title: Bacteria from gut microbiota associated with diarrheal infections in children promote virulence of Shiga toxin-producing and enteroaggregative Escherichia coli pathotypes.

city: Santiago

first: Mauricio

middle: J.

last: Farfan

address: Antonio Varas 360, Providencia

department: Departamento de Pediatria y Cirugia Infantil

country: Chile

institute: Universidad de Chile

summary:
Purpose: In this work, we evaluated the role of two indicative species, Citrobacter werkmanii (CW) and Escherichia albertii (EA), in the virulence of two DEC pathotypes, Shiga toxin-producing (STEC) and enteroaggregative (EAEC) Escherichia coli.
Methods: To determine the effect of supernatant obtained from CW and EA cultures in STEC strain 86-24 and EAEC strain 042 gene expression, a RNA-seq analysis was performed. T84 cells were infected with DEC strains in the presence or absence of supernatant from EA and IL-8 secretion was evaluated. The effect of supernatant from EA on the growth and adherence of STEC and EAEC to T84 cells was also evaluated. Finally, we studied the participation of long polar fimbriae (Lpf) in STEC and plasmid-encoded toxin (Pet) in EAEC during DEC infection in the presence of supernatant from EA.
Results: RNA-seq analysis revealed that several virulence factors in STEC and EAEC were up-regulated in the presence of supernatants from CW and EA. Interestingly, an increase in the secretion of IL-8 was observed in T84 cells infected with STEC or EAEC in the presence of a supernatant from EA. Similar results were observed with the supernatants obtained from clinical strains of E. albertii. Supernatant from EA had no effect on the growth of STEC and EAEC, or on the ability of these DEC strains to adhere to intestinal epithelial cells. Finally, we found that Pet toxin in EAEC was up-regulated in the presence of a supernatant from EA. In STEC, using mutant strains for Lpf fimbriae, our data suggested that these fimbriae might be participating in the increase of IL-8 induced by STEC on intestinal epithelial cells in the presence of a supernatant from EA.
Conclusion:Supernatant obtained from an indicative species of DEC-positive diarrhea could modulate gene expression in STEC and EAEC, and IL-8 secretion induced by these bacteria. These data provide new insights into the effect of gut microbiota species in the pathogenicity of STEC and EAEC.

overall_design: Evaluate changes in gene expression for STEC and EAEC after an incubation with supernantant obtained from the culture of intestinal bacteria Citrobacter werkmanii and Escherichia albertii

first: Mariana

last: Izquierdo

first: Joaquín

last: Lopez

first: Pablo

last: Gallardo

first: Roberto

last: Vidal

first: Juan

last: Ossa


title: A systematic exploration reveals the potential of spermidine for hypopigmentation treatment through the stabilization of melanogenesis-associated proteins

status: Public on Jul 25 2022

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

country: South Korea

institute: Kangwon National University

type: Expression profiling by high throughput sequencing

summary: Spermidine (SPD), a polyamine naturally present in living organisms, is known to prolong lifespan in animals. In this study, the role of SPD in melanogenesis were investigated and showed the possibility as a pigmenting agent. SPD treatment increased melanin production in melanocytes in a dose dependent manner. Computational analysis with RNA-sequencing data revealed the alteration of protein degradation by SPD treatment without changing the expressions of melanogenesis-related genes. Indeed, SPD treatment significantly increased the stabilities of tyrosinase-related protein (TRP)-1 and -2 while inhibiting ubiquitination, which was confirmed by treatment of proteasome inhibitor MG132. Inhibition of protein synthesis by cycloheximide (CHX) showed that SPD treatment increased the resistance of TRP-1 and TRP-2 to protein degradation. To identify the proteins involved in SPD transportation in melanocytes, the expression of several solute carrier (SLC) membrane transporters was assessed and, among 27 transporter genes, SLC3A2, SLC7A1, SLC18B1, and SLC22A18 were highly expressed, implying they are putative SPD transporters in melanocytes. Furthermore, SLC7A1 and SLC22A18 were downregulated by SPD treatment, indicating their active involvement in polyamine homeostasis. Finally, we applied SPD to a human skin equivalent and observed elevated melanin production. Our results identify SPD as a potential natural product to alleviate hypopigmentation.

overall_design: The transcriptomic profiles of human primary melanocytes under SPD administration

first: Sofia

last: Brito

first: Hyojin

last: Heo

first: Mi-Gi

last: Lee

first: Bum-Ho

last: Bin


title: Effect of bantam knockdown on mRNA levels in the the γ5β′2a/β′2mp/β′2mp_bilateral Mushroom Body Output Neurons (MBONs) in Drosophila Melanogaster

status: Public on Jul 21 2022

city: Waltham

first: Leslie

middle: C

last: Griffith

state: MA

address: 415 South St.

department: Volen National Center for Complex Systems/ Neuroscience

country: USA

institute: Brandeis University

summary: In order to knockdown bantam in the  γ5β′2a/β′2mp/β′2mp_bilateral Mushroom Body Output Neurons (MBONs), we expressed the bantam microRNA-sponge (or the control scrambled-sponge) under the MB011B-split-Gal4 driver. Additionally, we expressed a membrane localized GFP transgene. At ZT12-13.5, MB011B>ban-spg, GFP and MB011B>scramble-spg, GFP female fly brains were diseccted, homogenized and FACS sorted using GFP flourescence to isolate the MBONs of interest. mRNA was extracted and used to construct Illumina RNAseq libraries

overall_design: A modified SMART-seq2 protocol was used to generate Illumina libraries from the isolated neurons (Li et al., 2017; Picelli et al., 2014).  mRNA was purified using a Dynabead mRNA kit (Invitrogen). The Poly(A)-tailed mRNAs underwent reverse transcribtion and PCR amplification (25 cycles). AMPure beads (Agencourt) were used to clean the resultant cDNA libraries, which were then processed with the Nextera XT (Illumina) protocol to generate sequencing Illumina libraries. Two biological replications were sequenced on a Next-seq 500 platform with paired-end 75bp reads and one biological replication was sequenced on a Hi-seq platform with paired-end 150bp reads. Reads were aligned to the Drosophila genome (dm6) using STAR (Dobin et al., 2013). EdgeR was used to perform DGE analysis on the aligned reads of the three biological replicates (Robinson et al., 2010).

first: Michael

last: Hobin


title: Elevated Myl9 reflects the Myl9-containing microthrombi in SARS-CoV-2-induced exudative vasculitis and predicts COVID-19 severity

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

summary: The mortality of coronavirus disease 2019 (COVID-19) is strongly correlated with pulmonary vascular pathology accompanied by SARS-CoV-2 infection-triggered immune dysregulation and aberrant activation of platelets. We combined histological analyses using field emission scanning electron microscopy with energy-dispersive X-ray spectroscopy analyses of the lungs from autopsy samples and single-cell RNA sequencing of peripheral blood mononuclear cells to investigate the pathogenesis of vasculitis and immunothrombosis in COVID-19. We found that SARS-CoV-2 accumulated in the pulmonary vessels, causing exudative vasculitis accompanied by the emergence of thrombospondin-1 (THBS-1)-expressing non-canonical monocytes and the formation of Myosin light chain 9 (Myl9)-containing microthrombi in the lung of COVID-19 patients with fatal disease. The amount of plasma Myl9 in COVID-19 was correlated with the clinical severity and measuring plasma Myl9 together with other markers allowed us to predict the severity of the disease more accurately. This study provides detailed insight into the pathogenesis of vasculitis and immunothrombosis, which may lead to optimal medical treatment for COVID-19.

overall_design: PBMC samples recovered from COVID-19 patients at admission (n=13) or within 10 days after admission (n=8), were stained with anti-human CD45 antibody. Propidiumiodine was also added to samples to remove dead cells. Live CD45+ cells were sorted using a SONY SH800S (4,000-10,000 cells each, cell viability >98%) and then encapsulated into droplets.  Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 following the manufacturer’s protocol (10X Genomics, CA,USA). The generated scRNA-seq libraries were sequenced using a total of 127 cycles (paired-end reads) with a NovaSeq 6000 (Illumina, Inc., CA, USA).

first: Chiaki

last: Iwamura

first: Kiyoshi

last: Hirahara

first: Sanae

last: Ikehara

first: Kazuhiko

last: Azuma

first: Tadanaga

last: Shimada

first: Sachiko

last: Kuriyama

first: Syota

last: Ohki

first: Emiri

last: Yamamoto

first: Yousuke

last: Inaba

first: Yuki

last: Shiko

first: Ami

last: Aoki

first: Kota

last: Kokubo

first: Rui

last: Hirasawa

first: Takahisa

last: Hishiya

first: Kaori

last: Tsuji

first: Tetsutaro

last: Nagaoka

first: Satoru

last: Ishikawa

first: Akira

last: Kojima

first: Ryota

last: Hase

first: Yasunori

last: Kasahara

first: Naohide

first: Tetsuya

last: Tsukamoto

first: Sukeyuki

last: Nakamura

first: Takashi

last: Urushibara

last: Kaneda

first: Seiichiro

last: Sakao

first: Minoru

last: Tobiume

first: Yoshio

last: Suzuki

first: Mitsuhiko

last: Tsujiwaki

first: Teruhumi

last: Kubo

first: Tadashi

last: Hasegawa

first: Hiroshi

last: Nakase

first: Osamu

last: Nishida

first: Kazuhisa

last: Takahashi

first: Komei

last: Baba

first: Yoko

last: Iizumi

first: Toshiya

last: Okazaki

first: Motoko

middle: Y

last: Kimura

first: Ichiro

last: Yoshino

first: Hidetoshi

last: Igari

last: Nakajima

first: Takuji

first: Hideki

last: Hanaoka

first: Taka-Aki

last: Nakada

first: Yuzuru


title: Endothelial Gsα regulates post-ischemia angiogenesis

city: Jinan,

first: Lifan

last: He

state: Shandong

address: No. 107, Wen Hua Xi Rd,

country: China

institute: Shandong University

summary: In the present study, we investigated the role of endothelial Gsα in post-ischemic angiogenesis.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 replicates cells respectly treated by GFP or Gsα virus.

first: Wencheng

last: Zhang

first: Hanlin

last: Lu

first: Xiaoteng

last: Qin


title: Effect of native or citrullinated histone peptides on gene expression of THP-1 cells

city: Seoul

first: Lucy Eunju

last: Lee

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

department: Division of Rheumatology, Department of Internal Medicine

institute: Yonsei University College of Medicine

summary: To examine the cellular effects of histones, we analyzed the RNA-seq data of THP-1 cells treated with native or citrullinated H2B-α1 peptide.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP-1 cells treated with H2B-α1 peptide or its citrullinated form.

