title: Cellular Indexing of Transcriptomes and epitopes sequencing (CITE-seq) analysis to investigate the impact of granulocyte-colony stimulating factor on CRISPR/Cas9 gene edited human hematopoietic stem cell function

status: Public on Jun 30 2023

city: Bethesda

first: Daisuke

last: Araki

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: Our research has demonstrated that G-CSF impedes engraftment of CRISPR-Cas9 gene edited human hematopoietic stem cells (HSCs) by exacerbating p53-mediated DNA damage response. Results in this study suggest that the potential for G-CSF to exacerbate HSC toxicity mediated by DNA-damaging nucleases should be considered in autologous HSC gene therapy clinical trials.

overall_design: Human CD34+ cells edited with Cas9 alone (Cas9 group), Cas9+AAVS1-targeting gRNA (RNP group), or Cas9+AAVS1-targeting gRNA+GSE56 (RNP/GSE56 group) were transplanted into busulfan-conditioned NSG mice, and these mice subsequently received 3 days of PBS or G-CSF. Then, each mouse was euthanized and harvested for bone marrow cells and human CD34+cells were isolated using immunomagnetic beads. These CD34+ cells from a total of 6 mice were individually stained with Total seq B CITE-seq antibodies (CD38, CD45RA, CD90, CD49f) + hashtag oligo antibodies 1-6. Then, FACS sort was used to purify ~2,500 cells from each group, and subsequently pooled for CITE-seq library preparation/sequencing. Seurat was used to demultiplex data into 6 individual groups, and differential gene expression analysis was performed to evaluate the impact of G-CSF within Cas9, RNP and RNP/GSE56 groups.

first: Andre

last: Larochelle

first: Neelam

last: Redekar

first: Vicky

last: Chen


title: Hearing of malaria mosquitoes is modulated by a beta-adrenergic-like octopamine receptor and serves as insecticide target

status: Public on Jul 05 2023

city: London

first: Marta

last: Andrés

address: 332 Grays Inn Rd

department: Ear Institute

country: United Kingdom

institute: University College London

type: Expression profiling by high throughput sequencing

summary: Malaria mosquitoes acoustically detect their mating partners within large swarms that form transiently at dusk. Indeed, male malaria mosquitoes preferably respond to female flight tones during swarm time. This phenomenon implies a sophisticated context- and time-dependent modulation of mosquito audition, the mechanisms of which are largely unknown. Using transcriptomics, we identify a complex network of candidate neuromodulators regulating mosquito hearing in the species Anopheles gambiae. Among them, octopamine stands out as auditory modulator during swarm time. In-depth analysis of octopamine auditory function shows that it affects the mosquito ear on multiple levels: it modulates the tuning and stiffness of the flagellar sound receiver and controls the erection of antennal fibrillae. We show that two α- and β-adrenergic-like octopamine receptors drive octopamine’s auditory roles and demonstrate that the octopaminergic auditory control system can be targeted by insecticides. Our findings highlight octopamine as key for mosquito hearing and mating partner detection, and as a potential novel target for mosquito control.

overall_design: To investigate expression, and circadian pattern of expression of transcripts in Anopheles gambiae mosquito ears we conducted the following: First, we entrained mosquitoes, in environmental incubators, to 12H:12H light/dark cycle with 1-hour ramped light transition to simulated dawn and dusk (ZT0-ZT1 and ZT12-ZT13, respectively; ZTX is the formalised notation of an entrained circadian cycle's phase). Temperature and relative humidity were set constantinside the incubators throughout the circadian day, at 28 °C and 80% respectively. Mosquitoes were exposed to the circadian entrainment in the incubators for three days before performing any experiment. Then, on day four of circadian entrainment, 35 male and 35 female mosquitoes were removed from the incubators at six different circadian time points (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20), and we collected their Johnston's organs (JO; the mosquito's "internal ear"). This procedure was repeated 3 times, resulting in three biological replicates of JO samples at each circadian time point. Finally, we performed RNA sequencing of the samples, and conducted transcript expression, differential expression (between males and females), and circadian expression analyses on the sequenced data.

first: Marcos

last: Georgiades

first: Alexandros

middle: C

last: Alampounti

first: Jason

last: Somers

first: Matthew

middle: P

last: Su

first: David

middle: A

last: Ellis

first: Judit

last: Bagi

first: Scott

last: Tytheridge

first: Watson

last: Ntabaliba

first: Sarah

middle: J

last: Moore

first: Joerg

middle: T

last: Albert


title: Metabolic and molecular effects of intermittent fasting in humans: results from a randomized clinical trial

status: Public on Jul 01 2023

first: Ruteja

last: Barve

state: MO

address: 4515 McKinley Ave

department: Genetics

country: USA

institute: Washington University

summary: This study describes the effects of intermittent fasting induced weight loss on metabolic and molecular pathways

overall_design: 6 month randomized controlled clinical trial. The study included an extension period, during which the Intervention group continued the intervention for an additional 6 months (for a total of 12 months) and the control group crossed-over to receive the delayed intervention. A total of 41 participants (20 Controls and 21 intervention) were tested at Baseline, and after 6 months of intervention.

