title: Analysis of differential gene expression in the choroid plexus (ChP) of E16.5 and P60 mice

status: Public on Nov 28 2020

city: Boston

first: Maria

last: Lehtinen

address: 300 Longwood Ave

department: Pathology

institute: Boston Children's Hospital

summary: Age-appropriate regulation of cerebrospinal fluid (CSF) dynamics including production, flow, and clearance (e.g. via glymphatics and dural lymphatics) is essential for brain health. The choroid plexus (ChP) is an important compartment in CSF dynamics but its contribution is poorly understood. To identify temporally regulated ChP epithelial cell functions that may relate to increased ATP demand, we investigated transcripts that are prioritized for translation, therefore reflecting the functional preference of the ChP tissue. We employed Translating Ribosomal Affinity Purification.  We identified ChP Na-K-Cl co-transporter [NKCC1] as developmentally regulated, in both expression and function, by mechanisms ranging from epigenetic (NuRD) to post-translational, coupled with increased ATP production. Premature NKCC1 overexpression in ChP accelerated CSF [K+] reduction, reduced ventricle size, and increased intracranial compliance by adulthood as measured by a murine intracranial pressu  re monitor paired serially with MRI. Our data point to a critical developmental period when ChP transiently absorbs CSF through NKCC1-mediated K+ transport, which bears implications on lifelong brain fluid homeostasis and health.

overall_design:
3 mice per age (collected at 9am)
TRAP mRNAs were isolated and sequenced from the choroid plexus (ChP) of E16.5 and P60 mice

middle: K

first: Ryann

last: Fame

first: Myriam

last: Heiman

first: Amanda

last: Vernon

first: Fan

last: Gao


title: Transcriptomic analysis of osmotic stress response in yeast xrn1 mutant

status: Public on Nov 27 2020

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary: The goal of the project was to study the response in transcription rates after 0.6M KCl addition genome wide. We used Genomic Run-On (GRO) experiment taking samples at 0, 8, 15, 30, and 45 minutes after salt addition in wild type and xrn1 mutant strains.

overall_design: Cells were grown in YPD at 30ºC to 0.4 OD600. Then, we added KCl to 0.6M. At the indicated times after KCl addition cells were spun-down and collected. Note that each sample record represents three replicates.

first: José

middle: E

last: Pérez-Ortín

last: García-Martínez

first: María

last: Pérez-Martínez

first: Paula

last: Alepuz

first: Nicki

last: De Clercq


title: Ythdf modulates Fmr1 target selection and restricts axonal growth in Drosophila

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

type: Expression profiling by high throughput sequencing

summary: RIP-seq of Fmr1 in D. melanogaster whole brains.

overall_design: A total of 27 biological samples were used. Four biological replicates for CG6422 input, Fmr1 IP and IgG IP. Five biological samples for w1118 input, Fmr1 IP and IgG IP.

first: Alessia

last: Soldano

first: Alessandro

last: Quattrone


title: Transcriptomic Analysis of Equine Placenta Reveals Key Regulators and Pathways Involved in Ascending Placentitis

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

country: USA

institute: University of Kentucky

summary: Placentitis was induced in six mares at approximately 290d of gestation (placentitis group), and six mares with gestationally age-matched (290 d) pregnancies did not receive any treatment (control group).  For induction of placentitis in the former group, Streptococcus equi subsp. zooepidemicus was introduced intracervically.

overall_design: Placental samples were collected from the caudal pole of the placenta from mares with experimentally induced placentitis (290 d GA, n =6) and normal pregnant mares (290 d GA, n=6). Total RNA was isolated from all samples using RNeasy Mini Kit (#74104; Qiagen), and DNA digestion was performed on-column using RNase-free DNase I (#79254: Qiagen), followed by cleanup procedures. All procedures were performed according to the manufacturer’s instructions. After extraction, RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). All samples had a 260/280 ratio >2.0 and RNA integrity number (RIN) > 8.0.

first: Hossam

last: El-Sheikh Ali

first: Pouya

last: Dini

first: Shavahn

middle: C

last: Loux

first: Carleigh

last: Fedorka

first: Kirsten

last: Scoggin

first: Yatta

middle: L

last: Boakari

first: Alejandro

last: Esteller-Vico

first: Ted

last: Kalbfleisch

middle: A


title: RRBS profiling and Transcriptome profiling of Stat3 wild-type, Stat3 knock-out, Dnmt3a/b wild-type and Dnmt3a/b knock-out mouse embryonic stem cells (mES cells)

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

institute: University of Padua

type: Methylation profiling by high throughput sequencing

summary: Naive pluripotent epiblast cells of the preimplantation murine embryo and their in vitro counterpart, embryonic stem (ES) cells, have the capacity to give rise to all cells of the adult. Such developmental plasticity is associated with global genome hypomethylation. It is unclear whether genome methylation is dynamically regulated only via differential expression of DNA methyltransferases (DNMTs) and Ten-eleven Translocation (TET) enzymes, which oxidase methylated DNA. Here we show that LIF/Stat3 signalling induces genomic hypomethylation via metabolic reconfiguration. In Stat3-/- ES cells we observed decreased alpha-ketoglutarate (ɑKG) production from reductive Glutamine metabolism, leading to decreased TET activity, increased Dnmt3a/b expression and to a global increase in DNA methylation. Notably, genome methylation is dynamically controlled by simply modulating αKG availability, mitochondrial activity or Stat3 activation in mitochondria, indicating an effective crosstalk between metabolism and the epigenome. Stat3-/- ES cells also show increased methylation at Imprinting Control Regions accompanied with differential expression of >50% of imprinted genes. Single-cell transcriptome analysis of Stat3-/- embryos confirmed dysregulated expression of Dnmt3a/b, Tet2, and imprinted genes in vivo. Our results reveal that the LIF/Stat3 signal bridges the metabolic and epigenetic profiles of naive pluripotent cells, ultimately controlling genome methylation and imprinted gene expression. Several imprinted genes regulate cell proliferation and are often misregulated in tumours. Moreover, a wide range of cancers display Stat3-overactivation, raising the possibility that the molecular module we described here is exploited under pathological conditions.

overall_design:
RRBS profiles of wild-type (S3+/+) and knock-out (S3-/-)  mES cells were generated by high-throughput sequencing, using Illumina NextSeq 500. Cells were either cultured in 2iLIF; 2 experimental replicates for each condition.  Total RNA profiles of wild-type (S3+/+), knock-out (S3-/-) and mitochondrial Stat3 (MitoS3.A, MitoS3.B) mESCs were generated by high-throughput sequencing, using Illumina HiSeq4000. Cells were either cultured in 2i, 2iLIF or without 2iLIF for 48 hours; 2 experimental replicates for each condition.
RRBS profiles of wild-type (WT) and Dmmt3a/b knock-out (Dnmt3a/b dKO) mES cells were generated by high-throughput sequencing, using Illumina NextSeq 500. Wild-type E14 cells were stably cultured either in 2iLIF or 2i; Dnmt3a/b dKO cells were stably cultured in 2i; 2 different KO clones were used (Dnmt3a/b dKO.A, Dnmt3a/b dKO.B); 2 experimental replicates for each condition.

first: Salvatore

last: Oliviero

first: Riccardo

middle: M

last: Betto

first: Linda

last: Diamante

first: Valentina

last: Perrera

first: Stefania

last: Rapelli

first: Andrea

last: Lauria

first: Danny

last: Incarnato

first: Mattia

last: Arboit


title: Functional Network Profiles In Arsacs Disclosed By Aptamer-Based Proteomic Technology

status: Public on Nov 26 2020

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

summary: Although the genetic basis of autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) has been uncovered, the cellular and molecular mechanisms characterizing this rare neurodegenerative disease are still under investigation, and no cure has yet been developed. In this study, we analyzed proteomics data obtained using the SomaLogic technology, comparing cell lysates from ARSACS patients and from a SACS KO SH-SY5Y neuroblastoma cell model. Single-stranded deoxyoligonucleotides, selected in vitro from large random libraries, bound and quantified molecular targets related to the neuroinflammation signaling pathway and to neuronal development. Changes in protein levels were further analyzed by bioinformatics and network approaches to identify biomarkers of ARSACS and functional pathways impaired in the disease. We identified novel significantly dysregulated biological processes related to neuroinflammation, synaptogenesis and engulfment of cells in patients and in KO cells compared with controls. Among the differential expressed proteins found in this work, we identified several proteins encoded by genes already known to be mutated in other forms of neurodegeneration. This finding suggests that common dysfunctional networks could be therapeutic targets for future investigations.

overall_design: Human fibroblasts were collected from diagnostic punch skin biopsies using standard procedures and with signed informed consent. Primary fibroblast cell lines from three ARSACS patients presenting severe disease status and carrying different mutations in SACS and from three healthy subjects were grown at 37 °C with 5% CO2 in Dulbecco’s modified Eagle’s medium, containing 10% FBS, 4.5 g/L glucose and 1% antibiotics/antimycotics.

first: Federica

last: Morani

first: Stefano

last: Doccini

first: Giovanna

last: Chiorino

first: Elisa

last: Sciarrillo

first: Fabiana

last: Fattori

first: Daniele

last: Galatolo

last: Gemignani

first: Enrico

middle: S

last: Bertini

first: Filippo

last: Santorelli


title: Mammalian SWI/SNF continuously restores local accessibility to chromatin [MNase-Seq]

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Open chromatin is a hallmark of regulatory regions and serves as a feature for their identification. Accessible genomic sites are mediated by the activity of transcription factors (TFs) that can engage with nucleosomes to enable stable gene expression changes that underlie development. While the variability of open chromatin between tissues has been studied in large detail, we have limited knowledge on the dynamics of accessible chromatin in any given cell. Answering this question is critical to better understand cellular memory but also to discern actual kinetics of TF binding and its consequence on local nucleosomal organization. Here we use small molecule inhibition of the catalytic subunit of the mouse SWI/SNF remodeler complex to show that accessibility at sites of TF binding critically relies on persistent activity of nucleosome remodelers. Within minutes of remodeler inhibition, accessibility decreases excluding that remodeler activity is only necessary in defined cell cycle transitions. Moreover, this surprisingly fast response is irrespective of TF function as it is similar for the pluripotency factor and activating TF Oct4 and the repressive TF Rest. Importantly, accessibility is rapidly restored upon inhibitor removal demonstrating that open chromatin is regenerated continuously and in a cell-autonomous fashion. Combined, this establishes a model where TF binding to chromatin and remodeler-mediated nucleosomal removal do not represent an initial opening event leading to a stable situation but instead open chromatin reflects an average of a highly dynamic situation that requires continued reestablishment. This argues against a model where open chromatin can persist in absence of continuous TF binding and remodeler activity.

overall_design: MNase-Seq (2 replicates per condition) profiling of wildtype mouse embryonic stem cells treated with BRM014 compound, DMSO (control), or with BRM014 followed by wash-out of the compound.

