title: Genetic-epigenetic interactions in paternal transgenerational inheritance of metabolic disorders

city: Sainte-Anne-de-Bellevue

first: Anne-Sophie

last: Pépin

state: QC

address: 21111 Lakeshore road

department: Department of Pharmacology and Therapeutics

institute: McGill University

summary: Parental environmental exposures can strongly influence descendant risks for adult disease. Metabolic disorders arise from the intersection of environmental and genetic risk factors, with epigenetic inheritance being at the center of the familial cycle of transgenerational disease. How paternal high-fat diet changes the sperm chromatin leading to the acquisition of metabolic disease in offspring remains controversial and ill-defined. Using a genetic model of epigenetic inheritance, we investigated the role of histone H3 lysine 4 methylation (H3K4me3) in the paternal transmission of metabolic dysfunction. We show that obesity-induced alterations in sperm H3K4me3 associated with offspring phenotypes and corresponded to embryonic and placental chromatin profiles and gene expression. Transgenerational susceptibility to metabolic disease was only observed when grandsires had a pre-existing genetic predisposition to metabolic dysfunction that was associated with enhanced alterations to sperm H3K4me3. This non-DNA based knowledge of inheritance has the potential to improve our understanding of how environment shapes heritability and may lead to novel routes for the prevention of disease.

overall_design: Examination of sperm H3K4me3 in wildtype or KDM1A transgenic male mice fed either a low-fat or high-fat diet, examination of liver total RNA in wildtype KDM1A transgenic male mice fed either a low-fat or high-fat diet and in their male and female descendants (F1 and F2)

last: Pepin

first: Sarah

last: Kimmins


title: Deficiency of myeloid PHD proteins aggravates atherogenesis via macrophage apoptosis and paracrine fibrotic signaling

status: Public on Mar 30 2022

city: Heidelberg

first: Javier

last: Perales-Paton

state: Baden-Württemberg

address: Im Neuenheimer Feld 267

department: Faculty of Medicine

country: Germany

institute: Heidelberg University

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Circulating miR 218-5p, alone or in combination, predicts corticosteroid failure in ulcerative colitis. Study through computational strategies based on Systems Biology.

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

type: Non-coding RNA profiling by high throughput sequencing

summary: Our group used rectal biopsies from patients with active ulcerative colitis (UC) and differential response to glucocorticoid treatment, to generate a predictive computational strategy based on systems biology. Contrasting mRNA and miRNAs intestinal expression profiles with updated molecular information related to UC and glucocorticoids, we were able to identify a mechanism of action (MoA) associated with corticosteroid failure in UC. ith the aim of transferring these results to clinical practice, the MoA-models created previously were implemented with plasmatic miRNAs profiles, to describe in silico non-invasive potential biomarkers of glucocorticoid refractoriness. Small RNA-seq analysis was perfomed using Illumina next generation sequencing and standard statistical criteria were applied to compare the miRNA profiles, incluidng paired samples  before clucocorticoid treatment to the third day of the steroidal treatment. The selection these miRNA with predictive capacity was done using two complementary strategies: the first one using all the obtained miRNAs, and the second taking into account those miRNAs that are directly related to MoA, through various statistical restrictions (RELIEF, ENTROPY + CORRELATION, WILCOXON, ROC, and simple REGRESSION). These computational approaches from all miRNAs identified hsa-miR218-5p as the best to classify patients according their respond at basal time (Accuracy = 84.21%, Generalization Capability = 84.21%, Sensitivity = 100% and Specificity = 66.67%). In addition, the combination of this miRNA with hsa-miR6754-5p and hsa-miR4767, increases the diagnosis accuracy of the disease (Accuracy = 94.74%, Generalization Capability = 75.44%, Sensitivity = 70% and specificity = 81.48%). On the other hand, the combination of hsa-miR218-5p and the plasma levels of the Protein C Reactive increases the ability to classify patients towards their response to glucocorticoids up to 89%. Taking in account all this data, we can conclude that by means of a computer strategy based on Biology of Systems we have identified the plasmatic miR-218-5p as a potential biomarker to glucocorticoid response in UC before start the treatment.

overall_design: In total 46 samples were analyzed: 7 reference and 39 UC patient samples, derived from 27 different individuals (7 healthy controls and 20 patients). There were two patient groups based on glucocorticoid treatment response, composed of 10 responders and 10 non-responders respectively. Patient samples were collected at two different times: before and three days after glucocorticoid treatment. In total there were 19 sets of paired patient samples, before and after treatment from each of 19 diferent individual patients, and a single odd sample taken after treatment from the 20th patient.

first: Violeta

last: Lorén

first: Josep

last: Manyé


title: Gene expression profiles of variants of B16OVA melanoma cells established from different host immunological conditions

status: Public on Mar 29 2022

city: Toyama

first: Ichiro

last: Takasaki

address: 3190 Gofuku

country: Japan

institute: University of Toyama

summary: To establish cancer cells escaping from host immunity, we used murine B16 melanoma cell line expressing ovalbumin (B16OVA) and inoculated into mice immunized with OVA. Using this model, we established cell lines after the in vivo passage through distinct immunological condition. B16OVA tumor exposed to OVA-specific CD8+ T cell immunity in OVA-immunized B6 mice were isolated and established five variants (IMM1, 2, 8). For comparison, B16OVA tumors from non-immunized naïve B6 mice or OVA-immunized IFN-gamma-deficient mice were also isolated and established four variants, namely NIMM (1, 3, 4) cell lines or GKO-IMM (1, 2, 3) cell lines, respectively.

overall_design: Regarding the immunogenicity of different variants of B16OVA cells (NIMM, IMM. GKO-IMM) to tumor antigen-specific immunity, IMM, NIMM or GKO-IMM cell lines were re-challenged to OVA-immunized B6 mice. Contrary to NIMM and GKO-IMM cell lines, IMM cell lines showed progressive growth in OVA-immunized mice upon re-challenge. These results suggest IMM cell lines acquire the ability to escape from OVA-specific anti-tumor immune response. In order to understand the molecular mechanism behind in IMM cell lines to acquire the resistance to host immunity, we analyzed comprehensive gene expression of those cell lines using DNA microarray.

first: Yoshihiro

last: Hayakawa

first: Kohei

last: Oki


title: Macrophage infiltration induced by donor hypovolemia protects against severe primary graft dysfunction in mouse lung transplantation

city: Pittsburgh

first: XINGAN

last: WANG

state: Pennsylvania (PA)

address: 200 Lothrop Street, W1206A

department: Medicine

country: USA

institute: University of Pittsburgh

summary:
BACKGROUND: Hypovolemia is common in lung donors before or after brain death. However, its impact on primary graft function (PGD) remains obscure.
METHODS: A clinically relevant two-hit model of PGD was established by integrating hypovolemic shock (HS) and cold ischemia-reperfusion in a mouse model of orthotopic lung transplantation (LTx) from C57BL/6 to Balb/c. At -48 hours, HS was induced to donor by withdrawal of blood from femoral artery and keeping the mean arterial pressure at 15±5 mmHg for 4 h. At -24 hours, donor lungs were retrieved from mice with or without HS and stored at 0ºC until transplantation. CD11b-DTR mice were used as donor and treated with Diphtheria Toxin (DT) to deplete graft-infiltrating macrophages.
RESULTS: HS mainly caused macrophage-predominant infiltration around pulmonary artery injury systemic inflammatory response, but little impairment of lung function even if in combination with cold ischemia-reperfusion. Transcriptional profiling showed HS pretreatment increased pulmonary damage and alveolar remodeling but ameliorated inflammatory infiltration when compared to one-hit model of 12 hours cold ischemia-reperfusion injury. The allografts with donor DT-treatment one day ahead of HS showed injury and dysfunction at donation and worsened further at 24 hours reperfusion, whereas the allografts with recipient DT-treatment immediately after transplantation showed similar function and histology to the control treated with saline.
CONCLUSION: Donor hypovolemia causes pulmonary artery injury and infiltration but has little impact on allograft function, even in combination with 24 h cold ischemia. Graft-infiltrating macrophages are critical in protecting graft from HS-induced injury and cold ischemia-reperfusion injury.

overall_design: Transcriptional profiling were performed on three naïve lung samples, three lung allografts that experienced 24 hours of cold ischemia and 2 hours of reperfusion, and three lung allografts that experienced  additionally 4 hours of hypovolemic shock and 20 hours recovery before ischemia-reperfusion.

first: Xingan

last: Wang


title: Mitochondrial calcium uniporter in pancreatic cancer metastasis and cystine adiction

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: The effect of MCU overexpression on gene expression profile in PANC-1 pancreatic cancer cells were examined. Control or MCU overexpressing PANC-1 cells were cultured in media containing 1 mM Glucose for overnight and gene expression profile betweent the two groups were compared through RNA sequencing analysis.

overall_design: Total 6 samples were analyzed; 3 samples from the control group and 3 samples from the MCU overexpressing group

first: Xiuchao

middle: I

last: Kawasawa

first: Shengyu

last: Yang


title: Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells

city: Evry Cedex

first: Robert

last: Olaso

address: 2 rue Gaston Cremieux

department: CNRGH

country: France

institute: CEA-DRF

summary: Human doublecortin (DCX) mutations are associated with severe brain malformations leading to aberrant neuron positioning (heterotopia), intellectual disability and epilepsy. DCX is a microtubule-associated protein which plays a key role during neurodevelopment in neuronal migration and differentiation. Dcx knockout (KO) mice show disorganized hippocampal pyramidal neurons. The CA2/CA3 pyramidal cell layer is present as two abnormal layers and disorganized CA3 KO pyramidal neurons are also more excitable than wild-type (WT) cells. To further identify abnormalities, we characterized Dcx KO hippocampal neurons at subcellular, molecular and ultrastructural levels. Severe defects were observed in mitochondria, affecting number and distribution. Also, the Golgi apparatus was visibly abnormal, increased in volume and abnormally organized. Transcriptome analyses from laser microdissected hippocampal tissue at postnatal day 60 (P60) highlighted organelle abnormalities. Ultrastructural studies of CA3 cells performed in P60 (young adult) and > 9 months (mature) tissue showed that organelle defects are persistent throughout life. Locomotor activity and fear conditioning behavior of young and mature adults was also abnormal: KO mice consistently performed less well than WT littermates, with defects becoming more severe with age. Thus, we show that disruption of a neurodevelopmentally-regulated gene can lead to permanent organelle anomalies contributing to abnormal adult behavior

overall_design: 14 samples analyzed that included 5 WT and 9 mutant doublecortin (Dcx). In WT animals, the hippocampal CA3 region was microdissected in one piece.  In Dcx KO animals, internal stratum pyramidale (SPI) and external stratum pyramidale (SPE) CA3 cells in the two layers were separated.

first: Melissa

last: Stouffer

first: Reham

last: Khalaf-Nazzal

first: Carmen

last: Diaz-Cifuentes

first: Giulia

last: Albertini

first: Elise

last: Bandet

first: Gael

last: Grannec

first: Virginie

last: Lavilla

first: Jean-François

last: Deleuze

first: Marika

last: Nosten-Bertrand

first: Fiona

last: Francis


title: Deficiency of myeloid PHD proteins aggravates atherogenesis via macrophage apoptosis and paracrine fibrotic signaling [single-cell RNA-seq]

first: Javier

last: Perales-Paton

summary: Atherosclerotic plaque hypoxia is detrimental for macrophage function. Prolyl hydroxylases (PHDs) initiate cellular responses to hypoxia and may therefore govern macrophage function in plaque hypoxia. PHD inhibitors are clinically investigated to treat anemia in patients with chronic kidney disease, but the consequences for cardiovascular disease are not clear. Hence, we studied the influence of myeloid specific PHD deficiency on atherosclerotic plaque development and stability.

