title: The NALCN channel regulates metastasis and non-malignant cell dissemination (scRNA-Seq)

city: Cambridge

first: Amir

last: Jassim

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: We identify the Sodium Leak Channel Non-Selective Protein (NALCN) as a key regulator of cancer metastasis and non-malignant cell dissemination. Among 10,022 human cancers, NALCN loss-of-function mutations were enriched in gastric and colorectal cancers. Deletion of Nalcn from gastric, intestinal or pancreatic adenocarcinomas in mice did not alter tumour incidence, but markedly increased the number of circulating tumour cells (CTCs) and metastases. Treatment of these mice with gadolinium–a NALCN channel blocker–similarly increased CTCs and metastases. Deletion of Nalcn from mice that lacked oncogenic mutations and never developed cancer, caused shedding of epithelial cells into the blood at levels equivalent to those seen in tumour-bearing animals. These cells trafficked to distant organs to form normal structures including lung epithelium and kidney glomeruli and tubules. Thus, NALCN regulates cell shedding from solid tissues independent of cancer, divorcing this process from tumourigenesis and unmasking a potential new target for anti-metastatic therapies.

overall_design: Single cell RNAseq from normal tissues (kidney, lung, liver, epididymis, uterus, stomach), tumours (small intestine, gastric), metastases, circulating ZSG+ cells from tumour and non-tumour bearing animals, PBMCs

first: Eric

last: Rahrmann


title: Gene expression profiling of Human C2 and C1 iNKT cell subset

status: Public on Aug 08 2022

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

type: Expression profiling by high throughput sequencing

summary: We identified two novel subsets of iNKT cells in mouse, C2 iNKT cells (the circulating subset) and C1 iNKT cells (the tissue-resident subset). Here, we characterized the cells of these two subsets in human peripheral blood.

overall_design: Two hundred cells of each subset of iNKT cells were sorted from the peripheral blood of human.

first: Guangwei

last: Cui

first: Jianshi

last: Jin

first: Koichi

last: Ikuta


title: Gene expression profiling of C2, C1 and C0 iNKT cell subset

summary: We identified a novel subset of iNKT cells, C2 iNKT cells, that circulate in the periphery. Correspondingly, we characterized the tissue-resident iNKT cell subset, C1 iNKT cells. We also found the precursor of these two subsets of iNKT cells, C0 iNKT cells in thymus. The development and terminal maturation of C2 iNKT cells completely depended on the thymic epithelial IL-15 niche, whereas C1 iNKT cells were regulated also by local IL-15 niches in peripheral tissues. C2 iNKT cells expressed high levels of genes related to cytotoxicity and exhibited more NK cell-like features. Here we characterized the C2 iNKT cells, C1 iNKT cells, and C0 iNKT cells using RNA-seq. We also performed RNA-seq for CD4+ T cells, CD8+ T cells and NK cells as a comparison. To investigate the effect of CD4, we performed the RNA-seq for the CD4+ and CD4- C2 iNKT cells.

overall_design: Two hundred cells of each cell type were sorted from the thymus of mice at 6 weeks


title: The effect of Olaparib or MNA on bone marrow derived macrophage gene expression during induction

status: Public on Aug 05 2022

city: Boston

first: Gerburg

last: Wulf

state: MA

address: 330 Brookine Ave

department: Medicine

country: USA

institute: Beth Israel Deaconess Medical Center

summary: To investigate the effect of olaparib or MNA on macrophage, we treated bone marrow with olaparib or MNA during BMDM induction for 6 days.

overall_design: Induce bone marrow cells with cytokines (IL4&IL10&MCSF) together with olaparib or MNA for 6 days. Compare gene expression between ola and control or MNA and control.

first: Lin

last: Wang

first: Felipe

last: Batalini


title: RNA seq for CD4 T cells in lymph nodes from rhesus macaques

first: Xuan

last: He

address: 3 Blackfan Circle,  E/CLS 1024-B8

institute: BIDMC

summary: We evaluated transcriptional profiling of CD4 T cells from mesenteric and genital lymph nodes following SIV infection by RNA-seq.

overall_design: CD4 T cells from mesenteric LNs (mLNs) and genital LNs (gLNs) in monkeys necropsied on day 0, 3, 7 and 10 following SIV infection were enriched and sorted.

first: Malika

last: Boudries

first: Dan

last: Barouch


title: Membrane potential drives the exit from pluripotency and the ontogeny of cell fate via calcium  and mTOR

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

country: United Kingdom

institute: University of Exeter Medical School

summary: High temporal resoultion profiling of Xenopus tropicalis transcriptome in control and High K+ conditions.

overall_design: Synchronously developing embryos collected, harvesting 10 embryos every 30 minutes starting at  Stage 8 and concluding at Stage 13 in control and high K+ conditions.

first: Emily

last: Sempou

first: Mustafa

last: Khokha


title: Gene expression profiles of islets of Langerhans isolated from 7 weeks wt and Wnt4 conditional knock outs.

status: Public on Aug 04 2022

city: Dresden

first: Anne

last: Grapin-Botton

state: Saxony

address: Pfotenhauerstrasse 108

country: Germany

institute: Max Planck Institute of Molecular Cell Biology and Genetics, Dresde

summary: To check the role of Wnt4 in murine β cells function, we inactivated Wnt4 in β cells from 4-5 weeks using tamoxifen. After 2 weeks tamoxifen treatment, we collected islets from control and mutant mice. We found that Wnt4 knock out islets show significant reduction of oxidation-reduction processes, cysteine and methionine metabolism, fatty acid beta-oxidation and fatty acid biosynthesis, as well as transport mechanisms. On the contrary, ribosome related genes, as well as oxidative stress and apoptosis genes were up-regulated.

overall_design: To inactivate Wnt4 in β cells, Wnt4 fl/fl mice (Wnt4tm1Svo/tm1Svo) were crossed with Pdx1CreER (Tg(Ifp1-cre/Esr1)35.10Dam) mice to generate Pdx1CreER;Wnt4 fl/fl (Wnt4 βKO) and Wnt4 fl/fl littermates, which were used as controls. 3 control and 4 Wnt4βKO mice were used for the analysis . 4-5 week-old control and Wnt4βKO mice were injected with 200 mL Tamoxifen solution (50mg/mL) twice every other day by gavage. These mice were euthanized at 7 weeks islet collection.

middle: G

last: Botton

first: Keiichi

last: Katsumoto


title: Integrated transcriptome and trajectory analysis of cutaneous T-cell identifies putative precancer cell populations

city: New Haven

first: jingjing

last: Ren

state: Connecticut

address: 200 S Frontage Rd, #0618: Hunter Building

institute: Yale University

summary: We used human peripheral blood samples as scRNA seq resource.

overall_design: CD4+ T cells from periphera blood are directly isolated for scRNA and paired TCR seq

first: Jingjing

first: Michael

last: Girardi


title: A neutrophil - B-cell axis impacts tissue damage control during sepsis via Cxcr4

city: Vienna

first: Sylvia

last: Knapp

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

summary: Sepsis is a life-threatening condition characterized by uncontrolled systemic inflammation and coagulation, leading to multi-organ failure. Therapeutic options to prevent sepsis-associated immunopathology remain scarce.   Here, we established a mouse model of long-lasting disease tolerance during severe sepsis, manifested by diminished immunothrombosis and organ damage in spite of a high pathogen burden. We found that, both neutrophils and B cells emerged as key regulators of tissue integrity. Enduring changes in the transcriptional profile of neutrophils, included upregulated Cxcr4 expression in protected, tolerant hosts. Neutrophil Cxcr4 upregulation required the presence of B cells, suggesting that B cells promoted disease tolerance by improving tissue damage control via the suppression of neutrophils’ tissue damaging properties. Finally, therapeutic administration of a Cxcr4 agonist successfully promoted tissue damage control and prevented liver damage during sepsis. Our findings highlight the importance of a critical B-cell/neutrophil interaction during sepsis and establish neutrophil Cxcr4 activation as a potential means to promote disease tolerance during sepsis.

overall_design: 200 neutrophils (single/live/CD45+/CD3-/CD19-/Ly6G+/Ly-6Cint+) were sorted from mouse bone marrow or blood single cell suspensions into cell lysis buffer (0.2% Triton X-100 and 2 U/µl RNase Inhibitor) using a FACSAria Fusion cytometer. Cell lysates were stored at -80°C. Library preparation was performed according to Smart-Seq2, followed by sequencing of pooled libraries on the Illumina HiSeq 2000/2500 (50 bp single‐read setup) at the Biomedical Sequencing Facility of the Medical University of Vienna and CeMM. For analysis, reads were adapter-trimmed (Trimmomatic) and aligned to the mm10 reference genome (STAR aligner). Counting of reads mapping to genes was performed using the summarizeOverlaps function (Bioconductor R package GenomicAlignments). Differentially expressed genes were identified using DESeq2, whereby separate models per organ and condition and formulated for all pairwise comparisons. Filtering was performed by independent hypothesis weighting (ihw R package).

first: Riem

last: Gawish

first: Anna-Dorothea

last: Gorki

first: Martin

last: Watzenboeck

first: Asma

last: Farhat


title: The NALCN channel regulates metastasis and non-malignant cell dissemination

status: Public on Aug 06 2022

first: Amir

last: Jassim

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

overall_design: Refer to individual Series


title: Absolute quantification of single-base m6A methylation in the mammalian transcriptome

city: BeiJing

first: Kai

last: Li

address: Yi He Yuan Street No.5

department: School of Life Science

country: China

institute: Peking University

type: Methylation profiling by high throughput sequencing

summary:
To investigate the m6A methylation in the mammalian transcriptome, we developed a quantitative method, names GLORI, that could detect m6A stoichiometry at single-base resolution.  We then performed GLORI on cells with different treatment, such as stress, knockdown and inhibitor.
We next analysis m6A methyloms of different  celllines and cells under different treatment to investigate the fuctional role of m6A.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparation m6A profiling analysis of RNA-seq data for HEK293T/HeLa/MEF/cells and its KD derivatives (Heatshock, hypoxia, siMETTL3, siMETTL14, siWTAP, siYTHDF2, and inhibition of METTL3).

