title: Cynomolgus macaques as a translational model of human immune responses to yellow fever 17D vaccination

city: Marcy L'Etoile

first: Emilie

last: Chautard

address: 1541 Avenue Marcel Mérieux

country: France

institute: Sanofi

summary: The non-human primate (NHP) model (specifically rhesus and cynomolgus macaques) has facilitated our understanding of the pathogenic mechanisms of yellow fever (YF) disease and allowed evaluation of safety and efficacy of YF-17D vaccines. However, the accuracy of this model in mimicking vaccine-induced immunity in humans remains to be fully determined. We used a system biology approach to compare hematological, biochemical, transcriptomic, innate and antibody-mediated immune responses in cynomolgus macaques and human participants following YF-17D vaccination. Immune response progression in cynomolgus macaques followed a similar course as in adult humans, but with slightly earlier onset. Yellow fever virus neutralizing antibody responses occurred earlier in cynomolgus macaques (by Day 7 [D7]), but titers >10 were reached in both species by D14 post-vaccination and were not significantly different by D28 (PRNT50 titers 3.6 Log vs 3.5 Log in cynomolgus macaques and human participants, respectively; p = 0.821). Changes in neutrophils, NK cells, monocytes, T and B cell frequency were higher in cynomolgus macaques and persisted for four weeks versus less than two weeks in humans. Low levels of systemic inflammatory cytokines (IL-1Ra, IL-8, MIP-1α, IP-10, MCP-1 or VEGF) were detected in either or both species, but with no or only slight changes versus baseline. Similar changes in gene expression profiles were elicited in both species. These included enriched and up-regulated type I IFN-associated viral sensing, antiviral innate response, and dendritic cell activation pathways D3–D7 post-vaccination in both species. Hematological and blood biochemical parameters remained relatively unchanged versus baseline in both species. Low level YF-17D viremia (RNAemia) was transiently detected in some cynomolgus macaques (28% [5/18]) but generally absent in humans (except one participant [5%; 1/20]). Importance: Cynomolgus macaques were confirmed as a valid surrogate model for replicating YF-17D vaccine-induced responses in humans, and suggest a key role for type I IFN.

overall_design: Whole blood from 12 male cynomolgus macaques (Macaca fascicularis; Noveprim, Mauritius) aged 2.7 to 5.4 years was collected before vaccination at D –21, and after vaccination at D1, D3, D7, D14 and D28.

first: Nathalie

last: Mantel

first: Fabienne

last: Piras

first: Virgine

last: Courtois

first: Franck

last: Raynal


title: m1A inhibition fuels oncolytic virus-elicited antitumor immunity via downregulating PD-L1 expression

status: Public on Mar 31 2024

city: Wuhan

first: Shu-Jin

last: Li

state: Hubei

address: 237 Luoyu Road

country: China

institute: School & Hospital of Stomatology, Wuhan University

type: Expression profiling by high throughput sequencing

summary: RNA N1-methyladenosine methylation (m1A) modification is critical in regulating mRNA translation and thus protein synthesis, but the role of m1A modification in the occurrence, progression, and immunotherapy of head and neck squamous cell cancer (HNSCC) remains largely unknown. In Tgfbr1/Pten 2cKO mice, we found that the spontaneous neoplastic transformation of oral mucosa is accompanied by elevated levels of m1A modification. Analysis of m1A-associated genes identified TRMT61A as the key m1A writer associated with cancer progression, and poor prognosis. Mechanically, TRMT61A-induced tRNA-m1A modification promotes MYC protein synthesis and subsequent programmed death-ligand 1 (PD-L1) expression. In Tgfbr1/Pten 2cKO mice, RNA-m1A modification levels are also elevated in tumors that developed resistance to oncolytic herpes simplex virus (oHSV) treatment. Therapeutic inhibition of m1A modification sustains oncolytic virus-induced antitumor immunity and reduces tumor growth, providing a promising strategy for alleviating resistance to oHSV therapy. These findings indicate that m1A inhibition can prevent immune escape after oHSV therapy by reducing the expression of PD-L1. Our results provide a mutually reinforcing strategy for clinical combination immunotherapy.

overall_design: To explore whether TRMT61A plays a critical role in tumorigenesis, we screened and employed  lentivirus-mediated short hairpins RNAs (shRNAs) through their depletion efficiencies to silence TRMT61A expression in CAL-27/WSU-HN6 cell lines and treat shCtrl/shTRMT61A CAL-27 cells with either PBS or IFNγ.


title: Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3’ UTR of FAIM2 (snRNA-Seq)

status: Public on Mar 29 2024

city: Philadelphia

first: Sheridan

middle: Hope

last: Littleton

state: PA

address: 3615 Civic Center Blvd

department: Genetics

country: USA

institute: University of Pennsylvania

summary: The ch12q13 obesity locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via an influence on cis-regulation within the genomic region. We implicated rs7132908 as a putative causal variant at this locus leveraging a combination of our inhouse 3D genomic data, public domain datasets, and several computational approaches. Using a luciferase reporter assay in human primary astrocytes, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. Motivated by this finding, we went on to generate isogenic human embryonic stem cell lines homozygous for either rs7132908 allele with CRISPR-Cas9 homology-directed repair to assess changes in gene expression due to genotype and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. We observed that the rs7132908 obesity risk allele influenced the expression of FAIM2 along with other genes, decreased the proportion of neurons produced during differentiation, up-regulated cell death gene sets, and conversely down-regulated neuron differentiation gene sets. We have therefore functionally validated rs7132908 as a causal obesity variant which temporally regulates nearby effector genes at the ch12q13 locus and influences neurodevelopment and survival.

overall_design: To investigate the cis-regulatory and cellular effects of rs7132908 genotype on hypothalamic neuron differentiation and gene expression, we established H9 ESC lines homozygous for the rs7132908 obesity risk A allele with CRISPR-Cas9 homology-directed repair while the parent line is homozygous for the non-risk G allele. We performed single-nucleus RNA-seq on hypothalamic cells derived from these ESCs after 40 days of differentiation. We identified cell types found in our data and genes significantly differentially expressed due to rs7132908 genotype in each cell type. We also compared average TPMs from each homozygous rs7132908 non-risk G allele hypothalamic cell sample to average TPMs from primary human pediatric hypothalamus tissue and GTEx primary tissue expression profiles.

middle: H

first: Khanh

middle: B

last: Trang

first: Struan

middle: F

last: Grant


title: Nr2f6 electroporation in tibialis anterior promotes muscle weakness

city: Campinas

first: Dimitrius Santiago

middle: Passos Simoes Froes

last: Guimaraes

state: Sao Paulo

address: Carl von Linneaus

department: BFM

country: Brazil

institute: Unicamp

summary: Mouse tibialis anterior muscles were electroporated with Nr2f6-myc plasmid or pCMV6 empty vector in the contralateral leg. After 9 days, muscles were collected, and the RNA extracted and processed for microarray analysis.

overall_design: Tibialis anterior muscle (TA) of male adult C57Bl6/J mice were electroporated with 40 ug of pCMV6-Entry empty vector as control in the left limb (L samples) and pCVM6-Nr2f2-myc-flag plasmid in the contralateral limb (R samples. After 10 days, the animals were euthanized and total RNA extracted in TRIzol and collumn purified (RNeasy Mini Kit, Qiagen).

first: Dimitrius

middle: S

first: Leonardo

middle: R

last: Silveira

first: Juleen

last: Zierath

first: Anna

last: Krook


title: Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3’ UTR of FAIM2 (HiC)

overall_design: To identify putative cis-regulatory elements harboring childhood obesity GWAS variants and implicate their effector genes, we performed Hi-C using a human primary astrocyte cell line. During downstream analyses, this data was used in combination with ATAC-seq and RNA-seq in the same cell type, following our established 'variant-to-gene' mapping approach.


title: Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3’ UTR of FAIM2

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of the in vivo effects of CDK8/19 inactivation in 22Rv1 xenografts growing in intact and castrated NSG mice

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: RNA-Seq analysis was carried out to investigate the effects of CDK8/19 inactivation in the tumors formed in intact and castrated NSG mice by different 22Rv1 derivatives, with or without SNX631 treatment. The 22Rv1 derivatives were generated as following: Parental 22Rv1 (Rv1-WT) were transduced with a lentivirus expressing luciferase, yielding the derivative Rv1-Luc. 22Rv1 cells with a double knockout of CDK8 and CDK19 (Rv1-dKO) were made via CRISPR/Cas9.  Rv1-dKO cells were further transduced with lentiviruses to generate Rv1-dKO re-expression derivatives that express wild-type CDK19 (Rv1-dKO-CDK19) and the kinase-inactive D173A mutant (Rv1-dKO-CDK19M).  SNX631 is a selective and orally bioavalable CDK8/19 inhibtor.

overall_design: Rv1-WT, Rv1-Luc, Rv1-dKO-19 and Rv1-dKO-19M cells were inoculated s.c. (2x10^6 cells in 0.1 mL 50% Matrigel per animal) in the right flank of intact or castrated male NSG mice (8-10 weeks old). Castration was performed by either surgical orchiectomy (for Rv1-WT study) or Degarelix treatment (administered s.c. at 10 mg/kg monthly, for Rv1-Luc, Rv1-dKO-19, Rv1-dKO-19M studies), and tumor inoculation was done 10-14 days post castration. For SNX631 treatment studies, animals were randomly allocated to two study groups when the mean tumor size reached 100-200 mm^3. For Rv1-WT study, the treatment group received SNX631-medicated diet (500 ppm, producing 30-60 mg/kg/day dosage on average) and the control group received the control diet.  For Rv1-Luc study, the animals in the control group were dosed with vehicle (70% PEG-400/30% Propylene Glycol, 5 mL/kg, p.o., b.i.d.) and the treatment group was dosed with SNX631 (6 mg/mL solution in the vehicle, 5 mL/kg, p.o., b.i.d.) at 60 mg/kg/day.  At the end of studies, tumor xenografts were dissected from euthanized animals using sterilized surgical tools. Pieces of non-necrotic tumor tissues 50~100mm^3 were excised at the margin near midline section for RNA extraction.  At least four biological replicates (xenograft tumors from different animals) per study group were analyzed.

first: Jing

first: Hao

last: Ji

first: Igor

last: Roninson

first: Mengqian

last: Chen


title: Single cell RNA-seq analysis revealed molecular regulation of hematopoietic stem cell fate decisions in response to hypoxia

city: Xining

first: Haijing

last: Wang

address: 23 Xinning Road

institute: Northwest Institute of Plateau Biology, Chinese Academy of Sciences

summary: Here, we conducted single-cell RNA Seq to establish the atlas of hematopoietic stem progenitor cells (HSPC) and acquire the difference between the choice of cell fate.This study reports how the hypoxic condition influences the HSPCs, revealing the fate of erythroid and monocyte lineage. The immunomodulatory of MSCs was also affected, enhancing the development of monocytes. In addition, stem cells maintain quiescence in hypoxia. This would contribute to understanding regulatory mechanisms for hematopoiesis under a hypoxic state, favouring our comprehension of perturbation, facilitating the manipulation of cell-based therapies.

