title: Differentially expressed ncRNAs derived from circulating exosomes in the pathogenesis of rat spinal cord injury

city: Tian Jin

first: Jian an

last: Li

address: Jie fang road #406

country: China

institute: Tian Jin hospital

summary: This study was originally designed to have a general overview of differentially expressed ncRNAs including miRNAs, circRNAs and lncRNAs, from circulating exosomes in SCI rats in comparison with the control rats.

overall_design: Rat SCI model is utilised and exosomes are collected. Exosomal circRNAs are obtained, functional enrichment analyses including KEGG pathway and GO ontology are performed, and several differentially expressed circRNAs are confirmed through RT-PCR. Furthermore, the interaction network of circRNA-miRNA-mRNA is constructed.

first: Jianan

first: Chunfang

last: Zan

first: Fengsong

last: Lin

first: Zengliang

last: Wang


title: The role of gltS in biofilm

status: Public on Nov 07 2022

city: Boston

first: Koichi

last: Yuki

state: MA

address: 300 Longwood Avenue

country: USA

institute: Boston Children's Hospital

type: Expression profiling by high throughput sequencing

summary: gltS is glutamate transporter. We examined the role of gltS in staphylococcus aureus biofilm formation.

overall_design: We cultured staphylococcus JE2 and gltS transposon strains in vitro for biofilm formation, and obtained samples at 4, 24 and 48 hours for RNA sequencing.

first: Miho

last: Shibamura-Fujiogi


title: Mapping separase-mediated cleavage in situ

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Macaca fascicularis
Homo sapiens

platform_organism:
Macaca fascicularis
Homo sapiens

overall_design: Refer to individual Series


title: scRNA-seq and bulk RNA-seq analysis of normoxic and hyperoxic lung in mice [scRNA-seq]

city: ChengDu

first: Yanrong

last: Long

address: No. 17, Section 3, Renmin South Road, Wuhou District

department: State Key Laboratory of Biotherapy

institute: Sichuan University

summary: To explore the key molecules and mechanisms involved in the occurrence and development of BPD by using a hyperoxia-based BPD model in neonatal mice, providing new ideas for discovering new therapeutic target to approach the clinical prevention and treatment for BPD.

overall_design: We performed single-cell RNA-seq (scRNA-seq) profiling analysis of whole lung cells from mice reared in normoxia or hyperoxia.

first: Zhongwei

last: Cao


title: Chip-seq analysis of meiotic Cohesin (mei-Cohesins) subunit REC8 cleaved by separase (REC8*), and SMC3 in Macaca fascicularis testis

summary: The study aimed to map epigenomic locations of separase-cleaved REC8 using chromatin IP analyzed by high-throughput sequencing  on purified germ cells from M. fascicularis testis

overall_design: M. fascicularis is a monkey with non-seasonal male germ cells production, and the most comon primate used for preclinical animal studies. The ChIP-on-CHEP study was done with proprienaly mAbs developed against the COOH-terminal peptides of REC8* after cleavage by separase: X-LLEIPR* and X-EIEVPR*

first: AbdelHalim

last: Boukaba

first: Jian

last: Liu

first: Cheng

last: Chen

first: Jierong

last: Liang

first: Jinjin

first: Qiongfang

last: Wu

middle: V


title: ARID1A loss shapes immunosuppression tumor microenvironment via NF-kB induced MDSC chemotaxis to promote prostate Cancer metastasis [ATAC-seq]

city: Shanghai

first: Ni

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

summary: Chronic inflammation and immunosuppressive microenvironment promote prostate cancer (PCa) metastasis and diminish the responses to immune checkpoint blockade (ICB) therapies. However, it remains unclear how and to what extent these two events are coordinated. Here we show that ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, functions downstream of inflammation induced IKKb activation to shape immunosuppressive tumor microenvironment (TME). Prostate-specific deletion of Arid1a cooperates with Pten loss to produce a metastasis-prone tumors. We identify that polymorphonuclear myeloid-derived suppressor cells (MDSCs) as the major infiltrating immune cell type to cause immune evasion, and neutralization of MDSCs restricts metastasis of Arid1a deficient tumors. Mechanistically, inflammation cues activate IKKβ to phosphorylate ARID1A, leading to its degradation via b-TRCP. ARID1A downregulation in turn silences the enhancer of A20 deubiquitinase, a critical negative regulator of NF-kB signaling, and thereby unleashing CXCR2 ligands-mediated MDSC chemotaxis. Importantly, our results support the therapeutic strategy of anti-NF-kB or CXCR2 combined with ICB for advanced PCa. Together, our findings highlight a critical role of ARID1A in MDSCs recruitment and demonstrate IKKb/ARID1A/NF-kB feedback axis integrating inflammation and the immunosuppression to drive PCa metastasis.

overall_design: Examination of chromatin accessibility in Myc-CaP cells with or without Arid1a deletion.

first: Jun

last: Qin


title: ARID1A loss shapes immunosuppression tumor microenvironment via NF-kB induced MDSC chemotaxis to promote prostate Cancer metastasis [RNA-seq II]

overall_design: Myc-CaP expressing sgARID1A and control vectors inoculated subcutaneously into FVB mice and treated with or without JSH-23 and epithelial cells were sorted for RNA-seq.


title: ARID1A loss shapes immunosuppression tumor microenvironment via NF-kB induced MDSC chemotaxis to promote prostate Cancer metastasis [RNA-seq]

overall_design: mRNA profiles of prostate epithelium (EpCAM+; CD45− cells) collected from 3-month-old PtenPC−/− and PtenPC−/−; Arid1aPC−/− mice  and Myc-CaP cells with or without Arid1a deletion.


title: ARID1A loss shapes immunosuppression tumor microenvironment via NF-kB induced MDSC chemotaxis to promote prostate Cancer metastasis [ChIP-seq]

overall_design: Examination of BRG1 binding and  histone modifications in Myc-CaP cells.


title: Intelectin-1 binds a select group of bacteria and regulates mucus thickness promoting colitis

first: Magdalena

middle: Barbara

last: Flak

address: New Research Building, Room 641, 77 Avenue Louis Pasteur

department: Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine

institute: Brigham and Women’s Hospital, Harvard Medical School

summary: We report that ITLN1 production is induced by ER stress in IBD, binds to A. muciniphila, regulates mucus thickness, promoting barrier breach and inflammation. RNAseq analysis indicated transcriptional regulation of Itln1 by Xbp1.

overall_design: Comparison of gene expression in Paneth cells of XBP1-deleted (Xbp1ΔIEC) inestinal epithelia of germ-free C57BL/6 mice versus Paneth cells in intestinal epithelia of wild-type germ-free controls.

middle: B

first: Juan

middle: D

last: Matute


title: ARID1A loss shapes immunosuppression tumor microenvironment via NF-kB induced MDSC chemotaxis to promote prostate Cancer metastasis

last: Li


title: Activation of RXRα reprograms chromatin accessibility to protect against acute kidney injury [H3K27ac ChIP-seq]

status: Public on Nov 05 2022

city: Tianjin

first: Xinyi

state: State...

address: Qi Xiangtai Road, HePing District, Tianjin, P.R. China

institute: Tianjin Medical University

summary:
Purpose: To explore the differences in H3K27ac distribution in PTCs after MI and SI
Methods: Proximal tubules were isolated for H3K27ac ChIP-seq
Results: Using an optimized data analysis workflow, we mapped reads to the mouse genome (mm10).
Conclusions: We mapped the chromatin occupancy of H3K27ac.

overall_design: ChIP sequencing with H3K27ac antibodies for proximal tubular cells isolated in injury kidneys

first: Yupeng


title: Activation of RXRα reprograms chromatin accessibility to protect against acute kidney injury [ChIP-seq]

summary:
Purpose: To explore whether the differences in chromatin occupancy of RXRα correlate with distinct gene expression in PTCs of MI and SI
Methods: Proximal tubules were isolated for RXRα ChIP-seq
Results: Using an optimized data analysis workflow, we mapped reads to the mouse genome (mm10).
Conclusions: We mapped the chromatin occupancy of RXRα.

overall_design: ChIP sequencing with RXRα antibodies for proximal tubular cells isolated in injury kidneys


title: Activation of RXRα reprograms chromatin accessibility to protect against acute kidney injury [ATAC-seq]

summary:
Purpose: To explore the differences in chromatin openness of PTCs between MI and SI
Methods: Kidney proximal tubules were isolated for ATAC-seq
Results: Using an optimized data analysis workflow, we mapped reads to the mouse genome (mm10).


title: Activation of RXRα reprograms chromatin accessibility to protect against acute kidney injury [RNA-seq]

summary:
Purpose: To explore whether the differences in chromatin openness correlate with distinct gene expression in PTCs of MI and SI
Methods: Proximal tubules were isolated for RNA-seq
Results: Using an optimized data analysis workflow, we mapped reads to the mouse genome (mm10). Approximately 2%-13% of the transcripts showed differential expression within the different groups, with a fold change >= 1.5 and p value <0.05.

overall_design: RNA-sequencing of different conditions: Sham and bilateral ischemia-reperfusion injury (bIRI) mice with or without bexoratene


title: Activation of RXRα reprograms chromatin accessibility to protect against acute kidney injury.


title: CXCL13 is a predictive biomarker in idiopathic multicentric Castleman disease

status: Public on Nov 04 2022

city: Philadelphia

first: David

last: Fajgenbaum

state: PA

address: 3535 Market St, 717

department: Medicine

institute: University of Pennsylvania

summary: Idiopathic multicentric Castleman disease (iMCD) is a rare and poorly-understood cytokine storm-driven inflammatory disorder. Interleukin-6 (IL-6) is a known disease driver in some patients, but anti-IL-6 therapy with siltuximab is not effective in all patients, and biomarkers indicating success at an early time point following treatment initiation are lacking. Here we show, by comparison of levels of 1,178 proteins in sera of healthy participants (N=42), patients with iMCD (N=88), and with related diseases (N=60), a comprehensive landscape of candidate disease mediators and predictors of siltuximab response. C-X-C Motif Chemokine Ligand-13 (CXCL13) is identified and validated as the protein most prominently up-regulated in iMCD. Early and significant decrease in CXCL13 levels clearly distinguishes siltuximab responders from non-responders; a 17% reduction by day 8 following siltuximab therapy initiation is predictive of response at later time points. Our study thus suggests that CXCL13 is a predictive biomarker of response to siltuximab in iMCD.

overall_design: Samples were collected from 98 iMCD patients – including 79 patients who participated in the phase II registrational trial for siltuximab (NCT01024036) and 19 additional patients experiencing active disease. The 79 patients in the trial were randomized to placebo (N=26) or to siltuximab (N=53). Samples were collected from all iMCD patients before siltuximab treatment. Additionally, longitudinal samples at day 8 and day 64 of siltuximab treatment were collected from the iMCD patients in the phase II trial. One time samples were collected from comparator groups including 44 healthy donors, recruited to serve as age- and sex-matched comparators to the iMCD group and 20 patients each with clinico-pathologically overlapping disorders rheumatoid arthritis (RA), Hodgkin lymphoma (HL), and HIV-positive, HHV8-associated MCD (HHV8-MCD)—a form of MCD that is caused by uncontrolled infection with HHV8— representing diseases of autoimmune, neoplastic, and infectious origin respectively. Quantification of 1,305 protein analytes in the Primary cohort was performed by SomaLogic SOMAscan 1.3k version, a DNA-based aptamer technology per manufacturer’s protocol. Due to the number of samples, quantification was performed in two batches, and five technical replicates were included between the two batches. Batches were bridged together by the average log ratio of technical replicates for each analyte. SomaLogic SOMAscan pre-processing was performed, and 1,178 analytes passed quality control. Following quality control sample exclusion, pretreatment samples available for analysis included 88 iMCD patients, 42 healthy donors, and 20 each of RA, HL, and HHV8-MCD. Longitudinal samples available for analysis included samples from day 8 and day 64 of treatment from 73 iMCD patients.

