title: Regulation of Immunological Tolerance by the p53-Inhibitor iASPP

summary: Maintenance of immunological homeostasis between tolerance and autoimmunity is essential for the prevention of human diseases ranging from autoimmune disease to cancer. Accumulating evidence suggests that p53 can mitigate phagocytosis-induced adjuvanticity thereby promoting immunological tolerance following programmed cell death. Here we identify Inhibitor of Apoptosis Stimulating p53 Protein (iASPP), a negative regulator of p53 transcriptional activity, as a regulator of immunological tolerance. iASPP-deficiency promoted lung adenocarcinoma and pancreatic cancer tumorigenesis, while iASPP-deficient mice were less susceptible to autoimmune disease. Immune responses to iASPP-deficient tumors exhibited hallmarks of immunosuppression, including activated regulatory T cells and exhausted CD8+ T cells. Interestingly, iASPP-deficient tumor cells and tumor-infiltrating myeloid cells, CD4+, and γδ T cells expressed elevated levels of PD-1H, a recently identified transcriptional target of p53 that promotes tolerogenic phagocytosis. Identification of an iASPP/p53 axis of immune homeostasis provides a therapeutic opportunity for both autoimmune disease and cancer.

overall_design:
Refer to individual Series

ChIP-seq of p53 and total RNA polymerase II in A549 WT or PPP1R13L KO cell lines. mNET-seq of total RNA polymerase II in A549 WT or PPP1R13L KO cell lines.


title: Generation and characterization of NGLY1 patient-derived midbrain organoids

status: Public on Feb 03 2023

city: Rockville

first: Wei

last: Zheng

state: MD

address: 9800 Medical Center Dr

department: National Center for Translational Sciences

country: USA

institute: National Institutes of Health

type: Expression profiling by high throughput sequencing

summary: NGlY1 deficiency is an ultra-rare, autosomal recessive genetic disease caused by mutations in the NGLY1 gene encoding N-glycanase one that removes N-linked glycan. Patients with pathogenic mutations in NGLY1 have complex clinical symptoms including global developmental delay, motor disorder, and liver dysfunction. To better understand disease pathogensis and neurological symptoms of NGLY1 deficiency we generated and characterized midbrain organoids using patient-derived iPSCs from two patients with disease causing mutations.

overall_design: RNA-seq was performed on wild-type midbrain organoids, NGLY1-Knockout and two NGLY1 deficient midbrain organoids generated from patient derived iPSCs.

first: Joshua

last: Abbott


title: Transcriptomic landscape of the retrosplenial cortex of the mouse

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

summary: Here, we examined diversity in the cell-type composition of the mouse retrosplenial cortex using single-cell RNA-seq.

overall_design: Examination of retrosplenial cortex neuron transcriptomes.


title: Regulation of Immunological Tolerance by the p53-Inhibitor iASPP [ChIP-seq]

status: Public on Feb 02 2023

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Maintenance of immunological homeostasis between tolerance and autoimmunity is essential for the prevention of human diseases ranging from autoimmune disease to cancer.  Accumulating evidence suggests that p53 can mitigate phagocytosis-induced adjuvanticity thereby promoting immunological tolerance following programmed cell death.  Here we identify Inhibitor of Apoptosis Stimulating p53 Protein (iASPP), a negative regulator of p53 transcriptional activity, as a regulator of immunological tolerance.  iASPP-deficiency promoted lung adenocarcinoma and pancreatic cancer tumorigenesis, while iASPP-deficient mice were less susceptible to autoimmune disease.  Immune responses to iASPP-deficient tumors exhibited hallmarks of immunosuppression, including activated regulatory T cells and exhausted CD8+ T cells.  Interestingly, iASPP-deficient tumor cells and tumor-infiltrating myeloid cells, CD4+, and gamma-delta T cells expressed elevated levels of PD-1H, a recently identified transcriptional target of p53 that promotes tolerogenic phagocytosis.  Identification of an iASPP/p53 axis of immune homeostasis provides a therapeutic opportunity for both autoimmune disease and cancer.

overall_design: ChIP-seq of p53 and total RNA polymerase II in A549 wild-type cells or A549 PPP1R13L knockdown cells.

first: Elliot

middle: H

last: Akama-Garren

first: Paul

last: Miller

first: Thomas

middle: M

last: Carroll

first: Gopinath

last: Sutendra

first: Ludovico

last: Buti

first: Justyna

last: Zaborowska

first: Robert

middle: D

last: Goldin

first: Elizabeth

last: Slee

first: Francis

last: Szele

first: Shona

last: Murphy

first: Xin

last: Lu


title: Adipocyte YTH N(6)-methyladenosine RNA-binding protein 1 protects against obesity by promoting white adipose tissue beiging in male mice

city: Hangzhou

first: Sujun

last: Yan

state: Zhejiang

address: 866 Yuhangtang Rd

country: China

institute: Zhejiang University

summary: Obesity, one of the most serious public health issues, is caused by energy imbalance of energy intake and expenditure. N(6)-methyladenosine (m6A) RNA modification has been recently identified as a key regulator of obesity, while the detailed mechanism is elusive. Here, we found that YTH RNA binding protein 1 (YTHDF1), an m6A reader, acts as an essential regulator of white adipose tissue metabolism. The expression of YTHDF1 decreased in adipose tissue of mice fed a high-fat diet. Adipocyte-specific Ythdf1 deficiency exacerbated obesity-induced metabolic defects and inhibited beiging of inguinal white adipose tissue (iWAT) in mice. By contrast, mice with WAT-specific Ythdf1 overexpression were resistant to obesity and showed promotion of beiging. Mechanistically, YTHDF1 regulated the translation of diverse m6A-modified mRNAs. In particular, YTHDF1 facilitated the translation of bone morphogenetic protein 8b (Bmp8b) in an m6A-dependent manner to induce the beiging process. Together, these findings suggested that YTHDF1 may be an attractive therapeutic target for the management of obesity-associated diseases.

overall_design: White adipose tissue mRNA profiles of wild type (Y1CTL) and Ythdf1 adipose conditional knockout mice (Y1cKO) after cold stimulation.

first: Xiaoling

last: Zhou

first: Canlan

last: Wu

first: Yunyi

last: Gao

first: Yu

last: Qian

first: Jingyu

last: Hou

first: Renxiang

last: Xie

first: Shanghai

last: Chen

first: Saisai

last: Wei

first: Xiangwei


title: miR-101a-3p impairs synaptic plasticity and contributes to synucleinopathy

city: Goettingen

first: Tiago

middle: Fleming

last: Outeiro

address: Waldweg 33

department: Experimental Neurodegeneration

country: Germany

institute: University Medical Center Goettingen

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed small RNA-Sequencing of midbrain from 6-month-old transgenic (Tg) mice expressing A30P mutant aSyn, followed by comparative expression analysis, and found that several deregulated biological processes were linked with the synapse.

overall_design: Examination of midbrain miRNAome in 6 month old mice wild type (WT) and A30P mutant alpha-synuclein mice

first: Mary

last: Xylaki

first: Isabel

last: Paiva

first: Guarav

last: Jain


title: DOT-1.1 (DOT1L) deficiency in C. elegans leads to small RNA-dependent gene activation [small RNA, L3]

city: Boston

first: Alla

last: Grishok

address: 72 E Concord

institute: Boston University

summary: Methylation of histone H3 at lysine 79 (H3K79) is conserved from yeast to humans and is accomplished by Dot1 (disruptor of telomeric silencing-1) methyltransferases. The C. elegans enzyme DOT-1.1 and its interacting partners are similar to the mammalian DOT1L (Dot1-like) complex. The C. elegans DOT-1.1 complex has been functionally connected to RNA interference. Specifically, we have previously shown that embryonic and larval lethality of dot-1.1 mutant worms deficient in H3K79 methylation was suppressed by mutations in the RNAi pathway genes responsible for generation (rde-4) and function (rde-1) of primary small interfering RNAs (siRNAs). This suggests that dot-1.1 mutant lethality is dependent on the enhanced production of some siRNAs. We have also found that this lethality is suppressed by a loss-of-function of CED-3, a conserved apoptotic protease. Here, we describe a comparison of gene expression and primary siRNA production changes between control and dot-1.1 deletion mutant embryos. We found that elevated antisense siRNA production occurred more often at upregulated than downregulated genes. Importantly, gene expression changes were dependent on RDE-4 in both instances. Moreover, the upregulated group, which is potentially activated by ectopic siRNAs, was enriched in protease-coding genes. Our findings are consistent with a model where in the absence of H3K79 methylation there is a small RNA-dependent activation of protease genes, which leads to embryonic and larval lethality. DOT1 enzymes’ conservation suggests that the interplay between H3K79 methylation and small RNA pathways may exist in higher organisms.

overall_design: Synchronized populations of L3 stage wild-type C. elegans worms were lysed, their RNA was extracted, and small RNA sequencing was performed.

first: Thomas

last: Liontis

first: Karisma

last: Verma


title: SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry [4C]

status: Public on Feb 01 2023

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

summary: The pediatric extra-cranial tumor neuroblastoma displays a low mutational burden while recurrent copy number alterations are present in most high-risk cases. We identify SOX11 as a dependency transcription factor in adrenergic neuroblastoma based on recurrent chromosome 2p focal gains and amplifications, specific expression in the normal sympatho-adrenal lineage and adrenergic neuroblastoma, regulation by multiple adrenergic specific (super-)enhancers and strong dependency on high SOX11 expression in adrenergic neuroblastomas. SOX11 regulated direct targets include genes implicated in epigenetic control, cytoskeleton and neurodevelopment. Most notably, SOX11 controls chromatin regulatory complexes, including 10 SWI/SNF core components among which SMARCC1, SMARCA4/BRG1 and ARID1A. Additionally, the histone deacetylase HDAC2, PRC1 complex component CBX2, chromatin-modifying enzyme KDM1A/LSD1 and pioneer factor c-MYB are regulated by SOX11. Finally, SOX11 is identified as a core transcription factor of the core regulatory circuitry (CRC) in adrenergic high-risk neuroblastoma with a potential role as epigenetic master regulator upstream of the CRC.

overall_design: 4C sequencing for the SOX11 promoter in the neuroblastoma cell lines CLB-GA, KELLY, SK-N-AS and SH-EP.

first: Amber

last: Louwagie

first: Bieke

last: Decaesteker

first: Katleen

last: De Preter

first: Frank

last: Speleman


title: SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry

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

overall_design: Refer to individual Series


title: SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry [ATAC-Seq]

overall_design: ATAC-seq to define open and closed chromatin in the human IMR-32, CLB-GA and SH-EP neuroblastoma cell lines in an untreated way.


title: Deficient radiation transcription response in COVID-19 patients

city: Cambridgeshire

first: Veronika

last: Goriacha

address: 5 The Quay, St. Ives

institute: HQ Science

summary:
The ongoing SARS-CoV-2 pandemic has resulted in over 6.3 million deaths and 560 million COVID-19 cases worldwide.
Clinical management of hospitalised patients is complex due to the heterogeneous course of COVID-19.
Low-dose radiotherapy (LD-RT) is known to dampen localised chronic inflammation, and has been suggested to be used to reduce lung inflammation  in COVID-19 patients.
However, it is unknown whether SARS-CoV-2 alters the radiation response and associated radiation exposure related risk.
We generated gene expression profiles from circulating leukocytes of hospitalised COVID-19 patients and healthy donors.
The p53 signalling pathway was found to be dysregulated, with mRNA levels of p53, ATM and CHK2 being lower in COVID-19 patients.
Several key p53 target genes involved in cell cycle arrest, apoptosis and p53 feedback inhibition were up-regulated in COVID-19 patients, while other p53 target genes were downregulated.
This dysregulation has functional consequences as the transcription of p53-dependant genes (CCNG1, GADD45A, DDB2, SESN1, FDXR, APOBEC) was reduced 24 h after X-ray exposure ex-vivo to both low (100 mGy) or high (2 Gy) doses.
In conclusion, SARS-CoV-2 infection affects a DNA damage response that may modify radiation-induced health risks in exposed COVID-19 patients.

