title: Histone bivalency regulates the timing of cerebellar granule cell development in vivo [RNA-seq]

summary: Developing neurons undergo a progression of morphological and gene expression changes as they transition from neuronal progenitors to mature, multipolar neurons. Here we use RNA-seq and ChIP-seq to analyze how chromatin modifications control gene expression in a specific type of CNS neuron, the mouse cerebellar granule cell (GC). We find that in proliferating GC progenitors, H3K4me3/H3K27me3 bivalency is common at neuronal genes and undergoes dynamic changes that correlate with gene expression during migration and circuit formation. Inhibiting H3K27 methyltransferases EZH1 and EZH2 in vitro and in organotypic cerebellar slices dramatically altered the expression of bivalent genes and induced the downregulation of migration-related genes and upregulation of synaptic genes, inhibited glial-guided migration and accelerated dendrite formation. These data show that histone bivalency is required to regulate the timing of the progression from progenitor cells to mature neurons.

overall_design: Gene expression profiling of mouse cerebellar granule cells

first: Eve-Ellen

last: Govek

first: Matthew

middle: R

last: Paul

first: C

last: Allis

first: Mary

middle: E

last: Hatten


title: Histone bivalency regulates the timing of cerebellar granule cell development in vivo [ChIP-seq]

status: Public on Feb 06 2023

city: New York

first: Kärt

last: Mätlik

state: NY

address: 1230 York Ave

country: USA

institute: Rockefeller University

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: H3K4me3 and H3K27me3 ChIPseq in postnatal mouse cerebellar granule cells

middle: D


title: Single-cell genomics improves the discovery of risk variants and genes of Atrial Fibrillation [snRNA-seq]

status: Public on Feb 12 2023

city: Chicago

first: Sebastian

last: Pott

state: IL

address: 920 E 58th St

institute: The University of Chicago

type: Expression profiling by high throughput sequencing

summary: Genome-wide association studies (GWAS) have linked hundreds of loci to cardiac diseases. However, in most loci the causal variants and their target genes remain unknown. We developed a combined experimental and analytical approach that integrates single cell epigenomics with GWAS to prioritize risk variants and genes. We profiled accessible chromatin in single cells obtained from human hearts and leveraged the data to study genetics of Atrial Fibrillation (AF), the most common cardiac arrhythmia. Enrichment analysis of AF risk variants using cell-type-resolved open chromatin regions (OCRs) implicated cardiomyocytes as the main mediator of AF risk. We then performed statistical fine-mapping, leveraging the information in OCRs, and identified putative causal variants in 122 AF-associated loci. Taking advantage of the fine-mapping results, our novel statistical procedure for gene discovery prioritized 45 high-confidence risk genes, highlighting transcription factors and signal transduction pathways important for heart development. We further leveraged our single-cell data to study genetics of gene expression. An unexpected finding from earlier studies is that expression QTLs (eQTLs) are often shared across tissues even though most regulatory elements are cell-type specific. We found that this sharing is largely driven by the limited power of eQTL studies using bulk tissues to detect cell-type-specific regulatory variants. This finding points to an important limitation of using eQTLs to interpret GWAS of complex traits. In summary, our analysis provides a comprehensive map of AF risk variants and genes, and a general framework to integrate single-cell genomics with genetic studies of complex traits.

overall_design: snRNA-seq

first: Alan

last: Selewa

first: Kaixuan

last: Luo

first: Xin

last: He


title: Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons [ATAC-seq]

status: Public on Feb 13 2023

city: Baltimore

first: Andrew

middle: S.

last: McCallion

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary: To overcome the ethical and technical limitations of in vivo human disease models, the broader scientific community frequently employs model organism-derived cell lines to investigate of disease mechanisms, pathways, and therapeutic strategies. Despite the widespread use of certain in vitro models, many still lack contemporary genomic analysis supporting their use as a proxy for the affected human cells and tissues. Consequently, it is imperative to determine how accurately and effectively any proposed biological surrogate may reflect the biological processes it is assumed to model. One such cellular surrogate of human disease is the established mouse neural precursor cell line, SN4741, which has been used to elucidate mechanisms of neurotoxicity in Parkinson disease for over 25 years. Here, we are using a combination of classic and contemporary genomic techniques – karyotyping, RT-qPCR, single cell RNA-seq, bulk RNA-seq, and ATAC-seq – to characterize the transcriptional landscape, chromatin landscape, and genomic architecture of this cell line, and evaluate its suitability as a proxy for midbrain dopaminergic neurons in the study of Parkinson disease. We find that SN4741 cells possess an unstable triploidy and consistently exhibits low expression of dopaminergic neuron markers across assays, even when the cell line is shifted to the non-permissive temperature that drives differentiation. The transcriptional signatures of SN4741 cells suggest that they are maintained in an undifferentiated state at the permissive temperature and differentiate into immature neurons at the non-permissive temperature; however, they may not be dopaminergic neuron precursors, as previously suggested. Additionally, the chromatin landscapes of SN4741 cells, in both the differentiated and undifferentiated states, are not concordant with the open chromatin profiles of ex vivo, mouse E15.5 forebrain- or midbrain-derived dopaminergic neurons. Overall, our data suggest that SN4741 cells may reflect early aspects of neuronal differentiation but are likely not a suitable a proxy for dopaminergic neurons as previously thought. The implications of this study extend broadly, illuminating the need for robust biological and genomic rationale underpinning the use of in vitro models of molecular processes.

overall_design: 8 ATAC-seq samples: 4 from SN4741 cells cultured at 37C, 4 from SN4741 cells cultured at 39C

first: Rachel

middle: J

last: Boyd

first: Sarah

middle: A

last: McClymont

first: Nelson

middle: B

last: Barrientos

first: Paul

middle: W

last: Hook

first: William

last: Law

first: Rebecca

last: Rose

first: Eric

middle: L

last: Waite

first: Jay

last: Rathinavelu

first: Dimitrios

last: Avramopoulos

middle: S


title: scRNAseq gene expression profile of zebrafish jaw joint cells after IOM ligament transection.

status: Public on Feb 05 2023

first: Joanna

last: Smeeton

address: 650 W 168TH ST, ROOM 1103A, William Black Building

department: Rehabilitation and Regenerative Medicine

institute: Columbia University Irving Medical Center

summary: Adult zebrafish have the capacity to regenerate craniofacial ligament tissue following a complete transection injury. How this robust skeletal regeneration is achieved remains undefined. Here, we use single cell RNA sequencing to profile RNA expression from FACS sorted cranial neural crest lineage and non-cranial neural crest lineage cells (including skin and immune populations) in the first 3 days after ligament injury.

overall_design: To understand the cellular contributors and molecular regulation of craniofacial ligament regeneration in adult zebrafish, we collected jaw joint cells for single cell RNA sequencing following ligament injury. After IOM ligament transection injury and in uninjured and SHAM surgical controls, neural crest lineage cells (DsRed) and non-neural crest lineage cells (BFP) were isolated using Fluorescence-activated cell sorting (FACS) from jaw joints microdissected from Sox10:Cre;actb2:loxP-BFP-STOP-loxP-DsRed transgenic fish and analyzed using scRNAseq.


title: Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection

status: Public on Feb 08 2023

city: San Francisco

first: Joel

last: Ernst

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: UC, San Francisco

summary: Mycobacterium tuberculosis (Mtb) infects multiple lung myeloid cell subsets and persists despite innate and adaptive immune responses. However, the mechanisms allowing Mtb to evade elimination by these subsets are not fully understood. Here, we determined that four weeks post infection, after development of adaptive immune responses, CD11clo monocyte-derived lung cells termed MNC1 (mononuclear cell subset 1), harbor more live Mtb compared to alveolar macrophages (AM), neutrophils, and less permissive CD11chi MNC2. Bulk RNA-seq analysis for these subsets identified that lysosome biogenesis pathway is underexpressed in MNC1. Functional assays confirmed that Mtb-permissive MNC1 are deficient in lysosome content, lysosomal acidification, and lysosomal activity compared to AM, and have less nuclear TFEB, a master regulator of lysosome biogenesis. Mtb infection does not alter lysosome deficiency in MNC1. Instead, Mtb recruits MNC1 and MNC2 to the lungs for its spread from AM to these subsets, which depend on Mtb ESX-1 secretion system. Furthermore, nilotinib-mediated TFEB activation enhances lysosome function of primary macrophages in vitro, and MNC1 and MNC2 in vivo, improving control of Mtb infection. Our results suggest that Mtb exploits lysosome-poor monocyte-derived lung cells for persistence; targeting lysosome biogenesis may be an effective approach to host-directed therapy for tuberculosis, enabling permissive lung cells to restrict and kill Mtb through autophagy and other mechanisms.

overall_design: We performed transcriptomic analysis of four cell subtypes from M. tuberculosis infected mice

first: Weihao

last: Zheng

first: I-Chang

last: Chang

first: Jason

last: Limberis

first: Jonathan

middle: M

last: Budzik

first: B

last: Zha

first: Zach

last: Howard


title: Single cell quantification of ribosome occupancy in early mouse development

city: Austin

first: Can

last: Cenik

state: TX

address: Moffett Molecular Biology Building 2.122 2500 Speedway

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: Technological limitations precluded transcriptome-wide analyses of translation at single cell resolution. To solve this challenge, we developed a novel microfluidic isotachophoresis approach, named RIBOsome profiling via IsoTachoPhoresis (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key regulatory mechanism of genes involved in centrosome organization and N6-methyladenosine modification of RNAs. Our high coverage measurements enabled the first analysis of allele-specific ribosome engagement in early development and led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts with allelic-biased expression. Finally, by integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle stage oocytes is the predominant determinant of protein abundance in the zygote. The novel Ribo-ITP approach will enable numerous applications by providing high coverage and high resolution ribosome occupancy measurements from ultra-low input samples including single cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To study translation in mouse development, we performed our novel low-input ribosome profiling method (named Ribo-ITP) and RNA sequencing (Smart-seq3) in mouse oocytes and early stage embryos. To validate our method, we performed Ribo-ITP and conventional ribosome profiling using human K562 cells.
Ribosome profiling by isotachophoresis (Ribo-ITP) of single K562 cells

first: Hakan

last: Ozadam

first: Tori

last: Tonn

first: Crystal

last: Han

first: Alia

last: Segura

first: Ian

last: Hoskins

first: Shilpa

last: Rao

first: Vighnesh

last: Ghatpande

first: Duc

last: Tran

first: David

last: Catoe

first: Marc

last: Salit


title: Endogenous retrovirus MER50-derived enhancers confer the transcriptional regulation of human trophoblast syncytialization [ChIP-Seq]

status: Public on Feb 03 2023

city: Yangzhou

first: Cui

last: Du

state: Jiangsu

address: NO.88 University South Road

country: China

institute: Yangzhou University

summary: Multinucleated syncytiotrophoblasts (STBs), which are in direct contact with maternal blood, constitute the maternal-fetal interface critical for nutrient allocation, hormone production and immunological modulation during pregnancy. However, the genetic and epigenetic regulatory mechanisms governing trophoblast syncytialization remain largely elusive. We delineate that endogenous retroviruses (ERVs), which have been exapted as regulatory sequences for specific functional adaptations in placenta, profoundly rewire transcriptional program of trophoblast syncytialization. Here, we first determined dynamic bivalent ERV-derived enhancers with dual occupancy of H3K9me3 and H3K27ac in human trophoblast stem cells (hTSCs), which emerge as cell specific regulators of gene expression with markedly resolved H3K9me3 during differentiation towards STBs. Of note, bivalent enhancers derived from the Simiiformes-specific MER50 transposons were linked to a cluster of STB-specific genes. Importantly, depletions of MER50 elements adjacent to several STB genes, including MFSD2A, TNFAIP2 and RAI14, significantly attenuated their expression concomitant to dysregulated syncytium formation. Together, we propose that ERV-derived enhancers, MER50 specifically, fine-tune the transcriptional program accounting for human trophoblast syncytialization, which sheds light on novel epigenetic regulatory mechanisms underlying placental development.

