title: Pro-immunogenic impact of MEK inhibition synergizes with agonist anti-CD40 immunostimulatory antibodies in tumor therapy [PDA30364 treated with MEKi, CD40, in vivo]

first: Michael

last: Volkmar

summary:
Cancer types with lower mutational load and a non-permissive tumor microenvironment are intrinsically resistant to immune checkpoint blockade. While the combination of cytostatic drugs and immunostimulatory antibodies constitutes an attractive concept for overcoming this refractoriness, suppression of immune cell function by cytostatic drugs may limit therapeutic efficacy. Here we show that targeted inhibition of mitogen-activated protein kinase (MAPK) kinase (MEK) does not impair dendritic cell-mediated T-cell priming and activation. Accordingly, combining MEK inhibitors (MEKi) with agonist antibodies (Abs) targeting the immunostimulatory CD40 receptor resulted in potent synergistic anti-tumor efficacy. Detailed analysis of the mechanism of action of MEKi GDC-0623 by means of flow cytometric analysis of the tumor immune infiltrate and whole tumor transcriptomics showed that, in addition to its cytostatic impact on tumor cells, this drug exerts multiple pro-immunogenic effects, including the suppression of M2-type macrophages, myeloid derived suppressor cells and CD4+ T-regulatory cells. In addition, MEKi was found to induce tumor-cell intrinsic interferon signaling, which contributed to antigen presentation by tumor cells. Finally, the tumoridical impact of MEKi involves the activation of multiple pro-inflammatory pathways involved in immune cell effector function in the tumor microenvironment. Our data therefore indicate that the combination of MEK inhibition with agonist anti-CD40 Ab is a promising therapeutic concept, especially for the treatment of mutant Kras-driven tumors such as pancreatic ductal adenocarcinoma.
We used microarrays to monitor transcriptional and cell-type composition changes in murine transplantable tumor models of pancreatic ductal adenocarcinoma (PDA30364), colon cancer (MC38) and melanoma (B16-OVA) upon treatment with MEK inhibitor (GDC-0623), anti-CD40 antibody or the combination of GDC-0623 and anti-CD40 antibody.

overall_design: RNA was isolated from PDA30364 tumor pieces of at 3-4 animals per treatment group at the end of the treatment period and subjected to transcriptome analyses. After quality control, samples were normalized by applying the Robust Multichip Averaging (RMA) normalization method.

first: Daniel

last: Baumann

first: Rienk

last: Offringa


title: Gene expression in DCIS.COM with BCL9 knockdown

status: Public on Jan 17 2020

city: Kansas City

first: Hanan

last: Elsarraj

state: KS

address: 3901 Rainbow Blvd.

department: Pathology and Laboratory Medicine

country: USA

institute: University of Kansas Medical Center

type: Expression profiling by high throughput sequencing

summary: There is limited research on which specific Wnt targets are regulated by B-Cell Lymphoma-9 (BCL9) and whether BCL9 regulates other signaling pathways to drive cancer malignancy. Here we demonstrated that BCL9 drives DCIS invasive progression by regulation of  genes involved in cellular growth, invasion and migration.

overall_design: RNA-seq was performed on the DCIS cell line (DCIS.COM) control and BCL9-knockdown (BCL9 KD) to elucidate gene expression changes with BCL9 knockdown

middle: S

first: Yan

last: Hong

first: Jeffrey

last: Thompson

first: Fariba

last: Behbod


title: Single-cell RNA-seq of the mouse lymph node lymphatic vasculature: SMART-seq2

status: Public on Jan 18 2020

city: Stanford

first: Menglan

last: Xiang

state: CA

address: 450 Serra Mall

institute: Stanford University

summary: Lymph nodes (LNs) serve as hubs for the interaction and communication between tissue-derived and blood-derived immune cells. Here we analyzed mouse lymph node (LN) lymphatic endothelial cells (LEC) at single cell resolution. Clustering identifies five well-delineated subsets, including two medullary sinus subsets not recognized previously as distinct. Nearest neighbor alignments in trajectory space position the major subsets in a sequence that recapitulates known and suggests novel features of LN lymphatic organization, providing a transcriptional map of the lymphatic endothelial niches and of the transitions between them. Differences in gene expression reveal specialized programs for (1) subcapsular ceiling endothelial interactions with the capsule connective tissue and cells, (2) subcapsular floor regulation of lymph borne cell entry into the LN parenchyma and antigen presentation, and (3) medullary subset specialization for pathogen interactions and LN remodeling. LEC of the subcapsular sinus floor and medulla, which represent major sites of cell entry and exit from the LN parenchyma respectively, respond robustly to oxazolone inflammation challenge with enriched signaling pathways that converge on both innate and adaptive immune responses.

overall_design: Female 20-week-old Prox1-GFP/C57BL/6J inguinal LNs were processed by the SMART-seq2 workflow for scRNA-seq.

first: Maria

middle: H

last: Ulvmar

first: Eugene

middle: C

last: Butcher


title: Pro-immunogenic impact of MEK inhibition synergizes with agonist anti-CD40 immunostimulatory antibodies in tumor therapy [MC38 treated with MEKi, CD40, in vivo]

status: Public on Jan 24 2020

city: Heidelberg

state: BW

address: Im Neuenheimer Feld 280

department: D200 Molecular Oncology of Gastrointestinal Tumors

country: Germany

institute: German Cancer Research Center (DKFZ)

overall_design: RNA was isolated from MC38 tumor pieces of at least four animals per treatment group at the end of the treatment period and subjected to transcriptome analyses. After quality control, samples were normalized by applying the Robust Multichip Averaging (RMA) normalization method.


title: Amino acid metabolism regulated by DNA Methylation in Mycobacterium bovis BCG str. Tokyo 172 induced by vitamins

status: Public on Jan 16 2020

city: harbin

first: Ningning

last: Song

address: No.678. Haping Road

country: China

institute: Harbin Veterinary Research Institute

summary: Vitamins are organic compounds and essential nutrients required by host organism. Recent studies have shown that vitamin B1(VB1) and vitamin C (Vc) could inhibit Mycobacterium tuberculosis growth. However, the precise role of VB1 and Vc in M.tuberculosis are still not well understand. Therefore, in this study, the transcriptional, metabolic and methylation profiles of VB1 and VC treated Mycobacterium. bovis BCG were analyzed by RNA-sequencing, LC-MS (Liquid chromatography coupled to mass spectrometry) and SMRT. The RNA-seq show that gene encoding cysteine synthase A was significantly up-regulated under both vitamins treatment, metabolic study show that most of amino acids decreased in VB1 treated BCG, in constrast, most of amino acids increased in VC treated samples. Methylome data show that m4c modificatiion partically is present in VC treated BCG and the expression of most genes harboring m4c methylation modificaiton increased. In all, these data imply that potentially increased concentration of cysteine might lead to BCG growth inhibition induced by VB1 and VC duing to produce superoxide which could cause DNA damage via Fetions reacition. The m4c methylation modification could promote gene transcription to some extent. In all, this study will benefit for us to futher understand the roles of VB1 and VC which could be used as potential anti-tuberculosis drugs.

sample_organism: Mycobacterium tuberculosis variant bovis

overall_design: 2 groups (control and treated group), each group contain triplicates

first: Guanghui

last: Dang

first: Ziyin

last: Cui

first: Huajun

last: Zheng

first: Siguo

last: Liu


title: The regeneration transcriptome of corticospinal neurons

status: Public on Jan 21 2020

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: In the present study, we identify transcriptional mechanisms associated with corticospinal regeneration. We took advantage of the ability of NPC grafts to support corticospinal regeneration, together with a genetic mouse model (Glt25d2-GFP-L10a mice, in which a bacterial artificial chromosome (BAC) codes for GFP-tagged polyribosomes in layer 5b cortical neurons) to selectively enrich actively translated mRNA pools from layer Vb cortical projection neurons containing corticospinal neurons (Doyle et al., Cell 2008).

overall_design: We examined the regeneration transcriptome of the corticospinal neuron triggered by growth-promoting neural progenitor cell grafts compared to ungrafted, lesioned controls. We utilized mice with layer 5 neuron specific expression of EGFP-L10a under the Glt25d2 promoter. We pooled 3 mice for mRNA harvesting per condition for each of 3 time points plus 3 mice for a MSC control-graft condition.

first: Gunnar

last: Poplawski

first: Giovanni

last: Coppola

first: Mark

last: Tuszynski


title: Extensive DNA methylation variation across a single ADPKD kidney

status: Public on Jan 14 2020

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

type: Methylation profiling by high throughput sequencing

summary: We have previously described global hypomethylation and site-specific DNA methylation changes which are associated with disease-state renal tissue in Autosomal Dominant Polycystic Kidney Disease (ADPKD). However, to-date there are no available data on the pattern of DNA methylation across an ADPKD kidney. Here we describe the methylome of eight individual cysts from a single ADPKD patient and peform an intra-individual analysis to identify regions of DNA methylation variability.

overall_design: Here we generated single-nucleotide resolution methylomes of eight individual ADPKD cysts from a single patient using Reduced Representation Bisulfite Sequencing (RRBS).

first: Sarah

last: Bowden

first: Peter

last: Stockwell

first: Euan

last: Rodger

first: Michael

last: Eccles

first: Cherie

last: Stayner


title: Induction of Recurrent Break Cluster Genes in Neural Progenitor Cells Differentiated from Embryonic Stem Cells In Culture

status: Public on Jan 11 2020

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

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: Profiling of APEX-NLS and APEX-PMLca associated regions

status: Public on Jan 10 2020

city: Okazaki

first: Misuzu

last: Kurihara

state: Aichi

address: 5-1 Higashiyama, Myodaiji

country: Japan

institute: National Institute for Basic Biology

summary: To address specificity of ALaP-seq for PMLwt, we performed genome-wide profiling of genomic regions associated with NLS-APEX or PMLca-APEX. Cells were treated with H2O2 to trigger labeling of chromatin with biotin (H2O2+). Experimental negative control for PMLca (H2O2-), where the H2O2 treatment was omitted, was also analyzed.

overall_design: Genome-wide profiling of genomic regions associated with APEX-NLS or APEX-PMLca were analyzed by ALaP-seq.

first: Kagayaki

last: Kato

first: Chiaki

last: Sanbo

first: Shuji

last: Shigenobu

first: Yasuyuki

last: Ohkawa

first: Takeshi

last: Fuchigami

first: Yusuke

last: Miyanari


title: Investigate the role of MLKL in regulating TNF-induced endothelial cell inflammatory response

status: Public on Jan 04 2020

city: Shanghai

first: Dai

last: Jialin

state: Shanghai

address: Room 507-1, Build 6, QiuYue Rd 26, PuDong District

institute: Interdisciplinary Research Center of Biology and Chemistry

summary:
Purpose: Analyze the potential signaling pathways regulated by MLKL under TNF-induced endothelial cell inflammatory response
Methods: HUVECs were allowed to grow to confluency and were starved with basal medium containing 0.5% FBS for 6h. Then treat HUVECs with vehicle, NSA, TNF-alpha, TNF-alpha+NSA for 6h and extract RNA.
Results: NSA reduces the mRNA level of TNF-induced inflammation-related genes and most of these genes are downstream of NF-kappa B signaling pathway.

