title: Blood transcriptomics mirror regulatory mechanisms during hibernation

status: Public on Jul 30 2023

city: Neuherberg

first: Yiming

last: cheng

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

summary: Hibernation enables many species of the mammalian kingdom to overcome periods of harsh environmental conditions. During this physically inactive state metabolic rate and body temperature are drastically downregulated, thereby reducing energy requirements (torpor) also over shorter time periods. Since blood cells reflect the organism's current condition, it was suggested that transcriptomic alterations in blood cells mirror the torpor-associated physiological state. Transcriptomics on blood cells of torpid and non-torpid Djungarian hamsters and QIAGEN Ingenuity Pathway Analysis (IPA) revealed key target molecules (TMIPA), which were subjected to a comparative literature analysis on transcriptomic alterations during torpor/hibernation in other mammals. Gene expression similarities were identified in 148 TMIPA during torpor nadir among various organs and phylogenetically different mammalian species. Based on TMIPA, IPA network analyses corresponded with described inhibitions of basic cellular mechanisms and immune system-associated processes in torpid mammals. Moreover, protection against damage of heart, kidney, and liver was deduced from this gene expression pattern in blood cells. This study shows that blood cell transcriptomics can reflect the general physiological state during torpor nadir. Furthermore, the understanding of molecular processes for torpor initiation and organ preservation may have beneficial implications for humans in extremely challenging environments, such as in medical intensive care units and in space.

overall_design: All 36 SP-acclimated hamsters were observed to express spontaneous daily torpor, which is a drop of Tb <32 °C for at least 30 minutes. Over different sampling times, 18 hamsters were hypothermic (HT) and expressed torpor and the other 18 hamsters did not and served as normothermic controls (NT). During torpor entry (ZT01) samples were obtained from 6 NT and 5 HT animals; during torpor nadir/ or mid torpor (ZT04) samples from 4 NT and 5 HT animals; during torpor arousal (ZT07) samples from 4 NT and 4 HT animals, and post-torpor (ZT16) from 4 NT and 4 HT animals. For sampling, hamsters were sacrificed by carbon dioxide inhalation inside their home cage at an age of 32 ± 4 weeks. 5 hamsters didn’t perform torpor for their whole life served as overall control. Each sample is the blood sample of one animal.

last: Cheng

first: Dominique

last: Moser

first: Victoria

last: Diedrich

first: Alexander

last: Chouker


title: RNAseq of WT pMSP3535-PnisA-6his-ftsH(H456Y) and WT pMSP3535-PnisA-6his-ftsH

status: Public on Aug 01 2023

city: Singapore

first: Zeus

middle: Jaren

last: Nair

address: 60 Nanyang Dr

country: Singapore

institute: Singapore Centre for Environmental Life Sciences Engineering

type: Expression profiling by high throughput sequencing

summary: We report the transcriptome of cultures of WT pMSP3535-PnisA-6his-ftsH(H456Y) and WT pMSP3535-PnisA-6his-ftsH following overnight induction with 125 ng/mL nisin

overall_design: WT pMSP3535-PnisA-6his-ftsH(H456Y) and WT pMSP3535-PnisA-6his-ftsH were grown to mid-log phase and expression induced with nisin at 125 ng/mL, and RNA harvested. 3 replicates each were prepared.

middle: J

first: Hanxing

last: Gao

first: Aslam

last: Firras

first: Kelvin Kian Long

last: Chong

first: Pei Yi

last: Choo

first: Kevin

last: Pethe

first: Kimberly

middle: A

last: Kline


title: Transcriptomics analysis of iron chelator deferoxamine treated human tumor colonoids.

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

country: USA

institute: University of Michigan

summary: To investigate the detailed molecular mechanisms for the regulatory role of iron in colorectal cancer, RNA-seq analysis was performed on RNA isolated from untreated control and deferoxamine treated human tumor colonoids.

overall_design: Global gene expression profiling in RNAs isolated from pooled untreated control (n=3; CON) and  deferoxamine (n=3; DFO) human tumor colonoids.

first: Xiang

last: Xue


title: Study on m6A methylation modification of keratoconus

city: qingdao

first: HUIJIN

last: WANG

state: shandong province

address: yanerdao road

country: China

institute: Qingdao Eye Hospital of  Shandong First Medical University

summary: Transcriptional analysis of human keratoconus compared differentiated expression between normal and cone corneas. m6a modification plays an as yet unclear role in cone corneas, and here we aim to identify variations in m6a modification in cone corneas and the potential role it plays.

overall_design:
Two-condition experiment, normal cornea vs. keratoconus. Biological replicates: 5 control replicates, 5 keratoconus replicates.

Please note that experiments were technically performed as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed the results as though they are single channel and  raw data file is linked to the corresponding IP sample records.

first: Hua


title: Reducing NADPH synthesis counteracts diabetic nephropathy through restoration of AMPK activity

city: ChongQing

first: Xiao

last: Wei

address: ChangJiang Zhi Road 10, YuZhong District

department: Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases

institute: Daping Hospital, Army Medical University of PLA

summary: Wei et al. performed microarray analysis to explore the metabolism change in diabetes and RYGB surgery treated rats.

overall_design: Control and diabetes rats were treated with Sham or Roux-en-Y gastric bypass (RYGB) surgery.

first: Zhiming

last: Zhu


title: Sex shapes cell-type-specific transcriptional signatures of stress exposure in the mouse hypothalamus

status: Public on Jul 31 2023

city: Rehovot

first: Alon

last: Chen

address: Arison Neurobiology Building

department: Brain Sciences

country: Israel

institute: Weizmann Institute of Science

summary: Stress-related psychiatric disorders and the stress system show prominent differences between men and women. These sex differences are detectable at the transcriptional level but we lack cell-type specific information. Here, using single-cell transcriptomics, we identify cell-type-specific signatures of acute restraint stress in the paraventricular nucleus of the hypothalamus - a central hub of the stress response - in male and female mice. Further, we show that a history of chronic mild stress alters these acute stress signatures in a sex-specific way. Using this dataset, we identified oligodendrocytes as a major target for sex-specific effects of stress. This dataset provides the first molecular resource for an in-depth dissection of the interplay between cell types and sex on the mechanisms of the stress response, offering the transcriptomes of thousands of individual cells.

overall_design: Single-cell RNA-sequencing of male and female mice without (controls) or after stress exposure (acute restraint stress (ARS) or acute restraint stress after chronic mild stress (CMS ARS))

first: Elena

last: Brivio

first: Juan Pablo

last: Lopez


title: Thymine DNA glycosylase regulates cell-cycle-driven p53

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cell cycle progression is linked to transcriptome dynamics and variations in the response of pluripotent cells to differentiation cues, mostly through unknown determinants. Here, we characterized the cell-cycleassociated transcriptome and proteome of mouse embryonic stem cells (mESCs) in naive ground state. We found that the thymine DNA glycosylase (TDG) is a cell-cycle-regulated co-factor of the tumor suppressor p53. Furthermore, TDG and p53 co-bind ESC-specific cis-regulatory elements and thereby control transcription of p53-dependent genes during self-renewal. We determined that the dynamic expression of TDG is required to promote the cell-cycle-associated transcriptional heterogeneity. Moreover, we demonstrated that transient depletion of TDG influences cell fate decisions during the early differentiation of mESCs. Our findings reveal an unanticipated role of TDG in promoting molecular heterogeneity during the cell cycle and highlight the central role of protein dynamics for the temporal control of cell fate during development.

overall_design: ChIP-seq (10 samples), DIP-seq (12 samples), RNA-seq (36 samples), ATAC-seq (1 sample). Nomenclature: siC means Control (Wild-type) and siTdg/shTdg mean knocking-down the Tdg gene; SG2M means cells in S/G2/M phases, G1 means cells in G1 phase of the cell cycle.

first: Sergi

last: Aranda


title: Next Generation Sequencing of EGFR-mutant non-small cell lung cancer (NSCLC) cells with tyrosine kinase inhibitor (TKI)-resistance

city: New Taipei

first: Shiao-Ya

last: Hong

address: 362, Zhongzheng Rd., Xindian Dist.

country: Taiwan

institute: Cardinal Tien Hospital

summary:
Purpose: The aim of this study is to compare the differentially expressed transcriptome of TKI resistance NSCLC cells and their parental cells
Methods: mRNA profiles of the TKI-resistant NSCLC cells and their parental cells were generated by deep sequencing using Illumina HiSeq4000. Clean RNA-seq data was quantified and analyzed using the CLC genomics workbench software version 11.0 (Qiagen, Hilden, Germany).
Results: In the current study, we established three EGFR-TKI-resistant cell lines and analyzed their expression profiles by RNA sequencing. We mapped about 30 million sequence reads per sample to the human genome (hg38) sequence and identified 21,463 transcripts in the parental and TKI-resistant NSCLC cells. Over 10% of the transcripts showed differential expression between the parental andTKI-resistant NSCLC cells, with a fold change ≥1.5 and p value <0.05. Transcriptome data analysis revealed the existence of significant overlaps and significant upregulation of epithelial-mesenchymal transition (EMT) pathway in the three cell lines with EGFR-TKI resistance.
Conclusions: Our results showed that RNA-seq based transcriptome characterization offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within TKI-resistant NSCLC cells.

overall_design: mRNA profiles of TKI-resistant NSCLC cells and their parental cells

first: Cheng-Wen

last: Wu


title: Effects of chronic morphine exposure on the transcriptome of nucleus accumbens (NAc) in mice

status: Public on Jul 28 2023

city: Haikou

first: Feifan

last: Zhou

address: 58 Renmin Avenue

institute: Hainan University

summary: Morphine addiction causes major medical and social problems worldwide. Chronic morphine exposure results in the development of behavioral sensitization, accompanied by the disruption of brain homeostasis. As a key brain reward region, nucleus accumbens (NAc) plays a central role in brain reward mechanisms. However, the contribution of morphine exposure to NAc is poorly understood. Here we indicated that chronic morphine exposure induced neuroinflammation, abnormal neuronal physiology, and dysregulation of glycolytic metabolism in NAc. In summary, our findings illustrate the effects of morphine in NAc, and provide a new insight for development of future morphine addiction therapeutics.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for nucleus accumbens (NAc) of C57BL/6 male mice receiving morphine vs. saline exposure.

first: Jie

last: Rao

first: Weikang

last: Sun

first: Xinran

last: Wang


title: RNA sequencing of hydrogen peroxide (H2O2)-treated melanocytes

city: Seoul

first: Eun Jung

last: Lee

address: 50-1 Yonsei-Ro, Seodaemun-Gu

country: South Korea

institute: Yonsei University College of Medicine

summary:
Purpose: Determine the mechanism of H2O2-induced signaling in melanocytes.
Method: Primary human epidermal melanocytes were treated with H2O2 (200 μM) and incubated for 24 h. Total RNA (500 ng) from melanocytes were extracted and subjected to library synthesis.
Results: H2O2-treated melanocytes exhibited upregulation of cell death and type 1 interferon-related genes.
Conclusion: H2O2-induced melanocyte signaling was well evaluated using RNA sequencing.