overall_design: We generated ChIP-Seq and RNA-Seq data in this study. ChIP-Seq data are for H3K27ac, H3K4me3 in hTSC (human trophoblast stem cell) and differentiated STB(syncytiotrophoblast) at 24h, 48h. RNA-Seq data are for hTSC and STB at four time points: 24h, 48h, 72h, 96h.

first: Miao

last: Yu

first: Xiaoqian

last: Hu

first: Zihang

last: Pan

first: Wanshan

last: Zhen

first: Wenzhe

first: Xiaogang

last: Chen

first: Qibing

last: Yang

first: Wenbo

last: Deng

first: Jinhua

last: Lu

first: Haibin

last: Wang

first: Ming-an

last: Sun

first: Bin

last: Cao


title: Endogenous retrovirus MER50-derived enhancers confer the transcriptional regulation of human trophoblast syncytialization [RNA-Seq]


title: Expression data from lymphocytes (CD3+ cells) from severe, mild allergic patients and a non allergic group.

status: Public on Feb 02 2023

city: Boadilla del Monte

first: CARMELA

last: PABLO-TORRES JIMÉNEZ

state: Urbanización Montepríncipe

address: Urbanización Montepríncipe

country: Spain

institute: SAN PABLO CEU UNIVERSITY

summary:
The causes underlyed the acquisition and maintainance of a severe allergic phenotype remain unknown. Here, we study the cd3+ complete transcriptomic fingerprint from severity-stratified patients to understand the involvement of these cells in the development of severe allergy.
We used microarrays to detail the global programme of gene expression of CD3+ cells from severity-stratified allergic patients

overall_design: We recruited respiratory allergic patients and stratified them acording to severity. A non allergic group was also recruited. Blood samples were obtained by plateletpheresis. PBMCs were isolated by a ficoll graadient. CD3+ cells were isolated by magnetic bead separation. RNA was extracted from CD3+ cells and used for transcriptomics by affymetrix.

first: Carmela

last: Pablo-Torres

first: Martina

last: Romeo

first: Cristina

last: Gómez-Casado

first: José

last: Bueno-Cabrera

first: M

last: del Mar Reaño-Martos

first: Alfredo

last: Iglesias-Cadarso

first: Carlos

last: Tarín

first: Ioana

last: Agache

first: Tomas

last: Chivato

first: Domingo

last: Barber

first: María

last: Escribese

first: Elena

last: Izquierdo


title: Sex-biased gene and microRNA expression in the developing mouse brain is associated with neurodevelopmental functions and neurological phenotypes (RNA-Seq)

city: Dunedin

first: Susanna

last: Szakats

address: 270 Great King St

country: New Zealand

institute: University of Otago

summary: Compare miRNA expression between the sexes in normal mouse brain development at embryonic day 15.5 (E15.5).

overall_design: Small RNA-seq of 3 biological replicates per sex followed by differential expression analysis of known miRNAs.

first: Hugh

last: Cross

first: Megan

last: Wilson


title: Sex-biased gene and microRNA expression in the developing mouse brain is associated with neurodevelopmental functions and neurological phenotypes

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: MYC causes Suppression of Anti-Tumor Immune Response

status: Public on Feb 01 2023

city: Stanford

first: Renumathy

last: Dhanasekaran

address: 300 Pasteur Drive, Alway M211

institute: Stanford University

summary: Comparative transcriptional profiling of murine HCC with MYC activation and inactivation

first: Dean

last: Felsher


title: Yeast meiotic transcriptional profile

city: DC

first: Zachory

last: Park

state: Washington DC

address: 37th and O Streets NW

department: Biology

institute: Georgetown University

summary: RNAseq across a time cours of meiosis of cells with and without Kar4p. The overexpression of either IME1 or both IME1 and RIM4 was used to determine how overexpression of the two genes functions to resuce the meiotic defect associated with the loss of Kar4p.

overall_design: Samples were induced to sporulated and harvested across the first 12 hours of meiosis at 2-4 hour intervals. Each sample has two biological replicates.

first: Mark

last: Rose


title: Yeast meiotic transcriptom kar4 delete v. wild type

summary: Transcriptional profiling of wild type and kar4 deletion yeast mutants across a meiotic time course. Including samples with IME1 and RIM4 overexpression

overall_design: Time course of wild type and kar4 mutants across the first 12 to 16 hours of meiosis under varying genetic conditions including overexpression of IME1 and IME1/RIM4

first: Matthew

last: Remillard


title: single cell ATACseq of control and AngII challenged mouse ascending aorta

city: Houston

first: Yanming

last: Li

address: One Baylor Plaza

department: Michael E. DeBakey Department of Surgery

institute: Baylor College of Medicine

summary: OBJECTIVE: When aortic cells are under stress, such as increased hemodynamic pressure, they adapt to the environment by modifying their functions, allowing the aorta to maintain its strength. To understand the regulation of this adaptive response, we examined the transcriptomic and epigenomic programs in aortic smooth muscle cells (SMCs) during the adaptive response to angiotensin II (AngII) infusion and determined its importance in protecting against aortic aneurysm and dissection. APPROACH AND RESULTS: In wild-type mice, AngII infusion increased medial thickness in the thoracic aorta. Single-cell RNA sequencing analysis revealed an adaptive response in thoracic SMCs characterized by the upregulation of genes with roles in wound healing, elastin and collagen production, proliferation, migration, cytoskeleton organization, cell-matrix focal adhesion, and AKT and TGF-β signaling. Further single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) analysis showed increased chromatin accessibility at the regulatory regions of adaptive genes and revealed the mechanical sensor YAP/TEADs as a top candidate transcription complex driving the increased abundance of these gene transcripts (e.g., Lox, Col5a2 and Tgfb2). In cultured human aortic SMCs, cyclic stretch activated YAP, which directly bound to the regulatory regions of the adaptive genes (e.g., Lox) and increased the abundance of their transcripts. Finally, SMC-specific Yap deletion in mice compromised this adaptive response in SMCs, leading to an increased incidence of aortic aneurysm and dissection and a trend of increased rupture. CONCLUSIONS: Aortic stress triggers the systemic epigenetic induction of adaptive response (e.g., wound healing, proliferation, and matrix organization) in thoracic aortic SMCs, that depends on functional biomechanical signal transduction (e.g., YAP signaling). Our study highlights the importance of the adaptive response in maintaining aortic homeostasis and preventing aortic disease development in mice.

overall_design: Four-week-old male WT mice were fed with a high fat diet (HFD) for 8 weeks and AngII infusion during the last 4 weeks through an osmotic minipump were used to challenge the mice inducing aortic aneurysm and dissection. Mice fed a standard rodent laboratory diet for 8 weeks and infused with saline during the last 4 weeks were used as controls. We collected ascending aortic tissues after 7 days of AngII infusion for sc-ATACseq to capture the early response to aortic stress.

first: Chen

last: Zhang

first: Scott

last: LeMaire

first: Ying

middle: H

last: Shen


title: MYC-HCC treated with immunotherapy

summary: Murine MYC-HCC were treated with control IgG or anti PDL1 or anti CTLA4, or their combination. Tumors were sequenced using Nanostring IO360.

overall_design: Murine MYC-HCC were treated with control IgG or anti PDL1 or anti CTLA4, or their combination, 3 mice in each group. Tumors were sequenced using Nanostring IO360.


title: Evolution of antagonism among DUX family members from an ancestral toxic single homeodomain protein

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: Double homeobox genes are unique to eutherian mammals, transiently expressed in early blastomere-stage embryos, and comprise 3 clades (DUXA, B, and C) evolved by homeodomain duplication and divergence from an ancestral single homeobox gene, sDUX, present in non-eutherian mammals and other vertebrates.  We test platypus sDUX and find that it drives cellular phenotypes identical to DUX4, the human DUXC gene, including cytotoxicity and inhibition of myogenic differentiation.  sDUX binds DNA as a head-to-head dimer, showing near overlap of protein core and DNA to the DUX4-DNA crystal structure.  DUXA and sDUX bind both palindromic and nonpalindromic TAAT/TGAT double homeodomain motifs against DUX4 preference for non-palindromic.  Although DUXA lacks transcriptional activation potential, we find significant similarities in transcriptional and chromatin profiles of sDUX with DUX4 and DUXA-VP64, including expression of ZGA genes and LTR elements.  Furthermore, DUXA binds to a significant fraction of DUX4 target sites and is able to counteract transcriptional activation of DUX4 on its targets, potentiating a feedback inhibitory loop, including in cells from patients with facioscapulohumeral muscular dystrophy (FSHD).  The DUX gene family therefore comprises cross-regulating members of opposing function, with implications for their roles in ZGA, FSHD, and cancer.

overall_design: Doxycycline induced expression of DUX factor and uninduced control LHCN-M2 cells analyzed by RNA-seq and ATAC-seq with replicates.

first: Michael

last: Kyba

first: Darko

last: Bosnakovski


title: The transcription factor DUX4 orchestrates translational reprogramming by broadly suppressing translation efficiency and promoting expression of DUX4-induced mRNAs

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center


title: Evaluation of transcriptional changes in the duodenal tissue during acute pancreatitis

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

country: Germany

institute: Universitätsmedizin Greifswald

summary:
mRNA was isolated from duodenal tissue 3d after induction of acute pancreatitis in C57Bl/6 wild type mice to investigate transcriptional changes, untreated C57Bl/6 refer as controls
we used microarrays to investigate the duodenal barrier function during acute pancreatitis

overall_design: acute pancreatitis was induced by partial pancreatic duct ligation, duodenal tissue was removed 3d after onset of disease, mRNA was isolated by Trizol

first: Matthias

last: Sendler

first: Georg

last: Homuth

first: Frank

last: Ulrich Weiss


title: Expression Data from regulatory T-cells in a model of acute pancreatitis

summary:
Foxp3 positive regulatory T-cells were isolated by FACS from spleen of mice with acute pancreatitis induced by partial pancreatic duct ligation, mice without pancreatitis refer as controls
we used microarrays to investigate the activation of Tregs during acute pancreatitis

overall_design: We use FACS sorting to isolate Tregs by their GFP expression from DEREG mice which express GFP under the control of Foxp3, 3d after partial pancreatic duct ligation and untreated controls


title: Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability

status: Public on Feb 07 2023

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

address: 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, and as a translational repressor, but their functions in cells are incompletely understood. We have analyzed these questions by a combination of ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs.

