title: Whole genome bisulfite sequencing of young and old satellite cells

first: Vahab

last: Soleimani

type: Methylation profiling by high throughput sequencing

summary: The function of skeletal muscle stem cells (MuSC) declines during aging, contributing to the advent of age-related myopathies. However, whether this decline is the result of accumulating cellular damage, altered heterogeneity in stem cell populations or due to the effect of the changing niche environment remains largely unknown. By scRNA-Seq, we show that the age-related reduction in the MuSC pool is not stochastic, with different subpopulations being distinctly affected in aging. Using an in vivo allogeneic stem cell transplantation model, we show that exposure of MuSCs from old mice to a youthful niche environment significantly restores the gene expression of genes that are altered in aging. We show that age-related changes in the MuSC transcriptome are mainly driven by alterations in chromatin and transcription but are not due to posttranscriptional mechanisms affecting RNA stability. Furthermore, our data indicates that the portion of the genome that is activated in aging is significantly more responsive to restoration by niche factors compared to the repressed counterpart. Taken together, our data reveals that the niche environment plays a decisive role in controlling the transcriptional activity of MuSCs.

overall_design: Satellite cells were isolated from 3 young and 3 aged male C57Bl/6J mice by Fluorescence-Activated Cell Sorting (FACS). The sorted cells were cultured into myoblasts and expanded in vitro to passage 5. Genomic DNA was extracted using phenol-chloroform extraction. Genomic DNA underwent bisulfite treatment and library preparation before sequencing.

first: Hamed

last: Najafabadi


title: Gene expression profiling of kidneys derived from Pkd1 conditional knock-out (KO) mice treated by salsalate, tolvaptan, and in combination

status: Public on Jan 16 2023

city: Toronto

first: York

middle: PC

last: Pei

state: Ontario

address: 8N838, 585 University Avenue

department: Department of Medicine

country: Canada

institute: University of Toronto

summary: Computational identification of gene expression pathways or key regulatory factors in the Pkd1 KO kidneys treated by salsalate, tolvaptan, and in combination

overall_design: Using Affymetrix Mouse Gene 2.0 ST Arrays, the global gene profiling of 57 kidneys samples from wild type (n=10), KO (n=12), KO mice treated by salsalate (n=11), KO mice treated by tolvaptan (n=12), KO mice treated by salsalate plus tolvaptan (n=12) was performed

first: Xuewen

last: Song

first: Wouter

last: Leonhard

first: Dorien

last: Peters


title: Specificity of the innate immune responses to different classes of non-tuberculous mycobacteria

status: Public on Jan 12 2023

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

type: Expression profiling by high throughput sequencing

summary:
Mycobacterium avium is the most common nontuberculous mycobacterium (NTM) species causing infectious disease. Here, we characterized a M. avium infection model in zebrafish larvae, and compared it to M. marinum infection, a model of tuberculosis.
Using RNAseq analysis, we found a distinct transcriptome response in cytokine-cytokine receptor interaction for M. avium and M. marinum infection. In addition, we found substantial differences in gene expression in metabolic pathways, phagosome formation, matrix remodeling, and apoptosis in response to these mycobacterial infections.

overall_design: Zebrafish larvae at 5 dpf from line AB/TL were collected for RNAseq

middle: P

first: Wanbin

last: Hu


title: Redox-Dependent Igfbp2 Signaling Controls Brca1 DNA Damage Response to Govern Neural Stem Cell Fate

status: Public on Jan 17 2023

city: Iowa City

first: John

middle: F

last: Engelhardt

state: IA

address: 51 Newton Road

department: Anatomy and Cell Biology

country: USA

institute: University of Iowa

summary: Neural stem cell (NSC) maintenance and functions are regulated by reactive oxygen species (ROS). However, the mechanisms by which ROS control NSC behavior remain unclear. Here we report that ROS-dependent Igfbp2 signaling controls DNA repair pathways which balance NSC self-renewal and lineage commitment. Ncf1 or Igfbp2 deficiency constrained NSCs to a self-renewing state and prevented neurosphere formation due to absent Igfbp2 cysteine-43 oxidation. Ncf1-dependent oxidation of Igfbp2 promoted neurogenesis by NSCs in vitro and in vivo, while repressing Brca1 DNA damage response genes and inducing DNA double-strand breaks (DDSBs). By contrast, Ncf1–/– and Igfbp2–/– NSCs favored the formation of oligodendrocytes in vitro and in vivo. Notably, transient repression of Brca1 DNA repair pathway genes induced DDSBs and was sufficient to rescue the ability of Ncf1–/– and Igfbp2–/– NSCs to lineage-commit to form neurospheres and neurons. Our study highlights the role of DNA damage/repair in orchestrating NSC fate decisions downstream of redox-regulated Igfbp2.

overall_design: NCF1KO, NCF1KO+IGFBP2, and WT neurospheres were subjected to RNAseq analysis

first: Weam

middle: S

last: Shahin

first: Scott

middle: R

last: Tyler


title: Periosteal skeletal stem cells can migrate into the bone marrow and support hematopoiesis after injury

city: Bronx

first: Kira

last: Gritsman

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

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

overall_design: Refer to individual Series


title: Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Transposable elements (TEs) are major contributors of genetic material in mammalian genomes. These often include binding sites for architectural proteins, including the multifarious master protein, CTCF, which shapes the 3D genome by creating loops, domains, compartment borders and RNA-DNA interactions, all of which play a role in the compact packaging of DNA and have the potential to facilitate regulatory function.

In this study, we explore the widespread contribution of TEs to mammalian 3D genomes by quantifying the extent to which they give rise to loops and domain border differences across various cell types and species using several 3D genome mapping technologies. We show that specific (sub-)families of TEs have contributed to lineage-specific 3D chromatin structures across mammalian species. In many cases, these loops may facilitate interaction between distant cis-regulatory elements and target genes, and domains may segregate chromatin state to impact gene expression in a lineage-specific manner. An experimental validation of our analytical findings using CRISPR-Cas9 to delete a candidate TE resulted in disruption of species-specific 3D chromatin structure.

Taken together, we comprehensively quantify and selectively validate our finding that TEs contribute to 3D genome organization and may, in some cases, impact gene regulation during the course of mammalian evolution.

overall_design: HiC^2, (chr7:157.1-159.1MB), RNA-seq, and ATAC-seq on GM12878 WT and knockouts of region with L1MC1 loop anchor

first: Mayank

last: Choudhary

first: Kara

last: Quaid

first: Xiaoyun

last: Xing

first: Heather

last: Schmidt

first: Ting

last: Wang


title: The Staphylococcus aureus iron-regulated surface determinant A (IsdA) increases SARS CoV-2 replication by modulating JAK-STAT signaling

city: London

first: David

last: Heinrichs

state: ON

address: Microbiology and Immunology, 3014 Dental Sciences Building, 1151 Richmond Street

institute: University of Western Ontario

overall_design: RNA-Seq

first: Mariya

last: Goncheva


title: Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line

status: Public on Jan 15 2023

city: Saint-Petersburg

first: Antonina

last: Maslova

address: 7-9 Universitetskaya Embankment

country: Russia

institute: Saint-Petersburg State University

summary: The chicken LSCC-HD3 cell line (HD3) generated from erythroid precursors is an established avian model for erythroid differentiation and lineage-specific gene expression. We obtained Hi-C maps of genomic interactions for HD3 cell line and revealed A/B compartments and topologically-associating domains. By analysis of contact patterns in the Hi-C maps of HD3 cells we identified more than 25 interchromosomal translocations of regions ≥200 Kb on both micro- and macrochromosomes. Intrachromosomal inversions, deletions and duplications were also detected in HD3 cells. Hi-C data obtained for HD3 chicken cell line demonstrate that it has a highly rearranged karyotype, with most of the chromosomes involved in unbalanced translocations.

overall_design: Hi-C of chicken HD3 cell line (LSCC-HD3) (2 replicates)

first: Vladimir

last: Plotnikov

first: Miroslav

last: Nuriddinov

first: Maria

last: Gridina

first: Veniamin

last: Fishman

first: Alla

last: Krasikova


title: Single-cell ATAC profiles of the somites and myotomes at embryonic stages  E18, E21, and E28 from Tibetan pigs (ZZ) and Duroc x Tibetan  pigs (DZ)

city: Guangzhou

first: Delin

last: Mo

address: Xingang Road

country: China

institute: Sun Yat-sen University

summary: To investigate the upstream regulatory networks in myogenesis that lead to the establishment of the myogenic lineage and subsequent differentiation, we proformed scATAC-seq of pig somite and myotome cells from Tibetan pigs (ZZ) and Duroc×Tibetan pigs (DZ) at several embryonic stages (E18, E21, and E28).

overall_design: Somite tissues [a mixture of embryos (n=5) from the same sow] of ZZ and DZ at  E18, E21, and myotome tissues [a mixture of embryos (n=5) from the same sow] at E28 were isolated, and the tissues were digested with collagenase for single-cell RNA sequencing.

first: Shufang

last: Cai

first: Xiaoyu


title: Single-cell RNA gene expression profiles of the somites and myotomes at embryonic stages  E18, E21, and E28 from Tibetan pigs (ZZ) and Duroc x Tibetan  pigs (DZ)

summary: To investigate the upstream regulatory networks in myogenesis that lead to the establishment of the myogenic lineage and subsequent differentiation, we proformed scRNA-seq of pig somite and myotome cells from Tibetan pigs (ZZ) and Duroc×Tibetan pigs (DZ) at several embryonic stages (E16, E18, E21, and E28).

overall_design: Somite tissues [a mixture of embryos (n=5) from the same sow] of ZZ and DZ at E16, E18, E21, and myotome tissues [a mixture of embryos (n=5) from the same sow] at E28 were isolated, and the tissues were digested with collagenase for single-cell RNA sequencing.


title: Conventional DC1 (cDC1) are Strongly Enriched, Quiescent and Relatively Tolerogenic in Local Inflammatory Arthritis

status: Public on Jan 13 2023

city: Utrecht

first: Arjan

last: Boltjes

address: Heidelberglaan 25

institute: Princess Máxima Center

summary: We sequenced (bulk RNA-seq) conventional (c)DC1, cDC2 and monocytes from a local inflammatory site, namely synovial fluid (SF) from patients suffering from a chronic inflammatory condition, Juvenile Idiopathic Arthritis (JIA). To be able to compare to steady state, we also sequenced cDC2 and monocyte subsets from peripheral blood of healthy controls.

overall_design:
We isolated these antigen-presenting cells from synovial fluid by FASCsort, and then analysed gene expression using data from RNA-seq of n=4 patients, 3 cell types each, and n=4 healthy controls, 3-4 cell types each.
-------------------------------------
Authors state "The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent."

