title: Disease-associated KBTBD4 mutations in medulloblastoma elicit neomorphic ubiquitylation activity to promote CoREST degradation

city: Oxford

first: Vincenzo

last: D'Angiolella

state: Oxfordshire

address: Old Road Campus Research Building, Old Road Campus, Off, Roosevelt Dr

institute: University of Oxford

summary: E3 ubiquitin ligases of the Cullin RING Ligase (CRL) family assemble into multiprotein complexes to diversify substrate adaptors and ensure selectivity in substrate engagement for degradation. Here we show a novel mechanism whereby mutations in substrate adaptors can drive neo-substrate degradation in cancer. KBTBD4 is a CRL3 substrate adaptor harbouring recurrent indel mutations in a subset of non-WNT/non-SHH medulloblastomas. We show that these mutations, arising in the substrate recognition domain of KBTBD4, promote the recruitment and ubiquitylation of the REST Corepressor (CoREST), which forms a complex to modulate chromatin accessibility and transcriptional programmes. We observe that this neomorphic activity of KBTBD4 mutants induces changes in epigenetic markers and significant alterations in transcription, diverting normal cellular programmes towards increased stemness. These results highlight mutation-driven neomorphic E3 ligase activity as a previously unrecognised mechanism in tumorigenesis, with implications for medulloblastoma pathogenesis and treatment.

overall_design: D283MED cell lines conditionally expressing KBTBD4 WT, R313PRR or P311PR

first: Zhuoyao

last: Chen

first: Rafael

last: Ioris

first: Alex

middle: N

last: Bullock


title: Evaluation of tofacitinib in cutaneous sarcoidosis [Olink Explore 1536]

status: Public on Mar 30 2022

city: New Haven

first: William

last: Damsky

state: CT

address: 333 Cedar St

country: USA

institute: Yale School of Medicine

summary: Sarcoidosis is a multisystem inflammatory disease and no molecularly targeted therapies exist. Here we evaluate the efficacy of tofacitinib (a JAK1/3 inhibitor) in an open-label trial of 10 patients with sarcoidosis and correlate clinical improvement with molecular parameters in blood and skin.

overall_design: Blood samples were collected from participants at baseline and again after 6 months of therapy. Samples were compared to 11 healthy, roughly age matched controls. Blood was collected in EDTA-coated tubes and centrifuged; the buffy coat was removed and stored separately from the plasma, which was aliquoted and stored at -80ºC. Plasma was analyzed using the Olink Explore 1536 panel.

first: Alice

last: Wang

first: Bryan

middle: D

last: Young

first: Ruveyda

last: Ayasun

first: Changwan

last: Ryu

first: Meaghan

middle: K

last: McGeary

first: Ramesh

last: Fazzone-Chettiar

first: Darko

last: Pucar

first: Mridu

last: Gulati

first: Edward

middle: J

last: Miller

first: Marcus

last: Bosenberg

first: Richard

middle: A

last: Flavell

first: Brett

last: King


title: A genome-wide CRISPR activation screen identifies PRRX2 as a regulator of enzalutamide resistance in prostate cancer [ATAC-seq]

city: Chicago

first: Sarki

last: Abdulkadir

state: IL

address: 303 E Superior St

institute: Northwestern University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report that PRRX2 mediates enzalutamide resistance by activating the anti-apoptotic BCL2 and theE2F/RB1 cell cycle pathways.

overall_design: We used LNCaP cells to over-express the transcription factor PRRX2 using CRISPR activation. Negative Control (LNCaP-sgNC) and PRRX2 over-expressing cells (LNCaP-sgPRRX2) were treated with the AR inhibitor enzalutamide (5uM) for 4 days. We then studied gene expression changes in both cell lines treated with enzalutamide or DMSO.

first: Yara

last: Rodriguez


title: Single-cell ATAC of WT thymic IEL precursors (IELp)

city: Bethesda

first: Jia

last: Nie

state: Maryland

address: Building 37, Room 3016

department: Center for Cancer Research

institute: National Cancer Institute

summary: To examine the chromatin accessibility of IELp, single cell epigenomic analysis of IELp from control mice (Cd4 Cre–Lrffl/fl) were determined by scATACseq

overall_design: IELp from control (Cd4 Cre–Lrffl/fl) mice were sorted and single cell transcriptomic analysis was determined by scATAC

first: Remy

last: Bosselut


title: Single-cell Gene expression of WT CD8aa IEL and LRF-deficient CD8aa splenocytes

type: Expression profiling by high throughput sequencing

summary: To examine how the cluster composition of CD8aa IEL and their transcriptomic signatures were affected by LRF disruption, single-cell gene expression of CD8aa IEL from control (Cd4 Cre–Lrffl/fl)  and CD8aa splenocytes from LRF KO (Cd4 Cre+Lrffl/fl ) mice were determined by scRNAseq.

overall_design: CD8aa IEL from control (Cd4 Cre–Lrffl/fl) and CD8aa splenocytes from LRF KO(Cd4 Cre+Lrffl/fl ) mice were sorted, and their gene expression was determined by scRNAseq.


title: Trib1 promotes the development of acute myeloid leukemia in the Ts1Cje Down syndrome model mouse

status: Public on Mar 29 2022

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

summary:
Down syndrome (DS) is caused by trisomy of chromosome 21 and it predisposes to hematological disorders such as transient myeloproliferative disorder and acute megakaryocytic leukemia. Our previous study identified a gain-of-function mutation of TRIB1 encoding a pseudokinase that suppresses C/EBP and enhances MEK/ERK signaling. In this study, we aimed to examine whether Trib1 expression cooperates with trisomy 21 in the development of leukemia. The wild type or R107L mutant Trib1 was retrovirally introduced into bone marrow cells derived from the Ts1Cje Down syndrome model mice or C57Bl6/J mice. Trib1 expression in hematopoietic cells of Ts1Cje mice accelerated the onset of AML development compared with that in wild type mice. Gene expression analysis showed up-regulation of Hox downstream genes and down-regulation of genes for the myeloid differentiation program and C/EBP targets. These results suggest that Trib1-mediated signaling plays an important role in promoting leukemogenesis in Down syndrome.
We used microarrays to detail the global program of gene expression in mouse AML

overall_design: Murine AML cell lines expressing Trib1 were examined.

first: Seiko

last: Yoshino


title: Developmental dynamics of two bipotent progenitors of thymic epithelium

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

summary: T cell development in the thymus is essential for cellular immunity and depends on the organotypic thymic epithelial microenvironment. Compared to other organs, the size and cellular composition of the thymus is unusually dynamic, exemplified by rapid growth and high T cell output during early stages of development, followed by a gradual loss of functional thymic epithelial cells and diminished naïve T cell production with age. Single-cell RNA sequencing (scRNA-seq) has uncovered an unexpected heterogeneity of cell types in the thymic epithelium of young and aged adult mice; however, the identities and developmental dynamics of putative pre- and postnatal epithelial progenitors have remained unresolved. Here, we combine scRNA-seq and a novel CRISPR/Cas9-based cellular barcoding system in mice to determine qualitative and quantitative changes in the thymic epithelium over time. This dual approach enabled us to identify two principal progenitor populations: an early bi-potent progenitor type biased towards cortical epithelium, and a postnatal bi-potent progenitor population biased towards medullary epithelium. We further demonstrate that continuous autocrine provision of Fgf7 leads to sustained expansion of thymic microenvironments without exhausting the epithelial progenitor pools, suggesting a strategy to modulate the extent of thymopoietic activity.

overall_design: Single cell RNA sequencing was performed on thymic epithelial cells after enzymatic dissociation of the thymi of 4 week old mice from C57BL/6 WT mice as CD45-EpCAM+, UEA1+ as well as Ly51+ cells. Furthermore, scRNA-Seq was also performed on Fgf7-stimulated TECs isolated as CD45-EpCAM+ cells.

last: Sagar

first: Anja

last: Nusser

first: Dominic

last: Gruen

first: Thomas

last: Boehm


title: Heavy oil exposure suppresses antiviral activities in Japanese flounder   Paralichthys olivaceus infected with viral hemorrhagic septicemia virus (VHSV)

city: Matsuyama

first: Kei

last: Nakayama

address: 2-5 Bunkyo-cho

department: Center for Marine Environmental Studies

institute: Ehime University

summary: The genes detected with 3143 probes were significantly affected by VHSV infection and/or heavy oil exposure.

overall_design: Fish were treated with VHSV and/or heavy oil, and total RNA was isolated from kidney of the fish to detect the differentially expressed genes.

first: Shin-Ichi

last: Kitamura


title: Evaluation of tofacitinib in cutaneous sarcoidosis [scRNA-seq]

first: William

last: Damsky

overall_design: 4 mm punch biopsies of skin were obtained on separate days from 3 patients with GA and 3 healthy volunteers. Biopsies were immediately dissociated using dispase (10 mg/mL) followed by liberase. Live single cells were purified by FACS and single cell libraries were prepared using a 10X chromium controller according to the manufacturer’s instructions and sequenced using an Illumina Hiseq 4000.

first: Alice

last: Wang

first: Bryan

last: Young

first: Ruveyda

last: Ayasun

first: Changwan

last: Ryu

first: Meaghan

last: McGeary

first: Ramesh

last: Fazzone-Chettiar

first: Darko

last: Pucar

first: Mridu

last: Gulati


title: ATAC-seq changes induced by YAP, and TAZ knock down in DU145 cell lines

status: Public on Mar 28 2022

city: New York

first: Ekta

last: Khurana

address: 1305 York Ave

institute: Weill Cornell Medicine

summary: Chromatin accessibility of DU145 cell line upon knock down of YAP, and TAZ

overall_design: Chromatin accessibility analysis was performed in DU145 cell line knock down of YAP, YAP/TAZ, TAZ

first: Yu

last: Chen

first: Chen

last: Khuan Wong

first: Duo

last: Xu


title: ATAC-seq changes induced by FOSL1, YAP, and TAZ overexpression in LNCaP Prostate Cancer Cells

summary: Chromatin accessibility of LNCaP cells upon overexpression of FOSL1, YAP, and TAZ

overall_design: Chromatin accessibility analysis was performed in LNCaP cells stably expressing FOSL1, YAP, YAP/FOSL1, TAZ, or TAZ/FOSL1


title: Evaluation of tofacitinib in cutaneous sarcoidosis [bulk RNA-seq]

overall_design: Total RNA was extracted with Qiagen RNeasy Fibrous Tissue Mini kits (Qiagen cat# 74704) according to the manufacturer’s instructions. Homogenization of the tissue was achieved using a rotor-homogenizer (PowerGen 125, ThermoFisher). RNA was submitted to the Yale Stem Cell Center and complementary DNA libraries were prepared and 100-base pair paired-end stranded sequencing was performed on an Illumina HiSeq 4000, also at Yale Stem Cell Center.

