title: Multi-omics analysis of small RNA, transcriptome and degradome in T. turgidum – regulatory networks of grain development and abiotic stress response

city: Urrbrae

first: Haipei

last: Liu

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

summary: Crop reproduction is highly sensitive to water-deficit and heat stress. The molecular networks of stress adaptation and grain development in tetraploid wheat (T. turgidum durum) are not well understood. Small RNAs (sRNAs) are important epigenetic regulators connecting the transcriptional and post-transcriptional regulatory networks. This study presents the first multi-omics analysis of the sRNAome, transcriptome and degradome in T. turgidum developing grains, under single and combined water-deficit and heat stress. We identified 690 microRNAs (miRNAs), with 84 being novel, from 118 sRNA libraries. Complete profiles of differentially expressed miRNA (DEMs) specific to genotypes, stress types and different reproductive time-points are provided. The first degradome-seq report for developing durum grains discovered a significant number of new target genes regulated by miRNAs post-transcriptionally. Transcriptome-seq profiled 53,146 T. turgidum genes, with differentially expressed genes (DEGs) enriched in functional categories such as nutrient metabolism, cellular differentiation, transport, reproductive development and hormone transduction pathways. miRNA-mRNA networks that affect grain characteristics such as starch synthesis and protein metabolism were constructed, based on integrated analysis of the three omics. This study provides a substantial amount of novel information on the post-transcriptional networks in T. turgidum grains, which will facilitate innovations for breeding programs aiming to improve crop resilience and grain quality.

overall_design: Analysis of small RNA transcriptome in 118 samples (2 genotypes × 4 treatments × 5 time-points × 3 biological replicates); Analysis of mRNA transcriptome in eight libraries (2 genotypes × 4 treatments × 1 time-point × 1 pool of 3 biological replicates); Analysis of mRNA degradome in eight libraries (2 genotypes × 4 treatments × 1 time-point × 1 pool of 3 biological replicates)

first: Amanda

middle: J

last: Able

first: Jason

middle: A


title: Tcf1 and Lef1 regulate follicular helper T cell function eliciated by vaccination

status: Public on Oct 19 2020

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

country: USA

institute: Roswell Park Comprehensive Cancer Center

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Tcf1 and Lef1 regulate follicular helper T cell function eliciated by vaccination [CUTnRUN]

summary: The goal of this study is to determine the impact of Tcf1 and Lef1 deficiency on T follicular helper (Tfh) cells elicited by protein immunization. We demonstrate that although phenotypic Tcf1/Lef1-deficient Tfh cells were able to develop in response to vaccination, they are functionally impaired. Mechanisc studies reveal the direct regulatory effect by Tcf1 and Lef1 on transcriptome and chromatin accessibility in vaccine-elicited Tfh cells.

overall_design: Genome-wide mapping of Tcf1 binding in WT Tfh cells eliciated by vaccination.

first: Hai-Hui

last: Xue


title: The sea urchin larval response to metaloxide nanoparticule exposure

status: Public on Oct 17 2020

city: Banyuls-sur-mer

first: Anne-M

middle: Marie

last: GENEVIERE

address: Avenue Pierre Fabre

department: BIOM

country: France

institute: CNRS

summary: Engineered nanoparticles (ENPs) are increasingly used to generate innovative industrial and medical goods. Because of their broad applications, they form a new class of pollutants with potential eco-toxicological impacts on marine ecosystems. Attempting to evaluate the risk, we investigated the toxicity of Iron and Zinc oxide ENPs on Paracentrotus lividus sea urchin embryos. Sea urchin embryos are sensitive to both ENPs with a much stronger impact of ZnO ENPs. Transcriptome-wide analyses were conducted after exposure to ENPs or the corresponding ions. Only a very limited number of genes are differentially expressed in response to Fe2O3 ENPs or FeCl3. In contrast, both ZnO ENPs and ZnSO4 caused alteration of biological processes with stronger perturbation of gene expression for the ionic form (higher LFC). Comparison of GO term enrichment of the differentially expressed  genes indicated that ENP and ions elicited partly different mechanisms, suggesting that a nanoparticule-dependent response was induced. Remarkably, the expression of the metal binding and ROS scavenging Metallothioneins were massively induced by ZnO ENPs and ZnSO4 while ZnO ENPs and ions mainly repressed the transcription regulation processes which control embryo development.

overall_design: mRNA profiles of  24h post-fertilization control or treated embryos were generated by deep sequencing, using Illumina HiSeq 2500

first: Anne-Marie

last: Genevière

first: Christophe

last: Klopp


title: Tcf1 and Lef1 regulate follicular helper T cell function eliciated by vaccination [RNA-Seq]

overall_design: Transcriptomic analysis of WT and Tcf1/Lef1-deficient Tfh cells eliciated by vaccination.


title: Analysis of the response to PD1 therapy in B16R2L mouse melanoma tumors knockdown for Mdk.

status: Public on Oct 18 2020

city: Madrid

first: David

last: Olmeda

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

summary: Gene expression analysis in tumors generated by B16R2L cells injected in C57BL/6J mice and treated with anti-PD1 (clone RMP1-14, 10 gr/Kg) or the corresponding IgG2a control.

overall_design: 5x105 B16R2L mouse melanoma cells  control (shCtrl; Non-Target shRNA (CAACAAGATGAAGAGCACCAA)) or knockdown for mouse Mdk (shMdk-5 (NM_010784.4-734s1c1). When the tumor reached 100 mm3 the anaimals injected for each of the cell types were subdivided in 2 groups to be treated twice per week for 2 weeks with anti-PD1 (clone RMP1-14, 10 gr/Kg) or the corresponding IgG2a control. Quadriplicted tumors were excised and total RNA was extracted. 500ng of total RNA samples were used. Each condition was analyzed in quadruplicates.  Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions.

first: D

last: Cerezo-Wallis

first: O

last: Graña-Castro

first: M

middle: S

last: Soengas


title: Mouse transcriptome of two genetic mutations of Grm1

status: Public on Oct 16 2020

city: San Francisco

first: Zenghua

last: Fan

state: CA

address: 1550 4th Street

institute: University of California, San Francisco

summary: We report two genetic mutations of GRM1, which are Grm1-S458A and Grm1b-R889W, identified from two natural short sleep families. The introduction of these mutations into mouse models also causes the mice to sleepless. Thus, these findings suggest GRM1 is another short sleep gene and highlight the essential roles of mGluRs in regulating human sleep.

overall_design: Hippocampus transcriptome of four wildtype (WT) mice, four Grm1-S458A mice, and four Grm1b-R889W mice.

first: Guangsen

last: Shi

first: Lijuan

last: Xing

first: Ying-Hui

last: Fu


title: The Micomonas commoda response to metaloxide nanoparticule exposure

summary: Engineered nanoparticles (ENPs) are increasingly used to generate innovative industrial and medical goods. Because of their broad applications, they form a new class of pollutants with potential eco-toxicological impacts on marine ecosystems. Attempting to evaluate the risk, we investigated the toxicity of Iron and Zinc oxide ENPs on three picophytoplanktonic strains of algae: Micromonas commoda, Ostreococcus tauri and Nannochloris sp. Microalgae responses are highly species-dependent, Micromonas commoda growth being severely impaired by both ENP types whereas Ostreococcus tauri or Nannochloris sp. are resistant. ZnO ENPs have higher toxicity than iron ENPs though growth of M. commoda was severely inhibited by Fe2O3 ENPs. Transcriptome-wide analysis after exposure of M. commoda to ENPs shows that the altered biological processes mainly take place in the cytoplasm and that the response to ENPs is largely metabolic in nature: stimulation of carbohydrate metabolism, light harvesting processes and alteration of the nitrogen pathway.  In addition, a severe disruption of ribosome structure and translation processes is observed.

overall_design: mRNA profiles of Micromonas commoda cultures either control or after 48h metaloxide nanoparticles exposure were generated using Illumina HiSeq 3000


title: Gene expression profiles in CT26 syngeneic tumor tissues after EP4 antagonist TP-16(BY001), anti-PD-1 antibody or combination treatment

city: shanghai

first: lu

last: weiqiang

state: shanghai

address: 500 dongchuan

country: China

institute: East China Normal University

summary:
To explore the mechanisms resposible for the synergistic effect between  EP4 antagonist BY001 and anti-PD-1 antibody, we conducted a microarray analysis on gene expression profiles in CT26 syngenetic tumor tissues.
We used  Agilent SurePrint G3 Mouse GE V2.0 Array to detail gene expression after indicated treatments and identified the molecular mechanism during this process to facilitate further studies.

overall_design: Mice bearing CT26 tumors were treated with vehicle, TP-16(BY001), PD-1 antibody or TP-16(BY001) plus PD-1 antibody for two weeks. Samples were obtained from two independent biological replicates. RNA from each sample was labeled and hybridized using Agilent SurePrint G3 Mouse GE V2.0 Array.

first: Weiwei

last: Yu

first: Mingyao

first: Weiqiang

last: Lu


title: MaTAR25 lncRNA regulates the Tensin1 gene to impact breast cancer progression

city: Dunedin

first: Sarah

middle: D

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

summary: Misregulation of long non-coding RNA genes has been linked to a wide variety of cancer types. Here we report on Mammary Tumor Associated RNA 25 (MaTAR25), a nuclear enriched and chromatin associated lncRNA that plays a role in mammary tumor cell proliferation, migration, and invasion, both in vitro and in vivo. MaTAR25 functions by interacting with purine rich element binding protein B, and associating with a major downstream target gene Tensin 1 (Tns1) to regulate its expression in trans.  Knockout of MaTAR25 results in down-regulation of Tns1 leading to a reorganization of the actin cytoskeleton, and a reduction of focal adhesions and microvilli. The human ortholog of MaTAR25, LINC01271, is upregulated with human breast cancer stage and metastasis.

overall_design:
RNA-seq: Transcriptome profiles of MaTAR25 control and KO cells
ChIRP-seq: Chromatin Immunoprecipitation by RNA Purification (ChIRP) - seq of MaTAR25 in mammary tumor cells to identify MaTAR25 target genes

first: Kung-Chi

last: Chang

middle: L

last: Spector


title: Humanizing the Yeast Origin Recognition Complex

city: Hong Kong

first: Danny

last: Leung

address: Clear Water Bay

department: Division of Life Science

country: Hong Kong

institute: The Hong Kong University of Science & Technology

summary: The evolutionarily conserved Origin Recognition Complex (ORC), plays a key role in origin selection in eukaryotes. However, ORC is strikingly divergent in its DNA binding specificity, ranging from base-specific interactions in Saccharomyces cerevisiae to base-agnostic interactions in humans. The mechanisms underlying this distinct selectivity is unknown.  Atomic model of the yeast ORC showed that base-specific interaction with the invariant thymines of the ARS consensus sequence (ACS) is encoded by a 19-amino acid insertion helix (IH) embedded in the winged helix domain (WHD) of Orc4. This IH is absent in the Orc4 of metazoans including humans, suggesting that removal of the IH might give the yeast ORC “human-like” properties. Indeed, yeast strain engineered with IH deficient Orc4 has completely altered ORC-binding sites enriched in poly-dT tracts located in larger nucleosome-depleted and intergenic open chromatin.  In vivo and in vitro assays show that the mutant ORC loads MCM efficiently, in spite of its altered specificity in favor of binding patterns more characteristic of those observed in humans/metazoans. This work provides insights for understanding how ORC evolves to adopt a life cycle that requires plasticity in origin selection during development.

