title: Pneumosepsis survival in the setting of obesity leads to persistent steatohepatitis and metabolic dysfunction.

city: La Jolla

first: Avnee

middle: Jaya

last: Kumar

address: 9500 Campus Point Drive MC 7381

institute: University of California San Diego

overall_design: To evaluate the effect of obesity and infection, we utilized a murine model of Klebsiella Pneumosepsis and diet induced obesity.

first: Chitra

last: Parthasarathy

first: Hallie

middle: C

last: Prescott

first: Scott

last: Denstaedt

first: Michael

last: Newstead

first: Dave

last: Bridges

first: Angela

last: Bustamante

first: Kanakadurga

last: Singer

first: Benjamin


title: Costimulatory domains direct distinct fates of CAR-drivenT cell dysfunction [scRNA-seq]

status: Public on May 02 2023

city: St. Louis

first: Nathan

last: Singh

state: MO

country: USA

institute: Washington University School of Medicine

type: Expression profiling by high throughput sequencing

summary: Chimeric antigen receptor (CAR) engineered T cells often fail to enact effector functions after infusion into patients. Understanding the biological pathways that lead CAR T cells to failure is of critical importance in the design of more effective therapies. We developed and validated an in vitro model that drives T cell dysfunction by chronic CAR stimulation and interrogated how CAR costimulatory domains contribute to T cell failure. We found that dysfunctional CD28-based CARs targeting CD19 bear hallmarks of classical T cell exhaustion while dysfunctional 41BB-based CARs are phenotypically, transcriptionally and epigenetically distinct. We confirmed activation of this unique transcriptional program in CAR T cells that failed to control clinical disease. Further, we demonstrate that 41BB-dependent activation of the transcription factor FOXO3 is a significant contributor to this dysfunction and disruption of FOXO3 significantly improves 41BB-based CAR T cell function. These findings identify that chronic activation of 41BB leads to novel state of T cell dysfunction that can be alleviated by genetic modification of FOXO3.

overall_design:
Comparative gene expression profiling analysis of scRNA-seq data for CD19-directed human CAR T cells with CD28 and 41BB during chronic activation by CD19+ ALL cell line Nalm6.
CD19-directed human CAR T cells containing either CD28 (19/28) or 41BB (19/BB) domains were combined with the CD19+ ALL cell line Nalm6

first: Mehmet

middle: E

last: Selli

first: Jack

last: Landmann

first: John

last: Lattin

first: Amanda

last: Heard

first: Yu-Sung

last: Hsu

first: Tien-Ching

last: Chang

first: Jufang

last: Warrington

first: Helen

last: Ha

first: Natalie

last: Kingston

first: Graham

last: Hogg

last: Slade

first: Melissa

last: Berrien-Elliot

first: Mark

last: Foster

first: Samantha

last: Kersting-Schadek

first: Agata

last: Gruszczynska

first: Marina

last: Terekhova

first: David

last: DeNardo

first: Todd

middle: A

last: Fehniger

first: Maxim

last: Artyomov


title: Transcriptional dynamics of delaminating neuroblasts in the mouse otic vesicle

city: Stanford

first: Alan

last: Cheng

state: CA

address: 240 Pasteur Drive

institute: Stanford University

summary: An abundance of research has recently highlighted the susceptibility of cochleovestibular ganglion (CVG) neurons to noise damage and aging in the adult cochlea, resulting in hearing deficits. Furthering our understanding of the transcriptional cascades that contribute to CVG development may provide insight into how these cells can be regenerated to treat inner ear dysfunction. Here we perform a high-depth single-cell RNA sequencing analysis of the E10.5 otic vesicle and its surrounding tissues, including CVG precursor neuroblasts and emerging CVG neurons. Clustering and trajectory analysis of otic lineage cells reveals otic markers and the changes in gene expression that occur from neuroblast delamination towards the development of the CVG. This dataset provides a valuable resource for further identifying the mechanisms associated with CVG development from neurosensory competent cells within the otic vesicle.

overall_design: tdTomato+ cells from E10.5 Pax2Cre/+;Ai14tdTomato/+ microdissected mouse otic vesicles were isolated by flourescence activated cell sorting (FACS) and lysed. cDNA for each cell was generated using the Clontech SMARTer Ultra Low Input RNA kit V3, followed by library construction using the Nextera XT DNA Sample Preparation kit. Cells were sequenced on an Illumina HiSeq 2500 sequencer using 75 base pair (bp) paired-end reads.

first: Maggie

last: Matern

first: Robert

last: Durruthy-Durruthy

first: Mirko

last: Scheibinger

first: Spyros

last: Darmanis

first: Stefan

last: Heller


title: Costimulatory domains direct distinct fates of CAR-drivenT cell dysfunction

first: Nathan

last: Singh

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: SRC2 controls CD4+ T cell activation via stimulating c-Myc-mediated up-regulation of amino acid transporter Slc7a5

status: Public on May 01 2023

city: Duarte

first: ZUOMING

last: SUN

address: 1500 E Duarte Rd, Duarte, CA 91010

institute: City of Hope Medical Center

summary: Purpose: Since SRC2 is a transcriptional co-activator that is believed to regulate cellular function by controlling gene expression, RNA-seq analysis was performed to detect the transcriptome of SRC2fl/fl  and SRC2fl/fl/CD4-Cre CD4+ cells 4 weeks post adoptive transferred to Rag1-/-

first: Zuoming

last: Sun

first: Wencan

last: Zhang


title: Costimulatory domains direct distinct fates of CAR-drivenT cell dysfunction [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD19-directed human CAR T cells with CD28 and 41BB during chronic activation by CD19+ ALL cell line Nalm6. T cells were collected from five different donors and each sample was sequenced in technical triplicate.

first: Mehmet

last: Selli

first: Jack

last: Landmann

first: John

last: Lattin

first: Amanda

last: Heard

first: Yu-Sung

last: Hsu

first: Tien-Ching

last: Chang

first: Jufang

last: Warrington

first: Helen

last: Ha

first: Natalie

last: Kingston

first: Graham

last: Hogg

first: Michael

last: Slade

first: Melissa

last: Berrien-Elliot

first: Mark

last: Foster


title: Repurposing DPP4-Inhibition to Improve Hair Follicle Activation and Regeneration

city: Leipzig

first: Maria

last: Schmidt

address: Härtelstr. 16-18

country: Germany

institute: IZBI

summary: Skin-injury and several diseases elicit fibrosis and induce hair follicle (HF)-growth arrest and loss. Resulting alopecia and disfiguration represent a severe burden for patients both physically and psychologically. Reduction of pro-fibrotic factors such as DPP4 might be a strategy to tackle this issue. We demonstrate DPP4-overrepresentation in settings with HF-growth arrest (telogen), HF-loss and non-regenerative wound areas in mice skin and human scalp. Topical DPP4-inhibition (DPP4i) with FDA/EMA-approved Sitagliptin (Sit) on preclinical models of murine HF-activation/regeneration results in accelerated anagen-progress, while treatment of wounds with Sit results in reduced expression of fibrosis markers, increased induction of anagen around wounds, and HF-regeneration in the wound center. These effects are associated with higher expression of Wnt-target Lef1, known to be required for HF-anagen (HF-activation)/regeneration. Sit-treatment decreases pro-fibrotic signaling in the skin, induce a differentiation trajectory of HF-cells, and activate Wnt-targets related to HF-activation/growth but not those supporting fibrosis. Taken together, our study demonstrates a role for DPP4 in HF biology and shows how DPP4i, currently used as oral medication to treat diabetes, could be repurposed into a topical treatment agent to potentially reverse HF-loss in alopecia and after injury.

overall_design: Intradermal injection of Sitagliptin or PBS (conrol), 48 h after processing of the skin for scRNAseq

last: Helm

first: Ester

last: Del Duca

first: Ying

last: Liu

first: Lena

middle: S

last: Mortensen

first: Juliane

last: Loui

last: Zheng

first: Hans

last: Binder

first: Emma

last: Guttman-Yassky

first: George

last: Cotsarelis

first: Jan

last: Simon

first: Ruben

last: Ferrer


title: Massively parallel base editing to map variant effects in human hematopoiesis

city: Cambridge

first: Jorge Diego

last: Martin Rufino

state: MA

address: 415 Main Street

institute: Harvard University / Broad Institute of MIT and Harvard / Boston Children's Hospital

summary: Systematic evaluation of the impact of genetic variants is critical for the study and treatment of human physiology and disease. While specific mutations can be introduced by genome engineering, we still lack scalable approaches that are applicable to the important setting of primary cells, such as blood and immune cells. Here, we describe the development of massively parallel base-editing screens in human hematopoietic stem and progenitor cells. Such approaches enable functional screens for variant effects across any hematopoietic differentiation state. Moreover, they allow rich phenotyping through single-cell RNA sequencing readouts, and separately, characterization of editing outcomes through pooled single-cell genotyping. We efficiently design improved leukemia immunotherapy approaches, comprehensively identify non-coding variants modulating fetal hemoglobin expression, define mechanisms regulating hematopoietic differentiation, and probe the pathogenicity of uncharacterized disease-associated variants. These strategies will advance effective and high-throughput variant-to-function mapping in human hematopoiesis to identify the causes of diverse diseases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Hematopoietic stem and progenitor cells transduced with lentiviruses expressing pooled library sgRNAs were electroporated with high purity genome editor protein

first: Jorge

middle: D

last: Martin-Rufino

first: Vijay

middle: G

last: Sankaran


title: Spatiotemporally organized immunomodulatory response to SARS-CoV-2 virus in primary human broncho-alveolar epithelia [GeoMx]

city: Farmington

first: Carolyn

last: Paisie

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

summary: The COVID-19 pandemic continues to be a health crisis with major unmet medical needs. The early responses from airway epithelial cells, the first target of the virus regulating the progression towards severe disease, are not fully understood. Primary human air-liquid interface cultures representing the broncho-alveolar epithelia were used to study the kinetics and dynamics of SARS-CoV-2 variants infection. The infection measured by nucleoprotein expression, was a late event appearing between day 4-6 post infection for Wuhan-like virus. Other variants demonstrated increasingly accelerated timelines of infection. All variants triggered similar transcriptional signatures, an “early” inflammatory/immune signature preceding a “late” type I/III IFN, but differences in the quality and kinetics were found, consistent with the timing of nucleoprotein expression. Response to virus was spatially organized: CSF3 expression in basal cells and CCL20 in apical cells. Thus, SARS-CoV-2 virus triggers specific responses modulated over time to engage different arms of immune response.

overall_design: To investigate the spatiotemporal response to SARS-CoV-2 virus in primary human broncho-alveolar epithelia We then performed gene expression profiling analysis using data obtained from RNA-seq of ALi cultures infected with SARS-CoV-2 virus Comparative gene expression profiling analysis of RNA-seq data for SARS-CoV-2 variants.