overall_design: Comparative transcripts obtained from COVID-19 patients and healthy donors, which allows the identification of differentially expressed, up-and-down-regulated genes. We used Nanopore technology to sequence cDNA libraries prepared from whole blood RNA obtained from COVID-19 patients and healthy donors. This approach allows the identification and quantification of full-length transcripts.

first: Stanislav

last: Polozov

first: Lourdes

last: Cruz-Garcia

first: Grainne

last: O’Brien

first: Serge

last: Candeias

first: Christophe

last: Badie

first: Penny

last: Jeggo

first: Farah

last: Nasser


title: First-in-Human Study in Healthy Subjects with the Non-Cytotoxic Monoclonal Antibody OSE-127, a Strict Antagonist of the IL-7Rα

city: NANTES

first: Isabelle

last: Girault

state: PAYS-DE-LA-LOIRE

address: 22 BOULEVARD BENONI GOULIN

country: France

institute: OSE IMMUNOTHERAPEUTICS

summary: OSE-127 is a humanized monoclonal antibody targeting the IL-7Rα chain (CD127), under development for inflammatory and autoimmune disease treatment. It is a strict antagonist of the IL-7R pathway, is not internalized by target cells and is non-cytotoxic. Here, a first-in-human, phase I, randomized, double-blind, placebo-controlled, single-center study was carried out to determine the safety, pharmacokinetics, pharmacodynamics, and immunogenicity of OSE-127 administration.Sixty-three healthy subjects were randomly assigned to nine groups: six single ascending dose groups with intravenous (IV) administration (0.002-10 mg/kg), a single subcutaneous treatment group (1 mg/kg), and two double IV injection groups (6 or 10 mg/kg). Subjects were followed during < 146 days. OSE-127’s pharmacokinetic half-life after a single dose increased from 4.6 days (1mg/kg) to 11.7 days (10 mg/kg) and, after a second dose, from 12.5 days (6 mg/kg) to 16.25 days (10 mg/kg). Receptor occupancy was ≥ 95% at doses ≥ 0.02 mg/kg and this saturation level was maintained >100 days after two IV infusions at 10 mg/kg. IL-7 consumption was inhibited by OSE-127 administration, as demonstrated by a decreased IL-7 pathway gene signature in peripheral blood cells and by ex-vivo T-lymphocyte restimulation experiments. OSE-127 was well tolerated, with no evidence of cytokine-release syndrome and no significant alteration of blood lymphocyte counts or subset populations.Altogether, the observed lack of significant lymphopenia or serious adverse events, concomitant with the dose-dependent inhibition of IL-7 consumption by target cells highlight that OSE-127 may show clinical activity in IL-7R pathway-involved diseases.

overall_design: 22 paired samples (at baseline, Day15, Day57) were collected on Day 15 after administration, and 4 paired samples were collected on Day 57 for transcriptomic analysis to follow the antiIL7R signature on Healthy volunteers.

first: Nicolas

last: Poirier

first: Irène

last: Baccelli

first: Lyssia

last: Belarif

first: Riad

last: Abès

first: Géraldine

last: Teppaz

first: Caroline

last: Mary

first: Sonia

last: Poli

first: Claudia

last: Fromond

first: Sabrina

last: Pengam

first: Emilienne

last: Soma

first: Fanny

last: De Sa

first: Jean-Pascal

last: Conduzorgues

first: Cécile

last: Braudeau

first: Regis

last: Josien

first: Bram

last: Volckaert

first: Dominique

last: Costantini

first: Frédérique

last: Corallo


title: Impaired neurovascular remodeling mediated by Apelin signaling and Cdc42 activity in endothelial Rbpj deficient brain arteriovenous malformation [ChIP-seq]

city: Athens

first: Corinne

last: Nielsen

address: Irvine Hall

department: Biological Sciences

institute: Ohio University

summary: Brain arteriovenous malformations (bAVM) are characterized by enlarged blood vessels, which direct blood through arteriovenous AV shunts, bypassing the artery-capillary-vein network and disrupting blood flow. Clinically, bAVM treatments are invasive and not routinely applicable. There is critical need to understand mechanisms of bAVM pathologies and develop pharmacological therapies.  We used an in vivo mouse model of Rbpj-mediated bAVM, which develops pathologies in the early postnatal period and an siRNA in vitro system to knockdown RBPJ in human brain microvascular endothelial cells (ECs). To understand molecular events regulated by endothelial Rbpj, we conducted RNA-Seq and ChIP-Seq analyses from isolated brain ECs.  Rbpj-deficient (mutant) brain ECs acquired abnormally rounded shape (with no change to cell area), altered basement membrane dynamics, and increased EC density along AV shunts, compared to controls, suggesting impaired remodeling of neonatal brain vasculature. Consistent with impaired EC dynamics, we found increased Cdc42 activity in isolated mutant ECs, suggesting that Rbpj regulates small GTPase-mediated cellular functions in brain ECs. siRNA treated, RBPJ-deficient human brain ECs displayed increased Cdc42 activity, disrupted cell polarity and focal adhesion properties, and impaired migration in vitro. RNA-Seq analysis from isolated brain ECs identified differentially expressed genes in mutants, including Apelin, which encodes a ligand for G protein-coupled receptor signaling known to influence small GTPase activity. ChIP-Seq analysis revealed chromatin loci occupied by Rbpj in brain ECs that corresponded to G-protein and Apelin signaling molecules. In vivo administration of a competitive peptide antagonist against the Apelin receptor (Aplnr/Apj) attenuated Cdc42 activity and restored EC morphology and AV connection diameter in Rbpj-mutant brain vessels. Conclusions: Our data suggest that endothelial Rbpj promotes rearrangement of brain ECs during cerebrovascular remodeling, through Apelin/Apj-mediated small GTPase activity, and prevents bAVM. By inhibiting Apelin/Apj signaling in vivo, we demonstrated pharmacological prevention of Rbpj mediated bAVM.

overall_design: Chromatin immunoprecipitation was performed against Rbpj (Cell Signaling 1:50, #5313) from brain endothelial cells (ECs) isolated from P7 FVB/NJ mice (The Jackson Laboratories Strain 001800). Pooled isolated brain ECs from 15 biological samples per ChIP cohort were crosslinked at a final concentration of 1% formaldehyde for 10 min at RT, and crosslinking reaction quenched with glycine solution, for 5 min at RT. Nuclei from lysed cell were isolated and chromatin was digested around nucleosomal boundaries using Micrococcal nuclease (Cell Signaling). Additionally, MNase digested DNA was sonicated with a probe sonicator (20 kHz, Fisherbrand) for three sets of 10 sec pulses, at 20% amplitude. Sheared DNA fragments were electrophoresed on a 1.5% agarose gel to check DNA fragment size, ideally between 150- 800 base pairs for IP. 5 μg chromatin preparation was used for immunoprecipitation reaction overnight with rotation, at 4°C. Protein-G agarose beads (Active Motif) were added for 2 hrs with rotation, at 4°C to pulldown chromatin-Rbpj IP reaction. Bound DNA was eluted from antibody-Protein G beads and formaldehyde crosslinks were reversed at 65°C in buffer containing 5 M NaCl, 0.5 M EDTA and Proteinase K. Recovered nucleotides were treated with RNase A, and DNA was purified using silica membrane spin columns (Cell Signaling). IP-DNA and 2% Input samples were paired-end sequenced in duplicates on a NovaSeq 6000 platform.

first: Subhodip

last: Adhicary

first: Kayleigh

last: Fanelli

first: Sera

last: Nakisli

first: Brittney

last: Ward

first: Isaac

last: Pearce


title: Impaired neurovascular remodeling mediated by Apelin signaling and Cdc42 activity in endothelial Rbpj deficient brain arteriovenous malformation


title: Gene Expression Changes in Therapeutic Ultrasound-Treated Human Chronic Wound Tissue

city: Lewisburg

first: Olivia

last: Boerman

state: PA

address: One Dent Drive

department: Biomedical Engineering

institute: Bucknell University

summary: The purpose of this study was to evaluate gene expression differences in debrided human venous ulcer tissue from patients treated with low-frequency (20 kHz), low-intensity (100 mW/cm2) ultrasound compared to a sham treatment in an effort to better understand the potential biological mechanisms.

overall_design: Debrided venous ulcer tissue was collected from 32 subjects one week after sham treatment or low-frequency, low-intensity ultrasound treatment. Of these samples, 7 samples (3 ultrasound treated and 4 sham treated) yielded sufficient quality total RNA for analysis by ultra-high multiplexed PCR (Ampliseq) and expression of more than 24,000 genes was analyzed.

first: Boerman

last: Olivia

first: Abedin

last: Zahidur

first: DiMaria-Ghalili

last: Rose

first: Weingarten

last: Michael

first: Neidrauer

first: Lewin

last: Peter

first: Spiller

last: Kara


title: Identification of circular RNAs in amyotrophic lateral sclerosis

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH


title: Identification of circular RNAs in amyotrophic lateral sclerosis I

summary: Circular RNAs are abundant, covalently closed transcripts that arise in cells through back-splicing and display distinct expression patterns across cells and developmental stages.  While their functions are largely unknown, their intrinsic stability has made them valuable biomarkers in diseases like cancer.  Here, we set out to examine circRNA patterns in amyotrophic lateral sclerosis (ALS).  By RNA-sequencing analysis, we first identified circRNAs and linear RNAs that were differentially abundant in skeletal muscle biopsies from ALS and normal individuals.  Among these, 8 circRNAs were significantly elevated and 10 significantly reduced in ALS, while the linear counterparts, arising from shared precursor RNAs, did not change.  Several of these circRNAs were also differentially abundant in motor neurons derived from human induced pluripotent stem cells (iPSCs) bearing ALS mutations, and across different disease stages in skeletal muscle from a mouse model of ALS (SOD1G93A).  Interestingly, several of the circRNAs significantly elevated in muscle were significantly reduced in the spinal cord from ALS patients and ALS (SOD1G93A) mice.  In sum, we have identified differentially abundant circRNAs in ALS-relevant tissues (muscle and spinal cord) that could inform about neuromuscular molecular programs in ALS and guide the development of therapies.

overall_design: Comparative gene expression analysis of RNA-seq data from muscle biopsies from healthy (N=5) and ALS (N=5) individuals

first: Dimitrios

last: Tsitsipatis

first: Krystyna

last: Mazan-Mamczarz

first: Ying

last: Si

first: Alison

middle: B

last: Herman

first: Jen-Hao

last: Yang

first: Abhishek

last: Guha

first: Yulan

last: Piao

first: Jinshui

last: Fan

first: Jennifer

middle: L

last: Martindale

first: Rachel

last: Munk

first: Xiaoling

first: Brijesh

middle: K

last: Singh

first: Ritchie

last: Ho

first: Myriam

last: Gorospe

first: Peter

last: King


title: BaM-seq and TBaM-seq, highly multiplexed and targeted RNA-seq protocols for rapid, low-cost library generation from bacterial samples [TBaM-seq]

city: Cambridge

first: Gene-Wei

last: Li

state: MA

address: 77 Massachusetts Ave.

