title: Exosome-mediated transfer of lncRUNX2-AS1 from multiple myeloma cells to MSCs contributes to osteogenesis

city: Suzhou

first: Wenzhuo

last: Zhuang

state: Jiangsu

address: Ren Ai Road 199

department: Department of Cell Biology, School of Biology & Basic Medical Sciences

institute: Soochow University

summary: Multiple myeloma (MM) is characterized by the impaired osteogenic differentiation of mesenchymal stem cells (MSCs). Stromal communication with cancer cells can influence treatment response. Understanding the cellular interactions within the tumor-bone milieu is critical to the development of novel agents that can reverse bone diseases. Here we identified that bioactive lncRNA RUNX2-AS1 in myeloma cells could be incorporated into exosomes and transmitted to MSCs, thus repressing the osteogenesis of MSCs. RUNX2-AS1, which arises from the antisense strand of RUNX2, was enriched in MSCs derived from MM patients (MM-MSCs). RUNX2-AS1 was capable of forming an RNA duplex with RUNX2 pre-mRNA at overlapping regions and this duplex transcriptionally repressed RUNX2 expression by reducing the splicing efficiency, resulting in decreased osteogenic potential of MSCs. In vivo mouse models, intraperitoneally administered GW4869, an inhibitor of exosome secretion, was found to be effective in prevention of bone loss, sustained by both bone-forming and anticatabolic activities. Therefore, exosomic lncRNA RUNX2-AS1 may serve as a potential therapeutic target for bone lesions in MM. In summary, our results indicated a unique role of exosomic lncRUNX2-AS1 in transferring from MM cells to MSCs in osteogenic differentiation, through a novel exosomic lncRUNX2-AS1/RUNX2 signaling pathway.

overall_design: Examination of 6 different expression in 2 cell types.

first: Zhuang

last: Wenzhuo

first: Bingzong

last: Li

first: Hongxia

last: Xu

first: Huiying

last: Han

first: Sha

last: Song

first: Xiaojuan

last: Zhang

first: Lu

last: Ouyang

first: Chen’ao

last: Qian

first: Yating

last: Hong

first: Yingchun

last: Qiu

first: Wenqi

last: Zhou

first: Moli

last: Huang


title: Human Pluripotent Stem Cell-Derived Kidney Organoids for Modeling Epithelial Transport and Injury

status: Public on Dec 15 2020

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

country: USA

institute: Washington University in St. Louis

type: Expression profiling by high throughput sequencing

summary: Maximizing the potential of human kidney organoids for drug testing, regenerative medicine and to model development and disease requires addressing cell immaturity, the lack of a branching collecting system and the off target cell types. Here we establish methods to independently generate the two kidney progenitor cell populations – metanephric mesenchyme and ureteric bud. Combining these two progenitor cell types results in organoids with an improved branched collecting system. We also identified the hormones aldosterone and arginine vasopressin as critical to promote maturation of collecting duct cell types. The resulting organoids contain the full range of epithelial cells in the nephron, including principal and intercalated cells. By scRNA-seq, we demonstrate superior proximal tubule maturation and reduced off-target cell populations using this protocol.

overall_design: Single cell profiling of kidney organoids using 10x Chromium

first: Benjamin

middle: D

last: Humphreys


title: HMGA2 links promoter-specific H2A.X deposition and active DNA demethylation [TGFB1-ChIP-seq]

status: Public on Dec 14 2020

city: Nancy Cedex

first: Guillermo

last: Barreto

address: 9, Avenue de la Forêt de Haye ‐ BP 20199

department: Campus Biologie-Santé. Faculté de Médecine

country: France

institute: CNRS Director of Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: During transcriptional activation, chromatin undergoes structural changes with the help of various proteins such as chromatin remodeling factors and histone modifiers in order to make the DNA accessible for the transcription factors and RNA polymerase. We combined ChIP-, MNase- and RNA-sequencing analyzing the Hmga2 knock-out mice and found that HMGA2 is required for promoter specific deposition of the histone variant H2A.X. Consequently, the promoter specific H2A.X deposition resulted in an accumulation of active RNA Polymerase II at these promoters. Stimulation with TGFB1 resulted in increased accumulation of pH2A.X and expression of those “primed” target genes, whereas cells expressing no Hmga2 where not able to respond.

overall_design: Examination of pH2A.X levels in Hmga2+/+ and Hmga2-/- mouse embryonic fibroblasts treated with TGFB1. Further, the global enrichment of FACT in Hmga2+/+ and Hmga2-/- MEFs was assayed.

first: Stephanie

last: Dobersch

first: Stephan

last: Günther


title: Day23_exon3lines

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

summary: Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD), predicting gene regulatory network (GRN) imbalances. Here, we define transcriptional responses to reduced transcription factor dosage in human iPSCs heterozygous or homozygous for loss of the CHD gene TBX5.

overall_design: Single cell RNA sequencing of day 23 cells from exon3 lines (WTC11, Control, TBX5Het and TBX5Hom) in duplicate

middle: G

first: Irfan

middle: S

last: Kathiriya

first: Kavitha

last: Rao


title: Single cell transcriptomics of TBX5 allelic series during human cardiac differentiation

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

overall_design: Refer to individual Series


title: Day11_exon3lines

overall_design: Single cell RNA sequencing of day 11 cells from exon3 lines (WTC11, Control, TBX5Het and TBX5Hom) in duplicate


title: Identifying candidate genes whose expression is regulated by CbrAB and NtrBC in Pseudomonas fluorescens SBW25

status: Public on Dec 12 2020

city: Auckland

first: Xue-Xian

address: 14.02 The Station Cre., Albany

department: School of Natural and Computational Sciences

country: New Zealand

institute: Massey University

summary: Histidine is a good source of nutrient for many bacteria, but its utilization poses a significant challenge as it delivers excess nitrogen over carbon. The rate of histidine catabolism (hut) must thus be tightly regulated. Here, in Pseudomonas fluorescens SBW25, we show that the CbrAB two-component system directly activates the transcription of hut genes, while mediating succinate-induced carbon catabolite repression of hut at the translational level via the CbrAB-CrcYZ-Hfq/Crc regulatory cascade. When growing in minimal salt medium supplemented with histidine and succinate (the most preferred carbon source), the CbrAB-mediated promoter activity is weak; and the global nitrogen regulator NtrBC plays the dominant role in directly activating hut transcription.

overall_design: Gene expression was compared between wild-type P. fluorescens SBW25 and each of the three mutants devoid of cbrB, ntrC and hutC, respectively. RNA-seq analyses of these four strains were performed in parellel. However, the data for wild type and the del-hutC mutant have been deposited in NCBI’s Gene Expression Omnibus with accession number GSE146488.

first: Naran

last: Naren


title: Clostridium difficile transcriptome of strain R20291 in response to cysteine by using a time-resolved RNA-seqencing

city: Guangzhou

first: Jufang

last: Wang

address: Guangzhou Higher Education Mega Center, Panyu District, Guangzhou

department: School of Bioscience and Bioengineering

country: China

institute: South China University of Technology

summary: The incidence of Clostridium difficile infection has been steadily rising over the past decade. Its increased rate is associated with the specific NAP1/BI/027 strains which are “hypervirulent” and have led to several large outbreaks since their emergence. However, the relation between their outbreaks and virulence regulation mechanisms remains unclear. It has been reported that the major virulence factor TcdA and TcdB in C. difficile could be repressed by cysteine. Here, we investigated functional and virulence-associated regulation of C. difficile R20291 in response to cysteine stress by using a time-resolved genome-wide transcriptional analysis. Dramatic changes of gene expression in C. difficile were revealed in functional categories related to transport, metabolism, and regulators under cysteine stress during different phases of growth.

overall_design: mRNA profiles of Clostridium difficile R20291 Cells treated or untreated with cysteine for 4h,8h and 12h were generated by RNA-sequencing

first: Huawei

last: Gu


title: Gene expression analysis of rat macrophages

status: Public on Dec 13 2020

city: Edinburgh

first: Clare

last: Pridans

address: 47 Little France Crescent

department: University of Edinburgh

country: United Kingdom

institute: Centre for Inflammation Research

summary: We used microarray to compare gene expression between bone marrow-derived (BMDM), monocyte-derived (MDM), alveolar (AM), peritoneal (PM) and embryonic stem cell (ESC) derived rat macrophages. The expression of liver macrophages (Kupffer cells) were inferred by analysis of whole livers from Csf1r deficient rats. The transcriptional response of BMDM to LPS was also examined.

overall_design: RNA was isolated from 3-4 biological samples and included technical replicates for in vitro macrophages. For ESC-derived macrophages, technical replicates (n = 3) were used as the ESC were derived from a single clone.

first: David

middle: A

last: Hume


title: Skeletal muscle injury-responsive macrophage subsets in larval zebrafish

status: Public on Dec 11 2020

city: Melbourne

first: Fernando

last: Rossello

state: VIC

address: L 10, 305 Grattan Street

country: Australia

institute: The University of Melbourne

summary: Single-cell RNA-sequencing (scRNA-seq)  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tg(mpeg1:mCherry) transgenic zebrafish line was utilised to isolate mCherry-expressing macrophages by FACS. Following needle-stab muscle injury of a 4 days post fertilisation (dpf) larvae, the wound site was dissected out at 1, 2, and 3 days post injury (dpi) for macrophage isolation. Macrophages isolated from 4 dpf-uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages, one of which corresponded to uninjured macrophages. The 7 wound-present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context.

overall_design: Total of 4 different time points were assayed, including a 4 dpf uninjured control and 3 time points during injury-resolution (1-3 dpi).

first: Dhanushika

last: Ratnayake

first: Phong

last: Nguyen

middle: J

first: Jeroen

last: Bakkers

first: Peter

last: Currie


title: Day6_exon3lines

overall_design:
Single cell RNA sequencing of day 6 cells from exon3 lines (WTC11, Control, TBX5Het and TBX5Hom) in duplicate

Please note that the 'Day6_Day11_Day23_matrix.csv' processed data was generated from Day6_exon3lines, Day11_exon3lines, and Day23_exon3lines_rep1 datasets together (as detailed in the sample data processing field).


title: Day23_exon7lines_scRNAseq

overall_design: Single cell RNA sequencing of day 23 cells from 3 lines (PGP1, TBX5Het_exon7 and TBX5Hom_exon7)


title: Expression profile of 58As9 cells upon PLEKHA5 knockdown

city: TOKYO

first: Hideki

last: Yamaguchi

address: 2-2, KANDASURUGADAI, CHIYODA-KU

department: Cancer Cell Research

country: Japan

institute: Sasaki Institute

summary:
Phosphoproteomic analysis of diffuse-type gastric carcinoma cells with Met gene amplification identified Pleckstrin Homology Domain Containing A5 (PLEKHA5) as a protein that is tyrosine-phosphorylated downstream of Met.
We used DNA microarray analysis to explore the signaling pathways downstream of PLEKHA5 that regulates the survival and peritoneal dissemination of Met-amplified 58As9 diffuse-type gastric carcinoma cells.

