title: Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses

city: Boston

first: Songlei

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard University

summary: We present Barcoded Oligonucleotides Ligated On RNA Amplified for Multiplexed and parallel In Situ analyses (BOLORAMIS), a reverse transcription-free method for spatially-resolved, targeted, in situ RNA identification of single or multiple targets. BOLORAMIS was demonstrated on a range of cell types and human cerebral organoids. Singleplex experiments to detect coding and non-coding RNAs in human iPSCs showed a stem-cell signature pattern. Specificity of BOLORAMIS was found to be 92% as illustrated by a clear distinction between human and mouse housekeeping genes in a co-culture system, as well as by recapitulation of subcellular localization of lncRNA MALAT1. Sensitivity of BOLORAMIS was quantified by comparing with single molecule FISH experiments and found to be 11%, 12% and 35% for GAPDH, TFRC and POL2RA respectively. To demonstrate BOLORAMIS for multiplexed gene analysis, we targeted 96 mRNAs within a co-culture of iNGN neurons and HMC3 human microglia cells. We used fluorescence in situ sequencing to detect error-robust 8-base barcodes associated with each of these genes. We then used this data to uncover the spatial relationship among cells and transcripts by performing single-cell clustering and gene-gene proximity analyses. We anticipate the BOLORAMIS technology for in situ RNA detection to find applications in basic and translational research.

overall_design: Paired end RNA sequencing of HMC3 cells, PGP1 fibroblasts, and MCF7 cells. Sequencing was performed on Illumina platforms. Reads were aligned to GRCh38 GENCODE release 27. Counts for PGP1 fibroblasts and MCF7 cells were used in the probe number test experiments. Counts for HMC3 were used in the multiplexed RNA detection experiments.


title: long RNA sequencing analysis of TRMT1L KO vs WT brain

status: Public on Feb 08 2021

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

type: Expression profiling by high throughput sequencing

summary: TRMT1L is a paralog of the tRNA m22G-methyltransferase TRMT1 and, similarly to TRMT1, it is involved in cognitive functioning. To functionally dissect the biological role of TRMT1L, here we have employed a combined strategy of LC-MS/MS and next-generation sequencing of both long and short RNAs, to compare the levels and locations of m2,2G in brain tissues from TRMT1L knock-out mice, relative to wild-type.

overall_design: long RNASeq for 2 conditions (KO and WT), with biological triplicates.

first: Eva

middle: M

first: Sonia

last: Cruciani

first: Nicky

last: Jonkhout


title: Critical role of Jmjd3 in the maintenance and function of the thymic medulla for immunological tolerance

city: Shanghai

first: haohao

last: zhang

state: Shanghai

address: 320 Yueyang Road

country: China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Swapping the DNA binding domain of MeCP2 with that of MBD2 to abolish binding to non-CG methlyation results in RTT-like phenotypes in mice [ATAC-seq]

status: Public on Feb 07 2021

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: Mutations in the MECP2 gene cause the profound neurological disorder Rett syndrome. MeCP2 protein is an epigenetic reader that recruits the NCOR1/2 corepressor complexes to methylated cytosine in its canonical CG setting, but also to methylated CA motifs, which are abundant in neurons but rare in other cell types. In this study we set out to test the biological significance of this non-canonical mode of DNA binding. To achieve this, we replaced the endogenous MeCP2 DNA binding domain with that of MBD2, which only binds mCG. Knock-in mice expressing the hybrid “MM2” protein created by this domain-swap displayed severe Rett syndrome-like phenotypes. This indicates that binding to mCA, specifically the mCAC trinucleotide, is critical for normal brain function and it offers a plausible explanation for the delayed onset of Rett syndrome, due to the coincident late accumulation of mCAC and its cognate interpreter, MeCP2. We show that the small subset of genes aberrantly expressed in both Mecp2-null and MM2 mice is strikingly enriched for genes implicated in neurological disorders, highlighting targets with potential relevance to the Rett syndrome phenotype

overall_design: Hypothalamus tissue taken at 6 week of age (same as whole genome bisulphite dataset from Lagger et al., 2017 PLoS Genetics, used for analysis). Mecp2 -/y (KO), Mecp2 MM2/y (MM2) and WT (MM2 littermates), n = 3 per genotype

first: Cholewa-Waclaw

last: Justyna

first: Webb

last: Shaun


title: RNA-seq profiles of brains of Qk-Rosa26-iCKO mice and control mice.

city: Houston

first: Jian

last: Hu

state: Texas

address: 1881 East Rd

department: Department of Cancer Biology, Division of Basic Sciences

country: USA

institute: The University of Texas MD Anderson Cancer Center

summary: This study is to analyze the transcriptomic profiles of Rosa26-CreERT2;QkLoxP/LoxP (Qk-Rosa26-iCKO) mice and littermate controls to determine the differentially expressed genes after Qk deletion.

overall_design: The Rosa26-CreERT2;QkLoxP/LoxP (Qk-Rosa26-iCKO) mice and littermate controls were injected with tamoxifen at postnatal day 1 and their brains were collected at postnatal day 7. Total RNA was extracted by RNeasy Mini Kit and used for sequencing with Illumina HiSeq 2000 Sequencer.

first: Takashi

last: Shingu

first: Xin

last: Zhou


title: Next Generation Sequencing Facilitates Quantitative Analysis of MSMEG_2225 mutant and wild-type strains Transcriptomes in Mycobacterium smegmatis

city: Wu han

first: Xu

last: Hui

address: 1st shizishan

institute: Huazhong Agricultural University

summary: Compare the gene expression difference between MSMEG_2225 knockout strains and wild-type strains by RNA sequencing in Mycobacterium smegmatis. The goal of this study is that detection MSMEG_2225 acts as a transcriptional factor and regulates the target genes expression.

overall_design: Two samples in triplicate are analyzed. The control sample is the wild-type strains in Mycobacterium smegmatis.

first: Zhengguo

last: He

first: Hui

last: Xu


title: RNA-seq analysis of intestinal organoids treated with SGC-CBP30 or vehicle at 36 hours post-irradiation

status: Public on Feb 06 2021

first: Tang

last: peiyuan

address: Xietu road

institute: Fudan university

summary: CBP/P300 inhibitors have been shown to be remarkably effective in mitigating radiation-induced GI syndrome both in ex vivo 3D organoid systemand animal studies. To further figure out the underlying mechanisms of improved radio-resistance by CBP/P300 inhibition, RNA sequencing (RNA-seq) was performed on crypt organoids treated with SGC-CBP30 or vehicle post 8Gy irradiation. RNA-seq analysis of crypt organoids demonstrated that a few radiation-activated pathways are significantly affected by SC treatment, such as E2F targets, G2M checkpoint, Myc targets, and DNA Repair. We speculate that the significant upregulation of genes in DNA repair pathway after CBP/P300 inhibition may help epithelial cells recovery from radiation damage.

overall_design: Total RNA from organoids treated with SGC-CBP30 and vehicle(n=2, respectively) was extracted

first: Peiyuan

last: Tang

first: Guoqiang

last: Hua

first: Xinxin

last: Rao


title: Capture and metabolomic analysis of the human endometrial epithelial organoid secretome

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: We report the isolation and metabolomic profiling of human endometrial epithelial intra-organoid and extra-organoid fluids, derived from organoids, in turn derived from 3 donors, and subjected to a brief hormonal [estradiol (e2)] exposure. rna-sequencing was conducted on the cells from which organoid fluids were sampled.

overall_design: rna sequencing of cells isolated from endometrial organoid cultures at their 12th in vitro passage. total 3 samples are sequenced.

first: THOMAS

middle: E

first: CONSTANTINE

middle: A

last: Simintiras


title: RNA-seq profiles of brains of Qk-Plp-iCKO mice and control mice.

summary: This study is to analyze the transcriptomic profiles of Plp-CreERT2;QkLoxP/LoxP (Qk-Plp-iCKO) mice and littermate controls to determine the differentially expressed genes after Qk deletion.

overall_design: The Plp-CreERT2;QkLoxP/LoxP (Qk-Plp-iCKO) mice and littermate controls were injected with tamoxifen at postnatal day 7 and day 8 and their brains were collected at postnatal day 30. Total RNA was extracted by RNeasy Mini Kit and used for sequencing with Illumina HiSeq 2000 Sequencer.

first: Qiang

last: Zhang


title: Swapping the DNA binding domain of MeCP2 with that of MBD2 to abolish binding to non-CG methlyation results in RTT-like phenotypes in mice [RNA-seq]

first: Shaun

overall_design: Hypothalamus tissue taken at 6-15 weeks of age. Mecp2 -/y (KO), Mecp2 MM2/y (MM2) and WT (MM2 littermates).

first: Justyna

last: Cholewa-Waclaw

first: Kashyap

last: Chhatbar


title: Txnip C247S Mouse Heart Analysis

city: NY

first: Yoshinobu

last: Nakayama

state: NY

address: 160 Convent Ave

institute: City College of New York

summary: Cardiomyocyte specific knock in mouse heart with Txnip Cysteine 247 to Serine Mutation

overall_design: Wild type mouse hearts versus Knock-in mouse hearts, n=3 each

first: Jun

last: Yoshioka


title: Maternal transcriptome in response to expression of a gain-of-function MEK mutant

status: Public on Feb 05 2021

city: Princeton

first: Stanislav

middle: Y

last: Shvartsman

state: NJ

address: Carl Icahn Lab, Washington Road

department: Chemical and Biological Engineering

institute: Princeton University/ Lewis-Sigler Institute for Integrative Genomics

summary: We analyze the transcriptional response of the early Drosophila embryo by comparison between WT-MEK and F53S-MEK via maternal overexpression

overall_design: We generated two fly lines with overexpression constructs inserted in the same genomic location. One line contained wild-type MEK while the other contained a RASopathy MEK mutant. Maternal overexpression was driven by MTD-GAL4 and females were mated to sterile males. One half-hour collections of ~20 embryos were conducted and stored in RNA-later. There are three biological replicates for each experiment.

first: Robert

last: Marmion

first: Joshua

middle: L

last: Wetzel


title: Decoding Cortical Glial Cell Development

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary: Mouse cortical radial glial cells (RGCs) are primary neural stem cells that give rise to cortical oligodendrocytes, astrocytes, and olfactory bulb (OB) GABAergic interneurons in late embryogenesis. There are fundamental gaps in understanding how these diverse cell subtypes are generated. Here, by combining single-cell RNA-Seq with intersectional lineage analyses, we show that beginning at around E16.5, neocortical RGCs start to generate ASCL1+EGFR+ apical multipotent intermediate progenitors (MIPCs), which then differentiate into basal MIPCs that express ASCL1, EGFR, OLIG2, and MKI67. These basal MIPCs undergo several rounds of divisions to generate most of the cortical oligodendrocytes and astrocytes and a subpopulation of OB interneurons. Finally, single-cell ATAC-Seq supported our model for the genetic logic underlying the specification and differentiation of cortical glial cells and OB interneurons. Taken together, this work reveals the process of cortical radial glial cell lineage progression and the developmental origins of cortical astrocytes and oligodendrocytes.

