title: Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Nuclear Factor I Family Proteins for Medulloblastoma Progression

city: Paris

first: Jacob

last: Torrejon Diaz

address: 26 Rue d'Ulm

country: France

institute: Curie Institute

summary: The cancer-specific epigenome is the critical scaffold on which genetic programs work to positively promote cancer growth and progression. Understanding and appropriately disrupting this epigenome will lead to the discovery of new, more extensive and effective therapies in addition to conventional personalized medicine that relies on genomic mutations. However, the epigenomic changes during the process from normal cells to cancer formation as well as the molecules involved in the maintenance of the aberrant epigenome are still poorly characterized, and the development of epigenome-based therapeutics is therefore undeniably stagnant. To address this issue, we here focus on SHH-subgroup medulloblastoma, a representative pediatric brain tumor for which we developed a reliable mouse model to capture the epigenomic changes that cerebellar granule cells, the cells of origin, undergo during tumorigenesis. By comparing the epigenomes of the different stages of transforming cells, we identified NFI family of developmental factors as oncogenic regulators in the epigenome of pre-cancerous and cancerous cells, which they also contribute to maintain. Furthermore, we report pharmacological experiments demonstrating that inhibition of NFIB methylation blocks tumor growth and increases sensitivity to molecularly targeted drugs by disrupting the cancer epigenome. Thus, this study is a unique example of how epigenomic studies of cancer have led directly to therapeutic insights, and similar approaches in various cancers would accelerate the establishment of novel therapies.

overall_design: To identify the transcriptional targets of NFIA and NFIB in the context of Sonic Hedgehog medulloblastoma (SHH-MB), we performed knockdown of these genes using shRNAs and checked which genes were differentially expressed. The knockdown was performed in two human SHH-MB PDXs and on cultured murine SHH-MB cells derived from a spontaneous SHH-MB mouse model, in order to allow cross-species comparisons. The data from RNA-seq were also crossed and integrated with ATAC-seq and CUT&Tag data to identify direct targets of NFIA and NFIB.


title: Single-cell RNA sequencing of patient-derived xenograft meningiomas

status: Public on May 03 2024

city: San Francisco

first: Abrar

last: Choudhury

state: California

country: USA

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

summary: We report single-cell RNA sequencing of 23 PDX meningiomas that underwent radiation therapy, were treated with a Notch3 neutralizing antibody, or overexpressed Notch3.

overall_design: A total of 23 PDX meningiomas were sequenced, with 5 unradiated controls and 3 replicates each of Notch3 overexpression alone, Notch3 overexpression with radiation at an early timepoint, Notch3 overexpression at a late timepoint, Notch3 neutralizing antibody alone, controls with radiation at an early timepoint, and controls with radiation at a late timepoint.

first: Martha

middle: A

last: Cady

first: David

middle: R

last: Raleigh


title: Functional multi-organelle units control inflammatory lipid metabolism of macrophages

city: Freiburg im Breisgau

first: Angelika

last: Rambold

address: Stübeweg 51

department: Department of Developmental Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Eukaryotic cells contain several membrane-separated organelles to compartmentalize distinct metabolic reactions. However, it has remained unclear how these organelle systems are coordinated, when cells adapt metabolic pathways to support their development, survival or effector functions. Here we present OrgaPlexing, a multispectral organelle imaging approach for the comprehensive mapping of six key metabolic organelles and their interactions. We use this analysis on macrophages, immune cells that undergo rapid metabolic switches upon sensing bacterial and inflammatory stimuli. Our results identify lipid droplets (LDs) as primary inflammatory responder organelle, which forms three- and four-way interactions with other organelles. While clusters with endoplasmic reticulum (ER) and mitochondria (M-ER-LD unit) help supply fatty acids for LD growth, the additional recruitment of peroxisomes (M-ER-P-LD unit) supports fatty acid efflux from LDs. Interference with individual components of these units has direct functional consequences for inflammatory lipid synthesis. Together, we show that macrophages form functional multi-organellar units (MOUs) to support metabolic adaptation, and provide an experimental strategy to identify organelle-metabolic signaling hubs.

overall_design: bone marrow-derived mouse macrophages treated with LPS/IFNg for 0, 2, 6 and 24 hours

first: Julia

last: Zimmermann

first: Ward

last: Deboutte

first: Thomas

last: Manke

first: Anna

last: Bremser


title: Single-cell RNA sequencing of human meningioma

summary: We report single-cell RNA sequencing of 1 human meningioma sample with NF2 loss

overall_design: One tissue samples from a human meningioma patient was analyzed.


title: In vitro pigmentation of human iPSC-derived retinal pigment epithelium cells is not indicative of their quality for cell transplantation

status: Public on May 04 2024

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

summary: Retinal pigment epithelium (RPE) cells show heterogeneous level of pigmentation when cultured in vitro. We used Automated Live imaging and cell Picking System (ALPS) with single cell RNA sequencing (scRNA-seq) to analyze the correlation between color intensities and gene expression profiles of human-induced pluripotent stem (iPS) cell-derived RPE cells.

overall_design: The color intensity of each RPE cell and its gene expression profile were obtained by the Automated Live imaging and cell Picking System (ALPS) combined with scRNA-seq.

first: Yoko

middle: N

last: Futatsugi

first: Jianshi

last: Jin

first: Taisaku

last: Ogawa

first: Noriko

last: Sakai

first: Akiko

last: Maeda

first: Ken-ichi

last: Hironaka

first: Masakazu

last: Fukuda

first: Hiroki

last: Danno

first: Yuji

last: Tanaka

first: Seiji

last: Hori

first: Masayo

last: Takahashi


title: The application of ChIP-seq to study LSD1 and hematopoietic TF binding on enhancers upon LSD1 inhibition.

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We conducted ChIP-seq studies to study the effects of LSD1 inhibition on ehancer activation, LSD1 and hematopoietic TF binding in SET-2 cell line.

overall_design:
ChIP-seq was performed in duplicate for H3K27ac, LSD1 and hematopoietic TFs following vehicle or GSK-LSD1 treatment in SET-2 cells.
Please note that processed data generated from both replicates is linked to the corresponding Rep1 sample records.

middle: B


title: Targeted site integration in plants using a transposon system [insertion-seq]

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

summary: Genome editing tools with high precision are key to develop improved crops but current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone. Transposable elements (TEs) evolved to insert their DNA seamlessly into genomes, albeit in a quasi-random pattern. We developed a genome engineering tool that controls the TE insertion site and subsequently the delivery of any cargo attached to this TE. Using our tool, we demonstrated sequence-specific targeted delivery (guided by the CRISPR gRNA) of enhancers, an open reading frame and gene expression cassette into the genome of the model plant Arabidopsis, and we translated this technology to the crop soybean. We have engineered a ‘junk’ TE into a useful and accessible toolkit that enables the sequence-specific targeting of custom DNA into plant genomes.

sample_organism:
Arabidopsis thaliana
Glycine max

platform_organism:
Arabidopsis thaliana
Glycine max

overall_design: Insertion-Seq was performed to detect genome-wide insertion sites of the transposable element mPing in various transgenic lines of both Arabidopsis and soybean. Custom libraries were constructed using an adapted HtStuf protocol (PMID: 33228280) with modifications as mentioned below.

first: Peng

last: Liu

first: Kaushik

last: Panda

first: R

middle: K


title: Notch3 drives meningioma tumorigenesis and resistance to radiotherapy

first: Abrar

last: Choudhury

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

sample_organism:
Homo sapiens
Canis lupus familiaris

platform_organism:
Homo sapiens
Canis lupus familiaris

overall_design: Refer to individual Series


title: Targeted site integration in plants using a transposon system [Amplicon]

overall_design: Specific PCR amplicons from multiple samples capturing the junctions between mPing and the PDS3 locus of targeted insertion were investigated by using high throughput sequencing.


title: Targeted site integration in plants using a transposon system


title: Combination of a SOS1-KRAS interaction inhibitor with a KRASG12C inhibitor combination can address intrinsic and acquired resistance leading to stronger and more durable response (RNA-Seq).

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary:
To investigate the transcriptomic changes associated with KRAS G12C inhibitor Adagrasib resistance and Adagrasib + SOS1 inhibitor (BI-3406) or Adagrasib + EGFR inhibitor (Cetuximab) combination treatment to overcome resistance.
We performed differential gene expression analysis using RNA-seq generated from cell line derived xenograft (CDX) in vivo models. We compared different treatment conditions with DMSO treated condition.

overall_design: CDX models were generated using NSCLC cell line NCI-H2122 and CRC cell line SW837. For each CDX category, expression data with DMSO treated and either single agent and combination treatment was generated.

first: Venu

last: Thatikonda

first: Oliver

last: Bergner

first: Donat

last: Alpar

first: Marco

last: Hofmann


title: Combination of a SOS1-KRAS interaction inhibitor with a KRASG12C inhibitor combination can address intrinsic and acquired resistance leading to stronger and more durable response (Quant-Seq).


title: Combination of a SOS1-KRAS interaction inhibitor with a KRASG12C inhibitor combination can address intrinsic and acquired resistance leading to stronger and more durable response


title: Single-cell RNA sequencing of canine meningiomas

summary: We report single-cell RNA sequencing of 54,607 cells from 3 canine meningioma and 2 canine dura samples.

overall_design: A total of 5 tissue samples from 3 canine meningioma patients were analyzed. Two patients had dura tissue from their meninges analyzed as a normal tissue control.

first: Martha

last: Cady

first: David

last: Raleigh


title: Tuft cell-derived acetylcholine promotes epithelial chloride secretion and intestinal helminth clearance

status: Public on May 02 2024

city: Seattle

first: Jakob

middle: Helmuth

last: von Moltke

state: Washington

address: 750 Republican Street

department: Immunology

institute: University of Washington

summary: Epithelial cells secrete chloride to regulate water release at mucosal barriers, supporting both homeostatic hydration and the “weep” response that is critical for Type 2 immune defense against parasitic worms (helminths). Epithelial tuft cells in the small intestine sense helminths and release cytokines and lipids to activate Type 2 immune cells, but whether they regulate epithelial secretion is unknown. Here we found that tuft cell activation rapidly induced epithelial chloride secretion in the small intestine. This response required tuft cell sensory functions and tuft-cell-derived acetylcholine (ACh), which acted directly on neighboring epithelial cells to stimulate chloride secretion, independent of neurons. Maximal tuft cell-induced chloride secretion coincided with immune restriction of helminths, and clearance was delayed in mice lacking tuft cell-derived ACh, despite normal Type 2 inflammation. Thus, we have uncovered an epithelium-intrinsic response unit that uses ACh to couple tuft cell sensing to the secretory defenses of neighboring epithelial cells.