middle: C

first: Sheila

middle: K

last: Pierson

first: Laura

last: Katz


title: SRSF10 is essential for progenitor spermatogonia expansion by regulating alternative splicing

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Alternative splicing expands the proteome complexity and plays essential roles in tissue development and human diseases. However, how spermatogenesis is regulated by alternative splicing remains largely unknown. Here, using germ cell-specific knockout mouse model, we demonstrate that the splicing factor Srsf10 is essential for spermatogenesis and male fertility. Depletion of Srsf10 in germ cells had little effect on the formation of SSCs but impeded the expansion of progenitor spermatogonia, leading to the failure of spermatogonia differentiation and meiosis initiation. This was evidenced by the decreased expression of progenitor cell markers in bulk RNA-seq, and much less progenitor and differentiating spermatogonia in single-cell RNA-seq data. Furthermore, the expression of genes involved in cell cycle was abnormal in all subtypes of spermatogonia identified in single-cell RNA-seq data. Notably, using isolated spermatogonia, we found that Srsf10 depletion disturbed the alternative splicing of hundreds of genes, which were preferentially associated with cell cycle, mitotic cell cycle checkpoint and germ cell development, including Dazl, Kit, Ret, Sycp1, Nasp and Bora. These data suggest that SRSF10 is critical for the expansion of progenitor spermatogonia by regulating alternative splicing, expanding our understanding of the novel mechanism underlying spermatogenesis.

overall_design:
Transcriptional profiles of P3, P6 and P8 testes from Control and Srsf10-cKO mice; Transcriptional profiles of isolated THY1+ cells  from Control and Srsf10-cKO mice at P6; Single-cell RNA seq profiles of isolated spermatogonia (THY1+ or Kit+) from Control and Srsf10-cKO mice at P8; PacBio Isoform Sequencing (Iso-seq) profiles of isolated THY1+ cells  from Control and Srsf10-cKO mice at P6

LACE-seq of isolated THY1+ cells  from Control and Srsf10-cKO mice at P6

first: Wenbo

first: Xukun

last: Lu

first: Zhenghui

last: Zhao

first: Jianqiao


title: Transcriptomic profiling of MCF7 cells overexpressing JMJD6 (Jumonji domain containing protein 6)

city: Kalyani

first: Kartiki

last: Desai

state: West Bengal

address: N.S.S kalyani

country: India

institute: National Institute of Biomedical Genomics

summary: V5 tagged JMJD6 was stably overexpressed in MCF7 cells (JOE); empty vector transfected MCF7 cells were used as a control (Vec). Transcription profiling was carried out is duplicate.

overall_design: Comparison of gene expression profiles using RNA-seq data of  JOE cells with Vec cells

first: Partha

last: Das

first: Aritra

last: Gupta


title: Host response of human epidermis to Methicillin-resistant Staphylococcus aureus biofilm infection and synthetic antibiofilm peptide treatment

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

country: Canada

institute: Simon Fraser University

summary: Bacterial biofilm infections associated with wounded skin are prevalent, recalcitrant and in urgent need of treatments. Additionally, host responses in the skin to biofilm infections are not well understood. Here we employed a human organoid skin model to explore the transcriptomic changes of thermally-injured epidermis to Methicillin-resistant Staphylococcus aureus (MRSA) biofilm colonization. MRSA biofilm impaired skin barrier function, enhanced extracellular matrix remodelling, elicited inflammatory responses including IL-17, IL-12 family and IL-6 family interleukin signalling and modulated skin metabolism. Synthetic antibiofilm peptide DJK-5 effectively diminished MRSA biofilm associated with wounded human ex vivo skin. In the epidermis, DJK-5 shifted the overall skin transcriptome towards homeostasis including modulating the biofilm induced inflammatory response, promoting the skin DNA repair function, and downregulating MRSA invasion of thermally damaged skin. These data revealed the intrinsic promise of synthetic peptides in treating inflammation and biofilm infections.

overall_design: Samples are RNA-Seq libraries, based on a human skin organoid model of burn wounds, bacterial infection, and treatment with synthetic peptides. Included sample types are: untreated skin (control); burned skin; burned skin + MRSA infection; and burned skin + MRSA infection + peptide treatment

first: Bing

first: Evan

middle: F

last: Haney

first: Reza

last: Falsafi

first: Noushin

last: Akhoundsadegh

first: Robert

middle: E

last: Hancock


title: The transcription factor c-Jun inhibits RBM39 to reprogram pre-mRNA splicing during genotoxic stress

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

summary: Gene expression and pre-mRNA splicing events were examined in human breast adenocarcinoma (MCF7) cells treated or not with cisplatin and various siRNAs.

overall_design: Triplicate samples of MCF7 cells were treated with siRNA to knock down c-Jun or RBM39, or control siRNA, and treated or not with cisplatin.

first: Yvette

last: Habraken


title: Transcriptome profiling of human bone marrow stem cells (HBMSC) and tumorigenic sublines

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: We generated a novel subline (clone 6; Sample B) from the human bone marrow stem cell culture [HBMSC 3.5 (Sample A)] and demonstrated its in vivo tumorigenicity by growth as xenograft tumors both in the mammary fat pad (MFP; Sample C) pad and subcutaneously (Sample D). In order to gain insight into the molecular basis of their biological properties, phenotypic differences, and correlation to clinical cancer, we performed RNA-Sequencing (RNA-Seq) analysis of each of the samples to comprehensively characterize the transcriptome of each of the samples.

overall_design: A total of 4 samples were analyzed in this study. The study included a total of 4 samples: human bone marrow stem cells (HBMSC 3.5, Sample A) culture, a novel subline (clone 6; Sample B) culture, and two xenograft tumors grown in the mammary fat pad (MFP; Sample C) pad and subcutaneously (Sample D). Following the growth of cell cultures to ~70% confluency or growth of tumors to 500 mm^3, cells or tumors, respectively, were harvested, total RNA was isolated, and then submitted for RNA-sequencing analysis.

first: Jian

middle: J

last: Li

first: Ming

last: Fan

middle: G


title: Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity

city: Toronto

first: Caitriona

last: McEvoy

address: 200 Elizabeth St

institute: University Health Network

summary: We present a single-cell perspective of healthy human kidney from 19 living donors, with equal contribution from males and females, profiling the transcriptome of 27677 high-quality cells to map healthy kidney at high resolution. Our sex-balanced dataset revealed sex-based differences in gene expression within proximal tubular cells, specifically, increased anti-oxidant metallothionein genes in females and the predominance of aerobic metabolism-related genes in males. Using CD45+ enrichment in 10 samples, we profile the immune niche of the kidney, identifying kidney-specific lymphocyte populations with unique transcriptional profiles indicative of kidney-adapted functions. We observed significant heterogeneity in resident myeloid populations and identified an MRC1+ LYVE1+ FOLR2+ C1QC+ population as the predominant myeloid population in healthy kidney. This study provides a broad cellular map of healthy human kidney, revealing novel insights into the complexity of renal parenchymal cells and kidney-resident immune populations.

overall_design: Single -cell RNA sequencing (10X Genomics Single Cell 3’ v3) was performed on 19 core biopsies from human living donor kidneys, 9 biopsies from males and 10 from females. 10 samples (5 males, 5 females) were subjected to CD45-enrichment using magnetic EasySep Human CD45 depletion kit II (STEMCELL, cat# 17898).

first: Julia

last: Murphy

first: Ana

last: Konvalinka

first: Sarah

middle: Q

last: Crome


title: Loss of GM-CSF-dependent instruction of alveolar macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment

status: Public on Nov 03 2022

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

sample_organism:
Homo sapiens
Mus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Epigenome of an adult Ridgeia piscesae vestimentum

status: Public on Nov 06 2022

city: Montreal

first: Maeva

last: Perez

state: Qc

address: 1375 Avenue Thérèse-Lavoie-Roux

institute: Université de Montréal

type: Methylation profiling by high throughput sequencing

summary: 5mCpG methylation for Ridgeia piscesae.

overall_design: Methylation data were obtained from Oxford Nanopore reads and Whole-Genome-Shotgun sequencing.

first: Bernard

last: Angers

first: Oluchi

last: Aroh

first: Yannan

last: Sun

first: Yi

last: Lan

first: Pei-Yuan

last: Qian


title: Protective interaction of human phagocytic APC subsets with Cryptococcus neoformans induces genes associated with metabolism and antigen presentation

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: We determined the effect of conditional deletion of Menin in MLL-AF9 transformed leukemia cells

overall_design: Human BAL cells were enriched for APCs (lineage removal), then incubated for 2h with Cryptococcus neoformans. Cells were then used for single-cell RNA sequencing

first: Benjamin

middle: N

last: Nelson

first: Cheyenne

middle: S

last: Daugherty

first: Rachel

middle: R

last: Sharp

first: J

last: Booth

first: Vineet

middle: I

last: Patel

first: Jordan

middle: P

last: Metcalf

first: Karen

last: Wozniak


title: Loss of GM-CSF-dependent instruction of alveolar macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment (RNA-Seq)

summary: Systemic GM-CSF promotes myelopoiesis and inflammation and GM-CSF blockade is being evaluated as treatment for COVID-19-associated hyperinflammation. Alveolar GM-CSF is however required for monocytes to differentiate into alveolar macrophages (AM) that control alveolar homeostasis and dampen inflammation. By mapping cross-species AM development stages to clinical lung samples, we discovered that COVID-19 is marked by defective GM-CSF-dependent AM instruction and accumulation of proinflammatory macrophages. In a multi-center, open-label, randomized, controlled trial in 81 non-ventilated COVID-19 patients with respiratory failure, we found that inhalation of rhu-GM-CSF did not improve mean oxygenation parameters compared with standard treatment. However, more patients on GM-CSF had a clinical response, and GM-CSF inhalation induced higher numbers of virus-specific CD8 effector lymphocytes and class-switched B cells, without exacerbating systemic hyperinflammation. This translational proof-of-concept study provides rationale for further testing of inhaled GM-CSF as non-invasive treatment to improve alveolar gas exchange and simultaneously boost anti-viral immunity in COVID-19

overall_design: CiteSeq on BAL samples with 277 antibodies of  COVID-19 (n=8), non-COVID-19 pulmonary infection (n=8), interstitial lung disease (ILD) (n=1) and control non-infected individuals undergoing diagnostic bronchoscopy (n=2)