overall_design: PHD mRNA and protein levels were expressed by human plaque macrophages, and murine bone-marrow-derived macrophages, thus myeloid specific PHD knockout (PHDko) mice were fed 0.25% cholesterol diet for 6-12 weeks to induce atherosclerosis. Aortic root plaque size was augmented 2.6fold in PHD2cko, and 1.4-fold in PHD3ko, but not in PHD1ko mice compared to controls, independent of plasma cholesterol levels. Macrophage apoptosis was promoted in PHD2cko and PHD3ko mice in vitro and in vivo via the HIF1α/BNIP3 axis as shown by pathway analysis of bulk and single cell RNA sequencing of murine bone-marrow-derived macrophages and plaque macrophages, respectively, and validated by siRNA silencing. Human plaque BNIP3 mRNA associated with carotid plaque necrotic core content, suggesting similar adverse effects in humans. Further, PHD2cko plaques -not PHD1 or PHD3ko- displayed enhanced fibrosis at two different disease stages, and across vascular beds, independent of macrophage function. We show PHD2cko bone-marrow-derived macrophages enhanced collagen secretion by fibroblasts in a paracrine manner, while smooth muscle cell function was unchanged. In silico analysis of macrophage-fibroblast communication predicted SPP1 signaling by PDH2cko macrophages to regulate the fibroblast transcriptome, in line with enhanced SPP1 protein content in plaques of PDH2cko mice

first: Judith

middle: C

last: Sluimer


title: Dual RNA-Sequencing of Vitis vinifera During Lasiodiplodia theobromae Infection Unveils Host-Pathogen Interactions

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

summary: We report the use of a Dual RNA-Seq approach to investigate the interaction of grapevine with the Botryosphaeria dieback agent L. theobromae. The aim of this work was to (1) identify pathogenicity factors produced by L. theobromae, and (2) determine the V. vinifera defence response to the pathogen.

sample_organism:
Vitis vinifera
Lasiodiplodia theobromae

platform_organism:
Vitis vinifera
Lasiodiplodia theobromae

overall_design: 1-year-old seedlings of V. vinifera were inoculated with L. theobromae and four sampling points were defined: 1, 3, 7, and 10 days post inoculation (dpi). Dual RNA-sequencing was performed to characterise both host and pathogen transcriptomes during infection.

first: Micael

middle: F

last: Gonçalves

first: Rui

middle: B

last: Nunes

first: Yves

middle: V

last: Peer

first: Dieter

last: Deforce

first: Filip

last: Nieuwerburgh

first: Ana

last: Esteves

first: Artur

last: Alves


title: RNA deep sequencing data of the whole transcriptomes of the wild-type, sigB and sigE mutant strains of Mycobacterium smegmatis MC2 155

city: Busan 46241, Republic of Korea

first: Yuna

last: Oh

address: Busandaehakro63bun-gil, 2

department: Department of Integrated Biological Science

country: South Korea

institute: Pusan national university

summary: To identify the SigB and SigE regulons in Mycobacterium smegmatis MC2 155, we constructed the sigB and sigE mutant strains and profiled the transcriptomes of the wild-type and mutant strains. Differentially expressed genes were identified pair-wisely by means of the DEGseq package in R language. 110 and 271 genes are differentially expressed in the sigB and sigE mutant strains relative to the wild-type strain, respectively.

overall_design: Comparison of gene expression between the wild-type, sigB, and sigE mutant strains of mycobacterium smegmatis that are aerobically grown.

first: Ji-A

last: Jeong


title: In vitro culture at 39° C during hepatic maturation of human ES cells facilitates hepatocyte-like cell functions

city: Kyoto

first: Ken-ichiro

last: Kamei

state: Kyoto

address: Yoshida-Ushinomiya-cho, Sakyo-ku

department: iCeMS

institute: Kyoto University

summary: Hepatocyte-like cells derived from human pluripotent stem cells (hPSC-HLCs) offer an alternative to primary hepatocytes commonly used for drug screenings and toxicological tests. However, these cells do not have hepatic functions comparable to those of hepatocytes in vivo due to insufficient hepatic differentiation. Here we showed that the hepatic functions of hPSC-HLCs were facilitated by applying physiological liver temperatures during hepatic differentiation. We identified the optimal temperature by treating HLCs derived from H9 human embryonic stem cells (hESC-HLCs) at 39 °C; the 42 °C treatment caused significantly greater cell death than the 39 °C treatment. We confirmed the improvement of hepatic functions, such as albumin secretion, cytochrome P450 3A activity, and collagen production, without severe cell damage. In combination with existing hepatic differentiation protocols, the method proposed here may further improve hepatic functions for hPSCs and lead to the realization of drug discovery efforts and drug toxicological tests.

overall_design: We analyzed cDNA profiles amplified with PCR-cDNA Barcoding Kit  generated from RNAs in Hepatocyte-like cells derived from H9 human embryonic stem cells with 37˚C or 39˚C treatment using Nanopore Flow Cell (v9.4.1).

first: Satoshi

last: Imamura

first: Koki

last: Yoshimoto

first: Shiho

last: Terada

first: Kaho

last: Takamuro


title: Mitochondrial dysfunction and consequences in calpain-3-deficient muscle

status: Public on Mar 28 2022

city: Toledo

first: Jennifer

middle: M

last: Peterson

state: OH

address: 2801 W Bancroft St

department: SERS

institute: The University of Toledo

summary: Microarray profiling  to determine muscle cell-specific consequences of calpain-3 deficiency

overall_design: Total RNA was obtained from wild-type and calpain-3 deficient myotubes after 5 days of differentiation in culture. Expression levels were compared between groups

first: V

middle: E

last: Jahnke

first: J

middle: H

last: Van Der Meulen

last: Boehler

first: K

last: Uaesoontrachoon

first: H

middle: K

last: Johnston

first: A

last: Defour

last: Phadke

first: Q

last: Yu

last: Jaiswal

last: Nagaraju


title: Mitochondrial dysfunction and consequences in calpain-3-deficient muscle myoblasts

overall_design: Total RNA was obtained from wild-type and calpain-3 deficient proliferating myoblasts in culture. Expression levels were compared between groups


title: Transcriptomic analysis of rsp deficient Staphylococcus aureus

city: Tampa

first: Lindsey

middle: N

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

institute: University of South Florida

summary: We provide the transcriptomic profile of rsp deficient Staphylococcus aureus in order to elucidate the impact upon virulence.

overall_design: S. aureus RNA was extracted to compare global gene expression of two samples: HOU wildtype and HOU rsp transposon mutant. HOU wildtype serves as the parental control strain. Each sample was generated by pooling three independent biological replicate RNA preps.

first: Brooke

middle: R

last: Tomlinson

first: Sarah

middle: J

last: Kennedy


title: Conditional knockout of ERα in CD11c+ cells, impact on survival and inflammatory cytokines in murine lupus

city: Charleston

first: Melissa

last: Cunningham

state: SC

address: 96 Jonathan Lucas Street

institute: Medical University of South Carolina

summary: Estrogen and estrogen receptor alpha (ERα) have been implicated in systemic lupus erythematosus (SLE) pathogenesis. ERα signaling influences B cell and dendritic cell (DC) development and function, as well as inflammation and downstream immune responses. We previously reported that ERα modulates TLR-stimulated inflammatory pathways in conventional and plasmacytoid DCs in lupus-prone mice. CD11chiMHCII+ cell numbers are reduced in mice with global ERα deficiency or when expressing a short variant of ERα. RNA-seq analysis in CD11chi cells from bone marrow of NZM2410 mice expressing WT ERα vs. an ERα short (AF-1 mutant) vs. ERα null, revealed differentially expressed complement genes, interferon-related genes and cytokine signaling (e.g., IL-17 and Th17 pathways). Cytokine levels varied among different genotypes, demonstrating the complex nature of ERα regulation. To better understand the role of ERα in CD11c+ cells, lupus prone NZM2410 mice with selective deletion of the Esr1 gene in CD11c+ cells were generated. Phenotype and survival of these mice were similar with the exception of Cre positive (CrePos) female mice. CrePos females, but not males, all died prior to 35 weeks. Surprisingly, DC populations were not significantly different between groups. Since ERα is necessary for optimal development of most DC subsets, this result suggests that DC fate was determined prior to CD11c expression and subsequent ERα deletion (i.e. proximally in DC ontogeny). Overall, findings point to a clear functional role for ERα in regulating cytokine signaling and inflammation, suggesting that further study into ERα-mediated regulatory mechanisms in DCs is warranted.

overall_design: RNA-seq analysis in CD11chi cells from bone marrow of NZM2410 mice expressing wild type (WT) estrogen receptor alpha (Erα) vs. an ERα short (AF-1 mutant) vs. ERα null.

first: Aastha

last: Khatiwada

first: Dongjun

last: Chung

first: Mara

last: Richard Lennard


title: Identification of circular RNAs and mRNAs expression profiles in microglia M2 polarization [mRNA]

city: Changsha

first: longyan

last: Li

state: Hunan

address: 87 Xiangya Road

country: China

institute: Xiangya hospital, Central South University

summary: Microglia M2 polarization plays an important role in the regulation of neuroinflammation, but the molecular mechanisms behind it remain unclear. This study researched the expression profiles of mRNAs in microglia M2 polarization cell model.

overall_design: Microarray expression profiling of mRNAs were conducted using RNA extracted from the BV2 cell treated by 10ng/ml IL-4 for 24 hr and the untreated control, in triplicate.

first: Manyu

last: Xing

first: Wangyuan

last: Zou

first: Zhong

last: Zhang

first: Qian

first: Zhi

last: Ye

first: E

last: Wang

first: Longyan


title: Identification of circular RNAs and mRNAs expression profiles in microglia M2 polarization [CircRNA]

summary: Microglia M2 polarization plays an important role in the regulation of neuroinflammation, but the molecular mechanisms behind it remain unclear. This study researched the expression profiles of circRNAs in microglia M2 polarization cell model.

overall_design: Microarray expression profiling of circRNAs were conducted using RNA extracted from the BV2 cell treated by 10ng/ml IL-4 for 24 hr and the untreated control, in triplicate.


title: ZWC Complex-Mediated SPT5 Phosphorylation Suppresses Divergent Antisense RNA Transcription at the Active Gene Promoters