overall_design: mRNA profiles of HUVECs treated with vehicle, NSA, TNF-alpha, TNF-alpha+NSA  were generated by sequencing.


title: Plant toxin treatment of neonatal mouse cholangiocytes

status: Public on Jan 01 2020

city: Philadelphia

first: Rebecca

last: Wells

state: PA

address: 905 BRB, 421 Curie Blvd.

department: Medicine

institute: University of Pennsylvania

summary: Extrahepatic bile ducts were isolated from mouse pups at days 0-3 and primary cholangiocytes were isolated. Cholangiocytes were treated with DMSO, bilatresone (TOX4), betavulgarin (TOX2), and isoflavanone (TOX3), as per Lorent et al, Science Translationa Medicine 2015;286:286ra67 (Fig. 1), all in DMSO. Treatment concentrations were 2.0 micrograms/ml, for 6 hours.

middle: G


title: Pro-immunogenic impact of MEK inhibition synergizes with agonist anti-CD40 immunostimulatory antibodies in tumor therapy [PDA30364 treated with GEM, CD40, in vivo]

status: Public on Jan 27 2020

last: Volkmar

summary:
Cancer types with lower mutational load and a non-permissive tumor microenvironment are intrinsically resistant to immune checkpoint blockade. While the combination of cytostatic drugs and immunostimulatory antibodies constitutes an attractive concept for overcoming this refractoriness, suppression of immune cell function by cytostatic drugs may limit therapeutic efficacy. Here we show that targeted inhibition of mitogen-activated protein kinase (MAPK) kinase (MEK) does not impair dendritic cell-mediated T-cell priming and activation. Accordingly, combining MEK inhibitors (MEKi) with agonist antibodies (Abs) targeting the immunostimulatory CD40 receptor resulted in potent synergistic anti-tumor efficacy. Detailed analysis of the mechanism of action of MEKi GDC-0623 by means of flow cytometric analysis of the tumor immune infiltrate and whole tumor transcriptomics showed that, in addition to its cytostatic impact on tumor cells, this drug exerts multiple pro-immunogenic effects, including the suppression of M2-type macrophages, myeloid derived suppressor cells and CD4+ T-regulatory cells. In addition, MEKi was found to induce tumor-cell intrinsic interferon signaling, which contributed to antigen presentation by tumor cells. Finally, the tumoridical impact of MEKi involves the activation of multiple pro-inflammatory pathways involved in immune cell effector function in the tumor microenvironment. Our data therefore indicate that the combination of MEK inhibition with agonist anti-CD40 Ab is a promising therapeutic concept, especially for the treatment of mutant Kras-driven tumors such as pancreatic ductal adenocarcinoma.
We used microarrays to monitor transcriptional and cell-type composition changes in murine transplantable tumor models of pancreatic ductal adenocarcinoma (PDA30364), colon cancer (MC38) and melanoma (B16-OVA) upon treatment with MEK inhibitor (GDC-0623), chemotherapeutic agent gemcitabine (GEM), anti-CD40 antibody or the combination of GDC-0623 or chemotherapy Gemcitabine (GEM) and anti-CD40 antibody.

overall_design: RNA was isolated from PDA30364 tumor pieces of at 4 animals per treatment group at the end of the treatment period and subjected to transcriptome analyses. After quality control, samples were normalized by applying the Robust Multichip Averaging (RMA) normalization method.

first: Daniel

last: Baumann

first: Rienk

last: Offringa


title: Skeletal muscle regeneration is compromised in advanced diabetic peripheral neuropathy

status: Public on Jan 22 2020

city: Saint Louis

first: Bo

last: Zhang

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

summary: DPN muscle exhibits features of degeneration with attempted regeneration.  In the most severely pathological muscle samples, regeneration appears to be stymied and our data suggest that this may be partly due to intrinsic dysfunction of the satellite cell pool in addition to extrinsic structural pathology (e.g. nerve damage).

overall_design:
Biopsies were acquired from two muscles in individuals with and without diabetic neuropathy undergoing below knee amputation surgery.  Biopsies were subdivided for histological analysis, transcriptional profiling and satellite cell isolation and culture.

DPN: diabetic peripheral neuropathy
MNC: metabolically normal control

first: Gretchen

middle: A

last: Meyer

first: Kathryn

middle: L

last: Bohnert

first: Paul

last: Gontarz


title: Bedaquiline remodels the macrophage response

city: Paris

first: Alexandre

last: Giraud-Gatineau

address: 25-28 rue du docteur roux

department: Microbiology

country: France

institute: Institut Pasteur

summary:
Background: Infectious diseases are still a leading cause of death and, with the emergence of drug resistance, pose a great threat to human health. New drugs are thus continually being developed, without their effects on the immune system being studied in-depth. Here we aim to evaluate the impact of a recently release anti-TB drug, named bedaquiline (BDQ), on the response of human macrophages infected with Mycobacterium tuberculosis (MTB).

Results: Here, we used MTB resistant to BDQ as a model of bacterial infection to examine the impact of BDQ on the human macrophage response. Gene expression profiling has revealed about 1,500 genes differentially expressed in MTB infected macrophages incubated with BDQ. The expression of 499 genes was upregulated and that of 996 downregulated upon treatment. The gene set up-regulated by BDQ was significantly enriched for genes involved in glucose/phospholipid metabolism, lysosome and autophagy. We found similar results with uninfected macrophages-treated with BDQ.

Conclusions: Our results highlight the importance to study the interactions between antibiotics and host cells at the molecular level to better understand the consequences of antibiotic treatment during infection

overall_design: Evaluation of host response to BDQ treatment in infected and uninfected human macrophages.

first: Ludovic

last: Tailleux


title: Preservation of stemness in high-grade serous ovarian cancer organoids requires low Wnt environment

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: High-grade serous ovarian cancer (HGSOC) creates a unique clinical challenge due to late detection, limited therapeutic options and wide-spread resistance to chemotherapy, all of which lead to very low survival rates. It is now widely recognized that this cancer emerges as metastasis from the fallopian tube and the lack of suitable in vitro disease models poses a major obstacle for efforts to improve our understanding of this deadly disease. We used organoids of healthy human FT epithelium as a model for stepwise genetic modification towards malignancy, using shRNA-mediated knockdown (KD) of three major HGSOC driver genes: p53, PTEN and Retinoblastoma (Rb). These pathways are known to be disrupted in the vast majority of HGSOC patients (>95%, 45% and 67% of cases, respectively as reported by TCGA consortium). Unexpectedly, combined loss of function of the three tumor suppressor proteins, p53, PTEN and Rb, led to a growth arrest and loss of stemness if organoids are cultured in medium optimized for healthy FT epithelium, which maintains high Wnt signaling and BMP pathway inhibition. This designates a requirement for alterations in the exogenous signaling cues to facilitate transformation. Indeed, we show that successful expansion of patient-derived HGSOC organoids from solid tumor deposits depends on the absence of exogenous Wnt3A in the medium. Using a combinatorial screening approach of different medium compositions, we have established 15 organoid lines, which closely resemble the parental tumor tissue and express hallmarks of HGSOC phenotype as revealed by histology and global gene expression profiles. Strikingly, the medium optimized for ovarian cancer organoids also rescued the growth of the modified organoid lines, showing that changes within the niche environment are required to promote stemness upon depletion of p53/PTEN/RB. Likewise, surface expression of the stemness marker CD133 was strongly increased in triple KD organoids in the absence of Wnt3A/Rspo1. Complementary to this finding, the addition of Wnt agonists to cancer organoids led to rapid growth arrest and a sharp drop in stemness, as evidenced by cell viability assay and the number of CD133 positive cells, respectively. Taken together, our data reveal that critical changes in the paracrine environment constitute early events during HGSOC development.

overall_design:
Microarray experiments were performed as dual-color hybridizations on Agilent whole human catalog 4x44K (Agilent-0126652) arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

To compensate for dye-specific effects, dye-reversal color-swap hybridizations were applied. The polarity (indicated in the sample description field) is used for combining color-swap replicates.

first: Mirjana

last: Kessler

first: Karen

last: Hoffmann

first: Thomas


title: microRNA Profiling during endoderm differentiation from mouse embryonic stem cells

status: Public on Dec 31 2019

city: Chuo-ku

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

institute: National cancer center research institute

summary: The role of microRNAs (miRNAs) during mouse early development, especially in endoderm germ layer formation, is largely unknown. Here, using miRNA profiling, we discovered that miR-124a negatively regulates endoderm lineage commitment in mouse embryonic stem cells (mESCs). We showed that miR-124a inhibits endoderm differentiation in vitro through targeting the 3’ untranslated region (UTR) of Sox17 and Gata6, revealing the existence of an interplay between miR-124a and Sox17/Gata6 transcription factors in hepato-specific gene regulation. Besides, we proposed an in vivo system that utilizes teratoma to evaluate the functional role of miRNA in lineage specification. We demonstrated that ectopic expression of miR-124a in teratomas suppressed endoderm and mesoderm lineage differentiation while augmented the differentiation of ectoderm lineage. Collectively, our findings suggested that miR-124a plays a significant role in mESCs lineage commitment.

overall_design: To study the miRNA expression profiles during endoderm differentiation in mouse, we first induced definitive endoderm (DE) from mESC using Activin A, Noggin, and GSK-3 inhibitor (CHIR99021) (ActA-NG-CHIR). Next, RNA samples were harvested at 6 different time points along endoderm differentiation (Day 0, 2, 3, 4, 5 and 6). Experiment was performed in duplicate.

first: Lee

last: Liew

first: Takahiro

last: Ochiya


title: Molecular targets of HIV integrase inhibitor, MK-2048, on ATL cells

city: Musashimurayama-shi

first: Emi

last: Ikebe

address: 4-7-1, Gakuen

institute: National Institute of Infectious Diseases

summary: Adult T-cell Leukemia (ATL) is a highly chemoresistant malignancy of peripheral T lymphocytes, associated with retrovirus human T-cell leukemia virus type I (HTLV-1). To elucidate the complex molecular mechanism of anti-Growth effect of the HIV integrase inhibitor, MK-2048 in ATL cells, we attempted to perform gene expression profiling.

overall_design: Four ATL cell lines were cultured with or without MK-2048, then analysed.


title: Circadian clock regulation of alternative splicing and alternative polyadenylation in Arabidopsis thaliana

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

summary:
Purpose: Circadian clock in plants temporally coordinates biological processes throughout the day synchronizing gene expression with environmental changes. Here, we examined the genome-wide circadian and diurnal control of Arabidopsis transcriptome using high throughout RNA-seq approach.
Methods: Transcriptional and posttranscritional profiles were identified and characterized for Arabidopsis seedlings grown under continuous light or long-day condition (16 h light/8 h dark) for one day (each condition has two biological replicates).
Results: We show that rhythmic posttranscriptional regulation is also a significant factor for genome-wide profile of circadian plant transcriptome. Two major posttranscriptioal mechanisms alternative splicing (AS) and alternative polyadenylation (APA) show circadian rhythmicity, resulting from the oscillation in the genes invovled in AS and APA.
Conclusions: Arabidopsis circadian clock not only controls the transcription of genes, but also affects their posttranscriptional regulation through regulating AS and APA.