first: Cedric

last: Bosteels

first: Karel

middle: A

last: Van Damme

first: Elisabeth

last: De Leeuw

first: Jozefien

last: Declercq

first: Bastiaan

last: Maes

first: Victor

first: Levi

last: Hoste

first: Leslie

last: Naesens

first: Nincy

last: Debeuf

first: Julie

last: Deckers

first: Basiel

last: Cole

first: Marion

last: Pardons

first: Daniela

last: Weiskopf

first: Alessandro

last: Sette

first: Yannick

last: Vande Weygaerde

first: Thomas

last: Malfait

first: Stefaan

last: Vandecasteele

first: Ingel

last: Demedts

first: Hans

last: Slabbynck

first: Sabine

last: Allard

first: Pieter

last: Depuydt

first: Eva

last: Van Braeckel

last: De Clercq

first: Sam

last: Dupont

first: Ruth

last: Seurinck

first: Niels

last: Vandamme

first: Filomeen

last: Haerynck

first: Debasish

last: Roychowdhury

first: Linos

last: Vandekerckhove

first: Martin

last: Guilliams

first: Simon

last: Tavernier

first: Bart

last: Lambrecht


title: Stabilization of virgin naïve hESCs in two distinct substates along the continuum of pluripotency [RNA-seq]

city: La Jolla

first: Robert

last: Morey

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

summary: A detailed understanding of the developmental substates of human pluripotent stem cells (hPSCs) is needed to optimize their use in cell therapy and models of early development. Genetic instability and risk of tumorigenicity of primed hPSCs are well documented, but a systematic isogenic comparison between primed and naive substates has not been previously performed. We derived four hESC lines in naïve conditions and generated isogenic pairs of naïve and primed cultures. Through phenotypic, mRNA, miRNA, and DNA methylation profiling, we identified changes that arose during the naïve-primed transition and over extended culture. Although early naïve hESC cultures showed greater proliferation and clonogenic potential compared to primed cultures, they drifted toward a more primed-like substate over time, including accumulation of genetic abnormalities. Overall, we show that transcriptomic and epigenomic profiling can be used to place naïve/primed cultures along a developmental continuum, and may inform their utility for clinical and research applications.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the four hESC lines Lis38, Lis39, Lis45, and Lis46. All lines were derived in naive conditions and kept in naive conditions or switched to primed conditions and sampled at passage 20 (naive only), 30, and 50. Triplicates of all timepoints for a total of 60 samples.

first: Chen

last: Dekel

first: Hadar

last: Amir

first: Dalit

last: Ben-Yosef

first: Louise

last: Laurent


title: mTORC1 signaling facilitates differential stem cell differentiation to shape the developing murine lung and is associated with mitochondrial capacity

city: San Francisco

first: Pao-Tien

last: Chuang

address: 555 Mission Bay Blvd. South

institute: University of California, San Francisco

summary: Formation of branched organs requires sequential differentiation of stem cells. In this work, we find that the conducting airways derived from SOX2+ progenitors in the murine lungs fail to form without mTOR complex 1 (mTORC1) signaling and are replaced by lung cysts. Proximal-distal patterning through transitioning of distal SOX9+ progenitors to the proximal SOX2+ cells is disrupted. Mitochondria number and ATP production are reduced. Compromised mitochondrial capacity results in a similar defect as that in mTORC1-deficient lungs. This suggests that mTORC1 promotes differentiation of SOX9+ progenitors to form the conducting airways by modulating mitochondrial capacity. Surprisingly, in all mutants saccules are produced from lung cysts at the proper developmental time despite defective branching. SOX9+ progenitors also differentiate into alveolar epithelial type I and type II cells within saccules. These findings highlight selective utilization of energy and regulatory programs during stem cell differentiation to produce distinct structures of the mammalian lungs.

overall_design: Examine the difference of gene expression among Rptor-, Tfam-, Cox10-deficient and their littermate control lungs

first: Kuan

last: Zhang

first: Erica

last: Yao

first: Ethan

first: Biao

last: Chen

first: Evelyn

middle: Y


title: Stabilization of hESCs in two distinct substates along the continuum of pluripotency

type: Methylation profiling by genome tiling array

type: Non-coding RNA profiling by high throughput sequencing

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


title: Stabilization of virgin naïve hESCs in two distinct substates along the continuum of pluripotency [miRNA-seq]

overall_design: Comparative gene expression profiling analysis of small RNA-seq data for the four hESC lines Lis38, Lis39, Lis45, and Lis46. All lines were derived in naive conditions and kept in naive conditions or switched to primed conditions and sampled at passage 20 (naive only), 30, and 50. Triplicates of all timepoints for a total of 60 samples.

middle: C


title: Stabilization of virgin naïve hESCs in two distinct substates along the continuum of pluripotency [methArray]

overall_design: Bisulphite converted DNA from every line and timepoint (24 samples – late female cultures have duplicates) were hybridised to the Illumina Infinium MethylationEPIC array (850k probes)


title: Elective nodal irradiation mitigates local and systemic immunity generated by combination radiation and immunotherapy in head and neck tumors

status: Public on Nov 02 2022

city: Aurora

first: Sana

middle: D

last: Karam

state: CO

address: 1665 Aurora Ct.

department: Radiation Oncology

institute: CU Denver Anschutz

summary: Lymph nodes from canine patients with head and neck caner were sequenced to determine differences in gene expression after irradiation.

overall_design: RNA was extracted from frozen tumor tissues using Rneasy Plus Mini Kit (QIAGEN) following manufactures protocol. Depending on starting material, samples were eluted in 30-50L RNase-Free water. Samples were initially checked for quantity and purity on a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher) prior to being stored at -80oC until further processing. Samples were additionally quantity and quality checked using the RNA High Sensitivity assays on the Qubit 2.0 Fluorometer (Invitrogen/LifeTechnologies) and 5200 Fragment Analyzer Automated CE System (Agilent), respectively. NanoString gene expression analysis was performed using the Canine IO 360 panel. Nanostring analysis was performed with the nCounter Analysis FLEX system at the University of Arizona Genetics Core. Gene expression count data was analyzed via nSolver software.

first: Mary-Keara

last: Boss


title: Transcriptomic analysis of human laryngeal carcinoma cell line LIU-LSC-1 with depletion of ITGA5

city: Hefei

first: Dapeng

last: Li

institute: The First Affiliated Hospital of Anhui Medical University

summary: Recent studies have shown that integrins have a promotive effect on cancer. In our clinical work, we found that integrin subunit alpha 5 (ITGA5) was highly expressed in laryngeal cancer tissues. Further in vitro functional assays showed that ITGA5 promotes proliferation, migration and metastasis of laryngeal cancer cells. To investigate how ITGA5 exerts these functions and its downstream regulatory genes, we knocked down ITGA5 in the laryngeal cancer cell line LIU-LSC-1 and sequenced the transcriptome of wild-type and ITGA5 knockdown cells.

overall_design: Retinal mRNA profiles of wild type (WT) and ITGA5-/-LIU-LSC-1 cells

first: Yehai

last: Liu


title: Plastid and cytoplasmic origins of 1O2-mediated gene responses

city: Singapore

first: Eugene

last: Koh

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratories

summary: Effect of low and high light in Arabidopsis Ch1 mutant

overall_design: Total RNA obtained from 2-week old Ch1 Arabidopsis seedlings subjected to 0, 1, 2, 4 hours of low light (30 µE) or high light (1000 µE)

last: Fluhr


title: Transcriptomic analysis of human laryngeal carcinoma cell line LIU-LSC-1 with depletion of Raptor

summary: Recent studies have shown that mTOR signalling have a promotive effect on cancer. In our clinical work, we found that mTOR signalling is commonly activated in  laryngeal cancer tissues and influence the metabolism of cancer cells. To investigate how mTORC1 exerts these functions and its downstream regulatory genes, we knocked down Raptor in the  laryngeal cancer cell line LIU-LSC-1 and sequenced the transcriptome of wild-type and Raptor knockdown cells.

overall_design: Retinal mRNA profiles of wild type (WT) and shRaptor LIU-LSC-1 cells


title: Loss of evolutionary conserved GM-CSF-dependent signature in pulmonary macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment (microarray)

first: Liesbet

last: Martens

summary: Alveolar GM-CSF is required for monocytes to differentiate into alveolar macrophages (AM) that control alveolar homeostasis and dampen inflammation. By mapping cross-species AM development stages to clinical lung samples, we discovered that COVID-19 is marked by defective GM-CSF-dependent AM instruction and accumulation of proinflammatory macrophages. In a multi-center, open-label, randomized, controlled trial in 81 non-ventilated COVID-19 patients with respiratory failure, we found that inhalation of rhu-GM-CSF did not improve mean oxygenation parameters compared with standard treatment. However, more patients on GM-CSF had a clinical response, and GM-CSF inhalation induced higher numbers of virus-specific CD8 effector lymphocytes and class-switched B cells, without exacerbating systemic hyperinflammation. This translational proof-of-concept study provides rationale for further testing of inhaled GM-CSF as non-invasive treatment to improve alveolar gas exchange and simultaneously boost anti-viral immunity in COVID-19

sample_organism:
Mus
Mus musculus

overall_design: Compare microarrays of GM-CSF KO mice and microarrays covering the AMF development: Fetal liver monocyte (E15.5), Bone Marrow monocyte (adult), lung macrophage on E15.5, E17.5 and E19.5, Pre-AMF on day of birth, AMF on day 9 after birth and adult AMF to identify a GM-CSF gene signature. Some of these microarrays were already published in GSE117081 and GSE76999.

first: Cedric

last: Bosteels

first: Karel

last: Van Damme

first: Elisabeth

last: De Leeuw

first: Jozefien

last: Declercq

first: Bastiaan

last: Maes

first: Victor

first: Levi

last: Hoste

first: Leslie

last: Naesens

first: Nincy

last: Debeuf

first: Julie

last: Deckers

first: Basiel

last: Cole

first: Marion

last: Pardons

first: Daniela

last: Weiskopf

first: Alessandro

last: Sette

first: Yannick

last: Vande Weygaerde

first: Thomas

last: Malfait

first: Stefaan

last: Vandecasteele

first: Ingel

middle: K

last: Demedts

first: Hans

last: Slabbynck

first: Sabine

last: Allard

first: Pieter

last: Depuydt

first: Eva

last: Van Braeckel

last: De Clercq

first: Sam

last: Dupont

first: Ruth

last: Seurinck

first: Niels

last: Vandamme

first: Filomeen

last: Haerynck

first: Debasish

middle: F

last: Roychowdhury

first: Linos

last: Vandekerckhove

first: Martin

last: Guilliams

first: Simon

last: Tavernier

first: Bart


title: Mapping prohormone processing by proteases in human enteroendocrine cells using genetically engineered organoid models

status: Public on Nov 01 2022

city: Utrecht

first: Joep

last: Beumer

address: Uppsalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Bulk RNA sequencing was performed on organoids differentiated towards enteroendocrine cells in the presence and absence of BMP

overall_design: RNA was extracted from intestinal organoids that were differentiated towards enteroendocrine cells in -BMP or +BMP containing containing conditions for 5 days.