overall_design: 2 replicates for Myc-tag ORC ChIP-seq for G2/M arrested WT and mutant yeast cells. 2 replicates for FLAG-tag MCM ChIP-seq for G1 arrested WT and mutant yeast. 1 replicate for BrdU IP-seq for early S arrested WT and mutant yeast cells. 1 replicate for MNase-seq for G1 arrested WT and mutant yeast cells.  1 replicate for ATAC-seq for G2M arrested WT and mutant yeast cells.

first: Eric

middle: F

last: Cheung

first: Clare

middle: K

last: Lee

first: Vincy

last: Ho

first: YL

last: Zhai

first: BK

last: Tye


title: 4C-seq HD project

city: Basel

first: Jonathan

last: Seguin

address: Spitalstrasse 33

country: Switzerland

institute: UKBB-DBM

summary: Temporal dynamics and mechanisms underlying epigenetic changes in Huntington’s disease (HD),a neurodegenerative disease primarily affecting the striatum, remain unclear. Using slow progressing HDknockinmice,we have generated chromatin immunoprecipitation coupled with sequencing data for RNA polymerase II and histone modifications associated with active enhancers (H3K27ac) and repressive chromatin (H3K27me3), from neuronal, non-neuronal and bulk striatal tissue at two early disease stages. Data integration with cell type-specific transcriptomic databases shows that the HD mutation early accelerates age-related reprogramming of neuronal and glial cell identities at both epigenetic and transcriptional levels. Circular chromosome conformation capture followed by sequencing data using HD mouse striatum showed alterations both at neuronal super-enhancer and CAG expanded disease loci. Using these data to model higher-order chromatin architecture indicated that HD CAG expansion mutation impairs chromatin insulation and gene regulation. Thus, both age-dependent and disease locus-specific mechanisms contribute to early remodelling of chromatin structure in HD striatum.

overall_design: 4C-seq experiment in WT (2 replicates, 9 baits) and Knock-in Q140 homozygous (2 replicates, 9 baits) mice striatum at 6 months of age; WT (1 replicate, 3 baits) and R6/1 (1 replicate, 3 baits) mice striatum at 14 weeks of age and mouse ESC (1 replicate, 1 bait).

first: Karine

last: Merienne

first: Rafael

last: Alcala-Vida


title: DWARF WITH SLENDER LEAF1 encoding a histone deacetylase plays diverse roles in rice development

city: Tokyo

first: Fumika

middle: Clara

last: Kubo

address: 7-3-1 Hongo, Bunkyo-ku

department: School of Science, Department of Biological Sciences

country: Japan

institute: The University of Tokyo

summary:
To detect the genes that differentially expressed between dsl1 and wild type at the vegetative stage, we performed microarray analysis using Rice (US) gene 1.0 ST array.
We analyzed gene expression profiles of the shoot apices of WT and dsl1.

overall_design: The shoot apices including the SAM and P1-P4 primordia were sampled from the plants at the stage when the tips of the fifth leaves were just emerged.

middle: C

first: Sugisawa

last: Yukiko

first: Hiro-Yuki

last: Hirano


title: ChIP_HD_KI_3

overall_design: ChIP-sequencing of H3K27ac, H3K27me3 and RNA Pol II for WT and Knock-In Q140 mice striatum at 2 and 6 months of age (2 replicates per condition);  H3K9me3 for WT and Knock-In Q140 mice striatum at 6 months of age (1 replicate) and of H3K27ac and H3K27me3 in striatal NeuN sorted nuclei from WT mice at 20 weeks of age (2 replicates)


title: HIF1A signaling selectively supports proliferation of breast cancer in the brain

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital


title: Transcriptomes of ATG7 Knockout Microglia

status: Public on Oct 15 2020

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Multiple Sclerosis (MS) is a leading cause of incurable progressive disability in young adults caused by inflammation in the central nervous system (CNS) that triggers demyelination, glial cell dysfunction and irreversible neuro-axonal damage1. While considerable progress has been made in treating early inflammatory relapsing-remitting MS, the mechanisms underpinning the progressive stage remain largely unknown. The capacity of microglia, the CNS-resident phagocytes, to clear tissue debris is essential for both maintaining and restoring CNS homeostasis2,3 and this capacity diminishes with age4-6. Age strongly associates with the risk of developing progressive MS7,8. Herein we demonstrate that the recovery from inflammation is dependent on the ability of microglia to clear tissue debris and that blocking this process leads to development of progressive disease in a murine model of MS. Microglia-specific deletion of the general autophagy regulator Atg7, but not the canonical macroautophagy protein Ulk1, led to increased intracellular accumulation of phagocytosed myelin. This further associated with the alteration of the microglial phenotype towards that previously described in other neurodegenerative diseases2,3,9. Moreover, Atg7 deficient microglia showed striking similarities with microglia from aged wild type mice, which also demonstrated accumulation of myelin debris and inability to recover from MS-like disease. In contrast, the induction of autophagy using the disaccharide Trehalose in aged mice led to functional myelin clearance and remission from MS-like disease. Our results demonstrate that a non-canonical form of autophagy in microglia is responsible for myelin clearance and that impairment of this pathway markedly changes microglial phenotype and prevents recovery from MS-like disease. Importantly, we show that using a disaccharide ubiquitously found in plant-derived foods to boost autophagy in cells in which this process is naturally diminished can be utilized for therapeutic purposes.Project was run on 4 lanes with a 10M sequencing depth

overall_design: Transcriptome sequencing of WT and ATG7 knockout microglia during EAE on young and old mice.

first: Rasmus

last: Berglund


title: A Wnt-induced phenotypic switch in cancer-associated fibroblasts inhibits EMT in colorectal cancer

city: Frankfurt am Main

first: Mohammed

middle: Hossameldin

last: Mosa

state: Hessen

address: Paul-Ehrlich Str. 42-44

country: Germany

summary: Tumor progression is recognized as a result of an evolving crosstalk between tumor cells and their surrounding non-transformed stroma. Although Wnt signaling has been intensively studied in colorectal cancer (CRC), it remains unclear whether activity in the tumor-associated stroma contributes to malignancy. To specifically interfere with stromal signals, we generated Wnt-independent tumor organoids that secrete the Wnt antagonist Sfrp1. Upon subcutaneous transplantation into immuno-competent as well as -deficient mice, we observed strong reduction of tumor growth. Histological and transcriptomic analyses revealed that Sfrp1 induces an EMT (epithelial-mesenchymal transition) phenotype in tumor cells without affecting tumor-intrinsic Wnt signaling, suggesting involvement of non-immune stromal cells. Indeed, blockage of canonical signaling using Sfrp1, Dkk1, or fibroblast-specific genetic ablation of β-catenin strongly decreased the number of cancer-associated myofibroblasts (myCAFs). Interestingly, we found that the Wnt activity in CAFs is linked with distinct subtypes, where low and high levels induce an inflammatory-like CAF (iCAF) subtype or contractile myCAFs, respectively. Co-culture of tumor organoids with iCAFs resulted in massive upregulation of EMT markers, while myCAFs reverted this phenotype. In summary, we show that tumor growth and malignancy are differentially regulated via district fibroblast subtypes under the influence of juxtacrine Wnt signals.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Generation of Wnt-independent mouse tumor organoids that overexpress the Wnt antagonist Sfrp1 to block stromal Wnt signals and study the consequences on tumor growth and progression. Generated tumor lines were sequenced in vitro and upon sorting of Epcam+ and Pdgfrα+ cells from subcutaneous tumors. Stromal consequences were also studied of human xenografts after Sfrp1 overexpression. Moreover, mouse fibroblasts were cultured in the presence and absence of Wnt stimulation for validation.

middle: H

first: Birgitta

middle: E

last: Michels

first: Constantin

last: Menche

first: Adele

middle: M

last: Nicolas

first: Tahmineh

last: Darvishi

first: Florian

middle: R

last: Greten

first: Henner

last: Farin


title: Genome-wide Chromatin Accessibility and Sequencing of HPEKs

first: Guglielmo

last: Roma

address: Fabrikstrasse 22

institute: Novartis Institutes for Biomedical Research

summary: We report ATAC-seq (Assay for Transposase-Accessible Chromatin) on HPEKs treated in culture for 6h and 48h (6h+42h wash-out) with either 125nM NVS-BET1, 125nM NVS-BET2, or 0.0125% DMSO as control in triplicate per condition.

overall_design: Examination of genome-wide chormatin accessibility

first: Susan

last: Kirkland

first: Christian

last: Hauer

first: Sebastian

last: Bergling

first: Felix

last: Lohmann


title: Racial Disparities in Epigenetic Aging of the Right versus the Left Colon

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

type: Methylation profiling by genome tiling array

summary: Here, we present the first study showing race and side-specific differences in the trajectories of epigenetic aging in normal colonic mucosa. The cohort conisted of matched biopsies of left/right colon from healthy individuals (n=129). The majority of individuals were African American (n=89). Methylation arrays (Illumina EPIC) were performed on DNA extracted from fresh frozen biopsies taken at the time of colonoscopy. Our results provide novel insight of epigenetic aging underlying racial disparities in CRC. Side-specific colonic epigenetic aging may be a promising marker to guide interventions to reduce CRC burden.

overall_design: Matched left and right colon biopsies from 129 individuals were analyzed using the Illumina EPIC array.

first: Xiangqing

last: Sun

first: Fangcheng

last: Yuan

first: Gregory

last: Cooper

first: Joseph

last: Willis

first: Daniel

last: Weisenberger

first: Graham

last: Casey

first: Li

last: Li


title: Tcf1 and Lef1 regulate follicular helper T cell function eliciated by vaccination [ATAC-Seq]

first: Jianmin

last: Wang

summary:
The goal of this study is to determine the impact of Tcf1 and Lef1 deficiency on T follicular helper (Tfh) cells elicited by protein immunization. We demonstrate that although phenotypic Tcf1/Lef1-deficient Tfh cells were able to develop in response to vaccination, they are functionally impaired. Mechanisc studies reveal the direct regulatory effect by Tcf1 and Lef1 on transcriptome and chromatin accessibility in vaccine-elicited Tfh cells.
Analysis of chromatin accessibility in WT and Tcf1/Lef1-deficient Tfh cells eliciated by vaccination.

overall_design: WT or WT or Tcf1/Lef1-deficient Tfh cells were sort-purified from the lymph nodes, treated with TN5 transposase to generate tagged DNA fragments.

first: Hai-Hui

last: Xue


title: Gene expression of the A375 melanoma cell line treated with RAF inhibitors Vemurafenib  and  time-course with EGF stimulation during Vemurafenib RAF inhibitor treatment alone or with the MEK inhibitor Cobimetinib

first: Luca

last: Gerosa

address: 200 Longwood Avenue Warren Alpert Bldg, Apt2

department: Laboratory of Systems Pharmacology

institute: Harvard Medical School

summary: We treated for 24 hours the BRAF-V600E  melanoma cell line A375 with 7 doses of the RAF inhibitor Vemurafenib and, in a second experimental desing, we treated for 24 hours the BRAF-V600E  melanoma cell line A375 with Vemurafenib (1 uM) alone or in combination with the MEK inhibitor Cobimetinib (1 uM) and subsequently stimulated with EGF in a time-course of 7 time points for up to 8 hours (0, 0.5, 1, 2, 3, 4, 8 hours).

