title: FACT orchestrates the interplay between chromatin structure and transcription

city: Göttingen

first: Kristina

last: Žumer

address: Am Faßberg 11

department: Department of Molecular Biology

institute: Max Planck Institute for Multidisciplinary Sciences

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

overall_design: Refer to individual Series


title: FACT orchestrates the interplay between chromatin structure and transcription [mNET-Seq]

status: Public on May 30 2024

country: Germany

type: Non-coding RNA profiling by high throughput sequencing

summary: Transcription by RNA polymerase II (RNA Pol II) depends on transcription factors and chromatin factors. Here we use rapid factor depletion and multiomics analysis to investigate how a histone chaperone, FAcilitates Chromatin Transcription (FACT), influence nascent transcription by RNA PolII in human cells. Depletion of a FACT subunit, SSRP1, led to rapid changes in chromatin structure and concomitantly strongly compromised RNA synthesis. FACT depletion led to a multilayered transcriptional defect, including loss of promoter proximal pausing, deregulated release into elongation and drop-off of RNA Pol II in promoter-distant gene regions. We combined these analyses with biochemical dissection of transcription of a chromatinized template to show that FACT supports both elongation and pausing of RNA Pol II. Our study also provides new evidence how the position of promoter proximal pausing is defined by the +1 nucleosome in human cells.

overall_design: Samples for each condition were collected in biological duplicates. Cells were treated with dTAG7 for 1 or 4 hours, the corresponding control cells were treated for the same duration with vehicle only (DMSO) at the same vol/vol dilution.

last: Zumer

first: Aiturgan

last: Zheenbekova

first: Moritz

last: Ochmann

first: Arjun

last: Devadas

first: Kerstin

middle: C

last: Maier

first: Petra

last: Rus

first: Neef

last: Ute

first: Abrar

last: Aljahani

first: Marieke

last: Oudelaar

first: Patrick

last: Cramer


title: Epstein-Barr virus protein EBNA-LP engages YY1 through [RNA-seq] leucine-rich motifs to promote naïve B cell transformation

city: Durham

first: Jana

last: Cable

state: NC

address: 213 Research Dr.

department: Molecular Genetics and Microbiology

country: USA

institute: Duke University

type: Expression profiling by high throughput sequencing

summary: Epstein-Barr Virus (EBV) is associated with numerous cancers including B cell lymphomas. In vitro, EBV transforms primary B cells into immortalized Lymphoblastoid Cell Lines (LCLs) which serves as a model to study the role of viral proteins in EBV malignancies. EBV induced cellular transformation is driven by viral proteins including EBV-Nuclear Antigens (EBNAs). EBNA-LP is important for the transformation of naïve but not memory B cells. While EBNA-LP was thought to promote gene activation by EBNA2, EBNA-LP Knock Out (LPKO) virus-infected cells express EBNA2-activated cellular genes efficiently. Therefore, a gap in knowledge exists as to what roles EBNA-LP plays in naïve B cell transformation. We developed a trans-complementation assay wherein transfection with wild-type EBNA-LP rescues the transformation of peripheral blood- and cord blood-derived naïve B cells by LPKO virus. Despite EBNA-LP phosphorylation sites being important in EBNA2 co-activation; neither phospho-mutant nor phospho-mimetic EBNA-LP was defective in rescuing naïve B cell outgrowth. However, we identified conserved leucine-rich motifs in EBNA-LP that were required for transformation of adult naïve and cord blood B cells. Because cellular PPAR-g coactivator (PGC) proteins use leucine-rich motifs to engage transcription factors including YY1, a key regulator of DNA looping and metabolism, we examined the role of EBNA-LP in engaging cellular transcription factors. We found a significant overlap between EBNA-LP and YY1 in ChIP-Seq data. By Cut&Run, YY1 peaks unique to WT compared to LPKO LCLs occur at more highly expressed genes.  Moreover, Cas9 knockout of YY1 in primary B cells prior to EBV infection indicted YY1 to be essential for EBV-mediated transformation. We confirmed EBNA-LP and YY1and confirmed their biochemical association in LCLs by endogenous co-immunoprecipitation and. Moreover, we found that the EBNA-LP leucine-rich motifs were required for YY1 interaction in LCLs. Finally, we used Cas9 to knockout YY1 in primary total B cells and naïve B cells prior to EBV infection and found YY1 to be essential for EBV-mediated transformation. We propose that EBNA-LP engages YY1 through conserved leucine-rich motifs to promote EBV transformation of naïve B cells.

overall_design: To investigate the role of EBNA-LP in gene expression of LCLs, RNA from three donor-matched LCLs were sequenced.

middle: M

first: Nicolas

last: Reinoso-Vizcaino

first: Robert

middle: E

last: White

first: Micah

middle: A

last: Luftig


title: Gene Amplification of Mediator Subunit 30 Redirects the MYC Transcriptional Program and Oncogenesis [Pro-Seq]

city: La Jolla

first: Chunyu

last: Jin

address: 9500 Gilman Dr. MC0648

institute: University of California, San Diego

summary: Understanding the molecular mechanisms underlying tumorigenesis is crucial for developing effective cancer therapies. Here, we investigate the common co-amplification of MED30 and MYC across diverse cancer types and its impact on oncogenic transcriptional programs. Transcriptional profiling of MYC and MED30 single or both overexpression/amplification revealed the over amount of MED30 lead MYC to a new transcriptional program that associate with poor prognosis. Mechanistically, MED30 overexpression/amplification recruits other Mediator components and binding of MYC to a small subset of novel genomic regulatory sites, changing the epigenetic marks and inducing the formation of new enhancers, which drive the expression of target genes crucial for cancer progression. In vivo studies in pancreatic ductal adenocarcinoma (PDAC) further validate the oncogenic potential of MED30, as its overexpression promotes tumor growth and can be attenuated by knockdown of MYC. Using another cancer type, MED30 knockdown reduces tumor growth particularly in MYC high-expressed glioblastoma (GBM) cell lines. Overall, our study elucidates the critical role of MED30 overexprssion in orchestrating oncogenic transcriptional programs and highlights its potential as a therapeutic target for MYC-amplified cancer.

overall_design: Transcriptional activity was measured by PRO-seq in doxycycline (Dox) inducible MED30, MYC-3xHA or MED30&MYC-3xHA double integrated Mia PaCa-2 cell line with or without 0.5μg/ml Dox treatment for 1 day. Samples with Dox treatment were labeled as OE (overexpression). Processed files are feature counts per gene.

first: Likun

last: Yao

first: Michael

middle: G

last: Rosenfeld


title: BCAT1 contributes to the developmentproliferation and leukemogenesis of TKI-resistant CML

city: Shanghai

first: yu

last: Jiang

address: 280 Chongqing South Road, Shanghai

department: Faculty of Basic Medicine

country: China

institute: Shanghai Jiao Tong University School of Medicine

summary: In this report, we revealed that branched chain amino acid transaminase 1 (BCAT1) is highly enriched in both mouse and human TKI-resistant CML cells. Leukemia was almost completely abrogated upon BCAT1 knockdown during transplantation in a BCR-ABLT315I-induced murine TKI-resistant CML model . Moreover, knockdown of BCAT1 led to a dramatic decrease in the proliferation of TKI-resistant human leukemia cell lines. BCAA/BCAT1 signaling enhanced the phosphorylation of CREB, which is required for maintenance of TKI-resistant CML cells. Importantly, blockade of BCAA/BCAT1 signaling efficiently inhibited leukemogenesis both in vivo and in vitro.

overall_design: We performed transcriptome sequencing (RNA-seq) using BCAT1-knockdown and Scramble 32Dcl3 cells

first: Yu

first: Dan

last: Huang


title: Gene expression profiling of Elastin (ELN) knock-down in human fibroblast MRC5

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

country: France

institute: Inserm 1052

summary: The ELN gene encodes tropoelastin which is used to generate elastic fibers that insure proper tissue elasticity. Decreased amounts of elastic fibers and/or accumulation of bioactive products of their cleavage, named elastokines, are thought to contribute to aging. Cellular senescence, characterized by a stable proliferation arrest and by the senescence-associated secretory phenotype (SASP), increases with aging. Here, we identified that decrease in ELN either by siRNA in normal human fibroblasts results in premature senescence. Surprisingly this effect is independent of elastic fiber degradation or elastokines production, but it relies on the rapid increase in HMOX1 after ELN downregulation. These results unveil a role for ELN in protecting cells from cellular senescence through a non-canonical mechanism.

overall_design: Normal human fibroblast cells (MRC5) were transfected with siRNA against Elastin gene (siELN) or with scramble siRNA (siCTRL). Gene expression profiling was performed 1 day or 4 days after transfection. Three independent replicates have been performed.

first: Jean-Michel

last: Flaman

first: Joanna

last: Czarnecka-Herok

first: Nadine

last: Martin

first: David

last: Bernard


title: Microfluidic immuno-serolomic assay reveals systems level association with COVID-19 pathology and vaccine protection

city: New Haven

first: Rong

last: Fan

state: CT

address: 55 Prospect Street

department: Department of Biomedical Engineering

institute: Yale University

summary: How to develop highly informative serology assays to evaluate the quality of immune protection against COVID-19 has been a global pursuit over the past years including the NCI SeroNet initiative. Despite the wide-spread adoption of vaccination that has demonstrated exceptional efficacy, patients with altered immunity such as hematologic malignancies and autoimmune disease remain at risk, requiring rapid serological as well as immunological evaluation at the full range to manage these patients. Here, we develop a microfluidic high-plex immuno-serolomic assay to simultaneously measure up to 50 plasma or serum samples for up to 50 soluble markers including 35 plasma proteins, 11 anti-spike/RBD IgG antibodies spanning all major variants, and controls. Our assay demonstrates the quintuplicate test in a single run with high throughput, low sample volume input, high reproducibility and high accuracy. It is applied to the measurement of 1,012 blood samples including in-depth analysis of sera from 127 patients and 21 healthy donors over multiple time points, either with acute COVID infection or vaccination. The protein association matrix analysis reveals distinct immune mediator protein modules that exhibit a reduced degree of diversity in protein-protein cooperation in patients with hematologic malignancies and patients with autoimmune disorders receiving B cell depletion therapy. Serological analysis identifies that COVID infected patients with hematologic malignancies display impaired anti-RBD antibody response despite high level of anti-spike IgG, which could be associated with limited clonotype diversity and functional deficiency in B cells and is further confirmed by single-cell BCR and transcriptome sequencing. These findings underscore the importance to individualize immunization strategy for these high-risk patients and provide an informative tool to monitor their responses at the systems level.

overall_design: By combining single-cell RNA sequencing (scRNA-seq) and co-measurement of B cell receptor (BCR) repertoires, we characterized the heterogeneity of circulating B cells from the one COVID infected patient with chronic lymphocytic leukemia and one COVID patient with non-hematologic cancer.

first: Zhiliang

last: Bai

first: Dongjoo

last: Kim

first: Giulia

last: Biancon

first: Stephanie

last: Halene


title: Gene expression profiling of endothelial-mesenchymal transition in cerebral arteriovenous malformation

city: Los Angeles

first: Xiuju

last: Wu

state: CA

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

institute: University of California, Los Angeles

summary:
To investigate the endothelial-mesenchymal transition in cerebral arteriovenous malformation.
We performed gene expression profiling analysis using the data obtained from RNA-seq of CD31+CD45- brain cells in Cdh5cre;Mgpflox/flox mice with or without tamoxifen induction.