first: Valeria

last: Tosti

first: R

first: Beatrice

last: Bertozzi

first: Nicola

last: Veronese

first: Francesco

last: Spelta

first: Edda

last: Cava

first: Mark

last: Mattson

first: Laura

last: Piccio

first: Diana

middle: S

last: Early

first: Richard

middle: D

last: Head

first: Luigi

last: Fontana


title: Gene expression data from biological replicates of imatinib and nilotinib resistant K-562 cells.

city: Kiel

first: Meike

last: Kaehler

state: Schleswig-Holstein

address: Hospitalstraße 4

department: Institute of Experimental and Clinical Pharmacology

country: Germany

institute: University Hospital Schleswig-Holstein, Campus Kiel

summary:
Resistant cells were generated by stepwise exposure to increasing concentrations of imatinib or nilotinib to establish 0.5 and 2 µM imatinib and 0.05 µM nilotinib resistant cells. This procedure was performed twice independently to establish biological replicates of TKI resistance.
We performed microarrays (Clariom S) to analyze the changes in gene expression during the development of TKI resistance.

overall_design: RNA from cells was isolated and microarrays were run using two biological replicates of each resistance as well as four technical replicates. In addition, 4 controls were analyzed.


title: Loss of endothelial cell heterogeneity in arteries after obesogenic diet [scRNA-seq]

status: Public on Jun 26 2023

city: Charlottesville

first: Brant

middle: E

last: Isakson

state: Virginia

department: Cardiovascular Research Center

institute: University of Virginia

summary: Background: It is well recognized that obesity leads to arterial endothelial dysfunction and cardiovascular disease. However, the progression to endothelial dysfunction is not clear. Endothelial cells (ECs) adapt to the unique needs of their resident tissue and respond to systemic metabolic perturbations. We sought to better understand how obesity affects EC phenotypes in different tissues specifically focusing on mitochondrial gene expression.  Methods: We performed bulk RNA sequencing (RNA-seq) and single cell RNA-seq (scRNA-seq) on mesenteric and adipose ECs isolated from normal chow (NC) and high fat diet (HFD) fed mice. Differential gene expression, gene ontology pathway, and transcription factor analyses were performed. We further investigated our hypothesis in humans using published human adipose single nuclei RNA-seq (snRNA-seq) data.   Results: Bulk RNA-seq revealed higher mitochondrial gene expression in adipose ECs compared to mesenteric ECs in both NC and HFD mice. We then performed scRNA-seq and categorized EC clusters as arterial, capillary, venous, or lymphatic. HFD decreased the number of differentially expressed genes between mesenteric and adipose ECs in all subtypes, but the largest effect was seen in arterial ECs. Further analysis of arterial ECs revealed genes coding for mitochondrial oxidative phosphorylation proteins were enriched in adipose compared to mesentery under NC conditions. In HFD mice, these genes were decreased in adipose ECs becoming similar to mesenteric ECs. Transcription factor analysis revealed C/EBP and PPAR, both known to regulate lipid handling and metabolism, had high specificity scores in the NC adipose artery ECs. These findings were recapitulated in snRNA-seq data from human adipose.  Conclusions: These data suggest mesenteric and adipose arterial ECs metabolize lipids differently and the transcriptional phenotype of these two vascular beds converge in obesity, in part, due to downregulation of PPARand C/EBP in adipose artery ECs. This work lays the foundation for investigating vascular bed specific adaptations to obesity.

overall_design: Endothelial cells of ROSA26-eYFP+/+ Cdh5-CreERT2+ mice were isolated from the mesentery and adipose by fluorescence activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Luke

last: Dunaway

first: Melissa

last: Luse

first: Shruthi

last: Nyshadham

first: Gamze

last: Bulut

first: Nicholas

middle: W

last: Chavkin

first: Karen

middle: K

last: Hirschi

first: Gary

last: Owens


title: Loss of endothelial cell heterogeneity in arteries after obesogenic diet [Bulk-seq]

overall_design: Endothelial cells of ROSA26-eYFP+/+ Cdh5-CreERT2+ mice were isolated from the mesentery and adipose by fluorescence activated cell sorting (FACS) and analyzed using bulk RNA-seq.