first: Jaeyong

last: Jung

first: Lucy

middle: E

first: Hanna

last: Kim

first: Ji

first: Sung

middle: H

last: Jang

first: Jong

middle: S

last: Roh

first: Beomgu

first: William

last: Robinson

first: Dong

last: Sohn

first: Jae-Chul

last: Pyun

first: Jason

middle: J

last: Song


title: BASEMENT MEMBRANE OF SMALL DIAMETER XENOGENEIC EXTRACELLULAR MATRIX SCAFFOLDS MODULATE QUIESCENT HUMAN ENDOTHELIAL CELL MONOLAYER FORMATION

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

summary: Off-the shelf small diameter vascular grafts are an attractive alternative to eliminate the need and shortcomings of autologous tissue for vascular grafting. Bovine saphenous vein (SV) extracellular matrix (ECM) scaffolds from are potentially ideal small diameter vascular grafts, due to their inherit architecture and signaling molecules capable of driving proper cell behavior and regeneration. However, harnessing this potential is predicated on the ability of the scaffold generation technique to maintain the delicate structure, composition and associated function of native vascular ECM. Previous decellularization methods have been uniformly demonstrated to distupt the delicate basement membrane (BM) components of native vascular ECM. Here we demonstrate bovine SV ECM scaffolds generated using the novel antigen removal (AR) approach results in retention of native BM protein composition (e.g., Collagen IV and laminin), structure and cell modulatory function. Presence of BM proteins in AR vascular ECM scaffolds increases endothelial cell migration and proliferation, appropriate formation of adherence junction and apicobasal polarization, increased secretion of nitric oxide, and modulates endothelial cell quiescence. We conclude that presence of intact native vascular BM in AR SV ECM scaffolds modulate human endothelial cell behaviors which are essential for vessel homeostasis.

overall_design: Gene expression profiling of ECM scaffolds that are treated with TNFa or simvastatin. Sham treated scaffold (i.e. controls) and untreated scaffolds (Scaffolds) were also profiled for gene expression.

first: Leigh

last: Griffiths

first: Manuela

last: Lopera-Higuita

first: Nicholas

last: Shortreed


title: MiR-155 deficiency alters heterogeneity of lung immune cells in a mouse model of severe asthma

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

summary: The lung is a complex tissue comprised of more than 40 cell populations. The interplay among the heterogeneous pulmonary cells is required for proper function and long-term maintenance of lung homeostasis. Because each of the cell populations has a distinct transcriptome, bulk RNA-seq could mask cell-cell crosstalk, cell-type-specific contributions, and relevant networking changes in the lung. To overcome the limitations of bulk tissue analysis, we performed single cell RNA sequencing (scRNA-seq) to investigate the transcriptional profiles of lungs affected by miR-155. Unsupervised clustering analysis revealed 27 different clusters corresponding to distinct cell types of the lung, including epithelial, stromal, endothelial, and leukocyte lineages with specific molecular markers. The miR-155 knockout mice subjected to the severe asthma model showed a decrease in lung immune cells, whereas the numbers of structural cells such as epithelial and endothelial cells were slightly increased compared to their wild type counterparts. We also showed that the transcripts of extracellular trap formation-related genes were substantially down-regulated in miR-155 knockout mice subjected to the severe asthma model.

overall_design: Single cell RNA sequencing (scRNA-seq) from wild type and miR-155 knockout mice subjected to the SA model (N=3 each). Library preparation was carried out using 10x Genomics Chromium controller. Chromium 10x Genomics single cell library was sequenced as 150 base pair single-end reads on an Illumina NovaSeq 6000.

first: Sangwoon

last: Chung

first: Patrick

last: Stevens


title: 16S V3-V4 -based microbial profiling of matched healthy and inflamed ileal mucosa from patients affected by Crohn’s disease (set 2)

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Crohn’s Disease (CD) pathogenesis is still unclear. Disorders in the mucosal immunoregulation and its crosstalk with the microbiota may represent an important component in tissue injury. We aimed to characterize the molecular immune response distribution within the ileal layers ( mucosa, submucosa and serosa) and to evaluate the correlated microbiota in pathological/healthy settings comparing first surgery/relapse clinical conditions.

overall_design: 26 matched pairs of paraffin-embedded ileal tissue specimens was extracted and 16S rDNA amplicons (V3-V4 region)

first: Amedeo

last: Amedei


title: Effect of knockdown of RKIP(=PEBP1) on gene expression in mouse breast cancer cells

city: Toledo

first: Robert

last: Trumbly

address: 3000 Arlington Avenue

department: Biochemistry and Cancer Biology

institute: University of Toledo

summary: Raf-1 kinase inhibitor protein (RKIP = PEBP1) has been shown to negatively regulate signaling pathways including the MAPK and NFkappaB pathways involved in cancer progression and metastasis. RKIP acts as a suppressor of metastasis, but the exact mechanisms are unclear. In this study, knockdown of RKIP expression was used to identify the targets of RKIP expression. GSEA analysis identified interferon response genes as downregulated in the RKIP knockdown cells.

overall_design: The mouse breast cancer cell line 168FARN was transfected with expression vectors for either RKIP or control luciferase siRNAs. Total RNA was extracted from biological triplicates and hybridized to Affymetrix Mouse Gene 2.0 ST microarray chips.

first: Kam

last: Yeung


title: Environmental sensing by fibroblasts regulates tissue composition

city: New Haven

first: Scott

middle: Dean

last: Pope

state: Connecticut

address: 300 Cedar St

department: Immunobiology

institute: Yale School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Diverse cell types comprise animal tissues. However, the mechanisms controlling the number of each cell type within tissue compartments remain poorly understood. Here, we reported that different cell types utilize distinct strategies to control population numbers. Proliferation of fibroblasts, stromal cells important for tissue integrity, is limited by space availability. In contrast, proliferation of macrophages, innate immune cells involved in defense, repair, and homeostasis, is constrained by growth factor availability. Examination of density-dependent gene expression in fibroblasts revealed that Hippo and Tgf-b signaling are both regulated by cell density. We found YAP1, the transcriptional activator of the Hippo signaling pathway, directly regulate expression of Csf1, the lineage-specific growth factor for macrophages, through binding of YAP1 to a conserved enhancer of Csf1 that is specifically active in fibroblasts. Activation of YAP1 in fibroblasts elevates Csf1 expression, and is sufficient to increase the number of macrophages at steady state. Our data also suggest that expression programs in fibroblasts that change with density may result from sensing of mechanical pressure through actin-dependent mechanisms. Altogether, we demonstrate that two different modes of population control are connected and coordinated to regulate cell numbers of distinct cell types. Sensing of the tissue environment may serve as a general strategy to control tissue composition.

overall_design: Murine embryonic fibroblast were cultured at high and low densitys and perfomed ChIP-seq on endogenous Yap1 proteins.

first: Xu

last: Zhou

first: Ruslan

last: Medzhitov


title: Single cell sequencing facilitates quantitative analysis of transcriptomes of proliferative alveolar epithelial type 2 (AT2) cells in adult mouse lungs

city: Philadelphia

first: Ying

last: Tian

state: PA

address: 3500 N. Broad Street

department: Pharmacology, Center for Translational Medicine

institute: Lewis Katz School of Medicine at Temple University

summary:
Purpose: The goals of this study are to generate transcriptome profiling at single cell level (scRNA-seq) of proliferative AT2 cells
Methods: Lungs of 6- to 10-week-old SPC-EGFP, Ki67-creRT2, Rosa26-tdTomato mice before and 4 days after Streptococcus pneumoniae infection-induced lung injury were dissociated using dispase digesting method. Proliferative AT2 cells (GFP+/tdTomato+) and non-proliferative AT2 cells (GFP+/tdTomato-) were sorted using a BD influx LSRII. AT2 cell mRNA profiles were generated by scRNA-seq. Sequencing was performed on an Illumina Nextseq 500 system operated by the Next Generation Sequencing at GENEWIZ using the HiSeq 2x150 bp  high output sequencing kit.  The scRNAseq data was processed by Cell Ranger (v.3.0.2, 10X Genomics) followed by Seurat suite (version 4.0.1).
Results: Our results show a distinctive transcriptome profile of proliferative AT2 cells in adult mouse lungs
Conclusions: Our study represents the first detailed analysis of transcriptomes of proliferative and non-proliferative AT2 cells in adult mouse lungs generated by scRNA-seq technology.

overall_design: mRNA profiles of proliferative AT2 cells (GFP+/tdTomato+) and non-proliferative AT2 cells (GFP+/tdTomato-) in adult mouse lungs at homeostasis and after injury

first: Tian

last: Ying


title: HiChIP data for HNSCC subtypes

status: Public on Jul 20 2022

city: Madison

first: Scot

middle: Carson

last: Callahan

state: WI

address: 600 highland ave

institute: UW Health

summary: Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease with significant morbidity and mortality and frequent recurrence. Pre-NGS efforts to transcriptionally classify HNSCC into groups of varying prognosis have identified four accepted molecular subtypes of disease: Atypical (AT), Basal (BA), Classical (CL), and Mesenchymal (MS). Here, we investigated the active enhancer landscapes of these subtypes using representative HNSCC cell lines and identified samples belonging to the AT subtype as having increased enhancer activity compared to the other 3 HNSCC subtypes. Cell lines belonging to atypical subtype were more resistant to bromodomain inhibitors (BETi). PRO-Seq experiments that both TCGA tumors and AT cell lines showed higher eRNA transcripts for enhancers controlling BETi resistance pathways, such as lipid metabolism and MAPK signaling. Additionally, HiChIP experiments suggested higher enhancer-promoter (E-P) contacts in the AT subtype, including on genes identified in the eRNA analysis. Consistently, known BETi resistance pathways were upregulated upon exposure to these inhibitors. Together, our results identify that the AT subtype of HNSCC is associated with high enhancer activity, resistance to BET inhibition, and signaling pathways that could serve as future targets for sensitizing HNSCC to BET inhibition.

overall_design: H3K27ac HiChIP data for four HNSCC cell lines were generated with deep sequencing using the Novoseq6000 sequencer.  ***Authors state: Please note that the raw sequence data cannot be provided due to these being old cell lines without proper consents. Please contact krai@mdanderson.org for the sequence data***

first: S

first: Kunal

last: Rai


title: Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli

city: Tampere

first: Andre

last: Ribeiro

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Cold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators, while their single-cell protein numbers’ variability increases after cold shock. We hypothesized that some cold shock repressed genes could be triggered by high propensity for transcription locking due to changes in DNA supercoiling (likely due to DNA relaxation caused by an overall reduction in negative supercoiling). Concomitantly, we found that nearly half of cold shock repressed genes are also highly responsive to gyrase inhibition (albeit most genes responsive to gyrase inhibition are not cold shock responsive). Further, their response strengths to cold shock and gyrase inhibition correlate. Meanwhile, under cold shock, nucleoid density increases, and gyrases and nucleoid become more colocalized. Moreover, the cellular energy decreases, which may hinder positive supercoils resolution. Overall, we conclude that sensitivity to diminished negative supercoiling is a core feature of E. coli’s short-term, cold shock transcriptional program, and could be used to regulate the temperature sensitivity of synthetic circuits.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Examination of genome-wide responses over time (optimal and CS temperature) and under the effects of Novobicion (50 ng/μl). Data contains three samples per condition.