overall_design: RNA profiles of H2O2-treated human melanocyte

first: Sang

middle: H

last: Oh

first: Eun


title: PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription [CRISPR_screen]

status: Public on Jul 22 2023

city: Amsterdam

first: Isabel

last: Mayayo-Peralta

address: Plesmanlaan 121

country: Netherlands

institute: NKI

summary: How steroid hormone receptors (SHRs) orchestrate transcriptional activity remains only partly understood. Upon activation, SHRs bind the genome and recruit their co-regulators, crucial to induce gene expression. However, it remains unknown which components of the SHR-recruited coregulator complex are essential to drive transcription following hormonal stimuli. Through a FACS-based genome-wide CRISPR screen, we comprehensively dissected the Glucocorticoid Receptor (GR) co-regulatory complex involved in gene-target regulation. We describe a novel functional cross-talk between PAXIP1 and the cohesin subunit STAG2 that is critical for regulation of gene expression by GR. Without altering the GR cistrome, PAXIP1 and STAG2 depletion alter the GR transcriptome, by impairing the recruitment of 3D-genome organization proteins to the GR complex. Importantly, we demonstrate that PAXIP1 is required for stability of cohesin on the genome, its localization to GR-occupied sites, and maintenance of enhancer-promoter interactions. Moreover, in lung cancer, where GR acts as tumor suppressor, PAXIP1/STAG2 loss enhances GR-mediated tumor suppressor activity by modifying local chromatin interactions. All together, we introduce PAXIP1 and STAG2 as novel co-regulators of GR, required to maintain 3D-genome architecture and drive the GR transcriptional programme following hormonal stimuli.

overall_design: FACS-based genome-wide CRISPR screen to identify essential co-regulators of the Glucocorticoid Receptor. Human CRISPR Brunello library was used. 3 biological replicates for FKBP5 high and FKBP5 low populations were included.

first: Sebastian

last: Gregoricchio

first: Karianne

last: Schuurman

first: Selçuk

last: Yavuz

first: Anniek

last: Zaalberg

first: Bart

last: Geverts

first: Aleksandar

last: Kojic

first: Nina

last: Abbott

first: Suzanne

last: Beerthuijzen

first: Joseph

last: Siefert

first: Tesa

middle: M

last: Severson

first: Martijn

last: van Baalen

first: Liesbeth

last: Hoekman

first: Cor

last: Lieftink

first: Maarten

last: Altelaar

first: Roderick

last: Beijersbergen

first: Adriaan

middle: B

last: Houtsmuller

first: Stefan

last: Prekovic

first: Wilbert

last: Zwart


title: Gene expression of MDCK cells with antivirals treatment

status: Public on Jul 17 2023

city: Shenzhen

first: jianhui

last: liang

state: Guangdong

address: 1068 Xueyuan Avenue, Nanshan District

institute: Shenzhen Institute of Science and Technology

summary: In addition to directly inhibiting viral proteins, some antiviral drugs inhibit virus replication through regulation of host gene expression. Here we test whether antiviral activity of antivirals is independent of modulating gene expression in infected host cells.

overall_design: Transcriptional profiling was employed to test whether antivirals inhibit viral replication through the modulation of host gene expression in MDCK cells.

first: Yan

last: Wang

first: Mingfeng

last: He

first: Jianhui

last: Liang


title: Single-cell profiling of hematopoietic cells in VEXAS syndrome

status: Public on Jul 18 2023

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

summary:
Background and methods: VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome has been recently recognized as an adult-onset autoinflammatory syndrome due to somatic mutations affecting Ubiquitin Like Modifier Activating Enzyme 1 (UBA1) gene. Following-up studies have been mostly limited to case reports; transcriptome of especially hematopoiesis in VEXAS syndrome has not been well characterized.
Results: We performed whole transcriptome sequencing of single bone marrow cells (BMMNCs) and enriched Lineage-CD34+ hematopoietic stem and progenitor cells (HSPCs) from nine patients included in the original VEXAS cohort. We profiled inflammation and hematopoietic differentiation in these patients, and found activation of inflammatory gene programs particularly in marrow myeloid cells; HSPCs showed a preferred myeloid dominance. Patients had profound abnormalities in gene expression involved in pathways of inflammation, cell cycling and activation, and protein synthesis. We defined single bone marrow cells with expressed UBA1 mutations, and characterized gene expression of mutant myeloid cells as compared to that of wild-type, and observed upregulation of inflammatory pathways and immune activation; increased cell cycling might contribute to clonal dominance of UBA1 mutant cells. We were also able to profile other somatic mutations (DNMT3A) in two patients who had concurrent DNMT3A mutations at a high frequency. With coupled single cell T/B-cell receptor (TCR/BCR) sequencing, we characterized TCR and BCR repertoire in four patients, two of whom had B cell lymphocytosis. Cell-cell interaction analysis revealed enhanced interactions of myeloid cells with HSPCs, and interferons interaction with their receptors were frequent. We also performed bulk RNA sequencing of several leukemic cell lines with UBA1 knockdown, and observed upregulation of inflammatory pathways in these UBA1 knockdown cell lines.
Conclusion: Our study discloses transcriptome signatures of hematopoietic cells in VEXAS syndrome, providing a broad perspective into potential pathogenesis of this novel disease.

overall_design: RNA profiles of single bone marrow hematopoietic cells of 9 VEXAS patients and 4 healthy donors were generated by deep sequencing using Illumina NovaSeq. Bulk RNA sequencing was performed with several leukemic cell lines (U937, Raji, Jurkat, and THP1) with UBA1 knockdown using Illumina NovaSeq.

first: Zhijie

last: Wu


title: Homeodomain-interacting protein kinase maintains neuronal homeostasis during normal Caenorhabditis elegans aging and systemically regulates longevity from serotonergic and GABAergic neurons

city: Rochester

first: Andrew

middle: V

last: Samuelson

state: NY

address: 601 Elmwood Ave

department: Biomedical Genetics

institute: University of Rochester Medical Center

summary: Aging and the age-associated decline of the proteome is determined in part through neuronal control of evolutionarily conserved transcriptional effectors, which safeguard homeostasis under fluctuating metabolic and stress conditions by regulating an expansive proteostatic network. We have discovered the Caenorhabditis elegans homeodomain-interacting protein kinase (HPK-1) acts as a key transcriptional effector to preserve neuronal integrity, function, and proteostasis during aging. Loss of hpk-1 results in drastic dysregulation in expression of neuronal genes, including premature upregulation of genes associated with neuronal aging. During normal aging hpk-1 expression increases throughout the nervous system and in more cell-clusters than any other kinase. Within the aging nervous system, hpk-1 is co-expressed with key longevity transcription factors, including daf-16 (FOXO), hlh-30 (TFEB), skn-1 (Nrf2), and hif-1, which suggests hpk-1 expression mitigates natural age-associated physiological decline. Consistently, pan-neuronal overexpression of hpk-1 extends longevity, preserves proteostasis both within and outside of the nervous system, and improves stress resistance. Neuronal HPK-1 improves proteostasis through kinase activity. HPK-1 functions cell non-autonomously within serotonergic and GABAergic neurons to improve proteostasis in distal tissues by specifically regulating divergent components of the proteostatic network. Increased serotonergic HPK-1 enhances the heat shock response and survival to acute stress. In contrast, GABAergic HPK-1 induces basal autophagy and extends longevity. Our work establishes hpk-1 as a key neuronal transcriptional regulator that is critical for the preservation of neuronal function during aging and insight as to how the nervous system partitions acute and chronic adaptive response pathways to delay aging by maintaining organismal homeostasis.

overall_design: Approximately 3000 total C. elegans hermaphrodite animals of either N2 (WT) or hpk-1 (pk1393) mutants were collected at day 2 of adulthood for RNA isolation from populations that were synchronized at L1 and then treated with FUdR at L4 to prevent formation of progeny. Three biological replicates were prepared for each genotype, each consisting of a separate synchronized population of animals. Libraries for RNA-Seq were prepared and sequenced on a HiSeq2500 in 1x100bp mode at the University of Rochester Genomics Research Center.

first: Maria

middle: I

last: Lazaro-Pena

first: Adam

last: Cornwell

first: Carlos

last: Diaz-Balzac

first: Ritika

last: Das

first: Nicholas

last: Macoretta

first: Juilee

last: Thakar


title: RNA sequencing of high mobility group box 1-treated melanocytes [hmgb1]

first: Eun Jung

last: Lee

summary:
Purpose: Determine the mechanism of high mobility group box 1 (HMGB1)-induced signaling in melanocytes.
Method: Primary human epidermal melanocytes were treated with HMGB1 (1 μg/ml) and incubated for 24 h. Total RNA (500 ng) from melanocytes were extracted and subjected to library synthesis.
Results: HMGB1-treated melanocytes exhibited upregulation of cell death and type 1 interferon-related genes.
Conclusion: HMGB1-induced melanocyte signaling was well evaluated using RNA sequencing.

overall_design: RNA profiles of HMGB1-treated human melanocyte

first: Sang

last: Oh

first: Eun


title: Tumor-derived exosomal miR-204 enhances white adipose tissue browning to promote cancer associated cachexia

status: Public on Jul 13 2023

city: Wuhan

first: Yong

last: Hu

state: State...

address: Wuhan

institute: Wuhan university

summary:
Cachexia is a wasting disorder of adipose tissues that leads to profound weight loss and frailty. One key characteristic of cachexia is elevated resting energy expenditure, which has been linked to increased fat lipolysis and thermogenesis.
Extracellular vesicles (EVs) are serving as new messengers to mediate cell-cell communication in vivo. How tumors induce brown fat activity is unknown. Here, we found that breast cancer increased hypoxia inducible factor 1 subunit alpha (HIF1A) protein modification through extracellular-vesicle-encapsulated miR-204 targeting von Hippel-Lindau tumor suppressor (VHL), plays an important role in wasting by driving lipolysis and thermogenic gene expression in adipose tissues.

overall_design: adipose tissue mRNA profiles upon 10 times of EV (MDA-MB-231 EV) injection treatment through tail vein injection of NSG mice and adipose tissue mRNA from tumour bearing mice

first: Wei

last: Yan


title: Single-Cell Analysis of Dorsal Root Ganglia Reveals Metalloproteinase Signaling in Satellite Glial Cells and Pain

status: Public on Jul 12 2023

city: Cincinnati

first: Temugin

last: Berta

state: OH

address: 231 Albert Sabin Way, MSB 3408

department: Anesthesiology

institute: University of Cincinnati

summary: Although satellite glial cells (SGCs) are among the most abundant non-neuronal cells in dorsal root ganglia (DRG), little is known about their heterogenity and functions. We used single cell RNA sequencing (scRNA-seq) to analyze the heterogenity and unique functions of SGCs.

overall_design: DRG tissues from three CD-1 mice were dissected and pooled, single cell suspension was generated by  enzymatic and mechanical dissociation, and analyzed using scRNA-seq.