overall_design: Comparative gene expression analysis of RNA sequencing in CD31+CD45- brain cells.

first: Wu

last: Xiuju

first: Yan

last: Zhao


title: Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size

city: Riverside

first: Sika

last: Zheng

address: University Ave 900

department: School of Medicine

institute: University of California, Riverside


title: Cysteine Rich Protein 2 is a copper-responsive regulator of skeletal muscle differentiation.

city: Pittsburgh

last: Klein

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

type: Genome binding/occupancy profiling by high throughput sequencing


title: Cysteine Rich Protein 2 is a copper-responsive regulator of skeletal muscle differentiation. [RNA-Seq]

summary: Copper (Cu) is an essential trace element for diverse biological reactions such as respiration, neurotransmitter synthesis, oxidative stress and transcriptional regulation. If Cu homeostasis is disrupted, several pathological conditions can develop, leading to alterations of neuronal, cognitive, and muscular development.  Known Cu+-binding transcription factors in mammalian cells are Atox1, Mtf1 and Sp1. We identified Crip2 as a novel Cu+-responsive transcriptional regulator that is required for the differentiation of primary myoblasts derived from mouse satellite cells. Functional characterization of CRISPR/Cas9-mediated deletion of Crip2 showed that myoblasts fail to differentiate and manifest a decrease in expression of the differentiation markers Myogenin and Myosin heavy chain. RNA-seq and CUT&RUN analysis were performed to understand the effect on Crip2 in the regulation of gene expression in proliferating and differentiating primary myoblasts stimulated with Cu.

overall_design: Total strand-specific RNA-seq libraries isolated from differentiating (Diff) and proliferating (Prol) myoblasts. CRIP2 knockout myoblasts were generated via lentiviral transduction. Each CRIP2 KO library was paired with a scrambled (SCR) control experiment and completed in duplicate.

first: Verdejo-Torres

last: Odette

first: Klein

last: David C.

first: Hainer

last: Sarah J.

first: Padilla-Benavides

last: Teresita


title: CUT&Tag analysis of R-loops in Ube2t knockdown P19 cells (optimized)

city: Jinan

first: Yongze

last: Yu

email: lwyyzsdu@163.com, lwyyzsdu@hotmail.com

state: Shandong

address: 文化西路44号国家辅助生殖与优生工程技术研究中心

institute: Shandong University

summary: DNA sequencing of libraries from CUT&Tag with R-loops antibody (S9.6) in Ube2t knockdown and control P19 cells

overall_design: To understand the role of UBE2T in resolving R-loops. Mouse P19 cells were used. Two kinds of Ube2t knockdown adenovirus were used. No antibody group was regarded as control sample.

first: Shidou

first: Yajuan

last: Yang

first: Weiwei

last: Xu


title: Single-cell RNA-sequencing analysis for the molecular taxonomy of primate Anterior cingulate cortex (ACC) and Retro splenial cortex (RSC), as well as rodents

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: We thus isolated Anterior cingulate cortex (ACC) and Retro splenial cortex (RSC) from rhesus macaques and mice and performed single-cell RNA-sequencing analysis.The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V2 Reagent Kits (10X Genomics, Pleasanton, USA).

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus

overall_design: four groups（mouse-ACC; mouse-RSC; monkey-ACC; monkey-RSC), two mice were included in group mouse-ACC and group mouse-RSC; two macaques (a 17-month-old one and an 18- month-old one). Tissues of mice were mixed in one sample. Tissues of macaques were mixed and devided into 2 or 3 samples.

first: Lei

last: Zhang


title: tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [WGBS]

status: Public on May 29 2024

city: Ottawa

first: Kim

last: Kobar

state: Ontario

address: 401 Smyth Rd

country: Canada

institute: Children's Hospital of Eastern Ontario Research Institute

type: Methylation profiling by high throughput sequencing

summary: Li-Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development, we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants (human R248 and R273H). These mutants have lost several key wildtype p53 functions and recapitulate many LFS phenotypes. Specifically, we have shown that the R217H and R242H alleles result in partial-to-no activation of key p53 target genes, are resistant to apoptosis in a dominant negative manner and exhibit a defective G1 cell-cycle checkpoint in vivo. The loss of these wildtype p53 functions predisposed the fish to develop spontaneous tumors as early as 6 months of age. Tumor histology resembles human sarcomas, a predominant LFS tumor type. tp53 R242H mutants developed tumors earlier with a higher lifetime incidence than tp53 null or R217H mutants, suggesting it is a more aggressive mutation, while the R217H allele may be hypomorphic. Additionally, we observed mutation-specific differences both in the tumor type and sex bias across tp53 null, R217H, and R242H genotypes with associated diverse transcriptomic and DNA methylome profiles, impacting metabolism, cell signalling, and biological macromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics, which may inform more tailored tumor surveillance approaches and novel therapeutic targets in LFS.

overall_design: We generated tp53 zebrafish mutants representing two of the most common mutation residues found in human cancers, tp53 R217H and R242H (human R248 and R273) using CRISPR to knock in the mutations and also obtained a CG1 tp53 null line from the Langenau lab (Ignatius et al., 2018). We also used the transparent casper strain as a comparison to zebrafish with wildtype p53. Of note, the tp53 null fish are in the CG1 background while the casper, tp53 R217H, and tp53 R242H fish are in the AB background. We performed whole genome bi-sulfite sequencing on thirty pooled 5 days post-fertilization (dpf) for each sample with biological replicates each for a total of 12 samples (casper, tp53 null, tp53 R217H/R217H, tp53 R242H/R242H).

first: Sergey

middle: V

last: Prykhozhij

first: Jason

middle: N

last: Berman

first: Martin

last: Hirst

first: Michelle

last: Moksa

first: Annaick

last: Carles

first: Qi

last: Cao

first: Brianne

last: Laverty

first: Vallijah

last: Subasri

first: David

last: Malkin


title: Cysteine Rich Protein 2 is a copper-responsive regulator of skeletal muscle differentiation. [CUT&Run]

last: Klein

overall_design: CUT&RUN targeting CRIP2 binding in differentiating (Diff) and proliferating (Prol) myoblasts, each paired with an untargeted IgG control experiment and completed in triplicate. Differentiating myoblasts were treated with Cu, Insulin, or no treatment, while proliferating myoblasts were treated with either Cu or no treatment.

first: Verdejo-Torres

last: Odette

first: Klein

last: David C.

first: Hainer

last: Sarah J.

first: Padilla-Benavides


title: Expression analysis of human umbilical cord blood (hUCB) cells affected by OSA

city: Palma

first: Josep

last: Muncunill Farreny

address: Carretera de Valldemossa, 79. Hospital Universitario Son Espases

country: Spain

institute: IdISBa

summary: Obstructive sleep apnea (OSA) is common during pregnancy and is associated with adverse perinatal consequences, but it is not known whether it can also modulate fetal development processes. To understand the effects of OSA-affected mothers on fetus we analyzed the expression profile of hUCB cells under OSA conditions.

overall_design: To deeper study the potential molecular events triggered under OSA conditions during pregnancy, we compared the expression profile in hUCB cells obtained from five OSA and five non-OSA affected newborns.


title: FACT orchestrates the interplay between chromatin structure and transcription [MNase-Seq]

first: Kristina

last: Žumer

last: Zumer

first: Aiturgan

last: Zheenbekova

first: Moritz

last: Ochmann

first: Arjun

last: Devadas

first: Kerstin

last: Maier

first: Petra

last: Rus

first: Neef

last: Ute

first: Abrar

last: Aljahani

first: Marieke

last: Oudelaar

first: Patrick

last: Cramer


title: Dysregulated innate immune signaling cooperates with RUNX1 mutations to transform an MDS-like disease to AML

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center


title: Single-nuclei expression of canine veins during carotid-cartoid vein bypass implantation

city: Cartersville

first: Marina

last: Michaud

state: GA

address: 28 Cass Station Dr NW

institute: Emory University

summary: Vein graft failure (VGF) following cardiovascular bypass surgery results in significant patient morbidity and cost to the healthcare system. Vein graft injury can occur during autogenous vein harvest and preparation, as well as after implantation into the arterial system, leading to the development of intimal hyperplasia, vein graft stenosis, and, ultimately, bypass graft failure. While previous studies have identified maladaptive pathways that occur shortly after implantation, the specific signaling pathways that occur during vein graft preparation are not well defined and may result in a cumulative impact on VGF. We, therefore, aimed to elucidate the response of the vein conduit wall during harvest and following implantation, probing the key maladaptive pathways driving graft failure with the overarching goal of identifying therapeutic targets for biologic intervention to minimize these natural responses to surgical vein graft injury. Employing a novel approach to investigating vascular pathologies, we harnessed both single-nuclei RNA-sequencing (snRNA-seq) and spatial transcriptomics (ST) analyses to profile the genomic effects of vein grafts after harvest and distension, then compared these findings to vein grafts obtained 24 hours after carotid-cartoid vein bypass implantation in a canine model (n=4). Collectively, we find that vein conduit harvest and distension elicit a prompt genomic response facilitated by distinct cellular subpopulations heterogeneously distributed throughout the vein wall. This response was found to be further exacerbated following vein graft implantation, resulting in a cascade of maladaptive gene regulatory networks. Together, these results suggest that distension initiates the upregulation of pathological pathways that may ultimately contribute to bypass graft failure and presents potential early targets warranting investigation for targeted therapies.

overall_design: Bilateral upper limb cephalic vein harvest and carotid-cartoid vein bypass implantation were performed on 25 kg male (n=3) or female (n=1) mongrel dogs. Samples (15 cm) of distended vein were taken following distension during graft harvesting and at 24 hours post-bypass, alongside untouched control vein samples, and snap-frozen in cryovials using liquid nitrogen for single-nuclei analysis.

first: Michaud

last: Marina

first: Mota

last: Lucas

first: Liang

last: Patric

first: Bhasin

last: Manoj


title: FACT orchestrates the interplay between chromatin structure and transcription [ChIP-Seq]

last: Žumer


title: FACT orchestrates the interplay between chromatin structure and transcription [TT-Seq]

last: Zumer


title: FACT orchestrates the interplay between chromatin structure and transcription [5Cap-Seq]

last: Zheenbekova


title: Gene expression analysis of normal oral keratinocytes cells and oral squamous cell carcinoma (OSCC) cells

city: Chengdu

first: Yangfan

last: Liu

state: Sichuan

address: People South Street

institute: Sichuan University

summary: Gene expression profiling of normal oral keratinocytes (NOK) cells (n=3) and Cal27 cells (n=3)

overall_design: We performed gene expression profiling analysis using data from RNA-seq of normal oral keratinocytes (NOK) cells (n=3) and Cal27 cells (n=3)

first: Jingjing

last: Luo

first: Hongmei

last: Zhou


title: Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size (RNA-seq e13invivo)

first: Sika

last: Zheng

summary: To determine the transcriptomic impacts of NMD on lineage transition in vivo, we performed mRNA-Seq of neocortices from E13.5 Emx1-Upf2cKO and their control littermates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for neocorices from E13.5 Emx1-Upf2cKO and their control littermates.