first: Suchintak

last: Dash

first: Cristina

middle: D

last: Palma

first: Ines

last: Baptista

first: Bilena

middle: B

last: Almeida

first: Mohamed

middle: M

last: Bahrudeen

first: Vatsala

last: Chauhan

first: Rahul

last: Jagadeesan


title: mRNA-seq data HNSCC cell line PLX51107 treatment for HNSCC subtypes

overall_design: There are 15 samples – 5 different conditions with 3 replicates each. ***Authors state: Please note that the raw sequence data cannot be provided due to these being old cell lines without proper consents. Please contact krai@mdanderson.org for the sequence data***


title: Bulk RNA-seq of alveolar macrophages from WT (Lepr+/+, Lyz2-Cre) and Lepr KO (Leprfl/fl, Lyz2-Cre) mice

city: Beijing

first: Ziyi

last: Guo

state: Beijing

address: Medicial Science Building, Tsinghua University

department: School of Medicine

institute: Institute for Immunology

summary: To study the regulation of Lepr on transcriptome in WT and Lepr KO AMs under resting state and after LPS stimulation, Lepr-sufficient (Lepr+/+, Lyz2-Cre) and Lepr-deficient (Leprfl/fl, Lyz2-Cre) alveolar macrophages (AMs) were isolated by collecting BALF. Lipopolysaccharide (LPS) was added in vitro for 1h or cells were left untreated. Total RNA was extracted for deep sequencing. Gene expression in WT and Lepr KO cells were analyzed.

overall_design: WT and Lepr KO AMs were isolated. After attaching to plate, cells were left unstimulated or stimulated with LPS for 1h. Total RNA was isolated and libraries were prepapred for high throughput sequencing.


title: PRO-seq data for HNSCC subtypes

overall_design: 8 samples of PRO-seq. ***Authors state: Please note that the raw sequence data cannot be provided due to these being old cell lines without proper consents. Please contact krai@mdanderson.org for the sequence data***


title: Next generation sequencing facilitates quantitative analysis of transcriptomes of adult mouse alveolar epithelial type 2 (AT2) cells with Atf3 or Thra overexpression

summary:
Purpose: The goals of this study are to generate transcriptome profiling (RNA-seq) of AT2 cells with over expression of Atf3 and Thra.
Methods: AT2 cell mRNA profiles of 5 or 6-week-old wild-type mice were generated by deep sequencing, in triplicate. The Illumina Nextseq 500 system was used to generate raw data at 75 cycles.  Fastq files was aligned to the reference genome and DEseq2 was used to analyze the differentially expressed genes.
Results: Our results show that Atf3 or Thra overexpression promotes the expression of genes associated AT2 cell proliferation.
Conclusions: Our study represents the first detailed analysis of transcriptomes of mouse AT2 cell with Atf3 or Thra overexpression, with biologic replicates, generated by RNA-seq technology.

overall_design: Mouse AT2 cell mRNA profiles of Ad-Cre (Ctrl), Ad-Atf3, and Ad-Thra AT2 cells


title: Microarray analyses of mRNA in PCDH1 knockdown cells

city: Zhongshan

first: Junkai

last: Zhang

address: Zhongshan

institute: Zhongshan People's Hospital

summary:
Uncontrolled growth, distant metastasis and chemoresistance are critical characteristics of pancreatic ductal adenocarcinoma (PDAC). We identified PCDH1 acting as a novel prognostic marker for PDAC.
PCDH1 enhanced p65 nuclear localization by interacting with KPNB1, therefore activates NF-κB signaling pathway and function during the progression of PDAC.

overall_design: We comparied mRNA expression profile of PCDH1 knockdown cells with negative control (siNC) group.

first: Zhihua

last: Ye


title: Staphylococcus aureus induces a muted host response in human blood that blunts the recruitment of neutrophils

city: New York City

first: Ze

last: Chen

state: New York

address: 430 East 29th Street

institute: NYU Grossman School of Medicine

summary: Methicillin resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen chief amongst bloodstream infecting pathogens. MRSA produces an array of human specific virulence factors that may contribute to immune suppression. Here, we defined the response of primary human phagocytes to infection with MRSA using RNA-Seq. We found that the overall transcriptional response to MRSA was weak both in the number of genes and the magnitude of response. Using an ex vivo bacteremia model with fresh human blood, we found that infection with live MRSA resulted in the down-regulation of genes related to innate immune response, and cytokine and chemokine signaling. This muted transcriptional response was conserved across diverse S. aureus clones but absent in heat-killed MRSA or blood infected with live Staphylococcus epidermidis. Importantly, the muted signature was also present in patients with S. aureus bacteremia. We next identified the master regulator SaeRS and the SaeRS-regulated pore-forming toxins as key mediators of transcriptional suppression. The impaired chemokine and cytokine responses were reflected by circulating protein levels in the plasma. MRSA elicits a soluble milieu that is restrictive in the recruitment of human neutrophils compared to strains lacking saeRS. Thus, MRSA blunts the inflammatory response resulting in impaired neutrophil recruitment, which could promote the survival of S. aureus during invasive infection.

overall_design: Stimulation of 4 myeloid cell types with Staph of 3 anonymous healthy human donors; mRNA profile of whole blood responding to 2 different concentrations of staph; mRNA profile of whole blood responding to 17 subtypes or mutants of staph

first: Erin

last: Zwack

first: Joseph

last: Devlin

first: Zhi

last: Li

first: Xuhui

last: Zheng

first: Mei

last: Tang

first: Ada

last: Weinstock

first: Keenan

middle: A

last: Lacey

first: Edward

last: Fisher

first: David

last: Fenyo

first: Kelly

middle: V

last: Ruggles

first: P’ng

last: Loke

first: Victor

last: Torres


title: A Drug Repurposing Screen Identifies Fludarabine Phosphate as a Potential Therapeutic Agent for N-MYC Overexpressing Neuroendocrine Prostate Cancers

city: Saskatoon

first: Franco

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

summary: Neuroendocrine prostate cancer (NEPC) represents a highly aggressive form of prostate tumors. NEPC results from trans-differentiated castration-resistant prostate cancer (CRPC) with increasing evidence indicating that the incidence of NEPC often results from the adaptive response to androgen deprivation therapy. Recent studies have shown that a subset of NEPC exhibits overexpression of the MYCN oncogene along with the loss of tumor suppressing TP53 and RB1 activities. N-MYC is structurally disordered with no binding pockets available on its surface and so far, no clinically approved drug is available. We adopted a drug-repurposing strategy, screened ~1800 drug molecules and identified Fludarabine Phosphate to preferentially inhibit proliferation of N-MYC overexpressing NEPC cells by inducing ROS. We also show that Fludarabine phosphate affects N-MYC protein levels and N-MYC transcriptional targets in NEPC cells. Moreover, enhanced ROS production destabilizes N-MYC protein by inhibiting AKT signaling and is responsible for the reduced survival of NEPC cells and tumors. Our results indicate that increasing ROS production by administration of Fludarabine Phosphate may represent an effective treatment option for patients with N-MYC overexpressing NEPC tumors.

overall_design: Two biological replicates were analyzed for each of 2 conditions (Control and Treated)

first: Hussain

last: Elhasasna

first: Frederick

first: Andrew

last: Freywald


title: Chip-seq data for HNSCC subtypes

first: Scot

last: Callahan

overall_design: 28 unique HNSCC cell line samples. ***Authors state: Please note that the raw sequence data cannot be provided due to these being old cell lines without proper consents. Please contact krai@mdanderson.org for the sequence data***

first: S

first: Kunal

last: Rai

first: Zhiyi

last: Liu


title: miRNA expression in kidneys

status: Public on Jul 19 2022

city: Dallas

first: harini

last: ramalingam

state: Texas

address: 5323 Harry Hines Boulevard

department: IMN

institute: UTSW

summary:
The goal of this project is to obtain the expression pattern of miRNAs in wild type kidneys at various ages during development. The data is obtained from mouse kidneys of ages P0, P7, P14, P21 and P35.
The analysis compares the expression levels of miRNAs between the age groups.

overall_design: There were 4 biological replicates from P0 and 3 biological replicates from P7, P14, P21 and P35.

first: Vishal

last: Patel


title: RNA-seq for inflamed and non-inflamed mucosa in patients with Crohn's disease

first: Sung Noh

last: Hong

state: South Korea

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

institute: Samsung Medical Center

summary:
To investigate the gene expression profile of inflamed and non-inflamed mucosa in patients with Crohn's disease.
To investigate TCR repertoires in the intestinal mucosa, the expression profile of the TCR repertoire gene was analyzed.

overall_design:
We prospectively enrolled 13 patients with active CD (mean age: 30.9 ± 10.9 years; 9 were males) who underwent diagnostic or surveillance colonoscopy. Clinical characteristics of the enrolled patients were as follows: Montreal classification A1 / A2 / A3, n = 2 / n = 8 / n = 3; L1 / L2 / L3, n = 6 / n = 2 / n = 5; B1 / B2 / B3, n = 5 / n = 5 / n = 3. During colonoscopy, 2-4 biopsy samples were taken from active ulcer margins (inflamed intestinal mucosa, n = 13) and endoscopically normal-appearing mucosa (non-inflamed intestinal mucosa, n = 13) from each patient with CD.   As controls, 9 non-IBD patients were enrolled prospectively (mean age: 49.7 ± 14.9 years; 6 were males) who underwent colonoscopies for colorectal polyp removal. Endoscopically normal-appearing healthy colonic mucosa specimens were obtained from the ascending colon of each non-IBD control (healthy mucosa of non-IBD control, n = 9).
*** Submitter declares that institutional policy restricts the deposit of patient raw data outside the institution. ***

first: Sung

middle: N

first: Chnasu

last: Lee

first: Je-Gun

last: Joung


title: RBFOX1 overexpression in the human glioblastoma cell line A172

city: Montreal

first: Gabrielle

last: Perron

state: Quebec

address: 845 Sherbrooke St W

department: Human Genetics

institute: McGill University

summary: The goal of this study was to investigate the regulatory events underlying post-transcriptional changes in gene expression, and more specifically in mRNA stability, in cancer. We observed that the stability of RBFOX1 targets was decreased in glioblastoma and, given that RBFOX1 is known to stabilize its targets mRNAs, we hypothesized that RBFOX1 down-regulation is responsible at least in part for alterations in the glioblastoma transcriptome. We overexpressed RBFOX1 in the A172 human glioblastoma cell line and performed RNA-sequencing on extracted RNA. We computed differential gene expression in the cell line overexpressing RBFOX1, compared to the control samples. We confirmed that RBFOX1 overexpression leads to an upregulation of  the RBFOX1 regulon, including the majority of RBFOX1 targets that are destabilized in tumors. The results suggest that RBFOX1 downregulation in glioblastoma leads to the destabilization of its targets, which can be partially rescused through overexpression of RBFOX1.