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing


title: ZWC Complex-Mediated SPT5 Phosphorylation Suppresses Divergent Antisense RNA Transcription at the Active Gene Promoters [ChIP-Seq]

summary:
Purpose: The goals of this study are to understand the mechanistic roles of newly identified ZWC chromatin complex on the regulation of transcriptional process in actively transcribed genes. The novel ZWC complex is composed of ZC3H4, WDR82, and casein kinase II (CK2) subunits.
Methods: Two biological replicates of ChIP-seq data for ZC3H4, WDR82, CK2, and SPT5 were generated from HEK293 cells. And one replicate of ChIP-seq data for RNAPII, H3K4me3, H3K27me3, and H3K36me3 was generated in HEK293 cells. Two biological replicates of ChIP-seq data were generated for RNAPII, S5p RNAPII, S2p RNAPII, SPT5, H3K4me3, H3K36me3, H3K27me3 after HEK293 cells were treated with control or ZC3H4 siRNAs.
Results: The ZWC complex preferentially localizes at TSSs of active genes through the direct interactions of ZC3H4 and WDR82 subunits with S5p RNAPII CTD. ZC3H4 depletion leads to increased divergent antisense transcription.
Conclusion: Our study provides evidence that the newly identified ZWC-DSIF axis regulates the direction of transcription during the transition from early to productive elongation

overall_design: HEK293 cells were cultured in DMEM (10% serum). ChIP-seq experiments were performed as two replicates in HEK293 cells or after depletion of ZC3H4 subunit (a scaffold protein of the ZWC complex) in HEK293 cells.

last: Jian


title: Identification of circular RNAs and mRNAs expression profiles in microglia M2 polarization

type:
Expression profiling by array
Non-coding RNA profiling by array

overall_design: Refer to individual Series


title: ZWC Complex-Mediated SPT5 Phosphorylation Suppresses Divergent Antisense RNA Transcription at the Active Gene Promoters [RNA-Seq]

summary:
Purpose: The goals of this study are to understand the mechanistic roles of newly identified ZWC chromatin complex on the regulation of transcriptional process in actively transcribed genes. The novel ZWC complex is composed of ZC3H4, WDR82, and casein kinase II (CK2) subunits.
Methods: Three biological replicates of RNA-seq data were generated after HEK293 cells were treated with control or ZC3H4 siRNAs. The RNA-Seq libraries were generated from 200 ng of total RNA using TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer's protocol.
Results: The ZWC complex preferentially localizes at TSSs of active genes through the direct interactions of ZC3H4 and WDR82 subunits with S5p RNAPII CTD. ZC3H4 depletion leads to increased divergent antisense transcription.
Conclusion: Our study provides evidence that the newly identified ZWC-DSIF axis regulates the direction of transcription during the transition from early to productive elongation

overall_design: HEK293 cells were cultured in DMEM (10% serum). Strand-specfic RNA-seq was performed as triplicates in HEK293 cells treated with control or ZC3H4 siRNAs.

first: Jang

last: Jin Sung


title: Exosome gene expression technology to understand human health risks in space exploration: applications for SANS

city: Waltham

first: Johan

last: Skog

state: MA

address: 266 Second Avenue, Suite 200

institute: ExosomeDx

summary: Molecular profiling to characterize the effects of environmental exposures is important from the human health and performance as well as the occupational medicine perspective in space exploration. We have developed a novel exosome-based approach that allows profiling of biological processes in the body from a variety of body fluids. The technology is suitable for diagnostic applications as well as studying the pathophysiology of the Space Associated Neuro-Ocular Syndrome in astronauts and monitoring patients with chronically impaired CSF drainage or elevated intracranial pressure. In this proof-of-concept, we demonstrate that: a) exosomes from different biofluids contain a specific population of RNA transcripts; b) urine collection hardware aboard the ISS is compatible with exosome gene expression technology; c) cDNA libraries from exosomal RNA can be stored in dry form and at room temperature, representing an interesting option for the creation of longitudinal molecular catalogs that can be stored as a repository for retrospective analysis.

overall_design: 1. Comparison of high ICP patient's whole blood RNA, plasma exosomal RNA, CSF and urine exosomal RNA (in tripliates) with matched post-treatment low ICP samples or healthy (low ICP) control samples. 2. Comparison of two different urine collection tubes (in triplicates). 3. Comparison of three different DNA preservatives pre and post preservation of RNASeq libraries (one replicate per preservative).

first: Sudipto

last: Chakrabortty

first: Steven

middle: P

last: Lang

first: Yevgenia

middle: L

last: Khodor

first: Dulaney

last: Miller

first: Kailey

last: Babcock

first: Robert

last: Kitchen

first: Vasisht

last: Tadigotla

first: Wei

last: Yu

first: Eric

last: Bershad

first: Susanna

last: Zanello


title: Methylation profiles predict ATI outcome in the kick-and-kill therapeutic vaccine BCN02 clinical trial

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

institute: Josep Carreras Leukemia Research Institute

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


title: Effects of miRNA overexpression on keratinocytes in mice

city: Taigu

first: Lijun

last: Zhao

state: Shanxi

address: No. 1 Mingxian South Road,Taigu,  Shanxi Province, China

department: College of Veterinary Medicine

institute: Shanxi Agricultural University

summary: Extracellular vesicle(EV) secretion and capture is an important method of communication between cells. Melanocytes and their surrounding keratinocytes form epidermal melanin units in the thin, outermost layer of the skin to protect the skin from ultraviolet radiation damage. It is important to understand the mechanisms by which changes in melanocyte EV signal transduction influence pigmentation. EVs from melanocytes were extracted and used to investigate changes in the miRNA profile of EVs, and the effect of exosomal miR-28-3p on keratinocyte with transcriptomics was analyzed by RNA-seq analysis.Our results indicate that the content of miR-28 in EVs may be reduced to induce keratinocytes to prevent carcinogenesis, resist infection and prevent premature apoptosis.

overall_design: mRNA profiles of miR-28-3p overexpression and Control in mice melanocytes

first: Quanhai

last: Pang

first: Hongyu

last: Han

first: Yang

last: Li


title: Methylation profiles predict ATI outcome in the kick-and-kill therapeutic vaccine BCN02 clinical trial [450K]

summary: BCN02 was an exploratory, single arm study designed to evaluate a kick-and-kill therapeutic vaccine strategy in early-treated HIV infected individuals. The participants in the study received a MVA.HIVconsv vaccination before and after three cycles of infusion of romidepsin (RMD), an inhibitor of histone deacetylases that acts as a viral latency reversing agent. The inclusion of a monitored antiretroviral pause (MAP) identified 8 individuals with an early viral rebound (pVL > 2,000 HIV RNA copies/mL, < 4 weeks of MAP initiation) and 4, with a late viral rebound (pVL > 2,000 HIV RNA copies/mL, > 4 weeks of MAP initiation). In the present study, a systems biology analysis was conducted to identify the pathways modulated at transcriptomic and epigenetic level during the clinical intervention, involving vaccination and RMD, and to identify biomarkers predictive of HIV viral rebound during MAP. To this end, we studied gene expression and whole-genome DNA methylation in longitudinal PBMC samples prior and after the intervention. The main impact on host transcriptional and epigenetic signatures was observed after vaccination and RMD infusion (Vacc+RMD) with multiple pathways related to HIV infection and immune response showing changes at gene expression and DNA methylation level. Analysis of an independent cohort of individuals treated with RMD alone, showed that these changes were mainly driven by CD4 T cells. DNA methylation patterns in full PBMC obtained after full intervention (Vacc+RMD) allowed to discriminate individuals with an Early versus Late viral rebound. These individuals also showed a differential enrichment on chromatin accessibility and transcription factor binding sites. Intriguingly, 30 of the DMPs between Early and Late rebounders at Vacc+RMD were present already at baseline and were more accentuated after RMD infusion. Overall, this study provides with a deeper understanding of the mechanisms modulated during the BCN02 study and highlights the importance of DNA methylation profiles in HIV cure.

overall_design: DNA methylation was assessed with 450K array in 60 PBMC samples from 15 individuals in 4 different timepoints from the BCN02 clinical trial. Specifically, PBMCs samples from the 15 individuals were taken at baseline (w0), one week after 1st vaccination with HIVconsv (w1), one week after the 3-cycle treatment with romidepsin (w6) and one week after the 2nd vaccination with HIVconsv (w10).

first: Bruna

last: Oriol-Tordera

first: Anna

last: Esteve-Codina

first: María

last: Berdasco

first: Míriam

last: Rosas-Umbert

first: Elena

last: Gonçalves

first: Clara

last: Duran-Castells

first: Francesc

last: Català-Moll

first: Anuska

last: Llano

first: Samandhy

last: Cedeño

first: Maria

last: Puertas

first: Martin

last: Tolstrup

first: Ole

middle: S

last: Søgaard

first: Bonaventura

last: Clotet

first: Javier

last: Martínez-Picado

first: Tomas

last: Hanke

first: Behazine

last: Combadiere

first: Roger

last: Paredes

first: Dennis

last: Hartigan-O’Connor

first: Manel

last: Esteller

first: Michael

last: Meulbroek

last: Calle

first: Alex

last: Sanchez-Pla

first: José

last: Moltó

first: Beatriz

last: Mothe

first: Christian

last: Brander

first: Marta

last: Ruiz-Riol


title: Methylation profiles predict ATI outcome in the kick-and-kill therapeutic vaccine BCN02 clinical trial  [EPIC array]

first: IJC

last: Bioinformatics

overall_design: DNA methylation in 32  PBMCs samples from 15 individuals toatl was assessed with the Illumina EPIC array in three timepoints: before cART intiation (only in 6 out of 15 individuals), at MAP timepoint (14 individuals) and 24 weeks after cART resumption (12 individuals).

first: Bruna

last: Oriol-Tordera

first: Anna

last: Esteve-Codina

first: María

last: Berdasco

first: Míriam

last: Rosas-Umbert

first: Elena

last: Gonçalves

first: Clara

last: Duran-Castells

first: Francesc

last: Català-Moll

first: Anuska

last: Llano

first: Samandhy

last: Cedeño

last: Puertas


title: Monocyte subpopulation miRNA profiling

city: Münster

first: Anika

last: Witten

address: Domagkstrasse 3

institute: Institute for Human Genetics

summary: miRNA profiling of classical, non-classical and intermediate monocyte subpopulations

overall_design: profiling in n=3 samples per group (controls, myocardial infarction, stable coronary artery disease), 3 monocyte subsets per sample

first: Leonie

last: Martens

first: Ann-Christin

last: Schäfer

last: Troidl

first: Sabine

last: Pankuweit

first: Ann-Kathrin

last: Vlacil

first: Raghav

last: Oberoi

first: Bernhard

last: Schieffer

first: Grote

last: Karsten

first: Monika

last: Stoll

first: Birgit

last: Markus


title: Genome-wide analysis of TERC occupancy in MRC5 fibroblast cells by ChIRP-seq

city: Guangzhou

first: Shu

last: Wu

address: No.601, West Huangpu Avenue

institute: Jinan University

summary: TERC is the core subunit of telomerase which is responsible for adding telomeric sequences to the telomere ends. Besides being the RNA temple of telomerase, TERC is a typical Lnc RNA and ubiquitously expressed in normal somatic cells without telomerase activity. It is very likely that TERC has other, yet to be discovered functions in normal somatic cells independent of telomerase activity. Identifying the genomic occupancy of TERC helps to understand its functional mechanism on chromosomal DNA. Then, we analyzed the genome occupancy of TERC in MRC5 fibroblast cells that is without telomerase activity by ChIRP-seq, and found that there was not apparent enrichment of TERC on telomere sequences in normal somatic cells, but showed a significant enrichment on gene promoters/transcription start sites. This study provides a mechanistic insight of TERC on transcriptional regulation in normal somatic cells.