first: Julia

last: Bauza-Martinez

first: Tim

last: Veth

first: Veerle

last: Geurts

first: Charelle

last: Boot

first: Filip

last: Knop

first: Wei

last: Wu

last: Clevers


title: scRNA-seq and bulk RNA-seq analysis of normoxic and hyperoxic lung in  mice [bulk RNA-seq]

city: ChengDu

first: Yanrong

last: Long

address: No. 17, Section 3, Renmin South Road, Wuhou District

institute: Sichuan University

summary:
To explore the key molecules and mechanisms involved in the occurrence and development of BPD by using a hyperoxia-based BPD model in neonatal mice, providing new ideas for discovering new therapeutic target to approach the clinical prevention and treatment for BPD.
We performed  whole transcriptome sequencing (RNA-seq) profiling analysis of lung endothelial cells from mouse normoxic or hyperoxic mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data for normoxia and hyperxic mouse lung endothelial cells

first: Zhongwei

last: Cao


title: RNA sequencing of intestinal enterocytes pre- and post-Roux-en-Y gastric bypass reveals alteration in gene expression related to enterocyte differentiation, restitution, and obesity

city: Grand Forks

first: Sandeep

last: Singhal

state: NORTH DAKOTA

address: 1301 N Columbia Rd Stop 9037

institute: University of North Dakota

summary:
Background: The intestinal lining renews itself in a programmed fashion that can be affected by adaptation to surgical procedures such as gastric bypass.
Results: RNA sequencing suggested significant decreases of gene expression associated with G2/M DNA damage checkpoint regulation of the cell cycle pathway, and significant increases in gene expression associated with CDP-diacylglycerol biosynthesis pathway TCA cycle II pathway, and pyrimidine ribonucleotide salvage pathway after RYGB.  Since SLFN12 is reported to influence enterocytic differentiation, we stained mucosa for SLFN12 and observed increased SLFN12 immunoreactivity.  We investigated SLFN12 overexpression in HIEC-6 and FHs 74 Int intestinal epithelial cells and observed similar increased expression of the following genes that were also increased after RYGB: HES2, CARD9, SLC19A2, FBXW7, STXBP4, SPARCL1, and UTS.
Conclusions: Our data suggests that RYGB promotes SLFN12 protein expression, cellular mechanism and replication pathways, and genes associated with differentiation and restitution (HES2, CARD9, SLC19A2) and obesity-related genes (FBXW7, STXBP4, SPARCL1, UTS).

overall_design: Methods: To assess adaptive mechanisms in the human intestine after Roux-en-Y gastric bypass (RYGB), we biopsied proximal jejunum at the anastomotic site at surgery to establish a baseline and endoscopically re-biopsied the same area 6-9 months after bypass for comparison.  Laser microdissection was performed on pre- and post-RYGB biopsies to isolate enterocytes for RNA sequencing.

first: Emilie

middle: E

last: Vomhof-DeKrey

first: Sonalika

first: Allie

last: Stover

first: Odele

last: Rajpathy

first: Elizabeth

last: Preszler

first: Luis

last: Garcia

first: Marc

last: Basson


title: Lung transcriptome profile of a severe COVID-19 mice model with SARS-CoV-2 spike protein and Poly (I:C)

status: Public on Oct 31 2022

city: Yokohama

first: Kentaro

last: Tojo

state: Kanagawa

address: 3-9, Fukuura, Kanazawa Ward

department: Department of Anesthesiology and Critical Care Medicine

country: Japan

institute: Yokohama City University School of Medicine

summary: Acute respiratory distress syndrome (ARDS) with COVID-19 is aggravated by hyperinflammatory responses even after the peak of viral load has passed; however, its underlying mechanisms remain unclear. In the present study, analysis of the alveolar tissue injury markers and epithelial cell death markers in patients with COVID-19 revealed that COVID-19-induced ARDS was characterized by alveolar epithelial necrosis at an early disease stage. Serum levels of HMGB-1, one of DAMPs released from necrotic cells, were also significantly elevated in these patients. In addition, we established animal models of COVID-19 by intratracheal instillation with the SARS-CoV-2 spike protein and poly (I:C), a synthetic analog of double-stranded RNA. We performed bioinformatic analysis of lung tissue transcriptomes and confirmed that this COVID-19 model using SARS-CoV-2 spike protein and poly (I:C) recapitulated the biological responses seen in mice infected with SARS-CoV-2. Analysis of the mice model showed that the alveolar epithelial cell necrosis involved two forms of programmed necrosis: necroptosis and pyroptosis, Finally, neutralization of HMGB-1 attenuated alveolar tissue injury in the mouse model. Collectively, necrosis, including necroptosis and pyroptosis, seems to be the predominant form of alveolar epithelial cell death at an early disease stage and subsequent release of DAMPs is a potential driver of COVID-19-induced ARDS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lung tissues of a severe COVID-19 mice model with SARS-CoV-2 spike protein and Poly (I:C) and control mice.


title: Single-cell transcriptomic characterization reveals the landscape of airway remodeling and inflammation in a cynomolgus monkey model of asthma

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

institute: Children’s Hospital Zhejiang University School of Medicine

summary: Monkey disease models, which are comparable to humans in terms of genetic, anatomical, and physiological characteristics, are important for understanding disease mechanisms and evaluating the efficiency of biological treatments. Here, we established an A.suum-induced model of asthma in cynomolgus monkeys to profile airway inflammation and remodeling in the lungs by single-cell transcriptomic sequencing (scRNA-seq). The asthma model results in airway hyperresponsiveness and remodeling, demonstrated by pulmonary function test and histological characterization. scRNA-seq reveals that the model elevates the numbers of stromal, epithelial and mesenchymal cells (MCs). Particularly, the model increases the numbers of endothelial cells (ECs), fibroblasts (Fibs) and smooth muscle cells (SMCs) in the lungs, with upregulated gene expression associated with cell functions enriched in cell migration and angiogenesis in ECs and Fibs, and VEGF-driven cell proliferation, apoptotic process and complement activation in SMCs. Interestingly, we discover a novel Fib subtype that mediates type I inflammation in the asthmatic lungs. Moreover, MCs cells in the asthmatic lungs are found to regulate airway remodeling and immunological responses, with elevated gene expression enriched in cell migration, proliferation, angiogenesis and innate immunological responses. Despite the fact that the numbers of epithelial cells in the asthma lungs do not change at the time of lung tissue collection, their gene expressions are significantly altered, with an enrichment in the biological processes of IL-17 signaling pathway and apoptosis in the majority of subtypes of epithelial cells. Moreover, the ubiquitin process and DNA repair are more prevalent in ciliated epithelial cells. Last, cell-to-cell interaction analysis reveals a complex network among stromal cells, MCs and macrophages that contribute to the development of asthma and airway remodeling. Our findings provide a critical resource for understanding the principle underlying airway remodeling and inflammation in a monkey model of asthma, as well as valuable hints for the future treatment of asthma, especially the airway remodeling-characterized refractory asthma.

overall_design: Lung tissues were obtained from the control and asthma groups.The tissues were dissociated into single cells in dissociation solution.Single cell suspensions were loaded to 10× Chromium (10× Genomics, USA) to capture more than 3,000 single cells for the Single-cell 3′ Library using Gel Bead Kit V3 (1000075, 10× Genomics, USA) according to the manufacturer’s instructions. The following cDNA amplification and library construction steps were performed according to the manufacturer’s recommendation. Sequencing was performed on the NovaSeq6000 sequencer (Illumina, USA) with a minimum depth of 60,000~90,000 reads per cell and 150 bp (PE150) paired-end reads performed by LC-Bio Technology Co., Ltd (China).

first: Shuxian

last: Li

first: Huijuan

last: Shen

first: Yingshuo

last: Wang

first: Xinyan

last: Dong

first: Caizhe

last: Pan

first: Cihang

last: Zhu

first: Hantao

last: Qi

first: Yifan

first: Hao

last: Wei

first: Qiangmin

first: Lei


title: Type I interferons govern Zika virus resistance of human macrophages and microglia

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

summary: The role of the human type I interferon (IFN-I) system in restricting Zika virus (ZIKV) is uncertain. Here, genetic and pharmacological ablation of IFN-I signalling enhanced ZIKV replication and cytopathicity in macrophages and microglia, key cells in ZIKV transmission and pathogenesis. Thus, despite the extensive IFN-I countermeasures employed by ZIKV, IFN-I dictates the outcome of infection in macrophages. Therapeutic manipulation of the IFN-I system may bring clinical benefit in ZIKV.

overall_design: 12 samples of macrophages derived from induced pluripotent stem cells were processed for RNA-Sequencing on the Illumina NextSeq 500. Samples from an IFNAR2-deficient patient and 2 healthy controls. IFNAR2+ and IFNAR2- samples each infected with Asian lineage ZIKV H/FP/2013 and mock infected in triplicate.

first: Aidan

middle: T

last: Hanrath

first: Catherine

last: Hatton

first: Florian

last: Gothe

first: Cathy

last: Browne

first: Jane

last: Vowles

first: Peter

last: Leary

first: Sally

last: Cowley

first: William

last: James

first: Sophie

last: Hambleton

first: Christopher

last: Duncan


title: Total RNA analysis in extracellular vescicle of dystrophic, hypertrophic and wild type mice.

status: Public on Oct 29 2022

city: Leuven

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

institute: Genomics Core Leuven

summary: Total RNA analysis of extracellular vescicles coming from blood of dystrophic , hypertrophic and wild type mice was performed in order to detect most expressed genes in the extracellular vescicles and , if any, which differentially expressed genes would be identified between the three conditions. our analysis revealed that the amount of RNA extracted from blood-derived lurine extracellular vescicles was rather low and did not allow for az differential expression analysis even with extensive amplification of the transcripts. However, total RNA could be isolated and identified in the extracellular vescicles which allowed for a descriptive analysis of the content.

overall_design: Extracellular vescicles were isolated from the plasma ( blood) of dystrophic ( sgcb null) hypertrophic ( MAGIC-F1) and WT ( black 6) mice. Subsequently, total RNA was extracted from these samples. Total RNA was processed and run on a HiSeq2500 sequencer were analyzed with DeSeq in order to detect differentially expressed genes in the three mice groups.

first: Giorgia

last: Giacomazzi

first: Ester

last: Martinez Sarrà

first: Laura

last: Yedigaryan

first: Maurilio

last: Sampaolesi

first: Álvaro


title: Expression data from renal fibrotic tissues in two rat models induced by unilateral ureteral obstruction (UUO) and adenine

city: hangzhou

first: yueqin

last: cai

state: zhejiang

address: 548 Binwen Road, Binjiang District

institute: zhejiang chinese medical university

summary: Renal fibrosis (RF) is the common pathological outcome and central treatment target of multiple chronic kidney diseases. Currently, the molecular mechanisms of RF remain poorly understood. Therefore, this study aimed to established the adenine- and UUO-induced rat models, identified differentially expressed genes in their renal tissues using RNA-Seq analysis, and screened RF-related hub targets and key pathways.

overall_design: Three individual renal tissues of rats in the control, adenine, sham, and UUO groups were analyzed (n = 3 / group).

first: Yueqin

last: Cai

first: Jingan

last: Chen


title: Epigenetic and transcriptomic remodeling in monocytes of severe COVID-19 patients mirrors systemic changes in cytokines and immune cell crosstalk

