title: Human IRF1 governs phagocytic IFN-γ immunity to mycobacteria but not cell-intrinsic IFN-a/b immunity to viruses [CITEseq]

city: MONTREAL

first: David

last: Langlais

state: QC

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

department: Human Genetics

country: Canada

institute: McGill University

summary: Inborn errors of human IFN-γ immunity underlie mycobacterial diseases, while inborn errors of IFN-a/b immunity underlie viral diseases. Both types of IFNs induce the transcription factor IRF1. We describe two unrelated children with inherited complete IRF1 deficiency and early-onset, multiple, life-threatening diseases caused by weakly virulent mycobacteria. They have no history of severe viral disease, despite exposure to many viruses, including SARS-CoV-2 that is life-threatening in individuals with deficient IFN-a/b. There is a much greater IRF1-dependent response to IFN-γ than IFN-a/b in vitro, both quantitatively and qualitatively. Monocyte-derived macrophages and iPSC-derived macrophages of both patients do not upregulate at least 40% of target genes normally induced by IFN-γ. In contrast, cell-intrinsic IFN-a/b immunity to a wide range of viruses, including HIV and SARS-CoV-2, is maintained. Human IRF1 is thus largely redundant for antiviral IFN-a/b immunity across cell types. By contrast, human IRF1 is essential for IFN-γ immunity to mycobacteria in mononuclear myeloid cells.

overall_design: To investigate the impact of IRF1 loss-of-function on the development of immune cells and their transcriptional program, we have performed scRNA-seq on PBMC from 1 pediatric IRF1 deficient patient (P1.1). This dataset has been combined with CITE-seq for a second sample obtained for this patient (P1.2) and a second IRF1 deficient patient (P2), together with healthy controls.  To investigate the impact of IRF1 loss-of-function on the development of immune cells and their transcriptional program, we have performed scRNA-seq on PBMC from 1 pediatric IRF1 deficient patient. This dataset has been combined with CITE-seq for a second sample obtained for this patient and a second IRF1 deficient patient, together with healthy controls.

first: Mathieu

last: Mancini

last: Bourgey

first: Jérémie

last: Rosain

first: Philippe

last: Gros

first: Jean-Laurent

last: Casanova

first: Jacinta

last: Bustamante


title: Poly (A) Click-seq for U937 control and PMA-treated (6h and 24h) cells

status: Public on Jan 12 2023

city: Boston

first: Srimoyee

last: Mukherjee

state: MA

address: 150 Harrison Ave., Jaharis Bldg., Room #401A

department: Department of Developmental, Molecular & Chemical Biology

country: USA

institute: Tufts University

type: Expression profiling by high throughput sequencing

summary: Poly(A)-ClickSeq: click-chemistry for next-generation 3'-end sequencing without RNA enrichment or fragmentation enabling simultaneous genomewide poly(A)-site identification and differential expression analysis

overall_design: poly(A)-directed RNA-seq experiments: Deep-sequencing for control vs 6h PMA-treated U937 cells, and control vs 24h PMA-treated U937 cells.

first: Elizabeth

middle: A

last: Jaworski

first: Andrew

last: Routh


title: Whole genome doubling drives oncogenic loss of chromatin segregation [Hi-C]

city: Lausanne

first: Luca

last: Nanni

state: Vaud

address: Quartier Sorge

department: Computational Biology

country: Switzerland

institute: Université de Lausanne

summary: Whole genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies. However, the 3D organization of the chromatin in WGD cells and its contribution to oncogenic phenotypes are currently unknown. Here, we show that in p53 deficient cells WGD induces loss of chromatin segregation (LCS), characterized by reduced segregation between short and long chromosomes, A and B sub-compartments, and adjacent chromatin domains. LCS is driven by downregulation of CTCF and H3K9me3 in cells that bypassed activation of the tetraploid checkpoint. Longitudinal analyses revealed that LCS primed genomic regions for sub-compartment repositioning in WGD cells, which resulted in chromatin and epigenetic changes associated with oncogene activation in tumours ensuing from WGD cells. Importantly, sub-compartment repositioning events were largely independent of chromosomal alterations, indicating that these were complementary mechanisms contributing to tumour development and progression. Overall, LCS initiates chromatin conformation changes that ultimately result in oncogenic epigenetic and transcriptional modifications, suggesting that chromatin evolution is a hallmark of WGD-driven cancer.

overall_design: For assessing chromatin organization immediately after WGD, chromatin conformation capture (Hi-C) was performed in pre- and post-WGD cells in RPE TP53-/-, CP-A TP53-/- (clone 3 and clone 19), and K562 cells. Distinct WGD inductions were used to exclude that the treatment itself and not WGD is responsible for changes observed at chromatin level. Additionally, cells exhibiting chromosomal instability only, but not WGD, (CIN-only) were considered to check whether CIN and WGD are leading to the same phenotype. Spontaneous high ploidy cells detected in the CP-A TP53-/- were sorted and assessed by Hi-C. Considering LCS was hypothesized to be caused by CTCF and H3K9me3 insufficiency due to defective tetraploidy checkpoint after WGD, Hi-C was performed in CP-A TP53-/- WGD cells were treated with CDK4/6 inhibitor to mimic the G1 extension assciated with a p53-induced tetraploidy checkpoint, as well as in CP-A p53 wild type WGD cells, since in both cases CTCF and H3K9me3 levels were rescued. Long-term post-WGD cells with tumorigenic properties were then assessed. Cells were grown both in vivo in NSG mice from RPE TP53-/- 20w pWGD cells (T1, T2, T3), and in vitro in soft agar as colonies, derived from CP-A TP53-/- clone 3 6w pWGD (C1, C2) and CP-A TP53-/- 20w pWGD (C1, C2). Each experiment was performed in replicates, as indicated. Samples derived from distinct WGD inductions are marked as "experiment 1/2" in the sample sheet. All conditions were compared to their respective controls.

first: Ruxandra

last: Lambuta

first: Yuanlong

last: Liu

first: Juan

last: Diaz-Miyar

first: Arvind

last: Iyer

first: Daniele

last: Tavernari

first: Natalya

last: Katanayeva

first: Giovanni

last: Ciriello

first: Elisa

last: Oricchio


title: Widespread perturbation of ETS factor binding sites in cancer

status: Public on Jan 09 2023

first: Trevor

last: Siggers

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

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

overall_design: Refer to individual Series


title: Whole genome doubling drives oncogenic loss of chromatin segregation

type: Genome binding/occupancy profiling by high throughput sequencing


title: Whole genome doubling drives oncogenic loss of chromatin segregation [ChIP-seq]

overall_design: To assess the epigenetic landscape of pre- and post-WGD cells, in vitro and in vivo, chromatin immunoprecipitation sequencing was performed in RPE TP53-/- and CP-A TP53-/- in control and WGD cells, as well as in 20w pWGD tumours derived from RPE TP53-/- cells. WGD samples were assessed for H3K9me3 and CTCF, whereas control and post-WGD in vivo samples were assessed for CTCF, H3K9me3, H3K27ac, H3K27me3, H3K4me3. All samples were performed in one replicate. Mouse spike-in chromatin was included in a fraction of samples, as indicated.


title: Human IRF1 governs phagocytic IFN-gamma immunity to mycobacteria

city: Paris

first: Jeremie

last: Rosain

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine

summary: Inborn errors of human IFN-γ immunity underlie mycobacterial diseases, whereas inborn errors of IFN-/ immunity underlie viral diseases. Both types of IFNs induce the transcription factor IRF1. We describe two unrelated children with inherited complete IRF1 deficiency and early-onset, multiple, life-threatening diseases caused by weakly virulent mycobacteria. These children have no history of severe viral disease, despite exposure to many viruses, including SARS-CoV-2, which is life-threatening in individuals with impaired IFN-/ immunity. The IRF1-dependent cellular responses to IFN-γ are, both quantitatively and qualitatively, much greater than those to IFN-/ in vitro. Monocyte- and iPSC-derived macrophages from the two patients show no upregulation of at least 20% of the target genes normally induced by IFN-γ. By contrast, cell-intrinsic IFN-/ immunity to diverse viruses, including SARS-CoV-2, is intact. Human IRF1 is, thus, largely redundant for antiviral IFN-/ immunity. By contrast, human IRF1 is essential for IFN-γ immunity to mycobacteria in myeloid cells.

overall_design: Primary fibroblasts, M-CSF-iPSC-derived macrophages, and M-CSF-IL-4-monocytes-derived macrophages were stimulated or not 30 minutes, 2 hours, or 8 hours with 1000 IU/mL of IFN-alpha or IFN-gamma


title: Widespread perturbation of ETS factor binding sites in cancer [SCREEN_HOOK_SIGGERS_v2]

summary: Although >90% of somatic mutations reside in non-coding regions, few have been reported as cancer drivers. To predict driver non-coding variants (NCVs), we present a novel transcription factor (TF)-aware burden test (TFA-BT) based on a model of coherent TF function in promoters. We applied our TFA-BT to NCVs from the Pan-Cancer Analysis of Whole Genomes cohort and predicted 2,555 driver NCVs in the promoters of 813 genes across 20 cancer-types. These genes are enriched in cancer-related gene ontologies, essential genes, and genes associated with cancer prognosis. We found that 765 candidate driver NCVs alter transcriptional activity, 510 lead to differential binding of TF-cofactor regulatory complexes, and that they primarily impact the binding of ETS factors. Finally, we show that different NCVs within a promoter often affect transcriptional activity through shared mechanisms. Our integrated computational and experimental approach shows that cancer NCVs are widespread and that ETS factors are commonly disrupted.

overall_design: Differential Cofactor (COF) recruitment screen to cancer non-coding variants (NCVs) (ID: 086310) – These experiments profiled recruitment of a panel of six COFs (SRC1/NCOA1, BRD4, KAT8/MOF, NCOR1, RBBP5, TBL1XR1) to 2,956 pairs of reference and alternate alleles predicted by our transcription factor-aware burden test (TFA-BT). COF recruitment was profiled using nuclear extracts from SK-MEL-28 and Jurkat cells. Technical replicates were performed (REP1 and REP2) for each COF screened. NCV CASCADE (ID: 086772) – These experiments use the CASCADE approach to characterize COF recruitment motifs for target loci by profiling recruitment to all single-nucleotide variants across each locus. Motifs were determined for 395 NCV loci identified as differentially bound between reference and alternate alleles in our initial screen. COF recruitment was profiled using the same six COFs and nuclear extracts from Jurkat cells. Technical replicates were performed for each COF screened.