overall_design: We measured mRNA levels of the A375 cell line treated for 24 hours with 7 doses of the RAF inhibitor Vemurafenib in the range 0.001-10 uM and, in a second experimental design, mRNA levels of the A375 cell line treated for 24 hours with the RAF inhibitor Vemurafenib (1 uM) alone or in combination with the MEK inhibitor Cobimetinib (1 uM) and subsequently stimulated with EGF (100 ng/mL) in a time-course up to 8 hours


title: Immuno-priming with bevacizumab: durvalumab plus bevacizumab after prolonged exposition to bevacizumab in breast cancer

first: Orlando

last: Domínguez

address: Melchor F. Almagro 3

summary:
Purpose: To study the potential priming benefit of bevacizumab from subsequent immunotherapy (durvalumab) in advanced breast cancer patients
Methods: We tested this hypothesis by adding durvalumab after progression to maintenance single-agent bevacizumab treatment in advanced HER2-negative patients (average 3 treatment lines). In order to study the potential priming benefit, patients had to experience disease progression while on bevacizumab maintenance prior to entering the trial. In addition, we sought to find traits in peripheral-blood mononuclear cells (PBMCs) and tumor biopsies that informed about this immuno-priming, in an attempt to search for novel biomarkers of efficacy of the combo and obtain a better understanding of the biology of this clinical scenario.
Results: Patients that experienced clinical benefit, compared with the remaining patients, displayed a lymphocyte pattern in PBMCs consisting on increased T-effector subpopulations (CD4- and CD8- effector and effector-memory) and decreased immunosuppressive T-regulatory cells. Gene-expression studies in tumor samples showed a congruent pattern, with increased T-effector and memory T cell signatures in responders, and increased T-regulatory and decreased active dendritic cells in non-responders. These events were observed in patients that displayed vascular normalization features as a result of previous bevacizumab, supporting the immuno-priming effects of this strategy.

overall_design: mRNA profiles of 3 advanced breast patient samples that do not respond to therapy (non-Responders) and 3 patient samples that respond to therapy (Responders) samples were generated by deep sequencing.  Differential gene expression (DGE) analyses were performed.

first: Miguel

last: Quintela-Fandino

first: Esther

last: Holgado

first: Luis

last: Manso

first: Serafin

last: Morales

first: Begoña

last: Bermejo

first: Ramon

last: Colomer

first: Juan

last: Apala

first: Raquel

last: Blanco

first: Manuel

last: Muñoz

first: Eduardo

last: Caleiras

first: Vega

last: Iranzo

first: Mario

last: Martinez

last: Dominguez

first: Javier

last: Hornedo

first: Lucia

last: Gonzalez-Cortijo

last: Cortes

first: Ariadna

middle: G

last: Cudos

first: Diego

last: Malon

first: Antonio

last: Lopez-Alonso

first: Maria

last: Moreno-Ortiz

first: Silvana

last: Mouron

first: Santos

last: Mañes


title: The transcription factor ETS1 is a master regulator of human NK cell differentiation [ChIP-seq]

city: Ghent

first: Wouter

last: Van Loocke

state: East Flanders

address: C. Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Ghent University

summary: Natural killer (NK) cells are innate lymphoid cells that play a critical role in the direct immune defense against tumor cells and pathogens, and additionally have important immune regulatory functions by cytokine secretion. Whereas NK cell biology has been extensively studied in mouse models, transcriptional control of human NK cell differentiation is poorly understood. In this study, we generated ETS1-deficient human embryonic stem cell (hESC) clones using the CRISPR/Cas9 technology. In a complementary approach, we generated ETS1 loss-of-function cord blood hematopoietic stem cells (HSCs) by retroviral transduction of the dominant-negative ETS1 p27 isoform. We show that the transcription factor ETS1 is required for human NK cell differentiation. Transcriptome and ChIP analysis reveal that ETS1 directly regulates expression of several NK cell-linked transcription factors. Also, expression of genes involved in cytokine secretion and cytotoxic activity is ETS1-dependent, whereby these effector functions are decreased in residual NK cells developing from ETS1 loss-of-function cord blood hematopoietic stem cells. Our data show that ETS1 is a critical regulator of human NK cell development and function, and provide important insights in the underlying molecular mechanisms.

overall_design: For ChIP-seq peripheral blood mononuclear cells were first depleted of CD3 and CD19 cells by anti-CD3/19-biotine labeling followed by anti-biotin MACS depletion. NK cells were subsequently sorted as CD56+CD3- (residual CD3+ and CD19+ cells were identified via streptavidin staining) using a BD FACSAria III cell sorter. ChIP-seq was performed by Active Motif (Carlsbad, CA, U.S.A.) using 10 µl of anti-ETS1 Ab to precipitate protein-DNA complexes in 30 µg of chromatin.

first: Sylvie

last: Taveirne

first: Laurentijn

last: Tilleman

first: Filip

last: Van Nieuwerburgh

first: Georges

last: Leclercq


title: BRD4 Chromatin immunoprecipitation and Sequencing

first: Guglielmo

last: Roma

summary: We report BET bromodomain inhibitors (BETi) as regulators of keratinocyte stem cell fate. BETi displace BET proteins, including BRD4 from chromatin, inducing acute transcriptional changes at selected target genes. To gain insight into the compound mechanism of action, we assayed BRD4 chromatin occupancy genome-wide in keratinocytes subjected to BETi treatment. Specifically, BRD4 chromatin binding was analyzed following two treatments [125nM (low) versus 1250nM (high)] and three time points (30min, 6h and 6h treatment followed by compound removal for 3h (6m3h)).

overall_design: Examination of genome-wide BRD4 binding sites

first: Susan

last: Kirkland

first: Christian

last: Hauer

first: Sebastian

last: Bergling


title: Remodelling of whole-body lipid metabolism and a diabetic-like phenotype caused by loss of hepatic CDK1 and hepatocyte division

status: Public on Oct 14 2020

city: Singapore

first: Jin Rong

last: Ow

state: Singapore

address: 61 Biopolis Drive

department: Institute of Molecular and Cell Biology

country: Singapore

institute: A*STAR

summary: Purpose was to identify transcriptomic changes in whole liver and isolated hepatocytes from 12 month old wild type and Cdk1 liver-specific knock-out (Cdk1 Liv-/-) mice.

overall_design: RNA-seq of mRNA extracted from whole liver of 12 month old wild type or Cdk1 Liv-/- mice.

first: Matias

middle: J

last: Caldez

first: Soumita

last: Ghosh

first: Heike

last: Wollmann

first: Hyungwon

last: Choi


title: circRNA expression data from human non-small cell lung cancer tissues and the correponding non-cancerous tissues

city: Shanghai

first: Botai

last: Li

address: No. 25/Ln 2200 Xie-Tu Road

institute: Shanghai Jiao Tong University

summary: Circular RNAs (circRNAs) are a class of covalently closed single-stranded RNAs that have been demonstrated to involve in cancer progression. Here, we identify circNDUFB2 is downregulated in non-small cell lung cancer (NSCLC) tissues, and it negatively correlates with the malignant features. Elevated circNDUFB2 inhibits growth and metastasis of NSCLC cells. circNDUFB2 functions as a scaffold to enhance interaction of TRIM25 with IGF2BPs by forming a TRIM25/circNDUFB2/IGF2BPs ternary complex. The resultant ternary complex facilitates ubiquitination degradation of IGF2BPs, and N6-methyladenosine (m6A) modification of circNDUFB2 increases ubiquitination efficiency of TRIM25 for IGF2BPs. Moreover, circNDUFB2 can be recognized by RIG-I, then activates RIG-I-MAVS signaling cascades and recruits immune cells into tumor microenvironment (TME). Our data provide evidences that circNDUFB2 participates in degradation of IGF2BPs and activation of anti-tumor immunity in NSCLC progression. These findings reveal a dual-role pattern of circNDUFB2 action involved in protein ubiquitination degradation and cellular immune response.

overall_design: Total RNA from three pairs human non-small cell lung cancer tissues and correponding non-cancerous tissues were isolated and purified. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar’s Super RNA Labeling protocol (Arraystar Inc.). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (6x7K, Arraystar). After having washed the slides, the arrays were scanned by the Axon GenePix 4000B microarray scanner.

first: Lili

last: Zhu

first: Wenxin

last: Qin


title: A defect in G-quadruplex binding disrupts AID chromatin localization

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: Activation-induced cytidine deaminase (AID) plays a vital role in adaptive immunity by enabling class switch recombination (CSR) and somatic hypermutation (SHM). While many molecular factors affect AID targeting and function, mounting evidence implicates G-quadruplex (G4) nucleic acid structures as critical effectors of AID biology. To examine the function of AID-G4 binding in vivo, we generated a knock-in mouse with a mutation in Aicda (AIDG133V) that disrupts AID-G4 binding without altering DNA deaminase activity. AIDG133V mice completely lack CSR and SHM, modeling the pathology of hyper-IgM syndrome patients with an orthologous mutation. ChIP-sequencing experiments reveal a broad defect in AIDG133V chromatin localization, implicating AID-G4 binding in genome-wide AID targeting. We find that major histocompatibility complex (MHC) class II genes are AID targets, and that increased AID expression in diffuse large B-cell lymphomas (DLBCLs) correlates with decreased MHC class II expression. Given that loss of MHC class II expression in DLBCLs is highly correlated with adverse outcomes, AID-dependent gene regulation may provide a novel therapeutic target.

overall_design: WT, AID-/- or AID G133V/G133V splenic B cells were stimulated with LPS (30 μg/ml) plus mouse IL-4 (12.5ng/ml) for 72 hours and prepared for ChIP-seq assay.

first: Jayanta

last: Chaudhuri


title: Single-cell RNA sequencing and total RNA sequencing data, respectively, evaluating the expression of selective genes from C57BL/6 mouse-derived small intestinal organoids and whole ileal tissue from naïve Il22Ra1fl/fl;Defa6-cre+/- mice

city: Stony Brook

first: Pawan

last: Kumar

address: 100 Nicolls Road

institute: Stony Brook University

summary: All intestinal epithelial lineages express the IL-22 receptor; however, it is not known whether IL-22-dependent regulation of small intestinal host defense is dependent on ISCs or a specific epithelial lineages. To examine differences in gene expression among small intestinal enterocytes, single cell RNA sequencing was performed on primary small intestinal organoids derived from naïve C57BL/6 mice. Our scRNA-seq results demonstrate that Paneth cells express the highest level of Il22ra1 when compared to ISCs as well as enterocyte, goblet, tuft, and endocrine lineages. Additionally, total RNA sequencing (RNA-seq) of the terminal ileum of naïve Il22Ra1fl/fl;Defa6-cre+ (Paneth cell-specific IL22Ra1 knockout) and littermate cre- mice was performed. Our sequencing data revealed reduced expression of Paneth cell-specific Lyz1, Mmp7, and select alpha-defensin antimicrobial peptides but increased expression of IL-22 inducible Reg3g and serum amyloid genes (Saa1 and Saa3) in the terminal ileum of naïve Il22Ra1fl/fl;Defa6-cre+ mice

overall_design: N = 1 C57BL/6 mouse (4 replicates of organoids were pooled). N = 3 Il22Ra1fl/fl;Defa6-cre+ mice. N = 3 Il22Ra1fl/fl;Defa6-cre- mice

first: Stephen

last: Gaudino

first: Semir

last: Beyaz

first: Onur

last: Eskiocak

first: Brian

last: Yueh


title: Identification of a Midkine-associated gene expression profile in melanoma cells

first: David

last: Olmeda

address: Melchor Fernandez Almagro 3

institute: CNIO

summary: We performed gain-of-function (GoF) and loss-of-function (LoF) analyses of Midkine in melanoma cells by RNA-seq.