overall_design: Posttranscriptional profiles of Arabidopsis seedlings grown under continuous light or long-day condition (16 h light/8 h dark) for one day were generated using Illumina HiSeq 4000.

first: Onur

last: Oztas


title: HIV-1 RNA structure and heterogeneity analysis

city: Cambridge

first: Silvi

last: Rouskin

address: 455 Main Street

institute: Whitehead Institute

summary:
The goal of this set of experiments is to determine the structure of HIV-1 NL4-3 and NHG RNA structure using a novel algorithm that allows for the identification of multiple RNA folding conformations. The input data used for this algorithm is DMS-MaPseq data. We focused on two specific areas of the HIV-1 genome, the Rev Response Element (RRE) and A3 splice acceptor site, as well as probing the whole HIV-1 genome. RNA is DMS-modified in vitro and in vivo as indicated.
The goal of this data set was to test the novel alternative RNA structure detecting algorithm (DREEM) using RNA molecules with known structures.

sample_organism:
Vibrio vulnificus
Homo sapiens
Human immunodeficiency virus 1
synthetic construct

overall_design:
DMS-Modification and targeted sequencing of the HIV-1 A3 splice acceptor site in CD4+ T-cells or transfected HEK293t cells. 1 sample in CD4 T cells, 3 in HEK293t.
DMS-modification and targeted sequencing of the HIV-1 A3 splice acceptor site in transfected HEK293t cells using two designed mutant viruses. 1 sample per mutant.
HEK293t cells were transfected with a plasmid containing HIV-1 NHG. The cells were DMS-modified and RNA was extracted and sequenced. RNA strucural models were generated using a novel algorithm for regions of interest across the HIV-1 genome.
Two HIV-1 RRE mutants were transfected in a HIV-1NHG plasmid into HEK293. Structure of both mutants were analyzed and mixed computationally in order to validate the DREEM pipeline.
HIV-1 RNA structure of RRE was analyzed after DMS modification in vitro, in vivo and in the virion. For in vitro samples, HIV-1 RRE was in vitro transcribed. For in vivo and in virion, isolated CD4+ T-cells were infected with HIV-1 NL4-3.
U4-6 core-domain was in vitro transcribed, refolded and DMS modified. The RNA was then prepared for sequencing following the DMS-MaPseq library generation protocol and clustered by DREEM.
Adenine Riboswitch was in vitro transcribed, refolded and DMS modified with and without 5 mM adenine. The RNA was then prepared for sequencing following the DMS-MaPseq library generation protocol and clustered by DREEM.

Samples StemA_C_mix_1-5: The goal of this set of experiments is to validate a novel RNA structure clustering algorithm. Two closely related structured RNAs were in vitro transcribed and mixed at different proportions. The RNA was DMS-modified and used for DMS-MaPseq and clustering by the algorithm DREEM.
Two RNAs the form different structures within  the human gene MRPS21 we in vitro transcribed, mixed at different proportions and DMS-modified. The RNA structure was determined by DMS-MaPseq and clustering with the DREEM algorithm.

first: Phillip

last: Tomezsko

first: Paromita

last: Gupta


title: ALaP-seq and RNA-seq analyses of paraquat treated mESCs

first: Misuzu

last: Kurihara

summary: To address the roles of PML bodies in transcription under stress condition, we performed ALaP-seq and RNA-seq with paraquat treated mESCs.

overall_design: Paraquat treated mESCs were analyzed by ALaP-seq or RNA-seq.

first: Kagayaki

last: Kato

first: Chiaki

last: Sanbo

first: Shuji

last: Shigenobu

first: Yasuyuki

last: Ohkawa

first: Takeshi

last: Fuchigami

first: Yusuke

last: Miyanari


title: Miswired enhancer logic drives translocation positive rhabdomyosarcoma

status: Public on Dec 25 2019

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: Core regularity transcription factors (CR TFs) define cell identity and lineage through an exquisitely precise and logical order during embryogenesis and development.  These CR TFs regulated one another in three-dimensional space via distal enhancers that serve as logic gates embedded in their TF recognition sequences. Aberrant chromatin organization resulting in miswired circuitry of enhancer logic is a newly recognized feature in many cancers.  Here, we report that PAX3-FOXO1 expression is driven by a translocated FOXO1 distal super enhancer (SE).  ChIP-seq in tumors bearing rare PAX translocations implicate enhancer miswiring is a pervasive feature across all FP-RMS tumors.  Therefore, our data reveal a mechanism of a translocated hijacked enhancer which disrupts the normal CR TF logic during skeletal muscle development (PAX3 to MYOD to MYOG), replacing it with an infinite loop logic that makes rhabdomyosarcoma cells unable to exit the undifferentiated proliferating stage.

overall_design: Genome-wide profiles for active genes and enhancers via ChIP-seq for H3K27ac in Rhabdomyosarcoma (RMS) primary tumor samples.

first: Berkley

middle: E

last: Gryder

first: Xinyu

last: Wen


title: Fibrosis growth factor 23 is a promoting factor for cardiac fibrosis in the presence of transforming growth factor-β1

status: Public on Dec 10 2019

city: Tokyo

first: Toru

last: Akaike

address: 3-25-8 Nishi-Shimbashi, Minato-ku

department: Cell Physiology

institute: The Jikei University

summary:
We demonstrated that, four weeks after the pulmonary artery banding (PAB) operation, rats could be divided into two groups: an F+ group in which the fibrotic area occupied more than 6.5% of the whole area of the heart tissues, and an F- group in which the fibrotic area occupied less than 6.5% of this area.
We used microarrays to elucidate the fibrosis initiating master factor using heart samples obtained from PAB or sham-operated rats.

overall_design: Frozen rat right ventricles in the Sham, F- (no fibrosis), and F+ (fibrosis) groups were used (n=3 each). Then microarray analysis was performed.

first: Ken

last: Uesugi

first: Susumu

last: Minamisawa


title: Chemical reprogramming of fibroblasts to photoreceptor like cells [RNA-Seq]

status: Public on Dec 11 2019

first: Koray Dogan

last: Kaya

address: 6 CENTER DR

department: NEI

institute: NIH

summary: Reprogramming of mouse embryonic fibroblasts (MEFs) to photorereceptor like cells by five chemicals.

overall_design: Total RNA from MEFs, reprogramming intermediates (days 5,8) and reprogrammed photoreceptors (day 11) were extracted for library preparation and RNA Sequencing. All the data analyzed together with WT samples of GSE74660

first: Biraj

last: Mahato

first: Yan

last: Fan

first: Nathalie

last: Sumien

first: Ritu

last: Shetty

first: Zhang

last: Wei

first: Delaney

last: Davis

first: Thomas

last: Mock

first: Subrata

last: Batabyal

first: Aiguo

last: Ni

first: Samarendra

last: Mohanty

first: Zongchao

last: Han

first: Rafal

last: Farjo

first: Michael

middle: J

last: Forster

first: Anand

last: Swaroop

first: Sai

last: Chavala


title: Homeostasis and transitional activation of regulatory T cells require c-Myc

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
Regulatory T (Treg) cell activation and expansion during neonatal life and in response to inflammation are critical for immunosuppression, yet the mechanisms governing these events are incompletely understood. We report that the oncogene and transcriptional regulator c-Myc (Myc) controls immune homeostasis through regulation of Treg cell accumulation and functional activation. Myc activity is enriched in Treg cells generated during neonatal life and responding to inflammation. Myc-deficient Treg cells show cell-intrinsic defects in overall accumulation and ability to transition to an activated state during early life or acute inflammation. Consequently, loss of Myc in Treg cells results in a rapid, early-onset autoimmune disorder accompanied by uncontrolled effector CD4+ and CD8+ T cell responses. We also provide evidence that Myc regulates mitochondrial oxidative metabolism but is dispensable for fatty acid oxidation (FAO). Indeed, Treg cell-specific deletion of Cox10, which is required for oxidative phosphorylation, but not Cpt1a, the rate-limiting enzyme for FAO, results in impaired Treg cell function and maturation. Thus, Myc coordinates Treg cell accumulation, transitional activation and metabolic programming to orchestrate immune homeostasis.
We used microarrays to compare the global transcription profiles of WT and Myc-null Treg cells.

overall_design: In total 8 samples were analyzed: FACS-sorted Treg cells from WT mice (n = 4); FACS-sorted Myc-null Treg cells from Foxp3CreMycfl/fl mice (n = 4)

first: Jordy

last: Saravia

first: Hu

last: Zeng

first: Yogesh

last: Dhungana

first: Peter

last: Carmeliet

first: Hongbo

last: Chi


title: An intrinsic oscillator drives the blood stage cycle of the malaria parasite, Plasmodium falciparum

city: Durham

first: Steven

last: Haase

state: North Carolina

department: Biology

institute: Duke University

summary: The blood-stage infection of the malaria parasite, Plasmodium falciparum, exhibits a 48-hour developmental cycle that culminates in the synchronous release of parasites from red blood cells, triggering 48-hour fever cycles in the host. This cycle could be driven extrinsically by host circadian processes, or by a parasite-intrinsic oscillator. To distinguish between hypotheses, we examined the P. falciparum cycle in an in vitro culture system that lacks extrinsic cues from the host and show that P. falciparum has molecular signatures associated with circadian and cell-cycle oscillators. Each of four strains examined has a unique period, indicating strain-intrinsic period control. Finally, we demonstrate that parasites have low cell-to-cell variance in cycle period, on par with a circadian oscillator. We conclude that an intrinsic oscillator is responsible for Plasmodium’s rhythmic life cycle.

overall_design: Time-series sampling of four strains of Plasmodium falciparum cultured in vitro. Cultures were sampled every three hours for up to 69 hours, allowing capture of at least one entire developmental cycle.

first: Lauren

middle: M

last: Smith

first: Francis

last: Motta

first: Garima

last: Chopra

first: J

middle: K

last: Moch

first: Robert

middle: R

last: Nerem

first: Bree

last: Cummins

first: Kimberly

last: Roche

first: Christina

last: Kelliher

first: Adam

last: Leman

first: John

last: Harer

first: Tomas

last: Gedeon

first: Norman

last: Waters

middle: B


title: MeRIP sequencing reveals angiogenic properties of vascular endothelial cells

status: Public on Dec 20 2019

city: Beijing

first: Lin-jian

last: Wang

address: No.119 South 4th Ring West Road

institute: Beijing Tiantan Hospital, Capital Medical University

summary: We report the application of MeRIP sequencing technology for high-throughput profiling of RNA m6A modifications in wide-type and knock-down METTL3 or WTAP Human Umbilical Vein Endothelial Cells (HUVECs). Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads. Clean reads of all libraries were aligned to the reference genome (HG19) by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. And, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. qRT-PCR validation was performed using SYBR Green assays. Finally, we find that METTL3/WTAP can regulate the expression level of target genes through m6A modification in HUVECs. This study provides a framework for applying MeRIP sequencing profiles to characterize vascular endothelial cells.

overall_design: Examination of  m6A modification in wide-type and knock-down METTL3 or WTAP HUVECs, each with 2 replicates.