first: Cong

last: Liu


title: Identification and Characterization of a MAPT-targeting Locked Nucleic Acid Antisense Oligonucleotide Therapeutic for Tauopathies II

city: South San Francisco

first: Amy

last: Easton

state: CA

address: 1 DNA Way

department: Department of Neuroscience

institute: Genentech, Inc

summary: Tau is a microtubule-associated protein (MAPT, tau) implicated in the pathogenesis of Tauopathies, a spectrum of neurodegenerative disorders characterized by accumulation of hyperphosphorylated, aggregated tau.  Because tau pathology can be distinct across diseases, a pragmatic therapeutic approach may be to intervene at the level of the tau transcript, as it makes no assumptions to mechanisms of tau toxicity. Here we performed a large library screen of locked-nucleic acid-modified antisense oligonucleotides (LNA-ASOs), where careful tiling of the MAPT locus resulted in the identification of hot spots for activity in the 3’UTR.  Further modifications to the LNA design resulted in the generation of ASO-001933, which selectively and potently reduces tau in primary cultures from hTau mice, monkey, and human neurons.  ASO-001933 was well-tolerated and produced a robust, long lasting reduction in tau protein in both mouse and cynomolgus monkey brain. In monkey, tau protein reduction was maintained in brain for 20 weeks post-injection and corresponded with tau protein reduction in the CSF.  Our results demonstrate that LNA-ASOs exhibit excellent drug-like properties and sustained efficacy likely translating to infrequent, intrathecal dosing in patients. These data further support the development of LNA-ASOs against tau for the treatment of tauopathies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSC-derived  neurons  (SA001; NIH Registration Number 0085; Cellectis, Sweden) treated with 1uM ASO-001933 or 1uM ASO-NT for 42 days

first: Marianne

middle: L

last: Jensen

first: Congwei

last: Wang

first: Peter

middle: H

last: Hagedorn

first: Yuwen

last: Weed

first: Jere

middle: E

last: Meredith

first: Valerie

last: Guss

first: Kelli

last: Jones

last: Gill

first: Carol

last: Krause

first: Jeffrey

middle: M

last: Brown

first: Lisa

last: Hunihan

first: Alda

last: Fernandes

first: Yifeng

last: Lu

first: Joe

last: Polino

first: Mark

last: Bookbinder

first: Greg

last: Cadelina

first: Yulia

last: Benitex

first: Ramola

last: Sane

first: John

last: Morrison

first: Dieter

last: Drexler

first: Stephen

last: Mercer

first: Charlotte

last: Bon

first: Nikhil

middle: J

last: Pandya

first: Ravi

last: Jagasia

first: Tai-Hsien

middle: O

last: Yang

first: Tania

last: Distler

first: Fiona

last: Grüninger

last: Meldgaard

first: Marco

last: Terrigno

last: Macor

first: Charles

middle: F

last: Albright

first: James

last: Loy

first: Anja

last: Hoeg

first: Richard

last: Olson

first: Angela

last: Cacace


title: Blockade of pentraxin 3/CD44 interaction on attenuation and reversal of lung injury-induced fibrosis

city: Tainan

first: HSIN-YIN

last: LIANG

address: No.1 university Rd

department: Department of Biotechnology and Bioindustry Sciences

country: Taiwan

institute: National Cheng Kung University

summary: Fibrosing interstitial lung disease (fILD) is a fatal fibrotic lung disease with limited therapeutic options and no effective therapeutic strategies to reverse pulmonary fibrosis. Here, we found that PTX3 is upregulated in the lungs of bleomycin-treated mice and fILD patients. Lung injury and fibrosis were significantly attenuated in inducible conditional Ptx3-deficient mice in response to bleomycin treatment. Moreover, we dissected mechanistic insights into PTX3/CD44-dependent fibrotic pathways and effectors in lung myofibroblast activation and collagen production. Importantly, αPTX3i disrupts the interaction of PTX3 and CD44 and effectively attenuated bleomycin-treated lung injury and fibrosis in vivo and myofibroblast activation in vitro. Our study provides new insight into the regulation of PTX3 in pulmonary fibrosis and a potential target for developing future novel therapy for fILDs.

overall_design: C57BL/6 mice were exposed to either saline or bleomycin (2 mg/kg) via intratracheal instillation. Administration of αPTX3i (10 mg/kg) or IgG1κ (10 mg/kg) was performed on days 14 and 21 after bleomycin administration by intraperitoneal injection. At day 28, the lungs were harvested, total RNA was extracted and subjected to RNA-sequencing.

first: Jhih-Ying

last: Chi

first: Yu-Wei

last: Hsiao

first: Hsin-Yin

last: Liang

first: Tang-Hsiu

last: Huang

first: Feng-Wei

last: Chen

first: Chen-Yang

first: Ju-Ming

last: Wang


title: Identification and Characterization of a MAPT-targeting Locked Nucleic Acid Antisense Oligonucleotide Therapeutic for Tauopathies I

first: Amy

last: Easton

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSC-derived glutamatergic neurons (FujiFilm Cellular Dynamics; Cat.R1034) after 72 hrs of treatment with ASO-001933 5uM or vehicle.

first: Marianne

last: Jensen

first: Congwei

first: Peter

last: Hagedorn

first: Yuwen

last: Li

first: Michael

last: Weed

first: Jere

last: Meredith

first: Valerie

last: Guss

first: Kelli

last: Jones

first: Martin

last: Gill

first: Carol

last: Krause

first: Jeffrey

last: Brown

first: Lisa

last: Hunihan

first: Alda

last: Fernandes

first: Yifeng

last: Lu

first: Joe

last: Polino

first: Mark

last: Bookbinder

first: Greg

last: Cadelina

first: Yulia

last: Benitex

first: Ramola

last: Sane

first: John

last: Morrison

first: Dieter

last: Drexler

first: Stephen

last: Mercer

first: Charlotte

last: Bon

first: Nikhil

last: Pandya

first: Ravi

last: Jagasia

first: Tai-Hsien

last: Yang

last: Distler


title: DNMT3A and TET2 restrain mitochondrial DNA-mediated interferon signaling in macrophages

city: La Jolla

first: Isidoro

last: Cobo

address: Dept. of Cellular & Molecular Medicine, GPL210 9500 Gilman Drive, MC 0651

department: Cellular and Molecular Medicine

institute: University California San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Deleterious somatic mutations in DNMT3A or TET2 are associated with clonal expansion of haematopoietic cells and higher risk of cardiovascular disease (CVD). In mice, most studies have indicated an over-activation of the inflammatory program in myeloid cells with reduced DNMT3A or TET2 expression. However, the effect of loss of function of DNMT3A and TET2 in human myeloid cells remains poorly understood. Here, we investigated the roles of DNMT3A and TET2 in normal human monocyte- derived macrophages (mDM), in mDM isolated from individuals with DNMT3A or TET2 mutations and in macrophages isolated from human atherosclerotic plaques. Using a combination of transcriptomic, epigenetic, and imaging assays, we provide evidence that, in addition to distinct roles in regulation of macrophage gene expression, DNMT3A and TET2 share a common role in maintaining mitochondrial DNA integrity by regulating the expression of Transcription Factor A, Mitochondria ( TFAM ). This shared function is dependent on interactions of DNMT3A and TET2 with RBPJ and ZNF143 at regulatory elements in the TFAM gene. Experimental reduction of DNMT3A or TET2 expression in normal human mDMs results in downregulation of TFAM, release of mtDNA into the cytoplasm and consequent activation of a type I interferon response mediated by cGAS. Single-cell RNA-seq analysis of mDMs from individuals with heterozygous loss-of-function mutations in DNMT3A and TET2 revealed a similar transcriptional signature. In addition, single-cell RNA-seq analysis of normal mDM and macrophages residing in human atherosclerotic plaques revealed higher expression of type I IFN signature genes specifically in cells with lower DNMT3A or TET2 expression. The production of IFN as a component of the type I IFN response induces activation of interferon-stimulated genes in neighbouring cells, representing a mechanism by which partial loss of function of DNMT3A or TET2 in a small fraction of cells could exert pathogenic effects in the artery wall. These findings suggest that targeting the type I IFN pathway may have therapeutic value in reducing risk of cardiovascular disease in patients with DNMT3A or TET2 mutations.

overall_design: RNA-Seq, scRNA-Seq, ChIP-Seq and Hi-C

first: Tiffany

middle: N

last: Tanaka

first: Kailash

middle: C

last: Mangalhara

first: Addison

last: Lana

first: Calvin

last: Yeang

first: Claudia

last: Han

first: Johannes

last: Schlachetzki

first: Jean

last: Challcombe

first: Bethany

last: Fixsen

first: Rick

middle: Z

last: Li

first: Mashito

last: Sakai

first: Hannah

last: Fields

first: Michal

last: Mokry

first: Randy

last: Tsai

first: Rafael

last: Bejar

first: Koen

last: Prange

first: Menno

last: de Winther

first: Gerald

middle: S

last: Shadel

first: Christopher

middle: K

last: Glass


title: Inferring gene regulation from stochastic transcriptional variation across single cells at steady-state

first: Jorge Diego

last: Martin Rufino

address: 415 Main Street

institute: Harvard University / Broad Institute of MIT and Harvard / Boston Children's Hospital

summary: Regulatory relationships between transcription factors (TFs) and their target genes lie at the heart of cellular identity and function; however, uncovering these relationships is often labor-intensive and requires perturbations. Here, we propose a principled framework to systematically infer gene regulation for all TFs simultaneously in cells at steady-state by leveraging the intrinsic variation in the transcriptional abundance across single cells. Through modeling and simulations, we characterize how transcriptional bursts of a TF gene are propagated to its target genes, including the expected ranges of time delay and magnitude of maximum covariation. We distinguish these temporal trends from the time-invariant covariation arising from cell states, and we delineate the experimental and technical requirements for leveraging these small but meaningful co-fluctuations in the presence of measurement noise. While current technology does not yet allow adequate power for definitively detecting regulatory relationships for all TFs simultaneously in cells at steady-state, we investigate a small-scale dataset to inform future experimental design. This study supports the potential value of mapping regulatory connections through stochastic variation, and it motivates further technological development to achieve its full potential.

overall_design: For 4-thiouridine (4sU) experiments, cells were plated in 6-well plates ~12h before the start the experiment at a density of 5x 10^5 – 8 x 10^5 cells/mL in 5mL of fresh media. 4sU (Sigma, T4509-25MG) in DMSO was added to culture wells at a final concentration of 100μM for 24h, with renewal every 6-8h. Between the pulse and chase phases, the cells were washed twice to remove any residual traces of 4sU. Subsequently, media with saturating concentrations of uridine (Sigma, U6381) at 10mM was added. Cells were collected at 0h, 2h, 4h, 6h, 8h, and 10h. All the samples from each pulse-chase experiment were processed the same day to minimize batch effects. To control for genes induced by the long exposure to 4sU and to uridine, two control samples with chase only or DMSO only were included.

first: Jorge

middle: D

last: Martin-Rufino

first: Anika

last: Gupta

first: Brian

last: Cleary

first: Sharon

last: Grossman

first: Eric

last: Lander


title: Molecular and behavioral consequences of Ube3a gene overdosage in mice

city: Rotterdam

first: Mattijs

last: Punt

state: Zuid-Holland

address: Dr. Molewaterplein 40

department: Clinical Genetics

country: Netherlands

institute: Erasmus MC

summary:
Here, we investigated the neurodevelopmental impact of Ube3a gene overdosage using bacterial artificial chromosome-based transgenic mouse models (Ube3aOE) that recapitulate the increases in Ube3a copy number most often observed in Dup15q.Here, we investigated the neurodevelopmental impact of Ube3a gene overdosage using bacterial artificial chromosome-based transgenic mouse models (Ube3aOE) that recapitulate the increases in Ube3a copy number most often observed in Dup15q.
Hereto we performed gene expression profiling analysis using data obtained from RNA-seq of cortical and hippocampal tissue from wildtype and Ube3aOE mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cortical and hippocampal brain tissue of 5 wildtype and 5 Ube3aOE mice

first: A

first: Matthew

last: Judson

first: Michael

last: Sidorov

first: Naomi

last: Johnson

first: Sabine

last: Belder

first: Dion

last: den Hertog

first: Courtney

middle: R

last: Davis

first: Maximillian

last: Feygin

first: Mehrnoush

middle: A

last: Jolfaei

first: Wilfred

last: van Ijcken

first: Ype

last: Elgersma

first: Benjamin

last: Philpot


title: The NALCN channel regulates metastasis and non-malignant cell dissemination (Bulk RNA-Seq)

first: Amir

last: Jassim

overall_design: RNA extracted from primary tumours and matched metastases from genetically engineered mouse tumour models

last: Rahrmann


title: Resolution of the curse of dimensionality in single-cell RNA-sequencing data analysis

