title: Extracellular matrix modulates T cell clearance of malignant cells in vitro

city: Livermore

first: Claire

last: Robertson

state: CA

address: 7000 East Ave.

institute: Lawrence Livermore National Lab

summary: We describe changes to the transcriptomes of 4t1 mammary gland carcinoma cells in different matrix environments and with and without T cells

overall_design: 4t1 mammary gland carcinoma cultured with or without C57Bl6 splenic T cells on either: tissue culture polystyrene, tissue culture polystyrene coated with Collagen 1,tissue culture polystyrene coated with Collagen 4, tissue culture polystyrene coated with Fibronectin, or tissue culture polystyrene coated with Vitronectin.

first: Aimy

last: Sebastian

first: Aubree

last: Hinckley


title: Transcriptomic responses to submergence in elongating and non-elongating leaves of rice with and without SUB1A

status: Public on Aug 01 2022

city: Blacksburg

first: Song

last: Li

state: VA

country: USA

institute: Virginia Tech

type: Expression profiling by high throughput sequencing

summary: This study evaluated transcriptomic responses to submergence in elongating and non-elongating leaves of rice near-isogenic lines with and without SUB1A using RNA-Seq. SUB1A is an ERF transcription factor gene and the key regulator of submergence tolerance in rice, restricting underwater elongation and avoiding starvation under the stress. Submergence induces mRNA accumulation of SUB1A similarly in elongating and non-elongating leaves. This study uncovered SUB1A-dependent and independent regulation of adaptive responses to submergence in the two functionally distinct leaves at the global level.

overall_design: mRNAs extracted from elongating and non-elongating leaves of rice plants [M202 and M202(Sub1)] submerged for 0, 1, 3, and 6 days. Three independent biological replicates.

first: Takeshi

last: Fukao

first: Jasper

middle: B

last: Alpuerto


title: Epigenetic and transcriptomic signature reveals Sox8 as an otic master regulator

city: London

first: Andrea

last: Streit

address: Centre for Craniofacial & Regenerative Biology, King's College London

country: United Kingdom

institute: Kings College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Previously FGF signalling has been shown to specify otic fate from multipotent pre-placodal ectoderm. Though many FGF target genes have been identified in subsequent studies, none of them is sufficient to induce otic lineage. Profiling and analysing the transcriptome and epigenomical signature during otic specification, we predicted and confirmed Sox8 as an otic master regulator, able to specify otic fate in the pre-placodal ectoderm. This is achieved by activating the expression of otic identity markers and compromising the fate towards lens and trigeminal ganglion. In the combat to differentiate ESCs/iPSCs or convert other cell lineage into otic lineage, our discovery may add another weaponry to tame these cells towards otic cells.

overall_design: ChIPseq of H3K27ac,  H3K4me3, H3K27me3, and ATACseq were performed with a single biological replicate. Input was included for the ChIPseq experiments.

first: Jingchen

last: Chen

first: Alexandre

last: Thiery


title: Ex Utero Development of Post-Gastrulation Synthetic Mouse Embryos Generated Solely from Naïve Pluripotent Stem Cells [RNA-seq]

status: Public on Jul 31 2022

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Different types of in vitro expanded stem cells can contribute to embryonic or extra-embryonic compartments after microinjection into blastocysts. However, whether stem cells could give rise to advanced gastrulating whole embryo-like structures with both embryonic and extra-embryonic compartments, without relying on a micro-injected host embryo, remains to be achieved. Thus far, in vitro aggregated stem cells have failed to generate post-gastrulation embryos ex utero or in utero, which partially resulted from the lack of methods for prolonged expansion of embryos until advanced developmental stages ex utero. Here we adapt recently optimized platform and conditions for ex utero growth of natural embryos, to generate complete mouse synthetic embryos, with both embryonic and extra-embryonic compartments, and by starting solely from naïve ESCs. The latter is achieved following co-aggregating non-transduced naïve ESCs, with Cdx2- and Gata4- transiently pulsed naïve ESCs, to promote their trophoblast and primitive endoderm lineage induction, respectively. The obtained synthetic embryos adequately advance in this platform through developmental milestones and accomplish gastrulation and develop organs progenitors within normally developed extra-embryonic compartments.  Our findings highlight the plastic developmental potential of the naïve pluripotent state to functionally self-organize and reconstitute the entire early mammalian embryo.

overall_design: In this study, we induced mouse embryonic stem cells (ESC) into trophoblast stem cell (TSC) fate. We used the KH2 collagen flip-in ESC system that carriers M2RtTa allele in the Rosa26 locus, and flipped-in Cdx2 into the collagen locus under the regulation of Doxycycline (DOX) inducible Tet-On promoter. These iCdx2 ESCs were treated with Doxycyclne in different durations, with and without LPA, a Hippo pathway inhibitor that induces YAP nuclear localization. In addition to iCdx2 ESCs, we used established TSCs, WT ESCs, MEF (mouse embryonic fibroblasts) and XEN (mouse extra-embryonic endoderm) cells as control.

first: Shadi

last: Tarazi

first: Alejandro

last: Aguilera-Castejon

first: Jacob

last: Hanna


title: Depletion of m6A reader protein YTHDC1 induces dilated cardiomyopathy by abnormal splicing of Titin

city: Nanjing City

first: Haifeng

last: Sun

state: JiangSu province

address: Tianyuan East Road 818

country: China

institute: Nanjing Medical University

summary: N6-methyladenosine (m6A) is the most common internal modification in eukaryotic messenger RNAs (mRNAs) and plays essential roles in mammals. The function of this chemical modification is deciphered by m6A-specific binding proteins of the YTH family. Recent studies indicated that m6A methyltransferase METTL3 ('writer') and demethylase FTO ('eraser') play critical roles in cardiovascular diseases. However, function of m6A 'reader' proteins in the heart is still largely unknown. Here, we report that cardiac-speciﬁc ablation of Ythdc1 in postnatal heart exhibits progressive dilated cardiomyopathy, heart failure and dramatically increases the incidence of postnatal lethality. Mechanically, the transcript of Titin-the major DCM and heart failure related gene-is decorated by m6A modification and directly recognized by YTHDC1, deficiency of Ythdc1 in heart results in abnormal splicing of TTN and disarray of sarcomeric structures in the cardiomyocytes subsequently. Collectively, we demonstrated that YTHDC1-dependent TTN splicing is crucial for the postnatal heart development and cardiac function, which probably provides a potential target for treating DCM through tuning m6A modification of TTN mRNA.

overall_design: Examination the mRNA expression of left ventricular tissue in wild type / ythdc1 ko mouse

first: Siyun

last: Gao

first: Liudan

last: Jiang

first: Bin

last: Shen

first: Honghui

last: Ma

first: Yi-Han


title: Generation of functional rat spermatozoa in sterile mice utilizing blastocyst complementation with pluripotent stem cells [scRNAseq_mouse]

city: Schwerzenbach

first: Ori

last: Bar-Nur

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: Pluripotent stem cells (PSCs) provide a powerful tool to produce transgenic animals for biomedical research. However, impaired PSC contribution to chimerism and most notably the germline oftentimes impedes production of genetically modified animals, rendering techniques that expediate PSC contribution to the germline highly desirable. Blastocyst complementation denotes a technique which purposes to generate organs, tissues or cells in animal chimeras via microinjection of PSCs into genetically compromised blastocyst-stage embryos. Here we report on successful blastocyst complementation of the male germline in adult chimeras following microinjection of mouse or rat PSCs into mouse blastocysts mutated for Tsc22d3, an essential gene for spermatozoa production. Microinjection of mouse embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) into Tsc22d3-KnockOut (KO) blastocyst-stage embryos gave rise to intraspecies chimeras embodying functional spermatozoa, which were solely derived from microinjected PSCs. Furthermore, microinjection of rat ESCs into Tsc22d3-KO mouse embryos gave rise to viable mouse-rat chimeras that exhibited extensive contribution of rat cells to various organs. Notably, multiple mouse-rat chimeras showed contribution of rat ESCs to the male germline, solely harboring rat spermatids and spermatozoa that were rat ESC-derived and could fertilize rat oocytes. Collectively, this study reports a method for exclusive production of functional germ cells of one species in another via blastocyst complementation with PSCs. Implications of this study extend to development of transgenic rats via sterile mice, and may further assist efforts to generate xenogeneic gametes from endangered animal species.

overall_design: Cauda samples were isolated via percutaneous epididymal sperm aspiration from a Tsc22d3-KO and a Tsc22d3-KO chimera complemented with mouse induced pluripotent stem cells.  Testis samples were isolated from an adult Tsc22d3KO mouse testis (goGermline, Ozgene) via the protocol published by Valli et al, Fertility and Sterility, 2014

first: Joel

last: Zvick

first: Adhideb

last: Ghosh

first: Falko

last: Noé


title: Generation of functional rat spermatozoa in sterile mice utilizing blastocyst complementation with pluripotent stem cells

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Characterization and application of patient derived Glial Enriched Progenitors to repair functional deficits due to white matter stroke.

city: Los Angeles

first: William

last: Lowry

address: 621 Charles Young Drive South

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: Subcortical white matter stroke (WMS) accounts for up to 30% of all stroke events. WMS damages astrocytes, axons, oligodendrocytes, and myelin. We hypothesized that an astrocytic therapy would be ideally suited for brain repair after WMS. We characterized the molecular profile, epigenetic patterns and in vivo tissue repair activity of a novel glial enriched progentior cell differentiated from human induced pluripotent stem cells (hiPSCs). hiPSC-GEPs are derived from hiPSCs with an experimental manipulation of HIF activity by brief treatment with a prolyl hydroxylase inhibitor. This treatment permanently biased these cells toward an immature astrocyte fate. hiPSC-GEPs transplanted into the brain in the subacute period after WMS migrate widely, mature into astrocytes and induced endogenous oligodendrocyte precursor proliferation and re-myelination. hiPSC-GEPs enhanced motor recovery compared to other hiPSC-differentiated cell types. This approach establishes a hiPSC-derived product with easy scale-up capabilities and efficacy in a common and untreatable brain disease.

overall_design: Human neural progenitors were stimulated with low oxygen or drugs that increase HIF activity, and then processed to determine where H3K27ac and H3K9me3 histone marks are applied throughout the genome with ChIP_SEQ

first: S

middle: T

last: Carmichael


title: PU.1-dependent enhancer inhibition separates clonal hematopoiesis from malignant transformation (oxBS-Seq)

city: Bronx

first: Britta

last: Will

state: NY

address: 1300 Morris Park Avenue, Chanin Bldg., Rm. #401

department: Cell Biology

institute: Albert Einstein College of Medicine

type: Methylation profiling by high throughput sequencing

summary: Hematopoietic stem cells sustain life-long blood production. While they are the known cellular origin of aging-associated myeloid malignancies, such as acute myeloid leukemia (AML), mechanisms driving their malignant transformation have remained elusive. Epigenetic dysregulation following acquired loss-of-function mutations of DNA methyl-cytosine dioxygenase Ten-Eleven Translocation-2 (TET2) occurs frequently in the elderly leading to cytosine hypermethylation in and around DNA binding sites of master transcription factors, including PU.1. Here we show that Tet2 deficient hematopoietic stem and progenitor cells (HSPC) undergo malignant transformation upon compromised PU.1 gene regulation. Leukemic stem and progenitor cells show hypermethylation at PU.1 binding sites and fail to activate PU.1-depenent myeloid enhancers, and are hallmarked by a defined signature of impaired genes shared with human AML. Our study demonstrates that Tet2 and PU.1 cooperate in suppressing leukemogenesis in HSPC and establishes a methylation sensitive PU.1-dependent gene network as a unifying feature in acute myeloid leukemia.

