title: Metabolic support of tumor-infiltrating regulatory T cells by lactic acid

status: Public on Oct 01 2020

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

summary: Regulatory T (Treg) cells are vital for maintaining immune homeostasis and preventing autoimmunity, but represent a major barrier to robust cancer immunity as the tumor microenvironment (TME) actively recruits, activates, and promotes their differentiation1,2. Tumor cells have deregulated cellular metabolism leading to a metabolite-depleted, hypoxic, and acidic TME3. Highly glycolytic tumor infiltrating CD8 T cells are in direct competition with the tumor for glucose and oxygen which impairs their effector function4–6. In contrast, Treg cells maintain their high suppressive function within the TME7,8. Further, studies of in vitro induced and directly ex vivo Treg cells reveal a distinct metabolic profile compared to effector T cells9–11. Thus, we hypothesized that the altered metabolic landscape of the TME and the increased activity of intratumoral Treg cells are linked. Here we show Treg cells display heterogeneity in terms of their glucose metabolism and can engage an alternative metabolic pathway to maintain their high suppressive function and proliferation within the TME and other tissues. Tissue derived Treg cells (both at the steady state and under inflammatory conditions) show broad heterogeneity in their ability to take up glucose. However, glucose uptake correlates with poorer suppressive function and long-term functional stability, and culture of Treg cells in high glucose conditions decreased suppressive function. Treg cells under low glucose conditions upregulate genes associated with the uptake and metabolism of the glycolytic end-product lactic acid. Treg cells withstand high lactate conditions, and lactate treatment prevents the destabilizing effects of high glucose culture. Treg cells utilize lactate within the TCA cycle and generate phosphoenolpyruvate (PEP), a critical intermediate that can fuel intratumoral Treg cell proliferation in vivo. Using mice with a Treg cell-restricted deletion of lactate transporter Slc16a1 (MCT1) we show MCT1 is dispensable for peripheral Treg cell function but required intratumorally, resulting in slowed tumor growth and prolonged survival. These data support a model in which Treg cells are metabolically flexible such that they can utilize ‘alternative’ metabolites present in the TME to maintain their suppressive identity. Further, our studies support the notion that tumors avoid immune destruction not only by depriving effector T cells of essential nutrients, but also by metabolically supporting regulatory T cells.

overall_design: mRNA profiles of 2NBDG High and Low regulatory T cells subsets and bulk conventional T cells (CD4+ Foxp3-) sorted ex vivo from lymph nodes and B16 tumors. (6 replicates per subset and tissue)

first: McLane

middle: J

last: Watson

first: Paolo

last: Vignali

first: Steven

last: Mullett

first: Abigail

middle: E

last: Overacre-Delgoffe

first: Ronal

last: Peralta

first: Stephanie

last: Grebinoski

first: Ashley

middle: V

last: Menk

first: Natalie

last: Rittenhouse

first: Kristin

last: DePeaux

last: Whetstone

first: Dario

first: Timothy

last: Hand

first: Brett

last: Morrison

first: Jeffrey

last: Rothstein

first: Stacy

middle: G

last: Wendell

first: Greg

last: Delgoffe


title: The molecular subtype in colorectal cancer

status: Public on Sep 30 2020

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

type: Expression profiling by high throughput sequencing

summary: To dissect the the molecular subtype of colorectal cancer, we performed  RNA expression profiling in 53 CRC tissues.

overall_design: RNA-seq was performed in 53 colorectal cancer tissue


title: Determination of the regulons of 7 XRE-cupin regulators by RNA-seq

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

summary: Determination of the impact of the individual deletion of 7 transcription factors (PA0535, PA1359, PA1884, PA2312, PA4499 (PsdR), PA4987 and PA5301 (PauR)) in Pseudomonas aeruginosa PAO1.

overall_design: RNA-seq analysis of WT vs. mutants, in P. aeruginosa PAO1, in LB liquid cultures at 37°C at OD=1, in duplicates.

first: Ina

last: Attrée

first: Sylvie

last: Elsen


title: The mTORC1-mediated activation of ATF4 promotes protein and glutathione synthesis (Tunicamycin)

status: Public on Sep 28 2020

city: Schwerzenbach

first: Michael

middle: Robert

last: MacArthur

address: Schorenstrasse 16

department: D-HEST

summary: In response to a variety of upstream growth and oncogenic signals, the mechanistic target of rapamycin complex 1 (mTORC1) promotes anabolic metabolism, in part, through activation of downstream transcription factors. The transcription factor activating transcription factor 4 (ATF4) has been previously shown to function downstream of mTORC1 signaling to promote de novo purine synthesis and this activation of ATF4 can occur independently of the canonical activation of ATF4 through the integrated stress response (ISR). Here, we show that ATF4 activation through mTORC1 signaling drives a specific transcriptional program through ATF4 which is comprised of only a subset of genes involved in the broader cellular stress response. We find genes involved in amino acid uptake, biosynthesis, and charging by tRNA synthetases display transcriptional changes downstream of both mTORC1 and ATF4. We discovered that ATF4 activation contributes to the mTORC1-stimulated increase in protein synthesis, highlighting the importance of these transcriptional changes. Additionally, we observe regulation of the cystine transporter SLC7A11 by ATF4. We show that SLC7A11 is important for cell survival and is one mechanism by which cells with active mTORC1 signaling produce glutathione. Thus, ATF4 downstream of mTORC1 signaling regulates protein and glutathione synthesis.

overall_design: Atf4 WT and KO MEFs were grown to 70% confluence in 6 cm plates and were serum-starved in the presence of 2-mercaptoethanol and 1X MEM NEAA mixture and treated with vehicle (DMSO) or 20 nM rapamycin (LC Laboratories, R5000) for 30 min prior to additional treatment with vehicle (water) or 500 nM insulin (Alpha Diagnostic, INSL 16-N-5 ) for 16 h, or treated with vehicle (DMSO) or 2 mg/mL  tunicamycin (Sigma-Aldrich, T7765) for 4, 8 or 16 h

middle: R

first: Margaret

last: Torrence

first: Brendan

middle: D

last: Manning


title: Single guide RNA CRISPR /Cas(sg) editing 3 nucleotides and  prime editing (pe) single nucleotide of CArG element in Tspan2 promoter effect on transcriptome in aortas

status: Public on Sep 23 2020

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

country: USA

institute: University of Rochester

summary: Aortas from sgCArG WT versus sg CArG homozygous mice at 12 wks and peCArGWT and peCArG homozygenous mutant mice at 8 weeks were isolated  for total RNA extraction. RNA samples were then subjected to deeping sequencing to profile gene expression in aortas.

overall_design: We will compare the transcriptome of aortas from  sg CArG WT versus sg CArG mutant as well as peCArG WT versus peCArG mutant to determine the genes consistently regulated by CArG mutation  of TSPAN2 gene in mice.

first: Xiaochun

last: Long

first: Joseph

last: Miano


title: Determination of the regulons of 7 XRE-cupin regulators

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: RNAseq analysis of genes activated 90 minutes, or 7 days post irradiation or untreated cells with knockdown of NFKBIA

city: Berlin

first: Marina

last: Kolesnichenko

address: Robert Roessle str 10

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

summary: Goal of the study was to investigate genes regulated differentially after 90 minutes versus 7 days after irradiation.  7 day time point corresponds to cellular senescence. U2OS cells were irradiated with 20 Gy and harvested either 90 minutes or 7 days. In addition cells were left untreated (control) or had knockdown of NFKBIA (protein name Ikappa B alpha).  Ikappa B alpha is the main inhibitor of the transcription factor NFkappa B. NFkappa B regulates transcription of many factors constituting the SASP (senescence associated secretory phenotype).

overall_design: cell were grown in DMEM supplemented with 10 percent FCS and antibiotics.  Cells (in quintuplicates) were irradiated with 20 Gy and harvested using Trizol reagent at time points indicated above (so that cell harvesting took place at the same time). RNA was analyzed for integrity and subseqently 500 ng was used from each sample for sequencing.

first: Bora

last: Uyar

first: Eva

last: Kaergel

first: Claus

last: Scheidereit


title: Colonization of distant organs by mechanosensitive tumor cells via generation of stable circulating homotypic clusters

status: Public on Oct 03 2020

city: Kumamoto-shi

first: Manabu

last: Maeshiro

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Molecular Laboratory Medicine

country: Japan

institute: Kumamoto University

summary: Mechanisms governing cancer metastasis remain poorly understood. Once disseminated tumor cells (DTCs) arrive at a metastatic organ, they remain there, latent, and become seeds of metastasis. However, the clonal composition of DTCs in a latent state remains unclear. Here, we applied high-resolution DNA barcode tracking to a mouse model that recapitulated the metastatic dormancy of head and neck squamous cell carcinoma (HNSCC). We found that clones that had abundant circulating tumor cells (CTCs) but were rare in the primary site dominated DTCs. We obtained a specific subclone that dominated CTCs and subsequent DTCs in lungs and bone marrow. Despite no notable features under static conditions, this clone significantly generated stable cell aggregates that were resistant to anoikis in suspension culture under fluid shear stress conditions. Even as a heterogeneous population, this clone generated almost monoclonal CTC clusters. Via transcriptome analyses, we identified E-cadherin to be indispensable but not sufficient for such stable cell-cell adhesion. Instead, our data indicated that mutual regulation of cortical actin-myosin dynamics according to mechanostress in the cells within each aggregate governed stable adhesion. Furthermore, the gene expression signature of the mechanosensitive clone, which originated clustered CTCs, was associated with locoregional and metastatic recurrence in patients with HNSCC. These results reveal that intrinsically mechanosensitive rare clones in the parental population dominantly colonize distant sites via homotypic CTC cluster formation. This novel clonal selection mechanism based on intrinsic tumor cell mechanosensitivity may lead to promising cancer therapies.

overall_design: Analyze global gene expression in 3 different clones by comparing its gene expression.

first: Satoru

last: Shinriki


title: Multi-transcription factor reporter mice delineate early precursors to the LTi and ILC lineages

city: Chicago

first: Albert

last: Bendelac

state: IL

address: 924 E. 57th Street BSLC

department: Pathology

institute: University of Chicago

summary: Transcription factor (TF) reporter mice have proved integral to the characterization of murine innate lymphoid cell (ILC) development and function. Here, we implemented a CRISPR/Cas9-generated combinatorial reporter approach for the simultaneous resolution of several key TFs throughout ILC development in both the fetal liver and adult bone marrow. We demonstrate that the Tcf7-expressing early innate lymphoid progenitor (EILP) and the common helper innate lymphoid progenitor (CHILP) both contain a heterogeneous mixture of committed ILC and Lymphoid Tissue-inducer (LTi) precursors, rather than a shared precursor to these lineages. Moreover, the earliest specified precursor to the LTi lineage was identified upstream of these populations, prior to the expression of Tcf7. These findings match dynamic changes in chromatin accessibility associated with the expression of key TFs (ie. Gata3 and Rorc), highlighting the distinct origins of ILC and LTi lineages at the epigenetic and functional levels, and provide a revised map for ILC development.