overall_design: 58As9 cells were transfected with conrol or PLEKHA5 siRNA for RNA extraction and hybridization on Affymetrix microarrays.

first: Yuko

last: Nagamura

first: Makoto

last: Miyazaki

first: Yoshiko

last: Nagano

first: Masako

last: Yuki

first: Kiyoko

last: Fukami

first: Kazuyoshi

last: Yanagihara

first: Kazuki

last: Sasaki

first: Ryuichi

last: Sakai


title: RNAseq analysis of FAP cell states isolated from mdx mice and cultured in vitro

city: Rome

first: Giulio

last: Giuliani

address: Via della ricerca scientifica 1

country: Italy

institute: Univerisity of Rome Tor Vergata

summary: We investigated the transcriptome of cell states identified in fibro/adipogenic progenitors (FAPs) isolated from mdx mice using as a criterion SCA-1 expression. We found that after 5 days in growth medium FAP cell states have different transcriptomes. In particular, among the "Biological process" GO terms enriched in genes up-regulated in SCA1-High-FAPs we found genes correlated with adipogenic differentiation. Indeed, several genes directly regulated by PPAR-gamma are up-regulated in SCA1-High-FAPs. This experiment demonstrates that the adipogenic propensity of SCA1-High-FAPs arise spontaneously in vitro.

overall_design: The experiment was performed in four biological replicates (FAP cell states, called SCA1-High-FAPs and SCA1-Low-FAPs, isolated from 4 mdx mice for a total of 8 samples). FAP cell states were cultured 5 days in growth medium ad next we isolated total RNA. SCA1-Low-FAPs were used as a control.

first: Alessandro

last: Palma

first: Gianni

last: Cesareni


title: HMGA2 links promoter-specific H2A.X deposition and active DNA demethylation [RNA-Seq]

first: Guillermo

last: Barreto

overall_design: RNA-seq of Hmga2+/+ and Hmga2-/- mouse embryonic fibroblasts treated with TGFB1

first: Stephanie

last: Dobersch

first: Stephan

last: Günther


title: Identification of direct transcriptional targets of BMP signaling during zebrafish dorsal-ventral axial patterning

city: Philadelphia

first: Hannah

last: Greenfeld

state: PA

address: 421 Curie Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: To determine the mechanism of BMP morphogen interpretation in the zebrafish gastrula, we identified genes that are dependent on BMP signaling for their expression, as well as the genes directly regulated by BMP signaling using RNA-sequencing.

overall_design: BMP-dependent genes were identified by comparing transcript levels in wild-type and bmp7-/- mutant embryos at 6 and 8 hours post fertillization (hpf) using RNA-sequencing. Two biological replicates of 40 embryos each were analyzed per condition. Direct targets of BMP signaling were identified by comparing transcript levels by RNA-sequencing of bmp7-/- embryos treated with cycloheximide at 4 hpf and bmp7-/- embryos treated with cycloheximide and injected with 10 pg BMP2/7 protein at 4 hpf. Three biological replicates of 50 embryos each were analyzed per condition.

first: Mary

middle: C

last: Mullins


title: Impaired phosphatidylethanolamine metabolism activates a reversible stress response that detects   and resolves mutant mitochondrial precursors

city: Baltimore

first: Michelle Grace

last: Acoba

state: MD

address: 725 N Wolfe St

department: Physiology

institute: Johns Hopkins University

summary: Phosphatidylethanolamine made in mitochondria has long been recognized as an important precursor for phosphatidylcholine production that occurs in the endoplasmic reticulum (ER). Recently, the strict mitochondrial localization of the enzyme that makes PE in the mitochondrion, phosphatidylserine decarboxylase 1 (Psd1), was questioned. Since a dual localization of Psd1 to the ER would have far-reaching implications, we initiated our study to independently re-assess the subcellular distribution of Psd1. Our results support the unavoidable conclusion that the vast majority, if not all, of functional Psd1 resides in the mitochondrion. Through our efforts, we discovered that mutant forms of Psd1 that impair a self-processing step needed for it to become functional are dually localized to the ER when expressed in a PE-limiting environment. We conclude that severely impaired cellular PE metabolism provokes an ER-assisted adaptive response that is capable of identifying and resolving nonfunctional mitochondrial precursors.

overall_design: Two yeast strains, a control (WT) and a mutant (LGS), with three replicates were grown in YPD (D), YPD containing 2 mM ethanolamine (E), YPD containing 2 mM choline (C), or YPD containing 1% (v/v) tergitol and 0.5 mM lyso-phosphatidylethanolamine (L). RNA was extracted and sent to Novogen Corporation Inc. to perform quality tests, prepare the library, and sequence.

first: Pingdewinde

middle: N

last: Sam

first: Steven

middle: M

last: Claypool


title: WHSC1/NSD2 regulates immune infiltration in prostate cancer

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE


title: (bulk RNAseq) An extracellular vesicle-related gene expression signature identifies high-risk patients in medulloblastoma

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

summary: Background: Medulloblastoma (MB) is a malignant brain tumor in childhood. It comprises four subgroups with different clinical behaviors. The aim of this study was to characterize the transcriptomic landscape of MB, both at the level of individual tumors as well as in large patient cohorts. Methods: We used a combination of single-cell transcriptomics, cell culture models and biophysical methods such as nanoparticle tracking analysis (NTA) and electron microscopy (EM), to investigate intercellular communication in the MB tumor niche. Results: Tumor cells of the SHH-MB subgroup show a differentiation blockade. These cells undergo extensive metabolic reprogramming. The gene expression profiles of individual tumor cells show a partial convergence with those of tumor-associated glial and immune cells. One possible cause is the transfer of extracellular vesicles (EVs) between cells in the tumor niche. We were able to detect EVs in co-culture models of MB tumor cells and oligodendrocytes. We also identified a gene expression signature, EVS, which shows overlap with the proteome profile of large oncosomes from prostate cancer cells. This signature is also present in MB patient samples. A high EVS expression is one common characteristic of tumors that occur in high-risk patients from otherwise very different MB subgroups or subtypes. Conclusions: With EVS, our study uncovered a novel gene expression signature that has a high prognostic significance across MB subgroups.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For bulk mRNA sequencing, total RNA was isolated using RNeasy mini Kit (Qiagen) from three different cell lines: murine oligodendrocytic cell line Oli-neu (gift of Tanja Kuhlmann, Institute of Neuropathology, University Münster), murine SHH-MB tumor cells MB1, and human Group 3 medulloblastoma cell line D341 (purchased from ATCC via LGC Standards GmBH, Wesel, Germany). MB1 cells were established from tumors of Atoh1-cre:SmoM2 mice at P12. Cells were maintained at 37°C and 5% CO2 in DMEM/F-12 medium containing B-27 and N-2 supplements (Gibco, Thermo Fisher Scientific), 20 ng/mL of recombinant murine EGF and basic fibroblast growth factor (bFGF) (PeproTech Germany), and 1% penicillin/streptomycin (Gibco). For co-culture experiments 30 mm Millicell cell culture inserts with hydrophilic PTFE membranes (0.4 µm pore size) were used (Millipore, Merck). Two biological replicates for each of the following experimental conditions were used: Oli-neu cells, MB1 cells and D341 cells grown in mono-culture (sample designations O_d1/2, M_d1/2, D_d1/2, respectively), Oli-neu cells grown in co-culture with MB1 cells (sample designations Om_d1/2 and Mo_d1/2, respectively), or Oli-neu cells grown in co-culture with D341 cells (sample designations Od_d1/2 and Do_d1/2, respectively). mRNA was extracted using the NEBNext Poly(A) mRNA Magnetic Isolation module, libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), and sequencing was done using Illumina’s High Output Kit v2.5 with 75 cycles on an NextSeq500 instrument.

first: Thomas

last: Albert

first: Marta

last: Interlandi


title: WHSC1/NSD2 regulates immune infiltration in prostate cancer [ATAC-Seq]

summary: the WHSC1 enzymes controls immune infiltration in prostate cancer by regulating the expression of genes in immune pathways and genes in the antigen processng and presentation machinery

overall_design: ATAC-seq, n = 1/group, shCTR used as reference

first: Sebastiano

last: Battaglia

first: Muzamil

middle: Y

last: Want

first: Prashant

middle: K

last: Singh

first: James

middle: L

last: Thorne

first: Junko

last: Matsuzaki

first: Ellen

last: Karasik

first: Bryan

last: Gillard

last: Gomez

first: Richard

last: Koya

first: Amit

last: Lugade

first: Kunle

last: Odunsi


title: WHSC1/NSD2 regulates immune infiltration in prostate cancer [RNA-Seq]

overall_design: RNA-seq, n = 3/group, shCTR used as reference


title: An extracellular vesicle-related gene expression signature identifies high-risk patients in medulloblastoma


title: Memory like NK cells display stem cell like properties after Zika virus infection

city: Tyler

first: Sachin

last: Mulik

state: Texas

department: Pulmonary Immunology

institute: The University of Texas Health Science Center at Tyler

summary: In this study, we show that CD27+ memory like NK cells generated following Zika virus infection exhibited stem-like features viz., self-renewal pathway, differentiation into effector cells and longer telomeres, and greater therapeutic potential than CD27- and naive CD27+ NK cells when adoptively transferred to Zika virus infected mice. In addition, epigenetic landscape of CD27+ memory like NK is markedly different compared to CD27- NK cells.

overall_design: ATACseq of naive, CD27+ (stem cell like memory) and CD27- (nonmemory) NK cells in triplicates using Illumina HiseqX.

first: Weshely

last: Kujur

first: Oscar

last: Murillo

first: Raju

last: Adduri


title: Memory like NK cells display stem cell like properties after Zika virus Infection

summary: Here we show that Zika virus infection induces memory like NK cells that express CD27. This subset shared transcriptional changes with memory CD8 T cells, stem cells and stem like T cells. These NK cells with memory and stemness features which we term NK memory stem cells (SCMNK) demonstrated greater antiviral potential. Transcriptional data of SCMNK and non-memory NK cells is presented.

overall_design: RNA seq of CD27+ and CD27- NK cells in triplicates using Illumina platform


title: (single-cell RNAseq) An extracellular vesicle-related gene expression signature identifies high-risk patients in medulloblastoma

first: Kornelius

last: Kerl

overall_design: We used a mouse model, Atoh1-cre:SmoM2, to profile the transcriptome of SHH-MB by single cell RNA-sequencing (scRNA-seq). In this system, Atoh1-cre drives expression of a constitutively active Smo allele (SmoM2) in granule neuron precursors (GNPs), resulting in fortuitous activation of downstream target genes and subsequent formation of SHH-MB in the cerebellum. Tumors from four littermates were isolated at postnatal day 20, dispersed into single cells and further processed for scRNA-seq. Quality-filtered sequence data were merged and subjected to dimensionality reduction and cell cycle regression to mitigate the effects of cell cycle heterogeneity. This resulted in a total of 4,749 cells (mean sequence reads 59,566 ± 7,821 per cell), which represent tumor cells as well as tumor-associated non-tumor cells including immune cells and glia cells.