first: Traquel

last: Tonello

first: Aditi

last: Paranjpe


title: Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils [HI-C]

city: Philadelphia

first: Alexandra

last: Zezulin

address: 421 Curie Blvd 544 BRB II/III

institute: University of Pennsylvania

summary: Epigenome and transcriptome characterization of RUNX1 deficient hematopoietic cells. We hypothesized that epigenetic alterations in key inflammatory pathway genes are acquired in RUNX1 deficient granulocyte-monocyte progenitors (GMPs) and are propagated to neutrophils. We deleted RUNX1 using Cebpa-Cre, which deletes primarily in GMPs. We analyzed the basal transcriptional changes caused by the loss of RUNX1 in purified GMPs and neutrophils by bulk RNA-seq. We evaluated if the loss of RUNX1 leads to changes in chromatin accessibility in GMPs and neutrophils by ATAC-seq. We determined that there was increased chromatin accessibility of transposable elements (TEs) in RUNX1 deficient cells. To determine if we could detect dsRNA from TEs, we pulled down dsRNA using the 9D5 antibody and performed RNA-seq. To gain insight into how RUNX1 loss affects active enhancers, we performed H3K27ac ChIP-seq on control and Runx1 deficient neutrophils. We also evaluated if RUNX1 mutations in patient neutrophils lead to changes in chromatin accessibility by ATAC-seq. We then performed Hi-C to evaluate the global high-order chromatin organization in GMPs and neutrophils. Finally, we performed RUNX1 CUT&RUN to determine RUNX1 occupancy sites in GMPs.

overall_design: Examination of transcriptome, chromatin accessibility, and histone modifications in RUNX1 mouse deficient GMPs and neutrophils, and patient neutrophils. Please note that each processed data file was generated from both A and B replicates, and is linked to the corresponding *_A sample records.

middle: U

first: Elizabeth

middle: D

last: Howell

first: Darwin

last: Ye

first: Kai

last: Tan

first: Wenboa

last: Yu

first: Nancy

last: Speck


title: Effect of Neat1 knockdown on gene expression in the rat dorsal root ganglion (DRG) after spinal nerve ligation

status: Public on Jul 27 2023

city: Tokyo

first: Atsushi

last: Sakai

address: 1-1-5 Sendagi, Bunkyo-ku

country: Japan

institute: Nippon Medical School

summary: To investigate the involvement of Neat1 in neuropathic pain, Neat1 was knocked down in DRG neurons by the injection of AAV vector encoding shRNA for Neat1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in the rat DRG after SNL and/or Neat1 knockdown.

first: Motoyo

last: Maruyama

first: Tsukasa

last: Fukunaga

first: Yoshitaka

last: Miyagawa

first: Takashi

last: Okada

first: Michiaki

last: Hamada

first: Hidenori

last: Suzuki


title: Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils [CUT&RUN]


title: The effect of anti-MPO and anti-PR3 IgG from patients with ANCA vasculitis on human monocytes.

status: Public on Jul 24 2023

city: London

first: Michael

last: Robson

address: Great Maze Pond

country: United Kingdom

institute: King's College London

summary: These data are part of a body of work exploring the effect of IgG from patients with ANCA vasculitis on human monocytes in vitro. Please see the relevant publication for a full description.

overall_design: In each experiment, purified IgG from patients with ANCA vasculitis (anti antibodies to MPO or PR3) or IgG from healthy controls were incubated with human monocytes. Experiments were performed with or without TLR agonists, and timepoints and conditions are described below. The 'donor' refers to the healthy monocyte donor and is the same as in the associated publication. Each group had n=8, except in three cases n=7 for technical reasons. These were 202 (control, donor D, LPS), 513 (anti-MPO, donor F, R848) and 418 (anti-PR3, donor F, LPS).

first: Fernanda

last: Florez-Barros

first: Siobhan

last: Bearder

first: Pavlidis

last: Polychronis


title: PLSCR1 is a cell-autonomous defense factor against SARS-CoV-2 infection

city: West Haven

first: John

middle: David

last: MacMicking

state: CT

address: 850 West Campus Dr.

department: Microbial pathogenesis and immunobiology

institute: Yale University

summary: To investigate whether PLSCR1 knockout affects the gene expression in the presence or absence of  IFN-γ treatment, we compared the gene expression profile in WT and PLSCR1-KO cells using RNA-seq analysis.

overall_design: RNA-seq analysis of gene expression level in WT and PLSCR1-KO Huh7.5 cells treated or untreated with IFN-γ. Three biological replicates were performed for each group, resulting in a total 12 samples.

first: Dijin

last: Xu

first: Weiqian

last: Jiang


title: C5aR+ dendritic cells fine-tune the Peyer’s patch microenvironment to induce antigen-specific CD8+ T cells

city: Jeonju-si, Jeollabuk-do,

first: Saehae

last: Kim

address: 567 Baekje-daero, Deokjin-gu,

department: Molecular biology

institute: Jeonbuk National University

summary: The mucosa is an ideal route for vaccination against pathogen infection, but the effective adjuvant capable of overcoming the tolerogenic dendritic cell (DC) environment is unavailable. We characterized type 2 conventional DCs and lysozyme-expressing monocyte-derived DCs (LysoDCs) of Peyer’s patches to identify the vaccination target cells through single-cell RNA sequencing. Based on functional analysis of the data, we suggest that C5aR+ LysoDCs and Co1 peptide, a C5aR ligand, as a target cell and an adjuvant, respectively, for mucosal vaccination. Co1-mediated stimulation of C5aR+ LysoDCs increased the level of reactive oxygen species, leading to CCL3-mediated chemotaxis and exogenous antigen cross-presentation, which elicited an antigen-specific CD8+ T cell response. In a SARS-CoV-2 vaccine model, Co1 peptide increased the frequency of antigen-specific polyfunctional CD8+ T cells in systemic as well as mucosal compartments. Collectively, LysoDC activation by Co1 peptide potentiates vaccination efficiency by constructing an immunostimulatory environment in the mucosal immune inductive site.

overall_design: To observe the DEGs in PP CD11chiMHCclassIIhi SIRP+ cells treated with Co1 peptide, cells were sorted and then in vitro cultured with or without Co1 peptide in RPMI-1640 supplemented with 10% heat inactivated fetal bovine serum, colony stimulating factor 1 (0.1 g/ml), colony stimulating factor 2 (0.5 g/ml). After 6 h, the scRNA-seq were performed by geninus (Seoul, Korea) according to protocol provided by the 10x Genomics.

first: Sae-Hae

first: Yong-Suk

last: Jang


title: miR-15/16 clusters restrict effector Treg cell differentiation and function

status: Public on Jul 21 2023

city: La Jolla

first: Li-Fan

last: Lu

state: CA

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

summary: Effector regulatory T cells (eTregs) exhibit distinct homeostatic properties and superior suppressor capacities pivotal for controlling immune responses mediated by their conventional T cell counterpart. While the role of microRNAs (miRNAs) in Tregs has been well-established, how miRNAs regulate eTregs remains poorly understood. Here, we demonstrate that miR-15/16 clusters act as key regulators in limiting eTreg responses. Loss of miR-15/16 clusters leads to increased eTreg frequencies with enhanced suppressor function. Consequently, mice with Treg-specific ablation of miR-15/16 clusters display attenuated immune responses during neuroinflammation and upon both infectious and non-infectious challenges. Mechanistically, miR-15/16 clusters exert their regulatory effect in part through repressing IRF4, a transcription factor essential for eTreg differentiation and function. Moreover, miR-15/16 clusters also directly target neuritin, an IRF4-dependent molecule, known for its role in Treg-mediated regulation of plasma cell responses. Together, we identify an miRNA family that controls an important Treg subset and further demonstrate that eTreg responses are tightly regulated at both transcriptional and posttranscriptional levels.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Treg cells with or without deletion of miR-15/16 clusters.

first: Jiayi

last: Dong

first: William

last: Huth

first: Nimi

last: Marcel

first: Ziyue

last: Zhang

first: Ling-Li

last: Lin


title: Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils [dsRNA-seq]

first: Alexandra

last: Zezulin

overall_design: Examination of transcriptome, chromatin accessibility, and histone modifications RUNX1 mouse deficient GMPs and neutrophils, and patient neutrophils.

first: Elizabeth

last: Howell

first: Darwin

last: Ye

first: Kai

last: Tan

first: Wenboa

last: Yu

first: Nancy

last: Speck


title: Multi-scale epigenomic priming of inflammatory genes enables rapid recall in human memory T helper cells

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

institute: Erasmus Medical Center

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

overall_design: Refer to individual Series


title: Transgene-free direct conversion of murine fibroblasts into functional muscle stem cells [bulkRNA]

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: Transcription factor-based reprogramming provides an attractive approach to produce desired cell types for regenerative medicine purposes. Such cellular conversions are widely dependent on viral vectors to efficiently deliver and express defined factors in target cells. However, use of viral vectors is associated with unfavorable genomic integrations that can trigger deleterious molecular consequences, rendering this method a potential impediment to clinical applications. Here, we report on a highly efficient transgene-free approach to directly convert mouse fibroblasts into induced myogenic progenitor cells (iMPCs) by overexpression of synthetic MyoD-mRNA in concert with an enhanced small molecule cocktail. First, we performed a candidate compound screen and identified two molecules that enhance fibroblast reprogramming into iMPCs by suppression of the JNK and JAK/STAT pathways. Simultaneously, we developed an optimal transfection protocol to transiently overexpress synthetic MyoD-mRNA in fibroblasts. Combining these two techniques enabled robust and rapid reprogramming of fibroblasts into Pax7 positive iMPCs in as little as 10 days. Nascent transgene-free iMPCs proliferated extensively in vitro, expressed a suite of myogenic stem cell markers, and could differentiate into highly multinucleated and contractile myotubes. Furthermore, using global and single-cell transcriptome assays, we delineated gene expression changes associated with JNK and JAK/STAT pathway inhibition during reprogramming, and identified in iMPCs a Pax7+ stem cell subpopulation resembling satellite cells. Last, transgene-free iMPCs robustly engrafted skeletal muscles of a Duchenne muscular dystrophy mouse model, restoring dystrophin expression in hundreds of myofibers. In summary, this study reports on an improved and clinically safer approach to convert fibroblasts into myogenic stem cells that can efficiently contribute to muscle regeneration in vivo.

overall_design: Global transcriptional analysis of MEFs transfected with synthetic MyoD-mRNA with or without treatment of the small molecule cocktails containing F/R/C, F/R/C+SP or F/R/C+CP. This analysis was performed at day 10 of reprogramming.

