title: Vorasidenib and ivosidenib in IDH1-mutant low-grade glioma: a randomized, perioperative phase 1 trial

city: Boston

first: Ania

last: Tassinari

state: MA

address: 200 Pier 4 Blvd

department: Data Science

institute: Servier Pharmaceuticals

summary:
A phase-1, multi-center study in recurrent non-enhancing gliomas with IDH1 R132H mutation for patients who require surgery. The purpose of this study is to evaluate the suppression of 2-HG (2-hydroxyglutarate) by comparing the concentration of 2-HG in resected tumors from IDH1 mutant glioma subjects following AG-120 or AG-881 treatment with the 2-HG concentration in untreated, control tumors. The safety, tolerability, PK/PD, and anti tumor activity data from the study in subjects with recurrent non-enhancing Grade 2/3 LGG with an IDH1 R132H mutation for whom surgical resection is indicated will identify the recommended dose of AG-120 and AG-881 for future studies in glioma.
Vorasidenib and ivosidenib inhibit mutant forms of isocitrate dehydrogenase (mIDH) and have shown preliminary clinical activity against mIDHglioma. We evaluated both agents in a perioperative phase 1 trial to explore the mechanism of action in recurrent low-grade glioma (IGG) and select a molecule for phase 3 testing. Primary end-point was concentration ofD-2-hydroxyglutarate (2-HG), the metabolic product of mIDH enzymes, measured in tumor tissue from 49 patients with mIDH1-R132H nonenhancing gliomas following randomized treatment with vorasidenib (50 mg or 10 mg once daily, q.d.), ivosidenib (500 mg q.d. or 250 mg twice daily) or no treatment before surgery. Tumor 2-HG concentrations were reduced by 92.6% (95% credible interval (CrI), 76.1–97.6) and 91.1% (95% CrI, 72.0–97.0) in patients treated with vorasidenib 50 mg q.d. and ivosidenib 500 mg q.d., respectively. Both agents were well tolerated and follow-up is ongoing. In exploratory analyses, 2-HG reduction was associated with increased DNA 5-hydroxymethylcytosine, reversal of ‘proneural’ and ‘stemness’ gene expression signatures, decreased tumor cell proliferation and immune cell activation. Vorasidenib, which showed brain penetrance and more consistent 2-HG suppression than ivosidenib, was advanced to phase 3 testing in patients with mIDHLGGs. Funded by Agios Pharmaceuticals, Inc. and Servier Pharmaceuticals LLC; ClinicalTrials.gov number NCT03343197.

overall_design:
Patients with IDH1-mutated low-grade glioma were treated with AG-120 (ivosidenib), AG-881 (vorasidenib), or Placebo for 28 days before surgical resection. A portion of the surgical sample was submitted for exome capture-based transcriptome sequencing (Personalis ACE Whole Transcriptome). Following surgery, subjects had the option to continue (or initiate) treatment with AG-120 or AG-881.
dbGaP Study Accession: phs003148.v1.p1

first: Sung

last: Choe


title: The Role of Uridine Glucuronosyl transferase 2B28 (UGT2B28) in Prostate Cancer Progression

status: Public on May 12 2023

city: Houston

first: Danthasinghe

middle: Badrajee

last: Piyarathna

state: United States

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

type: Expression profiling by high throughput sequencing

summary:
To understand the effect of UGT2B28 on organoid formation, we generated lentiviral-mediated UGT2B28 knockdown and rescue (by overexpressing UGT2B28  in the knockdown background) in LNCaP cells.
These engineered cells were then allowed to spontaneously form organoids in a low attachment setting. We then performed transcriptomics on the organoids.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LNCaP control (NT), LNCaP KD (2B28 knockdown), and LNCaP rescue (overexpression of 2B28 in KD background)

first: Anindita

last: Ravindran

first: Badrajee

last: Waduge

first: Arun

last: Sreekumar


title: Identification of m6A-mediated changes in mouse liver after exposure to polychlorinated biphenyls (PCB126 and Aroclor1260) and high fat diet

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Exposure to polychlorinated biphenyls (PCBs) has been associated with liver injury in human cohorts and with nonalcoholic steatohepatitis (NASH) in mice fed a high fat diet (HFD). N(6)-methyladenosine (m6A) modification of mRNA regulates transcript fate, but the contribution of m6A modification on regulation of transcription in PCB-induced steatosis and fibrosis is unknown. This study tested the hypothesis that PCB and HFD exposure alters the levels of m6A modification in transcripts that play a role in NASH in vivo. Male C57Bl6/J mice were fed a HFD (12 wks.) and administered a single oral dose of Aroclor1260, PCB126, or Aroclor1260 + PCB126. Genome-wide identification of m6A peaks was accomplished by m6A mRNA immunoprecipitation sequencing (m6A-RIP) and the mRNA transcriptome identified by RNA-seq. Exposure of HFD-fed mice to Aroclor1260 decreased the number of m6A peaks and m6A-containing genes relative to HFD control whereas PCB126 or the combination of Aroclor1260+PCB126 increased m6A modification frequency. ~ 41% of genes had one m6A peak and ~49% had 2-4 m6A peaks. 117 m6A peaks were common in the four experimental groups. The Aroclor1260 + PCB126 exposure group showed the highest number (52) of m6A-peaks. qRT-PCR confirmed enrichment of m6A-containing fragments of the Apob transcript with PCB exposure. Integrated analysis of m6A-RIP-seq and mRNA-seq identified 242 differentially expressed genes (DEGs) with increased or reduced number of m6A peaks. Comparative pathway analysis identified “Immune response: IL-6-induced acute-phase response in hepatocytes” in the Aroclor1260 + PCB126 samples, consistent with steatohepatitis in human PCB epidemiological studies. These data show that PCB exposure in HFD-fed mice alters the m6A landscape offering an additional layer of regulation of gene expression affecting a subset of gene responses in NASH.

overall_design: Male C57Bl/6J mice were fed a HFD (42% kCal from fat) and treated with Aroclor 1260, PCB 126, and the combination of Aroclor 1260 + PCB 126 for 12 weeks. Livers were harvested and snap frozen. RNAs isolated were subjected to MeRIP m6A Assay with the Magna MeRIP™ m6A Kit (Millipore, Catalog No. 17-10499). 44 samples, 4 treatment groups, 5 replicates for each group, Input and m6A IP for each sample, plus 1 Ctrl IgG IP for each group were sequenced.

first: Belinda

middle: J

last: Petri

first: Kelianne

middle: M

last: Piell

first: Banrida

last: Wahlang

first: Kimberly

middle: Z

last: Head

first: Kalina

last: Andreeva

middle: C

first: Matthew

last: Cave

first: Carolyn

last: Klinge


title: Gene expression profile of liver metasized tumor tissue in HFD-fed and LFD-fed mice

status: Public on May 11 2023

city: Los Angeles

first: Ekihiro

last: Seki

state: CA

address: 8700 Beverly Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

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

relation:
SuperSeries of: GSE227913
SuperSeries of: GSE227914

overall_design: Refer to individual Series


title: Gene expression profile at single cell level of immune cells from the liver metasized tumor tissue [scRNA-seq]

summary:
To investigate the effect of diet and Yap KD on liver matastasis, we injected MC38 cells in LFD-fed or HFD-fed mice, and MC38 with shCon or shRNA for Yap (shYap1) in HFD-fed mice
We then performed gene expression profiling analysis in various cell types using data obtained from single cell RNA-seq of these 4 different conditions

overall_design: Comparative gene expression profiling analysis of single cell RNA-seq data for LFD-fed and HFD-fed liver metastatic tumors and its KD derivative (shYap)

first: So

middle: Y

last: Kim


title: Gene expression profile of the liver metastatic tumor tissue in HFD-fed and LFD-fed mice [RNA-seq]

summary:
To investigate the effect of diet and Yap KD on liver matastasis, we injected MC38 cells in LFD-fed or HFD-fed mice, and MC38 with shCon or shRNA for Yap (shYap1) in HFD-fed mice
We then performed gene expression profiling analysis using data obtained from RNA-seq of these 4 different conditions

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LFD-fed and HFD-fed liver metastatic tumors and its KD derivative (shYap)


title: Vemurafenib can induce senescence via HIPPO signaling pathway: An alternative targeted therapy against AML and MDS

city: Chongqing

first: Qiao

last: Zhou

state: State...

address: 1 Youyi Road, Yuzhong, Chongqing,China

country: China

institute: The First Affiliated Hospital of Chongqing Medical University

summary: The outcome of Acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) remain dismal despite the development of treatment. Exploration of alternative targeted gene therapy gradually become a new hot field in improving prognosis. We found BRAF was overexpressed in AML and MDS, which is correlated with poor prognosis. The BRAF inhibitor-Vemurafenib (VEM) could significantly induce senescence and therefore resulted in proliferation inhibition and apoptosis of AML cells. Moreover, this inhibitory effect was verified in CD34+ cells derived from AML patients, and enhanced by Bortezomib (BOR). Mechanistically, we showed that VEM combined with BOR could upregulate MST2 and turned on HIPPO signaling pathway, thereby inducing cellular senescence in vitro and vivo. Our data implicated BRAF expression in the biology of AML patients. We reported clinical correlates and provide a potential biological basis for these correlations. Analyzing the expression of BRAF may help predict prognosis and provide potential therapeutic target for AML and MDS patients.

overall_design: SAMPLE1 and SAMPLE5 was SKM-1 as control; SAMPLE2 and SAMPLE6 was SKM-1 treated with BOR; SAMPLE3 was SKM-1 treated with VEM;SAMPLE 4 was SKM-1 treated with VEM combined BOR.


title: RNA-seq profiling of WT and LKB1 knockout mouse embryonic fibroblasts treated with the HAT inhibitor A485

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Investigating transcriptional profile of WT and LKB1 knockout mouse embryonic fibroblasts untreated, stimulated with IL-1β, treated with A485 alone, or stimulated with IL-1β and A485

overall_design: RNA-seq was performed on WT and LKB1 knockout MEFs that were pre-treated with the HAT inhibitor A485 for 30 minutes prior to 6 hour vehicle or IL-1β treatment.

first: Shelby

middle: E

last: Compton

middle: G


title: Mesenchymal Osr1 cells orchestrate lymph node initiation

city: Berlin

first: Pedro

last: Vallecillo García

state: Berlin

address: Augustenburger Platz 1

department: Hematology and Oncology

country: Germany

institute: Charité Berlin

summary: We isolated Osr1-expressing cells (Osr1 GCE/+) via FACS-sorting from E13.5 axillary, inguinal and cervical regions of a mouse embryo and analysed the gene expression profile of 10,000 cells through single-cell RNA-seq.

overall_design: Transcriptional heterogeneity of Osr1+ cells at the developmental stage 13.5

last: Vallecillo-García

first: Mickael

last: Orgeur

first: Cornelius

last: Fischer

first: Sascha

last: Sauer

first: Sigmar

last: Stricker


title: Cis-regulatory atlas of primary human CD4+ T cells

city: Cincinnati

first: Kurtis

last: Stefan

state: OH

address: 3333 Burnet Ave

department: Dept Allergy & Immunology

institute: University of Cincinnati

summary: Naïve CD4+ T Cells are capable of differentiating into numerous T helper effector lineages depending on the provided local cytokines during activation. Cis-regulatory elements (CRE) are critical for cell differentiation, homeostasis, and function; however, CRE functional annotation (e.g. silencers, enhancers, and insulators) from existing genomic libraries remains an active need. Genome wide screens, including Transcribing Active Regulatory Region Sequencing (STARR-Seq) provides quantifies enhancer activity. However, these screens are mainly conducted in immortalized cell lines. Therefore, we have modified STARR-Seq using a non-integrating lentiviral transduction system (Lenti-STARR-seq) to investigate CRE in human CD4+ T cells. We identify and validate functional enhancers and negative regulatory elements (NRE). These elements differences stark differences in chromatin modification, TF binding, and nucleosome positioning. Additionally, STARR-Seq enhancers, but not NRE, exhibit transcription of enhancer RNA. Collectively these data suggest that Lenti-STARR-Seq may be a useful tool in the screening of primary human cell types for CRE function, and provides an atlas of functional CRE in human CD4+ T Cells.