overall_design: Examination of TERC genomic occupancy in fibroblast cells that is telomerase negative

first: Yuanlong

last: Ge

first: Kaixuan

last: Lin

first: Qianqian

last: Liu

first: Haoxian

last: Zhou

first: Qian

last: Hu

first: Yong

last: Zhao

first: Weifeng

last: He

first: Zhenyu

last: Ju


title: RNAseq expression of p53-null and p53-null/PLK2-null mammary tumors

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Bulk tumor samples from p53-null and p53-null/ PLK2-null tumors that have been serially transplanted in Balb/c mice

first: Jonathan

last: Shepherd

first: Matthew

middle: G

last: Soloway

first: Jeffrey

last: Rosen


title: Gene expression of PBMC and isolated CD4 T cells from participants in Part A REDUC clinical trial

city: Badalona

first: Marta

last: Ruiz-Riol

state: Catalonia/Barcelona

address: Ctra. del Canyet s/n

institute: IrsiCaixa

summary: REDUC Part A (NCT02092116) assessed the effect of romidepsin in ART-treated chronically HIV-1 infected individuals. Here, we studied the gene expression on PBMCs or isolated CD4 before and after the 3-cycle infusion of Romidepsin

overall_design: Samples of PBMCs and isolated CD4 T cells from 6 participants in the part A REDUC clinical trial were taken before (v1) and 1 week after the 3 cycles of romidepsin infusion (v9). We identified differentially expressed genes between v9-v1. We did not include the only woman of the study in the analysis, but we upload the data for transparency

first: Anna

last: Esteve-Codina

first: Christian

last: Brander

first: Bruna

last: Oriol-Tordera

first: Martin

last: Tolstrup


title: PBMC Gene expression of participants in the kick and kill clinical trial BCN02

summary: The BCN02 (NCT02616874)  was a pilot study to evaluate the kick and kill therapy on 15 early-treated individuals that were rolled-over from the BCN01 Study.  The participants in the study received two MVA.HIVconsv vaccination before and after the 3-cycle infusion of Romidepsin, an inhibitor of histone deacetylases that act as a latency reversing agent. Additionally, the inclusion of a monitored antiretroviral pause (MAP) allowed tthe identification of 8 individuals with an Early Rebound (pVL > 2,000 HIV RNA copies/mL, < 4 weeks of MAP initiation) and 4, with a Late Rebound (pVL > 2,000 HIV RNA copies/mL, > 4 weeks of MAP initiation).  In the present study we studied gene expression at 3 different timepoints: w0 (Bsl), w1 (Vacc),  w6 (Vacc+RMD) and applied pairwise comparisons.

overall_design: PBMCs from the 15 individuals enrolled in BCN02 clinical trial were taken at 5 different timepoints: w0, w1, w6, MAP and w24.


title: Impact of vancomycin on the ileum and colon of  mice-bearing singeneic mammary carcinoma expressing human HER2

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Starting from the evidences of gut microbiota role in tumor development, progression and response to therapy, this project was aimed at evaluating the effect of antibiotic treatment on intestine. The intestinal flora of FVB mice was altered by the oral administration of vancomicyn, mice were then injected with MI6 cells, a singeneic tumor cells line established from spontanueous mammary tumor developped in transgenic d16HER2-transgenic mice [Castagnoli L, 2014].  To analyze the impact of vancomycin on intestinal mucosa, a gene expression profile was performed on colon and ileum samples.

overall_design: FVB female mice were treated with vancomycin starting from four weeks of age until the end of the experiment. Vancomycin was administered in the drinking water at a concentration of 200 mg/L. Mice were sacrificed upon 9 weeks when tumors reached a volume of 150 mm3. For gene expression profile, colon and ileum from NoA and Vancomycin mice  were harvested, washed in clean PBS 1x and immediately fronzen in dry ice. Sample were then stored at -80°C until RNA extraction.


title: Expression profiling of Mouse inv(16):TET2ko and AML patient granulocyte macrophage progenitor (GMP) cells

city: Copenhagen

first: Kim

last: Theilgaard-Mönch

address: Ole Maaløes Vej 5

country: Denmark

institute: Rigshospitalet/National Univ. Hospital and Biotech Research and Innovation Centre

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Heterogeneity of  liver group 1 ILC1s

status: Public on Mar 27 2022

city: 合肥市

first: yawen

last: chen

state: 蜀山区

address: 稻香村街道

institute: USTC

summary: RNA sequencing  demonstrated that liver Ly49E+ and Ly49E- ILC1s exhibited unique transcriptional profiles and phenotypic features. scRNA-seq analysis revealed heterogeneity within both cNK and ILC1 subsets in liver. cNK cells could be further divided into three clusters, which corresponded to different developmental stages. Ly49E expression could dissect ILC1s into two subsets: Ly49E+ ILC1s and Ly49E- ILC1s, which exhibited different functional characteristics.

overall_design: Purified liver group 1 ILCs (CD45+ NK1.1+NKp46+ CD3-CD19-)  from adult WT mice were stained with 0.4% Trypan blue to check their viability, and processed for scRNA-seq (10X Genomics). One samples from murine liver  Ly49E+  ILC1s and three samples from Ly49E?  ILC1s for bulk RNA-seq.

first: Yawen

last: Chen

first: Xianwei

last: Wang

first: Hui

last: Peng

first: Zhigang

last: Tian


title: Expression data from human normal fibroblasts (NFs) and cancer associated fibroblasts (CAFs)

city: Nanjing

first: Junlong

last: Zhuang

address: 321# Zhongshan Road

institute: Institute of Urology, Drum Tower hospital

summary:
CAFs are the major regulators in tumor microenviroment which promote cancer progression. We want to know which miRNAs changed in human CAFs compared to NFs.
We used microarrays to detail the mature miRNA expression and identified distinct classes of 2-fold changed miRNAs during this process.

overall_design: NFs and CAFs were isolated from normal or bladder cancer tissues, respectively from 3 individuals. And cells were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Jun

last: Yan


title: Expression data of LT-HSC from Irf8+/+ and Irf8-/- mice

city: Shanghai

first: Qingsong

last: Qiu

address: Ruijin er road No.197

institute: SIH

summary: Deletion of IRF8 results in gene expression changes in lineage-c-kit+Sca-1+ CD48- CD150+ cells from mouse bone marrow.

overall_design: We analyzed lineage- c-kit+ Sca-1+  CD48- CD150+ cells from the bone marrow of IRF8 wild-type or knockout mice using the Affymetrix mouse 430 2.0 array platform. Array data was processed by Affymetrix Mouse Genome 430 2.0 Array Computational Tool. No technical replicates were performed.

first: Ruibao

last: Ren


title: Ybx1 is required for Survival of Leukemia Stem Cells and the Development of Chronic Myeloid Leukemia

city: wuhan

first: Qifan

address: donghu road

institute: wuhan university

summary: Chronic myeloid leukemia (CML) is a myeloproliferative disorder derived from hematopoietic stem cells (HSCs) that harbor Philadelphia chromosome (Ph chromosome). Leukemia stem cells (LSCs) in CML are insensitive to TKIs treatment, and are responsible for disease relapse. However, the molecular mechanisms for LSCs survival remains elusive. Here we show that YBX1 plays an important role in regulating survival of CML LSCs. We find that YBX1 expression is significantly increased in CML cells. Using CML patient-derived cell lines and a BCR-ABL-induced CML mouse model, we confirm that YBX1 is required for survival maintenance of LSCs. Deletion of YBX1 impairs the propagation of CML through impairing cell cycle and inducing apoptosis of LSCs. Mechanistically, we find that YBX1 regulates expression of apoptosis-related genes, and YBX1 binds MYC and BCL2 transcripts. YBX1 loss decreases expression of MYC and BCL2 by accelerating their mRNA decay. In addition, restoration of MYC and BCL2 efficiently rescue the defects of YBX1-deficient CML cells. Overall, our findings reveal a critical role of YBX1 in maintaining survival of CML LSCs, which may provide a rationale for targeting YBX1 in CML treatment.

overall_design: RNAseq of  WT and YBX1cKO LSCs

first: Jihua

last: Chai

first: Qiang

first: Guoqiang

last: Han

first: Yilin

first: Haojian

last: Zhang


title: Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides

status: Public on Mar 26 2022

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

summary:
Yeast Saccharomyces cerevisiae has been widely used as a model system for studying genome instability. Here, heterozygous S. cerevisiae zygotes were generated to determine the genomic alterations induced by sudden introduction of active RNase H2. In combination of a custom SNP microarray, the patterns of chromosomal instability could be explored at a whole genome level.
Ribonucleotides can be incorporated into DNA during replication by the replicative DNA polymerases.  These aberrant DNA subunits are efficiently recognized and removed by Ribonucleotide Excision Repair, which is initiated by the heterotrimeric enzyme RNase H2. While RNase H2 is essential in higher eukaryotes, the yeast Saccharomyces cerevisiae can survive without RNase H2 enzyme, although the genome undergoes mutation, recombination and other genome instability events at an increased rate.  Although RNase H2 can be considered as a protector of the genome from the deleterious events that can ensue from recognition and removal of embedded ribonucleotides, under conditions of high ribonucleotide incorporation and retention in the genome in a RNase H2-negative strain, sudden introduction of active RNase H2 causes massive DNA breaks and genome instability in a condition which we term “ribodysgenesis”. The DNA breaks and genome instability arise solely from RNase H2 cleavage directed to the ribonucleotide-containing genome.  Survivors of ribodysgenesis have massive loss of heterozygosity events stemming from recombinogenic lesions on the ribonucleotide-containing DNA, with increases of over 1000X from wild-type.  DNA breaks are produced over one to two divisions and subsequently cells adapt to RNase H2 and ribonucleotides in the genome and grow with normal levels of genome instability.

overall_design: Zygotes were grown on on solid YPD medium or in liquid YPD medium at 30°C. Genomic DNA from independent zygotes was extracted and analyzed by the whole-genome microarrays.

first: Dao-Qiong

first: Thomas

middle: D

last: Petes


title: Long non-coding RNA profiling of Simple steatosis and Non-alcoholic steatohepatitis in the liver of mice

first: Xiang

last: Liping

address: 180 Fenglin Road, Xuhui, Shanghai

institute: Fudan university

summary: In our study, C57BL/6 male mice were fed a normal chow diet or high-fat diet additionally containing high-fructose and high-cholesterol (HFHC diet) for 12 weeks and 28 weeks to construct simple steatosis (NAFL) and Non-alcoholic steatohepatitis (NASH) models respectively. Through lncRNA sequencing, a total of 1131 lncRNAs (798 up-regulated and 333 down-regulated) and 5161 lncRNAs (3168 up-regulated and 1993 down-regulated) were differentially expressed in livers of NAFL and NASH mice respectively. A total of 614 lncRNAs (455 up-regulated and 159 down-regulated) were dysregulated in both NASH and NAFL mice, while 4547 lncRNAs (2713 up-regulated; 1834 down-regulated) were altered specifically in NASH mice.