first: Mario

last: Iurlaro

first: Michael

middle: B

last: Stadler

first: Francesca

last: Masoni

first: Zainab

last: Jagani

first: Giorgio

middle: G

last: Galli

last: Schübeler


title: The dynamic methylome of the broiler chicken as a resource for livestock performance biomarker development

status: Public on Nov 30 2020

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

summary: The broiler chicken is the globally most important source of commercially produced meat. While genetic approaches have played an important role in the development of chicken stocks, little is known about chicken epigenetics. We have now systematically analyzed the chicken DNA methylation toolkit and DNA methylation landscape. While overall DNA methylation patterns were similar to mammals, sperm DNA appeared distinctly hypomethylated, which correlates with the absence of the DNMT3L cofactor in the chicken genome. Additional analysis also revealed the presence of low-methylated regions in the chicken methylome, which are conserved gene regulatory elements that show tissue-specific methylation patterns. We also used whole-genome bisulfite sequencing to establish 56 single-base resolution methylomes of the broiler chicken from various tissues and developmental time points. Data analysis confirmed tissue-specific and time-dependent methylation patterns that were used to establish a DNA methylation clock to predict sample age and measure stock performance. Our study thus provides a comprehensive resource for the chicken methylome and establishes a novel epigenetic tool for livestock performance analysis.

overall_design: Whole genome methylation analysis of G. gallus. Four tissues were sequenced and analyzed, all at different time points after birth. For jejunum tissue healthy and inflamed subjects were used. All combinations of tissues and time points were analyzed using replicates.

first: F

last: Lyko


title: Mammalian SWI/SNF continuously restores local accessibility to chromatin [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq (Oct4 or Rest, 2 replicates per condition) profiling of wildtype mouse embryonic stem cells treated with compound BRM014 or DMSO (control)


title: Activity-dependent regulome and transcriptome of human GABAergic neurons reveal new patterns of gene regulation and neurological disease heritability

first: Gabriella

middle: Lutz

last: Boulting

state: MA

address: 200 Longwood Ave.

department: Neurobiology

institute: Harvard Medical School

summary: Neuronal activity-dependent gene expression is essential for healthy brain development. Emerging studies implicate alterations in GABAergic neuronal circuits in neurodevelopmental and psychiatric disorders. We conducted an activity-dependent transcriptional and epigenetic profiling of human iPSC-derived GABAergic neurons.

overall_design: iCell GABAneurons were characterized by total and single-cell RNA sequencing and found to have similar transcriptional profiles to developing subcortical GABAergic neurons. These cultures were grown for 14-16 days in vitro prior to silencing with 2-amino-5-phosphonopentanoic acid and tetrodotoxin for 12 hours, followed by stimulation with 55mM potassium chloride for various time points prior to harvesting cells for RNA sequencing, ATAC sequencing or ChIP sequencing.

first: Ershela

last: Duressi

first: Bulent

last: Ataman

first: David

last: Harmin

first: Kevin

last: Mei

first: Ava

last: Carter

last: Greenberg


title: The reducing equivalent NADPH dictates histone acetylation via direct inactivation of HDAC3

city: beijing

first: wei

last: li

address: No.5 Dongdansantiao street, Dongcheng district

country: China

institute: Peking Union Medical College

summary: NADPH has been long well-recognized as a key cofactor for antioxidant defense and reductive biosynthesis. Here we report a metabolism-independent function of NADPH in modulating epigenetic status and transcription. We found that reduction of cellular NADPH levels by silencing malic enzyme (ME) or G6PD impairs global histone acetylation and transcription in both adipocytes and tumor cells. These effects can be reversed by supplementation of exogenous NADPH or inhibition of histone deacetylase 3 (HDAC3). Mechanistically, NADPH or inhibition of histone deacetylase 3 (HDAC3). Mechanistically,NADPH directly interacts with HDAC3 and interrupts the association between HDAC3 and its co-activator Ncor2 (SMRT) or Ncor1, thereby impairs HDAC3 activation. Interestingly, it appears that NADPH and  Ins(1,4,5,6)P4 bind to the same domains on HDAC3, and NADPH has relatively higher affinity towards HDAC3. Thus, while Ins(1,4,5,6)P4 acts as an ‘intermolecular glue’, NADPH may function as a HDAC3-Ncor assembly inhibitor. Collectively, our findings uncovered a previous unidentified and metabolism-independent role of NADPH in controlling epigenetic change and gene expression by acting as an endogenous inhibitor of HDAC3.

overall_design: Briefly, 3T3-L1 preadipocytes cells were transfected with control, ME1, or ME2 siRNAs as indicated and two days later induced to differentiate into adipocytes. After another 7 days, cells were washed in PBS buffer and subsequently cross-linked with 1% formaldehyde solution at room temperature (RT) for 15 min. After washing in cold PBS, cross-linking reaction was stopped by the addition of 0.125M glycine with gently shaking for 5min. Cells were then centrifuged and lysed in 300 μL SDS lysis buffer (50mM Tris-HCl pH 8.0, 10mM EDTA pH 8.0 , 1% SDS, protease inhibitors) for 15 minutes on ice. Cell lysates were sonicated to generate DNA fragments approximately 200-1000 bp and subjected to immunoprecipitation with indicated antibodies against Ac-H2B and Ac-H3. Immunoprecipitations were carried out overnight, samples were then washed with low salt buffer, high salt buffer, LiCl salt buffer and TE buffer sequentially. Histone-DNA complexes were eluted using elution buffer (1%SDS, 100 mM NaHCO3), incubated at 65ºC for overnight in the presence of 0.54 M NaCl. The next day, DNase-free RNase(10 mg/ml)was added into samples and incubated for 1 hour at 37℃.Samples were then incubated with Proteinase K for another 1 hour at 55ºC.Finally, DNA were purified using Qiaex II beads (Qiagen) and analyzed by quantitative PCR (qPCR). For ChIP-seq analysis, briefly, 3T3-L1 cells were treated with siRNA for 2 days and confluent cells were induced to differentiate into adipocytes. Cell were cross-linked, and the cell lysates were sonicated to generate DNA fragments and subjected to immunoprecipitation using Ac-H2B, Ac-H3 or HDAC3 antibodies as described above. Bound DNA fragments were eluted for ChIP-seq library construction and sequencing.

first: Wei

last: Li

first: Junjie

last: Kou

first: Junying

last: Qin

first: Li

first: Zhengxi

last: Zhang

first: Ying

last: Pan

first: Yi

last: Xue

first: Wenjing

last: Du


title: Mammalian SWI/SNF continuously restores local accessibility to chromatin [ATAC-Seq2]

first: Dirk

last: Schuebeler

overall_design: ATAC-seq (2 replicates per condition) profiling of wildtype mouse embryonic stem cells of different genetic backgrounds treated with compounds or DMSO (control) for different amounts of time.

first: Mario

last: Iurlaro

first: Michael

last: Stadler

first: Francesca

last: Masoni

first: Zainab

last: Jagani

first: Giorgio

last: Galli

last: Schübeler


title: Mammalian SWI/SNF continuously restores local accessibility to chromatin

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

overall_design: Refer to individual Series


title: Single-Cell RNA Sequencing Reveals Human iPS Cell-derived Alveolar Type 1 Cells in Alveolar Organoids [2D_EpCAM+ scRNA-seq]

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

summary: We induced differentiation from human induced pluripotent stem cell (hiPSC)-derived alveolar type2 (AT2) cells into hiPSC-derived 2D alveoalr type 1 (2D-iAT1) cells. Single cell RNA sequencing revealed that 2D-iAT1 cells were composed of three clusters.

overall_design:
After isolation of hiPSC-derived AT2 cells, hiPSC-dervied AT2 cells were cultured in two-demensional condition for 7 days, and then  single cell libraries were generated using Fluidigm C1 system.
Single "2D_EpCAM+" cells were captured and separated on the each chamber of medium-sized (17-25 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

first: Shuhei

last: Kanagaki

first: Yutaka

last: Suzuki


title: Mammalian SWI/SNF continuously restores local accessibility to chromatin [RNA-Seq]

overall_design: RNA-seq (2 to 4 replicates per condition) profiling of wildtype mouse embryonic stem cells treated with compounds or DMSO (control) for different amounts of time.


city: Seville

first: Villalba

last: Leticia

address: Avda. Manuel Siurot s/n

institute: FISEVI

summary: With the aim to elucidate the mechanism underlying the PAX6 role in such processes, we have performed a chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) analysis to identify the PAX6 target genes in enteric precursor cells (EPCs) from mice.

overall_design: Identification of PAX6 target genes in enteric precursor cells. 16 ChIPs, 16 Inputs and 4 IGG samples were sequenced and analyzed.

first: Salud

last: Borrego

first: Leticia

last: Villalba-Benito

first: Ana

last: Torroglosa


title: Identification of Hepatic Genes Regulated by ATF3 using Next Generation Sequencing

city: Rootstown

first: Yanqiao

last: Zhang

state: OH

address: 4209 State Route 44

institute: Northeast Ohio Medical University

summary: This study aimed to investigate how many genes were regulated by hepatocyte ATF3. C57BL/6J mice were injected intravenously with adeno-associated virus (AAV) expressing human activating transcription factor 3 (ATF3) under the control of an albumin promoter (AAV8-ALB-ATF3) or AAV8-ALB-Null). After 8 weeks, liver samples were used for RNA sequencing using Illumina NextSeq 500. Over 3000 genes were found to be up- or down-regulated by ATF3.

overall_design: Ten weeks old C57BL/6J mice were intravenoulsy injected with AAV8-ALB-ATF3 or AAV8-ALB-Null (control) (n=8 per group). After 8 weeks, total RNA was extracted and cDNA libraries were prepared. RNA sequencing was carried out using Next-Seq 500. Data were analyzed using Illumina Softwares in BaseSpace.

first: Yingdong

last: Zhu

first: Yanyong

last: Xu


title: Adaptation of Pseudomonas aeruginosa to cultivation in standard laboratory conditions

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

summary:
We studied adaptation of the metabolically versatile bacterium Pseudomonas aeruginosa to standard laboratory conditions by propagating mismatch repair-deficient P. aeruginosa in exponential phase for 24 days in rich medium. In the selective environment of this large-bottleneck mutation accumulation experiment, the bacteria developed shorter lag phases, higher growth rates and higher maximum cell densities. Transcriptional profiling and phenotyping for growth in different media revealed that higher fitness under laboratory conditions evolved via different pathways. Although common adaptive mutations or mutations that define trade-offs were not identified, there was a convergent evolution of transcriptional profiles associated with a shift from biofilm-associated to planktonic lifestyles. Our results indicate that under constant planktonic conditions P. aeruginosa uses several genetic pathways in order to fine-tune adaptation towards faster growth. The selected mutations in the different genetic pathways show a great variety of biofilm, virulence and motility phenotypic trade-offs, thus implying that on the population level, the adaptation of P. aeruginosa to constant conditions does not compromise its versatility.
Methods: mRNA profiles were generated for Pseudomonas aeruginosa samples derived from LB-cultures grown to an OD600 =0.4-0.6. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina). The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with default settings.