overall_design: ScATAC-seq were performed on FACS sorted GFP+ cells from the E18.5 hGFAP-GFP cortex. ScRNA-seq were performed on FACS sorted RFP+ cells from the P1 IS cortex which were electroporated of pCAG-Cre plasmid at E15.

first: Zhengang

last: Yang


title: The AMBRA1 E3 ligase adaptor regulates Cyclin D protein stability [U2OS cells]

city: Stanford

first: Andrea

middle: Christine

last: Chaikovsky

state: California

address: 265 Campus Drive

institute: Stanford University

summary: The initiation of cell division is a fundamental process that integrates a large number of intra- and extra-cellular inputs. In mammalian cells, D-type cyclins (Cyclin D) couple these inputs to the decision to initiate DNA replication. Increased levels of Cyclin D promote cell cycle progression by activating cyclin-dependent kinases 4 and 6 (CDK4/6). Accordingly, increased levels and activity of Cyclin D and their associated kinases are strongly linked to unchecked cell proliferation and tumor development. Despite this central role of Cyclin D in cell cycle progression, the mechanisms regulating their levels remain incompletely understood. Here we describe AMBRA1 as the main regulator of Cyclin D protein degradation. We first identify AMBRA1 as the top candidate in a genome-wide CRISPR/Cas9 loss-of-function screen investigating the genetic basis of resistance to chemical CDK4/6 inhibition. AMBRA1 loss results in high protein levels of Cyclin D in cells and in mice. AMBRA1 loss further promotes lung cancer development in a mouse model, and low levels of AMBRA1 correlate with worse survival in lung cancer patients. Mechanistically, AMBRA1 acts as a substrate receptor for the Cullin 4 E3 ligase complex to promote ubiquitylation and proteasomal degradation of the three Cyclin D family members. Thus, AMBRA1 regulates Cyclin D protein levels and contributes to the development of cancer as well as the response of cancer cells to CDK4/6 inhibitors.

overall_design: Two determine whether AMBRA1 loss impacts transcriptional programs, control and AMBRA1 knockout U2OS cells were examined by RNA sequencing. The transcriptomes from populations of cells expressing either non-targeting sgRNA or AMBRA1 sgRNAs were sequenced.

middle: C

first: Alexandros

middle: P

last: Drainas

first: Julien

last: Sage


title: Immunotherapy for breast cancer using EpCAM aptamer tumor-targeted gene knockdown efficacy

first: Ying

address: 200 Longwood Avenue, Warren Alpert Building Room 260

department: PCMM

institute: Boston Children's Hospital

summary: New strategies for cancer immunotherapy are needed since most solid tumors do not respond to current approaches. Here, we used EpCAM aptamer-linked small interfering RNAs (aptamer-siRNA chimeras (AsiCs)) to knockdown genes selectively in EpCAM+ tumors with the goal of making cancers more visible to the immune system to improve anti-tumor immunity. Gene targets were chosen whose knockdown was predicted to promote tumor neoantigen expression (Upf2 and Parp1), phagocytosis and antigen presentation (Cd47), or cause tumor cell death (Mcl1).  Using scRNA-seq, we showed that knocking down the four targets simutaeoulsy potently improved the anti-tumor immunity mediated T cells and macrophage/monocytes, demonstrating the immunostimulatory capacity of EpCAM-AsiCs.

overall_design: BALB/c mice were orthotopically implanted with ~105 4T1E cells/mouse. Three days post tumor challenge mice were treated with either EpCAM aptamer or EpCAM-AsiCs cocktail targeting Upf2, Parp1, Cd47 and Mcl1 by s.c. injection every third day. On day 14, CD45+ tumor infiltrating lymphocytes were enriched from tumors (two biological samples/group) for single cell encapsulation, RNA capture and libary construction.

first: Xuemei

last: Xie

first: Judy

last: Lieberman


title: Immunotherapy for breast cancer using EpCAM aptamer tumor-targeted gene knockdown efficacy_UPF2 knockdown in EpCAMhi MDA-MB-231 breast cancer cell lines

address: 200 Longwood Ave

summary:
Knocking down Upf2, which encodes a protein that binds to prematurely terminated mRNAs to activate NMD, has been postulated to induce tumor cell expression of neoantigens to promote tumor recognition by T cells. To investigate whether Upf2 knockdown in breast cancer generates novel mRNA isoforms, we performed bulk RNA sequencing (RNA-seq) to compare an EpCAMhi MDA-MB-231 human breast cancer cell line transfected with noncoding control or UPF2 siRNA for 72 h.
Results: 222 examples of differential exon usage (DEU) within 281 genes were identified. The number and diversity of DEUs suggest that UPF2 knockdown could have caused novel alternative splicing. To test this idea, UPF2 knockdown-related transcriptional diversity was deconvoluted to identify and estimate the abundance of transcript isoforms. 42 genes with potential differential isoform usage (DIU) were identified. Collectively, our data suggest that reducing NMD activity by UPF2 knockdown may induce expression of tumor neoantigens.

overall_design: mRNA profiles of control and Upf2 knocked down EpCAMhi MDA-MB-231 breast cancer cells

first: Pourya

last: Naderi Yeganeh

first: Winston

last: Hide


title: The AMBRA1 E3 ligase adaptor regulates Cyclin D protein stability


title: Integrated requirement of non-specific and sequence-specific DNA binding for transcriptional regulation by Myc (RNA-seq)

city: Milano

first: Mattia

last: Dalsass

state: MI

address: Via Adamello, 16

country: Italy

institute: IEO

summary: Eukaryotic transcription factors recognize specific DNA sequence motifs, but are also endowed with generic, non-specific DNA-binding activity: how these binding modes are integrated to determine select transcriptional outputs remains unresolved. We designed mutants of the MYC transcription factor bearing substitutions in residues that contact either the DNA backbone or specific bases within the consensus motif (E-box), and profiled their DNA-binding and gene-regulatory properties in cultured cells. Our data reveal that non-specific DNA binding is required for MYC to target genomic regulatory regions, and a prerequisite for sequence recognition; beyond merely stabilizing MYC onto select target loci, sequence-specific binding contributes to its precise positioning and – most unexpectedly – to transcriptional activity per se. Hence, seemingly promiscuous genome interaction profiles encompass diverse binding modalities and drive defined, sequence-dependent transcriptional responses.

overall_design: Mapping genomic distribution and transcriptional activity of Myc mutants proteins

first: Marco

last: Filipuzzi


title: Murine hippocampus: Scramble (control) vs Antagomir-134

status: Public on Feb 04 2021

city: Dublin

first: Cristina

last: Reschke

address: 123 St Stephens Green, Dublin 2

country: Ireland

institute: Royal College of Surgeons in Ireland

summary: Transcriptional profiling of mouse ipsilateral hippocampi at 24 hours after intra-amygdala kainic acid-induced status epilepticus followed by either Antagomir-134 or Scramble (control) treatment (intraperitoneal; 30 mg.kg-1)

overall_design: Two-condition experiment, Scramble (control) vs Antagomir-134. Biological replicates: 4 scramble (controls) and 4 antagomir-134. Each biological replicate is the homogeneate of one ipsilateral hippampus of the respective treated mouse.

first: Vamshidhar

middle: R

last: Vangoor

first: Jeroen

last: Pasterkamp

first: Niamh

last: Connolly

first: Catherine

last: Mooney

first: Amaya

last: Sanz Rodriguez


title: Integrated requirement of non-specific and sequence-specific DNA binding for transcriptional regulation by Myc (ChIP-seq)


title: Cell-autonomous retinoic acid receptor signaling alters enteric nervous system development with stage-specific effects in mice

city: Philadelphia

first: Robert

middle: O

last: Heuckeroth

state: PENNSYLVANIA

address: 3615 Civic Center Blvd

department: Research Institute

institute: Children's Hospital of Philadelphia

summary:
Purpose: Determine how blocking retinoic acid receptor (RAR) signaling within enteric neural crest-derived cells (ENCDC) from E11.5 stomach or E13.5 colon alters mRNA abundance. These ENCDC become the enteric nervous system.
Methods: Enteric nervous system precursors were isolated from mouse E11.5 stomach or E13.5 colon using fluorescence activated cell sorting to purify TdTomato or EYFP expressing cells respectively from fetal bowel. The RarαDN allele encodes a potent RAR dominant negative protein that is expressed after CRE-mediated DNA recombination. Tamoxifen-activated CRE-ERT2 was expressed from the Ret locus for E13.5 colon studies and mice were tamoxifen treated at E10.5 prior to cell sorting. The Wnt1Cre allele was employed for E11.5 stomach studies. RNA-SEQ was performed in quadruplicate using Illumina HiSeq 4000. Sequence reads that passed quality filters were aligned to remove repeat sequences and ribosomal RNA reads and then processed using RNA-Seq unified mapper (RUM) package. RUM files were visualized in the TessLA browser for subsequent analyses.
Results: Transcriptional profiling shows RarαDN differentially impacts gene expression in E11.5 stomach and E13.5 colon enteric neural crest-derived cells (ENCDC) that become the enteric nervous system.
Conclusions: Blocking of RAR signaling in ENCDC causes dramatic changes in gene expression during early development in a stage-specific manner.

overall_design: Gene expression profiles for ENCDC that expressed a dominant negative RAR protein were compared to ENCDC that did not express this dominant negative RAR. All ENCDC expressed a fluorescent reporter (EYFP for E13.5 colon and TdTomato for E11.5 stomach ENCDC). Mice used for E13.5 colon studies had been tamoxifen-treated at E10.5.

first: Tao

last: Gao


title: A dual omics approach to evaluate transcriptional and metabolic responses during lipid deprivation in an oyster parasite Perkinsus marinus

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

summary: In this study, we explored the metabolic processes of P. marinus under lipid deprived conditions to elucidate the interchanging flux of lipid and carbohydrate metabolism. Though P. marinus can synthesize their own lipids from available nutrients, they display a slower growth in media not supplemented with lipids as opposed to media with lipids. Under these conditions, using transcriptomics, we surprisingly observed evidence of stimulated lipid degradation through increased transcription of two core β-oxidation pathway enzymes.

overall_design: We sought to examine the transciptional effects of lipid withdrawal from growth media using RNA seq methodologies.

first: Kristin

last: Noell

first: Joseph

last: Pitula


title: A functional taxonomy of tumor suppression in oncogenic KRAS-driven lung cancer

first: Chuan

last: Li

state: CA

address: 327 Campus Drive

department: Biology

summary: Extensive cancer genotyping has identified a large number of putative tumor suppressor genes. However, genome sequencing data alone is insufficient to uncover the importance or the specific functional roles of these genes during carcinogenesis. It is generally unclear whether more frequently mutated tumor suppressors are also more consequential for tumor development. Furthermore, whether tumor suppressors restrict the rate of tumor growth, decrease the probability of incipient tumorigenesis, or limit the emergence of particularly fast-growing clones remains unknown for even the most well-studied tumor suppressors. Here we use a multiplexed autochthonous mouse model of oncogenic Kras-driven human lung adenocarcinoma to quantify the impact of forty-eight known and putative tumor suppressor genes on diverse aspects of carcinogenesis at an unprecedented scale and resolution. We discover many previously understudied functional tumor suppressors that constrain multiple aspects of carcinogenesis in vivo. Inactivation of some genes substantially elevates tumor growth rate, while the inactivation of others increases the probability of tumor initiation and/or the emergence of exceptionally large tumors. While some known and novel functional tumor suppressor genes exert particularly strong effects during specific phases of tumorigenesis, others impact multiple facets of tumor development. These direct and causal analyses uncover an unexpectedly complex functional landscape of tumor suppression. This map of carcinogenesis has implications for understanding cancer evolution, interpreting clinical cancer genome sequencing data, and directing approaches to limit tumor initiation and progression.