overall_design: oxidative bisulfite sequencing of cKit+ HSPC purified from UREHETTet2HET and UREHETTet2KO mice and age-matched controls

first: Maria

middle: M

last: Aivalioti

first: Kith

last: Pradhan


title: PU.1-dependent enhancer inhibition separates clonal hematopoiesis from malignant transformation (ATAC-Seq)

overall_design: Chromatin accessibility of cKit+ HSPC purified from UREHETTet2HET and UREHETTet2KO mice and age-matched controls

first: Boris

last: Bartholdy


title: PU.1-dependent enhancer inhibition separates Tet2 deficient clonal hematopoiesis from malignant transformation


title: Cohesin modulates DNA replication to preserve genome integrity [EdU-BrdU]

city: Beijing

first: Zhengrong

last: Zhangding

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: Cohesin participates in loop formation by extruding DNA fibers from its ring-shaped structure. Cohesin dysfunction eliminates chromatin loops but only causes modest transcription perturbation, which cannot fully explain the frequently observed mutations of cohesin in various cancers. Here, we found that DNA replication initiates at more than one thousand extra dormant origins after acute depletion of RAD21, a core subunit of cohesin, resulting in earlier replicating timing at approximately 30% of the human genomic regions. In contrast, CTCF is dispensable for suppressing the early firing of dormant origins that are distributed away from the loop boundaries. Furthermore, greatly elevated levels of gross DNA breaks and genome-wide chromosomal translocations arise in RAD21-depleted cells, accompanied by dysregulated replication timing at dozens of hotspot genes. Thus, we conclude that cohesin coordinates DNA replication initiation to ensure proper replication timing and safeguards genome integrity.

overall_design: We applied NAIL-seq to identify the early replication initiation zones in RAD21-depleted cells.

first: Jinchun

last: Wu

first: Yang

last: Liu

first: Xuhao

first: Jiazhi

last: Hu


title: Cohesin modulates DNA replication to preserve genome integrity [Repli-seq-series1]


title: Cohesin modulates DNA replication to preserve genome integrity [ChIP_seq]

overall_design: We applied ChIP-seq to depict the distribution of chromatin-bound MCM5 with and without RAD21 during G1 phase.


title: Cohesin modulates DNA replication to preserve genome integrity [PRO_seq]

overall_design: We applied PRO-seq to compare the expression difference of WT and RAD21-depleted cells.


title: Cohesin modulates DNA replication to preserve genome integrity [PEM-seq]

overall_design: We employed  primer-extension-mediated sequencing (PEM-seq) to study the level of genome instability after RAD21-depletion.


title: Cohesin modulates DNA replication to preserve genome integrity  [Replication_signal]


title: Cohesin modulates DNA replication to preserve genome integrity

overall_design:
Refer to individual Series

Submitter states: Data in this SuperSeries were revised and resubmitted in GSE198285.


title: PU.1-dependent enhancer inhibition separates clonal hematopoiesis from malignant transformation (RNA-Seq)

overall_design: cKit+ HSPC mRNA profiles of UREHETTet2HET and UREHETTet2KO mice and age-matched controls


title: Altered Genome-Wide Hippocampal Gene Expression Profiles Following Early Life Lead Exposure and their Potential for Reversal by Environmental Enrichment

city: Philadelphia

first: Jay

middle: S

last: Schneider

state: PA

address: 1020 Locust St

department: Anatomy,Pathology and Cell biology

institute: Thomas Jefferson University

summary: Developmental lead (Pb) exposure results in persistent cognitive/behavioral impairments as well as an elevated risk for developing a variety of diseases in later life. The quality of the environment can modify negative influences from Pb exposure. How the interaction between Pb and quality of the environment influences gene expression pattern in the brain affecting the development treajectory is unexplored. We used RNA-seq to examine how the interaction between developmental Pb exposure and living in an enriched versus a non-enriched environment affects genome-wide gene expression pattern in Hippocampus (HIPP) CA1.

overall_design: Female Long Evans rats were exposed to 0 ppm or 150 ppm Pb through early postnatal exposure (birth through weaning). Post-weaning, rats were randomly housed 3 to a standard cage with no added stimuli (non-enriched) or 6 to a cage containing enrichment stimuli (enriched group) resulting into four experimental groups: Control (0ppm)_non-enriched, Control (0ppm)_enriched, EPN Pb (150ppm)_non-enriched and EPN Pb (150ppm)_enriched.  At PND55, rats were euthanized and HIPP CA1 was dissected for RNA-seq analysis.

first: Garima

last: Singh

first: Vikrant

first: Taehyong

last: Kim

first: Adam

last: Ertel

first: Weixuan

last: Fu

first: J


title: Methylome of galls formed by Meloidogyne javanica in Arabidopsis thaliana at 3 days post infection

city: Toledo

first: Carolina

last: Escobar

address: Avenida Carlos III, s/n

country: Spain

institute: University of Castilla-La Mancha

summary: The goal of this study is to compare the methylation state of galls formed in Arabidopsis roots infected by Meloidogyne javanica at 3 days post infection compared to uninfected root segments (RC).

overall_design:
MethylC-seq samples were collected from galls induced by Meloidogyne javanica in Arabidopsis at 3 days post-infection (dpi) and from uninfected root segments (negative controls).
Arabidopsis thaliana plants were grown in controlled environment chambers under 16 h/8 h of light/dark at 23ºC. Arabidopsis plants were inoculated at 5 days post germination at the root tip with approximately 20 freshly-hatched Meloidogyne J2 each plant. The inoculated and non-inoculated plants were then kept in the dark for 2 days, in plates horizontally orientated. During the first 48 hours, the infections and control roots growth were assessed. After 2 days, the plates containing both inoculated and non-inoculated plants were maintained in the light, vertically orientated and covered by a gauze. For more details concerning this protocol please see Olmo et al. (2017; doi: 10.1007/978-1-4939-6831-2_5). Galls and control root segments were collected at 3 days post infection and frozen on liquid nitrogen. Galls and control root segments (RC) from at least three independent experiments were pooled together per sample. For each treatment, three independent biological samples (G1, G2 and G3 for galls; RC1, RC2 and RC3 for RC) were used for genomic DNA extraction. Genomic DNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen with several adaptations (Silva et al., 2019; doi: 10.3389/fpls.2019.00657).
The libraries were prepared using the NEXTflex Bisulfite-Seq Library Prep Kit (BiooScientific), following the manufacturer's instructions. The fragment size distribution of the libraries were checked in the Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA Kit. The libraries were then sequenced in one lane of an Illumina HiSeq 4000 PE100 platform. Two of the libraries (RC2 and RC3) were sequenced in an Illumina® HiSeq X PE150 (San Diego, California, USA). Both steps were performed by the company AllGenetics & Biology SL. (Spain).
MethylC-seq data was processed using the pipeline available at https://github.com/seb-mueller/snakemake-bisulfite (commit f12bb6) in GitHub. The pipeline performed quality control using FastQC (version 0.11.8). Raw reads were trimmed for adapters, quality-trimmed and filtered using Trim Galore (version 0.5.0). A combined genome was constructed by concatenation the genomes (in fasta format) of A. thaliana (TAIR10, including the chloroplast and mitochondrial genome), M. javanica (Assembly GCA_900003945.1; Blanc-Mathieu et al., 2017) and Lambda phage into a single fasta format reference. Reads were then mapped to the constructed reference with Bismark (version 0.20.0; Krueger and Andrews, 2011), using the following parameters: L,0,-0.4. The SAM alignment generated by Bismark were further processed into BAM format and subsequently imported for further processing into the R package methylKit version 0.99.2 (Akalin et al., 2012). To identify differential methylated regions (DMRs), we  defined various regions in form of adjacent non-overlapping window of 200 base pairs (referred to as bins), which were posteriorly checked for overlapping different genomic regions, including genes, promoters and transposable elements as specified in Araport11 (06/2016; Cheng et al., 2017). Promoters were considered as 1000 base pairs (bp) upstream until 200 bp downstream of the transcription start site. For each region, the containing methylated and unmethylated cytosines were counted (separately for each library, each region and each context [CHH, CHG, CG]) and tested for differential methylation using a logistic regression approach using the “MN” over-dispersion correction as implemented in MethylKit. DMRs are then defined if the difference of methylation proportion between the gall samples and the controls was higher than 15% and a FDR (q-value) of less than 0.05 and covered by at least two biological replicates of the treatment or control.

first: Ana

middle: C

last: Silva

first: Virginia

last: Ruiz-Ferrer

first: Sebastian

last: Eves-van den Akker

last: Müller


title: Methylome of galls formed by Meloidogyne javanica in Arabidopsis thaliana at 14 days post infection

summary: The goal of this study is to compare the methylation state of galls formed in Arabidopsis roots infected by Meloidogyne javanica at 14 days post infection compared to uninfected root segments (RC).