overall_design: Freshly isolated hCD4 T Cells are suspended to 6.6E6 cells per mL in CTS Optimizer, then combined 0.33mL concentrated lentivirus per mL cells. Cells are spinfected in low-bind 6-well plates (Corning #3471) ant 7ug/mL polybrene (MilliporeSigma #TR1003G) at 950g, 32°C, for 2 hours. Immediately following spinfection, cells are gently resuspended and cultured for 2 hours at 37°C, 5% CO2. Cells collected and centrifuged and suspended cultured for 24 hours. Cells are treated with 100U DNaseI (NEB M0303S) for 30 minutes at 37°C.     Total RNA is purified from transduced cells (Qiagen #75144) and concentrated 7.5x using RNA Cleanup (NEB #T2040L). RNA was Reverse Transcribed according to manufacturer guidelines for STARR-Seq transcript specific primers (Supplemental File 1) with SuperScript IV (Invitrogen #18090010), using twice the recommended RNA input. cDNA was purified using a Reaction Cleanup Kit (Qiagen #28206). cDNA was amplified using custom library primers (Supplemental File 1) as previously described.1 Diluted Plasmid control was amplified using an input concentration which yielded the same amplification cycle number as the STARR library for hCD4+ Donor I. Library was purified using PCR cleanup columns (Qiagen #28206), and quantified for PE-150bp sequencing (Novogene).

first: Artem

last: Barski


title: Genome wide screen of H3K27ac enrichment in WT, LKB1 KO, and LKB1/CRTC2 KO mouse embryonic fibroblasts

type: Genome binding/occupancy profiling by high throughput sequencing

summary: H3K27ac ChIP-seq analysis in WT, LKB1 KO, and LKB1/CRTC2 KO mouse embryonic fibroblasts untreated or stimulated with IL-1β

overall_design: WT, LKB1 KO, and LKB1/CRTC2 KO MEFs were untreated or stimulated with IL-1β for 6 hours and H3K27ac ChIP was performed


title: RNA-seq profiling of WT, LKB1 KO, and LKB1/CRTC2 KO mouse embryonic fibroblasts

summary: Investigating transcriptional profile of WT, LKB1 KO, and LKB1/CRTC2 KO mouse embryonic fibroblasts untreated or stimulated with IL-1β

overall_design: RNA-seq was performed on WT, LKB1 KO, and LKB1/CRTC2 KO MEFs either untreated or stimulated with IL-1β for 6 hours


title: Bulk TCRseq analysis on CD8+ T cells in FSCN1-KI bone marrow chimera mice following anti-CD4 and anti-PDL1 mAb treatment

city: Noda

first: Hiroyasu

last: Aoki

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

summary: The repertoire of tumor-infiltrating T cells is a novel perspective to characterize effective anti-tumor T cell responses. Previous studies reported that the oligoclonal expansion in tumor T-cell repertoire is associated with anti-tumor effects. However, the contribution of the expansion of diverse T-cell clones remained unclear. We demonstrated that the polyclonal fraction of tumor-reactive T-cell repertoire consisting of relatively minor clones, increased in tumor-bearing mice treated with anti-PD-L1 or anti-CD4 monoclonal antibodies (mAbs), while the oligoclonal fraction consisting of major clones was unchanged. Moreover, the polyclonal fraction was enriched with progenitor exhausted T cells, essential for a durable anti-tumor response, and more dependent on CCR7+ migratory dendritic cells, responsible for priming tumor-reactive T cells in the tumor-draining lymph node (dLN). These results proposed that the expansion of diverse tumor-reactive clones, “clonal spreading,” is an important mechanism by which anti-PD-L1 and anti-CD4 treatments exert robust and durable anti-tumor T-cell responses.

overall_design: CD8+ T cells from tumor, and CD8+ CD44high T cells from draining lymph node (dLN) were collected from B16F10 tumor-bearing Fscn1 knock-in BMC mice treated with anti-CD4 monoclonal antibody (mAb), anti-PD-L1 mAb or combination of anti-CD4 and anti-PD-L1 mAbs, with or without diphtheria toxin (DT) administration. Bulk TCR sequencing was performed, and T cell clones that overlap between tumor and dLN were identified.

first: Mikiya

last: Tsunoda

first: Haru

last: Ogiwara

first: Haruka

last: Shimizu

last: Abe

first: Takaya

first: Shigeyuki

last: Shichino

first: Kouji

last: Matsushima

first: Satoshi

last: Ueha


title: Cell atlas of trabecular meshwork in glaucomatous non-human primates and DEGs related to tissue contraction based on single-cell transcriptomics

status: Public on May 10 2023

city: Beijing

first: Jian

last: Wu

address: Beijing Tongren Eye Center, Beijing Key Laboratory of Ophthalmology and Visual Sciences, No. 1 Dong Jiao Min Xiang Street, Dongcheng District, Beijing 100730, P.R. China.

institute: Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University

summary: Dysfunction of TM, which is the main channel of aqueous humor outflow, can lead to elevated intraocular pressure (IOP) and result in primary open-angle glaucoma (POAG), but the molecular mechanism is still unclear. In this research, single-cell RNA sequencing (scRNAseq) analysis of TM were performed in spontaneous POAG and healthy macaques to compare cellular heterogeneity, thus exploring differentially expressed genes (DEGs) and pathways associated with dysfunction of TM contraction. Here, we show a comprehensive cell atlas of TM upon clustering analysis based on single-cell transcriptomics, which 14 distinct cell types were identified and some of them were associated with tissue contraction. The proportions of each cell types between spontaneous POAG and healthy macaques were different. Multiple genes associated with TM contraction were identified in Beam A, Beam B, Beam C and SMC cell types, with TPM1 and its associated ACTC1 and TNNT1 being first found. TPM1, ACTC 1 and TNNT1 were considered to be important protein in the regulation of tissue contraction, and the expressions of them were confirmed to be located in the sieve-like region of TM, which expressions in POAG models were lower than that in normal models. Altered levels of TPM1 expression have significant impact on TNNT1 and ACTC1 expression downstream of it. In addition, the microstructural alterations in TM of POAG non-human primate were observed, which was compact and collapsed. Thus, our study indicated that TPM1 may be a key target for regulating TM structure, contraction function and resistance of aqueous humor outflow.

overall_design: To explore the cell types and related genes and pathways involved in the relaxation and contraction of the sieve pore of TM in POAG, we screened spontaneous POAG monkey models. We analyzed the scRNAseq results and the healthy controls in our study. Having carefully compared the two groups in cell types, cell proportion, and differentially expressed genes, we unveiled the principal pathways regulating the aqueous outflow in the TM tissue.

first: Xu

last: Jia

first: Xiaohong

last: Chen

first: Simeng

last: Hou

first: Yangyang

last: Li

first: Ling

last: Zhao

first: Yingting

last: Zhu

first: Zhidong

first: Caibin

last: Deng

first: Wenru

last: Su

first: Yehong

last: Zhuo


title: Clonal spreading of tumor-infiltrating T cells underlies the durable antitumor effects of PD-1 blockade and anti-CD4 monoclonal antibody

first: Hiroyasu

last: Aoki


title: Identification and characterization of miRNAs in spleens of sheep subjected to repetitive vaccination

city: Leioa

first: Begoña

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

type: Non-coding RNA profiling by high throughput sequencing

summary: Spleen miRNA profiles of twelve age-matched Rasa sheep after inoculation of nine different commercial vaccines based of aluminium hydroxide (the vaccine group composed of 4 animals), with the aluminium adjuvant alone in an equivalent dose (the adjuvant group composed of 4 animals) or PBS (the control group composed of 5 animals) were generated by deep sequencing on an Illumina HiSeq2500 sequencer.

first: Endika

last: Varela-Martínez

first: Martín

last: Bilbao-Arribas

first: Naiara

last: Abendaño

first: Javier

last: Asín

first: Marta

last: Pérez

first: Damián

last: de Andrés

first: Lluís

last: Luján


title: Clonal spreading of tumor-infiltrating T cells underlies the durable antitumor effects of PD-1 blockade and anti-CD4 monoclonal antibody: Bulk TCR sequencing

overall_design: CD8+ PD1-, CD8+ PD1+ Ly108+ Tim3-, CD8+ PD1+ Ly108+ Tim3+, and CD8+ PD1+ Ly108- Tim3+ T cells from tumor, and CD8+ CD44high T cells from dLN were collected from B16F10 tumor-bearing mouse treated with anti-CD4 mAb, anti-PD-L1 mAb or combination of anti-CD4 and anti-PD-L1 mAbs. Bulk TCR sequencing was performed, and T cell clones that overlap between tumor and dLN were identified.

first: Mikiya

last: Tsunoda

first: Haru

last: Ogiwara

first: Haruka

last: Shimizu

last: Abe

first: Tatsuro

last: Ogawa

first: Takaya

first: Shigeyuki

last: Shichino

first: Kouji

last: Matsushima

first: Satoshi

last: Ueha


title: Integrated RNA-seq and functional analyses reveal the potential role of microRNAs in rainbow trout (Oncorhynchus mykiss) adapting to acute hypoxia and reoxygenation stress

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

summary: Hypoxia negatively affects the behavior, growth, reproduction, and survival of fish, causing serious economic losses to aquaculture. Rainbow trout (Oncorhynchus mykiss), an important economic fish worldwide, belongs to a hypoxia-sensitive fish species. However, the regulatory mechanisms of miRNAs under hypoxia stress response of rainbow trout remains unclear. In this study, rainbow trout were subjected to hypoxia stress (DO: 3.5 mg/L) for 3 h (H3h_L), 12 h (H12h_L), 24 h (H24h_L) and 3 h reoxygenation (R3h_L) to systemically evaluate the changes of miRNA expression profiles in liver, and the functions of sha-miR-92a_L+2R+4 were investigated. We found 17, 144, 57 and 55 differentially expressed (DE) miRNAs in H3h_L vs. control (N_L), H12h_L vs. N_L, H24h_L vs. N_L and R3h_L vs. N_L comparisons, respectively. Enrichment analysis revealed that the targets of these DE miRNAs were significantly enriched in HIF signaling pathway, VEGF signaling pathway, FoxO signaling pathway and glycolysis/gluconeogenesis. Through miRNA-mRNA nteraction and weighted gene co-expression network analysis (WGCNA), five key DE miRNAs (sha-miR-92a_L+2R+4, ssa-miR-128-3p, ssa-miR-101b-3p_R+1, ola-miR-199a-5p_R+2 and tni-miR-199_1ss18CG) were identified, which can target at least two hypoxia-responsive genes, such as vegfaa, ho, glut1a and junb. Functional analysis found that sha-miR-92a_L+2R+4 directly regulated vegfaa expression by targeting its 3′-UTR, overexpression of sha-miR-92a_L+2R+4 significantly decreased vegfaa expression in rainbow trout liver cells, while opposite results were obtained after transfection of sha-miR-92a_L+2R+4 inhibitor. Furthermore, overexpression of sha-miR-92a_L+2R+4 promoted rainbow trout liver cell proliferation and inhibited apoptosis. These results deepen our understanding of the crucial roles of miRNAs under hypoxia stress in rainbow trout, and provide valuable information for further studying the regulatory mechanisms of key hypoxia-responsive miRNAs and breeding hypoxia-tolerant rainbow trout species.