department: Biology

institute: Massachusetts Institute of Technology

summary: Here, we report the development of two RNA-seq library preparation protocols that increase the throughput and decrease the cost of converting RNA to cDNA libraries compatible for sequencing on high-throughput platforms. BaM-seq allows for early barcoding of samples such that many biological samples can be processed simultaneously. TBaM-seq allows for enrichment of target RNAs to decrease the required sequencing depth. Both methods are able to accurately measure gene expression changes with high technical reproducibility and agreement with gold standard, lower throughput approaches.

overall_design: Libraries prepared with TBaM-seq protocol.

first: Grace

middle: E

last: Johnson

first: Darren

middle: J

last: Parker

first: Jean-Benoit

last: Lalanne

first: Mirae


title: BaM-seq and TBaM-seq, highly multiplexed and targeted RNA-seq protocols for rapid, low-cost library generation from bacterial samples [BaM-seq]

sample_organism:
Escherichia coli
Bacillus subtilis

platform_organism:
Escherichia coli
Bacillus subtilis

overall_design: Libraries prepared with BaM-seq protocol.


title: OnePot-seq and OPT-seq, highly multiplexed and targeted RNA-seq protocols for rapid, low-cost library generation


title: Transcription factor c-Maf deletion improves streptozotocin-induced diabetic nephropathy by directly regulating Sglt2 and Glut2

city: Tsukuba

first: Akihiro

last: Kuno

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary: The transcription factor c-Maf has been widely studied and has been reported to play a critical role in embryonic kidney development; however, the postnatal functions of c-Maf in adult kidneys remain unknown as c-Maf null C57BL/6J mice exhibit embryonic lethality. In this study, we investigated the role of c-Maf in adult mouse kidneys by comparing the phenotypes of tamoxifen (TAM)-inducible c-Maf knockout mice (c-Maf flox/flox; CAG-Cre-ERTM mice named “c-Maf ΔTAM”) with that of c-Maf flox/flox control mice, 10 days after TAM injection (TAM(10d)). In addition, we examined the effects of c-Maf deletion on diabetic conditions by injecting the mice with streptozotocin (STZ), 4 weeks before TAM injection. c-Maf ΔTAM mice displayed primary glycosuria caused by Sglt2 and Glut2 downregulation in the kidneys without diabetes, as well as morphological changes and life-threatening injuries in the kidneys on TAM(10d). Under diabetic conditions, c-Maf deletion promoted recovery from hyperglycemia and suppressed albuminuria and diabetic nephropathy by causing similar effects as did Sglt2 knockout and SGLT2 inhibitors. In addition to demonstrating the unique gene regulation of c-Maf, these findings highlight the renoprotective effects of c-Maf deficiency under diabetic conditions and suggest that c-Maf could be a novel therapeutic target gene for treating diabetic nephropathy.

overall_design: Kidney mRNA profiles of 8w old c-Maf flox/flox mice (WT) and c-Maf-/- mice

first: Satoru

last: Takahashi

first: Mitsunori

last: Fujino


title: Loss of Fatty Acid Degradation by Astrocytic Mitochondria Triggers Neuroinflammation and Neurodegeneration

city: Tucson

first: Fei

last: Yin

state: Arizona

address: 1230 N Cherry Ave BSRL 471

institute: University of Arizona

summary:
To investiaged the role of astrocytic mitochondrial function in regulating brain function, we depleted the Tfam gene specifically in astrocytes of mouse brains (TfamAKO).
Gene expression profiling analysis was performed using data obtained from the RNA-seq of the hippocampus of WT and TfamAKO mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data generated from five WT and five TfamAKO mice at 6-month-of-age.

first: Yashi

last: Mi

first: Guoyuan

last: Qi

first: Yuan

last: Shang


title: Infection of bats and cell cultures with Marburg, Ebola and Rabies viruses

city: Oakland

first: Ravi

last: Sachidanandam

state: CA

address: 2945 Webster St

institute: Girihlet Inc.

summary: The response of bats to filoviral infections was studied to understand how they avoid getting sick

overall_design:
Bat cell lines, as well as live bats were infected with Marburg, Ebola and Rabies viruses to understand the innate response of bats and understand how they differ from the human response.

Grant ID: HDTRA11610033
Grant title: Comparative Immunology of Rousettus aegyptiacus Reservoir with Filovirus
Grantee: Christopher Basler
Funding source: Defense Threat Reduction Agency (DTRA)

first: Anitha

last: Jayaprakash

first: Adam

last: Ronk

first: Abhishek

middle: N

last: Prasad

first: Michael

middle: F

last: Covington

first: Kathryn

middle: R

last: Stein

first: Toni

last: Schwarz

first: Saboor

last: Hekmaty

first: Karla

middle: A

last: Fenton

first: Thomas

middle: W

last: Geisbert

first: Christopher

last: Basler

first: Alexander

last: Bukreyev


title: State- and stimulus-specific dynamics of SMAD signaling determine fate decisions in individual cells

city: Stuttgart

first: Stefan

last: Legewie

address: Allmandring 30E

department: Institute of Biomedical Genetics, Systems Biology

institute: University of Stuttgart

summary:
SMAD-mediated signaling regulates a broad range of cell fate decisions  including apoptosis, cell cycle arrest and EMT.
To elucidate how this relatively simple pathway realizes this complexity, we systematically investigate how SMAD-mediated responses are modulated by various ligands of the TGFβ family, and compare these ligand responses in quiescent and proliferating MCF10A cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for proliferating and quiescent MCF10A cells after treatment with different doses of TGFβ or GDF11.

last: Bohn

first: Lorenz

last: Hexemer

first: Zixin

last: Huang

first: Laura

last: Strohmaier

first: Sonja

last: Lenhardt

last: Loewer


title: SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry [Cut & Run]

first: Sarah-Lee

last: Bekaert

overall_design: Identification of CTCF binding sites through CUT&RUN sequencing in the neuroblastoma cell line CLB-GA.

first: Amber

last: Louwagie

first: Bieke

last: Decaesteker

first: Katleen

last: De Preter

first: Frank

last: Speleman


title: Environmentally relevant exposure to TBBPA and its analogues may not drastically affect human early cardiac development

city: 北京市

first: Renjun

last: Yang

state: 北京

address: 双清路18号林业大学北门

institute: RCEES

summary: Tetrabromobisphenol A (TBBPA) and its substitutes and derivatives have been widely used as halogenated flame retardants (HFRs), in the past few decades. As a consequence, these compounds are frequently detected in the environment, as well as human bodily fluids, especially umbilical cord blood and breast milk. This has raised awareness of their potential risks to fetuses and infants. In this study, we employed human embryonic stem cell differentiation models to assess the potential developmental toxicity of six TBBPA-like compounds, at human relevant nanomolar concentrations. To mimic early embryonic development, we utilized embryoid body-based 3D differentiation in presence of the six HFRs. Transcriptomics data showed that HFR exposure over 16 days of differentiation only interfered with the expression of a few genes, indicating those six HFRs may not have specific tissue/organ targets during embryonic development. Nevertheless, further analyses revealed that some cardiac-related genes were dysregulated. Since the heart is also the first organ to develop, we employed a cardiac differentiation model to analyze the six HFRs' potential developmental toxicity in more depth. Overall, HFRs of interest did not significantly disturb the canonical WNT pathway, which is an essential signal transduction pathway for cardiac development. In addition, the six HFRs showed only mild changes in gene expression levels for cardiomyocyte markers, such as NKX2.5, MYH7, and MYL4, as well as a significant down-regulation of some but not all the epicardial and smooth muscle cell markers selected. Taken together, our results show that the six studied HFRs, at human relevant concentrations, may impose negligible effects on embryogenesis and heart development. Nevertheless, higher exposure doses might affect the early stages of heart development.

overall_design: The differences of RNA expression in embryoid bodies after exposure to different compounds were examined.

first: Miaomiao

last: Zhao

first: Nuoya

last: Yin

first: Shichang

last: Li

first: Shuxian

last: Zhang

first: Francesco

last: Faiola


title: Toll-like receptor 3 mediates calcific aortic valve disease via a conserved mechanism of calcification

city: Innsbruck

first: Can

last: Gollmann-Tepeköylü

address: Anichstraße 35

department: Department for Cardiac Surgery

country: Austria

institute: Medical University of Innsbruck

summary: The molecular mechanisms underlying valvular immunaging are not well understood. Toll-like receptors (TLRs) are evolutionary conserved pattern recognition receptors at the interface between innate immunity and tissue repair. Here, we identify TLR3 as a central molecular regulator of calcification in cells exposed to mechanical strain. TLR3 is responsible for the phenotypic switch of valvular interstitial cells (VICs) to bone-forming cells in aortic valves and drives bone formation in vertebrates. Tlr3-/- mice exhibit an osteoporotic phenotype and are protected from CAVD. Moreover, we uncover biglycan (BGN), an extracellular matrix protein released upon mechanical tissue damage, as the first known endogenous TLR3-ligand and provide compelling evidence for receptor-ligand interaction. Our results reveal novel insights in the pathogenesis of CAVD and uncover TLR3 as a potential therapeutic target to prevent cardiovascular calcification and death.

overall_design: Gene expression profiling of human valvular interstitial cells (untreated  and treated with 20  µg/mL Poly (I:C) for 72h),  human osteoblasts, human dermal fibroblasts  (untreated  and treated with 20  µg/mL Poly (I:C) for 72h)

first: Hubert

last: Hackl

first: Johannes

last: Holfeld


title: Patient-derived organoid fibroblast co-cultures closely mimic tumor cell heterogeneity of colorectal cancer

city: Brno

first: Vaclav

last: Hejret

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

summary: Here we compare RNA expression profiles of colorectal cancer organoids grown in four different conditions, namely standard organoids medium, minimal medium without growth factors or with normal or cancer associated fibroblasts. We found majorly different expression profiles between conditions and more heterogeneous tumor cell population in organoids grown with fibroblasts.

overall_design: Evaluation of RNA expression changed caused by co-culturing of tumor cells and fibroblasts

first: Velina

middle: S

last: Atanasova

first: Crhistian

last: de Jesus Cardona

first: Carina

last: Binder

first: Julijan

last: Kabiljo

first: Andreas

last: Tiefenbacher

first: Loan

last: Tran

first: Janik

last: Clement

first: Leonhard

last: Müllauer

first: Boris

last: Tichy

first: Katharina

last: Woeran

first: Barbara

last: Neudert

first: Markus

last: Hengstschläger

last: Mitterhauser

first: Michael

last: Bergmann

first: Gabriele

last: Schweikert

first: Helmut

last: Dolznig

first: Gerda

last: Egger

last: Hartl


title: Wound memory of epidermal stem cells

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

overall_design: Refer to individual Series


title: Impaired neurovascular remodeling mediated by Apelin signaling and Cdc42 activity in endothelial Rbpj deficient brain arteriovenous malformation [RNA-seq]

first: Corinne

last: Nielsen

overall_design: Differential gene expression anlayses from isolated brain endothelial cells from P7 Cdh5(PAC)-CreERT2; Rbpjflox/WT (control) and Cdh5(PAC)-CreERT2; Rbpjflox/flox (mutant) mice in experimental triplicates (total 6 samples). Each experimental cohort included 13-15 biological samples from >3 independent litters.

