title: Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (cHi-C)

first: Ivana

last: Jerkovic

summary: Upon differentiation chromatin rewires in order to reflect its new cellular identity and function. Zfp608 locus is rewired following the differentiation from the ESCs to the NPCs. During this process the local chromatin content is remodelled with activating marks littering the region, local 3D chromatin conformation compacts the region through local chromatin contacts and the Zfp608 expression amplifies. This study investigates the cis genetic elements as well as trans elements that drive this process in order to better understand how differentiation rewiring occurs.

overall_design: cHi-C experiments of mouse ESC or NPC wt cells. cHi-C experiments of partial Zfp608 deletion, polyA insertion at the Zfp608 TSS, deletion of element A, deletion of element B, dual deletion of element A and B, deletion of CTCF motif at the element A - all in ESC and NPC cells. cHi-C of mouse ESCs that overexpress Pax6.

last: Jerković

first: Marco

last: Di Stefano

first: Hadrien

last: Reboul

first: Michael

middle: F

last: Szalay

first: Davide

last: Normanno

first: Giorgio

middle: L

last: Papadopoulos

first: Frederic

last: Bantignies

first: Giacomo

last: Cavalli

first: Flora

last: Paldi

first: Quentin

last: Szabo


title: Identification of hepatocyte-primed biliary epithelial cells in the homeostatic liver by in vivo lentiviral gene transfer to mice and non-human primates

status: Public on May 11 2024

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

type: Expression profiling by high throughput sequencing

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

sample_organism:
Macaca nemestrina
Mus musculus

platform_organism:
Macaca nemestrina
Mus musculus

overall_design: Refer to individual Series


title: Analysis of gene expression in Mel Z cells grown on Matrigel (MM).

status: Public on May 10 2024

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: RNA-Seq procedure was used for analysis of expression in melanoma cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with  BioAnalyser and  RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 14.8 millions of reads were generated for each sample.

overall_design: Analysis of gene expression in Mel Z cells grown on plastic (MP), Matrigel (MM), and on Matrigel in the presence of inhibitor(MMI).

middle: A

first: Yuri

middle: V

last: Kravatsky

first: Amalia

last: Vartanian


title: Analysis of gene expression in Mel Z cells grown on MM, MP, and with MMI


title: Long-term Urolithin A treatment ameliorates disease pathology in Alzheimer's Disease mouse models

status: Public on Jul 01 2024

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Antagonistic conflict between transposon-encoded introns and guide RNAs (RNA-Seq)

status: Public on May 06 2024

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

summary: TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function in bacteria as programmable RNA-guided homing endonucleases driving transposon maintenance through DSB-stimulated homologous recombination. Here we uncover molecular mechanisms of transposition lifecycle of IS607-family elements that, remarkably, also encode group I introns. We discover molecular features for a candidate ‘IStron’ from Clostridium botulinum that allow the element to carefully control the relative levels of spliced products versus functional guide RNAs. Our results suggest that IStron transcripts have evolved a sensitive equilibrium to balance competing and mutually exclusive activities that promote transposon maintenance while limiting adverse fitness costs on the host. Collectively, this work highlights molecular innovation in the multi-functional utility of transposon-encoded noncoding RNAs.

sample_organism:
Escherichia coli
Clostridium senegalense

overall_design: E. coli total RNA-seq profiles for CboIStron and CseIStrons, as well as total RNA-seq of C. senegalense.

first: Rimantė

last: Žedaveinytė

first: Chance

last: Meers

first: Hoang

middle: C

last: Le

first: Edan

middle: E

last: Mortman

first: Stephen

last: Tang

first: George

middle: D

last: Lampe

first: Sanjana

middle: R

last: Pesari

first: Diego

last: Gelsinger

first: Tanner

last: Wiegand

middle: H


title: Antagonistic conflict between transposon-encoded introns and guide RNAs (RIP-Seq)

overall_design: E. coli RIP-seq profiles for CboTnpB.


title: NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors (ChIP-Seq)

status: Public on May 01 2024

city: Philadelphia

first: Alessandro

last: Gardini

state: PA

address: 3601 Spruce St, Room 230

institute: The Wistar Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The pathogenesis of many rare tumor types is poorly understood, preventing the design of effective treatments. Solitary Fibrous Tumors (SFTs) are neoplasms of mesenchymal origin that affect 1/1,000,000  individuals every year and are clinically assimilated to sarcomas. SFTs are commonly found throughout the body and can be surgically removed upon diagnosis. However, 30-40% of tumors become aggressive and can locally relapse or metastasize. There are no effective treatments for malignant SFTs to date. The molecular hallmark of SFTs is a gene fusion between the NAB2 and STAT6 loci on chromosome 12, resulting in a chimeric protein of poorly characterized function called NAB2-STAT6. We use primary samples and an inducible cell model to discover that NAB2-STAT6 operates as a transcriptional coactivator for a specific set of enhancers and promoters that are normally targeted by the EGR1 transcription factor. In physiological conditions, NAB2 is primarily localized to the cytoplasm and only a small nuclear fraction is available to operate as a co-activator of EGR1 targets. NAB2-STAT6 redirects NAB1, NAB2, and additional EGR1 to the nucleus and bolster the expression of neuronal EGR1 targets. The STAT6 moiety of the fusion protein is a major driver of its nuclear localization and further contributes to NAB2’s co-activating abilities. In primary tumors, NAB2-STAT6 activates a neuroendocrine gene signature that sets it apart from most sarcomas. These discoveries provide new insight into the pathogenesis of SFTs and reveal new targets with therapeutic potential.

overall_design: NAB2-STAT6 (FLAG) and EGR1 was ChIPed in U2OS cells infected with doxycycline inducible NAB2-STAT6 expression plasmids without doxycycline treatment and after 2 days of 1ug/mL doxycycline.

first: Connor

last: Hill


title: NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors (RNA-Seq)

overall_design: 3' - mRNA Seq was done in U2OS cells infected with doxycycline inducible NAB2-STAT6 expression plasmids without doxycycline treatment and after 1, 2, and 3 days of 1ug/mL doxycycline.


title: NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors


title: An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus [snRNA-seq]

status: Public on Apr 27 2024

first: Keri

last: Martinowich

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

summary: The hippocampus contains many unique cell types, which serve the structure’s specialized functions, including learning, memory and cognition. These cells have distinct spatial topography, morphology, physiology, and connectivity, highlighting the need for transcriptome-wide profiling strategies that retain cytoarchitectural organization. Here, we generated spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. We defined molecular profiles for hippocampal cell types and spatial domains. Using non-negative matrix factorization and transfer learning, we integrated these data to define gene expression patterns within the snRNA-seq data and probe their expression in the SRT data. Using this approach, we leveraged existing rodent datasets that feature information on circuit connectivity and neural activity induction to make predictions about axonal projection targets and likelihood of ensemble recruitment in spatially-defined cellular populations of the human hippocampus. Finally, we integrated genome-wide association studies with transcriptomic data to identify enrichment of genetic components for neurodevelopmental, neuropsychiatric, and neurodegenerative disorders across cell types, spatial domains, and gene expression patterns of the human hippocampus. To make this comprehensive molecular atlas accessible to the scientific community, both raw and processed data are freely available, including through interactive web applications.

overall_design: We obtained tissue blocks of postmortem human brain containing anterior hippocampus from 10 neurotypical adult brain donors. We used the 10x Genomics Visium and 3’ Single Cell Gene Expression platforms to generate paired spatial transcriptomics and single-nucleus RNA-seq data of the human hippocampus. We performed a second spatial transcriptomics experiment using the Visium Spatial Proteogenomics (Visium-SPG) platform for two of the 10 donors.

first: Erik

last: Nelson

first: Madhavi

last: Tippani

first: Anthony

last: Ramnauth

first: Heena

last: Divecha

first: Ryan

last: Miller

first: Nicholas

middle: J

last: Eagles

first: Elizabeth

last: Pattie

first: Sang

last: Kwon

first: Svitlana

last: Bach

first: Uma

middle: M

last: Kaipa

first: Jianing

last: Yao

first: Joel

last: Kleinman

first: Leonardo

last: Collado-Torres

first: Shizhong

last: Han

first: Kristen

last: Maynard

first: Thomas

last: Hyde

first: Stephanie

last: Page

last: Hicks


title: Antagonistic conflict between transposon-encoded introns and guide RNAs

first: Samuel

last: Sternberg

platform_organism:
Escherichia coli
Clostridium senegalense


title: Linking single cell genomes and transcriptomes at scale to decode breast cancer progression [scRNA-seq]

status: Public on Apr 22 2024

city: Houston

last: Navin

state: Texas

address: 6565 MD Anderson Blvd

department: Systems Biology

institute: MD anderson Cancer Center

summary: Understanding the epithelial lineages of breast cancer and genotype-phenotype relationships requires direct measurements of the genome and transcriptome of the same single cells at scale. To achieve this, we developed wellDR-seq, the first high-genomic resolution, high-throughput method to simultaneously profile the genome and transcriptome of thousands of single cells in parallel. We profiled 33,646 single cells from 12 estrogen receptor-positive breast cancers, and identified ancestral subclones in multiple patients that showed a luminal hormone responsive lineage, indicating a potential cell-of-origin. Our data also identified sporadic copy number aberrations (CNAs) in the two luminal epithelial lineages and stromal cells. While gene expression was highly correlated with copy number in larger chromosome segments, our data reveals extensive variation at the single gene-level, reflecting differences in dosage-sensitive and dosage-insensitive genes. Overall, these data reveal the complex relationships between CNAs and gene expression in single cancer cells, improving our understanding of breast cancer progression.

overall_design:
We developed a high-genomic resolution, high-throughput nanowell single cell DNA & RNA sequencing method (wellDR-seq), that can simultaneously profile the whole genome and transcriptome from thousands of single cells. We first demonstrated wellDR-seq was capable of generating comparable data quality as unimodal scRNA-seq and scDNA-seq technologies using MDA-MB-231 cell line. We then applied it to profile 12 ER+ breast cancer patients, which identified ancestral cancer subclones and their epithelial lineages, normal epithelial cell states with somatic CNAs and revealed the impact of subclonal CNAs on gene dosage, providing insight into the complex relationship between DNA copy number and gene expression in cancer cells.
Please note that the DNA raw data was deposited to SRA (PRJNA1086561).