overall_design: We use a multiplexed autochthonous mouse model of oncogenic Kras-driven human lung adenocarcinoma to quantify the impact of forty-eight known and putative tumour suppressor genes on diverse aspects of carcinogenesis at an unprecedented scale and resolution.

first: Hongchen

last: Cai

first: Su

middle: K

last: Chew

first: Min

last: Tsai

first: Laura

last: Andrejka

first: Christopher

middle: W

last: Murray

first: Nicholas

last: Hughes

first: Emily

middle: G

last: Shuldiner

first: Rui

last: Tang

first: King

last: Hung

first: Leo

last: Chen

first: Shi

last: Lee

first: Maryam

last: Yousefi

middle: D

last: McFarland

first: Wen-Yang

last: Lin

first: Christian

last: Kunder

first: Le

last: Cong

first: Dmitri

last: Petrov

first: Charles

last: Swanton

first: Monte

last: Winslow


title: RNA seq on tumors from two groups of mice myofibroblast-collagen1 knockout group and control group)

first: Yang

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

summary: RNA sequencing analysis on tumor samples from two groups of mice (1) KPPF;Col1smaKO myfibroblast-collagen1 knockout group and (2) KPPF control group. Collagen1 is the most abundant extracellular matrix protein component in desmoplastic pancreatic tumors. In this study, we establish the transgenic mouse model KPPF;Col1smaKO mice with pancreatic tumors deleted for myofibroblast-derived collagen1. Then we use RNA-seq to examine the global changes of gene expression profile in tumors of KPPF;Col1smaKO mice (as compared to control KPPF mice).

overall_design: A total of 7 RNA samples from tumors from two groups of age-matched mice (1) KPPF;Col1smaKO myfibroblast-collagen1 knockout group, 4 mice; and (2) KPPF control group, 3 mice.

first: Raghu

last: Kalluri


title: Expression data from Sos1 and Sos2-depleted (individally or combined) mouse primary keratinocytes

status: Public on Feb 03 2021

city: SALAMANCA

first: FERNANDO

last: BALTANAS

state: SALAMANCA

address: CAMPUS MIGUEL DE UNAMUNO

institute: CANCER RESEARCH CENTER

summary:
Sos proteins are involved in the maintaining of skin homeostasis and participate in the initiation/progression of chemically-induced skin cancer. However, the precise role of these proteins in specific skin cellular compartments remains undetermined. Here, we examined the role of Sos1 and Sos2 in the overall transcriptional profile of mouse primary keratinocytes in order to unveil the specific functions of these Ras activators in keratinocyte population.
We used microarrays to detail the impact of Sos1/2 depletion (individual or combined) in the transcriptional signature of mouse primary keratinocytes

overall_design: Mouse primary keratinocytes (WT, Sos1KO, Sos2KO and Sos1/2DKO) at actively growing conditions were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of keratinocytes in order to increase the temporal resolution of expression profiles. Subconfluent cells were infected with GFP Adeno-Cre adenovirus for 72 hours and RNA was isolated and hybridated following manufacturer's recommendations.

first: Fernando

last: Baltanas

first: Eugenio

last: Santos


title: Transcriptional profiling of LNGFR.FOXP3-expressing scurfy CD4+ T cells

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We reported transcriptional characterization of LNGFR.FOXP3-expressing scurfy CD4+ T cells from lymph nodes, at day 35 after transfer in scurfy males, where they were able to rescue mice from scurfy autoimmune disease.

overall_design: We describe development and implementation of a full preclinical strategy for transferring FOXP3 into scurfy (Foxp3 deficient) CD4+ T cells. Them, we have established a novel in vivo assay of Treg functionality, based on adoptive transfer of these cells into scurfy mice and a combination of cyclophosphamide conditioning and interleukin-2 treatment. This model highlighted the possibility of rescuing scurfy disease after the latter’s onset. By using this in vivo model and an optimized lentiviral vector expressing human Foxp3 and as a reporter a truncated form of the 5 low-affinity nerve growth factor receptor (LNGFR), we demonstrated that the adoptive transfer of FOXP3-transduced scurfy CD4+ T cells enabled the long-term rescue of scurfy autoimmune disease. The efficiency was similar to that seen with wild-type Treg. After in vivo expansion, the converted CD4FOXP3 cells recapitulated the transcriptomic core signature for Treg.

first: Marianne

last: Delville

first: Juliette

last: Leon

first: Diane

last: Mathis

first: Christophe

last: Benoist

first: Isabelle

last: André

first: Marina

last: Cavazzana

first: Emmanuelle

last: Six


title: Genome-wide transcriptomic data from Streptococcus agalactiae strain CNCTC 10/84 wild type and an allelic exchange isogenic mutant lacking the GntR-class putative transcription factor mrvR

city: Pittsburgh

first: Thomas

middle: Alexander

last: Hooven

state: PA

address: 4401 Penn Ave., Rangos Research Bldg #8128

department: Pediatrics

institute: University of Pittsburgh

summary: As part of a broader study to identify genes that contribute to fitness of the human pathobiont Streptococcus agalacitae (group B Streptococcus), we identified a GntR-class transcription factor, named mrvR, which contributes to bacterial persistence in human amniotic fluid and multipe virulence phenotypes. In order to understand the transcriptome of mrvR, whole-genome transcriptomic analysis was performed with wild type group B Streptococcus and an mrvR deletion mutant at three growth phases.

overall_design: Wild type and mrvR knockout CNCTC 10/84 at early-log, late-log, and stationary growth; 2 independent samples per condition; 12 samples total.

first: Allison

middle: N

last: Dammann

first: Kyle

last: Davidson


title: Transcriptional Expression in Human Periodontal Ligament Cells Subjected to Orthodontic Force: An RNA-Sequencing Study

city: Seoul

first: PI EN

last: CHANG

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Department of Orthodontics

country: South Korea

institute: Yonsei University College of Dentistry

summary:
Purpose : This study was performed to investigate the changes in gene expression in periodontal ligament (PDL) cells following mechanical stimulus through RNA sequencing.
Method : Premolars extracted for orthodontic treatment were used. To stimulate the PDL cells, an orthodontic force of 100× g was applied to the premolar (experimental group; n = 11), whereas the tooth on the other side was left untreated (control group; n = 11). After the PDL cells were isolated from the extracted teeth, gene set enrichment analysis (GSEA), differentially expressed gene (DEG) analysis, and real-time PCR were performed to compare the two groups.
Result : GSEA demonstrated that gene sets related to the cell cycle pathway were upregulated in PDL. Thirteen upregulated and twenty downregulated genes were found through DEG analysis. Real-time PCR results confirmed that five upregulated genes (CC2D1B, CPNE3, OPHN1, TANGO2, and UAP-1) and six downregulated genes (MYOM2, PPM1F, PCDP1, ATP2A1, GPR171, and RP1-34H18.1-1) were consistent with RNA sequencing results.
Conclusion : Two upregulated genes, CPNE3 and OPHN1, and one downregulated gene, PPM1F, play an important role in PDL regeneration in humans when orthodontic force is applied.

overall_design: Examination of the gene expression between orthodontic force and no force stimulation in huMAN premolar PDL

first: Kyunam

last: Kim

first: Hee

last: Kang

first: Jong

middle: I

last: Yook

first: Hyung-Seog

last: Yu

first: Euiseong

first: Jung-Yul

last: Cha

first: Yoon

middle: J

last: Choi


title: Integrated requirement of non-specific and sequence-specific DNA binding for transcriptional regulation by Myc

first: Mattia

last: Dalsass

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

overall_design: Refer to individual Series


title: Smc5/6 functions with Sgs1-Top3-Rmi1 to complete chromosome replication at natural pause sites

city: Milan

first: Dana

last: Branzei

address: Via Adamello 16

institute: IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation

type: Genome binding/occupancy profiling by genome tiling array

summary: Smc5/6 is essential for genome structural integrity by yet unknown mechanisms. Here we find that Smc5/6 co-localizes with the DNA crossed-strand processing complex Sgs1-Top3-Rmi1 (STR) at genomic regions known as natural pausing sites (NPSs) where it facilitates Top3 retention. Individual depletions of STR subunits and Smc5/6 cause similar accumulation of joint molecules (JMs) composed of reversed forks, double Holliday Junctions and hemicatenanes, indicative of Smc5/6 regulating Sgs1 and Top3 DNA processing activities. We isolate an intra-allelic suppressor of smc6-56 proficient in Top3 retention but affected in pathways that act complementarily with Sgs1 and Top3 to resolve JMs arising at replication termination. Upon replication stress, the smc6-56 suppressor requires STR and Mus81-Mms4 functions for recovery, but not Srs2 and Mph1 helicases that prevent maturation of recombination intermediates. Thus, Smc5/6 functions jointly with Top3 and STR to mediate replication completion and influences the function of other DNA crossed-strand processing enzymes at NPSs.

overall_design: Protein binding profiles by ChIP-on-chip analysis were generated as described in (Bermejo et al., 2009). Labeled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

first: Sumedha

last: Agashe

first: Chinnu

last: Joseph

first: Teresa

last: Reyes

first: Demis

last: Menolfi

first: Michele

last: Giannattasio

first: Anja

last: Waizenegger

first: Barnabas

last: Szakal


title: The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics (ChIP-seq dataset)

city: Geneva 4

first: Patrick

last: Viollier

address: Rue Michel Servet 1

department: Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva UNIGE

summary: The regulatory roles of proteins associating with DNA-dependent RNA polymerase (RNAP) during transcription elongation are poorly characterized in bacteria. A forward genetic selection for Caulobacter crescentus cell cycle mutants revealed the uncharacterized DUF1013 protein (TrcR, transcriptional cell cycle regulator). TrcR associates with promoters and coding sequences (CDSs) and tracks with active RNAP. Loss of TrcR causes a cell division cycle and growth defect and an insufficiency in the essential cell cycle regulator CtrA. TrcR also protects cells from the quinolone antibiotic nalidixic acid that induces a multi-drug efflux pump and from the RNAP inhibitor rifampicin (Rif) that prevents transcription elongation. TrcR interacts biochemically and genetically with RNAP and no longer associates with chromatin when RNAP is inhibited with Rif. We show that these TrcR functions and its RNAP-dependent chromatin recruitment are conserved in symbiotic Sinorhizobium sp. and pathogenic Brucella sp., indicating that TrcR represents a new antibiotic target.

sample_organism:
Caulobacter vibrioides NA1000
Sinorhizobium meliloti 2011

overall_design: Examination of TrcR, RpoD and RNAP holoenzyme whole genome binding/occupancy (ChIP-Seq) in WT Caulobacter crescentus and mutants in PYE and following Rifampicin and Nalidixic Acid treatments and TrcR whole genome occupancy/binding in WT Sinorhizobium meliloti before and after Rifampicin treatment.

