title: Transcriptome metabolic characterization of Tuber borchii SP1, a new Spanish strain for in vitro studies of the Bianchetto truffle

city: Pamplona

first: Emilia

middle: Chuina

last: Tomazeli

state: Navarre

address: Av Calatuña s/n

department: Institute for Multisdisciplinary REsearch in Applied Biology

institute: Public University of Navarra

summary: Truffles are ascomycete hypogeous fungi belonging to the Tuberaceae family of the Pezizales order that grow in ectomycorrhizal symbiosis with tree roots and are known for their peculiar aromas and flavors. Axenic culture of truffle mycelium is problematic because it is not possible in many cases, and the growth rate is meager when it is possible. This limitation prompts searching and characterizing new strains that can be handled in laboratory conditions for basic and applied studies. In this work, a new strain of Tuber borchii (strain SP1) has been isolated and cultured, and its transcriptome has been analyzed under different in vitro culture conditions. The results show that the best T. borchii SP1 growth was obtained using maltose-enriched cultures made with soft-agar and in static submerged cultures made at 22ºC. The transcriptome analysis of this strain cultured in different media indicated that most of the gene transcription effort is due to a limited number of genes (20% of genes account for 80% of the transcription), that the transcription profile of the central metabolism genes was similar in the different conditions analyzed with a transcription signal detected for around 80% of the annotated genes. The gene expression profile suggests that T. borchii uses a fermentative rather than respiratory metabolism, even in aerobic conditions. Finally, there is a reduced expression of genes belonging to secondary metabolite clusters, whereas there is a significative transcription of those involved in producing volatile aromatic compounds.

overall_design: Gene expression profiling from RNA-seq data in truffle mycelium, Tuber borchii.

last: Chuina Tomazeli

first: Manuel

last: Alfaro

first: Alessandra

last: Zambonelii

first: Edurne

last: Garde

first: Gumer

last: Perez

first: Lucia

last: Ramirez

first: Hesham

last: Salman

first: Antonio

middle: G

last: Pisabarro


title: Effect of depletion of MIR222HG on gene expression of GSC267 glioma stem cells

status: Public on May 31 2023

city: Jinan

first: Gang

last: Li

state: Shandong

address: 107 Wenhua Xi Road

department: Neurosurgery

country: China

institute: Qilu Hospital of Shandong University

type: Expression profiling by high throughput sequencing

summary: To investigate the function of MIR222HG in the regulation of proneural-to-mesenchymal transition in glioma stem cells, we performed RNA sequencing in GSC267 after knocking down the target gene with shRNA

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GSC267 cells and its KD derivatives (shMIR222HG).

first: Xing

last: Guo


title: RNA Sequencing and Lipidomics Uncovers Novel Pathomechanisms in Recessive X-Linked Ichthyosis

status: Public on May 30 2023

city: London

first: Matthew

middle: Peter

last: Caley

state: london

address: Centre for Cutaneous Research, BLizard Building, Newark Street

country: United Kingdom

institute: QMUL

summary: Recessive X-linked ichthyosis (RXLI), a genetic disorder caused by deletion or point mutations of the steroid sulfatase (STS) gene, is the second most common form of ichthyosis. It is a disorder of keratinocyte cholesterol sulphate retention and the mechanism of extracutaneous phenotypes such as corneal opacities and attention deficit hyperactivity disorder are poorly understood. To understand the pathomechanisms of RXLI, the transcriptome of differentiated primary keratinocytes with STS knockdown was sequenced.   The results were validated at the protein level in a stable knockdown model of STS, to confirm STS specificity, and in RXLI skin.  The results show that there was significantly reduced expression of genes related to epidermal differentiation and lipid metabolism, including ceramide and sphingolipid synthesis. In addition, there was significant downregulation of aldehyde dehydrogenase family members and the oxytocin receptor which have been linked to corneal transparency and behavioural disorders respectively, both of which are extracutaneous phenotypes of RXLI. These data provide a greater understanding of the causative mechanisms of RXLI’s cutaneous phenotype, and show that the keratinocyte transcriptome and lipidomics can give novel insights into the phenotype of patients with RXLI.

overall_design: RNASeq analysis of primary keratnocytes with siRNA mediated knockdown of STS and NT control

first: Edel

middle: A

last: O'Toole

middle: P

first: Farrell

last: Mcgeoghan

first: Emanuela

last: Camera

first: Miriam

last: Maiellaro

first: Manasi

last: Menon

first: Mei

last: Huang

first: Priya

last: Dewan

first: Stela

last: Ziaj

first: Michael

last: Donaldson

first: Anton

last: Enright


title: Tumor-specific CD4 T cells instruct monocyte differentiation in pancreatic ductal adenocarcinoma [bulk RNA-seq]

city: Minneapolis

first: Jesse

middle: W

last: Williams

state: MN

address: 2101 6th St. SE

department: Dept. Integrative Biology & Physiology

country: USA

institute: University of Minnesota

summary: The function of IFNg on macrophage MHC-II differentiation in PDA was investigated using BULK RNA sequencing.

overall_design: CD45+CD11b+F4/80+ macrophages from IFNgKO or WT mouse PDA were collected for bulk RNA sequencing

last: Patterson

first: Yingzheng

last: Xu

first: Ingunn

last: Stromnes


title: Tumor-specific CD4 T cells instruct monocyte differentiation in pancreatic ductal adenocarcinoma [CITE-seq]

summary: To elucidate how CD4 T-cells impact monocyte differentaion in pancreatic ductal adenocarcinoma

overall_design: We sequenced CD45+ from mice bearing KPC pancreatic tumors, either untreated or CD4 depleted.


title: Steroid receptor coactivator 3 is a key modulator of regulatory T cell–mediated tumor evasionT Cells

city: Houston

first: Prashi

last: Jain

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor college of Medicine

summary: SMART-seq analysis is used for single cells or for a small amount of purified total RNA from low number of cells. The goal of this study to compare the quantitative differences between the SRC-3+ and SRC-3-/- Tregs cell transcriptomes.

overall_design: Transcriptome differences between WT and SRC-3KO Tregs explored to explain the anti-tumor effects of SRC-3KO Tregs

first: Sang

middle: J

last: Han

first: John

last: Lydon

first: David

last: Lonard

first: Bert

last: O'Malley


title: Transcriptomic analysis of Notch (N) induced [NΔecd] Drosophila larval primary CNS tumours vs N allograft tumours in w1118 host flies

city: Heraklion

first: Christos

last: Delidakis

address: 100 N Plastira St

country: Greece

institute: FORTH-IMBB

summary: The goal of this project was to compare NGS derived transciptional profiles of primary larval CNS tumours and allograft tumours from two stages (first-T0 and forth-T3) in Drosophila that are induced by overactivation of N pathway  in order to decipher if N regulates similar or different sets of genes as primary hypeplasias transition to malignant tumours. The results of this study show that overactivation of N negatively regulates genes related to neuronal differentiation processes genes as N hyperplasias become more malignant and that genes related to stress, metabolsim and immunity are upregulated

overall_design: mRNA profiles from FACS sorted, GFP positive Drosophila larval CNS N tumours (N FACS) vs the first (T0) allograft N tumours (N T0) vs the fourth (T3) serial allograft N tumours (N T3)

first: E

last: Zacharioudaki

first: C

last: Voutyraki

first: V

last: Theodorou


title: CD200R signaling regulates myeloid cell production of chemokines in tumor microenvironment

city: Columbus

first: Xue-Feng

last: Bai

state: OH

address: 281 W. Lane Ave

department: Department of Pathology

institute: Ohio State University Medical Center

summary: CD200 is overexpressed in human solid tumors such as neuroblastoma and melanoma and considered to be a checkpoint molecule to be targeted for cancer immunotherapy. However, its role in tumor microenvironment (TME) is not well understood. In this study, we evaluated the role of CD200-CD200R pathway in TME using two human relevant, CD200-positive murine tumor models, i.e. the mouse neuroblastoma NB9464D, and melanoma Yummer1.7 models. We found that in CD200R-/- mice, both tumor types grew significantly slower than in wild type mice. TME analyses using scRNAseq and flow cytometry revealed that tumors from CD200R-/- mice overall recruited more CD45+ immune cells including CD4+ and CD8+ T cells and NK cells but less neutrophils into tumors. Antibody depletion experiments revealed that immune effectors including CD4+ and CD8+ T cells, and NK cells are crucial in inhibiting tumor growth in CD200R-/- mice. Mechanistically, we found that CD200R signaling differentially regulates the expression of chemokines in TAMs. In the absence of CD200R, TAMs upregulate CCL24 and CCL8 and downregulate CXCL3, CXCL2 and CCL3 via activation of Erk and/or P38 MAP kinases. Increased expression of CCL24 in TAMs resulted in increased recruitment of eosinophils, which contributes to anti-tumor activity. Thus, CD200R signaling regulates myeloid cell production of chemokines in TME, which explains the differential recruitment of immune effectors and downregulation of neutrophils.

overall_design: The single cell mRNA profiles of NB9464D Tumor microenviroment in wild type and CD200R-/- mice

first: Cho-Hao

last: Lin

first: Fatemeh

last: Talebian

first: Yang

last: Li

first: Jianmin

last: Zhu

first: Jin-Qing

last: Liu

first: Ramesh

last: Ganju

first: Sujit

last: Basu

first: William

middle: E

last: Carson

first: Zihai

first: Ruoning

last: Wang

first: Haitao

last: Wen

first: Qin

last: Ma


title: Opposing transcriptional circuits governing skeletal muscle development and maturation revealed at single nuclear resolution [ChIP-seq]

city: Dallas

first: kenian

last: chen

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
During the maturation of myofibers, the expression and activity of the basic leucine zipper TF Maf are increased compared to developmental stages.
To determine the gene program regulated by this TF, we performed ChIP-seq against Maf and H3K27ac in adult gastrocnemius and quadriceps skeletal muscles.

overall_design: Matthieu ,Dos Santos

first: Akansha

last: Shah

first: Yichi

last: Zhang

first: Kenian

last: Chen

first: Lin

last: Xu

first: Weichun

first: Rhonda

last: Bassel-Duby

first: Ning

first: Eric

middle: N

last: Olson


title: Effectiveness of irinotecan plus trabectedin in a desmoplastic small round cell tumor patient-derived xenograft [II]

status: Public on May 29 2023

city: Milano

first: Stefano

last: Percio

address: VIa Amadeo 42

country: Italy

institute: Istituto Nazionale dei Tumori

summary: Desmoplastic small round cell tumor (DSRCT) is a rare and incurable malignancy characterized by the oncogenic EWSR1-WT1 transcription factor. This study exploited a novel DSRCT patient-derived xenograft (PDX), which reproduces histomorphological and molecular characteristics of the paired clinical tumor, to comparatively assess the activity of cytotoxic and targeted anticancer agents. Anti-tumor effect was moderate for single-agent doxorubicin, pazopanib and larotrectenib [maximum tumor volume inhibition (max TVI): 55-66%] while trabectedin had a higher effect (max TVI: 82%). Single-agent vinorelbine, irinotecan and eribulin achieved a nearly complete tumor growth inhibition (max TVI: 96-98%), although tumors started to re-growth after the end of treatment. Combination of irinotecan with either eribulin or trabectedin resulted in complete responses which were maintained until the end of the experiment for irinotecan plus trabectedin. Irinotecan-based combinations almost completely abrogated the expression of proteins involved in the G2/M checkpoint preventing cell entrance in mitosis and induced apoptotic and necroptotic cell death. This study emphasizes the importance of patient-derived pre-clinical models to explore new treatments in DSRCT and fosters clinical investigation in the activity of irinotecan plus trabectedin.