last: Albert


title: Analysis of differentially expressed genes in endothelial cells following tumor cell adhesion and role of PRKAA2 and miR-124-3p

status: Public on Dec 10 2020

city: Beijing

first: Yan

last: PAN

address: 38 Xueyuan Rd, Haidian District

department: Pharmacology

institute: Peking University

summary:
Tumor cell adhesion to endothelium is one pattern of tumor-endothelium interaction and one key step during tumor metastasis. The endothelium integrity is an important barrier to prevent tumor invasion and metastasis. Changes happened in ECs according to tumor cells adhesion provide important signaling mechanisms for the angiogenesis and metastasis of tumor cells. However, it is unclarified by now. In this present study we used Affymetrix Gene Chip Human Transcriptome Array 2.0. and quantitative real-time PCR (qPCR) to clarify the detailed genes alteration in endothelial cell adhered by prostate tumor cells PC-3M.
A total of 504 differentially expressed mRNAs and 444 lncRNAs were obtained through chip data analysis.

overall_design: Human umbilical vein endothelial cells (HUVECs) were cultured in 96-well dishes coated with 1 % gelatin. When HUVECs reached an approximate confluence of 100 %, PC-3M cells were washed and resuspended in culture medium (10e5 cells/ml). One hundred microliters of the tumor cell suspension were added to HUVECs monolayers in 96-well dishes and co-cultured with HUVECs for 30 min at 37°C. At the end of the incubation, wells were washed three times with PBS to try to remove adherent and non-adherent PC-3M cells.

last: Pan

first: Marhaba

last: Abdureyim


title: Relative DNA methylation and demethylation efficiencies during postnatal liver development regulate hepatitis B virus biosynthesis

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

type: Methylation profiling by high throughput sequencing

summary: HBV transcription and replication increases progressively throughout postnatal liver development with maximal viral biosynthesis occurring at around four weeks of age in the HBV transgenic mouse model of chronic infection.  Increasing viral biosynthesis is associated with a corresponding progressive loss of DNA methylation.  The loss of DNA methylation is associated with increasing levels of 5-hydroxymethylcytosine (5hmC) residues which correlates with increased liver-enriched pioneer transcription factor Forkhead box protein A (FoxA) RNA levels, a rapid decline in postnatal liver DNA methyltransferase (Dnmt) transcripts and a very modest reduction in Ten-eleven translocation (Tet) methylcytosine dioxygenase expression.  These observations are consistent with the suggestion that the balance between active HBV DNA methylation and demethylation is regulated by FoxA recruitment of Tet in the presence of declining Dnmt activity.  These changes lead to demethylation of the viral genome during hepatocyte maturation with associated increases in viral biosynthesis.  Consequently, manipulation of the relative activities of these two counter-balancing processes might permit the specific silencing of HBV gene expression with the loss of viral biosynthesis and the resolution of chronic HBV infections.

sample_organism:
Mus musculus
Hepatitis B virus

platform_organism:
Mus musculus
Hepatitis B virus

overall_design: Bisulfite and oxidative bisulfite sequencing by amplicon. 58 total samples analyzed in 120 separate libraries. Some bisulfite libraries were prepared in conjunction with oxidative bisulfite libraries and constitute paired samples – these are labeled as "OxBS + BS" in the library protocol. Others were only processed for bisulfite and are labeled "BS only". Amplicons were processed for different regions of the HBV genome, as well as several mouse promoters. Not all samples covered the same total set of amplicons; CpGs with 0 coverage in the processed data file indicate regions that were not covered in a particular file.

first: Claudia

middle: E

last: Oropeza

first: Grant

last: Tarnow

first: Taha

last: Taha

first: Rasha

last: Shalaby

first: Marieta

middle: V

last: Hyde

first: Stefan

last: Green

first: Alan

last: McLachlan


title: Gene expression differences among human natural killer cells and recombinant expression hosts

city: Athens

first: Adam

middle: W.

last: Barb

state: GA

address: 180 E. Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: This study was designed to identify gene expression differences in activatable cells used to test therapeutic monoclonal antibody efficacy in vitro. We characterized the types of glycans attached to CD16a that were expressed by four cell types and compared these compositional differences to gene expression.

overall_design: At least three biological replicates of each cell type were performed. RNA was recovered from the primary human NK cells of three donors, and RNA was recovered from NK92, YTS and HEK293F cells grown in culture and analyzed by RNA-Seq.

middle: W


title: MATR3 ChIP-seq analysis from C2C12 differentiated myotubes upon pCharme lncRNA knockdown

first: Andrea

last: Cipriano

state: Italy

address: Piazzale Aldo Moro 5

department: Biologia e Biotecnologue C. Darwin

institute: La Sapienza

summary: Identification of pCharme dependent Matrin3  chromatin binding sites by ChIP-seq analysis performed in pCharme depleted vs control myoutubes

overall_design: C2C12 cells were transfected wirth GAP-scr vs GAP-1 LNA gapmers against pCharme lncRNA and induced to differentiate. Cells were collected at day2 upon the induction of differentiation, the chromatin was collected and sonicated, and ChIP-Seq was performed.

first: Alessio

last: Colantoni

first: Monica

last: Ballarino


title: Elongin A displays widespread association with actively transcribed genes and modulates enhancer RNA transcripiton.

city: Boston

first: Manashree

last: Damle

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Elongin A (EloA) is an essential transcription factor that stimulates the rate of RNA polymerase II (Pol II) transcription elongation in vitro. However, its role as a transcription factor in vivo has remained underexplored. Here we show that in mouse embryonic stem cells, EloA localizes both to thousands of Pol II transcribed genes with a preference for sites of Pol II pausing and as well as a large number of active enhancers across the genome. EloA loss results in accumulation of transcripts at a subset of enhancers and their adjacent genes. However, EloA deletion results in only a modest decrease in the average elongation rate of Pol II globally. We also show that EloA localizes to the nucleoli and associates with RNA polymerase I transcribed ribosomal RNA gene, Rn45s. EloA is a highly disordered protein, which we demonstrate forms phase-separated condensates in vitro, and truncation mutations in the intrinsically disordered regions (IDR) of EloA interferes with its targeting and localization to the nucleoli. We conclude that EloA broadly associates with transcribed regions, tunes RNA Pol II transcription levels via impacts on eRNA synthesis and interacts with the rRNA producing/processing machinery in the nucleolus.

overall_design: We performed Cut&Run-seq and ChIP-seq  experiments on murine CCE28 embryonic stem cells (wild-type & ELoA null, Kind gift of Dr. Teijiro Aso at Kochi Medical School) to investigate the genome wide distribution of EloA .  We also investigated the effect of EloA loss on  transcription and transcription elongation rate by performing Bru-seq to detect nascent transcription in wild-type and EloA null mESC.

first: Behfar

last: Ardehali

first: Robert

last: Kingston


title: MAT2A inhibitor in cancer cell lines

status: Public on Dec 09 2020

city: Cambridge

first: Katya

last: Marjon

address: 88 Sidney Street

institute: Agios

summary: MAT2A inhibitor is dosed to MTAP null cell lines, samples are collected for transcriptome profiling

first: Chichao

last: Chen

last: Fletcher


title: ZNF410 uniquely activates the NuRD component CHD4 to silence fetal hemoglobin expression [RNA-Seq]

first: xianjiang

last: lan

state: Pennsylvania

address: 315A Abramson Research Center 3615 Civic Center Blvd

department: Hematology

institute: children's hospital of philadelphia

summary: Metazoan transcription factors typically regulate large numbers of genes. Here we identify via a CRISPR-Cas9 genetic screen ZNF410, a pentadactyl DNA binding protein that in human erythroid cells directly and measurably activates only one gene, the NuRD component CHD4. Specificity is conveyed by two highly evolutionarily conserved clusters of ZNF410 binding sites near the CHD4 gene with no counterparts elsewhere in the genome. Loss of ZNF410 in adult type human erythroid cell culture systems and xenotransplant settings diminishes CHD4 levels and derepresses the fetal hemoglobin genes. While previously known to be silenced by CHD4, the fetal globin genes are exposed here as among the most sensitive to reduced CHD4 levels. In vitro DNA binding assays and crystallographic studies reveal the ZNF410-DNA binding mode. ZNF410 is a remarkably selective transcriptional activator in erythroid cells whose perturbation might offer new therapeutic opportunities in the treatment of hemoglobinopathies.

overall_design: Differentiated HUDEP-2 cells and primary human CD34+ derived erythroblasts mRNA profiles of ZNF410 depleted and control cells or CHD4 overexpressed and control cells, in replicates, using illumina

first: Xianjiang

last: Lan

first: Gerd

last: Blobel


title: RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (ChIRP-Seq)

city: Shanghai

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

summary: N6-methyladenosine (m6A) methyltransferase METTL3 mainly mediates mRNA m6A methylation and plays important roles in various biological processes. Here we report a chromatin-based role for METTL3 in heterochromatin integrity regulation in mouse embryonic stem cells (mESCs). We show that in mESCs METTL3 predominantly localizes to one of the most active endogenous retroviruses (ERVs) families, the intracisternal A-type particles (IAPs). We further show that METTL3 knockout (KO) impairs deposition of multiple heterochromatin marks on METTL3-targeted IAPs, and upregulates IAP transcription without affecting the stability of the resulting RNAs. De-repression can be rescued by wildtype but not catalytically inactive METTL3, suggesting that METTL3-mediated methylation is important for heterochromatin silencing. Mechanistically, we demonstrate that METTL3 physically interacts with the H3K9 tri-methyltransferase SETDB1 and its regulator TRIM28, and reciprocally promote each other’s localization to IAPs. Importantly, we show that m6A catalytical activity of METTL3 is necessary for its own recruitment to chromatin but not its interactions with SETDB1 and TRIM28. Taken together, our findings demonstrate that RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs.

overall_design: Examination of METTL3 binding and histone modifications in Parental, METTL3 KO and rescue mESCs and in mESCs treated with transcriptional inhibitors.

first: Hongjie

last: Shen

first: Wenqi

last: Xu


title: RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (total RNA-Seq 2)

overall_design: Examination of total RNA in YTHDC1 WT, YTHDC1 KO and YTHDC1 W428A mESCs.


title: RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (MeRIP-Seq)

overall_design: MeRIP of chromatin RNA in Parental, METTL3 KO and SETDB1 KO mESCs.