title: Overexpression of the receptor-like kinase BIR1 gene causes SOBIR1- and EDS1-dependent cell death phenotypes in Arabidopsis

status: Public on Jun 15 2023

city: Lausanne

first: Irene

last: Guzmán-Benito

state: Vaud

address: Biophore, UNIL-SORGE

department: DBMV

country: Switzerland

institute: UNIL

summary: In order to understand the downstream biological processes and pathways associated to BIR1 induction, we conducted a global transcriptome RNA-Seq assay in Arabidopsis wild-type (WT) and transgenic plants with a dexamethasone (DEX)  inducible BIR1-mCherry transgene (ine 9, L9).

overall_design: Comparative gene expression profiling of RNA-seq data from Arabidopsis thaliana WT and L9 plants. Samples were collected at 4 and 12 days of daily treatment with DEX to induce the BIR1 expression. Mock-treated plants (water) ere used as controls.

first: César

last: Llave


title: Erythropoietin re-wires cognition-associated transcriptional networks

status: Public on Jun 16 2023

city: Göttingen

first: Hannelore

last: Ehrenreich

address: Hermann-Rein-Str 3

department: Clinical Neuroscience

institute: Max Planck Institute for Multidisciplinary Sciences

summary: Recombinant human erythropoietin (rhEPO) has potent procognitive effects, likely hematopoiesis-independent, but underlying mechanisms and physiological role of brain-expressed EPO remained obscure. Here, we provide transcriptional hippocampal profiling of male mice treated with rhEPO. Based on ~108,000 single nuclei, we unmask multiple pyramidal lineages with their comprehensive molecular signatures. By temporal profiling and gene regulatory analysis, we build developmental trajectory of CA1 pyramidal neurons derived from multiple predecessor lineages and elucidate gene regulatory networks underlying their fate determination. With EPO as ꞌtoolꞌ, we discover populations of newly differentiating pyramidal neurons, overpopulating to ~200% upon rhEPO with upregulation of genes crucial for neurodifferentiation, dendrite growth, synaptogenesis, memory formation, and cognition. Using a Cre-based approach to visually distinguish pre-existing from newly formed pyramidal neurons for patch-clamp recordings, we learn that rhEPO treatment differentially affects excitatory and inhibitory inputs. Our findings provide mechanistic insight into how EPO modulates neuronal functions and networks.

overall_design: C57BL6/N (WT) male mice received 5000 IU/kg i.p. EPO (12 mice) or solvent control (12 mice). Injections go from age P28 to P48, performed every other day for a total of 11 times. Mice are sacrificed 24 h after the last injection, on P49.

first: Manvendra

last: Singh

first: Ying

last: Zhao

first: Vinicius

last: Daguano Gastaldi

first: Sonja

last: Wojcik

first: Yasmina

last: Curto

first: Riki

last: Kawaguchi

first: Ricardo

middle: M

last: Merino

last: Fernandez Garcia-Agudo

first: Holger

last: Taschenberger

first: Nils

last: Brose

first: Daniel

last: Geschwind

first: Klaus-Armin

last: Nave


title: Single cell transcriptomic expression profiling by single cell RNA sequencing for human induced pluripotent stem cells (iPSCs) derived cortical organoids

status: Public on Jun 19 2023

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

summary: The pupose of this study is to explore the single cell transcriptome profiling changes of cortical organoids differentiated from POLG patient iPSCs compoared to control organoids.

overall_design:
Examination of singel cell transcriptomic profile in iPSC-derived cortical organoids
NOTE FROM SUBMITTER: According to the local law, the raw fastq data can not be uploaded due to the sensitivity of the data.

first: Kristina

middle: X

first: Anbin

last: Chen


title: Evidence of a role for CutRS and actinorhodin in the secretion stress response in Streptomyces coelicolor M145

status: Public on Jun 12 2023

city: Norwich

first: Ainsley

last: Beaton

address: Norwich Research Park

institute: John Innes Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CutRS was the first two-component system to be identified in Streptomyces species and is highly conserved in this genus. It was reported >25 years ago that deletion of cutRS increases the production of the antibiotic actinorhodin in Streptomyces coelicolor but despite this early work the function of CutRS has remained enigmatic until now. Here we show that deletion of cutRS upregulates the production of the actinorhodin biosynthetic enzymes up to 260-fold in the cutRS mutant, explaining the increase in actinorhodin production. However, while ChIP-seq identified 86 CutR binding sites in S. coelicolor none of these are in the actinorhodin BGC, so the effect is indirect. The directly regulated CutR targets identified in this study are implicated in extracellular protein folding, including two of the four highly conserved the HtrA-family foldases, HtrA3 and HtrB and a putative VKOR enzyme which is predicted to recycle DsbA following its catalysis of disulphide bond formation in secreted proteins. We thus tentatively propose a role for CutRS in sensing and responding to protein misfolding outside the cell. Since actinorhodin can oxidise cysteine residues and induce disulphide bond formation in proteins its over production in the ∆cutRS mutant may be a response to protein misfolding on the extracellular face of the membrane.