overall_design:
MethylC-seq samples were collected from galls induced by Meloidogyne javanica en Arabidopsis at 14 days post-infection (dpi) and from uninfected root segments (negative controls).
Arabidopsis thaliana plants were grown in controlled environment chambers under 16 h/8 h of light/dark at 23ºC. Arabidopsis plants were inoculated at 5 days post germination at the root tip with approximately 20 freshly-hatched Meloidogyne J2 each plant. The inoculated and non-inoculated plants were then kept in the dark for 2 days, in plates horizontally orientated. During the first 48 hours, the infections and control roots growth were assessed. After 2 days, the plates containing both inoculated and non-inoculated plants were maintained in the light, vertically orientated and covered by a gauze. For more details concerning this protocol please see Olmo et al. (2017; doi: 10.1007/978-1-4939-6831-2_5). Galls and control root segments were collected at 14 days post infection and frozen on liquid nitrogen. Galls and control root segments (RC) from at least three independent experiments were pooled together per sample. For each treatment, three independent biological samples (G1, G2 and G3 for galls; RC1, RC2 and RC3 for RC) were used for genomic DNA extraction. Genomic DNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen with several adaptations (Silva et al., 2019; doi: 10.3389/fpls.2019.00657).
The libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit EZ DNA Methylation-Gold Kit (Zymo Research) following the library protocol Accel-NGS Methyl-Seq DNA Library Kit for Illumina Platforms. The fragment size distribution of the libraries were checked in an Agilent® 2100 Bioanalyzer using DNA 1000 chip (Agilent® Technologies, Inc., Santa Clara, CA, USA). The libraries were quantified using using qPCR according to the Illumina qPCR Quantification Protocol Guide (Bioanalyzer DNA High Sensitivity chip & LightCycle qPCR). The libraries were sequenced using an Illumina® HiSeq X PE150 (San Diego, California, USA). Library preparation and sequencing were performed by the company Macrogen Inc. (South Korea).
MethylC-seq data was processed using the pipeline available at https://github.com/seb-mueller/snakemake-bisulfite (commit f12bb6) in GitHub. The pipeline performed quality control using FastQC (version 0.11.8). Raw reads were trimmed for adapters, quality-trimmed and filtered using Trim Galore (version 0.5.0). A combined genome was constructed by concatenation the genomes (in fasta format) of A. thaliana (TAIR10, including the chloroplast and mitochondrial genome), M. javanica (Assembly GCA_900003945.1; Blanc-Mathieu et al., 2017) and Lambda phage into a single fasta format reference. Reads were then mapped to the constructed reference with Bismark (version 0.20.0; Krueger and Andrews, 2011), using the following parameters: L,0,-0.4. The SAM alignment generated by Bismark were further processed into BAM format and subsequently imported for further processing into the R package methylKit version 0.99.2 (Akalin et al., 2012). To identify differential methylated regions (DMRs), we defined various regions in form of adjacent non-overlapping window of 200 base pairs (referred to as bins), which were posteriorly checked for overlapping different genomic regions, including genes, promoters and transposable elements as specified in Araport11 (06/2016; Cheng et al., 2017). Promoters were considered as 1000 base pairs (bp) upstream until 200 bp downstream of the transcription start site. For each region, the containing methylated and unmethylated cytosines were counted (separately for each library, each region and each context [CHH, CHG, CG]) and tested for differential methylation using a logistic regression approach using the “MN” over-dispersion correction as implemented in MethylKit. DMRs are then defined if the difference of methylation proportion between the gall samples and the controls was higher than 15% and a FDR (q-value) of less than 0.05 and covered by at least two biological replicates of the treatment or control.


title: Transcriptome of galls formed by Meloidogyne javanica in Arabidopsis thaliana at 3 days post infection

summary: The goal of this study is to compare the transcriptome profilling (RNA-seq) of galls (G) formed in Arabidopsis roots infected by Meloidogyne javanica at 3 days post infection compared to uninfected root segments (RC).

overall_design:
Meloidogyne javanica-induced galls and control roots mRNA profiles were generated by deep sequencing with Illumina HiSeq X PE150.
Arabidopsis thaliana plants were grown in controlled environment chambers under 16 h/8 h of light/dark at 23ºC. Arabidopsis plants were inoculated at 5 days post germination at the root tip with approximately 20 freshly-hatched Meloidogyne J2 each plant. The inoculated and non-inoculated plants were then kept in the dark for 2 days, in plates horizontally orientated. During the first 48 hours, the infections and control roots growth were assessed. After 2 days, the plates containing both inoculated and non-inoculated plants were maintained in the light, vertically orientated and covered by a gauze. For more details concerning this protocol please see Olmo et al. (2017; doi: 10.1007/978-1-4939-6831-2_5). Galls and control root segments were collected at 3 days post infection and frozen on liquid nitrogen. Galls and control root segments (RC) from at least three independent experiments were pooled together per sample. For each treatment, three independent biological samples (G1, G2 and G3 for galls; RC1, RC2 and RC3 for RC) were used for total RNA extraction. Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen with several adaptations (Silva et al., 2019; doi: 10.3389/fpls.2019.00657).
Illumina's TruSeq Stranded mRNA Library Prep Kit was used to prepare the libraries, strictly following the manufacturer's instructions. The fragment size distribution of the libraries were checked in the Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA Kit. The libraries were then sequenced in a fraction of an Illumina HiSeq X PE150. Both steps were performed by the company AllGenetics & Biology SL.(Spain).
For the bioinformatic analysis, the reads were firstly checked for quality using FastQC (version 0.11.8). Trimming was then performed using BBDuk (version 38.39). Trimmed reads were mapped to the combined A. thaliana (TAIR10) and M. javanica (Assembly GCA_900003945.1; Blanc-Mathieu et al., 2017) genomes using STAR (version 2.7.0d; Dobin et al., 2013) and the following parameters: --outFilterMismatchNmax 7, --outFilterMultimapNmax 5. The BAM files produced with STAR where then used by HTSeq (version 0.11.2), in order to produce the count tables used for the differentially expressed analysis. The normalized count tables and the posterior differentially expression analysis were performed with DESeq2 (version 1.20.0; Love et al., 2014) using R (version 3.5.2) and RStudio (version 1.1.463). Genes with a |log2-fold change|>0.5 and an adjusted p value <0.01 were considered as differentially expressed.

first: Clement

last: Pellegrin


title: Gene expression profile on the single cell level of atherosclerotic plaque from mice with MCP1 knockout in Lgals3-transitioned smooth muscle cells

status: Public on Jul 30 2022

city: Charlottesville

first: Katherine

last: Owsiany

address: 415 Lane Rd

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: Many different subsets of smooth muscle cells  (SMC) are present in advanced atherosclerotic plaque. We used single cell sequencing to interrogate the impact of MCP1 made by Lgals+ smooth muscle cells on smooth muscle and immune cell subsets in advanced atherosclerotic plaque

overall_design: Advanced atherosclerotic plaques were microdissected from the brachiocephalic artery of dual lineage smooth muscle lineage tracing mice with wild-type, heterozygous, or homozygous MCP1 knockout alleles. Part of the sample was sequenced directly and a portion underwent sorting for Myh11+ SMC (marked by tdTomato) and Lgals3-transitioned SMC (marked by GFP) to enrich for these smooth muscle subsets.

first: Rebecca

last: Deaton

first: Gary

last: Owens


title: Robust methylation based classification of brain tumors using nanopore sequencing

city: Berlin

first: Luis

middle: Philipp

last: Kuschel

address: Robert-Koch-Platz 4

department: Abteilung für experimentelle Neurologie

country: Germany

institute: Charité Universitätsmedizin Berlin

summary: Using a public reference data set of 82 unique entities, 382 nanopore-sequenced brain tumor samples were classified based on their methylation status through an ad hoc random forest algorithm. As a measure of confidence, score recalibration was performed and platform-specific thresholds were defined.

overall_design:
382 brain tumor tissue samples were submitted to DNA extraction, quality control and library preparation. Subsequently, nanopore whole genome sequencing was performed. Samples were randomly divided into a discovery and validation cohort in order to establish and validate an implemented classification score and the resulting cut-off values.
***The raw data will be uploaded to EGA due to data privacy and local legislation***

middle: P

first: Jürgen

last: Hench

first: Stephan

last: Frank

first: Ivana

last: Bratic Hench

first: Elodie

last: Girard

first: Maud

last: Blanluet

first: Julien

last: Masliah-Planchon

first: Martin

last: Misch

first: Julia

last: Onken

first: Marcus

last: Czabanka

first: Dongsheng

last: Yuan

first: Sören

last: Lukassen

first: Philipp

last: Karau

first: Naveed

last: Ishaque

first: Elisabeth

middle: G

last: Hain

first: Frank

last: Heppner

first: Ahmed

last: Idbaih

first: Nikolaus

last: Behr

first: Christoph

last: Harms

first: David

last: Capper

last: Euskirchen


title: Efficacy of CD40 agonists is mediated by distinct cDC subsets and subverted by suppressive macrophages

status: Public on Jul 29 2022

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Agonistic αCD40 therapy has been shown to inhibit cancer progression in only a fraction of patients. Understanding the cancer cell-intrinsic and microenvironmental determinants of αCD40 therapy response is therefore crucial to identify responsive patient populations and design efficient combinatorial treatments. Here, we show that the therapeutic efficacy of αCD40 in subcutaneous melanoma relies on pre-existing, type 1 classical dendritic cell (cDC1)-primed CD8+ T cells. However, after administration of αCD40, cDC1s were dispensable for anti-tumour efficacy. Instead, the abundance of activated cDCs, potentially derived from cDC2 cells, increased and further activated antitumour CD8+ T cells. Hence, distinct cDC subsets contributed to the induction of αCD40 responses. By contrast, lung carcinomas, characterized by a high abundance of macrophages, were resistant to αCD40 therapy. Combining αCD40 therapy with macrophage depletion led to tumour growth inhibition only in the presence of strong neoantigens. Accordingly, treatment with immunogenic cell death-inducing chemotherapy sensitized lung tumours to αCD40 therapy in subcutaneous and orthotopic settings. These insights into the microenvironmental regulators of response to αCD40 suggest that different tumour types would benefit from different combinations of therapies to optimize the clinical application of CD40 agonists.

overall_design:
Subcutaneous LLC and B16 tumors (pooled from 3 mice per sample)
Please note that processed data generated from LLC_tumour Citeseq_DL16* samples are linked to the LLC_tumour Citeseq_DL16_CDNA sample records.

first: Aleksandar

last: Murgaski

first: Máté

last: Kiss

first: Helena

last: Van Damme

first: Isaure

last: Vanmeerbeek

first: Jiri

last: Keirsse

first: Eva

last: Hadadi

first: Jan

last: Brughmans

first: Sana

last: Arnouk

middle: E

last: Hamouda

first: Ayla

last: Debraekeleer

first: Victor

last: Bosteels

first: Yvon

last: Elkrim

first: Louis

last: Boon

first: Sabine

last: Hoves

first: Niels

last: Vandamme

first: Sofie

last: Deschoemaeker

first: Sophie

last: Janssens

first: Abhishek

middle: D

last: Garg

first: Greetje

middle: V

last: Velde

first: Martina

last: Schmittnägel

first: Carola

middle: H

last: Ries

first: Damya

last: Laoui


title: Role of PC1 on Evs release in mDCT15 cells

city: Nijmegen

first: Valentina

last: Carotti

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboudumc

summary: To investigate the role of the loss Pkd1 in mDCT15 cells we compared the transcriptome of wild type and Pkd1-/- mCT15 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mDCT15 wild type and Pkd1-/- cells

first: Jenny

last: van der Wijst

first: Eric

last: Verschuren

first: Nico

last: Sommerdijk

first: Charlotte

last: Kaffa

first: Vera

last: Sommers

first: Juan

last: Rigalli

first: Joost

last: Hoenderop

first: Luco

last: Rutten


title: Influence of Sox4 on chromatin accessibility of adult hepatocytes

first: Takeshi

last: Katsuda

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

summary: Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. An earlier work in our laboratory nominated Sox4 as an initiation factor of this reprogramming event To investigate the effect of Sox4 on the change of chromatin landscape of hepatocytes, we performed ATAC-seq of Sox4-overexpressed (OE) hepatocytes.

