title: Microenvironment commits breast tumor ECs to dedifferentiation by micro-RNA-200-b-3p regulation and extracellular matrix remodelling (miRNA-Seq)

city: Warsaw

first: Klaudia

last: Brodaczewska

address: Szaserow 128

institute: Military Institute of Medicine

summary: Hypoxia  shapes the tumor microenvironment and modulates distinct cell populations  activity. Low pO2 activates pathological angiogenesis in cancer-  process in which endothelial cells  (ECs)  are the most important players. The main goal of the study was to evidence  the hypoxic  tumor  microenvironment influence on the global gene expression pattern characteristic for ECs and evidence  the  distinct  and  specific  responses  displayed  by  the  tumor-derived  ECs  compared  to  the  healthy  endothelium during the endothelial to mesenchymal transition  (EndMT)  and its regulation by miR-200-b-3p. Immortalized lines of ECs from the same patient with diagnosed breast cancer- healthy  breast  tissue  (HBH.MEC)  and  primary  tumor  (HBCa.MEC)  were  used.  The  experiments  were  performed in normoxia and hypoxia for 48 hours. By wound healing test,  we investigated the migration  abilities of ECs. Using the established model, global gene expression analysis with NGS was carried  out to detect new pathways altered in pathological ECs and to find the most changed miRNAs. The  validation of NGS data from RNA and miRNA was estimated by qPCRs.  Hypoxia influences ECs migration properties  in  wound healing assay. In hypoxia, healthy  ECs migrate slower than in normoxia, as opposed to HBCa.MEC  where no decreased migration ability  was induced by hypoxia, due to  EndMT  features. NGS data identified this process to be altered in  cancer ECs through extracellular matrix (ECM) organization. The deregulated genes, confirmed by  qPCR,  included:  SPP1,  ITGB6,  COL4A4,  ADAMST2,  LAMA1,  GAS6,  AGTR2,  PECAM1,  ELN,  FBLN2, COL6A3, COL9A3. NGS also identified collagens, laminin, fibronectin and integrin, as being  deregulated in tumor-derived ECs. Moreover,  the  analysis of ten most intensively modified miRNAs  when  breast tumor-derived ECs were compared to healthy ECs, put a light on miR-200b-3p which is  strongly up-regulated in HBCa.MECs as compared to HBH.MECs.   Microenvironment influences on ECs dedifferentiation by miR-200-b-3p and ECM.  The  pathological ECs  differed significantly, both phenotypically and  functionally, from the normal corresponding tissue, thus influencing their microenvironment cross- talk. The gene expression profile confirms the EndMT phenotype of tumor-derived ECs and migratory  properties  acquisition.  Moreover,  it  indicates  the  role  of  miR-200b-3p,  regulating  EndMT  in  pathological ECs, silencing several angiogenic growth factors and their receptors by directly targeting  their mRNA transcripts.

overall_design: small RNA-Seq for healthy breast tissue endothelial (2 replicates),breast cancer endothelial (2 replicates) cells

first: Kinga

last: Wilkus

first: Aleksandra

last: Majewska

first: Claudine

last: Kieda


title: YY1 complex in tumor-associated macrophage promotes prostate cancer progression by upregulating IL-6 [RNA-seq]

status: Public on Apr 01 2023

city: Nanjing

first: Bin

last: Xu

address: Dingjiaqiao 87

country: China

institute: Southeast University

type: Expression profiling by high throughput sequencing

summary: Tumor-associated macrophages are mainly polarized into the M2 phenotype, which remodels the tumor microenvironment and promotes tumor progression by secreting various cytokines. Herein, we reported that Yin Yang 1 (YY1) was highly expressed on tumor-infiltrated M2 macrophages in prostate cancer and was associated with poorer clinical outcomes. Using transgenic mice overexpressing YY1, we found that the tumor-promoting effects of oe-YY1 mice could be suppressed by macrophage depletion. Further in-vitro and in-vivo experiments using YY1 overexpressing and knocked down M2 macrophages demonstrated that YY1 induced M2 polarization and increased macrophages-induced prostate cancer progression by the IL-6/STAT3 pathway. Furthermore, YY1 promoted phase-separated condensates and upregulated IL-6 by modulating p300, p300 and CEBPB as a transcription complex. By conducting chromatin immunoprecipitation sequencing of M2 macrophages and monocytes, an M2-specific IL-6 enhancer associated with the YY1 complex was shown to upregulate IL-6 expression in M2 macrophages, and H3K27ac and YY1 signals significantly increased around this enhancer. In conclusion, YY1 complex promotes the M2 macrophages polarization and upregulates IL-6 in macrophages by inducing phase separation and a M2-specific enhancer, thereby increasing prostate cancer progression. These findings might lead to novel therapies targeting YY1 in prostate tumor-associated macrophages.

overall_design:
We  performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.
Comparative gene expression profiling analysis of RNA-seq data for oe/nc-YY1 M2 macrophages CM cocultured LNCaP cells

first: Wenchao

last: Li

first: Ming

last: Chen

first: Yue

last: Hou


title: YY1 complex in tumor-associated macrophage promotes prostate cancer progression by upregulating IL-6

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Exploring differentially expressed genes of staphylococcus aureus exposed to human tonsillar cells using RNA sequencing

status: Public on Mar 30 2023

city: Tromsø

first: Anne

middle: Merethe

last: Hanssen

address: Hansine Hansens veg 18

department: Medical Biology

country: Norway

institute: University of Tromsø

summary: Nasal colonization is well described; however, we have limited knowledge about S. aureus throat colonization. The main objective of this project was to explore differentially expressed genes (DEGs) in S. aureus throat isolate TR145 exposed for 1 or 3 hours (h) to human tonsil epithelial cells (HTEpiC) by using RNA sequencing (RNA-seq) and pathway analysis. We have shown the suitability of using HTEpiC as an in vitro model for investigating key determinants in S. aureus during co-incubation with the HTEpiC cells. Among the DEGs were genes encoding proteins involved in adhesion and immune evasion, as well as iron acquisition and transport. As their expression is induced upon meeting with the HTEpiC, they might be explored further for future targets for intervention to prevent either colonization or infection in the throat region.

overall_design: In this study, a Staphylococcus aureus throat isolate was cultured with or without a tonsillar cell line prior to RNA sequencing to find differentially expressed genes (DEGs). Test samples were defined as S. aureus strains exposed to HTEpiC and control samples were defined as S. aureus without HTEpiC cells. Three independent experiments were run in triplicates. Total RNA extracted from three replicates of S. aureus TR145 grown in absence of HTEpiC cells collected at time point of 0h, 1h and 3h (bacteriaonly, control samples (C)) and three replicas of S. aureus TR145 after 1h and 3h exposure to HTEpiC cells (bacteriaVSHTEpiC, test samples (T)) were selected for RNA-seq library preparation

first: Srijana

last: Bastakoti

first: Clement

last: Ajayi

first: Kjersti

last: Julin

last: Merethe Hanssen

first: Mona

last: Johannessen


title: Doxorubicin Changes the Spatial Organization of the Genome around Active Promoters

status: Public on Mar 31 2023

city: Berlin

first: Maria

last: Valieva

address: Ihnestraße 63

country: Germany

institute: MPIMG

summary: To investigate the function of the doxorubicin treatment in differentiation expression of human genes, we performed gene expression profiling analysis using data obtained from RNA-seq of three different conditions: control (DMSO-treatment) and doxorubicin treatment (200 nM and 340 nM).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RPE1 cells treated with DMSO and doxorubicin.

middle: E

first: Stefan

last: Stefanov

first: Heathcliff

last: Dorado Garcia

first: Anton

middle: G

last: Henssen

last: Mundlos

first: Juanma

last: Vaquerizas

first: Lis

last: Ing-Simmons


summary: To investigate the function of the TOP2 inhibitors treatment in binding of chromatin architecture factors, we performed ChIP-seq. We used chromatin from RPE1 cells treated with four different conditions: control (DMSO-treatment), doxorubicin treatment (200 nM and 340 nM) and ICRF193 treatment (5uM).

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CTCF and RAD21.


summary: To investigate the function of TOP2 on chromatin structure of human cells, we performed Hi-C using chromatin obtained from RPE1 cells.

overall_design: Pairwise comparison of the Hi-C maps of four different conditions: 1) control (DMSO-treatment), 2) treated with ICRF193  in final concentration 5uM or treated with doxorubicin in final concentration 3) 200 nM and 4) 340 nM.


title: Single-cell RNA-Seq (scRNA-Seq) of mouse basal cell carcinoma (BCC) immune cells.

status: Public on Mar 29 2023

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

country: USA

institute: Stanford University

summary: We used scRNA-Seq to examine BCC immune cell heterogeneity.

overall_design: Mouse BCC tumors were dissociated, immune cell fractions isolated, and were processed for scRNA-Seq. For the Sample 1/ , the tumor was simply dissociated, FACS sorted for immune cells and processed for scRNA-Seq. For Sample 2/Mouse_BCC_CD45.2+ and Sample 3/Mouse_BCC_CD45.2-, transplanted tumor was dissociated, FACS sorted for immune cells and processed for scRNA-Seq.

first: Daniel

last: Haensel

first: Sadhana

last: Gaddam


title: Transcriptomes Analysis of LHX2-knockdown in KYSE30 and KYSE510 cells

status: Public on Apr 07 2023

city: Beijing

first: Xukun

last: Li

address: No.17 Panjiayuan Nanli, Chaoyang District

department: Department of Radiation Oncology

institute: NCC

summary:
Purpose: To fully realize the potential molecular mechanism that LHX2 promotes ESCC progression
Methods: Total RNA of LHX2-knockdown KYSE30/KYSE510  and control cells was extracted with TRIzol Reagent. RNA libraries were constructed using an Illumina TruSeq RNA Sample Preparation kit according to the manufacturer’s protocol. A total of 150 base paired-end reads were sequenced using the Novaseq 6000 S4 platform.
Results: We identified 26008 transcripts in KYSE30 control and KYSE30 LHX2-knockdown cells ,and 25561 transcripts in KYSE510 control and KYSE510 LHX2-knockdown cells.
Conclusions: Our study represents the analysis of LHX2-knockdown ESCC cells, generated by RNA-seq.

overall_design: mRNA profiles of LHX2-knockdown in KYSE30 and KYSE510 cells

first: Xueling

last: Wu


title: Investigation of the direct activity of type I interferon on Ifnar1 KO ID8 ovarian cancer cells in vitro.

status: Public on Mar 28 2023

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

summary: This experiment is part of a larger study examining the anti-tumour properties of interferon epsilon in ovarian cancer. The goal of this experiment was to assess whether interferon signalling had been ablated in Ifnar1 CRISPR knockout (KO) ID8 cell lines, so that they could be used for in vivo models of ovarian cancer.