first: Jing

middle: R

last: Zhao

first: Naoto

last: Kubota

last: Chen


title: Epigenetic modifications of white blood cell DNA caused by transient fetal infection with bovine viral diarrhea virus

city: Fort Collins

first: Thomas

last: Hansen

state: CO

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: The impact of late-term fetal bovine viral diarrhea virus (BVDV) transient infections (TI) on fetal growth and methylome was examined by inoculating pregnant heifers with a noncytopathic (ncp) type 2 BVDV suspended in media or media alone (sham-inoculated controls) on day 175 of gestation to generate TI (n=11) and control heifer calves (n=12).  Blood samples were collected at birth. White blood cells (WBC) were separated for DNA extraction.  Fetal infection in calves was confirmed by positive virus serum neutralizing antibody titers at birth and control calves were seronegative. Both control and TI calves were negative for BVDV RNA in WBCs by RT-PCR.   DNA methyl seq analysis of WBC DNA demonstrated 2,349 differentially methylated cytosines (p≤0.05) including 1,277 hypomethylated cytosines, 1.072 hypermethylated cytosines, 84 differentially methylated regions based on CpGs in promoters and 89 DMRs based on CpGs in exons of TI WBC DNA compared to controls.  Fetal BVDV infection during late gestation resulted in epigenomic modifications predicted to affect fetal and organ development pathways suggesting potential consequences for postnatal growth and health of TI cattle.

overall_design: Reduced-representation bisulfite sequencing (RRBS-Seq ) for five randomly selected newborn calves from heifers that were inoculated with BVDV on day 175 of gestation and five randomly selected newborn calves from heifers that were inoculated with sham media on day 175 of gestation. Jugular vein was collected, and PMBC were collected for DNA analysis.

first: Hana

last: Van Campen

first: Jeanette

last: Bishop

first: Zella

last: Brink

first: Terry

last: Engle

first: Carolina

middle: L

last: Gonzalez-Berrios

first: Hanah

last: Georges

first: Jessica

last: Kincade

first: Dilyara

last: Murtazina


title: Curcumin improves atrial fibrillation susceptibility by regulating tsRNA expression in aging mouse atrium

city: Guangzhou

first: Xueshan

address: Dongchuan Road

institute: South China University of Technology

summary: Age is an independent risk factor for atrial fibrillation (AF), and curcumin can delay aging related disease through reducing oxidative stress and inflammation. However, its target in aging-related AF remains unclear. Transfer RNA-derived small RNA (tsRNA) is a novel short non-coding RNA (sncRNA), and exerts a potential regulatory function in aging. This study was to explore the therapeutic targets of curcumin in atrium of aged mice by PANDORA-seq. Aged mice (18 month) were treated with curcumin (100mg/kg). Rapid transjugular atrial pacing was performed to observe AF inducibility. SA-β-gal staining, ROS detection and qRT-PCR were used to assess the degree of aging and oxidative stress/inflammation levels. PANDORA-seq was performed to reveal the differentially expressed sncRNAs in the atrium of mice. The results showed that curcumin reduced the susceptibility AF of aged mice by improving aging-related atrial fibrosis. Compared to young mice (5 month) group, aged mice yielded 473 significantly altered tsRNA sequences, while 947 tsRNA sequences were significantly altered after treated with curcumin. Enrichment analysis revealed that the target genes were mainly related to DNA damage and protein modification. Compared with the 5mo group, the expression levels of mature-mt_tRNA-Val-TAC_CCA_end, mature-mt_tRNA-Glu-TTC_CCA_end, and mature-tRNA-Asp-GTC_CCA_end were up-regulated in the 18mo group, while the expression of mature-mt_tRNA-Thr-TGT_5_end was down-regulated. This trend was reversed in the 18mo+curcumin group. Increased cellular ROS levels, inflammation expression and senescence in aged mice atrium were improved by the down-regulation of mature-mt_tRNA-Val-TAC_CCA_end. In conclusion, our findings identified mature-mt_tRNA-Val-TAC_CCA_end participated in the mechanism of aging-related atrial fibrosis, providing new intervention target of aging-related AF.

overall_design: The mice were randomly divided into three groups (n = 3) : 5-month-old (young), 18-month-old (old) and curcumin treated 18-month-old mice. curcumin treated 18-month-old mice were received 100mg/kg curcumin daily in the non-fat skim milk, starting from the age of 12 months until 18 months.

first: Xingdong

last: Ye

first: Panyue

first: Yingyu

last: Lai

first: Jintao

last: He

first: Yidong

last: Lv

first: Xiongbin

last: Wu

first: Yang

first: Qianhuan

last: Zhang

first: Hui

last: Yang

first: Hai

last: Deng

first: Wei

last: Wei

first: Chunyu

first: Sujuan

last: Kuang

first: Shulin

first: Yumei

last: Xue

first: Fang

last: Rao


title: A 5:2 intermittent fasting regimen initiated in the active phase ameliorates NASH, fibrosis and blunts HCC development via hepatic PPARα and PCK1

city: Heidelberg

first: Mathias

last: Heikenwälder

address: Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ) and University of Tuebingen

summary: The role and molecular mechanisms of intermittent fasting (IF) in non-alcoholic steatohepatitis (NASH) and its transition to hepatocellular carcinoma (HCC) are unknown. Here, we identified that an IF 5:2 regimen (two non-consecutive days of food deprivation per week), initiated in the active phase of mice, prevents NASH development as well as ameliorates established NASH and fibrosis without affecting total calorie intake. Furthermore, the IF 5:2 regimen also blunted NASH-HCC transition when applied therapeutically in two independent models of diet-induced NASH and NASH-HCC. The timing (7pm-7pm > 7am-7am), length (24h > 12h) and number (5:2 > 6:1) of fasting cycles as well as the type (WD / CDHFD) of NASH diet were all critical parameters determining the effectiveness of the fasting benefits. Combined proteome, transcriptome and metabolome analyses identified that PPARα and glucocorticoid signalling-induced phosphoenolpyruvate carboxykinase 1 (PCK1) act co-operatively as hepatic executors of the fasting response by promoting fatty acid catabolism and gluconeogenesis while suppressing anabolic lipogenesis. In line, PPARα targets and PCK1 were reduced in human NASH. Notably, only fasting during the active phase (7pm-7pm) of mice robustly induced glucocorticoid signalling in hepatocytes including PCK1 expression; while both active and inactive phase (7am-7am) fasting induced free fatty acid-induced PPARα signalling, highlighting the increased efficacy of fasting during the active phase. However, hepatocyte-specific glucocorticoid receptor (GR) deletion only partially abrogated the hepatic fasting response, illustrating the need for both glucocorticoid-induced PCK1 expression and free fatty acid-induced PPARα activation for mediating the benefits of fasting. In support, the combined knockdown of Ppara and Pck1 in vivo abolished the beneficial outcomes of fasting against inflammation and fibrosis, confirming their causal relationship in integrating systemic signalling in hepatocytes. Moreover, overexpression of Pck1 alone or together with Ppara in vivo lowered hepatic triglycerides and steatosis upon Western-diet feeding. Altogether, our data support that the IF 5:2 regimen could be a promising and viable intervention against NASH and subsequent liver cancer.

overall_design: Transcriptomics data from whole liver homogenates from C57BL/6 mice with AAV8 viral vectors - sh_Scramble, sh_Ppara, sh_Pck1 and sh_Combo. Mice were fed a Western diet (WD) and underwent either ad libitum feeding or an intermittent fasting 5:2 regimen. Mice under ad libitum conditions were sacrificed in a fed state while mice undergoing IF 5:2 regimen were sacrificed in a fasted state.

first: M

last: Heikenwalder


title: Single-Cell RNA-SeqSingle cell RNA-sequencing reveals low-dose radiation effects.

city: Suzhou

first: Yidi

last: Wang

address: Ren'ai Road

department: School of Radiation Medicine and Protection

institute: Soochow University

summary: Single-cell sequencing was performed on the irradiated cell lines to accurately map the biological information triggered by low-dose radiation to each individual cell.

overall_design: The BEAS-2B cell line was exposed to the Cs-137 gamma-ray source. The Cs-137 irradiation equipment was designed and manufactured by Hopewell Designs company. The irradiation doses used were 10 mGy, 100 mGy, and 1 Gy.


title: Differential gene expression analysis of  wild type and heterozygous RB1 mutant human iPSC derived retinal organoids.

city: CHENNAI

first: SOWMYA

last: PARAMESWARAN

address: 41 COLLEGE ROAD

country: India

institute: VISION RESEARCH FOUNDATION

summary: Recent in vitro studies using RB1+/- fibroblasts and MSCs have shown molecular and functional disruptions without the need for biallelic loss of RB1. However, this was not reflected in the recent in vitro studies employing RB1+/- retinal organoids. To gain further insights into the molecular disruptions in the RB1+/- retinal organoids we performed a high throughput RNA-sequencing analysis.iPSCs were generated from RB1+/+ and RB1+/- Orbital adipose mesenchymal stem cells (OAMSCs) derived from retinoblastoma patients. RB1+/+ and RB1+/- iPSCs were subjected to step-wise retinal differentiation protocol and high throughput RNA-sequencing followed by differential gene expression analysis and Gene set enrichment analysis (GSEA) was performed.The analysis revealed that even though there are no gross observable differences, subtle molecular changes in RB1+/- retinal organoids were observed. We report that there is mild shift from the regular metabolic process of glycolysis to oxidative phosphorylation in the RB1+/- retinal organoids which could be setting a premise for tumorigenesis.

overall_design: RNA sequencing was performed on the RB-iPSC derived retinal organoids

first: Sowmya

last: Parameswaran

first: Ambily

last: Vincent


title: Molecular analysis of platinum-resistant and -sensitive  ovarian cacner based on RNA-Seq  analysis

first: Wu

middle: yang

last: jun

address: shanghai dongan road 270

department: Fudan university shanghai cancer center

institute: Fudan university

summary: Ovarian cancer (OC) is the leading cause of death from gynecologic malignancies. The most difficult issue in the treatment of ovarian cancer is the eventual development of platinum resistance. Accumulating studies have shown that circRNAs are abnormally aberrantly expressed in tumors and play critical roles in tumor growth, metastasis, stemness and resistance to therapy.To identify circRNAs that play crucial roles in maintaining the platinum resistance of ovarian cacner, we performed RNA-seq analysis in platinum-resistant（n=9） and -sensitive（n=10） ovarian cacner tissues. Candidate genes were identified by bioinformatic analysis and literature review.

overall_design: Tumor tissues from platinum-sensitive (n = 10) or platinum-resistance ( n = 9) ovarian cancer  patients were prospectively collected before platinum-based therapies  and analyzed by  RNA-Seq on Illumina NovaSeq 6000 platform.  Potential expression profile were compared between  platinum-sensitive and platinum-resistance groups. Candidate genes were identified by bioinformatic analysis and literature review.