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Single-cell RNA sequencing (scRNA-seq) can determine gene expression in numerous individual cells simultaneously, promoting progress in the biomedical sciences. However, scRNA-seq data are high-dimensional with substantial technical noise, including dropouts. During analysis of scRNA-seq data, such noise engenders a statistical problem known as the curse of dimensionality (COD). Based on high-dimensional statistics, we herein formulate a noise reduction method, RECODE (resolution of the curse of dimensionality), for high-dimensional data with random sampling noise. We show that RECODE consistently resolves COD in relevant scRNA-seq data with unique molecular identifiers. RECODE does not involve dimension reduction and recovers expression values for all genes, including lowly expressed genes, realizing precise delineation of cell-fate transitions and identification of rare cells with all gene information. Compared to representative imputation methods, RECODE employs different principles and exhibits superior overall performance in cell-clustering, expression-value recovery, and single-cell level analysis. The RECODE algorithm is parameter-free, data-driven, deterministic, and high-speed, and its applicability can be predicted based on the variance normalization performance. We propose RECODE as a powerful strategy for preprocessing noisy high-dimensional data.

overall_design: Single cell transcriptome analysis of human primodial germ cell like cell (PGCLC) induction process using 10x chromium Single Cell Gene expression system.

first: Yusuke

last: Imoto

first: Tomonori

last: Nakamura

first: Emerson

last: Escolar

first: Michio

last: Yoshiwaki

first: Yoji

last: Kojima

first: Yoshitaka

last: Katou

first: Takuya

last: Yamamoto

first: Yasuaki

last: Hiraoka

first: Mitinori

last: Saitou


title: Systemic RNA interference-defective (SID) genes modulate dopaminergic neurodegeneration in C. elegans

city: Tuscaloosa

first: Guy

last: Caldwell

state: AL

address: 300 Hackberry Lane

department: Biological Sciences

institute: The University of Alabama

summary:
To investigate mutations in genes involved in the cellular import of dsRNA neuroprotection, we generated a profile of individual genes affected when dsRNA transport is incapacitated and established a foundation for the systemic analysis of their distinct contributions to neuroprotection.
We then identified a set of previously unreported neuroprotective proteins using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C. elegans in an a-synuclein background with and without the sid-1 mutation, 3 biological replicates.

first: Anthony

last: Gaeta

first: J

middle: B

last: Nourse Jr

first: Karolina

last: Willicott

first: Luke

last: McKay

first: Candice

last: Keogh

first: Kylie

last: Peter

first: Shannon

last: Russell

first: Shusei

last: Hamamichi

first: Laura

last: Berkowitz

first: Kim


title: The transcriptional terminator XRN2 and the RNA binding protein Sam68 link alternative polyadenylation to cell cycle progression in prostate cancer

city: Rome

first: Marco

last: Pieraccioli

address: Largo Francesco Vito 1

country: Italy

institute: Catholic University of the Sacred Heart rome

summary: Alternative cleavage and polyadenylation (APA) of pre-mRNAs yields multiple transcripts differing in their 3' end and its regulation is often aberrant in human cancers, including prostate cancer (PC). In this study, we  have uncovered a novel mechanism of APA regulation which impinges on the functional interaction between the 5'-3' exonuclease XRN2 and the A/U-rich motif RNA binding protein Sam68 in PC cells. XRN2 promotes recruitment of Sam68 to its target transcripts, where it competes with the cleavage and polyadenylation specificity factor (CPSF) for the recognition of the AAUAAA core polyadenylation signal (PAS) motif. In particular, the Sam68/XRN2 complex suppresses the usage of strong canonical PASs at distal ends of genes and, consequently, promotes the usage of suboptimal proximal PASs.

overall_design: We have profiled the global effect of Sam68 and XRN2 on alternative polyadenylation by 3’READS-seq analysis using RNA isolated from LNCaP cells after 48 hours of RNAi, with 2 biological replicates.

first: Cinzia

last: Caggiano

first: Luca

last: Mignini

first: Chuwei

last: Zhong

first: Gabriele

last: Babini

first: Rossano

last: Lattanzio

first: Savino

last: Di Stasi

first: Bin

last: Tian

first: Claudio

last: Sette

first: Pamela

last: Bielli


title: A SlCLV3-SlWUS module regulates auxin and ethylene homeostasis in low light–induced tomato flower abscission

status: Public on Aug 03 2022

city: shenyang

first: lina

last: cheng

address: dongling road NO.120

department: college of Horticulture

institute: shenyang agriculture university

summary: DNA affinity purification sequencing for WUSCHEL in tomato flower abscission zone

overall_design: The DAP genomic DNA (gDNA) library was prepared using the kit from NEBNext® DNA Library Prep Master Mix Set for Illumina

first: Tao

last: Xu

first: Tianlai

last: Li

first: Lina

last: Cheng


title: Altered costimulatory signaling and hypoxia support chromatin landscapes that limit the functional potential of exhausted T cells in cancer [CUT&RUN]

city: Pittsburgh

first: B. Rhodes

last: Ford

state: PA

address: 4401 Penn Ave.

department: Department of Pediatrics

institute: University of Pittsburgh

summary: Increases in terminally exhausted T cells in the tumor are associated with poor responses to immunotherapy, yet the mechanisms that promote progression to terminal exhaustion remain undefined. We profiled the chromatin landscape of subsets of tumor-infiltrating CD8+ T cells using CUT&RUN.  CD8 T cells were sorted from the murine  B16 melanoma tumor using PD1 and Tim3 expression to define four subsets: PD1lo, PD1mid, PD1hi, and PD1hiTim3+. Additional control samples include paired CD44+ cells from the tumor-draining lymph node of tumor bearing mice, and OT-I effector CD8 T cells isolated from Vaccinia-ova infection. We performed CUT&RUN for H3K4me3, H3K27me3, H3K27ac, and H3K9ac, as well as the transcription factors Tox and Batf.

overall_design: Two individual biological replicates of each sorted population (dLN CD8+ CD44+; TIL CD8+ PD1lo; TIL CD8+ PD1mid; TIL CD8+ PD1hi; TIL CD8+ PD1hi Tim3+; OT-I CD8+ effector from d10 Vaccinia-Ova infection) per histone modification mark (H3K4me3; H3K27me3; H3K27ac; H3K9ac) or transcription factor (Tox) profiled, except Batf which has one replicate.

first: B

first: Natalie

last: Rittenhouse

first: Nicole

last: Scharping

first: Paolo

last: Vignali

first: Greg

last: Delgoffe

first: Amanda

last: Poholek


title: An internally normalized approach to comparing RNA levels between samples using nucleoside recoding chemistry

city: West Haven

first: Matthew

last: Simon

address: PO Box 27392

department: Molecular Biophysics and Biochemistry

summary: RNA sequencing allows for transcriptome-wide comparative studies of RNA levels, including gene expression, localization in subcellular compartments, or content of ribonucleoprotein complexes. It is often challenging, however, to separate real biological variation from technical artifacts arising from variable sample preparation, uneven contamination and difficulties normalizing sequencing counts between samples. These challenges are magnified in complex biochemical preparations, such as isolating polysomes to study translation. To address these challenges, we developed TILAC, an approach to compare RNA content between samples with internal controls and normalization. TILAC uses two different metabolic labels (4-thiouridine, s4U, and 6-thioguanisine, s6G) to differentially label RNA from each condition, allowing the samples to be pooled prior to downstream processing. TILAC uses nucleotide-recoding chemistry and sequencing to determine which RNAs are enriched in each sample. TILAC accurately identifies known changes in the transcriptome during RNA polymerase II inhibition and heat shock response. Using TILAC, we discovered a set of transcripts that are enriched in actively-translating ribosome complexes during stress, including MCM2 and DDX5, and verified their translational upregulation. These results demonstrate the power of TILAC to uncover differences between samples revealing new biology.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: RNA isolated from Drosophila S2 cells +/- heat shock and +/- s4U or s6G, and from 293t cells +/- flavopiridol inhibitor and +/- s4U or s6G or +/- sodium arsenite and +/- s4U or s6G. RNA was also isolated from 293t cells +/- sodium arsenite and +/- s4U or s6G whose cell lysate was treated with +/- puromycin. RNA was subjected to oxidative-nucleophilic-aromatic-substitution chemistry. Sequencing libraries were prepared from all RNA or polysome-associated RNA.

first: Meaghan

last: Sullivan

first: Isaac

middle: W

last: Vock

first: Rachel

last: Niederer

first: Lea

last: Kiefer

first: Wendy

middle: V

last: Gilbert


title: transcriptomic data in the spinal cord of Taiwanese type I SMA mice

city: nantong

first: junjie

last: sun

state: jiangsu province

address: 19 Qixiu Road

institute: nantong university

summary: SMA is a neurodegenerative disease of unknown pathogenesis characterized by degeneration of motor neurons in the anterior horn of the spinal cord. Here we performed transcriptome sequencing of the spinal cord of a severe SMA mouse model.

overall_design: Transcriptome sequencing of spinal cords of postnatal day 4 SMA mice (mSmn-/-, hSMN22tg/0), heterozygous mice  (mSmn+/-, hSMN22tg/0) as controls.

first: Junjie

last: Sun

first: Liucheng

last: Wu


title: Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages (ChIP-Seq II)

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago

summary: We report that Hedgehog signaling is a heterochronic pathway that determines the timing of the transition from specified cardiac progenitor to differentiated cardiomyocyte, a function distinct from its previously described roles affecting cellular patterning or proliferation. Hedgehog signaling was required to prevent premature differentiation and disruption of cardiac morphogenesis in vivo and the Hedgehog signaling transcription factor GLI1 was sufficient to delay differentiation in stem cell-derived cardiac progenitors in vitro. GLI1 directly activated a de novo progenitor-specific network in vitro that inhibited the induction of the cardiac differentiation program. The GLI1-driven gene regulatory network is sufficient to induce Hedgehog-naive in vitro cardiac progenitors to adopt an epigenomic state reminiscent of second heart field cardiac progenitors in vivo. A Hh-dependent GLI transcription factor switch functions as a differentiation timer, restricting activity of the progenitor network to the second heart field and permitting cardiomyocyte differentiation in the heart. GLI1 expression is broadly associated with the progenitor state, and its activity also delayed the differentiation of specified neural progenitors in vitro. We posit that Hedgehog signaling functions as a heterochronic regulator that transiently maintains diverse progenitor populations for complex organ development and that may explain diverse Hedgehog signaling-dependent phenomena.