overall_design: mRNA profiles of treated and untreated PDX samples were generated on an Illumina NovaSeq.

first: Valentina

last: Zuco


title: Tumor-specific CD4 T cells instruct monocyte differentiation in pancreatic ductal adenocarcinoma.

first: Jesse

last: Williams

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

overall_design: Refer to individual Series


title: A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB [ChIP-seq]

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: North Carolina

address: 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina at Chapel Hill

summary: The Polycomb Repressive Complex 2 (PRC2) is a conserved enzyme that tri-methylates Lysine 27 on Histone 3 (H3K27me3) to promote gene silencing. PRC2 is remarkably responsive to the expression of certain long noncoding RNAs (lncRNAs). In the most notable example, PRC2 is recruited to the X-chromosome shortly after expression of the lncRNA Xist begins during X-chromosome inactivation. However, the mechanisms by which lncRNAs recruit PRC2 to chromatin are not yet clear. We report that a broadly used rabbit monoclonal antibody raised against human EZH2, a catalytic subunit of PRC2, cross-reacts with an RNA-binding protein called Scaffold Attachment Factor B (SAFB) in mouse embryonic stem cells (ESCs) under buffer conditions that are commonly used for chromatin immunoprecipitation (ChIP). Knockout of EZH2 in ESCs demonstrated that the antibody is specific for EZH2 by western blot (no cross-reactivity). Likewise, comparison to previously published datasets confirmed that the antibody recovers PRC2-bound sites by ChIP-Seq. However, RNA-IP from formaldehyde-crosslinked ESCs using ChIP wash conditions recovers distinct peaks of RNA association that co-localize with peaks of SAFB and whose enrichment disappears upon knockout of SAFB but not EZH2. IP and mass spectrometry-based proteomics in wild-type and EZH2 knockout ESCs confirm that the EZH2 antibody recovers SAFB in an EZH2-independent manner. Our data highlight the importance of orthogonal assays when studying interactions between chromatin-modifying enzymes and RNA.

overall_design: CS5246 EZH2 ChIP in WT mESCs

first: Rachel

last: Cherney

first: Christine

last: Mills

first: Laura

last: Herring

first: Aki

middle: K

last: Braceros

first: J Mauro


title: Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: This study investigated the mechanisms and novel engineering strategy of locus- specific transgenerational epigenetic inheritance by depositing centromere repeats

overall_design:
(Bisulfite-Seq)  A. thaliana plants were growth on 1/2 X MS agar (0.8%) + 1% sucrose. 1-week-old seedlings were frozen in liquid nitrogen before DNA extraction for sequencing.
(Small RNA-Seq)  A. thaliana plants were grown on 1/2 X MS agar (0.8%) + 1% sucrose. 1-week-old seedlings were frozen in liquid nitrogen before RNA extraction for sequencing.

first: Zhang-wei

last: Liu

first: Jie


title: A Minimal Circadian Clock Network for Glucose Tolerance in Mice

city: barcelona

first: aintzane

last: rueda

state: Choose State

address: C/ del Dr. Trueta, 179, 08005 Barcelona

country: Spain

institute: Sequentia Biotech SL.

summary: Physiology is regulated by interconnected cell and tissue circadian clocks.  Disruption of the rhythms generated by this interconnectedness is associated with  metabolic disease. Here we tested the interactions between clocks in two critical  components of organismal metabolism – liver and skeletal muscle – by rescuing  clock function either in each organ separately, or in both organs simultaneously,  in otherwise clock-less mice. Experiments revealed that individual clocks are  partially sufficient for tissue glucose metabolism, yet the connections between  both tissue clocks coupled with daily feeding rhythms maximizes systemic  glucose tolerance. This synergy relies in part on local transcriptional control of  the glucose machinery, feeding-responsive signals such as insulin, and metabolic  cycles that connect the muscle and liver. We posit that spatiotemporal  mechanisms of muscle and liver play an essential role in the maintenance of  systemic glucose homeostasis, and that disrupting this diurnal coordination can  contribute to the metabolic disease.

overall_design: Gastocnemius muscle and livers were harvested from WT, Bmal1-KO, Liver-RE, Muscle-RE and Liver+Muscle-RE mice after 2 weeks of food access only during the 12 hour dark phase. Bulk RNA-seq was performed on harvested tissues. ZT refers to time in hours since the start of the 12 hour light dark cycle.

first: Jacob

last: Smith

first: Kevin

middle: B

last: Koronowski

first: Thomas

last: Mortimer

first: Tomoki

last: Sato

first: Carolina

middle: M

last: Greco

first: Paul

last: Petrus

first: Amandine

last: Verlande

first: Siwei

first: Muntaha

last: Samad

first: Ekaterina

last: Deyneka

first: Lavina

last: Mathur

first: Ronnie

last: Blazev

first: Jeffrey

last: Molendijk

first: Arun

last: Kumar

first: Oleg

last: Deryagin

first: Mireia

last: Vaca-Dempere

last: Sica

first: Peng

first: Valerio

last: Orlando

first: Benjamin

middle: L

last: Parker

first: Pierre

last: Baldi

first: Patrick-Simon

last: Welz

first: Cholsoon

last: Jang

first: Selma

last: Masri

first: Salvador

last: Aznar Benitah

first: Pura

last: Muñoz-Cánoves Cánoves

first: Paolo

last: Sassone-Corsi


title: A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB [RIP-seq]

first: Joseph

last: Calabrese

overall_design: RIP-seq

first: Rachel

last: Cherney

first: Christine

last: Mills

first: Laura

last: Herring

first: Aki

last: Braceros

first: J Mauro


title: A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB


title: Effectiveness of irinotecan plus trabectedin in a desmoplastic small round cell tumor patient-derived xenograft

first: Stefano

last: Percio

overall_design: mRNA profiles of PDX and clinical sample were generated on an Illumina NextSeq500 sequencer.

first: Valentina

last: Zuco


title: Low temperature and mTOR inhibition favor stem cell maintenance in human keratinocyte cultures

city: Singapore

first: Jun-Ichi

last: Sakabe

address: Blk4 Lv3, Outram Rd

department: Plastic Reconstructive and Aesthetic Surgery

country: Singapore

institute: Singapore General Hospital (SGH)


title: Low temperature and mTOR inhibition favor stem cell maintenance in human keratinocyte cultures [miRNA-seq]

summary:
Purpose: Comparison of genes expression pattern in normal human epidermal keratinocytes (NHEKs) which were cultured at several specific temperatures or with rapamycin.
Methods: Basically, NHEKs were cultured with irradiated 3T3J2 feeder cells in cFAD medium (Pr Green's method) for 1 week. NHEKs were cultured at 32, 35, 36, 37 and 38 degrees C from beginning to end of cell culture, respectively. Furthermore, 100 nM rapamycin-added cFAD medium and ed at 37 degrees C.  7days after cell cuture, NHEKs were harvested for RNAseq analysis.
Results: The culture condition at 32 degrees C and 37 degrees C with rapamycin maintained human epidermal keratinocyte stem cells.
Conclusions: mTORC1 inhibition via temperature changes favors ex vivo maintenance of human epidermal keratinocyte stem cells.

overall_design: miRNA profiles in human epidermal keratinocytes which were cultured at some specific temperatures or with 100 nM rapamycin.

first: Yann

last: Barrandon

first: Jun-ichi

first: Daisuke

last: Nanba

first: Mariko

last: Shimokawa


title: Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response (Mouse Lung scRNA-seq Data)

status: Public on May 28 2023

city: Xiamen

first: Jinhang

last: He

state: Fujian

address: No.4221, South Xiang'an Road

institute: Xiamen University

summary:
The emergence of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) variants and “anatomical escape” characteristics threaten the effectiveness of current coronavirus disease (COVID-19) vaccines. There is an urgent need to understand the immunological mechanism of broad-spectrum respiratory tract protection to guide broader vaccines development. In this study, we investigated immune responses induced by an NS1-deleted influenza virus vectored intranasal COVID-19 vaccine (dNS1-RBD) which provides broad-spectrum protection against SARS-CoV-2 variants. Intranasal delivery of dNS1-RBD induced innate immunity, trained immunity and tissue-resident memory T cells covering the upper and lower respiratory tract. It restrained the inflammatory response by suppressing early phase viral load post SARS-CoV-2 challenge and attenuating pro-inflammatory cytokine (IL-6, IL-1B, and IFN-γ) levels, thereby reducing excess immune-induced tissue injury compared with the control group. By inducing local cellular immunity and trained immunity, intranasal delivery of NS1-deleted influenza virus vectored vaccine represents a broad-spectrum COVID-19 vaccine strategy to reduce disease burden.
To investigate the immune response generated by dNS1-RBD, dNS1-Vector and wild type Influenza virus CA04 in C57BL/6 mouse lung, we vaccinated/infected C57BL/6 mice and collected the lung samples at different time point post vaccinated/infected to sequence for the single cell RNA-seq data, then performed normalization, clustering, reduction, cell type annotation, differential expression analysis and enrichment analysis based on this dataset.

overall_design: Comparative gene expression and enrichment analysis of C57BL/6 mice lung scRNA-seq data at different time points(1, 7, 44 dpi) post vaccinated/infected with dNS1-RBD, dNS1-Vector and wild type Influenza virus CA04.

first: Liang

last: Zhang

first: Yao

last: Jiang


title: Low temperature and mTOR inhibition favor stem cell maintenance in human keratinocyte cultures [RNA-seq]

overall_design: mRNA profiles in human epidermal keratinocytes which were cultured at some specific temperatures or with 100 nM rapamycin.


title: Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response (Hamster AMs ATAC-seq Data)

summary:
The emergence of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) variants and “anatomical escape” characteristics threaten the effectiveness of current coronavirus disease (COVID-19) vaccines. There is an urgent need to understand the immunological mechanism of broad-spectrum respiratory tract protection to guide broader vaccines development. In this study, we investigated immune responses induced by an NS1-deleted influenza virus vectored intranasal COVID-19 vaccine (dNS1-RBD) which provides broad-spectrum protection against SARS-CoV-2 variants. Intranasal delivery of dNS1-RBD induced innate immunity, trained immunity and tissue-resident memory T cells covering the upper and lower respiratory tract. It restrained the inflammatory response by suppressing early phase viral load post SARS-CoV-2 challenge and attenuating pro-inflammatory cytokine (IL-6, IL-1B, and IFN-γ) levels, thereby reducing excess immune-induced tissue injury compared with the control group. By inducing local cellular immunity and trained immunity, intranasal delivery of NS1-deleted influenza virus vectored vaccine represents a broad-spectrum COVID-19 vaccine strategy to reduce disease burden.
To investigate the trainned-immunity of alveolar macrophage generated by dNS1-RBD vaccine in Golden Hamster, we vaccinated Golden Hamster with dNS1-RBD/dNS1-Vector/PBS and collect the alveolar macrophage samples to sequence for the ATAC-seq data 2 months post vaccinated. Then performed the differential peak and igv track visualization with this dataset.

