title: Blood-derived lysophospholipid sustains hepatic phospholipids and fat storage necessary for hepatoprotection in overnutrition

city: Singapore

first: Cheen Fei

last: Chin

address: 8 College Road, Level 8

department: Cardiovascular and Metabolic Disorders

country: Singapore

institute: Duke-NUS Medical School

summary: The liver has a high demand for phosphatidylcholine (PC) particularly in overnutrition where reduced phospholipid levels have been implicated in the development of non-alcoholic fatty liver disease (NAFLD). Whether other pathways exist in addition to de novo PC synthesis that contribute to hepatic PC pools remains unknown. Here, we identified the lysophosphatidylcholine (LPC) transporter Mfsd2a as critical for maintaining hepatic phospholipid pools. Hepatic Mfsd2a expression was induced in patients having NAFLD and in mice in response to dietary fat via glucocorticoid receptor action. Mfsd2a liver-specific deficiency in mice (L2aKO) led to a robust NASH-like phenotype within just two weeks of dietary fat challenge associated with reduced hepatic phospholipids containing linoleic acid. Reducing dietary choline intake in L2aKO mice exacerbated liver pathology and deficiency of liver phospholipids containing polyunsaturated fatty acids (PUFA). Treating hepatocytes with LPC containing oleate and linoleate, two abundant blood-derived LPCs, specifically induced lipid droplet biogenesis and contributed to phospholipid pools, while LPC containing the omega-3 fatty acid DHA promoted lipid droplet formation and suppressed lipogenesis. This study revealed that PUFA containing LPCs drive both hepatic lipid droplet formation, suppress lipogenesis and sustain hepatic phospholipid pools--processes that are critical for protecting the liver from excess dietary fat.

overall_design: Liver mRNA profiles of 2afl/fl and L2aKO mice fed with NASH diet.

first: David

middle: L

last: Silver


title: Genome-wide mapping of MLL1, CRM1, and NUP-fusion derivatives in human leukemia or mouse ES cell lines

status: Public on Jul 27 2023

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We used ChIP-seq to examine the genome-wide binding of MLL1, CRM1, and NUP-fusions in human leukemia or mouse ES cell lines. Our analysis revealed that MLL1, CRM1, and NUP-fusions are preferentially co-localized on the genome.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Chromatin immunoprecipitation-sequencing (ChIP-seq) for the drug-treated human leukemia LOUCY cells or mouse embryonic stem cells (mESCs) expressing FLAG-NUP98-HOXA9 or its mutants (AG or N51S).

first: Masahiro

last: Oka

first: Mayumi

last: Ohtani


title: The distinct transcriptome of virulence-associated phylogenetic group B2 Escherichia coli

city: Richardson

first: Zhenyu

last: Xuan

state: TX

address: 800 West Campbell

country: USA

institute: UT Dallas

type: Expression profiling by high throughput sequencing

summary: Strains of urinary tract associated E. coli both recent isolates and from the ECOR collection and non pathogenic E. coli strains were analyzed. Replicates were performed to establish the reproduciblity, then single experiments were performed there on.

overall_design: RNA-Seq

first: Jacob

middle: B

last: Hogins

first: Philippe

middle: E

last: Zimmern

first: Larry

middle: J

last: Reitzer


title: Anatomy of footprint extension in ribosome profiling reveals translational landscape mediated by S1 protein in bacteria

status: Public on Jul 28 2023

city: Wako

first: tomoya

last: fujita

state: Saitama

address: 2-1, Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

type: Non-coding RNA profiling by high throughput sequencing

summary: Ribosome profiling — RNase footprinting of ribosome-bound mRNA — has been a unique and powerful method, applied to widespread organisms to survey ribosome traversal along mRNAs. In contrast to eukaryotes, bacterial ribosome footprints show a broad range of sizes, reflecting the differential states of ribosomes. However, the origin remains unclear. Here, we show that rotated state of ribosomes and intramolecular RNA duplexes each extend bacterial ribosome footprints at the 5′ end. Combining elongation inhibitors, cryo-electron microscopy, and ribosome profiling, we demonstrated that the rotated state of ribosomes results in long footprints. Along the subunit rotation, ribosomal protein S1 — a 30S-subunit RNA-binding protein — sterically protects mRNA at the 5′ end of the ribosome from RNase digestion and facilitates elongation of the ribosome. Moreover, we found that ribosomes stalled on ycbZ mRNA generate prolonged footprints because of their unique RNA secondary structure proximal to ribosomes. Through the studies of footprint extension, our results revealed S1-mediated stabilization of translation elongation and provide ribosome profiling approach to probe the conformational diversity of ribosomes in bacteria.

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

overall_design: Ribosome profiling, tRNA-seq, and irCLIP-seq

first: Tomoya

last: Fujita

first: Takeshi

last: Yokoyama

first: Mikako

last: Shirouzu

first: Hideki

last: Taguchi

first: Takuhiro

last: Ito

first: Shintaro

last: Iwasaki


title: Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity [DRB/TT-seq]

city: London

first: Sara

last: Rohban

state: London

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: To investigate the role of catalytic subunit of the Integrator complex, INTS11, during the transcription cycle, we established U2OS cell line in which INTS11 has been knock down by siRNA.

overall_design: We performed DRB/TT-seq on siCtrl- and siINTS11-transfected cells at different timepoints (10, 20 and 30 min) after DRB release in duplicates.

first: Mahmoud

middle: R

last: Rafiee

first: Jernej

last: Ule

first: Nicholas

last: Luscombe


title: Effects of rapamycin, torin1, and rapalink1 on RNA levels

city: Chicago

first: Sejeong

last: Shin

state: IL

address: 909 S Wolcott Ave.

institute: University of Illinois at Chicago

summary: This study aimed to identify changes in RNA levels after inhibiting the mechanistic target of rapamycin using RNA sequencing.

overall_design: Mouse embryonic fibroblasts were treated with inhibitors of the mechanistic target of rapamycin for 24 hours.

first: Sang-Oh

last: Yoon


title: Deficiency of neutrophil high-mobility group box-1 in liver transplant recipients exacerbates early allograft injury in mice

first: Natalia

last: Nieto

address: 909 South Wolcott Avenue

summary: To investigate the role of recipient neutrophil intracellular HMGB1 in early allograft injury after liver transplant. Using a mouse orthotopic liver transplant model, as well as LPS injection, we found that neutrophils significantly infiltrate the liver after liver transplant and LPS challenge. Deficiency of neutrophil HMGB1 enhances their activation, boosts their pro-oxidant and pro-inflammatory phenotype, and hinders biosynthesis and metabolism of inositol polyphosphates. Overall, these events exacerbate early allograft injury after liver transplant.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from neutrophils of WT and Hmgb1ΔMye mice treated with saline or LPS.

first: Zhuolun

last: Song


title: lncRNA expression reveals the potential regulatory roles in ox-LDL induced macrophage-derived foam cells

city: beijing

first: wenjuan

last: xu

address: Beijing University of Chinese Medicine, No.11 North 3rd Ring East Road, Chao-Yang District, Beijing

country: China

institute: Beijing University of Chinese Medicine

summary: The goals of this study are to analysis the potential regulatory roles in ox-LDL induced macrophage-derived foam cells by lncRNA. A total of 50688 mRNA and 1514 lncRNA were found, and including 51 lncRNAs and 1730 mRNAs were significantly dysregulated in the model group (p-adjust < 0.05 and |log2FC| > 2). Then the result of GO and KEGG pathways showed that this dysregulated genes were significantly enriched in molecular function and biological processes and they were associated cell proliferation, cell apoptosis and inflammatory response. Additionally, the results of the lncRNA-mRNA co-expression network showed that 15 mRNAs and 9 lncRNAs were identified as the key regulatory factors, which may play crucial roles in AS development. Especially, the lncRNAs, Brip1os, Gm15472, Gm16586, Gm20703, and AU020206 could be seen as the potential biomarkers in macrophage-derived foam cells. This study revealed the dysregulated lncRNAs and mRNAs in AS development and the lncRNAs, Brip1os, Gm15472, Gm16586, Gm20703, and AU020206 were identified as the key regulatory factors. The dysregulated genes may be consider as the potential diagnostic biomarkers of AS, and it needs more verification in future studies.

overall_design: lncRNA and mRNA profiles of ox-LDL induced macrophage cells

first: Wenjuan

last: Xu


title: Accessibility and activity of transcriptional regulatory elements during sea urchin embryogenesis and differentiation [PRO-seq]

city: Staten Island

first: Cesar

last: Arenas-Mena

state: New York

address: 2800 Victory Boulevard

department: Biology

institute: CSI CUNY

type:
Other
Third-party reanalysis

summary: Transcriptional regulatory elements (TREs) are the primary nodes of the gene regulatory networks that control development.   TREs are identified by PRO-seq and their accessibility by ATAC-seq during sea urchin embryonic development and differentiation.  Our analysis identifies surprisingly early accessibility in 4-cell cleavage embryo TREs that is not necessarily followed by subsequent transcription, and an excess of ATAC-seq peaks transcriptionally disengaged during the stages analyzed.  Embryonic accessibility shifts are driven by transcriptionally engaged TREs, and PRO-seq transcriptional differences at TREs provide more contrast among embryonic stages than ATAC-seq accessibility differences.  TRE accessibility reaches a maximum around the 20-hour late blastula, which coincides with major embryo regionalizations. At the same time, a large number of distal TREs become transcriptionally disengaged, in support of an early Pol II primed model for developmental gene regulation that eventually resolves in transcriptional activation or silencing.  A transcriptional potency model based on labile nucleosome TRE occupancy driven by DNA sequences and the prevalence of histone variants is proposed in order to explain the basal accessibility of transcriptionally inactive TREs during early embryogenesis.

overall_design: PRO-seq in embryos and larvae followed previously stablished protocols (Arenas-Mena et al., 2021), except that for red spherule cells the lysis buffer during the nuclear prep was supplemented with 0.1 % NP40, 0.1% Tween-20, and 1% BSA, and the density gradient solutions were supplemented with 1% BSA to diminish nuclear shearing. Red spherule cells were purified from the coelomic fluid of adult sea urchins following a previously stablished method (Smith et al., 2019).  OmniATAC in 72 hour embryos raised at 15 degrees C and red spherule cells was performed as previously described (Corces et al., 2017).    Quick PRO-seq in red spherule cells was performed according to a previously stablished method (Judd et al., 2019) with minor modifications.  Permeabilization and wash buffers were supplemented with 1% BSA, cells were collected in a fixed angle centrifuge at 0 oC and 1,000 G for 10 minutes.  The run-on reaction was done at 15 oC for 15 minutes.  Dynabeads Myone ® Streptoavidin T1 beads were used to pull down the biotinylated RNAs. Free biotinylated nucleotides were removed by filtration with SigmaspinTM post-reaction clean-up columns.  On-Bead 5’ Decapping reaction was done using NEBuffer 2 buffer (NEB, B7002S ®). Off-Bead Reverse Transcription followed the instructions in SuperScript ® IV Reverse transcriptase kit. The Quick PRO-seq PRO-seq libraries were purified from 5% acrylamide gel to remove adaptor dimers.