overall_design: single-cell RNA seq of bone marrow HSPCs from 7~8 week old mice with hypoxic treatment for 13 days and control


title: Effect of MetAP2 the inhibitor SDX-7320 on gene expression in BT-474 xenografts

city: Cambridge

first: Peter

last: Cornelius

state: MA

address: One Broadway, 14th Floor

department: Translational Research

institute: SynDevRx, Inc.

summary:
Analysis of gene expression using bulk RNASeq was performed on tumors dissected from vehicle-treated and SDX-7320-treated mice (12 mg/kg).
The analysis of RNASeq data showed that a several pathways were modulated in tumors from mice treated with SDX-7320.

overall_design: Comparative gene expression profiling of RNA-seq data for BT-474 tumors treated with the MetAP2 inhibitor SDX-7320.

first: Pierre

last: Dufour


title: Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue

status: Public on Mar 28 2024

city: London

first: Jo

last: Spencer

state: Kent

address: Guy’s Hospital Campus

country: United Kingdom

institute: King's College London

summary: Intestinal homeostasis is maintained by the response of gut-associated lymphoid tissue to bacteria transported across the follicle associated epithelium into the subepithelial dome. The initial response to antigens and how bacteria are handled is incompletely understood. By iterative application of spatial transcriptomics and multiplexed single-cell technologies, we identify that the double negative 2 subset of B cells, previously associated with autoimmune diseases, is present in the subepithelial dome in health. We show that in this location double negative 2 B cells interact with dendritic cells co-expressing the lupus autoantigens DNASE1L3 and C1q and microbicides.  We observe that in humans, but not in mice, dendritic cells expressing DNASE1L3 are associated with sampled bacteria but not DNA derived from apoptotic cells. We propose that fundamental features of autoimmune diseases are microbiota-associated, interacting components of normal intestinal immunity.

overall_design: Two FFPE blocks (STA and STB) containing normal colon were used to perform Visium spatial transcriptomics according manufacturer’s instructions as per demonstrated protocol CG000408 Revision A and CG000409 Revision A.

first: Lucia

last: Montorsi

first: Michael

middle: J

last: Pitcher


title: Transfer learning enables identification of multiple types of RNA modification using nanopore direct RNA sequencing

city: Shanghai

first: Xiang

last: Yu

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: RNA internal modifications play critical role in development of multicellular organisms and their response to environmental cues. Using nanopore direct RNA sequencing (DRS), we constructed a large in vitro epitranscriptome (IVET) resource from plant cDNA library labeled with m6A, m1A and m5C respectively. Furthermore, after transfer learning, the pre-trained model was used to detect additional RNA internal modification such as m1A, hm5C, m7G and Ψ modification. Finally, we illustrated a global view of epitranscriptome with m6A, m1A, m5C, m7G and Ψ modification in rice seedlings under normal and high salinity environment. In summary, we provided a strategy for creating IVET resource from cDNA library and developed a computational method that use IVET-based transfer learning termed TandemMod for profiling epitranscriptome landscape with co-occupancy of multiple types of RNA modification in plants responsive to environmental signal.

sample_organism:
Oryza sativa
synthetic construct

platform_organism:
Oryza sativa
synthetic construct

overall_design: Comparative epitranscriptome profiling analysis of DRS data for rice seedings under normal and high salinity environment.

first: You

last: Wu

first: Wenna

last: Shao

first: Mengxiao

last: Yan

first: Hongxia


title: Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function [RNA-Seq]

first: Matthew

middle: C

last: Pahl

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia

summary: We investigated the role of Ikaros in regulatory Tcell identity and function during stimulation using RNA-seq, ATAC-seq, and H3K27ac/Foxp3/Ikzf1 ChIP-seq

overall_design: We performed ATAC-seq, RNA-seq, and ChIPseq against H3K27ac, Foxp3, and Ikzf1 on mouse Tregs

first: Rajan

last: Thomas

first: Andrew

middle: D

last: Wells


title: Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function [ATAC-Seq]

middle: M


title: Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function


title: TFE3-SLC36A1 axis promotes resistance to glucose starvation in kidney cancer cells

first: suli

last: LV

address: Wuhan, Hubei, China

institute: Huazhong University of Science and Technology


title: Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells

status: Public on Mar 27 2024

city: Pittsburgh

first: Jian

last: Ma

address: 5000 Forbes Ave

institute: Carnegie Mellon University

summary: The organization of mammalian genomes within the nucleus features a complex, multiscale three-dimensional (3D) architecture. The functional significance of these 3D genome features, however, remains largely elusive due to limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we report GAGE-seq, a highly scalable, robust single-cell co-assay that simultaneously measures 3D genome structure and transcriptome within the same cell. Employing GAGE-seq on mouse brain cortex and human bone marrow CD34+ cells, we comprehensively characterized the intricate relationships between 3D genome and gene expression. We found that these multiscale 3D genome features collectively inform cell type-specific gene expressions, hence contributing to defining cell identity at the single-cell level. Integration of GAGE-seq data with spatial transcriptomic data revealed in situ variations of the 3D genome in mouse cortex. Moreover, our observations of lineage commitment in normal human hematopoiesis unveiled notable discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level that is more nuanced than previously appreciated. Together, GAGE-seq provides a powerful, cost-effective approach for interrogating genome structure and gene expression relationships at the single-cell level across diverse biological contexts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: GAGE-seq of cell lines (K562, GM12878, NIH3T3 and MDS-L) and  primary tissues (mouse brain cortex and human bone marrow CD34+ cells)

first: Zhijun

last: Duan

first: Tianming

last: Zhou


title: Peripheral T-cell lymphomas expressing CD30 and CD15 expand the spectrum of anaplastic large cell lymphoma, ALK-negative

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: RNAseq of 14 samples of human primary T cell lymphoma

overall_design: Genome-wide profiling of total RNA transcript levels in human T cell lymphoma

first: Karthik

last: Ganapathi


title: iPSC-based modeling of preeclampsia identifies defects in extravillous trophoblast differentiation

city: La Jolla

first: Robert

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: Preeclampsia (PE) is a hypertensive pregnancy disorder with increased risk of maternal and fetal morbidity and mortality. Abnormal extravillous trophoblast (EVT) development and function is considered to be the underlying cause of PE, but has not previously been modeled in vitro. We previously derived induced pluripotent stem cells (iPSC) from placentas of PE patients and characterized abnormalities in formation of syncytiotrophoblast and responses to changes in oxygen tension. In this study, we converted these primed iPSC to naïve iPSC, then derived trophoblast stem cells (TSC) and EVT to evaluate molecular mechanisms underlying PE. We found that primed (but not naïve) iPSC-derived PE-EVT have reduced surface HLA-G, blunted invasive capacity, and altered EVT-specific gene expression. These abnormalities correlated with promotor hypermethylation of genes associated with the epithelial-mesenchymal transition pathway, specifically in primed-iPSC derived PE-EVT. Our findings indicate that abnormal epigenetic regulation might play a role in the PE pathogenesis.

overall_design: To investigate the mechanisms underlying preeclampsia (PE) we used iPSC derived from the placentas of three PE patients (1932, 1933, 1981) and three control patients (1754, 1938, 1947), converted these primed iPSC to naive iPSC and then differentiated the primed and naive iPSC lines to  trophoblast stem cells (TSC) and extravillous trophoblast (EVT).  We then performed gene expression profiling on all of  these samples using RNA-seq. For each timepoint and patient, we sequenced 3 replicates.

first: Mariko

last: Horii


title: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions [Hi-C]

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

summary: Estrogen Receptor 1 (ESR1; also known as ERα, encoded by ESR1 gene) is the main driver and prime drug target in luminal breast cancer. ESR1 chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ESR1 chromatin action, along with its biological implications. Here, we use a large set of ESR1 ChIP-seq data from 70 ESR1+ breast cancers to explore inter-patient heterogeneity in ESR1 DNA binding to reveal a striking inter-tumor heterogeneity of ESR1 action. Of note, commonly shared ESR1 sites show the highest estrogen-driven enhancer activity and are most engaged in long-range chromatin interactions. In addition, the most commonly shared ESR1-occupied enhancers are enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ESR1 and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we can confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ESR1–chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ESR1 landscape, with the most common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.

overall_design: Hi-C was performed on MCF7 breast cancer cell lines in full-media condition. 4 biological replicates have been used.

first: Stacey

last: Joosten

first: Sebastian

last: Gregoricchio

first: Suzan

last: Stelloo

first: Elif

last: Yapıcı

first: Chia-Chi

last: Huang

first: Maria

last: Donaldson Collier

first: Tunc

last: Morova

first: Umut Berkay

last: Altintas

first: Yongsoo

last: Kim

first: Sander

last: Canisius

first: Gozde

last: Korkmaz

first: Nathan

middle: A

last: Lack

first: Michiel

last: Vermeulen

first: Sabine

last: Linn


title: Targeting of REST with rationally-designed small-molecule compounds exhibits synergetic therapeutic potential in human glioblastoma cells

city: Austin

first: Svetlana

last: Panina

state: TX

address: 101 East 21st St.

department: Molecular Biosciences

institute: The University of Texas at Austin

summary:
To validate role of REST (RE-1 silencing transcription factor) in glioblastoma (GBM) growth, we used CRISPR/Cas9 gene editing to generate REST-null single-cell clonal lines from GBM cell line (T98G) and non-neural HEK293 cells.
We then performed gene expression profiling using data obtained from Tag-Seq of 8 cell lines: T98G CRISRP Control and 4 T98G REST-KO clones (C10, F7, G2, D4); HEK293 CRISPR Control and 2 HEK293 REST-KO clones (D10, E6).

overall_design: Comparative gene expression analysis of Tag-Seq data for T98G and HEK293 cells and their REST-KO clones, two biological replicates per cell line.