overall_design: Differential peak and igv track visualization and enrichment analysis analysis of alveolar macrophage ATAC-seq data in dNS1-RBD/dNS1-Vector/PBS vaccinated group at 2 weeks post immunization.


title: Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response (Hamster Lung RNA-seq Data)

summary:
The emergence of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) variants and “anatomical escape” characteristics threaten the effectiveness of current coronavirus disease (COVID-19) vaccines. There is an urgent need to understand the immunological mechanism of broad-spectrum respiratory tract protection to guide broader vaccines development. In this study, we investigated immune responses induced by an NS1-deleted influenza virus vectored intranasal COVID-19 vaccine (dNS1-RBD) which provides broad-spectrum protection against SARS-CoV-2 variants. Intranasal delivery of dNS1-RBD induced innate immunity, trained immunity and tissue-resident memory T cells covering the upper and lower respiratory tract. It restrained the inflammatory response by suppressing early phase viral load post SARS-CoV-2 challenge and attenuating pro-inflammatory cytokine (IL-6, IL-1B, and IFN-γ) levels, thereby reducing excess immune-induced tissue injury compared with the control group. By inducing local cellular immunity and trained immunity, intranasal delivery of NS1-deleted influenza virus vectored vaccine represents a broad-spectrum COVID-19 vaccine strategy to reduce disease burden.
To investigate the immune response, pathological process caused by SARS-CoV-2 Beta variants infection in Golden Hamster lung. Golden hamsters were vaccinated with dNS1-RBD vaccine at day0 and day 14, and 2 months later the vccinated hamster were challenged with SARS-CoV-2 Beta varians together with control group hamster. Then the lung samples were collected at 0, 1, 3, 5 post infection to sequence for the RNA-seq data, then performed gene expression analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression analysis and enrichment analysis analysis of lung RNA-seq data of control group and vaccinated group at different time point (day 0, 1, 3, 5) post SARS-CoV-2 Beta Virus challenge.


title: Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response (Mouse Lung RNA-seq Data)

summary:
The emergence of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) variants and “anatomical escape” characteristics threaten the effectiveness of current coronavirus disease (COVID-19) vaccines. There is an urgent need to understand the immunological mechanism of broad-spectrum respiratory tract protection to guide broader vaccines development. In this study, we investigated immune responses induced by an NS1-deleted influenza virus vectored intranasal COVID-19 vaccine (dNS1-RBD) which provides broad-spectrum protection against SARS-CoV-2 variants. Intranasal delivery of dNS1-RBD induced innate immunity, trained immunity and tissue-resident memory T cells covering the upper and lower respiratory tract. It restrained the inflammatory response by suppressing early phase viral load post SARS-CoV-2 challenge and attenuating pro-inflammatory cytokine (IL-6, IL-1B, and IFN-γ) levels, thereby reducing excess immune-induced tissue injury compared with the control group. By inducing local cellular immunity and trained immunity, intranasal delivery of NS1-deleted influenza virus vectored vaccine represents a broad-spectrum COVID-19 vaccine strategy to reduce disease burden.
To investigate the immune response generated by dNS1-RBD vaccine in C57BL/6 mouse lung, we vaccinated C57BL/6 mice and collect the lung samples to sequence for the RNA-seq data, then performed gene expression analysis using data obtained from RNA-seq of 5 different time points before and after vaccinated with dNS1-RBD vaccine.

overall_design: Comparative gene expression analysis and enrichment analysis analysis of lung RNA-seq data for non-vaccinated and different time points(1,7,14,28 days post vaccinated)


title: Use of the dTAG system in vivo to degrade CDK2 and CDK5 in adult mice and explore potential safety liabilities

city: Groton

first: Seda

last: Arat

state: CT

address: 445 Eastern Point Road

institute: Pfizer


title: Use of the dTAG system in vivo to degrade CDK2 and CDK5 in adult mice and explore potential safety liabilities [Bone marrow]

summary: The degradation tag (dTAG) system for target protein degradation can remove proteins from biological systems without the drawbacks of some genetic methods, such as slow kinetics, lack of reversibility, low specificity, and the inability to titrate dosage. These drawbacks can make it difficult to compare toxicity resulting from genetic and pharmacological interventions, especially in vivo. Because the dTAG system has not been studied extensively in vivo, we explored the use of this system to study the physiological sequalae resulting from CDK2 or CDK5 degradation in adult mice. Mice with knock-in of the dTAG sequence onto the C-terminus of CDK2 and CDK5 were born at Mendelian ratios despite decreased CDK2 or CDK5 protein levels in comparison to wild-type mice. In bone marrow cells and duodenum organoids derived from these mice, treatment with the dTAG degrader dTAG-13 resulted in rapid and robust protein degradation but caused no appreciable change in viability or the transcriptome. Repeated delivery of dTAG-13 in vivo for toxicity studies proved challenging; we explored multiple formulations in an effort to maximize degradation while minimizing formulation-related toxicity. Degradation of CDK2 or CDK5 in all organs except the brain, where dTAG-13 likely did not cross the blood brain barrier, only caused microscopic changes in the testis of CDK2dTAG mice. These findings were corroborated with conditional CDK2 knockout in adult mice. Our results suggest that the dTAG system can provide robust protein degradation in vivo and that loss of CDK2 or CDK5 in adult mice causes no previously unknown phenotypes.

overall_design: Samples were washed in PBS and then RNA was harvested using the RNeasy Mini Micro Kit from Qiagen. Libraries were prepped using Lexogen QuantSeq 3' mRNA-seq library preparation kit for Illumina (FWD) (Lexogen, catalog # 015.96) and sequenced on an Illumina machine

first: Paul

last: Yenerall

first: Jessie

last: Qian


title: Use of the dTAG system in vivo to degrade CDK2 and CDK5 in adult mice and explore potential safety liabilities [Duodenum]


title: A genome-wide screening in pluripotent cells identifies Mtf1 as a suppressor of mutant huntingtin toxicity

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

institute: University of Padua

summary: Huntington’s disease (HD) is an inherited and incurable neurodegenerative disorder caused by CAG repeat expansions in the huntingtin (HTT) gene. The resulting mutant HTT protein alters cellular physiology at multiple levels, inducing toxicity and cell death. The mechanisms directly causing toxicity are partially understood, thus precluding the development of effective therapeutic strategies. Here we identified novel suppressors of mutant HTT toxicity by performing a genome-wide screen in pluripotent stem cells, followed by hit validation both in zebrafish and mouse HD models. The candidate suppressors identified were strongly enriched for HD-associated processes. We focused on Metal regulatory transcription factor 1 (Mtf1), a transcription factor controlling metal homeostasis in the cell. Forced expression of Mtf1 counteracts cell death, oxidative stress and transcriptional alterations caused by mutant HTT in pluripotent cells. In zebrafish, Mtf1 reduces malformations and apoptosis induced by mutant HTT, while Mtf1 delivery by Adeno-Associated viral (AAV) vectors ablated motor defects observed in an HD mouse model. Our data reveal that delivery of Mtf1 might act as a novel therapeutic strategy against HD and potentially other neurodegenerative disorders.

overall_design: Library Preparation  Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific). Libraries were prepared from (125* - 250** - 250***) ng of total RNA using a 3'DGE mRNA-seq (research*/clinical**/diagnostic***) grade sequencing service (Next Generation Diagnostics srl)1 which included library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing system using a single-end, 100 cycle strategy (Illumina Inc.).     Bioinformatics workflow  The raw data were analyzed by Next Generation Diagnostics srl proprietary 3'DGE mRNA-seq pipeline (v2.0) which involves a cleaning step by quality filtering and trimming, alignment to the reference genome and counting by gene.  We have filtered out all genes having < 1 cpm in less than n_min samples and Perc MM reads > 20% simultaneously. Differential expression analysis was performed using edgeR.


title: The NCOR-HDAC3 co-repressive complex modulates the leukemogenic  potential of ERG.

status: Public on May 26 2023

city: Petah Tikva

first: Eitan

last: Kugler

state: Please make your selection

address: Zeev Jabutinsky Rd 39

department: Hematology

country: Israel

institute: Rabin medical center

summary: The ETS transcription factor ERG is involved in several cancers including leukemia. However, ERG domains and co-factors involved in leukemogenesis remain largely uncharacterized and as a transcription factor it is currently undruggable. Here, we report a critical role for the conserved amino-acid proline at position 199, at the 3’ end of the PNT domain, for ERG’s leukemogenic activity. Specifically, we demonstrate that it is required for ERG-induced self-renewal and restriction of myeloid differentiation in hematopoietic progenitor cells and for initiation of leukemia in mouse transduction/transplantation models. Mechanistically, we show that P199 facilitates the interaction of ERG with the NCoR-HDAC3 co-repressor complex. Inhibition of HDAC3 reduced in vitro and in vivo growth of human ERG-dependent leukemic cells as well as growth of ERG dependent prostate cancer cells. Thus, the interaction of ERG with the NCoR-HDAC3 co-repressor complex is required for its oncogenic activity and modulation of this interaction may provide an opportunity for therapeutic intervention.

overall_design: Murine fetal liver derived HSCP transduced with ERG variants, RNA sequencing

first: Shreyas

last: Madiwale

first: Darren

last: Yong

first: Julie

last: Thoms

first: Yehudit

last: Birger

first: David

last: Sykes

first: Johannes

last: Schmoellerl

first: Aneta

last: Drakul

first: Valdemar

last: Priebe

first: Muhammad

last: Yassin

first: Nasma

last: Aqaqe

first: Avigail

last: Rein

first: Hila

last: Fishman

first: Ifat

last: Geron

first: Chun-Wei

last: Chen

first: Brian

last: Raught

first: Qiao

last: Liu

first: Heather

last: Ogana

first: Elisabeth

last: Liedke

first: Jean-Pierre

last: Bourquin

last: Zuber

first: Michael

last: Milyavsky

first: John

last: Pimanda

first: Gilbert

last: Privé

first: Shai

last: Izraeli


title: Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response

first: Jinhang

last: He

sample_organism:
Mesocricetus auratus
Mus musculus

platform_organism:
Mesocricetus auratus
Mus musculus


first: Eitan

last: Kugler

overall_design: ER-Hoxb8 cells stably expressing ERG variants and an empty vector for control were carefully washed to remove beta-estradiol followed by treatment with either 5µM BRD3308 or DMSO. For each sample type, we conducted four independent experiments. Cells were incubated for 36 hours, fluidized in TRIzol, and prepared for RNA sequencing

first: Shreyas

last: Madiwale

first: Darren

last: Yong

first: Julie

last: Thoms

first: Yehudit

last: Birger

first: David

last: Sykes

first: Johannes

last: Schmoellerl

first: Aneta

last: Drakul

first: Valdemar

last: Priebe

last: Yassin


title: Effect of Aβ40 or PBS induced migrasome on endotheliel cells

status: Public on May 25 2023

city: Guangzhou

first: Mengyan

last: Hu

address: guangzhou,china

institute: SYSU

summary: To investigate the effect of Aβ40  induced migrasome on endotheliel cells, We treat Aβ40 or PBS induced migrasome  to brain blood vessel endothelial cells at a concentration of 50μg/ml for 2h.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Aβ40 or PBS induced migrasome on endotheliel cells.