first: Kaile

last: Wang

first: Rui

last: Ye


title: Microglia - astrocyte cross-talk in the amyloid plaque niche of an Alzheimer’s disease mouse model as revealed by spatial transcriptomics (CosMx)

status: Public on Apr 19 2024

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

summary: In this study, we characterize the transcriptomic alterations, cellular compositions, and signaling perturbations in the amyloid plaque niche in an AD mouse model using high-resolution spatial transcriptomics (CosMx and Stereo-seq).  We discover a wide heterogeneity in the cellular composition of amyloid plaque niches, marked by an increase in microglial accumulation over time. We profile the alterations of glial cells as they are exposed to plaques, and conclude that the microglial response to plaques is consistent across different brain regions, while the astrocytic response is more heterogeneous. In turn, as the microglial density of plaque niches increases, astrocytes acquire a more neurotoxic phenotype and play a key role in inducing GABAergic signaling and decreasing glutamatergic signaling in neurons of the hippocampus. Taken together, we show that astrocytic signaling around plaque pathology is disrupted with increasing microglial density, which in turn induces an imbalance in synaptic signaling in neurons in the hippocampus.

overall_design: CosMx technology [CosMx Mouse Neuroscience Panel (950-plex); Nanostring, USA] was applied to the hippocampus and adjacent regions of AppNL-G-F KI mice at 18 months of age. Briefly, 10 µm thick tissue sections were fixed, antigen retrieval was performed and the tissue was permeabilized. Tissues from two mice were fixed onto each slide. In situ hybridisation was performed with the RNA mouse neuroscience panel, including the 18s RNA probe, and antibody morphology stain was performed with antibodies for Histone, glial fibrillary acidic protein (GFAP), 4′,6-diamidino-2-phenylindole (DAPI) and MOAB-2 for amyloid-β. Information from 84 FOV, with each FOV the size of 510 µm x  510 µm, were analyzed. After data acquisition, decoding of individual transcripts and segmentation of cells, based on Cellpose, was performed

first: Anna

last: Mallach

first: Magdalena

last: Zielonka

first: Veerle

last: van Lieshout

first: Yanru

last: An

first: Jia

last: Khoo

first: Marisa

last: Vanheusden

first: Wei-Ting

last: Chen

first: Daan

last: Moechars

last: Moechar

first: Lorena

last: Arancibia-Carcamo

first: Mark

last: Fiers

last: De Strooper


title: Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (RNA-Seq)

status: Public on May 23 2024

city: Montpellier

first: Ivana

last: Jerkovic

state: Occitanie

address: 141 rue de la Cardonille

country: France

institute: IGH, CNRS

last: Jerković

first: Marco

last: Di Stefano

first: Hadrien

last: Reboul

first: Michael

last: Szalay

first: Davide

last: Normanno

first: Giorgio

last: Papadopoulos

first: Frederic

last: Bantignies

first: Giacomo

last: Cavalli

first: Flora

last: Paldi

first: Quentin

last: Szabo


title: Increased hepatoprotective effects of the novel farnesoid X receptor agonist INT-787 versus obeticholic acid in a mouse model of nonalcoholic steatohepatitis

status: Public on Apr 11 2024

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

summary: We applied RNA sequencing to study the hepatic gene expression profile of Lep(ob/ob) mice fed the Amylin liver NASH (AMLN) diet for 14 weeks and then treated for 2 weeks with vehicle (n=10), obeticholic acid (OCA) (n=9), or INT-787 (n=9). INT-787, which is equipotent to OCA but more hydrophilic, modulated a substantially greater number of genes associated with FXR signaling, lipid metabolism, and stellate cell activation relative to OCA.

overall_design: RNA-seq of poly A-enriched RNA isolated from ob/ob NASH mice treated with vehicle (n=10), obeticholic acid (n=9), or INT-787 (n=9).

first: Kristoffer

last: Rigbolt

first: Luciano

last: Adorini

last: Feigh

first: Jonathan

last: Roth

first: Mary

last: Erickson


title: Spatiotemporal immune atlas of a clinical-grade gene-edited pig-to-human kidney xenotransplant

status: Public on Mar 27 2024

city: Birmingham

first: Rebecca

last: Asiimwe

state: Alabama

address: 1720 2nd Ave South

department: Surgery

institute: The University of Alabama at Birmingham

summary: Pig-to-human xenotransplantation is rapidly approaching the clinical arena; however, it is unclear which immunomodulatory regimens will effectively control human immune responses to pig xenografts. Here, we transplant a gene-edited pig kidney into a brain-dead human recipient on pharmacologic immunosuppression and study the human immune response to the xenograft using spatial transcriptomics and single-cell RNA sequencing. Human immune cells are uncommon in the porcine kidney cortex early after xenotransplantation and consist of primarily myeloid cells. Both the porcine resident macrophages and human infiltrating macrophages express genes consistent with an alternatively activated, anti-inflammatory phenotype. No significant infiltration of human B or T cells into the porcine kidney xenograft is detectable. Altogether, these findings provide proof of concept that conventional pharmacologic immunosuppression is sufficient to restrict infiltration of human immune cells into the xenograft early after compatible pig-to-human kidney xenotransplantation.

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design:
Wild-type pig and human kidneys were procured. Porcine kidney biopsies were flash frozen in optimal cutting temperature, then processed and analyzed using the 10X Genomics Visium Spatial Transcriptomics platform
Please note that the C9WTB* processed data is generated from all Wild Type Pig Kidney_L* samples and is linked to the Wild Type Pig Kidney_L1 sample records.

first: Matthew

last: Cheung

first: Elise

middle: N

last: Erman

first: Christopher

last: Fucile

first: Shanrun

last: Liu

first: Chiao-Wang

last: Sun

first: Vidya

middle: S

last: Hanumanthu

first: Harish

last: Pal

first: Emma

last: Wright

first: Gelare

last: Ghajar-Rahimi

first: Daniel

last: Epstein

first: Babak

last: Orandi

first: Vineeta

last: Kumar

first: Douglas

last: Anderson

first: Morgan

last: Greene

first: Markayla

last: Bell

first: Stefani

last: Yates

first: Kyle

last: Moore

first: Jennifer

last: LaFontaine

first: John

middle: T

last: Killian Jr.

first: Gavin

last: Baker

first: Jackson

last: Perry

first: Zayd

last: Khan

first: Rhiannon

last: Reed

first: Shawn

last: Little

first: Alexander

last: Rosenberg

first: James

last: George

first: Jayme

last: Locke

first: Paige

last: Porrett


title: Microglia - astrocyte cross-talk in the amyloid plaque niche of an Alzheimer's disease mouse model as revealed by spatial transcriptomics

first: Bart

last: de Strooper


title: TnpB homologs exapted from transposons are RNA-guided transcription factors

first: Samuel

last: Sternberg

summary: Transposon-encoded tnpB and iscB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination. These widespread gene families were repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas12. We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas. Here, using phylogenetics, structural predictions, comparative genomics, and functional assays, we uncover multiple instances of programmable transcription factors that we name TnpB-like nuclease-dead repressors (TldR). These proteins employ naturally occurring guide RNAs to specifically target conserved promoter regions of the genome, leading to potent gene repression in a mechanism akin to CRISPRi technologies invented by humans. Focusing on a TldR clade found broadly in Enterobacteriaceae, we discover that bacteriophages exploit the combined action of TldR and an adjacently encoded phage gene to alter the expression and composition of the host flagellar assembly, a transformation with the potential to impact motility, phage susceptibility, and host immunity. Collectively, this work showcases the diverse molecular innovations that were enabled through repeated exaptation of transposon-encoded genes, and reveals the evolutionary trajectory of diverse RNA-guided transcription factors.

sample_organism:
Enterobacter cloacae
Escherichia coli
Enterobacter sp. BIDMC93

overall_design:
E. coli genome ChIP-seq profiles for 16 RNA-guided endonuclease-dead proteins. 17 samples were sequenced in total. The raw read file "Input_Eco_dTnpB_ChIP-seq_paired_raw" is a control sample which was used as a reference sample for MACS3 peak calling.

RIP-seq for a subset of the 16 RNA-guided endonuclease-dead proteins tested using ChIP. Total RNA-seq of several Enterobacter species encoding endogenous RNA-guided endonuclease-dead proteins.

first: Tanner

last: Wiegand

first: Florian

last: Hoffmann

first: Matthew

middle: W

last: Walker

first: Stephen

last: Tang

first: Egill

last: Richard

first: Hoang

last: Le

first: Chance

last: Meers


title: Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq)

first: Ivana

last: Jerkovic

last: Jerković

first: Marco

last: Di Stefano

first: Hadrien

last: Reboul

first: Michael

last: Szalay

first: Davide

last: Normanno

first: Giorgio

last: Papadopoulos

first: Frederic

last: Bantignies

first: Giacomo

last: Cavalli

first: Flora

last: Paldi

first: Quentin

last: Szabo


title: NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors (ATAC-Seq)

first: Alessandro

last: Gardini

overall_design: Omni-ATAC-seq was done in U2OS cells infected with doxycycline inducible NAB2-STAT6 expression plasmids without doxycycline treatment and after 2 days of 1ug/mL doxycycline.

first: Connor

last: Hill


title: Single cell approaches define two mammalian oligodendrocyte precursor cell populations and their evolution over developmental time [scRNA-seq]

status: Public on Mar 05 2024

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

department: Division of Neurology

country: Canada

institute: The University of British Columbia

summary: Here, we have used single-cell RNA sequencing (scRNA-seq), single-cell ATAC sequencing (scATAC-seq) and spatial transcriptomics to characterize murine cortical OPCs throughout postnatal life. During development, we identify two differentially-localized PDGFRα-positive OPC populations that are transcriptionally and epigenetically distinct. One population (active or actOPCs) is metabolically active and is enriched in white matter. The second (homeostatic or hOPCs) is less active, enriched in grey matter, and predicted to derive from actOPCs. In adulthood, these two groups are transcriptionally but not epigenetically distinct, and relative to developing OPCs are less active metabolically with much less open chromatin. When adult oligodendrogenesis is enhanced following experimental demyelination, adult OPCs do not reacquire a developmental open chromatin state, and the oligodendrogenesis trajectory is distinct from that seen neonatally. These data support a model where two OPC populations subserve distinct postnatal functions, and where neonatal and adult OPC-mediated oligodendrogenesis are fundamentally different.

overall_design: High-throughput single cell transcriptomic profiles of P2, P7, P15 and P60 from the mouse brain (SVZ and cortex) generated by single cell RNA sequencing using the 10X Genomics platform.

first: Daniel

last: Dennis

first: Beatrix

last: Wang

first: Konstantina

last: Karamboulas

first: David

last: Kaplan


title: Identification and targeting of extremely high-risk gamma delta T-ALL in children

status: Public on Mar 01 2024

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL


title: Targeting Immune-Fibroblast Crosstalk in Myocardial Infarction and Cardiac Fibrosis II

city: South San Francisco

first: Xin

last: Luo

state: CA

address: 750 Gateway Blvd

department: Research and Development

institute: Amgen Inc

summary: To examine whether commonly used human cultured fibroblast systems model human cardiac fibroblasts, we tested three different fibroblast cell preparations: primary human cardiac fibroblasts (NHCF), human dermal fibroblasts (NHDF), and immortalized human cardiac fibroblasts (iHCF).