overall_design: In the present study, the miRNA expression profiles changes in the liver of rainbow trout under hypoxia for different durations and reoxygenation stress were detected using the Illumina HiSeq 2500 sequencing platform, and the functions of sha-miR-92a_L+2R+4 were further investigated.

first: Jinqiang

last: Huang

first: Shenji

last: Wu


title: BRG1 facilitates the development of porcine somatic cell nuclear transfer embryos [RNA-Seq]

city: nanning

first: Ren

last: xuan

address: xixiangtang street

institute: guangxi university

summary:
To investigate the effect of BRG1 overexpression in donor cells on the efficiency of porcine somatic cell nuclear transplantation.
In total, 2358 differentially expressed genes were identified by the RNA-seq, with 1336 up- and 1022 down-regulated genes in the experimental group. The up-regulated genes were mainly enriched in PI3K/AKT signaling pathway and WNT signaling pathway, and the down-regulated genes were mainly enriched in disease development.

overall_design: BRG1 was over-expressed in donor cells (porcine fetal fibroblasts) to examine its effect on the epigenetic modification levels and chromatin openness, subsequently, the effect of BRG1 overexpression in donor cells on the development of cloned embryos was investigated.

first: Xiangping

last: Li

first: Xuan

last: Ren

first: Yi

last: Tong


title: BRG1 facilitates the development of porcine somatic cell nuclear transfer embryos [ATAC-Seq]

summary:
To investigate the effect of BRG1 overexpression in donor cells on the efficiency of porcine somatic cell nuclear transplantation.
ATAC-seq results revealed that more open chromatin peaks at SMARCA4、NANOG、SOX2、MAP2K6、HIF1A sites were observed in the experimental group.


title: The establishment of HP1-independent heterochromatin reveals an essential role for HP1 proteins in maintaining epigenetic memory

city: Waltham

first: Melissa

last: Seman

address: 415 South St

institute: Brandeis University

summary: H3K9 methylation (H3K9me) marks transcriptionally silent genomic regions called heterochromatin. A conserved class of HP1 proteins are critically required to establish and maintain heterochromatin. HP1 proteins bind to H3K9me, recruit factors that promote heterochromatin formation, and oligomerize to form phase-separated condensates. We do not understand how HP1 protein binding to heterochromatin establishes and maintains transcriptional silencing. Here, we demonstrate that the S.pombe HP1 homolog, Swi6, can be completely bypassed to establish silencing at ectopic and endogenous loci when an H3K4 methyltransferase, Set1 and an H3K14 acetyltransferase, Mst2 are deleted. Deleting Set1 and Mst2 enhances Clr4 enzymatic activity, leading to higher H3K9me levels and increased spreading. In contrast, Swi6 and its capacity to oligomerize were indispensable during epigenetic maintenance. Our results demonstrate the role of HP1 proteins in regulating histone modification crosstalk during establishment and identifies a genetically separable function in maintaining epigenetic memory.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for H3K9me2 and H3K9me3

first: Alexander

last: Levashkevich

first: Ajay

last: Larkin

first: Fengting

first: Kaushik

last: Ragunathan


title: RNA sequencing on a cohort of Poor Risk AML samples

city: London

first: Findlay

last: Bewicke-Copley

address: John Vane Science Centre, Barts Cancer Institute

country: United Kingdom

institute: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London

summary: A cohort of 54 samples from the Barts Health NHS Trust (London) harbouring poor-risk cytogenetic aberrations including -7/del(7), -5/del(5), KMT2A rearrangements (other than t(9;11)), t(6;9), inv(3), -17/del(17) and complex karyotypes (≥ 3 chromosomal aberrations)

overall_design: Gene expression analysis of 54 poor risk AML patients

first: Ana

last: Rio-Machin

first: Pedro

last: Casado

middle: R

last: Cutillas

first: Jude

last: Fitzgibbon


title: WT, LKB1 KO, and LKB1/CRTC2 KO mouse embryonic fibroblasts

first: Russell

last: Jones

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


title: Comprehensive transcriptional analysis of pig facial skin development

city: Ya'an

first: Yu

middle: jing

state: Sichuan

address: Xinkang street num 46

department: Department of Zoology, College of Life  Science

institute: Sichuan Agricultural University

summary: To study the development of pig facial skin after birth, we use the facial skin tissues of healthy Chenghua sows as experimental materials. we then performed gene expression profiling analysis using data obtained from RNA-seq of pig facial skin tissues at four time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for skin tissues at four time points.

first: Yujing

first: Rui

last: Shi

first: Rong

last: Yuan

first: Yanzhi

last: Jiang


title: Global Release of Translational Repression Across Plasmodium’s Host-to-Vector Transmission Event

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

summary: Malaria parasites must be able to respond quickly to their environment, including during their transmission between mammalian hosts and mosquito vectors. Therefore, before transmission, female gametocytes proactively produce and translationally repress mRNAs that encode essential proteins that the zygote requires to establish a new infection. This essential regulatory control requires the orthologues of DDX6 (DOZI) and LSM14 (CITH), which along with ALBA proteins, form a translationally repressive complex in female gametocytes that associates with many of the affected mRNAs. However, while the release of translational repression of individual mRNAs has been documented, the details of the global release of translational repression have not. Moreover, the changes in spatial arrangement and composition of the DOZI/CITH/ALBA complex that contribute to translational control are also not known. Therefore, we have conducted the first comparative transcriptomics and proteomics of Plasmodium parasites across the host-to-vector transmission event to document the global release of translational repression. Using female gametocytes and zygotes of P. yoelii, we find that over 200 transcripts are released for translation soon after fertilization, including those with essential functions for the zygote. However, we also observed that some transcripts remain repressed beyond this point. In addition, we have used TurboID-based proximity proteomics to interrogate the spatial and compositional changes in the DOZI/CITH/ALBA complex across this transmission event. Consistent with recent models of translational control, proteins that associate with either the 5’ or 3’ end of mRNAs are in close proximity to one another during translational repression in female gametocytes and then dissociate upon release of repression in zygotes. These protein interactions in female gametocytes were further validated through structured illumination microscopy and ultrastructure expansion microscopy. Together, these data provide a model for the essential translational control mechanisms used by malaria parasites to promote their efficient transmission.

overall_design: Female gametocytes and zygotes were purified by flow cytometry, RNA was purified by a Qiagen Rneasy kit with in-solution DNaseI digestion, and used for library preparation using the Illumina stranded mRNA kit for 150nt single end reads.

first: Scott

last: Lindner

first: Kelly

middle: T

last: Rios


title: Bulk TCRseq analysis on CD8+ T cells in wild type mice following anti-CD4 and anti-PDL1 mAb treatment

first: Hiroyasu

last: Aoki

overall_design: CD8+, CD8+ PD1-, CD8+ PD1+ Ly108+ Tim3-, CD8+ PD1+ Ly108+ Tim3+, and CD8+ PD1+ Ly108- Tim3+ T cells from tumor, and CD8+ CD44high T cells from dLN were collected from B16F10 or Lewis lung carcinoma (LLC) tumor-bearing mouse treated with anti-CD4 mAb, anti-PD-L1 mAb or combination of anti-CD4 and anti-PD-L1 mAbs. Bulk TCR sequencing was performed, and T cell clones that overlap between tumor and dLN were identified.

first: Mikiya

last: Tsunoda

first: Haru

last: Ogiwara

first: Haruka

last: Shimizu

last: Abe

first: Takaya

first: Shigeyuki

last: Shichino

first: Kouji

last: Matsushima

first: Satoshi

last: Ueha


title: Macrophage recipient WGBS data: Donors infected with Porphyromonas gingivali (WDPg) or sham-infected (WD) and fed a western diet (WD)

city: Edmonton

first: Maria

last: Febbraio

state: AB

department: Dentistry

country: Canada

institute: University of Alberta

type: Methylation profiling by high throughput sequencing

summary: Our understanding of how atherosclerosisr risk factors persist after risk factor mitigation is incomplete. Here, we use oral infection with Porphyromonas gingivalis (Pg) as a model risk factor. Atherosclerosis-prone LDLR Komice were infected with Pg or sham infected, and fed a high fat diet for 16 weeks. Their bone marrow was then injected into lethally irradiated naive LDLR KO mice. After 16 weeks of high fat diet feeding, macrophages were elicited into the peritoneal cavity with thioglycollate. DNA from these macrophages was isolated for WGBS sequencing. We hypothesize that oral infection with Pg caused methylation differences in genes that contribute to increased atherosclerosis.

overall_design: DNA from elicited macrophages. 5 mice were pooled/group. WD=sham infected mice. WD+Pg=mice orally infected with Pg.

first: Mohamed

last: Omar


title: Epigenome-wide association study of diabetic chronic kidney disease progression

city: Seoul

first: Sue K.

last: Park

address: 103, Daehak-ro, Jongno-gu

department: Preventive Medicine

country: South Korea

institute: Seoul National University

summary:
Since the etiology of diabetic chronic kidney disease (CKD) is multifactorial, studies on DNA methylation for kidney function deterioration have rarely been performed despite the need for an epigenetic approach.
Therefore, this study aimed to identify epigenetic markers associated with CKD progression based on the decline in the estimated glomerular filtration rate in diabetic CKD in Korea.

overall_design: We profiled genome-wide DNA methylation using Infinium MethylationEPIC array using whole blood samples from 180 CKD patients

first: Hye

last: Sung

first: Sangjun

last: Lee

first: Miyeun

last: Han

first: Woo

last: An

first: Hyunjin

last: Ryu

first: Eunjeong

last: Kang

first: Yong

first: Seung

first: Curie

last: Ahn

first: Kook-Hwan

last: Oh

first: Sue

middle: K

first: Jung-Hyuck


title: Long-range genomic contacts and spatiotemporal chromatin landscape of human histone gene clusters at Histone Locus Bodies during the cell cycle in breast cancer [cHiC]

city: Burlington

first: Joseph

last: Boyd

state: Vermont

address: University of Vermont

department: Biomedical and Health Sciences

institute: University of Vermont

summary: Cell cycle controlled mechanistic remodeling of chromatin architecture at HLBs as non-membranous phase-separated nuclear domains represents a novel dimension to regulation of cell proliferation. Therefore, we sought to resolve a gap in our understanding of how 3D higher-order genomic organization supports the activation of multiple clustered histone genes. Our findings are consistent model that the HINFP/NPAT complex controls the formation and dynamic remodeling of higher-order genomic organization of histone gene clusters at HLBs in early to late G1 phase to support production of histone mRNAs in S phase. that the two principal histone gene regulators HINFP and NPAT are located at anchor-points for chromatin loops reflecting their obligatory functions in remodeling the spatiotemporal genomic organization at HLBs during the G1 phase to accommodate histone gene expression in S phase.

overall_design: cHiC in the MCF10DCIS cell, 2 biological replicates enriched for the histone locus body on chr6.