first: Heather

last: Hook

first: David

last: Bray


title: Widespread perturbation of ETS factor binding sites in cancer [CASCADE_HOOK_SIGGERS_v3]


title: Human IRF1 governs phagocytic IFN-γ immunity to mycobacteria but not cell-intrinsic IFN-a/b immunity to viruses

last: Langlais


title: Human IRF1 governs phagocytic IFN-γ immunity to mycobacteria but not cell-intrinsic IFN-a/b immunity to viruses [scRNAseq]

first: Mathieu

last: Mancini

last: Bourgey

first: Jérémie

first: Philippe

last: Gros

first: Jean-Laurent

last: Casanova

first: Jacinta

last: Bustamante


title: Caspase-4 mediates SREBP1 activation in macrophages

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

summary: We identified caspase-4/S1P/SREBP1 pathway that is activated in LPS-treated macrophages. To analyze the functions of caspase-4 and SREBP1 in gene expression in macrophages, we analyzed the effects of deletions of Casp4 and Srebf1 in bone marrow-derived macrophages by RNA-seq.

overall_design: RNA-seq profiling of effects of the knockdown and deletion of Casp4 and Srebf1 in BMDMs.

first: Oishi

last: Yumiko

first: Manabe

last: Ichiro


title: RNAseq analysis of iSB09 treated seedlings

status: Public on Jan 11 2023

city: Valencia

first: Jorge

last: Lozano-Juste

address: Ingeniero Fausto Elio s/n Edificio 8E

country: Spain

institute: IBMCP-UPV-CSIC

summary: wt and plants overxpressing CsPYL1_5m treated with iSB09 for 3 hours

overall_design: 3 biological replicates, control and iSB09 treated seedlings, wt and CsPYL1_5m genotypes


title: Gene differential expression of autophagy-related gene ablation in 562 vascular tumor cells

city: Cincinnati

first: FUCHUN

last: YANG

state: OH

address: 3125 Eden Ave.

department: Cancer Biology

institute: University of Cincinnati

summary: To explore the mechanisms of autophagy in the regulation of vascular tumour cells, we generated three autophagy-related genes, Fip200, Atg5 and Atg7, knockout vascular tumor cells in 562 cell line by CRISPR-Cas9-based sgRNAs. Three independent replicates of mRNA samples were prepared from each KO cells and subjected to RNA-sequencing in comparison to three samples from control 562 cells. We examined changes in gene expression by transcriptional profiling of Fip200 KO, Atg5 KO, and Atg7 KO cells, compared to control 562 cells respectively.

overall_design: Transcriptional profiling of Fip200 KO, Atg5 KO, Atg7 KO and control 562 vascular tumor cells

first: Fuchun

last: Yang

first: Jun-Lin

last: Guan


status: Public on Jan 10 2023

city: Bar Harbor

first: Ryan

last: Tewhey

state: ME

address: 600 Main Street

institute: Jackson Laboratory

overall_design: The study consists of a single MPRA experiment testing somatic variants identified in cancers. Variants for screening were selected using a transcription factor aware burden test (TFA-BT). For each library we processed independent transfections in three unique cell lines; in total we completed 5 replicates of Jurkat (lymphoma), SK-MEL-28 (melanoma), and HT-29 (colorectal) cell lines. Raw data is provided as Illumina reads of the 20 bp barcode from the RNA extracted 24 hours post transfection as well as from the plasmid library used for transfection. We also provide Illumina paired-end reads used to link oligo/barcode combinations from the ∆gfp vector. Processed count files are unnormalized counts for each oligo reported per barcode (uncollapsed).

first: R

first: D

last: Berenzy


title: Whole transcriptome analysis of mouse first molar enamel organ cells at P5 and P12

status: Public on Jan 08 2023

city: San Francisco

first: Yan

last: Zhang

state: CA

address: 513 Parnassus Avenue

department: Orofacial Sciences

institute: UCSF

summary: We report the bulk RNA-se analysis of  the wild type mouse first molar enamel organ cells at P5 and P12

overall_design:
Profile the overall gene expression pattern of enamel organ cells from wild type mouse first molars at days of P5 and P12
*** Submitter declares that raw data are no longer available. ***


title: Transcription factor TFII-I fine tunes innate properties of B lymphocytes

status: Public on Jan 06 2023

city: Baltimore

first: Amit

middle: Kumar

last: Singh

state: Maryland

address: 251 Baview Blvd

department: Laboratory of Molecular Biology Immunology

institute: National Institute on Aging

summary: The ubiquitously expressed transcription factor TFII-I is a multifunctional protein with  pleiotropic roles in gene regulation. TFII-I associated polymorphisms are implicated in Sjögren’s  syndrome and Lupus in humans and, germline deletion of the Gtf2i gene in mice leads to embryonic lethality. Here we report a unique role for TFII-I in homeostasis of innate properties of B lymphocytes. Loss of Gtf2i in murine B lineage cells leads to an alteration in transcriptome, chromatin landscape and associated transcription factor binding sites, which exhibits myeloid like features and coincides with enhanced sensitivity to LPS induced gene expression. TFII-I deficient B cells also show increased switching to IgG3, a phenotype associated with inflammation. These results demonstrate a role for TFII-I in maintaining immune homeostasis and provide clues for GTF2I polymorphisms associated with B cell dominated autoimmune diseases in humans.

overall_design: RNA-seq from mouse splenic B cells, FACS sorted FO and MZ B cell subsets. ATAC-seq from FO and MZ B cells.

first: Mary

last: Kaileh

first: Supriyo

last: De

first: Krystyna

last: Mazan-Mamczarz

first: Dashzeveg

last: Bayarsaihan

first: Ranjan

last: Sen

first: Ananda

middle: L

last: Roy


title: Differential cell composition and split epidermal differentiation in human palm, sole, and hip skin

status: Public on Jan 05 2023

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary: Palmoplantar skin is structurally and functionally unique, but the transcriptional programs driving this specialization are unknown. Here, we exploit bulk and single-cell RNA-sequencing of human palm, sole, and hip skin to describe the distinguishing characteristics of palmoplantar and non-palmoplantar skin while also uncovering previously unappreciated differences between palmar and plantar sites. Our approach reveals downregulation of diverse immunological processes and decreased immune cell populations in palmoplantar skin, highlighting an altered immune environment in the skin of the palms and soles. Further, we identify specific palmoplantar and non-palmoplantar fibroblast populations that appear to orchestrate key differences in cell-cell communication in palm, sole, and hip. Dedicated analysis of epidermal keratinocytes highlights major differences in basal cell fraction among the three sites and validates the presence of a more differentiated, cycling basal population. Finally, our data demonstrate the existence of two spinous keratinocyte populations that constitute two parallel, site-selective epidermal differentiation trajectories. Together, these results provide a deep characterization of the highly adapted palmoplantar skin and contribute new insights into the fundamental biology of human skin.

overall_design: Bulk RNA-seq was performed using RNA extracted from 4 mm punch biopsies obtained from 15 healthy research subjects. Of the 15 subjects, 10 contributed hip and palm biopsies and 5 contributed hip and sole. We performed pairwise comparisons between the hip and palm, hip and sole, and palm and sole to identify differentially expressed genes.

first: Allison

middle: C

last: Billi

first: Johann

middle: E

last: Gudjonsson


title: Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences


title: Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells (RNA-Seq II)

status: Public on Jan 04 2023

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

summary:
Purpose: The goals of this study are to analyze global transcriptional, epigenetic and topological changes in dendritic cells under LPS treatment condition and to investigate how CTCF regulates three-dimensional chromatin interaction in inflammatory response.
Conclusions: Our study provides the detailed analysis of transcriptional, epigenetic and topological genome profiles in mouse dendritic cells under LPS treatment condition. Moreover, our data show how three-dimensional enhancer networks control gene expression during DC activation.

overall_design: NF-κB inhibitor (JSH23) and LPS treated RNA profiles of CTCF-WT cells with biological replicates.

first: Bobae

first: Kyungwoo


title: Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells (HiChIP II)

overall_design: NF-κB inhibitor (JSH23) and LPS treated HiChIP profiles of CTCF-WT cells with biological replicates.

last: Yang


title: NFIC overexpression perturbs normal haematopoeisis by promoting myeloid differentiaon

city: Cardiff

first: Namrata

last: Rastogi

address: Hadyn Ellis Building, Maindy Rd

department: European Cancer Stem Cell Research Institute, School of Biosciences

country: United Kingdom

institute: Cardiff University

summary: Nuclear factor I-C belongs to a family of CTF binding transcription factor which is known for its role cellular differentiation. In our recent study we identified increased expression of  NFIC in. AML samples as compared to normal haematpoitic stem and progenitor cells (HSPCs). We also found that overexpression of NFIC in cord blood derived HSPCs perturbed normal haematopoiesis by increasing monocyte production. Therefore in this analysis we aimed to identify the effect of NFIC overexpression in normal HSPCs at single cell level using single cell RNA (scRNA) sequencing. Cluster analysis based on the cellular and functional identities, identified eight clusters according to their terminal differentiation as monocytes, erythrocytes, dendritic cells (DC), megakaryocytes, neutrophils, megakaryocyte-erythroid progenitor cells, basophil/mast progenitor cells and eosinophils. We found that NFIC overexpressing CD34+ HSPCs had increased percentage of monocytes as compared to control. To understand the molecular basis of this, we focussed our analysis on monocytes to determine changes in mRNA expression following NFIC overexpression. We identified 164 and 88 significantly up-regulated and down-regulated genes, respectively (p<0.05, FDR<0.05) in NFIC overexpressing monocytes as compared to control. Pathway analysis identified enrichment in genes involved in mTOR signalling, cancer cell death and survival, energy metabolism pathways and oxidative phosphorylation. Therefore our scRNA suggested that NFIC play a role in monocytic growth development and its overexpression may lead to monocytic bias in normal haematopoiesis.

overall_design: Human CD34 positive haematopoietic stem and progenitor cells (HSPCs) were infected with either control vector or NFIC overexpression using retronectin. Four days post infection cells were sorted for GFP and processed for single cells RNA sequencing using 10x Genomics.

first: Alex

last: Tonks


title: Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells (ChiP-Seq II)

overall_design: NF-κB inhibitor (JSH23) and LPS treated ChIP-seq profiles of CTCF-WT cells with biological replicates.


title: RNA sequencing of THP-1 cells after Nuclear factor I-C knockdown

summary: Nuclear factor I-C (NFIC) is a transcription factor involved cell growth and differentiation has been found to be upregulated in certain cancers. We also found upregulation of NFIC in Acute myleoid leukemia (AML) as compared to normal blood cells. We also foudn that its shRNA mediated knockdown inhibited growth and induced cell death in AML cell lines and primary samples. Therefore, we next became intersetde to find precise role AML, for this we performed bulk mRNA sequencing using THP-1 cells. Our sequencing resuts revealed 10,083 genes being significantly differentially expressed in NFIC knock down cells as compared to scambled control. Pathway analysis revealed upregulation of genes involved in G2M cell cycle regulation, apoptosis, DNA repair and epigenetic regulation of gene expression as well as downregulation of genes involved in cell survival such as Myc targets, MLL targets, cell adhesion, migration and invasion. All together these results suggests that NFIC promotes growth and survival of AML cells by regulation gene expression.

