title: Microbiome-specific T follicular helper cells drive tertiary lympohid structures and anti-tumor immunity against colorectal cancer

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

institute: University of Pittsburgh

summary: Advanced or metastatic colorectal cancer is largely refractory to current therapeutic regimens and correspondingly has poor prognosis. The microbiota plays an important role in controlling the host immune response, with unique bacterial species able to activate and differenation specific subpopulations of T cells in the colon. Using an orthotopic carcinogen-induced murine model of colorectal cancer, we found that pertubation of the microbiome with Helicobacter hepaticus led to increased antitumor immunity and disease control. Single-cell RNAseq analysis was used to interrogate the tumor microenvironment and lamina propria in Helicobacter hepaticus colonized and control mice.

overall_design: Colitis-associated colon cancer was induced in 6 week old mice using the azoxymethane-dextran sodium sulfate (AOM-DSS) model. Mice were injected intraperitoneally with azoxymethane (AOM) followed by 3 cycles of 1 week of treatment with DSS in drinking water and 2 weeks without. One group of mice were colonized with Helicobacter hepaticus (AOM-DSS+HHep) on week 7 post tumor inducation, and uncolonized mice were carried forward as a control. Single cell suspensions were generated  from the epithelial layer containing the tumor and  the lamina propria of mice 12 weeks after tumor induction. Three mice were used in each group, and cells from individual mice for each tissue were cell hashed with Biolegend TotalSeq-C. TotalSeq-C 1-3 labeled the individual mice from the AOM-DSS group, and TotalSeq-C 4-6 labeled the individual mice from the AOM-DSS+HHep group.

first: Abigail

last: Overacre-Delgoffe

first: Timothy

last: Hand


title: Targeting MYC Transcription with Small Peptide Derived from KSHV Transactivator (RNA-Seq analysis of PDX tumors)

status: Public on Dec 01 2021

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

country: USA

institute: UC Davis School of Medicine

type: Expression profiling by high throughput sequencing

summary: Herpesviruses rely on host cell transcription and translation machineries for replication. Viral proteins thus function to redirect multiple cellular proteins for viral replication. In herpesvirus replicating cells, host cell gene transcription is frequently down-regulated because important transcriptional apparatuses are appropriated by viral transcription factors. Here we show that an evolutionally-shaped viral protein sequence is a great starting material for unique drug development to modulate cellular transcription. Cellular c-Myc protein (MYC) is overexpressed in over 70% of all types of cancer cells and therefore a very attractive target to control cancer cell growth. We identified a small functional peptide derived from the Kaposi's sarcoma-associated herpesvirus transactivator (K-Rta), which strongly attenuates MYC expression, reduces cell proliferation, and selectively kills cancer cells in both tissue culture and a xenograft tumor mouse model. Mechanistically, the peptide blocks promoter-enhancer interactions by preventing coactivator complex consisting of Nuclear receptor coactivator 2, p300, and SWI/SNF proteins from engaging the MYC promoter in leukemia cells. Target gene profiling with SLAM-seq suggests that the viral peptide attenuates MYC expression through a mechanism likely different from that of BET bromodomain inhibitors. Furthermore, fusing the 13 amino acids peptide with humanized anti-CD22 single chain armed the antibody drug with cell killing ability, and inhibited cell growth in soft agar. Our studies thus demonstrate the utility of the peptide sequence as a therapeutics module, which may be used to modulate MYC activity in a cell type-specific manner.

overall_design: The goal of these studies was to utilize comprehensive transcriptomic profiling in order to determine the gene expression and pathway alterations mediated by treatment of human xenograft tumors with MBK50, a novel small functional peptide therapeutic derived from the Kaposi's sarcoma-associated herpesvirus (KSHV)-transactivator (K-Rta), and which strongly attenuates MYC expression. This was performed in the context of xenograft tumors generated by intraperitoneal injection of KSHV-infected human primary effusion lymphomas (PEL) BCBL-1 cells, into NRG mice. For this study, NRG mice were randomized into three groups and then treated with either PBS vehicle control, the MBK50 wild type peptide (10 mg/kg), or an inactive mutant peptide (10 mg/kg). The mice were treated once daily for 10 days. Following treatment, tumors were harvested for isolation of total RNA and followed by library preparation and next-generation sequencing (NGS).

first: Yoshihiro

last: Izumiya

middle: G


title: Characterization of a newly-identified myelinating oligodendroglial population expressing NDRG1 in the adult mouse central nervous system

city: New York

first: Sarah

last: Moyon

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: CUNY ASRC

summary: Oligodendrocytes are the main myelinating and remyelinating cells of the central nervous system. We identified N-myc downstream regulated gene family member 1 (NDRG1) as a specific mature marker of the oligodendroglial lineage, regulated by mTORC2 kinase activity. By generating a transgenic reporter murine line, we managed to precisely characterize the effect of cuprizone-induced treatment on myelinating cells. We also created a new and adult-specific whole genome transcriptomic profile of the oligodendroglial lineage, from proliferative OPC (using P60 PDGFRa::GFP sorted cells), to pre-myelinating OL (using P60 PLP::GFP sorted cells) and then mature OL (using P60 NDRG1-eGFP sorted cells). This new reporter murine line and its associated RNA-Sequencing dataset could help us better understand the specific biology of adult myelinating oligodendrocytes, compared to previously published developmental tools and databases.

overall_design: mRNA profiles of FAC-sorted P60 PDGFRa::GFP, P60 PLP::GFP and P60 NDRG1-eGFP purified cell samples from mouse brains were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2500.

first: S

first: K

last: Castro

first: J

last: Patzig

first: M

last: Gacias

first: L

last: Magri

first: P

last: Casaccia


title: Expression data from intestinal mucosa of patients with Crohn disease

status: Public on Dec 05 2021

city: Paris

first: Marjolaine

last: Ngollo

address: 1 avenue Claude Vellefaux

department: Gastroenterology

country: France

institute: INSERM

summary: We used microarrays to detail the global signature of gene expression underlying endoscopic recurrence of CD and identified distinct gene signature predicting postoperative recurrence.

overall_design: Ileal samples from Crohn's disease patients and healthy samples from non-inflammatory controls were collected for RNA extraction and hybridization on Affymetrix microarrays. Inclusion criteria were age >18 years, ileal or ileocolonic CD and indication of CD‐related intestinal surgery. Endoscopic recurrence was defined by the presence of any ulcerated lesions at the anastomosis and/or on the neo-terminal ileum (Rutgeerts score > i0). Five hundred and twenty samples (520) were collected from the inflamed ileum (M0I) and the ileal margin (M0M) at time of surgery, and during post-operative endoscopy six month later (M6). We also collected 25 ileal non-IBD control biopsies (Ctrl) from patients who underwent ileocecal resection for colonic tumour with a healthy ileum.

first: Ngollo

last: Marjolaine

first: Allez

last: Matthieu


title: Effects of Methylprednisolone (MP) to Spinal Cord Injury

city: Taipei

first: Yuan-Chii

last: Lee

address: 250, Wuxing Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

summary: Spinal cord injury (SCI) causes serious and complex secondary injury mechanism that leads to function deficit in daily life. How to treat devastating SCI is a critical issue in clinical medicine. This study explores effect of Methylprednisolone (MP) in temporal change of gene expression to look for candidate genes that have potential to develop effective treatment.

overall_design: There is a total of 60 duplicate samples with and without SCI, respectively. In the whole experiment, we used MP medication in a time series from 2, 4, 6, 8, 12, 24, and 48 hours.

first: Meng-Yu

last: Tsai

first: Liang-Yo

last: Yang

first: Shwu-Fen

last: Chang

first: Yang

middle: C

last: Fann


title: Next Generation Sequencing Facilitates Quantitative Analysis of Brown Adipose Tissues from 3bKO and fl/fl Control Mice after 20-week High-Fat Diet Feeding

city: Atlanta

first: Bingzhong

last: Xue

state: Georgia

address: 50 Decatur St SE

department: Biology

institute: Georgia State University

summary: A persistent influx of energy due to intake over expenditure leads to obesity. Increasing energy expenditure through activation of brown fat thermogenesis is a promising therapeutic strategy for the treatment of obesity. Epigenetic regulation has emerged as a key player in regulating brown fat development and thermogenic program. Here we aimed to study the role of DNA methyltransferase 3b (Dnmt3b), a DNA methyltransferase involved in de novo DNA methylation, in the regulation of brown fat function and energy homeostasis during diet-induced obesity (DIO). We have generated a genetic model with Dnmt3b deletion in brown fat-skeletal lineage precursor cells (3bKO mice) by crossing Dnmt3b-floxed (fl/fl) mice with Myf5-Cre mice. Female 3bKO mice were prone to diet-induced obesity and were insulin resistant. This was associated with decreased energy expenditure, which may largely account for the obese phenotype as there was no difference in food intake and locomotor activity between 3bKO and fl/fl mice. Dnmt3b deficiency impaired mitochondrial and thermogenic program in brown fat. Surprisingly, further RNA-seq analysis revealed a profound up-regulation of myogenic markers in the brown fat of 3bKO mice, suggesting a myocyte-like remodeling in brown fat, which may explain the impaired thermogenic program in brown fat. Further motif enrichment and pyrosequencing analysis suggested myocyte enhancer factor 2C (Mef2c) as a mediator for the myogenic alteration in Dnmt3b-deficient brown fat as indicated by decreased methylation at its promoter. Our data demonstrate that brown fat Dnmt3b is a key regulator of brown fat development, energy metabolism and obesity in female mice.

overall_design: Brwon adiipocytes mRNA profiles of fl/fl and 3bKO mice after 20-Week High-fat diet feeding

first: Hang

last: Shi


title: Targeting MYC Transcription with Small Peptide Derived from KSHV Transactivator (CUT&RUN)

first: Clifford

last: Tepper

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Homo sapiens
Human gammaherpesvirus 8

platform_organism:
Homo sapiens
Human gammaherpesvirus 8

overall_design: The goal of these studies was to define the genome-wide binding sites host cellular proteins and sites of histone modifications on the human and Kaposi's sarcoma-associated herpesvirus (KSHV) genome using CUT&RUN. This was performed in the context of the BCBL-1, (TREx)BCBL-1, and BC-1 cell line models, which are derived from KSHV-infected human primary effusion lymphomas (PEL) and contain latent KSHV genomes. TREx-K-Rta BCBL-1, also referred to as (TREx)BCBL-1, is an engineered subline, which contains a Tetracycline/Doxycycline (Dox)-inducible Flagx3- and HAx3-tagged K-Rta expression cassette. Viral reactivation can be stimulated by inducing K-Rta expression in individual TREx-K-Rta BCBL-1 cultures by treatment with Dox for 24 hours. For this study, replicate cell cultures were grown to 75% confluence and then harvested for CUT&RUN analyses for binding sites of SMARCC1, SMARCA5, RNA polymerase II, and sites of H3K27Ac and H3K4me1 histone modifications. Non-specific IgG was used as a control.