title: Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid Leukemia

status: Public on Dec 05 2019

city: FARMINGTON

first: Yijun

last: Ruan

state: CT

address: 10 DISCOVERY DR

department: Ruan

institute: The Jackson Laboratory

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

overall_design: Refer to individual Series


title: Neutrophil extracellular trap induced dendritic cell activation leads to Th1 polarization in type 1 diabetes

status: Public on Jan 07 2020

city: Prague

last: Klocperk

address: V Uvalu 84

department: Department of Immunology

country: Czech Republic

institute: University Hospital in Motol

summary: We performed a comparison of transcriptome between monocyte-derived dendritic cells (moDC) cultured with neutrophil extracellular traps (NETs) from healthy donors or type 1 diabetes (T1D) patients. The source of moDCs is healthy donors and T1D patients

overall_design: T1D moDCs were cultivated with healthy NETs, autologous T1D NETs or left untreated. Simularly, healthy moDCs were treated with own healthy NETs, T1D NETs or left untreated

first: Zuzana

last: Parackova

first: Anna

last: Sediva


title: Slo2 potassium channel function depends on a SCYL1 protein

status: Public on Dec 03 2019

city: Denton

first: Bojun

last: Chen

state: TX

address: 1511 W Sycamore St

department: Biological Sciences

institute: University of North Texas

summary: Slo2 potassium channels play important roles in neuronal function, and their mutations in humans cause epilepsies and profound cognitive defects. However, little is known how Slo2 function is regulated by other proteins. In a genetic screen for suppressors of a sluggish phenotype caused by a hyperactive C. elegans Slo2 (SLO-2), mutants of adr-1, a gene important to RNA editing, were isolated. SLO-2 current in motor neurons is substantially decreased in the mutants. However, slo-2 transcripts have no detectable RNA editing events and exhibit a similar expression level in wild type and adr-1 mutants. In contrast, mRNA level of scyl-1, which encodes an orthologue of mammalian SCYL1 (a pseudokinase), is greatly reduced in adr-1 mutants due to deficient RNA editing at a single adenosine in its 3’-UTR. SCYL-1 physically interacts with SLO-2 in neurons. Single-channel open probability of SLO-2 in neurons is reduced by ~50% in scyl-1 knockout whereas that of human Slo2.2/Slack is doubled by SCYL1 in a heterologous expression system. These results suggest that SCYL-1/SCYL1 is an evolutionarily conserved regulator of Slo2 channels.

overall_design: Examination of gene expression in wild type and adr-1 mutant worms in three biological replicates.

first: Longgang

last: Niu

first: Ping

last: Liu

first: Zhao-Wen


title: Laboratory mice housed in the natural environment identifies genetic and environmental contributions to immune variation

status: Public on Dec 01 2019

city: New York

first: Joseph

last: Devlin

state: NY

address: 430 East 29th Street

institute: New York University Langone Health

summary: The relative contribution of genetic and environmental factors to variation in immune response is still poorly understood. Here, we performed a deep phenotypic analysis of immunological parameters and molecular profiles of laboratory mice released into an outdoor enclosure, carrying genetic susceptibility genes (Nod2 and Atg16l1) implicated in the development of inflammatory bowel diseases. Differences in lymphocyte populations were largely driven by the lab and wild environment. However, cytokine production after stimulation with microbial antigens showed a stronger genetic component in the lab, which was reduced after exposure to the wild environment. Multi-omic models identified key transcriptional factors associated with lymphocyte changes predictive of the environment, as well as sub-networks associated with cytokine responses against Candida albicans and Bacteroides vulgatus. Hence, exposing laboratory mice of different genetic backgrounds to the outdoor environment may identify important contributors to immune variation.

overall_design: Bulk transcriptome of mesenteric lymph nodes from laboratory and rewilded mice

first: Jian-Da

last: Lin

first: Frank

last: Yeung

first: Ken

last: Cadwell

first: Andrea

last: Graham

first: P'ng

last: Loke


title: Expression data from livers of 6 and 10-weeks garlic-fed mice

city: Urla

first: Bunyamin

last: Akgul

state: izmir

address: Gulbahcekoyu

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

summary:
Garlic is a popular flavor enhancer in modern cuisines. Although anti-atherosclerotic, anti-proliferative, hypolipidemic and chemopreventative effects of garlic are known for a long time, the mechanisms of garlic as a dietary supplement ramain largely unknown.
We used microarrays to analyze the global programme of gene expression in control (cellulose) and garlic-fed C57BL/6J mice serendipitously infected with Pasteurella multocida and identified acute phase response genes, particularly Lcn2 and Orm2, as the major players in the innate response. Also dieraty garlic suppressed pasteurella infection in C57BL/6J mice.

overall_design: 8-week old male C57BL/6J mice were divided into two diet groups (two cages of each diet) and maintained at a non-barrier facility. Mice were fed (ad libitum) a special diet (Yeh and Yeh, 1994) with 4% cellulose (Control group, 3 mice) or 4% lyophilized raw garlic powder (Treatment group, 3 mice). At the end of the 6 and 10-week treatment, liver organs were used for RNA isolation and arraying.

first: Bünyamin

last: Akgül

first: Chen-Pei

middle: D

last: Tu


title: Autologous microgratf accelerates endogenous wound healing response through ERK-induced cell migration.

city: Leuven

first: Frederic

last: Lluis

state: Leuven

address: Herestraat 49

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

summary: Defective fibroblast migration cause delayed wound healing (WH) and chronic skin lesions. Autologous micrograft (AMG) therapies have recently emerged as a new effective treatment able to improve wound healing capacity. However, the molecular mechanisms connecting their beneficial outcomes with the wound healing process are still unrevealed. Here, we show that AMG modulates primary fibroblast migration and accelerates skin re-epithelialization without affecting cell proliferation. We demonstrate that AMG is enriched in a pool of WH-associated growth factors that may provide the initiation signal for faster endogenous wound healing response. This, in turn leads to increased cell migration rate by elevating activity of ERK and subsequent activation of matrix metalloproteinase expression and their extracellular enzymatic activity. Moreover, AMG-treated wounds showed increased granulation tissue formation and organized collagen content. Overall, we shed light on AMG molecular mechanism supporting its potential to trigger highly improved wound healing process.

overall_design: A total of 14 samples have been used to analyse transcriptome changes in wounded murine primary fibroblasts upon Autologous Micrograft (AMG) treatment. Samples have been divided in two groups: Untreated and AMG-treated. Samples have been exposed to AMG treatment for different time periods (1, 5, 12 and 24 hours). Each time of treatment includes 1 biological sample, except for 5 hours of treatment where we included three additional biological replicates.

first: Martina

last: Balli

first: Francesca

last: Vitali

first: Adrian

last: Janiszewski

first: Ellen

last: Calawé

first: Alvaro

last: Cortés-Calabuig

first: Sebastien

last: Carpentier

first: Robin

last: Duelen

first: Flavio

last: Ronzoni

first: Gabriele

last: Ceccarelli

first: Maria

last: De Angelis

first: Aernout

last: Luttun

first: Riccardo

last: Bellazzi

first: Maurilio

last: Sampaolesi


title: Transcriptome profiling of CXCR2+ neuroendocrine (NE) tumor cells purified from patients' fresh prostate adenocarcinoma

first: Yanjing

last: Li

state: NC

address: 905 S. LaSalle Street GSRB1, 3038

summary: The development of therapy resistance is inevitable in prostate cancer (PCa) despite maximal inhibition of androgen receptor (AR) signaling. Here, we for the first time purified a rare AR-negative NE-cell subset from primary fresh human PCa tissue based on cell-surface receptor CXCR2 and showed that they possess gene signatures of lethal cancer through transcriptional profiling. Functional studies demonstrate CXCR2 to be a driver of NE cells’ key phenotypes, including loss of AR expression, lineage plasticity, and resistance to hormonal-therapy. Furthermore, CXCR2-driven NE cells are critical for the tumor microenvironment by providing a survival niche for the bulk AR+ luminal cells. Importantly, inhibition of CXCR2 by a chemical inhibitor or genetic manipulation dramatically inhibits aggressive PCa cells in-vitro and in-vivo, demonstrating a central role of NE cells in human PCa. Therefore, we firmly established that targeting NE cells through CXCR2 represents a novel, AR-independent therapeutic strategy that will eliminate all tumor cells (NE and luminal), achieving superior therapeutic efficacy.

overall_design: We performed RNA-seq analysis of theTrop2+CXCR2+ (NE tumor cells) and Trop2+CXCR2- (luminal type tumor cells) populations isolated from patients’ fresh PCa tissue immediately after radical prostatectomy. We also did RNA-seq on basal cells population purified through Trop2+CXCR2-CD49f+ markers from benign prostate tissue for comparison. To study the CXCR2-induced gene network, we established CXCR2 overexpressed LNCaP (LNCaP-CXCR2) cell line and examined the gene expression profiles in LNCaP and LNCaP-CXCR2 cells.

first: Suzette

last: Farber-Katz

first: Rachid

last: Karam

first: Tyler

last: Landrith

first: Bing

first: Sitao

last: Wu

first: Vickie

last: Hsuan

first: David

last: Corcoran


title: Optimization of NaIO4 Oxidation and Deep-sequencing Methodology for Detection of 3' End Methylation of Small RNAs in low-input RNA Samples

city: Shanghai

first: Ligang

address: 320 Yueyang Road

department: Shanghai Institutes for biological Sciences

institute: Chinese Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: The 2'-O-methylation is present at the 3' end of various small RNAs and has important biological functions. At present, NaIO4 oxidation treatment combined with deep sequencing is one of the most powerful method to study the 2'-O-methylation of small RNAs. However, currently used protocol requires 3 μg of total RNA and is not suitable for studying 3' terminal 2'-O-methylation of small RNAs in limited number of cells. In this study, We optimized the oxidation condition, and omitted the glycerol addition when we stop the oxidation reaction. With these improvements, we are able to identify the small RNAs bearing 3’ terminal 2'-O-methylation using as little as 10 ng total RNA from mouse testis, providing a robust protocol suitable for investigating 3’ terminal 2'-O-methylation of small RNAs in a small number of cells.

overall_design: We optimized the oxidation condition, and omitted the glycerol adding when we stop the oxidation reaction. With these improvements, we are able to identify the small RNAs bearing 3’ terminal 2'-O-methylation using as little as 10 ng total RNA from mouse testis, providing a robust protocol suitable for investigating 3’ terminal 2'-O-methylation of small RNAs in a small number of cells

first: Wanqiang

last: Xue

first: Li

last: Hou

first: Ronghong


title: Poor maternal nutrition during gestation alters prenatal muscle growth and development in offspring

city: Storrs

first: Kriste

last: Govoni

address: 3636 Horsebarn Road Ext., Unit 4040

department: Animal Science

institute: University of Connecticut

summary: We hypothesized that poor maternal nutrition during gestation would reduce the growth and development of offspring muscle prenatally, reduce the number of myogenic progenitor cells, and result in changes in the global expression of genes involved in prenatal muscle development and function. Ewes were fed a control (100% NRC)-, restricted (60% NRC),- or over-fed (140% NRC) diet beginning at day 30 of gestation until day 45, 90, and 135 of gestation or until parturition.  In offspring, we report altered secondary: primary muscle fiber ratios and percent PAX7 positive cells during fetal development. In addition, changes in muscle mRNA expression were observed between maternal dietary treatments and over timepoints during gestation. In conclusion, poor maternal nutrition during gestation contributes to altered offspring muscle growth during early fetal development which persists throughout the fetal stage.

