title: Transcriptomic analysis of lung tissue from db/db mice treated with or without MSDC-0602K following influenza virus infection

summary: To identify molecular characteristics of lung tissue from db/db mice treated with DMSO or  a new insulin sensitizer MSDC-0602K at day 5 post influenza virus infection, we isolated RNA from lungs with various treatments and examined by bulk RNA-seq. We found a large number of gene profiles were altered following MSDC-0602K treatment in lungs. Interestingly, a number of genes accounting for pulmonary inflammatory responses were significantly decreased following MSDC-0602K treatment in lungs of db/db mice at day 5 post influenza virus infection. Moreover,  MSDC-0602K treated lung tissue showed lower levels of genes related to glucose metabolism.

overall_design: Influenza virus infected-db/db mice were administrated with DMSO or MSDC-0602K daily from day 1 to day 4 post viral infection.  Lungs were obtained at day 5 post influenza virus infection for sequencing.


title: Monocyte signature as a predictor of chronic lung disease in the preterm infant

status: Public on Feb 22 2023

city: Braunschweig

first: Prof. Hamid

last: Hossain

state: Lower Saxony

address: Celler Str. 38

department: Microbiology

country: Germany

institute: Klinikum Braunschweig

summary: The early changes in innate immunity associated with BPD (bronchopulmonary dysplasia) development are incompletely understood. Transcriptome analyses from cord blood of preterm infants indicate a monocyte-centered, profibrotic signature at birth confirming TNFalpha as a critical upstream regulator for the development of BPD.

overall_design: Differential expression analyses of perterm infants with no BPD versus mild or moderate/severe BPD

first: Hamid

first: Anne

last: Hilgendorff


title: Mitochondrial pyruvate metabolism and glutaminolysis toggle steady-state and emergency myelopoiesis

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

country: USA

institute: University of Arizona

type: Expression profiling by high throughput sequencing

summary: RNA-sequencing was performed to look for transcriptional differences between wild-type and Mpc2-deficient granulocyte-macrophage progenitors immediately following the deletion of Mpc2. Paper abstract: Hematopoietic stem and progenitor cells likely engage specific metabolic pathways to promote homeostasis of downstream mature lineages. We examined hematopoiesis in mice conditionally deficient in genes required for long-chain fatty acid oxidation (Cpt2), glutaminolysis (Gls), or mitochondrial pyruvate import (Mpc2). Genetic ablation of Cpt2 or Gls minimally impacted most blood lineages. Deletion of Mpc2 led to a sharp decline in mature myeloid cells and a slower reduction in T cells, whereas other hematopoietic lineages were unaffected. Yet MPC2-deficient monocytes and neutrophils rapidly recovered due to a transient increase in proliferation of myeloid but not other progenitors. Competitive bone marrow chimera and stable isotope tracing experiments demonstrated that this proliferative burst was progenitor-intrinsic and accompanied by a metabolic switch to glutaminolysis. Myeloid recovery after loss of MPC2 or cyclophosphamide treatment was delayed in the absence of GLS. Reciprocally, MPC2 was not required for myeloid recovery after cyclophosphamide treatment. Thus, whereas mitochondrial pyruvate metabolism maintains myelopoiesis under steady-state conditions, rapid recovery from acute loss of myeloid cells requires a switch to glutaminolysis in progenitors.

overall_design: RNA-sequencing of wild-type and Mpc2 knockout granulocyte-macrophage progenitors immediately following Mpc2 deletion

first: Hannah

middle: A

last: Pizzato


title: Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes

status: Public on Feb 23 2023

city: Copenhagen N

first: Chunarum

last: Choudhary

state: --- Select a state ---

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: University of Copenhagen

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin features are widely used for genome-scale mapping of enhancers. However, discriminating active enhancers from other cis-regulatory elements, predicting enhancer strength, and identifying their target genes remains challenging. Here we establish histone H2B N-terminus multisite lysine acetylation (H2BNTac) as a genuine signature of active enhancers. H2BNTac prominently marks candidate active enhancers and a subset of promoters and discriminates them from ubiquitously active promoters. Two mechanisms afford the distinct H2BNTac specificity. (1) Unlike H3K27ac, H2BNTac is specifically catalyzed by CBP/p300. (2) H2A-H2B, but not H3-H4, are rapidly exchanged through transcription-induced nucleosome remodeling. H2BNTac-positive candidate enhancers show a high validation rate in orthogonal enhancer activity assays, and a vast majority of endogenously active enhancers are marked by H2BNTac and H3K27ac. Notably, H2BNTac intensity predicts enhancer strength and outperforms the current state-of-the-art models in predicting CBP/p300 target genes. These findings have broad implications for generating fine-grained enhancer maps and modeling CBP/p300-dependent gene regulation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
H2BNTac ChIP-seq before and after A-485  treatment in mES cell grown in 2i. As a reference, H3K9ac, H3K4me3, H3K27ac, H3K27me3, Med1 ChIP-seq are included. H2BK20ac and H3K27ac ChIP-seq in K562 cell are included.
H3K27ac and H2BK20ac ChIP seq were performed in mouse ESC and human K562 cell lines.

first: Takeo

last: Narita

first: Yoshiki

last: Higashijima


title: Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3 [scRNA-seq]

city: Berlin

first: Giulia

last: Cova

address: 63-73 Ihnestrasse

institute: Max Planck Institute

summary: Split-Hand/Foot Malformation type 3 (SHFM3) is a congenital limb malformation associated with tandem duplications at the LBX1/FGF8 locus. Yet, the disease patho-mechanism remains unsolved. Here we investigated the functional consequences of SHFM3-associated rearrangements on chromatin conformation and gene expression in vivo in transgenic mice. We show that the Lbx1/Fgf8 locus consists of two separate, but interacting, regulatory domains. Re-engineering of a SHFM3-associated duplication and a newly reported inversion in mice resulted in restructuring of the chromatin architecture. This led to an ectopic activation of the Lbx1 and Btrc genes in the apical ectodermal ridge (AER) in an Fgf8-like pattern.  Artificial repositioning of the AER-specific enhancers of Fgf8 was sufficient to induce misexpression of Lbx1 and Btrc. We provide evidence that the SHFM3 phenotype is the result of a combinatorial effect on gene misexpression and dosage in the developing limb. Our results reveal new insights into the molecular mechanism underlying SHFM3 and provide novel conceptual framework for how genomic rearrangements can cause gene misexpression and disease.

overall_design: We performed scRNA-seq to investigate the effect of the SHFM3-associated duplication on gene expression specifically in the AER cell cluster.


title: Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3 [RNA-seq]

overall_design: We performed transcriptome analysis to investigate the effect of the SHFM3-associated duplications and inversion on gene expression


title: Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3 [4C-seq]

overall_design: We used 4C-seq to investigate interactions specific to Lbx1, Btrc and Fgf8 in a patient carrying a SHFM3 duplication versus a healthy control


title: Moxibustion Improves Hypothalamus Aqp4 Polarization in APP/PS1 Mice: Evidence from Spatial Transcriptomics

city: Chendu

first: Qiaofeng

last: Wu

address: No. 37, Twelfth Bridge Road, Jinniu District

country: China

institute: Chengdu University of Traditional Chinese Medicine

summary: Aquaporin-4 (AQP4) is highly polarized to perivascular astrocytic endfeet. Loss of AQP4 polarization is associated with many diseases. In Alzheimer's disease (AD), it is found that AQP4 loos its normal location and thus reduce the clearance of amyloid-β plaques and Tau protein. Clinical and experimental studies show that moxibustion can improve the learning and memory abilities of AD. In order to explore whether moxibustion can affect the polarization of AQP4 around blood brain barrier (BBB), we used spatial transcriptomics (ST) to analyze the expression and polarization of Aqp4 in wild type mice, APP/PS1 mice and APP/PS1 mice intervened by moxibustion. The results showed that moxibustion improved the loss of abnormal polarization of AQP4 in APP/PS1 mice, especially in the hypothalamic BBB. Besides, there are other 31 genes with Aqp4 as the core have the similar depolarization in APP/PS1 mice, most of which are also membrane proteins. The majority of them have been reversed by moxibustion. At the same time, we employed the cerebrospinal fluid circulation gene set, which was found being on a higher level in the group of APP/PS1 mice with moxibustion treatment. Finally, in order to further explore its mechanism, we analyzed the mitochondrial respiratory chain complex enzymes closely related to energy metabolism, and found that moxibustion can significantly increase the expression of mitochondrial respiratory chain enzymes such as Cox6a2 in the hypothalamus, which could provide energy for mRNA transport. Our research shows that increasing the polarization of hypothalamic Aqp4 through mitochondrial energy supply may be an important target for moxibustion to improve APP/PS1 mice’s cognitive impairment.

overall_design: The WT mice were male C57BL/6J mice, while AD model mice were male APP/PS1 double transgenic mice. All the mice were screened by Morris water maze test after a week of adaptation. Then APP/PS1 mice were randomly divided into AD model group (APP/PS1) and moxibustion group (APP/PS1+MOX), C57BL/6J wild-type mice were used as control group (WT group). Spatial Transcriptomics were generated by deep sequencing, using Illumina NovaSeq 6000.

first: Shuqing

last: Liu

first: Ning

last: Zhang

first: Hongying

last: Li


title: Yeast Lachancea Kluyveri uses tripartite mechanism for haploid specific gene repression [ChIP-seq]

city: SAN FRANCISCO

first: Francesca

middle: Silvia

last: Del Frate

state: CA

address: 329 Church St

department: Department of Biochemistry and Biophysics

institute: University of California, San Francisco

summary: Over evolutionary timescales, the logic and pattern of cell-type specific gene expression can remain constant, yet the molecular mechanisms underlying such regulation can drift between alternative forms.  Here, we document a new, especially clear example of this principle in the regulation of the haploid-specific genes across a wide group of fungal species. For most species, transcription of these genes is repressed in the a/ a cell type by a heterodimer of two homeodomain proteins, Mata1 and Mata2.  We show that in the species Lachancea kluveri, repression of one haploid-specific gene (GPA1) requires, in addition to Mata1 and Mata2, a third regulatory protein, Mcm1.  Model building, based on x-ray crystal structures of the three proteins, rationalizes the requirement for all three proteins: no single pair of the proteins is optimally arranged and we show that no single pair can bring about repression.  Although the three-part solution is used to regulate GPA1 in L. kluveri, the other haploid specific genes in this species are regulated by the more conventional two-protein mechanism. This case study exemplifies the idea that the energy of DNA binding can be “shared out” in different ways and can result is different DNA-binding solutions across different genes—while maintaining the same pattern of gene expression.