first: Edward

last: Miller

first: Marcus

last: Bosenberg

first: Richard

last: Flavell

first: Brett

last: King


title: Single-cell Gene expression of WT and LRF-deficient thymic IEL precusors (IELp)

first: Jia

last: Nie

summary: To examine how the cluster composition of IELp and their transcriptomic signatures were affected by LRF disruption, single-cell gene expression of IELp  from control (Cd4 Cre–Lrffl/fl) and LRF KO(Cd4 Cre+Lrffl/fl )mice were determined by scRNAseq

overall_design: IELp from control (Cd4 Cre–Lrffl/fl) and LRF KO(Cd4 Cre+Lrffl/fl )mice were sorted and gene expression was determined by scRNAseq

first: Remy

last: Bosselut


title: LRF genome-wide occupancy in CD4+ T cells

summary: To examine whether LRF protein could bind cis-regulatory elements in the genes that LRF regulates. We performed Chromatin immunoprecipitation followed by deep-sequencing (ChIPseq) on activated T cells using  an in vivo biotinylation and streptavidin pull-down approach.

overall_design: Splenic CD4+ T cells from Rosa26BirA animals were activated and  transduced with pMRX-LRFbio-tag-IRES-Thy1.1 retrovirus, or with a control retrovirus expressing Thy1.1 only. Streptavidin immunoprecipitation from transduced cells  were performed.


title: Gene expression in WT and LRF-deficient thymic IEL precusors (IELp) and their progeny CD8aa IEL

summary: Gene expression of IELp and CD8aa IEL was determined by RNAseq

overall_design: 40000 IELp, CD8aa IEL and CD8aa splenocytes in control (Cd4 Cre–Lrffl/fl) or LRF KO(Cd4 Cre+Lrffl/fl ) mice were sorted and gene expression was determined by RNAseq


title: Evaluation of tofacitinib in cutaneous sarcoidosis

first: William

last: Damsky

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

overall_design: Refer to individual Series


title: Changes in tumor infiltrating leukocytes following TA99 CAR T cell treatment

city: Lebanon

first: Yina

last: Huang

state: NH

address: 1 Medical Center Drive

institute: Dartmouth College

summary: Tumor infiltrating leukocytes were analyzed by scRNAseq 9 days after treatment with TA99 (anti-TRP-1) CAR T cells with or without Super2 and IL-33 co-expression.

overall_design: To identify changes in tumor infiltrating CAR T cells and host leukocytes, C57BL/6 mice inoculated with 2 x 10^5 B16F10 cells were treated with 7x10^6 CAR T cells after 6 days, and then tumors were harvested on day 15, digested and purified by percoll gradient prior to single cell RNA-seq and Antibody-derived tags.

first: Rachel

last: Brog

first: Courtney

last: Schiebout

first: Hildreth

last: Frost


title: Genes differentially expressed by Haemophilus ducreyi during anaerobic growth significantly overlap with those differentially expressed during experimental infection of human volunteers

city: Indianapolis

first: Stanley

middle: M

last: Spinola

state: Indiana

address: 635 Barnhill Dr., MS420

department: Department of Microbiology & Immunology

institute: Indiana University

summary: The transcriptional response of Haemophilus ducreyi to anaerobiosis was determined over the course of 18 h. Cells were collected from aerobic and anaerobic cultures at 4, 8, or 18 hours .

overall_design: Overnight aerobic cultures of H. ducreyi were subcultured into GC broth plus hemin, FBS, and IsoVitalex that contained either the commercial product Oxyrase or the buffer components of Oxyrase to yield anaerobic and aerobic growth conditions, respectively, and grown for up to 18 h.

first: Julie

last: Brothwell


title: The fused methionine sulfoxide reductase MsrAB promotes oxidative stress defense and bacterial virulence in Fusobacterium nucleatum

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

institute: Bielefeld University

summary: Recognizably associated with oral infections, adverse pregnancy outcomes, and colorectal cancer, the Gram-negative oral bacterium Fusobacterium nucleatum is known to colonize many extraoral sites including placenta and colon. How this anaerobe copes with oxidative stress imposed by the host immune response in various tissues is unknown. Here, we revealed that F. nucleatum harbors a gene locus coding for a single, fused methionine sulfoxide reductase (MsrAB), a two-component transduction system (ModRS), thioredoxin (Trx)-  and cytochrome c (CcdA)-like proteins. Considering their role in oxidative stress responses, we demonstrated that these genes were increasingly expressed when fusobacterial cells were exposed to hydrogen peroxide. Comparative transcriptome analysis of the parental and modR mutant strains revealed that the response regulator ModR regulates a large regulon including trx, ccdA, and many metabolic genes. Significantly, mutants lacking individual genes within the msrAB locus, including msrAB, were sensitive to reactive oxygen species and defective in adherence/invasion of colorectal epithelial cells, as compared to the parental strain. The msrAB mutant was also defective in survival in macrophage, unlike the rescued and parental strains. Strikingly, in an experimental model of preterm birth this mutant was severely attenuated in virulence, for it failed to colonize the placenta and spread to the amniotic fluid. The results support that the MsrAB system represents a major pathway that protects fusobacteria against oxidative damage and confers virulence and that MsrAB-mediated oxidative stress defense is subjected to regulation by the two-component transduction system ModRS.

sample_organism: Fusobacterium nucleatum subsp. nucleatum

overall_design: Examination of modR deficient mutant compared to parental strain under normal growth or H2O2 stress in biological triplicates

first: Matthew

last: Scheible

first: Cuong

middle: T

last: Nguyen

first: Truc

last: Luong

first: Ju

middle: H

last: Lee

first: Martha

middle: I

last: Camacho

first: Yi-Wei

first: Bethany

middle: L

last: Tiner

first: Chenggang

last: Wu

first: Andreas

last: Tauch

first: Asis

last: Das

first: Hung

last: Ton-That


title: Bulk RNA-seq of lung-resident memory B cells and comparison to splenic memory and naive B cells

first: Oliver

last: Bannard

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

summary:
The aim was to utilise bulk RNAseq to compare the transcriptional profiles of memory B cells (Bmem) from the lung tissue to circulatory Bmem derived from spleen, in the context of X31 influenza-induced immune memory.
In this study we utilise AID-Cre Rosa-Stop-YFP reporter mice to track previously activated B cell populations, and combine this with an X31-influenza-specific HA probe to isolate flu-specific Bmem.
We find that lung Bmem express a number of tissue retention-associated genes (Cd44, Cd69) and downregulate circulatory genes (Sell, S1pr1), in comparison to splenic Bmem.
We also identify a number of chemotactic factors (Cxcr3, Ccr1, Ccr5) that are expressed at higher levels in lung Bmem than splenic Bmem.

overall_design:
Bmem were FACS-sorted from the lungs (IV CD45- B220+ AID-YFP+ GL7- CD69+ infuenza HA+) or spleens (B220+ CD38+ AID-YFP+ GL7- Infuenza HA+) of influenza-infected AID-cre Rosa26-Stop-dTomato mice at day 45 postinfection.
These memory populations were isolated the same animals and compared to naïve B cells (Live B220+ CD38+ AID-YFP- GL7- spleen cells) from the same donors.
in vivo labelling (IV Cd45) was used in lung samples to allow distinction of Bmem cells in the tissue parenchyma.
Lung cells from 6 mice were pooled per biological replicate. Three experiments were performed, each containing a single biological replicate. Technical replicates were acquired in two of these experiments.
Each sample has 4x raw fastq files, representing the sample being spread across 4 sequencing lanes

first: Tal

last: Arnon

first: Andrew

last: MacLean

first: Emmanouela

last: Repapi

first: Nicki

last: Gray


title: ATAC-seq changes induced by YAP, and TAZ knock down in MSKPCa3 organoid

first: Ekta

last: Khurana

summary: Chromatin accessibility of MSKPCa3 organoids upon knock down of YAP, and TAZ

overall_design: Chromatin accessibility analysis was performed in MSKPCa3 organoid knock down of YAP, YAP/TAZ, TAZ

first: Yu

last: Chen

first: Chen

last: Khuan Wong

first: Duo

last: Xu


title: Increased expression of SPRR1A is associated with a poor prognosis in pancreatic ductal adenocarcinoma

status: Public on Mar 27 2022

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

summary: SPRR1A-overexpression did not alter the gene expression profiles associated with aggressive progression of PDAC

overall_design: Comparison of the gene expression profiles between SPRR1A-overexpressing PK-1 and control using the stable and transient SPRR1A-overexpression models

first: Kohei

last: Yamakawa

first: Takashi

last: Aoi


title: CITE-seq analysis of mouse LSK cells

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: We performed cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) of the LSK compartment of TdT-reporter and TdT-fate mapping mice, in order to elucidate the heterogeneity and developmental trajectories within the MPP (lymphoid-primed multipotent progenitor) and HSC (hematopoietic stem cell) compartments.

overall_design: Lineage-Sca1+cKit+ (LSK) cells from 4 TdT[hCD4]-TdT[iCre]-Rosa26[YFP] mice were sorted,  stained with antibodies coupled to oligonucleotides directed against hCD4, Flt3, CD48, CD150, CD9, CD41, CD55, CD105, CD115, CXCR4, and ESAM, and loaded on separate wells of a 10X Genomics Chromium Single Cell Controller.

first: Fabian

last: Klein

first: Roxane

last: Tussiwand

first: Julien

last: Roux


title: Single-cell sequencing of wt and Rbx1-deficient Treg cells from mice

status: Public on Mar 26 2022

city: Hangzhou

first: Di

last: Wu

state: Zhejiang

address: No. 268, Kaixuan Road

country: China

institute: Zhejiang University

summary: Single-cell RNA sequencing (scRNA-seq) was utilized to unbiasedly dissect the cellular heterogeneity of wt vs. Rbx1-deficient CD4+YFP+ Treg cells from the peripheral lymph nodes of inflammation-free female Foxp3cre/wt and Foxp3cre/wt;Rbx1fl/fl mice.

overall_design: wt and Rbx1-deficient Treg cells from peripheral lymph nodes of C57 mice were analysed by sc-RNA sequencing.

first: Yi

last: Sun


title: Agrobacterium-mediated cassava transformation for the Asian-elite variety KU50

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

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

department: CSRS

institute: RIKEN

summary: Agrobacterium-mediated cassava transformation via friable embryogenic callus (FEC) has allowed the robust production of transgenic cassava. So far, the transformation has been performed mostly for 60444 (the model cassava variety for transformation) and African varieties due to the high ability of callus induction and good regeneration capacity from embryogenic tissues. It is important to develop the transformation methods for elite cassava varieties in Asian area which is one of main cassava production area in the world, however, the suitable transformation method for Asian elite variety via FEC has not been reported. Here, we developed the transformation method in Kasetsart 50 (KU50) which has the highest planting area in Thailand and Vietnam. In cassava transformation, the preparation of FEC is considered as a key step. The ability of FEC induction from KU50 was improved efficiently by the use of media with reduced nutrients and excess vitamin B1, even if the FEC-inducible efficiency was 5 times lower compared with cv. 60444. The optimal concentration of NAA for regeneration from FEC to cotyledon was 1.0 mg/L and the optimal concentration of BAP for shoot formation from cotyledon was 0.4 mg/L. The transformation efficiency was estimated as 45% for 60444 and 22% for KU50. Transcriptome analysis indicated that KU50 FEC is out of balance between cell wall production and assembly, because the expression of the genes related to loosing cell wall was upregulated in the FEC from KU50 compared with 60444. We hope that the developed technology will contribute to molecular breeding of useful cassava plants in Asia by the simultaneous use of genome-editing technology.