overall_design: For LoF, midkine was depleted in SK-Mel-147 (a melanoma cell line with high midkine levels and inherent metastatic potential) using MDK-sh5 (NM_002391.3-621s21c1). In turn, GoF studies were performed by overexpressing midkine in non-metastatic WM164 melanoma cells using ORF lentiviral expression vector pReceiver-Lv105-A0792 (MDK) .

first: D

last: Cerezo-Wallis

first: O

last: Graña

first: M

last: Soengas


title: BRAFV600E or mutant MAP2K1 human CD34+ cells establish Langerhans cell-like histiocytosis in immunodeficient mice

status: Public on Oct 12 2020

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

summary: We describe a xenograft model for human LCH-like disease in which we transduced human Cord Blood CD34+ HSPCs with a virus coding for BRAF-V600E - the most abundant pathognomonic somatic mutation occuiring in LCH. Cells were subsequently subjected to RNA-sequencing or transplanted into humanized MISTRG or NSG mice.

overall_design: CD34+ Cord Blood HSPCs were transduced with a Lentivirus coding for BRAF-V600E and GFP or with a control virus containing a GFP- and a Luciferase contruct instead of BRAF-V600E and were then kept in vitro for 5 days. Samples were then sorted for GFP expression and subjected to bulk RNA sequencing.

first: Anahita

last: Rafiei

first: Christian

last: Wilk

first: Patrick

last: Helbling

first: Markus

last: Manz


title: Smc3 regulates B-cell transit through germinal centers and restricts their malignant transformation (RNA-seq)

status: Public on Oct 13 2020

city: New York

first: Cem

last: Meydan

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

summary: During the germinal center (GC) reaction, B-cells undergo extensive redistribution of cohesin complex and 3D re-organization of their genomes. Yet, the significance of cohesin and architectural programming in the humoral immune response is unknown. Herein we report that conditional homozygous deletion of cohesin subunit Smc3 abrogated GC formation, yet in marked contrast, Smc3 haploinsufficiency induced GC hyperplasia, skewing of GC polarity and impaired plasma cell differentiation. Transcriptional and architectural profiling revealed defects in GC terminal differentiation programs controlled by lymphoma epigenetic tumor suppressors Tet2 and Kmt2d, and failure of Smc3+/- GC B-cells to switch from B-cell to plasma cell lineage factors. There was also impaired connectivity of gene regulatory elements controlling tumor suppressor genes, and accordingly Smc3 haploinsufficiency accelerated lymphomagenesis in mice with constitutive Bcl6 expression. Collectively, our data indicate a dose dependent function for cohesin in humoral immunity to facilitate the B-cell to plasma cell lineage switch, while restricting their malignant transformation.

overall_design: RNA from the spleen centrocytes was processed using the TruSeqRNA seq kit from Illumina to produce RNA-seq libraries

first: Martín

middle: A

last: Rivas

first: Christopher

last: Chin

first: Matt

last: Challman

first: Daleum

last: Kim

first: Bhavneet

last: Binder

first: Andreas

last: Kloetgen

first: Aaron

last: Viny

last: Teater

first: Dylan

last: McNally

first: Ashley

last: Doane

first: Wendy

last: Béguelin

first: María

middle: T

last: Calvo Fernández

first: Hao

last: Shen

first: Ross

last: Levine

first: Zhengming

last: Chen

first: Aristotelis

last: Tsirigos

first: Olivier

last: Elemento

last: Mason

first: Ari

last: Melnick


title: Smc3 regulates B-cell transit through germinal centers and restricts their malignant transformation (Mint-ChIP)

first: Cem

last: Meydan

overall_design: Mint-ChIP sequencing was performed with 3 replicates of wild-type germinal center (GC) cells using H3K27Ac antibody (Cat#39133, lot 31814008) from Active Motif following the protocol from the Berstein lab.

first: Martín

last: Rivas

last: Chin

last: Challman

middle: S


title: Nociceptive nerves regulate haematopoietic stem cell mobilization

city: Bronx

first: Paul

last: Frenette

address: 1301 Morris Park Avenue , Room 101

department: Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research

institute: Albert Einstein College of Medicine

summary: Nociceptive neuropeptide CGRP acts directly on HSCs via the its receptor RAMP1/CALCRL, to promote egress by activating Gαs/Adenylyl cyclase/cAMP pathway.

overall_design: mRNA profiles of sorted bone marrow hematopoietic stem cells were generated from Ramp1+/+ and Ramp-/- mice in triplicates by Illumina Platform

first: Xin

last: Gao


title: Expression data from female C57BL/6J and B6.Cg-Mir146atm1.1Bal/J mice after 10 weeks of normal or high fat diet

city: Ulm

first: Julian

last: Roos

department: Department of Pediatrics and Adolescent Medicine

institute: Ulm University Medical Center

summary: The pathogenesis of obesity-related metabolic diseases has been linked to the inflammation of white adipose tissue (WAT), but the molecular interconnections are still not fully understood. MiR-146a controls inflammatory processes by suppressing pro-inflammatory signaling pathways. The aim of this study was to characterize the role of miR-146a in obesity and insulin sensitivityresistance  . MiR-146a-/- mice were subjected to a high fat diet followed by metabolic tests and WAT transcriptomics. Gain- and loss-of-function studies were performed using human Simpson-Golabi-Behmel syndrome (SGBS) adipocytes. Compared to controls, miR-146a-/- mice gained significantly more body weight on a high fat diet with increased fat mass and adipocyte hypertrophy. This was accompanied by exacerbated liver steatosis, insulin resistance, and glucose intolerance. Likewise, adipocytes transfected with an inhibitor of miR-146a displayed a decrease in insulin-stimulated glucose uptake, while transfecting miR-146a mimics caused the opposite effect. Natriuretic peptide receptor 3 (NPR3) was identified as a direct target gene of miR-146a in adipocytes and CRISPR/Cas9-mediated knockout of NPR3 increased insulin-stimulated glucose uptake and enhanced de-novo lipogenesis.  In summary, miR-146a regulates systemic and adipocyte insulin sensitivity via downregulation of NPR3.

overall_design: 5 samples/group; groups: C57BL/6J normal diet (ND), C57BL/6J high fat diet (HFD), B6.Cg-Mir146atm1.1Bal/J ND , B6.Cg-Mir146atm1.1Bal/J HFD

first: J

first: M

last: Dahlhaus

middle: B

last: Funcke

last: Kustermann

first: G

last: Strauss

first: D

last: Halbgebauer

first: E

last: Boldrin

first: K

last: Holzmann

first: P

last: Möller

first: BM

last: Trojanowski

first: B

last: Baumann

last: Debatin

last: Wabitsch

last: Fischer-Posovszky


title: meCLICK-Seq -  substrate-hijacking and RNA degradation strategy for the study of RNA methylation

city: Cambridge

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: University of Cambridge

type: Methylation profiling by high throughput sequencing

summary: The method hijacks RNA methyltransferase activity to introduce an alkyne, instead of a methyl, moiety on RNA. Subsequent copper(I)-catalyzed azide–alkyne cycloaddition (CuAAC) with an imidazole-degrader leads to RNA cleavage and degradation, exploiting a mechanism used by endogenous ribonucleases. Focusing on N6-methyladenosine (m6A), we compare Slick-Seq to current state-of-the-art methods used to study of this modification, and show that the platform identifies methylated transcripts, determines RNA methylase specificity, and reliably maps modification sites in intronic and intergenic regions. Importantly, we discovered that METTL16 deposits m6A to intronic polyadenylation (IPA) sites, which suggests a potential role of METTL16 in IPA and, in turn, splicing. Unlike previously reported methods, Slick-Seq allows a comprehensive and dynamic study of RNA modifications throughout the transcriptome, including regions of low abundance.

overall_design: We have developed Slick-Seq (Surrogate-Click-Degradation-Sequencing), a small-molecule-based method for the study RNA methylation, the most abundant RNA modification.

first: Sigitas

last: Mikutis

first: Eliza

last: Yankova

first: Hannah

last: Kiely-Collins

first: Demetrios

last: Aspris

first: George

last: Vassiliou

first: Konstantinos

last: Tzelepis

first: Gonçalo

last: Bernardes


title: Effect of folic acid deprivation on on transcriptome upon OTX treatment

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

institute: Inserm

summary: Deciphering the impact of metabolic intervention on response to anticancer therapy represents a path toward improved clinical responses. Here, we identify amino acid-related pathways connected to the folate cycle whose activation predicts sensitivity to MYC-targeting therapies in acute myeloid leukemia (AML). We establish that folate restriction and deficiency of the rate-limiting folate-cycle enzyme, MTHFR ― which exhibits reduced-function polymorphisms in about 10% of Caucasians ― enhance resistance to MYC targeting by BET and CDK7 inhibitors in cell lines, primary patient samples and syngeneic mouse models of AML. Further, this effect is abrogated by supplementation with the MTHFR enzymatic product, CH3-THF. Mechanistically, folate cycle disturbance reduces H3K27/K9 histone methylation, and activates a SPI1 transcriptional program counteracting the effect of BET inhibition. Our data provide a rationale for screening MTHFR polymorphisms and the folate cycle status to exclude patients least likely and nominate those most likely to benefit from MYC-targeting therapies.

overall_design: Two AML cell lines IMS-M2 and U937, supplemented with or without FA, were treated with OTX. RNAseq was performed on these samples using TruSeq Stranded mRNA LT Sample Prep Kit for library preparation.

first: Alexandre

last: Puissant


title: Defining totipotency using criteria of increasing stringency

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

institute: KU Leuven

summary: Totipotency is the ability of a single cell to give rise to all the differentiated cells that build the conceptus, yet how to capture this property in vitro remains incompletely understood. Defining totipotency relies upon a variety of assays of variable stringency. Here we describe criteria to define totipotency. We illustrate how distinct criteria of increasing stringency can be used to judge totipotency by evaluating candidate totipotent cell types in the mouse, including early blastomeres and expanded or extended pluripotent stem cells. Our data challenge the notion that expanded or extended pluripotent states harbor increased totipotent potential relative to conventional embryonic stem cells under in vivo conditions.

overall_design: Mouse ESCs grown in 2i/LIF are switched to L-EPSC medium and total RNA was collected at day (D) 0, D3, D5, D7, D9, D11, D13 and D15.