first: Diana

last: Castaneda

first: Sonia

last: Jangra

first: Marina

last: Yurieva

last: Martinek

first: Megan

last: Callender

first: Matthew

last: Coxe

first: Angela

last: Choi

first: Juan

last: García-Bernalt

first: Jianan

last: Lin

first: Te-Chia

last: Wu

first: Florentina

last: Marches

first: Damien

last: Chaussabel

first: Peter

last: Yu

first: Andrew

last: Salner

first: Gabrielle

last: Aucello

first: Jonathan

last: Koff

first: Briana

last: Hudson

first: Sarah

last: Church

first: Kara

last: Gorman

first: Esperanza

last: Anguiano

first: Adolfo

last: García-Sastre

first: Adam

last: Williams

last: Schotsaert

first: Karolina

last: Palucka


title: Mechanisms for HIV containment in CD4 T cells under homeostatic proliferation

city: Minato-ku

first: Mie

last: Koabyashi-Ishihara

state: Tokyo

address: 4-6-1 Shirokanedai

department: UTOPIA

country: Japan

institute: The University of Tokyo

summary: The main obstacle in curing an established HIV-1 infection is the long-lived reservoir of latently infected CD4+ T cells. This reservoir is maintained by T cell expansion that can be activated by several mechanisms including antigen-driven proliferation and homeostatic proliferation (HSP). Antigen-driven proliferation triggered by T cell receptor (TCR) signaling is a strong physiological inducer of CD4+ T cell expansion. This also reactivates latent HIV-1 and thus, can be the source of viral rebound. Unlike antigen-driven proliferation, HSP allows the expansion of HIV-1-infected CD4+ T cells without activating HIV-1 expression. While this condition strongly activates STAT5 signaling, the mechanisms for HIV-1 containment are unknown. Our previous work using HIV-infected primarily CD4+ T cells maintained under HSP conditions suggested a post-transcriptional block as a cause of the containment (Tsunetsugu-Yokota et al. 2016 Front Microbiol). To decipher the mechanisms that contribute to the HIV-1 refractory state in homeostatic proliferating CD4+ T cells, we analyzed differentially expressed genes in primary CD4 + cells that were cultured either under HSP conditions (culture with IL-7 and IL-15) or after TCR-stimulation (culture with IL-2 after anti-CD3/CD28 activation).

overall_design: RNA-seq of total RNAs from naive CD4+ T cells cultured under four different conditions

first: Yasuko

last: Tsunetsugu-Yokota

first: Anna

last: Esteve-Codina

first: Jordi

last: Argilaguet

last: Kobayashi-Ishihara

first: Andreas

last: Meyerhans


title: Spatiotemporally organized immunomodulatory response to SARS-CoV-2 virus in primary human broncho-alveolar epithelia [RNA-seq]

first: Carolyn

last: Paisie

first: Diana

last: Castaneda

first: Sonia

last: Jangra

first: Marina

last: Yurieva

first: Jan

last: Martinek

first: Megan

last: Callender

first: Matthew

last: Coxe

first: Angela

last: Choi

first: Juan

last: García-Bernalt

first: Jianan

last: Lin

first: Te-Chia

last: Wu

first: Florentina

last: Marches

first: Damien

last: Chaussabel

last: Yu

last: Salner

first: Michael


title: Establish a rapid and efficient chemical reprogramming platform (CUT&Tag)

status: Public on May 03 2023

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

country: China

institute: Zhejiang University

summary: Chemically reprogramming somatic cells to iPSCs is time-consuming and low-efficiency. Here, we discribe a rapid chemical reprogramming condition enabling generating iPSCs from MEFs in 12 days. To further investigate the mechemisms and draw an epigenetic maps during the rapid chemical reprogramming, we performed time-course RNA-seq, ATAC-seq, RRBS and CUT&Tag (H3K4me3, H3K18la, H3K9me3, H3K27me3 and H3K27ac).

overall_design: Cells were collected every 2 days of reprogramming along with riPSCs were used for CUT&Tag.

first: Xi

last: Chen

first: Saiyong

last: Zhu


title: Intranasal administration of adenoviral vaccines expressing SARS-CoV-2 spike protein improves vaccine immunity in mouse models

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

summary: Intranasal vaccines can prime or recruit to the respiratory epithelium mucosal immune cells capable of preventing transmission of SARS-CoV-2. We found that a single intranasal dose of serotype 5-based adenoviral vectors expressing either the receptor binding domain (Ad5-RBD) or the complete ectodomain (Ad5-S) of the SARS-CoV-2 spike protein was effective in inducing i) secretory and serum anti-spike IgA and IgG, ii) robust SARS-CoV-2-neutralizing activity in the serum and in respiratory secretions, iii) rigorous spike-directed T helper 1 cell/cytotoxic T cell immunity, and iv) protection of wild-type mice from a challenge with the SARS-CoV-2 beta variant. Our data confirm and extend previous studies reporting promising preclinical results on vector-based intranasal SARS-CoV-2 vaccination, and support the potential of this approach to elicit mucosal immunity for preventing reinfection and transmission of SARS-CoV-2 more effectively than the currently available vaccines.

overall_design: Here we report a comprehensive series of studies to explore the intranasal vaccines using various mouse models, including HLA class II-humanized transgenic strains. To improve SARS-CoV-2 vaccine efficacy, and to better address the global demand for safe and affordable vaccines against COVID-19, we have developed two human adenovirus 5-vectored vaccines, one expressing an RBD fragment (Ad5-RBD) and the other a long version of the spike protein (Ad5-S). To test the efficacy of an Ad5-vectored, codon-optimized RBD vaccine (Ad5-RBD), we performed dose testing by single treatment via the nose (intranasal, i.n.) or muscle (intramuscular, i.m.) of wildtype Balb/c and HLA-DQB1*06:02 transgenic Ab0 NOD (HLA-DQ6) mice.

first: Katarzyna

last: Leskinen

first: Tobias

last: Freitag


title: Vitamin D inhibition of metastasis and oxidative stress in osteosarcoma

city: Coral Gables

first: Thomas

last: Lisse

state: Florida

address: 1801 Memorial Drive

department: Biology

institute: University of Miami

summary:
We investigated how the biologically active form of vitamin D (1,25(OH)2D3) inhibits the epithelial-to-mesenchymal transition (EMT), a critical step in the development of a migratory phenotype in epithelial tumor cells, as well as migration in general, using osteosarcoma (OS) as a model. We looked at how 1,25(OH)2D3 affected pre- and post-EMT migratory states in non-metastatic MG63 and metastatic LM7 OS cell models. In scratch and Boyden chamber assays, 1,25(OH)2D3 inhibited cell migration and invasion, but LM7 cells responded significantly less than MG63 cells (50 vs 26 percent decrease, respectively). 1,25(OH)2D3 inhibited the expression of EMT-inducing genes (e.g., SNAI2) and extracellular contact regulatory genes in MG63 cells but not in LM7 cells (e.g., CD44, MMP3). In comparison to MG63 cells, LM7 cells had significantly lower baseline VDR transcript levels but higher SNAI2 transcript levels. Furthermore, ATAC-seq analysis revealed that 1,25(OH)2D3 epigenetically repressed SNAI2 in MG63 cells, implying that LM7 cells may be constitutively induced to undergo EMT via VDR de-repression mediated by increased SNAI2 levels. Both cell lines appeared to activate an antioxidative pathway involving SOD2 upregulation and concurrent reactive oxygen species (ROS) reduction (e.g., H2O2). ATAC-seq analysis revealed that 1,25(OH)2D3 does not epigenetically regulate SOD2 in MG63 cells, implying a previously unknown indirect link promoting anti-EMT and anti-metastatic oxidation states in both OS cell lines. We studied the fate and migration of mouse hair follicle stem cell progenitor cells after wounding with or without the Vdr because cutaneous wounding and metastasis involve similar signaling factors that regulate cell migration. Conditional loss of Vdr in epithelial progenitor cells promoted cell migration and wound healing in comparison to control animals, indicating that Vdr signaling inhibits cell migration in general. Our findings show that vitamin D signaling inhibits cell migration both in vivo and in vitro, and that inhibiting reactive oxygen species (ROS) in both pre-EMT and post-EMT OS cells is a possible vitamin D mechanism and therapeutic strategy for preventing the onset and progression of OS.
MG63 human osteosarcoma cell line treated with vehicle (ethanol) or 1,25(OH)D (10nM) for 24 and 48 hours.

overall_design: RNA-seq

first: Sandra

last: Rieger

first: Enrico

last: Campobianco


title: The landscape of immune cells in the mouse HCC model with F1 and F3 subtype

city: Nanjing

first: Binghua

last: Li

state: Jiangsu

address: Zhongshan road 321, Nanjing, Jiangsu, China

department: Department of Hepatobiliary Surgery

institute: the Affiliated Drum Tower Hospital, Medical School of Nanjing University

summary: In this study, we identified and validated a molecular classification of hepatocellular carcinoma (HCC) patients based on 42 fatty acid degradation (FAD) genes. The F1 subtype was characterized by the lowest expression of FAD genes, whereas F3 subtype had the highest expression levels, and F2 had the intermediate expression levels of FAD genes. We characterized the immune microenvironment in HCC patients from different FAD subtypes. To further explore the immune landscape of HCC, we generated the Nras-driven HCC model (belonging to the F1 subtype) and the Akt1-driven HCC model (belonging to the F3 subtype) by hydrodynamic tail vein injection (HTVi) of oncogenes together with the sleeping beauty transposase. The tumor tissues were resected from the liver 14 weeks after the hydrodynamic delivery of the plasmids, isolated for single cells, and prepared for scRNA-seq.

overall_design: Mouse liver tumors were induced by hydrodynamic tail vein injection (HTVi) of oncogenes together with the sleeping beauty transposase. To generate the Nras-driven HCC model, two expression constructs for human N-Ras (19 μg/mouse) and human c-Myc (1 μg/mouse), together with a plasmid expressing Sleeping Beauty transposase (2 μg/mouse) were co-transfected. To generate the AKT1.MYC model, two expression constructs for Akt1 (10 μg/mouse) and human c-Myc (10 μg/mouse), together with a plasmid expressing Sleeping Beauty transposase (5 μg/mouse) were co-injected. All plasmid DNAs were diluted in phosphate-buffered saline (PBS) and injected at a final volume of 10% of the mouse’s body weight through the tail vein in less than 8 seconds. The tumor tissues were resected from the liver 14 weeks after the hydrodynamic delivery of the plasmids.

first: Yunzheng

first: Decai


title: Single-cell RNA sequencing analysis of blood B cells from human allogeneic hematopoietic transplant patients

city: Durham

first: Stefanie

last: Sarantopoulos

state: NC

address: 2 Genome Ct, MSRB2

department: Department of Medicine

institute: Duke University Medical Center

summary: Single cell analysis of gene expression in blood B cells from allogeneic hematopoietic stem cell transpant (HCT) patients that either developed chronic GVHD, or never developed chronic GVHD.

overall_design: B cells were purified from viably cryopreserved PBMC samples of de-identified HCT patients by magnetic bead negative sorting (Miltenyi Human B Cell Isolation Kit II). Following an 18h culture period as resting B cells or ATRA-treated B cells, dead cells were eliminated (STEMCELL Technologies Dead Cell Removal Kit) and the samples immediately submitted for single-cell RNA-Seq library preparation (Duke Molecular Genomics Core).