first: Yangjun

first: Shengli

last: Li

first: Xiaohua


title: Epigenetic Modulation of GPER Expression in Gastric and Colonic Smooth Muscle of Male and Female Non-obese Diabetic (NOD) Mice: Insights into H3K4me3 and H3K27ac Modifications

city: Tuskegee

first: Sunila

last: Mahavadi

state: Alabama

address: 1200 W. Montgomery Rd, Carver Research Building, Room #1

department: Biology

institute: Tuskegee University

summary: Introduction: Type 1 diabetes (T1D) significantly affects gastrointestinal (GI) motility and contributes to complications, such as gastroparesis, constipation, and fecal incontinence. Notably, these complications have a higher prevalence in female patients, underscoring a critical knowledge gap in the understanding of the underlying mechanisms. Given the emerging role of the G-protein-coupled estrogen receptor (GPER) in GI motility regulation, our study investigated the potential contribution of diabetes-induced changes in GPER expression to pathophysiology. Hypothesis: We hypothesized that diabetes-induced perturbations in GPER expression contribute to pathophysiological mechanisms affecting GI motility in T1D, with notable sex-dependent variations. Methods: we assessed GPER mRNA and protein expression levels using quantitative reverse-transcription PCR and western blot analyses, and quantified the changes in nuclear DNA methyltransferases and histone modifications (H3K4Me3, H3Ac, and H3K27Ac) were quantified using ELISA kits. Targeted bisulfite and chromatin immunoprecipitation sequencing were used to evaluate DNA methylation and histone modifications around the GPER promoter by chromatin immunoprecipitation assays in gastric and colonic smooth muscle tissues of male and female control (CTR) and non-obese diabetic (NOD) mice. Results: Our results revealed significant downregulation of GPER in NOD mice, with marked sex-dependent variations. Mechanistically, this downregulation was associated with reduced H3K4me3, H3ac, and H3K27ac levels in NOD male gastric smooth muscle. In contrast, downregulation in female gastric smooth muscle cells has been linked to decreased H3K4me3 and H3ac levels. Male NOD colonic smooth muscle exhibited elevated H3ac and H3K27ac levels, whereas female NOD colonic smooth muscle demonstrated diminished enrichment of H3ac and H3K27ac at the GPER promoter. Additionally, DNA methylation is elevated in NOD male colonic smooth muscle compared to NOD females. Conclusion: Our findings elucidate sex-specific epigenetic mechanisms contributing to T1D-mediated suppression of GPER expression in the gastrointestinal tract. These insights not only advance our understanding of T1D complications but also suggest promising avenues for targeted therapeutic interventions.

overall_design: To investigate the GPER expression in male and female gastric and colonic smooth muscle of Control and NOD mice, we performed DNA-methylation measurement at the GPER promoter region by targeted bisulfite sequencing assay. This was performed in the colonic and gastric tissue of 5 male Control, 5 male NOD, 5 female Control and 5 NOD female mice. The DNA methylation data was analyzed by comparative analysis, using ANOVA.

first: Aliyu

last: Muhammad


title: Gastrocnemius muscle-Deletion of TECRL promotes skeletal muscle repair

first: Wei

last: He

state: Jiangsu

address: 199 RenAi Road

department: Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology

summary: Myogenic regeneration relies on the proliferation and differentiation of satellite cells. TECRL (Trans-2,3-Enoyl-CoA Reductase Like) is an endoplasmic reticulum protein only expressed in cardiac and skeletal muscle. However, its role in myogenesis remains unknown. We show that TECRL expression is increased in response to ischemic injury. Satellite cell-specific deletion of TECRL enhances muscle repair by increasing the expression of EGR2 through the activation of the ERK1/2 signaling pathway, which in turn promotes the expression of PAX7. We further showed that TECRL deletion led to the upregulation of the histone acetyltransferase general control non-derepressible 5 (GCN5), which enhances the transcription of EGR2 through acetylation.

overall_design: Total RNA from TECRLflox/flox and TECRLscko gastrocnemius muscle.  TECRLscko mice (satellite cell – specific TECRL knockout mice) were generated by crossing Pax7-Cre mice (Stock Number: 010530, Pax7tm1 (cre) Mrc/J; The Jackson Laboratory, Bar Harbor, ME) with TECRLflox/flox mice (generated by Cyagen, Guangzhou, China).

first: Yao-Hua

last: Song

first: Sha

last: Geng


title: Longitudinal trajectories of mild/moderate SARS-CoV2 infection reveals key precursors and predictors of convalescent virus-specific immunity

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: SARS-CoV2 infection results in clinically heterogeneous manifestations that are partially driven by complex longitudinal interactions with the immune system. The public health burden of mild COVID-19 is massive given the >100 million infected worldwide, but most research has focused on severe and fatal COVID-19. We recruited a mild COVID-19 cohort for multimodal immunophenotyping of single immune cells (scRNAseq, scATACseq, flow cytometry), serum proteins, virus-specific cellular and humoral immune responses, and clinical annotation from early acute infection to convalescence. Samples were acquired longitudinally from early acute infection before 15 days to >100 days post-symptom onset. Comparison to uninfected controls revealed marked immune activation consistent with acute response to viral infection at 15 days post-symptom onset with stronger inflammatory responses in older (>=40) compared to younger (<40) participants. Type I, II, and III interferon responses were most consistently upregulated in nearly all PBMC subsets. Plasmablasts were expanded in early infection with signatures of active IFNL and IFNG signaling, linking early inflammation and IFN responses to control of viral replication via antibodies.  Longitudinal models of scRNAseq confirmed most inflammatory pathways decreased over time, including type I and II IFN signaling, as well as signaling by innate danger sensors (TLR, RIG-I) that detect viral replication. By contrast, genes with increasing expression over time were enriched for EMT and wound healing pathways. Most participants showed consistent decay of inflammatory signatures by convalescence at >d 30 post-symptom onset except those presenting with PASC. Despite similar virus-specific adaptive immune responses between post-acute sequelae PASC and recovered convalescent participants, PASC participants showed persistent serum cytokine and chemokine differences including elevated IL5, TNF, IL-12p70, and soluble CD28 at >30 d post-symptom onset. scRNAseq, scATACseq, and network analyses provided more signs of persistent inflammatory activation in multiple cell types, with multimodal evidence pointing to increased activity of innate cells (CD14 monocytes, DCs) and effector T cells (CD4 TEM, CD8 TEMRA). Cytokines at day 7 PSO were highly correlated with and predictive of both virus-specific IgG and neutralizing antibody titers. Integrative network analyses defined the most enriched ligand-receptor pathways across PBMC subsets including LTA/TNF𝛃, TNF, and IFNg in early infection, and these also showed signs of persistent activation in PASC. Common downstream targets of these pathways in PASC point to novel therapeutic targets and mechanistic hypotheses, including IL-1Ꞵ, AP-1, ZFP36/TTP, and CEBP/ꞵ. These findings revealed dynamics of immune activation and critical early signals correlated with adaptive immune responses. Serum protein signatures predicting antibody responses and correlating with PASC may provide opportunities for enhanced immunomonitoring and personalized treatment.

overall_design:
We recruited a mild COVID-19 cohort for multimodal immunophenotyping of single immune cells (scRNAseq, scATACseq, flow cytometry), serum proteins, virus-specific cellular and humoral immune responses, and clinical annotation from early acute infection to convalescence. Samples were acquired longitudinally from early acute infection before 15 days to >100 days post-symptom onset.
NOTE from submitter: The FASTQs are from human subjects and they will be submitted to dbGAP.

first: Gregory

last: Szeto

first: Aarthi

last: Talla

first: Mark-Phillip

last: Pebworth

first: Suhas

last: Vasaikar

first: Kathy

last: Henderson

first: Alexander

middle: T

last: Heubeck

first: Mark

last: Gillespie

first: Palak

last: Genge

first: Elliot

last: Swanson

first: Charles

last: Roll

first: Adam

middle: K

last: Savage

first: Ernest

last: Coffey

first: Lynne

last: Becker

first: Julian

last: Reading

first: Peter

middle: J

last: Skene

first: Xiaojun

first: Troy

last: Torgeson

first: Thomas

middle: F

last: Bumol

last: McElrath

first: Kristen

middle: W

last: Cohen

first: Evan

last: Newell

first: Maria

middle: P

last: Lemos

first: Stephen

last: DeRosa

first: Julie

last: Czartoski

first: Lamar

last: Ballweber-Fleming


title: Transcriptomic analyses of bacterial growth on fungal necromass reveals different microbial community niches during degradation

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

summary: Bacteria are major drivers of organic matter decomposition and play crucial roles in global nutrient cycling. Although the degradation of dead fungal biomass (necromass) is increasingly recognized as an important contributor to soil carbon (C) and nitrogen (N) cycling, the genes and metabolic pathways involved in necromass degradation are under characterized. In particular, how bacteria degrade necromass containing different quantities of melanin, which largely control rates of necromass decomposition in situ, is largely unknown. To address this gap, we conducted a multi-timepoint transcriptomic analysis using three Gram-negative, bacterial species grown on low or high melanin necromass of Hyaloscypha bicolor. The bacterial species, Cellvibrio japonicus, Chitinophaga pinensis, and Serratia marcescens, belong to genera known to degrade necromass in situ. We found that while bacterial growth was consistently higher on low than high melanin necromass, the CAZyme-encoding gene expression response of the three species was similar between the two necromass types. Interestingly, this trend was not shared for genes encoding nitrogen utilization, which varied in C. pinensis and S. marcescens during growth on high versus low melanin necromass. Additionally, this study tested the metabolic capabilities of these bacterial species to grow on a diversity of C and N sources and found that the three bacteria have substantially different abilities to utilize carbon and nitrogen compounds. Collectively, our data suggests that as necromass changes chemically over the course of degradation, certain bacterial species are favored based on their differential metabolic capacities.

sample_organism:
Serratia marcescens
Chitinophaga pinensis
Cellvibrio japonicus

overall_design: Bacterial cell pellets were collected during exponential growth or stationary phase in biolgical triplicate during the degradation of high or low melanin fungal necromass. Reference conditon was growth using glucose as sole carbon source.


title: Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size (RNA-seq NPC)

city: Riverside

first: Sika

last: Zheng

address: University Ave 900

institute: University of California, Riverside

summary: We performed mRNA-Seq of Upf2 KO, Trp53 KO, and dKO NPC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Upf2 KO, Trp53 KO, and dKO NPC.

first: Jing

last: Zhao

first: Naoto

last: Kubota

first: Liang

last: Chen


title: Longitudinal DNA methylation in serially passaged BJ Fibroblasts to investigate the latent aging of cells

city: San Diego

first: Morgan

middle: E.

last: Levine

address: 5510 Morehouse Dr

department: Institute of Sciences San Diego

institute: Altos Labs

type: Methylation profiling by genome tiling array

summary: As epigenetic clocks have evolved from powerful estimators of chronological aging to predictors of mortality and disease risk, it begs the question of what role DNA methylation plays in the aging process. We hypothesize that while it has the potential to serve as an informative biomarker, DNA methylation could also be a key to understanding the  biology entangled between aging, (de)differentiation, and epigenetic reprogramming. Here we use an unsupervised approach to analyze time associated DNA methylation from both in vivo and in vitro samples to measure an underlying signal that ties these phenomena together. We identify a methylation pattern shared across all three, as well as a signal that tracks aging in tissues but appears refractory to reprogramming, suggesting that aging and reprogramming may not be fully mirrored processes.