first: Joshua

middle: V

last: Schweer

first: Qian

last: Zhang

first: Gaurav

last: Raina

first: Haley

last: Hardtke

first: Seungjin

first: Wanjie

last: Yang

first: Dionicio

last: Siegel

first: Jessie

middle: Y


title: Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3’ UTR of FAIM2 (snATAC-Seq)

first: Sheridan

last: Littleton

overall_design: To investigate the cis-regulatory effects of rs7132908 genotype on chromatin accessibility, we established H9 ESC lines homozygous for the rs7132908 obesity risk A allele with CRISPR-Cas9 homology-directed repair while the parent line is homozygous for the non-risk G allele. We performed single-nucleus ATAC-seq on hypothalamic cells derived from these ESCs after 40 days of differentiation. We identified cell types found in our data using paired single-nucleus RNA-seq profiles and then detected significantly differentially accessible peaks due to rs7132908 genotype in each cell type. We also identified transcription factor motifs significantly enriched in each differentially accessible peak.

first: Khanh

last: Trang

first: Struan

last: Grant


title: Cell-mediated cytotoxicity surrounding the brain in spinal muscular atrophy

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

summary: We here longitudinally investigated how SMA and nusinersen shaped local immune responses in the cerebrospinal fluid (CSF) using single cell RNA-sequencing and single cell TCR-sequencing.

overall_design: Single-cell RNA and TCR sequencing data of 23 individual CSF cell samples from 7 individual SMA patients that were longitudinally (baseline: n = 7; 2 months: n = 2; 6 months: n = 6; 10 months: n = 6)  and 2 additional SMA patients at 10 months post_treatment.

first: Michael

last: Heming

first: Gerd

last: Meyer zu Hörste


title: Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3’ UTR of FAIM2 (ATAC-Seq)

overall_design: First, to identify putative cis-regulatory elements harboring childhood obesity GWAS variants and implicate their effector genes, we performed ATAC-seq using a human primary astrocyte cell line. During downstream analyses, this data was used in combination with RNA-seq and Hi-C in the same cell type, following our established 'variant-to-gene' mapping approach. Then, to investigate the cis-regulatory effect of rs7132908 genotype on chromatin accessibility, we established H9 ESC lines homozygous for the rs7132908 obesity risk A allele with CRISPR-Cas9 homology-directed repair while the parent line is homozygous for the non-risk G allele. Next, we performed ATAC-seq on these ESCs. We identified peaks that had significantly differentially accessibility due to rs7132908.

first: Matthew

last: Pahl


title: scRNAseq of adult iECs

status: Public on Mar 26 2024

city: Chapel Hill

first: Li

last: Qian

state: North Carolina

address: 111 Mason Farm Road, MBRB

department: Department of Pathology

institute: UNC

summary: Evaluation of Sox17-Erg adult cardiac fibroblast reprogramming at Day 3, Day 7, 2 weeks, and 4 weeks

overall_design: Isolated adult murine cardiac fibroblasts were infected with GFP or Sox17-Erg-GFP retroviruses at Day 0 of reprogramming.  Two replicates were pooled at each specified timepoint to evaluate iEC reprogramming. Each timepoint contained multiplexed samples of GFP (control) and Sox17-Erg-GFP infected cells.

first: Gregory

last: Farber


title: ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions [RNA-seq]

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

institute: Cancer Research Center of Lyon

summary: Cell plasticity sustains intra-tumor heterogeneity and treatment resistance in melanoma. Deciphering the transcriptional mechanisms governing reversible phenotypic transitions between proliferative/differentiated and invasive/stem-like states is required. Expression of the ZEB1 transcription factor is frequently activated in melanoma, where it fosters adaptive resistance to targeted therapies. Here, we performed a genome-wide characterization of ZEB1 transcriptional targets, by combining ChIP-sequencing and RNA-sequencing, upon phenotype switching in melanoma models. We identified and validated ZEB1 binding peaks in the promoter of key lineage-specific genes crucial for melanoma cell identity. Mechanistically, ZEB1 negatively regulates SOX10-MITF dependent proliferative/melanocytic programs and positively regulates AP-1 driven invasive and stem-like programs. Comparative analyses with breast carcinoma cells revealed lineage-specific ZEB1 binding, leading to the design of a more reliable melanoma-specific ZEB1 regulon. We then developed single-cell spatial multiplexed analyses to characterize melanoma cell states intra-tumoral heterogeneity in human melanoma samples. Combined with scRNA-Seq analyses, our findings confirmed increased ZEB1 expression in Neural-Crest-like cells and mesenchymal cells, underscoring its significance in vivo in both populations. Overall, our results define ZEB1 as a major transcriptional regulator of cell states transitions and provide a better understanding of lineage-specific transcriptional programs sustaining intra-tumor heterogeneity in melanoma.

overall_design: ZEB1 expression was enhanced using TNF-α treatment alone or in combination with TGF-β for 14 days in the melanoma cell line GLO.

first: Simon

last: Durand

first: Yaqi

last: Tang

first: Roxane

last: Pommier

first: Valentin

last: Benboubker

first: Maxime

last: Grimont

first: Felix

last: Boivin

first: Laetitia

last: Barbollat

first: Eric

last: Cumunel

first: Florian

last: Dupeuble

first: Anaïs

last: Eberhardt

first: Maud

last: Plaschka

first: Stéphane

last: Dalle

last: Caramel


title: Predictive biomarkers and maternal immune alterations in postpartum preeclampsia reveal an immune-driven pathology

city: Rochester

first: Sylvie

last: Girard

state: Minnesota

address: 200 First Street

institute: Mayo Clinic

summary: Postpartum preeclampsia (PPPE) is an under-diagnosed condition, developing within 48 hours to 6 weeks following an uncomplicated pregnancy. The etiology of PPPE is still unknown, leaving patients vulnerable and making the identification and treatment of patients requiring postpartum care an unmet need. We aimed to understand the immune contribution to PPPE at the time of diagnosis, as well as uncover the predictive potential of perinatal biomarkers for the early postnatal identification of high-risk patients. Placentas were collected at delivery from uncomplicated pregnancies (CTL) and PPPE patients for immunohistochemistry analysis. In this initial study, blood samples in PPPE patients were collected at the time of PPPE diagnosis (48h-25 days postpartum; mean 7.4 days) and compared to CTL blood samples taken 24h after delivery. Single-cell transcriptomics, flow cytometry, intracellular cytokine staining, and the circulating levels of inflammatory mediators were evaluated in the blood. Placental CD163+ cells and 1st trimester blood pressures can be valuable non-invasive and predictive biomarkers of PPPE with strong clinical application prospects. Furthermore, changes in immune cell populations, as well as cytokine production by CD14+, CD4+, and CD8+ cells, suggested a dampened response with an exhausted phenotype including decreased IL1b, IL12, and IFNg as well as elevated IL10. Understanding maternal immune changes at the time of diagnosis and prenatally within the placenta in our sizable cohort will serve as groundwork for pre-clinical and clinical research, as well as guiding clinical practice for example in the development of immune-targeted therapies, and early postnatal identification of patients who would benefit from more thorough follow-ups and risk education in the weeks following an uncomplicated pregnancy.

overall_design: Peripheral blood mononuclear cells (PBMC) were isolated from patients blood and analyzed using scRNAseq

first: Camille

last: Couture

first: Marie-Eve

last: Brien

first: Jade

last: Rechtzigel

first: SuYun

last: Ling

first: Cecilia

last: Ledezma-Soto

first: Gilberto

last: Bishop

first: Ines

last: Boufaied

first: Dorothée

last: Dal Soglio

first: Evelyne

last: Rey

first: Serge

last: McGraw

first: Charles

last: Graham


title: Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3’ UTR of FAIM2 (RNA-Seq)

first: Sheridan

last: Littleton

address: 3615 Civic Center Blvd

institute: University of Pennsylvania

summary: The ch12q13 obesity locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via an influence on cis-regulation within the genomic region. We implicated rs7132908 as a putative causal variant at this locus leveraging a combination of our inhouse 3D genomic data, public domain datasets, and several computational approaches. Using a luciferase reporter assay in human primary astrocytes, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. Motivated by this finding, we went on to generate isogenic human embryonic stem cell lines homozygous for either rs7132908 allele with CRISPR-Cas9 homology-directed repair to assess changes in gene expression due to genotype and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. We observed that the rs7132908 obesity risk allele influenced the expression of FAIM2 along with other genes, decreased the proportion of neurons produced during differentiation, up-regulated cell death gene sets, and conversely down-regulated neuron differentiation gene sets. We have therefore functionally validated rs7132908 as a causal obesity variant which temporally regulates nearby effector genes at the ch12q13 locus and influences neurodevelopment and survival.

overall_design: First, to identify putative cis-regulatory elements harboring childhood obesity GWAS variants and implicate their effector genes, we performed RNA-seq using a human primary astrocyte cell line. During downstream analyses, this data was used in combination with ATAC-seq and Hi-C in the same cell type, following our established 'variant-to-gene' mapping approach. Then, to investigate the cis-regulatory effect of rs7132908 genotype on gene expression, we established H9 ESC lines homozygous for the rs7132908 obesity risk A allele with CRISPR-Cas9 homology-directed repair while the parent line is homozygous for the non-risk G allele. We performed RNA-seq on these ESCs as well as hypothalamic neural prgenitors derived from these ESCs after 14 days of differentiation. We identified genes significantly differentially expressed due to rs7132908 in each cell type. We also obtained primary human pediatric hypothalamus tissue from 4 donors from the NIH NeuroBiobank to serve as a reference to validate the identity of our ESC-derived hypothalamic neural progenitors. We compared average TPMs from each homozygous rs7132908 non-risk G allele hypothalamic neural progenitor sample to average TPMs from each donor homozygous for the rs7132908 non-risk G allele.

first: Struan

last: Grant

first: Khanh

last: Trang

first: Alessandra

last: Chesi


title: Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [CLIP-seq]

city: Würzburg

first: Laura

last: Jenniches

address: Josef-Schneider-Straße 2/D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post-transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. We developed a hierarchical Bayesian model that corrects for confounding factors in rifampicin RNA stability assays and enables us to identify differentially decaying transcripts transcriptome-wide. Our analysis revealed that the median RNA half-life in Salmonella in early stationary phase is less than 1 minute, a third of previous estimates. We found that over half of the 500 most long-lived transcripts are bound by at least one major RBP, suggesting a general role for RBPs in shaping the transcriptome. Integrating differential stability estimates with CLIP-seq revealed that approximately 30% of transcripts with ProQ binding sites and more than 40% with CspC/E binding sites in coding or 3' untranslated regions decay differentially in the absence of the respective RBP. Analysis of differentially destabilized transcripts identified a role for both proteins in the control of respiration, and for ProQ in the oxidative stress response. Our findings provide new insights into post-transcriptional regulation by ProQ and CspC/E, and the importance of RBPs in regulating gene expression.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design:
Sample 1-12: CLIP-seq, Sample 13-132 RIF-seq
Cross-linking immunoprecipitation-high-throughput sequencing (CLIP-seq) to detect CspC and CspE binding sites in Salmonella (SL1344)

first: Charlotte

last: Michaux

first: Linda

last: Popella

first: Sarah

last: Reichardt

first: Jörg

last: Vogel

first: Alexander

last: Westermann

first: Lars

last: Barquist


title: CAR affinity modulates the sensitivity of CAR-T cells to PD-1/PD-L1-mediated inhibition.