first: Eszter

last: Posfai

first: John

middle: P

last: Schell

first: Adrian

last: Janiszewski

first: Isidora

last: Rovic

first: Alex

last: Murray

first: Brian

last: Bradshaw

first: Tine

last: Pardon

first: Mouna

last: Bakkali

first: Irene

last: Talon

first: Natalie

last: De Geest

first: Pankaj

last: Kumar

first: Sophie

last: Petropoulos

first: Andrea

last: Jurisicova

first: Fredrik

last: Lanner

first: Janet

last: Rossant


title: Epigenetic Profiling of Cardiac Pacemaker Cells Reveals a Conserved Isl1 Enhancer That Regulates Sinoatrial Node Development and Function

city: San Francisco

first: Ravi

last: Mandla

address: 555 Mission Bay Blvd South

department: Medicine - Cardiology

institute: UC San Francisco

summary: Cardiac pacemaker cells (PCs) in the sinoatrial node (SAN) have a distinct gene expression program that allows them to fire automatically and initiate the heartbeat. Although critical SAN transcription factors, including Isl1, have been identified, the cis-regulatory architecture that governs PC-specific gene expression is not understood, and discrete enhancers required for gene regulation in the SAN have not been identified. We used ATAC-Seq on sorted neonatal mouse SAN to define regions of open chromatin in PCs and neighboring right atrial cardiomyocytes. PC-specific ATAC-seq peaks were located near established SAN genes and were enriched for distinct sets of transcription factor binding sites. In-vivo testing of a novel ATAC-seq peak at the Isl1 locus defined a regulatory element that was active specifically in the cardiac inflow at E8.5 and throughout later SAN development and maturation. Deletion of the enhancer uncovered a role for this cis-regulatory element in SAN development and function. The mouse SAN enhancer also directed reporter activity to the inflow tract in developing zebrafish hearts, demonstrating deep conservation of its upstream regulatory network.  Finally, single nucleotide polymorphisms in the human genome that occur near the region syntenic to the mouse enhancer exhibit significant associations with resting heart rate in human populations.

overall_design: Examination of regions of open chromatin in isolated RNA-seq validated cardiac SAN PCs and RACMs from neonatal mouse hearts (p0) using ATAC-seq.

first: Giselle

last: Galang

first: Nicole

last: Stone

first: Kevin

last: Chang

first: Marie

last: Shi

first: Vasanth

last: Vedantham


title: Effect of folic acid deprivation on H3K27me3 and H3K9me2 upon OTX treatment

first: Camille

last: Lobry

overall_design: Two AML cell lines IMS-M2 and U937, supplemented with or without FA, were treated with OTX. ChIP was performed on these samples using H3K27Me3- and H3K9Me2-directed antibodies prior to library preparation.

first: Alexandre

last: Puissant


title: Unravelling the developmental and functional significance of an ancient Argonaute duplication

city: Maale-AdumimJerusalem

first: Arie

last: Fridrich

state: Israel

department: EEB

country: Israel

institute: The Hebrew University of Jerusalem

type: Non-coding RNA profiling by high throughput sequencing

summary: Knockdown of NveAGO1 and NveAGO2 in Nematostella results in severe developmental defects.  NveAGO1 and NveAGO2 immunoprecipitation reveals subfunctionalization for differential miRNA sorting as well as siRNA specialization.

overall_design: small RNA highthroghput sequencing after AGO immunoprecipitations and AGO knockdowns.

first: A

first: V

last: Modepalli

first: M

last: Lewandowska

first: R

last: Aharoni

first: Y

last: Moran


title: Smc3 regulates B-cell transit through germinal centers and restricts their malignant transformation

first: Cem

last: Meydan

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

overall_design: Refer to individual Series


title: Smc3 regulates B-cell transit through germinal centers and restricts their malignant transformation (HiC)

summary: During the germinal center (GC) reaction, B-cells undergo extensive redistribution of cohesin complex and 3D re-organization of their genomes. Yet, the significance of cohesin and architectural programming in the humoral immune response is unknown.  Herein we report that conditional homozygous deletion of cohesin subunit Smc3 abrogated GC formation, yet in marked contrast, Smc3 haploinsufficiency induced GC hyperplasia, skewing of GC polarity and impaired plasma cell differentiation.  Transcriptional and architectural profiling revealed defects in GC terminal differentiation programs controlled by lymphoma epigenetic tumor suppressors Tet2 and Kmt2d, and failure of Smc3+/- GC B-cells to switch from B-cell to plasma cell lineage factors.  There was also impaired connectivity of gene regulatory elements controlling tumor suppressor genes, and accordingly Smc3 haploinsufficiency accelerated lymphomagenesis in mice with constitutive Bcl6 expression.  Collectively, our data indicate a dose dependent function for cohesin in humoral immunity to facilitate the B-cell to plasma cell lineage switch, while restricting their malignant transformation.

overall_design: Splenocytes from 8 day immunized Smc3 haploinsufficient or wildtype mice were FACS sorted using antibodies against B220, IgD, Fas, CD38, CXCR4, CD86 and stained with DAPI. Centroblasts were defined as DAPI-, B220+, Fas+, CD38-, CXCR4+ and CD86-. Centrocytes were defined as DAPI- lymphocytes, B220+, Fas+, CD38-, CXCR4- and CD86+. Naïve B cells were defined as DAPI-, B220+, Fas-, CD38+ and IgD+. One million cells were processed using the in situ HiC protocol and processed in duplicates. THB7 and MPC11OUAr were acquired from the ATCC and 1.5 million cells (in triplicate) were processed using the in situ HiC protocol.

first: Martin

last: Rivas

first: Christopher

last: Chin

first: Matt

middle: F

last: Challman

first: Bhavneet

last: Binder

first: Andreas

last: Kloetgen

first: Daleum

last: Kim

first: Aaron

last: Viny

last: Teater

first: Ashley

last: Doane

first: Dylan

last: McNally

first: Wendy

last: Beguelin

first: Maria

last: Fernandez

first: Hao

last: Shen

first: Ross

middle: L

last: Levine

first: Zhenming

last: Chen

first: Aris

last: Tsirigos

first: Olivier

last: Elemento

last: Mason

first: Ari

last: Melnick


title: A complementary study pipeline unravels novel players in the pathoetiology of Hirschsprung's disease

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: Purpose: Hirschsprung’s disease (HSCR, OMIM 142623) represents one of the main causes of neonatal intestinal obstruction. It is caused by dysfunction of neural crest cells (NCCs) and their progeny during development of the enteric nervous system (ENS). HSCR is considered a multifactorial disorder, however, associated risk genes only account for a minority of cases. Consequently, defining disease-relevant variants is still a demanding task. Methods: To reduce the number of candidate genes identified by Whole Exome Sequencing (WES) and to examine their disease-causing relevance, we established a complementary study pipeline including transcriptome data of murine embryonic ENS-relevant tissues, literature and database searches, in silico network analyses as well as functional assays using genome-edited candidate-specific cell clones.   Results: Applying this strategy on a pilot set of two HSCR patients and their non-affected parents led to the identification of four novel HSCR candidate genes: ATP7A, SREBF1, ABCD1 and PIAS2. This candidate gene selection was corroborated by the discovery of further rare variants in additional HSCR cases. Moreover, expression analyses revealed that all four genes are expressed in embryonic murine gastrointestinal tissues. Functional analyses using candidate gene-specific, neuronal-like CRISPR/Cas9-edited knockout cell clones demonstrated impaired differentiation, proliferation and/or cell survival capacity.   Conclusions: Taken together, the presented study pipeline was proven to be suitable for the selection and validation of candidate genes as well as to gain insight into underlying pathomechanisms of HSCR.

overall_design: For mRNA expression analyses by microarray profiling, murine embryonic regions of interest (pre-migratory vagal NCCs at stages E8.75 and E9.5; embryonic gut at E13.5, without stomach) were prepared. Embryonic tissues from each litter were pooled and three litters were analyzed per stage.

first: Stefanie

last: Schmitteckert

first: Beate

last: Niesler


title: Genetic alterations of SUGP1 mimic mutant-SF3B1 splice pattern in lung adenocarcinoma and other cancers

status: Public on Oct 10 2020

first: Alexandre

last: Houy

address: 26 rue d'Ulm

institute: Institut Curie

summary: RNA-sequencing data from HEK293T and HAP1 cell models: Hek293T (SF3B1-K700E, SF3B1-WT, SUGP1-KD and siContol), HAP1 CRISPR-isogenic cell lines WT and SUGP1-P636L

overall_design: In cellulo examination of SUGP1 loss, SUGP1 mutation and SF3B1 mutation in HAP1 and HEK293T cell lines.

first: Samar

last: Alsafadi

first: Stephan

last: Dayot

first: Marc-Henri

last: Stern

first: Tatiana

last: Popova


title: Smc3 regulates B-cell transit through germinal centers and restricts their malignant transformation (single-cell RNA-seq)

first: Cem

last: Meydan

overall_design: Six samples total: germinal center and post-germinal center B-cells R26-LSL-YFPwt/fl;Smc3wt/fl;Cγ1-cre (WT, three biological replicates); germinal center and post-germinal center B-cells R26-LSL-YFPwt/fl;Cγ1-cre (SMC3, three biological replicates) of 10 weeks-old female mice immunized with SRBC and euthanized 8 days post-immunization. Samples were multiplexed.

first: Martín

last: Rivas

first: Christopher

last: Chin

first: Matt

last: Challman

first: Daleum

last: Kim

first: Bhavneet

last: Binder

first: Andreas

last: Kloetgen

first: Aaron

last: Viny

last: Teater

first: Dylan

last: McNally

first: Ashley

last: Doane

last: Béguelin

first: María

last: Calvo Fernández

first: Zhengming

first: Aristotelis


title: RNAsequencing of the ventral rhombomere 1 of the developing mouse [bulk RNA-seq]

city: Helsinki

first: Kaia

last: Achim

address: Viikinkaari 9

department: Faculty of Biological and Environmental Sciences

country: Finland

institute: University of Helsinki

summary: Sequencing of the mouse ventral rhombomere 1 tissues and cells to characterize the Tal1-dependent and -independent neuronal precursor groups. The data allowed to describe the cell types in the R1 brain region, and map gene expression dynamics during bifurcation of the GABAergic and glutamatergic lineages. Our results provide a framework for understanding the development of cellular diversity in the tegmental nuclei.

overall_design: Rhombomere 1 tissues were collected from 6 wild type controls and from 6 Tal1cko animals, and subjected to RNA-sequencing, in order to identify the target genes of the transcription factor Tal1.

first: Juha

last: Partanen

first: Daniel

last: Borshagovski

first: Ogli

last: Samir-Sadik


title: RNA sequencing of the ventral rhombomere 1 of the developing mouse


title: Whole transcriptome sequencing in human cervical adenocarcinoma and normal cervical tissues

city: Hangzhou

first: Junfen

last: Xu

state: Other (Non U.S.)

address: No.1 Xueshi Road

department: Department of Gynecologic Oncology

institute: Women’s Hospital, Zhejiang University School of Medicine

summary: mRNA, lncRNA, and miRNA signatures were identified to discriminate cervical adenocarcinoma from normal cervix by whole transcriptome sequencing. We confirmed the RNA-seq data in another cohort of clinical cervical tissue samples by qRT-PCR.We demonstrated that miR-192-5p/HNF1A-AS1/VIL1 panel could accurately discriminates adenocarcinoma from normal cervix. Moreover,we also identified the circRNA expression profiles in cervical adenocarcinoma tissues and explored the function roles and mechanisms of circular RNA circEYA1 and circSPIDR in cervical adenocarcinoma cells.