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) of tagged Matalpha2 to assay Mata1 dependent Matalpha2 binding in a/alpha cell in the yeast Lachancea Kluyveri. To assay binding, ChIP-seq from tagged a/alpha  cells was compared to untagged a/alpha cells and input. The same was done for alpha cells. Then results from alpha cell ChIP-seq were used as a control for Matalpha2 binding events that occur in both a/alpha and alpha cells, allowing us to find a/alpha cell specific binding of Matalpha2.

middle: S

first: Megan

last: Garber

first: Alexander

middle: D

last: Johnson


title: Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3 [Capture Hi-C, Virtual4C]

overall_design: We used Capture Hi-C enriching a 2 Mb region at the Lbx1/Fgf8 locus in Mus musculus to study the effects of CRISPR/Cas9-induced duplication and inversions on the genomic landscape. We analysed wildtype and homozygous mutant limb buds. Embryonic E11.5 limb tissue was used.


title: Yeast Lachancea Kluyveri uses tripartite mechanism for haploid specific gene repression [RNA-seq]

overall_design: Genome-wide transcriptional profiling of L.kluyveri a cell, alpha cell, and a/cell by RNAseq, to determine haploid specific gene expression in this yeast species. Haploid specific genes are genes expressed in both haploid cell types (a cell and alpha cell) but not the diploid a/alpha cell


title: Nutrient regulation of the islet epigenome controls adaptive insulin secretion

status: Public on Feb 24 2023

city: La Jolla

first: Matthew

last: Wortham

address: 2880 Torrey Pines Scenic Drive, Sanford Consortium for Regenerative Medicine, Room 3102

institute: University of California, San Diego

summary: Adaptation of the islet β-cell insulin secretory response to changing insulin demand is critical for blood glucose homeostasis, yet the mechanisms underlying this adaptation are unknown. Here, we show that nutrient cues adapt insulin secretion by modulating chromatin state and transcription of genes regulating β-cell nutrient sensing and metabolism. Feeding stimulates histone acetylation at sites occupied by the chromatin-modifying enzyme Lsd1 in islets. We demonstrate that β-cell-specific deletion of Lsd1 leads to insulin hypersecretion, aberrant expression of nutrient response genes, and histone hyperacetylation, features we also observed in the db/db model of chronically increased insulin demand. Moreover, genetic variants associated with fasting glucose levels and type 2 diabetes risk are enriched at LSD1-bound sites in human islets, suggesting interindividual variation in β-cell functional adaptation in humans. These findings reveal nutrient state-dependent modulation of the islet epigenome and identify Lsd1 as a regulator of feeding-stimulated chromatin modification and adaptive insulin secretion.

sample_organism:
Homo sapiens
Mus
Mus musculus

platform_organism:
Homo sapiens
Mus
Mus musculus

overall_design: Human or mouse pancreatic islets were assessed for genomewide enrichment of H3K27ac under different conditions or for binding by the histone demethylase Lsd1 using ChIP-seq. mRNA-seq was used to assess transcriptional changes in islets under different nutrient states or following inactivation of the histone demethylase Lsd1.


title: Role of epigenetics in the clinical evolution of COVID-19 disease. Epigenome-wide association study identifies markers of severe outcome.

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

type: Methylation profiling by genome tiling array

summary: We performed a whole-genome DNA methylation analysis using EPIC Illumina BeadArrays on a cohort of 187 “Italian” COVID-19 patients (123 mild and 64 severe) to identify epigenetic markers underlying the worst evolution of the disease (death or Intensive Care Unit admission for mechanical ventilation support).

overall_design: Genome-wide DNA methylation analysis of a cohort of COVID-19 patients with a different clinical evolution (123 mild vs 64 severe) using Illumina Human Methylation EPIC Beadchips.

first: Davide

last: Gentilini

first: Gianfranco

last: Parati

first: Francesco

last: Scaglione


title: shox2 is required for inner ear development

city: Piscataway

first: Kelvin

middle: Y.

last: Kwan

state: NJ

address: 604 Allison Rd.

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Zebrafish tissue around the inner ear was dissected from wild-type, heterozygote and mutant ~16-22 hpf embryos and subjected to single cell RNAseq

overall_design: Single cell RNAseq was compared for WT, shox2 heterozygotes and shox2 homozygote mutants.

middle: Y

first: Alejandra

last: Laureano


title: Effect of depletion of Rac1 and Rac3 GTPases on gene expression in cells from the medial ganglionic eminence (MGE)

city: Heraklion

first: ZOUZANA

last: KOUNOUPA

state: Crete

address: Vassilika Vouton

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology Hellas

summary: Το investigate the role of Rac1 and Rac3 GTPases in the development of MGE-derived cortical interneurons we generated a  transgenic mice where both Rac1 and 3  were depleted from the medial ganglionic eminence. First we generated a conditional knockout for Rac1 (Vidaki et al. 2012) by crossing animals carrying a floxed allele of Rac1 (Rac1fl/fl) (the fourth and fifth exon of the Rac1 gene are flanked with loxP sites, Walmsley et al. 2003) to the Nkx2.1Tg(Cre) mice (Nkx2.1 transgenic Cre, Fogarty et al. 2007). The ROSA26fl-STOP-fl-YFP allele was also inserted as an independent marker (Srinivas et al. 2001).  Next, we crossed the Rac1 conditional knockout with the Rac3 KO line (Corbetta et al. 2005) and obtained a mouse line where Rac1 and Rac3 were both depleted from the MGE-derived interneurons.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MGEs from controls, E13.5 Rac1/Rac3 wt embryos (Rac1+/+;Rac3+/+;Nkx2.1Tg(Cre);R26RYFP+/- ) and  Rac1/Rac3 dmut  embryos (Rac1fl/fl;Rac3-/-; Nkx2.1Tg(Cre); R26R-YFP+/- ). Triplicates of each genotype were used and each sample consisted of MGEs from 3 embryos.

first: Zouzana

last: Κounoupa

first: Simona

last: Tivodar

first: Kostas

last: Theodorakis

first: Dimitrios

last: Kyriakis

first: Myrto

last: Denaxa

first: Domna

last: Karagogeos


title: Yeast Lachancea Kluyveri uses tripartite mechanism for haploid specific gene repression.

first: Francesca

last: Del Frate

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

overall_design: Refer to individual Series


title: Targeting cathepsin B by cycloastragenol enhances anti-tumor immunity via inhibiting MHC-1 degradation and promoting the presentation of tumor antigen

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University


title: Targeting cathepsin B by cycloastragenol enhances anti-tumor immunity via inhibiting MHC-1 degradation and promoting the presentation of tumor antigen  [ATAC-seq]

summary: Purpose:We want to elaborate the specific mechanism of CAG inhibiting the growth of transplanted mouse colon cancer cell MC38.  Methods:After MC38 cells were inoculated into C57BL/6 mice for 6 days, the mice were evenly divided into PBS group and CAG group, and PBS and CAG (50mg / kg) were administered by gavage every day. On the 18th day, the mouse tumors were removed, and one tumor was selected to prepare single cell suspension for 10x-scRNA-seq and 10x-scATAC-seq. Results:We found that CAG promoted the antigen-presenting function of tumor cells and enhanced the killing ability of CD8 T cells. Conclusions:CAG enhances the antitumor immunity of CD8 T cells by promoting the antigen presentation of tumor cells.

overall_design: scATAC-seq profiling of total tumor cells in MC38 mouse transplanted tumor.

first: Guoliang

last: Deng

first: Lisha

last: Zhou

first: Bingling

last: Wang

first: Yang

last: Sun


title: Transcriptomic analysis of lung tissue from WT mice treated with or without MSDC-0602K following influenza virus infection

city: Rochester

first: Bibo

last: Zhu

state: MN

address: 200 1st ST SW

department: Pulmonary and Critical Care Medicine

institute: Mayo Clinic

summary: To identify molecular characteristics of lung tissue from WT mice treated with DMSO or  a new insulin sensitizer MSDC-0602K at day 4 post influenza virus infection, we isolated RNA from lungs with various treatments and examined by bulk RNA-seq. We found a large number of gene profiles were altered following MSDC-0602K treatment in lungs. Interestingly, gene sets involved inflammatory responses were enriched in DMSO treatd mouse lungs whereas gene set of fatty acid metabolism was enriched in MSDC-0602K treated mouse lung, suggesting MSDC-0602K treatment diminshed pulmonary inflammation and altered metabolic status during influenza virus infection.

overall_design: Influenza virus infected-WT mice were administrated with DMSO or MSDC-0602K daily from day 1 to day 3 post viral infection.  Lungs were obtained at day 4 post influenza virus infection for sequencing.

first: Jie


title: Genome-wide occupancy of  ATX2 in Arabidopsis

city: shanghai

first: li

last: peng

institute: PSC

summary: ChIP-seq was performed to detect genome-wide binding sites of  ATX2

overall_design: Arabidopsis wild-type Col-0, ATX2-3Flag plants were subject to ChIP-seq analysis using the Flag antibodies.

first: Si-Si

last: Xie

first: Li

last: Peng

first: Cheng-Guo

last: Duan


title: Targeting cathepsin B by cycloastragenol enhances anti-tumor immunity via inhibiting MHC-1 degradation and promoting the presentation of tumor antigen [RNA-seq]

overall_design: scRNA-seq profiling of total tumor cells in MC38 mouse transplanted tumor.


title: Arabidopsis mutants

sample_organism:
Arabidopsis
Arabidopsis thaliana

platform_organism:
Arabidopsis
Arabidopsis thaliana


title: RNA-seq analysis of Col-0 and jmj28-2 in Arabidopsis

summary: RNA-seq was performed to detect transcripts level of WT and mutants

overall_design: Total RNAs were extracted from 12-day-old seedlings grown during long days using a RNeasy Plant Mini kit (Qiagen)


title: Case Report: Deep Immune Profiling Links Neutrophil and Plasmablast Dysregulation to Microvascular Damage in post-COVID-19 Multisystem Inflammatory Syndrome of Adults (MIS-A).

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

summary: Despite surviving a SARS-CoV-2 infection, some individuals experience an intense post-infectious Multisystem Inflammatory Syndrome (MIS) of uncertain etiology. Children with this syndrome (MIS-C) can experience a Kawasaki-like disease, but mechanisms in adults (MIS-A) are not clearly defined. Here we utilize a deep phenotyping approach to examine immunologic responses in an individual with MIS-A. Results are contextualized to healthy, convalescent, and acute COVID-19 patients. The findings reveal systemic inflammatory changes involving novel neutrophil and B-cell subsets, autoantibodies, complement, and hypercoagulability that are linked to systemic vascular dysfunction. This deep patient profiling generates new mechanistic insight into this rare clinical entity and provides potential insight into other post-infectious syndromes.

overall_design:
Single-cell RNA-Seq library construction, alignment, and quality control:

A total of 15,000 single cells (containing an equal proportion of leukocytes and lymphocytes) were loaded for partitioning using 10X Genomics NextGEM Gel Bead emulsions. All samples were processed as per manufacturer’s protocol (with both PCR amplification steps run 12X). Quality control and pre-loading cDNA quantification was performed using TapeStation D1000 ScreenTape assay. Sequencing was performed using Illumina NovaSeq S2 and SP 100 cycle dual lane flow cells over multiple rounds to ensure each sample received approximately 32,000 reads per cell. Sequencing reads were aligned using CellRanger 3.1.0 pipeline to the standard pre-built GRCh38 reference genome. Samples that passed alignment QC were aggregated into single datasets using CellRanger aggr with between-sample normalization to ensure each sample received an equal number of mapped reads per cell. Aggregated healthy (n = 3) and recovered COVID-19 (n = 3) samples recovered 30,514 cells that were sequenced to 17,157 post-normalization reads per cell.