overall_design: Mice were injected with adeno-associated viruses (AAVs) packaged with mouse Sox4 (AAV8-TBG-HA-Sox4-P2A-Cre) or empty virus (AAV8-TBG-Cre), and hepatocytes were harvested 4 days post injection by a standard 2-step liberase digestion method followed by a Percoll enrichment step.

first: Jonathan

last: Sussman

first: Ben

middle: Z

last: Stanger


title: Expression data from allergy and non allergy humans

city: Madrid

first: María Isabel

last: Delgado Dolset

address: Urb. Montepríncipe s/n

department: Instituto de Medicina Molecular Aplicada Nemesio Díez

institute: Universidad CEU-San Pablo

summary:
In previous studies with peripheral blood cells, platelet factors were found to be associated with severe allergic phenotypes. A reliable method yielding highly concentrated and pure platelet samples is usually not available for immunological studies. Plateletpheresis is widely used in the clinics for donation purposes.
In this study, we designed a protocol based on plateletpheresis to obtain platelet-rich plasma (PRP), Platelet Poor Plasma (PPP) as well as CD3+ and CD14+ cells matched samples from a waste plateletpheresis product for immunological studies.

overall_design: Twenty-seven subjects were voluntarily subjected to plateletpheresis. Platelet-rich plasma (PRP) and blood cell concentrate contained in a leukocyte reduction system chamber (LRSC) were obtained in this process. CD3+ and CD14+ cells were isolated from the LRSC by density-gradient centrifugation and positive magnetic bead isolation. RNA was isolated from PRP, CD3+ and CD14+ cell samples and used for transcriptomic studies by Affymetrix.

first: Carmela

last: Pablo-Torres

first: Maria

middle: I

first: Javier

last: Sanchez-Solares

first: Leticia

last: Mera-Berriatua

first: Lucía

last: Nuñez Martin Buitrago

first: Mar

last: Reaño Martos

first: Jose

middle: L

last: Bueno

last: Escribese

first: Domingo

last: Barber

first: Cristina

last: Gomez-Casado


title: DHODH is an independent prognostic marker and potent therapeutic target in neuroblastoma

status: Public on Jul 27 2022

city: Stockholm

first: Ninib

last: Baryawno

address: Tomtebodavägen 18a

department: Department of Women's and Children's health

country: Sweden

institute: Karolinska institutet

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: DHODH is an independent prognostic marker and potent therapeutic target in neuroblastoma [RNA-seq]

summary: Despite intensive therapy, children with high-risk neuroblastoma are at risk of treatment failure. We applied a multi-omic system approach to evaluate metabolic vulnerabilities in human neuroblastoma. We combined metabolomics, CRISPR screening and transcriptomic data across >700 solid tumor cell lines and identified dihydroorotate dehydrogenase (DHODH), a critical enzyme in pyrimidine synthesis, as a potential treatment target. Of note, DHODH inhibition is currently under clinical investigation in patients with hematologic malignancies. In neuroblastoma, DHODH expression was identified as an independent risk factor for aggressive disease, and high DHODH levels correlated to worse overall and event-free survival. A subset of tumors with the highest DHODH expression was associated with a dismal prognosis, with a 5-year survival of <10%. In xenograft and transgenic neuroblastoma mouse models treated with the DHODH inhibitor brequinar, tumor growth was dramatically reduced, and survival was extended. Furthermore, brequinar treatment was shown to reduce the expression of MYC targets in three different neuroblastoma models in vivo. A combination of brequinar and temozolomide was curative in the majority of transgenic TH-MYCN neuroblastoma mice, indicating a highly active clinical combination therapy. Overall, DHODH inhibition combined with temozolomide has therapeutic potential in neuroblastoma and we propose this combination for clinical testing.

overall_design: These samples represent tumor tissue of three neuroblastoma mouse models treated with the DHODH inhibitor brequinar. Three replicates from each experimental condition is included. The models used were: 1) SK-N-BE(2)C cell-line derived subcutaneous xenografts; 2) SK-N-AS cell-line derived subcutaneous xenografts; 3) tumor tissue from homozygous mice of the transgenic TH-MYCN neuroblastoma mouse model. Xenograft mice were given one dose of brequinar 50 mg/kg i.p. and tumor tissue was sampled after 24 and 72 hours; tumor tissue from untreated mice were used as control. TH-MYCN mice were treated with one dose of brequinar 50 mg/kg i.p and tumors sampled after 72 hours; tumor tissue from vehicle treated mice were used as control. In addition, we sampled three tumors from mice which suffered from disease relapse after 120 days of brequinar treatment.

first: Thale

middle: K

last: Olsen


title: Single-cell analysis of Kaposi’s sarcoma-associated herpesvirus infection in three-dimensional air-liquid interface culture model

status: Public on Jul 28 2022

city: Cleveland

first: Kyle

last: Jung

email: jungk@ccf.org, kxj240@case.edu

state: OH

address: 9500 Euclid Ave. NE2-251

department: Cancer Biology

institute: Cleveland Clinic

summary: The oral cavity has previously been identified as the major site for transmission of Kaposi’s sarcoma-associated herpesvirus (KSHV), but how KSHV establishes infection and replication in the oral epithelia remains unclear. Here, we report a KSHV spontaneous lytic replication model using fully differentiated, three-dimensional (3D) oral epithelial organoids at an air-liquid interface (ALI). This model revealed that KSHV infected the oral epithelia when the basal epithelial cells were exposed by damage. Unlike two-dimensional (2D) cell culture, 3D oral epithelial organoid ALI culture allowed high levels of spontaneous KSHV lytic replication, where lytically replicating cells were enriched at the superficial layer of epithelial organoid. Single cell RNA sequencing (scRNAseq) showed that KSHV infection induced drastic changes of host gene expression in infected as well as uninfected cells at the different epithelial layers, resulting in altered epithelial differentiation and morphogenesis. Moreover, we identified a unique population of infected cells containing lytic gene expression at the KSHV K2-K5 gene locus and distinct host and viral gene expression compared to latency or lytic replication. This study demonstrates an in vitro 3D epithelial organoid ALI culture model that recapitulates KSHV infection in the oral cavity, where KSHV undergoes the epithelial differentiation-dependent spontaneous lytic replication with a unique cell population carrying distinct viral gene expression.

overall_design: 3D oral epithelial organoids were wounded and then infected with either PBS (Mock) or KSHV (rKSHV.219). These tissues were harvested at 3dpi or 6dpi for single cell RNA sequencing with the 10X Single Cell Gene Expression v2 (Set 1 and 2) or v3 (Set 3).

first: Un

middle: Y

last: Choi

first: Angela

last: Park

first: Suan-Sin

last: Foo

first: Stephanie

last: Kim

first: Shin-Ae

last: Lee

first: Jae

middle: U


title: DHODH is an independent prognostic marker and potent therapeutic target in neuroblastoma [ChIP-seq]

overall_design: These samples represent H3K27Ac ChIP-seq of tumor tissue from transgenic TH-MYCN mice  treated with the DHODH inhibitor brequinar. Three biological replicates from each experimental condition is included. Mice were treated with brequinar or vehicle, one dose of 50 mg/kg i.p., and tumors were sampled after 72h.


title: Counterintuitive effect of extracellular fluid viscosity on enhancing motility and metastasis

city: Washington

first: Jiaxiang

last: Tao

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

summary: Cells respond to physical stimuli, such as stiffness, fluid shear stress and hydraulic pressure. Extracellular fluid viscosity is a key physical cue that varies under physiological and pathological conditions, such as cancer. However, its impact on cancer biology and the mechanism by which cells sense and respond to changes in viscosity is unknown. We demonstrate that elevated viscosity counterintuitively increases the motility of various cell types on two-dimensional (2D) surfaces, in confinement, and cell dissemination from 3D tumor spheroids. Increased mechanical loading imposed by elevated viscosity induces an Actin Related Protein 2/3 (Arp2/3) complex-dependent dense actin network, which enhances Na+/H+ exchanger 1 (NHE1) polarization via its actin-binding partner ezrin. NHE1 promotes cell swelling and increased membrane tension which, in turn, activates transient receptor potential cation vanilloid 4 (TRPV4) and mediates calcium influx, leading to increased RhoA-dependent cell contractility. The coordinated action of actin remodeling/dynamics, NHE1-mediated swelling and RhoA-based contractility facilitates enhanced motility at elevated viscosities. Breast cancer cells pre-exposed to elevated viscosity acquire TRPV4-dependent mechanical memory via transcriptional control of the Hippo pathway, leading to increased migration in zebrafish, extravasation in chick embryos and lung metastasis in mice. Cumulatively, extracellular viscosity is a physical cue that regulates both short- and long-term cellular processes with pathophysiological relevance to cancer biology.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for scramble or shTRPV4 MDA-MB-231 cells subjected to media at 0.77 cP or 8 cP.

first: Konstantopoulos

last: Konstantinos


title: HOTAIR interacts with PRC2 complex regulating the regional preadipocyte transcriptome and human fat distribution

status: Public on Jul 26 2022

city: Oxford

first: Katherine

last: Pinnick

state: Oxon

address: OCDEM, Churchill Hospital

institute: University of Oxford

summary: Mechanisms governing regional human adipose tissue (AT) development remain undefined. Here, we show that the long non-coding RNA, HOTAIR (HOX transcript antisense RNA), is exclusively expressed in gluteofemoral AT, where it is essential for adipocyte development. We find that HOTAIR interacts with Polycomb Repressive Complex 2 (PRC2) and identify core HOTAIR-PRC2 target genes involved in adipocyte lineage determination. Repression of target genes coincides with PRC2 promoter occupancy and H3K27 tri-methylation. HOTAIR is also involved in modifying the gluteal adipocyte transcriptome through alternative splicing. Gluteal-specific expression of HOTAIR is maintained by defined regions of open chromatin across the HOTAIR promoter. HOTAIR expression levels can be modified by hormonal (oestrogen, glucocorticoids) and genetic variation (rs1443512 is a HOTAIR eQTL associated with reduced gynoid fat mass in 25,200 individuals). These data identify HOTAIR as a dynamic regulator of the gluteal adipocyte transcriptome and epigenome with functional importance for human regional AT development.

overall_design: Human immortalized gluteal preadipocytes were transduced with HOTAIR shRNA and transcriptional profiling was performed at Day0, Day4 and Day14 of adipogenic differentiation compared to shControl cells


title: Neutrophils restrain sepsis associated coagulopathy via extracellular vesicles carrying superoxide dismutase 2 in a murine model of lipopolysaccharide induced sepsis