first: Xhem

last: Qabrati

first: Inseon

first: Falko

last: Noé

first: Ori

last: Bar-Nur


title: Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains

status: Public on Jul 19 2023

city: Quebec

first: Steve

last: Bilodeau

state: Quebec

address: 2260 boul. Henri-Bourassa

country: Canada

institute: Centre de recherche du CHU de Québec-Université Laval

summary: Transcription-factor binding to cis-regulatory regions regulates the gene expression program of a cell, but occupancy is often a poor predictor of the gene response. Here, we show that glucocorticoid stimulation led to the reorganization of transcriptional coregulators MED1 and BRD4 within topologically associating domains (TADs), resulting in active or repressive gene environments. Indeed, we observed a bias toward the activation or repression of a TAD when their activities were defined by the number of regions gaining and losing MED1 and BRD4 following dexamethasone (Dex) stimulation. Variations in Dex-responsive genes at the RNA levels were consistent with the redistribution of MED1 and BRD4 at the associated cis-regulatory regions. Interestingly, Dex-responsive genes without the differential recruitment of MED1 and BRD4 or binding by the glucocorticoid receptor were found within TADs, which gained or lost MED1 and BRD4, suggesting a role of the surrounding environment in gene regulation. However, the amplitude of the response of Dex-regulated genes was higher when the differential recruitment of the glucocorticoid receptor and transcriptional coregulators was observed, reaffirming the role of transcription factor-driven gene regulation and attributing a lesser role to the TAD environment. These results support a model where a signal-induced transcription factor induces a regionalized effect throughout the TAD, redefining the notion of direct and indirect effects of transcription factors on target genes.

overall_design: Genome-wide binding of transcriptional coregulators (MED1 and BRD4) in control and Dex-stimulated A549 cells

first: Christophe

last: Tav

first: Éric

last: Fournier

first: Michèle

first: Fatemeh

last: Khadangi

first: Audrey

last: Baguette

first: Maxime

middle: C

last: Côté

first: Maruhen

last: Silveira

first: Félix-Antoine

last: Bérubé-Simard

first: Guillaume

last: Bourque

first: Arnaud

last: Droit


title: Transgene-free direct conversion of murine fibroblasts into functional muscle stem cells


title: Single-Cell Analysis Reveals Cellular Reprogramming in Advanced Colon Cancer Following FOLFOX-Bevacizumab Treatment

status: Public on Jul 20 2023

city: Guangzhou

first: Meiling

last: Yang

address: No. 106, Zhongshan Road,Yuexiu District

institute: Guangdong Provincial People’s Hospital（Guangdong Academy of Medical Sciences）

summary: The combination of FOLFOX and bevacizumab (FOLFOX-Bev) is a promising treatment for advanced colorectal cancer (CRC). To gain insights into the cellular changes associated with FOLFOX-Bev treatment, we conducted single-cell transcriptomic analysis of CRC samples derived from a patient before and after treatment. Our results show that cancer cells with high proliferative, metastatic, and pro-angiogenic properties respond better to FOLFOX-Bev treatment. Moreover, FOLFOX-Bev enhances CD8+ T cell cytotoxicity, thereby boosting the anti-tumor immune response. Conversely, FOLFOX-Bev impairs the functionality of tumor-associated macrophages, plasma cells, and cancer-associated fibroblasts, leading to a decrease in VEGFB-mediated angiogenesis. Furthermore, FOLFOX-Bev treatment reset intercellular communication, which could potentially affect the function of non-cancer cells. Our findings provide valuable insights into the molecular mechanisms underlying the response of advanced CRC to FOLFOX-Bev treatment and highlight potential targets for improving the efficacy of this treatment strategy.

overall_design: The primary biopsy samples from advanced colon cancer patient before and after FOLFOX-bevacizumab therapy were used for single-cell RNA sequencing by 10X Genomics.

first: Wei

last: Zhao

first: Dongyang


title: Inosine enhances mitochondria respiration to promote cancer survival under starvation

first: Li

last: Mei-Xin

address: College of Life Science, Wuhan University, Luojiashan Road, Wuchang District, Wuhan City, Hubei Province, China

institute: Wuhan University

summary:
To investigate mechanism of inosine promotes the survival and metabolism of MDA-MB-231 cells under starvation conditions, MDA-MB-231 cells were treated with inosine and glucose for 12h  under starvation conditions.
We then performed gene expression profiling analysis using data obtained from RNA-seq of MDA-MB-231 cells under three different treatments（-G-Q,Inosine,Glucose）.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDA-MB-231 cells under three different treatments（-G-Q,Inosine,Glucose）.

first: Mei-Xin

last: Li

first: Xiaoting

last: Wu

first: Wenqiang

last: Jing

last: Yan


title: Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils [RNA-seq]

first: Alexandra

last: Zezulin

overall_design:
Examination of transcriptome, chromatin accessibility, and histone modifications in RUNX1 mouse deficient GMPs and neutrophils, and patient neutrophils.
Please note that the  processed data file (generated from all replicates) is linked to the corresponding *_A sample records.

first: Elizabeth

last: Howell

first: Darwin

last: Ye

first: Kai

last: Tan

first: Wenboa

last: Yu

first: Nancy

last: Speck


title: Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transgene-free direct conversion of murine fibroblasts into functional muscle stem cells [scRNA]

first: Adhideb

last: Ghosh

overall_design: Global transcriptional analysis of stable iMPCs clones derived from synthetic MyoD-mRNA with treatment of the small molecule cocktails containing F/R/C or F/R/C+CP.

first: Xhem

last: Qabrati

first: Inseon

last: Kim

first: Falko

last: Noé

first: Ori

last: Bar-Nur


title: Dynamic nucleosome remodeling mediated by YY1 underlies early mouse development

status: Public on Jul 16 2023

city: Kofu

first: Mizuki

last: Sakamoto

institute: University of Yamanashi

summary: Nucleosome positioning can alter the accessibility of DNA-binding proteins to their cognate DNA elements, and thus its precise control is essential for cell identity and function. Mammalian preimplantation embryos undergo temporal changes in gene expression and cell potency, suggesting the involvement of dynamic epigenetic control during this developmental phase. However, the dynamics of nucleosome organization during early development are poorly understood. In this study, using a low-input MNase-seq method, we show that nucleosome positioning is globally obscure in zygotes but becomes well defined during subsequent development. Downregulation of the chromatin assembly in embryonic stem cells can partially reverse nucleosome organization into a zygote-like pattern, suggesting that the chromatin assembly pathway might be linked to fuzzy nucleosomes in zygotes. We also reveal that YY1, a zinc finger containing transcription factor expressed upon zygotic genome activation, regulates the de novo formation of well-positioned nucleosome arrays at the regulatory elements, through identifying YY1-binding sites in 8-cell embryos. The YY1-binding regions acquire H3K27ac enrichment around the 8-cell and morula stages and YY1 depletion impairs the morula-to-blastocyst transition. Thus, our study delineates the remodeling of nucleosome organization and its underlying mechanism during early mouse development.

overall_design: Low-input MNase-seq, RNA-seq, and CUT&RUN have been performed for mouse early embryos and ESCs.

first: Takashi

last: Ishiuchi


title: Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils [ATAC-seq]

overall_design:
Examination of transcriptome, chromatin accessibility, and histone modifications in RUNX1 mouse deficient GMPs and neutrophils, and patient neutrophils.
Please note that each processed data file was generated from both A and B replicates, and is linked to the corresponding *_A sample records.


title: The non-redundant functions of PIWI family proteins in gametogenesis in golden hamsters

city: Shanghai

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

type: Non-coding RNA profiling by high throughput sequencing

summary: The piRNA pathway is essential for female fertility in golden hamsters and likely humans, but not in mice. However, the role of individual PIWIs in reproduction remains poorly understood outside of mice. Here, using golden hamsters, we establish dynamic expression profiles and subcellular localization for all four PIWIs and characterize their associated reproductive defects in knockout mutants. In female golden hamsters, PIWIL1 and PIWIL3 are highly expressed throughout oogenesis and early embryogenesis, while PIWIL1 knockout leads to sterility, and PIWIL3 deficiency results in subfertility with lagging zygotic development. PIWIL1 can partially compensate for TE silencing and transcriptional regulation in PIWIL3 knockout females, but not vice versa. PIWIL1 and PIWIL4 are the predominant PIWIs expressed in adult or postnatal testes, respectively, while PIWIL2 is present in both stages. Notably, in golden hamsters, none of the differences were found between pre-pachytene and pachytene piRNAs characteristic of mice. Loss of any PIWI expressed in testes leads to sterility and severe but distinct spermatogenesis disorders, which are markedly less severe in mice. These findings expand our understanding of the non-redundant PIWI-piRNA regulatory functions in gametogenesis and early embryogenesis in golden hamster, increasing the value of this model for studying human fertility.

sample_organism:
Mesocricetus auratus
Mus musculus

platform_organism:
Mesocricetus auratus
Mus musculus

overall_design: Using golden hamsters, establish dynamic expression profiles and subcellular localization for all four PIWIs and characterize their associated reproductive defects in knockout mutants.

first: Xiaolong

last: Lv

first: Hongdao

last: Zhang

first: Ligang


title: Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils [Human ATAC-seq]

first: Alexandra

overall_design: Examination of transcriptome, chromatin accessibility, and histone modifications in RUNX1 mouse deficient GMPs and neutrophils, and patient neutrophils.


title: Whole genome tomato transcriptional response to Tetranychus evansi herbivory.

status: Public on Jul 10 2023

first: Vladimir

last: Zhurov

state: ON

address: 1151 Richmond Street

department: Biology

institute: University of Western Ontario

summary:
The red spider mite, Tetranychus evansi, is a oligophagous specialist mite pest of Solanaceae plants. Here, we described tomato transcriptional responses to T. evansi feeding and compared them to responses to tomato-adapted and -non-adapted strains of generalist herbivorous spider mite Tetranychus urticae.
We used microarray to assess global gene expression in Solanum lycopersicum cv. Heinz 1706 upon T. evansi attack.

overall_design: 1 month old tomato plants were subjected to Tetranychus evansi attack through application of 100 adult mites on a terminal leaflet of leaf 3 for 24 hours.

first: Marie

last: Navarro

first: Manuel

last: Martinez

first: Marc

last: Cazaux

first: Philippe

last: Auger

first: Alain

last: Migeon

first: Maria

middle: E

last: Santamaria

first: Nicky

last: Wybouw

first: Isabel

last: Diaz

first: Thomas

last: Van Leeuwen

last: Navajas

first: Miodrag

last: Grbic

first: Vojislava


title: Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils [H3K27ac ChIP-seq]

last: Zezulin

overall_design:
Examination of transcriptome, chromatin accessibility, and histone modifications in RUNX1 mouse deficient GMPs and neutrophils, and patient neutrophils.
Please note that the  processed data file (generated from both replicates) is linked to the corresponding *_IP1 sample records.