overall_design: Two Ifnar1 CRISPR KO ID8 cell line clones (1CF10 and 2CD7), as well as CRISPR empty vector (EV) and untransfected (WT) controls, were stimulated with 10,000 IU/ml recombinant mouse interferon (IFN) beta. Untreated (UT) cells were used as a reference sample for baseline gene expression. Three technical replicates were performed per cell line, treated on the same date.

first: Zoe

middle: R

last: Marks

first: Nicole

middle: K

last: Campbell

first: Linden

middle: J

first: Jodee

middle: A

last: Gould

first: Paul

last: Hertzog


title: YY1 complex in tumor-associated macrophage promotes prostate cancer progression by upregulating IL-6 [ChIP-seq]

first: Bin

last: Xu

summary: Tumor-associated macrophages are mainly polarized into the M2 phenotype, which remodels the tumor microenvironment and promotes tumor progression by secreting various cytokines. Herein, we reported that Yin Yang 1 (YY1) was highly expressed on tumor-infiltrated M2 macrophages in prostate cancer and was associated with poorer clinical outcomes. Using transgenic mice overexpressing YY1, we found that the tumor-promoting effects of oe-YY1 mice could be suppressed by macrophage depletion. Further in-vitro and in-vivo experiments using YY1 overexpressing and knocked down M2 macrophages demonstrated that YY1 induced M2 polarization and increased macrophages-induced prostate cancer progression by the IL-6/STAT3 pathway. Furthermore, YY1 promoted phase-separated condensates and upregulated IL-6 by modulating p300, NF-κB and CEBPB as a transcription complex. By conducting chromatin immunoprecipitation sequencing of M2 macrophages and monocytes, an M2-specific IL-6 enhancer associated with the YY1 complex was shown to upregulate IL-6 expression in M2 macrophages, and H3K27ac and YY1 signals significantly increased around this enhancer. In conclusion, YY1 complex promotes the M2 macrophages polarization and upregulates IL-6 in macrophages by inducing phase separation and a M2-specific enhancer, thereby increasing prostate cancer progression. These findings might lead to novel therapies targeting YY1 in prostate tumor-associated macrophages.

overall_design:
Chromatin immunoprecipitation sequencing comparing THP-1 and M2 cells
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for YY1 and H3K27ac in THP-1 and M2 cells.

first: Wenchao

first: Ming

last: Chen

first: Yue

last: Hou


title: Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche


title: RNAseq of tumor endothelial cells isolated from CT2A glioma under control or LGK974 treatment

city: Xi’an

first: Lei

last: Zhang

address: No. 620, West Chang'an Avenue

institute: Shaanxi Normal University

summary: The Wnt signaling pathway regulates blood-brain barrier (BBB) formation and function in both development and pathogenesis of diseases, and is essential for CNS angiogenesis and BBB formation in both embryonic and postnatal development. However, how Wnt signaling affects brain tumor endothelial cells is largely unknown. We isolated endothelial cells from tumors in control or LGK974 treated mice, and analyzed the role of Wnt signaling inhibition on tumor endothelial cells.

overall_design: We injected GFP-labeled CT2A glioma cells intracranially to C57BL/6 mice of 6 weeks old. 21 days after tumor induction, mice were administrated with saline or 2.5mg/kg LGK974 by oral gavage for 4 consecutive days. 25 days after tumor injection, tumor were dissected under a stereological microscope according to GFP expression. Magnetic-activated cell sorting (MACS) was used for isolating endothelial cells, based on expression of CD31 and CD45 (CD45-/CD31+), from tumors in control or LGK974 treated mice. Isolated endothelial cells were further prepared for RNAseq analysis.

first: Yuan

last: Xie

first: Fan

last: Yang


title: Investigation of the direct activity of interferon epsilon on ID8 ovarian cancer cells in vitro.

summary: This experiment is part of a larger study examining the anti-tumour properties of interferon epsilon in ovarian cancer. The objective of this experiment was to examine the direct activity of interferon epsilon on the mouse ovarian cancer cell line, ID8, and compare it to equivalent unit concentrations of interferon beta. The goal was to determine whether interferon epsilon and interferon beta induce different patterns of gene expression in ID8 cells.

overall_design: ID8 cells were stimulated with 10, 100, or 1000 IU/ml recombinant mouse interferon beta or interferon epsilon in vitro for three hours. Untreated (UT) ID8 cells were used as a reference sample for baseline gene expression. Three biological replicates were performed on separate dates, with three technical replicates for each treatment per n. Technical replicates were combined into a single sample for sequencing.


title: TRained Immunity induced by Bcg in UroThElial carcinoma (Tribute) associated epigenetic remodeling

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

institute: Murdoch Children's Research Institute

summary: Trained immunity is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, altering their responses to future exposures. Intravesical instillation with Bacillus Calmette-Guérin (BCG) is the most effective adjuvant therapy in patients with high-risk non-muscle invasive bladder cancer (HR-NMIBC). HR-NMIBC is associated with a high risk of tumor recurrence and progression to muscle-invasive bladder cancer. The precise immunological mechanisms through which BCG mediates anti-tumor immunity are still unclear. The aim of our study was to investigate the (long-term) induction of trained immunity by repeated BCG instillations in NMIBC patients and elucidate the immunological and epigenetic mechanisms that are involved. Another aim was to assess the relationship between trained immunity response and clinical response of NMIBC patients, in terms of recurrence free survival and progression free survival. To determine whether BCG instillations induce trained immunity in peripheral blood mononuclear cells (PBMCs) we performed a prospective cohort study (‘Tribute’) and isolated PBMCs collected before BCG therapy and at 8 time points during BCG therapy. A total of 17 BCG-naïve HR-NMIBC patients were included. After isolation of PBMCs, monocytes were further purified using an isolation procotol with a percoll gradient. RNA was isolated from these purified monocytes were and used as input for RNA-seq analysis.

overall_design: Blood was collected using venapuncture and PBMCs were isolated at three time points during the BCG induction cycle: pre-BCG1, BCG2 and BCG6; and two time points during each subsequent BCG maintenance cycle: pre-BCG7, BCG9, pre-BCG10, BCG12, pre-BCG13 and BCG15. For each donor one replicate for each time point was included. RNA from purified monocytes was isolated for the time points pre-BCG1, BCG6, and pre-BCG7 and the RNA-seq data was analysed. For some patients RNA-seq data for the pre-BCG10 time point was also available, but this time point was not included in the analysis because not every patient had data available for this time point. Comparisons for differentially expressed genes were made using the pre-BCG1 time point as a reference.

first: Jelmer

last: van Puffelen

first: Liesbeth

last: van Emst

first: Denise

last: Kooper

first: Tahlita

last: Zuiverloon

first: Ursula

last: Oldenhof

first: Alfred

last: Witjes

first: Tessel

last: Galesloot

first: Alina

last: Vrieling

first: Katja

last: Aben

first: Lambertus

last: Kiemeney

first: Egbert

last: Oosterwijk

first: Mihai

last: Netea

first: Joost

last: Boormans

first: Antoine

last: van der Heijden

first: Leo

last: Joosten

first: Sita

last: Vermeulen


title: Synergistic effect of CD47 blockade in combination with cordycepin treatment against cancer

city: Chang Zhou

first: Rongzhang

last: Chen

address: 185 Juqian Street

institute: Soochow University

summary: Cordycepin was widely considered as a direct tumor-suppressive drug, however, and as of now few studies have been presented to investigate the effect of cordycepin therapy to the tumor microenvironment (TME). In our study, we demonstrated that cordycepin would decrease the function of M1-like macrophage in TME, and also contribute to macrophage polarization (M2-macrophage). Herein, we tried to establish a combined therapeutic strategy of cordycepin and anti-CD47 antibody. Using single cell RNA sequencing, we improved that the combined treatment would significantly increase the effect of cordycepin, which would reactivate macrophages and reverse macrophage polarization. And then, the combined treatment would regulate the proportion of CD8+T cells to increase the PFS for digestive tract malignancy patients. Finally, Flow cytometry was used to validate the change of percentage for TAM and TIL. Our finding suggests the combined treatment of cordycepin and anti-CD47 mAb could significantly increase tumor suppression, which could increase M1-macrophage and decrease M2-macrophage. The PFS for digestive tract malignancy patients would be increased though regulation of CD8+T cells.

overall_design: In C57BL/6J mice, 1×10^6 MC38 cells were injected under the skin (s.c.) on the right flank. .Different treatment sub-groups were performed when the maximal diameter of the tumor became greater than 5mm. The tumor-bearing mice of cordycepin group were treated everyday by cordycepin (500 μg/mice, i.g.). In combination therapy (anti-CD47+cordycepin) group, the mice were treated by CD47 antibody (200 μg/mice, i.p.)  on Day0, Day4, Day8, Day12 during the treatment and cordycepin (500 μg/mice, i.g.) everyday. On day 8 after treatment, tumor were isolated, digested and isolated CD45+ cells. Libraries were constructed using 10x Genomics.

first: Chen

last: Feng

first: Jingting

last: Jiang


title: Transcriptome sequencing data sets for mice brain infected with Sindbis virus and treated with glucosylceramide synthase inhibitor

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

summary: The goal of this study is to determine the brain pathology upon infection of mice with neuroinvasine Sindbis virus (SVNI) and the affect of treatmant wuth the glucosylceramide inhibitor GZ-161 . For this purpose, C57BL/6 mice wasinfected with SVNI and treted or not with GZ-161. 5 days post infection, brains were harvested and total RNA was extracted. RNA-seq libraries were constructed and sequencing of 100bp paired-end was performed on the Illumina NovaSeq 6000 system. Sequencing yielded about 30M reads per sample that were mapped to the mouse genome

overall_design: The experiment includes four groups: Control (Naive, untreated), GZ-161 (Naïve, treated with GZ-161), SVNI (infected with SVNI, untreated), and SVNI+GZ-161 (infected with SVNI, treated with GZ-161).

first: Einat

middle: B

last: Vitner


title: Selection of endogenous control and identification of significant microRNA deregulations in cervical cancer

status: Public on Mar 25 2023

city: Hradec Králové

first: Tereza

last: Stverakova

address: Sokolská 581

department: Department of Clinical Biochemistry and Diagnostics

country: Czech Republic

institute: Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Czech Republic

type: Non-coding RNA profiling by high throughput sequencing

summary: Cervical cancer is a malignant disease that causes around 350 000 deaths annually. One of the essential things in enhancing the survival rates of cervical cancer is the availability of high-quality, sensitive, and specific diagnostic tests capturing the early stages of the disease. In this study, we analyzed the differential expression of microRNA in cervical cancer FFPE tissue samples. The comprehensive miRNA expression profile was detected using modern small-RNA sequencing technology, and the results were validated by real-time PCR. The relative expression of selected miRNAs was determined using the 2-ΔΔCt method. Moreover, two strategies for endogenous control selection were compared. miRNA profiling by small-RNA sequencing and a commercially supplied microfluidic card with 30recommended endogenous controls predesigned by the manufacturer. The RefFinder algorithm and coefficient of variation were used for endogenous control selection. A combination of miR-181a-5p and miR-423-3p was chosen as the most optimal normalizer. Statistically significant upregulation ofmiR-320a-3p, miR-7704, and downregulation of miR-26a-5p was detected, so we propose the combination as a new potential miRNA cervical cancer diagnostic panel. Using ROC curve analysis, the proposed panel showed 93.33% specificity and 96.97% sensitivity with AUC = 0.985. Inconclusion, our study suggests an optimal combination of two endogenous miRNAs for data normalization of miRNA expression studies in the cervical tissue (miR-181a-5p and miR-423-3p) and a novel diagnostic marker panel of three miRNAs (miR-320a-3p, miR-7704, miR-26a-5p) for cervical cancer.