title: Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs

city: Shenzhen

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity [TT-seq]

overall_design: We performed nascent RNA-seq analysis on siCtrl- and siINTS11-transfected cells at 48h post transfection in triplicates.


title: Presence of mutant p53 increases stem cell frequency and is associated with reduced binding to classic TP53 binding sites in cell lines and primary AMLs [ChIP-seq]

status: Public on Jul 26 2023

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: With an overall 5%-10% incidence rate in acute myeloid leukemia (AML), the occurrence of TP53 mutations is low compared with that in solid tumors. However, when focusing on high-risk groups including secondary AML (sAML) and therapy-related AMLs, the frequency of mutations reaches up to 35%. Mutations may include loss of heterozygosity (LOH) or deletion of the 17p allele, but are mostly missense substitutions that are located in the DNA-binding domain. Despite elaborate research on the effects of TP53 mutations in solid tumors, in hematological malignancies, the effects of TP53 mutations versus loss of TP53 remain unclear and under debate. Here, we compared the cellular effects of a TP53 mutant and loss of TP53 in human hematopoietic stem and progenitor cells (HSPCs). We found that when expressing TP53 mutant or loss of TP53 using siRNA, CD34+/CD38- cells have a significantly enhanced replating potential, which could not be demonstrated for the CD34+/CD38+ population. Using RNA-sequencing analysis, we found a loss of expression of p53 target genes in cells with TP53 knockdown. In contrast, an increased expression of a large number of genes was observed when expressing TP53 mutant, resulting in an increase in expression of genes involved in megakaryocytic differentiation, plasma membrane binding, and extracellular structure organization. When binding of p53 wild type and p53 mutant was compared in cell lines, we found that mutant p53 binds to a large number of binding sites genomewide, contrary to wild-type p53, for which binding is restricted to genes with a p53 binding motif. These findings were verified in primary AMLs with and without mutated TP53. In conclusion, in our models, we identified overlapping effects of TP53 mutant and loss of TP53 on in vitro stem cell properties but distinct effects on DNA binding and gene expression.

overall_design: ChIP sequencing of TP53 in primary patient AML cells and of histone modifications in AML cell lines

first: Mylène

last: Gerritsen

first: Susan

last: Hilgendorf

first: Guoqiang

last: Yi

first: Albertus

middle: T

last: Wierenga

first: Jan-Jacob

last: Schuringa

middle: H

first: Edo

last: Vellenga


title: Blocking the activation of TGFβ signaling in liver sinusoidal endothelial cells alleviates liver fibrosis in mice

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

summary: Purpose: To detect the alterations in transcriptional profile of primary LSECs isolated from Tgfbr2 ECKO mice and Tgfbr2f/f mice in CCl4-induced liver fibrosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LSECs from Tgfbr2 ECKO mice and Tgfbr2f/f mice treated with CCl4. Methods: we generated endothelial-specific Tgfbr2 knockout mice. We then subjected Tgfbr2 ECKO and its littermates Tgfbr2f/f mice to CCl4 injection for 6 weeks.

first: Ru

last: Huang


title: Presence of mutant p53 increases stem cell frequency and is associated with reduced binding to classic TP53 binding sites in cell lines and primary AMLs


title: PARylated PDHE1α generates acetyl-CoA for local chromatin acetylation and DNA damage repair

first: Jun

last: Zhang

state: Guangdong Province

address: Xueyuan Avenue

department: School of Medicine

institute: Shenzhen University

summary: Chromatin relaxation is a prerequisite step for allowing DNA repair machinery to access double-strand breaks (DSBs), and local histones around the DNA breaks suffer from prompt acetylation changes. However, an intriguing question remains as to where the quick and robust acetyl-CoA is produced. Here, we report that pyruvate dehydrogenase 1α (PDHE1α) catalyzes pyruvate metabolic processes and provides acetyl-CoA promptly in response to DNA damage. PDHE1α was quickly recruited to chromatin in a PARylation-dependent manner, which further drove the local acetyl-CoA generation to support local chromatin acetylation around the DSB regions. In turn, this process increased the formation of relaxed chromatin to benefit repair factor loading, thus promote DSB repair to ultimately maintain genome stability and contribute to the resistance of cancer cells to DNA-damaging treatments in vitro and in vivo. Consistent with this, blocking PARylation-based PDHE1α chromatin recruitment markedly attenuated chromatin relaxation and the DSB repair efficiency, and resulted in genome instability and radio re-sensitivity. Collectively, these findings identified an undescribed mechanism that underlies site-directed acetyl-CoA generation involving chromatin-associated PDHE1α and its instrumental function in DNA repair and regulating local chromatin acetylation around DSB sites. The findings provide potential routes to disrupt a key mechanism of cancer cell resistance to genotoxic damage.

overall_design: Examination of pan-Lysine acetylation signal distribution upon DNA damage.


title: Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity

first: Sara

last: Rohban


title: Gene expression profile at single cell level of glial cells from mouse nodose ganglia at postnatal day 4.

city: Boston

first: Elijah

middle: D.

last: Lowenstein

state: MA

address: 3 Blackfan Circle

institute: BIDMC

summary: The nodose ganglia contain sensory neurons that play key roles in homeostatic behaviors and are supported by nodose glial cells. We used single cell RNA sequencing (scRNA-seq) to interrogate the molecular diversity of nodose glial cells shortly after birth.

overall_design: Nodose glial cells from Phox2bCre;Ai14 mice were isolated by fluorescence activated cell sorting (FACS) according to the presence of cytoplasmic tdTomato at P4 and analyzed using scRNA-seq (CEL-Seq2).

middle: D

first: Aristotelis

last: Misios


title: Single cell RNAseq analysis of Igbpl1 treatment on microbead-induced glaucoma in mice

city: Cambridge

first: Guangan

last: Hu

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: IGFBPL1 deficiency leads  to progressive retinal neuron loss and phosphorylated Tau accumulation in the brain. To investigate the role of IGFBL1 in retina microglia homestasis and function. Total immune cells were sorted from microbead (MB)-induced glaucoma mice and glucoma mice treated with recombinant  Igfbpl1 protein for single cell RNAseq analysis by 10X genomics technology.

overall_design: scRNA-seq was performed for immune cells isolated from retinas of 10 MB and 10 Igfbpl1-treated MB mice (at 8-10 months of age), using FACS. Mice were transcardially perfused with saline, and digested into single cell suspension  in a dissociation solution that included collagenase/dispase (1 mg/ml), papain (80 units), and Dnase (0.5mg/ml) in DMEM for 1 hour at 37oC.

first: Jianzhu

last: Chen


title: Conserved roles of B-GATAs in the regulation of photosynthesis and high-light stress response

city: Freising

first: Peter

middle: Michael

last: Schröder

state: Bavaria

address: Emil-Ramann-Straße 8, Gebäude 4223

department: School of Life Sciences

country: Germany

institute: Technical University of Munich

sample_organism:
Marchantia polymorpha
Arabidopsis thaliana


title: A mechano-dependent senescence associated secretory phenotype triggers the recruitment of endothelial and immune cells by Cerebral Cavernous Malformation 2 deficient endothelial cells

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

country: France

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

summary: Cerebral Cavernous Malformations (CCM) is a cerebrovascular disease in which stacks of dilated haemorrhagic blood-filled capillaries form focally in the brain. Endothelial loss-of-function mutations on any of the three CCM genes (CCM1-3) are responsible for the familial form of the disease. Whether and how the defective mechanotransduction, inflammatory response and mosaic state characteristic of these lesions interplay to sustain the progression of CCM diseases is unknown. Here, we show that CCM1- and CCM2-silenced endothelial cells enter into a senescence associated with secretory phenotype (SASP) that they use to invade the extracellular matrix and attract surrounding wild-type endothelial and immune cells. Further, we demonstrate that this SASP is driven by the mechanical and molecular disorders provoked by ROCKs dysfunctions when CCM2 is lost. This discovery reconciles all the known dysregulated traits of CCM1/2-deficient endothelial cells into a unique mechano-dependent SASP that links perturbed cellular mechanics to microenvironment remodelling and long-range activation of WT endothelial and immune cells.

overall_design: RNA-seq analysis of monolayers of HUVEC silenced for CCM2 and/or ROCK1 or ROCK2 (3 replicates per condition; 6 conditions. NT used as the reference sample).

first: Daphné

last: Vannier

first: Apeksha

last: Shapeti

first: Emmanuelle

last: Planus

first: Sandra

last: Manet

first: Paul

last: Rivier

first: Olivier

last: Destaing

first: Corinne

last: Albiges-Rizo

first: Hans

last: Van Oosterwyck

first: Eva

last: Faurobert


title: High-light stress RNA-seq Marchantia polymorpha

summary: In order to elucidate the role of the single Marchantia B-GATA ortholog in response to high light intensities, a transcriptomic analysis of Marchantia polymorpha BoGa, Mpb-gata1 mutants and MpB-GATA1ox under high-ligh stress conditions was performed.

overall_design: Transcriptome comparison including three replicate measurements of three biological samples. Plants were subjected to three different conditions: six hours of high-light (HL) with 1200 µmol m-2 s-1 at 20-22°C (t6HL), six hours of mock treatment with 60-70 µmol m-2 s-1 at 20-22°C (t6GL), or at time point 0h (t0).

middle: M

first: Claus

last: Schwechheimer


title: High-light stress RNA-seq Arabidopsis thaliana

summary: In order to elucidate the role of the Arabidopsis thaliana LLM-domain B-GATAs in response to high light intensities, a transcriptomic analysis of Col-0, a hexuple LLM-domain B-GATA mutant hex (gnc gnl gata15 gata16 gata17 gata17l) and GNLox under high-ligh stress conditions was performed.


title: Comparative transcriptomic analysis of  Marchantia polymorpha BoGa and the MpB-GATA1 mutants Mpb-gata1-1 and Mpb-gata1-2

summary: RNA-seq of Marchantia polymorpha Mpb-gata1 mutants was performed in order to investigate their molecular signature of gene expression changes.

overall_design: Transcriptome comparison including three replicate measurements of three biological samples. BoGa, Mpb-gata1-1 and Mpb-gata1-2 were grown on 1/2 Gamborg's B5 medium in long day conditions (16L/8D) at 40 µmol m-2 s-1 and 22°C for three weeks.


title: Folate deficiency reduced aberrant level of DOT1L-mediated histone H3K79 methylation causes disruptive SHH gene expression involved in neural tube defects

status: Public on Jul 25 2023

city: Beijing

first: Pei

last: Pei

address: 2 Yabao Road

department: The Central Lab

institute: Capital Institute of Pediatrics

summary: Neural tube defects (NTDs) are one of the most severe congenital abnormalities. Maternal folate deficiency could impact the occurrence of NTDs. Histone H3 methyltransferase disruptor of telomeric silencing 1-like (DOT1L) expression was significantly downregulated, and low levels of H3K79me2 were found in the corresponding NTDs samples with their maternal serum folate under low levels. Using ChIP-seq assays, we found that a decrease of H3K79me2 downregulates the expression of Shh and Sufu in mouse embryonic stem cells (mESC) under folate deficiency. Our results indicate that abnormal Shh and Sufu genes expression reduced by aberrant Dot1l-mediated H3K79me2 levels could be the cause of NTDs occurrence.