overall_design: Pseudomonas aeruginosa PA14 mutS::Tn mismatch repair-deficient strain was subjected to in vitro evolution in this study. This strain was obtained from a PA14 transposon insertion library. Cultures WBN1, 2, 4, 5, 6 were obtained from single colonies of PA14 mutS::Tn and passaged in exponential phase in LB for 24 days using 100-cell bottlenecks. The last passage of each WBN culture was streaked on LB agar to obtain 6 single-colony-derived clones, which were saved in liquid nitrogen. RNA sequencing was performed for three randomly selected clonal isolates from each WBN line. The first number in the name of each clone (e.g. "4" in WBN4-1) refers to the culture the clone is derived from. The second number in the name of each clone (e.g. "1" in WBN4-1) refers to the clone itself. The RNA of non-evolved PA14 mutS::Tn was sequenced as control.

first: Igor

last: Grekov

first: Janne

last: Thöming

first: Adrian

last: Kordes


title: Mammalian SWI/SNF continuously restores local accessibility to chromatin [ATAC-seq1]

first: Dirk

last: Schuebeler

overall_design: ATAC-seq (2 to 4 replicates per condition) profiling of wildtype mouse embryonic stem cells treated with compounds or DMSO (control) for different amounts of time.

first: Mario

last: Iurlaro

first: Michael

last: Stadler

first: Francesca

last: Masoni

last: Jagani


title: Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients [Drop-seq]

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

institute: Hannover Medical School

summary: Single-cell transcriptomics from dissociated organs lack information regarding the spatial origin of each cell, which limits their interpretation, particularly in complex and regionally heterogeneous tissues. This is relevant in the kidney, where cell types are exposed to a wide spectrum of cellular microenvironments along the corticomedullary axis, including steep gradients of extracellular osmolality and oxygen tension. Whether kidney single-cell transcriptomes can be exploited to predict spatial origins of cells and to provide physiological readouts of the cellular microenvironment is unknown. Here, we obtained single-cell transcriptomes of mouse kidney tissue from whole organs and from defined kidney zones (cortex, outer and inner medulla) and applied computational methods to reconstruct the spatial position of kidney tubule cells along the corticomedullary axis based on their transcriptomes. Our approach enabled a spatially resolved analysis of gene expression, showed a coordinated activation of osmolality-and hypoxia-associated genes towards the kidney medulla, and predicted that transcriptomes of a given cell type across different kidney zones change gradually rather than being clearly distinct in different anatomical zones. In genetically modified mice with a tubular concentration defect, spatial reconstruction of single-cell transcriptomics and osmogene expression quantitation accurately predicted reduced medullary osmolality. We conclude that our approach, which can be applied to any mouse whole kidney single-cell transcriptomic dataset, uncovers previously underappreciated information regarding spatial origin and microenvironment-dependent cellular states, adding improved readouts to existing and future datasets.

overall_design: The provided data comprise one sample of scRNA-seq from mouse renal cortex, outer medulla and inner medulla and two mouse whole kidney scRNA-seq datasets.

first: Nikos

last: Karaiskos

first: Anastasiya

last: Boltengagen

first: Katharina

last: Walentin

first: Klea

last: Redo

first: Nina

last: Himmerkus

first: Markus

last: Bleich

first: Steve

last: Potter

first: Andrew

first: Kai-Uwe

last: Eckardt

first: Christine

last: Kocks

first: Nikolaus

last: Rajewsky

first: Kai

last: Schmidt-Ott


title: Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients


title: Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients [bulk RNA-seq]

overall_design: The provided data comprise bulk RNA-sequencing data from microdissected cortex, OM, IM from wild type C56BL/6N male mice.


title: Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients [single nuclei]

overall_design: The provided data comprise one sample of whole kidney single-nuclei data from a collecting duct-specific knockout of Grainyhead-like 2 and one control littermate.


title: Single-Cell RNA Sequencing Reveals Human iPS Cell-derived Alveolar Type 1 Cells in Alveolar Organoids

first: Shimpei

last: Gotoh

summary: Human induced pluripotent stem cells (hiPSCs) were differentiated into alveolar epithelial cells in  the fibroblast-dependent (FD) or fibroblast-free (FF) alveolar organoids (AO). Then the epithelial cells in FD-AOs or FF-AOs were subjected to scRNA-seq. Then, human iPSC-derived AT1 (iAT1) cells were demonstrated to be included in FD-AOs, not in FF-AOs. In addition, XAV-939 increased iAT1 cell population in FD-AOs.

overall_design: After isolation of alveolar epihtelial cells (EpCAM+) cells from FD-AOs or FF-AOs,  single cell libraries were generated using Fluidigm C1 system. For XAV-939 treatment, FD-AOs treated XAV-939 from day 2 to 14.

first: Shuhei

last: Kanagaki

first: Yutaka

last: Suzuki


title: Inherent Motor Impulsivity Associates with Specific Gene Targets in the Rat Medial Prefrontal Cortex

city: Galveston

first: Kathryn

last: Cunningham

state: Texas

address: 301 University blvd, route 0615

department: Pharmacology and Toxicology

institute: UTMB

summary: The present study profiled the complete set of mRNA expressed from genes (transcriptome) in the medial prefrontal cortex of male, outbred rats stably expressing high (HI) or low (LI) motor impulsivity identified in the 1-choice serial reaction time (1-CSRT) task.

overall_design: HI and LI rats were defined as falling within the upper and lower quartiles of premature responses in the 1-CSRT task (n = 4-6/phenotype), respectively. RNA-sequencing was performed on isolated mPFC homogenate. Gene expression differences in HI vs. LI rats were identified using Fisher’s exact test (α = 0.1).

first: Dennis

middle: J

last: Sholler


title: Transcriptome analysis of liver tissue from Tm7sf2-KO mouse

status: Public on Nov 25 2020

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

summary: The nuclear envelope protein Tm7sf2/NET47, a paralog of Lbr preferentially expressed in liver, was knocked out in mouse (C57/B6 background). The transcriptome of livers from WT and KO mice were compared by microarray.

overall_design: Total RNA from liver of 6-week old WT and Tm7sf2-KO male mice was isolated, converted to cDNA, labelled with biotin and hybridized in duplicate to Affymetrix MOE430 v2 microarrays.

first: Rita

last: Roberti

first: Tommaso

last: Beccari

first: Giuseppe

last: Servillo

first: Maria

last: Dellafazia

first: Leonardo

last: Gatticchi


title: DMXAA (STING agonist) efficacy on tumor microenvironment after CAR-T therapy

city: Chapel Hill

first: Jonathan

last: Serody

state: NC

address: 125 Mason Farm Rd.

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: This study is designed to uncover the mechanism by which STING agonist (DMXAA) changes the tumor microenivorment of mammary tumor to support Th/Tc17 CAR-T cells treatment.

overall_design: Single-cell RNA-seq profiling for tumor infiltrating CD45 expressing cells are isolated from mice receiving Th/Tc17 CAR-T cells therapy with or without DMXAA (STING agonist) treatment.

first: Nuo

last: Xu


title: An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis [Set3]

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Damaged tissues have increased risk of cancer development through poorly understood mechanisms. In the pancreas, tissue damage collaborates with activating mutations in the Kras oncogene to dramatically accelerate the formation of early neoplastic lesions and ultimately pancreatic cancer. By integrating genomics, single-cell chromatin assays and spatiotemporally-controlled functional perturbations in autochthonous mouse models, we show that the combination of Kras mutation and tissue damage promotes a unique chromatin state in the pancreatic epithelium that distinguishes neoplastic transformation from normal regeneration and is selected for throughout malignant evolution. This cancer-associated epigenetic state emerges within 48 hours of pancreatic injury, and involves large-scale chromatin accessibility changes that contribute to the early dysregulation of genes defining human pancreatic cancer. Among the genes most rapidly activated by tissue damage in the pre-malignant pancreatic epithelium is the alarmin cytokine IL33, which cooperates with mutant Kras in unleashing the epigenetic remodeling program of early neoplasia and neoplastic transformation in the absence of injury. Collectively, our study demonstrates how gene-environment interactions can rapidly produce gene regulatory programs that dictate early neoplastic commitment and provides a molecular framework for understanding the interplay between genetics and environmental cues in cancer initiation.

overall_design: Characterization of the transcriptional profiles (RNA-seq) of bulk lineage-traced Kras-mutant pancreatic epithelial cells isolated by FACS-sorting from pancreata of Kras-mutant KC (p48-Cre;RIK;LSLKrasG12D) or Kras wild-type C (p48-Cre;RIK) mice treated with murine recombinant IL-33 (rIL-33) or PBS.

first: Direna

last: Curbelo

first: Scott

middle: W

last: Lowe


title: LaminB1-DamID analysis of primary hepatocytes from wild type and Tmem7sf2/NET47 knock-out mouse

summary: Maps of genomic regions in proximity to the nuclear lamina were determined in primary hepatocytes from wild type and Tm7sf2/NET47 KO mouse, C57BL/6 strain, using DamID with a Dam-Lamin B1-encoding lentivirus.

overall_design: Examination of Lamin B1-chromatin contacts in primary hepatocytes from wild type and Tmem7sf2/NET47 knock-out mouse.

middle: I

first: Eric

last: Schirmer


title: The expression of Rpb10, a small subunit common to RNA polymerases, is modulated by the R3H domain-containing Rbs1 protein and the Upf1 helicase

city: Warsaw

first: Tomasz

middle: Wojciech

last: Turowski

address: Pawinskiego 5a

department: Laboratory of Transcription Mechanisms

country: Poland

institute: Insitute of Biochemistry and Biophysics PAS

summary: The biogenesis of eukaryotic RNA polymerases is poorly understood. The present study used a combination of genetic and molecular approaches to explore the assembly of RNA polymerase III (Pol III) in yeast cells. We identified a regulatory link between Rbs1, a Pol III assembly factor, and Rpb10, a small subunit that is common to all three RNA polymerases Overexpression of Rbs1 increased the abundance of both RBP10 mRNA and the Rbp10 protein, which correlated with suppression of Pol III assembly defects. Rbs1 is a poly(A) mRNA-binding protein and mutational analysis identified R3H domain to be required for mRNA interactions and genetic enhancement of Pol III biogenesis. Rbs1 also binds to Upf1 protein, a key component in nonsense-mediated mRNA decay (NMD) and levels of RBP10 mRNA were increased in a upf1∆ strain. Genome-wide RNA binding by Rbs1 was characterized by UV cross-linking based approach (CRAC). We demonstrated that Rbs1 directly binds to the 3’ untranslated regions (3’UTRs) of many mRNAs including transcripts encoding Pol III subunits Rpb10 and Rpc19. We propose that Rbs1 functions by opposing mRNA degradation, at least in part mediated by NMD pathway. Orthologues of Rbs1 protein are present in other eukaryotes, including humans, suggesting that this is a conserved regulatory mechanism.

overall_design: Samples were analyzed in total from a strain carrying HTP tagged Rbs1 and untagged strain as a negative control. Duplicate experiments was carried out.