overall_design: Each fibroblast cell line was treated with vehicle, TGF-β, or IL-1β for 72 hours and scRNAseq performed. Multiple biological and technical replicates were included, individually hash tagged, and pooled to minimize any potential batch effects.

first: Kory

last: Lavine

first: Junedh

last: Amrute

first: Tracy

last: Yamawaki

first: Chi-Ming

last: Li

first: Brandon

last: Ason

first: Sally

middle: Y

last: Shi


title: Single cell RNA seq data of normal and DMED rat corpus cavernosum

status: Public on Feb 26 2024

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

country: China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

summary: we profiled the scRNA-seq of 4 DMED and 2 normal rat corpus cavernosum. Corpus cavernosum tissue was collected 4 weeks after successful modeling.

overall_design: Single cell RNA seq data of normal and diabetes mellitus erection dysfunction (DMED) SD rat corpus cavernosum


title: Identification and targeting of extremely high-risk gamma delta T-ALL in children [HiChIP, ChIP and ATAC]

summary: STAG2/LMO2 subtype in T-ALL was investigated through integrative genomic analysis.  H3K27ac HiChIP was used to investigate the impact of LMO2::STAG2 translocations in MOLT-14 and PER-117 cell lines.  ChIP-seq was used to explore the effects of STAG2 inactivation by using gene-edited MOLT-14 and PF382 cell lines.

overall_design: Chromatin interactions in leukemia cell lines using H3K27ac HiChIP. Effects of STAG2 inactivation in gene-edited leukemia cell lines using ChIP-seq (H3K27ac, STAG1, STAG2).

first: Shunsuke

last: Kimura

first: Charles

last: Mullighan


title: Blood gene expression biomarkers of response to anti-TNF drugs in pediatric patients before initiation of treatment

city: Madrid

first: Luis

middle: Andrés

last: López Fernández

state: Madrid

address: Servicio Farmacia, Doctor Esquerdo 46

country: Spain

institute: Hospital General Universitario Gregorio Marañón

summary:
Background/aims: Changes in gene expression profiles among individuals with inflammatory bowel diseases (IBDs) could potentially influence the responsiveness to anti-TNF treatment. The aim of this study was to identify genes that could serve as predictors of early response to anti-TNF therapies in pediatric IBD patients prior to the initiation of treatment.Methods: We conducted a prospective, longitudinal, and multicenter study, enrolling 24 pediatric IBD patients aged less than 18 years who were initiating treatment with either infliximab or adalimumab. RNA-seq from blood samples was analyzed using the DESeq2 library by comparing responders and non-responders to anti-TNF drugs.
Results: Bioinformatic analyses unveiled 102 differentially expressed genes, with 99 genes exhibiting higher expression in responders compared to non-responders prior to the initiation of anti-TNF therapy. Functional enrichment analyses highlighted defense response to Gram-negative bacteria (FDR =2.3 ×10–7) as the most significant biological processes, and hemoglobin binding (FDR =0.002), as the most significant molecular function. Gene Set Enrichment Analysis (GSEA) revealed notable enrichment in transcriptional misregulation in cancer (FDR =0.016). Notably, 13 genes (CEACAM8, CEACAM6, CILP2, COL17A1, OLFM4, INHBA, LCN2, LTF, MMP8, DEFA4, PRTN3, AZU1, and ELANE) were selected for validation, and a consistent trend of increased expression in responders prior to drug administration was observed for most of these genes, with findings for 4 of them being statistically significant (CEACAM8, LCN2, LTF2, and PRTN3).
Conclusions: We identified 102 differentially expressed genes involved in the response to anti-TNF drugs in children with IBDs and validated CEACAM8, LCN2, LTF2, and PRTN3. Genes participating in defense response to Gram-negative bacterium, serine-type endopeptidase activity, and transcriptional misregulation in cancer are good candidates for anticipating the response to anti-TNF drugs in children with IBDs.

overall_design: Expression profiling by high throughput sequencing. Whole gene expression profiles from total RNA isolated from whole-blood samples of children with inflammatory bowel disease of 12 responders and 12 non-responders taken before biologic administration were analyzed by RNA next-generation sequencing. The other 12 samples were taken from GSE159034.

last: López-Fernández

first: S

last: Salvador-Martín

first: Perceval

last: Velosillo


title: CASZ1 is essential for activation of epidermal terminal differentiation

city: Evanston

first: Stephenie

last: Droll

state: IL

address: Hogan 2-100 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

summary: CASZ1 is a novel and potent activator of terminal epidermal differentiation. CASZ1 knockdown inhibits transcription of the epidermal differentiation program. p63 and p300 are required to activate CASZ1 expression.

overall_design:
RNA-sequencing of control and CASZ1 siRNA-treated keratinocytes in the differentiated condition. 2 replicates per condition.
ChIP-sequencing of p63 and H3K27ac in progenitor and differentiated keratinocytes. 2 replicates per condition.

first: Xiaomin

last: Bao


title: Single-cell analysis of tobacco-associated lung adenocarcinoma development

status: Public on Feb 16 2024

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Understanding cellular processes underlying early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies. Here, we performed single-cell RNA sequencing (scRNA-seq) of mouse lungs from Gprc5a-/- mice during lung tumor development. We coupled scRNA-seq analysis with spatial transcriptomics of tumor-bearing lungs.

overall_design: scRNA-seq profiling was performed on lungs from Gprc5a-/- mice treated with nicotine-derived nitrosamine ketone (NNK) or saline at the end of exposure (EOE, timepoint at which lungs are still clear of lesions), at 3 months and at 7 months post-exposure, the time point of Kras-mutant LUAD onset in all mice (n = 4 mice per group and time point). We also performed scRNA-seq of GFP+ and GFP- fractions of lungs from Gprc5a-/- mice carrying alveolar type II reporter (Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+) at three months post-exposure to saline of NNK (n = 2 mice per group). scRNA-seq was performed using the 10X Genomics platform. Spatial transcriptomics of tumor-bearing lungs from Gprc5a-/- mice at 7 months post-exposure to NNK (n = 3) was performed using the Visium platform from 10X Genomics to further characterize and validate scRNA-seq findings in a spatial context.

first: Guangchun

last: Han

first: Fuduan

last: Peng


title: PanIN and CAF Transitions in Pancreatic Carcinogenesis Revealed with Spatial Data Integration

status: Public on Feb 06 2024

first: Luciane

middle: Tsukamoto

last: Kagohara

state: MD

address: 1650 Orleans St - Rm 485

department: Oncology

institute: Johns Hopkins University

summary: This study introduces a new imaging, spatial transcriptomics (ST), and single-cell RNA-sequencing (scRNA-seq) integration pipeline to characterize neoplastic cell state transitions during tumorigenesis. Our semi-supervised analysis pipeline was applied to examine pancreatic intraepithelial neoplasias (PanIN), the most frequent premalignant lesions that can develop into pancreatic adenocarcinoma (PDAC). Their strict diagnosis on FFPE samples has limited previous characterization of human PanINs within their microenvironment through single-cell approaches. We leverage unbiased whole transcriptome FFPE spatial profiling to enable this characterization in a rare cohort of matched low-grade and high-grade PanIN lesions to track progression and map cellular phenotypes relative to scRNA-seq data of advanced PDAC tumors. We demonstrate that cancer associated fibroblasts (CAF), including antigen-presenting CAFs (apCAF), are located close to PanINs. We further observed a transition from CAF-related inflammatory signaling to cellular proliferation during PanIN progression. We use these findings to guide panel design to perform single-cell validation with high-dimensional imaging proteomics and transcriptomics technologies. Altogether, our pipeline for spatial multi-omics characterization provides a resource for future PanIN studies. Moreover, our semi-supervised learning framework to spatial multi-omics has broad applicability across cancer types to decipher the spatiotemporal dynamics of carcinogenesis.

overall_design:
Spatial transcriptomics with Visium (10x Genomics) was performed on pancreatic intraepithelial neoplasia (PanIN) lesions from surgical specimens obtained from patients with pancreatic ductal adenocarcinoma. Spatial gene expression analyses was performed between normal epithelial cells and PanIN lesions.

NOTE:
The Xenium data input data (of 5 tissue sections from surgical sections of resected primary pancreatic ductal adenocarcinoma from 3 unique human subjects) are available in GSE267680, which is to recreate results of validation experiments conducted as an extension of analyses conducted with GSM8058242-GSM8058255).

***************************************************************
human raw data not provided due to privacy concern. Submitter states that missing raw data are being made available for controlled access in dbGaP.
***************************************************************

first: Alexander

last: Bell

first: Jacob

last: Mitchell

first: Ashley

last: Kiemen

first: Elana

last: Fertig


title: Transcription–replication conflicts underlie sensitivity to PARP inhibitors

status: Public on Apr 12 2024

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

summary: To examine replication fork progression firing upon TIMELESS/TIPIN knockdown, EdUseq was performed in HeLa cells transfected with siCTRL, siTIMELESS or siTIPIN, synchronised with Thymidine and then released for 120 min in S phase, with the last 30 minutes being labeled with EdU.

overall_design: Cells were collected by mitotic shake-off and allowed to progress through the cell cycle for 12 hours in the presence of 5-ethynyl2′-deoxyuridine (EdU) and hydroxyurea (HU). EdU-labelled DNA was then isolated and subjected to high-throughput sequencing (EdUseq-HU)

first: Michalis

last: Petropoulos

first: Angeliki

last: Karamichali

first: Giacomo

middle: G

last: Rossetti

first: Alena

last: Freudenmann

first: Luca

last: Iacovino

first: Sotirios

middle: K

last: Sotiriou

first: Thanos

last: Halazonetis


title: Senescence progression in the normal human fibroblast, WI-38 cells induced with plasma membrane damage, calcium influx, DNA damage and telomere shortening.

status: Public on Jan 24 2024

city: Onna-son, Kunigami-gun

first: Nurhanani

last: Razali

state: Okinawa

address: 1919-1 Tancha

department: Membranology

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University (OIST)

summary: To investigate the comparison of senescence progression in plasma membrane damage-, calcium influx-, DNA damage- and telomere shortening-induced senescence in the normal human fibroblast cells.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of these four senescence inducers in human normal fibroblast cells at day 0, 1, 2, 3, 4, 6, 8 and 16 days after inducing with the senescence inducers.