overall_design: Sv/129 mouse embryonic stem cells (mESCs) were cultured under normal folate medium for at least 2 passages before 1uM methotrexate(MTX) was applied for 24hours. 10^7 mESC cells from normal folate group and MTX group were used to obtain DNA with a concentration of 1 ng / ul and fragments were digested into100-500bp for CHIP(chromatin immunoprecipitation) sequencing. SimpleChip KIT (Cell Signaling Technology, America). CHIP-Seq libraries were prepared according to the protocol. Two IPs( Normal folate group and MTX group)precipitated with H3K79me2 antibody and two inputs(normal folate group and MTXgroup)were sequenced using Illumina NovaSeq 6000.

first: Xue

last: Li

first: Yuexi

last: Cheng

first: Juan

last: Yu

first: Fang

last: Wang

first: Lei

first: Changyun

last: Liu

first: Shan


title: Presence of mutant p53 increases stem cell frequency and is associated with reduced binding to classic TP53 binding sites in cell lines and primary AMLs [RNA-seq]

first: Joost

last: Martens

overall_design: RNA sequencing of Cordblood cells transfected with TP53 shRNA constructs or TP53 mutants

first: Mylène

last: Gerritsen

first: Susan

last: Hilgendorf

first: Guoqiang

last: Yi

first: Albertus

last: Wierenga

first: Jan-Jacob

last: Schuringa

first: Edo

last: Vellenga


title: Vascular calcification is accelerated by hyponatremia and low osmolality condition via activating Rac1-Akt pathway

first: Matsueda

last: Shumei

address: 3-1-1, Maidashi, Higashi-ku

institute: Kyushu universuty

summary:
Hyponatremia, one of the most frequently observed electrolyte disorders in patients with chronic kidney disease (CKD), is associated with increased mortality. Lower sodium concentrations or low osmolar conditions are shown to induce cell damages via apoptosis and oxidative stress, both of accelerate vascular calcification (VC), a critical phenotype of CKD patients.  It is unknown whether hyponatremia or low osmolar condition plays roles in the pathogenesis of VC.Human vascular smooth muscle cells (VSMCs) were cultured with calcifying medium, which was supplemented high calcium and phosphate. Concentrations of sodium in the culture media were further modified to determine the impacts of osmotic pressure on VC.
Microarray analysis of VSMCs revealed low osmolality activated Rac1-Akt pathway and reduced expression of NCX1, which is calcium-sodium exchanger.Lower osmolality including hyponatremic condition promotes high-phosphate-induced VC through multiple cellular processes including Rac1-Akt pathway activation.

overall_design: Human VSMCs was incubated for 4 days in normal medium or calcifying medium(CM), and further divided into 'Low' sodium(Na) concentration (126 mmol/L) or 'High' (170 mmol/L) Na groups for a total of 4 groups. mRNA expression of each groups was analyzed by microarray.

first: Shumei

last: Matsueda

first: Shunsuke

last: Yamada

first: Kumiko

last: Torisu

first: Toshiaki

last: Nakano

first: Takanari

last: Kitazono


title: Ascorbic acid induces transient global active chromatin remodelling, providing clues for its anti-cancer effect

first: Xiangyue

state: Shanghai

address: 131 Dong'an Road

institute: Fudan university

summary: In addition to the role of antioxidant, ascorbic acid (reducing Vitamin C) is an important cofactor for Fe2+ and α-ketoglutarate (α-KG) dependent dioxygenases (Fe2+/α-KGDDs) that comprise many diverse enzymes, including collagen prolyl hydroxylases, jmjC (Jumonji C) domain containing histone demethylases, Ten-eleven translocation (TET) 5-methyl cytosine (5mC) dioxygenases, and N6-methyl adenosine (m6A) demethylase FTO and ALKBH5. Ascorbic acid was reported to induce global epigenetic reprogramming. Here we optimized the library construction flow chart of single-stranded DNA profiling method KAS-seq and utilized KAS-seq to profile transient chromatin states changes upon ascorbic acid treatment for 10 min. We identified several critical pathways affected by ascorbic acid treatment, providing some clues for explaining the reported positive impact of anti-cancer, anti-depression, and anti-obesity for taking ascorbic acid.

overall_design: Cells were incubated in completed culture medium at 37 °C, 5% CO2. For vitamin C treatment experiments, cells were treated with/without 0.5 mM vitamin C in the culture medium for 10 min before being subjected to 5 mM N3-kethoxal labeling for another 10 min incubation.

first: Weizhi

last: He

first: Lulu

last: Hu


title: Transcriptional adaptation facilitates host specialization in a wheat pathogen

city: Kiel

first: Janine

last: Haueisen

address: Am Botanischen Garten 1-9

department: Botanical Institute

institute: Christian-Albrechts University of Kiel

summary: Host-pathogen co-evolutionary dynamics force microbial plant pathogens to constantly develop and adjust specific adaptations to thrive in their plant host, and therefore also act as strong drivers of divergence and speciation in pathogens. Factors that confer host specialization and determine host specificity are very diverse and range from molecular and morphological strategies to metabolic and reproductive adaptations. Identification of these key factors is a major goal in the study of pathogen evolution and may aid the development of sustainable crops and crop protection strategies. We here took a novel experimental approach and conducted comparative microscopy and transcriptome analyses of the closely related, recently diverged fungal pathogens Zymoseptoria tritici, Z. pseudotritici, and Z. ardabiliae that establish compatible and incompatible interactions with wheat. Although infections of the incompatible species induce plant defense response during invasion of stomatal openings, we found a highly conserved early-infection program among the three species. The transcriptional programs of the three pathogens are conserved to a large extent, as only 9.2% of the 8,885 orthologous genes are significantly differentially expressed during initial infection of wheat. The genes up-regulated in the compatible pathogen reflect adaptation to growth in wheat tissue e.g., by re-programming of fungal metabolism. In contrast, genes primarily involved in counteracting cell stress and damage are strongly induced in the incompatible species. Based on the species-specific gene expression profiles, we further identified nine candidate genes encoding putative effectors and host-specificity determinants in Z. tritici. These effectors are strongly induced in the compatible species and may interfere with host immune suppression. We also identify putative necrotrophic effectors which are induced at the onset of necrotrophic growth. Together, the results presented here indicate that host specialization has involved transcriptional adaptation of a relatively small number of genes. Our findings demonstrate the potential comparative analyses of compatible and incompatible infections present for identifying traits involved in pathogen evolution and host specialization.

sample_organism:
Zymoseptoria pseudotritici
Zymoseptoria ardabiliae

overall_design: High-quality total RNA from wheat leaves inoculated with Zp13, and Za17 was isolated. Strand-specific RNA-seq libraries including polyA enrichment were prepared and sequenced using an Illumina HiSeq 2500 platform. We further used published in planta and in vitro RNA-seq data (Grandaubert et al., 2015; Haueisen et al., 2019b; Möller et al., 2019). Differential gene expression analyses for 8,885 orthologous Zymoseptoria spp. genes (Feurtey et al., 2020) were performed in R (R Core Team, 2017) using DESeq2 v1.28.1 (Love et al., 2014). Genes with Padj ≤ 0.01 and |log2 fold-change | ≥ 2 were considered significantly differentially expressed.

first: Mareike

last: Moeller

first: Heike

last: Seybold

first: Eva

last: Stukenbrock


title: Transcriptional characterization of primary tumors and liver metastasis from 4T1-derived liver-metastatic cells

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

summary:
Metabolic rewiring is essential for breast tumor growth and progression to metastatic disease, yet little is known regarding how cancer cells modify their acquired metabolic programs in response to different metastatic microenvironments. Transcriptional and metabolomic analysis have previously shown that liver-metastatic breast cancer cells adopt an intrinsic metabolic profile characterized by increased HIF-1α activity and dependence on glycolysis. Stable isotope tracing analysis (SITA) performed in vivo confirmed that the glycolytic nature of liver-metastatic breast cancer cells is retained when these cells are grown as primary tumors or as liver metastases. However, our data also reveal that unique metabolic adaptations are specifically induced by the liver microenvironment. Indeed, liver metastases display elevated expression of genes involved in glutathione (GSH) biosynthesis and reactive oxygen species (ROS) detoxification when compared to primary tumors. Moreover, breast cancer liver metastases rely strongly on glucose and glutamine-derived carbons to support de novo GSH synthesis. Glutathione is a tripeptide that acts as a major scavenger for reactive oxygen species (ROS). Liver metastases display reduced levels of 8-Oxo-2'-deoxyguanosine, confirming their increased capacity to buffer ROS. We demonstrated the dependence of liver metastases formation on these distinct metabolic adaptations by depleting glutamate-cysteine ligase (Gcl), the rate-limiting enzyme in glutathione biosynthesis. Gcl depletion, and decreased GSH levels, strongly reduced the capacity of liver-metastatic cells to form distant metastasis within the liver.
We performed gene expression analysis of liver metastasis and primary tumors from liver-metastatic breast cancer cells derived from 4T1 cells. 4T1-2776 (76) and 4T1-2792 (92) cells were injected in the mammary fat pads of BALB/c and grown as primary tumors or were grown as liver metastasis after splenic injection. Tissues were harvested from primary tumors and liver metastasis and submitted to laser-capture microdissection (LCM). For liver metastasis, tumour tissue was harvested at 10 days, 2 weeks and 3 weeks after splenic injection. For each time point, tissue was isolated from the tumor centre (core), a peripheral area of the tumor (margin), a region of the liver proximal to the tumor (adjacent) and a region of the liver far from the tumor (distant). For primary tumors from 4T1-2776 cells (1034, 1036, 1043) and 4T1-2792 (MFP2L, MFP3L, MFP5L) tissue was collected from the tumor core and margin, at the experimental endpoint.

overall_design: Gene expression profile comparison from liver metastasis and primary tumors of 4T1-2776 and 4T1-2792  liver metastatic sub-populations of 4T1 cells.

first: Peter

last: Siegel

first: Sébastien

last: Tabariès


title: MicroRNA expression profile of human umbilical vein endothelial cells in response to Coxsackievirus A10 infection

city: Kunming

first: Jie

last: Song

state: Yunnan

address: Number 935 Jiaoling Load

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

summary: Coxsackievirus A10 (CV-A10) constitutes one of the major pathogens of hand, foot, and mouth disease (HFMD), which can cause mild to severe illness and even death. Most of these severe and death cases were closely associated with their neurological impairments, but the underlying mechanism of neuropathological injury induced by CV-A10 infection has not been elucidated. MicroRNAs (miRNAs), implicated in the regulation of gene expression in a posttranscriptional manner, play a vital role in the pathogenesis of various central nervous systems (CNS) diseases; thereby they are served as diagnostic biomarkers and are emerging as novel therapeutic targets for CNS injuries. To gain insights in the CV-A10-induced regulation of host miRNA-processing machinery, we employed high-throughput sequencing to identify differentially expressed miRNAs in CV-A10-infected HUVEC cells and further analyzed the potential functions of these miRNAs during CV-A10 infection. The results showed that CV-A10 infection could elicit 189 and 302 significantly differentially expressed miRNAs in HUVEC cells at 24 hpi and 72 hpi, respectively, as compared with the uninfected control.