overall_design: Two pools of extracted RNA from malignant and non-malignant samples were prepared for sequencing analysis. The RealSeq®-Biofluids, Plasma/Serum miRNA Library Kit for Illumina® sequencing (RealSeq Biosciences, Santa Cruz, CA, USA) was used for library preparation.

first: Ivana

last: Baranova

first: Petra

last: Mikyskova

first: Barbora

last: Gajdosova

first: Hana

last: Vosmikova

first: Jan

last: Laco

first: Vladimir

last: Palicka

first: Helena

last: Parova


title: Investigation of the anti-tumour properties of interferon epsilon in high grade serous ovarian cancer

first: Jamie

last: Gearing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Bulk ATAC-Seq of Trem2+ cells from mouse skin, mouse wound, and mouse basal cell carcinoma (BCC).

first: Anthony

last: Oro

summary: We used ATAC-Seq to exmaine the Trem2+ cells from different sources.

overall_design: Mouse skin, mouse wounds, and mouse BCC tumors were dissociated, the Trem2+ cells were FACS sorted and then processed for ATAC-Seq using the Omni-ATAC pipeline.

first: Daniel

last: Haensel

first: Sadhana

last: Gaddam


title: Single-cell ATAC-Seq (scATAC-Seq) of mouse basal cell carcinoma (BCC) immune cells.

summary: We used scATAC-Seq to examine BCC immune cell heterogeneity.

overall_design: Mouse BCC tumors were dissociated, immune cell fractions isolated, and were processed for scATAC-Seq. For both samples, the tumor was simply dissociated, FACS sorted for immune cells and processed for scATAC-Seq.


title: Cell plasticity in neuroblastoma

status: Public on Mar 27 2023

city: Paris

first: Agathe

last: Peltier

address: 26 rue d'Ulm

department: Centre de recherche

country: France

institute: Institut Curie

summary: Two cell identities, noradrenergic and mesenchymal, have been characterized in neuroblastoma cell lines according to their epigenetic landscapes relying on specific circuitries of transcription factors. Yet, their relationship and relative contribution in patient tumors remain poorly defined. Our results now document spontaneous plasticity in several neuroblastoma models between noradrenergic and mesenchymal tumor states and show that this plasticity is reversible and relies on epigenetic reprogramming. We demonstrate that an in vivo microenvironment provides a powerful pressure towards a noradrenergic identity for these models. Interestingly, single-cell RNA-seq analyses of 18 tumor biopsies and 15 PDX models revealed that tumor cells systematically exhibit a noradrenergic identity. Yet, our data highlight a population of noradrenergic tumor cells with mesenchymal features, demonstrating that the plasticity described in cellular models between both identities is relevant in neuroblastoma patients. Our work also emphasizes that both external cues of the environment and intrinsic factors influence plasticity and cell identity in neuroblastoma.

overall_design: ChIP-seq data of neuroblastoma cell lines and xenografts (H3K27ac)

first: Cécile

last: Thirant

first: Isabelle

last: Janoueix-Lerosey


title: Investigation of the anti-tumour properties of interferon epsilon in high grade serous ovarian cancer in vivo.

summary: This experiment is part of a larger study examining the anti-tumour properties of interferon epsilon in ovarian cancer. The goal of this experiment was to test the direct effects of interferon epsilon and interferon beta on human ovarian tumours in vivo, using patient derived xenografts (PDX) in immunocompromised (NSG) mice.

overall_design: NSG mice bearing two different PDX were treated with i.p. recombinant human interferon epsilon (300 IU), recombinant human interferon beta (300 IU), recombinant mouse interferon epsilon (3 IU, equivalent to 300 IU of human interferon epsilon), or PBS thrice weekly for 6 weeks after first detectable evidence of tumour growth in sentinel mice. Peritoneal exudate cells were harvested from mice at endpoint and snap frozen, and stored at −80°C until RNA extraction. n=6 mice were used for each treatment group for each of the two PDX tumours.

first: Zoe

last: Marks

first: Nicole

last: Campbell

first: Linden

first: Jodee

last: Gould

first: Paul

last: Hertzog


title: Population-level antagonism between FGF and BMP signaling steers mesoderm differentiation in embryonic stem cells

status: Public on Mar 24 2023

city: Leiden

first: Christian

last: Schröter

state: Zuid-Holland

address: Einsteinweg 55

department: Cell Systems and Drug Safety

country: Netherlands

institute: Leiden University, Leiden Academic Centre for Drug Research

summary: The mesodermal precursor populations for different internal organ systems are specified during gastrulation by the combined activity of extracellular signaling systems such as BMP, Wnt, Nodal, and FGF. The BMP, Wnt and Nodal signaling requirements for the differentiation of specific mesoderm subtypes in mammals have been mapped in detail, but which mesodermal cell types depend on FGF signaling is not precisely known. It is also not clear how FGF signaling modulates the activity of orthogonal signaling systems involved in mesoderm differentiation. Here, we address these questions by analyzing the effects of targeted signaling manipulations in differentiating stem cell populations with single cell resolution. We identify opposing functions of BMP and FGF, and map the boundary between FGF-dependent and -independent mesodermal lineages. Stimulation with exogenous FGF boosts the expression of endogenous Fgfs while repressing Bmp ligands. This intercellular positive autoregulation of FGF signaling coupled to the repression of BMP signaling may contribute to the specification of reproducible and coherent cohorts of cells with the same identity via a community effect, both in the embryo and in synthetic embryo-like systems.

overall_design: Mouse epiblast stem cells were differentiated towards a mix of mesodermal cell types in N2B27 medium supplemented with BMP4, CHIR99201 and different doses of FGF2 or the FGF receptor inhibitor AZD4547, and analyzed by scRNAseq.

first: Marina

last: Gattiglio

first: Michelle

last: Protzek


title: Education of tumour-associated macrophages by the tumour matrisome inhibits immune surveillance

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Metastatic ovarian tissues represent a complex tumour microenviroment. We analysed the tumour matrisome and immune cell environment in 39 metastatic ovarian tissues. We developed a disease score system, which positively correlated with the tumour matrisome. A distinct matrisome signature was identfied with increasing disease. Immune abundance and phenotype positively correaletd with tumour matrisome components. We developed a decellularised tissue model using metastatic ovarian omental tissues that maintained ECM protein content and architecture and cultured human blood-derived macrophages derived from four different donors. Monocytes cultured on high diseased tissues differerntiated into a distinct macrophage population, different from uninvovled (low disease) samples. Tumour ECM cultured macrophages had pro-tumorgenic phenotype and function.

overall_design: Decellularised tissue from ovarian high grade serous omental metastasis (n = 4) or from adjacent normal omenum (n =4)  was used as substrate for culture of human blood-derived macrophages derived from four different donors.

first: Elliott

middle: H

last: Puttock

first: Oliver

last: Pearce


title: scRNAseq of healthy and irradiated mouse parotid glands highlights crosstalk between immune and secretory cells during chronic injury

status: Public on Mar 23 2023

city: San Francisco

first: Alejandro

last: Martinez Chibly

state: CALIFORNIA

address: 330A Guerrero Street

institute: Genentech

summary: Translational frameworks to understand the chronic loss of salivary dysfunction that follows after clinical irradiation, and the development of regenerative therapies remain an unmet need. Advances in single cell (sc)RNAseq has made it possible to identify previously uncharacterized cell types within tissues and to uncover gene regulatory networks that mediate cell-cell communication and drive specific cell states. scRNAseq studies have been performed for virtually all major tissues including salivary glands; however, there are currently no scRNAseq studies on chronically irradiated salivary glands. Here, we present scRNAseq from control and irradiated parotid glands from mouse collected 10 months post-irradiation. We identify a previously uncharacterized population of epithelial cells in the gland defined by expression of Etv1, which could be a possible salivary precursor. Furthermore, our data suggests that CD8+ T-cells and secretory cells are the most transcriptionally affected during chronic injury with radiation, suggesting active immune involvement during chronic irradiation injury. Notably, scRNAseq of in vivo models of chronic IR injury has only been performed in liver, lung, and skin, and data is only publicly available for lung and skin. Thus, our study will also be an essential resource to better understand cell-specific responses to chronic irradiation in general.

overall_design: irradiated and control parotig glands drom C3H mice were dissociated and analyzed by scRNAseq 10-months post-irradiation. SEURAT workflow for scRNAseq analysis was followed by differential expression between control and irradiated.

first: Brenna

last: Rheinheimer

first: Mary

middle: C

last: Pasquale

last: Martin

first: Kirsten

last: Limesand

first: Matthew

middle: P

last: Hoffman

middle: M

last: Chibly


title: EDG-5506 Single Cell Sequencing

status: Public on Mar 21 2023

city: Boulder

first: Ben

last: Barthel

institute: Edgewise Therapeutics

summary: We used single nucleus RNA sequencing (snRNA-seq) to analyze the changes in gene expression in treated vs untreated mdx mice and compared them to WT expression

overall_design: Gastrocnemius muscles were dissected and nuclei isolated via homogenization, counted, and analyzed using snRNAseq

first: Ashleigh

last: Van Deusen

first: Alan

last: Russell

first: Monica

last: Hall

first: Brad

last: Olwin


title: Differential gene expression in the grf10Δ mutant of Candida albicans in rich growth medium

status: Public on Mar 20 2023

city: Washington

first: Ronda

middle: Joan

last: Rolfes

state: DC

address: 3700 O Street NW

department: Biology

institute: Georgetown University

summary: To identify genes regulated by the transcription factor Grf10, we compared expression patterns of a grf10-null mutant relative to the isogenic WT at 1-hr and 4-hr after innoculation in YPD medium.

overall_design: Isogenic strains OHWT and grf10Δ were grown in triplicate cultures in YPD medium, and cells harvested at 1-hr or 4-hr.  Total RNA was prepared.