overall_design: ATAC-seq was performed in ILC and LTi precursors from E15 Fetal Liver of Zbtb16-EGFP or Zbtb16-EGFP Tcf7-mCherry Rorc-Thy1.1 reporter mice

first: Darshan

middle: N

last: Kasal


title: Chromothripsis drives DNA amplification in cancer cells developing drug resistance

city: La Jolla

first: Ofer

last: Shoshani

state: California

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

summary: Gene amplification leading to increased oncogene expression or anticancer drug resistance is a frequent event in cancer. Cytogenetic, genomic, and transcriptomic analyses were used to determine the initiating events of gene amplification in a tunable cell culture system developing resistance to chemotherapy. Chromosome shattering (chromothripsis) was found to be a major resistance driver through the production of extra-chromosomal double minutes either directly or subsequent to formation of a homogenous staining region (HSR). Formation and maintenance of double minutes were enhanced by PARP and DNA-PK activities. Double minutes were found to be highly dynamic, undergoing structural evolution to produce increased drug tolerance or re-integration into ectopic chromosomes under conditions of DNA damage. Genome rearrangement profiles produced through acquired drug resistance are similar to human cancer examples with oncogene amplification. Thus, chromothripsis is a driver of genome evolution that enables rapid acquisition of tolerance to altered growth conditions.

overall_design: Examination of DNA interactions using in situ Hi-C in two different cells (with double minutes or with HSRs) and in control cells

first: Don

last: Cleveland

first: Rongxin

last: Fang

first: Miao

last: Yu

first: Bing

last: Ren


title: Immune determinants for the mesenchymal identity of ovarian cancer via exosome-mediated microRNA transfer

status: Public on Sep 22 2020

city: Chengdu

first: Shentao

last: Zhou

address: Chengdu

institute: West China Second University Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Ovarian cancer is a heterogeneous disease that constitutes great menace to female health and poses tremendous clinical challenge. Based on unsupervised classification of whole-genome gene expression profiles, four molecular subtypes of ovarian cancer were recently identified. However, currently it is still unelucidated on the immune infiltration pattern of different molecular subtypes of ovarian cancer. we used a computational approach (CIBERSORT) to bulk gene expression profiles of ovarian cancer datasets to infer the proportions of 22 subsets of immune cells in the four subtypes. We found that plasma cells are enriched in the mesenchymal subtype of ovarian cancer and the content of plasma cells was correlated with the density of mesenchymal cells in clinical specimens of ovarian cancer. Co-culture of non-mesenchymal subtype ovarian cancer cell lines with plasma cells could induce a mesenchymal phenotype and enhance the metastatic potential of ovarian cancer cells. Mechanistically, this phenotypic switch was mediated by the transfer of miR-330-3p-containing exosomes to the non-mesenchymal ovarian cancer cells.miR-330-3p, which subsequently activate gene transcription of junctional adhesion molecule B(JAM2) epigenetically as an enhancer trigger. Collectively, our work identifies an immune-associated cellular, molecular, and clinical network that highlights the defining role of plasma cells in the mesenchymal identify of ovarian cancer.

overall_design: For Small RNA Sequencing, small RNA was isolated from three groups of plasma cells cultured medium. For RNA Sequenceing, total RNA was isolated after that the cells transfected with control miRNA mimic or miR-330-3p mimic in OVTOKO and OVCAR3 cell lines. Gene expression profiles were analyzed.

first: Shengtao


title: Transcriptional landscape of BE disease progression

status: Public on Sep 17 2020

city: München

first: Michael

last: Quante

address: Ismaninger Str 22

department: II Medizinische Klinik

institute: Technische Universität München

summary: Our mouse model of BE in which overexpression of IL-1b in the squamous esophagus induces chronic inflammation leads to metaplasia and dysplasia at the squamo-columnar junction (SCJ) in the mouse gastro-esophageal junction resembles the human disease. Adult L2-IL1b mice were employed to investigate changes to the transcriptional landscape at the SCJ during disease progression from BE to EAC following pharmaceutical or genetic perturbations of interest to BE biology.

overall_design: Barrett Esophagus (BE) is a risk factor for the development of esophageal adenocarcinoma (EAC). Disease progression, however, is not well understood. Here, we utilized our IL-1b mouse model of BE to study the impact of following risk factors on progression of BE to EAC: high fat diet (HFD) and overexpression of IL-8, modulations of the bile acid receptor FXR, modifications of Notch signaling in intestinal Lgr5-positive intestinal stem cells and modifications of Notch signaling in intestinal Dclk1-positive post-mitotic tuft cells.

first: H

middle: C

last: Maurer


title: Expression data from Hela cells that express wt or SUMOylation-deficient IRF2BP1 and which are treated with or without EGF after serum starvation

status: Public on Sep 15 2020

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
The transcriptional co-regulator IRF2BP1 gets de-SUMOylated after EGF treatment in Hela cells. SUMOylation of IRF2BP1 occurs at position K579.
We used microarray analysis to investigate which genes are under control of IRF2BP1 SUMOylation in dependence of EGF treatment.

overall_design: Hela cells stably expressing low levels of siRNA-resistant, untagged IRF2BP1 wildtype (wt) or IRF2BP1 K579R (KR) were treated with siRNA against the endogenous IRF2BP1. Following that, cells were serum starved, serum starved and treated with100 ng/ml EGF for 1 hour. As a control, cells were also kept in full medium containing serum.

first: Nicolas

last: Stankovic-Valentin

first: Sina-Victoria

last: Barysch

first: Frauke

last: Melchior


title: SIN3A regulates porcine early embryonic development by modulating CCNB1 expression

status: Public on Sep 16 2020

city: Hangzhou

first: Kun

last: Zhang

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: SIN3A is the central scaffold protein of the SIN3/HDAC transcriptional repressor complex. We previously found that SIN3A participates in the mouse preimplantation development by finetuning HDAC1 expression. However, it remains unresolved if this functional significance of SIN3A was conserved in other mammals. The objective of this work was thus to characterize the expression profiles and the functional role of SIN3A in preimplantation development using non-rodent animal models. RNA-seq results show a large amount of SIN3A mRNA is present in oocytes and early embryos prior to embryonic genome activation and a low amount thereafter, suggesting a maternal origin of SIN3A in all species examined. Interestingly, immunofluorescence data show that SIN3A protein level peaks at 4-cell stage in pigs compared with morula stage in cattle, suggesting a differential role of SIN3A among species. Indeed, SIN3A depletion in early embryos causes a developmental arrest at 2-cell stage in pigs but does not affect bovine early embryonic development. In contrast with mouse data, SIN3A depletion results in only a slight decrease and even no difference in HDAC1 expression in porcine and bovine early embryos, respectively. In addition, HDAC1 knockdown does not cause 2-cell block, however, leads to a reduced blastocyst rate, suggesting the effect of SIN3A depletion on porcine early embryos is independent of HDAC1. By using un-biased RNA-seq approach, we found that CCNB1 transcript level is dramatically reduced. Moreover, CCNB1 knockdown results in a similar phenotype as SIN3A depletion. Injection of exogenous CCNB1 into SIN3A-depleted embryos could partly rescue embryonic development beyond 2-cell stage. In conclusion, our results indicate SIN3A plays an essential role in porcine early embryonic development, which probably involving the regulation of CCNB1 expression.

overall_design: 2-cell porcine embryos (32 h after parthenogenetic activation) were harvested from NC and KD groups (n=3; 20 embryos/group/replicate). Total RNA extraction was performed using Picopure RNA isolation kit (Life Technologies, Grand Island, NY, USA) based on the manufacturer's manual. Before RNA isolation, equal amount of GFP and RFP mRNA  were added to each group as a spike-in control. mRNAs separation was achieved using oligo(dT)25 beads. Sequencing libraries were constructed with NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the instruction. In brief, mRNAs were fragmented followed by reverse transcription. The cDNA library underwent end repair, poly(A)-tailing, adaptor ligation, and PCR amplification for 12–15 cycles to prepare sequencing libraries. Libraries were sequenced using Illumina Hiseq X Ten at the Novogene Co. Ltd.

first: Lei

last: Luo

first: Yanna

last: Dang


title: Transcriptomic Characterization of neuroblastoma by Single Cell RNA Sequencing

status: Public on Sep 18 2020

first: rui

last: Dong

address: 399 Wan Yuan Road

institute: Department of Pediatric Surgery, Children’s Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defect

summary: Neuroblastoma (NB) is the most common malignant solid tumor in the abdomen of children, with high degree of malignancy, poor prognosis and unknown pathogenesis. So we aim to investigate intra-tumor heterogeneity of neuroblastoma at single cell resolution.

overall_design: Single cell mRNA profiles of sixteen primary tumors from sixteen patients with neuroblastoma, four adrenal tissue and two embryos from six aborted fetus were generated by 10X Genomics plartform, without technical replication, and sequenced by NovaSeq 6000 (Illumina)

first: Rui

first: Jia

last: Wang

first: Kai

last: Li

first: Kuiran

first: Yong

last: Zhan

first: Chunjing

last: Ye


status: Public on Sep 14 2020

first: Don

middle: W.

last: Cleveland

state: CA

overall_design: Examination gene expression changes in cancer cells developing methotrexate resistance through gen amplification

first: Ofer

last: Shoshani

first: Ying

last: Sun


title: Gene expression of primary Glioblastoma cell lines

status: Public on Oct 02 2020

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: We investigated the gene expression profiles of primary Human GBM cell lines. To represent the complexity of the GBM tissues, we uesd cell lines belonging to two different subtypes (HuTu10, proneural; HuTu13, Mesenchymal).

overall_design: Two primary Glioblastoma cell lines were transfected with control siRNAs. Each sample was in quadruplicate. Two days after transfection, cells were harvested for RNA extraction; total RNA was then used for Affymetrix Microarray profiling.