overall_design: Transcriptomic and epigenomic analyses of Hedgehog/GLI dependent-networks in cardiac and neural progenitors

first: Megan

last: Rowton

first: Carlos

last: Perez-Cervantes

first: Sebastian

last: Pott


title: Transcriptional comparison of adult human primary Retinal Pigment Epithelium, human pluripotent stem cell-derived Retinal Pigment Epithelium, and ARPE19 cells

city: New York City

first: Timothy

last: Blenkinsop

address: 1 Gustave L Levy Place

department: Ophthalmology Cell Development and Regenerative Biology, Black Family Stem Cell Institute

institute: Icahn School of Medicine at Mount Sinai

summary: The therapeutic potential of pluripotent stem cells is great as they promise to Q7  usher in a new era of medicine where cells or organs may be prescribed to  replace dysfunctional tissue. At the forefront are efforts in the eye to develop Q8  this technology as it lends itself to in vivo monitoring and sophisticated imaging  modalities. In the retina, retinal pigment epithelium (RPE) is the most promising  replacement cell as it has a single layer, is relatively simple to transplant, and is  associated with dozens of eye diseases. However, after transplantation, they  may transform and cause complications. This transformation may be partially  due to incomplete maturation. With the goal of learning how to mature RPE, we  compared iPSC-RPE with adult primary RPE and the immortalized ARPE-19 line.  We cultured ARPE-19, iPSC-RPE, and adult human RPE for one month,  evaluating morphology, RPE marker staining, and transepithelial electrical  resistance as quality control indicators. We then isolated RNA for bulk RNAsequencing  and DNA for genotyping. We genotyped adult RPE lines for the top  age-related macular degeneration (AMD) and proliferative vitreoretinopathy  (PVR) risk allele polymorphisms. Transcriptome data verified that both adult and  iPSC-RPE exhibit similar RPE gene expression signatures, significantly more  than ARPE-19. In addition, in iPSC-RPE, gene networks relating to epithelial to  mesenchymal transition (EMT), stem cell maintenance, retina development, and  muscle contraction were significantly elevated compared to those of adult RPE.  We compared adult human RPE to iPSC-RPE in a model of EMT and observed an  increased sensitivity of iPSC-RPE to producing contractile aggregates in vitro  which resembles incident reports upon transplantation. P38 inhibition was  capable of inhibiting iPSC-RPE–derived aggregates. In summary, we find  that the transcriptomic signature of iPSC-RPE conveys an immature RPE state  which may be ameliorated by targeting “immature” gene regulatory networks.

overall_design: Comparative gene expression profiling by RNASeq of ahRPE, iPSC-RPE and ARPE19 cells.

first: Elke

last: Markert

first: Holger

last: Klein

first: Stefan

last: Kauschke

first: Remko

last: Bakker

first: Benjamin

last: Strobel

first: Coralie

last: Viollet

first: Ba

last: r Makovoz

first: Werner

last: Rust

first: Heike

last: Neubauer


title: Gene expression analysis after GPR17 silencing in oligodendrocyte precursor cells (OPCs)

city: Milano

first: Davide

last: Marangon

state: MI

address: Via Giuseppe Balzaretti 9

institute: Università degli studi di Milano

summary: GPR17 silencing in OPCs accelerates their differentiation into fully mature oligodendrocytes. We performed a whole microarray profiling to identify altered signaling pathways after GPR17 silencing that are responsible for its effect on oligodendrocyte maturation.

overall_design: Gene expression was measured in OPCs 48h after transfection of GPR17 siRNA (or negative control). 2 independent samples were used for each condition.

last: Lecca

first: Maria

middle: P

last: Abbracchio


title: TLR7 sensing of SARS-CoV-2 and IFN-I response by plasmacytoid dendritic cells leads to the hyperactivation of macrophages.

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: To gain a comprehensive understanding of type I IFN or SARS-CoV-2 activated pDCs priming macrophages in regulating TLR4 meidated gene expression, we treated primary human blood monocytes with 30ng/ml IFNα or the supernatant of SARS-CoV-2 activated pDCs  for 24 h and followed by 2 ng/ml LPS for 3 h. Cells were harvested and performed transcriptomic analysis via RNA-seq. We found that IFNα and supernatant of SARS-CoV-2 activated pDCs had similar effects on priming macrophages to induce massive inflammatory gene expression mediated by LPS.

overall_design: mRNA of human primary monoyctes from 4 healthy donors treated with 30ng/ml IFNα or the supernatant of SARS-CoV-2 activated pDCs  for 24 h and followed by 2 ng/ml LPS for 3 h were used for library preparing and RNA sequencing.

first: Chao

last: Yang

first: David

last: Oliver

first: Franck

last: Barrat


title: Transcriptional regulation of the thymus master regulator Foxn1 [ChIP-seq]

city: Rehovot

first: Jakub

last: Abramson

address: 234 Herzl st.

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

summary: FOXN1 is a transcription factor critical for the development of both thymic epithelial cell (TEC) and hair follicle cell (HFC) compartments. However, mechanisms controlling its expression remain poorly understood. To address this question, we performed thorough analyses of the conservation and chromatin status of the Foxn1 locus in different tissues and states, and identified several putative cis-regulatory regions unique to TEC vs. HFC. Furthermore, experiments using genetically modified mice with specific deletions in the Foxn1 locus and additional bioinformatic analyses helped us identify key regions and transcription factors involved in either positive or negative regulation of Foxn1 in both TEC and HFC. Specifically, we identified SIX1 and FOXN1 itself, as key factors inducing Foxn1 expression in embryonic and neonatal TECs. Together, our data provide important mechanistic insights into the transcriptional regulation of the Foxn1 gene in TEC vs. HFC and highlight the role of FOXN1 in its autoregulation

overall_design: ChIPseq profiles of Six1 and Sox9 binding in sorted thymic epithelial cells from embryonic or adult mice, respectively.

first: Noam

last: Kadouri


title: The Impact of T cell Immunity on Chemotherapy Response in Childhood Acute Lymphoblastic Leukemia

city: Memphis

first: Jun

state: TN

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: Although acute lymphoblastic leukemia (ALL) is highly responsive to chemotherapy, it is unknown how and which host immune factors influence the long-term remission of this cancer. To this end, we systematically evaluated the effects of T cell immunity on ALL chemotherapy outcomes. Using murine BCR-ABL1 ALL model, we showed that loss of total T cells, CD4 cells, or CD8 cells in the host drastically increased leukemia relapse following dasatinib or cytotoxic chemotherapy. Although ABL1 mutations emerged early during dasatinib treatment in both immunocompetent and immunocompromised hosts, T cell immunity was essential for suppressing the outgrowth of drug-resistant leukemia. Bulk and single-cell transcriptome profiling of T cells during therapy pointed to the activation Type I immunity-related cytokine signaling linked to long-term leukemia remission in mice. Consistent with these observations, IFNG and IL12 directly modulated dasatinib anti-leukemia efficacy in vivo. Finally, we evaluated peripheral blood immune cell composition in 102 children with ALL during chemotherapy and observed a significant association of T cell abundance with treatment outcomes. Together, these results suggest that T cell immunity plays pivotal roles in maintaining long-term remission of ALL, highlighting that the interplay between host immunity and drug resistance can be harnessed to improve ALL chemotherapy outcomes.

overall_design: To explore the mechanisms underlying host immune response against ALL, we performed molecular profiling experiments in immunocompetent mice to compare features that distinguish those that did vs. did not relapse after dasatinib therapy. To this end, we collected peripheral blood leukocytes one week after the initiation of dasatinib treatment from all mice, and cryo into liquid nitrogen. At that time, they were all in remission and then continued dasatinib treatment for 4 additional weeks. Mice were retrospectively classified as “cured” or “relapsed” based on their survival status at 100 days post leukemia inoculation, i.e., the “cured group” and the “relapsed group”. After 100 days of the experiment, six mice remained in remission, and six mice relapsed. Cells were thawed from liquid nitrogen, and live cells were collected by BD Biosciences Aria cell sorters. We mixed the peripheral blood leukocyte from three mice as one scRNA-seq sample. Thus, we have two cured and two relapsed samples in total.

first: Yizhen

last: Li

first: Xu


title: Molecular classificaiton of ALL with whole transcriptome sequencing analysis in a Taiwan cohort

first: Gang

last: Wu

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

summary: Purpose: Next-generation sequencing (NGS) has revolutionized accurate molecular classification of leukemia. The goal of this study is to show the value of a sequential approach to classify the leukemia with various data types.

overall_design: Gene expression profiles of pediatric acute lymphoblastic leukemia

first: Yung-Li

first: Chih-Hsiang

last: Yu

first: Sung-Liang

first: Ching-Hon

last: Pui


title: CD55 facilitates immune evasion by Borrelia crocidurae, an agent of relapsing fever

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

institute: Zhejiang University

summary: Effect of CD55 deletion on host response following Borrelia crocidurae infection in mice

overall_design: Examination of the immune responses associated with Borrelia crocidurae, using RNA-seq

first: Gunjan

last: Arora

first: Erol

last: Fikrig


title: Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages (RNA-Seq III)

first: Ivan

last: Moskowitz

first: Megan

last: Rowton

first: Carlos

last: Perez-Cervantes

first: Sebastian

last: Pott


title: A cap 0-dependent mRNA capture method to analyze the yeast transcriptome

city: Warsaw

first: Maria

last: Górna

address: Żwirki i Wigury 101

department: Department of Chemistry

country: Poland

institute: Biological and Chemical Research Centre, University of Warsaw

summary: Analysis of the protein coding transcriptome by the RNA sequencing requires either enrichment of the desired fraction of coding transcripts or depletion of the abundant non-coding fraction consisting mainly of rRNA. We propose an alternative mRNA enrichment strategy based on the RNA-binding properties of the human IFIT1, an antiviral protein recognizing cap 0 RNA. Here, we compare for Saccharomyces cerevisiae an IFIT1-based mRNA pull-down with yeast targeted rRNA depletion by the RiboMinus method. IFIT1-based RNA capture depletes rRNA more effectively, producing high quality RNA-seq data with an excellent coverage of the protein coding transcriptome, while depleting cap-less transcripts such as mitochondrial or some non-coding RNAs. We propose IFIT1 as a cost effective and versatile tool to prepare mRNA libraries for a variety of organisms with cap 0 mRNA ends, including diverse plants, fungi and eukaryotic microbes.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for Saccharomyces cerevisiae BY4741 with IFIT1-based mRNA pull-down (Cin-S,Con-B) and yeast targeted rRNA depletion by the RiboMinus (RiboMinus) method.
Please note that raw data has been deposited in ENA (ERP133696).