title: ZNF410 uniquely activates the NuRD component CHD4 to silence fetal hemoglobin expression

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

overall_design: Refer to individual Series


title: Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells

city: New York

first: Gabriel

last: Victora

address: 1230 York Avenue

institute: The Rockefeller University

summary: Germinal centers (GCs) are the sites of affinity maturation, the process by which antibodies improve their affinity for antigen over time (Cyster and Allen, 2019; De Silva and Klein, 2015; Eisen, 2014; Mesin et al., 2016; Rajewsky, 1996; Shlomchik et al., 2019; Victora and Nussenzweig, 2012). For efficient affinity maturation, GC B cells must cycle between two major transcriptional states, associated with localization of B cells to each of the two microanatomical “zones” of the GC. When in the dark zone (DZ), B cells proliferate vigorously while they mutate their immunoglobulin genes by somatic hypermutation (SHM). After transition to the light zone (LZ), B cells bearing advantageous mutations are selectively driven to clonally expand, based at least in part on their ability to bind and present antigen to GC-resident T follicular helper (Tfh) cells (Victora et al., 2010). Successive cycles of somatic hypermutation and affinity-based selection ultimately enrich for higher-affinity cells in among the GC B cell population, in a process known as cyclic re-entry (MacLennan, 1994; Victora and Nussenzweig, 2012).

overall_design: SmartSeq2:  Libraries were prepared as previously described (Trombetta et al., 2014). Briefly, nucleic acids were extracted from sorted single cell using RNAClean XP SPRI beads (Beckman Coulter), and RNA was hybridized first using RT primer (/5BiosG/AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN) then reverse-transcribed into cDNA using TSO primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG) and RT maxima reverse transcriptase (Thermo Fisher Scientific). cDNA was amplified using ISPCR primer (AAGCAGTGGTATCAACGCAGAGT) and KAPA HiFi HotStart ReadyMix (Fisher Scientific), cleaned up using RNAClean XP SPRI beads three times, and tagmented using Nextera XT DNA Library Preparation Kit (Illumina). For each sequencing batch, up to four plates were barcoded at a time with Nextera XT Index Kit v2 Sets A-D (Illumina). Finally, dual-barcoded libraries were pooled and sequenced using Illumina Hiseq2500 (experiment 1)/Nextseq 550 (experiments 2-4) platform.

first: Juhee

last: Pae

first: Jonatan

last: Ersching

first: Tiago

middle: B

last: Castro

first: Marta

last: Schips

first: Luka

last: Mesin

first: Samuel

last: Allon

first: Jose

last: Ordovas-Montanes

first: Coraline

last: Mlynarczyk

first: Ari

last: Melnick

first: Alejo

last: Efeyan

first: Alex

last: Shalek

first: Michael

last: Meyer-Hermann


title: RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (ChIP-Seq 2)


title: ZNF410 uniquely activates the NuRD component CHD4 to silence fetal hemoglobin expression [ChIP-Seq]

first: xianjiang

last: lan

overall_design: Examination of transcription factor ZNF410 binding profiles in 3 cell types.

first: Xianjiang

last: Lan

first: Gerd

last: Blobel


title: Comparative genomic analysis revealed twenty-six candidate genes involved in the air-breathing function of the broadhead catfish Clarias macrocephalus

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: Walking catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater fish species of the Siluriformes order. C. macrocephalus has both gills and modified gill structures serving as an air breathing organ (ABO) which allows them aerial breathing (AB), while I. punctatus does not possess an air-breathing organ (ABO), and thus cannot breathe in air. These two species provide an excellent model for studying the molecular basis of accessory air-breathing organ development in teleost fish. In this study, seven development stages in C. macrocephalus were selected for RNA-seq analysis to compare with channel catfish as the time when air breathing organ developed and became functional. Through comparative genetic contents analysis, 1,458 genes were identified to be present in C. macrocephalus, but absent from I. punctatus. Gene expression analysis and protein-protein intersection (PPI) analysis were performed, 26 genes were selected in C. macrocephalus, including mb, ngb, hbae genes, which are mainly associated with oxygen carrier activity, oxygen binding and heme binding activities.  Our work provides a large data resource for exploring the genomic basis of air breathing function in C. macrocephalus and offers an insight into the adaption of aquatic organisms to hypoxia and high ammonia environment.

overall_design: Profile of transcriptome-wide gene expression levels in seven early development stages of Clarias macrocephalus

first: Xiaoli

last: Ma

first: Rex

last: Dunham


title: Intraductal Xenografts Model Lobular Carcinoma of the Breast and Reveal Matrix Remodeling by LOXL1 as a Targetable Hallmark II

city: Lausanne

first: George

last: Sflomos

address: SV 2815, Batiment SV, Station 19

department: ISREC

country: Switzerland

institute: EPFL

summary: Invasive lobular carcinoma (ILC) is the most frequent specific histological subtype of breast cancer (BC). It has distinct clinical features from other estrogen receptor positive (ER+) BCs but the molecular mechanisms underlying the characteristic biology are unclear because we lack experimental models to study it. Here, we generate xenograft models with ILC-derived SUM-44 PE and MDA-MB-134-VI cells by grafting them to mouse milk ducts that recapitulate the human disease including metastasis to visceral organs. Transcriptomic analysis of intraductal ER+ PDXs reveals extracellular matrix modulation as an ILC-specific trait. This signature confirms in patient datasets. The collagen modifying enzyme LOXL1 is overexpressed specifically in ILCs by tumor cells; treatment with a LOX inhibitor, BAPN, and LOXL1 silencing decrease tumor growth and inhibit metastasis by disrupting ECM structure/fibrils with down modulation of ER, IGFR, and FGFR signaling. Hence inhibition of LOXL1 is a promising therapeutic strategy for ILC.

overall_design: Expression profile of 6 FACS sorting RFP+ SUM44 intraductally xenografted mammary glands treated with PBS or BAPN


title: RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs [YTHDC1_ChIP]

first: Yang

last: Shi

first: Hongjie

last: Shen

first: Wenqi

last: Xu


title: To study the function of KLF5 in squamous cancers and gastrointestinal cancers [ChIP-seq]

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

summary: To identify KLF5 target genes and study the gene regulation function of KLF5 by integrating ChIP-seq, HiChIP and RNA-seq assays

overall_design: ChIP-seq to identify KLF5 binding site in squamous cancer and gastrointestinal cell lines; ChIP-seq to define BRD4 and phosphorylated POL2 binding profiles in HARA cells with and without KLF5 knockout. Samples with 'sgAAVS1' use a sgRNA targeting an intronic region of AAVS1, which serves a negative control for CRISPR knockout.

first: Yanli

last: Liu


title: RNA-seq analysis of gestationally Cd-exposed hepatic transcriptome

city: Raleigh

first: Scott

last: Belcher

state: NC

address: 127 David Clark Labs, Campus box 7617

department: Biological Sciences

institute: North Carolina State University

summary: We report the RNA-sequencing analysis of hepatic RNA isolated from CD-1 mice following gestational exposure to 500ppb CdCl2. We show that gestational Cd exposure alters the hepatic gene expression of female, but not male offspring in numerous pathways related to oxidative stress and mitochondrial dysfunction leading to endoplasmic reticulum stress that ultimately drives metabolic disruption of insulin signaling.

overall_design: Examination of three different timepoints and one exposure group

first: Thomas

last: Jackson


title: RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (total RNA-seq)

overall_design: Examination of total RNA in Parental, METTL3 KO and rescue mESCs.


title: Single-cell RNA sequencing of escort cells (ECs) in Drosophila ovaries

first: xi

last: rongwen

address: No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,

institute: National Institute of Biological Sciences, Beijing

summary: Escort cells (ECs) in the Drosophila ovaries showed important functions in modulate germline cysts differentiation, as germline cysts differentiation niche, yet their subtypes and functions to germline cysts were still little known. Through single cell RNA-sequencing analysis, here we provide a comprehensive analysis of cellular diversity and functions of ECs in adult Drosophila germariums. We identify 2 EC subtypes with different gene expression and functions, further tested through EC subtypes-specific gene RNAi. Our single-cell data should greatly facilitate understanding of the functions of ECs as differentiation niche.

overall_design: FACS sort ECs through C587-GAL4> UAS-GFP line and perform 10X genomics single cell sequencing. Raw data was further processed by Seurat3 algorithm and EC subtypes were visualized by generating a UMAP plot.

first: Shi

last: Jingyuan

first: Fu

last: Yang

first: Yongchao

first: Rongwen

last: Xi


title: The genomic underpinnings of oscillatory biomarkers supporting successful memory encoding in humans

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Brain oscillations are remarkable components of brain activity that support memory encoding. However, it remains a major challenge to determine the molecular mechanisms underlining this activity in humans. Here, we used direct intracranial electroencephalography recordings from patients performing free recall tasks of verbal memory encoding in temporal cortex. Using resected tissue transcriptomics from the same patients, we linked gene expression with brain oscillations, identifying genes correlated with oscillatory signatures of memory formation across six frequency bands. Co-expression analysis isolated biomarker-specific modules associated with neuropsychiatric disorders as well as ion channel activity. Using single-nuclei transcriptomic data from resected tissue, we further revealed that biomarker-specific modules are enriched for both excitatory and inhibitory neurons. This unprecedented dataset of patient-specific brain oscillations coupled to genomics unlocks new insights into the genetic mechanisms that support memory encoding.  By linking brain expression of these genes to oscillatory patterns, our data help overcome limitations of phenotypic methods to uncover genetic links to memory performance.

overall_design: Transcriptomic data obtained from resected human Brodmann Area 38 tissue were integrated with intracranial electroencephalography (iEEG) data from the same subjects to link memory-related oscillations with gene expression in 16 subjects. Matched post-mortem tissues from healthy and epileptic individuals were used for cross-validations. Single-nuclei RNA-sequencing and single-nuclei chromatin accessibility obtained from similar Brodmann Area 38 samples were used to define the cell-type composition of genes and coexpressed gene expression modules associated with memory oscillation. Resected tissues were obtained from living donors.

first: Stefano

last: Berto

first: Miles

last: Fontenot

first: Fatma

last: Ayhan

first: Emre

last: Caglayan

first: Connor

last: Douglas


title: Intraductal Xenografts Model Lobular Carcinoma of the Breast and Reveal Matrix Remodeling by LOXL1 as a Targetable Hallmark I

first: George

last: Sflomos

overall_design: Expression profile of 6 GFP+ FACS-sorted intraductally injected Patient Derived Xenografts_PDXs


title: RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (ChIP-seq)

first: Yang

last: Shi

first: Hongjie

last: Shen

first: Wenqi


title: RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs [YTHDC1_ChIRP-Seq]

last: Xu


title: RNA-seq analysis to profile TGF-beta/Activin signaling-dependent gene expression in Drosophila larval skeletal muscle

status: Public on Dec 08 2020

city: Minneapolis

first: Myung-jun

last: Kim

state: MN

address: 5-235 Moos tower, 515 Delaware st. SE

department: GCD

institute: University of minnesota

summary: We performed RNA-seq analysis to identify genes whose expression is regulted or influenced by TGF-beta/Activin signaling in Drosophila larval skeletal muscle. We used two sample sets. One is composed of wild-type and smox (the sole R-smad of TGF-beta/Activin signaling in Drosophila). The other is composed of control and larvae of muscle-specific expression of activated Baboo (Type I receptor). By comparing differential expressions from these two sets, we were able to identify genes whose expression is regulated by TGF-beta/Activin pathway in the skeletal muscle of Drosophila larvae.