first: Marie

last: DELABY

first: Lydia

middle: M

last: VARESIO

first: Laurence

last: DEGEORGES

first: Sean

last: CROSSON

middle: H

last: VIOLLIER


title: Reduced Nucleoprotein availability impairs negative-sense RNA virus replication and promotes host recognition

status: Public on Feb 02 2021

city: New York

first: Daniel

last: Blanco Melo

address: One Gustave L. Levy Place, Box 1124

department: Microbiology

institute: Icahn School of Medicine at Mount Sina

summary: Negative-sense RNA viruses (NSVs) rely on prepackaged viral RNA-dependent RNA polymerases (RdRp) to replicate and transcribe their viral genomes. Their replication machinery consists of an RdRp bound to viral RNA which is wound around a nucleoprotein (NP) scaffold, forming a viral ribonucleoprotein complex. NSV NP is known to regulate transcription and replication of genomic RNA, however its role in maintaining and protecting the viral genetic material is unknown. Here, we exploited host microRNA expression to target NP of influenza A virus and Sendai virus to ascertain how this would impact genomic levels and the host response to infection. We find that in addition to inducing a drastic decrease in genome replication, the antiviral host response in the absence of NP is dramatically enhanced. Additionally, our data shows that insufficient levels of NP prevent the replication machinery of these NSVs to process full-length genomes, resulting in aberrant replication products which form pathogen-associated molecular patterns in the process. These dynamics facilitate immune recognition by cellular pattern recognition receptors leading to a strong host antiviral response. Moreover, we observe that the consequences of limiting NP levels are universal amongst NSVs including Ebola virus, Lassa virus and Measles virus. Overall, these results provide new insights into viral genome replication of negative-sense RNA viruses and highlight novel avenues towards developing effective antiviral strategies, adjuvants, and/or live-attenuated vaccines.

overall_design: Independent biological duplicates of Lung adenocarcinoma-derived cell lines (A549) were mock treated or infected with wild-type IAV (A/Puerto Rico/8/1934 (H1N1)), SeV (Fushimi), or recombinant IAV and SeV containing a microRNA cassette targeting their correspondant NP/N mRNAs. Additionally, Independent biological triplicates of Lung adenocarcinoma-derived cell lines (A549) transduced with a vector expressing human ACE2, were transfected with siRNAs targeting the SARS-CoV-2 N mRNAs (or a scramble control) and infected with SARS-CoV-2 (USA-WA1/2020).

first: Benjamin

last: tenOever

last: Blanco-Melo


title: PPARγ is essential for the development of erythroblastic island macrophages and red pulp macrophages

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

institute: ETH Zürich

summary: Macrophages in the bone marrow erythroblastic island (EIM) and splenic red pulp (RPM) are required for terminal erythropoiesis and removal of aged erythrocytes, respectively. This manuscript shows that EIM and RPM development require both PPARg and Spi-C.

overall_design: Analysis of the few remaining Pparg-deficient RPM-like and EIM-like cells

first: Katarzyna

last: Okreglicka

first: Irina

last: Iten

first: Lea

last: Pohlmeier

first: Lucas

last: Onder

first: Qian

last: Feng

first: Michael

last: Kurrer

first: Burkhard

last: Ludewig

first: Peter

last: Nielsen

first: Christoph

last: Schneider


title: Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules [RNA-seq]

city: Bethesda

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Angiotensin-Converting Enzyme 2 (ACE2) binds SARS-CoV-2 spike protein and facilitates viral entry into the cell. ACE2 is expressed in the kidney and renal injury strongly impacts COVID-19 prognosis. In addition, a short, interferon-inducible isoform of ACE2, dACE2 was recently identified. Change in ACE2 expression has already been linked to several human nephropathies. However, these changes were not analyzed in context of dACE2 and regulation of ACE2 expression in the kidney remains unclear. Human primary Renal Proximal Tubule cells were used for all experiments. ChIP-seq analysis of histone modifications (H3K27ac, H3K4me3, K3K4me1), RNA polymerase loading and DNAse hypersensitive sites (DHS) were used to identify gene regulatory elements in the ACE2 locus. qRT-PCR was used to assess mRNA expression of ACE2, dACE2, TMPRSS2 and STAT1. RNA-seq was used to identify changes in global gene expression after cytokine treatment. Putative regulatory elements controlling dACE2 expression were identified using ChIP-seq profiles and RNA-seq mapping. qRT-PCR differentiating between ACE2 and dACE2 revealed that only dACE2 is interferon inducible. dACE2 mRNA was upregulated 300- and 600-fold by IFNα and IFNβ, respectively, while full length ACE2 was unchanged. Interferon stimulation also resulted in elevated STAT1 expression. JAK inhibitor ruxolitinib ablated both STAT1 and dACE2 expression after interferon treatment. RNA-seq analysis revealed approximately 1200 genes induced by IFNβ, largely innate immune response-related. We showed that human primary proximal tubules express ACE2 and its interferon-inducible short isoform, dACE2, from an intronic promoter. We also deliver new datasets identifying cytokine response genes in proximal tubule cells.

overall_design: RNA-seq was used to characterize ACE2 locus and gene expression profiles in cytokine stimulation.

first: Hye

first: Jakub

last: Jankowski


title: IL-6 promotes MYC-induced B cell lymphomagenesis independent of STAT3

city: Stony Brook

first: Jinyu

last: Li

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

summary: The inflammatory cytokine IL-6 is known to play a causal role in the promotion of cancer, although the underlying mechanisms remain to be completely understood. Interplay between endogenous and environmental cues determines the fate of cancer development. The Eμ-myc transgenic mouse expresses elevated levels of c-Myc in the B cell lineage and develops B cell lymphomas with associated mutations in p53 or other genes linked to apoptosis. We generated Eμ-myc mice that either lacked the IL-6 gene, or lacked the STAT3 gene specifically in B cells to determine the role of the IL-6/JAK/STAT3 pathway in tumor development. Using the Eμ-myc lymphoma mouse model, we demonstrate that IL-6 is a critical tumor promoter during early stages of B cell lymphomagenesis. IL-6 is shown to inhibit the expression of tumor suppressors, notably BIM and PTEN, thereby advancing MYC-driven B cell tumorigenesis. Several miRNAs known to target BIM and PTEN are upregulated by IL-6 and likely lead to the stable suppression of pro-apoptotic pathways early during the tumorigenic process. STAT3, a classical downstream effector of IL-6, appears dispensable for Eμ-myc driven lymphomagenesis. We conclude that the growth-promoting and anti-apoptotic mechanisms activated by IL-6 are critically involved in Eμ-myc driven tumor initiation and progression, but the B cell intrinsic expression of STAT3 is not required.

overall_design: B cells were isolated from bone marrow of 1 month old C57Bl/6 mice with genotype IL6+/+, IL6-/-, IL6+/+;EuMyc transgene, or IL6+/+; EuMyc transgene. Samples were pools from 3-5 mice and RNA was isolated by miRNeasy from Qiagen and analyzed by the Stony Brook University Affymetrix core facility. The Affymetrix GeneChip miRNA 4.0 array was used. Hierarchical clustering and pairwaise comparison between B cell populations was performed.

first: Oleksi

last: Petrenko

first: Velasco

last: Cimica

first: Patricio

last: Mena-Taboada

first: Ha

middle: Y

last: Shin

first: Stephen

last: D'Amico

first: Nancy

last: Reich


title: The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics (RNA-seq dataset)

first: Patrick

last: Viollier

overall_design: Examination of gene expression in the DtrcR mutant versus WT C. crescentus cells.

first: Marie

last: DELABY

first: Lydia

last: VARESIO

first: Laurence

last: DEGEORGES

first: Sean

last: CROSSON

last: VIOLLIER


title: Linking the KIR phenotype with STAT3 and TET2 mutations to identify chronic lymphoproliferative disorders of NK cells

city: Rennes

first: Cedric

last: PASTORET

address: 2 rue Henri Le Guilloux

country: France

institute: University Hospital Rennes

summary: We report two transcriptomic profile for Chronic lymphoproliferative disorders of NK cells: STAT3-like and AITL-like

overall_design: FACS-sorted NK cell samples from 7 patients with CLPD-NK (2 STAT3 mutated, 3 TET2 mutated and 2 Wild type)

last: Pastoret

first: Thierry

last: Fest

last: Lamy


title: Urinary single cell profiling captures cellular diversity of the kidney

first: Katalin

last: Susztak

state: Pennsylvania

address: 3400 Civic Center Blvd

department: Department of Medicine

institute: University of Pennsylvania

summary: We performed single cell transcriptomic analysis on 17 urine samples obtained from five subjects at two different occasions using both spot and 24-hour urine collection. In addition, we used a combined spot urine samples of five healthy individuals as a control sample. We sequenced a total of 71,667 cells. After quality control and downstream analysis, we found that epithelial cells were the most common cell types in the urine. We were also able to identify most kidney cell types in the urine, such as podocyte, proximal, and collecting duct (CD), in addition to macrophages, monocytes and lymphocytes.

overall_design: Single cell RNA sequencing for 17 urine samples collected from 5 DKD patients of TRIDENT cohort and a pooled urine sample of five healthy individuals

first: Shatakshee

last: Chatterjee

first: Amin

last: Abedini

first: Yuan

last: Zhu

first: Gabor

last: Halasz

first: Kishor

last: Devalaraja-Narashimha

first: Rojesh

last: Shrestha

first: Jihwan

last: Park

first: Tong

last: Zhou

first: Katie

last: Sullivan

first: Hailong

last: Hu

first: Xin

last: Sheng

first: Hongbo

last: Liu

first: Yi

last: Wei

first: Carine

last: Boustany-Kari

first: Uptal

last: Patel

first: Salem

last: Almaani

first: Matthew

last: Palmer

first: Raymond

last: Townsend

first: Shira

last: Blady

first: Jonathan

last: Hogan

first: Lori

last: Morton


title: The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D

first: Chuan

last: Li

institute: Stanford University

summary: The initiation of cell division integrates a large number of intra- and extracellular inputs. D-type cyclins (hereafter, cyclin D) couple these inputs to the initiation of DNA replication1. Increased levels of cyclin D promote cell division by activating cyclin-dependent kinases 4 and 6 (hereafter, CDK4/6), which in turn phosphorylate and inactivate the retinoblastoma tumour suppressor. Accordingly, increased levels and activity of cyclin D-CDK4/6 complexes are strongly linked to unchecked cell proliferation and cancer2,3. However, the mechanisms that regulate levels of cyclin D are incompletely understood4,5. Here we show that autophagy and beclin 1 regulator 1 (AMBRA1) is the main regulator of the degradation of cyclin D. We identified AMBRA1 in a genome-wide screen to investigate the genetic basis of the response to CDK4/6 inhibition. Loss of AMBRA1 results in high levels of cyclin D in cells and in mice, which promotes proliferation and decreases sensitivity to CDK4/6 inhibition. Mechanistically, AMBRA1 mediates ubiquitylation and proteasomal degradation of cyclin D as a substrate receptor for the cullin 4 E3 ligase complex. Loss of AMBRA1 enhances the growth of lung adenocarcinoma in a mouse model, and low levels of AMBRA1 correlate with worse survival in patients with lung adenocarcinoma. Thus, AMBRA1 regulates cellular levels of cyclin D, and contributes to cancer development and the response of cancer cells to CDK4/6 inhibitors.