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

summary: COVID-19 manifests with a wide spectrum of clinical phenotypes ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by a marked dysregulation in the myeloid compartment,  especially monocytes; however, little is known about the epigenetic regulation of these cells in relation to hyperinflammatory responses in severe COVID-19 patients. In this study, we obtained the DNA methylome and transcriptome of monocytes from severe COVID-19 patients. We observed drastic DNA methylation changes encompassing impairment of type-I interferons (IFN), antigen presentation functions among others, in concordance with gene expression changes supporting the relevance of DNA methylation alterations in the dysregulation of the myeloid compartment. These changes were similar to those occurring in bacterial sepsis, although specific functions resulting from viral infection were also identified. Also, a progressive relationship of DNA methylation alterations and Sequential Organ Failure Assessment (SOFA) score was found related with IFNγ production and T-helper 1 cell cytokine production. Analysis of the single cell transcriptomes of other immune cell types allowed inferring dysregulation of communication between monocytes and other cell types like NK cells, plasma B cells and T cells, which can partly explain monocyte epigenome dysregulation, perpetuating a dysregulated response in these patients.

overall_design: Monocytes from 48 severe COVID19 patients and 11 healthy donors were sorted and DNA methylation analysis was performed.

first: Gerard

last: Godoy-Tena

first: Anis

last: Barmada

first: Octavio

last: Morante-Palacios

first: Carlos

last: de la Calle-Fabregat

last: Ciudad

first: Adolfo

last: Ruiz-Sanmartín

first: Mónica

last: Martínez-Gallo

first: Mojca

last: Frank-Bertoncelj

first: Ricard

last: Ferrer

first: Juan

last: Ruiz-Rodriguez

first: Javier

last: Rodríguez-Ubreva

first: Roser

last: Vento-Tormo


title: Genome-wide identification of H3K27ac & H3K4me3-binding sequences upon LPS & CSF1 stimuli in mouse oocytes

status: Public on Oct 30 2022

city: Nanjing

first: yang

last: wang

address: 101 Longmian Avenue, Jiangning District, Nanjing

institute: Nanjing medical university

summary: We found that oocytes could arrange IgG production against adverse enviromental stimuli. We want to use chip-seq (cut-and-tag kit)  to identify how different stimuli (LPS, CSF1) impact the binding of H3K27ac & H3K4me3 to transcription-regulation sequences of IgG gene

overall_design: Identify how two major modified histones, H3K27ac & H3K4me3, bind to the regulating sequences of IgG gene upon different stimuli (LPS, CSF1) through chip-seq in mouse oocytes

first: Yang

last: Wang

first: Dong

last: Zhang


title: The effect of Monophosphoryl Lipid A (MPLA) on gene expression of wild type, MyD88 KO, and TRIF KO bone marrow-derived macrophages

status: Public on Oct 28 2022

city: Lexington

first: Allison

middle: M

last: Owen

state: KY

address: 441/CTW, 900 S. Limestone St.

institute: University of Kentucky

summary: We aimed to determine the relative contributions of MyD88- and TRIF-dependent signaling in Toll-like receptor-induced trained immunity in macrophages.

overall_design: Bone marrow-derived macrophages were obtained from wild type (WT), MyD88 KO (MKO), and TRIF KO (TKO) mice (3 biological replicates each) and treated with the TLR4 agonist monophosphoryl lipid A (1ug/mL MPLA; _M) or left unstimulated as negative controls (_US) for 24h before washoff. Macrophages were then rested for 3 days before RNA was harvested and processed for RNAseq.

first: Julia

last: Bohannon


title: Primate-specific Transcription Factors & Cis-Regulatory Elements Regulate Human Developmental Evolution.

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

summary: The human genome is composed of 4.5 million transposable elements (TE). The requirement for a TE to propagate through the genome during evolution is to be expressed to be retro-transpose into germ cells or pre-implantation embryo. Thus, many evolutionarily young TEs still contain DNA binding sites for pluripotency factors and are transiently expressed in the pre-implantation embryo. We observed that these and many other primate-restricted transposable elements have alternative binding sites for cell-type-specific transcription factors that allow them to be transcribed during human gastrulation. Furthermore, we have demonstrated that they can also serve as cell-type-specific enhancers and induce the expression of KRAB-Zinc Finger repressors of similar evolutionary age. This mechanism allows the domestication of TEs containing cell-type-specific binding sites and their incorporation into the shaping of human developmental-specific transcription networks.

overall_design: RNA-seq and Single-nuclei Multi-omic (ATAC and RNA) in endoderm and gastruloid differentiated human embryonic stem cells

first: Julien

last: Pontis

first: Delphine

last: Grun


title: mTORC1 signaling facilitates differential stem cell differentiation to shape the developing murine lung and is associated with mitochondrial capacity

first: Pao-Tien

last: Chuang

summary: Formation of branched organs requires sequential differentiation of stem cells. In this work, we find that the conducting airways derived from SOX2+ progenitors in the murine lungs fail to form without mTOR complex 1 (mTORC1) signaling and are replaced by lung cysts. Proximal-distal patterning through transitioning of distal SOX9+ progenitors to the proximal SOX2+ cells is disrupted. Mitochondria number and ATP production are reduced. Compromised mitochondrial capacity results in a similar defect as that in mTORC1-deficient lungs. This suggests that mTORC1 promotes differentiation of SOX9+ progenitors to form the conducting airways by modulating mitochondrial capacity. Surprisingly, in all mutants saccules are produced from lung cysts at the proper developmental time despite defective branching. SOX9+ progenitors also differentiate into alveolar epithelial type I and type II cells within saccules. These findings highlight selective utilization of energy and regulatory programs during stem cell differentiation to produce distinct structures of the mammalian lungs.

overall_design: Examination the gene expression difference between Control and mTORC1 deficient lungs

first: Kuan

first: Erica

last: Yao

first: Ethan

first: Biao

last: Chen

first: Evelyn


title: PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation

status: Public on Oct 27 2022

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: In this setup we have used RNA-seq, ChIP-seq, and ATAC-seq to identify how natural mutations in PPARg, which leads to lipodystrophy, cause changes in transcription, chromatin landscape, transcription factor binding and enhancer activity.

overall_design: Global gene expression analysis, HA-PPARg ChIP-seq, Med1 ChIP-seq, H3K27ac ChIP-seq, and ATAC-seq in PPARg-/- MEF-coxsackievirus-adenovirus receptor (CAR) cells acutely transduced with adenovirus expressing PPARg2-WT, PPARg2-E379K, or PPARg2-R212Q. All experiments are performed in duplicates.

first: Maria

last: Madsen

first: Marjoleine

last: Broekema

first: Martin

first: Arjen

last: Koppen

first: Anouska

last: Borgman

first: Cathrin

last: Gräwe

first: Elisabeth

middle: G

last: Thomsen

first: Mariette

last: Kranendonk

first: Marian

last: Koerkamp

first: Nicole

last: Hamers

first: Alexandre

last: Bonvin

first: José

last: Pittol

first: Kedar

last: Natarajan

first: Sander

last: Kersten

first: Frank

last: Holstege

first: Houshang

last: Monajemi

first: Saskia

middle: W

last: van Mil

first: Wilco

last: Spiering

first: Michiel

last: Vermeulen

first: Birthe

last: Kragelund

first: David

last: Cassiman

first: Eric

last: Kalkhoven


title: Polyploidy, regular patterning of genome copies, and unusual control of DNA partitioning in the Lyme disease spirochete

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

summary: Borrelia burgdorferi, the tick-transmitted spirochete agent of Lyme disease, has a highly segmented genome with a linear chromosome and various linear or circular plasmids. Here, by imaging several chromosomal loci and 16 distinct plasmids, we show that B. burgdorferi is polyploid during growth in culture and that the number of genome copies decreases during stationary phase. B. burgdorferi is also polyploid inside fed ticks and chromosome copies are regularly spaced along the spirochete’s length in both growing cultures and ticks. This patterning involves the conserved DNA partitioning protein ParA whose localization is controlled by a potentially phage-derived protein, ParZ, instead of its usual partner ParB. ParZ binds its owe coding region and acts as a centromere-binding protein. While ParA works with ParZ, ParB controls the localization of the condensin, SMC. Together, the ParA/ParZ and ParB/SMC pairs ensure faithful chromosome inheritance. Our findings underscore the plasticity of cellular functions, even those as fundamental as chromosome segregation.

overall_design: ChIP-seq experiments were performed on wild type and mutant cells of Borrelia burgdorferi S9 or M31 growing in BSK-II. WGS files were used as input control samples for ChIP-seq experiments.

first: X


title: Differential H3K9me2 heterochromatin levels and concordant mRNA expression in postmortem brain tissue of individuals with schizophrenia, bipolar, and controls

status: Public on Oct 25 2022

city: Chicago

first: Rajiv

middle: P.

last: Sharma

state: Illinois (IL)

address: 1601 West Taylor St room 285

institute: Univ Illinois Chicago

summary: The existence of repressive and durable chromatin assemblies along gene promoters or networks, especially in the brain, is of theoretical and therapeutic relevance in a subset of individuals diagnosed with schizophrenia who experience a chronic, persistent, and treatment-resistant trajectory. We used chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) to generate an epigenomic map that includes differential sites occupied by di-methylated lysine 9 of histone 3 (H3K9me2), a repressive modification that is yet unexplored in human postmortem brain tissue. We have discovered over 150 significantly differential promoter sites in the postmortem prefrontal cortex tissue of individuals diagnosed with schizophrenia (n=15) when compared to controls (n=15). Potentially dysregulated gene categories include postsynaptic proteins, processing enzymes (for proproteins, lipids, and oxidative stress), cadherin family genes, the complement system, and peptide hormones. Ten genes with significantly increased or decreased H3K9me2 promoter occupation were selected through statistical analysis, function, or previous GWAS association, and qRT-PCR was performed on an extended sample of postmortem brain tissue, adding an additional 17 controls, 7 individuals with schizophrenia, and 19 individuals with bipolar samples (n=32 control, 22 schizophrenia, 19 bipolar). This approach revealed that mRNA expression levels correlated with chromatin modification levels in eight of ten selected genes, and mRNA expression in the total sample could be predicted by the occupancy of H3K9me2. Utilization of this method and replication in a larger sample open a pathway to durable and restrictive epigenomic assemblies whose accumulation across the lifespan of individuals diagnosed with schizophrenia may explain treatment resistance, and advance therapeutic options.

overall_design: ChIP-seq for histone variant H3K9me2 is used to compare levels of H3K9me2 modification in schizophrenia and non-psychiatric controls in human postmortem brain tissue.

first: Hooriyah

last: Rizavi

first: Kayla

last: Chase

first: Chunyu

last: Liu


title: Primate gastrulation and early organogenesis at single-cell resolution

status: Public on Oct 26 2022

city: Beijing

first: Xiangxiang

last: Jiang

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Our understanding of human early development is severely hampered by limited access to embryonic tissues. Due to their close evolutionary relationship with humans, non-human primates (NHPs) are often used as surrogates to understand human development but currently suffer from a lack of in vivo datasets, especially from gastrulation to early organogenesis during which the major embryonic cell types are dynamically specified. To fill this gap, we have collected six Carnegie stage (CS) 8-CS11 cynomolgus monkey embryos and performed in-depth transcriptome analyses of 56,636 single cells. Our analyses reveal transcriptomic features of major peri-gastrulation cell types, which help shed light on morphogenetic events including primitive streak (PS) development, somitogenesis, gut tube formation, neural tube patterning, and neural crest regionalization in primates. In addition, comparative analyses with mouse embryos and human embryoids uncover conserved and divergent features of peri-gastrulation development across species, e.g. species-specific dependency on Hippo signaling during presomitic mesoderm differentiation, and provide an initial assessment of relevant stem cell models of human early organogenesis. This comprehensive single-cell transcriptome atlas not only fills the knowledge gap in the NHP research field but also serves as an invaluable resource for understanding human embryogenesis and developmental disorders.