overall_design: Transcript profiles of larval carcass (muscle-epidermis complex) of wild-type and smox mutant as well as muscle specific expression of activated baboon and control animals

first: Myung-Jun

first: Michael

last: O'Connor


title: RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (WGBS)

overall_design: Examination of DNA methylation in Parental, METTL3 KO and rescue mESCs.


title: Effect of DMF and MEF on gene expression in select mouse organs:  Single-dosing regimen

first: Suzanne

last: Szak

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

summary: Delayed-release dimethyl fumarate (DMF) is approved in the United States, European Union, Canada, and Australia for the treatment of multiple sclerosis. DMF is also a component in a defined-mixture product with three salts of monoethyl fumarate (MEF) that is approved in Germany for the treatment of psoriasis. Characterizing common or distinct pharmacodynamic properties of DMF and MEF would provide insights into the mechanisms of action of delayed-release DMF versus fixed combination products containing DMF and MEF salts. In this study we evaluated the pharmacodynamic effects and pharmacokinetics of DMF and MEF in central nervous system and peripheral tissues of naïve mice following a single dose or 10 daily doses of DMF, MEF, or a combination of the two. DMF and MEF exhibited similar pharmacokinetic profiles, but differences were noted in biodistribution: monomethyl fumarate (MMF, the primary metabolite of DMF) exhibited a higher degree of brain penetration, whereas MEF was preferentially partitioned into kidney. Both common and distinct pharmacodynamic responses were observed in all assessed tissues for DMF and MEF alone or in combination. These findings indicate that all fumaric acid esters cannot be considered equivalent, and combinations of compounds may exert effects not observed when agents are used individually.

overall_design: C57BL/6 mice were administered vehicle (0.8% hydroxypropyl methylcellulose), DMF (100 mg/kg or 179.2 mg/kg), a mixture of MEF salts (Ca2+, Mg2+, Zn2+; 79.2 mg/kg), or a combination of DMF (100 mg/kg) and MEF salts (79.2 mg/kg) as a single acute dose (n = 6−10 mice per dose group). Global transcriptional profiling was performed on whole blood and a panel of tissues (brain, inguinal lymph node, mesenteric lymph node, jejunum and spleen) to identify genes that were significantly modulated relative to vehicle controls 6 and 12 hours after the single dose.

first: Brian

middle: T

last: Wipke

first: Kristopher

last: King

first: Melanie

last: Brennan

first: Norm

last: Allaire

first: Patrick

last: Cullen

first: Alice

last: Thai

first: Ankur

last: Thomas

first: Davide

last: Gianni

first: Alex

last: Chou

first: Theresa

last: Hillery

first: Kejie

last: Li

first: Liyu

first: John

middle: P

last: Carulli

first: Chaoran

last: Huang

first: Mark

last: Rogge

first: Norman

first: Kenneth

last: Rhodes

first: Robert

middle: H

last: Scannevin


title: Genetic interaction mapping informs integrative structure determination of protein complexes

city: San Francisco

first: Hannes

last: Braberg

institute: UCSF

summary: Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for point mutations crossed against gene deletions or exposed to environmental perturbations, followed by converting similarities between two profiles into an upper bound on the distance between the mutated residues. We determine the structure of the yeast histone H3/4 complex based on ~500,000 genetic interactions of 350 mutants. We then apply the method to subunits Rpb1-Rpb2 of yeast RNA polymerase II, and subunits RpoB-RpoC of bacterial RNA polymerase. The accuracy is comparable to that based on chemical cross-links; using restraints from both genetic interactions and cross-links further improves model accuracy and precision. The approach provides an efficient means to augment integrative structure determination with in vivo observations.

overall_design: RNA-seq expression analysis of 29 histone H3/H4 point mutants and wild-type. 2-4 replicates per sample; ATAC-seq analysis of 2 histone H3/H4 point mutants, set2 deletion, and wild-type. 3-4 replicates per sample.

first: Ignacia

last: Echeverria

first: Stefan

last: Bohn

first: Peter

last: Cimermancic

first: Anthony

last: Shiver

first: Richard

last: Alexander

first: Jiewei

last: Xu

first: Michael

last: Shales

first: Raghuvar

last: Dronamraju

first: Shuangying

last: Jiang

first: Gajendradhar

last: Dwivedi

first: Derek

last: Bogdanoff

first: Kaitlin

last: Chaung

first: Ruth

last: Hüttenhain

first: Shuyi

last: Wang

first: David

last: Mavor

first: Riccardo

last: Pellarin

first: Dina

last: Schneidman

first: Joel

middle: S

last: Bader

first: James

last: Fraser

last: Morris

last: Haber

first: Brian

middle: D

last: Strahl

first: Carol

last: Gross

first: Junbiao

last: Dai

first: Jef

last: Boeke

first: Andrej

last: Sali

first: Nevan

last: Krogan


title: Apolipoprotein A-I mimetic peptide L37pA attenuates IFNα-induced inflamation and promotes antiviral activity

city: Pamplona

first: Pedro

last: Berraondo

address: Avenida Pio XII 55

department: Program of Immunology and Immunotherapy

country: Spain

institute: Cima Universidad de Navarra

summary: Apolipoprotein A-I mimetic peptides are amphipathic alpha helix peptides that display similar functions to apolipoprotein A-I, and preclinical studies have evaluated . In this study, we evaluated the effect of the long-term expression of L37pA in the liver by an adeno-associated virus (AAV-L37pA) on the expression of an adeno-associated virus encoding interferon-alpha (AAV-IFNα). Long-term IFNα expression in the liver leads to lethal hematological toxicity one month after AAV administration. Concomitant administration of AAV-L37pA prevented the lethal toxicity since the IFNα expression was reduced one month after AAV administration by decreasing the expression of IFNα. To identify the mechanism of action of L37pA, a genomic and proteomic analysis was performed fifteen days after AAV administration when a similar level of IFNα and interferon-stimulated genes were observed in mice treated with AAV-IFNα alone and in mice treated with AAV-IFNα and AAV-L37pA. The coexpression of the apolipoprotein A-I mimetic peptide L37pA with IFNα modulated the gene expression program of IFNα, inducing a significant reduction in inflammatory pathways affecting pathogen-associated molecular patterns receptor, dendritic cells, NK cells and Th1 immune response. The proteomic analysis confirmed the impact of the L37pA activity on several inflammatory pathways and indicated an activation of LXR/RXR and PPPARα/γ nuclear receptors. Thus, long-term expression of L37pA induces an anti-inflammatory effect in the liver that allows silencing of IFNα expression mediated by an adeno-associated virus.

overall_design: We administered intravenously AAV- IFNα or AAV- IFNα + AAV-L37pA to wild type mice, and 15 days later, livers were extracted and homogenized. RNA was obtained and used to analyze the gene expression profile induced by the different treatments using Affymetrix Mouse Gene 1.0 ST array.


title: Transcriptomic landscape of radiation-induced murine thyroid proliferative lesions

city: Neuherberg

first: Martin

last: Selmansberger

state: Bavaria

address: Ingolstaedter Landstrasse 1

department: Department of Radiation Cytogenetics

institute: Helmholtz Zentrum Muenchen

summary: This study aims at the identification and characterization of early-state radiation-associated neoplastic processes by histologic and transcriptomic analyses of thyroid tissues derived from a mouse model. Comprehensive histological examination of 246 thyroids (164 exposed, 82 non-exposed) was carried out. Proliferative and normal tissues from exposed cases and normal tissue from non-exposed cases were collected by laser-capture microdissection, followed by RNAseq transcriptomic profiling using a low input 3`-library preparation protocol, differential gene expression analysis and functional association by Gene Set Enrichment Analysis.

overall_design:
9 individual samples of normal thyroid tissue from non-exposed mice (nromal control tissue, NCT)
9 samples of normal thyroid tissue from exposed mice with adjacent histologic abnormalities (normal tissue, NT)
9 samples of proliferative lesions tissue (PL), paired with NT samples

first: Elena

last: Stauffer

first: Kristian

last: Unger

first: Peter

last: Weber


title: Transcriptional profiing of cultured adherent and non-adherent monocytes

city: Amsterdam

first: Joe

last: Butler

address: Meibergdreef 9

department: Infectious diseases

country: Netherlands

institute: Amsterdam UMC

summary: To determine the effect of adherence on the metabolic and functional response of human monocytes. Monocytes were stimulated with lipopolysaccharide (LPS) under non-adherent and adherent conditions. To determine the role of glycolysis in LPS-induced immune responses, this pathway was inhibited by glucose deprivation or the glucose analog 2-deoxy-D-glucose (2DG).

overall_design: Monocytes were isolated from 6 healthy volunteers. Each donor's monocytes were exposed to every combination of the three treatment conditions (2 adherene conditions, 2 LPS conditions, 3 glucose conditions).


title: Next Generation Sequencing Facilitates Quantitative Analysis of Il17ra villin cre -/+ colon transcriptomes at day 10 post C. rodentium infection

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: We report analysis of colonic transcriptome in gut epithelial cells specific deficient mouse (Il17ra villin cre +) and littermate control mouse (Il17ra villin cre -) infected with Citrobater rodentium (C. rodentium) for 10 days. We found RNA-seq data show Nox family genes and defensin genes are downregulated in Il17ra villin cre + mice. It is interestingly Tnfsf13 was also downregulated in Il17ra villin cre + mice. These genes expressions were confirmed by qRT–PCR validation was performed using TaqMan assays. Finally, this study provides first detailed analysis of C. rodentium infected colonic transctiptome in Il17ra villin cre + mice, with biologic replicates, generated by RNA-seq technology.

overall_design: colonic mRNA profiles of  Il17ra villin cre -/+ at day 10 post C. rodentium infection

first: Yasuka

last: Matsunaga


title: RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (ChIP-Seq 3)

first: Yang

last: Shi

overall_design: Examination of METTL3 binding and histone modifications in Parental, METTL3 KO and rescue mESCs and in mESCs treated with transcriptional inhibitors.

first: Hongjie

last: Shen

first: Wenqi

last: Xu


title: Effects of novel selective androgen receptor modulator, TEI-SARM2, on gene expression profile changes in skeletal muscle