status: Public on Mar 25 2024

city: Barcelona

first: Sònia

last: Guedan

address: Carrer Roselló 153

country: Spain

institute: Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS)

summary: The objective of this experiment was to characterized the molecular mechanisms behind the different effects of PD-1 disruption in low affinity (LA) and high affinity (HA) HER2-28z CAR-T cells. The transcriptomic profile of mock and PD-1 KO CAR-T cells following antigen recognition was compared by using the nCounter® CAR-T Characterization Gene Expression Panel (Nanostring). RNA samples were isolated from CAR-T cells generated from three independent donors.

overall_design: CAR-T cells were cocultured with SKOV3 tumour cells (effector/target ratio of 1:3) for 48h. CD45+ cells were then flow sorted and total RNA was extracted using the RNeasy Mini kit (Qiagen). Samples were prepared according to the manufacturer’s protocols for the nCounter CAR-T Characterization Panel (Nanostring). Cartridges were run on the nCounter Sprint Profiler. Gene expression levels were normalized against the housekeeping genes and data analysis was conducted using the Rosalind Platform

first: Irene

last: Andreu-Saumell

first: Alba

last: Rodriguez-Garcia

first: Sonia


title: Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives

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

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Refer to individual Series


title: Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function [ChIP-Seq]

city: Philadelphia

first: Matthew

last: Pahl

overall_design: We performed ATAC-seq, RNA-seq, and ChIPseq against H3K27ac, Foxp3, and Ikzf1 on mouse ex vivo Tregs isolated from spleens

first: Rajan

last: Thomas

first: Andrew

last: Wells


title: Mutant FOXO1 Controls an Oncogenic Network via Enhancer Accessibility and RNA Polymerase Pause Release

city: Nashville

first: Scott

last: Hiebert

state: Tennessee

address: 2220 Pierce Ave, Hiebert Lab PRB 512

institute: Vanderbilt University


title: Multiscale architecture design of 3D printed biodegradable Zn-based porous scaffolds for immunomodulatory osteogenesis

status: Public on Mar 23 2024

city: Beijing

first: Shuang

last: Li

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

summary: We studied gene expression changes in the transcriptome of RAW264.7 cells treated with extracts of Zn-0.8Li alloys Gyroid scaffolds for 48 hours and compared them to RAW264.7 (control) without the addition of extracts. The aim of this study was to determine the regulation of macrophage inflammatory responses by ions released from Gyroid scaffolds.

overall_design: To investigate the effect of degradable Zn-0.8Li Gyroid scaffolds on RAW264.7 cells, we collected extracts of Gyroid scaffolds. Then, we co-cultured RAW264.7 cells using the extract for 48 h. Cells without added extract were the control group, and total cellular RNA was collected for gene expression profiling using RNA-seq data.


title: SWI/SNF Chromatin Remodeling Complex Orchestrates Sequential Binding of Key Transcription Factors in B Cells and Restricts Aggressive Lymphoma [human CUT&RUN]

status: Public on Mar 22 2024

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

summary: ARID1A, a subunit of the canonical BAF nucleosome remodeling complex, is commonly mutated in lymphomas. Our study shows that ARID1A orchestrates B-cell fate during the germinal center (GC) response, facilitating cooperative and sequential binding of PU.1 and NF-kB at crucial genes for cytokine and CD signaling. The absence of ARID1A tilts GC cell-fate towards immature IgM+CD80-PDL2- memory B-cells, known for their potential to re-enter new GCs. When combined with BCL2 oncogene, ARID1A haploinsufficiency hastens the progression of aggressive follicular lymphomas in mice. Remarkably, follicular lymphoma patients with ARID1A-inactivating mutations preferentially display an immature memory B-cell-like state with increased transformation risk to aggressive disease. These observations offer mechanistic understanding into the emergence of both indolent and aggressive lymphomas in ARID1A-mutant patients through formation of immature memory-like clonal precursors. Lastly, we demonstrate that ARID1A mutation induces synthetic lethality to SMARCA2/4 inhibition, paving the way for potential precision therapy for high-risk patients.

overall_design: CUT&RUN was performed using Epicypher protocol with a light fixation protocol (1min 0.1% PFA). Antibodies used; ARID1A (1235S), IgG (ABIN101961), BRD9 (137245), PU.1 (2266S), H3.3 (91191), H3K27me3 (13027S). Two genotypes were used; ARID1A WT and HET. All experiments were done in RIVA cell line.

first: Barisic

last: Darko

first: Chris

first: Meydan

last: Cem

first: Teater

last: Matt

first: Melnick

last: Ari


title: Mutant FOXO1 Controls an Oncogenic Network via Enhancer Accessibility and RNA Polymerase Pause Release [RNA-Seq]

summary: Transcriptional dysregulation is a hallmark of diffuse large B-cell lymphoma (DLBCL), as multiple transcriptional regulators are mutated. However, our mechanistic understanding of how normal transcriptional programs are co-opted in DLBCL has been hindered by a lack of methodologies that provide the temporal resolution required to separate direct and indirect effects in transcriptional control. Here, we applied a chemical-genetic approach to engineer the inducible degradation of the transcription factor FOXO1, which is recurrently mutated in DLBCL. The combination of rapid degradation of FOXO1, nascent transcript detection, and accessible chromatin allowed us to identify the direct targets of FOXO1. FOXO1 degradation impaired RNA polymerase pause-release at many target genes. Furthermore, FOXO1 was required to maintain accessibility at specific enhancers associated with target genes. Importantly, many direct targets of FOXO1 were oncogenes including several effectors of the PI3K pathway, which creates a dependency on AKT signaling.

overall_design: RNA-seq was performed on 3 DLBCL cell lines (parental or expressing endogenous FOXO1-FKBPF36V) at specified time points after treatment with dTAG-47..

first: Hillary

last: Layden

middle: W


title: Evaluating cell culture reliability in pediatric brain tumor primary cells through DNA methylation profiling

city: Rome

first: Evelina

last: Miele

address: Viale Baldelli 38

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

type: Methylation profiling by genome tiling array

summary: In vitro models of pediatric brain tumors (pBT) are tools instrumental for better understanding the mechanisms contributing to oncogenesis and testing new therapies; and thus, ideally, they should recapitulate the original tumor. We applied  DNA methylation (DNAm) and copy number variation (CNV) profiling to characterize 241 pBT samples, including 155 tumors and 86 pBT-derived cell cultures, and considering serum vs serum-free conditions, late vs early passages, and dimensionality (2D vs 3D cultures). We performed a t-SNE classification and identified differentially methylated regions in tumors compared to cell models.    Early cell cultures recapitulate the original tumor, but serum media and 2D culturing were demonstrated to significant contribute to the divergence of DNAm profiles from the parental ones. All divergent cells clustered together acquiring a common deregulated epigenetic signature, suggesting a shared selective pressure.   In conclusion, DNAm and CNV are informative tools that should be used to assess the recapitulation of pBT-cells from parental tumors.

overall_design: Pediatric brain tumors (pBT)-cellular in vitro models were analyzed to check if they recapitulate the original tumors. Using bisulphite converted DNA hybridised to Illumina EPIC Beadchip, we applied genome-wide (~850K CpGs) methylation of DNA (DNAm) and Copy Number Variation (CNV) profiling to characterize both pBT cell cultures and tumors, analyzing 241 pBT samples (155 tissues and 86 cells) by means of clustering (t-SNE/HDSCAN) and functional analysis. For cell models three variables were considered: method (serum/serum free), time (early/late), and dimensionality (2D/3D).

first: Lucia

last: Pedace

first: Simone

last: Pizzi

first: Luana

last: Abballe

first: Maria

last: Vinci

first: Celeste

last: Antonacci

first: Sara

last: Patrizi

first: Francesca

last: Del Bufalo

first: Sabrina

last: Rossi

first: Giulia

last: Pericoli

last: Gianno

first: Zein

last: Besharat

first: Luca

last: Tiberi

first: Angela

last: Mastronuzzi

first: Elisabetta

last: Ferretti

first: Marco

last: Tartaglia

first: Franco

last: Locatelli

first: Andrea

last: Ciolfi


title: SWI/SNF Chromatin Remodeling Complex Orchestrates Sequential Binding of Key Transcription Factors in B Cells and Restricts Aggressive Lymphoma [human ChIP-seq]

first: Christopher

last: Chin

overall_design: ChIP-seq was perfomred using standard ChIP-seq protocol (see Barisic et al 2019 Nature) with a few modifications (described in Barisic et al 2024 Cancer Cell). Antibodies used: PBRM1 (A301-591A), IgG (ABIN101961), SMARCA4 (A300-813A), PU.1 (2266S), H3K27ac (39133).

first: Barisic

last: Darko

first: Chris

first: Meydan

last: Cem

first: Teater

last: Matt

first: Melnick

last: Ari


title: Mutant FOXO1 Controls an Oncogenic Network via Enhancer Accessibility and RNA Polymerase Pause Release [ATAC-Seq]

first: Scott

last: Hiebert

overall_design: ATAC-seq was performed on 3 DLBCL cell lines expressing endogenous FOXO1-FKBPF36V at specified time points after treatment with dTAG-47.

first: Hillary

last: Layden


title: Iron oxide nanoparticles inhibit tumor progression and suppress lung metastases in mouse models of breast cancer

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University


title: The spatially resolved transcriptome signatures of glomeruli in chronic kidney disease

city: Los Angeles

first: Sargis

last: Sedrakyan

address: 4650 Sunset Blvd

institute: Children's Hospital Los Angeles

summary: Here, we used Digital Spatial Profiling (DSP) to describe the glomerular transcriptomic signatures that may characterize the complex molecular mechanisms underlying progressive kidney disease in Alport syndrome, focal segmental glomerulosclerosis, and membranous nephropathy. Our results revealed significant transcriptional heterogeneity among diseased glomeruli, and this analysis showed that histologically similar glomeruli manifested different transcriptional profiles. Using glomerular pathology scores to establish an axis of progression, we identified molecular pathways that progressively decreased with increasing pathology scores, including Signal Recognition Particle-dependent co-translational protein targeting to membrane and selenocysteine synthesis pathways. We also identified a distinct signature of upregulated and downregulated genes common to all the diseases investigated when compared to non-diseased tissue from nephrectomies. These analyses using DSP at the single glomerulus level could help to gain insight into the pathophysiology of kidney disease

overall_design: Serially sectioned formalin fixed and paraffin embedded kidney biopsies from healthy control pateints (n=3) and patients affected with Alport syndrome (n=3), focal segmental glomerulosclerosis (n=2), membranous nephropathy (n=2) were processed for digital spatial profiling to explore compartment-specific transcriptional programs of the selected 75 glomeruar and 31 tubular regions.