first: Tanaporn

last: Wangsanut

first: Sarah

last: Marzec


title: A tumor suppressive-molecular axis EP300/circRERE/miR-6837-3p/MAVS activates type I interferon pathway and anti-tumor immunity to suppress colorectal cancer

status: Public on Mar 17 2023

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

summary: Purpose: The oncogenic role of circRNAs has been well-studied in cancers including colorectal cancer (CRC). However, tumor-suppressive circRNAs and the mechanism through which they exert their anti-tumor effects remain largely unknown. We aim to find out the critical tumor-suppressive circRNAs and their possibility to serve as gene therapy targets.  Experimental Design: CircRNA sequencing, gain- and loss- of function experiments，and transcriptomic analysis were performed to find tumor-suppressive and anti-tumor immunity effects of circRERE. Molecular biology experiments were conducted for mechanism exploration. Finally, we conducted adeno-associated virus to deliver circRERE (circRERE-AAV) and evaluated circRERE-AAV alone and in combination with anti-PD-1 antibody in C57BL/6J mice bearing subcutaneous MC38 tumors.  Results: CircRERE is lowly expressed in CRC and its lower expression predicts worse prognosis of CRC patients in clinic. Overexpression of circRERE inhibits the malignant behaviors of CRC in vitro and in vivo, while knockdown exhibits the opposite effects. The expression of circRERE is regulated by EP300, a histone acetyltransferase downregulated in CRC as well. Mechanistically, circRERE acts as a ceRNA to sponge miR-6837-3p to upregulate MAVS expression, thereby activating type I IFN signaling and promoting anti-tumor immunity. Delivery of circRERE-AAV elicits significant anti-tumor effects, and combination treatment with circRERE-AAV and anti-PD-1 antibody exhibits synergistic effects on tumor growth in preclinical models of CRC.  Conclusions: These results uncover modulatory axis constituting of EP300/circRERE/miR-6837-3p/MAVS and its essential roles in anti-tumor immunity, and demonstrate that circRERE-AAV might represent a new therapeutic avenue to prime immune responses and boost the effects of immunotherapy in clinic.

overall_design: RNA-seq performed in this study was designed to understand the molecular mechanisms underlying SiNC/sicircRERE in gene transcriptional activation.

last: Ding

first: A

middle: b

last: You

first: Hu

last: Yang

first: Guo

middle: s

first: Chun

last: Lai

first: Wen

last: Liu

first: Feng

last: Ye


title: Type I Interferon Response in Astrocytes Promotes Brain Metastasis by Enhancing Monocytic Myeloid Cell Recruitment

status: Public on Mar 16 2023

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Cancer metastasis to the brain is a significant clinical problem.  Metastasis is the consequence of favorable interactions between invaded cancer cells and the microenvironment.  Here, we demonstrate that cancer-activated astrocytes create a sustained low-level activated type I interferon (IFN) microenvironment in brain metastatic lesions.  We further confirm that the IFN response in astrocytes facilitate brain metastasis.  Mechanistically, IFN signaling in astrocytes activates C-C Motif Chemokine Ligand 2 (CCL2) production, which further increases the recruitment of monocytic myeloid cells.  The correlation between CCL2 and monocytic myeloid cells is confirmed in clinical brain metastasis samples.  Lastly, genetically or pharmacologically inhibiting C-C Motif Chemokine Receptor 2 (CCR2) significantly reduces brain metastases.  Our study clarifies a pro-metastatic effect of type I IFN in the brain even though IFN response has been considered to have anti-tumor effects.  Moreover, this work expands our understandings on the interactions between cancer-activated astrocytes and immune cells in brain metastasis.

overall_design: RNA seq in astrocytes and MDA231 tumor cells alone or cocultured

first: Weili

last: Ma

first: Qing

last: Chen


title: Mitochondrial protein import clogging as a mechanism of disease

city: Syracuse

first: Liam

last: Coyne

state: NY

address: 750 E Adams St

institute: SUNY Upstate Medical University

summary: Mitochondrial biogenesis requires the import of >1,000 mitochondrial preproteins from the cytosol.  Most studies on mitochondrial protein import are focused on the core import machinery.  Whether and how the biophysical properties of substrate preproteins affect overall import efficiency is underexplored.  Here, we show that protein traffic into mitochondria can be disrupted by amino acid substitutions in a single substrate preprotein.  Pathogenic missense mutations in adenine nucleotide translocase 1 (Ant1), and its yeast homolog Aac2, cause the protein to accumulate along the protein import pathway, thereby obstructing general protein translocation into mitochondria. This impairs mitochondrial respiration, cytosolic proteostasis and cell viability independent of Ant1’s nucleotide transport activity.  The mutations act synergistically, as double mutant Aac2/Ant1 cause severe clogging primarily at the Translocase of the Outer Membrane (TOM) complex.  This confers extreme toxicity in yeast.  In mice, expression of a super-clogger Ant1 variant led to neurodegeneration and an age-dependent dominant myopathy that phenocopy Ant1-induced human disease, suggesting clogging as a mechanism of disease. More broadly, this work implies the existence of uncharacterized amino acid requirements for mitochondrial carrier proteins to avoid clogging and subsequent disease.

overall_design: Gene expression profiling analysis of RNA-seq data from Ant1A114P,A123D/+ mouse skeletal muscle compared with wild-type

first: Xin


title: Grf10 regulates the response to copper, iron, and phosphate in Candida albicans.

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

overall_design: Refer to individual Series


title: ESC_HiC

status: Public on Mar 18 2023

city: Tianjin

first: Zhenzhen

last: Lin

address: No. 22, Qixiangtai Road

institute: Tianjin Medical University

summary: To determine the chromatin structural change after telomere shortening in ESC.

overall_design: HiC of WT and Terc-/- ESCs.

first: Zhe


title: Cis-regulation between Irf8 enhancers during cDC1 development (CUT&RUN)

status: Public on Mar 15 2023

city: Saint Louis

first: Tiantian

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: Type 1 classical dendritic cells (cDC1s) development requires the transcription factor IRF8, and IRF8 mutations cause severe combined immunodeficiency, including disseminated bacille Calmette-Guérin (BCG) disease. IRF8 regulated enhancers are required for Irf8 expression in early DC progenitors and mature cDC1s. The E-protein-dependent +41 kb enhancer gains accessibility and activates transcription in common DC progenitors (CDPs), and its depletion abrogated pre-cDC1s specification. The Batf3-dependent +32 kb enhancer gains accessibility and activates transcription in pre-cDC1 progenitors, and its depletion impaired cDC1 maturation. The +32 kb Irf8 enhancer locus bears an enhancer transcript, and the production of enhancer RNA (eRNA) Gm39266 is dependent on +41 kb Irf8 enhancer. It was unclear whether the +32 kb and +41 kb enhancers act independently or cooperate to regulate Irf8 expression. We dissected the mechanisms using +32/+41 compound heterozygous mice, and found that while the +41 kb enhancer suffices for pre-cDC1 progenitor specification, the +32 kb and +41 kb enhancers must reside on one allele to support cDC1 maturation. The +41 kb enhancer cis-regulates chromatin accessibility and BATF3 binding at +32 kb enhancer, independent of eRNA Gm39266 transcripts or transcription across +32 kb Irf8 enhancer.

overall_design: Examination of BATF3 binding in the cDC1 and cDC2 progenitor cells by CUT&RUN.

first: Tian-Tian

first: Kenneth

last: Murphy


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

status: Public on Mar 12 2023

city: Shanghai

first: Wenyong

address: No. 528, Zhangheng Road, Pudong New Area

department: Cardiovascular Research Institute of Traditional Chinese Medicine

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

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

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

first: Dongyuan

last: Wang

first: Ruixia

last: Lu

first: Chunling

last: Zhang

first: Zhenchao

last: Niu

first: Jie

first: Xiaofen

last: Ruan

first: Xiaolong


title: Effects of co-culture EBV-miR-BART1-3p on proliferation and invasion of gastric cancer cells based on exosomes

status: Public on Mar 13 2023

city: Fuzhou

first: Shun

last: Hu

address: Chazhong Road

department: Department of Pathology

institute: The First Affiliated Hospital of Fujian Medical University

summary:
Aim: EBV encode at least 44 miRNAs involved in immune regulation and disease progression. Exosomes can be used as carriers of EBV-miRNA-BART intercellular transmission and affect the biological behavior of cells. We characterized exosomes and established a co-culture experiment of exosomes to explore the mechanism of miR-BART1-3p transmission through the exosome pathway and its influence on tumor cell proliferation and invasion.
Materials and methods: Exosomes of EBV-positive and EBV-negative gastric cancer cells were characterized by transmission electron microscopy, Nanosight and western blotting, and miRNA expression profiles in exosomes were sequenced with high throughput. Exosomes with high or low expression of miR-BART1-3p were co-cultured with AGS cells to study the effects on proliferation, invasion and migration of gastric cancer cells. The target genes of EBV-miR-BART1-3p were screened and predicted by PITA, miRanda, RNAhybrid, virBase and Diana-Tarbase v.8 databases, and the expression of the target genes after co-culture was detected by qPCR.
Results：The exosomes secreted by EBV positive and negative gastric cancer cells range in diameter from 30 nm to 150nm and express the exosomal signature proteins CD63 and CD81. High throughput sequencing showed that exosomes expressed some human miRNAs, among which has-miR-23b-3p, has-miR-320a-3p and has-miR-4521 were highly expressed in AGS-exo. has-miR-21-5p, has-miR-148a-3p and has-miR-7-5p were highly expressed in SNU-719-exo. All EBV miRNAs were expressed in SNU-719 cells and their exosomes, among which EBV- miR-Bart1-5p, EBV- miR-bart22 and EBV- miR-bart16 were the highest in SNU-719 cells. EBV-miR-BART1-5p, EBV-miR-BART10-3p and EBV-miR-BART16 were the highest in SNU-719-exo. After miR-BART1-3p silencing in gastric cancer cells, the proliferation, healing, migration and invasion of tumor cells were significantly improved. Laser confocal microscopy showed that exosomes could carry miRNA into recipient cells. After co-culture with miR-BART1-3p silenced exosomes, the proliferation, healing, migration and invasion of gastric cancer cells were significantly improved. The target gene of miR-BART1-3p was FMA168A, MACC1, CPEB3, ANKRD28 and USP37 after screening by targeted database. CPEB3 was not expressed in all exosome co-cultured cells, while ANKRD28, USP37, MACC1 and FAM168A were all expressed to varying degrees. USP37 and MACC1 are down-regulated after up-regulation of miR-BART1-3p, which may be the key target genes for miR-BART1-3p to regulate the proliferation of gastric cancer cells through exosomes.
Conclusions: miR-BART1-3p can affect the growth of tumor cells through exosome pathway. The proliferation, healing, migration and invasion of gastric cancer cells were significantly improved after co-culture with exosomes of miR-BART1-3p silenced expression. USP37 and MACC1 may be potential target genes of miR-BART1-3p in regulating cell proliferation.

overall_design: Exosomes of EBV-positive and EBV-negative gastric cancer cells were sequenced with high throughput.