overall_design: Liver lncRNA profiles of NAFL and NASH mice

first: Liping

last: Xiang

first: Xiaoyan

last: Li

first: Yunchen

last: Luo

first: Lu


title: First-in-class microbial ecosystem therapeutics 4 (MET4) in combination with immune checkpoint inhibitors in patients with advanced solid tumours (MET4-IO Trial)

city: Guelph

first: Kyla

last: Cochrane

state: ntario

address: 488 Gordon Street

country: Canada

institute: NuBiyota

summary: The intestinal microbiome has been associated with response to immune checkpoint inhibitors (ICI) in humans, and causally implicated in ICI responsiveness in animal models.  Therapeutic augmentation of the microbiome in ICI recipients is being investigated in multiple ongoing human clinical trials. We conducted an early phase clinical trial of a cultivated, orally-delivered 30-species microbial consortium (microbial ecosystem therapeutic-4, MET4) designed for co-administration with ICIs and assessed safety, tolerability and ecological responses in patients with advanced solid tumors.

overall_design:
Examine the bacterial cumulative relative abundance of immunotherapy-responsiveness associated with MET4 strains between baseline, day 12 (during treatment), week 24 (after treatment) and to determine the bacterial taxonomic diversity between baseline and follow-up samples.
16S rRNA gene amplicon sequencing was used for identification, classification and quantitation of microbes within complex patient fecal mixtures (human gut mircobiome)


title: Small RNA profiling of Simple steatosis and Non-alcoholic steatohepatitis in the liver of mice [miRNA-seq]

summary: In our study, C57BL/6 male mice were fed a normal chow diet or high-fat diet additionally containing high-fructose and high-cholesterol (HFHC diet) for 12 weeks and 28 weeks to construct simple steatosis (NAFL) and Non-alcoholic steatohepatitis (NASH) models respectively. Through miRNA sequencing, 420 miRNAs were detected. A total of 148 miRNAs (14 up-regulated and 34 down-regulated) and 146 miRNAs (74 up-regulated and 72 down-regulated) were differentially expressed in livers of NAFL and NASH mice, respectively. A total of 36 miRNAs (8 up-regulated; 28 down-regulated) were dysregulated in both NASH and NAFL mice, while 110 miRNAs (66 up-regulated; 44 down-regulated) were altered specifically in NASH mice.

overall_design: Liver miRNA profiles of NAFL and NASH mice


title: Microglial Piezo1 senses  Aβ fibrils stiffness to restrict Alzheimer’s disease

city: Xiamen

first: Hongrui

last: Zhu

state: Fujian

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District, Xiamen, Fujian Province, China

institute: Xiamen University

summary: Alzheimer's disease (AD) is associated with the formation of extracellular amyloid-β (Aβ) plaque, perturbing the mechanical properties of brain tissue. Microglia sense and integrate biochemical and mechanical cues in their local microenvironment, intimately linked with AD progress. However, little is known about how microglial mechanosensing pathways are implicated in AD pathogenesis. Gene Ontology (GO) analysis of the significantly down-regulated genes in Piezo1 conditional knockout microglia revealed a significant functional reduction in synapse organization, cell-substrate adhesion, and cytoskeleton system-based events (morphogenesis, migration, and endocytosis) in 5×FAD mice.

overall_design: 1. 5×FAD mice were crossed with Cx3cr1CreER-EYFP; Piezo1fl/fl mice to develop Cx3cr1CreER-EYFP; Piezo1fl/fl; 5×FAD. Cx3cr1CreER-EYFP; Piezo1fl/fl; 5×FAD and Piezo1fl/fl; 5×FAD male littermates aged at 4.5 weeks were subjected with four daily intraperitoneal 20 mg/kg tamoxifen  to generate microglial Piezo1 knockout in 5×FAD mice (Piezo1MGKO; FAD) and the control littermate mice (Piezo1fl/fl; FAD); 2.Microglia isolation from adult mouse brain of Piezo1MGKO; FAD and Piezo1fl/fl; FAD. RNA were extracted from the indicated groups for RNA profiles.

first: Jin

last: Hu


title: Mouse inv(16):TET2ko granulocyte macrophage progenitor (GMP) cells

first: Kim

last: Theilgaard-Mönch

type:
Expression profiling by array
Third-party reanalysis

summary:
inv(16)/Tet2-/- GMPs (Lin- Sca1- ckit+ CD41- FcgR+ CD150-) were FACS sorted as described in Supplementary Information (Reckzeh, K et al 2020)
TET2 deficiency cooperates with CBFB-MYH11 to induce acute myeloid leukemia and represents an early leukemogenic event. Reckzeh, K et al.

overall_design: TET2 deficiency cooperates with CBFB-MYH11 to induce acute myeloid leukemia and represents an early leukemogenic event. This series includes re-analyzed samples from: GSE15907

first: Kristian

last: Reckzeh


title: Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440

city: Golden

first: Gregg

middle: T.

last: Beckham

address: 15013 Denver West Parkway

institute: National Renewable Energy Laboratory

summary: Pseudomonas putida KT2440 has received increasing attention as an important biocatalyst for the conversion of diverse carbon sources to multiple products, including the olefinic diacid, cis,cis-muconic acid (muconate). P. putida has been previously engineered to produce muconate from glucose; however, periplasmic oxidation of glucose causes substantial 2-ketogluconate accumulation, reducing product yield and selectivity. Deletion of the glucose dehydrogenase gene (gcd) prevents 2-ketogluconate accumulation, but dramatically slows growth and muconate production. In this work, we employed adaptive laboratory evolution to improve muconate production in strains incapable of producing 2-ketogluconate. Growth-based selection improved growth, but reduced muconate titer. A new muconate-responsive biosensor was therefore developed to enable muconate-based screening using fluorescence activated cell sorting. Sorted clones demonstrated both improved growth and muconate production. Mutations identified by whole genome resequencing of these isolates indicated that glucose metabolism may be dysregulated in strains lacking gcd. Using this information, we used targeted engineering to recapitulate improvements achieved by evolution. Deletion of the transcriptional repressor gene hexR improved strain growth and increased the muconate production rate, and the impact of this deletion was investigated using transcriptomics. The genes gntZ and gacS were also disrupted in several evolved clones, and deletion of these genes further improved strain growth and muconate production. Together, these targets provide a suite of modifications that improve glucose conversion to muconate by P. putida in the context of gcd deletion. Prior to this work, our engineered strain lacking gcd generated 7.0 g/L muconate at a productivity of 0.07 g/L/h and a 38% yield (mol/mol) in a fed-batch bioreactor. Here, the resulting strain with the deletion of hexR, gntZ, and gacS achieved 22.0 g/L at 0.21 g/L/h and a 35.6% yield (mol/mol) from glucose in similar conditions. These strategies enabled enhanced muconic acid production and may also improve production of other target molecules from glucose in P. putida.

overall_design: Ribosomal RNA removed RNA prepared from cell cultures of Pseudomonas putida KT2440 at the exponential phase.

first: Gayle

last: Bentley

first: Christopher

middle: W

last: Johnson

middle: T


title: Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple mutated AML

city: Heidelberg

first: Caroline

last: Pabst

address: Im Neuenheimer Feld 400

department: Department of Medicine V, Hematology, Oncology and Rheumatology

institute: University Hospital Heidelberg

summary: HLF was knocked down in a primary human triple mutated AML sample using shRNA against human HLF versus shRNA against luciferase (shLuc) as control to determine gene expression changes 72 hours after lentiviral transduction.

overall_design: Transcriptome profiling of shRNA mediated HLF knockdown cells in primary AML cells.

first: Swati

last: Garg

first: Armando

last: Reyes-Palomares

first: Judith

middle: B

last: Zaugg


title: H3K9 Me3 occupancy of Control and AMPK knockdown Hep3B cells

city: Winston-Salem

first: zhen

last: cai

address: 391 Technology way

institute: wake forest baptist medical center

overall_design: Control and two AMPK knockdown clones in Hep3B were involved. Chromatin-immunoprecipitation was performed by H3K9 Me3 antibody. The sheared chromatin samples were subjected to high-throughput sequencing the unravel the H3K9 Me3 occupancy through whole genome of Control and AMPK knockdown cells

first: Zhen

last: Cai

first: Hui-kuan

last: Lin


title: Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer

city: Saugus

first: Michael

last: Raabe

address: 3214 Founders Way

institute: Massachusetts General Hospital

summary: Colorectal cancer aberrant repeat RNA expression can be therapeutically targeted with reverse transcriptase inhibitors.

overall_design: The experiments performed were on colorectal cancer (CRC) cell lines in different conditions to characterize the effects of P53 status and therapy on CRC.  Cell lines in vitro were grown in 3D tumorsphere conditions and treated with DMSO control or 3TC with biological replicates at Day 1 and Day 7 post-treatment for a total of 96 RNA-seq samples.  Cell lines grown as xenografts in Nu/Nu mice were treated with PBS control, 3TC, AZA, or 3TC + AZA for a total of 51 tumors with RNA-seq.  ChIP-seq was performed on cell lines in vitro comparing input and p53 immunoprecipitation (IP) for a total of 12 samples.

first: Mihir

last: Rajurkar

first: Aparna

last: Parikh

first: Alexander

last: Solovyov

first: Eunae

last: You

first: Anupriya

last: Kulkarni

first: Chu

last: Chong

first: Katherine

last: Xu

last: Jaicks

first: Martin

last: Taylor

first: Connie

last: Wu

middle: A

last: Alexander

first: Charly

last: Good

first: Annamaria

last: Szabolcs

first: Stefanie

last: Gertsberger

first: Antuan

last: Tran

first: Nova

first: Richard

middle: Y

last: Ebright

first: Emily

last: Van Seventer

first: Kevin

last: Vo

first: Eric

middle: C

last: Tai

first: Chenyue

last: Lu

first: Jasmin

last: Joseph-Chazan

first: Linda

last: Nieman

first: Niyati

last: Desai

first: Kshitij

last: Arora

first: Matteo

last: Ligorio

first: Vishal

last: Thapar

first: Limor

last: Cohen

first: Padric

middle: M

last: Garden

first: Yasmeen

last: Senussi

first: Hui

last: Zheng

first: Jill

last: Allen

first: Lawrence

last: Blaszkowsky

first: Jeffrey

last: Clark

first: Lipika

last: Goyal

first: Jennifer

last: Wo


title: H3K4 Me3 occupancy of Control and AMPK knockdown Hep3B cells

first: zhen

last: cai

overall_design: Control and two AMPK knockdown clones in Hep3B were involved. Chromatin-immunoprecipitation was performed by H3K4 Me3 antibody. The sheared chromatin samples were subjected to  high-throughput sequencing the unravel the H3K4 Me3 occupancy through whole genome of Control and AMPK knockdown cells

first: Zhen

last: Cai

first: Hui-kuan

last: Lin


title: H3K27 Me3 occupancy of Control and AMPK knockdown Hep3B cells

overall_design: Control and two AMPK knockdown clones in Hep3B were involved. Chromatin-immunoprecipitation was performed by H3K27 Me3 antibody. The sheared chromatin samples were subjected to high-throughput sequencing the unravel the H3K27 Me3 occupancy through whole genome of Control and AMPK knockdown cells


title: CD4 T cell response to MHC-II-restricted APOB epitope in human cardiovascular disease revealed by single cell transcriptomics and TCR reconstruction

city: La Jolla

first: Vasantika

last: Suryawanshi

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

summary: We sorted T-helper-1 (Th1), memory (Tmem), Treg and APOB-specific CD4 T cells, detected and sorted by a validated MHC-II tetramer DRB1*07:01 APOB-p18 (Tet+ cells) from peripheral blood mononuclear cell samples from 8 DRB1*07:01+ women with and without subclinical cardiovascular disease (sCVD) as documented by carotid artery ultrasound. We subjected them to 10x Genomics 5’ single cell RNA-sequencing with T cell receptor (TCR) sequencing.