first: Subhodip

last: Adhicary

first: Kayleigh

last: Fanelli

first: Sera

last: Nakisli

first: Brittney

last: Ward

first: Isaac

last: Pearce


title: CALHM6 is an immunological synapse ion channel required for macrophage-natural killer cell communication upon bacterial infection

city: Oxford

first: Sara

last: Danielli

state: Oxon

address: Roosevelt Dr, headington

department: NDORMS

institute: Kennedy Institute of rheumatology

summary: Membrane ion channels of the calcium homeostasis modulator (CALHM) family promote cell-cell crosstalk at synapses via ATP release, where ATP acts as a neurotransmitter. CALHM6, the only CALHM highly expressed in immune cells, has been linked to induction of natural killer (NK) cell anti-tumour activity. Its mechanism of action and broader functions in the immune system are, however, unclear.  Here we generated Calhm6-/- mice and report that CALHM6 is important for regulating the early innate control of Listeria monocytogenes infection in vivo. We find that CALHM6 is upregulated in macrophages by pathogen-derived signals, and that it relocates from intracellular compartment to the macrophage-NK cell synapse, facilitating ATP release and controlling the kinetics of NK cell activation. Anti-inflammatory cytokines terminate CALHM6 expression. CALHM6 forms an ion channel when expressed in the plasma membrane of Xenopus oocytes, where channel opening is controlled by a conserved acidic residue, E119, but CALHM6 is localized to intracellular compartments in mammalian cells. Our results contribute to understanding of neurotransmitter-like signal exchange between immune cells that fine-tunes the timing of innate immune responses.

overall_design: Bone marrow derived macrophages from WT and CALHM6 KO mice were left unstimulated or cultured for 24 hours in the presence of Poly(I:C) (50 ug/ml), LPS (100 ng/ml), IFN-g (10 ng/ml), Zymosan  (100ug/ml) or a combination of the above. 3 biological replicates were sequenced for every stimulation. RNA was collected and sequenced to determine differentially expressed genes between WT and CALHM6 KO BMDM for each treatment.

first: Zhongming

last: Ma

first: Eirini

last: Pantazi

first: Amrendra

last: Kumar

first: Benjamin

last: Demarco

first: Fabian

last: Fisher

first: Usha

last: Paudel

first: Jillian

last: Weissenrieder

first: Robert

last: Lee

first: Sebastian

last: Joycce

first: Kevin

last: Foskett

first: Jelena

last: Bezbradica


title: RNA-seq of U2OS treated with Harmine or INDY and their controls

city: Cologne

first: Björn

last: Schumacher

address: Joseph-Stelzmann-Str. 26

institute: CECAD Research Center

summary: RNA-seq was applied for identifying the change of transcriptome between U2OS cells with starvation-induced quiescence treated with Harmine Hydrochloride or INDY and the untreated controls.

overall_design: U2OS cells were starved for 48 hours and treated for 24 hours with Harmine 10 µM, INDY 25 µM or the equivalent amount of water or DMSO (for the Harmine control and INDY control respectively). Four samples per condition were analysed. mRNA Seq (PolyA+ selection). Paired End, 2x100bp. 50 million reads per sample. RIN = 10 for all samples.

first: Arturo

last: Bujarrabal

first: Georg

last: Sendtner

first: David

last: Meyer

first: Bjoern


title: CDK7 controls E2F- and MYC-driven proliferative and metabolic vulnerabilities in multiple myeloma

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Therapeutic targeting of CDK7 has proven beneficial in pre-clinical studies, yet the off-target effects of currently available CDK7 inhibitors make it difficult to pinpoint the exact mechanisms behind MM cell death mediated by CDK7 inhibition. Here, we show that CDK7 expression positively correlates with E2F and MYC transcriptional programs in multiple myeloma (MM) patient cells; and its selective targeting counteracts E2F activity via perturbation of the CDKs/Rb axis and impairs MYC-regulated metabolic gene signatures translating into defects in glycolysis and reduced levels of lactate production in MM cells. CDK7 inhibition using the covalent small molecule inhibitor YKL-5-124 elicits a strong therapeutic response with minimal effects on normal cells, and causes in vivo tumor regression increasing survival in several MM mouse models including a genetically engineered mouse model of MYC-dependent MM. Through its role as a critical cofactor and regulator of MYC and E2F activity, CDK7 is therefore a master regulator of oncogenic cellular programs supporting MM growth and survival, and a valuable therapeutic target providing rationale for development of YKL-5-124 for clinical use.

overall_design: Cell count normalized RNA-seq in PBMCs (24 total samples; 3 technical replicates) upon treatment with the selective covalent CDK7 inhibitor YKL-5-124

first: Mariateresa

last: Fulciniti

first: Nikhil

last: Munshi

middle: Y

first: Yao

last: Yao

first: Woojun

last: Park


title: RNA-seq for C.elegans lin-52 vs N2 (UV & non-UV)

summary: RNA-seq was applied for identifying the change of transcriptome between L1 stage lin-52 mutants and N2, with and without UV after 6h of irradiation.

overall_design: Biological triplicate of each Strain and Condition were analysed. That is, 3 samples N2 without UV, 3 with UV, 3 samples lin-52(n771) without UV, 3 with UV. Ribo-zero was applied to RNA samples, 25M pairs per sample. RIN ≥9.4 for all samples


title: Adaptive and non-adaptive gene expression changes in prostate cancer during androgen deprivation

city: Tampere

first: Reetta

last: Nätkin

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology, Prostate Cancer Research Center

country: Finland

institute: Tampere University and Tays Cancer Center

summary: In this study long-term cell cultures were used to model castration resistant prostate cancer (CRPC) and to understand the cellular mechanisms leading to CRPC. Study included a testosterone-dependent cell line (VCaP-T) and more antiandrogen resistant and AR upregulating cell line adapted to grow in low testosterone (VCaP-CT). They were used uncover persistent and adaptive responses to testosterone level. RNA was sequenced to study AR-regulated genes. To evaluate their significance for CRPC growth, we compared which of them were adaptive i.e., restored expression level in VCaP-CT. The goal was to identify novel risk genes that could be possibly used as biomarkers or therapeutic targets in the future.

overall_design: Altogether 12 samples were sequenced including 3 replicates from each VCaP-T 10nM T, VCaP-T treated with 0.1 nM T for 48h, VCaP-CT 0.1nM T and VCaP-CT treated with 10 nM T for 48h.

first: Pasi

last: Pennanen

first: Heimo

last: Syvälä

first: Merja

last: Bläuer

first: Juha

last: Kesseli

first: Teuvo

last: Tammela

first: Matti

last: Nykter

first: Teemu

last: Murtola


title: Bladder cancer organoids as a functional system to model different disease stages and therapy response

city: Bern

first: Daniel

middle: Walter

last: Hanhart

state: Bern

address: Murtenstrasse 24

department: Department for BioMedical Research (DBMR)

country: Switzerland

institute: UroGenus

summary: Bladder Cancer (BLCa) inter-patient heterogeneity is the primary cause of treatment failure, suggesting that patients could benefit from a more personalized treatment approach. Patient-derived organoids (PDOs) have been successfully used as a functional model for predicting drug response in different cancers. In our study, we established PDO cultures from different BLCa stages and grades. PDOs preserve the histological and molecular heterogeneity of the parental tumors (PTs), including their multiclonal genetic landscapes, and consistently share key genetic alterations, mirroring tumor evolution in longitudinal sampling. Our drug screening pipeline was implemented using PDOs, testing both standard-of-care and FDA-approved compounds for other tumors. Integrative analysis of drug response profiles with matched PDO genomic analysis was used to determine enrichment thresholds for candidate markers of therapy response and resistance. Finally, by assessing the clinical history of longitudinally sampled cases we were able to assess the disease clonal evolution matched with drug response.

overall_design: Single cell mRNA profile of three primary tumor samples, and from the three tumor sample grown organoids.

first: Martina

last: Minoli

first: Thomas

last: Cantore

first: Mirjam

last: Kiener

first: Tarcisio

last: Fedrizzi

first: Federico

last: La Manna

first: Sofia

last: Karkampouna

first: Panagiotis

last: Chouvardas

first: Vera

last: Genitisch

first: Antonio

last: Rodriguez-Calero

first: Eva

last: Compérat

first: Irena

last: Klima

first: Paola

last: Gasperini

first: Bernhard

last: Kiss

first: Roland

last: Seiler-Blarer

first: Francesca

last: Demichelis

first: George

last: Thalmann

first: Marianna

last: Kruithof-de Juli


title: Identification of circular RNAs in amyotrophic lateral sclerosis II

first: Supriyo

last: De

overall_design: Comparative gene expression analysis of RNA-seq data from muscle biopsies from healthy (N=5) and ALS (N=5) individuals

first: Dimitrios

last: Tsitsipatis

first: Krystyna

last: Mazan-Mamczarz

first: Ying

last: Si

first: Alison

last: Herman

first: Jen-Hao

last: Yang

first: Abhishek

last: Guha

first: Yulan

last: Piao

first: Jinshui

last: Fan

first: Jennifer

last: Martindale

first: Rachel

last: Munk

first: Xiaoling

first: Brijesh

last: Singh

first: Ritchie

last: Ho

first: Myriam

last: Gorospe

first: Peter

middle: H

last: King


title: Mitochondria Metabolism Sets the Species-Specific Tempo of Neuronal Development

city: Leuven

first: Emir

last: Erkol

address: ON5 Herestraat 49

department: Department of Neuroscience

institute: KU Leuven-VIB

summary: Neuronal development in the human cerebral cortex is considerably prolonged compared to that of other mammals. We explored whether mitochondria influence the species-specific timing of cortical neuron maturation. By comparing human and mouse cortical neuronal maturation at high temporal and cell resolution, we found a slower mitochondria development in human cortical neurons compared with that in the mouse, together with lower mitochondria metabolic activity, particularly that of oxidative phosphorylation. Stimulation of mitochondria metabolism in human neurons resulted in accelerated development in vitro and in vivo, leading to maturation of cells weeks ahead of time, whereas its inhibition in mouse neurons led to decreased rates of maturation. Mitochondria are thus important regulators of the pace of neuronal development underlying human-specific brain neoteny.