first: Yoshihiro

last: Izumiya

first: Mel

last: Campell

first: Ashish

last: Kumar

first: Yuanzhi

last: Lyu

first: Yuichi

last: Yanagihashi

first: Chanikarn

last: Chantarasrivong

first: Kazushi

last: Nakano

first: Ryan

middle: R

last: Davis


title: Targeting MYC Transcription with Small Peptide Derived from KSHV Transactivator

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

overall_design: Refer to individual Series


title: Effect of Ssrp1 KO on chromatin accessibility in mouse adipose stem cells [ATAC-seq]

status: Public on Nov 30 2021

city: Buffalo

first: Katerina

last: Gurova

address: Elm and Carlton Str

institute: Roswell Park Cancer Institute

summary: Preservation of nucleosomes during replication has been extensively studied, while the maintenance of nucleosomes during transcription has gotten less attention. The histone chaperone FACT is involved in transcription elongation, although whether it disassembles or assembles nucleosomes during the passage of RNA polymerase is still unclear. We deleted the FACT subunit in adult mice to clarify the function of FACT in mammals. FACT loss was lethal due to bone marrow and intestinal failure, where the earliest progenitors completely vanished, while several other cell types were increased or decreased. Using cells isolated from several tissues, we showed that FACT loss was lethal only for stem cells but not cells differentiated in vitro. FACT depletion led to increased chromatin accessibility in a transcription-dependent manner, suggesting that nucleosomes are lost from transcribed regions in the absence of FACT. The most prominent response to the loss of chromatin integrity was the activation of interferon signaling and the accumulation of immunocytes in sensitive organs. FACT maintained chromatin integrity during transcription in mammalian adult stem cells, suggesting that chromatin transcription in these cells is different from more differentiated cells.

overall_design: Mouse adipose mesenchymal stem cells (MSC) were isolated from Ssrp1fl/fl;CreERT2+/+ or Ssrp1fl/+; CreERT2+/+ cells. Cells were treated with 4-OHTor vehicle  in vitro for 5 days, then split. After attchment cells were kept at 0.5% serum for 48 hours and then used for ATAC-seq.


title: Reprogramming of RNA silencing triggered by Cucumber Mosaic Virus infection in Arabidopsis

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA silencing has an important role mediating sequence-specific virus resistance. Here, we analyzed in detail the interference of Cucumber Mosaic Virus (CMV) with the RNA silencing machinery of Arabidopsis thaliana. We detected that CMV infection induced the production of viral small interfering RNAs (vsiRNAs) that account for a significant part of the sRNome affecting the levels of other sRNA classes. Furthermore, we analyzed the incorporation of vsiRNAs into the main ARGONAUTE (AGO) proteins with a described antiviral role and the viral RNA silencing suppressor (VRS) 2b, by combining protein immunoprecipitation with sRNA high-throughput sequencing. vsiRNAs accumulated to high levels in AGO2, followed by AGO1, AGO5 and AGO7. Interestingly, vsiRNAs represented a significant percentage of AGO-loaded sRNAs and displaced other endogenous sRNAs. As a countermeasure, the VSR 2b loaded vsiRNAs and mRNA-derived siRNAs, which affected the expression of the genes they derived from. Additionally, we analyzed how vsiRNAs incorporated into the endogenous RNA silencing pathways by exploring their target mRNAs using parallel analysis of RNA end (PARE) sequencing. This strategy allowed us to identify 61 genes with degradome data supporting their vsiRNA-mediated cleavage. This work exemplifies the complex relationship of RNA viruses with the endogenous RNA silencing machinery and the multiple aspects of virus resistance and virulence that this interaction induces.

overall_design: Analysis of sRNA (infected and mock tissues including AGO and 2b-IPed) and PARE sequencing during CMV infection in Arabidopsis thaliana rosette leaves


title: Methods for Cardiac Fibroblast Generation from iPSCs: Updates and Characterization

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

summary: Since the initial isolation of human embryonic stem cells and subsequent discovery of reprogramming methods for somatic cells, thousands of protocols have been developed to create each of the hundreds of cell types found in vivo with significant focus on disease-prone systems, e.g. cardiovascular. Robust protocols exist for many of these cell types, save cardiac fibroblasts (CF). Very recently, several competing methods have been developed to generate these cells through a developmentally conserved epicardial pathway. Such methods generate epicardial cells, but here we report that prolonged exposure to growth factors such as bFGF induces a more native morphology and similar chromatin architecture to primary CFs. Media conditions for growth and assays are provided, as well as suggestions for seeding densities and timepoints for protein harvest of extracellular matrix. We demonstrate marker expression and matrix competency of resultant cells as shown next to primary human cardiac fibroblasts. These methods provide additional guidance to the original protocol and result in an increasingly stable phenotype

overall_design: ATAC-sequencing of two clones of human iPSCs, cardiac progenitor cells, epicardial cells, and cardiac fibroblasts in addition to primary human cardiac fibroblasts.

first: Alexander

middle: J

last: Whitehead

first: James

middle: D

last: Hocker

first: Bing

last: Ren


title: miR181a is a novel key player in the STAT3 mediated survival network of TCRab CD8+ T-LGL leukemia

city: Rotterdam

first: Anton

middle: W

last: Langerak

state: Zuid Holland

address: Dr. Molewaterplein 40

department: Immunology

country: Netherlands

institute: ErasmusMC


title: Macrophage-targeted Therapy Unlocks Antitumoral Crosstalk Between IFN𝜸-secreting Lymphocytes and IL12-producing Dendritic Cells

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

summary: Macrophages often abound within tumors, express colony-stimulating factor 1 receptor (CSF1R), and are linked to adverse patient survival. Drugs blocking CSF1R signaling have been used to suppress tumor-promoting macrophage responses; however, their mechanisms of action remain incompletely understood. Here, we assessed the lung tumor immune microenvironment in mice treated with BLZ945, a prototypical small-molecule CSF1R inhibitor, using single-cell RNA sequencing and mechanistic validation approaches. We showed that tumor control was not caused by CSF1R+ cell depletion; instead, CSF1R targeting reshaped the CSF1R+ cell landscape, which unlocked crosstalk between antitumoral CSF1R- cells. These cells included IFN𝜸-producing natural killer and T cells, and an IL12-producing dendritic cell subset, denoted as DC3, which were all necessary for CSF1R inhibitor–mediated lung tumor control. These data indicate that CSF1R targeting can activate a cardinal crosstalk between cells that are not macrophages and that are essential to mediate the effects of T cell–targeted immunotherapies and promote antitumor immunity.

overall_design: Single-cell RNA sequencing (scRNAseq) of lung-infiltrating CD45+ cells from healthy mice (n=2), and lung adenocarcinoma-bearing mice treated with the CSF1R inhibitor BLZ945 (n=2) or vehicle alone (n=2).

first: Christina

last: Pfirschke

first: Camilla

last: Engblom

first: Marius

last: Messemaker

first: Angela

middle: E

last: Zou

first: Steffen

last: Rickelt

first: Nicolas

middle: A

last: Gort-Freitas

first: Yunkang

last: Lin

first: Ruben

last: Bill

first: Marie

last: Siwicki

first: Jeremy

last: Gungabeesoon

first: Melissa

middle: M

last: Sprachman

middle: N

last: Marquard

first: Christopher

middle: B

last: Rodell

first: Michael

middle: F

last: Cuccarese

last: Quintana

first: Maaz

middle: S

last: Ahmed

first: Rainer

middle: H

last: Kohler

first: Virginia

last: Savova

first: Ralph

last: Weissleder

first: Allon

last: Klein

first: Mikael

last: Pittet


title: miR181a is a novel key player in the STAT3 mediated survival network of TCRab CD8+ T-LGL leukemia [sRNA-Seq]

first: Anton

last: Langerak

summary: TCRαβ CD8 large granular lymphocyte (LGL) leukemia is a rare heterogeneous hematological disorder with a chronic disease course that mostly affects elderly. It is generally accepted that LGL cells arise as a consequence of chronic antigenic stimulation and inflammation and thrive because of dysregulation of mainly the STAT3 but also to some extent the ERK pathway, which are constitutively activated. In approximately 40% of patients this is due to STAT3 activating mutations, but for the other 60% it remains to be elucidated, why the STAT3 pathway is chronically activated. miRNAs are one of the most potent regulators in health and disease and are also linked with various leukemias. Therefore, we hypothesized that aberrant miRNA expression could contribute to dysregulation of the STAT3 pathway. miRNA sequencing in LGL leukemia cases and aged-matched healthy control TEMRA cells revealed overexpression of miRNA181a. Furthermore, gene set enrichment analysis (GSEA) of miRNA181a implicated its involvement in the STAT3 and ERK1/2 pathways. Phosphoflow analysis of STAT3, ERK1/2 in miR181a-transfected human CD8 T cells revealed that miR181a overexpression results in STAT3 and ERK1/2 phosphorylation. By using TL1, a human T-LGL cell line model, we have now established that miR181a is the common actor in T-LGL leukemia, driving STAT3 activation by SOCS3 inhibition in LGL leukemia patients. Additionally, miR181a induces ERK1/2 phosphorylation by inhibition of DUSP6. Taken together, our data show that miR181a is the missing link to explain why STAT3-unmutated patients show hyperactive STAT3.

overall_design: Small non coding RNA sequencing of T-LGL patients compared to healthy control TEMRA CD8+ T cells

first: Jorn

middle: L

last: Assmann

first: Leticia

last: Leon


title: Mammary Tumor-Derived Transplants as Breast Cancer Models to Evaluate Tumor-Immune Interactions and Therapeutic Responses

city: San Francisco

first: Jade

last: Moore

state: California

address: 2340 Sutter St, S371

institute: University of California San Francisco

summary: To investigate mTDT transcriptional features using the Nanostring pancancer io 360 gene expression panel that consists of 770 unique genes involved in the interplay between the tumor, microenvironment and immune response.

overall_design: Mammary tumor tissue.

first: Lin

last: Ma

first: Ann

last: Lazar

first: Mary

last: Barcellos-Hoff


title: Effector Memory CD4 T cells engage the innate immune system through CD40 and TNFR to trigger cytokine storm and autoimmune pathology II

city: Cincinnati

first: Chandrashekhar

last: Pasare

state: Ohio

address: 250 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary:
Introduction: DCs sense and respond to a variety of pathogen-dependent and independent features. We found that DCs can directly sense the presence of immunological memory in the form of effector memory T cells via TNFRSF signaling. Expression of CD40L and TNF by effector memory T cells specifically led to a robust inflammatory signature in interacting DCs.
Method: Bone marrow derived DCs (BMDCs) were differentiated in the presence of GMCSF for 7 days. WT naïve T cells were polarized to Th0 (platebound anti-CD3 and anti-CD28 and soluble IL-2) for 5 days, followed by 2 days of rest in low IL-2 containing media to mimic generation of effector memory T cells. CD11c+ BMDCs were sorted via AutoMacs and activated with effector memory T cells (ratio of 1:4) in the presence or absence of soluble anti-CD3 (200ng/mL) for 3 hours. Cells were pretreated with blocking and neutralizing antibodies for CD40L and TNF (20ug/mL for 30 minutes) when indicated. Cells were blocked with FC block and stained with flourophores to distinguish DCs from T cells. DCs were FACS sorted and lysed in Trizol.
Conclusion: Effector memory T cells activate interacting BMDCs via CD40 and TNF signaling. When these pathways are blocked, BMDCs fail to upregulate the transcriptional program associated with effector memory T cell induced activation.