first: Yatzu

last: Chiu

first: Yohsuke

last: Moriyama

first: Keiko

last: Kono


title: Verification of Molecular Subtyping of Bladder Cancer in the GUSTO Clinical Trial

status: Public on Jan 18 2024

city: Sheffield

first: Jon

last: Griffin

address: Beech Hill Road

department: School of Medicine and Population Health

country: United Kingdom

institute: University of Sheffield

summary: The GUSTO clinical trial (Gene expression subtypes of Urothelial carcinoma: Stratified Treatment and Oncological outcomes) uses molecular subtypes to guide neoadjuvant therapies in participants with muscle-invasive bladder cancer (MIBC). Before commencing the GUSTO trial, we needed to determine the reliability of a commercial subtyping platform (Decipher Bladder; Veracyte) when performed in an external trial laboratory as this has not been done previously. Here we report our pre-trial verification of the TCGA molecular subtyping model using gene expression profiling. Formalin fixed paraffin embedded tissue blocks of MIBC were used for gene expression subtyping by gene expression microarrays. Intra- and inter-laboratory technical reproducibility, together with quality control of laboratory and bioinformatics processes were assessed. Eighteen samples underwent analysis. RNA of sufficient quality and quantity was successfully extracted from all samples. All subtypes were represented in the cohort. Each sample was subtyped twice in our laboratory and once in a separate reference laboratory. No clinically significant discordance in subtype occurred between intra- or inter-laboratory replicates. Examination of sample histopathology showed variability of morphological appearances within and between subtypes. Overall, these results show that molecular subtyping by gene expression profiling is reproducible, robust, and suitable for use in the GUSTO clinical trial.

overall_design: In this study we did gene expression subtyping using gene expression microarrays. Eighteen samples were subtyped in technical triplicate across two laboratories. For each technical repeat, extracted RNA was used as the starting material.


title: Primary human preadipocyte differentiation using bulk RNA-sequencing

city: Los Angeles

first: Asha

last: Kar

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: University of California Los Angeles

summary: We performed bulk RNA-sequencing on primary human preadipocytes in which we induced differentiation, and collected samples at 6 timepoints across 14 days. The purpose of our study was to study gene expression during the course of preadipocyte differentiation into adipocytes.

overall_design: We induced a 14 day differentiation in cryopreserved human subcutaneous primary white preadipocytes. We collected RNA at the 0, 1, 2, 7, and 14 day timepoints with four replicates at each time point. RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA kit and sequenced on one lane of an Illumina NovaSeq S1 flowcell to produce an average of 42 million reads per sample.

first: Kristina

last: Garske

first: Päivi

last: Pajukanta


title: Engineering Large-Scale and Innervated Functional Human Gut for Transplantation

status: Public on Dec 01 2023

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: In this study, we utilize a scaffolding tray for organoid development. Conventional organoids are compared to those generated using the scaffolding tray.

overall_design: Single nucleus RNA sequencing was preformed on transplanted organoids.

first: Holly

last: Poling

first: Akaljot

last: Singh


title: Abnormal Immune Programming in Neutrophils of Cystic Fibrosis

status: Public on Nov 09 2023

city: New Orleans

first: Guoshun

last: Wang

state: LA

address: CSRB 607, 533 Bolivar Street

institute: Louisiana State University Health Sciences Center

summary: This study performed single-cell RNA sequencing (scRNA-seq) analyses on peripheral blood neutrophils from cystic fibrosis (CF) patients and healthy controls (HC) in their native state and LPS-activated state. Differences in global gene transcription were interrogated and compared. Results demonstrate that CFTR loss of function in CF neutrophils led to abnormal immune programming, exemplified by precocious priming at their native state, and abnormal immune response to LPS.

overall_design: Peripheral blood (~10 cc) from cystic fibrosis patients and healthy controls was drawn using a BD EDTA-purple top Vacutainer tube. Neutrophils were isolated by Percoll-density gradient centrifugation method, and were split into two aliquots. One was immediately processed for sc-RNA-seq, and the other was cultured and stimulated with Pseudomonas aeruginosa LPS (40 µg/ml) for 16 hours, followed by scRNA-seq.

first: Yawen

last: Hu


title: HILPS, a novel long non-coding RNA essential for global oxygen sensing in human

status: Public on Oct 18 2023

city: Chapel Hill

first: Donghai

state: North Carolina

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill (UNC)

summary: Adaptation to low levels of O2 (hypoxia) is a universal biological feature across metazoans. Yet the underlying mechanisms how different species sense O2 deprivation remain to be deciphered. Here we functionally characterize a novel long non-coding RNA (lncRNA), LOC105369301, which we termed hypoxia-induced lncRNA for PLK1 stabilization or HILPS. HILPS exhibits appreciable basal expression exclusively in a broad range of human normal and cancer cells and is robustly induced by hypoxia inducible factor 1α (HIF1α). HILPS binds PLK1 and sequesters it from proteasome degradation. Stabilized PLK1 directly phosphorylates HIF1α and enhance its stability, constituting a positive feedforward circuit that reinforces oxygen sensing by HIF1α. HILPS inactivation triggers catastrophic adaptation defect during hypoxia in both normal and cancer cells. These findings introduce a mechanism that underlies the HIF1α identity deeply interconnected with PLK1 integrity, and identify the HILPS-PLK1-HIF1α pathway as a crucial oxygen-sensing axis in regulation of human physiological and pathogenic processes.

overall_design: We performed RNA-Seq analysis in two normal cell lines (H9 and NCM460) and two cancer cell lines (RKO and MDA-MB-231) to screen and identify hypoxia/HIF1α/HIF1β-induced lncRNAs. We further performed RNA-Seq analysis in H9 cells and human colorectal cancer organoids to investigate the function of HILPS under 1% O2.

first: Zhi

last: chen

first: Guoliang

last: Qing


title: Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

status: Public on Oct 17 2023

city: Uppsala

first: Olga

last: Krali

address: Husargatan 3

country: Sweden

institute: Uppsala University

summary: Genomic analyses have redefined the molecular subgrouping of pediatric acute lymphoblastic leukemia (ALL). Molecular subgroups guide risk-stratification and targeted therapies, but outcomes of recently identified subtypes are often unclear, owing to limited cases with comprehensive profiling and cross-protocol studies. We developed a machine learning tool (ALLIUM) for the molecular subclassification of ALL in retrospective cohorts as well as for up-front diagnostics. ALLIUM uses DNA methylation and gene expression data from 1131 Nordic ALL patients to predict 17 ALL subtypes with high accuracy. ALLIUM was used to revise and verify the molecular subtype of 281 B-cell precursor ALL (BCP-ALL) cases with previously undefined molecular phenotype, resulting in a single revised subtype for 81.5% of these cases. Our study shows the power of combining DNA methylation and gene expression data for resolving ALL subtypes and provides a comprehensive population-based retrospective cohort study of molecular subtype frequencies in the Nordic countries.

overall_design:
Gene expression profiling of primary pediatric ALL samples taken at diagnosis (n = 315), relapse (n = 8), fractionated blood cells from healthy blood donors (n = 10) and remission samples (n = 2).
Technical replicates were generated from four patients.
***Please nota that raw FASTQ files will not be submitted to a repository because the patients providing the samples were not consented for raw data deposition****

first: Jessica

last: Nordlund

first: Gudmar

last: Lönnerholm

first: Yanara

last: Marincevic-Zuniga

first: Gustav

last: Arvidsson


title: Identification and targeting of extremely high-risk gamma delta T-ALL in children [RNA-seq]

first: QINGSONG

last: GAO

overall_design: Effects of STAG2 inactivation in gene-edited leukemia cell lines using RNAseq.

first: Shunsuke

last: Kimura

first: Charles

last: Mullighan


title: Sepsis-associated acute kidney injury in mice and humans elicits heterogeneous renal microvascular microRNA responses

status: Public on Dec 31 2023

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

type: Non-coding RNA profiling by high throughput sequencing

summary: Microvascular endothelial cells play important roles in sepsis-associated acute kidney injury (SA-AKI). In this study, we focused on microvascular microRNAs changes following SA-AKI to identify microRNAs as novel druggable targets and microvasculature-related early biomarkers of SA-AKI. Using small RNA sequencing we identified 40 differentially expressed microRNAs in the renal microvasculature in response to SA-AKI. While the induction of most microRNAs was restricted to a single microvascular compartment, miR-21-5p levels were increased across the renal microvasculature in both mice and humans following SA-AKI. Functional assessment in vitro revealed that inhibition of hsa-miR-21-5p exacerbated endothelial inflammatory activation, suggesting a protective role of this microRNA in endothelial cells. Furthermore, patients with SA-AKI exhibited elevated hsa-miR-21-5p levels in plasma compared with critically ill sepsis patients without AKI. These results highlight the potential of hsa-miR-21-5p and other microRNAs as therapeutic targets and biomarkers in SA-AKI.

overall_design: MicroRNA analysis in microvascular compartments from mouse kidney cortex (arterioles, glomeruli, peritubular capillaries, post-capillary venules) to reveal altered microRNA transcription in response to sepsis-induced acute kidney injury

first: Matthijs

last: Luxen

first: Tamar

last: van der Aart

first: Rianne

last: Jongman

first: Peter

last: Zwiers

first: Jill

last: Moser

first: Marianne

last: Pultar

first: Susanna

last: Skalicky

first: Hjalmar

last: Bouma

first: Jacqueline

last: Koeze

first: Matthias

last: Hackl

first: Grietje

last: Molema

first: Matijs

last: van Meurs


title: Transcriptomic clock predicts vascular changes of prodromal diabetic retinopathy

status: Public on Aug 10 2023

city: Cleveland

first: Peng

last: Jiang

address: 2121 Euclid Ave

institute: Cleveland State University

summary: We performed RNA-Seq on fresh whole retinal vasculature from 28 Nile rats with a large dynamic range of acellular capillary density (ACD).

overall_design: Whole retinal vasculature was used for RNA-seq.

first: Jiang

last: Peng


title: Human gingival immune cell atlas unveils the impaired B cell development in aggressive periodontitis

status: Public on Apr 02 2024

city: Seoul

first: Byeongsoo

last: Eom

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

summary: Aggressive periodontitis (AP; Grade C, Stage 3-4) is rapid destructive condition of periodontium triggered by an imbalanced immune reaction with dysbiosis of periodontal pathogens. AP is characterized by extensive tooth loss in early ages due to its severe nature and rapid progression, significantly impacting the affected individual's quality of life. Despite the severity and refractoriness of the disease, the precise pathophysiology of this hyper-reactive phenotype remains unclear. In this study, we dissected the distinct immunological features in AP by establishing the comprehensive human gingival cell atlas on individuals with AP, chronic periodontitis (CP), and healthy controls (HC). Iterative clustering analysis based on the single-cell transcriptome revealed the distinct populations in B and plasma cells upon the periodontal conditions. AP group exhibited a significant rise in B cells including a unique cell cluster dominantly expressing ID3, a key suppressor of plasma cell development. This observation is coordinated with the impaired phenotypes of antibody class switching in AP patients. Remarkably, the secreted IgM gingival crevicular fluid from AP patients exhibited the autoreactivity to gingival tissues, suggesting a potential autoimmune mechanism that involved in AP pathogenesis. These findings highlight distinct immune cell and antibody profiles in AP, providing the insights into the groundwork for personalized monitoring and proactive intervention approaches to mitigate irreversible tissue damage.