first: Anoushka

last: Samat

first: Michal

last: Mokry

first: Femke

last: van Wijk


title: The mechanism underlying the “unified model” of YTHDF proteins

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St, Room E319B

institute: University of Chicago

summary: The YTH N6-methyladenosine RNA Binding Proteins (YTHDFs) mediate the functions of N6-methyladenosine (m6A) in RNA. Recently, a report proposed that all YTHDFs work redundantly to facilitate RNA decay, raising questions about the exact functions of individual YTHDFs, especially YTHDF1 and YTHDF2. We show that YTHDF1 and YTHDF2 differ in their low-complexity domains (LCDs), and this causes different behaviors in condensate formation and subsequent physiological functions. Biologically, we find that the global stabilization of RNA after depletion of all YTHDFs is a result of increased P-body formation and is independent of mRNA m6A methylation.

overall_design: [Dataset 1] 10 samples. Duplicates for RNA-Seq samples with ERCC spike-in calibration in HeLa cells transfected with siRNAs targeting different genes (Non-targeting control, YTHDF1, YTHDF2, YTHDF3 and YTHDF1-3)  [Dataset 2] 6 samples. Duplicates for RNA-Seq samples with ERCC spike-in calibration in HeLa cells transfected with siRNAs targeting different genes (Non-targeting control, DDX6 and DDX6/YTHDF1-3)  [Dataset 3] 6 samples. Duplicates for P-body isolations with two different antibodies (EDC3 and EDC4). RNA-sq were performed

first: Zhongyu

last: Zou


title: Temporal iCLIP captures co-transcriptional RNA-protein interactions

city: Aarhus

first: Ross

middle: Andrew Alex

last: Cordiner

address: Universitetsbyen 81

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. Yet, our current understanding of this process in vivo primarily stems from steady state analysis. To remedy this, we here conduct temporal-iCLIP (tiCLIP), combining RNAPII transcriptional synchronisation with UV cross-linking of RNA-protein complexes at serial timepoints. We apply tiCLIP to the RNA export adaptor, ALYREF; a component of the Nuclear Exosome Targeting (NEXT) complex, RBM7; and the nuclear cap binding complex (CBC). Regardless of function, all tested factors interact with nascent RNA as it exits RNAPII. Moreover, we demonstrate that the two transesterification steps of pre-mRNA splicing temporally separate ALYREF and RBM7 binding to splicing intermediates, and that exon-exon junction density drives RNA 5’end binding of ALYREF. Finally, we identify underappreciated steps in snoRNA 3’end processing performed by RBM7. Altogether, our data provide an unprecedented temporal view of RNA-protein interactions during the early phases of transcription.

overall_design: [i] Synchronise RNAPII transcription with a 3h DRB block. [ii] Release block and UV cross-link at serial timepoints to capture temporal association of ALYREF, RBM7 and the CBC

middle: A

first: Sander

last: Granneman

first: Torben

middle: H

last: Jensen


title: Mouse genetic background controls the severity of kidney injury

status: Public on Jan 11 2023

city: Lausanne

first: Jean-David

middle: Horacio

last: Morel

state: Vaud

address: Station 15

department: SV/IBI

country: Switzerland

institute: Ecole Ploytechnique Fédérale de Lausanne

summary: Acute kidney failure and chronic kidney disease are global health issues steadily rising in incidence and prevalence. Animal models are critically needed to better understand these diseases and develop new therapies. These models are typically restricted to a single genetic background, thus fail to recapitulate the hallmarks of human nephropathies and the diversity of their associated clinical presentations. Here, we used a simple model of folic acid-induced kidney injury in 7 highly diverse mouse strains. We measure plasma and urine parameters, as well as renal histopathology and mRNA expression data at 1-, 2- and 6-weeks after folic acid administration, covering the early response and subsequent recovery from injury. We observe an extensive strain-specific response ranging from complete resistance of the CAST/EiJ to high sensitivity of the C57BL/6J, DBA/2J, and PWK/PhJ strains. We show that in these susceptible strains, the severe early kidney injury is accompanied by the induction of mitochondrial stress genes, which is associated with delayed healing and a prolonged inflammatory and adaptive immune responses 6 weeks after the insult, heralding a transition to chronic kidney disease. Our data catalogue the variability in predisposition to acute kidney injury, recovery, and transition to chronic kidney disease in laboratory strains, enabling better selection of mouse strains to study kidney disease.

overall_design: This study used 7 domesticated (C57BL/6J, DBA/2J, A/J, 129S1/SvlmJ,WSB/EiJ) or wild-derived (CAST/EiJ, PWK/PhJ) inbred mouse strains drawn from founders the well-characterized BXD and collaborative cross panels, that are well known for their diversity in genetics, as well as in molecular and cardio-metabolic phenotypes. Mouse strains were imported from Charles River and bred at the École Polytechnique Fédérale de Lausanne (EPFL) animal facility for more than two generations before incorporation into the study. All research was approved by the Swiss cantonal veterinary authorities of Vaud under license 30759.The mice were fed a chow diet (Harlan 2018 (6% kCal of fat, 20% kCal of protein, and 74% kCal of carbohydrates). Mice were housed at 2-4 animals per cage under 12 hours light/dark cycle, with ad libitum access to food and water at all times. Body weight was measured weekly from 8 weeks of age until killing. We examined 7 mouse inbred strains. At 9 weeks of age, 3 groups of mice were treated with 125mg/kg of folic acid in 3M sodium bicarbonate and two groups with bicarbonate alone (vehicle controls). Strains were entered into each group randomly, then observed daily to monitor their health. The mice were scored weekly according to body weight/food intake, Coat condition, movement and signs of pain. Mice scoring above 1 were monitored three times a week and mice scoring above 2 were monitored daily. Mice with a score of 3 were sacrificed.  Mice were sacrificed at week 1,2 and 6 (folic acid treated) or weeks 2 and 6 (controls). The sacrifices took place from 8:30 a.m. until 12 a.m., with isoflurane anesthesia followed by a complete blood draw (~1 mL) from the vena cava, followed by perfusion with phosphate-buffered saline. The kidney was collected and flash-frozen in liquid nitrogen

first: Maroun

middle: B

last: Sleiman

first: Alexis

middle: M

last: Bachmann

first: Johan

last: Auwerx


title: Somites and myotomes at embryonic stages  E18, E21, and E28 from Tibetan pigs (ZZ) and Duroc x Tibetan  pigs (DZ)

status: Public on Jan 14 2023


title: Effect of hypoxia and normoxia in Pancreatic Ductal Adenocarcinoma

city: Oegstgeest

first: Marlene

last: Geyer

state: Please Select

address: De Limes 7

institute: Mimetas

summary: To study the differences in gene expression between PDAC organoids grown either as monocultures or co-cultures with panctreatic stellate cells in normoxia and hypoxia.

overall_design: Comparative gene expression profiling between PDAC mono-, and co-culture in hypoxia and normoxia.

first: Karla

last: Queiroz


title: RNA Seq analysis of the response of fisetin and rapamycin treatment on TNFα plus IL17A-stimulated primary human keratinocytes

status: Public on Jan 10 2023

city: Monroe

first: Jean Christopher

last: Chamcheu

state: Louisiana

address: 1800 Bienville drive

department: Basic Pharmaceutical and Toxicological Sciences

institute: University of Louisiana Monroe

summary: Chronic autoimmune skin disease characterized by epidermal proliferation with hyper- and para-keratosis. The aberrant background immune response involves helper T-lymphocyte types 1 and 17 and their respective secreted cytokines tumor necrosis factor alpha (TNF) and interleukin 17 (IL-17). These pro-inflammatory cytokines stimulate the activation of keratinocytes, resulting in the release of acute phase cytokines, followed by chronic phase cytokines thus promotes induced hyperplasia of keratinocyte. The pro-differentiative action of fisetin on dual cytokine-induced abnormally proliferating keratinocyte revealed downregulation of psoriasis-associated genes and activation of autophagic genes, as well as normalization of genes involved in keratinocyte terminal differentiation. These result supports the effect of fisetin on improving psoriasis like inflammatory flareups in cultured keratinocyte in vitro.

overall_design: Monolayer of primary adult Human epidermal keratinocyte were stimulated with dual cytokine TNFα (10ng/mL) and IL-17A (20ng/mL) for 24h. Cells were treated with Fisetin and Rapamycin for their particular concentration. Control group of cells were maintained in their growth medium (Primary keratinocyte growth medium: 1% Human Keratinocyte Growth Factor (HKGS) and 1% Penicillin Streptomycin (PEST) containing EpiLife Medium).

first: Jean

middle: C

first: Bolni

last: Nagalo

first: Tithi

last: Roy


title: The antitumor activity of human Vγ9Vδ2 T cells is impaired by TGF-β through significant phenotype, transcriptomic and metabolic changes

city: Solna

first: Chirine

last: RAFIA

address: Bioclinicum

department: Medicin Solna

country: Sweden

institute: Karolinska Institutet

summary: Despite significant advances, the eradication of cancer remains a clinical challenge which justifies the urgent exploration of additional therapeutic strategies such as immunotherapies. Human peripheral Vg9Vd2 T cells represent an attractive candidate subset for designing safe, feasible and effective adoptive T cell transfer-based therapies. However, following their infiltration within tumors, gd T cells are exposed to various regulating constituents and signals from the tumor microenvironment (TME), which severely alter their antitumor functions. Here, we show that TGF-b, whose elevated production in some solid tumors is linked to a poor prognosis, interferes with the antigenic activation of human Vg9Vd2 T cells in vitro. This regulatory cytokine strongly impairs their cytolytic activity, which is accompanied by the induction of particular phenotypic, transcriptomic and metabolic changes. Collectively, these observations provide informations for better understanding and targeting the impact of TME components to regulate the antitumor activity of human T cell effectors.

overall_design:
Vg9Vd2 T cells obtained from healthy donor blood have been treated or not with TGF-b (10ng/mL) for 3 days and activated or not for 6 hours with BrHPP. RNA was extracted and DGE-sequencing was performed.
BIRD, core facility (contributor)

last: Rafia

first: Noémie

last: Joalland

first: Emmanuel

last: Scotet


title: Single-cell RNA sequencing of developing mouse small intestine

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

summary: The mammalian intestine is a self-renewing organ that processes ingested food, absorbing nutrients from a sea of biochemical, mechanical, and pathogenic insults. To understand the developmental specification of diverse cell types in the small intestine, we performed time-resolved single-cell transcriptomics across five stages intestinal development: embryonic days (E) 12.5, 14.5, 16.5, and 18.5, and postnatal day (P) 1.5. By dissociating cells from whole organ preparations, we captured the full range of cellular diversity across all intestinal cell lineages. This allowed us to reconstruct the mesenchymal differentiation trajectory and identify the specific genetic programs that give rise to the diverse musculature of the gut wall and villus stroma.

overall_design: Time-resolved single-cell transcriptomics across five stages during intestinal development: embryonic days (E) 12.5, 14.5, 16.5, and 18.5, and postnatal day (P) 1.5.