overall_design: mRNA profiles of BMDCs stimulated with Th0 cells via CD3 in the presence or absence of TNF and CD40L blocking antibodies for 3 hours by Illumina sequencing in duplicate.

first: Margaret

last: McDaniel

first: Amanpreet

last: Chawla

first: Hannah

last: Meibers


title: Effector Memory CD4 T cells engage the innate immune system through CD40 and TNFR to trigger cytokine storm and autoimmune pathology I

summary:
Introduction: DCs sense and respond to a variety of pathogen-dependent and independent features. We found that DCs can directly sense the presence of immunological memory in the form of effector memory T cells. This activation by effector memory T cells led to a robust inflammatory signature in interacting DCs.
Method: Bone marrow derived DCs (BMDCs) were differentiated in the presence of GMCSF for 7 days. WT naïve T cells were polarized to Th0 (platebound anti-CD3 and anti-CD28 and soluble IL-2) for 5 days, followed by 2 days of rest in low IL-2 containing media to mimic generation of effector memory T cells. CD11c+ BMDCs were sorted via AutoMacs and activated with LPS (100ng/mL) or effector memory T cells (ratio of 1:4) in the presence or absence of soluble anti-CD3 (200ng/mL) for 3 hours. Cells were blocked with FC block and stained with flourophores to distinguish DCs from T cells. DCs were FACS sorted and lysed in Trizol.
Conclusion: BMDCs activated with LPS or effector memory T cells had a distict transcriptional response. When activated with effector memory T cells, BMDCs upregulated genes associated with TNFRSF signaling. BMDCs activated with LPS or effector memory T cells also shared certain transcriptional features of upregulated cytokine and chemokine expression.

overall_design: mRNA profiles of BMDCs stimulated with LPS or effector memory Th0 cells via CD3 for 3 hours by Illumina sequencing in triplicate.

first: Aakanksha

last: Jain


title: RNA-Seq analysis of Rpl22l1-deficient murine CD4-CD-CD44-CD25+ (DN3) thymocytes

city: PHILADELPHIA

first: David

middle: Lynn

last: Wiest

address: 333 COTTMAN AVENUE, REIMANN BUILDING, LAB  R364

department: Nuclear Dynamics and Cancer Program

institute: FOX CHASE CANCER CENTER

summary: Rpl22l1 is a highly conserved ribosomal protein paralog that plays a regulatory role in certain hematopoietic cell lineages. Rpl22l1-deficiency arrests the development of T cells at the DN3 stage. RNA-seq analysis was performed to identify the molecular basis for the arrest

overall_design: Adult DN3 thymocytes were isolated from Vav-Cre- Rpl22l1fl/fl (L1 KO) and Vav-Cre+ Rpl22l1fl/fl mice (WT).  Triplicate samples were lysed in Trizol. Total RNA was isolated and processed as previously described (Miyazaki et al., 2017).

first: Shawn

middle: P

last: Fahl


title: Tetramerization of Transcription Factor STAT5 in Monocytes Promotes Autoimmune-mediated Neuroinflammation via the Regulation of CCL17

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: STAT5 plays a critical role in mediating cellular responses following cytokine stimulation. The activated STAT5 proteins can form dimers and tetramers with distinct biological functions. The role of STAT5 tetramerization in autoimmune-mediated neuroinflammation has not been investigated. Using the STAT5 tetramer-deficient Stat5a-Stat5b N-domain double knock-in (DKI) mouse strain, we report here that STAT5 tetramers promote the pathogenesis of experimental autoimmune encephalomyelitis (EAE). The mild EAE phenotype observed in DKI mice correlates with the impaired extravasation of pathogenic Th17 cells and interactions between Th17 cells and monocyte-derived cells (MDCs) in the meninges. We further demonstrated that STAT5 tetramerization regulates the GM-CSF-dependent production of CCL17 by MDCs. Importantly, DKI Th17 cells expanded with CCL17 exhibit more severe EAE. Mechanistically, the effect of CCL17 is dependent on the activity of the integrin VLA-4. Thus, our study uncovered a novel GM-CSF-STAT5 tetramer-CCL17 pathway that promotes autoimmune neuroinflammation via the regulation of Th17 cell migration.

overall_design: For isolating monoyctes and monoycte-derived APCs from the mice, EAE was induced in STAT5 tetramer-deficient (DKI) mice by active immunization with MOG35-55 in CFA and pertussis toxin. Bone marronw monocytes, and spinal cord monocytes, and spinal cord APCs were isolated on day 14 after immunization by cell sorting. For the isolation of pathogenic Th17 cells, WT and DKI mice were immunized with MOG35-55 in CFA without pertussis toxin administration. Cells from the spleens and lymph nodes were isolated on day 14 following immunization and expanded with MOG35-55 peptide under Th17 conditions, with or without the addition of CCL17. CD4+ T cells were isolated 3 days following expansion by cell sorting.

first: Kelly

last: Monaghan

first: Drake

last: Aesoph

first: Edwin

middle: C

last: Wan


title: Expression profiles of SOX11-positive and SOX11-negative Mantle Cell Lymphoma (MCL) primary samples from lymph node and reactive lymph nodes (RLN).

city: Barcelona

first: Virginia

last: Amador

email: VAMADOR@clinic.cat, PBALSAS@clinic.cat

state: Barcelona

address: Roselló 149-153

country: Spain

institute: IDIBAPS

summary: Gene expression profiles were obtained via Nanostring nCounter Expression Assay (PanCancer Immune Profiling Panel, Nanostring Technologies, Hamburg, Germany). We aimed to obtain the differential immune gene expression comparing the lymph node microenvironment of SOX11-positive and SOX11-negative MCL primary samples and non-neoplastic nodal samples (RLN).

overall_design: In this study, 11 SOX11-positive nodal MCL primary samples, 3 SOX11-negative nodal MCL primary samples and 6 reactive lymph nodes were screened for gene expression of immune response-related genes (770 genes including 40 housekeeping genes). Nucleic acids were extracted from 10-µm sections of FFPE biopsies from lymph nodes using the QIAGEN AllPrep DNA/RNA FFPE kit (QIAGEN, Hilden, Germany) after deparaffinization according to the manufacturer´s instructions. The quality and concentration were assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Inc., Waltham, MA, USA).  Isolated RNA (400 ng) was processed through the NanoString nCounter Prep Station.  Subsequently, samples were processed according to the manufacturer’s instructions and signals of reporter probes were counted and tabulated using the nCounter Digital Analyzer (NanoString Technologies). Gene expression analysis was performed using the human nCounter® PanCancer Immune Profiling Panel (NanoString Technologies). Finally, housekeeping gene (geometric mean of 40 genes) normalization for quantitating gene expression levels, positive control normalization for background noise correction and data analysis was performed using nSolver™ Analysis Software 4.0 (NanoString Technologies, Hamburg, Germany) and standard settings.

first: Patricia

last: Balsas

first: Luis

last: Veloza

first: Elías

last: Campo


title: Multifaceted Pathomolecular Mechanism of a VWF Large Deletion Involved in the Pathogenesis of Severe VWD

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

country: Germany

institute: University Clinic Bonn

summary: An in-frame heterozygous large deletion of exons 4-34 of the von Willebrand factor (VWF) gene was identified in an index patient (IP) with type 3 von Willebrand disease (VWD), as the only mutation. The IP exhibited severe bleeding episodes despite prophylaxis treatment, with a short VWF half-life after infusion of VWF/FVIII concentrates.  This study intends to elucidate the causal molecular mechanism of this large deletion. Transcript analysis confirmed transcription of normal VWF mRNA besides an aberrant deleted transcript. The amount of secreted VWF from blood outgrowth endothelial cells (BOECs) isolated from the IP was not significantly different from that of controls. However, IP-BOECs exhibited a deficiency in the assembly of VWF multimers and biogenesis of the Weibel-Palade bodies (WPBs). Furthermore, immunostaining of IP-BOECs demonstrated subcellular mislocalization of WPBs pro-inflammatory cargos angiopoietin-2 (Ang2) and P-selectin. Additionally, whole-transcriptome RNA-sequencing of the BOECs and subsequent Ingenuity Pathway Analysis indicated the significant alterations of canonical pathways in IP-BOECs related to inflammatory responses, cell adhesion, extracellular organization, and angiogenesis (e.g. granulocyte adhesion and Rho-related signaling pathways), which are known downstream signaling pathways induced by Ang2. Accordingly, the IP-BOECs exhibited an increased adhesiveness to leukocytes which may contribute to accelerated VWF clearance.  In conclusion, deleted VWF has a dominant-negative impact on the elongation of multimers and biogenesis of WPBs. Aberrant WPBs lead to the alternative trafficking of its cargos in a specific way, which, in turn, may cause distinctive perturbations in cellular signaling pathways, resulting in the exceptional phenotypes in the current patient.

overall_design: 6 samples

first: Hamideh

last: Yadegari

first: Muhammad

last: Ahmer Jamil


title: Targeting MYC Transcription with Small Peptide Derived from KSHV Transactivator (SLAM-Seq)

first: Clifford

middle: G.

last: Tepper

summary: Herpesviruses rely on host cell transcription and translation machineries for replication. Viral proteins thus function to redirect multiple cellular proteins for viral replication. In herpesvirus replicating cells, host cell gene transcription is frequently down-regulated because important transcriptional apparatuses are appropriated by viral transcription factors. Here we show that an evolutionally-shaped viral protein sequence is a great starting material for unique drug development to modulate cellular transcription. Cellular c-Myc protein (MYC) is overexpressed in over 70% of all types of cancer cells and therefore a very attractive target to control cancer cell growth. We identified a small functional peptide derived from the Kaposi's sarcoma-associated herpesvirus transactivator (K-Rta), which strongly attenuates MYC expression, reduces cell proliferation, and selectively kills cancer cells in both tissue culture and a xenograft tumor mouse model. Mechanistically, the peptide blocks promoter-enhancer interactions by preventing coactivator complex consisting of Nuclear receptor coactivator 2, p300, and SWI/SNF proteins from engaging the MYC promoter in leukemia cells. Target gene profiling with SLAM-seq suggests that the viral peptide attenuates MYC expression through a mechanism likely different from that of BET bromodomain inhibitors. Furthermore, fusing the 13 amino acids peptide with humanized anti-CD22 single chain armed the antibody drug with cell killing ability, and inhibited cell growth in soft agar. Our studies thus demonstrate the utility of the peptide sequence as a therapeutics module, which may be used to modulate MYC activity in a cell type-specific manner.