overall_design: Comparative gene expression profiling analysis of RNA-seq data

first: Seung Cheol

last: Lee

first: Byeong Soo

first: Jin Man

last: Kim

first: Jae-Kook

last: Cha


title: miR-9-5p is downregulated in serum extracellular vesicles of patients treated with biperiden after traumatic brain injury

status: Public on Dec 09 2023

city: Sao Paulo

first: Sintia

last: Belangero

address: Rua Botucatu

department: Morphology and Genetics

country: Brazil

institute: UNIFESP

summary: Traumatic brain injury (TBI) is a prevalent and debilitating condition, which often leads to the development of post-traumatic epilepsy (PTE), a condition that yet lacks preventive strategies. Biperiden, an anticholinergic drug, is a promising candidate that has shown efficacy in murine models of PTE. MicroRNAs (miRNAs), small regulatory RNAs, can help in understanding the biological basis of PTE, and act as TBI- and PTE-relevant biomarkers that can be detected peripherally, as they are present in extracellular vesicles (EVs) that cross the blood brain barrier. This study aimed to investigate miRNAs in serum EVs from patients with TBI, and their association with biperiden treatment and PTE. Blood samples of 37 TBI patients were collected 10 days after trauma and treatment initiation in a double-blind clinical trial. A total of 18 patients received biperiden, with 3 subjects developing PTE, and 19 received placebo, with 2 developing PTE. Serum EVs were characterized by size distribution and protein profiling, followed by high-throughput sequencing of the EV miRNome. Differential expression analysis revealed no significant differences in miRNA expression between TBI patients with and without PTE. Interestingly, miR-9-5p displayed decreased expression in biperiden-treated patients compared to the placebo group. This miRNA regulates genes enriched in stress response pathways, including axonogenesis and neuronal death, relevant to both PTE and TBI. These findings suggest serum miR-9-5p as a possible marker for biperiden treatment, which may play a role in TBI resolution.

overall_design: Within approximately 12 hours following TBI, patients began receving, every 6 hours, either placebo or biperiden, intravenously. A total of 40 doses (5 mg of biperiden per dose) were administered per patient, as described in the clinical trial NCT01048138. Approximately 10 hours after the last biperiden or placebo dose, blood samples were collected from each patient. Serum was obtained after centrifugation, then frozen and maintained in -80C until processing. Serum extracellular vesicles (EVs) were isolated, and microRNAs (miRNAs) were extracted. miRNA concentration was determined using nanodrop, and miRNA libraries were then prepared and sequenced. Differential expression analysis of miRNA-Seq was performed between placebo- and biperiden-treated patients, as well as between patients that did or did not develop PTE.

first: Gustavo

last: Kajitani

first: Beatriz

last: Villena-Rueda

first: Paula

middle: F

last: Asprino

middle: I


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [lncRNA-seq]

status: Public on Aug 03 2023

city: Guangzhou

first: Yuming

last: Wang

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

summary: The hereditary information encoded in DNA sequence is intrinsically susceptible to alterations, being continually threatened by a variety of genotoxic perturbations. To safeguard the stability of the genome, eukaryotic cells have evolved a set of sophisticated surveillance system that controls several aspects of the cellular response, including the detection of DNA lesions, a temporary cell cycle arrest, regulation of transcription, and the repair of the damaged DNA. However, it is still poorly understood how the DNA damage checkpoints and stalled RNAPII molecules convert a very limited amount of molecular-level information (even a single DNA lesion) in the context of an otherwise genome into regulation that halts and resumes the cell-cycle engine in a coordinated way. In this study, we reveal a map of extensive lncRNA transcription during DDR by using synchronized cells, leading to the unexpected identification of a poorly characterized mammalian lncRNA-ZFAS1. We describe that ZFAS1 functions as a key player of cellular response to DNA damage in both human and rodent cells by fine tuning RNAPII kinetics, suggesting a lncRNA-dependent transcriptional regulatory axis that maintains genomic stability upon DNA damage in mammalian cells.

overall_design: To illustrate the transcriptome map for both mRNAs and lncRNAs during DNA damage response, we synchronized human fibroblasts MRC5_VA at G1/S block and UV irradiated prior to release from the arrested cell cycle phase. We then performed gene expression profiling analysis using data obtained from RNA-seq of 14 samples, including undisturbed (6 samples) and UV-irradiated (8 samples) cell lines at the indicated time intervals after release from G1/S block.

first: Jiena

last: Liu

first: Tingting

last: Zhu

first: Zhaoya

last: Han

first: Qing

last: Lu


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation

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

overall_design: Refer to individual Series


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for phosphorylated isoforms of RNA polymerase II (RNAPII-Ser5P and RNAPII-Ser2P) in the WT and ZFAS1-depleted cells with or without UV-C irradiation.


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [ZFAS1 ChIRP-seq]

overall_design: To illustrate the genome wide binding capacity of ZFAS1, ChIRP (chromatin isolation by RNA purification) was performed using biotinylated probes against ZFAS1. Independent even and odd probe pools were used to ensure ZFAS1 specific retrieval. High-throughput sequencing libraries were constructed from ChIRPed DNA according to ChIP-seq protocol.


title: scRNA-seq in adipocyte progenitors in Azin-/- and wild-type mice

status: Public on Jul 03 2023

city: Dresden

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

country: Germany

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

summary: AZIN2 regulates adipocyte progenitor differentiation. Here we investigated how AZIN2 deficiency affects the profile of adipocyte progenitors. To this end, Azin2-/- and wild-type male mice were fed for 8 weeks a high-fat diet, subcutaneous adipose tissue was isolated and single-cell RNA-seq was performed in CD45-CD31- cells of the stromal vascular fraction.

overall_design: Azin2-/- and wild-type littermate mice were fed for 8 weeks a high-fat diet, then subcutaneous adipose tissue was excised, incubated for 45 min with collagenase type I (2 mg/ml/g tissue) at 37 °C under continuous rotation. Cells were then passed through a 100-μm pore-sized cell strainer and centrifuged at 300 g for 10 min. Erythrocytes were removed from the SVF through lysis with a red blood cell lysis buffer (Biolegend) and CD31-CD45- cells were isolated using anti-CD31 and anti-CD45 MicroBeads (Miltenyi Biotec), according to manufacturer’s instructions. Two mice were pooled per genotype. 10,275 wt and 11,004 Azin2-/- cells were FACS sorted.

first: VI

first: Anupam

last: Sinha


title: Mechanical confinement governs phenotypic plasticity in melanoma

city: New York

first: Miranda

last: Hunter

state: NY

address: 418 E 68th St

institute: Memorial Sloan Kettering Cancer Center


title: Tet2 deficiency altered hematopoietic stem and progenitor cells ageing process

status: Public on Aug 11 2023

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

type: Methylation profiling by high throughput sequencing

summary: we compared self-renewal and lineage specification of WT and Tet2-deficient HSPCs during ageing and demonstrated that Tet2 ablation alters age-dependent HSC functional decline, revealing a disparate ageing process in the Tet2-deficient haemopoietic system.

overall_design: We collected hematopoietic progenitor and stem cells (HSPCs) from young and aged WT/ Tet2KO/Dnmt3aKO mice for WGBS, 5hmC mapping (CMSIP), SMART-seq, H3K9me3 CHIP seq, and scATAC seq. We captured and compared the 3D genome structure among four groups ( WT-young, WT-old, T2KO-young and T2KO-old).

last: Hong

first: Shaohai

last: Fang

first: Anna

last: Guzman

first: Wei

first: Yubin

last: Zhou

first: Margaret

middle: A

last: Goodell

first: Yun

last: Huang


title: HFD versus LFD [RNA-seq]

summary: Obesity alters the transcriptional profile of the adipose tissue. Our aim was to characterize the metabolic adaptations induced by diet-induced obesity in the adipose tissue. To this end wild-type mice were fed for 20 weeks a high-fat diet and subcutaneous adipose tissue was analyzed by RNA sequencing.

overall_design: For HFD versus ND/LFD: C57BL/6J male mice were fed for 20 weeks a low-fat diet (10% kcal fat) or a high-fat diet (60% kcal fat), subcutaneous adipose tissue (SAT) was isolated and RNA sequencing was performed in whole SAT.  For SAT_WT versus SAT_KO :  Azin2-/- and wild-type littermate male mice were fed for 8 weeks a high-fat diet (60% kcal fat), subcutaneous adipose tissue (SAT) was isolated and RNA sequencing was performed in whole SAT. For GAT_WT versus GAT_KO: Azin2-/- and wild-type littermate male mice were fed for 8 weeks a high-fat diet (60% kcal fat), epigonadal adipose tissue (GAT) was isolated and RNA sequencing was performed in whole GAT.


title: Azin2-dependent transcriptional and epigenetic regulation in adipose tissue and adipocyte progenitors


title: Interactions between the genome and the nuclear lamina are multivalent and cooperative (RNA-seq)

status: Public on Dec 19 2023

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Mammalian genomes contain hundreds of lamina-associated domains (LADs), which are large, often megabase-sized heterochromatin domains that are anchored to the nuclear lamina (NL). Even though LADs play a key role in the spatial organization of the genome and potently repress gene activity, it is not yet understood how their interactions with the NL are encoded in their DNA. Here, we investigated the principles that govern LAD-NL interactions by taking a "LAD scrambling" approach. This approach relies on 1) local "hopping" of a Sleeping Beauty transposon to randomly insert loxP sites within and around a LAD of choice; and 2) Cre-mediated recombination between the loxP sites. This approach is highly efficient, enabling us to establish a large collection of clonal cell lines with deletions and inversions up to ~2Mb in size, spanning LAD and their flanking inter-LAD sequences. Mapping of NL interactions in these clones revealed that a single LAD contacts the NL through multiple regions. These regions act cooperatively and redundantly; however, some have more affinity for the NL and can boost NL contacts of neighbouring sequences. We also observed a crosstalk between two neighbouring LADs, when close enough to each other. Finally, changes in the heterochromatin mark H3K9me3 only partially mirrored changes in NL contacts. They also correlated more with gene expression changes than NL contacts did. These principles of LAD - NL interactions provide insight into the overall architecture of the genome and the impact on gene regulation.