overall_design: 10x single cell RNA on the cortical differentiated H9 cell line sorted with magnetic-activated cell sorting (MACS)

first: Ryohei

last: Iwata

first: Pierre

last: Vanderhaeghen


title: A Randomized, Placebo-Controlled, Phase III Trial Evaluating Motixafortide and G-CSF to Mobilize Hematopoietic Stem Cells for Autologous Transplantation in Multiple Myeloma – The Genesis Trial

status: Public on Jan 31 2023

city: Saint Louis

first: Li

last: Ding

state: MO

address: 660 S. Euclid Avenue

institute: Washington University in St. Louis

summary: Autologous hematopoietic stem cell transplantation (ASCT) improves survival in multiple myeloma (MM). However, up to 30% of MM patients are unable to collect optimal numbers of peripheral blood (PB) CD34+ hematopoietic stem and progenitor cells (HSPCs) with standard G-CSF mobilization. Motixafortide is a novel cyclic-peptide CXCR4 inhibitor with extended receptor occupancy and enhanced in-vivo activity. The GENESIS Trial is a prospective, phase III, double-blind, placebo-controlled, international, multicenter, superiority trial with 122 adult patients randomized (2:1) to motixafortide+G-CSF or placebo+G-CSF for HSPC mobilization for ASCT in MM (NCT03246529). The primary endpoint of the study was met, with motixafortide+G-CSF enabling 92.5% of patients to collect ≥6x106 CD34+ cells/kg within 2 apheresis procedures versus 26.2% with placebo+G-CSF (p<0.0001). A key, prespecified secondary endpoint was also met, with motixafortide+G-CSF enabling 88.8% of patients to collect ≥6x106 CD34+ cells/kg in 1 apheresis versus 9.5% with placebo+G-CSF (p<0.0001). Motixafortide+G-CSF was safe and well-tolerated, with the most common treatment-emergent adverse events observed being transient, Grade 1/2 injection site reactions (pain: 50%, erythema: 27.5%, pruritis: 21.3%). In addition, extended immunophenotyping and single-cell transcriptional profiling were performed on CD34+ HSPCs mobilized on the GENESIS Trial, as well as a contemporaneous MM cohort undergoing plerixafor+G-CSF mobilization for ASCT and 3 cohorts of allogeneic HSPC donors undergoing single-agent mobilization with motixafortide, plerixafor or G-CSF alone. Motixafortide+G-CSF resulted in a 10.5-fold increase in primitive HSPCs collected versus placebo+G-CSF (p<0.0001); and significantly greater numbers of early stem and progenitors versus both placebo+G-CSF (p<0.0001) and plerixafor+G-CSF (p=0.0327). Motixafortide also preferentially mobilized HSPC subsets with upregulated gene expression pathways associated with enhanced self-renewal, regeneration and quiescence (EGF, NFB/TNF and HBO1). In conclusion, motixafortide+G-CSF mobilized significantly greater CD34+ HSPC numbers within 2 apheresis procedures versus placebo+G-CSF. Motixafortide also preferentially mobilized primitive stem and early progenitor cells with unique transcriptional profiles versus plerixafor and G-CSF.

overall_design:
As a pre-specified correlative study to further define the transcriptional profiles of CD34+ HSPCs mobilized and to specifically elucidate the impact of extended CXCR4i with motixafortide +/- G-CSF as compared to short-acting CXCR4i with plerixafor +/- G-CSF and G-CSF alone, we performed scRNA-seq on CD34+ HSPCs from the apheresis products of MM patients (N=12 total) mobilized with placebo+G-CSF (N=4), plerixafor+G-CSF (N=4) and motixafortide+G-CSF (N=4); along with CD34+ HSPCs from the apheresis product of healthy allo-donors (N=6 total) mobilized with G-CSF alone (N=2), plerixafor alone (N=2) and motixafortide alone (N=2).

Submitter states: Raw data will be submitted to dbGaP

first: Zachary

last: Crees

first: John

last: DiPersio

first: Reyka

middle: G

last: Jayasinghe


title: Comparison of NAT-lncRNA knockout effect by Next Generation Sequencing

city: Shenzhen

first: Shikuan

last: Zhang

state: Guangdong

address: Tsinghua Shenzhen International Graduate School, University Town of Shenzhen, Nanshan District

department: iBHE

institute: Tsinghua

summary: Analysis of different expression of mRNAs and lncRNAs after lncRNA DHRS4-AS1 knockout with two strategies in immortalized human pancreatic duct epithelial cell line HPDE6-C7. The strategies include promoter-exon1(PE) and branch point and 3‘ splicing site(BESST). The results provide transcriptome comparison between PE and BESST knockout approach, indicating the superior effect of BESST.

overall_design: The HPDE-C7 cell line was used in this study, CRISPR-based PE and BESST were applied to knockout DHRS4-RS1 lncRNA. Triplicates were done for each group.

first: Yue

last: Chen

first: Kunzhe

last: Dong

first: Yiwan

last: Zhao

first: Yanzhi

last: Wang

first: Songmao

first: Chen

last: Qu

first: Naihan

last: Xu

first: Weidong

last: Xie

first: Chunyu

last: Zeng

first: Qing

last: Lyu

first: Yaou


title: The effects of WTAP on m6A mRNA modification pancreatic islets

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary: Through  m6A mRNA-profiling, we aim to characterize the  m6A mRNA changes in pancreatic islets between Wtapflox/flox and Wtap-βKO mice.

overall_design:
To map the mRNA m6A modification caused by WTAP in pancreatic islets, MeRIP-seq was performed in pancreatic islets obtained from Wtapflox/flox and Wtap-βKO mice.
Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from pancreatic islets of Wtapflox/flox and Wtap-βKO mice at 7 weeks old. A total of 2 μg RNAs were pooled from ten Wtapflox/flox mice and nineteen Wtap-βKO mice, respectively. Fragmented RNA (~100 nt) was incubated for 2 hr at 4℃ with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs or Input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols. After mapping reads to the reference genome, exomePeak R package (version 2.16.0) was used for the m6A peak identification in each anti-m6A immunoprecipitation group with the corresponding input samples serving as a control, and q-value threshold of enrichment of 0.05 was used for all data sets. The m6A-enriched motifs of each group were identified by HOMER (version 4.9.1).
The islet mRNA m6A profiles in Wtapflox/flox and Wtap-βKO mice were characterized.

first: Xinzhi

last: Li

first: Ying

last: Yang


title: Chronic developmental hypoxia alters rat lung immune cell transcriptomes during allergic airway inflammation

city: Indianapolis

first: Michelle

last: Chu

state: IN

address: 635 Barnhill Drive

institute: Indiana University

summary: It is unknown how hypoxia exposure beginning at conception and maintained through adulthood, chronic developmental hypoxia (CDH), effects immune cell populations in the lung. This study utilized single cell RNA sequencing in a rat model of CDH combined with a model of OVA-induced asthma or a non-allergic model to assess the effect of CDH on lung immune cell populations in the context of allergic airway disease and in a non-allergic state.

overall_design: Rat breeding pairs were acclimated to either hypoxic (15% FiO2) (CDH) or normoxic/room air (RA) conditions for 3 weeks. Pups born to the breeding pairs were then weaned and raised in the same conditions in which they were born for. At 4-6 weeks of age, both hypoxic and normoxic animals received IP OVA (250ug in PBS) and pertussis toxin (50ng) followed by a booster 8-12 days later.  Both hypoxic and normoxic rats were then challenged with either intranasal OVA or a PBS vehicle control for 3 days. Rats were euthanized, and lungs were digested with 1% Collagenase A and processed into single-cell suspensions prior to sequencing on the 10X Gennomics Chromium platform.

first: Patricia

last: Esparza

first: Abigail

last: Pajulas

first: Rakshin

last: Kharwadkar

first: Jocelyn

first: Mark

last: Kaplan

first: Robert

last: Tepper


title: Spatial transcriptomics on human lumbar spinal cord

city: New York

first: Vilas

last: Menon

state: NY

department: Neurology

institute: Columbia University Medical Center

summary: This study includes spatial transcriptomics on the human lumbar spinal cord using the 10x Genomics Visium platform. Frozen sections of spinal cord were placed on Visium slide arrays and processed using the 10x Genomics workflow, followed by alignment and quantification using the spaceranger package.

overall_design: Spatial transcriptomics using the 10x Genomics Visium array, on 20 sections from 4 donors

first: Ariel

last: Levine


title: The effects of WTAP on islet β-cell function

last: Chen

summary:
The goal of this study is to investigate how WTAP regulates islet β-cell function.
Islets were isolated from pancreatic islets of Wtapflox/flox and Wtap-βKO mice at 7 weeks old. One islet sample was combined from three mice. Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany).  Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm38/mm10) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3.
Our study represents the first detailed analysis of islet transcriptomes from Wtapflox/flox and Wtap-βKO mice, generated by RNA-seq technology. The RNA-seq analysis showed that 3015 genes were downregulated and 2900 genes were upregulated in the pancreatic islets of Wtap-βKO mice.

overall_design: mRNA profiles in pancreatic islets of Wtapflox/flox and Wtap-βKO mice were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).


title: Dense, systematic mutagenesis to identify the features required for CSEs

city: Jamaica Plain

first: Xiaoran

last: Zhang

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

summary: Investigate the sequence features required for CSE activity and selectivity.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Candidate region was synthesized as 80 190 nt oligonucleotides tiled in 5 nt steps. Each wild type 190 nt oligonucleotide was mirrored by a matching mutant in which the central 5 nt were deleted. The activity of mutant and mirrored wt oligos was compared to identify the import sequence.

first: Yangpo

last: Cao

first: Brynn

last: Akerberg

first: William

middle: T

last: Pu


title: Osteopontin-producing microglia contribute to Alzheimer’s disease (AD) pathology and severity

city: Chongqing

first: Yiguo

last: Qiu

state: Chongqing

address: 13 Tianchi Road, Banan Distri

institute: Chongqing International Institute for Immunology

summary: We define a pathogenic subset of microglia that is distinguished by expression of the CD11c protein and by production of osteopontin (OPN). OPN production by this CD11c+ microglial subset correlates positively with disease pathology and severity in the 5XFAD mouse model and in AD patients. Genetic ablation of OPN in 5XFAD mice leads to reduced development of pro-inflammatory CD11c+ microglia, increased amyloid beta (Aβ) phagocytosis and improved cognitive function.

overall_design: Transcriptome profile of CD11c+ microglial subset of 9-mo old 5XFAD mice versus OPN-KO.5XFAD mice and the mRNA profile of CD11c+ microglia versus  CD11c- microglia of 9-mo old 5XFAD mice.

first: Xianli

last: Shen

first: Hye-Jung

last: Kim

first: Harvey

last: Cantor


title: Generate 3D genome database for atrial and ventricles and using chamber selective chromatin loops link a subset of CSEs to target genes

summary: Measurement the contribution of 3D genome structure to chamber specific transcriptional programs and CSE activity.

overall_design: P0 aCMs and vCMs were isolated and purified for H3K27ac HiChIP.


title: Transposase-accessible chromatin with high-throughput sequencing for purified neonatal aCMs and vCMs

summary: Examination of chamber selective chromatin accessibility and investigate if chromatin accessibility regulates CSEs.

overall_design: Neonatal atrial and ventricular cardiomyocytes were isolated and purified for ATAC-seq to identify the chamber selective chromatin accessibility regions.


title: Absence of the eisosome causes general transcriptome remodeling of the yeast cell

city: Prague

first: Jakub

last: Zahumensky

address: Videnska 1083

department: Functional Organization of Biomembranes

institute: Institute of Experimental Medicine, CAS

summary: We investigated the effect of the absence of the eisosome on the overall yeast transcriptome by gene expression profiling analysis. We used data obtained from RNA-seq (polyA enrichment of total RNA isolates) of 3 different strains, specifically wild type (BY4742), a strain missing PIL1 gene that forms eisosome remanants instead of eisosome and our newly described seg1Δnce102Δpil1Δ strain, which forms neither eisosomes, nor eisosome remnants, even in the response to stress.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type (BY4742), pil1Δ and seg1Δnce102Δpil1Δ cells grown in SC for 24 hours.