Single-cell RNA-Seq computational analyses and workflows:

Filtered feature-barcode HDF5 matrices from aggregated datasets were imported into the R package Seurat v.3.9 for normalization, scaling, integration, multi-modal reference mapping, louvain clustering, dimensionality reduction, differential expression analysis, and visualization. Briefly, cells with abnormal transcriptional complexity (fewer than 500 UMIs, greater than 25,000 UMIs, or greater than 15% of mitochondrial reads) were considered artifacts and were removed from subsequent analysis. Cell identity was classified by mapping single cell profiles to the recently published PBMC single-cell joint RNA/CITE-Seq multi-omic AZIMUTH reference. Since no published reference automates granulocyte annotations, neutrophil clusters were manually annotated by querying known markers (i.e. CSF3R, S100A8, S100A9, MMP8, MMP9, ELANE, MPO). A cell state-specific ‘perturbation score’ was calculated to reflect the magnitude of response elicited by factoring in number and cumulative FC of consensus DEGs. Perturbation scores were visualized using Nebulosa-generated density plots. Cells with high mitochondrial read were subsetted to enable further characterization of these cells, as there were high mitochondrial reads specifically in the first MIS-A sample.

first: Mark

middle: R

last: Gillrie

first: Nicole

last: Rosin

first: Sarthak

last: Sinha

first: Hellen

last: Kang

first: Raquel

last: Farias

first: Angela

last: Nguyen

first: Kelsie

last: Volek

first: Jordan

last: Mah

first: Etienne

last: Mahe

first: Marvin

middle: J

last: Fritzler

first: Bryan

middle: G

last: Yipp


title: Genome-wide occupancy of JMJ28 in Arabidopsis [JMJ28_ChIP_seq]

summary: ChIP-seq was performed to detect genome-wide binding sites of JMJ28

overall_design: Arabidopsis wild-type Col-0 and JMJ28-4Myc plants were subject to ChIP-seq analysis using the Myc antibody.


title: Genome-wide occupancy of ATX2 in Arabidopsis 2

summary: ChIP-seq was performed to detect genome-wide binding sites of ATX2 in different background

overall_design: Arabidopsis wild-type Col-0, ATX2-3Flag/Col-0, ATX2-3Flag/atx1, ATX2-3Flag/atx1 jmj28 plants were subject to ChIP-seq analysis using Flag antibodies.


title: Genome graphs detect human polymorphisms in active epigenomic state during influenza infection [ChIP-seq]

status: Public on Feb 21 2023

city: Montréal

first: Guillaume

last: Bourque

state: QC

address: 740, Dr. Penfield Avenue Room 6103

department: Human Genetics

institute: McGill University

summary: Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that the use of a genome graph, which encapsulates genetic diversity, could reveal missing epigenomic signal. We tested this in a dataset obtained by sequencing the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after Influenza virus infection, which also allowed us to investigate the potential role of MEIs in immunity. After characterizing genetic variants in this cohort using linked-reads, including 5140 Alu, 316 L1, 94 SVAs and 48 ERVs, we incorporated them into a genome graph. Mapping epigenetic data to this graph revealed 2.5%, 3.0% and 2.3% novel peaks for H3K4me1 and H3K27ac ChIP-seq and ATAC-seq respectively. Notably, using a genome graph also modified quantitative trait loci estimates and we observed 375 polymorphic MEIs in active epigenomic state. For example, we found an AluYh3 polymorphism whose chromatin state changed after infection and that was associated with the expression of TRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches.

overall_design: ChIP-seq

first: Marie-Michelle

last: Simon

first: Albena

last: Pramatarova

first: Cristian

last: Groza


title: Organotypic Human Lung Bud Microarrays Identify BMP-dependent SARS-CoV-2 Infection in Lung Cells

city: New York

first: Edwin

last: Rosado-Olivieri

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: Although lung disease is the primary clinical outcome in COVID-19 patients, how SARS-CoV-2 induces lung pathology remains elusive. Here we describe a high-throughput platform to generate self-organizing ad commensurate human lung buds derived from hESCs cultured on micropatterned substrates. Lung buds resemble human fetal lungs and display proximo-distal patterning of alveolar and airway tissue directed by KGF. These lung buds are susceptible to infection by SARS-CoV-2 and endemic coronaviruses and can be used to track cell type-specific cytopathic effects in hundreds of lung buds in parallel. Transcriptomic comparisons of infected lung buds and postmortem tissue of COVID-19 patients identified an induction of BMP signaling pathway. BMP activity renders lung cells more susceptible to SARS-CoV-2 infection and its pharmacological inhibition impairs infection by this virus. These data highlight the rapid and scalable access to disease-relevant tissue using lung buds that recapitulate key features of human lung morphogenesis and viral infection biology.

overall_design: In vitro-differentiated organotypic lung buds were infected with SARS-CoV-2, 229E and OC43 and RNA was collected at multiple time-points post-infection for RNA-sequencing analysis.

last: Rosado Olivieri

first: Brandon

last: Razooky

first: Jeremie

last: Le Pen

first: Riccardo

last: De Santis

first: Douglas

last: Barrows

first: Ziad

last: Sabry

first: Hans-Heinrich

last: Hoffmann

first: Jiwoon

last: Park

first: Thomas

last: Carroll

first: John

middle: T

last: Poirier

first: Charles

middle: M

last: Rice

first: Ali

middle: H

last: Brivanlou


title: Effect of endothelial depletion of Wt1 on gene expression during coronary plexus sprouting in the heart

city: Barcelona

first: Ofelia

middle: M.

last: Martínez Estrada

state: Barcelona

address: Avinguda Diagonal, 643, Edifici Prevosti, Planta 1, Laboratori 2

department: Cell Biology, Physiology and Immunology

country: Spain

institute: University of Barcelona

summary: Coronary blood vessel formation is a highly regulated process in which endothelial cells (ECs) play an essential role. During the last years, new pieces of evidence have demonstrated WT1 expression in coronary ECs. However, its role in coronary blood vessel formation was almost unknown. Here we generated an inducible endothelial-specific Wt1KO mouse model (Wt1KOΔEC). The analysis of these mutant mice has demonstrated that deletion of Wt1 in coronary ECs impairs coronary blood vessels and myocardium development. The transcriptomic analysis of coronary ECs from Wt1KOΔEC mice demonstrated that deletion of Wt1 has a great impact on the molecular signature of coronary ECs that correlate with defects in cell proliferation, migration, and differentiation.  These results provide novel insights into the role of WT1 in heart development and demonstrate that WT1 in ECs is required for  coronary blood vessel formation.

overall_design: To investigate the role of WT1 in coronary endothelial cells from the coronary plexus during initial stages of sprouting angiogenesis of the heart, we generated an inducible endothelial-specific Wt1KO mouse model (Wt1KOΔEC) in which both lineage tracing expression of membrane GFP (mGFP) and deletion of Wt1 is induced upon tamoxifen administration. We administered pregnant mice during E11.5-13.5 stages, isolated embryo hearts at E15.5 and FACS-sorted mGFP+ cells.  We then performed gene expression profiling analysis using data obtained from RNA-seq of ControlΔEC (n=3) and Wt1KOΔEC (n=3) coronary endothelial cells

first: Marina

last: Ramiro-Pareta

first: Anna

last: Esteve-Codina

last: Martínez-Estrada


title: H3K9me2 level in WT, jmj28-2.

first: li

last: peng

summary: ChIP-seq was performed to detect  histone H3K9me2 level in WT, jmj28-2.

overall_design: Arabidopsis wild-type Col-0, jmj28-2 plants were subject to ChIP-seq analysis using the H3K9me2  antibody.

first: Si-Si

last: Xie

first: Li

last: Peng

first: Cheng-Guo

last: Duan


title: Transcription profiles of young and old HSCs

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

summary: Here we examine the transriptomes of HSCs from young (2 months) vs old (24 months) mice bone marrow.

overall_design: To determine the transcriptional changes in HSCs during ageing, we FACS sorted HSCs (LSKCD150+CD48-) from young and old mouse bone marrow for bulk RNA-seq.

first: Yiran

last: Meng

first: Simona

last: Valletta


title: Murine lenses:βB2-crystallin W151C knock-in mice vs.wild type control mice

city: Guangzhou

first: Wei

last: Xiao

state: Guangdong

address: S 54 Xianlie Rd, Yuexiu District

institute: Zhongshan Ophthalmic Center

summary: Transcriptional profiling of the lens in βB2-crystallin W151C mutation mice compared with wild type lenses

overall_design: Two-condition experiment, βB2-crystallin W151C knock-in vs.wild type ,Biological replicates: 3 control replicates, 3 knock-in replicates.

first: Xiaoyun

last: Chen


title: Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3

first: Giulia

last: Cova


title: Adipophilin as a metabolic biomarker for Uveal Melanoma

city: Turku

first: Arfa

last: Mehmood

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology, UTU

summary: In this study, we designed four adipophilin-based multigene signatures for uveal melanoma prognostication using a transcriptomic and secretome survival-functional network approach. To validate the adipophilin-based multigenes and adipophilin expression levels in the context of BAP1, we used next generation RNA sequencing approach.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for two uveal melanoma cell lines, Mel285 (BAP1 positive) and MP46 (BAP1 negative) cells lines

first: Rogerio

last: De Figueiredo


title: Rapid protection induced by a single-shot Lassa vaccine in cynomolgus monkeys

city: Paris

first: Sylvain

last: Baize

address: 25-28 rue du Docteur Roux, CEDEX 15

country: France

institute: Institut Pasteur

summary: Lassa fever outbreaks hit West African countries every year and there is still no licensed vaccine to limit the burden of this viral hemorrhagic fever. We previously developed MeV-NP, a single-shot vaccine that induces protective immunity in cynomolgus monkeys one month or more than a year before Lassa virus infection and that is able to protect against divergent viral strains. Given the limited dissemination area of Lassa virus during outbreaks and the high risk of nosocomial transmission, a vaccine that induces rapid protection could be useful to protect exposed people during outbreaks in the absence of preventive vaccination. We tested whether the time to protection could be reduced after immunization by challenging MeV pre-immune cynomolgus monkeys 16 or 8 days after a single shot of MeV-NP. None of the immunized monkeys developed disease and they rapidly controlled viral replication. Animals immunized eight days before the challenge were the best controllers, producing a strong CD8 T-cell response against the viral glycoprotein. A group of animals was also vaccinated an hour after the challenge. These animals did not develop any protective immune responses and presented the same lethal disease as the control animals. This study demonstrates that MeV-NP can induce a rapid protective immune response against Lassa fever in presence of MeV pre-existing immunity but can likely not be used as therapeutic vaccine.