first: Małgorzata

last: Cieśla

first: Marcin

last: Nowotny

first: David

last: Tollervey

first: Magdalena

last: Boguta


title: Transcriptome alterations in the cerebellum of manganese (Mn)-deficient mice

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

summary: RNAseq was performed using cerebellum tissue of mice with either normal (35 ppm) or Mn-deficient (0 ppm) diet

overall_design: Three mice per group

first: Young

last: Seo


title: Loss of endocytosis-associated RabGEF1 causes aberrant morphogenesis and altered autophagy in photoreceptors leading to retinal degeneration

city: Bethesda

first: Anand

last: Swaroop

state: MD

address: 6 Center Dr, Bldg 6, Room 303

department: NEI

institute: NIH

summary: Rab and associated effector proteins are involved in all steps of cargo transport through subcellular compartments during the endocytic pathway that participates in multiple cellular processes including signal transduction, protein recycling and degradation. We identified Rabgef1 (also called Rabex-5) as the only differentially expressed Rab-associated gene that exhibits strong concordance with photoreceptor maturation by mining the retinal transcriptome data. The retinas of Rabgef1-/- mice exhibit defects in photoreceptor morphology, followed by cell death, and almost complete loss of both rod and cone photoreceptor function within 3 weeks after birth. Like other cells/tissues, Rabgef1 interacts with Rabaptin5 in the retina and its loss leads to reduced early endosomes in the photoreceptor inner segments as indicated by EEA1 immunostaining. Rabgef1-/- photoreceptors abnormally accumulate autophagosomes, and proteomic profiling of endosome-enriched fractions demonstrate significant depletion of phototransduction and mitochondrial proteins. Transcriptome analysis of developing retina before the degeneration is evident reveals energy metabolism modules and gene regulatory landscape that likely suggest the trajectory of cellular changes leading to photoreceptor degeneration. Our results directly implicate endocytic pathway in outer segment biogenesis and photoreceptor development and provide strong evidence that endocytosis defects in the retina can trigger upregulation of autophagic mechanisms. We also suggest that Rabgef1 and components of the endocytic and autophagic pathways should be considered as candidates for human retinopathies.

overall_design: Retinal transcriptome of Rabgef1 WT and KO mutants were profiles at three different ages: P6, P10, P14. All samples had at least two replicates. Transcriptome landscape were compared to determine the pathway changes associated with Rabgef1 loss of function.

first: Passley

last: Hargrove-Grimes

first: Anupam

middle: K

last: Mondal

first: Jessica

last: Gumerson

first: Jacob

last: Nellissery

first: Angel

last: Aponté

first: Linn

last: Gieser

first: Robert

last: Farris

first: Juan

last: Bonifacino

first: Tiansen

last: Li

first: Haohua

last: Qian


title: RNA-sequencing analysis of Drosophila yki tumor tissue

city: Daejeon

first: Kyu-Sun

last: Lee

address: 125 Gwahak-ro

country: South Korea

institute: KRIBB

summary: In this study, we showed Drosophila Dilp8 is secreted from tumor tissue and caused anorexia through Lgr3 receptor in the brain. To find the feeding neuropeptides regulated by Dilp8, RNA-sequencing analysis was processed using yki-induced tumor tissue.

overall_design: 2 samples each for GMR-Gal4 control head tissue and GMR>ykiSA tumor head tissue

first: Kweon

last: Yu


title: Targeting aberrant DNA methylation in mesenchymal stromal cells as a treatment for myeloma bone disease [methylation II]

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

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

institute: Josep Carreras Research Institute (IJC)

summary: Genome wide DNA methylation profiling of bone marrow-derived mesenchymal stromal cells from healthy donors (n=11), monoclonal gammopathy of undetermined significance (MGUS) (n=10), smoldering myeloma (SMM) (n=8), multiple myeloma (MM) (n=9) patients, and healthy donors exposed to the MM.1S cell line (n=3). The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in this cell type.

overall_design: Bisulphite converted DNA from all samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip.

first: Antonio

last: Garcia-Gomez

first: Tianlu

first: Javier

last: Rodríguez-Ubreva

first: Laura

last: Ciudad

first: Francesc

last: Català-Moll

first: Montserrat

last: Martín

last: San-Segundo

first: Xabier

last: Morales

first: Carlos

last: Ortiz de Solórzano

first: Julen

last: Oyarzabal

first: Edurne

last: San-José Enériz

last: Agirre

first: Felipe

last: Prosper

first: Mercedes

last: Garayoa


title: Targeting aberrant DNA methylation in mesenchymal stromal cells as a treatment for myeloma bone disease [expression]

summary: Gene expression profiling of bone marrow-derived mesenchymal stromal cells from healthy donors (n=8), monoclonal gammopathy of undetermined significance (MGUS) (n=10), smoldering myeloma (SMM) (n=10) and multiple myeloma (MM) (n=24) patients. Gene expression profile of MSCs was obtained using high density oligonucleotide microarrays (Human Gene 1.0 ST Array from Affymetrix).

overall_design: Primary MSCs from bone marrow (BM) samples of healthy donors, MGUS, smoldering myeloma and multiple myeloma (MM) patients were generated as described by Garayoa et al. 2009 (PMID:19357701). Ficoll-Paque density gradient separation medium was used to isolate mononuclear cells from BM aspirates. MSCs were selected by adherence to plastic and subsequently expanded until passage 2 when they were used for experiments.

last: Li

last: Martín-Sánchez


title: Targeting aberrant DNA methylation in mesenchymal stromal cells as a treatment for myeloma bone disease [methylation]


title: Targeting aberrant DNA methylation in mesenchymal stromal cells as a treatment for myeloma bone disease

type:
Methylation profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis  [ATAC-seq]

first: Richard

last: Koche

state: NY

address: 417 East 68th St

department: Center for Epigenetic research

summary: Damaged tissues have increased risk of cancer development through poorly understood mechanisms. For example, in the pancreas, tissue damage collaborates with activating mutations in the Kras oncogene to dramatically accelerate the formation of early neoplastic lesions and, ultimately, pancreatic cancer. By integrating genomics, single-cell chromatin assays and spatiotemporally-controlled functional perturbations in autochthonous tumor models, we show that the combination of Kras mutation and tissue damage promotes a functionally relevant chromatin state in the pancreatic epithelium that distinguishes neoplastic transformation from normal regeneration and is inherited throughout malignant evolution. This cancer-associated epigenetic state emerges remarkably fast, involves chromatin accessibility changes not induced by pancreatic injury alone, and contributes to the early activation of neoplasia specific genes that define advanced human pancreatic cancer. Among the genes activated by injury-facilitated chromatin reprogramming are a series of known and novel cancer-related factors, including the alarmin cytokine IL33, which cooperates with mutant Kras in driving neoplastic transformation in the absence of tissue damage. Collectively, our study demonstrates how gene-environment interactions can rapidly produce gene regulatory programs that dictate early neoplastic commitment and provides a molecular framework for understanding the cooperation between genetics and environmental cues in cancer initiation.

overall_design: Characterization of the chromatin accessibility profiles of lineage-traced pancreatic epithelial cells isolated directly by FACS-sorting (mKate2+ or GFP+) from normal, regenerating, early neoplastic and malignant murine pancreatic tissues: To compare the effects of tissue injury in mutant Kras-expressing or Kras wild-type pancreatic epithelial cells, cells were sorted from KC;RIK (p48-Cre;RIK;LSLKrasG12D) or C;RIK (p48-Cre;RIK) male mice treated with caerulein or PBS (vehicle control) at 5 weeks of age, using littermates when possibe. To characterize invasive disease, pancreatic ductal adenocarcinoma (PDAC) cells were isolated from cancer lesions arising in autochthonous transgenic models (KPflC;RIK (p48Cre;RIK;LSL-KrasG12D;p53fl/+) or in immunocompetent mice upon orthotopic transplantation of pre-malignant Kras-mutated;p53-null pancreatic organoids. 3-6 biological replicates (independent mice) were used per experimental condition.

first: Direna

last: Curbelo

first: Scott

last: Lowe


title: An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis  [Set1]

first: Yu-Jui

last: Ho

overall_design: Characterization of the transcriptional profiles of bulk lineage-traced pancreatic epithelial cells isolated directly by FACS-sorting (mKate2+ or GFP+) from normal, regenerating, early neoplastic and malignant murine pancreatic tissues: To compare the effects of tissue injury in mutant Kras-expressing or Kras wild-type pancreatic epithelial cells, cells were sorted from KC;RIK (p48-Cre;RIK;LSLKrasG12D) or C;RIK (p48-Cre;RIK) male mice treated with caerulein or PBS (vehicle control) at 5 weeks of age, using littermates when possibe. To characterize invasive disease, pancreatic ductal adenocarcinoma (PDAC) cells were isolated from cancer lesions arising in autochthonous transgenic models (KPflC;RIK (p48Cre;RIK;LSL-KrasG12D;p53fl/+). 3-6 biological replicates (independent mice) were used per experimental condition.


title: An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis [scATAC-Seq]

city: New York City

first: Cassandra

last: Burdziak

overall_design: Characterization of single-cell chromatin accessibility profiles of lineage-traced pancreatic epithelial cells isolated directly by FACS-sorting (mKate2+) from early neoplastic pancreatic tissues: To assess the effects of tissue injury in mutant Kras-expressing pancreata, lineage-traced (mKate2+) pancreatic epithelial cells were sorted from KC;RIK (p48-Cre;RIK;LSLKrasG12D) littermate male mice treated with caerulein or PBS (vehicle control) at 5 weeks of age.

last: Alonso Curbelo


title: RNAseq analysis of MM13 and MM2 metastatic melanoma PDX cells overexpressing TINCR

city: Milano

first: Marine

last: Melixetian

address: via Adamello 16

institute: European Institute of Oncology

summary:
Purpose: Study the changes in cell transcriptome upon overexpression of lncRNA TINCR
Methods: Primary melanoma cell line WM902B was transduced with lientiviruses expressing Scrambled and TINCR directed shRNA hairpins
Results: we found that TINCR overexpression induces partial reversion of invasive phenotype

overall_design: Analysis of differential gene expression in control and TINCR overexpressing MM2 and MM13 metastsatic melanoma PDX cells

first: Daniela

last: Bossi

first: Marija

last: Mihalovich

first: Simona

last: Punzi

first: Iros

last: Barozzi

first: Giuseppe

last: Testa

first: Alessandro

last: Cuomo

first: Tiziana

last: Bonaldi

first: Eleonora

last: Leucci

first: Jean-Chrisophe

last: Marine

first: Saverio

last: Minucci

first: Pier

last: Pelicci

first: Luisa

last: Lanfrancone


title: An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis [Set2]

overall_design: Identification of the transcriptional changes induced upon doxycycline (dox)-inducible Brd4 knockdown in either wild-type or mutant Kras bulk pancreatic epithelial cells triggered to undergo regenerative (Injury condition) or proneoplastic (Kras*+Injury condition) transitions, respectively: Brd4-suppressed vs Brd4-expressing pancreatic epithelial cells were FACS-sorted (mKate2+;GFP+) from pancreata from p48Cre;RIK;TRE-GFP-shRNA (Kras wild-type) or p48Cre;RIK;TRE-GFP-shRNA;LSL-KrasG12D (Kras mutant) mice (harbouring Brd4 shRNA -1448, 552- or control Renilla shRNA -713-) at day 2 after treatment with caerulein. Brd4-expressing (shRen) pancreatic epithelial cells FACS-sorted from p48Cre;RIK;TRE-GFP-shRNA (Kras wild-type) mice which were placed on dox diet but not subjected to caerulein treatment served as additional control to pinpoint caerulein- and mutant Kras-specific effects. 3 biological replicates (independent mice) were used per experimental condition.