first: Gary

last: Stein

first: Prachi

last: Ghule

first: Seth

last: Frietze


title: Single-cell analysis of the dLN-tumor OL clones following anti-CD4 mAb treatment

first: Hiroyasu

last: Aoki

overall_design: CD8+ TILs and CD8+ CD44high T cells in dLN were collected from a B16F10 tumor-bearing mouse treated with anti-CD4 mAb. Single-cell targeted RNA sequencing combined with TCR sequencing (scRNA/TCRseq) was perfomed on CD8+ TILs. Bulk TCR sequencing was performed on dLN CD8+ CD44high T cells. T cell clones that overlap between tumor and dLN were identified.

first: Mikiya

last: Tsunoda

first: Haru

last: Ogiwara

first: Haruka

last: Shimizu

last: Abe

first: Tatsuro

last: Ogawa

first: Takaya

first: Shigeyuki

last: Shichino

first: Kouji

last: Matsushima

first: Satoshi


title: Single-cell transcriptomic analysis uncovers diverse and dynamic senescent cell populations

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Senescence is a state of enduring growth arrest triggered by sublethal cell damage.  Given that senescent cells actively secrete proinflammatory and matrix-remodeling proteins, their accumulation in tissues of older persons has been linked to many diseases of aging.  Despite intense interest in identifying robust markers of senescence, the highly heterogenous and dynamic nature of the senescent phenotype has made this task difficult.  Here, we set out to comprehensively analyze the senescent transcriptome of human diploid fibroblasts at the individual-cell scale by using single-cell RNA-sequencing analysis through two approaches.  First, we characterized the different cell states in cultures undergoing senescence triggered by different stresses; we found distinct cell subpopulations that expressed mRNAs with roles in growth arrest, survival, and the secretory phenotype.  Second, we characterized the dynamic changes in the transcriptomes of cells as they developed etoposide-induced senescence; by tracking cell transitions across this process, we found two different senescence programs that developed divergently, one in which cells expressed traditional senescence markers and one in which cells expressed long noncoding RNAs and splicing was dysregulated.  Finally, we obtained evidence that the proliferation status at the time of senescence initiation affected the path of senescence, as determined based on the expressed RNAs.  We propose that a deeper understanding the transcriptomes of different senescent cell programs will help develop more effective interventions directed at this detrimental cell population.

overall_design: WI-38 proliferating (PDL 24, CTRL) fibroblasts were grown until their replicative potential was exhausted (PDL 57) and they reached replicative senescence (RS), exposed to 10 Gray of Ionizing Radiation (IR) then cultured 10 days, treated with 50 μM Etoposide (ETO) for 10 days. Additionally, WI-38 cells were either treated with DMSO or 50 μM etoposide and collected at 0 (untreated) 1, 2, 4, 7, and 10 days after treatment. Then, cells were analyzed using single-cell RNA sequencing.

first: Noah

last: Wechter

first: Martina

last: Rossi

first: Carlos

last: Anerillas

first: Dimitrios

last: Tsitsipatis

first: Yulan

last: Piao

first: Jinshui

last: Fan

first: Jennifer

middle: L

last: Martindale

first: Krystyna

last: Mazan-Mamczarz

first: Myriam

last: Gorospe


title: Chloroplast nucleoid is organized by membrane association of transcribed genes [HIC]

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

summary: Chloroplasts are organelles responsible for photosynthesis. They originated form a procaryotic ancestor in the process of endosymbiosis and contain their own genomes. The chloroplast genome is packaged into a chromatin-like structure known as the nucleoid. The internal arrangement of the nucleoid, molecular mechanisms of DNA packaging and connection of the nucleoid structure to gene expression remain poorly understood. We show that Arabidopsis thaliana chloroplast nucleoids have a unique organization driven by DNA binding to the thylakoid membranes. Membrane association of specific DNA regions is correlated with high levels of transcription, high protein occupancy and reduced DNA accessibility. Genes with low levels of transcription are further away from the membranes, have lower protein occupancy and higher DNA accessibility. Gene-specific disruption of transcription in sigma factor mutants causes a corresponding reduction in membrane association, indicating that RNA polymerase activity causes DNA tethering to the membranes. We propose that transcription organizes the chloroplast nucleoid into a transcriptionally active membrane-associated core and a less active Periphery.

overall_design: The data consists of 4 replicates of HI-C performed on chloroplast membranes. Non-crosslinked controls are included as negative controls

first: V

first: Andrzej

last: Wierzbicki


title: BRG1 facilitates the development of porcine somatic cell nuclear transfer embryos

first: Ren

last: xuan

overall_design: Refer to individual Series


title: H3K27ac, H3K4me3 ChIPseq of A549 (T/T) and A549 (C/C) cells

city: 天津市

first: Xinyue

last: Lei

state: 天津市

address: 天津市和平区气象台路22号天津医科大学

institute: 天津医科大学

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications, H3K27ac, H3K4me3 in A549 (T/T) and A549 (C/C) cells;

first: Zhe

last: Liu


title: Effect of site directed mutagenesis on transcriptomic difference between A549 (T/T) and A549 (C/C) cells

address: 天津市和平区气象台路22号天津医科大学

summary: To study the effect of rs1663689 on lung cancer cells, we generated A549(C/C) from A549(T/T) using CRISPR/Cas9 technology and performed RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A549(T/T) and A549(C/C) cells


title: rs1663689 interchromosomally regulates ADGRG6 and modulates the malignant progression of lung cancer

address: 天津市和平区气象台路22号天津医科大学


title: The acetylcarnitine shuttle links mitochondrial metabolism to histone acetylation and lipogenesis

city: Durham

first: Luke

last: Izzo

state: NC

address: 308 Research Drive

institute: Duke University

summary: To understand the contribution of acetyl-CoA generating enzymes to epigenetic regulation we generated ACLY knockout, ACSS2 knockout, and ACLY/ACSS2 double knockout cell lines

overall_design: Gene expression profiling analysis using data obtained from RNA-seq of 4 different cell lines (WT, ACLY KO, ACSS2 KO, DKO)

first: Sophie

last: Trefely

first: Christina

last: Demetriadou

first: Jack

last: Drummond

first: Takuya

last: Mizukami

first: Nina

last: Kurpasertkul

first: Aimee

last: Farria

first: Phuong

last: Nguyen

first: Nivitha

last: Murali

first: Lauren

last: Reich

first: Daniel

last: Kantner

first: Joshua

last: Shaffer

first: Hayley

last: Affronti

first: Alessandro

last: Carrer

first: Andrew

last: Andrews

first: Brian

last: Capell

first: Nathaniel

middle: W

last: Snyder

first: Kathryn

last: Wellen


title: Anti-asthmatic effect of nafamostat is associated with modulated expression of pro-inflammatory genes, reduced eosinophil infiltration and attenuated airway hyperreactivity

city: Uppsala

first: Venkata Sita Rama Raju

middle: Sita Rama Raju

last: Allam

state: Sweden

address: Husargatan 3

department: IMBIM

country: Sweden

institute: Biomedical Center Uppsala University

summary: Asthma is typically characterized by an imbalance between the expression of proteases and of inhibitors capable of neutralizing such enzymes. Hence, an attractive option for intervening with asthma could be to interfere with asthma-associated proteases. In this study, we exploited this option by assessing the impact of nafamostat, a serine protease inhibitor with known capacity to neutralize mast cell tryptase, on the manifestations of airway responses in a house dust mite (HDM)-based model of experimental asthma. Our findings reveal that nafamostat efficiently suppressed the airway hyperreactivity in HDM-sensitized mice, which was accompanied by a profound reduction in the infiltration of eosinophils and lymphocytes to the airways, and also by suppression of the levels of proinflammatory compounds within the airway lumen.Further, nafamostat caused a marked reduction of eosinophil inflammation in the lung tissue, and we also show that nafamostat had a dampening impact on goblet cell hyperplasia and smooth muscle layer thickening in the lungs of HDM-sensitized animals. To obtain deeper insight into the mechanism by which nafamostat affects parameters of allergic airway inflammation, a transcriptomic analysis was conducted. This analysis revealed, as expected, that the HDM sensitization caused an upregulated expression of numerous proinflammatory genes. Further, the transcriptomic analysis showed that nafamostat suppressed the levels of multiple proinflammatory genes, with a particular impact on genes related to asthma. Altogether, this study provides extensive insight into the ameliorating effect of nafamostat on experimental asthma, and our findings can thereby provide a basis for the further evaluation of nafamostat as a potential therapeutic agent in human asthma.

overall_design:
Mice were lightly anesthetized with isoflurane and the anesthetized mice were instilled with 10 mg of house dust mite (HDM) extract reconstituted in 30 ml PBS (Dermatophagoides pteronyssinus) intranasally twice a week for three weeks. Control mice received 30 ml PBS via the intranasal route. To investigate the efficacy of nafamostat on asthmatic features, nafamostat (20 mg/kg in 3% acetic acid in PBS) were administered thirty minutes before each PBS and/or HDM instillation via the intraperitoneal route. 24 hr mice were euthanized and the left lung was snap frozen and the upper portion of the left lung lobes from separate experiments were grounded in liquid nitrogen, and RNA was extracted using the Qiagen RNeasy® plus mini kit. cDNA libraries were created and amplified using the Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit (Life Technologies, Carlsbad, CA) following the protocol of the manufacturer; the sequencing was performed on an Ion S5™ XL Sequencer
*** Submitter declares that raw data are no longer available. ***

first: Venkata

middle: S

first: Ida

last: Waern

first: Sowsan

last: Taha

first: Srinivas

last: Akula

first: Sara

last: Wernersson

first: Gunnar

last: Pejler


title: Integrative analysis of transcriptome, microRNA-seq and metabolome reveals an essential role of exogenous melatonin in enhancing salt stress tolerance during seed germination in maize [miRNA-seq]

city: Yangzhou

first: Rujia

last: Chen

address: Wenhui

institute: Yangzhou unversity

summary:
To investigate the role of melatonin in salt tolerance of maize, we determine the seed germinated rate of maize under CK, NaCl and NaCl+melatonin.
We then performed miRNA profiling analysis using data obtained from miRNA-seq of the seeds of three different treatments.

overall_design: Comparative miRNA expression profiling analysis of miRNA-seq data for the seeds among thress different comparisons.

first: Zefeng

last: Yang


title: Integrative analysis of transcriptome, microRNA-seq and metabolome reveals an essential role of exogenous melatonin in enhancing salt stress tolerance during seed germination in maize [RNA-seq]

summary:
To investigate the role of melatonin in salt tolerance of maize, we determine the seed germinated rate of maize under CK, NaCl and NaCl+melatonin.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the seeds of three different treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the seeds among thress different comparisons.


title: Lineage tracing of mutant granulosa cells reveals in vivo protective mechanisms that prevent granulosa cell tumorigenesis

city: Beijing

first: Kaixin

last: Cheng

state: 北京

address: Yuanmingyuan West Road 2#

department: State Key Laboratory of Agrobiotechnology, College of Biological Sciences

institute: China Agricultural University

summary: In the current study, we combined a multi-fluorescent reporter mouse model with a conditional knockout mouse model, in which the tumor suppressor genes Pten and p27 were deleted in GCs, to perform cell lineage tracing of mutant GCs. We found that only 30% of ovaries with substantial mutant GCs developed into GCTs that derived from a single mutant GC. In-depth molecular analysis of the process of tumorigenesis demonstrated that up-regulation of immune evasion genes Cd24a and Cd47 led, in part, to the transition of mutant GCs to GCTs. Therefore, treatment with the Cd47 inhibitor RRX-001 was tested and found to efficiently suppress the growth of GCTs in vivo.

overall_design: To reveal key cellular components and pathways responsible for the single cell derivation of GCT, we collected mutant GCs from ovaries of PD23 DKO mice (MT-GCs) and GCT cells from four-month-old DKO females with tumors (GCTs). GCs from ovaries of PD23 control mice (WT-GCs) were used as normal controls. RNA-Seq was performed to analyze the transcriptomic gene expression profiles of those cells.