overall_design: BJ fibroblasts with and without hTert expression were serially passaged, with samples being frozen every other passage for potential DNA methylation analysis until senescence. Senescent cells were maintained in culture and passaged to check cell counts, lastly being harvested after 200 days of senescence. From the initial vial, two sets of flasks were passaged independently, called Trajectory A and B. Wild-type serially passaged BJ Fibroblasts were done at separate locations from different original vials from ATCC.

last: Niimi

first: Victoria

last: Gould

first: Kyra

last: Thrush-Evensen


title: Deficiency of P2RY11 causes narcolepsy and attenuates recruitment of neutrophils and macrophages of inflammatory response in zebrafish

city: Tianjin

first: 林

last: 赵

state: 南开区

address: 学府街道卫津路南开大学医学协同创新中心

institute: 医学院

summary: Purinergic receptor P2Y11, a G protein-coupled receptor that is stimulated by the endogenous ATP, has been demonstrated to be related with the chemotaxis of granulocytes, apoptosis of neutrophils, and secretion of cytokines in vitro. P2Y11 mutations were associated with narcolepsy. However, little is known about the roles of P2RY11 in the occurrence of narcolepsy and inflammatory response in vivo. In this study, we generated zebrafish P2Y11 mutant by CRISPR/Cas9 genome editing and performed gene expression profiling analysis.To analyze the P2RY11 function, we performed GO term analysis of the up-regulated and down-regulated DE genes of P2RY11-8bp versus their WT controls. The results showed that plasma membrane signaling receptor complex (GO:0098802), calcium ion binding (GO:0005509), and protein refolding (GO:0042026) were most enriched terms in up-regulated DE genes. While metabolic process (GO:008152), location (Go:0051179) and cellular process (GO:009987) were most enriched terms in down-regulated DE genes . In addition, immune system process (GO:0002376) was also enriched in down-regulated DE genes of P2RY11-8bp versus WT controls . Basic on the genes related with immune system process, we further performed GO term enrichment analysis and found that the defense response, leukocyte chemiotaxis, and inflammatory response were the main enriched terms.

overall_design: The p2ry11(-/-) mutant and  wild-type (WT) sibling were produced from p2ry11 heterozygous (+/-) intercross embryos. Subsequently, RNA was extracted from the p2ry11(-/-) mutant and the WT sibling embryos using TRIzol reagent.We then performed gene expression profiling analysis using data obtained from RNA-seq of the mutant and WT siblings.

first: Zhao

last: Lin

first: Wang

last: Li-feng

first: Chen

last: Dong-yan


title: Spatial gene expression of canine veins during carotid-cartoid vein bypass implantation

first: Marina

last: Michaud

overall_design: Bilateral upper limb cephalic vein harvest and carotid-cartoid vein bypass implantation were performed on 25 kg male (n=3) or female (n=1) mongrel dogs. Samples (15 cm) of distended vein were taken following distension during graft harvesting and at 24 hours post-bypass, alongside untouched control vein samples, and embedded in OCT blocks and flash-frozen in an isopentane and liquid nitrogen bath for spatial transcriptomics analysis.

first: Michaud

last: Marina

first: Mota

last: Lucas

last: Patric

first: Bhasin

last: Manoj


title: Dysregulated innate immune signaling cooperates with RUNX1 mutations to transform an MDS-like disease to AML (RNA-Seq)

first: Kwangmin

last: Choi

summary: Dysregulated innate immune signaling is linked to preleukemic conditions and myeloid malignancies like MDS and AML. However, it is unknown whether sustained innate immune signaling contributes to malignant transformation. Here we show that cell-intrinsic innate immune signaling driven by miR-146a deletion (miR-146aKO), a commonly deleted gene in MDS and AML, cooperates with mutant RUNX1 (RUNX1mut) to initially induce marrow failure and features of MDS. However, miR-146aKO HSPCs expressing RUNX1mut eventually progress to a fatal AML. miR-146aKO HSPCs exhaust during serial transplantation, while expression of RUNX1mut restored their hematopoietic cell function. Thus, HSPCs exhibiting dysregulated innate immune signaling require a second hit to develop AML. Inhibiting the dysregulated innate immune pathways with a TRAF6-UBE2N inhibitor suppressed leukemic miR-146aKO/RUNX1mut HSPCs, highlighting the necessity of TRAF6-dependent cell-intrinsic innate immune signaling in initiating and maintaining AML. These findings underscore the critical role of dysregulated cell-intrinsic innate immune signaling in driving preleukemic cells toward AML progression.

overall_design: RNA sequencing on LSK (GFP+) isolated from secondary recipient mice engrafted with miR-146aKO/RUNX1mut, miR-146aKO, RUNX1mut, or wildtype hematopoietic stem and progenitor cells

first: Laura

last: Barreyro

first: Daniel

last: Starczynowski


title: Transcriptome profiling of wild type and DNMT3L-overexpressing Drosophila larvae brains

city: Shenyang

first: JIE

last: LU

state: Liaoning

address: 77 Puhe Road, Shenbei Xiqu

department: Human Anatomy

institute: China Medical University

summary: The objective of the study was to examine the gene expression changes caused by human DNMT3L overexpression in Drosophila melanogaster brains. There were 6 samples in total- C1, C2, C3, D1, D2, and D3. C1-C3 were larvae brains from the strain of elavC155-Gal4, which were used as the control group (C). D1-D3 were larvae brains from the strain with DNMT3L overexpression, which were bred by crossing the strains of elavC155-Gal4 and w/w;P(UAS-DNMT3L,w+)/Cyo;TM2/TM6B and used as the DNMT3L overexpressing group (D). The total RNA of each sample was extracted from 30 brains of the 3rd instar larvae of Drosophila by using TRIzol reagent. Then the RNA samples were processed for high throughput transcriptome sequencing on Illumina HiSeq 3000 platform. Results: among 17737 cleaned RNAs, 267 RNAs were differentially expressed in DNMT3L overexpressing group compared with control group, with q-value ≤ 0.05 and |fold change|≥2 , with more down-regulation  (151) than up-regulation (116). They corresponded to 655 human homologous genes. The differential expressed genes distributed in all chromosomes. Functional annotation with  GO and KEGG enrichment revealed the top functional groups including calcium ion transport, voltage gated channel, choilnergic synapse, serotonergic synapse, and drug metabolism.

overall_design: Transcriptome profiling of 3 control (elavC155-Gal4) and 3 experimental (DNMT3L overexpression,  elavC155-Gal4 X w/w;P(UAS-DNMT3L,w+)/Cyo;TM2/TM6B ) 3rd instar larvae brain samples.

first: Jie

last: Lu

first: Tingting

last: Miao


title: Dysregulated innate immune signaling cooperates with RUNX1 mutations to transform an MDS-like disease to AML (WES)

overall_design: Genomic DNA isolated from FACS sorted BM GFP+/lin-/ckit+/Sca+ cells from WT/vector (n=3), WT/RUNX1mut (n=3), miR-146aKO/vector (n = 3), and miR-146aKO/RUNX1mut secondary transplanted mice were submitted to Otogenetics Corporation (Atlanta, GA, USA) for mouse exome capture and sequencing


title: A tantalum-containing zirconium-based metallic glass with superior endosseous implant relevent properties (xenograft)

city: Beijing

first: Yunshu

last: Wu

address: No.22 Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

summary: Tantalum (Ta) metal is well known for its ideal corrosion resistance and biological effects as endosseous implants. However, the metal has a elastic modulus as high as 186GPa which is not comparable to the natural bone (10-40GPa), and it also has a relative high cost. Here, to fully exploit the advantages of Ta as endosseous implants, a small amount of Ta (as low as 3 at.%) was successfully added into a zirconium-based metallic glass (MG) to generate an advanced functional endosseous implant, Zr58Cu25Al14Ta3 MG, with superior comprehensive properties. Upon carefully dissecting the surface chemistry and atomic structure, the results show that amorphization of Ta enable the uniform distribution in material surface, leading to a significantly improved chemical stability and extensive material-cell contact regulation. Systematical analyses on the immunological, angiogenesis and osteogenesis capability of the material is carried out by utilizing the next-generation sequencing, revealing that Zr58Cu25Al14Ta3 MG can regulate angiogenesis through VEFG signaling pathway and osteogenesis via BMP signaling pathway. Animal experiment further confirms a sound osseointegration of Zr58Cu25Al14Ta3 MG in achieving better bone-implant-contact and inducing faster peri-implant bone formation.

overall_design: To investigate the response of primary mouse bone marrow-derived macrophages to cp Ti, Zr61Cu25Al14 MG and Zr58Cu25Al14Ta3 MG after 48h of co-culturing

first: Feifei

last: Wang

first: Songlin

first: Yuchun

last: Sun


title: Hepatocellular carcinoma specific epigenetic checkpoint bi-directionally regulates antitumor immunity of CD4+T cell

city: Hang Zhou

last: Xu

address: Huansha Roud

institute: Zhejiang University

summary: To investigate the effect of Matr3 CKO of CD4+ T cells on HCC of mice.

overall_design: A 25 μL mixture of PBS and Matrigel (Corning, USA) (1:1) containing 5 × 10^5 Hepa1-6 cells were injected into the left liver lobe of the C57BL/6 mice to establish the HCC orthotopic transplantation mice model. To investigate the effect of Matr3 on tumor infiltrating cells and TCR of T cell, Matr3 CKO and WT mice of CD4+ T cell carried HCC were isolated and analyzed using scRNAseq and TCRseq on the fifth and fourteenth day.

first: Shuai


title: Rutin attenuates ensartinib-induced hepatotoxicity by non-transcriptional regulation of TXNIP

city: Hangzhou

first: Wu

middle: Wen

last: Tong

state: Zhejiang

address: 866 Yuhangtang Road

summary: Ensartinib, an approved ALK inhibitor, is used as the first-line therapy for advanced ALK-positive non-small cell lung cancer in China. Ensartinib shows superior efficacy to crizotinib in both systemic and intracranial disease and is prepared to be reviewed overseas. In future, more patients would benefit from it based on its efficacy.  However, a high incidence of hepatotoxicity has been observed in clinic, which often demands dose reduction or discontinuation of the drug, hampering its overall efficacy. Hence, it is inevitably valuable to study the mechanism which would be benefit to overcome the ensartinib-induced hepatotoxicity. In addition, based on the toxicity model, it is well established to understand the process of drug-induced liver injury and hepatic function-related molecules. Our findings discovered the level and location of TXNIP in liver homeostasis regulatory, clarified the molecular mechanism for ensartinib-induced hepatotoxicity and identified rutin as a potential strategy for the first time. We find a novel mode of rutin in intervening ROS production and apoptosis by binding TXNIP. Our study is of great significance to the basic theories and clinical practice. And this work is of broad interest to the readers from drug discovery, hepatologists in this filed and biologists in redox homeostasis.

overall_design: In order to explore the key marker of ensartinib-induced hepatotoxicity, HL-7702 cells were treated with 2 μM ensatinib or dimethyl sulfoxide for 24 hours.We then performed gene expression profiling analysis using data obtained from RNA-seq of treated or not ensartinib cells . Comparative gene expression profiling analysis of RNA-seq data between ensartinib treatment group and control group.