first: Bhargav

middle: D

last: Sanketi

first: Madhav

last: Mantri

first: Natasza

last: Kurpios


title: Volatile metabolome and floral transcriptome analyses reveal the volatile components of strongly fragrant progeny of Malus robusta Rehder

city: Baoding

first: Guofang

last: Li

address: No.289 street

institute: Hebei Agricultural University

summary: To study the floral volatile compounds of standard Malus robusta flowers (Mr), and its progeny with strongly and weakly fragrant flowers

overall_design: We performed gene expression profiling analysis using data obtained from flowers of three different stages

first: Jia

last: Liu

first: He

last: Zhang

first: Jianzhu

last: Shao


title: Mechanisms underlying MAIT cell ability to promote skin wound repair

city: Paris

first: Martin

last: MESTDAGH

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: Tissue repair processes maintain proper organ function following mechanical or infection related damage. In addition to anti-bacterial properties, MAIT cells express a tissue repair transcriptomic program and promote skin wound healing when expanded. Herein, we use a human‑like full‑thickness skin excision mouse model to assess the underlying mechanisms of MAIT cell tissue repair function. Single-cell RNAseq analysis suggests that skin MAIT cells already express a repair program at steady state. Following skin excision, MAIT cells promote keratinocyte proliferation thereby accelerating healing. Using skin grafts, parabiosis and adoptive transfer experiments, we show that MAIT cells migrate into the wound from other tissues in a TCR independent but CXCR6 dependent manner. Amphiregulin secreted by MAIT cells following excision promotes wound healing. The repair function is independent of sustained TCR stimulation. Overall, our study provides mechanistic insight into MAIT cell wound healing function in the skin.

overall_design: scRNA-seq of skin MAIT cells at steady state or in skin wound repair.

first: Marion

last: Salou

first: Olivier

last: Lantz

first: Anastasia

last: De Halgouet

last: Mestdagh


title: Chromatin occupancy profiling of AML transcription factors upon SWI/SNF inhibition [ChIP-seq]

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

summary: To reveal the effects of SWI/SNF inhibition on genome-wide transcription factor occupancy in AML cells, we performed ChIP-seq in THP-1 cells, and compared the effects of BRM014 with DMSO vehicle control. We also examined the effects of SMARCA4 chromatin targeting via treatment with the PU.1 inhibitor DB2313. Analysis of genome-wide occupancy by ChIP-seq reveals that SWI/SNF inhibition impairs PU.1-directed enhancer programs in AML cells.

overall_design: Comparative chromatin occupancy profiling of transcription factors in AML cells treated with inhibitors of SWI/SNF or PU.1

first: Courtney

last: Chambers

first: H


title: Transcriptional changes in bone marrow cells upon SWI/SNF inhibition [scRNA-seq]

summary: Despite significant therapeutic potential of SWI/SNF inhibition therapy, the off-tumor effects of SWI/SNF inhibition remain largely unknown. Here, we quantify the effects of the dual SWI/SNF ATPase inhibitor BRM014 on bone marrow cells in mice. We identify lineage-dependent effects on the B and monocyte lineages within the bone marrow.

overall_design: Single-cell 5' RNA-seq (scRNA-seq) of bone marrow cells from C57BL/6 mice that received 14-day treatment of daily 20 mg/kg BRM014 or vehicle control via oral gavage. All samples are pooled from 3 independent mice in the same condition and processed using 10x Chromium 5’v2 kit according to the manufacturer's instructions.

first: Rachel

middle: E

last: Rau


title: Periosteal skeletal stem cells can migrate into the bone marrow and support hematopoiesis after injury [II]

first: Kira

last: Gritsman

summary: To investigate the transcriptomic differences between bone marrow mesenchymals stem cells and periosteal skeletal stem cells at steady state, and graft bone marrow mesenchymal stem cells 5 months after transplantation

overall_design: Comparative gene expression profiling of RNA-seq data for steady state BM MSCs, periosteal SSCs and tomato+ graft BM-MSCs 5 months after transplantation

first: Tony

last: Marchand

first: Kemi

last: Akinnola

first: Shoichiro

last: Takeishi

first: Maria

last: Maryanovich

first: Sandra

last: Pinho

first: Julien

last: Saint-Vanne

first: Alexander

last: Birbrair

first: Thierry

last: Lamy

first: Karin

last: Tarte

first: Paul

last: Frenette


title: Transcriptional effects of SWI/SNF inhibition in acute myeloid leukemia cells [RNA-seq]

summary: To reveal the effects of SWI/SNF inhibition in KMT2Ar leukemic cells, we performed RNA-seq in THP-1, MOLM-13, and MV-4-11 cells, and compared the effects of BRM014 with DMSO vehicle control. We also compared these effects to PMA-induced differentiation in THP-1 cells, as well as treatment with the PU.1 inhibitor DB2313. Analysis of transcripts reveal that SMARCA4 inhibition promotes differentiation, down-regulation of MYC and its target genes, and reduced expression of CD44, consistent with loss of self-renewal.

overall_design: RNA-seq


title: SWI/SNF-dependent regulation of chromatin and transcription in AML

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

overall_design: Refer to individual Series


title: Periosteal skeletal stem cells can migrate into the bone marrow and support hematopoiesis after injury [I]

summary: To investigate the transcriptomic differences between bone marrow mesenchymals stem cells and periosteal skeletal stem cells at steady state, and periosteal skeletal stem cells 72 hours after bone transplantation

overall_design: Comparative gene expression profiling of RNA-seq data for steady state BM MSCs, Periosteal SSCs and Periosteal SSCs three days after bone transplantation


title: DNA accessibility sites requiring SWI/SNF activity in AML [ATAC-seq]

summary: To reveal the genome-wide targets of SWI/SNF complexes in AML cells, we performed ATAC-seq in THP-1, MOLM-13, and MV-4-11 cells with or without the SWI/SNF ATPase BRM014. Analysis of the locations decreased following 24 or 72 h after addition of BRM014 revealed that SWI/SNF-dependent sites are located at enhancers occupied by PU.1, especially the blood enhancer cluster (BENC), a set of enhancers that drives expression of MYC.

overall_design: Comparative genome accessibility profiling of AML cells treated with inhibitors of SWI/SNF or PU.1. For comparison to THP-1 differentiation, treatment by phorbol 12-myristate 13-acetate (PMA) was separately assessed.


title: Expression data from rat prefrontal cortex administrated with MK-801

status: Public on Jan 09 2023

city: Yangzhou

first: Bo

last: Pan

state: Jiangsu

address: No.136, JiangYangZhongLu

department: Department of Pharmacy

institute: Yangzhou University Medical College

summary: Schizophrenia is a group of severe mental disorders. MK-801 is a common chemical that is used to construct schizophrenic animal model. In the present study, male SD rats were received MK-801 (0.2 mg/kg) intraperitoneal injections for 2 weeks. PFC tissue samples were collected freshly when sacrificing the rats and then quickly frozen and stored under -80°C for RNA sequencing. Differentially-expressed genes (DEGs) were determined by using DESeq2. A total of 129 DEGs, including 50 down-regulated and 79 up-regulated DEGs, were determined. By comparing with the online database TargetScanHuman (Release 8.0) and miRDB (Version 6.0), we found 4 genes (SIK1, TWIST1, BTG2, EGR2) that were altered in the schizophrenic model rat PFC and also are potential targets of miR-25.

overall_design: Male SD rats (aging 21 days and weighing 60 ± 5 g) were randomly assigned into two groups (n = 5 per group). After habituating for 1-week, the two groups received either MK-801 (0.2 mg/kg) or saline (0.9%) intraperitoneal injections for 2 weeks. PFC tissue samples were collected freshly when sacrificing the rats and then quickly frozen and stored under -80°C for RNA sequencing. The RNA-seq test was performed by Novogene (Beijing, China). Briefly, the RNA-seq library for sequencing was prepared by Novogene following the standard Illumina protocols. Reads were aligned to the genome using HISAT2 (Version 2.2.1) and SAMtools (Version 1.15.1) with referencing the gene annotation file from Ensembl (Release 105). FeatureCounts (Subread package Version 2.0.1) was employed to count the reads and then to create the expression matrix. Differentially-expressed genes (DEGs) were determined by using DESeq2 (Version 1.36.0) with P value < 0.05 and |logFC| ≥ 1 as the selection criteria.

first: Xiaoli

last: Zhu

first: Bing

last: Han

first: Jianjun

last: Weng

first: Yuting

last: Wang

first: Yanqing

last: Liu


title: Epithelial Disruption Drives Mesendoderm Differentiation in Human Pluripotent Stem Cells by Enabling TGF-β Protein Sensing

city: Marseille

first: Thomas

last: Vannier

address: Campus de Luminy, 163 Av. de Luminy

institute: Aix-Marseille University

summary: The processes of primitive streak formation and fate specification in the mammalian epiblast rely on complex interactions between morphogens and tissue organization. Little is known about how these instructive cues functionally interact to regulate gastrulation. We interrogated the interplay between tissue organization and morphogens by using human induced pluripotent stem cells (hiPSCs) down-regulated for the morphogen regulator GLYPICAN-4, in which defects in tight junctions result in areas of disrupted epithelial integrity. Remarkably, this phenotype does not affect hiPSC stemness, but impacts on cell fate acquisition. Strikingly, cells within disrupted areas become competent to perceive the gastrulation signals BMP4 and ACTIVIN A, (an in vitro surrogate for NODAL), and thus differentiate into mesendoderm. Yet, disruption of epithelial integrity sustains activation of BMP4 and ACTIVIN A downstream effectors and correlates with enhanced hiPSC endoderm/mesoderm differentiation. Altogether, our results disclose epithelial integrity as a key determinant of TGF-β activity and highlight an additional mechanism guiding morphogen sensing and spatial cell fate change within an epithelium.

overall_design: mRNA profiles of a human induced pluripotent cell (hiPSC) line down-regulated for GPC4 (shGPC4) and 2 control lines (WT and shCTRL)  were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500 technology.

first: Rosanna

last: Dono


title: Genetic and pharmacologic inhibition of ALDH1A3 as a treatment of β-cell failure

city: NEW YORK

first: Jinsook

last: Son

address: 1150 st Nicholas ave, Russ Berrie Pavilion, Ste. 238

institute: Columbia University

summary: Type 2 diabetes (T2D) is associated with defective insulin secretion, reduced β-cell mass, and β-cell dedifferentiation. Aldehyde dehydrogenase 1 isoform A3 (ALHD1A3) serves as a marker of β-cell dedifferentiation and correlates with T2D progression. ALDH1A3-positive β-cells (A+) demonstrate impaired insulin secretion, and their numbers decrease when diabetic mice are rendered euglycemic by pair-feeding. It is unknown whether ALDH1A3 activity contributes to β-cell failure, and whether the decrease of A+ cells under pair-feeding is due to β-cell restoration. To tackle these questions, we (i) investigated the fate of A+ cells during pair-feeding by lineage-tracing, (ii) somatically ablated ALDH1A3 in diabetic β-cells, and (iii) used a novel selective ALDH1A3 inhibitor to treat diabetes. Lineage tracing and functional characterization show that A+ cells can be reconverted to functional, mature β-cells. Genetic or pharmacological inhibition of ALDH1A3 in diabetic mice lowers glycemia and increases insulin secretion. Molecular interrogation of β-cells following ALDH1A3 inhibition show a reactivation of differentiation as well as regeneration pathways through the REG gene family. We conclude that ALDH1A3 inhibition offers a therapeutic strategy for β-cell dysfunction in diabetes.