first: Shudong

last: Niu


title: Integrative analysis of transcriptome, microRNA-seq and metabolome reveals an essential role of exogenous melatonin in enhancing salt stress tolerance during seed germination in maize


title: Naringenin and beta-carotene induce energy expenditure and insulin sensitizing genes in human white adipocytes

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

summary: Changes in expressed genes will be sequenced for regulatory pathway analysis in human adipocytes

overall_design: Subcutaneous human adipocyte cultures from  female overweight and obese donors treated were for treated 7 days with 8μM naringenin extract and 2μM beta-carotene

first: Ann

middle: A

last: Coulter

first: Richard

last: Carmouche

first: Jasleen

last: Kaur

first: Candida

last: Rebello


title: Estrogen alleviates acute and chronic itch in mice [exp2]

first: jinhua

last: jin

state: Beijing

address: 33 Ba-Da-Chu Road, Shi-Jing-Shan District

institute: Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: RNAseq analysis showed that estrogen-treatment caused significantly reduced expression level of itch-related molecules

overall_design: female mice ovariectomized ,then  a slow–release pellet of 17β-estradiol and their placebo were placed back to its ovary position in estrogen or placebo group respectively.   Placebo group displayed significantly increased itch signaling moleculars,

first: Jinhua

last: Jin

first: Li

last: Li

first: Yuhui

last: Wang

first: Keyan

first: Weiou

first: Qing

last: Liu

first: Chao

last: Wen

first: Quanle

first: Guanghai

last: Yan

first: Fushan

last: Xue


title: Deletion of CSF2RA in the bovine preimplantation embryo reduces development and affects embryonic gene expression in utero

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

summary: The hypothesis that CSF2 plays a role in the preimplantation development of the bovine embryo was tested by evaluating consequences of deletion of CSF2RA (the functional receptor in the embryo) for development of embryos in utero. CRISPR/Cas9 was used to delete exon 5 and intron 5 of CSF2RA on chromosome 3. Control embryos were injected with Cas9 mRNA only. Embryos > 16 cells at day 5 after insemination were transferred to synchronized recipient females in groups of 7 to 24. Embryos were flushed from the uterus two days later. The proportion of recovered embryos that developed to the blastocyst stage was lower for knockout embryos (39%) than for control embryos (63%).  RNA sequencing of individual morulae and blastocysts indicated  a total of 27 (morula) or 15 (blastocyst) differentially-expressed genes (false discovery rate <0.05). Differentially-expressed genes as well as regulated gene sets identified by gene set enrichment analysis indicated that knockout affected genes playing roles in several functions including cell signaling and glycosylation. It was concluded that signaling through CSF2RA is not obligatory for development of the bovine preimplantation embryo to the blastocyst stage but that CSF2 signaling does enhance the likelihood that the embryo can become a blastocyst and result in specific changes in gene expression.

overall_design: Bovine embryos at the blastocyst stage produced in vivo either knockout or control

first: Peter

last: Hansen

first: Froylan

last: Sosa

first: Kyungjun

last: Uh

first: Jessica

middle: N

last: Drum

first: Katy

last: Stoecklein

first: Kim

last: Davenport

first: M

first: Kiho

last: Lee


title: Sham vs.BCAS microarray for brain

city: Nanjing

first: Qian

last: Cao

address: 358 Zhongshan Road, Nanjing Drum Tower Hospital, Nanjing City, Jiangsu Province

department: Neurology

institute: Nanjing Drum Tower Hospital

summary: The Agilent SurePrint G3 Mouse GE V2.0 Microarray was used in this experiment to analyze data of the 6 samples. Goal was to determine the differential genes of Sham and Bilateral carotid artery stenosis (BCAS).

overall_design: Sham vs. BCAS groups. Biological replicates: 3 BCAS replicates, 3 Sham replicates

first: Shuwei

last: Qiu


title: Maladaptive upregulation of aminoprocalcitonin fuels seizure self-sustaining by boosting energy supply in refractory status epilepticus

city: Xi’an city

first: Changgeng

last: Song

state: Shaanxi Province

address: 169 Changle Xi Road, Xincheng District

department: Department of Neurology, Xijing Hospital

institute: Fourth Militarty Medical University

summary: To investigate the biological functions of aminoprocalcitonin (NPCT) and its parent peptide procalcitonin (PCT) in neurons, we stimulated rat primary hippocampal neurons at DIV7 with 1 nM NPCT and 1 nM PCT for 24 h, respectively. Alterations in transcriptomes were analyzed with RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for rat primary hippocampal neurons at DIV7 stimulated with 1 nM NPCT and 1 nM PCT for 24 h, respectively.

first: Yu

last: liu

first: Jingjing

last: Zhao

first: Jianmin

last: Hao

first: Dan

last: Mi

first: Jiajia

last: Zhang

first: Yingying

first: Fang

last: Gao

first: Shengxi

last: Wu

first: Wen

last: Jiang


title: Electroconductive and mechano-competent PUCL@CNT nanohybrid scaffolds guiding neuronal specification of neural stem/progenitor cells

city: Cheonan

middle: Meng

last: Li

address: Pharmacy Bldg, Cheonan 31116, Republic of Korea

department: Department of Nanobiomedical Science

institute: Institute of Tissue Regeneration Engineering (ITREN)

summary: Neural stem/progenitor cells (NSPCs) exhibited a selective neuron and oligodendrocyte differentiation on the novel conductive, flexible biopolymer composite (PUCL@CNT).

overall_design:
To investigate the potential mechanisms in the regulation of directional differentiation, gene expression profiling analysis uses data obtained from RNA Quant-seq of NSPCs at two points.
Comparative gene expression profiling analysis of RNA Quant-seq data for rat NSPCs cultured on the bare PUCL and PUCL@CNT1 platforms under before and after differentiation conditions.

first: Yu-Meng

first: Jung-Hwan

first: Hae-Won

last: Kim


title: Serum Amyloid A proteins reduce bone mass during mycobacterial infections

city: Porto

first: Ana

middle: Cordeiro

last: Gomes

state: Porto

address: Rua Alfredo Allen, 208

country: Portugal

institute: I3S: Universidade do Porto Instituto de Investigacao e Inovacao em Saude

summary: To investigate the molecular mechanisms responsible for bone loss during mycobacterial infections

overall_design: Comparative gene expression profiling analysis of RNA-seq data for whole bone in mice infected with M. avium compared with non-infected littermate controls.

last: Cordeiro Gomes

first: Ricardo

last: Pinto

first: Luisa

last: Pereira

first: Maria


title: Effect of site directed mutagenesis on transcriptomic difference between H460 (T/T) and H460 (C/C) cells

first: Xinyue

last: Lei

address: 天津市和平区气象台路22号天津医科大学

summary: To study the effect of rs1663689 on lung cancer cells, we generated H460(C/C) from H460(A/A) using CRISPR/Cas9 technology and performed RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H460 (T/T) and H460 (C/C) cells

first: Zhe

last: Liu


title: circularized chromosome conformation capture followed by sequencing (4C-seq) in the heterozygous (T/C) A549 cell line

address: 天津市和平区气象台路22号天津医科大学

summary: To examine target genes that interact with different alleles of rs1663689 in a heterozygous cell line A549(A/C).

overall_design: 4Cseq of A549 cells


title: Gene expression changes in human triple negative breast cancer cells with loss of MDM2

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

summary: RNA-sequencing was performed on p53-inactivated human triple negative breat cancer cells to evaluate gene expression changes following MDM2 loss. Genes and pathways that are regulated by p53/p73 were induced with MDM2 loss.

overall_design: Gene expression profiles from RNA-sequencing were generated from human triple negative breast cancer cells with and without loss of MDM2 compared to contols

first: Christine

middle: M

last: Eischen

first: Clare

last: Adams


title: Optimized metrics for combinatorial and orthogonal CRISPR screens

city: Frankfurt am Main

first: Martin

last: Wegner

state: Hessen

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry II

institute: University Hospital Frankfurt am Main, Germany

summary: CRISPR-based gene perturbation enables unbiased investigations of single and combinatorial genotype-to-phenotype associations. In light of efforts to map combinatorial gene dependencies at scale, choosing an efficient and robust CRISPR-associated (Cas) nuclease is of utmost importance. Even though SpCas9 and AsCas12a are widely used for single, combinatorial, and orthogonal screenings, side-by-side comparisons remain sparse. Here, we systematically compared combinatorial SpCas9, AsCas12a, and CHyMErA in hTERT-immortalized retinal pigment epithelial cells and extracted performance-critical parameters for combinatorial and orthogonal CRISPR screens. Our analyses identified SpCas9 to be superior to enhanced and optimized AsCas12a, with CHyMErA being largely inactive in the tested conditions. Since AsCas12a contains RNA processing activity, we used arrayed dual-gRNAs to improve AsCas12a and CHyMErA applications. While this negatively influenced the effect size of combinatorial AsCas12a applications, it enhanced the performance of CHyMErA. This improved performance, however, was limited to AsCas12a dual-gRNAs, as SpCas9 gRNAs remained largely inactive. To avoid the use of hybrid gRNAs for orthogonal applications, we engineered the multiplex SpCas9-enAsCas12a system (multiSPAS) that avoids RNA processing for efficient orthogonal gene editing.

overall_design: CRISPR-based screening experiments comparing end time point to control time point.

first: Ronay

last: Cetin

first: Leah

last: Luwisch

first: Sarada

last: Saud

first: Simone

last: Schaubeck

first: Eva

last: Quandt

first: Tatjana

last: Achmedov

first: Chase

last: Beisel

first: Manuel

last: Kaulich


title: H3K27ac, H3K4me3, H3K27me3 and H3K9me3 ChIPseq of H460 (T/T) and H460 (C/C) cells

address: 天津市和平区气象台路22号天津医科大学

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications, H3K27ac, H3K4me3, H3K27me3 and H3K9me3 in H460 (T/T) and H460 (C/C) cells


title: Circularized chromosome conformation capture followed by sequencing (4C-seq) in A549 cell line

address: 天津市和平区气象台路22号天津医科大学

summary: To examine target genes that interact with different alleles of rs1663689 in a heterozygous cell line A549(T/T),A549(C/C).


title: KDM5B occupancy profiling by CUT&Tag from murine BMDMs untreated (UT) or stimulated with LPS

city: Shanghai

first: Xingguang

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

summary: To identify the potential genes that regulated by KDM5B, we performed the CUT&Tag in murine primary BMDMs stimulated with LPS for 1h or not, and analyzed the precipitated DNA with deep sequencing.

overall_design: CUT&Tag using antibody against KDM5B in murine primary BMDMs stimulated with LPS for 1h or not.

first: Yunkai

last: Zhang


title: Developmentally regulated isoform of HNF4α reprograms the adult liver

city: Riverside

first: Frances

last: Sladek

state: CA

address: 900 University Avenue

institute: University of California

summary: Hepatocyte Nuclear Factor 4α (HNF4α), master regulator of hepatocyte differentiation, is regulated by two promoters (P1 and P2). P1-HNF4α but not P2-HNF4α is expressed in normal adult liver in fed conditions. Both P1- and P2-HNF4α are expressed in fetal liver. P2-HNF4α expression is increased in fasted conditions, high fat diet, alcoholic liver and liver cancer. To determine the target genes of the P1- and P2-HNF4α isoforms, we compared P2-HNF4α-expressing exon swap mice (a7HMZ) to wildtype (WT) male mice. Liver ChIP-seq samples were taken at 10:30 AM (ZT 3.5)

overall_design: Liver ChIP-seq samples from adult WT (P1-HNF4a1) and a7HMZ (P2-HNF4a7) male mice were analyzed in triplicate at 10:30 AM (ZT 3.5).