first: Martyna

last: Nowacka

first: Przemysław

last: Latoch

first: Matylda

last: Izert

first: Natalia

last: Karolak

first: Rafal

last: Tomecki

first: Michał

last: Koper

first: Agnieszka

last: Tudek

first: Agata

middle: L

last: Starosta


title: Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages (Drop-Seq)


title: Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages (RNA-Seq I)


title: Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages (in vitro ATAC-Seq)


title: Impaired gene expression in ATRX-depleted cells following interferon signaling

city: Ulm

first: Thomas

last: Stamminger

address: Albert-Einstein-Allee 11

department: Institute of Virology

institute: Ulm University Medical Center

summary: We investigated the role of the chromatin remodeling protein ATRX on ISG expression upon stimulation with IFN-β utilizing doxycycline-inducible ATRX knockdown cells.

overall_design: Examination of differential gene expression by RNA-seq in human foreskin fibroblasts (doxycycline-inducible ATRX knockdown cells and control cells) treated with IFN-β.

first: Anne-Charlotte

last: Stilp

first: Axel

last: Fürstberger

first: Hans

last: Kestler


title: Alterations in chromatin accessibility in ATRX-depleted cells following interferon signaling

summary: We investigated the role of the chromatin remodeling protein ATRX on chromatin accessibility specifically upon IFN-β stimulation utilizing stable ATRX knockdown cells.

overall_design: Examination of chromatin accessibilty by ATAC-seq in human foreskin fibroblasts (ATRX knockdown and control) treated with IFN-β.


title: Transcriptional regulation of the thymus master regulator Foxn1 [RNAseq_dev_HFC]

first: Jakub

last: Abramson

overall_design: mRNA profiles of sorted thymic epithelial populations at different developmental time points as well as sorted HFC from Foxn1 EGFP mice, were generated by MARSeq Method.

first: J

first: N

last: Kadouri


title: The chromatin remodeling protein ATRX positively regulates IRF3-dependent type I interferon production and interferon-induced gene expression

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

overall_design: Refer to individual Series


title: Transcriptional regulation of the thymus master regulator Foxn1


title: Transcriptional regulation of the thymus master regulator Foxn1 [ATAC-Seq]

overall_design: Chromatin accessibility profiles of sorted thymic epithelial populations at different developmental time points, were generated by deep sequencing, using the ATACseq method.


title: Transcriptional regulation of the thymus master regulator Foxn1 [RNAseq_AR3_vs_nude]

overall_design: mRNA profiles of sorted total thymic epithelial cells (TEC) from young (4-5 weeks old) of Foxn1 del AR3 mutant and heterozygous control (generated in this study) as well as of nu/nu,were generated by deep sequencing, using the MARSseq method.


title: NanoDam identifies novel temporal transcription factors conserved between the Drosophilacentral brain and visual system

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Rd

institute: The Gurdon Institute

summary: Temporal patterning of neural progenitors is an evolutionarily conserved strategy for generating neuronal diversity. Type II neural stem cells in the Drosophilacentral brain produce transit-amplifying intermediate neural progenitors (INPs) that exhibit temporal patterning. However, the known temporal factors cannotaccount for the neuronal diversity in the adult brain. To search for new temporal factors, we developed NanoDam, which enablesrapid genome-wide profiling of endogenously-tagged proteins in vivowith a singlegenetic cross.Mapping the targets of known temporal transcription factorswith NanoDamidentified Homeobrain and Scarecrow (ARX and NKX2.1 orthologues) as novel temporal factors. We show that Homeobrainand Scarecrow define middle-aged and late INP temporal windows and play a role in cellular longevity. Strikingly, Homeobrain and Scarecrow have conserved functions as temporal factors in the developing visual system.NanoDam enables rapid cell type-specific genome-wideprofiling with temporal resolution and can be easily adapted for use in higher organisms.

overall_design: To establish and assess the efficiency and reproducibility of NanoDam, Chronophage-NanoDam was compared to Chronophage-Targeted DamID in Neural Stem Cells of Drosophila embryos. NanoDam was performed for Dichaete, Grainyhead and Eyeless in TypeII Neural Stem Cell-derived Intermediate Progenitors of the Drosophila L3 larval brain to identify novel temporal factors. scRNAseq was conducted to assess expression of the respective temporal factor candidates in Intermediate Progenitors and their offspring. In parallel, NanoDam for Dichaete and Eyeless in the Optic lobe medulla Neural Stem Cells allowed a comparative analysis between the two temporal cascades.

first: Jocelyn

last: Tang

first: Anna

middle: E

last: Hakes

first: Robert

last: Krautz

first: Takumi

last: Suzuki

first: Esteban

middle: G

last: Contreras

first: Paul

middle: M

last: Fox

middle: H


title: Transcriptional regulation of the thymus master regulator Foxn1 [WGBS]

overall_design: WGBS profiles of sorted total thymic epithelial  (TEC) and type II airway epithelial cells (ATII)

first: Joschka

last: Hey

first: Christoph

last: Plass

first: Michelle

last: Paulsen

first: Noam


title: Integrated host-microbe metagenomics of cell-free nucleic acid for sepsis diagnosis in critically ill adults [plasma]

city: San Francisco

first: Charles

last: Langelier

address: HSE 401, 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

summary: Here we developed a new approach to sepsis diagnosis that integrates host transcriptional profiling with metagenomic broad-range pathogen detection from cell-free plasma RNA and DNA.

overall_design:
Comparing gene expression in patients with sepsis versus those without
Raw data not provided due to patient privacy concerns.

first: Lucile

last: Neyton

first: Katrina

last: Kalantar


title: Integrated host-microbe metagenomics of cell-free nucleic acid for sepsis diagnosis in critically ill adults [paxgene]


title: Super-enhancer landscape profiling in primary colorectal carcinoma

first: Royce

last: Zhou

address: 1470 Madison Avenue

summary:
Purpose: Examine H3K27ac enhancer and super-enhancer landscape differences between primary colorectal carcinoma and adjacent normal mucosa towards the identification of novel downstream targets.
Methods: H3K27ac ChIP-seq and RNA-seq were performed on fresh primary colorectal carcinoma samples and normal colonic mucosa, from human patient samples.
Results: We identified 2026 total super-enhancers in our cohort, between primary colorectal and normal mucosa. We quantified differences in H3K27ac signal within this space, between tumor and normal, and identified putative downstream target genes through integration with sample matched RNA-seq using a positive linear correlation model to identifty putative target genes.

overall_design: Examination of H3K27ac landscape differences, particularly at super-enhancers, between primary colorectal carcinoma and patient-matched adjacent normal mucosa.

first: Ramon

last: Parsons


title: Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages (RNA-Seq IV)

first: Ivan

last: Moskowitz

overall_design: Transcriptomic and epigenomic analyses of Hedgehog/GLI dependent-networks in cardiac and neural progenitors

first: Megan

last: Rowton

first: Carlos

last: Perez-Cervantes

first: Sebastian

last: Pott


title: Gene expression profiles of Wnt4 high and Wnt4 low populations of murine islets at postnatal day 1 (P1).

status: Public on Aug 02 2022

city: Dresden

first: Anne

last: Grapin-Botton

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics, Dresde

summary: To find the differences between  β cells expressing Wnt4 and those that do not express it (or express it at low levels) at neonatal stage, murine islets at postnatal day 1 (P1) were collected. Based on a reporter expressing Cre recombinase from the Wnt4 locus, we observed that Wnt4 expression starts in a small subset of β cells at embryonic day (E) 18.5. At neonatal stages, around 50% of β cells express Wnt4 at P0 and most of cells express it by P5. We collected Wnt4 high and Wnt4 low islet cells by FACS and compared their gene expression profile. Wnt4 high islet cell population showed a significant increase of β-cell maturation and function related genes, including transcription factors such as Pdx1 and Nkx6.1, insulin 2, glucokinase (Gck), and the glucose transporter Slc2a2. On the contrary, Wnt4 low islet cell population showed significant increasing of proliferation markers such as Pcna, Mki67 and the positive cell cycle regulators Ccnd1, Ccnd3, Ccna2, Cdk1, Cdk2 and Cdk6. Taken together, these results show that Wnt4 expression is higher in more mature but less proliferative β cells.

overall_design: To follow the Wnt4 expression in β cells, Wnt4eGFPCre (Wnt4 tm2(EGFP/cre)Svo) mice were crossed with mTmG (Gt(ROSA)26Sor tm4(ACTB−tdTomato,−EGFP)Luo) mice to generate Wnt4eGFPCre;mTmG mice. The islets were collected at P1. The islets from 3-4 pups were pooled together into 1 sample. Wnt4 high and low islet cells were sorted by FACS based on mGFP expression.

last: Botton

first: Keiichi

last: Katsumoto


title: Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages (RNA-Seq V)


title: The dependency factor RRM2 at the nexus of a copy number driven regulatory network and a target for synthetic lethal interactions with replication stress checkpoint addiction in high-risk neuroblastoma

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University


title: Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages (RNA-Seq II)


title: Characterization of a novel hormone-responsive endometrial cancer cell line: HCI-EC-23

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah


title: Characterization of a novel hormone-responsive endometrial cancer cell line: HCI-EC-23 [ChIP-seq]

summary: Most endometrial cancers are driven by excess estrogen signaling and express the hormone receptor estrogen receptor alpha (ER). Evaluation of the estrogen response in endometrial cancer cells has been limited by the availability of hormonally responsive in vitro models, with one cell line, Ishikawa, being used in most studies. Here, we describe a novel, adherent endometrioid endometrial cancer (EEC) cell line model, HCI-EC-23. We show that HCI-EC-23 retains ER expression and that ER functionally responds to 17b-estradiol (E2) induction over a range of passages. We also demonstrate that this cell line retains paradoxical activation of ER by tamoxifen, which is also observed in Ishikawa and is consistent with clinical data. The mutational landscape shows that HCI-EC-23 is mutated at many of the commonly altered genes in EEC, has relatively few copy-number alterations, and is microsatellite instable high (MSI-high). In vitro proliferation of HCI-EC-23 is modestly enhanced by E2 but is strongly reduced upon combination E2 and progesterone (P4) treatment. HCI-EC-23 exhibit strong E2 dependence for tumor growth in vivo and tumor size is reduced by combination E2 + P4 treatment. Molecular characterization of E2 induction in HCI-EC-23 revealed hundreds of estrogen-responsive genes that significantly overlapped with those regulated in Ishikawa. Analysis of ER genome binding identified similar patterns in HCI-EC-23 and Ishikawa, although ER exhibited more bound sites in Ishikawa. This study demonstrates that HCI-EC-23 is estrogen-responsive and can be used to study the hormonal aspects of endometrial cancer.

overall_design: ChIP-seq was used to study genomic binding of estrogen receptor and baseline H3K27ac in the endometrial cancer cell lines HCI-EC-23 and Ishikawa

first: Craig

last: Rush


title: Histone deacetylase inhibitors (HDACi) enhance oncolytic herpes simplex virus in malignant meningioma.