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

summary: TEI-SARM2 is a novel selective androgen receptor modulator. To assess the effects of TEI-SARM2 on skeletal muscle, we generated myofiber specific ARKO using HSA-Cre and AR flox mice (mARKO). Male mARKO and littermate control (ARL2/Y) mice underwent ORX or not. Nine days after ORX, the mice were treated with TEI-SARM2 (10 mg/kg weekly, p.o.) or vehicle (weekly, p.o.) for another 2 weeks. After euthanasia, the bulbocavernosus (BC) muscles were collected and total RNA was extracted.

overall_design: mRNA profiles of bulbocavernosus (BC) muscles obtained from control  and mARKO mice treated with 1) sham operation, 2) ORX and vehicle administration or 3) ORX and TEI-SARM2 administration, were generated by sequencing using Illumina Myseq separately for control and mARKO.

first: Masanobu

last: Kanou


title: Global examination of LncMyoD binding sites using ChIRP-seq

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

summary: We report the application of ChIRP-seq on examination of LncMyoD binding sittes in differentiated myotubes  We observed the global binding sites of LncMyoD in differentiated myotubes.

overall_design: Examination of LncMyoD binding sites in differentiated myotubes.

first: Anqi

last: Dong


title: Antigen-specific and bystander epidermal CD8+ resident memory T cells

city: Pittsburgh

first: Daniel

last: Kaplan

address: 200 Lothrop Street

institute: University of Pittsburgh

summary: RNAseq analysis of epidermal OT-I Trm generated by VV-OVA infection or DNFB-pull

overall_design: Thy1.1 OT-I cells were adoptively transferred into WT mice.  Mice were infected on 1 flank with VV-OVA followed 5 days later by DNFB-pull on the opposite flank. 57-70 days later, OT-I cells were isolated by enzymatic digestion from the epidermis and FACS sorted.

first: Toshiro

last: Hirai


title: In situ HiC of primary mouse B cell progenitor populations after activation with LPS

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Naive resting B-cells were purified from the bone marrow of C57BL/6 mice using flow cytometry sorting. Naive B cells were activated with LPS. Activated but undivided cells were harvested 3 hours, 10 hours or 33 hours after the LPS treatment. The Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) system was also used to isolate imminently dividing B cells specifically in the G1 stage of the cell cycle prior to the S phase.

overall_design: Two biological replicates were prepared at each activation time. In situ Hi-C libraries were sequenced on an Illumina NextSeq 500 to produce paired-end 81bp reads.

first: Hannah

last: Coughlan


title: RNA-seq of primary mouse B cell progenitor populations after activation with LPS

summary: Naive resting B-cells were purified from bone marrow from C57BL/6 mice using flow cytometry sorting. Naive B cells were activated with LPS and harvested 3 hours, 10 hours or 33 hours after the LPS treatment. Expanded activated B cells (CD22+ CD138-) and plasmablasts (CD22- CD138+) were  also harvested on day 4 post-stimulation.

overall_design: Two biological replicates were prepared of naive B cells, activated B cells after each LPS treatment time and plasmablasts. All 12 samples were RNA-seq profiled by sequencing on an Illumina NextSeq 500 to produce 81bp paired-end reads.


title: Characterization of the role of Elongin A in transcription regulation in DLD1 cell

first: Brian

middle: David

last: Dynlacht

address: 522 1st Ave, Smilow 1104

department: Dept. of Pathology and Cancer Center

institute: NYU School of Medicine

summary: We performed RNA-seq, 4sU-seq, ChIP-seq and Cut&Run to characterize how Elongin A regulates different steps during the transcription cycle.

overall_design: RNA-seq, 4sU-seq, ChIP-seq for Pol II, Pol II-ser2p, Pol II-ser5p were performed in control and Elongin A depleted DLD1 cells. Elongin A Cut&Run was performed to determine the genome-wide localization of Elongin A. All experiments were performed in replicates.

first: Yating

last: Wang

first: Liming

last: Hou


title: Alzheimer’s-associated PU.1 expression levels regulate microglial inflammatory response

status: Public on Dec 07 2020

first: Alison

last: Goate

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: More than forty loci contribute to genetic risk for Alzheimer’s disease (AD). These risk alleles are enriched in myeloid cell enhancers suggesting that microglia, the brain-resident macrophages, contribute to AD risk. We have previously identified SPI1/PU.1, a master regulator of myeloid cell development in the brain and periphery, as a genetic risk factor for AD. Higher expression of SPI1 is associated with increased risk for AD, while lower expression is protective. To investigate the molecular and cellular phenotypes associated with higher and lower expression of PU.1 in microglia, we used stable overexpression and knock-down of PU.1 in BV2, an immortalized mouse microglial cell line. Transcriptome analysis suggests that reduced PU.1 expression suppresses expression of homeostatic genes similar to the disease-associated microglia response to amyloid plaques in mouse models of AD. Moreover, PU.1 knock-down resulted in activation of protein translation, antioxidant action and cholesterol/lipid metabolism pathways with a concomitant decrease of pro-inflammatory gene expression. PU.1 overexpression upregulated and knock-down downregulated phagocytic uptake in BV2 cells independent of the nature of the engulfed material. However, cells with reduced PU.1 expression retained their ability to internalize myelin similar to control albeit with a delay, which aligns with their anti-inflammatory profile. Here we identified several microglial responses that are modulated by PU.1 expression levels and propose that risk association of PU.1 to AD is driven by increased pro-inflammatory response due to increased viability of cells under cytotoxic conditions. In contrast, low expression of PU.1 leads to increased cell death under cytotoxic conditions accompanied by reduced pro-inflammatory signaling that decreased A1 reactive astrocytes signature supporting the protective effect of SPI1 genotype in AD. These findings inform future in vivo validation studies and design of small molecule screens for therapeutic discovery in AD.

overall_design: We performed bulk RNA-sequencing of FACS-sorted BV2 cells with transient shRNA-mediated knock-down and cDNA overexpression of mouse Spi1.

first: Anna

middle: A

last: Pimenova


title: RNA-seq and in situ Hi-C of primary mouse B cell progenitor populations after activation with LPS

summary: During cellular differentiation, chromosome conformation is intricately remodelled to support the lineage-specific transcriptional programs required for initiating and maintaining lineage identity. When these changes occur in relation to cell cycle, division and time is unclear although it has been proposed they would occur during DNA synthesis 5 or after mitosis. Here we elucidate the chromosome conformational changes in B lymphocytes as they differentiate and massively expand from a naïve, quiescent state into antibody secreting plasma cells. Unexpectedly, we find dramatic gene-regulatory chromosome reorganization in late G1 phase prior to the first division, and that this configuration is remarkably stable as the cells massively 10 and rapidly clonally expansion. A second wave of conformational change occurs as cells terminally differentiate into plasma cells, coincident with increased time in G1 phase. In this study we stimulated naive B cells with LPS and harvested activated B cells or plasmablasts at different time points after stimulation. RNA-seq was used to profile gene expression and in situ Hi-C was used to profile DNA-DNA interactions at each time point.

overall_design: Naive resting B-cells were purified from the bone marrow of C57BL/6 mice using flow cytometry sorting. Naive B cells were activated with LPS and harvested 3 hours, 10 hours or 33 hours after the LPS treatment. Expanded activated B cells (CD22+ CD138-) and plasmablasts (CD22- CD138+) were also harvested on day 4 post-stimulation. Two biological replicates from different mice were prepared of each cell population.


title: Tumor-infiltrating mast cells are associated with resistance to anti-PD-1 therapy. [TCR]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: TCR clonotypes in spleen and melanoma tumor from humanized mice.

overall_design: Expression of TCR clonotypes in spleen and tumor of humanized mice.

first: Rajasekharan

last: Somasundaram

first: Meenhard

last: Herlyn


title: Tumor-infiltrating mast cells are associated with resistance to anti-PD-1 therapy.

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

overall_design: Refer to individual Series


title: Tumor-infiltrating mast cells are associated with resistance to anti-PD-1 therapy. [RNA-Seq]

summary: Increased expression of mast cell related genes in melanoma tumors obtained from humanized mice after anti-PD-1 therapy.

overall_design: Expression levels of mast cell related genes in tumors obtained after anti-PD-1 therapy and compared to control Ig treated tumors.


title: Transcriptiome dynamics of cyanopodovirus S-SBP1 and its host Synechococcus sp. WH7803

city: Guangzhou

first: Sijun

last: Huang

state: Guangdong

address: 164 Xingangxi St

institute: Chinese Academy of Sciences

summary: Whole-genome expression dynamics of cyanopodovirus P-SSP7 and its host Prochlorococcus strain MED4 have been reported. To investigate whether cyanopodoviruses infecting Prochlorococcus and Synechococcus have similar transcription strategy and host response to phage infection, genomic and transcriptomic analyses were conducted on cyanopodovirus S-SBP1 that infects Synechococcus strain WH7803. S-SBP1 has a latent period of 8 h and a burst size of 30 progeny phages per cell. S-SBP1 was most similar to cyanopodovirus S-RIP2 that also infects Synechococcus WH7803, in terms of whole genome phylogenetic relationship and average nucleotide identity (ANI). Three hypervariable genomic islands were found when comparing the genomes of S-SBP1 and S-RIP2, and single nucleotide variants (SNV) were observed on three genes of S-SBP1, which are located within the island regions. Based on RNA-seq analysis, genes of S-SBP1 were clustered into three temporal express classes, with gene content within each class similar to that of P-SSP7. Thirty-two host genes were upregulated during phage infection, including those involved in carbon metabolism, ribosome component and stress response. These upregulated genes were also similar to those of Prochlorococcus MED4 in response to infection by P-SSP7. Our study demonstrates a programmed temporal expression pattern of cyanopodoviruses and hosts during infection.

sample_organism:
Synechococcus sp. WH 7803
Synechococcus phage S-SBP1

overall_design: Exponentially growing Synechococcus WH7803 culture was inoculated with phage S-SBP1 at a multiplicity of infection (MOI) of two. At the time points 15 min, 1 h, 3 h, 5 h and 7 h after phage lysate additon, cells from single treatment were collected for transcriptomic analysis. A parallel of control group without phage addition was also sampled at the time point of 30 min and 8 h. Seven RNA-seq libraries, which are five time points of phage addition treatment and two time points of control, were sequenced using the Illumina HiSeq platform.

first: Yingting

last: Sun

first: Si

last: Zhang

first: Lijuan

last: Long


title: Single cells RNA-Seq of CD45+ cells during Staphylococcus aureus craniotomy infection

