title: Activity-induced gene expression and long-range enhancer-promoter contacts in cohesin-deficient neurons (Ribo Tag)

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: RNA-seq of ribosome associated mRNA from Rad21lox/lox;NexCre/+;RiboTag+ and Rad21+/+;NexCre/+;RiboTag+ dissociated cortical neurons at Day In Vitro (DIV10)

overall_design: RNA-Seq was performed on mRNA  from immunoprecipitated polysomes of DIV10 cortical dissociated neurons. Three replicates of Rad21lox/lox;NexCre/+;RiboTag+ and three replicates of  Rad21+/+;NexCre/+;RiboTag+ DIV10 cortical dissociated neurons were used. Neurons were heterozygous for the Rpl22-HA (RiboTag) allele, which expresses an HA-tagged ribosomal protein specifically in Cre-expressing neurons.

first: Lesly

last: Calderon

first: Thomas

last: Carroll

first: Matthias

last: Merkenschlager

first: Felix

last: Weiss

first: Yi-Fang

last: Wang


title: Activity-induced gene expression and long-range enhancer-promoter contacts in cohesin-deficient neurons with BDNF

status: Public on Apr 26 2022

city: London

country: United Kingdom

type: Expression profiling by high throughput sequencing

summary: RNA-seq of total RNA from RAD21-TEV depleted and expressing cortical neurons at day in vitro (DIV11) without stimulation or after treatment with BDNF (10ng/ml) for 30 or 120 minutes. Minimum of three replicates were used in each condition

overall_design: RNA-seq was performed on total RNA from DIV11 cortical dissociated neurons. Neurons were left without stimulation or treated with BDNF (50ng/ml) for either 30 or 120 minutes where indicated.


title: Single Cell Sequencing of MITF-GFP sorted cells at 28

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 51 Newton Road 100 Bowen Science Building Iowa

department: Anatomy and Cell Biology

country: USA

institute: University of Iowa

summary: scRNA-seq on GFP + cells sorted from the Tg(mitfa:GFP) transgenic zebrafish embryos at 28 hours post fertilization (hpf) using the 10x Chromium system

overall_design: Single cell RNA-sequencing (scRNA-seq) was used to investigate the temporal order of gene expression in cells of the melanocyte lineage which were included among GFP-expressing cells isolated from Tg(mitfa-GFP) zebrafish embryos at 28 hours post fertilization (hpf)

first: Robert

middle: A

last: Cornell


title: Activity-induced gene expression and long-range enhancer-promoter contacts in cohesin-deficient neurons

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

overall_design: Refer to individual Series


title: Epigenetic reversal of lineage plasticity enhances responsiveness to anti-GD2 therapy in neuroblastoma [RNA-seq SKNBE2 or KPNYN]

city: West Lafayette

first: Nathaniel

middle: Wesley

last: Mabe

state: Indiana

address: 201 S. University St.

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

summary: GD2 is a disialoganglioside that is highly expressed on the surface of neuroblastoma cells. Immunotherapy with anti-GD2 antibodies has revolutionized the treatment of children with high-risk neuroblastoma, but nearly half of patients relapse and little is known about mechanisms of resistance to anti-GD2. Neuroblastomas harbor intrinsic transcriptional plasticity by co-opting divergent lineage-specific developmental programs between adrenergic and mesenchymal cell states. We found that reduced GD2 expression was significantly correlated with the adrenergic cell state in neuroblastoma and that an Adrenergic-to-Mesenchymal Transition (AMT) conferred downregulation of GD2 and resistance to anti-GD2 antibody. Induced reprogramming of adrenergic cells with the master AMT regulator PRRX1 was sufficient to promote transcriptional rewiring in isogenic models and downregulate GD2 expression. Mechanistically, low-GD2 expressing cell lines demonstrate significantly reduced expression of the ganglioside synthesis enzyme ST8SIA1 (GD3 synthase), resulting in a bottlenecking of GD2 synthesis. Primary neuroblastoma tumors enriched for mesenchymal features show demonstrably lower GD3 synthase expression as compared to adrenergic tumors. Pharmacologic inhibition of EZH2 resulted in epigenetic rewiring of mesenchymal neuroblastoma cells and re-expression of ST8SIA1, restoring surface expression of GD2 and sensitivity to an anti-GD2 antibody. These data identify developmental lineage as a key determinant of sensitivity to anti-GD2 based immunotherapies and credential EZH2 inhibitors for clinical testing in combination with anti-GD2 antibody to enhance outcomes for children with neuroblastoma.

overall_design: SKNBE2;tetON-PRRX1 or KP-N-YN;tetON-PRRX1 cells were treated with 0.5 mg / mL doxycycline or vehicle for 21 days

middle: W


title: Activity-induced gene expression and long-range enhancer-promoter contacts in cohesin-deficient neurons (NexCre)

summary: RNA-seq of total RNA from Rad21lox/lox;NexCre/+ and Rad21+/+;NexCre/+ dissociated cortical neurons at Day In Vitro (DIV10) without stimulation or after treatment with TTX/D-AP5 and 1h or 6h of KCl depolarization.

overall_design: RNA-Seq was performed on total RNA from DIV10 cortical dissociated neurons. Neurons were left without stimulation, treated overnight with TTX/D-AP5 or treated overnight with TTX/D-AP5 and then depolarized for 1h or 6h with KCl. Three replicates of Rad21lox/lox;NexCre/+ and three replicates of  Rad21+/+;NexCre/+ DIV10 cortical dissociated neurons in each condition were used.


title: The Phytotoxin Myrigalone A Triggers a Phased Detoxification Programme and Inhibits Lepidium sativum Seed Germination via Multiple Mechanisms Including Interference with Auxin Homeostasis

status: Public on Apr 23 2022

city: Egham

first: Gerhard

last: Leubner-Metzger

state: Surrey

address: Bourne Building 3-30

department: Biological Sciences

institute: Royal Holloway University of London

summary: Molecular responses of plants to natural phytotoxins comprise more general and com-pound-specific mechanisms. How phytotoxic chalcones and other flavonoids inhibit seedling growth was widely studied, but how they interfere with seed germination is largely unknown. The dihydrochalcone and putative allelochemical myrigalone A (MyA) inhibits seed germination and seedling growth. Transcriptome (RNAseq) and hormone analyses of Lepidium sativum seed re-sponses to MyA were compared to other bioactive and inactive compounds. MyA treatment of imbibed seeds triggered the phased induction of a detoxification programme, altered gibberellin, cis-(+)-12-oxophytodienoic acid and jasmonate metabolism, and affected the expression of hor-mone transporter genes. The MyA-mediated inhibition involved interference with the antioxidant system, oxidative signalling, aquaporins and water uptake, but not uncoupling of oxidative phosphorylation or p-hydroxyphenylpyruvate dioxygenase expression/activity. MyA specifically affected the expression of auxin-related signalling genes, and various transporter genes, including for auxin transport (PIN7, ABCG37, ABCG4, WAT1). Responses to auxin-specific inhibitors further supported the conclusion that MyA interferes with auxin homeostasis during seed germination. Comparative analysis of MyA and other phytotoxins revealed differences in the specific regulatory mechanisms and auxin transporter genes targeted to interfere with auxin homestasis. We conclude that MyA exerts its phytotoxic activity by multiple auxin-dependent and independent molecular mechanisms.

overall_design: L. sativum seeds were treated with Myrigalone A or control solution and sampled for RNA extraction at 6,12, and 18 hours after treatment.  Five biological replicates for each sample were harvested for RNAseq

first: Kazumi

last: Nakabayashi

first: Jonathan

last: Cohn

first: Stephanie

middle: M

last: Guida-English

first: Lucio

last: Garcia

first: Iva

last: Pavlovic

first: Ondrej

last: Novak

first: Danuse

last: Tarkowska

first: Miroslav

last: Strnad

first: Marta

last: Perez

first: Anne

last: Seville

first: David

last: Stock


title: Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [DNA-Seq]

status: Public on Apr 22 2022

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

type: Genome variation profiling by high throughput sequencing

summary: Large offspring syndrome (LOS) and Beckwith-Wiedemann syndrome are a similar epigenetic congenital overgrowth conditions in ruminants and humans, respectively.  We have reported global loss-of-imprinting, methylome epimutations, and global misregulation of genes in LOS.  However, less than 4% of gene misregulation can be explained with short range (<20Kb) alterations in DNA methylation.  Therefore, we hypothesized that methylome epimutations in LOS affect chromosome architecture which results in misregulation of genes located at distances >20Kb in cis and also in trans (other chromosomes). Our analyses focused on two imprinted domains that frequently show misregulation in these syndromes, namely KvDMR1 and IGF2R. Using bovine fetal fibroblasts, we identified CTCF binding at IGF2R but not KvDMR1, and allele-specific chromosome architecture of these domains in controls.  In LOS, analyses identified erroneous long-range contacts and clustering tendency in the direction of expression of misregulated genes. In conclusion, altered chromosome architecture is involved in the etiology of LOS.

overall_design: DNA sequencing for semen DNA of the bull (Brahman breed, JDH MR. MANSO 7 860958 154BR599 11200 EBS/INC CSS 2) used to sire all the fetuses in this study.

first: Yahan

last: Li

first: Frimpong

last: Boadu

first: Max

middle: R

last: Highsmith

first: Darren

middle: E

last: Hagen

first: Jianlin

last: Cheng


title: Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [WGBS]

type: Methylation profiling by high throughput sequencing

overall_design: Whole genome bisulfite sequencing (WGBS) for skin fibroblast primary cells derived from four control and four LOS bovine day 105 fetuses.


title: Effect of CSPG stimulation on Fibcd1 WT and KO primary hippocampal neurons

status: Public on Apr 25 2022

city: Vienna

first: Vanja

last: Nagy

address: Lazarettgasse 14

country: Austria

institute: LBI-RUD

summary: To investigate if Fibcd1 mediates CSPG signalling to neurons, we established a primary mouse hippocampal neuron culture plated +/- a coating of CSPGs. After determining that Fibcd1 KO neurons are partially resistant to CSPG signals, we sought to identify the transcriptional finger print of CSPG-Fibcd1 signalling by nulk RNA-seq.

overall_design: Primary hippocampal neurons were isolated from Fibcd1 WT and KO mice and plated on coverslips +/- a coating of CSPGs

first: Christopher

last: Fell


title: Comparative transcriptomic analysis of Drosophila melanogaster adult brains

status: Public on Apr 21 2022

city: Lisboa

first: Mariana

middle: Batista

last: Santos

address: Av Brasilia

department: Champalimaud Physiology and Cancer Programme

country: Portugal

institute: Champalimaud Foundation

summary: We identified genes whose expression is upregulated in adult Drosophila m. brain 48h after a stab lesion by microarray analysis of RNA extracted from injured and intact wild-type brains (Oregon-R).