overall_design: To examine the effects of Ambra1 loss on lung adenocarcinoma development in in vivo model, we integrated CRISPR/Cas9 genome editing with tumor barcoding and high-throughput barcode sequencing (Tuba-seq), a highly quantitative method that controls for the variability associated with viral infection. In this approach, pooling lenti-sgRNA-Cre vectors that target different genes allows for a direct comparison of each gene’s effect on tumor growth relative to inert controls in a cohort of mice. KPTC and KTC (p53 wild-type) mice were infected with lenti-sgRNA-Cre pools consisting of guides against Ambra1 and three other known lung cancer tumor suppressors (Rb1, Apc, and Rbm10), as well as 5 inert sgRNAs (sgRNAs targeting Neomycin loci or non-targeting). KT mice (lacking Cas9) were also infected with the same lentiviral pool to control for differences in virus titer and/or infectivity. 14-15 weeks after tumor initiation, we harvested the lungs and quantified cell number per tumor by sequencing the integrated barcodes (sgID-BCs).

first: Andrea

last: Chaikovsky

first: Edwin

middle: E

last: Jeng

first: Samuel

last: Loebell

first: Myung

last: Lee

first: Christopher

last: Murray

first: Alexandros

last: Drainas

first: Susan

last: Hipkins

first: Yan

middle: T

last: Shue

first: Edel

last: McCrea

first: J

middle: A

last: Diehl

first: Christina

last: Kong

first: Dmitri

last: Petrov

first: Michael

last: Bassik

first: Monte

last: Winslow

first: Julien

last: Sage


title: The AMBRA1 E3 ligase adaptor regulates Cyclin D protein stability [U937 cells]

middle: Christine

address: 265 Campus Drive

summary: The initiation of cell division is a fundamental process that integrates a large number of intra- and extra-cellular inputs. In mammalian cells, D-type cyclins (Cyclin D) couple these inputs to the decision to initiate DNA replication. Increased levels of Cyclin D promote cell cycle progression by activating cyclin-dependent kinases 4 and 6 (CDK4/6). Accordingly, increased levels and activity of Cyclin D and their associated kinases are strongly linked to unchecked cell proliferation and tumor development. Despite this central role of Cyclin D in cell cycle progression, the mechanisms regulating their levels remain incompletely understood. Here we describe AMBRA1 as the main regulator of Cyclin D protein degradation. We first identify AMBRA1 as the top candidate in a genome-wide CRISPR/Cas9 loss-of-function screen investigating the genetic basis of resistance to chemical CDK4/6 inhibition. AMBRA1 loss results in high protein levels of Cyclin D in cells and in mice. AMBRA1 loss further promotes lung cancer development in a mouse model, and low levels of AMBRA1 correlate with worse survival in lung cancer patients. Mechanistically, AMBRA1 acts as a substrate receptor for the Cullin 4 E3 ligase complex to promote ubiquitylation and proteasomal degradation of the three Cyclin D family members. Thus, AMBRA1 regulates Cyclin D protein levels and contributes to the development of cancer as well as the response of cancer cells to CDK4/6 inhibitors.

overall_design: Two determine whether AMBRA1 loss impacts transcriptional programs, control and AMBRA1 knockout U937 cells were examined by RNA sequencing. The transcriptomes from 2 isogenic clones for each sgRNA (1 non-targeting sgRNA and 2 AMBRA1 sgRNAs) were sequenced.

middle: C

middle: P


title: LncRNA ASTILCS as an important regulator of liver carcinoma cell survival

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

type: Non-coding RNA profiling by high throughput sequencing


title: LncRNA ASTILCS as an important regulator of liver carcinoma cell survival [non-coding RNA-Seq]

summary: Extensive genomic studies have significantly improved our understanding of hepatocellular carcinoma (HCC) biology and have led to the discovery of multiple protein-coding genes driving hepatocarcinogenesis. In addition, these studies have identified thousands of new non-coding transcripts deregulated in HCC, suggesting these transcripts are important for disease progression. Long non-coding RNA is a large class of non-coding transcripts which participate in the regulation of virtually all cellular functions. However, a majority of lncRNAs remain dramatically understudied. Here, we applied a pooled shRNA-based screen to identify lncRNAs essential for HCC cell survival. We validated our screening results using RNAi, CRISPRi, and antisense oligonucleotides. We found a lncRNA, termed ASTILCS, is critical for HCC cell growth and is overexpressed in tumors from HCC patients. We demonstrated that HCC cell death upon ASTILCS knockdown is associated with apoptosis induction and downregulation of a neighboring gene, Protein Tyrosine Kinase 2 (PTK2), a crucial protein for HCC cell survival. Taken together, our study describes a novel regulator of HCC progression providing valuable insight in HCC biology.

overall_design:
RNA-Seq of Huh7 liver cell line RNA
Sample title "H" and "L" are internal nomenclature and do not represent variables used in analysis.

first: Yulia

last: Rybakova

first: John

last: Gonzalez

first: Roman

last: Bogorad

first: Vikash

last: Chauhan

first: Yize

middle: L

last: Dong

first: Victor

last: Kotelianski

first: Daniel

last: Anderson


title: Sexual dimorphism in cancer: insights from transcriptional signatures in kidney tissues and renal cell carcinoma

status: Public on Feb 20 2021

city: Lyon

first: Jean-Noel

last: Hubert

address: 150 cours Albert Thomas

department: Genetics

institute: International Agency For Research on Cancer

type:
Expression profiling by array
Third-party reanalysis

summary:
We have characterized genome-wide expression and regulatory networks of 609 renal tumors and 256 non-tumor renal tissues using the Illumina HumanHT-12 v4 Expression BeadChips.
Data show remarkable sexual dimorphism at transcriptional level including sex-specific signatures associated with RCC progression and survival.

overall_design:
Total RNA obtained from frozen RCC tumour and/or adjacent non-tumour renal tissue.
Note that 202 samples (from 101 patients) analyzed were already submitted (see PMID: 23526956 and GSE40435).

first: Ruhina

middle: S

last: Laskar

first: Jean-Noël

first: Estelle

last: Chanudet


title: RNA-seq analysis of NIL-GAF1 and NIL-gaf1 grains of 15 DAF at filling stage

city: Shanghai

first: Ma

last: Bin

address: Fenglin 300 Road, Shanghai, China

institute: National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences

summary: Favorable grain filling ability is crucial for seed development and plant yield1, with less fertilizer applying is the most urgent goals to meet the growing demands of green and safe food. However, the balance mechanism between grain filling and nutrient elements is still unclear so far. Here, we describe a gene GAF1, specially expressed in endosperm aleurone layer, encoding a phosphate transporter, positively controls rice grain filling and seed development and also contributes to phosphate balance was mapped in our study. To study the regulation pattern of GAF1, we performed the RNA-seq analysis of NIL-GAF1 and NIL-gaf1 at middle grain filling stage in seeds. The data shows that many pathways related to starch and sugar metabolism were enriched, and many starch synthesis related genes and phosphate response genes were up-regulated or down-regulated. These data further support that seed specific expressed GAF1 plays a key role in regulating both phosphate homeostasis and seed development. More importantly, overexpression of GAF1 can significantly improve grain filling and thus yield enhanced plant production in field.

overall_design: mRNA profiles of NILs filling seeds (15DAF)  were sequenced

first: Bin

last: Ma


title: The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics

first: Patrick

last: Viollier

platform_organism:
Caulobacter vibrioides NA1000
Sinorhizobium meliloti 2011


title: LncRNA ASTILCS as an important regulator of liver carcinoma cell survival [shRNA cassette seq]

overall_design:
shRNA cassette seq of Huh7 liver cell line RNA
Input library - The input pooled shRNA plasmid library before virus production consisting of 7873 shRNA vectors allowing to do knockdown of the 1618 lncRNAs based on RNAi.
Selected - The shRNA plasmid library packaged in lentivirus and applied on Huh7 cells. Two days after exposure, infected cells were selected for four days on puromycin and then maintained for four weeks under selection followed by DNA isolation.

middle: G


title: N6-methyladenosine Modification of lncRNA Pvt1 Governs Epidermal Stemness

status: Public on Feb 01 2021

city: Chicago

first: Bryan

last: Harada

state: IL

address: 929 E 57th St

department: Chemistry

institute: University of Chicago

type: Methylation profiling by high throughput sequencing

summary: Dynamic chemical modifications of RNA represent novel and fundamental mechanisms that regulate stemness and tissue homeostasis. Rejuvenation and wound repair of mammalian skin are sustained by epidermal progenitor cells, which are localized within the basal layer of the skin epidermis. N6-methyladenosine (m6A) is one of the most abundant modifications found in eukaryotic mRNA and lncRNA (long non-coding RNA). In this report, we survey changes of m6A RNA methylomes upon epidermal differentiation, and identify Pvt1, a lncRNA whose m6A modification is critically involved in sustaining stemness of epidermal progenitor cells. With genome-editing and a mouse genetics approach, we show that ablation of m6A methyltransferase or Pvt1 impairs the self-renewal and wound healing capability of skin. Mechanistically, methylation of Pvt1 transcripts enhances its interaction with MYC and stabilizes the MYC protein in epidermal progenitor cells. Our study presents a global view of epitranscriptomic dynamics that occur during epidermal differentiation and identifies the m6A modification of Pvt1 as a key signaling event involved in skin tissue homeostasis and wound repair.

overall_design: In order to uncover how changes in the RNA methylomes regulate self-renewal and differentiation of epidermal progenitor cells, we performed m6A-sequencing and RNA-sequencing of polyadenylated RNAs isolated from undifferentiated and differentiated cells

first: Jimmy

last: Lee

first: Chuan

last: He

first: Xiaoyang

last: Wu


title: TMEFF2 isoform detection in LNCaP prostate cancer cells

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

summary: Deep sequencing was performed in LNCaP cells

overall_design: Analysis of deep sequencing data from LNCaP prostate cancer cells enabled the identification of low expressed TMEFF2 isoforms

first: Joshua

last: Corbin

first: M

last: Ruiz-Echevarria


title: SEED-MEDIATED RNA INTERFERENCE OF ANDROGEN SIGNALING AND SURVIVAL NETWORKS INDUCES CELL DEATH IN PROSTATE CANCER CELLS

overall_design: Refer to individual Series


title: Distinct DNA methylation patterns of rheumatoid arthritis peripheral blood and synovial tissue T cells

city: La Jolla

first: Gary

last: Firestein

address: 9500 Gilman Dr

institute: UCSD

summary:
Objective:   To study epigenetic patterns in T lymphocytes that accumulate in rheumatoid arthritis (RA) synovium, we characterized DNA methylation of CD3+ T cells in peripheral blood and synovial tissue in RA and osteoarthritis (OA) patients.
Methods:   Genomic DNA of CD3+ T cells was isolated from RA (n = 8) and OA (n = 5) patients from blood or synovium at the time of arthroplasty using antibodies and magnetic beads. Methylation was measured using Illumina Infinium MethylationEPIC Kit. Differentially methylated loci (DMLs) and genes (DMGs) were identified using Welch’s t-test. Principal component analysis (PCA), hierarchical clustering and pathway analysis were used to determine relationships among groups.
Results:   Comparing DNA methylation of CD3+ T cells between peripheral blood and synovial tissue within each disease, 4615 and 164 DMLs were identified in RA and OA samples respectively, resulting in 832 and 36 DMGs. PCA showed that methylation differences in T cells were greater based on location (blood vs. synovium) than based on disease (RA vs. OA). Differentially modified pathways were significantly enriched between RA blood and synovial T cells, especially in genes related to complement, integrin cell surface interactions and P53 pathway. The limited number of DMGs identified between OA blood and synovial T cells did not conform to biologic pathways.
Conclusion:   The patterns of DNA methylation in RA show location-specific differences related to immune pathways, while methylation differences in OA are limited. The RA joint-specific signatures could be due to selective accumulation of T cell populations or expansion of differentially marked adaptive immune cells. Understanding epigenetic patterns could provide clues to the types of T cells that accumulate in the RA joint and identify potential therapeutic targets.