overall_design: single cells from cynomolgus monkey embryo tissues spanning different developmental stages during early pregnancy were used to do single-cell RNA-Seq experiments

first: JingLei

last: Zhai

first: Jing

last: Guo

first: Haifeng

last: Wan

first: Luqing

last: Qi

first: Lizhong

first: Long

last: Yan

first: Zhenyu

last: Xiao

first: Yanhong

last: Xu

first: Dainan

last: Yu

first: Xulun

last: Wu

first: Wentao

last: Zhao

first: Kunyuan

first: Fan

first: Jun

first: Hongmei


title: Pulmonary parasite infection: do trypanosomes take your breath away?

first: Johan

last: Van Weyenbergh

address: Herestraat 49

department: DMIT

institute: KU Leuven

summary: Approximately 20% of sleeping sickness patients exhibit respiratory complications which are commonly attributed to secondary bacterial infections, with an unknown role of the parasite. Using a Glossina morsitans tsetse fly initiated Trypansoma brucei infection in mice we found that parasites rapidly and permanently colonize the lungs, representing one of the major target organs next to the adipose tissue. Trypanosomes were found by immunofluorescence staining and scanning electron microscopy to occupy the extravascular spaces surrounding the blood vessels of the alveoli and bronchi. Parasites were even found in the lung cartilage. Trypanosomes were often observed as nests of multiplying parasites exhibiting close interactions with collagen and highly active secretion of extracellular vesicles that are engaged in intercellular communication. The local immune response was analysed by flow cytometry after 10 and 21 days of infection and was characterized by a substantial increase of CD11b+ Ly6C+ monocytes, CD11b+ Ly6C+ F4/80+ macrophages and CD11b+ CD11c+ dendritic cells. CD11b+ Ly6G+ neutrophils only accumulated prominently at the late infection time point. Interestingly, parasite presence resulted in a significant reduction of B220+ IgM+ B cells, CD11b+ CD11clo/- SiglecF+ eosinophils and TcR-β- NK1.1+ natural killer cells. Digital transcriptomics revealed infection-induced upregulation of Il-10, IFN-ɣ- and IFN-α-responses, IL-2-, IL-6- and TNF-signalling, a Th1 pro-inflammatory signature, negative immune checkpoint regulators and a predominant M1 macrophage polarization. Il12a and genes associated with complement and the B cell receptor were downregulated. No infection-associated pulmonary dysfunction could be detected by in vivo lung function measurements, mirroring the limited pulmonary complications during sleeping sickness. However, the substantial reduction of eosinophils, B cells and NK cells may render individuals more susceptible to opportunistic infections. Collectively, these observations provide essential insights in the peculiar parasite biology, immunological reactions and physiological function of a largely overlooked target organ which may trigger new diagnostic approaches for sleeping sickness.

overall_design: C57BL/6JRj mice were kept in quarantine for at least 5 days before infection and were randomly allocated to the experimental units. Trypanosoma brucei brucei AnTAR1 were used for infection and total RNA from lung tissue extracted at 10dpi and 21 dpi.

first: Guy

last: Caljon


title: Transcriptome Analysis of Synovial CD14+ cells in Rheumatoid Arthritis Patients

city: Seoul

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

summary: To understand the pathogenic mechanisms of bone erosion in rheumatoid arthritis (RA), we investigated osteoclast-specific epigenetic programs, RANKL-responsive super-enhancers (SEs) and SE-associated enhancer RNAs (SE-eRNAs) in human osteoclasts. In this dataset, we sought for functional SE-eRNAs in RA patients' synovial monocytes.

overall_design: RNA_MCSF and RANKL

first: Seyeon

last: Bae

first: Kyung-Hyun

last: Park-Min

first: SungHo

last: Park


title: Impacts of ciliary neurotrophic factor on the retinal transcriptome in a mouse model of photoreceptor degeneration

city: CULVER CITY US

first: XIAN-JIE

last: YANG

address: 4037 Coogan Circle, Culver City, Culver City, Culver City

department: Ophthalmology

institute: Stein Eye Institute, UCLA School of Medicine

summary: Ciliary neurotrophic factor (CNTF) has been tested in clinical trials for human retinal degeneration due to its potent neuroprotective effects in various animal models.  To decipher CNTF-triggered molecular events in the degenerating retina, high-throughput RNA sequencing analyses were performed using the Rds/Prph2 (P216L) transgenic mouse as a preclinical model for retinitis pigmentosa.  Retinal transcriptome data was obtained for untreated wild type retinas, Rds retinas treated with a lentivirus expressing CNTF from postnatal day 25 to 35, and Rds retinas similarly treated with a control lentivirus expressing GFP.  Comparisons of transcriptome data detect significant changes between wild type and Rds retinas.  In addition, RNA-seq data reveal elevation of transcripts in the innate immune system and growth factor signaling, as well as altered neuronal transmission and metabolism in CNTF-treated Rds retinas.  These results demonstrate the influence of exogenous CNTF on the retinal transcriptome landscape and illuminate likely CNTF impacts in degenerating human retinas.

overall_design: Mouse retinas carried an rds mutation was treated with CNTF for 10 days by lentivirues-mediated delivery.  Retinal transcriptomes of wild type and rds mutant retinas treated with lentivurs expressing CNTF or control lentivirus expressing GFP were analyzed by high throughput sequnecing.

first: Yanjie

last: Wang

first: Kun-Do

last: Rhee

first: Matteo

last: Pellegrini

first: Xian-Jie

last: Yang


title: An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation

city: barcelona

first: benedetta

last: bolognesi

state: Barcelona

address: c comte borrell 232 5a-1a

institute: IBEC

summary: Multiplexed assays of variant effects (MAVEs) guide clinical variant interpretation and reveal disease mechanisms.  To date, MAVEs have focussed on a single mutation type - amino acid (AA) substitutions - despite the diversity of coding variants that cause disease.  Here we use Deep Indel Mutagenesis (DIM) to generate the first comprehensive atlas of diverse variant effects for a disease protein, amyloid beta (Aß) that aggregates in Alzheimer’s disease (AD) and is mutated in familial AD (fAD). The atlas identifies known fAD variants and many mutations beyond substitutions that accelerate Aß aggregation. Truncations, substitutions, insertions,  single- and multi-AA deletions differ in their propensity to enhance or impair aggregation, but likely pathogenic variants from all classes are strongly enriched in the polar N-terminus of Aß. This first comparative atlas for any disease gene highlights the importance of including diverse mutation types in MAVEs and provides important mechanistic insights into amyloid nucleation.

overall_design: Systematic measurement of the nucleation of substitutions, insertions, deletions and truncations in Aβ42

first: Benedetta

last: Bolognesi

first: Ben

last: Lehner


title: Single-cell RNA sequencing reveals a novel inhibitory effect of ApoA4 on NAFL mediated by liver-specific subsets of myeloid cells

city: Shaanxi

first: Xiaoming

last: Li

address: Zhuque Street

institute: xian jiaotong univercity

summary: The liver immune microenvironment is a key element in the development of hepatic inflammation in NAFLD. However, the precise immune cell subsets that exacerbate fatty liver remain elusive. ApoA4 deficiency increases the hepatic lipid burden, insulin resistance, and metabolic inflammation. The aim of this study was to profile the hepatic immune cells affected by ApoA4 in NAFL. We performed scRNA-seq on liver immune cells from WT and ApoA4-deficient mice administered a high-fat diet.

overall_design: Liver immune cells isolated from WT and KO mice (n=3/group) were subjected to scRNA-seq

first: Xiao-Huan

last: Liu

first: Jin-Ting

last: Zhou

first: Cheng

last: Cheng

first: Jing-Na

last: Fan


title: Global knock out of Sirt3 gene in Alzheimer’s transgenic mice with amyloid pathology

status: Public on Oct 24 2022

city: Aurora

first: Subbiah

last: Pugazhenthi

address: 1700 N Wheeling St

department: Endocrinology

institute: RMRVA & Anschutz Campus - Sch of Med - Endocrinology

summary: We have previously demonstrated that Sirt3 gene deletion, a model for metabolic syndrome, leads to brain mitochondrial dysfunction and neuroinflammation. We also reported that silencing of Sirt3 gene in APP/PS1 mice results in exacerbation of insulin resistance, neuroinflammation and β amyloid plaque deposition. To further understand how metabolic syndrome and amyloid pathology interact, we performed RNA-seq analysis of the brain samples from wild type, Sirt3-/- , APP/PS1 and APP/PS1/Sirt3-/- mice.

overall_design: Comparative gene expression profiling analysis of  RNA-seq data from the brain of  C57/BL6 (WT), Sirt3-/- (S3),  APP/PS1 (AP) and  APP/PS1/Sirt3-/- (AP_S3) mice

first: Alpna

last: Tyagi


title: WWP2 regulates Ly6Chigh monocyte infiltration and activity in heart fibrosis

city: Singapore

first: Gabriel

last: Chew

address: 8 College Road

institute: Duke-NUS Medical School

summary: Non-ischemic cardiomyopathy (NICM) can cause left ventricular dysfunction through interstitial fibrosis, which corresponds to the failure of cardiac remodelling. Recent evidence implicates monocytes/macrophages modulating cardiac fibrosis but targeting these is convoluted, giving their tissue heterogeneity and the antagonizing roles of macrophage subtypes in fibrosis. Here we focus on the role of WWP2, an E3 ubiquitin ligase that acts as a positive genetic regulator of human and murine cardiac fibrosis, and show that its myeloid-specific deletion reduces cardiac fibrosis in hypertension-induced NICM. Using the same model, we establish the functional heterogeneity of macrophages and define an early pro-fibrogenic phase driven by Ccl5-expressing Ly6chigh monocytes. Among other cardiac macrophage subtypes, WWP2 dysfunction primarily affects the Ccl5-dependent infiltration and activation of Ly6chigh monocytes, which causes reduced myofibroblast trans-differentiation. WWP2 interacts with IRF7, promoting its non-degradative monoubiquitination, nuclear translocation and transcriptional activity, including upstream Ccl5. Thus, we identify WWP2 as a key regulator of IRF7-mediated Ccl5/Ly6chigh monocyte axis in heart fibrosis.

overall_design: Isolated single cell suspensions were converted to barcoded scRNA-seq libraries (WT, WT Ang-II, WWP2Mut/Mut, and WWP2Mut/Mut Ang-II) by using the Chromium Single Cell 3' Library, Gel Bead & Multiplex Kit, and Chip Kit V3, loading an estimated 7,000-12,000 cells per library/well and following the manufacturer's instructions. Indexed libraries were sequenced using Illumina HiSeq 4000 sequencer, where 150bp pair-end sequences were obtained. Sequencing reads were aligned and quantified to the mouse genome GRCm38 (mm10-3.0.0 provided by 10x Genomics) using Cellranger count (v3.1.0).