overall_design: 7-day-old adult wild-type flies (Oregon-R) were injured on the right optic lobe with a stab lesion or left non-injured (controls) and kept at 25ºC. 48h after damage, brains (with the lamina removed) were collected in chilled PBS, transferred to TRIzol and snap frozen. Experimental and control samples (25 brains each) were prepared in quadruplicates. Samples were sent to the FlyChip Drosophila functional genomics unit (Cambridge) for extraction of total RNA, reverse transcription and labeling and hybridization to Drosophila whole transcriptome long-oligonucleotide array FL003 (GEO:GPL14121). Dye-swapping (2 arrays Cy5, 2 arrays Cy2) was performed to control for bias due to dye allocation. Genes showing at least fold change of -1.3 ≤ FC ≥ 1.3 and with p-value of ≤0.05 were selected for further bioinformatic analyses. Gene ontology analyses and enrichment was performed based on STRING and networks visualized with Cytoscape. Redundancy of the GO-terms was reduced with ReviGO.

first: Christa

last: Rhiner

first: Ismael

last: Fernández-Hernández


title: Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome

sample_organism:
Bos indicus
Bos indicus x Bos taurus

platform_organism:
Bos indicus
Bos indicus x Bos taurus


title: Binary outcomes of enhancer activity underlie stable random monoallelic expression

city: Berkeley

first: Djem

middle: Ulian

last: Kissiov

state: CA

address: 485 Weill Hall

department: MCB

institute: UC Berkeley

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We analyzed the natural killer (NK) cell receptor genes as in vivo genetic model to study random monoallelic gene expression (RME). These genes are expressed randomly, and largely monoallelically, in subsets of NK cells to generate a repertoire of specificities. We found that enhancers directly controlled the probability of expression of both RME and related, broadly expressed genes. We present an analysis of the accessibility (ATAC-seq) and  both active and repressive histone modifications of elements associated with both expressed and silent alleles of the NK receptor genes in primary cells. The goals of this study were to assess the chromatin state of the silent and active alleles of the monoallelically expressed natural killer (NK) cell receptor genes.

overall_design:
We examined chromatin accessibility and histone modifications in primary NK cells sorted to be homogenous with respect to allelic expression status of the variegated/monoallelically expressed NK receptor genes, Klrc1/Nkg2a, Klrk1/Nkg2d and Klra7/Ly49g. ATAC-seq data were aligned to the mm10 genome, or separately aligned to a SNP-masked genome and allele-informative reads were binned into B6 (genome1) or BALB/c (genome2) .bam files and processed to .bw files. CUT&RUN files were all aligned to the mm10 genome.

Funding source for Stefan Muljo: Intramural Research Program of NIH, NIAID.

middle: U

middle: H

last: Raulet

first: Stefan

last: Muljo


title: Transcriptome sequencing of CD8αα T cells and CD8αβ T cells in liver of dnTGFβRII mice.

city: GuangZhou

first: bian

last: zhenhua

state: GuangDong

address: Panyu University Town

country: China

institute: South China University of Technology

summary: We characterized the tcr repertoire diversity of CD8αα T cells and CD8αβ T cells in liver microenvironment of in dnTGFβRII mice, a classical Primary Biliary Cirrhosis mouse model .

overall_design: CD8αα T cells and CD8αβ T cells sorted from liver of  dnTGFβRII mice.

first: Zhen-Hua

last: Bian

first: Yi-Chen

last: Han


title: The SARS-CoV-2 receptor ACE2 is expressed in mouse pericytes but not endothelial cells – implications for COVID-19 vascular research

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

summary: Humanized mouse models and mouse-adapted SARS-CoV-2 virus are increasingly used to study COVID-19 pathogenesis, and it is therefore important to learn where the SARS-CoV-2 receptor ACE2 is expressed. Here we mapped ACE2 expression during mouse postnatal development and in adulthood. Pericytes in the central nervous system, heart and pancreas express ACE2 strongly, as do perineurial and adrenal fibroblasts, whereas endothelial cells do not at any location analyzed. In a number of other organs pericytes do not express ACE2, including in the lung where ACE2 instead is expressed in bronchial epithelium and alveolar type-II cells. The onset of ACE2 expression is organ-specific: in bronchial epithelium already at birth, in brain pericytes before and in heart pericytes after postnatal day 10.5. Establishing the vascular localization of ACE2 expression is central to correctly interpret data from modelling COVID-19 in the mouse and may shed light on the cause of vascular COVID-19 complications.

overall_design: single-cell transcriptomes were generated of individual cells captured from adult male mice (10-20 weeks of age) by single-cell RNA-sequencing

first: Liqun

last: He

first: Ying

last: Sun

first: Jianping

last: Liu

first: Guillem

last: Genové

first: Stefanos

last: Leptidis

first: Giuseppe

last: Mocci

first: Emil

last: Hansson

first: Johan

middle: L

last: Björkegren

first: Michael

last: Vanlandewijck

first: Xiao-Rong

last: Peng

first: Urban

last: Lendahl

first: Christer

last: Betsholtz


title: Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [4C-Seq]

first: Rocío

last: Rivera

overall_design: Circular chromosome conformation capture (4C) sequencing of KvDMR1 and IGF2R imprinting control region (ICR) in skin fibroblast primary cells derived from four control and four LOS bovine day 105 fetuses.

first: Yahan

last: Li

first: Frimpong

last: Boadu

first: Max

last: Highsmith

first: Darren

last: Hagen

first: Jianlin

last: Cheng


title: Bap1 shapes the bone marrow niche for lymphopoiesis by fine-tuning epigenetic profiles in endosteal mesenchymal stromal cells [ChIP-Seq]

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: Hematopoiesis occurs within a unique bone marrow (BM) microenvironment which consists of various niche cells, cytokines, growth factors and extracellular matrix components. These multiple components directly or indirectly regulate the maintenance and differentiation of hematopoietic stem cells (HSCs). Here we report that Bap1 in BM mesenchymal stromal cells (MSCs) is critical for the maintenance of HSCs and B lymphopoiesis. Mice lacking Bap1 in MSCs show aberrant differentiation of hematopoietic stem and progenitor cells, impaired B lymphoid differentiation, and expansion of myeloid lineages. Mechanistically, Bap1 loss in distinct endosteal MSCs, expressing Prx1 but not Lepr, leads to aberrant expression of genes affiliated with BM niche functions. Bap1 deficiency leads to a reduced expression of pro-hematopoietic factors such as Scf, caused by increased H2AK119-ub1 and H3K27-me3 levels on the promoter region of these genes. On the other hand, the expression of myelopoiesis stimulating factors including Csf3 was increased by enriched H3K4-me3 and H3K27-ac levels on their promoter, causing myeloid skewing. Notably, loss of Bap1 substantially blocks B lymphopoiesis and skews the differentiation of hematopoietic precursors toward myeloid lineages in vitro, which is reversed by G-CSF neutralization. Thus, our study uncovers a key role for Bap1 expressed in endosteal MSCs in controlling normal hematopoiesis in mice by modulating expression of various niche factors governing lymphopoiesis and myelopoiesis via histone modifications.

overall_design: ChIP sequencing of endosteal mesenchymal stromal cells (MSCs) isolated from control mice (Bap1 WT) or Bap1 cKO mice which were then incubated with anti-ubiquityl-H2AK119, anti-trimethyl-H3K27, anti-acetyl-H3K27, or anti-trimethyl-H3K4 antibodies.

first: Rho

last: Seong

first: Daehee

last: Hwang


title: Comparison of genomic binding profile for RNA polyII in control and CFIm25 KD hESCs (H9 cell line)

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

institute: sysu

summary: To understand how CFIm25 depletion affects gene expression at the transcription level, we carried out ChIP-seq analysis for RNAPII in control and CFIm25 KD cells.

overall_design: To examine differential binding pattern of transcription factor RNAPII on transcribed genes in control and CFIm25 KD hESCs

first: Yi

last: Ran

first: Shanshan

last: Huang

first: Chengguo

last: Yao


title: Comparison of genomic binding profile for RNA polyII in control and Rex1 RNAi hESCs (H9 cell line)

summary: To understand if rex1 is directly involved in CFIm25-regulated transcription at the transcription level, we carried out ChIP-seq analysis for RNAPII in control and rex1 RNAi cells.

overall_design: To examine differential binding pattern of transcription factor RNAPII on transcribed genes in control and rex1 RNAi hESCs


title: Global PAS-seq (polyA-site-sequencing) profiling in control and CFIm25 KD human embryonic stem cells (H9 cell line)

summary: To understand how CFIm25, an mRNA 3' processing regulator, affects global mRNA alternative polyadenylation (APA) profiling in H9 cells. We performed PAS-seq (polyadenylation site sequencing) in control (2 samples) and CFIm25 KD cells (3 samples). PAS-seq library was prepared using a lexogen kit (3'-seq, Catolog. 016.024). Sequencing was performed using Novaseq PE150.

overall_design: We used 2 control and 3 CFIm25 KD H9 cell line samples for PAS-seq


title: poly(A+)-seq profiling of gene expression in control H9 and (CFIm25 KD+ 3Flag-CFIm25 overexpression) H9 cell lines

summary: We carried out CFIm25 KD experiments in H9 cell line (hESCs). After poly(A+)-seq, we found the expression of hundreds of genes were changed. To investigate if the effect is a direct or indirect effect of CFIm25 KD, we next carried out 3Flag-CFIm25 overexpression in CFIm25 KD cells for gene-rescue experiments. After we obtained this cell line, here we performed poly(A+)-seq in control H9 and (CFIm25 KD+ 3Flag-CFIm25 overexpression)H9 cell lines. The goal of this experiment is to investigate if CFIm25 overexpression could rescue the gene expression phenotype caused by CFIm25 KD.

overall_design: poly(A+)-seq profiling of gene expression in two cell lines


title: Global poly(A+) RNA-seq profiling in control and CFIm25 KD human embryonic stem cells (H9 cell line)

summary: To understand how CFIm25, an mRNA 3' processing regulator, affects the global poly(A+) RNAs profiling in hESCs (H9 cell line). We carried out poly(A+)-seq in control (2 samples) and CFIm25 KD (3 samples) hESCs.Using a cutoff value (P<0.05, fold change>1), in total, 577 differentially expressed genes (268 down-regulated genes and 309 up-regulated genes) were found upon CFIm25 KD, and the number of down-regulated genes and up-regulated genes were 84 and 128 respectively if using the cutoff value (P<0.05, fold change>2).

overall_design: We used 2 control and 3 CFIm25 KD H9 cell line samples for poly(A+)-seq profiling


title: Acute Inflammatory Response via Neutrophil Activation Protects Against the Development of Chronic Pain

city: Montreal

first: Marc

last: Parisien

state: Quebec

address: 740 Dr. Penfield Avenue

department: Dentistry

country: Canada

institute: McGill University

summary: We used transcriptome-wide data to investigate the molecular pathophysiological mechanisms in peripheral blood immune cells at the transcriptome-wide level that underlie the transition of acute to chronic low back pain.

overall_design: A total of 98 participants with acute low back pain (LBP) were followed for three months, with blood drawn at the beginning and ending of the study. Transcriptomic changes were compared between patients whose LBP was resolved at three months with those whose LBP persisted.