first: Mengyao

first: Tianyi

first: Jiezhen

last: Li

first: Feng

last: Gao

first: Ke

last: Zheng

first: Guoping

first: Caihong

last: Re

first: Xiangna

first: Fang

last: Guo

first: Sheng


title: Cis-regulation between Irf8 enhancers during cDC1 development

status: Public on Mar 14 2023

first: Tiantian

last: Liu


title: Effect of Escherichia coli O157: H7 on gene expression before and after citric acid-induced antibiotic tolerance

status: Public on Mar 10 2023

city: Changchun

first: Xue-song

address: Xincheng Street No. 2888

institute: Jilin Agricultural University

summary: In order to explore the differentially expressed genes of E. coli O157: H7 after citric acid induced antibiotic tolerance, we artificially induced the antibiotic tolerance of E. coli O157: H7 and verified its phenotype.

overall_design: In vitro, citric acid was added during bacterial culture to artificially induce antibiotic tolerance of E.coli O157: H7 bacteria.


title: Revisiting chromatin packaging in mouse sperm [ChIP-Seq]

city: Boston

first: Qiangzong

last: Yin

state: MA

address: 3 Blackfan St, CLS building 440A

department: Medicine

institute: BIDMC/Harvard Medical School

summary: Mammalian sperm exhibit an unusual and heavily-compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression in the early embryo. Scores of genome-wide surveys in sperm have reported patterns of chromatin accessibility, histone localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low levels of cell-free chromatin. In the absence of proper sperm lysis we readily recapitulate multiple prominent genome-wide surveys of sperm chromatin, suggesting that these profiles primarily reflect contaminating cell-free chromatin. Removal of cell-free DNA, along with appropriate lysis conditions, are required to reveal a sperm chromatin state distinct from any yet reported. Using ATAC-Seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with genes expressed during late spermiogenesis. Histone modification and chromosome folding studies also strongly support the hypothesis that prior studies suffer from contamination, but technical challenges associated with reliably preserving the architecture of the compacted sperm head prevent us from confidently assaying true localization patterns for these epigenetic marks. Together, our studies strongly argue that our knowledge of mammalian chromosome packaging remains largely incomplete, and motivate future efforts to more accurately characterize genome organization in mature sperm.

overall_design: Histone modification profiling in mouse sperm samples that are pre-treated with Dnase or DTT using ChIP-Seq

first: Chih-Hsiang

last: Yang

first: Olga

middle: S

last: Strelkova

first: Yu

last: Sun

first: Sneha

last: Gopalan

first: Liyan

first: Job

last: Dekker

first: Thomas

last: Fazzio

first: Xin

middle: Z

first: Johan

last: Gibcus

first: Oliver

last: Rando


title: Cis-regulation between Irf8 enhancers during cDC1 development (ATAC-Seq)

overall_design: Examination of chromatin accessibility in the pre-cDC1 progenitors from Irf8 +32+/- and +32/+41 compound heterozygous mice by ATAC-seq.

first: Tian-Tian

first: Julia

last: Belk

first: Ansuman

middle: T

last: Satpathy

first: Kenneth

last: Murphy


title: MicroRNA‑130a‑3p inhibition suppresses cervical cancer cell progression

city: Barretos

first: Rhafaela

middle: Lima

last: Causin

state: SP

address: Antenor Duarte Villela, 1331

department: Molecular Oncology Research Center

country: Brazil

institute: Barretos Cancer Hospital

summary: MicroRNAs (miRNAs or miRs) play essential roles in the initiation and progression of human tumors, including cervical cancer. However, the mechanisms underlying their actions in cervical cancer remain unclear. The present study aimed to evaluate the functional role of miR‑130a‑3p in cervical cancer. Cervical cancer cells were transfected with a miRNA inhibitor (anti‑miR‑130a‑3p) and a negative control. Adhesion‑independent cell proliferation, migration and invasion were evaluated. The findings presented herein demonstrated that miR‑130a‑3p was overexpressed in HeLa, SiHa, CaSki, C‑4I and HCB‑514 cervical cancer cells. The inhibition of miR‑130a‑3p significantly reduced the proliferation, migration and invasion of cervical cancer cells. The canonical delta‑like Notch1 ligand (DLL1) was identified as a possible direct target of miR‑103a‑3p. The DLL1 gene was further found to be significantly downregulated in cervical cancer tissues. On the whole, the present study demonstrates that miR‑130a‑3p contributes to the proliferation, migration and invasion of cervical cancer cells. Therefore, miR‑130a‑3p may be used as a biomarker to determine cervical cancer progression.

overall_design: Three replicates of the HCB-514 cervical cancer cell line and three replicates of the non-tumorigenic cell line HaCaT

first: Rui

last: Reis

first: Marcela

middle: N

last: Rosa

middle: L

first: Márcia

last: Marques.


title: Time trajectory analysis reveals age-modulated small RNA cargo of circulating extracellular vesicles

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

summary: Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across the lifespan from 2-18 months: (1) sncRNAs that are free-circulating (fc-RNA) and (2) sncRNAs bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit unique ageing patterns that vary between the fcRNA and EV-RNA fractions. While tRNAs showed the highest correlation with ageing in both fractions, rRNAs exhibited inverse correlation trajectories between the EV- and fc-fractions. For miRNAs, the EV-RNA fraction was exceptionally strongly associated with ageing, especially the miR-29 family in adipose tissues. Sequencing of sncRNAs and coding genes in fat tissue of an independent cohort of aged mice up to 27 months highlighted the pivotal role of miR-29a-3p and miR-29b-3p in ageing-related gene regulation that we validated in a third cohort by RT-qPCR.

overall_design: The main aim of our study was to provide a data resource of small non-coding RNAs included in EV cargo and freely circulating in plasma (fc-RNAs) in mice of different ages and to identify differences between the molecular information in these fractions associated with ageing that might advance our understanding of the systemic ageing process. Therefore, plasma fc-RNA and EV-RNA of individual mice were sequenced for noncoding RNA profiling and contrasted by computational approaches. We initially conducted the EV-RNA and fc-RNA isolation workflow on 18 female C57BL/6N mice, 14 of which resulted in a sufficient amount of biological material. Overall, we thus generated non-coding RNA-sequencing samples from mice at the age of 2 months (n = 3; body weight (bw): 19-20 g), 6 months (n = 4; bw: 25-29 g), 8 months (n = 3; bw: 23-26 g), 12 months (n = 2; bw: 31 g) and 18 months (n = 2; bw: 34 & 41 g).

last: Kuhn

first: Nicole

last: Ludwig

first: Martin

last: Simon

first: Laura

last: Gröger

first: Natalie

last: Fabis

first: Abdulrahman

last: Salhab

first: Tobias

last: Fehlmann

last: Hahn

first: Annika

last: Engel

first: Marcus

last: Koch

first: Jana

last: Koehler

first: Katarzyna

last: Winek

first: Hermona

last: Soreq

first: Irina

last: Nazarenko

first: Gregor

last: Fuhrmann

first: Tony

last: Wyss-Coray

first: Eckart

last: Meese

first: Verena

last: Keller

first: Matthias

middle: W

last: Laschke

first: Andreas


title: Differential gene expression in the grf10Δ mutant of Candida albicans in high copper containing growth medium

first: Ronda

last: Rolfes

summary: To identify genes in that are misregulated in the grf10Δ mutant of Candida albicans in response to growth in high copper, we compared expression patterns of the grf10-null mutant relative to the isogenic WT in YPD medium supplemented with and without 12 mM CuSO4.

overall_design: Isogenic strains OHWT and grf10Δ were grown in triplicate cultures in YPD medium until an OD600 of 1.0, and split in half.  One set remained in YPD medium and other into in YPD medium supplemented with 12 mM CuSO4.  Total RNA was prepared for RNA sequencing.

first: Sylvia

middle: J

last: Arnold

first: Sarah

last: Marzec


title: MOV10 knockout and gene expression

status: Public on Mar 07 2023

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

summary: Transposable elements constitute nearly half of the mammalian genome and play important roles in genome evolution. While a multitude of both transcriptional and post-transcriptional mechanisms exist to silence transposable elements, control of transposition in vivo remains poorly understood. MOV10, an RNA helicase, is an inhibitor of mobilization of retrotransposons and retroviruses in cell culture assays. Here we report that MOV10 restricts LINE1 retrotransposition in mice. Although MOV10 is broadly expressed, its loss causes only incomplete penetrance of embryonic lethality, and the surviving MOV10-deficient mice are healthy and fertile. Biochemically, MOV10 forms a complex with UPF1, a key component of the nonsense-mediated mRNA decay pathway, and primarily binds to the 3' UTR of somatically expressed transcripts in testis. Consequently, loss of MOV10 results in an altered transcriptome in testis. Analyses using a LINE1 reporter transgene reveal that loss of MOV10 leads to increased LINE1 retrotransposition in somatic and reproductive tissues from both embryos and adult mice. Moreover, the degree of LINE1 retrotransposition inhibition is dependent on the Mov10 gene dosage. Furthermore, MOV10 deficiency reduces reproductive fitness over successive generations. Our findings demonstrate that MOV10 attenuates LINE1 retrotransposition in a dosage-dependent manner in mice.

overall_design: Total RNA was isolated from 6 pairs of PND21 mouse testes (3 pairs of wild type and 3 pairs of Mov10-/-) using TRIzol reagents (Thermo Fisher Scientific). A total of 1 μg of RNA from each sample was used to generate RNA-seq libraries using TruSeq Stranded mRNA Library Preparation Kit Set A (Cat. No. RS-122-2101, Illumina) according to the manufacturer’s instruction. The quality of libraries was evaluated using the Agilent 4200 TapeStation (Agilent Technologies). All 6 individual libraries were pooled in equal amount and sequenced with HiSeq 4000 system (Illumina).

first: Yongjuan

last: Guan

first: Jeremy

last: Wang


title: Longitudinal study of the human sperm methylome aging through whole-genome bisulfite sequencing

status: Public on Mar 01 2023

city: Los Angeles

first: Guilherme

last: de Sena Brandine

address: 1050 Child's Way

department: Quantitative and Computational Biology

institute: University of Southern California

type: Methylation profiling by high throughput sequencing

summary: The average age of fatherhood has increased in recent years. Various genetic diseases are also known to be more likely in children with older fathers. This leads to a need to investigate age-related changes to the sperm DNA. The sperm methylome can be used to accurately predict fertility and embryo viability, and it also changes continuously with age. To date, most population studies that investigate age-related changes to the sperm methylome use microarrays, which are less expensive but, compared to sequencing-based approaches, investigate the methylome at much lower spatial resolution.

overall_design: We generated whole-genome bisulfite sequencing of sperm DNA for 10 donors. For each donor, two samples were collected, separated by 10 to 18 years.