first: Elizabeth

last: Howell

first: Darwin

last: Ye

first: Kai

last: Tan

first: Wenboa

last: Yu

first: Nancy

last: Speck


title: Generation of patient-relevant p63 gene signature to identify novel oncogenes and tumor suppressors that contribute to HNSCC development and progression

city: Buffalo

first: Rose-Anne

last: Romano

address: 3435 Main Street

department: Oral Biology

institute: State University of New York at Buffalo

summary: To identify novel targets of p63 as part of a patient-centric meta analysis, we performed RNA-sequencing on control and p63-depleted cancer cells (A253 and SCC25). In addition, we performed ChIP-sequencing analysis using multiple p63-specific antibodies, as well as antibodies targeting specific histone modifications(H3K27ac,H3K4me3 and H3K4me1) to evaluate mechanism(s) by which p63 regulates these novel targets. Our analysis identified known and novel oncogenic factors that influence various aspects of cancer development and progression.

overall_design: 1. RNA-sequencing of A253 and SCC25 control, and p63 depleted cells. 2. p63 ChIP-Sequencing performed on control A253 and SCC25 cells 3. Histone ChIP-sequencing performed on control A253 and SCC25 cells

first: Akinsola

last: Oyelakin

first: Satrajit

last: Sinha


title: Hallmarks of CD8 T cell dysfunction are established within hours of tumor antigen encounter

city: Nashville

first: Mary

last: Philip

state: TN

address: 777 PRB, 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

summary: ATAC-SEQ analysis of antigen-specific CD8 T cells sorted from murine liver tumors and from the spleens of Listeria-infected mice at different early timepoints following adoptive transfer. We sequenced naive antigen-specific CD8 T cells from spleens for comparison. We also sorted tumor-infiltrating antigen-specific CD8 T cells that were removed from tumors and parked in tumor-free hosts for 5 days. The overall goal of this study was to determine the earliest chromatin remodeling events in CD8 T cells activated and differentiating in late tumor-bearing hosts or in infected mice and to determine the extent to which tumor-induced chromatin remodeling was "imprinted."

overall_design: CD8+CD90.1+ TAG-specific T cells were (1) sorted from murine liver tumors (TAG-expressing tumors) at 6, 12, and 24 hours and 5 and 10 days of exposure or (2) sorted from B6 mice spleens that had previously been adoptively transferred with tumor-exposed TAG-specific T cells removed from tumors after 24 hours, 5 days, and 10 days or (3) sorted from spleens of Listeria-TAG infected mice at 6, 12, and 24 hours of antigen exposure or (4) sorted from spleens of transgenic TCRTAG mice and ATAC-SEQ was performed.

first: Michael

middle: W

last: Rudloff


summary: RNA-SEQ analysis of antigen-specific CD8 T cells sorted from murine liver tumors and from the spleens of Listeria-infected mice at different early timepoints following adoptive transfer. We sequenced naive antigen-specific CD8 T cells from spleens for comparison.

overall_design: CD8+CD90.1+ TAG-specific T cells (1) sorted from murine liver tumors (TAG-expressing tumors) at 6, 12, and 24 hours or (2) sroted from spleens of Listeria-TAG infected mice at 6, 12, and 24 hours of antigen exposure or (3) sorted from spleens of transgenic TCRTAG mice, and RNA-SEQ was performed.


title: Microarray expression data of E7386-treated HSC3 cells

city: Medford

first: Eric

middle: R

last: Reed

state: MA

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

summary: E7386 inhibits interaction between B-catenin and CREB-binding protein (CBP), which drives oncogenic gene expression and aggressive cancer phenotypes in oral squamous cell carcinomas (OSCC). We use microarrays to profile the effects of E7386 treatment on gene expression of HSC3 human OSCC cells.

overall_design: Three separate wells (triplicate) in 6-well plates were seeded with HSC3 cells (at 5 × 104/well). After 12–24 hours (ie, ∼ 50% confluency), the cells were treated with either 0.1% dimethyl sulfoxide (DMSO) or 0.1 μM E7386 in DMSO. After 48–64 h, the cells were trypsinized and harvested for RNA purification using the miRNeasy Micro Kit (QIAGEN no. 217084).

first: Stefano

last: Monti

last: Kukuruzinska

first: Xaralabos

last: Varelas


title: A lignin-derived material improves plant nutrient bioavailability and growth through its metal chelating capacity

status: Public on Jul 04 2023

city: Hangzhou

first: Qiang

last: Liu

state: Zhejiang

address: Xihu District, Yuhangtang road 866

department: College of Environmental & Resource Science

institute: Zhejiang University

summary:
To pinpoint the molecular and biological processes that are targeted by HSAL and lead to enhanced root growth in nutrient poor environments.
We performed a genome-wide transcript analysis of the root tip of 7-day-old seedlings treated with or without HSAL for 12 h using RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the Oryza Sativa L root tip of 7-day-old seedlings treated with or without HSAL for 12 h.

first: Baohai

last: Li

first: Tsubasa

last: Kawai

first: Yoshiaki

last: Inukai

first: Zhihang

last: Feng

first: Yasuyuki

last: Matsushita


title: Chronic pulmonary bacterial infections facilitate breast cancer lung metastasis with tumor-promoting MHCIIhi neutrophils II

city: Chengdu

first: Teng

last: Ma

address: No.17 People's South Road

institute: sichuan university

summary: In order to explore whether the tumor-promoting phenotype of MHCIIhi neutrophils was directly affected by bacterial chronic infection, we isolated MHCIIhi neutrophils cells from the lungs of both of CI tumor-bearing mice and CTRL tumor-bearing mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MHCIIhi neutrophils isolated from the lungs of both of CI tumor-bearing mice and CTRL tumor-bearing mice.

first: Taolin

last: Wang

first: Yang

last: Yang

first: Yu

last: Tang


title: Chronic pulmonary bacterial infections facilitate breast cancer lung metastasis with tumor-promoting MHCIIhi neutrophils

summary: To investigate whether MHCIIhi neutrophils have tumor-promoting properties, we performed RNA-sequencing (RNA-seq) on MHCIIhi neutrophils and MHCIIlow neutrophils isolated from the lung and peripheral blood of tumor-bearing mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MHCIIhi neutrophils and MHCIIlow neutrophils (LP, LN, BP)


title: Effect of pulmonary hypertension due to left heart disease on gene expression in pulmonary arteries

status: Public on Jul 03 2023

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Pulmonary hypertension worsens outcome in left heart disease. Stiffening of the pulmonary artery may drive this pathology by increasing right ventricular dysfunction and lung vascular remodeling. We showed that pulmonary arteries from patients with left heart disease are characterized by increased stiffness that correlates with impaired pulmonary hemodynamics. Pulmonary arteries in left heart disease patients with pulmonary hypertension were characterized by degradation of elastic fibers paralleled by an accumulation of fibrillar collagens. We utilized RNA sequencing to identify differentially expressed genes regulating extracellular matrix remodeling in pulmonary arteries of left heart disease patients with or without pulmonary hypertension, in comparison to healthy-heart donor controls. As such we identified that transcriptional deregulation of extracellular matrix constituents and their regulators precedes clinical pulmonary hypertension, and therefore might be a pathomechanism that drives pulmonary arterial remodeling and stiffening in left heart disease.

overall_design: To identify genes that are differentially expressed in pulmonary arteries of left heart disease patients without or with pulmonary hypertension (LHD w/o PH or PH-LHD respectively), in comparison to healthy-heart controls (donor), human pulmonary trunk samples were collected during heart transplantation and snap-frozen in liquid nitrogen, followed by TRIzol-RNA extraction and bulk RNA sequencing.

first: Mariya

last: Kucherenko

first: Orr

last: Shomroni

first: Christoph

last: Knosalla


title: MiR-16 and miR-519 suppress tumor cell proliferation in meningiomas via HuR inhibition

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

country: France

institute: INSERM

summary:
We investigated the relative expression levels of these miRs in a series of meningioma and normal meningeal tissues. The effects of miR-16 and miR-519 on cell growth and transcriptome were assessed in vitro using two human cell lines (Ben-Men-1 and IOMM-Lee).
Both miR-16 and miR-519 were significantly downregulated in meningioma compared with normal meningeal tissue. Overexpression of either miR in IOMM-Lee and Ben-Men-1 cells significantly reduced cell growth. The transfection of miR-16 and miR-519 significantly downregulated HuR mRNA, and genes involved in various functions such as pre-replicative complex, mitotic recombination, S phase and M phase of cell cycle, and upregulated genes implicated in cell junction, and positive regulation of cell death. Cell-cycle-related genes associated cluster included HuR mRNA (ELAVL1), and was highly enriched with HuR gene targets.

overall_design: IOMM-Lee cells transfected with either miR Mimic hsa-miR-16-5p (miR16 ; n=6 ; biological replicates), miR Mimic hsa-miR-519a-3p (miR519 ; n=6 ; biological replicates) and mirVana miR Mimic Negative Control (ctrl ; n=6 ; biological replicates).

first: Sébastien

first: Guillaume

last: Gauchotte

first: Shyue-Fang

last: Battaglia-Hsu

first: Jean-Matthieu

last: Casse


title: Arid1a is essential in cardiomyocytes for neonatal heart maturation

status: Public on Jul 05 2023

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

institute: Hubrecht Institute

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

overall_design: Refer to individual Series


title: Remote neuronal activity drives glioma progression via Sema4F

status: Public on Jun 30 2023

city: HOUSTON

first: emmet

last: huang-hobbs

state: TX

address: 1 baylor plaza, N1120

department: CAGT

institute: Baylor College of Medicine

summary: The goal of the study was to find the effect of neural stimulation via DREADDs in a distal site from tumor, then comparing these results to Semaphorin-4F gain of function tumors. Saline treated tumors were used as a control

overall_design: mice were treated with CNO or Saline for 30 days post weaning and tumors were harvested at 50 days

first: Yi-Ting

last: Cheng

first: Emmet

last: Huang-Hobbs

first: Benjamin

last: Deneen


title: Immune landscape of mouse heart in steady state

status: Public on Jul 01 2023

city: Saint Louis

first: Pan

last: Ma

state: United States

address: CSRB, Room 9918, 425 S Euclid, Saint Louis, MO, 63110

institute: Washington University in Saint Louis

summary: To reveal the cardiac  immune landscape of mouse heart in steady state, we performed single-cell RNA-sequencing (scRNA-seq) with heart tissue from wide type mice and immune subsets were analyzed to reveal cardiac immune features.

overall_design: We performed single-cell RNA-sequencing (scRNA-seq) with heart tissue from wide type C57BL/6 mice (n=6). We constructed one library with CD45+DAPI- cells purified from pooled enzymatically digested hearts by FACS.

first: Jesus

last: Jimenez

first: Kory

last: Lavine


title: Transcriptomic analysis of the effects of expression of CDK8/CDK19 and their kinase-inactive mutants in HEK293 cells (WT) and their CDK8/19 double-knockout (dKO) derivatives