overall_design: 3 groups of 3 animals ; 4 to 6 timepoints by animals

first: Mathieu

last: Mateo

first: Natalia

last: Pietrosemoli

first: Emeline

last: Perthame


title: Pathogenic Mutation that Dislocates GATA2 Zinc Fingers Establishes a Hematopoiesis-Disrupting Signaling Network

city: Ottawa

first: Marjorie

last: Brand

state: Onatrio

address: 501 Smyth Road

department: Regenerative Medicine Program

institute: Ottawa Hospital Research Institute

summary: While certain human genetic variants are conspicuously loss-of-function, decoding the functional impact of many variants is challenging. Previously, we described a leukemia predisposition syndrome (GATA2-deficiency) patient with a germline GATA2 variant that inserts nine amino acids between the two zinc fingers (9aa-Ins). Here, we conducted mechanistic analyses using genomic technologies in Gata2 enhancer-mutant hematopoietic progenitor cells to reveal how the insertion impacts GATA2 function genome-wide. Despite being nuclear-localized, 9aa-Ins was severely defective, with activation more impaired than repression. Variation of the inter-zinc finger spacer length revealed that repression tolerated insertions that were detrimental to activation. GATA2 deficiency generated a hematopoiesis-disrupting signaling network in progenitor cells with reduced Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) signaling and elevated Interleukin-6 (IL-6) signaling. As insufficient GM-CSF signaling causes pulmonary alveolar proteinosis and excessive IL-6 signaling causes bone marrow failure, hallmark phenotypes of GATA2-deficiency patients, these results establish molecular mechanisms underlying GATA2-linked pathologies.

overall_design: 25000 Hoxb8-immortalized wild type hematopoietic progenitors (hi−77+/+) infected with control (empty) retrovirus, Gata2 -77 enhancer deleted mutant progenitors (hi−77−/−) infected with empty retrovirus or GATA2- or 9aa-Ins-expressing retrovirus were FACS isolated for GFP+

first: Mabel

last: Jung

first: Thomas

last: Olender

first: Qingzhou

last: Zhang

first: Emery

last: Bresnick


title: Epigenetic profiles of young vs old Vwf+ HSCs at single cell level

first: Claus

last: Nerlov

summary: Here we examine the chromatin landscapes of Vwf+ HSCs from young (2 months) vs old (24 months) mouse bone marrow.

overall_design: To determine the change of HSC subtype composition during ageing, we used scATAC-seq to profiled Vwf+ HSCs (LKSCD150+CD48-CD34-Vwf+) from young and old mouse bone marrow.

first: Bowen


title: Cerebral malaria is regulated by host mediated changes in Plasmodium gene expression

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Cerebral Malaria (CM), the deadliest complication of Plasmodium infection, is a complex and unpredictable disease. Currently, our understanding of the factors that trigger progression of malaria to CM is limited. Here, by infecting experimental CM (ECM) resistant (Balb/c) and ECM susceptible (C57BL/6) mice with ECM causing (ANKA) and non-ECM causing (NK65) Plasmodium berghei (Pb) parasite strains, we revealed that in resistant host, infection by ECM causing parasite develops similar to infection by non-ECM causing parasite in susceptible host in terms of parasite growth in host, disease course and host immune response against parasite. Our comparative gene expression analysis revealed that in Balb/c host, gene expression of Pb ANKA parasite is remarkably different from, the gene expression of Pb ANKA in C57BL/6 but similar to the gene expression of non-ECM causing Pb NK65 in C57BL/6. Thus, host has a critical influence on parasite behavior which ultimately determines the course of malaria disease.

sample_organism:
Plasmodium berghei
Mus musculus

platform_organism:
Plasmodium berghei
Mus musculus

overall_design: different treatments of Plasmodium compared

first: Clare

middle: K

last: Cimperman

first: Mirna

last: Pena

first: Sohret

last: Gokcek

first: Brandon

middle: P

last: Theall

first: Meha

middle: V

last: Patel

first: Anisha

last: Sharma

first: ChenFeng

last: Qi

first: Daniel

first: Patrick

middle: L

last: Collins

first: Susan

last: Pierce

first: Munir

last: Akkaya


title: The N-terminal extension of Arabidopsis ARGONAUTE 1 is essential for microRNA activities II

city: Riverside

first: Ye

last: Xu

address: 900 University Ave

institute: University of California, Riverside

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Spontaneous Development of an Autoimmune Hepatitis – Primary Biliary Cirrhosis Overlap Syndrome in dnTGFβRII Aire-/- mice

first: Jie

last: Long

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

summary: Autoimmune regulator (Aire) and TGF-β signaling play an important role in central tolerance and peripheral tolerance respectively, by eliminating or suppressing the activity of autoreactive T cells. We have previously demonstrated that dnTGFβRII mice develop a defect in peripheral tolerance and a primary biliary cirrhosis (PBC) like disease. We hypothesized that by introducing the AIRE gene to this model, we would observe a more severe PBC phenotype. Interestingly, however, we demonstrate that while dnTGFβRII Aire-/- mice do manifest key histologic and serologic features of autoimmune cholangitis, they also develop mild to moderate interface hepatitis and show high levels of alanine transaminase (ALT) and antinuclear antibodies (ANA), characteristics of autoimmune hepatitis (AIH). To further understand this unique phenotype, we performed RNA-seq and flow cytometry to explore the functional pathways and immune cell pathways in the liver of dnTGFβRII Aire-/- mice. Our data revealed enrichments of programmed cell death pathways and predominant CD8+ T cell infiltrates. Depleting CD8+ T cells using an anti-CD8α antibody significantly alleviated hepatic inflammation and prolonged the lifespan of these mice. Finally, RNA-seq data indicated the clonal expansion of hepatic CD8+ T cells. In conclusion, these mice develop an autoreactive CD8+ T cell mediated autoimmune cholangitis with concurrent hepatitis that exhibits key histological and serological features of the AIH-PBC overlap syndrome, representing a novel model for the study of tolerance and autoimmune liver disease.

overall_design: To explore the function state of hepatic cells in different groups, we extracted the total RNA of liver and thymus tissues or 5×10^5 hepatic CD8+ T cells from dnTGFβRII Aire-/- mice and their control littermates, then we build the cDNA library and performed the bulk RNA sequencing.

first: Si-Yu

last: Yang


title: Directed Differentiation of Human iPSCs to Functional Ovarian Granulosa-Like Cells via Transcription Factor Overexpression

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

institute: Harvard University


title: The N-terminal extension of Arabidopsis ARGONAUTE 1 is essential for microRNA activities [ncRNA_seq]

summary: We profiled the small RNA of AGO1 NTE truncation mutant lines, and the small RNA associated with AGO1 NTE truncation mutant to study the roles of the NTE region in Arabidopsis AGO1 involved RNA-induced silencing complex (RISC) formation.

overall_design: sRNA-seq to examine the total small RNA profile in Arabidopsis AGO1 NTE truncation mutants, and small RNA associated with Arabidopsis AGO1 NTE truncation mutants.

first: Xuemei

last: Chen


title: The N-terminal extension of Arabidopsis ARGONAUTE 1 is essential for microRNA activities


title: The N-terminal extension of Arabidopsis ARGONAUTE 1 is essential for microRNA activities [RNA_seq]

summary: We profiled gene expression of AGO1 NTE truncation mutant lines to study the roles of the NTE region in Arabidopsis AGO1 involved RNA-induced silencing complex (RISC) formation.

overall_design: RNA-seq to examine the mRNA in AGO1 NTE truncation mutants.


title: Genome-wide maps of chromatin state in Col-0, jmj28 mutant, and atx1/2 mutant [Histone ChIP-seq]

first: li

last: peng

summary: ChIP-seq was performed to detect two different histone modifications in WT, jmj28-2, and atx1/2.

overall_design: Arabidopsis wild-type Col-0, jmj28-2, atx1/2 plants were subject to ChIP-seq analysis using the H3K4me1, H3K4me3 and H3 antibody respectivly.

first: Si-Si

last: Xie

first: Li

last: Peng

first: Cheng-Guo

last: Duan


title: Bulk RNA sequencing of DGKa deficient and wildtype P14 CD8 T cells after LCMV Clone 13 infection

city: Wauwatosa

first: Matthew

last: Kudek

state: WI

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

summary: exposure to LCMV Clone 13 infection in the absence of DGKa leads to excessive inflammation and mortality

overall_design: Four samples of DGKa deficient and three samples of C57Bl/6 P14+ CD8+ T cells were enriched from mouse splenocytes on day 8 post infection with LCMV clone 13 and were analyzed by bulk RNA sequencing

first: Weiguo

last: Cui


title: Graded BMP signaling within intestinal crypt architecture directs self-organization of the Wnt-secreting stem cell niche

first: Ramesh

middle: A.

last: Shivdasani

address: 450 Brookline Ave. SM1060

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Signals from the surrounding niche drive proliferation and suppress differentiation of intestinal stem cells (ISCs) at the bottom of intestinal crypts. Among sub-epithelial support cells, deep sub-cryptal CD81+ PDGFRAlo trophocytes capably sustain ISC functions ex vivo. Here we show that mRNA and chromatin profiles of abundant CD81- PDGFRAlo mouse stromal cells resemble those of trophocytes and that both populations provide crucial canonical Wnt ligands. Mesenchymal expression of key ISC-supportive factors extends along a spatial and molecular continuum from trophocytes into peri-cryptal CD81- CD55hi cells, which mimic trophocyte activity in organoid co-cultures. Graded expression of essential niche factors is not cell-autonomous but dictated by the distance from bone morphogenetic protein (BMP)-secreting PDGFRAhi myofibroblast aggregates. BMP signaling inhibits ISC-trophic genes in PDGFRAlo cells near high crypt tiers; that suppression is relieved in stromal cells near and below the crypt base, including trophocytes. Cell distances thus underlie a self-organized and polar ISC niche.

overall_design: Mesenchymal cells from the small and large intestine of adult PdgfraH2BeGFP (JAX strain 007669) mice were isolated and sorted for level of Pdgfra (eGFP, high or low) and among Pdgfra_low cells for CD81+ or CD81-  to obtain three different cell types in biological replicates per location.

first: Judith

last: Kraiczy

first: Neil

last: McCarthy

first: Ermanno

last: Malagola

first: Guodong

last: Tie

first: Shariq

last: Madha

first: Dario

last: Boffelli

last: Wagner

first: Timothy

middle: C

last: Wang

middle: A


title: Genome graphs detect human polymorphisms in active epigenomic state during influenza infection

first: Guillaume

last: Bourque


title: Genome graphs detect human polymorphisms in active epigenomic state during influenza infection [ATAC-seq]

summary: Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that the use of a genome graph, which encapsulates genetic diversity, could reveal missing epigenomic signal. We tested this in a dataset obtained by sequencing the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after Influenza virus infection, which also allowed us to investigate the potential role of MEIs in immunity. After characterizing genetic variants in this cohort using linked-reads, including 5140 Alu, 316 L1, 94 SVAs and 48 ERVs, we incorporated them into a genome graph. Mapping epigenetic data to this graph revealed 2.5%, 3.0% and 2.3% novel peaks for H3K4me1 and H3K27ac ChIP-seq and ATAC-seq respectively. Notably, using a genome graph also modified quantitative trait loci estimates and we observed 375 polymorphic MEIs in active epigenomic state. For example, we found an AluYh3 polymorphism whose chromatin state changed after infection and that was associated with the expression of TRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches.