overall_design: The goal of these studies was to utilize thiol(SH )-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) in order to determine the dynamics of gene expression in response to treatment with a novel small functional peptide therapeutic derived from the Kaposi's sarcoma-associated herpesvirus (KSHV)-transactivator (K-Rta), which strongly attenuates MYC expression. This was performed in the context of the BCBL-1 and BC-1 cell line models, which are derived from KSHV-infected human primary effusion lymphomas (PEL) and contain latent KSHV genomes. For this study, replicate cultures from each cell line were treated with either vehicle control, wild-type peptide (24 uM), or mutant peptide (24 uM) for 30 minutes, and then for an additional 1 hour in the presence of 4-Thiouridine (s4U; 300 uM) in order to label nascent transcripts. Following treatment, the cells were then harvested for isolation of total RNA (containing s4Uracil-labeled transcripts) and followed by library preparation and next-generation sequencing (NGS).

first: Yoshihiro

last: Izumiya

middle: G


title: Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies

city: Houston

first: James

middle: Cushing

last: Bayley

state: Texas

address: One Baylor Plaza

department: Neurosurgery

institute: Baylor College of Medicine

type: Methylation profiling by genome tiling array


title: Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies [RNA-Seq]

summary:
Purpose: Clustering of meningiomas using DNA methylation and RNA-sequencing data yields groups which predict clinical behavior than the current clinical standard of histopathologic grading. Both techniques segregate many common genomic features seen in meningiomas similarly, raising the question of whether they were identifying the same underyling groups.
Methods: DNA methylation profiling (EPIC 850K array) and RNA-sequencing of 110 primary meningiomas was performed. Unsupervised clustering was performed using each type of data, followed by computational modeling which explored correlations of promoter methylation and copy number variation (CNV) with gene expression.
Results: We performed unsupervised clustering of the DNA methylation data and gound three clusters to be optimal. These clusters aligned closely with our prior transcriptional classification (Patel et al. PNAS 2019). These groups also closely aligned with groups defined by large-scale cytogenetic changes and merlin expression/genomic instability, suggesting the presence of three biologic groups of meningioma that can be identified by multiple methods. Computational modeling demonstrated that both promoter methylation and CNV correlated closely with gene expression differences seen in meningioma and our biologic groups, although cytogenetic changes (particularly chr 1p loss) was predominant in the clinically aggressive tumors.
Conclusions: Our anaylsis suggests the presence of three biologic groups of meningioma (MenG A, B, and C) which can be accurately identified through DNA methylation, RNA-seq, and cytogenetic profiling.

overall_design: DNA methylation, RNA-sequencing, and whole exome-sequencing was performed on 110 primary meningiomas

first: Akash

middle: J

last: Patel


title: Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies [Methylation array]

summary:
Purpose: Clustering of meningiomas using DNA methylation and RNA-sequencing data yields groups which predict clinical behavior than the current clinical standard of histopathologic grading. Both techniques segregate many common genomic features seen in meningiomas similarly, raising the question of whether they were identifying the same underyling groups.
Methods: DNA methylation profiling (EPIC 850K array) and RNA-sequencing of 110 primary meningiomas was performed. Unsupervised clustering was performed using each type of data, followed by computational modeling which explored correlations of promoter methylation and copy number variation (CNV) with gene expression.
Results: We performed unsupervised clustering of the DNA methylation data and gound three clusters to be optimal. These clusters aligned closely with our prior transcriptional classification (Patel et al. PNAS 2019). These groups also closely aligned with groups defined by large-scale cytogenetic changes and merlin expression/genomic instability, suggesting the presence of three biologic groups of meningioma that can be identified by multiple methods. Computational modeling demonstrated that both promoter methylation and CNV correlated closely with gene expression differences seen in meningioma and our biologic groups, although cytogenetic changes (particularly chr 1p loss) was predominant in the clinically aggressive tumors.
Conclusions: Our analysis suggests the presence of three biologic groups of meningioma (MenG A, B, and C) which can be accurately identified through DNA methylation, RNA-seq, and cytogenetic profiling.


title: Muscle-secreted neurturin couples fiber oxidative metabolism and slow motor neuron identity

city: Stockholm

first: Jorge

middle: C.

last: Correia

address: Biomedicum - Solnavägen 9

department: Dept. Physiology and Pharmacology

institute: Karolinska Institutet

summary: In this study we evaluate the effects of muscle-derived neurturin on skeletal muscle innervation, metabolism, and performance.

overall_design: RNA-sequencing analysis of gastrocnemius muscles from muscle-specific NRTN transgenic mice (with NRTN expression driven by the human alpha-skeletal actin promoter) and wild-type littermates.

first: Yildiz

last: Kelahmetoglu

first: Paulo

middle: R

last: Jannig

last: Ruas


title: Gene expression in Lucilia sericata (Diptera: Calliphoridae) larvae exposed to Pseudomonas aeruginosa and Acinetobacter baumannii

first: Richard

last: Meisel

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: RNA-seq was used to measure gene expression in second instar larvae of the blow fly Lucilia sericata after feeding exposure (1 hour or 4 hours) to Pseudomonas aeruginosa and Acinetobacter baumanii. RNA-seq measurements were also collected from control larvae from each time point that were not exposed to bacteria.

overall_design: 4 replicates in each of 3 batches were collected from second instar blow fly larvae fed either PBS (negative control), Pseudomonas aeruginosa, or Acinetobacter baumannii.

first: C

last: McKenna

first: D

last: Asgari

first: T

middle: K

last: Crippen

first: R

last: Sherman

first: J

last: Tomberlin

first: A

last: Tarone


title: Effect of Ssrp1 KO on transcriptome in mouse adipose stem cells [RNA-seq]

first: Katerina

last: Gurova

summary: Preservation of nucleosomes during replication has been extensively studied, while the maintenance of nucleosomes during transcription has gotten less attention. The histone chaperone FACT is involved in transcription elongation, although whether it disassembles or assembles nucleosomes during the passage of RNA polymerase is still unclear. We deleted the FACT subunit in adult mice to clarify the function of FACT in mammals. FACT loss was lethal due to bone marrow and intestinal failure, where the earliest progenitors completely vanished, while several other cell types were increased or decreased. Using cells isolated from several tissues, we showed that FACT loss was lethal only for stem cells but not cells differentiated in vitro. FACT depletion led to increased chromatin accessibility in a transcription-dependent manner, suggesting that nucleosomes are lost from transcribed regions in the absence of FACT. The most prominent response to the loss of chromatin integrity was the activation of interferon signaling and the accumulation of immunocytes in sensitive organs. FACT maintained chromatin integrity during transcription in mammalian adult stem cells, suggesting that chromatin transcription in these cells is different from more differentiated cells.

overall_design: Mouse adipose mesenchymal stem cells (MSC) were isolated from Ssrp1fl/fl;CreERT2+/+ or Ssrp1fl/+; CreERT2+/+ cells. Cells were treated with 4-OHTor vehicle  in vitro for 5 days, then split. Next day cells were used for RNA-seq.


title: Effect of Ssrp1 KO in mouse adipose stem cells

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

overall_design: Refer to individual Series


title: Comparative Transcriptome Analysis Reveals immunoregulation mechanism of lncRNA-mRNA in Large Yellow Croaker (Larimichthys crocea) in Response to Cryptocaryon irritans Infection

status: Public on Nov 28 2021

city: Xiamen

first: Yulin

last: Bai

address: Xiang'an South Road

country: China

institute: Xiamen University

summary: Cryptocaryonosis caused by Cryptocaryon irritans is one of the major diseases of large yellow croaker (Larimichthys crocea), which lead to massive economic losses annually. The pathogenesis for cryptocaryonosis has been researched by a series of transcriptome studies under different infection conditions. However, little is known about the roles of tissue-specifically expressed genes during the infection of C. irritans. In this study, we analyzed the tissue-specific expression of transcripts in the major infection organs including gill and skin of L. crocea after C. irritans infection. we constructed transcriptome expression profiles of L. crocea gill and skin, including 23,172 protein-coding genes and 7,503 long noncoding RNAs (lncRNAs). By comparing transcriptome data from different tissues of L. crocea, we observed tissue specificity of transcripts in gill and skin, including 3,003 protein coding genes and 639 lncRNAs. A total of 212 of the protein coding genes were involved in immune system. Further analysis revealed that the tissue-specific DEGs in gill and skin were mainly involved in HIF-1 signaling pathway and Complement and coagulation cascades, respectively. In addition, 9 non-tissue-specific hub genes, including CCL4, DDIT4, LEP, ect., which are highly associated with C. irritans infection were identified. To our knowledge, this is the first comparative transcriptome analysis of gill and skin after C. irritans infection. Our results are helpful to understand the molecular mechanism of pathogenesis for cryptocaryonosis, espec-tissue specificity of protein-coding genes and lncRNAs involved in immune regulation.

overall_design: The expression of large yellow croaker gill tissue at different time points after infection with Cryptocaryon irritans


title: Spatial Organization of Transcribed Eukaryotic Genes

city: Worcester

first: Job

last: Dekker

state: MA

address: 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School/HHMI

summary: The nuclear organization of the genome is accepted as an important feature of gene expression regulation. However, it has remained unknown what the spatial organization of a single transcribed gene is. Here, we made use of several long highly expressed mammalian genes to describe their structure and spatial arrangement during transcription. We demonstrate that an expressed gene forms a transcription loop with RNA polymerases moving along the loop and carrying nascent RNAs that undergo co-transcriptional splicing. Transcription loops dynamically modify their harboring loci and extend into the nuclear interior due to their intrinsic stiffness. We hypothesize that the stiffness of the transcription loop arises due to  a dense decoration of gene-axis with multiple voluminous nascent ribonucleoprotein particles and provide  supporting evidence to this hypothesis. Our work suggests that transcription loop formation is a universal principle of eukaryotic gene expression.

overall_design: Hi-C dataset

first: Susanne

last: Leidescher

first: Johannes

last: Nübler

first: Yana

last: Feodorova

first: Erica

last: Hildebrand

first: Simon

last: Ullrich

first: Sebastian

last: Bultmann

first: Stephanie

last: Link

first: Katharina

last: Thanisch

first: Heinrich

last: Leonhardt

first: Leonid

last: Mirny

first: Irina

last: Solovei


title: In vitro culture of ovine embryos up to gastrulating stages

city: Madrid

first: Priscila

last: Ramos-Ibeas

address: Avda. Puerta de Hierro, 12, local 10

department: Animal Reproduction

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

summary: Developmental failures occurring shortly after blastocyst hatching from the zona pellucida constitute a major cause of pregnancy losses in both humans and farm ungulates. The developmental events occurring following hatching in ungulates include the proliferation and maturation of extra-embryonic membranes –trophoblast and hypoblast- and the formation of a flat embryonic disc, similar to that found in humans, that initiates gastrulation prior to implantation. Unfortunately, our understanding of these key processes for embryo survival is limited because current culture systems are unable to sustain ungulate embryo development beyond hatching. Herein, we report a culture system that recapitulates most developmental landmarks that characterize ovine development up to gastrulating stages: trophoblast maturation, hypoblast migration, embryonic disc formation, Rauber´s layer removal, epiblast polarization and mesoderm differentiation. In this dataset we compare the transcriptional profile of ovine day (D) 14 in vitro cultured embryos and embryonic day (E) 11 and 12.5 in vivo derived embryos by RNA-seq.