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo

first: Atsushi

last: Fujimura


title: Radiation induces dynamic changes to the T cell repertoire in renal cell carcinoma patients

status: Public on Sep 08 2020

city: Buffalo

first: Jacky

middle: Louis

last: chow

state: New York

address: Elm and Carlton Streets

department: Immunology

institute: Roswell Park

summary: Strong evidence supports the tumor immune landscape as a determinant of patient responses to immunotherapy. Readily available therapies, including radiation, are being investigated as modifying agents with immune checkpoint blockade. However, surprisingly little is known regarding radiotherapy’s impact within the tumor microenvironment and intratumoral T cell repertoires of patients, leaving critical gaps to guided design of clinical protocols. Here, samples from renal cell carcinoma (RCC) patients underwent high-throughput analysis to reveal transcriptional immune activation and increased clonality in irradiated tumors.

overall_design: Comparing transcriptomes of treatment-naïve, resected patient primary renal cell carcinoma (RCC) tumors versus patient primary RCC tumors treated with 1 x 15 Gy radiation by SBRT, followed by nephrectomy at 4 weeks post radiation.

last: Chow

first: Nicholas

last: Hoffend

first: Scott

middle: I

last: Abrams

first: Thomas

last: Schwaab

first: Anurag

middle: K

last: Singh

first: Jason

middle: B

last: Muhitch


title: RNA Sequencing and characterization of the transcriptomes regulated by KSHV-encoded vIRF1

status: Public on Sep 09 2020

city: Nanjing

first: Liuxue

last: Sheng

state: Jiangsu

address: Tian Yuan East Road

institute: Nanjing Medical University

summary: To understand the regulatory work of KSHV vIRF1, we profiled dysregulated RNAs by RNA-seq.

overall_design: We identified vIRF1-regulated RNAs through RNA sequencing in established KSHV and vIRF1 mutant virus infected EA.HY926 cell line.

first: Xiangya

last: Ding


title: Longitudinal profiling of the human immune response to Plasmodium falciparum

status: Public on Sep 07 2020

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

summary:
The diversity of human immune responses to P. falciparum is unknown and yet immune decision-making likely dictates outcome of infection
We infected 15 malaria-naïve human volunteers with P. falciparum and used longitudinal whole blood transcriptional profiling to independently analyse the immune response in every volunteer

overall_design: Timecourse analysis of the whole blood transcriptome in 15 malaria-infected human volunteers and 4 uninfected controls (120 samples in total, median = 6 samples per volunteer)

first: Phil

last: Spence

first: Kathryn

last: Milne


title: High-throughput sequencing identified differentially expressed RNAs  between MALAT1 knockdown C3H10 adipocyte  and control cells

first: LEI

last: SHEN

state: State...

address: Feng lin road 180

department: Department of General Surgery

institute: Zhongshan Hospital, Fudan University

summary: Although MALAT1 is a lncRNA highly expressed in many tissues and participates in a series of physiological and pathological processes, the potential role of MALAT1 in adipogenesis is not clear. To gain full insights into MALAT1 function in the adipogenic differention of C3H10 cell, we performed RNA-seq to antisense oligonucleotides(ASO) treated C3H10 cells and found numerous differentially expressed RNAs  between MALAT1 knockdown C3H10 adipocyte  and control cells.

overall_design: Transcriptome profiling of MALAT1 knockdown C3H10 adipocyte  and control cells

first: Lei

last: Shen


title: Epigenetic gene silencing by heterochromatin primes fungal resistance

first: Sito

last: Torres-Garcia

address: 6.4 Michael Swann Building. Max Born Crescent

institute: Wellcome Centre for Cell Biology. University of Edinburgh

summary: Genes embedded in H3 lysine 9 methylation (H3K9me)-dependent heterochromatin are transcriptionally silenced. In fission yeast, Schizosaccharomyces pombe, H3K9me-mediated heterochromatin silencing can be transmitted through cell division provided the counteracting demethylase Epe1 is absent. It is possible that under certain conditions wild-type cells might utilize heterochromatin heritability to form epimutations, phenotypes mediated by unstable silencing rather than DNA changes. Here we show that resistant heterochromatin-dependent epimutants are formed in response to threshold levels of caffeine. Unstable resistant isolates exhibit distinct heterochromatin islands, which reduce the expression of underlying genes, one of which is known to confer resistance when deleted. Targeting synthetic heterochromatin to implicated loci confirms that resistance results from heterochromatin-mediated silencing. Our analyses reveal that epigenetic processes promote phenotypic plasticity, allowing wild-type fission yeast to adapt to non-favorable environments without altering their genotype. In some isolates, subsequent or co-occurring gene amplification events enhance resistance. Caffeine impacts two anti-silencing factors: levels of Epe1 are downregulated, reducing its chromatin association; and expression of the Mst2 histone acetyltransferase is switched to a shortened isoform. Thus, heterochromatin-dependent epimutant formation provides a bet-hedging strategy that allows cells to remain genetically wild-type but transiently adapt to external insults. As unstable caffeine-resistant isolates show cross-resistance to fungicides it is likely that related heterochromatin-dependent processes contribute to anti-fungal resistance in both plant and human pathogenic fungi.

overall_design: H3K9me2 ChIP-seq, total small RNA-seq and total RNA-seq of isolates identified in this study

first: Robin

last: Allshire


title: Evolutionarily conserved sequence motif analysis guided development of chemically defined hydrogels for therapeutic angiogenesis

status: Public on Sep 21 2020

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

summary: Biologically ligands (e.g., RGDS from fibronectin: Fn-RGD) play a critical role in the development of chemically defined biomaterials. However, there has been limited progress in recent decades towards discovering novel extracellular-matrix-protein-derived ligands for translational applications. Here, by combining motif analysis of evolutionarily conserved RGD-containing regions in laminin (Ln) with functional microarray screening, we identified a Ln-derived angiogenic peptide (LDAP) that showed enhanced proangiogenic activities over commonly used Fn-RGD. Mechanistic studies using RNA-sequencing of LDAP functionalized hydrogels showed an improved angiogenic transcriptome over Fn-RGD functionalized hydrogels and high similarity to Matrigel, attributed to the ability of LDAP to engage both Ln- and Fn-binding integrins. Injectable hydrogels functionalized with LDAP, along with MMP-QK (a VEGF-mimetic peptide), exhibited increased functional recovery over decellularized extracellular matrix (dECM) and alginates functionalized with Fn-RGD and MMP-QK in a mouse ischemic hindlimb model, illustrating the power of the strategy to rapidly develop potent chemically-defined biomaterials for therapeutic applications.

overall_design: HUVECs (p2-p3) were encapsulated into 0.125mmol/g peptide-modified alginate (at alginate concentration = 1% (w/v)) at the density of 2 million cells/mL with EGM for 24 hours. Groups include HUVECs cultured in LDAP(laminin derived angiogenic peptide)-peptide modified alginate compared to in RGDS-peptide modified alginate hydrogels.

first: Jia

last: Jia

first: Dylan

last: Richards

first: Ying

last: Mei

first: E

middle: S

last: Hazard


title: Defective mitochondrial dynamics underlie manganese-induced neurotoxicity

city: New York

first: Hector

last: Cordero

address: 650W 168th Street

institute: Columbia University

summary: Rats were exposed to manganese (Mn) at 25mg/kg for 15 days. After the exposure, the RNA was collected from the striatum tissue (specific part the brain) of the control group (untreated) and Mn-exposed group, and submitted for RNA sequencing to elucidate the transcriptional changes of Mn-induced toxicity in the striatum.

overall_design: Examination of the transcriptomic profile of striatum exposed to Mn.


title: CVB3 infected fetal mice

status: Public on Sep 05 2020

city: St. Louis

first: Vipul

last: Sharma

state: Missouri

address: Campus Box 8234, 600 S. Euclid

department: Surgery

institute: Washington University in St.Louis

summary: Difference in RNA sequencing in CVB3 infected and control mice fetuses

overall_design: Pregnant mice were infected with CVB3 at E9 and fetuses were collected at E14. These fetuses were divided into 3 groups – control (uninfected) and infected. Fetuses were cryosectioned and using laser microdissection heart tissue (left ventricle, right ventricle, and interventricular septum) was collected for RNA extraction. This RNA was used to examine signaling pathways using RNAseq.

first: Pirooz

last: Eghtesady


title: Genome-wide analysis of targets for post-transcriptional regulation by Rsm proteins in Pseudomonas putida KT2440

status: Public on Sep 03 2020

city: Granada

first: Manuel

last: Espinosa-Urgel

address: Profesor Albareda, 1

department: Environmental Protection

country: Spain

institute: Estacion Experimental del Zaidin. CSIC

summary: Pseudomonas putida KT2440 harbors three known members of the CsrA/RsmA family of post-transcriptional regulators: RsmA, RsmE and RsmI. We have carried out a global analysis to identify RNA sequences that are bound in vivo by Rsm proteins, in order to identify potential regulatory targets for each of them. Affinity purification and sequencing of RNA molecules associated with Rsm proteins were used to identify 709 targets, 75 of them common to the three proteins. Relevant targets include genes encoding proteins involved in metabolism, transport and secretion, stress responses, signal transduction and regulation, and the turnover of the second messenger c-di-GMP. The role of Rsm proteins in the utilization of basic amino acids and bacterial fitness in the plant rhizosphere are also exposed.

overall_design: Previously constructed derivatives of expression vector pME6032 harboring each rsm gene were used to express His-tagged Rsm proteins in P. putida KT2440. Overnight cultures (10 ml) of KT2440 harbouring each construct were inoculated in 500 ml of LB medium, and incubated at 30°C under shaking to an OD660 of 0.8. At that point, expression of His-tagged-Rsm proteins was induced for 6 h by the addition of IPTG to a final concentration of 0.5 mM. Three biological replicates were run in parallel. Aliquots of 1.5 ml were harvested by centrifugation, instantly frozen with liquid nitrogen and stored at -80C for total RNA purification. Cells from the remaining cultures were also harvested and cell pellets stored at -80C. His-tagged Rsm-RNA complex purification were isolated using Ni-NTA Fast Start Kit (Qiagen). Three replicate extractions were done for each culture replica.  Total RNA and RNA from Rsm-RNA complex was extracted using RNA isolation kit (Macherey-Nagel) following the manufacturer´s instructions. RNA samples were subsequently treated with RNase-free DNase I (Turbo DNA-free kit, Ambion) to remove DNA traces, as specified by the supplier. Total RNA quality was assessed using Agilent RNA 6000 Nano Kit (Agilent Technologies) in the Agilent 2100 Bioanalyzer. RNA concentration was measured using Qubit RNA BR assay kit (Life Technologies). 1µg of RNA was used for rRNA depletion using Ribo-Zero rRNA Removal Kit (Illumina). One of the biological replicates of RsmA and one of RsmI did not meet the required quality and quantity standards and were discarded.