overall_design: RNA-seq experiments were performed on various recombined clones and their respective parental cell lines to assess gene expression changes upon recombination. For recombination d3, we analysed two recombined clones: clone 12 and 21. For recombination d6, we analysed one recombined clone: clone 16. For recombination i7, we analysed two recombined clones: clone 7 and 12. For recombination i10, we analysed one recombined clone: clone 18. For recombination i12, we analysed one recombined clone: clone 10. All experiments were performed in biological duplicates.

first: Lise

last: Dauban

first: Marcel

last: de Haas

first: Mathias

last: Eder

first: Vinícius

last: Franceschini-Santos

first: Tom

last: van Schaik

first: Christ

last: Leemans

first: Koen

last: Rademaker

first: Moreno

last: Martinovic

first: J

middle: O

last: Yañez-Cuna


title: Interactions between the genome and the nuclear lamina are multivalent and cooperative


title: Longitudinal analysis of birthweight and epigenetic aging among children from birth to age three in the Democratic Republic of Congo

status: Public on Jun 26 2023

city: GAINESVILLE

first: Edward

last: Quinn

state: FL

address: 2033 Mowry Road

department: Anthropology

institute: University of Florida

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of venous blood samples from children in the Eastern Democratic Republic of Congo from birth to age three. DNA methylation data were noob normalized and uploaded to Steve Horvath's epigenetic age calculator website to calculate Horvath epigenetic age acceleration for each participant at each timepoint for which they had data available. Replicates were averaged and a single outlier at birth was removed as described in the manuscript, leaving 155 observations from 67 unique individuals. Sample size at each timepoint was as follows: n = 64 at birth, n = 8 at six months, n= 35 at one year, n = 32 at two years, and n = 16 at three years.

overall_design: Bisulphite converted DNA from 164 samples were hybridised to the Illumina Infinium MethylationEPIC v1.0 Beadchip

first: Connie

middle: J

last: Mulligan


title: Genome-Wide Epigenomic Profiling of Primary Non-Small Cell Lung Cancer Reveals Specific and Recurrent DNA Methylation Alterations in Smoker Versus Never-Smoker Patients

status: Public on Sep 16 2023

city: St. Louis

first: Ting

last: Wang

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

summary: Epigenetic alterations are widespread in cancer and can complement genetic alterations to influence cancer progression and treatment. To better understand the potential contribution of DNA methylation alterations to tumor phenotype in non-small cell lung cancer (NSCLC) in both smoker and never-smoker patients, we performed a comprehensive, genome-wide profiling of DNA methylation in 17 primary non-small cell lung cancer and 10 matched normal lung samples using the complementary methylation assays MeDIP-seq and MRE-seq. Compared to patient-matched non-malignant lung tissue, we report recurrent methylation changes of several gene promoters, many previously implicated in cancer, including FAM83A and SEPT9 (hypomethylation), and PCDH7, NKX2-1, and SOX17 (hypermethylation). Although smoker and never-smoker patients shared many methylation changes, several were specific and recurrent within a particular smoking status. In particular, never-smokers displayed a greater proportion of hypoDMRs and exhibited a greater number of recurrently hypomethylated promoters, including the promoter of the oncogene ASPSCR1, and others previously linked to cancer, including TOP2A, DPP9, and USP39. Methylation changes outside of promoters were also widespread and often recurrent, particularly the loss of methylation over repetitive elements, highly enriched for ERV1 subfamilies. Recurrent hypoDMRs were also enriched for several transcription factor (TF) binding motifs, often for genes involved in signaling and cell proliferation, including 71% encoding a binding site of NKX2-1, which was found to be significantly upregulated in TCGA LUAD samples. Furthermore, the overwhelming majority of DMRs identified in this study were found to reside in an active chromatin state in at least one tissue profiled using the Roadmap Epigenome data, suggesting that methylation changes may contribute to altered regulatory programs through the adaptation of cell type-specific expression programs.

overall_design: We performed methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation sensitive restriction enzyme sequencing (MRE-seq), which profile methylated and unmethyalted CpG sites, respecitvely, for 17 lung adenocarcinoma tumors and 10 matched normal lung samples. MeDIP-seq and MRE-seq data were integrated using the M&M algorithm to identify regions differentially methylated between two samples, and were also integrated using methylCRF to calculate methylation value across indivual CpGs for each sample.

first: Jennifer

last: Karlow

first: Erica

middle: C

last: Pehrsson

first: Xiaoyun

last: Xing

first: Mark

last: Watson

first: Siddhartha

last: Devarakonda

first: Ramaswamy

last: Govindan


title: Starvation induced circulating miR-33a secretion remodeled extracellular matrix of tumor microenvironment by altering polyamine metabolism [TC TM]

status: Public on Aug 09 2023

city: Wuhan

first: Yan

last: Wei

address: Bayi road 229

institute: wuhan university

summary: Breast cancer cells secret different kinds of cargoes through extracellular vesicles (EVs) especially under stress conditions. However, the underling mechanism and function is poorly defined. Here, we found RNA binding protein ACO1 could bind miR-33a and assist their package into EVs in tumor core region. Thereby, miR-33a suppressed putrescine metabolism in cancer-associated fibroblasts (CAFs)  and reprogrammed H3K4me3 mediated epigenetic regulation. Chip-seq data suggested stress granules related genes were downregulated and ECM related genes were upregulated. Most notably, putrescine inhibited KDM5C expression level but did not altered activity. Finally, our study provides a novel mechanism of how cancer EVs reprogrammed polyamine metabolism in tumor stroma, leading to spatially different distribution of ECM in tumor microenvironment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor core and margin established by injecting MDA-MB-231 orthotopically of NSG mice

first: Sheng

last: Hu

first: Wei

last: Yan


title: Epigenetic analysis of psychosocial stress among mother-newborn dyads in the Democratic Republic of Congo (EWA reanalysis)

status: Public on Jun 08 2023

summary: Prenatal maternal stress has a negative impact on child health but the mechanisms through which maternal stress affects child health are unclear. Epigenetic variation, such as DNA methylation, is a likely mechanistic candidate as DNA methylation is sensitive to environmental insults and can regulate long-term changes in gene expression. We recruited mother-newborn dyads in the Democratic Republic of Congo to investigate the effects of maternal stress on DNA methylation in mothers and newborns. We used four measures of maternal stress to capture a range of stressful experiences: general trauma, sexual trauma, war trauma, and chronic stress. We identified differentially methylated positions (DMPs) associated with general trauma, sexual trauma, and war trauma in both mothers and newborns. No DMPs were associated with chronic stress. Sexual trauma was positively associated with epigenetic age acceleration across several epigenetic clocks in mothers. General trauma and war trauma were positively associated with newborn epigenetic age acceleration using the extrinsic epigenetic age clock. We tested the top DMPs for enrichment of DNase I hypersensitive sites (DHS) and found no enrichment in mothers. In newborns, top DMPs associated with war trauma were enriched for DHS in embryonic and fetal cell types. Finally, one of the top DMPs associated with war trauma in newborns also predicted birthweight, completing the cycle from maternal stress to DNA methylation to newborn health outcome. Our results indicate that maternal stress is associated with site-specific changes in DNAm and epigenetic age acceleration in both mothers and newborns.

overall_design: Bisulphite converted DNA from the 356 samples were hybridised to the Illumina Infinium MethylationEPIC v1.0 Beadchip


title: Starvation induced circulating miR-33a secretion remodeled extracellular matrix of tumor microenvironment by altering polyamine metabolism


title: Epigenetic analysis of psychosocial stress among mother-newborn dyads in the Democratic Republic of Congo


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [ZFAS1-mRNA-seq]

first: Yuming

overall_design: To study the effect of ZFAS1 lncRNA on mature RNA synthesis upon DNA damage, we knocked down ZFAS1 in MRC5_VA cells by using lentiviral shRNA plasmids targeting two distinct regions of ZFAS1. Cells were UV irradiated and recovered for the indicated time intervals (3 h and 24 h), total RNA was extracted from the three cell lines (empty vector, ZFAS1-sh1, and ZFAS1-sh2). We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 samples.

first: Jiena

last: Liu

first: Tingting

last: Zhu

first: Zhaoya

last: Han

first: Qing

last: Lu


title: Transposon-encoded nucleases use guide RNAs to selfishly bias their inheritance

status: Public on Jun 01 2023

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

summary: Insertion sequences (IS) are compact and pervasive transposable elements found in bacteria, which encode only the genes necessary for their mobilization and maintenance. IS200/IS605 elements undergo ‘peel-and-paste’ transposition catalyzed by a TnpA transposase, but intriguingly, they also encode diverse, TnpB-family genes that are evolutionarily related to the CRISPR-associated effectors Cas9 and Cas12. Recent studies demonstrated that TnpB-family enzymes function as RNA-guided DNA endonucleases, but the broader biological role of this activity has remained enigmatic. Here we show that IscB and TnpB are essential to prevent loss of the donor IS element and potential transposon extinction as a consequence of the TnpA transposition mechanism. We first performed phylogenetic analysis of IscB/TnpB proteins and selected a family of related IS elements from Geobacillus stearothermophilus that we predicted would be mobilized by a common TnpA homolog. After reconstituting transposition using a heterologous expression system in E. coli, we found that IS elements were readily lost from the donor site due to the activity of TnpA in rejoining the flanking sequences back together upon excision. However, these IS elements also encode non-coding RNAs that guide TnpB and IscB nucleases  to precisely recognize and cleave these excision products, leading either to elimination of the excision product or re-installation of the transposon through recombination. Indeed, under experimental conditions in which TnpA and TnpB-RNA complexes were co-expressed together with a genomically integrated IS element, transposon retention was significantly increased relative to conditions expressing TnpA alone. Remarkably, both TnpA and TnpB recognize the same AT-rich transposon-adjacent motif (TAM) during transposon excision and RNA-guided DNA cleavage, respectively, revealing a striking convergence in the evolution of DNA sequence specificity between transposase and nuclease. Collectively, our study reveals that RNA-guided DNA cleavage is a primal biochemical activity that arose to bias the selfish inheritance of transposable elements, which was later co-opted during the evolution of CRISPR-Cas adaptive immunity for antiviral defense.

overall_design: E. coli genome ChIP-seq profiles for 4 proteins for RNA-guided endonucleases. 18 samples were sequenced in total. The raw read files "Input_TnpB3_targeting_ChIP-seq_paired_raw" and "Input_Cas9_targeting_ChIP-seq_paired_raw" are control samples which were used as reference samples for MACS3 peak calling. Biological replicate samples are indicated as "rep1" or "rep2".