overall_design: Small intestinal tuft cells were sorted from naïve mice expressing an Il25-RFP reporter and a Chat-GFP reporter. Tuft cells were identified as CD45- EPCAM+ and IL25-RFP+ and then sorted into Chat-GFP+ and Chat-GFP- populations for RNA sequencing

first: Tyler

last: Billipp

first: John

last: McGinty


title: Euo is a developmental regulator that represses late genes and activates midcycle genes in C. trachomatis

city: Irvine

first: Syed

middle: Meraj Azhar

last: Rizvi

address: University of California Irvine

department: Microbiology and Molecular Genetics

country: India

institute: University of California Irvine

summary: The pathogenic bacterium Chlamydia reproduces via an unusual intracellular developmental cycle in which it converts from a dividing form (reticulate body or RB) to an infectious form (elementary body or EB). The transcription factor Euo has been proposed as a developmental regulator in C. trachomatis because it repressed a number of late chlamydial promoters, which are transcribed during RB-to-EB conversion. To define the Euo regulon, we performed a genome-wide study that combined Euo DNA Immunoprecipitation-seq (DIP-seq) studies with RNA-seq analysis of HeLa cells infected with an Euo-overexpressing C. trachomatis strain. We demonstrate that Euo directly regulates ~7% of C. trachomatis genes. However, only about half were downregulated (28/61; 45.9%) by Euo overexpression while paradoxically the other half were upregulated (33/61; 54.1%). Intriguingly, all downregulated genes were late genes, while the majority of upregulated genes were midcycle genes, which are transcribed during RB replication. DIP analysis showed that Euo occupancy sites were restricted to the core promoter region for downregulated genes, but were located over a wider region immediately upstream of the promoter for upregulated genes. We also found that Euo controls its own expression through a negative feedback mechanism. Electron microscopy analysis of cells infected with the Euo-overexpressing strain showed fewer EBs, consistent with a block in RB-to-EB conversion, as well as fewer and larger RBs. Together, these findings broaden the role of Euo as a developmental regulator that functions as both a transcriptional repressor of late genes and a transcriptional activator of midcycle genes in C. trachomatis.

overall_design: Total RNA from C. trachomatis infected HeLa cells purified, rRNA depleted, total cDNA constructed and sequenced

first: Owais

middle: H

last: Rashid

middle: M

first: Ming

last: Tan


title: Mouse Vascularized Adipose Spheroids: An Organotypic Model for Thermogenic Adipocytes

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Adipose tissues, particularly beige and brown adipose tissue, play crucial roles in energy metabolism. Brown adipose tissues’ thermogenic capacity and the appearance of beige cells within white adipose tissue have spurred interest in their metabolic impact and therapeutic potential. Brown and beige fat cells, activated by factors like cold exposure, share mechanisms that drive non-shivering thermogenesis. Understanding their behavior requires sophisticated, yet universal in vitro models that replicate the complex microenvironment and vasculature of adipose tissues. Here we present mouse vascularized adipose spheroids of the stromal vascular microenvironment from inguinal white adipose tissue. We show that scaffold embedding improves vascular sprouting, enhances spheroid growth, and upregulates adipogenic markers. Transcriptional profiling via RNA sequencing revealed distinct metabolic pathways upregulated in our vascularized adipose spheroids, with increased expression of genes involved in glucose metabolism, lipid metabolism, and thermogenesis. Functional assessment demonstrated increased oxygen consumption in vascularized adipose spheroids compared to 2D cultures, which was further enhanced by β-adrenergic receptor stimulation via isoproterenol correlating with elevated β-adrenergic receptor expression. Moreover, stimulation with the naturally occurring adipokine, FGF21, induced Ucp1 mRNA expression in the vascularized adipose spheroids. In conclusion, our vascularized inguinal white adipose tissue spheroids provide a physiologically relevant platform to study how the stromal vascular microenvironment shapes adipocyte responses and influence activated thermogenesis in beige adipocytes.

overall_design:
We investigated whether the stromal vascular fraction from mouse inguinal white adipose tissue cultured in 3D as spheroids were providing a more favorable adipogenic microenvironment than 2D cultures.
We utilized RNA sequencing to compare transcriptional profiles between 3D cultures and conventional in vitro differentiated adipocytes in 2D cultures.
Furthermore, we stimulated 2D and 3D cultures with Isoproteronol, a pan beta-adrenergic agonist to induce thermogenesis and compared transcriptional profiles using RNA sequencing.

first: Laura

middle: I

last: Davidsen

first: Carolina

middle: E

last: Hagberg

first: Victor

last: Goitea

first: Stine

last: Lundby

first: Steen

last: Larsen

first: Morten

middle: F

last: Ebbesen

first: Jan-Wilhelm


title: Characterisation of the epidermal diurnal transcriptome of mice with K14-Cre-driven Bmal1 knockout

city: Barcelona

first: Thomas

last: Mortimer

address: Carrer Baldiri Reixac 10-12

country: Spain

institute: IRB Barcelona

summary: To preserve a state of health, mammals employ an integrated network of molecular oscillators to drive daily rhythms of tissue-specific homeostatic processes. Importantly, the output, structure and coherence of this network is compromised by physiological ageing, disease and lifestyle changes. Yet, the key signalling nodes in this network, their underlying mechanisms of communication, and potential for therapeutic intervention, remain undefined. To dissect this system, we construct a minimal clock network consisting of two communicating nodes: the peripheral epidermal clock and central brain clock. We show that communication between the brain and epidermal clocks is sufficient for wild-type core clock activity and specific homeostatic processes, but inputs from other clock nodes are essential for full daily physiology. Unexpectedly, we find evidence that the epidermal clock selectively suppresses or interprets systemic signals to ensure coherence of specific homeostatic processes, identifying an unrecognised gatekeeper role for peripheral clocks. Together, we introduce a novel approach for dissecting a tissues daily physiology, and in turn identify key signalling nodes required to maintain epidermal homeostasis.

overall_design: The diurnal transcriptome of the skin epidermis was profiled for mice in which circadian clock activity was absent in the skin epidermis, but present in all other tissues. Profiling was undertaken by performing RNA-seq of epidermis samples taken at four hour intervals throughout the day (four biological replicates per timepoint). Subsequently, a comparison with gene expression rhythmicity in WT epidermis was performed using the DryR algorithm.


title: Decoding Endothelial MPL and JAK2V617F Mutation: Insight into Cardiovascular Dysfunction in Myeloproliferative Neoplasms

city: Stony Brook

first: Huichun

last: Zhan

state: NY

address: 101 Nicolls Rd

institute: Stony Brook Univeristy

summary: Background: Patients with JAK2V617F-positive myeloproliferative neoplasms (MPNs) and clonal hematopoiesis of indeterminate potential (CHIP) face a significantly elevated risk of cardiovascular diseases (CVDs). Endothelial cells (ECs) carrying the JAK2V617F mutation have been detected in many MPN patients. In this study, we investigated the molecular basis for the high incidence of cardiovascular complications in MPN patients. Methods: We investigated the impact of endothelial JAK2V617F mutation on CVD development using both transgenic murine models and MPN patient-derived induced pluripotent stem cell lines. Results and Conclusions: Our investigations revealed that JAK2V617F mutant ECs promote CVDs by impairing endothelial function and undergoing endothelial-to-mesenchymal transition (EndMT). Importantly, we discovered that inhibiting the endothelial thrombopoietin receptor MPL suppressed JAK2V617F-induced EndMT and prevented cardiovascular dysfunction caused by mutant ECs. Notably, the endothelial MPL receptor is not essential for the normal physiological regulation of blood cell counts and cardiac function, rendering it a promising therapeutic target for preventing or ameliorating cardiovascular complications in patients with MPNs.

overall_design: To gain insight into the transcriptomic changes associated with the JAK2V617F mutation and MPL inhibition on endothelial cells, we performed RNA sequencing on untreated and AMM2 MPL inhibitor treated endothelial cells of wild-type and JAK2V617F mutant mice.

first: Haotian

last: Zhang

first: Nicholas

last: Kafeiti

first: Kyla

last: Masarik

first: Sandy

last: Lee

first: Xiaoxi

last: Yang

first: Haoyi

last: Zheng


title: Transcriptomes of high-grade serous ovarian cancer cell lines cultured in monolayer and in spheroids.

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: HGSOC cancer cell lines OvCAR3 and G164 were cultured in monolayer and spheroids and subjected to RNA-sequencing.

overall_design: RNA sequencing on the G164 and OvCAR3 HGSOC malignant cell lines grown in monolayer (n = 2) or in spheroids (n =2).

first: Joash

middle: D

last: Joy

first: Frances

last: Balkwill


title: CRWN nuclear lamina components maintain the H3K27me3 landscape and promote successful reproduction in Arabidopsis

first: JUNSIK

last: CHOI

address: 455 MainSt

institute: WHITEHEAD INSTITUTE

summary: The nuclear lamina, a crucial sub-nuclear protein matrix, maintains nuclear structure and genomic function. Our study centers on the Arabidopsis lamina component CROWDED NUCLEIs (CRWNs), unveiling their extensive role in the development of the reproductive system with a specific focus on the endosperm, which is pivotal in seed development. We showed that quadruple crwn null gametophytes exhibit limited viability, and crwn1 crwn2 (crwn1/2) mutations lead to defective seeds often having enlarged chalazal cysts and variable timing of endosperm cellularization. crwn1/2 endosperm also exhibit perturbations of level of tri-methylation of lysin 27 on histone H3 (H3K27me3) and transcriptomics. In addition, we found that PHERES1 (PHE1) targets and defense-related genes are mis-regulated in crwn1/2 endosperm, showing that both development and stress responses are affected by CRWNs simultaneously. The data also suggest that CRWNs affect various aspects of physiology of both vegetative and reproductive tissues but there are tissue-specific roles.

overall_design: To assess effect of loss of plant nuclear lamina protein CRWN1 and CRWN2 in endosperm, H3K27me3 CUT&RUN libraries for WT and crwn1/2 mutants in both endosperm (6C nuclei) and leaf tissues (combining 2,4,8,16C nuclei) were sequenced. mRNA-seq libraries were also sequenced for WT and crwn1/2 mutants in endosperm (6C nuclei). mRNA-seq libraries for leaves are available as 'SRA BioProject ID PRJNA485018'.

first: Junsi

last: Choi

first: Mary

last: Gehring


title: Spatial transcriptomics of mouse spleens during malaria convalescence.

city: Melbourne

first: Hyun Jae

address: 792 Elizabeth Street

department: Department of Microbiology and Immunology

country: Australia

institute: University of Melbourne

summary: Naturally-acquired immunity to blood-stage malaria is associated with several effector CD4 + T subsets including germinal centre (GC) Tfh, Th1 and Tr1 cells. Here, we mapped the locations of effector CD4+ T cell subsets during post-Plasmodium convalescence using Slide-seqV2.

overall_design: Mice were infected with Plasmodium chabaudi chabaudi AS (PcAS) parasites and mice were administered with artesunate (intermittent artesunate therapy - IAT) at Day 7. At Day 30, whole spleens were recovered and fresh frozen to generate Slide-seqV2 datasets.