first: Jonathan

last: Deans

first: Linh

last: Vuong

first: Poonam

middle: J

last: Deol

first: Jose

last: Martinez Lomeli


title: Porcine DUXC and human DUX4 activate similar embryonic programs cross species: implications for preclinical model of FSHD

city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

summary: DUX4 and its mouse ortholog Dux are normally expressed in the early embryo—the 4 cell or 2 cell cleavage stage embryo, respectively—and activate a portion of the first wave of zygotic gene expression. DUX4 is epigenetically suppressed in nearly all somatic tissue, whereas FSHD-causing mutations result in its aberrant expression in skeletal muscle, transcriptional activation of the early embryonic program, and subsequent muscle pathology. Although DUX4 and Dux both activate an early totipotent transcriptional program, divergence of their DNA binding domains limits the use of DUX4 expressed in mice as a pre-clinical model for FSHD. In this study, we identify the porcine DUXC mRNA expressed in early development and show that both pig DUXC and human DUX4 robustly activate a highly similar early embryonic program in pig muscle cells. These results support further investigation of pig preclinical models for FSHD.

overall_design: Overexpression of human DUX4, pig DUXC, or GFP control in primary pig myoblasts.

first: Yee

last: Nip

first: Sean

last: Bennett


title: Super enhancers orchestrate osteogenesis program through navigation and initiation effects of Brd4 on Zbtb16 [CUT&TAG]

city: Shenzhen

first: Wenhui

last: Yu

address: Shennan middle road #3025

department: Department of Orthopedics

institute: The Eighth Affiliated Hospital of Sun Yat-sen University

summary: We performed multiomic high-throughput sequencing to recapitulated the primary mechanism of mesenchymal stem cells osteogenesis. We analysed the H3K27ac ChIP-seq, BRD4 CUT&Tag and RNA-seq data before and after osteogenesis, and identified super enhancers (SEs) regulated osteogenic identity genes in MSCs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of the BRD4 binding to genome in MSCs

first: Huiyong

last: Shen

first: Zhongyu

last: Xie

first: Yanfeng

last: Wu


title: Transcriptomic analysis of Acinetobacter baumannii exposed to sub-lethal  Sono-Fenton inactivation

city: Bhubaneswar

first: Suraj

middle: Kumar

last: Tripathy

state: Odisha

address: Campus 11

department: Biotechnology

country: India

institute: KIIT-DU

summary: The trancriptomic changes in Acinetobacter baumannii after Sono-Fenton inactivation was reported. A total of 148 genes were significantly expressed after the treatment. The genes involved in stress related response were up-regulated while the genes responsible for vital cell functioning were down-regulated.

overall_design:
Examination of Acinetobacter baumannii treated with sub lethal Sono-Fenton and its comparison with untreated bacteria.
contributor: Pranjal

first: A

middle: P

last: Habeeb Rahman

first: Amrita

last: Mishra

first: Cecilia

last: Stalsby Lundborg

last: Kumar Tripathy


title: BMPR2 Regulates Hypoxic Extracellular Vesicle Signaling to Maintain Vascular Homeostasis.

city: Palo Alto

first: Kevin

last: Van Bortle

address: 3165 Porter Dr

department: Genetics

institute: Stanford University

summary: To investiage the BMPR2 dependent effects of extracellular vesicle (EV) treatment, we compared the miRNA composition of EV derived from pulmonary arteerial endothelial cells after BMPR2 knockdown and 24 hours hypoxia.

overall_design: Comparative miRNA expression profiling analysis of extracellular vesicles derived from pulmonary arterial endothelial cells treated with 24 hours hypoxia and either siRNA targeting BMPR2 or scrambled control.

first: David

last: Marciano

first: Marlene

last: Rabinovitch

first: Michael

last: Snyder


title: The regeneration-responsive careg element monitors activation of Müller glia after MNU-induced damage in the zebrafish retina

city: Fribourg

first: Anna

last: Jazwinska

address: Chemin du Musée 10

country: Switzerland

institute: University of Fribourg

summary: We found that the zebrafish non-coding element careg, which is induced in regenerating fins and heart, also participates in retina regeneration. Its activation persisted mostly in Müller glia from the onset to the termination of retina restoration. To assess the involvement of the careg:EGFP reporter during retina regeneration, we used a chemical injury model with MNU treatment. To identify the molecular profile of these cells, we performed a single-cell RNA sequencing (scRNA-seq) experiment of retinas dissected from adult careg:EGFP zebrafish at 3, 7, and 10 dpMNU. Our control retinas were dissected from fish at 3 days after treatment with heat-inactivated MNU

overall_design: Adult careg:EGFP-transgenic zebrafish retinas after MNU-induced injury were isolated for scRNA-sequencing

first: Thomas

last: Bise

first: Catherine

last: Pfefferli

first: Marylène

last: Bovin


title: Light dependent gene expression in D. shibae wildtype compared to the gene expression in the transposonmutant D. shibae clpX::Tn

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: Transcriptomes of Dinoroseobacter shibae DSM16493 wild type and clpX  knockout mutant were recorded under white and blue light and in dark.

platform_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design: Dinoroseobacter shibae DFL12T (DSM 16493T) and  the transposonmutant D. shibae clpX::Tn  were grown in artificial saltwater minimal medium (SWM) in baffled flasks shaking at 180 rpm and 30 °C and incubation was performed under light, dark and bluelight conditions. D. shibae wild type and mutant strain were grown under aerobic conditions up to the mid exponential growth phase (OD578 nM 0.5).

first: Alina

last: Rommerskirch

first: Elisabeth

last: Härtig

first: Dieter

last: Jahn


title: ChIP-seq of healthy human thymus

city: Paris

first: Vahid

last: Asnafi

address: 149 rue de Sèvres

country: France

institute: APHP

summary: ChIP-sequencing samples to improve our understanding of how genes are activated or repressed in healthy and diseased human cells.

overall_design: ChIP-Seq for H3K27ac and H3K4me3 on healthy thymus

first: Agata

last: Cieslak

first: Charlotte

last: Smith

first: Guillaume

last: Charbonnier

first: Salvatore

last: Spicuglia


overall_design: ChIP-Seq for H3K27ac and H3K4me3 on T-Acute Lymphoblastic Leukemia as a complement of samples produced in the Blueprint consortium


title: TAL1 activation in T-ALL: A novel oncogenic 3' Neo-enhancer

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

overall_design: Refer to individual Series


title: RNA-sequencing of T-cell Acute Lymphoblastic Leukemia (T-ALL) and human CD34+ thymocytes

summary: RNA-sequencing samples to improve our understanding of gene expression and gene expression changes between healthy and diseased leukemic primary samples.

overall_design: RNA-sequencing of 8 T-cell Acute Lymphoblastic Leukemia (T-ALL) and 1 CD34+ thymocytes, as a complement of samples produced in the Blueprint consortium


title: The KDM5B lysine demethylase regulates androgen receptor function and expression in prostate cancer cells

city: Nottingham

first: Nigel

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham

summary: KDM5B/JARID1B is an 2-oxoglutarate and Fe(2+) dependent oxygenase that demethylates the di- and tri-methylated histone H3 lysine 4 (H3K3) generally associated with transcriptional activation. KDM5B is also implicated in numerous pro-oncogenic mechanisms in many different types of cancer, including the hypoxic response, immune evasion and PI3/AKT signalling. We show that the CPI-455 KDM5B inhibitor impairs androgen regulated transcription and splicing.

overall_design: RNAseq was used to identify differentially expressed and spliced transcripts in LNCaP prostate cancer cells treated with androgen (R1881, 1nM) vs cells treated with both R1881 (1nM) and CPI-455 (50 µM).

first: Veronika

last: Metzler

first: Simone

last: de Brot

first: Daisy

last: Haigh

first: Corinne

last: Woodcock

first: Jennifer

last: Lothion-Roy

middle: E

last: Harris

first: Emeli

last: Nilsson

first: Atara

last: Ntekim

first: Jenny

last: Persson

first: Brian

middle: D

last: Robinson

first: Francesca

last: Khani

first: Kristian

middle: B

last: Laursen

first: Lorraine

last: Gudas

last: Toss

first: Emad

last: Rakha

last: Heery

first: Catrin

last: Rutland

first: Jennie

last: Jeyapalan


title: Transretinal migration of astrocytes and brain/spinal cord-like cells arising from subretinally transplanted human retinal organoids

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

address: 1622 Locust Street

department: Ophthalmology

institute: University of Pittsburgh

summary: Subretinal transplantation of human retinal organoid-derived cells can potentially restore vision lost in photoreceptor dystrophies. Prior studies analyzed the maturation, integration, and function of transplanted organoid cells in the subretinal region, but detailed molecular analysis of transplanted photoreceptor and of cells that migrate to other retinal layers has not been conducted. Here, we characterized migratory and non-migratory organoid-derived cells following subretinal transplantation into a dystrophic host. Retinal organoids derived from Crx-tdTomato+ H9 human embryonic stem cells (hESC) (aged D134) were transplanted into immunodeficient Rd1/NS mice. Graft-derived cells using single-cell RNA sequencing and histological analysis were analyzed 4.5 months later.  Age-matched human retinal organoids maintained in vitro served as controls. Graft-derived cells migrated to all retinal layers, and underwent long-distance tangential migration.  Transcriptomic analysis of transplanted cells identified two cell types not found in cultured controls – PAX2-positive retinal astrocytes, and ARX/NKX2-2/HOXC8-positive brain/spinal cord-like neural precursors.  Some migrating cells were proliferative, but overall less proliferation was observed in the transplants than the cultured organoids.  Transplanted rod and cone photoreceptors remained in the subretinal space, and were more mature than age-matched photoreceptors in cultured organoids. This study shows that extrinsic signals present in the degenerative subretinal space promote maturation of photoreceptors in transplanted retinal organoids, while also inducing formation of migratory cell populations that are not normally derived from retinal progenitors, either in cultured organoids or in vivo.  This has important implications for the design and safety of cell-based therapies for treating photoreceptor dystrophies.

overall_design: Human retinal organoids transplanted into the rd1 mouse retina or age matched cultured organoids were dissociated into a single cell suspension and run on the 10x Genomics Chromium Single Cell System platform using ver3.1 chemistry. Libraries were sequenced on Illumina NextSeq 500 and processed through the Cell Ranger pipeline using the GRCh38 reference genome.

first: Ying

middle: V

last: Liu

first: Akin

last: Sogunro

first: Gregory

last: Konar

first: Ming-Wen

last: Hu

first: Minda

last: McNally

first: Yuchen

last: Lu

first: Zhuolin

last: Li

first: Dzhalal

last: Agakishiev

first: Sarah

last: Hadyniak

first: Katarzyna

last: Hussey

first: Tyler

last: Creamer

first: Linda

last: Orzolek

first: Derek

last: Teng

first: Jiang

last: Qian

first: Zheng

last: Jiang

first: Robert

last: Johnston Jr

first: Seth

last: Blackshaw

first: Mandeep

last: Singh


title: Super enhancers orchestrate osteogenesis program through navigation and initiation effects of Brd4 on Zbtb16 [RNA-Seq]

first: Wenhui

last: Yu

summary: We performed multiomic high-throughput sequencing to recapitulated the primary mechanism of mesenchymal stem cells osteogenesis. We analysed the H3K27ac ChIP-seq and RNA-seq data before and after osteogenesis, and identified super enhancers (SEs) regulated osteogenic identity genes in MSCs.

overall_design: Examination of the H3K27ac modification in MSCs before and after osteogenesis.

first: Huiyong

last: Shen

first: Zhongyu

last: Xie

first: Yanfeng

last: Wu


title: Super enhancers orchestrate osteogenesis program through navigation and initiation effects of Brd4 on Zbtb16


title: Oncogenic role and target properties of the lysine-specific demethylase KDM1A in chronic lymphocytic leukemia

city: Köln

first: Alicja

last: Pacholewska

address: Weyertal 115b

institute: Uniklinik Köln

summary: We report the alteration in H3K4me3 profile in Eµ-TCL1A leukemic splenocytes with or without KDM1A knockdown.

overall_design: H3K4me3 ChIP-seq in KDM1A wildtype and KDM1A knockdown Eµ-TCL1A leukemic splenocytes

first: Marco

last: Herling

first: Qu


title: Super enhancers orchestrate osteogenesis program through navigation and initiation effects of Brd4 on Zbtb16 [ChIP-Seq]


title: Western diet unmasks tumorigenic potential of transient vinyl chloride exposure at sub-OSHA level concentrations; potential role of the (epi-)transcriptome.

