title: Bulk RNAseq expression data of colon biopsies from intestinal mucosa of non-IBD controls and patients with Crohn's disease or ulcerative colitis

status: Public on Jun 20 2023

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

institute: IDIBAPS

summary: Ulcerative colitis and Crohn’s disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in manifestations and response to treatment. While the molecular basis for this heterogeneity remains uncharacterized, single-cell technologies allow us to explore the transcriptional states within tissues at an unprecedented resolution which could further understanding of these complex diseases. Here, we apply single-cell RNA-sequencing to human inflamed intestine and show that the largest differences among patients are present within the myeloid compartment including macrophages and neutrophils. Using spatial transcriptomics in human tissue at single-cell resolution (CosMx Spatial Molecular Imaging) we spatially localized each of the macrophage and neutrophil subsets identified by single-cell RNA-sequencing and unravel further macrophage diversity based on their tissue localization. Finally, single-cell RNA-sequencing combined with single-cell spatial analysis reveals a strong communication network involving macrophages and inflammatory fibroblasts. Our data sheds light on the cellular complexity of these diseases and points towards the myeloid and stromal compartments as important cellular subsets for understanding patient-to-patient heterogeneity.

overall_design: Barcoded RNAseq libraries were prepared from total RNA using a TruSeq stranded mRNA kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were subjected to single-end sequencing (100 bp) on a HighSeq-3000 platform (Illumina, CA, USA) at the Translational Medicine and Genomics group (Boehringer-Ingelheim GmbH & Co, Biberach, Germany). Quality filtering and adapter trimming was performed using Skewer version 2.2.8 Reads were mapped against the human reference genome using the STAR aligner version 2.5.2a. The genome used was GRCh38.p10, and gene annotation was based on Gencode version 27 (EMBL-EBI, Hinxton, UK). Read counts per gene were obtained using RSEM version 1.2.31 and the Ensembl GTF annotation file (EMBL-EBI, Hinxton, UK).

first: Alba

last: Garrido-Trigo


title: TET2 deficiency maintains leukemia stem cell self-renewal and subverts tumor immunity [model 2]

status: Public on Jun 23 2023

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

country: USA

institute: Beckman Research Institute of City of Hope

type: Expression profiling by high throughput sequencing

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

overall_design: We established NRAS/AE9a leukemic cells with bone marrow-derived hematopoietic stem cells from wildtype (WT) and Tet2-/- mice which was with the deletion of exon 3. We then performed comparative gene expression profiling analysis of RNA-seq for these AML cells.

first: Yangchan

last: Li

first: Rui

last: Su

first: Lei

last: Dong


title: Assessing the influence of distinct IVF culture media on human pre-implantation development using single-embryo transcriptomics

status: Public on Jun 19 2023

city: DIJON

first: Bastien

last: Ducreux

address: Batiment B3, 15 boulevard Maréchal de Lattre de Tassigny

country: France

institute: Inserm U1231

summary: The use of Assisted Reproductive Technologies (ART) is rising consistently across the world. However, making an informed consent on the choice of which embryo culture media should be preferred to ensure satisfactory success rates and the future children to be healthy lacks scientific knowledge. Particularly, embryos within their first days are highly sensitive to their micro-environment with limited stress tolerance mechanisms. Here, we aimed to determine whether culture media that differed markedly in their composition used before compaction would affect gene expression and subsequent human embryonic development.

overall_design: We employed single-embryo RNA-seq on human embryos cultured until day-2 or day-5 in distinct culture media.

first: Julie

last: Barberet

first: Magali

last: Guilleman

first: Raquel

last: Pérez-Palacios

first: Céline

last: Bruno

first: Aurélie

last: Teissandier

first: Déborah

last: Bourc’his

first: Patricia

last: Fauque


title: Transcriptional remodeling of primary human monocytes exposed to itaconate and its derivatives in the context of trained immunity

status: Public on Jun 26 2023

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

summary: Trained immunity is a phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, altering their responses to future exposures. This study profiled the transcriptome of human monocytes and in vitro differentiated macrophages, exposed to a combination of LPS, BG, DMI, or Itaconate.

overall_design: Human primary monocytes were isolated using Ficoll and Percoll gradient separation. Baseline monocytes were collected after 1 hour in culture (attached). Samples for media alone, LPS, BG, DMI, itaconate, or a combination of LPS+DMI and BG+DMI, were collected at 4 hours post stimulation (4h sample), 24 hours post stimulation (day 1 sample). Additionally,exposed RNA was collected from monocytes were allowed to differentiate to macrophages for 5 days (day 6 sample) and then re-exposed to LPS for 4 hours (restimulation sample).

first: Anaisa

last: Ferreira

first: Mihai

last: Netea

first: Jorge

last: Dominguez Andres


title: TET2 deficiency

status: Public on Jun 22 2023

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

overall_design: Refer to individual Series


title: Intrinsic sexual dimorphism in the placenta determines the differential response to benzene exposure

status: Public on Jun 21 2023

city: Detroit

first: Gil

middle: G.

last: Mor

state: Michigan

address: 275 E. Hancock

department: C.S. Mott Center for Human Growth and Development

institute: Wayne State University School of Medicine

summary: To investigate the impact of benzene exposure during pregnancy on the placenta and fetal development

overall_design: C57/BL6 mice were exposed to 50ppm benzene for 5 hours a day from E0.5 to E17.5. Tissues were collected on E17.5

first: Jiahui

last: Ding

first: Anthony

last: Maxwell

first: Nicholas

last: Adzibolosu

first: Katherine

last: Gurdziel

first: Douglas

last: Ruden


title: Tet2 regulates Sin3a recruitment at active enhancers in embryonic stem cells

city: New York

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

type: Methylation profiling by high throughput sequencing

summary: In this study: (1) we distinguished Tet2 target genes that are regulated by its catalytic vs. noncatalytic functions in ESCs by transcriptomic profiling of Tet2 wildtype (WT), Tet2 catalytic mutant (Mut), and Tet2 knockout (KO) mouse ESCs by RNA-seq. (2) We mapped genome-wide DNA methylation of Tet2-WT, Tet2-Mut, and Tet2-KO ESCs by WGBS, to establish a critical role for Tet2 in demethylating promoters and enhancers of its catalytic target genes. (3) We determined how the genome-wide occupancy of the epigenetic modifiers Sin3a and Sap30 and the enrichment of H3K27ac, are affected in Tet2-Mut and Tet2-KO ESCs versus Tet2-WT by CUT&Tag and identified that Tet2 deficiency diminishes Sin3a occupancy at promoters and enhancers. (4) We mapped Sin3a levels genome-wide in Tet1/2 double catalytic mutant (DMUT) and Tet1/2 double knockout (DKO) ESCs, and found that deficiency of both Tet1 and Tet2 resulted in decreased levels of Sin3a in a subset of active enhancers.

overall_design: We studied the role of Tet2 noncatalytic functions in the regulation of ESC gene expression by performing transcriptomic analysis of Tet2-WT, Tet2-Mut, and Tet2-KO ESCs by RNA-seq to identify differentially expressed genes. RNA-Seq: Three independent ESC for Tet2-WT and two clones for each Tet2-Mut and Tet2-KO were cultured on feeders, pre-plated to remove feeders, and seeded on gelatin overnight. Total RNA was extracted (Omega E.Z.N.A Total RNA kit). Library preparation and RNA-seq were performed at Novogene (https://en.novogene.com/) on an Illumina Novoseq 6000 platform. About 20-30 million reads were generated per sample. Details of RNA-seq and data analysis are described in the methods sections of the manuscript.  WGBS: One clone of each genotype of ESCs was seeded on feeders and plated on gelatin overnight. High-quality DNA was extracted (Quick-DNA miniprep kit (Zymo, D3024) and sent for WGBS analysis at BGI genomics company (https://en.genomics.cn/). Lamda DNA spike-in was added to confirm the bisulfite conversion efficiency. Details of WGBS and data analysis are described in the methods sections of the manuscript. CUT&Tag: For Sin3a, Sap30 and H3K27ac genome-wide occupancy experiments, one ESC line of each genotype (Tet2-WT, Tet2-Mut, and Tet2-KO) was cultured on feeders, pre-plated to remove feeders, and seeded on gelatin overnight. For Tet1/2 DMUT and DKO ESCs, two independent clones of each genotype were used. ESCs were crosslinked, bound to Con-A beads, incubated with primary antibody and treated with pre-loaded pA-Tn5 adapter complex. Details of CUT&Tag procedure and data analysis are described in detail in the methods section of the manuscript. Libraries were prepared using NEBNext HiFi 2x PCR Master and subjected to 75-bp paired-end sequencing using Illumina NextSeq 500 platform at the Einstein Epigenomics core following their protocols.

first: Julio

middle: C

last: Flores

first: Simone

last: Sidoli


title: TET2 deficiency maintains leukemia stem cell self-renewal and subverts tumor immunity [model 1]

first: Jianjun

last: Chen

overall_design: We established NRAS/AE9a leukemic cells with bone marrow-derived hematopoietic stem cells from wildtype (WT) and Tet2-/- mice which was absent of exons 8 to 10. We then performed comparative gene expression profiling analysis of RNA-seq for these AML cells.

first: Yangchan

last: Li

first: Rui

last: Su

first: Lei

last: Dong


title: Sugar accumulation enhancement in sorghum stem is associated with reduced reproductive sink strength and increased phloem unloading activity

status: Public on Jun 17 2023

city: Urbana

first: Gabriel

last: Beuchat

email: beuchat2@illinois.edu, beuchag@uw.edu

state: IL

address: 1201 W Gregory Dr

department: Plant Biology

institute: University of Illinois at Urbana Champaign

summary: Sweet sorghum has emerged as a promising source of bioenergy mainly due to its high biomass and high soluble sugar yield in stems. Studies have shown that loss-of-function Dry locus alleles have been selected during sweet sorghum domestication, and decapitation can further boost sugar accumulation in sweet sorghum, indicating that the potential for improving sugar yields is yet to be fully realized. To maximize sugar accumulation, it is essential to gain a better understanding of the mechanism underlying the massive accumulation of soluble sugars in sweet sorghum stems in addition to the Dry locus. We performed a transcriptomic analysis upon decapitation of near-isogenic lines for mutant (d, juicy stems, and green leaf midrib) and functional (D, dry stems and white leaf midrib) alleles at the Dry locus. Our analysis revealed that decapitation suppressed photosynthesis in leaves, but accelerated starch metabolic processes in stems. SbbHLH093 negatively correlates with sugar levels supported by genotypes (DD vs. dd), treatments (control vs. decapitation), and developmental stage post anthesis (3d vs.10d). D locus gene SbNAC074A and other programmed cell death-related genes were downregulated by decapitation, while sugar transporter-encoding gene SbSWEET1A was induced. Both SbSWEET1A and Invertase 5 were detected in phloem companion cells by RNA in situ assay. Loss of the SbbHLH093 homolog, AtbHLH093, in Arabidopsis led to a sugar accumulation increase. This study provides new insights into sugar accumulation enhancement in bioenergy crops, which can be potentially achieved by reducing reproductive sink strength and enhancing phloem unloading.

overall_design: 64 Samples from the stem and a leaf from two genotypes (D and d), a control and decapitation treatment, and two lengths of treatment before collecting (3d and 10d).

first: Xueyi

last: Xue

first: Ya-Chi

last: Yu

first: Jiang

last: Wang

first: Stephen

last: Moose

first: Jin

first: Li-Qing


title: Mitochondria- and polyribosome-interacting lncRNA sequencing analysis in human embryonic stem cells, iPSCs and fibroblasts

status: Public on Jun 16 2023

city: Palo Alto

first: Ji-Fan

last: Hu

state: California

address: 3801 Miranda Ave

institute: Stanford University

summary: RNA-seq reveals the differentially distributed mitochondrial and polyribosome related lncRNAs in human pluripotent stem cells versus fibroblasts

overall_design: The human H9 embryo stem cell line, human induced pluripotent stem cell and human fibroblast cells  (C11/S0730 line, PMID: 21636641) were  used to isolate RNAs from the whole cell, mitochondria, polyribosomes for Illumina Library sequencing.

first: Jifan

last: Zhou

first: Miguel

middle: A

last: Esteban

first: Jiuwei

last: Cui


title: Pharmacological targeting Netrin-1 inhibits EMT in cancer

status: Public on Jun 13 2023

city: Brussels

first: Sebastiaan

last: Vanuytven

address: Campus Erasme CP 637

country: Belgium

institute: Université Libre de Bruxelles


title: A contamination focused approach for optimizing the single-cell RNA-seq experiment

status: Public on Jun 14 2023

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: created metrics to measure quality of scRNA seq datasets

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: compared contamination QC metrics and standard QC metrics on multiple experimental conditions

first: Alan

last: Simmons

first: Deronisha

last: Arceneaux


title: Pharmacological targeting Netrin-1 inhibits EMT in cancer [scRNA-seq]

summary: Epithelial-to-Mesenchymal transition (EMT) regulates tumor initiation, progression, metastasis and resistance to anti-cancer therapy. Whereas great progress had recently been made in understanding the role and mechanisms that regulate EMT in cancer, no therapeutic strategy to pharmacologically target EMT had been identified so far. Here, we found that Netrin-1 is upregulated in a primary mouse model of skin squamous cell carcinoma (SCCs) presenting spontaneous EMT. Pharmacological inhibition of Netrin-1 by administrating NP137, an anti-Netrin-1 blocking monoclonal antibody currently used in clinical trials in human cancer, decreased the proportion EMT tumor cells in skin SCCs, as well as decreased the number of metastasis and increased the sensitivity of tumor cells to chemotherapy. Single-cell RNA-seq revealed the presence of different EMT states including epithelial, early and late hybrid EMT as well as fully EMT states in control SCCs. In contrast, administration of NP137 prevents the progression of cancer cells towards a late EMT state and sustains tumor epithelial states. ShRNA knockdown (KD) of Netrin-1 and its receptor Unc5b in EPCAM+ tumor cells inhibited EMT in vitro in the absence of stromal cells and regulated a common gene signature promoting tumor epithelial state and restricting EMT. To assess the relevance of these findings to human cancers, we treated mice transplanted with A549 human cancer cell line that undergoes EMT following TGF-b1 administration with NP137. Netrin-1 inhibition decreased EMT in A549 cells in vivo. Altogether, our results identify a new pharmacological strategy to target EMT in cancer opening novel therapeutic interventions for anti-cancer therapy.

overall_design: To induce tumorigenesis on Lgr5CreER/ KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ (LKPR), Tamoxifen was diluted at 25 mg/ml in sunflower seed oil, 10% EtOH (Sigma). Four daily intraperitoneal (IP) injections of 2.5 mg tamoxifen were administered at P28 to LKPR mice. After 7-9 week after Tamoxifen injection tumor appearance and size were detected by daily observation and palpation. Mice were euthanized when tumor size was reached or when mice presented signs of distress. To determine the effect of anti-Netrin-1 molecule (NP137) on primary tumor, LKPR mice were treated intraperitoneally at 10 mg/kg every two days from 4 weeks after Tamoxifen injection and until the death of animal.  Control and NP137-treated skin tumors from LKPR mice were dissected, rinsed and digested in collagenase type I (Sigma) at 3,5mg/ml in HBSS (Gibco) for 1h at 37°C on a rocking plate protected from the light. Collagenase was blocked by the addition of EDTA (5mM) and then the cells were rinsed 1 time in PBS supplemented with 10% FBS and the cell suspension were filtered through a 70-μm cell trainer (BD Bioscience). For the wash next and antibody incubation, cells were resuspended in PBS supplemented with 2% FBS (facs buffer). Cells were incubated with BV711- conjugated anti-EPCAM (rat, clone G8.8, BD Bioscience Cat#563134, dilution 1:100), PE-conjugated anti-CD45 (rat, clone 30-F11, BD, Cat#553081, dilution 1:100) and PE-conjugated anti-CD31 (rat, clone MEC 13.3, BD, Cat#553373, dilution 1:100) antibodies for 30 min at 4 °C protected from light. For cell sorting, cells were also filtered through a 40-μm cell trainer (BD Bioscience). Living single tumor cells were selected by forward and side scatter, doublet discrimination and Hoestch exclusion. Profile of the tumors was analyzed following viability and profile of YFP, Lin- (CD45/CD31) and EPCAM expression. Once screened all lived cells were sorted for single cell RNA sequencing experiment using FACSAria and FACSDiva software (BD Bioscience). After FACS isolation, lived cells were loaded onto each channel of the Chromium Single Cell 3’ microfluidic chips (V2-chemistry, 10X Genomics) and individually barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics).

first: Justine

last: Lengrand

first: Yura

last: Song

first: Cédric

last: Blanpain


title: Multimodal immune cell phenotyping in gastrointestinal biopsies reveals microbiome-related T cell modulations in human GvHD patients

status: Public on Jun 18 2023

city: Munich

first: Sebastian

last: Jarosch

state: Bavaria

address: Trogerstr. 30

department: institut für Medizinische Mikrobiologie, Immunologie und Hygiene

country: Germany

institute: TU Munich

summary: Acute graft-versus-host disease (aGvHD) is a significant complication after allogeneic hematopoietic stem cell transplantation (aHSCT), but major factors determining disease severity are not well defined yet. By combining multiplexed tissue imaging and single-cell RNA sequencing on gastrointestinal biopsies from aHSCT patients with fecal microbiome analysis, we could link high microbiome diversity and the abundance of short-chain fatty acid-producing bacteria to the sustenance of suppressive regulatory T cells. Furthermore, aGvHD severity was strongly associated with the clonal expansion of mainly CD8 T cells, which we found distributed over anatomically distant regions of the gut, persistent over time, and inversely correlated with the presence of suppressive Tregs. Overall, our study highlights the pathophysiological importance of expanded CD8 T cell clones in the progression of aGvHD towards more severe clinical manifestations and strongly supports the further development of microbiome interventions as GvHD treatment via repopulation of the gut Treg niche to suppress inflammation.

overall_design: scRNA sequencing data for gastrointestinal immune cells from HSCT patients

first: Jan

last: Köhlen

first: Sakhila

last: Ghimire

first: Erik

middle: T

last: Orberg

first: Ludwig

last: Pachmayr

first: Monika

last: Hammel

first: Doris

last: Gaag

first: Matthias

last: Evert

first: Klaus-Peter

last: Janssen

first: Andreas

last: Hiergeist

first: André

last: Gessner

first: Daniela

last: Weber

first: Elisabeth

last: Meedt

first: Hendrik

last: Poeck

first: Elvira

last: D’Ippolito

first: Ernst

last: Holler

first: Dirk

middle: H

last: Busch


title: RNA sequencing of myelod derived suppressor cells (MDSCs) and Bone marrow (BM)

status: Public on Jun 09 2023

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

summary: Myeloid-derived suppressor cells were subjected to polysome profiling analysis to identify the expressed membrane-tethered proteins involved in their recruitment into prostate cancer.

overall_design: Bone marrow-derived MDSCs were sorted in Cd11bhigh; Ly6Ghigh;Ly6Cint and Cd11bhigh; Ly6Gneg;Ly6Chigh after 5 days of in vitro differentiation. Then, polysome profiling of three independent biological replicates was performed.

first: Martina

last: Troiani


title: Pharmacological targeting Netrin-1 inhibits EMT in cancer [Visium]

first: Sebastiaan

last: Vanuytven

summary: Epithelial-to-Mesenchymal transition (EMT) regulates tumour initiation, progression, metastasis and resistance to anti-cancer therapy. Whereas great progress had recently been made in understanding the role and mechanisms that regulate EMT in cancer, no therapeutic strategy to pharmacologically target EMT had been identified so far. Here, we found that Netrin-1 is upregulated in a primary mouse model of skin squamous cell carcinoma (SCCs) presenting spontaneous EMT. Pharmacological inhibition of Netrin-1 by administrating NP137, an anti-Netrin-1 blocking monoclonal antibody currently used in clinical trials in human cancer, decreased the proportion EMT tumour cells in skin SCCs, as well as decreased the number of metastasis and increased the sensitivity of tumour cells to chemotherapy. Single-cell RNA-seq revealed the presence of different EMT states including epithelial, early and late hybrid EMT as well as fully EMT states in control SCCs. In contrast, administration of NP137 prevents the progression of cancer cells towards a late EMT state and sustains tumour epithelial states. ShRNA knockdown (KD) of Netrin-1 and its receptor Unc5b in EPCAM+ tumour cells inhibited EMT in vitro in the absence of stromal cells and regulated a common gene signature promoting tumour epithelial state and restricting EMT. To assess the relevance of these findings to human cancers, we treated mice transplanted with A549 human cancer cell line that undergoes EMT following TGF-b1 administration with NP137. Netrin-1 inhibition decreased EMT in A549 cells in vivo. Altogether, our results identify a new pharmacological strategy to target EMT in cancer opening novel therapeutic interventions for anti-cancer therapy.

overall_design: To induce tumorigenesis on Lgr5CreER/ KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ (LKPR), Tamoxifen was diluted at 25 mg/ml in sunflower seed oil, 10% EtOH (Sigma). Four daily intraperitoneal (IP) injections of 2.5 mg tamoxifen were administered at P28 to LKPR mice. After 7-9 week after Tamoxifen injection tumour appearance and size were detected by daily observation and palpation. Mice were euthanized when tumour size was reached or when mice presented signs of distress. To determine the effect of anti-Netrin-1 molecule (NP137) on primary tumour, LKPR mice were treated intraperitoneally at 10 mg/kg every two days from 4 weeks after Tamoxifen injection and until the death of animal. Control and NP137-treated skin tumours from LKPR mice were dissected, rinsed one part of the tumors has been kept for immunochemistry. Tumour tissues were pre-fixed in 4% PFA for 2 h at room temperature, rinsed in PBS, before to be embedded in FFPE.  To analyze the spatial distribution and localization of different EMT tumors states previously described by scRNA-seq in Control and anti-Netrin-1 treated skin SCC tumors, we used VISIUM technology for spatial transcriptomic analysis (10X Genomics). FFPE tissue section were places on Visium slides and prepared according to 10X Genomics protocols. After H&E staining, imaging and decrosslinking steps, tissue sections were incubated with human specific probes targeting 10,551 genes (10X genomics, Visium Mouse Transcriptome probe Set v1.0).

first: Justine

last: Lengrand

first: Yura

last: Song

first: Cédric

last: Blanpain


title: Autophagy ablation in skeletal muscles worsens sepsis-induced muscle wasting, impairs whole-body metabolism, and decreases survival

city: Montreal

first: Gilles

last: Gouspillou

state: Québec

address: 141 Avenue du Président Kennedy

department: Département des sciences de l'activité physique

country: Canada

institute: UQAM

summary: mRNA expression data for the mouse tibialis anterior (TA) muscle (n=5 per group) were obtained using Affymetrix Mouse Clariom S Assay (Affymetrix, Santa Carla, CA) according to the manufacturer’s recommendations.

overall_design: Female Atg7f/f and Atg7iSkM-KO mice (~16-wk-old) were sacrificed 6 days CLP post-surgery and total RNA was extracted from TA muscles.

first: JP

last: Leduc-Gaudet

first: S

last: Hussain

first: G


title: Pharmacological targeting Netrin-1 inhibits EMT in cancer [BulkRNA-seq]

overall_design: FACS isolated EPCAM+ Primary mouse skin SCC cell line derived from LKPR tumors was cultured in Modified eagle medium (MEM) (Capricorn scientific, Cat#SP-2002-500ml) supplemented with 10% Foetal bovine serum (FBS) (Serana, Cat#S-FBS- SA-015), 4μg/ml hydrocortisone (Sigma, Cat#H0888) 1% penicillin/streptomycin (100X) (Capricorn 2 scientific, Cat#PS-B), 2mM L-glutamine, 2ml amphotericin B (100X) (Capricorn scientific, Cat#AMP- B) and 500μl T3 (Sigma, Cat#T6397). _x000B_For generation of Netrin-1 and Unc5b Knock-down Epcam+ cell lines,  of HEK 293T (Human embryonic kidney 293T) (ATCC) were used as packaging cells. Transfer plasmid pLKO.1-puro, carrying our gene of interest Unc5b or Ntn1 (Sigma), TRC1 as empty vector, PPAX and PMDG packaging plasmids were transfected into the cells with lipofectamine 2000 (Thermo Fisher Scientific) using Opti-Medium (Capricorn scientific). EPCAM+ cell lins was plated and transduced with Opti-medium (Capricorn scientific). Puromycin resistance test has been realized after transduction.   For bulk RNA-sequencing experiement, cells were plated 100% Epcam+ and after 6 days, washed in PBS and detached from the cell culture plate with trypsin. Cells were resuspended and washed with PBS supplemented with 2% FBS (Facs buffer) and incubated with BV711- conjugated anti-EPCAM (rat, clone G8.8, BD Bioscience Cat#563134, dilution 1:100) 30min at room temperature and protected from the light. For cell sorting, cells were washed 2 times in Facs buffer and filtered through a 40- um cell trainer (BD Bioscience). Living single YFP+/ EPCAM+ tumour cells were selected by forward and side scatter, doublet discrimination and Hoestch exclusion. Cells were sorted in lysis buffer for RNA extraction from RNeasy micro kit (Qiagen) and RNA quality was evaluated by Bioanalyzer 2100 (Agilent) prior sequencing.


title: DNA Methylation Signatures Differentiate Meningiomas from Normal Dura [HumanMethylation450]

city: Los Angeles

first: Michelle

middle: Ariana

last: Wedemeyer

address: 1200 N State St, Suite 3300

department: Neurosurgery

institute: University of Southern California

type: Methylation profiling by genome tiling array

summary: Meningiomas are the most common primary brain tumor.  Though typically benign with a low mutational burden, histopathologic analysis has poor predictive value for malignant behavior and there are no proven chemotherapies.  Although DNA methylation patterns distinguish subgroups of meningiomas and have higher predictive value for tumor behavior than histologic classification, little is known about differences in DNA methylation between meningiomas and surrounding normal dura tissue.  Using multimodal studies of meningioma/dura pairs, we identified 4 distinct DNA methylation patterns.  Diffuse DNA hypomethylation of malignant meningiomas readily facilitated their identification from lower grade tumors by unsupervised clustering.  All clusters and 12/12 meningioma-dura pairs exhibited hypomethylation of the gene promoters of a module associated with the craniofacial patterning transcription factor FOXC1 and its upstream lncRNA FOXCUT.  Furthermore, we identified an epigenetic continuum of increasing hypermethylation of polycomb repressive complex target promoters with increased histopathologic grade suggesting progressive epigenetic dysregulation is associated with increasing tumor aggressiveness.  These findings are a starting point for future investigations of the role of epigenetic dysregulation of FOXC1 and cranial patterning genes in early stages of meningioma formation as well as studies of the utility of polycomb inhibitors for treatment of aggressive meningiomas.

overall_design: DNA methylation of matched meningioma/dura samples from 12 patients (11 WHO grade I, 1 WHO grade II) and 19 meningiomaswere assessed using Illumina HM450K methylation arrays. Also analyzed including were DNA methylation array data from 19 meningiomas (11 WHO grade I, 6 WHO grade II, and 4 WHO grade III) previously reported in GEO (GSE42882).

first: Gabriel

last: Zada

first: Suhn

middle: K

last: Rhie

first: Ivo

last: Muskins

first: Joseph

middle: L

last: Wiemels

first: Daniel

middle: J

last: Weisenberg

first: Kai

last: Wang

first: Debraj

last: Mukerjee

first: Ben

last: Strickland


title: Gene expression profile at single cell level of aortic cells from 2 adult R26-DreER;Ki67-CrexER;R26-GFP;Kdr rox/rox (Kdr-KO) mice after 8weeks of tamoxifen treatment.

status: Public on Jun 12 2023

city: Shanghai

first: zixin

last: liu

address: 320 Yueyang road, Life Science Research Building A2112

country: China

institute: Center for Excellence in Molecular Cell Science

summary: The heterogeneity of endothelial cell proliferation is not addressed. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of aortic endothelial cell proliferation.

overall_design: Aortic cells were isolated by digestion with Collagenase type 1 at 37℃ for 30 minutes. The cell suspension was filtered through a 70 µm cell strainer and then pelleted by centrifugation at 300g for 5 minutes.  After washing cells with 500ml HBSS, cells were loaded onto the 10x Chromium controller the generate Gel Bead-in-Emulsions (GEMs), which were further processed into single cell 5’ gene expression libraries using Chromium Single Cell 5’ Library Kit (v2). Sequencing was performed on Illumina Nova6000 PE150 platform. Fastq files were processed by CellRanger (v.6.1.1) pipeline.

first: Yi

last: Li

first: Zixin

last: Liu

first: Ximeng

last: Han

first: Feng

last: Liang

last: He

first: Bin

last: Zhou


title: Transcriptomic analysis of double-negative B cell subsets in IgG4-related disease

status: Public on Jun 08 2023

city: Cambridge

first: Vinay

middle: S

last: Mahajan

state: MA

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

summary: IgD-CD27- “double negative” (DN) B cells are known to be expanded in the blood in many disease contexts and the IgD-CD27-CXCR5-CD11c+ DN2 B cell subset has been most widely studied in autoimmune diseases. In addition to DN2 B cells, a distinct IgD-CD27-CXCR5-CD11c- DN3 B cell subset accumulates in the blood both in IgG4-related disease, an autoimmune disease in which inflammation and fibrosis can be reversed by B cell depletion, and in severe COVID-19. DN3 B cells, but not DN2 B cells, prominently accumulate in the blood and end-organs of IgG4-related disease.

overall_design:
Total RNA was extracted from IgD-CD27- double negative (DN) B cell subsets from subjects with IgG4-related disease and subjected to mRNA sequencing using the SmartSeq2 protocol. IgD-CD27- DN B cell subsets were defined using the following flow cytometry markers:
DN1: CXCR5pos CD11Cneg
DN2: CXCR5neg CD11Cpos
DN3: CXCR5pos CD11Cpos
DN4: CXCR5neg CD11Cneg

first: Pillai

last: Shiv

first: Allard

last: Hugues


title: RNA sequencing of different GEMMs of prostate cancer

first: Andrea

last: Alimonti

summary: Prostate cancers of different genetic backgrounds were subjected to polysome profiling analysis to identify the extracellular interactome between prostate cancer and myeloid-derived suppressor cells.

overall_design: Polysome profiles analysis of prostate was performed in six different genetic backgrounds: wild-type, Ptenpc-/-, Ptenpc-/-;TMPRSS2-ERGpc+/+,  Ptenpc-/-;CDCP1pc+/+, Ptenpc-/-;TIMP1-/- and Ptenpc-/-;Trp53pc-/-. Polysome profiling of the prostate of three mice for genotype was performed.

first: Martina

last: Troiani


title: Genome-wide DNA methylation analysis of leukoplakia and oral cancers

status: Public on Jun 05 2023

city: Navi Mumbai

first: Manoj

middle: Balkrishna

last: Mahimkar

state: Maharashtra

address: Sector-22, Owe Village, Kharghar Node

country: India

institute: Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre

summary: Genomewide DNA methylation profiling of oral leukoplakia and oral sqamous cell carcinoma (OSCC) was performed to delineate candidate gene associated with progression and clinicopathological parameters. All tissue samples were collected after obtaining written informed consent. The DNA methylation profile of 74 OSCC and 22 leukoplakia were compared with 22 normal control tissues from healthy donor.

overall_design: Genome-wide DNA methylation profiling was performed on 74 early- and late-stage OSCC samples, 22 histologically confirmed leukoplakia samples and 22 healthy normal tissues using Infinium Methylation EPIC (850K) BeadChips (Illumina, San Diego, CA, USA).

middle: B

first: Mayuri

last: Inchanalkar


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [mouseD35-ChIPseq-mm10]

status: Public on Jun 04 2023

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: TRIM28 interacts with PGR and ESR1 in both human and mouse uterus to modulate estrogen and progesterone signaling. Knocking down of TRIM28 in the human endometrial stromal cells imparied decidualization in vitro. Deletion of TRIM28 from mouse uterus disrupted uterine stromal decidualization leading to infertility. Addtionally, TRIM28 deletion caused abnormal accumulation of TRIM28 postive and PGR negative cells in the stroma.

overall_design: Wild type mouse uterus were collected at Pregnancy day 3.5 for TRIM28 ChIP-Seq analysis.

first: Rong

first: Tianyuan

last: Wang

first: San-Pin

last: Wu

first: John

middle: P

last: Lydon

first: Francesco

last: DeMayo


title: Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [ATAC-seq]

city: Loma Linda

first: Isaac

middle: Jacob

last: Kremsky

address: 11175 Campus St., Chan Shun Pavilion, Room A1022

department: Basic Sciences

institute: Loma Linda University

overall_design: Mice were housed in standard cages on a 12: 12 h light:dark cycle and given ad lib access to food and water. Healthy 8-week old CD-1 mice (Charles River Labs) were used. Gestating females (F0) were administered daily intraperitoneal injections of Bisphenol A (Sigma 239658, 50 mg/kg) or sesame oil (Sigma S3547) to prevent irritation at the injection site. Injections were performed from embryonic day 7.5 through 13.5. No sibling breeding was used to avoid inbreeding artifacts.

first: Yoon-Hee

last: Jung

first: Hsiao-Lin

middle: V

first: Samir

last: Ali

first: Victor

middle: G

last: Corces


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [ATACseq-hg38]

overall_design: Primary human endometrial stromal cells from three donors were treated with either non-targeting siRNA (siNT) or TRIM28 siRNA (siTRIM28) for 48h then treated with either vehicle or EPC (17beta-estradiol, progesterone and cAMP) for 72h to generate pre-decidual (Pre-dec) and decidaul (Dec) cells and collected for ATAC-Seq analysis.

last: Li


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [HESC-CUT+RUN-hg38]

overall_design: Primary human endometrial stromal cells from three donors were treated with EPC (17beta-estradiol, progesterone and cAMP) to generate decidaul (Dec) cells and collected for PGR and TRIM28 Cut and run analysis.


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [mouse-D3.5-scRNAseq]

overall_design: 3-4 TRIM28f/f (TRff) and TRIM28d/d (TRdd) mouse uterus were collected at pregnancy day 3.5 and the uterus from the mice with the same genotype were pooled for scRNA-Seq analysis


title: Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability

type: Genome variation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: ScRNA-seq of immune cells in tumors or during EAE from Pglyrp1 KO and wildtype mice.

city: Boston

first: Linglin

last: Huang

address: 60 Fenwood Road, HBTM 10016F

department: Neurology

institute: Brigham and Women’s Hospital

summary: PGLYRP1 is highly co-expressed with known co-inhibitory molecules and might be a promising novel target for immunotherapy. Indeed, genetic deletion of PGLYRP1 in mice led to decreased tumor growth and an increased activation/effector phenotype in CD8+ T cells, suggesting an inhibitory function of PGLYRP1 in CD8+ T cells. Surprisingly, genetic deletion of PGLYRP1 strongly protected against experimental autoimmune encephalomyelitis (EAE), a model of autoimmune disease in the central nervous system (CNS). Pglyrp1-deficient myeloid cells had a defect in antigen-presentation and T cell activation, indicating that PGLYRP1 might act as a proinflammatory molecule in myeloid cells during autoimmunity. Our results highlight PGLYRP1 as a promising novel target for immunotherapy, that, when targeted, elicits a potent anti-tumor immune response while protecting against tissue inflammation and autoimmunity.

overall_design: To characterize the role of PGLYRP1 in immune cells during tumor progression, we profiled the leukocytes in the MC38-OVA tumor and lymph nodes from 2 wild type (WT) and 2 PGLYRP1 knockout (KO) mice. For each genotype and tissue origin, cells from 2 mice were hashtagged respectively, pooled, and then split into 2 channels for combined singlecell RNA- and TCR-sequencing.  Similarly, to characterize the role of PGLYRP1 in EAE, we profiled leukocytes in the CNS from 3 WT and 3 KO mice. For each genotype, cells from 3 mice were hashtagged individually, pooled, and then split into 2 channels for combined single-cell RNA- and TCR-sequencing.

first: Alexandra

last: Schnell

first: Brianna

last: Regan

first: Vasundhara

last: Singh

first: Vijay

last: Kuchroo


title: CD4 T cell intrinsic Arginase 1 controls the kinetics of Th1 induction and contraction

city: Bethesda

first: Jack

last: Bibby

address: 10 Center Drive

institute: National Institutes of Health

overall_design: Total CD4 T cells of two patients with Arginase 1 deficiency and two age - and sex-matched healthy controls were isolated and activated for 6 hours in vitro with immobilized antibodies to CD3 and CD46 in the presence of 25U/ml IL-2. Total RNA was isolated and gene array analyses performed.

first: Erin

middle: E

last: West

first: Claudia

last: Kemper


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [HESC-ChIPseq-hg38]

first: Franco

last: Demayo

overall_design: Primary human endometrial stromal cells two patients were collected for TRIM28, H3K27AC and H3K27me3 ChIP-Seq analysis.

first: Rong

first: Tianyuan

last: Wang


title: Prolonged cytopenia following  CD19 CAR T cell therapy is linked with bone marrow infiltration of clonally expanded IFNγ-expressing CD8 T cells

city: Houston

first: Michael

last: Green

state: TX

address: 1515 Holcombe Blvd

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

summary: Autologous anti-CD19 chimeric antigen receptor T-cell (CAR T) therapy is highly effective in relapsed/refractory large B-cell lymphoma (rrLBCL) but is associated with toxicities that delay recovery. While the biological mechanisms of cytokine release syndrome and neurotoxicity have been investigated, the pathophysiology is poorly understood for prolonged cytopenia, defined as grade ≥3 cytopenia lasting beyond 30 days after CAR T infusion. By performing single-cell RNA-sequencing analysis of bone marrow samples from healthy donors and rrLBCL patients with and without prolonged cytopenia, we identified a significantly increased frequency of clonally expanded CX3CR1hi cytotoxic T-cells, expressing high interferon (IFN)-γ and cytokine signaling gene sets, associated with prolonged cytopenia. In line with this, hematopoietic stem cells from these patients expressed IFN-γ response signatures. IFN-γ deregulates hematopoietic stem cell self-renewal and differentiation and can be targeted with thrombopoietin agonists or IFN-γ neutralizing antibodies, highlighting a potential mechanism-based approach for the treatment of CAR T-associated prolonged cytopenia.

overall_design: Single cell gene expression profiles for 22 bone marrow samples from patients treated with CAR T-cell product, chemotherapy, and healthy donors. Due to patient privacy concerns the raw data is available through the European Genome-Phenome Archive.

middle: R


title: Transcriptional reprogramming underpinning resistance to endocrine therapy and CDK4/6 inhibitors in ER+ breast cancer cell lines

city: Naples

first: Luigi

last: Formisano

address: Via Sergio Pansini, 5

department: Department of Clinical Medicine and Surgery

country: Italy

institute: University of Naples "Federico II"

summary:
To investigate the molecular mechanisms of resistance to ER downregulator and CDK4/6 inhibitors in ER+ breast cancer, we generated two cell lines, MCF7 and T47D, resistant to fulvestrant and abemaciclib after 6-8 months of exposure to increasing doses of the drug combination
We performed gene expression profiling analysis using data obtained from RNA-seq of parental MCF7 or T47D and the respective fulvestrant and abemaciclib resistant cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF7 vs MCF7-FAR and T47D vs T47D-FAR

first: Stefania

last: Belli

first: Daniela

last: Esposito


title: Netrin-1 blockade induces tumor growth inhibition and EMT reversion in endometrial cancer [Mouse_Pten]

status: Public on Jun 02 2023

city: LYON

first: Nicolas

last: Rama

address: 28 rue Laennec

institute: CRCL

summary: Netrin-1 is up-regulated in a large fraction of human cancers as a pro-tumoralmechanism. Therefore, a phase I trial assessing netrin-1 blockade using an anti- netrin-1 monoclonal antibody (NP137) in patients with advanced solid cancer is ongoing. We analyzed here the potential implication of netrin-1 in endometrial carcinoma. We show that netrin-1 is up-regulated in the vast majority of human endometrial carcinomas, and demonstrate that NP137 treatment is effective in reducing tumor progression in preclinical mouse models of endometrial carcinoma. We report here a confirmed objective response in a patient with endometrial carcinoma (EC) treated in monotherapy with NP137. A 51.16% reduction of target lesions at 6 weeks and up to 54.65% reduction during the next 6 months of NP137 treatment was observed for a 74 years old woman. To evaluate the mechanism of action of the anti-netrin-1 mAb, we performed gene profiling of mouse PTENf/f endometrial tumors treated with NP137 and observed that, in addition to cell death induction, NP137 induced a reversion of the Epithelial-to-Mesenchymal Transition (EMT). Of interest, by analyzing 13 pre/post paired biopsies of the patients with endometrial carcinoma treated in the NP137 trial, we confirmed a significant reduction of EMT in tumors. We thus performed pre/post NP137 treatment biopsy- based single cell RNA sequencing in a patient with endometrial carcinoma, and showed a net decrease of neoplastic cells and a reversion of EMT markers in the remaining tumor cells, with associated change in the tumor microenvironment. Given the importance of EMT in resistance to the current standard of care including chemotherapy or immune-checkpoint inhibitors, we showed in a PTENf/f endometrial cancer mouse model that combining NP137 with carboplatin paclitaxel outperformed carboplatin paclitaxel alone. Our results thus identify for the first time, in preclinical models and in patients, netrin-1 blockade as a clinical strategy triggering both tumor debulking and reversion of EMT, thus potentially alleviating resistance to standard treatments.

overall_design: RNAseq analysis of CAG-CreERT2:PTENlox/lox treated with anti-Netrin-1 (n=3) or with control (n=3) antibody.

first: Philippe

last: Cassier

first: Raul

last: Navaridas

first: Benjamin

last: Ducarouge

first: Jean-Pierre

last: Delord

first: Melanie

last: Bellina

first: Andrea

last: Paradisi

first: Gwenaelle

last: Garin

first: Hanane

last: Gheit

first: David

last: Neves

first: Remy

last: Jelin

last: Gadot

first: Sophie

last: Léon

first: Cyril

last: Degletagne

first: Mojgan

last: Devouassoux-Shisheboran

first: Eliane

last: Mery-Lamarche

last: Perol

first: Xavi

last: Dolcet

first: Isabelle

last: Ray-Coquard

first: Agnès

last: Bernet

first: Patrick

last: Mehlen

first: Hector

last: Hernandez-Vargas


title: Netrin-1 blockade induces tumor growth inhibition and EMT reversion in endometrial cancer [scRNA-seq]

first: Nicolas

last: Rama

overall_design: Single cell RNAseq analysis of pre/upon biopsy of a patient with endometrial adenocarcinoma. 2 lung metastasis biopsies were collected : C1D1 (at inclusion) and C3D1 (after one month of treatment with NP137).

first: Philippe

last: Cassier

first: Raul

last: Navaridas

first: Benjamin

last: Ducarouge

last: Delord

last: Bellina


title: Netrin-1 blockade induces tumor growth inhibition and EMT reversion in endometrial cancer.


title: Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [gDNA]

first: Isaac

last: Kremsky

overall_design: Adult (2-5 months old) CD-1 IGS mice (Charles River Lab, USA) were used for all experiments. Mice were housed in standard cages on a 12 h light:dark cycle and given ad libitum access to food and water. Five randomly picked male animals were euthanized by cervical dislocation before the cortex tissueswere retrieved for DNA extraction and genomic library preparations. All animal experiments were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).

first: Yoon-Hee

last: Jung

first: Hsiao-Lin

last: Wang

first: Samir

last: Ali


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [HESC-RNAseq-hg19]

first: Franco

last: Demayo

overall_design: Primary human endometrial stromal cells from three donors were treated with either non-targeting siRNA (siNT) or TRIM28 siRNA (siTRIM28) for 48h then treated with either vehicle or EPC (17beta-estradiol, progesterone and cAMP) for 72h to generate pre-decidual (Pre-dec) and decidaul (Dec) cells and collected for RNA-Seq analysis.

first: Rong

last: Li

first: Tianyuan

first: San-Pin

last: Wu

first: John

last: Lydon

first: Francesco

last: DeMayo


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [mouseP4-RNAseq-mm10]

overall_design: Pgrcre/+ mice were ovariectomized for 2 weeks treated with either oil or Progesterone (P4) for 6h. The uterus were collected for RNA-Seq analyais.


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [mouseD3.5-RNAseq-mm10]

overall_design: Four TRIM28f/f (TRff) and TRIM28d/d (TRdd) mouse uterus were collected at pregnancy day 3.5 for RNA-Seq analysis


title: Gene expression profile at single cell level of murine macrophages infected with Mtb (-/+ TLR2)

status: Public on Jun 01 2023

first: Bryan

last: Bryson

address: 400 Technology Square

department: Biological Engineering

institute: MIT

summary: The macrophage is a cellular reservoir for Mtb infection. We profiled BMDM following Mtb infection.

overall_design: Murine macrophages (-/+ TLR2) were infected with H37Rv Mtb and profiled by 10X genomics,

first: Amy

last: Barczak


title: Generation and characterization of Myc knockin mouse model of osteosarcoma

first: Jason

last: Yustein

address: 1102 Bates Ave

department: Pediatrics-Oncology

institute: Texas Children's Hospital

summary: To understand the mechanisms that underlie the ability of Myc to alter both the tumor and its surrounding tumor microenvironment (TME) of osteosarcoma, we generated and molecularly characterized an osteoblast-specific Cre-Lox-Stop-Lox;(LSL)-c-MycT58A;p53fl/+ knockin genetically engineered mouse model (GEMM). Phenotypically, the Myc knockin-GEMM had rapid tumor development with a high incidence of metastasis.

overall_design: Myc knockin genetically engineered mouse model (GEMM) were generated by crossing Col2.3-Cre/Trp53fl/+and Lox-Stop-Lox (LSL)-MycT58A mice. Col2.3-Cre/Trp53fl/+ mouse model was generated by crossing mice expressing Cre recombinase under the transcriptional regulation of the osteoblast-specific promoter Col2.3 with Trp53-floxed mice. After development of the spontaneous tumor, tumors were resected, mRNA was isolated using Qiagen RNAeasy Plus Mini kit, and RNA sequencing was performed.

first: Bikesh

last: Nirala

first: Lyazat

last: Kurenbekova

first: Tajhal

middle: D

last: Patel


title: Transcriptome profiles of wild-type, IRF8KO, IRF8cKO, Batf3KO, 5xFAD, and 5xFAD/IRF8KO microglia [RNA-seq]

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

institute: NIH/NICHD

summary: The role of the lineage-determining transcription factor IRF8 in microglia remains unelucidated. We report the genome-wide, transcriptome profiles of wild-type, IRF8KO, IRF8cKO, Batf3KO, 5xFAD, and 5xFAD/IRF8KO microglia. Deep-sequencing and subsequent differential analysis revealed the impacts of IRF8 on microglia-specific transcription programs, such as cell identity. Sall1 and Batf3 genes were identified as a downstream transcription factor of IRF8, and Batf3 dependent genes showed correlation with IRF8-dependent genes in microglia. The conditional depletion of IRF8 gene after microglial maturation (P14) increased or decreased the gene expression, most of which were shared with those of IRF8KO. This study provides a novel insight into understanding transcriptional programs in microglia.

overall_design: Transcriptome profiles of adult WT, IRF8KO, 5xFAD, 5xFAD/IRF8KO, IRF8cKO, and Batf3KO mice were analyzed. The conditional deletion of IRF8 gene was achieved with 5 consecutive days of Tamoxifen injection to an IRF8flox-Cx3cr1CreERT2-Rosa26LSL-EYFP mouse at the age of P12-14 and YFP-positive microglia at 3-month-old of age were sorted and analyzed.

first: Richard

last: Pan

first: Keiko

last: Ozato


title: Netrin-1 blockade induces tumor growth inhibition and EMT reversion in endometrial cancer [visium data]

first: Nicolas

last: Rama

overall_design: Spatial transcriptomic analysis by Visum technology of pre/upon biopsy of a patient with endometrial adenocarcinoma. 2  metastasis biopsies were collected : C1D1 (at inclusion) and C3D1 (after one month of treatment with NP137).

first: Philippe

middle: A

last: Cassier

first: Raul

last: Navaridas

first: Benjamin

last: Ducarouge

first: Jean-Pierre

last: Delord

first: Melanie

last: Bellina

first: Andrea

last: Paradisi

first: Gwenaelle

last: Garin

first: Hanane

last: Gheit

first: David

last: Neves

first: Remy

last: Jelin

last: Gadot

first: Sophie

last: Léon

first: Cyril

last: Degletagne

first: Mojgan

last: Devouassoux-Shisheboran

first: Eliane

last: Mery-Lamarche

last: Perol

first: Xavi

last: Dolcet

first: Isabelle

last: Ray-Coquard

first: Agnès

last: Bernet

first: Patrick

last: Mehlen

first: Hector

last: Hernandez-Vargas


title: Zika virus co-opts miRNA networks to persist in placental microenvironments detected by spatial transcriptomics

status: Public on Jun 03 2023

first: Michael

last: Jochum

address: 1 Baylor Plaza

department: Obstetrics and Gynecology

institute: Baylor College of Medicine

type: Non-coding RNA profiling by high throughput sequencing


title: Netrin-1 blockade induces tumor growth inhibition and EMT reversion in endometrial cancer [RNAseqPatient]

first: Nicolas

last: Rama

overall_design: RNAseq analysis of metastasis microbiopsy from Endometrial cancer patient before and after2 cycle of NP137 treatment (n=13).

first: Philippe

last: Cassier

first: Raul

last: Navaridas

first: Benjamin

last: Ducarouge

first: Jean-Pierre

last: Delord

last: Bellina

last: Paradisi


title: Single-cell transcriptome profiles of wild-type and IRF8KO microglia [scRNA-seq]

first: Keita

last: Saeki

summary: The role of the lineage-determining transcription factor IRF8 in microglia remains unelucidated. We analyzed the transcriptome diversity of wild-type and IRF8KO microglia. Deep-sequencing and subsequent differential analysis revealed the significance of the IRF8-dependent transcription on microglial heterogeneity and self-renewing. This study provides a novel insight into understanding IRF8-mediated transcriptional programs in microglia.

overall_design: Transcriptome profiles of adult WT and IRF8KO microglia were analyzed at a single-cell level using 10xGenomics.

first: Keiko

last: Ozato


title: Bulk RNA-sequencing of articular cartilage from DMM-treated mice

city: Vienna

first: Kazuhiko

last: Matsuoka

address: Borschkegasse 8a

department: Cellular and Molecular Tumor biology

country: Austria

institute: CeCenter for Cancer research, Medical University of Vienna

summary: Identify the therapeutic targets/pathways of Osteoarthritis (OA),  the most frequent joint disease. Surgery-induced cartilage degeneration is used as an experimental model for OA in mice. An inducible cartilage-specific c-Fos loss-of-function model is generated by combining c-fos floxed and Col2a1-CreERT mice. Since c-Fos mutant mice have more severe phenotype than c-Fos wild type mice, we focused on c-Fos-related signaling pathway in the articular cartilage.

overall_design: Contralateral side from c-FosWT mice: n = 4, DMM-treated side from c-FosWT  mice: n = 3 and DMMptreated isde from  c-FosDCh mice: n = 4

first: Martin

last: Bilban

first: Sophia

last: Derdak

first: Markus

last: Jeitler


title: Genome-wide methylated CpG status in WT and IRF8KO microglia [WGBS]

summary: The role of the lineage-determining transcription factor, Interferon regulatory factor (IRF8), in microglia remains elucidated. We report the genome-wide methyl-CpG status in adult wild-type (WT) and IRF8-knockout (IRF8KO) microglia by whole-genome bisulfite-Seq (WGBS). Deep-sequencing and subsequent differential analysis revealed that IRF8KO microglia exhibited a cell-intrinsic methylation profile. Furthermore, the differentially methylated regions showed a significant correlation with IRF8-dependent chromatin accessibility in microglia. This study provides a novel insight into understanding epigenetic regulation in microglia.

overall_design: WGBS in WT and IRF8KO microglia.


title: Pituitary Gigantism ArrayCGH

city: Tokyo

first: Maki

last: Fukami

address: 2-10-1 Okura, Setagaya

department: Molecular Endocrinology

country: Japan

institute: National Research Institute for Child Health and Development

type: Genome variation profiling by genome tiling array

summary:
Germline chromosomal microdeletion leading to pituitary gigantism through hormone-gene overexpression
We detected a hitherto unreported heterozygous deletion involving a 752,023-bp genomic interval at 20q11.23 (chr20:35,899,203–36,651,225, hg19/GRCh37.p13)

overall_design: Copy-number variations (CNVs) in the genome using array-based comparative genomic hybridization (aCGH) were examined


title: Transplanting FVIII/ET3-Secreting Cells in Fetal Sheep Increases FVIII Levels Long-Term Without Inducing Immunity or Toxicity

city: Winston Salem

first: Maria Graça

last: Almeida-Porada

address: 391 Technology Way

institute: Wake Forest Institute for Regnerative Medicine

summary: To investigate the differentiative fate of human PLCs following transplantation into fetal sheep and engraftment in various tissues/organs, we performed gene expression profiling analysis using data obtained from RNA-seq of human PLCs prior to in utero transplantation and of each engrafted fetal sheep tissue after filtering to remove any cross-reactivity with orthologous sheep transcripts

sample_organism:
Homo sapiens
Ovis aries

platform_organism:
Homo sapiens
Ovis aries

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human placental cells (PLCs) prior to and following engraftment within various sheep tissues after in utero transplantation

first: Graça


title: Genome-wide open chromatin status in WT and IRF8KO microglia [ATAC-seq]

summary: The role of the lineage-determining transcription factor, Interferon regulatory factor (IRF8), in microglia remains unelucidated. We report the genome-wide chromatin status in adult wild-type (WT) and IRF8-knockout (IRF8KO) microglia by ATAC-Seq. Deep-sequencing and subsequent differential analysis revealed that chromatin accessibility in microglia requires IRF8. At the same time, the loss of IRF8 gains aberrant chromatin accessibility that potentially confers mRNA transcription of the genes upregulated in IRF8KO microglia. This study provides a novel insight into understanding epigenetic regulation in microglia.

overall_design: Examination of chromatin accessibility in microglia.

first: Richard

last: Pan


title: TRAF7 is an essential regulator of vascular integrity

city: Oklahoma City

first: Alla

last: Tsytsykova

state: OK

address: 1122 NE 13th Street

institute: OUHSC

summary:
Targeted deletion of TRAF7 revealed that it is a crucial part of shear stress-responsive MEKK3-MEK5-ERK5 signaling pathway induced in endothelial cells by blood flow. Similarly, to Mekk3-, Mek5- or Erk5-deficient mice, Traf7-deficient embryos died in utero around midgestation due to impaired endothelial cell integrity. They displayed significantly lower expression of transcription factor Klf2, an essential regulator of vascular hemodynamic forces downstream of the MEKK3-MEK-ERK5 signaling pathway. Deletion of Traf7 in endothelial cells of postnatal mice was also associated with severe cerebral hemorrhage. Here, we show that besides MEKK3 and MEK5, TRAF7 associates with a planar cell polarity protein SCRIB. SCRIB binds with an N-terminal region of TRAF7, while MEKK3 associates with the C-terminal WD40 domain. Downregulation of TRAF7 as well as SCRIB inhibited fluid shear stress-induced phosphorylation of ERK5 in cultured endothelial cells. These findings suggest that TRAF7 and SCRIB may comprise an upstream part of the MEKK3-MEK5-ERK5 signaling pathway.
Objective: to present first in vivo experimental evidence of TRAF7 function by using global and endothelium-specific TRAF7 knockout mice and comparing transcriptomes of developing embryos.

overall_design: RNA-seq was performed to determine and compare transcriptome profiles in whole mouse embryos of different genotypes at E9.5. Genotypes include wild type, global, and endothelium-specific TRAF7 knockouts.

first: Erdyni

last: Tsitsikov

first: Khanh

last: Phan

first: Yufeng

last: Liu

first: Mike

last: Kinter

first: Lauren

last: Selland

first: Lori

last: Garman

first: Courtney

last: Griffin

first: Ian

middle: F

last: Dunn


title: Early loss of microglial p38alpha in the APPswe/PS1dE9 mouse model of Alzheimer’s disease reduces microglial uptake of amyloid beta without exacerbating amyloid-associated neuropathology

city: Lexington

first: Linda

last: Van Eldik

state: KY

address: 789 S. Limestone St.

department: Sanders-Brown Center on Aging

institute: University of Kentucky

summary: Background: The p38 alpha mitogen-activated protein kinase (p38a) pathway is linked to both innate and adaptive immune responses, and as such, is currently under active investigation as a target for drug development in the context of Alzheimer’s disease (AD) and other conditions with neuroinflammatory dysfunction. While preclinical data has shown that p38a inhibition can protect against AD-associated neuropathology, the underlying mechanisms are only partially elucidated. Inhibitors of p38a may provide benefit via modulation of microglial-associated neuroinflammatory responses that contribute to the development of AD pathology. The present study tests this hypothesis by knocking out microglial p38a and assessing early-stage pathological changes.  Materials and methods: Conditional knockout of microglial p38a was accomplished in 5-month-old C57BL/6J wild-type and amyloidogenic AD model (APPswe/PS1dE9) mice using a tamoxifen-inducible Cre/loxP system. Beginning at 7.5 months of age, animals underwent behavioral assessment on the open field and radial arm water maze tests, followed by collection of cortical and hippocampal tissues at 11 months. Additional endpoint measures included microglial RNA-seq analysis, quantification of pro-inflammatory cytokines, assessment of amyloid burden and plaque deposition, and characterization of microglia-plaque dynamics using a combination of ELISA, immunohistochemical, and immunofluorescent techniques.  Results: Loss of microglial p38a did not alter behavioral outcomes, pro-inflammatory cytokine levels, or overall amyloid plaque burden. However, this manipulation did significantly increase hippocampal levels of soluble Abeta42 and reduce colocalization of Iba1 and 6E10 in a subset microglia in close proximity to plaques, indicating that p38a suppression may alter microglial phagocytosis.  Conclusion: The data presented here suggest that rather than reducing inflammation per se, the net effect of microglial p38a inhibition in the context of AD-type amyloid pathology could be an alteration of phagocytosis and/or plaque deposition. Additionally, these results support future investigations of microglial p38a signaling at different stages of disease, as well as its relationship to phagocytic processes in this particular cell-type.

overall_design: Comparative gene expression profiling analysis of RNA-seq data extracted from isolated microglia obtained in wild-type (WT) and Alzheimer's disease model (AD) mice with or without microglial expression of p38alpha (genetic KO).

first: David

last: Braun

first: Hilaree

middle: N

last: Frazier

first: Verda

last: Davis

first: Meggie

last: Coleman

first: Colin

last: Rogers


title: MFAP5 regulates skin scar formation and fibroblast activation

city: Chicago

first: Trevor

last: Leonardo

state: Illinois

address: 801 South Paulina Street

department: Medicine

institute: University of Illinois at Chicago

summary: A subset of human skin fibroblasts are phagocytic. To investigate the gene expression changes between phagocytosing and non-phagocytosing fibroblasts, fibroblasts were incubated with apoptotic human dermal microvascular endothelial cells expressing green fluorescent protein or no treatment. Treated fibroblasts were then collected after 8 hours and sorted by FACS to identify phagocytic and non-phagocytic fibroblasts. We then performed gene expression profiling analysis using data obtained from RNA-seq of these three groups of cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human skin fibroblasts with or without engulfed apoptotic human dermal microvascular endothelial cells and untreated control fibroblasts, three groups and three replicates per group.

first: Bruna

last: Romana-Souza

first: Chen

last: Han

first: Lin

last: Chen

first: Luisa

last: DiPietro


title: Genome-wide profiles of IRF8 and PU.1 bindings, and H3K4me1 and H3K27ac histone marks in wild-type and IRF8-knockout microglia [CHIP-seq]

first: Keita

last: Saeki

summary: The role of the lineage-determining transcription factor Interferon regulatory factor 8 (IRF8) in microglia remains elucidated. Here we report the genome-wide IRF8 binding profiles in microglia at various ages. CUT&RUN methodology revealed that IRF8 starts to bind to the genome around postnatal day 9 (P9), and its number increases with age. In comparison to peritoneal macrophages, microglia IRF8 showed a cell-intrinsic binding pattern. By co-occurrence analysis, most IRF8 was H3K4me1/H3K27ac-marked enhancers, and many of them bind to the H3K27ac(high) super-enhancer regions. In IRF8KO microglia, H3K4me1 and H3K27ac profiles were altered and deposited aberrantly on the genome. This study provides a novel insight into understanding epigenetic regulation in microglia.

overall_design: Analyzed IRF8 binding profile in WT P9, three P14, adult microglia, and peritoneal macrophages using CUT&RUN. Additionally, profiles of PU.1 binding, H3K4me1, and H3K27ac histone marks in adult microglia in the presence or absence of IRF8 were analyzed similarly. Four corresponding IgG controls were included.

first: Keiko

last: Ozato


title: NASH time course study (Ldlr-/- mice on reference or Western diet)

city: Corvallis

first: Andrey

last: Morgun

state: Oregon

address: Pharmacy Building, 1601 SW Jefferson Way

institute: Oregon State University

summary: Mice on a reference (RD) or western diet (WD)

overall_design: 96 samples, 3-8 replicates per treatment, including a control (RD), a WD over a timecourse from 1 week to 10 months

first: Jump

last: Donald

first: Shulzhenko

last: Natalia


title: Comparative analysis of Tet2 catalytic deficient and knockout bone marrow over time

city: New York

first: Meelad

middle: M

last: Dawlaty

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

summary: In this study, we investigated the role of Tet2 in regulation of hematopoietic genes by performing transcriptomic analysis of Tet2 WT, Mut, and KO LSK and Lin– cells at 3, 6, 9, and 12 months by RNA-seq, and mapping the DNA methylation landscape of 3-month-old Tet2 WT, Mut, and KO LSK and Lin– cells. (1) We find that loss of Tet2 (Tet2 KO) vs. a loss of Tet2 catalytic function (Tet2 Mut) at different time points and cell types causes distinct gene expression changes when compared to WT samples as assessed by RNA-seq. (2) Additionally, we find that many genes implicated in lymphoma and leukemia are deregulated in Tet2 Mut and KO LSK and Lin– cells, consistent with the phenotypes observed in mice transplanted with Tet2 Mut and KO bone marrow. (3) We also mapped genome-wide DNA methylation levels of WT, Tet2 Mut, and KO LSK and Lin– cells at 3 months by WGBS and establish a role for Tet2 in demethylating genes implicated in lymphoma and leukemia initiation and progression.

overall_design: We studied the role of Tet2 in regulation of hematopoietic genes by performing transcriptomic analysis of Tet2 WT, Mut, and KO LSK and Lin– cells at 3, 6, 9, and 12 months by RNA-seq. Bone marrow from three mice was pooled and LSK and Lin– fractions were sorted by FACS. Total RNA was extracted (Qaigen RNeasy Total RNA kit). Library preparation and RNA-seq were performed at Novogene (https://en.novogene.com/) on an Illumina Novoseq 6000 platform. About 20-30 million reads were generated per sample. Details of RNA-seq and data analysis are described in the methods sections of the manuscript. We also performed WGBS to assess changes in DNA methylation in the absence of Tet2 or its catalytic function alone. We isolated LSK and Lin– cells from Tet2 WT, Mut, and KO 3-month-old mouse bone marrow and subjected them to WGBS. High-quality DNA was extracted (Quick-DNA miniprep kit (Zymo, D3024) and sent for WGBS analysis at BGI genomics company (https://en.genomics.cn/). Lamda DNA spike-in was added to confirm the bisulfite conversion efficiency. Details of WGBS and data analysis are described in the methods sections of the manuscript.

first: Keisuke

last: Ito

first: Julio

middle: C

last: Flores


title: Transcriptomic characterization of hepatobiliary plasticity of hepCLiPs and bilCLiPs

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

summary: Recent studies have demonstrated extensive proliferative capacity of adult hepatocytes and biliary epithelial cells (BECs) in vitro, thereby allowing derivation of clonal cell lines named hepCLiPs and bilCLiPs, respectively. Both cell lines undergo hepatobiliary plastiticity in that they exhibit a BEC-like phenotype under a 2D culture condition, while they exhibit a hepatocyte-like phenotype under a 3D culture condition. This data set was obtained to comprehensively characterize the gene expression profiles of hepCLiPs and bilCLiPs which were cultured under 2D and 3D culture conditions.

overall_design: RNA was isolated from hepCLiPs and bilCLiPs which were either cultured under the 2D condition (hepCLiP_2D and bilCLiP_2D) or the 3D suspension condition (hepCLiP_3D and bilCLiP_3D).

first: Ben

middle: Z

last: Stanger


title: Mature tertiary lymphoid structures are key niches of tumor-specific immune responses in pancreatic ductal adenocarcinomas

city: Sao Paulo

first: Gabriela

middle: Sarti

last: Kinker

state: SP

address: 440 Tagua street

department: International Research Center

country: Brazil

institute: A. C. Camargo Cancer Center

summary: Objective: To better understand the immune microenvironment of pancreatic ductal adenocarcinomas (PDACs), here we explored the relevance of T and B cell compartmentalization into tertiary lymphoid structures (TLSs) for the generation of local antitumor immunity.     Design: We characterized the functional states and spatial organization of PDAC-infiltrating T and B cells using single-cell RNA sequencing (scRNA-seq), flow cytometry, multicolor immunofluorescence, gene expression profiling of microdissected TLSs, as well as in vitro assays. Additionally, we performed a pan-cancer analysis of tumor-infiltrating T cells using scRNA-seq and single-cell T cell receptor sequencing (scTCR-seq) datasets from 8 cancer types. To evaluate the clinical relevance of our findings we used PDAC bulk RNA-seq data from The Cancer Genome Atlas and the PRINCE chemoimmunotherapy trial.     Results: We found that a subset of PDACs harbors fully developed TLSs where B cells proliferate and differentiate to plasma cells. These mature TLSs also support T cell activity and are enriched with tumor-reactive T cells. Importantly, we showed that chronically activated, tumor-reactive T cells exposed to fibroblast-derived TGF-β may act as TLS organizers by producing the B cell chemoattractant CXCL13. Identification of highly similar subsets of clonally expanded CXCL13+ tumor-infiltrating T cells across multiple cancer types further indicated a conserved link between tumor-antigen recognition and the allocation of B cells within sheltered hubs in the tumor microenvironment. Finally, we showed that the expression of a gene signature reflecting mature TLSs was enriched in pre-treatment biopsies from PDAC patients with longer survival after receiving different chemoimmunotherapy regimens.     Conclusion: We provided a framework for understanding the biological role of PDAC-associated TLSs and revealed their potential to guide the selection of patients for future immunotherapy trials.

overall_design: We evaluated the expression profile of immune-related genes in microdissected PDAC-associated TLSs in different maturation stages.

first: G

first: T

last: Medina


title: Gene expression profile at single cell level of lung-tumor bearing KrasG12D mice with or without defective cholesterol efflux

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Impaired cholesterol efflux pathways is a hallmark of lung adenocarcinoma. We used single cell RNA sequencing (scRNA-seq) to analyze the impact of defective cholesterol efflux on cell diversity in lung tumor

overall_design: Lung cells were disociated by proteolytic digestion with collagenase D from whole lung (n=3/4 mice per group)

first: Emma

last: Guilbaud

first: Laurent

last: Yvan-Charvet


title: Epigenetic analysis in a murine genetic model of Gulf War illness

city: Memphis

first: Khyobeni

last: Mozhui

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

summary: Of the nearly 1 million military personnel who participated in the 1990-1991 Gulf War, between 25% and 35% became ill with what now is referred to as Gulf War Illness (GWI), by the Department of Defense.  Symptoms varied from gastrointestinal distress to lethargy, memory loss, inability to concentrate, depression, respiratory and reproductive problems. The symptoms have persisted for 30 years in those afflicted but the basis of the illness remains largely unknown.  Nerve agents and other chemical exposures in theater have been implicated but the long-term effects of these acute exposures have left few if any identifiable signatures.  The major aim of this study is to elucidate the possible genomic basis for the persistence, especially of the neurological and behavioral effects.  To address this, we performed a whole genome epigenetic analysis of the proposed cause of GWI, viz., exposure to organophosphate neurotoxicants combined with high circulating glucocorticoids in two inbred mouse strains, C57BL/6J and DBA/2J. The animals received corticosterone in their drinking water (20mg%, w/v) for 7 days followed by injection of diisopropylfluorophosphate, a nerve agent surrogate (DFP, 4mg/kg, i.p.). Control mice were maintained under normal husbandry. Six weeks after DFP injection, the animals were euthanized and medial prefrontal cortex harvested for genomic methylation analysis by MBD-seq. We observed 67 differentially methylated genes, notably among them, Ttll7, Akr1c14, Slc44a4, and Rusc2, all related to different symptoms of GWI. Our results support proof of principle of genetic differences in the chronic effects of GWI-related exposures and may reveal why the disease has persisted in many of the now aging Gulf War veterans.

overall_design: 23 male and female C57BL/6J and DBA/2J mice. Treatment consisted of corticosterone in the drinking water (20 mg% w/v) for 7 days followed by i.p. injection of 4.0 mg kg-1 diisopropyl fluorophosphate (DFP, a sarin surrogate).

first: K

first: B

last: Jones


title: Dysregulation of the Wnt/β-catenin signaling pathway via Rnf146 upregulation in a VPA-induced mouse model of autism spectrum disorder

city: Seongbuk-gu, Seoul

first: Seoyeon

last: Kim

address: 145, Anam-ro

country: South Korea

institute: Korea University

summary: To investigate the function of RNF146 on gene expression and signaling pathways, we overexpressed RNF146 in mouse prefrontal cortex (PFC) using AAV and performed RNA-seq analysis. We found that genes in Wnt signaling pathway are differentially expressed in RNF146 expressed PFC compared to control.

overall_design: 4 RNF146-expressed PFC samples were compared with 4 eGFP-expressed control samples.

first: Gaeun

last: Park

first: Yong-Seok

last: Lee

first: Joon-Yong

last: An


title: Gene expression profiling in hepatocellular carcinoma cell lines PRC/PRF/5 and SNU-449 after a treatment with Transforming Growth Factor beta (TGF-beta) and Galunisertib, alone or in combination

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

summary: Transforming Growth Factor beta (TGF-beta) is a pleiotropic cytokine playing a key role in liver carcinogenesis. The goal of this study was to identify genes differentially expressed in hepatocellular carcinoma cell lines PRC/PRF/5 and SNU-449 after a treatment with TGF-beta and/or Galunisertib, an inhibitor of the type I TGF-beta receptor (TGFBRI). Thus, cells were treated for 16 hours with 1 ng/mL recombinant human TGF-β1 (R&D Systems, Minneapolis, MN) and/or 10 μM LY2157299 (Sigma-Aldrich, St. Louis, MO) after overnight serum starvation. Gene expression profiling was performed using Agilent SurePrint G3 Human GE 8x60K microarrays.

overall_design: Gene expression profiling was performed to identify genes differentially expressed between in hepatocellular carcinoma cell lines PRC/PRF/5 and SNU-449 after a treatment with Transforming Growth Factor beta (TGF-beta) and Galunisertib, alone or in combination


title: Single-cell profiling of a clinically applicable lentiviral vector for the treatment of Diamond-Blackfan anemia

city: Lund

first: Yang

last: Liu

address: A12 BMC

country: Sweden

institute: Lund University, Stem Cell Center

summary: We applied single-cell RNA sequencing analysis to study the transcriptomic landscapes of a clinically applicable lentiviral vector in RPS19-deficient CD34+ hematopoietic stem and progenitor cells

overall_design:
Single cell transcriptional profiling using the 10x Genomics platform was performed on CRISPR edited RPS19-dedicient CD34+ hematopoietic stem and progenitor cells with or without treatment of lentiviral therapeutic vector. The cells were generated using FACS isolated from 2 RPS19-deficient samples, 2 vector treated samples, and 1 normal control.

Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns.

first: Stefan

last: Karlsson


title: Reduced PGC-1α expression and mitochondrial biogenesis predisposes gliomas to radiation resistance

city: Nanjing

first: Xu

last: Qian

state: Jiangsu

address: 101 Longmian Ave

institute: Nanjing Medical University

summary: To investigate the role of mitochondrial metabolic pathways in glioma radioresistance, we established the radioresistant (RR) glioblastoma (GBM) cells in vitro and collected 2 self-pairs of primary and recurrent GBM samples. We then performed gene expression profiling analysis using data obtained from RNA-seq of GBM cells and tissue samples.

overall_design: Comparative gene expression profiling analysis, gene set enrichment analysis and gene set variation analysis of RNA-seq data were performed in GBM cells (U87, U251) versus their paired RR cells (U87-RR, U251-RR) and primary GBM tissue samples (Primary_1, Primary_2) versus their paired recurrent tissue samples (Recurrent_1, Recurreny_2), with 3 replicates for each type of GBM cell.


title: Repurposing of the multiciliation gene regulatory network in fate specification of Cajal-Retzius neurons

city: paris

first: Frederic

last: Causeret

address: 24 bd de montparnasse

department: Imagine Institute

institute: Inserm

summary: Cajal-Retzius (CR) neurons are key players of cortical development that display a very unique transcriptomic identity. However, little is known about the mechanisms involved in their fate specification. Here we use scRNAseq to reconstruct the differentiation trajectory of hem-derived CR cells (CRs) and unravel the transient expression of a complete gene module previously known to control the cellular process of multiciliogenesis. However, we find that CRs do not undergo centriole amplification or multiciliation. We show that upon genetic disruption of Gmnc, the master regulator of the multiciliation cascade, CRs are initially produced but fail to reach their normal identity and lean towards an aberrant fate resulting in their massive apoptosis. We further dissect the contribution of multiciliation effector genes and identify Trp73 as a key determinant. Finally, we use in utero electroporation to demonstrate that the intrinsic competence of hem progenitors as well as the heterochronic expression of Gmnc prevent centriole amplification in the CR lineage. Our work exemplifies how the co-option of a complete gene module, repurposed to control a completely distinct process, may contribute to the emergence of novel cell identities.

overall_design: The hem region of four E11.5 PGKCre;Rosa26YFP  and four E12.5 Wnt3aCre;Rosa26tdTomato mouse embryos were dissected and subjected to scRNAseq. Two libraries were generated from the initial single cell suspension. A third library was obtained from four E12.5 Gmnc-/- embryos

first: Matthieu

middle: X

last: Moreau

first: Frédéric


title: Transcriptional effects of the myeloid cell-derived growth factor Oncomodulin on human monocytes and ipSC-derived sensory neurons

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: To evaluate the possible translational relevance of oncomodulin (Ocm) and its receptor, we investigated the effect of Ocm on human peripheral blood monocytes and human induced pluripotent stem cells (iPSCs) derived sensory neurons

overall_design: we performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells treated with control vehicle, forskolin, mannose and/or oncomodulin

first: Lili

last: Xie

first: Qing

last: Wang

first: Selwyn

last: Jayakar

first: Larry

last: Benowitz

first: Daniel

last: Geschwind


city: Shanghai

first: Xingguang

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

summary: We report the application of RNA sequencing technology for high-throughput profiling in mouse bone marrow-derived macrophages pre-treated with MB-3(50μM) or DMSO, and stimulated with LPS(100ng/ml) for 4 hours. The goal of this study is to search differential gene in indicated groups. Through differential gene analysis, we can find out the specific mechanism of MB-3 inhibits LPS-induced pro-inflammatory gene transcription but promotes the expression of gene involved in NRF2 pathway and anti-oxidation acitivity.

overall_design: RNA sequencing of LPS-stimulated bone marrow-derived macrophages pre-treated with MB-3 or DMSO. Finding out differential gene.

first: Liu

last: Xingguang

first: Zhang

last: Yunkai

first: Gao

last: Ying


title: Excess glucose or fat differentially affects gene expression and appetite regulation during zebrafish embryogenesis

city: Jackson

first: Michael

middle: R.

last: Garrett

state: MISSISSIPPI

address: 2500 N State Street, Department of Pharmacology and Toxicology

department: Pharmacology and Toxicology

institute: University of Mississippi Medical Center

summary: Zebrafish embryos were exposed to  3% glucose (24-72 hpf) and injected 2 nL of BODIPY-FL C12:0 dissolved in canola oil directly into the yolk sac at 24 hpf. At 72 hpf embryos were collected for analysis. Quantitative PCR analysis of glucose exposed embryos demonstrated that glucose exposure activates the insulin pathway while FFA/TAG injection activates the lipolysis and beta-oxidation pathways. At 72 hpf embryos were collected and bulk RNAseq was performed on control, glucose exposed and FFA/TAGs injected embryos.

overall_design: Embryos were treated with 3% glucose or injected into yolk sac with BODIPY-labeled fluorescent lipid dissolve in canola oil solution (1 mg/ml) at 24 hpf. At 72 hpf, samples were flash frozen. 10 embryos were used per condition with a total of six replicates (60 embryos total) for our experimental groups: glucose exposed or FFA/TAG injected embryos. A total of five replicates were used for the control group. Zebrafish embryos were sent to the UMMC Molecular and Genomics Core Facility (www.umc.edu/genomicscore) for RNA isolation, QC, and bulk RNAseq.

first: Yann

last: Gibert

first: Bridget

last: Konadu

first: Carol

middle: K

last: Cox


title: H19X-encoded microRNAs induced by IL-4 in adipocyte precursors regulate proliferation to facilitate differentiation

city: Bongmyeongdong

first: Mihye

last: Lee

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

summary:
Type 2 cytokine, interleukin (IL)-4 promotes the proliferation of adipocyte precursors and their commitment to the beige adipocyte lineage in white adipose tissue, which leads to the growth of beige fat and subsequent metabolic benefits. However, the underlying mechanism that mediates such context specific cell proliferation and lineage commitment is largely unknown and genome wide investigation has not yet been reported.
Here, we performed the global analysis of gene expressions altered by IL4 stimulation in mouse adipocyte precursors through high-throughput sequencing of mRNAs and small RNAs.

overall_design:
For mRNA sequencing, a total of 6 samples were prepared, 3 biological replicates in control group and IL4 treated group.
For small RNA sequencing, a total of 4 samples were prepared: 2 biological replicates in control group and IL4 treated group

first: Min-Woo

first: Choijamts

last: Munkzhul


title: Multi-omic colon organoid analysis highlight MSH4 as a marker of Lynch syndrome and microsatellite instability [methylation array]

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

summary: Approximately 15% of colorectal cancer (CRC) patients present with high levels of microsatellite instability (MSI-H), which is driven by defective mismatch repair (dMMR). While about 20% of MSI-H tumors are associated with the hereditary condition, Lynch syndrome (LS), the majority develop through non-hereditary mechanisms. In recent years, the molecular processes underpinning tumor development in LS patients has been debated, with the longstanding view that dMMR is a secondary process in CRC development of LS patients being questioned. Here, we performed the first multi-omic analysis of normal colon organoids developed from LS and healthy patients to address questions regarding the development of dMMR in LS colon epithelial cells from cancer-free individuals.

overall_design:
Illumina EPIC array protocols were performed on healthy and lynch syndrome colon organoids derived from left and right colon at the time of colonoscopy.
Pleae note that files from each colon location were processed independently. As such, two processed beta files of differing probe lengths were generated.

first: Mourad

middle: W

last: Ali

first: Stephen

last: Eaton

first: Dan

last: Weisenberger

first: Steven

last: Powell

first: Li

last: Li

first: Graham

last: Casey


title: Single-cell transcriptomics reveal a hyperacute cytokine and immune checkpoint axis after cardiac arrest in patients with poor neurological outcome

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

institute: University of Alabama at Birmingham

summary: Neurological injury is a major driver for mortality among patients hospitalized after cardiac arrest (CA). The early systemic inflammatory response after CA is associated with neurological injury and mortality but remains poorly defined. We determine the innate immune network induced by clinical CA at single-cell resolution. Immune cell states diverge as early as 6h post-arrest between patients with good or poor neurological outcomes at hospital discharge. Nectin-2+ monocytes and Tim-3+ natural killer (NK) cell subpopulations associate with poor outcomes, and interactome analysis highlight their cross-talk via cytokines and immune checkpoints. Ex vivo studies on peripheral blood cells from CA patients demonstrate that immune checkpoints are a compensatory mechanism for the resolution of inflammation after CA. IFNγ/IL-10 induce Nectin-2 on monocytes; in a negative feedback loop, Nectin-2 suppresses IFNγ production by NK cells. The initial hours after CA may represent a window for therapeutic intervention in the resolution of inflammation via  immune checkpoints.

overall_design: PBMC from 12 healthy subjects and 28 post-CA were analyzed and sorted by flow cytometry into Tim-3+ NK cells, Tim-3- NK cells, Nectin-2+ monocytes, and Nectin-2- monocytes. Sorted PBMC were subsequently preparated for RNA sequencing.

first: Edy

middle: Y

last: Kim

first: Tomoyoshi

last: Tamura


title: Maturation of sympathetic innervation in the lung facilitates the establishment of T helper 2 resident memory cells

city: Boston

first: Xingbin

last: Ai

state: MA

address: 55 Fruit St

department: Pediatrics

institute: MASSACHUSETTS GENERAL HOSPITAL

summary: Allergic asthma develops from allergen exposure in early childhood and progresses into adulthood. The central mediator of progressive allergic asthma is allergen-specific, T helper 2 (Th2) resident memory cells (TRMs). However, whether the immature lung facilitates residence of Th2-TRMs is unknown. Employing a mouse model of progressive allergic inflammation from neonates to adults, we found that maturing sympathetic nerves enable a dopamine-enriched lung environment in early life that promotes establishment of allergen-specific Th2-TRMs. To expore the molecular mechanism, we apply bulk RNA-seq to test the transcriptome changes in mouse Th2 cells after dopamine treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse Th2 cells with/without dopamine treatment.

first: Wei

last: Wang


title: BCAS2 regulates granulosa cell survival via participating in Flt3l mRNA splicing

city: Beijing

first: xiaohong

last: Yao

address: No. 2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

summary: Granulosa cell proliferation and differentiation are essential for follicle development. Breast cancer amplified sequence 2 (BCAS2) is necessary for spermatogenesis, oocyte development, and maintaining the genome integrity of early embryos in mice. However, the function of BCAS2 in granulosa cells is still unknown. We show that conditional disruption of BCAS2 causes follicles development failure; cell proliferation markers PCNA and Ki67 positive cell ratio are unchanged in granulosa cells. However, specific deletion of BCAS2 causes BrdU positive cell ratio to decrease, cell cycle arrest appearance, DNA damage, and cell apoptosis increase in granulosa cells, RPA1 was abnormally stained in granulosa cells. Furthermore, RNA-Seq results reveal that knockout of BCAS2 results in cellular senescence gene unusual expression. BCAS2 participates in the PRP19 complex to mediate alternative splicing (AS) of E2f3 and Flt3l mRNA to inhibit the cell cycle. Knock down of BCAS2 results in a significantly decrease of BrdU positive cell ratio in Human granulosa-like tumor(KGN) cell line. Thus, BCAS2 regulates granulosa cell proliferation, DNA damage repair, and cell apoptosis. BCAS2 is vital for female fertility.

overall_design: BCAS2 was knocked out in ovarian granulosa cells, and 8dpp ovaries were taken to analyze and compare the gene expression profiles of RNA-SEQ data between WT and knockout groups.

first: Xiaohong

first: Jiali

last: Liu


title: ATAC-seq in myelinating oligodendrocytes from wt and Lmna knockout mice

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: We showed that the composition of the nuclear lamina changes with the differentiation state of oligodendrocyte lineage cells, with Lamin B highly expressed in progenitor cells and Lamin A highly expressed in mature oligodendrocytes. The genetic deletion of LMNA in mice results in the onset of a progressive motor phenotype in adult mice. We performed ATAC-Seq in myelinating Oligodendrocytes expressing the myelin marker NDRG1-EGFP ( Marechal et al., 2021) in the presence or absence of LMNA. The goal is to identify regions of chromatin accessibility that distinguish the LMNA KO mutant cells from the WT.

overall_design: Open chromatin profiles (ATAC-seq assay) in wild-type mice and knockdown LMNA mice.

first: Panos

last: Roussos

first: John

last: Fullard

first: Julia

last: Patzig


title: AMYLOIDOGENIC LIGHT CHAINS IMPAIR PLASMA CELL SURVIVAL

city: Jerusalem

first: Marjorie

last: Pick

address: Kiryat Hadassah p.o.b 12000

department: Hematology

country: Israel

institute: Hadassah Medical Organization

summary: We used lentiviral vectors to generate cell lines expressing LCs from patients suffering from AL amyloidosis.

overall_design: Compare AL LC to MM LC

first: Moshe

last: Gatt


title: Mitochondrial aconitase inhibits immunity via reducing mitochondrial unfolded protein response

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

institute: KAIST

summary: We show that mitochondrial aconitase, ACO-2, a Krebs cycle enzyme that catalyzes the conversion of citrate to isocitrate, inhibits immunity against pathogenic bacteria in C. elegans. We found that genetic inhibition of aco-2 enhanced mitochondrial unfolded protein response, subsequently upregulating ATFS-1 transcription factor, which contributed to enhanced immunity against pathogenic bacteria.

overall_design: The investigation of the changes of gene expression upon knockdown of aco-2 or infection with PA14.

first: Hae-Eun

middle: H

last: Park

first: Seokjin

last: Ham


title: Effect of Rheb depletion of Rheb and Ribo-HA knock-in on gene expression of neurons

status: Public on May 31 2023

city: Baltimore

first: Alexander

last: Platero

state: MD

address: 725 N. Wolfe st

institute: Johns Hopkins SOM

summary: To examine the effect of neuronal Rheb on brain myelination, we generated a conditional neuronal Rheb knockout mouse line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Control and Rheb cKO mice.

first: Ping

last: Tang

first: Liliana

last: Florea

first: Corina

last: Antonescu


title: Transcriptome profiles of lymphoma cell lines after treatment with MZ1 compunds

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

summary: 4 lymphoma cell lines (DOHH2, OCILy10, TMD8 and Toledo) have been treated with MZ1. The transcriptome has been sequenced after 6hrs from the treatment

overall_design: Transcriptome profiles of 6hrs for 4 lymphoma cell lines treated with MZ1

first: Francesco

last: Bertoni


title: Enhanced phosphorylation of c-Jun by cisplatin treatment as a potential predictive biomarker for cisplatin response in combination with patient-derived tumor organoids.

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

institute: Oita university, Faculty of Medicine

summary: Despite recent advancement in sequencing technologies and large-scale drug screenings with hundreds of cell lines, the predictive accuracy of mutation-based biomarkers is still insufficient to guide cancer therapy. Therefore, novel types of diagnostic methods with alternative biomarkers are highly appreciated. To develop the novel methods, we hypothesized that sensitivity-specific changes in phosphorylations of signaling molecules could be useful as predictive biomarkers. Here, we aimed to develop predictive methods for cisplatin with a combination of such type of biomarker(s) and patient-derived tumor organoids (PDOs). We found that cisplatin sensitive cell lines or PDOs showed enhanced phosphorylation of c-Jun (p-c-Jun) within 24 h in response to cisplatin treatment. We also compared responses to cisplatin in 6 PDOs with therapeutic effect of neoadjuvant chemotherapy (docetaxel/cisplatin/5-fluorouracil) in 6 matched patients. Mechanistically, the c-Jun induction was partly related to TNF signaling induced by cisplatin. Thus, our data implicates the feasibility of enhanced p-c-Jun by cisplatin treatment as a predictive biomarker for the efficacy.

overall_design: To identify genes that are regulated by JNK/c-Jun after a cisplatin treatment, we explored global gene expression profile after 24 h cisplatin treatment with or without JNK inhibitor (SP600125) for the last 3h of the treatment.

first: Shusaku

last: Kurogi

first: Tomotaka

last: Shibata

first: Kosuke

last: Suzuki

first: Shoichi

last: Fumoto

first: Yuka

last: Hirashita


title: eIF4E/mTOR-independent mRNA translation plasticity conferred by DAP5/eIF3d is required for breast cancer cell mesenchymal transition and metastasis

first: Robert

middle: J

last: Schneider

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

summary: We report the application of polysome profiling sequencing technology for high-throughput transcriptomics and translatomics in 4T1 cells.  We compare reduction of Dap5 to control in a BALB/c mouse breast cancer cell line in transcription and polysome enriched translation using RNA sequencing. Genome-wide transcriptomic and translatomic analyses indicate that DAP5 is required for translation of many transcription factors and their mRNA targets involved in EMT, angiogenesis, DNA repair and translation initiation, among other mRNAs. Metastatic potential of cells is significanlty decreased upon Dap5 silencing as confirmed by different in vivo models.

overall_design: Examination of transcriptomics and translatomics in mouse breast cancer cells.

first: Olga

last: Katsara

first: Amandine

last: Allard

first: Columba

last: dela Parra