overall_design: ChIP-seq was carried out to determine the DNA binding sites of the response regulator CutR, part of the two component system CutRS, in Streptomyces coelicolor. This is a conserved two component system found in all member of the genus. CutRS knock out mutants show a different phenotype in the presence of glucose compared to the wild type - and so to understand this further these expirments were carried out on samples grown on DNA (no glucose) and DNAD (with glucose). Being analysed in this experiment is DNA binding of the response regulator CutR in S. coelicolor. S. coelicolor ΔcutRS containing pSS170-Cterm3xFLAG-CutRS (CutS and FLAG-tagged CutR under the native promotor) and S. coelicolor ΔcutRS containing pSS170-Cterm3x_vnz_FLAG-CutRS (CutS and FLAG-tagged CutR from S. venezuelae under the native promotor) grown in the presence and absence of glucose. This was compared to S. coelicolor WT (no FLAG) grown in the same way and each was carried out and analysed in duplicate.

first: Thomas

last: McLean

first: Carlo

last: de Oliveira Martins

first: Govind

last: Chandra

first: Barrie

last: Wilkinson

first: Matthew

middle: I

last: Hutchings


title: Keratin 19 binds and regulates cytoplasmic HNRNPK mRNA targets in triple-negative breast cancer

status: Public on Jul 06 2023

first: Markus

last: Hafner

address: 50 South Drive

department: NIAMS

institute: NIH

summary: This study identifies how a cytoskeletal protein can directly regulate gene expression by controlling the subcellular localization of RNA-binding proteins to support pathways involved in cancer progression.

overall_design: We used parental and K19 KO cell lines to study the impact of cytoskeleton in gene expression regulation.

first: Arwa

last: Fallatah

first: Dimitrios

middle: G

last: Anastasakis

first: Amirhossein

last: Manzourolajdad

first: Pooja

last: Sharma

first: Xiantao

last: Wang

first: Alexis

last: Jacob

first: Sarah

last: Alsharif

first: Ahmed

last: Elgerbi

first: Pierre

last: Coulombe

first: Byung

last: Chung


title: Single-cell sequencing dissects the transcriptional identity of activated fibroblasts and identifies novel persistent distal tubular injury patterns in kidney

status: Public on Jun 14 2023

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Mouse E18.5 wildtype kidney single-cell reference.

overall_design: E18.5 wildtype kidneys were analyzed by single-cell RNA-seq.

first: Joo-seop

last: Park


title: A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes

city: Nashville

first: David

last: Miller

state: TN

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Motor neurons (MNs) are the cellular targets of multiple adult-onset diseases. Because distinct MN populations differ in disease susceptibility, it is important to define in animal models the degree of diversity within adult MNs. Here, we generated a comprehensive molecular resource of adult MNs in C. elegans. Single-cell RNA-sequencing of 12,603 cells revealed that all eight morphologically defined MN classes of the ventral nerve cord and its flanking ganglia subdivide into 29 distinct subclasses, almost quadrupling the degree of their previously described diversity. We find that four of the six C. elegans Hox genes delineate most, but not all MN subclasses. Strikingly, all 29 subclasses are delineated by unique expression codes of neuropeptide genes and receptors, critical for extra-synaptic (wireless) signaling. Leveraging the C. elegans connectome, we found a strong correlation between molecularly and connectivity defined MN subclasses. Beyond providing a valuable resource and searchable database (spinalcordatlas.com), our study identifies Hox and neuropeptide codes as key molecular descriptors of adult MN diversity, codes likely conserved in MNs across species.

overall_design: Ventral nerve cord MNs were isolated from two strains of worms. Two samples were collected from both CZ631 juIs14 [acr-2::GFP] and KRA257 kasIs2 [lin-39p::RFP] worms. MNs were isolated by FACS and analyzed by 10X Genomics 3' single-cell RNA sequencing.

first: Seth

middle: R

last: Taylor

first: Jayson

last: Smith

first: Paschalis

last: Kratsios


title: Hox gene activity directs physical forces to differentially shape chick small and large intestinal epithelia

city: Boston

first: Hasreet

last: Gill

state: MA

address: 77 Avenue Louis Pasteur, NRB 360

institute: Harvard Medical School

summary: Hox genes are highly conserved, master regulators of spatial patterning in the embryo, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of the small and large intestines early in embryogenesis, which ultimately leads to their specialization in both form and function. While the midgut forms villi, the hindgut develops flat, brain-like sulci that resolve into heterogeneous outgrowths. Combining mechanical measurements and mathematical modeling, we demonstrate that the posterior Hox gene Hoxd13 regulates biophysical phenomena that shape the hindgut lumen. We further show that Hoxd13 acts through the TGFβ pathway to thicken, stiffen, and promote isotropic growth of the subepithelial mesenchyme; together, these features lead to hindgut surface buckling. TGFβ, in turn, promotes collagen deposition to affect mesenchymal geometry and growth. We thus identify a cascade of events downstream of positional genetic identity that direct posterior intestinal morphogenesis.