first: Hyun

middle: J

first: Cameron

last: Williams

first: Irving

last: Barrera

first: Marcela

last: Moreira


title: Bidirection activation of stem-like programs in metastatic cancer and alveolar type II cells within the niche

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

institute: The Francis Crick Institute

summary: A key step for metastatic outgrowth involves the generation of a deeply altered microenvironment (niche) that supports the malignant behavior of cancer cells. The complexity of the metastatic niche has posed a significant challenge in elucidating the underlying programs driving its origin. Here, by focusing on early stages of breast cancer metastasis to the lung in mice, we describe a cancer-dependent chromatin remodeling and activation of developmental programs in alveolar type 2 (AT2) cells within the niche. We show that metastatic cells can prime AT2 cells into a reprogrammed multilineage state. In turn, this cancer-induced reprogramming of AT2 cells promoted stem-like features in cancer cells and enhanced their initiation capacity. In conclusion, we propose the concept of "reflected stemness" as an early phenomenon during metastatic niche initiation, wherein metastatic cells reprogram the local tissue into a stem-like state that enhances intrinsic cancer-initiating potential, creating a positive feedback loop where tumorigenic programs are amplified.

overall_design:
ATAC-seq data of AT2 cells in the distal lung or the metastatic niche of breast and colon cancer pulmunary metastasis.
RNA-seq data of EpCAM+ cells isolated from the distal lung, the metastatic niche of 4T1 shControl and  of 4T1 shSox9 cell's niche.
RNA-seq of 4T1 cancer cells growing in the dish (in vitro) and 4T1 cancer cells isolated from the lungs of BALB/c mice (in vivo) 7 days after tail vein injection.

first: Felipe

middle: S

last: Rodrigues


title: scRNA-seq of mouse Plasmodium-specific TCR-transgenic CD4+ T cells prior to and after re-infection.

summary: Naturally-acquired immunity to blood-stage malaria is associated with several effector CD4 + T subsets including germinal centre (GC) Tfh, Th1 and Tr1 cells. Children in malaria-endemic regions can experience repeated Plasmodium infections over short periods of time; yet the effect of reinfection on multiple co-existing effector and memory subsets remains unclear. Here, we tracked antigen-experienced TCR-transgenic CD4+ T cells during Plasmodium re-infection in mice using scRNA-seq.

overall_design: Mice were infected with Plasmodium chabaudi chabaudi AS (PcAS) parasites and mice were administered with artesunate (intermittent artesunate therapy - IAT) at Day 7. At Day 28, mice were re-infected with PcAS parasites. Plasmodium-specific CD4+ T cells were recovered at Day 28, and Days 1, 2, and 3 after re-infection to undergo processing and generate scRNA-seq dataset.

first: Megan

last: Soon

first: Jessica

last: Engel


title: scRNA-seq + TCR-seq of mouse polyclonal CD4+ T cells prior to and after re-infection.

summary: Naturally-acquired immunity to blood-stage malaria is associated with several effector CD4 + T subsets including germinal centre (GC) Tfh, Th1 and Tr1 cells. Children in malaria-endemic regions can experience repeated Plasmodium infections over short periods of time; yet the effect of reinfection on multiple co-existing effector and memory subsets remains unclear. Here, we tracked antigen-experienced polyclonal CD4+ T cells during Plasmodium re-infection in mice using scRNA-seq/TCR-seq.

overall_design: Mice were infected with Plasmodium chabaudi chabaudi AS (PcAS) parasites and mice were administered with artesunate (intermittent artesunate therapy - IAT) at Day 7. At Day 27, mice were re-infected with PcAS parasites. CD4+ T cells were recovered at Day 30, and Day 3 after re-infection to undergo processing and generate scRNA-seq dataset.

middle: L


title: CITE-seq of LSK cells from aged mice after long-term iron chelator regimen

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Department of Cell Biology

institute: Albert Einstein College of Medicine

summary: We found that iron chelation restored functional defects in aged HSC, including engraftment potential and platelet bias. To gain molecular insights into iron-dependent mechanism for sustaining HSC identity during aging, we performed Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) with lineage (Lin)− Sca-1+ cKit+ (LSK) cells isolated from aged mice after long-term regimens with iron chelator Deferoxamine or vehicle control.

overall_design: To investigate the effect of long-term iron chelation during HSC aging, mice aged ~6 months were subjected to iron chelator (Deferoxamine, 50 mg/kg) or vehicle control (HBSS) daily regimens for consecutive 7 days, repeated every 4 weeks for a total of 13 months. Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) was performed to examine the molecular regulation by iron chelation. Briefly, lineage depleted bone marrow cells were stained for 30 min with antibodies for lineage, Sca-1, c-Kit, TotalSeq-C Mouse Universal Cocktail and sample-specific hashing antibodies. Stained cells were then sorted on Moflo Astrios EQ (Beckman Coulter), and approximately 20,000 Lin-Sca1+ckit+ (LSK) cells were acquired per sample. Single cell CITE-seq libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics, Pleasanton, CA, USA). FACS-sorted LSK cells from bone marrow were stained and pooled in equal amounts prior to chip loading. Libraries were constructed according to manufacturer instructions. Libraries were purified and paired-end sequenced using NovaSeq 6000 S4 Reagent Kit v1.5 with 150 cycles (Illumina, San Diego, CA, USA).

first: Yun-Ruei

last: Kao


title: scRNA-seq of CD4+ T cells prior to and after re-infection.

last: Lee


title: Vascular architecture regulates mesenchymal stromal cell heterogeneity via P53-PDGF signaling in the mouse incisor

city: Los Angeles

first: Tingwei

last: Guo

state: CA

address: 2250 Alcazar St

department: CCMB

institute: usc

summary:
To investigate the the role of Trp53 in the adult mouse incisor
We performed gene expression profiling analysis using data obtained from RNA-seq of 6 samples

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and Trp53 mutant samples


title: Propionate and butyrate counteract renal damage and progression to chronic kidney disease

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary:
Background: Short-chain fatty acids (SCFAs), mainly acetate, propionate and butyrate, are produced by gut microbiota through fermentation of complex carbohydrates that cannot be digested by the human host. They affect gut health and can contribute at the distal level to the pathophysiology of several diseases, including renal pathologies.
Methods: SCFA levels were measured in chronic kidney disease (CKD) patients (n = 54) at different stages of the disease and associations with renal function and inflammation parameters were examined. The impact of propionate and butyrate in pathways triggered in tubular cells under inflammatory conditions was analysed using genome-wide expression assays. Finally, a pre-clinical mouse model of folic acid-induced transition from acute kidney injury to CKD was used to analyse the preventive and therapeutic potential of these microbial metabolites in the development of CKD.
Results: Faecal levels of propionate and butyrate in CKD patients gradually reduce as the disease progresses, and do so in close association with established clinical parameters for serum creatinine, blood urea nitrogen and the estimated glomerular filtration rate. Propionate and butyrate jointly downregulated the expression of 103 genes related to inflammatory processes and immune system activation triggered by TNF-α in tubular cells. In vivo, the administration of propionate and butyrate, either before or soon after injury, respectively prevented and slowed the progression of damage. This was indicated by a decrease in renal injury markers, the expression of pro-inflammatory and pro-fibrotic markers, and recovery of renal function over the long term.
Conclusions: Propionate and butyrate levels are associated with a progressive loss of renal function in CKD patients. Early administration of these SCFAs prevents disease advancement in a pre-clinical model of acute renal damage, demonstrating their therapeutic potential independently of the gut microbiota.

overall_design: Samples were analyzed by duplicate using biological repliques. Untreated  cells were used as control cells. Cells stimulated with TNF-α (5ng/ml) for 3h  were used to induce inflammation. Propionate (15mM) and butyrate (3mM) were added for 24h, before and after activation of the cells with TNF-α. Analyzed conditions were: untreated and unstimulated cells. cells estimulated with TNF-α, cells stimulated with TNF-α and treated with propionate and butyrate, before and after activation of the inflammation with TNF-α.

first: Viviana-Diaz

last: Corte

first: Ramon

last: Rodriguez Lopez

first: Juan

last: Lozano

first: Maria

last: Sainz Alvarez

first: Beatriz

last: Suarez Alvarez

first: Carlos

last: López Larrea


title: Liver-specific DICER1 syndrome model mice develop cystic liver tumors with defective primary cilia

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

institute: Tokyo Medical University

summary: DICER1 syndrome is a tumor predisposition syndrome caused by familial genetic mutations in DICER1. Pathogenic variants of DICER1 have been discovered in many rare cancers, including cystic liver tumors. However, the molecular mechanisms underlying liver lesions induced by these variants remain unclear. In the present study, we sought to gain a better understanding of the pathogenesis of these variants by generating a mouse model of liver-specific DICER1 syndrome. The mouse model developed bile duct hyperplasia with fibrosis, similar to congenital hepatic fibrosis, as well as cystic liver tumors resembling those in Caroli's syndrome, intrahepatic cholangiocarcinoma, and hepatocellular carcinoma. Interestingly, the mouse model of DICER1 syndrome showed abnormal formation of primary cilia in the bile duct epithelium, which is a known cause of bile duct hyperplasia and cyst formation. These results indicated that DICER1 mutations contribute to cystic liver tumors by inducing defective primary cilia. The mouse model generated in this study will be useful for elucidating the potential mechanisms of tumorigenesis induced by DICER1 variants and for obtaining a comprehensive understanding of DICER1 syndrome.

overall_design: RNA profiles of liver from DICER1 syndrome model mouse. 4-weeks-old, female, two WT and two DICER1 syndrome model mice.

first: Masahiko

last: Kuroda


title: Characterisation of the epidermal diurnal and circadian transcriptomes of mice with tissue-specific circadian clock activity

first: Thomas

last: Mortimer

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

overall_design: Refer to individual Series


title: Characterisation of the epidermal diurnal transcriptome of mice with tissue-specific circadian clock activity [LD]

overall_design: The diurnal transcriptome of the skin epidermis was profiled for mice in which circadian clock activity was present only in the skin epidermis, only in the brain, only in the skin and brain, or all tissues. Profiling was undertaken by performing RNA-seq of epidermis samples taken at four hour intervals throughout the day (four biological replicates per timepoint), and subsequently the algorithms JTK_CYCLE and BIOCYCLE were used to generate a consensus diurnal transcriptome for each condition. In addition, the algorithm DryR was used to identify groups of genes with specific rhythmic parameters either shared or differing between the different conditions.


title: CD40 stimulation + dasatinib treatment of chronic lymphocytic leukemia (CLL) cells

status: Public on May 01 2024

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC (AMC)

summary: In this experiment we in vitro activated CLL cells on a layer of fibroblasts expressing CD40L (3T40) in the presence of 100 nM Dasatinib for 48 hours. After the 48 hours, cells were taken off the fibroblasts and sorted for viable CD19+ cells. Then we performed RNA sequencing.