overall_design: Examination of mRNA, lncRNA, miRNA, and circRNA signatures in 4 cervical adenocarcinoma tissues and 4 normal cervical tissues

first: Weiguo

last: Lu


title: Differences in Toxic Response induced by three Variants of the Diarrheic Shellfish Poisoning Phycotoxins in Human Intestinal Caco-2 Cells

city: Fougères

first: Antoine

last: Huguet

address: 10B rue Claude Bourgelat

institute: Anses

summary: Diarrheic shellfish poisoning (DSP) is caused by the consumption of shellfish contaminated with a group of phycotoxins that includes okadaic acid (OA), dinophysistoxin-1 (DTX-1), and dinophysistoxin-2 (DTX-2). These toxins are inhibitors of serine/threonine protein phosphatases 1 (PP1) and 2A (PP2A), but show distinct levels of toxicity. Aside from a difference in PP inhibition potency that would explain these differences in toxicity, others mechanisms of action are thought to be involved. Therefore, we investigated and compared which mechanisms are involved in the toxicity of these three analogues. As the intestine is one of the target organs, we studied the transcriptomic profiles of human intestinal Caco-2 cells exposed to OA, DTX-1, and DTX-2. The pathways specifically affected by each toxin treatment were further confirmed through the expression of key genes and markers of toxicity. Our results did not identify any distinct biological mechanism for OA and DTX-2. However, only DTX-1 induced up-regulation of the MAPK transduction signalling pathway, and down-regulation of gene products involved in the regulation of DNA repair. As a consequence, based on transcriptomic results, we demonstrated that the higher toxicity of DTX-1 compared to OA and DTX-2 was consistent with certain specific pathways involved in intestinal cell response.

overall_design: Modulation of gene expression in undifferentiated Caco-2 cells was measured at 24 hours after exposure to doses of 0, 13.8 nM of okadaic acid, 6.9 nM of dinophysistoxin-1, and 27.7 nM of dinophysistoxin-2. Six independent experiments were performed, and 24 samples (6 controls,  6 exposed to okadaic acid, 6 exposed to dinophysistoxin-1, 6 exposed to dinophysistoxin-2) had an RNA quality indicator ≥ 9 and were used for the microarray experiments.


title: H3 K27M and EZHIP impede H3K27-methylation spreading by inhibiting allosterically stimulated PRC2.

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus


title: Single-cell RNAsequencing of the ventral rhombomere 1 of the developing mouse [10X Genomics]

summary: Sequencing of the mouse ventral rhombomere 1 tissues and cells to characterize the Tal1-dependent and -independent neuronal precursor groups. The data allowed to describe the cell types in the R1 brain region, and map gene expression dynamics during bifurcation of the GABAergic and glutamatergic lineagesOur results provide a framework for understanding the development of cellular diversity in the tegmental nuclei.

overall_design: Unlabelled single cells were dissociated from selected brain regions and collected on 10xgenomics Chromium platform.


title: Single-cell RNAsequencing of the ventral rhombomere 1 of the developing mouse [INDROPS]

overall_design: Unlabelled single cells were dissociated from R1 brain region and collected using in-house InDrops single-cell collection setup.


title: TDP-43 aggregation induced by oxidative stress causes global mitochondrial imbalance in ALS

city: Wuhan

first: Yu

last: Zhou

state: Hubei

address: Luojia Hill

department: College of Life Sciences

institute: Wuhan University

summary: When mutant superoxide dismutase 1 (SOD1) was first linked to amyotrophic lateral sclerosis (ALS), it was thought that ALS is a disease of oxidative stress, but this idea has taken a back seat since the discovery of multiple ALS-linked genes involved in RNA processing and proteostasis. Strikingly, a hallmark of both familial and sporadic ALS is the aggregation of the essential DNA/RNA binding protein TDP-43, which is thought to cause simultaneous loss-of-nuclear function and gain-of-cytoplasmic toxicity. A central unanswered question is what triggers ALS in adult followed by rapid and irreversible progression? Here we report that neuronal cells are particularly prone to oxidative stress to trigger TDP-43 aggregation, which in turn sponges a large subset of microRNAs and proteins, resulting in global mitochondrial imbalance that further elevates the oxidative stress. We propose that this ferocious cycle may underlie ALS onset and progression with oxidative stress as a key disease-driving event.

overall_design: PolyA RNA-seq, small RNA-seq and RIP-seq of N2a cells

first: Xinxin

last: Zuo

first: Jie

first: Xiang-Dong

last: Fu


title: Calcium Signaling Prompts NIPBL Recruitment at Active Enhancers and Promoters via Distinct Mechanisms to Reconstruct Genome Compartmentalization

city: La Jolla

first: Cornelis

last: Murre

address: 9500 Gilman Drive

department: Molecular Biology

institute: UCSD

summary: During developmental progression the genomes of immune cells undergo large-scale changes in chromatin folding. However, insights into the signals and epigenetics that induce alterations in nuclear architecture remain rudimentary. Here, we found that calcium influx rapidly recruited the cohesin-loading factor NIPBL to thousands of binding sites to dictate widespread changes in compartment segregation. The induction of NIPBL-binding was coordinate with increased P300, BRG1 and RNA Polymerase II co-occupancy, via different kinetics at active enhancers and promoters. Through acute degradation system, we found that enhancers, rather than promoters, are dependent on BAF complexes to induce NIPBL recruitment. Finally, we found that calcium signaling acts universally to orchestrate rapid redistribution of NIPBL in both primary innate and adaptive immune cells. Collectively, these data reveal how calcium signaling regulates NIPBL occupancy to orchestrate nuclear architecture.

overall_design: Performed in situ Hi-C, ChIP-Seq, GRO-Seq and ATAC-Seq to pinpoint the underlying molecular mechanisms by which calcium signaling modulates nuclear architecture.

first: Yina

last: Zhu

first: Matthew

last: Denholtz

first: Hanbin


title: Global analysis of kidney gene expression by RNA-Seq of aged CTRP1-deficient mice on high-fat diet

city: Baltimore

first: Guang

middle: William

last: Wong

state: MD

address: 855 N Wolfe Street

department: School of Medicine

institute: The Johns Hopkins University

summary: Aging and obesity profoundly influence organ system health by altering circulating levels of hormones, growth factors, and cytokines. C1q/TNF-related protein 1 (CTRP1) is an endocrine factor with important metabolic, cardiovascular, and renal functions. We sought to determine the impact of CTRP1 deficiency on heart and kidney function in the context of aging and obesity using aged and obese wild-type (WT) and Ctrp1 knockout (KO) mice fed a high-fat diet for eight months or longer. Surprisingly, no differences were observed in blood pressure, heart function, or vascular stiffness between genotypes. Loss of CTRP1, however, resulted in renal enlargement (relative to body weight), reduced urinary creatinine, elevated urinary total protein content and pH, and changes in renal gene expression affecting sugar, fat, and amino acid metabolism pathways. Assessment of glomerular integrity, the extent of podocyte foot process effacement, as well as renal response to water restriction and salt loading did not reveal significant differences between WT and Ctrp1-KO mice. Interestingly, blood platelet, white blood cell, neutrophil, lymphocyte, and eosinophil counts were significantly elevated, whereas mean corpuscular volume and hemoglobin were reduced in Ctrp1-KO mice. Cytokine profiling revealed increased circulating levels of CCL17 and TIMP-1 in KO mice. Compared to a previous study, our current data suggest that chronic high-fat feeding affects renal phenotypes differently than similarly aged mice fed a control low-fat diet, highlighting a diet-dependent contribution of CTRP1 deficiency to age-related changes in renal structure and function.

overall_design: Kidney RNA sequenceing and bioinformatics analyesis was performed on age-matched 40 week-old wildtype (WT) and CTRP1-/- mice fed a high-fat diet, with 4 biological replicates for each genotype for a total of 8 mice. Thus, 4 KO mice were compared to 4 WT.

first: Susana

last: Rodriguez

first: Hannah

middle: C

last: Little

first: Parnaz

last: Daneshpajouhnejad

first: Paride

last: Fenaroli

first: Stefanie

middle: Y

last: Tan

first: Dylan

last: Sarver

first: Saneedp

last: Jandu

first: Michael

last: Delannoy

first: C

last: Talbot Jr

first: Dan

last: Berkowitz

first: Avi

middle: Z

last: Rosenberg

first: Jennifer

last: Pluznick

first: G


title: Membrane tension regulated mechanotransduction drives fate transitions in embryonic stem cells

first: Celine

last: Labouesse

address: Puddicombe Way

department: Cambridge Stem Cell Institute

summary: Changes in cell shape and mechanics frequently accompany cell fate transitions. Yet how cellular  mechanics affects the regulatory pathways controlling cell fate is poorly understood. To probe the  interplay between shape, mechanics and fate, we used embryonic stem (ES) cells, which spread as  they undergo early differentiation. We found that this spreading is regulated by a β-catenin  mediated decrease in RhoA activity and subsequent decrease in the plasma membrane tension.  Strikingly, preventing the membrane tension decrease resulted in early differentiation defects in  ES cells and gastruloids. We further find that the decrease in membrane tension facilitates  endocytosis of FGF signaling components, which activates ERK signaling and directs exit from  the ES cell state. The early differentiation defects we observed can be rescued by increasing Rab5afacilitated  endocytosis. Thus, we show that a mechanically-triggered increase in endocytosis  regulates early differentiation. Our findings are of fundamental importance for understanding how  cell mechanics regulates biochemical signaling, and therefore cell fate.

overall_design: mESC from parental cell line E14 wt and from inducible constitutively active Ezrin (iEZR_CA) were seeded on gelatin-coated plates in 2i+LIF (naive medium) or N2B27 (differentiation medium). The expression of Ezrin was induced ~16hr before exit by the addition of doxycycline to the medium. RNA lysates were collected at 24hr and 48hr of exit from the naive and differentiated cells in both cell lines. 3 replicates per condition were processed.

first: Henry

last: De Belly

first: Céline

first: Kevin

last: Chalut

first: Ewa

middle: K

last: Paluch


title: Expression profile of mouse primary and recurrent breast cancer cell lines

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Dr., 2133 CIEMAS Box 3382 DUMC

department: Center for Genomic and Computational Biology

institute: Duke University

summary: The molecular basis of tumor recurrence remain poorly understood. Here, we performed RNA microarrays to study the genetic basis of the phenotypic differences between the primary and recurrent breast cancer cells.

overall_design:
Primary and recurrent tumor cells were isolated and expanded from Her2 driven murine model of MTB/TAN tumor before the oncogenic withdrawal (primary tumors) and after the recurrence (recurrent tumors).
biological replicate: 54074-1, 54074-2
biological replicate: 99142-1, 99142-2
biological replicate: 42929-1, 42929-2
biological replicate: 48316-1, 48316-2

first: Chao-Chieh

last: Lin

first: James

middle: V

last: Alvarez


title: RNA-seq Analysis of bone marrow mesenchymal stromal cells from DPBS-treated vs FAP inhibitor-treated mice

city: Shanghai

first: Rui

last: Yue

address: 1239 Siping Road

department: School of Life Sciences and Technology

institute: Tongji University

summary:
Purpose: The goal of this study is to compare the transcriptomic differences between bone marrow mesenchymal stromal cells (BMSCs) from DPBS-treated mice and FAP inhibitor (FAPi)-treated mice, in order to find out the differentially expressed genes and pathways underlying the bone phenotypes after FAPi treatment.
Methods: The mRNA profiles of BMSCs from DPBS treated mice (n=3) and FAPi treated mice (n=4) were generated by deep sequencing on a HiSeq X Ten system (Illumina) as paired-end 150-bp reads. The sequence reads that passed quality filters were analyzed by STAR and HTSeq. Raw gene counts for each gene was determined by UMI numbers.
Results: Using an optimized data analysis workflow, we mapped more than 40 million sequence reads per sample to the mouse genome (mm10) and identified about 9 million raw counts (removing the duplicates by UMIs from Read2) in the BMSCs of DPBS treated mice and FAPi treated mice with HTSeq.  Approximately 3% of the genes showed differential expression between BMSCs from DPBS treated mice and FAPi treated mice (fold change > 2.0 or < -2.0 and p value <0.05).
Conclusions: Our study revealed the molecular mechanisms underlying the bone-forming activity of FAPi in BMSCs after in vivo administration.