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Disseminated intravascular coagulation (DIC) is a deadly complication of sepsis lacking effective managements. Although excessive inflammatory responses are emerging as key triggers of coagulopathy in sepsis, the interplays between immune system and coagulation are not fully understood. In a murine model of sepsis induced by intraperitoneal lipopolysaccharide (LPS), we found neutrophils in circulation mitigate the occurrence of DIC, thereby preventing the subsequent septic death. We found circulating neutrophils constantly release extracellular vesicles (EVs) containing mitochondria, which carry substantial amount of Superoxide Dismutase 2 (Sod2) upon LPS exposure. The extracellular Sod2 is necessary to bring about neutrophils’ antithrombotic function by eliminating endothelial reactive oxygen species (ROS) accumulation and alleviating endothelial dysfunction. Intervening endothelial ROS accumulation by antioxidants significantly ameliorates DIC with correspondingly improved survival in sepsis. These findings revealed a novel interaction between neutrophils and vascular endothelium which critically regulates coagulation in sepsis and had potential implications for the management of septic DIC.

overall_design: Single cell suspensions of peripheral blood and bone marrow were prepared as previously described. Neutrophils were isolated by EasySepTM Mouse Neutrophil Enrichment Kit (Stem Cell). The isolated neutrophils were washed twice with PBS and maintained on ice for further experiments.

first: Wenjie

last: Bao

first: Huayue

last: Xing

first: Shiwei

last: Cao

first: Xin

last: Long

first: Haifeng

last: Liu

first: Junwei

last: Ma

first: Zimu

last: Deng

first: Xiaolong


title: Transcriptional repression of GTL1 by water-deficit stress promotes anthocyanin and polyamine biosynthesis to enhance drought tolerance

status: Public on Jul 25 2022

city: WEST LAFAYETTE

first: Noel

middle: Anthony

last: Mano

state: IN

address: 170 S University Street

institute: Purdue University

summary: GT2-LIKE 1 (GTL1) is a negative regulator of stomatal development and its repressed expression under water deficit can result in enhanced drought tolerance. As a transcription factor, GTL1 has been implicated in diverse developmental roles. We hypothesized that GTL1 represses multiple drought tolerance pathways, leading to the drought tolerance phenotype of the gtl1-4 knockout mutant. RNA-Seq data indicates that GTL1 regulates genes involved in ribosome biogenesis in emerging leaves and secondary metabolite synthesis in expanding leaves.

overall_design: RNA was collected from emerging and expanding leaves of Col-0 wildtype Arabidopsis thaliana and the knockout mutant gtl1-4 that had been maintained under well-watered or a 30% media water content water-deficit stress. There were three biological replicates per genotype/treatment/leaf age combination, with 10 plants were pooled into a replicate. Emerging leaves were sampled one-day post-emergence and expanding leaves sampled at 14/15 days post-emergence.

middle: A


title: SOX transcription factors direct TCF-independent Wnt/beta-catenin transcription

city: Cincinnati

first: Shreyasi

last: Mukherjee

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: We report ChIP-Seq experiments to profile the genomic binding dynamics  of ß-catenin, SOX17, SOX2 and TCF/LEF TFs in definitive endoderm and neuromesodermal progenitor cells and RNA-Seq/ATAC-Seq experiments for transcriptomic and chromatin profiling of these cell types.

overall_design: ChIP-Seq, RNA-Seq and ATAC-Seq experiments were performed every 24hrs during DE specification in WT and SOX17KO cells. ChIP-Seq, RNA-Seq and ATAC-Seq was performed in NMP cells after Day 3 of differentiation in WT and SOX2KD conditions. ChIP-Seq and RNA-Seq experiments were performed at day 3 of DE specification in WT and SOX17KO iPSCs or in HEK293T cells.

first: Aaron

middle: M

last: Zorn


title: Cell division drives DNA methylation loss in late-replicating domains in primary human cells [methylation array]

city: Grand Rapids

first: Peter

middle: W

last: Laird

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

type: Methylation profiling by genome tiling array

summary: We present the first experimental evidence that loss of DNA methylation at late-replicating regions, widely documented in aging and cancer, is directly driven by cell division. DNA hypomethylation, particularly at low-density CpGs in A:T-rich, partially methylated domains (PMD solo-WCGWs), tracks cumulative population doublings in primary cell culture. Cell cycle deceleration or full arrest resulted in a proportional decrease in the rate of DNA methylation loss.   Lower culture oxygen conditions resulted in a slowed rate of methylation loss, suggesting that these CpGs may also be vulnerable to methylation loss during unscheduled, repair-associated methylation maintenance as well as scheduled, replication-associated methylation maintenance.  By studying this methylation context in immortalized primary cells, we identified genomic and epigenomic features that are resistant or more susceptible to methylation loss. Finally, we leveraged this extensive DNA methylation dataset to develop a refined metric for the relative cumulative mitotic histories of human cells. These RNA-sequencing data accompany the larger DNA methylation dataset.

overall_design: DNA methylation in serially passaged primary human cell lines was profiled via human methylationEPIC array. Multiple sub-experiments are included: primary cells were either cultured under standard conditions, under low oxygen, with growth arresting agent mitomycin C, with differential serum concentrations , or after lentiviral transduction with TERT expression vector. Controls are included within each sub-experiment.

first: Jamie

last: Endicott

first: Hui

last: Shen

first: Paula

last: Nolte


title: Cell division drives DNA methylation loss in late-replicating domains in primary human cells [RNA-seq]

overall_design: RNA-sequencing was performed on total RNA extracted from serially-passaged human primary cells.


title: Single-cell transcriptomic data in the spinal cord of Taiwanese type I SMA mice

status: Public on Jul 23 2022

city: nantong

first: junjie

last: sun

state: jiangsu province

address: 19 Qixiu Road

institute: nantong university

summary: Although spinal muscular atrophy (SMA) is a motor neuron disease caused by the loss of survival of motor neuron protein, there is growing evidence that non-neuronal cells play important roles in SMA pathogenesis. However, transcriptome alterations occurring at the single-cell level in SMA spinal cord remain unknown, preventing us from fully comprehending the role of specific cells. Here, we performed single-cell RNA sequencing of the spinal cord of a severe SMA mouse model, and identified ten cell types as well as their differentially expressed genes.

overall_design: Single-cell sequencing of spinal cords of postnatal day 4 SMA mice (mSmn-/-, hSMN22tg/0), heterozygous mice  (mSmn+/-, hSMN22tg/0) as controls.

first: Junjie

last: Sun

first: Liucheng

last: Wu

first: Lingyan


title: Genome-wide transcriptome analysis of SARS-CoV-2 positive patients' mucosa, compared with negative controls.

status: Public on Jul 24 2022

city: Pozzuoli

first: Francesco

last: Panariello

state: Napoli

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

summary: We report the application of genome-wide RNA-sequencing analysis for SARS-CoV-2 positive patients' mucosa. We analyzed the correlation between gene expression levels and viral load (assessed with qPCR) and found a gene signature that might be relevant for diagnosis and treatment of SARS-CoV-2 infection. We performed such analyses in samples with assigned lineage B.1 or B.1.617 (Delta). We compared the expression of these genes in negative patients and observed low abundance, thus confirming their significance.

overall_design: mRNA profiles of SARS-CoV-2 positive patients' mucosa and negative controls.

first: Antonio

last: Grimaldi


title: RNA-Seq in peripheral blood samples of atopic dermatitis patients of the TREATgermany registry before and after initiation of systemic therapy with Dupilumab

status: Public on Jul 21 2022

city: Kiel

first: Matthias

last: Hübenthal

state: SH

address: Rosalind-Franklin-Str. 9

department: Dermatology, Venereology and Allergy

institute: University Hospital Schleswig-Holstein

summary: Background: Few studies have analyzed the blood transcriptome in atopic dermatitis (AD). Objective: We explored blood transcriptomic features of moderate to severe AD. Results: AD patients showed pronounced inflammatory expression signatures with increased myeloid and IL-5-related patterns, and clearly segregated into 2 distinct clusters, with striking differences in particular for transcripts involved in eosinophil signaling. The eosinophil-high endotype showed a more pronounced global dysregulation, a positive correlation between disease activity and signatures related to IL-5 signaling, and strong correlations with several target proteins of antibodies or small molecules under development for AD. In contrast, the eosinophil-low endotype showed little transcriptomic dysregulation and no association between disease activity and gene expression. Clinical improvement with receipt of dupilumab was accompanied by a decrease of innate immune responses and an increase of lymphocyte signatures including B-cell activation and natural killer cell composition and/or function. The proportion of super responders was higher in the eosinophil-low endotype (32% vs 11%). Continued downregulation of IL18RAP, IFNG, and granzyme A in the eosinophil-high endotype suggests a residual disturbance of natural killer cell function despite clinical improvement. Conclusion: AD can be stratified into eosinophilic and noneosinophilic endotypes; such stratification may be useful when assessing stratified trial designs and treatment strategies.

overall_design: Blood messenger RNA sequencing on 60 adults from the TREATgermany registry including 49 patients before and after dupilumab treatment, as well as from an independent cohort of 31 patients and 43 controls was performed. Patient clustering, differential expression, correlation and coexpression network analysis, and unsupervised learning were conducted.

first: Lena

last: Möbus

first: Elke

last: Rodriguez

first: Stephan

last: Weidinger


title: CHD7 regulates otic lineage differentiation and sensory epithelium generation in human inner ear organoids

city: Indianapolis

first: Tsubasa

last: Saeki

address: 980 W Walnut St

department: Otolaryngology-Head and Neck Surgery

institute: Indiana University School of Medicine

summary: Mutations in the chromatin remodeling enzyme CHD7 cause CHARGE syndrome, which affects multiple organs including the inner ear. We investigated how CHD7 mutations affect otic development in human inner ear organoids. We found loss of CHD7 or its chromatin remodeling activity leads to complete absence of hair cells and supporting cells, which can be explained by dysregulation of key otic development-associated genes in mutant otic progenitors. Further analysis of the mutant otic progenitors suggested that CHD7 can regulate otic genes through a chromatin remodeling-independent mechanism. Results from transcriptome profiling of hair cells revealed disruption of deafness gene expression as a potential underlying mechanism of CHARGE-associated sensorineural hearing loss. Notably, co-differentiating CHD7 knockout and wild-type cells in chimeric organoids partially rescued mutant phenotypes by restoring otherwise severely dysregulated otic genes. Taken together, our results suggest that CHD7 plays a critical role in regulating human otic lineage differentiation and deafness gene expression.

overall_design: For day 20 samples, dissociated cells from WT and CHD7 KO/KO human inner ear organoids were isolated by fluorescence-activated cell sorting (FACS) according to the presence or absence of PAX2-2A-nGFP signal and analyzed using scRNA-seq. For day 70 samples, dissociated cells from WT, CHD7 KO/+, and CHD7 KO/KO human inner ear organoids were isolated by FACS according to the presence or absence of POU4F3-2A-ntdTomato signal, or the presence or absence of EPCAM-PE signal and analyzed using scRNA-seq.