overall_design: The cassava calli were prepared in RIKEN at Japan. Total RNA was prepared from the cassava callus and used for the microarray hybridization. Four replicative hybridization experiments were carried out using the independent biological sample.

first: Yoshinori

last: Utsumi

first: Chikako

first: Maho

last: Tanaka

first: Yoshie

last: Okamoto

first: Anh

last: Vu Nguyen

first: Satoshi

last: Takahashi

first: Hiroki

last: Tokunaga

first: Nigel

last: Taylor

first: Motoaki

last: Seki


title: Secondary influenza challenge triggers lung resident memory B cell mobilization and rapid relocation for antibody secretion at infected loci

first: Stephen

last: Sansom

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

summary: Resident memory B (BRM) cells develop and persist in the lungs of influenza infected mice and humans but their contribution to recall responses following rechallenge has not been defined. We used scRNA-seq to identify early changes in lung immune cell composition and gene expression following secondary influenza infection and tested the effect of alveolar macrophage depletion (using intranasally delivered CLL). We found an alveolar macrophage dependent upregulation of IFNG-associated pathways after influenza rechallenge, that included increased expression of CXCL9, CXCL10 and CCL5 in myeloid cells.

overall_design:
B6 mice were infected with X31 influenza and were allowed to reach a memory phase (day 42 post primary infection). The mice were divided into 3 groups (n=3).
One group was assessed without rechallenge. The second group was pre-treated with PBS intranasally on days 6 and 3 before being rechallenged with X31 influenza.
The third group was pre-treated with CLL 3- and 6-days before rechallenge with X31 influenza. One day after rechallenge, the mice were in vivo labelled with anti-CD45 for 4min prior to tissue collection.
Cells were sorted as (live, IV CD45-, ex vivo CD45+) and stained with a CITESEQ antibody panel to facilitate population identification.
Samples were multiplexed in three pools using barcoded antibodies with one replicate of each condition present in each pool. There was a different assignment of HTO id to condition in pool 2. Each pool was captured on a seperate 10X channel.

first: Andrew

last: MacLean

first: Niamh

last: Richmond

first: Lada

last: Koneva

first: Moustafa

last: Attar

first: Tal

last: Arnon


title: Time-series RNAseq analysis following lateral root induction by gravistimulation

status: Public on Mar 25 2022

city: Montpellier

first: Soazig

last: GUYOMARC'H

address: 911 avenue Agropolis

country: France

institute: University of Montpellier

summary: We report the comparison of transcriptomic profiles in specific lateral root tissues for Col-0 wild type and puchi-1 mutant seedlings. Lateral root organogenesis is a key process in plant root system development and adaptation to the environment. To dissect the molecular events occurring during the early phase, we generated time-series transcriptomic datasets profiling lateral root development in puchi-1 and wild type backgrounds. Consistent with a mutually inhibitory mechanism, transcriptomic and reporter analysis revealed meristem-related genes were ectopically expressed during early stages of lateral root primordium formation in puchi-1. We conclude that PUCHI participates to the coordination of lateral root patterning and represses ectopic establishment of meristematic cell identities during early stages of organ development.

overall_design: The experiment comprises 36 samples: 2 genotypes (Col-0 wild type and puchi-1 mutant), and 6 treatments (no treatment, 12h, 18h, 24h, 30h and 36h gravistimulation), with 3 replicates per condition (genotype and treatment).

first: Kevin

last: BELLANDE

first: Laurent

last: LAPLAZE

first: Anne-Alicia

last: GONZALEZ

first: Emeric

last: DUBOIS


title: Clec4a4+ and Clec4a4- eosinophils in the small intestine

city: St. Louis

first: Wei-Le

last: Wang

state: MO

address: BJCIH, 8th Floor, Room 8107, 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University

summary: Eosinophils contribute to parasitic helminths- and allergens-induced type 2 immune responses. Although the gastrointestinal tract harbors a substantial number of eosinophils, the pathophysiological roles of intestinal eosinophils remain unclear. Here we identify a novel subset of eosinophil that expresses a repertoire of inhibitory molecules, including Clec4a4 and PD-L1. These Clec4a4+ leukocytes are blood-derived and exclusively present in the small intestine. Accordingly, this subset acquires imprinted features by the instruction of AHR signaling, which modulates immune responses to establish gut homeostasis. Selective depletion of AHR in eosinophils leads to a marked reduction of Clec4a4+PD-L1+ eosinophils and enhances the worm clearance accompanied by an increased type 2 immune response. Our findings may open new therapeutic avenues on primary eosinophilic gastrointestinal disorders.

overall_design: 1. Profile the gene expression in sorted mCherry+ and mCherry- eosinophils from Clec4a4-mCherry reporter mice. 2. Profile the gene expression from sorted A. WT Clec4a4+ eosinophils, B. WT Clec4a4- eosinophils, and C. Ahr KO Clec4a4- eosinophils.

first: Wei

first: Jun

last: Kasamatsu

first: Satoru

last: Joshita

first: Marco

last: Colonna


title: Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression

city: Aarhus C

first: William

last: Garland

address: C.F. Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: Transposable elements (TEs) are widespread genetic parasites known to be kept under tight transcriptional control. Here, we describe a functional connection between the mouse-orthologous ‘nuclear exosome targeting (NEXT)’ and ‘human silencing hub (HUSH)’ complexes, involved in nuclear RNA decay and the epigenetic silencing of TEs, respectively. Knocking out the NEXT component ZCCHC8 in embryonic stem cells results in elevated TE RNA levels. We identify a physical interaction between ZCCHC8 and the MPP8 protein of HUSH and establish that HUSH recruits NEXT to chromatin at TE loci. However, while NEXT and HUSH both dampen TE RNA expression, their activities predominantly affect shorter non-polyadenylated and full-length polyadenylated transcripts, respectively. Indeed, our data suggest that the repressive action of HUSH promotes a condition, favouring NEXT RNA decay activity. In this way, transcriptional and post-transcriptional machineries synergise to suppress the genotoxic potential of TE RNAs.

overall_design: 28 samples (9 RNA-seq, 12 3P-seq, 7 ChIP-seq)

first: Iris

last: Müller

first: Mengjun

last: Wu

first: Manfred

last: Schmid

first: Katsutoshi

last: Imamura

first: Leonor

last: Rib

first: Albin

last: Sandelin

first: Kristian

last: Helin

first: Torben

last: Heick Jensen


title: Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple mutated AML

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: RNA-Seq of primary human AML samples sorted based on GPR56 and CD34 expression.

overall_design: RNA-Seq of sorted AML fractions.

first: Swati

last: Garg

first: Armando

last: Reyes-Palomares

first: Lixiazi

last: He

first: Anne

last: Bergeron

first: Vincent-Philippe

last: Lavalée

first: Sébastien

last: Lemieux

first: Patrick

last: Gendron

first: Christian

last: Rhode

first: Jianglong

last: Xia

first: Prarabdha

last: Jagdhane

first: Carsten

last: Müller-Tidow

first: Daniel

middle: B

last: Lipka

first: Suzan

last: Imren

first: Keith

last: Humphries

first: Guillaume

last: Richard-Carpentier

first: Claudia

last: Waskow

first: Josée

last: Hébert

first: Judith

last: Zaugg

first: Fréderic

last: Barabé

first: Caroline

last: Pabst


title: Human CAR T cells expressing Super2 and IL-33 retain subset identity

first: Yina

last: Huang

department: Microbiology and Immunology

summary: Single cell RNAseq analysis was conducted on human TZ47 CAR T cells with or without Super2 and IL-33 co-expression eight days post in vitro manufacturing.

overall_design: PBMCs were stimulated for two days starting with anti-CD3 in RPMI complete media with 100 U/ml human IL-2 for 2 days prior to transduction with TZ47 CAR and Super2 + IL33 viral supernatants on sequential days. Human CAR T cells were expanded for a total of 8 days before cells were analyzed by scRNAseq

first: James

last: Cook

first: Cameron

last: Messier

first: Shannon

last: Ferry

first: Leena

last: Abdullah


title: RNF43 G659fs is an oncogenic colorectal cancer mutation and sensitizes tumor cells to PI3K/mTOR inhibition

city: Boston

first: Marios

last: Giannakis

state: Massachusetts

address: Brookline Ave 450

institute: Dana Farber Cancer Institute

summary: The RNF43_G659fs mutation occurs frequently in colorectal cancer, however, its function remains poorly understood. In addition, there are no specific therapies directed against this alteration. In this study, we found that RNF43_G659fs is not a passenger mutation, but rather promotes cell growth independent of Wnt signaling. We performed a drug repurposing library screen and discovered that cells with RNF43_G659 mutations were selectively killed by inhibition of PI3K signaling. PI3K/mTOR inhibitors yielded promising antitumor activity in RNF43659mut isogenic cell lines and xenograft models, as well as in patient-derived organoids harboring RNF43_G659fs mutations. We found that RNF43659mut binds p85 leading to increased PI3K signaling through p85 ubiquitination. Additionally, RNA-sequencing of RNF43659mut isogenic cells revealed decreased interferon signaling that may alter tumor immunity. Our findings suggest a novel therapeutic application for PI3K/mTOR inhibitors in treating RNF43_G659fs mutant cancers.

overall_design: mRNA profiles of HT29-sgCtrl and HT29_RNF43_G659 mutations

first: Lishan

last: Fang


title: ZNF333 ChIP-seq in HCT116

city: Singapore

first: Roger

last: Foo

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: ZNF333 ChIP-seq in HCT116

overall_design: ZNF333 ChIP-seq in HCT116

first: Marie

last: Loh


title: Transcriptomic and fatty acid analyses of Neochloris aquatica grown under different nitrogen concentration

city: Istanbul

first: Hande

last: Morgil

state: Fatih

address: Beyazit St.

department: Biology

country: Turkey

institute: Istanbul University

summary: In this study, we characterized the fatty acid production in Neochloris aquatica at transcriptomics and biochemical levels under limiting, normal, and excess nitrate concentrations in different growth phases. At the stationary phase, N. aquatica mainly produced saturated fatty acids such as stearic acid under the limiting nitrate concentration, which is suitable for biodiesel production. However, it produced polyunsaturated fatty acids such as α-linolenic acid under the excess nitrate concentration, which has nutritional values as food supplements. In addition, RNA-seq was employed to identify genes and pathways that were being affected in N. aquatica for three growth phases in the presence of the different nitrate amounts. Genes that are responsible for the production of saturated fatty acids were upregulated in the cells grown under a limiting nitrogen amount while genes that are responsible for the production of polyunsaturated fatty acid were upregulated in the cells grown under excess nitrogen amount. Further analysis showed more genes differentially expressed (DEGs) at the loga- rithmic phase in all conditions while a relatively steady trend was observed during the transition from the logarithmic phase to the stationary phase under limiting and excess nitrogen. Our results provide a foundation for identifying developmentally important genes and understanding the biological processes in the different growth phases of the N. aquatica in terms of biomass and lipid production.

overall_design: We performed de novo transcriptome analysis of Neochloris aquatica cells growth in nitrogen abundance and deficiency with  18 mmol/L nitrogen concentration for control. Deep sequencing technique was utilized via Illumina HiSeq2500 platfrom. Genes that participated in many biosynthesis were significantly changed in the logarithmic phase of the cells at 3 and 27 mmol/L of nitrate.