first: Enrico

last: Petretto


title: Bulk RNA-Seq of human thyroid organoids

city: Bruxelles

first: Sabine

last: Costagliola

address: 808 route de lennik

department: IRIBHM

institute: Université Libre de Bruxelles

summary: The function of the thyroid gland is to metabolize iodide to synthesize hormones that act on almost all tissues and are essential for normal growth and metabolism. Low plasma levels of thyroid hormones lead to hypothyroidism, which is one of the most common diseases in the general population and cannot be always satisfactorily treated by lifelong hormone replacement. Therefore, in addition to the lack of in vitro tractable models to study human thyroid development, differentiation and maturation, there is a need for new therapeutic approaches that involve replacement of thyroid tissue to better control hormone balance. Here we report the first model of thyroid organoids derived from human embryonic stem cells that produce thyroid hormones in vitro and are capable of restoring plasma thyroid hormone levels when transplanted into athyreotic mice.

overall_design: Bulk RNA-seq was performed in NKX2-1GFP+  hESC-differentiated cells every week from day 16 to day 45 of our differentiation protocol. 10,000 NKX2-1GFP+ cells were directly sorted into 700µl of Qiazol lysis reagent (Qiagen) and RNA isolation was performed using the miRNeasy micro kit (Qiagen) according to the manufacturer's instructions. Ovarion Solo RNA-seq Systems (NuGen) was used as indicated by the manufacturer. Multiplexed libraries (10ρM) were loaded onto flow cells and sequenced on the HiSeq 1500 system (Illumina) in high-output mode using the HiSeq Cluster Kit v4 (Illumina).


title: Bulk RNA-Seq of human thyroid organoids II


title: Transplantable human thyroid organoids generated from embryonic stem cells to rescue hypothyroidism

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

overall_design: Refer to individual Series


title: Differential Immune Transcriptomic Profiles between Vaccinated and Resolved HCV Reinfected Subjects

city: Montreal

first: Naglaa

last: Shoukry

state: QC

address: Tour Viger, Local 09.414, 900 rue St-Denis

institute: CRCHUM

summary:
We applied a systems immunology approach to characterize longitudinal changes
in the peripheral blood transcriptomic signatures in eight subjects who spontaneously resolved two HCV infections Furthermore, we compared these signatures with those induced by an HCV T cell-based vaccine regimen.

overall_design:
Comparative gene expression analyses of different time points (4 total - Pre-reinfection, EA, LA, FU) pertinent to secondary HCV infection. And comparison with HCV T cell-based vaccine regimen.
Note: SR stands for Spontaneous Resolver.

first: Sabrina

last: Mazouz

first: Eduardo

last: Salinas

first: Nathalie

last: Bédard

first: Ali

last: Filali

first: Omar

last: Khedr

first: Leo

last: Swadling

first: Mohamed

last: Abdel-Hakeem

first: Asiyah

last: Siddique

first: Eleanor

last: Barnes

first: Julie

last: Bruneau

first: Arash

last: Grakoui

middle: H


title: Single-cell RNA-Seq of human thyroid organoid

overall_design: Cells originating from human thyroid differentiation protocol, at day 45, were isolated for scRNAseq profiling. Different proportions of viable NKX2-1/GFP+ (60 %) and NKX2-1/GFP- (40 %) cells were sorted. Around 6,000 cells were loaded onto a channel of the Chromium Single Cell 3′ microfluidic chip and barcoded with a 10X Chromium controller followed by RNA reverse transcription and amplification according to manufacturer’s recommendations (10X Genomics).


title: Single-cell RNA-Seq of human thyroid organoid II

overall_design: Cells originating from human thyroid differentiation protocol, at day 58, were isolated for scRNAseq profiling. Different proportions of viable NKX2-1/GFP+ (60 %) and NKX2-1/GFP- (40 %) cells were sorted and combined in a single tube. Around 6,000 cells were loaded onto a channel of the Chromium Single Cell 3′ microfluidic chip and barcoded with a 10X Chromium controller followed by RNA reverse transcription and amplification according to manufacturer’s recommendations (10X Genomics).


title: PPM1D suppresses p53-dependent transactivation and cell death by inhibiting the HRI-eIF2alpha-ATF4 pathway [RNA-seq]

first: Joaquin

last: Espinosa

department: Pharmacology, Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: The p53 transcription factor is a master regulator of cellular stress responses restrained by repressors such as MDM2 and the phosphatase PPM1D. Activation of p53 with pharmacological inhibitors of its repressors is being tested in clinical trials for cancer therapy, but efficacy has been limited by poor induction of tumor cell death. We demonstrate that dual inhibition of MDM2 and PPM1D induces cell death in multiple cancer cell types via amplification of the p53 transcriptional program through the eIF2alpha -ATF4 pathway. PPM1D inhibition induces phosphorylation of eIF2alpha, ATF4 accumulation, and ATF4-dependent enhancement of p53-dependent transactivation upon MDM2 inhibition. Dual inhibition of p53 repressors depletes heme and induces HRI-dependent eIF2alpha phosphorylation. Pharmacological induction of eIF2alpha phosphorylation synergizes with MDM2 inhibition to induce cell death and halt tumor growth in mice. These results demonstrate that PPM1D inhibits both the p53 network and the integrated stress response controlled by eIF2alpha, with clear therapeutic implications.

overall_design: Effects of MDM2 and PPM1D inhibition on transcriptomes in TPC1 and K1 cell lines.

first: Zdenek

last: Andrysik


title: Molecular identity of proprioceptor subtypes innervating different muscle groups in mice

status: Public on Oct 23 2022

city: Berlin

first: Niccolò

last: Zampieri

address: Robert-Rössle-Str. 10

department: Development and Function of Neural Circuits

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine

summary: The precise execution of coordinated movements depends on proprioception, the sense of body position in space. However, the molecular underpinnings of proprioceptive neuron subtype identities are not fully understood. Here we used a single-cell transcriptomic approach to define mouse proprioceptor subtypes according to the identity of the muscle they innervate. We identified and validated molecular signatures associated with proprioceptors innervating back (Tox, Epha3), abdominal (C1ql2), and hindlimb (Gabrg1, Efna5) muscles. We also found that proprioceptor muscle identity precedes acquisition of receptor character and comprise programs controlling wiring specificity. These findings indicate that muscle-type identity is a fundamental aspect of proprioceptor subtype differentiation that is acquired during early development and includes molecular programs involved in the control of muscle target specificity.

overall_design: scRNA transcriptomic analysis of proprioceptive sensory neurons (pSN) at embryonic day 15.5 and postnatal day 1.

first: Stephan

last: Dietrich


title: Differential gene expression analysis of PTGS2-inducing and PTGS2-non-inducing oropharyngeal carcinoma cell lines.

status: Public on Oct 21 2022

city: Manhasset

first: Vincent

last: Bonagura

state: New York

address: 350 Community Drive

department: Pediatric Immunology

institute: Northwell Health

summary: Prostaglandin E2 (PGE2) is a powerful immunomodulator synthesized by the COX2 enzyme, coded by human gene PTGS2. PGE2 is known to possess angiogenic, protumor and immunosuppressive functionality in the microenviornment of oropharyngeal carcinomas (OPC). Differential induction of PTGS2 in infiltrating myeloid-derived immunocytes has been observed with media conditioned by cultured OPC biopsies and OPC-derived cell lines alike. To identify PTGS2-inducing, OPC-derived gene products, we utilized bluk RNA sequencing on 4 OPC-derived cell lines to compare expression profiles of PTGS2-inducing (SCC154, SCC25) with that of PTGS2-non-inducing (2A3, SCC152) cell lines. Interleukin-1α (IL-1α) was among the differentially expressed candidates between cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of 2A3 and SCC152 vs. SCC154 and SCC25 cell lines.

first: Bettie

last: Steinberg

first: James

last: DeVoti

first: Mohd

last: Israr

first: Fung

last: Lam

first: Christopher

middle: J

last: Papayannakos


title: Loss of autism-candidate CHD8 perturbs neural crest development and intestinal homeostatic balance

city: Illkirch

first: Christelle

last: Golzio

state: Alsace

address: 1 rue Laurent Fries

country: France

institute: IGBMC


title: Single Cell Analysis of Docosahexaenoic Acid Suppression of Sequential LPS-Induced Proinflammatory and Interferon-Regulated Gene Expression in the Macrophage

status: Public on Oct 20 2022

city: Utrecht

first: Kathryn

middle: A.

last: Wierenga

state: Utrecht

address: Uppsalalaan 8

institute: Universitiet Utrecht

summary: Preclinical and clinical studies suggest that consumption of long chain omega-3 polyunsaturated fatty acids (PUFAs) reduces severity chronic and autoimmune diseases.  These ameliorative effects have been conventionally linked in part to downregulation of expression of proinflammatory cytokine and chemokine genes and more recently, associated with inhibition of Type 1 interferon (IFN1)-regulated gene expression. Here we used single cell RNA sequencing (scRNAseq) to gain new mechanistic perspectives of how the omega-3 PUFA docosahexaenoic acid (DHA) influences TLR4-driven proinflammatory and IFN1-regulated gene expression in a novel self-renewing murine fetal liver-derived macrophage (FLM) model. FLMs were cultured with 25 µM DHA or vehicle for 24 h, treated with modest concentration of  LPS (20 ng/ml) for 1 and 4 h, and then subjected to scRNAseq using 10X Chromium System.  At 0 h (i.e., in the absence of LPS), DHA increased expression of genes associated with the NRF2 antioxidant response (Sqstm1, Hmox1, Chchd10) and metal homeostasis (Mt1, Mt2, Ftl1, Fth1) suggesting cells are polarized towards a more anti-inflammatory phenotype. At 1 h post-treatment, DHA inhibited LPS-induced cholesterol synthesis genes (Scd1, Scd2, Pmvk, Cyp51, Hmgcs1, and Fdps)  which potentially could contribute to interference with TLR4-mediated inflammatory signaling. At 4 h post-treatment, LPS-treated FLMs reflected a robust proinflammatory response including upregulation of cytokine (Il1a, Il1b, Tnf) and  chemokine (Ccl2, Ccl3, Ccl4, Ccl7) genes as well as  IFN1-regulated (Irf7, Mx1, Oasl1, Ifit1) genes, many of which were suppressed by DHA. Using SCENIC analysis to identify gene expression networks, we found DHA modestly downregulated LPS-induced expression of NF-κB-target genes. Moreover, LPS induced a subset of FLMs simultaneously expressing NF-κB- and IRF7/STAT1/STAT2-target genes  that were conspicuously absent in DHA-pretreated FLMs, suggesting that DHA more potently targets the IFN1 response over the NF-kB response.  Altogether, scRNAseq generated a valuable dataset that provides new insights into multiple overlapping mechanisms by which DHA may transcriptionally or post-transcriptionally regulate LPS-induced proinflammatory and IFN1-driven responses in macrophages

overall_design: Primary macrophages treated with omega-3 docosahexaenoic acid and/or lipopolysachharide

last: Pestka

first: Bart

last: Westendorp

first: Frank

last: Riemers


title: SENP1 prevents steatohepatitis by suppressing RIPK1-driven apoptosis and inflammation

city: Shanghai

first: yan

middle: ling

last: jie

address: No. 100 Haike Road, Pudong, Shanghai

institute: Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences

summary: The mechanism underlying RIPK1-driven cell death and inflammation, a key process in the progression of nonalcoholic steatohepatitis, remains unclear. Here we identified SENP1, a SUMO-specific protease, as a key endogenous inhibitor of RIPK1. SENP1 is progressively reduced in proportion to NASH severity in patients. Hepatocyte-specific SENP1-knockout mice develop spontaneous NASH-related phenotypes in a RIPK1 kinase-dependent manner. We demonstrate that SENP1 deficiency sensitizes cells to RIPK1 kinase-dependent apoptosis by promoting RIPK1 activation following TNFα stimulation. Mechanistically, SENP1 deSUMOylates RIPK1 in TNF-R1 signaling complex (TNF-RSC), keeping RIPK1 in check. Loss of SENP1 leads to SUMOylation of RIPK1, which re-orchestrates TNF-RSC and modulates the ubiquitination patterns and activity of RIPK1. Notably, genetic inhibition of RIPK1 effectively reverses disease progression in hepatocyte-specific SENP1-knockout male mice with high-fat-diet-induced nonalcoholic fatty liver. We propose that deSUMOylation of RIPK1 by SENP1 provides a pathophysiologically relevant cell death-restricting checkpoint that modulates RIPK1 activation in the pathogenesis of nonalcoholic steatohepatitis.