overall_design: RNA-seq of A172 cell lines overexpressing RBFOX1 or GFP, performed using Illumina NovaSeq 6000

first: Yasser

last: Riazalhosseini

first: Hamed

last: Najafabadi


title: Single-cell transcriptional profiles of lung CD45+ immune cells from WT and Ptgs2-cKO mice

city: Bar Harbor

first: Guangwen

last: Ren

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: To better understand the role of the COX-2-dependent lung fibroblast program in modulating the lung immune microenvironment, we generated fibroblast-targeted Ptgs2 conditional knockout (cKO) mice by crossing Pdgfra-Cre mice with Ptgs2flox/flox mice. Then we determined how Ptgs2 deficiency in CD140a+ fibroblasts alters the lung immune microenvironment by performing single-cell RNA sequencing on lung CD45+ immune cells from WT and Ptgs2-cKO mice.

overall_design: Lung CD45+ immune cells from WT and Ptgs2-cKO mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Zheng

last: Gong

first: Qing

last: Li

first: Jiayuan

last: Shi


title: Leishmania parasites exchange drug-resistance genes through extracellular vesicles

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

summary: Leishmania are ancient eukaryotes that have retained the ability to produce extracellular vesicles (EVs) through evolution. Until date, it was unclear if different DNA entities could be associated to Leishmania EVs, and whether these could constitute a novel mechanism of horizontal gene transfer (HGT). Herein, we investigated the DNA content of EVs derived from drug-resistant parasites, as well as the potential of EVs as shuttles for DNA transfer. Next-generation sequencing, and PCR assays confirmed the enrichment of amplicons carrying drug-resistance genes associated to EVs. Transfer assays of drug-resistant EVs highlighted a significant impact in the phenotype of recipient parasites induced by the expression of the transferred DNA. Recipient parasites displayed an enhanced growth and better control of oxidative stress. We provide the first evidence that eukaryotic EVs function as efficient mediators in HGT, thereby facilitating the transmission of drug-resistance genes and increasing the fitness of cells when encountering stressful environments.

overall_design: Extracellular vesicles (EVs) were isolated from the wild type (WT) and the antimony (Sb) resistant Leishmania infantum and their DNA content was analyzed using DNA sequencing (Illumina NovaSeq 6000).

first: Christopher

last: Fernandez-Prada

first: Atia

last: Amin

first: Noélie

last: Douanne


title: Mouse model of weak depression exhibiting suppressed cAMP signaling in amygdala, lower lipid catabolism in liver and correlated gut microbiota

city: Matsudo

first: Akihito

last: Yausoka

state: Chiba

address: Iwase 550

department: Human nutrition

institute: Seitoku University

summary: To establish a mouse model of weak depression, we raised six-week-old C57BL/6N mice in single (SH) or group housing (GH) conditions for two weeks. The SH group showed less social interaction with stranger mice, learning disability in behavioral tests, and lower plasma corticosterone level. The cecal microbiota of the SH group showed significant segregation from the GH group in principal coordinate analysis. Transcriptome analysis of the amygdala, and liver detected multiple differentially expressed genes (DEGs). In the amygdala of SH mice, suppression of the cyclic adenine monophosphate (cAMP) signal was predicted and confirmed by the reduced immunoreactivity of phosphorylated cAMP-responsive element binding protein. In the liver of SH mice, down-regulation of beta-oxidation was predicted. Interestingly, the expression levels of over 100 DEGs showed significant correlation with the occupancy of two bacterial genera, Lactobacillus (Lactobacillaceae) and Anaerostipes (Lachnospiraceae). These bacteria-correlated DEGs included JunB, the downstream component of cAMP signaling in the amygdala, and carnitine palmitoyltransferase 1A, a key enzyme of beta-oxidation in the liver. This trans-omical analysis also suggested that NAD synthesis in the liver may be linked to the occupancy of Lactobacillus through the regulation of nicotinamide phosphoribosyltransferase and kynureninase genes. Our results suggested that SH condition along with the presence of correlated bacteria species causes weak depression phenotype in young mice and provide suitable model to study food ingredient that is able to cure weak depression.

overall_design: Transcriptome analysis of amygdala, hypothalamus, and liver. MIcrobiome analysis of cecal content. Correlational analysis between transcriptome and micorbiome.

first: Kousuke

last: Shimada

first: Masakatsu

last: Nohara

last: Yasuoka

first: Asuka

last: Kamei

first: Fumika

last: Shinozaki

first: Kaori

last: Kondo

first: Ryo

last: Inoue

first: Takashi

first: Keiko

last: Abe


title: The effect of CBX2 knockdown on gene expression in MDA-MB-231 cells

city: Hull

first: Mark

last: Wade

state: Humberside

address: Room 121, Hardy Building, University of Hull, Cottingham Road

country: United Kingdom

institute: University of Hull

summary: To identify potential CBX2-regulated genes in triple negative breast cancer cells we assessed global gene expression changes in CBX2-depleted MDA-MB-231 cells by RNA-sequencing analysis using the Illumina NovaSeq 6000 platform. Through Gene Set Enrichment Analysis we identified that CBX2 promotes cell growth, mTORC1 activation, E2F signalling and inhibits RBL2-mediated DREAM-complex activity.

overall_design: MDA-MB-231 cells were transfected with either a non-silencing scrambled control siRNA (siSCR) or CBX2 targeting siRNAs (siCBX2#2/siCBX2#3), using Lipfectamine RNAiMAX (Invitrogen) to a final concentration of 25 nM. Cells were grown for 72 hours prior to RNA extraction using the RNeasy mini kit (Qiagen). Library preparation and sequencing using the Illumina NovaSeq 6000 platform was performed by Novogene Co Ltd (Cambridge, UK). Read alignment was performed using the HISAT2 algorithm and FPKM calculated to estimate gene expression in each sample.

first: Lucie

last: Bilton

first: Chloe

last: Warren

first: Ella

last: Waters

first: Thomas

last: Francis

first: Pedro

last: Beltran-Alvarez

first: Rebecca

last: Humphries


title: The effect of CBX2 knockdown on gene expression in MCF-7 cells

summary: To identify potential CBX2-regulated genes in ER positive cancer cells we assessed global gene expression changes in CBX2-depleted MCF-7 cells by RNA-sequencing analysis using the Illumina NovaSeq 6000 platform. Through Gene Set Enrichment Analysis we identified that CBX2 promotes cell growth, mTORC1 activation, E2F signalling.

overall_design: MCF-7 cells were transfected with either a non-silencing scrambled control siRNA (siSCR) or CBX2 targeting siRNA (siCBX2#3), using Lipfectamine RNAiMAX (Invitrogen) to a final concentration of 25 nM. Cells were grown for 72 hours prior to RNA extraction using the RNeasy mini kit (Qiagen). Library preparation and sequencing using the Illumina NovaSeq 6000 platform was performed by Novogene Co Ltd (Cambridge, UK). Read alignment was performed using the HISAT2 algorithm and FPKM calculated to estimate gene expression in each sample.


title: The effect of CBX2 knockdown on gene expression in MDA-MB-231 and MCF-7 cells

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

overall_design: Refer to individual Series


title: High-throughput microarray reveals the epitranscriptome-wide landscape of m6A-circRNA in oral squamous cell carcinoma

city: Tianjin

first: Wei

last: Zhao

address: Qixiangtai Road

institute: Tianjin medical university

summary:
We report an epitranscriptome-wide mapping of m6A-modified circRNAs (m6A-circRNA) in oral squamous cell carcinoma (OSCC). Utilizing the data of m6A-circRNAs epitranscriptomic microarray analysis, we found that m6A-circRNAs exhibited their particular modification style in OSCC.
anti-m6A antibody Synaptic Systems, cat. No. 202003)

overall_design: SCC25 vs. HOK cells. Biological replicates: 3 tumor replicates, 3 normal replicates.


title: COVID-19 DNA methylation analysis

city: Granada

first: Guillermo

last: Barturen

state: Andalucia

address: Faculty of Science. Fuente nueva s/n

department: Department of Genetics

country: Spain

institute: University of Granada

type: Methylation profiling by genome tiling array

summary: Whole blood genome wide DNA methylation profiling from RT-PCR 473 positive and 101 negative SARS-CoV-2 individuals was performed.

overall_design: Bisulphite converted DNA samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip.

first: Marta

last: Alarcón-Riquelme


title: Characterization and analysis of the promoter region of Monodehydroascorbate reductase 4 (CpMDAR4) in papaya

status: Public on Jul 18 2022

city: Urbana

first: Dessiree

middle: Patricia

last: Zerpa Catanho

state: Illinois

address: 1201 W. Gregory Dr, 279 ERML

institute: University of Illinois at Urbana-Champaign

summary: The aim of this research was to study the effects of cis-element differences between the X, Y and Yh alleles on the expression of CpMDAR4, a potential candidate gene for sex differentiation in papaya, using a transcriptional reporter system in a model species Arabidopsis thaliana. Possible effects of a retrotransposon insertion in the Y and Yh alleles on the transcription and expression of CpMDAR4 alleles in papaya flowers were also examined. When comparing promoters and cis-regulatory elements among genes in the non-recombining region of the sex chromosomes, paired genes exhibited differences. Our results showed that differences in the promoter sequences of the CpMDAR4 alleles drove the expression of a reporter gene to different flower tissues in Arabidopsis. β-glucuronidase staining analysis of T2 and T3 lines for constructs containing 5’ deletions of native Y and Yh allele promoters showed the loss of specific expression of the reporter gene in the anthers, confirming the existence and location of cis-regulatory element POLLEN1LELAT52. The expression analysis of CpMDAR4 alleles in papaya flowers also showed that all alleles are actively expressed in different flower tissues, with the existence of a shorter truncated isoform, with unknown function, for the Y and Yh alleles due to an LTR-RT insertion in the Y and Yh chromosomes. The observed expression patterns in Arabidopsis thaliana flowers and the expression patterns of CpMDAR4 alleles in papaya flowers, suggest that MDAR4 might have a role on development of reproductive organs in papaya, and that it constitutes an important candidate for sex differentiation.

overall_design: To evaluate tissue-specific expression of CpMDAR4 alleles in papaya flowers, total RNA was extracted from small flower buds (< 1 mm), reproductive organs of pre-meiotic (1-6 mm) and post-meiotic (7-12 mm) flower buds (including aborted pistils or “pistillode”), mature flowers (15-20 mm) and gametophytes of mature ‘AU9’ female flowers and ‘AU9’ male flowers.