overall_design: For virus infection, single-cell suspension at a density of 5 × 105 cells/ml was added into 6-well plates. When the cells were reached 80% confluences, the cells were incubated with CV-A10 (sub-genotype C, GenBank: MN557275), which isolated from an epidemic in Xiangyang, China, in 2017, at a multiplicity of infection (MOI) of 1 at 37°C for 2 h absorption. Subsequently, the infected-cells were continued to culture in RPMI-1640 containing 2% FBS and antibiotics at 37 °C in an atmosphere of 5% CO2, and collected with a cell scraper at 0, 24 and 72 h. Cells infected with CV-A10 at 0 hpi were regarded as control.

first: Yajie


title: Flexible and scalable control of T cell memory by a reversible epigenetic switch (RNA-seq)

city: Seattle

first: Kathleen

last: Abadie

state: Washington

address: 3720 15th Ave NE

department: Bioengineering

institute: University of Washington

summary: In this study, we find that the Tcf7+ CD8 T cells present following acute challenge can form either from cells that maintain Tcf7 expression throughout activation or from cells that silence Tcf7 and reactivate it after stimulation removal. In this experiment, we asked whether both pathways can give rise to cells with genomic characteristics of memory. To do this, we activated naive CD8 T cells ex vivo for 2 days followed by 1 day of culture without TCR stimulation. On day 3, we sorted Tcf7-YFP high and low populations, all from a single CellTrace peak representing cells that had undergone the same number of divisions. The sorted populations were cultured for an additional 6 days and sorted again on day 9 by Tcf7-YFP levels. These samples, as well as control naive, antigen-experienced, and effector samples, were processed for RNA-seq analysis.

overall_design: Control naïve samples were sorted from splenoyctes as CD8+CD44-CD62L+Tcf7-YFP+ (2 replicates); antigen-experienced samples were sorted from splenocytes as  CD8+CD44+CD62L+Tcf7-YFP+ (2 replicates); effector control samples were activated ex vivo for 3 days (2 replicates). Cells sorted as Tcf7-YFP high and low at day 3 were recultured and sorted as Tcf7-YFP high or low at day 9: Day9 Tcf7-YFP high, sorted Tcf7-YFP high at Day3 (2 replicates); Day9 Tcf7-YFP low, sorted Tcf7-YFP low at Day3 (2 replicates); Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3 , 1 (2 replicates).

first: Elisa

middle: C

last: Clark

first: Hao-Yuan

last: Kueh


title: Effect of siRNA depletion of SPRTN gene on gene expression in HepG2 cells

city: Split

first: Anja

last: Batel

address: Soltanska 2

country: Croatia

institute: MEFST

summary: A biallelic mutation in the SPRTN gene is currently the only known single-gene mutation implicated in early-onset HCC, contributing to the development of liver cancer. The precise mechanism by which SPRTN mutations lead to HCC is not fully understood. The SPRTN protein is involved in repair of DNA damage caused by DNA-protein crosslinks (DPC). Spartan was silenced in HepG2 cells with siRNA that targets mRNA of Spartan using Lipofectamine RNAiMAX (Thermo Fisher).Total RNA was extracted with QIAzol (Qiagen) according to the manufacturer's protocol and transcribed into cDNA with High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems) according to the manufacturer's protocol to test level of silencing with RT-qPCR .  The quality of RNA was tested with agarose electrophoresis and concentration was determined using Nanodrop. Samples were send to company providing RNA sequencing. Company did RNA quality check, sequencing and analysis of the results.

overall_design: siRNA knockdown of SPRTN gene (siRNA-SPRTN-1, 5'-GUC AGG AAG UUC UGG UUA A-UA-3')  in HepG2 cell line

first: Ivana

last: Terzić


title: Functional interrogation of lymphocyte subsets in alopecia areata using single-cell RNA sequencing

city: San Francisco

first: Eunice

middle: Y

last: Lee

address: 505 Parnassus Ave

institute: University of California, San Francisco

summary: Alopecia areata (AA) is among the most prevalent autoimmune diseases, but the development of innovative therapeutic strategies has lagged due to an incomplete understanding of the immunological underpinnings of disease. Here, we performed single-cell RNA sequencing (scRNAseq) of skin-infiltrating immune cells from the graft-induced C3H/HeJ mouse model of AA, coupled with antibody-based depletion to interrogate the functional role of specific cell types in AA in vivo. Since AA is predominantly T cell-mediated, we focused on dissecting lymphocyte function in AA. Both our scRNAseq and functional studies established CD8+ T cells as the primary disease-driving cell type in AA. Only the depletion of CD8+ T cells, but not CD4+ T cells, NK, B, or γδ T cells, was sufficient to prevent and reverse AA. Selective depletion of regulatory T cells (Treg) showed that Treg are protective against AA in C3H/HeJ mice, suggesting that AA failure of Treg-mediated immunosuppression is not a major disease mechanism. Focused analyses of CD8+ T cells revealed five subsets, whose heterogeneity is defined by an ‘effectorness gradient’ of interrelated transcriptional states that culminate in increased effector function and tissue residency. scRNAseq of human AA skin showed that CD8+ T cells in human AA follow a similar trajectory, underscoring that shared mechanisms drive disease in both murine and human AA. Our study represents a comprehensive, systematic interrogation of lymphocyte heterogeneity in AA, and uncovers a framework for AA-associated CD8+ T cells with implications for the design of future therapeutics.

overall_design: Expression profiling by high throughput sequencing

first: Zhenpeng

last: Dai

first: Eddy

last: Wang

first: Angela

last: Christiano


title: Amoeba Predation of Cryptococcus: A Quantitative and Population Genomic Evaluation of the Accidental Pathogen Hypothesis

city: Durham

first: Paul

last: Magwene

state: North Carolina

address: 124 Science dr.

institute: Duke University

summary: The “Amoeboid Predator-Fungal Animal Virulence Hypothesis” posits that interactions with environmental phagocytes shape the evolution of virulence traits in fungal pathogens. In this hypothesis, selection to avoid predation by amoeba inadvertently selects for traits that contribute to fungal escape from phagocytic immune cells. Here, we investigate this hypothesis in the human fungalpathogens Cryptococcus neoformans and Cryptococcus deneoformans. Applying quantitative trait locus (QTL) mapping and comparative genomics, we discovered a cross-species QTL region that is responsible for variation in resistance to amoeba predation. In C. neoformans, this same QTL was found to have pleiotropic effects on melanization, an established virulence factor. Through fine mapping and population genomic comparisons, we identified the gene encoding the transcription factor BZP4 that underlies this pleiotropic QTL and we show that decreased expression of this gene reduces melanization and increases susceptibility to amoeba predation. Despite the joint effects of BZP4 on amoeba resistance and melanin production, we find no relationship between BZP4 genotype and escape from macrophages or virulence in murine models of disease. Our findings provide new perspectives on how microbial ecology shapes the genetic architecture of fungal virulence, and suggests the need for more nuanced models for the evolution of pathogenesis that account for the complexities of both microbe-microbe and microbe-host interactions.

overall_design: The goal of the RNAseq experiment was to determine the change in expression when Cryptococcus neoformans cells are in coculture with Acanthamoeba castellanii or alone. This was accomplished by growing C. neoformans cells on V8 media and either adding amoeba or a control to the plate they are on. Cells were then left to interact for 48 hours. Cells were then collected for sequencing. 14 strains in total were used. With two of those strains having a single duplicate. The two strains with the duplicates are the parent strains a cross that generated the other 12 samples.

first: Thomas

last: Sauters

first: Cullen

last: Roth

first: Debra

last: Murray

first: Sheng

last: Sun

first: Anna

last: Floyd-Averette

first: Chinaemerem

last: Oniyishi

first: Robin

last: May

first: Joseph

last: Heitman


title: Gene expression in 1133 HCCs

city: RENNES CEDEX 9

first: Musso

last: Orlando

state: FRANCE

address: rue Henri Le Guilloux

institute: UMR-1317 INSERM - INRAe - Université de Rennes

type:
Expression profiling by array
Third-party reanalysis

summary:
Hepatocellular carcinomas (HCCs) exhibit a diversity of molecular
phenotypes, raising major challenges in clinical management. HCCs detected
by surveillance programs at an early stage are candidates for potentially
curative therapies (local ablation, resection, or transplantation). In the
long term, transplantation provides the lowest recurrence rates. Treatment
allocation is based on tumor number, size, vascular invasion, performance
status, functional liver reserve, and the prediction of early (<2 years)
recurrence, which reflects the intrinsic aggressiveness of the tumor.
Well-differentiated, potentially low-aggressiveness tumors form the
heterogeneous molecular class of nonproliferative HCCs, characterized by an
approximate 50% beta-catenin mutation rate. To define the clinical,
pathological, and molecular features and the outcome of nonproliferative
HCCs, we constructed a 1,133-HCC transcriptomic metadata set and validated
findings in a publically available 210-HCC RNA sequencing set. We show that
nonproliferative HCCs preserve the zonation program that distributes
metabolic functions along the portocentral axis in normal liver. More
precisely, we identified two well-differentiated, nonproliferation
subclasses, namely periportal-type (wild-type beta-catenin) and
perivenous-type (mutant beta-catenin), which expressed negatively correlated
gene networks. The new periportal-type subclass represented 29% of all HCCs;
expressed a hepatocyte nuclear factor 4A-driven gene network, which was
down-regulated in mouse hepatocyte nuclear factor 4A knockout mice; were
early-stage tumors by Barcelona Clinic Liver Cancer, Cancer of the Liver
Italian Program, and tumor-node-metastasis staging systems; had no
macrovascular invasion; and showed the lowest metastasis-specific gene
expression levels and TP53 mutation rates. Also, we identified an eight-gene
periportal-type HCC signature, which was independently associated with the
highest 2-year recurrence-free survival by multivariate analyses in two
independent cohorts of 247 and 210 patients. CONCLUSION: Well-differentiated
HCCs display mutually exclusive periportal or perivenous zonation programs.
Among all HCCs, periportal-type tumors have the lowest intrinsic potential
for early recurrence after curative resection. (Hepatology
2017;66:1502-1518).