first: Wentong

first: Jinjin

last: Li

first: Yiming

last: Yin

first: Yourong

last: Zhou


title: Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size (scRNA-seq)

first: Sika

last: Zheng

summary: To examine the transcriptomic changes in Upf2 KO neural progenitors at a single cell level, we performed scRNA-seq using the 10x Chromium platform.

overall_design: Upf2 fl/fl NPC were infected with GFP or CRE lentivirus and used for scRNA-seq.

first: Jing

last: Zhao

first: Naoto

last: Kubota

first: Liang

last: Chen


title: Epstein-Barr virus protein EBNA-LP engages YY1 through leucine-rich motifs to promote naïve B cell transformation [Cut&Run]

city: Durham

first: Jana

last: Cable

state: NC

address: 213 Research Dr.

institute: Duke University

summary: Epstein-Barr Virus (EBV) is associated with numerous cancers including B cell lymphomas. In vitro, EBV transforms primary B cells into immortalized Lymphoblastoid Cell Lines (LCLs) which serves as a model to study the role of viral proteins in EBV malignancies. EBV induced cellular transformation is driven by viral proteins including EBV-Nuclear Antigens (EBNAs). EBNA-LP is important for the transformation of naïve but not memory B cells. While EBNA-LP was thought to promote gene activation by EBNA2, EBNA-LP Knock Out (LPKO) virus-infected cells express EBNA2-activated cellular genes efficiently. Therefore, a gap in knowledge exists as to what roles EBNA-LP plays in naïve B cell transformation. We developed a trans-complementation assay wherein transfection with wild-type EBNA-LP rescues the transformation of peripheral blood- and cord blood-derived naïve B cells by LPKO virus. Despite EBNA-LP phosphorylation sites being important in EBNA2 co-activation; neither phospho-mutant nor phospho-mimetic EBNA-LP was defective in rescuing naïve B cell outgrowth. However, we identified conserved leucine-rich motifs in EBNA-LP that were required for transformation of adult naïve and cord blood B cells. Because cellular PPAR-g coactivator (PGC) proteins use leucine-rich motifs to engage transcription factors including YY1, a key regulator of DNA looping and metabolism, we examined the role of EBNA-LP in engaging cellular transcription factors. We found a significant overlap between EBNA-LP and YY1 in ChIP-Seq data. By Cut&Run, YY1 peaks unique to WT compared to LPKO LCLs occur at more highly expressed genes.  Moreover, Cas9 knockout of YY1 in primary B cells prior to EBV infection indicted YY1 to be essential for EBV-mediated transformation. We confirmed EBNA-LP and YY1and confirmed their biochemical association in LCLs by endogenous co-immunoprecipitation and. Moreover, we found that the EBNA-LP leucine-rich motifs were required for YY1 interaction in LCLs. Finally, we used Cas9 to knockout YY1 in primary total B cells and naïve B cells prior to EBV infection and found YY1 to be essential for EBV-mediated transformation. We propose that EBNA-LP engages YY1 through conserved leucine-rich motifs to promote EBV transformation of naïve B cells.

overall_design: To investigate the role of EBNA-LP leucine-rich motifs in modulating the association of YY1 with chromatin, Cut&Run was performed in LPKO LCLs trans-complemented with wild type EBNA-LP, LRM Mutant, or control vector.

middle: M

first: Nicolas

last: Reinoso-Vizcaino

first: Robert

middle: E

last: White

first: Micah

last: Luftig


title: Epigenetic profiling in adult brain after prenatal BPA exposure [RRBS]

city: Shanghai

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

summary: We reported that, in C57BL/6Slac mice, prenatally exposure to low-dose BPA induces up-regulation of genes associated with neuronal function and down-regulation of genes related to mitochondrial oxidative phosphorylation. Three-dimensional chromatin organization of these differential expressed genes revealed that up-regulated genes are primarily under control of remote enhancers, while down-regulated genes appear to be regulated by chromatin interactions among relative adjacent genes. Further examination of genome-wide repressive epigenetic modifications, specifically DNA methylation, H3K27me3, and H3K9me3 revealed that  transcription of down-regulated genes might be repressed directly by enhanced DNA methylation and H3K27me3 modifications at promoter regions and indirectly by increased DNA methylation at their corresponding interaction regions, while up-regulated genes might be regulated by loss of H3K9me3 occupancy on distal regulatory regions.

overall_design: Examination of whole genome DNA methylation in adult male cortex.

first: Jie

last: Weng

first: Wenzhu

last: Peng


title: Structural determinants for tRNA selective cleavage by RNase 2/EDN

city: Barcelona

first: Jiarui

address: Campus UAB  Cerdanyola del Valles (Bellaterra)

institute: Universitat Autònoma de Barcelona

summary: tRNA-derived fragments (tRFs) have emerged as key players of immunoregulation. Some RNase A superfamily members participate in the shaping of tRFs population. By comparing wild-type and knock-out macrophage cell lines our previous work (Lu L, et al. CMLS, 2022, 79: 209) revealed that RNase 2 can selectively cleave tRNAs. Here, we confirm the in vitro protein cleavage pattern by screening synthetic tRNAs, single-mutant variants and anticodon-loop DNA/RNA hairpins. By sequencing the tRFs products, we identified the cleavage selectivity by recombinant RNase 2 with base specificity at B1 (U/C) and B2 (A) sites, consistent with a previous cellular study. Knowledge of RNase 2 specific tRFs generation might guide new therapeutic approaches for infectious and immune-related diseases.

overall_design: To identify the corresponding tRFs degraded by RNase 2 in vitro, we used a crude method which mimicked next-generation sequencing technology to process our in vitro samples including the teminal treatment on tRFs with enzymes to enable the adaptors to ligate onto the fragments

first: Ester

last: Boix


title: UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency 1

city: Bethesda

first: J. Robert

last: Hogg

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

summary: The RNA helicase UPF1 interacts with mRNAs, mRNA decay machinery, and the terminating ribosome to promote nonsense-mediated mRNA decay (NMD). Structural and biochemical data have revealed that UPF1 exists in an enzymatically autoinhibited “closed” state. Upon binding the NMD protein UPF2, UPF1 undergoes an extensive conformational change into a more enzymatically active “open” state, which exhibits enhanced ATPase and helicase activity. However, mechanically deficient UPF1 mutants can support efficient NMD, bringing into question the roles of UPF1 enzymatic autoinhibition and activation in NMD. Here, we identify two additional important features of the activated open state: slower nucleic acid binding kinetics and enhanced ATP-stimulated nucleic acid dissociation kinetics. Computational modeling based on empirical measurements of UPF1, UPF2, and RNA interaction kinetics predicts that the majority of UPF1-RNA binding and dissociation events in cells occur independently of UPF2 binding. We find that UPF1 mutants with either reduced or accelerated dissociation from RNA have NMD defects, whereas UPF1 mutants that are more dependent on UPF2 for catalytic activity remain active on well-established NMD targets. These findings support a model in which the kinetics of UPF1-mRNA interactions are important determinants of cellular NMD efficiency.

overall_design: Paired-end high-throughput RNA sequencing of rRNA depleted RNA from triplicate biological replicates of Flp-In 293 T-REx  cell lines stably expressing a CLIP-tagged UPF1 mutant transfected with non-targeting control siRNA or siRNA against endogenous UPF1. Cells were reverse-transfected with the indicated siRNAs and harvested 72 hrs post-transfection.

first: Joseph

middle: H

last: Chapman

first: J


title: Epigenetic profiling in adult brain after prenatal BPA exposure [ATAC-seq]

overall_design: Examination of chromatin accessibility in adult male cortical neuron


title: DSS-colitis induced in young age accelerates the onset of cognitive defects in Tg2576 mice, a model of Alzheimer disease

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: In this study we explored if colitis induced by dextran sulfate sodium (DSS) in young, presymptomatic/preplaque mice worse and/or anticipate age-dependent cognitive impairment in Tg2576, a widely used mouse model of Alzheimer disease.

overall_design: Total DNA was extracted from the stool of the mice, amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

first: Amedeo

last: Amedei

first: Simone

last: Baldi

first: Leandro

last: Di Gloria


title: Transcriptional profiling of CD11b+ microglia isolated from cerebellum and olfactory bulb-removed brains of SAMP8 and SAMR1 mice at 2, 5, and 9 months of age.

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: SAMP8 mice serve as an accelerated aging model characterized by inflammation and neurological memory deficits, in contrast to their control SAMR1 counterparts. To investigate the role of microglia in aging, we conducted a comprehensive analysis of microglial heterogeneity using CITE-seq. CD11b positive cells were extracted from cerebellum and olfactory bulb-removed brains at key time points: 2 months, 5 months, and 9 months of age.

overall_design: At 2, 5, and 9 months of age, brains of SAMP8 and SAMR1 mice were prepared by removing the cerebellum and olfactory bulbs. The remaining brain tissue was then physically and enzymatically dissociated in presence of Actinomycin D and Brefeldin A. Following dissociation, CITE-seq antibodies (ADTs and HTOs) and CD11b-PE/Cy5 staining were used. The DAPI-CD11b+ cells were subsequently isolated using fluorescence-activated cell sorting (FACS).

first: Roxane

last: Gruel

first: Baukje

last: Bijnens

first: Johanna

last: Van Den Daele

first: Sofie

last: Thys

first: Peter

last: Verstraelen

last: Roels

first: Renzo

last: Mancuso

first: Niels

last: Vandamme

first: Winnok

last: De Vos


title: A tantalum-containing zirconium-based metallic glass with superior endosseous implant relevant properties (HUVEC)

first: Yunshu

last: Wu

overall_design: To investigate the angiogenesis reaction  of HUVECs to cpTi, Zr61Cu25Al14 MG and Zr58Cu25Al14Ta3 MG after 3 days of co-culturing

first: Feifei

last: Wang

first: Songlin

first: Yuchun

last: Sun


title: UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency

first: J. Robert

last: Hogg

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

overall_design: Refer to individual Series


title: Transcriptional profiling of CD11b+ microglia isolated from cerebellum and olfactory bulb-removed brains of K18-seeded P301L, PBS-injected P301L and PBS-injected FVB  at 1-week, 1-month, and 3-months post-injection.

summary: To gain deeper insights into the relationship between Tau spreading and microglial response, we conducted a comprehensive analysis of microglial heterogeneity in K18-seeded P301L mice at 1 week, 1 month, and 3 months post-injection.  We compared these findings with those from control groups:  P301L mice injected with PBS and  their non-transgenic counterparts, the FVB mice also subjected to PBS injection. For this purpose, we employed CITE-seq to investigate CD11b positive cells isolated from cerebellum and olfactory bulb-removed brains.