first: Riza

last: Akgul

first: Inci

last: Kizilkaya

first: Ehsan

last: Sarayloo

first: Gul

last: Oz

first: Fusun

first: Halil

last: Kavakli


title: RNA sequencing of endothelial cells from mouse brain of WT and EC-specific Nf2-deleted mice

status: Public on Mar 24 2022

city: Daejeon

first: JUNGMO

last: KIM

state: -- None selected --

address: 291 Daehak-ro, Yuseong-gu

department: Center for Vascular Research

country: South Korea

institute: Institute for Basic Science

summary: Understanding of transciptome changes of endothelial cells (ECs) in mouse brain by Nf2/Merlin is unknown. Here, we performed bulk RNA sequencing to investigate the changes of expression patterns by Nf2/Merlin deletion in mouse brain ECs

overall_design: ECs from mouse brain of WT and EC-specific Nf2-deleted mice were isolated and transciptome libraries were generated

first: Gou-Young

last: Koh

first: Jung-Mo

last: Kim

first: Jung-Hyun

last: Bae


title: ARGONAUTE proteins regulate a specific network of genes through KLF4 in mESCs [ChIP-seq]

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

institute: ETH

summary: Purpose: Study of H3K27me3 histone methylation for mouse embryonic stem cells (mESC) depleted for Argonaute proteins

overall_design: H3K27me3 histone methylation has been assessed for double Ago2&1 knockout mESCs in biological duplicates

first: Madlen

last: Müller

first: Moritz

last: Schaefer

first: Rodrigo

last: Peña-Hernández

first: Raffaella

last: Santoro


title: Transcriptome of Ago1_KO mESCs

summary: The goal was to identfiy the transcriptomics changes in mESCs upon Ago1 depletion. WT duplicate samples that are experimentally comparable, have been uploaded to GEO previously (GSM2082855, GSM2082856)

overall_design: mRNA profiles of Ago1 KO E14 mESCs were generated in duplicates


title: The formation of mineralized scaffolds in Bacillus subtilis biofilms is driven by a controlled calcium-concentrating subcellular niche

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

summary: In nature, bacteria reside in biofilms - multicellular differentiated communities held together by extracellular matrix. In this work, we identified a novel subpopulation essential for biofilm formation – mineral-forming cells in Bacillus subtilis biofilms. This subpopulation contains an intracellular calcium-accumulating niche, in which the formation of a calcium carbonate mineral is initiated. As the biofilm colony develops, this mineral grows in a controlled manner, forming a functional macrostructure that serves the entire community. Consistently, biofilm development is prevented by inhibition of calcium uptake. Taken together, our results provide a clear demonstration of the orchestrated production of calcite exoskeleton, critical to morphogenesis in simple prokaryotes. We expect future research exploring this newly discovered process to shed further light on mechanisms of bacterial development.

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: For accessing the effect of deletion of cueR gene on overall gene expression  - WT (3 replictes) was compared to delta cueR (3 replicates)

first: Ilana

last: Kolodkin-Gal

first: Alona

last: Keren-Paz

first: Iris

last: Karunker


title: Single-cell RNA sequencing of metastatic testicular seminoma reveals the cellular and molecular characteristics of metastatic cell lineage

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: Testicular cancer is the most common solid malignancy in young men. Given the many histological classifications of testicular tumours, seminoma is one of the most treatable cancers. The survival rate in early-stage disease was more than 90%. Thus, seminoma at the cellular and molecular levels, especially at the single-cell level, is worth studying. We performed a single-cell RNA sequencing (scRNA-seq) study on a patient who was diagnosed with testicular seminoma with lymph node metastasis. This study presented tumour tissue, PBMC, pelvic and renal hilus lymph node in a total of 18,206 high-quality single-cell transcriptome information. The characteristics of metastatic cell lineage were revealed by the comparison between different tumour cell subtypes at the scRNA level. A single-cell map of testicular seminoma with lymph node metastasis was constructed by scRNA-seq. We discovered the gene expression characteristics of the tumour cells in testicular seminoma, especially metastatic tumour cells. KRT8 and KRT18 were commonly expressed in the three tumour cell subtypes. However, TCF7L1, SCG3 and SV2C were the specifically expressed genes of tumour cell subtypes in primary tumour sites. Some molecular markers specifically expressed by the metastatic cell lineage, such as POU5F1, were identified. We revealed the molecular characteristics of testicular seminoma at the single-cell level, especially the metastatic tumour cells. This study could provide new insights into the diagnosis and treatment of testicular seminoma.

overall_design: Primary testicular cancer (tumor), pelvic lymph node (LN1), renal hilus lymph node (LN2) metastases and PBMC samples from 1 patient were used for single-cell RNA sequencing by 10X Genomics.

first: Linjian

last: Mo

first: Yufang

last: Lv

first: Jiwen

last: Cheng

first: Haibiao

last: Yan

first: Wenhao

last: Lu

first: Cheng

last: Su

first: Qiang

last: Ling

first: Zengnan


title: A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

department: Biological Sciences

institute: RNA Institute

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis [Polysome-seq]

summary: Ribosomal defects perturb stem cell differentiation, causing diseases called ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, we discovered three RNA helicases are required for ribosome biogenesis and for Drosophila oogenesis. Loss of these helicases, which we named Aramis, Athos and Porthos, lead to aberrant stabilization of p53, cell cycle arrest and stalled GSC differentiation. Unexpectedly, Aramis is required for efficient translation of a cohort of mRNAs containing a 5’-Terminal-Oligo-Pyrimidine (TOP)-motif, including mRNAs that encode ribosomal proteins and a conserved p53 inhibitor, Novel Nucleolar protein 1 (Non1). The TOP-motif co-regulates the translation of growth-related mRNAs in mammals. As in mammals, the La-related protein co-regulates the translation of TOP-motif containing RNAs during Drosophila oogenesis. Thus, a previously unappreciated TOP-motif in Drosophila responds to reduced ribosome biogenesis to co-regulate the translation of ribosomal proteins and a p53 repressor, thus coupling ribosome biogenesis to GSC differentiation.

overall_design: polysome-seq of duplicate samples of ovaries from germline aramis RNAi and germline bam RNAi as a developmental control and germline driven UAS-tkv as a developmental control

first: Elliot

last: Martin

first: Patrick

last: Blatt

first: Elaine

last: Ngyuen

first: Roni

last: Lahr

first: Sangeetha

last: Selvam

first: Hyun

last: Yoon

first: Tyler

last: Pocchiari

first: Shamsi

last: Emtenani

first: Daria

middle: E

last: Siekhaus

first: Andrea

last: Berman

first: Gabriele

last: Fuchs


title: A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis [RNA-seq]

overall_design: mRNA-seq of duplicate samples of ovaries from germline aramis RNAi and germline bam RNAi as a developmental control


title: A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis [rRNA_RIP-seq]

overall_design: Total RNA-seq of triplicate samples of ovaries expressing FLAG-tagged versions of Aramis, Athos, or Porthos subjected to RNA immunoprecipitation using anti-FLAG antibody or IgG as a negative control, with 10% of lysate reserved for input.


title: RNA Sequencing Analysis of liver from Normal Chow, HFD Control and SZ-A-treated HFD mice

status: Public on Mar 23 2022

city: Beijing

first: Yanmin

last: Chen

address: 1 Xian Nong Tan Street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Ramulus Mori  (Sangzhi) alkaloids (SZ-A) alleviates nonalcoholic fatty liver disease in mice. This study compares transcriptome profiling (RNA-seq) in the liver of normal chow, high-fat diet (HFD) control and SZ-A-treated HFD mice to verify the regulatory mechanisms of SZ-A. These results demonstrated that SZ-A regulates lipid metabolism and metabolic stress-induced inflammation and fibrosis.

overall_design: C57 mice were fed with normal chow or HFD for 14 weeks, and the HFD mice were treated with saline or SZ-A for another 8weeks. We performed RNA-Sequencing of the liver of normal chow, HFD control and SZ-A-treated HFD mice (n=6 per group).

first: Chunfang

last: Lian

first: Yuling

last: Liu


title: Gene expression changes caused by treatment of TPC1 cells with RET, FGFR inhibitor

city: New York

first: Yariv

last: Houvras

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College


title: Identification of the transcriptional biomarkers set linked to pathological remodelling of the eye tissues in various HD mouse models.

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary:
Our study aims to identify transcriptional deregulation of the oculomotor transcriptome in various HD mouse models using an Affymetrix array analysis
This study identified transciptome deregulation in the eye tissue of two HD mouse models, namely R6/1 and R6/2.

overall_design: All HD mouse lines were purchased from Jackson Laboratories (US). The R6/2, R6/1  mouse lines were bred and genotyped. The cumulative CAG counts for all time-points were as follow: R6/2 (162 ± 2.8 SD); R6/1 (131 ± 3.1 SD; HdhQ150 homozygote (165 ± 1.7 SD). All experimental procedures were conducted under a project license from the Home Office, UK and approved by the Animal Welfare and Ethical Review Body of Imperial College London. Experimental groups included: the R6/2 mouse model at  9 and weeks of age and their C57BL/6J littermates; the R6/1 mouse model at  6 months of age  and their C57BL/6J littermates. Tissues were harvested at specific time points, snap-frozen in liquid nitrogen and stored at -80OC for further analysis.

first: Iwona

last: Michałek-Mazur

first: Marta

last: Leśniczak

first: Paulina

last: Pietras

first: Mateusz

last: Sowinski

first: Witold

last: Szaflarski

first: Mark

last: Isalan

first: Michal

last: Mielcarek


title: Time-course RNA-Seq analysis of UVC exposed Ramazzottius varieornatus.