overall_design: ATAC-seq

first: Marie-Michelle

last: Simon

first: Albena

last: Pramatarova

first: Cristian

last: Groza


title: Transcriptomic analyzes of paps1 pollen tube/style complexes

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary: Polyadenylation of mRNAs is critical for their export from the nucleus, stability and efficient translation. The Arabidopsis thaliana genome encodes three isoforms of canonical nuclear poly(A) polymerase (PAPS) that redundantly polyadenylate the bulk of pre-mRNAs. However, their distinct mutant phenotypes and transcriptome studies have indicated that subsets of pre-mRNAs are preferentially polyadenylated by either PAPS1 or the two very similar PAPS2 and PAPS4 proteins. Such functional specialization raises the possibility of modulating the balance of activities between the isoforms to alter poly(A) lengths of sets of transcripts, providing an additional level of gene-expression control in plants. Here we test this notion by studying the function of PAPS1 in pollen-tube growth and guidance. Pollen tubes growing through female tissue acquire the competence to find ovules efficiently and upregulate PAPS1 expression more strongly than in vitro grown pollen tubes. Using the temperature-sensitive paps1-1 allele we show that PAPS1 activity during pollen-tube growth is required for full acquisition of competence, resulting in inefficient fertilization by paps1-1 mutant pollen tubes. While these mutant pollen tubes germinate and grow at the same rates as wild-type pollen tubes, they are compromised in locating the micropyles of ovules. Transcriptomic analyses indicate that previously identified competence-associated genes are less expressed in paps1-1 mutant than in wild-type pollen tubes. Estimating the poly(A)-tail lengths of transcripts in mutant and wild-type pollen tubes suggests that polyadenylation by PAPS1 is associated with reduced transcript abundance. Our results therefore suggest that PAPS1 upregulation during pollen-tube growth through the style plays a key role in the acquisition of competence and support the notion that plants can modulate the balance of activity between PAPS isoforms to regulate gene expression.

overall_design: Gene expression profiling in pollen tube/style complexes in A. thaliana paps1-1 mutants and wild type.

first: Anna

last: Ramming

first: Christian

last: Kappel


title: Transcriptomic analyses to estimated poly(A)-tail lengths in paps1-1 mutant pollen tubes

overall_design: Gene expression profiling in pollen tubes in A. thaliana paps1-1 mutants and wild type using either oligo(dT) or random hexamer priming.


title: Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states [snRNA]

first: Osama

last: Al Dalahmah

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

summary: Glioblastoma is an aggressive diffusely infiltrating neoplasm that spreads beyond surgical resection margins, where it intermingles with non-neoplastic brain cells. This complex microenvironment harbouring infiltrating glioma and non-neoplastic brain cells is the origin of tumor recurrence. Thus, understanding the cellular and molecular features of the glioma microenvironment is therapeutically and prognostically important. Here, we used single-nucleus RNA sequencing (snRNAseq) of primary and recurrent glioma to define three compositional ‘tissue-states’ rooted in cohabitation of cell-types and transcriptional states. These comprise a state featuring A) minimally infiltrated-brain, B) reactive inflamed infiltrated tissue, and C) cellular tumor. Spatial transcriptomics confirmed that the cell-types and transcriptomics states which compositionally cohabitate indeed do colocalize in space. Tissue states are clinically significant because they correlate with radiographic, histopathologic, and prognostic features. We found that in addition to enrichment of tissue state B signature, enrichment of both neoplastic and non-neoplastic cell-type gene signatures in tissue state B correlated with decreased survival. Importantly, we found that our compositionally defined tissue states are enriched in distinct metabolic pathways. One such pathway is fatty acid biosynthesis, which was enriched in tissue state B – a state enriched in recurrent glioblastoma and composed of astrocyte-like/mesenchymal glioma cells, reactive astrocytes resembling those seen in neurodegeneration, and monocyte-like myeloid cells. We discovered that targeting fatty acid synthesis was sufficient to deplete the transcriptional signature of tissue state B. Our findings define a novel compositional approach to the glioma infiltrated tissue which allows us to discover prognostic and targetable features, paving the way to new mechanistic and therapeutic discoveries.

overall_design: Comparative gene expression and molecular analysis on GBM tissue that are primary glioma versus a recurrent glioma.

last: Al-Dalahmah

last: Argenziano

first: Aayushi

last: Mahajan

first: Julia

last: Furnari

first: Fahad

last: Paryani

first: Deborah

last: Boyett

first: Akshay

last: Save

first: Fatima

last: Khan

first: Juncheng

last: Li

first: Hong

last: Lu

first: Yu

last: Sun

first: John

middle: F

last: Tuddenham

first: Alexander

last: Goldberg

first: Athanassios

last: Dovas

first: Matei

last: Banu

first: Tejaswi

last: Sudhakar

first: Erin

last: Bush

first: Andrew

middle: B

last: Lassman

first: Jeffrey

middle: N

last: Bruce

first: Peter

last: A Sims

first: Vilas

last: Menon

last: Canoll

first: Adithya

last: Kannan

first: Nelson

last: Humala

first: Guy

last: McKhann

first: Brian

last: A Gill

first: Brett

last: Youngerman

last: Sisti


title: Hepatocyte mARC1 Promotes Fatty Liver Disease

status: Public on Feb 20 2023

first: Enrique

last: Toledo

address: Innovation Building, Old Road Campus, Roosevelt Drive

department: R&D

institute: Novo Nordisk

summary: Non-alcoholic fatty liver disease (NAFLD) has a prevalence of ~25% worldwide, with significant public health consequences, yet  few effective treatments.  Human genetics can help elucidate novel biology and identify targets of new therapeutics. Genetic variants in mitochondrial amidoxime reducing component 1 (MTARC1) have been associated with NAFLD and liver-related mortality, however, its pathophysiological role and the cell type(s) mediating these effects remain unclear. We aimed to investigate how MTARC1 exerts its effects on NAFLD by integrating human genetics with in vitro and in vivo studies of mARC1 knockdown. Methods: Analyses including multi-trait colocalization and mendelian randomization were used to assess the genetic associations of MTARC1. In addition, we established an in vitro long-term primary human hepatocyte model with metabolic readouts and used the Gubra GAN-diet NASH mouse model treated with hepatocyte specific GalNAc-siRNA to understand the in vivo impacts of MTARC1. Results: We show that genetic variants within the MTARC1 locus are associated with liver enzymes, liver fat, plasma lipids and body composition and these associations are due to the same causal variant (p.A165T, rs2642438 G>A), suggesting a shared mechanism. We demonstrated that increased MTARC1 mRNA had an adverse effect on these traits using Mendelian Randomization, implying therapeutic inhibition of mARC1 could be beneficial.  In vitro mARC1 knockdown decreased lipid accumulation and increased triglyceride secretion and in vivo GalNAc-siRNA mediated knockdown of mARC1 lowered hepatic, but increased plasma triglycerides. We found alterations in pathways regulating lipid metabolism and decreased secretion of 3-hydroxybutyrate upon mARC1 knockdown in vitro and in vivo. Conclusions: Collectively, our findings from human genetics, and in vitro and in vivo hepatocyte-specific mARC1 knockdown support the potential efficacy of hepatocyte-specific targeting of mARC1 for treatment of NAFLD.

overall_design: DIO-NASH Mouse Liver bulk RNA-seq Vehicle and siRNA

first: Lara

last: Lewis

first: Lingyan

last: Chen

first: L

middle: S

last: Hameed

first: Robert

middle: R

last: Kitchen

first: Cyrielle

last: Maroteau

first: Shilpa

last: Nagarajan

first: Jenny

last: Norlin

first: Charlotte

middle: E

last: Daly

first: Iwona

last: Szczerbinska

first: Sara

last: Hjuler

first: Rahul

last: Patel

first: Eilidh

middle: J

last: Livingstone

first: Tom

last: Durrant

first: Elisabeth

last: Wondimu

first: Soumik

last: BasuRay

first: Anandhakumar

last: Chandran

first: Wan-Hung

last: Lee

first: Sile

last: Hu

first: Barak

last: Gilboa

first: Megan

last: Grandi

first: Abdullah

last: Erikat

first: Leanne

last: Hodson

first: William

last: Haynes

first: Natalie

middle: W

last: Pursel

first: Ken

last: Coppieters

first: Jan

last: Fleckner

first: Joanna

last: Howson

first: Birgitte

last: Andersen

first: Maxwell

last: Ruby


title: Mechanisms of AICAR in lung cancer

city: Orlando

first: Wencai

last: Zhang

state: FL

address: 6900 Lake Nona Blvd

institute: University of Central Florida

summary: The purpose of the research is to delineate the mechanism behind AICAR-induced cytotoxicity by understanding the genetic pathways that are affected with AICAR treatment.

overall_design: H1975 non-small lung cancer cell line was treated with AICAR 0 or 1mM for four hours before total RNA extraction using MirVana RNA Isolation kit. There are two groups. A vehicle treatment and 1mM AICAR treatment. Each group contains three biological replicates.

first: Fareesa

last: Aftab


title: Effect of depletion of GPRC5A on gene expression in HT-29 cells upon the treatment of 7-fluorotryptamine and/or TNFa

city: La Jolla

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

summary: To investigate the function of GPRC5A and aromatic monoamine, we generated GPRC5A knock-out HT-29 colorectal cancer cells by CRISPR-Cas9 gene editing and evaluated changes in gene expression by RNA sequencing. Wild-type and GPRC5A knock-out cells revealed significant differences in gene expression patterns, particularly the immune- and cancer-related genes. The regulation of gene expression by GPRC5A is not significantly affected by 7-fluorotryptamine and/or TNFa.

overall_design: Wild-type and GPRC5A knock-out HT-29 cells were treated with DMSO, 7FTA, TNFa or 7FTA+TNFa in three replicates for each condition.

first: Xiaohui

last: Zhao

first: Kathryn

last: Stein

first: Steven

last: Head

first: John

last: Shimashita

first: Aishwarya

last: Sundaresan

first: Padmaja


title: Human Germline Heterozygous Gain-of-Function STAT6 Variants Cause Severe Allergic Disease

city: Vancouver

first: Stuart

last: Turvey

state: BC

address: 938 W 28th Ave

institute: BC Children's Hospital Research Institute

summary: We descrie a cohort of 10 families, with 16 patients, that presented with severe early onset allergic disease since birth. Disease inhertance was in an autosomal dominant manner and heterozygous variants in STAT6 were identified in all patients. Whole blood bulk RNAsequencing was done on patient 6 to understand treatment specific transcriptomic changes in this patient.

overall_design: Bulk RNA sequencing was done on Jurkat T cell transduced with Wild-Type STAT6, p.E382Q STAT6, and p.D419G STAT6. These cells were either left untreated or stimulated with IL-4 (100ng/mL) for 4 hours

first: Mehul

last: Sharma

first: Maggie

last: Fu

first: Ashish


title: The N-terminal extension of Arabidopsis ARGONAUTE 1 is essential for microRNA activities [sRNA-seq]

first: Ye

last: Xu

state: CA

first: Xuemei

last: Chen


title: The N-terminal extension of Arabidopsis ARGONAUTE 1 is essential for microRNA activities [mRNA]


title: Function of BRD9 during osteoclastogenesis [ChIP-Seq]

city: Shanghai

first: Jiahui

last: Du

address: Zhizaoju Road 639

institute: Shanghai Jiao Tong University

summary: We show that BRD9 suppresses osteoclastogenesis through negative feedback mechanism.