first: Timothy

last: Jenkins

first: Kenneth

middle: I

last: Aston

first: Andrew

middle: D

last: Smith


title: LPS induced CXCL10 chemokine production via IFN- α receptor and toll-like receptor 4 signalling

city: Fitzroy

first: Helen

last: Thomas

address: 9 Princes Street

department: Immunology and Diabetes

institute: St Vincent's Institute

summary: CXCL10 is a chemokine induced by IFN-γ and implicated in the pathogenesis of type 1 diabetes (T1D). It attracts IFN-γ-producing T cells to the pancreatic islets, forming a positive feed-forward loop where T cells induce CXCL10 and attract themselves, but it is unclear what attracts the first IFN-γ-producing T cells in islets. Lipopolysaccharide induced CXCL10 production in cultured islets of nonobese diabetic (NOD) mice, and the lack of its inhibition in islets from NOD mice deficient for RAG1 or IFN-g receptor revealed its dissociation from the requirement of T cells and IFN-γ. To further investigate the mechanism of LPS induced CXCL10 production, the gene expression profile of pancreatic beta cells after culture of whole islets in LPS was analysed. Overall a gene expression signature of cytokine signalling, particularly by type I IFNs and TLR4 was upregulated after culture of islets in LPS.

overall_design: Islets were isolated from 6-8 week old male NOD mice and cultured for 48 hours with 50ng/ml lipopolysaccharide. Islets were then dispersed to single cells with trypsin and beta cells were sorted using FACS. RNA was isolated and subjected to RNA sequencing. There were n=5 independent samples per group, untreated and LPS-treated.


title: Genome-wide CRISPR loss-of-function screen for α-amanitin

city: Shenzhen

first: Bei

address: No.66,Gongchang Road,Guangming District

department: School of Pharmaceutical Sciences (Shenzhen)

institute: Sun Yat-sen University

summary: The “death cap”, Amanita phalloides, is the world’s most poisonous mushroom, responsible for 90% of mushroom-related fatalities. The most fatal component of the death cap is α-amanitin(AMA). Despite its lethal effect, the exact mechanisms of how α-amanitin poisons humans remain unclear, leading to no specific antidote available for treatment. Here, we performed a genome-wide CRISPR loss-of-function screen to identify genes and pathways involved in AMA cytotoxicity.

overall_design: The mutant cell pools were treated by AMA for 7 days and the surviving cells were recovered and harvested for genomic DNA analysis. Two replicates for control group and AMA group.

first: Guo-Hui

last: Wan

first: Qiao-Ping


title: Chemoresistance in acute myeloid leukemia: a single-cell RNA sequencing approach

city: Taichung City

first: thh

last: lab

address: 1650 Taiwan Boulevard Sect. 4, Taichung, Taiwan 40705, ROC

country: Taiwan

institute: TCVGH

summary: Introduction  Our previous study demonstrated that myc, mitochondrial oxidative phosphorylation, mTOR, and stemness were independently responsible for chemoresistance in AML. The current study aimed to further identify the potential mechanisms of chemoresistance of the “7+3” induction in AML using a single-cell RNA sequencing (scRNA-seq) approach.   Methods  Thirteen untreated de novo AML patients were enrolled and stratified into the complete remission (CR) (n = 8) and the non-CR (n = 5) groups. We used scRNA-seq to analyze the genetic profiles of 28950 AML cells from these 13 patients. A previously published bulk RNA-seq dataset validated our results.   Results  Chemoresistant AML cells had more premature accumulation in early hematopoiesis. The hematopoietic stem cell-like cells from the non-CR group expressed more leukemic stem cell markers (CD9, CD82, IL3RA and, IL1RAP) than those from the CR group. Besides, chemoresistant progenitor cells had impaired myeloid differentiation due to early hematopoiesis arrest. Importantly, the AML cells analyzed by the scRNA-seq and bulk RNA-seq honored comparable myeloid lineage cell fraction, which internally validated our results. Using the TCGA database, our analysis demonstrated that AML patients with a higher expression of chemoresistant genetic markers (IL3RA and IL1RAP had a worse overall survival (p < 0.01 for IL3RA; p < 0.05 for IL1RAP).

overall_design: Examination of 2 different clinical outcome in Bone marrow cells of Acute myeloid leukemia

first: Po-Liang

last: Cheng

first: Tzu-Hung

last: Hsiao

first: Miao-Neng

last: Hung

first: Pei-Pei

last: Jhan

first: Li-Wen

last: Lee

first: Chieh-Lin

last: Teng


title: UVDE-HS-seq mapping of UV-induced 6-4PPs and atypical TA photoproducts

status: Public on Feb 28 2023

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: We used a novel high-throughput sequencing method known as UVDE-HS-seq to map the formation of UV-induced 6-4 photoproducts (6-4PP) and atypical thymidine-adenine (TA) photoproducts at single nucleotide resolution across the yeast genome in wild-type cells. We also analyzed 6-4PP and TA photoproducts in UV-irradiated yeast genomic DNA (i.e., naked DNA).

overall_design: Mapping UV-induced 6-4PPs and TA photoproducts in wild-type BY4741 yeast cells and isolated yeast genomic DNA. Yeast cells were irradiated with 600J/m2 of UVC, while the isolated genomic DNA was irradiated with 500 J/m2 of UVC.

first: Kaitlynne

last: Bohm


title: UVDE-seq mapping of UV-induced 6-4PPs and atypical TA photoproducts

summary: We used a novel high-throughput sequencing method known as UVDE-seq to map the formation of UV-induced 6-4 photoproducts (6-4PP) and atypical thymidine-adenine (TA) photoproducts at single nucleotide resolution across the yeast genome in wild-type and rad16 mutant cells, which are deficient in GG-NER. We also analyzed 6-4PP and TA photoproducts in UV-irradiated yeast genomic DNA (i.e., naked DNA).

overall_design: Mapping UV-induced 6-4PPs and TA photoproducts in wild-type BY4741 yeast cells, mutant yeast cells deleted for the RAD16 gene. (i.e., rad16?), and isolated yeast genomic DNA. Yeast cells were irradiated with 600J/m2 of UVC, while the isolated genomic DNA was irradiated with either 400 or 500 J/m2 of UVC.


title: Dual-action host-guest chemistry suppresses PAO1 virulence in A549 cell line model

status: Public on Feb 27 2023

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

summary: Our study showed that selected pillararene was able to decrease the level of cell death and demage caused to human A549 epithelial cells by Pseudomonas aeruginosa PAO1 infection. To further understand the protective effects of pillararene during bacterial infections, we analyzed total mRNA isolated from the A549 epithelial cells. Our study showed that pillararene alone had minimal effect on A549 epithelial cells. The addition of PAO1 to A549 cells greatly altered expression levels. The addition of pillararene to infected A549 epithelial cells displayed a concentration-dependent reduction in the inflammatory response.

overall_design:
Human epithelial lung cells (A549)were grown in the presence and absence of Pseudomonas aeruginosa PAO1 and two different concentrations of pillararene (0.1 and 0.5 mM).

The raw data files for each sample in this submission are not de-multiplexed. All sample metadata are included in the file sample_information.xls linked to to the foot of this record.

first: Katarzyna

last: Leskinen

first: Christopher

last: Jonkergouw

first: Markus

last: Linder


title: Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development.

status: Public on Feb 15 2023

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

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

overall_design: Refer to individual Series


title: PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans

status: Public on Feb 22 2023

first: Zinan

last: Li

address: #16 Hepingli Middle Street

institute: Beijing center for disease prevention and control

summary: To elucidate the molecular mechanism underlying lifespan reduction induced by PM2.5 exposure in Caenorhabditis elegans, we performed global gene expression profiling by RNA-sequencing technology, and compared the gene expression pattern change induced by PM2.5 exposure.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from PM2.5 exposed worms and corresponding sham-treated worms


title: MacroH2A2 modulates the self-renewal of glioblastoma cells

city: Calgary

first: Marco

last: Gallo

state: AB

address: 2500 University Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

summary: Self-renewal is a crucial property of glioblastoma cells and is enabled by the choreographed function of chromatin regulators and transcription factors. Identifying targetable epigenetic mechanisms of self-renewal could represent an important step toward developing new and effective treatments for this universally lethal cancer. Here we uncover a targetable epigenetic axis of self-renewal mediated by the histone variant macroH2A2.

overall_design: ChIP-seq of macroH2A2-FLAG in endogenously tagged primary glioblastoma cells

first: Ana

last: Nikolic

first: Katrina

last: Ellestad


title: Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [ATAC-seq]

summary: Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential expressions and the proportion of distal ACRs were increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages, and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed lights on the improvement of wheat yields and qualities.

overall_design: It is reported that the CRE variants are associated with many important agronomic traits. In this study, we unravelling the transcriptional network underlying wheat grain development by combing ATAC-seq (Assay for Transposase Accessible Chromatin sequencing) and RNA-seq with samples from a series of time points.


title: Durable Alterations of Hematopoiesis and Chromatin post-COVID-19

city: New York

first: Jin-Gyu

last: Cheong

address: 1300 York Avenue

institute: Weill Cornell Medicine


title: Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [RNA-seq]


title: Glioblastoma cells treated with MI3 or DMSO

overall_design: RNA-seq of primary glioblastoma cells with MI3 treatment or control after 7 days of treatment

first: Anna

last: Bobyn

first: Xuequng

last: Lun

first: Michael

last: Johnston

last: Gafiuk

first: Franz

last: Zemp

first: Nicolleta

last: Ninkovic

first: N

last: Berger

first: Peter

middle: B

last: Dirks

first: Darren

last: Derksen

first: Donna

last: Senger

first: Jennifer

middle: A

last: Chan

first: Douglas

last: Mahoney


title: The small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti

status: Public on Feb 14 2023

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

institute: Albert-Ludwigs-University Freiburg

summary: Ribosome profiling was applied for the first time on S. meliloti to generate a translatome map. Our work reveals active translation for several ORFs including small ORFs (sORFs). In addition, our ribosome profiling data led to the discovery of several translated non-annotated sORFs. Translation of these non-annotated sORFs was validated by proteomics and western blotting.

overall_design: 2 replicates of Total RNA-seq and two replicates of Ribo-seq of S. meliloti

first: Lydia

last: Hadjeras

first: Sandra

last: Maaß

first: Elena

last: Evguenieva-Hackenberg

first: Cynthia

middle: M

last: Sharma

first: Christian

middle: H

last: Ahrens


title: Abatacept/Ruxolitinib and Screening for Concomitant Respiratory Muscle Failure to Mitigate Fatality of Immune-Checkpoint Inhibitor Myocarditis

status: Public on Feb 13 2023

city: San Francisco

first: Juan

last: Qin

state: CA

address: 555 Mission Bay Boulevard South

institute: UCSF

summary: we performed bulk RNA sequencing assessing transcriptomics and pathways affected in our mouse model. In ICI-myocarditis mice (ctla4+/-pd1-/-), bulk RNA sequencing showed very distinct affected pathways in ICI-myocarditis mice compared to unaffected control mice (ctla4+/+ pd1-/-).

overall_design: ICI-myocarditis mice (n=3, ctla4+/- pd-1-/-) were compared to unaffected control mice (n=4, ctla4+/+ pd-1-/-).