overall_design: This experiment was analyzed together with another GEO submission (GSE201341), the comparison was between 3T40 and 3T40 + DAS conditions.

first: Jacco

middle: A

last: van Bruggen

first: Arnon

middle: P

last: Kater


title: A spatial transcriptomics based Label-free Method for Assessment of Human Stem Cell Distribution and Effects in a Mouse Model of Lung Fibrosis

city: Seoul

first: Jeongbin

last: Park

state: Not US or Canada

address: 23, Sinhyeon-ro 38beon-gil, Siheung-si, Gyeonggi-do, 14957, Rep. of KOREA

department: Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea

country: South Korea

institute: Seoul National University

summary: Recently, cell therapy has emerged as a promising treatment option for various disorders. Given the intricate mechanisms of action (MOA) and heterogenous distribution in target tissues inherent to cell therapy, it is necessary to develop more sophisticated, unbiased approaches to evaluate the distribution of administered cells and the molecular changes at a microscopic level. This study introduces a label-free approach for assessing the tissue distribution of administered human mesenchymal stem cells (hMSCs) and their MOA, leveraging spatially resolved transcriptomics (ST) analysis. The hMSCs were introduced into a mouse model with lung fibrosis, followed by the manipulation of ST to visualize the spatial distribution of hMSCs within the tissue. This was achieved by capitalizing on interspecies transcript differences between human and mouse. Furthermore, the method allowed for the examination of molecular changes associated with the spatial distribution of hMSCs. Therefore, our method has the potential to serve as an effective tool for various cell-based therapeutic agents.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We administered human mesenchymal stem cells (hMSC) in a mouse model of lung fibrosis and presented a method for evaluating both the tissue-level distribution of the administered stem cells and their effect on treated tissue by using Visium Spatial Transcriptomics.

first: Dongjoo

first: Jae

first: Daeseung

first: In

last: Song

first: Hyun

first: Hongyoon

last: Choi

first: Hyung-Jun

last: Im


title: Single cell RNA-seq of mouse HSC treated with iron chelator deferoxamine (DFO)

first: Britta

last: Will

summary: We characterized longer-term effects of iron homeostasis activation on hematopoietic stem cells by characterizing transcriptomic chagnes at the singe cell level 48hrs after iron chelatior treatement (vehicle treatemnt as controls).

overall_design: For isolation of mouse HSC, bone marrow cells were isolated from tibiae, femurs, pelvic bones and vertebrae of wildtype C57/B6 mice at the age of 6 to 8-weeks. Lineage-depleted bone marrow cells from 8 mice were pooled and prospective HSC (Lin−Sca-1+c-Kit+CD150+CD48−) were sorted on MoFlo Astrios (Beckman Coulter). Thereafter, FACS-sorted HSC were exposed to iron chelator (DFO, Sigma) or vehicle (water) for 48 hours. Treated cells were collected and viability of >95% was determined by trypan blue exclusion. Twenty thousand (20,000) cells from each treatment group were then subjected to 10x Genomics platform for library preparation. Following quality control assessment with Agilent 2100 Bioanalyzer, approximately 50ng libraries were sequenced on BGISEQ-500 platform.

first: Yun-Ruei

last: Kao


title: Origins and diversity of pan-isotype human bone marrow plasma cells

city: Boston

first: Duane

middle: R.

last: Wesemann

address: 77 Avenue Louis Pasteur

department: Medicine, Division of Allergy and Clinical Immunology

institute: Brigham and Women's Hospital

summary: Bone marrow plasma cells (BMPCs) produce durable, infection-resistant IgM, IgG, and IgA antibodies, but in some cases, pro-allergic IgE. Despite this, BMPC sources are unclear. We charted single BMPC transcriptional and clonal heterogeneity in peanut-allergic and non-allergic humans across CD19 protein expression—due to CD19’s inverse correlation to BMPC longevity. Transcriptional and clonal diversity revealed distinct functional modules. Additionally, distributions of somatic hypermutation and intraclonal antibody sequence variance suggest CD19low and CD19high BMPCs arise from recalled memory and germinal center B cells, respectively. Most IgE BMPCs were from peanut-allergic individuals; some bound peanut and potently prevented peanut-driven anaphylaxis in a mouse model. These findings shed light on BMPC origins and identify the bone marrow as a likely source for long-lived pathogenic IgE in peanut allergy.

overall_design: Human bone marrow samples were obtained from the iliac crest of food-allergic or non-allergic controls. Samples were RBC-lysed, magentically-erniched for CD138+ cells, and FACS sorted (DAPI-, IgD-, CD3-, CD14-, CD138+, CD38+). Some samples were further FACS-sorted into CD19low and CD19mid/high populations. Some samples also contain B cells magnetically-enriched with positive selection CD19 beads from peripheral blood.

first: Gaspar

last: Pacheco

first: Vishal

last: Rao

first: DuckKyun

last: Yoo

first: Shahab

last: Saghaei

first: Pei

last: Tong

first: Sachin

last: Kumar

first: Orlee

last: Marini-Rapoport

first: Zahra

last: Allahyari

first: Ali

last: Moghaddam

first: Romina

last: Esbati

first: Aida

last: Alirezaee

first: Sarita

middle: U

last: Patil

middle: R


title: CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Tail Fin Regeneration (RNA-Seq)

city: Rochester, NY

first: Phu

middle: T

last: Duong

state: New York

address: 601 Elmwood Ave

institute: University of Rochester

summary: The regenerative potential is governed by a complex process of transcriptional reprogramming, involving nuclear reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes influence this process remains only partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of epigenetic changes during of zebrafish caudal fin regeneration. Data generated from our protocol recapitulates results from previously published ChIP-Seq methods, requires far fewer cells as input, and significantly improves signal to noise ratios during profiling. We deliver high-resolution enrichment maps for H3K4me3 at 0 days post amputation (DPA) and 2DPA using tissue isolated from caudal fins. During regeneration, we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and H3K4me3 is lost at genes which are silenced. Remarkably, these epigenetic alterations partially recapitulate H3K4me3 patterns that occur normally in 24 hour old embryos. Our results demonstrate that the CUT&Tag method is an effective tool for profiling chromatin landscapes in regenerating fins, and that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programming.

overall_design: RNA sequencing and analysis in 24 hpf zebrafish caudal fin folds

first: Duong

last: Phu

first: Anjelica

last: Rodriguez-Parks

first: Junsu

last: Kang

first: Patrick

last: Murphy


title: CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Adult Tail Fin Regeneration (CUT&Tag)

summary: Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization   and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes contribute to this process remains partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of epigenetic changes during adult fin regeneration in zebrafish. Data generated from our protocol recapitulates results from previously published ChIP-Seq methods, requires far fewer cells as input, and significantly improves signal to noise ratios. We deliver high-resolution enrichment maps for H3K4me3 of uninjured and regenerating fin tissues. During regeneration, we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and H3K4me3 is lost at genes which become silenced  . Interestingly, these epigenetic reprogramming events recapitulate the H3K4me3 patterns observed in developing fin folds of 24 hour old zebrafish embryos. Our results indicate that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programs, demonstrating CUT&Tag to be an effective tool for profiling chromatin landscapes in regenerating tissues.

overall_design: Cleavage Under Targets and Tagmentation sequencing and analysis for histone H3K4me3 in 24 hpf zebrafish fin fold, 0dpa, and 2dpa zebrafish adult caudal fins


title: Myeloid and lymphoid lineage C9orf72 regulates the IL-17 inflammatory axis in mice

city: Cambridge

first: Francesco

last: Limone

state: Massachusetts

address: 7 divinity avenue, Bauer Laboratory 008

institute: harvard university

summary: The goal of this study was to identify cell types and pathways that contribute to autoimmunity and inflammation in C9orf72 loss of function mice.

overall_design: The experimental design involved age matched euthanasia of C9orf72 mutant and control mice paired with mass cytometry, flow cytometry, single cell sequencing, antibody-based therapeutic neutralization and cellular and biofluidic analyses. Pre-defined euthanasia criteria, age for euthanasia and sample sizes were determined based on power calculations and temporal characterization of systemic and neural inflammation in this model. Neutrophil counts, platelet counts, and rotarod performance was used to assign mice into isotype antibody or anti-IL17A antibody treatment groups so these disease measures did not differ between C9or72-/- mice prior to treatment. All subjects were coded so operators remained blinded to genotype during behavioral testing, tissue harvest and outcome assessments. Numbers of mice and well replicates are indicated in figure legends.

first: Alexander

last: Couto

first: Jin-Yuan

last: Wang

first: Yingying

last: Zhang

first: Blake

last: McCourt

first: Cerianne

last: Huang

first: Adina

last: Minkin

first: Marghi

last: Jani

first: Sarah

last: McNeer

first: James

last: Keaney

first: Gaëlle

last: Gillet

first: Rodrigo

last: Lopez Gonzalez

first: Wendy

last: Goodman

first: Irena

last: Kadiu

first: Kevin

last: Eggan

first: Aaron

last: Burberry


title: CUT&Tag Reveals a Return of Embryonic H3K4me3 Patterns During Zebrafish Tail Fin Regeneration

first: Phu

last: Duong


title: Characterisation of the epidermal circadian transcriptome of mice with tissue-specific circadian clock activity [DD]

first: Thomas

last: Mortimer

summary: To preserve a state of health, mammals employ an integrated network of molecular oscillators to drive daily rhythms of tissue-specific homeostatic processes. Importantly, the output, structure and coherence of this network is compromised by physiological ageing, disease and lifestyle changes. Yet, the key signalling nodes in this network, their underlying mechanisms of communication, and potential for therapeutic intervention, remain undefined. To dissect this system, we construct a minimal clock network consisting of two communicating nodes: the peripheral epidermal clock and central brain clock. We show that communication between the brain and epidermal clocks is sufficient for wiDD-type core clock activity and specific homeostatic processes, but inputs from other clock nodes are essential for full daily physiology. Unexpectedly, we find evidence that the epidermal clock selectively suppresses or interprets systemic signals to ensure coherence of specific homeostatic processes, identifying an unrecognised gatekeeper role for peripheral clocks. Together, we introduce a novel approach for dissecting a tissues daily physiology, and in turn identify key signalling nodes required to maintain epidermal homeostasis.

overall_design: The circadian transcriptome of the skin epidermis was profiled for mice in which circadian clock activity was present only in the skin epidermis, only in the brain, only in the skin and brain, or all tissues. After a 1 week exposure to constant darkness, RNA-seq of epidermis samples were taken at four hour intervals throughout the day (four biological replicates per timepoint), and subsequently the algorithms JTK_CYCLE and BIOCYCLE were used to generate a consensus circadian transcriptome for each condition. In addition, the algorithm DryR was used to identify groups of genes with specific rhythmic parameters either shared or differing between the different conditions.