city: Boston

first: Hiroaki

last: Wakimoto

address: 185 Cambridge Street, CPZN-3800

department: Neurosurgery

institute: Massachusetts General Hospital

summary: The goal of the study was to determine whether low dose HDACi sensitizes human malignant meningioma cells to the cytotoxic capacity of oncolytic herpes simplex virus G47delta. RNA sequencing was used to examine transcriptomic changes mediated by HDACi preexposure before oncolytic virus infection.

overall_design: RNAseq data for CH-157 cells (CH) and IOMM-Lee cells (IOMM). Cells were untreated control (C; 1 and 2), or treated with G47delta (G; 3 and 4), Panobinostat (P, 5 and 6), or TrichostatinA (T, 7 and 8), Panobinostat and G47delta (P_G, 9 and 10), and TrichostatinA and G47delta (T_G, 11 and 12) before RNA extraction. Samples were labeled as CH1, CH2, CH3, CH4, CH5, CH6, CH7, CH8, CH9, CH10, CH11 CH12.

first: Joshua

last: Gorham

first: Hiroko


title: Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages (in vivo ATAC-Seq)

address: 900 East 57th Street, KCBD Room 5102

summary: We report that Hedgehog signaling is a heterochronic pathway that determines the timing of the transition from specified cardiac progenitor to differentiated cardiomyocyte, a function distinct from its previously described roles affecting cellular patterning or proliferation. Hedgehog signaling was required to prevent premature differentiation and disruption of cardiac morphogenesis in vivo and the Hedgehog signaling transcription factor GLI1 was sufficient to delay differentiation in stem cell-derived cardiac progenitors in vitro. GLI1 directly activated a de novo progenitor-specific network in vitro that inhibited the induction of the cardiac differentiation program. The GLI1-driven gene regulatory network is sufficient to induce Hedgehog-naive in vitro cardiac progenitors to adopt an epigenomic state reminiscent of second heart field cardiac progenitors in vivo. A Hh-dependent GLI transcription factor switch functions as a differentiation timer, restricting activity of the progenitor network to the second heart field and permitting cardiomyocyte differentiation in the heart. GLI1 expression is broadly associated with the progenitor state, and its activity also delayed the differentiation of specified neural progenitors in vitro. We posit that Hedgehog signaling functions as a heterochronic regulator that transiently maintains diverse progenitor populations for complex organ development and that may explain diverse Hedgehog signaling-dependent phenomena.


title: Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages (ChIP-Seq)


title: DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: WT_nude_and_NSG_4T1_BC250000]

city: Darlinghurst

first: Alexander

last: Swarbrick

state: NSW

address: 384 Victoria St

department: Cancer Ecosystems Program

country: Australia

institute: Garvan Institute of Medical Research

summary: To investigate immunoediting at the primary tumour, we used DNA barcoding combined with NGS. By stably integrating 4T1 murine cancer cell line with 250000 unique DNA barcodes (1 barcode per cell), we can trace how barcode (and therefore subclonal) diversity changes over time and in the presence of the endogenous immune system, compared to immunocompromised mice.

overall_design: The data provided are generated by targete barcode sequencing of primary tumours and matching lungs generated in mice from barcoded 4T1 cells. Samples are generated from immunocompetent BALB/c mice or immunocompromised NSG mice. Both the primary tumour and matching draining lymph node was collected for analysis.

first: Louise

last: Baldwin

first: Simon

last: Junankar

first: Jessica

last: Yang

first: Nenad

last: Bartonicek

first: Dan

last: Roden

first: Alex


title: DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [Bulk RNAseq]

summary: To investigate immunoediting at the primary tumour, we used DNA barcoding combined with NGS to identify individual cancer cells wthin the 4T1 murine model of cancer. We isolated two highly immune evasive clones from the parental population and carried out buk RNA sequencing

overall_design: We sequenced bulk RNA derived from 4 biological replates of the bulk parental population, immune evasive clone 1, clone 2, and two non target clones (1 and 2).


title: DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [WGS of target clones]

summary: By using DNA barcoding to trace individual cancer cells from the 4T1 murine model of cancer, we were able to identify two cancer cell clones that were highly immune evasive and resistant to immune destruction both by the endogenous immune system and when treating with immunotherapy. We isolated these clones (IE1 and IE2) from the bulk parental population for further characterisation. We wondered if copy number variations could explain the phenotype we observed, so we carried out WGS to investigate this.

overall_design: We carried out whole genome sequencing on one replicate per derived cell line (IE1, IE2, NT1 and NT2) at 30x sequencing depth.


title: DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: WT_nude_and_NSG_4T1_BC5000]

summary: To investigate immunoediting at the primary tumour, we used DNA barcoding combined with NGS. By stably integrating 4T1 murine cancer cell line with 5000 unique DNA barcodes (1 barcode per cell), we can trace how barcode (and therefore subclonal) diversity changes over time and in reponse to the endogenous immune system in immunocompetent mice compared to immunocompromised mice.

overall_design: The data provided are generated by targete barcode sequencing of primary tumours and matching lungs generated in mice from barcoded 4T1 cells. Samples are generated from immunocompetent BALB/c mice or immunocompromised NSG mce, with both primary tumour and matching lung tissue analysed.


title: DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: IT_and_cont_4T1_BC5000]

summary: To investigate immunoediting at the primary tumour, we used DNA barcoding combined with NGS. By stably integrating 4T1 murine cancer cell line with 5000 unique DNA barcodes (1 barcode per cell), we can trace how barcode (and therefore subclonal) diversity changes over time and after treatment with immunotherapy.

overall_design: The data provided are generated by targete barcode sequencing of primary tumours and matching lungs generated in mice from barcoded 4T1 cells. Samples are generated from immunocompetent BALB/c mice treated with eihter control IgG of combination immunotherapy (anti-Pd1 and anti-CTLA4). One sample was generated from the cell pellet left over after surgery


title: Integrated host-microbe metagenomics of cell-free nucleic acid for sepsis diagnosis in critically ill adults

first: Charles

last: Langelier


title: Elevating SOX2 downregulates MYC through a SOX2:MYC signaling axis and induces a slowly cycling proliferative state in human tumor cells

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

summary: Quiescent/slowly circling tumor cells present a clinical challenge due to their ability to evade treatement. Recent studies have demonstrated that quiescent/slow circling tumor cells hijack embryonic growth arrest mechanisms and consequently resist chemotherapy. Significantly, earlier studies established that high levels of SOX2 in both fetal and tumor cells restrict cell proliferation and induce a slowly cycling state. However, the mechanisms through which elevated SOX2 levels inhibit tumor cell proliferation have not been identified. To identify common mechanisms through which SOX2 elevation restricts tumor cell proliferation, we performed RNA-seq using ONS76 medulloblastoma and LNCaP prostate tumor cells engineered to express SOX2 from an inducible promoter. SOX2 elevation in both cell lines significantly downregulated MYC target genes. Consistent with these findings, elevating SOX2 in five cell lines representing three different human cancer types decreases MYC mRNA and protein levels. Importantly, the expression of a dominant-negative MYC variant, omomyc, recapitulated many of the effects of SOX2 on proliferation, cell cycle, and gene expression. As predicted by our Gene   Ontology analysis, elevating SOX2 decreases biosynthetic activity, in particular protein translation. We also demonstrate that rescuing MYC activity in the context of elevated SOX2 induces cell death, indicating that the downregulation of MYC is a critical mechanistic step necessary to maintain survival in the slowly cycling state induced by elevated SOX2. Altogether, our findings uncover a novel SOX2: MYC signaling axis and provide novel insights into the molecular mechanisms through  which SOX2 elevation induces a slowly cycling proliferative state.

overall_design: SOX2 elevation in multiple tumor cell types downregulates MYC and the expression of MYC target genes.

first: Ethan

last: Metz

first: Achyuth

last: Kalluchi

first: Angie

last: Rizzino


title: Characterization of a novel hormone-responsive endometrial cancer cell line: HCI-EC-23 [RNA-seq]

first: Jason

overall_design: RNAseq was used to study the estrogen response of the endometrial cancer cell lines HCI-EC-23 and Ishikawa


title: DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: All_EMT6_BC5000]

summary: To investigate immunoediting at the primary tumour, we used DNA barcoding combined with NGS. By stably integrating EMT6 murine cancer cell line with 5000 unique DNA barcodes (1 barcode per cell), we can trace how barcode (and therefore subclonal) diversity changes over time and after treatment with immunotherapy.

overall_design: The data provided are generated by targeted barcode sequencing of primary tumours generated in mice from barcoded EMT6 cells. Samples are generated from 6 severely immunocompromised (NSG) mice, 5 wildtype (immunocompetent) control treated mice, and 6 wildtype immunotherapy treated mice. One sample is generated from the cell pellet left over after surgery


title: Cryobanking of human distal lung epithelial cells for preservation of their phenotypic and functional characteristics

city: Los Angeles

first: Gianni

last: Carraro

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: The epithelium lining airspaces of the human lung is maintained by regional stem cells including basal cells of pseudostratified airways and alveolar type 2 pneumocytes (AT2) of the gas-exchange region. Despite effective techniques for long-term preservation of airway basal cells, procedures for efficient preservation of functional epithelial cell types of the distal gas-exchange region are lacking. Here we detail a method for cryobanking of epithelial cells from either mouse or human lung tissue for preservation of their phenotypic and functional characteristics. Flow cytometric profiling, epithelial organoid-forming efficiency, and single cell transcriptomic analysis, were used to compare cells recovered from cryobanked tissue with those of freshly dissociated tissue. Alveolar type 2 cells within single cell suspensions of enzymatically digested cryobanked distal lung tissue retained expression of the pan-epithelial marker CD326 and the AT2 cell surface antigen recognized by monoclonal antibody HTII-280, allowing antibody-mediated  enrichment and downstream analysis. Isolated AT2 cells from cryobanked tissue were comparable with those of freshly dissociated tissue both in their single cell transcriptome and their capacity for in vitro organoid formation in 3D cultures. We conclude that the cryobanking method described herein allows long-term preservation of distal human lung tissue for downstream analysis of lung cell function and molecular phenotype, and is ideally suited for creation of an easily accessible tissue resource for the research community.

overall_design: Single cell RNA-seq using 10x chromium system on freshly isolated and cryo-preserved lung explant tissue. The barcoded sequencing libraries were quantified by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems). Sequencing libraries were loaded on a NovaSeq 6000 (Illumina).

first: Bindu

last: Konda

first: Barry

last: Stripp


title: Multiomics analysis of the NAD+ -PARP1 axis reveals a role for site specific ADP ribosylation in splicing in embryonic stem cells

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: RNA-seq was performed in WT or Parp1-/- mESC cells over a time course of differentiation performed by LIF removal and suspension culture starting at 0 hour.  for a total of 20 samples, including 2 replicates

overall_design: Cells were harvested at 0hr, 6hr, 12hr, 24hr, and 72hrs of LIF removal. Sequencing done in paired-end manner 150bp insert lenght. Biological Replicate 1&2 - however biological replicate #1 didn't recieve enough reads and another replicate will be processed.