first: Concetta

last: Dagostino

first: Massimo

last: Allegri

first: Luda

last: Diatchenko


title: Next Generation Sequencing facilitating quantitative analysis of Wild Type and osbzip47dsRNAi transcriptome

status: Public on Apr 20 2022

city: Bangalore

first: Usha

last: Vijayraghavan

state: Karnataka

address: New biological Science building

department: Microbiology and cell biology

country: India

institute: Indian Institute of Science

summary:
Purpose:  The goals of this study is to compare NGS-derived inflorescence transcriptome profiling (RNA-seq) between wild type and transgenic rice line #14 silenced for endogenous OsbZIP47 gene through RNA interference
Methods: mRNA profiles of tissue pool from 0.1-0.5 cm inflorscences of wild-type (WT) and osbzip47dsRNAi transgenic line #14 were generated by sequencing, in duplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed at the transcript level with STAR2 aligner followed by featureCounts and edgeR
Results: we mapped about 30 million sequence reads per sample to the rice genome (RAP Database) and identified 29532 expressed genes

first: P

last: Raghavaram


title: Omega 3, 6 long-chain fatty acid imbalance delays neurovascular development in hyperglycemia-associated retinopathy

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

summary: There is a gap in our understanding of the protective effect of the essential ω-3 long-chain polyunsaturated fatty acid (LCPUFA) docosahexaenoic acid (DHA) on proliferative retinopathies. In retinopathy of prematurity (ROP), DHA supplementation alone may not reduce the risk for severe disease. We found that in mouse neonates with hyperglycemia-associated retinopathy (HAR) with impaired retinal vessel growth modeling Phase I ROP versus controls, there was a strong metabolic shift in almost all types of retinal neuronal cells identified with single-cell transcriptomics. Loss of adiponectin (Apn-/-), modeling low APN seen in premature infants, caused a ω-3 and ω-6 LCPUFA imbalance in HAR mouse retinas. Dietary intake of ω-3 vs ω-6 LCPUFA promoted retinal vessel growth, associated with increased APN levels and increased retinal APN receptor AdipoR1 gene expression. Interestingly, we found that ω-6 vs. ω-3 LCPUFA was essential in maintaining retinal metabolism and neuronal development. Our findings suggest that both ω-3 and ω-6 LCPUFA are essential in protecting against retinal neurovascular dysfunction in Phase I ROP model. Maintaining adequate ω-6 LCPUFA levels is required while supplementing ω-3 LCPUFA to prevent retinopathy.

overall_design: P10 control (n=3 mice), P10 stz (n=3 mice), P10 stz omega3 (n=2 mice), P10 stz omega6 (n=3 mice)

first: Zhongjie

last: Fu

first: Chuck

middle: T

last: Chen

first: Anders

last: Nilsson

first: Edward

last: Bull

first: William

last: Allen

first: John

middle: P

last: SanGiovanni

first: James

middle: D

last: Akula

first: Saswata

last: Talukdar

first: Ann

last: Hellström

first: Lois

last: Smith


title: Human Pluripotent Stem Cell-derived Medium Spiny Neurons (hMSNs) Exhibit Acute and Chronic Responses to Dopamine

city: Raleigh

first: Ryan

last: Tam

state: North Carolina

address: 840 Main Campus Drive, Building Partners II, Room 3700

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: Here, we performed RNA-seq of hMSNs in triplicate (20-30 million reads per sample) exposed to dopamine, assessed their responses over time, and also compared their transcriptomic and functional responses to acute and chronic exposures. We also identified responses to agonists of interest. From this work, we identified ranges of experimental conditions that elicited cellular responses, identified specific genes and ontological functions induced by dopamine exposure, and observed desensitization to chronic exposures. These results provide a foundation on which to further develop hMSN models and to derive context for and comparisons between human and rodent responses.

overall_design: mRNA profiles of human medium spiny neurons dosed with acute dopamine, chronic dopamine, SKF82958, Quinpirole, CGS21680 and PBS, Ascorbic Acid (AA), and Water controls.

first: Albert

middle: J

last: Keung


title: Comparison of genomic binding profile for CFIm25 in control and CFIm25 KD hESCs (H9 cell line)

first: chengguo

last: yao

summary: To understand how CFIm25 associates with genomic DNA during co-transcriptional mRNA processing,we carried out ChIP-seq analysis for CFIm25 in control and CFIm25 KD cells (CFIm25 KD cells as normalization background)

overall_design: To understand how CFIm25 interacts with genomic DNA at the transcriptional level, we carried out CFIm25 ChIP-seq analysis in control and CFIm25 KD H9 cells. CFIm25 KD cells serves as background control

first: Yi

last: Ran

first: Shanshan

last: Huang

first: Chengguo

last: Yao


title: CFIm25 regulates human stem cell function independently of its role in mRNA alternative polyadenylation

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

overall_design: Refer to individual Series


title: Comparison of genomic binding profile for several transcription factors and 3' processing factors in control and CFIm25 KD hESCs (H9 cell line)

summary: To understand how CFIm25 depletion affects gene expression at the transcription level, we carried out ChIP-seq analysis for several transcription factors and 3' processing factors in control and CFIm25 KD cells.


title: Gene regulation by gonadal hormone receptors defines brain sex differences-[snRNA-Seq]

city: Cold Spring Harbor

first: Melody

last: Wu

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

summary: Estradiol establishes neural sex differences in many vertebrates and modulates mood, behavior, and energy balance in adulthood. In the canonical pathway, estradiol exerts its effects through the transcription factor estrogen receptor α (ERα). While ERα has been extensively characterized in breast cancer, the neuronal targets of ERα, and their involvement in brain sex differences, remain largely unknown. Here we generate a comprehensive map of genomic ERα-binding sites within a sexually dimorphic neural circuit that mediates social behaviors. We conclude that ERα orchestrates sexual differentiation of the mouse brain through two mechanisms: establishing two male-biased neuron types and activating a sustained male-biased gene expression program. Collectively, our findings reveal that sex differences in gene expression are defined by hormonal activation of neuronal steroid receptors. The molecular targets we identify may underlie the effects of estradiol on brain development, behavior, and disease.

overall_design: Genomic response to estradiol in mouse brain

first: Bruno

last: Gegenhuber

first: Robert

last: Bronstein

first: Jessica

last: Tollkuhn


title: Gene regulation by gonadal hormone receptors defines brain sex differences-[Multiome-Seq]


title: Gene regulation by gonadal hormone receptors defines brain sex differences-[CUT&RUN]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene regulation by gonadal hormone receptors defines brain sex differences-[RNA-Seq]


title: Gene regulation by gonadal hormone receptors defines brain sex differences-[ATAC-Seq]


title: Gene regulation by gonadal hormone receptors defines brain sex differences


title: Refining Colorectal Cancer Classification and Clinical Stratification Through a Single-Cell Atlas

status: Public on Apr 19 2022

city: INDIANAPOLIS

first: Ashiq

last: Masood

address: 410 W. 10th Street

department: Heamatology and oncology

institute: Indiana University

summary: To determine and dissect the extent of tumor, immunological, and stromal heterogeneity in CRC patients, we performed droplet-based scRNA-seq on 16 racially diverse, treatment naïve CRC patient tissue samples and seven adjacent normal colonic tissue samples (totaling 23 samples), yielded 49,589 single cells enabling high-resolution depiction of the cellular diversity and heterogeneity within the tumor and microenvironmental cells.

overall_design:
Patients with resectable untreated CRC who underwent curative colon resection at Rush University Medical Center (Chicago, IL, USA) were included in this Institutional Review Board (IRB)-approved study. CRC specimens from 16 patients, including nine Caucasian, six African American and one Asian patient with corresponding 8 adjacent normal tissue samples were processed immediately after collection at Rush University Medical Center Biorepository and sent for scRNA-seq.  Thus, our scRNA-seq atlas represents a diverse patient population. The study was conducted in accordance with ethical standards and all patients provided written informed consent. Single-cell RNA sequencing (scRNA-seq) was performed using 10X Genomics Single Cell 5' Platform. Tumors and normal colon samples were enzymatically dissociated (Miltenyi), filtered through a 70-micron cell strainer, pelleted after centrifugation at 300 xg and resuspended in DAPI-FACS buffer (PBS, 0.04% BSA). Samples were sorted and viable singlets were gated on the basis of scatter properties and DAPI exclusion. Approximately 3000 cells were pelleted and resuspended in PBS, and cells underwent single cell droplet-based capture on 10X Chromium instruments according to the 10X Genomics Single Cell 5' Platform protocol. Transcriptome libraries were prepared post-fragmentation, end-repair, and A-tailing double-sided size selection, and subsequent adaptor ligation as per the manufacturer’s protocol. Illumina NextSeq 550 was used for library sequencing and data were mapped and counted using Cellranger-v3.1.0 (GRCh38/hg38).
-----------------------------------
Author state "we have privacy issues with raw data can we submit only count file and annotation files to the GEO database".

first: Ateeq

last: Khaliq


title: Profiling of H3K9cr and H3K9ac in the P19 embryonal carcinoma cells

status: Public on Apr 17 2022

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

summary: To gain a deeper insight into dynamic changes of H3K9cr and H3K9ac during cell fate commitment, ChIP-seq was performed to analyze the genome-wide changes of H3K9cr and H3K9ac during neuroectodermal differentiation of the P19 embryonal carcinoma cells.

overall_design: ChIP-seq was performed with two biological replicates, and sequenced on Illumina NovaSeq 6000 platform.

first: Shang-Kun

last: Dai


title: Calcium bursts allow rapid reorganization of EFhD2/Swip-1 crosslinked actin networks in epithelial wound closure

city: Marburg

first: Katja

last: Rust

address: Emil-Mannkopff-Str. 2

country: Germany

institute: Phillips-University Marburg

summary: Changes in cell morphology require the dynamic remodeling of the actin cytoskeleton. Calcium fluxes have been suggested as an important signal to rapidly relay information to the actin cytoskeleton, but the underlying mechanisms remain poorly understood. Here, we identify the EF-hand domain containing protein EFhD2/Swip-1 as a conserved lamellipodial protein strongly upregulated in Drosophila macrophages at the onset of metamorphosis when macrophage behavior shifts from quiescent to migratory state. Loss- and gain-of-function analysis confirm a critical function of EFhD2/Swip-1 in lamellipodial cell migration in fly and mouse melanoma cells. Contrary to previous assumptions, TIRF-analyses unambiguously demonstrate that EFhD2/Swip-1 proteins efficiently cross-link actin filaments in a calcium-dependent manner. Using a single-cell wounding model, we show that EFhD2/Swip-1 promotes wound closure in a calcium-dependent manner. Mechanistically, our data suggest that transient calcium bursts reduce EFhD2/Swip-1 cross-linking activity and thereby promote rapid reorganization of existing actin networks to drive epithelial wound closure.

overall_design: RNA-sequencing of larval and prepupal Drosophila melanogaster hemocytes.