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: RNA-Seq analysis was carried out to investigate the effects of expression of wild-type CDK8 (CDK8) or CDK19 (CDK19) or their kinase-inactive D173A mutants (CDK8M and CDK19M) in HEK293 cells (WT) and their CDK8/19 double-knockout (dKO) derivatives

overall_design: Two different sets of the re-expression derivatives of dKO cells generated with pHIV-dTomato or pHIV-luc-Blast based lentiviral constructs (dKO-V, dKO-8, dKO-8M, dKO-19 and dKO-19M; dKO-V_2, dKO-8_2, dKO-8M_2, dKO-19_2 and dKO-19M_2) and a set of the over-expression derivatives of WT cells generated with pHIV-luc-Blast based lentiviral constructs (WT-V, WT-8, WT-8M, WT-8M, WT-19 and WT-19M) were analyzed by RNA-Seq for transcriptomic profiles under regular culture condition. Each condition (expression derivative) was done in biological triplicate or more.

first: Mengqian

last: Chen

first: Hao

last: Ji

first: Igor

last: Roninson


title: Transcriptomic changes in cervical cells during the menstrual cycle are evident but insufficient to predict window of implantation

status: Public on Jul 09 2023

city: tartu

first: Maire

last: Peters

department: Dept. of Obstetrics and gynecology

country: Estonia

institute: University of Tartu

summary: Current endometrial receptivity tests require an invasive method of collecting of endometrial biopsies that can cause general discomfort and adverse events such as infections, pain, and bleeding. Therefore, minimally-invasive methodologies for receptivity evaluation are needed. Cervical cells could offer a great potential for endometrial receptivity testing because cervical cell collection by cytobrush is a standardized, quick, simple, well tolerated, minimally invasive and routinely used sampling technique in everyday gynaecological practice. To date, no studies have evaluated the suitability of cervical cells for endometrial receptivity testing based on transcriptional profiling throughout the menstrual cycle. In this study, paired samples of the endometrium and cervical cells were obtained from 20 women in different menstrual cycle time-points in natural cycles and women undergoing hormonal replacement cycles. The gene expression profiles of cervical cells showed no apparent clustering according to their collection time and menstrual cycle phase. Transcriptome analysis identified only four (KIF2C, CENPF, HLA-DRB5 and CUTALP) differentially expressed genes between the early- and mid-secretory samples, suggesting that the transcriptomes of cervical cells, in contrast to endometrial tissue, do not exhibit significant differences during the window of implantation opening. The largest differences in the transcriptome of cervical cells were noticed in late-secretory phase, before initiation of menstruation. The results of our study suggested that cervical cells’ transcriptome does not reflect the gene expression pattern of endometrial tissue during the WOI and these cells offer little or no potential for endometrial receptivity diagnostics.

overall_design: Cervical cells from healthy women from proliferative phase (n=3), two days after luteinizing hormone (LH) peak (n=4), seven days after LH peak (n=5),  eleven days after LH peak (n=3)  and from hormone replacement cycle, after 5 days of progesterone (P4) administration were analyzed using RNA-seq.

first: Amruta

last: Pathare

first: Merli

last: Saare

first: Alvin

last: Meltsov

first: Ankita

last: Lawarde

first: Vijayachitra

last: Modhukur

first: Aive

last: Kalinina

first: Aire

last: Sekavin

first: Viktorija

last: Kukushkina

first: Helle

last: Karro

first: Andres

last: Salumets


title: Effects of CDK8/19 mediator kinase inhibition by Senexin B in HAP-1 cells treated with or without interferon-gamma

summary: RNA-Seq analysis was carried out to investigate the effects of selective CDK8/19 inhibitor Senexin B on gene transcription mediated by IFN-gamma signaling pathway in HAP-1 cells.

overall_design: HAP-1 cells were pre-treated with or without 1 μM Senexin B for 1 hour, followed by treatment with or without 10ng/mL IFN-gamma for 4 hours. Each treatment condition was done in biological triplicate.


title: Hallmarks of CD8 T cell dysfunction are established within hours of tumor antigen encounter prior to cell division

first: Mary

last: Philip


title: Effects of CDK8/19 mediator kinase inhibition by didehydrocortistatin A (dCA) and 15w on gene expression in HEK293 cells

summary: RNA-Seq analysis was carried out to investigate the effects of selective CDK8/19 inhibitor didehydrocortistatin A (dCA) and 15w on gene expression in HEK293 cells (293-WT) or the CDK8/19 double-knockout (293-dKO) derivatives.

overall_design: 293-WT and 293-dKO cells were treated with 0.1% DMSO, 1 μM dCA or 1 μM 15w for 72 hours. Each treatment condition was done in biological triplicate.


title: Effects of CDK8/19 Mediator Kinase inhibition by Senexin B on gene expression in HEK293 cells

summary: RNA-Seq analysis was carried out to investigate the effects of selective CDK8/19 inhibitor Senexin B on gene expression in HEK293 cells (293-WT) or the CDK8/19 double-knockout (293-dKO) derivatives.

overall_design: 293-WT or 293-dKO cells were treated with 0.1% DMSO (vehicle control) or 1 μM Senexin B for 24 or 72 hours. Each treatment condition was done in biological triplicate.


title: Effects of inhibition of CDK8/19 mediator kinase on signal-regulated gene expression in 293 cells (treated with PMA for 24 hours)

summary: We have investigated the effects of CDK8/19 inhibitor Senexin B on the gene expression regulated by PMA 24hr-treatment in 293 cells.

overall_design: HEK293 cells were treated with vehicle control (0.1% DMSO), 1 μM Senexin B, 30nM PMA or combination for 24 hours. Each treatment condition was done in biological triplicate.


title: Differential Expression Spectrum  of tRNA-Derived small RNAs in Idiopathic Pulmonary Arterial Hypertension

city: Changsha

first: Yusi

state: Hunan

address: 139 Renmin Road

institute: The Second Xiangya Hospital of Central South University

summary: Microarray detected 816 statistically differentially expressed tsRNAs, of which 243 tsRNAs were upregulated and 573 were downregulated. Eight validated tsRNAs in the results of Real Time-PCR were consistent with the small RNA microarray: four upregulations (tRF3a-AspGTC-9, 5'tiRNA-31-GluCTC-16, i-tRF-31:54-Val-CAC-1 and tRF3b-TyrGTA-4) and four downregulation (5'tiRNA-33-LysTTT-4, i-tRF-8:32-Val-AAC-2, i-tRF-2:30-His-GTG-1, and i-tRF-15:31-Lys-CTT-1).

overall_design: Small RNA microarray was implemented on three pairs of plasma of IPAH patients and healthy controls to investigate and compare tsRNAs expression profiles.

last: chen

first: Jiang

last: Li


title: Effects of Inhibition of CDK8/19 Mediator Kinase on serum-regulated gene expression in 293 cells

first: HAO

last: JI

summary: We have investigated the effects of CDK8/19 inhibitor Senexin B on the gene expression regulated by serum stimulation in 293 cells

overall_design: HEK293 cells were serum starved for 48 hrs and then treated with serum (FBS added to 10% final concentration) for 30 min.  Serum-starved cells were pre-treated with or without 1 μM Senexin B for 1 hour, followed by 30 min serum stimulation. Each treatment condition was done in biological triplicate.

first: Mengqian

last: Chen


title: spinDrop: a modular droplet microfluidic platform to maximise single-cell RNA sequencing information content

status: Public on Jul 02 2023

city: Cambridge

first: Florian

last: Hollfelder

address: 80 tennis court road

institute: University of Cambridge

summary: Droplet microfluidic methods have massively increased the throughput of single-cell RNA sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples as well as lower overall RNA capture efficiency. These drawbacks stem from the lack of strategies to enrich for high-quality material at the moment of cell encapsulation and the lack of implementable multi-step enzymatic processes that increase RNA capture. Here we alleviate both bottlenecks by deploying fluorescence-activated droplet sorting to enrich for droplets that contain single viable cells, intact nuclei or fixed cells and use reagent addition to droplets by picoinjection to perform multi-step lysis and reverse transcription. Our methodology increases gene detection rates fivefold, while reducing background noise by up to half, depending on sample quality. We harness these unique properties to deliver a high-quality molecular atlas of mouse brain development using highly damaged input material. Our method is broadly applicable to other droplet-based workflows to deliver sensitive and accurate single-cell profiling at a reduced cost.

overall_design: Mouse ES, HEK293T cells and mouse embryonic brain sections at stage E10.5 were dissociated and processed for single-cell RNA-sequencing using the spinDrop workflow.

first: Joachim

last: De Jonghe

first: Tomasz

last: Kaminski


title: Single-cell multiomic analysis of thymocyte development reveals drivers of CD4+ T cell and CD8+ T cell lineage commitment

city: Berkeley

first: Zoë

last: Steier

address: 378 Stanley Hall

institute: UC Berkeley

summary: The development of CD4+ T cells and CD8+ T cells  in the thymus is critical to adaptive immunity and is widely studied as a model of lineage commitment. Recognition of self-MHCI or MHCII by the T cell antigen receptor (TCR) determines the CD8+ T cell or CD4+ T cell lineage choice, respectively, but how distinct TCR signals drive transcriptional programs of lineage commitment remains largely unknown. Here we applied CITE-seq to measure RNA and surface proteins in thymocytes from wild-type and T cell lineage-restricted mice to generate a comprehensive timeline of cell state for each T cell lineage. These analyses identified a sequential process whereby all thymocytes initiate CD4+ T cell lineage differentiation during an initial wave of TCR signaling, followed by a second TCR signaling wave that coincides with CD8+ T cell lineage specification. CITE-seq and pharmaceutical inhibition experiments implicated a TCR-calcineurin-NFAT-GATA3 axis in driving the CD4+ T cell fate. Our data provide a resource for understanding cell fate decisions and implicate multiple redundant mechanisms in guiding lineage choice.

overall_design: CITE-seq with a panel of 111 antibodies was performed on cells from the thymus of wild-type and lineage-restricted mice at age 4-8 weeks. Each of 19 samples was processed in a separate lane of 10x Chromium. Samples included six lineage-restricted mouse genotypes (two biological replicates each) and wild-type mice (five biological replicates processed in seven samples). 72,042 cells were captured across all samples.

first: Dominik

last: Aylard

first: Laura

middle: L

last: McIntyre

first: Isabel

last: Baldwin

first: Esther

last: Kim

first: Lydia

middle: K

last: Lutes

first: Can

last: Ergen

first: Tse-Shun

last: Huang

first: Ellen

last: Robey

first: Nir

last: Yosef

first: Aaron

last: Streets


title: Effects of inhibition of CDK8/19 mediator kinase on signal-regulated gene expression in 293 cells (treated with PMA for 2 hours)

summary: RNA-Seq analysis was carried out to investigate the effects of CDK8/19 inhibitor Senexin B on the gene expression regulated by 2hr-treatment with PMA in 293 cells.

overall_design: HEK293 cells were pre-treated with or without 1 μM Senexin B for 1 hour, followed by treatment with or without 30nM PMA for 2 hours. Each treatment condition was done in biological triplicate.