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

overall_design: CD45+ cells were isolated from the brain, subcutaneous galea, bone flap, and blood at day 7 post-infection by FACS, whereupon single cell RNA sequencing was performed using a 10X Genomics platform

first: Horn

last: Chris

first: Heim

last: Cortney

first: Kielian

last: Tammy


title: The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress [ChIP-seq]

city: Lausanne

first: Terytty Yang

last: Li

address: EPFL SV IBI-SV LISP AI 1145

institute: EPFL

summary: Organisms respond to mitochondrial stress by activating multiple defense pathways including the mitochondrial unfolded protein response (UPRmt). However, how different layers of UPRmt regulators are orchestrated to transcriptionally activate the stress responses remains largely unknown. Here we identified CBP-1, the worm ortholog of the mammalian acetyltransferases CBP/p300, as an essential regulator for UPRmt activation, as well as for mitochondrial stress-induced immune response, amyloid-β aggregation reduction and lifespan extension in Caenorhabditis elegans. Mechanistically, CBP-1 acts downstream of histone demethylases, JMJD-1.2/JMJD-3.1, and upstream of UPRmt transcription factors including ATFS-1, to systematically induce a broad spectrum of UPRmt genes and execute multiple beneficial functions. In mouse and human populations, transcript levels of CBP/p300 positively correlate with UPRmt transcripts and longevity. Furthermore, CBP/p300 inhibition disrupts, while forced expression of p300 is sufficient to activate, the UPRmt in mammalian cells. These results highlight an evolutionarily conserved mechanism that determines mitochondrial stress response, and promotes health and longevity through CBP/p300.

overall_design: N2 worms carrying a hsp-6::GFP reporter fed with control or cco-1 RNAi, and ChIP with H3K18Ac or H3K27Ac

first: Terytty

first: Maroun

last: Bou Sleiman

first: Hao

first: Arwen

last: Gao

first: Adrienne

last: Mottis

first: Alexis

last: Bachmann

first: Gaby

last: Alam

first: Kristina

last: Schoonjans

first: Johan

last: Auwerx


title: The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress [HepG2]

overall_design: Human HepG2 cells treated with or without CBP/p300 Inhibitor A-485 and/or Dox


title: Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A

city: Wakoshi

first: Mingming

last: Chen

state: Saitama

address: Hirisawa 2-2

department: CPR

institute: RIKEN

summary: Small molecule compounds that sense the nucleic acid sequences, promise the attractive venue for drug development. Such an unusual effect has been observed in the natural product Rocaglamide A (RocA) from Aglaia plant, proving to exhibit anti-tumor effects by clamping eukaryotic initiation factor (eIF) 4A onto mRNA polypurine sequences. Although eIF4A has been speculated the unique target of RocA, the insensitization of eIF4A in human cells only partially rescued the translation repression from RocA, suggesting another alternative target of this compound. Here, we revealed that DDX3 is an alternative target of RocA. Developing a RocA derivative with an O-nitrobenzoxadiazole unit (RocA-O-NBD), which can covalently bind to proximate proteins and provide fluorescence to them, we identified DDX3 bound to RocA. As observed in eIF4A, RocA locked the DDX3 protein onto polypurine sequences of RNA in an ATP-independent manner. De novo assembled Aglaia plant transcriptome uncovered the natural amino acid substitutions in Aglaia DDX3 to protect itself from RocA toxicity. Because of the dominant negative effect of RocA, we also proved the protein abundance of eIF4A and DDX3 in cancer cells determines their sensitivity to RocA. Overall, this study discovered DDX3 as another target of RocA and suggests the probability to predict tumor toxicity of RocA by the target abundance.

overall_design: Ribosome profiling

first: Yuichi

last: Shichino

first: Shintaro

last: Iwasaki


title: Genome editing demonstrates that the -5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin


title: The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress

sample_organism:
Caenorhabditis elegans
Homo sapiens
Mus musculus


title: The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress [C. elegans]

overall_design: N2 worms carrying a hsp-6::GFP reporter fed with cco-1, mrps-5, cbp-1, atfs-1 RNAi


title: NK cell expansion on uAPC helper cells

status: Public on Dec 06 2020

city: Houston

first: Katy

last: Rezvani

state: Texas

address: 1400 Pressler St

department: Stem Cell Transplantation

institute: University of Texas MD Anderson Cancer Center

summary: Natural killer (NK) cells are innate lymphocytes recognized for their important role against tumor cells. NK cells expressing chimeric antigen receptors (CARs) have enhanced effector function against various type of cancer and are attractive contenders for the next generation of cancer immunotherapies. However, a number of factors have hindered the application of NK cells for cellular therapy, including their poor in vitro growth kinetics and relatively low starting percentages within the mononuclear cell fraction of peripheral blood or cord blood (CB). To overcome these limitations, we genetically-engineered human leukocyte antigen (HLA)-A- and HLA-B- K562 cells to enforce the expression of CD48, 4-1BBL, and membrane-bound IL-21 (mbIL21), creating a universal antigen presenting cell (uAPC) capable of stimulating their cognate receptors on NK cells. We have shown that uAPC can drive the expansion of both non-transduced (NT) and CAR-transduced CB derived NK cells by greater than 900-fold in 2 weeks of co-culture with excellent purity (>99.9%) and without indications of senescence/exhaustion. We confirmed that uAPC-expanded research- and clinical-grade NT and CAR-transduced NK cells have higher metabolic fitness and display enhanced effector function against tumor targets compared to the corresponding cell fractions cultured without uAPCs. This novel approach allowed the expansion of highly pure GMP-grade CAR NK cells at optimal cell numbers to be used for adoptive CAR NK cell-based cancer immunotherapy.

overall_design: We report the application of next-gen sequencing technology for high-throughput RNA profiling of NK cells. Comparison of RNA profiles 1) between freshly isolated NK cells with those repeated exposed to uAPC, and 2) between freshly isolated NK cells with those repeated exposed to uAPC over the course of 2 weeks after CAR19-transduction

first: Enli

last: Liu

first: Sonny

middle: O

last: Ang

first: Lucila

last: Kerbauy

first: Rafet

last: Basar

first: Indreshpal

last: Kaur

first: Mecit

last: Kaplan

first: Li

first: Yijiu

last: Tong

first: May

last: Daher

first: Ana

last: Nunez Cortes

first: Ryan

middle: Z

last: Yang

first: Ye

first: Hila

last: Shaim

first: Francia

last: Reyes Silva

first: Paul

last: Lin

first: Vakul

last: Mohanty

first: Sunil

last: Acharya

first: Mayra

last: Shanley

first: Luis

last: Muniz-Feliciano

first: Pinaki

last: Banerjee

first: Ken

first: Richard

last: Champlin

first: Elizabeth

last: Shpall

first: Katayoun


title: The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress [Mus musculus]

first: Terytty Yang

last: Li

overall_design: Wild-type and CBP/p300 KO MEFs treated with or without Dox

first: Terytty

middle: Y

first: Maroun

last: Bou Sleiman

first: Hao

first: Arwen

last: Gao

first: Adrienne

last: Mottis

first: Alexis

last: Bachmann

first: Kristina

last: Schoonjans

first: Johan

last: Auwerx


title: The effects of transcriptional activator engineering on the transcriptome of Penicillium oxalicum

status: Public on Dec 05 2020

city: Qingdao

first: Guodong

last: Liu

state: Shandong

address: Binhai Road 72

department: State Key Laboratory of Microbial Technology

institute: Shandong University

summary: The filamentous fungus Penicillium oxalicum can secret various enzymes for efficient saccharification of plant biomass materials. Expression of the constitutively active forms of transcriptional activators ClrB, XlnR and AraR could trigger the production of different sets of lignocellulolytic enzymes. Here, the transcriptomes of the three engineered strains were compared with that of wild type in the medium without carbon source.

overall_design: A total of 12 samples were analyzed, which include biological triplicates. The wild-type strain 114-2 was used as a control.

first: Liwei


title: Footprints of global change in marine life: inferring past environment based on DNA methylation and gene expression marks

city: Barcelona

first: Dafni

last: Anastasiadi

address: Pg. Marítim de la Barceloneta 37-49

department: Renewable Marine Resources

institute: Institute of Marine Sciences-CSIC

summary: Ocean global warming affects the distribution, life history and physiology of marine life. Extreme events, like marine heatwaves, are increasing in frequency and intensity. During sensitive developmental windows of fish, the consequences may be long-lasting and mediated by epigenetic mechanisms. Here, we used adult European sea bass as a model to study the effects of a marine heatwave during development. We measured DNA methylation and gene expression in four tissues (brain, muscle, liver and testis) and detected differentially methylated regions (DMRs). Six genes were differentially expressed and contained DMRs three years after exposure to increased temperature, indicating direct phenotypic consequences and representing persistent changes. Interestingly, nine genes contained DMRs around the same genomic regions across tissues, therefore consisting of common footprints of developmental temperature in environmentally responsive loci. These loci are, to our knowledge, the first metastable epialleles (MEs) described in fish. MEs may serve as biomarkers to infer past life history events linked with persistent consequences. These results highlight the importance of subtle phenotypic changes mediated by epigenetics to extreme weather events during sensitive life stages. Also, to our knowledge, it is the first time the molecular effects of a marine heatwave during the lifetime of individuals are assessed. MEs could be used in surveillance programs aimed at determining the footprints of climate change on marine life. Our study paves the way for the identification of conserved MEs that respond equally to environmental perturbations across species. Conserved MEs would constitute a tool of assessment of global change effects in marine life at a large scale.

overall_design:
We analyzed genome-wide methylation and gene expression patterns in adult fish that had experienced 4°C of developmental temperature differences. At seven days post fertilization (dpf), temperature increased from 13.5±1°C to 16.5±1°C in the low temperature group and from 13.5±1°C to 20.5±1°C in the high temperature group. The temperature differences were maintained until 68 dpf when temperature started following natural conditions until fish were 3 years old adults and sampled. Genome-wide methylation patterns were analyzed by performing Reduced Representation Sequencing (RRBS) of four tissues representative of the embryonic layers: brain (ectoderm), muscle (paraxial mesoderm), testis (intermediate mesoderm) and liver (endoderm) from three fish reared at low and three fish reared at high temperature. Gene expression patterns were analyzed by RNA-seq in the brain, muscle, testis and liver of five low and five high temperature fish. The RRBS and RNA-seq data of fish reared at low temperature are already published under the GEO Series accession number GSE125124 and are the samples of farmed fish from this series.
Please note that each *Feature_Counts.txt was generated from all replicates and is linked to the corresponding repl1 sample records (e.g. *1-RNAseq-HighTemperature).

first: Changwei

last: Shao

first: Songlin

last: Chen

first: Francesc

last: Piferrer


title: Genome-wide profiling of SESAME complex and related regulators

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute


title: Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A [Bind-n-Seq]

first: Mingming

overall_design: Bind-n-Seq

first: Yuichi

last: Shichino

first: Shintaro

last: Iwasaki


title: Nuclear ESM1 promotes prostate cancer stemness through β-catenin signaling

city: Taipei City

first: KeFan

last: Pan

state: Please Select

address: Rm. 539, 5F., No.1, Sec. 1, Ren’ai Rd.