overall_design: Liver mRNA profiles of E14.5d  Senp1+/+ ,Senp1-/-, Senp1-/-;RIPK1D138N/D138N mice and 4-month old Senp1flox/flox, Senp1flox/flox;AlbCre/+ mice

first: Daichao

last: Xu

first: Lingjie

last: Yan


title: Loss of autism-candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA-seq]

summary: Individuals with mutations in CHD8 present with gastrointestinal complaints, yet the underlying mechanisms are understudied. Here, utilizing a stable constitutive chd8 mutant zebrafish model, we found that the loss of chd8 leads to reduced number of vagal neural crest cells (NCCs), enteric neural and glial progenitors, emigrating from the neural tube and that their early migration capability was altered. At later stages, although the intestinal colonization by the NCCs was complete, we found decreased numbers of both serotonin-producing enterochromaffin cells and NCC-derived serotonergic neurons, suggesting an intestinal hyposerotonemia in absence of chd8. Further, transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last, single-cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8, NCC development, intestinal homeostasis, and autism-associated gastrointestinal complaints.

overall_design: 8 samples were analyzed: 4 tg(phox2bb:GFP);chd8+/+ (wild-type) and 4 tg(phox2bb:GFP);chd8sa19827/+ (heterozygous mutants). Each sample is comprised of a clutch of at least 80 4 days post-fertilization larvae.

first: Gaëlle

last: Hayot

first: Mathieu

last: Massonot

first: Céline

last: Keime

first: Elodie

last: Faure


title: A metabolic associated fatty liver disease risk variant in MBOAT7 regulates toll like receptor induced outcomes.

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research


title: Comprehensive analysis of differentially expressed miRNAs in mice with kidney injury induced by chronic intermittent hypoxia

city: 泉州

first: 清石

last: 陈

state: 福建省

address: 福建省泉州市鲤城区中山北路34号

institute: 医科大学附属第二医院

summary: In this study, the altered miRNA profiles in a chronic intermittent hypoxia (CIH) mouse model were investigated, aiming to provide novel clues for delineating the underlying mechanisms of OSA-induced kidney injury.

overall_design: A CIH mouse model was established. miRNA microarray was then applied to profile miRNA expression in kidney samples from CIH groups and controls.

first: Yunan

last: Su

first: Chaowei

last: Li

first: Weifeng

last: Liu

first: Yibin

first: Liangyi

first: Qingshi

last: Chen


title: Multiomic analysis reveals conservation of cancer associated fibroblast phenotypes across species and tissue of origin [multiome]

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

institute: Stanford University

summary: Cancer associated fibroblasts (CAFs) are integral to the solid tumor microenvironment. Once thought to be a relatively uniform population of matrix-producing cells, the arrival of single cell RNA sequencing has revealed diverse CAF phenotypes. Here, we further probe CAF heterogeneity with a comprehensive multiome approach. Using paired, same-cell chromatin accessibility and transcriptome analysis, we provide an integrated analysis of CAF subpopulations over a complex spatial transcriptomic and proteomic landscape to identify three superclusters – steady state-like (SSL), mechanoresponsive (MR) and immunomodulatory (IM) CAFs. These superclusters are recapitulated across multiple tissue types and species. Selective disruption of underlying mechanical force or immune checkpoint inhibition therapy results in shifts in CAF subpopulation distributions and impacts tumor growth. As such, the balance among CAF superclusters may have considerable translational implications. Collectively, this research expands our understanding of CAF biology, identifying regulatory pathways in CAF differentiation and elucidating novel therapeutic targets in a species- and tumor-agnostic manner.

sample_organism:
Homo sapiens
Mus musculus

overall_design:
multiomic analysis (scRNA-seq + scATAC-seq of material from the same/paired cells) of unsorted cells from tumor samples from mouse and human breast cancer using the 10X Genomics Multiome platform

The raw data for mouse samples have been split into separate samples. GSM6543819-GSM6543827 contains scRNA-seq raw data. GSM6774763-GSM6774771 contains scATAC-seq raw data. Human samples are associated with raw data for both scRNA-seq and scATAC-seq reads.

first: Deshka

last: Foster

first: Daniel

last: Delitto


title: RNAseq of triple negative breast cancer samples

city: Pamplona

first: Pablo

last: Sarobe

address: Avda. Pio XII, 55

institute: CIMA

summary:
We report RNAseq data from tumors obtained from patients with triple negative breast cancer
Eight patients with II-III stageTNBC diagnosis (only one patient with IV oligometastatic stage) were included in the study.  All patients received neoadjuvant chemotherapy based on sequential anthracyclines and taxanes ± platinum salts plus radiation therapy. Seven patients were evaluable for response and pathological complete response (RCB=0) was reached in 71.4% of the patients (2 patients with RCB=2). No patients received adjuvant systemic therapy.Tumor biopsies were obtained for RNAseq studies.

overall_design: RNAseq of tumor samples obtained from patients with TNBC

first: Sandra

last: Hervas


title: Inducible costimulator ligand (ICOSL) on CD19+ B cells is involved in immunopathological damage of rheumatoid arthritis (RA)

city: Suzhou

first: Cuiping

state: Jiangsu

address: Ganjiang Road 178#

institute: Jiang Su institue of immunology

summary: To explore the potential function of CD19+ICOSL- B-cell-subset, the whole transcriptome of sorted CD19+ICOSL+ and CD19+ICOSL- B cells was profiled by using Microarray analysis.

overall_design: CD19+ICOSL+ B cell and CD19+ICOSL- B cell subsets were sorted by FACSAriaTM Ⅱ Cell Sorter (BD Biosciences). Microarray analysis of sorted CD19+ICOSL+ B and CD19+ICOSL- B cells were carried out by Capitalbio Technology Corporation (Changping District, Beijing, China).

first: Sisi

last: Ding

first: Zhiyong

last: Sun

first: Juean

last: Jiang

first: Xin

last: Chang

first: Yu

last: Shen

first: Yanzheng

last: Gu


title: Breast cancer plasticity is restrictedby a LATS1-NCOR1 repressive axis

status: Public on Oct 19 2022

city: Rehovot

first: Yael

last: Aylon

address: 234 Herzl St

department: MCB

country: Israel

institute: Weizmann Institute of Science


title: Breast cancer plasticity is restrictedby a LATS1-NCOR1 repressive axis [ATAC-seq]

summary: The tumor suppressor LATS1, whose expression is often downregulated in human breast  cancer,  helps  maintain  luminal  breast  cancer  cell  identity  by  keeping  basal-specific genes in a closed chromatin state, preventing their spurious activation. This is achieved via interaction of LATS1 with the NCOR1 nuclear corepressor and  recruitment  of HDAC1,driving  histone H3K27  deacetylation near NCOR1-repressed “basal” genes. Consequently, decreased expression of LATS1 elevates the expression of such “basal” genes and promotes luminal-to-basal slippage.

overall_design: 4 samples X 2 replicates = 8 samples total

first: Noa

last: Furth

first: Gilgi

last: Friedlander

first: Moshe

last: Oren


title: BCL6 is regulated by the RAS/MAPK/ELK axis and promotes KRAS-driven lung cancers

city: China

first: Yanan

last: Liu

address: 500 Dongchuan Road, Minhang District, Shanghai, China

department: School of Life Sciences

country: China

institute: East China Normal University

summary: Mutational activation of KRAS represents a common oncogenic event in lung cancers and still lacks effective treatments so far. Here, we identify the proto-oncogene B-cell lymphoma 6 (BCL6) as a lynchpin for KRAS dependence. BCL6 transcription was markedly promoted upon inducible activation of KRAS in either LSL-KrasG12D mice lung tumor tissue or engineered KRAS isogenic cell lines. Constitutive expression of BCL6 was also observed in patients with KRAS-mutant lung adenocarcinoma and associated with poor survival. Employing chemical and genetic screens, we characterized that the MAPK/ELK1 axis downstream of KRAS directly regulated BCL6 expression. Genetic depletion or pharmacological inhibitor targeting BCL6 preferentially impedes the proliferation of KRAS-mutant lung cancer cells by suppressing pre-RC protein expression in cycling cells, ultimately leading to stalled replication and DNA damage in vitro. Accordingly, targeted inhibition of BCL6 significantly reduced tumor burden and mortality in LSL-KrasG12D/+ and patient-derived lung cancer xenograft mouse models in vivo. Taken together, these findings reveal an oncogenic role of BCL6 in promoting KRAS-addicted lung cancers and define that BCL6 inhibition confers a targetable vulnerability for this kind of disease.

overall_design: 7 samples are uploaded. RNA-seq was performed for HPNE cells,HPNE/KRAS G12V cells (HK) and HK/siBCL6 cells (HK cells treated with siBCL6); MEF1 cells and MEF1/KRAS G12D cells, MEF2/KRAS G12D cells and MEF2/ KRAS G12D/siBCL6 cells (MEF2/ KRAS G12D cells treated with siBCL6); each sample has three biological replicates.

first: Kun

last: Li

first: Xiufeng

last: Pang


title: Transcriptomic landscape of the central amygdala of the mouse

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: University of British Columbia

summary: Inhibitory neurons are the predominant type of neuron in the mouse central amygdala. Here, we examined diversity in this cell type using single-cell RNA-seq.

overall_design: Examination of inhibitory central amygdala neuron transcriptomes.


title: Breast cancer plasticity is restrictedby a LATS1-NCOR1 repressive axis [MARS-seq]


title: Analyses of transcriptomic profile of peritoneal macrophages

city: London

first: Patricia

last: Barral

address: London

institute: King's College London

summary: To investigate the function of CD1d in the regulation of macrophage homeostasis we performed transcriptomic analyses of cells isolated from the peritoneal cavity of WT and CD1d-deicient mice

overall_design: Macrophages were isolated from the peritoneal cavity of WT (C57BL/6) and CD1d-KO mice. Four biological replicates were performed