overall_design: RNA-seq analysis was performed in 3 ovine whole embryos in vitro-produced and cultured until D14, 3 E11 and 3 E12.5 in vivo-derived embryos.

first: Pablo

last: Bermejo-Álvarez


title: Differential Expression Profile of MicroRNAs and Tight Junction in Lung Tissue of Rat with Mitomycin-C Induced Pulmonary Veno-Occlusive Disease

city: Hunan

first: Qing

last: Song

address: Renmin Road 139

institute: Central South University

summary: Pulmonary veno-occlusive disease (PVOD) is characterized by increased pulmonary vascular resistance. Currently, there is a lack of effective treatment. It is of great significance to explore molecular targets for treatment of the disease. This study investigated the differentially expressed profile of miRNAs and tight junction in the lung tissue of rats with mitomycin-C induced PVOD.

overall_design: Fourteen 8-week-old male SD rats were purchased from the SJA Lab Animals Corporation (Hunan, China) and were divided into two groups: the control group (N = 4 rats per group) and the PVOD group (N = 10 rats per group).

first: Ping

last: Chen

first: Shang-Jie

last: Wu

first: Yan

last: Zhang


title: Transcriptome analysis of naive CD4T cells from Granulomatosis with Polyangiitis(GPA) patients and healthy control (HC)

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

country: United Kingdom

institute: King's College London

summary: Analysis of transcriptional profile of GPA and HC naive CD4 T cells to understand intrinsic molecular differences after early TCR activation that may explain different effector T cell genereation.

overall_design: Total RNA was isolated from rested and 2 hour TCR activated naive CD4 T cells from GPA and HC peripheral blood.

first: Sangmi

last: Kim

first: Susan

last: John


title: Induced cell-autonomous neutropenia systemically perturbs hematopoiesis in Cebpa enhancer-null mice

status: Public on Nov 24 2021

first: Roger

last: Mulet-Lazaro

address: Doctor Molewaterplein 40

institute: Erasmus MC

summary: Knockouts of the Cebpa gene or its +37kb enhancer in mice show two major findings: (1) neutropenia in bone marrow and blood; (2) decrease in long-term hematopoietic stem cell (LT-HSC) numbers. To study mechanisms linking the two observed events, we applied RNA sequencing on +37kbWT and +37kbHOM bone marrow cells. The analysis of these data revealed that myeloid priming in HSPCs occurs before Cebpa activation and that a neutrophil differentiation block in these progenitors potentially leads to HSC quiescence exit.

overall_design: RNA-seq of hematopoietic stem and progenitor cells (HSPCs) isolated with LSK markers and common myeloid progenitors (CMP) from Cebpa null mice and wild type mice

first: Mulet-Lazaro

last: Roger

first: Avellino

last: Roberto

first: Delwel

last: Ruud


title: CD158a+/CD158b+ NK Cell Imbalance Correlates with Hypertension in Patients with Pre-eclampsia

status: Public on Nov 22 2021

city: Hefei

first: xiuxiu

last: xu

state: Anhui

address: No.96, JinZhai Road Baohe District

institute: university of science and technology of china

summary: Background: Preeclampsia, a pregnancy complication with hypertension and proteinuria, seriously threats the health and lives of the mother and the baby. The role of peripheral natural killer cells (NK cells) in the pre-eclampsia is unclear.  Methods: Flow cytometry was performed to detect the expression of CD158a (KIR2DL1) and CD158b (KIR2DL2/3) in peripheral NK cells of non-pregnant healthy women (HW), healthy pregnant women (HP), and patients with pre-eclampsia (PE). Differentially expressed genes (DEGs) in CD158a+ and CD158b+ NK cells were identified by RNA-sequencing and real-time PCR. Protein array analysis was used to identify altered protein levels in the serum of study participants.  Findings: CD158a+ NK cell numbers were significantly increased in the peripheral blood of patients with pre-eclampsia while the number of CD158b+ NK cells was significantly reduced. The percentage of CD158a+ NK cells was positively correlated with systolic blood pressure while the percentage of CD158b+ NK cells was negatively correlated with systolic blood pressure. RNA-seq and real-time PCR showed that the expression of ERAP2 and GCH1, the genes that regulate blood pressure and angiogenesis, was decreased in CD158a+ compared to CD158b+ NK cells.   Interpretation: CD158a+ and CD158b+ NK cell numbers are altered in the peripheral blood of patients with pre-eclampsia compared to healthy individuals, which is associated with the increase in blood pressure.

overall_design: RNA-seq of CD45+CD3−CD56+CD158b+CD158a− NK cells sorted from the peripheral blood of healthy pregnant women and CD45+CD3−CD56+CD158a+CD158b− NK cells sorted from the peripheral blood of patients with pre-eclampsia

first: Xiuxiu

last: Xu

first: Xirui

last: Zhao

first: Yonggang

last: Zhou

first: Haiming

last: Wei


title: Interferon (IFN)-γ promotes monocyte-mediated lung injury during influenza pathogenesis

status: Public on Nov 25 2021

city: Grand Forks

first: Kai

last: Guo

state: ND

address: 1301 N Columbia Rd Stop 9037

institute: University of North Dakota

summary: Influenza A Virus (IAV) triggers an exuberant host response that promotes acute lung injury. However, the determinants of the pathological host response to IAV remain incompletely understood. In the current study, we identified interferon (IFN)-γ-regulated subset of monocytes, CCR2+ monocytes, as a driver of lung damage during IAV pathogenesis. IFN-γ regulated the recruitment and inflammatory phenotype of CCR2+ monocytes, and CCR2 (CCR2-/-) and IFN-γ (IFN-γ-/-) deficient mice exhibited reduced lung inflammation, pathology, and increased resistance against bacterial co-infection by Streptococcus pneumoniae (Spn). Adoptive transfer of WT (IFN-γR1+), but not IFN-γR1 deficient (IFN-γR1-) CCR2+ monocytes, restored the wild-type (WT)-like pathological phenotype of lung damage in IAV-infected CCR2-/- mice. The CD8+ T cells were the most significant source of IFN-γ in IAV-infected lungs. Collectively, our data highlight that IFN-γ regulates CCR2+ monocyte-mediated lung pathology during IAV pathogenesis.

overall_design: scRNAseq profiles of mock, 7 days post-viral infection

first: M

last: Khan


title: Transcriptome-Wide Analysis of Human Liver Reveals Age-Related Differences in the Expression of Select Functional Gene Clusters and Evidence for a PPP1R10-Governed ‘Aging Cascade’.

city: Magdeburg

first: Ramiro

last: Vichez-Vargas

state: Saxony Anhalt

address: Leipzigerstr. 44

department: Gastroenterology, Hepatology and infectious diseases

institute: Otto-von-Guericke-Universität Magdeburg

summary: A transcriptome-wide analysis of human liver for demonstrating differences between young and old humans has not yet been performed. However, pinpointing major age-related alterations in hepatic gene expression may identify ontogenetic shifts with important hepatic and systemic con-sequences, provide novel pharmacogenetic information, offer clues to efficiently counteract symptoms of old age, and improve the overarching understanding of ontogeny and individual decline. By applying next-generation sequencing and subsequent statistical and bioinformatic [Ensemble Feature Selection (EFS)] analysis, we identified 44 transcripts among 60,617 total and 19,986 protein-encoding transcripts that significantly (p = 0.0003 to 0.0464; EFS score >0.3: 16 transcripts; EFS score >0.2: 28 transcripts) differ between young and old livers. Genes encoding for 25 of these highly age-related transcripts were assigned to the categories ‘regulome’, ‘in-flammaging’, ‘regeneration’, and ‘pharmacogenes’, plus two genes that did not match these cate-gories. Our results have major implications in the area of ontogeny/aging and for the age-dependently increased occurrence of non-alcoholic fatty liver, steatohepatitis, and hepatocellular carcinoma. In addition, we present a broadly substantiated and testable hypothesis on a genetical-ly governed ‘aging cascade’, wherein the protein phosphatase 1 regulatory subunit 10 (PPP1R10) gene acts as a putative ontogenetic master regulator, which is prominently flanked by the genes for the insulin-like growth factor-binding protein acid labile subunit (IGFALS) and dual specificity phosphatase 1 (DUSP1). The results of this transcriptome-wide analysis of human liver offer potential clues towards developing better therapeutic interventions against major liver diseases and increased insight into key mechanisms underlying aging.

overall_design: Examination of differences in gene expression of human livers from 9 patients below age of 49 years and 8 patients older than 74 years.

first: Thomas

last: Schreiter

first: Robert

last: Gieseler

last: Vílchez-Vargas

first: Ruy

last: Jauregui

first: Jan-Peter

last: Sowa

first: Susanne

last: Klein-Scory

first: Ruth

last: Broering

first: Roland

last: Croner

first: Jürgen

middle: W

last: Treckmann

first: Alexander

last: Link

first: Ali

last: Canbay


title: Muscle-secreted neurturin couples myofiber oxidative metabolism and slow motor neuron identity

first: Jorge

last: Correia

summary: Endurance exercise promotes skeletal muscle vascularization, oxidative metabolism, fiber-type switching, and neuromuscular junction integrity. Importantly, the metabolic and contractile properties of the muscle fiber must be coupled to the identity of the innervating motor neuron (MN). Here, we show that muscle-derived neurturin (NRTN) acts on muscle fibers and MNs to couple their characteristics. Using a muscle-specific NRTN transgenic mouse (HSA-NRTN) and RNA-sequencing of MN somas, we observed that retrograde NRTN signaling promotes a shift towards a slow MN identity. In muscle, NRTN increased capillary density, oxidative capacity, and induced a transcriptional reprograming favoring fatty acid metabolism over glycolysis. This combination of effects on muscle and MNs, makes HSA-NRTN mice lean with remarkable exercise performance and motor coordination. Interestingly, HSA-NRTN mice largely recapitulate the phenotype of mice with muscle-specific expression of its upstream regulator PGC-1ɑ1. This work identifies NRTN as a myokine that couples muscle oxidative capacity to slow MN identity.

overall_design: We used laser capture microdissection to isolate discrete motor neurons from the lumbar spinal cord of HSA-NRTN mice and wild-type littermates. We performed RNA-sequencing analysis in pools of approximately 50 motor neurons per mouse (5 HSA-NRTN and 5 wild-type controls).

first: Yildiz

last: Kelahmetoglu

first: Christoph

last: Schweingruber

first: Igor

last: Cervenka

first: Eva

last: Hedlund

last: Ruas


title: Multi-omics integration analysis identifies novel genes for alcoholism with potential link to neurodegenerative diseases

status: Public on Nov 20 2021

city: New York

first: Alison

last: Goate

state: New York

address: 1 Gustave L. Levy Place

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Alcohol use disorders (AUD) are complex, moderately heritable, psychiatric disorders associated with heightened morbidity and mortality. Genome-wide association studies of AUD and drinks per week (DPW) have identified multiple risk loci however few studies have examined the intersection between the loci and genes associated with AUD and DPW, especially with respect to their functional and regulatory significance.  In this study we use a muti-omics systems approach to identify causal variants and genes associated with AUD and DPW.