first: Aarin

last: Jones

first: W


title: DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: CD8_NK_depletion_4T1_BC5000_rpt]

first: Alexander

overall_design: The data provided are generated by targeted barcode sequencing of the primary tumour and  lungs collected from barcoded 4T1 tumour bearing mice treated with ket-cell type depleting antibodies, either anti-CD8 to deplete CD8+ cells, anti-asialo GM1 to deplete NK cells, anti-CD4 to deplete CD4 cells, or control anitbodies.

first: Louise

first: Simon


title: A New Gene Set Identifies Senescent Cells and Predicts Senescence Associated Pathways Across Tissues

city: Rochester

first: Sundeep

last: Khosla

state: MN

address: 200 1st St SW

department: Endocrinology Research

institute: Mayo Clinic

summary: Young (6-12 months old) INK-ATTAC mice were untreated. Old (20 months old) mice were treated with either Veh or AP (twice weekly, beginning at 20 months, for a total of 4 months). Centrifuged tibial diaphyses were harvested.

overall_design: INK-ATTAC mice (6-12 months=young) were compared to INK-ATTAC mice (20 months=old), treated with either Vehicle or 10 mg of AP20187 per kg body mass [drug/body mass]) twice weekly beginning at 20 months of age for a total of 4 months.

first: Dominik

last: Saul

first: Joshua

middle: N

last: Farr


title: Wound healing in aged skin exhibits systems-level alterations in cellular composition and cell-cell communication

city: Irvine

first: Remy

last: Vu

address: D288 Med Sci I Health Sciences Rd

institute: University of California, Irvine

summary: Delayed and often impaired wound healing in the elderly presents major medical, social, and economic challenges. A systematic understanding of the cellular and molecular changes that shape complex cell-cell communications in aged skin wounds is lacking. Here we use single-cell RNA sequencing to define baseline differences across epithelial/fibroblast/immune cell types in young and aged skin during homeostasis and identify major changes in their subset compositions, kinetics, and molecular profiles during wound healing. Our data uncover a more pronounced inflammatory phenotype in aged skin wounds, featuring more neutrophils, a previously unknown inflammatory/glycolytic Arg1Hi macrophage subset, and fewer dendritic cells, compared to young counterparts. Generalizing our computational tool CellChat to compare signaling changes in young vs. aged skin wounds, we find specific alterations in Arg1Hi macrophage-fibroblast signaling interactions and the overall cell-cell communication networks. Finally, our systems-level and experimental analyses uncover dysregulated growth factor, chemokine, and cytokine pathways (e.g., IL-1, Ccl19-Ccr7) in aged skin wounds. Our study exposes numerous cellular and molecular targets for future functional interrogation.

overall_design: Droplet-based single cell RNA-seq experiments were performed to identify molecular differences between young (7-week-old) and aged (88-week-old) skin from unwounded, 4-, and 7-day post-wounding skin.

first: Xing

last: Dai

first: Souqin

last: Jin

first: Peng

last: Sun


title: DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: CD8 NK depletion 4T1 BC5000]

last: Swarbrick

overall_design: The data provided are generated by targeted barcode sequencing of the primary tumour and  lungs collected from barcoded 4T1 tumour bearing mice treated with ket-cell type depleting antibodies, either anti-CD8 to deplete CD8+ cells, anti-asialo GM1 to deplete NK cells or control anitbodies.

last: Baldwin

last: Junankar

first: Jessica

last: Yang

first: Nenad

last: Bartonicek

first: Dan

last: Roden

first: Alex


title: Oncohistone mutations occur at functional sites of regulatory ADP-ribosylation: the role of oncohistone mutations in transcriptional regulation [RNA-Seq]

first: W. Lee

summary: RNA-seq were performed in MDA-MB-231 cells ectopically expressing FLAG-tagged WT, D51A, or D51N H2B, and WT, D68A, or D68N H4

last: Huang

first: Sara

last: Martire

first: Cristel

last: Camacho

first: Anusha

last: Nagari

first: Rohit

last: Setlem

first: Laura

last: Banaszynski


title: Oncohistone mutations occur at functional sites of regulatory ADP-ribosylation: the role of oncohistone mutations in transcriptional regulation [ChIP-Seq]

last: Kraus

summary: H2BK12ac ChIP-seq were performed in MDA-MB-231 cells ectopically expressing FLAG-tagged WT, D51A, or D51N H2B ± treatment with A485 (5 M, 2 hours) or vehicle (DMSO).

first: W


title: Characterization of Basal and Estrogen-Regulated  Antisense Transcription in Breast Cancer Cells:  Role in Regulating Sense Transcription

summary: We have mined genomic data to define three classes of antisense transcription in MCF-7 cells based on where their antisense transcription termination sites reside relative to their cognate sense mRNA and lncRNA genes.  These three classes differ in their response to estrogen treatment, the enrichment of a number of genomic features associated with active promoters (H3K4me3, RNA polymerase II, open chromatin architecture), and the biological functions of their cognate sense genes as analyzed by DAVID gene ontology.  We further characterized two estrogen-regulated antisense transcripts arising from the MYC gene in MCF-7 cells, showing that these antisense transcripts are five-prime capped, three-prime polyadenylated, and localized to different compartments of the cell.

overall_design: MCF-7 cells treated with ethanol (vehicle) or 17beta-estradiol (E2; 100 nM).

first: Tim

middle: Y

last: Hou

first: Tulip

last: Nandu

first: Rui

last: Li

first: Minho

last: Chae

first: Shino

last: Murakami

first: Kraus

last: Lee


title: A long non-coding RNA specifically expressed in early embryos programs the metabolic balance in adult mice

city: shanghai

first: HONG

last: QIN

address: 130# Dongan road

institute: Fudan Univercity

summary: Long non-coding RNAs (lncRNAs) display higher tissue-specificity than mRNAs. In particular, many lncRNAs are specifically expressed in early embryos, but the physiological functions of most of them remain largely unknown. Here, we show that deficiency of Lncenc1, a lncRNA specifically expressed in early embryos, results in an altered glucose and lipid balance in adult mice. Newly weaned lncenc1-deficient mice have been shown to display higher fasting blood glucose levels and to prefer to use lipids as a fuel source. When mice were fed a normal chow diet (NCD), in which glucose was the main energy source, glucose intolerance and insulin resistance were observed in adult lncenc1-deficient mice. Under high-fat diet (HFD) conditions, however, lncenc1-deficient mice became healthier and could resist food-induced obesity and metabolic disturbances, including liver steatosis and hypercholesterolmia. Furthermore, PPARγ-regulated lipogenesis in liver was reduced in lncenc1-deficient mice fed an HFD, as shown by transcriptome analyses. Interestingly, lncenc1-deficient mouse embryonic fibroblasts (MEFs) showed impaired glycolysis and lipogenesis, suggesting that the metabolic defects may already exist in embryos. Our study provides the first piece of evidence showing the essential roles of embryo-specific lncRNAs in adult metabolism, verifying the “fetal origin” of adult metabolic disorders.

overall_design: RNAseq data in wild type and lncenc1 knockout mice livers.


title: DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: IT_and_cont_4T1_BC250000]

first: Alexander

last: Swarbrick

summary: To investigate immunoediting at the primary tumour, we used DNA barcoding combined with NGS. By stably integrating 4T1 murine cancer cell line with 250000 unique DNA barcodes (1 barcode per cell), we can trace how barcode (and therefore subclonal) diversity changes over time and after treatment with immunotherapy.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: The data provided are generated by targete barcode sequencing of primary tumours and matching lungs generated in mice from barcoded 4T1 cells. Samples are generated from immunocompetent BALB/c mice treated with eihter control IgG of combination immunotherapy (anti-Pd1 and anti-CTLA4). Three samples were generated from the cell pellets left over after surgery.

first: Louise

last: Baldwin

first: Simon

last: Junankar

first: Jessica

last: Yang

first: Nenad


title: Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells

first: David

last: Wu

state: California

address: 35 Medical Center Way

institute: UCSF

summary: Human chromosomes are pervasively transcribed, but systematic understanding of coding and lncRNA genome function in cell differentiation is lacking. Using CRISPR interference (CRISPRi) in human induced pluripotent stem cells, we performed dual genome-wide screens – assessing 18,905 protein-coding and 10,678 lncRNA loci – and identified 419 coding and 201 lncRNA genes that regulate neural induction. Integrative analyses revealed distinct properties of coding and lncRNA genome function, including a 10-fold enrichment of lncRNA genes for roles in differentiation compared to proliferation. Further, we applied Perturb-Seq to obtain granular insights into neural induction phenotypes. While most coding hits stalled or aborted differentiation, lncRNA hits were enriched for the genesis of diverse cellular states, including those outside the neural lineage. In addition to providing a rich resource (danlimlab.shinyapps.io/dualgenomewide) for understanding coding and lncRNA gene function in development, these results indicate that the lncRNA genome regulates lineage commitment in a manner fundamentally distinct from coding genes.

overall_design: Time-series RNA-Seq, Perturb-Seq, CUT&Tag, and PLAC-Seq.

first: Daniel

last: Lim


title: Combinatorial Treatment of Poly (ADP-ribose) Polymerase-1 Inhibitors and Cisplatin Attenuates Cervical Cancer Growth Through FOS-Driven Changes in Gene Expression

first: W. Lee

summary: Cervical cancer is the one of the most prevalent types of cancers in women and is the second highest cause of death in women aged 20-39.  The most common chemotherapy for cervical cancer involves the use of the drug cisplatin in conjunction with other therapeutics.  However, the development of cisplatin resistance in patients can hinder the efficacy of these treatments.  This highlights the need to explore different therapeutic approaches for cervical cancer treatment.  We found that inhibitors targeting the enzyme Poly (ADP-ribose) Polymearse (PARP)-1 can attenuate cell growth of cervical adenocarcinoma and squamous cell carcinoma.  Furthermore, combinatorial therapy of PARP inhibitors (PARPi) with cisplatin increases the cisplatin-mediated cell toxicity in cervical cancer cells.  This is accompanied by a rewiring of the transcriptome in response to the cisplatin and PARPi together.  Surprisingly, we observed that the Fos gene is upregulated in the dual treatment condition leading to the subsequent induction of its target genes.  Importantly, increased the expression of Fos is sufficient to hinder cervical cancer growth.  We conclude that by inducing Fos expression, PARPi treatment with cisplatin leads to inhibition of cervical cancer.

overall_design: RNA-Seq was perfomed in HeLa cells treated with the PARP inhibitor BYK204165  or Cisplatin or both for 6 hours or vehicle control (DMSO).

first: Lin

last: Ken

first: Gupte

last: Rebecca

first: Nandu

last: Tulip

last: W Lee


title: Single-cell RNA-seq reveals early heterogeneity during aging in yeast

status: Public on Aug 01 2022

city: Beijing

first: Jincheng

last: Wang

address: yiheyuan road No5

institute: BIOPIC, Peking University

summary:
we carried out a systematic and quantitative investigation of yeast aging with single-cell resolution through transcriptomic sequencing. We optimized a single-cell RNA sequencing (scRNA-seq) protocol to quantitatively study the whole transcriptome profiles of single yeast cells at different ages, finding increased cell-to-cell transcriptional variability during aging.
The single-cell transcriptome analysis also highlighted key biological processes or cellular components, including oxidation-reduction process, oxidative stress response (OSR), translation, ribosome biogenesis and mitochondrion that underlie aging in yeast. We uncovered a molecular marker of FIT3, indicating the early heterogeneity during aging in yeast. We also analyzed the regulation of transcription factors and further characterized the distinctive temporal regulation of the OSR by YAP1 and proteasome activity by RPN4 during aging in yeast. Overall, our data profoundly reveal early heterogeneity during aging in yeast and shed light on the aging dynamics at the single cell level.