overall_design: Human AML THP-1 cells were  infected with either scrambled shRNA or shRNA against NFIC using retronectin. Four days post infection cells were sorted for GFP and processed for sequencing with three replicates for each sample.


title: Innate tolerance is mediated by inhibition of specific signaling pathways rather than by epigenetic silencing of effector genes

city: Moscow

first: Mikhail

last: Pashenkov

address: Kashirskoe shosse 24

country: Russia

institute: Institute of Immunology

summary: Macrophages activated through a pattern-recognition receptor (PRR) enter a transient state of tolerance characterized by hyporesponsiveness to restimulation of the same receptor. Signaling-based and epigenetic mechanisms are invoked to explain tolerance. The epigenetic scenario predicts that: (i) activation of a PRR should cross-tolerize to agonists of unrelated PRRs; (ii) some genes become hyperresponsive to homologous rechallenge due to distinct chromatin modifications. We show that in human macrophages tolerized by TLR4 or NOD1 agonists, signaling and transcriptional responses to homologous stimuli are inhibited partially or completely. Many genes are upregulated due to primary stimulation, but are unresponsive to homologous restimulation. Gene hyperresponsiveness to homologous rechallenge is a rare and inconsistent phenomenon. However, most genes that have become unresponsive to homologous stimuli show unchanged or elevated responses to agonists of PRRs signaling via distinct pathways. Thus, inhibition of specific signaling pathways rather than epigenetic silencing is the dominant mechanism of innate tolerance.

overall_design: Human macrophages were generated by culturing blood monocytes from a healthy donor with GM-CSF (40 ng/ml) for 6 days. To induce tolerance, macrophages were treated for 24 h with a NOD1 agonist (M-triDAP), a TLR4 agonist (LPS) or medium as a control. After 24 h, cells were washed and recultured with medium, M-triDAP or LPS for 1 h or 4 h, at which points total RNA samples were collected. Two identically designed independent experiments using macrophages generated from the same donor at two different occasions were performed (two biological replicates)

first: Anna

middle: M

last: Masyutina

middle: V


title: URB1 ensures 3' end processing of pre-rRNAs to prevent exosome-dependent degradation and is required for development

city: Shanghai

first: Li

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: The nucleolus composes hundreds of proteins that play distinct roles in ribosomal RNA (rRNA) processing within Fibrillar Center/Dense Fibrillar Component (FC/DFC) units and ribosome assembly in Granular Component (GC). The sub-nucleolar localization of most proteins and how their unique localization facilitates rRNA processing have remained elusive. By screening 200 nucleolar candidate proteins with high-resolution, live-cell microscopy, we identified a previously undescribed sub-nucleolar compartment, named the periphery of DFC (PDFC). Among the 12 proteins identified in PDFC, URB1 (unhealthy ribosome biogenesis 1) is required for PDFC organization and proper 3' end processing of 47S pre-rRNA. URB1 binds between the 28S rRNA and the 3' external transcribed spacer (3' ETS) to ensure 3' ETS removal, which occurs at the DFC/PDFC boundary. Loss of URB1 leads to accumulation of aberrant 3' ETS-retained 32S pre-rRNA variants, which activates exosome-dependent nucleolar surveillance. This causes decreased 28S rRNA production, reduced cell proliferation and retarded mouse embryonic pre-implementation development. Furthermore, urb1 depletion results in developmental craniofacial disorder in zebrafish, which can be at least partially rescued by further depleting exosome components. Together, this study provides new insights into functional sub-nucleolar organizations, identifies a physiologically essential step in rRNA maturation and emphasizes the exosome-dependent pre-rRNA surveillance pathway.

overall_design: iCLIP-seq of Flag-tagged URB1 protein in HeLa cells and mapped with pre-rRNA. Each experiment was performed in biological duplicate. Control libraries for size-match inputs (SMI) were prepared in parallel.

first: Lin

last: Shan

first: Guang

last: Xu

first: Youkui

last: Huang

first: Run-Wen

last: Yao

last: Zhang

first: Peng-Fei

last: Luan

first: Xiang

last: Gao

first: Pei-Hong

first: Shuai-Xin

first: Siqi

last: Li

first: Liang-zhong

first: Ying

last: Wang

first: Jinsong

first: Catharine

last: Wong

first: Ling-Ling

last: Chen


title: URB1 ensures 3' end processing of pre-rRNAs to prevent exosome-dependent degradation and is required for development [SHAPE-MaP]

overall_design: SHAPE-MaP of in vivo 28S-3' ETS region with/without URB1


title: Influenza-trained mucosal-resident alveolar macrophages confer long-term antitumor immunity in the lungs [RNA-seq]

city: Hangzhou

first: Yushi

state: Zhejiang

address: 866 Yu Hang Tang Road

institute: Zhejiang University

summary: Respiratory viral infections reprogram pulmonary macrophages with altered anti-infectious functions. However, the potential function of virus-trained macrophages in antitumor immunity in the lung, a preferential target of both primary and metastatic malignancies, is not well understood. Using mouse models of influenza and lung metastatic tumors, we show here that influenza trains respiratory mucosal-resident alveolar macrophages (AMs) to exert long-lasting and tissue-specific antitumor immunity. Trained AMs infiltrate tumor lesions and have enhanced phagocytic and tumor cell cytotoxic functions, which are associated with epigenetic, transcriptional and metabolic resistance to tumor-induced immune suppression. Generation of antitumor trained immunity in AMs is dependent on interferon-γ and natural killer cells. Notably, human AMs with trained immunity traits in non-small cell lung cancer tissue are associated with a favorable immune microenvironment. These data reveal a function for trained resident macrophages in pulmonary mucosal antitumor immune surveillance. Induction of trained immunity in tissue-resident macrophages might thereby be a potential antitumor strategy.

overall_design: AMs from different groups  were isolated from mouse lung BAL, and resuspended in Trizol for RNA-seq

first: Tao

first: Jinjing

first: Yanling

first: Lu

first: Yangle

last: Yu


title: Influenza-trained mucosal-resident alveolar macrophages confer long-term antitumor immunity in the lungs

overall_design: Refer to individual Series


title: Influenza-trained mucosal-resident alveolar macrophages confer long-term antitumor immunity in the lungs [ATAC-seq]

overall_design: AMs from different groups  were isolated from mouse lung BAL, and processed with standard ATAC-seq protocol


title: Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells (HiChIP)

first: Hyoung-Pyo

last: Kim

overall_design: LPS treated and non-treated Hi-ChIP profiles of CTCF-WT and CTCF-KO cells with biological replicates.

first: Bobae

last: Yang

first: Woong-Jae

last: Jung


title: Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells (RNA-seq)

overall_design: LPS treated and non-treated RNA profiles of CTCF-WT and CTCF-KO cells with biological triplicates.


title: Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells (HiC)

overall_design: LPS treated and non-treated Hi-C profiles of CTCF-WT and CTCF-KO cells with biological replicates.


title: Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells (ChIP-seq)

overall_design: LPS treated and non-treated ChIP-seq profiles of CTCF-WT and CTCF-KO cells with biological replicates.


title: Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells


title: Effect of genetic deletion of Slc37a2 on gene expression of mouse bone marrow macrophage-derived osteoclasts

status: Public on Jan 03 2023

city: Crawley

first: Nathan

middle: J

last: Pavlos

state: WA

address: 35 Stirling Highway

department: School of Biomedical Sciences

country: Australia

institute: The University of Western Australia

summary: To investigate the mechanism(s) by which Slc37a2 regulates osteoclasts, we performed gene expression profiling analysis using data obtained from RNA-seq of osteoclasts derived from wild-type and Slc37a2-knockout mice (C57BL/6N-SLC37A2 tm2a(KOMP)Wtsi)

overall_design: Comparative gene expression profiling analysis using data obtained from RNA-seq of Slc37a2-knockout  and wild-type osteoclasts derived from bone-marrow macrophages

first: Jamie

middle: W

last: Tan

first: Amy

middle: B

last: Ribet


title: Abiraterone resistance in prostate cancer cells

status: Public on Jan 01 2023

city: Cleveland

first: Shiv

last: Verma

state: Ohio

address: 10900 Euclid Avenue, 2

department: Urology

institute: Case Western Reserve University

summary: Castration resistant prostate cancer (CRPC) develops resistance to antiandrogens affecting Androgen Receptor (AR) signaling through a variety of mechanism. Because of this, the efficacy of androgen receptor targeted therapy remains limited for many patients with CRPC. We  developed C42B-Abiraterone (Abi) and resistance cells to study changes in transcriptomic profile compared to parental cells.

overall_design:
Genome wide expression of prostate cancer cells (C42B and C42B-Abiraterone resistant cells) were determined using RNA-seq. The RNA-seq experiment were performed with C42B cells were recurrently exposed to increasing concentrations of Abiraterone (1~ 20 μM) by passage in media containing Abiraterone for 6 months in 10% FBS and stored for further analysis. The resistant cells generated from 20 µM Abiraterone were always maintained in media containing 5µM Abiraterone were referred to as C42B Abi (C42B Abiraterone resistance). Parental C42B cells treated with 1% DMSO were passaged alongside the Abiraterone treated cells as an appropriate control.C42B and C42B-Abi cells were maintained in RPMI 1640 with 10% FBS. All cells were maintained at 37°C in a humidified incubator with 5% carbon dioxide.