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

institute: NARO

summary: Time-course RNA-Seq analysis of  Ramazzottius varieornatus exposed to UVC for up to 72 hours

overall_design: 48 samples were sequenced for 16 time points, with 3 replicates each.

first: Kazuharu

last: Arakawa


title: Single cell RNA sequencing and TCR repertoire analysis of Adult T-cell Leukemia/Lymphoma (ATLL)

city: Seoul

first: EUN-HYE

last: JOO

address: 81, Irwon-ro, Gangnam-gu

department: Samsung Genome Institute

institute: Samsung Medical Center

summary: We examined ATLL using archived fresh frozen tissue after the biopsy by single-cell RNA sequencing (scRNA-seq) with T-cell receptor (TCR) clonal analysis. Highly clonal tumor cells showed multiple activating pathways, suggesting dynamic evolution of the malignancy. Dissecting diverse cell types comprising the TME led to the identification of a novel subset of cancer-associated fibroblast which showed enriched epidermal growth factor receptor (EGFR)-related transcripts.

overall_design: Human skin samples were obtained using remnants of biopsy tissue taken for diagnostic purposes.Specimens were placed in phosphate-buffered saline (PBS) on ice. Biopsy samples were cryopreserved in optimal cutting temperature (OCT) compound and stored at -80ºC. Single cell dissociates were loaded into the Chromium system (10x Genomics, USA) targeting 25,000 cells. The Chromium Single Cell 5’ Kit (10x Genomics, USA) was used to generate scRNA-seq and TCR libraries, according to the manufacturer’s instructions. scRNA-seq and TCR-seq data were aligned to the human reference genome (GRCh38) and processed using the CellRanger 4.0.0 pipeline (10x Genomics). In this study, we observed that the clonally expanded malignant tumor cells in ATLL are CD4 T-cells through scRNA-seq combined with TCR clonal analysis.

first: Hyun

last: Kim


title: A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis [bam-aramis double mRNAseq]

first: Prashanth

last: Rangan

first: Elliot

last: Martin

first: Patrick

last: Blatt

first: Elaine

last: Ngyuen

first: Roni

last: Lahr

first: Sangeetha

last: Selvam

last: Yoon

first: Tyler

last: Pocchiari

first: Shamsi

last: Emtenani

first: Daria

last: Siekhaus

first: Andrea

last: Berman

first: Gabriele

last: Fuchs


title: Gene expression changes induced by transgenic expression of CCDC6-RET or BRAF(V600E) oncogenes in zebrafish thyroid tumors [Zebrafish RET vs BRAF adult tumors]

first: Yariv

last: Houvras

summary: We used RNAseq to examine gene expression changes in thyroid tumors arising in transgenic zebrafish engineered to expression human CCDC6-RET or BRAF(V600E) oncogenes

overall_design: A zebrafish thyroglobulin promoter is used to express oncogenes in zebrafish thyroid

first: Renuka

last: Raman


title: A plant immune protein enables broad antitumor response by rescuing microRNA deficiency in cancers [RNA-seq and smallRNA-seq]

first: Li

last: Ding

state: Beijing

address: No.5, Yiheyuan Road

institute: Peking University

summary: Cancer cells are featured with uncontrollable activation of cell cycle and proliferation,and microRNA deficiency drives tumorigenesis. The RNA-dependent RNA polymerase (RDR) is essential for small RNA-mediated immune response in plants, but absent in vertebrates with adaptive immunity. Here we show that ectopic expression of plant RDR1 can generally inhibit the proliferation of different cancer cells. Interestingly, we find that abnormal AGO2-free microRNA isoforms with 1-nucleotide shortening at the 3’ end are widely accumulated in many tumors. RDR1 with nucleotidyltransferase activity can recognize and modify these problematic microRNAs with mononucleotides to restore their AGO2 loading efficiency, which eventually rescues microRNA deficiency and elevates microRNA expression to target cell cycle in cancer specifically. The wide antitumor effects of RDR1 can be visualized in multiple xenograft tumor models in vivo, which can be realized by adeno-associated virus-mediated delivery. Altogether, we develop a broad microRNA-mediated antitumor stratagem using the plant immune protein RDR1.

overall_design: Five tumors cell lines (A549, HepG2, HeLa, H1299), three leukemia (K562) with or without RDR1 expression were used for RNA-seq at different time points. siRNA-mediated AGO2 knockdown in cancer A549 cells with or without RDR1 expression were used for small RNA-seq to analyze the tailing percentage of miRNAs (siNC, Negative control). AGO2-IP followed by small RNA-seq analysis was performed from the A549 cell lines and HepG2 cell lines with inducible RDR1 expression (including miR-34c transfection assay). HeLa cells were treated with 0.5 uM palbociclib and DMSO for 48h followed by small RNA-seq. Tumor samples from the A549, H1299, PC-3, Jurkat and NALM-6 xenograft models were used for RNA-seq analysis (including AAV-mediated RDR1 delivery in A549 xenografts). For nanoparticle-mediated RDR1 delivery, A549, HeLa cells were transfected with RDR1-containing nanoparticles and used for RNA-seq.

first: Ye

last: Qi

first: Peng

last: Du


title: CUT & RUN H3K27me3 of Human Naïve and Primed Pluripotent Stem Cells with and without EZH2 inhibition.

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: To assess the effect of EZH2i in primed and naïve human pluripotent stem cells.


title: Analysis of non-relapsed and relapsed adult type granulosa cell tumors suggests stable transcriptomes during tumor progression

city: Helsinki

first: Katja

last: Eloranta

address: Tukholmankatu 8

department: Children's Hospital

country: Finland

institute: University of Helsinki

summary: Adult-type granulosa cell tumor (AGCT) is a rare ovarian malignancy characterized by slow growth and hormonal activity. The prognosis of AGCT is generally favorable, but one-third of patients with low-stage disease experience a late relapse, and over half of them die of AGCT. To identify markers that would distinguish patients at risk for relapse, we performed Lexogen QuantSeq 3’ mRNA sequencing on formalin-fixed paraffin-embedded, archival AGCT tissue samples tested positive for the pathognomonic FOXL2-mutation. We compared the transcriptomic profiles of 14 non-relapsed archival primary AGCTs (follow-up time 17-26 years after diagnosis) with 13 relapsed primary AGCTs (follow-up time 1.7-18 years) and eight relapsed tumors (follow-up time 2.8-18.9 years). Non-relapsed and relapsed primary AGCTs had similar transcriptomic profiles. In relapsed tumors three genes were differentially expressed: plasmalemma vesicle associated protein (PLVAP) was upregulated (p=0.01), whereas argininosuccinate synthase 1 (ASS1) (p=0.01) and perilipin 4 (PLIN4) (p=0.02) were downregulated. PLVAP upregulation was validated using tissue microarray RNA in situ hybridization. In our patient cohort with extremely long follow-up, we observed similar gene expression patterns in both primary AGCT groups suggesting that relapse is not driven by transcriptomic changes. These results reinforce earlier findings that molecular markers do not predict AGCT behavior or risk of relapse.

overall_design: Comparison of the transcriptomes of non-relapsed and relapsed adult type granulosa cell tumors

first: Noora

last: Andersson

first: Ulla-Maija

last: Haltia

first: Anniina

last: Färkkilä

first: Swee

last: Chong Wong

first: David

last: Wilson

first: Leila

last: Unkila-Kallio

first: Marjut

last: Pihlajoki

first: Antti

last: Kyrönlahti

first: Markku

last: Heikinheimo


title: DANCE-MaP probing of the adenine riboswitch

city: Houston

first: Anthony

last: Mustoe

state: TX

address: 1 Baylor Plaza

department: Biochemistry and Molecular Biology

institute: Baylor College of Medicine

summary: We show that DANCE-MaP permits measurement of state-specific per-nucleotide reactivities, direct secondary structure PAIRs, and tertiary RINGs for RNA structural ensembles. Here, we demonstrate DANCE-MaP on the V. vulnificus add riboswitch.

overall_design: Riboswitch constructs were in vitro transcribed and folded in the presence of variable amounts of adenine.

first: J

middle: W

last: Arney

first: Kevin

last: Weeks


title: Global transcriptomic analysis of bacteriophage-host interactions between Kayvirus therapeutic phage and Staphylococcus aureus

city: Brno

first: Adela

last: Finstrlova

address: Kamenice 5

department: Department of Experimental Biology

country: Czech Republic

institute: Masaryk University

summary: We analyzed RNA-Seq data of two Staphylococcus aureus strains, Newman and SH1000, infected by Kayvirus phage K. Staphylococcus virus K is used in the phage therapy, its genome is 148 kb long consisting of dsDNA with long terminal repeats, and encodes 233 ORFs and 4 tRNAs. The sampling times 0, 2, 5, 10, 20, and 30 minutes after infection were chosen based on the growth characteristics of the phage K at the two S. aureus strains. From the RNA-Seq data we determined transcriptional profile of the phage K and its hosts, which allowed us to identify differentially expressed genes, ncRNAs, and promotor and terminator sites. Transcription of the phage K genes starts immediately after the infection of bacterial cells and we found a gradual take-over by phage K transcripts in the infected cells. The temporal transcriptional profile of phage K was similar in both strains and the relative expression of phage K genes shows three distinct transcript types – early, middle, and late based on the time they reach maximum expression. The bacterial response to phage K infection is similar to the general stress response. It includes the upregulation of nucleotide, amino acid and energy synthesis and transporter genes and the downregulation of transcription factors. The expression of particular virulence genes involved in adhesion and immune system evasion as well as prophage integrases were marginally affected. This work unveils the versatile nature of phage K infection leading to its broad host range

overall_design: Infection of two S. aureus strains, SH1000 and Newman, with Staphylococcus virus K sampled in biological triplicates at  0, 2, 5, 10, 20, and 30 minutes after infection.

first: Ivana

last: Maslanova


title: A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis [aramis mRNA IP]

first: Prashanth

last: Rangan

country: USA

overall_design: mRNA-seq of triplicate samples of ovaries expressing FLAG-tagged Larp subjected to RNA immunoprecipitation using anti-FLAG antibody or IgG as a negative control, with 10% of lysate reserved for input.

first: Elliot

last: Martin

first: Patrick

last: Blatt

first: Elaine

last: Ngyuen

first: Roni

last: Lahr

first: Sangeetha

last: Selvam

first: Hyun

last: Yoon

first: Tyler

last: Pocchiari

first: Shamsi

last: Emtenani

first: Daria

last: Siekhaus

first: Andrea

last: Berman

first: Gabriele

last: Fuchs


title: 24-nt phasiRNAs move from tapetal to meiotic cells in maize anthers

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: In maize, 24-nt phased, secondary small interfering RNAs (phasiRNAs) are abundant in meiotic stage anthers, but their distribution and functions are not precisely known. Using laser capture microdissection (LCM), we analyzed tapetal cells, meiocytes, and other somatic cells at several stages of anther development to establish the timing of 24-PHAS precursor transcripts and the 24-nt phasiRNA products. This dataset includes 24-nt phasiRNA part of data. 24-nt phasiRNAs are found to accumulate in all cell types, with the highest levels in meiocytes, followed by tapetum.

overall_design: small RNA profiling of fixed single W23 inbred maize anther and isolated meiocyte, tapetum, and outer cell layers.

first: Virginia

last: Walbot

first: Xue

last: Zhou

middle: C

first: Chong

last: Teng


title: NFI factors repress fetal hemoglobin in adult erythorid cells [RNA-seq]

city: Philadelphia

first: KUNHUA

last: QIN

email: qink@chop.edu, kunhua.qin@gmail.com

state: PA

address: 3615 Civic Center Blvd, 315H

institute: Children's Hospital of Philadelphia

summary: The mechanisms by which the fetal type b-globin-like genes HBG1 and HBG2 are silenced in adult erythroid precursor cells is a basic biology question in human development. Reversal of such mechanisms is beneficial for b hemoglobinopathies, such as sickle cell disease (SCD). A CRISPR-Cas9 genetic screen uncovered two members of the NFI transcription factor family – NFIA and NFIX – as novel HBG1/2 repressors. Both factors are expressed at elevated levels in adult erythroid cells, and their single or combined depletion revealed cooperativity in HBG1/2 regulation in cultured cells and human-to-mouse xenotransplant experiments, as well as in preventing sickling of SCD-derived erythroblasts. Genomic profiling, gene editing and in vitro binding assays demonstrated that the potent concerted activity of NFIA and NFIX factors is explained in part by their ability to activate expression of BCL11A, a known silencer of the HBG1/2 genes, and in part by repressing the HBG1/2 genes via two direct binding sites. NFI factors emerge as versatile regulators of the fetal-to-adult switch in b-globin production.