country: Taiwan

institute: National Taiwan University

summary: Abberant expression and protein localization of ESM1 were found in prostate cancer. The high expression of ESM1 is associated with prostate cancer stemness and progression. Thus, ESM1 is clinically relevant to poor overall survival and metastasis. However, the molecular mechanisms by which ESM1 contribute to prostate cancer is not yet understood. To discover the role of ESM1 mislocalization in prostate cancer, RNA-seq analysis was performed on 22Rv1 cells overexpressing with different ESM1. Our study demonstrate that nuclear ESM1 may support prostate cancer stemness by interacting with the ARM domain of β-catenin to stabilize β-catenin-Tcf4 complex and facilitate the transactivation of Wnt/β-catenin signaling targets. Our results establish the significance of ESM1 in driving metastasis in prostate cancer by coordinating the Wnt/β-catenin pathway, with implication for its potential use as a diagnostic or prognostic biomarker and as a candidate therapeutic target in prostate cancer.

overall_design: RNA-seq of ESM1-overexpressing prostate cancer cells (22Rv1). We have two vector groups which are different controls to overexpression group. Vector-1 is the control for ESM1 group while Vector-2 is control of ESM1-NLS and ESM1-NES group.

first: Ke-Fan

first: Kuo-Tai

last: Hua


title: RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs

city: Shanghai

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university


title: Next Generation Sequencing of transfected NC K1 cells and transfected si-NEAT1_2 K1 cells

city: Shenyang

first: WEI

last: SUN

state: Liaoning

address: No.155 Nanjing Bei Street

institute: the First Hospital of China Medical University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of transfected NC K1 cells and transfected si-NEAT1_2 K1 cells. The goals of this study are to analysis the different mRNA expression between transfected NC K1 cells and transfected si-NEAT1_2 K1 cells. Quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. We performed mRNA-seq in the NEAT1_2 knockdown group and NC group in the K1 cell line. We found that after knockdown of NEAT1_2, 615 mRNAs were upregulated and 2364 mRNAs were downregulated.

overall_design: K1 cell lines mRNA profiles of transfected NC K1 cells and transfected si-NEAT1_2 K1 cells

first: Wei

last: Sun

first: Yuan

last: Qin

first: Hao

last: Zhang


title: ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis

city: San Francisco

first: Michael

middle: Ryan

last: Corces

state: CA

address: 1650 Owens Street

department: Neurological Disease

institute: Gladstone Institute

summary: The advent of large-scale single-cell chromatin accessibility profiling has accelerated our ability to map gene regulatory landscapes, but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; www.ArchRProject.com) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element to gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility, and multi-omic integration with scRNA-seq. Enabling the analysis of over 1.2 million single cells within 8 hours on a standard Unix laptop, ArchR is a comprehensive analytical suite for end-to-end analysis of single-cell chromatin accessibility data that will accelerate the understanding of gene regulation at the resolution of individual cells.

overall_design: 10x Genomics single-nucleus ATAC-seq and bulk ATAC-seq data obtained from 10 different cell lines. These cell lines include K562, Jurkat, THP1, GM12878, MCF7, MCF10A, HeLa, HT1080, T24, and 293T. In the context of 10x Genomics snATAC-seq, all cell lines were mixed together to enable detection of multiplet droplets based on genotype.

first: Jeff

last: Granja

first: Ryan


title: Conserved Gsx2/Ind homeodomain monomer versus homodimer DNA binding defines regulatory outcomes in the fly and mouse

status: Public on Dec 04 2020

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Identification of Gsx2 genomic binding patterns from E12.5 mouse lateral ganglionic eminence (LGEs).

overall_design: CUT&RUN analysis was performed to identify Gsx2 genomic binding patterns from dissected E12.5 mouse lateral ganglionic eminence (LGEs) using an endogenously tagged Gsx2-2xFLAG mouse line.

first: Brian

last: Gebelein

first: Kenneth

last: Campbell

first: Joseph

last: Salomone

first: Shenyue


title: Fat1 deletion promotes hybrid EMT state with enhanced tumor progression, stemness, and metastasis (exome)

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary: FAT1, a protocadherin, is among the most frequently mutated genes in human cancers. However, the role and the molecular mechanisms by which FAT1 mutations control tumor initiation and progression are poorly understood. Here, using different mouse cancer models including skin squamous cell carcinoma (SCC) and lung tumors we found that Fat1 deletion accelerated tumor initiation and malignant progression and promoted hybrid epithelial to mesenchymal transition (EMT) phenotype. This hybrid EMT state was also found in FAT1 mutated human SCCs. Fat1 deleted skin SCCs presented increased tumor stemness and spontaneous metastasis. Transcriptional and chromatin profiling combined with proteomic analyses and mechanistic studies revealed that FAT1 loss of function activates a CAMK2/CD44/SRC axis that promotes YAP/ZEB1 nuclear translocation and stimulates the mesenchymal state, as well as a CAMK2-EZH2 axis that promotes activation of SOX2, which sustains the epithelial state. This comprehensive analysis also identified drug resistance and vulnerabilities in FAT1 deficient tumors with important implications for cancer therapy. Altogether, our studies revealed that Fat1 loss of function promotes tumor initiation, progression, invasiveness, stemness and metastasis through the induction of a hybrid EMT state.

overall_design: We FACS isolated tumor cells from PDX by excluding CD45+, CD31+ and PDGFRb+ (lin-) non-tumoral cells. The germline DNA was extracted from the corresponding blood sample.

first: Ievgenia

last: Pastushenko

first: Federico

last: Mauri

first: Cédric

last: Blanpain


title: A Strategic Expression Method of MiR-29b and Its Anti-Fibrotic Effect Based on RNA-Sequencing Analysis

city: Huntington

first: Jiang

last: Tian

state: WV

address: 1 John Marshall Dr

department: Biomedical Sciences

institute: Marshall University

summary: Tissue fibrosis is a significant health issue associated with organ dysfunction and failure. Increased deposition of collagen and other extracellular matrix (ECM) proteins in the interstitial area is a major process in the formation of tissue fibrosis. The microRNA-29 (miR-29) family has been demonstrated as anti-fibrotic microRNAs. Our recent work also showed that dysregulation of miR-29 contributes to the formation of cardiac fibrosis in animal models of uremic cardiomyopathy and replenish of miR-29 attenuated cardiac fibrosis in these animals. However, due to the multi-targeting effect, overexpression of miR-29 could result in unexpected side effect. In the current study, we constructed a novel col1a1-miR-29b vector using collagen 1a1 promoter, which can strategically express miR-29b-3p (miR-29b) in cells with high expression of collagen and thus minimize the side effect of excessive miR-29b. Because of the similarity between the col1a1 promoter in the plasmid and the endogenous col1a1 promoter in the cell, pro-fibrotic factors that stimulate endogenous collagen expression will simultaneously activate the col1a1 promoter in the plasmid vector and thus stimulate the anti-fibrotic miR-29b expression. The increased miR-29b will then contra-regulate the collagen synthesis and maintain a dynamic balance of collagen. To evaluate the anti-fibrotic effect of miR-29b overexpression, we performed RNA sequencing in MEF cells transfected with the col1a1-miR-29b vector with or without TGF-β treatment. A CMV-miR-29b vector was used as positive control. The RNA-sequencing data showed that TGF-β treatment upregulated a broad spectrum of extracellular matrix (ECM) genes. In accordance, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using GAGE package showed that the top 5 upregulated pathways after TGF-β treatment were mostly fibrosis-related, including focal adhesion, ECM reaction, and TGF-β signaling pathways, while transfection of miR-29b expression vectors attenuated the activation of these pathways, suggesting their anti-fibrotic effect. However, despite that the expression of miR-29b in CMV-miR-29b transfected cells were about 1000 times higher compared to the col1a1-miR-29b transfected cells, there was no significant difference in the anti-fibrotic effect in these cells. In summary, our work demonstrated that the col1a1-miR-29b vector expresses much lower miR-29b compared to the CMV-miR-29b vector, but it is as effective as the CMV-miR-29b vector in blocking the fibrosis-related signaling pathways in response to TGF-β treatment. Our results also suggest that miR-29b has a moderate effect on each of its targeting genes, and its anti-fibrotic effect may result from perturbation of a broad spectrum of fibrosis-related signaling pathways.

overall_design: Study gene expression after miR29b overexpression and TGF-β treatment in Mouse Embryonic Fibroblasts(MEF)

first: Xiaoming

last: Fan

first: Yingnyu

last: Gao

first: Xiaolu


title: Transcriptomic analysis from lateral ganglionic eminence (LGE) of wild type and Gsx2 germline knock-out mice.

summary: RNA-seq analysis was used to identify genes that are differentially expressed between wild type and Gsx2 null mouse LGEs.

overall_design: Bulk RNA-seq was performed on dissected E12.5 mouse LGE from wild type and Gsx2 null embryos in quadruplicate


title: Fat1 deletion promotes hybrid EMT state with enhanced tumor progression, stemness, and metastasis

overall_design: Refer to individual Series


title: Fat1 deletion promotes hybrid EMT state with enhanced tumor progression, stemness, and metastasis (ATAC-Seq)

overall_design: FACS isolated Epcam+ and Epcam- tumor cells from DMBA/TPA K14Cre;RYFP and K14Cre;Fat1fl/fl;RYFP skin SCCs.


title: Metabolic regulation of telomere silencing by SESAME complex-catalyzed H3T11 phosphorylation

first: Madelaine

last: Gogol

summary: Telomeres are organized into a heterochromatin structure and maintenance of silent  heterochromatin is required for chromosome stability. How telomere heterochromatin is  dynamically regulated in response to stimuli remains unknown. Pyruvate kinase Pyk1 forms a  complex, named SESAME (Serine-responsive SAM-containing Metabolic Enzyme complex) to  regulate gene expression by phosphorylating histone H3T11 (H3pT11). Here, we identified a  novel function of SESAME in regulating telomere heterochromatin structure. SESAME  phosphorylates H3T11 at telomeres, which promotes SIR (silent information regulator) complex  assembly at telomeres and protects Sir2 from degradation by autophagy. Moreover, SESAMEcatalyzed H3pT11 directly represses autophagy-related gene expression to further prevent  autophagy-mediated Sir2 degradation. By promoting H3pT11, serine increases Sir2 protein  levels and enhances telomere silencing. Loss of H3pT11 leads to reduced Sir2 and compromised  telomere silencing during chronological aging. Together, our study provides insights into  dynamic regulation of silent heterochromatin by histone modifications and autophagy in  response to cell metabolism and aging.

overall_design: Examination of H3pt11 in yeast cells. H3 was used a control.

first: Shanshan

last: Li