title: Detecting intragenic trans-splicing events with hybrid transcriptome sequencing in cancer cells

city: Taipei

first: Trees-Juen

last: Chuang

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: Analysis of high-throughput transcriptome sequencing (RNA-seq) data often observed numerous 'non-co-linear' (NCL) transcripts

overall_design:
The generated MCF7 Illumina RNA-seq data of ribosomal RNA-depleted
RNAs without poly(A) selection. The datasets were generated to eliminate potential false positives, fusion events, and circRNAs.


title: A single amino acid at the PNT domain of ERG mediates its leukemogenic activity through interaction with the NCoR-HDAC3 co-repressor complex.

overall_design: Refer to individual Series


title: Coupling of co-transcriptional splicing and 3’ end Pol II pause during termination in Arabidopsis

status: Public on May 27 2023

city: Hangzhou

first: Fengli

last: Zhao

state: Zhejiang

address: No. 28 of Shuidaosuo Road

department: State Key Laboratory of Rice Biology and Breeding

institute: China National Rice Research Institute

summary: In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pause is regulated remains largely elusive. Here, we studied Pol II dynamics at gene 3’ end by combining comprehensive experiments with mathematical modelling. We generated high-resolution Ser2P Pol II positioning data specifically enriched at gene 3’ end and defined a 3’ end pause index (3’PI).  The position but not the extent of the 3’ end pause correlates with termination window size. The 3’PI is not decreased but even mildly increased in the termination deficient mutant xrn3, indicating 3’ end pause is a regulatory step early during the termination and before XRN3 mediated RNA decay that releases the Pol II. Unexpectedly, 3’PI is closely associated with gene exon numbers and co-transcriptional splicing efficiency. Multiple exons genes often display stronger 3’ end pauses and more efficient on-chromatin splicing than genes with few exons. Chemical inhibition of splicing strongly reduces the 3’PI and disrupts its correlation with exon numbers but does not globally impact 3’ end readthrough levels. These results were further confirmed by fitting Pol II positioning data with a mathematical model, which enables the estimation of parameters that define Pol II dynamics. Our work highlights that the number of exons via co-transcriptional splicing is a major determinant of Pol II pausing levels at gene 3’ end in plants.

overall_design: pNET-seq was performed using Pol II Ser 2P antibody 3E10 to profile the elongating transcripts genome wide in Arabidopsis. As a complementary, RNA-seq was performed in the same conditions to measure the nascent RNA.

first: Sixian

last: Zhou

first: Danling

last: Zhu

first: Qiqi

last: Zhang

first: Ziwei

last: Dai

first: Zhe

last: Wu


title: Gene expression in AML12 cells after Uhrf2 knock-down

city: Zurich

first: Sabine

last: Werner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

summary: We identified the ubiquitin ligase Uhrf2 as a key regulator of liver regeneration. To determine the underlying mechanisms of action, we performed siRNA-mediated knockdown of Uhrf2 in AML12 cells and analysed the transcriptome of the Uhrf2-deficient cells.

overall_design: AML12 cells were treated with siRNA against Uhrf2 or scrambled siRNA for 72h andd gene expression profiling was determined using RNA-seq.

first: Coenraad

middle: F

last: Slabber

first: Andrii

last: Kuklin


title: Murine colonic epithelial cells: Trabid(Zranb1) C443S hetero knock-in mouse (KI/+) vs. homo knock-in mouse (KI/KI)

status: Public on May 24 2023

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Transcriptional profiling of colonic epithelial cells comparing control Trabid KI/+ with KI/KI

overall_design: Two-condition experiment, KI/+ vs. KI/KI. Biological replicates: 3 KI/+, 2 KI/KI. One replicate per array.

first: Akiko

last: Tamura

first: Shigeru

last: Oshima


title: Transcriptomic signatures of feline chronic gingivostomatitis are influenced by upregulated IL6

city: Ithaca

first: Jennifer

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: Feline chronic gingivostomatitis (FCGS) is a relatively common and debilitating disease characterized by bilateral inflammation and ulceration of the caudal oral mucosa, alveolar and buccal mucosa, and varying degrees of periodontal disease. The etiopathogenesis of FCGS remains unresolved. In this study, we performed bulk RNA-seq molecular profiling of affected tissues derived from a cohort of client-owned cats with FCGS compared to tissues from unaffected animals, to identify candidate genes and pathways that can help guide future exploration of novel clinical solutions. We complemented transcriptomic findings with immunohistochemistry and in situ hybridization assays to better understand the biological significance of the results and performed RNA-seq validation of selected differentially expressed genes using qPCR assays to demonstrate technical reproducibility. Transcriptomic profiles of oral mucosal tissues in cats with FCGS are enriched with immune- and inflammation-related genes and pathways that appear to be largely influenced by IL6, and include NFKB, JAK/STAT, IL-17 and IFN type I and II signaling, offering new opportunities to develop novel clinical applications based on a more rational understanding of the disease.

overall_design: Gene expression analysis using RNAseq for 4 groups of samples: Feline chronic gingivostomatitis (8 cases), healthy oral mucosa (8 samples from 5 control animals), periodontitis (6 cases), and healthy gingiva (3 controls).

first: Santiago

last: Peralta


title: A viral ADP-ribosyltransferase attaches RNA chains to host proteins

city: Marburg

first: Katharina

last: Höfer

address: Karl-von-Frisch-Str. 14

country: Germany

institute: Max-Planck-Institute for terrestrial Microbiology

summary: The mechanisms by which viruses hijack their host’s genetic machinery are of current interest. When bacteriophage T4 infects Escherichia coli, three different ARTs (ADP-ribosyltransferases) reprogram the host’s transcriptional and translational apparatus through ADP-ribosylation using nicotinamide adenine dinucleotide (NAD) as substrate. Recently, NAD was identified as a 5’-modification of cellular RNAs. Here, we report that T4 ART ModB accepts not only NAD but also NAD-capped RNA (NAD-RNA) as substrate and attaches entire RNA chains to acceptor proteins in an “RNAylation” reaction. ModB specifically RNAylates ribosomal proteins rS1 and rL2 at defined arginine residues, and selected E. coli and T4 phage RNAs are linked to rS1 in vivo. T4 phages that express an inactive mutant of ModB show a decreased burst size and slowed lysis of E. coli. Our findings reveal a distinct biological role of NAD-RNA, namely activation of the RNA for enzymatic transfer to proteins. The attachment of specific RNAs to ribosomal proteins might provide a strategy for the phage to modulate the host’s translation machinery. This work exemplifies the first direct connection between RNA modification and post-translational protein modification. As ARTs play important roles far beyond viral infections, RNAylation may have far-reaching implications.

overall_design: Exponentially growing E. coli with endogenously His-tagged rS1 were infected with T4 phage WT or T4 phage ModB R73A,G74A or not infected for 8 minutes. His-tagged rS1 was captured and covalently bound RNA was reverse transcribed and sequenced using our RNAylomeSeq pipeline. His-tagged rS1 RNAylated with NAD-RNAI was used as a spike-in to monitor success of capture of RNAylated RNAs by RNAylomeSeq. Uninfected and ModB R73A,G74A infected samples serve as negative controls for the WT infected samples.

first: Maik

last: Wolfram-Schauerte


title: Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response (Mouse AMs ATAC-seq Data)

first: Jinhang

last: He

summary:
The emergence of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) variants and “anatomical escape” characteristics threaten the effectiveness of current coronavirus disease (COVID-19) vaccines. There is an urgent need to understand the immunological mechanism of broad-spectrum respiratory tract protection to guide broader vaccines development. In this study, we investigated immune responses induced by an NS1-deleted influenza virus vectored intranasal COVID-19 vaccine (dNS1-RBD) which provides broad-spectrum protection against SARS-CoV-2 variants. Intranasal delivery of dNS1-RBD induced innate immunity, trained immunity and tissue-resident memory T cells covering the upper and lower respiratory tract. It restrained the inflammatory response by suppressing early phase viral load post SARS-CoV-2 challenge and attenuating pro-inflammatory cytokine (IL-6, IL-1B, and IFN-γ) levels, thereby reducing excess immune-induced tissue injury compared with the control group. By inducing local cellular immunity and trained immunity, intranasal delivery of NS1-deleted influenza virus vectored vaccine represents a broad-spectrum COVID-19 vaccine strategy to reduce disease burden.
To investigate the trainned-immunity of alveolar macrophage generated by dNS1-RBD vaccine in C57BL/6 mouse, we vaccinated C57BL/6 mice with dNS1-RBD/dNS1-Vector/PBS and collect the alveolar macrophage samples to sequence for the ATAC-seq data 2 months post vaccinated. Then performed the differential peak and igv track visualization with this dataset.

overall_design: Differential peak and igv track visualization and enrichment analysis analysis of alveolar macrophage ATAC-seq data in dNS1-RBD/dNS1-Vector/PBS vaccinated group at 2 months post immunization.

first: Liang

first: Yao

last: Jiang


title: Aberrant gene activation in synovial sarcoma relies on SSX specificity and increased PRC1.1 stability

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

institute: University of Edinburgh

summary: The SS18-SSX fusion drives oncogenic transformation in synovial sarcoma by bridging SS18, a member of the mSWI/SNF (BAF) complex, to Polycomb repressive complex 1 (PRC1) target genes. Here we show that the ability of SS18-SSX to occupy H2AK119ub1-rich regions is an intrinsic property of its SSX C terminus, which can be exploited by fusion to transcriptional regulators beyond SS18. Accordingly, SS18-SSX recruitment occurs in a manner that is independent of the core components and catalytic activity of BAF. Alternative SSX fusions are also recruited to H2AK119ub1-rich chromatin and reproduce the expression signatures of SS18-SSX by engaging with transcriptional activators. Variant Polycomb repressive complex 1.1 (PRC1.1) acts as the main depositor of H2AK119ub1 and is therefore required for SS18-SSX occupancy. Importantly, the SSX C terminus not only depends on H2AK119ub1 for localization, but also further increases it by promoting PRC1.1 complex stability. Consequently, high H2AK119ub1 levels are a feature of murine and human synovial sarcomas. These results uncover a critical role for SSX-C in mediating gene deregulation in synovial sarcoma by providing specificity to chromatin and further enabling oncofusion binding by enhancing PRC1.1 stability and H2AK119ub1 deposition.