overall_design: We used Mendelian randomization to integrate AUD and drinks per week GWAS summary statistics with gene expression and methylation quantitative trait loci in the largest brain and myeloid datasets as well as AUD-related single cell epigenetic data to nominate candidate causal variants and genes associated with DPW and AUD.

first: Manav

last: Kapoor

middle: M

first: Jessica

last: Schulman


title: Single Cell sequencing of tumor infiltrating immune cells upon E2 treatment

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Estrogens (E2) has been shown to affect growth, differentiation and polarization of different immune cell types in different context. To understand how E2 treatment affects immune microenvironment during cancer (melanoma) progression, we profiled tumor infiltration immune cells from placebo and E2 treated tumors isolated from female mTyrCreERT2;BrafCA/WT;Ptenf/f. We identified diverse immune cell types and their underlying transcriptomic changes that are manifest upon E2 treatment in the tumor microenvironment.

first: Donald

last: McDonnell

first: Weida

last: Gong

first: Binita

last: Chakraborty


title: Transcriptomic Analysis of Human Epidermal Keratinocytes Stimulated with TWEAK, TNF and IL-17A

status: Public on Nov 19 2021

city: La Jolla

first: Rinkesh

last: Gupta

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Here, we identified psoriasis-associated genes upregulated by TWEAK stimulation, alone or in combination with either TNF or IL-17, in human keratinocytes.

overall_design: Human epidermal keratinocytes were treated with human TWEAK, IL-17A, or TNF, alone, or TWEAK in combination with IL-17A or TNF, and analyzed by RNA-seq.

first: Kai

last: Fung

first: Michael

last: Croft


title: Cell-Specific Transcriptome of the COPD Alveolar Niche

city: New Haven

first: John

last: McDonough

state: CT

address: 300 Cedar St

institute: Yale School of Medicine

summary: The study aimed to compare the gene expression profiles at a single cell level in lung tissues between patients with COPD and donor controls.

overall_design: Single-cell RNA sequencing data was generated from lungs of 4 cigarette smoke exposed and 4 room air exposed mice.

first: Maor

last: Sauler

first: Jonas

last: Schupp

first: Naftali

last: Kaminski

first: Ivan

last: Rosas


title: Estimating and predicting the resolution of HiC libraries

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary:
High resolution HiC libraries are usually lightly sequenced before investing in a deep sequencing. We modeled HiC resolution in function of the sequencing depth to predict accurately the resolution of any high resolution HiC library given a small sequnecing batch of the library.
To test our tool, we used public datasets as well as a newly generated dataset using Arima kit on mouse purified rods photoreceptors.

overall_design: Modeling HiC resolution using public datasets and HiC produced on mouse rods photoreceptors.

first: Claire

last: Marchal

first: Nivedita

last: Singh

first: Ximena

last: Corso-Díaz

first: Anand

last: Swaroop


title: Genome binding/occupancy profiling of ccRCC cell line upon SETD2 rescue [ChIPseq_JHRCC12]

status: Public on Nov 15 2021

first: Christina

middle: S

last: Leslie

state: NY

address: 417 E 68th St

department: Computational Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: SETD2, a H3K36 trimethyltransferase, is frequently mutated in human cancers with the highest prevalence (13%) in clear cell renal cell carcinoma (ccRCC). Genomic profiling of primary ccRCC tumors reveals a positive correlation between SETD2 mutations and metastasis. However, whether and how SETD2-loss promotes metastasis remains unclear. Here, we detected SETD2 mutations in 24 of 51 (47%) metastatic ccRCC tumors. Using SETD2-mutant metastatic ccRCC patient-derived cell line and xenograft models, we showed that H3K36me3 restoration greatly reduced distant metastases of ccRCC in mice. An integrated ATAC-seq, ChIP-seq, and transcriptome analysis concluded a tumor suppressor model in which loss of SETD2-mediated H3K36me3 activates enhancers to drive oncogenic transcription through dysregulating histone chaperone recruitment, enhancing histone exchange, and expanding chromatin accessibility. Furthermore, we uncovered mechanism-based therapeutic strategies for SETD2-deficient cancer through inhibition of histone chaperones. Overall, SETD2-loss creates a permissive epigenetic landscape for cooperating oncogenic drivers to amplify transcriptional output, providing unique therapeutic opportunities.

overall_design: ChIP-Seq was performed in SETD2-proficient and SETD2-deficient JHRCC12 cells in 2 replicates.

first: Yuchen

last: Xie

first: Merve

last: Sahin

first: Emily

last: Cheng


title: Temporally controlled Scn1a gene reconstitution rescues seizures, behavioral deficits and altered gene expression after symptom onset in Dravet syndrome mice

status: Public on Nov 29 2021

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

summary: Dravet Syndrome (DS) is a severe epileptic encephalopathy caused primarily by haploinsufficiency of the SCN1A gene. While different therapeutic strategies based on the upregulation of the healthy gene copy are being developed, repetitive seizures might lead to endurable and hardly treatable neural deficits. In fact, whether and to which extent this severe pathology is reversible after symptom onset remains unknown and the lack of this knowledge prevents the development of more effective therapies. We generated a novel Scn1a conditional knock-in mouse model (Scn1aStop) where Scn1a expression could be re-activated on-demand during the mouse lifetime. Scn1a gene disruption leads to the development of seizures, often associated with SUDEP and behavioral alterations including hyperactivity, social interaction deficits and cognitive impairment starting from the second/third week of age. However, we showed that Scn1a gene reconstitution when symptoms were already manifested (P30) led to a complete rescue of both spontaneous and thermic inducible seizures and marked amelioration of behavioral abnormalities. Normalization of firing of hippocampal parvalbumin interneurons was observed after reactivation of the Scn1a mutant allele. We also identified dramatic gene expression alterations associated with astrogliosis in DS mice, rescued by Scn1a gene expression normalization at P30. Interestingly, regaining of Nav1.1 physiological levels rescued epileptic seizures also in adult DS mice (P90) after months of repetitive seizure events. These results uncover the principles governing the reversibility of a severe epileptic encephalopathy as DS and they are central for accelerating therapeutic translation, providing key insights on the timing of delivery of the disease modifying therapies in DS.

overall_design: n=4 Scn1a wt Cortex, n=4 Scn1a wt  Hippocampus, n=4 Scn1a het Cortex, n=4 Scn1a het  Hippocampus, n=4 Scn1a rec Cortex, n=4 Scn1a rec Hippocampus

first: Gaia

last: Colasante

first: Vania

last: Broccoli


title: Chromatin landscape analysis of ccRCC cell line upon SETD2 rescue [ATACseq_JHRCC12]

overall_design: ATAC-Seq was performed in SETD2-proficient and SETD2-deficient JHRCC12 cells in 3 replicates.

middle: H


title: SETD2 Loss Creates A Permissive Epigenetic Landscape that Promotes Kidney Cancer Metastasis and Engenders Therapeutic Vulnerabilities

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Chromatin landscape analysis of murine renal tubular epithelial cells upon SETD2 knockout [ATACseq_RTE]

overall_design: ATAC-Seq was performed in primary renal tubular epithelial (RTE) cells cultured from Setd2(F/F)Ksp-Cre+ or littermate Setd2(F/F) mice in 3 replicates.


title: Transcriptomic profiling of MCF-7 breast cancer cells treated with G1, a G-protein coupled estrogen receptor (GPER1) agonist

status: Public on Nov 27 2021

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Guwahati

summary: Application of next generation sequencing (NGS) technology to identify G1-modulated genes in MCF-7 breast cancer cells

overall_design: MCF-7 breast cancer cells were treated with 100 nM G1 (n=3), 1 μM G1 (n=3) or vehicle (0.1% Ethanol, n=3) for 48 h.

first: Uttariya

last: Pal

first: Ankur

last: Sahu

first: Pankaj

last: Barah


title: Dicer promotes genome stability via the bromodomain transcriptional co-activator BRD4

status: Public on Nov 13 2021

city: Cold Spring Harbor

first: Robert

last: Martienssen

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

summary: RNA interference is required for post-transcriptional silencing, but also has additional roles in transcriptional silencing of centromeres and genome stability. However, these roles have been difficult to detect in mammals. Strikingly, we found that Dicer-deficient embryonic stem cells have strong proliferation and chromosome segregation defects as well as increased transcription of centromeric satellite repeats, which triggers the interferon response. We conducted a CRISPR-Cas9 genetic screen to restore viability and identified transcriptional activators, histone H3K9 methyltransferases, and chromosome segregation factors as suppressors, resembling Dicer suppressors identified in independent screens in fission yeast. The strongest suppressors were mutations in the transcriptional co-activator Brd4, which reversed the strand-specific transcription of major satellite repeats suppressing the interferon response, and in the histone acetyltransferase Elp3. We show that identical mutations in the second bromodomain of Brd4 rescue Dicer-dependent silencing and chromosome segregation defects in both mammalian cells and fission yeast. This remarkable conservation demonstrates that RNA interference has an ancient role in transcriptional silencing of satellite repeats, which is essential for cell cycle progression and proper chromosome segregation. Our results have pharmacological implications for cancer and autoimmune diseases characterized by unregulated transcription of satellite repeats.

overall_design: RNA-seq of Dicer1 mutant mouse embryonic stem cell (mESC) clones and induced populations at day 8, Brd4 mutant mESCs, Elp3 mutant mESCs, double mutant Dicer1/Brd4 mutant clones and induced populations, double mutant Dicer1/Elp3 mutant clones; small RNA sequencing of wild type mESCs, Dicer1 induced population, Dicer1 mutant clones, and Dgcr8 knockout mESCs; BRD4 ChIP-seq of wild type mESCs, Dicer1 induced mutant population, and Dicer1 mutant clones; H3K9 me2 and me3 ChIP-seq of wild type mESCs, Dicer1 induced populations of mESCs, and Dicer1 mutant mESC clones with input and H3 control

first: Michael

last: Gutbrod

first: Andrea

last: Schorn

first: Joshua

middle: I

last: Steinberg


title: Comparative analysis of chromatin state in monocytes from HIV+ individuals on ART

status: Public on Nov 26 2021

city: New Orleans

first: Francesca

last: Peruzzi

state: LA

address: 1700 Tulane Ave.