first: Jonathan

last: Poe

first: Jiyuan

last: Fang

first: Dadong

last: Zhang

first: Jichun

last: Xie

first: Kouros

last: Owzar


title: naive T vs imm_sol Ab treated and LatA treated

city: Gwangju

first: Changduk

last: Jun

state: Not US or Canada

address: Bukgu oryongdong GIST

department: life science

country: South Korea

institute: Gwangju institute of science and technology(GIST)

summary:
Although T cell activation is closely linked to internalization of the T cell antigen receptor (TCR), relatively few studies have examined the release of TCRs via shedding of T cell microvilli following physical interaction with cognate antigen-presenting cells. In this study, we investigated the physiological implications of the release of TCRs and other external membrane components. We term this event “trogocytic molting”, as it occurs through a combined process of trogocytosis and enzymatic vesiculation of microvillar membrane structures. Surprisingly, in contrast to TCR internalization, this event leads to rapid upregulation of surface TCRs and remarkable metabolic reprogramming of cholesterol and fatty acids synthesis to meet the demands of clonal expansion, which drives multiple rounds of division and cell survival. These findings suggest that, contrary to the long-standing paradigm that emphasizes the importance of TCR internalization, external membrane loss, including TCRs, is a significant mechanism for clonal expansion
We mimicked the internalization and release of TCR through the sab iab condition.

overall_design: In mouse CD3 T cells, we analyzed gene expression in each stimulation at three time points: 0 h (NT),  3 h, and 24 h time point.

first: Hye-Ran

last: Kim

first: ChangDuk

first: JeongSu

last: Park


title: Cx3cr1 controls kidney resident macrophage heterogeneity

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

institute: University of Oklahoma Health Sciences Center

summary: Kidney macrophages are comprised of both monocyte-derived and tissue resident populations; however, the heterogeneity of kidney macrophages and factors that regulate their heterogeneity are poorly understood. Herein, we performed single cell RNA sequencing (scRNAseq), fate mapping, and parabiosis to define the cellular heterogeneity of kidney macrophages in healthy mice. Our data indicate that healthy mouse kidneys contain four major subsets of monocytes and two major subsets of kidney resident macrophages (KRM) including a population with enriched Ccr2 expression, suggesting monocyte origin. Surprisingly, fate mapping data using the newly developed Ms4a3Cre Rosa Stopf/f TdT model indicate that less than 50% of Ccr2+ KRM are derived from Ly6chi monocytes. Instead, we find that Ccr2 expression in KRM reflects their spatial distribution as this cell population is almost exclusively found in the kidney cortex. We also identified Cx3cr1 as a gene that governs cortex specific accumulation of Ccr2+ KRM and show that loss of Ccr2+ KRM reduces the severity of cystic kidney disease in a mouse model where cysts are mainly localized to the kidney cortex. Collectively, our data indicate that Cx3cr1 regulates KRM heterogeneity and niche-specific disease progression.

overall_design: 4 samples were analyzed, all from 6 week old female mice. Two biological duplicates for each genotype.

first: Alex

last: Yashchenko

first: Sarah

middle: J

last: Bland

first: Cheng

last: Song

first: Ummey

middle: K

last: Ahmed

first: Rachel

last: Sharp

first: Jeremie

middle: M

last: Lever

first: Zhang

first: Nancy

last: Gonzalez

first: Dustin

middle: Z

last: Revell

first: Ernald

last: Aloria

first: Shanrun

last: Liu

first: Michael

middle: R

last: Crowley

first: Kenneth

middle: L

last: Jones

first: James

middle: F

last: George

first: Michal

last: Mrug

first: David

last: Crossman

first: Katharina

last: Hopp

first: Mary

middle: B

last: Humphrey

first: Florent

last: Ginhoux

first: Morgan

last: Smith


title: Obesity and dyslipidemia are associated with partially reversible modifications to DNA hydroxymethylation of apoptosis- and senescence-related genes in swine adipose-derived mesenchymal stem/stromal cells

city: Rochester

first: Lilach

middle: O

last: O Lerman

state: Minnesota

address: 200 First St. SW

department: Division of Nephrology & Hypertension

institute: Mayo Clinic

type: Methylation profiling by high throughput sequencing

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa


title: Identification of HNF1A targets in WT hPSC-derived kidney organoids

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

summary: To determine the transcriptional targets of HNF1A in human kidney cells, we performed chromatin immunoprecipitation sequencing on D28 kidney organoids generated from WT hPSCs using an established protocol by Morizane et al. (2015) doi: 10.1038/nbt.3392. ChIP-Seq analysis revealed that HNF1A preferentially bound onto the promoter regions of various genes that are predominantly expressed in renal proximal epithelial cells. qRT-PCR validation was performed on various human kidney cell models to confirm that HNF1A binds to promoter regions of selected target genes to regulate their gene expression.

overall_design: ChIP-Seq was performed on end-stage kidney organoids obtained on day 28 of the directed differentiation of WT hPSCs (1 clone from H9).

first: Jun

middle: W

last: CHAN

first: Claire

last: NEO

first: Soumita

last: GHOSH

last: TEO


title: Nonsense-mediated decay constrains nociceptive responses through repression of the integrated stress response

city: Madison

first: Zachary

middle: T

last: Campbell

state: WI

address: 1111 Highland Avenue

department: Anesthesiology

institute: University of Wisconsin - Madison

summary: RNA stability is meticulously controlled. Here, we sought to determine if an essential post-transcriptional regulatory mechanism plays a role in pain. Nonsense-mediated decay (NMD  ) safeguards against translation of mRNAs that harbor premature termination codons and controls the stability of roughly 10% of typical protein-coding mRNAs. It hinges on the activity of the conserved kinase SMG1. Both SMG1 and its target UPF1 are expressed in sensory neurons throughout the dorsal root ganglion (DRG). SMG1 protein is present in DRG neurons and their fibers in the sciatic nerve. Using high-throughput sequencing, we examined changes in mRNA abundance following inhibition of SMG1. Among the characteristics of NMD substrates, the most prominent is structure specifically in the 3′UTR. We confirmed multiple NMD stability targets in sensory neurons including ATF4. AFT4 is preferentially translated during the integrated stress response (ISR). This led us to ask if suspension of NMD induces the ISR. Indeed, blockade of NMD increases eIF2-alpha phosphorylation, a key marker of the integrated stress response. Next, we examined the effects of SMG1 inhibition on pain-associated behaviors. Peripheral inhibition of SMG1 result in mechanical hypersensitivity that persists for several days and priming to a subthreshold dose of PGE2. Priming was fully rescued by a small molecule inhibitor of the ISR. Collectively, our results indicate that suspension of NMD promotes pain through activation of the ISR.

overall_design: RNA-sequencing of mouse DRG cultures.

first: June

last: de la Peña

first: Rebecca

last: Chase

first: Nikesh

last: Kunder

first: Tzu-Fang

last: Lou

first: Alexander

last: Stanowick

first: Prarthana

last: Suresh

first: Patrick

first: Tarjani

last: Shukla

first: Theodore

last: Price


title: Does heat stroke induces heat intolerance?: What genes tell us

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: RNA samples of each group, extracted from PBMCs (Peripheral blood mononuclear cell) , were hybridized on two dye array. Within groups and between groups analyses to identify canonical pathways and enriched biological annotations were conducted.

overall_design:
3 experimental groups ; 2 months after heat stroke prior to performance of the HTT-R test termed basal (0) , HTT-R test end after 120 minutes (1) and Recovery from HTT-R test after 180 minutes (2). Each of the experimental groups includes 3 repeats that are composed of a pool of 3 subjects that were determined as Tolerant (HT) or Intolerant (HI) to heat by the HTT-R test outcomes .
*** Submitter declares raw data files are no longer available.

first: Michal

last: Horowitz

first: Dani

last: Kopeliovich

first: Yoav

first: Sharona

last: Elgavish

first: Hagai

last: Shermann

last: Moran


title: Identification of Trichomonas vaginalis 5-nitroimidazole resistance targets

status: Public on Apr 30 2023

city: Birmingham

first: Keonte

middle: Jamel

last: Graves

state: AL

address: 1900 University Blvd, THT 230

department: Medicine-Infectious Diseases

institute: The University of Alabama at Birmingham

summary: We aimed to delineate mechanisms of T. vaginalis resistance using transcriptome profiling of metronidazole (MTZ)-resistant and sensitive T. vaginalis clinical isolates.

overall_design: RNA sequencing, bioinformatics, and biostatistical analyses were performed to identify differentially expressed genes (DEGs) in the MTZ-resistant vs. sensitive T. vaginalis isolates.

first: Colin

last: Reily

first: Hemant

last: Tiwari

first: Vinodh

last: Srinivasasainagendra

first: W

middle: E

last: Secor

first: Jan

last: Novak

first: Christina

last: Muzny


title: naive T vs conA treated sample

first: Changduk

last: Jun

summary:
Although T cell activation is closely linked to internalization of the T cell antigen receptor (TCR), relatively few studies have examined the release of TCRs via shedding of T cell microvilli following physical interaction with cognate antigen-presenting cells. In this study, we investigated the physiological implications of the release of TCRs and other external membrane components. We term this event “trogocytic molting”, as it occurs through a combined process of trogocytosis and enzymatic vesiculation of microvillar membrane structures.
Surprisingly, in contrast to TCR internalization, this event leads to rapid upregulation of surface TCRs and remarkable metabolic reprogramming of cholesterol and fatty acids synthesis to meet the demands of clonal expansion, which drives multiple rounds of division and cell survival. These findings suggest that, contrary to the long-standing paradigm that emphasizes the importance of TCR internalization, external membrane loss, including TCRs, is a significant mechanism for clonal expansion

first: Hye-Ran

last: Kim

first: Chang-Duk

first: Jeong-Su

last: Park


title: Deletion of taf1 and taf5 in Zebrafish Capitulate Cardiac and Craniofacial Abnormalities Associated with TAFopathies through Perturbations in Metabolism

city: St. Louis

first: Kory

last: Lavine

address: 660 S Euclid Ave

department: Cardiology

institute: Washington University School of Medicine

summary: Intellectual disability is a neurodevelopmental disorder that affects 2-3% of the general population. Syndromic forms of intellectual disability frequently have a genetic basis and are often accompanied by additional developmental anomalies. Pathogenic variants in components of TATA-binding protein associated factors (TAFs) have recently been identified in a subset of patients with intellectual disability, craniofacial hypoplasia, and congenital heart disease. This syndrome has been termed as a TAFopathy and includes mutations in TATA binding protein (TBP), TAF1, TAF2, and TAF6. The underlying mechanism by which TAFopathies give rise to neurodevelopmental, craniofacial, and cardiac abnormalities remains to be defined. Through a forward genetic screen in zebrafish, we have recovered a recessive mutant phenotype characterized by craniofacial hypoplasia, ventricular hypoplasia, heart failure at 96 hours post-fertilization and lethality, and show it is caused by a nonsense mutation in taf5. CRISPR/CAS9 mediated gene editing revealed that these defects where phenocopied by  mutations in taf1 and taf5. Mechanistically, taf5-/- zebrafish displayed misregulation in metabolic gene expression and metabolism as evidenced by RNA sequencing, respiration assays, and metabolite studies. Collectively, these findings suggest that the TAF complex may contribute to neurologic, craniofacial, and cardiac development through regulation of metabolism.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for corastl325 embryos and their unaffected clutchmates.