title: RNAi-mediated rheostat for dynamic control of AAV-delivered transgenes

city: Cambridge

first: Joseph

last: Barry

address: 675 West Kendall St

institute: Alnylam Pharmaceuticals

summary: Adeno-associated virus (AAV)-based gene therapy could be facilitated by the development of molecular switches to control the magnitude and timing of expression of therapeutic transgenes. RNA interference (RNAi)-based approaches hold unique potential as a clinically proven modality to pharmacologically regulate AAV gene dosage in a sequence-specific manner. We present a generalizable RNAi-based rheostat wherein AAV transgene expression is silenced using the clinically validated modality of chemically modified short interfering RNA (siRNA) conjugates or vectorized co-expression of short hairpin RNA (shRNA). For transgene induction, we employ REVERSIR technology, a synthetic high-affinity oligonucleotide complementary to the siRNA or shRNA guide strand to reverse RNAi activity and rapidly recover transgene expression. For potential clinical development, we report potent and specific siRNA sequences that may allow selective regulation of transgenes while minimizing unintended off-target effects. Our results establish a conceptual framework for RNAi-based regulatory switches with potential for infrequent dosing in clinical settings to dynamically modulate expression of virally-delivered gene therapies.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The high specificity of transgene-targeting siRNAs is demonstrated in vitro using measures of differential expression derived from RNA-seq data.

first: Megha

last: Subramanian

first: James

last: McIninch

first: Ivan

last: Zlatev

last: Schlegel

first: Charalambos

last: Kaittanis

first: Tuyen

last: Nguyen

first: Saket

last: Agarwal

first: Timothy

last: Racie

first: Martha

last: Alvarado

first: Kelly

last: Wassarman

first: Thomas

last: Collins

first: Tyler

last: Chickering

first: Christopher

last: Brown

first: Karyn

last: Schmidt

first: Adam

middle: B

last: Castoreno

first: Svetlana

last: Shulga-Morskaya

first: Elena

last: Stamenova

first: Kira

last: Buckowing

first: Daniel

last: Berman

middle: D

first: Anna

last: Bisbe

first: Martin

last: Maier

first: Kevin

last: Fitzgerald

first: Vasant

last: Jadhav


title: Anemia Activates a Network of Cis-Regulatory Elements in Red Blood Cell Regeneration

city: Omaha

first: Yichao

last: Zhou

state: NE

department: Genetics, Cell Biology and Anatomy

institute: University of Nebraska Medical Center

summary: Acute anemia elicits broad transcriptional changes in erythroid progenitors and precursors. We previously discovered a cis-regulatory transcriptional enhancer at the Samd14 locus (S14E) is required for survival in severe anemia. The S14E contains DNA binding motifs for GATA and TAL1, two transcription factors which bind to the enhancer and activate transcription during stress erythropoiesis. However, Samd14 is only one of dozens of anemia-activated genes. In a mouse model of acute anemia, we used single cell RNA sequencing to identify erythroid cell types which expanded and increased expression of genes that contain S14E-like cis-elements. Through orthogonal loss-of-function approaches (shRNA, sgRNA-guided Cas9 and Cas9-KRAB), we reveal that several S14E-like cis-elements are important for the expression of newly identified anemia induced genes, including the poorly studied Ssx-2 interacting protein (Ssx2ip). Ssx2ip expression was determined to play an important role in erythroid progenitor activity, cell cycle progression, and proliferation in anemia. Our results define a genome-wide mechanism in which S14E-like enhancers control transcriptional responses during erythroid regeneration. Furthermore, time course analysis of erythroid precursor gene activation in anemia revealed distinct transcriptional programs are established at earlier time points, distinct from S14E-like elements. These findings provide a framework to understand anemia-specific transcriptional mechanisms, ineffective erythropoiesis, anemia recovery and phenotypic variability within human populations.

overall_design: Single cell suspensions of 15,000 Kit+ cells isolated from female untreated control mice and Days 1, 3, 7 post-PHZ treatment were added to arrays containing 110,000 mRNA capture beads to perform Seq-well. Two replicate mice were analyzed for control and PHZ-Day3 group.

first: Venkatasai

last: Dogiparthi

first: M

last: Rowley

first: Kyle

last: Hewitt


title: Next Generation Sequencing Facilitates Quantitative Analysis of LSEC and Hepa1-6 mono- and co-cultured

city: Osaka

first: Hoang

middle: Huu

last: Truong

state: Select a State or Province

address: 1-4-3 Asahi-machi, Abeno-ku, Osaka-City, Osaka, Japan

department: Hepatology

institute: Graduate School of Medicine, Osaka City University

summary:
Purpose: investigating paracrine effects of mono- and/or co-cultured LSEC and Hepa1-6
Method: mRNA profiles of  mono- and co-cultured LSEC and Hepa1-6 were generated by deep sequencing.
Results: The RNA-seq data  confirmed that extracellular matrix-encoding genes were up-regulated by co-cultured LSEC with Hepa1-6.

first: Norifumi

last: Kawada

first: Misako

last: Sato-Matsubara

first: Truong

last: Hoang


title: Impaired iron recycling from erythrocytes is an early hallmark of aging

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: Aging affects iron homeostasis and erythropoiesis, as evidenced by tissue iron loading in rodents and common anemia in the elderly. Given thatred pulp macrophages (RPMs) continuously process iron, their cellular functions might be susceptible to age-dependent decline, affecting organismal iron metabolism and red blood cell (RBCs) parameters. However, little is known about the effects of aging on the functioning of RPMs. To study aging RPMs, we employed 10-11-months-old female mice that show serum iron deficiency and iron overload primarily in spleens compared to young controls. We observed that this is associated with iron loading, oxidative stress, diminished lysosomal activity, and decreased erythrophagocytosis rate in RPMs. We uncovered that these impairments of RPMs lead to the retention of senescent RBCs in the spleen, their excessive local hemolysis, and the formation of iron- and heme-rich large extracellular protein aggregates, likely derived from damaged ferroptotic RPMs. We further found that feeding mice an iron-reduced diet alleviates iron accumulation and reactive oxygen species build-up in RPMs, improves their ability to clear and degrade erythrocytes, and limits ferroptosis. Consequently, this diet improves splenic RBCs fitness, limits hemolysis and the formation of iron-rich protein aggregates, and increases serum iron availability in aging mice. Using RPM-like cells, we show that diminished erythrophagocytic and lysosomal activities of RPMs can be attributed to a combination of increased iron levels and reduced expression of heme-catabolizing enzyme heme oxygenase 1 (HO-1). Taken together, we identified RPM dysfunction as an early hallmark of physiological aging and demonstrated that dietary iron reduction improves iron turnover efficacy.

overall_design: RNA sequencing of samples obtained from FACS-sorted red pulp macrophages, derived from young (8-weeks-old) and aged (10-months-old) mice. Aged mice were maintained either on standard diet (200 ppm iron, denoted as Aged) or iron-reduced diet (25 ppm iron, denoted as Aged IR). Four biological replicates per experimental group were sequenced.

first: Patryk

last: Slusarczyk

first: Pratik

middle: K

last: Mandal

first: Gabriela

last: Zurawska

first: Marta

last: Niklewicz

first: Komal

last: Chouhan

first: Matylda

last: Macias

first: Aleksandra

last: Szybinska

first: Magdalena

last: Cybulska

first: Olga

last: Krawczyk

first: Sylwia

last: Herman

first: Malgorzata

last: Lenartowicz

first: Wojciech

last: Pokrzywa

first: Katarzyna

last: Mleczko-Sanecka


title: CRaTER enrichment for on-target gene-editing enables generation of variant libraries in hiPSCs

city: Seattle

first: Kai-Chun

last: Yang

state: Washington

address: 850 Republican Street

department: University of Washington, School of Medicine

institute: Institute for Stem Cell and Regenerative Medicine

summary: Generation of transgenic cell lines is limited by inefficient gene editing requiring genotypic screening of hundreds to thousands of colonies to isolate correctly gene-edited cells. Here, we describe a novel method called CRISPRa On-Target Editing Retrieval (CRaTER) that enriches for cells with on-target knock-in of a promoterless cDNA-fluorescent reporter transgene by transiently overexpressing the targeted endogenous genetic locus and sorting for fluorescent cells. We use CRaTER to enrich for rare cells with heterozygous, biallelic-editing of the endogenous, transcriptionally-inactive MYH7 locus in human induced pluripotent stem cells (hiPSC), resulting in a 9-fold enrichment compared to antibiotics selection alone. We leveraged CRaTER to enrich for heterozygous knock-in of a library of single nucleotide variants (SNV) in MYH7, a gene encoding for sarcomeric MHC-β wherein autosomal dominant missense mutations cause cardiac and skeletal myopathies. CRaTER enabled 90% enrichment of heterozygous, biallelically-edited hiPSCs – a 38.6-fold enrichment compared to antibiotics selection alone – to generate 113 SNVs comprising 78 missense variants in MYH7. hiPSCs that have undergone CRaTER enrichment can differentiate to cardiomyocytes and exhibit expected localization and expression of MHC-β fusion proteins. Together, CRaTER substantially reduces the screening required for isolation of gene-edited cells, enabling the generation of transgenic cell lines at unprecedented scale.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: pDNA, hiPSC, and cardiomyocyte MYH7 variant libraries

first: Clayton

last: Friedman

first: Shawn

last: Fayer

first: Sriram

last: Pendyala

first: Wei-Ming

last: Chien

first: Linda

last: Tran

first: Sy-Ling

last: Chao

first: Ashley

last: Mckinstry

first: Elaheh

last: Karbassi

first: Aidan

last: Fenix

first: Alexander

last: Loiben

first: Charles

last: Murry

first: Lea

last: Starita

first: Douglas

last: Fowler


title: Next-generation sequencing facilitates quantitative analysis of atrial and ventricular cardiomyocytes transcriptomes

first: Xiaoran

last: Zhang

state: MA

summary: To investigate the chamber selective transcriptional programs, we performed RNA-seq on purified cardiomyocytes. Totally we have 5 replicates for atrial cardiomyocytes and 5 replicates for ventricular cardiomyocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for atrial cardiomyocytes and ventricular cardiomyocytes.