overall_design: scRNA-Seq study of APOB-specific Tet+ cells in individuals with and without sCVD, using a recombinant APOB-p18 DRB1*07:01 tetramer for detecting the naturally occurring population of CD4 T cells in humans that recognize a human APOB peptide, determining their transcriptomes and TCRα and β sequences.

first: Klaus

last: Ley

first: Ryosuke

last: Saigusa


title: ZMO1162 Overexpression Boosts Phenolic Aldehyde Conversion and Ethanol Production of Zymomonas mobilis ZM4

status: Public on Mar 25 2022

city: Changzhou

first: Xia

last: Yi

address: 21 Gehu Middle Road

institute: Changzhou University

summary: we aimed to screen candidate kinase genes under the stress of phenolic aldehydes during ethanol fermentation for Zymomonas mobilis ZM4

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: Effect of kinase genes on transcriptional profiling of Zymomonas mobilis ZM4

first: Jianfang

last: Wu

first: He

last: Jiang

first: Yan

last: Zhao

first: Jun

last: Mei


title: Liver Transcriptomes of Simple steatosis in Mice

first: Xiang

last: Liping

summary: In our study, we constructed a Simple steatosis (NAFL) mouse model with a high-fructose and high-cholesterol (HFHC diet) for 12 weeks. Next, we performed RNA Sequencing analysis to reveal molecular features of Simple steatosis. As a result, we obtained hepatic genome-wide mRNA expression in the livers from two groups of mice (NAFL versus Normal).Using FDR < 0.01 and fold change > 2 as the threshold, we identified 176 differentially expressed genes (DEGs) in the livers of NAFL mice relative to the normal control mice, of which 118 up-regulated and 58 down-regulated. The top 5 up-regulated genes in NAFL mice included the genes encoding for Themis, Cfd, Aqp8, Osbpi3 and Scd1.

overall_design: Liver mRNA profiles of NAFL and Normal mice

first: Liping

last: Xiang

first: Xiaoyan

last: Li

first: Yunchen

last: Luo

first: Lu

last: Yan


title: Evaluation the effects of ectopic expression of TaF5H1 in Arabidopsis driven by its native promoter on the the cell wall biosynthesis and salt tolerance by RNA-seq

city: Shijiazhuang

first: Caili

last: Bi

state: Hebei

address: No.20 Road East. 2nd Ring South, Yuhua District

department: College of life sciences

institute: Hebei Normal University

summary:
Purpose: The goals of this study are to compare the transcriptome of Arabidopsis seedlings expressing pTaF5H1:TaF5H1(expression of TaF5H1 driven by its native promoter) with the wild-type control(Col-0) under/without salt treatment, which may give us clues to whether and how cell wall composition changes affect salt tolerance.
Transcriptomes profiles of 14-day-old Arabidopsis seedlings of wild-type (Col-0) and  seedlings harbour pTaF5H1:TaF5H1 without and under NaCl treatment for 6 hours  were generated by RNA-seq, in triplicate, using Illumina a HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150 paired-end (PE) configuration; image analysis and base calling was conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format was processed by Cutadapt (V1.9.1) to be high quality clean data. For mapping, firstly, reference genome sequences and gene model annotation files of relative species were downloaded  from ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1). For expression analysis,  in the beginning, transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data. For differential expression analysis, DESeq2 Bioconductor package was used, a model based on the negative binomial distribution, the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Results: we mapped about 43.5 million sequence reads per sample to the Arabidopsis genome (TAIR10). Significant differential expressed genes(DEG) between samples was sreened for fold change≥2 and  p-value (fdr, padj)≤0.05.Totally 7713 significant DEGs were discovered with 3430 up -regulated and 4483 down-regulated, no significant  changes were detected as for the remaining 26505 genes among samples.
Conclusions:   Our study presents the detailed analysis of transcriptomes of Arabidopsis wild-type control(Col-0) and Arabidopsis seedlings expressing pTaF5H1:TaF5H1, with three biologic replicates, generated by RNA-seq technology. Our results show that ectopic expressing pTaF5H1:TaF5H1 in Arabidopsis changed the expression of some cell-wall related genes as well as genes related to salt stress response, inferring that changes in cell wall components may affect the salt tolerance of plants somehow.

overall_design: 14-day old Arabidopsis seedlings of wild-type(Col-0) and seedlings harbour pTaF5H1:TaF5H1 under/without NaCl (200 mM) treatment for 6 hours were sampled for RNA-seq analysis with three biological replicates.


title: Expression profile and Histone H3 K4, K9, K27, K36 tri-methylation occupancy through the whole genome between control and AMPK knockdown Hep3B cells

first: zhen

last: cai

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

overall_design: Refer to individual Series


title: Cancer specific tissue-resident memory T cells expressed ZNF683 up-regulated by autocrine IFN-γin colorectal cancer

city: Suita

first: Masatoshi

last: Kitakaze

state: Osaka

address: Yamadanishi, 4-2-88-703

institute: Osaka University

summary: Tissue-resident memory T (Trm) cells express CD103 to be maintained in the local microenvironment and to be strongly involved in local immunity of epithelial tissue.  Trm has been associated with cytotoxicity in pathologies of not only virus infection and autoimmune disease but also many cancers. Tumor infiltration by CD103+ Trm cells was associated with patient survival in colorectal cancer. Tumor infiltrating CD103+ Trm cells were comprised predominantly of CD8 T cells expressing cytotoxic activation and immune check-point molecules called exhausted markers. Therefore, we focused on ZNF683 as a marker of cancer-specific Trm. The expression of ZNF683 in Trm was up-regulated by TCR and IFN-γ signaling that was positive feedback by autocrine IFN-γ. These results indicate that IFN-γ and TCR signaling and ZNF683 are involved in the activation of Trm in tumor and would be promising targets for regulation of cancer immunity.

overall_design: Samples were obtained from colorectal cancer tissue and normal colon tissue in the intact area from two patients. CD45 positive cells in the sample were obtained by isolation and separation. These cells were targeted for single-cell RNA-seq analysis using the BD Rhapsody Single-Cell Analysis System

first: Hideshi

last: Ishii

first: Masamitsu

last: Konno

first: Ayumu

last: Asai


title: AML patient granulocyte macrophage progenitor (GMP) cells

first: Kim

last: Theilgaard-Mönch

address: Ole Maaløes Vej 5

institute: Rigshospitalet/National Univ. Hospital and Biotech Research and Innovation Centre

summary:
AML patient GMPs or CMPs were FACS sorted as described in Supplementary Information (Reckzeh, K et al. 2020)
TET2 deficiency cooperates with CBFB-MYH11 to induce acute myeloid leukemia and represents an early leukemogenic event.  Reckzeh, K et al

overall_design: TET2 deficiency cooperates with CBFB-MYH11 to induce acute myeloid leukemia and represents an early leukemogenic event.  This series includes re-analyzed samples from: GSE11864, GSE19599 and GSE42519. Two samples were re-analyzed from ArrayExpress E-MEXP-1242

first: Kristian

last: Reckzeh


title: A novel anti-hepatitis B virus regent iCDM-34 reveals suppression of cccDNA accompanied with aryl hydrocarbon receptor activation

city: Wako-shi

first: Yutaka

last: Furutani

state: Saitama

address: 2-1 Hirosawa

department: Center for Integrative Medical Sciences

institute: RIKEN

summary:
Background & Aims: IFN-alpha and -gamma have been reported to suppress cccDNA via APOBEC3 cytidine deaminase activity, and CDM-3008, an IFNAR2 agonist, also suppress cccDNA through interferon signaling. In order to develop a novel anti-HBV drug for functional or complete cure, we performed in silico screening using a structure of CDM-3008-binding pocket in IFNAR2.
Approach & Results: The binding pocket of CDM-3008 in IFNAR2 was determined by LC-MS/MS using a CDM-3008-based molecular probe, CDM-3095 and a recombinant protein of IFNAR2 extracellular region. We conducted in silico screening of the binding compounds fitting the steric structure of the pocket. We identified 37 compounds and named them iCDM-1–37. We found that iCDM-34 showed anti-HCV and anti-HBV activities. We measured the anti-HBV activity of iCDM-34 with or without entecavir (ETV). iCDM-34 suppressed pregenome RNA, covalently closed circular DNA (cccDNA), HBsAg, and HBeAg and clearly exhibited synergistic inhibitory effects with ETV. Metabolic stability of iCDM-34 was measured in human, mouse, and rat microsomal fractions. iCDM-34 was stable in human liver microsomal fraction. Furthermore, anti-HBV activity in human hepatocyte-chimeric mice revealed that iCDM-34 was not effective as a single agent, but when combined with ETV, it suppressed HBV DNA and cccDNA compared to ETV alone. Phosphoproteome analysis showed no activation of IFN signaling with iCDM-34 treatment. Transcriptome analysis of interferon-stimulated genes (ISGs) revealed no increase in the expression, while downstream factors of aryl hydrocarbon receptor (AhR) showed increased expression.  Conclusion: iCDM-34 is a novel anti-HBV drug that induces AhR activation and suppresses cccDNA.
Conclusion: iCDM-34 is a novel anti-HBV drug that induces AhR activation and suppresses cccDNA.

overall_design: Overall, 12 samples were analyzed. PXB cells cultured in 24-well plates were infected with 3 genome equivalents per cell of HBV C_AT. After 24 days of infection, the cells were treated with DMSO, 0.3 and 30 microM iCDM-34 or 1000 IU/ml IFNalpha for 7 days (n=3).

first: Xian

last: Qin

first: Harukazu

last: Suzuki


title: scRNA-seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish

city: Shenzhen

first: Zhao

last: Shizheng

address: Shenzhen

department: LIFS

institute: Undefined

summary: In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells (ECs) of the dorsal aorta (DA) in zebrafish, we isolated single ECs from the DA roof and the floor respectively using the Tg(flk1:eGFP;flk1:NLS-Eos) zebrafish after photoconversion, and then performed scRNA sequencing. These single ECs were isolated at two different time points, 21 hpf and 28 hpf, when the lumen of the DA is established and the EHT begins , respectively.

overall_design: Spatial photoconversion (DA roof versus DA floor), cell dissociation and mannual picking of photoconverted ECs

first: Shizheng

last: Zhao

first: Shachuan

last: Feng

first: Ye

last: Tian

first: Zilong

last: Wen


title: H3K36 Me3 occupancy of Control and AMPK knockdown Hep3B cells

overall_design: Control and two AMPK knockdown clones in Hep3B were involved. Chromatin-immunoprecipitation was performed by H3K36 Me3 antibody. The sheared chromatin samples were subjected to high-throughput sequencing the unravel the H3K36 Me3 occupancy through whole genome of Control and AMPK knockdown cells

first: Zhen

last: Cai

first: Hui-kuan

last: Lin


title: Gene expression profiling of control and AMPK knockdown Hep3B cells

first: zhen

last: cai

overall_design: Control and two AMPK knockdown clones in Hep3B were involved and triplicate RNA samples obtained from each group were subjected to gene expression profiling analysis by array


title: Hepatic Transcriptome Profiling of A Multiethnic Cohort of Pediatric Non-Alcoholic Fatty Liver Disease Patients Reveals Novel Genes and Pathways Associated With Disease Stages