first: Geremy

last: Clair

first: Hasmik

last: Soloyan

first: Paolo

last: Cravedi

last: Angeletti

first: Fadi

last: Salem

first: Laith

last: Al-Rabadi

first: Roger

last: De Filippo

first: Stefano

last: Da Sacco

first: Kevin

last: Lemley

first: Laura

last: Perin


title: Intragraft memory-like CD127hiCD4+Foxp3+ regulatory T cells maintain transplant tolerance

city: Westmead

first: Brian

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

summary: CD4+Foxp3+ regulatory T cells (Tregs) play an essential role in suppressing transplant rejection but their role within the graft, is poorly understood. To address this, we compared phenotypic and transcriptomic characteristics of Treg populations within lymphoid-organs and grafts in an islet xenotransplant model of tolerance induced by co-stimulation blockade. In this study, Tregs were essential for tolerance induction and their numbers increased over time. Tregs demonstrated phenotypic and transcriptional heterogeneity within the graft, and lymphoid organs of tolerant mice. A sub-population of CD127highTreg with memory-like and suppressive features were present in high proportions within long surviving islet-grafts of tolerant mice and had a transcriptomic profile consistent with tissue-Tregs. Importantly these CD127highTregs were better able to prevent rejection by effector T cells, after adoptive transfer into secondary Rag-/- hosts, than naïve Tregs, or unselected Tregs isolated from tolerant mice. We propose that after initial development within the draining lymph node they undergo further genetic reprogramming within the graft towards a phenotype that has shared characteristics with other tissue or tumour Tregs. These findings provide a new focus for engineering such cells either in vivo or for adoptive transfer for inducing tolerance.

overall_design: To determine if there were distinctive molecular profiles for memory-like CD127highTregs and graft-Tregs in this transplant tolerant model, and to explored possible precursor relationships between secondary lymphoid-organ Tregs and non-lymphoid tissue-Tregs, as well as among CD127highTregs, CD127-/lowTregs, graft-Tregs and naïve-Tregs

first: Min

last: Hu

first: Philip

last: O'Connell

first: Joey

last: Lai

first: Yuanfie

last: Zhao

first: Leigh

last: Nicholson

first: Yi

last: Qian


title: RNA-seq of muscle tissue from 9-week-old control and LSD1 mutant mice

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

institute: IGBMC

summary: Deciphering the genes regulated by LSD1 in muscle.

overall_design: RNA-Seq

first: Qingshuang

last: CAI

last: DUTEIL

first: Daniel

last: METZGER


title: ChIP-seq of NRF1 in skeletal muscle

summary: Charaterize NRF1 cistrome in mouse muscle

overall_design: 2 samples

first: Tao

last: YE


title: Mutant FOXO1 Controls an Oncogenic Network via Enhancer Accessibility and RNA Polymerase Pause Release [PRO-Seq]

first: Scott

last: Hiebert

overall_design: PRO-seq was performed on 3 DLBCL cell lines expressing endogenous FOXO1-FKBPF36V at specified time points after treatment with dTAG-47..

first: Hillary

last: Layden


title: Mutant FOXO1 Controls an Oncogenic Network via Enhancer Accessibility and RNA Polymerase Pause Release [ChIP-seq/CUT&RUN]

overall_design: ChIP-seq (H3K27ac, Abcam ab4729) or CUT&RUN (H3K4me3 Abcam ab12209) was performed in the OCI-LY1 cell line expressing endogenous FOXO1-FKBPF36V at specified time points after treatment with dTAG-47.


title: A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations [ATAC-seq]

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

summary: Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.

overall_design: 51 ATAC-seq datasets from hESCs differntiation toward trunk neural crest and sympathoadrenal derivatives at 5 key stages (day 0, 3, 9, 14, 19) and in four different experimental conditions (wt, 17q gain, 17q+1q gain, 17q+1q gain and MYCN overexpression); most sample groups are represented by 3 replicates (independent differentiation experiments with the same cell lines)

first: Ingrid

last: Saldana-Guerrero

first: Luis

last: Montano-Gutierrez

first: Katy

last: Boswell

first: Christoph

last: Hafemeister

first: Evon

last: Poon

first: Lisa

last: Shaw

first: Dylan

last: Stavish

first: Rebecca

last: Lea

first: Sara

last: Wernig-Zorc

first: Eva

last: Bozsaky

first: Irfete

last: Fetahu

first: Peter

last: Zoescher

first: Ulrike

last: Pötschger

first: Marie

last: Bernkopf

first: Andrea

last: Wenninger-Weinzierl

first: Caterina

last: Sturtzel

first: Celine

last: Souilhol

first: Sophia

last: Tarelli

first: Mohamed

last: Shoeb

first: Polyxeni

last: Bozatzi

first: Magdalena

last: Rados

first: Maria

last: Guarini

first: Michelle

last: Buri

first: Wolfgang

last: Weninger

last: Putz

first: Miller

last: Huang

first: Ruth

last: Ladenstein

last: Andrews

first: Ivana

last: Barbaric

first: George

last: Cresswell

first: Helen

last: Bryant

first: Martin

last: Distel

first: Louis

last: Chesler

first: Sabine

last: Taschner-Mandl

first: Matthias

last: Farlik

first: Anestis

last: Tsakiridis


title: A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations [RNA-seq]

first: Florian

last: Halbritter

overall_design: 64 RNA-seq datasets from hESCs differentiation toward trunk neural crest and sympathoadrenal derivatives at 5 key stages (day 0, 3, 9, 14, 19) and in four different experimental conditions (wt, 17q gain, 17q+1q gain, 17q+1q gain and MYCN overexpression); most sample groups are represented by 3-4 replicates (independent differentiation experiments with the same cell lines)

first: Ingrid

last: Saldana-Guerrero

first: Luis

last: Montano-Gutierrez

first: Katy

last: Boswell

first: Christoph

last: Hafemeister

first: Evon

last: Poon

first: Lisa

last: Shaw

first: Dylan

last: Stavish

first: Rebecca

last: Lea

first: Sara

last: Wernig-Zorc

first: Eva

last: Bozsaky

first: Irfete

last: Fetahu

first: Peter

last: Zoescher

first: Ulrike

last: Pötschger

first: Marie

last: GuariniBernkopf

first: Andrea

last: Wenninger-Weinzierl

first: Caterina

last: Sturtzel

first: Celine

last: Souilhol

first: Sophia

last: Tarelli

last: Shoeb

last: Bozatzi


title: scRNAseq of Sox17-Erg and Etv2 iECs at Day 3 and Day 7

first: Li

last: Qian

summary: Evaluation of direct reprogramming heterogeneity of neonatal murine cardiac fibroblasts into iECs at Day 3 and Day 7

overall_design: Isolated neonatal murine cardiac fibroblasts were infected with control, Etv2, or Sox17 and Erg retroviruses at Day 0 of reprogramming.  Two replicates were pooled at each specified timepoint to evaluate iEC reprogramming. Each timepoint contained multiplexed samples of control, Etv2, and Sox17-Erg infected cells.

first: Gregory

last: Farber


title: A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations [10x scRNA-seq]

first: Florian

last: Halbritter

overall_design: 26 scRNA-seq datasets from hESCs differentiation toward trunk neural crest and sympathoadrenal derivatives at 9 key stages (day 0, 3, 6, 9, 10,12, 14, 19, 28) and in four different experimental conditions (wt, 17q gain, 17q+1q gain, 17q+1q gain and MYCN overexpression); most sample groups are represented by at least 3 replicates (independent differentiation experiments with the same cell lines). 3-4 samples were multiplexed per 10x Genomics reaction using CellPlex, or with the barcoding technology of Parse Biosciences where indicated.

first: Ingrid

last: Saldana-Guerrero

first: Luis

last: Montano-Gutierrez

first: Katy

last: Boswell

first: Christoph

last: Hafemeister

last: Poon

last: Shaw

last: Bernkopf

first: Mohamed

first: Polyxeni

first: Magdalena

last: Rados

first: Maria

last: Guarini

first: Michelle

last: Buri

first: Wolfgang

last: Weninger

last: Putz

first: Miller

last: Huang

first: Ruth

last: Ladenstein

last: Andrews

first: Ivana

last: Barbaric

first: George

last: Cresswell

first: Helen

last: Bryant

first: Martin

last: Distel

first: Louis

last: Chesler

first: Sabine

last: Taschner-Mandl

first: Matthias

last: Farlik

first: Anestis

last: Tsakiridis


title: Bulk RNAseq of Day 3, Day 7, and 4 week iECs

first: Li

last: Qian

summary: Sox17-Erg direct reprogramming converts neonatal murine cardiac fibroblasts into induced endothelial cells. This data evaluates the conversion over time of the Sox17-Erg iECs compared to control condition.

overall_design: Sox17-Erg iECs or control fibroblasts were harvested  at Day 3, Day 7, and Week 4.  Gene expression of each condition was then compared to look at the acquisition of endothelial identity.

first: Gregory

last: Farber


title: Genomic Analysis of Human Brain Metastases Treated with Stereotactic Radiosurgery Reveals Unique Signature Based on Treatment Failure. [WES]

status: Public on Mar 21 2024

city: Madison

first: Jack

last: Shireman

state: WI

address: 600 Highland Ave

institute: UW-Madison

summary: Stereotactic radiosurgery (SRS) has been shown to be efficacious for treatment of limited brain metastasis (BM), however, the effects of SRS on human brain metastases have yet to be studied. We performed genomic analysis of resected brain metastases from patients whose resected lesion was previously treated with SRS. Our analyses demonstrated for the first time that patients possess a distinct genomic signature based on type of treatment failure including local failure, leptomeningeal spread, and radio-necrosis. Examination of the center and peripheral edge of the tumors treated with SRS indicated differential DNA damage distribution and an enrichment for tumor suppressor mutations and DNA damage repair pathways along the peripheral edge. Furthermore, the two clinical modalities used to deliver SRS, LINAC and GK, demonstrated differential effects on the tumor landscape even between controlled primary sites. Our study provides, in humans, biological evidence of differential effects of SRS across BM’s.