overall_design: Bisulphite converted DNA from the 22 samples were hybridised to the Illumina Infinium MethylationEPIC Kit chip

first: Rizi

last: Ai

first: David

last: Boyle

first: Wei

last: Wang


title: Gene expression profiling of LNCaP cells following short term shRNA-mediated knockdown of TMEFF2 and growth in presence and absence of dihydrotestosterone

summary: Analysis of RNA expression in LNCaP cells expressing shTMEFF2 to define its trancriptome. We report global changes in the AR-signaling transcriptome in response to shRNA targeted to TMEFF2.

overall_design: LNCaP cells expressing shScramble or shTMEFF2-3. Cells were grown in RPMI containing 10% charcoal-stripped FBS for 24 hours beginning at 24 hours after transductions. Cells were then grown in RPMI containing 10% charcoal-stripped FBS with the addition of 10 nM DHT or .0001% EtOH for 24 hours prior to RNA extraction. Each sample was run in tiplicate.


title: RNA sequencing of Harpegnathos saltator workers and gamergates' non-visual brains, ovaries, and fat bodies at 0, 3, and 10 days after initiation of the dueling tournament

city: Paris

first: NIKOLAOS

last: KONSTANTINIDES

address: 15 rue Helene Brion

institute: Institut Jacques Monod

summary: Ant societies exhibit a division of labor in which a queen is in charge of reproduction while non-reproductive workers maintain the colony. In Harpegnathos saltator, workers retain reproductive ability, inhibited by the queen pheromones. Following the queen loss, the colony undergoes social unrest with an antenna dueling tournament. Most workers quickly abandon the tournament while a few workers continue the dueling for months and become gamergates (pseudoqueens). However, the temporal dynamics of the molecular mechanisms underlining the caste transition and social dominance remain unclear. To identify genetic factors responsible for this transition, we compared transcriptomes of ovary, fat body, and non-visual brains between dueling and non-dueling workers.

overall_design: We sequenced five replicates of the three tissues (fat body, ovary, and non-visual brains) at day 0. We then sequenced five replicates for each tissue at day 3 and day 10 from two groups of ants, prospective workers and prospective gamergates.

first: Nikos

last: Konstantinides

first: Comzit

last: Opachaloemphan

first: Giacomo

last: Mancini

first: Hua

last: Yan

first: Danny

last: Reinberg

first: Claude

last: Desplan


title: A first exon termination checkpoint that preferentially suppresses extragenic transcription [RNASEQ_ZC3H4_C]

city: Milano

first: Viviana

last: Piccolo

state: Milano

department: Department of Experimental Oncology

institute: European Institute of Oncology (IEO)

summary: Wdr82 and Zc3h4 repress transcription at extragenic sites.

overall_design: Transcriptome analysis to measure transcription in cells depleted of Wdr82, Zc3h4or other known termination factors.

first: Liv

last: Austenaa

first: Marta

last: Russo

first: Elena

last: Prosperini

first: Sara

last: Polletti

first: Iros

last: Barozzi

first: Giuseppe

last: Diaferia

first: Gioacchino

last: Natoli


title: Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

summary: The adult liver has exceptional ability to regenerate, but how it sustains normal metabolic activities during regeneration remains unclear. Here, we use partial hepatectomy (PHx) in tandem with single-cell transcriptomics to track cellular transitions and heterogeneities of ~22,000 liver cells through the initiation, progression, and termination phases of mouse liver regeneration. Our results reveal that following PHx, a subset of hepatocytes transiently reactivates an early-postnatal-like gene expression program to proliferate, while a distinct population of metabolically hyperactive cells appears to compensate for any temporary deficits in liver function. Importantly, through combined analysis of gene regulatory networks and cell- cell interaction maps, we find that regenerating hepatocytes redeploy key developmental gene regulons, which are guided by extensive ligand–receptor mediated signaling events between hepatocytes and non-parenchymal cells. Altogether, our study offers a detailed blueprint of the intercellular crosstalk and cellular reprogramming that balances the metabolic and proliferation requirements of a regenerating liver.

overall_design: Mice underwent 2/3rd partial hepatectomy, and after surgery at the set times liver cells were isolated using the 2 step perfusion protocol. And then cells were passed through the 10x processing pipeline.

first: Ullas

middle: V

last: Chembazhi

first: Auinash

last: Kalsotra


title: TLR7/8 Agonist Treatment Induces an Increase in Bone Marrow Resident Dendritic Cells and Hematopoietic Progenitor Expansion and Mobilization

city: Saint Louis

first: Daniel

last: Link

address: 660 S. Euclid Avenue

department: Department of Medicine, Division of Oncology

institute: Washington University School of Medicine

summary: Treatment with the TLR7/8 agonist R848 results in a significant increase in classic dendritic cells (DCs) in the bone marrow, but a decrease in common dendritic cell progenitors and pre-DCs. Phenotypic analysis of DCs showed that R848 treatment is associated with altered expression of certain chemokines, activation markers, and migratory receptors.

overall_design: Wildtype mice were treated with a single dose of the TLR7/8 agonist R848 and then dendritic cells were purified from the bone marrow for RNA sequencing

first: Sidan

last: Li

first: Juo-Chin

last: Yao

first: Justin

last: Lli


title: TMEFF2 and CD95L derived shRNAs promote prostate cancer cell death by targeting the essential androgen receptor pathway

first: Jonathan

last: Wren

summary: A novel mechanism, Death Induced by Survival gene Elimination (DISE), has recently been described as a potential cancer therapy. DISE kills cancer cells through an RNA interference (RNAi) mechanism. We show that expression of certain shRNAs developed to target TMEFF2 promotes prostate cancer (PCa) cell death similar to DISE, and independently of TMEFF2 targeting/expression. In PCa cells, these shRNAs downregulate the androgen receptor (AR) and AR coregulatory genes, an effect that correlates with the presence of short seed matches in their 3’UTRs and which results in global androgen signaling inhibition and cell death. We have termed this mechanism Androgen Network DISE (AN-DISE). shL3, an shRNA to CD95L known to promote DISE in non-PCa cells,  promotes AN-DISE in PCa cells by targeting the AR-signaling pathway.

overall_design: LNCaPcells expressing control shRNA (shScramble), shL3 shRNA (against CD95L) or three different shRNAs to TMEFF2, shTMEFF2-3, shTMEFF2-4 and shTMEFF2-9  were grown in complete RPMI. RNA was extracted 55 hours after transductions and the differences in the transcriptome for each of the shRNAs were evaluated with respect to the shScramble control.

first: Joshua

last: Corbin

first: M

last: Ruiz-Echevarria


title: Engineered Peptide-Functionalized Hydrogels Modulate RNA Transcriptome of Human Nucleus Pulposus Cells In Vitro

city: St Louis

first: Lori

last: Setton

address: 1 Brookings Drive, Campus box 1097

department: Department of Biomedical Engineering

institute: Washington University in St. Louis

summary:
Purpose: Degeneration and aging of the nucleus pulposus (NP) of the intervertebral disc (IVD) is accompanied by alterations in NP cell phenotype marked by reduced cellularity and a shift towards a fibroblast-like state. We have recently demonstrated an ability to manipulate the phenotypic expression of adult degenerative NP cells by culture upon poly(ethylene glycol) (PEG) based hydrogels dually functionalized with integrin- and syndecan-binding laminin-mimetic peptides. In the present study, we seek to understand the transcriptome changes elicited by NP cell interactions with the presented hydrogel system.
Methods: mRNA profiles of NP from 3 human tissue samples were cultured for 4 days on either tissue culture polysyrene (TCPS) or the functionalized gel before RNA was isolated and sequenced, using Illumina NovaSeq. Unaligned reads were trimmed based on quality score (minimum quality level (Phred) = 20, minimum read length = 25) and aligned to the whole human genome (STAR 2.6.1d; hg19) using Partek Flow software. This software suite was also used to calculate the counts/normalized counts of genes and to perform gene specific analysis (GSA), principle component analysis (PCA), hierarchical clustering, and gene set enrichment. Differentially regulated genes were considered to be those with a fold change value (gel/TCPS) that was greater than or equal to 2 or less than or equal to negative 2 and a p-value of less than or equal to 0.05.
Results: The data corroborate and expand on the previous findings by demonstrating that degenerative adult human NP cells cultured upon these gels have upregulations in some markers of NP and notochordal cells but also downregulations of some NP-specific markers and several fibroblastic markers. Furthermore, through gene set enrichment analysis we have shown that pathways related to cell differentiation and notochord morphogenesis were upregulated in the gel condition. Additionally, 13 genes associated with G protein-coupled receptors, many of which are known drug targets, were identified as up or downregulated following periods of culture upon the gel condition.
Conclusions: The data from this RNA-sequencing demonstrate that culture on laminin-mimetic-peptide presenting gels can modulate cell phenotype and promotes upregulation of NP and notochordal markers.

overall_design: Nucleus pulposus (NP) cells from 3 human patients (24F, 55M, 53F; all below passage 4) were used for this study. Cells of each patient were seeded on TCPS or gels and allowed to culture for 4 days with no media changes before cells were harvested and lysed and RNA extracted. RNA sequencing was performed and Partek flow was used to analyze the data.

first: Marcos

middle: N

last: Barcellona

first: Julie

last: Speer

first: Liufang

last: Jing

first: Munish

last: Gupta

first: Jacob

last: Buchowski

first: Michael

last: Kelly


title: RNA-seq analysis of transcriptomic changes in WT and MPHOSPH8 KO MOLM-13 leukemia cells

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

summary: Human cancers including acute myeloid leukemia (AML) hijack epigenetic machinery to drive malignant self-renewal, whereas dysregulated epigenetic states also create selective and targetable liabilities. We performed domain-based CRISPR/Cas9 screens of human chromatin regulators and identified MPHOSPH8 (or MPP8), a component of the HUSH complex and repressor of LINE-1 retrotransposons, as a selective epigenetic dependency of AML cells. While dispensable for normal hematopoiesis, MPP8 loss inhibited AML initiation and maintenance by reactivating LINE-1 retrotransposons. Activation of endogenous or ectopic LINE-1 photocopied MPP8 loss, whereas blocking LINE-1 retrotransposition abrogated MPP8-deficiency-induced phenotypes. Reactivated LINE-1 retrotransposition increased DNA damage, activated cyclin-dependent kinase inhibitor p21 (or CDKN1A), and induced AML differentiation. Enhanced L1 suppression in AML stem cells is associated with therapy resistance and poor prognosis. Hence, while retrotransposons are historically recognized as sources of genetic instability and somatic mutations, we uncover an unexpected role for HUSH/MPP8 in promoting cancer by suppressing genomic transposable elements.