overall_design: This study includes total 24 samples, 6 for ribosome profiling and 6 for RNA-Seq derived from duplicates of WT, dcp2D and dcp2-EE. Separately, total RNA of WT, dcp2, and xrn1 in duplicates,  were subjected to CAGE-Seq (6 samples) and total RNA-Seq (6 samples). All strains were grown in YPD at 30ºC till the OD600 ~0.6

first: Anil

last: Kumar Vijjamarri

first: Xiao

last: Niu

last: Vandermeulen

first: Chisom

last: Onu

first: Fan

first: Hongfang

last: Qui

first: Neha

last: Gupta

first: Swati

last: Gaikwad

first: Miriam

last: Greenberg

first: Paul

last: Cullen

first: Zhenguo

last: Lin


city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research


title: Therapeutic modulation of the blood-brain barrier and ischemic stroke by a bioengineered FZD4-selective WNT surrogate (bulk)

status: Public on Jan 31 2023

city: New York City

first: Lukas

last: Vlahos

state: New York

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

summary: Derangements of the blood-brain barrier (BBB) or blood-retinal barrier (BRB) occur in disorders ranging from stroke, cancer, diabetic retinopathy, and Alzheimer's disease. The Norrin/FZD4/TSPAN12 pathway activates WNT/-catenin signaling, which is essential for BBB and BRB function. However, systemic pharmacologic FZD4 stimulation is hindered by obligate palmitoylation and insolubility of native WNTs and suboptimal properties of the FZD4-selective ligand Norrin. Here, we developed L6-F4-2, a non-lipidated, FZD4-specific surrogate with significantly improved sub-picomolar affinity versus native Norrin. In Norrin knockout (NdpKO) mice, L6-F4-2 not only potently reversed neonatal retinal angiogenesis deficits, but also restored BRB and BBB function. In adult C57Bl/6J mice, post-stroke systemic delivery of L6-F4-2 strongly reduced BBB permeability, infarction, and edema, while improving neurologic score and capillary pericyte coverage. Our findings reveal systemic efficacy of a bioengineered FZD4-selective WNT surrogate during ischemic BBB dysfunction, with general applicability to adult CNS disorders characterized by an aberrant blood-brain barrier.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ndp WT/KO with PBS/L6-F4-2 treatment

first: Jie

last: Ding

first: Kanako

last: Yuki

first: Calvin

last: Kuo


title: Therapeutic modulation of the blood-brain barrier and ischemic stroke by a bioengineered FZD4-selective WNT surrogate

overall_design: Retina endothelia cells were isolated by Fluorescence-activated cell sorting (FACS) by CD31 positive and 7-AAD negative stainings

first: Vincent

last: van Unen


title: Single-cell gene expression profiling (sc-RNA-seq) of CD34+ hematopoietic stem cells from Myeloproliferative Neoplasm (MPN) patients

city: New Haven

first: Dongjoo

last: Kim

state: CT

address: 55 Prospect st.

department: BME

institute: Yale University

summary: To explore specific cytokine pathways in MPN patients with enriched NF-kB activation (and thus fibrosis), we carried out single-cell gene expression profiling (sc-RNA-seq) on isolated CD34+ cells from 7 separate individual MPN patients across MPN sub-types with varying degress of fibrosis using an enclosed microwell array platform with a focus on NF-kB pathway-associated cytokine mediators.

overall_design: Single cell gene expressio profiling of CD34+ hematopoietic stem cells by different fibrotic level in MPN patients

first: Rong

last: Fan


title: Single-Cell RNA Transcriptome of the Human Endometrium Reveals Epithelial Characterizations Associated with Recurrent Implantation Failure

status: Public on Jan 30 2023

city: Chongqing

first: Shen

last: Zhang

address: No. 288 Tianwen avenue, Nanan district

department: Obstetrics and Gynecology Department

institute: The Second Affiliated Hospital of Chongqing Medical University

summary: To investigated the characteristics of the endometrium from RIF patients during WOI at single-cell resolution.

overall_design: Both stromal fibroblasts-enriched and epithelium-enriched populations were collected by a two-step dissociation. We characterized the mid-secretory endometrium of RIF patients at single-cell solution.

first: Hong

first: Chanyu


title: Activation of tissue-resident NK and conventional NK are fundamentally different as indicated by their particular genesets

city: Beijing

first: Chao

last: Zhong

address: 38 Xueyuan Rd , Haidian District

department: Institute of Systems Biomedicine

institute: Peking University

summary: Residential natural killer cells in peripheral tissues (trNK) act as pioneering responders during infectious challenges, and thus have attracted increasing attention recently. However, their discrimination with conventional NK (cNK) cells is still problematical, limiting the further knowledge of this particular NK subgroup. Here, through an integrative transcriptome comparison of the two NK subgroups from different tissues, two genesets are defined to efficiently distinguish them. From these genesets, we have also discovered a fundamental difference of the two NK subgroups in activation. Transcriptomic profiling of trNK and cNK activated in vivo after MCMV infection and in vitro by PMA/ionomycin stimulation further confirms this difference, and reveals a particular role of chromatin landscape in regulating the trNK activation. Additionally, trNK and cNK respectively highly express IL-21R and IL-18R, indicating that their activation is differentially regulated by cytokine milieu. Indeed, IL-21 is particular critical in accessorily promoting trNK activation, while IL-18 mainly facilitates cNK activation. Further, IL-21 is found to direct transcriptome changes in activated trNK using a bunch of bifunctional transcription factors. Together, our study sheds light on the bona fide difference between trNK and cNK, which will enrich our understanding of their distinct functionalities during immune responses.

overall_design: RNA-Seq was performed on trNK and cNK from liver, uterus, salivary glands and spleen. RNA-Seq was also performed on ex-vivo trNK and cNK stimulated  with and without PMA/Ionomycin, PMA/Ionomycin+IL-21, PMA/Ionomycin+IL-18.ATAC-seq was performed on ex-vivo trNK stimulated with and without PMA/Ionomycin, PMA/Ionomycin+IL-21.

first: Mengwei

last: Han

first: Luni

last: Hu


title: polyA RNA-seq of SMCHD1 and LRIF1 knock-out immortalized myoblasts

city: Leiden

first: Darina

last: Sikrova

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Centre

summary: polyA RNA-seq was performed on different SMCHD1 and LRIF1 knock-out myoblast clones to assess the role of SMCHD1 and LRIF1 in transcriptioanl regulation in somatic cells

overall_design: 3 independent CRISPR clones were derived for each knock-out genotype and used as biological triplicate for RNA-seq and downstream statistical analysis

first: Silvere

last: van der Maarel


title: Sex-biased gene and microRNA expression in the developing mouse brain is associated with neurodevelopmental functions and neurological phenotypes (miRNA-Seq)

first: Susanna

last: Szakats

first: Hugh

last: Cross

first: Megan

last: Wilson


title: Chronic Prenatal Delta-9-tetrahydrocannabinol Exposure Adversely Impacts Placental Function

status: Public on Jan 26 2023

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

institute: Oregon Health and Science University

platform_organism:
Macaca mulatta
Homo sapiens


title: THE IDENTIFICATION OF THE METHYLATION PATTERNS OF TOMATO CURLY STUNT VIRUS IN RESISTANT AND SUSCEPTIBLE TOMATO LINES

city: Johannesburg

first: Gerrit

last: Koorsen

address: Corner of Kingsway and University Avenue

country: South Africa

institute: University of Johannesburg

type: Methylation profiling by high throughput sequencing

summary: Tomato curly stunt virus (ToCSV) is a monopartite begomovirus infecting tomatoes in South Africa, with sequence similarity to tomato yellow leaf curl virus (TYLCV). While there are numerous reports on the mechanism of TYLCV resistance in tomato, the underlying mechanisms in the tomato-ToCSV pathosystem is still relatively unknown. The main aim of this study was to investigate and compare the global methylation profile of ToCSV in two near-isogenic tomato lines, one with a tolerant phenotype (T, NIL396) and one with a susceptible phenotype (S, NIL395). Bisulfite conversion and PCR amplification, coupled with a next-generation sequencing approach, were used to elucidate the global pattern of methylation of ToCSV cytosine residues in T and S leave tissue at 35 days post-infection (dpi). The extent of methylation was more pronounced in tolerant plants compared to susceptible plants in all sequence (CG, CHG and CHH) contexts, however, the overall methylation levels were relatively low (<3%). Notably, a significant interaction (p < 0.05) was observed between the viral genomic region and susceptible vs. tolerant status for CG methylated regions where it was observed that the 3'IR CG methylation was significantly (p < 0.05) higher than CG methylation of other genomic regions in tolerant and susceptible plants. Additionally, statistically significant (EdgeR p < 0.05) differentially methylated cytosines were located primarily in the genomic regions V2/V1 and C4/C1 of ToCSV. The relative expression, using RT-qPCR, was also employed in order to quantify the expression of various key methylation-related genes, MET1, CMT2, KYP4/SUVH4, DML2, RDM1, AGO4 and AGO6 in T vs. S plants at 35dpi. The differential expression between T and S was significant for MET1, KYP4/SUVH4 and RDM1 at p<0.05 which further supports more pronounced methylation observed in ToCSV from T plants vs. S plants. While this study provides new insights into the differences in methylation profiles of ToCSV in S vs. T tomato plants, further research is required to link tolerance and susceptibility to ToCSV.

overall_design: Differential cytosine methylation of ToCSV (Accession: OK813888.1) isolated from a tolerant (T,NIL396) and susceptible (S, NIL395) tomato line. Viral samples from 3 biological replicates of each line were analysed (S1-3 and T1-3, respectively) at 35 dpi.

first: Precious Earldom

last: Mulaudzi

first: Farhahna

last: Allie


title: Endogenous retrovirus MER50-derived enhancers confer the transcriptional regulation of human trophoblast syncytialization

city: Yangzhou

first: Cui

last: Du

address: NO.88 University South Road

institute: Yangzhou University


title: A combinatorial approach to uncover a novel Integrator subunit

status: Public on Jan 25 2023

city: Philadelphia

first: Sarah

last: Offley

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute


title: A combinatorial approach to uncover a novel Integrator subunit [ChIP-seq II]

summary: The Integrator complex is one of the most elusive transcriptional regulators in metazoans, deemed to be recruited after initiation to help establish and modulate paused RNAPII. Recent structural, biochemical, and functional evidence suggest that Integrator is composed of 14 subunits, assembling, and operating in a modular fashion. We employed proteomics and machine-learning (alphafold2) approaches to discover a novel Integrator subunit, INTS15. We report that INTS15 assembles primarily with the INTS10-INTS13-INTS14 module and interfaces with the Int-PP2A phosphatase module. Functional genomics analysis further reveals a role for INTS15 in modulating RNAPII pausing at a subset of genes in human cell lines.

overall_design: C7orf26 (INTS15) was ChIPed in WT HeLa and HL-60 cells after stimulation. ChIP-seq for RNA polymerase II was done in HeLa cells that were treated with shRNAs for C7orf26 or Luciferase (control).