overall_design: P301L mice represent a transgenic lineage originating from FVB mice, characterized by their expression of the human tau protein, specifically the 4R/2N isoform. At the age of 3 months, both the transgenic P301L mice and their non-transgenic FVB counterparts were injected with either PBS or K18. Subsequently, the brains of K18-seeded P301L, PBS-injected P301L, and PBS-injected FVB mice were extracted at 1-week, 1-month, and 3-month time points post-injection. After removing the cerebellum and olfactory bulbs, the remaining brain tissue was physically and enzymatically dissociated in the presence of Actinomycin D and Brefeldin A. Following dissociation, CITE-seq antibodies (ADTs and HTOs) and CD11b-PE/Cy5 staining were used. The DAPI-CD11b+ cells were subsequently isolated using fluorescence-activated cell sorting (FACS).

first: Roland

last: Willems

first: Dirk

last: Wuyts

first: Jana

first: Juan

middle: D

last: Pita-Almenar


title: Endothelial Cell Expression of a STING Gain-of-function Mutation Initiates Pulmonary Lymphocytic Infiltration

city: Worcester

first: Kate

last: Fitzgerald

state: MA

address: 364 Plantation street, LRB 260E

institute: UMASS Chan Medical School

summary: Patients afflicted with STING gain-of-function mutations frequently present with debilitating interstitial lung disease (ILD) that is recapitulated in mice expressing the STINGV154M mutation (VM). Prior radiation chimera studies revealed an unexpected and critical role for non-hematopoietic cells in initiating ILD. To identify STING-expressing non-hematopoietic cell types required for the development of ILD, we generated a conditional knock-in (CKI) model and directed expression of the VM allele to hematopoietic cells, fibroblasts, epithelial cells, or endothelial cells. Only endothelial cell-targeted VM expression resulted in enhanced recruitment of immune cells to the lung associated with chemokine expression and the formation of bronchus-associated lymphoid tissue, as seen in the parental VM strain. These findings reveal the importance of endothelial cells as instigators of STING-driven lung disease and suggest that therapeutic targeting of STING inhibitors to endothelial cells could potentially mitigate inflammation in the lungs of SAVI patients or patients afflicted with other ILD-related disorders.

overall_design: To investigate role of the STING gain-of-function mutation V154M (VM), in endothelial cells, we generated a conditioal knock-in (CKI) mouse model of the VM mutation in all cells (CKI x CAGG-cre ERTM) and endothelial cells (CKI x Cdh5-cre ERT2). To understand how ubiquitous and endothelial targeting of VM alters gene expression within lung stromal and parenchymal cells, we depleted hematopoietic (CD45+) and erythrocytes (Ter119+) from the lungs and performed RNA-seq.

first: Kristy

last: Chiang

first: Kevin

last: Gao

first: Katherine

middle: A

first: Ann

last: Marshak-Rothstein


title: C1Q+macrophage interacts with activated CD8+ promoting atherosclerosis development [DC]

last: Xu

summary:
To investigated how SPI1 inhibitor (DB2313) affected the function of DCs , we treated BMDM derived DCs,with DB2313.
We then performed gene expression profiling analysis using data obtained from RNA-seq of peritoneal DCs with DB2313

overall_design: Comparative gene expression profiling analysis of RNA-seq data for treated with DB2313.

first: Shuai


title: A tantalum-containing zirconium-based metallic glass with superior endosseous implant relevent properties

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: C1Q+macrophage interacts with activated CD8+ promoting atherosclerosis development


title: C1Q+macrophage interacts with activated CD8+ promoting atherosclerosis development [T cell]

summary:
To investigate how DC cells treated with SPI1 inhibitor (DB2313) affected the function of primary T cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq of primary T cells incubated with DC cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary T cells incubated with DC cells treated with DB2313.


title: Unravelling the etiology of dilated cardiomyopathy through differential miRNA-mRNA interactome

city: Granada

first: Francisco

last: Hernandez-Torres

state: Granada

address: Avda. de la Investigación, 11

department: Dept. of Biochemistry, Molecular Biology III and Immunology

institute: Universidad de Granada

summary: Dilated cardiomyopathy (DCM) entails a broad group of diseases, acquired or genetic, that share a similar phenotype. The understanding of gene-specific pathogenetic mechanisms and the determination of the functional effects of each variant may tailor different therapeutic strategies. MicroRNAs (miRNAs) are short sequences of non-coding RNA that play an important role in the development of several cardiovascular diseases, including DCM. Here, we applied mRNA and small RNA sequencing to identify the gene and miRNA signature from myocardial biopsies from four patients with DCM caused by volume overload (VCM) and four with ischemic DCM (ICM). Analysis showed five miRNAs and 112 mRNAs dysregulated in VCM vs ICM. Differentially expressed genes were positively enriched for extracellular matrix (ECM), mitochondria respiration-related, cardiac muscle contraction and fatty acid pathways in VCM vs ICM, and negatively enriched for immune response-related pathways, JAK-STAT and NF-kappa B signaling pathways in VCM vs ICM. miRNA-mRNA interaction analysis revealed four negatively correlated miRNA-target transcript pairs, miR-218-5p-DDX6, miR-218-5p-TT39C, miR-218-5p-SEMA4A and miR-494-3p-SGMS2. qRT-PCR validation showed a strong correlation between RNA-seq and qRT-PCR for these genes and miRNAs. These findings suggest that transcriptome signatures may distinguish distinct etiologies of DCM shedding light on underlying biological differences between VCM and ICM.

overall_design: We used RNA-seq and small RNA-seq to identify etiology-specific transcriptome signatures in myocardial biopsies from volume overload dilated cardiomyopathy (VCM) and ischemic  cardiomyopathy (ICM) patients without any valve disease

first: Bonet

last: Fernando

first: Hernandez-Torres

last: Francisco

first: Toro

last: Rocío


title: Genome-wide analysis of long noncoding RNAs as cis-acting regulators of transcription factor-encoding genes in IgA nephropathy

city: Zhengzhou

first: huijuan

last: Tian

state: Henan

address: No.1 Jianshe East Road, Zhengzhou, (China)

institute: The First Affiliated Hospital of Zhengzhou University

summary: IgA nephropathy (IgAN) is the most common form of primary glomerulonephritis in the world, but the disease pathogenesis noncoding is yet to be elucidated.Previous studies have revealed regulatory functions for long noncoding RNA (lncRNA) in various diseases; however, the roles of lncRNA in IgAN and regulation of transcription factors (TFs) have been scarcely investigated.

overall_design: Renal tissue samples (n = 5) from patients with IgAN and control samples (n = 4) were collected and RNA sequencing (RNA-seq) was performed.

last: tian

first: yaling

last: zhai

first: zhanzheng

last: zhao


title: Transcriptional profiling of Rhodotorula toruloides IST536 and derived evolved strain IST536 MM15 under non-stressing conditions

city: Lisbon

first: Isabel

last: Sá-Correia

address: Avenida Rovisco Pais, 1

department: Department of Bioengineering

country: Portugal

institute: Instituto Superior Técnico

summary: The oleaginous red yeast species Rhodotorula toruloides, a prominent environmental basidiomycetous yeast, has garnered significant interest for its remarkable capacity to utilize main carbon sources present in lignocellulosic hydrolysates, such as glucose, xylose, and acetic acid, and to efficiently produce lipids and carotenoids. This species can also efficiently use other less usual and difficult-to-catabolize C-sources, as is the case of the acid sugar D-galacturonic acid and the neutral sugar L-arabinose, present in hydrolysates from pectin-rich agro-industrial residues. Strain R. toruloides IST536 (alias PYCC 5615) was previously selected in our laboratory for sugar beet pulp valorization based on its ability to produce lipids and carotenoids through the complete catabolism of the major C-sources present in the hydrolysates (1). This strain, whose genome has been recently sequenced in our laboratory, is a conjugated strain derived from IFO 0559 (isolated from wood-pulp; GCA_000988805.1) × IFO 0880 (isolated from air; GCA_001255795.1) (2). Despite its potential, the metabolism of this promising strain can be limited by the presence of acetic acid in the hydrolysates as well as other inhibitors present in lignocellulosic hydrolysates. To increase IST536 (PYCC 5615) strain robustness, an adaptive laboratory evolution (ALE) strategy was used. The selected evolved strain IST536 MM15 exhibits increased tolerance to several inhibitors of biotechnological relevance: methanol and the four main inhibitors present in lignocellulosic hydrolysates: acetic and formic acids, hydroxymethylfurfural (HMF), and furfural (3). The superior performance of this evolved multi-stress tolerant strain for lipid production from non-detoxified lignocellulosic biomass hydrolysates was confirmed. To obtain mechanistic insights underlying such multi-tolerant phenotype, the genomes of the original and the evolved strains, IST536 (PYCC 5615) and IST536 MM15, respectively, were sequenced and the transcriptomic profiling of both strains under non-stressing conditions was performed.  References:  1. Martins LC, et, al. Journal of Fungi. 2021; 7(3):215. https://doi.org/10.3390/jof7030215  2. Banno, I. (1967). The Journal of General and Applied Microbiology, 13(2), 167-196. https://doi.org/10.2323/jgam.13.167  3. Fernandes, M. A., Mota, M. N., et al,  Journal of Fungi, 2023, 9(11), 1073 https://doi.org/10.3390/jof9111073

overall_design: mRNA profiling of R. toruloides IST536 and the derived evolved strain IST536 MM15 unstressed cells. A total of 4 samples were analysed (2 biological replicates)

first: Miguel

last: Antunes

first: Marta

middle: N

last: Mota


title: Transcriptomic changes in eutopic endometrium and ectopic lesions in mouse model during progression of endometriosis-related infertility

city: Columbia

first: Rong

last: Li

state: MO

address: 1030 Hitt Str

department: OBGYN

institute: University of Missouri

summary: In this study, we performed transcriptomic analysis in ectopic lesions and eutopic endometrial tissues from both fertile and subfertile mice with endometriosis. We identified the positive correlation of the gene signatures between the mouse and human in ectopic lesions. Conserved gene networks were activated in all the ectopic lesions including estradiol, immune, fibrosis, and angiogenesis pathways. The interactions mediated through hormone, cytokine, and growth factor as well as their corresponding receptors were predicted between the ectopic and eutopic endometrium. EGF and WNT signaling were more suppressed in the eutopic endometrium from subfertile mice. Our results revealed that our mouse endometriosis model recapitulates the important transcriptomic changes of endometriosis progression in human ectopic lesions including the essential regulator network and intensive inter-communications between ectopic and eutopic endometrium. Our preclinical animal model for endometriosis will be invaluable to understand etiology and pathophysiology on endometriosis.

overall_design: Four fertile and four subfertile Pgrcre/+Rosa26mTmG/+ mice with endometriosis, and four sham mice for each group of endometriosis mice as control. These mice underwent either surgery to induce endometriosis or sham surgery. Fertile sham and mice with endometriosis were used one month after surgery, while subfertile ones were used three months after surgery. RNA-Seq analysis and identification of differential expressed genes and pathways in the ectopic lesions and eutopic uteri from mice with endometriosis and sham mice at day of pregnancy 3.5.

first: Tae

last: Kim

first: Dinh

last: Tran

first: Bruce

last: Lessey

first: Steve

middle: L

last: Young

first: Jae

last: Jeong


title: Epigenome analysis of normal oral keratinocytes cells and oral squamous cell carcinoma (OSCC) cells

city: Chengdu

first: Yangfan

last: Liu

address: People South Street

institute: Sichuan University

overall_design:
Genome wide DNA methylation profiling of normal oral keratinocytes (NOK) cells (n=3), Cal27 cells (n=3), DNMT1 silenced (sh-DNMT1) Cal27 cells (n=4) and short hairpin RNA negative control (sh-NC) Cal27 cells (n=3).
The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in cell pellets.
Bisulphite converted DNA from the 13 samples were hybridized to the Illumina Infinium 850k Human Methylation Beadchip.