overall_design: Calibrated Native Chromatin immunoprecipitation DNA-sequencing (cChIP-seq) for H2AK119ub1 in human synovial sarcoma cells HS-SY-II after PCGF1 knockout

middle: S

first: Ana

last: Banito


first: Eitan

last: Kugler

overall_design: ChIP material was prepared from ER-Hoxb8 cells stably expressing ERG variants and an empty vector for control. Immunoprecipitation was preform using polyclonal antibody raised against H3K27ac, H3K4me1, H3K4me3, H3K9ac (Abcam). As a control, nonspecific rabbit IgG (I5006; Sigma Aldrich) was used.

first: Shreyas

last: Madiwale

first: Darren

last: Yong

first: Julie

last: Thoms

first: Yehudit

last: Birger

first: David

last: Sykes

first: Johannes

last: Schmoellerl

first: Aneta

last: Drakul

first: Valdemar

last: Priebe

first: Muhammad

last: Yassin

first: Nasma

last: Aqaqe

first: Avigail

last: Rein

first: Hila

last: Fishman

first: Ifat

last: Geron

first: Chun-Wei

last: Chen

first: Brian

last: Raught

first: Qiao

last: Liu

first: Heather

last: Ogana

first: Elisabeth

last: Liedke

first: Jean-Pierre

last: Bourquin

last: Zuber

first: Michael

last: Milyavsky

first: John

last: Pimanda

first: Gilbert

last: Privé

first: Shai

last: Izraeli


title: Genome-wide occupancy map of NFIC in mouse pancreas

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

summary: In order to identify direct NFIC target genes, in the context of pancreatic homeostasis, ChIP-seq was performed using pancreata from 8-10 week-old wild type mice.

overall_design: Assessment of NFIC binding in 8-12 week-old mouse pancreas genome

first: Sumit

last: Paliwal

first: Isidoro

last: Cobo

last: de Villarreal

first: Francisco

middle: X

last: Real


title: Identification of KMT5A regulated genes in prostate cancer

city: Newcastle upon Tyne

first: Kelly

last: Coffey

address: Framlington Place

department: Biosciences Institute

institute: Newcastle University

summary: The methyltransferase, KMT5A, is suggested as an oncogene in prostate cancer but the mechanisms underlying its oncogenic properties are poorly understood. This study uncovers genes and cellular pathways which are regulated by KMT5A in LNCaP-AI cells, a model of androgen independence.

overall_design: LNCaP-AI cells were grown in steroid depleted media whilst knockdown was performed using 2 independent siKMT5A sequences or a non-silencing sequence over 72 hours. Dihydrotestosterone (DHT) or DMSO vehicle control was then applied for a further 24 hours. RNA was isolated using TRIzol. 4 biological replicates for each sample was carried out. Total of 24 samples.

first: Zainab

last: Alebady

first: Mahsa

last: Azizyan

first: Sirintra

last: Nakjang

first: Emma

last: Lishman-Walker

first: Dhuha

last: Al-Karaif

first: Hui

last: Choo

first: Rebeccs

last: Garnham

last: Scott

first: Katya

last: Johnson

first: Craig

last: Robson


title: RNA-Seq of wild type and Nfic-/- mice pancreata

summary: To assess the role of Nfic in pancreatic development and homeostasis we used constitutive Nfic knockout mice.

overall_design: RNA-Seq of  4 wild type  and  3 Nfic-/- pancreata from 8-10 week-old mice

last: Villarreal


title: SEC-seq human plasma cells in nanovials

status: Public on May 23 2023

city: Seattle

first: Rene

last: Cheng

state: WA

address: 1900 9th AVE

institute: Seattle children research institute

summary: SEC-seq human plasma cells in nanovials

overall_design: Ex vivo differentiated B cells day 10 and day13 in nanovial.

middle: Y

first: Richard

last: James

first: Dino

last: Di Carlo

first: Joe

last: de Rutte


title: Transcriptome expression in Paspalum vaginatum under salt stress

city: Haikou

first: Xu

last: Hu

state: Hainan

address: 58 Renmin Avenue, Meila

institute: Hainan University

summary: Lipid metabolism and antioxidant system contributed to salt salinity tolerance induced by Na+ accumulation in halophytic grass seashore paspalum

overall_design: Two-month-old plants were treated with 400 mM NaCl or water as a control for 8, 12, 24, or 48 h or 5 days before harvesting tissues. Total RNAs were isolated from leaves with three biological replicates at each stress stage.

first: Zhiyong

last: Wang

first: Minqiang

last: Tang


title: Broadly-applicable control approaches improve accuracy of ChIP-seq data

city: Los Angeles

first: Meghan

middle: V

last: Petrie

state: CA

address: 1050 Childs Way

department: Molecular Biology

institute: University of Southern California

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) with and without designed internal controls.

first: Yiwei

last: He

first: Yan

last: Gan

first: A

middle: Z

last: Ostrow

first: Oscar

last: Aparicio


title: The response of WT, ∆rip1, and ∆sigL strains of Mycobacterium tuberculosis to dipyridyl treatment

city: Worcester

first: Christopher

last: Sassetti

state: MA

address: 55 Lake Ave North

institute: University of Massachusetts Chan Medical School

summary: Mycobacterium tuberculosis is exposed to a variety of stresses during a chronic infection, as the immune system simultaneously produces bactericidal compounds and starves the pathogen for essential nutrients. The intramembrane protease, Rip1, plays an important role in the adaptation to these stresses, at least partially by the cleavage of membrane bound transcriptional regulators. Although Rip1 is known to be critical for surviving copper intoxication and nitric oxide exposure, these stresses do not fully account the regulatory protein’s essentiality during infection.  In this work, we demonstrate that Rip1 is also necessary for growth in low iron and zinc conditions, similar to those imposed by the immune system.  Using a newly generated library of sigma factor mutants, we show that the known regulatory target of Rip1, SigL, shares this defect.  Transcriptional profiling under iron limiting conditions supported the coordinated activity of Rip1 and SigL and demonstrated that the loss of these proteins produces an exaggerated iron starvation response. These observations demonstrate that Rip1 coordinates several aspects of metal homeostasis and suggest that a Rip1- and SigL-dependent pathway is involved in the adaptation to the iron deficient environments encountered during infection.

overall_design: Gene expression profiling of Mycobacterium tuberculosis WT H37Rv and knockout mutants in response to dipryidyl treatment

first: Samantha

last: Nelson

first: Thomas

middle: R

last: Ioerger


title: The identification of protein and RNA interactors of the splicing factor Caper in the adult Drosophila nervous system

city: Colorado Springs

first: Michael

middle: Brandon

last: Titus

state: Colorado

address: 1420 Austin Bluffs Pkwy  Colorado Springs, CO  USA 80918

institute: University of Colorado Colorado Springs

summary: Post-transcriptional gene regulation is a fundamental mechanism that helps regulate the development and healthy aging of the nervous system. Mutations that disrupt the function of RNA-binding proteins (RBPs), which regulate post-transcriptional gene regulation, have increasingly been implicated in neurological disorders including amyotrophic lateral sclerosis, Fragile X Syndrome, and spinal muscular atrophy. Interestingly, although the majority of RBPs are expressed widely within diverse tissue types, the nervous system is often particularly sensitive to their dysfunction. It is therefore critical to elucidate how aberrant RNA regulation that results from the dysfunction of ubiquitously expressed RBPs leads to tissue specific pathologies that underlie neurological diseases. The highly conserved RBP and alternative splicing factor Caper is widely expressed throughout development and is required for the development of Drosophila sensory and motor neurons. Furthermore, caper dysfunction results in larval and adult locomotor deficits. Nonetheless, little is known about which proteins interact with Caper, and which RNAs are regulated by Caper. Here we identify proteins that interact with Caper in both neural and muscle tissue, along with neural specific Caper target RNAs. Furthermore, we show that a subset of these Caper-interacting proteins and RNAs genetically interact with caper to regulate Drosophila gravitaxis behavior.

overall_design: RIPSeq experiment performed on Drosophila heads with FLAG-tagged Caper using either Caper or FLAG antibody.

first: M

first: Adeline

middle: W

last: Chang

first: Niko

last: Popitsch

middle: C

last: Ebmeier

first: Jeremy

last: Bono

first: Eugenia

last: Olesnicky


first: Nezha

last: Benabdallah

overall_design: RNA sequencing of human mesenchymal stem cells expressing various oncofusions

first: Ana

last: Banito


title: Genotoxic aldehyde stress prematurely ages hematopoietic stem cells in a p53-driven manner

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

summary:
Aged hematopoietic stem cells (HSC) display diminished self-renewal and a myeloid differentiation bias. However, the physiological drivers and molecular processes that underpin this fundamental switch are not understood. HSCs produce formaldehyde and are protected from this metabolite by two tiers of protection: the detoxification enzymes ALDH2 and ADH5 and the Fanconi anemia (FA) DNA repair pathway. Using single cell RNA sequencing, we find that the HSC and progenitor cells in young Aldh2-/- Fancd2-/- mice harbor a transcriptomic signature equivalent to aged wild-type HSCs, along with increased epigenetic age, telomere attrition and myeloid-biased progenitors. In addition, the p53 response is vigorously activated in Aldh2-/- Fancd2-/- HSCs, whilst p53 deletion rescued this aged transcriptomic signature and telomere attrition. Transplantation of single Aldh2-/- Fancd2-/- HSCs also reveals a predominantly myeloid output, which is reversed upon p53 deletion. To further define the origins of the myeloid differentiation bias, a GFP genetic reporter which detects Vwf+ myeloid primed HSCs was crossed into Aldh2-/- Fancd2-/- mice, revealing a striking enrichment
of these lineage-biased Vwf+ HSCs. These results indicate that metabolism derived formaldehyde causes endogenous DNA damage which stimulates the p53 response in HSCs, which then accelerates their aging, resulting in a myeloid lineage biased output.