overall_design: We detected the function of BRD9 in bone marrow-derived monocytes (BMDMs) during osteoclastic differentiation with M-CSF and RANKL.


title: Function of BRD9 during osteoclastogenesis [RNA-seq-2]


title: Function of BRD9 during osteoclastogenesis [ATAC-seq]


title: Function of BRD9 during osteoclastogenesis


title: Pro-fibrotic and pro-inflammatory genes driven by steroid hormone imbalance in the prostate

city: Norfolk

first: Petra

last: Popovics

state: Virginia

address: 651 Colley Avenue Room 422

institute: Eastern Virginia Medical School

summary: The study involved analysis of the effect of testosterone and estradiol hormone pellet implantation with the mouse fibrosis Nanostring panel

overall_design: Mice were implanted with 25 mg testosterone and 2.5 mg estradiol slow-release pellets or underwent sham surgery. Prostates were collected two weeks later.

first: William

last: Ricke


title: HIV-1 integration in microglia (ChIP-seq of CTCF-KD/-NT)

city: Heidelberg

first: Carl

last: Herrmann

address: INF 267

department: Medical Faculty

institute: University Heidelberg

summary: We performed ChIP-seq in a microglia cell line (C20) upon CTCF-KD and CTCF-NT (wild-type) to understand the impact of CTCF loss on chromatin and HIV-1 integration pattern in the C20 cell line.

overall_design: ChIP-seq from the C20 cell line on the histone modifications H3K36me3 and on CTCF (and the respective inputs) for the CTCF-KD and NT.

first: Marina

last: Lusic

first: Bojana

last: Lucic


title: Genome-wide CRISPR/Cas9 Screens Reveal Shared and Bespoke Mechanisms of Resistance to SHP2 Inhibition

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

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

overall_design: Refer to individual Series


title: HIV-1 integration in microglia (RNA-seq)

summary: We performed RNA-seq in a microglia cell line (C20). Our aim was to understand how expression in the uninfected state will impact integration site selection on microglia.

overall_design: RNA-seq from microglia (C20 cell line)


title: Human Germline Heterozygous Gain-of-Function STAT6 Variants Cause Severe Allergic Disease [bulk_RNAseq]

city: Hongkong

first: Zhongyi

last: Liu

state: Hongkong

address: L7-55 Paediatrics, Lab Block, Faculty of Medicine, 21 Sassoon Road, Pokfulam, HK

institute: The University of Hong Kong

overall_design: Whole blood RNA sequencing was done on 10 samples: 1 patient sample before Dupilumab treatment initiation, 4 patient samples post Dupilumab treatment initiation, and 5 healthy controls

first: Daniel

last: Leung

first: Yu

last: Lau


sample_organism:
Homo
Homo sapiens

platform_organism:
Homo
Homo sapiens


title: HIV-1 integration in microglia (ATAC-seq)

summary: We performed ATAC-seq in a microglia cell line (C20) to assess chromatin accessibility alterations upon HIV-1 infection in latent and active status in comparison with the uninfected status.

overall_design: ATAC-seq of 3 sorted cell populations in C20 cell line infected with HIVGKO reporter virus: uninfected cells (eGFP-mKO2-), actively infected (eGFP+mKO2+) and latently infected (eGFP-mKO2+).


title: HIV-1 integration in microglia (ChIP-seq)

summary: We performed ChIP-seq in a microglia cell line (C20) to understand integration patterns of HIV-1. We characterised the uninfected epigenetic cellular landscape in order to assess how integration is affected by distinct chromatin states and to understand the features defining integration-permissible regions.

overall_design: ChIP-seq from the C20 cell line on the histone modifications H3K9me3, H3K4me1, H3K27me3, H3K36me3, H3K9me2, and H3K27ac (and the respective inputs)


title: HIV-1 integration in microglia (LM-PCR)

summary: We performed LM-PCR in an infected microglia cell line (C20) to map HIV-1 integration sites. Our aim was to compare the IS obtained through this method with ChIP-seq, ATAC-seq, and RNA-seq data obtained in the uninfected cells, allowing the assessment of integration preferences.

overall_design: LM-PCR of the C20 cell line infected with HIV-1.


title: Sensory nerves in melanoma impede the formation of tertiary lymphoid structures and anti-tumor immune responses

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd.

department: Department of Biomedical Informatics

institute: University of Pittsburgh

summary: Utilizing surgical and chemical skin sensory denervation methods, we show that afferent neurons support the growth of melanoma tumors in vivo. We demonstrate that sensory innervation limits the activation of effective anti-tumor immune response. Specifically, sensory ablation led to improved leukocyte recruitment and infiltration into tumors, decreased intratumoral lymphoid and myeloid immunosuppressive cells, and the activation of T effector cells within the TME. We found that cutaneous sensory nerves hinder the maturation of intratumoral high endothelial venules and the formation of mature tertriary lymphoid-like structures containing organized clusters of CD4+ T cells and B cells. Denervation further increased T cell clonality and expanded the B cell repertoire in the TME. Importantly, CD8a depletion prevented the denervation-dependent anti-tumor effects. Finally, we observed that the gene signatures associated with immune function and sensory innervation were inversely correlated in human primary cutaneous melanomas, and the latter was a negative prognostic marker of the overall survival in the examined cohort. Our results suggest that tumor-associated sensory neurons negatively regulate the development of effective anti-tumor immune responses, thereby defining a novel target for therapeutic intervention in the cancer setting.

overall_design: mRNA profiles of innervated versus denervated B16F10 tumors established in C57Bl/6 mice.

first: Yuri

last: Bunimovich

first: Kavita

last: Vats

first: Vishal

last: Soman


title: Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [RNA-Seq]

city: Charlestown

first: Rui

last: Dong

address: 149 13th Street

institute: Massachusetts General Hospital

summary: Intrinsically disordered regions (IDRs) in DNA-associated proteins have recently been shown to play important roles in gene regulation. To better understand these domains we developed an antibody-independent assay to map disordered proteins genome-wide by combining b-isox mediated precipitation and next-generation sequencing (DisP-seq, disordered protein precipitation followed by DNA sequencing).  We first analyzed Ewing sarcoma cells as a proof of principle given that the prion-like IDR of the oncogenic fusion protein EWS-FLI1 has been shown to play a critical role in this cancer. We find that DisP-seq produces thousands of strong peaks associated with diverse chromatin states in Ewing sarcoma and other cell types tested. These locations are highly enriched for DNA binding motifs matching EWS-FLI1 and other transcription factors with prominent IDRs. Moreover, depletion of EWS-FLI1 in Ewing sarcoma cells leads to a widespread reorganization of DisP-seq signals, including decreases at EWS-FLI1 binding sites and marked increases at sites associated with mesenchymal differentiation. Analysis of these new DisP-seq signals shows that they arise from redistribution of the transcription factor NFIB, which initially overlaps EWS-FLI1 and has an IDR that is required for proper localization and function. Our results thus show that antibody-independent precipitation mapping can enable genome-wide profiling and identification of disordered transcription factors to uncover their roles in complex gene regulation programs.

overall_design: Examination of gene expression in Ewing sarcoma SKNMC cells (empty expression vector, NFIB wildtype expression vector and NFIB deletion expression vector).

first: Yu-Hang

last: Xing

first: Miguel

last: Rivera


title: A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

summary: Plants often generate secondary metabolites with antifungal properties as defense mechanisms against parasites. Although some fungi may potentially overcome the barrier of antimicrobial compounds, only a limited number of examples and molecular mechanisms of resistance have been reported. Here, we found an Aglaia plant-parasitizing fungus that overcomes the toxicity of rocalgates, which are translation inhibitors synthesized by the plant, through an amino acid substitution in a translation initiation factor (eIF). De novo transcriptome assembly of the fungus revealed that eIF4A, a molecular target of rocaglates, replaces a critical amino acid in the rocaglate binding site. Moreover, genome-wide ribosome profiling harnessing a cucumber-infecting fungus, Colletotrichum orbiculare, demonstrated that the translational inhibitory effects of rocaglates were largely attenuated by the mutation found in the Aglaia parasite. The engineered Colletotrichum orbiculare showed a survival advantage on cucumber plants with rocaglates. Our study exemplifies a plant-fungus tug-of-war centered on secondary metabolites produced by host plants.

overall_design: Ribosome profiling and RNA-Seq of Colletotrichum orbiculare treated with aglafoline

first: Mingming

last: Chen

first: Naoyoshi

last: Kumakura

first: Hironori

last: Saito

first: Ryan

last: Muller

first: Madoka

last: Nishimoto

first: Mari

last: Mito

first: Pamela

last: Gan

first: Nicholas

middle: T

last: Ingolia

first: Ken

last: Shirasu

first: Takuhiro

last: Ito

first: Yuichi

last: Shichino


title: Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [ChIP-seq]

overall_design: Examination of histone markers and transcription factors in small cell lung cancer NCI-H446 cells (wildtype, shGFP control and NFIB knockdown) and Ewing sarcoma SKNMC cells (wildtype; shGFP control, EWS-FLI1 knockdown; empty expression vector, NFIB wildtype expression vector and NFIB deletion expression vector).


title: Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [DisP-Seq]

overall_design: DisP-seq profiles of small cell lung cancer NCI-H446 cells (wildtype, shGFP control and NFIB knockdown), Ewing sarcoma SKNMC cells (wildtype; shGFP control, EWS-FLI1 knockdown; empty expression vector, NFIB wildtype expression vector and NFIB deletion expression vector) and wild type embryonic fibroblast MRC5 cells.


title: Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [ATAC-seq]

overall_design: We examined chromatin structure using ATAC-seq in small cell lung cancer NCI-H446 cells (wildtype, shGFP control and NFIB knockdown) and Ewing sarcoma SKNMC cells (wildtype; shGFP control, EWS-FLI1 knockdown; empty expression vector, NFIB wildtype expression vector and NFIB deletion expression vector).