first: Jing

last: Nie

first: Yoshitomo

last: Ueda

first: Alexander

middle: J

last: Solivais

first: Eri

last: Hashino


title: A ketogenic diet in combination with gemcitabine increases survival in pancreatic cancer KPC mice

city: Davis

first: Gerardo

middle: Guillermo

last: Mackenzie

state: California

address: One Shields Ave

department: Nutrition

institute: University of California, Davis

summary: Pancreatic ductal adenocarcinoma (PDAC) continues to be a major health problem. A ketogenic diet (KD), characterized by a very low carbohydrate and high fat composition, has gained attention for its anti-tumor potential. We evaluated the effect and mechanisms of feeding a strict KD alone or in combination with gemcitabine in the autochthonous LSL-KrasG12D/+; LSL- Trp53 R172H/+; Pdx1-Cre (KPC) mouse model. For this purpose, both male and female pancreatic tumor-bearing KPC mice were allocated to a control diet (CD; %kcal: 70% carb, 14% protein, 16% fat), a KD (%kcal: 14% protein, 1% carb, 85% fat), a CD + gemcitabine (CG), or a KD + gemcitabine (KG) group. Mice fed a KD alone or in combination with gemcitabine showed significantly increased blood β-hydroxybutyrate levels compared to mice fed a CD or CG. KPC mice fed a KG had a significant increase in overall median survival compared to KPC mice fed a CD (increased overall median survival by 42%). Interestingly, when the data was disaggregated by sex, the effect of a KG was significant in female KPC mice (60% increase in median overall survival), but not in male KPC mice (28% increase in median overall survival). Mechanistically, the enhanced survival response to a KD combined with gemcitabine was multifactorial, including inhibition of ERK and AKT pathways, regulation of fatty acid metabolism and the modulation of the gut microbiota. In summary, a KD in combination with gemcitabine appears beneficial as a treatment strategy in PDAC in KPC mice, deserving further clinical evaluation.

overall_design: Female pancreas/tumor samples from KPC mice treated with or without a ketogenic diet and gemcitabine

first: Natalia

last: Cortez

first: Cecilia

last: Rodriguez Lanzi

first: Brian

last: Hong

first: Jihao

last: Xu

first: Fangyi

last: Wang

first: Shuai

last: Chen

first: Jon

last: Ramsey

first: Matthew

last: Pontifex

first: Michael

last: Müller

first: David

last: Vauzour

first: Payam

last: Vahmani

first: Chang-il

last: Hwang

first: Karen

last: Matsukuma


title: Common chromosome gains and losses in acute lymphoblastic leukemia [RNA-seq]

city: Guadalajara

first: Adriana

middle: Del Carmen

last: Aguilar Lemarroy

state: Jalisco

address: Sierra Mojada 800, Independencia Oriente, 44340 Guadalajara, Jal.

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

summary: To evaluate chromosomal aberrations that were first detected with aCGH at the transcriptome level, we obtained total RNA from a sample derived from an individual with untreated acute lymphoblastic leukemia (which we named M5) and from the JURKAT and CEM cell lines. Sequencing was performed by NOVOGEN Bioinformatics Technology Co., Ltd., in Beijing, China. The platform used was Illumina NovaSeq 6000.

overall_design: We evaluate altered chromosomal regions with loss in chromosomes 2,9 and 14 and with amplification in chromosomes 13 and 17

last: Aguilar-Lemarroy

first: Jessica

last: Zapata-García

first: Luis

middle: F

last: Jave-Suárez

first: Alma

last: Riveros-Magaña


title: DNA sequence and chromatin modifiers determine epigenetic bistability at imprinting control regions

status: Public on Jul 20 2022

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

institute: Utrecht University

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

overall_design: Refer to individual Series


title: Mapping the mouse developmental and aging atlas by single cell mRNA-seq

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

summary: Single-cell mRNA sequencing (mRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built a comprehensive mouse cell atlas to catalog all cell types by collecting scRNA-seq data in the fetal and adult stages. Howerver, systematically study for organism-level dynamic changes of cellular states across mouse life span are still lacking. Here, We made an updated version of mouse cell atlas (MCA) by adding scRNA-seq data covering 14 major mouse organs during different mouse development period. We revealed aging related regulatory networks and pathways that have not been well characterized previously. We found that the expressions of immune-related genes, such as antigen-presenting genes and immunoglobulin genes, appeared in non-immune cell types in aging process. We also focused on the expression of lung epithelial immunoglobulin genes and revealed their related transcriptional regulation mechanisms. The updated MCA resource provides a valuable resource for studying mammalian development, maturation and aging.

overall_design: Microwell datasets for ten mouse tissues (brain, heart, intestine, kidney, liver, lung, pancreas, stomach, testis and uterus) covering 8 stages  including E14.5, neonatal, 10d, 3w, 6-8w, 12m, 18m and 24m, four mouse tissues (bladder, spleen and prostate) covering aging stages including 6-8w, 12m, 18m, 24m, one tissue (thymus) covering aging stages including 6-8w, 12m, 18m and some mouse tissues used in GSE134355 and GSE108097.

first: Xiaoping

last: Han

first: Renying

first: Huiyu

last: Sun


title: Mesenchymal stromal cell secretome in preserving myocardial transcriptome profile following ex vivo cold storage

first: Meijing

last: Wang

state: Indiana

address: 950 W Walnut St. R2 E319

department: Surgery

summary: Deep RNA sequencing analysis revealed that compared to control (no cold storage/ischemia), 6h-cold storage led to 266 differentially expressed genes, many of which were implicated in modulating mitochondrial performance, oxidative stress response, myocardial function, and apoptosis. Either bone marrow- (BM) or adipose tissue-derived (Ad) mesencymal stromal cell conditioned medium (MSC-CM) restored these gene expression towards control.

overall_design: Total RNAseq was performed from the RNA isolated from mouse hearts without storage or stored in cold presrevation soultion +/- BM-MSC CM or Ad-MSC CM for 6 hours.

first: Keith

last: March


title: Early suppression of antiviral host response and protocadherins by SARS-CoV-2 Spike protein in monocyte-derived macrophages

status: Public on Jul 18 2022

city: Nyíregyháza

first: Judit

last: Dobránszki

state: Szabolcs-Szatmár-Bereg

address: Westsik Vilmos út 4-6.

department: Centre for Agricultural Genomics and Biotechnology

country: Hungary

institute: University of Debrecen

summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease-19 (COVID-19). The spike protein (S) of SARS-CoV-2 plays a crucial role in mediating viral infectivity; hence, in an extensive effort to curb the pandemic, many urgently approved vaccines rely on the expression of the S protein, aiming to induce a humoral and cellular response to protect against the infection. Given the very limited information about the effects of intracellular expression of the S protein in host cells, we aimed to characterize the early cellular transcriptomic changes induced by expression of the S protein in THP-1 monocyte-derived macrophages (MDMs). The results showed that a wide variety of genes were differentially expressed, products of which are mainly mostly involved in cell adhesion, homeostasis, and most notably, antiviral and immune responses, depicted by significant downregulation of protocadherins and type I alpha interferons. Our study highlights the intrinsic pathogenic role of the S protein and sheds some light on the potential drawbacks of its utilization in the context of vaccination strategies

overall_design: Characterization of the early cellular transcriptomic changes induced by expression of S protein in THP-1-derived macrophages

first: Noémi

last: Miltner

first: Tamás

middle: R

last: Linkner

first: Viktor

last: Ambrus

first: János

last: Mótyán

first: József

last: Tőzsér

first: Mohamed

last: Mahdi


title: Mutant KRAS regulates transposable element RNA and innate immunity via KRAB zinc-finger genes

status: Public on Jul 19 2022

city: Santa Cruz

first: Daniel

last: Kim

address: McLaughlin Dr

department: Biomolecular Engineering

institute: UC Santa Cruz

summary: RAS genes are the most frequently mutated oncogenes in cancer, yet the effects of oncogenic RAS signaling on the noncoding transcriptome remain unclear. We analyzed the transcriptomes of human airway and bronchial epithelial cells transformed with mutant KRAS to define the landscape of KRAS-regulated noncoding RNAs. We found that oncogenic KRAS signaling upregulates noncoding transcripts throughout the genome, many of which arise from transposable elements (TEs). These TE RNAs exhibit differential expression, are preferentially released in extracellular vesicles, and are regulated by KRAB zinc-finger (KZNF) genes, which are broadly downregulated in mutant KRAS cells and lung adenocarcinomas in vivo. Moreover, mutant KRAS induces the epigenetic reprogramming of IFN-stimulated genes (ISGs), some of which are also regulated by KZNFs. Our results reveal that mutant KRAS remodels the noncoding transcriptome via KZNF-mediated epigenomic reprogramming, revealing the broad scope of intracellular and extracellular RNAs regulated by this oncogenic signaling pathway.

overall_design: Comparative gene expression analysis of cell lines (6x AALE and 6x HBEC) expressing mutant KRAS (3x G12D and 3x G12V, resp) and extracellular vesicles secreted from AALE (6x).

first: Roman

middle: E

last: Reggiardo

first: Angela

last: Brooks


title: DNA sequence determines epigenetic bistability at imprinting control regions [ChIP-Seq]

first: Tuncay

summary: Genomic imprinting is regulated by parental-specific epigenetic marks that differentiate between maternal and paternal chromosomes. Despite identical DNA sequence, the presence or absence of DNA methylation leads to the establishment of two distinct epigenetic states at Imprinting Control Regions (ICR). Here we combine targeted epigenome engineering to generate ectopic loci in the mouse embryonic stem cell genome that recapitulate the epigenetic properties of ICRs. We describe these ectopic ICRs as strong cis-regulatory sequences that can adopt and memorise one of two opposing epigenetic states, dependent of pre-imposed DNA methylation. This bistability is unique to ICRs and enabled us to systematically study the genetic and epigenetic determinants required for creating and maintaining the observed states. Through sequence manipulation we show that the ICR DNA sequence confers autonomy of ICRs and is required for creating epigenetic bistability. Genetic screens using DNA-methylation-sensitive reporters identify key components involved in regulating maintenance of epigenetic states. Besides DNMT1, UHRF1 and ZFP57, we identify novel factors that prevent switching between methylated and unmethylated states and validate two of these candidates, ATF7IP and ZMYM2, to be important for epigenetic memory at ICRs. In summary we show that the DNA sequence of ICRs provides the prerequisite for establishment of two distinct epigenetic states, while DNA and histone modifications ensure their stable propagation.