overall_design: Pre-operative SRS samples analyzed during surgical reception from the center and peripheral edges of the tumor

first: Christina

last: Kendziorski

first: Mahua

last: Dey


title: H3K27ac CUT&Tag iEC reprogramming

summary: H3K27ac CUT&Tag analysis of Sox17-Erg and Etv2 reprogramming of cardiac fibroblasts into endothelial cells

overall_design: H3K27ac CUT&Tag sample preperation of Day 3 control, Sox17-Erg retrovirally infected neonatal murine  cardiac fibroblasts, Etv2 retrovirally infected neonatal cardiac fibroblasts, and isolated primary neonatal cardiac endothelial cells (Pecam1+)


title: LSD1 in skeletal muscle

first: Delphine

last: Duteil

overall_design: Refer to individual Series


title: The functional role of L-fucose on dendritic cell function and polarization

status: Public on Mar 20 2024

city: Tampa

first: Dongliang

last: Du

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

summary: Despite significant advances in the development and refinement of immunotherapies administered to combat cancer over the past decades, a number of barriers continue to limit their efficacy. One significant clinical barrier is the inability to mount initial immune responses towards the tumor. As dendritic cells are central initiators of immune responses in the body, the elucidation of mechanisms that can be therapeutically leveraged to enhance their functions to drive anti-tumor immune responses is urgently needed. Here, we report that the dietary sugar L-fucose can be used to enhance the immunostimulatory activity of dendritic cells (DCs). L-fucose polarizes immature myeloid cells towards specific DC subsets, specifically cDC1 and moDC subsets. In vitro, L-fucose treatment enhances antigen uptake and processing of DCs. Furthermore, our data suggests that L-fucose-treated DCs increase stimulation of T cell populations. Consistent with our functional assays, single-cell RNA sequencing of intratumoral DCs from tumor-bearing mice confirmed transcriptional regulation and antigen processing as pathways that are significantly altered by dietary L-fucose. Together, this study provides the first evidence of the ability of L-fucose to bolster DC functionality and provides rational to further investigate how L-fucose can be used to leverage DC function in order to enhance current immunotherapy.

overall_design: To investigate the effect of L-fucose on immune subsets we took intratumoral CD45+ cells treated +\- L-fucose. We then preformed gene expression profiling comparing L-fucose-treated tumors to control-treated tumors at three time points. Comparative gene expression profiling analysis of RNA-seq data for intratumoral CD45+ cells with L-fucose-treated groups compared to control-treated groups.


title: Iron oxide nanoparticles inhibit tumor progression and suppress lung metastases in mouse models of breast cancer [NanoString]

first: Lu

last: Jin

summary:
Systemic exposure to starch-coated iron oxide nanoparticles (IONPs) can stimulate antitumor T cell responses, even when little IONP is retained within the tumor. Here, we demonstrate in mouse models of metastatic breast cancer that IONPs can alter the host immune landscape leading to systemic immune-mediated disease suppression. We report that a single intravenous injection of IONPs can inhibit primary tumor growth, suppress metastases, and extend survival. Gene expression analysis revealed activation of Toll-like receptor (TLR) pathways involving signaling via Toll/Interleukin-1 Receptor domain-containing adaptor-inducing IFN-β (TRIF), a TLR pathway adaptor protein. Requisite participation of TRIF in suppressing tumor progression was demonstrated with histopathologic evidence of upregulated IFN-regulatory factor 3 (IRF3), a downstream protein, and confirmed in a TRIF knockout syngeneic mouse model of metastatic breast cancer. Neither starch-coated polystyrene nanoparticles lacking iron, nor iron-containing dextran-coated parenteral iron replacement agent induced significant antitumor effects suggesting a dependence on the type of IONP formulation. Analysis of multiple independent clinical databases support a hypothesis that upregulation of TLR3 and IRF3 correlates with increased overall survival among breast cancer patients. Taken together, these data support a compelling rationale to re-examine IONP formulations as harboring anti-cancer immune (nano)adjuvant properties to generate therapeutic benefit without requiring uptake by cancer cells.
HuHER2 transgenic mice that developed palpable primary mammary tumors were assigned randomly into one of two groups (n = 3/group) to receive either PBS or BP (5 mg Fe/mouse). Mice were sacrificed 7 days after treatment and tumors, lungs, livers, spleens, lymph nodes, and bone marrows were collected. All nanoparticle-containing organs collected from BP treated mice were divided into two equal sections except for lungs (no detectable nanoparticle accumulation). One section was processed for RNA isolation from whole organ. The other tissue/organ section was further processed for magnetic sorting. These were digested to provide single cells as described before28,38 and nanoparticle associated cells were separated magnetically to obtain the nanoparticle-associated fraction (BP-NA). RNA was isolated from BP-NA cells from each organ and tumor and used for sequencing. For Nanostring analysis, HuHER2 transgenic tumor bearing mice were treated with PBS or BP (5 mg Fe) on the day of tumor detection (n = 12/group). Three mice from each group were sacrificed on day 1, 3, 7, or 31 and primary tumors collected for RNA isolation and gene expression analysis by Nanostring using the pan-immune cell marker panel.

overall_design: Preethi,Korangath

first: Robert

last: Ivkov

last: Clarke


title: Sox17-Erg cardiac iEC reprogramming

city: Chapel Hill

address: 111 Mason Farm Road, MBRB

institute: UNC

summary: Bioinformatic Analyses of Sox17-Erg reprogramming


title: LSD1/GR crosstalk

summary: Characterize GR/LSD1 cistrome in skeletal muscle in mice fed or starved for 24h

overall_design: ChIP-Seq

first: Qingshuang

last: CAI

last: DUTEIL

first: Daniel

last: METZGER


title: Effect of deletion of SPTLC1 on gene expression and differentiation of mouse Th17 cells in vitro

city: Frederick

first: Thiruvaimozhi

last: Abimannan

state: MD

address: Building 560, Room 22-6

department: CDBL

institute: National Cancer Institute

summary: Th17 cells are implicated in autoimmune diseases and several metabolic processes are shown to be important for their development and function. However, the role of de novo sphingolipid biosynthesis in their differentiation and function is less known. To investigate the role of SPTLC1(major subunit of serine palmitoyl transferase enzyme (SPT) that catalyzes the first and rate limiting step of de novo sphingolipid synthesis) in mouse Th17 cell differentiation, we have activated the WT and SPTLC1 defecient (KO) naïve CD4+ T cells, isolated  from mouse spleen and lymph nodes, in Th17 differentiating condition in the precence and absence of NAC ( N-acetyl cysteine) and 3-KDS (3-ketodihydrosphingosine).

overall_design: To investigate the role of SPTLC1 in Th17 differentiation, total RNA was extracted for each of the 3 biological replicates from WT and KO naive CD4+ T cells and Th17 cells. To understand the specificity of the de novo sphingolipid biosynthetic pathway in the observed effect KO Th17 cells, RNA was isolated from WT and KO naive CD4+T cells cultured under Th17 polarizing condition in the presence and absense of 3-KDS (product of SPT enzyme). Further, to understand role of ROS in the observed defect in KO Th17 cells,  RNA was isolated from WT and KO naive CD4+T cells cultured under Th17 polarizing condition in the presence and absense of 3-KDS (product of SPT enzyme)

first: Usha

last: Acharya

first: Jairaj

middle: K


title: BayesAge: A Maximum Likelihood Algorithm To Predict Epigenetic Age

first: Matteo

last: Pellegrini

address: 610 Charles Young Drive East

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a reaction that results in the formation of 5-methylcytosine when a methyl group is added to the cytosine’s C5 position. As organisms age, DNA methylation patterns change in a reproducible fashion. This phenomenon has established DNA methylation as a valuable biomarker in aging studies. Epigenetic clocks based on weighted combinations of methylation sites have been developed to accurately predict the age of an individual from their methylome. However, many epigenetic clocks, particularly those that utilize penalized regression, model the changes in methylation linearly with age. Moreover, these models, which use methylation levels as features, are not robust to missing data and do not account for the count-based nature of bisulfite sequence data. Additionally, the models are generally not interpretable. To overcome these challenges, we present BayesAge, an extension of the previously developed scAge approach that was developed for the analysis of single cell DNA methylation datasets. BayesAge utilizes maximum likelihood estimation (MLE) to infer ages, models count data using binomial distributions, and uses LOWESS smoothing to capture the non-linear dynamics between methylation and age. Our approach is designed for use with bulk bisulfite sequencing datasets. BayesAge outperforms scAge in several respects. Specifically, BayesAge’s age residuals are not age associated, thus providing a less biased representation of epigenetic age variation across populations. Moreover, BayesAge enables the estimation of error bounds on age inference and, when run on downsampled data, its coefficient of determination between predicted and actual ages surpasses both scAge and penalized regression.

overall_design: We collected targeted bisulfite sequence data fom blood and buccak swabs of 458 Individuals

first: Lajoyce

last: Mboning

first: Michael

last: Thompson

first: Liudmilla

last: Rubbi


title: Genomic Analysis of Human Brain Metastases Treated with Stereotactic Radiosurgery Reveals Unique Signature Based on Treatment Failure.

last: Shireman

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


title: Reverse translational discovery reveals dysregulation of CD4+ and CD8+ resident memory T, myeloid, and stromal cells in steroid-refractory, checkpoint inhibitor colitis [blood CITE_TCR-seq]

city: San Francisco

middle: George

last: Kattah

address: 513 Parnassus Ave

department: Medicine-Gastroenterology

institute: UCSF

summary: Checkpoint inhibitor colitis (CPI colitis) is a frequent immune-related adverse event resulting from cancer immunotherapy that is currently treated with empiric immunosuppression such as corticosteroids. A greater understanding of the pathogenesis of CPI colitis in the steroid-refractory setting is required to develop better colitis interventions targeted to each patient. Using paired colon biopsies and blood from steroid-experienced patients with endoscopically confirmed CPI colitis, combined with control patients, we performed multiplexed single-cell transcriptomics (scRNA/TCRseq) and proteomics (CITEseq, CyTOF) to identify contributing immune and non-immune populations. In CPI colitis patient biopsies compared to healthy controls, we found enrichment of resident memory (RM) T cells in both the CD8+ and unexpectedly the CD4+ compartments, as well as cytotoxic CD8+ T cells. These 3 populations expressed exact matching TCR, suggesting that CD4+ RM and CD8+ RM T cells are clonal progenitors that give rise to tissue-destructive cytotoxic effectors. Unbiased CyTOF and confirmatory scRNAseq and CITEseq analysis identifies specific mobilized subpopulations of both cytotoxic CD8+ and CD4+ RM cells that express both activation markers CD38 and HLA-DR, underscoring their pathogenic potential. CPI colitis induces global upregulation of interferon signaling and antigen presentation, as well as epithelial-specific dysregulation of homeostatic pathways (aquaporin/solute transporters) which is shared with ulcerative colitis. However, distinct from ulcerative colitis, CPI colitis involves specific alterations in stromal cell metabolic (NAD+, tryptophan) or extracellular signaling (BMP) pathways that directly impact epithelial cell survival, arguing for distinct therapeutic targeting. Finally, endothelial cells in CPI colitis demonstrate enrichment of the integrin 47 ligand MADCAM-1 (which is targeted by anti-47 antibody vedolizumab to treat colitis). This ligand is enriched in CPI colitis patients who received TNF blockade and anti-CTLA-4, identifying subsets of patients who may be more responsive to vedolizumab treatment. This work identifies putative pathogenic resident memory and cytotoxic T cells, and non-immune stromal and endothelial populations, whose properties may nominate subsets of CPI colitis patients amenable to distinct targeting strategies.