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

summary: Vinyl chloride (VC) monomer is a volatile organic compound commonly used in industry to produce polyvinyl chloride (PVC). At high exposure levels, VC causes hepatic angiosarcoma and toxicant-associated steatohepatitis. However, our group has recently shown that lower exposure levels (i.e., < OSHA exposure limits), which do not directly damage the liver, enhance injury caused by a Western diet (WD). Although these lower exposure levels are currently considered 'safe,' it is unknown if the long-term impact of transient low-concentration VC enhances the risk of liver cancer development. Low-concentration VC is especially a concern given that fatty liver disease is in and of itself a risk factor for the development of liver cancer. To evaluate the long-term effects of VC exposure C57Bl/6J, mice were fed WD or control diet (CD) for 1 year. During the first 12 weeks of feeding, mice were also exposed to VC via inhalation at concentrations below the current OSHA limit (<1 ppm) or air for 6 hours/day, 5 days/week. During the remaining 9 months of feeding, mice were not exposed to VC. Feeding WD for 1 year caused significant hepatic injury, including steatohepatitis and moderate fibrosis, which was exacerbated by VC. Additionally, VC increased the number of tumors ranging from moderately to poorly differentiated HCC. Transcriptomic analysis demonstrated VC-induced changes in metabolic but also ribosomal processes. Epitranscriptomic analysis showed a VC-induced shift of the modification pattern that has been associated with metabolic disease, mitochondrial dysfunction and cancer.  These data indicate that VC sensitizes the liver to other stressors (e.g., WD), resulting in enhanced tumorigenesis. These data raise concerns about a potential interaction between VC exposure and WD. Furthermore, it also emphasizes that current OSHA safety restrictions may be insufficient to account for other factors that can influence hepatotoxicity.

overall_design: 12-week (w12) and 12-month (m12) for mice in the following conditions: Control Diet (CD), Control Diet + Vinyl Chloride (CD+VC), Western Diet (WD), and Western Diet + Vinyl Chloride (WD+VC).

first: Silvia

first: Liqing

last: He

first: Olivia

last: Bannister

first: Regina

last: Schnegelberger

first: Andrew

last: Althouse

first: Francisco

last: Schopfer

first: Banrida

last: Wahlang

first: Matthew

middle: C

last: Cave

first: Satdarshan

last: Monga

first: Xiang

last: Zhang

first: Gavin

last: Arteel

first: Juliane

middle: I

last: Beier


title: Investigated the responses of ZM532 and wild-type ZM4 to acetic acid and furfural by using RNA-seq

city: Haidian

first: Samina

last: Shabbir

address: Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu

department: Biomass Energy Technology Research Centre

institute: Graduate School of Chinese Academy of Agricultural Science,

summary: In our previous study, we successfully constructed an engineered Zymomonas mobilis ZM532 strain tolerant these double inhibitors by genome shuffling, but the molecular mechanisms of tolerance to these inhibitors are still unknown. The goal of this study investigated the responses of ZM532 and wild-type ZM4 to acetic acid and furfural using Transcriptome

overall_design: ZM532 and wild-type ZM4 cultured in RM and AF medium in triplicate and then extracted the RNA. The concentrations of acetic acid and furfural combinations were set at 5.0 g/L and 3.0 g/L to study the responses of ZM4 and mutant ZM532.

first: Mingxiong


title: Increased sinusoidal pressure impairs liver endothelial mechanosensing pathways uncovering specific plasma biomarkers of portal hypertension.

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Abstract: Background and aims: Portal hypertension (PH) is the most frequent and severe clinical syndrome associated to chronic liver disease (CLD), defined by a pathological increase in the hepatic venous pressure gradient (HVPG). Considering the known mechanobiological effects of hydrostatic pressure and shear stress on endothelial cells, we hypothesized that PH could not only be a consequence of, but significantly influence the phenotype of liver sinusoidal endothelial cells (LSECs) during disease progression. The aim of this study was to investigate the effects of pathological hydrodynamic pressure on LSECs and to identify endothelial-derived biomarkers of PH. Methods: Primary LSECs were cultured under normal or increased hydrodynamic pressure within a pathophysiological range (1 vs 12 mmHg) using a microfluidic liver-on-a-chip device. RNAseq was used to identify pressure-sensitive genes, which were validated in liver biopsies from two independent cohorts of CLD patients with PH (n=73) vs subjects without PH (n=23). Biomarker discovery was performed in plasma from a third independent cohort of 64 patients (46 with PH vs 18 w/o). Results: Transcriptomic analysis revealed a marked deleterious effect of pathological pressure in LSECs and identified chromobox 7 (CBX7) as a key transcription factor diminished by pressure. Hepatic CBX7 downregulation was validated in patients with PH and significantly correlated with HVPG. MicroRNA 181a-5p was identified as pressure-induced upstream regulator of CBX7. Analysis of two downstream targets of CBX7, ECAD and SPINK1, were found increased in the bloodstream of patients with PH and were highly predictive of PH and clinically significant PH, with a sensitivity of 91.3% and 91.4% respectively. Conclusions: We describe the detrimental effects of increased hydrodynamic pressure on the sinusoidal endothelium, identify CBX7 as a pressure-sensitive transcription factor, and propose that the combination of two of its reported products could be used as plasma biomarkers of PH.

overall_design: Primary liver sinusoidal endothelial cells (LSEC) isolated from Han Wistar Rats using the 4 in 1 protocol (Fernández-Iglesias A et al 2019 J Cel Mol Med). LSEC, together with primary hepatocytes, stellate cells and hepatic macrophages, were cultured within the Exoliver device (Ortega-Ribera M 2018 Biotechnol Bioeng) under physiological (1mmHg - Samples 2,11 and 22) or pathological (12 mmHg - Samples 3, 9 and 23) pressure and dynamic shear stress stimulation of 1.15 dyn/cm2 for 48h.

first: M

last: Ortega-Ribera

first: A

last: Fernández-Iglesias

first: J

last: Gracia


title: VAL1/2 recruit PKL to target sites in arabidopsis genome

city: Guangzhou

first: Liang

last: Zhenwei

state: Guangdong

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen University

summary: PICKLE (PKL), a Chromodomain Helicase DNA binding domain type 3-type (CHD3) chromatin remodeler, noted for an embryonic structure called pickle root in primary root tip in pkl mutant, has been studied for decades. we obtained a comprehensive genome occupancy of PKL by Chromatin immunoprecipitation-sequencing (ChIP-seq), and found PKL co-occupy with the major repressors of seed maturation program, VIVIPAROUS1/ABI3-LIKE1/2 (VAL1/2) in genome. Furthermore, PKL physically interacts with VAL1/2 in vivo and phenotype and transcriptome data indicated that PKL and VAL1/2 function in a common pathway. Moreover, ChIP-seq and ChIP-qPCR results showed that VAL1/2 are necessary for the recruitment of PKL to co-target genes

overall_design:
Examination of PKL occupancy in 14-day-old WT and val1 val2 seedlings.
Examination of GFP occupancy in 14-day-old WT

first: Zhenwei

last: Liang

first: Chenlong

last: Li


title: ChIP-reChIP-seq data in mESCs show ZFP661 co-binds target regions with CTCF

status: Public on May 09 2023

city: Bethesda

first: Jinpu

last: Jin

address: Building 6B, Room 2B-211, 6 Center Drive

institute: NICHD

summary: In this assay, we aimed to investigate whether ZFP661 co-binds target regions with CTCF. To achieve this, we performed ChIP-reChIP-seq in ZFP661-3HA overexpressing (OE) mESCs, where the 1st ChIP utilized anti-HA antibody, and the 2nd ChIP involved the use of anti-IgG and anti-CTCF antibodies, respectively. Our results demonstrate that ZFP661 co-binds target regions with CTCF.

overall_design: To assess whether ZFP661-3HA peaks co-occupied with CTCF exhibit distinct signal patterns in the 2nd ChIP (CTCF ChIP signal minus IgG signals), we compared them to CTCF-only peaks and ZFP661-3HA-only peaks as controls. Two biological replicates were used in this assay.

first: Todd

last: Macfarlan


title: Integration of p16/HPV DNA status with a 24-miRNA-defined molecular phenotype improves clinically relevant stratification of head and neck cancer patients

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary:
Head and neck squamous cell carcinomas (HNSCC) driven by human papillomavirus (HPV) generally have a more favourable prognosis. We hypothesized that HPV-positive HNSCC may be identified based on a miRNA signature according to their specific molecular pathogenesis and are characterized by a unique transcriptome compared to HPV-negative HNSCC.
We characterized the miRNA-expression patterns of the tumors from 229 head and neck squamous cell carcinoma patients by Agilent miRNA microarrays in order to define a HPV-predicting miRNA signature.

overall_design: n=229 HNSCC tumor samples for which HPV-status was known were analyzed.

first: Julia

last: Heß

first: Helmholtz

middle: Z

last: München


title: FTO regulated genes in Hepatocellular Carcinoma

city: Shanghai

first: Yinghao

last: Shen

address: 180 Fenlin Road

institute: Zhongshan Hospital

summary: To investigate the global genes regulated by FTO high-throughput mRNA sequencing (RNA-Seq) was performed to compare the expression profile between HepG2 cells transfected with control siRNA or FTO siRNA.

overall_design: RNA-seq was performed in HepG2 liver cells after control siRNA or FTO siRNA transfection

first: Shen

last: Yinghao


title: Oct4 is a gatekeeper of epithelial identity by regulating cytoskeletal dynamics in skin keratinocytes [ATAC-Seq]

city: Nicosia

first: Katerina

last: Strati

state: Nicosia

address: 1 Panepistimiou Avenue - Aglantzia

department: Biological Sciences

country: Cyprus

institute: University of Cyprus

summary: Oct4 is arguably a pioneer transcription factor regulating pluripotency. However, it is poorly known whether Oct4 has an impact on somatic cells. We generated OCT4 knockout clonal cell lines using immortalized human skin keratinocytes to identify a functional role for the protein. Here we report that Oct4-deficient cells transitioned into a mesenchymal-like phenotype with enlarged size and shape, exhibited accelerated migratory behavior, decreased adhesion and appeared arrested at G2/M cell cycle checkpoint. Oct4 absence had a profound impact on cortical actin organization, with loss of microfilaments from cell periphery, increased puncta deposition in the cytoplasm and stress fiber formation. E-cadherin, β-catenin and ZO1 were almost absent from cell-cell contacts while fibronectin deposition was markedly increased in ECM. Mapping of the transcriptional and chromatin profiles of Oct4-deficient cells revealed that Oct4 controls the levels of cytoskeletal, ECM and differentiation related genes, whereas epithelial identity is preserved through transcriptional and non-transcriptional mechanisms.