overall_design: FAP ihibitor treated (n=4, 500 ug/kg daily intraperitoneal injection for 35 days). DPBS-treated mice (n=3, DPBS injected daily intraperitoneal injection for 35 days). Bone marrow cells were digested and sorted for BMSCs.

first: Yue

last: Rui

first: Wang

last: Yibin

first: Wei

last: Hanjing

first: Xu

last: Liting


title: DeepTFactor, a deep learning-based tool for the identification of transcription factors

status: Public on Oct 09 2020

first: Ye

last: Gao

address: 9500 Gilman Dr.

summary: We report the development of a deep learning-based tool, DeepTFactor, that predicts whether a protein of question is a transcription factor. DeepTFactor uses a convolutional neural network to extract features of protein sequences. We characterized the genome-wide binding sites of three TFs (i.e., YqhC, YiaU, and YahB), which are predicted by DeepTFactor

overall_design: Identification of genome-wide bindings for uncharacterized transcription factors in E. coli K-12 MG1655, using ChIP-exo technology

first: Gi Bae

last: Kim

first: Bernhard

last: Palsson

first: Sang Yup

last: Lee


title: RNA Sequencing and characterization of the linear and circular transcriptomes from healthy controls' and multiple sclerosis patients' leukocytes

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

institute: Biodonostia Institute

summary:
Background and aim: The disease course and clinical phenotype in multiple sclerosis (MS) are highly variable and therefore, biomarkers are needed. Studies have shown a dysregulation in the coding and non-coding RNAs and proposed some as biomarkers. However, still none of them have reached the clinical practice. Recently, circular RNAs (circRNAs) have emerged as new players in the transcriptome that hold a great potential as biomarkers in several diseases. In this study we have performed a RNASeq profiling of patients (N=50) and healthy controls' (N=20) leukocytes in order to characterize their linear and circular transcriptomes with the final aim of finding some new potential biomarkers.
Methods: Differential expression analysis was performed by DESeq and circRNA candidates were studied in a second cohort (70MS and 46HC) by RT-qPCR and in paired samples drawn during the relapse and remission phases (20 patients).
Results: Among the differentially expressed circRNAs, the 96.1% is are upregulated in patients compared to controls, but similar circRNA profiles are found between MS types. The same upregulation trend was observed in females but not in males or in the linear transcriptome. The upregulation of 6 circRNAs was validated and a change in their expression was found between relapse and remission. The 6 circRNAs showed a good performance to discriminate patients from HC with a combined AUC of 0.852.
Conclusion: There is global, specific and sex dependent increase of circRNA expression in MS and 6 circRNAs are proposed as potential biomarkers.

overall_design: Linear and circularRNA profile from 30 MS patients' and 20 healthy controls' leukocytes

first: Leire

last: Iparraguirre

first: Ainhoa

last: Alberro

first: Lucía

last: Sepúlveda

first: Iñaki

last: Osorio

first: Laura

last: Moles

first: Tamara

last: Castillo-Triviño

first: Thomas

last: Hansen

first: David

last: Otaegui


title: Loss of the RNA trimethylguanosine cap is compatible with nuclear accumulation of spliceosomal snRNAs but not pre-mRNA splicing or snRNA processing during animal development

city: Guangzhou

first: Lin

last: Cheng

state: Guangdong

address: No.132, East Outer Ring Road, Guangzhou University City

institute: Sun Yat-sen University

summary: The 2,2,7-trimethylguanosine (TMG) cap is synthesized by the conserved Tgs1 enzyme, which is abundantly present on snRNAs essential for pre-mRNA splicing. In our study, we characterize new mutations in the Drosophila tgs1 gene and studied their effects on development and on splicing. Utilizing a hypomorphic tgs1 mutation, we uncovered a prominent role of Tgs1 in pre-mRNA splicing, particularly of introns with smaller sizes and weaker splice sites. Remarkably, stronger tgs1 mutations generated by CRISPR-Cas9 cause lethality without disrupting splicing, likely due to the preponderance of a maternal contribution and stable TMG capped snRNAs maintaining a near normal level of TMG modified snRNAs, which further proved that the TMG modification is important in splicing.

overall_design: 8 samples in total; 4 kinds of RNA samples from wildtype and tgs1 mutant animals were prepared and sequenced with two replicates.

first: Yu

last: Zhang

first: Yi

first: Tao

last: Chen

first: Yong-Zhen

last: Xu

first: Yikang

last: Rong


title: Cancer Stem Cell Phenotypes in ER + Breast Cancer Models Are Promoted by PELP1/AIB1 Complexes

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

summary: Trascriptome analysis of mcf7 cell lines were performed

overall_design: MCF-7 PELP1 cells expressing LXSN, WT PELP1, or cytoplasmic (cyto) PELP1 were hormone-starved in modified IMEM containing 5% DCC for 16 hours prior to hormone treatment. Cells (in triplicate) were treated with vehicle (ethanol) or E2 (10-9 mol/L) for 6 hours, RNA was extracted with RNAeasy Mini Kit and sequenced with Illumina HiSeq 2000

first: Carol

middle: E

last: Lange

first: Julie

middle: H

last: Ostrander


title: Induced organoids derived from patients with ulcerative colitis recapitulate the colitic reactivity

city: Cleveland

first: Bo

last: Hu

state: Ohio

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: We report the application of single nucleus RNA-seq technology for transcriptomic-wide profiling of the induced organoids derived from patients with ulcerative colitis (iHUCO) and normal induced organoids derived from the healthy colon (iHNO), along with their parental fibroblasts. By comapring the nucleus profiles of both iHUCOs and their parental fibroblasts (UC FBs) to iHNOs and normal fibroblasts (NL FBs), we found unique signatures exclusive to the UC samples but not the controls. We also report that UC FBs and iHUCOs share the layers of similarities in their single nucleus profile. This study provides a framework for the application of the induced patient-derived organoids as a more comprehensive model to study human UC.

overall_design:
Examination of the single-nucleus profiles of fibroblats isolated from the colon of the patients with UC along with their corresponding induced organoids
contributor: LRI Genomics Core

first: Emina

last: Huang

first: Samaneh

last: Sarvestani

first: Hao

last: Feng


title: Bulk RNA-seq data from the aIPg, pC1d, and pC1e neurons in adult Drosophila

city: Ashburn

first: Catherine

middle: Elizabeth

last: Schretter

state: VA

address: 19700 Helix Dr

institute: HHMI - Janelia

summary: We analyzed transcriptome of aIPg and pC1 neurons cell types to identify their neurotransmitters. We found that the aIPg, pC1d, and pC1e neurons all expressed transcripts consistent with being cholinergic, which has been reported previously for the pC1 neurons.

overall_design: Specific cell types were marked by split-GAL4 drivers, and sorted by hand or FACS

first: Yoshinori

last: Aso

first: Alice

last: Robie

first: Marisa

last: Dreher

first: Michael-John

last: Dolan

first: Masayoshi

last: Ito

first: Tansy

last: Yang

first: Ruchi

last: Parekh

first: Kristin

last: Branson

first: Gerald

middle: M

last: Rubin


title: Effect of p16 deficiency on gene expression in primary hepatocytes

city: Lille

first: Joel

last: Haas

address: 1 Rue du Professeur Calmette

institute: Institut Pasteur de Lille

summary:
*Objectives:* In addition to their well-known role in the control of cellular proliferation and cancer, cell cycle regulators are increasingly identified as important metabolic modulators. Genome wide association  studies identified SNPs near the cell cycle regulator CDKN2A/p16INK4a (p16)  as strongly associated with risk of developing type 2 diabetes (T2D). T2D  is associated with numerous perturbations of hepatic lipid and glucose metabolism. We have recently shown that p16 controls fasting-induced hepatic gluconeogenesis in mice. However, whether p16 may also affect hepatic lipid homeostasis is unknown.
*Results:* In primary hepatocytes, p16-deficiency was associated with elevated expression of genes involved in fatty acid catabolism and enhanced activation of PPAR. This led to increased mitochondrial fatty acid oxidation (FAO) through a mechanism requiring the catalytic AMPK  2 subunit and SIRT1. By contrast, *p16* overexpression was associated with triglyceride accumulation and increased lipid droplet numbers *in vitro*, and decreased ketogenesis and hepatic mitochondrial activity *in vivo*. Gene expression analysis of human liver samples revealed a negative correlation between *CDKN2A* expression and *PPARA* and its target genes, suggesting a potential association between hepatic p16 expression and FAO in obese humans.
*Conclusions:* Our findings demonstrate that p16 plays a key role in hepatic lipid metabolism and may thus contribute to the development of metabolic diseases.

overall_design: Primary hepatocytes were isolated by two step collagenase perfusion from p16+/+ and p16-/- littermate mice and RNA was harvested after 24 hours.

first: Réjane

last: Paumelle


title: The mole genome reveals regulatory rearrangements associated with adaptive intersexuality (Hi-C)

city: Berlin

first: Francisca

last: Martinez Real

address: Ihnestrasse 73

institute: Max Planck Institute for Molecular Genetics

summary: Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. These include a tandem triplication involving CYP17A1, a gene controlling androgen synthesis, and an intrachromosomal inversion involving the pro-testicular growth factor FGF9, which is heterochronically expressed in mole ovotestes. Transgenic mice with a knock-in mole CYP17A1 enhancer or overexpressing FGF9 showed phenotypes recapitulating mole sexual features. Our results highlight how integrative genomic approaches can reveal the phenotypic impact of noncoding sequence changes.

overall_design: We used HiC-seq to define the topologically associated domains (TADs) in the mole genome.


title: "TRADES": Targeted RNA demethylation by Suntag system

city: Beijing

first: Zonggui

last: Chen

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: Academy for Advanced Interdisciplinary Studies

institute: Peking University

summary: We engineered a new m6A editing system consisting of GCN4 (SunTag)-dCas13b, anti-GCN4 single chain variable fragment (scFv)-FTO or ALKBH5-GBI and sgRNA to provide an applicable method to remove m6A modification at specific loci.

overall_design: m6A-seq were performed to evaluate the demethylation results of targeted SON demethylation samples (WT (sg-SON)), off-target control (WT (sg-control)) and mutant FTO control (Mut (sg-SON)). RNA lifetime profiling was conducted by collecting and analyzing RNA-seq data on targeted SON demethylation and control samples, the transcription of which were inhibited with actinomycin D at different time points.

first: Jing

last: Mo

first: Yu

last: Zhou

first: Xiang


title: The mole genome reveals regulatory rearrangements associated with adaptive intersexuality (ATAC-Seq)

overall_design: We used ATAC-seq to detect open chromatin and associate it to regulatory elements in moles compared to mouse.