title: Exploiting a subtype-specific mitochondrial vulnerability for successful treatment of colorectal peritoneal metastases

first: Sander

middle: Roeland

last: van Hooff

department: Center for Experimental and Molecular Medicine (CEMM),

institute: AUMC

summary: Peritoneal metastases (PM) in colorectal cancer (CRC) present a significant challenge due to limited treatment options and poor patient prognosis. While cytoreductive surgery with hyperthermic intraperitoneal chemotherapy (CRS-HIPEC) offers curative potential for selected patients, its overall benefit remains limited compared to surgery alone. In this study we show that the majority of CRC-PM represent the CMS4-subtype. Despite CRS-HIPEC treatment, CMS4 patients had high rates of recurrent disease and mortality, indicating limited effectiveness of the treatment. To explore alternative treatment approaches, we queried large-scale compound screens and discovered the copper (Cu)-ionophore elesclomol (ES) as a highly effective agent against CMS4-specific disease models. ES exhibited rapid and selective cytotoxicity against CMS4 cells by targeting the oxidative phosphorylation machinery. CMS4 cells had reduced absolute mitochondrial content and lower expression of genes involved in oxidative phosphorylation, making them vulnerable to ES-induced cytotoxicity. Short exposures to ES combined with Cu (ES-Cu) resulted in near-complete growth inhibition of cancer cells, suggesting its potential for HIPEC-like intra-abdominal treatment procedures. Furthermore, ES-Cu demonstrated efficacy in preclinical models of PM, including CRC-PM and ovarian cancer organoids, and a HIPEC rat model of PM. These findings highlight ES-Cu as promising candidate for the local treatment of CRC-PM, with broader implications for other cancer types characterized by high incidence of PM.

overall_design:
Set of 48 colorectal peritoneal metastases
-----------------------
Authors state "raw data are unavailable due to patient privacy concerns".

first: Sanne

last: Bootsma

first: Mark

middle: G

last: Dings

first: Louis

last: Vermeulen

first: Maarten

last: Bijlsma


title: Microarray analysis of regenerating parietal cells (PCs) in murine gastric epithelium recovering from Diphtheria toxin injury

city: Houston

first: Jason

middle: C

last: Mills

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Highly specialized, acid-secreting PCs are one of many epithelial lineages that line the gastric epithelium. Even though PCs are functionally and structurally distinct from other lineages in the stomach, the molecular mechanisms that govern their specification and maturation from the gastric stem cells are relatively unknown. We used microarray analysis  to interrogate transcriptional changes that occur in regenerating PCs and to identify candidate regulators of PC fate specification and maturation.

overall_design: Transgenic Atp4b-DTR mice were treated daily with diphtheria toxin for 3 days to induce reversible PC ablation. The gastric corpus was harvested at 24, 36, 48, or 72 hours after the final injection for the experimental groups and from vehicle treated mice for the uninjured control sample. Two independent samples were collected for 48 and72h timepoints; all others had 1 sample. The corpus was collected, snap frozen, then RNA isolated using Qiagen RNeasy Micro Kit and qulality assesed with Nanodrop.

first: Steven

last: Bark

first: Mahliyah

last: Adkins-Threats


title: Single cell transcriptional analysis of regenerating parietal cells (PCs) in murine gastric epithelium recovering from Diphtheria toxin injury

state: TX

department: Gastroenterology

summary: Highly specialized, acid-secreting PCs are one of many epithelial lineages that line the gastric epithelium. Even though PCs are functionally and structurally distinct from other lineages in the stomach, the molecular mechanisms that govern their specification and maturation from the gastric stem cells are relatively unknown. We used single cell RNA sequencing (scRNA-seq) to construct a transcriptional profile for regenerating PCs and identify candidate regulators of PC fate specification and maturation.

overall_design: Transgenic Atp4b-DTR mice were treated daily with diphtheria toxin for 3 days to induce reversible PC ablation. The gastric corpus was harvested at 36, 48, or 72 hours after the final injection for the experimental groups and from vehicle treated mice for the uninjured control sample. The corpus was dissociated to the single cell level using a combination of mechanical and chemical techniques. Three mice were used per sample group/condition.

first: Jenie

middle: Y

last: Hwang


title: Gene expression profile at single cell level of neuroblastoma tumors

summary: Single cell expression data used for training the deconvolution algorithm

overall_design:
Fresh pre-treatment neuroblastoma tumor samples (n=4) were enzymatically digested and single-cell FACS sorted into plates for scRNA-seq.
***raw data are unavailable due to patient privacy concerns***

first: K

middle: K

last: Keller

first: S

first: J

last: Molenaar

first: P

last: Mestdagh

first: F

last: Cobos


title: Disease-specific T cell receptors maintain pathogenic T helper cell responses in postinfectious Lyme arthritis

city: Würzburg

first: Johannes

last: Dirks

state: DE

address: Josef-Schneider-Straße 2

department: Pediatric Immunology

institute: University Hospital Julius-Maximilians University Würzburg

summary: Antibiotic-refractory Lyme arthritis (ARLA) is defined by persistent arthritis after sufficient antibiotic treatment of acute Lyme arthritis and is seen in approximately 10 % of patients with Lyme arthritis. Although some clinical and genetic risk markers for ARLA have been elucidated, whether chronic inflammation is sustained by persistent Borrelial antigens or triggered by autoantigens is not elucidated yet. Here, we show an oligoclonal expansion of peripheral T helper (TPH) cells in synovial fluid (SF) of pediatric ARLA patients. By in-depth bioinformatics analysis we identify a group of T cell receptors (TCRs) in this cell population shared between ARLA patients with a HLA-DRB1*11 background. By delineating surrogate markers for this convergent T cell response, we can show that these TCRs are specific for ARLA patients with HLA-DRB1*11 background compared to different autoimmune and infectious causes of arthritis and that those markers persist throughout disease course. Furthermore, combined single cell transcriptome and paired TCRα/β sequencing links the ARLA specific surrogate markers to cells with an inflammatory transcriptional program driven by TCR signaling – revealing possible therapeutic targets. Concluding, this study reveals an HLA-DRB1 restricted convergent TPH cell response in the joints of pediatric ARLA patients – suggesting a common persisting antigen as causative agent.

overall_design: Ex vivo CD4+ T cells from Synovial Fluid mononuclear cells from patients with anitbiotic refractors Lyme arthritis were used for 10X genomics 5' scRNA and VDJ TCR sequencing. For two patients samples were multiplexed using  Hashtag Oligos prior to preparation of single cell suspensions. The third patient (ARLA02) was seqeunced in a separate run.

first: Henner

last: Morbach


title: Microbial short-chain fatty acids regulate drug seeking and transcriptional control in a model of cocaine seeking.

city: Winston-Salem

first: Drew

last: Kiraly

state: NC

address: 115 South Chestnut Street

department: Physiology, Pharmacology, Psychiatry

institute: Wake Forest University School of Medicine

summary: Cocaine use disorder represents a public health crisis with no FDA-approved medications for its treatment. A growing body of research has detailed the important connections between the brain and the resident population of bacteria in the gut, the gut microbiome in psychiatric disease models. Acute depletion of gut bacteria results in enhanced reward in a mouse cocaine place preference model, and repletion of bacterially-derived short-chain fatty acid (SCFA) metabolites reverses this effect. However, the role of the gut microbiome and its metabolites in modulating cocaine-seeking behavior after prolonged abstinence is unknown. Given that relapse prevention is the most clinically challenging issue in treating substance use disorders, studies examining the effects of microbiome manipulations in relapse-relevant models are critical. Here, Sprague-Dawley rats received either untreated water or antibiotics to deplete the gut microbiome and its metabolites. Rats were trained to self-administer cocaine and subjected to either within-session threshold testing to evaluate motivation for cocaine or 21 days of abstinence followed by a cue-induced cocaine-seeking task to model relapse behavior. Microbiome depletion did not affect cocaine acquisition on an FR1 schedule. However, microbiome-depleted subjects exhibited significantly enhanced motivation for low dose cocaine on a within-session threshold task. Similarly, microbiome depletion increased cue-induced cocaine-seeking following prolonged abstinence. In the absence of a normal microbiome, repletion of bacterially-derived SCFA metabolites reversed the behavioral and transcriptional changes associated with microbiome depletion. These findings suggest that gut bacteria, via their metabolites, are key regulators of drug-seeking behaviors, positioning the microbiome as a potential translational research target.

overall_design: Comparative gene expression profiling analysis of cocaine self-administering Sprague-Dawley rats with normal microbiomes (control), depleted microbiomes, supplemented with short-chain fatty acids, or depleted microbiome with short-chain fatty acids.

first: Katherine

last: Meckel

first: Sierra

last: Simpson

first: Arthur

last: Godino

first: Emily

last: Peck

first: Olivier

last: George

first: Erin

last: Calipari

first: Rebecca

last: Hofford


title: Safety and reactogenicity of a controlled human infection model of sand fly-transmitted cutaneous leishmaniasis

status: Public on Apr 30 2024

city: York

first: Paul

middle: M

last: Kaye

state: North Yorkshire

address: University of York, Heslington

institute: Hull York Medical School, University of York

summary: The leishmaniases are globally important parasitic diseases for which no human vaccines are currently available. To facilitate vaccine development, we conducted an open label observational study to establish a controlled human infection model of sand fly-transmitted cutaneous leishmaniasis caused by L. major. Between 24th January and 12th August 2022, we exposed 14 (8F, 6M) participants to infected sand flies. The primary objective was to demonstrate effectiveness (attack rate) and safety (absence of CL lesion at 12 months), whereas secondary and exploratory objectives included rate of lesion development, parasite load and analysis of local immune responses using immunohistology and spatial transcriptomics. We estimated a take rate for CL development of 64% (9/14) based on all participants, increasing to 82% (9/11) if only participants with confirmed bites are included. Lesion development was terminated by therapeutic biopsy in 10 participants with confirmed bites. 30% (3/10) had either one (2/10) or two (1/10) lesion recurrences between 4-8 months after biopsy that were treated successfully with cryotherapy. No severe or serious adverse events were recorded, but scarring was evident as expected.  All participants were lesion-free at long-term (>12 month) follow up.  We provide the first comprehensive map of immune cell distribution and cytokine/chemokine expression in human CL lesions, revealing discrete immune niches.  This controlled human infection model offers opportunities for rapid vaccine candidate selection and a greater understanding of immune-mediated protection and pathology.

overall_design: Evaluating a new controlled human infection model of cutaenous leishmaniasis that incorporates natural sand fly transmission. The study was designed with the primary objectives of determining take rate (defined as lesion development) after exposure to infected sand flies and safety in terms of lesion clearance at 12 month follow up.