title: Targeting Glutaminolysis Shows Efficacy in Both Prednisolone-Sensitive and in Metabolically Rewired Prednisolone-Resistant B-Cell Childhood Acute Lymphoblastic Leukaemia Cells

status: Public on Feb 19 2023

city: Plovdiv

first: Yordan

last: Sbirkov

address: 15 A Vassil Aprilov Blvd

department: Medical Biology

country: Bulgaria

institute: Medical University of Plovdiv

summary: In spite of the considerable progress in risk stratification and therapeutic regimens in childhood acute lymphoblastic leukaemia (cALL), which has led to cure rates of above 90%, prognosis for patients with relapsed disease remains poor. The main cause of therapy failure is drug resistance, most commonly to glucocorticoids (GCs). While alterations of cell metabolism in cALL are considered a hallmark of this malignancy as well, the molecular differences between prednisolone sensitive and resistant lymphoblasts are not well-studied, thereby precluding the development of novel and targeted therapies. Therefore, the aim of this work was to investigate the biology of matched pairs of cell lines where GCs are effective and such with acquired lack of response to prednisolone. In order to address this, we took advantage of the molecular characterisation of an in vitro model of GC resistance we had previously developed. An integrated transcriptomic and metabolomic analysis revealed alterations in oxidative phosphorylation, glycolysis, amino acid, pyruvate and nucleotide biosynthesis, as well as activation of mTORC1 and MYC signaling, which are also known to control cell metabolism. In attempt to explore the potential therapeutic effect of inhibiting one of the hits from our analysis, we targeted the glutamine-glutamate-α-ketoglutarate axis by three different strategies, all of which impaired mitochondrial respiration and ATP production and induced apoptosis in both GC-sensitive and resistant cell lines. In summary, we report that prednisolone resistance may be accompanied by considerable rewiring of transcriptional and biosynthesis programs. We suggest that targeting glutamine metabolism presents a novel therapeutic approach in cALL.

overall_design: Comparing biological triplicates of prednisolone sensitive (Sup-B15) and resistant (Sup-PR) childhood acute lymphoblastic leukaemia cells.


title: Ensheathing glia promote healthy brain aging

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Drosophila ensheathing glia decline in relative numbers during normal aging. Using p35, we inhibit apoptosis specifically in ensheathing glia, and show that this is sufficient to rescue the decline in ensheathing glia, improve neuromotor performance of aged flies, and increase lifespan. Remaining ensheathing glia from aged brains exhibit transcriptomes exhibiting signs of lipid metabolism and apoptosis dysregulation. Expanding ensheathing glia with p35 also prevented the accumulation of amyloid plaques and delayed premature death in a fly model of Alzheimer's disease.

overall_design: Transcriptomes of Drosophila brains or sorted ensheathing glia or astrocytes from Drosophila brains were sequenced and analyzed. Samples come from whole brains (3 replicates each at ages d5 and d70 for each driver line of 10E12, 56F03, and 86E01 - 18 samples), sorted ensheathing glia (3 replicates each at ages d5 and d70 for each driver line of 10E12 and 56F03 - 12 samples), and sorted astrocytes (3 replicates each at ages d5 and d70 from driver line 86E01 - 6 samples). Total: 36 samples.

first: Lihong

last: Sheng

first: Roberto

last: Bonasio


title: Function of BRD9 during osteoclastogenesis [RNA-seq]

first: Jiahui

last: Du

overall_design: We detected the function of BRD9 in bone marrow-derived monocytes (BMDMs) during osteoclastic differentiation with M-CSF and RANKL.


title: LncRNA/mRNA expression profile of rat bone marrow mesenchymal stem cells (BMSCs) under hypoxia condition

status: Public on Feb 18 2023

city: Guiyang

first: Tao

last: Wang

state: Guizhou

address: 9 Beijing Road

institute: Guizhou Medical University

summary: The osteonecrotic area of steroid-induced avascular necrosis of the femoral head (SANFH) is a hypoxic microenvironment that leads to apoptosis of transplanted bone marrow mesenchymal stem cells (BMSCs). However, the underlying mechanism remains unclear. Here, we explore the mechanism of hypoxic-induced apoptosis of BMSCs, and use the mechanism to improve the transplantation efficacy of BMSCs. We analyzed LncRNA/mRNA expression profile of BMSCs under hypoxia conditions, and successfully screened the key long non-coding RNA AABR07053481 (LncAABR07053481) which mediated hypoxic apoptosis of BMSCs, we further determined its regulatory mechanism. Importantly, overexpression of LncAABR07053481 can improve the survival rate and repair efficacy of BMSCs under hypoxia conditions.

overall_design: In this study, BMSCs were treated under normoxia and hypoxia conditions for 48 h respectively, with 3 biological replicates in each group. Then, the cells were lysed to collect total RNA.

first: Fei

last: Zhang

first: Wuxun

last: Peng


title: Spatiotemporal transcriptomes of mouse embryo

first: Ji

last: Qi

state: Shanghai

address: E401, Life Science Building, Jiangwan Campus, Fudan University, 2005 Songhu Rd.

department: School of Life Sciences

institute: Fudan University

summary: We performed spatial transcriptome sequencing of mouse embryos to provide spatial cell atlas of mouse organogenesis.

overall_design: C57BL/6 mouse embryos at the stages of E9.5, E10.5, E11.5 and E12.5 on 10X Visium platform

first: Yamao

last: Chen

first: Shengyu

last: Zhou

first: Ming

last: Li

first: Fangqing

last: Zhao


title: An HNRNPC-PABPC4 axis governs translational control from the nucleus

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

overall_design: Refer to individual Series


title: Monocyte - neutrophil interplay drives mesenchymal transition in GBM

first: Dolores

last: Hambardzumyan

state: NY

address: 1425 Madison Ave.

department: Oncological Sciences

institute: Icahn School of Medicine

summary: Myeloid cells comprise the majority of immune cells in tumors, where their content and composition is not only driver mutation-specific, but also tumor type-dependent. While these cells are essential for shaping the tumor microenvironment, promoting tumor growth, and contributing to therapeutic resistance, targeting tumor-associated myeloid cells, including bone-marrow-derived monocytes and neutrophils, has not been successful. To eliminate monocyte recruitment, we employed CRISPR/Cas9-based methods to delete the region on murine chromosome 11 harboring the monocyte chemoattractant protein family (MCP) genes, Ccl2, Ccl7, Ccl8, Ccl12, and Ccl11, which we termed qMCP-KO. Using these qMCP-knockout mice in combination with genetically engineered mouse models (GEMM) of glioblastoma (GBM),  we investigated myeloid infiltraion by sc-RNA seq. We found that when monocyte infiltraion was abolisehd, a compensatory influx of nuetrophil in these tumor occured. These neutrophil promote tumor growth by releasing TNF, contributing to tumor hypoxic responses and aggression.

overall_design: We induced de novo brain tumor in WT, qMCP-KO mice of both genders. We isolated brain tumor cells at the humane endstage of these mice and ran sc-RNA seq on these cells to compare their functional differences.

first: Zhihong

first: Alexander

middle: M

last: Tsankov

first: Bruno

last: Giotti


title: Human Germline Heterozygous Gain-of-Function STAT6 Variants Cause Severe Allergic Disease [scRNAseq]

first: Zhongyi

last: Liu

summary: We descrie a cohort of 10 families, with 16 patients, that presented with severe early onset allergic disease since birth. Disease inhertance was in an autosomal dominant manner and heterozygous variants in STAT6 were identified in all patients. Whole blood bulk RNAsequencing was done on patient 6 to understand treatment specific transcriptomic changes in this patient.

overall_design: Single cell RNA sequencing was done on PBMCs and enriched T cells from the patient sample pre- and two years post- dupilumab treatment, along with one age matched healthy control.

first: Mehul

last: Sharma

first: Maggie

middle: P

last: Fu

first: Ashish

first: Stuart

last: Turvey

first: Daniel

last: Leung

first: Yu

last: Lau


title: Identification of genes regulated by treatment with MEK inhibitor

city: Yufu

first: Naoki

last: Hijiya

state: Oita

address: 1-1, Idaigaoka Hasama-machi

department: Medicine

institute: Oita University

summary: In this study, we compared expression profiles between luciferase-expressing pancreatic cancer cell line MIA/luc with and without MEK inhibitor PD325901treatment in vivo.

overall_design: MIA/luc tumors treated with MEK inhibitor PD325901 (n = 4) vs those with vehicle only (n = 4)


title: Total RNA-Seq in control and TRAF4-overexpressing LNCaP cells

status: Public on Feb 17 2023

city: Houston

first: Huan

last: Meng

state: Texas

address: One Baylor Plaza BCM 130

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

summary: We reported the total gene expression in control and TRAF4-overexpressing LNCaP cells

overall_design: TRAF4 overexpressing or control LNCaP cells were analyzed by RNA-Seq.


title: scRNA-seq of cancer and CD8+ cells during early metastasis identifies targetable subpopulations and immune evasion mechanisms

city: Singapore

first: Yiqun Elaine

last: Cao

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: Profiling tumors at single-cell resolution provides an opportunity to understand complexities underpinning lymph-node metastases in head and neck squamous-cell carcinoma. Single-cell RNAseq (scRNAseq) analysis of cancer-cell trajectories identifies a sub-population of pre-metastatic cells, driven by actionable pathways including AXL and AURK. Blocking these two proteins blunts tumor invasion in patient-derived cultures. Furthermore, scRNAseq analyses of tumor-infiltrating CD8+ T-lymphocytes show two distinct trajectories to T-cell dysfunction, corroborated by their clonal architecture based on single-cell T-cell receptor sequencing. By determining key modulators of these trajectories, followed by validation using external datasets and functional experiments, we uncover a role for SOX4 in mediating T-cell exhaustion. Finally, interactome-analyses between pre-metastatic tumor-cells and CD8+ T-lymphocytes uncover a putative role for the Midkine pathway in immune-modulation and this is confirmed by scRNAseq of tumors from humanized mice. Aside from specific findings, this study demonstrates the importance of tumor heterogeneity analyses in identifying key vulnerabilities during early metastasis.

overall_design: Examining the tumor microenvironment of humanized mouse model of head and neck squamous cell cancer (HNSCC) treated with Pembrolizumab (anti-PD1)

first: Hong

last: Quah

first: Elaine

middle: Y

first: N

middle: G

last: Iyer


title: Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping

first: Rui

last: Dong

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


title: Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila [CUT&RUN]

city: Planegg-Martinsried

first: Nicolas

last: Gompel

address: Grosshaderner Str. 2

department: Faculty of Biology

institute: Ludwig Maximilian University of Munich

summary: The loss of discrete morphological traits, the most common evolutionary transition, is typically driven by changes in expression of developmental genes. Mutations accumulating in regulatory elements of these genes can disrupt DNA binding sites for transcription factors patterning their spatial expression, or delete entire enhancers. Regulatory elements, however, may in principle be silenced through other mechanisms, including changes in chromatin accessibility, or the emergence of repressive elements. Here, we show that an increase in chromatin accessibility at the pigmentation gene yellow, combined with the gain of a repressor site, underlie the evolutionary loss of a spot pigmentation pattern on the wings of a Drosophila species. The evolutionary gain of accessibility of this repressive element is regulated by E93, a transcription factor governing the progress of metamorphosis. This convoluted evolutionary scenario contrasts with the classical parsimonious mutational paths generally envisioned and often documented for morphological losses. It illustrates for the first time how evolutionary changes in chromatin accessibility may directly contribute to morphological diversification.

overall_design: We profiled the signal enrichment of H3K27ac at the stage (67% of pupal development) when spot activity was repressed in D. melanogaster using CUT&RUN.