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Non-alcoholic Fatty Liver Disease (NAFLD) is the most common type of chronic liver disease in children. The mechanisms that drive NAFLD disease progression in this specific patient population remains poorly defined. In this study, we gathered liver biopsy samples from a multiethnic cohort (71% Hispanic) of pediatric NAFLD patients (n=52, mean age=13.6 years) plus healthy liver controls (n=5). We analyzed transcriptomic changes associated with NAFLD disease progression using high-throughput RNA-sequencing. Unsupervised clustering as well as pairwise transcriptome comparison distinguished NAFLD from healthy livers. We identified perturbations in calcium and insulin/glucose signaling occurring early in NAFLD disease, prior to the presence of histopathologic evidence of advanced disease. Transcriptomic comparisons between low and advanced fibrosis identified a 25-gene signature associated with pediatric fibrotic liver progression. We also identified expression of the IGFBP gene family (1/2/3/7) as correlating with disease progression and it has the potential to be used as a peripheral biomarker in NAFLD. Comparing our dataset with publicly available adult transcriptomic data, we identified similarities and differences in pathway enrichment and gene expression profiles between adult and pediatric NAFLD patients. Regulation of genes including IL32, IGFBP1, IGFBP2, IGFBP7 was consistently found in both NAFLD populations, while IGFBP3 was specific to pediatric NAFLD. Conclusions: This paper expands our knowledge on the molecular mechanisms driving NAFLD and fibrosis in the pediatric population and aids future biomarker and therapeutics discovery.

first: Kangning

last: Yao

first: Elena

last: Tarabra

first: Daniela

last: Sia

first: Raffaella

last: Morotti

first: Rima

last: Fawaz

first: Nicola

last: Santoro

first: Sonia

last: Caprio

first: Silvia

first: Dean

last: Yimlamai


title: Human placental tissues:control group vs non-diabetic fetal macrosomia (NDFMS) group

city: Nanjing

first: Shanshan

last: Yang

address: 101 Longmian Avenue

department: Institute of Toxicology

institute: Nanjing Medical University

summary:
To investigate whether aberrant lncRNA expression in the placenta is involved in the pathogenesis of NDFMS and to elucidate its biological mechanisms.
The expression profile of lncRNAs in the placentas of pregnant women with NDFMS was investigated using an Agilent Human LncRNA Microarray. Differentially expressed lncRNAs were selected for validation using reverse transcription-quantitative polymerase chain reaction (RT-qPCR).

overall_design: eight samples from the NDFMS group and eight samples from the control group were prepared into two merged RNA samples, one per each group, for microarray screening. RNA labeling and microarray hybridization were performed

first: Yiwen

last: Lu

first: Dan

last: Guo


title: RNA-Seq on Eca109 and KYSE450 cell lines with DMSO and Elaiophylin treatment

city: Wuhan

first: Gao

last: Lijuan

address: Luojiashan

institute: Wuhan University

summary: Esophageal cancer remains a dominating cause of cancer-associated death and has shown a sharp increase of more than 6-fold increase rates all over the world. It is divided into two main pathological types: esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). Though the treatment has been improved a lot, the prognosis is still very poor with overall survival rate at 5 year was 15%-25%. Elaiophylin is a novel autophagy inhibitor at the late stage, which is a C2 symmetric macrolides separated from Streptomyces niger. However, the function of it in esophageal cancer was never explored. EIF4B is an important component of eukaryotic transcription initiation complex, which can be recruited to the 5’ untranslated region (5’UTR) of the mRNA. In recent years, eIF4B was suggested to play an important role in the progression of a various cancer cells. In the study we presented here, we firstly confirmed that the Elaiophylin was a novel autophagy inhibitor in ESCC cells. Moreover, Elaiophylin can inhibit the proliferation and migration of ESCCs, and promotes apoptosis. Then, we using RNA-seq to identify the genes which were regulated by Elaiophylin and verify them by RT-qPCR assay. Finally, we found the activity of PI3K/AKT pathway was inhibited by Elaiophylin. And the mRNA and protein expression level of eIF4B was both downregulated by Elaiophylin. In order to further confirm whether eIF4B is a target of Elaiophylin, we transfected a EIF4B-OE plasmid to ESCC cells, and found that the eIF4B overexpression could block the effect which was resulted from Elaiophylin. And by transfecting a shRNA to ESCC cells, we found that knockdown of eIF4B could inhibit the proliferation and migration of ESCC cells and promotes apoptosis when compared with the control group. All the results suggest that Elaiophylin could inhibit the proliferation, invasion of ESCC cells and promote its apoptosis by targeting the eIF4B via PI3K/AKT signaling pathway. This result identified that the Elaiophylin might serve as a promising therapeutic medicine for esophageal cancer.

overall_design: Eca109 and KYSE450 cell line mRNA profiles of DMSO and Elaiophylin were generated by deep sequencing, in double, using Illumina NovaSeq 6000.

first: Lijuan

last: Gao

first: Bin

last: Li

first: Yongshun

last: Chen


title: Transcriptomics study of excess Mn (1000 uM) in Chlamydomonas reinhardtii

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

summary: Liquid cultures of the unicellular green alga, Chlamydomonas reinhardtii were grown in media with 6 uM Mn (control) or 1000 uM Mn (experimental), and analyzed by RNA-Seq to identify genes that are differentially expressed in response to excess Mn.

overall_design: Six flasks containing Tris-Acetate-Phosphorus (TAP) medium were innoculated with C. reinhardtii from a starter culture. Three of the flasks contained 6 uM Mn and three flasks contained 1000 uM Mn. These were grown on a shaker platform under continuous light until they reached a cell density of 3x10^6 cells/mL (mid-log). Total RNA was purified from each culture and subjected to RNA-Seq analysis on the Illumina HiSeq2000 platform.

first: Munkhtsetseg

last: Tsednee

first: Madeli

last: Castruita

first: Sabeeha

last: Merchant


title: Small-RNA sequencing of WUS-induced RNA degradation in Arabidopsis thaliana

city: Hefei

first: Zhong

last: Zhao

state: Anhui

address: Huangshan Road 443

department: School of Life Sciences

institute: University of Science and Technology of China

summary: WUS is the key regulator in stem cell induction and maintenance. We performed the small RNA high throughput sequencing to test whether WUS is involved in stabilizing RNA structure in Arabidopsis thaliana.

overall_design: For analyzing the degradation of RNA induced by WUS, the pUBI10:mCherry-GR-linker-WUS plants sprayed with or without DEX (15μM) for 2 days, and then total RNA were isolated from the shoot apexes. 18-60 nt small RNA were selected for library building.Two biological replicates were used for small RNA library preparation. To annotate reads of small RNA from Arabidopsis, we first map clean reads to the Arabidopsis genome.

first: Haijun

last: Wu

first: Zhicheng

last: Dong


title: RNA-Seq of DU145 cell line upon knockdown of  YAP, TAZ, or YAP/TAZ

status: Public on Mar 24 2022

city: New York

first: Yu

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: Transcriptome analysis of prostate cancer patient derived organoid DU145 cell line upon knockdown of YAP, TAZ, or YAP/TAZ mediated by siRNAs

overall_design: Transcriptome analysis was performed in DU145 cell line treated with siYAP, siTAZ, or siYAP/TAZ for 48 hours

first: Ekta

last: Khurana

first: Chen

middle: K

last: Wong

first: Duo

last: Xu


title: Arid1a loss potentiates pancreatic beta-cell regeneration through activation of EGF signaling

city: Dallas

first: Hao

last: Zhu

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Cetern


title: Isoform-specific functions of PPARg in gene regulation and adipose metabolism

city: Philadelphia

first: Chunjie

last: Jiang

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

summary: Peroxisome proliferator-activated receptor g (PPARg) is a nuclear receptor that is a vital regulator of adipogenesis, insulin sensitivity, and lipid metabolism. Activation of PPARg by antidiabetic thiazolidinediones (TZD) reverses insulin resistance but also leads to weight gain that limits the use of these drugs. There are two main PPARg isoforms, but the specific functions of each are not established. Here we generated mouse lines in which endogenous PPARg1 and PPARg2 were epitope-tagged to interrogate isoform-specific genomic binding, and mice deficient in either PPARg1 or PPARg2 to assess isoform-specific gene regulation. Strikingly, although PPARg1 and PPARg2 contain identical DNA binding domains, we uncovered isoform-specific genomic binding sites in addition to shared sites. Moreover, PPARg1 and PPARg2 regulated different set of genes in adipose tissue depots, suggesting distinct roles in adipocyte biology. Indeed, mice with selective deficiency of PPARg1 maintained body temperature better than wild type or PPARg2-deficient mice. Most remarkably, although TZD treatment improved glucose toleranceinsulin resistance in mice lacking either PPARg1 or PPARg2, the PPARg1-deficient mice were protected from TZD-induced body weight gain compared to PPARg2-deficient mice. Thus, PPARg isoforms have specific and separable metabolic functions that may be targeted to improve therapy for insulin resistance and diabetes.

overall_design: Adipose tissues were collected from 3HA-PPARg1, HHA-PPARg2, PPARg1 KO, PPARg2 KO and their littermate control mice

first: Wenxiang

last: Hu


title: The miRNAs in plasma exosomes may serve as markers for segmental vitiligo

first: Dong

state: Hubei

address: No.1095 Jie Fang Avenue

institute: Tongji Hospital, Tongji Medical College,Huazhong University of Science and Technology

summary: More and more studies have showed that plasma exosomal miRNAs are biomarkers for disease. The aim of the study were to investigate the miRNA profiling in plasma exosomes of patients with segmental vitiligo (SV) and to find biomarkers in plasma exosomes for patients with SV. Plasma exosomes and exosomal RNA of 7 SV patients and 8 health persons were purified by exoRNeasy Serum/Plasma Maxi Kit. The miRNA profiles of the 15 samples were sequenced using HiSeq 2500 (Illumina) and analyzed by Reads Per Million (RPM) values and edgeR algorithm. Some differently expressed miRNAs in plasma exosomes and skin tissues of the two sets were validated by qRT–PCR.A total of 85 miRNAs in plasma exosomes showed differential expression between SV patients and health persons, with a |log2（Fold Change）|≥1 and P-value < 0.05. Several miRNAs were confirmed by qRT–PCR and showed similar expression patterns between plasma exosomes and skin tissues. Our study depict the miRNAs expression profiles in plasma exosomes of SV patients and suggest that several miRNAs in plasma exosomes may serve as biomarkers for SV.

overall_design: To investigate the miRNA profiling in plasma exosomes of patients with segmental vitiligo (SV) and health persons and to find biomarkers in plasma exosomes for SV.

first: Yunhua

last: Deng


title: L1 chimeric transcripts are expressed in healthy brain and their deregulation in glioma follows that of their host locus.