first: Alessandro

last: Gardini


title: RNA Sequencing of two Breast Cancer Cell Lines in Comparison to Healthy Epithelial Breast Cells

city: Kaunas

first: Monika

last: Pankevičiūtė-Bukauskienė

address: Sukilėlių pr. 15

department: Institute of Cardiology

country: Lithuania

institute: Lithuanian University of Health Sciences

summary: We studied genes, that are differentially expressed between malignant and normal breast tissue, to find weak spots for anti-cancer therapy development. RNA sequencing of three cell lines was performed: MCF-7 (epithelial breast cancer cell line), BCC (primary breast tumour cell line) and MCF-10A (epithelial breast cell line).

overall_design: Three biological replicates were analyzed for each of 3 studied cell lines

first: Sergio

last: Bordel Velasco


title: Regulatory T-cells and duodenal tissue in acute pancreatitis

first: Sabine

last: Ameling

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

overall_design: Refer to individual Series


title: Integrated single-cell multiomics reveals novel immune candidate markers for post-traumatic coagulopathy

city: Shanghai

first: Ping

last: Zheng

state: Shanghai

address: 490 South Chuanhuan Road

department: Neurosurgery

institute: Shanghai Pudong New area People's Hospital

summary:
Introduction: Post-traumatic coagulopathy (PTC) is a critical pathology in traumatic brain injury (TBI), however, its potential mechanism is not clear. To explore this in peripheral samples, we integrated single cell RNA-sequencing and T cell repertoire (TCR)-sequencing across a cohort of patients with TBI.
Methods: Clinical samples from patients with more brain severity demonstrated  altered mRNAs.

overall_design: 12 TBI patients and 4 healthy controls collected with PBMC for ceRNA chipset

first: Wanju

last: Sun


title: Evolutionary barriers to horizontal gene transfer in macrophage associated Salmonella

status: Public on Jan 27 2023

city: Liverpool

first: Jonathan

middle: Paul

last: Bollback

address: Crown Street

country: United Kingdom

institute: University of Liverpool

summary: To investigate which of the intrinsic of a horizontally acquired gene and the environment can be a barrier to HGT, we transferred and expressed 44 E.coli orthologs into S. Typhimurium strain 4/74.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

overall_design:
We estimated relative fitness effects in four infection relevant environments for the 44 Salmonella mutants  with changes in gene frequencies estimated using Next-Generation Sequencing.
Pooled growth assays for the 44 mutants in four infection relevant environments that are representative of an intra-macrophage environment during an infection.

first: Rama

middle: P

last: Bhatia

first: Hande

last: Kirit

first: Cecil

last: Lewis Jr

first: Krithivasan

last: Sankarnarayanan


title: Tissue-resident memory T-cells in pancreatic ductal adenocarcinoma co-express PD-1 and TIGIT and inhibition is reversible by dual antibody blockade

status: Public on Jan 24 2023

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

institute: University of Birmingham

summary: An in-depth investigation of the pancreatic ductal adenocarcinoma tumour microenvironment highlights PD-1 and TIGIT, or their corresponding ligands, as potential targets for combinatorial monoclonal antibody therapy to treat this devastating disease.

overall_design: Single Cell RNA profile of cells in the PDAC tumor microenvironment

first: Hayden

last: Pearce

first: Wayne

last: Croft

first: Samantha

last: Nicol

first: Sandra

last: Margielewska-Davies

first: Richard

last: Powell

last: Cornall

first: Simon

last: Davis

first: Francesca

last: Marcon

first: Matthew

last: Pugh

first: Éanna

last: Fennell

last: Powell-Brett

first: Rachel

last: Brown

first: Gary

last: Middleton

first: Brinder

last: Mahon


title: A combinatorial approach to uncover a novel Integrator subunit [ChIP-seq I]

first: Sarah

last: Offley

first: Alessandro

last: Gardini


title: Gene expression profile of FACS-sorted CD63lo and CD63hi beta cells from 10 weeks-old C57BL/6J male mice.

status: Public on Jan 23 2023

city: New York

first: Friederike

last: Dündar

address: 1300 York Ave

department: Physiology & Biophysics

institute: Weill Cornell Medicine

summary:
To evaluate the transcriptome of CD63lo and CD63hi beta cells, we FACS-sorted beta cells based on CD63 expression. We then performed gene expression profiling analysis using data obtained from RNA-seq.
For details of the analyses, see https://github.com/abcwcm/RubioNavarro_Pancreas

overall_design: Mouse pancreatic islets from 10 weeks-old C57BL/6J male mice were isolated. After dissociation, pancreatic islets were FACS-sorted to obtain two population of beta cells based on CD63 expression

first: Alfonso

last: Rubio-Navarro

first: Nicolás

last: Gómez-Banoy

first: Lisa

last: Stoll

first: Alex

last: Mawla

first: Lunkun

last: Ma

first: Nathalia

last: Montoya-Oviedo

last: Zumbo

first: Moritz

last: Reiterer

first: Norihiro

last: Imai

first: Ankit

last: Gilani

first: Boris

last: Yang

first: Eric

last: Cortada

first: Angie

middle: C

last: Chong

first: David

last: Cohen

first: Shuibing

last: Chen

first: Jingli

last: Cao

first: Geoffrey

last: Pitt

first: Mark

middle: O

last: Huising

first: Doron

last: Betel

first: James

last: Lo


title: A Critical Role of RUNX1 in Governing Megakaryocyte-Primed Hematopoietic Stem Cell Differentiation [CUT&RUN Chip-seq]

status: Public on Jan 20 2023

city: Cincinnati

first: Chen

last: Wang

state: OH

address: 3333 Burnet Avenue

department: Experimental Hematology/Oncology

institute: CCHMC

summary:
RUNX1 is crucial for multiple stages of hematopoiesis and its mutation can cause familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML). We aim to study the role of RUNX1 in megakaryocyte-biased HSCs differentiation to megakaryocytes.
Here, by using Runx1F/FMx1-Cre mouse model ,we sorted CD41pos HSCs and CD41neg HSCs in both RUNX1 WT and KO, and tested the RUNX1 direct binding targets in these cells genome.

overall_design: Comparative RUNX1 binding target genes acquired from CUT&RUN for RUNX1and H3K4me3 in CD41pos HSCs and CD41neg HSCs from both RUNX1 KO and WT mice.

first: Yi

last: Zheng


title: A Critical Role of RUNX1 in Governing Megakaryocyte-Primed Hematopoietic Stem Cell Differentiation


title: Genome-wide Map of R-loops Reveals its interplays with Transcription and Genome Integrity during Germ Cell Meiosis

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: R-loop is a naturally formed three-strand nucleic acid structure that was reported to take part in multiple biological processes. In our study, we firstly mapped R-loop genomic distribution in mammalian meiotic cells by genome-wide S9.6 CUT & Tag seq. R-loop mainly distributed at promoter-related regions, and combined with systematically transcriptome analysis showed R-loop was closely related to transcription in the meiotic process. Moreover, we verified the conclusion by constructing conditional knockout mice of Rnaseh1, which delete the R-loop endonuclease before meiosis entry. Lack of RNase H1 caused mice completely sterile with R-loop accumulation and abnormal DSB repairing in spermatocytes. Further analysis showed R-loop accumulation in leptotene/zygotene influenced transcriptional regulation in the pachytene stage. Thus, mutual regulation of R-loop and transcription plays an essential role in spermatogenesis.

overall_design: Genome-wide R-loop profiling during spermatogenesis generated by S9.6 CUT&Tag deep sequencing

first: Yu

last: Jiang

first: Fei

last: Huang

first: Li

last: Shen

first: Hengyu


title: Ecological interactions in breast cancer: Cell facilitation promotes growth and survival under drug pressure

status: Public on Jan 18 2023

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: The interplay of positive and negative interactions between drug sensitive and resistant cells determines the efficacy of treatment in heterogeneous cancer cell populations. We studied isogenic estrogen receptor positive (ER+) breast cancer cell lineages sensitive and resistant to ribociclib-induced CDK4/6 inhibition in monoculture and coculture, finding that sensitive cells grow and compete more effectively in the absence of treatment. During treatment with ribociclib, sensitive cells survive and proliferate better when grown together with resistant cells than when grown in monoculture, termed facilitation in ecology. Several lines of evidence indicate estradiol production by resistant cells as the mechanism of facilitation, with both liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays and single cell RNA-seq showing higher production by resistant cells, and sensitive cells shifting phenotype to become more like resistant cells when grown in coculture.  Adding estradiol in monoculture provides sensitive cells with partial resistance, and cancels facilitation in coculture. Mathematical modeling quantifies the strength of competition and facilitation, and predicts that blocking facilitation has the potential to control both resistant and sensitive cell populations and inhibit the emergence of a refractory population.

overall_design: Spheroids of different composition (100% sensitive, 50% sensitive – 50% resistant, 100% resistant) were initiated from Venus-labeled CAMA-1 and mCherry-labeled CAMA-1_ribociclib_resistant cells and were subjected to 1 uM ribociclib treatment. After 11 days, speroids were harvested, washed and cell suspensions were viably frozen for single cell RNA-seq analysis.

first: Rena

last: Emond

first: Jason

last: Griffiths

first: Vince

last: Grolmusz

first: Aritro

last: Nath

last: Castaneda

first: Rachel

last: Sousa

first: Andrea

last: Bild

first: Frederick

last: Adler


title: A Critical Role of RUNX1 in Governing Megakaryocyte-Primed Hematopoietic Stem Cell Differentiation [10x scRNAseq]

summary: RUNX1 is crucial for multiple stages of hematopoiesis and its mutation can cause familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML). We aim to study the role of RUNX1 in megakaryocyte-biased HSCs differentiation to megakaryocytes.

overall_design:
Here, by using Runx1F/F Mx1-Cre mouse model, we sorted LSKCD150+ HSCs in both RUNX1 WT and KO, and performed 10x scRNA seq to compare their population composition.
10X scRNA sequencing for LSKCD150+ HSCs from both RUNX1 KO and WT mice.


title: Albumosomes formed by pre-folding albumin in cytoplasm of hepatocytes maintain mitochondrial homeostasis and inhibit nonalcoholic fatty liver disease

first: Boyuan

last: Ma

address: Qinghuayuan 1

institute: Tsinghua University

summary:
Wildtype (WT) and albumin-knockout (AKO) were fed with normal diet. We harvested the liver tissues from WT and AKO mice at 3-week, 8-week, and 10-month of age. We then performed gene expression profiling analysis using data obtained from RNA-seq of the six different liver tissues.
Wildtype (WT) and albumin-knockout (AKO) mice were fed with Normal diet (ND) or Western diet (WD) for 8 weeks from the age of 8 weeks. We harvested the liver tissues from WT-ND, WT-WD, AKO-ND, AKO-WD mice . We then performed gene expression profiling analysis using data obtained from RNA-seq of the four different liver tissues.
Wildtype (WT) mice fed with HFD from the age of 8 weeks were injected by 17-AAG at the 3rd, 4th, 5th, 6.5th, and 8th weeks of the HFD feeding process. The control group was injected by the solvent. Another group of mice at the same age was fed with normal diet (ND). We harvested the liver tissues ND, Ctrl, and 17-AAG mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of the three different liver tissues.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of liver tissues.