overall_design: To identify genes and pathways that are directly or indirectly regulated by Hoxd13 to affect posterior gut morphogenesis in the chick, we compared mesodermal transcriptomes of wild-type midgut and hindgut intestinal samples, as well as mesodermal samples from a Hoxd13-overexpressing midgut. Tissues were dissected and endoderm layers were removed manually before RNA extraction and downstream processing. Unbiased clustering was used to identify genes commonly differentially expressed in the hindgut and Hoxd13-misexpressing midgut.

first: Sifan

last: Yin

first: Nandan

middle: L

last: Nerurkar

first: John

last: Lawlor

first: ChangHee

last: Lee

first: Tyler

last: Huycke

first: L

last: Mahadevan

first: Clifford

last: Tabin


title: IgM from common variable immunodeficiency patients narrowly recognizes erythrocyte and platelet glycans

status: Public on Jun 09 2023

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

summary: Autoantibody-mediated cytopenias (AICs) regularly occur in profoundly IgG-deficient common variable immunodeficiency (CVID) patients. The isotypes, antigenic targets, and origin(s) of disease-causing autoantibodies in this patient population are unclear. Herein, we report that erythrocytes and platelets from CVID patients with AICs (CVID+AIC) are coated with autoreactive IgM. Glycan array-based analyses of CVID+AIC plasma IgM revealed narrow reactivities to erythrocytic I/i antigens and platelet expressed I/i antigen-related glycans but starkly lower binding to hundreds of other pathogen and tumor-associated carbohydrates. Polyclonal B-cell receptors with corresponding I/i antigen reactivities were highly enriched among CVID+AIC circulating marginal zone (MZ) B cells. Within secondary lymphoid tissues, MZ B cells secreted copious IgM when activated by IL-10 secreting FOXP3-CD25hiTfh cells. In lymph nodes from immunocompetent controls, MZ B cells localized outside of GCs near rare FOXP3-CD25+ cells and plentiful FOXP3+ regulatory T cells. In CVID+AIC lymph nodes, counterpart cells localized to similar anatomic positions but CD25hiTfh cells greatly outnumbered regulatory T cells. In total, our findings indicate glycan-reactive IgM autoantibodies produced outside of GC borders may contribute to the autoimmune pathogenesis of CVID.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS-isolated tonsillar GC B cells and marginal zone B cells

first: Carole

last: Le Coz

first: Samuel

last: Yoon

first: Hakon

last: Hakonarson

first: Neil

last: Romberg


title: ELONGATED HYPOCOTYL (HY5) AND HY5 HOMOLOG (HYH) maintain shade avoidance suppression in sunlight

status: Public on Jun 07 2023

city: Bristol

first: Keara

last: Franklin

address: 24 Tyndall Avenue

department: School of Biological Sciences

institute: University of Bristol

summary: We show that longer-term inhibition of shade avoidance in Arabidopsis is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOG (HYH) which, together, regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification.

overall_design: Monitoring of gene expression in Arabidopsis thaliana wild type (Wassilewskija) individuals and hy5/hyh mutants under different light conditions.


title: Different chromatin scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2

status: Public on Jun 06 2023

first: Kenneth

middle: S.

last: Zaret

address: 9-132, SCTR, 3400 Civic Center Boulevard

institute: University of Pennsylvania School of Medicine

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

overall_design: Refer to individual Series


title: A ligation-independent sequencing method reveals tRNA fragments with blocked 3' termini

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

type: Non-coding RNA profiling by high throughput sequencing

summary: Despite the numerous sequencing methods available, the vast diversity in size and chemical modifications of RNA molecules makes the capture of the full spectrum of cellular RNAs a difficult task. By combining quasirandom hexamer priming with a custom template switching strategy, we developed a method to construct sequencing libraries from RNA molecules of any length and with any type of 3’ terminal modification, allowing the sequencing and analysis of virtually all RNA species. Ligation-independent detection of all types of RNA (LIDAR) is a simple, effective tool to comprehensively characterize changes in small non-coding RNAs and mRNAs simultaneously, with performance comparable to separate dedicated methods. With LIDAR, we comprehensively characterized the coding and non- coding transcriptome of mouse embryonic stem cells, neural progenitor cells, and sperm. LIDAR detected a much larger variety of tRNA-derived RNAs (tDRs) compared to traditional ligation-dependent sequencing methods, and uncovered the presence of tDRs with blocked 3’ ends that had previously escaped detection. Our findings highlight the potential of LIDAR to systematically detect all RNAs in a sample and uncover new RNA species with potential regulatory functions.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Gene expression in mES cells +/- serum, NPC, and sperm using traditional pA sequencing, LIDAR, TAKARA, or NEB ligation-based sequencing.