relation:
Reanalysis of: GSE14520
Reanalysis of: GSE15765
Reanalysis of: GSE16757
Reanalysis of: GSE17856
Reanalysis of: GSE19977
Reanalysis of: GSE20017
Reanalysis of: GSE25097
Reanalysis of: GSE54236
Reanalysis of: GSE56140

overall_design: Raw feature data from Gene Expression Omnibus (GSE16757, GSE20017, GSE14520, GSE25097, GSE17856, GSE54236, GSE20140 (subSeries GSE19977, subSeries GSE56140), GSE15765) were normalized and log 2 intensity  expression summary values for each probe set were calculated using Robust Multiarray Average (RMA, packages Affy or Limma). Each dataset was assessed for  the detection of outliers and inter-array, experiment-related batch effects by principal component analysis (PCA) and density plots. The outliers removed were: one sample  from GSE17856, one sample from GSE15765 and two samples from GSE54236. When clear-cut inter-array experiment-related batch effects were observed within a  dataset, this effect was corrected by the COMBAT method (package sva). GSE25097 was corrected for 2-batch effect and GSE14520 for 3-batch effect. Then,  probes being detected over the background noise in at least one HCC were retained and quantile normalized (package preprocessCore). When raw data were not  available, normalized data were directly used. The final metadata set include 1,133 HCCs and 9,542 genes.

first: Orlando

last: Musso

first: Romain

last: Désert

first: Lise

last: Desquilles

first: Fabien

last: Foucher


title: Mechanism of TP53 and RB1 inactivation-induced neuroendocrine phenotype transformation in TKI-resistant lung adenocarcinoma

city: Guangzhou

first: Ying

last: Zhang

address: No. 613, Huangpu Avenue West

institute: Jinan University First Affiliated Hospital

summary: In order to study the mechanism of co-inactivation of RB1 and TP53 in the transformation of lung adenocarcinoma to small cell lung cancer, we established the NCI-H1975 cell line with RB1 knockdown.NCI-H1975 cells were cultured and infected with lentivirus expressing RB1-shRNA (n=3) or pLKO.1-shRNA (n=3), We then performed transcriptome sequencing (RNA-seq) on the above cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NCI-H1975 cells and its KD derivatives (shRB).

first: Yuanzhi

last: Lu

first: Qiang

last: Chen

first: Ting

last: Huang

first: Di

last: Zhu


title: Flexible and scalable control of T cell memory by a reversible epigenetic switch (ATAC-seq)

first: Kathleen

last: Abadie

summary: In this study, we find that the Tcf7+ CD8 T cells present following acute challenge can form either from cells that maintain Tcf7 expression throughout activation or from cells that silence Tcf7 and reactivate it after stimulation removal. In this experiment, we asked whether both pathways can give rise to cells with genomic characteristics of memory. To do this, we activated naive CD8 T cells ex vivo for 2 days followed by 1 day of culture without TCR stimulation. On day 3, we sorted Tcf7-YFP high and low populations, all from a single CellTrace peak representing cells that had undergone the same number of divisions. The sorted populations were cultured for an additional 6 days and sorted again on day 9 by Tcf7-YFP levels. These samples, as well as control naive, antigen-experienced, and effector samples, were processed for ATAC-seq analysis.

overall_design: Control naïve samples were sorted from splenoyctes as CD8+CD44-CD62L+Tcf7-YFP+ (1 replicate); antigen-experienced samples were sorted from splenocytes as  CD8+CD44+CD62L+Tcf7-YFP+ (1 replicate); effector control samples were activated ex vivo for 3 days (1 replicate). Cells sorted as Tcf7-YFP high and low at day 3 were recultured and sorted as Tcf7-YFP high or low at day 9: Day9 Tcf7-YFP high, sorted Tcf7-YFP high at Day3 (2 replicates); Day9 Tcf7-YFP low, sorted Tcf7-YFP low at Day3 (3 replicates); Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3 , 1 (3 replicates).

first: Elisa

last: Clark

first: Riza

last: Daza

first: Jay

last: Shendure

first: Hao-Yuan

last: Kueh


title: NFIA in adipocytes reciprocally regulates mitochondrial and inflammatory gene program to improve glucose homeostasis [flox RNA-Seq]

city: Tokyo

first: Yuta

last: Hiraike

address: Hongo 7-3-1, Bunkyo-ku

institute: The University of Tokyo

summary: Adipose tissue is central to regulation of systemic energy homeostasis. Adaptive thermogenesis in brown and beige adipocytes, which relies on mitochondrial oxidative phosphorylation, dissipates energy to counteract obesity. On the other hand, chronic inflammation in adipose tissue is linked to insulin resistance, type 2 diabetes and obesity. Here we show that nuclear factor I-A (NFIA), a transcriptional regulator of brown and beige adipocytes, improves systemic glucose homeostasis via up-regulation of oxidative phosphorylation and reciprocal down-regulation of inflammation. Mice with transgenic expression of NFIA in adipocytes exhibited improved glucose tolerance, increased energy expenditure and limited weight gain on high fat diet. NFIA coordinately up-regulate genes involved in oxidative phosphorylation as well as a battery of brown-fat-specific genes through enhancer activation that involves facilitated genomic binding of PPARγ. In contrast, NFIA in adipocytes, but not in macrophages, down-regulate pro-inflammatory cytokine genes to ameliorate adipose tissue inflammation in vivo. NFIA binds to enhancer/promoter region of Ccl2 gene that encodes pro-inflammatory cytokine MCP-1, to down-regulate its transcription. NFIA expression and CCL2 expression was negatively correlated in human adipose tissue. These results indicate that NFIA in adipocytes reciprocally regulate mitochondrial and inflammatory gene program to improve systemic glucose homeostasis.

overall_design: RNA-seq analysis of Nfiaflox/flox adipocytes, Cre- and 3xFLAG-NFIA-expressing Nfiaflox/flox adipocytes, and Cre- and 3xFLAG-Δpro#3 mutant-expressing Nfiaflox/flox adipocytes.

first: Kaede

last: Saito

first: Misato

last: Oguchi

first: Toshimasa

last: Yamauchi


title: Gibberellin and the microRNA156/SlSBP module synergistically regulate tomato floral meristem activity and fruit patterning

city: Piracicaba

first: Guilherme

middle: Bovi

last: Ambrosano

address: Av. Pádua Dias, 11

country: Brazil

institute: ESALQ

summary: Most developmental processes associated with fruit patterning take place at the floral meristem (FM). Age-regulated microRNA156 (miR156) and gibberellins (GA) integrate to control flowering time, but it is unclear how GA and miR156 interplay during fruit patterning. Here, we used genetic, molecular, and imaging tools to demonstrate that GA and age synergistically control tomato reproductive development. We found that low levels of miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL/SBP) transcripts or high GA responses/levels led to enlarged FMs, defects in FM determinacy, and fruits with increased locule number. Conversely, low GA responses reduced locule number and indeterminacy, and the expression of a miR156-resistant form of SlSBP15 (rSBP15) reduces FM size by decreasing cell size and cell number. Importantly, we discovered that GA levels/responses may be partially responsible for the fruit defects observed in 156OE and rSBP15 plants. GA and miR156-targeted SlSBPs regulate classical genes associated with floral determinacy, such as CRABS CLAWa (SlCRCa), and GA and SlSBPs act synergistically with tomato CLAVATA3 (SlCLV3) to control early flower and fruit development. Our findings indicate that gibberellins and age-dependent miR156-targeted SlSBPs co-operate to regulate FM activity and locule formation, thereby offering a novel mechanism of controlling fruit patterning.

overall_design: Differential expression analyses between WT and miR156-overexpressing plants

first: Leticia

middle: F

last: Ferigolo

first: Mateus

last: Vicente

first: Joao

middle: P

last: Correa

first: Carlos

last: Barrera-Rojas

first: Airton

last: Carvalho Jr

first: Eder

last: Silva

first: Geraldo

first: Lazaro

last: Peres

first: Gabriel

last: Margarido

first: Robert

last: Sablowski

first: Fabio

last: Nogueira


title: Flexible and scalable control of T cell memory by a reversible epigenetic switch

first: Kathleen

last: Abadie

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

overall_design: Refer to individual Series


title: Hypomethylating agents sensitize diffuse large B-cell lymphoma to venetoclax

city: Madison

first: Lixin

last: Rui

state: WI - Wisconsin

address: 1111 Highland Ave R.4060

department: Medicine

institute: University of Wisconsin-Madison

summary: We established acquired venetoclax resistant OCI-LY1R cell line by treating venetoclax sensitive parental OCI-Ly1 cell line with increasing doses of venetoclax up till 1µM. Parental OCI-Ly1 and venetoiclax-resistant OCI-Ly1R cells were treated with vehicle control or decitabine at 1uM for 3 days. We found that decitabine differantially regulated gene expression in venetoclax sensitive and resistant cells. With gene set enrichment analysis, we identified two pathways that were deregulated by decitabine in both cell lines.

overall_design: We established acquired venetoclax resistant OCI-LY1R cell line by treating venetoclax sensitive parental OCI-Ly1 cell line with increasing doses of venetoclax up till 1µM. Parental OCI-Ly1 and venetoiclax-resistant OCI-Ly1R cells were treated with vehicle control or decitabine at 1uM for 3 days before RNA was isolated.

first: Matthew

middle: S

last: Davids

first: Fen

last: Zhu

first: Nguyet-Minh

last: Hoang


title: Identification of human exTregs as CD16+CD56+ cytotoxic CD4+ T cells.

city: La Jolla

first: Klaus

last: Ley

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: In chronic inflammatory diseases with an autoimmune component like atherosclerosis, some  regulatory T cells (Tregs) lose their regulatory function and become exTregs. The present study  was designed to identify surface markers specific of human exTregs, using an integrated  approach from sorted mouse exTregs bulk RNA-Seq to human scRNA-Seq with CITE-Seq, to  sort human exTregs and characterize them by transcriptome and function. We crossed inducible  Treg lineage tracker mice (FoxP3-eGFP-Cre-ERT2 ROSA26CAG-fl-stop-fl-tdTomato) to  atherosclerosis-prone Apoe -/- mice, sorted Tregs and exTregs from lymph nodes and spleens of  replicate mice and determined their transcriptomes by bulk RNA sequencing (RNA-Seq). A  support vector machine (SVM) approach identified the leading signature genes for exTregs as  CST7, NKG7, GZMA, PRF1, TBX21 and CCL4. Projecting these genes onto feature maps of  human PBMC single cell (sc)RNA-Seq with CITE-Seq from 61 subjects with and without  atherosclerosis showed that CST7, NKG7, GZMA, PRF1, TBX21 and CCL4 mapped to CD4 T  cells that expressed CD56 and CD16. This finding was validated in a second, independent  scRNA- and CITE-Seq dataset. Even in healthy volunteers, a subpopulation of CD4 T cells  expressed both CD56 and CD16. Bulk RNA-Seq identified these cells as cytotoxic CD4 T cells,  which was functionally confirmed in a cell killing assay. DNA sequencing for TCRβ showed  clonal expansion of Treg CDR3 sequences in CD16 + CD56 + exTregs. Taken together, we identify  mouse and human exTregs as cytotoxic CD4 T cells.