first: Direna

last: Curbelo

last: Lowe


title: Long non-coding RNA TINCR suppresses metastatic  melanoma dissemination by preventing ATF4 translation

type: Non-coding RNA profiling by high throughput sequencing


title: RNAseq analysis   of lncRNA  silenced  primary melanoma cell line WM902B

summary:
Purpose:  Study   the  changes in gene expression  upon  silencing of lncRNA TINCR
Methods:        Primary melanoma cell line WM902B  was transduced with lientiviruses expressing  Scrambled and TINCR directed shRNA hairpins
Results:  we found that TINCR silencing  induces switch  to invasive phenotype in WM902B  primary melanoma cells

overall_design: Analysis of differential gene  expression  in shscrambled and shTINCR expressing WM902B cells


title: Ribosome profiling analysis of lncRNA TINCR silenced primary melanoma cell line WM902B

summary:
Purpose: Study the changes in mRNA translation upon silencing of lncRNA TINCR
Methods: Primary melanoma cell line WM902B was transduced with lientiviruses expressing Scrambled and TINCR directed shRNA hairpins
Results: we found that TINCR silencing induces activation of ATF4 translation

overall_design: Analysis of differential translation in shScrambled and shTINCR expressing WM902B cells


title: Metabolic reprogramming and epigenetic changes of vital organs in SARS-CoV-2 induced systemic toxicity

status: Public on Nov 24 2020

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: SARS-CoV-2 primarily affects the respiratory system but extra-pulmonary manifestations in individuals with COVID-19 are commonly seen. All major organ systems have been reported to be affected by SARS-CoV-2 and complications arising from ensuing organ dysfunction significantly increase the mortality rate of COVID-19. Yet, despite the clinical importance of systemic involvement of SARS-CoV-2, little is known about the pathogenesis of extra-pulmonary complications of COVID-19. Here, we create a murine model of SARS-CoV-2 induced severe systemic toxicity and multi- organ involvement by expressing the human ACE2 transgene in multiple tissues using an adeno associated virus (serotype 9) followed by administration of the SARS-CoV-2 virus intra-peritoneally. The animals develop a profound phenotype within 7 days of SARS-CoV-2 infection with severe weight loss, morbidity and failure to thrive, that necessitated euthanasia. We demonstrate that following a robust anti-viral immune response, there is metabolic suppression of oxidative phosphorylation and the tri- carboxylic acid (TCA) cycle in multiple organs with neutrophilia, lymphopenia and splenic atrophy mirroring human COVID-19 phenotypes with adverse prognosis. Animals had a significantly lower heart rate and electron microscopy demonstrated myofibrillar disarray and myocardial edema, a common pathogenic cardiac phenotype in human COVID-19. An organ wide metabolic reprogramming consistent with depression of oxidative phosphorylation led to utilization of peripheral fat stores and gross accumulation of fat in the heart and other vital organs. We perform metabolomic profiling of peripheral blood and identify a panel of TCA cycle metabolites that serve as biomarkers of depressed oxidative phosphorylation, several of these markers been noted in human clinical studies to be associated with adverse prognosis. Finally, we observed that SARS-CoV-2 induces epigenetic changes with a significant number of differentially methylated sites in vital organs, across the whole host cell genome, that affects expression of immune response genes and could in part contribute to dysregulated gene expression in affected tissues. Our model suggests that SARS-CoV- 2 induced metabolic reprogramming and epigenetic changes in internal organs could contribute to systemic toxicity and lethality in COVID-19.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of expression changes of mouse organs with nCOV2 infection

first: Shen

last: Li

first: Matteo

last: Pellegrini

first: Arjun

last: Deb


title: lncRNA TINCR antisense pulldown of interacting RNAs

first: Marine

last: Melixetian

summary:
Purpose: Identify RNA interactome of lncRNA TINCR
Methods: Primary melanoma cell lines WM902B and MMC70 lysates hybridized with TINCR antisense DNA oligos
Results: we found that TINCR silencing induces activation of translation of ATF4 and other stress responsive RNAs.

overall_design: RNA Peak Analysis in two independent replicates ( even and odd sets of DNA antisense oligos) in WM902B and MMC70 melanoma cells

first: Daniela

last: Bossi

last: Mihalovich


title: Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors

first: John

last: Poirier

address: 550 1st Ave

institute: NYU Langone Health

summary: The ongoing SARS-CoV-2 pandemic has devastated the global economy and claimed more than one million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a focused high-coverage CRISPR-Cas9 library targeting 332 members of a recently published SARS-CoV-2 protein interactome. We leveraged the compact nature of this library to systematically screen SARS-CoV-2 at two physiologically relevant temperatures (33 ºC and 37 ºC) along with three related coronaviruses (HCoV-229E, HCoV-NL63, and HCoV-OC43), allowing us to probe this interactome at a much higher resolution relative to genome scale studies. This approach yielded several new insights, including unexpected virus-specific differences in Rab GTPase requirements and GPI anchor biosynthesis, as well as identification of multiple pan-coronavirus factors involved in cholesterol homeostasis. This coronavirus essentiality catalog could inform ongoing drug development efforts aimed at intercepting and treating COVID-19, and help prepare for future coronavirus outbreaks.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Focused CRISPR screens targeting host factors in the SARS-CoV-2 interactome were performed for SARS-CoV-2, HCoV-229E, HCoV-NL63, and HCoV-OC43 coronaviruses.

first: Hans-Heinrich

last: Hoffmann

first: Francisco

last: Sánchez-Rivera

first: William

last: Schneider

first: Joseph

last: Luna

first: Yadira

last: Soto-Feliciano

first: Alison

last: Ashbrook

first: Jérémie

last: Le Pen

first: Andrew

last: Leal

first: Inna

last: Ricardo-Lax

first: Eleftherios

last: Michailidis

first: Yuan

last: Hao

first: Ansgar

middle: F

last: Stenzel

first: Avery

last: Peace

first: Johannes

last: Zuber

first: C

middle: D

last: Allis

first: Scott

first: Margaret

middle: R

last: MacDonald

middle: T

first: Charles

last: Rice


title: RNA Sequencing  Analysis of wild type (WT) and Mrp4 knock out (Mrp4-/-) mice adipose tissue Transcriptomes

city: Storrs

first: Jose

middle: E

last: Manautou

state: Connecticut

address: 69 N Eagleville Rd, Room 517

department: Pharmaceutical Sciences

institute: University of Connecticut

summary: The goal of this study is to idenitfy the role of multi drug resistance-associated protein- 4 ( Mrp4), a drug transorter, in adipose tissue phyisiology and adipogenesis processes. In this study we aim to identify gene expression changes in adipose tissue that are altered due to lack of Mrp4 in mice. These gene expression changes observed will aid us in idenitifying the role of Mrp4 in adipose tissue physiology and its role in adipogenesis processes.

overall_design: We have analysed white adipose tissue mRNA profiles of 16 week old wild type (WT) and Mrp4 knock out (Mrp4-/-) mice. In this experiment we have n=4 samples per genotype

first: Ajay

middle: C

last: Donepudi


title: Expression date from mouse peritoneum after intraperitoneal injection of chlorhexidine gluconate

city: Kyoto

first: Takuya

last: Ishimura

state: Kyoto

address: Sakyo-ku Syogoinkawaharatyo 54

department: Nephrology

institute: Kyoto University

summary: To study angiogenesis and inflammatory mediators in peritoneal fibrosis, we used microarray analysis and compared gene expression profiles of the peritoneum in control and chlorhexidine gluconate (CG)-induced peritoneal fibrosis mice.

overall_design:
Peritoneum was obtained after intraperitoneal injection of 0.01 mL/gBW of 0.1% CG in 15% ethanol and 85% PBS 3 times per week for 21 days. Control mice received intraperitoneal injection of ethanol/PBS. WT; wild-type mice, SAP-BNP-Tg; serum amyloid P promoter-driven brain natriuretic peptide transgenic mice (J Clin Invest. 93, 1911-1921, 1994).
Please note that raw data CEL files are not provided as they have been lost.

first: Hideki

last: Yokoi


title: Iron Deficiency Triggered Transcriptome Changes in Bread Wheat

city: Hefei

first: Meng

last: Wang

address: School of Life Sciences, West Campus of University of Science and Technology of China, No. 443 Huangshan Road, Shushan District, Hefei, Anhui, China

institute: USTC

summary: Iron (Fe) plays a pivotal role in several metabolic and biosynthetic pathways essential for plant growth. Fe deficiency in plants severely affects the overall crop yield. Despite several studies on iron deficiency responses in different plant species, these mechanisms remain unclear in the allohexaploid wheat, which is the most widely cultivated commercial crop. In order to gain a comprehensive insight into molecular responses of bread wheat when exposed to iron deficiency, we studied transcriptomic changes in the roots and flag leaves of wheat plants subjected to iron-deficient and iron-sufficient conditions during early grain filling.

overall_design: Triticum aestivum cv. Bobwhite S26 seeds were germinated on wet filter paper for 7 days and then transferred to the hydroponic system in the greenhouse conditions (22˚C/18˚C with 16-hour-light/8-hour-dark cycle, 60% relative humidity). All the seedlings were first maintained in iron-sufficient hydroponic solution for 7 days and then half of the plants were transferred to iron-deficient hydroponic solutions (iron-sufficient condition: 100.0 μM Fe; iron-deficient condition: 10.0 μM Fe). Roots and flag leaves were collected at 8-10 days post anthesis (DPA), i.e., around the commencement of grain filling. Three biological replicates were collected for each sample. Twelve samples were collected in total.