first: Ray

last: Ming

first: Juan

last: Liu

first: Ping

last: Zhou

last: Zerpa


title: Peripheral whole blood: Healthy control and Major depression disorder patients

first: Zijing

address: No. 9, Dongdan

institute: Chinese Academy of Medical Sciences

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Transcriptional profiling in the whole blood samples of healthy controls and major depression disorder (MDD) patients who have never been treated with depression medication. Samples included 20 healthy controls and 20 MDD patients who have never been treated with depression medication. Goal was to discover the differentially expressed genes.

overall_design: 20 Healthy controls vs. 20 major depression disorder (MDD) patients

first: Futing

last: Du

first: Rongrong

last: Han


title: MeRIP-Seq reveals the genome-wide maps of m6A modification on mRNA and lncRNA in OSCC

first: Xi

last: Wang

address: Qixiangtai Road, No. 12

department: The School and Hospital of Stomatology

institute: Tianjin Medical University

type: Methylation profiling by high throughput sequencing

summary: We report the application of Methylated RNA Immunoprecipitation with Next Generation Sequencing and R software package in SCC25 and HAEC. By analysis the m6A peak areas which decorated in the 3' untranslated regions of target functional mRNAs and the entire interval of lncRNA, after that use gene ontology enrichment analysis and pathway enrichment analysis to indicate the explicit correlation to transcription, DNA-templated and pathways, we detect a series of m6A modification in mRNAs and lncRNAs, and explore some key clues in pathways related to OSCC which can guide the further studies on OSCC tumorigenesis and potential targeting.

overall_design: Examination of m6A modification in human aortic endothelial cells and human tongue phosphorus carcinoma cells.


title: Shifts in the Immunoepigenomic Landscape of Monocytes in Response to a Diabetes-Specific Social Support Intervention: A Pilot Study Among Native Hawaiian Adults with Diabetes

city: Honolulu

first: Christian

middle: Ka'ikekuponoaloha

last: Dye

state: HI

address: 641 Ilalo St. BSB 222K

department: Native Hawaiian Health

institute: University of Hawaii at Manoa

summary: Genome-wide DNA methylation profiling of bead-enriched total monocytes collected from Native Hawaiian participants with known type 2 diabetes mellitus enrolled in a 3 month diabetes-specific social support education intervention. DNA methylation profiling was performed across ~450,000 CpGs from monocytes using the Illumina Infinium HumanMethylation450 BeadChip. Samples included 8 participants with paired DNA methylation data collected at pre-intervention and post-intervention (3 months), and 2 non-diabetic donors.

overall_design: 500 ng of genomic DNA from enriched total monocytes were bisulfite converted (EZ DNA Methylation Kit - Zymo Research), bisulfite converted DNA was randomly assigned to a chip well on the HumanMethylation450 BeadChip, and imaged with the iScan SQ instrument (Illumina) to obtain raw image intensities.

middle: K

first: Michael

last: Corley

first: Alika

last: Maunakea


title: Deficiency of the RNA-binding protein Cth2 extends yeast replicative lifespan by alleviating its repressive effects on mitochondrial function

city: Boston

first: Vyacheslav

last: Labunskyy

state: MA

address: 609 Albany St

department: Department of Dermatology

institute: Boston University School of Medicine

summary: Iron dyshomeostasis contributes to aging, but little information is available about the molecular mechanisms. Here, we provide evidence that, in Saccharomyces cerevisiae, aging is associated with altered expression of genes involved in iron homeostasis. We further demonstrate that defects in the conserved mRNA-binding protein Cth2, which controls stability and translation of mRNAs encoding iron-containing proteins, increase lifespan by alleviating its repressive effects on mitochondrial function. Mutation of the conserved cysteine residue in Cth2 that inhibits its RNA-binding activity is sufficient to confer longevity, whereas Cth2 gain-of-function shortens replicative lifespan. Consistent with its function in RNA degradation, we demonstrate that Cth2 deficiency relieves Cth2-mediated post-transcriptional repression of nuclear-encoded components of the electron transport chain. Our findings uncover a major role of the RNA-binding protein Cth2 in the regulation of lifespan and suggest that modulation of iron starvation signaling can serve as a target for potential aging interventions.

overall_design: RNA-Seq and Ribo-Seq analyses of replicatively aged (OLD) and young (YNG) wild-type and cth2 knockout strains

first: Praveen

last: Patnaik

first: Carine

last: Beaupere

first: Hanna

last: Barlit


title: Genome-wide profiling of the DNA methylome in the peripheral blood of MDD patients

summary: Genome wide DNA methylation profiling in the whole blood samples of healthy controls and major depression disorder (MDD) patients who have never been treated with depression medication. The Illumina Infinium 450k Human DNA methylation Beadchip can assay over 480K CpG sites with bisulfite-converted genomic DNA and has been widely used in methylome-wide association studies (MWAS). Samples included 40 healthy controls and 40 MDD patients who have never been treated with depression medication.

overall_design: Bisulphite converted DNA from the 80 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip v1.0

first: Zeyue


title: Chr21 protein-protein interactions: enrichment in proteins involved in intellectual disability, autism and late-onset Alzheimer’s disease

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

summary: Down syndrome (DS) is caused by human chromosome 21 (HSA21) trisomy. It is characterized by a poorly understood intellectual disability (ID). We studied two mouse models of DS, one with an extra copy of the Dyrk1A gene (189N3) and the other with an extra copy of the mouse Chr16 syntenic region (Dp(16)1Yey). RNA-seq analysis of the transcripts deregulated in the embryonic hippocampus revealed an enrichment in genes associated with chromatin for the 189N3 model and synapses for the Dp(16)1Yey model

overall_design: We investigated the respective contributions of Dyrk1a and other HSA21 gene products to the pathways underlying ID in DS, using embryonic hippocampus (E16-E18).

first: Michel

last: Simonneau

first: Julia

last: Viard


title: Proximal sciatic nerve stumps exhibit sexually dimorphic transcriptome changes  in mice after peripheral nerve injury (axotomy)

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: Transcriptional changes are distinct in female and male mice in the time course of peripheral nerve injury response. Here, we present sexually dimorphic transcriptome profiles established in the space of 24 h period after sciatic nerve axotomy.

overall_design: Compare transcriptomes of female and male mice after sciatic nerve axotomy to identify sexually dimorphic molecular signatures, upstream regulators and signaling pathways.

first: Veronica

last: Shubayev


title: Inhibition of TWEAK/Tnfrsf12a axis protects against acute liver failure by suppressing RIPK1-dependent apoptosis

city: Shanghai

first: Zhijie

last: Li

state: Other

address: Haike Road 230

institute: ShanghaiTech University

summary: To explore the potential molecular basis of acute liver failure and identify new therapeutic targets, we performed a transcriptome sequencing analysis of liver samples from acute liver failure mice induced by APAP or TAA toxicity and PBS-treated controls.

overall_design: Liver tissues were harvested 24 hours after PBS, APAP or TAA administration for analysis. RNA was extracted using Trizol reagent.The transcriptome sequencing was performed using the high throughput sequencing platform of Illumina HiSeq, n=2 for each group.

first: Heming

first: Junjin

last: Zhu

first: Pengyu

last: Huang


title: Prenatal diagnosis of genetic aberrations in fetuses with pulmonary stenosis using ultrasound in Southern China

status: Public on Jul 16 2022

city: Fuzhou

first: Hailong

state: Fujian

address: No.18 Daoshan Road, Gulou District

institute: Fujian Maternity and Child Health Hospital

summary: Although pulmonary stenosis (PS) is relatively common, the genetic etiology of congenital PS in fetuses is poorly studied. We used karyotype analysis and chromosomal microarray analysis (CMA) to investigate the genetic aberrations associated with PS in fetuses.

overall_design: Fetal amniotic fluid and umbilical cord blood samples were extracted for chromosomal karyotype analysis and CMA.

first: Meiying

last: Cai


title: Temporal changes in the transcriptome (RNA-seq) and genome-wide chromatin accessibility (ATAC-seq) after Sinorhizobium meliloti LCO treatment, in Medicago truncatula roots

city: Gainesville

first: Daniel

last: Conde

state: FL

address: 2033 Mowry road

institute: University of Florida

summary: The extend of chromatin accessibility changes and its consequent impact on the transcriptional control of rhizobial infection, colonization, and nodule development, remain unknown. This understanding requires that the dynamic behavior of gene expression and chromatin accessibility be quantified. Thus, we uncovered the gene regulatory network in response to LCOs in M. truncatula roots by quantifying temporal changes in the transcriptome (RNA-seq) and genome-wide chromatin accessibility (ATAC-seq) after Sinorhizobium meliloti LCO treatment.

overall_design: Seeds of M. truncatula wild-type reference accession Jemalong A17 were sterilized and germinated in 1% agar plates, including 1µM GA3. Plates were stored at 4°C for three days in the dark and placed at room temperature overnight for germination. Seedlings were grown vertically for five days on a modified Fahraeus medium with no nitrogen, in a growth chamber (24°C, 16 h light/8h dark cycle, 70 µmol m-2 s-1 photosynthetic photon flux). LCOs were purified from Sinorhizobium meliloti strain 2011. Next, seedling roots were immersed in a solution of purified LCOs (10-8 M) or 0.005% ethanol (control) for 1 h. Roots were cut and immediately used for nuclei extraction and generation of ATAC-seq libraries, or snap-frozen in liquid nitrogen for posterior RNA isolation and sequencing. Roots were collected at 0 h (control), 15 min, 30 min, 1 h, 2 h, 4 h, 8 h after LCOs treatment. Roots from seven plants were pooled for each of three biological replicates used in RNA sequencing, while roots from 15 plants were pooled for one replicate used in ATAC-seq, in each time point of the experiment.

first: Sara

last: Knaack

first: Kelly

last: Balmant

first: Thomas

last: Irving

first: Lucas

middle: G

last: Maia

first: Christopher

last: Dervinis

first: Henry

last: Schmidt

first: Jean-Michel

last: Ané

first: Sushmita

last: Roy

first: Matias

last: Kirst


title: Differential dependencies of human RNA polymerase II promoters on TBP, TAF1, TFIIB, and XPB.

status: Public on Jul 17 2022

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road, 260 EMRB

department: Biochemistry

institute: University of Iowa

summary: General transcription factors (GTFs) are required for RNA polymerase II (Pol II) to initiate transcription at promoters. In this study, we determined the effects of acute depletion of TBP, TAF1, TAF4, TFIIB, and XPB in HAP1 cells. We performed precision nuclear run-on sequencing (PRO-Seq) and quantified nascent transcripts arising from more than 70,000 promoters. The average dependencies for each factor across all promoters varied widely even though levels of depletions were similar. Many of the effects could be attributed to the presence or absence of core promoter elements. Depletion of TBP had a large effect on only a small fraction of Pol II and Pol III promoters. TFIIB depletion also led to readthrough transcription downstream of the 3′ ends of genes. We conclude that promoter activity is influenced by recruitment of TFIID, sequence-specific transcription factors, and interaction of the preinitiation complex (PIC) with the +1 nucleosome.