first: Franziska

last: Lehne

first: Thomas

last: Prokrant

first: Sabnam

last: Parbin

first: Gabriela

last: Salinas-Riester

first: Jörg

last: Großhans

first: Jan

last: Faix

first: Sven

last: Bogdan


title: Duper is a Cryptochrome 1 null mutation in Syrian hamsters

status: Public on Apr 18 2022

city: Cincinnati

first: Yin Yeng

last: Lee

state: Ohio

address: 3333 Burnet Avenue

department: Department of Pediatrics

institute: Cincinnati Children's Hospital Medical Center

summary: The duper mutation is a recessive mutation that shortens the period length of the circadian rhythm in Syrian hamsters. These animals show a large phase shift when responding to light pulses. Using two distinct ecotypes and a fast homozygosity mapping strategy, we identified duper as an early nonsense allele of Cryptochrome 1 (Cry1) leading to a short, unstable protein.

overall_design: Liver, cortex and SCN tissues from 4 duper and 4 wild type hamsters, were collected at CT15. For cortex and SCN, RNA extracted from the 4 hamsters of the same genotypes were pooled together before library preparations. For liver, RNA extracted from each hamster was used to prepare library separately. In total, 12 libraries (2x1 for cortex, 2x1 for SCN and 2x4 for liver) were pooled for sequencing.

first: Yin

middle: Y

first: Eric

last: Bittman

first: John

middle: B

last: Hogenesch


title: Temporal placental genome wide expression profiles reflect three phases of utero-placental blood flow during early to mid human gestation

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

summary: During early human placental development, extravillous cytotrophoblasts (EVT) invade the uterine vasculature to sequester a maternal blood supply. The impact of this on placental gene expression has not been established for normal pregnancy. Using RNA sequencing, we profiled placental chorionic villous tissues from 96 pregnancies at 6-23 weeks of gestation. We identified 1,048 genes that were differentially expressed between 6-10 weeks’ and 11-23 weeks’ of gestation. These are predominantly genes that are enriched in transcription factor signalling, inflammatory response and cell adhesion. Using a co-expression network and gene set enrichment analyses, we reveal three distinct phases of gene expression coincident with phases of maternal blood flow to the placenta that impact immune function and are likely driven by oxygen tension, potentially in a sex-specific manner. These data represent a comprehensive transcriptional profile of early placental development and point to significant environmental, genetic and regulatory triggers that drive gene expression.

overall_design: RNA-seq analysis of multiple cohorts of placenta tissues

first: Melanie

last: Smith

first: Dale

last: McAninch

first: Tanja

last: Jankovic-Karasoulos

first: Dylan

last: McCullough

first: K

last: Bogias

first: Qianhui

last: Wan

first: Awais

last: Choudhry

first: Nhi

last: Hin

first: Stephen

last: Pederson

first: Tina

last: Bianco-Miotto

first: Claire

last: Roberts


title: Chromatin states in glioblastoma stem cells (HOXA-AS2 depletion)

status: Public on Apr 15 2022

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

country: France

institute: GReD CNRS

summary: Glioblastoma multiform account for about half of all gliomas and are the most deadly and aggressive forms. Its therapeutic resistance and tumor relapse rely on a subpopulation of cells, the so-called Glioma-stem Cells (GSCs). Here, we investigated for the role of the long non-coding RNA HOXA-AS2 in GSC biology by conducting descriptive and functional analyses of glioma samples classified according to their isocitrate dehydrogenase (IDH1) gene mutation status, and of glioma stem cells. We found that HOXA-AS2 is overexpressed only in aggressive (IDHwt) glioma and GSC. Sh-RNA-based depletion of HOXA-AS2 affects GSC both at the cellular and molecular levels with a decrease in proliferation and altered expression of several hundreds of their genes. Integrative analysis revealed that these changes is expression are not associated to changes in DNA methylation or chromatin signature at the promoter of most deregulated genes following HOXA-AS2 silencing in GSC, supporting a post-transcriptional regulation. In addition, transcription factor motif enrichment and correlation analyses sustained that HOXA-AS2 affect, directly or indirectly, expression of key transcription factors of GCS biology, including E2F8, E2F1, STAT1 and ATF3 to, in fine, contributes to their pathological status by promoting proliferation and modulating the inflammation pathway of Glioma Stem Cell.

overall_design: HOXA-AS2 was depleted in human glioblastoma stem cells, and ChIP-seq was performed using anti-H3K27ac, anti-H3K4me3, and anti-H3K27me3 antibodies.

first: Franck

last: Court

first: Elisa

last: Le Boiteux

first: Pierre

middle: O

last: Guichet

first: Philippe

last: Arnaud


title: EPIC-based DNA methylation analysis of glioblastoma stem cells and H9NSC (HOXA-AS2 depletion or overexpression)

type: Methylation profiling by genome tiling array

summary: Glioblastoma multiform account for about half of all gliomas and are the most deadly and aggressive forms. Its therapeutic resistance and tumor relapse rely on a subpopulation of cells, the so-called Glioma-stem Cells (GSCs). Here, we investigated for the role of the long non-coding RNA HOXA-AS2 in GSC biology by conducting descriptive and functional analyses of glioma samples classified according to their isocitrate dehydrogenase (IDH1) gene mutation status, and of glioma stem cells. We found that HOXA-AS2 is overexpressed only in aggressive (IDHwt) glioma and GSC. Sh-RNA-based depletion of HOXA-AS2 affects GSC both at the cellular and molecular levels with a decrease in proliferation and altered expression of several hundreds of their genes. Integrative analysis revealed that these changes is expression are not associated to changes in DNA methylation or chromatin signature at the promoter of most deregulated genes following HOXA-AS2 silencing in GSC, supporting a post-transcriptional regulation. In addition, transcription factor motif enrichment and correlation analyses sustained that HOXA-AS2 affect, directly or indirectly, expression of key transcription factors of GCS biology, including E2F8, E2F1, STAT1 and ATF3 to, in fine, contributes to their pathological status by promoting proliferation and modulating the inflammation pathway of Glioma Stem Cell.

overall_design: HOXA-AS2 was depleted in human glioblastoma stem cells. HOXA-AS2 was overexpressed in human neural stem cells.


title: Transcriptome of glioblastoma stem cells and H9NSC (HOXA-AS2 depletion or overexpression)


title: Transcriptome and EPIC-based DNA methylation analysis of glioblastoma stem cells and H9NSC (HOXA-AS2 depletion or overexpression), and chromatin states in glioblastoma stem cells (HOXA-AS2 depletion)


title: Transcriptomic analysis of low-density neutrophils (LDNs) in acute generalized pustular psoriasis (GPP)

city: Shanghai

first: Ning

last: Yu

state: Shanghai

address: Baode Road 1278

institute: Shanghai Skin Disease Hospital

summary: Generalized pustular psoriasis (GPP) is a severe disease featured by neutrophilic pustules and enhanced IL-36 inflammatory pathway in skin. Recently, a transcriptomic analysis of PBMCs and neutrophils in MPO-deficient GPP patients has been performed in stable disease state. However, transcriptomic profiling of PBMCs during acute flare of GPP is unclear. Here, we reported a predominant neutrophil signature in GPP PBMC and a marked increase in the CD66+CD16+ low-density neutrophils (LDNs) within the PBMC fraction of acute GPP patients. Transcriptomic and functional analysis of LDNs revealed a hypoinflammatory phenotype yet enhanced release of neutrophil granule proteases, implicating that LDNs might contribute to the IL-36-mediated inflammation in GPP patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for low-density neutrophils (LDNs) and autologous normal-density neutrophils (NDNs) from 4 generalized pustular psoriasis (GPP) patients, and NDNs from 3 healthy donors

first: Yuling

last: Shi


title: Millimeter Waves Modulate the Transcriptome in Human Fibroblasts

city: Perth

first: Nicholas

last: Lawler

state: Western Australia

address: 35 Stirling Hwy

institute: University of Western Australia

summary: Millimetre-wave (MMW) frequencies of the electromagnetic spectrum are increasingly being adopted in modern technologies including mobile communications, networking, and security screening. These frequencies are absorbed by the outer layers of the skin, however the biological effects are not well characterised. Thus, as emerging technologies increase human exposure, understanding the effects of MMWs on biological material and cell biology in the skin is critical in determining safe exposure levels. Here, we report on the exposure of primary human dermal fibroblasts to MMWs; we find that the radiation triggers genomic and transcriptomic alterations. In particular, repeated 60 GHz MMW exposures at 2.6 mW cm-2, 46.8 J cm-2 doses, trigger a physiological response in human fibroblasts distinct from conventional cytokine-induced stimulation. Our results show that high dose MMWs induce non-thermal transcriptomic alterations with simultaneous changes in DNA structural dynamics including formation of G-quadruplex and i-motif secondary structures, but not DNA damage.

overall_design: RNA-seq of primary human fibroblasts exposed to 60 GHz MMWs for 5 h/day for 2 days

first: Cameron

middle: W

last: Evans

first: Sergii

last: Romanenko

first: Nutan

last: Chaudhari

first: Mark

last: Fear

first: Fiona

last: Wood

first: Nicole

middle: M

last: Smith

first: Vincent

last: Wallace

middle: S

last: Iyer


title: The interaction of influenza A NS1 and cellular TRBP protein modulates the function of RNA interference machinery

first: Qi

last: Wang

address: Anshun Road 350

institute: Shanghai Institute of Biological Products

type: Non-coding RNA profiling by high throughput sequencing

summary: Influenza A virus (IAV), one of the most prevalent respiratory diseases, causes pandemics around the world. The multifunctional non-structural protein 1 (NS1) of IAV is a viral antagonist that suppresses host antiviral response. However, the mechanism by which NS1 modulates the RNA interference (RNAi) pathway remains unclear. Here, we identified interactions between NS1 proteins of Influenza A/PR8/34 (H1N1; IAV-PR8) and Influenza A/WSN/1/33 (H1N1; IAV-WSN) and Dicer’s cofactor TAR-RNA binding protein (TRBP). We found that the N-terminal RNA binding domain (RBD) of NS1 and the first two domains of TRBP protein mediated this interaction. Furthermore, two amino acid residues (Arg at position 38 and Lys at position 41) in NS1 were essential for the interaction. We generated TRBP knockout cells and found that NS1 instead of NS1 mutants (two-point mutations within NS1, R38A/K41A) inhibited the process of microRNA (miRNA) maturation by binding with TRBP. PR8-infected cells showed masking of short hairpin RNA (shRNA)-mediated RNAi, which was not observed after mutant virus-containing NS1 mutation (R38A/K41A, termed PR8/3841) infection. Moreover, abundant viral small interfering RNAs (vsiRNAs) were detected in vitro and in vivo upon PR8/3841 infection. We identify, for the first time, the interaction between NS1 and TRBP that affects host RNAi machinery.

overall_design: 5 virus-derived small RNA from 293T cells or mice lung infected with PR8/3841 or PR8-WT was detected by small RNA-seq.

first: Jiaxin

first: Yan

last: Xu

first: Zhe

last: Li

first: Binbin

first: Yang


title: 4C-seq protocol in mice macrophages

status: Public on Apr 14 2022

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

summary: A protocol for performing the 4C library and the analysis in mice macrophages.

overall_design: We used the ChIP-seq data to mark the DNA element regions (Silencer) and used the 4C-seq technique to investigate all the interactions with specific bait.