overall_design: Sorted beta cells from db/db, db/+ or Aldh1a3 KO_db/db mice

first: Hongxu

last: Ding

first: Domenico

last: Accili


title: LINC00607 is essential to maintain the endothelial phenotype through SWI/SNF chromatin remodeler BRG1

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe Universität Frankfurt am Main

summary: Long non-coding RNAs (lncRNAs) are regulatory RNAs, which by altering gene expression impact on the cellular phenotype and cardiovascular disease development. The pool of endothelial lncRNAs and their vascular function is largely undefined. Deep-endothelial RNA-Seq and FANTOM5 CAGE analysis revealed LINC00607 as a specifically enriched and highly expressed lncRNA in human endothelial cells. LINC00607 was induced in response to hypoxia, arteriosclerosis regression in non-human primates and also in response to propranolol used to induce regression of human arteriovenous malformations. siRNA Knockdown or CRISPR/Cas9 knockout of LINC00607 attenuated VEGF-A-induced angiogenic sprouting. LINC00607 knockout HUVEC also integrated less into newly formed vascular networks in an in vivo assay in SCID mice. Overexpression of LINC00607 in CRISPR knockout cells restored the normal function. RNA- and ATAC-Seq of the LINC00607 knockout revealed changes in transcription of endothelial gene sets particularly linked to the endothelial phenotype. This was most likely the consequence of a reduced chromatin accessibility of the ERG binding motif. Mechanistically, LINC00607 interacts with the SWI/SNF chromatin remodeling protein BRG1. CRISPR/Cas9-mediated knockout of BRG1 in HUVEC followed by CUT&RUN revealed that BRG1 is required to secure a stable chromatin state, mainly on ERG-binding sites. In conclusion, LINC00607 is a highly expressed endothelial-specific lncRNA important for efficient endothelial gene transcription through sustaining ERG target gene transcription by interaction with the chromatin remodeler BRG1.

overall_design: BRG1 CUT&RUN in Human Umbilical Vein Endothelial Cells (HUVEC) subjected to either CRISPR-Cas9-mediated knockout of BRG1 or non-targeting control.

first: Frederike

last: Boos

first: James

last: Oo

first: Stefan

last: Günther

first: Judit

last: Izquierdo Ponce

first: Tianfu

last: Li

first: Shaza

last: Haydar

first: Sepide

last: Kashefiolasl

first: Giulia

last: Buchmann

first: Andrew

last: Baker

first: Reinier

last: A Boon

first: Marcel

last: Schulz

first: Ilka

last: Wittig

first: Francis

middle: J

last: Miller

first: Ralf

last: Brandes

first: Matthias

last: Leisegang


title: CALR mutation-induced transcriptional changes in cord blood-derived hematopoietic stem and progenitor cells

city: Graz

first: Johannes

last: Foßelteder

address: Auenbruggerplatz 48

department: Blood Group Serology and Transfusion Medicine

country: Austria

institute: Medical University of Graz

summary: Recurrent mutations in calreticulin (CALR) are present in 70-80% of JAK2 unmutated myeloproliferative neoplasms (MPN). Current models of CALR mutant MPNs are mainly based on cancer cell lines with ectopic overexpression or transgenic mouse models with a lack of data for primary human hematopoietic stem and progenitor cells (HSPCs) with endogenous CALR expression. Thus, we developed a CRISPR/Cas9 and AAV6-mediated knock-in approach to introduce the two most common CALR mutations (52 bp deletion, DEL; 5 bp insertion, INS) at the endogenous gene locus in human cord blood-derived HSPCs. We used these cells to investigate transcriptional changes induced upon CALR mutation acquisition in HSPCs in a prospective manner by performing RNA-sequencing 4 days after CRISPR-mediated knock-in.

overall_design: Examination of mRNA profiles of primary human HSPCs, which were CRISPR-modified to carry either calreticulin wildtype or mutant sequences with 3 samples per genotype.

first: Slave

last: Trajanoski

first: Andreas

last: Reinisch


title: CPEB1-dependent disruption of the mRNA translation program in oocytes during maternal aging

city: San Francisco

first: Xuan

last: Luong

state: CA

address: 505 Parnassus Ave

institute: UCSF

summary: The molecular causes of deteriorating oocyte quality during aging are poorly defined. Since oocyte developmental competence relies on post-transcriptional regulations, we tested whether defective mRNA translation contributes to this decline in quality. Disruption in ribosome loading on maternal transcripts is present in old oocytes. Using a candidate approach, we detect altered translation of 3’-UTR-reporters and altered poly(A) length of the endogenous mRNAs. mRNA polyadenylation depends on the cytoplasmic polyadenylation binding protein 1 (CPEB1). Cpeb1 mRNA translation and protein levels are decreased in old oocytes. This decrease causes de-repression of Ccnb1 translation in quiescent oocytes, premature CDK1 activation, and accelerated reentry into meiosis. De-repression of Ccnb1 is corrected by Cpeb1 mRNA injection in old oocytes. Oocyte-specific Cpeb1 haploinsufficiency in young oocytes recapitulates all the translation phenotypes of old oocytes. These findings demonstrate that a dysfunction in the oocyte translation program is associated with the decline in oocyte quality during aging.

overall_design: Examination of ribosome-bound mRNA in MII oocytes (in duplicate) collected from young and old RiboTagF/F;Zp3-Cre mice via RiboTag IP followed by RNA-Seq

first: Nozomi

last: Takahashi

first: Federica

last: Franciosi

first: Enrico

last: Daldello

middle: G

first: Peter

last: Althoff

first: Xiaotian

last: Wang

first: Marco

last: Conti


title: Chromatin accessibility changes after CRISPR/Cas9-mediated knock-out of lncRNA LINC00607 in HUVEC [ATAC-seq]

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Long non-coding RNAs (lncRNAs) are molecular switches in cellular differentiation, movement and in the reprogramming of cell states by altering gene expression patterns. However, in endothelial cells their role is not well understood. LINC00607 is an endothelial-enriched lncRNA. In order to uncover the functional relevance of LINC00607, an endothelial lentiCRISPR/Cas9-mediated knock-out was created and subjected to RNA- and ATAC-Seq, which revealed that LINC00607 is important for many pathways, among them VEGF- and TGF-beta-signalling.

overall_design: 3 biolocial replicates of HUVEC non-target control (CTL) and LINC00607 CRISPR/Cas9 knock-out (KO), respectively.

first: Frederike

last: Boos


title: ATAC-seq and RNA-seq after CRISPR/Cas9-mediated knock-out of lncRNA LINC00607 in HUVEC


title: Mitigating reprogramming stress with dominant negative BET deletion fragments

status: Public on Jan 08 2023

city: Fort Worth

first: Kejin

last: Hu

address: 3400 Camp Bowie Boulevard

department: Microbiology, Immunology and Genetics

institute: UNT Health Science Center

summary: The iPSC reprogramming is very inefficient and has an early stochastic stage. The cause of the low efficiency and stochastic nature are poorly understood. The bromo- and extra-terminal domain (BET) proteins have impacts on cellular reprogramming, but the molecular mechanisms are elusive. Here we show that the reprogramming factors cause dramatic reprogramming stresses including massive transcriptional turbulence, massive and random dysregulation of stress response genes, cell cycle impairment, and cytotoxicity. BET dominant negative (DN) mutants lacking the characteristic ET and bromo- domain enhanced iPSC reprogramming and downregulated a large set of stress response genes over-activated by the reprogramming factors. These DN BET mutants also restored the cell cycle profile and mitotic genes impaired by the reprogramming factors, and mitigate the reprogramming-associated cytotoxicity. The DN BET fragments additionally reduced illegitimate transcriptional reprogramming imposed by the reprogramming factors. Both the DN BET mutants and the BET chemical inhibitors target a similar set of the stress response genes in the reprogramming cells although their targeting mechanism are different. In human  naive fibroblasts, these DN BET fragments also commonly target a large set of stress response genes including inflammatory genes, implying general roles of BET proteins in stress responses. These DN BET peptides constitute a novel approach to targeting BET proteins for disease managements.

overall_design: To understand the molecular mechanisms underlying the gained reprogramming activities of the short isoform of human BRD3 (BRD3R), we overexpressed the domain-deletion proteins of BRD2, BRD3 and BRD4S in human normal fibroblasts (BJ cells) in their naive state or in the reprogramming cells (BJ expressing OCT4, SOX2 and KLF4). These deletion mutants lack the ET-containing C terminus and one or both bromodomain (BD). All the domain-deletion mutants enhance reprogramming efficiencies. We then extract total RNA under different conditions (various BET mutants) and conducted RNA-seq.

first: Emon

last: Hossain

first: Ricardo

last: Cevallos


title: RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells

status: Public on Jan 07 2023

city: LYON

first: Mathieu

last: GABUT

address: 28 rue laennec

department: Cancer Initiation and Tumor cell Identity

institute: Cancer Research Centre of Lyon, Inserm U1052

summary: Embryonic stem cell (ESC) fate decisions are regulated by a complex molecular circuitry that requires tightly coordinated gene expression regulations at multiple levels from chromatin organization to mRNA processing. Recently, ribosome biogenesis and translation have emerged as key pathways that efficiently control stem cell homeostasis. However, the molecular mechanisms underlying the regulation of these pathways remain largely unknown to date. Here, we analyzed the expression of over 300 genes involved in ribosome biogenesis between self-renewing and differentiated mouse ESCs.   We identified RSL24D1 as highly expressed in multiple mouse pluripotent stem cell models and showed that its expression profile is conserved in human ESCs. RSL24D1 is associated with nuclear pre-ribosomes and is required for the maturation and the biogenesis of 60S subunits in mouse ESCs. Interestingly, RSL24D1 depletion resulted in a significant modification of ESC’s proteome by impairing global translation, particularly of key pluripotency factors, including POU5F1 and NANOG, as well as components of the polycomb repressive complex 2 (PRC2). Consistently, while having a moderate impact on lineage commitment and cell differentiation, RSL24D1 depletion significantly altered mouse ESC self-renewal and proliferation, a phenotype largely alleviated by RSL24D1 knockdown rescue. Taken together, these results demonstrate that RSL24D1-dependant ribosome biogenesis is both required to sustain the expression of pluripotent transcriptional programs and to silence PRC2-dependant developmental programs, which concertedly dictate ESC homeostasis.