first: Óscar

last: Huertas-Rosales

last: Romero

first: Kok-Gan

last: Chan

first: Kar-Wai

last: Hong

first: Miguel

last: Cámara

first: Stephan

last: Heeb

first: Laura

last: Barrientos-Moreno

first: María

middle: A

last: Molina-Henares

middle: L

last: Travieso

last: Ramos-González


title: The Tudor-domain protein TDRD7, mutated in congenital cataract, controls the heat shock protein HSPB1 (HSP27) and lens fiber cell morphology

status: Public on Sep 01 2020

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

summary: Mutations of the RNA-granule component TDRD7 (OMIM: 611258) cause pediatric cataract in humans. Here, we applied an integrated approach to elucidate the molecular pathology of cataract in Tdrd7 targeted-knockout (Tdrd7-/-) mice. Tdrd7-/- animals precipitously develop lens fiber cell abnormalities early in life, suggesting a global-level breakdown/mis-regulation of key cellular processes. High-throughput RNA-sequencing followed by iSyTE-integrated bioinformatics-based analysis identified the molecular chaperone and cytoskeletal-modulator, HSPB1 (HSP27), among the high-priority down-regulated candidates in Tdrd7-/- lens. Moreover, a protein 2-D fluorescence difference gel electrophoresis-coupled mass spectrometry screen also identified HSPB1 to be reduced in Tdrd7-/- lens, offering independent support for focusing efforts on this factor to explain Tdrd7-/- cataract. Reduction of HSPB1 preceded lens morphological abnormalities, suggesting that cytoskeletal defects underlie the Tdrd7-/- cataract phenotype. In agreement, scanning electron microscopy revealed abnormal fiber cell membrane protrusions in Tdrd7-/- lenses. Significantly, abnormal F-actin staining was detected specifically in Tdrd7-/- fiber cells that exhibit nuclear degradation, thereby revealing that there are distinct mechanisms based on pre- or post-nuclear degradation differentiation stage for F-actin cytoskeletal maintenance in fiber cells. Further, RNA-immunoprecipitation identified Hspb1 mRNA in wild-type lens lysate TDRD7-pulldowns, and single-molecule RNA-imaging showed co-localization of TDRD7 protein with cytoplasmic Hspb1 mRNA in a specific pre-nuclear degradation area of differentiating fiber cells, indicating that TDRD7-ribonucleoprotein complexes are necessary for controlling optimal levels of key factors in lens development. Together, these data uncover a novel role for TDRD7 in regulating elevation of stress-responsive chaperones for cytoskeletal maintenance in post-nuclear degradation lens fiber cells, perturbation of which causes early-onset cataracts.

overall_design: For RNA-sequencing (RNA-Seq) experiments, mouse lenses at stage P4 (n = 15 lenses per biological replicate) were collected from  Tdrd7-/- or control mice. RNA isolation was performed using the mirVanaTM RNA isolation kit (Life Technologies, Grand Island, NY). Total RNA isolation, followed by removal of small molecular weight RNA was performed according to manufacturer’s instructions. Library was prepared using TruSeq RNA Library Prep Kit v2 (Illumina), and sequencing was performed on a 2x75 paired end run using standard protocols on an Illumina HiSeq 2500 sequencing system. Briefly, mRNA was purified from the total RNA samples using Oligo dT conjugated magnetic beads, converted to adaptor-tagged, paired-end fragments which were then used for cluster generation onto a TruSeq v3 flow cell according to the Illumina® TruSeq™ RNA Sample Preparation Kit v2. Sequencing was carried out using the SBS Sequencing Kit. Images were analyzed using the Illumina Pipeline software (version RTA 1.13.48/CASAVA 1.8.2), and bases were called and translated to generate FASTQ sequence files.

first: Anand

last: Deepti

first: Lachke

last: Salil


title: Impact of liver-specific deletion of Dhcr24 gene on tissue gene expression

status: Public on Sep 04 2020

city: Cincinnati

first: Shailendra

last: Patel

state: OH

address: 231 Albet Sabin Way

department: Endorcrinology

institute: University of Cincinnati

summary: Genetic loss of the enzyme 3ß-hydroxysterol-∆24 reductase (DHCR24) results in Desmosterolosis (MIM #602398), a rare disease that presents with multiple congenital anomalies. Earlier studies to create a Dhcr24 global knockout mouse have failed as the pups died within 24 h of birth from lethal dermopathy. We generated a conditional knockout mouse model (Dhcr24flx/flx) and validated it by creating a liver-specific knockout Dhcr24flx/flx, Alb-Cre mouse using a mouse expressing cre recombinase driven by the albumin promoter. Despite increased circulatory and liver desmosterol due to loss of cholesterol synthesis in the liver, these mice demonstrated no marked changes in growth, fertility, hepatic architecture, lipoprotein secretion, etc. RNA-Seq analysis of the female mouse liver revealed no notable perturbations in pathways participating in cholesterol biosynthesis.

overall_design: RNA was isolated from liver, adrenal and macrophage of 1 mouse in each group.  KO mouse from each sex were compared to floxed Cre negative control mouse of the same sex.

first: Babunageswararao

last: Kanuri

first: Vincent

last: Fong

first: Ranjuna

last: Weerasekera

first: Sithara

last: Ponny


title: murine jejunal and ileal epithelial tissue

status: Public on Aug 31 2020

city: Tokyo

first: Masataka

last: Suzuki

address: 35, Shinanomachi, Shinjuku-ku

department: Pharmacology

institute: KEIO University, School of Medicine

summary:
Transcriptional profiling of mouse jejunal epithelia comparing Tcrbd-/-, DAOwt/wt mouse and Tcrbd-/-, DAOG181R/G181R
Intestinal microbiota produce D-amino acids, which are bacteria-specific    metabolites, for regulation of bacterial cell wall integrity. Host    intestine releases D-amino acid oxidase (DAO) to degrade bacterial D-amino    acids, which shapes gut microbial community. However, it is not clarified    whether bacterial D-amino acids affect host   s immunity. In the present    study, we compared mRNA expression in ileal epithelial tissue of DAO null    mice with that of control mice in the absence of both T cell receptor beta    and delta (Tcrb/d). Transcriptome analysis revealed up-regulation of    inflammatory cytokines such as TNFa, IL1b, and IFNg in the epithelial    tissue. Up-regulation of such cytokines could promote survival of na  ve B    cells and increase IgA-producing plasma cells, which in turn results in    enhancement of IgA production. These results indicate that DAO controls    intestinal immune responses through regulation of na  ve B cells and    differentiation of mature B cells.

overall_design:
Total RNA from 5 mice of each genotype were mixed.
Epithelial tissue of jejunum and ileum from Two genotype, Tcrbd-/-, DAOwt/wt vs.  Tcrbd-/-, DAOG181R/G181R, Total RNA from 5 mice were mixed in one sample.

first: Jumpei

last: Sasabe


title: Functional plasticity and reversible growth behavior of patients’ acute myeloid leukemia stem cells growing in mice

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

summary: Resistance against chemotherapy remains a major obstacle in treating patients with acute myeloid leukemia (AML). Novel therapeutic concepts are especially desired to target and eliminate resistant AML stem cells. Here we show that AML stem cells harbor the plasticity to switch from a low-cycling, therapy resistant state into an actively proliferating state associated with treatment response.   We used patient-derived xenograft (PDX) cells from patients with high risk or relapsed AML, which were lentivirally transduced for marker expression, stained with the proliferation-sensitive dye Carboxyfluorescein succinimidyl ester (CFSE), and re-transplanted into next-recipient mice. A rare subpopulation of AML cells displayed reduced proliferation in vivo, associated with increased treatment resistance. The proportion of AML cells with stem cell potential was identical in both, the highly and lowly proliferative sub-fraction. In re-transplantation experiments, proliferation behavior proved reversible, and AML stem cells were able to switch between a high and low proliferation state. Our data indicate that AML stem cells display functional plasticity in vivo, which might be exploited for therapeutic purposes, to prevent AML relapse and ultimately improve the prognosis of patients with AML.

overall_design: LRC and nLRC populations were sorted from samples AML-393 and AML-491. In summary, 12 LRC and 12 nLRC samples were analysed.

first: Sarah

last: Ebinger

first: Binje

last: Vick

first: Johannes

last: Bagnoli

first: Irmela

last: Jeremias


title: Targeting steroid receptor co-activator 3 sensitizes myeloma cell to proteasome inhibitor treatment through NSD2-mediated phase separation and chromatin remodeling [RNA-Seq]

status: Public on Aug 26 2020

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

summary: Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we demonstrate that some drug resistant genes were activated during myeloma resistant to bortezomib.  Mechanistically, NSD2 can interact with SRC-3, its SET domain is responsible to H3K36me2 to enhance the transcriptional activity of SRC-3 target gene. The inhibitor of SRC-3, SI-2, can impaired the interaction between NSD2 and SRC-3, caused the distribution of H3K36me2 changed on the genome-wide, and inhibit the transcription of those drug resistant genes.

overall_design: For myeloma cell, LP-1, we established bortezomib-resistant cell line which IC50 to bortezomib have been augmented over 5 folds, and the anti-apoptotic capacity remarkably enhanced. In this condition, we treated the LP-1 wild-type cell and bortezomib-resistant cell with 25nM SI-2, and cells were harvested for gene expression profiling when SI-2 was treated for 24h. Two replicates were performed.

first: Jing

last: Liu

first: Ying

last: Xie


title: In situ Hi-C profile of neutrophils from human peripheral blood

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Neutrophils were enriched from the peripheral blood of one healthy male human donor. High-throughput chromosome confirmation capture (Hi-C) was used to examine DNA interactions between chromosomes.

overall_design: The data consists of one Hi-C profile of neutrophil cells isolated from one healthy human male donor.

first: Hannah

last: Coughlan

first: Timothy

middle: M

last: Johanson


title: RNA-seq Analysis Reveals Different Drought Tolerance Mechanisms in Two Broadly Adapted Wheat Cultivars ‘TAM 111’ and ‘TAM 112’

status: Public on Aug 29 2020

city: Amarillo

first: Shuyu

state: Texas

address: 6500 Amarillo Blvd West

department: Texas A&M AgriLife Research

institute: Texas A&M University System

summary: Wheat cultivars ‘TAM 111’ and ‘TAM 112’ have been dominantly grown in the Southern U.S. Great Plains for many years due to their excellent, yet variable, drought tolerance. To identify the molecular basis and genetic control of drought tolerance in these two landmark cultivars, RNA-seq analysis was conducted to compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions. Of the 122,017 gene sequences assembled, 2,254 genes showed significantly altered expression patterns under dry and wet conditions in the two cultivars.  TAM 111 had 593 and 1,532 dry-wet differentially expressed genes (DEGs), and TAM 112 had 777 and 1,670 at heading and grain-filling stages, respectively. The two cultivars have 1,214 (53.9%) dry-wet DEGs in common, which agreed with their excellent adaption to drought, but 438 and 602 dry-wet DEGs were respectively shown only in TAM 111 and TAM 112 suggested that each may have a specific mechanism to cope with drought. Annotation of all 2,254 genes with dry-wet expression difference found 1,855 have functions related to biosynthesis, stress responses, defense responses, transcription factors and cellular components related to ion or protein transportation and signal transduction. Comparing hierarchical structure of biological processes, molecule functions and cellular components revealed the significant regulation differences between TAM 111 and TAM 112, particularly for genes of phosphorylation and adenyl ribonucleotide binding, and proteins located in nucleus and plasma membrane. Comparing gene expressions involved in responses to stresses of water deprivation, heat and oxidative, ABA-induced signal pathway and transcription regulation found TAM 112 have more specific dry-wet DEGs than TAM 111 with most of them up-regulated, indicating that TAM 112  is more active than TAM 111 in response to drought. In addition, 399 dry-wet DEGs with unknown functions included 258 genes encoding predicted uncharacterized proteins and 141 unannotated genes with no similar sequences identified in the databases. These may represent novel genes related to drought response in TAM 111 or TAM 112. This research thus revealed different drought-tolerance mechanisms in TAM 111 and TAM 112 and identified useful drought tolerance genes for wheat adaption.