first: Anji

last: Ju

first: Shaosen

last: Zhang

first: Qi

last: An

first: Siran

last: Xu

first: Jie

last: Liu

last: Yu

first: Yan

last: Fu

first: Yongzhang

last: Luo


title: A Critical Role of RUNX1 in Governing Megakaryocyte-Primed Hematopoietic Stem Cell Differentiation [RNA-seq]

first: Chen

last: Wang

summary:
RUNX1 is crucial for multiple stages of hematopoiesis and its mutation can cause familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML). We aim to study the role of RUNX1 in megakaryocyte-biased HSCs differentiation to megakaryocytes.
Here, by using Runx1F/FMx1-Cre mouse model, we sorted CD41pos HSCs and CD41neg HSCs in both RUNX1 WT and KO, and compared their gene expression profiles.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD41pos HSCs and CD41neg HSCs from both RUNX1 KO and WT mice.

first: Yi

last: Zheng


title: Novel transcriptomic signatures associated with premature kidney allograft failure

status: Public on Jan 16 2023

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

summary:
Prediction power of kidney allograft outcomes based on non-invasive assays is limited. Assessments of operational tolerance (OT) patients allow to identify transcriptomic signatures of true non-responders for construction of predictive models.
In the discovery cohort, RNA sequencing was used to identify protective set of transcripts by comparison of 15 OT patients from TOMOGRAM Study (NCT05124444)  with 14 chronic active antibody-mediated rejection (CABMR) and 23 stable graft function ≥15 years (STA). Archetypal analysis and classifier performance of RNA sequencing data showed that OT is clearly distinguishable from CABMR, but similar to STA. Selected differentially expressed transcripts between OT and CABMR were used in validation cohort (n=396) to predict 3-year kidney allograft loss at 3 time-points using RT-qPCR. Based on significant transcripts in univariable analysis, 2 multivariable Cox models were created. 3-transcripts (ADGRG3, ATG2A and GNLY) model from POD 7 predicted graft loss with C C-statistics (C) 0.727  (95% CI, 0.638-0.820). Another 3-transcript (IGHM, CD5, GNLY) model from M3 predicted graft loss with C 0.786 (95% CI, 0.785-0.865). Combining 3-transcript model with eGFR at month 3 improved C-statistics to 0.860 (95% CI, 0.778-0.944) and 0.868 (95% CI, 0.790-0.944), respectively. The model based on DGF, acute rejection, HLA mismatch and eGFR reached similar performance (C 0.846).
In conclusion, identification of transcripts distinguishing OT from CABMR allowed to construct models predicting premature graft loss. Predictive statistics of these models reach same performance as well known-clinical models. Identified transcripts reflect mechanisms of injury/repair and alloimmune response when assessed at day 7 or with a loss of protective phenotype when assessed at month 3.

overall_design: To identify protective set of peripheral blood transcripts by expression profiling (RNAseq) of operationally tolerant patients (OT) with chronic active antibody-mediated rejection (CABMR) as “high-responders” and  stable graft function ≥15 years (STA) as “low responders”.  Other controls involved CNI-treated patients with primary glomerulopathies and healthy people.

first: Jiri

last: Klema

first: Anh

last: Vu Le

first: Eva

last: Girmanova

last: Mrazova

first: Annick

last: Massart

first: Dita

last: Maixnerová

first: Ludek

last: Voska

first: Gian

last: Benedetto Piredda

first: Luigi

last: Biancone

first: Ana

last: Ramirez Puga

first: Miguel

last: Angel Gentil

first: Nurhan

last: Seyahi

first: Mehmet

last: Sukru Sever

first: Laurent

last: Weeckers

first: Anja

last: Muhfeld

first: Klemens

last: Budde

first: Bruno

last: Watschinger

first: Marius

last: Miglinas

first: Marc

last: Abramowicz

first: Daniel

first: Ondrej

last: Viklicky


title: Genome-wide DNA methylation analysis of peripheral blood samples of psychiatric patients and healthy controls

status: Public on Jan 14 2023

city: Munich

first: Natan

last: Yusupov

address: Kraepelinstr. 2-10

department: Dept. Genes and Environment

institute: Max Planck Institute of Psychiatry

type: Methylation profiling by genome tiling array

summary: We evaluated biological aging using five epigenetic clocks (Horvath, Hannum, PhenoAge, GrimAge and DunedinPoAm) calculated from DNA methylation measured in peripheral blood cells in a trans-diagnostic psychiatric sample including healthy controls. We found that burden of psychiatric disease, represented by a weighted score, was significantly associated with biological age acceleration as measured by GrimAge and DunedinPoAm. The faster pace of aging was even further accelerated in individuals exposed to physical abuse in childhood

overall_design:
The study sample included subjects with psychiatric disorders and self-reported healthy controls of two studies conducted at the Max Planck Institute of Psychiatry in Munich, Germany: the Biological Classification of Mental Disorders study (BeCOME, registered on ClinicalTrials.gov, TRN: NCT03984084) and a subset of patients recruited for major depression from a clinical psychotherapy study (OPTIMA, registered on ClinicalTrials.gov, TRN: NCT03287362) who agreed to participate in an additional biobanking project. Epigenetic age was calcualted with Horvaths’ New Methylation Age Calculator (https://dnamage.genetics.ucla.edu/new). DunedinPoAm was calculated with the DunedinPoAm38 R package (https://github.com/danbelsky/DunedinPoAm38). Final DNA methylation data comprised of 420 subjects.

***Please note that the algorithms to calculate epigenetic age need only small part of the CpGs on the array and due to privacy concerns, a partial dataset (i.e. only the necessary CpGs (N = 1922) for the calculation of the epigentic age by the 5 tools) was included in the records.

first: Linda

last: Dieckmann

first: Mira

last: Erhart

first: Susann

last: Sauer

first: Monika

last: Rex-Haffner

first: Johannes

last: Kopf-Beck

first: Tanja

last: Brückl

first: Darina

last: Czamara

first: Elisabeth

last: Binder


title: A Critical Role of RUNX1 in Governing Megakaryocyte-Primed Hematopoietic Stem Cell Differentiation [Single MK RNAseq]

first: Chen

last: Wang

overall_design:
Here, by using Runx1F/FMx1-Cre mouse model, we sorted CD41pos HSCs from both RUNX1 WT and KO, and cultured the cells in 2 days, selected the differentiated MK like cells and non MK like cells for RNA sequencing to determine their differentiation potential.
Comparative gene expression profiling analysis of RNA-seq data for cultured cells from CD41pos HSCs from both RUNX1 KO and WT mice.

first: Yi

last: Zheng


title: A combinatorial approach to uncover a novel Integrator subunit [RNA-seq]

first: Sarah

middle: R

last: Offley

overall_design: C7orf26 (INTS15) was knocked down in HeLa cells, serum starved, and transcription was induced through the addition of Epidermal Growth Factor (EGF) to the media. After 15 minutes, the cells were collected for total RNA-seq.

first: Alessandro

last: Gardini


title: RNA-seq of decitabine-treated AML cell line panel

status: Public on Jan 13 2023

city: Palo Alto

first: Abolfazl

last: Arab

address: 3160 Porter Dr

institute: Arc Institute

summary: We assessed differential RNA expression and stability by treatment condition (decitabine and DMSO) in each cell line.

overall_design: We performed stranded RNA-seq on SKM-1, MOLM-13, THP-1, OCI-AML2, OCI-AML3 and KG-1 cell lines treated with decitabine or DMSO for 72 hours in three replicates.

first: Alex

last: Ge

first: Raymond

last: Dai


title: Tissue-specific chromatin binding patterns of C. elegans heterochromatin proteins HPL-1 and HPL-2 reveal differential roles in the regulation of gene expression.

status: Public on Jan 09 2023

city: Seville

first: Patricia

last: De La Cruz Ruiz

address: Ctra. de Utrera, km 1

institute: 1Andalusian Centre for Developmental Biology. Universidad Pablo de Olavide

overall_design: DNA adenine methyltransferase identification-sequencing (DamID-seq) for HPL-1 in the intestine and HPL-2 in the hypodermis and intestine in L4 larval stage.

first: Peter

last: Askjaer

first: Marta

last: Artal-Sanz

last: de la Cruz-Ruiz


title: Role of eEF2 diphthamide modification in translational fidelity

status: Public on Jan 10 2023

city: Bethesda

first: Byung-Sik

last: Shin

address: 6 Center Dr, BLDG 6, RM 227

institute: NIH

summary: Diphthamide (DPH) is a conserved amino acid modification on eukaryotic translation elongation factor eEF2. We show that loss of DPH increases -1 ribosomal frameshifting at both programmed, including in SARS-CoV-2, and non-programmed sites. Ribosome profiling of yeast and mammalian cells lacking DPH reveals increased ribosomal drop-off during elongation. The drop-off defect on the long yeast MDN1 gene was suppressed by eliminating out-of-frame stop codons. Our data reveal that loss of DPH impairs the fidelity of translocation during translation elongation resulting in increased rates of ribosomal frameshifting and premature termination at out-of-frame stop codons.

sample_organism:
Saccharomyces cerevisiae
Cricetulus griseus

overall_design: Examination of yeast and mammalian cells lacking diphthamide modification in eEF2

first: Ivaylo

last: Ivanov

first: Joo-Ran

last: Kim

first: Terri

last: Kinzy

first: Thomas

middle: E

last: Dever


title: Gene expression profile at single embryo level of 0-3h old Drosophila embryos

status: Public on Jan 12 2023

city: Grand Rapids

first: Adelheid

last: Lempradl

state: Michigan

address: 333 Bostwick Ave NE

department: Metabolism and Nutritional Programing

institute: Van Andel Institute

summary: We used single-embryo sequencing to characterize early zygotic gene expression in Drosophila. The data provide the first continuous timeline of transcript levels during early development (≤ 3 hours) in Drosophila melanogaster.

overall_design: RNA from single Drosophila embryos was isolated and subjected to a modified CelSeq2 single-cell RNA-sequencing protocol. Pseudo-temporal analysis of the single embryo transcriptomes provides a high-resolution, time-sensitive picture of transcriptional events during early embryonic development.

first: J

last: Perez-Mojica

first: Kin

last: Lau


title: Characteristics of Human and Microbiome RNA Profiles in Saliva

status: Public on Jan 07 2023

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

summary: Saliva is a convenient non-invasive source of liquid biopsy to monitor human health and diagnose diseases. In particular, extracellular vesicles (EVs) in saliva can potentially reveal clinically relevant information for systemic health. Recent studies have shown that RNA in saliva EVs could be exploited as biomarkers for disease diagnosis. However, there is no standardized protocol for profiling RNA in saliva EV nor clear guideline on selecting saliva fractions for biomarker analysis. To address these issues, we established a robust protocol for small RNA profiling from fractionated saliva. With this method, we performed comprehensive small RNA sequencing of four saliva fractions, including cell-free saliva (CFS), EV-depleted saliva (EV-D), exosome (EXO), and microvesicle (MV) from ten healthy volunteers.   Methods: To address these issues, we established a robust protocol for small RNA profiling from fractionated saliva. With this method, we performed comprehensive small RNA sequencing of four saliva fractions, including cell-free saliva (CFS), EV-depleted saliva (EV-D), exosome (EXO), and microvesicle (MV) from ten healthy volunteers.