overall_design: RSL24D1 was downregulated using a pool of siRNAs in the presence or absence of expression of a rescue RSL24D1 protein induced by Doxycyline. CGR8 mouse ESCs were treated with a pool of non targeting siRNAs, in absence (siControl_nores) or in presence of RSL24D1 rescue (siControl_RESCUE), or with Rsl24d1 targetting siRNAs in absence (siRSL24D1_nores) or in presence of RSL24D1 rescue (siRSL24D1_RESCUE). After 72h all RNA samples were collected and extracted. The same experiment was conducted in serum+LIF contain media propomiting ESC self renewal ("ESC" condition ) or in LIF + RA containing media promoting ESC differentiation ("DIF" condition). Iindependant triplicate samples were produced for each group (R1, R2, R3).

first: Sébastien

last: Durand

first: Marion

last: Bruelle

first: Fleur

last: Bourdelais

first: Bigitha

last: Bennychen

first: Juliana

last: Blin-Gonthier

first: Caroline

last: Isaac

first: Aurélia

last: Huyghe

first: Sylvie

last: Martel

first: Antoine

last: Seyve

first: Christophe

last: Vanbelle

first: Annie

last: Adrait

first: Yohann

last: Couté

first: David

last: Meyronet

first: Frédéric

last: Catez

first: Jean-Jacques

last: Diaz

first: Fabrice

last: Lavial

first: Emiliano

last: Ricci

first: François

last: Ducray

last: Gabut


title: Transcriptomic changes after CRISPR/Cas9-mediated knock-out of lncRNA LINC00607 in HUVEC [RNA-seq]

first: Stefan

last: Günther

first: Frederike

last: Boos

first: Ralf

last: Brandes

first: Matthias

last: Leisegang


title: Host blood-based biosignatures for subclinical TB: a prospective study of household contacts of adult pulmonary TB index cases in Southern India.

city: Bergen

first: Harleen

last: Grewal

address: The Laboratory Building, 5th floor, 5021

department: Department of Clinical Science

country: Norway

institute: University of Bergen

summary: Identification of blood transcriptional biomarkers linked to different phases of tuberculosis. The discovery of a transcriptional signature that distinguishes subclinical TB from incipient TB at baseline could lead to tuberculosis interventions that combat the tuberculosis epidemic in the context of household contacts.

overall_design: All household contacts were followed up for one year. Samples were collected at 0, 2, 6, and 12 months. Some people go on to develop TB (Subclinical TB) whereas some others do not (Incipient TB). Household controls were carefully selected from the same incipient TB and sub-clinical TB families and age-matched to either incipient or subclinical TB cases. We used the same method as for the controls to pick the active TB cases in the adult index TB. In this study, for incipient TB baseline and 12 month or last available samples were selected, for sub-clinical TB baseline and culture-postive for Mtb time point samples or closely available time-point samples were selected, whereas for active TB and household controls baseline samples were selected and sent for RNA-sequencing. Within families/households of TB index cases, the present study aimed to i) identify differentially expressed transcriptional biomarkers associated with distinct stages of TB in samples acquired at baseline contact investigation. ii) identify transcriptional signatures with the ability to distinguish subclinical TB from incipient TB in samples acquired at baseline, iii) evaluate the performance of identified transcriptional signature(s) in active TB disease cases and asymptomatic household controls in samples acquired at baseline.

first: Dhanasekaran

last: Sivakumaran

first: Aashish

last: Srivastava

first: Mario

last: Vaz


title: Changes of DNA accessibility and RNA transcription upon SWI/SNF inhibition in peripheral blood and bone marrow cells [multiome]

first: H. Courtney

last: Hodges

summary: Despite significant therapeutic potential of SWI/SNF inhibition therapy, the off-tumor effects of SWI/SNF inhibition remain largely unknown. Here, we quantify the effects of the dual SWI/SNF ATPase inhibitor BRM014 on peripheral blood (PB) and bone marrow (BM) cells in mice. We identify altered chromatin regulatory mechanisms in B cells and monocytes.

overall_design: Single-nuclei joint RNA-seq (snRNA-seq) and ATAC-seq (snATAC-seq) of peripheral blood (PB) or bone marrow (BM) cells from C57BL/6 mice that received 14-day treatment of daily 20 mg/kg BRM014 or vehicle control via oral gavage. All samples are pooled from 3 independent mice in the same condition and processed using 10x Multiome ATAC + Gene Expression kit according to the manufacturer's instructions.

first: Courtney

last: Chambers

first: Rachel

last: Rau

first: H


title: Effects of SWI/SNF inhibition on hematopoiesis


title: Differential serum microRNAs in premotor LRRK2 G2019S carriers from Parkinson’s disease

status: Public on Jan 06 2023

city: Barcelona

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

country: Spain

institute: Fundacio Clinic/IDIBAPS

summary: The LRRK2 G2019S pathogenic mutation causes LRRK2-associated Parkinson’s disease (L2PD) with incomplete penetrance. LRRK2 non-manifesting carriers (L2NMC) are at PD high risk but predicting pheno-conversion is challenging given the lack of progression biomarkers. To investigate novel biomarkers for PD premotor stages, we performed a longitudinal microRNA (miRNA) assessment of serum samples from G2019S L2NMC followed-up over 8 years. Our cohort consisted of G2019S L2NMC stratified by dopamine transporter single-photon emission computed tomography (DaT-SPECT) into DaT-negative (n=20) and DaT-positive L2NMC (n=20), pheno-converted G2019S L2PD patients (n=20), idiopathic PD (iPD) (n=19), and controls (n=40). We also screened a second cohort of L2PD patients (n=19) and controls (n=20) (Total n=158). Compared to healthy controls, we identified 8 deregulated miRNAs in DaT-negative L2NMC, 6 in DaT-positive L2NMC, and one in L2PD. Between groups, the highest miRNA differences, 24 candidate miRNAs, occurred between DaT-positive L2NMC and L2PD. Longitudinally, we found 11 common miRNAs with sustained variation in DaT-negative and DaT-positive L2NMCs compared to their baselines. Our study identifies novel miRNA alterations in premotor stages of PD co-occurring with progressive DaT-SPECT decline before motor manifestation, whose deregulation seems to attenuate after the diagnosis of L2PD. Moreover, we identified 4 miRNAs with relatively high discriminative ability (AUC=0.82) between non-pheno-converted DaT-positive G2019S carriers and pheno-converted L2PD patients (miR-4505, miR-8069, miR-6125, and miR-451a), which hold potential as early progression biomarkers for PD.

overall_design: No replicates. For differential miRNA expression analysis (4 groups), we used the global normalization method adjusting by gender, age, and hybridization date.

first: Marta

last: Soto

first: Manel

last: Fernández

first: Paloma

last: Bravo

first: Sara

last: Lahoz

first: Alicia

last: Garrido

first: Antonio

last: Sánchez-Rodríguez

first: María

last: Rivera-Sánchez

last: Sierra

first: Paula

last: Melón

first: Ana

last: Roig-García

first: Anna

last: Naito

first: Bradford

last: Casey

first: Jordi

last: Camps

first: Eduardo

last: Tolosa

first: María-José

last: Martí

first: Jon

last: Infante

first: Rubén

last: Fernández-Santiago


title: Postharvest chilling diminishes melon flavor via effects on volatile acetate ester biosynthesis.

city: Gainesville

first: Xiang

last: Li

state: FL

department: Horticultural Sciences

institute: UNIVERSITY OF FLORIDA

summary:
To investigate transcript abundance of flavor-associated genes in fatty acid and amino acid pathways after chilling.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different treatments [(A) stored at 4°C for 7 d (without chilling injury), and then transferred to room temperature (~22°C) for 1 d; (B) held at 4°C for 8 d until use (without chilling injury); (C) harvested on day 8 (8 d after the fruits of first two groups). Three replicates of each group were performed, and each replicate has three fruits)].

overall_design: Comparative gene expression profiling analysis of RNA-seq data for flavor-associated genes in 3 treatments on melon fruits.

first: Huijun

last: Zhang


title: Global cardiac gene expression in left ventricles from 20 day-old and 60 day-old Efnb1 CMspe KO and WT male mice

city: Toulouse

first: Celine

last: GALES

address: 1 Avenue du Pr. Jean Poulhès

institute: INSERM

summary:
To identify a physiologic postanal transcriptomic program between postnatal day 20 and 60, we first analyzed  the gene expression profile in 60 day-old ( young adult) wild-type mice (WT)   and compared it to 20 day-old  WT mice
To identify the gene expression between postnatal day 20 and 60 under the strict dependence of cardiac ephrin-B1, we compared gene expression in  20 day-old and 60 day-old Efnb1 CMspe KO (a-MHC-Cre-/+ Efnb1 flox/flox or) to 20 day-old and 60 day-old  WT mice

overall_design: There are 23 Cardiac left ventricle samples, each from an individual mouse. The samples (left ventricles) are from Efnb1 cardiac KO (Efnb1cKO) and WT male mice of 20 day-old or 60 day-old from the same genetic background (mixed S129/S4 × C57BL/6). N=6 mice for P20 (postnatal day 20 - 20 day-old) WT and Efnb1 cKO genotypes , n=6 for P60 Efnb1 cKO genotype, n=5 for P60 WT genotype,

first: Karsenty

last: Clément

first: Lippi

last: Yannick

first: Claire

last: Naylies

first: Alexandra

last: Montagner

first: Céline

last: Galés


title: The ribose methylation enzyme FTSJ1 has a conserved role in neuron morphology and learning performance

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

type: Non-coding RNA profiling by high throughput sequencing

summary: FTSJ1 is a conserved human 2’-O-methyltransferase (Nm-MTase) that modifies several transfer RNAs (tRNAs) at position 32 and the wobble position 34 in the AntiCodon Loop (ACL). Its loss of function has been linked to Non-Syndromic X-Linked Intellectual Disability (NSXLID), and more recently to cancers. However, the molecular mechanisms underlying these pathologies are currently unclear. Here we report a novel FTSJ1 pathogenic variant from a NSXLID patient. Using blood cells derived from this patient and other affected individuals carrying FTSJ1 mutations, we performed an unbiased and comprehensive RiboMethSeq analysis to map the ribose methylation (Nm) on all tRNAs and identify novel targets. In addition, we performed a transcriptome analysis in these cells and found that several genes previously associated with intellectual disability and cancers were deregulated. We also found changes in the miRNA population that suggest potential cross-regulation of some miRNAs with these key mRNA targets. Finally, we show that differentiation of FTSJ1-depleted human neuronal progenitor cells (NPC) into neurons displays long and thin spine neurites compared to control cells. These defects are also observed in Drosophila and are associated with long term memory deficit in this organism. Altogether, our study adds insight into FTSJ1 pathologies in human by the identification of novel FTSJ1 targets and the defect in neuron morphology.

overall_design: small RNA sequencing of patients cell lines carying a mutation of methyltransferase FTSJ1 and control cells. The experiment was performed in triplicates for all cell lines.