overall_design: Lin-Sca1+cKit+ cells from WT, Aldh2 knock-outs, Fancd2 knock-outs, p53 knock-outs, Aldh2 & Fancd2 double knock-outs, Aldh2 & Fancd2 & p53 triple knock-outs

first: Meng

first: Laura

middle: T

last: Brandt

first: Holly

last: Russel

first: Emily

last: Mitchell

first: Ashley

middle: N

last: Kamimae-Lanning

first: Jill

last: Brown

first: Felix

middle: A

last: Dingler

first: Juan

middle: I

last: Garaycoechea

first: Tomoya

last: Isobe

first: Sarah

middle: J

last: Kinston

first: Muxin

last: Gu

first: George

last: Vassiliou

first: Nicola

last: Wilson

first: Berthold

last: Göttgens

first: Ketan

last: Patel


title: ACK1/TNK2 Epigenetically Regulates Cell Cycle Program to Promote Breast Cancer Resistance to CDK4/6 inhibitor

city: St Louis

first: Tiandao

last: Li

address: 4444 Forest Park Ave

institute: Washington University

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

overall_design: Refer to individual Series


title: ACK1/TNK2 Epigenetically Regulates Cell Cycle Program to Promote Breast Cancer Resistance to CDK4/6 inhibitor (ChIP-Seq)

summary: Over-activation of oncogenes by aberrant expression of epigenetic modulators, overcoming cell cycle checkpoints and bestowing infinite multiplication potency acts as the mainstay of malignancy. We identified one such non-receptor tyrosine kinase ACK1 as an epigenetic regulator of cell cycle genes governing the G2/M transition of breast cancer cells. ACK1 was found to be over-activated (pY264-ACK1) in most of the breast cancer sub-types, independent of their hormone receptor status, as assessed by the Tissue-microarray analysis of nearly 400 breast cancer patient samples. ACK1 primed the epigenetic landscape surrounding the genes CCNB1, CCNB2 and CDC20 by depositing Y88-H4 histone activation marks, in turn initiating their efficient transcription. Pharmacological inhibition of ACK1 using small molecular inhibitor (R)-9b not only reversed this transcriptional potential but also sensitized the cells to a G2/M arrest, culminating in breast cancer cell death and tumor regression in in vivo xenograft models of breast cancer. Further, ACK1 was also found to modulate expression of the gene CXCR4, circumventing breast cancer metastasis on ACK1 ablation.  In addition, ACK1 inhibition was also found to counteract the resistance of RB1 deficient breast cancer cells to the CDK4/6 inhibitor palbociclib, overcoming road blocks to conventional therapeutics. Overall, our data warrants the identification of ACK1 as an epigenetic controller of genes essential for the successful establishment and progression of breast cancer and signifies development of therapeutics against ACK1 to combat intrinsic and acquired breast cancer resistance.

overall_design: MDA-MB-453 cells were treated overnight with 5µM (R)-9b (also known dz67) and the lysates were subjected to chromatin immunoprecipitation using pY88-H4 antibody. The immunoprecipitated chromatin was further subjected to high throughput sequencing.

first: Nupam

middle: P

last: Mahajan


title: ACK1/TNK2 Epigenetically Regulates Cell Cycle Program to Promote Breast Cancer Resistance to CDK4/6 inhibitor (RNA-Seq)

overall_design: MDA-MB-453 and HCC-1395 breast cancer cells were treated overnight with 5µM (R)-9b (also known as dz67) and RNA was prepared from these cells.


title: 10x genomics single cell sequencing of yak testis

status: Public on May 22 2023

city: Lanzhou

first: Xingdong

last: Wang

state: 未选择

address: No.335 Jiangouyan, Qilihe District

institute: CAAS: Chinese Academy of Agricultural Sciences

summary: Testis is the most important male reproductive organ, and the integrity of its physiological function is crucial to the successful production of sperm. In this study, the expression profiles of 11 991 and 8 930 cells in testicular tissue of yak and cattle-yak after sexual maturity were established using Single-cell RNA sequencing. The identification results of cell subpopulations and marker genes were analyzed and their possible mechanisms were predicted.

sample_organism:
Bos grunniens
Bos grunniens x Bos taurus

overall_design: Single-cell RNA sequencing was conducted for testis tissues of yak and cattle-yak after sexual maturity.

first: Xian

last: Guo

first: Ping

last: Yan

first: Jie

last: Pei


title: DNA methylation dynamics during pregnancy

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

country: France

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation analysis of 36 pregnant women during pregnancy. DNA methylation was investigated in maternal blood at two time points (1st and 3rd trimester) and in cord blood at birth using the Illumina EPIC array.

overall_design: Bisulphite converted DNA from the 36 pregnant women at two time points were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip.

first: Jorg

last: Tost


title: Determining genomic localization of SIX1 in EWS-502 cells with SIX1 depletion

city: Aurora

first: Heide

last: Ford

state: CO

institute: University of Colorado Anschutz Medical Campus

summary: Investigating genomic binding of SIX1 in EWS-502 cells transduced with shSCR or one of two shSIX1 shRNAs to deplete SIX1.

overall_design: Performed CUT&RUN on EWS-502 shSCR and shSIX1 KD samples. Probed genomic localization of SIX1 in EWS-502 shSCR and shSIX1 KD samples and FLI1 in EWS-502 shSCR samples

first: Connor

last: Hughes

first: Annika

middle: L

last: Gustafson

first: Etienne

last: Danis

first: James

last: Costello


title: Interventional hydrogel microsphere vaccine as an immune amplifier for activated antitumour immunity after ablation therapy

first: Xiaoyu

last: Liu

state: Shanghai

address: 180 Yue-yang road

department: Department of Interventional Radiology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Current chemotherapy or immunotherapy regimens for pancreatic cancer are limited. Although minimally invasive irreversible electroporation (IRE) ablation is a promising option for unresectable pancreatic cancers, the typical immunosuppressive tumour microenvironment promotes immune evasion and rapid tumour recurrence. Thus, triggering efficient amplification of endogenous adaptive antitumour immunity is critical for improving immunotherapy after ablation therapy. Here, we developed a hydrogel microsphere vaccine as an immune amplifier for post-ablation cancer immunotherapy. The vaccine acts as a general immune amplifier to trigger a rocket-like amplification of the cDC1-mediated antigen cross-presentation cascade, resulting in dramatic amplification of the antitumour immunity of endogenous CD8+ T cells. We also showed that the hydrogel microsphere vaccine promoted the transformation of pancreatic cancer from "cold" to "hot" tumours in a safe and efficient manner, significantly increased the survival of mice bearing orthotopic pancreatic tumours, and induced strong systemic antitumour immunity, which inhibited the growth of distant metastases.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for irreversible electroporation (IRE) treated or non-treated pancreatic cancer

first: Yaping

last: Zhuang

first: Zhuozhuo

last: Wu

first: Zhongmin

first: Wenguo

last: Cui


title: Determining genomic localization of SIX1 in A673 cells with SIX1 depletion

summary: Investigating genomic binding of SIX1 in A673 cells transduced with shSCR or one of two shSIX1 shRNAs to deplete SIX1.

overall_design: Performed CUT&RUN on A673 shSCR and shSIX1 KD samples. Probed genomic localization of SIX1 in A673 shSCR and shSIX1 KD samples and FLI1 in A673 shSCR samples

first: Jessica

last: Hsu


title: Effect of shRNA-mediated knockdown of SIX1 in A673 cells in vitro

summary: To investigate gene expression changes associated with SIX1 in the A673 cell line

overall_design: Comparative gene expression profiling of A673 SCR and shSIX1 knockdown cells in biological triplicates


title: Effect of shRNA-mediated knockdown of SIX1 in EWS-502 cells in vitro

summary: To investigate gene expression changes associated with SIX1 in the EWS-502 cell line


title: Exploring the role of SIX1 in Ewing Sarcoma


title: TET2 and TET3 loss disrupts small intestine differentiation and homeostasis [RNA-seq]

city: Heidelberg

first: Llorenç

last: Solé Boldo

address: Im Neuenheimer Feld, 580

institute: DKFZ

summary: The Ten-eleven translocation (TET) DNA demethylases play a well-known role in epigenetic regulation and mouse development. However, their function in cellular differentiation and tissue homeostasis remains poorly understood . Since previous results have implied Tet2/3 in mouse intestinal inflammation, we ablated both enzymes in intestinal epithelial cells (IECs). Our results show that the corresponding mice developed a novel phenotype displaying a severe homeostasis imbalance and a blockage in differentiation trajectories. Transcriptomic, single-cell RNA sequencing (scRNA-seq), single-molecule fluorescence in situ hybridization (sm-FISH), and immunohistochemical analyses revealed that the Tet2/3-deleted mice show a massive loss of mature Paneth cells concomitant with fewer Tuft and more enteroendocrine cells. Further results showed major changes in DNA methylation at putative enhancers, which were associated with cell fate-determining transcription factors and functional effector genes. Notably, pharmacological inhibition of DNA methylation partially rescued the methylation and cellular phenotypes. Moreover, the loss of Tet2/3 results in an altered microbiome, presumably increasing gut susceptibility to inflammatory signals (Ansari et al., 2020). Together, our results uncovered previously unrecognized critical roles for DNA demethylation in intestinal development and function, culminating in the establishment of normal intestinal crypts in mice.

overall_design: Overall 6 small intestine crypts samples from eleven-weeks old mice were analyzed. Three of them correspond to WT mice (Tet2/3 fl/fl) and three correspond to Tet2/3-depleted mice (Tet2/3 fl/fl VillinCre)

first: F

last: Lyko

first: Y

last: Bergman


title: TET2 and TET3 loss disrupts small intestine differentiation and homeostasis


title: TET2 and TET3 loss disrupts small intestine differentiation and homeostasis [Bisulfite-seq]

overall_design: Overall 6 small intestine crypts samples from eleven-weeks old mice were analyzed. Three of them correspond to WT mice (Tet2/3 fl/fl and three correspond to Tet2/3-depleted mice (Tet2/3 fl/fl VillinCre)


title: TET2 and TET3 loss disrupts small intestine differentiation and homeostasis [scRNA-seq]


title: Gene expression profiling of drought-sensitive (ICC1882) and tolerant (ICC4958) chickpea genotypes

status: Public on May 20 2023

city: Gautam Buddha Nagar

first: Rohini

last: Garg

state: UP

address: Shiv Nadar University, NH - 91, Tehsil Dadri

country: India

institute: Shiv Nadar University

summary: We generated the global transcriptome profile of the two chickpea genotypes under control and drought conditions. Approximately 12 million high-quality reads were obtained for each cultivar and different conditions using the Illumina platform. Reference-based assembly was generated for each cultivar and condition. Differentially expressed genes were identified between drought and control conditions for each cultivar.

overall_design: We collected 27-day-old seedlings of the drought sensitive (ICC1882) and tolerant (ICC4958) chickpea genotypes under drought and control conditions. The RNA-seq libraries were prepared for sequencing using standard Illumina protocols and sequencing was performed on the Illumina HiSeq platform by a commercial sequencing service provider. The raw reads were filtered using NGSQC Toolkit (v2.3.3) at default parameters. Kabuli chickpea genome (v1.0) was indexed using bowtie (v2.3.3.1) and filtered reads were mapped against the chickpea genome using TopHat2 pipeline (v2.1.1) at default parameters. Reference-based transcriptome assembly was performed using cufflinks (v2.2.1), followed by cuffmerge. The FPKM for each transcript was calculated using cufflinks by fragments per kilobase of transcript per million mapped fragments. Differential gene expression (log2 fold change ± 1 and FDR ≤ 0.05) analysis was performed using cufdiff (2.2.1).

first: Khushboo

last: Gupta


title: Molecular profiling and specific targeting of gemcitabine-resistant subclones in heterogeneous pancreatic cancer cell populations