overall_design: Five HAP1 cell lines were developed in which the endogenous locus for TBP, TAF1, TAF4, TFIIB or XPB were tagged with FKBP12 as described in the methods. To assay the effects of depleting each of the GTFs on nascent transcription we performed PRO-Seq as described in the methods. Briefly, each of the cell lines were treated with either DMSO (control) or 400 nM dTAGV-1 for 2 h. Nuclei was then isolated and PRO-Seq libraries were prepared in duplicates (one experiment was performed for TAF4).

first: Juan

middle: F

last: Santana

first: Mrutyunjaya

last: Parida

first: Geoffrey

last: Collins

first: Donal

last: Luse


title: Longitudinal analysis of phenotype-transcriptome correlations in AAV-TGFb1- and Bleomycin-induced lung fibrosis

status: Public on Jul 15 2022

city: Biberach an der Riß

first: Holger

last: Klein

state: Rhineland Palatinate

address: Birkendorfer Str. 65

department: global Computational Biology and Digital Sciences

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co KG

type: Non-coding RNA profiling by high throughput sequencing

summary: We have previously established a novel mouse model of lung fibrosis based on Adeno-associated virus (AAV)-mediated pulmonary overexpression of TGFβ1. Here, we provide an in-depth characterization of phenotypic and transcriptomic changes (mRNA and miRNA) in a head-to-head comparison with Bleomycin-induced lung injury over a 4-week disease course. The analyses delineate the temporal state of model-specific and commonly altered pathways, thereby providing detailed insights into the processes underlying disease development. They further guide appropriate model selection as well as interventional study design. Overall, Bleomycin-induced fibrosis resembles a biphasic process of acute inflammation and subsequent transition into fibrosis (with partial resolution), whereas the TGFβ1-driven model is characterized by pronounced and persistent fibrosis with concomitant inflammation and an equally complex disease phenotype as observed upon Bleomycin instillation. Finally, based on an integrative approach combining lung function data, mRNA/miRNA profiles, their correlation and miRNA target predictions, we identify putative drug targets and miRNAs to be explored as therapeutic candidates for fibrotic diseases. Taken together, we provide a comprehensive analysis and rich data resource based on RNA-sequencing, along with a strategy for transcriptome-phenotype coupling. The results will be of value for TGFβ research, drug discovery and biomarker identification in progressive fibrosing interstitial lung diseases.

overall_design: mRNA-Seq of time course of two lung fibrosis inducing animal models

first: Benjamin

last: Strobel

first: German

last: Leparc

first: Birgit

middle: E

last: Stierstorfer

first: Florian

last: Gantner

first: Sebastian

last: Kreuz


title: Functional neuronal circuitry and oscillatory dynamics in human brain organoids

city: Santa Barbara

first: Stella

middle: M. K.

last: Glasauer

address: Biological Sciences II

department: Neuroscience Research Institute

institute: University of California Santa Barbara

summary: Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiology of neuronal circuits within organoids remains under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we captured spontaneous extracellular activity from brain organoids derived from human induced pluripotent stem cells. We inferred functional connectivity from spike timing, revealing a large number of weak connections within a skeleton of significantly fewer strong connections. A benzodiazepine increased the uniformity of firing patterns and decreased the relative fraction of weakly connected edges. Our analysis of the local field potential demonstrate that brain organoids contain neuronal assemblies of sufficient size and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug action, and the effects of external stimuli upon neuronal networks.

overall_design: Droplet-based single-cell RNA sequencing was performed on 7-month-old cerebral organoids

first: Tal

last: Sharf

first: Kenneth

last: Kosik


title: Expression data from 1. leucine deprivation and 2. ATF4 overexpression on HepG2 cells

city: Tokyo

first: Sihui

last: Ma

address: Yayoi 1-1-1

institute: The university of Tokyo

summary: The mechanistic target of rapamycin complex 1 (mTORC1) is involved in nutrient-induced signaling and is a master regulator of cell growth and metabolism. Amino acid-deficient conditions affect mTORC1 activity; however, its upstream regulators warrant further investigation. MicroRNAs are key regulators of nutrient-related responses; therefore, the present study aimed to assess the leucine starvation-induced microRNA profile and its impact on mTORC1 activity. Transcriptome analysis of human hepatocellular carcinoma cells (HepG2) under leucine deprivation revealed that hsa-miR-663a and hsa-miR-1469 were altered in a transcription factor 4-dependent manner. Overexpression of these microRNAs induced phosphorylation of the ribosomal protein S6 kinase beta-1, a mTORC1 downstream target. Furthermore, hsa-miR-663a downregulated proline-rich Akt1 substrate of 40 kDa (PRAS40), one of the mTORC1 components. In summary, this study provides new insights into the regulatory role of microRNAs in amino acid metabolism and demonstrate alterations in microRNA profile under leucine deprivation in human hepatocytes.

overall_design: Leucine deprivation and ATF4 overexpression treated HepG2 cells were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Junki

last: Yamamura

first: Huijuan

last: Jia

first: Hisanori

last: Kato


title: Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis [ChIP-seq MEFs]

city: Durham

first: Eda

last: Yildirim

state: NC

address: DUMC Box 3709

department: Cell Biology

institute: Duke University School of Medicine

summary: X chromosome inactivation (XCI) is a dosage compensation phenomenon that occurs in females. Initiation of XCI depends on Xist RNA, which triggers silencing of one of the two X chromosomes, except for XCI escape genes that continue to be biallelically expressed. In the soma XCI is stably maintained with continuous Xist expression. How Xist impacts XCI maintenance remains an open question. Here we conditionally deleted Xist in hematopoietic system of mice and report differentiation and cell cycle defects in female hematopoietic stem and progenitor cells (HPSCs). By utilizing female HSPCs and mouse embryonic fibroblasts, we find that X-linked genes show variable tolerance to Xist loss. Specifically, XCI escape genes exhibit preferential transcriptional upregulation, which associates with low H3K27me3 occupancy, and high chromatin accessibility that accommodates preexisting binding of transcription factors such as Yin Yang 1 (YY1) at the basal state. We conclude that Xist is necessary for gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis.

overall_design: H3K27me3, H3K27ac and YY1 ChIP-seq in mouse embryonic fibroblasts (MEFs).

first: Tianqi

last: Yang

first: Jianhong

last: Ou


title: Sham operated mouse sciatic nerve for studies of sexual dimorphism of peripheral nerve injury (PNI)

first: Andrei

last: Chernov

summary: Accumulating evidence suggests that transcriptional changes are distinct in females and males in the time course of peripheral nerve injury response. Here, we present sexually dimorphic transcriptome profiles established within 24 h period after sham operation.

overall_design: Compare transcriptomes of female and male mice after sciatic nerve sham operation to identify sexually dimorphic molecular signatures, upstream regulators and signaling pathways.

first: Veronica

last: Shubayev


title: Gene expression profiling of lignin biosynthetic mutants of Arabidopsis

city: West Lafayette

first: Clint

last: Chapple

address: 175 S. University St.

institute: Purdue University

summary:
Purpose: To investigate the global impact of lignin perturbation on transcription in plants, we analyzed transcriptomes from rapidly lignifying stem tissue in wild-type Arabidopsis and 13 selected mutants.
Methods: RNA-sequencing was conducted to profile the transcriptome in basal stem tissue of Arabidopsis plants. PolyA+ RNA libraries were constructed and paired-end sequencing was performed on Illumina NovaSeq 6000. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using HISAT2. Gene counts were analyzed using HTSeq-count program and differential gene expression using DESeq2.
Results: The whole dataset contains 20974 expressed genes and 5581 differentially expressed genes in at least one mutant (ANOVA, FDR < 0.05, Fold change ≥ 2 fold).

overall_design: Gene expression profiles of 8 biological replicates of wild type and 4 biological replicates of 13 mutants with perturbed lignification were generated from inflorescence stem tissue of 28-day-old Arabidopsis by RNA-sequencing.

first: Peng

last: Wang


title: TET proteins regulate T cell and iNKT cell lineage specification in a TET2 catalytic dependent manner [CATCH-SEQ]

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

summary: TET proteins mediate DNA demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) and other oxidative derivatives. We have previously demonstrated a dynamic enrichment of 5hmC during T and invariant natural killer T cell lineage specification. Here, we investigate shared signatures in gene expression of Tet2/3 DKO CD4 single positive (SP) and iNKT cells in the thymus. We discover that TET proteins exert a fundamental role in regulating the expression of the lineage specifying factor Th-POK, which is encoded by Zbtb7b. We demonstrate that TET proteins mediate DNA demethylation - surrounding a proximal enhancer, critical for the intensity of Th-POK expression. In addition, TET proteins drive the DNA demethylation of site A at the Zbtb7b locus to facilitate GATA3 binding. GATA3 induces Th-POK expression in CD4 SP cells. Finally, by introducing a novel mouse model that lacks TET3 and expresses full length, catalytically inactive TET2, we establish a causal link between TET2 catalytic activity and lineage specification of both conventional and unconventional T cells.

overall_design: We compared the methylation status across the Zbtb7b locus, that encodes for Th-POK,  in CD4 SP  cells isolated from  4  control (wt), 3  Tet2-/-Tet3flx/flxCD4 cre (DKO) mice and 1 Tet2CDTet3flx/flxCD4 cre (TET2CDTET3KO) mouse by using CATCHseq

first: Ageliki

last: Tsagaratou


title: Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis [ChIP-seq Lin-]

overall_design: Bone marrow lineage negative (Lin-) cells in wild type (WT) and Xist knockout (XistΔ/Δ) female mice were utilized to determine genome-wide occupancy of H3K27me3, H3K4me3 and YY1 by ChIP-Seq.


title: Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis [RNA-seq]

overall_design: Bone marrow Lin- (lineage negative), LSK+ (Lin- SCA-1+ c-KIT+)  and LSK- (Lin- SCA-1- c-KIT+) cells in wild type (WT) and Xist knockout (XistΔ/Δ) female mice were sorted by FACS and utiliized for gene expression profiling by RNA-Seq.


title: Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis [ATAC-seq]

overall_design: Bone marrow LSK+ (Lin- SCA-1+ c-KIT+) or LSK- (Lin- SCA-1- c-KIT+) cells in wild type (WT) and Xist knockout (XistΔ/Δ) female mice were sorted by FACS . Approximately 10,000 cells were utilized per sample for chromatin accessibility profiling by ATAC-seq.


title: Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis

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

overall_design: Refer to individual Series


title: Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis [RNA-seq MEFs]

overall_design: RNA-seq of mouse embryonic fibroblasts (MEFs)


title: Single cell RNA sequencing profile of progeny of a unique mesenchymal progenitor subset traced to adult mouse skeletal muscle

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

institute: University of British Columbia

summary: During mouse embryonic development, as the limb bud expands, several populations of cells are thought to migrate into the emerging limb and contribute to various specialized structures therein. A unique subset has been identified among the migrating populations that contributes to enduring stromal compartments in various tissues. Using a lineage tracing tool, this population was sampled from limb muscle after post-natal development was complete and gene expression was profiled at the single cell level to determine the fate and function of this cell subtype and the genetic programs involved.