overall_design: Low input bulk RNA-seq of on sorted cells from Mus musculus and Homo sapiens

first: Antoine

last: Freuchet

first: Sujit

last: Armstrong

first: Payel

last: Roy

first: Jeffrey

last: Makings

first: Erpei

last: Wang

first: Christopher

last: Durant

first: Amal

last: Ali

first: Yanal

last: Ghosheh

first: Rishab

last: Gulati


title: NFIA in adipocytes reciprocally regulates mitochondrial and inflammatory gene program to improve glucose homeostasis [RNA-seq]

first: Yuta

last: Hiraike

overall_design: RNA-seq analysis of WT and NFIA-Tg inguinal adipose tissue as well as WT and NFIA-Tg adipocytes before and after differentiation

first: Kaede

last: Saito

first: Misato

last: Oguchi

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Hironori

last: Waki

first: Toshimasa

last: Yamauchi


title: Arginine dependency is a therapeutically exploitable vulnerability in chronic myeloid leukaemic stem cells

city: Glasgow

first: Kevin

last: Rattigan

address: Wolfson Wohl Cancer Research Centre, Garscube Estate, Glasgow, Bearsden

department: School of Cancer Sciences

institute: University of Glasgow

summary:
We tested the effect of arginine depleting enzyme BCT-100 (24 hours) on primary normal and CML cells (100ng/mL for primary) as well as the wildtype or ASS1 knock-out K562 cell lines (1000ng/mL for cell lines)
Cells were cultured in Plasmax
Primary groups were Normal, Normal+bct, CML, CML+BCT
Cell line groups were WT, WT+bct, ASS1KO, ASS1KO+BCT

overall_design:
Comparative gene expression profiling analysis of RNA-seq data of primary and cell lines
Samples were profiled across 2 runs on sequencer. Data was merged to give 20 million reads/sample

first: Vignir

last: Helasgon


title: NFIA in adipocytes reciprocally regulates mitochondrial and inflammatory gene program to improve glucose homeostasis


title: NFIA in adipocytes reciprocally regulates mitochondrial and inflammatory gene program to improve glucose homeostasis [ChIP-seq]

overall_design: ChIP-seq analysis of WT and NFIA-Tg adipocytes


title: NFIA in adipocytes reciprocally regulates mitochondrial and inflammatory gene program to improve glucose homeostasis [flox ChIP-Seq]

overall_design: ChIP-seq analysis of Nfiaflox/flox adipocytes, Cre- and 3xFLAG-NFIA-expressing Nfiaflox/flox adipocytes, and Cre- and 3xFLAG-Δpro#3 mutant-expressing Nfiaflox/flox adipocytes.


title: Flexible and scalable control of T cell memory by a reversible epigenetic switch (sci-fate-seq)

first: Kathleen

last: Abadie

summary: In this study, we use a minimal ex vivo culture system to track CD8 T cell differentiation at the single cell and clonal lineage level during activation. To characterize early heterogeneity in memory and effector differentiation in this system, we subjected cells to temporally-resolved single-cell transcriptomic profiling using sci-fate-seq (Cao et al., Nature Biotech, 202).

overall_design: Cells were activated ex vivo and subjected at days 1, 2, and 4 to 4-thiouridine (4sU) pulse-labeling for 2 hrs, enabling detection of newly synthesized mRNA at each time point.

first: Wei

last: Yang

first: Junyue

last: Cao

first: Jay

last: Shendure

first: Hao-Yuan

last: Kueh


title: Zeb2 regulates the balance between retinal interneurons and Muller glia by inhibition of BMP-Smad signaling

city: Tel Aviv

first: Ruth

last: Ashery-Padan

department: Department of Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel-Aviv University

summary: In order to identify the roles of the transcription factor Zeb2, Zeb2 was inactivated in the peripheral retina of Zeb2 mouse embryos using the αCre transgene which is acrive in the peripheral retina as early as E10.5. RNA was extracted from the whole retinae of control and Zeb2 mutant mice pups at P2.

overall_design: Examination of the transcriptome of in the retinea of 3 control and 3 Zeb2 loxp/loxp αCre (Zeb2 mutants) P2 old mice.

first: Yotam

last: Menuchin-Lasowski

first: Bar

last: Dagan


title: Small cell neuroendocrine transdifferentiation in EGFR-mutant lung cancer evolving from mesenchymal drug-tolerant state

city: Tainan

first: SHANG-YIN

last: WU

address: No.138,Sheng Li Road

department: Oncology

country: Taiwan

institute: National Cheng Kung University Hospital

summary: Small-cell neuroendocrine (SCN) transdifferentiation and epithelial-mesenchymal transition (EMT) are recognized as two kinds of lineage plasticity and they emerged as a model of targeted therapy evasion in a subset of EGFR-mutated NSCLC. Whether SCN transdifferentiation could phenocopy in isogenic acquired resistant clinically relevant cells and the association between EMT and SCN transdifferentiation remain unknown. 　We established several mesenchymal gefitinib-acquired resistant cells from HCC827 and showed SCN transdifferentiation could evolve from mesenchymal drug-tolerant state. The SCN property and the mesenchymal property in cancer cells are negatively correlated. Dynamic IL-6, correlated with mesenchymal property, could reflect this process and it might be a ready-to-use biomarker to monitor this process.

overall_design: By long term step-wise treatment with gefitinib, we established serial gefitinib-acquired resistant sublines (HCC827GRs) from HCC827 lung adenocarcinoma cells, harboring EGFR exon 19 deletion. HCC827GR was a parental resistant subline with unstable gefitinib-resistant ability while it was cultured in drug-free medium by passages. To obtain stable gefitinib-resistant sublines, we maintained HCC827GR in culture medium with or without gefitinib (1 μM) over 6 months to obtain two different sublines, HCC827GR+ and HCC827GR.M6, respectively.

first: S

last: Wu

first: H

last: Yeh

first: W

middle: L

last: Huang

last: Su


title: Epigenome analysis of normal and FHRCC samples

city: Chengdu

first: Zhenhua

last: Liu

state: Sichuan

address: 37# Guoxue Alley

department: Urology

institute: West China Hospital Sichuan University

summary: Genome wide DNA methylation profiling of 32 hereditary leiomyomatosis and renal cell cancer patient-derived samples. The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in nine breast HMECs samples.

overall_design: Bisulphite converted DNA from the 32 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip

first: Guangxi

last: Sun

first: Hao

last: Zeng


title: Bulk RNA sequencing and analysis of sorted fetal liver hematopoietic stem cells from VavCre+Jag1 f/f and WT E14.5 C57bl/6 embryos

city: Chicago

first: Kostandin

middle: V

last: Pajcini

address: 909 S Wolcott Ave.

department: Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

summary: We assesed the transcriptional profiles of sorted SLAM-LSK hematopoietic stem cells (HSCs) during expansion in the murine fetal liver from WT and Jag1-null mutants at embryonic day 14.5 post-conception. The goals of the study are to compare the expression profiles of rapidly proliferating fetal HSCs when the Notch ligand Jag1 is specifically deleted in the hematopoietic compartment.  We find that hematopoietic deletion of Jag1 negatively impacts the expression of critical hematopoietic cell fate and identity genes such as GATA2, Mllt3 and Hoxa7. Our study establishes a unique role for Notch signaling activation in the fetal liver by the hematopoietic Jag1 ligand.

overall_design:
Hematopoietic stem cell mRNA expression profiles from sorted E14.5 fetal liver HSCs of VavCre+Jag1 f/f and  VavCre-Jag1 f/f littermates.
Macrophage mRNA expression profiles from sorted E14.5 fetal livers in Jag1f/fVav-Cre- and Jag1f/fVav-Cre+ embryos

first: Lijian

last: Shao

first: Mark

last: Sanborn


title: A novel CRISPR/Cas9 screening platform identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and anti-tumor immunity (Human RNA-Seq)

status: Public on Jul 24 2023

city: Melbourne

first: Kevin

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Investigation and validation of genes that regulate CXCL9 expression by RNA sequencing

overall_design: Human monocytes were gene-edited and then derived into macrophages using M-CSF. Macrophages were stimulated with 1ng/mL IFNg for 17 hours.

first: Imran

last: House

first: Emily

last: Derrick

first: Paul

last: Beavis

last: Sek


title: A novel CRISPR/Cas9 screening platform identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and anti-tumor immunity (AT3 RNA-Seq)

overall_design: AT-3 cells were stimulated with IFNg/TNF for 8 or 14 hours.


title: A novel CRISPR/Cas9 screening platform identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and anti-tumor immunity (IRF1 ChIP-Seq)

summary: CHIPseq of mouse IRF1 in macrophage and AT-3 breast cancer

overall_design: Murine bone marrow derived into macrophages using GM-CSF. Macrophages were stimulated with 1ng/mL IFNg for 3 hours. AT-3 cells were stimulated for 5ng/mL IFNg/TNF for 3 hours. Anti-Irf1 immunoprecipitation was performed.


title: Embryonic stem cell-derived neurons as a model system for epigenome maturation during development

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

institute: The University of Western Australia

summary: DNA methylation in neurons is directly linked to neuronal genome regulation and maturation. Unlike other tissues, vertebrate neurons accumulate high levels of atypical DNA methylation in the CH sequence context (mCH) during early postnatal brain development. Here we investigate to what extent neurons derived in vitro from both mouse and human pluripotent stem cells recapitulate in vivo DNA methylation patterns. While human ESC-derived neurons did not accumulate mCH in either 2D culture or 3D organoid models, even after prolonged culture, neurons derived from mouse ESCs in vitro acquire in vivo levels of mCH over a similar time period as both primary neuron cultures and in vivo development. mESC-derived neuron mCH deposition occurs concurrently with a transient increase in Dnmt3a expression, is preceded by expression of the post-mitotic marker Rbfox3 (NeuN), is enriched at the nuclear lamina, and negatively correlates with gene expression. We further show that CG- and CH-methylation patterning subtly differs between in vitro mES-derived and in vivo neurons, suggesting the involvement of additional non-cell autonomous processes. As our findings show mouse ESC-derived neurons are capable of recapitulating the unique DNA methylation landscape of adult mammalian neurons in vitro over experimentally tractable timeframes, identification of such external cues, and elucidation of the writing-reading mechanisms and functional consequences of these different types and patterns of DNA methylation events, is now achievable.

overall_design: Whole genome bisulfite sequencing of 49 different mouse cell culture and primary cell samples, and RNA-seq of a subset of samples

first: Sally

last: Martin

first: Daniel

last: Poppe

first: Nelly

last: Olova

first: Conor

last: O'Leary

first: Elena

last: Ivanova

first: Jahnvi

last: Pflueger

first: Jennifer

last: Dechka

first: Rebecca

middle: K

last: Simmons

first: Helen

last: Cooper

first: Wolf

last: Reik

first: Ernst

last: Wolvetang


title: Salvianolic acid B attenuates inflammation and prevent pathologic fibrosis by inhibiting CD36-mediated activation of the PI3K-Akt signaling pathway in frozen shoulder.