first: Dilyana

last: Dimitrova

first: Mira

last: Brazane

first: Julien

last: Pigeon

first: Chiara

last: Paolantoni

last: Ye

first: Virginie

last: Marchand

first: Bruno

last: Da Silva

first: Elise

last: Schaefer

first: Margarita

middle: T

last: Angelova

first: Zornitza

last: Stark

first: Martin

last: Delatycki

first: Tracy

last: Dudding-Byth

first: Jozef

last: Gecz

first: Pierre-Yves

last: Placais

first: Laure

last: Teysset

first: Thomas

last: Preat

first: Amélie

last: Piton

first: Bassem

last: Hassan

first: Jean-Yves

last: Roignant

first: Yuri

last: Motorin

first: Clément

last: Carré


title: Rapid nuclear deadenylation of mammalian messenger RNA

city: Berlin

first: Jonathan

last: Alles

state: Berlin

address: Hannoversche Straße 28

department: Berlin Institute for Medical Systems Biology (BIMSB)

institute: Max Delbruck Center Berlin

summary: Poly(A) tails protect RNAs from degradation and deadenylation rates determine RNA stability. Deadenylation has mostly been investigated within the cytoplasm and the dynamics of poly(A) tail length after transcription are not well understood. Combining long-read sequencing with metabolic labeling and cell fractionations, we investigate deadenylation dynamics of newly synthesized poly(A) tails in vitro and in vivo. We report evidence for genome-wide synthesis of poly(A) tails longer than 200 nt which are enriched upon splicing inhibition. Metabolic labeling reveals rapid deadenylation of poly(A) tails within minutes after transcription. Fractionation experiments show that initial deadenylation is a nuclear process, and that different classes of transcripts, including long noncoding RNAs, have distinctive nuclear poly(A) tail lengths. Modelling deadenylation dynamics predicts that deadenylation in the nucleus is by an order of magnitude faster than in the cytoplasm. In summary, we suggest nuclear deadenylation as a novel regulatory layer which may determine stability and abundance before mRNAs reach the cytoplasm.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Full length poly(A) and mRNA sequencing (FLAM-seq) analysis of PlaB treated HeLa nuclei, pulldown experiments, SLAM-seq, and biochemical fractionation

first: Ivano

last: Legnini

first: Maddalena

last: Pacelli

first: Nikolaus

last: Rajewsky


title: Whole exome sequencing data from cholangiocarcinoma

status: Public on Jan 05 2023

city: SEOUL

first: hee seung

last: lee

state: --- Select ---

address: SEOUL

country: South Korea

institute: Yonsei University

summary: whole exome sequening

overall_design: whole exome sequening

first: Hee

last: Lee

first: Jun

middle: Y

last: Park


title: Single-cell RNA seq of aging peripheral blood

city: Providence

first: Nicola

last: Neretti

state: RI

address: 70 Ship St

department: Department of Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

summary: We use single-cell RNA-sequencing to investigate and identify immune cell types and transcriptomic changes with age

overall_design: Blood samples from young and old mice

first: Teo

last: Yee Voan

first: Samuel

last: Hinthorn

first: Ashley

last: Webb

first: Neretti

last: Nicola


title: A Transcription Factor Atlas of Directed Differentiation [191225_astrocyte]

city: Cambridge

first: Julia

last: Joung

state: MA

address: 75 Ames St

institute: Broad Institute

summary: Transcription factor overexpression screen in neural progenitors for astrocyte differentiation

overall_design: hESCs were differentiated into neural progenitors by overexpressing RFX4 with dual SMAD inhibition, transduced with a library of 54 transcription factor ORFs, and cultured for 7 days before flow cytometry

first: Feng

last: Zhang


title: A Transcription Factor Atlas of Directed Differentiation [190830_cardiomyocyte]

summary: Transcription factor overexpression screen in cardiomyocytes for differentiation into atrial, ventricular, or mature cardiomyocytes

overall_design: hESCs were differentiated into cardiomyocytes by overexpressing EOMES, transduced with a library of 80 transcription factor ORFs, and cultured for 4 weeks before flow cytometry


title: A Transcription Factor Atlas of Directed Differentiation [171022_reporter]

summary: Transcription factor overexpression screen with reporter cell line readout

overall_design: hESCs reporter cell lines were transduced with a library of 90 transcription factor ORFs and cultured for 7 days before flow cytometry


title: A Transcription Factor Atlas of Directed Differentiation [180509_FlowFISH]

summary: Transcription factor overexpression screen with flow-FISH readout

overall_design: hESCs were transduced with a library of 90 transcription factor ORFs and cultured for 7 days before flow-FISH


title: A Transcription Factor Atlas of Directed Differentiation [190712_media]

summary: Transcription factor overexpression screen in different cell culture media

sample_organism:
Escherichia coli
Homo sapiens
Lentivirus

overall_design: hESCs were transduced with a library of 3,548 transcription factor ORFs and cultured for 7 days in different cell culture media before flow cytometry


title: A Transcription Factor Atlas of Directed Differentiation [10XscRNA_180124_perturb]

summary: 10X single-cell RNA-seq data profiling hESCs overexpressing transcription factors

overall_design: hESCs were transduced with a library of 90 transcription factor ORFs and cultured for 7 days before single-cell RNA-seq


title: A Transcription Factor Atlas of Directed Differentiation [ChIP-seq]

summary: ChIP-seq data for candidate transcription factors identified from targeted screen for neural progenitor differentiation

overall_design: V5 tagged transcription factors were overexpressed in HUES66 cells. ChIP was performed using V5 antibody.


title: A Transcription Factor Atlas of Directed Differentiation [10XscRNA_180726_TFd56]

summary: 10X single-cell RNA-seq data profiling spontaneously differentiated cells from induced neural progenitors produced by overexpressing transcription factors

overall_design: Induced neural progenitors were differentiated from hESCs by overexpressing transcription factors and spontaneously differentiating before single-cell RNA-seq


title: Mapping of DNA methylation-sensitive cellular processes in gingival fibroblasts using the DNMT inhibitor decitabine

city: Krakow

first: Aleksander

last: Grabiec

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

summary: Epigenetic changes in DNA methylation are involved in periodontitis pathogenesis and recent studies indicate that DNA methyltransferase (DNMT) inhibitors may protect against bone resorption and disruption of the epithelial barrier. To assess the impact of DNMT inhibition on gingival fibroblasts (GFs), cells were cultured with decitabine (5-aza-2’-deoxycytidine, DAC) for 12 days to induce DNA hypomethylation. Analysis of DAC-induced genes in resting or P. gingivalis-infected GFs identified by RNA sequencing revealed increased expression of CCL20, CCL5, CCL8, CCL13, TNF, IL1A, IL18, IL33, and CSF3, and showed that the most affected processes were related to immune and inflammatory responses. In contrast, the genes downregulated by DAC were associated with extracellular matrix and collagen fibril organization.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GFs that were subjected to 12-day culture with DMSO or DAC (5 μM) and then were either left untreated or were infected with P. gingivalis (MOI 20) for 4 h.

first: Katarzyna

last: Lagosz-Cwik


title: A Transcription Factor Atlas of Directed Differentiation [10XscRNA_180525_CM]

summary: 10X single-cell RNA-seq data profiling induced cardiomyocytes

overall_design: Induced cardiomyocytes were differentiated from hESCs by overexpressing EOMES or by small molecule inhibition of GSK and WNT before single-cell RNA-seq


title: A Transcription Factor Atlas of Directed Differentiation [10XscRNA_191108_TFv2d56]

summary: 10X single-cell RNA-seq data profiling spontaneously differentiated cells from induced neural progenitors produced by combining RFX4 overexpression and dual SMAD inhibition

overall_design: Induced neural progenitors were differentiated from hESCs using RFX4 overexpression combined with dual SMAD inhibition and spontaneously differentiated before single-cell RNA-seq


title: A Transcription Factor Atlas of Directed Differentiation [SHAREseq_201218_ATAC]

summary: SHARE-seq single-cell ATAC- and RNA-seq data profiling hESCs overexpressing transcription factors

overall_design: hESCs were transduced with a library of 198 transcription factor ORFs and cultured for 7 days before single-cell ATAC- and RNA-seq joint profiling


title: A Transcription Factor Atlas of Directed Differentiation [bulk RNA-seq]

summary: Bulk RNA-seq data for candidate transcription factors and DYRK1A perturbations

overall_design: Candidate transcription factors and DYRK1A perturbations were introduced into pluripotent stem cells for 7 days before RNA-seq


title: A Transcription Factor Atlas of Directed Differentiation [10XscRNA_200209_NP]

summary: 10X single-cell RNA-seq data comparing induced neural progenitors produced by different methods

overall_design: Induced neural progenitors were differentiated from hESCs using RFX4 overexpression combined with dual SMAD inhibition, embryoid body, and dual SMAD inhibition before single-cell RNA-seq


title: General transcription factor TAF4 antagonizes epigenetic silencing by Polycomb to maintain intestine stem cell functions [RNA-seq]

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

summary: Taf4 (TATA-box binding protein-associated factor 4) is a subunit of the general transcription factor TFIID, a component of the RNA polymerase II pre-initiation complex that interacts with tissue-specific transcription factors to regulate gene expression. Properly regulated gene expression is particularly important in the intestinal epithelium that is constantly renewed from stem cells. We investigated the role of Taf4 in the murine intestinal epithelium using tissue-specific inactivation. Taf4 inactivation during embryogenesis compromised gut morphogenesis and the emergence of adult-type stem cells, ultimately leading to death. In adults, Taf4 loss perturbed the stem cell compartment and the associated Paneth cells in the stem cell niche, epithelial turnover and differentiation of mature cells, thus exacerbating the response to inflammatory challenge and potentiating Apc-driven tumorigenesis. In addition, Taf4 inactivation ex vivo in organoids prevented budding formation and maintenance. Combining immunohistology with bulk RNA-seq, ATAC-seq and single-cell RNA-seq, showed that Taf4 loss caused broad chromatin remodeling, and a strong reduction in the numbers of stem and progenitor cells with a concomitant increase in an undifferentiated cell population that displayed high activity of the Ezh2 and Suz12 components of Polycomb Repressive Complex 2 (PRC2). In line with this observation, treatment of Taf4-mutant organoids with a specific Ezh2 inhibitor restored buddings, cell proliferation and the stem/progenitor compartment. Our results reveal the critical role of Taf4 in intestinal development and homeostasis and a novel mechanism by which Taf4 acts to maintain the stem/progenitor compartment by counteracting PRC2 repression of the stem cell gene expression program.

overall_design: Assessing the effect of genetic deletion of the Taf4 subunit of general transcription factor TFIID on gene expression in embryonic and adult mouse intestine as well as ileum derived intestine organoids. RNA-seq conditions are in triplicates. For organoids samples conditions are TAF4-WT, TAF4-KO and EPZ-treated. For mice samples conditions are TAF4-WT and TAF4-KO for both embryo and adult mice.