first: Eckardt

last: Treuter

first: Rongrong

last: Fan


title: N3 induced reprogramming and ShWT1 knock-down in DSRCT cell lines

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: The object of this study is to identify the molecular signature underlying the therapeutic potential of N3-induced growth arrest in Desmoplastic Small Round Cell Tumor (DSRCT).  The molecular hallmark of DSRCT is the EWS-WT1 fusion protein formed by chromosomal translocations found in DSRCT. The N-terminal transactivation domain of EWS is fused to the C-terminal DNA binding domain of WT1, creating an oncogenic transcription factor. We have recently discovered that addition of N3 supplement to growing DSRCT cells leads to a rapid cessation of cell growth.

overall_design: To identify the effect of N3 induced growth arrest, U2OS (control) or DSRCT cells will be cultured in regular media or media containing N3 supplement. Three independent experiments will be performed for each cell line with indicated media. A second set of experiment will be to examine the effects of depleting the EWS/WT1 oncogene with a short hairpin ShWT1 or shControl in DSRCT cell lines grown in the absence or presence of N3 Supplement. Total RNA will be isolated and analyzed by microarray analysis.  The untreated (no N3) will serve as a reference point for the first experiment, and the shControl transfected samples will serve as a reference for the second experiment. We will probe Affymetrix human genome U133 plus 2.0 arrays with total RNA samples. For all experiments, we will use total RNA isolated in triplicate (biological triplicates).

first: S

last: Lee


title: Dissecting the transcriptomic landscape of the human papillary thyroid carcinoma by single cell RNA-sequencing

status: Public on Apr 13 2022

city: Jinan

first: Lei

last: Sheng

state: Shandong Province

address: 107, Wenhuaxi Road

department: Department of General Surgery

institute: Qilu Hospital, Shandong University

summary: Papillary thyroid carcinoma (PTC) is the most common malignant phenotype of thyroid cancer, with a rapidly increasing number of new cases globally. Multifocality is a common phenomenon in patients with PTC. The tumor microenvironment (TME) plays a pivotal role in cancer progression in papillary thyroid carcinoma (PTC), yet the composition and phenotype of cells within TME in bilateral PTCs are poorly understood.

overall_design: To comprehensively elucidate the inter-tumor heterogeneity of bilateral PTC, we employed single-cell RNA sequencing (scRNA-seq) to profile 29,561 cells from 3 pairs of bilateral PTCs and 1 non-tumor thyroid sample. Our integrative analyses revealed great inter-tumor heterogeneity within tumor microenvironment in bilateral PTCs, which will offer assistance for precise diagnosis and treatment.

first: Tiantian


title: Stable inheritance of H3.3-containing nucleosomes during mitotic cell divisions

city: New York

first: Zhiguo

last: Zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: It is known that newly synthesized H3.1/H3.2 and H3.3 histones, differing by four or five amino acids, are assembled into nucleosomes via replication-coupled and replication-independent pathways, respectively. However, it is not clear how parental H3.3 is transferred following DNA replication, especially when compared to H3.1. Here, we show that parental H3.3, like H3.1, are stably transferred into daughter cells. Moreover, Mcm2, Pole3 and Pole4, proteins known to engage in parental histone transfer based upon analysis of parental histone modifications, participate in the transfer of H3.3 following DNA replication. Lastly, we found that Mcm2, Pole3 and Pole4 mutants defective in parental histone transfer show defects in chromosome segregations. We propose that parental H3.3 is also stably transferred into daughter cells, contributing to the epigenetic memory of gene expression and the maintenance of genome stability.

overall_design: The CUT&TAG and eSPAN experiments were conducted in WT, Mcm2-2A mutant, Pole3 KO and Pole4 KO mES cells. The histone markers performed by CUT&TAG and eSPAN methods in mES cells included H3.3 and H3K36me3.  For the regulation of gene expression, we performed total RNA-seq experiments in WT, Mcm2-2A mutant, Pole3 KO and Pole4 KO mES cells.

first: Xiaowei

first: Shoufu

last: Duan

first: Xu

last: Hua

first: Zhiming

first: Richard

last: He


title: Faster growth enhances low carbon fuels and commodity chemcial production through gas fermentation

status: Public on Apr 12 2022

city: Tartu

first: Kaspar

last: Valgepea

state: Tartu

address: Nooruse 1, room 520

department: Institute of Technology

country: Estonia

institute: University of Tartu

summary: Gas fermentation offers both fossil carbon-free sustainable production of fuels and chemicals and recycling of gaseous and solid waste using gas-fermenting microbes. Bioprocess development, systems-level analysis of biocatalyst metabolism, and engineering of cell factories are advancing the widespread deployment of the commercialised technology. Acetogens are particularly attractive biocatalysts but effects of the key physiological parameter – specific growth rate (μ) – on acetogen metabolism and the gas fermentation bioprocess have not been established yet. Here, we investigate the μ-dependent bioprocess performance of the model-acetogen Clostridium autoethanogenum in CO and syngas (CO+CO2+H2) grown chemostat cultures and assess systems-level metabolic responses using gas analysis, metabolomics, transcriptomics, and metabolic modelling. We were able to obtain steady-states up to μ ~2.8 day-1 (~0.12 h-1) and show that faster growth supports both higher yields and productivities for reduced by-products ethanol and 2,3-butanediol. Transcriptomics data revealed differential expression of 1,337 genes with increasing μ and suggest that C. autoethanogenum uses transcriptional regulation to a large extent for facilitating faster growth. Metabolic modelling showed significantly increased fluxes for faster growing cells that were, however, not accompanied by gene expression changes in key catabolic pathways for CO and H2 metabolism. Cells thus seem to maintain sufficient “baseline” gene expression to rapidly respond to CO and H2 availability without delays to kick-start metabolism. Our work advances understanding of transcriptional regulation in acetogens and shows that faster growth of the biocatalyst improves the gas fermentation bioprocess.

overall_design: RNA sequencing of CO-grown or syngas-grown Clostridium autoethanogenum chemostat cultures at three specific growth rates; 20 samples in total with various number of biological replicate samples

first: Lorena

middle: A

last: Lima

first: Henri

last: Ingelman

first: Kush

last: Brahmbhatt

first: Kristina

last: Reinmets

first: Craig

last: Barry

first: Audrey

last: Harris

first: Esteban

last: Marcellin

first: Michael

last: Köpke


title: H3K4me3 recognition by the COMPASS complex guides de novo histone methylation to restore the symmetric distribution of H3K4me3 following DNA replication

summary: During DNA replication, histones in nucleosomes ahead of DNA replication forks are evicted and then distributed equally onto leading and lagging strands. Mcm2, a subunit of the replicative MCM helicase, participates in the transfer of parental H3-H4 marked by H3K4me3 to lagging strands. Mutations in Mcm2 (Mcm2-3A) result in enrichment of H3K4me3 at leading strands following DNA replication. Here, we show that mcm2-3A mutant cells partially recover the H3K4me3 lost at lagging strands, with a faster recovery at highly transcribed genes than lowly ones, before mitosis. Furthermore, the H3K4 methyltransferase complex COMPASS is essential in the recovery of H3K4me3, irrespective of transcription status. Finally, H3K4me3 recognition (read) by COMPASS is also important for the restoration (write) of this mark. We suggest that both gene transcription and the “read and write” mechanism contribute to the restoration of H3K4me3, with the later mechanism more important for lowly transcribed chromatin.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae W303

overall_design: We synchronized yeast cells (Wild type, mcm2-3A mutant and Swd1 KO and Spp1 KO using the conditional degradation system) at G1 and released into early S phase in the presence of BrdU. We then performed BrdU immunoprecipitation using anti-BrdU antibodies following single-strand DNA library preparation and sequencing (ssSeq). we also performed protein ChIP followed by single-strand DNA sequencing (ChIP-ssSeq) for RNA Pol II (RNA Pol II CTD Ser5p), H3K4me3, H3K56ac. And eSPAN for H3K4me3, H3K56ac. The sequencing tag was mapped to both Watson (red) and Crick (blue) strands of the reference genome.

first: Albert

last: Serra-Cardona


title: Single cell transcriptional profiling of native, transplanted, or organoid SCA1+ and SCA1- lung epithelial cells

city: Boston

first: Aaron

middle: L.

last: Moye

address: 1 Blackfan Circle

department: Stem Cell Program

institute: Boston Children's Hospital

summary: The study examined the ability of SCA1+ and SCA1- lung epithelial organoids to be transplanted and retained by donor mice.

overall_design: SCA1- and SCA1+ lung epithelial organoids were grown then transplanted into bleomycin pre-treated nude mice. Native cells, transplanted cells, and primary organoid cells were collected and analyzed using single-cell RNA-seq to determine the ability of transplanted organoid cells to re-establish a native transcriptional profile.

first: Irene

middle: G

last: Wong

first: Sharon

last: Louie

first: Carla

middle: F

last: Kim


title: Reorganization of postmitotic neuronal chromatin accessibility for maturation of serotonergic identity

city: Cleveland

first: Evan

last: Deneris

address: 2210 Circle Dr., Robbins E640

department: Neurosciences

institute: Case Western Reserve University

summary: Assembly of transcriptomes encoding unique neuronal identities requires selective accessibility of transcription factors to cis-regulatory sequences in nucleosome-embedded postmitotic chromatin. Yet, the mechanisms controlling postmitotic neuronal chromatin accessibility are poorly understood. Here, we show that unique distal enhancers define the Pet1 neuron lineage that generates serotonin (5-HT) neurons. Heterogeneous single cell chromatin landscapes are established early in postmitotic Pet1 neurons and reveal the putative regulatory programs driving Pet1 neuron subtype identities. Distal enhancer accessibility is highly dynamic as Pet1 neurons mature, suggesting the existence of regulatory factors that reorganize postmitotic neuronal chromatin. We find that Pet1 and Lmx1b control chromatin accessibility to select Pet1-lineage specific enhancers for 5-HT neurotransmission. Additionally, these factors are required to maintain chromatin accessibility during early maturation suggesting that postmitotic neuronal open chromatin is unstable and requires continuous regulatory input. Together our findings reveal postmitotic transcription factors that reorganize accessible chromatin for neuron specialization.

overall_design: 5-HT neuron ATAC-seq profiles of control (CON), Pet1 null, Lmx1bCKO, Pet1CKO, and Pet1/Lmx1b CKO (control and Pet1 null at E11.5, E14.5 and E17.5 (Pet1CKO, Lmx1bCKO, and DKO only at E14.5)) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 550. The sequence reads that passed quality filters were processed using the ENCODE ATAC-seq pipeline and compared for differential accessibility using DESeq2. ChIPmentation for histone marks and CUT&RUN for the transcription factors Pet1 and Lmx1b were deep sequenced using an Illumina HiSeq 550. RNA-seq for control and DKO Pet1-neurons at E17.5 were deep sequenced using an Illumina HiSeq 550.