overall_design: Compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions.

first: Chenggen

last: Chu


title: Targeting steroid receptor co-activator 3 sensitizes myeloma cell to proteasome inhibitor treatment through NSD2-mediated phase separation and chromatin remodeling [ChIP-Seq]

summary: Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we demonstrate that NSD2/SRC-3 complex coordinates histone H3 lysine 36 dimethylation (H3K36me2) and transcriptional elongation factor Pol II to regulate chromatin dynamic and gene transcription during myeloma resistant to bortezomib. Mechanistically, NSD2 can interact with SRC-3, its SET domain is responsible to H3K36me2 to enhance the transcriptional activity of SRC-3 target gene. The inhibitor of SRC-3, SI-2, can impaired the interaction between NSD2 and SRC-3, caused the distribution of H3K36me2 on the genome-wide.

overall_design: Examination of histone modification in multiple myeloma bortezomib-resistant cell line


title: Gene expression profilings of  naive B cell,  memory B cell and plasmablast of healthy donors and SLE patients

status: Public on Aug 25 2020

city: Sendai

first: Hiroshi

last: Fujii

state: MIyagi

address: Seiryo 1-1, Aoba-ku

department: Department of Hematotology and Rheumatology

institute: Tohoku University, School of Medicine

summary: Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by production of various pathogenic autoantibodies. Increased type I interferon signature is suggested as a trigger of the disease. Previous studies identify increased plasmablasts in peripheral blood of SLE patients. In spite of the unique cellular properties of the plasmablasts compared with other B cell subsets and plasma cells, the biological characteristics of SLE plasmblast remain unknown and few therapeutic strategies targeting SLE plasmablasts have been applicated. We performed microarray analysis of naive, memory B cells and plasmablasts (CD38+CD43+ B cells) freshly isolated from healthy controls and active SLE (n=4, each) to find the unique biological properties of SLE plasmablast.

overall_design: Naive B cell,  memory B cell and plasmablast were isolated from freshly separated peripheral blood mononuclear cell derived from 4 healthy donors and 4 systemic lupus erythematosus patients

first: Kanae

last: Akita


title: Characterization of SALL2 gene isoforms and its targets across cell types reveals highly conserved networks

status: Public on Aug 28 2020

city: Concepción

first: Carlos

last: Farkas

state: Biobío

address: Chacabuco 1140, 1808

department: Bioquímica y Biología Molecular

country: Chile

institute: Universidad de Concepción (UDEC)

summary:
The SALL2 transcription factor (TF), an evolutionarily conserved gene through vertebrates, is involved in normal development and neuronal differentiation and considered as a tumor suppressor in certain human cancers. Several transcriptional targets of SALL2 are identified, these include the p21CDKN1A and p16INK4A cyclin-dependent kinase inhibitors, and the PMAIP1 and Bax pro-apoptotic genes, among others in various cell types. The human and mouse SALL2 gene loci contain two promoters, each one controlling the expression of a different protein isoform (namely E1 and E1A). However, several improvements on the human genome assembly and gene annotation through next-generation sequencing technologies over time reveal correction and annotation of additional isoforms, obscuring dissection of SALL2 isoform-specific transcriptional targets. We here integrated current data of normal/tumor gene expression databases along with ChIP-seq binding profiles to analyze SALL2 isoforms expression distribution and infer isoform-specific SALL2 targets. We found that the canonical SALL2 isoform (E1) is one of the lowest expressed, while isoform E1A is highly predominant across cell types. To dissect SALL2 isoform-specific targets, we analyzed publicly available ChIP-seq data from glioblastoma multiforme (GBM) and in-house ChIP-seq datasets performed in SALL2 wild-type and isoform E1A knockout HEK293 cells. Another available ChIP-seq data in HEK293 cells (ENCODE Consortium Phase III) overexpressing a non-canonical SALL2 isoform (herein named short_E1A) was analyzed but not included in the final analysis because we demonstrated that short_E1A is mostly localized in the cytoplasm, making impractical to dissect its direct transcriptional targets in this cell model. Regardless of cell type, our analysis reveals a highly conserved network of brain-specific TFs (i.e., SALL3, POU3F2, and NPAS3) and PODXL as a gene that is likely regulated by SALL2 across cell types. Our data integration identified a conserved molecular network in which SALL2 regulates target genes and encourages validation of publicly available ChIP-seq datasets for assessing transcriptional targets of a specific gene/isoform.

Financial support: This work was supported by Fondecyt Regular Grants #1151031, #1191172 to Roxana Pincheira Fondecyt Regular Grant #120 to Ariel Castro, Postdoctorate Fondecyt Grant #3160129 and Fondecyt de Iniciacion # 1119028 to Matias I.Hepp.

overall_design: ChIP-seq of endogenous SALL2 performed in wild-type HEK293 cells, SALL2 E1A knockout isoforms in HEK293 cells and SALL2 total knockout in HEK293 cells

first: Matias

last: Hepp

first: Roxana

last: Pincheira


title: Multi-omics and Machine Learning Accurately Predicts Clinical Response to Adalimumab and Etanercept Therapy in Patients with Rheumatoid Arthritis

status: Public on Aug 24 2020

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Targeting steroid receptor co-activator 3 sensitizes myeloma cell to proteasome inhibitor treatment through NSD2-mediated phase separation and chromatin remodeling


title: Multi-omics and Machine Learning Accurately Predicts Clinical Response to Adalimumab and Etanercept Therapy in Patients with Rheumatoid Arthritis [RNA-Seq]

summary: Objectives: To predict response prior to anti-TNF treatment and comprehensively understand the mechanism how patients respond differently to anti-TNF treatment in rheumatoid arthritis (RA). Methods: Gene expression and/or DNA methylation profiling on PBMC, monocytes, and CD4+ T cells, from 80 RA patients before initiating either adalimumab (ADA) or etanercept (ETN) therapy was studied. After 6-month treatment response was evaluated according to the EULAR criteria of disease response. Differential expression and methylation analyses were performed to identify the response-associated transcriptional and epigenetic signatures. Machine learning models were built using these signatures by random forest algorithm to predict response prior to anti-TNF treatment and were further validated by a follow-up study. Results: Transcriptional signatures in ADA and ETN responders are divergent in PBMCs, and this phenomenon was reproduced in monocytes and CD4+ T cells. The genes upregulated in CD4+ T cells of ADA responders were enriched in the TNF signaling pathway, while very few pathways were differential in monocytes. Differential methylation positions (DMPs) of responders to ETN but not to ADA are majorly hypermethylated. The machine learning models to predict the response to ADA and ETN using differential genes reached overall accuracy of 85.9% and 79%, respectively. The models using DMPs reached overall accuracy of 84.7% and 88% for ADA and ETN, respectively. A follow-up study validated the high performance of these models. Conclusions: Machine learning models based on these molecular signatures could accurately predict response before ADA and ETN treatment, paving the path towards personalized anti-TNF treatment.

overall_design: From the observational (BiOCURA) cohort, we selected 80 patients with RA, treated with ADA (38) or ETN(42) and a follow-up period of at least 6 months. Blood was drawn shortly before treatment initiation in a Lithium-heparinized tube (BD Vacutainer®). We first isolated peripheral blood mononuclear cells (PBMCs) from these blood samples prior to ADA or ETN treatments. And then genome-wide gene expression were performed on these PBMCs, using RNA-sequencing. RNA-sequencing on CD14+ monocytes and CD4+ T cells isolated from the PBMCs were performed to gain more insights into different anti-TNF response. After 6-month treatment, patients’ responses were evaluated according to EULAR criteria.

first: Weiyang

last: Tao

first: Arno

last: Concepcion

first: Marieke

last: Vianen

first: Anne

last: Marijnissen

first: Floris

middle: P

last: Lafeber

last: Radstake


title: Circulating miRNA sequencing in serum of patients with Cushing's syndrome and related controls

first: sharmilee

last: vetrivel

state: Bayern

address: ziemssenstraße 1, DG

institute: Ludwig Maximilian University of Munich (Universität München)

summary: Cushing’s syndrome (CS) is a rare disease with high morbidity and mortality. Diagnosis and subtyping are complex and challenging. Circulating microRNAs were described to be useful as minimally invasive diagnostic markers. Our aim was to determine and compare the circulating microRNA expression profiles of patients with CS and controls. We included three groups of patients of the German Cushing’s registry: A.) patients with florid adrenal dependent CS scheduled for adrenalectomy (CPA); B.) patients with florid pituitary dependent CS scheduled for surgery (CD); and C.) patients in whom CS had been ruled out (controls). Next-generation sequencing was performed in the 30 CS serum samples before and after curative surgery, respectively, and in 10 baseline samples of controls. No significant differential expression was observed between all the CS samples and controls by NGS as well as by QPCR. The sequencing of the preoperative samples revealed a significant differential expression of miR-182-5p (p=0.02) between CD and controls. The differential expression was validated by QPCR in the discovery cohort and in an independent validation cohort. MiR-96-5p, miR-146b-5p, miR-183-5p, miR-185-5p, miR-616-5p and miR-629-5p were found to be significantly upregulated in CPA samples in comparison to CD group of the preoperative group in NGS. However, similar upregulation pattern could not be observed by QPCR in the discovery and validation cohorts. Additionally, miR-96-5p and miR-185-5p were found to be modulated by dexamethasone in controls. Thus, our study reports miR-182-5p as a possible biomarker for CD, which has to be validated in a prospective cohort.

overall_design: Circulating miRNA profile in patient serum samples for identifcation of potential biomarkers

first: Anna

last: Riester

first: Martin

last: Reincke

first: Alon

last: Chen

first: Sharmilee

last: Vetrivel


title: DEX Induced effector RiNLE1 expression inhibited plant defense genes expression

status: Public on Aug 05 2020

city: WAGENINGEN

first: Peng

last: Wang

address: Hoevestein 239 12B007

institute: Wageningen university

summary: Since we reasoned that RiNLE1 exerts its functions inside host nuclei, we explored the influence of RiNLE1 on plant gene expression. Therefore, we applied a dexamethasone (DEX) inducible promoter system (Borghi, 2010) to induce RiNLE1 expression (lacking signal peptide) in Medicago roots. As a control we replaced the RiNLE1 coding sequence by a short nonsense sequence.