overall_design: Chromatin Immunoprecipitation - sequencing for H3K9me3 in wild type ES cells

first: Stefan

last: Butz


title: PAX9 regulates periodontal ligament stem cell-like differentiation of human induced pluripotent stem cells

city: Fukuoka

first: Risa

last: Sugiura

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

country: Japan

institute: Kyushu University

summary: Periodontal ligament stem cells (PDLSCs) play central roles in periodontal ligament (PDL) tissue homeostasis, repair, and regeneration. Previously, we established a protocol to differentiate human induced pluripotent stem cell-derived neural crest-like cells (iNCs) into PDLSC-like cells (iPDLSCs) using human PDL cell-derived extracellular matrix (ECM). However it remained unclear what factors principally regulate the differentiation of iNCs into iPDLSCs. In this study, we aimed to identify the transcription factor regulating production of human PDL cell-derived ECM, which is responsible for the generation of iPDLSCs. We cultured iNCs on two human PDL cell lines (HPDLC-3S and HPDLC-3U) and human dermal fibroblasts (HDF). iNCs cultured on HPDLC-3U showed higher iPDLSC-associated gene expression and mesenchymal differentiation capacity than cells cultured on HDF or HPDLC-3S. The transcription factor PAX9 was highly expressed in HPDLC-3U compared with HDF and HPDLC-3S. iNCs cultured on siPAX9-transfected HPDLC-3U displayed downregulation of iPDLSC-associated marker expression and adipocytic differentiation capacity relative to controls. Our findings suggest that PAX9 is one of the transcription factors regulating ECM production in human PDL cells, which is responsible for the differentiation of iNCs into iPDLSCs.

overall_design: Examination of CAGE method in 3 cell types.

first: Sayuri

last: Hamano

first: Atsushi

last: Tomokiyo

first: Daigaku

last: Hasegawa

first: Shinichiro

last: Yoshida

first: Hideki

last: Sugii

first: Shoko

last: Fujino

first: Orie

last: Adachi

first: Masataka

last: Kadowaki

first: Daiki

last: Yamashita

first: Hidefumi

last: Maeda


title: AAV-mediated LRG1 overexpression in diabetic mice

city: New York

first: Chan Hee

last: Choi

address: 1230 York Ave

institute: The Rockefeller University

summary: To investigate the effect of LRG1 overexpression on gene expression of eWAT from db/db mice, we transduced 4-week-old db/db mice with AAV8-eGFP or AAV8-LRG1-FL and harvested eWAT at 7 weeks and 10 weeks of age. We then performed gene expression profiling analysis using data obtained from RNA-seq of eWAT from eGFP- and LRG1-overexpressing mice at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from eWAT of db/db mice transduced with AAV8-eGFP or AAV8-LRG1-FL.

first: Chanhee

first: Paul

last: Cohen


title: miR-29 mimic and inhibitor expression in the clear cell renal cell carcinoma cell lines 786-O, A-498 and ACHN

city: Montreal

first: Gabrielle

last: Perron

state: Quebec

address: 845 Sherbrooke St W

department: Human Genetics

country: Canada

institute: McGill University

summary: The goal of this study was to investigate the regulatory events underlying post-transcriptional changes in gene expression in cancer. We observed that the miR-29 regulon had reccurently increased mRNA stability across multiple cancer types and hypothesized that its down-regulation is responsible at least in part for alterations in the cancer transcriptome. To verify if restoring miR-29 activity can partially reverse these changes, we expressed a miR-29 mimic in the 786-O and A-498 clear cell renal cell carcinoma (ccRCC) lines and performed RNA-sequencing on extracted RNA. We computed differential gene expression in the cell lines expressing the miR-29 mimic, compared to the control sample. We observed that expression of miR-29 mimic partially shifts the transcriptome of cells toward a normal cell state, primarily by down-regulating the majority of genes that are up-regulated in ccRCC tumors, most of which are also miR-29 targets. We observed opposite trends when expressing a miR-29 inhibitor in the ACHN ccRCC cell line. The results suggest that miR-29 downregulation is responsible for changes in the mRNA stability of a considerable number of genes in ccRCC, which can be partially rescued when miR-29 activity is restored.

overall_design: RNA-seq of 786-O and A-498 cells expressing a miR-29 mimic or a miRNA mimic control, and ACHN cells expressing a miR-29 inhibitor or miRNA inhibitor control, performed using Illumina NovaSeq 6000 S4 PE100

first: Yasser

last: Riazalhosseini

first: Hamed

middle: S

last: Najafabadi


title: Cell division drives DNA methylation loss in late-replicating domains in primary human cells

first: Peter

last: Laird


title: RNA-seq analysis of heat resonse in M. polymorpha and K. nitens

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Life Science Laboratory

summary: Purpose: To understand the dynamic heat-sress response in M. polymorpha and K. nitens

sample_organism:
Marchantia polymorpha
Klebsormidium nitens

overall_design: 7-day old M. polymorpha gemmalings and one-month full K. nitens were subjected to  37°C  for 0, 1, 2 and 5 hr, 2-3  biological replicates

first: Ting-Ying

last: Wu


title: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: Argonaute 2 (AGO2) is a ubiquitously expressed protein critical for regulation of mRNA translation and vital to animal development. AGO2 protein is found in both cytoplasmic and nuclear compartments, and while its cytoplasmic role is well studied, the biological relevance of nuclear AGO2 is unclear. Here, we address this problem in vivo, using developing spermatogenic cells as a model. We find that AGO2 transiently binds both chromatin and nucleus-specific mRNA transcripts of hundreds of genes required for sperm production during male meiosis in mice, and that germline conditional knockout (cKO) of Ago2 causes depletion of the encoded proteins. Correspondingly, Ago2 cKO males exhibit abnormal sperm head morphology and reduced sperm count, along with reduced postnatal viability of offspring. Together, our data reveal an unexpected nuclear role for AGO2 in enhancing expression of developmentally important genes during mammalian male reproduction.

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design: RNA-seq, eCLIP, and ChIP-seq data for AGO2 in mESCs and spermatogenic cells; eCLIP in whole testis cytoplasmic fraction

first: Kimberly

middle: N

last: Griffin

first: Haixin

last: Li

first: Benjamin

last: Walters


title: Expression Profiling of Circular RNAs in Early Pregnant Jianghuai Buffaloes

city: Hefei

first: Zubing

last: Cao

state: Anhui

address: 130 changjiang west road

department: Animal Science

institute: Anhui Agricultural University

summary: The long reproductive cycle of buffalo is a key factor limiting the expansion of buffalo populations. Early and accurate pregnancy diagnosis in breeding heifers can shorten calving intervals and improve reproductive efficiency. Circular RNA (circRNA) is expressed in cells and tissues of several species. However, the expression of circRNAs in the blood of Jianghuai buffaloes during early pregnancy has not been reported. In this study, we identified the differentially expressed circRNAs (DECs) in the blood of Jianghuai buffaloes and annotated the functions of these DECs. The results showed that there were 890 differentially expressed circRNAs between the pregnant and non-pregnant groups, of which more than 80% were exon-derived circRNAs, including 323 up-regulated circRNAs and 567 down-regulated circRNAs. Enrichment analysis revealed that DECs were mainly enriched in the epidermal growth factor receptor signaling pathway important for embryonic development and pregnancy maintenance. In addition, most DECs have multiple miRNA targets, suggesting that these DECs have the potential to function as miRNA sponges. In conclusion, a number of DECs are present between pregnant and non-pregnant Jianghuai buffaloes, and these DECs are associated with embryo implantation and pregnancy establishment.

overall_design: control buffalo and pregnancy buffalo

first: Qiuchen

last: Liu

first: Mengya

last: Zhang

first: Tenglong

last: Guo


title: Light regulates xylem cell differentiation via PIF in Arabidopsis

city: Durham

first: Miguel

last: de Lucas

state: Durham

address: South Road

department: Biosciences

institute: Durham University

summary: Water transport is required for photosynthesis; thus plant vascular development must proceed such that water demands can be met during formation of new organs. Precise regulation of the balance between cell proliferation and differentiation in the cambial meristem defines formation of xylem and phloem, which constitute the vascular tissues. The TDIF-PXY/TDR signalling pathway is central to this process1. Peptide ligand, TDIF, encoded by CLE41 and CLE44 2, activates PXY/TDR receptors to maintain proliferative cambium. Cambium cells differentiate to xylem or phloem in the absence of active TDIF-PXY/TDR complexes. Vascular development is stimulated by light. After gemination, light induces the establishment of photoautotrophic growth via photosynthesis. Consequently, the differentiation of vascular cells must occur to favour the transport of water and minerals from the soil to the green tissues and newly developing organs. Plants perceive light through the action of photoreceptors, which modulate the activity of the transcription factors that orchestrate development. Despite the association between light signalling and vascular development, molecular mechanisms linking the two are unknown. Our work shows that vascular differentiation is inhibited in the dark by a mechanism that depends on PIF transcription factors. The dark accumulation of PIFs is necessary for CLE44 induction and thus maintenance of undifferentiated vasculature. In illuminated environments, PIF inactivation by photoreceptors causes a decrease in CLE44 expression. CLE44 reduction, in turn, leads to reduced PXY/TDR signalling which induces the xylem differentiation required to fulfil the water demands associated with photoautotrophic development.

overall_design: Arabidopsis seedlings were grown in the dark for 5 days, then exposed to white light for varying lengths of time (15, 30, 60, 150, and 360 min) before tissue collection. Three biological replicates were taken for each light condition.

first: Shraboni

last: Ghosh

first: Joseph

last: Nelson

first: Geoffrey

last: Cobb

first: John

middle: P

last: Etchells


title: Histone H2B.8 compacts flowering plant sperm through chromatin phase separation

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

summary: We characterised a sperm-expressed histone variant, H2B.8 in Arabidopsis by performing ChIP-seq, RNA-seq, and Hi-C. The data show that H2B.8 is exclusively deposited to unexpressed euchromatin and that gene expression is not significantly affected either by h2b.8 mutation in sperm or overexpression in soma. The deposition of H2B.8increases the contact probability of short range intrachromosomal interactions and contacts between pericentomeric regions and chromosome arms of different chromosomes.

overall_design: ChIP-seq profiles of H2B.8 in sperm and ectopic H2B.8 in seedlings. Native ChIP-seq of H2B.8p::H2B.8-eGFP pollen and 35Sp::H2B.8-eGFP seedlings was used with GFP-Trap beads for immunoprecipitation. The ChIP-seq data includes two replicates of IP and respective inputs each. RNA-seq data comparing WT and h2b.8 mutant sperm cells and WT and H2B.8 ectopic expression (35Sp::H2B.8-eGFP) seedlings. The data includes two replicates of sperm cells and three replicates of seedlings for each. Hi-C data for WT and H2B.8 ectopic expression (35Sp::H2B.8-eGFP) seedlings.

first: Toby

last: Buttress

first: Shengbo

last: He

first: Liang

last: Wang

first: Shaoli

last: Zhou

first: Gerhard

last: Saalbach

first: Martin

last: Vickers

first: Guohong

first: Pilong


title: Unscheduled DNA replication in G1 causes genome instability and damage signatures indicative of replication collisions

city: Martinsried

first: Karl-Uwe

last: Reusswig

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry


title: Gene expression profile at single cell level of human TILs treated with PD1-TIM3, PD1-LAG3, anti-PD1 or control isotype.