first: Hao

last: Ji

first: Igor

last: Roninson


title: Transcriptomic and Proteomic Effects of CDK8 and CDK19 Mediator Kinases

first: HAO

last: JI


title: Multi-Omic Analysis of CIC’s Functional Networks Reveals Novel Interaction Partners and a Potential Role in Mitotic Fidelity

status: Public on Jun 29 2023

city: Vancouver

first: Marco

last: Marra

state: BC

address: 675 W 10th Ave, 7th Floor

institute: Canada's Michael Smith Genome Sciences Centre

summary: CIC encodes a transcriptional repressor and MAPK signalling effector that is inactivated by loss-of-function mutations in several cancer types, consistent with a role as a tumour suppressor. Here, we used bioinformatic, genomic, and proteomic approaches to investigate CIC’s interaction networks. We observed both previously identified and novel candidate interactions between CIC and SWI/SNF complex members, as well as novel interactions between CIC and cell cycle regulators and RNA processing factors. We found that CIC loss is associated with an increased frequency of mitotic defects in human cell lines and an in vivo mouse model and with dysregulated expression of mitotic regulators. We also observed aberrant splicing in CIC-deficient cell lines, predominantly at 3′ and 5′ untranslated regions of genes, including genes involved in MAPK signalling, DNA repair, and cell cycle regulation. Our study thus characterises the complexity of CIC’s functional network and describes the effect of its loss on cell cycle regulation, mitotic integrity, and transcriptional splicing, thereby expanding our understanding of CIC’s potential roles in cancer. In addition, our work exemplifies how multi-omic, network-based analyses can be used to uncover novel insights into the interconnected functions of pleiotropic genes/proteins across cellular contexts.

overall_design: Single-cell RNA-seq profiles of CIC wild type and CIC knockout NHA cells

first: Yuka

last: Takemon

first: Veronique

middle: G

last: LeBlanc

first: Jungeun

last: Song

first: Susanna

middle: Y

last: Chan

first: Stephen

last: Lee

first: Diane

last: Trinh

first: Shiekh

middle: T

last: Ahmad

first: William

last: Brothers

first: Richard

last: Corbett

first: Alessia

last: Gagliardi

first: Annie

last: Moradian

first: J

last: Cairncross

last: Yip

first: Jennifer

first: Christopher

middle: S

last: Hughes

first: Gregg

last: Morin

first: Sharon

last: Gorski

first: Suganthi

last: Chittaranjan


title: Transcriptomic analysis reveals distinct adaptive molecular mechanism in the hippocampal CA3 from rats susceptible or not-susceptible to hyperthermia-induced seizures

status: Public on Jun 28 2023

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: This study aimed to identify the genomic differences - through differential gene expression, miRNAs, and WGCNA transcriptional modules among animals with or without seizure after insult and non-insulted controls.

overall_design: Use of a rat (Rattus norvegicus) model of hyperthermia-induced seizure to characterize the genomic mechanism underlying febrile seizures in epilepsy. The aim of the study is to identify the genomic differences in hippocampal ventral CA3 region - through differential gene expression, miRNAs, and WGCNA transcriptional modules among animals with (HS) or without (HNS) seizure after insult and non-insulted controls (CT). Here, samples from the animal of all groups in the P60 time-interval.

first: Silvia

last: Bando

first: Fernanda

middle: B

last: Bertonha

first: Pedro

middle: H

last: Menezes

first: André

last: Takahara

first: Nathália

middle: A

last: Khaled

first: Paula

last: Santos

first: Mara

last: Junqueira

first: Roberto

middle: M

last: Cesar Jr


summary: Here we conducted a temporal analysis of the transcriptomic and microRNA changes in the ventral CA3 of rats that develop (HS group) or not-develop (HNS group) seizures after hyperthermic insult on the eleventh postnatal day. The selected time intervals corresponded to acute, latent, and chronic phases of the disease.


overall_design: Use of a rat (Rattus norvegicus) model of hyperthermia-induced seizure to characterize the genomic mechanism underlying febrile seizures in epilepsy. The aim of the study is to identify the genomic differences in hippocampal ventral CA3 region - through differential gene expression, miRNAs, and WGCNA transcriptional modules among animals with (HS) or without (HNS) seizure after insult and non-insulted controls (CT). Here, samples from the animal of all groups in the P120 time-interval.


title: Fast single-cell joint analysis of histone modifications and transcriptome by Droplet Paired-Tag

city: La Jolla

first: Yang

last: Xie

address: Rm.2071, 9500 Gilman Dr

department: Department of Cellular and Molecular Medicine

institute: UC San Diego

summary: Analysis of histone modifications at single-cell resolution can provide insights into the cellular heterogeneity in activity states of regulatory elements. However, current methods are hindered by lengthy procedures and insufficient sensitivity. Here we present Droplet Paired-Tag, a microfluidic cell barcoding-based method for fast and robust joint analysis of histone modifications and gene expression from single cells. We applied Droplet Paired-Tag to mouse brain and demonstrated its utility in accurately identifying active or repressive regulatory elements, and resolving the dynamic interactions between candidate regulatory elements and putative target genes.

overall_design: Combined analysis of RNA and histone modifcations in single-cells

first: Bing

last: Ren


title: Developmental emergence of cortical neurogliaform cell diversity

city: Geneva

first: Denis

last: Jabaudon

state: Geneva

address: Centre Medical Universitaire, Rue Michel Servet 1

department: Department of Basic Neurosciences

institute: Geneva University

summary: GABAergic interneurons are key regulators of cortical circuit function. Among the dozens of reported transcriptionally distinct subtypes of cortical interneurons, neurogliaform cells (NGC) are unique: are recruited by long-range excitatory inputs and the primary source of slow cortical inhibition. Despite their functional importance, the developmental emergence and cellular diversity of NGCs remains unclear. Here, combining single-cell transcriptomics, genetic fate-mapping, electrophysiological morphological characterization, we reveal that discrete molecular subtypes of NGCs, with distinctive functional and anatomic profiles, populate the neocortex. Furthermore, we show that NGC subtypes emerge gradually through development, as incipient differential molecular signatures are apparent in Preoptic Area (POA) born NGC precursors. By identifying NGC developmentally-conserved transcriptional programs, we report that the transcription factor Tox2 constitutes an identity hallmark across NGC subtypes. Using CRISPR-Cas9-mediated genetic loss-of-function, we show that Tox2 is critical for NGC development: POA-born cells lacking Tox2 fail to differentiate into NGCs. Together, these results reveal that NGCs are born from a spatially restricted pool of Tox2+ POA precursors, after which intra-type diverging molecular programs are gradually acquired post-mitotically and result in functionally and molecularly discrete NGC cortical subtypes.

overall_design: Two scRNA-seq collection types were used: microfluidic-based scRNA-seq for experiments involving FACS (P15, P30 and E14.5 Hmx3-Cre::Htr3a-GFP; R26R-tdTOMfl/fl ; E14.5 FlashTag) and droplet-based for experiments on WT cells (E14.5). For each time-point, several biological replicates where included (3 to 5). Analyzed cell populations include diverse subtypes of interneurons at several ages and differentiation stages.

first: Lucia

last: Gomez

first: Christelle

last: Cadilhac

first: Julien

last: Prados

first: Nand

last: Mule

first: Alexandre

last: Dayer


first: Carlos

last: Moreira-Filho

overall_design: Use of a rat (Rattus norvegicus) model of hyperthermia-induced seizure to characterize the genomic mechanism underlying febrile seizures in epilepsy. The aim of the study is to identify the genomic differences in hippocampal ventral CA3 region - through differential gene expression, miRNAs, and WGCNA transcriptional modules among animals with (HS) or without (HNS) seizure after insult and non-insulted controls (CT). Here, samples from the animal of all groups in the P12 time-interval.


title: Arid1a is essential in cardiomyocytes for neonatal heart maturation [RNA-seq]

status: Public on Jul 06 2023

first: Cornelis

last: Boogerd

summary: Adult mammalian hearts do not regenerate following ischemic injury, causing permanent damage to the myocardium, often leading to heart failure. In contrast, neonatal mouse hearts can fully regenerate after injury, however this ability is lost shortly after birth. Loss of regenerative capacity coincides with profound changes in the epigenetic landscape. Yet, the mechanisms controlling cardiomyocyte proliferation remain poorly understood.     To identify epigenetic mechanisms that underlie cardiomyocyte regeneration in response to ischemic injury, we subjected mice to sham or ischemia-reperfusion injury (IR) and performed RNA-Seq at multiple timepoints after injury. Multiple SWI/SNF chromatin remodeling complex subunits were upregulated after IR, including the AT-rich interactive domain-containing protein 1A (Arid1a), which has previously been implicated in tissue regeneration. Here, we show that Arid1a is abundantly expressed in cardiomyocytes during development, and is reactivated in a subset of adult cardiomyocytes after IR. Moreover, ARID1A is highly expressed in cardiomyocytes in human failing hearts, suggesting an important function in injury response.    Cardiomyocyte-specific Arid1a ablation in neonatal mice induced  cardiomyocyte hyperplasia, and severe cardiac enlargement at 2 weeks of age. Arid1a mutant hearts display increased expression of key cell cycle genes. Using ChIP-Seq and protein interaction studies we show that Arid1a functionally interacts with HIPPO signaling, thereby regulating neonatal cardiomyocyte proliferation. Furthermore, suppression of Arid1a in adult cardiomyocytes after IR induced cell cycle activity in border zone cardiomyocytes.  These data suggest that Arid1a regulates cardiomyocyte proliferation and function. Upregulation of Arid1a in cardiomyocytes after injury may  suppress proliferation and regeneration. Modulation of ARID1A after ischemic injury may be a novel therapeutic target to enhance cardiac regeneration.

overall_design: RNA-Seq on aMHC-Cre;Arid1a cKO and littermate control cardiac ventricles at postnatal day 7 (P7)

middle: J


overall_design: Use of a rat (Rattus norvegicus) model of hyperthermia-induced seizure to characterize the genomic mechanism underlying febrile seizures in epilepsy. The aim of the study is to identify the genomic differences in hippocampal ventral CA3 region - through differential gene expression, miRNAs, and WGCNA transcriptional modules among animals with or without seizure after insult  and non-insulted controls (which would be impossible to study in humans). Here, samples from the animal with seizure.

first: Silvia

last: Bando

first: Fernanda

last: Bertonha


overall_design: Use of a rat (Rattus norvegicus) model of hyperthermia-induced seizure to characterize the genomic mechanism underlying febrile seizures in epilepsy. The aim of the study is to identify the genomic differences in hippocampal ventral CA3 region - through differential gene expression, miRNAs, and WGCNA transcriptional modules among animals with (HS) or without (HNS) seizure after insult and non-insulted controls (CT). Here, samples from the animal of all groups in the P30 time-interval.