first: Liucong

last: Ling


title: Profiling cancer cells during early metastasis identifies targetable subpopulations [cell line scRNA-seq]

summary: Profiling tumors at single-cell resolution provides an opportunity to understand complexities underpinning lymph-node metastases in head and neck squamous-cell carcinoma. Single-cell RNAseq (scRNAseq) analysis of cancer-cell trajectories identifies a sub-population of pre-metastatic cells, driven by actionable pathways including AXL and AURK. Blocking these two proteins blunts tumor invasion in patient-derived cultures. This study demonstrates the importance of tumor heterogeneity analyses in identifying key vulnerabilities during early metastasis.

overall_design: Examining the primary and metastatic cell cultures derived from treatment-naïve patients with head and neck squamous cell cancer (HNSCC)


title: Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila [greenCUT&RUN]

overall_design: We profiled genome wide binding sites of Eip93F (E93) at the stage (72% of pupal development) when spot activity was repressed in D. melanogaster using a modified CUT&RUN: greenCUT&RUN.


title: Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila.

sample_organism:
Drosophila melanogaster
Drosophila biarmipes


title: Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila [ATAC-seq]

summary:
The loss of discrete morphological traits, the most common evolutionary transition, is typically driven by changes in expression of developmental genes. Mutations accumulating in regulatory elements of these genes can disrupt DNA binding sites for transcription factors patterning their spatial expression, or delete entire enhancers. Regulatory elements, however, may in principle be silenced through other mechanisms, including changes in chromatin accessibility, or the emergence of repressive elements. Here, we show that an increase in chromatin accessibility at the pigmentation gene yellow, combined with the gain of a repressor site, underlie the evolutionary loss of a spot pigmentation pattern on the wings of a Drosophila species. The evolutionary gain of accessibility of this repressive element is regulated by E93, a transcription factor governing the progress of metamorphosis. This convoluted evolutionary scenario contrasts with the classical parsimonious mutational paths generally envisioned and often documented for morphological losses. It illustrates for the first time how evolutionary changes in chromatin accessibility may directly contribute to morphological diversification.
We profiled chromatin accessibility at selected stages in the pupal wings of D. melanogaster and D. biarmipes using ATAC-seq.

platform_organism:
Drosophila melanogaster
Drosophila biarmipes

overall_design: Chromatin accessibility was profiled at five time points during pupal development based on the expression dynamics of yellow in the wings of both species. The five time points include: 0%, 48%, 60%, 69%, and 78% of pupal development. Two biological replicates were prepared for each stage.


title: Human Hematopoietic Stem Cell Vulnerability to Ferroptosis [scRNA-seq]

city: Boston

first: Jiawei

last: Zhao

state: Massachusetts

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: To investigate differential gene expression of CD34+CD45RA-CD90+ cells with MYSM1 deficiency achieved by CRISPR editing

overall_design: Single cell transcriptomic profiling of CD34+CD45RA-CD90+ cells edited by AAVS1 and MYSM1 guide RNAs

first: Vijay

last: Sankaran


title: A point mutation in the kinase domain of CRK10 leads to xylem vessel collapse and activation of defence responses in Arabidopsis

city: Harpenden

last: Smith

state: Hertfordshire

address: West Common

department: IDE

institute: Rothamsted Research

summary: Cysteine-rich receptor-like kinases (CRKs) are a large family of plasma membrane-bound receptors ubiquitous in higher plants. However, despite their prominence, their biological roles have remained largely elusive so far. In this study we report the characterization of an Arabidopsis mutant named crk10-A397T in which alanine 397 has been replaced by a threonine in the αC helix of the kinase domain of CRK10, known to be a crucial regulatory module in mammalian kinases. The crk10-A397T mutant is a dwarf that displays collapsed xylem vessels in the root and hypocotyl, whereas the vasculature of the inflorescence develops normally. In situ phosphorylation assays with His-tagged wild type and crk10-A397T versions of the CRK10 kinase domain revealed that both alleles are active kinases capable of autophosphorylation, with the newly introduced threonine acting as an additional phosphorylation site in crk10-A397T. Transcriptomic analysis of wild type and crk10-A397T mutant hypocotyls revealed that biotic and abiotic stress-responsive genes are constitutively up-regulated in the mutant, and a root-infection assay with the vascular pathogen Fusarium oxysporum demonstrated that the mutant has enhanced resistance to this pathogen compared with wild type plants. Taken together our results suggest that crk10-A397T is a gain-of-function allele of CRK10, the first such mutant to have been identified for a CRK in Arabidopsis.

overall_design: Expression analysis of WT and CRK10 mutant hypocotyls at day 15, day 21 and day 35 after germination

first: Maiara

last: Piovesana

first: Michaela

last: Matthes


title: Human Hematopoietic Stem Cell Vulnerability to Ferroptosis [Ribosome profiling]

summary:
To investigate the translatome change due to loss of MYSM1 in CD34+CD45RA-CD90+ cells
We performed ribosome profiling followed by NGS sequencing where only ribosome protected RNA was extracted to make the library, which mostly are in active translation

overall_design: comparative ribosome profiling assay of MYSM1 or AAVS1 edited CD34+CD45RA-CD90+ cells with three biological replicates of each group


title: A druggable signaling hub of choroid plexus immune-secretory function

city: New Haven

first: Kristopher

last: Kahle

state: Connecticut

address: 333 Cedar St

institute: Yale University Department of Neurosurgery

summary: Integrated multi-omics investigation of novel rat models of acquired hydrocephalus, Blood or bacteria in CSF trigger similar choroid plexus (ChP) immune-secretory responses, Crosstalk between ChP immune and epithelial cells drives CSF hypersecretion and ventriculomegaly, Repurposed systemic immunomodulators ameliorate acquired hydrocephalus, Identification of a druggable hub of ChP function relevant for multiple neurological diseases.

overall_design: Examine the effect of IVH and LPS on ChP

first: Emre

last: Kiziltug

first: Stephanie

last: Robert

first: Ben

last: Reeves


title: Single-cell RNA sequencing identifies hippocampal microglial dysregulation in diet-induced obesity

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

summary: Obesity is a growing global concern in adults and youth along with a parallel rise in associated complications, including cognitive impairment. Obesity induces brain inflammation and activates microglia, which contribute to cognitive impairment by aberrantly phagocytosing synaptic spines. Local and systemic signals, such as inflammatory cytokines and metabolites likely participate in obesity-induced microglial activation. However, the precise mechanisms mediating microglial activation during obesity remain incompletely understood. Herein, we leveraged our mouse model of high-fat diet (HFD)-induced obesity, which mirrors human obesity, and develops hippocampal-dependent cognitive impairment. We assessed hippocampal microglial activation by morphological and single-cell transcriptomic analysis to evaluate this heterogeneous, functionally diverse, and dynamic class of cells over time after 1 and 3 months of HFD. HFD altered cell-to-cell communication, particularly immune modulation and cellular adhesion signaling, and induced a differential gene expression signature of protein processing in the endoplasmic reticulum in a time-dependent manner.

overall_design: Single cell RNA sequencing analysis of microglia isolated from hippocampus of either a 60% HFD enriched with saturated fatty acids (HFD) or a control diet containing 10% fat (SD) beginning at 5-wk-old male C57BL/6J mice. To determine time-dependent changes in microglia in response to HFD, mice were divided into two cohorts and fed for 1 mo or 3 mo. Hashtagging was used to multiple cells from three animals into each run.

first: Eva

middle: L

last: Feldman


title: Alternative Splicing of HDAC7 Regulates its Interaction with 14-3-3 Proteins to Alter Histone Marks and Target Gene Expression

first: Kristen

last: Lynch

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

summary: Epigenetics  and  Alternative  Splicing  are  both  critical  mechanisms  guiding  gene  expression.  Several  studies  have  demonstrated  that  epigenetic  marks  can  influence alternative  splicing decisions,  but  less  is  known  about  how  alternative  splicing may  impact epigenetics.  Here,  we demonstrate  that  several  genes  encoding  histone  modifying  enzymes  are  alternatively  spliced downstream  of  T  cell  activation  signaling  pathways,  including HDAC7, a  gene  previously implicated in controlling gene expression programs and differentiation in T cells. Using CRISPR-Cas9 gene  editing  and  cDNA  expression,  we  show  that  differential  inclusion  of HDAC7 exon  9 controls  the  interaction  of  HDAC7  with  protein  chaperones  with  resulting  impact  on  histone modifications  and  gene  expression.  Notably,  the  long  isoform,  which  is  favored  upon  JNK signaling,  promotes  expression  of  several  critical  T  cell  surface  proteins  including  CD3,  CD28, CD69.  Thus,  we  demonstrate  that  alternative  splicing  of HDAC7 has  a  global  impact  on epigenetics and gene expression, and may contribute to T cell regulation.

overall_design: To investigate the functional consequences of HDAC7 exon 9 pre-mRNA alternative splicing, we utilized CRISPR-Cas9 technologies to establish Jurkat T cell lines that endogenously express the HDAC7 protein with or without exon 9 encoded peptide (isoforms termed iE9 or dE9, respectively). We then performed gene expression profiling analyses using data obtained from polyA-selected RNA-seq of 3 different HDAC7 genotypes (wild type, iE9 and dE9) at two time points (0 hr vs 48 hr post-PMA stimulation). Differential gene expression analyses were performed by comparing a) WT Jurkat cells vs iE9 or dE9 cells (matched by time point), b) stimulated vs unstimulated condition (matched by cell line), and c) iE9 vs dE9 cells (matched by time point).

first: Laura

last: Agosto

first: Max

last: Ferretti


title: In vivo analysis of circRNA expression alterations in response to influenza virus infection

city: Fuzhou

first: JiLong

last: Chen

address: Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University

summary: Our study's objective was to determine circRNA expression alterations following in vivo influenza virus infection. We challenged C57BL/6 for 48 hours with IAV-PR8. Lung samples were obtained, RNA-Seq was utilized, and the circRNAs transcriptome data was compared to the control.

overall_design: Ten SPF C57BL/6 mice were divided into two groups (mock-infected and IAV PR8 infected). The infected group was inoculated with 1x104 PFU/ml of IAV PR8 viral stock through intranasal instillation. Mice were euthanized, and lung samples were collected 48 hours post-infection (hpi). Mice lungs were sent for circRNAs transcriptome analysis RNA-Seq by Shanghai OE Biotech Co., Ltd. (Shanghai, China) using an Illumina NovaSeq 6000 instrument.

first: Chen

last: Yuhai

first: Maarouf

last: Mohamed

last: Ji-Long


title: Bulk RNA-seq of interleukin-23 receptor (IL-23R) -deficient and IL-23R-sufficient colonic mouse regulatory T cells

city: Nashville

first: Justin

last: Jacobse

state: Tennessee

address: 2215 Garland Avenue

institute: Vanderbilt University Medical Center

summary: To define the IL-23R-dependent changes in intestinal regulatory T cells (Treg cells) that might contribute to the impact on Treg cell function and selective advantage

overall_design: RNA-seq of flow cytometry sorted colonic Treg cells (live CD45+CD4+Foxp3+ from colon lamina propria) from Foxp3YFP-Cre (wt) and Il23rflflFoxp3YFP-Cre (ko) mice. Colonic Treg cells from multiple mice were pooled; each replicate (n=3 per group)  is reflective of at least 5 mice.

first: Jeremy

last: Goettel