overall_design: Offspring longissimus dorsi muscle samples from ewes fed control, restricted, and over-fed diet during gestation were collected from offspring at day 90 and 135 of gesetation and at birth. RNA-Seq analysis was performed on all samples at each time point to determine the effect of diet and time on gene expression.

first: M

last: Gauvin

first: S

last: Pillai

last: Reed

first: J

last: Stevens

last: Hoffman

first: A

last: Jones

last: Zinn

first: K


title: CpG DNA methylation is altered in the PKD1 gene body but not promoter in autosomal dominant polycystic kidney disease

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

institute: University of Otago

summary: Limited data exists on alterations in DNA methylation that are associated with Autosomal Dominant Polycystic Kidney Disease (ADPKD). Given there are similarities between cystic kidney disease and neoplasia, and that DNA methylation inhibitors are FDA-approved for the treatment of myelodysplastic syndrome, we performed genome-scale methylation analysis of cortical kidney tissue from four ADPKD patients and nonADPKD cortical kidney tissue from three individuals to identify the methylation patterns of ADPKD tissue.

overall_design: He re we generated single-nucleotide resolution methylomes of seven cortical kidney tissue samples using Reduced Representation Bisulfite Sequencing (RRBS). We have two groups, nonADPKD (n =3) and ADPKD (n=4).

first: Sarah

last: Bowden

first: Micheal

last: Eccles

first: Michael

last: Bates

first: Euan

last: Rodger

first: Cherie

last: Stayner


title: Model-driven generation of artificial yeast promoters

city: Stanford

first: Christina

last: Smolke

state: CA

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

summary: Promoters play a central role in controlling gene regulation; however, a small set of promoters is used for most genetic construct design in the yeast Saccharomyces cerevisiae. The ability to generate and utilize models that accurately predict protein expression from promoter sequence may enable rapid generation of novel useful promoters, facilitating synthetic biology efforts in this model organism. We measured the activity of over 675,000 unique sequences in a constitutive promoter library, and over 327,000 sequences in a library of inducible promoters. Training an ensemble of convolutional neural networks jointly on the two datasets enabled very high (R2 > 0.79) predictive accuracies on multiple prediction tasks. We developed model-guided design strategies which yielded large, sequence-diverse sets of novel promoters exhibiting activities similar to current best-in-class sequences. In addition to providing large sets of new promoters, our results show the value of model-guided design as an approach for generating DNA parts.

overall_design: Promoter activity was measured using a “FACS-seq” reporter-based assay. Libraries of yeast cells harboring a plasmid in which mCherry expression was driven by PTEF1 (as a control for expression noise) and GFP expression was driven by a member of a sequence library were grown in synthetic complete media containing 2 percent dextrose and lacking uracil, and were FACS-sorted on the basis of the ratio of GFP to mCherry expression. Plasmid DNA was extracted from each bin, and bin-specific barcodes were applied by PCR. PCR amplicons were pooled and sequenced to derive read counts for each sequence in each bin; this data was used to extract quantitative estimates of promoter activity for each sequence. This was first done for a library of constituitive promoters based on natural pGPD, then for one of beta-estradiol-inducible promoters based on the pZEV system (McIsaac et al. 2014, PMID 24445804). Neural network models of promoter activity were then trained on results from the first two libraries and leveraged to generate sets of novel promoters designed to fulfill a variety of objectives. These designs, and control promoters from the first two libraries, were assayed in the third experiment. In the first two experiments, samples were sequenced on Illumina Miseq (2x300) and Nextseq (1x75) platforms. In the third, only Miseq was used. In the GPD experiment, 2 replicates of 12 bins each were collected; in the following experiments, 12 bins each in the presence and absence of 1 uM beta-estradiol inducer were collected. In some experiments, aliquots of the original library were also prepared for sequencing.

first: Benjamin

last: Kotopka


title: Transcriptomic signature of spinal cord from CHMP2Bintron5 mice

status: Public on Dec 26 2019

city: Strasbourg

first: Frédérique

last: René

address: 11 rue Humann

department: U1118 INSERM

institute: INSERM  - University of Strasbourg

summary: We report transcriptomic dysregulations in the spinal cord of asymptomatic (A: 1.5 months) symptomatic (S: 6 months) and end stage (E: 10-12 months) CHMP2Bintron5 mice by RNA sequencing. We found that genes related to immune system  and  lipid metabolism  had altered expression levels at 1.5 month.  Expression of genes related to neuronal system was atletred at 6months and expression of genes related to neuronal system and extracellular matrix xere dfound deregulated at the end-stage. These results were used to determine the change of transcriptomic profile throughout the course of the disease.

overall_design: At 1.5 month: 4 spinal cord samples from CHMP2Bintron5 mice and 6 spinal cord samples of non-transgenic control mice were analyzed. At 6 months: 4 spinal cord samples from CHMP2Bintron5 mice and 5 spinal cord samples of non-transgenic control mice were analyzed. At 12 months: 6 spinal cord samples from CHMP2Bintron5 mice and 6 spinal cord samples of non-transgenic control mice were analyzed.

last: RENE

first: Céline

last: Keime


title: Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid Leukemia (ChIA-PET)

first: Yijun

last: Ruan

summary: Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML/RARα, a major etiological agent in APL. Although PML/RARα is critical, the molecular mechanisms remains largely unknown. Here, using an inducible system, we comprehensively analyzed the 3D genome organization in myloid cells and its reorganizationn after PML/RARα induction, and performed additional analysis in patient-derived APL cells with native PML/RARα. We discovered that PML/RARα mediate extensive chromatin interactions genome-wide. Globally, it redefine the chromatin topology of the in myloid genome toward a more condensed configuration in APL cells; locally, it intrude RNAPII-associated interaction dmains, interrupt myeloid-specific transcription factors binding at enhancers and super-enahncers, and lead to transcriptional repression of genes critical for myeloid differentiation and maturation. Together, our results provide novel insights of a topological framework for PML/RARα’s roles in transforming myeloid into leukemia, likely a general mechanism for oncogenic fusion proteins in cancers.

overall_design:
Three factors (PML/RARA fusion protein, CTCF and RNAPII)  associated chromatin interaction maps are generated and used for exploring 3D genome architecture changes with two APL cell lines (U937-PR9 and NB4) during the APL leukogenesis.
Paired-end sequencing (2 ×150bp) was used for ChIA-PET libraries  with Illumina Hiseq 2500 or Illumina Nextseq 500.

first: Ping

last: Wang

first: Zhonghui

last: Tang

first: Byoungkoo

last: Lee


title: Transcriptome analysis of germinal center B cells of WT and SAP-deficient mice

status: Public on Dec 28 2019

city: Rehovot

first: Ziv

last: Shulman

address: 234 Herzl st.

country: Israel

institute: Weizmann Institute of Science

summary: Analysis of germinal center B cells derived from WT and SAP-deficient mice revealed that SAP-deficient mice have reduced Myc signature

overall_design: Peyer's patches from WT and SAP-deficient mice were removed and germinal center B cells were sorted and sequenced.

first: Adi

last: Biram


title: Gene expression profiles between miRNA Negative control-treated and miR-124a-3p mimic treated-teratomas

city: Chuo-ku

first: Yusuke

last: Yamamoto

address: 5-1-1, Tsukiji, Chuo-ku

institute: National cancer center research institute

summary: The role of microRNAs (miRNAs) during mouse early development, especially in endoderm germ layer formation, is largely unknown. Here, using miRNA profiling, we discovered that miR-124a negatively regulates endoderm lineage commitment in mouse embryonic stem cells (mESCs). We showed that miR-124a inhibits endoderm differentiation in vitro through targeting the 3’ untranslated region (UTR) of Sox17 and Gata6, revealing the existence of an interplay between miR-124a and Sox17/Gata6 transcription factors in hepato-specific gene regulation. Besides, we proposed an in vivo system that utilizes teratoma to evaluate the functional role of miRNA in lineage specification. We demonstrated that ectopic expression of miR-124a in teratomas suppressed endoderm and mesoderm lineage differentiation while augmented the differentiation of ectoderm lineage. Collectively, our findings suggested that miR-124a plays a significant role in mESCs lineage commitment.

overall_design: Formation of teratomas derived from mESCs was performed in immunodeficiency mouse (BALB/c Nude). Mice were randomly divided into 2 groups (miR-124a vs Control) for in vivo miRNA transfection experiment (n=3 in each group). In vivo miRNA transfection was performed by intratumoral administration of miRNAs: “Atelogen QG” complexes at a final concentration of 15 µg/100 µL. In vivo delivery of miRNAs was performed once every 3 days until Day 28. At the end of the experiment, teratomas were harvested for histological analysis and microarray analysis.

first: Lee

last: Liew

first: Takahiro

last: Ochiya


title: Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid Leukemia (RNA-seq)

status: Public on Dec 17 2019

overall_design:
Three factors (PML/RARA fusion protein, CTCF and RNAPII)  associated chromatin interaction maps are generated and used for exploring 3D genome architecture changes with two APL cell lines (U937-PR9 and NB4) during the APL leukogenesis.
Paired-end sequencing (2 × 34bp) was used for RNA-seq libraries  with Illumina Nextseq 500.


title: Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid Leukemia (ChIP-seq)

overall_design:
Three factors (PML/RARA fusion protein, CTCF and RNAPII)  associated chromatin interaction maps are generated and used for exploring 3D genome architecture changes with two APL cell lines (U937-PR9 and NB4) during the APL leukogenesis.
Paired-end sequencing (2 ×150bp) was used for ChIP-Seq libraries  with  Illumina Nextseq 500.


title: Heterodimerization of Tfap2 pioneer factors drives epigenomic remodeling during neural crest specification

status: Public on Dec 12 2019

city: Ithaca

first: Marcos

last: Simoes-Costa

state: New York

address: 526 Campus Rd

institute: Cornell University

summary: Cell fate commitment is a stepwise process, in which multipotent progenitors transition through sequential regulatory states as they become fate restricted. Recent studies have highlighted the extensive transcriptomic shifts that typify cell differentiation, but our understanding of the epigenetic mechanisms underlying these changes is still superficial. To examine how chromatin states are reorganized during cell fate commitment in an in vivo system, we examined the function of pioneer factor Tfap2a at discrete stages of neural crest development. Our results show that TFAP2a activates distinct sets of genomic regions during induction and specification of neural crest cells. Genomic occupancy analysis revealed that the repertoire of TFAP2a targets depends upon its dimerization with paralogous proteins TFAP2c and TFAP2b. During gastrula stages, TFAP2a/c heterodimers activate components of the neural plate border induction program. As neurulation begins, TFAP2a trades partners, and TFAP2a/b heterodimers reorganize the epigenomic landscape of progenitor cells to promote neural crest specification. We propose that this molecular switch acts to drive progressive cell commitment, remodeling the epigenomic landscape to define the presumptive neural crest. Our findings show how pioneer factors regulate distinct genomic targets in a stage-specific manner, and highlight how paralogy can serve as an evolutionary strategy to diversify the function of the regulators that control embryonic development.

overall_design:
CUT&RUN data for transcription factors TFAP2a, TFAP2b, and TFAP2c, and modified histone mark H3K27ac in chick neural crest cells at two developmental timepoints.