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

institute: University of Lübeck

summary: Purpose: Chemotherapy is pivotal in the multimodal treatment of pancreatic cancer patients. In recent years, technical advances have developed experimental methods that unveiled a high degree of inter- and intratumoral heterogeneity in pancreatic cancer. We hypothesized that intratumoral heterogeneity (ITH) impacts response to gemcitabine treatment and demands specific targeting of resistant subclones.  Results: Individual SCDCLs of the parental tumor cell populations of BxPC3 and Panc-1 showed considerable heterogeneity in response to gemcitabine. Unsupervised principal component analysis (PCA) including the 1,000 most variably expressed genes showed a clustering of the SCDCLs according to their respective sensitivity to gemcitabine treatment for BxPC3, while this clustering was less clear for Panc-1. In BxPC3 SCDCLs, enriched signaling pathways EMT, TNF signaling via NfKB, and IL2STAT5 signaling correlated with more resistant behavior to gemcitabine. In Panc-1 SCDCLs MYC targets V1 and V2 as well as E2F targets were associated with stronger resistance to gemcitabine. Feature extraction of proteomes again identified less proteins whose expression was associated with the response of individual SCDCLs in Panc-1 compared to BxPC3. Based on molecular profiles, we could show that the gemcitabine-resistant SCDCLs of both BxPC3 and Panc-1 are more sensitive to the BET inhibitor JQ1 compared to the respective gemcitabine-sensitive SCDCLs.  Conclusions: Our model system of SCDCLs identified gemcitabine-resistant subclones within a parental tumor population and provides evidence for the critical role of ITH for treatment response in pancreatic cancer. Through molecular profiling, we identified specific signaling pathways and protein signatures that might help to explain the differential response to treatment among clones. We exploited these molecular differences for an improved and more targeted therapy of resistant subclones of a heterogeneous tumor.

overall_design: We addressed the effect of ITH on response to gemcitabine treatment using single cell-derived cell lines (SCDCL) from the classical-like cell line BxPC3 and the basal-like cell line Panc-1 which were analyzed by mRNA-seq and mass spectrometry.

first: Bendikt

last: Färber

first: Rüdiger

last: Braun

first: Hauke

last: Busch


title: m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency [SLAM-seq]

status: Public on May 19 2023

city: Toronto

first: Evelyne

middle: Anne

last: Collignon

state: ON

address: 60 Murray Street, Box42,

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

summary: Development is often assumed to be a sequential unfolding of genetic programs towards increased complexity and occurring with a very stereotypical timing. However, embryos across all lineages of metazoans can enter reversible states of developmental pausing in response to adverse environmental conditions. In mammals, pausing manifests as a delayed implantation of the blastocyst, the source of embryonic stem cells (ESCs). Paused pluripotency can be induced in mouse blastocysts and ESCs by inhibition of mTOR, a conserved growth-promoting kinase, and is characterized by a drastic global decrease in biosynthetic activity, including gene transcription. The molecular mechanisms by which this remarkable dormant cellular state is achieved remain largely unknown. Here we show that m6A RNA methylation by Mettl3 is essential for transcriptional dormancy and maintenance of the paused pluripotent state in vitro and in vivo. Mass spectrometry and transcriptome-wide sequencing revealed an increase in m6A in paused ESCs. Knockout of the RNA methyltransferase Mettl3 suppresses transcriptional and proliferation dormancy of ESC specifically in the paused state, and leads to loss of paused blastocysts. Integration of several datasets in vitro and in vivo identified the transcriptional amplifier and oncogene Mycn as a key “anti-pausing factor” regulated by m6A mRNA methylation. Mett3-mediated methylation at a specific site of the Mycn mRNA is essential for its destabilization, which in turns mediates suppression of nascent transcription and proliferation in paused conditions. Our results highlight an intricate feedback between signaling, regulation of RNA stability and nascent transcription during pausing, with Mettl3 as an essential integrator and Mycn as a key downstream anti-pausing factor. These findings shed light on the mechanisms that underlie tuning of global transcriptional output during mammalian developmental pausing, and that may be redeployed in adult stem cells or during cancer dormancy.

overall_design:
ESCs were grown on gelatin for 2 weeks in FBS/LIF media, under paused condition (200 nM INK128).
Cells were pre-incubated with 100μM S4U, protected from light and with media exchange every 3h, for a total of 12h. Then, the medium was changed back to standard (no S4U), and cells were collected at different times (0h, 1h, 3h, 8h).
RNA was extracted from  ESCs (5x10^5 cells).

first: Miguel

last: Ramalho-Santos


title: A framework to identify functional interactors that contribute to disrupted early retinal development in Vsx2 mutant mice III

city: Nashville

first: EDWARD

middle: M

last: LEVINE

state: TN

address: 1161 21st Ave S

department: Vanderbilt Eye Institute

institute: Vanderbilt University Medical Center

summary: These datasets contain the transcriptomes from E12.5 mouse retinal tissues from embryos carrying three different combinations of the Vsx2 ocular retardation J (orJ) allele and the Mitf mi (mi) allele: orJ-heterozygous, which serves as the control, orJ-homozygous, and orJ-homozygous; mi-heterozygous. The orJ allele is a recessive loss of function and the mi allele is semi-dominant. Mitf is direct target of repression by Vsx2 in the retina and is an established causal factor in the orJ ocular phenotype of microphthalmia. The goal of this analysis was to determine if blocking Mitf function in the orJ mutant would restore retinal gene expression to wild type levels. All libraries were prepared and sequenced together, facilitating direct comparisons of the gene expression profiles across the 3 genotypes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for biological replicates of E12.5 Vsx2<orJ/orj> retinas,  E12.5 Vsx2<orJ/orj>; Mitf<mi/+> retinas, and E12.5 Vsx2<orJ/+>; Mitf<+/+> retinas (control)

first: Amanda

last: Leung

first: Mahesh

last: Rao

first: Edward

last: Levine


title: A framework to identify functional interactors that contribute to disrupted early retinal development in Vsx2 mutant mice II

summary: These datasets contain the transcriptomes from E12.5 orJ-homozygous (orJ mutant) retinal tissues after organotypic culture of retina and lens for 24 hours in the presence or absence of the Retinoid-X-Receptor (RXR) antagonist HX531. The Retinoid X receptor gamma (Rxrg) gene was identified as a highly upregulated gene from the retinal RNA-Seq profile of the E12.5 orJ mutant compared to the orJ-heterozygous (control) (add in GEO accession numbers for that data). The goal of this analysis was to determine if blocking RXR activity would restore gene expression to wild type levels by comparing the retinal gene expression profiles of biological replicates from 100 nM HX531-treated and vehicle-treated (0.1% DMSO) cultures.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for biological replicates of E12.5 Vsx2<orJ/orj> mutant retinas treated with the Retinoid X Receptor antagonist HX531 compared to vehicle control (Dimethyl Sulfoxide).


title: A framework to identify functional interactors that contribute to disrupted early retinal development in Vsx2 mutant mice

summary:
This SuperSeries is composed of the SubSeries listed below.
The Vsx2 homeobox gene is expressed in the newly formed retinal domain during early eye development and mutations in the Vsx2 gene cause congenital microphthalmia. The primary disruptions in the early retina are compromised retinal identity (lineage infidelity), reduced proliferation, and delayed neurogenesis. One goal of the study was to use gene expression profiling to predict genetic interactions between Vsx2 and candidate functional interactors that contribute to the early retinal phenotype of the Vsx2-null mouse strain ocular retardation J (orJ). The orJ allele is a spontaneous, recessive allele caused by the presence of a premature stop codon in the Vsx2 homeodomain. The datasets contained within are from three independent experimental designs. One was to compare the retinal gene expression profiles from E12.5 embryos that are one of three genotypes: the orJ-homozygous mutant, the combinatorial orJ; Mitfmi heterozygous mutant, and the orJ-heterozygous mouse (control).
Another analysis was to compare the gene expression profiles of E12.5 orJ-homozygous mutant retinal tissues cultured for 24 hour in the presence or absence of the RXR antagonist HX531. The other analysis was to compare the gene expression profiles of E12.5 orJ-homozygous mutant retinal tissues cultured for 24 hour in the presence or absence of the gamma-Secretase antagonist Dibenzazipine (DBZ).


title: Analysis of mRNA-miRNA interaction network reveals the role of CAFs-derived exosomes in the immune regulation of oral squamous cell carcinoma [Exo-miRNA]

city: Kunming

first: Weizhou

last: Wang

state: Yunnan

address: Chunrong West Road

institute: Kunming Medical University

summary: To investigate the miRNA differences in the exosomes released from cells after hOMF is activated by PDGF to become CAFs, and to clarify the regulatory role.

overall_design: miRNA-seq data of CAFs-Exo and hOMF-Exo were analyzed and compared for gene expression profiling.

first: Wei

first: Xue

last: Cao

first: Li

last: Bian

first: Gao

last: Yue

first: Ming

last: Yu

first: Yi

last: Li

first: Jian

middle: G

last: Xu

first: Yang

middle: H

first: He

middle: F

last: Yang

first: Ding

last: You

first: Yong

last: He


title: A framework to identify functional interactors that contribute to disrupted early retinal development in Vsx2 mutant mice I

summary: These datasets contain the transcriptomes from E12.5 orJ-homozygous (orJ mutant) retinal tissues after organotypic culture of retina and lens for 24 hours in the presence or absence of the gamma-Secretase inhibitor Dibenzazipine (DBZ). A trait of the orJ mutant retina is the persistence of retinal progenitor cells (RPCs) during development despite greatly reduced proliferation and delayed neurogenesis. This led us to test whether gamma secretase activity was maintaining the RPC population in the orJ mutant retina, possibly through Notch signaling. The goal of this analysis was to determine if blocking gamma-Secretase activity would shift RPCs from a progenitor to a neurogenic state by comparing the retinal gene expression profiles of biological replicates from 300 nM DBZ-treated and vehicle-treated (0.1% DMSO) cultures.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for biological replicates of E12.5 Vsx2<orJ/orj> mutant retinas treated with the gamma secretase inhibitor Dibenzazepine (DBZ) compared to vehicle control (Dimethyl Sulfoxide).


title: Analysis of mRNA-miRNA interaction network reveals the role of CAFs-derived exosomes in the immune regulation of oral squamous cell carcinoma [Exo-mRNA]

summary: To investigate the mRNA differences in the exosomes released from cells after hOMF is activated by PDGF to become CAFs, and to clarify the regulatory role.

overall_design: RNA-seq data of CAFs-Exo and hOMF-Exo were analyzed and compared for gene expression profiling.

middle: Z

middle: Y


title: m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency [MeRIP-seq]

first: Evelyne

summary: Development is often assumed to be a sequential unfolding of genetic programs towards increased complexity and occurring with a very stereotypical timing. However, embryos across all lineages of metazoans can enter reversible states of developmental pausing in response to adverse environmental conditions. In mammals, pausing manifests as a delayed implantation of the blastocyst, the source of embryonic stem cells (ESCs). Paused pluripotency can be induced in mouse blastocysts and ESCs by inhibition of mTOR, a conserved growth-promoting kinase,  and is characterized by a drastic global decrease in biosynthetic activity, including gene transcription. The molecular mechanisms by which this remarkable dormant cellular state is achieved remain largely unknown. Here we show that m6A RNA methylation by Mettl3 is essential for transcriptional dormancy and maintenance of the paused pluripotent state in vitro and in vivo. Mass spectrometry and transcriptome-wide sequencing revealed an increase in m6A in paused ESCs. Knockout of the RNA methyltransferase Mettl3 suppresses transcriptional and proliferation dormancy of ESC specifically in the paused state, and leads to loss of paused blastocysts. Integration of several datasets in vitro and in vivo identified the transcriptional amplifier and oncogene Mycn  as a key “anti-pausing factor” regulated by m6A mRNA methylation. Mett3-mediated methylation at a specific site of the Mycn mRNA is essential for its destabilization, which in turns mediates suppression of nascent transcription and proliferation in paused conditions. Our results highlight an intricate feedback between signaling, regulation of RNA stability and nascent transcription during pausing, with Mettl3 as an essential integrator and Mycn as a key downstream anti-pausing factor. These findings shed light on the mechanisms that underlie tuning of global transcriptional output during mammalian developmental pausing, and that may be redeployed in adult stem cells or during cancer dormancy.