first: Javid

last: Moslehi


title: RNA stability controlled by m6A methylation provides X to autosome compensation in mammals [SLAM-seq]

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

institute: Würzburg University

summary: In therian mammals, X-chromosomal genes are expressed only from a single active X chromosome, both in males (XY) as well as females (XX). To compensate for this reduction in dosage compared to the evolutionary ancestral state on two autosomes, it has been proposed that genes from the active X chromosome exhibit dosage compensation (“Ohno’s hypothesis”). However, the existence and mechanism of X-to-autosome dosage compensation are still under debate. Here, we show that dosage compensation is achieved via differential N6-methyladenosine (m6A) RNA modification. X-chromosomal transcripts are reduced in m6A modifications and more stable compared to the autosomal counterparts. Acute depletion of m6A using a small molecule inhibitor differentially affects autosomal and X-chromosomal transcripts across sexes, cell types, tissues and species, resulting in perturbed dosage compensation. We propose that higher stability of X-chromosomal transcripts is directed by lower levels of m6A, indicating that mammalian dosage compensation occurs via epitranscriptomic RNA regulation.

overall_design: SLAMseq experiment was performed for total RNA of male mES cells in 4 replicates per condition.

first: Cornelia

last: Rücklé

first: Nadine

last: Körtel

first: Felicia

last: Basilicata

first: Kathi

last: Zarnack

first: Claudia

middle: K

last: Valsecchi

last: König


title: RNA sequencing analysis of wild-type and Scd1-deficient CD4+ early iTregs

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

country: Belgium

summary:
Analysis of differentially expressed genes in CD4+ early iTregs isolated from wild-type and Scd1-deficient mice.
The goal of this study was to elucidate the effect of Scd1 on Treg differentation.

overall_design: CD4+ T cells were purified from splenocytes (collected from 11-week-old wild-type and Scd1-deficient C57BL/6 mice) using magnetic separation. Subsequent fluorescence-activated cell sorted naïve T cells (CD4+ CD44med CD25- CD62L+) were differentiated for 1 day in Treg-polarizing conditions (CD3, CD28, TGFb). After 1 day, cells were lysed using QIAzol.

first: Jeroen

middle: F

last: Bogie

first: Jerome

last: Hendriks

first: Melanie

last: Loix


title: RNA stability controlled by m6A methylation provides X to autosome compensation in mammals [DNA-seq]

overall_design: DNAseq experiments on female mESC clones were performed on genomic DNA.

first: Anke

last: Busch

first: You

last: Zhou


title: Effect of hypoxia and treatment with cyclosporine A on chemotaxis of RAMOS B cells

city: Rochester

first: Juilee

last: Thakar

state: New York

address: 601 Elmwood Ave

department: Microbiology and Immunology

institute: University of Rochester

summary: To investigate the effect of changes in oxygen tension and treatment with cyclosporine A on the chemotactic migration of B cells, we grew RAMOS B cells at 19% and 1% oxygen levels, and at 19% and 1% oxygen levels after treatment with cyclosporine A. We then performed RNA-seq on these RAMOS B cells and subequently gene expression profiling analysis on this RNA-seq data.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RAMOS B cells grown at 19% and 1% O2 levels with and without treatment with cyclosporine A.

first: Shannon

last: Hilchey

first: Mukta

middle: G

last: Palshikar

first: Martin

last: Zand


title: Effect of cell-penetrating TLR decoy peptide on LPS-stimulated Bone marrow derived macrophages

status: Public on Feb 10 2023

city: Chuncheon

first: Keunwook

last: Lee

department: Biomedical Science

country: South Korea

institute: Hallym University

summary:
To investigate the effects of the cell-penetrating TLR decoy peptide, M-CSF generated bone marrow derived macrophages obtained from C57BL6/J mice were pretreated  with two different concentrations of the peptide followed by stimulation with LPS for 2 hours.
The cells were lyzed and analyzed by RNA Sequencing.

overall_design: RNA sequencing was performed using BMDM cells grown under 4 different conditions (Control, LPS, LPS with 1uM peptide and LPS with 10 uM peptide) with triplicate samples in each group.

first: Pak

last: Seongwon

first: Thapa

last: Bikash

first: Lee

last: Keunwook


title: Comparative genomics of the sea urchin P. lividus highlights contrasting trends of genome and regulatory evolution in deuterostomes

status: Public on Feb 09 2023

city: London

first: Ferdinand

last: Marlétaz

address: Gower Street

department: Genetics, Evolution & Environment

institute: University College London

summary: Sea urchins are emblematic marine animals with a rich fossil record and represent instrumental models for developmental biology. As echinoderms, sea urchins display several characteristics that set them apart from other deuterostomes such as their highly regulative embryonic development and their unique pentaradial adult body plan. To determine whether these characteristics are linked to particular genomic rearrangement or gene regulatory rewiring, we introduce a chromosome-scale genome assembly for sea urchin Paracentrotus lividus as well as extensive transcriptomic and epigenetic profiling during its embryonic development. We found that sea urchins show opposite modalities of genome evolution as compared to those of vertebrates: they retained ancestral chromosomal linkages that otherwise underwent mixing in vertebrates, while their intrachromosomal gene order has evolved much faster between sea urchin species that split 60 Myr ago than it did in vertebrates. We further assessed the conservation of the cis-regulatory program between sea urchins and chordates and identified conserved modules despite the developmental and body plan differences. We documented regulatory events underlying processes like zygotic genome activation and transition to larval stage in sea urchins. We also identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes are involved in organismal novelties, such as Aristotle's lantern, tube feet, or in the specification of   lineages through for instance the pmar1 and pop genes.  Altogether, our results suggest that gene regulatory networks controlling development can be conserved despite extensive gene order rearrangement.

overall_design:
Staged RNA-seq from P.lividus embryonic and larval stages

Staged ATAC-seq from P.lividus embryonic and larval stages

first: Thierry

last: Lepage


title: Whole body Knockout of PC-TP (Pctp-/-), Hepatic whole RNAseq comparing Wild Type (WT) and knock out mic (KO) as well as Chow Fed and Methionine and choline depleted (MCD) fed mice.

status: Public on Feb 12 2023

city: Atlanta

first: Samuel

middle: Adam

last: Druzak

state: GA

address: 1510 clifton RD NE

department: Biochemistry

institute: Emory University

summary:
Previous studies have used this model to show that PC-TP has a protective effect when challenged with a methionine and choline depleted diet, known to induce NAFLD. We performed transcription factor binding experiments and show that PPARs are dysregulated in the contect of PC-TP depletion
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 Mice for WT and KO fed either normal chow or methionine and choline depleted chow.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and KO Livers fed MCD or Chow diet

first: Eric

last: Ortlund

first: David

last: Cohen


title: Evaluation of gene expressions in epididymal white adipose tissue (eWAT) of genetic and diet-induced NASH model.

status: Public on Feb 11 2023

city: Kobe

first: Yusei

last: Hosokawa

address: 7-5-2 Kusunoki-cho, Chuo-ku

department: Division of Diabetes and Endocrinology, Department of internal medicine

country: Japan

institute: Kobe University graduate school of medicine

summary:
To investigate the alterlation of eWAT gene expression in diet-induced NASH model with adipose tissue insulin resistance, we evaluated eWAT of control mice
and adipocyte-specific PDK1 knockout (PDK1KO) mice  fed either normal chow(NC) or  Gubra amylin NASH (GAN) diet for 16weeks after weaning
at 4 weeks old. We then performed gene expression profiling analysis using data obtained from RNA-seq of these 4 groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for eWAT of 4 groups[Control(NC), Contro(GAN), PDK1KO(NC),PDK1KO(GAN)].

first: Tetsuya

last: Hosooka

first: Wataru

last: Ogawa


title: MacroH2A2 knockdown vs control RNA-seq in primary glioblastoma cells

first: Marco

last: Gallo

overall_design: RNA-seq of primary glioblastoma cells with macroH2A2 knockdown shRNA or control after 7 days of doxycycline induction

first: Ana

last: Nikolic

first: Anna

last: Bobyn

first: Katrina

last: Ellestad

first: Xuequng

last: Lun

first: Michael

last: Johnston

first: Christopher

last: Gafiuk

first: Franz

last: Zemp

first: Nicolleta

last: Ninkovic

first: N

last: Berger

first: Peter

last: Dirks

first: Darren

last: Derksen

first: Donna

last: Senger

first: Jennifer

last: Chan

first: Douglas

last: Mahoney


title: Broad-spectrum antiviral inhibitors targeting pandemic potential RNA viruses

status: Public on Feb 08 2023

city: Irvine

first: Arunachalam

last: Ramaiah

address: McGaugh Hall

department: Ecology and Evolutionary Biology

institute: University of California, Irvine

summary: We report RNA-seq analysis of Vehicle control, cAIMP, or scleroglucan treated human fibroblasts  under uninfected (mock) and Chikungunya virus infected conditions.

overall_design: Vehicle, cAIMP, or scleroglucan treated human fibroblasts cells were either uninfected (mock) or infected with Chikungunya virus at MOI 0.1 for 24 hrs

first: Gustavo

last: Garcia Jr

first: Joseph

last: Irudayam

first: Arjit

middle: V

last: Jeyachandran

first: Christina

last: Chang

first: Sebastian

last: Castillo Cario

first: Nate

last: Price

first: Sathya

last: Arumugam

first: Angelica

last: Marquez

first: Amir

last: Fanae

first: Nikhil

last: Chakravarty

first: Sanjeev

last: Sinha

first: Samuel

last: French

first: Mark

last: Parcells

first: Vaithilingaraja

last: Arumugaswami


title: MacroH2A2 knockdown vs control ATAC-seq

first: Marco

last: Gallo

overall_design: ATAC-seq of primary glioblastoma cells with macroH2A2 knockdown shRNA or control after 7 days of doxycycline induction

first: Ana

last: Nikolic

first: Anna

last: Bobyn

first: Katrina

last: Ellestad

first: Xuequng

last: Lun

first: Michael

last: Johnston

first: Christopher

last: Gafiuk

first: Franz

last: Zemp

first: Nicolleta

last: Ninkovic

first: N

last: Berger

first: Peter

last: Dirks

first: Darren

last: Derksen

first: Donna

last: Senger

first: Jennifer

last: Chan


title: Transcriptomics-driven characterization of novel T7-like temperate Pseudomonas phage LUZ100

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

institute: KU Leuven

summary: The global transcriptional profile of novel T7-like Pseudomonas aeruginosa phage LUZ100 was obtained using the long read RNA sequencing technique ONT-cappable-seq. Using this approach we obtained a comprehensive genome-wide map of viral transcription start sites, terminators and transcription units and gained new insights in the molecular mechanisms of transcriptional regulation of T7-like temperate phages.