overall_design: small RNA expression profiles of fractionated saliva

first: Fangjia

last: Tong

first: Gongyu

last: Tang


title: FOXA1 O-GlcNAcylation-mediated transcriptional switch governs metastasis capacity in breast cancer [ChIP-seq]

status: Public on Jan 02 2023

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

institute: Dalian University of Technology

summary: The transcription factor FOXA1, which functions in epigenetic reprogramming, plays a critical role in breast cancer progression. However, the molecular mechanisms by which FOXA1 achieves its oncogenic functions remain elusive. Here, we demonstrate that the O-GlcNAcylation of FOXA1 increases breast cancer metastasis capacity by orchestrating the transcription of numerous metastasis regulators. O-GlcNAcylation at Thr432, Ser441 and Ser443 regulates the stability of FOXA1 and promotes its assembly with chromatin in breast cancer cells. We provide evidence that O-GlcNAcylation shapes the FOXA1 interactome, especially triggering the recruitment of the transcriptional repressor MECP2 and consequently stimulating FOXA1 chromatin-binding sites to switch to chromatin loci of adhesion-related genes, including EPB41L3 and COL9A2. Site-specific depletion of O-GlcNAcylation on FOXA1 affects the expression of various downstream genes and thus inhibits breast cancer proliferation and metastasis both in vitro and in vivo.

overall_design: We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using anti-HA magnetic beads in HA-FOXA1-WT or HA-FOXA1-3A stably expressed MCF-7 FOXA1 KO cells. MECP2 ChIP-seq was performed using anti-MECP2 antibody in the above cells. Next, MECP2 was knockdown by shRNA in FOXA1 rescued MCF-7 FOXA1 KO cells. HA-FOXA1-WT and HA-FOXA1-3A ChIP-seq were performed using anti-HA magnetic beads in MECP2 knockdown cells. Next-generation sequencing libraries were generated and amplified for 15 cycles. 100-300 bp DNA fragments were gel-purified and sequenced with an Illumina NovaSeq 6000 instrument by Novogene Technology (Beijing, China). Two biological replicates of each ChIP-seq were performed. We also analyzed gene expression in FOXA1-WT and FOXA1-3A expressed cells by RNA-seq.

first: Yajie

first: Lingyan


title: The porcine piRNA transcriptome response to Senecavirus A infection

status: Public on Jan 05 2023

city: 北碚区

first: 王

last: 晨

state: 重庆市

address: 天生路2号

department: 动物医学院

institute: 西南大学

summary: Senecavirus A (SVA) belongs to the family of small RNA viruses, the genus Senecavirus, and has become a research hotspot because of the oncolytic viral characteristics. PIWI-interacting RNAs (piRNAs) are a class of small RNAs found in mammalian cells in recent years; however, the host piRNA expression profile during SVA infection and their role in viral infection is not well understood. In this study, we obtained small RNA transcriptome expression profiles from SVA-infected pig kidney cell lines (PK-15) by high-throughput sequencing. Differential expression (DE) analysis, GO annotation, and KEGG analysis of piRNAs in SVA-infected and non-infected PK-15 cells were performed. qRT-PCR was used to validate the DE of piRNAs. The results showed that 981 and 1,370 novel piRNAs were identified in SVA-infected and non-infected PK-15 cells; expression of 129 piRNAs was upregulated while that of 44 piRNAs was downregulated after SVA infection. The DE of 10 piRNAs was further verified by qRT-PCR. GO annotation analysis results showed the metabolism, proliferation, and differentiation were significantly activated after SVA infection. KEGG results showed that after SVA infection, piRNA was mainly enriched in AMPK signaling pathway, Rap1 signaling pathway, circadian rhythm, and VEGF signaling pathway, which suggested that piRNAs may play a role in regulating antiviral immunity, intracellular homeostasis, and tumor processes during SVA infection. This is the first report of the piRNA transcriptome in pig kidney cells and will contribute to the research of piRNA regulatory mechanism during SVA infections and provide an important reference for the prevention and treatment of SVA.

overall_design: SVA southwest strain was used to infect PK-15 cells. Cell culture in DMEM nutrient solution containing 10% FBS, which also contains 50 mg/mL penicillin/streptomycin antibiotic solution, cultured under standard conditions of 5% CO2 and 37°C. PK-15 cells were infected by SVA (1.26×108 TCID50/mL), and cells were collected for high-throughput sequencing and stem ring PCR validation after 72 h infection.Total RNA was extracted from the above SVA-infected and non-infected PK-15 cells using Trizol reagent. The purity and concentration of the total RNA sample were determined using a NanoPhotometer® spectrophotometer. The integrity of total RNA samples was determined using the Agilent 2100 Bioanalyzer system.

first: Chen


title: FOXA1 O-GlcNAcylation-mediated transcriptional switch governs metastasis capacity in breast cancer [RNA-seq]


title: Cell circuits between leukemic cells and mesenchymal stem cells block lymphopoiesis by activating lymphotoxin-beta receptor signaling

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Korea University College of Medicine

summary: Acute lymphoblastic and myeloblastic leukemias (ALL and AML) have been known to modify the bone marrow microenvironment and disrupt non-malignant hematopoiesis. However, the molecular mechanisms driving these alterations remain poorly defined. Here we show that leukemic cells turn-off lymphopoiesis and erythropoiesis shortly after colonizing the bone marrow. ALL and AML cells express lymphotoxin-a1b2 and activate LTbR signaling in mesenchymal stem cells (MSCs), which turns off IL7 production and prevents non-malignant lymphopoiesis. Genetic or pharmacologic disruption of LTbR signaling in MSCs restores lymphopoiesis but not erythropoiesis, reduces leukemic cell growth, and extends survival of transplant recipients significantly. These studies demonstrate that acute leukemias exploit physiological mechanisms governing hematopoietic output as a strategy for gaining competitive advantage. Our studies also reveal that disrupting the cross-talk between leukemia cells and bone marrow niche cells, and specifically the LTbR pathway, offers new therapeutic opportunities.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mesenchymal stem cells and its treatment derivatives.

first: Xing

last: Feng

first: Moonyoung

last: Lee

first: Joao

last: Pereira


title: A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation

first: Abolfazl

last: Arab

state: CA

summary:
The search for new approaches in cancer therapy requires a mechanistic understanding of cancer vulnerabilities and anti-cancer drug mechanisms of action. Problematically, some effective therapeutics target cancer vulnerabilities that we do not understand and have poorly defined mechanisms of anti-cancer activity. One such drug is decitabine, which is a frontline therapeutic approved for the treatment of high-risk acute myeloid leukemia (AML). Decitabine is thought to kill cancer cells selectively via inhibition of DNA methyltransferase enzymes, but the genes and mechanisms involved remain unclear. Here, we apply an integrated multiomics and CRISPR functional genomics approach to identify genes and processes associated with response to decitabine in AML cells. Our integrated multiomics approach reveals RNA dynamics are key regulators of DNA hypomethylation induced cell death. Specifically, regulation of RNA decapping, splicing and RNA methylation emerge as critical regulators of decitabine killing. Our results provide insights into the mechanisms of decitabine anti-cancer activity in treatment of AML and identify combination therapies which could potentiate decitabine anti-cancer activity.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: scRNAseq MS023-treated MuSCs

city: montreal

first: Stephane

last: Richard

address: 3999 chemin de la cote sainte catherine

country: Canada

institute: McGill University

summary: scRNAseq of MS023-treated muscle stem cells.

overall_design: Muscle stem cells were isolated from wildtype C57Bl6 mice and cultured for 0, 4, and 6 days with MS023 or DMSO.

first: Claudia

last: Dominici


title: FOXA1 O-GlcNAcylation-mediated transcriptional switch governs metastasis capacity in breast cancer.

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


title: Loss of Arntl promotes PDAC

city: Madison

first: Sean

last: Ronnekleiv-Kelly

state: Wisconsin

address: 1400 University Ave

department: Surgery

institute: University of Wisconsin

summary: The circadian clock regulates metabolism and other critical cellular functions. We used CRISPR-Cas9 to knockout the core clock gene Arntl in KPC cells

overall_design: We used RNA-seq to compare wildtype and Arntl KO KPC cells

first: Patrick

last: Schwartz

first: Mark

last: Berres


title: mRNA-seq of wild-type or XAF1 knockout HT29 cells after vesicular stomatitis virus infection

status: Public on Jan 01 2023

city: Beijing

first: Ming

last: Kuang

address: Xueyuan Road 38 #, Haidian District

institute: Peking University

summary:
To investigate the function of XAF1 in immune response, we established XAF1 knockout cell lines in which XAF1 gene has been knockout by sgRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of WT or XAF1 knockout HT29 cells with or without VSV infection

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  WT or XAF1 knockout HT29 cells that were infected by VSV for 0 or 6 hours.


title: H3K27Ac ChIP-seq in wild-type and XAF1 knockout HT29 cells after vesicular stomatitis virus infection

summary:
To investigate the function of XAF1 in chromatin openning. Wild-type or XAF1 knockout HT29 cells were infected with  VSV  for 0 or 3 hours, ChIP-seq was did with H3K27Ac antibody.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27Ac in HT29 cells.

overall_design: Ming Kuang


title: Identification of cell types in medial vestibular nucleus and their response to unilateral vestibular loss

city: Shanghai

first: Pengjun

address: 600 Yishan Rd

institute: Sixth People's Hospital affiliated to Shanghai Jiaotong University

summary: We performed single-cell RNA-seq of mouse medial vestibular nucleus to reveal the cell diversity of this region.

overall_design: Medial vestibular nucleus of mice in normal condition and acute vestibular loss were dissected for single-cell RNA-seq through Drop-seq technique.

first: Haibo

last: Shi


title: Reprogramming of fish somatic cells for nuclear transfer is primed by Xenopus egg extract

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

summary: Somatic cell reprogramming in vitro prior to nuclear transfer is one strategy expected to improve clone survival during development. In this study, we investigated the reprogramming extent of fish fin somatic cells after in vitro exposure to Xenopus egg extract and subsequent culture. Using a cDNA microarray approach, we observed drastic changes in the gene expression profile of the treated cells. Several actors of the TGFbeta and Wnt/beta-catenin signaling pathways, as well as some mesenchymal markers, were inhibited in treated cells, while several epithelial markers were upregulated. This was associated with morphological changes of the cells in culture, suggesting that egg extract drove somatic cells towards a mesenchymal-epithelial transition (MET), the hallmark of somatic reprogramming in iPSCs. However, treated cells were also characterized by a strong decrease in de novo lipid biosynthesis metabolism, the lack of re-expression of pou2 and nanog pluripotency markers, and absence of DNA methylation remodeling of their promoter region. In all, this study showed that Xenopus egg extract treatment initiated an in vitro reprogramming of fin somatic cells in culture. Although not thorough, the induced changes have primed the somatic chromatin for a better embryonic reprogramming upon nuclear transfer.