first: Susanna

last: Säisä-Borreill

first: Thomas

last: Kleiber

first: Andréa

last: Thevenot

first: Elisabeth

last: Martin

first: Stanislas

last: Mondot

first: Hervé

last: Blottière

first: Alexandra

last: Helleux

first: Gabrielle

last: Mengus

first: Michela

last: Plateroti

first: Isabelle

last: Duluc

first: Irwin

first: Jean-Noel

last: Freund


title: Effect of AR isoform and total AR depletion and AR-v19 oeverexpression in UM-UC-3 bladder cancer cells

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: To investigate AR regulated transcription, full length, AR-v19 splice variant or total AR was siRNA depleted or AR-V19 was overexpressed in UM-UC-3 cells.

overall_design: Following ribosome depletion for transcript enrichment we then performed gene expression profiling analysis using data obtained from RNA-seq of 6 conditions.

first: Maria

last: Mudryj


title: General transcription factor TAF4 antagonizes epigenetic silencing by Polycomb to maintain intestine stem cell functions [scRNA-seq]

overall_design: Assessing the effect of genetic deletion of the Taf4 subunit of general transcription factor TFIID on gene expression in ileum derived intestine organoids. Two scRNA-seq samples from organoids with either TAF4-WT or TAF-KO.


title: General transcription factor TAF4 antagonizes epigenetic silencing by Polycomb to maintain intestine stem cell functions

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

overall_design: Refer to individual Series


title: Clinical and molecular significance of the RNA m6A methyltransferase complex in prostate cancer

status: Public on Jan 04 2023

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

summary: shRNAs targeting METTL3 used to deplete METTL3 in castrate-resistant LNCaP:C42 prostate cancer cells and the effect on gene expression and splicing determined.

overall_design: shRNA targeting METTL3 was used to deplete METTL3 in castrate-resistant but enzalutamide-sensitive LNCaP:C42 and the effect on basal gene expression and alternative splicing determined using RNA sequencing.

first: Daisy

last: Haigh

first: Corinne

middle: L

last: Woodcock

first: Veronika

last: Metzler

first: Jennifer

last: Lothion-Roy

first: Anna

last: Harris

first: Atara

last: Ntekim

first: Jenny

last: Persson

first: Brian

last: Robinson

first: Francesca

last: Khani

first: Lorraine

last: Gudas

first: Michael

last: Toss

first: Emad

last: Rakha

first: Catrin

last: Rutland

first: Rupert

last: Fray

first: Jennie

middle: N

last: Jeyapalan


title: High level and nature of transcriptional noise in yeast cells [MNase-Seq]

city: Boston

first: Zlata

last: Gvozdenov

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

summary: “Biological noise” is defined as functionally insignificant events that occur in living cells due to imperfect fidelity of biological processes.  Distinguishing between biological function and biological noise is often difficult, and experiments to measure biological noise have not been performed.  Here, we measure biological noise in yeast cells by analyzing chromatin structure and transcription of an 18 kb region of DNA whose sequence was randomly generated and hence is functionally irrelevant.  Nucleosome occupancy on random-sequence DNA is comparable to that on yeast genomic DNA.  However, nucleosome-depleted regions are much less frequent, and there are fewer well-positioned nucleosomes and shorter nucleosome arrays.  Steady-state levels of RNAs expressed from random-sequence DNA are comparable to those of yeast mRNAs, although transcription and mRNA decay rates are at higher levels.  Transcriptional initiation (5’ ends) from random-sequence DNA occurs at numerous sites at low levels, indicating very low intrinsic specificity of the Pol II machinery.  In contrast, poly(A) profiles (relative levels and clustering of 3’ isoforms) of random-sequence RNAs are roughly comparable to those of endogenous yeast RNAs, which are restricted to 3’ untranslated regions.   RNAs expressed from random-sequence DNA show higher cell-to-cell variability than RNAs expressed from yeast genomic DNA, suggesting that functional elements limit the variability among individual cells within a population.  These observations indicate that transcriptional noise occurs at high levels in yeast, and they provide insight into how chromatin and transcription patterns arise from the evolved yeast genome.

overall_design: MNase-Seq of the strain harboring random-sequence artificial chromosome (ChrXVII).

first: Kevin

last: Struhl


title: General transcription factor TAF4 antagonizes epigenetic silencing by Polycomb to maintain intestine stem cell functions [ATAC-seq]

first: Guillaume

last: Davidson

overall_design: Assessing the effect of genetic deletion of the Taf4 subunit of general transcription factor TFIID on chromatin accessibility in ileum derived intestine organoids. Two ATAC-seq samples with TAF4 either WT or KO.

first: Susanna

last: Säisä-Borreill

first: Thomas

last: Kleiber

first: Andréa

last: Thevenot

first: Elisabeth

last: Martin

first: Stanislas

last: Mondot

first: Hervé

last: Blottière

first: Alexandra

last: Helleux

first: Gabrielle

last: Mengus

first: Michela

last: Plateroti

first: Isabelle

last: Duluc

first: Irwin

first: Jean-Noel

last: Freund


title: Gene expression data from left ventricular free wall of male adult Macaca fascicularis with and without chronic atrioventricular block

city: Ota-ku

first: Hiroko

last: Izumi-Nakaseko

state: Tokyo

address: 5-21-16 Omori-Nishi

department: Faculty of Medicine

country: Japan

institute: Toho University

summary:
We studied time course of pathological remodeling occurring in the hearts of cynomolgus monkey, Macaca fascicularis against atrioventricular block condition.
We used microarrays to detail the pathological changes in the hearts which had obtained sensitivity for detecting dl-sotalol-induced TdP by 7th month after the production of atrioventricular block.

overall_design: The 14 male cynomolgus monkeys were divided into non-operated (intact) group (n=4) and operated (atrioventricular block) one (n=10). Two out of 10 operated monkeys had developed TdP ≥3 times in total by monthly dl-sotalol challenge by 7th month after the surgery, the left ventricular free wall of which were adopted to microarray assay together with ones of 4 non-operated monkeys.


title: MCT1-dependent energetic failure and neuroinflammation underlie optic nerve degeneration in Wolfram syndrome mice

city: Milan

first: Edoardo

middle: Niccolò

last: Bellini

state: Lombardia

address: Via Olgettina 58

department: Neuroscience

country: Italy

institute: San Raffaele Hospital

summary:
Purpose: The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) from WT and Wfs1-/- mices.
Methods: Retinal mRNA profiles of 240-day-old wild-type (WT) and retina Wolframin knockout (Wfs1−/−) mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were aligned to reference genome

overall_design: Retinal mRNA profiles of 240-day old wild type (WT) and Wfs1-/- mice

first: Vania

last: Broccoli


title: Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19 [single-cell CITEseq]

city: Bethesda

first: William

middle: W

last: Lau

state: MD

address: 4 Memorial Drive

department: Laboratory of Immune System Biology

institute: National Institute of Allergy and Infectious Diseases

summary: Acute viral infections can have durable functional impacts on the immune system long after recovery, but how they affect homeostatic immune states and responses to future perturbations remain poorly understood. Here we use systems immunology approaches, including longitudinal multimodal single cell analysis (surface proteins, transcriptome, and V(D)J sequences), to comparatively assess baseline immune statuses and responses to influenza vaccination in 33 healthy individuals after recovery from mild, non-hospitalized COVID-19 (mean: 151 days after diagnosis) and 40 age- and sex-matched controls who never had COVID-19. At baseline and independent of time since COVID-19, recoverees had elevated T-cell activation signatures and lower expression of innate immune genes in monocytes. COVID-19-recovered males had coordinately higher innate, influenza-specific plasmablast, and antibody responses after vaccination compared to healthy male and COVID-19-recovered females, partly because male recoverees had monocytes with higher IL-15 responses early after vaccination coupled with elevated pre-vaccination frequencies of "virtual memory" like CD8+ T-cells poised to produce more IFNg upon IL-15 stimulation. In addition, the expression of the repressed innate immune genes in monocytes increased by day 1 through day 28 post-vaccination in recoverees, thus moving towards the pre-vaccination baseline of healthy controls. In contrast, these genes decreased on day 1 and returned to the baseline by day 28 in controls. Our study reveals sex-dimorphic impacts of prior mild COVID-19 and suggests that viral infections in humans can establish new immunological set-points impacting future immune responses in an antigen-agnostic manner.

overall_design:
Blood samples were collected on 33 subjects with prior symptomatic SARS-CoV-2 infection (diagnosed by nasal PCR test) or asymptomatic infection (by antibody test), and 40 age- and sex-matched healthy controls with no history of COVID-19, at each of the following timepoints relative to seasonal influenza vaccination (day 0): days -7, 0, 1, 7, 14, 28, 70, 100. Subjects between ages 18 – 64 years were administered the Flucelvax Quadrivalent seasonal influenza vaccine (2020-2021; Seqirus Inc, Summit, NJ), whereas those aged 65 years old and above were administered the high-dose Fluzone Quadrivalent seasonal influenza vaccine (2020-2021; Sanofi Pasteur Inc, Swiftwater, PA).

Peripheral blood mononuclear cells from days 0, 1, and 28 among a selected group of 24 COVID19 patients and 16 healthy controls were profiled using multi-modal single cell CITE-seq, including surface protein staining (Biolegend TotalSeq-C lyophilized panel) and mRNA, on the 10x Genomics Chromium system. Samples from different donors were pooled and different timepoints from the same donor were pooled separately so that each pool contains only one timepoint from one donor. Assignment of the individual cells to a donor and timepoint was done using a combination of SNP and antibody hashtags. SNP calls per donor were determined from bulk level RNAseq data of the individual samples. A single sample, Control, was included across the three batches as a technical control.

first: Rachel

last: Sparks

first: Can

last: Liu

first: Kyu-Lee

last: Han

first: Kiera

last: Vrindten

first: Guangping

last: Sun

first: Milann

last: Cox

first: Sarah

last: Andrews

first: Neha

last: Bansal

first: Laura

last: Failla

first: Jody

last: Manischewitz

last: Grubbs

first: Lisa

middle: R

last: King

first: Galina

last: Koroleva

first: Stephanie

last: Leimenstoll

first: LaQuita

last: Snow

first: Elizabeth

last: Wendell

first: Princess

last: Barber

first: Daly

last: Cantave

first: Valerie

last: Mohammed

first: Alaina

last: Magnani

first: Cindy

last: Palmer

first: Dirk

last: Darnell

first: Deitra

last: Shipman

first: Anne

last: Carmona

first: Jean

last: Hammer

first: Ericka

last: Garrett

first: Jinguo

last: Chen

first: Juanjie

last: Tang

first: Amrita

last: Mukherjee

first: Brian

last: Sellers

first: Richard

last: Apps

first: Adrian

last: McDermott

first: Andrew

last: Martins

first: Evan

last: Bloch

first: Hana

last: Golding

first: Surender

last: Khurana

first: John

middle: S

last: Tsang


title: Elucidating transcriptional regulation of nitrogen metabolism with systems approaches

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

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


title: Elucidating transcriptional regulation of nitrogen metabolism with systems approaches [ChIP-Seq]

summary: NtrC and Nac have been known to be responsible for responding to nitrogen limitting conditions. In order to elucidate NtrC and Nac regulons in a genome-wide manner, RNA-seq and ChIP-exo experiments were performed for those two transcription factors under 4 different nitrogen sources, ammonia, glutamine, cytidine and cytosine.