first: Jamison

last: Leid

first: Ryan

middle: S

last: Gray

first: Lila

last: Solnica-Krezel


title: UBE2C expression is elevated in hepatoblastoma and correlates with inferior patient survival

first: Ruth

last: Nousiainen

address: Tuhkolmankatu 8

summary: To gain insight into the pathobiology of hepatoblastoma (HB), RNA sequence analysis and protein-protein interaction analysis of previously established and sequenced HB samples were conducted. Ubiquitination was identified as a key pathway dysregulated in HB and UBE2C, encoding an E2 ubiquitin ligase often overexpressed in cancer cells, was markedly upregulated in 5 of the 6 HB cell lines. The silencing of UBE2C in HUH6 HB cell model resulted in decreased cell viability and migration. RNA sequencing analysis showed alterations in cell cycle regulation after UBE2C knockdown.

overall_design: RNA-seq data analysis of HUH6 cells after UBE2C knockdown.

first: Katja

last: Eloranta

first: Noora

last: Isoaho

first: Stefano

last: Cairo

first: David

last: Wilson

first: Markku

last: Heikinheimo

first: Marjut

last: Pihlajoki


title: Synergistic Targeting of Menin in AML

city: Mainz

first: Johanna

last: Rausch

address: Langenbeckstraße 1

department: Department of Hematology and Medical Oncology

institute: University Medical Center, Johannes Gutenberg-University Mainz

summary: Menin inhibitors have demonstrated profound preclinical activity in MLL1-rearranged and NPM1 mutated AML and in this context, ziftomenib is a novel compound currently assessed in a clinical phase I/II trials. We assessed preclinical effects of ziftomenib and demonstrate profound synergy in combination with compounds targeting chromatin regulation and apoptosis including the BCL2 inhibitor venetoclax which was validated in primary AML samples and an MLL-r and NPM1 mutated AML xenograft model.

overall_design: RNA sequencing of indicated cell lines treated with 150nM ziftomenib (KO-539) or DMSO for 4 days in OCI-AML3 and MOLM13  and 3 days in MV411. OCI-AML3 were additionally treated with 100nM VTP-50469 or DMSO for 4 days. All experiments performed in triplicates.

first: Margarita

last: Dzama

first: Nadezda

last: Dolgikh

first: Hanna

last: Stiller

first: Stephan

last: Bohl

first: Catharina

last: Lahrmann

first: Kerstin

last: Kunz

first: Linda

last: Kessler

first: Hakim

last: Echchannaoui

first: Chun-Wie

last: Chen

first: Thomas

last: Kinder

first: Konstanze

last: Döhner

first: Francis

last: Burrows

first: Matthias

last: Theobald

first: Daniel

last: Sasca

first: Michael

last: Kühn


title: A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer

city: San Francisco

first: Valerie

last: Weaver

address: 513 Parnassus Avenue, HSE 560

department: Surgery

institute: UCSF

summary: Intratumor heterogeneity associates with poor patient outcome. Stromal stiffening also accompanies cancer. Whether cancers demonstrate stiffness heterogeneity, and if this is linked to tumor cell heterogeneity remains unclear. We developed a method to measure the stiffness heterogeneity in human breast tumors that quantifies the stromal stiffness each cell experiences and permits visual registration with biomarkers of tumor progression. We present Spatially Transformed Inferential Force Map (STIFMap) which exploits computer vision to precisely automate atomic force microscopy (AFM) indentation combined with a trained convolutional neural network to predict stromal elasticity with micron-resolution using collagen morphological features and ground truth AFM data. We registered high-elasticity regions within human breast tumors colocalizing with markers of mechanical activation and an epithelial-to-mesenchymal transition (EMT). The findings highlight the utility of STIFMaps to assess mechanical heterogeneity of human tumors across length scales from single cells to whole tissues and implicates stromal stiffness in tumor cell heterogeneity.

overall_design: RNAseq of soft and stiff patient-derived xenograft tumors from three different patients. Each patient-stiffness combination has three replicates for 18 samples total.

first: Jason

last: Northey

first: Connor

last: Stashko


title: Modulation of lncRNA links endothelial glycocalyx to vascular dysfunction of tyrosine kinase inhibitors [dataset 1]

city: Chicago

first: Jordan

last: Jousma

state: Illinois

address: 909 South Wolcott

department: Pharmacology and Regenerative Medicine

institute: University of Illinois

summary:
Aims: Novel cancer therapies leading to increased survivorship of cancer patients have been negated by a concomitant rise in cancer therapies-related cardiovascular toxicities. Sunitinib, a first line multi receptor tyrosine kinase inhibitor (TKI), has been reported to cause vascular dysfunction although the initiating mechanisms contributing to this side effect remain unknown. Long non-coding RNAs (lncRNAs) are emerging regulators of biological processes in endothelial cells (ECs); however, their roles in cancer therapies-related vascular toxicities remain underexplored.
Methods and Results: We performed lncRNA expression profiling to identify potential lncRNAs that are dysregulated in human induced pluripotent stem cells-derived ECs (iPSC-ECs) treated with sunitinib. We show that the lncRNA hyaluronan synthase 2 antisense 1 (HAS2-AS1) is significantly diminished in sunitinib-treated iPSC-ECs. Sunitinib was found to downregulate HAS2-AS1 by an epigenetic mechanism involving hypermethylation. Depletion of HAS2-AS1 recapitulated sunitinib-induced detrimental effects on iPSC-ECs, whereas CRISPR-mediated activation of HAS2-AS1 reversed sunitinib-induced dysfunction. We confirm that HAS2-AS1 stabilizes the expression of its sense gene HAS2 via an RNA/mRNA heteroduplex formation. Knockdown of HAS2-AS1 led to reduced synthesis of hyaluronic acid (HA) and upregulation of ADAMTS5, an enzyme involved in extracellular matrix degradation, resulting in disruption of the endothelial glycocalyx which is critical for ECs. In vivo, sunitinib-treated mice showed reduced coronary flow reserve, accompanied by a reduction in has2os and degradation of the endothelial glycocalyx. Finally, we identify that treatment with high molecular-weight HA can prevent the deleterious effects of sunitinib both in vitro and in vivo by preserving the endothelial glycocalyx.
Conclusions: Our findings highlight the importance of lncRNA-mediated regulation of the endothelial glycocalyx as an important determinant of sunitinib-induced vascular toxicity and reveal potential novel therapeutic avenues to attenuate sunitinib-induced vascular dysfunction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three lines of hiPSC-EC  treated with either DMSO or 1µM SUN for 72 hours

first: Sarath Babu

last: Nukala

first: Sang-Ging

last: Ong


title: Multiple paths of plant host toxicity are associated with the fungal toxin cercosporin

first: Eugene

last: Koh

address: 1 Research Link

institute: Temasek Life Sciences Laboratories

summary: Effect of various Cercosporin concentrations on gene expression in Arabidopsis

overall_design: Total RNA obtained from 2-week old WT (Col-0) Arabidopsis seedlings incubated with various concentrations of cercosporin before exposure to light (30 µE) for 30min

first: Robert

last: Fluhr


title: Helicase-like transcription factor (Hltf)-deletion activates Hmgb1-Rage axis and granzyme A-mediated killing of pancreatic β cells resulting in neonatal lethality

city: Lubbock

first: Beverly

last: Chilton

state: TX

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

summary: Epigenetic mechanisms are integral to pancreatic β cell function. Promoter hypermethylation of the helicase like-transcription factor (HLTF) gene—a component of the cellular DNA damage response that contributes to genome stability—has been implicated in age-associated changes in β cells.  To study HLTF, we generated global and β cell-specific (β) Hltf knockout (KO) immune competent (IC) and immune deficient (ID) Rag2-/IL2- mice. IC global and β Hltf KO mice were neonatal lethal whereas ID global and β Hltf KO newborn mice had normal survival. This focused our investigation on the effects of Rag2 interruption with common gamma chain interruption on β cell function/survival. Three-way transcriptomic (RNAseq) analyses of whole pancreata from IC and ID newborn β Hltf KO and wild type (Hltf +/+) controls combined with spatially resolved transcriptomic analysis of formalin fixed paraffin embedded tissue, immunohistochemistry and laser scanning confocal microscopy showed DNA damage caused by β Hltf KO in IC mice upregulated the Hmgb1-Rage axis and a gene signature for innate immune cells. Perforin-delivered granzyme A (GzmA) activation of DNase, Nme1, showed damaged nuclear single-stranded DNA (γH2AX immunostaining). This caspase-independent method of cell death was supported by transcriptional downregulation of Serpinc1 gene that encodes a serine protease inhibitor of GzmA. Increased transcriptional availability of complement receptors C3ar1 and C5ar1 likely invited crosstalk with Hmgb1 to amplify inflammation. This study explores the complex dialog between β cells and immune cells during development. It has implications for the initiation of type I diabetes in utero when altered gene expression that compromises genome stability invokes a localized inflammatory response.

overall_design:
Global and β cell-specific (β) Hltf knockout (KO) immune competent (IC) and immune deficient (ID) Rag2-/IL2- mice were generated for this study. Three-way transcriptomic (RNAseq) data of whole pancreata from IC and ID newborn β Hltf KO and wild type (Hltf +/+) controls are presented here.
Five basic steps were necessary to implement spatial transcriptomics technology. Step 1, placement of FFPE tissue (abdominal segments) on capture areas of a Visium gene expression (GEX) slide. Step 2, H&E staining followed by brightfield microscopic imaging with ZEISS Axioscan 7 high-performance slide scanner (White Plains, NY). Step 3, permeabilization of tissue and construction of barcoded libraries with a final sample index PCR all according to the manufacturer?s instructions. Step 4, NGS short-read sequencing (Illumina NovaSeq) of barcoded libraries by Genewiz (Azenta US, Inc, South Plainfield, NJ). Step 5, data analysis of tissue images and sequencing files in FASTQ format with Space Ranger run on Ubuntu 22.04 LTS ?Thelio Mira-b3 by System76, Inc. (Denver, CO). The space ranger aggr pipeline was used to aggregate data from replicate samples and from samples from the different biological conditions (IC, ID). Loupe browser visualization software was accessed in a desktop application via Windows (Dell Optiplex 990).
CPRIT Grant # RP190524 (TTUHSC Cancer Animal Facility Core, PI Dr. Scott L. Trasti):
This infrastructure grant provided funding for the ZEISS Axioscan 7 high-performance slide scanner.

first: Gurvinder

last: Kaur

first: Rebecca

middle: A

last: Helmer

first: Dalia

last: Martinez-Marin

first: Souad

last: Sennoune

first: Rachel

last: Washburn

first: Raul

last: Martinez-Zaguilan

first: Jannette

last: Dufour


title: Enhanced chondrogenic differentiation of iPS cell-derived mesenchymal stem/stromal cells via neural crest cell induction for hyaline cartilage repair