first: Alessandro

last: Scacchetti

first: Roberto

last: Bonasio


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [mouseD3.5-RNAseq-mm10]

status: Public on Jun 04 2023

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: TRIM28 interacts with PGR and ESR1 in both human and mouse uterus to modulate estrogen and progesterone signaling. Knocking down of TRIM28 in the human endometrial stromal cells imparied decidualization in vitro. Deletion of TRIM28 from mouse uterus disrupted uterine stromal decidualization leading to infertility. Addtionally, TRIM28 deletion caused abnormal accumulation of TRIM28 postive and PGR negative cells in the stroma.

overall_design: Four TRIM28f/f (TRff) and TRIM28d/d (TRdd) mouse uterus were collected at pregnancy day 3.5 for RNA-Seq analysis

first: Rong

last: Li

first: Tianyuan

last: Wang

first: San-Pin

last: Wu

last: Lydon

first: Francesco

last: DeMayo


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [mouse-D3.5-scRNAseq]

overall_design: 3-4 TRIM28f/f (TRff) and TRIM28d/d (TRdd) mouse uterus were collected at pregnancy day 3.5 and the uterus from the mice with the same genotype were pooled for scRNA-Seq analysis

first: John


title: Distinct Chromatin Scanning Modes Lead to Targeting of Compacted Chromatin by Pioneer Factors FOXA1 and SOX2 [Cut&Run]

summary:
Pioneer transcription factors, by interacting with nucleosomes, scan silent, compact chromatin to target regulatory sequences, enabling cooperative binding events that modulate local chromatin structure and gene activity.  However, not all cognate motifs are targeted by pioneer factors and dynamic scanning parameters required to scan compact chromatin are unknown. A combined genomics and single-molecule tracking approach shows that to target DNase-resistant, low-histone turnover sites, pioneer factors FOXA1 and SOX2 display opposite dynamics of chromatin scanning: slow, with low nucleoplasmic diffusion and stable interactions, versus fast, with high nucleoplasmic diffusion and transient interactions, respectively. Despite such differences, the ability of FOXA1 and SOX2 to scan low-mobility chromatin, mediated by protein domains outside of the respective DNA binding domains, leads to targeting silent chromatin. By contrast, non-pioneer HNF4A predominantly targets DNase-sensitive, nucleosome-depleted regions. We conclude that the targeting of compact chromatin sites by pioneer factors can be performed through diverse dynamic processes.
Cleavage under Targets and Release Using Nuclease (CUT&RUN) of SOX2 and SOX2-DBD after ectopic expression in BJ fibroblasts.

overall_design: Andrew,Katznelson

first: Jonathan

last: Lerner


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [mouseD35-ChIPseq-mm10]

overall_design: Wild type mouse uterus were collected at Pregnancy day 3.5 for TRIM28 ChIP-Seq analysis.


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [HESC-RNAseq-hg19]

overall_design: Primary human endometrial stromal cells from three donors were treated with either non-targeting siRNA (siNT) or TRIM28 siRNA (siTRIM28) for 48h then treated with either vehicle or EPC (17beta-estradiol, progesterone and cAMP) for 72h to generate pre-decidual (Pre-dec) and decidaul (Dec) cells and collected for RNA-Seq analysis.


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [mouseP4-RNAseq-mm10]

overall_design: Pgrcre/+ mice were ovariectomized for 2 weeks treated with either oil or Progesterone (P4) for 6h. The uterus were collected for RNA-Seq analyais.


title: TRIM28 modulates progesterone and estrogen signaling in endometrium

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: TRIM28 modulates progesterone and estrogen signaling in endometrium [mouseD35-PGR-ChIPseq-mm10]

summary: TRIM28 interacts with PGR and ESR1 in both human and mouse uterus to modulate estrogen and progesterone signaling. Knocking down of TRIM28 in the human endometrial stromal cells impaired decidualization in vitro. Deletion of TRIM28 from mouse uterus disrupted uterine stromal decidualization leading to infertility. Additionally, TRIM28 deletion caused abnormal accumulation of TRIM28 positive and PGR negative cells in the stroma.

overall_design: Mouse uteri were collected at D3.5 and performed PGR ChIP-seq using sc7208 PGR antibody by Santa Cruz Biotechnology.