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

overall_design: A total of eight samples were analyzed. E. coli K-12 MG1655 WT, nac-8myc, ntrC-8myc strains were cultured in the 4 different nitrogen sources, ammonia, glutamine, cytidine and cytosine, and glucose carbon source with biological duplicates.

first: Kim

last: Donghyuk

first: Ebrahim

last: Ali

first: Seo

last: Sang Woo


title: HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [RNA-seq 2]

status: Public on Jan 03 2023

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

institute: Universite Paris Saclay

summary:
We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops.
We performed gene expression profiling analysis using data obtained from RNA-seq of 4 weeks old tomato (Solanum lycopersicum cv. Moneymaker background ) plants (wild type and RNAi knock-down lines) which were treated at 45°C for 0h, 1h and 6h.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tomato MM wild type and RNAi knock-down lines after 0h and 1h of heat stress. 3 biological replicates for each time point.

first: Ying

last: Huang

first: Moussa

last: Benhamed

first: David

last: Latrasse

first: Xiaoning

last: HE


title: HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [HiChIP]

summary:
We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops.
To validate the presence of transcription factories we performed a HiChIP experiment, which is a sensitive and efficient method to analyze protein-centric chromosome conformation, using an anti-RNA polymerase II antibody.

overall_design: Comparative interaction profiling analysis of HiChIP_RNAPII assay data for tomato M82 wild type after 0h and 1h of heat stress.

first: Sanchari

last: Sicar


title: The submandibular and sublingual glands maintain oral microbial homeostasis through multiple antimicrobial proteins

city: Chongqing

first: yanan

last: li

state: Chongqing

address: 426 Songshi North Road, Yubei Distrinct, Chongqing

department: Department of Endodontics

institute: Stomatological Hospital of Chongqing Medical University

summary: Oral microbial homeostasis is a key factor affecting oral health, and saliva plays a significant role in maintaining oral microbial homeostasis. The submandibular gland (SMG) and sublingual gland (SLG) together produce the most saliva at rest. Organic ingredients, including antimicrobial proteins, are rich and distinctive and depend on the type of acinar cells in the SMG and SLG. However, the functions of the SMG and SLG in maintaining oral microbial homeostasis have been difficult to identify and distinguish, given their unique anatomical structures. Therefore, we analyzed each gland using  single-cell RNA sequencing.

overall_design: Single-cell suspensions from freshly isolated submandibular glands and sublingual glands from two female C57BL/6N (6–8 weeks old) mice were generated for scRNA-seq analysis.

first: Yanan

last: Li

first: Jingming

last: Liu

first: Wenping

last: Luo

first: Tianyu

last: Zhao


title: HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [RNA-seq 1]

summary:
We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops.
To confirm that the temperature and timing used for the heat stress are relevant, we generated RNA-seq data and analyzed changes in gene expression induced by the heat stress treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tomato M82 wild type after 0h, 1h and 6h of heat stress. 2 biological replicates for each time point.


title: HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [DAP-seq]

summary:
We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops.
We performed Amplified DNA affinity purification sequencing assay to determine HSFA1a binding sites.

overall_design: Comparative analysis of DNA affinity profiling of HSFA1a-Halo tag with control Halo-tag.


title: Gender and prior exposure shape innate immune responses to a replication-defective herpes virus vaccine

first: Foo

last: Cheung

address: Bethesda

institute: NIH

summary:
Here we integrate immune profiling and computational approaches to study responses to a replication-defective herpes simplex virus (HSV) 2 vaccine, in men and women either naive or previously exposed to HSV.
Subjects were recipients of a herpes simplex virus (HSV) 2 vaccine in a phase 1 clinical trial where comparisons could be made between three groups of human volunteers based on their HSV serostatus prior to vaccination: HSV1-/HSV2- , HSV1+/HSV2-, or HSV1±/HSV2+
Peripheral blood transcriptomics and cell population frequencies showed the greatest changes on day 1 after vaccination.  Prior exposure status and gender were independently associated with responses, but the magnitude of innate responses including type I interferon signatures and TLR7 were greatest in HSV naive women.  In contrast, subjects previously infected with HSV had more prominent interferon-I responses.  Thus, prior exposure and gender interact to shape innate responses that may also impact adaptive immune phenotypes, such as the neutralizing antibody response which was also faster in HSV naive women than men.


title: HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [Hi-C]

summary:
We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops.
To map the three-dimensional chromatin interactions we performed in situ Hi-C, a genome-wide method that detects DNA-DNA physical interactions.

overall_design: Comparative interaction profiling analysis of in situ Hi-C data for tomato M82 wild type  after 0h, 1h and 6h of heat stress. 2 biological replicates for each time point.


title: Elucidating transcriptional regulation of nitrogen metabolism with systems approaches [RNA-Seq]

overall_design: A total of eight samples were analyzed. E. coli K-12 MG1655 WT strain was cultured in the 4 different nitrogen sources, ammonia, glutamine, cytidine and cytosine, and glucose carbon source with biological duplicates.

first: Park

last: JoonYoung


title: HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions.


title: HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [ATAC-seq]

summary:
We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops.
We performed ATAC-seq experiments which provide accessible chromatin sites that can be used to identify putative regulatory elements coming in physical contact with promoters when they are actived.

overall_design: Comparative chromatin accessibility patterns analysis of ATAC-seq data for tomato M82 wild type after 0h, 1h and 6h of heat stress. 2 biological replicates for each time point.


title: HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [ChIP-seq]

summary:
To investigate the HSFA1a, a master regulator of heat stress response, plays a key role in this reorganization by promoting the formation of promoter/enhancer chromatin loops.
To determine if a typical chromatin signature could differentiate distal and proximal REs, we performed ChIP-seq experiments and analyzed the levels of four histone covalent modifications that are permissive for transcription: H3K4me3, H3K9ac, H3K18ac and H3K27ac at 0, 1 and 6 hours after heat stress on both proximal and distal REs specifically active at 1 hour after HS. In addition, To assess if RNAPII could also by recruited at distal active enhancers in plants, we performed an RNAPII ChIP-seq on plant subjected to 0, 1 and 6 hours of heat stress and analyzed its accumulation on distal REs specifically active at 1 hour after HS. Moreover, we did ChIP-seq of H3K27me1 associated constitutive heterochromatin at normal condition.

overall_design: Comparative analysis of ChIP-seq data for tomato M82 wild type at heat stress 0h, 1h and 6h.


title: SRSF6 in HeLa cells grown under normoxic and hypoxic conditions

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

institute: Goethe University Frankfurt

overall_design: Refer to individual Series


title: RNA-seq of HeLa cells stably overexpressing SRSF6-GFP grown under normoxic and hypoxic conditions

summary: We used HeLa cells that overexpress GFP-tagged SRSF6 (4-fold) were grown in normal conditions (Normoxia, 21% oxygen) or hypoxic conditions (Hypoxia, 0.2% oxygen).  compared the binding pattern of SRSF6 between normoxia, 4h hypoxia and 24h hypoxia.

overall_design: 2 biological replicates for each conditions. Total RNA after ribodepletion was sequenced with 150-bp paired end reads.


title: HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [Capture Hi-C]

summary:
We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops.
To determine whether distal REs come into contact with promoters, instead of using a classical Hi-C, we further combined Hi-C with a capture enrichment step. We generated a biotinylated RNA bait library specifically targeting 212,735 promoter regions and performed a capture Hi-C after 0h, 1h and 6h after stress.

overall_design: Comparative interaction profiling analysis of Capture Hi-C data for tomato M82 wild type after 0h, 1h and 6h of heat stress. 2 biological replicates for each time point.


title: Transcriptome-wide mapping of RNA:protein interactions of SRSF6 in HeLa cells grown under normoxic and hypoxic conditions by iCLIP

summary: We used HeLa cells that express GFP-tagged SRSF6 at physiological levels and subjected them to 4 h or 24 h hypoxia (0.2% oxygen). Cells grown in normal conditions were used as control (Normoxia, 21% oxygen). We performed iCLIP using anti-GFP antibodies and compared the binding pattern of SRSF6 between normoxia, 4h hypoxia and 24h hypoxia.

overall_design: 3 biological replicates per condition were subjected to the iCLIP procedure with UV-crosslinking at 254 nm. For IPs either an anti-GFP antibody was used. No UV treatment served as negative control.


title: Releasing the restraints of Vγ9Vδ2 T-cells in cancer immunotherapy

status: Public on Jan 02 2023

city: London

first: JONATHAN

last: CARON

state: Greater London

address: New Hunt's House, Newcomen St

department: Cancer Studies

institute: KING'S COLLEGE LONDON

summary:
Objectives: Vγ9Vδ2 T-cells are a subset of T-cells with a crucial role in immunosurveillance which
can be activated and expanded by multiple means to stimulate effector responses. Little is known
about the expression of checkpoint molecules on this cell population and whether the ligation of
these molecules can regulate their activity. The aim of this study was to assess the expression of both
activatory and inhibitory receptors on Vγ9Vδ2 T-cells to assess potential avenues of regulation to
target with immunotherapy.
Methods: Expression of various activatory and inhibitory receptors was assessed on Vγ9Vδ2 T-cells
by flow cytometry following activation and expansion using zoledronic acid (ZA) and Bacillus
Calmette-Guérin (BCG). Expression of these markers and production of effector molecules was also
examined following co-culture with various tumour cell targets. The effect of immune checkpoint
blockade on Vγ9Vδ2 T-cells was also explored.
Results: Vγ9Vδ2 T-cells expressed high levels of activatory markers both at baseline and following
stimulation. Vγ9Vδ2 T-cells expressed variable levels of inhibitory checkpoint receptors with many
being upregulated following stimulation. Expression of these markers is further modulated upon co-
culture with tumour cells with changes reflecting activation and effector functions. Despite their high
expression of inhibitory receptors when cultured with tumour cells expressing cognate ligands there
was no effect on Vδ2+ T-cell cytotoxic capacity or cytokine production with immune checkpoint
blockade.
Conclusions: Our work suggests the expression of checkpoint receptors present on Vγ9Vδ2 T-cells
which may provide a mechanism with the potential to be utilised by tumour cells to subvert Vγ9Vδ2
T-cell cytotoxicity. This work suggests important candidates for blockade by ICI therapy in order to
increase the successful use of Vγ9Vδ2 T-cells in immunotherapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for blood human gamma-delta t cells activated with either IL2 only, IL2+ZA, IL2+BCG, or IL2+KBCG for 13 days, and day 0 controls.

first: Jonathan

last: Caron

first: Mark

last: Bodman-Smith

first: Laura

last: Ridgley