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

summary: Generate high-quality cartilage spheroids in vitro from iMSCs for regenerative medicine and tissue engineering

overall_design: The genes and signaling pathways regulating the chondrogenic susceptibility of iMSCs generated under different conditions were studied

first: Ikeya

last: Makoto

first: Denise

last: Zujur

first: Ziadoon

last: Al-Akashi


title: Anti-GD2 CAR-NKT cells in patients with relapsed or refractory neuroblastoma – a first-in-human phase 1 trial

city: HOUSTON

first: Leonid

last: Metelitsa

address: 3639 Skyline Dr1102 Bates Ave., Ste. 1570

department: Pediatrics

institute: BAYLOR COLLEGE OF MEDICINE/Texas Children's Hospital

summary: Vα24-invariant natural killer T cells (NKTs) have antitumor properties that can be enhanced by transgenic expression of tumor-specific receptors. Here, we report the results of the first-in-human clinical evaluation of autologous NKTs co-expressing a GD2-specific chimeric antigen receptor with interleukin (IL)15 (GD2-CAR.15) in 12 children with neuroblastoma (NB) treated on four dose levels (NCT03294954). Objectives included assessing safety, antitumor activity, and immune response. No dose-limiting toxicities occurred, and one patient had grade 2 cytokine release syndrome resolved by tocilizumab. The overall response rate was 25% (3/12) and disease control rate was 58% (7/12) including four patients with stable disease, two partial responses, and one complete response. CD62L+ NKT frequency in infused products correlated with CAR-NKT expansion in patients and was higher in responders than non-responders (71% vs 35.3%, p=0.002). Singe-cell RNA sequencing analysis identified B cell translocation gene 1 (BTG1) as one of the top upregulated genes in GD2-CAR.15-NKTs after in vitro serial tumor challenge. Genetic gain- and loss-of-function experiments revealed that BTG1 is a key driver of hyporesponsiveness in exhausted NKT and T cells. Crucially, NKTs co-expressing GD2-CAR.15 and BTG1-specific shRNA eradicated metastatic NB in mice. These results indicate that CAR-NKTs are safe, produce objective responses in NB patients, and that targeting BTG1 can enhance their therapeutic potency.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NKTs with BTG1 overexpression versus control luciferase overexpression

first: Chunchao

last: Zhang

first: Andras

last: Heczey


title: Genes expression  profiles of postmenopausal osteoporosis

status: Public on Apr 29 2023

city: Fuzhou

first: LH

last: Xie

address: 282hao,Wusi Road ,Gulou distract

institute: Fujian Academy of Traditional Chinese Medicine

summary: Investigate  genes expression  profiles of postmenopausal osteoporosis in bone(femur)

overall_design: 15 patients were divided into 12 patients with postmenopausal osteoporosis, another 3 healthy postmenopausal women as control group. Whole human genome oligo microarray were applied to explore gene expression difference of the two groups.

first: Shengqiang

last: Li

first: Jirong

last: Ge

first: Lihua

first: Juan

last: Chen


title: Identification of FAD subtypes in mouse HCC models

city: Nanjing

first: Binghua

address: Zhongshan road 321, Nanjing, Jiangsu, China

institute: the Affiliated Drum Tower Hospital, Medical School of Nanjing University

summary: In this study, we identified and validated a molecular classification of hepatocellular carcinoma (HCC) based on 42 fatty acid degradation (FAD) genes in clinical samples. We further searched PubMed for the RNA sequencing datasets of mouse models to identify the FAD subtypes in mouse HCC models. A total of 90 samples were collected from five publicly available datasets including 11 mouse HCC models. In addition, the transcriptome sequencing data of 8 samples from our two mouse models (NRAS.MYC.ND and AKT1.MYC.KD) were also included. This dataset aims to explore the transcriptomic characteristics of these two models.

overall_design: To generate the Nras-driven HCC model, two expression constructs for human N-Ras (19 μg/mouse) and human c-Myc (1 μg/mouse), together with a plasmid expressing Sleeping Beauty transposase (SB) (2 μg/mouse) were co-transfected. After 4 weeks, the NRAS.MYC.KD group was fed with a ketogenic diet (KD) purchased from Dyets (http://www.dyets-cn.com/, #HF89.5), which consisted of 0.1% carbohydrates, 89.5% fat, and 10.4% protein for another 4 weeks, whereas the NRAS.MYC.ND group was fed with the normal diet (ND) for another 4 weeks. The tumor tissues and nontumor tissues from eight mice were resected from the liver 8 weeks after the hydrodynamic delivery of the plasmids, isolated for RNA, and prepared for RNA-seq.

first: Yunzheng

first: Decai

last: Yu


title: Brain and Blood Hydroxymethylation in Mice after Lead (Pb) and DEHP Exposure

status: Public on Apr 28 2023

city: Ann Arbor

first: Maureen

last: Sartor

state: MI

address: 100 Washtenaw Ave

department: Computational Medicine and Bioinformatics

institute: University of Michigan

summary: The developing epigenome changes rapidly, potentially making it more sensitive to toxicant exposures. DNA modifications, including methylation and hydroxymethylation, are important parts of the epigenome that may be affected by environmental exposures. However, most studies do not differentiate between these two DNA modifications, possibly masking significant effects. To investigate the relationship between DNA hydroxymethylation and developmental exposure to common contaminants, a collaborative, NIEHS-sponsored consortium, TaRGET II, initiated longitudinal mouse studies of developmental exposure to human-relevant levels of the phthalate plasticizer di(2-ethylhexyl) phthalate (DEHP), and the metal lead (Pb). Exposures to 25 mg DEHP/kg of food (approximately 5 mg DEHP/kg body weight) or 32 ppm Pb-acetate in drinking water were administered to nulliparous adult female mice. Exposure began 2 weeks before breeding, and continued throughout pregnancy and lactation, until offspring were 21 days old. At 5 months, perinatally exposed offspring blood and cortex tissue were collected, for a total of 25 male mice and 17 female mice (n=5-7 per tissue and exposure). DNA was extracted and hydroxymethylation was measured using hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq). Differential peak and pathway analysis was conducted comparing across exposure groups, tissue types, and animal sex, using an FDR cutoff of 0.15. DEHP-exposed females had two genomic regions with lower hydroxymethylation in blood and no differences in cortex hydroxymethylation. For DEHP-exposed males, ten regions in blood (six higher and four lower) and 246 regions (242 higher and four lower) and four pathways in cortex were identified. Pb-exposed females had no statistically significant differences in blood or cortex hydroxymethylation compared to controls. Pb-exposed males, however, had 385 regions (all higher) and six pathways altered in cortex, but no differential hydroxymethylation was identified in blood. Overall, perinatal exposure to human-relevant levels of two common toxicants showed differences in DNA hydroxymethylation specific to sex, exposure type, and tissue, but male cortex was most susceptible to hydroxymethylation differences by exposure. Future assessments should focus on understanding if these findings indicate potential biomarkers of exposure or are related to functional long-term health effects.

overall_design: Hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq) genomic DNA from 5 month old mouse brain and blood perinatally exposed to DEHP (25 mg per kg chow), Pb (32 ppm in drinking water), and Control

first: Rebekah

last: Petroff

first: Kai

last: Wang

first: Raymond

last: Cavalcante

first: Claudia

last: Lalancette

last: Sautor


title: Maintenance of epithelial traits and resistance to mesenchymal reprogramming promote proliferation in metastatic breast cancer

city: Basel

first: Massimo

last: Saini

state: Basel Canton

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: Despite important advances in the treatment of breast cancer, the 5-year survival rate for patients with distant metastasis remains less than 30%. Metastasis is a complex, multi-step process beginning with local invasion and ending with the outgrowth of systemically disseminated cells into actively proliferating metastases that ultimately cause the destruction of vital organs. It is this last step that limits patient survival and, at the same time, remains the least understood mechanistically. Here, we focus on understanding determinants of metastatic outgrowth using metastatic effusion biopsies from stage IV breast cancer patients. By modelling metastatic outgrowth through xenograft transplantation, we show that tumour initiation potential of patient-derived metastatic breast cancer cells across breast cancer subtypes is strongly linked to high levels of EPCAM expression. Breast cancer cells with high EPCAM levels are highly plastic and, upon induction of epithelial-mesenchymal transition (EMT), readily adopt mesenchymal traits while maintaining epithelial identity. In contrast, low EPCAM levels are caused by the irreversible reprogramming to a mesenchymal state with concomitant suppression of metastatic outgrowth. The ability of breast cancer cells to retain epithelial traits is tied to a global epigenetic program that limits the actions of EMT-transcription factor ZEB1, a suppressor of epithelial genes. Our results provide direct evidence that maintenance of epithelial identity is required for metastatic outgrowth while concomitant expression of mesenchymal markers enables plasticity. In contrast, loss of epithelial traits is characteristic of an irreversible mesenchymal reprogramming associated to a deficiency for metastatic outgrowth. Collectively, our data provide a framework for the intricate intercalation of mesenchymal and epithelial traits in metastatic growth.

overall_design: Omni-ATAC-sequencing and RNA-sequencing on EMT-sensitive (M1-M3) and EMT-resistant (E1-E3) HMLE-TWIST1-ER single-cell clones.  RNA-seq on sorted EPCAM fractions of metastatic breast cancer cells from effusion biopsies from an ER+ (Patient 6, BPE22) and an ER- (Patient 1, BPE7) stage IV breast cancer patient.

first: Laura

last: Eichelberger

first: Helena

middle: D

last: Moreno

first: Corinna

last: Klein

first: Johanna

last: Bartsch

first: Mattia

last: Falcone

first: Manuel

last: Reitberger

first: Elisa

last: Espinet

first: Vanessa

last: Vogel

first: Elisabeth

last: Graf

first: Thomas

last: Schwarzmayr

first: Tim-Matthias

last: Strom

first: Mareike

last: Lehmann

first: Melanie

last: Königshoff

first: Nicole

last: Pfarr

first: Roberto

last: Würth

last: Donato

first: Simon

last: Haas

first: Saskia

last: Spaich

first: Marc

last: Sütterlin

first: Andreas

last: Schneeweiss

first: Wilko

last: Weichert

first: Gunnar

last: Schotta

last: Trumpp

first: Martin

last: Sprick

first: Christina

middle: H

last: Scheel


title: Single-cell transcriptomics reveals conserved regulatory networks in human and mouse interneuron development

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

country: United Kingdom

institute: UK Dementia Research Institute at Cardiff University

summary: Inhibitory GABAergic interneurons originate in the embryonic medial ganglionic eminence (MGE) and control network activity in the neocortex. Dysfunction of these cells is believed to lead to runaway excitation underlying seizure-based neurological disorders such as epilepsy, autism and schizophrenia. Despite their importance in heath and disease, our knowledge about the development of this diverse neuronal population remains incomplete. Here we conducted single cell RNA sequencing (scRNA-seq) of human fetal MGE from 10 to 15 weeks post conception. These MGE tissues are composed of largely cycling progenitors and immature post-mitotic interneurons with characteristic regional marker expression. Analysis of integrated human and mouse MGE data revealed species conserved transcriptomic profiles and regulatory program. Moreover, we identified novel candidate transcription regulators for human interneuron differentiation. These findings provide a framework for in vitro modelling of interneuron development and strategy for potentially enhance interneurons production from human pluripotent stem cells.