*** THIS SUBMISSION IS LACKING RAW DATA BECAUSE SUBMITTER FAILED TO COMPLY WITH GEO REQUIREMENTS ***

first: Sanjay

last: Gupta

middle: S


title: Synthetic self-adjuvanted lipopeptide vaccines conferred protection against Helicobacter pylori infection

city: chongqing

first: ruoyi

last: xue

address: GaoTanYan street

institute: unknown

summary: Helicobacter pylori (H. pylori) colonize the stomach epithelium of half the world's population and are responsible for a variety of digestive diseases and even stomach cancer. The protection against H. pylori infection depends primarily on the antigen-mediated mucosal and T cell responses. We hypothesized that lipopeptide vaccines obtained by covalently conjugation of Pam2Cys with strong mucosal adjuvant activity to the immunodominant epitope from protective antigens could induce protective responses against H. pylori infection. In this study, the synthetic lipopeptide vaccines, Hp4 (Pam2Cys modified UreB T cell epitope) and Hp10 (Pam2Cys modified CagA T/B cell combined epitope), induced the BMDCs maturation in vitro by activating a variety of pattern recognition receptors such as TLR, NLR and RLR. In addition, lipopeptide vaccines stimulated BMDCs to secret cytokines that have the potential to modulate T cell activation and differentiation. Although intranasal immunization with Hp4 or Hp10 elicited robust epitope-specific T cell responses in mice, only Hp10 conferred protection against H. pylori infection, possibly due to the fact that Hp10 also induced substantial specific sIgA response at mucosal sites. Interestingly, when two lipopeptide vaccines were administrated in combination, Hp4 elevated the protective response against H. pylori infection of Hp10, which was characterized by better protective effect and enhanced specific T cell and mucosal antibody responses. Our results suggest that synthetic lipopeptide vaccines based on the epitopes derived from the protective antigens are promising candidates for protection against H. pylori infection.

overall_design: BMDCs were co-incubated with PBS, Hp4 or Hp10 for 48 hours, and 1ml Trizol was added to each well for re-suspension before collection. RNA-seq [22] library was generated and sequenced by Shanghai Sangon. The raw data of sequencing were evaluated by FastQC. Trimmomatic was used for quality cutting to obtain relatively accurate and effective data.

first: Ruo-Yi

last: Xue

first: Chang

last: Liu

first: Jia-Qi

first: Hai-Bo


title: Effect of GATA3 suppression gene expression in breast cancer cells.

city: Nanjing

first: Zhen

last: Zhu

address: 101Longmian Avenue

institute: Nanjing medical university

summary: Neoadjuvant chemotherapy (NAC) is the major pre-treatment for breast cancer before surgery. Patients who achieve pathologic complete response (pCR) have a higher chance to receive lumpectomy and a better quality of life after neoadjuvant treatment. Luminal subtype breast cancer has poor NAC response compared with triple-negative breast cancer (TNBC) subtype. The molecular and cellular mechanisms underlying this chemoresistance are not fully understood. Here we report that the 17 featured transcriptional factors (TFs) in luminal and TNBC were identified. The association between 17 TFs and NAC pCR were analysis and exogenous luminal featured TF GATA3 overexpression promotes chemotherapy resistance in TNBC cell lines whereas its knockdown promotes sensitivity. In mechanism, we found that anthracycline based chemotherapy induces robust cellular ROS and Fe2+ overload in sensitivity cells; GATA3 mediates cell survival through repress CYB5R2 expression and Fenton reducing in DOX recycle which reduce cellular ROS and Fe2+ level during chemotherapy procedure. These founding altogether indicate that luminal featured transcription factor GATA3 enhance NAC resistance thorough repress ROS production and Fenton reducing. Breast cancer patient with GATA3 high expression might not suit for anthracycline based NAC regimen.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of control and GATA3 vector overexpresion cells.


title: Gene regulatory loops at lamina-associated domains

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are repressed, approximately ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to contact regulatory elements in LADs or outside LADs remains unclear. Here, we integrate transcriptomic, chromatin states, microscopy and publicly available enhancer-capture Hi-C data to show that expressed genes in LADs are able to connect to enhancers in LADs and inter-LADs. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with transcriptional regulation in this dynamic nuclear compartment.

overall_design: Using public enhancer capture Hi-C (ECHI-C) data for differentating adipocytes, we have analyzed enhancer connections in chromatin at the nuclear lamina in human primary adipose stem cells (ASCs).  We have mapped lamin A/C (LMNA/C) enrichment throughout the genome by ChIP-seq of lamin AC on Day 0, 1 and 3 of in vitro adipogenic differentiation. Six histone modifications (H3K4me3, H3K4me1, H3K27ac, H3K27me3, H3K36me3, and H3K9me3) were also mapped from proliferating ASC (Pro; day minus 2 before induction of differentiation) in culture to learn chromatin states. These datasets provide a genomic context to characterize sites of chromatin (enhancer) interactions in lamina-associated domains in the adipose lineage.

first: Sarah

middle: H

last: Pickering

first: Mohamed

last: Abdelhalim

first: Julia

last: Madsen-Østerbye


title: ATF3 Inhibits Cardiac Ferroptosis  by Directly Binding FANCD2 in Response to Myocardial Ischemia/Reperfusion Injury [RNA-Seq 2]

city: Guangzhou

first: Haiqiong

state: Guangdong

address: Gongye Avenue 253

institute: Zhujiang Hospoital, Southern Medical University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived neonatal mouse cells' transcriptome profiling (RNA-seq) to microarray method and to evaluate protocols for optimal high-throughput data analysis, to find the trageted genes regulated by ATF3 in Hypoxia/Reoxygenation(H/R)

overall_design: mRNA profiles of WT and ATF3-KO mouse neonatal cells with ATF3 re-expression after H/R model(WT_HR, KO_HR, KO_HA)

first: Aihua

last: Chen


title: Mammalian Pumilio Proteins Control Cellular Morphology, Migration, and Adhesion

city: Riverside

first: Fedor

last: Karginov

state: California

address: 900 University Ave

department: MCSB

institute: UC Riverside

summary: Pumilio proteins are RNA-binding proteins that control mRNA translation and stability by binding to the 3' UTR of target mRNAs. Mammals have two canonical Pumilio proteins, PUM1 and PUM2, which are known to act in many biological processes, including embryonic development, neurogenesis, cell cycle regulation and genomic stability. Here, we characterized a new role of both PUM1 and PUM2 in regulating cell morphology, migration, and adhesion in T-REx-293 cells, in addition to previously known defects in growth rate. Gene ontology analysis of differentially expressed genes in PUM double knockout (PDKO) cells for both cellular component and biological process showed enrichment in categories related to adhesion and migration. PDKO cells had a collective cell migration rate significantly lower than that of WT cells and displayed changes in actin morphology. In addition, during growth, PDKO cells aggregated into clusters (clumps) due to an inability to escape cell-cell contacts. Addition of extracellular matrix (Matrigel) alleviated the clumping phenotype. Collagen IV (ColIV), a major component of Matrigel, was shown to be the driving force in allowing PDKO cells to monolayer appropriately, however, ColIV protein levels remained unperturbed in PDKO cells. This study characterizes a novel cellular phenotype associated with cellular morphology, migration, and adhesion which can aid in developing better models for PUM function in both developmental processes and disease.

overall_design: RNAseq of WT and PUM1,2 KO T-Rex-293 and HCT116 cells, and GFP-, PUM1-, and PUM2-rescue lines of PUM1,2 KO T-Rex-293 cells

first: Erin

last: Sternburg

first: Jordan

last: Lillibridge


title: ATF3 Inhibits Cardiac Ferroptosis  by Directly Binding FANCD2 in Response to Myocardial Ischemia/Reperfusion Injury [RNA-Seq 1]

summary: The goals of this study are to compare  mice heart tissues' transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis, and find the potential molecule implicating in myocardial ischemia/reperfusion injury.

overall_design: mRNA profiles of wild-type (WT) mouse heart tissues after ischemia for 45 min followed by different reperfusion durations(I/R 0.5h, 1.0g, 1.5h, 3.0h, 6.0h, 12h) by deep sequencing, in triplicate.


title: Analysis of the expression profiles of back skin and spontaneous back skin tumor-derived fibroblasts FACS-sorted from mice overexpressing oncogenes of human papilloma virus 8 in keratinocytes.

city: Chicago

first: Mateusz

last: Wietecha

state: IL

address: 801 S Paulina St

department: Oral Biology

institute: University of Illinois Chicago

summary: Overexpression of the oncogene HPV8 in keratinocytes of mice causes spontaneous papillomas to form in the skin. To study the expression profiles of skin cancer-associated fibroblasts, we performed RNA-sequencing of fibroblasts FACS-sorted from back skin tumors of HPV8 overexpressing mice.

overall_design: CD45-negative/CD140a-positive live cells (fibroblasts) were FACS-sorted from back skin papillomas/tumors (Tu) of  HPV8 overexpressing mice and the intact back skin (BS) of their age-matched littermates. Two tumors of 70- and 78-week-old animas were analyzed, along with six BS samples of 68-, 69- and 70-week-old animals, which were pooled to achieve adequate fibroblast cell numbers. The expression profiles of the sorted fibroblasts were analyzed by RNA-sequencing.

first: Sabine

last: Werner


title: Transcriptomic profiling of freshly isolated primary adult human alveolar epithelial type 2 cells (AEC2s), their isogenic cultured progeny, and human iPSC-derived AEC2s (iAEC2s)

city: Boston

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: We performed transcriptomic profiling of freshly isolated primary adult human alveolar epithelial type 2 cells (AEC2s), their isogenic cultured progeny, and human induced pluripotent stem cell-derived AEC2s (iAEC2s). Distal lung preparations from adult donor lung explants from two individuals were cryopreserved using methods we have previously described. Primary AEC2s were purified using fluorescence activated cell sorting (FACS) to isolate cells co-expressing EPCAM and HTII-280. To establish cultures of primary AEC2s, these cells were combined with MRC5 fibroblasts at an 1:10 ratio on cell culture inserts in CK+DCI medium. iAEC2s were derived using our previously published lung directed differentiation protocol. We used the SPC2 human iPSC line and specifically the SPC2-ST-B2 (SFTPC tdT/WT ) clone containing a SFTPC tdTomato knock-in reporter. SFTPC tdTomato+ cells were sorted on day 41 of differentiation. iAEC2s were single-cell passaged in self-renewing feeder-free 3D cultures approximately every 2 weeks. We used the 10X Chromium System to generate single-cell transcriptomic data from 5 samples prepared in parallel and sequenced on the same day. We profiled (a) preculture primary AEC2s, (b) cultured primary AEC2s, (c) 3D feeder-free iAEC2s, (d) feeder-free iAEC2 cultured on cell culture inserts, and (e) iAEC2s cultured on cell inserts with MRC5 fibroblasts. The cultured primary AEC2 samples and the iAEC2 sample co-cultured with MRC5s were sorted for live EPCAM+ cells prior to encapsulation. All other samples were sorted for live cells. We find that although each population (fresh, primary cultured, and iPSC-derived AEC2s) occupies a distinct transcriptomic space, both cultured primary AEC2s and cultured feeder-free iAEC2s closely resemble their primary pre-cultured counterparts. We also find a continuum of progressively more proliferative states (from fresh primary to cultured primary to cultured iAEC2s) inversely associated with progressively less mature AEC2 states.