first: San


title: Loss of endothelial cell heterogeneity in arteries after obesogenic diet

status: Public on Jun 24 2023

first: Brant

last: Isakson


title: Distinct Chromatin Scanning Modes Lead to Targeting of Compacted Chromatin by Pioneer Factors FOXA1 and SOX2 [ChIP-seq]

summary:
Pioneer transcription factors, by interacting with nucleosomes, scan silent, compact chromatin to target regulatory sequences, enabling cooperative binding events that modulate local chromatin structure and gene activity.  However, not all cognate motifs are targeted by pioneer factors and dynamic scanning parameters required to scan compact chromatin are unknown. A combined genomics and single-molecule tracking approach shows that to target DNase-resistant, low-histone turnover sites, pioneer factors FOXA1 and SOX2 display opposite dynamics of chromatin scanning: slow, with low nucleoplasmic diffusion and stable interactions, versus fast, with high nucleoplasmic diffusion and transient interactions, respectively. Despite such differences, the ability of FOXA1 and SOX2 to scan low-mobility chromatin, mediated by protein domains outside of the respective DNA binding domains, leads to targeting silent chromatin. By contrast, non-pioneer HNF4A predominantly targets DNase-sensitive, nucleosome-depleted regions. We conclude that the targeting of compact chromatin sites by pioneer factors can be performed through diverse dynamic processes.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HNF4A, FOXA1, FOXA1-DBD, FOXA1-NHAA, FOXA1-RRAA, as well as H2B-HALO after ectopic expression in human BJ fibroblast cells.

overall_design: Jonathan,Lerner

first: Andrew

last: Katznelson


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [HESC-CUT+RUN-hg38]

overall_design: Primary human endometrial stromal cells from three donors were treated with EPC (17beta-estradiol, progesterone and cAMP) to generate decidaul (Dec) cells and collected for PGR and TRIM28 Cut and run analysis.


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [ATACseq-hg38]

overall_design: Primary human endometrial stromal cells from three donors were treated with either non-targeting siRNA (siNT) or TRIM28 siRNA (siTRIM28) for 48h then treated with either vehicle or EPC (17beta-estradiol, progesterone and cAMP) for 72h to generate pre-decidual (Pre-dec) and decidaul (Dec) cells and collected for ATAC-Seq analysis.


title: TRIM28 modulates progesterone and estrogne signaling in endometrium [HESC-ChIPseq-hg38]

overall_design: Primary human endometrial stromal cells two patients were collected for TRIM28, H3K27AC and H3K27me3 ChIP-Seq analysis.


title: Transcriptional activity of an MPRA library containing sequences of genomic origin bound by the transcription factor CRX measured in retinas from mice carrying pathogenic CRX variants

status: Public on May 27 2023

city: Saint Louis

first: Michael

middle: Aaron

last: White

address: 660 South Euclid Ave

institute: Washington University in St. Louis School of Medicine

summary: Dozens of mutations in the photoreceptor-specific transcription factor CRX are linked with different human blinding diseases that vary in their severity and age of onset. How these mutations in a single TF cause a range of pathological phenotypes is not understood. We deployed massively parallel reporter assays (MPRAs) in live mouse retina to directly measure changes to CRX cis-regulatory function caused by two disease-causing mutations, one in the DNA binding domain (p.R90W) and the other in the activation domain (p.E168d2).

overall_design: Two MPRA libraries were constructed containing 1,723 candidate cis-regulatory elment (CRE) sequences each 164 bp in length. The CREs were cloned upstream of one of two minimal promoters: rhodopsin (rho library) and hsp68 (hsp68 library). Each library was electroporated into mouse retinal explants from mice carrying each of six Crx genotypes: +/+, R90W/+, E168d2/+, R90W/R90W, E168d2/E168d2, -/-, with three biological replicates per combination. Additionally, each of the two input plasmid DNA libraries were sequenced.

first: James

last: Shepherdson

first: Ryan

middle: Z

last: Friedman

first: Yiqiao

last: Zheng

first: Chi

last: Sun

first: Inez

middle: Y

last: Oh

first: David

last: Granas

first: Barak

last: Cohen

first: Shiming

last: Chen


title: Symmetric self-renewal and dormancy define functional fetal liver hematopoietic stem cells at single cell resolution

status: Public on May 24 2023

city: Seattle

first: Brandon

last: Hadland

state: WA

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Center

summary: Our study disclosed previously unrecognized heterogeneity in fetal liver (FL) hematopoietic stem cells (HSC), highlighting biosynthetic dormancy as a key to symmetric self-renewal of engraftable HSC and supports recent studies demonstrating distinct developmental origins for multipotent progenitors and HSC in definitive hematopoiesis.

overall_design: single cell RNA-sequencing (10X Genomics platform) of murine E12 FL-derived cultured endothelial cells expressing mAkt (FL-EC) used as stroma to support HSC developemnt/expansion ex vivo; and murine E13.5 FL-derived FACS-isolated VEcadherin-/low,CD45+,Gra1-F4/80-,Sca1+,EPCR+  cells enriched for HSCs (primary cells and progeny following co-culture with FL-EC). Sample 4 also included CD11b-ESAM expression in sorting.

