title: Transcriptome in rat kidneys exposed to a fetal low-protein diet on postnatal days 5, 10, and 28

city: Tokyo

first: Xuguang

last: Li

address: 1-1-1 Yayoi, Bunkyo-ku

institute: Tokyo University

summary:
Early in fetal development, maternal nutritional environments are expected to induce changes in epigenetic regulation in offspring.In the present study, we integrated methylome and transcriptome data to identify potential salt-sensitive hypertension genes using the kidneys of pups exposed to a low-protein diet throughout their fetal life. We aimed to uncover how specific candidate marker genes are modified over time and under different nutritional interventions at an early age.
Using the kidneys of pups exposed to a low-protein diet (LP) compared to those exposed to a control diet (CN) during fetal life, we searched for candidate genes by integrating data from both methylome and transcriptome profiling.Transcriptome analyses were used to identify genes with differential expression.

overall_design: Offspring exposed to a low-protein diet during fetal life were selected at postnatal days 5, 10, and 28 for RNA extraction and hybridization on Affymetrix microarrays.

first: Huijuan

last: Jia

first: Moe

last: Miyoshi

first: Kyohei

last: Furukawa

first: Lila

last: Otani

first: Katsuhiko

last: Shirahige

first: Fumihito

last: Miura

first: Takashi

last: Ito

first: Hisanori

last: Kato


title: Transcriptional profiling by 3' digital gene expression of huCD45+CD34+ HSPCs isolated from the bone marrow of humanized NSG mice

status: Public on Oct 04 2023

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

type: Expression profiling by high throughput sequencing

summary: This study aims to establish the gene signatures of the indicated cell fractions and follow their time-depedent variations

overall_design:
The indicated huCD45+CD34+ HSPC subsets were sorted from the BM of  NSG mice between weeks 1-5 after grafting with cord blood CD34+ HSCs
***Raw data will be submitted to EGA***

first: Bruno

last: Canque

first: Kutaiba

last: Alhaj Hussen

first: Aurélie

last: Lardenois


title: Single-cell transcriptional profiling of human CD45+CD34+ HSPCs isolated from the bone marrow of humanized NSG mice

summary: This study aims at establishing a map a clonal resolution of primary hematopoietic diversification in humans

overall_design:
The indicated huCD45+CD34+ HSPC subsets were sorted from the BM of  NSG mice at week-3 after grafting with cord blood CD34+ HSCs

**Raw data will be submitted to EGA**


title: Alteration and Reprogramming of Renal Ptger1 DNA Methylation Induced by Maternal Protein Restriction in SHRSP Offspring

country: Japan

type: Methylation profiling by high throughput sequencing

summary: Nutrient imbalances during gestation are a risk factor for hypertension in offspring. In this study, we found that, in spontaneously hypertensive stroke-prone (SHRSP) rats, maternal protein restriction during gestation modulates the DNA methylation status and significantly upregulates the expression of renal prostaglandin E receptor 1 (Ptger1), which is associated with hypertension in offspring. Renal Ptger1 DNA methylation is characterized by hypermethylation of CpG islands within the gene and a tendency toward hypomethylation in promoter regions. Furthermore, we observed that changes in fetal Ptger1 DNA methylation status after birth were preserved and enhanced, strongly supporting the stable conservation of this epigenetic marker. However, post-weaning low- or high-protein diets ameliorated Ptger1 DNA hypermethylation caused by fetal malnutrition, indicating postnatal nutritional environment interventions can alter and reprogram epigenetic modifications. These findings provide new insights into hypertension prevention and prospective therapeutic strategies.

overall_design: Kidneys of offspring exposed to a low-protein diet during fetal life were selected at postnatal day 28 for DNA extraction and  bisulfite sequencing. we searched for candidate genes by integrating data from both methylome and transcriptome profiling.


title: The RIP-seq  of SiHa and KOYTHDF3 cells

status: Public on Oct 09 2023

city: Shenzhen

first: sheng

last: zhong

address: The Xinhu Road 1333

country: China

institute: The Sourthern Medical University

summary: We  find different genes that bind to the YTHDF3 by comparing the wild type SiHa with knockout YTHDF3 SiHa

overall_design: We then performed gene expression profiling analysis using data obtained from the RIP-seq of 2 different cells.

first: Sheng

last: Zhong

first: Xiaona

last: Chen


title: Hyperactive PI3K-delta in Th1 and Th2 differentiation

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

country: USA

institute: NIAID

summary: We are examining the consequences of activating mutations in PI3K-delta in Th1 vs. Th2 differentiation. Using the house dust mite (HDM) model of allergic airway inflammation, which drives potent Th2 responses in vivo, we have found mice expressing hyper-activated PI3K-delta show impaired Th2 differentiation and instead favor Th1 cell differentiation. We would like to further investigate this aberrant CD4 differentiation profile using scRNA-seq to characterize PI3K-delta regulated aspects of type II immunity.

overall_design: PBMCs isolated from Mouse spleens in 4 samples. Each sample consists of cells from 3 mice, sequenced as one pool per sample. Comparisons made between WT & MT, & between Naïve & HDM.

first: Pamela

last: Schwartzberg

first: Dominic

last: Golec

first: Pedro

last: Gazzinelli Guimaraes

first: Thomas


title: Detection of the expression profiles of mRNA and miRNA between dermal papilla cells and hair matrix cells of yak hair follicle

city: lanzhou

first: zhang

last: xiaolan

address: Lanzhou Institute of Husbandry and Pharmaceutical Sciences

institute: Chinese Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Detection of the expression profiles of mRNA and miRNA between dermal papilla cells and hair matrix cells of yak hair follicle [RNA-seq]

summary: Dermal papilla cells (DPCs) and epidermal hair matrix cells (HMCs) located in hair bulb are the key cell types during the hair follicles (HFs) development. To explore the mRNA and miRNA expression of DPCs and HMCs of yak hair follicle, illustrating the mocular basis of the interaction and cellular communication between DPCs and HMCs during the hair follicle development, the DPCs and HMCs of yak were isolated and cultured, RNA-seq was used to identify the differentially expressed mRNAs and miRNAs between DPCs and HMCs.

overall_design: The dermal papilla cells (DPCs) and hair matrix cells (HMCs) from yak skin were isolated and cultured. Then a total of six samples, including three DPCs and three HMCs samples were used to RNA sequencing.

first: Xiaolan

last: Zhang

first: Pengjia

last: Bao

first: Qingbo

last: Zheng

first: Min

last: chu

first: Chunnian

last: Liang

first: Xian

last: Guo

first: Xiaoyun

last: Wu

first: Hemei

last: Lan

first: Chengfang

last: Pei

first: Ping

last: Yan


title: Detection of the expression profiles of mRNA and miRNA between dermal papilla cells and hair matrix cells of yak hair follicle [miRNA-seq]


title: Transcriptomic changes associated with specific Dhps deletion in intestinal epithelial cells

city: Nashville

first: Alain

middle: P

last: Gobert

address: 2215B Garland Ave

institute: VUMC

summary: RNA sequencing by Illumina NovaSeq6000 was performed from isolated epithelial cells from the colon of C57BL/6J Dhpsfl/fl and Dhpsfl/fl;Vil1cre/+ mice.

overall_design: There was three mice per group

first: Keith

middle: T

last: Wilson

first: Yvonne

middle: L

last: Latour


title: Clemastine suppresses proneural glioblastoma stem cell growth

city: durham

first: Yiping

last: He

state: NC

address: 199A MSRB1, Research Drive

department: Pathology

institute: Duke University

summary: Glioblastoma (GBM) cells’ stemness-like features and lineage plasticity promote tumor progression. Here, we demonstrate that Clemastine, a drug for treating hay fever and allergy symptoms, effectively attenuated the stemness and suppressed the propagation of primary GBM cultures bearing PDGFRA amplification. We show that these effects of GBM cells were accompanied by altered gene expression profiling indicative of a more differentiated state of tumor cells, in resonating with Clemastine’s activity in promoting the differentiation of normal oligodendrocyte progenitors (OPCs) into mature oligodendrocyte. Functional assays for proteins that can be pharmacologically targeted by Clemastine, including histamine receptors, muscarinic receptors, and Emopamil binding protein (EBP), revealed the essential roles of these proteins in sustaining GBM cell propagation and suggested that Clemastine likely impairs tumor cells via targeting multiple pathways. Finally, we showed that a PDGFB-driven mouse glioma model, representing the proneural subtype GBMs, was similarly susceptible to Clemastine treatment. Collectively, these results identify pathways that are essential for maintaining the proneural progenitor features of GBMs, and suggest that non-oncology, low toxicity drugs with OPC differentiation promoting effects, such as Clemastine, can be exploited for targeting GBM cell’s progenitor property.

overall_design: a mouse GBM cell line was treated with vehcle control or clemastine or cw3388

first: Rui

last: Yang

first: Michael

last: Sun


title: Clemastine suppresses proneural glioblastoma stem cell growth II

overall_design: two human primary GBM cell lines were treated with vehcle control or 4uM clemastine for 15 days


title: Epression Data from HUVEC and HUAEC

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

summary:
To assess if HUVEC and HUAEC differ in suscptibility to inflammation and inflammation resolution, the cells were stimulated for 24 hrs with TNF followed by RNA isolation. Two additional groups were first stimulated with TNF (24 hr) followed by TNF removal  (12 and 24 hrs). Expression profiles were compared to basal conditions, i.e. cells cultured in normal medium
We used micro-arrays to assess if Gene-xpression profiles between HUVEC and HUAEC differ under inflammatory conditions and under conditions of inflammation resolution

overall_design: Geneitcally identical HUVEC (n=3) and HUAEC (n=3) were isolated and cultured until Passage 2. The cells were treated as above and gene-expression profiles were assessed using the Affymetrix platform

first: Benito

last: Yard

last: De La Torre


title: Transcriptome analysis of untreated multiple myeloma cells and multiple myeloma cells treated with T6, F2, I3C and DIM

city: 南京

first: yang

last: shu

state: 江苏

address: xianlin road

institute: Nanjin university of Chinese medicin

summary: Transcriptome sequencing was used to analyze the changes of related signaling pathways and gene expression in multiple myeloma cells after the addition of T6, F2, I3C and DIM.

overall_design: Five cell types were examined

first: Shu

first: Mengjie


title: Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci [RNA-Seq]

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

institute: Goehte University Frankfurt

summary: The noncoding genome presents a largely untapped source of new biological insights, including thousands of long noncoding RNA (lncRNA) loci. While some produce bona fide functional transcripts, others exert transcript-independent regulatory effects, and the lack of predictive features renders mechanistic dissection a major challenge. Here, we describe MYNRL15: a noncoding regulatory locus on chromosome 15 and pan-myeloid leukemia dependency identified by a CRISPR screen of lncRNA signatures from hematopoietic stem and progenitor cells (HSPCs) and acute myeloid leukemia (AML) samples We demonstrate that the loss of cis-regulatory DNA elements in the locus, rather than its transcriptional products, drives its perturbation phenotype, triggering a global downregulation of oncogenic pathways, coordinated dysregulation of chromosome 15 neighborhoods, and formation of a tumor-suppressive, long-range chromatin interaction with the base of a distal loop. In addition, MYNRL15 perturbation selectively impaired primary AML blasts over normal HSPCs in vitro, and depleted patient-derived xenografts in vivo, providing evidence for oncogenic vulnerabilities at chromatin-regulating, noncoding loci. MYNRL15 is characterized by elevated CTCF binding, low expression, and short span - features shared by hundreds of lncRNA genes, nearly half of which associate with clinical aspects in AML patient cohorts. We propose these as a new class of functional genetic elements carrying both therapeutic potential for AML and profound implications for cancer pathophysiology in general, as exemplified by MYNRL15.