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

institute: GReD CNRS

summary:
Background:
Besides the consequences of retrotransposition, long interspersed element 1 (L1) retrotransposons can affect the host genome though their antisense promoter. In addition to the sense promoter, the evolutionarily recent L1 retrotransposons, which are present in several thousand copies, also possess an anti-sense promoter that can produce L1 chimeric transcripts (LCT) composed of the L1 5’ UTR followed by the adjacent genomic sequence. The full extent to which LCT expression occurs in a given tissue and whether disruption of the defense mechanisms that normally control L1 retrotransposons affect their expression and function in cancer cells, remain to be established.

Results:
By using CLIFinder, a dedicated bioinformatics tool, we found that LCT expression was widespread in normal brain and aggressive glioma samples, and that approximately 17% of recent L1 retrotransposons, from the L1PA1 to L1PA7 subfamilies, were involved in their production. Importantly, the transcriptional activities of the L1 antisense promoters and of their host loci were coupled. Accordingly, we detected LCT-producing L1 retrotransposons mainly in transcriptionally active genes and genomic loci. Moreover, changes in the host genomic locus expression level in glioma was associated with a similar change in LCT expression level, regardless of the L1 promoter methylation status.

Conclusions:
Our findings support a model in which the host genomic locus transcriptional activity is the main driving force of LCT expression. We hypothesize that this model is more applicable when host gene and LCT are transcribed from the same strand.

overall_design: RNA-seq of GSC2 NS

first: Franck

last: Court

first: Elisa

last: Le Boiteux

first: Pierre

middle: O

last: Guichet

first: Philippe

last: Arnaud


title: Longer read lengths are required for RNA velocity analysis of single-cell RNA-sequencing with paired immune repertoire and transcriptome profiling

city: Los Angeles

first: Kenneth

middle: Howard

last: Gouin III

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: Increasing numbers of studies utilize single cell sequencing (scSeq) technologies that are capable of simultaneously profiling T/B-cell receptor (TCR/BCR) sequences and RNA expression. Here we show that standard sequencing of commonly-used 5’-biased scSeq chemistry precludes the ability to perform RNA velocity analysis; however extended sequencing lengths that allow for paired-end genome alignment alleviates these issues. This study provides important practical implications for paired TCR/BCR and RNA scSeq experiments.

overall_design: Single-cell RNA-sequencing of untreated human triple negative breast cancer samples (n = 5 patients) enriched for CD45+ cells.

middle: H

first: Stephen

last: Shiao

first: Simon

middle: R

last: Knott


title: The licorice metabolite enoxolone attenuates Clostridioides difficile pathophysiology by corrupting its metabolic and toxin production networks

city: Memphis

first: Richard

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

summary: Toxins TcdA and TcdB are the main virulence factors of Clostridioides difficile, a leading cause of hospital-acquired diarrhea. We investigated the therapeutic potential of inhibiting the biosynthesis of TcdA and TcdB. Accordingly, screening of structurally diverse phytochemicals with medicinal properties identified 18b-glycyrrhetinic acid (enoxolone) as an inhibitor of TcdA and TcdB biosynthesis. Enoxolone also inhibited sporulation. In a CDI colitis model, enoxolone when combined with vancomycin protected mice from becoming moribund and the combination was more effective than vancomycin alone, a standard of care antibiotic for CDI. While enoxolone alone reduced the in vivo load of toxins, the monotherapy did not protect mice from CDI. Affinity based proteomics identified ATP synthase subunit alpha (AtpA) and adenine deaminase (Ade) as possible molecular targets for enoxolone. Silencing of mRNA for Ade and AtpA also reduced toxin biosynthesis, while molecular interaction analysis showed that enoxolone directly bound to Ade. Ade converts adenine to hypoxanthine as an early step in the purine salvage pathway. Metabolomics revealed enoxolone caused cells to accumulate adenosine and deplete hypoxanthine and ATP. Accordingly, supplementation with hypoxanthine partly restored toxin production. Enoxolone also impacted phosphate metabolism by reducing the amounts of cellular phosphate. Thus, supplementation with triethyl phosphate as a source of phosphate also partly restored toxin production. When hypoxanthine and triethyl phosphate were combined, toxin production was fully restored in the presence of enoxolone. Taken together, studies with enoxolone revealed metabolic pathways that affect C. difficile toxin production and could represent potential anti-virulence drug targets.

overall_design: mRNA profiles of C. difficile R20291 upon exposure to enoxolone (16 µM) or DMSO for 30 minutes.

first: Julian

last: Hurdle

first: Ravi

last: Marreddy

middle: E

first: Gregory

last: Phelps


title: Integrated multi-omics reveals putative biomarkers of bacterial-fungal co-infections

city: Vienna

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

country: Austria

institute: Max Perutz Labs

summary: Transcriptomic analysis of Aspergillus fumigatus and Klebsiella pneumoniae grown as single and mixed biofilms.

sample_organism:
Klebsiella pneumoniae
Aspergillus fumigatus

overall_design: RNA Sequencing was performed of Aspergillus fumigatus and Klebsiella pneumoniae grown as single and mixed biofilms for 24 hours at 37 °C in YPD medium. For mixed biofilms, Aspergillus fumigatus was pre-cultured for 12 hours to allow germination prior addition of Klebsiella pneumoniae.  Cultures were harvested and three biological replicates were subjected for RNA isolation and sequencing library preparation.

first: Filomena

last: Nogueira

first: Karl

last: Kuchler

first: Thomas

last: Lion


title: Chicory: cutting the effects and the effectors for a functional food

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

institute: University of Lille

summary: Whole chicory flour (Chic) and three compounds of chicory roots: fructose (Fru), chlorogenic acids (CGA) and sesquiterpene lactones (STL) were separately analyzed for their health effects in mice. A whole transcriptomic analysis was conducted using Agilent DNA microarrays to investigate their nutrigenomic effects.

overall_design: Mice were fed with an aqueous decoction of the roots flour, with fructose, chlorogenic acids and sesquiterpene lactones solutions. The mice gavages consisted in a daily force-feeding of 500 µl of stemming solution decoctions of Chic, Fru, CGA or STL water solution besides the standard chow. As experiments were conducted for two different periods of time, two control sets were used: first control group (Ctr1) in parallel with chicory and fructose and a second control group (Ctr2) in parallel with CGA and STL. Three mice for each condition were sacrificed, 2 mice for Ctr1 and 2 mice for Ctr2. The central core of the liver left lobe was cut into cubes, a short segment (1 cm) of colon was also cut and enterocytes were harvested from upper ileal segments by mucosa scraping method. All these tissues were immediately frozen on liquid azote and stored as individual samples at -80°C for transcriptomics.

first: Céline

last: Pouille


title: Megakaryocyte derived immunoregulatory cells regulate host-defense immunity against bacterial pathogens

city: Guangzhou

first: Jiayi

last: Xie

state: Guangdong

address: North Campus, Sun Yat-sen University

institute: Sun Yat-sen University

summary: Here, using single-cell sequencing we identified an MK derived immunoregulatory cell population, which plays an important role in host-protective responses against bacteria. In contrast to platelet-generating MKs, MK derived immunoregulatory cells highly express immune response genes and chemokines.

overall_design: Single-cell RNA-seq on bone marrow megakaryocytes

first: Meng

last: Zhao

first: Jin

last: Wang

first: Daosong

first: Xue

last: Han


title: ZNF521 enhances MLL-AF9-dependent hematopoietic stem cell transformation in acute myeloid leukemias by altering the gene expression landscape

city: Milan

first: Antonino

last: Neri

state: Milan

address: Via Francesco Sforza, 35

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

summary:
Leukemias derived from the MLL-AF9 rearrangement rely on deranged transcriptional networks. ZNF521, a transcription co-factor implicated in the control of hematopoiesis, has been proposed to sustain leukemic transformation in collaboration with other oncogenes.  We demonstrate here that ZNF521 mRNA levels correlate with specific genetic aberrations: in particular, the highest expression is observed in AMLs bearing MLL rearrangements, while the lowest is detected in AMLs with FLT3-ITD, NPM1 or CEBPα double mutations. In cord blood-derived CD34+ cells, enforced expression of ZNF521 provides a significant proliferative advantage, and acts synergistically when co-expressed with MLL-AF9 throughout the proliferation and expansion of leukemic progenitor cells.
Transcriptome analysis of primary CD34+ cultures displayed subsets of genes upregulated by MLL-AF9 or ZNF521 single transgene overexpression as well as in MLL-AF9/ZNF521 combinations, either at early or late time points of an in vitro model of leukemogenesis. Silencing of ZNF521 in MLL-AF9+ THP-1 cell line coherently results in an impairment of growth and clonogenicity, recapitulating effects observed in primary cells. Taken together, these results underscore a role for ZNF521 in sustaining self-renewal of the AML immature compartment, most likely through the perturbation of the gene expression landscape which ultimately favors the expansion of MLL-AF9 transformed leukemic clones.

overall_design: Cord blood (CB)-CD34+ cells were trasformed by lentiviral vectors expressing the MLL/AF9 fusion gene (UMG-LV6-MA9) alone or in combination with ZNF521 (UMG-LV6-ZNF521).Global transcript expression profiles of ZNF521, MA9 single transduction conditions were investigated in comparison to control cells at 23 days, whereas ZNF521-MA9 double transduced cells were analyzed both at the 23 and 58 day time points. Duplicate samples were analyzed for each condition.

first: Emanuela

last: Chiarella

first: Annamaria

last: Aloisio

first: Stefania

last: Scicchitano

first: Katia

last: Todoerti

middle: G

last: Cosentino

first: Daniela

last: Lico

first: Nicola

last: Amodio

first: Giovanni

last: Morrone

first: Heather

last: Bond

first: Maria

last: Mesuraca


title: Treatment of a human lymphoblastoid cell line with the iron chelator deferoxamine

status: Public on Mar 23 2022

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St, Box G

department: Molecular Biology, Cell Biology and Biochemistry

institute: Brown University

summary: We treated lymphoblast cells with the iron chelator deferoxamine (DFO) for 60 hours to determine if iron chelation would affect the levels of intron lariats.

overall_design: Duplicate samples of treated and control cells

first: John

middle: D

last: Phillips

first: Allison

last: Taggart

first: Luke

last: Buerer


title: TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana

city: Heidelberg

first: Alexis

last: Maizel

address: Im Neuenheimer Feld 230

department: Center for Organismal Studies

institute: Heidelberg University

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

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199202
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199203

overall_design: Refer to individual Series


title: Venetoclax cooperates with ionizing radiation to attenuate Diffuse Midline Glioma tumor growth

city: Aurora

first: Bridget

last: Sanford

state: CO

department: Pediatrics

institute: University of Colorado

summary: This article highlights the radiation induced cytotoxic effect of the BCL2 inhibitor, venetoclax, in diffuse midline gliomas (DMG). 1. RNA-seq: We performed bulk RNA sequencing of DMG cells exposed to 6Gy radiation and found the genes upregulated after radiation compared to unirradiated controls. 2. DNA Repair shRNA screen: We also performed a DNA Repair shRNA screen and identified the genes which are responsible for radioresistance in DMG.

overall_design: 1. RNA-seq samples were obtained from SF8628 DIPG cells radiated at 6Gy and unirradiated controls. 2. DNA Repair shRNA samples obtained from SF8628 cells transduced with DNA Repair shRNA pool and then either radiated at 6Gy or not radiated. Genomic DNA was collected at Day 21 after radiation.

first: Ilango

last: Balakrishnan

first: Rajeev

last: Vibhakar

first: Sujatha

last: Venkataraman