first: Xinrui

last: Zhang

first: William

middle: C

last: Spencer

first: Nobuko

last: Tabuchi


title: Single cell RNA-Seq analysis of circulating red cells

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382, CIEMAS 2177A, Duke University, SOM

department: Molecular Genetics and Microbiology

institute: Duke University

summary: single RBC RNA-Seq to capture and discover known and unexpected heterogeneity of RBC population

overall_design: the blood from three healthy donors were processed according to the typical blood bank processing protocol and stored at 4 C in AS-1. Aliquots from the RBC stored at day 1 and day 15 were withdrawn and subjected to single cell RNA-Seq analysis.

first: Vaibhav

last: Jain

first: Wen-Hsuan

last: Yang

first: Simon

last: Gregory


title: A dynamic single cell-based framework for digital twins to prioritize disease genes and drug targets

city: Linköping

first: Sandra

last: Lilja

address: Sandbäcksgatan 7

department: BKV

institute: Linköping University

summary: A major health care problems today is that drug treatment is ineffective for many patients. This may depend on the involvement of thousands of genes, which vary between patients with the same diagnosis at different time points. Identification and prioritization of upstream regulatory (UR) genes for precision medicine are therefore great challenges. In this study, we present a framework to model dynamic cellulome- and genome-wide changes in digital twins, to prioritize UR genes. We used seasonal allergic rhinitis (SAR) as a disease model because the external trigger (pollen) is known, so that the disease process can be mimicked by time series analyses of in vitro allergen-stimulated PBMC from SAR patients. Based on single cell profiling data from different stages of the disease, we constructed network models, hypothesizing that the directed molecular interactions between cell types could be traced to find an UR cell type and gene. This hypothesis was rejected because the cellular interactions formed multi-directional networks, rather than linear hierarchies. Instead, we were successfully able to rank and prioritize the URs based on their relative effects on the different cell types. We propose that this ranking strategy is a scalable approach for organizing and analyzing cellulome- and genome-wide data in digital twins.

overall_design: Data from scRNA-seq analysis of peripheral blood mononuclear cells (PBMCs), from patients with seasonal allergic rhinitis (SAR) as well as healthy controls. The samples (retrieved outside of the pollen season) were stimulated with pollen extract or diluent, for different time points, 0h (before stimulation), 12 hours, 1 day, 2 days, 3 days, 5 days, and 7 days.

first: Xinxiu

last: Li

first: Eun Jung

last: Lee

first: Huan

first: Joseph

last: Loscalzo

first: Samuel

last: Schäfer

first: Martin

last: Smelik

first: Maria

middle: R

last: Strobl

first: Oleg

last: Sysoev

first: Hui

last: Wang

first: Yelin

first: Danuta

last: Gawel

first: Barbara

last: Bohle

first: Mikael

last: Benson


title: A mesenchymal to epithelial switch in Fgf10 expression specifies an evolutionary-conserved population of ionocytes in salivary gland

city: La Jolla

first: Helen

last: Makarenkova

state: CA

address: 10550 N Torrey Pines Rd, MB-218

department: Molecular Medicine

institute: The Scripps Research Institute

summary: Salivary glands are essential structures that secrete saliva to the oral cavity and maintain oral health. Development of salivary glands in mice and humans is controlled by mesenchymally expressed fibroblast growth factor-10 (FGF10). Using single cell RNA-seq atlas of the salivary gland and a tamoxifen inducible Fgf10CreERT2:R26-tdTomato  mouse we show that FGF10pos  cells are exclusively mesenchymal until postnatal day 5 (P5), but after P7, there is a switch in expression and only epithelial FGF10pos  cells are observed after P15. Further RNAseq analysis of sorted mesenchymal and epithelial FGF10pos cells shows that the epithelial FGF10pos  populations express the hallmark of ancient ionocyte signature  Foxi1,    Foxi2, Ascl3 and  the cystic fibrosis transmembrane conductance regulator (Cftr). We propose that epithelial FGF10pos cells are specialized salivary gland ionocytes that are important for the ionic modification of saliva. In addition, they maintain FGF10-dependent glands homeostasis via communication with FGFR2b-expressing epithelial progenitor and myoepithelial cells

overall_design: Comparison of Fgf10+ expressing cell mRNA profiles from submandibular glands of 7 day old pups and 60 days old mice in duplicate

first: Olivier

last: Mauduit

first: Marit

middle: H

last: Aure

first: Vanessa

last: Delcroix

first: Liana

last: Basova

first: Amrita

last: Srivastava

first: Takeshi

last: Umazume

first: Jacqueline

last: Mays

first: Saverio

last: Bellusci

first: Abigail

last: Tucker

first: Mohammad

middle: K

last: Hajihosseini

first: Matthew

last: Hoffman


title: Ribosome profiling and RNA-seq of an acute glucose starvation timecourse and 5 day growth course in S. cerevisiae

status: Public on Apr 11 2022

first: Brian

middle: Matthew

last: Zid

state: California

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

summary: Ribosome profiling provides an opportunity to not only assess how the relative abundance of ribosome association with mRNAs changes in different conditions, but to look more closely at where along mRNAs those ribosomes bind. Here, we used ribosome profiling to calculate the ribosome polarity scores and changes in ribosome footprint read density in both aggregate and gene-specific ways. We profiled a time course of acute glucose starvation followed by glucose readdition and a multi-day growth course through the diauxic shift into stationary phase. We found that ribosome polarity became positive in postdiauxic shift conditions relative to log phase. In acute starvation, polarity shifted positive at our earliest time points but did not continue to do so at later time points. This is consistent with a read density analysis which demonstrated increased density on the 3’ half of genes after glucose starvation. Additionally, we performed ribosome profiling in samples that had glucose added back following acute starvation and observed a wave of new ribosome movement near the start codon and approximately 2,000 nucleotides downstream on open reading frames after one and five minutes of readdition, respectively. Our ribosome profiling analysis suggested that elongation slows during starvation which leads to a buildup of ribosomes on the 3’ halves of mRNAs. Further, it also indicated ribosomes previously built up can resume translation upon glucose readdition. We used reporter assays to corroborate these findings in vivo. Together, these results demonstrate how yeast regulate translation in response to glucose starvation.

overall_design: mRNA and ribosome occupancy profiles of S. cerevisiae in actue glucose starvation, glucose readdition, and mutli-day growth conditions

first: Anna

last: Guzikowski

first: Jingxiao

last: Zhang

first: Kyle

last: Begovich

first: Shihui

last: Zhu

first: Molly

last: Cohn


title: RNA-seq data of JN and BER-DSRCT dox inducible shSIK1 cell lines

city: New Orleasn

first: Sean

middle: Bong

last: Lee

state: LA

address: 1700 Tulane Ave

department: Pathology and Laboratory Medicine

institute: Tulane University

summary: Depletion of SIK1 expression in DSRCT cell lines affected expressions of genes in cell cycle regulation pathways.

overall_design: JN and BER-DSRCT dox inducible shSIK1 cell lines were either not treated (NT) or treated with 1ug/mL of doxycycline for five days.

first: Nathan

last: Ungerleider

first: Lawrence

last: Shi


title: A Zebrafish-Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: A reliable animal model that can mimic the GBM intracranial infiltration and Blood-brain barrier (BBB) interaction is necessary for effective therapeutics development. Here, we report a zebrafish-based orthotopic GBM xenograft model, in which GBM cells from different species and even patients, can robustly propagate and faithfully reproduce their histological characteristics. Single-cell RNA-seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals, which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients’ samples, we further generate zebrafish patient-derived orthotopic xenografts (z-PDOX) and proof-of-concept experiments indicate the short-term temozolomide response in z-PDOX can predict the long-term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: 1.Single-cell RNA seq for endothelial cells of zebrafish 2.Single-cell RNA seq for GBM cells implanted in zebrafish brain

first: Xiaolin

last: Ai

first: Zengpanpan

last: Ye

first: Chaoxin

last: Xiao

first: Jian

last: Zhong

first: Xuelan

last: Chen

first: Xiangyu

first: Chong

first: Chengjian

last: Zhao


title: Placental abnormalities are associated with specific windows of embryo culture in a mouse model

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Assisted Reproductive Technologies (ART) employ gamete/embryo handling and culture in vitro to produce offspring. ART pregnancies have increased risk of low birth weight, abnormal placentation, pregnancy complications, and imprinting disorders. We and others have previously shown that embryo culture induces low birth weight, abnormal placental morphology, and lower levels of DNA methylation in placentas in a mouse model of ART. We hypothesized that these adverse effects are linked to a subtle disruption of specific biological processes during preimplantation development. To test this hypothesis, we performed embryo culture for several discrete periods of preimplantation development and assessed fetal and placental outcomes at term. We observed a reduction in fetal:placental ratio in two distinct windows of preimplantation embryo development, while placental morphological abnormalities and reduced imprinting control region methylation were associated with culture prior to the morula stage. We also provide evidence that extended culture to the blastocyst stage induces additional placental DNA methylation changes compared to embryos transferred at the morula stage, and that female concepti exhibited a higher loss of DNA methylation than males. Altogether, this study identifies specific developmental windows of susceptibility and potential targets for embryo culture optimization.

overall_design: Mouse (Mus musculus) term placentas from 1-cell-morula group (n=12, 6 females and 6 males), 1-cell-blastocyst group (n=12, 6 females and 6 males) and Natural group (n=10, 5 females and 5 males) were analyzed.

first: Lisa

last: Vrooman

first: Eric

last: Rhon-Calderon

first: Kashviya

middle: V

last: Suri

first: Asha

last: Dahiya

first: Richard

last: Schultz

first: Marisa

last: Bartolomei


title: A Chromatin Accessibility Landscape During Early Adipogenesis of Human Adipose-Derived Stem Cells

status: Public on Apr 10 2022

city: shanghai

first: sen

last: li

address: shanghai

institute: B

summary: We depict a time series genome‐wide accessible chromatin atlas during adipogenesis of human adipose-derived stem cells.

overall_design: ATAC-seq analysis was performed to map a four time points (0h, 2h, 8h and 24h) high-quality genome‐wide time-resolved accessible chromatin atlas during adipogenesis of human adipose-derived stem cells.  Two biological replicates were conducted for each time point.

first: Sen

last: Li

first: Liheng

last: Zhang

first: Jianxin

last: Wu


title: H3.3 S31 phosphorylation ChIP-seq in mitotic WT mouse ES cells

city: Clayton

first: Hsiao Phin

middle: Joanna

last: Voon

state: Victoria

address: Monash University, Wellington Road

department: Biochemistry and Molecular Biology

institute: Monash University

summary: The serine 31 (S31) residue of histone H3.3 is phosphorylated during mitosis and this modification is enriched at repetitive DNA. ChIP-seq of H3.3 S31Ph was carried out in a mitotic population of synchronised mouse ES cells. We find that H3.3 S31Ph is enriched at telomeres and IAP repeats in mitotic mouse ES cells.