overall_design: We selected relatively young and small sized cells from the yeast colonies and aligned them on the same agar plate and dissected daughter cells per 1.5 hours. After 2/16/36 hours, we isolated yeast mother cell and conducted scRNA-seq process. The data analysis reveal transcriptional change during aging.

first: Yuchen

last: Sang

first: Shengxian

last: Jin

first: Xuezheng

first: Gajendra

last: Azad

first: Mark

last: McCormic

first: Brian

last: Kennedy

first: Qing

first: Jianbin

first: Xiannian

last: Zhang

first: Yi

first: Yanyi

last: Huang


title: RNA-sequence on prostates of wild type (C57BL/6J) and ARNoC/Y mice that underwent orchidectomy and testosterone (or vehicle) replacement for 4 days

city: Heverlee

first: Sarah

last: El Kharraz

address: Herestraat 49

institute: KU Leuven

summary: We generated a mouse model (ARNoC/Y) with a mutation in the FQNLF motif located on the aminoterminal domain (NTD) that disrupts the N/C interactions of the androgen receptor (AR). These mice exhibit a normal male phenotype. To be able to compare WT males and ARNoC/Y mice more directly, we performed a castration experiment with testosterone (T) supplementation for 4 days. Since slightly differences in prostate weight were observed, we performed RNA-seq on these prostate to evaluate the biological relevance.

overall_design: Sample = ventral prostate; 5 samples per group: WT + vehicle, WT + testosterone, ARNoC/Y + vehicle, ARNoC/Y + testosterone


title: Single-cell multi-omic velocity infers dynamic and decoupled gene regulation

city: Ann Arbor

first: Joshua

last: Welch

address: 500 S State St

department: DCMB

institute: University of Michigan

summary: Single-cell multi-omic datasets, in which multiple molecular modalities are profiled within the same cell, provide a unique opportunity to discover the interplay between cellular epigenomic and transcriptomic changes. To realize this potential, we developed MultiVelo, a mechanistic model of gene expression that extends the popular RNA velocity framework by incorporating epigenomic data. MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of gene regulation, providing a quantitative summary of the temporal relationship between epigenomic and transcriptomic changes. Fitting MultiVelo on single-cell multi-omic datasets revealed two distinct mechanisms of regulation by chromatin accessibility, quantified the degree of concordance or discordance between transcriptomic and epigenomic states within each cell, and inferred the lengths of time lags between transcriptomic and epigenomic changes.

overall_design:
Human HSPC multi-omic sequences on 10X Genomics platform.
**Raw data has been deposited to dbGAP phs002915.v1.p1**

first: Chen

last: Li

first: Maria

middle: C

last: Virgilio

first: Kathleen

last: Collins


title: Oncohistone mutations occur at functional sites of regulatory ADP-ribosylation: the role of oncohistone mutations in transcriptional regulation [ATAC-Seq]

first: W. Lee

last: Kraus

summary: ATAC-seq were performed in MDA-MB-231 cells ectopically expressing FLAG-tagged WT, D51A, or D51N H2B, and WT, D68A, or D68N H4

first: Dan

first: Sara

last: Martire

first: Cristel

last: Camacho

first: Anusha

last: Nagari

first: Rohit

last: Setlem

first: Laura

last: Banaszynski

first: W


title: An ancestral Wnt-Brachyury feedback loop and vertebrate-specific recruitment of mesoderm-determining target genes revealed by comparative Brachyury target screens

city: Napoli

first: Maria Ina

last: Arnone

address: Villa Comunale 1

department: Biology and Evolution of Marine Organisms

institute: Stazione Zoologica Anton Dohrn

summary: Transcription factor brachyury plays a key role during mesoderm development in vertebrates. In this study we study study the effect of this transcription factor in the purple sea urchin S. purpuratus.

overall_design: Brachyury binding sites were identified with ChIP-seq and effect of brachyury binding on gene expression was studied with RNA-seq.

first: Carmen

last: Andrikou

first: Danila

last: Voronov

last: Dnyansagar

first: Michaela

last: Schwaiger

first: Periklis

last: Paganos

first: Ulrich

last: Technau


title: Single-cell immune profiling reveals thymus-seeding populations, T cell commitment, and multi-lineage development in the human thymus

city: Leiden

first: Martijn

last: Cordes

address: Albinusdreef 2

department: Immunology

institute: Leiden University Medical Centre

summary: Development of T lymphocytes in the thymus has been widely studied in mice, but our insights into human T cell development are scarce. Using a combination of single-cell techniques and functional assays, we report deep immune profiling of human T cell development, with a focus on the initial development stages of pre-lineage commitment. We identified three thymus-seeding progenitor populations that also have a counterpart in the bone marrow. We found that the human thymus physiologically supports development of monocytes, DCs, NK cells, and limited development of B lymphocytes. These insights are important to monitor and guide regenerative therapies after hematopoietic stem cell transplantation.

overall_design: To get more insight into human T cell development, we performed single-cell RNA-seq on sorted thymocytes from six healthy donors. We used flow cytometry to sort the DN1 (CD34+CD38-CD1a-), DN2 (CD34+CD38+CD1a-), DN3 (CD34-CD38+CD1a+) thymocytes. Maturating CD4 and CD8 thymocytes were also analyzed from the sorted subsets: CD4 immature single-positive (ISP), CD4/CD8 double-positive (DP), CD4 SP and CD8 SP. From the 8 sorted populations we generated 8 scRNA-seq libraries for gene expression profiling using the 10x Genomics platform.

first: Kirsten

last: Canté-Barrett

first: Erik

last: van den Akker

first: Federico

last: Moretti

first: Szymon

last: Kiełbasa

first: Sandra

last: Vloemans

last: Garcia-Perez

first: Cristina

last: Teodosio

first: Jacques

middle: J

last: van Dongen

first: Karin

last: Pike-Overzet

first: Marcel

last: Reinders

first: Frank

last: Staal


title: RNA-seq study on the placentomes collected from the cows with or without retained placenta

city: Karaj

first: Mehdi

last: Moradi

state: Alborz

address: Daneshkadeh st.

department: Animal Science

country: Iran

institute: University of Tehran

summary: We conducted an RNA-sequencing on the placentomes that were collected from 4 and 3 cows with and without retained placenta, respectively. Placentomes were collected from the cows within 30 minutes after parturition and samples were taken from the feto-maternal junction sites of the placentomes. These samples were used for RNA-sequencing and the results showed 240 genes that were differentially expressed between the two groups. These genes could be candidate genes that are involved in the development of placental retention in cattle.

overall_design: Identifying the genes that are differentially expressed in the placentome of cows with or without retained placenta.

first: Mahdi

last: Zhandi

first: Mohsen

last: Sharafi

first: Arvand

last: Akbari

first: Mohammad

last: Jafari Atrabi

last: Totonchi


title: DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy

first: Alexander

last: Swarbrick

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

overall_design: Refer to individual Series


title: Oncohistone mutations occur at functional sites of regulatory ADP-ribosylation: the role of oncohistone mutations in transcriptional regulation

first: W. Lee

last: Kraus


title: Domain-specific mutations in dyskerin disrupt 3´end processing of snoRNAs

first: Suneet

last: Agarwal

state: MA

address: Karp 07214, 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: Mutations in genes encoding components of the telomerase holoenzyme complex result in a spectrum of rare genetic disorders known as telomere diseases, including dyskeratosis congenita (DC). A consistent finding in DC due to pathogenic mutations in DKC1, which encodes dyskerin, is decreased steady-state levels of the non-coding RNA component of telomerase (TERC) and thus impaired telomere maintenance. Dyskerin binds hundreds of other small nucleolar RNAs (snoRNAs). However, the mechanisms by which DKC1 mutations cause variable impacts on these snoRNAs are poorly understood, which is a barrier to understanding disease mechanisms in DC beyond impaired telomere maintenance. Here, using somatic and induced pluripotent stem cells (iPSCs) from DC patients with DKC1 mutations and CRISPR-Cas9-engineered iPSCs, we show that mutations in the N-terminal extension domain (NTE) of dyskerin dysregulate the biogenesis of a subset of snoRNAs, with the most prominent effect on scaRNA13 (small Cajal body-specific RNA 13). In patient iPSCs carrying the del37L dyskerin NTE-domain mutation but not in those with C-terminal mutations, nascent scaRNA13 transcripts showed a discrete population of 3´-extended forms, as seen in the setting of DC-causing mutations in the PARN (polyA-specific ribonuclease) gene. By deep sequencing of RNA 3´ ends, we found that aberrant scaRNA13 transcripts were composed of genomically-encoded extensions and post-transcriptionally oligoadenylated species, mediated by the noncanonical polymerase PAPD5, which counters PARN. NTE domain mutations generated using CRISPR-Cas9 engineering of the endogenous DKC1 recapitulated the scaRNA13 3´-end processing defects seen in del37L patient cells. Conversely, repair of the DKC1 del37L mutation and genetic or pharmacological manipulation of PAPD5 rescued scaRNA13 end processing defects and steady-state levels. Analysis of the human telomerase cryo-EM structure showed that the dyskerin NTE interacts with 3´ end of bound RNA, suggesting that mutations in this domain impair 3´ end protection of nascent scaRNA13 in addition to canonical functions in snoRNA stabilization. Our results provide mechanistic insights into the interplay of dyskerin and the PARN/PAPD5 axis in the biogenesis and accumulation of snoRNAs beyond TERC, which has important implications for our broader understanding of ncRNA dysregulation in human diseases.

overall_design: Total RNA profile of PARN mutant patient iPSCs

first: Neha

last: Nagpal

first: Albert

middle: K

last: Tai

first: Jayakrishnan

last: Nandakumar


title: Targets for renal carcinoma growth control identified by screening FOXD1 cell proliferation pathways

city: New York

first: Leif

last: Oxburgh

state: NY

address: 310 E 67th Street

institute: The Rogosin Institute

summary: FOXD1 regulates proliferation of clear cell renal cell carcinoma (ccRCC) cells, and ccRCC cells in which FOXD1 has been inactivated do not form tumors efficiently in an animal model. Reproducing growth inhibition in tumor cells by inhibiting FOXD1 pathways presents an possible therapeutic approach for ccRCC and other cancers. We have established an analysis strategy to identify FOXD1-regulated target pathways that may be therapeutically tractable and compounds that modulate these pathways were selected for testing.

overall_design: Biological triplicate total RNA extracts from cell lines 786-O and 786-OFOXD1null were paired-end sequenced.

first: Kyle

last: Bond