overall_design:
Healthy control (HC), ulcerative colitis (UC) patients, and patients with immune-checkpoint inhibitor (CPI) colitis, blood CITE-seq, biopsy scRNA-seq, biopsy CITE-seq, and TCR analysis of blood leukocytes and biopsies. Samples were pooled and subsequently deconvoluted with freemuxlet/demuxlet

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Junyan

last: He

first: Alexis

last: Combes

first: David

last: Oh


title: Gene expression profile in monocyte of PsA patients

city: Kaohsiung

first: Sung-Chou

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

summary: We examined gene expression variations in monocyte between PsA patients and healthy control subjects

overall_design: We had the RNA samples prepared and examined microarray assays.

first: Shang-Hung

last: Lin


title: Reverse translational discovery reveals dysregulation of CD4+ and CD8+ resident memory T, myeloid, and stromal cells in steroid-refractory, checkpoint inhibitor colitis


title: Iron oxide nanoparticles inhibit tumor progression and suppress lung metastases in mouse models of breast cancer [RNA-seq]

last: Jin

summary: Systemic exposure to starch-coated iron oxide nanoparticles (IONPs) can stimulate antitumor T cell responses, even when little IONP is retained within the tumor. Here, we demonstrate in mouse models of metastatic breast cancer that IONPs can alter the host immune landscape leading to systemic immune-mediated disease suppression. We report that a single intravenous injection of IONPs can inhibit primary tumor growth, suppress metastases, and extend survival. Gene expression analysis revealed activation of Toll-like receptor (TLR) pathways involving signaling via Toll/Interleukin-1 Receptor domain-containing adaptor-inducing IFN-β (TRIF), a TLR pathway adaptor protein. Requisite participation of TRIF in suppressing tumor progression was demonstrated with histopathologic evidence of upregulated IFN-regulatory factor 3 (IRF3), a downstream protein, and confirmed in a TRIF knockout syngeneic mouse model of metastatic breast cancer. Neither starch-coated polystyrene nanoparticles lacking iron, nor iron-containing dextran-coated parenteral iron replacement agent induced significant antitumor effects suggesting a dependence on the type of IONP formulation. Analysis of multiple independent clinical databases support a hypothesis that upregulation of TLR3 and IRF3 correlates with increased overall survival among breast cancer patients. Taken together, these data support a compelling rationale to re-examine IONP formulations as harboring anti-cancer immune (nano)adjuvant properties to generate therapeutic benefit without requiring uptake by cancer cells.

overall_design: HuHER2 transgenic mice that developed palpable primary mammary tumors were assigned randomly into one of two groups (n = 3/group) to receive either PBS or BP (5 mg Fe/mouse). Mice were sacrificed 7 days after treatment and tumors, lungs, livers, spleens, lymph nodes, and bone marrows were collected. All nanoparticle-containing organs collected from BP treated mice were divided into two equal sections except for lungs (no detectable nanoparticle accumulation). One section was processed for RNA isolation from whole organ. The other tissue/organ section was further processed for magnetic sorting. These were digested to provide single cells as described before28,38 and nanoparticle associated cells were separated magnetically to obtain the nanoparticle-associated fraction (BP-NA). RNA was isolated from BP-NA cells from each organ and tumor and used for sequencing. For Nanostring analysis, HuHER2 transgenic tumor bearing mice were treated with PBS or BP (5 mg Fe) on the day of tumor detection (n = 12/group). Three mice from each group were sacrificed on day 1, 3, 7, or 31 and primary tumors collected for RNA isolation and gene expression analysis by Nanostring using the pan-immune cell marker panel.

first: Preethi

last: Korangath

last: Ivkov

last: Clarke


title: Endocardial HDAC3 is required for myocardial trabeculation [bulk RNA-seq]

city: COLUMBUS

first: Deqiang

state: Ohio

address: 575 Children’s Crossroad, WB4321

institute: Nationwide Children's Hospital

summary: To investigate the growth factors regulated in the endocardial cells, we performed gene expression profiling analysis using RNA-Seq data obtained from Hdac3 CRISPR knockout mouse cardiac endothelail cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CTL (EV) and HDAC3 knockout (Hdac3 KO) in mouse cardiac endothelial cell

first: Jihyun

last: Jang


title: Reverse translational discovery reveals dysregulation of CD4+ and CD8+ resident memory T, myeloid, and stromal cells in steroid-refractory, checkpoint inhibitor colitis [biopsy scRNA_TCR-seq]


title: Endocardial HDAC3 is required for myocardial trabeculation [single-cell RNA-seq]

summary: To investigate the signal communication from the endocardium to the trabecular myocardium, we performed single cell RNA sequencing (scRNA-seq) in E11.5 Hdac3 Tie2 knockout hearts and littermate control hearts

overall_design: In E11.5 Hdac3 Tie2 knockout hearts and littermate control hearts, single cells are isolated and analyzed using single cell RNA sequencing (scRNA-seq)


title: Endocardial HDAC3 is required for myocardial trabeculation [miRNA-seq]

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the microRNA regulated in the endocardial cells, we performed high-throughput profiling analysis using small RNA-Seq data obtained from Hdac3 CRISPR knockout mouse cardiac endothelail cells

overall_design: Comparative profiling analysis of RNA-seq data for CTL (EV) and HDAC3 knockout (Hdac3 KO) in mouse cardiac endothelial cell


title: Endocardial HDAC3 is required for myocardial trabeculation


title: RNA-seq of Monocyte-derived Macrophages and Hepatic Stellate Cell Activation after 72hr

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim Pharma GmbH & Co KG


title: Hepatic Stellate Cell Activation after 72hr

summary: Chronic liver diseases as non-alcoholic steatohepatitis (NASH)-induced cirrhosis are characterized by an increasing accumulation of stressed, damaged, or dying hepatocytes. Hepatocyte damage triggers the activation of resident immune cells, such as Kupffer cells (KC), as well as the recruitment of immune cells from the circulation towards areas of inflammation. After infiltration, monocytes differentiate into monocyte-derived macrophages (MoMF) which are functionally distinct from resident KC. We herein aim to compare in vitro signatures of polarized macrophages and activated hepatic stellate cells (HSC) with ex vivo derived disease signatures from human NASH. Secondly, we investigate the effects of the secretome of primary human monocytes, macrophages and NK cells on HSC activation, as in particular monocytes and macrophages have often been linked to liver fibrosis progression. IL-4 and IL-13 treatment induced TGF-β1 secretion by macrophages. However, the supernatant transfer did not induce HSC activation. Interestingly, PMA-activated macrophages showed a strong induction of the fibrosis response genes COL10A1 and CTGF, while supernatant of IL-4/IL-13 treated monocytes induced the upregulation of COL3A1 in HSC. Supernatant of PMA-activated NK cells had the strongest effect on COL10A1 induction in HSC, while IL-15 stimulated NK cells reduced the expression of COL1A1 and CTGF. These data indicate that other factors, aside the well-known cytokines and chemokines, are potentially stronger contributors to activation of HSCs and induction of a fibrotic response, indicating a more diverse and complex role of monocytes, macrophages and NK cells in liver fibrosis progression.

overall_design: Primary human hepatic stellate cells were treated with supernatant from macrophages stimulated with either IL4+IL13, TNFA or TGFB1 for 72 hours and then processed for RNASequencing.

first: Julia

last: Sauer

first: Agnes

last: Steixner-Kumar

first: Ehsan

last: Bahrami

first: Maciej

last: Motyka

first: Jörg

last: Rippmann

first: Oliver

last: Krenkel


title: Long-term haplodeficency of DSPP causes temporomandibular joint osteoarthritis in mice

status: Public on Mar 19 2024

city: Changchun

first: Qilin

last: Liu

address: 1500 Tsinghua Road

institute: Jilin University

summary: Background Extracellular matrix (ECM) protein malfunction or defect may lead to temporomandibular joint osteoarthritis (TMJ OA). Dentin sialophophoprotein (DSPP) is a mandibular condylar cartilage ECM protein, and its deletion impacted cell proliferation and other extracellular matrix alterations of postnatal condylar cartilage. However, it remains unclear if long-term loss of function of DSPP leads to TMJ OA. The study aimed to test the hypothesis that long-term haploinsufficiency of DSPP causes TMJ OA. Materials and Methods To determine whether Dspp+/- mice exhibit TMJ OA but no severe tooth defects, mandibles of wild-type (WT), Dspp+/-, and Dspp homozygous (Dspp-/-) mice were analyzed by Micro-computed tomography (micro-CT). To characterize the progression and possible mechanisms of osteoarthritic degeneration over time in Dspp+/- mice over time, condyles of Dspp+/- and WT mice were analyzed radiologically, histologically, and immunohistochemically. Results Micro-CT and histomorphometric analyses revealed that Dspp+/- and Dspp-/- mice had significantly lower subchondral bone mass, bone volume fraction, bone mineral density, and trabecular thickness compared to WT mice at 12 months. Interestingly, in contrast to Dspp-/- mice which exhibited tooth loss, Dspp+/- mice had minor tooth defects. RNA sequencing data showed that haplodeficency of DSPP affects the biological process of ossification and osteoclast differentiation. Additionally, histological analysis showed that Dspp+/- mice had condylar cartilage fissures, reduced cartilage thickness, decreased articular cell numbers and severe subchondral bone cavities, and with signs that were exaggerated with age. Radiographic data showed an increase in subchondral osteoporosis up to 18 months and osteophyte formation at 21 months. Moreover, Dspp+/- mice showed increased distribution of osteoclast in the subchondal bone and increased expression of MMP2, IL-6, FN-1, and TLR4 in the mandibular condylar cartilage. Conclusions Dspp+/- mice exhibit TMJ OA in a time-dependent manner, with lesions in the mandibular condyle attributed to hypomineralization of subchondral bone and breakdown of the mandibular condylar cartilage, accompanied by upregulation of inflammatory markers.