overall_design: 12 samples (5 Control; 3 MII; 4 MII-late)

first: Nathalie

last: Chenais

last: Le Cam

first: Brigitte

last: Guillet

first: Jean-Jacques

last: Lareyre

first: Catherine

last: Labbe


title: XAF1 knockout HT29 cells after vesicular stomatitis virus infection


title: An efficacious and safe rescue of GM3 synthase deficiency in mice by spatially regulated AAV-mediated ST3GAL5 delivery

city: Worcester

first: Huiya

last: Yang

state: MA

address: 368 Plantation street

department: Gene therapy center

institute: UMass Chan Medical School

summary: The first-generation rAAV-ST3GAL5 replacement vector employing a ubiquitous promoter led to hepatic injury and death caused by high off-target ST3GAL5 expression when administered systemically. In contract, a seconed-geneeration vector optimized for CNS-restricted expression of ST3GAL5 eliminated liver toxicity while preserving neurotherapeutic effects.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype mouse livers treated with PBS, or AAV9.empty, or AAV9.CB.EGFP, or AAV9.CB.hST3GAL5, or AAV9.CB.hST3GAL5_E332K or AAV9.Syn1.hST3GAL5.miR122BS vectors

first: Guangping

last: Gao


title: Heterosis of mule was revealed by induced pluripotent stem cells

city: Hohhot

first: Yuting

last: Fu

address: university west road

institute: Inner Mongolia University

summary: We examined the growth curve, cell cycle, apoptosis and glycolysis of donkey, horse and mule adult fibroblasts (DAFs, HAFs and MAFs), which indicated there are differences in cell proliferation and metabolism. We also derived mule, donkey and horse iPSCs from their respective adult fibroblasts by piggyBac transposition, and we found the induced reprogramming efficiency of mule iPSCs was significantly higher than donkey and horse iPSCs (78.3% vs 58.2% vs 47.9%). miPSCs, diPSCs and hiPSCs all expressed high levels of key endogenous pluripotency genes such as Oct4, Sox2 and Nanog, propagated robustly in single cell passaging and miPSCs were found to proliferated significantly faster than diPSCs and hiPSCs. Furthermore, miPSCs/MAFs clustered closer to diPSCs/DAFs than to hiPSCs/HAFs by RNA-seq. The establishment of miPSCs provide unique experimental materials for further investigation of understanding the “heterosis” and reproductive isolation during speciation.

sample_organism:
Equus asinus
Equus caballus
Equus asinus x Equus caballus

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mule,donkey and horse iPSCs and their respectively adult fibroblasts.

first: Jia

last: Zhang

first: Lixia

last: Zhao


title: ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion [HTGTS]

status: Public on Dec 31 2022

city: New York

first: Shan

last: Zha

state: NY

address: 1130 Saint Nicholas Ave.

institute: Columbia University

summary: The ATR kinase, which coordinates cellular responses to DNA replication stress, is also   essential for the proliferation of normal unstressed cells. Although its role in the replication stress   response is well defined, the mechanisms by which ATR supports normal cell proliferation remain   elusive. Here, we show that Atr is dispensable for the viability of G0-arrested naïve B cells. However,   upon cytokine-induced proliferation, Atr-deficient B cells initiate DNA replication efficiently in early S   phase, but by mid-S phase they display dNTP depletion, fork stalling, and replication failure.   Nonetheless, productive DNA replication can be restored in Atr-deficient cells by pathways that  suppress origin firing, such as downregulation of CDC7 and CDK1 kinase activities. Together, these   findings indicate that ATR supports the proliferation of normal unstressed cells by tempering the pace   of origin firing during the early S phase to avoid exhaustion of dNTPs and other replication factors.

overall_design: To determine how ATR protein affects the repair phase of CSR, we analyzed thousands of CSR and internal deletion junctions from activated control, CD21-Cre AtrC/- and CD21-Cre AtrC/KD B cells using the high-throughput genome-wide translocation sequencing (HTGTS) technology. Cells were cultured in RPMI medium plus IL-4 and anti-CD40 cytokines for 4 days and total genomic DNA was collected for HTGTS.

first: Demis

last: Menolfi

first: Brian

last: Lee

first: Hanwen


title: Cell-free DNA methylation as a predictive biomarker of response to neoadjuvant chemotherapy for patients with muscle invasive bladder cancer in SWOG S1314

city: Alhambra

first: Yi-Tsung

last: Lu

address: 516 SAN PASQUAL DR

institute: University of Southern California

summary: cfDNA methylation analysis to predict cisplatin treatment response in bladder cancer

overall_design: cfDNA was collected from 72 patients in SWOG S1314 before neoadjuvant chemotherapy and was analyzed using EPIC microarray.


title: SIPA1 expression in breast cancer patient

city: Wuhan

first: Li

last: Su

state: Hubei

address: Luoyu Road 1037

institute: Huazhong university of science and technology

summary: To study the expression of SIPA1 in patients with metastatic triple-negative breast cancer, we obtained a subcutaneous metastatic sample from a patient with stage III triple-negative breast cancer and performed single-cell transcriptome sequencing

first: Lijuan

last: Guo

first: Wanjun


title: Exploring mechanism the transcription factor SIPA1 promote the progression of triple-negative breast cancer

summary:
To further study the regulation of SIPA1 on cells, the transcriptome sequencing on BT549 cells, BT549/shSIPA1 cells and si-dDBR cells were performed.
We then performed gene expression profiling analysis using data obtained from RNA-seq of BT549 cells, BT549/shSIPA1 cells and si-dDBR cells to find the genes regulated by SIPA1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BT549 cells and its KD derivatives (shSIPA1, shSIPA1-dBD).


title: SIPA1 Functions as a Transcription Regulator to Sustain Progression of Triple-Negative Breast Cancer


title: ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion [CRISPR-Cas9 gRNA screen]

summary: The ATR kinase, which coordinates cellular responses to DNA replication stress, is also essential for the proliferation of normal unstressed cells. Although its role in the replication stress response is well defined, the mechanisms by which ATR supports normal cell proliferation remain elusive. Here, we show that Atr is dispensable for the viability of G0-arrested naïve B cells. However, upon cytokine-induced proliferation, Atr-deficient B cells initiate DNA replication efficiently in early S phase, but by mid-S phase they display dNTP depletion, fork stalling, and replication failure. Nonetheless, productive DNA replication can be restored in Atr-deficient cells by pathways that suppress origin firing, such as downregulation of CDC7 and CDK1 kinase activities. Together, these findings indicate that ATR supports the proliferation of normal unstressed cells by tempering the pace of origin firing during the early S phase to avoid exhaustion of dNTPs and other replication factors.

overall_design: We set up a genome-wide CRISPR-Cas9 screen targeting 18,424 different genes with 4-5 gRNAs each in v-abl transformed wild-type mouse B cells treated with the IC90 dose of 1 of 2 ATR inhibitors (VE821 or AZD6738) or a Chk1 inhibitor (LY2603618), in triplicates, for 6 days and compared gRNA representation to DMSO-treated controls.

first: Yunyue

last: Wang


title: Dominance in gene expression variability during ontogeny reveals the importance of canalization in adaptive divergence and speciation.

city: Reykjavík

first: Quentin

last: Horta-Lacueva

address: Sturlugötu 7

country: Iceland

institute: University of Iceland

summary: We investigated whether two sympatric Arctic charr morphs (Salvelinus alpinus) with contrasting feeding ecology, the small-benthic (SB) and the planktivorous (PL) charr of Thingvallavatn in Iceland, exhibit genetically based differences in gene expression variability, and how dominance would affect their hybrids. Through a common-garden experiment, we identified genes clusters with similar expression variability, most differing among the two morphs. In the hybrids, gene expression variability was substantially affected by maternal effects and biases towards the PL charr, while the expression of a minority of genes felt outside the range of parental values. These profiles of expression variability were consistent across mRNA and miRNA datasets. Predominant maternal effects and PL charr biases were also observed at the level of average gene expression, including candidate genes involved in the lower jaw development.

overall_design: RNA-seq on embryos from two charr morph and their hybrids reared in common-garden conditions

first: Zophonías

last: Jónsson

first: Dagny

last: Thorholludottir

first: Benedikt

last: Hallgrímsson

first: Kalina

last: Kapralova


title: ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion.


title: Integrative dissection of gene regulatory elements at base resolution

city: Boston

first: Nauman

middle: Muhammad

last: Javed

address: 450 BROOKLINE AVE

department: Cancer Biology

institute: DANA-FARBER CANCER INSTITUTE INC


title: Integrative dissection of gene regulatory elements at base resolution [RNA-seq]

summary: Although vast numbers of putative gene regulatory elements have been cataloged, the sequence motifs and individual bases that underlie their functions remain largely unknown. Here we combine deep learning, epigenetic perturbations and base editing to dissect regulatory sequences within the exemplar immune locus encoding CD69. Focusing on a differentially accessible and acetylated upstream enhancer, we find that the complementary strategies converge on a ~150 base interval as critical for CD69 induction in stimulated Jurkat T cells. We pinpoint individual cytosine to thymine base edits that markedly reduce element accessibility and acetylation, with corresponding reduction of CD69 expression. The most potent base edits may be explained by their effect on binding competition between the transcriptional activator GATA3 and the repressor BHLHE40. Systematic analysis of GATA3 and BHLHE40 binding suggests that interplay between these factors plays a general role in rapid T cell transcriptional responses. Our study provides a framework for parsing gene regulatory elements in their endogenous chromatin contexts and identifying operative engineered variants.

overall_design:
ChIP-seq (GATA3, BHLHE40, and H3K27ac) and ATAC-seq were performed on base edited (sg70_P260) and wild-type (sgCtrl_P258) Jurkat T lymphocytes in the resting and stimulated (PMA/ionomycin) states. ATAC-seq was additionally performed in BHLHE40 over-expressing (BHLHE40-OE) or BHLHE40-ctrl/Ctrl-lentivirus in edited (sg70_P260) Jurkats. RNA-seq was performed in BHLHE40 over-expressing (BHLHE40-OE) or wild-type (BHLHE40-ctrl/Ctrl-lentivirus) in wild-type Jurkats.
This dataset includes the RNA-seq data.

first: Zeyu

last: Chen

first: Fadi

last: Najm

first: Bradley

last: Bernstein


title: ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion [RNA-seq]

first: Shan

overall_design: We studied gene expression profiles in murine primary B cells ATR-proficient (CD21-Cre Atr+/C) or ATR-deficient (CD21-Cre AtrC/-) at different time points and cell cycle stages, namely G0 (0 h), G1 (10 h) and S (24 h) phase. Furthermore, we also analyzed the gene expression profile upon 14 hour treatment with CDC7 and CDK1 inhibitors.

first: Demis

middle: J

last: Zhang


title: Single cell RNA-seq in chicken's lung and DF-1 cell line

first: Chan

last: Ding

address: No.518 Ziyue Road

institute: Shanghai Veterinary Research Institute,Chinese Academy of Agricultural Sciences

summary: Newcastle disease virus (NDV) is an avian paramyxovirus that causes major economic losses to the poultry industry around the world, with NDV pathogenicity varying due to strain virulence differences. However, the impact of intracellular viral replication and the heterogeneity of host responses among cell types are unknown. Here, we investigated the heterogeneity of lung tissue cells in response to NDV infection in vivo and that of chicken embryo fibroblast cell line DF-1 to NDV infection in vitro using single-cell RNA sequencing.