ATAC-seq on isolated neural crest cells using AP2aE1

RNA-seq on isolated neural crest cells using AP2aE1

CUT&RUN for Tfap2a in control tissue or Tfap2b knockdown

first: Megan

last: Rothstein


title: Chemical reprogramming of fibroblasts to photoreceptor like cells [ATAC-Seq]

city: Bethesda

first: Koray Dogan

last: Kaya

address: 6 CENTER DR

institute: NIH

summary: Reprogramming of mouse embryonic fibroblasts (MEFs) to photorereceptor like cells by five chemicals.

overall_design: Genomic DNA from MEFs, reprogramming intermediates (day 8) and reprogrammed photoreceptors (day 11) were collected and sent to Active motifs for sequencing and analysis.

first: Biraj

last: Mahato

first: Yan

last: Fan

first: Nathalie

last: Sumien

first: Ritu

last: Shetty

first: Zhang

last: Wei

first: Delaney

last: Davis

first: Thomas

last: Mock

first: Subrata

last: Batabyal

first: Aiguo

last: Ni

first: Samarendra

last: Mohanty

first: Zongchao

last: Han

first: Rafal

last: Farjo

first: Michael

last: Forster

first: Anand

last: Swaroop

first: Sai

last: Chavala


title: VIPR2 activation has an inhibitory effect on ILC3

status: Public on Dec 19 2019

first: Dan

last: Littman

address: 430 East 29th St Room 403

institute: New York University School of Medicine

summary: We report that VIPR2 is an inhibitory receptor for CCR6+ ILC3

overall_design: Examination of the transcriptome of WT and VIPR2 KO CCR6+ isolated from the same mice using a bone marrow chimera strategy

first: Jhimmy

last: Talbot

first: Lina

last: Kroehling


title: ASA-750K array genotyping of Northern Han Chinese and Southern Han Chinhttps://www.ncbi.nlm.nih.gov/geo/subsese

status: Public on Dec 13 2019

city: Nanjing

first: Peng

last: Chen

state: Jiangsu

address: China

department: Department of Forensic

institute: Nanjing Medical University

summary: ASA-750K is a commercial array developed by Novogene Bioinformatics Technology Co.Ltd. The array contains 738980 sites in total including Illumina Asian Screening Arrary with additional 50k SNP sites (see http://www.novogene.com for more information).

overall_design: To investigate whether Northern Han Chinese Southern Han Chinese is genetic distinguishable, we genotyped 50 Northern Han and 50 Southern Han by Illumina ASA-750K BeadChip. The array sequencing results of all samples are uploaded to GEO database.

first: Jiawen

last: Yang

first: Chuwei

last: Deng

first: Feng


title: RNA-sequencing of human vascular endothelial cells after si-RNA mediated gene silencing of interleukin-6 (IL6)

city: Orebro

first: Liza

middle: U

last: Ljungberg

address: Sodra Grev Rosengatan 32

department: Medical Sciences

country: Sweden

institute: Örebro University

summary:
Purpose: To characterize the autocrine functions of IL6 in human endothelial cells
Methods: Knockdown of interleukin-6 in cultured human umbilical vein endothelial cells were performed using stealth-siRNA and lipofectamine 2000. Total RNA was isolated 48h after siRNA introduction. RNA sequencing libraries were prepared using TruSeq stranded mRNA sample prep kit including poly-A selection. Sequencing was performed on a Illumina HiSeq2500 instrument.
Results: Knockdown of IL6 in human endothelial cells resulted in 84-92% reduction in the release of IL6. Knockdown of IL6 in the absence of soluble IL6Rα (sIL6Rα) lead to differential regulation of 1915 genes (using a fold change 1.5, q < 0.05), and 1967 differentially regulated genes in the presence of sIL6Rα. Treatment with sIL6Rα alone had a limited effect and resulted only in 59 differentially expressed genes.
Conclusion: Knockdown of IL6 in human endothelial cells results in dramatic changes in transcriptional patterns, which seem to be independent of sIL6Rα, indicating that the autocrine functions of IL6 in human endothelial cells are mainly mediated via classic IL6 signaling.

overall_design: siRNA mediated gene silencing of interleukin-6 followed by RNA sequencing was performed in cultured human endothelial cells.

first: Dirk

last: Repsilber

first: Allan

last: Sirsjö


title: Temporal Expression Profiling of Global Long Noncoding RNA and mRNA during Development in Pig Whole-blood

city: Chengdu

first: Zhou

last: rui

state: Sichuan

address: 211 huimin road, wenjiang district

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary: Blood is the pipeline of the immune system. Assessing changes in transcript abundance in blood on a genome-wide scale affords a comprehensive view of the status of the immune system during development. However, little is known about the changes of gene expression in blood across multiple developmental stages in pigs. In this study, we performed transcriptomic analysis of messenger RNA (mRNA) and long noncoding RNA (lncRNA) expressed in whole-blood tissue from pigs of natal, suckling, weaning, sexual maturity and adult stages. A total of 5,946 lncRNA and 12,354 mRNA transcripts were identified to be substantially expressed. Short time-series expression miner (STEM) and functional enrichment analysis showed that genes with the greatest variation of expression levels between suckling period (0, 7 and 28 days) and the late stage of development (180 days and 2 years) might function in transcription, immune function, and apoptotic process. Functional prediction indicated the expression correlation and functional relatedness between mRNAs and lncRNAs. Additionally, a number of T cell-related genes were continuously up-regulated during lactation, suggesting this phase is significant for the establishment of piglet adaptive immunity. Notably, the TCONS_00192752 and TCONS-00086451 lncRNA might promote blood immune development by up-regulating the tumor necrosis factor receptor-associated factor 3 (TRAF3) and nuclear factor of activated T-cells cytoplasmic 2 (NFATC2) expression, respectively. Our research provides the first catalog of the developing pig whole-blood, and will accelerate clinical researches of immune system development with pig models.

overall_design: Ten healthy female pigs were used to simulate the blood immune system development.   In the 0 day, 7 day, 28day, 180day and 2 year groups, there were two pigs of similar weight obtained after birth in each group. Pig whole-blood tissues collected from each pig and frozen immediately in liquid nitrogen and stored at -80°C until required for RNA extraction, sequencing and transcriptome analysis.

first: Yiren

last: Gu

first: Rui

last: Zhou

first: Long

last: Jin

first: Mingzhou

last: Li

first: Xuebin

last: Lv


title: ATAC-Seq analysis of Mouse Embryonic Fibroblasts (MEFs) to understand the role of β-actin in regulating chromatin states

status: Public on Jan 01 2020

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: β-actin is a crucial component of several chromatin remodeling complexes which control chromatin structure and accessibility. The mammalian Brahma-associated factor (BAF) is one such complex that plays essential roles in development and differentiation by regulating the chromatin state of critical genes and opposing the repressive activity of polycomb repressive complexes. While previous work has shown that β-actin loss can lead to extensive changes in gene expression and heterochromatin organization, it is not known if changes in β-actin levels can directly influence chromatin remodeling activities of BAF and polycomb proteins. Here we conduct a comprehensive genomic analysis of β-actin knockout mouse embryonic fibroblasts (MEFs) using ATAC-Seq, HiC-seq, RNA-Seq and ChIP-Seq of various epigenetic marks. We demonstrate that β-actin levels can affect the complex interplay between chromatin remodelers such as BAF/BRG1 and EZH2 in a dosage-dependent manner. Our results show that changes in β-actin levels and associated chromatin remodeling activities can not only impact local chromatin accessibility but also induce reversable changes in 3D genome architecture. Our findings support a novel role for β-actin levels in shaping the chromatin landscape during development and differentiation.

overall_design: ATAC-Seq analysis was performed for 3 samples using two replicates for each condition. Samples included MEFs wildtype, knockout or heterozygous for β-actin.

first: Xin

last: Xie

first: Syed

last: Mahmood


title: Lipoic acid induced endoplasmic reticulum stress-mediated apoptosis in rat hepatoma cells:identification of new ER stress aggravator (ERSA)

city: Cagliari

first: Gabriella

last: Simbula

address: Porcel 4

country: Italy

institute: THE UNIVERSITY OF CAGLIARI

summary: Study gene expression during apoptotic process α Lipoic acid-induced.

overall_design: 3 controls, 2 Thapsigargin, 7 Lipoic acid. Time course analysis

first: Pia

last: Sulas


title: Transcriptome profiling of human thymic and peripheral blood CD4 + and CD8+ T cells, using RNA-seq

status: Public on Nov 11 2019

city: OSLO

first: Benedicte

middle: Alexandra

last: Lie

address: Kirkeveien 166, Laboratoriebygget

department: Department of Medical Genetics

country: Norway

institute: OUS

summary: We have performed high-throughput RNA sequencing to characterize the transcriptomes of primary single positive (SP) CD4+ and CD8+ T cells from infant thymic tissue, as well as primary CD4+ and CD8+ T cells from infant and adult peripheral blood, to enable the comparisons across tissues and ages

overall_design:
RNA-seq of 18 samples, using Illumina HiSeq2000/2500; thymic T cells - 4 replicates of CD4+ and 5 replicats of CD8+,  infant blood T cells - 4 replicates of CD4+ and 3 replicates of CD8+, and 2 adult blood pools, one of CD4+ and one of CD8+ T cells.
>>>Raw data are not available for this series due to patient privacy concerns<<<

first: Hanna

last: Helgeland


title: HIV-CRISPR screen of HIV-1 CA-P90A and CA-N74D mutant viruses with the PIKAHIV library

status: Public on Nov 16 2019

city: Seattle

first: Molly

last: Ohainle

state: WA

address: 1100 Fairview Ave N, C2-023

institute: Fred Hutchinson Cancer Research Center

summary: Illumina sequencing data used in HIV-CRISPR screen with an ISG-specific sgRNA library (PIKAHIV) to find genes that block infection by the N74D and P90A HIV-1 capsid mutant viruses in THP-1 monocytic cells. For more information on the library and approach see Ohainle et al. eLife 2018 (PMID: 30520725). All screens performed here were done in a clonal ZAP-KO cell line (ZAP may inhibit the HIV-CRISPR vector used in the screen). Here we screen the Cyclophilin A-binding deficient mutant P90A and the CPSF6-binding deficient mutant N74D together with a wild type HIV-1 virus. The N74D screen was performed both with IFN treatment and without. These two HIV-1 capsid mutant viruses are hypersensitive to the effects of IFN.