overall_design: Comparative gene expression profiling analysis of ATAC-seq data for HaCaT cells and  OCT4 KO derivatives (Clone1 and Clone4) generated using CRISPR-Cas9 editing technology

first: Elena

last: Christofidou

first: Marios

last: Tomazou

first: Chrysovalantis

last: Voutouri

first: Christina

last: Michael

first: Triantafyllos

last: Stylianopulos

first: George

last: Spyrou


title: Oct4 is a gatekeeper of epithelial identity by regulating cytoskeletal dynamics in skin keratinocytes


title: Understanding transcriptional profile of alveolar Type I, Type II and double positive (Type I/II+) cells upon KrasG12D activation in mouse lungs during lung adenocarcinoma.

city: La Jolla

first: Mark

last: Onaitis

state: California

address: 855 Health Sciences Dr

department: Surgery

institute: University of California San Diego

summary: Previously, we identifed alveolar Type II cells as cell-of-origin for Kras induced lung adenocarcinoma. In the current study, we examined the phenotype of Type II cells after Kras activation and found evidence for proliferation of cells that co-express Type I and Type II markers. Using RNAseq, we are trying to charcterize these different alveolar epithelial cells (Type I, Type II and double positive (Type I/II+)) upon KrasG12D activation during lung adenocarcinoma.

overall_design: Comparative gene-expression analysis for single positive Type I cells (Pdpn+, Tdtm-) and Type II cells (Pdpn-, Tdtm+); and double positive cells (Pdpn+, Tdtm+) from Sftpc-CreER; LSL-KrasG12D, LSL-Rosa26-Tdtm mice after 4 weeks of tamoxifen administration.

first: Xia

last: Xu

first: Jacob

last: Hoj

first: william

last: Kim

first: Priyanka

last: Chaudhary


title: Metabolic Reprogramming Driven by IGF2BP3 Promotes Acquired Resistance to EGFR Inhibitors in Non–Small Cell Lung Cancer

first: Xiaolei

last: Zhang

address: 132 East Waihuan Road, Higher Education Mega Center, Panyu District

summary: Acquired resistance represents a bottleneck for effective molecular targeted therapy in lung cancer. Metabolic adaptation is a distinct hallmark of human lung cancer that might contribute to acquired resistance. In this study, we discovered a novel mechanism of acquired resistance to EGFR tyrosine kinase inhibitors (TKI) mediated by IGF2BP3-dependent cross-talk between epigenetic modifications and metabolic reprogramming through the IGF2BP3–COX6B2 axis. IGF2BP3 was upregulated in patients with TKI-resistant non–small cell lung cancer, and high IGF2BP3 expression correlated with reduced overall survival. Upregulated expression of the RNA binding protein IGF2BP3 in lung cancer cells reduced sensitivity to TKI treatment and exacerbated the development of drug resistance via promoting oxidative phosphorylation (OXPHOS). COX6B2 mRNA bound IGF2BP3, and COX6B2 was required for increased OXPHOS and acquired EGFR-TKI resistance mediated by IGF2BP3. Mechanistically, IGF2BP3 bound to the untranslated region of COX6B2 in an m6A-dependent manner to increase COX6B2 mRNA stability. Moreover, the IGF2BP3–COX6B2 axis regulated nicotinamide metabolism, which can alter OXPHOS and promote EGFR-TKI acquired resistance. Inhibition of OXPHOS with IACS-010759, a small-molecule inhibitor, resulted in strong growth suppression in vitro and in vivo in a gefitinib-resistant patient-derived xenograft model. Collectively, these findings suggest that metabolic reprogramming by the IGF2BP3–COX6B2 axis plays a critical role in TKI resistance and confers a targetable metabolic vulnerability to overcome acquired resistance to EGFR-TKIs in lung cancer.

overall_design:
RNA-Seq in NSCLC patients with TKI-sensitive and TKI-resistant.
RNA-Seq in two conditions were investigated: (1) untreated PC-9/GR cells, (2) PC-9/GR cells with IGF2BP3 stable knockdown.
RIP-Seq in two conditions were investigated: (1)  PC-9/GR cells, (2) PC-9/GR cells with IGF2BP3 stable overexpression.

first: Ziyou

last: Lin

first: Jingwei

last: Li

first: Jian

first: Weineng

last: Feng


title: Tiered Sympathetic Control of Cardiac Function Revealed by Viral Tracing and Single Cell Transcriptome Profiling

city: Los Angeles

first: Olujimi

last: Ajijola

address: 100 Medical Plaza

department: Cardiovascular Center

institute: UCLA

summary: The cell bodies of postganglionic sympathetic neurons innervating the heart primarily reside in the stellate ganglion (SG), alongside neurons innervating other organs and tissues. Whether cardiac-innervating stellate ganglionic neurons (SGNs) exhibit diversity and distinction from those innervating other tissues is not known. To identify and resolve the transcriptomic profiles of SGNs innervating the heart we leveraged retrograde tracing techniques using adeno-associated virus (AAV) expressing fluorescent proteins (GFP or Td-tomato) with single cell RNA sequencing. We investigated electrophysiologic, morphologic, and physiologic roles for subsets of cardiac-specific neurons and found that three of five adrenergic SGN subtypes innervate the heart. These three subtypes stratify into two subpopulations; high (NA1a) and low (NA1b and NA1c) Npy-expressing cells, exhibit distinct morphological, neurochemical, and electrophysiologic characteristics. In physiologic studies in transgenic mouse models modulating NPY signaling, we identified differential control of cardiac responses by these two subpopulations to high and low stress states. These findings provide novel insights into the unique properties of neurons responsible for cardiac sympathetic regulation, with implications for novel strategies to target specific neuronal subtypes for sympathetic blockade in cardiac disease.

first: Sachin

last: Sharma

first: Russell

last: Littman


title: Oct4 is a gatekeeper of epithelial identity by regulating cytoskeletal dynamics in skin keratinocytes [RNA-Seq]

first: Katerina

last: Strati

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT HaCaT cells and  OCT4 KO derivatives (Clone1 and Clone4) generated by CRISPR-Cas9 editing technology

first: Elena

last: Christofidou

first: Marios

last: Tomazou

first: Chrysovalantis


title: ChIP-seq data in mESCs show ZFP661 suppresses cohesin binding at CTCF barriers

first: Jinpu

last: Jin

summary: In this assay, we aimed to investigate the occupancy of ZFP661 in the mouse genome and its possible role in regulating the occupancies of CTCF and cohesin, which are two key factors in establishing 3D chromatin structures. To achieve this, we performed ChIP-seq in ZFP661-3HA endogenously tagged mESCs (for ZFP661), Zfp661 knockout (KO) mESCs (for CTCF and RAD21), and ZFP661-3HA overexpressing (OE) mESCs (for ZFP661, CTCF, RAD21, KAP1, and H3K9me3). Our results reveal that 1) ZFP661 binding peaks were co-occupied with those of CTCF; 2) ZFP661 binds exclusively inside the CTCF loop anchors; and 3) ZFP661 can suppress cohesin binding at CTCF barriers without altering CTCF binding.

overall_design: We compared the binding of CTCF and RAD21 on CTCF barriers co-occupied with ZFP661 between wild-type (WT) and Zfp661 KO, as well as between empty vector (EV) control and ZFP661-3HA OE. Each type included two biological replicates.

first: Todd

last: Macfarlan


title: PC3T: a signature-driven predictor of chemical compounds for cellular transition

first: Xiuliang

last: Cui

state: Shanghai

address: Changhai Road 225

institute: Second Military Medicine University

summary: Cellular transitions hold great promise in translational medicine research. However, therapeutic applications are limited by the low efficiency and safety concerns of using transcription factors. Small molecules provide a temporal and highly tuneable approach to overcome these issues. Here, we present PC3T, a computational framework to identify enrich molecules that induce desired cellular transitions, and PC3T was able to consistently identify enrich small molecules that had been experimentally validated in both bulk and single cell datasets. We then predicted and experimentally validated small molecules reprogramming of fibroblasts into hepatocyte-like cells and found that the fibroblasts exhibited epithelial cell morphology and hepatocyte-like specific gene expression pattern after treatment.

overall_design: Examine RNA expression profile of MEFs, and MEFs treated by 3 molecules: Carbidopa, CHIR-99021 and LY-364747.

first: Lu

last: Han

first: Wenxia

last: Zhou

first: Peilin


title: Effect of norepinephrine and UK 14,304 treatment on murine small intestinal organoids

city: Amsterdam

first: Anne

last: ten Hove

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal Research

country: Netherlands

institute: Amsterdam UMC

summary: Murine small intestinal organoids were stimulated with the general α and β adrenergic receptor agonist norepinephrine and the complete potent and specific α2 adrenergic agonist UK 14,304 (both 1uM) or vehicle controls for 4 days. Afterwards, they were harvested for RNA isolation and proliferation and differentiation gene expression patterns were assessed.

overall_design: Organoids treated with vehicle control or agonist: vehicle control HCl for norepinephrine (n=4), vehicle control DMSO for UK 14,304 (n=4), norepinephrine 1uM (n=5), UK 14,304 1uM (n=5)

first: A

middle: F

last: Li Yim

first: T

last: Hakvoort

first: J

last: Seppen

first: W

last: de Jonge

middle: S


title: Convergence of YAP/TAZ, TEAD and P63 activity directs premalignant lung gene expression

city: BOSTON

first: Boting

last: Ning

state: Massachusetts

address: 72 E Concord St

country: USA

institute: BOSTON UNIVERSITY

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

overall_design: Refer to individual Series


title: Human DUX4 and mouse Dux interact with STAT1 and broadly inhibit interferon-stimulated gene induction [CUT&TAG]

city: Seattle

first: Stephen

last: Tapscott

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

summary: DUX4 activates the first wave of zygotic gene expression in the early embryo. Mis-expression of DUX4 in skeletal muscle causes facioscapulohumeral dystrophy (FSHD), whereas expression in cancers suppresses IFNg-induction of MHC Class I and contributes to immune evasion. We show that the DUX4 protein broadly suppresses immune signaling pathways—including IFNg, IFNb, DDX58, IFIH1 and cGAS mediated pathways. A conserved region containing (L)LxxL(L) motifs in the DUX4 carboxyterminal domain (CTD) was necessary to suppress interferon stimulated genes (ISGs). Co-immunoprecipitation identified DUX4-CTD interaction with multiple immune signaling factors, including STAT1. The DUX4-CTD (L)LxxL(L) region interacts with phosphorylated STAT1, sequesters it in the nucleus, modestly reduces its DNA binding, and prevents STAT1 from inducing ISG transcription. Mouse Dux similarly interacted with STAT1 and suppressed IFNg induction of ISGs. These findings identify an evolved role of the DUXC family in modulating immune signaling pathways with implications for development, cancers, and FSHD.

overall_design: Sequencing of CUT&Tag targeting phosphorylated RNA Polymerase II using the phospho-RpB1 CTD (Ser5) (D9N51) Antibody)

first: Amy

last: Spens

first: Nicholas

last: Sutliff

first: Sean

last: Bennett