overall_design: Global transcriptomic profiling of freshly isolated primary adult human alveolar epithelial type 2 cells (AEC2s), their isogenic cultured progeny, and human iPSC-derived AEC2s (iAEC2s) by single-cell RNA sequencing (scRNA-seq).

first: Konstantinos-Dionysios

last: Alysandratos

first: Darrell

middle: N

last: Kotton

first: Carolina

last: Garcia de Alba Rivas

first: Barry

last: Stripp

first: Carla

middle: F

last: Kim


title: Effect of Tubeimoside I (TA) on the innate immunity in C57BL/6 mice

status: Public on Dec 31 2022

first: Xiangfeng

address: Yuhangtang Road

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

summary: A saponin monomer Tubeimoside I (TA) was found to have potential adjuvant activity. Since the adaptive immune response is mediated by innate immunity, we took the immune injection site (quadriceps femoris muscle) as the local immune microenvironment, and injected TA (50 μg) into quadriceps muscle to prepare samples. Muscles injected with PBS were served as the negative control. RNA was extracted 4 hours after drug treatment, and samples were prepared for whole-gene transcriptome expression profile microarray detection.

overall_design: Mice were intramuscularly injected in the quadriceps with 50 μg TA dissolved in 50 µL of PBS, with each mouse injected in one leg only. The corresponding contralateral quadriceps were injected with an equal volume of PBS serving as the negative control. Quadriceps muscles were collected at 4 h after injection. The total RNA was extracted for microarray detection.

first: Z

middle: Y

last: Han

first: H

middle: X

last: Sun


title: MNase-seq facilitates quantitative analysis of nucleosome positioning of wild type and mutant SWI/SNF complexes

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

institute: University of Cambridge

summary:
Purpose: The goal of this study is to evaluate potentially direct targets of altered chromatin remodeller SWI/SNF on nucleosome positioning at gene promoters by means of MNase-sequencing from synchronised L1-staged swsn‑1 single mutant, swsn‑1; snfc‑5 double mutants, swsn‑1; snfc‑5; ubr‑5 triple mutants compared to wild-type animals to achieve genome-wide nucleosome coverage profiles.
Methods: In vivo MNAse-seq profiles of WT (N2), swsn-1-/- (MH2354, SX3714), swsn-1-/-; snfc-5-/- (SX3622, SX3715), swsn-1-/-; snfc-5-/-; ubr-5-/- (SX3627) C. elegans L1s were generated by deep sequencing, in duplicate, using Illumina NextSeq 2000. The sequence reads that passed quality filters were mapped to C. elegans (ce11) genome using bowtie2 aligner v.2.2.9. The resulting bam files were converted to bigwig tracks using deeptools bamCoverage.
Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the C elegans genome (build ce11). MNase-Seq data was further analysed locus-by-locus for nucleosome positioning around transcription start site of ubiquitous genes in the mutants relative to wild-type coverage. Swsn-1 single mutants showed strongly reduced +1 nucleosome coverage in compare to the wild-type animals. The +1-nucleosome coverage in both the swsn-1; snfc-5 double and swsn-1; snfc-5; ubr-5 triple suppressor mutants was higher than in swsn-1 single mutants. We also established that the subsets of ubiquitously up and downregulated SWI/SNF-dependent genes have a higher nucleosome coverage in wild-type animals when compared to all ubiquitous genes in wild-type animals.

overall_design: In vivo MNAse-Seq profiles of WT, swsn-1-/-, swsn-1-/-; snfc-5-/- , swsn-1-/-; snfc-5-/-; ubr-5-/- C. elegans L1

first: Subhanita

last: Ghosh

first: Peter

last: Sarkies

first: Lisa

last: Lampersberger

first: Nicholas

middle: O

last: Burton


title: The Sesquiterpene Lactone-Rich Fraction of Inula helenium L. Enhances the Antitumor Effect of Anti-PD-1 Antibody in   Colorectal Cancer: Integrative Phytochemical, Transcriptomic, and Experimental Analyses

status: Public on Dec 30 2022

city: Daejeon

first: Sang-Min

last: Park

address: Youseong-Daero

department: College of Pharmacy

institute: Chungnam National University

summary: Treatment strategies combining immune checkpoint inhibitors with sesquiterpene lactones have attracted much attention as a promising approach for cancer treatment. We systemically analyzed gene expression profiles of cells in response to two major sesquiterpene lactones, alantolactone and isoalantolactone, and determined whether the sesquiterpene lactone-rich fraction of Inula helenium L. (SFIH) enhances the antitumor effect of anti-PD-1 antibody in MC38 colorectal can-cer-bearing mice. Gene expression and pathway analysis using RNA sequencing data were used to identify the SFIH-driven combined activity with anti-PD-1 antibody. The results showed that SFIH significantly enhanced the antitumor effect of anti-PD-1 antibody by reducing tumor growth and increasing the survival time of mice. Specifically, SFIH exhibited antitumor activity when com-bined with anti-PD-1 antibody, and the effects were further enhanced compared with monotherapy. An analysis of immune cells indicated that combination treatment with SFIH and anti-PD-1 an-tibody significantly increased the proportion of CD8+ T cells. Moreover, combination treatment enhanced antitumor immunity by decreasing the population of myeloid-derived suppressor cells and increasing the number of M1-like macrophages. Pathway enrichment analysis revealed that combination therapy activated immune-related pathways to a greater extent than monotherapy. In conclusion, our integrative analysis demonstrates that SFIH enhances the response of murine tumors to anti-PD-1 antibody. These findings provide insight into developing integrative ther-apeutics and molecular data for the use of natural products as an adjunct treatment for colorectal cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MC38 tumor tissues by SFIH and/or anti-PD-1 antibody treatment

first: Jaemoo

last: Chun


title: ATF3 Inhibits Cardiac Ferroptosis by Directly Binding FANCD2 in Response to Myocardial Ischemia/Reperfusion Injury

first: Haiqiong

last: Liu

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: ATF3 Inhibits Cardiac Ferroptosis by Directly Binding FANCD2 in Response to Myocardial Ischemia/Reperfusion Injury [ChIP-Seq]

summary: We performed ChIP-seq to find the trageted genes regulated by ATF3 in hypoxia/reoxygenation (H/R)using ATF3 antibody for ChIP.

overall_design: AC16 cells were divided to 2 groups, Control and H/R, after H/R, samples were collected for the subsequent protocols.

first: Aihua

last: Chen


title: P-TEFb promotes cell survival upon p53 activation by suppressing intrinsic apoptosis pathway

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: We used RNA sequencing to deciphere a molecular basis for the synthethic lethality of non-genotoxic p53 activation and P-TEFb inhibition.

overall_design: We treated HCT116 cell line in biological triplicates with DMSO, Nutlin-3a (10 uM), NVP-2 (20 nM), and Nutlin-3a (10 uM) together with NVP-2 (20 nM) for 8 hours.

first: Andrii

last: Bugai

first: Matjaz

last: Barboric


title: Transcriptomic and epigenomic signatures of bone marrow-derived myeloid cells and microglia in CNS autoimmunity [ATAC-seq]

city: Dallas

first: Victor

last: Salinas

address: 5323 Harry Hines Blvd.

department: Neurology

institute: University of Texas Southwestern Medical Center

summary: We previously identified a myeloid cell subset expressing the markers CD88 and CD317 upon induction of inflammation in a mouse model of CNS autoimmunity. Here, we use single cell transcriptomics and epigenomics to extensively phenotype these cells and determine their compartment of origin.

overall_design: CD88+CD317+ myeloid cells from CNS tissue of bone marrow chimeric mice were isolated at peak of disease by cell sorting and subject to single cell transcriptomic and epigenomic analysis.

first: Navid

last: Manouchehri

first: Rehana

last: Hussain

first: Olaf

last: Stüve


title: Transcriptomic and epigenomic signatures of bone marrow-derived myeloid cells and microglia in CNS autoimmunity [RNA-seq]


title: Role of CCN3 on Hs578T triple negative breast cancer cell line

city: Seoul

first: Incheol

last: Shin

address: Wangsimni-ro 222

department: Life science

institute: Hanyang university

summary: Transcriptome sequencing analysis of Hs578T control (CTRL sh) and CCN3 knockdown (CCN3 sh) cell lines. CCN3, also known as nephroblastoma overexpressed (NOV, NOVH), has been associated with cell migration, invasion, angiogenesis, adhesion and proliferation in several cancer types like Ewing’s sarcoma, glioma, prostate cancer, hepatocellular carcinoma, clear cell renal cell carcinoma, chondrosarcoma and melanoma. These results provide information about gene expression affected by CCN3 in triple-negative breast cancer cell lines.

overall_design: CCN3 knockdown and control cell lines were generated by retroviral transduction of control shRNA (pSUPER-CTRL) and CCN3 shRNA (pSUPER-CCN3 sh). Total RNA of each cell line was extracted by Tri-RNA Reagent (Favorgen). Each experimental group was analyzed using three independent biological replicates.

first: Seogho

last: Son


title: Novel metabolic adaptation promotes enhanced macrophage efferocytosis under a limited-oxygen environment

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

summary: Apoptotic cell clearance (efferocytosis), a process essential for organismal homeostasis, is performed by phagocytes that inhabit a wide range of environments, including physiologic hypoxia. Here, we find macrophages, the predominant tissue-resident phagocyte, display enhanced efferocytosis under chronic hypoxia, characterized by increased internalization and accelerated degradation of apoptotic cells. Analysis of mRNA and protein programs revealed that chronic hypoxia induces two distinct but complimentary states in macrophages. The first, ‘primed’ state consists of concomitant induction of transcriptional and translational programs broadly associated with metabolism in apoptotic cell-naïve macrophages that persist during efferocytosis. The second, ‘poised’ state consists of transcription, but not translation, of phagocyte function programs in apoptotic cell-naïve macrophages that are subsequently translated during efferocytosis. We discovered that one such primed state consists of the efficient flux of glucose into a noncanonical pentose phosphate pathway (PPP) loop, whereby PPP-derived intermediates cycle back through the PPP to enhance production of NADPH. Mechanistically, we found that PPP-derived NADPH directly supports enhanced efferocytosis under chronic hypoxia via its role in phagolysosomal maturation, while simultaneously maintaining cellular redox homeostasis. Thus, macrophages adapt to chronic hypoxia by adopting states that both support cell fitness and ensure ability to rapidly and safely perform essential homeostatic functions.

overall_design: The experiment consists of three conditions: Phagocytes (primary macrophages) condition in standard oxygen, acute hypoxia, or chronic hypoxia.  All conditions consisted of three biological replicates.

first: Ya-Ting

last: Wang

first: Alissa

last: Trzeciak

first: Waleska

last: Rojas

first: Pedro

last: Saavedra

first: Yan-Ting

first: Rachel

last: Chirayil

first: Jon

middle: I

last: Etchegaray

first: Christopher

middle: D

last: Lucas

first: Daniel

last: Puleston

first: Kayvan

last: Keshari


title: Extracellular vesicle microRNA profiling in synovial fluids and plasma from Oligoarticular Juvenile Idiopathic Arthritis patients: methodological challenges and identification of putative disease biomarkers

city: Genova

first: Federica

last: Raggi

address: via genrolamo gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

summary: New early low-invasive biomarkers are demanded for the management of Oligoarticular Juvenile Idiopathic Arthritis (OJIA), the most common chronic inflammatory arthritis in childhood and a leading cause of disability. Extracellular vesicles (EVs) released in the synovial fluid (SF) of inflamed joints have gained increased recognition as mediators of arthritis pathogenesis and as a source of biomarkers. No standardized protocol is available, yet, for the analysis of EV-derived microRNAs (EV-miRs) in human SF specimens, and their potential as biomarkers in OJIA has not been explored. This study proposes an optimized procedure for profiling EV-miRs in SF and represents the first investigation of the miRNome in EV isolated from OJIA patients at disease onset. We present data showing efficient recovery of EVs from SF aspirates and optimal profiling of their miRNA content. We identified a subset of 15 EV-miRs whose expression was deregulated in SF. Analysis of EV-miRs target genes evidenced the enrichemnt of processes related to inflammation, cartilage/bone homeostasis, hypoxia, and hormone metabolism, suggesting their contribution to disease pathogenesis and potential as new putative biomarkers. In addition, we detected altered expression levels of several circulating EV-miRs able to discriminate new-onset OJIA patients from control children. Among them, 16 were consensually overexpressed in both PL and SF from OJIA patients respect to controls, potentially representing a disease-associated molecular “fingerprint” measurable at both the systemic and local levels with high diagnostic potential. These results improve our understanding of OJIA molecular mechanisms and provide an important contribution in the search of new candidate biomarkers for early OJIA diagnosis and the design of novel tailored therapies.

overall_design: Thirteen patients newly diagnosed with OJIA at the Pediatric and Rheumatologic Department of the Gaslini Institute, Genova, Italy on the basis of the 2001 International League of Associations for Rheumatology (ILAR) classification criteria 1 were enrolled consecutively in the study from october 2018 through February 2020 (Table I). All patients  had clinically active disease, with joint effusion, swelling, pain, and stiffness, and underwent arthrocentesis and intra-articular steroid administration as part of routine clinical care. Arthrocentesis was performed with ultrasound guidance under local anesthesia or, in case of younger patients or multiple joints, under general anesthesia. Patients who were having anti-inflammatory treatment (steroids, disease-modifying anti-rheumatic drugs-DMARDs, or biological therapy) at the time of arthrocentesis were excluded from the study  . Eight age- and gender-matched children undergoing minor orthopedic procedures at the Gaslini Institute were enrolled as control group. Detailed clinical and laboratory examination of control subjects was carried out to rule out infections, inflammatory, and chronic diseases. The protocol of the study was reviewed and approved by the Ethical Committee of the Liguria Region (Approval 165/2018), and the procedures were carried out according to the approved guidelines and in adherence to the general ethical principles set forth in the Declaration of Helsinki. Written informed consent to participate to the study was obtained from the parents or the patient legal guardian prior to sample collection.

first: Davide

last: Cangelosi

first: Maria

middle: C

last: Bosco


title: Dual Targeting of EGFR and MTOR pathways inhibits glioblastoma growth by modulating the tumor microenvironment

city: San Francisco

first: Liliana

last: Soroceanu

address: 475 Brannan Street

institute: California Pacific Medical Center Research Institute

summary: In the current study we focused on identifying an effective therapeutic regimen for a cohort of human-derived GBM models driven by alterations in the EGFR pathway. Pharmacological testing based on the genomics characteristic of each patient-derived model demonstrated that no single drug is efficacious in inhibiting tumor cell viability in culture. Combining two targeting agents Erlotinib (Tarceva) and MLN0128 (investigational MTOR inhibitor) resulted in effective tumor cell killing across several GBM PDX- derived culture models. Mechanistically, inhibition of p-ERK, p-AKT and RSK pathways underlie the combinatorial drug effects in culture. Using an orthotopic primary-GBM model, we show that the two drugs combined resulted in significant improvement in survival, superior to either drug alone. Microarray RNA profiling of tumor tissues from treated mice showed that the anti-tumor efficacy of co-inhibiting EGFR and MTOR pathways was in part due to modulation of the tumor microenvironment, including downregulation of CCL2 and Periostin, and subsequent inhibition of TAM infiltration in treated tumors.

overall_design: RNA extracted from PDX samples from treated mice was used for microarray profiling. The samples include the following: 2 sham treated, 2 treated with the EGFR inhibitor Erlotinib, 2 treated with the MTOR inhibitor MLN0128 and 3 treated with a combination of Erlotinib and MLN0128. Analysis was focused on identifying DEG between treatment groups.

first: Mehdi

last: Nosrati


title: Myelodysplastic Syndrome-associated TET2/IDH mutations in Natural Killer cells disrupt their anti-tumor activity

city: Paris

first: Nicolas

last: Dulphy

address: 1, avenue Claude Vellefaux

department: Institut de Recherche Saint-Louis

institute: UNIV PARIS

type: Methylation profiling by high throughput sequencing

summary:
Myelodysplastic syndromes (MDS) are clonal hematopoietic disorders, representing high risk of progression to acute myeloid leukaemia, and frequently associated to somatic mutations, notably in the epigenetic regulator TET2. Natural Killer (NK) cells play a role in the anti-leukemic immune response via their cytolytic activity.
Here we show that patients with MDS clones harbouring mutations in the TET2 gene are characterised by phenotypic defects in their circulating NK cells. Remarkably, NK cells and MDS clones from the same patient share the TET2 genotype, and the NK cells are characterised by increased methylation of genomic DNA and reduced expression of Killer Immunoglobulin-like receptors (KIR), perforin, and TNF-α. In vitro inhibition of TET2 in NK cells of healthy donors reduces their cytotoxicity, supporting its critical role in NK cell function. Conversely, NK cells from patients treated with azacytidine (#NCT02985190; https://clinicaltrials.gov/) show increased KIR and cytolytic protein expression, and IFN-γ production. Altogether, our findings show that, in addition to their oncogenic consequences in the myeloid cell subsets, TET2 mutations contribute to repressing NK-cell function in MDS patients.

overall_design: Reduced representation bisulfite sequencing analysis were performed on NK cells and T cells sorted from TET2 wt and TET2 mut MDS/CMML patients, Three TET2 mut MDS/CMML patients were chosen based on a KIR2D expression on NK cells below 25%, and a TET2 mutation VAF superior to 45% in the cell bulk at diagnosis (TET2 mut KIR low patients: MUT22, MUT27, MUT33). One TET2 mut was chosen because of aKIR2D expression on NK cells at 90% to serve as control (TET2 mut KIR high patient: MUT14) with the TET2 wt patient (TET2 wt KIR high patient: WT13).

first: Maxime

last: Boy

first: Valeria

last: Bisio

first: Fabien

last: Guidez


title: Effects of functional ingredients on gut inflammation in Atlantic salmon (Salmo salar L)

status: Public on Dec 28 2022

city: Ås

first: Aleksei

last: Krasnov

state: Viken

address: Øreveien, 47B

institute: Nofima AS

summary: Intestinal inflammation, which is often observed in farmed salmon, is caused by anti nutrient in feed ingredients of plant origin. The aim of this study is to increase knowledge of this patholology and to assess effects of physiologically active compounds applied as feed additives.Feeding trial was followed with metabolomic, transcriptomic and bacterial meta genomic analyses.

overall_design: Six diets were tested including a feed with high level of fish meal (control). Package 1 (P1) contained 0.01% butyrate and 1.5% arginine and package 2 (P2) contained 0.1% β-glucan, 0.01% butyrate and 0.05% nucleotides. Soybean meal and corn gluten were tested alone and in combination with P1 and P2 (soybean meal) and P2 (corn gluten). Fish weighing 177 g was distributed in 18 tanks and reared during 67 days at 11.2C°.

first: Krasnov

last: Aleksei

first: Krogdahl

last: Åshild

first: Kortner

last: Trond


title: Transcriptomic Profiling of JEG-3 cells using human leiomyoma derived matrix.

status: Public on Dec 29 2022

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

summary: We studied morphological and transcriptional changes of JEG-3 cells, a trophoblast model, using a hypoxia microchip and human leiomyoma-derived matrix Myogel that mimics human tumor microenvironment.

overall_design:
We tested the influence of Myogel, fibrin, and poly-di-methyl-siloxane (PDMS) on cell morphology, adhesion, invasion, and RNA expression.

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: Samineh

last: Barmaki

first: Satu

last: Wedenoja


title: Construction of an artificial diploid Escherichia coli using a CRISPR-based chromosome-doubling technique

city: Tianjin

first: Pengju

last: Wang

address: 32 West Seventh Road, Airport Economic Zone, Dongli District

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: we designed a CRISPR-based chromosome-doubling technique to construct an artificial diploid Escherichia coli cell. The stable diploid E. coli was confirmed by quantitative PCR and third-generation genome sequencing.

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

overall_design: Total mRNA profiles of haploid and diploid Escherichia coli

first: Dongdong

last: Zhao

first: Ju

last: Li

first: Junchang

last: Su

first: Chunzhi

last: Zhang

first: Siwei

first: Zhubo

last: Dai

first: Xiaoping

last: Liao

first: Zhitao

last: Mao

first: Changhao

last: Bi

first: Xueli


title: Transcriptomics profiling of ccc_R08 for mechanism-of-action investigation with forward pharmacology

city: Basel

first: Jitao David

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

institute: F. Hoffmann-La Roche

summary: To investigate the mode of action of ccc_R08, a first-in-class orally available HBV cccDNA inhibitor, we designed and implemented two orthogonal and complementary approaches: a forward pharmacology approach and a reverse pharmacology approach. Bioinformatics analysis integrating biological knowledge with the observations from both approaches offered us preliminary insights into the mode of action of ccc_R08.

overall_design: In the forward pharmacology approach, we characterized the transcriptome profiles of HBV-infected PHH treated with the active compound ccc_R08, a less active compound ccc_R07 derived from the same chemical series with an identical backbone and with side-chain modifications, and DMSO as control.

first: Jitao

first: Yaling

first: Qihui

last: Zhu

first: Li


title: Transcriptomic and epigenomic signatures of bone marrow-derived myeloid cells and microglia in CNS autoimmunity

first: Victor

last: Salinas


title: Transcriptome analysis using RNA sequencing of the perilesional cortex in traumatic brain injury mice treated with CSF1R inhibitor or vehicle

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

summary: C57BL6 mice were subjected to a controlled cortical impact (CCI) to induce a unilateral traumatic brain injury (TBI). After surgery, mice were treated for 5 days with the CSF1R antagonist, PLX3397 or vehicle by daily i.p. injections. PLX3397 is an inhibitor of Colony Stimulating Factor receptor 1 (CSF1R) that leads to a depletion of microglial cells which was confirmed by immunohistochemistry in a subgroup of mice at day 5. Termination of PLX3397 allows for a repopulation of microglial cells which was near complete at 30 days, as assessed by immunofluorescence studies. Perilesional cortical tissue was obtained at the late time point of 30 days after TBI to assess lasting effects of microglia depletion for cortical reorganization that manifested at the transcriptional level. The RNAseq study was done in male and female mice (PLX3397 n = 5 male, 5 female; vehicle n = 5 male, 5 female). Behavioral scores for well-being and motor functions were obatined repeatedly during the observation time. Histology of brain lesion size, indices of neuronal damage and neuroinflammation were obtained at 5d and 30d after TBI. Microglia depletion (PLX3397 treatment) did not reduce the lesion volume and hindered phagocytosis and removal of the hematoma at 5 days, but reduced structural brain damage and neuron loss at 30 days after the injury. Neuroinflammatory markers tended to be lower in PLX3397 treated male than female mice which was associated with better neurological outcome. Overall, CSF1R inhibition provided only subtle lasting beneficial effects.

overall_design: RNA was extracted from perilesional cortex 30d after TBI in mice treated with PLX3397 (n = 10) or vehicle (n = 10) from d1-d5. RNA and was analyzed by RNA sequencing in 10 biological replicates per treatment group using an Illumina NovaSeq 6000 system.

first: Michael

middle: E

last: Schäfer

first: Matthias

last: Klein


title: Mapping of clonal lineages across developmental stages in human neural differentiation (Biological Replicates #2 and #3)

status: Public on Dec 27 2022

city: Shanghai

first: Zhiwen

last: You

address: 320 Yueyang Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

summary: The cell lineages across developmental stages remains to be elucidated. We developed single-cell split barcoding (SISBAR) to allow clonally tracking single-cell transcriptomes across stages in an in vitro model of human ventral midbrain-hindbrain differentiation. We developed “potential-spective” and “origin-spective” analysis to interrogate the cross-stage lineage relationships, and mapped a multi-level clonal lineage landscape depicting the whole differentiation process. We uncovered many previously uncharacterized converging and diverging trajectories. We demonstrated that a transcriptome-defined cell type can arise from distinct lineages that leave molecular imprints on their progenies, and the multi-lineage fates of a progenitor cell type represent the collective results of distinct rather than similar clonal fates of individual progenitors, each with distinct molecular signatures. Specifically, we uncovered a ventral midbrain progenitor cluster as the common clonal origin of midbrain dopaminergic (mDA) neurons, midbrain glutamatergic neurons, and vascular and leptomeningeal cells, and identified surface markers that can predict its lineage fate after transplantation and improve graft outcomes.

overall_design: We developed SISBAR method, which integrated virus-mediated cellular barcoding, clonal splitting, and scRNA-seq, to investigate the lineage relationships among cells across developmental stages in hPSC-based neural differentiation. SISBAR works by genetically labelling each progenitor cell with a unique viral barcode at an earlier differentiation stage, followed by limited cell division, and then randomly splitting the cells into two parts. Half of the cells are immediately subjected to scRNA-seq and viral barcode recovery, and the remaining cells are allowed to continue differentiating to a later stage, followed by scRNA-seq and viral barcode recovery. We designed three successive but independent labelling experiments to investigate the lineage relationships between stage I-II (Exp #1), stage II-III (Exp #2), and stage III-IV (Exp #3), respectively.

first: Luyue

first: Wu

last: Wei

first: Yuejun

last: Chen


title: Targeted down regulation of core mitochondrial genes during SARS-CoV-2 infection

city: Chapel Hill

first: Jonathan

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

summary:
SARS-CoV-2 polypeptides bind mitochondrial proteins, and the virus inhibits oxidative phosphorylation (OXPHOS) nuclear DNA (nDNA) gene transcription by blocking coordinately expressed genes of modular components of the OXPHOS holoenzymes. While initial nasopharyngeal infection is associated with the down regulation of OXPHOS genes, at death lung OXPHOS is up regulated. By contrast, heart, kidney, and liver nDNA gene expression remains suppressed, likely contributing to mortality. The virus also induces miR-2392 which inhibits mitochondrial DNA (mtDNA) transcription and the translation of mitochondrial cytosolic mRNAs. This concerted inhibition of OXPHOS activates HIF-1α inducing a pseudo-hypoxic state favoring viral biogenesis.
We interrogated the effects of SARS-CoV-2 infection by infecting BALB/c and C57BL/6 mice with the mouse-adapted SARS-CoV-2 MA10 virus and analyzed their lung transcripts at day 4 post infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from lungs isolated from two strains of mice, a subset of each infected with the mouse adapated SARS-n-CoV-2 MA10 virus strain.

first: Wes

last: Sanders

first: Victoria

middle: K

last: Baxter

first: Mark

middle: T

last: Heise


title: HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia [RNA-seq]

city: Cambridge

first: Sarah

middle: J

last: Horton

state: Cambridgeshire

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute - Department of Haematology

summary: This study identifies HOXA9 protein interactome in acute myeloid leukemia cells. Integrated genomic, transcriptomic and proteomic analyses further demonstrated that the HOXA9-SAFB-chromatin complex associates with NuRD and HP1γ to repress the expression of factors associated with differentiation and apoptosis in leukemia maintenance.

overall_design: Fusion oncoprotein MLL-AF9 positive acute myeloid leukemia cell line MOLM13, RNA-seq.

first: Brian

last: Huntly

first: Shuchi

last: Agrawal Singh

first: Dhoyazan

last: Azazi


title: HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia [CUT&RUN/ChIP-Seq]

overall_design: Fusion oncoprotein MLL-AF9 positive acute myeloid leukemia cell line MOLM13 and primary AML cells are used for all the genomics experiments. Genome-wide binding of 5 chromatin factors (HOXA9, SAFB, MTA2, GATAD2A. HP1g) and 3 histone H3 modifications (H3K27me3, H3K9me2, H3K9me3) were investigated using CUT&RUN approach in MOLM13 cells. All experiments performed and sequenced in replicates.


title: Explore the transcriptomic profiles of double-positive TAMs

city: Nanjing

first: Qianghu

last: Wang

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

summary: Several studies have described the existence of cells that co-express TAMs markers and tumor cell markers. Double-positive cells are formed by the hybridization of TAMs and GBM cells. The hybrids exhibit unique transcriptome profiles via nuclear reprogramming and contribute to GBM invasion. Another report stated that the double-positive cells are formed by the fusion of neoplastic cells and macrophages, and the fusion cells contribute to tumor heterogeneity and metastasis. However, few studies have investigated the immune regulatory functions of the double-positive cells in the GBM TME. Here, we isolated F4/80+GFP+ cells and F4/80+GFP– cells to explore the immune functions of double-positive TAMs.

overall_design: We isolated F4/80+GFP+ cells and F4/80+GFP– cells for RNA-seq.

first: Jian


title: Recycling of parental histones preserves the epigenetic landscape during embryonic development (RNA-seq)

city: Göttingen

first: Ufuk

last: Günesdogan

address: Justus-von-Liebig Weg 11

institute: University of Göttingen

summary: Epigenetic inheritance during DNA replication requires an orchestrated assembly of nucleosomes from parental and newly synthesized histones. We analyzed Drosophila HisC mutant embryos harboring a deletion of all canonical histone genes, in which nucleosome assembly relies on parental histones from cell cycle 14 onwards. Lack of new histone synthesis and parental histone recycling leads to more accessible chromatin and reduced nucleosome occupancy. This leads to upregulated and spurious transcription, whereas the control of the developmental transcriptional program is partially maintained. Importantly, the genomic positions of modified parental H2A, H2B, and H3 are restored during DNA replication. Therefore, the results suggest that parental histones with active or repressive marks are recycled to preserve the epigenetic landscape during DNA replication in vivo.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type embryos (w1118) and mutant embryos (Df(2L)HisC) lacking newly synthesized histones.

first: Herbert

last: Jäckle

first: Xiaojuan

last: Li

first: Oleksandr

last: Dovgusha

first: Dominik

last: Mühlen


title: Generation of functional oocytes from male mice in vitro.

city: Fukuoka

first: Kenta

last: Murakami

address: 3-1-1, Maidashi, Higashi-ku

department: Stem Cell Biology and Medicine

institute: Kyushu University

summary: Sex chromosome disorder greatly compromises gametogenesis in both males and females. In oogenesis, the presence of a Y chromosome or the loss of an X chromosome disturbs the robust production of oocytes. In this study, we efficiently converted the XY chromosome set into two X chromosomes without an extra Y chromosome in mouse pluripotent stem cells (PSCs). In addition, this chromosomal alteration successfully eradicated trisomy 16 in PSCs, which is a model of Down syndrome. The artificially produced euploid XX PSCs differentiated into mature oocytes in culture as efficiently as native XX PSCs. Importantly, by this means, induced pluripotent stem cells (iPSCs) from the tail of a sexually mature male differentiated into fully potent oocytes, which gave rise to offspring after fertilization. This study provides insights that could lead to a cure for infertility caused by sex chromosome or autosomal disorders, and paves a way forward to bipaternal reproduction.

overall_design: Examination of transcriptomes in GV and MII oocytes derived from sex converted and native XX ESCs

first: Katsuhiko

last: Hayashi


title: Recycling of parental histones preserves the epigenetic landscape during embryonic development

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

overall_design: Refer to individual Series


title: Gene expression profile at single cell level of DKO and TKO prostate tumor

status: Public on Dec 26 2022

city: Notre Dame

first: Xin

last: Lu

address: 109 Galvin Life Science Center

institute: University of Notre Dame

summary: To explore how Pygo2 expression in tumor cells regulate the TME, we used single cell RNA sequencing (scRNA-seq) to analyze  the  immune cell composition and activity change in tumor area

overall_design: Single cell suspension were obtained from nDKOLuc or nTKOLuc tumor at 10 week or 17 week post tamoxifen inducing,  singlce cells were labeled with hashtag and sent combined to load for 10xGenomics scRNA-seq

first: Yini

last: Zhu

first: Sheng

last: Liu

first: Jun

last: Wan


title: Recycling of parental histones preserves the epigenetic landscape during embryonic development (STRIPE-seq)

overall_design: Profiling of 5'capped mRNA and transcriptional initiation sites (transcription start regions) in whole Drosophila melanogaster embryos between 5.5 to 7 hours after egg laying. Wild type embryos (w1118) are compared with mutant embryos (Df(2L)HisC) lacking newly synthesized histones. Each analysis was conducted in quadruplicates or quintuplicates.