sample_organism:
Homo sapiens
Human immunodeficiency virus

overall_design: An HIV-CRISPR screen targeting Interferon-Stimulated Genes in which enrichment of 20bp sgRNA sequences is compared in viral RNA to the library representation of the sgRNA sequences in genomic DNA. 2 biological replicates were performed in ZAP Knockout THP-1 clonal cell lines for all screens, except the HIV-1 CA-P90A mutant screen with IFN and the HIV-1 CA-N74D mutant screen without IFN in which only a single replicate for the viral RNA was performed. Cells were infected following treatment overnight with IFN and viral supernatants and cell pellets collected 3 days post-infection. sgRNA representation in viral RNA is compared to genomic DNA to determine which sgRNAs are over- or under-represented in the viral population.

first: Michael

last: Emerman


title: Transcriptome analysis of dark zone (DZ) and light zone (LZ) compartments of Wild type (WT) and SykY317F mice

status: Public on Nov 13 2019

first: Ziv

last: Shulman

summary: Analysis of DZ and LZ compartments in the germinal center of WT and SykY317F mice revealed that Syk degradation regulates the gene expression in the light zone compartment.

overall_design: Chimeric mice (50% WT, 50% SykY317F) were immunized with NP-KLH. 14 days after the immunization popliteal lymph nodes were harvested and dz and lz gc b cells were sorted and sequenced.

first: Natalia

last: Davidzohn


title: Whole spleen transcriptome during acute phase of infection in an avirulent Plasmodium chabaudi chabaudi AS infection.

status: Public on Nov 19 2019

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

summary: The spleen is considered as the major lymphoid organ involved in generating immune responses to the erythrocytic stages of the malaria parasite, Plasmodium, but access to human spleens is not practical and most studies rely on peripheral blood for assessing immune responses. However, the suitability of peripheral blood as a proxy for splenic immune responses is unknown. Here, we have  analysed transcriptome activity for whole  spleens over 12 days of erythrocytic stage Plasmodium chabaudi infection in C57BL/6 mice. These data will be compared with comparable data taken from whole blood: and previously published:  GSE93631

overall_design: Spleens were collected from infected C57BL/6 mice on at 2, 4, 6, 8, (9), 10, 12 days post infection. Naïve samples were collected from age matched mice at the beginning (day 0) and the end (day 12) of the experiment. 3-4 replicates per condition.

first: Calos

last: Talavera-Lopez

first: Jingwen

last: Lin

first: Yaw

last: Bediako

first: Jean

last: Langhorne


title: Single cell transcriptome atlas of the Drosophila larval brain

status: Public on Nov 15 2019

city: Fribourg

first: Simon

last: Sprecher

state: Fribourg

address: Chemin du Musée 10

department: Biology

country: Switzerland

institute: University of Fribourg

summary: The cellular composition of the brain and how it is affected by starvation, remains largely unknown. Here we introduce a single-cell transcriptome atlas of the entire Drosophila melanogaster first instar larval brain. We first assigned cell type identity based on the expression of previously characterized marker genes, allowing us to distinguish five major groups: neural progenitors cells, differentiated neurons, glial cells, undifferentiated neurons as well as non-neural cells corresponding to organs and structures located adjacent to the brain. All major classes were further subdivided into multiple subtypes based on cluster analysis, revealing critical biological features of various cell types. Moreover, we included two different feeding conditions: normal fed versus starved. After starvation, the transcriptional profile of several cell clusters were altered, while the overall composition of the brain remains unaffected. Intriguingly, different cell clusters show very distinct responses to starvation, suggesting the presence of cell-specific programs for nutrition availability. Establishing a single-cell transcriptome atlas of the larval brain provides a powerful tool to explore cell diversity, assess genetic profiles of neurogenic, neuronal and glial cell types. The analysis of neurotransmitters, neuropeptides and their respective receptors may further open the doors for functional studies.

overall_design: scRNA-seq (10x Genomics - Single Cell 3’ Chemistry v2 ) of the Drosophila larval brain at different feeding conditions

first: Clarisse

last: Brunet Avalos

first: Rémy

last: Bruggmann

first: Sprecher

last: Simon

first: G Larisa

last: Maier


title: WUSCHEL acts as a rheostat on the auxin pathway to maintain apical stem cells in Arabidopsis

city: Heidelberg

first: Jan

last: Lohmann

address: Im Neuenheimer Feld 230

department: Stem Cell Biology

institute: Centre for Organismal Studies

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

overall_design: Refer to individual Series


title: WUSCHEL acts as a rheostat on the auxin pathway to maintain apical stem cells in Arabidopsis [RNA-seq]

summary: During development and growth, dynamic signals need to be translated into spatially precise and temporally stable gene expression states, which define cell fate. In the context of the apical plant stem cell system, local accumulation of the small, highly mobile phytohormone auxin triggers organ initiation. Here we show that the WUSCHEL transcription factor locally protects stem cells from differentiation by controlling the auxin signaling and response pathways via regulation of Histone acetylation. Conversely, low levels of signaling are required for stem cell maintenance, demonstrating that WUSCHEL acts as a rheostat on the auxin pathway. Our results reveal an important mechanism that allows cells to differentially translate a potent and highly mobile developmental signal into appropriate cell behavior with high spatial precision and temporal robustness.

overall_design: pUBI10::mCherry-GR-linker-WUS (WUS-GR); seedling; 2hours; ChIP-Seq profile of WUS-GR binding (duplicate), and RNA-Seq profile after WUS-GR induction (triplicate)

first: Olga

last: Ermakova


title: WUSCHEL acts as a rheostat on the auxin pathway to maintain apical stem cells in Arabidopsis [ChIP-seq]


title: Phospho-antibody microarray analyses for islets of control and IFT88 knockout mice [PEX100]

status: Public on Oct 30 2019

city: St Louis

first: Jing

last: Hughes

state: Missouri

address: 660 S Euclid

department: Internal Medicine

institute: Washington University

summary:
β-cell specific IFT88 knock-out mice recapitulate human diabetes with impaired insulin secretion and altered islet hormone paracrine regulation. To examine the signaling pathways regulating islet cell function, we subjected protein lysates of whole islets from control and IFT88 knockout mice to a commercial phospho-antibody array analysis (Full Moon Bio, Inc).
Samples were probed against 1318 site-specific and phospho-specific antibodies with 2 replicates per antibody on 76 x 25 x 1mm glass slides.

overall_design: IFT88 fl/fl mice and INS1-Cre mice on a C57BL/6 background were crossed to generate β-cell specific IFT88 knockout mice. Animals were weaned at age 3 weeks and maintained on a standard chow diet. Islets were isolated using modified Lacy protocol and allowed to recover in culture overnight before collection and lysis. Total protein lysates were prepared from 240 size-matched islets per sample (2 controls and 2 knockouts, each pooled from 2 mice) and used for FullMoonBio Phospho Explorer Array (PEX100) analysis.


title: A Single-Cell Transcriptomic Atlas of Artery Aging in Cynomolgus Monkey

status: Public on Nov 30 2019

city: Beijing

first: Shu

last: Zhang

state: Beijing

address: Peking University, No.5 Yiheyuan Road Haidian District

institute: BIOPIC

summary: Aging is one of the major risk factors for cardiovascular diseases; however, our understanding of how aging affects the cellular and molecular components of vasculatures and contributes to cardiovascular diseases is still limited. Compared with other model organisms, monkeys are more similar to humans in terms of their genetic, anatomical and physiological features, thus representing an ideal model for studying vascular aging and its effect on diseases.

overall_design: Here, we report a single-cell transcriptomic survey of aortic and coronary arteries from eight young and eight old cynomolgus monkeys.

first: Weiqi

first: Guanghui

last: Liu

first: Fuchou

last: Tang


title: Characterization of Fetal Specific Transcriptional Programs in Thymic Epithelial Cells Identifies Myc as a Critical Determinant of Thymus Size

first: Margaret

last: Cam

state: MD


title: Metastatic conditioning of myeloid cells at a subcutaneous synthetic niche reflects disease progression and predicts therapeutic outcomes

status: Public on Oct 31 2019

city: College Park

first: Robert

middle: Smith

last: Oakes

address: 8278 Paint Branch Drive

institute: University of Maryland, College Park

summary:
Microporous polymer (PCL) implants were implanted into BALB/c mice. After 2 weeks mice were inoculated with 4T1 tumor cells. Then after 7, 14, and 21 days the implant and tissue infiltrate which develops into a synthetic niche was biopsied, total RNA was isolated, reverse transcribed into cDNA and analyzed using a high throughput RT-qPCR platform (Applied Biosystems™ TaqMan™ OpenArray™ Mouse Inflammation Panel).
The goal of the studies was to identify genes that progressively change at a synthetic site during disease progression.

overall_design: A total of 28 biological replicates were analyzed for the expression of 648 genes. Conditions include 4T1 tumor-bearing (n=14) and healthy time-matched control (n=14) mice analyzed over Days 7 (n=3 per condition), 14 (n=8 per condition), and 21 (n=3 per condition).

middle: S

first: Grace

last: Bushnell

first: Sophia

last: Orbach

first: Pridvi

last: Kandagatla

first: Yining

first: Aaron

last: Morris

first: Matthew

last: Hall

first: Petrina

last: LaFaire

first: Joseph

middle: T

last: Decker

first: Michael

last: Brooks

first: Max

last: Wicha

first: Rachel

last: Hartfield

first: Jacqueline

last: Jeruss

first: Lonnie

last: Shea


title: A Nine-gene Signature for Predicting the Response to Preoperative Chemoradiotherapy in Patients with Locally Advanced Rectal Cancer

status: Public on Oct 23 2019

city: Daejeon

first: Jin Young

last: Park

address: 24,Techno 11-ro, Yuseong-gu

country: South Korea

institute: CbsBioscience

summary: A total of 156 LARC patients (training cohort n = 60; validation cohort n = 96) were included in the study who underwent surgical resection post PCRT. By using univariate and multivariate logistic regression, we identified a 9-gene signature that differentiated between responders and non-responders. ; The novel 9-gene signature is robust in predicting response to PCRT in LARC patients. Tailored treatment approaches in good and poor responders to PCRT may improve the oncologic outcomes of patients with LARC.

overall_design: The study included 156 randomly selected rectal cancer patients (n = 156) divided into a training cohort (n = 60) and a validation cohort (n = 96). Surgical resection was performed 6–8 weeks after completion of PCRT and included local excision and radical resection performed according to the principles of total mesorectal excision. Gene expression analysis was performed using the nCounter PanCancer Pathway Panel (NanoString Technologies, Seattle, WA). The panel analyzed 770 genes including 40 control genes.

first: Inja

first: Yun Suk

last: Yu

first: Bilal

last: Mustafa

first: Yong Bae

last: Seo

first: Gun-Do

last: Kim

first: Jinpyo

first: Chang Min

first: Hyun Deok

last: Noh

first: Seung-Mo

last: Hong

first: Yeon Wook

first: Mi-Ju

first: Luigi

last: Buonaguro

first: Adnan Ahmad

last: Ansari

first: Sung-Min

last: Ahn

first: Chang-Sik


title: Dissecting cell composition and cell-cell interaction network of normal human heart tissue by single-cell sequencing

status: Public on Oct 21 2019

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

country: USA

summary: We studied the cell compositon of normal human heart by single-cell sequencing. Distint subgroups of cardiac muscle, fibroblast cell and endothelial cell were detected. We drawed a cell-cell interaction network using specific expressed ligands and receptors of cells. And we also observed the change of interaction and cell transformation with age.