institute: LSU Health Sciences Center

summary: We report ChIP-sequencing data obtained of freshly isolated human CD14+ monocytes obtained from 3 HIV- controls and 6 HIV+ subjects. Persons living with HIV (PLWH) are at higher risk of developing secondary illnesses than their uninfected counterparts, suggestive of a dysfunctional immune system in these individuals. Upon exposure to pathogens, monocytes undergo epigenetic remodeling that results in either a trained or a tolerant phenotype, characterized by hyper-responsiveness or hypo-responsiveness to secondary stimuli, respectively. We utilized CD14+ monocytes from virally suppressed HIV+ patients and healthy controls for in vitro analysis following polarization of these cells toward a pro-inflammatory monocyte-derived macrophage (MDM) phenotype. We found that in HIV-derived MDMs, pro-inflammatory signals (TNFA, IL6, IL1B, miR-155-5p, and IDO1) dominate over negative feedback signals (NCOR2, GSN, MSC, BIN1, and miR-146a-5p), favoring an abnormally trained phenotype. The mechanism of this reduction in negative feedback involves the attenuated expression of IKZF1, a transcription factor required for de novo synthesis of RELA during LPS-induced inflammatory responses. Furthermore, restoring IKZF1 expression in HIV-MDMs partially reinstated expression of negative regulators of inflammation and lowered the expression of pro-inflammatory cytokines. Overall, this mechanism may provide a link between dysfunctional immune responses and susceptibility to co-morbidities in HIV+ individuals with low or undetectable viral load.

overall_design: Examination of 2 different histone modifications in CD14+ monocytes.


title: Tcf1 preprograms glycolysis mobilization   in central memory CD8+ T cells in recall response

status: Public on Nov 10 2021

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

summary: The goal of this study is to determine the impact of Tcf1 deficiency on recall capacity of central memory CD8+ T (Tcm) cells. We demonstrate that loss of Tcf1 shows limited impact on Tcm cells at resting state, but severely comprimises activation of glycolysis  and other key regulators during recall response. Based on these findings, we propose that Tcf1 preprograms the responsiveness of Tcm cells to secondary challenges.

overall_design: Genome-wide expression,  chromatin accessibility, TCF1 binding and chromatin interaction profiles of central memory CD8+ T cells.

first: Shan

last: Qiang

first: Hu

last: Sheng'en

first: Zang

last: Chongzhi

first: Xue

last: Hai-Hui


title: Biological response of adrenal carcinoma and melanoma cells to mitotane treatment

status: Public on Nov 02 2021

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary: A previous case study described an adrenal incidentaloma initially misdiagnosed as adrenocortical carcinoma (ACC) and treated with mitotane. The final diagnosis was metastatic melanoma of unknown primary origin. However, the patient developed rapid disease progression after mitotane withdrawal, suggesting a protective role for mitotane in a non-adrenal derived tumour. The aim of the present study was to determine the biological response of primary melanoma cells obtained from that patient and in two other established melanoma and ACC cell lines treated with mitotane. Although mitotane inhibited proliferation of both ACC and melanoma cells, its role in melanoma treatment appears to be limited. Flow cytometry analysis and transcriptomic studies indicated that the ACC cell line was highly responsive to mitotane treatment, although the primary melanoma cell line showed a moderate response in vitro. Mitotane modified activity in several key biological processes, including “mitotic nuclear division”, “DNA repair”, “angiogenesis”, and “negative regulation of ERK1 and ERK2 cascade”.

overall_design: The isolated RNA was pooled into two samples per group, consisting of the following: 1) untreated primary melanoma cell culture; 2) mitotane-treated primary melanoma cell culture; 3) untreated WM266-4 cell line; 4) mitotane-treated WM266-4 cell line; 5) untreated HAC15 cell line; 6) mitotane-treated HAC15 cell line. The cells were treated with mitotane (final concentration 50 μM) within 24 hours.

first: Ewelina

last: Stelcer

first: Karol

last: Jopek


title: High-throughput screen reveals purinergic receptor as a therapeutic target in circadian β-cell failure

status: Public on Nov 03 2021

city: Chicago

first: Benjamin

last: Weidemann

state: IL

address: 303 E. Superior St.

department: Medicine

institute: NORTHWESTERN UNIVERSITY

summary: We report a screen of 2,640 pharmacologically-active compounds in clock-deficient pancreatic β cells and reveal a mechanism by which ivermectin induces insulin secretion and regulates transcription in wild type and P2ry1 receptor knockout BetaTC6 β-cell lines by mRNA-seq.

overall_design:
Examination of mRNA expression changes in wild type and P2ry1 receptor knockout BetaTC6 β-cell lines treated with 20 mM glucose in the presence or absence of ivermectin.

The records have been updated with third-party re-analysis data as described below, on Jan 11, 2022:
Sequencing data from the study under SRA accession ERP017126 (Bioproject: PRJEB15401; ENA-SUBMISSION: ERA705448) (PMID: 27667667) was downloaded and converted to fastq files using the commands 'prefetch' followed by 'fastq-dump' via sra-toolkit (v2.10.5). Each individual cell/file was aligned and transcript abundance quantified using RSEM (v1.3.3) with Hg38 (GRCh38.p12) as a reference. Raw single-cell expression count values were imported into Rstudio and count files were aggregated into count matrices for each condition (ctrl.data.txt, t2d.data.txt) for analysis using Seurat. Following low-quality cell removal using the author-provided metadata (https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5061/E-MTAB-5061.sdrf.txt), normalized expression values were used in uniform manifold approximation and projection (UMAP) dimensional reduction analyses to cluster distinct cell types (As outlined in E-MTAB-5061_analysis.R).

E-MTAB-5061.sdrf.txt: Direct downloaded file from original authors including metadata on single-cell RNA-sequencing data. Available through https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5061/E-MTAB-5061.sdrf.txt
ctrl.data.txt: Single-cell RNA count matrix for cells from non-type 2 diabetic donors
t2d.data.txt: Single-cell RNA count matrix for cells from type 2 diabetic donors
E-MTAB-5061_analysis.R: Custom script for Seurat analysis of single-cell RNA count data from the study E-MTAB-5061

first: B


title: Impact of fluoxetine treatment and folic acid supplementation on the mammary gland transcriptome during peak lactation

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Lactation causes dramatic maternal calcemic adaptations where up to 10% of maternal bone density is mobilized for milk calcium. Serotonin plays a role in regulating this calcemic demand through alterations in DNA methylation. Selective serotonin reuptake inhibitors used to treat peripartum depression exacerbate this signaling. The first objective of this study was to determine the impact of fluoxetine, one of the most popular selective serotonin reuptake inhibitors, on the transcriptome of the mouse mammary gland during peak lactation. The second objective was to determine whether supplementation with folic acid, a well-known methyl donor, would mitigate the gene expression changes induced by fluoxetine.

overall_design: Two weeks before mating, C57BL/6 female mice were randomly assigned into breeder diet (4mg/kg folic acid, n = 16) or folic acid supplemented diet (24 mg/kg folic acid, n = 16). Female mice were bred overnight, and pregnancy was determined by observing a seminal plug, at which time the mice were housed individually and randomly assigned to fluoxetine or saline treatment. This resulted in 4 treatments (n = 8 mice per treatment): breeder diet + saline, breeder diet + fluoxetine, folic acid supplemented diet + saline, or folic acid supplemented diet + fluoxetine. Beginning on embryonic day 13 of pregnancy through day 10 of lactation, dams received a daily intraperitoneal injection of either 20 mg/kg bodyweight fluoxetine hydrochloride or saline. At day 10 of lactation, dams were euthanized, and mammary glands were rapidly extracted and stored at -80°C until RNA extraction.

first: Laura

last: Hernandez


title: The interaction of secreted phospholipase A2-IIA with the microbiota alters its lipidome and promotes inflammation

city: Québec

first: Antoine

last: BODEIN

state: QC

address: 2705 Bd Laurier

institute: Université Laval

summary: Secreted phospholipase A2-IIA (sPLA2-IIA) hydrolyzes phospholipids to liberate lysophospholipids and fatty acids. Given its poor activity toward eukaryotic cell membranes, its role in the generation of proinflammatory lipid mediators is unclear. Conversely, sPLA2-IIA efficiently hydrolyzes bacterial membranes. Here, we show that sPLA2-IIA impacts on the immune system by acting on the intestinal microbial flora. Using mice overexpressing transgene-driven human sPLA2-IIA, we found that the intestinal microbiota was critical for both induction of an immune phenotype and promotion of inflammatory arthritis. The expression of sPLA2-IIA led to alterations of the intestinal microbiota composition, but housing in a more stringent pathogen-free facility revealed that its expression could affect the immune system in the absence of changes to the composition of this flora. In contrast, untargeted lipidomic analysis focusing on bacteria-derived lipid mediators revealed that sPLA2-IIA could profoundly alter the fecal lipidome. The data suggest that a singular protein, sPLA2-IIA, produces systemic effects on the immune system through its activity on the microbiota and its lipidome.

overall_design: Identification of the microbiota composition of WT and sPLA2-IIATGN mice in different conditions. Conditions 1: at three different timepoint of a fecal microbiota transplantation: initial flora (Day 0), reconstituted flora (Day 21) and flora during arthritis (Day 29) (n = 5-7). Condition 2: in mice housed in an SPF animal facility (n = 7-8). Condition 3: in mice housed in an Elite SPF+ animal facility at two timepoints: at 14 weeks of age and at 14 months of age.

first: Etienne

last: Doré

first: Charles

last: Joly-Beauparlant

first: Satoshi

last: Morozumi

first: Alban

last: Mathieu

first: Tania

last: Lévesque

first: Isabelle

last: Allaeys

first: Anne-Claire

last: Duchez

first: Nathalie

last: Cloutier

first: Mickaël

last: Leclercq

last: Bodein

first: Christine

last: Payré

first: Cyril

last: Martin

first: Agnes

last: Petit-Paitel

last: Gelb

first: Manu

last: Rangachari

first: Makoto

last: Murakami

first: Laetitia

last: Davidovic

first: Nicolas

last: Flamand

last: Arita

first: Gérard

last: Lambeau

first: Arnaud

last: Droit

first: Eric

last: Boilard


title: Expression data of the mouse heart of a nose-only HCN inhalation model and a subcutaneous KCN injection model

city: Aberdeen Proving Ground

first: Ki

middle: Hwan

last: Ma

address: 8350 Ricketts Point Road

department: Medical Toxicology

institute: US Army Medical Research Institute of Chemical Defense

summary:
Smoke inhalation from a structure fire is a common route of cyanide poisoning in the U.S. Cyanide inhibits cellular respiration, often leading to death. Its rapid distribution throughout the body can result in injuries to multiple organs, and cyanide victims were reported to experience myocardial infarction and other cardiac complications.
We performed oligonucleotide microarrays to establish cardiac transcriptomes of an animal model of nose-only inhalation exposure to hydrogen cyanide (HCN), which is relevant to smoke inhalation. We also profiled cardiac transcriptomes after subcutaneous injection of potassium cyanide (KCN). Although the KCN injection model has been often used to evaluate medical countermeasures, this study demonstrated that cardiac transcriptomes are largely different from that of the HCN inhalation model at multiple time points within 24 hours after exposure.

overall_design: Non-anesthetized CD-1 adult male mice (20-35 g) were subjected to a subcutaneous injection of KCN (8.0 mg/kg) or a nose-only HCN inhalation, and volume-matched saline and air were used as control, respectively. The heart samples were harvested at several time points after exposure and total RNA was isolated for hybridization on Affymetrix microarrays.