status: Public on Jul 16 2022

city: Basel

first: Marina

last: Natoli

state: Basel city

address: Hebelstrasse 20

department: DBM

institute: University Hospital Basel

summary: Several next-generation cancer immunotherapies are designed to target LAG3 and TIM3 checkpoints, though the molecular and cellular mechanisms by which both receptors operate to mediate their anti-tumour effects are still poorly understood. Here, we examined the phenotypical and transcriptional consequences of treatment with bispecific antibodies (bsAbs), currently being tested in clinical trials, which co-target PD1 and either TIM3 or LAG3, respectively, using scRNAseq.

overall_design: CD45+ cells were sorted from tumour suspensions from four different patients treated with PD1-TIM3, PD1-LAG3, anti-PD1 or control isotype for 48 and 96 hours. A total of 31 samples was ultimately sequenced from the four different conditions, 2 timepoints and 4 patients (1 sample failed at library preparation).

first: Natoli

last: Marina


title: Blood transcriptomes of SARS-CoV-2 infected kidney transplant recipients demonstrate immune insufficiency

status: Public on Jul 15 2022

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: Kidney transplant recipients (KTRs) are reported to have worse outcomes with COVID-19, and empiric reduction of T-cell directed immunosuppression has been pursued. Here we evaluated the peripheral blood transcriptome of 64 KTRs either during and after acute COVID-19. We identified transcriptomic signatures of suppression of adaptive T-cell responses which significantly associated with disease severity and showed evidence of recovery after acute disease. These findings were consistent with public data from non-KTR cohorts.

overall_design: A total of 64 cases of COVID-19 in KTRs were enrolled, including 31 acute cases (< 4 weeks from diagnosis PCR) and 33 post-acute cases (>4 weeks from PCR). Eight COVID-19 KTRs died, and three graft losses occurred during follow-up.  In the blood transcriptome of acute cases, we identified differentially expressed genes (DEGs) in positive or negative association with increasing COVID-19 severity. Functional enrichment analyses showed upregulation of neutrophil and innate immune pathways, but downregulation of adaptive immune activation pathways with increasing severity score, independent of lymphocyte count despite reduction in immunosuppression (IS) in most KTRs. Interestingly, comparison with post-acute cases showed “normalization” of these enriched pathways after >4 weeks, suggesting recovery of adaptive immune system activation despite reinstitution of IS. The latter analysis was adjusted for COVID-19 severity. Similar pathways enriched in DEGs associated with worsening disease severity was identifiable from a public dataset of non-KTRs with COVID-19 (GSE152418).

first: Zhongyang

last: Zhang

first: Khadija

last: Banu

first: Madhav

middle: C

last: Menon


title: The transcriptome of paired major and minor salivary gland tissue in patients with primary Sjögren's syndrome

city: Summit

first: Rida

last: Khan

state: NJ

address: 556 Morris Ave

department: Knowledge Science Research, IPS

institute: Bristol-Myers Squibb

summary: While all salivary glands (SGs) can be involved in primary Sjögren’s syndrome (pSS), their respective role in pathogenesis remains unclear. To assess immunopathway activation in paired parotid and labial gland tissue from biopsy-positive and biopsy-negative pSS and non-SS sicca patients, paraffin-embedded, paired parotid and labial salivary gland tissue and peripheral blood mononuclear cells were obtained from 39 pSS and 20 non-SS sicca patients. The patients were subdivided based on fulfillment of ACR-EULAR criteria and histopathology and the samples were analyzed for differentially expressed genes (DEGs).  The principal component analysis of SG gene expression could only separate biopsy-positive pSS from non-SS sicca patients. However, when comparing the transcriptome of biopsy-positive pSS and biopsy-negative non-SS sicca patients, 1235 and 624 DEGs (FDR<-1 or >1) were identified for parotid and labial glands, respectively. The number of DEGs between biopsy negative pSS and non-SS sicca patients was scarce. The overall, transcript expression levels correlated strongly between parotid and labial glands (R2=0.86, p‐value<0.0001). Gene signatures present in both glands of biopsy‐positive pSS patients included IFN‐α signaling, IL-12/IL-18 signaling, CD3/CD28 T-cell activation, CD40 signaling in B-cells, DN2 B-cells, and FcRL4+ B-cells. Signature scores varied considerably amongst pSS patients. In conclusion, the transcriptomes of paired major and minor SGs in pSS were overall comparable, although significant inter-individual heterogeneity in immunopathway activation existed. The SG transcriptome of biopsy-negative pSS was indistinguishable from non-SS sicca patients. The different patterns of SG immunopathway activation in pSS argue for personalized treatment approaches.

overall_design:
Differential expression analysis of a cohort of 39 patients with primary Sjogren's syndrome and 20 non-SS sicca patients.
characteristics: ACR EULAR = positive -> patients with primary Sjogren's syndrome
characteristics: ACR EULAR = negative -> non-SS sicca patients

first: Gwenny

last: Verstappen

first: Lu

last: Gao

first: Sarah

last: Pringle

first: Erlin

last: Haacke

first: Bert

last: van der Vegt

first: Silvia

last: Liefers

first: Vishal

last: Patel

first: Yanhua

last: Hu

first: Sumanta

last: Mukherjee

first: Julie

last: Carman

first: Laurence

last: Menard

first: Frederik

middle: K

last: Spijkervet

first: Arjan

last: Vissink

first: Hendrika

last: Bootsma

first: Frans

middle: G

last: Kroese


title: Systematic analysis of imprinting defects in female and male mouse iPSCs

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Reprogramming of somatic cells into Induced Pluripotent Stem Cells (iPSCs) provided a major leap towards more personalized cellular models for disease modelling and offers great prospects for regenerative medicine. Despite their considerable success, we still lack the ability to control the state of iPSCs fully, especially at the epigenetic level. This can be appreciated at chromosomal regions regulated by genomic imprinting which provides a good read-out for epigenetic fidelity in iPSCs. Indeed, imprinting defects have already been reported in both mouse and human iPSCs. However, the extent, nature, causes and consequences of these defects still remain to be analysed in a systematic manner. To fill this gap in knowledge, we used a controlled secondary reprogramming system whereby the donor mouse embryonic fibroblasts (MEFs) contain a doxycycline (DOX)-inducible Yamanaka cassette and also Single Nucleotide Polymorphisms (SNPs) to distinguish between the two parental alleles. Several female and male isogenic mouse iPSCs (miPSCs) were obtained using independent culture conditions (defined versus serum) and screened by allelic-specific IMPLICON, a targeted next-generation method to measure DNA methylation at imprinted regions with unprecedented genomic coverage of 1000-fold. Our results showed that imprinting defects are remarkably common in miPSCs. Interestingly, we found important differences in gender responses to culture conditions. In particular, female iPSCs exhibit widespread hypomethylation defects regardless of culture conditions, while male miPSCs show tendency for hypomethylation defects under defined conditions, and hypermethylation defects under serum conditions in particular loci. As expected, methylation defects at imprinted regions resulted in dysregulation of monoallelic expression of imprinted genes. Our results are of utmost importance to devise future reprogramming strategies to generate epigenetic error-free iPSCs

overall_design: RNA profiles of parental MEFs, female and male miPSCs, and mESCs were generated by deep sequencing, in triplicates, using Illumina HiSeq platform. Methylation profile of specific genomic regions in female and male miPSCs generated in two different culture conditions, parental MEFs and mESCs, using Illumina MiSeq platform.

first: Maria

last: Arez

first: Melanie

last: Eckersley-Maslin

first: Tajda

last: Klobucar

first: João

last: von Gilsa Lopes

first: Ana

last: Raposo

first: Domenico

last: Aprille

first: Anne-Valerie

last: Gendrel

first: Simão

middle: T

last: da Rocha


title: PCGF6 activates SOX2 and contributes to lineage differentiation of human pluripotent stem cells

city: Wuhan

first: Chun

middle: Xian

last: Lan

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

institute: Wuhan University

summary: To assess and distinguish the molecular role of PCGF6 in the self-renewal and early differentiation of PSCs, we established PCGF6-knockout PSCs. Although the absence of PCGF6 could maintain self-renewal and colony-formation capacity, it induced abnormal early differentiation in PSCs. PCGF6 deficiency in PSCs promoted the development of mesendoderm, and impaired the development of neuroectoderm during differentiation process in vitro. RNA-seq and ChIP-seq experiments revealed that PCGF6 plays different roles in distinct lineage specification. On the one hand, PCGF6 worked as a transcription activator that maintain early neuroectoderm differentiation by regulating the expression of SOX2. On the other hand, PCGF6 resists skewed differentiation toward mesendoderm through the PRC1-dependent inhibition of WNT/β-catenin signaling pathways.

overall_design: We performed RNA-seq and PCGF6 ChIP-seq using PSC (two replicates for each), Ub Chip-seq using PSC (only one replicates for each).

first: Xianchun

first: Wei

last: Jiang


title: Single cell RNA sequencing profile of a unique mesenchymal progenitor subset from the developing murine forelimb

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

institute: University of British Columbia

summary: During mouse embryonic development, the limbs emanate from primordial buds of lateral plate mesoderm as proliferating mesenchymal cells cause protrusions of the overlying ectoderm. As the bud expands, several populations of cells are thought to migrate into the emerging limb and contribute to various specialized structures therein. A unique subset has been identified among the migrating populations that contributes to enduring stromal compartments in various tissues and is responsible for aspects of secondary morphogenesis including the formation of entheses throughout the limb. Using a lineage tracing tool, this population was sampled at various stages along the developmental continuum and gene expression was profiled at the single cell level to determine the fate and function of this cell subtype and the genetic programs involved.

overall_design: Single cell RNA-seq analyes of mesenchymal progenitors from the developing murine forelimb.

first: M

last: Arostegui

first: R

last: Scott

first: T


title: RNA sequencing analysis of WT and Dusp6-/- rat cardiac infiltrated macrophages transcriptomes

status: Public on Jul 13 2022

city: Beijing

first: Chenyang

last: Zhang

address: 5 Yiheyuan Road

institute: College of Future Technology, Peking University

summary: Dual-specificity phosphatase 6 (DUSP6), a member of MAPK phosphatase, serves a specific and conserved function on the dephosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2) in multiple species. Utilizing a rat strain harboring nonsense mutation of Dusp6, we found that Dusp6 deficiency improves cardiac function by attenuating cardiomyocyte death and fibrosis in acute inflammatory phase after MI. To investigate the effect of DUSP6 on macrophages in acute inflammatory phase of MI, we performed RNA-seq analysis using CD45+HIS36+ macrophages isolated from Dusp6-deficient and WT infarcted LV tissues 72 h after MI by fluorescent activated cell sorting (FACS).

overall_design: Cardiac infiltrated macrophage mRNA profiles of WT and Dusp6-/- rats.

first: Xiaohai

last: Zhou

first: Xueying

last: Wu