first: Yan

last: Yan

state: Guangdong province

address: yanjiang west road No.107

department: orthopaedic surgery

institute: No. 107, Yanjiang West Road, Yuexiu District, Guangzhou, Guangdong Province


title: Salvianolic acid B attenuates inflammation and prevent pathologic fibrosis by inhibiting CD36-mediated activation of the PI3K-Akt signaling pathway in frozen shoulder [dataset 2]

summary: Frozen shoulder (FS) is characterized by pain and limited range of motion (ROM).  Inflammation and fibrosis are accepted as main pathologic processes associated with the development of FS. However, the intrinsic mechanisms underlying pathologic fibrosis remain unclear. We aimed to elucidate the key molecules involved in pathologic fibrosis and explore new therapeutic targets for FS. Synovial fibroblasts isolated from patient biopsies were identified using immunofluorescence. Western blotting, RT-qPCR, cell adhesion tests, and would-healing assays were used to evaluate the fibrosis-related functions of synovial fibroblasts. Elevated cluster of differentiation 36 (CD36) expression was detected in FS using western blotting and immunohistochemistry. Salvianolic acid b (SaB) inhibited CD36, blocking synovial fibroblast-induced inflammation and fibrosis. Our RNA-seq data showed that knocking down CD36 dramatically impaired the capacity of synovial fibroblasts for cell adhesion and that the PI3K-Akt signaling pathway may be crucial to the fibrotic process of FS. By up-regulating CD36 and inhibiting the phosphorylation of Akt, we demonstrated that CD36 promotes pathologic fibrosis by activating the PI3k-Akt pathway. Finally, rats treated with SaB had improved ROM and less collagen fiber deposition than the FS model group. Conclusions: SaB attenuates inflammation and inhibited the CD36-mediated activation of the PI3K-Akt signaling pathway to block pathologic fibrosis of FS in in vitro and in vivo models.

overall_design: To further clarify the differences in gene expression of frozen shoulder patients and healthy people, we employed RNA-seq technology to examine the synovium transcriptome from 4 individuals with frozen shoulder and 4 healthy controls.

first: Xinhao

last: Li

first: Zhuo

last: Wang

first: Rui

last: Yang


title: A novel CRISPR/Cas9 screening platform identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and anti-tumor immunity (CRISPR screen)

first: Kevin

last: sek

summary: Investigation and validation of genes that regulate CXCL9 expression through a genome-wide in vitro CRISPR/Cas9 screen.

overall_design: AT-3 cells containing a GFP reporter for CXCL9 were transduced with a genome wide CRISPR library and stimulated with IFNg and TNF.

first: Imran

last: House

first: Emily

last: Derrick

first: Paul

last: Beavis

last: Sek


title: Comparison of gene expression in skeletal muscle between Baf155 WT and mutant

city: Seoul

first: jong-seol

last: kang

address: 1 Gwanak-ro, Gwanak-gu

department: Biological sciences

country: South Korea

institute: Seoul National University

summary: Baf155 is a core subunit of SWI/SNF complex, an ATP dependent chromatin remodeler. To explore the function of Baf155 in skeletal muscle, we deleted the Baf155 in skeletal muscle and compared the gene expression profiling between wild type control and Baf155 deleted mutant mice.

overall_design: Gene expression profiling of freshly isolated skeletal muscles (including TA, EDL, GA, SOL, and Q) from wild type control and Baf155 -/- mice.

first: Jong

last: Kang

first: Dongyeon

last: Cho

first: Young

last: Kong


title: A novel CRISPR/Cas9 screening platform identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and anti-tumor immunity (AT3 ATAC-Seq)

summary: Investigation and validation of genes that regulate CXCL9 expression by ATAC sequencing

overall_design: AT3 cells were stimulated with IFNg/TNF.


title: Histone ChIP-seq from prostate gland (ENCSR499FXI)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Alcohol promotes macrophage M2b polarization in colitis by modulating the TRPV1-MAPK/NF-kB pathways

city: Shanghai

first: Zehua

last: Zhang

state: --- Select One ---

address: No. 150 Jimo Road

institute: Tongji University School of Medicine

summary: Macrophages are key immune cells in inflammatory bowel disease (IBD) that can exhibit different phenotypes and promote inflammation. Alcohol consumption is associated with increased risk and severity of IBD. We performed in vitro and in vivo experiments with dextran sodium sulfate-induced mice colitis model, peritoneal macrophages and RAW264.7 cell line to investigate the effect and mechanism of alcohol on macrophages in colitis. Our study has found that alcohol exacerbates colitis in mice, increases the aggregation of colonic macrophages, and promotes the production of various inflammatory factors. Alcohol increases lipopolysaccharides (LPS)-induced calcium influx in macrophages, which is inhibited by the TRPV1 antagonist Capsazepine (CPZ). Alcohol and LPS together induce M2b polarization of macrophages and promote the phosphorylation and nuclear translocation of P38, ERK1/2 and NF-κB, and could be inhibited by CPZ and NOD2 inhibitor. Thus, alcohol can aggravate experimental colitis in mice and promote macrophage M2b polarization through the TRPV1-MAPK/NF-kB pathways.

overall_design: Peritoneal macrophages used for RNA-seq were cultured with RPMI 1640 with 1% streptomycin and penicillin for 1 h to keep the cell state consistent and stimulated by LPS 1μg/mL, LPS 1μg/mL with 5% EtOH, LPS 1μg/mL with CPZ 100 μM for 4 h.

first: Z


title: Salvianolic acid B attenuates inflammation and prevent pathologic fibrosis by inhibiting CD36-mediated activation of the PI3K-Akt signaling pathway in frozen shoulder  [dataset 1]

overall_design: To further clarify the relationship between CD36 and pathologic fibrosis, we employed RNA-seq technology to examine the synovial fibroblast transcriptome from 6 individuals with frozen shoulder; 3 of these underwent CD36 knockdown interference using siRNA.


title: The origin and dynamics of cellular heterogeneity vary across lineage subtypes of castrate resistant prostate cancer.

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

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

overall_design: Refer to individual Series


title: Cellular communication and fusion regulates cell fusion, trap morphogenesis, conidiation, and secondary metabolism in Arthrobotrys oligospora

city: Kunming

first: wenjie

last: wang

address: Kunming

institute: Yunnan University

summary: In this study, we characterized Aoadv-1, Aoso, Aoham-6, and Aoham-5 of A. oligospora, homologous to those involved in cellular communication and fusion in the model fungus Neurospora crassa. The deletion of four genes resulted in the complete loss of cell fusion, and traps produced by mutants do not close to form mycelial rings but are still capable of capturing nematodes. Meanwhile, the absence of these genes inhibited aerial mycelial extension, slowed colony growth, and increased mycelial branching. In addition, the mutants showed reduced sporulation capacity, reduced tolerance to oxidative stress, increased sensitivity to SDS, and altered lipid droplet accumulation and autophagy. Furthermore, transcriptome analysis revealed that Aoadv-1 and Aoso were involved in plasma membrane fusion, transmembrane transport of multiple nutrients, signal transduction, response to oxidative stress, cell wall, lipid metabolism, and autophagy. In addition, metabolomic analysis showed that Aoadv-1 and Aoso were involved in biosynthesis of secondary metabolites. Our results revealed that Aoadv-1, Aoso, Aoham-6, and Aoham-5 regulate mycelial growth and trap morphogenesis through cell fusion, which provides a valuable reference for the molecular mechanisms of cellular communication regulating the mycelia development and trap morphogenesis in NT fungi.

overall_design: The WT,ΔAoadv-1, and ΔAoso mutant strains, were cultured in PDA medium at 28 °C, 180 rpm for 3 days, and mycelium was collected. The mycelium was divided and induced with about 400 nematodes for 0 and 36 h, respectively. Three replicates were performed for each sample.

first: Wenjie

first: Yankun

last: Liu

first: Shipeng

last: Duan

last: Bai


title: A novel CRISPR/Cas9 screening platform identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and anti-tumor immunity (Mouse RNA-Seq)

overall_design: Murine bone marrow was gene edited and then derived into macrophages using GM-CSF. Macrophages were stimulated with 1ng/mL IFNg for 17 hours.


title: Tianeptine promotes lasting antiallodynic effects in a mouse model of neuropathic pain

city: New York

first: Molly

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Tricyclic antidepressants (TCAs), such as desipramine (DMI), are effective at managing neuropathic pain symptoms but often take several weeks to become effective and also lead to considerable side effects. Tianeptine (TIAN) is an atypical antidepressant that activates the mu-opioid receptor but does not produce analgesic tolerance or withdrawal in mice, nor euphoria in humans, at clinically-relevant doses. Here, we evaluate the efficacy of TIAN at persistently alleviating mechanical allodynia in the spared nerve injury (SNI) model of neuropathic pain, even well after drug clearance. After finding an accelerated onset of antiallodynic action compared to DMI, we used genetically modified mice to gain insight into RGS protein-associated pathways that modulate the efficacy of TIAN relative to DMI in models of neuropathic pain. Because we observed similar behavioral responses to both TIAN and DMI treatment in RGS4, RGSz1, and RGS9 knockout mice, we performed RNA sequencing on the NAc of TIAN- and DMI-treated mice after prolonged SNI to further clarify potential mechanisms underlying TIANs faster therapeutic actions. Our bioinformatic analysis revealed distinct transcriptomic signatures between the two drugs, with TIAN more directly reversing SNI-induced differentially expressed genes, and further predicted several upstream regulators that may be implicated in onset of action. This new understanding of the molecular pathways underlying TIAN action may enable the development of novel and more efficacious pharmacological approaches for the management of neuropathic pain.

overall_design: Bilateral nucleus accumbens punches from male C57Bl/6J mice were taken after Tibial SNI or Sham Surgery (4 weeks) followed by 3 weeks of Saline, 30 mg/kg Tianeptine, or 15 mg/kg Desipramine (intraperitoneal, twice daily) . Each sample reflects samples from an individual animal, with several biological replicates per condition. The control condition in this experiment is "Sham-Saline".

first: Randal

middle: A

last: Serafini

first: Elizabeth

last: Pekarskaya

first: Farhana

last: Sakloth

first: Li

last: Shen

first: Jonathan

last: Javitch

first: Venetia

last: Zachariou


title: RNA content of yeast nuclear mRNPs

city: Martinsried

first: Fabien

last: Bonneau

address: Am Klopferspitz 18

department: Structural Cell Biology

institute: Max Planck Institute of Biochemistry

summary:
We isolated nuclear mRNPs from yeast using an endogenous bi-molecular tagging approach on Sub2 and Hpr1.
To validate the nature of these isolated particles, extracted RNA was sequenced and differential enrichment, as well as metagene coverage analysis were performed.

overall_design: Two replicates each of RNA-Seq data for transcripts extracted from total lysate or from eluted particles.

first: Elena

last: Conti


title: Mitochondrial DNA sequences of familial (maternal vs. non-maternal) ALS cases in whole blood, platelets and white blood cells

city: Ulm

first: Karin

last: Danzer

address: Albert-Einstein-Allee 11

institute: DZNE

type: Genome variation profiling by genome tiling array

summary: To address the question of whether mtDNA mutations might play a role in familiar ALS (fALS), mtDNA was isolated from whole blood (WB), white blood cells (WBC) and platelets (PLT) from fALS patients and the mitochondrial genome was analyzed using a mtDNA resequencing array (Affymetrix MitoChip v2.0) that allows detection of low-level heteroplasmy in addition to the conventional homoplasmic or heteroplasmic mutations. We distinguished between fALS cases with a prominent maternal (mat) inheritance pattern and fALS cases that do not point to a maternal inheritance pattern (non-mat). As additional controls we compared our results to healthy age and sex matched individuals without any known neurodegenerative background. With this we are aiming to get a deeper insight into a possible role of mtDNA alterations acting as a disease modifier in a subgroup of ALS patients presenting with a maternal transmission of the disease.