first: Dennean

last: Lippner

first: Kelly

last: Basi

first: Susan

last: DeLeon

first: William

last: Cappuccio

first: Melissa

middle: O

last: Rhoomes

first: Diane

last: Hildenberger

first: Heidi

last: Hoard-Fruchey

first: Gary

last: Rockwood


title: Growth phase-associated changes in the proteome and transcriptome of Bifidobacterium animalis subsp. lactis A6

city: Beijing

first: Hui

last: Wang

address: No. 17 Tsing Hua East Road, HaiDian District

institute: China Agricultural University

summary: This study was aimed to further illustrate the expression files of BAA6 between the stationary phase and the exponential phase in MRSc broth, we combined the transcriptomic analysis with RNA sequencing and tandem mass tags (TMT) quantitative proteomic methods to quantitatively screen the differentially expressed genes and proteins. During the stationary phase, BAA6 expanded its carbon source utilizing profile and enhanced the transport of cellobiose, xylooligosaccharides (XOS), and raffinose to confront with glucose consumption. Meanwhile, the increased NH3 production, enhanced branched-chain amino acids (BCAAs) transport and biosynthesis, and upregulated GroEL/ES complex and Clp protease could contribute to respond to acid stress during fermentation. These findings provide a novel insight into the growth characteristics developed by B. animalis to environment changes.

overall_design: Sequencing libraries were generated using NEBNext® Ultra™ Directional  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations

first: Yanling

last: Hao


title: Vibrio vulnificus MARTX toxin effector domains differentially remodel the transcriptional response of intestinal epithelial cells

status: Public on Nov 21 2021

first: Karla

middle: Jean Fullner

last: Satchell

address: 303 East Chicago Ave

department: Microbiology-Immunology

institute: Northwestern University

summary: Vibrio vulnificus is an foodborne pathogen that can cause gastroenteritis and septicemia in humans. V. vulnificus secretes a multifunctional autoprocessing repeats-in-toxin (MARTX) toxin as an essential virulence factor to cause disease. MARTX toxins are pore-forming toxins that translocate multiple functionally independent effector domains into a target cell. MARTX toxins of V. vulnificus can contain anywhere from 3 to 5 of the 10 identified effector domains and strains with different effector repertories having varying virulence potential. The goal of this study was to compare how different effector combinations from an F-type MARTX toxin differentially remodel the transcriptional response of human intestinal epithelial cells (IECs). F-type MARTX toxins contain five effector domains – the actin crosslinking domain (ACD), two copies the makes caterpillar floppy-like domain (MCF), and alpha-beta hydrolase (ABH) domain, and the Ras/Rap1 specific endopeptidase (RRSP). Cultured human IECs were treated with V. vulnificus or strains modified to secrete a toxin with only ACD, ACD with MCF-ABH, ACD with RRSP, or no active effectors. We demonstrate that when no active effectors are present, the bacterium induces minimal changes in the transcriptional profile of IECs. However, the strains containing different effector combinations each uniquely remodeled the transcriptional profile of IECs. These data provide insight into how V. vulnificus strains with varying effector combinations can differentially regulate the host cell response to cause disease.

overall_design: T84 human colonic epithelial cells were inoculated with 98-783-DP-A1 Vibrio vulnificus containing the wild type F-type MARTX toxin or strains generated to contain MARTX toxins with varying effector combinations. mRNA from inoculated T84 cells was extracted for RNA-sequencing. Each processed file is in .xlsx file type and contain official gene symbol, fold changes compared to PBS treated controls, and p-vaules indicating statistically significant or non-significant changes in gene expression compared to PBS treated controls.

first: Patrick

last: Woida


title: Characterization of the zebrafish cell landscape at single-cell resolution

city: Hangzhou

first: Mengmeng

last: Jiang

address: Yuhangtang Road 866, Xihu Distric

institute: Zhejiang University

summary: Zebrafish have been found to be a premier model organism in biological and regeneration research. However, the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here, we utilized Microwell-seq to analyze more than 250,000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single-cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single-cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall, our single-cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research.

overall_design:
Expression profiling by high throughput sequencing of major zebrafish organ types.

Please note that 19 samples were added and 9 samples were deleted on Mar 1, 2022.

first: Guoji

last: Guo


title: The oxygen sensor Prolyl hydroxylase domain 2 regulates the in vivo suppressive capacity of regulatory T cells

status: Public on Nov 01 2021

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: The oxygen sensor PHD2 (prolyl hydroxylase domain 2) plays an important role in cell hypoxia adaptation by regulating the stability of HIF proteins (HIF1α and HIF2α) in numerous cell types including T lymphocytes. The role of oxygen sensor on immune cells, in particular on regulatory T cell (Treg) function, has not been fully elucidated. The purpose of our study was to evaluate the role of PHD2 in the regulation of Treg phenotype and function. We demonstrate herein that selective ablation of PHD2 expression in Treg (PHD2ΔTreg mice) leads to a spontaneous systemic inflammatory syndrome, as evidenced by weight loss, development of a rectal prolapse, splenomegaly, shortening of the colon and elevated expression of IFN-γ in the mesenteric lymph nodes, intestine and spleen. PHD2 deficiency in Tregs led to an increased number of activated CD4 conventional T cells expressing an effector/Th1-like phenotype. Concomitantly, the expression of innate-type cytokines such as IL1-β, IL-12p40, IL-12p35 and TNF-α was found to be elevated in peripheral (gut) tissues and spleen. PHD2ΔTreg mice also displayed an enhanced sensitivity to DSS-induced colitis and to toxoplasmosis, suggesting that PHD2-deficient Tregs do not efficiently control inflammatory response in vivo, in particular immune responses characterized by IFN-γ production. Further analysis revealed that Treg dysregulation is largely prevented in PHD2-HIF2α (PHD2-HIF2αΔTreg mice), but not in PHD2-HIF1α (PHD2-HIF1αΔTreg mice) double KOs, suggesting an important and possibly selective role of the PHD2-HIF2α axis in the control of Treg function. Finally, the transcriptomic analysis of PHD2-deficient Tregs revealed an altered expression of several chemokine receptors including CXCR3, a finding corroborated by the altered in vivo localization of PHD2-deficient Tregs in splenic tissues. Collectively, these findings uncover an important role of the PHD2-HIF2α axis in regulatory T cell positioning and trafficking.

overall_design:
The goal of this study was to compare transcriptome of Treg cells from different mouse strain (Foxp3cre, PHD2ΔTreg, PHD2-HIF1aΔTreg, PHD2-HIF2aΔTreg and PHD2-HIF1a-HIF2aΔTreg mice) to evaluate the role of PHD2-HIF2a axis on Treg phenotype.
Splenic Treg cells were purified with anti-CD4 antibody and expression of YFP using Cell Sorter. The sample purity was assessed by Foxp3 staining (purity > 97%) .Total RNA was extracted using the TRIzol method and subsequently used to prepare RNA-Seq library by using TruSeq RNA sample prep kit (Illumina).

first: Yousra

last: Ajouaou

last: Azouz

first: Anaelle

last: Taquin

first: Hind

last: Hussein

first: Fabienne

last: Andris

first: Muriel

last: Moser

first: Stanislas

last: Goriely

first: Oberdan

last: Leo


title: Mouse Osteoblast Differentiation RNA-seq analysis

status: Public on Oct 31 2021

city: Turku

first: Riku

last: Kiviranta

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: Analysis of the data indicated that there were clear changes in temporal expression which can also be observed through enriched pathways. K-means clustering reveals similarly behaving groups of genes which have the potential to be key players in the cell differe

overall_design: Investigation genome-wide expression and pathway changes in cells differentiating to mouse osteoblasts at 5 time points.

first: K

last: Tarkkonen

first: C

last: Valensisi

first: A

last: Dudakovic


title: Adult enteric Dclk1-positive glial and neuronal cells reveal distinct responses to acute intestinal injury

city: Munich

first: Moritz

last: Middelhoff

address: Ismaninger Str. 22

institute: TU München

summary: Intestinal ganglionic cells in the adult enteric nervous system (ENS) are continually exposed to stimuli from the surrounding microenvironment, and need at times to respond to disturbed homeostasis following acute intestinal injury. The kinase DCLK1 and intestinal Dclk1-positive cells have been reported to contribute to intestinal regeneration. While Dclk1-positive cells are present in adult enteric ganglia, their cellular identity and response to acute injury have not been investigated in detail. Here, we reveal the presence of distinct Dclk1-tdTom+/CD49b+ glial-like and Dclk1-tdTom+/CD49b- neuronal cell types in adult myenteric ganglia. These ganglionic cells demonstrate distinct patterns of tracing over time, yet show a similar expansion in response to elevated serotonergic signaling. Interestingly, Dclk1-tdTom+ glial-like and neuronal cell types appear resistant to acute irradiation injury-mediated cell death. Moreover, Dclk1-tdTom+/CD49b+ glial-like cells show prominent changes in gene expression profiles induced by injury, in contrast to Dclk1-tdTom+/CD49b- neuronal cell types. Finally, subsets of Dclk1-tdTom+/CD49b+ glial-like cells demonstrate prominent overlap with Nestin and p75NTR, and strong responses to elevated serotonergic signaling or acute injury. These findings, together with their role in early development and their neural-crest like gene expression signature, suggest the presence of reserve progenitor cells in the adult Dclk1 glial cell lineage.

overall_design: Single-cell RNA sequencing data are presented for sorted Dclk1-tdTom+/CD49b+ and Dclk1-tdTom/CD49b- cells from LMMP preparations of adult mice in homeostasis and following injury (n=6 mice per group, 2 mice pooled for each sorting)

first: Giovanni

last: Valenti

first: Lorenzo

last: Tomassoni

first: Pasquale

last: Laise

first: Timothy

middle: C

last: Wang


title: Comparative Analysis of Gene expression profile in the Adipose Tissue of Obese Adult Mice with Rapid Infantile Growth after Undernourishment in utero

status: Public on Nov 06 2021

city: Hamamatsu city

first: Misako

last: SUZUKI

state: Shizuoka, Japan

address: Higashi-ku 1-20-1 Handayama

country: Japan

institute: Hamamatsu University School of Medicine.

summary:
Rapid growth in infancy considerably increases the risk of obesity and metabolic disorders in adulthood especially among neonates born small. To investigate the molecular mechanism of rapid infantile growth (RG) following undernourishment in utero (UN) in the deterioration of the adult fat deposit, we developed a mouse animal UN model by maternal energy restriction, followed by RG by adjustment of 4 pups per litter soon after birth. High fat diet (FHD) was supplied to the weaned pups, with or without the treatment of tauroursodeoxycholic acid (TUDCA; TU).
UN-RG pups showed deterioration of diet-induced obesity and fat deposit, which was ameliorated by TU. We carried out microarray analysis of epidydimal adipose tissue.

overall_design: We carried out microarray analysis of epidydimal adipose tissue ;groups of NN-Veh,UN-RG-Veh, NN-TU, UN-RG-Veh.

first: Hiroaki

last: Itoh

first: Yukiko

last: Kohmura-Kobayashi

last: Suzuki