overall_design: RiNLE1 overexpression roots compared to EV toots

first: Erik

last: Limpens


title: scRCAT-seq: simultaneously profile RNA TSS and TES at single-cell level

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

summary: We developed a new single cell sequencing method to simultaneously identify RNA TSS and TES at single-cell level.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design:
Single DRG neurons, oocytes, hESC, HEk293T, ARPE, mESC, hESC_drived_organoid were sequenced by scRCAT-seq, a single cell transcriptomic protocol for identifying the transcription start sites and the transcription end sites. For comparison, Smart-seq2 and  Iso-seq were also used to construct the libraries.
scRCAT_seq_ERCC* samples are solely composed of the ERCC control RNAs. '100' and '1000' in the sample titles represent  dilution. 0.1ul  of 1:100 or 1:1000  dilution of ERCC was used to  construct the library.


title: PC3 cells gene expression after p-coumaric acid treatment

city: San Nicolás de los Garza

first: María

middle: Del Rayo

last: Camacho-Corona

state: Nuevo León

address: Av. Universidad S/N, Ciudad Universitaria

department: Facultad de Ciencias Químicas

country: Mexico

institute: Universidad Autónoma de Nuevo León

summary: Whole genome expression monitoring of human adenocarcinoma prostate cancer (PC3) cell line, after sub-lethal treatment with p-coumaric acid

overall_design: Treated vs untreated (control) cells, grown and harvested on a 6-well plate (1 million cells per well)

first: Tommaso

last: Stefani

first: Jorge

last: Ramírez-Salcedo


title: The effects of liver specific deletion of Dhcr7 on gene expression

first: Shailendra

last: Patel

summary: Smith-Lemli-Opitz Syndrome (SLOS) is a developmental disorder caused by autosomal recessive mutations in the Dhcr7 gene. SLOS patients present clinically with multiple dysmorphologies, neurological, behavioral and cognitive defects, and demonstrate impaired cholesterol biosynthesis resulting in markedly elevated 7-DHC in all bodily tissues and fluids. Previous rodent models of SLOS suffered from neonatal mortality or variation in the biochemical phenotype over time.  We generated a viable murine model bearing a conditional flosed allele of the Dhcr7 gene, and validated it by generating a mice with liver-specific deletion of Dhcr7 by breeding with a strain expressing Cre recombinase driven by an albumin promoter . These mice demonstrated elevated circulatory and liver 7-DHC levels, but phenotypic characterization of the knockout mice revealed no significant changes in viability, fertility, growth curves, liver architecture, hepatic triglyceride secretion, and parameters of systemic glucose homeostasis. Investigation in to changes in the liver transcriptome were investigated withe RNAseq, and identified enrichment in various pathways, including steroid hormone biosynthesis and various cell signaling and metabolism pathways. Most notably missing from the list are the genes related to cholesterol biosynthesis.  Generation of this Dhcr7 conditional knockout model will allow for better studies into the post natal effects of blocking cholesterol biosynthesis, accumulation of 7-DHC, and the role of DHCR7 in specific tissues.

overall_design: RNA was isolated from livers of 3 mice in each group.  KO mice from each sex were compared to floxed Cre negative control mice of the same sex.

first: Babunageswararao

last: Kanuri

first: Vincent

last: Fong

first: Sithara

last: Ponny


title: DK2, a newly synthesized chalcone, induced apoptosis and differential expression profiles of miRNA and mRNA on breast cancer MCF-7 cell line

status: Public on Jul 31 2020

city: Cheras

first: norlaily

last: mohd ali

state: Selangor

address: Universiti Tunku Abdul Rahman, Jln Sg Long

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

summary:
In this study, the cytotoxic effect of DK2, a newly synthesized chalcone and its underlying mechanism against breast cancer cell line, MCF-7 were investigated.
MCF-7 was treated with 8.2 μM of DK2 at several time points. The apoptotic analysis was carried out using MTT assay, morphology observation (using inverted microscope and fluorescent microscope) and flow cytometry analysis (using Annexin V/7ADD apoptosis analysis and cell cycle analysis).

overall_design: Triplicate of DK2-treated MCF-7 cell and control untreated MCF-7 were subjected to miRNA and mRNA microarray profiling (Affymetrix, USA).

first: Norlaily

last: Mohd Ali

first: M

last: Akhtar

first: Huynh

last: Ky

first: Han

last: Ong

first: Sheau

middle: W

last: Tan

first: Swee

last: Yeap

first: Tunku

last: Kamarul


title: Analysis of functions of Rlim during reproduction in male mice

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

summary: The transcriptomes of mouse testes isolated from 8 weeks old male littermates carrying germline Rlim-KO and Rlim-Fl alleles were determined via RNA-seq were elucidated. No major differences between wt and RlimKO with respect to pathways containing multiple genes was detected.

overall_design: Transcriptomes of testes isolated from male Rlim-KO and Rlim-Fl mice were compared.

first: Ingolf

last: Bach

first: Feng

last: Wang


title: A cell non-autonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism

status: Public on Jul 30 2020

city: Charlottesville

first: Jeffrey

last: Smith

state: Virginia

address: 1340 JPA  PO Box 800733 Charlottesville, VA 22908 Telephone:

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary:
Purpose: To gain additional insights to candidate factors promoting longevity in Caloric Restricted Conditioned Media (CRCM), we performed transcriptomics analysis (RNA-seq) on BY4741 yeast cells grown in non-restricted SC media supplemented with CRCM, Non-restricted Conditioned Media (NRCM), or water as a control with a goal of identifying physiological responses that could be linked to specific metabolites.
Methods: RNA profiles of NR (SC, 2% glucose) treated cells supplemented with water, 2% CRCM, or 2% NRCM at log phase, 24, and 96 hours post-inoculation. These samples were conducted in triplicate. Following inoculation, we harvested cells at log phase, 24 hrs (late diauxic shift), and 96 hrs (stationary phase).Total RNA was isolated using the hot acid phenol method and then processed into Illumina DNA sequencing libraries. Briefly, total RNA was treated with DNase I for 10 min at 37°C and then measured for concentration and quality with an Agilent Bioanalyzer. PolyA mRNA selection was performed on 5µg of the DNase-treated total RNA with the NEBNext Poly(A) mRNA magnetic isolation module (E7490). DNA sequencing libraries were then generated with the NEBNExt Ultra Directional RNA library Prep kit for Illumina (E7420). Libraries were sequenced on an Illumina NextSeq 500 by the UVA Genome Analysis and Technology Core.
Results: Sequencing reads were mapped to the sacCer3 genome using bowtie2 with default settings. We preprocessed sequencing data from the UVA genomics core and analyzed differential gene expression in R using DESeq2. We found that In log phase cells, there were no significantly upregulated or downregulated genes in the CRCM or NRCM samples as compared to the water supplemented control (FDR <0.05). At the 24 hr timepoint,  CRCM samples diverged from the NRCM and water supplemented control samples, and showed many more differentially regulated genes than the NRCM-treated samples. At the 96 hr timepoint, NRCM samples also became more clearly separated from the control in a PCA plot , though there were still a large number of genes exclusively altered in the CRCM samples. Furthermore, the YCL064C (CHA1) gene clearly stood out as being the most significantly upregulated in conditioned media supplementation.
Conclusions: RNAseq data led us to explore YCL064C (CHA1) gene clearly stood out as being the most significantly upregulated in the conditioned media experiments. CHA1 encodes a predominantly mitochondrial L-serine (L-threonine) deaminase that catabolizes these amino acids.  RNA-seq based transcriptome analysis allowed us to explore L-serine contribution to longevity phenotype we observed with CRCM.

overall_design: RNA profiles of log phase, 24, and 96 hour BY4741 yeast cells grown in SC and supplemented with CR conditioned media, NR conditioned media, or water.

first: Elisa

last: Enriquez-Hesles

first: Ryan

last: Fine


title: Multi-omics and Machine Learning Accurately Predicts Clinical Response to Adalimumab and Etanercept Therapy in Patients with Rheumatoid Arthritis [Methylation array]

first: Aridaman

last: Pandit

overall_design: From the observational (BiOCURA) cohort, we selected 80 patients with RA, treated with ADA (38) or ETN(42) and a follow-up period of at least 6 months. Blood was drawn shortly before treatment initiation in a Lithium-heparinized tube (BD Vacutainer®). We first isolated peripheral blood mononuclear cells (PBMCs) from these blood samples prior to ADA or ETN treatments. And then genome-wide DNA methylation profiling was performed on these PBMCs, using Infinium MethylationEPIC BeadChip array (Illumina). After 6-month treatment, patients’ responses were evaluated according to EULAR criteria.

first: Weiyang

last: Tao

first: Arno

last: Concepcion

first: Marieke

last: Vianen

first: Anne

last: Marijnissen

first: Floris

last: Lafeber

first: Timothy

last: Radstake


title: Structure-based analysis of the gene network controlled by the Salmonella RcsB response regulator

status: Public on Jul 18 2020

city: Pozuelo de Alarcón

first: joaquín

last: Giner Lamia

state: Madrid

address: Campus de Montegancedo

department: Biotecnologia

institute: CBGP-Universidad Politecnica de Madrid

summary: RcsB is a transcriptional regulator that controls expression of numerous genes in Enterobacteriaceae. RcsB accomplishes this role alone or in combination with auxiliary transcriptional factors independently or dependently of phosphorylation. To understand the mechanisms by which RcsB regulates such a large number of genes, we performed structural and in vitro and in vivo functional studies with different RcsB variants. Our structural data reveal that RcsB binds the promoters of rprA and flhDC genes in a dimeric active conformation, docking the DNA-binding domains into the major groove of the DNA that preform a weak read-out of the target sequence. Interestingly, comparative structural analysis shows that DNA binding may trigger the active conformation in unphosphorylated RcsB. Furthermore, RNAseq analysis performed in strains expressing wild-type or several RcsB variants provided new insights into the contribution of phosphorylation to gene regulation  and assign a potential role of RcsB in regulating iron and molybdenum metabolism. Finally, we delimited the RcsB box for homodimeric active RcsB binding with sequence TN(G/A)GAN4TC(T/C)NA that can be found in promoter and intragenic regions to regulate activation or inhibition of gene transcription.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: mRNA profiles of S. Typhimurium expressing RcsB wild type (WT)  or RcsB mutant variants in exponential phase (OD600 ~ 0.25) were generated by deep sequencing, in triplicate, using Illumina Hiseq 400 system.

first: Joaquín

last: Giner-Lamia

first: Juanjo

last: Huesa

first: M

last: Graciela Pucciarelli

first: Francisco

last: García-del Portillo

first: Alberto

last: Marina

first: Patricia

last: Casino


title: Screening for the key miRNAs of exosomes that promote tumor progression and metastasis

status: Public on Jul 17 2020

city: Beijing

first: Songjie

last: Shen

state: Beijing

address: No.1 Shuaifuyuan, Doncheng District

department: Department of Breast Surgery

institute: Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China

summary:
Intercellular communication is crucial for breast cancer progression and metastasis. Yet, the role of cancer-derived exosomes and their specific miRNAs cargo in mediating intercellular communications needed to be further elucidated.
MiRNAs control gene expression post-transcriptionally and are selectively packaged into cancer-derived exosomes. Therefore, we hypothesized that miRNAs in cancer-derived exosomes were most likely the essential components of intercellular communication. To identify the key miRNAs, we chose metastatic MDA-MB-231 and non-metastatic MCF-7 for comparison. The miRNAs profiling of exosomes derived from these two kinds of cells as well as the endogenous miRNAs profiling of the cells were conducted by microarrays.