overall_design: Transcriptome changes were analyzed by RNA-seq in 5 days-differeniated HUDEP2 cells targeted with CRISPR-Cas9 control sgRNA or NFIA and NFIX sgRNA.

first: Kunhua

last: Qin

first: Gerd

last: Blobel


title: ARGONAUTE proteins regulate a specific network of genes through KLF4 in mESCs.

first: Constance

last: Ciaudo

overall_design: Refer to individual Series


title: ARGONAUTE proteins regulate a specific network of genes through KLF4 in mESCs [ATAC-seq]

summary: Purpose: Study of chromatin accessibility for mouse embryonic stem cells (mESC) depleted for Argonaute proteins

overall_design: Chromatin accessibility has been assessed for single and double Ago2/Ago1 knockout mESCs in biological duplicates.

first: Madlen

last: Müller

first: Moritz

last: Schaefer


title: A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis [mRNA_RIP-seq]

first: Prashanth

last: Rangan

first: Elliot

last: Martin

first: Patrick

last: Blatt

first: Elaine

last: Ngyuen

first: Roni

last: Lahr

first: Sangeetha

last: Selvam


title: Gene expression changes caused by treatment of TPC1 cells with RET inhibitor BLU6864 [BLU6864_6H vs DMSO]

first: Yariv

last: Houvras

summary: NOT PROVIDED; REQUESTED

overall_design: We used RNAseq to examine gene expression changes in TPC1 cells after treatment with BLU6864 or BGJ398 or the combination of BLU6864 and BGJ398

first: Renuka

last: Raman


title: NFI factors repress fetal hemoglobin in adult erythorid cells [ATAC-seq]

overall_design: Open chromation regions were analyzed by ATAC-seq in undiffereniateed HUDEP2 cells targeted with CRISPR-Cas12a control sgRNA or NFIA&NFIX sgRNA.


title: Single-cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver

first: Jaime

last: Chu

address: 1 Gustave L. Levy Place, Annenberg 14-12

department: Pediatrics

institute: Icahn School of Medicine at Mount Sinai

summary: Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi-faceted and remain elusive with no approved antifibrotic treatments available. Here we use single-cell RNA sequencing (scRNA-seq) of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single-cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA-seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA-seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells (HSCs), the driver cell in liver fibrosis, specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel, conserved marker for zebrafish HSCs. To demonstrate the power of scRNA-seq to study liver fibrosis, we performed scRNA-seq on our zebrafish model of a pediatric liver disease with characteristic early, progressive liver fibrosis caused by mutation in mannose phosphate isomerase (MPI). Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor-ligand interactions within normal and fibrotic states. This study establishes the first scRNA-seq atlas of the adult zebrafish liver, highlights the high degree of similarity to the human liver, and strengthens its value as a model to study liver fibrosis.

sample_organism: Francisella tularensis subsp. tularensis SCHU S4

overall_design:
Single-cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/- (mss7) and WT siblings

Please note that the Series supplementary files were generated from multiple samples as following:
zf_WT_MPIMT_EC_HSC_subset - GSM5515731-GSM5515736
zf_WT_MPIMT_liver - GSM5515731-GSM5515736
zf_liver_atlas - GSM5515731-GSM5515733
joint_fish_human - GSM5515731-GSM5515733 as well as data from GSE115469 (samples GSM317872-317876).
and the description of each file is provided in the readme.txt.

first: Joshua

last: Morrison

first: Mamta

last: Giri


title: Gene expression changes caused by treatment of TPC1 cells with FGFR inhibitor BGJ398 [BGJ398_6H and BGJ398_24H]

summary: NOT PROVIDED; REQUESTED

overall_design: We used RNAseq to examine gene expression changes in TPC1 cells after treatment with BGJ398 at 6 and 24 hours


title: NFI factors repress fetal hemoglobin in adult erythorid cells [CUT&RUN]

first: KUNHUA

last: QIN

overall_design: Genomic occupancies of NFIA and NFIX proteins in HUDEP2 and primary erythroblasts were analyzed by CUT&RUN. IgG, NFIA KO and NFIX KO were used as control.


title: Gene expression changes caused by treatment of TPC1 cells with RET inhibitor BLU6864 in combination with FGFR inhibitor BGJ398 vs. BLU6864 alone [BGJ398_24H + BLU6864_24H vs BLU6864_24H]

summary: NOT PROVIDED; REQUESTED

overall_design: We used RNAseq to examine gene expression changes in TPC1 cells after treatment with the combination of a RET inhibitor (BLU68964) in combination with an FGFR inhibitor (BGJ398) compared to a RET inhibitor (BLU6864) alone


title: Relish-mediated lncRNA-CR33942 facilitates Drosophila Imd immune responses and promotes antimicrobial peptide expression via interacting with Relish

status: Public on Mar 22 2022

city: Nanjing

first: Hongjian

last: Zhou

address: No.1 Wenyuan Road, Xianlin University Town, Nanjing

institute: Nanjing Normal University

summary: Long noncoding RNAs (lncRNAs), as a class of emerging regulators, play crucial role in regulating the strength and duration of innate immunity. However, little is known about how these Drosophila Imd immunity-related lncRNAs are regulated. Herein, we firstly revealed that overexpression of lncRNA-CR33942 could strengthen the expression of Imd pathway antimicrobial peptides Diptericin (Dpt) and Attacin-A (AttA) after infection, and vice versa. Secondly, RNA-seq analysis of post-infected lncRNA-CR33942-overexpressing flies further confirmed that lncRNA-CR33942 positively regulates the Drosophila Imd pathway. Mechanistically, we indicated that lncRNA-CR33942 interacts with NF-κB transcription factor Relish to promote its binding to Dpt and AttA promoters, thereby facilitating Dpt and AttA expression. Interestingly, we found that Relish can also directly promote lncRNA-CR33942 transcription by binding to its promoter. Finally, rescue experiments and dynamic expression profiling post-infection demonstrated the vital role of the Relish/lncRNA-CR33942/AMPs regulatory axis in enhancing inadequate Imd immune responses and maintaining immune homeostasis. Taken together, our study not only elucidates a novel mechanism about lncRNA in Drosophila Imd immune regulation, but also has important guiding significance for elucidating the complex regulatory mechanism of animal innate immune response.

overall_design: the CR33942-overexpressing and control male adult flies were collected at 12 h after E. coli infection for subsequently RNA-seq

first: Shengjie

last: Li

first: Fei

last: Ma

first: Ping

last: Jin


title: Single-Cell RNAsequencing of Human Naïve Pluripotent Stem Cells to Trophoblast Stem Cells with and without EZH2 inhibition.

first: Vincent

last: Pasque

summary: Single-Cell RNAsequencing of the conversion of naïve iCas9 Sigma hiPSC line 1 (iCSIG-1 hiPSCs) into trophoblast stem cells with and without EZH2i (Abcam ab146152 UNC1999, EZH2 methyltransferase inhibitor) during 4 days preconversion and during 4 days during conversion (total of 8 days with or without PRC2i).

overall_design: Examination of the inhibition of EZH2 in human naïve pluripotent stem cells and day 4 of the conversion of naïve into trophoblast stem cells.

first: Dick

last: Zijlmans

first: Irene

last: Talon

first: Sigrid

last: Verhelst

first: Adam

last: Bendall

first: Karlien

last: VanNerum

first: SanKit

last: To

first: Adrian

last: Janiszewski

first: Joop

last: Jansen

first: Ruth

last: Knops

first: Danielle

last: Admiraal

first: Amitesh

last: Panda

first: Nataranjan

middle: V

last: Bhanu

first: Amanda

last: Collier

first: Charlene

last: Fabian

first: Dieter

last: Deforce

first: Benjamen

last: Garcia

first: Michiel

last: Vermeulen

first: Maarten

last: Dhaenens

first: Hendrik

last: Marks

first: Peter

last: Rugg-Gunn


title: Bulk RNA-seq analysis of WT and MPI MT LX-2 cells

first: Jaime

last: Chu

summary: The purpose of this study was to identify the changes in gene expression that occur in LX-2 human hepatic stellate cells in response to depletion of mannose phosphate isomerase enzymatic activity.

overall_design: Bulk RNA sequencing of WT and MPI MT LX-2s

first: Joshua

last: Morrison

first: Charles

last: DeRossi


title: Gene expression changes caused by treatment of TPC1 cells with RET inhibitor BLU6864 from 6 to 24 hours [BLU6864_24H vs BLU6864_6H]

first: Yariv

last: Houvras

summary: NOT PROVIDED; REQUESTED

overall_design: We used RNAseq to examine gene expression changes in TPC1 cells after treatment with RET inhibitor BLU6864 from 6 to 24 hours

first: Renuka

last: Raman


title: Transcriptome Analysis Reviewed a Two-step Transformation of VSMCs to Macrophage-like Cells

city: Xiamen

first: Wei

last: Shen

state: Fujian

address: 2999 Jinshan Rd, Huli District

institute: Xiamen University

summary: We report the transcriptome profiles of rat vascular smooth muscle cells (rVSMCs) treated by cholesterol loading or NOTCH inhibitor DAPT through RNA-Seq. rVSMCs were resistant to cholesterol loading alone that only promoted limited inflammatory responses. DAPT treatment alone also resulted in limited gene expression changes related with VSMC differentiations. Interestingly, cholesterol loading supplemented with DAPT resulted in significant changes of gene expression in rVSMCs and promoted VSMC-to-macrophage-like cell transformations.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Primary rVSMCs were cultured with water soluble cholesterol (Chol:MβCD) or NOTCH inhibitor DAPT or both for 48 hours to observe transcriptome profile changes in rVSMCs.


title: SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes [ChIP-Seq]

status: Public on Mar 21 2022

city: Atlanta

first: Sergio

last: Ramirez-Perez

state: Georgia

address: 615 Michael St NE

department: Orthopaedics

institute: Emory University

summary:
Purpose: Our goal was to evaluate the transcriptional profiles of FLS. We used genome wide approaches to uncover the interactions between SOX4 and RELA/p65, downstream of TNF signaling.
Methods: ChIP-seq of mouse FLS was used to compare the global DNA binding profiles of SOX4 and RELA.
Results: ChIP-seq revealed an overllap of SOX4 peak summits with RELA peak summits suggesting that both proteins bind in close-proximity on regulatory sequences, enabling them to co-operatively regulate gene expression.  By integrating the ChIP-seq results with RNA-seq from SoxC-knockout FLS we identified a set of TNF-responsive genes that are targets of the RELA-SOX4 transcriptional complex.
Conclusion: SOX4 and RELA, together orchestrate a multimodal regulation of gene expression downstream of TNF signaling. Their interdependent activities play a pivotal role in the transformation FLS in arthritis and in the inflammatory pathology of diverse tissues where RELA and SOX4 are co-expressed.