overall_design: RNA-seq was performed to determine the transcriptomic changes in WT and MPHOSPH8 (MPP8) KO MOLM-13 myeloid leukemia cells. MOLM-13 cells with inducible Cas9 were transduced with MPP8-targeting or control sgRNAs.

first: Zhimin

last: Gu

first: Yuxuan

last: Liu


title: Gain of toxic function by long-term SMN overexpression in the sensory-motor circuit.

city: New York

first: Livio

last: Pellizzoni

address: 630 W 168TH STREET, Physician & Surgeons Building Room 5-421, Mail Code #62, Physician & Surgeons Building Room 5-421

department: Pathology and Cell Biology

institute: Columbia University

summary: The neurodegenerative disease spinal muscular atrophy (SMA) is a leading genetic cause of infant death caused by deficiency in the survival motor neuron (SMN) protein. Currently approved SMA treatments aim to restore SMN, but the potential for expression of SMN beyond physiological levels is a unique feature of AAV9-SMN gene therapy. Here, we show that long-term AAV9-mediated SMN overexpression in mouse models induces dose-dependent, late-onset motor dysfunction associated with loss of proprioceptive synapses and neurodegeneration. Mechanistically, aggregation of overexpressed SMN in the cytoplasm of motor circuit neurons sequesters components of small nuclear ribonucleoproteins (snRNPs), leading to splicing dysregulation and widespread transcriptome abnormalities with prominent signatures of neuroinflammation and innate immune response. Thus, long-term SMN overexpression can interfere with its normal activity in RNA regulation and trigger SMA-like pathogenic events through toxic gain of function mechanisms. These unanticipated, SMN-dependent and neuron-specific liabilities of AAV9-SMN warrant further evaluation of the long-term safety of gene therapy in SMA.

overall_design: To determine the effects of AAV9-mediated long-term SMN overexpression on the transcriptome of dorsal root ganglia (DRGs) of wild type mice, we performed transcriptome analysis of DRGs from 300-day old wild type mice that were either uninjected or injected with AAV9-GFP or AAV9-SMN at P1 by deep sequencing in triplicates.

first: Meaghan

last: Van Alstyne

first: Chaolin

last: Zhang

first: Recinos

last: Yocelyn


title: Analysis of MPHOSPH8 chromatin occupancy and MPHOSPH8-dependent gene expression in MOLM-13 leukemia cells

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


title: ChIP-seq analysis of H3K4me3, H3K9me3 and MPHOSPH8 in MOLM-13 cells

overall_design: ChIP-seq was performed to determine the chromatin occupancy of histone marks (H3K4me3 and H3K9me3) and MPHOSPH8 (MPP8) in human myeloid leukemia cell line MOLM-13


title: The PfAP2-G2 transcription factor is a critical regulator of gametocyte maturation

city: University Park

first: Manuel

last: Llinas

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University


title: Inhibition of longevity regulator PAPP-A modulates tissue homeostasis via restraint of mesenchymal stromal cells [Fig. 1]

city: South San Francisco

first: Adam

last: Freund

address: 1170 Veterans Blvd

institute: Calico Life Sciences LLC

summary: Reducing insulin-like growth factor (IGF) signaling is one of the best conserved and characterized mechanisms to extend longevity. Pregnancy associated plasma protein A (PAPP-A) is a secreted metalloprotease that increases IGF availability by cleaving IGF binding proteins. PAPP-A inhibition reduces local IGF signaling, limits the progression of multiple age-related diseases, and extends lifespan, but the mechanisms behind these pleiotropic effects remains unknown. Here, we developed and utilized a PAPP-A neutralizing antibody to discover that adulthood inhibition of this protease reduced collagen and extracellular matrix (ECM) gene expression in multiple tissues in mice. Using bone marrow to explore this effect, we identified mesenchymal stromal cells (MSCs) as the source of PAPP-A and primary responders to PAPP-A inhibition. Short-term treatment with anti-PAPP-A reduced IGF signaling in MSCs, altered MSC expression of collagen/ECM, and decreased MSC number. This affected MSC-dependent functions, decreasing myelopoiesis and osteogenesis. Our data demonstrate that PAPP-A inhibition reduces the activity and number of IGF-dependent mesenchymal progenitor cells and their differentiated progeny, and that this reduction leads to functional changes at the tissue level. MSC-like cells are present in virtually all tissues, and aberrant collagen and ECM production from mesenchymal cells drives aspects of aging and age-related diseases, thus this may be a mechanism by which PAPP-A deficiency enhances lifespan and healthspan.

overall_design: Mice were treated with control or anti-PAPP-A antibody for 17 weeks, then sacrificied and nine tissues were harvested and processed for RNA-seq:  lung, liver, kidney, heart, spleen, bone marrow, gonadal fat, subscapular (subcutaneous) fat, skin

first: Mary

last: Mohrin

first: Justin

first: Jose

last: Zavala-Solorio

first: Sakshi

last: Bhargava

first: John

last: Trumble

first: Alyssa

last: Brito

first: Jonathan

last: Paw

first: Yuliya

last: Kutskova


title: A first exon termination checkpoint that preferentially suppresses extragenic transcription [RNASEQ_HELA_polyA]

first: Viviana

last: Piccolo

address: Via Adamello 16

first: Liv

last: Austenaa

first: Marta

last: Russo

first: Elena

last: Prosperini

first: Sara

last: Polletti

first: Iros

last: Barozzi

first: Giuseppe

last: Diaferia

first: Gioacchino

last: Natoli


title: Inhibition of longevity regulator PAPP-A modulates tissue homeostasis via restraint of mesenchymal stromal cells [Fig. 2]

first: Adam

overall_design: Mice were treated with control or anti-PAPP-A antibody for 4 weeks, then sacrificied and bone marrow was collected.  Bone marrow was sorted to isolate MSCs, HSCs, CLPs, GMPs, MEPs, and Myeloid cells

last: Liu


title: A first exon termination checkpoint that preferentially suppresses extragenic transcription

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A first exon termination checkpoint that preferentially suppresses extragenic transcription [RNASEQ_BMDM_polyA]


title: A first exon termination checkpoint that preferentially suppresses extragenic transcription [ChIP-seq Raw W ZC]


title: "Mirador" on the potential role of miRNAs in synergy of light and heat networks

city: Vasant Kunj

first: Neeti

last: Sanan-Mishra

state: Delhi

address: Aruna Asaf Ali Marg

department: Plant RNAi Biology

country: India

institute: ICGEB

summary: We report the application of small RNA sequencing (Illumina) technology  for the identification of miRNA from panical and flag leaf tissues of pusa basmati rice cultivar grown under normal and heat stress conditions. We used this data to predict and identify known and novel  miRNAs.

overall_design: Examination of 4 different dataset from different rice variety and tissues

first: Deepti

last: Mittal

first: Kavita

last: Goswami

first: Anita

last: Tripathi


title: A first exon termination checkpoint that preferentially suppresses extragenic transcription [RNASEQ_HELA_4sU]


title: Comparative miRomics of salt-tolerant and salt-sensitive rice

summary: We report the application of small RNA sequencing (Illumina) technology  for the identification of miRNA from  root and leaf and flower tissues of pusa basmati  rice cultivar grown under normal and salt stress conditions. We used this data to predict and identify known and novel  miRNAs.

overall_design: Examination of 9 different dataset from different rice variety and tissues


title: Trancriptome profiling of murine Hoxa9-transformed MigA9 cell line treated or not with DB818

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary:
Effect of DB818 treatment on murine Hoxa9-transformed MigA9 cell line
Effect of DB818 treatment on murine Hoxa9-transformed MigA9 cell line

overall_design: Murine Hoxa9-transformed MigA9 cell line treated with 2.5 µM of DB818 vs CTR for 6, 12 or 24H

first: M

last: DAVID-CORDONNIER


title: GDF11 rapidly increases lipid accumulation in liver cancer cells through ALK5-dependent signaling

status: Public on Jan 31 2021

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

institute: IRCCS Casa Sollievo della Sofferenza

summary: Here we used RNA-Seq to unravel the gene expression patterns and related signaling pathways that might be responsible for the observed changes in the lipidome upon GDF11 treatment of hepatocellular carcinoma cells (HCC), HepG2. RNA-seq analysis was performed after 24h of GDF11 (100ng/ml) treatment to investigate its involvement in lipid metabolism. Genes exhibiting absolute fold-change values >2 and p-values <0.05 were considered differentially expressed between contrasts and statistical differences in gene expression were assessed by the ANOVA test. The significance threshold was set to 0.05. Treatment with recombinant GDF11 had an extensive effect on the overall gene expression profile in HepG2 cells and heatmap analysis clearly segregated control and GDF11 treated samples. In total, we identified 3,357 differentially expressed genes, of which 2,422 were over-expressed, and 935 were downregulated. To gain more deep mechanistic insight into the biological processes and pathway associations with these differentially expressed genes, we analyzed our transcriptomic data by STRING pathway unbiased analysis for annotated molecular interactions of selected genes employing Kegg pathways database. The 5 top most significantly influenced canonical pathways/cellular processes were the ones related to TGF-β signaling, extracellular matrix remodeling, focal adhesion, PI3K-AKT signaling, and cytochrome P450-dependent metabolism.

overall_design: Profiling the transcriptome of hepatocelular cell line HepG2 after the treatment with recombinant GDF11 protein.

first: Manlio

last: Vinciguerra


title: Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays

first: Jeremiah

last: Li

address: 430 E 29th St 14th Floor, 14th Floor

institute: Gencove

summary: Low-pass sequencing (sequencing a genome to an average depth less than 1× coverage) combined with genotype imputation has been proposed as an alternative to genotyping arrays for trait mapping and calculation of polygenic scores. To empirically assess the relative performance of these technologies for different applications, we performed low-pass sequencing (targeting coverage levels of 0.5× and 1×) and array genotyping (using the Illumina Global Screening Array (GSA)) on 120 DNA samples derived from African and European-ancestry individuals that are part of the 1000 Genomes Project. We then imputed both the sequencing data and the genotyping array data to the 1000 Genomes Phase 3 haplotype reference panel using a leave- one-out design. We evaluated overall imputation accuracy from these different assays as well as overall power for GWAS from imputed data, and computed polygenic risk scores for coronary artery disease and breast cancer using previously derived weights. We conclude that low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ∼ 0.5× and higher compared to the Illumina GSA.

overall_design: We genotyped 60 EUR and 60 AFR individuals from the 1000 Genomes Phase 3 release using the Illumina GSA v3, each in triplicate.

first: Chase

last: Mazur

first: Tomaz

last: Berisa

first: Joseph

middle: K

last: Pickrell


title: Increased fitness of pancreatic cancer cells Adapted to nutrient deprivation

city: Boston

first: Nada

last: Kalaany

state: MA

address: 3 Blackfan Circle CLS 16067

institute: Boston Children's Hospital

summary: Pancreatic cancer cells adapted to low nutrient conditions share common transcriptional programs that correlate with alterations in open chromatin states.