overall_design: Single cell RNA-seq analyes of mesenchymal progenitors labelled in the developing murine embryo and traced through post natal development.

first: M

last: Arostegui

first: R

middle: W

last: Scott

first: T


title: Identification of RNA Markers in Red Blood Cells for Doping Control in Autologous Blood Transfusion

status: Public on Jul 14 2022

city: Tsukuba

first: takehito

last: sugasawa

state: Select State

address: Ibaraki

institute: University of tsukuba

summary:
We conducted an animal experiment and used total RNA sequencing (RNA-Seq) to identify novel RNA markers to detect autologous blood transfusion (ABT) doping within red blood cells (RBCs) as a pilot study before human trials.
The total RNA-Seq and bioinformatics were performed using rat RBCs that were stored 10- and 20-day periods with citrate–phosphate–dextrose solution with adenine (CPDA) at 4°C
In the results, we identified three significant genes whose expression levels were drastically decreased according to the storage period.
Our novel insights may allow future studies to develop a test method for ABT doping.

overall_design: RNAs of RBCs purified form the whole bloods were analyzed using total RNA-Seq, at each storage period.

first: Takehito

last: Sugasawa


title: Unraveling human T cell development using scRNA-seq

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

summary: T cells develop in the thymus from multipotent lymphoid precursors. During this gradual differentiation process thymocytes go through several decision points, before they fully mature into conventional and unconventional T cells. The underlying molecular mechanisms have been investigated in mice, but several details remain unclear in the human context. To be able to study the drivers of thymocyte differentiation in human, we have generated several 3' scRNA-seq libraries from enriched thymocyte populations.

overall_design: Single cell transcriptional libraries were generated from human CD34+, DP, ISP and gdTCR+ thymocytes obtained from a 4 month old donor using the 10X Genomics Chromium 3’ sequencing V3.1 kit.

first: Lena

last: Boehme

first: Marieke

last: Lavaert


title: Single cell ATAC sequencing profile of a unique mesenchymal progenitor subset from the developing murine forelimb

summary: During mouse embryonic development, the limbs emanate from primordial buds of lateral plate mesoderm as proliferating mesenchymal cells cause protrusions of the overlying ectoderm. As the bud expands, several populations of cells are thought to migrate into the emerging limb and contribute to various specialized structures therein. A unique subset has been identified among the migrating populations that contributes to enduring stromal compartments in various tissues and is responsible for aspects of secondary morphogenesis including the formation of entheses throughout the limb. Using a lineage tracing tool, this population was sampled at various stages along the developmental continuum and chromatin accessibility was profiled at the single cell level to determine the fate and function of this cell subtype and the epigenetic programs involved.

overall_design: Single cell ATAC-seq analyes of mesenchymal progenitors from the developing murine forelimb.


title: Elucidating cellular states of CD8+ T cells regulating anti-tumor response using multi-omic single cell sequencing

city: Princeton

first: Namit

last: Kumar

state: NJ

address: 3551 lawrenceville

department: Informatics & Predictive Sciences

institute: Bristol-Myers Squibb

summary: Immune checkpoint blockade (ICB) has led to durable clinical responses in multiple cancer types; however, biomarkers that identify which patients are most likely to respond to ICB are not well defined.  Many putative biomarkers developed from a small number of samples often fail to maintain their predictive status in larger validation cohorts.  We show across multiple human malignancies and syngeneic murine tumor models that neither pre-treatment T cell receptor (TCR) clonality nor changes in clonality after ICB correlate with response.  Dissection of tumor infiltrating lymphocytes pre- and post-ICB by paired single-cell RNA sequencing and single-cell TCR sequencing reveals conserved and distinct transcriptomic features in expanded TCR clonotypes between anti-PD1 responder and non-responder murine tumor models. Overall, our results indicate a productive anti-tumor response is agnostic of TCR clonal expansion. Further, we used single-cell transcriptomics to develop a CD8+ T cell specific gene signature for a productive anti-tumor response and show the response signature to be associated with clinical outcomes to nivolumab monotherapy in CheckMate-067, a phase 3 clinical trial in metastatic melanoma.  These results highlight the value of leveraging single-cell assays to dissect heterogeneous tumors and T cell subsets and define cell-type specific transcriptomic biomarkers of ICB response.

overall_design: Single cell transcriptomes were assessed in FACS sorted CD45+ immune cells, isolated from dissociated murine MC38 or CT26 tumors.  Each tumor type contained 4 treatment groups and each treatment group consisted of biological triplicates.  The four treatment groups were: Group #1) Early timepoint untreated mice (Day 6 in MC38, Day 10 in CT26), Group #2) Late timepoint untreated mice (Day 13 in MC38, Day 17 in CT26), Group #3) Mice treated with 10mg/kg isotype control antibody on Days 6 and 10 in MC38, and Days 10 and 14 in MC38 harvested at the same timepoint as group #2, Group #4)mice treated with 10 mg/kg anti-PD1 antibody on the same schedule as the isotype treatment in group #3 and harvested at the same timepoint as group #2.

first: Joseph

middle: L

last: Benci


title: Evaluation of TET1 non-catalytic functions reveals DNA demethylation independent gene and ERV regulation

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Surveillance of DNA methylation is critical for genome stability and epigenetic regulation in mammals. The discovery of the ten-eleven translocation (TET) proteins catalyzing the oxidation from 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) revolutionized the understanding of DNA methylation maintenance and remodeling. Interestingly in recent years evidence accumulated that TET1 also harbours non-catalytic functions. However, the role and mechanism of TET1 DNA demethylation independent functions still remain poorly understood. Here, we use genome engineering, mass spectrometry and quantitative multi-omics approaches to dissect the non-catalytic role of TET1. Strikingly, we find that the majority of transcriptional regulation depends on non-catalytic functions of TET1. Our study identifies TET1 as a scaffold protein and a global regulator of histone modifications. Moreover, we show that the establishment of H3K9me3 and H4K20me3 at ERV1, ERVK and ERVL is mediated by TET1 independent of DNA demethylation. Finally, we provide evidence that repression of endogenous retroviruses depends on the interaction between TET1 and SIN3A. In summary, we found that the non-catalytic functions of TET1 are critical for regulation of gene expression and the silencing of endogenous retroviruses in mESCs.

overall_design: ChIP-seq profiling of WT J1, Tet1 KO (clone H9) and Tet1 CM (clone D7) mESC lines.

first: Angelo

last: Salazar Mantero

first: Paul

last: Stolz

first: Yuying

last: Cheng

first: Carmen

last: Navarro

first: Sebastian

last: Bultmann


title: Circular RNA, long non-coding RNA and mRNA transcriptomic profiles in a rat lumbosacral spinal roots avulsion model

city: shanghai

first: zhibin

last: zhou

address: 415 Fengyang Road

department: orthopedics

institute: changzheng hospital

summary: To better understand the underlying pathogenic mechanisms and which circRNA/lncRNA/mRNA are involved in lumbosacral spinal roots avulsion (LSRA), we performed circRNA, lncRNA and mRNA expression profiling by high-throughput sequencing in a rat LSRA model

overall_design: CircRNA, LncRNA and mRNAs profiles of rat spinal cord inlumbosacral spinal roots avulsion were generated by high-throughput sequencing

first: Zhibin

last: Zhou

first: Lei

last: Zhu


title: Epigenetic consequences of DMSO treatment on the HepaRG cell line

city: Saarbrücken

first: Kathrin

last: Kattler-Lackes

state: non-US Resident

address: Campus A2.4 Raum 0.13

department: Epigenetics

institute: Saarland University

summary: DMSO treatment of HepaRG cells during differentiation

overall_design: The study contains ChIP-seq data in 2 replicates for H3K4me1, H3K4me3 and H3K27ac for HepaRG cells differentiated for 30 days with or without the presence of DMSO

last: Kattler


title: Transcriptome analysis of the hippocampus in late postnatal mice after repeated ketamine anesthesia

city: Daejeon

first: Woosuk

last: Chung

address: 282, Munhwa-ro

department: Department of Medical Science

institute: Chungnam National University School of Medicine

summary: Numerous recent studies showed that early anesthesia during neurodevelopment may induce changes in specific behaviors. We further studied the effects of early anesthetic exposures regarding addiction behavior later in life. Postnatal day (PND) 16 C57BL/6 mice received ketamine anesthesia for 5 consecutive days. Addiction behavior was evaluated 1 week after anesthesia treatment. Neurological changes after repeated anesthesia were evaluated using high-performance liquid chromatography, RNA sequencing, electrophysiology studies.  Repeated ketamine anesthesia during the critical neurodevelopment period increased the expression of genes involved with action potential, and induced excitatory/inhibitory (E/I) imbalance in hippocampal CA1 pyramidal neurons of male mice. Such neurological changes were associated with increases in drug-induced contextual addiction memory.

overall_design: Transcriptome profile of the hippocampus in late postnatal mice after repeated ketamine anesthesia

first: Hyojin

last: Kang

first: Jianchen

last: Cui

first: Xianshu

last: Ju


title: The soluble CD83 protein prevents bone destruction by inhibiting the formation of osteoclasts and inducting resolution of inflammation

status: Public on Jul 13 2022

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hanover Medical School

summary: Here we show that soluble CD83 induces resolution of inflammation in the antigen-induced arthritis (AIA) model. Joint swelling as well as arthritis related expression levels of IL‐1β, IL‐6, RANKL, MMP9 and OC‐Stamp were strongly reduced, while Foxp3 was induced. In addition, we observed a significant inhibition of TRAP+ osteoclast formation, correlating with the reduced arthritic disease score. In contrast, cell specific deletion of CD83 in human and murine precursor cells resulted in an enhanced formation of mature osteoclasts. RNA-sequencing analyses, comparing sCD83- with mock treated cells, revealed a strong downregulation of osteoclastogenic factors, such as OC-STAMP, MMP9, NFATC1, Ctsk and Trap. Concomitantly, transcripts typical for pro-resolving macrophages, e.g. Mrc1/2, Marco, Klf4 and Mertk, were upregulated. Interestingly, also members of the metallothionein (MT) family, which have been associated with a reduced arthritic disease severity, were highly induced by sCD83 also in samples derived from RA patients. Finally, we elucidated the sCD83-induced signalling cascade, downstream to its binding to the Toll-like receptor 4/(TLR4/MD2) receptor complex, using CRISPR/Cas9-induced knockdowns of TLR4/MyD88/TRIF and MTs, revealing that sCD83 acts via the TRIF-signalling cascade. In conclusion, sCD83 represents a promising therapeutic approach to induce resolution of inflammation and to prevent bone erosion in autoimmune arthritis.