overall_design: 184 MitoChips were performed in total. For each analysed group a n-number was included as follows (CTRL/ALS non-mat/ALS mant): whole blood (49/23/25), white blood cells (22/6/16), platelets (21/6/16). For the isolated cell types (PLT and WBC) freshly drawn EDTA blood was used to isolate the cell populations by differential centrifugation and cleaning up of the sample by magnetic bead separation. For whole blood samples one aliquot of frozen EDTA blood from the biobank was used.

first: Sarah

middle: J

last: Brockmann

first: Eva

last: Buck

first: Casoli

last: Tiziana

first: Joao

last: de Meirelles

first: Wolfgang

last: Ruf

first: Paolo

last: Fabietti

first: Karlheinz

last: Holzmann

first: Jochen

last: Weishaupt

first: Albert

last: Ludolph

first: Fiorenzo


title: MicroRNA expression in normal and inflamed endothelial cells derived exosomes.

city: Fuzhou

first: Pengli

last: Zhu

address: 134Dongjie St, Gulou District

institute: Fujian Provincial Hospital

summary: Exosomes research has been strongly promoted by the discovery of different classes of RNAs, mainly miRNAs, which are transfered to target cells and modulate various simgnaling pathways in target cells. Inflamed endothelial cells derived exosomes, acting as carriers for intercellular information exchange in atherosclerosis, are worthy of further research to investigate the disease pathophysiological mechanisms. This study aimed to investigate the differentially microRNA expression between normal and inflamed endothelial cells derived exosomes.

overall_design: Comparison of the microRNA expression  in normal endothelial cells derived exosomes and TNF-α-stimulated endothelial cells derived exosomes

first: Feng

last: Huang

first: Yin

last: Yuan

first: Wenwen

last: Lin


title: Effect of vitamin D supplementation on rats' liver

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

summary: In order to understand the molecular mechanism responsible for the therapeutic potential of vitamin D, we conducted an analysis of the liver transcriptome – a central place of metabolic changes. The experiment was carried out on adult female rats (about one year old), n=18, divided into three experimental subjects, receiving different doses of vitamin D for three months: group I - 0, group II - 1000 U/Kg, group III - 5000 U/Kg. After the experiment, the biochemical and haematological parameters of the blood were evaluated. RNA-seq was used to analyze the changes in the liver transcriptome, and Gene Set Enrichment Analysis (GSEA) was used to identify enrichments in gene expression profiles of experimental groups. qPCR was employed to evaluate the expression of several genes connected to cholesterol biosynthesis, metallothioneins, vitamin D metabolism and others. At the end of the experiment, 25(OH) vitamin D concentrations were as follows: group I: 29 ng/ml, group II 43: ng/ml, group III: 70 ng/mL. Considering blood parameters, we observed a lower platelet count (p<0,008) and significantly higher (p<0.02) number of WBC in rats supplemented with 1000 U/Kg than in rats from group III (5000 U/Kg), but no difference between rats from group I and III were detected in these parameters.  Moreover,  we noted a trend (p<0.06 ) in total cholesterol concentration, suggesting a linear decrease with increasing doses of vitamin D. RNA-seq analysis did not identify any differentially expressed genes with FDR<0.05 in any of the three comparisons. However, GSEA revealed significant activation of the number of processes and pathways. In the I vs III comparison, the most enriched were the genes from the “metallothionein, and TspO/MBR family” (Enrichment Score=8,170, FDR= 0.00006), the genes associated with “glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity” (Enrichment Score=5.13, FDR<00049) and the genes associated with  “Negative regulation of tumour necrosis factor production” (Enrichment score=1.26, FDR0.0064. qPCR analysis identified significant upregulation of  Mt1, Mt2 and Orm1 genes in animals receiving high doses of vitamin D (p<0.025, p<0.025, p<0009, respectively). Moreover, significant downregulation of Srebp2 and Insig2 was observed in both experimental groups when compared to the control group (p<0.003, p<0.036, respectively). Our results support the potential of vitamin D supplementation in ameliorating oxidative stress, inflammation and high blood cholesterol and underlie the need for further studies aimed at identifying optimal vitamin D doses with therapeutic effects.

overall_design: The experiment was carried out on adult female rats (about one year old), n=18, divided into three experimental groups, receiving different doses of vitamin D for three months: group I - 0, group II - 1000 U/Kg, group III - 5000 U/Kg. After the experiment, the biochemical and haematological parameters of the blood were evaluated. RNA-seq was used to analyze the changes in the liver transcriptome

first: Maria

last: Oczkowicz

first: Alicja

last: wierzbicka

first: Anna

last: Steg


title: Microglial repopulation reverses cognitive-associated deficits in an Alzheimer’s disease model by restoring the BDNF signaling

city: Xiamen

first: wanbing

last: Wang

state: Fujian Province

address: 4221 Xiang'an South Road, Xindian Town

department: Medical Department

institute: Xiamen University

summary: Over the past decade, genetic evidence has demonstrated that microglial dysregulation is likely to play a central role in the development of Alzheimer's disease (AD). As resident immune cells in the brain, microglia become dystrophic and senescent during the chronic progression of AD. To explore whether replenishing the brain with new microglia is beneficial to AD, we employed a CSF1R inhibitor PLX3397 to deplete microglia and induce repopulation after the inhibitor withdrawal in 5xFAD transgenic mice. We observed that microglial repopulation ameliorates AD-associated cognitive deficits, accompanied by elevation of synaptic proteins and hippocampal long-term potentiation (LTP). In addition, microglial morphology is restored after microglial self-renewal, and amyloid pathology is reduced with long-term repopulation but not short-term. Transcriptome analysis showed that repopulating microglia in 5xFAD mice recovers a gene expression profile that is highly similar to microglia from WT mice. Notably, the neurotrophic signaling pathway and hippocampal neurogenesis dysregulated in the AD brain are restored after microglial replenishment. At last, we confirmed that microglial repopulation rescues brain-derived neurotrophic factor (BDNF) expression to contribute to synaptic plasticity. Together, we conclude that microglial self-renewal benefits AD brain by restoring the BDNF neurotrophic signaling pathway. Thus, the proper replenishment of microglia may be an effective and novel therapeutic strategy for ameliorating cognition impairment in AD.

overall_design: 1. Four-month-old 5×FAD mice were fed with PLX3397 (Selleck, S7818, 290 mg/kg formulated in standard chow) for one month, then discontinued from PLX3377 feed and treated with a normal mouse diet for an additional one month, resulting in microglial repopulation. 2. Microglia (CD45lowCD11b+) were isolated from the hippocampi of WT and 5xFAD mice with or without microglial repopulation. Microglial RNA was extracted from the indicated groups for RNA sequencing.

first: Wanbing

first: Li

last: Zhong


title: intact Hi-C from dendritic cell (ENCSR456QYU)

first: ENCODE

last: DCC

summary:
Monocytes Dendritic cell day 4 LP23 intact mnase HiC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: intact Hi-C from heart right ventricle (ENCSR591SNM)

summary:
w76-heart-right-ventricle intact dnase hic

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment

city: Washington

first: Anton

last: Wellstein

state: DC

address: 3970 Reservoir Road, N.W.,

institute: Georgetown University


title: A recombinant vesicular stomatitis virus-based vaccine provides postexposure protection against Bundibugyo ebolavirus infection

city: Galveston

first: Thomas

last: Geisbert

state: TX

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: Bundibugyo virus (BDBV) is the most recently discovered pathogenic species of ebolavirus, with mortality rates of 25% and 51% reported in two identified. BDBV infection is non-uniformly lethal in macaques. The lack of uniform lethality offers the opportunity for identification of biomarkers that correlate with positive and negative outcomes following infection that can help define mechanisms of pathogenesis and potentially serve as guides for clinical care. In both the treatment and control groups, ~58% survived infection, an increase over lethality seen in historical controls. There was no differential advantage of the BDBV GP expressing vaccine, suggesting a general effect of rVSV. Our transcriptomic analysis identified strong initial responses to infection and treatment in all animals. This response returned to baseline in animals with mild disease by day 7. In animals with severe disease, fatal cases could be predicted beginning at day 5 post infection based on the expression of 5 circulating mRNAs. This study suggested a nonspecific effect of treating NHPs with VSV-based vectors as a postexposure therapy following BDBV infection and identified potential biomarkers of outcome.

overall_design: Seven cynomolgus macaques were challenged by intramuscular injection in the left quadriceps with a 1,000 PFU target dose of BDBV challenge stock (the actual dose was 913 PFU). Approximately 20-23 minutes post challenge, six animals were treated with ~ 2X10^7 PFU of rVSVΔG/BDBV-GP via i.m. injection. The inoculation was equally distributed between the left and right quadriceps. Animals were monitored for viremia and clinical signs of illness (temperature, weight loss, changes in blood count, and blood chemistries) during the treatment and BDBV challenge portions of the study. Blood was collected on days 0, 1, 5, 7, 9, 12, 15, 21, and 28 post challenge. Samples were also collected on the day of euthanasia.

first: Courtney

last: Woolsey

first: Jamie

last: Strampe

first: Karla

last: Fenton

first: Krystle

middle: N

last: Agans

first: Jasmine

last: Martinez

first: Viktoriya

last: Borisevich

first: Natalie

last: Dobias

first: Daniel

last: Deer

first: Joan

middle: B

first: Robert

middle: W

last: Cross

first: John

middle: H

last: Connor


title: The origin and dynamics of cellular heterogeneity vary across lineage subtypes of castrate resistant prostate cancer [scATAC-seq]

first: Adam

last: Sowalsky

summary: Cancer cells often adapt a stem-like state resulting in lineage plasticity and phenotypic heterogeneity. We assessed the dynamics of lineage determination and cellular subpopulation expansion in treatment-resistant adenocarcinoma, amphicrine, and small cell neuroendocrine castrate resistant prostate cancers.

overall_design:
We used single-cell ATAC-seq to delineate the subpopulation structure of the heterogeneous organoids and define the lineage hierarchy, determine potential transcriptional regulators of amphicrine lineage-plasticity, and identify subpopulation-specific molecular targets for therapeutic intervention.
***Submitter declares that the raw data is being submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns [accession ID phs001587.v2.p1]***

first: Michael

last: Beshiri

first: Brian

last: Capaldo

middle: G

first: Kathleen

last: Kelly


title: The origin and dynamics of cellular heterogeneity vary across lineage subtypes of castrate resistant prostate cancer [scRNA-seq]

overall_design:
We used single-cell RNA-seq and barcode lineage-tracing to delineate the subpopulation structure of the heterogeneous organoids and define the lineage hierarchy, determine potential transcriptional regulators of amphicrine lineage-plasticity, and identify subpopulation-specific molecular targets for therapeutic intervention.
***Submitter declares that the raw data is being submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns [accession ID phs001587.v2.p1]***