overall_design: RNA-seq, ATAC-seq and Whole Exome-seq (WES) analyses of pancreatic ductal adenocarcinoma cells adapted to low glucose and low glutamine conditions.

first: Pei-Yun

last: Tsai

first: Min-Sik

last: Lee

first: Unmesh

last: Jadhav

first: Insia

last: Naqvi

first: Shariq

last: Madha

first: Ashley

last: Adler

first: Meeta

last: Mistry

first: Sergey

last: Naumenko

first: Caroline

last: Lewis

first: Daniel

last: Hitchcock

first: Frederick

middle: R

last: Roberts

first: Peter

last: DelNero

first: Thomas

last: Hank

first: Kim

last: Honselmann

first: Vicente

last: Morales Oyarvide

first: Mari

last: Mino-Kenudson

first: Clary

middle: B

last: Clish

first: Ramesh

last: Shivdasani


title: Developing miRNA profiles for decoding salt stress tolerance in Pokkali rice

first: Neeti

last: Sanan-Mishra

summary: We report the application of small RNA sequencing (Illumina) technology  for the identification of miRNA from  root and leaf tissues of pokkali rice cultivar grown under normal and salt stress conditions. We used this data to predict and identify known and novel  miRNAs.

first: Deepti

last: Mittal

first: Kavita

last: Goswami

first: Anita

last: Tripathi


title: Loss of hepatic miR-33 improves metabolic homeostasis and liver function without altering body weight or atherosclerosis

city: New Haven

first: Nathan

last: Price

state: CT

address: 10 Amistad St Rm 320

department: CMED

institute: Yale University

summary: miR-33 is an intronic miRNA within the gene encoding the SREBP2 transcription factor. Like its host gene, miR-33 has been shown to be an important regulator of lipid metabolism. Inhibition of miR-33 has been shown to promote cholesterol efflux in macrophages by targeting the cholesterol transporter ABCA1, thus reducing atherosclerotic plaque burden. Inhibition of miR-33 has also been shown to improve HDL biogenesis in the liver and increase circulating HDL-C levels in both rodents and non-human primates. However, evaluating the extent to which these changes in HDL metabolism contribute to atherogenesis has been hindered by the obesity and metabolic dysfunction observed in whole body miR-33 knockout mice. To determine the impact of hepatic miR-33 deficiency on obesity, metabolic function and atherosclerosis, we have generated a conditional knockout mouse model that lacks miR-33 only in the liver. Characterization of this model demonstrates that loss of miR-33 in the liver does not lead to increased body weight or adiposity. Hepatic miR-33 deficiency actually improves regulation of glucose homeostasis and impedes the development of fibrosis and inflammation. We further demonstrate that hepatic miR-33 deficiency increases circulating HDL-C levels and reverse cholesterol transport capacity in mice fed a chow diet, but these changes are not sufficient to reduce atherosclerotic plaque size under hyperlipidemic conditions. By elucidating the role of miR-33 in the liver, and the impact of hepatic miR-33 deficiency on obesity and atherosclerosis, this work will help inform ongoing efforts to develop novel targeted therapies against cardio-metabolic diseases.

overall_design: Hepatic mRNA profiles from control and liver specific miR-33 knockout mice on standard diet or high fat diet

first: Carlos

last: Fernandez-Hernando


title: DNA Methylation Differences Associated with Social Anxiety Disorder and Early Life Adversity

city: Tuebingen

first: Vanessa

last: Nieratschker

address: Calwerstr. 14

department: Department of Psychiatry and Psychotherapy

country: Germany

institute: University of Tuebingen

summary: Social anxiety disorder (SAD) is a psychiatric disorder characterized by extensive fear in social situations. Multiple genetic and environmental factors are known to contribute to its pathogenesis. One of the main environmental risk factors is early life adversity (ELA). Evidence is emerging that epigenetic mechanisms such as DNA methylation might play an important role in the biological mechanisms underlying SAD and ELA. To investigate the relationship between ELA, DNA methylation, and SAD, we performed an epigenome-wide association study for SAD and ELA examining DNA from whole blood of a cohort of 143 individuals using DNA methylation arrays. We identified two differentially methylated regions (DMRs) associated with SAD located within the genes SLC43A2 and TNXB. As this was the first epigenome-wide association study for SAD, it is worth noting that both genes have previously been associated with panic disorder. Further, we identified two DMRs associated with ELA within the SLC17A3 promoter region and the SIAH3 gene and several DMRs that were associated with the interaction of SAD and ELA. Of these, the regions within C2CD2L and MRPL28 showed the largest difference in DNA methylation. Lastly, we found that two DMRs were associated with both the severity of social anxiety and ELA, however, neither of them was found to mediate the contribution of ELA to SAD later in life. Future studies are needed to replicate our findings in independent cohorts and to investigate the biological pathways underlying these effects.

overall_design: Genome-wide DNA methylation in whole blood from 143 participants was assessed with the HumanMethylationEPIC BeadChip array.

first: Ariane

last: Wiegand

first: Benjamin

last: Kreifelts

first: Matthias

middle: J

last: Munk

first: Nadja

last: Geiselhart

first: Katia

last: Ramadori

first: Julia

last: MacIsaac

first: Andreas

last: Fallgatter

first: Michael

last: Kobor


title: Chromatin binding and regulation by Oct4 and artificially evolved POU (ePOU) in pluripotency reprogramming

city: Guangzhou

first: Chen

last: yanpu

state: guangdong

address: Kaiyuan No. 190, Luogang district

department: drug discovery pipelines

institute: Guangzhou Institute of Biomedicine and Health

summary: We generated Oct4 libraries by randomizing selected amino acids and by recombining domains of paralogous POU family genes. These libraries were subjected to iterative rounds of pooled screens to select variants that enhance pluripotency induction. We identified an artificially evolved POU factor (ePOU) that substantially outperforms wild-type Oct4 in terms of mouse embryonic fibrobast (MEF) reprogramming. To probe whether the ePOU and Oct4 differentially engage the chromatin of reprogramming cells, we performed Assay for Transposase-Accessible Chromatin with highthroughput sequencing (ATACseq) for both factors and different combination. Two cocktails Sox2 (S), Klf4 (K), c-Myc (M) plus Oct4 (O) or ePOU(e) were transduced into OG2 MEF cells which is MEF cells with Oct4 promotor.

overall_design: Accessible Chromatin profiles of reprogramming intermediate cells in ePOU(e) and Oct4(O), Sox2(S), Klf4(K), c-Myc(M) condition at day 2, day 3, and day 6 were generated separately. Single and two factor cocktail compositions of eS, eK, OS, OK, e, O condition at day 3 were generated as well. The somatic cell reprogramming is based on retrovirus system, and sequenced by Illumina Hiseq X Ten.

first: Yuanjie

last: Wei

first: Daisylyn

middle: Y

last: Tan

first: Yanpu

last: Chen

first: Ralf

last: Jauch


title: Large-scale transcriptomics provides insights on the mycorrhizal symbiosis of the Mediterranean orchid Limodorum abortivum in nature

city: Udine

first: Fabio

last: Marroni

address: Via delle Scienze 208

institute: Università di Udine

summary: The study of orchid mycorrhizal interactions is particularly complex because of the peculiar life cycle of these plants and their diverse trophic strategies. Here, large-scale transcriptomics has been applied to investigate gene expression in the mycorrhizal roots of the terrestrial mixotrophic orchid Limodorum abortivum under natural conditions. Our results provide new insights into the mechanisms underlying plant-fungus interactions in orchids and in particular on the plant responses to the mycorrhizal symbiont(s) in adult roots. Comparison with gene expression in mycorrhizal roots of another orchid species, Oeceoclades maculata, suggests that amino acids may represent the main nitrogen source in both protocorms and adult orchids, at least for mixotrophic species. The upregulation, in mycorrhizal L. abortivum roots, of some symbiotic molecular marker genes identified in mycorrhizal roots from other orchids as well as in arbuscular mycorrhiza, suggests a common plant core of genes in endomycorrhizal symbioses. Further efforts will be required to understand whether the specificities of orchid mycorrhiza depend on fine-tuned regulation of these common components, or whether specific additional genes are involved.

overall_design: Examination of three mycorrhized and three non-mycorrhized orchid (Limodorum abortivum) samples.

first: Raffaella

last: Balestrini

first: Sivlia

last: Perotto


title: A first exon termination checkpoint that preferentially suppresses extragenic transcription [ChIPseq_BMDM_POLII]

first: Viviana

last: Piccolo

institute: European Institute of Oncology (IEO)

summary: Wdr82 and Zc3h4 repress transcription at extragenic sites.

overall_design: Transcriptome analysis to measure transcription in cells depleted of Wdr82, Zc3h4or other known termination factors.

first: Liv

middle: M

last: Austenaa

first: Marta

last: Russo

first: Elena

last: Prosperini

first: Sara

last: Polletti

first: Iros

last: Barozzi

first: Giuseppe

last: Diaferia

first: Gioacchino

last: Natoli


title: NOTCH signaling pathway is required for bovine early embryonic development

city: Hangzhou

first: Kun

last: Zhang

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: The NOTCH signaling pathway plays an important role in regulating various biological processes, including cell proliferation, lineage specification and apoptosis. Multiple components of the NOTCH pathway have been identified in mammalian preimplantation embryos. However, the precise role of NOTCH pathway in early embryonic development is poorly understood, especially in domestic animals. Here, we show that key transcripts of the NOTCH pathway exhibit a dynamic pattern throughout early embryonic development with an abundant level before embryonic genome activation in cattle. We also confirmed the presence of active NOTCH1 and RBPJ. By using pharmacological and RNAi tools, we demonstrated that the NOTCH pathway is required for the proper development of bovine early embryos. This functional consequence could be partly attributed to the major transcriptional mediator-RBPJ, whose deficiency also compromised the embryo quality. Indeed, we observed a significant increase of histone H3 serine 10 phosphorylation (pH3S10, a mitosis marker) positive blastomeres in not only NOTCH1 depleted embryos but RBPJ depleted ones. Importantly, RNA-seq analysis revealed that either NOTCH1 or RBPJ depletion triggers a reduction in H1FOO that encodes the oocyte-specific linker histone H1 variant. Interestingly, depleting H1FOO also results in detrimental effects on the developmental competence of early embryos, similar with NOTCH1 inhibition. Overall, our results reveal a crucial role for NOTCH pathway in regulating bovine preimplantation development, likely by controlling cell proliferation and maintaining H1FOO expression.

overall_design: Late morula (D6) were harvested from nonspecific siRNA-injected control and NOTCH1 or RBPJ KD groups (n = 2; 15 embryos/group/replicate). Total RNA extraction was performed with a PicoPure RNA Isolation Kit based on the manufacturer’s manual. Before RNA isolation, equal amounts of GFP and RFP mRNAs (2×106 copies) were added into each group as spike-in controls. mRNA separation was achieved using oligo(dT)25 beads. Sequencing libraries were constructed with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) based on the manufacturer’s instructions.

first: Shuang

last: Li

first: Yanna

last: Dang