first: Vivak

last: Parkash

first: Helen

last: Ashwin

first: Shoumit

last: Dey

first: Jovana

last: Sadlova

first: Barbora

last: Vojtkova

first: Kat

last: Van Bocxlaer

last: Wiggins

first: David

last: Thompson

first: Nidhi

first: Charles

last: Jaffe

first: Eli

last: Schwartz

first: Petr

last: Volf

last: Lacey

first: Alison

last: Layton


title: Translational control in the spinal cord regulates gene expression and pain hypersensitivity in the chronic phase of neuropathic pain

city: Montreal

first: Arkady

last: Khoutorsky

state: Quebec

address: 3655 Promenade Sir-William-Osler

country: Canada

institute: McGill University

summary: Sensitization of spinal nociceptive circuits plays a cardinal role in neuropathic pain. This sensitization depends on new gene expression that is primarily regulated via transcriptional and translational control mechanisms. The relative roles of these mechanisms in regulating gene expression in the clinically relevant chronic phase of neuropathic pain are not well understood. Here, we show that changes in gene expression in the spinal cord during the chronic phase of neuropathic pain are substantially regulated at the translational level. Downregulating spinal translation at the chronic phase alleviated pain hypersensitivity. Cell-type-specific profiling revealed that spinal inhibitory neurons exhibited greater changes in translation after peripheral nerve injury compared to excitatory neurons. Notably, increasing translation selectively in all inhibitory neurons or parvalbumin-positive (PV + ) interneurons, but not excitatory neurons, promoted mechanical pain hypersensitivity. Furthermore, increasing translation in PV + neurons decreased their intrinsic excitability and spiking activity, whereas reducing translation in spinal PV + neurons prevented the nerve injury-induced decrease in excitability. Thus, translational control mechanisms in the spinal cord, primarily in inhibitory neurons, play a critical role in mediating neuropathic pain hypersensitivity.

overall_design:
Translational regulation in chronic pain conditions was investigated at the tissue (exploratory stage) and cell level using two distinct workflows, namely Ribosome profiling and translating ribosome affinity purification (TRAP).
First, Ribosome profiling was used to identify the genes that are translationally regulated in dorsal root ganglia (DRG) and spinal cord (SC) in early (day 4) and late (day 63) stages of neuropathic pain and at day 4 of inflammatory pain. Spared nerve injury (SNI) surgery was used to establish a mouse model of neuropathic pain, with sham surgery as a control, and Complete Freund's Adjuvant (CFA)injection was used to establish the mouse model for inflammatory pain, with vehicle injection as a control. Ribosome footprints (RFP, ~28 nucleotide fragment of mRNA where ribosomes were bound during translation) and bulk mRNA were sequenced from DRG and SC tissues of mice undergone either SNI/Sham surgery at day 4 or day 63 time points or CFA/vehicle injections at day 3 time point. Each condition had two biological replicates for both RFP and mRNA samples.
Secondly, to identify the actively translating mRNAs in excitatory and inhibitory neuronal populations, we employed a translating ribosome affinity purification (TRAP) to study cell specific translational regulation. In TRAP, a ribosomal subunit L10a tagged with eGFP (L10a-eGFP) is expressed in specific cell types – GAD2 for inhibitory neurons and TAC1 for excitatory neurons. Immunoprecipitation (IP) with eGFP antibody was performed on cell lysates of spinal cord to capture the eGFP-tagged ribosomes and subsequent sequencing of immunoprecipitated ribosome-bound mRNAs was performed to identify actively translated mRNAs in the specific cell types. For each cell type, TRAP was performed on mice which underwent either SNI or sham surgery at two points (day 4 and day 60) post-surgery. For each condition the RNA obtained by immunoprecipitation (IP) and RNA extracted from a fraction of the input cell lysate (Input) were sequenced. The input sample was used to identify the mRNA and their abundance present in the tissue. Each of the IP and input samples had three biological replicates.

first: Kevin

last: Lister

first: Sonali

last: Uttam

first: Marc

last: Pairsien


title: Obesity Disrupts the Pituitary-Hepatic UPR Communication Leading to NAFLD Progression (pituitary scRNA seq)

city: Iowa City

first: Ling

last: Yang

state: Iowa

address: 169 Newton RD

department: Anatomy & Cell Biology

institute: university of Iowa

summary: Obesity alters circulating levels of pituitary hormones that govern hepatic immune-metabolic homeostasis, and dysregulation of which leads to NAFLD. Here, using diet induced obese and IRE1PKO mice, we uncovered an blunted unfolded protein response (UPR) but elevated inflammatory signatures in pituitary glands of obese mice. Mechanistically, we demonstrated that the pituitary IRE1alpha-XBP1 UPR branch is essential for protecting against pituitary endocrine defects and NAFLD progression in obesity.

overall_design: Pituitaries were collected from WT RD vs HFD, and IRE1 PKO vs IREfl RD male mice  (4 hrs feeding following a 16-hrs fasting).


title: Obesity Disrupts the Pituitary-Hepatic UPR Communication Leading to NAFLD Progression (pituitary bulk RNA seq)

summary: Obesity alters circulating levels of pituitary hormones that govern hepatic immune-metabolic homeostasis, and dysregulation of which leads to NAFLD. Here, using diet induced obese mouse, we uncovered an blunted unfolded protein response (UPR) but elevated inflammatory signatures in pituitary glands of obese mice. Mechanistically, we demonstrated that the pituitary IRE1alpha-XBP1 UPR branch is essential for protecting against pituitary endocrine defects and NAFLD progression in obesity.

overall_design: Pituitary were collected from RD or HFD male mice (4 hrs feeding following a 16-hrs fasting).


title: Obesity Disrupts the Pituitary-Hepatic UPR Communication Leading to NAFLD Progression (liver bulk RNA seq)

summary: Obesity alters circulating levels of pituitary hormones that govern hepatic immune-metabolic homeostasis, and dysregulation of which leads to NAFLD. Here, using diet induced obese mouse and IRE1PKO mice, we uncovered an blunted unfolded protein response (UPR) but elevated inflammatory signatures in pituitary glands of obese mice. Mechanistically, we demonstrated that the pituitary IRE1alpha-XBP1 UPR branch is essential for protecting against pituitary endocrine defects and NAFLD progression in obesity.

overall_design: Livers were collected from IRE1 PKO vs IREfl HFD male mice  (4 hrs feeding following a 16-hrs fasting).


title: A novel t(X;21) (p11.4;q22.12) translocation adds to the role of BCOR and RUNX1 in Myelodysplastic Syndromes/Acute Myeloid Leukemias [Copy number analysis]

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

summary: In this study we present a thus far undescribed, reciprocal, unbalanced chromosomal translocation between the long arm of chromosome 21 and the short arm of chromosome X, t(X;21)(p11.4;q22.12), in five cases with Myelodysplastic Syndromes and Acute Myeloid Leukemias (MDS/AML). The translocation was isolated or accompanied by one additional change and is not generating a fusion gene. Deletion of RUNX1 at chromosome 21 and of BCOR at chromosome X  was shown by Fluorescence In Situ Hybridization (FISH) and Single Nucleotide Polymorphism array (SNPa) analysis. BCOR was downregulated in all cases compared to the normal counterpart, as well as to normal karyotype AMLs (NK-AML). By contrast, RUNX1 expression was not altered, suggesting a compensatory effect of the remaining allele. Molecular analysis by Next Generation Sequencing showed that the translocation was accompanied by at least one somatic mutation at TET2, EZH2, RUNX1, DNMT3A and NRAS genes.

overall_design: Copy number analysis of 4 AML cases with t(X;21) by CytoScan HD Affymetrix platform


title: CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant [Hi-C]

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

summary: Functional enhancer annotation is a valuable first step for understanding tissue-specific transcriptional regulation and prioritizing disease-associated non-coding variants for investigation. However, unbiased enhancer discovery in physiologically relevant contexts remains a major challenge. To discover regulatory elements pertinent to diabetes, we conducted a CRISPR interference (CRISPRi) screen in the human pluripotent stem cell (hPSC) pancreatic differentiation system. Among the enhancers uncovered, we focused on a long-range enhancer ~664 kb from the ONECUT1 promoter, as coding mutations in ONECUT1 cause pancreatic hypoplasia and neonatal diabetes. Homozygous enhancer deletion in hPSCs was associated with a near-complete loss of ONECUT1 gene expression and compromised pancreatic differentiation. This enhancer contains a confidently fine-mapped type 2 diabetes (T2D) associated variant (rs528350911) which disrupts a GATA motif. Introduction of the risk variant into hPSCs revealed substantially reduced binding of key pancreatic transcription factors (GATA4, GATA6 and FOXA2) on the edited allele, accompanied by a slight reduction of ONECUT1 transcription, supporting a causal role for this risk variant in metabolic disease. This work expands our knowledge about transcriptional regulation in pancreatic development through the characterization of a long-range enhancer and highlights the utility of enhancer discovery in disease-relevant settings for understanding monogenic and complex disease.

overall_design: lab: Danwei Huangfu, MSKCC  award: 1U01DK128852-01  accession: 4DNESOGBAIC7  condition: pancreatic precursor cells - H1  dataset_label: in situ Hi-C on PDX1-GFP idCAS9-KRAB H1 human embryonic stem cells differentiated to pancreatic progenitor cells (PP)  experiment type: in situ Hi-C  url: https://data.4dnucleome.org/experiment-set-replicates/4DNESOGBAIC7/  number_of_experiments: 2  experiment: in situ Hi-C on PDX1-eGFP dCAS9-KRAB H1 differentiated to endoderm of foregut with Arima - A1, A2 - 4DNEXMHLGGWC experiment: in situ Hi-C on PDX1-eGFP dCAS9-KRAB H1 differentiated to endoderm of foregut with Arima - A1, A2 - 4DNEXUDU96VW   Series supplementary files:  ****** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/3e86c39e-47f3-4656-ac56-ab63aa493af7/  genome_assembly GRCh38  derived_from: 4DNFI823LSII.chrom.sizes, 4DNFITG6TM26.pairs.gz, 4DNFINK7ALPW.pairs.gz, 4DNFIU1RS39P.txt,  description: This is an output file of the Hi-C processing pipeline  file_type: contact list-combined  file_format: pairs  file_name: 4DNFIEAQ6DIR.pairs.gz ****** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/3e86c39e-47f3-4656-ac56-ab63aa493af7/  genome_assembly GRCh38  derived_from: 4DNFI823LSII.chrom.sizes, 4DNFITG6TM26.pairs.gz, 4DNFINK7ALPW.pairs.gz, 4DNFIU1RS39P.txt,  description: This is an output file of the Hi-C processing pipeline  file_type: contact matrix  file_format: mcool  file_name: 4DNFIYC4AJW5.mcool ****** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/4a5f3a30-c608-4367-953b-e5300001f22b/  genome_assembly GRCh38  derived_from: 4DNFIYC4AJW5.mcool,  description: Boundaries calls on Hi-C contact matrices  file_type: boundaries  file_format: bed  file_name: 4DNFINRZXAQF.bed.gz ****** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/4a5f3a30-c608-4367-953b-e5300001f22b/  genome_assembly GRCh38  derived_from: 4DNFIYC4AJW5.mcool,  description: Diamond insulation scores calls on Hi-C contact matrices  file_type: insulation score-diamond  file_format: bw  file_name: 4DNFI4F6P2UE.bw ****** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/d04948a9-1b41-47f2-80b0-8e3a74eb90af/  genome_assembly GRCh38  derived_from: 4DNFIYC4AJW5.mcool, 4DNFI7MCA4R6.bedGraph.gz,  description: Compartments signals on Hi-C contact matrices  file_type: compartments  file_format: bw  file_name: 4DNFI9C517H3.bw ******BED files: HiC-Pro (3.1.0) alignment, HiTC (1.34.0), HiCDC+(1.5.2), TopDom, 50 kb file_format: bed file_name: 4DNFIJI7XHPW.bed.gz

first: Danwei

last: Huangfu

first: Wilfred

middle: W

last: Wong

first: Samuel

last: Kaplan


title: A novel t(X;21) (p11.4;q22.12) translocation adds to the role of BCOR and RUNX1 in Myelodysplastic Syndromes/Acute Myeloid Leukemias [Gene expression analysis]

overall_design: Gene expresion analysis was carried out on 4 AML cases with t(X;21), 5 AML-Normal Karyotype cases, 3 Wild Type and 3 AML cases with t(8;21)


title: MYC promotes aggressive growth and metastasis of a WNT-medulloblastoma mouse model