overall_design: Time course single cell RNAseq from the human embryonic medial ganglionic eminence (MGE) from post-conceptional weeks 10, 13, 14 and 15.

first: Francesca

last: Keefe

first: Anne

last: Rosser

first: Caleb

last: Webber

first: Meng

last: Li


title: Adult murine intestine epithelial cell chromatin accessibility

city: San Diego

first: Wendy

last: Huang

state: CA

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: Chromatin accessibility (ATAC-seq) in wildtype and DDX5-deficient intestine epithelial cells from adult mice.

overall_design: Small intestine or colonic epithelial cells were obtained from two pairs of 8-12 week old cohouse littermates.

first: Tianyun

last: Long

first: Claire

last: Luo

first: Yuxin

middle: J


title: GRID-seq studies of small intestinal epithelial cells from wildtype mice

summary: Long non-coding RNAs (lncRNAs) are critical regulators of mammalian gene programs.   Metastasis Associated Lung Adenocarcinoma Transcript 1 (Malat1) is one of the most abundant lncRNA expressed in the mammalian genome. Here, we report that Malat1 regulates intestinal epithelial cell programs and contributes to tissue homeostasis and tumorigenesis. Global RNA interactions with DNA by deep sequencing (GRID-seq) experiments revealed Malat1 chromatin localization in intestinal epithelial cells from the wildtype small intestine.

overall_design: Two independent biological replicates were performed.

first: Shengyun

last: Ma

first: Bing

last: Zhou

first: Xiang-Dong

last: Fu

last: Jia Men Huang


title: Malat1 regulates intestinal epithelial cell function

summary: The long-non-coding RNA Malat1 is abundantly expressed in all subsets of the intestinal epithelial cells (IEC). Here, we compared the transcriptome of the small intestinal and colonic  epithelium of wildtype and Malat1-/- mice under steady state. We found that Malat1 is involved in IEC homeostasis, intestinal microbial balance, and regulates programs involved in intestinal cancer.

overall_design: Two intestine tissues from each genotype were obtained from 9-11 week old cohoused littermate. Results of epithelium from Malat1-deficient (Malat1-/-) mice were compared to those from their gender-matched controls (Malat1+/+ or Malat1+/-).

middle: M


title: Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes [cell mixtures bulk]

city: Houston

first: Pavel

last: Sumazin

address: 1102 Bates St

department: Pediatric

institute: Baylor College of Medicine

summary: RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-Seq and snRNA-Seq, scnRNA-Seq for short), can help characterize the composition of tissues and reveal cells that influence key healthy and disease functions. However, the use of these technologies is challenging because of their relatively high costs and exacting sample collection requirements. Computational deconvolution methods that infer the composition of RNA-Seq-profiled samples using scnRNA-Seq-characterized cell types can expand the benefit of these technologies, but their effectiveness remains controversial. We produced the first systematic evaluation of deconvolution methods on datasets with either known compositions or based on concurrent RNA-Seq and scnRNA-Seq profiles. Our analyses revealed biases that are common to scnRNA-Seq 10X Genomics assays and illustrated the importance of accurate and properly controlled data preprocessing and method selection and optimization. Moreover, our results suggested that concurrent RNA-Seq and scnRNA-Seq profiles can help improve the accuracy of both scnRNA-Seq preprocessing and the deconvolution methods that employ them. Indeed, our proposed method, Single-cell RNA Quantity Informed Deconvolution (SQUID), combined RNA-Seq transformation and a dampened weighted least squares deconvolution approach to consistently outperform other methods in predicting the composition of cell mixtures and tissue samples. Moreover, our analysis suggested that only SQUID could identify outcomes-predictive cancer cell subtypes in pediatric acute myeloid leukemia and neuroblastoma datasets.

overall_design: We developed a solid tumor model that includes multiple solid-tumor cell types, immune cells, and lower-abundance stem cells. Following this model, we established in vitro cell mixtures that are composed of varying proportions of cells from 3 breast cancer lines (T47D, BT474, MCF7), monocytes (Thp1), lymphocytes (Jurkat), and stem cells (hMSC). Mixture composition was recorded based on input cell counts. Cells from each 6 cell line and from each 6 mixture were profiled by bulk RNA-seq in triplicates (n=36).


title: Differentially expressed RNA levels in the liver of aged LoxP and SIRT2-KOhep mice

city: Shanghai

first: qinghua

last: zhao

address: No. 100, Hai Ning Road

department: Department of Orthopedics

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

summary:
To investigate the differentially expressed RNA levels in the liver of aged LoxP and SIRT2-KOhep mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq of liver of aged LoxP and SIRT2-KOhep mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the liver of aged LoxP and SIRT2-KOhep mice.

first: Longshuai

last: Lin

first: Zengya

last: Guo

first: Enjun

last: He

first: Xidai

first: Difei

last: Wang

first: Yingting

last: Zhang

first: Weihong

first: Qian

last: Wei

first: Wei

first: Wanying

last: Wu

first: Jingchi

first: Lulu

last: Wo

first: Dengli

last: Hong

first: Junke

last: Zheng

first: Ming

first: Qinghua

last: Zhao


title: Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos [scRNA-seq]

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

institute: EPFL

summary: During development, Hox genes are activated in a time sequence following their relative positions on their clusters, leading to the proper identities of structures along the rostral to caudal axis. To understand the mechanism operating this Hox timer, we used ES-cells derived stembryos and show that the core of the process involves the start of transcription at the anterior part of the cluster, following Wnt signaling, and a concomitant loading of cohesin complexes enriched on the transcribed DNA segments, i.e., with an asymmetric distribution in favor of the anterior part the gene cluster. Chromatin extrusion then occurs with, along with time, successively more posterior CTCF sites acting as transient insulators, thus generating a progressive time-delay in the activation of more posterior-located genes due to long-range contacts with a flanking TAD. Mutant stembryos support this model and reveal that the iterated presence of evolutionary conserved and regularly spaced intergenic CTCF sites control the precision and the pace of this temporal mechanism.

overall_design: Single Cell RNA-seq data of stembryos

first: Hocine

last: Rekaik

first: Bénédicte

last: Mascrez

first: Célia

last: Bochaton

first: Alexandre

last: Mayran

first: Denis

last: Duboule


title: Profiling dynamic RNA-protein interactions using small molecule-inducible RNA editing

city: Princeton

first: Ralph

last: Kleiner

state: NJ

address: Frick Laboratory on Washington Rd

department: Chemistry

institute: Princeton University

summary: We develop a small molecule-inducible dimerization strategy of RBP of interest and adenosine deaminase domain to profile dynamic RBP-RNA interactions.

overall_design: A-to-G mutation analysis to identify G3BP1 substrates with comparative analysis of RNA-Seq data

first: Kyung

last: Seo


title: m6A Modification Regulates Planarian Regeneration [scRNA-seq]

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: Regeneration is the regrowth of damaged tissues or organs, a vital mechanism in response to damages from primitive organisms to higher mammals. Planarian possesses active whole-body regenerative capability owning to its vast reservoir of adult stem cells, neoblasts, providing an ideal model to delineate the underlying mechanisms for regeneration. RNA N6-methyladenosine (m6A) modification participates in many biological processes, including stem cell self-renewal and differentiation, in particular the regeneration of hematopoietic stem cells and axons. However, how m6A controls regeneration at the whole-organism level remains largely unknown. Here, we demonstrate that the depletion of m6A methyltransferase regulatory subunit wtap abolishes planarian regeneration, potentially through regulating genes related to cell-cell communication and cell cycle. Single-cell RNA-seq (scRNA-seq) analysis unveils that the wtap knockdown induces a unique type of neural progenitor-like cells (NP-like cells), characterized by specific expression of the cell-cell communication ligand grn. Intriguingly, the depletion of m6A-modified transcripts grn/cdk9 (or cdk7) axis rescues the defective regeneration of planarian caused by wtap knockdown. Overall, our study reveals an indispensable role of m6A modification in regulating whole-organism regeneration.

overall_design: single cell RNA-seq of 5 samples from planarian at 0 hpa, 6 hpa, 3 dpa, 7 dpa and 11 dpa, and  5 samples from wtap knockdown planarian at  0 hpa, 6 hpa, 3 dpa, 7 dpa and 11 dpa.

first: Y

last: Yang


title: Maintenance of epithelial traits and resistance to mesenchymal reprogramming promote proliferation in metastatic breast cancer [ATAC-seq]

first: Massimo

last: Saini

overall_design: Omni-ATAC-sequencing on EMT-sensitive (M) and EMT-resistant (E) HMLE-Twist1-ER single-cell clones with a doxycyclin-inducible ZEB1 (NM00128128) or GUS construct.

first: Laura

last: Eichelberger

first: Helena

last: Moreno

first: Corinna

last: Klein

first: Johanna

last: Bartsch

first: Mattia

last: Falcone

first: Manuel

last: Reitberger

first: Elisa

last: Espinet

first: Vanessa

last: Vogel

first: Elisabeth

last: Graf

first: Thomas

last: Schwarzmayr

first: Tim-Matthias

last: Strom

first: Mareike

last: Lehmann

first: Melanie

last: Königshoff

first: Nicole

last: Pfarr

first: Roberto

last: Würth

last: Donato

first: Simon

last: Haas

first: Saskia

last: Spaich

first: Marc

last: Sütterlin

first: Andreas

last: Schneeweiss

first: Wilko

last: Weichert

first: Gunnar

last: Schotta

last: Trumpp

first: Martin

last: Sprick

first: Christina

last: Scheel


title: Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos [cHi-C]

first: Lucille

last: Lopez-Delisle

overall_design: Capture Hi-C data of wt and mutant stembryos

first: Hocine

last: Rekaik

first: Bénédicte

last: Mascrez

first: Célia

last: Bochaton

first: Alexandre

last: Mayran

first: Denis

last: Duboule


title: Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes [AML single-cell]

first: Pavel

last: Sumazin

overall_design: We profiled diagnosis-relapse pairs from 6 pediatric AML patients (n=12) that were enrolled in AAML1031 using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq). All patients were treated at Texas Children's Cancer Center and consented to banking of tissue for research.

first: Michele

last: Redell


title: Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos [HiChIP]

overall_design: H3K27ac HiChIP data of wt stembryos at 120h


title: Nucleosome position mapping by micrococcal nuclease analysis in S. cerevisiae of Top1-AID/Top2-AID strains with auxin in galactose-rich media

city: Amsterdam

first: Tineke

last: Lenstra

state: North Holland

address: Plesmanlaan 121

department: Division of Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: We analyed the nucleosome positions by using 2 concentrations of micrococcal nuclease of haploid yeast strains that were grown in galactose containing synthetic complete media. Strains contained AID-tags at the endogeous TOP1 and TOP2 genes. One strain contained OsTIR1 and these cells  were either untreated or treated for 60 min with 500 uM auxin.