overall_design: Transcriptome profiling was performed in K562 and ML-2 cells at early and late timepoints post-MYNRL15 perturbation.

first: Michelle

last: Ng

first: Dirk

last: Heckl


title: Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci [capture-C]

summary: he noncoding genome presents a largely untapped source of new biological insights, including thousands of long noncoding RNA (lncRNA) loci. While some produce bona fide functional transcripts, others exert transcript-independent regulatory effects, and the lack of predictive features renders mechanistic dissection a major challenge. Here, we describe MYNRL15: a noncoding regulatory locus on chromosome 15 and pan-myeloid leukemia dependency identified by a CRISPR screen of lncRNA signatures from hematopoietic stem and progenitor cells (HSPCs) and acute myeloid leukemia (AML) samples We demonstrate that the loss of cis-regulatory DNA elements in the locus, rather than its transcriptional products, drives its perturbation phenotype, triggering a global downregulation of oncogenic pathways, coordinated dysregulation of chromosome 15 neighborhoods, and formation of a tumor-suppressive, long-range chromatin interaction with the base of a distal loop. In addition, MYNRL15 perturbation selectively impaired primary AML blasts over normal HSPCs in vitro, and depleted patient-derived xenografts in vivo, providing evidence for oncogenic vulnerabilities at chromatin-regulating, noncoding loci. MYNRL15 is characterized by elevated CTCF binding, low expression, and short span - features shared by hundreds of lncRNA genes, nearly half of which associate with clinical aspects in AML patient cohorts. We propose these as a new class of functional genetic elements carrying both therapeutic potential for AML and profound implications for cancer pathophysiology in general, as exemplified by MYNRL15.

overall_design: NG Capture-C combines 3C library preparation with oligonucleotide capture to enrich for interactions involving regions of interest. In this case, one of the two cis-regulatory elements in MYNRL15 (C1) was used as the viewpoint. This method was applied to K562 and ML-2 cells, with and without Cas9-mediated MYNRL15 perturbation, as well as to CD34+ HSPCs.


title: RNA sequencing of CD19-directed chimeric antigen receptor T (CART19) cells with and without TP-0903 treatment

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: TP-0903 was obtained from Tolero Pharmaceuticals. CART19 cells from five biological replicates were thawed and stimulated with irradiated Jeko-1 cells (120 Gy) for 5 days. Jeko-1 is a human mantle cell lymphoma cell line that expresses the CD19 antigen (ATCC). Each sample was treated with either 30 nM TP0903 (treated condition) or DMSO (untreated control). CART19 were isolated to a purity of 100% using CD19 microbeads (Miltenyi).  RNA was isolated from the CART19 using QIAGEN RNeasy Plus Mini Kit (Cat. No. 74134). RNA was further treated with DNase I and purified using Zymo Research RNA Clean & Concentrator (Cat. No. R1015).

overall_design: RNA sequencing was performed on CD19-directed chimeric antigen receptor T (CART19) cells with and without TP-0903 treatment using five biological replicates for each condition.

first: Reona

last: Sakemura

last: Cox


title: Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci

type: Genome binding/occupancy profiling by high throughput sequencing


title: Gene expression profile (RNAseq) of H9 shCTL, shZEB1 and shZEB2 at day 2 post-CHIR treatment

city: Barcelona

first: Antonio

last: Postigo

state: BARCELONA

address: Casanova 143. Cellex 1B

country: Spain

institute: IDIBAPS/ICREA

summary:
Purpose: Characterize the gene expression profile of knocked-down ZEB1 and ZEB2 H9 cells during myogenic differentiation through RNA sequencing
Methods: RNA sequencing of RNA from cell cultures treated for 2 days with CHIR from the three genotypes used in this study: H9shCTL, H9shZEB1 and H9shZEB2
Results: Knock-down of ZEB1 and ZEB2 in H9 cells results in differential gene expression upon differentiation.
Conclusions: Compairson of knocked-down ZEB1 and ZEB2 H9 cells display differences in gene expression at day 2 of the differentiation protocol.

overall_design: RNA sequencing of total RNA from H9 shCTL, H9 shZEB1 and H9 shZEB2 cells at day 2 of the differentiation protocol. One sample of each genotype from one independent differentiation experiment (3 experiments).

first: Laura

last: Siles

first: Chiara

last: Ninfali

first: Anna

last: Esteve-Codina


title: Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci [CUT&RUN]

overall_design: NG Capture-C combines 3C library preparation with oligonucleotide capture to enrich for interactions involving regions of interest. In this case, one of the two cis-regulatory elements in MYNRL15 (C1) was used as the viewpoint. This method was applied to K562 and ML-2 cells, with and without Cas9-mediated MYNRL15 perturbation, as well as to differentiated monocytic cells.


title: Effect of blocking A2aR in sepsis on the Treg transcriptome

status: Public on Oct 03 2023

city: tianjin

first: Teng

last: Zhang

address: nanjing road

institute: Tianjin Medical University General Hospital

summary: In our study, blocking A2aR with ZM241385 was found to inhibit Foxp3 expression in Treg cells of septic mice. Therefore, we used flow cytometry to sort mouse spleen CD4+CD25+ cells for transcriptome sequencing in an attempt to discover the mechanism by which blocking A2aR affects Foxp3 expression. The specific groupings were as follows: naive groups (N1-N5), CLP groups (C1-C5), CLP+A2aR antagonist groups (Z1-Z6).

overall_design: This part of the data consists of the following three sections: splenic Treg cells from normal mice, splenic Treg cells from mice with sepsis CLP model, and splenic Treg cells from mice with sepsis CLP model treated with ZM241385.The Treg cells were labeled with CD4+CD25+ antibody and sorted using flow cytometry.

first: Tao

last: Ma


title: CCG-1423-derived compounds reduce global RNA synthesis and inhibit transcriptional responses (PRO-seq)

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

summary: Myocardin-related transcription factors (MRTFs) are coactivators of serum response factor (SRF), and thereby regulate cytoskeletal gene expression in response to actin dynamics. MRTFs have also been implicated in heat shock protein (hsp) transcription in fly ovaries, but the mechanisms remain unclear. Here we demonstrate that in mammalian cells, MRTFs are dispensable for hsp gene induction. However, the widely used small molecule inhibitors of MRTF/SRF transcription pathway, derived from CCG-1423, efficiently inhibit hsp gene transcription in both fly and mammalian cells also in absence of MRTFs.  Quantifying RNA synthesis and RNA polymerase distribution demonstrates that CCG-1423-derived compounds have a genome-wide effect on transcription. Indeed, tracking nascent transcription at nucleotide resolution reveals that CCG-1423-derived compounds reduce RNA polymerase II elongation, and severely dampen the transcriptional response to heat shock. The effects of CCG-1423-derived compounds therefore extend beyond the MRTF/SRF pathway into nascent transcription, opening novel opportunities for their use in transcription research.

overall_design: 2 replicates of PRO-seq was performed in S2R+ cells. Drug treatment was done for allocated timepoints (10 mins with the inhibitors at NH condition) followed by heat shock for 20 mins in 37°C waterbath.

first: Anniina

last: Vihervaara

first: Bina

last: Prajapati


title: Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci [ATAC-Seq]


title: Role of ANT1 in pulmonary fibrosis

city: Pittsburgh

first: Corrine

last: Kliment

state: PA

address: 200 Lothrop street

institute: University of Pittsburgh

summary: Crispr KO of ANT1 in Beas2b cells versus control cells were treated with media or bleomycin

overall_design: Three biological replicates were analyzed for each of 4 conditions (two genotypes; two treatments per genotype - media versus bleomycin)

first: Justin

last: Sui


title: The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development [FAIRE-seq]

city: Chapel Hill

first: Matthew

last: Niederhuber

address: 250 Bell Tower Dr.

institute: UNC-Chapel Hill

summary: Chromatin remodeling is central to the dynamic changes in gene expression that drive cell fate determination. During development, the sets of enhancers that are accessible for use change globally as cells transition between stages. While transcription factors and nucleosome remodelers are known to work together to control enhancer accessibility, it is unclear how the short stretches of DNA that they individually unmask yield the kilobase-sized accessible regions characteristic of active enhancers. Here, we performed a genetic screen to investigate the role of nucleosome remodelers in control of dynamic enhancer activity. We find that the Drosophila SWI/SNF complex, BAP, is required for repression of a temporally dynamic enhancer, brdisc. Contrary to expectations, we find that the BAP-specific subunit Osa is dispensable for mediating changes in chromatin accessibility between early and late stages of wing development. Instead, we find that Osa is required to constrain the levels of brdisc activity when the enhancer is normally active. Genome-wide profiling reveals that Osa directly binds brdisc as well as thousands of other developmentally dynamic regulatory sites, including multiple genes encoding components and targets of the Notch signaling pathway. Transgenic reporter analyses demonstrate that Osa is required for activation and for constraint of different sets of target enhancers in the same cells. Moreover, Osa loss results in hyperactivation of the Notch ligand Delta and development of ectopic sensory structures patterned by Notch signaling early in development. Together, these findings indicate that proper constraint of enhancer activity is necessary for regulation of dose-dependent developmental events.

overall_design: anti-GFP CUT&RUN from third larval wandering wing discs in Osa-GFP and yw females

first: M

middle: J

last: Leatham-Jensen

first: D

last: McKay


title: Myeloid Cell Derived IL1b Contributes to Pulmonary Vascular Remodeling in Heart Failure with Preserved Ejection Fraction

first: Vineet

last: Agrawal

address: 1310 24th Ave South

institute: Veterans Affairs Hospital in Nashville, TN

summary: Goals and objectives of this study were to determine on a single-cell level transcriptomic changes that occur in the lungs of a murine model of heart failure with preserved ejection fraction caused by administration of high fat diet and eNOS inhibitor L-NAME.

overall_design: Four C57/BL6 mice each were given either a combination of high fat diet and L-NAME or control (low fat diet with no L-NAME) for 5 weeks. Lungs were isolated after sacrifice, enzymatically digested, separately labeled with hashing antibodies, and submitted for single cell RNA sequencing.

first: Jonathan

last: Kropski

first: James

last: West


title: Cerebrospinal fluid immune cells appear similar across neuropathic and non-neuropathic pain conditions.

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

country: United Kingdom

institute: King's College London

summary: Microglia have been implicated in the pathophysiology of neuropathic pain. Here, we sought to investigate whether cerebrospinal fluid (CSF) might be used as a proxy-measure of microglial activation in human participants. For this, we preformed fluorescent-activated cell sorting (FACS) of CSF immune cell populations derived from individuals who experienced pain with neuropathic features. We sorted CD4+, CD8+ T cells and monocytes and analyzed their transcriptome using RNA sequencing. We also performed Cellular Indexing of Transcriptomes and Epitopes (CITE)-seq to characterize the expression of all CSF immune cells in a patient with postherpetic neuralgia and in a patient with neuropathic pain after failed back surgery.   Immune cell numbers and phenotypes were not obviously different between individuals regardless of the etiology of their pain. This was true when examining our own dataset, as well as when comparing it to previously published single-cell RNA sequencing data of human CSF. In all instances, CSF monocytes showed expression of myeloid cell markers commonly associated with microglia (P2RY12, TMEM119 and OLFML3), which will make it difficult to ascertain the origin of CSF proteins: do they derive directly from circulating CSF monocytes or could some originate in spinal cord microglia in the parenchyma? We conclude that it will not be straightforward to use CSF as a biomarker for microglial function in humans.

overall_design: Human CSF immune cell populations were sorted via FACS and either processed using bulk RNA sequencing of sorted populations or at single cell level using CITE-seq.


title: Household laundry detergents disrupt barrier integrity and induce inflammation in mouse and human skin

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary:
To investigate the effect of household detergents on the mouse skin barrier, we treated mouse's back skin with two household detergents (A and B) and collected the treated skin 24 hours after the application. We then performed gene expression profiling analysis using data obtained from RNA-seq of mouse skin treated with detergent A, detergent B, and PBS.
We performed gene expression profiling analysis using data obtained from RNA-seq of the skin biopsy at 24 hours after the application.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for detergent A treated skin and detergent B treated skin compared with PBS treated skin.


title: Epigenome-Wide DNA Methylation Profiling in Comparison between Pathological and Physiological Hypertrophy of Human Cardiomyocytes

first: Hangchuan

last: Shi

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

type: Methylation profiling by genome tiling array

summary: Physiological and pathological stimuli result in distinct anatomic forms of cardiac hypertrophy, but the head-to-head comparison of molecular regulation between physiological and pathological cardiac hypertrophy is less well understood, especially at the DNA methylation level. We conducted an in vitro study using human cardiomyocyte cell line AC16 exposed to angiotensin II (AngII) and insulin-like growth factor 1 (IGF-1) to mimic pathologically and physiologically hypertrophic heart models, respectively. Whole genome DNA methylation patterns were profiled by the Infinium human MethylationEPIC platform with >850K DNA methylation loci. We detected 194 loci that are significantly differentially methylated after AngII treatment (vs control) with 50.0% hypermethylated, and 206 significant loci after IGF-1 treatment (vs control) with 45.1% hypermethylated (Adjusted P < 0.05). Mapping the significant loci to genes, we identified 158 genes corresponding to AngII treatment and 175 genes to IGF-1 treatment, with 67 genes overlapping between AngII and IGF-1.

overall_design: We conducted an in vitro study using human cardiomyocyte cell line AC16 exposed to angiotensin II (AngII) and insulin-like growth factor 1 (IGF-1) for 12h and 24h to mimic pathologically and physiologically hypertrophic heart models, respectively. Whole genome DNA methylation patterns were profiled by the Infinium human MethylationEPIC platform with >850K DNA methylation loci.

first: Si

last: Chen

first: Fanju

middle: M

last: Meng

first: Deborah

last: Ossip

first: Chen

last: Yan

first: Dongmei

last: Li


title: Green tea polyphenols alleviate liver injury induced by di(2-ethylhexyl) phthalate in mice

city: Guangzhou

first: Shengyun

last: Sun

state: Guangdong

address: 613 West Huangpu Avenue

institute: The First Affiliated Hospital of Jinan University

summary: Di (2-ethylhexyl) phthalate (DEHP) is a common plasticizer. Studies have revealed that DEHP exposure can cause liver damage. Green tea is one of the most popular beverages in China. Green tea polyphenols (GTPs) have been proven to have therapeutic effects on organ damage induced by heavy metal exposure. However, few study report on GTP relieving DEHP-induced liver damage.

overall_design: C57BL/6J mice were treated with distilled water (control group), 1500 mg/kg/d DEHP + corn oil (model group), 1500 mg/kg/d DEHP + corn oil + 70 mg/kg GTP (treatment group), corn oil (oil group), and 70 mg/kg GTP (GTP group) by gavage for 8 weeks, respectively. The hepatic tissues histopathology of each group were measured. The hepatic tissues of mice in the model, treatment, and control groups were analyzed using high-throughput sequencing.

first: Heng

first: Shiping

last: Zhu


title: An optimized protocol for isolation of hepatic leukocytes retrieved from murine and NASH liver biopsies

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim Pharma GmbH & Co KG

summary: Immune dysregulation and inflammation by hepatic-resident leukocytes is considered a key step in disease progression of Non-alcoholic fatty liver disease (NAFLD) and Nonalcoholic steatohepatitis (NASH) toward cirrhosis and hepatocellular carcinoma (HCC). Here we provide a robust protocol for isolation and characterization of liver-resident immune cells from fine needle biopsies of rodent model and human. Various downstream applications can then be applied to gain an appreciation of the functional activity of liver-resident leukocyte populations.

overall_design: Immune-cell FACS of liver needle biopsy tissue from mice using varying input cell numbers: 2,500 (n=3), 5,000 (n=3), 10,000 (n=3) and 20,000 (n=3) cells and bulk liver tissue as control (n=2)

first: Bahrami

last: Ehsan

first: Geiger

last: Tobias

first: Steixner-Kumar

last: Agnes A.

first: Santacruz

last: Diana

first: Violett

last: Coralie

first: Dick

last: Alec

first: Roth

last: Yvonne

first: Schlingeloff

last: Patrycja

first: Schmidberger

last: Julian

first: Haenle

last: Mark

first: Kratzer

last: Wolfgang

first: Kitt

last: Kerstin

first: Neubauer

last: Heike

first: Simon

last: Eric

first: Krenkel

last: Oliver

first: Werner

last: Markus


title: Associations between pre-diagnostic aspirin use and ovarian tumor gene expression

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary:
Aspirin use has been associated with reduced ovarian cancer risk. However, the underlying biological mechanisms are not fully understood
We examined the association between gene expression profiles in ovarian tumors and current low and regular dose aspirin use in the 1-2 years prior to diagnosis

overall_design: Ovarian cancer case-only analysis, comparing gene expression profiles by current vs. never low or regular dose aspirin use

first: Naoko

last: Sasamoto

first: Shelley

middle: S

last: Tworoger


title: Role of TET1-mediated epigenetic modulation in Alzheimer's disease

city: Atlanta

first: Matthew

last: Armstrong

state: Georgia

address: 615 Michael St

institute: Emory University

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

overall_design: Refer to individual Series


title: RNA sequencing of resident human colonic gd T cells bearing the Vg2/3/4 receptor stimulated with butyrophilin-like (BTNL) 3 and BTNL8

first: Philip

last: East

address: Midland Road

institute: The Francis Crick Institute

summary: Purpose: to characterise the steady state gene expression and transcriptomic characteristic of tissue residernt human colonic mucosal gd T cells from controls undergoing routine colonoscopy.

overall_design: Methods: 12 fresh pinch biopsies were obtained per patient from 4 control patients underoing screening colonoscopy and immediately dissociated using a Miltenyl tumour dissociation protocol. Cells were FACS sorted according to their surface phenotype Vg2/3/4 CD103+ or CD103neg. For the first 3 donors these were frozen and sent to Genewiz for RNA extrraction library preparation and sequencing on an Illumina HiSeq. For the final donor, RNA was purified immediately after the sort and libraries were prepared and sequenced on an Illumina HiSeq 2500 at the Francis Crick Institute in London.

first: Robin

last: Dart

first: Adrian

last: Hayday

first: Tim

last: Recaldin


title: Effect of  liver-specific ABL2 knockout on model of alcohol-induced steatohepatitis

city: Maywood

first: wei

last: Qiu

state: IL

department: Surgery

institute: Loyola University Chicago

summary: We evaluated the effect of  liver-specific ABL2 knockout on model of alcohol-induced steatohepatitis

overall_design: Using three mice per group, we treated ABL2 KO and WT mice with the NIAAA alcohol model

first: Wei

first: Greg

last: Malnassy

first: Claudia

middle: R

last: Keating


title: Knockdown of ABL2 in HepG2 cells with EtOH treatment

summary: Evaluation of the effect of ABL2 knockdown in HepG2 cells following treatment with alcohol

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at one time point.


title: Role of TET1-mediated epigenetic modulation in Alzheimer’s disease [RNA-Seq]

summary:
To investigate the influence the partial loss of Tet1 has on AD pathogenesis in 5xFAD mice, we crossed a Tet1 KO mouse line with the 5xFAD mouse line to generate WT, 5xFAD, Tet1(+/-), and FAD/Tet1(+/-) mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq from biological replicates of mice comprised of 4 different genotypes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT, 5xFAD, Tet1(+/-), FAD/Tet1(+/-) mice to determine how the partial loss of Tet1 influences 5xFAD-associated gene expression and pathology.


title: Role of TET1-mediated epigenetic modulation in Alzheimer’s disease [5hmC-Capture]

summary: To investigate the influence the partial loss of Tet1 has on AD pathogenesis in 5xFAD mice, we crossed a Tet1 KO mouse line with the 5xFAD mouse line to generate WT, 5xFAD, Tet1(+/-), and FAD/Tet1(+/-) mice.

overall_design: 5hmC capature was performed to characterize the relative abundance and genomic location of 5hmC modifications, and how the partial loss of Tet1 influences 5xFAD-associated 5hmC profile and pathology.


title: Epigenetic dynamics during capacitation of naïve human pluripotent stem cells [PBAT]

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

summary: Human pluripotent stem cells (hPSCs) are of fundamental relevance in regenerative medicine and the primary source for many novel cellular therapies. The development of naïve culture conditions has led to the expectation that these naïve hPSCs could overcome some of the limitations found in conventional (primed) hPSCs culture conditions, including recurrent epigenetic anomalies. Recent work has shown that transition to the primed state (or capacitation) is necessary for naïve hPSCs to acquire multi-lineage differentiation competence. This pluripotent state transition may recapitulate essential features of human peri-implantation development. Here we studied epigenetic changes during the transition between naïve and primed pluripotency, examining global genomic redistribution of histone modifications, chromatin accessibility, and DNA methylation, and correlating these with gene expression. We identify CpG islands, enhancers, and retrotransposons as hotspots of epigenetic dynamics between pluripotency states. Our results further reveal that hPSC resetting and subsequent capacitation rescue X chromosome-linked epigenetic erosion and reduce the ectoderm-biased gene expression of conventional primed hPSCs.

overall_design: 2 lines of human naïve pluripotent stem cells (embryo-derived HNES1 and chemically reset cR-H9-EOS) were cultured in N2B27 and 2uM XAV939 for 10 days. After that the cells were split into two conditions: N2B27 + 2uM XAV939 + 3ng/ml Activin A + 10ng/ml FGF2 (XAF), or E8 medium, for extended maintenance. The experiment was performed with the cells on day 0 and 10, when the cells were cultured in XAV939; and one time point after transfer to maintenance conditions, at not less than 22 days of culture from the start of the experiment. Conventional hPSC cell line H9-EOS, which was a parental line for the chemically reset cR-H9-EOS was used as a control.

first: João

last: Agostinho de Sousa

first: Maria

last: Rostovskaya

first: Chee-Wai

last: Wong

first: Wolf

last: Reik

first: Austin

last: Smith

first: Ferdinand

last: von Meyenn


title: Epigenetic dynamics during capacitation of naïve human pluripotent stem cells


title: Gene expression analysis of Vg4+ vs Vg5/8/9+ gd T cells isolated from human gut

address: Great Maze Pond

department: Immunobiology

institute: King's  College London

summary: The aim of this experiment was to characterize the the gene expression profile of colonic Vg4+ cells and to compare it to that of Vg5/8/9+ tissue-resident gd T cells.

overall_design: Colonic biopsies (11 per donor) from 4 donors with no intestinal pathologies were dissociated with Miltenyi Biotec's tumour dissociation kit and stained with anti-Vg4 and anti-Vg2/3/4 antibodies. Vg4+Vg2/3/4+ (termed Vg4+) and Vg4-Vg2/3/4- (termed Vg5/8/9+) cells were flow sorted directly into lysis buffer and mRNA was used for library preparation and pair-end (PE100) sequencing on on Illumina NextSeq 2000.

first: Iva

last: Zlatareva

first: Shichina

last: Kannambath


title: Whole genome bisulfite sequencing (WGBS) and RNA-sequencing of preadipocytes from iWAT

city: California

first: Sona

last: Kang

state: Berkeley

address: Morgan Hall 321

department: Nutritional Sciences & Toxicology

institute: University of California, Berkeley

summary: C57BL/6J male mice received a high-fat diet. DNA methylation profiles by WGBS of preadipocytes from iWAT of Tet3 f/f and Pdgfra-Tet3 KO mice. Expression profiling by RNA-sequencing of preadipocytes from iWAT of Tet3 f/f and Pdgfra-Tet3 KO mice.

overall_design: Preadipocytes were isolated from SVF of iWAT using flow cytometry. Genomic DNA was purified using Dneasy Blood & Tissue kit (cat# 69506) and RNA was purified using RNAqueous®-Micro Kit (Cat#. AM1931).

first: Byung

middle: C

last: Jung


title: Transcriptional Metabolic Reprograming Drives Meiotic Fate Decision in Mammalian Germ Cells

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary:
Nitrogen starvation drives meiosis in yeasts1, while retinoic acid (RA) is required for mammalian meiosis through the activation of its germline-specific target, stimulated by retinoic acid gene 8 (Stra8).Here, by using single-cell transcriptome analysis of wild-type and Stra8-deficient testes, our data revealed that the expression of major metabolic genes are downregulated during germ cell entry into meiosis.
Recently, we collected mouse testicular cells from wild-type and Stra8-deficient mice at postnatal day 12 (P12) and P21 for single cell RNA-sequencing (scRNA-seq). Upon scRNA-seq, we obtained a total of 23,470 cells from these samples. Using stringent quality control, 22,839 cells were selected for further analysis. All cells, including both wild-type and Stra8-deficient testicular cells, were pooled together to perform clustering analysis, which revealed 6 major cell clusters based on their distinct gene expression patterns. We annotated these six clusters by using known marker genes, including spermatogonia (SPG; Stra8; 3,941 cells), spermatocyte (SPC; Syce1; 4,924 cells), spermatid (STD; Acrv1; 710 cells), Sertoli cell (SC; Sox9; 9,488 cells), Myeloid (MYD; Acta2; 3,531 cells), and Leydig Cells (LY; Star; 245 cells). There is an increase in the percentage of spermatogonia in Stra8-deficient testes at both P12 (28% versus 14% in wild-type) and P21 (17% versus 10% in wild-type). At P21, while spermatocytes are abundant and spermatid are formed in wild-type testes, there are only a few spermatocytes (0.2% versus 73% in wild-type), and spermatids are absent in Stra8-deficient testes. Signature genes are enriched for GO terms for distinct biological function and metabolic pathways in different cell types.

overall_design: Single cell RNA sequencing of wild-type and  stra8 deficient mouse testis were generated by deep sequencing using the 10x Genomics Chromium Single Cell Gene Expression Solution

first: Ning

last: Wang

first: Xiaoyu

last: Zhang

first: Gunewardena

last: Sumedha

first: Yan

last: Liu


title: The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development [H3K27ac Cut & Run]

first: Matthew

last: Niederhuber

summary: Chromatin remodeling is central to the dynamic changes in gene expression that drive cell fate determination. During development, the sets of enhancers that are accessible for use change globally as cells transition between stages. While transcription factors and nucleosome remodelers are known to work together to control enhancer accessibility, it is unclear how the short stretches of DNA that they individually unmask yield the kilobase-sized accessible regions characteristic of active enhancers. Here, we performed a genetic screen to investigate the role of nucleosome remodelers in control of dynamic enhancer activity. We find that the Drosophila SWI/SNF complex, BAP, is required for repression of a temporally dynamic enhancer, brdisc. Contrary to expectations, we find that the BAP-specific subunit Osa is dispensable for mediating changes in chromatin accessibility between early and late stages of wing development. Instead, we find that Osa is required to constrain the levels of brdisc activity when the enhancer is normally active. Genome-wide profiling reveals that Osa directly binds brdisc as well as thousands of other developmentally dynamic regulatory sites, including multiple genes encoding components and targets of the Notch signaling pathway. Transgenic reporter analyses demonstrate that Osa is required for activation and for constraint of different sets of target enhancers in the same cells. Moreover, Osa loss results in hyperactivation of the Notch ligand Delta and development of ectopic sensory structures patterned by Notch signaling early in development. Together, these findings indicate that proper constraint of enhancer activity is necessary for regulation of dose-dependent developmental events.

overall_design: anti-H3K27ac CUT&RUN from third larval wandering wing discs in Osa-GFP and yw females

first: M

last: Leatham-Jensen

first: D

last: McKay


title: MiR-137 and GOMAFU form a novel non-coding RNA pathway to regulate human neuron differentiation and molecular networks affected in neuropsychiatric diseases

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

summary: Increasing evidence suggests important roles of long noncoding RNAs (lncRNAs) in normal neuron development and neuropsychiatric disorders that disturb early neurodevelopmental processes. One such lncRNA is GOMAFU, which displays aberrant expression in schizophrenia postmortem brains and is known to regulate SCZ-associated splice variants in developing human neurons. However, molecular mechanisms that control expression and biological function of GOMAFU in human neuron development remain elusive. Here we report the identification of a novel miRNA-lncRNA pathway in which miR-137, a well-recognized risk factor for SCZ and autism spectrum disorder (ASD) that play key roles in promoting neuronal differentiation, enhances GOMAFU expression in human neurons through targeting transcription factors that suppress GOMAFU. In addition, loss of GOMAFU in cortical neurons derived from human induced pluripotent stem cells (hiPSCs) by CRISPR-cas9 mediated gene editing significantly reduces dendritic growth during early-stage differentiation. Moreover, GOMAFU deficiency elicited a broad influence on molecular pathways commonly affected in SCZ and ASD postmortem brains, including aberrantly increased expression of numerous genes known to govern neuroimmune responses. Our studies demonstrated essential roles of the lncRNA GOMAFU in human neuron development and connected GOMAFU malfunction with pathological molecular networks in neuropsychiatric disorders.

overall_design: GOMAFU knockdown M17 cells compared with control M17 cells

first: Peng

last: Teng

first: Yangping

last: Li

first: Yue

last: Feng


title: ADAR1 utilizes independent mechanisms to suppress MDA5 and PKR activation by cellular double-stranded RNA

city: Stanford

first: Shibin

last: Hu

state: CA

address: 240 pasteur drive, 4300

department: Genetics

institute: Stanford University

summary: The antiviral defense in vertebrates requires the innate immune system to sense foreign “non-self” nucleic acids while avoiding “self” nucleic acids, which is accomplished by an intricate system. Cellular double-stranded RNAs (dsRNAs) are edited by the RNA editing enzyme ADAR1 to prevent their dsRNA structure pattern from being recognized as viral dsRNA. Lack of RNA editing by ADAR1 enables activation of MDA5, a cytosolic dsRNA sensor, by cellular dsRNA. Additional RNA editing- independent functions of ADAR1 have been proposed, but the specific mechanism remains elusive. Here we demonstrate that RNA binding by ADAR1, independent of its editing activity, restricts the activation of PKR, another cytosolic dsRNA sensor, by cellular dsRNA. Mechanistically, the loss of ADAR1 editing caused MDA5 activation to induce interferon signaling, while a lack of ADAR1 protein or its dsRNA binding ability led to PKR activation, with subsequent stress granule formation and proliferation arrest. Based on these findings we rescued the Adar1−/− mice from embryonic lethality to adulthood by deleting both MDA5 and PKR, in contrast to the limited rescue of Adar1−/− mice by removing MDA5 or PKR alone. Our findings reveal a multifaceted contribution of ADAR1 in regulating the immunogenicity of “self” dsRNAs. Furthermore, ADAR1 is an immuno-oncology target for drug development, and the separation of ADAR1’s RNA editing and binding functions provides mechanistic insights for such developments.

overall_design: In order to study the effect of ADAR1 deficiency in human cells, HEK293T or U937 cells were transfected or infected with Cas9 and sgRNAs to make ADAR1 knockout (ADAR1KO) or ADAR1 editing deficient (ADAR1E912A) single clones. In HEK293T, wild type (WT), ADAR1KO, and ADAR1E912A cells were harvest and subjected to stranded, paired-end RNAseq. In U937, WT or ADAR1KO cells were treated with or without 50nM phorbol myristate acetate for three days to induce the differentiation of U937 cells to macrophages. After that, the cells were subjected to stranded, paired-end RNAseq. In order to identify the factors accounting for IFN-induced cell growth arrest in the absence of ADAR1, U937 ADAR1KO cells were infected with human CRISPR gRNA library followed by IFN treatment for 14 days. The genomic DNA was then purified for gRNA sequencing.  der to identify PKR-enriched endogenous RNAs, flag-PKR was overexpressed in WT and ADAR1 KO HEK293T cells . Then,  flag-PKR native RNA IP was performed to enrich RNAs. Flag-PKR-enriched RNAs were sequenced.

first: Hu

last: Shibin


title: MicroRNAs in plasma in metabolic syndrome.

status: Public on Oct 02 2023

city: Tlalpan

first: M Elizabeth

last: Tejero

state: Ciudad de MÃ©xico

address: Periferico sur 4809

country: Mexico

institute: Instituto Nacional de Medicina Genomica, Mexico City

summary:
Comparison between miRNA expression in plasma of women with and without metabolic syndrome.
We used microarrays to compare the composition of miRNAs in plasma of participants with and without metabolic syndrome (ATP III criteria).

overall_design: Case control study.

first: Marisol

middle: A

last: Solano Ramírez

first: Emilio

last: Córdova

first: Lorena

last: Orozco Orozco

middle: E


title: FBP1 overexpression in MDA-MB-231 breast cancer cells

city: Heidelberg

first: Stefan

last: Wolfl

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

institute: Heidelberg University, Heidelberg, Germany

summary: Fructose 1,6 bisphosphatase the key enzyme of gluconeogenesis has emerged as  a potential metabolic tumor suppressor. In breast cancer distinct FBP1 expression levels are found depending on subtype. In MDA-MB-231 FBP1 expression is suppressed. To get more insight into potential functions of FBP1 we introduced a vector to reintroduce expression of FBP1. These experiments are part of a more comprehensive study on expression of FBP1 in breast cancer cells.

overall_design: Transfection of MDA-MB231 cells with FBP1 expression vector and empty vector for control.

last: Wölfl

first: Ali

last: Ghanem


title: The leptin receptor has no role in delta-cell control of beta-cell function in the mouse

city: Baltimore

first: Maria

last: Golson

state: MD

address: 5501 Hopkins Bayview Circle, Allergy and Asthma 2A.20

institute: Johns Hopkins University

summary:
Introduction: Leptin inhibits insulin secretion from isolated islets from multiple species, but the cell type that mediates this process remains elusive. Several mouse models have been used to explore this question. Ablation of the leptin receptor (Lepr) throughout the pancreatic epithelium results in altered glucose homeostasis and ex vivo insulin secretion and Ca2+ dynamics. However, Lepr removal from neither alpha nor beta cells mimics this result. Moreover, scRNAseq data has revealed an enrichment of LEPR in human islet delta cells.

Methods: We confirmed LEPR upregulation in human delta cells by performing RNAseq on fixed, sorted beta and delta cells. We then used a mouse model to test whether delta cells mediate the diminished glucose-stimulated insulin secretion in response to leptin.

Results: Ablation of Lepr within mouse delta cells did not change glucose homeostasis or insulin secretion, whether mice were fed a chow or high-fat diet. We further show, using a publicly available scRNAseq dataset, that islet cells expressing Lepr lie within endothelial cell clusters.

Conclusions: In mice, leptin does not influence beta-cell function through delta cells.

overall_design: We aimed to understand the differences in expression between human beta and delta cells.  To complete this project, we obtained islet samples from five non-diabetic human donors. Current protocols for sorting live islets do not reliably distinguish beta and delta cells. Therefore, we used a procedure to sort cells using internal cell-specific markers. Islets were fixed and suspended into a single-cell suspension. The cell membranes were perforated, and cells were indirectly fluorescently immunolabeled using antibodies against insulin and somatostatin. We found that delta cells express the machinery that beta cells use to sense glucose and secrete insulin (except for insulin). Delta cells were also enriched for genes such as Somatostatin, HHex, Leptin Receptor, Erb-B2 Receptor Tyrosine Kinase 4 and Dopamine Receptor 2, Serpin Family A Member 1, Nuclear receptor coactivator 7, several GABA receptors, Growth Hormone Receptor, and several solute transporters. Characterization of differentially expressed cell-surface molecules could lead to better sorting of live human beta and delta cells.Islets from non-diabetic human donors were obtained from the IIDP, cultured in Prodo Complete Media, then fixed in 1% PFA, 01.% saponin, and 1:100 Rnasin before staining with Somatostatin and Insulin and FACS sorting

first: Jia

last: Zhang


title: Role of Histone H3 Lysine 27 Crotonylation in Gene Transcriptional Repression

city: New York

first: Rajal

last: Sharma

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

summary: Histone lysine acetylation and methylation regulate gene transcription through coordination of chromatin structure and transcriptional activity. However, our understanding of the role of histones in gene regulation is far from complete, in part due to newly discovered novel histone modifications, whose functions are yet to be uncovered1. Here we report that histone H3 lysine 27 crotonylation (H3K27cr) is selectively recognized by the YEATS domain of GAS41 in association with SIN3a-HDAC1/2 co-repressor complex for gene transcriptional repression. The GAS41 YEATS domain dimer binds proto-oncogenic transcription factor c-Myc, which recruits GAS41/SIN3a-HDAC1/2 complex to target gene loci in chromatin such as cell cycle inhibitor p21. Transcriptional de-repression of p21, directed by tumor suppressor p53 upon doxorubicin stimulation, entails dissociation of c-Myc/GAS41/SIN3a-HDAC1/2 complex from chromatin, reduced H3K27 crotonylation, and consequentially increased H3K27 acetylation at p21 locus. GAS41 knockout or H3K27cr binding depletion with CRISPR/Cas9 results in p21 activation, cell cycle arrest and tumor growth inhibition in mice. Our study explains mechanistically causal effect of GAS41 and c-Myc gene amplification on down-regulation of p21 in human colorectal cancer, and suggests GAS41 as an anti-cancer target. We propose that H3K27 crotonylation represents a previously unrecognized, distinct chromatin state for gene transcriptional repression in contrast to H3K27 trimethylation for long-term transcriptional silencing and H3K27 acetylation for transcriptional activation.

overall_design: The role of GAS41 in transcriptional repression and H3K27Cr binding was assessed by multiple approaches. The genomic localization of GAS41 and c-myc, as well as the distribution of the histone marks H3K27Ac and H3K27Cr, was assessed by ChIP-seq. The response in transcription to Doxorubicin was assessed by RNA-seq. Furthermore, the role of GAS41 in transcriptional regulation was further delineated by RNA-seq in WT, GAS41-KO, and GAS41-Rescue HCT116 colon cancer cells.

last: Liu

first: Tsuyoshi

last: Konuma

first: Qiang

first: Ming-Ming

last: Zhou


title: Retina-derived signals control pace of neurogenesis in visual brain areas but not circuit configuration

city: Martinsried

first: Herwig

last: Baier

address: Am Klopferspitz 18

department: Genes - Circuits - Behavior

institute: Max Planck Institute for Biological Intelligence

summary: Brain development is orchestrated by both innate and experience-dependent mechanisms, but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum, thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated, the complete set of 77 neuronal types develops in apparently normal proportions, at normal locations, and along normal differentiation trajectories. Strikingly, the cell-cycle exits of proliferating progenitors in these areas are delayed, and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion, we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas, but do not detectably affect the specification or wiring of downstream neurons.

overall_design: Tg(HGn12C:GFP) or [Tg(Gal4s1026t) X Tg(UAS:GFP)] larvae were sorted for GFP expression 24 hours after fertilization. All single-cell experiments were performed at 6 days after fertilization. To obtain unrelated WT, pigmented larvae were used from Tg(HGn12C:GFP) pigmented males or females crossed with WT TLN, which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae, Tg(HGn12C:GFP) lakritz heterozygote adults were crossed with adult lakritz heterozygotes. For experiments with lakritz larvae, only lakritz mutants were collected; for other experiments, they were discarded. For single-cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.

first: Shachar

last: Sherman

first: Irene

last: Arnold-Ammer

first: Martin

middle: W

last: Schneider

first: Koichi

last: Kawakami


title: Epigenetic dynamics during capacitation of naïve human pluripotent stem cells [ATAC-seq]

first: Laura

last: Biggins

first: João

last: Agostinho de Sousa

last: Rostovskaya

first: Chee-Wai

last: Wong

first: Wolf

last: Reik

first: Austin

last: Smith

first: Ferdinand

last: von Meyenn


title: Transcriptome analysis of  longissimus dorsi muscle treated with melatonin  in weaned piglets

city: Hangzhou

first: Chen

last: Wentao

state: Zhejiang

address: No. 866 Yuhangtang Road

institute: Zhejiang University

summary: Melatonin has been reported to play crucial roles in regulating meat quality, improving reproductive properties and maintaining intestinal health in animal production, but whether it regulates skeletal muscle development in weaned piglet is rarely studied. This study was conducted to investigate the effects of melatonin on growth performance, skeletal muscle development and lipid metabolism in animals by intragastric administration of melatonin solution. Twelve 28-day-old DLY (Duroc × Landrace × Yorkshire) weaned piglets with similar body weight were randomly divided into two groups: control group and melatonin group. The results showed that melatonin supplementation for 23 days had no effect on growth performance, but significantly reduced serum glucose content (P<0.05). Remarkably, melatonin increased longissimus dorsi muscle (LDM) weight, eye muscle area and decreased the liver weight in weaned piglets (P<0.05). In addition, the cross-sectional area of muscle fibers was increased (P<0.05), while triglyceride (TG) levels were decreased in LDM and psoas major muscle (PMM) by melatonin treatment (P<0.05). Transcriptome sequencing showed melatonin induced the expression of genes related to skeletal muscle hypertrophy and fatty acid oxidation. Enrichment analysis indicated that melatonin regulated cholesterol metabolism, protein digestion and absorption and mitophagy signaling pathways in muscle. Gene set enrichment analysis (GSEA) also confirmed the effects of melatonin on skeletal muscle development and mitochondrial structure and function. Moreover, quantitative real-time polymerase chain reaction (qPCR) analysis revealed that melatonin supplementation elevated the gene expression of cell differentiation and muscle fiber development, including paired box 7 (PAX7), myogenin (MYOG), myosin heavy chain (MYHC) ⅡA and MYHC ⅡB (P<0.05), which was accompanied by increased insulin like growth factor 1 (IGF1) and insulin like growth factor binding protein 5 (IGFBP5) expression in LDM (P<0.05). Additionally, melatonin regulated lipid metabolism and activated mitochondrial function in muscle by increasing the mRNA abundance of cytochrome c oxidase subunit 6A (COX6A), COX5B and carnitine palmitoyltransferase 2 (CPT2) and decreasing the mRNA expression of peroxisome proliferator activated receptor gamma (PPARG), Acetyl-CoA carboxylase (ACC) and fatty acid binding protein 4 (FABP4) (P<0.05). Together, our results suggest that melatonin could promote skeletal muscle growth and muscle fiber hypertrophy, improve mitochondrial function and decrease fat deposition in muscle.

overall_design: A total of 12 weaned piglets  at 28 d of age DLY (Duroc × Landrace × Yorkshire) were randomly divided into two groups (n = 6). All the piglets were fed the same basal diet and water throughout the experiment. Following 5 days for adaptive rearing, all the piglets were given fasting gavage at 9 a.m every morning. Piglets from melatonin-treated group were infused with 10 mL of the sterile saline solution dissolved with melatonin on basis of body weight (5 mg/kg) and the control group in which piglets received same volume of sterile saline solution daily for 23 days. Melatonin solution was prepared daily and kept with an aluminum foil cover to prevent light-induced degradation before use. We then performed gene expression  analysis using RNA from longissimus dorsi muscle after  melatonin supplementation


title: Transcriptome analysis of high potent DCs using small molecule compounds

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

institute: Kanazawa Medical University Hospital

summary: Comparative gene expression analysis of generated DCs on several condition with small molecule compounds

overall_design: Total RNA extracted from generated DCs on several conditon with small molecule compounds were used for library construction with NEB Next Ultra II Directional RNA Library Prep Kit. All libraries were sequenced (2x75 bp) usng Illumina NextSeq 500.

first: Yo

last: Niida

first: Nobuyuki

last: Onai

first: Shintaro

last: Matsuba


title: macroH2A1 ChIP-seq in G1/S phase and metaphase

city: Shanghai

first: Bi

middle: shan

last: Ye

state: Shanghai

address: Minhang district Dongchuan Road NO.800

department: School of Biomedical Engineering

institute: Shanghai JiaoTong University

summary: The histone variant macroH2A forms large chromatin domains and serves as a transcriptional repression marker. It has been found that the overall quantity of macroH2A deposition on chromatin undergoes dynamic changes during the cell cycle. However, the genomic features relevant to these dynamic changes in macroH2A1 deposition during the cell cycle remain poorly understood. We combined ChIP‑seq and cell synchronization in mouse NIH-3T3 cells to examine the dynamic changes of macroH2A1 deposition on the genome between G1/S phase and metaphase. Interestingly, we observed that macroH2A1 deposition dynamically changes within the large macroH2A1 domain at G1/S phase and metaphase, which was associated with transcriptional activity. These dynamic changes occurring at gene bodies can specifically mark cell-cycle-specific genes. Taken together, we propose that macroH2A1 is a dynamic histone variant associated with cell-cycle-specific genes and plays a crucial role in cell-cycle-specific transcriptional repression.

overall_design: Chromatin immunoprecipitation and DNA-sequencing (ChIP-seq) for histone variants macroH2A1 in NIH-3T3 cells in G1/S phase and metaphase.

first: Bishan

first: Zeqian

last: Xu

first: Xinhui

last: Li

first: Zhifeng

last: Shao


title: Spatial and temporal mapping of breast cancer lung metastases identify TREM2 macrophages at the metastatic boundary

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Cancer mortality is primarily caused by metastatic recurrence, whereby tumor cells evade immune surveillance. Better understanding of the molecular and cellular events that occur in metastatic niches is essential to develop effective immunotherapies targeting metastasis. We employed a model of spontaneous breast cancer lung metastasis to create a single-cell RNA-sequencing temporal and spatial atlas that spans different metastatic stages and regions. We found that pre-metastatic lungs are infiltrated by inflammatory neutrophils and monocytes, followed by accumulation of suppressive macrophages with the emergence of metastases. Metastasis-associated immune cells are present in the metastasis core, with the exception of Trem2+ regulatory macrophages uniquely enriched in the metastatic invasive margin. These regulatory macrophages contribute to the formation of an immune-suppressive niche, cloaking the tumor cells from immune surveillance. Our study provides a comprehensive chart of immune cell dynamics across metastatic stages and niches, which could inform the development of immunotherapies that target metastasis.

overall_design: We utilized photoactivatable GFP (PA-GFP) mice as recipients of EO771 breast cancer (BC) tumors and emergent spontaneous metastasis, thus enabling spatial analysis by application of the NICHE-seq technology (Medaglia et al., 2017). We performed photoactivation on metastases-bearing lungs, labeling either the metastasis core or the metastasis invasive margin (ADJ). We isolated immune cells from lungs of control PA-GFP mice (Normal), and also included in our atlas immune cells from EO771-tdTomato primary tumors. Cells from all samples were isolated by FACS, gating on CD31-CD45+ immune cells or CD31-GFP+ (PA+) cells following photoactivation of metastatic tissues. In total scRNA-seq was performed on 63 samples from 27 mice

first: Tomer

last: Landsberger

last: Yofe


title: Epigenetic dynamics during capacitation of naïve human pluripotent stem cells [ChIP-seq]

first: Laura

last: Biggins

first: João

last: Agostinho de Sousa

first: Maria

last: Rostovskaya


title: Effect of MelasolvTM treatment on human melanocytes

city: Yongin-si

first: Kyu-Han

last: Kim

state: Gyeonggi-do

address: 1920 Yonggu-daero, Giheung-gu, Gyeonggi-do, South Korea, AMOREPACIFIC Corp., R&D unit, BioScience Lab

country: South Korea

institute: AMOREPACIFIC Copr.

summary: To investigate the effect of MelasolvTM, we established human epidermal melanocytes cell lines in which MelasolvTM was treated for 1day. We then performed comparative gene expression profiling analysis using data obtained from RNA-seq of untreated and MelasolvTM-treated cells.

overall_design:
Comparative gene expression profiling analysis of RNA-seq for melanocyte cells with MelasolvTM treatment.

**Submitter declares that the raw data are no longer available**

first: Kyu

middle: H

first: Yeonju

last: Cho


title: Antibody-free fluorine assisted metabolic sequencing of RNA N4-acetylcytidine

city: Wuhan

first: Ziang

last: Lu

address: Wuhan University, No.299, Bayi Road, Wuchang District

institute: Wuhan University

summary: More researches have revealed that N4-acetylcytidine (ac4C) affected a variety of cellular and biological processes. In order to better understand the ac4C roles in biology and disease, we present an antibody-free, fluorine assisted metabolic sequencing method to detect RNA N4-acetylcytidine, called ‘FAM-seq’. We have successfully applied FAM-seq to profile ac4C landscapes in humans. By comparing with the classic ac4C antibody sequencing method, we demonstrated that FAM-seq is a convenient and specific method for transcriptome-wide detection of ac4C. This method holds promise to detect nascent RNA ac4C modifications.

overall_design: Cells were fed with the pro-metabolite sodium fluoroacetate, which can be converted to its CoA metabolite fluoroacetyl-CoA in vivo by enzymes. Cellular RNA could therefore be acetylated with the fluoroacetyl group at supposed N4-acetylcytidine sites. The resulting fluoroacetamides could be converted to biotin or fluorophore tags by fluorine-thiol displacement reaction with high yield.

first: Shen

last: Yan

first: Yuhao

last: Du

first: Xiang

last: Zhou


title: MHC Class Ib-restricted CD8+ T Cells Possess Strong Tumoricidal Activities

city: shanghai

first: Qing

address: 320 Yueyang Road

institute: Chinese Academy of sciences

summary: The tumoricidal effects of CD8+T cells are well acknowledged, but how MHC Ib-restricted CD8+T (Ib-CD8+T) cells contribute to anti-tumor immunity remains obscure. Here, we show that infusion of MHC Ia+ cells to Kb-/-Db-/- mice induced the expansion of Ib-CD8+T cells in tumors and potently inhibited tumor progression. Such priming of Ib-CD8+T cells by MHC-Ia is not MHC haplotype restricted and MHC Ia tetramers alone can prime Ib-CD8+T cells for activation. The MHC Ia priming promoted Tbet expression in Ib-CD8+T cells and in absence of Tbet, such priming effect diminished. Importantly, these tumoricidal Ib-CD8+T cells are positive for CX3CR1, and exhibit rapid proliferation, high expression of cytotoxic factors, and prolonged persistence at tumor sites. Adoptive transfer of CX3CR1+Ib-CD8+T cells to wild type mice resulted in potent anti-tumor effects. Our findings unravel an uncharacterized function of MHC Ia molecules in immunoregulation and raise the possibility of using Ib-CD8+T cells in tumor immunotherapy.

overall_design: Single cell RNA seq of CD8+ T cells isolated from tumor or spleen of C57 or Kb-/-Db-/- mice treated with MHC Ia+MCs or MHC Ia-MCs. Kb-/-Db-/- mice and C57BL/6 mice were i.v. injected with B16F10 cells (3× The tumor bearing Kb-/-Db-/- mice were i.p. injected with Ia-MSCs (1×or Ia+MSCs (1×every 3 days starting on day 0. After 9 days, splenic CD8+ T cells from Ia-MSCs treated Kb-/-Db-/- mice (Ia-MSCs-spleen), splenic CD8+ T cells from Ia+MSCs treated Kb-/-Db-/- mice (Ia+MSCs-spleen), tumor infiltrated CD8+ T cells from Ia+MSCs treated Kb-/-Db-/- mice (Ia+MSCs-tumor), splenic CD8+ T cells from C57BL/6 mice (C57BL/6-spleen), and tumor infiltrated CD8+ T cells from C57BL/6 mice (C57BL/6-tumor) were isolated using magnet beads and subjected to single cell RNA sequencing. *** Submitter was unable to provide valid raw data files for the following samples: GSM5005586 GSM5005589 GSM5005590.

first: Liangyu

last: Lin

first: Ying

last: Wang

first: Yufang

last: Shi


title: Retrospective DNA Methylation profiles collated from Nottingham, UK

city: Nottingham

first: Timothy

last: Ritzmann

address: Coates Road

department: Children's Brain Tumour Research Centre

institute: University of Nottingham

summary:
DNA Methylation profiles were generated for retrospective cases to support work into investigation of the immune environment in pediatric ependymoma. Samples were analyzed using the Illumina 450k beadchip and processed using the Heidelberg classifier (v11.2b and subsequently v12.3 for subgrouping/subtyping).
The aim of the study was to better understand the immune-tumor microenvironment in pediatric ependymoma and the methylation profiles support the diagnoses of each case.

overall_design: 74 samples were analyzed and found to be consistent with ependymoma.

first: Rebecca

last: Chapman

first: Andrea

last: Griesinger

first: Andrew

last: Donson

first: Simon

last: Paine

first: Richard

last: Grundy

first: Nicholas

last: Foreman


title: Epithelial Ovarian Cancer is infiltrated by activated effector T cells co-expressing CD39, PD-1, TIM-3, CD137 and interacting with cancer cells and myeloid cells

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

summary: Introduction: Despite predicted efficacy, immunotherapy in epithelial ovarian cancer (EOC) has limited clinical benefit and the prognosis of patients remains poor. There is thus a strong need for better identifying local immune dynamics and immune-suppressive pathways limiting T-cell mediated anti-tumor immunity.   Methods: In this observational study we analyzed by immunohistochemistry, gene expression profiling and flow cytometry the antigenic landscape and immune composition of 48 EOC specimens, with a focus on tumor-infiltrating lymphocytes (TILs).   Results: Activated T cells showing features of partial exhaustion with a CD137+CD39+PD-1+TIM-3+CD45RA-CD62L-CD95+ surface profile were exclusively present in EOC specimens but not in corresponding peripheral blood or ascitic fluid, indicating that the tumor microenvironment might sustain this peculiar phenotype. Interestingly, while neoplastic cells expressed several tumor-associated antigens possibly able to stimulate tumor-specific TILs, macrophages provided both co-stimulatory and inhibitory signals and were more abundant in TILs-enriched specimens harboring the CD137+CD39+PD-1+TIM-3+CD45RA-CD62L-CD95+ signature.   Conclusions: These data demonstrate that EOC is enriched in CD137+CD39+PD-1+TIM-3+CD45RA-CD62L-CD95+ T lymphocytes, a phenotype possibly modulated by antigen recognition on neoplastic cells and by a combination of inhibitory and co-stimulatory signals largely provided by infiltrating myeloid cells. Furthermore, we have identified immunosuppressive pathways potentially hampering local immunity which might be targeted by immunotherapeutic approaches

overall_design: 46 samples derived from epithelial ovarian cancer patients were analyzed

first: Elena

last: Tassi

first: Alice

last: Bergamini

first: Jessica

last: Wignall

first: Miriam

last: Sant’Angelo

first: Emanuela

last: Brunetto

last: Bonini


title: CYR61 orchestrates NASH fibrosis through SYK-NFκB-PDGF signaling in monocyte-derived macrophages [bulk RNA-seq]