title: Circulating tRNA-derived small RNAs (tsRNAs) signature for the diagnosis and prognosis of breast cancer

status: Public on Oct 08 2020

city: Nanjing

first: Shui

last: Wang

state: Jiangsu

address: 300 Guangzhou Road

institute: The First Affiliated Hospital with Nanjing Medical University

summary: Liquid biopsy is noninvasive and convenient to detect cancer-derived materials in blood or other body fluids. The aim of this study was to identify tRNA-derived small RNAs (tsRNAs) in plasma that could distinguish patients with breast cancer (BC) from healthy controls. Basing on high-throughput sequencing, 15 significantly upregulated tsRNAs were selected and assessed in cell supernatants and cell lines. 6 tsRNAs were identified and verified in a large cohort of 120 patients with BC and 112 healthy controls. tRF-Arg-CCT-017, tRF-Gly-CCC-001 and tiRNA-Phe-GAA-003 could serve as novel diagnostic biomarkers. Meanwhile, tRF-Arg-CCT-017 and tiRNA-Phe-GAA-003 could also act as prognostic biomarkers. Target genes of these tsRNAs were related to the development of cancer. These results suggest that specific tsRNAs in plasma might serve as diagnostic and prognostic biomarkers of BC.

overall_design: Expression profiling of tsRNAs in plasma samples of patiens with breast cancer

first: Jingyi

first: Ge

last: Ma

first: Han

last: Ge

first: Xu

last: Han

first: Xinrui

last: Mao

first: Xinyang

first: Jordee

middle: S

last: Veeramootoo

first: Tiansong

last: Xia

first: Xiaoan

last: Liu


title: The mole genome reveals regulatory rearrangements associated with adaptive intersexuality (RNA-Seq)

sample_organism:
Mus musculus
Talpa occidentalis

platform_organism:
Mus musculus
Talpa occidentalis

overall_design: We perform transcriptome analysis on different developmental stages in gonads from moles and mouse to find candidates genes responsibles for the formation of the ovotestis in female moles.


title: The mole genome reveals regulatory rearrangements associated with adaptive intersexuality (4C-Seq)

overall_design: We have performed Circular Chromosome Conformation Capture (4C seq) on mole embryonic tissues to determine the regulatory domain of FGF9.


title: Inhibition of the SUV4-20 H1 histone methyltransferase increases frataxin expression in Friedreich’s ataxia patient cells

city: Oxford

first: Gabriela

last: Vilema-Enríquez

address: South Parks Road

department: Physiology, Anatomy and Genetics

institute: University of Oxford

summary: The molecular mechanisms of reduced frataxin (FXN) expression in Friedreich's ataxia (FRDA) are linked to epigenetic modification of the FXN locus caused by the disease-associated GAA expansion. Here, we identify that SUV4-20 histone methyltransferases, specifically SUV4-20 H1, play an important role in the regulation of FXN expression and represent a novel therapeutic target. Using a human FXN-GAA-Luciferase repeat expansion genomic DNA reporter model of FRDA, we screened the Structural Genomics Consortium epigenetic probe collection. We found that pharmacological inhibition of the SUV4-20 methyltransferases by the tool compound A-196 increased the expression of FXN by ∼1.5-fold in the reporter cell line. In several FRDA cell lines and patient-derived primary peripheral blood mononuclear cells, A-196 increased FXN expression by up to 2-fold, an effect not seen in WT cells. SUV4-20 inhibition was accompanied by a reduction in H4K20me2 and H4K20me3 and an increase in H4K20me1, but only modest (1.4-7.8%) perturbation in genome-wide expression was observed. Finally, based on the structural activity relationship and crystal structure of A-196, novel small molecule A-196 analogs were synthesized and shown to give a 20-fold increase in potency for increasing FXN expression. Overall, our results suggest that histone methylation is important in the regulation of FXN expression and highlight SUV4-20 H1 as a potential novel therapeutic target for FRDA.

overall_design:
24 samples derived from two cell lines; a Friedrich's ataxia cell line (GM04078) and a healthy control line (GM03440). Untreated, DMSO treated, inactive compound treated and A-196 treated (3 different concentrations) analysed. Three cell culture replicates of each condition included.
A-196 is the lead compound
SGC2043 is the inactive structural analogue of A-196

first: Robert

last: Quinlan

first: Peter

last: Kilfeather

first: Roberta

last: Mazzone

first: Saba

last: Saqlain

first: Irene

last: del Molino del Barrio

first: Annalidia

last: Donato

first: Gabriele

last: Corda

first: Fengling

last: Li

first: Masoud

last: Vedadi

first: Andrea H

last: Németh

first: Paul E

last: Brennan

first: Richard

last: Wade-Martins


title: Repurposing bioactive aporphine alkaloids as efflux pump inhibitors

city: İstanbul

first: Fatma

middle: Gizem

last: Avci

address: Marmara Uni, Bioengineering  Dep., No:404  Kadıköy

department: Bioengineering

country: Turkey

institute: Marmara University

summary: In the current study, RNA sequencing was used to investigate the synergistic effects of the berberine and roemerine on Bacillus subtilis cells.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Comparison of one-hour berberine+roemerine treated cells with the control (DMSO treated) cells.

middle: G

first: Berna

last: Sarıyar-Akbulut


title: A Genome-wide CRISPR-Based Screen Identifies KAT7 as a Senescence Driver

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: Understanding the genetic and epigenetic bases of cellular senescence is instrumental to aging intervention. We performed genome-wide CRISPR/Cas9-based screens in two human mesenchymal precursor cell (hMPC) models of progeroid syndromes and identified hundreds of genes whose deficiency alleviated cellular senescence. Among them, KAT7, a histone acetyltransferase, ranked as a top hit in both models. Inactivation of KAT7 decreased H3 lysine 14 acetylation (H3K14ac), repressed p15INK4b transcription, and rejuvenated both physiologically and pathologically aged cells. Moreover, lentiviral vectors encoding Cas9/sg-Kat7 alleviated liver senescence and extended healthspan and lifespan of mice. Our findings demonstrate that CRISPR/Cas9-based genetic screening is a robust method for systematically uncovering unknown senescence genes, of which KAT7 may represent a new therapeutic target for aging intervention.

overall_design: CRISPR screen, RNA-seq, ChIP-seq and Hi-C


title: EGFR/Src/Erk-Stabilized YTHDF2 Promotes Cholesterol Dysregulation and Invasive Growth of Glioblastoma [RNA-Seq]

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

summary: Epidermal growth factor receptor (EGFR) signaling is constitutively activated in majority of GBM and is associated with a worse prognosis. Here we show that EGFR is responsible for overexpression of the m6A "reader" YTHDF2 in GBM through the EGFR/Src/ERK signaling pathway. YTHDF2 overexpression clinically correlates with poor glioma patient prognosis. EGFR signaling stabilizes YTHDF2 protein through phosphorylation of YTHDF2 serine 39 and threonine 381 by ERK1/2. YTHDF2 is required for GBM cell proliferation, invasion and tumorigenesis. YTHDF2 facilitates m6A-dependent mRNA decay of LXRA and HIVEP2, both are genes impacting glioma patient survival. YTHDF2 promotes tumorigenesis of GBM cells largely through downregulation of LXRA and HIVEP2.  Further, YTHDF2 inhibits LXRA-dependent cholesterol homeostasis in GBM cells. Together, our findings extend the landscape of EGFR downstream circuit, uncover novel function for YTHDF2 in GBM tumorigenesis, and highlight an essential role of RNA m6A methylation in cholesterol homeostasis.

overall_design: Expression profiles were generated from GSC11 human glioblastoma stem cell lines transfected with control or YTHDF2 siRNA, which were collected to extract total RNA, and mRNA sequencing was performed.

first: Suyun

last: Huang


title: Urinary exosomal small non-coding RNA expression of prostate cancer patients

city: Rensselaer

first: Martin

last: Tenniswood

address: 1 Discovery Drive

institute: miR Scientific LLC

summary: Small non-coding RNA profiling of urine exosomal total RNA from patients with or without prostate cancer were performed using Affymetrix miRNA Gene-Chip 4.0 to identify small non-coding RNA proflie that can be used for prostate cancer diagnosis.

overall_design:
Changes in small non-coding RNA expression in prostate cancer patients were determined by comparing the small non-coding RNA expression to the positive or negative results of core-needle biopsy of patients suspicious of prostate cancer.

Contributor: miR Scientific LLC


title: EGFR/Src/Erk-Stabilized YTHDF2 Promotes Cholesterol Dysregulation and Invasive Growth of Glioblastoma

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

overall_design: Refer to individual Series


title: EGFR/Src/Erk-Stabilized YTHDF2 Promotes Cholesterol Dysregulation and Invasive Growth of Glioblastoma [RIP-Seq]

overall_design: anti-YTHDF2 of mRNA from GSC11 cells


title: Global gene expression profiles of cellular response in human induced pluripotent stem cell-derived cardiomyocytes to melphalan treatment

status: Public on Oct 07 2020

city: Atlanta

first: Rui

last: Liu

state: GA

address: 2015 Uppergate Drive

department: Pediatrics

institute: Emory University

summary:
Purpose: Evaluate the molecular changes associated with melphalan-induced cardiotoxicity and rescue by N-acetyl-L-cysteine (NAC) supplementation.
Methods: RNA-Seq analysis was performed to analyze global transcriptome profiles of hiPSC-CMs treated with DMSO (Control group), 20 µM melphalan (Mel group), and 20 µM melphalan with 1 mM NAC (Mel+NAC group), respectively. The Illumina TruSeq technology was used to prepare RNA-Seq libraries, and next-generation sequencing was done via an Illumina HWI-ST1276. RNA sequence reads were aligned to the human reference genome (GRCh38) using STAR v2.5. HTSeq v0.6.1 was used to count the read numbers mapped of each gene, and then Fragments Per Kilobase Million (FPKM) was calculated to estimate gene abundance. Differential expression analysis was performed using the DESeq2 R package (2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg's approach.
Results: As detected by RNA-Seq, more genes were down-regulated than up-regulated by the treatment of melphalan, whereas NAC supplementation resulted in more genes being up-regulated than down-regulated. Among the top 10 up-regulated genes by melphalan treatment, 4 were direct p53 effectors (CDKN1A, EDXR, TNFRSF10C, and GDF15). And among the top 10 down-regulated genes by melphalan treatment, 5 were correlated to cell adhesion (CDH13, CNTN1, SDK1, CTNND2, and PARD3B). In addition, the up- and down-regulation of genes involved in oxidative stress (e.g., DUOX2 and NOX4) following melphalan treatment (Mel vs. control) was attenuated with NAC supplementation (Mel+NAC vs. Control). Similarly, the up- and down-regulation of genes involved in cardiac muscle contraction (e.g., Ca2+ handling proteins CACNA1C, RYR2 and CASQ2 and cardiac contractile proteins TNNC1, ACTC1, TNNC1) and cardiac conduction (e.g., ATP2B2 and ABCC9) following melphalan treatment (Mel vs. Control) was attenuated with NAC supplementation (Mel+NAC vs. Control).
Conclusion: NAC ameliorates melphalan-induced alteration of hiPSC-CM transcriptomic profiles.

overall_design: RNA-Seq analysis was performed to compare global gene expression profiles of hiPSC-CMs treated with DMSO, 20 µM melphalan, and 20 µM melphalan with 1 mM NAC, respectively, in triplicate.

first: Chunhui

last: Xu