first: Jingjing

last: Luo

first: Hongmei

last: Zhou


title: A tantalum-containing zirconium-based metallic glass with superior endosseous implant relevant properties (BMSC)

first: Yunshu

last: Wu

summary: Tantalum (Ta) metal is well known for its ideal corrosion resistance and biological effects as endosseous implants. However, the metal has a elastic modulus as high as 186GPa which is not comparable to the natural bone (10-40GPa), and it also has a relative high cost. Here, to fully exploit the advantages of Ta as endosseous implants, a small amount of Ta (as low as 3 at.%) was successfully added into a zirconium-based metallic glass (MG) to generate an advanced functional endosseous implant, Zr58Cu25Al14Ta3 MG, with superior comprehensive properties. Upon carefully dissecting the surface chemistry and atomic structure, the results show that amorphization of Ta enable the uniform distribution in material surface, leading to a significantly improved chemical stability and extensive material-cell contact regulation. Systematical analyses on the immunological, angiogenesis and osteogenesis capability of the material is carried out by utilizing the next-generation sequencing, revealing that Zr58Cu25Al14Ta3 MG can regulate angiogenesis through VEFG signaling pathway and osteogenesis via BMP signaling pathway. Animal experiment further confirms a sound osseointegration of Zr58Cu25Al14Ta3 MG in achieving better bone-implant-contact and inducing faster peri-implant bone formation.

overall_design: To investigate the angiogenesis reaction of BMSCs to cpTi, Zr61Cu25Al14 MG and Zr58Cu25Al14Ta3 MG after 3 days of co-culturing

first: Feifei

last: Wang

first: Songlin

first: Yuchun

last: Sun


title: Decoding at single cell resolution the molecular and functional program of pathogenic Th2 cells subsets in humans

first: Beatriz

last: León

state: Maryland

address: Building 10, Room 11N240A, 10 Center Drive

department: NIAID

institute: NIH

summary: Unraveling the diversity of Th2 effector cells subsets may help us to understand their pathogenic role in Type-2 associated inflammatory disorders, including allergic diseases and helminth infections. To characterize the heterogeneity and function of these effector Th2 cells, we analyzed 47 subjects’ PBMCs [23 filarial-infected (Fil+) with or without coincident HDM sensitization (Fil+HDM+ n=12; Fil+HDM-, n=11) and 24 subjects without filarial infection (Fil-) (Fil-HDM+ n=12; and Fil-HDM-, n=12) using multiparameter flow cytometry and two-level FlowSOM analysis. The frequency of 3 memory CD4+ T cell clusters, including CCR4+CCR6+CRTH2- (subset 1), CCR4+CCR6-CRTH2+ (subset 2), and CCR6+CCR4+CRTH2+ (subset 3) were markedly enriched among Fil+ subjects. The functional characterization indicated subset 2 and 3 as distinct Th2 cytokine producers, which together were responsible for the majority of IL-4, IL-5, or IL-13 produced among the Fil+ subjects. These subsets were sorted and analyzed by multiomic single cell RNA profiling. Indeed, both subset 2 and subset 3 presented features of pathogenic Th2 effector cells based on their single cell molecular signature, including downregulation of cd27 and high expression levels of itga4, il-17rb, hpgds, klrb1, ptgdr2, il-9r, il-4, il5 and il-13 genes when compared with conventional Th2 cells from healthy controls. When the Fil+ subjects were divided  based on allergic status, the Fil+HDM+ subjects had an expansion of both subset 2 (3.19% vs 1.28%, p=0.001) and subset 3 (0.39% vs 0.15%, p=0.002) Th2 cells when compared with Fil+HDM-. Gene expression analysis further demonstrated that concomitant HDM sensitization in the presence of filarial infection reshaped the molecular program of these pathogenic effector Th2 subsets by even further upregulating the expression of gata3, il17rb, clrf2, and klrb1. Notably, Fil+HDM+ patients’ cells showed higher responsiveness to filarial or HDM antigenic stimulation, producing even higher levels of IL-4, IL-5 and IL-13 when compared with Fil+HDM- patients. This distinct molecular and functional program of Th2 effector cells subsets sheds new light on the Th2 cell plasticity and their contribution to immune regulation in helminth infection and allergic diseases.

overall_design: From a previously described cohort of 49 subjects used to characterize the nature of the T cell response induced by parasite antigens and aeroallergens in the context of filarial-infected individuals with or without coincident allergic sensitization, 47 north American individuals, with no history of helminthic infection prior to this study were included in the current study population. Out of the 47 subjects, 24 patients were diagnosed with filarial infection, including either Loa loa, Wuchereria bancrofti or O. volvulus by clinical, parasitological, and molecular analysis. Moreover, 23 healthy volunteers (NIH blood bank donors) comprised the control group. Later, these individuals were divided in 4 groups based on their allergic status presenting or not concomitant HDM sensitization. Individuals with allergen-specific IgE levels >0.35 kUA/L by ImmunoCAPTM Phadiatop assay were considered allergic/atopic. Group 1: HDM-Filarial- (n=12), group 2: HDM+Filarial- (n=12), group 3: HDM-Filarial+ (n=11), and group 4: HDM+Filarial+ (n=12).

first: Pedro

last: Gazzinelli-Guimaraes

first: Brittany

last: Dulek

first: Justin

last: Lack

first: Phillip

last: Swanson

first: Mario

last: Roederer

first: Thomas

middle: B

last: Nutman


title: Epigenetic profiling in adult brain after prenatal BPA exposure [ChIP-seq]

first: Yan

last: Jiang

overall_design: Examination of histone H3K9me3 and H3K27me3 modification in  of adult male cortex.

first: Jie

last: Weng

first: Wenzhu

last: Peng


title: Epigenetic profiling in adult brain after prenatal BPA exposure [RNA-seq]

overall_design: mRNA profiles of prefrontal cortex from adult mice


title: Bulk RNA-seq of sham or alkali injury treated WT and Vegfr3 depletion mouse iris

city: Guangzhou

first: Zheng

address: No. 7 Jinsui Rd, Guangzhou, People 's Republic of China

institute: Zhongshan Ophthalmic center, Sun Yat-sen University

summary: We report conditional ablation of lymphatic Vegfr3 alleviated inflammatory process in alkali injured iris. Prox1CreERT2 mice were crossed with Vegfr3fl/fl to selectively target gene expression in Prox1+ lymphatic cells. Injury models were established at 6 weeks postnatally, and Vegfr3 gene depletion was conducted via Tamoxifen injection on the day 13th-17th after corneal alkali injury. Mice were sacrificed 28th days post-injury.

overall_design: To evaluate the pathological impact of Vegfr3 in alkali-injured mouse iris, we performed bulk RNA-sequencing analysis from PBS-treated Sham Vegfr3fl/fl mice, corneal alkali injury-treated Injured Vegfr3fl/fl and Injured Vegfr3fl/fl;Prox1CreERT2 mice. We conducted three experiments (3 identical genotype samples in each group).

first: Bingsheng

last: Lou

first: Feng

last: Zhang

first: Xiaofeng

last: Lin


title: Epigenetic profiling in adult brain after prenatal BPA exposure


title: Epigenetic checkpoint regulates anti-tumor immunity of CD4 T cell in Hepatocellular carcinoma

last: Xu

summary:
To investigated how Matr3 KO affected the function of CD4 T cells
We then performed gene expression profiling analysis using data obtained from Hi-C seq of Jurkat T cells knocked out of Matr3 or not.

overall_design: Comparative gene expression profiling analysis of Hi-C seq data for Jurkat T cells knocked out of Matr3 or not.

first: Shuai


title: Pharmacological inhibition of LIFR impairs ovarian cancer progression by blocking LIF/LIFR autocrine loop

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: We examined the transcriptional chagnes modulated by LIFR inhibitory compound EC359 by perfroming global transcriptome analysis. ES2 cells were treated with vehicle or EC359 for 12 h and the RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that EC359 modulated unique pathways  including oxidative phosphorylation, Glutathione signaling, JNK signaling, NRF2 signaling, ovarian cancer signaling, hypoxia signaling and apoptotic pathways.

overall_design: Total RNA was isolated from ES2 cells that are treated with vehicle (0.1% DMSO) or EC359 (10 nM) for 12 hours. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 2000 in duplicate. The combined raw reads were aligned to UCSC hg19 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Suryavathi

last: Viswanadhapalli

first: Ratna

last: Vadlamudi


address: Huansha Roud

summary:
To investigated how Matr3 KO affected the function of CD4 T cells
We then performed gene expression profiling analysis using data obtained from RNA-seq of Jurkat T cells knocked out of Matr3 or not.

overall_design: Comparative gene expression profiling analysis of RNA-seq data forJurkat T cells knocked out of Matr3 or not.

last: Wang


title: WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination

city: shanghai

first: Yaning

last: Du

address: shanghai

institute: Shanghai Jiao Tong University

summary: Proteasome-mediated degradation of chromatin-bound NF-κB is critical in terminating the transcription of pro-inflammatory genes and can be triggered by Set9-mediated lysine methylation of RelA subunit. However, the E3 ligase targeting methylated RelA remains unknown. Here, we identified two structurally similar WD-40 repeat (WDR) proteins, WSB1 and WSB2, as the E3s that recognize chromatin-bound methylated RelA for polyubiquitination and proteasomal degradation. WSB1/2 specifically recognized methylated lysines (K) 314 and 315 of RelA via their WDR domains. Deletion of WRD in WSB1/2 or mutation of K314/315 of RelA to arginines abolished the interaction between WSB1/2 and RelA. RNA-sequencing of TNF--stimulated WSB1/2 knockdown cells revealed that WSB1/2 negatively regulated a subset of NF-B target genes with reduced polyubiquitination of chromatin-bound RelA. TNF- stimulated the methylation of RelA and the subsequent recruitment of WSB1/2 to the promoters of these NF-B target genes to terminate the transcription. Computational modeling demonstrated that a highly conserved Asp within repeat 3 of WDR domains of WSB1/2 coordinated its interaction with K314/K315 of RelA, with a higher pKa when either of the lysines is methylated. Together, these findings identify novel E3 ligases that target chromatin-bound methylated RelA for proteolysis to prevent sustained NF-κB activation, providing new targets for therapeutic intervention of NF-κB-mediated inflammatory diseases.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for U2OS cells and its KD derivatives (shWSB2) under normal conditions and TNF-α stimulation (two replicates per sample)
Please note that each processed data file contains processed data for two samples and is linked to the corresponding '1' sample records.

first: Yuanyuan

last: Yu

first: Yurong

last: He

first: Dandan

last: Wu

first: Xiaoli

first: Matt

last: Sinclair

first: Emad

last: Tajkhorshid

first: Yuejuan

last: Zheng

first: Zhaoyuan

last: Hou

first: Lin-Feng

first: Xiao-Dong

last: Yang