first: Navreet

last: Bhullar

first: Jiazhen

last: Gong


title: Tumour Heterogeneity and Intercellular Networks of Nasopharyngeal Carcinoma at Single Cell Resolution

city: Guangzhou

first: Jin-Xin

last: Bei

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District, Guanzhou, P.R. China

institute: Sun Yat-sen University Cancer Center

summary: The heterogeneous nature of tumour microenvironment (TME) underlying diverse treatment responses remains unclear in nasopharyngeal carcinoma (NPC). Here, we profile 176,447 cells from 10 NPC tumour-blood pairs, using single-cell transcriptome coupled with T cell receptor sequencing. Our analyses reveal 53 cell subtypes, including tumour-infiltrating CD8+ T, regulatory T (Treg), and dendritic cells (DCs), as well as malignant cells with different Epstein-Barr virus infection status. Trajectory analyses reveal exhausted CD8+ T and immune-suppressive TNFRSF4+ Treg cells in tumours might derive from peripheral CX3CR1+CD8+ T and naïve Treg cells, respectively. Moreover, we identify immune-regulatory and tolerogenic LAMP3+ DCs. Noteworthily, intensive inter-cell interactions are observed among LAMP3+ DCs, Treg, exhausted CD8+ T, and malignant cells, suggesting potential cross-talks to foster an immune-suppressive niche for the TME. Collectively, our study uncovers the heterogeneity and interacting molecules of the TME in NPC at single-cell resolution, which provide insights into the mechanisms underlying NPC progression and the development of precise therapies for NPC.

overall_design: We profile 176,447 cells from 10 NPC tumour-blood pairs, using single-cell transcriptome coupled with T cell receptor sequencing.

first: Yang

last: Liu

first: Shuai

last: He

first: Xi-liang

first: Dong-Mei

last: Chi

first: Qiu-Yan

last: Chen

first: Wan

last: Peng

first: Jie-Rong

first: Bo-Wei

last: Han

first: Guo-Wang

last: Lin

first: Yi-Qi

last: Li

first: Qian-Yu

first: Rou-Jun

first: Pan-Pan

last: Wei

first: Xiang

last: Guo

first: Bo

first: Xiaojun

last: Xia

first: Hai-Qaing

last: Mai

first: Xue-Da

last: Hu

first: Zemin

last: Zhang


title: De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG island (T7-DNMT3B ChIP-Rx_seq)

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

summary: The aberrant gain of DNA methylation at CpG islands (CGIs) is frequently observed in colorectal tumours and may silence the expression of tumour suppressors such as MLH1. Current models propose that these CGIs are targeted by de novo DNA methyltransferases (DNMTs) in a sequence-specific manner but this has not been tested. Using ectopically integrated CGIs, we find that aberrantly methylated CGIs are subject to low levels of de novo DNMT activity in colorectal cancer cells. By delineating DNMT targets, we find that instead de novo DNMT activity is targeted primarily to CGIs marked by the histone modification H3K36me3, a mark associated with transcriptional elongation. These H3K36me3 marked CGIs are heavily methylated in colorectal tumours and the normal colon suggesting that de novo DNMT activity at CGIs in colorectal cancer is focused on similar targets to normal tissues and not greatly remodelled by tumourigenesis.

overall_design: This series contains t7_DNMT3B ChIP-Rx_seq from human cancer cell lines


title: De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG island


title: Locus-specific paramutation in Zea mays is maintained by a chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function

city: COLUMBUS

first: Natalie

middle: Christine

last: Deans

address: 318 W. 12th Ave, 500 Aronoff

department: Molecular Genetics

institute: The Ohio State University

summary: Paramutations represent directed and meiotically-heritable changes in gene regulation leading to apparent violations of Mendelian inheritance. Although the mechanism and evolutionary importance of paramutation behaviors remain largely unknown, genetic screens in maize (Zea mays) identify five components affecting 24 nucleotide RNA biogenesis as required to maintain repression of a paramutant purple plant1 (pl1) allele. Currently, the RNA polymerase IV largest subunit represents the only component also specifying proper development. Here we identify a chromodomain helicase DNA-binding 3 (CHD3) protein orthologous to Arabidopsis (Arabidopsis thaliana) PICKLE as a second component maintaining both pl1 paramutation, and normal somatic development. In addition, genetic tests show this protein contributes to proper male gametophyte function. The similar mutant phenotypes documented in Arabidopsis and maize implicate some evolutionarily-conserved gene regulation while developmental defects associated with the two paramutation mutants are largely distinct. Our results show that a CHD3 protein responsible for normal plant ontogeny and sperm transmission also maintains meiotically-heritable epigenetic regulatory variation for specific alleles. This finding implicates an intersection of RNA polymerase IV function and nucleosome positioning in the paramutation process.

overall_design: sRNA-seq comparing rmr12 mutant and non-mutant seedlings.

first: Jay

last: Hollick


title: De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG island (H3K36me3 ChIP-Rx_seq)

overall_design: This series contains H3K36me3 ChIP-Rx_seq from human cancer cell lines


title: Deciphering Endoderm-derived Macrophage-like Metaphocytes in Zebrafish Gill and Intestine

city: HK

first: Zilong

last: WEN

address: Academic Bld., HKUST, Clearwater Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

summary: In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine, we isolated endoderm-derived GFP+ cells and remaining DsRedx+ cells (hematopoiesis-derived macrophages) from the gill (sox17_gill_GFP, sox17_gill_DsRedx) and intestine (sox17_intestine_GFP, sox17_intestine_DsRedx) of 4-OHT treated Tg(sox17:CreERT2;mpeg1:loxP-DsRedx-loxP-GFP) fish and performed RNA-seq. Both T-SNE analysis and feature gene comparison indicate that the endoderm-derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm-derived mpeg1+ cells as metaphocytes.

overall_design: Different cell types form zebrafish gill and intestine, including GFP labelled metaphocytes and DsRedx labelled macrophages, were sorted by fluorescence-activated cell sorting (FACS). cDNA libraries were prepared according to standard Smart-seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair-end sequencing.

first: Xi

first: Qiuxia

last: Zhou

first: Guanzhen

first: Changlong

last: Zhao

last: Wen


title: The nuclear envelope protein Net39 is essential for nuclear integrity, chromatin organization, and muscle growth (RNA-Seq)

city: Dallas

first: Andres

last: Ramirez-Martinez

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UTSW Medical Center

summary: Lamins and transmembrane proteins within the nuclear envelope are regulators of nuclear structure and chromatin organization. Nuclear Envelope Transmembrane Protein 39 (Net39) is a muscle-restricted nuclear envelope protein. We show that mice lacking Net39 succumb to severe myopathy and neonatal lethality, with concomitant disruption in nuclear integrity, chromatin accessibility, gene expression and metabolism. These abnormalities resemble those of Emery-Dreifuss muscular dystrophy (EDMD), caused by mutations in A-type Lamins (LMNA) and other genes, like Emerin (EMD). We observe that Net39 is downregulated in EDMD patients, implicating Net39 in the pathogenesis of this disorder. Our findings reveal an intimate role for the nuclear envelope in maintaining muscle chromatin organization, gene expression and function, and highlight the importance of Net39 in these processes and in the molecular etiology of EDMD.

overall_design: Gene expression profile was generated comparing wild type (WT) and Net39 knockout(KO) mice, by deep sequencing, with three biological replicates, using Illumina HiSeq 2500. Two timepoints (9 days of age and 17 days of age) were analyzed.

first: Yichi


title: The nuclear envelope protein Net39 is essential for nuclear integrity, chromatin organization, and muscle growth (ATAC-Seq)

overall_design: ATAC-seq was performed in WT and Net39 KO muscle tissue at 17 days of age.


title: The nuclear envelope protein Net39 is essential for nuclear integrity, chromatin organization, and muscle growth (ChIP-Seq)

overall_design: Lamin A ChIP-seq was performed in WT and Net39 KO hindlimb muscle tissue at 17 days of age.


title: Transcriptional responses of wild-type and abr1 mutant Arabidopsis plants to infection with Pseudomonas syringae

city: Albany

first: Jennifer

last: Lewis

address: 800 Buchanan St

institute: University of California, Berkeley

summary: Pathogens secrete effector proteins into host cells in order to suppress host immunity and promote pathogen virulence, although many features at the molecular interface of host-pathogen interactions remain to be characterized.  In a yeast two-hybrid assay, we found that the Pseudomonas syringae effector HopZ1a interacts with the Arabidopsis transcriptional regulator Abscisic Acid Repressor 1 (ABR1).  Further analysis revealed that ABR1 interacts with multiple P. syringae effectors, suggesting that it may be targeted as a susceptibility hub.  Indeed, loss-of-function abr1 mutants exhibit reduced susceptibility to a number of P. syringae strains.  The ABR1 protein comprises a conserved APETALA2 (AP2) domain flanked by long regions of predicted structural disorder.  We verified the DNA-binding activity of the AP2 domain and demonstrated that the disordered domains act redundantly to enhance DNA binding and to facilitate transcriptional activation by ABR1.  Finally, we compared gene expression profiles from wild-type and abr1 plants following inoculation with P. syringae, which suggested that the reduced susceptibility of abr1 mutants is due to the loss of a virulence target rather than an enhanced immune response.  These data highlight ABR1 as a functionally important component at the host-pathogen interface.

overall_design: Wild-type and abr1 mutants infiltrated with either 10 mM MgCl2 (Control), 1 x 10^8 cfu/mL Pseudmonas syringae pv. tomato DC3000, or 1 x 10^8 cfu/mL P. syringae pv. tomato DC3000 ΔhrcC (three biological replicates each for a total of 18 samples)

first: Karl

last: Schreiber


title: Round 2 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

city: Nonoichi

first: Takanori

last: Kobayashi

state: Ishikawa

address: 1-308 Suematsu

department: Research Institute for Bioresources and Biotechnology

institute: Ishikawa Prefectural University

summary: We report the comparison of transcript expression of Fe-sufficient roots of OsIMA overexpression lines IMA1OX-4, IMA2OX-1, OsIMA knockdown lines IMA1i-2, IMA2i-3, and corresponding NT, as well as Fe-deficient roots of NT, by RNA-Seq.

overall_design: Total RNA was extracted from Fe-sufficient roots of OsIMA overexpression lines IMA1OX-4, IMA2OX-1, OsIMA knockdown lines IMA1i-2, IMA2i-3, and corresponding NT, as well as Fe-deficient roots of NT, and used for RNA-Seq library preparation, sequencing, mapping and quantification of each gene expression as read per million (RPM). Fe deficiency responses in NT was analyzed by the expression ratiios of NT1 -Fe/NT1 +Fe and NT3 -Fe/NT3 +Fe.

first: Atsushi

last: Nagano


title: Heterogeneity of monocytes/macrophages in skin wounds from non-diabetic and diabetic mice

city: Chicago

first: Timothy

middle: Jon

last: Koh

state: IL

address: 1919 W Taylor Room 650

institute: University of Illinois at Chicago

summary: Monocytes isolated from skin wounds on non-diabetic and diabetic mice on day 6 post-injury, subjected to enzymatic digestion to obtain single cells and pooled from two mice per strain. Fresh cells with viability over 85% processed using the 10x Chromium platform . Libraries sequenced on HiSeq with paired-end reads. Fastq files were generated and iesdemultiplexed into single cells using Cell Ranger software

overall_design: Single cell RNA-seq data from 10X Chromium. Two samples: Control and diabetic models

first: Jingbo

last: Pang

first: Mark

last: Maienschein-Cline


title: Round 1 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice.

summary: We report the comparison of transcript expression of Fe-sufficient roots and leaves of OsIMA overexpression lines IMA1OX-7, 9, IMA2OX-2, 5 and corresponding NTby RNA-Seq.