overall_design: MCF7 cells, MDA-MB-231 cells, exosomes isolated from the conditioned medium of MCF7 cells, and exosomes isolated from the conditioned medium of MDA-MB-231 cells were subjected to microarray analysis.

first: Yu

last: Song


title: A CTCF binding element regulates RA-induced early ESCs differentiation through orchestrating long-range chromatin interactions between its adjacent enhancers and HoxA

status: Public on Jul 16 2020

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

summary: Proper Homeobox A (HoxA) cluster genes expression is essential for embryonic stem cells (ESCs) differentiation and individual development. However, the mechanisms controlling the precise spatiotemporal expression of HoxA cluster genes during early ESCs differentiation remain largely unknown. Here, we find a CTCF binding element (CBE+47kb) closest to the 3'-end of HoxA locus within a topologically associated domains (TAD) in ESCs. CRISPR-Cas9 mediated the CBE+47kb knockout significantly promotes expression of HoxA cluster genes and early ESCs differentiation induced by RA compared with wild type cells. In mechanism, we found that there was a significant differently long-range chromatin interactions between its adjacent enhancers and HoxA in CBE+47kb knockout cells through chromosome conformation capture assay (Capture-C), indicating that CBE+47kb can precisely organize interactions between its adjacent enhancers and HoxA chromatins. Furthermore, we also showed that its adjacent enhancers deletion shows significantly synthetic inhibition effect on HoxA genes expression, suggesting that these enhancers are required for RA-induced HoxA genes expression. Our study reveals that a new functional CBE+47 can regulate HoxA genes expression through orchestrating long-range chromatin interactions between its adjacent enhancers and HoxA, thus maintaining RA-induced early ESCs proper differentiation.

overall_design: At least 2 biological replicates were analyzed for each experimental condition. WT  and CBE-KO were RNA-seq after RA treatment for 24h. Enhancer Capture-C was done in WT and CBE-KO cells, in triplicate, under RA induction.

first: Wange

last: Lu

first: Guangsong

last: Su

first: Jun

last: Chen

first: Dianhao

last: Guo

first: Wenbin

last: Wang


title: Transcriptome profiling of Clostridium tetani

city: Aarhus

first: Holger

last: Brueggemann

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

summary: Clostridium tetani produces the tetanus-causing tetanus toxin (TeNT), one of the most powerful bacterial toxins known to humankind. The regulation of toxin expression is complex and involves the alternative sigma factor TetR as well as other regulators. Here, we identified a novel regulatory molecule, a non-coding small regulatory RNA (sRNA), located in the 3’ untranslated region of the tent gene. We show with an antisense RNA approach and recombinant expression of the tent locus with and without the sRNA in C. tetani strains that the sRNA acts as a negative regulator of TeNT expression and modulates the growth pattern of C. tetani. Its possible role is to limit tetanus toxin levels in the exponential growth phase; thus, it might interlock bacterial growth and toxin production.

overall_design: Transcriptome of Clostridium tetani in two different media and two different growth phases

first: Michel

last: Popoff


title: Small RNAs during seed development in large-seeded chickpea

status: Public on Jul 13 2020

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: In this study, we sequenced small RNAs at seven successive stages of seed development and leaf tissue in a large-seeded chickpea cultivar (JGK 3) using Illumina platform. More than 500 million reads were generated in all the samples combined together with an average of 34 million reads in each sample. Data obtained in FASTQ files were pre-processed and unique reads representing small RNAs were identified at different stages of seed development.

overall_design: Total RNA was isolated from the seed stages and leaf tissues followed by preparation of small RNA libraries and sequencing using Illumina platform. The reads were pre-processed using modified perl scripts. After quality control, the identical reads were collapsed into a unique read and read count for each sequence was recorded. All the filtered unique reads from each sample were mapped on the chickpea genome to find their location.

first: Rohini

last: Garg

first: Niraj

last: Khemka

first: Mohan

last: Rajkumar


title: Integrated Assessment of Circulating Cell-Free MicroRNA Signatures in Plasma of Patients with Melanoma Brain Metastasis

status: Public on Jul 15 2020

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: We analyzed cell-free microRNAs (cfmiRs) in blood, tissue, and urine samples of melanoma patients to find potential biomarkers for monitoring and assessing early detection of melanoma metastasis. This study demonstrates that identifying cfmiR signatures in body fluids may allow for detection and assessment of melanoma brain metastasis (MBM) and metastatic melanoma patients undergoing checkpoint inhibitor immunotherapy treatments.

overall_design: Data was extracted from patients' blood, urine, and tissue. Samples were profiled for cfmiRs by using a next generation sequencing (NGS) probe-based HTG EdgeSeq miRNA whole transcriptome assay. 2083 microRNAs were profiled for 409 clinical specimens. Normal (cancer-free) donor plasma (n=48) and serum plasma (n=48) samples were analyzed in duplicates. Pre-surgery plasma from melanoma brain metastasis patients (MBM, n=36) were compared for differences in their cfmiR counts, and then verified in a second cohort of MBM plasma samples (n = 24). A cfmiR signature was identified in MBM plasma samples, and further verified in MBM tumor tissues (n=24). MBM cfmiR signature was specifically compared to patients with other cancer types that had brain metastasis (LuBM, n=6 and BCBM, n=7) and glioblastomas (n=36). In addition, the detection of cfmiRs in pre- and post-treatment plasma (n=20) and urine (n=14) samples collected from metastatic melanoma patients receiving checkpoint inhibitor immunotherapy (CII) showed potential utility in assessing CII responses. Normal urine samples (n=8) in duplicates were analyzed to demonstrate reproducibility and compared to urine from metastatic melanoma patients.

first: Matias

last: Bustos

first: Kevin

last: Tran

first: Negin

last: Rahimzadeh


title: Single cell RNA-seq analysis reveals compartment-specific heterogeneity and plasticity of microglia

status: Public on Jul 27 2020

city: Stony Brook

first: Shao-Jun

last: Tang

state: New York

address: 101 Nicolls Road

institute: Renaissance School of Medicine at Stony Brook University

summary: Microglia are heterogeneous and ubiquitous CNS-resident macrophages that maintain homeostasis of neural tissues and protect them from pathogen attacks. Yet, their differentiation in different compartments remains elusive. We performed single cell RNA-seq (scRNA-seq) analysis to compare the transcriptomes of microglia in adult mouse(C57/Bl) brains and spinal cords to identify microglial subtypes in these CNS compartments.Cortical microglia from 2-month mice consisted of a predominant population of the homeostatic subtype (HOM-M) and a small population (4%) of the inflammatory subtype (IFLAM-M), while spinal microglia consisted of HOM-M and IFLAM-M subtype. Comparison of cortical and spinal microglia at 2, 4 and 8 months revealed consistently a higher composition of the IFLAM-M subtype in the spinal cord. At 8-month, cortical microglia differentiated a small new subtype with interferon response phenotypes (INF-M), while spinal microglia polarized toward a proinflammatory phenotype, as indicated by the increase of microglia expressing IL-1β. To further characterize the differential plasticity of cortical and spinal microglial heterogeneity, we determined the microglial transcriptomes from HIV-1 gp120 transgenic (Tg) mice, a model of HIV-associated neurological disorders. Compared with wild-type (Wt) cortical microglia, the gp120Tg cortical microglia had three new subtypes, with signatures of interferon I response (INF-M), cell proliferation (PLF-M), and myelination or demyelination (MYE-M) respectively; while INF-M and PLF-M subtypes presented at all ages, the MYE-M only at 4-month. In contrast, only the INF-M subtype was observed in the spinal microglia from 2-and 4-month gp120tg mice. Bioinformatic analysis of regulated molecular pathways of individual microglial subtypes indicated that gp120 more severely impaired the biological function of microglia in cortices than in the spinal cord. The results collectively reveal differential heterogeneity and plasticity of cortical and spinal microglia, and suggest functional differentiation of microglia in different CNS compartments.

overall_design: Comparison of cell transcriptomes of wt and gp120 mice from brain cortex and whole spinal cord tissues across 2, 4, and 8 month timepoints.

first: Junying

last: Zheng

first: Wenjuan

last: Ru

first: Jay

last: Adolacion

first: Michael

last: Spurgat

first: Xin

last: Liu

first: Subo

last: Yuan

first: Rommel

middle: X

last: Liang

first: Jianli

last: Dong

first: Andrew

last: Potter

first: S

first: Ken

first: Rui

first: Navin

last: Varadarajan


title: Transcriptional profiling of brain tissues from a Q130 Long Evans Knock-in rat model of Huntington’s disease at 2-, 6- and 12-months of age

status: Public on Jul 14 2020

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt).  A collaboration between the CHDI Foundation and Dr. H.P. Nguyen (huu.nguyen-r7w@ruhr-uni-bochum.de) at Universitat Bochum focused on generating a knock-in rat model of HD that contains expanded CAG repeats inserted within the rat huntingtin gene (Hdh) in order to provide a genetic reconstruction of the human causative mutation within the rat model. The goal of this study is RNA expression profiling by RNA sequencing (RNA-seq) in brain tissues of 2-, 6- and 12-month-old heterozygous knock-in rats with uninterrupted CAG length approaching 130 along with littermate control wild-type animals.

overall_design: Transcriptomic analysis (RNASeq) was performed on samples from striatum, cortex, cerebellum, and hippocampus collected from wild type and heterozygous Q130KI rats at 2, 6, and 12 months; number of replicates 5 males/5 females for each timepoint/genotype/tissue combination. Twelve samples from batch1 were added to batch2 as pipeline controls to monitor for reproducibility and batch effect.

first: Jim

last: Rosinski


title: Dataset for Placental Genomic and Epigenomic Signatures in Infants Borns at Extremely Low Gestational Age [mRNA and microRNA sequencing]

status: Public on Jul 22 2020

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

summary: These analyses set out to evaluate placental genomic and epigenomic signatures in newborns from the Extremely Low Gestational Age Newborns (ELGAN) cohort. Genome-wide mRNA, microRNA, and DNA methylation profiles were obtained from placenta samples collected at birth. Analyses were conducted to better understand placental molecular signatures and relate these to placental, maternal, infant, and later-in-life health indices. Samples included in this GEO series reflect genome-wide mRNA and microRNA expression signatures.

overall_design:
This study involves the evaluation of patients from the ELGAN cohort, comprised of pregnancies that ended in livebirths prior to completing 28 weeks of gestation. Subjects were recruited from 2002 to 2004, and consisted of pregnant women scheduled to give birth at one of 14 participating institutions. Study procedures were approved by the Institutional Review Board at each of the 14 participating ELGAN sites, and consent was provided prior to hospital admission or soon after delivery. At or prior to delivery, maternal and demographic and clinical assessments were completed. A trained research nurse measured demographic and pregnancy variables after delivery using a structured questionnaire. Each infant’s anthropometric measures were recorded throughout hospitalization and at follow-up. Women participating in the ELGAN study also agreed to the collection of placenta samples. Immediately after delivery, placental tissue samples were collected and flash frozen in liquid nitrogen and stored at -80°C until processed. Placental tissue (~0.2g) was cut from the frozen biopsy sample and rinsed with sterile 1 X PBS to remove residual blood. Samples were then homogenized in Buffer RLT with β-mercaptoethanol (Qiagen, Valencia CA). An AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Valencia CA) was used to extract DNA and RNA. Illumina HiSeq 2500 was used to determine genome-wide mRNA expression profiles. The HTG EdgeSeq miRNA Whole Transcriptome Assay (HTG Molecular Diagnostics, Tucson, AZ) was used to evaluate genome-wide microRNA expression profiles. Extracted DNA samples were bisulfate-converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) and associated methylation levels quantification using the Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA).