overall_design: Mnase-seq of 1 strain grown in raffinose-rich or galactose-rich media. Mnase-seq of 1 strains grown in galactose-rich media with and without treatment with auxin.

first: Heta

last: Patel

first: Ineke

last: Brouwer


title: Absence of the proprotein convertase FURIN in naive and in vitro activated CD8+ T cells

city: Tampere

first: Markus

middle: Juhani Tapani

last: Ojanen

address: Arvo Ylpön katu 34

institute: Tampere University

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

overall_design: Refer to individual Series


title: Absence of the proprotein convertase FURIN in naive CD8+ T cells modifies the transcriptome of the cells

summary:
Purpose: FURIN is a member of the proprotein convertase subtilisin/kexin (PCSK) family of serine endoproteases important in converting immature proproteins into their functional form. While FURIN is important in various aspects of the immune response such as in CD4+ T cells, FURIN´s role in CD8+ T cells is unclear. Here, we isolated naive CD8+ T cells from conditional T cell specific Furin KO (Cd4-Cre-Furinflox/flox) and WT (Furinflox/flox) mice and studied the genome-wide gene expression pattern using RNA sequencing.
Methods: Total RNA was isolated from the naive CD8+ T cells and the RNA-sequencing data was produced by the Finnish Functional Genomics Centre of Turku Bioscience (University of Turku, Turku, Finland) using Illumina HiSeq 2000. Data processing pipeline was built on Snakemake wrappers, and used STAR to quantify features from quality and adapter trimmed reads in gene level. Prior the normalisation and differential gene expression analysis with DESeq2, the matrix of raw gene counts was prefiltered to keep only rows that have at least 10 reads total. Result tables were annotated with biomaRt.
Results: Snakemake preprocessing pipeline measured 55573 genes against GRCm38, ENSEMBL release 97. 15843 of them was used for statistical testing. Full result tables for each treatment were ranked by p-value and the normalized DESeq2 abundances in samples were included. The genes with BH-adjusted p-value <0.05 was considered differentially expressed.
Conclusions: Our study revealed that the abscence of FURIN from the naive CD8+ T cells causes an effector-like phenotype in comparison to the WT cells.

overall_design: Total of 8 samples were analyzed; 5 Furin KO samples and 3 WT samples

first: Meeri

last: Pekkarinen


title: Single-nucleus Ribonucleic Acid-sequencing and Spatial Transcriptomics Reveal the Cardioprotection of Shexiang Baoxin Pill (MUSKARDIA) in Mice with Myocardial Ischemia-Reperfusion Injury

status: Public on Apr 26 2023

first: Wenyong

last: Lin

address: No. 528, zhangheng Rd

department: Cardiovascular Research Institute of Traditional Chinese Medicine

institute: Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine

summary: The Shexiang Baoxin Pill (MUSKARDIA) has been extensively used to treat cardiovascular diseases in China for four decades, and its clinical efficacy has been widely approved. However, the mechanism by which this is achieved remains largely unexplored. Research attempting to understand the underlying mechanism is ongoing, but the findings are controversial. Here, we aimed to explore the possible mechanism of MUSKARDIA in myocardial ischemia-reperfusion (I/R) injury using heart single-nucleus and spatial ribonucleic acid (RNA) sequencing.

overall_design: Heart tissues of C57BL/6 mice were isolated from sham, I/R, and MUSKARDIA groups and analyzed using scRNAseq.

first: Xin

last: Chen

first: Dongyuan

last: Wang

first: Ruixia

last: Lu

first: Chunling

last: Zhang

first: Zhenchao

last: Niu

first: Jie

first: Xiaofen

last: Ruan

first: Xiaolong


title: Imatinib mesylate on Mycobacterium marinum induced tail granulomas in mice

status: Public on Apr 27 2023

city: Atlanta

first: Daniel

last: Kalman

state: GA

address: 144 Whitehead Bldg., 615 Michael St.

department: Pathology

institute: Emory University

summary: We report that imatinib induces gene signatures indicative of immune activation at early time points post infection that resemble those seen at later ones, suggesting that imatinib accelerates but does not substantially alter anti-mycobacterial immune responses.

overall_design: RNA was isolated from mouse tails from uninfected C57BL/6J mice +/- 100mg/kg/day imatinib (Noinfection_NT and Noinfection_Imatinib), or C57BL/6J mice infected with Mycobacteium marinum for 6 days +/- 100mg/kg/day imatinib (1Week_NT and 1Week_Imatinb), or C57BL/6J mice infected with M. marinum for 21 days +/- 100mg/kg/day imatinib for the last 7 days of infection (3Week_NT and 3Week_Imatinb).

first: T

last: Cleverley

first: D


title: Comparative transcriptomic anlaysis of postharvest stored ‘Bingtangcheng’ and ‘Tarocco’ Blood orange fruit differing in fruit citrate and anthocyanin accumulation

city: Changsha

first: Ling

last: Sheng

address: Donghu

institute: Hunan Agricultural University

summary: Organic acids and anthocyanins are the most important compounds for the flavor and nutritional quality of citrus fruit. In this study, a comparative transcriptome analysis was conducted to elucidate the genes and pathways involved in the accumulation of citrate and anthocyanins in postharvest citrus fruit using ‘Tarocco’ blood orange (TBO) and ‘Bingtangcheng’ sweet orange (BTSO). About 2397, 2677, 3067, 3131 and 2960 differentially expressed genes (DEGs) between two materials were identified at 0, 15, 30, 60, and 90 DAS (days after storage) respectively. A robust core set of 825 DEGs temporally associated with the citrate and anthocyanin accumulation throughout the storage period. Further function enrichment revealed the up-regulated DEGs in TBO were mainly related to UV protection, flavonoid biosynthesis process and transcription factors (TFs). And the down-regulated DEGs were mainly related to inositol biosynthesis process, carboxylic acid/organic acid transmembrane transport and transporters. Moreover, co-expression network and correlation analysis revealed that 23 differentially expressed TFs may be responsible for the simultaneously positively regulation of citrate and anthocyanin accumulation. And 19 differentially expressed transporters may be involved in citrate metabolism and negatively correlated with citrate content. These results suggesting that the high anthocyanis and citrate levels in TBO compared with BTSO were porbably attributed to the highly active of a group of core TFs and lowly active of transporters, which will accordingly provide novel insights into the molecular mechanisms underlying the difference accumulation of citrate and anthocyanin content in TBO and BTSO.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for postharvest ‘Tarocco’ Blood orange and ‘Bingtangcheng' sweet orange fruit.

first: Yan

last: Jin

first: Manyu

last: Liao

last: Li

first: Xiaoqian

last: Ma

first: Huimin

first: Jian

last: Han

first: Dazhi

first: Junfeng

last: Yang

first: Xiaopeng


title: ExpressAnalyst: a unified platform for RNA-seq analysis in non-model species

city: Ste-Anne-de-Bellevue

first: Yeon-Seon

last: Jeon

state: Quebec

address: 21111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

summary: The increasing application of RNA-seq to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst (www.expressanalyst.ca), a web-based tool for processing, analyzing, and interpreting RNA-seq data from any eukaryotic species. ExpressAnalyst contains a series of modules that enable raw data processing and annotation of FASTQ files, and statistical and functional analysis of counts tables and gene lists. All modules are integrated with EcoOmicsDB, an ortholog database that enables comprehensive analysis for species without a reference transcriptome. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, ExpressAnalyst enables researchers to obtain global expression profiles and gene-level insights from raw RNA-seq reads within 24 hours. Here, we present ExpressAnalyst and demonstrate its utility with a case study of RNA-seq data from multiple non-model salamander species, including two that do not have a reference transcriptome.

overall_design: ExpressAnalyst contains recently updated version 2.0 of the Seq2Fun algorithm. To ensure that Seq2Fun 2.0 also reproduces results obtained using traditional approaches, we carried out two case studies using organisms with reference transcriptomes (American lobster and zebrafish). Here, we publish the lobster data. Stage I lobster larvae were exposed for 24hrs to four doses of WAF (10%, 19%, 37% and 72%) a positive control (1-methylnaphthalene, at 0.3 mg/L corresponding to the estimated concentration of EC20) or a negative control (0.22 µm filtered seawater). Due to the lack of effects reported on survival, molting and respiration after WAF exposures, only the highest dose of WAF (72% WAF) was considered for transcriptomics analysis. RNA extraction of whole larvae exposed to 72% WAF (n = 7), methylnaphthalene (n = 6) and filtered seawater (n = 6) was performed using Trizol. The transcriptomes were sequenced using Novaseq Illumina at 28M reads per library.

first: Peng

last: Liu

first: Jessica

last: Ewald

first: Zhiqiang

last: Pang

first: Elena

last: Legrand

first: Jonathan

last: Sangiovanni

first: Orcun

last: Hacariz

first: Guangyan

last: Zhou

last: Head

first: Niladri

last: Basu

first: Jianguo

last: Xia


title: The invadopodial and cytoskeletal regulator glycine- and cysteine-rich protein 2 induces pro-metastatic matrix metalloproteinase expression in breast cancer cells

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Actin cytoskeleton has multiple functions in cancer cell invasion and metastasis; yet how these functions are coordinated remains unclear. In the cytoplasm, actin is necessary for the formation of specialized membrane protrusions, termed invadopodia, that concentrate and secrete extracellular matrix-degrading enzymes, particularly the matrix metalloproteinases (MMPs), facilitating tumor cell invasion. We recently identified cysteine- and glycine-rich protein 2 (CRP2) as an actin-crosslinking protein whose activity is required for the assembly and elongation of the invadopodium actin backbone. Here, we report that CRP2 is also located in the nucleus of breast cancer cells to induce a complementary pro-metastasis gene expression program mostly related to breast cancer cell invasion and metastasis. We showed in this present study that CRP2 interacts with the transcription factors SRF and GATA3 to regulated the expression of MMP-9 and MMP-13 respectively. Overall, our data indicate that CRP2 act a key mediator of tumor cell invasion.

overall_design: mRNA profiles between control and CSRP2 knocked down MDA-MB-231 cells

first: Takouhie

last: Mgrditchian

first: Clément

last: Thomas

first: Arnaud

last: Muller

last: Kaoma


title: m6A Modification Regulates Planarian Regeneration [MeRIP-seq]

first: Bao-Fa

last: Sun

summary: The fundamental of regeneration process of invertebrates involves the renewal, differentiation and reprogramming of stem cell in an orchestrated manner. It has been known that N6-methyladenosine (m6A) regulates stem cell renewal and differentiation. It is still unclear if m6A is crucial for the regeneration at whole-organism level. Here, we demonstrate that wtap knockdown mediated m6A depletion impairs planarian regeneration upon amputation. The cell cycle related genes displayed decreased m6A while increased expression levels in response to wtap knockdown. The m6A depletion induced phenotypes can be rescued by double-knocking down these genes together with wtap, suggesting that m6A-mediated cell cycle controls planarian regeneration. Further analysis combining the single-cell sequencing unveils a unique neuronal progenitor-like cell type, named NCC and characterized by specific expression of grn, which is indispensable for neuroregeneration. Overall, our study uncovered an essential role of wtap-mediated m6A modification in regulating stem cell population dynamics and homeostasis in terms of general-body regeneration.