first: Chance

last: Meers

first: Hoang

last: Le

first: Sanjana

middle: R

last: Pesari

first: Florian

last: Hoffmann

first: Matthew

last: Walker

middle: H


title: Construction of miRNA-mRNA Regulatory Network Indicates Potential Biomarkers for Primary Open-Angle Glaucoma

status: Public on May 05 2023

city: Changsha

first: Xiaoyu

last: Zhou

address: No. 188, Section 1, Furong South Road

department: Glaucoma Institute

institute: Changsha Aier Eye Hospital

summary: MicroRNAs were associated with the development and progression of glaucoma. Our study aims to identify the potential miRNAs and target genes in human trabecular meshwork related to primary open-angle glaucoma (POAG).

overall_design: MiRNA expression profiles in trabecular meshwork from 4 normal controls and 4 POAG patients were determined through microarray analysis.

first: Feng

last: Zhang

first: Xuanchu

last: Duan


title: The Chd4 helicase regulates chromatin accessibility and gene expression critical for β-cell function in vivo.

status: Public on May 31 2023

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

institute: Indiana University


title: The Chd4 helicase regulates chromatin accessibility and gene expression critical for β-cell function in vivo [RNA-seq]

summary: To establish the role of Chd4 on controlling gene expression programs in the beta cell, we generated a tamoxifen-inducible, beta-cell-specific knockout mouse model; control (MIP-CreERT; Chd4flox/+;R26RtdTomato) and Chd4Db (MIP-CreERT; Chd4flox/flox;R26RtdTomato.

overall_design: Dispersed islets from tamoxifen treated control and Chd4Db mice were flow-sorted, and RNASeq performed.

first: Rebecca

last: Davidson


title: Effect of Charme lncRNA knockout (KO) in cardiac development [RNA-seq]

status: Public on Mar 18 2023

city: Rome

first: Monica

last: Ballarino

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

summary:
To investigate the role of the lncRNA Charme in cardiac differentiation and physiology, total RNA was collected from  CharmeWT and CharmeKO hearts
RNA-seq analysis was performed on CharmeWT and CharmeKO postnatal hearts

overall_design: Comparative gene expression profiling analysis of RNA-seq data from murine WT and Charme-depleted hearts

first: Adriano

last: Setti


title: ChIP-seq in Azin2-/- and wt adipocyte progenitors

first: Ismini

last: Alexaki

summary: AZIN2 regulates adipogenesis and acetyl-coA levels in adipocyte progenitors. We investigated here how AZIN2 deficiency affects histone acetylation in adipocyte progenitors.

overall_design: Adipocyte progenitors were isolated from subcutaneous adipose tissue of Azin2-/- and wild-type mice and cultured for 1 week 4.5 g/L glucose Glutamax–DMEM with 10% FBS and 1% penicillin/streptomycin at 37°C and 5% CO2. Then, they were cultured in medium containing 5 µg/ml insulin , 0.5 mM 3-isobutyl-1-methylxantine, 1 µM dexamethasone and 1 µM rosiglitazone. After 2 days, they were switched to medium containing 5 µg/ml insulin and cultured for another 5 days. Medium was changed every 2 days. ChIP was performed using the EZ-Magna ChIP HiSens (Millipore) following manufacturer's instructions. An antibody  against H3K27Ac (Millipore 17- 683) was used. DNA was isolated and sequenced.

first: VI

first: Anupam

last: Sinha


title: Targeted DNA integration in human cells without double-strand breaks using CRISPR RNA-guided transposases

status: Public on Mar 09 2023

country: USA

summary: Traditional genome-editing reagents such as CRISPR-Cas9 achieve targeted DNA modification by introducing double-strand breaks (DSBs), thereby stimulating localized DNA repair by endogenous cellular repair factors. While highly effective at generating heterogenous knockout mutations, this approach suffers from undesirable byproducts and an inability to control product purity. Here we develop a system in human cells for programmable, DSB-free DNA integration using Type I CRISPR-associated transposons (CASTs). To adapt our previously described CAST systems, we optimized DNA targeting by the QCascade complex through a comprehensive assessment of protein design, and we developed potent transcriptional activators by exploiting the multi-valent recruitment of the AAA+ ATPase, TnsC, to genomic sites targeted by QCascade. After initial detection of plasmid-based transposition, we screened 15 homologous CAST systems from a wide range of bacterial hosts, identified a CAST homolog from Pseudoalteromonas that exhibited improved activity, and increased integration efficiencies through parameter optimization. We further discovered that bacterial ClpX enhances genomic integration by multiple orders of magnitude, and we propose that this critical accessory factor functions to drive active disassembly of the post-transposition CAST complex, akin to its demonstrated role in Mu transposition. Our work highlights the ability to functionally reconstitute complex, multi-component machineries in human cells, and establishes a strong foundation to realize the full potential of CRISPR-associated transposons for human genome engineering.

overall_design: Human genomic ChIP-seq profiles for eCAST-1 TnsC binding in the presence of either a crRNA targeting a region upstream of the TTN locus, or a non-targeting crRNA with a sequence not present in the human genome. Bioligical replicates are indicated as "biol rep #"

first: George

middle: D

last: Lampe

first: Rebeca

middle: T

last: King

first: Tyler

middle: S

last: Halpin-Healy

first: Sanne

middle: E

last: Klompe

first: Marcus

last: Hogan

first: PhucLeo

last: Vo

first: Stephen

last: Tang

first: Alejandro

last: Chavez


title: Interactions between the genome and the nuclear lamina are multivalent and cooperative (pA-DamID)

first: Bas

last: van Steensel

overall_design: pA-DamID experiment were performed on parental (non-edited), Cre-recombined or CRISPR/Cas9-edited clones. Lamina association and H3K9me3 deposition were probed using anti-LaminB1 (LB1) (Abcam, ab16048) and anti-H3K9me3 (Diagenone, C15410193) antibodies respectively.

first: Lise

last: Dauban

first: Marcel

last: de Haas

first: Mathias

last: Eder

first: Vinícius

last: Franceschini-Santos

first: Tom

last: van Schaik

first: Christ

last: Leemans

first: Koen

last: Rademaker

first: Moreno

last: Martinovic

first: J. Omar

last: Yañez-Cuna


title: Molecular fingerprints for bone marrow cells, pediatric acute lymphoblastic leukemia

status: Public on May 03 2023

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1E

department: School of Medicine, Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: The overall goal of this study was to characterize bone marrow cells based on their transcriptome, surface protein expression and BCR- and TCR VDJ-profile for accurate identification of clinically relevant cell states. This submission includes pediatric B-cell acute lymphoblastic leukemia samples. This project has received funding from the European Union Horizon 2020 research and innovation programme under grant agreement No 824110 (EASI-Genomics)

overall_design:
CITE-seq (scRNA-seq, scADT-seq) and scVDJ-seq samples were generated from bone marrow and blood mononuclear cells using the 10X Genomics Chromium platform and protocols. Bone marrow and blood samples were collected from donors treated with NOPHO2008 protocol at diagnosis and at day 2 (blood) and day 15 (bone marrow) during induction chemotherapy. Cells were stained with specific surface antibodies and hashtag antibodies to label donors. Single cell suspensions representing donor pools (2 per pool) were loaded and processed for sequencing. Sample annotation follows tissue term ontology from EFO https://www.ebi.ac.uk/efo/
---------------------------------------------------------
Authors state the following:
Submission of sensitive patient data, only processed cell ranger output files provided. Raw data with sample metadata is deposited to EGA (see Data Access Committee)

first: Olli

last: Lohi

first: Mari

last: Lahnalampi

first: Janne

last: Suhonen

first: Konstantin

last: Ivanov

first: Mikko

last: Sipola


title: Maintenance of pluripotency in the entire ectoderm enables neural crest formation  and challenges dogmatic viewpoints of gastrulation

status: Public on Mar 02 2023

city: Bethesda

first: Laura

last: Kerosuo-Pahlberg

address: 30 Convent Dr

institute: NIDCR

summary: The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like cells is obtained. We monitored transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. Unexpectedly, we find maintenance of undecided Nanog/Oct4-PouV/Klf4-positive pluripotent-like pan-ectodermal stem-cells spanning the entire ectoderm late in the neurulation process with ectodermal patterning completed only at the end of neurulation when pluripotency becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency is found at all axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond “ectodermal-capacity” in chick and mouse embryos.

overall_design: Chick embryo samples from all tissue at the midbrain axial level from, HH5, 1ss, 4ss, 7ss and HH11 stage were dissociated and analyzed by scRNAseq. SEURAT workflow for scRNAseq analysis was followed by differential expression between ectodermal cell types.

first: Ceren

last: Pajanoja

first: Jenny

last: Hsin

first: Bradley

last: Olinger

first: Andrew

last: Schiffmacher

first: Shaun

last: Abrams

first: Arvydas

last: Dapkunas

first: Zarin

last: Zainul

last: Doyle

first: Daniel

last: Martin

last: Kerosuo


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

overall_design: Refer to individual Series


title: Epigenetic analysis of psychosocial stress among mother-newborn dyads in the Democratic Republic of Congo (EAA)

first: Edward

last: Quinn

first: Connie

last: Mulligan


title: Single-cell RNA sequencing to dissect the immunological network of liver fibrosis in Schistosoma japonicum-infected mice

status: Public on Dec 16 2022

first: Yu

last: Zhang

address: No. 138 Tongzipo Road

department: Transplantation Center

institute: The Third Xiangya Hospital, Central South University

summary: Liver fibrosis is a poor outcome of patients with schistosomiasis, impacting the quality of life and even survival. Eggs deposited in the liver were the main pathogenic factors of hepatic fibrosis in Schistosomiasis japonica. However, the mechanism of hepatic fibrosis in schistosomiasis remains not well defined and there is no effective measure to prevent and treat schistosome-induced hepatic fibrosis. In this study, we applied single-cell sequencing to primarily explore the mechanism of hepatic fibrosis in murine schistosomiasis japonica(n=1) and normal mouse was served as control(n=1). A total of 10,403 cells were included in our analysis and grouped into 18 major cell clusters. Th2 cells and NKT cells were obviously increased and there was a close communication between NKT cells and FASLG signaling pathway. Flow cytometry analysis indicated that the expression of Fasl in NKT cells, CD8+ T cell and NK cell were higher in SJ groups. Arg1, Retnla and Chil3, marker genes of alternatively activated macrophages (M2), were mainly expressed in mononuclear phagocyte(1) (MP(1)), suggesting that Kupffer cells might undergo M2-like polarization in fibrotic liver of schistosomiasis. CXCL and CCL signaling pathway analysis with CellChat showed that Cxcl16-Cxcr6, Ccl6-Ccr2 and Ccl5-Ccr5 were the most dominant L−R and there were close interactions between T cells and MPs. Overall, our research profiled a preliminary immunological network of hepatic fibrosis in murine schistosomiasis japonica, which might contribute to a better understanding of the mechanisms of liver fibrosis in schistosomiasis. NKT cells and CXCL and CCL signaling pathway such as Cxcl16-Cxcr6, Ccl6-Ccr2 and Ccl5-Ccr5 might be potential targets to alleviate hepatic fibrosis of schistosomiasis.