Samples included in this GEO series reflect genome-wide mRNA and microRNA expression signatures. The range of gestational age for this subcohort was 23-27 weeks (median of 26 weeks).

middle: E

first: Kyle

last: Roell

first: Hudson

last: Santos

last: O-Shea

first: Rebecca

last: Fry


title: Gene expression profiles of wild type and Nr4a-triple knockout (Nr4a-TKO) Tnaive and iTreg 3 h

status: Public on Jul 08 2020

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

institute: National Center for Global Health and Medicine

summary: In this study, we investigated the roles of Nr4a family transcription factors in Th and Treg cell differentiation from Tnaive cells. Nr4a factors were found to promote Treg cell differentiation and repress Th1 and Th2 differentiation. During Treg cell differentiation, all Nr4a factors are transiently induced in Tnaive cells immediately after TCR stimulation, whereby they mediate epigenetic changes directly or by cooperating with other transcription factors. To reveal Nr4a factors' mediated transcrptional events, we analyzed gene expression of wild type and Nr4a-tripple knockout (Nr4a-TKO) Tnaive and iTreg cells by microarray analysis.

overall_design: Wild type and Nr4a-TKO Tnaive cells and iTreg cells at 3 h of differentiation were analyzed.

first: Shizuko

last: Kagawa

first: Katsunori

last: Masaki

first: Koichi

last: Fukunaga

first: Akihiko

last: Yoshimura

first: Satoshi

last: Takaki


title: Gene expression profiles of wild type, Nr4a-triple knockout (Nr4a-TKO), and Foxp3-KO iTreg 24 h

summary: In this study, we investigated the roles of Nr4a family transcription factors in Th and Treg cell differentiation from Tnaive cells. Nr4a factors were found to promote Treg cell differentiation and repress Th1 and Th2 differentiation. During Treg cell differentiation, all Nr4a factors are transiently induced in Tnaive cells immediately after TCR stimulation, whereby they mediate epigenetic changes directly or by cooperating with other transcription factors. To reveal Nr4a factors' mediated transcrptional events, we analyzed gene expression of wild type and Nr4a1,a2,a3-tripple knockout (Nr4a-TKO) iTreg cells by microarray analysis.

overall_design: Wild type, Nr4a-TKO, and Foxp3 KO iTreg cells after 24 h differentiation were analyzed.


title: Replication dynamics of recombination-dependent replication forks: leading and lagging strand synthesis are not coupled

status: Public on Jul 03 2020

city: Marseille

first: Karel

last: Naiman

address: BD Lei Roure

country: France

institute: CRCM

summary: DNA replication fidelity is essential for maintaining genetic stability. Forks arrested at replication fork barriers can be stabilised by the intra-S phase checkpoint, subsequently being rescued by a converging fork, or resuming when the barrier is removed. However, some arrested forks cannot be stabilised and fork convergence cannot rescue in all situations. Thus, cells have developed homologous recombination-dependent mechanisms to restart persistently inactive forks. To understand the dynamics of HR-restart, we visualized in vivo replication dynamics at an S. pombe replication barrier, RTS1, using polymerase usage sequencing and model replication dynamics by Monte Carlo simulation. We confirm that HR-restarted forks synthesise both strands with Pol d and that Pol a is not used significantly on either strand: the lagging strand template remains as a gap that is filled in later. We further demonstrate that HR-restarted forks progress for >30 kb kilobases without maturing to a d/e configuration and can progress through a fork barrier that arrests canonical forks. Finally, by manipulating lagging strand resection during HR-restart by deleting pku70, we show that the leading strand initiates replication at the same position, demonstrating the stability of the 3' single strand in the context of increased resection.

overall_design: We mapped ribonucleotide-incorporation by the mutated DNA polymerase delta and epsilon at single-nucleotide resolution and used the data for following the replication fork restart by subsequent informatics analysis.

first: Eduard

last: Campillo-Funolet

first: Adam

middle: T

last: Watson

first: Izumi

last: Miyabe

first: Alice

last: Budden

first: Antony

last: Carr


title: Copy number variation analysis in Japanese children with Autsim Spectrum Disorder by Affymetrix Genome-Wide Human SNP Array 6.0.

status: Public on Aug 01 2020

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

institute: Hirosaki University Graduate School of Medicine

summary:
Autism spectrum disorder (ASD) is an innate neurodevelopmental disorder characterized by impairments in social communication/interaction, repetitive and restrictive behavior. Copy number variation (CNV) is a one of the structural variation of the genomic sequence, including large multiplications and deletions ranging from kb to Mb of DNA. These multiplication-deletion provide genomic diversity, while CNV affects the amount of gene products or transcriptional regulation, and result in strong association with biological process, metabolism and disease. In facts, many studies reported that the mapping of CNVs which strongly associated with ASD.
The subjects of this study were the community-based 5 years old children because they might be able to except acquired effects after birth as much as possible and focus on the genetic background, and there are possibilities that the results will be specific to the Japanese patients with ASD.

overall_design: Genomic DNA from peripheral blood were isolated from 124 (boys: 62, girls: 62) healthy control subjects and 68 (boys: 45, girls: 23) patients with ASD.

first: Yui

last: Sakamoto


title: Next Generation Sequencing Facilitates Quantitative Analysis of Control and rhCYGB treated liver and HHSteC transcriptomes

status: Public on Aug 25 2020

city: Osaka

first: Le

middle: Thi Thanh

last: Thuy

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan

department: Department of Hepatology

institute: Osaka City University, Graduate School of Medicine

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptome profile of ZIP7 knockdown cells

city: Durham

first: Wei

last: Chen

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

summary: We analysed the transcriptome profile by RNA-seq when knockdown ZIP7 by two individual siRNAs in MDAMB231 cells.

overall_design: Compare the transcriptome profile between NC (nontargeting control) and two individual ZIP7 siRNA in MDAMB231 cells

first: Jen-Tsan

last: Chi

first: Po-Han

first: Yitong

last: Xu


title: Effect of SMYD3 on MDA-MB-231 breast cancer cells (RNA-seq)

status: Public on Jun 30 2020

city: Seoul

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

country: South Korea

institute: College of Medicine, Hanyang University

summary: RNA-sequencing analysis of control and SMYD3-knockdown MDA-MB-231 tumors from the mammary glands of orthotopic xenograft NOD/SCID mice. SMYD3 (also known as KMT3E), a hisone H3 lysine K4 methyltransferase, is highly expressed in several human cancers, including colorectal and breast carcinomas.  Results provide insight into the transcriptional regulation of SMYD3 in breast cancer.

overall_design: MDA-MB-231 cells stably infected with lentiviruses encoding either control (pGIPZ vectror) or SMYD3 shRNA (pGIPZ-shSMYD3) were orthotopically injected into mice. Total RNA was isolated from control and SMYD3 knockdown MDA-MB-231 tumors from the mammary glands of orthotopic xenograft NOD/SCID mice using Trizol reagent. For each of the 2 conditions, 2 biological replicates were included. In total, 4 RNA-sequencin samples were analyzed; 2 controls and 2 SMYD3 knockdown MDA-MB-231 tumors.

first: Jeong-Yeon

last: Lee

first: Hee-Joo

last: Choi


title: Single-cell Transcriptomics Combined With Interstitial Fluid Proteomics Defines Cell Type-Specific Immune Regulation in Atopic Dermatitis

status: Public on Jul 04 2020

city: Vienna

first: Patrick

last: Brunner

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary:
Background: Atopic dermatitis (AD) is the most common chronic inflammatory skin disease, but its complex pathogenesis is only insufficiently understood, resulting in still limited treatment options.
Objective: We sought to characterize AD on both transcriptomic and proteomic levels in humans.
Methods: We used skin suction blistering, a painless and nonscarring procedure that can simultaneously sample skin cells and interstitial fluid. We then compared results with conventional biopsies.
Results: Suction blistering captured epidermal and most immune cells equally well as biopsies, except for mast cells and nonmigratory CD163+ macrophages that were only present in biopsy isolates. Using single-cell RNA sequencing, we found comparable transcriptional profiles of key inflammatory pathways between blister and biopsy AD, but suction blistering was superior in cell-specific resolution for high-abundance transcripts (KRT1/KRT10, KRT16/KRT6A, S100A8/S100A9), which showed some background signals in biopsy isolates. Compared with healthy controls, we found characteristic upregulation of AD-typical cytokines such as IL13 and IL22 in Th2 and Th22 cells, respectively, but we also discovered these mediators in proliferating T cells and natural killer T cells, that also expressed the antimicrobial cytokine IL26. Overall, not T cells, but myeloid cells were most strongly enriched in AD, and we found dendritic cell (CLEC7A, amphiregulin/AREG, EREG) and macrophage products (CCL13) among the top upregulated proteins in AD blister fluid proteomic analyses.
Conclusion: These data show that by using cutting-edge technology, suction blistering offers several advantages over conventional biopsies, including better transcriptomic resolution of skin cells, combined with proteomic information from interstitial fluid, unraveling novel inflammatory players that shape the cellular and proteomic microenvironment of AD.

overall_design:
Comparison of skin cells obtained by skin suction blistering and conventional biopsy

>>>Raw data are unvailable due to patient privacy concerns<<<

first: Thomas

last: Rojahn

first: Vera

last: Vorstandlechner

last: Krausgruber

first: Wolfgang

last: Bauer

first: Natalia

last: Alkon

first: Christine

last: Bangert

first: Felix

last: Thaler

first: Farzaneh

last: Sadeghyar

first: Nikolaus

last: Fortelny

first: Victoria

last: Gernedl

first: Katharina

last: Rindler

first: Adelheid

last: Elbe-Bürger

first: Christoph

last: Bock

first: Michael

last: Mildner