first: Pallavi

last: Bhattaram


title: Esrrb Regulates Specific Feed-Forward Loops to Transit from Pluripotency into Early Stages of Differentiation  (RNA-Seq)

city: Barcelona

first: Ana

last: Sevilla

state: ESP

address: Avda Diagonal 643. Edificio Malagef 4rd Floor, Faculty of Biology

country: Spain

institute: Universidad de Barcelona

summary: Characterization of pluripotent states, in which cells can both self-renew or differentiate, with the irreversible loss of pluripotency, are important research areas in developmental biology. Although microRNAs (miRNAs) have been shown to be crucial for embryonic stem (ES) self-renewal maintenance and cellular differentiation, the role of miRNAs integrated into gene regulatory networks and its dynamic changes during these state transitions remain elusive. Here we describe the dynamic transcriptional regulatory circuitry of ES cells that incorporate protein-coding and miRNA genes based on microRNA array expression and quantitative sequencing of short transcripts upon the downregulation of the Estrogen Related Receptor Beta (Esrrb). The data reveals how Esrrb, a key stem cell transcription factor, regulates a specific ES cell miRNA expression program and integrates dynamic changes of feed forward loops contributing to the exit of the pluripotency state upon its downregulation. Together these findings provide new insights on the architecture of the combined transcriptional post-transcriptional regulatory network in stem cells.

overall_design: Total of 4 time course series data of a murine embryonic stem cell line with controllable Esrrb expression (Esrrb_R) samples; Esrrb day0, Esrrb kd day1, Esrrb kd day3 and Esrrb kd Day5.

first: Amin

middle: R

last: Mazloom

first: Huilei

last: Xu

first: Jaume

last: Reig

last: Vasileva

first: Avi

last: Ma’ayan

first: Ihor

last: Lemischka


title: Integrated Multi-Omics Reveal Polycomb Repressive Complex 2 Restricts Human Trophoblast Induction.

first: Vincent

last: Pasque

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


title: Identification of targets of Vegfc signaling during cardiac regeneration in zebrafish

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Purpose:to identify with transcriptomic analysis, gene targets of Vegfc signaling during cardiac regeneration in zebrafish.  Results: We were able to identify several differential expressed genes, many of which encode for immune related genes, as well as ECM components.

overall_design: Adult ventricles were extracted from cryoinjured WT and Tg(hsp70l:sflt4) fish at 24 hpci

first: Hadil

last: El-Sammak

last: Guenther


title: Differential vulnerability of adult neurogenic niches to dosage of the Neurodevelopmental-disorder linked gene FoxG1

city: Erlangen

first: Dieter

middle: Chichung

last: Lie

address: Fahrstr. 17

department: Institut für Biochemie

summary: We report that the two adult neurogenic niches of the mammalian brain – the dentate gyrus of the hippocampal formation and the subependymal zone of the lateral ventricles - displayed differential vulnerability to increased FoxG1 dosage: high FoxG1 levels severely compromised survival and glutamatergic dentate granule neuron fate acquisition in the hippocampal neurogenic niche, but left neurogenesis of GABAergic neurons in the subependymal zone / olfactory bulb system unaffected. Comparative transcriptomic analyses revealed a significantly higher expression of the apoptosis-linked nuclear receptor Nr4a1 in FoxG1-overexpressing hippocampal neural precursors. Our results reveal differential vulnerability of neuronal subtypes to increased FoxG1 dosage and suggest that activity of a FoxG1/Nr4a1 axis contributes to such subtype-specific response.

overall_design: Bulk RNA-sequencing from adult neural stem/progenitor cells (NSPCs) derived from either the dentate gyrus or the subepenymal zone of female adult C57BL/6.  Both groups were transduced with either a CAG-GFP control retrovirus or a FoxG1-overexpressing (CAG-FoxG1-IRES-GFP) retrovirus.

first: Iris

last: Schäffner

first: Marie-Theres

last: Wittmann

first: Tanja

last: Vogel


title: TRL-1 undergoes phase separation to regulate the reproduction and longevity tradeoff

city: Beijing

first: Dou

last: Wu

address: Haidian street

institute: Tsinghua university

summary: The antagonistic pleiotropy theory of aging proposes that genes enhancing fitness in early life limit lifespan, but the molecular evidence remains underexplored. By profiling translatome changes in Caenorhabditis elegans during starvation recovery, we demonstrate that an open reading frame (ORF) trl-1 'hidden' within an annotated pseudogene significantly translates upon refeeding. trl-1 mutant animals increase brood sizes but shorten lifespan and specifically impair the germline deficiency-induced longevity. The loss of trl-1 abnormally upregulates the translation of vitellogenin that produces copious yolk to provision eggs, whereas vitellogenin overexpression is known to reduce lifespan. We show that TRL-1 protein undergoes liquid-liquid phase separation, through which TRL-1 granules recruit vitellogenin mRNA and inhibit its translation. These results indicate that trl-1 functions as an antagonistic pleiotropic gene to regulate the reproduction-longevity tradeoff by optimizing nutrient production for the next generation.

overall_design: Ribo-Seq and RNA-Seq of starved six days C. elegans larvae refed with bacterial food for 0, 10, 30, and 60 minutes (min) in wide-type(N2) animals , trl-1(cas1077) animals and trl-1(cas1078) animals. A reference sample was collected from the same culture condition from the non-starved (NS) animals, each strain was analyzed in biological duplicate.

first: Jingying

last: Huang


title: A Drosophila toolkit for HA-tagged proteins unveils a block in autophagy flux in the last instar larval fat body

city: Yokohama

first: Tadayoshi

last: Murakawa

address: Midori Nagatsuta 4259 S2-201

department: Department of Life Science and Technology

country: Japan

institute: Tokyo Institute of Technology

summary: The lysosomal function is down-regulated in the white prepupal fat body, resulting in the enlargement of lysosomes in the tissue. The enlargement is blocked by the forced activation of lysosomes by the overexpression of mitf, a sole homolog of the MiTF/TFE family transcription factors. Thus, it is possible to speculate that mitf participates in the down-regulation of lysosomes in the fat body. To test this possibility, we performed a comparative mRNA-seq of (1) wild-type white prepupal fat body, (2) mitf overexpressed white prepupal fat body, and (3) wild-type third instar larval fat body. First, a comparison of (1) and (2) showed that the overexpression of mitf upregulated transcription of most of the lysosome-related genes in the fat body, consistent with previous studies. Next, a comparison of (1) and (3) indicated that the transcription level of several lysosome-related genes was decreased in (1) compared to (3). However, most of the genes regulated by Mitf were not transcriptionally affected. These results suggest that mitf is dispensable for the downregulation of lysosomes in the white prepupal fat body.

overall_design: Compare the effect of the overexpression of mitf at white prepupa. Or, compare the gene expression levels between third instar larvae and white prepupae in WT strain.

first: Naonobu

last: Fujita


title: Bulk RNAsequencing of H9 Primed and Naïve Pluripotent Stem Cells with and without EZH2 inhibition.

summary: Bulk RNAseq of 3 replicates of primed H9 +/- EZH2i (E8Flex) and 3 replicates of naive H9 +/- EZH2i (PXGL) to assess the effect of EZH2i in human pluripotent stem cells

overall_design: To assess the effect of EZH2i in primed and naïve human pluripotent stem cells.

first: Dick

last: Zijlmans

first: Irene

last: Talon

first: Sigrid

last: Verhelst

first: Adam

last: Bendall

first: Karlien

last: VanNerum

first: SanKit

last: To

first: Adrian

last: Janiszewski

first: Joop

last: Jansen

first: Ruth

last: Knops

first: Danielle

last: Admiraal

first: Amitesh

last: Panda

first: Nataranjan

last: Bhanu

first: Amanda

last: Collier

first: Charlene

last: Fabian

last: Deforce

first: Benjamen

last: Garcia

first: Michiel

last: Vermeulen

first: Maarten

last: Dhaenens

first: Hendrik

last: Marks

first: Peter

last: Rugg-Gunn


title: SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes

first: Sergio

last: Ramirez-Perez

overall_design: Refer to individual Series


title: NFI factors repress fetal hemoglobin in adult erythorid cells

first: KUNHUA

last: QIN


title: Astrocyte-targeted gene delivery of interleukin 2 specifically increases brain-resident regulatory T cell numbers and protects against pathological neuroinflammation

city: Cambridge

last: Liston

address: Babraham Research Campus

country: United Kingdom

institute: The Babraham Institute

summary: The ability of immune-modulating biologics to prevent and reverse pathology has transformed recent clinical practice. Full utility in the neuroinflammation space, however, requires identification of both effective targets for local immune-modulation and a delivery system capable of crossing the blood-brain-barrier. The recent identification and characterization of a small population of regulatory T (Treg) cells resident in the brain presents one such potential therapeutic target. Here we identified brain interleukin 2 (IL-2) levels as a limiting factor for brain-resident Treg cells. We developed a gene-delivery approach for astrocytes, with a small-molecule on-switch to allow temporal control, and enhanced production in reactive astrocytes to spatially direct delivery to inflammatory sites. Mice with brain-specific IL-2 delivery were protected from traumatic brain injury, stroke and multiple sclerosis models, without impacting the peripheral immune system. These results validate brain-specific IL-2 gene delivery as effective protection against neuroinflammation, and provide a versatile platform for delivery of diverse biologics to neuroinflammatory patients.

overall_design: 8 samples in total. 2 control replicates and 2 experimental replicates for brain , 2 control replicates and 2 experimental replicates for blood


title: Transcriptomics analysis of Huh7 hepatoma cells transfected with con-miR or miR-383 in the presence or absence of DENV infection

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

institute: University of Ottawa

summary: Investigating the role of miR-383 in the modulation of DENV infection and hepatic lipid metabolism

overall_design: Human liver heptoma cells were transfected with either con-miR or miR-383 in the presence or absence of DENV. RNA was extracted and analysed using a Affymetrix Human Gene ST.2.0 array.

first: Nadine

last: Ahmed

first: Noreen

middle: P


title: Sequence-dependent model of genes with dual σ factor preference

city: Tampere

first: Andre

middle: Sanches

last: Ribeiro

state: Pirkanmaa

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

institute: Tampere University

summary: Escherichia coli uses σ factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single σ factor, approximately 5% of them have dual σ factor preference. The most common are those responsive to both σ70, which controls housekeeping genes, and σ38, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that ‘σ70+38 genes’ are nearly as upregulated in stationary growth as ‘σ38 genes’. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in σ38 levels. We then propose and validate a sequence dependent model of σ70+38 genes, with dual sensitivity to σ38 and σ70, that is applicable in the exponential and stationary growth phases, as well in the transient period in between. We further propose a general model, applicable to other stresses and σ factor combinations. Given this, promoters controlling σ70+38 genes (and variants) could become important building blocks of synthetic circuits with predictable, sequence-dependent sensitivity to transitions between the exponential and stationary growth phases.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Examination of genome-wide responses under exponential and stationary growth phase conditions

first: Ines

middle: S

last: Baptista

first: Vinodh

last: Kandavalli

first: Vatsala

last: Chauhan

first: Mohamed

middle: N

last: Bahrudeen

first: Bilena

last: Almeida

first: Cristina

last: Palma

first: Suchintak

last: Dash


title: Small Noncoding RNAome Changes during macrophage polarization

status: Public on Mar 19 2022

city: Shanghai

first: Chuandong

last: Wang

address: NO.1665 Kongjiang Road

country: China

institute: Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Macrophages belong to a special phagocytic subgroup of human leukocytes and are one of the important cells of the human immune system. They participate in both specific and innate immune processes and play an important role in the host's resistance to pathogen invasion and the inflammatory response. Small noncoding RNAs are a group of small RNA molecules that can be transcribed without the ability to encode proteins but could play a specific function in cells. We used high-throughput sequencing analysis and qPCR to detect the expression changes of the small noncoding RNAome during macrophage polarization.