overall_design: MeRIP-seq of 15 samples from planarian at 0 hpa, 6 hpa, 3 dpa, 7 dpa and 11 dpa, and  15 samples from wtap knockdown planarian at  0 hpa, 6 hpa, 3 dpa, 7 dpa and 11 dpa, including three biological replicates.

first: Y

last: Yang


title: m6A Modification Regulates Planarian Regeneration [RNA-seq]

overall_design: RNA-seq of 15 samples from planarian at 0 hpa, 6 hpa, 3 dpa, 7 dpa and 11 dpa, and  15 samples from wtap knockdown planarian at  0 hpa, 6 hpa, 3 dpa, 7 dpa and 11 dpa, including three biological replicates.


title: Absence of the proprotein convertase FURIN in in vitro activated CD8+ T cells (+/- TGFB1 or IL12) modifies the transcriptome of the cells

first: Markus

last: Ojanen

summary:
Purpose: FURIN is a member of the proprotein convertase subtilisin/kexin (PCSK) family of serine endoproteases important in converting immature proproteins into their functional form. While FURIN is important in various aspects of the immune response such as in CD4+ T cells, FURIN´s role in CD8+ T cells is unclear. Here, we isolated naive CD8+ T cells from conditional T cell specific Furin KO (Cd4-Cre-Furinflox/flox) and WT (Furinflox/flox) mice and studied the genome-wide gene expression pattern upon in vitro anti-CD3/anti-CD28 activation (plate-bound, 5µg/ml each) using RNA sequencing. We also used recombinant TGFB1 (0.5ng/ml) or IL12 (10ng/ml) in the same experimental setting to study their impact on the CD8+ T cell transcriptome.
Methods: Total RNA was isolated from the stimulated CD8+ T cells and the RNA-sequencing data was produced by the Functional Genomics Unit of the HiLIFE Genome Analysis Infrastructure (University of Helsinki, Helsinki, Finland) using Illumina NextSeq High Output 1x75 bp. Data processing pipeline was built on Snakemake wrappers, and used STAR to quantify features from quality and adapter trimmed reads in gene level. Prior the normalisation and differential gene expression analysis with DESeq2, the matrix of raw gene counts was prefiltered to keep only rows that have at least 10 reads in total. Result tables were annotated with biomaRt.
Results: Snakemake preprocessing pipeline measured 55573 genes against GRCm38, ENSEMBL release 97. 17714 of them was used for statistical testing. Full result tables for each treatment were ranked by p-value and the normalized DESeq2 abundances in samples were included. The genes with BH-adjusted p-value <0.05 was considered differentially expressed.
Conclusions: Our study revealed that the abscence of FURIN influences the expression of several genes in activated CD8+ T cells. Additionally, although FURIN-deficient CD8+ T cells can respond to exogenous TGFB1 and IL12, administrating these cytokines further increases the number of differentially expressed genes between Furin KO and WT CD8+ T cells.

overall_design: Total of 30 samples were analyzed; 10 samples without added cytokines (3 dps), 10 samples treated with TGFB1 (3 dps + TGFB1) and 10 samples treated with IL12 (3 dps + IL12). n=5 for both genotypes in the experimental groups. Comparisons were made between Furin KO and WT CD8+ T cells as well as between 3 dps and 3 dps + IL12/TFGB1 groups in both genotypes.

first: Meeri

last: Pekkarinen


title: Genetic Predisposition to Neuroblastoma Results from a Regulatory Polymorphism that Promotes the Adrenergic Cell State

status: Public on Apr 25 2023

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like “mesenchymal” cell state and a more differentiated sympathetic “adrenergic” cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional co-factor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism G/T that affects a GATA motif in the first intron of LMO1. Here we showed that wild-type zebrafish with the GATA genotype developed adrenergic neuroblastoma, while knock-in of the protective TATA allele at this locus reduced the penetrance of MYCN-driven tumors, which were restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrated that TATA/TATA tumors also exhibited a mesenchymal cell state and were low risk at diagnosis. Thus, conversion of the regulatory GATA to a TATA allele in the first intron of LMO1 reduced the neuroblastoma initiation rate by preventing formation of the adrenergic cell state, a mechanism that was conserved over 400 million years of evolution separating zebrafish and humans.

overall_design: Ribosome-depleted RNA-seq in zebrafish bearing genomes with TATA/TATA or KO alleles of lmo1

first: Nina

last: Weichert-Leahey

first: Hui

last: Shi

first: Ting

last: Tao

first: Derek

last: Oldridge

first: Adam

last: Durbin

first: Brian

last: Abraham

first: Mark

last: Zimmerman

first: Shizhen

last: Zhu

first: Andrew

middle: C

last: Wood

first: Deepak

last: Reyon

first: J

middle: K

first: Sharon

last: Diskin

first: John

last: Maris

first: A

last: Look


title: Estrogen Receptor alpha DNA-binding in the arcuate and AVPV nuclei of the hypothalamus in female mice

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

summary: Coupling the release of pituitary hormones to the developmental stage of the oocyte is essential for female fertility. It requires estrogen to restrain kisspeptin (Kiss1) neuron pulsatility in the arcuate hypothalamic nucleus, while also exerting a surge-like effect on Kiss1 neuron activity in the AVPV hypothalamic nucleus. However, a mechanistic basis for this region-specific effect has remained elusive. Here, we provide functional insight into hypothalamic estrogen sensing by analyzing estrogen receptor alpha (ERα/ESR1) DNA binding events in the arcuate and AVPV nuclei of the hypothalamus in female mice.

overall_design: Comparison of Estrogen receptor alpha binding sites between the acruate and AVPV nuclei of the hypocampus in female mice.

first: Jose

last: Ramos-Pittol

first: Isabel

last: Fernandes-Freitas

first: Bryn

last: Owen


title: Transcriptomic analysis of Francisella tularensis infected lungs from human AT-1 receptor expressing mice I

city: Valhalla

first: Sudhir

last: Jain

state: New York

address: 15 Dana Rd

department: Pathology, Microbiology and Immunology

institute: New York Medical Collage

summary: Human angiotensin-II receptor type-I (hAT1R) over-expression may cause adverse pathological outcomes due to renin-angiotensin system overactivity. We have shown that transgenic (TG) mice containing Hap-I (hypertensive genotype) of hAT1R gene are more prone to develop metabolic syndrome (MetS) disorders as compared to the TG mice with Hap-II (normotensive genotype). Aging together with an increased risk of hypertension, can affect multiple organ systems, including increased susceptibility to various pathogenic infections. The current study, therefore, was designed to examine the potential role of aging and hypertension on lung pathology and altered transcriptome, in our TG mice, in response to Francisella tularensis live vaccine strain (LVS) intranasal infection. Our results showed that in comparison to Hap-II, aged Hap-I TG mice had a significantly higher mortality post-infection; elevated lung pathology; and altered gene expression profile. Consistent with worsened phenotype in aged Hap-I mice post LVS infection, RNA-seq data from their lungs revealed that >1400 genes (p <0.005) were significantly altered. Bioinformatics analysis identified major alterations in canonical pathways related to immune responses including interferon signaling, antigen presentation, agranulocyte adhesion and dendritic cell maturation. These alterations in turn resulted in disorders including, lung infection, inflammation, and immunological diseases. Importantly, IFNG, STAT1, STAT3 and TNF were among the top upstream regulators significantly affected by LVS infection. Overall, these results provide a deeper insight in molecular signaling associated with hypertension associated lung infections in aged subjects.

overall_design: overall 12 samples were analysed by RNA seq. These samples were devided into four groups in triplicate. These groups are #1 GroupA Hap-I adults; #2 GroupB Hap-II aged; #3 GroupC Hap-I aged; #4 GroupE Hap-I aged+LVS

first: Harshada

last: Ketkar

first: Weihua

last: Huang


title: m6A Modification Promotes Planarian Regeneration

first: Bao-Fa

last: Sun


title: Whole animal RNA Seq of wild type and RBP/TF mutants

status: Public on Apr 24 2023

city: Riverside

first: Adam

middle: David

last: Norris

address: 3401 Watkins Drive

institute: University of California, Riverside

summary: Gene expression is a multistep, carefully controlled process, and crosstalk between regulatory layers plays an important role in coordinating gene expression. To identify functionally relevant coordination between transcriptional and post-transcriptional gene regulation, we performed a systematic reverse-genetic interaction screen in C. elegans. We combined RNA binding protein (RBP) and transcription factor (TF) mutants, creating over 100 RBP; TF double mutants. This screen identified a variety of unexpected double mutant phenotypes, including two strong genetic interactions between the ALS-related RBPs, fust-1 and tdp-1, and the homeodomain TF ceh-14. Losing any one of these genes alone has no significant effect on the health of the organism. However, fust-1; ceh-14 and tdp-1; ceh-14 double mutants both exhibit strong temperature-sensitive fertility defects. Both double mutants exhibit defects in gonad morphology, sperm function, and oocyte function. RNA-seq analysis of double mutants identifies ceh-14 as the main controller of transcript levels, while fust-1 and tdp-1 control splicing through a shared role in exon inhibition. We identify a cassette exon in the polyglutamine-repeat protein pqn-41 which tdp-1 inhibits. Loss of tdp-1 causes the pqn-41 exon to be aberrantly included, and forced skipping of this exon in tdp-1; ceh-14 double mutants rescues fertility. Together our findings identify a novel shared physiological role for fust-1 and tdp-1 in promoting C. elegans fertility in a ceh-14 mutant background and reveal a shared molecular function of fust-1 and tdp-1 in exon inhibition.

overall_design: Biological triplicates of wild-type, TF mutant (ceh-14), two RBP mutants (fust-1 and tdp-1) and pairwise TF-RBP combinations


title: Bulk RNA-seq of a time series of hPSCs as they differentiate towards left ventricle cardiomyocytes

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

summary: We report that both hESCs and hiPSCs can be differentiated towrads left ventricle cardiomyocytes using an optimised protocol and that these cells transit via first heart field progenitors.

overall_design: Examination of the transcriptome of two hPSC lines as they differentiate towards left ventricle cardiomyocytes; critical time points were collected

first: Andreia

last: Bernardo

first: Nicola

last: Dark


title: The genomic landscape of sensitivity to Arsenic Trioxide characterized by Genome-wide CRISPR-Cas9 screening

city: guangzhou

first: Chen

last: Jun-Zhu

state: State...

address: 广州市越秀区中山二路58号中山大学附属第一医院

institute: Sun Yat-Sen University

summary: The key modifiers of sensitivity to  Arsenic Trioxide (ATO) remained unclear, and we presented a genome-wide scale loss-of-function screening to identify the modulators of cell response to ATO.

overall_design: Genome-wide CRISPR-Cas9 screening for HAP1 cells with different treatments (vehicle, and ATO).

first: Jun-Zhu

last: Chen

first: Xue-Qun

last: Luo