overall_design: Total RNA was extracted from Fe-sufficient roots and leaves of IMA1OX-7, 9, IMA2OX-2, 5 and corresponding NT, and used for RNA-Seq library preparation, sequencing, mapping and quantification of each gene expression as read per million (RPM).


title: Elevated NSD3 Histone Methylation Activity Drives Squamous Cell Lung Cancer

city: Houston

first: Pawel

last: Mazur

address: 6565 MD Anderson Blvd

department: Experimental Radiation Oncology

institute: MD Anderson

summary: Amplification of chromosomal region 8p11-12 is a frequent genetic alteration implicated in the etiology of lung squamous cell carcinoma (LUSC). FGFR1 (fibroblast growth factor receptor 1) is the main candidate driver within this region. However, clinical trials evaluating FGFR1 inhibition as a targeted therapy have been unsuccessful. Here we identify the H3K36 methyltransferase NSD3 (nuclear receptor binding SET domain protein 3), an 8p11-12-localized gene, as a key regulator of LUSC tumorigenesis. In contrast to other 8p11-12 candidate LUSC drivers, increased NSD3 expression strongly correlates with gene amplification. Ablation of NSD3, but not FGFR1, attenuates tumor growth and extends survival in a potent LUSC mouse model. We identify NSD3T1232A as an LUSC-associated variant that increases H3K36 dimethylation (H3K36me2) catalytic activity in vitro and in vivo. Structural dynamic analyses reveal that the T1232A substitution elicits localized mobility changes throughout NSD3’s catalytic domain to relieve auto-inhibition and increase H3 substrate accessibility. NSD3T1232A expression in vivo in LUSC mouse models accelerates tumorigenesis and decreases overall survival. Pathologic generation of H3K36me2 by NSD3T1232A rewires the chromatin landscape to promote oncogenic gene expression programming. Accordingly, depletion of NSD3 and H3K36me2 in patient derived xenografts (PDXs) from primary LUSC harboring NSD3 amplification or the NSD3T1232A variant attenuate neoplastic growth. Finally, NSD3-regulated LUSC PDXs are markedly and selectively sensitive to bromodomain inhibition (BETi). Together, our work identifies NSD3 as a principal 8p11-12 amplicon-associated oncogenic driver in LUSC and suggests that NSD3-dependency renders LUSC therapeutically vulnerable to BETi.

overall_design: RNA-seq from tumor biopsies form mouse model of lung squamous cell carcinoma with constitutively active PI3K (Pik3caH1047R), SOX2 overexpression (Sox2OE) and CDKN2A/B deletion (Cdkn2a/bKO) hereto referred to as PSC mice (control) and expression of NSD3T1242A mutant (named PSCN)

first: Shane

last: Lofgren


title: High (5X) 5-methyltetrahydrofolate (MTHF) vs folic acid (FA) pregnancy diets on  hypothalamic gene expression of Wistar rat dams upon birth.

status: Public on Nov 23 2020

city: Toronto

first: G. Harvey

last: Anderson

state: ON

address: 1 Kings College Circle

department: Nutritional Sciences

country: Canada

institute: University of Toronto

summary:
This study compared the effects of 5X requirements of FA (10mg/kg) vs equimolar 5-methyletetrahydrofolate (MTHF, 10.4mg/kg) provided during pregnancy on hypothalamic (arcuate nucleus of the hypothalamus) gene expression profiles of Wistar rat dams upon birth.
Methods: Whole-transcriptome analysis by RNA-sequencing was performed with Illumina HiSeq 2500 instrument (paired-end 2x125 bp sequencing  at a  depth of ≈20 million paired reads per sample). Sequence reads that passed quality filters were aligned to the rat genome using STAR aligner and differential gene expression was analyzed by DESeq2 using a padj <0.05. SYBR Green assay was used to validate candidate genes via qRT–PCR.
Results: A total of 279 genes were identified to be differentially expressed genes in the hypothalamus of dams at birth fed high (5X) MTHF compared to 5X-FA diets during pregnancy, with 170 up-regulated and 109 down-regulated genes. Using goseq for pathway enrichment analysis, we identified several  enriched pathways that associated with the long-term phenotype of the dam including the KEGG neuroactive-ligand receptor interaction pathway.
Conclusion: This study provides novel insight towards the differential effects of folate form during pregnancy on regulating dynamic changes in gene expression of the maternal brain upon birth. The results of our study may led to hypothesis testing to identify novel candidate genes and pathways targeted by folate during pregnancy that have a role in disease on-set and/or prevention.

overall_design: Hypothalamic (arcuate nucelus of the hypothalamus) mRNA profiles from  Wistar rat dams  immediately after giving birth.

first: Emanuela

last: Pannia

first: Ruslan

last: Kubant

first: G

middle: H


title: Transcriptome profiling of hydrogen-oxidizing Acidithiobacillus ferrooxidans

city: Brno

first: Jiri

last: Kucera

address: Kamenice 753/5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

summary: The study identified a total of 3169 gene transcripts (98.4% coverage). By comparing the anaerobic versus aerobic H2-oxidizing At. ferrooxidans cultures, a total of 371 DEGs were found. Of these, 168 DEGs were increased significantly during the aerobic growth on H2 (with O2 as the sole electron acceptor), while 203 DEGs increased significantly during anaerobic growth on H2 (with Fe3+ as the sole electron acceptor).

overall_design: Transcriptome profiling of gene expression during aerobic and anaerobic growth of Acidithiobacillus ferrooxidans cells on hydrogen.

first: Jan

last: Lochman

first: Pavel

last: Bouchal

first: Eva

last: Pakostova

first: Kamil

last: Mikulasek

first: Sabrina

last: Hedrich

first: Oldrich

last: Janiczek

first: Martin

last: Mandl

first: D

middle: B

last: Johnson


title: Effects of FOXN1 or AFF4 deficiency on gene expression in the skin

city: Brooklyn

first: Lorin

last: Weiner

address: 450 Clarkson Ave, MSC 5

department: Cell Biology

institute: State University of New York Downstate Health Sciences University

summary: Loss-of-function mutations in Foxn1 or Aff4 cause similar defects in skin morphology.  To determine whether these similar phenotypes result from similar changes in gene expression, skin from wild-type, Foxn1-null, or Aff4 conditional knockout (cko) mice was analysed by RNA-seq at a time when the animals were attempting to grow their first hair coats (P6).

overall_design: RNA preparations from Foxn1-null or Aff4-cko mutants were compared to RNA preparations from their respective wild-type littermates.

first: Janice

middle: L

last: Brissette


title: Dual Antimicrobial and Anti-inflammatory Activity of a Nitric Oxide-releasing Topical Medication in Atopic Dermatitis

city: New York

first: Ana

last: Pavel

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary: A clinical trial assessed the cutaneous immune response and short-term efficacy, safety, and tolerability in adults with mild to moderate AD who applied SB414 2% and 6% BID for 2 weeks.

overall_design: This was a phase 1b, multicenter, randomized, double-blind, vehicle-controlled study. Patients were randomized 3:3:2 to SB414 2%, SB414 6%, or vehicle applied twice daily to all affected areas including the scalp for 2 consecutive weeks. Approximately 0.5 g of study medication was applied for every 2% of BSA affected per application. Patients were instructed to apply study medication to any new AD lesions that appeared during the study, and to continue applying study treatment to lesions that appeared to resolve. Study visits occurred at screening, baseline, and weeks 1 and 2.

first: Emma

last: Guttman-Yassky

first: Richard

last: Gallo

first: Teruaki

last: Nakatsuji

first: Randall

last: Li

first: Ning

last: Zhang

first: Elizabeth

last: Messersmith

first: Tomoko

last: Maeda-Chubachi


title: The nuclear envelope protein Net39 is essential for muscle nuclear integrity and chromatin organization

first: Andres

last: Ramirez-Martinez

summary: Lamins and transmembrane proteins within the nuclear envelope regulate nuclear structure and chromatin organization. Nuclear Envelope Transmembrane Protein 39 (Net39) is muscle nuclear envelope protein whose functions in vivo have not been explored. We show that mice lacking Net39 succumb to severe myopathy and juvenile lethality, with concomitant disruption in nuclear integrity, chromatin accessibility, gene expression and metabolism. These abnormalities resemble those of Emery-Dreifuss muscular dystrophy (EDMD), caused by mutations in A-type Lamins (LMNA) and other genes, like Emerin (EMD). We observe that Net39 is downregulated in EDMD patients, implicating Net39 in the pathogenesis of this disorder. Our findings highlight the role of Net39 at the nuclear envelope in maintaining muscle chromatin organization, gene expression and function, and its potential contribution to the molecular etiology of EDMD.

overall_design: Refer to individual Series


title: Genetic screening and multipotency in rhesus monkey haploid neural progenitor cells

status: Public on Nov 21 2020

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

institute: Nankai University

summary: Haploid embryonic stem cells (haESCs) have been extensively applied in forward and reverse genetic screening. However, a mammalian haploid somatic cell line is difficult to achieve because of spontaneous diploidization in differentiation. As a non-human primate species, monkeys are widely used in basic and pre-clinical research in which haploid cells are restricted to ESCs. Here, we report that rhesus monkey haESCs in an optimized culture medium show naïve-state pluripotency and stable haploidy. This model facilitated the derivation of haploid neural progenitor cells (haNPCs), which maintained haploidy and differentiation potential into neurons and glia for a long period in vitro. High-throughput trapping mutations can be efficiently introduced into haNPCs via piggyBac transposons. This system proves useful when identifying gene targets of neural toxicants via a proof-of-concept experiment. Using CRISPR/Cas9 editing, we confirmed that B4GALT6, from the candidate gene list, is a resistance gene of A803467 (a tetrodotoxin-like toxicant). This model is the first non-human primate haploid somatic cell line with proliferative ability, multipotency and an intact genome, thus providing a cellular resource for recessive genetic and potential drug screening.

first: Haisong

last: Wang

first: Wenhao


title: Transplacental Innate Immune Training via Maternal Microbial Exposure: Role of XBP1-ERN1 Axis in Dendritic Cell Precursor Programming

status: Public on Nov 22 2020

city: Perth

first: Kyle

last: Mincham

address: Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands

country: Australia

institute: Telethon Kids Institute

summary:
Background: Maternal enviromnetal exposures during pregnancy can transplacentally train the developing fetal immune system. We have proviously shown that treatment of pregnant mice with the microbial-derived OM-85 can protect their offspring against allergic airways disease.
Purpose: To characterise the cellular/molecular mechanisms underpinning this protection, focusing on the fetal bone marrow as a potential mechanistic target.
Methods: Pregnant mice were orally treated with OM-85 from gestation day (GD) 9.5-17.5. Fetal bone marrow and thymus was collected from OM-85 treated and non-treated mothers at GD18.5. Cellular and molecular profiles were characterised by multi-colour flow cytometry and transcriptomics (RNA-Seq) respectively.. Molecular profiling utilised upstream regulator analysis .Protein-level validation of upstream regulator analysis results was performed by multi-colour flow cytometry.
Results: Maternal OM-85 treatment induces transplacental signals that manifest in fetal bone marrow as an enriched population of conventional dendric cells (cDC) displaying enhanced functional maturation. Moreover, the myeloid progenitor populations directly upstream of this cDC pool were significantly boosted in response to maternal treatment. Transcriptomic analysis of fetal bone marrow identified maternal OM-85-induced activation of X-box binding protein 1 (XBP1), with upregulation of active XBP1 localised to cDC precursors.
Conclusions: Maternal OM-85 treatment during pregnancy transplacentally accelerates functional immunocompetence of fetal bone marrow cDCs and for the first time we identify the transcription factor XBP1 as a putative driver of this immune training mechanism.