overall_design: RNA-seq analysis of osteoclasts derived from the blood of healthy donor- or RA patients (with each n=3) treated with 25 µg/ml sCD83 or the corresponding volume PBS for control

first: Dmytro

last: Royzman

first: Darja

last: Andreev


title: Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for precise termination of mtDNA replication

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

institute: University of Gothenburg

summary: The exact in vivo role for RNase H1 in mammalian mitochondria (mtDNA) has been much debated and we show here that it is essential for processing of RNA primers to provide site-specific initiation of mtDNA replication.  Without RNase H1, mtDNA replication is instead initiated at non-canonical sites and becomes impaired.  Furthermore, RNase H1 is also needed for replication completion and in its absence linear deleted mtDNA molecules extending between the two origins of mtDNA replication are formed.  Finally, we report the first patient with a homozygous pathogenic mutation in the hybrid-binding domain (HBD) of RNase H1 causing impaired mtDNA replication. In contrast to catalytically dead pathological variants of RNase H1, this mutant version has enhanced enzyme activity.  This finding shows that the RNase H1 activity must be strictly controlled to allow proper regulation of mtDNA replication.

overall_design: We used HydEn-seq to investigate the genome-wide distribution of ribonucleotides and 5' ends in hearts isolated from mice deficient in Rnase H1.

first: Jelena

last: Misic

first: Dusanka

last: Milenkovic

first: Ali

last: Al-Behadili

first: Xie

last: Xie

first: Min

last: Jiang

first: Shan

first: Roberta

last: Filograna

first: Camilla

last: Koolmeister

first: Stefan

last: Siira

first: Louise

last: Jenninger

first: Aleksandra

last: Filipovska

first: Anders

middle: R

first: Valerio

last: Carelli

first: Thomas

last: Nicholls

first: Anna

last: Wedell

first: Maria

last: Falkenberg

first: Nils-Göran

last: Larsson


title: Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer I

city: Houston

first: Chang-Jiun

last: Wu

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: University of Texas, MD Anderson Cancer Center

summary: We examined the pathways that are regulated by TDO2 in APC-deficient cancer cells by analyzing gene expression profiles of APC-WT and APC-KO MC38 cells that are transduced with inducible shTDO2 constructs. This study establishs that the TDO2-Kyn-AhR axis serves a critical role in promoting APC-deficient tumor growth via cancer cell autonomous (metabolism and proliferation) and non-autonomous mechanisms (tumor immunity).

overall_design: Transcriptomic analysis of APC-intact and APC-deleted MC38 cell lines after inducible knockdown of TDO2.

first: Rumi

last: Lee

first: Jiexi

last: Li

first: Ronald

last: DePinho


title: Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer II

summary: Comparative transcriptomic analysis of TAMs isolated from APC-WT and APC-KO MC38 orthotopic tumors express higher levels of multiple classical M2-like markers (CD163, CCL22, YM1) compared to APC-WT tumors after re-normalized the read counts of multiple M2 macrophage markers with housekeeping gene read counts (GAPDH and ACTB).

overall_design: Transcriptomic analysis of macrophages isolated from APC-WT and APC-KO MC38 orthotopic tumors.


title: RNA seq analysis on immune cells isolated from nGD mice brain

city: New Haven

first: Pramod

last: Mistry

address: 300 Cedar St

institute: Yale University

summary: We observed significant changes in gene expression between Wt and nGD brain. nGD brains are highly enriched for immune infiltrates, both microglia and immune infiltrates are activated in nGD brains. Through scRNA seq we identified that, microglia specific Gba deletion lead to higher activation and expression of DAM signature genes compared to control mice.

overall_design: The aim of the study is to identify immune microenvironment of of GD associated neuronopathy using single cell RNAseq technology. We developed mouse models that lack Gba gene in individual cell types with in the brain and evaluated gene expression changes using 10X scRNA seq.

first: Venkata

last: Boddupalli

first: Sameet

last: Mehta


title: RNA and scRNA seq analyses on immune cells isolated from nGD mice brain


title: Epithelial-mesenchymal plasticity determines estrogen receptor positive breast cancer dormancy and epithelial reconversion drives recurrence

city: Lausanne

first: Fabio

last: De Martino

address: EPFL SV ISREC UPBRI Station 19

country: Switzerland

institute: EPFL

summary: Estrogen receptor α-positive (ER+) breast cancers (BCs) represent more than 70% of all breast cancers and pose a particular clinical challenge because they recur up to decades after initial diagnosis and treatment. The mechanisms governing tumor cell dormancy and latent disease remain elusive due to a lack of adequate models. Here, we compare tumor progression of ER+ and triple-negative (TN) BC subtypes with a clinically relevant mouse intraductal  xenografting approach (MIND). Both ER+ and TN BC cells disseminate already during the in situ stage. However, TN disseminated tumor cells (DTCs) proliferate at the same rate as cells at the primary site and give rise to macro-metastases. ER+ DTCs have low proliferative indices, form only micro-metastases and lose epithelial characteristics. Single cell RNA sequencing reveals that dormant DTCs harbor different Epithelial-Mesenchymal Plasticity (EMP)-states, reflective of their heterogeneous and plastic nature. Dormant DTCs are in a mesenchymal-like state, with decreased CDH1 and increased ZEB2 and VIM expression levels, as well as matrisome-related genes, like FN1, ELN, COL3A1, and others. On the other hand, proliferative DTCs are epithelial-like, and express CDH1, EPCAM, KRT18, and ESR1. EMP is very rare in primary tumour cells and is not required for invasion or metastasis. In vivo, forced transition to the epithelial state through ectopic E-cadherin expression overcomes dormancy with increased growth of lung metastases. We conclude that EMP is essential for the generation of a dormant cell state and the development of latent disease. Targeting exit from EMP is of therapeutic potential.

overall_design: MCF7:RFP-Luc cells were injected in the ductal tree of NSG female mice. 6 months after intraductal injection, 2 mice were sacrificed; mammary glands and lungs were then collected and digested into single cells, which were subsequently FACS-sorted based on RFP.

first: Patrick

last: Aouad


title: EZH2 T367 phosphorylation activates p38 signaling through lysine methylation to promote breast cancer progression [RNA-seq]

status: Public on Jul 12 2022

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: To investigate the gene expression deregulation in Breast Cancer Tumors treated with P38i, EZH2i, the combination and controls.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 3 replicas of   BreastTumors treated with P38i, EZH2i, the combination and controls

last: Gonzalez

first: Shilpa

last: Tekula

first: Celina

last: Kleer


title: High-resolution mapping of transcribing RNAPIII by CRAC upon mutation of Sen1 in the G1 phase of the cell cycle [Experiment 3]

city: Paris

first: Odil

last: Porrua Fuerte

address: 15 rue Helene Brion

institute: Institut Jacques Monod-CNRS

summary: Here we report high-resolution analyses of transcribing RNAPIII in either a wild-type (WT) background or a sen1-3 mutant  in the G1 phase of the cell cycle. The mutations in Sen1-3 prevent the interaction of Sen1 with both RNAPIII and the replisome, raising the question whether the role of Sen1 in RNAPIII transcription termination could depend on the association of Sen1 with the replisome. Our data show that in the G1 phase of the cell cycle, where the replisome is not assembled, the sen1-3 mutant also exhibits transcription termination defects at RNAPIII-dependent genes, as in asynchronous cells. This result indicates that the role of Sen1 in termination at RNAPIII-dependent genes is independent on the association of Sen1 with the replisome.

overall_design: Analysis of the effect of the sen1-3 mutation on RNAPIII-dependent transcription in G1 by CRAC

last: Porrua


title: Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer

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

overall_design: Refer to individual Series


title: Intrinsic and extrinsic mechanisms cooperate to ensure efficient termination of RNAPIII transcription.


title: EZH2 T367 phosphorylation activates p38 signaling through lysine methylation to promote breast cancer progression


title: High-resolution mapping of transcribing RNAPIII by CRAC upon mutation or depletion of Sen1 [Experiment 1]

summary: Here we report high-resolution analyses of transcribing RNAPIII in either a wild-type (WT) background , a sen1-3 mutant or a Sen1 auxin-inducible degron (AID) strain in which Sen1 can be rapidly depleted upon addition of the auxin analogue Indole-3-acetic acid (IAA). Sen1 is a well-characterized transcription termination factor for RNAPII-dependent genes in budding yeast. Here we show that the presence of three point mutations in sen1-3 that abrogate the interaction of Sen1 with RNAPIII, as well as the depletion of Sen1 provoke global transcription termination defects at RNAPIII-dependent genes. These results indicate that Sen1 is also a transcription termination factor for RNAPIII transcription units.

overall_design: Analysis of the effect of the mutation or the depletion of Sen1 on RNAPIII-dependent transcription genome-wide using CRAC


title: scRNA seq analysis on immune cells isolated from nGD mice brain


title: Endothelial cell death after ionizing radiation does not impair vascular structure

city: Ljubljana

first: Bostjan

last: Markelc

email: bmarkelc@gmail.com, bmarkelc@onko-i.si

state: Ljubljana

address: Zaloska cesta 2

department: Department of Experimental Oncology

country: Slovenia

institute: Institute of Oncology Ljubljana

summary: The effect of radiation therapy on tumor vasculature has long been a subject of debate. Increased oxygenation and perfusion have been documented during radiation treatments. Conversely, apoptosis of irradiated tumor endothelial cells has been proposed as a major determinant of tumor control. To approach these contradictions, we used multiphoton microscopy in two murine tumor models: MC38, a highly vascularized and B16F10, a moderately vascularized model, grown in transgenic mice with tdTomato labelled endothelium. These tumors received either a single dose of radiation (15 Gy) or a fractionated dose (5x3 Gy). Unexpectedly, even these high doses led to little structural change of the perfused vasculature. However, non-perfused vessels and blind ends were substantially impaired after radiation accompanied by apoptosis of their endothelium. Additionally, proliferation of endothelium was blocked. Further, RNAseq confirmed the modification of gene expression in apoptotic and cell cycle regulation pathways. Therefore, we show that apoptosis of tumor endothelial cells after radiation does not impair vascular structure.

overall_design: Bulk and single cell RNA seq are performed on mouse tumor EC without irradiation as control and 48h after irradiation as treatment group.

first: Jakob

last: Kaeppler

first: Jianzhou

last: Chen

first: Mario

last: Buono

first: Jenny

last: Vermeer

first: Pavitra

last: Kannan

first: Wei-Chen

last: Cheng

first: Dimitrios

last: Voukantsis

first: James

last: Thompson

first: Mark

last: Hill

first: Danny

last: Allen

first: Ana

last: Gomes

first: Veerle

last: Kersemans

first: Paul

last: Kinchesh

first: Sean

last: Smart

first: Francesca

last: Buffa

first: Claus

last: Nerlov

first: Ruth

last: Muschel


title: Identification of recurrent chromosome breaks underlying structural rearrangements in mammary cancer cell lines

city: Syracuse

first: Wenyi

last: Feng

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University