overall_design: There are two groups in our study. Single cells were dissociated from a fibrotic liver of S. japonicum-infected mouse( SJ, n=1) and a normal mouse was served as control(HC, n=1).

first: Yingzi

last: Ming


title: Ovarian cancer mutational processes drive site-specific immune evasion

status: Public on Dec 14 2022

first: Florian

last: Uhlitz

address: 1275 York Avenue

department: Computational Oncology

summary: High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability patterned by distinct mutational processes, tumour heterogeneity and intraperitoneal spread. Immunotherapies have had limited efficacy in HGSOC, highlighting an unmet need to assess how mutational processes and the anatomical sites of tumour foci determine the immunological states of the tumour microenvironment. Here we carried out an integrative analysis of whole-genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumour sites from 42 treatment-naive patients with HGSOC. Homologous recombination-deficient HRD-Dup (BRCA1 mutant-like) and HRD-Del (BRCA2 mutant-like) tumours harboured inflammatory signalling and ongoing immunoediting, reflected in loss of HLA diversity and tumour infiltration with highly differentiated dysfunctional CD8+ T cells. By contrast, foldback inversion-bearing tumours exhibited elevated immunosuppressive TGFβ signalling and immune exclusion, with predominantly naive/stem-like and memory T cells. Phenotypic state associations were specific to anatomical sites, highlighting compositional, topological and functional differences between adnexal tumours and distal peritoneal foci. Our findings implicate anatomical sites and mutational processes as determinants of evolutionary phenotypic divergence and immune resistance mechanisms in HGSOC. Our study provides a multi-omic cellular phenotype data substrate from which to develop and interpret future personalized immunotherapeutic approaches and early detection research.

overall_design: We profile flow-sorted single-cell transcriptomes of 158 fresh tissue samples acquired from 41 newly-diagnosed, pre-treatment ovarian cancer patients. Anatomic site collections included adnexa (ovary and fallopian tube), omentum, peritoneum, bowel, ascites and other intra-peritoneal sites. Tissue samples were collected from laparoscopic biopsies or primary debulking surgeries, dissociated, flow-sorted for live CD45+ and CD45- cells to enrich immune cell populations, and processed for transcriptomic profiling using 10x 3’ single-cell RNA sequencing.

first: Ignacio

last: Vazquez-Garcia

first: Eliyahu

last: Havasov

first: Nicholas

last: Ceglia

last: McPherson

first: Dmitriy

last: Zamarin

first: Sohrab

last: Shah


title: Single-cell transcriptomic atlas of mouse gingival stroma in homeostasis and inflammation

status: Public on Oct 30 2022

city: chengdu

first: Yixuan

last: Huang

state: sichuan

address: West China Hospital of Stomatology

institute: Sichuan University

summary: The onset of periodontitis involves the response of gingival stroma to inflammatory stimulus. The cell constitution of gingival stroma, however, has never been mapped at the resolution of single cell. In this study, we used single-cell mRNA sequencing to establish cell atlas in mouse gingival stroma. Epithelial, mesenchymal, pericyte and neuronal clusters were successfully identified and their subpopulation and response to ligature-induced inflammation were also examined. While shifts in epithelial cell gene profile and proportion recapitulated the epithelium breakdown during periodontitis, mesenchymal cluster maintained its proportion and gene expression patterns.

overall_design: single cell mRNA profiles of 3-month old wild type (WT)  mice intact and inflammed gingiva tissue

first: Xing

last: Yin


title: RNA-sequencing of dsb-2, spo-11 and htp-3 mutants to identify mechanisms involved in somatic aging of C. elegans through meiotic dysfunction

status: Public on Nov 01 2022

city: Pittsburgh

first: Arjumand

last: Ghazi

state: Pennzylvania

address: 4401 Penn Avenue

institute: University of Pittsburgh

summary: We identified that mutations in meiotic genes dsb-2, htp-3, and spo-11 accelerated the rate of aging of the organims. In order to determine mechanisms responsible for this phenotype we conducted an RNA sequencing experiment to identify potential pathways.

overall_design: Comparison of adult day 1 whole worm NGS-derived transcriptomic profiles of AV157 spo-11(me44), TY4986 htp-3(y428), AV477 dsb-2(me96) animals to N2(WT) animals. For each strain, three biological replicates were collected.

first: Julia

last: Loose


title: Effect of isolevuglandin formation in high ros in endothelial cell immune activaiton

status: Public on Apr 08 2023

city: Nashville

first: Nestor

last: de la Visitacion

state: TN

address: 2213 GARLAND AVE

institute: Vanderbilt University Medical Center

summary: To observe the effects on cell programming that isolevulgandin adduct formation has on endothelial cells, we increased ROS with glucose oxidase

overall_design:
We scavenged the formed adducts with ethyl 2 hydroxybenzylamine
Comparative gene expression profiling analysis of RNA-seq data in endothelial cells

first: Néstor

last: de la Visitación

first: David

middle: M

last: Patrick

first: Shilin

last: Zhao


title: RNA-sequencing of pediatric acute lymphoblastic leukemia bone marrow mononuclear cells

status: Public on Apr 05 2023

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

institute: university of eastern finland

summary: The overall goal of this study was to profile pediatric acute lymphoblastic leukemia bone marrow tissue based on their transcriptome to characterize clinically relevant subtypes. This project has received funding from Cancer Society of Finland, Jane and Aatos Erkko Foundation and ERAPerMed (Reference Number: ERAPERMED2018-209) under the ERA-NET Cofund scheme of the Horizon 2020 Research and Innovation Framework Programme of the European Commission Research Directorate-General Grant Agreement No. 779282.

overall_design:
RNA-seq (bulk) samples were generated from bone marrow mononuclear cells using stranded total RNA protocols. Samples represent donors treated with NOPHO2008 protocol (NCT00819351). Sample annotation follows tissue term ontology from EFO https://www.ebi.ac.uk/efo/
*** Submitter declares that the raw data will be made available via EGA since the data corresponds to sequencing reads and sensitive patient data according to ethical consents will only be shared via controlled access data repository.***

first: Janne

last: Suhonen

first: Olli

last: Lohi

first: Laura

last: Oksa

first: Jessica

last: Nordlund

first: Olga

last: Krali


title: Molecular Networks in Atopic Mothers Impact the Atopy Risk of Infants

status: Public on Dec 15 2022

city: Denver

first: Sonia

last: Leach

state: Colorado

address: 1400 Jackson St

institute: National Jewish Health

summary: The prevalence of atopic diseases has increased with atopic dermatitis (AD) as the earliest manifestation. We assessed if molecular risk factors in atopic mothers influence their offsprings’ susceptibility to an atopic disease. Pairs of pregnant women and their infants with or without parental atopy were followed over the first 2 years of life. Global DNA methylation and differentially methylated regions (DMR) were determined in atopic and non-atopic mothers.  During the first 2 years of life, AD was more prevalent in children of atopic compared to non-atopic mothers with an increase in food sensitization in children with AD. 165 DMRs distinguished atopic from non-atopic mothers. Maternal atopy combined with DMRs increased the offsprings’ predicted risk to develop AD from an odds ratio of 2.56 to 4.26.

overall_design: Genome-wide DNA methylation profiles were determined using DNA extracted at ≥ 34 weeks gestational age from whole blood of 92 randomly selected mothers of infants with maternal or biparental history of atopy and 82 mothers of infants without parental history of atopy.

first: Pia

last: Hauk

first: Michaela

last: Schedel


title: Single-cell analysis of bone marrow B220+ cells from 56R and  LAPTM5 knockout (LAPTM5KO) 56R mice

status: Public on Aug 14 2022

city: Shanghai

first: Ying

last: Wang

state: Shanghai

address: 130 Dong’an Road

department: Immunology

institute: fudan university

summary: We used single-cell transcriptomics and BCR sequencing to analyze B cell development in 56R and LAPTM5KO 56R mice. We found increased proportions of immature B and mature B cells in LAPTM5KO 56R mice compared to 56R mice. QuSAGE analysis revealed that immature B cells from LAPTM5KO 56R mice were enriched in PI3K-Akt, mTOR, Ras and MAPK signaling pathways that contribute to cell survival. Moreover, mature B cells from LAPTM5KO 56R mice were enriched for activated autoimmune disease and transplant rejection pathways compared with those from 56R mice, suggesting that LAPTM5KO 56R mice might be more susceptible to autoimmunity. Single-cell BCR sequencing showed that LAPTM5 deficiency resulted in less reduction in LC diversity in mature B compared to immature B cells.

overall_design: Examination of bone marrow B lineage cells in 3 pairs of 56R and LAPTM5 deficient 56R mice

first: Ji-Yang


title: Role of RNA polymerase II "pausing" in Drosophila development

status: Public on Sep 10 2022

city: Moscow

first: Nadezhda

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

summary: According to previous studies, during Drosophila embryogenesis, RNA polymerase II is recruited to promoters at developmental stages preceding the stages of active transcription of genes. This work is aimed at exploring whether this mechanism is used during Drosophila metamorphosis. We performed ChIP-Seq analysis using antibodies to various modifications of RNA polymerase II (total, Pol II CTD Ser5P and Pol II CTD Ser2P), as well as to subunits of NELF, DSIF, PAF complexes and Brd4/Fs(1)h that control transcription elongation. We found that like in mid-embryogenesis during metamorphosis, promoters bind RNA polymerase II in the "paused" state preparing for activation at later stages of development. During mid-embryogenesis, RNA polymerase II in "pause" is phosphorylated at Ser5 and Ser2 of Rpb1 CTD and binds NELF, DSIF, and PAF complexes, but not Brd4/Fs(1)h. During metamorphosis, the "paused" RNA polymerase II complex includes Brd4/Fs(1)h in addition to NELF, DSIF, and PAF. The RNA polymerase II in this complex is phosphorylated at Ser5 at Rpb1 CTD, but not at Ser2.

overall_design: Whole embryos, larvae and prepupae were staged and collected for the ChIP-Seq experiments with antibodies against Rpb3, Pol II Ser2P, Pol II Ser5P, NELF-E (NELF complex), Spt5 (DSIF complex), PAF1 (PAF complex) and Brd4/Fs(1)h

first: N