overall_design: This study consisted of paired bone marrow (n=32) and thymus (n=32) samples from gestation day 18.5 fetuses from OM-85 treated or non-treated mothers. RNA-Seq profiles were generated by sequencing Illumina HiSeq2500, 50bp single-end reads, v4 chemistry.

first: Anya

last: Jones

first: Marie

last: Bodinier

first: Naomi

middle: M

last: Scott

first: Jean-Francois

last: Lauzon-Joset

first: Philip

middle: A

last: Stumbles

first: Anthony

last: Bosco

first: Patrick

middle: G

last: Holt

first: Deborah

last: Strickland


title: ChIP-nexus data for Oct4, Sox2, Nanog and Klf4 in mouse embryonic stem cells

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

summary:
The goal of this study was discover the transcription binding synthax for the key differentiation TFs in mouse embryonic stem cells.
Genes are regulated through enhancer sequences, in which transcription factor binding motifs and their specific arrangements (syntax) form a cis-regulatory code. To understand the relationship between motif syntax and transcription factor binding, we train a deep learning model that uses DNA sequence to predict base-resolution binding profiles of four pluripotency transcription factors Oct4, Sox2, Nanog, and Klf4. We interpret the model to accurately map hundreds of thousands of motifs in the genome, learn novel motif representations and identify rules by which motifs and syntax influence transcription factor binding. We find that instances of strict motif spacing are largely due to retrotransposons, but that soft motif syntax influences motif interactions at protein and nucleosome range. Most strikingly, Nanog binding is driven by motifs with a strong preference for ~10.5 bp spacings corresponding to helical periodicity. Interpreting deep learning models applied to high-resolution binding data is a powerful and versatile approach to uncover the motifs and syntax of cis-regulatory sequences.

overall_design: ChIP-nexus and ChIP-seq measurements in WT ESCs R1 cell line for 4 TFs. Additionally, ChIP-nexus of Nanog and Sox2 was performed on CRISPR perturbations of Sox2 (chr10: 85,539,634-85,539,643 (mm10) mutated from CCTTTGTTCC (wildtype) to CCTAGGTTCC (mutant) and Nanog (chr10: 85,539,756-85,539,765 (mm10) mutated from CTGATGGCT (wildtype) to CGGCTGGCT).

first: Ziga

last: Avsec

first: Melanie

last: Weilert


title: mRNA-seq of wild-type or Eral1 deficient primary peritoneal macrophages (PMs) after sendai virus infection

status: Public on Nov 20 2020

city: Beijing

first: Ming

last: Kuang

address: Xueyuan Road 38 #, Haidian District

institute: Peking University

summary: Analysis of mRNA-seq  reveals how wild-type and Eral1 deficient peritoneal macrophages  response to  SeV infection

overall_design: Primary peritoneal macrophages generated from  WT or Eral1 knock down C57BL/6 mice were infected by  SeV for 0 or 6 hours.

first: Siji

last: Li

first: Fuping

last: You


title: CD4+ follicular regulatory T cells optimize the influenza virus-specific B cell response

city: New Haven

first: Jiawei

state: CT

address: 300 George St, Suite 503

institute: Yale University

summary: CD4+ follicular regulatory T cells (Tfr cells) control B cell responses through the modulation of follicular helper T (Tfh) cells and germinal center development, while suppressing autoreactivity; however, their role in the regulation of productive germinal center B cell responses and humoral memory is incompletely defined. We show that Tfr cells promote antigen-specific germinal center B cell responses upon influenza virus infection. Following viral challenge, we found that Tfr cells are necessary for robust generation of virus-specific, long-lived plasma cells, antibody production against both hemagglutinin (HA) and neuraminidase (NA), the two major influenza virus glycoproteins, and appropriate regulation of the BCR repertoire. To further investigate the functional relevance of Tfr cells during viral challenge, we utilized a sequential immunization model with repeated exposure of antigenically partially conserved strains of influenza viruses, revealing that Tfr cells promote recall antibody responses against the conserved HA stalk region. Thus, Tfr cells promote antigen-specific B cell responses and are essential for the development of long-term humoral memory.

overall_design: Each group consisted of 3-4 mice pooled together Two replicates of each group were used for the HA+_GCB cell RNAseq Three replicates of each group were used for the Tfh cell RNAseq Tfr wildtype and Tfr knockout mice are the two groups studied

first: Yisi

last: Lu

first: Shirin

last: Strohmeier

first: Davide

last: Angeletti

first: Joe

last: Craft

first: Roy

last: Jiang

first: Katlyn

last: Lederer

first: Kevin

last: O’Connor

first: Alec

middle: W

last: Freyn

first: Michela

last: Locci

first: Steven

last: Kleinstein

first: Hongyu

last: Zhao

first: Raffael

last: Nachbagauer


title: Nucleotide resolution profiling of m3C RNA modification by HAC-seq

city: Boston

first: Qi

last: Liu

state: MASSACHUSETTS

address: Boston, 02115.USA

institute: Boston Children's Hospital

summary: We report a m3C-specific high-throughput sequencing techinque, Hydrazine-Aniline Cleavage sequencing (HAC-seq) to profile the m3C methylome at single-nucleotide resolution. We apply HAC-seq to analyze ribosomal RNA-depleted total RNA from MCF7 cells. We find that tRNA are the predominant m3C-modified RNA species. We find no evidence of m3C-modification of mRNA or other non-coding RNAs at comparable levels to tRNA in MCF7 cells.

overall_design: HAC-seq was performed in biological duplicates. After ribosomal RNA depletion, ribominus total RNA were randomly fragmented and end-repaired. The fragmented RNAs were treated with 10% hydrazine with 3M NaCl for 4h and then cleaved by aniline cleavage buffer at the m3C modification sites (HAC). Then RNAs were treated with AlkB before library preparation. Two controls were performed at the same time. Untreated control (CTRL) was carried out with AlkB demethylation but without hydrazine and aniline cleavage. DM-HAC was performed by treating the AlkB-demethylated RNA with hydrazine followed by aniline cleavage.

first: Jia

last: Cui

first: Richard

middle: I

last: Gregory


title: Human Innate Lymphoid Cell Precursors Express CD48 that Modulates ILC Differentiation through 2B4 Signaling

city: Aurora

first: George

middle: Devon

last: Trahan

state: CO

address: 1635 Aurora Ct

department: The Department of Pediatrics Section of Hematology, Oncology and Bone Marrow Transplantation

institute: University of Colorado Anschutz Medical Campus

summary: Innate lymphoid cells (ILCs) develop from common lymphoid progenitors (CLP), which further differentiate into the common ILC progenitor (CILP) that can give rise to both ILCs and NK cells. Murine ILC intermediates have recently been characterized, but the human counterparts and their developmental trajectories have not yet been identified, largely due to the lack of homologous surface receptors in both organisms. Here, we show that human CILPs (CD34+CD117+α4β7+Lin-) acquire CD48 and CD52, which define NK progenitors (NKPs) and innate lymphoid cell precursors (ILCPs). Two distinct NK cell subsets were generated in vitro from CD34+CD117+α4β7+Lin-CD48-CD52+ and CD34+CD117+α4β7+Lin-CD48+CD52+ NKPs, respectively. Independent of NKPs, ILCPs exist in the CD34+CD117+α4β7+Lin-CD48+CD52+ subset and give rise to ILC1s, ILC2s and NCR+ ILC3s, whereas CD34+CD117+α4β7+Lin-CD48+CD52- ILCPs give rise to a distinct subset of ILC3s that have lymphoid tissue inducer (LTi)-like properties. Additionally, CD48 expressing CD34+CD117+α4β7+Lin- precursors give rise to tissue-associated ILCs in vivo. We also observed that the interaction of 2B4 with CD48 induced differentiation of ILC2s, and together these findings show that expression of CD48 by human ILCPs modulates ILC differentiation.

overall_design: scRNA-Seq data for 4 CD34+a4b7+ sub-populations based on CD48 and CD52 expression

first: Dejene

last: Tufa

first: Michael

last: Verneris


title: Mitochondrial activity linked to CD34+CD90+EPCR+ phenotype determines the functional fitness of ex vivo expanded HSCs

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

summary: We report the transcritpome of purified CD34+ cells from cultures initiated with cord blood  CD34+ hematopoietic stem cells that were expanded ex vivo in Stemline II media supplemented with a cytokine cocktail in the presence or absence of  valproic acid for 6 days .

overall_design: Cord blood  CD34+ hemtopoietc stem cells were expanded ex vivo in Stemline II media supplemented with a cytokine cocktail in the presence or absence of  valproic acid for 6 days  and transcirptome of purified CD34+ cells determined by mRNA-seq

first: Luena

last: Papa

first: Mansour

last: Djedaini

first: Ramon

last: Parsons

first: Ronald

last: Hoffman

first: Rober

last: Sebra

first: Schaniel

last: Christoph

first: Kristin

last: Beaumount

first: Mahtab

last: Zangui


title: Gene expression analysis of normal primary human bronchial epithelial cells (pHBEC) stimulated by glucocorticoid, long-acting β2-adrenoceptor agonist or both combined.

city: Calgary

first: Robert

last: Newton

state: Alberta

address: 3330 Hospital Dr NW

department: Snyder Institute for Chronic Diseases

institute: University of Calgary

summary:
In 2019, the Global Initiative for Asthma treatment guidelines were updated to recommend that inhaled corticosteroid (ICS)/long-acting β2-adrenoceptor agonist (LABA) combination therapy should be a first-in-line treatment option for asthma. Although clinically superior to ICS, mechanisms underlying the efficacy of this combination therapy remain unclear. We hypothesised the existence of transcriptomic interactions, an effect that was tested in primary human bronchial epithelial cells (pHBECs) using formoterol and budesonide as representative LABA and ICS, respectively.
To investigate the gene expression changes by each condition, transcriptomic analysis was performed on RNA extracted from pHBECs treated with budesonide, formoterol, or both combined.

overall_design: Primary Human bronchial epithelial cells (pHBEC) were either not treated or treated with budesonide, formoterol or both combined for 6 h. Six independent experimental determinations, one from each different donor, were analyzed. Altogether, 24 arrays were hybridized.

first: Mahmoud

last: Mostafa

first: Christopher

middle: F

last: Rider