overall_design: We used RAW264.7 cells to induce macrophage polarization. For M1 macrophage polarization, we added LPS and IFN-γ stimulated RAW264.7 cells. For macrophage M2 polarization, we stimulated RAW264.7 cells with IL-4 and IL-10.

first: Ding

last: Ma

first: Xing

last: Zhou

first: Yu


title: Clr-f expression regulates kidney immune and metabolic homeostasis

city: Halifax

first: Francesca

last: Di Cara

state: Nova Scotia

address: 5850/5980 University Avenue

institute: Dalhousie University

summary: The C-type lectin-related protein, Clr-f, encoded by Clec2h in the mouse NK gene complex (NKC), is a member of a family of immune regulatory lectins that guide immune responses at distinct tissues of the body. Clr-f is highly expressed in the kidney; however, its activity in this organ is unknown. To assess the requirement for Clr-f in kidney health and function, we generated a Clr-f-deficient mouse (Clr-f−/−) by targeted deletions in the Clec2h gene. Mice lacking Clr-f exhibited glomerular and tubular lesions, immunoglobulin and C3 complement protein renal deposits, and significant abdominal and ectopic lipid accumulation. Whole kidney transcriptional profile analysis of Clr-f−/− mice at 7, 13, and 24 weeks of age revealed a dynamic dysregulation in lipid metabolic processes, stress responses, and inflammatory mediators. Examination of the immune contribution to the pathologies of Clr-f−/− mouse kidneys identified elevated IL-12 and IFNγ in cells of the tubulointerstitium, and an infiltrating population of neutrophils and T and B lymphocytes. The presence of these insults in a Rag1−/−Clr-f−/− background reveals that Clr-f−/− mice are susceptible to a T and B lymphocyte-independent renal pathogenesis. Our data reveal a role for Clr-f in the maintenance of kidney immune and metabolic homeostasis.

overall_design: Total kidney RNA of 7, 13, 24-week old wild type and Clr-f-/- mice. 3 replicates per age.

first: Andrew

last: Makrigiannis

first: Brendon

middle: D

last: Parsons

first: Haggag

last: Zein


title: Single-cell multiomics of  CD4+ T cell clones in HIV-1 infected individuals

city: New Haven

first: Jack

middle: Anthony

last: Collora

state: CT

address: 295 Congress Ave

department: Microbial Pathogenesis

institute: Yale University

summary: The clonal expansion of HIV-1-infected CD4+ T cells is a major barrier to cure. Using single-cell ECCITE-seq, we examined the transcriptional landscape, upstream immune regulators, HIV-1 RNA expression, and T cell clonal expansion dynamics of 215,458 CD4+ T cells (267 HIV-1 RNA+ cells and 68 expanded HIV-1 RNA+ T cell clones) from six HIV-1-infected individuals (during viremia and after suppressive antiretroviral therapy) and two uninfected individuals, in unstimulated conditions and after CMV and HIV-1 antigen stimulation. We found that despite antiretroviral therapy, antigen and TNF responses persisted and shaped T cell clonal expansion. HIV-1 resided in Th1 polarized, antigen-responding T cells expressing Bcl-2 family anti-apoptotic genes. HIV-1 RNA+ T cell clones were larger in clone size, established during viremia, persistent after viral suppression, and enriched in GZMB+ cytotoxic effector memory Th1 cells. Targeting HIV-1-infected cytotoxic CD4+ T cells and drivers of clonal expansion provides a new direction for HIV-1 eradication.

overall_design: Study was completed in two arms, unstimulated and antigen stimulated CD4+ T cells. Paired PBMC samples from 6 individuals from the Sabes cohort during acute/recent viremia were used in both arms, 2 uninfected controls were recruited for comparison. For the unstimulated arm, CD4+ T cells were isolated from PBMC by negative selection and stained with a CITE-seq panel. For the stimulated arm, CD8+ T cells were depleted from PBMC. CD8- PBMC were pulsed with either CMV peptides or HIV peptides for 9 hours in the presence of T20 ART. Cells were then stained and antigen specific cells sorted on a FACS ARIA sorter for CD3+CD8-CD19-CD56- Acitvation inducible Marker (AIM, CD69+CD154+). Memory cells were also sorted as CD3+CD8-CD19-CD56-CD69-CD154-CD45RO+. Sorted cells were then hashed and stained with the CITE panel as previous. In either case, labeled cells were loaded into the 10X chromium controler for 5' immune profiling with feature barcoding. This resulted in libraries for the single cell transcriptome, surface proteome, and T cell receptor sequences. Libraries were sequenced with either the minimum requirements (R1 26, R2 90 for transcriptome and CITE-seq) on a HiSeq 4000 or in 150PE mode on a Novaseq 6000. In parallel, bulk TCR repetiore libraries were generated from remaining unstimulated CD4+ T cells using the NEBNext Human ImmuneProfiling kit and sequence on a MiSeq in 300PE mode.

first: Ho

last: Ya-Chi

middle: A

first: Runxia

last: Liu


title: Single-cell RNA sequencing-based characterization of resident lung mesenchymal stromal cells in bronchopulmonary dysplasia

status: Public on Mar 20 2022

first: David

last: Cook

address: 501 Smyth Rd

department: Cancer Therapeutics Program

institute: Ottawa Hospital Research Institute

summary: Late lung development is a period of alveolar and microvascular formation, which is pivotal in ensuring sufficient and effective gas exchange. Defects in late lung development manifest in premature infants as a chronic lung disease named bronchopulmonary dysplasia (BPD). Numerous studies demonstrated the therapeutic properties of exogenous bone marrow and umbilical cord-derived mesenchymal stromal cells (MSCs) in experimental BPD. However, very little is known regarding the regenerative capacity of resident lung MSCs (L-MSCs) during normal development and in BPD. In this study we aimed to characterize the L-MSC population in homeostasis and upon injury. We used single-cell RNA sequencing (scRNA-seq) to profile in situ Ly6a+ L-MSCs in the lungs of normal and O2-exposed neonatal mice (a well-established model to mimic BPD) at three developmental timepoints (postnatal days 3, 7 and 14). Hyperoxia exposure increased the number, and altered the expression profile of L-MSCs, particularly by increasing the expression of multiple pro-inflammatory, pro-fibrotic, and anti-angiogenic genes. In order to identify potential changes induced in the L-MSCs transcriptome by storage and culture, we profiled 15,000 Ly6a+ L-MSCs after in vitroculture. We observed great differences in expression profiles of in situ and cultured L-MSCs, particularly those derived from healthy lungs. Additionally, we have identified the location of Ly6a+/Col14a1+ L-MSCs in the developing lung and propose Serpinf1 as a novel, culture-stable marker of L-MSCs. Finally, cell communication analysis suggests inflammatory signals from immune and endothelial cells as main drivers of hyperoxia-induced changes in L-MSCs transcriptome.

overall_design: Multiplexed scRNA-seq (MULTI-seq) of cultured normoxia and hyperoxia-derived LY6A+ and LY6A- L-MSCs

first: Ivana

last: Mižíková


first: Samar

middle: Hayat Khan

last: Tareen

address: Babraham Hall, Babraham

institute: Babraham Institute

overall_design: Wildtype mice, treated with PHP.GFAP-IL-2 (or PHP.GFAP-GFP control vector) on day -14, were given controlled cortical impacts to induce moderate traumatic brain injury (TBI) or sham surgery. Triplicate samples for were for TBI conditions. 14 days post-TBI, T cells (TCRβ+CD45+CD11b-) and microglia (CD11b+CD45+) were sorted from the perfused brains for 10x single cell transcriptomics. For each experiment, approximately 8,700 cells were added to each channel for a targeted cell recovery of 5,000 cells. Post-cell count and quality control, the samples were immediately loaded onto the Chromium Controller.

middle: H

first: Emanuela

last: Pasciuto

first: Pascal

last: Bielefeld

first: Lidia

last: Yshii

first: Adrian

last: Liston


title: Gene expression in engineered heart tissues exposed to THC and genistein

city: Aurora

first: Edward

last: Lau

state: CO

address: 12700 E19th Av RCII Rm 8004

department: Medicine/Cardiology

institute: University of Colorado

summary: The goal of the experiment is to identify gene expression changes in engineered heart tissues (EHT) composed of human induced pluripotent stem cell-derived cardiomyocytes and endothelial cells treatered with Δ9-tetrahydrocannabinol (THC) or THC with genistein.

overall_design: 6 samples are analyzed, containing 2 EHT constructs each (n=2) treated with vehicle control, THC, and THC plus genistein

first: Mark

last: Chandy

first: Joseph

last: Wu


title: Type I Innate Lymphoid Cells Control Leukemia Stem Cell Fate and Limit Development of Acute Myeloid Leukemia [2]

city: Duarte

first: Zhenlong

last: Li

address: 1500 East Duarte Road

institute: City of hope

summary: Type I innate lymphoid cells (ILC1s) are critical regulators of inflammation and immunity in mammalian tissues. However, their functional roles in cancer are largely undefined. We found that a high concentration of normal murine ILC1s induced leukemia stem cell (LSC) apoptosis. At a lower concentration, ILC1s prevented LSCs from differentiating into leukemia progenitors and promoted their differentiation into non-leukemic cells, thus blocking the production of terminal myeloid blasts. All of these effects, which required ILC1s to produce interferon-γ after cell–cell contact with LSCs, converged to suppress leukemogenesis in vivo. Conversely, ILC1s’ anti-leukemia potential waned when JAK-STAT and PI3K-AKT signaling was inhibited. The relevant anti-leukemic properties of normal ILC1s were operative in humans and impaired in AML patients. Collectively, our findings reveal crucial functions of ILC1s as anti-cancer immune cells seemingly suitable for AML immunotherapy, and provide a new potential strategy to treat AML and/or prevent relapse of the disease.

overall_design: Identification of the LSC regulatory pathways exploited by ILC1s or IFN-γ

first: Jianhua

last: Yu


title: Disordered N-Terminal DNMT3A Domain Is Required for Mouse Postnatal Development

city: Houston

first: Tianpeng

last: Gu

address: Cambridge steet

institute: Baylor College of Medicine

type: Methylation profiling by high throughput sequencing

summary: DNA methyltransferase 3a (DNMT3A) plays a crucial role in multiple biological processes during mouse development. We report that the longer isoform DNMT3A1, but not the shorter DNMT3A2, is essential for mouse postnatal development. DNMT3A1 binds to and regulates bivalent developmental genes in the brain. The disordered N-terminal domain is required for DNMT3A1-regulated development, DNA methylation and gene expression in the nervous system. A potential ubiquitin-interacting motif (UIM) in the N-terminus may bind to histone H2AK119 ubiquitination, mediating the recruitment of DNMT3A1 to its targets. These data reveal the N-terminus as a necessary regulatory domain for DNMT3A1 chromatin occupancy and functions.

overall_design: Comparation of transcriptomes and DNA methylomes between WT and Dnmt3a mutant mouse cortex / neuron nuclei; Examination of chromatin binding profiles of DNMT3A isoforms and mutants

first: Dapeng

last: Hao

first: Margaret

last: Goodell