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Obesity is increasing worldwide and leads to a multitude of metabolic diseases including non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatosis (NASH). Here we examine the role of CYR61 in liver fibrosis and inflammation and its potential as a therapeutic target. Loss of CYR61 during NASH injury improves glucose tolerance, decreases liver inflammation and reduces fibrosis. CYR61 activates signaling in monocytes and monocyte-derived macrophages promoting a pro-inflammatory/pro-fibrotic phenotype through a CYR61/SYK/NFKB signaling cascade. In vitro, CYR61 activates Pdgfa and Pdgfb expression in macrophages in a NFκB-dependent manner. Ultimately, we identify a potential therapeutic for NASH: a CYR61-blocking antibody that reduces fibrotic injury and CYR61-driven signaling in macrophages in vitro and in vivo. This study demonstrates that CYR61 is a key driver of liver inflammation and fibrosis and a strong therapeutic target for treatment of NAFLD/NASH.

overall_design: mRNA profiles of two conditions: Control and Cyr61 KO, with three repeats each.

first: Meghan

last: Mooring

first: Panu

last: Luukkonen

first: Silvia

first: Oluwashanu

last: Balogun

first: Rigen

last: Mo

first: Kari

last: Nejak-Bowen

first: Masha

last: Poyurovsky

first: Carmen

last: Booth

first: Liza

last: Konnikova

first: Gerald

middle: I

last: Shulman

first: Dean

last: Yimlamai


title: Identification of translational ncRNA biomarker candidates for nano-polystyrene induced brain injury using next-generation sequencing

city: Shijiazhuang

first: chu

last: chen

state: Hebei

address: 361 Zhongshan East Road

department: Department of Toxicology

institute: Hebei medical university

summary: The exposure to nano-plastics affects mammalian neurotoxic hazard characterization remains to be determined. Our aim was to investigate the neurotoxicity of nano-plastics in rodents. Animals were randomly divided into two groups: a control group and 50 mg/kg body weight PS NPs treatment groups. Before treatment, animals were fasted overnight. PS NPs were suspended into waters, vigorously stirred. The PS NPs via oral gavage once per day and for 6 months. The mice were treated with water in control group. We found that exposure to PS NPs caused cognitive decline. PS NPs exposure influenced the prefrontal cortex cells with more pathological alteration with increasing dosage. High-throughput RNA sequencing was conducted to explore miRNA expression in prefrontal cortex. Sixty-seven differentially expressed circRNAs were detected, including 25 upregulated and 42 downregulated circRNAs. We also explored 987 differentially expressed mRNAs, including 477 upregulated and 510 downregulated mRNAs.

overall_design: Mice exposure PS NPs for half year and identified of translational circRNA, LncRNA as well as mRNA

first: Chu

last: Chen

first: Zhang

last: Rong


title: RBPJ deficiency sensitizes pancreatic acinar cells to Kras-mediated PanIN initiation

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

summary: Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis and is among the most common causes of cancer death worldwide. KrasG12D mutation is the main driver mutation but insuffi-cient for progression of invasive cancer on its own indicating that other pathways, such as Notch signaling may participate in that process. RBPJ, the only transcription factor in Notch signaling, is frequently lost in human cancers and associated with more aggressive breast cancer phenotype. Notch-independently, in complex with P48, RBPJ initiates transcription of its paralogue RBPJL ensuring acinar differentiation. The RBPJ knockout has an embryonic lethal effect. Mice with pancreas-specific deletion of RBPJ presented with less acinar tissue and large duct-like structures suggesting a relevance of RBPJ for acinar to ductal reprogramming and even pancreatic neoplasia. Here, we found reduced RBPJ expression level in the human PDAC specimens. Analyses of transgenic mouse models of an inducible P48-dependent RBPJ knockout revealed that it is dispensable for the maintenance adult acinar cells. In the context of oncogenic KRAS expression, the RBPJ deficiency facilitated the development of PanIN lesions with massive fibrotic stroma. Interestingly, RNA seq data revealed corresponding transcription pattern prior to phenotypic alterations.

overall_design: RNA-seq was performed by whole RNA islation from pancreata harvested from 4 weeks after oil/tamoxifen treated 6-8 weeks old iCR (P48-CreERT;Rbpjflox/flox), iKC (P48-CreERT; LSL-KrasG12D), and iKCR (P48-CreERT; LSL-KrasG12D ;Rbpjflox/flox) mice (n=6/group).


title: Single-cell RNA sequencing of the spleen reveals differences in the mechanisms of resistance to bacterial infection between different chicken breeds

status: Public on Oct 01 2023

city: Bejing

first: Qi

last: Zhang

address: No2 Yuanmingyuan West Road, Haidian

institute: Chinese Academy of Agricultural Sciences Institute of Animal Science

summary: Bacterial infections remain an important cause of morbidity in poultry production. The molecular characteristics and dynamic changes in immune cell populations after bacterial infection have yet to be fully understood. Beijing-You chicken and Cobb broiler, two broiler breeds with different disease resistance, were infected with Salmonella typhimurium, and inflammation models were constructed. We characterized chicken spleen CD45+ immune cells by single-cell RNA sequencing.

overall_design: At 28 days old, 3 Cobb chicks and 1 Beijing-you chicks were randomly chosen and challenged orally with 1 mL PBS containing 1.83 × 1011 CFU Salmonella typhimurium (ST), 3 Cobb chicks and 3 Beijing-you chicks were randomly given orally with 1mL PBS.         At 3 days post-infection (dpi), we collected the splenic tissues and prepared the single-cell suspensions.    Collected CD45+ cells by flow cytometry and analyzed using scRNAseq.

first: Jumei

last: Zheng

first: Jin

first: Gaomeng

first: Jie

last: Wen

first: Qinghe

last: Li

first: Guiping

last: Zhao


title: Pre-piRNA trimming safeguards piRNAs against erroneous targeting by RNA-Dependent RNA Polymerase

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

summary: In animal germ lines, The Piwi/piRNA pathway plays a crucial role in safeguarding genome integrity and promoting fertility. Following transcription from discrete genomic loci, piRNA precursors undergo nucleolytic processing at both 5’ and 3’ ends. The ribonuclease PARN-1 and its orthologs mediate piRNA 3' trimming in worms, insects and mammals. Yet, the significance of this evolutionarily conserved processing step is not well understood. Employing C. elegans as a model organism, our recent work has demonstrated that 3' trimming protects piRNAs against non-templated nucleotide additions and degradation. In this study, we present an unexpected finding that C. elegans deficient for PARN-1 accumulate a heretofore uncharacterized RNA species termed anti-piRNAs, which are antisense to piRNAs. These anti-piRNAs associate with Piwi proteins and display the propensity for a length of 17-19 nucleotides and 5’ guanine and adenine residues. We show that untrimmed pre-piRNAs in parn-1 mutants are modified by the terminal nucleotidyl transferase RDE-3 and erroneously targeted by the RNA dependent RNA polymerase EGO-1, thereby giving rise to anti-piRNAs. Taken together, our work identifies a previously unknown class of small RNAs upon loss of parn-1 and provides mechanistic insight to activities of RDE-3, EGO-1 and Piwi proteins.

overall_design: Analysis of small RNAs from wild-type, parn-1 and various parn-1 double mutants

first: Benjamin

last: Pastore

first: Hannah

last: Hertz


title: Hydrogen sulfide treatment at the late growth stage of Saccharomyces cerevisiae extends chronological lifespan

city: Chengdu

first: Arman Ali

last: Shah

state: Sichuan

address: Wangjiang road 29, Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu

institute: Sichuan University

summary: Hydrogen sulfide (H2S), a traditionally known cytotoxic gas, has been recently included in the gasotransmitters family. Previous studies demonstrated that lifelong treatment with a slow H2S releasing donor extends yeast chronological lifespan (CLS), but it is not clear when the action of H2S benefits to CLS during yeast growth. Therefore, we investigated the effects of short H2S treatments at different time during yeast cell growth in the lifespan extension by using NaHS, a fast H2S-releasing donor. We show that short NaHS treatments at 4 days after inoculation extend yeast CLS while NaHS treatments earlier than 3 days after inoculation fail to do so. To reveal the mechanism of different consequences on yeast CLS of NaHS treatments at different times, we analyzed the transcriptome of Saccharomyces cerevisiae strain BY4742 with or without the early and late NaHS treatments. We found that the early and late NaHS treatments had similar effects on the expression of genes involved in pathways which are related to CLS regulation. Follow up qPCR and ROS analyses suggest that altered expression of some antioxidant genes by the early NaHS treatments were not stable enough to benefit CLS. Moreover, transcriptome data also indicated that some genes were regulated differently by the early and late H2S treatment such as genes involved in cell wall integrity. Specifically, we found that the expression of YPK2, a human SGK2 homolog and also a key regulator of the yeast cell wall synthesis, was significantly altered by the late NaHS treatment but not altered by the early NaHS treatment. Finally, the key role of YPK2 in CLS regulation by H2S is revealed by CLS data showing that the late NaHS treatment did not enhance the CLS of a ypk2 knockout mutant. This study sheds light on the molecular mechanism of CLS extension induced by H2S, and for the first time addresses the importance of H2S treatment timing for lifespan extension.

overall_design: Four samples, three replicates each. Names are Early_control, Early_NaHS_treatment, Late_control and Late_NaHS_treatment.

first: Arman

last: Ali Shah

first: Binghua

last: Liu

first: Wang

last: Wang

first: Ke


title: Genetic enhancers of partial PLK1 inhibition reveal hypersensitivity to kinetochore perturbations

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

summary: Polo-like kinase 1 (PLK1) is a serine/threonine kinase required for mitosis and cytokinesis. As cancer cells are often hypersensitive to partial PLK1 inactivation, chemical inhibitors of PLK1 have been developed and tested in clinical trials. However, these molecules alone were not completely effective. PLK1 promotes numerous molecular and cellular events in the cell division cycle. To date, it is unclear which of these events most crucially depend on PLK1 activity. We used a CRISPR-based genome-wide screening strategy to identify genes whose inactivation enhances cell proliferation defects upon partial chemical inhibition of PLK1. Genes identified encode proteins that are functionally linked to PLK1 in multiple ways. Among them, factors that promote centromere and kinetochore function were clearly enriched. In particular, inactivation of the kinesin KIF18A or SKA1 in PLK1-compromised cells results in mitotic defects, activation of the spindle assembly checkpoint and nuclear reassembly defects. Our results suggest that functions of PLK1 at kinetochores are most sensitive to its inhibition, and point at KIF18A as a possible target for combinatorial therapies using existing PLK1 inhibitors.

overall_design: Genome-wide CRISPR/Cas9 screens to test for gene deletions that affect fitness in human cells treated with PLK1 inhibitors BI2536, BI6727 and GSK461364A.