overall_design: ChIP-seq of H3.3 S31Ph in mitotic mouse ES cells with matched input sequencing

first: Hsiao

middle: P

first: Lee

last: Wong


title: Covid-19 Infection During Pregnancy Induces Differential Gene Expression in Human Cord Blood Cells from Term Neonates

status: Public on Apr 08 2022

first: Zubair

last: Aghai

address: 833 Chestnut Street East, Suite 1210,

department: Pediatrics

institute: Jefferson/Nemours Children's Health

summary:
Exposure to COVID-19 during pregnancy induces differential gene expression in cord blood cells. The early exposure and associated differentially expressed genes may potentially contribute to cardiac, hepatic, renal and immunological disorders in offspring. These findings lead to a further understanding of the effects of COVID-19 exposure at an early stage of life and its potential long-term consequences as well as therapeutic targets.
We have used microarray to find the global gene expression of Covid exposed cord blood compared to control samples

overall_design: Global Gene expression was compared between Covid exposed and control term neonates. The umbilical cord blood was collected in PAXgene blood RNA tube. Cord blood was collected from mothers with (8 Covid sample) or without (8 control) Covid exposure during or at the time of delivery. Total RNA was isolated using PAXgene Blood RNA Kit from PreAnalytiX and then fragmented biotin-labeled cDNA was prepared by GeneChip WT PLUS reagent kit. Genome-wide gene expression screening was performed using Human Clariom S gene chips. The COVID group was compared with the control group using Transcriptome array console software 4.0. Sst-RMA normalization was performed and Student’s t-test was employed for comparison of the two groups. Genes with fold change ≥ 1.5 and p ≤ 0.05 were identified as differentially expressed.

first: Suhita

last: Gayen nee’ Betal

first: Pedro

last: Urday

first: Huda

middle: B

last: Al-Kouatly

first: Kolawole

last: Solarin

first: Joanna

middle: Y

last: Chan

first: Sankar

last: Addya

first: Rupsa

last: Boelig


title: Airway microbiota in patients with synchronous multiple primary lung cancer: the bacterial topography of the respiratory tract

status: Public on Apr 09 2022

city: Kunming

first: Kai

last: Qian

address: Jinbi Road, 157#, Xishan District

institute: The First People’s Hospital of Yunnan Province

summary: we analyzed the characteristics of the respiratory microbiome, which was collected from different sites and using different sampling methods.

overall_design: We used the Antakli modifications as the basic criteria for the definition of sMPLC. The details are as follows: (1) one lesion in each patient must be diagnosed as an adenocarcinoma; (2) that the lesions are in anatomically distinct regions; (3) that there are no systemic metastases; (4) that there is no mediastinal spread as confirmed by postoperative pathology; and (5) possessing two or more of the following: (i) one tumor diagnosed as an adenomatous tumor, i.e., minimally invasive carcinoma, or invasive AD[3], and another tumor diagnosed as either squamous carcinoma or small cell lung cancer; (ii) different driver gene mutations; and (iii) different biomarker patterns[11]. The inclusion criteria were as follows: (1) patients diagnosed with sMPLC, as previously described, and all lesions located in the right upper lobe (RUL); (2) aged ≥18 years; (3) no contraindications for pulmonary surgery, i.e., distant metastasis, bleeding tendency, blood clotting disorders, cardiopulmonary insufficiency, severe arrhythmia or hypertension, pulmonary hypertension, and acute respiratory infection; (4) no other prior therapies; (5) expected survival >2 months; (6) without a history of other primary malignant tumors; (7) agreeing to participate in this study. Exclusion criteria included patients with poorly controlled diabetes, prior cerebrovascular events, active second malignancy, uncontrolled concommitant illness, or other conditions that might affect their participation in the study. We used the Antakli modifications as the basic criteria for the definition of sMPLC [10]. The details are as follows: (1) one lesion in each patient must be diagnosed as an adenocarcinoma; (2) that the lesions are in anatomically distinct regions; (3) that there are no systemic metastases; (4) that there is no mediastinal spread as confirmed by postoperative pathology; and (5) possessing two or more of the following: (i) one tumor diagnosed as an adenomatous tumor, i.e., minimally invasive carcinoma, or invasive AD[3], and another tumor diagnosed as either squamous carcinoma or small cell lung cancer; (ii) different driver gene mutations; and (iii) different biomarker patterns[11]. The inclusion criteria were as follows: (1) patients diagnosed with sMPLC, as previously described, and all lesions located in the right upper lobe (RUL); (2) aged ≥18 years; (3) no contraindications for pulmonary surgery, i.e., distant metastasis, bleeding tendency, blood clotting disorders, cardiopulmonary insufficiency, severe arrhythmia or hypertension, pulmonary hypertension, and acute respiratory infection; (4) no other prior therapies; (5) expected survival >2 months; (6) without a history of other primary malignant tumors; (7) agreeing to participate in this study. Exclusion criteria included patients with poorly controlled diabetes, prior cerebrovascular events, active second malignancy, uncontrolled concommitant illness, or other conditions that might affect their participation in the study.

first: Yi

last: Deng

first: William

last: Krimsky

first: Yong-Geng

last: Feng


title: Photoconversion of MC38

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

summary: MC38 tumors were photoconverted in Kade mice to assess the effect of photo conversion on the transcriptome

overall_design: 4 mice per group. Photoconversion vs no intervention

first: J

first: D

last: Withers

first: M

last: Clatworthy


title: RhoBTB1 Reverses Established Arterial Stiffness in Angiotensin II Hypertension

city: Wauwatosa

first: Shi

last: Fang

state: Wisconsin

address: 8701 W Watertown Plank Rd.

department: Physiology

institute: The Medical College of Wisconsin

summary:
We are investigating of role of RhoBTB1 in vascular smooth muscle cells. Restoring RhoBTB1 expression in mouse aorta reversed the established arterial stiffness but not hypertension caused by angiotensin II (Ang-II).
To investigate the underlying mechanism by which RhoBTB1 reversed arterial stiffness, we performed bulk RNA-sequencing using aorta from four groups: control /RhoBTB1 transgenic mice treated with/without Ang-II.

overall_design: aortic mRNA profile in vehicle/angiotensin II-treated mice expressing either smooth muscle specific Cre or smooth muscle specific RhoBTB1 transgene.

first: Curt

middle: D

last: Sigmund

first: Angela

middle: J

last: Mathison


title: A network-based approach to identify expression modules underlying rejection in pediatric liver transplantation

city: Pittsburgh

first: Jishnu

last: Das

address: 203 Lothrop Street

department: Immunology

institute: University of Pittsburgh

summary: Selecting the right immunosuppressant to ensure rejection-free outcomes poses unique challenges in pediatric liver transplant (LT) recipients. A molecular predictor can comprehensively address these challenges. Although early acute cellular rejection (ACR) is mediated by cytotoxic T-cells, late rejection also includes antibody-mediated damage in addition to cell-mediated injury. Currently, there are no well-validated blood-based biomarkers for pediatric LT recipients either pre- or post- transplant. Here, we discover and validate separate pre- and post- transplant molecular signatures of LT outcome from whole blood transcriptomes. Using an integrative machine learning approach, we combine transcriptomic data with the high-quality reference human protein interactome network to identify differentially regulated functional sub-components of the network, or “network module signatures”, which drive ACR. Unlike gene signatures, our approach is inherently multivariate, more robust to replication and captures the structure of the underlying molecular network, encapsulating additive effects. We also identify, in a patient-specific manner, network module signatures that can be targeted by current anti-rejection drugs and other mechanisms that can be repurposed. Overall, our approach can enable personalized adjustment of drug regimens for the dominant targetable pathways in pre- and post- LT in children.

overall_design: Whole blood samples were obtained from children undergoing liver transplantation at the UPMC-Children’s Hospital of Pittsburgh (CHP)

first: Rakesh

last: Sindhi

first: Mylarappa

last: Ningappa

first: Syed

last: Rahman


title: Single cell 3' RNA sequencing of B16 melanoma (B16F0 and B16F10)

city: Seoul

first: YOON-SEOB

last: KIM

state: Korea (the Republic of)

address: Banpodaero 222

institute: The Catholic University of Korea

summary: Under the hypothesis that subset of parental cells may already harbor metastasis potential, which leads progression of metastasis, we investigated single-cell expression of parental B16 melanoma cell (B16F0) and its highly metastatic subclone (B16F10) (N=4,156) using single-cell RNA sequencing

overall_design: Single-cell 3' mRNA sequencing data were obtained from B16F0 and B16F10 cells using Chromium Single-cell 3' Reagent Kits v2 (10x Genomics, Pleasanton, CA).

first: Yeun-Jun

last: Chung


title: Identification of key pathways associated with residual feed intake of beef cattle

status: Public on Apr 07 2022

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: The biological mechanisms associated with the residual feed intake in ruminants have been harnessed immensely via transcriptome analysis of liver and ruminal epithelium, however, this concept has not been fully explored using whole blood. We applied whole blood transcriptome analysis and gene set enrichment analysis to identify key pathways associated with divergent selection for low or high RFI in beef cattle. A group of 56 crossbred beef steers (average BW = 261.3 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake (RFI). After RFI determination, weekly whole blood samples were collected three times from beef steers with the lowest RFI (most efficient; low-RFI; n = 8) and highest RFI (least efficient; high-RFI; n = 8). Prior to RNA extraction, whole blood samples collected were composited for each steer. Sequencing was performed on an Illumina NextSeq2000 equipped with a P3 flow. Gene set enrichment analysis (GSEA) was used to analyze differentially expressed gene sets and pathways between the two groups of steers. Results of GSEA revealed pathways associated with metabolism of proteins, cellular responses to external stimuli, stress, and heat stress were differentially inhibited (false discovery rate (FDR) < 0.05) in high-RFI compared to low-RFI beef cattle, while pathways associated with binding and uptake of ligands by scavenger receptors, scavenging of heme from plasma, and erythrocytes release/take up oxygen were differentially enriched (FDR < 0.05) in high-RFI, relative to low-RFI beef cattle. Taken together, our results revealed that beef steers divergently selected for low or high RFI revealed differential expressions of genes related to protein metabolism and stress responsiveness.

overall_design: Whole blood mRNA expression profilig of 8 high residual food intake (RFI) beef cattle versus 8 low RFI beef cattle.

first: Godstime

middle: A

last: Taiwo

first: Modoluwamu

last: Idowu

first: Ibukun

middle: M

last: Ogunade


title: Gene expression pattern of primed human neutrophils

city: Heidelberg

first: Guido

last: Wabnitz

address: Im Neuenheimer Feld 305

department: Institute of Immunology

institute: University of Heidelberg

summary: Neutrophilic granulocytes change their functionality and phenotype in response to cytokines. This adaptation to the micro-milieu, also called priming, is eminent for an orchestrated defense against infection. However, in chronic inflammation, this process may be accompanied by a steady maintenance of inflammation and tissue destruction. To explore this in more detail, neutrophilic granulocytes were obtained from the peripheral blood of healthy adult donors and primed with cytokines in vitro. The gene expression profile of these cells was compared to resting cells using nCounter technology.

overall_design: Total RNA was isolated from 10.000 resting or primed human neutrophils using MagNA pure isolation according to the manufacturer's instructions. Three biological replicates were inlcuded.