first: Yangpo

last: Cao

first: Brynn

last: Akerberg

first: William

last: Pu


title: Deletion of miR-181ab1 reduces liver tumour progression via upregulation of CBX7

city: Sydney

first: Jinbiao

last: Chen

state: NSW

address: Building 93, RPA Hospital, Missenden Rd

country: Australia

institute: Centenary Institute

summary:
Purpose: miR-181 is upregulated in human liver cancer. The cancer genome atlas (TCGA) liver cancer data show that the iCluster1 subclass of hepatocellular carcinoma (HCC) has a higher expression of miR-181 than either the iCluster2 or iCluster3 subclass, suggesting it may be a driver of oncogenesis. However, the miR-181 family has also been reported to inhibit tumour progression. Thus, we aim to examine the function of miR-181 and its vital mediators in hepatocarcinogenesis.
Methods: Primary liver tumours were induced with diethylnitrosamine (DEN) in global (miR-181ab1GKO), liver-specific (miR-181ab1LKO) and hematopoietic & endothelial lineage-specific (miR-181ab1vavKO) miR-181ab1 deletion mice. The molecular and cellular characterization was carried out using immunohistochemistry and whole-genome transcriptome analysis. Liver-specific miR-181a and CBX7 double knockout mice were used to investigate the role of CBX7 in mediating miR-181 effects on liver tumour progression. An AAV/Transposase Hybrid-Vector System used in this study gave a reliable long-term expression of CBX7 in vivo. Relevant gene expression profiles and patient outcomes were downloaded from TCGA database, and their correlations were analysed. The mRNA profiles of miR-181ab1 wild-type (WT) and knockout (KO) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq. After quality control procedures, short reads were mapped to mouse genome assembly (mm10) by STAR version 2.7.3a. Mapped reads were quantified by featureCounts version 2.0.0 from Subread package. Ward’s hierarchical clustering method was applied to group the samples based on the gene expression matrix. Differential gene expression analysis was then conducted using R package Limma. Gene set enrichment analysis was subsequently performed with R package clusterProfiler. Overlaps between differential expressed gene sets and gene sets in MSigDB were computed with Gene Set Enrichment Analysis (GSEA).
Results: The number and size of liver tumours in 181ab1GKO mice were significantly reduced by 50% and 90%, respectively, compared to WT mice at 34-week post-DEN injection. The number of tumours in 181ab1LKO mice was no different from that of control mice, but the size of liver tumours was significantly reduced by 90%. The number and size of tumours were similar in miR-181ab1vavKO and WT mice. Consistent with the roles of miR-181 in the promotion of epithelial to mesenchymal transition (EMT), the TGF-beta signalling pathway was inhibited in 181ab1GKO tumours compared with WT tumours, and expression of E-Cadherin, an EMT marker, was significantly increased in miR-181ab1 KO tumours compared to WT tumours. CBX7 was reduced in WT liver tumours compared to non-tumours, and restored CBX7 expression inhibited the progression of liver tumours in WT mice. At the same time, CBX7 was upregulated in miR-181ab1 KO tumours compared to WT tumours, and CBX7 deletion turned the reduced progression of miR-181ab1 KO liver tumours back to WT liver tumours. MiR-181a expression was the lowest and CBX7 expression the highest in iCluster 2 & 3 subclasses of human HCC compared to iCluster 1. Gene expression profiles were significantly overlapped between human low proliferative periportal-type HCCs and miR-181ab1 KO tumours.
Conclusions: Primary liver tumour progression is inhibited by loss of miR-181ab1 via up-regulation of CBX7 expression at the level of the liver cancer cells themselves, but tumour induction requires both hepatic and non-hepatic expression. Tumours in miR-181ab1 KO mice resemble low-proliferative periportal-type human HCC and could represent a new model to study therapies for such difficult-to-treat tumours.

overall_design: Liver tumour mRNA profiles of miR-181ab1 wild type (WT) and knockout (KO) mice. Diethylnitrosamine (DEN)-induced liver cancer models were made in multiple miR-181ab1 and/or CBX7 KO mice. CBX7 was over-expressed in the liver with AAV.

first: Geoffrey

last: McCaughan


title: Effects of RDD4 overexpression in leaf sheaths

city: Tsukuba

first: Masao

last: Iwamoto

state: Ibaraki

address: 3-1-3 Kannondai

department: Division of Crop Genome Editing

institute: Institute of Agrobiological Sciences, NARO

summary: Transcriptional profiling of wild-type (WT) and RDD4 overexpressing plants (RDD4-OX) to examine function of RDD4 in rice

overall_design: WT(leaf sheath), RDD4-OX(leaf sheath). Three biological replicates (Three independent lines of RDD4-OX plants).

first: M


title: Mouse C2C12 cell line Mef2D ChIP-seq experiment

status: Public on Jan 30 2023

city: Debrecen

first: Endre

last: Barta

state: Hungary

address: Egyetem tér 1.

department: Institute of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary: DNA binding regions of MEF2D transcription factor associated with myogenic regulatory factors were investigated in differentiated myotubes using ChIP-seq analysis.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Mef2D transcription factor

first: Mónika

last: Szentandrássyné Gönczi

first: Zsolt

last: Ráduly

last: Fuxreiter


title: Interferon regulation of neonatal hematopoiesis

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

summary: single-cell RNA-seq for indicated genotypes

overall_design: Lineage neg, Kit positive and Lineage neg, Sca1 positive, Kit positive cells were isolated for CITE-seq

first: Jeffrey


title: Landscape of Prostate-Specific Membrane Antigen Heterogeneity in Metastatic Prostate Cancer [ChIP-Seq]

city: Boston

first: Himisha

last: Beltran

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana Farber Cancer Institute

summary: Prostate-specific membrane antigen (PSMA) has emerged as an important therapeutic target in metastatic castration-resistant prostate cancer (CRPC). However, not all patients respond to PSMA-targeted therapy, in part due to heterogeneity of tumor expression of the target PSMA. Furthermore, loss of PSMA expression develops in up to 15-20% of patients with CRPC, and the underlying mechanisms remain poorly defined. In this study,To investigate possible epigenetic regulation of PSMA in the context of HOXB13-independent PSMA-suppressed tumors, we performed ChIPseq to evaluate the activation mark Histone H3 Lysine 27 acetylation (H3K27ac)  on our previously characterized organoids. Similar to AR-positive, PSMA-positive 22Rv1 cells, the AR-negative, PSMA-positive NEPC model WCM1262 demonstrated H3K27ac at the PSMA (FOLH1) gene promotor corresponding with high PSMA expression, whereas other PSMA-negative NEPC models demonstrated low H3K27ac.

overall_design: We performed H3K27ac ChIPseq on 22Rv1 cell line and our previously NEPC organoids including WCM154, WCM155, WCM 1078 and WCM1262.

first: Martin

last: Bakht


title: Dynamic coding and noncoding RNA interactions coordinate gene expression during meiosis in wheat

city: Saskatoon

first: Sateesh

last: Kagale

state: SK

address: 110 Gymnasium Place

department: Aquatic and Crop Resource Development

institute: National Research Council Canada

summary: We present a high-resolution network of gene expression during meiosis and its regulatory control elements in polyploid wheat. MeioCapture method (Shunmugam et al. 2018 BMC Plant Biology 18: 293) was used for isolating high-purity sporogenous archesporial columns of synchronized male meiocytes from wheat anthers in different meiotic stages. Total RNA extracted from three independent biological replicates per developmental stage of the meiocytes, as well as vegetative flag leaf, young leaves, and reproductive anthers and pollen, was sequenced using Illumina platform, generating 548 million paired-end short mRNA reads. Filtered reads were aligned to the wheat reference genome (IWGSC v1.0) using STAR. Transcript abundance was estimated using the RSEM (v1.3.3) and the IWGSC v1.1 annotation, and read counts and transcripts per million (TPM) values that normalize counts to a consistent number per library (1 million) to facilitate the comparison of relative expression across various samples were generated.

overall_design: Gene expression analysis of meiotic stages, including pre-meiotic G2 (Pm), the sub-stages of prophase I [termed leptotene, zygotene, pachytene, and diplotene/diakinesis], metaphase I and metaphase II, as well as vegetative flag leaf and young leaves, and reproductive anthers and pollen


title: Transcriptional profiles of wild-type and dscaml1 mutant zebrafish larvae

city: Roanoke

first: Yuchin

middle: Albert

last: Pan

state: VA

address: 2 Riverside Circle

institute: Virginia Tech

summary: The purpose of the experiment was to identify the differentially expressed genes in dscaml1 mutants compared to wild-type controls

overall_design: Total RNA from 3.5-4 days-post fertizliation larvae. Each sample is from a pool of 6-11 larvae. 3 replicates each for wild-type and dscaml1 mutant.


title: Heterogeneity of islet-infiltrating interleukin-21+ CD4 T cells in a mouse model of type 1 diabetes

city: Milwaukee

first: Yi-Guang

state: WI

address: 9200 W. Wisconsin Ave.

department: Pediatrics

institute: Medical College of Wisconsin

summary: Interleukin (IL)-21 is essential for type 1 diabetes (T1D) development in the NOD mouse model. IL-21-expressing CD4 T cells are present in pancreatic islets where they contribute to disease progression. However, little is known about their phenotype and differentiation states. To fill this gap, we generated a novel IL-21 reporter NOD strain to further characterize IL-21+ CD4 T cells in T1D. IL-21+ CD4 T cells accumulate in pancreatic islets and recognize β-cell antigens. Single-cell RNA sequencing revealed that most CD4 T effector cells in islets actively express IL-21 and they are highly diabetogenic despite expressing multiple inhibitory molecules, including PD-1 and LAG3. Islet IL-21+ CD4 T cells segregate into four phenotypically and transcriptionally distinct differentiation states, less differentiated early effectors, Tfh-like cells, and two Th1 subsets. Trajectory analysis predicts that early effectors differentiate into both Tfh-like and terminal Th1 cells. We further demonstrated that intrinsic IL-27 signaling controls the differentiation of islet IL-21+ CD4 T cells, contributing to their helper function. Collectively, our study reveals the heterogeneity of islet-infiltrating IL-21+ CD4 T cells and indicates that both Tfh-like and Th1 subsets continuously produce IL-21 throughout their differentiation process, highlighting the important sources of IL-21 in T1D pathogenesis.

overall_design: Islet-infiltrating CD4 T cells from NOD.Il21V/+ mice were isolated by fluorescence-activated cell sorting (FACS) according to the presence of absence of Venus signal and analyzed by scRNA-seq.

first: Ashley

middle: E

last: Ciecko

first: Yu

last: Wang

first: Stephanie

last: Harleston

first: Amber

last: Drewek

first: David

middle: V

last: Serreze

first: Aron

middle: M

last: Geurts

first: Chien-Wei

last: Lin


title: Chamber selective enhancers identified in vivo by AAV-MPRA

first: Xiaoran

last: Zhang

summary: Measurement the activity of candidate CSEs in aCMs and vCMs.

overall_design: AAV library was delivered to P0 pups. Atria and ventricles were harvested at P7 for MPRA library construction.

first: Yangpo

last: Cao

first: Brynn

middle: N

last: Akerberg

first: William

last: Pu


title: Landscape of Prostate-Specific Membrane Antigen Heterogeneity in Metastatic Prostate Cancer  II

summary: Prostate-specific membrane antigen (PSMA) has emerged as an important therapeutic target in metastatic castration-resistant prostate cancer (CRPC). However, not all patients respond to PSMA-targeted therapy, in part due to heterogeneity of tumor expression of the target PSMA. Furthermore, loss of PSMA expression develops in up to 15-20% of patients with CRPC, and the underlying mechanisms remain poorly defined. In this study, we developed an orthotopic xenograft model of CRPC using 22Rv1 cell line, we observed lower PSMA expression in liver lesions versus other sites of metastatic disease, suggesting a potential role of the microenvironment in modulating PSMA expression. To facilitate investigation of PSMA-suppression, we cultured and immortalized a liver metastasis of 22Rv1 metastatic xenograft model in vitro as a new cell line (22Rv1-LMD) which remained AR-positive and PSMA-negative.

overall_design: Three biological replicates were analyzed for each of 3 conditions including wild type (WT) and Liver drived cell line (LV).


title: Landscape of Prostate-Specific Membrane Antigen Heterogeneity in Metastatic Prostate Cancer I

overall_design: Three orthotopic xenograft model replicates were analyzed metastatic tumors at lymph nodes (n=3) and liver (n=6).


title: RNA sequencing of lungs from WT and IFITM3 knockout mouse lungs after SARS-CoV-2 infection

city: Columbus

first: Jacob

last: Yount

state: OH

address: 460 W 12th Ave, BRT 790

department: Microbial Infection and Immunity

institute: The Ohio State University

summary: WT and IFITM3 KO mice were infected with 10^5 TCID50 SARS-CoV-2 MA10 (mouse adapted virus originally generated by the Baric Lab at UNC).  2 days post infection, RNA was extracted from lung tissue using TRIzol.  RNA library preparation and sequencing was performed by Genewiz.

overall_design: Lung mRNA analysis at 2 days post infection of WT and IFITM3 KO mice with SARS-CoV-2 MA10.


title: Replication origin mapping in the malaria parasite Plasmodium falciparum

first: Catherine

last: Merrick

address: Tennis Court road

department: Pathology

institute: University of Cambridge

summary: The malaria parasite Plasmodium falciparum replicates via schizogony: a fundamentally unusual type of cell cycle involving asynchronous replication of multiple nuclei within the same cytoplasm.  It also has one of the most A/T-biased genomes ever sequenced.  Here, we present the first comprehensive study of the specification and activation of DNA replication origins during Plasmodium schizogony.  Potential replication origins were found to be abundant, with ORC1-binding sites detected every ~800 bp throughout the genome.  They had no motif enrichment, but were biased towards areas of higher G/C content.  Origin activation was then measured at single-molecule resolution via DNAscent technology, and was much less dense than ORC1-binding sites, with origins activated preferentially in areas of low transcriptional activity.  Consistently, replication forks moved slowest through the most highly transcribed genes, suggesting that conflicts between transcription and origin firing inhibit efficient replication, and that P. falciparum has evolved its S-phase to minimise such conflicts.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HA-tagged ORC1 in Plasmodium falciparum 3D7 (ORC1-HA + pTK-BSD)

first: Francis Isidore

last: Totañes

first: Jonas

last: Gockel

first: Sarah

last: Chapman

first: Richárd

last: Bártfai

first: Michael

middle: A

last: Boemo

middle: J


title: Mapping the response of human osteocytes in native matrix to mechanical loading using RNA sequencing

city: Amsterdam

first: Chen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary: Aim: To identify differentially expressed genes by mapping the response of human primary osteocytes in their native matrix to mechanical loading using RNA sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of osteocytes in human cortical bone, which was not loaded or mechanically loaded by 2000 or 8000 µɛ for 5 min, followed by 0, 6, or 24 h post-culture without loading.

first: Huib

middle: W

last: van Essen

first: Daoud

last: Sie

first: Dimitra

last: Micha

first: Gerard

last: Pals

first: Jenneke

last: Klein-Nulend

first: Nathalie

last: Bravenboer


title: Tn5 tagments and transports oligos to single-strand DNA for high throughput sequencing

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

summary: Tn5 transposon tagments double-strand DNA and RNA/DNA hybrid to generate nucleic acids ready to be amplified for high throughput sequencing. The nucleic acid substrates of Tn5 transposon need to be explored to increase the applications of Tn5. Here, we find that Tn5 transposon is able to transport oligos into the 5’ end of single-strand DNA, which are more than 140 base pairs of nucleic acids. Based on this property of Tn5, we develop a tagmentation-based and ligation-enabled single-strand DNA sequencing method, TABLE-seq. Through a series of reaction temperature, time, and enzyme concentration tests, we managed to apply this TABLE-seq to strand-specific RNA sequencing, starting with as low as 30 picograms of total RNA. Moreover, compared with traditional dUTP based strand-specific RNA sequencing, this method detects more genes, has higher strand-specificity, and shows more evenly distributed reads across genes. Together, our results provide insights into the properties of Tn5 transposons and expand the applications of Tn5 in cutting-edge sequencing techniques.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Yanjun

last: Zhang

first: Yin

last: Tang


title: Effects of lactoferrin in PM2.5-induced nephrotoxicity

city: Taipei

first: Yung-Li

last: Wang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Graduate Institute of Clinical Medicine, Taipei Medical University

summary: Several epidemiological pieces of evidence on air pollution health effects have notably accelerated in recent years. They have described the relationship between PM2.5 (ambient fine particulate matter of <2.5 μm in diameter) and kidney diseases. Previous research has shown that lactoferrin showed renoprotective effects against some kidney diseases. In the current study, we analyzed the transcriptional profiles of PM2.5 and lactoferrin using RNA sequencing (RNA-seq) and identified the key signaling pathway in the human kidney proximal tubular epithelial cell line (HK-2 cells).

overall_design: RNA-seq of human kidney proximal tubular epithelial cell line (HK-2 cells) treated with PM2.5 and lactoferrin. Cells were pretreated with lactoferrin (40 mg/ml) for 6 h and then treated with PM2.5 (1 mg/ml) for 18 h.

first: Yu

last: Chiu

first: Wen

middle: C

last: Liu

last: Lee

first: Hui


title: BioChIP-seq analysis of atrial and ventricular cardiomyocytes

city: Jamaica Plain

first: Xiaoran

address: 14 Perkins Square, Apt 11

country: USA

institute: Boston Children's Hospital

summary: Cardiac TF and P300 chromatin occupancy in atria and ventricles.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for cardiac TFs: Gata4, Mef2a, Mef2c, Tead1, Srf, Nkx2-5, Tbx3 and P300 in atrium and ventricle cardiomyocytes cells.

first: Yangpo

last: Cao

first: Brynn

last: Akerberg

first: William

last: Pu


title: Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [RNA-Seq]

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

summary: Cohesin mediates sister chromatid cohesion and organizes the genome through the formation of chromatin loops. Two versions of the complex carrying either STAG1 or STAG2 show overlapping and specific functions and both are required to fulfill embryonic development. Cohesin-STAG1 displays longer residence time on chromatin that depends on CTCF and ESCO1 and establishes longer, long-lived chromatin loops together with CTCF. Cohesin-STAG2 shows a preferential interaction with WAPL and mediates shorter loops involved in tissue-specific transcription independently of CTCF. Here we show that the two variants respond in opposite ways to knock down of NIPBL, the putative cohesin loader that is also essential for loop extrusion. Cohesin-STAG1 levels increase on chromatin under this condition and the complex accumulates further at CTCF positions while cohesin-STAG2 is diminished genome-wide. Our data support a model in which NIPBL is not required for association of cohesin with chromatin but it is for loop extrusion, which in turn facilitates stabilization of cohesin-STAG2 at CTCF positions after being loaded elsewhere. In contrast, cohesin-STAG1 is preferentially loaded at CTCF sites independently of NIPBL. Nevertheless, loop formation by these chromatin-bound complexes is impaired and gene expression is severely affected, resembling alterations in Cornelia de Lange patients

overall_design: RNA-seq was performed in triplicates in MCF10A cells mock transfected or transfected with siRNAs for NIPBL.

last: Gimenez-Llorente

first: Ana

last: Cuadrado

first: Dácil

last: del Pilar Alonso-Gil

first: Miriam

last: Rodríguez-Corsino

last: Losada


title: LTA4H extensively associates with mRNAs and lncRNAs indicative of its novel regulatory targets

city: Wuhan

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

overall_design: The RNA-binding metabolic enzyme LTA4H is a new target for cancer chemoprevention and treatment. The elevated expression of LTA4H in laryngeal squamous cell carcinoma has been demonstrated in recent research to promote tumor proliferation, migration and metastasis without clear mechanism. To explore the potential roles of LTA4H in LSCC, we applied improved RNA immunoprecipitation and sequencing(iRIP-Seq) experiments to obtain LTA4H-bound RNA profile in modal HeLa cells and verified LTA4H-regulated genes using QRT-PCR. We found that LTA4H extensively binds to mRNAs/pre-mRNAs and lncRNAs. In the LTA4H binding peak, the frequency of AAGG motifs reported for TRA2β4 is high in both replicates. Notably, LTA4H-binding genes were significantly enriched in mitotic cell cycle, DNA repair, RNA splicing related pathways and RNA metabolism pathways, implicating a tumor-associated alternative splicing regulation mechanism. QRT-PCR validation confirmed LTA4H specifically binds to mRNAs of carcinogenesis-associated genes, including LTBP3, ROR2, EGFR, HSP90B1, and lncRNAs represented by NEAT1. These findings suggesting that LTA4H may combine with genes associated with Laryngeal squamous cell carcinoma (LSCC) as an RNA-binding protein to perform a cancer regulatory function. Our study further expanding the understanding of molecular mechanism of LTA4H as a possible LSCC clinical therapy target.

first: Tianjiao

last: Ren

first: Song

first: Wei

last: Zhou

first: Cansi


title: Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [ChIP-Seq]

overall_design: ChIP-seq for cohesin subunits SMC1A, STAG1 and STAG2 was performed in MCF10A cells mock transfected or transfected with siRNAs for NIPBL, CTCF or both. Input samples from all conditions were also sequenced.


title: Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels

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

overall_design: Refer to individual Series


title: Chemical conversion of human conventional Pluripotent Stem Cells to Trophoblast Stem Cells following transient naive genes activation.

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

institute: University of Padua

summary: In human embryos, naive pluripotent cells of the inner cell mass (ICM) generate epiblast, primitive endoderm and trophectoderm (TE) lineage, whence trophoblast cells derive. In vitro, naive pluripotent stem cells (PSCs) retain this potential and efficiently generate trophoblast stem cells (TSCs), while conventional PSCs form TSCs at low efficiency. Transient histone deacetylase and MEK inhibitions with LIF stimulation is used to chemically reset conventional to naive PSCs. Here we report that chemical resetting induces expression of both naive and TSC markers and of placental imprinted genes. A modified chemical resetting protocol allows for the fast and efficient conversion of conventional PSCs into TSCs, entailing shutdown of pluripotency genes and full activation of the trophoblast master regulators, without induction of amnion markers. Chemical resetting generates a plastic intermediate state, characterised by co-expression of naive and TSC markers, after which cells steer towards one of the two fates in response to the signalling environment. The efficiency and rapidity of our system will be useful to study cell fate transitions, and to generate models of placental disorders.

overall_design:
Study of transcriptional changes appearing after chemical resetting protocols from primed human iPSCs to naïve human iPSCs and trophoblast stem cells.
Samples analyzed: 3 replicates of H9 primed-ESCs (primed controls), 3 replicates of HPD00 primed-iPSCs (primed controls), 3 replicates of HPD01 naive-iPSCs (naïve controls), 3 replicates of HPD06 naive-iPSCs (naïve controls),  4 replicates of KiPS primed-iPSCs (primed controls), 4 replicates of KiPS-chemical resetting (post-chemical resetting samples). For the time-point analysis of the chemical conversion: 4 replicates of KiPS primed-iPSCs (primed controls), 3 replicates of H9 naive-TSCs (TSC controls), 3 replicates of HPD06 naive-TSCs (TSC controls), 3 replicates of ccTSC.01 (post-chemical resetting samples), 3 replicates of ccTSC.02 (post-chemical resetting samples), replicates of different timepoints during the chemical conversion (chemical resetting samples).

first: Irene

last: Zorzan

first: Riccardo

last: Betto

first: Giada

last: Rossignoli

first: Mattia

last: Arboit

first: Andrea

last: Drusin

first: Clelia

last: Corridori

first: Paolo

last: Martini


title: Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [Hi-C]

last: Gimenez

overall_design: In situ Hi-C was performed in mock transfected MCF10A cells (3 replicates) and cells transfected with a single oligonucleotide against NIPBL (2 replicates) or a mix of four oligonucleotides (smart pool, 2 replicates).


title: Landscape of prostate-specific membrane antigen heterogeneity and regulation in AR-positive and AR-negative metastatic prostate cancer

first: Himisha

last: Beltran