first: Pedro

last: Menezes

first: André

last: Takahara


title: Arid1a is essential in cardiomyocytes for neonatal heart maturation [ChIP-seq]

overall_design: H3K27Ac ChIP-Seq on hearts of aMHC-Cre;Arid1a conditional mutant mice and control littermates


title: Drug-class specific gene-based MAPK sensitivity scores predict sensitivity to MAPK inhibitors in pediatric low-grade gliomas

status: Public on Jun 27 2023

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

summary: Pediatric low-grade gliomas (pLGG) have shown heterogeneous responses to MAPK inhibitors (MAPKi) in clinical trials. A predictive feature for stratification is needed to identify patients likely to benefit from MAPKi therapy. MAPK-related genes differentially regulated between MAPKi sensitive and non-sensitive cell lines from the Genomics of Drug Sensitivity in Cancer dataset identified class-specific MAPKi sensitivity gene signatures used to calculate the MAPKi sensitivity score (MSS) via single sample gene set enrichment analysis. The MSS discerned gliomas with varying MAPK alterations from those without, and was higher in pLGG compared to other pediatric CNS tumors. As in clinical trials, the MSS was heterogeneous within pLGGs with a common MAPK alteration. A positive correlation between the MSS and the predicted immune infiltration determined by the ESTIMATE signature was observed. The MSS therefore represents a potential tool for the stratification of pLGG patients, worth of further investigation in upcoming clinical trials. Our data could support a role of microglia in the response to MAPKi, warranting further validation.

overall_design: We examined the single-cell transcriptomes of pLGG tumors from six different patients. For this purpose, single-cell suspensions were prepared from fresh biopsy material, which were then subjected to droplet-based single-cell RNA sequencing (scRNA-seq) using Chromium Next GEM Single Cell 3' Technology by 10x Genomics.

first: Romain

last: Sigaud

first: Thomas

last: Albert

first: Caroline

last: Heß

last: Hielscher

first: Nadine

last: Winkler

first: Daniel

last: Münter

first: Florian

last: Selt

first: Diren

last: Usta

first: Jonas

last: Ecker

first: Angela

last: Brentrup

first: Martin

last: Hasselblatt

first: Christian

last: Thomas

first: Julian

last: Varghese

first: David

last: Capper

first: Ulrich

last: Thomale

first: Pablo

last: Driever

first: Michèle

last: Simon

first: Arend

last: Koch

first: Felix

last: Sahm

first: Stefan

last: Hamelmann

first: Nada

last: Jabado

first: Augusto

middle: F

last: Andrade

first: Antoinette

middle: N

last: Schouten-van Meeteren

first: Eelco

last: Hoving

first: Tilman

last: Brummer

last: van Tilburg

last: Pfister

first: Olaf

last: Witt

last: Jones

first: Kornelius

last: Kerl

first: Till

last: Milde


title: TET2 deficiency subverts tumor immunity [model 3]

status: Public on Jun 23 2023

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: To investigate the function of TET2 in the development of acute myeloid leukemia (AML), we performed gene expression profiling analysis using data obtained from RNA-seq of AML cells carrying Tet2+/+ versus Tet2-/-.

overall_design: We established NRAS/AE9a leukemic cells with bone marrow-derived hematopoietic stem cells from wildtype (WT) and Tet2-/- mice. We then performed comparative gene expression profiling analysis of RNA-seq for these AML cells obtained from in vivo study.

first: Yangchan

last: Li

first: Rui

last: Su

first: Lei

last: Dong


first: Carlos

last: Moreira-Filho

overall_design: Use of a rat (Rattus norvegicus) model of hyperthermia-induced seizure to characterize the genomic mechanism underlying febrile seizures in epilepsy. The aim of the study is to identify the genomic differences in hippocampal ventral CA3 region - through differential gene expression, miRNAs, and WGCNA transcriptional modules - among animals with or without seizure after insult  and non-insulted controls (which would be impossible to study in humans). Here, samples from the animal with seizure.

first: Silvia

last: Bando

first: Fernanda

last: Bertonha

first: Pedro

last: Menezes

first: André

last: Takahara

first: Nathália

last: Khaled

first: Paula

last: Santos

first: Mara

last: Junqueira

first: Roberto

last: Cesar Jr


title: TET2-mediated mRNA in tumor immunity [m5C]

summary: To investigate the function of TET2 as an mRNA m5C demethylase in the development of acute myeloid leukemia (AML), we conducted RNA bisulfite sequencing of mRNA samples enriched from AML cells carrying Tet2+/+ versus Tet2-/- with actinomycin D treatment at different time point.

overall_design: Total RNA extraction from WT and Tet2-null NRAS/AE9a cells was performed using TRIzol reagent and then was enriched for poly(A) + RNA using polyATract mRNA isolation system IV kit (Z5310, Promega) following manufacturer’s instructions. The purified RNA was then subjected to bisulfite treatment using EZ RNA Methylation Kit (R5002, Zymo Research). The converted RNA was then subjected to column-based purification and next-generation sequencing using Illumina HiSeq 2500 platform with 70 million single end reads per sample.

first: Xiaolan

last: Deng

first: Meilin

last: Xue


title: TET2-mediated mRNA in leukemia stemness maintanence and homing [RNA-Seq]

status: Public on Jun 22 2023

summary: To assess the potential effect of Tet2 on RNA stability, mRNA half-life profiling was performed on samples enriched from AML cells with Tet2+/+ or Tet2-/- genotypes, following treatment with actinomycin D at different time points.

overall_design: WT and Tet2-null NRAS/AE9a cells were treated with 5 µg/ml actinomycin D for 0h, 4 h, and 8 h. At each time point, cells were rapidly harvested and total RNA was extracted using TRIzol reagent. The RNA samples were subsequently subjected to sequencing on Illumina NovaSeq 6000 platform with a paired-end 150-base pair (bp) read length.


title: TET2-mediated mRNA in leukemia stemness maintanence and homing

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

overall_design: Refer to individual Series


title: RNA-seq of myelinating oligodendrocytes in Lmna wt and knockout mice

status: Public on Jun 21 2023

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: We showed that the composition of  the nucler lamina changes with the differentiation state of oligodendrocyte lineage cells, with Lamin B highly expressed in progenitor cells and Lamin A highly expressed in mature oligodendrocytes.  The  genetic deletion of Lmna in oligodendrocytes results in the onset of a progressive motor phenotype in adult mice. We performed RNA-Seq in myelinating oligodendrocytes expressing the reporter myelin marker NDRG1-EGFP ( Marechal et al., 2021) in the presence or absence of LMNA. The goal is to identify the transcriptome profile in mice LMNA ablated cells compared to the controls.

overall_design: Transcriptome profiles (bulk RNA-seq assay) in wild-type mice and knockdown LMNA mice.

first: Mathilde

last: Pruvost

first: Ipek

last: Selcen

first: Sarah

last: Moyon

first: Julia

last: Patzig


title: Transcriptomic Identification of Genes expressed in Invasive S. aureus Diabetes Foot Ulcer infection

city: New Haven

first: Taiwo

last: Agidigbi

state: Connecticut

address: 330 Cedar street, Orhtopeadic and rehabilitation, Yale college of medicine

department: Orthopaedics and Rehabilitation,

institute: Yale university

summary: Infection in diabetic foot ulcers (DFU) are one of the major complications associated with diabetic patients.  Staphylococcus aureus is the most common offending pathogen in patients with infected DFU. Previous studies have suggested application of species-specific antibodies against S. aureus for diagnosis and monitoring treatment response. Early and accurate identification of the main pathogen is critical for management of DFU infection. Understanding the host immune response against species-specific infection may facilitate diagnosis and suggest potential intervention options to promote healing infected DFUs. We sought to investigate evolving host transcriptome associated with surgical treatment of S. aureus infected DFU. This study compared the transcriptome profile of twenty-one patients with S. aureus infected DFU who underwent initial foot salvage therapy with irrigation and debridement followed by intravenous antibiotics therapy. Blood samples were collected at the recruitment (0-weeks) and 8-week after therapy to isolate peripheral blood mononuclear cells (PBMC). We analyzed the PBMCs expression of transcriptomes at two different time points (0 vs 8-week). Subjects were further divided into two groups at 8-week: healed (n=17, 80.95%) versus non-healed (n=4,19.05%) based on the wound healing status. DESeq2 differential gene analysis was performed. An increased expression of IGHG1, IGHG2, IGHG3 and IGLV3-21, IGLV6-57 were noted during active infection at 0-week compared to 8-week. Lysine and arginine-rich histones (HIST1H2AJ, HIST1H2AL, HIST1H2BM, HIST1H3B and HIST1H3G) were upregulated at the initial phase of active infection at 0-week. CD177 and RRM2 were also upregulated at the initial phase of active infection (0-week) compared to 8-week follow-up. Genes of heat shock protein members (HSPA1A, HSPE1, and HSP90B1) were high in not-healed compared to healed patients 8-week after therapy. The outcome of our study suggests that identification of genes evolution based on a transcriptomic profiling could be a useful tool for diagnosing infection, assessing severity and assess host-immune response to therapies.

overall_design: We analyzed forty-two (42) samples from twenty-one (n=21) S. aureus infected DFU patients who underwent surgical debridement/treatment. Infection status was clinically determined based on the assessment of twelve signs and symptoms. Wound healing status (size), presence of infection such as purulent exudate, erythema, pain, or offensive odor were documented at 0-week and at 8-week after initiation of therapy. In this study, n=17 (80.95%) patients clinically healed the infection at 8-weeks follow-up, whereas n=4 (19.05%) patients failed to heal. Those patients who failed to heal underwent repeat debridement or amputation. Analysis of our results was based on the comparison between 0-week and 8-week among patients that were healed (n=17) before and after antibiotics therapy; and comparison between healers (n=17) and non-healers (n=3) at 8-week after antibiotics therapy. One sample (n=1) was contaminated and was excluded from further analysis.

first: Hyuk-K

last: Kwon

first: James

last: Knight

first: Dejian

last: Zhao

first: Francis

last: Lee

first: Irvin

last: Oh


title: An integrated proteome and transcriptome of B cell maturation defines poised activation states of transitional and mature B cells

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

summary: During B cell maturation, transitional and mature B cells acquire cell-intrinsic features that determine their ability to exit quiescence and mount effective immune responses. Here we use label-free proteomics to quantify the proteome of B cell subsets from the mouse spleen and map the differential expression of environmental sensing, transcription, and translation initiation factors that define cellular identity and function. Cross-examination of the full-length transcriptome and proteome identifies mRNAs related to B cell activation and antibody secretion that are not accompanied by detection of the encoded proteins. In addition, proteomic data further suggests that the translational repressor PDCD4 restrains B cell responses, in particular those from marginal zone B cells, to a T-cell independent antigen. In summary, our molecular characterization of B cell maturation presents a valuable resource to further explore the mechanisms underpinning the specialized functions of B cell subsets, and suggest the presence of 'poised' mRNAs that enable expedited B cell responses.

overall_design: Splenic transitional (T)1, T2, marginal zone (MZ) and follicular (FoB) B cells were FACS sorted from C57BL/6 mice (n= 4 biological replicates), based on the expression of CD19, CD93, IgM, CD23 and CD21 extracellular markers. The RNA for each sample was divided to prepare short-read Illumina mRNAseq libraries and long-read ONT RNA-seq libraries.

first: Fiamma

last: Salerno

first: Özge

last: Gizlenci

first: Martin

last: Turner