title: A G-protein-coupled receptor modulates gametogenesis via PKG-mediated signaling cascade in Plasmodium berghei

status: Public on Apr 06 2022

city: Shenyang

first: Xiaotong

last: Zhu

state: Liaoning

address: No. 77 Puhe Road Shenyang North NEW AREA

department: Department of Immunology

institute: China Medical University

summary: Gametogenesis is essential for malaria parasite transmission, but the molecular mechanism of this process remains to be refined. Here, we identified a G-protein-coupled receptor 180 (GPR180) that plays a critical role in signal transduction during gametogenesis in Plasmodium. P. berghei GPR180 was predominantly expressed in gametocytes and ookinetes and associated with the plasma membrane in female gametes and ookinetes. Knockout of pbgpr180 (Δpbgpr180) had no noticeable effect on blood-stage development but impaired gamete formation and reduced transmission of the parasites to mosquitoes. Transcriptome analysis revealed that a large proportion of the dysregulated genes in the Δpbgpr180 gametocytes had assigned functions in cyclic nucleotide signaling transduction. In the Δpbgpr180 gametocytes, the intracellular cGMP level was significantly reduced, and the cytosolic Ca2+ mobilization showed a delay and a reduction in the magnitude during gametocyte activation. These results suggest that PbGPR180 functions upstream of the cGMP-protein kinase G-Ca2+ signaling pathway. In line with this functional prediction, the PbGPR180 protein was found to interact with several transmembrane transporter proteins and the small GTPase Rab6 in activated gametocytes. Allele replacement of pbgpr180 with the P. vivax ortholog pvgpr180 showed equal competence of the transgenic parasite in sexual development, suggesting functional conservation of this gene in Plasmodium spp. Furthermore, an anti-PbGPR180 monoclonal antibody and the anti-PvGPR180 serum possessed robust transmission-blocking activities. These results indicate that GPR180 is involved in signal transduction during gametogenesis in malaria parasites and is a promising target for blocking parasite transmission.

overall_design: Total RNA was extracted from the 48% Nycodenz purified activated gametocytes (incubation at 25℃ for 15 min ) of the WT and Δpbgpr180 K1 parasites using the Qiagen RNeasy kit (Qiagen, Dusseldorf, Germany). The purity of RNA was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total of 1 µg total RNA was used to purify the mRNAs using poly-T oligo-attached magnetic beads, followed by fragmentation using divalent cations under elevated temperature in the first-strand synthesis reaction buffer. First-strand cDNA was synthesized using random hexamer primer and RNase H. To select cDNA fragments of 100~200 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Adapters were ligated at 25°C for 10 min before PCR. PCR was performed with the Phusion High-Fidelity DNA polymerase, universal PCR primers, and the index (X) primer. PCR products were purified (AMPure XP system), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina, San Diego, USA). After cluster generation, the libraries were sequenced on an Illumina platform, and 150 bp paired-end reads were generated. Raw reads in the fastq format were firstly processed through in-house Perl scripts to remove low-quality reads, reads containing adapter, and ploy-N. Meanwhile, the Q20, Q30 and GC content of the clean data were calculated. The UMI (Unique Molecular Identifiers) was extracted by the UMI-tools (v2.0.4). Only clean UMI reads were kept for further analysis. RNA-seq reads from each sample were mapped to the P. berghei ANKA genome obtained from the NCBI reference genome (PbANKA01) using the Hisat2 (v2.0.4) (68). The UMI-tools (v1.0.0) were used to deduplicate reads based on the mapping coordinates and the UMI attached to the read. Cuffdiff v2.1 was used as the default method for normalization (69), while differential expression analysis was conducted using DESeq package (1.18.0) in R (70). The resulting P-values were adjusted using Benjamini and Hochberg’s approach for controlling the FDR. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.

first: Peng-peng

last: Wang

first: Xuefeng

last: Jiang

first: Liying

first: Dan

last: Zhou

first: Mingyang

last: Hong

first: Lu

last: He

first: Lumeng

last: Chen

first: Shijie

last: Yao

first: Yan

last: Zhao

first: Guang

first: Chengqi

first: Liwang

last: Cui

first: Yaming

last: Cao


title: hUC-MSC-mediated recovery of subacute spinal cord injury through enhancing the pivotal subunits β3 and γ2 of the GABAA receptor

city: GuangZhou

first: Mangmang

last: Weiping

state: Guangdong

address: 1838 Guangzhou North Ave

department: Department of Cell Biology

institute: Southern Medical University

summary: We conducted a time-course RNA-seq of spinal cord segments at the lesion site without or with hUC-MSC treatment at subacute phase of SCI to identify genes involved in hUC-MSC-mediated recovery

overall_design: The compression injury in rat spinal cord was generated by an aneurysm clip with clamping force of 60 g at T10 for 1 min. Human umbilical cord mesenchymal stem cells (hUC-MSCs) were applied intrathecally into thoracic rat SCI models at 7 days post-injury. After transplantation, 5mm segments of spinal cord centered at the lesion site were collected from rats treated with or without hUC-MSCs at 0, 1, 2, 4 weeks post transplantation

first: Tingting

first: Huan

first: Weiping

last: Huang

last: Li


title: Generation of an RCVRN-eGFP reporter hiPSC line by CRISPR/Cas9 to monitor photoreceptor cell development and facilitate the cell enrichment for transplantation

city: Guangzhou

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: Stem cell based-cell therapies are considered to be promising treatments for retinal disorders with dysfunction or death of photoreceptors. However, the enrichment of human photoreceptors at specific developmental stage suitable for transplantation is highly challenging so far. This study aimed to generate a specific photoreceptor reporter human induced pluripotent stem cell (hiPSC) line using CRISPR/Cas9 genome editing, which harbored an enhanced green fluorescent protein (eGFP) sequence at the endogenous locus of the pan photoreceptor marker Recoverin  (RCVRN). After confirmation of the successful targeting and gene stability, three-dimensional retinal organoids were induced from this report line. The RCVRN-eGFP reporter faithfully replicated endogenous RCVRN  expression and revealed the developmental characteristics of photoreceptors during retinal differentiation. The RCVRN-eGFP specifically and steadily labeled photoreceptor cells from photoreceptor precursors to mature rods and cones. Additionally, abundant eGFP positive photoreceptors could be enriched by fluorescence activated cell sorting and the further RNA sequencing analysis of these purified cells revealed transcriptome signatures and gene networks of photoreceptors. Moreover, potential cluster of differentiation biomarkers  were extracted here for enrichment of photoreceptors for clinical applications. Altogether, the RCVRN-eGFP reporter hiPSC line was successfully established and the first global expression database of RCVRN positive photoreceptors was constructed. These achievements will provide a powerful tool for dynamically monitoring photoreceptor cell development and purification of human photoreceptors at specific developmental stage, thus facilitating the photoreceptor cell therapy for the advanced outer retinal disorders.

overall_design: At Day 150, ROs derived from the RCVRN-eGFP reporter hiPSCs (5 ROs per experiment, 2 independent experiments), FACS-sorted eGFP+ and eGFP- cells pooled from ROs derived from the reporter hiPSCs (30 ROs per experiment, 2 independent experiments) were collected in Trizol reagent. Total RNA was extracted using Trizol reagent kit and the quality of RNA was assessed by an Agilent 2100 Bioanalyzer and checked using RNase free agarose gel electrophoresis. Oligo (dT) beads were used to isolate the poly mRNA from the total RNA. Then the enriched mRNA was subjected to RNA-seq library construction from each two independent samples of three groups: unsorted (ROs), eGFP+ (FASC-sorted RCVRN-eGFP positive cells) and eGFP- (FASC-sorted RCVRN-eGFP negative cells).Paire-end sequencing was performed using Illumina Novaseq 6000. Reads were further filtered by fastp (Chen et al., 2018) (version 0.18.0). Clean reads were mapped to the reference genome using HISAT2. 2.4 (Kim et al., 2015). For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM (Li and Dewey, 2011) software.

first: Yuanyuan

last: Guan

first: Yuan

first: Dandan

last: Zheng

first: Bingbing

last: Xie

first: Ping

last: Xu

first: Guanjie

last: Gao


title: Silencing alanine transaminase 2 in diabetic liver attenuates hyperglycemia by reducing gluconeogenesis from amino acids

city: St. Louis

first: Brian

last: Finck

address: 660 Euclid Ave

institute: Washington University School of Medicine

summary: Hepatic gluconeogenesis from amino acids contributes significantly to diabetic hyperglycemia, but the molecular mechanisms involved are incompletely understood. Alanine transaminases (ALT1 and ALT2) catalyze the interconversion of alanine and pyruvate, which is required for gluconeogenesis from alanine. Hepatocyte-specific knockout of Gpt2 attenuated incorporation of 13C-alanine into newly synthesized glucose by hepatocytes. However, Gpt2 knockout in liver had no effect on glucose concentrations in lean mice, which may suggest that metabolic compensation is occurring.

overall_design: WT or liver specific alanine transaminase 2 knockout mice were either given ad libitum access to food or fasted for 18 h in a 2x2 factorial design.

first: Michael

last: Martino

first: Andrew

last: Lutkewitte


title: miR-138 controls interneuron function and short-term memory

city: Zürich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: D-HEST

country: Switzerland

institute: ETH Zürich

summary: Using a miR-138 loss-of-function mouse model, a role for the brain enriched microRNA miR-138 in the regulation of inhibitory synaptic transmission and short-term memory formation was shown.

overall_design: 3 replicates each from total hippocampal RNA obtained from transgenic mice expressing either an inhibitory sponge transcript (sponge 138) or a control (ctrl) were subjected to polyA-RNA sequencing, followed by differential gene expression analysis.

first: Reetu

last: Daswani

first: Cristoph

last: Dieterich


title: Neisseria genes required for persistence identified via in vivo screening of a transposon mutant library

city: Tucson

first: Katherine

last: Rhodes

state: AZ

address: 1657 East Helen street

department: Immunobiology

institute: University of Arizona

summary: Species of the Neisseria genus harbor close relationships with their mamallian hosts, including humans. The outcome of these interactions can result in commensalism, asymptomatic carriage, or acute inflammatory responses. Little is known of the mechanisms Neisseria use to maintain and shape their host niche in the context of asymptomatic infection or long term commensal colonization and persistence. To identify novel host interaction factors contributing to host persistence, a Tn5 transposon library was created in Neisseria musculi, and inoculated into a permissive strain of laboratory mice (CAST/EiJ). At various time points post inoculation, transposon mutants were recovered from fecal and oral samples, and analyzed to identifiy mutants incapable of maintaining a host niche at either site.

overall_design: A Tn5 transposon library was generated in Neisseria musculi (Nmus), and  inoculated into the oral cavity of mice.  Two library replicates were tested in 5 mice per replicate. For each library replicate, DNA was isolated from the initial stock passage and the inoculum. In host screen samples, bacteria were recovered from oral and fecal samples on selective media, and CFUs were pooled by timepoint, sample site and dose prior to DNA extraction.  Transposon junction sites were then amplified by PCR and sequenced.

first: Man

last: Ma

first: Maria

last: Rendon

first: Magdalene

last: So