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

summary: Medulloblastoma (MB), the most common malignant pediatric brain tumor, comprises of four molecularly and clinically distinct subgroups (termed WNT, SHH, Group3, and Group4). Prognosis varies based on genetic and pathological features associated with each molecular subgroup. WNT-MB, considered low-risk, are rarely metastatic and contain activating mutations in CTNNB1; Group3-MB, commonly classified as high-risk, are frequently metastatic and can contain genomic alterations resulting in elevated MYC expression. Here we compare model systems of low-risk WNT-MB to high-risk Group3-MB to identify tumor and microenvironment interactions that could contribute to features associated with poor outcome. Compared to Group3-MB, we find that WNT-MB display enrichment in gene sets related to extracellular matrix (ECM) regulation and cellular adhesion. Exogenous expression of MycT58A in murine WNT-MB models significantly accelerates growth and results in metastatic disease. In addition to down-regulation of ECM regulation and cell adhesion pathways, we also identified immune system interactions among the top down-regulated signaling pathways following MycT58A expression. Taken together, our data provides evidence that increased Myc signaling can promote the growth and metastasis of WNT-MB.

overall_design: Three biological replicates were analyzed for each of 3 conditions (control cerebellum, mWnt-MB + EV, mWnt-MB + MycT58A)

first: Rachel

last: Hartley


title: Best practices for differential accessibility analysis in   single-cell epigenomics

city: Geneve

first: Alan Yue Yang

last: Teo

address: Chem. des Mines 9, Campus Biotech

department: SV

country: Switzerland

institute: EPFL

summary: This submission is a dataset of single-nucleus multi-omics of uninjured and injured spinal cords of mice harvested and profiled using 10x Multiome ATAC + Gene Expression kit.

overall_design: We used single-nucleus RNA-sequencing and single-nucleus ATAC-sequencing to profile the mid thoracic spinal cord of uninjured and injured mice at acute and chronic post-spinal cord injury.

first: Michael

last: Skinnider

first: Matthieu

last: Gautier

first: Alan

first: Claudia

last: Kathe

first: Thomas

middle: H

last: Hutson

first: Achilleas

last: Laskaratos

first: Alexandra

last: de Coucy

first: Nicola

last: Regazzi

first: Viviana

last: Aureli

first: Nicholas

middle: D

last: James

first: Bernard

last: Schneider

middle: V

last: Sofroniew

first: Quentin

last: Barraud

first: Jocelyne

last: Bloch

first: Mark

last: Anderson

first: Jordan

last: Squair

first: Grégoire

last: Courtine


title: HIV-1 Vpr targets PU.1 to vastly alter the antiviral machinery of HIV infected primary human macrophages

city: Ann Arbor

first: Kathleen

middle: Loretta

last: Collins

state: MI

address: 1150 W. Medical Center Drive

institute: University of Michigan

summary: HIV-1 accessory protein, Vpr, is required for efficient HIV-1 infection of macrophages. Here we show that Vpr reprograms macrophage gene expression by altering the activity of master transcriptional regulator, PU.1, which is responsible for regulating the expression of host immune response genes and is necessary for normal hematopoiesis. In HIV-infected primary macrophages, Vpr-dependent changes in PU.1 levels result in suppression of known anti-viral targets of Vpr including IFITM3 and MRC1. Moreover, we find that PU.1 and its co-factor TET2 are co-recruited to DCAF1 by Vpr and targeted for accelerated degradation. Downmodulation of PU.1 is a highly conserved function of Vpr that is maintained across primate lentiviruses including HIV-2 and several SIVs. In contrast, this activity is not shared by the evolutionarily related accessory protein Vpx. Our findings demonstrate how Vpr dramatically enhances HIV spread in macrophages by targeting a myeloid-specific transcription factor needed for expression of multiple viral restriction factors.

overall_design:
Human MDM scRNA-seq sequences on 10X Genomics platform.

***RAW data has been deposited in dbGap (phs002915.v2.p1) due to patient privacy concerns.***

first: Maria

last: Virgilio

first: W

last: Disbennett

last: Chen

first: Jay

last: Lubow

first: Joshua

last: Welch

middle: L


title: Effects of vancomycin and ramoplanin on gene expression in Clostridioides difficile

first: Boris

last: Belitsky

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

summary: We compared transcriptomes of wild-type and ∆vanS strains of Clostridioides difficile 630 growing in the presence or absence of peptidoglycan-targeting antibiotics, vancomycin or ramoplanin. VanS is a histidine kinase of a two-component system that regulates expression of the vancomycin-induced vanG operon.

overall_design: Comparative RNAtag-Seq of wild-type and vanS null mutant cells in the presence or absence of vancomycin or ramoplanin


title: Prenatal phenotypes and pregnancy outcomes of fetuses with 16p11.2 microdeletion/microduplication

status: Public on Apr 29 2024

city: Changchun

first: Hongguo

last: Zhang

state: Jilin

address: 1 Xinmin Street, Changchun, Jilin 130021, P.R. China

department: Center for Reproductive Medicine and Center for Prenatal Diagnosis

country: China

institute: First Hospital, Jilin University, Changchun, China

summary:
Background: Chromosomal 16p11.2 deletions and duplications are genomic disorders which are characterized by neurobehavioral abnormalities, obesity, congenital abnormalities and so on. However, the prenatal phenotypes of 16p11.2 copy number variations (CNVs) are still not well described till now. This study aimed to provide an elaborate summary of intrauterine phenotypic features for such genomic disorders.     Methods: Twenty prenatal amniotic fluid samples diagnosed with 16p11.2 microdeletions/microduplications were obtained from pregnant women who opted for invasive prenatal testing. Karyotypic analysis and chromosomal microarray analysis (CMA) were performed in parallel. The pregnancy outcomes and health conditions after birth for all cases were followed up. Meanwhile, we made a pooled analysis on the prenatal phenotypes for the published cases carrying 16p11.2 CNVs.     Results: 20 fetuses (20/20884, 0.10%) with 16p11.2 CNVs were identified: five 16p11.2 BP2-BP3 deletion, ten 16p11.2 BP4-BP5 deletion and five 16p11.2 BP4-BP5 duplication. Abnormal ultrasound findings were recorded in ten participants with 16p11.2 deletions.Various degrees of intrauterine phenotypic features, ranging from normal to abnormal, were observed. No ultrasound abnormalities were observed for all 16p11.2 duplication cases during the pregnancy period. For 16p11.2 deletions, eleven cases terminated their pregnancies. For 16p11.2 duplications, four cases gave birth to healthy neonates except one was lost to follow up.    Conclusions: Diverse prenatal phenotypes were presented in 16p11.2 CNVs, ranging from normal to abnormal. For 16p11.2 BP4-BP5 deletion, the most common structural and non-structural abnormalities were the abnormality of the vertebral column or rib and thickened nuchal translucency, respectively. 16p11.2 BP2-BP3 deletion might be closely associated with fetal growth restriction and single umbilical artery. No representative ultrasound findings for 16p11.2 duplication were observed till now. Considering the variable expressivity and incomplete penetrance of 16p11.2 CNVs, long term follow up after birth should be carried out for these cases.
We identified 20 fetuses carrying the 16p11.2 microdeletions and microduplications using chromosomal microarray analysis. And diverse prenatal phenotypes and the critical genes involved in the deleted/duplicated regions were described in this study.

overall_design: 15 pregnancies with 16p11.2 microdeletions and five with 16p11.2 microduplications were included. **Please note that raw data CEL files for ？samples (out of total ？) have been lost and thus are not provided***

first: Fagui

last: Yue


title: A novel t(X;21) (p11.4;q22.12) translocation adds to the role of BCOR and RUNX1 in Myelodysplastic Syndromes/Acute Myeloid Leukemias

first: Cristina

last: Mecucci

type:
Expression profiling by array
Genome variation profiling by SNP array

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

overall_design: Refer to individual Series


title: Genetic dependencies associated with transcription factor activities in human cancer cell lines [CROP-seq]

city: Vienna

first: Malgorzata

middle: Emilia

last: Kamuda

address: Dr.Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

institute: Boehringer-Ingelheim

summary: Transcription factors (TFs) are important mediators of aberrant transcriptional programs in cancer cells. In this study, we focused on TF activity (TFa) as a new biomarker for cell line-selective anti-proliferative effects, in that high TFa predicts sensitivity to loss-of-function of a given gene (i.e., genetic dependencies (GD)). Our linear regression-based framework identified 3,047 pan-cancer and 3,952 cancer-typespecific candidate TFa-GD associations from cell line data, which were then crossexamined for impact on survival in patient cohorts. One of the most prominent biomarkers was TEAD1 activity, whose associations with its predicted GDs were validated through experimental evidence as proof of concept. Overall, these TFa-GD associations represent an attractive resource for identifying innovative, biomarkerdriven hypotheses for drug discovery programs in oncology.

overall_design: We performed a pooled CRISPRko screen followed by single cell RNA sequencing (CROP-seq) on human SNU-761 cell line using a library containing 450 sgRNAs targeting 108 genes and non-targeting controls. Cells were processed on 10X Genomics platform using 5’ HT chemistry on Day 5 and Day 10 timepoints. Whole transcriptome, sgRNA and cell hashing libraries were prepared from each time point and submitted for next-generation sequencing.