overall_design: To investigate the haploid deletion of DSPP affects the biological processes of ossification and osteoclast differentiation, We obtained the mandibular condyles from 4-month DSPP+/-, -/-, and wild-type mice.We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different tissues.Comparative gene expression profiling analysis of RNA-seq data for Osteoblast/osteoclast differentiation markers.

first: Yitong

last: zhao


title: Monocyte-derived Macrophages

overall_design: Human monocytes isolated from healthy donors were differentiated into monocyte-derived macrophages with M-CSF and polarized with either IL4+IL13 or LPS+IFN-gamma for 24h


title: Linear interaction between transcription and replication shapes DNA break dynamics

status: Public on Mar 18 2024

city: Heidelberg

first: Pei-Chi

last: Wei

state: Baden-Württemberg

address: Im Neuenheim Feld 280

department: Structural and functional genomics

institute: German Cancer Research Center

summary: Recurrent DNA break clusters (RDCs) are replication and transcription collision hotspots. Through high-resolution replication sequencing and a capture-ligation assay in mouse neural progenitor cells experiencing replication stress, we unraveled the replication fork architecture dictating RDC location and orientation. Most RDC occurs at the replication forks traversing timing transition regions (TTRs), where sparse replication origins connect unidirectional forks. Leftward-moving forks generate telomere-connected DNA double-strand breaks (DSB) while rightward-moving forks lead to centromere-connected DSBs. Strand-specific mapping for DNA-bounded RNA revealed transient DNA:RNA hybrids present at a higher density in RDC than in other actively transcribed long genes. In addition, mapping nascent RNA and RNA polymerase activity revealed that head-to-head interactions between replication and transcription machinery slow down DNA replication, resulting in 60% DSB contribution to the head-on as compared to 60% for co-directional . Our findings revealed TTR as a novel fragile class and highlighted how the linear interaction between transcription and replication impacts genome stability.

overall_design: We performed high-throughput sequencing to measure the linear movement of transcription and DNA replication in mouse neural progenitor cells.

first: Lorenzo

last: Corazzi

first: Li-Chin

last: Wang

first: Vivien

last: Ionasz


title: Epigenome-wide profiling of buccal DNAm in samples obtained from children of pregnant smokers enrolled in the VCSIP RCT: NCT03203603

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

institute: Oregon Health and Science University

summary: DNA methylation analysis was performed for buccal samples from children exposed in utero to maternal smoking during pregnancy (with or without vitamin C supplementation) and in a smaller number of non-smoker controls

overall_design: Illumina MethylationEPIC analysis of buccal samples collected in offspring near birth, 1 year, and/or 5 years of age.

first: Cindy

middle: T

last: McEvoy

first: Robert

last: Tepper

first: Eliot

last: Spindel


title: The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin tolerant Staphylococcus aureus [RNase III-CLASH]

city: Sydney

first: Jai

middle: Justin

last: Tree

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

summary: Small RNAs have been found to control a broad range of bacterial phenotypes including tolerance to antibiotics. Vancomycin tolerance in multidrug resistance Staphylococcus aureus is correlated with dysregulation of small RNAs although their contribution to antibiotic tolerance in poorly understood. RNA-RNA interactome profiling techniques are expanding our understanding of sRNA-mRNA interactions in bacteria; however, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. At steady-state, protein and mRNA abundances are often highly correlated and lower than expected protein abundance may indicate translational repression of an mRNA. To identify sRNA-mRNA interactions that regulate mRNA translation, we examined the correlation between gene transcript abundance, ribosome occupancy, and protein levels. We used the machine learning technique self-organising maps (SOMS) to cluster genes with similar transcription and translation patterns and identified a cluster of mRNAs that appeared to be post-transcriptionally repressed. By integrating our clustering with sRNA-mRNA interactome data generated in vancomycin tolerant S. aureus by RNase III-CLASH, we identified sRNAs that may be mediating translational repression. We have confirmed sRNA-dependant post-transcriptional repression of several mRNAs in this cluster. Two of these interactions are mediated by RsaOI, a sRNA that is highly upregulated by vancomycin. We demonstrate regulation of HPr and the cell-wall autolysin Atl. These findings suggest RsaOI coordinates carbon metabolism and cell wall turnover during vancomycin treatment.

sample_organism: Staphylococcus aureus subsp. aureus str. JKD6008

overall_design: This study uses a metaomics approach to predict sRNA function on mRNA transcription and translation, and identify genes that are post-transcriptionally regulated. The technique CLASH was used to identify sRNA-mRNA interactions in the cell and is presented in this entry. RNaseIII-CLASH was performed on biological duplicate cultures grown in Muller Hinton media to an OD of 0.8 with or without treatment with 2ug/ml vancomycin for 10mins.

first: Ignatius

last: Pang

first: Winton

last: Wu


title: ChIP-Seq of H4K4me1 in a panel of  ovarian cancer related cell lines.

first: Michelle

middle: Renee

last: Jones

state: CA

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

summary: In the current study we performed epigenomic characterization of 13 different in vitro models of  high-grade serous (HGSOC), low-grade serous (LGSOC), mucinous (MOC), endometrioid (ENOC) and clear cell (CCOC) carcinoma using ChIP-Seq for histone modication H3K4me1.

overall_design:
Chromatin Immuno Precipitation DNA Sequencing (ChIP-Seq) for histone modifications (H3K4me1 in 13 cell lines.
Please note that each processed data file was generated from *A, *B and *input samples together and is linked to the corresponding *A sample records.

first: Simon

last: Gayther


title: The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin tolerant Staphylococcus aureus [Ribo-seq]

platform_organism: Staphylococcus aureus subsp. aureus str. JKD6008

overall_design: This study uses a metaomics approach to assess gene transcription and translation, and identify genes that are post-transcriptionally regulated. Ribo-seq was used the assess translational of genes and is presented in this entry. Ribo-seq was performed on biological duplicate cultures grown in Muller Hinton media to an OD of 0.8.


title: Reverse translational discovery reveals dysregulation of CD4+ and CD8+ resident memory T, myeloid, and stromal cells in steroid-refractory, checkpoint inhibitor colitis [biopsy CITEseq]

first: Michael

last: Kattah

first: Junyan

last: He

first: Alexis

last: Combes

first: David

last: Oh


title: Effects of methionine, tryptophan, and niacin deficient diets on gene expression in intestinal cells in the DSS drinking IBD mouse model.

city: Suita

first: Tomoaki

last: Hara

state: Osaka

address: Yamadaoka 2-2

department: Graduate School of Medicine

country: Japan

institute: Osaka university

summary: Inflammatory bowel disease (IBD) is one of the intractable diseases. Nutritional components associated with IBD have been identified, and it is known that excessive methionine intake exacerbates inflammation and that tryptophan metabolism is involved in inflammation. In this study, we examined how temporary methionine, tryptophan, and niacin deficiencies alter gene expression in the intestinal cells of a dextran sulfate sodium (DSS)-fed IBD mouse model. The results showed that feeding amino acid deficient diets increased the expression of serine proteases and fat metabolizing enzymes. Amino acid deficiency also activated one-carbon metabolism and the PPAR pathway. These results suggest that temporary amino acid deficiency may be useful to enhance the antioxidant activity of the host.

overall_design: To examine the effects of amino acid deficiency, total RNA was extracted from mouse intestinal tracts for 9 conditions (R, 1K, 2K, 3K, RR, 1KR, 2KR, 3KR, C) and RNA- seq was performed. 1K, 2K, and 3K were fed amino acid-deficient diets until day 28 of rearing, and intestinal tracts were collected. The 1KR, 2KR, and 3KR were fed amino acid-deficient diet until day 28, and then fed normal diet until day 33, when their intestinal tracts were collected. R was fed normal diet until day 28 and their intestinal tract was collected. RR was fed normal diet until day 33 and the intestinal tract was collected. R, 1K, 2K, 3K, RR, 1KR, 2KR, and 3KR were free-drinking DSS from day 18 of rearing. C was control mice reared on normal feed, and their intestinal tract was collected on day 34. 1K and 1KR were fed methionine-deficient diet until day 28. 2K and 2KR were fed tryptophan- and niacin-deficient diet until day 28. 3K and 3KR were fed methionine-, tryptophan-, and niacin-deficient diet until day 28.

first: Sikun

last: Meng

first: Daisuke

last: Motooka

first: Yasuko

last: Arao

first: Hiromichi

last: Sato

first: Yoshiko

last: Tsuji

first: Chihiro

last: Otsuka

last: Saito

first: Yumiko

last: Hamano

first: Mirei

last: Ogita

first: Hideshi

last: Ishii


title: Age-associated accumulation of B cells promotes macrophage inflammation and inhibits lipolysis in adipose tissue during sepsis

city: Minneapolis

first: Anna

last: Carey

address: 312 Church Street SE

department: Biochemistry, Molecular Biology, and Biophysics

institute: University of Minnesota

summary: Noncanonical lipolysis induced by inflammatory cytokines or toll-like receptor ligands is required for the regulation of inflammation during endotoxemia and sepsis. Canonical lipolysis induced by catecholamines declines during aging, but the extent to which the noncanonical pathway of lipolysis is active during aging remains unknown. The immune compartment of visceral white adipose tissue (vWAT) changes during aging, including an expansion of lymphocytes, pro-inflammatory macrophage polarization, and an increase in chronic low-grade inflammation, all of which influence canonical lipolysis in old vWAT. Therefore, we aimed to define the extent to which immune cells from older hosts influence noncanonical lipolysis induced by sepsis. Here we show that models of polymicrobial sepsis and lipopolysaccharide (LPS)-induced endotoxemia induce vWAT lipolysis in young mice but fail to activate lipolytic pathways in vWAT from old mice. Characterization of vWAT B cells revealed an accumulation of dysfunctional B1 B cells and an amplified inflammatory signature induced by LPS in old B1 B cells compared to old B2 B cells. Short term depletion of B2 B cells from old mice and adoptive transfer of peritoneal B cells from old mice into young recipient mice were insufficient to alter LPS-stimulated lipolysis. However, life-long deficiency of B cells increased LPS-stimulated lipolysis, suggesting the suppressive role of B cells may be indirect and requires other cell types. Pro-inflammatory macrophages and NLRP3 inflammasome activation were significantly reduced in the old B cell knockout mice. These data collectively reveal a decline in noncanonical lipolysis in vWAT during aging that is regulated by resident immune cells. Additionally, our study suggests the B cell-macrophage signaling axis may offer new approaches to resolve metabolic dysfunction in aged vWAT and attenuate septic severity in older individuals.

overall_design: Bulk RNA sequencing on B1 (CD11b+) and B2 (CD11b-) B cell subsets isolated from the vWAT of 20 month old female mice challenged with PBS or 0.1 mg/kg LPS for 4 hours.

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