overall_design: Full-length transcriptional profiling of P. aeruginosa PaLo41 infected with phage LUZ100 using ONT-cappable-seq

first: Leena

last: Putzeys

first: Jorien

last: Poppeliers

first: Maarten

last: Boon

first: Cédric

last: Lood

first: Marta

last: Vallino


title: BRD9 is essential for ribosome biogenesis and survival of multiple myeloma cells.

city: Boston

first: Keiji

last: Kurata

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

overall_design: Refer to individual Series


title: RNA-seq analysis after dBRD9-A treatment in human multiple myeloma cell line OPM2 and H929

summary: BRD9 is a defining component of the non-canonical SWI/SNF complex, regulating gene expression by controlling chromatin dynamics.  We here identified high BRD9 expression as a poor prognostic factor in multiple myeloma (MM), which is positively correlated with activation of ribosome biogenesis. Genetic and pharmacological depletion of BRD9 downregulates expression of ribosome biogenesis genes and disrupts protein synthesis maintenance machinery, thereby inhibiting MM cell growth in both in vitro and in vivo preclinical models. Importantly, BRD9 interacts with BRD4 and MYC to form a transcription initiation complex that promotes transcription of ribosomal biogenesis genes. These results identify and validate BRD9 as a novel therapeutic target in MM which regulates ribosome biogenesis gene transcription, and provide the framework for clinical evaluation of BRD9 degraders to improve patient outcome in MM.  This SuperSeries is composed of the SubSeries listed below.

overall_design: OPM2 and H929 cells were treated with either dBRD9-A or DMSO in triplicate for RNA-seq analysis.

first: Kenneth

middle: C

last: Anderson


title: Chip-seq analysis after dBRD9-A treatment in human multiple myeloma cell line OPM2

overall_design: OPM2 cells were treated with either dBRD9-A or DMSO in triplicate for Chip-seq analysis.


title: Immune Response following Radiation Therapy in a MC38-luc Orthotopic Rectal Cancer Model

first: Scott

last: Gerber

summary: Specific immune subsets from orthotopic murine rectal tumors were sequenced to explore the effect that short course radiotherapy has on the immune response.

overall_design: MC38-luc tumor cells were orthotopically implanted in the rectum of C57BL6 female mice. Tumors were irradiated using a small animal irradiator from days 9-13 post tumor implantation. Tumors were treated with 5Gy radiation therapy for 5 consecutive daily fractions. Tumors were harvested on day 14 and myeloid subsets including tumor associated macrophages (CD45+, CD11b+, Ly6C-, Ly6G-, F480+), inflammatory monocytes (CD45+, CD11b+, Ly6C+, Ly6G-), and granulocytes (CD45+, CD11b+, Ly6C+, Ly6G+) were sorted and processed for RNA sequencing.

first: Taylor

last: Uccello


title: Transcriptomic profile of neutrophils and macrophages from APLAID mutant mice

status: Public on Feb 07 2023

city: Parkville

first: Nishika

last: Ranathunga

state: VIC

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

summary:
Missense mutations in the PLCg2 gene can cause autoinflammation, antibody deficiency and immune dysregulation (APLAID).
Clinical and laboratory features include recurrent blistering skin lesions, pulmonary manifestations, inflammatory eye – and bowel diseases accompanied by reduced class-switching memory B cell counts and recurrent infections. Disease onset occurs typically during childhood with varying degrees of severity. To date there is no known cure of APLAID.
The potential mechanism by which autoinflammation is promoted in APLAID remains elusive. However, neutrophils and macrophages are the main drivers of autoinflammation. In order to dissect the pathogenicity of disease we analyse the transcriptome of neutrophils and macrophages extracted from newly established APLAID mutant mice.

overall_design: Comparative gene expression profiling analysis of macrophages and neutrophils samples from skin and lung of APLAID mutant and control mice.

first: Elisabeth

last: Mulazzani

first: Waruni

last: Abeysekera

first: Alexandra

middle: L

last: Garnham


title: CircPVT1 promotes ER-positive breast tumorigenesis and drug resistance by targeting ESR1 and MAVS

status: Public on Feb 06 2023

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

country: China

institute: xiamen University

summary: The molecular mechanisms underlying estrogen receptor (ER)-positive breast carcinogenesis and endocrine therapy resistance remain incompletely understood. Here, we reported that circPVT1, a circular RNA generated from lncRNA PVT1, is highly expressed in ERalpha-positive breast cancer cell lines and tumor samples, which is functionally important in promoting ERalpha-positive breast tumorigenesis and endocrine therapy resistance. CircPVT1 acts as a competing endogenous RNA (ceRNA) to sponge miR-181a-2-3p, promoting the expression of ESR1 and downstream ERalpha-target genes and breast cancer cell growth. Meanwhile, circPVT1 directly interacts with MAVS to disrupt the RIGI-MAVS complex formation, inhibiting type I interferon (IFN) signaling pathway and anti-tumor immunity. The dual mechanisms both contribute to ERα-positive breast tumorigenesis. Anti-sense oligonucleotides (ASO) targeting circPVT1 was shown to inhibit ERalpha-positive breast cancer cell and tumor growth, and could re-sensitize tamoxifen-resistant ERalpha-positive breast cancer cells to tamoxifen treatment. Taken together, our data demonstrated that circPVT1 can work through both ceRNA and protein scaffold mechanisms to promote cancer, and in particular, circPVT1 may serve as a diagnosis biomarker and therapeutic target for ERalpha-positive breast cancer in the clinic.

overall_design: RNA-seq performed in this study was designed to understand the molecular mechanisms underlying circPVT1 in gene transcriptional regulation.

first: Wen

last: Liu

first: Jia

last: Yi

first: Lei

last: Wang


title: Comparison of de novo refilled to original lung interstitial macrophages by bulk RNA-sequencing

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

institute: PhyMedExp INSERM U1046

summary: Lung interstitium macrophages (IMs) are non-alveolar resident tissue macrophages which contribute to the lung homeostasis. These cells were reported to be heterogeneous by our group and other teams, which contains two main distinct subpopulations: CD206+ IMs and CD206- IMs. However, the exact origin of IMs and the transcriptional programs that regulate IM differentiation remains unclear. In recent report, we analyzed the refilled IMs in the course of time after induced IM depletion with single-cell RNA sequencing (10X Genomics Chromium) and bulk RNA sequencing.     In this study, the de novo refilled CD206+ and CD206- IMs on Day 14 post-depletion were compared to those without depletion. Alvelar macrophages (AMs) samples were also included in this analysis and served as a reference. Results of clustering and PCA analyses showed high similarity between de novo refilled and original IMs for both CD206+ and CD206- subsets. Only 9 genes were find upregulated in refilled IMs: AA467197, Cd109, Igf2r, Rarb and S100a4.

overall_design: Both CD206+ and CD206- lung IM subsets were FACS sorted from two groups of mice. Mice in Group “refilled” were IM-DTR mice that were treated with 50 ng diphtheria toxin (DT) 14 days before sacrifice. Group “control” was with litternate control mice without DT treatment. On the day of sacrifice, cells sorted by FACS  and directly subjected to RNA extraction and library construction.   Processed data then were analyzed with Bioconductor.

last: Bai

first: Shakir

last: Hasan

first: Domien

last: Vanneste

first: Thomas

last: Marichal


title: Single-cell RNAseq analysis (10X Genomics Chromium) of refilled lung interstium macrophages on day 4 after depletion

summary: Lung interstitium macrophages (IMs) are non-alveolar resident tissue macrophages which contribute to the lung homeostasis. These cells were reported to be heterogeneous by our group and other teams, which contains two main distinct subpopulations: CD206+ IMs and CD206- IMs. However, the exact origin of IMs and the transcriptional programs that regulate IM differentiation remains unclear. In recent report, we analyzed the refilled IMs in the course of time after induced IM depletion with single-cell RNA sequencing (10X Genomics Chromium) and bulk RNA sequencing.     The IMs in Day 4 post-depletion were compared to the those without depletion. Results showed that refilled IMs had a lower ratio of CD206+ IM vs CD206- subpopulation comparing to IMs without depletion, but they shared high similarity to each other, indicating that the de novo IM population had been established before Day 4 post-depletion.

overall_design: The lung IMs and monocytes were sorted from two groups of mice. Group “DT96h” contains 5 IM-DTR mice, which were treated with 50 ng diphtheria toxin (DT) 4 days before sacrifice. Group “NoTreatment” contains 5 litternate control mice without DT treatment. On the day of sacrifice, mice were sacrificed and lung monocytes and IMs were sorted by FACS and pooled before sending to 10X Chromium library construction.     Processed data then were analyzed with Bioconductor and Seurat package.


title: Gene expression profile at single cell level of hematopoietic progenitors of the bone marrow and spleen with or without the presence PyMT-B6 tumor

city: Saint Louis

first: Derek

middle: Arthur George

last: Barisas

state: Missouri

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: Hematopoietic stem and progenitors cells interact with organ specific stem cell niches. We used single cell RNA sequencing (scRNA-seq) to analyze the gene expression of hematopoietic and potential stromal cells in the bone marrow and spleen with or without PyMT-B6 breast cancer.

overall_design: Bone marrow and splenic hematopoietic stem and progenitor cells as well as a variety of stromal cell populations were isolated from mice with or without PyMT-B6 tumors using fluorescence-activated cell sorting (FACS).

first: Kyunghee

last: Choi


title: Lung interstitial macrophages

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


title: Muscle function in fit and (pre-)frail males and females

status: Public on Feb 04 2023

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

summary: AbstractBackground: A decreased intramuscular carnitine status with aging may contribute to frailty and fatigue, but studies are often confounded by sex-heterogeneity and lack of control groups. We hypothesize that muscle carnitine deficiency is associated with (pre-)frailty, diminished physical performance and altered mitochondrial function, possibly in a sex-dependent manner. This was tested in well-matched age groups, allowing gender-specific analyses.   Methods: A cross-sectional study was performed in well-matched fit (n = 15) and (pre-)frail (n = 13) old males as well as in fit (n = 15) and (pre-)frail (n = 11) old females, using young males (n = 13) and females (n = 13) as healthy controls. In the elderly, frailty was assessed according to the Fried criteria and physical performance was determined by 400-m walk test, short physical performance battery and handgrip strength. Acylcarnitine status was assessed in muscle biopsies and blood plasma using liquid chromatography-tandem mass spectrometry. Muscle mitochondrial gene expression was analyzed.  Results: Intramuscular total carnitine levels and short chain acylcarnitine levels were lower in (pre-)frail old females compared to fit old females and young females, whereas no differences were observed in males. Intramuscular short chain acylcarnitine levels were associated with low physical performance in females, even after correction for muscle mass (%), whereas in males no such association was found. The decline in short chain acylcarnitine levels in (pre-)frail old females was associated with low expression of genes involved in mitochondrial energy production and mitochondrial functionality.  Conclusions: In (pre-)frail old females, intramuscular total carnitine levels and short chain acylcarnitine levels are decreased and this decrease is accompanied by reduced physical performance and low expression of a wide range of genes involved in mitochondrial function.

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