first: Tatyana

last: Perlova

first: Lisa

last: Papp

first: Rahul

last: Sharma

first: Lukas

last: Badertscher

first: Verena

last: Supper

first: Venu

last: Thatikonda

first: Alexandra

last: Popa


title: PRMT1 Promotes Epigenetic Reprogramming Associated with Acquired Chemoresistance in Pancreatic Cancer

city: Washington

first: Chan

middle: Dinh Khac

last: Nguyen

state: DC

address: 3970 Reservoir Rd

department: Oncology

institute: Lombardi Comprehensive Cancer Center

summary: Pancreatic Ductal Adenocarcinoma (PDAC) is associated with extremely poor prognosis due to late diagnosis and therapeutic resistance. Here we show that PDAC cells undergo progressive reprogramming of the global epigenetic landscape during the process of acquiring chemoresistance. Through an epigenetic inhibitor screen, we identified Protein Arginine methyltransferase 1 (PRMT1) as a central driver of chemoresistance in PDAC. Genetic or pharmacological inhibition of PRMT1 impaired adaptive epigenetic reprogramming, sensitized PDAC cells to Gemcitabine and other commonly used chemo drugs, and delayed the development of acquired resistance both in vitro and in vivo. Mechanistically, we find that PRMT1, through its enzymatic activity, limits the accumulation of small bZIP transcription factor MAFF in the nucleus, and the assembly of chromatin-bound MAFF/BACH1 hetero-oligomeric complexes following Gemcitabine treatment. Genetic silencing of MAFF heightened the resistance of PDAC cells to Gemcitabine, and to combination of Gemcitabine and PRMT1 inhibitors. Cut&Tag chromatin profiling of H3K27Ac, MAFF and BACH1 suggests a pivotal role for MAFF/BACH1 in orchestrating global epigenetic reprogramming during the course of acquiring Gemcitabine resistance. Supporting the clinical relevance of our findings, predicted PRMT1 and MAFF/BACH1 genes signatures based on our Cut&Tag analysis were able to distinguish Gemcitabine-resistant from Gemcitabine-sensitive PDAC patient-derived xenografts according to expression changes induced by Gemcitabine. Together, our study reveals a novel epigenetic regulatory axis involving PRMT1 and MAFF/BACH1 that modulates Gemcitabine response, which could be potentially exploited for improving therapeutic response in advanced PDAC.

overall_design: Cut&Tag Chromatin Profiling of H3K27Ac, MAFF, and BACH1 for Pancreatic Ductal Adenocarcinoma (PDAC). (1) Time series analysis of PDAC under GEM treatment at D0,2,4,6,8,10. (2) KD

first: Shigekazu

last: Murakami

first: Alec

last: McIntosh

first: Rachel

last: Nas

first: Benjamin

last: Colon-Emeric

first: Chunling

last: Yi


title: Genetic dependencies associated with transcription factor activities in human cancer cell lines [SLAM-seq]

summary: Transcription factors (TFs) are important mediators of aberrant transcriptional programs in cancer cells. In this study, we focused on TF activity (TFa) as a new biomarker for cell line-selective anti-proliferative effects, in that high TFa predicts sensitivity to loss-of-function of a given gene (i.e., genetic dependencies (GD)). Our linear regression-based framework identified 3,043 pan-cancer and 3,952 cancer-type-specific candidate TFa-GD associations from cell line data, which were then cross-examined for impact on survival in patient data. One of the most prominent biomarkers was TEAD1 activity, whose associations with its predicted GDs were validated through experimental evidence as proof of concept. Overall, these TFa-GD pairs represent an attractive resource for identifying innovative, biomarker-driven hypotheses for drug discovery programs in oncology.

overall_design:
To investigate the immediate transcriptional effects induced by the pharmacological modulation with the pan-TEAD VT107 inhibitor and the ITGAV-targeting antibody, Intetumumab, we performed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) in the liver carcinoma cell lines: SNU-761. VT107 treatment was added at 0.1 uM and 2.15 uM concentrations and the respective amount of DMSO for samples to compare against. Samples were prepared in duplicates. Intetumumab Biosimilar – Anti-ITGAV_ITGB3 mAb (Prote Genix PX-TA1230) was added at 1.5 µg/ml and 5 µg/ml concentrations. We used  Isotype IgG1, Kappa from human myeloma plasma (Sigma -Aldrich I5154) as a control. For the Intetumumab treatment group, samples were prepared in triplicates. Samples were collected at 4h after treatment.
Samples were prepared for SLAM-seq using the protocol from Muhar et al., 2018. De novo transcript and data processing was performed with the SLAM DUNK pipeline (Neumann et al. 2019).

first: Onur

last: Kaya

first: Johannes

last: Wachter

first: Federico

last: Mauri


title: RNAseq of mRNA from splenic and hepatic CD8 T cell populations after resolved and during persistent AdV infection

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

institute: TUM

summary: We aimed at dissecting phenotype, functionality and regulation of antigen-specific hepatic and splenic CX3CR1-positive and hepatic CXCR6-positive CD8 T cells after resolved or during persistent viral infection of the liver.

overall_design: Comparison of splenic and hepatic CD8 T cell populations in two infection models (n=3 for each sample group). For resolved infection, hepatic T cells were sorted into CXCR6 and CX3CR1 populations. For persistent infection, hepatic T cells were sorted into CXCR6 and CXCR6-CX3CR1 populations.

first: Miriam

last: Bosch

first: Nina

last: Kallin

first: Sainitin

last: Donakonda

first: Rupert

last: Oellinger

first: Thomas

last: Engleitner

first: Percy

middle: A

last: Knolle


title: Pervasive nuclear envelope ruptures precede ECM signaling and disease onset without activating cGAS-STING in Lamin cardiomyopathy mice [sci-RNA-seq]

status: Public on Apr 26 2024

first: Kohta

last: Ikegami

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Nuclear envelope (NE) ruptures are emerging observations in Lamin-related dilated cardiomyopathy, an adult-onset disease caused by loss-of-function mutations in Lamin A/C, a nuclear lamina component. Here, we test a prevailing hypothesis that NE ruptures trigger the pathological cGAS-STING cytosolic DNA-sensing pathway using a mouse model of Lamin cardiomyopathy. The reduction of Lamin A/C in cardiomyocytes of adult mice causes pervasive NE ruptures in cardiomyocytes, preceding inflammatory transcription, fibrosis, and fatal dilated cardiomyopathy. NE ruptures are followed by DNA damage accumulation without causing immediate cardiomyocyte death. However, cGAS-STING-dependent inflammatory signaling remains inactive. Deleting cGas or Sting does not rescue cardiomyopathy. The lack of cGAS-STING activation is likely due to the near absence of cGAS expression in adult cardiomyocytes at baseline. Instead, extracellular matrix (ECM) signaling is activated and predicted to initiate pro-inflammatory communication from Lamin-reduced cardiomyocytes to fibroblasts. Our work nominates ECM signaling, not cGAS-STING, as a potential inflammatory contributor in Lamin cardiomyopathy.

overall_design: sci-RNA-seq.  Each Sample (GSM#) represents a mixture of biological samples, by design.

first: Atsuki

last: En


title: Endometrial transcriptomic changes after application of seminal plasma: a randomized controlled trial

status: Public on Apr 24 2024

city: Copenhagen N

first: Atul

last: Anand

address: Ole Maaløes Vej 5, building 2, 3 floor

department: Department of Pathology

institute: Rigshospitalet

summary:
We hypothesized that seminal plasma, the acellular seminal fluid component, influences the endometrium stimulating the immune system and facilitating the implantation. We designed a randomized, double-blinded, placebo-controlled trial, and we used microarray analysis to evaluate differences in the endometrial transcriptomic profile after vaginal seminal plasma application.
Differential gene pathways analysis showed an upregulation of pathways associated with the immune response, cell viability, proliferation and cellular movement, implantation, embryo development, oocyte maturation and angiogenesis. We compared our results with similar studies in pigs, mice and in vitro human endometrial cells and found similar and found comparable results.  Our data show that seminal plasma has a positive effect on the endometrium during the implantation window.

overall_design: 9 women without a male partner undergoing Gonadotropin-releasing hormone agonist long-protocol treatment at the fertility clinic were randomized into two treatment groups. 5 women received a vaginal application of seminal plasma and 4 received a placebo application with saline solution.  The application of seminal plasma/placebo was performed inside the vagina 2 days after induced ovulation in a normal cycle. After 5-8 days, an endometrial biopsy was collected for RNA extraction and hybridization on Affymetrix microarrays.  Inclusion criteria: no male partner; age between 20 and 40 years old. Exclusion criteria: FSH outside the normal range 3-9 IU/L; genital infections; severe endometriosis; severe polycystic ovarian syndrome; chronic diseases.

first: Laura

last: Catalini

first: Mark

last: Burton

first: Dorte

last: Egeberg

first: Tilde

last: Eskildsen

first: Mads

last: Thomassen

first: Jens

last: Fedder


title: Coordinated regulation of osmotic imbalance by c-di-AMP shapes ß-lactam tolerance in Group B Streptococcus

status: Public on Apr 25 2024

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: Streptococcus agalactiae is among the few pathogens that have not developed resistance to ß-lactam antibiotics despite decades of clinical use. The molecular basis of this long-lasting susceptibility has not been investigated, and it is uncertain whether specific mechanisms constraint the emergence of resistance. In this study, we first report a conserved role of the signaling nucleotide cyclic-di-AMP in the sensitivity of S. agalactiae to ß-lactam. Specifically, we demonstrate that inactivation of the phosphodiesterase GdpP confers ß-lactam tolerance. Characterizing the signaling pathway revealed an antagonistic regulation by the transcriptional factor BusR, which is activated by c-di-AMP and negatively regulates ß-lactam susceptibility. Furthermore, we show that simultaneous inhibition of osmolyte transporters activity and transcription by c-di-AMP has an additive effect, sustaining ß-lactam tolerance. Finally, transposon mutagenesis for ß-lactam reduced susceptibility reveals a convergent pattern of mutations, including in the KhpAB small RNA chaperone and the protein S immunomodulator. Overall, our findings suggest mechanisms that may foster antibiotic resistance in S. agalactiae and demonstrate that c-di-AMP acts as a turgor pressure rheostat, coordinating an integrated response to cell wall weakening due to ß-lactam activity.

sample_organism:
Streptococcus agalactiae
Streptococcus agalactiae NEM316

overall_design:
To investigate the c-di-AMP signaling pathway in Group B Streptococcus, we generated deletion mutants for the c-di-AMP phosphodiesterase GdpP (∆gdpP) and for the c-di-AMP regulated transcriptional repressor BusR (∆busR)
For comparative transcritomic analysis, ∆gdpP and ∆busR mutants were generated in two wild-type strains: NEM316 (capsular serotype III, CC-23) and BM110 (capsular serotype III, CC-17)
RNA are purified from exponentialy growing cultures (OD600 = 0.5) in rich media (THY) incubated at 37°C in static condition. Biological triplicate (Replicate 1, 2, and 3) are done on different days.

first: Terry

last: Brissac

first: Odile

last: Sismeiro

first: Elise

last: Jacquemet

first: Arnaud

last: Firon