overall_design: Three-day-old SPF chicks was challenged with the LaSota lentogenic strain of NDV (200 μl of 108 50% egg infectious dose [EID50]) by ocular and nasal routes (50 μl into each eye and nostril), whereas the other group was challenged with the highly virulent Herts/33 strain of NDV (200 μl of 103 EID50). The control group was treated with 200 μl phosphate-buffered saline (PBS) by the same routes. Chicks were sacrificed after 3 days of treatment. Finally, two chicks in each group (n = 2/each group) were used for single-cell sorting. DF-1 cell line infected with 1 MOI Herts/33 after 12 hours were uesd for single-cell sorting.

first: Weiwei

last: Liu


title: Loss of BraA09g066480.3C leads to a wax-less phenotype in flowering Chinese cabbage

status: Public on Dec 29 2022

city: Shenyang

first: chuanhong

last: liu

address: No. 120 Dongling Road, Shenhe District

institute: Shenyang Agricultural University

summary:
PURPOSE:To clarify the mechanism of the wax deficiency, the wax-less flowering Chinese cabbage doubled-haploid (DH) line ‘CX001’ and Chinese cabbage DH line ‘FT’, obtained from isolated microspore culture, were used in the experiments.
Transcriptome analysis indicated that BraA09g066480.3C was expressed in ‘FT’ but not in ‘CX001’.The work presented herein demonstrated that BraA09g066480.3C was the causal gene for wax-less flowering Chinese cabbage ‘CX001’

overall_design: Stems of ‘FT’ and ‘CX001’ were selected for RNA extraction, with three replicates per sample.

first: Chuanhong

first: Zhiyong


title: DJ-1 governs airway progenitor cell/eosinophil interactions to promote allergic inflammation

status: Public on Dec 21 2022

city: Tianjin

first: Kuan

last: Li

state: Tianjin

address: Jingu road 890

institute: Tianjin Key Laboratory of Pulmonary Regenerative Medicine

summary: Background  DJ-1 is an antioxidant protein known to regulate mast cell mediated allergic response, but its role in airway eosinophilic interactions and allergic inflammation is not known.  Objective  The aim of this study was to investigate the role of DJ-1 in airway eosinophilic inflammation in vitro and in vivo.  Methods  Ovalbumin-induced airway allergic inflammation was established in mice. ELISA was adopted to analyze DJ-1 and cytokine levels in mouse bronchoalveolar lavage fluid. Transcriptional profiling of mouse lung tissues was conducted by single-cell RNA sequencing technology. The role of DJ-1 in the differentiation of airway progenitor cells into goblet cells was examined by organoid cultures, immunofluorescence staining, quantitative PCR, and cell transplantation in normal, DJ-1 knockout (KO), or conditional DJ-1 KO mice.  Results  We observed that DJ-1 was increased in the lung tissues of ovalbumin-sensitized and challenged mice. DJ-1 KO mice exhibited reduced airway eosinophil infiltration and goblet cell differentiation. Mechanistically, we discovered that eosinophil-club cell interactions are reduced in the absence of DJ-1. Organoid cultures indicated that eosinophils impair the proliferative potential of club cells. Intratracheal transplantation of DJ-1-deficient eosinophils suppresses airway goblet cell differentiation. Loss of DJ-1 inhibits the metabolism of arachidonic acid into cysteinyl leukotrienes in eosinophils while these secreted metabolites promote airway goblet cell fate in organoid cultures and in vivo.  Conclusion  DJ-1-mediated interactions between airway epithelial progenitor cells and immune cells are essential in controlling airway goblet cell metaplasia and eosinophilia. Blockade of the DJ-1 pathway is protective against airway allergic inflammation.

overall_design: After PBS of OVA challenge, total lung cells from three randomly selected WT mice or DJ-1 KO mice were pooled for scRNA-seq analysis (1 sample of WT-PBS, 1 sample of WT-OVA, 1 sample of DJ-1 KO-OVA).

first: Qiuyang

first: Li

first: Shuangyan

first: Qing

last: Yue

first: Xue

first: Yu

first: Jianhai

first: Sisi

first: Zengqiang

last: Yuan

first: Huaiyong


title: Integrative dissection of gene regulatory elements at base resolution [ChIP-seq]

first: Nauman

overall_design:
ChIP-seq (GATA3, TAL1, BHLHE40, and H3K27ac) was performed on base edited (sg70_P260) and wild-type (sgCtrl_P258) Jurkat T lymphocytes in the resting and stimulated (PMA/ionomycin) states. ChIP-seq (BHLHE40, H3K27ac, H3K27me3) was additionally performed in BHLHE40 over-expressing (BHLHE40-OE) or BHLHE40-ctrl(Ctrl-LV) in WT Jurkats.
This dataset includes the ChIP-seq data.

first: Zeyu

first: Fadi

first: Bradley


title: Targeting macrophage M1 polarization suppression through PCAF inhibition alleviates autoimmune arthritis via synergistic NF-κB and H3K9Ac blockade

status: Public on Dec 20 2022

city: Shenzhen

first: Xiaojun

last: Xu

address: No. 3025, Shennan Middle Road

department: Department of Orthopedics

institute: The Eighth Affiliated Hospital of Sun Yat-sen University

summary: M1 macrophages are considered to contribute to autoimmune arthritis such as rheumatoid arthritis, spondyloarthritis. However, the exact role of M1 macrophage during inflammatory joint disease remain unclear. To explore the molecular mechanisms underlying M1 macrophage in autoimmune arthritis, we performed the whole transcriptome sequencing of 3 repeats of M0, 3 repeats of M1 without 20 μM Garcinol and 3 repeats of M1 with 20 μM Garcinol.

overall_design: Total 9 samples were analyzed. The whole transcriptome sequencing of 3 repeats of M0, 3 repeats of M1 without 20 μM Garcinol and 3 repeats of M1 with 20 μM Garcinol was performed.

first: Huiyong

last: Shen

first: Yanfeng

last: Wu

first: Jinteng

first: Feng

last: Ye


title: Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules (miRNAseq)

city: Guangxi

first: ben

last: huang

address: NO.100. DAXUE EAST RD, Nanning

institute: School of Animal Science and Technology, Guangxi University

summary: Mammary epithelial cells (MECs), the only cell type which could be capable of secreting milk in mammary gland, can be applied for the generation of transgenic mammary cell/gland bioreactor. However, continuously achieving large amount of high-quality goat MECs by non-invasion method, especially prepuberal MECs, in vitro has been a challenge. Here, we show that a small molecules cocktail enables the in vitro generation of chemically-induced mammary epithelial cells (CiMECs) with milk-secreting properties from goat ear fibroblasts. The properties of CiMECs were highly similar to those of naturally isolated MECs. Notably, the CiMECs lineage reprogramming process may partially imitate the MECs developmental process from embryonic to milk-secreting stages. Interestingly, fibroblasts were firstly reversed back to embryonic ectoderm/surface ectoderm-like state. Our findings constitute a substantial step toward further promoting the application of transgenic mammary bioreactors, moreover, also offer a new strategy for obtaining other cell types by reprogrammed fibroblasts.

overall_design: The four samples are analyzed. BERTV0d are control group with two replicates. BFRTV8d are treatment group with two replicates.

first: Dandan

first: Ben

last: Huang


title: Dissecting the Arabidopsis/downy mildew interaction by haustoriated cell-specific RNA profiling

status: Public on Dec 25 2022

city: Yokohama

first: Shuta

last: Asai

address: 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN

summary: The downy mildew oomycete Hyaloperonospora arabidopsidis, an obligate filamentous pathogen, infect Arabidopsis by forming feeding structures called haustoria inside the host cell. Previous transcriptome analysis revealed host genes specifically induced during infection. However, whole infected tissue-derived RNA profiling may fail to capture the key transcriptional events that may occur exclusively in haustoriated host cells where the pathogen injects virulence effectors to modulate host immunity for successful accommodation. To understand the interaction between Arabidopsis and H. arabidopsidis at the cellular level, we established a new translating ribosome affinity purification (TRAP) system applicable to pathogen-responsive promoters, enabling haustoriated cell-specific RNA profiling. Among the host genes specifically expressed in H. arabidopsidis-haustoriated cells, we found genes that promote either susceptibility or resistance to the pathogen, providing new insights into the Arabidopsis/downy mildew interaction. We also expect that our new TRAP system could be applicable to several stimulus-specific contexts as well as other plant–pathogen interactions.

overall_design: Three-week-old plants were spray-inoculated to saturation with a spore suspension of 1 x 104 conidiospores/ml. Plants were covered with a transparent lid to maintain high humidity (90-100%) conditions in a growth cabinet at 16°C under a 10-h photoperiod for 5 days. RNA sequencing was performed by deep sequencing on Illumina NextSeq 500 using EXPRSS tag-seq protocol (BMC Genomics 2014, 15:341). Each biological replicate set of samples were sequenced as one batch (biorep1, biorep2 and biorep3 in filenames).

first: Ken

last: Shirasu


title: Integrative dissection of gene regulatory elements at base resolution [ATAC-seq]

last: Javed

overall_design:
ChIP-seq (GATA3, BHLHE40, and H3K27ac) and ATAC-seq were performed on base edited (sg70_P260) and wild-type (sgCtrl_P258) Jurkat T lymphocytes in the resting and stimulated (PMA/ionomycin) states. ATAC-seq was additionally performed in BHLHE40 over-expressing (BHLHE40-OE) or BHLHE40-ctrl/Ctrl-lentivirus in edited (sg70_P260) Jurkats. RNA-seq was performed in BHLHE40 over-expressing (BHLHE40-OE) or wild-type (BHLHE40-ctrl/Ctrl-lentivirus) in wild-type Jurkats.
This dataset includes the ATAC-seq data.

last: Chen

last: Najm


title: Disulfiram/Cu induce ferroptosis in triple-negative breast cancer cells

status: Public on Dec 30 2022

city: ChangChun

first: Chu

last: Meiran

address: 5333 XI an road

department: Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education

institute: Jilin University

summary: To further explore the mechanism of DSF/Cu in TNBC, we conducted transcriptome sequencing experiments in MDA-MB-231 cells in response to 24 h treatment with DSF/Cu (0.2 µM). RNA-seq data revealed that 874 genes were upregulated and 764 genes were downregulated in DSF/Cu treated cells. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that TNBC cells death induced by DSF/Cu wais related to MAPK signaling pathway, p53 signaling pathway, mitophagy signaling pathway and ferroptosis.

overall_design: MDA-MB-231 cells were seeded in 6-well plates and incubated with culture mediums. The next day, cells were treated with DMSO or DSF/Cu and incubated for 24 h. The cells of three wells were maxed into one repeat,  and three repeats  were performed for RNA-sequencing.

first: Meiran

last: Chu

first: Xinglan

last: An

first: Hao

last: Yu

first: Daoyu

last: Zhang

first: Qi

first: Xiaxia

last: Man

first: Xiangpeng

last: Dai

first: Ziyi


title: Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules (WGBSseq)

overall_design: The two samples are analyzed. BERTV_0d are control group. BFRTV_8d are treatment group.


title: Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis.

status: Public on Dec 19 2022

city: Tucson

first: Bonnie

last: LaFleur

state: AZ

address: 4151 W Speedway Blvd

institute: University of Arizona

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

overall_design: Refer to individual Series


title: Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules