title: Immune landscape of PBMC based on single-cell rna sequancing in End Stage Renal Disease

city: taiyaun

first: ruijing

last: Zhang

address: Wuyi Road, Xinghualing District, Taiyuan City, Shanxi Province

institute: The Second Hospital of Shanxi Medical University

summary: Although an increase in studies has revealed the potential mechanisms underlying immune dysfunction during CKD progression, there are still many significant components that need to be clarified, such as the machinery of T-cell phenotype switching and the plasticity levels of different subsets. Fortunately, in the last decade, novel technologies such as single-cell RNA sequencing have enabled us to investigate transcriptomic profiles at the single-cell level and have enabled us to unravel the potential mechanisms of the heterogeneity of the cell phenotype underlying different diseases. In this study, we investigated the immune cell composition, function, and interaction with other cells in PBMCs (peripheral blood mononuclear cells) during the ESRD period, especially CD4+ T-cell plasticity and the involved signaling pathways and mediators, which could be potential therapeutic targets for preventing CKD progression and complications.

overall_design: In this case‒control study, 14 male and 6 female ESRD patients who underwent standard hemodialysis were enrolled. Twenty healthy volunteers who were sex- and age-matched to ESRD patients comprised the healthy control group. All the participants were involved between June 1, 2022, and September 1, 2022. ESRD patients were required to meet the following inclusion/exclusion criteria. Inclusion criteria: ESRD patients receiving standard hemodialysis (HD) with arteriovenous fistulas (AVFs) for 5-10 years; the cause of kidney damage was primary kidney disease or diabetic nephropathy; and the discontinuation of corticosteroid and immunosuppression therapy for at least 1 year. Exclusion criteria: infection, tumor (including parenchymal tumor and hematological system tumor), autoimmune disease, acute infection, and other diseases; vaccination for COVID-19, influenza, and other viruses in the past 3 months; and an unwillingness or inability to cooperate due to individual reasons. Ficoll-Paque density gradient centrifugation was applied for PBMC isolation. Dead cells were removed using a Miltenyi ® Dead Cell Removal Kit (MACS, 130-090-101). Cell suspensions were resuspended in 1× PBS buffer with 0.04% BSA and centrifuged at 300 × g for 3 min at 4 °C (repeated twice). The cell pellet was resuspended in 50 μl of 1× PBS buffer with 0.04% BSA. The overall cell viability was confirmed by trypan blue exclusion. Cell viability above 85% was required for scRNA sequencing using a Countess II Automated Cell Counter. The PBMCs were diluted to a concentration of 1*106 cells/mL with sorting buffer. The 20 cellular suspensions from patients and controls were separately pooled with an equal volume.

first: Ruijing

first: Xinyan

last: Liu

first: Rongshan

last: Li


title: Identification of differentially expressed genes in mice with chronic heart failure induced by pressure overload

status: Public on Oct 31 2023

city: Shanghai

first: YUE

last: CUI

state: Shanghai

address: 1678 Dongfang Road

country: China

institute: Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the mechanism of chronic heart failure induced by pressure overload, we established an animal model in mice by transverse aortic constriction (TAC), with mice undergoing sham surgery as control.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of left ventricle (LV) tissues isolated from mice. Comparative gene expression profiling analysis of RNA-seq data for LV tissues in TAC and Sham mice.

first: Yue

last: Cui

first: Bozhong

last: Shi

first: Zijie

last: Zhou

first: Bo

last: Chen

first: Xiaoyang

first: Cong

first: Kai

last: Luo

first: Zhongqun

last: Zhu

first: Jinghao

last: Zheng

first: Xiaomin

last: He


title: Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate motor cortex

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

country: USA

institute: UCSD

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Sequence divergence of cis-regulatory elements drives species-specific traits, but how this manifests in the evolution of neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 180,000 cells.  For each modality, we determined species-specific, divergent, and conserved gene expression and epigenetic features at multiple levels. We find that cell type-specific gene expression evolves more rapidly than broadly expressed genes, and that epigenetic status at distal candidate cis-regulatory elements (cCREs) evolves faster than  promoters. Strikingly, transposable elements (TEs) contribute to nearly 80% of the human-specific cCREs in cortical cells. Through machine learning, we develop sequence-based predictors of cCREs in different species, and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Lastly, we show that epigenetic conservation combined with sequence similarity help uncover functional  cis-regulatory elements and enhance our ability  to interpret genetic variants contributing to neurological disease and traits.

sample_organism:
Callithrix jacchus
Macaca mulatta
Homo sapiens
Mus musculus

overall_design: Analysis of single cell multiome ATAC + gene expression (10x Genomics) of motor cortex from human, macaque, marmoset, and mouse

first: Nathan

middle: R

last: Zemke


title: Outward-oriented sites within clustered CTCF boundaries are key for intraTAD chromatin interactions and gene regulation [4C-seq]

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

summary: CTCF plays an important role in 3D genome organization by adjusting insulation at TAD boundaries, where clustered CBS (CTCF-binding site) elements are often arranged in tandem array with a complex divergent or convergent orientation. Here using cPcdh and HOXD loci as a paradigm, we look into the clustered CTCF TAD boundaries and find that, counterintuitively, outward-oriented CBS elements are crucial for inward enhancer-promoter interactions as well as for gene regulation. Specifically, by combinatorial deletions of a series of putative enhancer elements in vivo or CBS elements in vitro, in conjunction with chromosome conformation capture and RNA-seq analyses, we show that deletions of outward-oriented CBS elements weaken the strength of long-distance intraTAD promoter-enhancer interactions and enhancer activation of target genes. Our data highlight the crucial role of outward-oriented CBS elements within the clustered CTCF TAD boundaries and have interesting implications on the organization principles of clustered CTCF sites within TAD boundaries.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: QHR4C-seq of P0 old wild type (WT) and several mouse line mice and HEK293T cells were seperately generated by deep sequencing using Illumina Novaseq 6000

first: X

first: H

last: Huang

first: K

last: Han

first: W

last: Xu

first: Z

last: Wang

first: Q

last: Wu


title: ATF4 marks quiescent reserve cells of gastric chief cells

city: Toon

first: Daisuke

last: Shiokawa

state: Ehime

address: 454 Shitsukawa

department: Translational Research Center

country: Japan

institute: Ehime University Hospital

summary: Hierarchically organized tissues, such as hematopoietic systems, muscle, or skin harbor deeply quiescent stem cells which start proliferating in response to external insults. In contrast, it remains obscure whether similar quiescent cells exist in epithelia of digestive organs. Here we identified a deeply quiescent population in gastric corpus but not in other gastrointestinal organs after systematic examination of H2b-GFP label-retaining cells. The label-retaining cells in corpus epithelia belonged to a subpopulation of chief cells that were located near basal layers of corpus and did not overlap with Troyhigh, Lgr5high, or Misthigh cell population. The identified quiescent cells were marked with activation of Atf4 and unfolded protein response. External damages by indomethacin treatment triggered proliferation of the quiescent populations, indicating that chief cells of gastric corpus harbor deeply quiescent reserve cells with high levels of internal stress response activity.

overall_design: Stomach epithelial cells of the H2b-GFP mice were isolated by Fluorescence-activated cell sorting (FACS) according to Epcam-PE and GFP signals and analyzed using scRNAseq.

first: Hiroaki

last: Honda

first: Koji

last: Okamoto


title: Outward-oriented sites within clustered CTCF boundaries are key for intraTAD chromatin interactions and gene regulation [4C]

overall_design: QHR-4C profiles of P0 wild type (WT) and CBS-deletion mouse cortex were generated by deep sequencing using Illumina HiSeq X-ten.


title: Outward-oriented sites within clustered CTCF boundaries are key for intraTAD chromatin interactions and gene regulation [ATAC-seq]

overall_design: ChIP-seq of P0 old wild type (WT) and several mouse line mice were seperately generated by deep sequencing using Illumina Novaseq 6000


title: Outward-oriented sites within clustered CTCF boundaries are key for intraTAD chromatin interactions and gene regulation [ChIP-seq]

overall_design:
ChIP-seq of P0 old wild type (WT) and several mouse line mice were seperately generated by deep sequencing using Illumina Novaseq 6000

NOTE: The processed data for GSM7042633 (ChIP_WT_H3K4me1_rep2) sample has been updated on Dec 5, 2023.


title: Loss of centrosomal gene ALMS1 alters lipid metabolism and the regulation of processes linked to the extracellular matrix.

city: Vigo

first: Brais

last: Bea Mascato

state: Pontevedra

address: Campus de Vigo As LagoasCtra. de Marcosende, 36310 Vigo, Pontevedra

country: Spain

institute: University of Vigo

summary:
To investigate the alterations that occur in the TGF-B signalling pathway in Alström syndrome, we established by lentiviral transduction with CRISPR an hTERT-BJ-5ta cell line with the ALMS1 gene inhibited.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells (WT and KO) after 24h of TGF-β stimulation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hTERT BJ-5ta cells and its KO derivatives for ALMS1 gene (ALMS1KO) after TGF-β stimulation.

last: Bea-Mascato


title: Leukemia-intrinsic determinants of CAR-T response revealed by in vivo genome-wide CRISPR screening [scRNA-seq]

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: CAR-T cells are a promising new treatment for B cell malignancies. However, the   majority of patients inevitably go on to experience disease relapse through largely   unknown means. To investigate leukemia-intrinsic CAR-T resistance mechanisms, we   performed genome-wide CRISPR-Cas9 loss-of-function screening in an immunocompetent   murine model of B cell acute lymphoblastic leukemia (B-ALL). We identified IFN𝝲/JAK/STAT   signaling and components of the antigen processing and presentation pathway as key   mediators of resistance to anti-CD19 CAR-T therapy in vivo, but not in vitro.   Transcriptional characterization of this model demonstrated an upregulation of these   pathways in CAR-T treated relapsed tumors, and examination of data from CAR-T treated   B-ALL patients revealed an association between poor outcomes and increased expression   of JAK/STAT/MHC-I in leukemia cells. Together, our data identify an unexpected   mechanism of resistance to immunotherapy, in which tumor cell interaction with   IFN𝝲-secreting CAR-T cells in vivo activates the expression of an MHC-I inhibitory   T cell program.

overall_design: Single cell RNAseq comparison of 3 biological replicates each of mouse B-ALL cells isolated from either spleen or bone marrow challenged with CAR-T cells targeting either CD19 or a EGFRvIII

first: Azucena

last: Ramos

first: Catherine

last: Koch

first: Yunpeng

last: Liu

first: Riley

middle: D

last: Hellinger

first: Taeyoon

last: Kyung

first: Rebeca

middle: C

last: Larson

first: Julia

last: Fröse

first: Daniel

last: Goulet

first: John

middle: G

last: Doench

first: Aviv

last: Regev

first: Marcela

middle: V

last: Maus

first: Michael

middle: E

last: Birnbaum

middle: T

last: Hemann


title: Leukemia-intrinsic determinants of CAR-T response revealed by in vivo genome-wide CRISPR screening [bulk RNA-seq]

overall_design: Bulk RNAseq comparison of 3 biological replicates each of mouse B-ALL cells isolated from either spleen or bone marrow challenged with CAR-T cells targeting either CD19 or a EGFRvIII


title: Epigenomic Profile of Lineage-Traced Mouse Horizontal Basal Cells Before and 24 Hours After Injury

status: Public on Oct 30 2023

city: Bethesda

first: Whitney

last: Heavner

state: MD

address: Building 35 Rm 2B-203

department: NINDS

institute: National Institutes of Health

summary: Wild-type horizontal basal cells (HBCs) from mouse olfactory epithelium were profiled using single-cell ATAC-seq (10x Genomics v2) to identify regions of accessible chromatin in individual cells before and 24 hours after acute injury.

overall_design: 24 hours after injury by intraperitoneal injection of methimazole, Krt5-CreER^T2; Rosa26-LSL-YFP/YFP lineage-traced cells were purified via fluorescence activated cell sorting (FACS). Uninjured YFP+ cells were also collected. Three biological replicates per condition (uninjured and 24 hours post-injury) were collected.

first: Hsin-Jung

last: Chou

last: Ngai

first: Koen

last: Van den Berge


title: Single-Nuclei Multiome (ATAC + Gene Expression) Sequencing of a Primary Canine Osteosarcoma Elucidates Intra-Tumoral Heterogeneity and Characterizes the Tumor Microenvironment

city: Auburn

first: Bruce

middle: F

last: Smith

state: AL

address: 1265 HC Morgan Dr

department: Pathobiology

institute: Auburn University College of Veterinary Medicine

summary: Osteosarcoma (OSA) is a highly aggressive bone tumor primarily affecting pediatric or adolescent humans and large breed dogs. Canine OSA shares striking similarities with its human counterpart, making it an invaluable translational model for uncovering the disease's complexities and de-veloping novel therapeutic strategies. Tumor heterogeneity, a hallmark of OSA, poses significant challenges to effective treatment due to the evolution of diverse cell populations that influence tumor growth, metastasis, and resistance to therapies. In this study, we apply single-nuclei mul-tiome sequencing, encompassing ATAC (Assay for Transposase-Accessible Chromatin) and GEX (Gene Expression, or RNA) sequencing, to a treatment-naïve primary canine osteosarcoma. This comprehensive approach reveals the complexity of the tumor microenvironment by simultane-ously capturing the transcriptomic and epigenomic profiles within the same nucleus. Furthermore, these results are analyzed in conjunction with bulk RNA sequencing and differential analysis of the same tumor and patient-matched normal bone. By delving into the intricacies of OSA at this un-precedented level of detail, we aim to unravel the underlying mechanisms driving intra-tumoral heterogeneity, opening new avenues for therapeutic interventions in both human and canine patients. This study pioneers an approach that is broadly applicable, while demonstrating sig-nificant heterogeneity in the context of a single individual’s tumor.

overall_design: Single nuclei were extracted from a primary, treatment-naive canine osteosarcoma tumor and subjected to 10x Genomics single nuclei multiome (ATAC + GEX) sequencing to evaluate intra-tumoral heterogeneity and characterize the tumor microenvironment.

first: Rebecca

middle: L

last: Nance

first: Xu

last: Wang

first: Maninder

last: Sandey

first: Brad

last: Matz


title: Transcriptomic changes from resulting from DARPP-32 modulation in breast cancer

city: Nottingham

first: Sarah

middle: Joanne

last: Storr

state: Nottinghamshire

address: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

summary: DARPP-32 expression was reduced in oestrogen receptor positive luminal B breast cancer cells (T47D) using siRNA and control and DARPP-32 knockdown cells were subject to stimulation with estradiol17β (E2) or inhibition of protein kinase A (PKA) with PKA inhibitor fragment (6-22) amide prior to RNA sequencing. A bioinformatics pipeline of Trim Galore, Kallisto, DESeq2 and Qiagen Ingenuity Pathway Analysis was used for pathway analysis.

overall_design: T47D cells were subject to siRNA knockdown of PPP1R1B (DARPP-32), or negative control siRNA prior to RNA-Seq. In addition, DARPP-32 knockdown or control cells were stimulated with 17-estradiol (E2) or inhibition of PKA with PKA inhibitor fragment (6-22) amide.


title: Leukemia-intrinsic determinants of CAR-T response revealed by in vivo genome-wide CRISPR screening

first: Charles

last: Whittaker

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

overall_design: Refer to individual Series


title: HOXC6 drives a therapeutically targetable pancreatic cancer growth and metastasis pathway via stimulating MSK1 kinase and suppressing PPP2R2B protein

city: Birmingham

first: Narendra

last: Wajapeyee

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers, which lacks effective therapies. Here, we demonstrate that the transcription factor, HOXC6, is overexpressed in most PDACs, and its inhibition blocks PDAC tumor growth and metastasis. HOXC6 transcriptionally activates tumor-promoting kinase MSK1 and suppresses tumor-inhibitory protein PPP2R2B in PDAC. HOXC6-induced PPP2R2B suppression causes mTOR pathway activation, which facilitates PDAC growth. Also, MSK1 upregulation by HOXC6 is necessary for PDAC growth due to its ability to suppress apoptosis via its substrate DDX17. Combinatorial pharmacological inhibition of MSK1 and mTOR potently suppressed PDAC tumor growth and metastasis in PDAC mouse models. PDAC cells with acquired resistance to MSK1/mTOR-inhibitors displayed activated IGF1R signaling and were successfully eradicated by IGF1R inhibitor. Furthermore, MEK inhibitor trametinib enhanced the efficacy of dual MSK1 and mTOR inhibition. Collectively, these results identify therapeutic vulnerabilities of PDAC and an approach to overcome acquired drug resistance to prolong therapeutic benefit.

overall_design: PANC1 cells stably expressing two individual shRNAs against HOXC6 were used to prepare the total RNA, which was then used to analyze for gene expression using RNA-sequencing analysis


overall_design: PANC1 cells stably expressing two individual shRNAs against MSK1 were used to prepare the total RNA, followed by RiboRNA depletion with random priming and RNASeq Illumina Hi-Seq 2500 platform, with three biological replicates for each sample.

first: Romi

last: Gupta

first: Parmanand

last: Malvi


overall_design: AsPC1 cells stably expressing two individual shRNAs against MSK1 were used to prepare the total RNA, followed by RiboRNA depletion with random priming and RNASeq Illumina Hi-Seq 2500 platform, with three biological replicates for each sample.


title: M2-like dermis resident macrophages regulate type 1 2 circuitries with ILC2s and eosinophils to exacerbate cutaneous leishmaniasis

first: Byunghyun

last: Kang

state: Maryland

address: 9000 Rockville Pike

institute: NIAID

summary: Tissue-resident macrophages (TRMs) are critical for tissue homeostasis/repair. We previously showed that dermal TRMs produce CCL24 which mediates their interaction with IL-4 producing eosinophils, required to maintain their M2-like properties in the TH1 environment of the Leishmania major infected skin. Here, we unveil another layer of TRM self-maintenance involving production of TSLP, an alarmin typically characterized as epithelial cell-derived. Both TSLP signaling and IL-5+ innate lymphoid cell 2 (ILC2s) were shown to maintain dermal TRM numbers  and promote infection. Single cell RNA sequencing identified the dermal TRMs as the sole source of TSLP and CCL24. Generation of Ccl24-cre mice permitted specific labeling of dermal TRMs, as well as interstitial TRMs from other organs. Genetic ablation of TSLP from dermal TRMs reduced the number of dermal TRMs and ameliorated infection. Here, we show that by orchestrating localized type 2 circuitries with ILC2s and eosinophils, dermal TRMs are self-maintained as a replicative niche for L. major.

overall_design: CD45+ hematopoietic and CD45- nonhematopoietic cells were FACs-sorted from the ears of either naïve or infected WT and eoCre : Il4/13f/f mice and mixed at 9:1 ratio (CD45+:CD45-),  and then processed through the Chromium Single cell 3’ v3.1 Library kit (10x Genomics) per the manufacturer’s protocol.  Samples were further stained with nucleotide sequence tagged antibodies for measuring surface protein expression and cell indexing: TotalSeqTM-B0182 anti-mouse CD3 (17A2, Biolegend), TotalSeqTM-B0001 anti-mouse CD4 (RM4-5, Biolegend); TotalSeqTM-B0014 anti-mouse CD11b (M1/70, Biolegend); TotalSeqTM-B0106 anti-mouse CD11c (N418, Biolegend); TotalSeqTM-B0093 anti-mouse CD19 (6D5, Biolegend); TotalSeqTM-B0118 anti-mouse NK1.1 (PK136, Biolegend); TotalSeqTM-B0015 anti-mouse Ly6G (1A8, Biolegend); TotalSeqTM-B0012 anti-mouse c-Kit (2B8, Biolegend); TotalSeqTM-B0847 anti-mouse ICOS (7E.17G9, Biolegend); TotalSeqTM-B0114 anti-mouse F4/80 (BM8, Biolegend); TotalSeqTM-B0157 anti-mouse CD45.2 (104, Biolegend); TotalSeqTM-B0115 anti-mouse FceR1a (MAR-1, Biolegend); TotalSeqTM-B0002 anti-mouse CD8a (53-6.7, Biolegend); TotalSeqTM-B0431 anti-mouse SiglecF (S17007L, Biolegend); TotalSeqTM-B0810 anti-mouse CD138 (281-2, Biolegend); TotalSeqTM-B0120 anti-mouse TCRb (H57-597, Biolegend); TotalSeqTM-B0211 anti-mouse TCRgd2 (UC3-10A6, Biolegend); TotalSeqTM-B0301 to 0304 anti-mouse Hashtag 1 to 4 (M1/42 and 30-F11, Biolegend). 8,300 sorted cells were loaded for GEM formation, targeting 5,000 single cells for analysis from each ear. The RNAs from lysed single cells in gel beads were reversed transcribed into cDNA with Barcodes. Library fragment-size distribution was assessed using the Bioanalyzer 2100 and the DNA high-sensitivity chip (Agilent Technologies), followed by amplification, fragmentation, adapter ligation, and size selection to generate both 3’ gene expression libraries and cell surface protein libraries. Libraries were sequenced on an Illumina NovaSeq 6000 by Psomagen, Inc.

first: SangHun

last: Lee

first: Byunhyun

first: Brian

last: Kelsall

first: David

last: Sacks


title: Identification of differential expression miRNAs profile in serum samples of high-grade serous ovarian patients

status: Public on Oct 29 2023

city: Bialystok

first: Magdalena

last: Niemira

address: Kilinskiego 1

country: Poland

institute: Medical University of Bialystok

summary: Developing a classification model based on differential expression miRNAs profile in serum HGSOC samples to improive diagnosis of HGCOS.

overall_design: In the study presented here, well-defined cohort of 34 HGSOS and 36 healthy subjects were used to acquire expression profiles of 798 miRNAs using NanoString platform.

first: Anna

last: Erol


title: Role of PDGFRA+ cells and a CD55+ PDGFRALo fraction in the gastric mesenchymal niche

city: Boston

first: RAMESH

last: SHIVDASANI

state: MASSACHUSETTS

address: 450 Brookline ave

institute: Dana-Farber Cancer Institute

summary: PDGFRA-expressing mesenchyme supports intestinal stem cells. Stomach epithelia have related niche dependencies, but their enabling mesenchymal cell populations are unknown, in part because previous studies pooled the gastric antrum and corpus. Our high-resolution imaging, transcriptional profiling, and organoid assays identified regional subpopulations and supportive capacities of purified mouse corpus and antral PDGFRA+ cells. Sub-epithelial PDGFRAHi myofibroblasts are principal sources of BMP ligands and two molecularly distinct pools distribute asymmetrically along antral glands but together fail to support epithelial growth in vitro. In contrast, PDGFRALo CD55+ cells strategically positioned beneath gastric glands promote epithelial expansion in the absence of other cells or factors. This population encompasses a small fraction expressing the BMP antagonist Grem1. Although Grem1+ cell ablation in vivo impairs intestinal stem cells, gastric stem cells are spared, implying that CD55+ cell activity in epithelial self-renewal derives from other subpopulations. Our findings shed light on spatial, molecular, and functional organization of gastric mesenchyme and the spectrum of signaling sources for epithelial support.

overall_design: Gastric intestinal mesenchymal cells from adult PdgfraH2BeGFP (JAX strain 007669) mice were isolated and sorted for level of Pdgfra (eGFP, high or low) to obtain two different cell types in biological replicates per location.

first: Elisa

last: Manieri

first: Guodong

last: Tie

first: Ermanno

last: Malagola

first: Davide

last: Seruggia

first: Shariq

last: Madha

first: Adrianna

last: Maglieri

first: Kun

last: Huang

first: Yuko

last: Fujiwara

first: Kevin

last: Zhang

first: Stuart

middle: H

last: Orkin

first: Timothy

first: Ruiyang

last: He

first: Neil

last: McCarthy

first: Ramesh

middle: A

last: Shivdasani


title: Circulating total extracellular vesicles cargo are associated with age-related oxidative stress and susceptibility to cardiovascular diseases: exploratory results from microarray data

status: Public on Oct 28 2023

city: Washington

first: Laura

last: Reck Cechinel

state: District of Columbia

address: 7144 13th Pl NW

institute: Children's National Medical Center

summary: Aging is a risk factor for many non-communicable diseases such as cardiovascular and neurodegenerative diseases. Aging could impact the extracellular vesicles and particles (EVPs) miRNA profile and impair redox homeostasis, contributing to chronic age-related diseases. We aimed to investigate the microRNA profiles of circulating total EVPs from aged and young adult animals. Plasma from 3- and 21-month-old male Wistar rats was collected and circulating total EVPs were isolated.  MicroRNA isolation and microarray expression analysis were performed on EVPs to determine the predicted regulation of targeted mRNAs. 31 mature miRNAs in circulating EVPs were impacted by age and predicted to target molecules in canonical pathways directly related to cardiovascular diseases and oxidative status.  Our data show that circulating total EVP cargo, specifically microRNAs, are involved in redox imbalance in the aging process and can potentially drive cardiovascular aging and consequently cardiac disease.

overall_design: EVPs miRNA was isolated from the plasma of young adult (3-month old, n=10) and aged (21-month-old, n=11) male Wistar rats. Total RNA was extracted using mirVana microRNA Isolation kits (Life Technologies). Total RNA was amplified with the Complete Seramir Exosome

first: Rachael

last: Batabyal

first: Giana

last: Blume Corssac

first: Madeleine

last: Goldberg

first: Brennan

last: Harmon

first: Virgínia

last: Mendes Carregal

first: Gisele

last: Bruch

first: André

last: Massensini

first: Adriane

last: Belló-Klein

first: Alex

middle: S

last: Araujo

first: Robert

middle: J

last: Freishtat

first: Ionara

last: Rodrigues Siqueira


title: ETV4-Dependent Transcriptional Plasticity Maintains MYC Expression and Results in IMiD Resistance in Multiple Myeloma

city: Atlanta

first: Benjamin

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University


title: Transcriptional and epigenetic reprogramming mediated by chronic IL1β exposure drives self-renewal ability and myeloid priming in TET2 deficient stem and progenitor cells [Bisulfite-Seq]

status: Public on Oct 27 2023

city: Portland

first: Anupriya

last: Agarwal

state: OR

address: 2730 S Moody Ave

department: OHSU Knight Cancer Institute/ CEDAR

institute: Oregon Health & Science Univ

type: Methylation profiling by high throughput sequencing

summary: Clonal hematopoiesis (CH) increases risk for the development of hematological malignancy and cardiovascular disease. IL1β is elevated in patients with CH and its inhibition mitigates cardiovascular risk in murine models with Tet2 loss-of-function. How IL1β alters population dynamics of hematopoietic cells upon Tet2 deletion (Tet2-KO) is not well understood. We demonstrated IL1β expands Tet2-KO neutrophils, monocytes/macrophages, and long-term hematopoietic stem cells with reduced lymphopoiesis. IL1β promotes myeloid bias over other lineages coinciding with failure to demethylate lineage associated enhancer and transcription factor binding sites in Tet2-KO HSPCs. IL1β enhanced self-renewal ability of Tet2-KO HSPCs by upregulating genes associated with self-renewal potential and by failure to demethylate binding sites of transcription factors promoting differentiation. IL1β-mediated premalignant phenotype is reversed by IL1β antagonist anakinra or deletion of the Il1 receptor, in vivo. Our results demonstrated that targeting IL-1 signaling could be an efficient early intervention strategy in preleukemic disorders.

overall_design: Whole genome bisulfite sequencing (WGBS) was performed on flow sorted live LSK (Lin-Sca1+cKit+7AAD-), CMP (Lin- Sca1- ckit+ CD34+ Fc Gamma-7AAD-), and GMP (Lin- Sca1- ckit+ CD34+ Fc Gamma+7AAD-) isolated from Tet2fl/fl (wild type, WT) or Vav-Cre-Tet2-/- knockout (KO) animals that were treated with either recombinant IL-1ß or vehicle for five weeks prior to collection. In total four biological replicates were performed for each genotype/treatment/cell type  (16 LSK, 16 CMP, and 16 GMP samples from 16 animals).

first: McClatchy

last: John

first: Strogantsev

last: Ruslan

first: Mohammed

last: Hisham

first: Agarwal

last: Anupriya


title: Music compensates for altered gene expression in age-related cognitive disorders

status: Public on Oct 26 2023

city: Santiago de Compostela

first: Alberto

last: Gómez-Carballa

state: A coruña

address: Choupana sn

department: Pediatrics

institute: GENVIP research group

summary: Extensive literature has explored the beneficial effects of music in age-related cognitive disorders (ACD), but limited knowledge exists regarding its impact on gene expression. We analyzed transcriptomes of ACD patients and healthy controls, pre-post a music session (n=60), and main genes/pathways were compared to those dysregulated in mild cognitive impairment (MCI) and Alzheimer’s disease (AD) as revealed by a multi-cohort study (n=1269 MCI/AD and controls). Music was associated with 2.3 times more whole-genome gene expression, particularly on neurodegeneration-related genes, in ACD than controls. Co-expressed gene-modules and pathways analysis demonstrated that music impacted autophagy, vesicle and endosome organization, biological processes commonly dysregulated in MCI/AD. Notably, the data indicated a strong negative correlation between musically-modified genes/pathways in ACD and those dysregulated in MCI/AD. These findings highlight the compensatory effect of music on genes/biological processes affected in MCI/AD, providing insights into the molecular mechanisms underlying the benefits of music on these disorders.

overall_design: Music exerts a profound influence on human brains, affecting emotions, activating the reward system, and inducing changes in brain anatomy. However, research on the impact of music on gene expression is still in its nascent stages. The present study represents the first attempt to analyze the effect of music on the transcriptome of ACD patients. Capillary blood samples were collected from ACD patients and healthy donors using a minimally invasive procedure before and after a 50-minute session of classical musical stimuli in an ecologically valid environment. Subsequently, we performed RNA sequencing on these samples, allowing for the analysis of gene expression information for over 35,000 transcripts. The analysis focused on differential expression between the two time points and cohorts, as well as the contextualization of gene expression changes within the framework of genes and pathways that exhibit dysregulated expression in MCI and AD

first: Antonio

last: Salas


title: Transcriptional and epigenetic reprogramming mediated by chronic IL1β exposure drives self-renewal ability and myeloid priming in TET2 deficient stem and progenitor cells


title: Ultradeep targeted methylation sequencing of BRCA1 promoter in paired tumor-normal samples from breast cancer patients

city: Bergen

first: Oleksii

last: Nikolaienko

state: Vestland

address: Jonas Lies veg 87

department: Department of Clinical Science

country: Norway

institute: University of Bergen

summary:
Background:  Normal cell BRCA1 epimutations have been associated with increased risk of triple-negative breast cancer (TNBC). However, the fraction of TNBCs that may have BRCA1 epimutations as their underlying cause is unknown. Neither are the time of occurrence and the potential inheritance patterns of BRCA1 epimutations established.
Methods: To address these questions, we analyzed BRCA1 methylation status in breast cancer tissue and matched white blood cells (WBC) from 408 patients with 411 primary breast cancers, including 66 TNBCs, applying a highly sensitive sequencing assay, allowing allele-resolved methylation assessment. Further, to assess the time of origin and the characteristics of normal cell BRCA1 methylation, we analyzed umbilical cord blood of 1260 newborn girls and 200 newborn boys. Finally, we assessed BRCA1 methylation status among 575 mothers and 531 fathers of girls with (n = 102) and without (n = 473) BRCA1 methylation.
Results: We found concordant tumor and mosaic WBC BRCA1 epimutations in 10 out of 66 patients with TNBC and in four out of six patients with estrogen receptor (ER)-low expression (<10%) tumors (combined: 14 out of 72; 19.4%; 95% CI 11.1–30.5). In contrast, we found concordance in only three out of 220 patients with 221 ER≥10% tumors and zero out of 114 patients with 116 HER2-positive tumors. Intraindividually, BRCA1 epimutations affected the same allele in normal and tumor cells. Assessing BRCA1 methylation in umbilical WBCs from girls, we found mosaic, predominantly monoallelic BRCA1 epimutations, with qualitative features similar to those in adults, in 113/1260 (9.0%) of individuals, but no correlation to BRCA1 methylation status either in mothers or fathers. A significantly lower fraction of newborn boys carried BRCA1 methylation (9 / 200; 4.5%) as compared to girls (p = 0.038). Similarly, WBC BRCA1 methylation was found less common among fathers (16/531; 3.0%), as compared to mothers (46 / 575; 8.0%; p = 0.0003).
Conclusions: Our findings suggest prenatal BRCA1 epimutations might be the underlying cause of around 20% of TNBC and low-ER expression breast cancers. Such constitutional mosaic BRCA1 methylation likely arise through gender-related mechanisms in utero, independent of Mendelian inheritance.

overall_design: Study includes 408 patients enrolled in three neoadjuvant breast cancer studies (EPITAX, DDP and PETREMAC) from which pretreatment tumor tissue and white blood cells DNA samples were available for analysis.

first: Nikolaienko

last: Oleksii

first: Knappskog

last: Stian

first: Lønning

last: Per Eystein


title: Large-scale analysis of cell-cell communication reveals angiogenin-dependent tumor progression in clear cell renal cell carcinoma

city: Paris

first: Lucile

last: Massenet-Regad

address: 1 avenue Claude Vellefaux

country: France

institute: INSERM

summary: Cellular crosstalk in the tumor microenvironment (TME) is still largely uncharacterized, while it plays an essential role in shaping immunosuppression or anti-tumor response. Large-scale analyses are needed to better decipher cell-cell communication in cancer. In this work, we used original and publicly available single-cell RNA sequencing (scRNAseq) data to characterize in-depth the communication networks in human clear cell renal cell carcinoma (ccRCC). We identified 50 putative communication channels specifically used by cancer cells to interact with other cells, including two novel angiogenin-mediated interactions. Expression of angiogenin and its receptors was validated at the protein level in primary ccRCC. Mechanistically, angiogenin enhanced ccRCC cell line proliferation and down-regulated secretion of IL-6, IL-8, and MCP-1 proinflammatory molecules. This study provides novel biological insights into molecular mechanisms of ccRCC, and suggests angiogenin and its receptors as potential therapeutic targets in clear cell renal cancer.

overall_design: Fresh samples of ccRCC human tumors and adjacent healthy tissue were obtained from the pathology departments of Saint-Louis and Bichat hospitals (Paris, France), from 3 patients that underwent partial or total nephrectomy for localized clear cell renal cell carcinoma. After tissue dissociation and single-cell suspension generation, cell sorting was done by FACS to enrich for rare immune and stromal cell types.  Single-cell libraries were generated using the Chromium 10X Next GEM Single-cell 3’ Kit (v3.1) according to the manufacturer instructions (10X Genomics).  Quality of the libraries was assessed by High Sensitivity D1000 ScreenTape assay and next-generation sequencing was performed on an Illumina NovaSeq 6000, with a sequencing depth of 200 000 reads/cell.

first: Justine

last: Poirot

first: Vassili

last: Soumelis


title: Transcriptional and epigenetic reprogramming mediated by chronic IL1β exposure drives self-renewal ability and myeloid priming in TET2 deficient stem and progenitor cells [10x_scRNAseq]

overall_design: High throughput single cell RNA sequencing (10x scRNA-seq) was performed for lineage depleted bone marrow cells (Lin-ve BM) isolated from Tet2 wild type (WT) or knockout (KO) animals that were treated with either recombinant IL-1ß or vehicle for five weeks prior to collection. In total four biological replicates  were performed for each genotype/ treatment condition  (16 Lin- BM samples from 16 animals).


title: Transcription induces context-dependent remodeling of chromatin architecture during differentiation

city: Illkirch

first: Tom

last: Sexton

address: 1 rue Laurent Fries

institute: IGBMC (Institute of Genetics and Molecular and Cellular Biology)

summary: Metazoan chromosomes are organized into discrete domains (TADs), believed to contribute to the regulation of transcriptional programs. Despite extensive correlation between TAD organization and gene activity, a direct mechanistic link is unclear, with perturbation studies often showing little effect. To follow TAD dynamics during development, we used Capture Hi-C to interrogate the TADs around key differentially expressed genes during mouse thymocyte maturation, uncovering specific remodeling events. Notably, one TAD boundary was broadened to accommodate RNA polymerase elongation past the border, and sub-domains were formed around some activated genes without changes in CTCF binding. The ectopic induction of one gene was sufficient to recapitulate microdomain formation in embryonic stem cells, providing strong evidence that transcription can directly remodel chromatin structure. These results suggest that transcriptional processes drive complex, but non-universal, chromosome folding patterns that can be important in certain genomic contexts.

overall_design: Capture Hi-C, Hi-C and 4C interrogation of specific TAD architectures in mouse thymocytes and ESCs before and after experimental manipulations to try and perturb specific TADs. Biological replicates performed for Hi-C and Capture Hi-C experiments.

first: Yousra

last: Ben Zouari


title: RNA sequencing of clonal cell lines derived from mouse digit P3 fibroblasts

city: College Station

first: Ling

last: Yu

state: Texas

address: Raymond Stotzer Pkwy

department: VTPP

institute: TAMU

summary: Here we present RNA sequencing data of 2 clonal cell lines (P3D8 and P3E3) treated with BMP2 and BMP9 to differentiate cartilage and control untreated clonal cells

overall_design: Each sample was prepared from three independent cultures. For chondrogenesis, cells were aggregated by BMP2 treatment in suspension culture then differentiated with BMP9. Control cells were cultured in monolayer.

first: Yu-Lieh

last: Lin

first: Minquan

last: Yan

first: Regina

last: Brunauer

first: Lindsay

last: Dawson

first: Katherine

last: Zimmel

first: Ken

last: Muneoka


title: Brain methylome remodeling sustains neuronal activity gene expression in mice exposed to maternal immune activation

status: Public on Oct 25 2023

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics


title: Ultradeep targeted methylation sequencing of BRCA1 promoter in white blood cell DNA samples from newborns and their parents

first: Oleksii

last: Nikolaienko

overall_design: Study includes 1260 newborn girls, 200 newborn boys, 575 samples from mothers and 531 samples from fathers of girls with and without BRCA1 methylation. 420 girls were born prematurely (before 36 weeks of gestation) and 840 girls were born at normal term (39–41 weeks of gestation).


title: Nod1-dependent NF-kB activation initiates hematopoietic stem cell specification in response to small Rho GTPases

city: Ames

first: Raquel

last: Espin-Palazon

state: Iowa

address: 2437 Pammel Drive

institute: Iowa State University

summary:
The possibility of specifying functional hematopoietic stem and progenitor cells (HSPCs) from human pluripotent stem cells (hPSCs) would overcome current limitations related to HSPC transplantation. However, generating hPSC-derived HSPCs has been elusive, necessitating a better understanding of the native developmental mechanisms that trigger HSPC specification. Here, we revealed in vivo an intrinsic inflammatory mechanism triggered by Nod1 that drives early hemogenic endothelium (HE) patterning to specify HSPCs. Our genetic and chemical experiments showed that HSPCs failed to specify in the absence of Nod1 and its downstream kinase Ripk2. Rescue experiments demonstrated that Nod1 and Ripk2 acted through NF-kB, and that small Rho GTPases are at the apex of this mechanism. Manipulation of NOD1 in a human system of hPSCs differentiation towards the definitive hematopoietic lineage indicated functional conservation. This work establishes the RAC1-NOD1-RIPK2-NFkB axis as the earliest inflammatory inductor that intrinsically primes the HE for proper HSPC specification. Manipulation of this pathway could help derive a competent HE amenable to specify functional patient specific HSPCs for the treatment of blood disorders.
Keywords: NOD1, RIPK2, NF-kB, RAC1, Rho GTPases, Hematopoietic Stem and Progenitor Cell Specification, Hemogenic Endothelium.

overall_design: AB wildtype x kdrl:mCherry zebrafish embryos were injected with Standard-MO, Nod1-MO2, Nod2-MO and Ripk2-MO at one-cell stage. Approximately 150 per morpholino injection 24hpf kdrl + zebrafish embryos were screened with Leica M165FC stereomicroscope, dechorionated with pronase, anesthetized in 1% tricane, gently shaken at 28C for 5 mins with 0.05mg/ml liberase TM(Roche) in PBS solution with Ca2+ and Mg2+. The resulting cell suspension was filtered and stained with Sytox Red to exclude dead cells. kdrl+ cells were sorted and collected with BD FACS Aria III. RNA was then isolated and purified with RNeasy Micro Kit (Qiagen) in triplicate per condition.

first: Xiaoyi

last: Cheng

first: Radwa

last: Barakat

first: Abigail

last: Gorden

first: Elizabeth

last: Snella

first: Yudi

last: Zhang

first: Karin

last: Dorman

first: Antonella

last: Fidanza

first: Clyde

last: Campbell


title: Brain methylome remodeling sustains neuronal activity gene expression in mice exposed to maternal immune activation [5hmc]

summary: Maternal infections have been linked to various neuropsychiatric disorders that may later emerge in offspring. 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) are key DNA modifications but their roles in maternal infection remain to be elucidated. It has been documented that Zika virus (ZIKV) infection during pregnancy leads to structural brain defects such as microcephaly in offspring. However, whether and how offspring exposed to maternal ZIKV infection develop neurocognitive complications remain largely unknown. Here we report that ZIKV infection during mouse pregnancy leads to offspring with depression- and anxiety-like behaviors, which are transmitted to the next generation. Single nucleus RNA sequencing in prefrontal cortex (PFC) of ZIKV offspring mice revealed cell type-specific gene dysregulation associated with neuropsychiatric lesions. Genome-wide 5hmC, 5mC, and transcriptome profiling in ZIKV PFC revealed an overall loss of 5hmC and an increase of 5mC in intragenic regions, associated with transcriptional changes in key functional genes. Gain-of-5hmC regions were mainly located in intergenic transposable elements (TEs) coupled with decreased 5mC and dynamic TE expression. These results provide the first 5hmC study in maternal infection and suggest that maternal ZIKV infection remodels methylome and gene expression in offspring mouse brains, contributing to transgenerational behavior changes.

overall_design: NeuN+ and NeuN- cell population from ZIKA virus treatment and mock group were subject for 5hmC-Seal-seq

first: Li

last: Ma

first: Feng

last: Wang

first: Yangping

last: Li


title: Brain methylome remodeling sustains neuronal activity gene expression in mice exposed to maternal immune activation [5mC]

overall_design: NeuN+ and NeuN- cell population from ZIKA virus treatment and mock group were subject for MeDIP-seq


title: Maternal Zika virus infection alters epigenetic DNA modifications and leads to transgenerational behavioral changes in offspring mice

overall_design: Refer to individual Series


title: Maternal Zika virus infection alters epigenetic DNA modifications and leads to transgenerational behavioral changes in offspring mice (5hmC)

summary: Female mouse was infected by zika virus, then subject to 5hmC capture and RNAseq, by comparing PBS treated mouse and zika infected mouse, we identified zika affected gene that regulated by 5hmC change

overall_design: 3 zika infected mouse and 3 PBS treated mouse for 5hmC capture; 4 zika infected mouse and 4 PBS treated mouse for RNAseq

first: Jianfu

last: Chen


title: Prenatal BRCA1 epimutations contribute significantly to triple-negative breast cancer development


title: Single-cell transcriptomics reveals the brain evolution of web-building spiders

status: Public on Oct 24 2023

city: Beijing

first: IOZ

last: CAS

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Spiders are renowned for their efficient capture of flying insects using intricate aerial webs. How the spider nervous systems evolved to cope with this specialized hunting strategy and various environmental clues in an aerial space remains unknown. Here, we report a brain cell atlas of >30,000 single-cell transcriptomes from a web-building spider (Hylyphantes graminicola). Our analysis revealed the preservation of ancestral neuron types in spiders, including the potential coexistence of noradrenergic and octopaminergic neurons, and many peptidergic neuronal types that are lost in insects. By comparing the genome of two newly sequenced plesiomorphic burrowing spiders with three aerial web-building spiders, we found that the positively selected genes in the ancestral branch of web-building spiders were preferentially expressed (42%) in the brain, especially in the three mushroom body-like neuronal types. By gene enrichment analysis and RNAi experiments, these genes were suggested to be involved in the learning and memory pathway and may influence the spiders’ web-building and hunting behavior. Our results provide key sources for understanding the evolution of behavior in spiders and reveal how molecular evolution drives neuron innovation and the diversification of associated complex behaviors.

overall_design: Five single-cell libraries (two from males and three from females) were constructed for 10X single-cell sequencing.

first: Pengyu

last: Jin

first: Bingyue

last: Zhu

first: Yiming

first: Shuqiang


title: Maternal Zika virus infection alters epigenetic DNA modifications and leads to transgenerational behavioral changes in offspring mice (RNA-Seq)

first: Bing

last: Yao


title: Genomic Exploration of Distinct Molecular Phenotypes Steering Temozolomide Resistance Development in  Patient-Derived Glioblastoma Cells

city: Rotterdam

first: Martine

last: Lamfers

address: Dr. Molewaterplein 40

department: Neurosurgery

country: Netherlands

institute: Erasmus MC

summary: Temozolomide resistance is a major obstacle in the therapy of glioblastoma. This is also due to the insufficient understanding of glioma heterogeneity in relation to temozolomide resistance. More in depth biological knowledge would benefit the development of different approaches to tackle the problem from its root. We explored the different outcomes derived from the long-term exposure to temozolomide and identified two different behavioral phenotypes associated to specific categories of pathways. In addition, we investigated the intra-tumoral heterogeneity of these phenotypes revealing the complexity of the temozolomide resistance phenomenon.

overall_design: Four cell cultures were selected for single cell RNA sequencing. For GS359, GS785, and GS789 the cells sequenced comprised five conditions: control prior treatment (T0-CTRL), control and temozolomide treatment after the first temozolomide exposure (T1-TMZ and T1-CTRL), control and treatment after the last temozolomide treatment (T2-TMZ and T2-CTRL). For GS772 the cells sequenced comprised three conditions: control prior treatment (T0-CTRL), control and temozolomide treatment after the first temozolomide exposure (T1-TMZ and T1-CTRL).

first: Federica

last: Fabro

first: Trisha

last: Kers

first: Kate

last: Feller

first: Cecile

last: Beerens

first: Miao-Ping

last: Chien

first: Sieger

last: Leenstra


title: DPPIV+ fibro-adipogenic progenitors form the niche of adult skeletal muscle self-renewing resident macrophages

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

summary: Depending on the tissue, adult tissue-resident macrophages (RMs) are either maintained by blood monocytes or through self-renewal at steady state. While the presence of a nurturing-niche is likely crucial to support the survival and function of self-renewing RMs, evidence regarding its nature is limited. Here, we aimed to characterize the niche for skeletal muscle RMs. We found stromal cells called Fibro-Adipogenic Progenitors (FAPs) to be the main source of colony-stimulating factor 1 (CSF1) in resting skeletal muscle. By utilizing parabiosis in combination with transgenic lines that deplete FAPs (PdgfrαCreERT2 ´ DTA) or conditionally delete FAP-derived CSF1 (PdgfrαCreERT2 ´  Csf1flox/null), we showed that local CSF1 from FAPs is required for the survival of both TIM4- monocyte-derived and TIM4+ self-renewing RMs at steady state in adult skeletal muscle. Following pharmacological depletion of RMs, local CSF1 increases significantly to facilitate their replenishment. Indeed, TIM4- RMs get replaced by blood monocytes following depletion and their numbers increase significantly beyond the normal levels. While a noticeable fraction of TIM4+ RMs also gets replaced by blood monocytes following depletion, their numbers are tightly controlled, which indicates the presence of regulatory mechanisms exclusive to TIM4+ cells. The spatial distribution and number of TIM4+ RMs match with a subpopulation of Dipeptidyl peptidase IV (DPPIV)+ FAPs, suggesting their role as nurturing CSF1-producing niche cells for self-renewing RMs. This finding offers novel opportunities to precisely manipulate the function of self-renewing RMs in situ to further unravel their role in health and disease.

overall_design: Characterization of the niche of muscle self-renewing resident macrophages.

first: Farshad

last: Babaeijandaghi

first: Lin

middle: W

last: Tung

first: Tara

last: Stach


title: Single-cell profiling coupled with lineage analysis reveals vagal and sacral neural crest contributions to the developing enteric nervous system

status: Public on Oct 23 2023

city: Pasadena

first: Jessica

last: Jacobs-Li

state: California

address: 1200 E. California Blvd

department: Biology

institute: California Institute of Technology

summary: During development, much of the enteric nervous system (ENS) arises from the vagal neural crest that emerges from the caudal hindbrain and colonizes the entire gastrointestinal tract. However, a second contribution to the ENS comes from the sacral neural crest that arises in the caudal neural tube and populates the post-umbilical gut. By coupling single cell transcriptomics with axial-level specific lineage tracing in avian embryos, we compared the contributions of embryonic vagal and sacral neural crest cells to the pre-umbilical and post-umbilical chick ENS and the associated peripheral ganglia (the Nerve of Remak and pelvic plexuses) at embryonic day (E) 10.

overall_design: Using replication incompetent avian (RIA) retroviruses, we indelibly labeled the vagal and sacral neural crest and collected their respective lineages in the E10 gut. The ENS of pre-umbilical gut is solely derived from vagal neural crest cells, which we collected for sequencing. The post-umbilical gut receives contributions from both vagal and sacral-derived neural crest cells and we collected both populations separately from this tissue.

first: Weiyi

last: Tang

first: Can

last: Li

first: Marianne

last: Bronner


title: Hypoxia promotes proliferation and inhibits myogenesis in broiler satellite cells

city: Knoxville

first: Brynn

last: Voy

state: Tennessee

address: 2506 River Drive

department: Animal Science

institute: The University of Tennessee

summary: Breast muscle myopathies in broilers compromise meat quality and continue to plague the poultry industry. Broiler breast muscle myopathies are characterized by impaired satellite cells (SC)-mediated repair, and localized tissue hypoxia and dysregulation of oxygen homeostasis have been implicated as contributing factors. The present study was designed to test the hypothesis that hypoxia disrupts the behavior of SC essential for multinucleated myotube formation in vitro, and to determine the extent to which effects are reversed by restoration of oxygen tension. Primary SC was isolated from pectoralis major of young (5 d) Cobb 700 chicks and maintained in growth conditions or induced to differentiate under normoxic (20% O2) or hypoxic (1% O2) conditions for up to 48 h. Hypoxia enhanced SC proliferation while inhibiting myogenic potential, with decreased fusion index and suppressed myotube formation. Reoxygenation after hypoxia partially reversed effects on both proliferation and myogenesis. Western blotting showed that hypoxia diminished myogenin expression, activated AMPK, upregulated proliferation markers, and increased molecular signaling of cellular stress. Hypoxia also promoted accumulation of lipid droplets in myotubes. Targeted RNAseq identified numerous differentially expressed genes across differentiation under hypoxia, including several genes that have been associated with myopathies in vivo. Altogether, these data demonstrate localized hypoxia may influence SC behavior in ways that disrupt muscle repair and promote the formation of myopathies in broilers.

overall_design: To investigate the impacts of cellular hypoxia on broiler satellite cells across 48 h myogenic differentiation, we cultured cells for 48 h under 1% or 20% O2 in a normal CO2 humidified incubator. We collected samples every 12 h.

first: Usuk

last: Jung

first: Kurt

last: Lamour


title: Targeting NHE6 gene expression identifies lysosome and neurodevelopmental mechanisms in Christianson Syndrome cell model

city: Providence

first: Eric

last: Morrow

address: 70 Ship Street

institute: Brown University

summary:
To investigate the function NHE6 protein, we established HAP1 CRISPR-CAS9 SLC9A6 Knockout lines and their paired controls .
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells, each with 6 replicates, at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HAP1 cells and its SLC9A6 CRIPSR/Cas9-mediated genome editing mutant.

first: Qing

last: Wu

first: Li

last: Ma

first: Lena

last: Joesch-Cohen

first: Michael

last: Schmidt

first: Ece

last: Gamsiz Uzun

middle: M


title: ELAVL3 stabilizes MYCN mRNA and provides a therapeutic target in neuroendocrine prostate cancer [LNCaP/AR/shTP53/shRB1]

city: Shanghai

first: Qi

last: Wang

state: Shanghai

address: Shanghai Pu Dong district, Dongfang Rd. No.1630

institute: Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine

summary: Here we demonstrated that the RNA-binding protein ELAVL3 is specifically upregulated in NEPC, and that overexpression of ELAVL3 alone sufficiently induce neuroendocrine phenotype in prostate adenocarcinoma. Pharmacological inhibition of ELAVL3 with pyrvinium pamoate, an FDA-approved drug, effectively suppressed tumor growth, reduced the risk of metastases, and improved the survival of NEPC mice models.

overall_design: mRNA profiles of LNCaP/AR/shTP53/shRB1 cells with shELAVL3 or shCtrl

first: Yiyi

last: Ji

first: Weiwei

last: Zhang

first: Kai

last: Shen

first: Wei

last: Xue


title: Evidence for Widespread Presence of Hidden yet Functional Novel and Non-canonical Human Transcripts

city: Xiamen

first: Dongyang

last: Xu

state: Fujian

address: 668 Jimei Road

institute: Huaqiao University

summary: Fraction of functional sequence in human genome remains a key unresolved question in Biology and the subject of vigorous debate. While a plethora of studies have connected a significant fraction of human DNA to various biochemical processes, like transcription, the classical definition of function requires evidence of effects on cellular or organismal fitness that such studies do not provide. Although multiple high-throughput reverse-genetics screens have been developed to address this issue, they are limited to annotated genomic elements and suffer from non-specific effects, arguing for a strong need to develop additional functional genomics approaches. In this work, we established a high-throughput lentivirus-based insertional mutagenesis strategy as a forward genetics screen tool in aneuploid cells. Application of this approach to human cell lines in multiple phenotypic screens suggested the presence of many uncharacterized functional elements in the human genome, represented at least in part by novel exons of known and novel genes. The novel transcripts containing these exons can be massively, up to thousands-fold, induced by specific stresses, and at least some can represent bi-cistronic protein-coding mRNAs. Altogether, these results argue that many unannotated human transcripts, including those that appear as aberrant splice products, have biological relevance under specific biological conditions.

overall_design: Used a high-throughput lentivirus-based insertional mutagenesis strategy as a forward genetics screen tool for identification of novel functional genomic elements

first: Lu

last: Tang

first: Philipp

last: Kapranov


title: Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex

first: Zili

last: Song

address: Beichen West Road 1

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Production of secondary metabolites is controlled by a complicated regulatory network in eukaryotic cells. Several layers of regulators are involved in this process, ranging from pathway-specific regulation, to epigenetic control, to global regulation. Unprecedentedly, we have discovered that interaction of an RNA-binding protein CsdA with a regulator RsdA coordinates fungal secondary metabolism. Employing a genetic deletion approach and transcriptome analysis as well as metabolomics analysis, we revealed that CsdA and RsdA synergistically regulate fungal secondary metabolism comprehensively. Mechanistically, comprehensive genetic and biochemical studies proved that RsdA and CsdA co-localize in the nucleus and physically interact to achieve their function. In particular, we have demonstrated that CsdA mediates rsdA expression by binding specific motif “GUCGGUAU” of its pre-mRNA at a post-transcriptional level. We thus uncover a general mechanism in which RNA-binding protein physically interacts with, and controls the expression level of, the RsdA to coordinate fungal secondary metabolism.

overall_design: Mycelial RNA from Pestalotiopsis fici wild type and mutants for 5 days.

first: Shuang

last: Zhou

first: Hongjiao

first: Nancy

last: P Keller

first: Berl

last: R Oakley

first: Xiao

last: Liu

first: Wen-Bing

last: Yin


title: ELAVL3 stabilizes MYCN mRNA and provides a therapeutic target in neuroendocrine prostate cancer [RIP-seq]

summary: Here we demonstrated that the RNA-binding protein ELAVL3 is specifically upregulated in NEPC, and that overexpression of ELAVL3 alone sufficiently induce neuroendocrine phenotype in prostate adenocarcinoma. We performed RIP-seq of ELAVL3-V5 from 2 prostate cancer cell lines.

overall_design: RIP-seq of ELAVL3-V5 from PC3/ELAVL3-V5 and DU145/ELAVL3-V5 cells.


title: ELAVL3 stabilizes MYCN mRNA and provides a therapeutic target in neuroendocrine prostate cancer [NCI-H660]

overall_design: mRNA profiles of NCI-H660 cells treated with PBS or PP


title: Milk fat miRNome changes in response to LPS challenge in Holstein cows

city: Saint Genès-Champanelle

first: christine

last: Leroux

address: Route de Theix

institute: INRAE

summary: Cows were fed a lactation diet at ad libitum intake (n = 6). At 27±3 days in milk, cows were injected with 50 µg of LPS E. coli in one healthy rear mammary quarter. Milk samples were collected just before LPS challenge (LPS-) and 6.5 h after LPS challenge (LPS+) from the same cows. Microarray analysis was performed using customized 8x60K ruminant miRNA microarrays to compare LPS- to LPS+ miRNome. MiRNome comparison between LPS- and LPS+ identified 37 differentially abundant miRNAs (q-value ≤ 0.05)

platform_organism:
Bos taurus
Capra hircus
Ovis aries

overall_design: Six miltiparous cows were fed ad libitum intake of a lactation diet. At 27±3 days in milk, one healthy rear mammary quarter of all cows was injected with 50 µg of LPS. Residual milk in mammary gland was collected after AM milking, just before infusion (LPS-) and the end of PM milking, corresponding to 6.5 h after LPS injection (LPS+). One g of MF was mixed with 2.0 mL of TRIzol LS solution, then 600 µL of chloroform were added before centrifugation at 12,000 x g for 20 min at 4°C. The upper aqueous layer was precipitated using 500 µL of isopropanol overnight. The pellet obtained by centrifugation at 12,000 x g for 10 min at 4°C was washed and RNA was dissolved in 50 μL of RNase-free water.

first: Karol

last: Pawlowski

first: Yannick

last: Faulconnier

first: Christine


title: Epigenetic reprogramming through KDM6B drives immunofibroblast early commitment and immune properties [CUT&RUN-seq]

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

institute: INSERM U1236-MOBIDIC

summary: TLS are composed of immune cells, including lymphocytes and myeloid cells, lymphatic and blood endothelial cells, and PDPN+ stromal cells with lymphoid stromal cells (LSC) features called immunofibroblasts. These LSC play a central role in the physiology of secondary lymphoid organs. Recent studies have focused on the heterogeneity of immunofibroblast and their cell of origin, but molecular and epigenetic mechanisms involved in their commitment are still unknown. In this study, we took advantage of the combination of an in vitro model of human ASC commitment to LSC/immunofibroblasts, and an in vivo model of murine TLS induction. We highlighted in both cases an early induction of KDM6B in stromal cells associated with an early epigenetic reprogramming. The KDM6B signature was enriched in sorted pathogenic stroma from patients with autoimmune diseases. Furthermore, using a KDM6 inhibitor, we demonstrated that KDM6B was required for the acquisition of immunofibroblast phenotype and functions, including upregulation of CCL2 production and monocyte recruitment. Overall, our results shed light on epigenetic mechanisms involved in the early commitment, but also immune properties of immunofibroblasts.

overall_design:
CUT&RUN analysis of KDM6B binding was performed on ASC coming from 2 different donors from two independents experiments. ASC were committed or not into LSC-like by TNF/LT treatment.

KDM6B_TNFLT.bw generated from adipose stromal cells, TNFLT-treated - KDM6B, Rep 1+2+3+4
KDM6B_untreated.bw generated from adipose stromal cells, untreated - KDM6B, Rep 1+2+3+4

first: Marvin

last: Sylvestre

first: Julien

last: Saint-Vanne

first: Karin

last: Tarte

first: David

last: Roulois


title: The Myc binding partner Spt5 is essential for brain tumor growth in Drosophila

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

summary: The transcription factor SPT5 physically interacts with MYC oncoproteins and is essential for the full transcriptional activation of MYC targets in cultured cells. Here, we use Drosophila to show that SPT5 is also required for MYC-dependent processes in vivo. Depletion of SPT5 strongly impairs the growth of a model neuronal tumor and substantially extends survival of tumor-bearing animals. This beneficial effect is also observed when SPT5 is knocked down systemically after tumor initiation, highlighting SPT5 is a potential drug target in human oncology.

overall_design: brat and/or Spt5 were knocked down in type II neuroblasts from larval stages on, using the genotypes: wor-GAL4 ase-GAL80 UAS-mCD8::GFP [UAS-brat-IR] [UAS-Spt5-IR]

first: Ayoola

last: Ogunleye

first: Julia

last: Hofstetter-Hadry

first: Elmar

last: Wolf

first: Thomas

last: Raabe

first: Peter

last: Gallant


title: ELAVL3 stabilizes MYCN mRNA and provides a therapeutic target in neuroendocrine prostate cancer [RIPseq-ELAVL3&R1D]

first: Qi

last: Wang

summary: Here we demonstrated that the RNA-binding protein ELAVL3 is specifically upregulated in NEPC, and that overexpression of ELAVL3 alone sufficiently induce neuroendocrine phenotype in prostate adenocarcinoma. We performed RIP-seq of ELAVL3-V5 from PC3 cell lines.

overall_design: RIP-seq of ELAVL3-V5 from PC3/ELAVL3-V5 and PC3/ELAVL3-RRM1-deletion-V5 cells.

first: Yiyi

last: Ji

first: Weiwei

last: Zhang

first: Kai

last: Shen

first: Wei

last: Xue


title: A Rat Liver Cell Atlas Reveals Intrahepatic Myeloid Heterogeneity.

city: Toronto

first: Delaram

last: Pouyabahar

state: ON

address: 160 College St

department: Molecular Genetics

institute: University of Toronto

summary: The large size and vascular accessibility of the laboratory rat (Rattus norvegicus) makes it an ideal hepatic animal model for diseases that require surgical manipulation. Often, the disease susceptibility and outcomes of inflammatory pathologies vary significantly between strains. This study uses single cell transcriptomics to better understand the complex cellular network of the rat liver, as well as to unravel the cellular and molecular sources of inter-strain hepatic variation. We generated single cell and single nucleus transcriptomic maps of the livers of healthy Dark Agouti and Lewis rat strains, and developed a factor analysis-based bioinformatics analysis pipeline to study data covariates, such as strain and batch. Using this approach, we discovered transcriptomic variation within the hepatocyte and myeloid populations that underlie distinct cell states between rat strains. This finding will help provide a reference for future investigations on strain-dependent outcomes of surgical experiment models.

overall_design: Four whole livers were acquired from 8-10 week-old healthy male Dark Agouti and Lewis strains and the resulting total liver homogenates went through 2-step collagenase digestion. To provide a more detailed resource of rat hepatic immune cells, two additional immune-enriched samples were collected.  These samples underwent additional washing steps and red blood cell depletion to reduce the hepatocyte-released ambient RNA. The size samples were analyzed using scRNAseq. Liver tissue from an additional two pairs of Lewis and Dark Agouti rats were taken and processed for 10x Genomics single nuclei RNA sequence (snRNA-seq) to further inform parenchymal cell identities.

first: Sai

last: Chung

first: Olivia

middle: I

last: Pezzutti

first: Catia

last: Perciani

first: Xinle

first: Xue-Zhong

last: Ma

first: Chao

last: Jiang

first: Damra

last: Camat

first: Trevor

first: Manmeet

last: Sekhon

first: Justin

last: Manuel

first: Xu-Chun

last: Chen

first: Ian

last: McGilvray

first: Sonya

last: MacParland

first: Gary

last: Bader


title: Epigenetic reprogramming through KDM6B drives immunofibroblast early commitment and immune properties [Mus_stromal_cells]

first: Delphine

last: Rossille

overall_design: Balb/c mice were bred and maintained under specific pathogen-free conditions in the Biomedical Service Unit at the University of Birmingham according to Home Office and local ethics committee regulations. The submandibular glands of mice (8-12 weeks old) were intraductally cannulated with 10^8 to 10^9 plaque forming units (p.f.u.) of replication-defective adenovirus (Ad5) to induce the formation of ectopic tertiary lymphoid structure (TLS). Salivary glands were harvested (as previously shown: Nayar S, et al.; PMID: 31213547), at various time points after cannulation and gp38+ fibroblasts were sorted and used for quantification of gene expression.

first: Marvin

last: Sylvestre

first: Vonick

last: Sibut

first: David

last: Roulois


title: Epigenetic reprogramming through KDM6B drives immunofibroblast early commitment and immune properties

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

overall_design: Refer to individual Series


title: Epigenetic reprogramming through KDM6B drives immunofibroblast early commitment and immune properties [Hum_ASC_native]

overall_design: Lipoaspiration from 4 healthy donors were collected and enzymatically dissociated. After depletion of hematopoietic cells, stromal cell subsets were sorted by FACS based on the phenotype: CD45[neg] /CD11b[neg] /CD235a[neg] /CD31[neg] /CD34[pos]/CD73[pos]/ /CD146[pos]/ RNA extraction was performed on 10 000 cells.

first: Karin

last: Tarte


title: Epigenetic reprogramming through KDM6B drives immunofibroblast early commitment and immune properties [Hum_ASC_TNFLT]

overall_design: RNA-seq analysis was performed on ASC coming from 3 different donors. ASC were committed or not into immunofibroblasts by TNF/LT treatment.


title: Prenatal Diagnosis and Clinical Analysis of Talipes Equinovarus by Chromosomal Microarray Analysis

status: Public on Oct 22 2023

city: Fuzhou

first: Xiaorui

last: Xie

address: No. 18 Daoshan Road

institute: Fujian Provincial Maternity and Children’s Hospital

summary: With the advancement of molecular technology, fetal talipes equinovarus (TE) is believed to be not only associated with chromosome aneuploidy, but also related to chromosomal microdeletion and microduplication. The study aimed to explore the molecular etiology of fetal TE and provide more information for the clinical screening and genetic counseling of TE by CMA.This retrospectively study included 131 fetuses with TE identified by ultrasonography. Conventional karyotyping and SNP array analysis were performed for all the subjects. They were divided into isolated TE group (n=55) and complex group (n=76) according to structural anomalies.Among the total of 131 fetuses, karyotype analysis found 12(9.2%) abnormal results, while SNP array found 27 (20.6%) cases. Trisomy 18 was detected most frequently among abnormal karyotypes. The detection rate of SNP array was significantly higher than that of traditional chromosome karyotype analysis.SNP array detected 15 (11.5%) cases of submicroscopic abnormalities that karyotype analysis did not find. The most common CNV was the 22q11.2 microdeletion. For both analyses, the overall detection rates were significantly higher in the complex TE group than in the isolated TE group. The incremental yield of chromosomal abnormalities in fetuses with unilateral TE (22.0%) was higher than in fetuses with bilateral TE (19.8%), but this difference was not statistically significant.Abnormal chromosomes were most frequently detected in fetuses with TE plus cardiovascular system abnormalities.Fetal TE is related to chromosomal microdeletion or microduplication. Prenatal diagnosis is recommended for fetuses with TE, and CMA testing is preferred. CMA can improve the detection rate of chromosomal abnormalities associated with fetal TE, especially in pregnancies with complex TE.

overall_design: Traditional karyotyping and SNP array analysis were performed for all the subjects.

first: Baojia

last: Huang

first: Liangpu

last: Xu

first: Xiaoqing

last: Wu


title: Generation of three-dimensional meat-like tissue from stable pig epiblast stem cells

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

institute: China Agricultural University

summary:
We performed RNA-seq using pgEpiSCs at passage 30 (P30) and at P200 to further comprehensively assess the cellular properties.
We subsequently employed the RNA-Seq dataset to focused on the expression level profiles of marker genes known to be involved in critical phases of myogenic lineage differentiation to determine if the differentiation scheme generates cells of the expected lineage at each stage.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pgEpiSCs cells (pgEpiSCs-Low and pgEpiSCs-high), its myogenic lineage differentiation derivatives (pgEpiSCs-MPCs, pgEpiSCs-MCs) and myogenic differentiation of porcine muscle stem cells (MPC-Dif)

first: Gaoxiang

last: Zhu

first: Dengfeng

last: Gao


title: GPR162 is a beta cell CART receptor [INS1_GPR162]

status: Public on Oct 20 2023

city: Malmo

first: Dmytro

last: Kryvokhyzha

address: Jan Waldenströms gata 35

department: Clinical Sciences

country: Sweden

institute: Lund University

summary: Cocaine and amphetamine-regulated transcript (CART) is expressed in pancreatic islet cells and neuronal elements. We have previously established insulinotropic actions of CART in human and rodent islets. The receptor for CART in the pancreatic beta cells is unidentified. We used RNA sequencing of Cartpt knock down (KD) INS-1 832/13 cells and identified GPR162 as the most Cartpt-regulated receptor. We therefore tested if GPR162 mediates the effects of CART in beta cells. Binding of CART to GPR162 was established using proximity ligation assay, radioactive binding and co-immunoprecipitation, and KD of Gpr162 mRNA caused reduced binding. Gpr162 KD cells had blunted CARTp-induced exocytosis, and reduced CARTp-induced insulin secretion. Furthermore, we identified a hitherto undescribed GPR162-dependent role of CART as a regulator of cytoskeletal arrangement. Thus, our findings provide mechanistic insight into the effect of CART on insulin secretion and show that GPR162 is the CART receptor in beta cells.

overall_design: To investigate how GPR162 affects insulin secrition and CART mediated processes in INS-1 cells, INS-1 cells were treated with negative control siRNA and an siRNA for GPR162.


title: Epigenetic reprogramming through KDM6B drives immunofibroblast early commitment and immune properties [Hum_ASC_GSKJ4]

overall_design: RNA-seq analysis was performed on ASC coming from 4 different donors. ASC were committed or not into immunofibroblasts by TNF/LT treatment, with or without KDM6 inhibition.


title: The ELAVL3/MYCN positive feedback loop provides a therapeutic target for neuroendocrine prostate cancer

first: Qi

last: Wang


title: The prenatal frontal and parietal bones are distinct organs.

status: Public on Oct 21 2023

city: Pittsburgh

first: Matthew

middle: Brian

last: Rogera

state: Pennsylvania

address: 325 Sutherland Drive

department: Oral and craniofacial sciences

institute: University of Pittsburgh

summary: The skull vault is composed of frontal and parietal bones that are connected by flexible sutures that protect the growing brain. Intramembranous ossification in the prenatal skull vault starts by mid-gestation in the mouse, and sutures must remain flexible for normal growth and development. Therefore, the balance of bone formation and remodeling needs to be precisely controlled because premature ossification in the sutures causes craniosynostosis (CS) to develop. CS has a variable clinical presentation where two frontal bones may be fused together, or a frontal bone may be fused to a parietal bone. While most studies focus on the premature suture ossification, we hypothesized that the process of intramembranous ossification in the frontal and parietal bones contributes to the etiology of CS. By bulk RNASeq we identified 536 unique transcripts between the frontal and parietal compartments.Taken together, we propose that the frontal bone is more active in bone remodeling than the parietal bone, and this control is important for temporal onset of intramembranous ossification in the skull vault.

overall_design: To determine the transcriptomic differences between the E15.5 frontal and parietal bones

first: H

last: Szabo-Rogers

first: M

middle: B

last: Rogers

first: Y

last: Wan


title: GPR162 is a beta cell CART receptor [CART_KD]

overall_design: To investigate how Cartpt affects insulin secretion in INS-1 cells, INS-1 cells were treated with negative control siRNA and an siRNA for Cartpt.


title: Impact of genetic depletion or pharmacological inhibition of LSD1 on gene expression in ovarian cancer cells [CUT&Tag]

city: Chengdu

first: Lei

last: Tao

address: No.17, Section 3, Renmin Nan Road

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: LSD1 is frequently overexpressed and correlates with poor prognosis in patients with ovarian cancer.  RNA-seq, CUT&Tag-seq and ATAC-seq were performed to determine the impact of genetic depletion or pharmacological inhibition of LSD1 on gene expresion profiles in ovarian cancer cells.

overall_design: LSD1 CUT&Tag-seq was performed in ES2 cells  treated with 1 µM LSD1 inhibitor ZY0511 or DMSO for 24 hours.   H3K9me2 and H3K4me2 CUT&Tag-seq were performed in ES2 cells  treated with non-targeted control (shCtrl) or shRNA targeting LSD1 (shLSD1).

first: L

first: X

last: Pan

last: Cen

last: Zhao


title: Impact of genetic depletion or pharmacological inhibition of LSD1 on gene expression in ovarian cancer cells [RNA-Seq]

overall_design: RNA-seq was performed in A2780 and ES2 cells  treated with 1 µM LSD1 inhibitor ZY0511 or DMSO for 24 hours.


title: Impact of genetic depletion or pharmacological inhibition of LSD1 on gene expression in ovarian cancer cells [ATAC-Seq]

overall_design: ATAC-seq was performed in ES2 cells under baseline conditions, treated with  1µM LSD1 inhibitor ZY0511 for 12 h, or treated with shRNA targeting LSD1 (shLSD1).


title: Effect of deletion of Sisssb and Sisdbp on DNA metabolic pathways of Saccharolobus islandicus REY15A

city: Qingdao

first: Qihong

state: Shandong

address: 72 Binhaidadao, Aoshanwei, Jimo

institute: Shandong University

summary: To investigate the putative functions of the ssDNA binding proteins SisSSB and SisDBP in DNA replication, DNA repair and DNA damage response, we constructed  Sisssb and Sisdbp deletion mutants of S. islandicus.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells, the wild type strain E233S, delta-Sisssb and delta-Sisdbp.

first: Yuanxi

last: Xiao

first: Zhichao

last: Jiang

first: Yulong

last: Shen


title: Impact of genetic depletion or pharmacological inhibition of LSD1 on gene expression in ovarian cancer cells


title: SMARCB1 loss creates patient-specific MYC topologies that drive malignant rhabdoid tumor growth [Hi-C]

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

institute: Erasmus University Medical Center Rotterdam

summary: Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer. Yet, their contribution to tumorigenesis remains in many cases poorly understood. Here, we studied derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids revealed a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently revealed patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 drives patient-specific epigenetic reprogramming underlying MRT tumorigenesis.

overall_design:
The MRT organoids were transduced with either a control or a full-length wildtype SMARCB1 lentiviral plasmid, followed by Hi-C as described (Liu et al., 2021).
*** Submitter declares that raw data will be deposited in EGA due to patient privacy concerns. ***

first: Ning

middle: Q

first: Irene

last: Paassen

first: Lars

last: Custers

first: Elzo

last: de Wit

first: Jarno

last: Drost


title: SMARCB1 loss creates patient-specific MYC topologies that drive malignant rhabdoid tumor growth [ChIP-seq]

overall_design:
The MRT organoids were transduced with either a control or a full-length wildtype SMARCB1 lentiviral plasmid, followed by ChIP-seq as described (Liu et al., 2017).
*** Submitter declares that raw data will be deposited in EGA due to patient privacy concerns. ***


title: SMARCB1 loss creates patient-specific MYC topologies that drive malignant rhabdoid tumor growth [ATAC-seq]

overall_design:
The MRT organoids were transduced with either a control or a full-length wildtype SMARCB1 lentiviral plasmid, followed by ATAC-seq as described (Liu et al., 2017).
*** Submitter declares that raw data will be deposited in EGA due to patient privacy concerns. ***


title: SMARCB1 loss creates patient-specific MYC topologies that drive malignant rhabdoid tumor growth [4C-seq]

overall_design:
The MRT organoids were transduced with either a control or a full-length wildtype SMARCB1 lentiviral plasmid, followed by 4C-seq as described (Liu et al., 2021).
*** Submitter declares that raw data will be deposited in EGA due to patient privacy concerns. ***


title: SMARCB1 loss creates patient-specific MYC topologies that drive malignant rhabdoid tumor growth [RNA-seq]

overall_design:
The MRT organoids were transduced with either a control or a full-length wildtype SMARCB1 lentiviral plasmid, or treated with either DMSO or iBRD9, followed by RNA-seq as described (Liu et al., 2021).
*** Submitter declares that raw data will be deposited in EGA due to patient privacy concerns. ***


title: Tamoxifen Response at Single Cell Resolution in Estrogen Receptor Positive Primary Human Breast Tumors

status: Public on Oct 19 2023

city: Chapel Hill

first: Philip

last: Spanheimer

state: NC

address: 101 Manning Drive (Campus Box 7213)

department: UNC School of Medicine - Surgery

institute: University of North Carolina at Chapel Hill

summary: In ER-positive, HER2-negative breast cancer, multiple measures of intra-tumor heterogeneity are associated with worse response to endocrine therapy. To investigate heterogeneity in response to treatment, we developed an operating room-to-laboratory pipeline for the collection of live human tumors and normal breast specimens immediately after surgical resection for processing into single-cell workflows for experimentation and genomic analyses. We demonstrate differences in tamoxifen response by cell type and identify distinctly responsive and resistant subpopulations within the malignant cell compartment of human tumors. Tamoxifen resistance signatures from 3 distinct resistant subpopulations are prognostic in large cohorts of ER-positive breast cancer patients and enriched in endocrine therapy resistant tumors. This novel ex vivo model system now provides a foundation to define responsive and resistant sub-populations within heterogeneous tumors, to develop precise single cell-based predictors of response to therapy, and to identify genes and pathways driving resistance to therapy.

overall_design: Primary breast tissue and cell lines, normal and cancerous, was collected immediately after resection. The tissue was dissociated and treated with 10uM tamoxifen or control media for 12 hours in suspension. Single cell libraries were then created using 10x Genomics gel bead droplet-based kit and sequenced via Illumina sequencing platforms. Differences in cell response to tamoxifen was observed between cell types and distinct responsive and unresponsive cell populations were determined.

first: P


title: SMARCB1 loss creates patient-specific MYC topologies that drive malignant rhabdoid tumor growth

city: Rotterdam

overall_design: Refer to individual Series


title: Mapping and modeling human colorectal carcinoma interactions with the tumor microenvironment

city: Philadelphia

last: Li

address: 3800 Spruce St.

department: Biomedical Sciences

institute: UPENN

summary: Tumoroid cultures suppress gene expression programs involved in communication with the TME, and introduction of human monocyte-derived macrophages into tumoroid cultures instructs macrophages to acquire pro-tumorigenic gene expression programs similar to those observed in vivo.

overall_design: We collected primary tumors, phenotypically normal adjacent colonic tissue, and liver metastases. Single cell profiling were done using 10x chromium single cell RNA sequencing library kit and Nova-Seq kit. The single cells derived from cultured organoid and organoid/Macrophage co-culture  were profiled same way and compared to its in vivo counterpart.

first: Li

last: Ning

first: Zhu

last: Qin

first: Tan

last: Kai

first: Lengner

last: Chris


title: Netrin-1 directs vascular patterning and maturity in the developing kidney

first: Lori

last: O'Brien

address: 111 Mason Farm Rd

department: Cell Biology and Physiology

summary: The kidneys intricate vascular system supports body fluid and organ homeostasis. However, little is known about how vascular architecture is established during kidney development. More specifically, how signals from the kidney influence vessel maturity and patterning remains poorly understood. Netrin-1 (Ntn1) is a secreted ligand critical for vessel and neuronal guidance. Here, we demonstrate that Ntn1 is expressed by Foxd1+ stromal progenitors in the developing kidney and conditional deletion (Foxd1GC/+;Ntn1fl/fl) results in hypoplastic kidneys with extended nephrogenesis. Wholemount 3D analyses additionally revealed the loss of a predictable vascular pattern in Foxd1GC/+;Ntn1fl/fl kidneys. As vascular patterning has been linked to vessel maturity, we investigated arterialization. Quantification of the CD31+ endothelium at E15.5 revealed no differences in metrics such as the number of branches or branch points, whereas the arterial vascular smooth muscle metrics were significantly reduced at both E15.5 and P0. In support of our observed phenotypes, whole kidney RNA-seq revealed disruptions to genes and programs associated with stromal cells, vasculature, and differentiating nephrons. Together, our findings highlight the significance of netrin-1 to proper vascularization and kidney development.

overall_design: Whole kidneys were collected at E15.5 from 3 separate Ntn1fl/fl x Foxd1GC/+;Ntn1fl/+ crosses. Three kidneys were collected of each genotype: Foxd1GC/+;Ntn1fl/+ (heterozygous), Foxd1GC/+;Ntn1fl/fl (homozygous), and Ntn1fl/fl (wildtype). Kidneys were placed in RNAlater (Thermo Fisher) until all samples were collected. RNA was extracted with TRIzol (Invitrogen). RNA was sent to Cancer Genetics Inc (Morrisville, NC) for sequencing and data processing. RNA samples were converted to sequencing libraries using the TruSeq Stranded mRNA kit (Illumina Cat. #20020595). Resulting libraries were assessed for quality via analysis on a 2100 Bioanalyzer (Agilent Technologies) and quantitated by qPCR (KAPA Library Quantification; Roche: KK4824, Cat# 07960140001). Normalized and pooled libraries were sequenced on the Illumina Nextseq 550 system. Alignment and analysis were performed following a modified Tuxedo workflow. Briefly, alignment was done with STAR aligner followed by cufflinks/cuffmerge for assembled transcripts. FPKM was calculated with CuffDiff and analyzed with the R package

first: Deanna

last: Hardesty

first: Samuel

last: Honeycutt

first: Matthew

last: Stevenson


title: The slan antigen identifies the prototypical non-classical CD16+-monocytes in human blood.

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona


title: The slan antigen identifies the prototypical non-classical CD16+-monocytes in human blood [Bulk RNA-seq]

summary: Peripheral monocytes in humans are conventionally divided into classical (CL, CD14++CD16−), intermediate (INT, CD14++CD16+) and non-classical (NC, CD14dim/−CD16++) cells, based on their expression levels of CD14 and CD16. A major fraction of the NC-monocytes has been shown to express the 6-sulfo LacNAc (slan) antigen, but whether these slan+/NC-monocytes represent the prototypical non-classical monocytes or whether they are simply a sub-fraction with identical features as the remainder of NC monocytes is still unclear. Therefore, we analysed transcriptome, proteome, cell surface markers and production of discrete cytokines by peripheral slan+/NC- and slan−/NC-monocytes, in comparison to total NC-, CL- and INT- monocytes. By bulk RNA-seq and proteomic analysis, we found that slan+/NC-monocytes express higher levels of genes and proteins specific of NC-monocytes than slan−/NC-monocytes do. Unsupervised clustering of scRNA-seq data generated one cluster of NC- and one of INT-monocytes, where all slan+/NC-monocytes were allocated to the NC-monocyte cluster, while slan−/NC-monocytes were found, in part (13.38 %), within the INT-monocyte cluster. In addition, total NC- and slan−/NC-monocytes, but not slan+/NC-monocytes, were found by both bulk RNA-seq and scRNA-seq to contain a small percentage of natural killer cells. Altogether, in addition to comparatively characterize total NC-, slan−/NC- and slan+/NC-monocyte transcriptomes and proteomes, our data prove that slan+/NC-, but not slan−/NC-, monocytes are more representative of prototypical NC-monocytes.

overall_design:
Monocytes subsets were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of CD14, CD16 and slan membrane markers and analyzed using Bulk RNA-seq.

slan−/NC-monocytes were isolated concurrently with other monocyte subsets (including slan+/NC-, total NC-, INT-, and CL-monocytes), which were previously investigated in our previous study by bulk RNA-seqs (GSE136107: GSM4041235, GSM4041236, GSM4041237, GSM4041243, GSM4041244, GSM4041245, GSM4041246, GSM4041247, GSM4041248, GSM4041249, GSM4041250, and GSM4041251), and compared with them.

Re-analysed Samples PRJNA561329/GSE136107:

GEO Sample  SRA Runs  BioSample Title
GSM4041235 SRX6747882 SAMN12614816 CL_mono_1
GSM4041236 SRX6747883 SAMN12614814 CL_mono_2
GSM4041237 SRX6747884 SAMN12614812 CL_mono_3
GSM4041243 SRX6747890 SAMN12614850 INT_mono_1
GSM4041244 SRX6747891 SAMN12614849 INT_mono_2
GSM4041245 SRX6747892 SAMN12614848 INT_mono_3
GSM4041246 SRX6747893 SAMN12614847 NC_mono_1
GSM4041247 SRX6747894 SAMN12614846 NC_mono_2
GSM4041248 SRX6747895 SAMN12614845 NC_mono_3
GSM4041249 SRX6747896 SAMN12614844 slan_plus_mono_1
GSM4041250 SRX6747897 SAMN12614843 slan_plus_mono_2
GSM4041251 SRX6747898 SAMN12614842 slan_plus_mono_3

first: Nicola

last: Tamassia

first: Marco

last: Cassatella


title: Expression of the CIC-DUX4 fusion oncoprotein mirrors human CIC-rearranged sarcoma in a transgenic mouse model

city: Durham

first: Peter

last: Hendrickson

state: North Carolina

address: 308 Research Drive

institute: Duke University


title: Expression of the CIC-DUX4 fusion oncoprotein mirrors human CIC-rearranged sarcoma in a transgenic mouse model (RNA-Seq)

summary: CIC-DUX4 sarcoma (CDS) is a rare but highly aggressive undifferentiated small round cell sarcoma driven by a fusion between the tumor suppressor Capicua (CIC) and DUX4. Currently, there are no effective treatments and efforts to identify and translate better therapies is limited by the scarcity of tissues and patients. To minimize, we made three genetically engineered mouse models of CDS (Ch7CDS, Ai9CDS, and TOPCDS). Remarkably, chimeric mice from all three models developed spontaneous tumors and widespread metastasis in the absence of Cre-recombinase. The penetrance of spontaneous (Cre-independent) tumor formation was complete irrespective of bi-allelic CIC function and loxP site proximity. Characterization of primary and metastatic mouse tumors showed that they consistently expressed the CIC-DUX4 fusion protein as well as other downstream markers of the disease authenticating them as CDS. Lastly, tumor-derived cell lines were generated and ChIP-seq was preformed to map fusion-gene specific binding using an N-terminal HA epitope tag. These datasets, along with paired H3K27ac ChIP-seq maps, validate CIC-DUX4 as a neomorphic transcriptional activator and point to ETS family transcription factors as cooperative and redundant drivers of the core regulatory circuitry.

overall_design: To authenticate the tumors and tumor-derived cell lines obtained from our genetically-engineered mouse models (Ch7CDS, Ai9CDS, TOPCDS), RNA-sequencing and ChIP-sequencing was performed. Comparative gene expression profiling analysis was carried out using KP (KrasG12D, p53fl/fl) tumors/cells and normal hindlimb skeletal muscle as controls.

middle: G

first: Kristianne

last: Oristian

first: MaKenna

middle: R

last: Browne

first: Lixia

last: Lou

first: Yan

last: Ma

first: Dianna

last: Cardona

first: Corinne

last: Linardic

first: David

last: Kirsch


title: The slan antigen identifies the prototypical non-classical CD16+-monocytes in human blood [scRNA-seq]

summary: Peripheral monocytes in humans are conventionally divided into classical (CL, CD14++CD16−), intermediate (INT, CD14++CD16+) and non-classical (NC, CD14dim/−CD16++) cells, based on their expression levels of CD14 and CD16. A major fraction of the NC-monocytes has been shown to express the 6-sulfo LacNAc (slan) antigen, but whether these slan+/NC-monocytes represent the prototypic non-classical monocytes or whether they are simply a sub-fraction with identical features as the remainder of NC monocytes is still unclear. Unsupervised clustering of scRNAseq data generated one cluster of NC- and one of INT-monocytes, where all slan+/NC-monocytes were allocated to the NC-monocyte cluster, while slan−/NC-monocytes were found, in part (13.38 %), within the INT-monocyte cluster. In addition, total NC- and slan−/NC-monocytes, but not slan+/NC-monocytes, were found to contain a small percentage of natural killer cells. Altogether, this data prove that slan+/NC-, but not slan−/NC-, monocytes are more representative of prototypical NC-monocytes.

overall_design: Monocytes subsets were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of CD14, CD16 and slan membrane markers and analyzed using scRNA-seq

last: Bianchetto


title: Transcriptome analysis of human iPSC-neurons treated with cardiac glycosides

city: Boston

first: Zhiyun

last: Wei

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: To investigate the molecular mechanisms of cardiac glycosides’ neuroprotection, we profiled transcriptomes of human iPSC-neurons after 72h of treatment with increasing doses of digoxin, oleandrin, proscillaridin A or vehicle alone (0.1% DMSO) using RNA sequencing.

overall_design: The NPC line MGH-2046-RC1 (P301L) was derived from a female individual in her 50s with FTD carrying the autosomal dominant mutation P301L (c.C1907T NCBI NM_001123066, rs63751273), and differentiated into neuronal cells over 6-8 weeks by growth factor withdrawal. The iPSC-neurons were treated with increasing doses of digoxin, oleandrin, proscillaridin A or vehicle alone (0.1% DMSO) for 72h, followed by RNA-seq.

first: Lien

middle: D

last: Nguyen

first: M

middle: C

last: Silva

first: Anna

last: Krichevsky