overall_design: Extract cells from left ateria and ventricle of normal heart and conduct single-cell sequencing of 9994 cells.

first: Peng

first: Zheng

last: Li

first: Zongna

last: Ren


title: Characterization of Fetal Specific Transcriptional Programs in Thymic Epithelial Cells Identifies Myc as a Critical Determinant of Thymus Size [bulk RNA-Seq]

first: Margaret

middle: C

last: Cam

summary: The thymus is the site of T cell development. Although much is known about the development and differentiation of the T lymphocyte compartment, less is known about the thymic epithelial cell (TEC) populations fostering their development. Here we use next generation sequencing approaches to identify transcriptional programs unique to TEC at specific stages of mouse life. This strategy identified Myc as a regulator of the fetal program, driving the rapid expansion in thymic size during fetal life.

overall_design: Next-generation sequencing approaches on a large data set enabled the identification of age-specific transcriptional programs; and established a key role for Myc in driving TEC proliferation, ribosomal biogenesis, and regulating thymic size.

first: Jennifer

last: Cowan

first: Maggie

first: Xiongfong

last: Chen

first: Yongge

last: Zhao

first: Justin

last: Malin

first: Avinash

last: bhandoola


title: Characterization of Fetal Specific Transcriptional Programs in Thymic Epithelial Cells Identifies Myc as a Critical Determinant of Thymus Size [single cell RNA-Seq]


title: Epigenetic reader complexes of the human malaria parasite, Plasmodium falciparum

status: Public on Oct 15 2019

city: Nijmegen

first: Christa

last: Toenhake

state: Netherlands

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

summary: Epigenetic regulatory mechanisms are central to the development and survival of all eukaryotic organisms. These mechanisms critically depend on the marking of chromatin domains with distinctive histone tail modifications (PTMs) and their recognition by effector protein complexes. In this project,  histone peptide pull-downs and protein-protein interaction quantitative proteomics were used to unveil interactions between PTMs and associated reader protein complexes of Plasmodium falciparum, a unicellular parasite causing malaria. One of the identified bromodomain proteins (BDP5, PF3D7_1234100) has previously been proposed to be the P. falciparum homologue of TBP-associated factor 1 (TAF1). As the bdp5/taf1 locus was refractory to disruption, knock-sideways strategy was employed to disrupt BDP5/TAF1 function by tethering it to the cell membrane (Birnbaum, 2017, Nature Methods). To gain insight in the transcriptional defects upon BDP5/TAF1 knock-sideways (KS), directional RNA seq libraries were generated at 2, 6 and 12 hours after knock-sideways induction.

overall_design: Asexual blood stage bdp5/taf1-2xFKBP-GF-2xFKBP P. falciparum 3D7 parasites with the Lyn-FRB-T2A-mCherry mislocalizer plasmid were synchronized (~4hr) and split in two at 14 hours post red blood cell invasion. One half was kept in normal medium ('control' condition) while the second half was put on 250 nM rapalog to induce knock-sideways. RNA was collected at 2, 6 and 12 hours post knock-sideways induction and prepared to directional RNA-seq libraries.  A culture of bdp5/taf1-2xFKBP-GF-2xFKBP parasites without the mislocalizer was treated in a similar fashion but collected 12 hours after rapalog addition to control for any effects of rapalog itself. RNA-seq libraries were sequenced paired-end for 42 bp on a NextSeq 500 system (Illumina).

first: Wieteke

last: Hoeijmakers

first: Richárd

last: Bártfai

middle: G


title: Next-generation hypomethylating agent SGI-110 primes acute myeloid leukemia cells to IAP antagonist by activating extrinsic and intrinsic apoptosis pathways

status: Public on Oct 03 2019

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Hospital Freiburg

summary: Therapeutic efficacy of first-generation hypomethylating agents (HMAs) is limited in elderly acute myeloid leukemia (AML) patients. Therefore, combination strategies with targeted therapies are urgently needed. Here, we discover that priming with SGI-110 (guadecitabine), a next-generation HMA, sensitizes AML cells to ASTX660, a novel antagonist of cellular Inhibitor of Apoptosis Protein 1 and 2 (cIAP1/2) and X-linked IAP (XIAP). Importantly, SGI-110 and ASTX660 synergistically induced cell death in a panel of AML cell lines as well as in primary AML samples while largely sparing normal CD34+ human progenitor cells, underlining the translational relevance of this combination. Unbiased transcriptome analysis revealed that SGI-110 alone or in combination with ASTX660 upregulated the expression of key regulators of both extrinsic and intrinsic apoptosis signaling pathways such as TNFRSF10B (DR5), FAS and BAX. Individual knockdown of the death receptors TNFR1, DR5 and FAS significantly reduced SGI-110/ASTX660-mediated cell death, whereas blocking antibodies for TRAIL or FASLG failed to provide protection. Also, TNF-blocking antibody Enbrel had little protective effect on SGI110/ASTX660-induced cell death. Further, SGI-110 and ASTX660 acted in concert to promote cleavage of caspase-8 and BID, thereby providing a link between extrinsic and intrinsic apoptotic pathways. Consistently, sequential treatment with SGI-110 and ASTX660 triggered loss of mitochondrial membrane potential (MMP) and BAX activation, which contributes to cell death as BAX silencing significantly protected from SGI-110/ASTX660-mediated apoptosis. Together, these events culminated in activation of caspases-3/-7, nuclear fragmentation and cell death. In conclusion, SGI-110 and ASTX660 cooperatively induced apoptosis in AML cells by engaging extrinsic and intrinsic apoptosis pathways, highlighting the therapeutic potential of this combination for AML.

overall_design: After pre-treatment with 2 µM SGI-110 for 24 h, ML-2 cells were treated with 5 µM ASTX660 for another 9 h. Samples (solvent-treated controls, SGI-110 single treatment, ASTX660 single treatment, SGI-110/ASTX660 combination treatment) were collected from three independent experiments.

first: Jessica

last: Dittmann

first: Melanie

last: Boerries

first: Simone

last: Fulda


title: Early RNA sequencing of human monocytes in presence of Candida albicans

status: Public on Oct 11 2019

city: Jena

first: Christine

last: Skerka

address: Beutenbergstraße 11A

department: Infection Biology

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: C.albicans induces the upregulation of inflammation related genes at the same time it also induces TGF-ß signalling pathway related genes from human blood derived monocytes. RNA sequencing was prerformed from Candida albicans co-incubated monoyctes from 3 different donors. Candida albicans significantly upregulates 6363 genes in human blood derived monocytes in 1h of co-incubation.

overall_design: Blood derived monocytes were treated with Candida albicans or DPBS, after 1h RNA was isolated, RNA of 3 donors were combined and sequenced

first: Luke

last: Halder


title: Exogenous expression analysis of U1 snRNA mutation

status: Public on Oct 09 2019

city: Toronto

first: Michael

middle: D.

last: Taylor

state: ON

address: 686 Bay Street

department: Developmental & Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

summary: To reveal the effect of U1 snRNA mutation, we performed exogenous expression analysis of U1 snRNA mutation. The pLKO.1-puro U6 sgRNA BfuAI stuffer lentiviral vector was modified by removing the internal U6 promoter. It was replaced by the U1 locus, including 393 bases of internal native U1 promoter, the U1 sequence, and 39 bases of 3’-flanking region. The r.3A>G mutation was introduced by site-directed mutagenesis. HEK-293T cells were transfected using Lipofectamine Plus with either pLKO.1-U1wt or pLKO.1-U1r.3a>g in duplicate. Messenger RNA library construction was performed based on oligo dT-based mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module. RNA Sequence was performed on NextSeq 550 using 100-bp paired-end mode.

overall_design: mRNA profiles of HEK293T with either U1 mutation or U1 wildtype vector.


title: The Set1 N-terminal domain and Swd2 interact with the RNA polymerase II CTD to recruit COMPASS

status: Public on Oct 02 2019

city: BOSTON

first: HYUN JIN

last: BAE

state: MA

address: 240 Longwood Ave, Building C1-207

department: BCMP

institute: Harvard Medical School

summary: Methylation of histone H3 lysine 4 (H3K4) by the Set1/COMPASS complex is coupled with active transcription, and this modification is important for regulating gene expression. Set1/COMPASS associates with the RNA polymerase II (RNApII) C-terminal domain (CTD) to establish proper levels and distribution of H3K4 methylations.To ask how the Set1-RNApII CTD binding affects the occupancy and overall level of H3K4 methylations, ChIP-Seq was pefromed in cells transformed with full length or N-terminal truncated Set1. Our results indicate that Set1-RNApII CTD interaction is necessary for maintaining H3K4 methylations throughout the genes.

overall_design: 27 samples of H3K4me3, H3K4me2, FLAG ChIP-Seq for S.cerevisiae transformed with Full length or mutant Set1. Input samples from gene deletions were included.

first: H

last: Bae

first: S

last: Buratowski


title: Urinary sediment transcriptomic and longitudinal data to investigate renal function decline in type 1 diabetes

city: Sao Paulo

first: Maria Beatriz

last: Monteiro

address: Av Dr Arnaldo 455

country: Brazil

institute: University of Sao Paulo Medical School

summary: Using a discovery/validation approach we investigated associations between a panel of genes selected from a transcriptomic study and the renal function decline across time in a cohort of type 1 diabetes patients.

overall_design: mRNA profiles of urine sediment cells from healthy volunteers and from type 1 diabetes patients with different rates of kidney funcion decline were used to select genes with the potential do predict renal function decline

first: Maria


title: Radiomic and transcriptomic analysis for understanding metastatic clear cell renal cell carcinoma

status: Public on Sep 30 2019

city: Seongnam-si

first: Je-Gun

last: Joung

address: 335, Pangyo-ro, Bundang-gu

institute: CHA University

summary: To understand the relationship of radiomic and transcriptomic features of metastatic clear cell renal cell carcinoma, we performed RNA-sequencing in clear cell renal cell carcinomas (ccRCCs).

overall_design:
Examination of 19 RNA samples of clear cell renal cell carcinoma
Raw data has not been provided to protect the privacy of the human subjects.

first: Seong-Il

last: Seo


title: Next Generation Sequencing of PKD2 mutant mice

status: Public on Sep 25 2019

city: Dallas

first: Ronak

last: Lakhia

state: Texas

address: 5323 Harry Hines

institute: UTSW

summary:
Purpose: Determine the differential gene expression pattern between wildtype, Pkd2-KO and Pkd2-miR-214 KO mice
Methods: kidney mRNA profiles of Pkd2-KO and Pkd2-mir-214-KO mice was sequenced with N of 3 in each group
Results: 972 differentially expressed transcripts were identified between Pkd2-KO kidneys and Pkd2-miR-214-KO kidneys
Conclusion: Deletion of miR-214 promotes interstitial inflammation in mouse models of ADPKD

overall_design: kidney mRNA profiles of Pkd2-KO and Pkd2-miR-214 KO were determined by polyA mRNA sequencing with an N=3 different biological replicates in each group

first: Vishal

last: Patel