overall_design: Wildtype mESCs were cultured under control (FBS/LIF) or paused (200nM INK128) conditions for 2 weeks and m6A methylated RNA immunoprecipitation (MeRIP-seq) was performed.

first: Miguel


title: m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency [dCas_RNAseq]

overall_design:
ESCs expressing dCas_Alkbh5 cells were grown on gelatin in FBS/LIF
Cells were transfected with 1μg lenti-sgRNA-BSD (coding for guide RNAs) and selected with 8μg/mL blasticidin for 3 days. Cells were then paused with 200 nM INK128 as mTor inhibitor for 5 days.
RNA was extracted from ESCs.


title: The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation

city: Rome

first: Stefano

last: Scalera

address: Via Elio Chianesi 53

institute: IRCCS Regina Elena National Cancer Institute

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

overall_design: Refer to individual Series


title: Analysis of mRNA-miRNA interaction network reveals the role of CAFs-derived exosomes in the immune regulation of oral squamous cell carcinoma [Cal27_mRNA]

summary: To investigate the regulatory effect of exosomes released from CAFs cells on Cal-27 cells after hOMF is activated by PDGF to become CAFs, high-throughput sequencing was performed on co-cultured Cal-27 cells.

overall_design: The RNA-seq data of Cal-27 cells co-cultured with CAFs-Exo or hOMF-Exo were analyzed and compared for gene expression profiling.


title: m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency [ChIP-seq]

last: Collignon

overall_design: Wildtype mESCs were cultured under control (FBS/LIF) or paused (200nM INK128) conditions for 2 weeks and Mettl3 ChIP-seq was performed.


title: Pharmacological Inhibition of TAK1 Prevents and Induces Regression of  fibrosis

status: Public on May 17 2023

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: To evaluate the effects of TAK1 inhibition on TGF-beta regulated fibrosis using a novel small molecule inhibitor of TAK1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for foreskin fibroblast and treated with TGFb1 and TAK1 inhibitor (Control, TGFb1 and TAK1 inhibitor (HS-276)+TGFb1).

first: Swarna

last: Bale

first: Priyanka

last: Verma

first: Swati

last: Bhattacharya

first: John

last: Varga


title: The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [ChIRP-seq]

summary: The transcription factor ΔNp63, a master regulator of epithelial biology, is involved in regulating epithelial stem cell function and maintaining the integrity of stratified epithelial tissues such as the epidermis. To this end, ΔNp63 acts as transcriptional repressor or activator towards a distinct subset of protein-coding genes and microRNAs. However, how and whether ∆Np63 regulates long non-coding RNA (lncRNAs) expression is not known. Here, we identified the lncRNAs NEAT1 and MALAT1 as a bona fide ΔNp63 transcriptional targets. We found that in proliferating human keratinocytes ∆Np63 represses NEAT1 and MALAT1 expression by recruiting the histone deacetylates HDAC1/HDAC2 to the p63 DNA binding site located in the proximal promoter of NEAT1 and MALAT1 genomic loci. Upon induction of differentiation, ∆Np63 down-regulation is associated by a marked increase of NEAT1 RNA levels, resulting in an increased assembly of paraspeckles foci both in vitro and in human skin tissues. RNA-seq analysis associated with global DNA binding profile (ChIRP-seq) revealed that NEAT1 associates with the promoter of key epithelial transcription factors sustaining their expression during epidermal differentiation. These molecular events might explain the inability of NEAT1-depleted keratinocytes to undergo the correct epidermal differentiation program. Remarkably, NEAT1 expression is dysregulated in those skin pathologies characterized by aberrant keratinocytes differentiation such as ichthyosis and psoriasis, suggesting its potential involvement in the pathogenesis of skin disorders.

overall_design: Profile of the genomic binding sites for endogenous NEAT1 in human primary keratinocytes (HEKn) maintanied for six days in high calcium-containing medium. Chromatin was isolated from gluteraldeyde-fixed nuclei of differentiated HEKn and NEAT1-associated DNA was purified by using biotinylated DNA probes targeting NEAT1 lncRNA and isolated by magnetic streptavidin beads. RT-qPCR was performed to validate the NEAT1 enrichment in the antisense NEAT1 sample.

first: Claudia

last: Fierro

first: Francesca

last: De Nicola

first: Veronica

last: Gatti

first: George

last: Calin

first: Gerry

last: Melino

first: Maurizio

last: Fanciulli

first: Angelo

last: Peschiaroli


title: The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [RNA-seq]

overall_design: RNA profiles of differentiated human primary keratinocytes (HEKn) transfected with LNA-GapmeR targeting NEAT1, MALAT1 or a non targeting lncRNA (scramble, SCR) were generated by deep sequencing using Illumina. We analyzed three biological replicates for each conditions. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. RT–qPCR validation was performed using SYBR Green assays


title: m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency [RNA-seq]

overall_design: Wildtype and Mettl3-KO mESCs were cultured under control (FBS/LIF) or paused (200nM INK128) conditions for 2 weeks and RNA-seq was performed.

last: Ramalho-Santos


title: RNA sequencing of isolated brain endothelial cells from Smad4, Alk1, or Eng endothelial cell-specific knock-out mutants, respective wildtypes (WTs), and Angiopoietin-2 inhibition transcriptional changes.

city: New Orleans

first: Xingyan

last: Zhou

address: 6823 St Charles Ave

institute: Tulane University

summary:
Purpose: Hereditary Hemorrhagic Telangiectasia (HHT) is an autosomal dominant vascular disorder characterized by arteriovenous malformations (AVMs). Over 90% of HHT patients carry heterozygous loss-of-function mutations in Transforming Growth Factor-beta (TGFb) signaling components activin receptor-like kinase 1 (ACVRL1/ALK1), endoglin (ENG), or mothers against decapentaplegic homolog 4 (SMAD4). Brain AVMs can be lethal for HHT patients. Here, we use an inducible endothelial (EC)-specific mouse line to investigate brain AVMs characteristics in Alk1-, Eng-, and Smad4-HHT mouse models. Angiopientin-2 (Ang2) inhibition diminishes HHT associated cerebral vascular defects. We aim to identify the shared transcriptional changes in brain ECs between these three HHT types, and provide insights for transcriptional changes upon Ang2 inhibition.
Methods: ECs were isolated from brains of both WT and HHT mutant mice at postnatal day 7 (P7) for Smad4 and Eng models, P6 for Alk1 model. Total RNA was extracted from isolated brain ECs and quantified using Qubit RNA High Sensitivity Assay Kit. RNA integrity was determined using the Bioanalyzer RNA 6000 Nano assay kit. RNA library construction was performed with the TruSeq RNA Library Prep Kit v2 from Illumina. The resulting mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit and verified using the Bioanalyzer DNA1000 assay kit. Verified samples were sequenced using the NextSeq 500/550 High Output Kit v2.5 (150 Cycles) on a Nextseq 550 system. Sequenced reads were aligned to the mouse (mm10) reference genome with RNA-seq alignment tool (version 2.0.1). The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-seq Differential Expression tool (version 1.0.1). Both alignment and differential expression analysis were performed using the tools in the BaseSpace Sequence Hub.
Results: We identified 5509, 5381, and 2663 differentially expressed genes in Smad4, Alk1, and Eng HHT models respectively. Also, Ang2 inhibition mainly funcioned through angiogenesis and cell migration processes to normalize cerebrovascular defects in Smad4-HHT model.
Conclusions: A common but unique pro-angiogenic program among all HHT models included 14 consistent upregulated and 5 consistent downregulated angiogic genes. Also, Ang2 inhibition mainly funcioned through angiogenesis and cell migration processes to normalize cerebrovascular defects in Smad4-HHT model.

overall_design: Isolated brain ECs mRNA profiles of postnatal day 7 (P7) for Smad4 and Eng models, P6 for Alk1 model, 5 samples in each WT/mutant group. IgG/LC10 treatments were administered at P2 and P4 for Smad4-HHT model.

first: Stryder

last: Meadows


title: The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [microarray]

last: Scalera

summary: Profile of the genomic binding sites for endogenous NEAT1 in human primary keratinocytes (HEKn) maintanied for six days in high calcium-containing medium. Chromatin was isolated from gluteraldeyde-fixed nuclei of differentiated HEKn and NEAT1-associated D


title: Parallel Genome-Wide CRISPR Screens Clarify Executors of Epithelial-Mesenchymal Transition Mediated Immune resistance to CD8+ T cells

status: Public on May 16 2023

city: Suzhou

first: Zhengkui

last: Zhang

address: No. 199, Renai Road, Suzhou Industrial Park

department: Institutes of Biology and Medical Science

institute: Soochow University

summary: To investigate the role of tumor epithelial-to-mesenchymal plasticity in CD8+ T cell cytotoxicity, we generated two types of tumor cells with epithelial-like (Epi) or mesenchymal-like (Mes) features through an inducible EMT system. The parental KPC3-OVA cells were transduced with constitutively kinase active ALK5 cDNA (ALK5 CA) in doxycycline-induced system by Nakao et al. and Itoh et al, which initiated TGF-β signaling induced EMT. In this system, we firstly treated cells with TGF-β (5 ng/mL) for 2 days, then removed TGF-β ligands and added doxycycline to sustain cancer cells with mesenchymal feature. We proved the mesenchymal-like phenotype could maintain more than 16 days, which was long enough for all our experiments. Then we performed RNA-seq to investigate the differences between these two types of KPC3-OVA :: Tet-On ALK5 CA cells co-cultured  with OT-1  CD8+ T cells or not.

overall_design: 2 × 10E6 KPC3-OVA cells (Epithelial or Mesenchymal type) were coculture with 1 × 10E6 OT-I T cells for 0, 6 or 24 hours. Each group has three biological independent replicates (three different donors derived OT-I T cells). OT-I T cells and culture medium was removed and washed three times with ice-cold PBS. Cancer cells were collected for RNA samples preparation by the NucleoSpin RNA kit. After mRNA enrichment by Oliogo dT selection and the following library preparation, RNA-seq was performed in the DNBseq platform (Beijing Genomics Institute, BGI, Hongkong).

first: Zhnegkui

first: Yuanzhuo

last: Gu

first: Peter

last: ten Dijke