first: Karine

last: Normandin

first: Jasmin

last: Coulombe-Huntington

first: Corrine

last: St-Denis

first: Alexandre

last: Bernard

first: Mohammed

last: Bourouh

first: Thierry

last: Bertomeu

first: Michael

first: Vincent

last: Archambault


title: CYR61 orchestrates NASH fibrosis through SYK-NFκB-PDGF signaling in monocyte-derived macrophages [HIVE single-cell RNA-seq]

first: Shuchang

state: PA

overall_design: HIVE single-cell RNA-seq with two conditions: Control and CYR61, with four repeats each.

first: Meghan

last: Mooring

first: Panu

last: Luukkonen

first: Silvia

first: Oluwashanu

last: Balogun

first: Rigen

last: Mo

first: Kari

last: Nejak-Bowen

first: Masha

last: Poyurovsky

first: Carmen

last: Booth

first: Liza

last: Konnikova

first: Gerald

last: Shulman

first: Dean

last: Yimlamai


title: Starving advanced prostate cancer cells by pharmacological gluose deprivation with a resveratrol trimer trans-Gnetin H [TGH]

city: New York

first: William

last: Oh

state: New York

address: 1 Gustave Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: Prostate cancer is a unique disease from a metabolic perspective. Early stage localized prostate cancer does not typically display increased aerobic glycolysis (the Warburg effect), as seen in other malignancies. However, increasing evidence suggests that advanced prostate cancer exhibits the Warburg effect and displays high glucose uptake. We describe here that trans-gnetin H (TGH), a naturally-occurring resveratrol trimer extracted from Paeonia suffruticosa, displays significant anti-cancer effects in advanced prostate cancer cells in vitro. TGH perturbs energy metabolism by blocking the availability of glucose, inducing unfolded protein response (UPR) and C-MYC pathway downregulation in  PC-3 cells. Our studies demonstrate the feasibility of targeting aerobic glucose metabolism in advanced prostate cancer and identify TGH as a potential therapeutic candidate.

overall_design: PC-3 treated with 2.5µM TGH for 24 hours in triplicates, PC-3 treated with DMSO as controls in triplicates

first: Gong

last: Yixuan

first: Oh

last: Wiliiam

first: Wang

last: Li

first: Yu

last: Haocheng


title: Genomic DNA copy number aberration in chromosome 18 of small intestinal tumors in B6/B6-Chr18MSM-F1 ApcMin/+ mice irradiated with ionizing radiation

city: Chiba

first: Daisuke

last: IIZUKA

address: 4-9-1, Anagawa, Inage-ku

institute: Research Institutes for Quantum Science and Technology

summary: To investigate DNA copy number changes in chromosome 18 of small intestinal tumors in B6/B6-Chr18MSM-F1 ApcMin/+ mice irradiated with ionizing radiation

overall_design: DNA copy number changes in radiation-induced small intestinal tumors of B6/B6-Chr18MSM-F1 ApcMin/+ mice were analyzed using CGH custom microarrays, an array specialized for chromosome 18 analysis.

last: Iizuka

first: Megumi

last: Sasatani


title: Targeting PRMT1-mediated SRSF1 Methylation to Suppress Exon Inclusion within Oncogenic Transcripts and Breast Tumorigenesis

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

summary: PRMT1 is highly expressed in breast tumors, and has been suggested to play a vital role in breast tumorigenesis, but the underlying molecular mechanisms remain to be fully characterized. Here, we reveal that PRMT1 exhibits a wide-spreading role in RNA alternative splicing based on transcriptome analysis, with a preference for exon inclusion in a large cohort of oncogenic genes. Profiling PRMT1 methylome reveals that the arginine/serine-rich splicing factor SRSF1 is heavily arginine-methylated by PRMT1, which is critical for SRSF1 phosphorylation, SRSF1 binding with RNA, and PRMT1-induced exon inclusion. In breast tumors, the overexpression of PRMT1 is associated with high levels of SRSF1 arginine methylation and aberrant exon inclusion in those oncogenic genes. Accordingly, PRMT1-mediated SRSF1 methylation and exon inclusion events are found to be critical for the malignant behaviors of breast cancer cells. Furthermore, we identified and characterized a selective PRMT1 inhibitor iPRMT1, which is potent in inhibiting PRMT1-mediated SRSF1 methylation and exon inclusion events, and breast cancer cell growth both in vitro and in vivo. Combination treatment with iPRMT1 and inhibitor targeting SRSF1 phosphorylation, SPHINX31 or SRPIN340, exhibits synergistic effects on suppressing breast cancer cell growth, strengthening the cross-talk between arginine methylation and phosphorylation in SRSF1. In conclusion, our data uncover a key mechanism underlying PRMT1-mediated gene alternative splicing, demonstrating targeting PRMT1 has great potential to treat breast cancer in clinic.

overall_design: RNA-seq performed in this study was designed to reveal the gene splicing events regulated by PRMT1

first: Wen

last: Liu

first: Wen-juan

first: Guo-sheng


title: Starving advanced prostate cancer cells by pharmacological gluose deprivation with a resveratrol trimer trans-Gnetin H [PDX]

summary: Prostate cancer is a unique disease from a metabolic perspective. Early stage localized prostate cancer does not typically display increased aerobic glycolysis (the Warburg effect), as seen in other malignancies. However, increasing evidence suggests that advanced prostate cancer exhibits the Warburg effect and displays high glucose uptake. We describe here that trans-gnetin H (TGH), a naturally-occurring resveratrol trimer extracted from Paeonia suffruticosa, displays significant anti-cancer effects in advanced prostate cancer cells xenografted PC-3 cells in vivo.TGH perturbs energy metabolism by blocking the availability of glucose and inducing profound metabolic and transcriptomic changes in prostate cancer cells as demonstrated by RNA-seq. C-MYC, a known driver oncogene in prostate cancer, is downregulated in TGH-treated cells. Our studies demonstrate the feasibility of targeting aerobic glucose metabolism in advanced prostate cancer and identify TGH as a potential therapeutic candidate.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: PC3 xenograft tumor performed on athymic nude mice. 9 were treated with TGH. 9 were treated with vehicle control


title: CYR61 orchestrates NASH fibrosis through SYK-NFκB-PDGF signaling in monocyte-derived macrophages

first: Shuchang

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

overall_design: Refer to individual Series


title: MicroRNA expression profile of Chicken liver in different stages during Histomonas meleagridis infection

city: Yangzhou

first: chen

last: qiaoguang

address: No.48 Wenchang East Road, Yangzhou

institute: College of Veterinary Medicine, Yangzhou University

summary:
Background: Histomonas meleagridis is an anaerobic, intercellular parasite, which infects gallinaceous birds such as turkeys and chickens. In recent years, the reemergence of Histomoniasis has caused serious economic losses as drugs to treat the disease have been banned. At present, research of H. meleagridis focuses on virulence, gene expression analysis, and the innate immunity of the host. However, there are no study on the differentially expressed miRNAs (DEMs) associated with the liver induced by H. meleagridis. In this research, high-throughput sequencing was used to analyze the expression profile of liver miRNA at 10 and 15 days post-infection (DPI) in chickens infected with Chinese JSYZ-F strain H. meleagridis.
Results: Compared with the uninfected control, 120 and 118 DEMs were found in the liver of infected chickens at 10 DPI and 15 DPI, respectively, of which 74 DEMs were shared at two-time points. Differentially expressed miRNAs were classified into three types according to the time of infection: L1, 45 miRNAs differentially expressed only at 10 DPI, were predicted to target 1646 genes; L2, 43 miRNAs differentially expressed only at 15 DPI, were predicted to target 2257 genes; L3, 75 miRNAs differentially expressed at both 10 DPI and 15 DPI, were predicted to target 1623 genes. A total of 89, 87 and 41 significantly enriched GO terms (p<0.05) were identified at L1, L2 and L3, respectively. The KEGG pathway analysis of differentially expressed miRNA target genes were shown that 3, 4 and 5 significantly enriched KEGG pathway (p<0.05) were identified at L1, L2 and L3, respectively.
Conclusion: This article suggested that liver miRNA expression was dynamically altered by H. meleagridis and host and showed that the expression pattern of the L1 class DEMs were more favourable for controlling the development of the inflammatory response, whereas the L2 class DEMs were more favourable for enhancing the inflammatory response. Inflammation-associated miRNA expression patterns were consistent with the liver inflammatory process after artificial infection. The results of the study laid the foundation for an in-depth analysis of the pathogenic mechanism of H. meleagridis from the perspective of host miRNAs.

overall_design: liver miRNA profiles of 10 and 15 days old infect/control chicken

first: Yu-Ming

last: Zhang

first: Jin-jun

last: Xu


title: Calponin 2 regulates ketogenesis to dictate the outcome of acute kidney injury

summary: Calponin 2 (CNN2) is a prominent actin stabilizer. It regulates fatty acid oxidation (FAO) by interacting with estrogen receptor 2 (ESR2) to determine kidney fibrosis. However, whether CNN2 is actively involved in acute kidney injury (AKI) remains unclear. Here, we report that CNN2 was induced in human and animal kidneys after AKI. Knockdown of CNN2 preserved kidney functions, mitigated tubular cell death and inflammation, and promoted cell proliferation. Distinct from kidney fibrosis, proteomics showed that the key elements in the FAO pathway have little changes in AKI, but we identified that hydroxymethylglutaryl-CoA synthase 2 (HMGCS2), a rate-limiting enzyme of endogenous ketogenesis that promotes cell self-renewal, was markedly increased in CNN2 knockdown kidneys. The ketone bodies β-hydroxybutyrate and ATP production were increased in CNN2 knockdown mice. Mechanistically, CNN2 interacts with ESR2 to activate mitochonrial sirtuin 5, subsequently desuccinylating HMGCS2 to produce energy for AKI repair. Understanding CNN2-mediated discrete fine-tuning of protein posttranslational modification is critical to optimize organ performance after AKI.

overall_design: RNA-seq data on mouse kidney after acute kidney injury at different time points

first: Yuan

last: Gui

first: Zachary

last: Palanza

first: Priya

last: Gupta

first: Hanwen

first: Yuchen

last: Pan

first: Yuanyuan

last: Wang

first: Yi

last: Qiao

first: Geneva

last: Hargis

first: Donald

last: Kreutzer

first: Sheldon

last: Bastacky

first: Yanlin

first: Yansheng

first: Silvia

first: Dong

last: Zhou


title: CYR61 orchestrates NASH fibrosis through SYK-NFκB-PDGF signaling in monocyte-derived macrophages [10X single-cell RNA-seq]

first: Shuchang

overall_design: Single-cell RNA-seq by 10X platform of two conditions: Control and KO, with two repeats each.

first: Meghan

last: Mooring

first: Panu

last: Luukkonen

first: Oluwashanu

last: Balogun

first: Rigen

last: Mo

first: Kari

last: Nejak-Bowen

first: Masha

last: Poyurovsky

first: Carmen

last: Booth

first: Liza

last: Konnikova

first: Gerald

last: Shulman

first: Dean

last: Yimlamai


title: Starving advanced prostate cancer cells by pharmacological gluose deprivation with a resveratrol trimer trans-Gnetin H

first: William

last: Oh