title: The Neurotoxin DSP-4 Dysregulates the Locus Coeruleus-Norepinephrine System and Recapitulates Molecular and Behavioral Aspects of Prodromal Neurodegenerative Disease

city: Atlanta

first: David

last: Weinshenker

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

summary:
To investigate changes in noradrenergic neurons of the LC following treatment with the specific neurotoxin DSP-4.
We then performed gene expression profiling analysis using data obtained from RNA-seq of Pre-IP and IP samples following DSP-4 or saline treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LC-mRNA (IP) for DSP-4 treated samples vs saline controls.

first: Alexa

last: Iannitelli


title: Dual host-pathogen RNA-sequencing of R. canadensis infected Vero cells in response to various compound treatments

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: The goal of this study is to utilize dual host-pathogen NGS to assess transcriptomic pertubations due to multiple drug compounds, and compare between compounds to identify putative mechanism of action for novel anti-Rickettsial compounds.

sample_organism:
Rickettsia canadensis
Chlorocebus sabaeus

overall_design: RNA sequencing of Vero cells infected with R. canadensis pRAM18dRGA+ and treated with multiple drug compounds (Doxycycline, Rifampin, Chloramphenicol, Duartin, JSF-3204) to assess comparative transcriptomes

first: Joel

last: Freundlich

first: Robert

last: Donnelly

first: Nancy

last: Connell


title: ZBTB12-HERVH-LncRNA axis is a molecular barrier for dedifferentiation of human pluripotent stem cells

city: Santa Barbara

first: Dasol

last: Han

address: University of California Santa Barbara

institute: University of California Santa Barbara


title: ZBTB12-HERVH-LncRNA axis is a molecular barrier for dedifferentiation of human pluripotent stem cells [RNA-seq]

summary: Development is generally viewed as one-way traffic of cell state transition from primitive to developmentally advanced states. However, molecular mechanisms that ensure the unidirectional transition remain largely unknown. NanoCAGE sequencing identified an evolutionarily conserved zinc finger repressor, ZBTB12, as a molecular barrier for dedifferentiation of human pluripotent stem cells (hPSCs). Single cell RNA sequencing revealed that ZBTB12 is essential for three germ layer differentiation by blocking hPSC dedifferentiation. Mechanistically, ZBTB12 cooperates with NANOG to fine-tune the expression of human endogenous retroviruses (HERVs). Active HERVH loci drive the expression of overlapping long non-coding RNAs (lncRNAs) whose downregulation by ZBTB12 is necessary for dedifferentiation blockage and pluripotency exit. Overall, we have identified a ZBTB12-HERVH-lncRNA axis as molecular machinery that safeguards the unidirectional transition of stem cell fates.

overall_design: Bulk RNA sequencing, Primed J1 mouse EpiSCs transduced with shControl or shZbtb12 lentivirus

first: Yujeong

last: Oh

first: Guojing


title: Recycling of parental histones preserves the epigenetic landscape during embryonic development (ATAC-seq)

first: Ufuk

last: Günesdogan

overall_design: Profiling of chromatin accessibility in whole Drosophila melanogaster embryos between 3.5 to 7 hours after egg laying. Wild type embryos (w1118) are compared with mutant embryos (Df(2L)HisC) lacking newly synthesized histones. Each timepoint and genotype was analyzed in triplicates.

first: Herbert

last: Jäckle

first: Xiaojuan

last: Li

first: Oleksandr


title: Identification of RNA information related to different skin color of golden-backed crucin carp

status: Public on Dec 25 2022

city: Wuxi

first: Mingkun

last: Luo

state: Jiangsu

address: East Shanshui Road 9

department: Wuxi Fisheries College

institute: Nanjing Agricultural University

type: Non-coding RNA profiling by high throughput sequencing


title: Malaria-driven expansion of adaptive-like functional CD56-negative NK cells correlates  with clinical immunity to malaria

city: Stanford

first: Prasanna

last: Jagannathan

state: CA

address: 240 Pasteur Drive Room 3456

department: Department of Medicine

institute: Stanford Universit

summary: Natural Killer (NK) cells likely play an important role in immunity to malaria, but whether repeated  malaria modifies the NK cell response remains unclear. Here, we comprehensively profiled the  NK cell response in a cohort of 264 Ugandan children. Repeated malaria exposure was  associated with expansion of an atypical, CD56neg population of NK cells that differed  transcriptionally, epigenetically, and phenotypically from CD56dim NK cells, including decreased  expression of PLZF and the Fc receptor g chain, increased histone methylation, and increased  protein expression of LAG-3, KIR and LILRB1. CD56neg NK cells were highly functional, displaying  greater antibody dependent cellular cytotoxicity than CD56dim NK cells, and higher frequencies of  these cells were associated with protection against symptomatic malaria and high parasite  densities. Importantly, following marked reductions in malaria transmission, frequencies of these  cells rapidly declined, suggesting that continuous exposure to malaria is required to maintain this  modified, adaptive-like NK cell subset.

overall_design:
Approximately 1,000,000 cells from 10 patient samples were stained with Human TruStain FcX Fc Blocking Reagent (BioLegend, 422302) for 10 min at room temperature. The cells were stained for 30 min at 4 °C. Cells were then washed twice with PBS supplemented with 2% FCS and 2 mM EDTA (Sigma) before resuspending in PBS and counting. Approximately 10,000 cells per sample were loaded onto the 10x Chromium controller.

ATAC-Seq was performed on 2 samples from the same Ugandan child: one in 2013 when malaria transmission was high, and one in 2015 when transmission had decreased due to insecticide spraying.

first: Maureen

last: Ty

first: Shenghuan

last: Sun


title: Inhibition of the ATM kinase rescues planarian regeneration after lethal radiation

city: ITHACA

first: Carolyn

last: Adler

state: NY

address: 930 Campus road

institute: Cornell University

summary: As stem cells divide, they acquire mutations that can be passed on to daughter cells. To mitigate potentially deleterious outcomes, cells activate the DNA damage response (DDR) network, which governs several potential cellular outcomes following DNA damage, including repairing DNA or undergoing apoptosis. At the helm of the DDR are three PI3-like kinases including Ataxia Telangiectasia Mutated (ATM). We report here that knockdown of ATM in planarian flatworms enables stem cells to withstand lethal doses of radiation which would otherwise induce cell death. In this context, stem cells circumvent apoptosis, replicate their DNA, and recover function using homologous recombination-mediated DNA repair. Despite radiation exposure, atm knockdown animals survive long-term and regenerate new tissues. These effects occur independently of ATM’s canonical downstream effector p53. Together, our results demonstrate that in planarians, ATM regulates radiation-induced apoptosis. This acute, ATM-dependent apoptosis is a key determinant of long-term animal survival. Our results suggest that inhibition of ATM in these organisms could therefore potentially favor cell survival after radiation without obvious effects on stem cell behavior.

overall_design: Transcriptional profiling of X1 cells to determine the effect of atm knockdown

first: Kuang-Tse

last: Wang

first: Divya

middle: A

last: Shiroor


title: Promiscuous splicing-derived hairpins are dominant substrates of tailing-mediated defense of miRNA biogenesis in mammals

city: New York

first: Seungjae

last: Lee

address: 430 East 67th St.

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

summary: A canonical pathway generates microRNAs (miRNAs) via stepwise cleavage of hairpin precursors by RNase III enzymes Drosha and Dicer, followed by loading of resultant ~22 nucleotide (nt) RNAs into an Argonaute (Ago) effector complex. In addition, non-canonical substrates can bypass either RNase III enzyme to yield functional small RNAs, including hundreds of intron-derived hairpins that comprise pre-miRNA mimics that bypass Drosha (i.e., mirtrons). Here, we show that mirtron breadth is much larger than currently appreciated, since hundreds of novel splicing-derived hairpins are detected in intermediate (~50-100 nt) but not small (20-30nt) RNA data. Since mirtrons were originally defined on the basis of small RNA duplexes, we term the larger set of loci as structured, splicing-derived RNAs (ssdRNAs). Although individual species generally accumulate modestly, these are broadly detected in Dicer and/or Ago complexes and can mediate repression in directed assays. Nevertheless, their extremely poor conservation suggests they do not generally benefit regulatory networks, and may instead contaminate the canonical miRNA pathway. In aggregate, ssdRNAs/mirtrons comprise the dominant hairpin substrates for 3' tailing by multiple terminal nucleotidyltransferases, notably TUT4/7 and TENT2. We provide evidence that hairpin tailing is inhibitory for ssdRNA/mirtron biogenesis and/or function, and that this pathway has restricted the evolution of canonical pre-miRNAs that resemble splicing products. Overall, the rampant proliferation of evolutionary young mammalian mirtrons, coupled with an attendant molecular defense, comprises a Red Queen's race of intragenomic conflict.

overall_design: Comparative small RNA expression profiling analysis for HEK293T cells and its TUTase KO derivatives. Ago2-associated intermediate (50-80 nt) RNA profiling from K562 cells

first: David

last: Jee

first: Sid

last: Srivastava

first: Acong

last: Yang

first: Abhinav

last: Ramidi

first: Renfu

last: Shang

first: Diane

last: Bortolamiol-Becet

first: Sebastian

last: Pfeffer

first: Shuo

last: Gu

first: Jiayu

last: Wen

first: Eric

last: Lai


title: Identification of mRNA information related to different skin color of golden-backed crucin carp

first: Mingkun

last: Luo

summary: In order to explore the regulatory information of the two different color associations in crucian carp, we identified the differential mRNAs of gold and greenish grey by transcriptome sequencing, and analyzed their functional and pathway enrichment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for gold and greenish grey skin of crucian carp.

first: Xianbo

last: Zhang

first: Webin

last: Zhu

first: Zaijie

last: Dong


title: The differential impact of maternal age on heart, brain, face, and placental development

status: Public on Dec 24 2022

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Drive NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

summary: Investigating the impact of maternal age on heart, brain, face, and placental development by using RNA-seq to compare these tissues at E10.5 from young vs. aged females

overall_design: Comparative gene expression profiling analysis based on RNA-seq data for the placenta, heart, brain, and face of E10.5 embryos from young vs. aged C57BL/6 females

first: C

last: Kokorudz

first: B

last: Radford

first: W

last: Dean

first: M