first: Hadland

last: Brandon


title: Mapping disease-associated regulatory circuits by cell type from single-cell multiomics data

status: Public on May 19 2023

city: New York

first: Elena

last: Zaslavsky

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai


title: Transcriptional profiling of regional intestinal tissue from mice with and without Apc deficiency

status: Public on Apr 28 2023

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

summary: A profile of gene expression differences along the length of the mouse intestine, in the presence and absence of functional Apc.

overall_design: Expression data from intestine at the noted locations with and without Apc deficiency.

last: Hodder

first: Owen

last: Sansom


title: PP2Ac Deficiency Enhances Tumor Immunogenicity by Activating STING-Type I Interferon Signaling in Glioblastoma [scRNA]

status: Public on May 17 2023

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: Glioblastoma (GBM) is an incurable cancer despite aggressive treatment paradigms. Current immunotherapies, such as CTLA-4 and/or PD-1 blockade, have yet to demonstrate benefits for GBM. A key barrier is the immunologically “cold” nature of GBM defined by insufficient tumor antigen presentation and lack of T cells infiltration. We previously demonstrated that pharmacologic inhibition of Protein Phosphatase-2A (PP2A), using a small molecule inhibitor, synergized with PD1 blockade in multiple preclinical tumor models including GBM. However, PP2A is ubiquitously expressed in many cell types and regulates many cellular pathways. The cell type or molecular mechanism responsible for PP2A-modulated tumor immunity is poorly understood. Here, we demonstrate that genetic ablation of PP2A in glioma cells sufficiently promotes tumor immunogenicity by enhancing 1) dsDNA production and thereby cGAS-Type I interferon (IFN) signaling, 2) MHC-I expression and 3) tumor mutational burden. PP2A deficient glioma enhances DC activation and cross presentation to promote clonal expansion of tumor antigen specific CD8 cells. PP2A deficiency also markedly sensitize tumors to immune checkpoint blockade and radiotherapy. Single cell analysis of murine glioma demonstrates that PP2A deficient tumors have 1) increased infiltration of CD8+ T cell, NK cell and cDC1 cells, 2) reduced infiltration of immunosuppressive tumor associated macrophages, 3) promotion of IFN signaling in both myeloid and tumor cells, and 4) reduced glioma-associated gene signature that predicts poor prognosis in glioma patients. This is the first study to establish a role for PP2A in regulating dsDNA-cGAS-STING signaling and collectively, our results suggest that PP2A is a promising novel target to enhance anti-tumor immunity for glioma.

overall_design: We implanted subcutanous or intracranial SB28 murine glioma in WT and LysMcrePP2Acfl/fl mice. 18 days after implantation, tumor tissue was harvested, and single cell suspensions were obtained and sent for sequencing.

first: Das

last: Oishika

first: Mondal

last: Isha

first: Xu

last: Beisi

first: Lu

last: Rongze

first: Ho

last: Winson


title: Spatial Transcriptomics of Liver tissue with Bcatenin exon3 genetic mutations.

summary: Gene expression was profiled in different regions of mouse liver with either Bcatenin exon3 mutation or Bcatenin exon3/Myc mutation at the noted time points.

overall_design: Spatial transcriptomic data of the noted regions in mouse liver with the noted genetic mutations.

first: Alexander

last: Raven

first: Nigel

last: Jamieson


title: PP2Ac Deficiency Enhances Tumor Immunogenicity by Activating STING-Type I Interferon Signaling in Glioblastoma [RNA]


title: RNA-seq data for tumor and adjacent non-tumor tissues from hepatocellular carcinoma patients with anti-PD-1 therapy

status: Public on May 01 2023

city: Nanjing

first: Binghua

last: Li

state: Jiangsu

address: Zhongshan road 321, Nanjing, Jiangsu, China

department: Department of Hepatobiliary Surgery

country: China

institute: the Affiliated Drum Tower Hospital, Medical School of Nanjing University

summary: Immune checkpoint inhibitors elicit durable antitumor effects in multiple cancers, yet not all patients respond. Here, we aimed to develop and validate a molecular classification of  hepatocellular carcinoma (HCC) patients based on 42 fatty acid degradation genes and demonstrate its predictive ability in the clinical response of anti-PD1 therapy in HCC patients. We studied global mRNA expression profiles from 41 primary tumor tissues and 25 nontumor tissues derived from 41 HCC patients. 17 patients received anti-PD1 therapy and were available with clinical response. 63 samples were also sent for lipidomics analysis. Methods for the study included gene expression analysis, consensus clustering analysis, pathway enrichment analysis, and Single-Sample Gene Set Enrichment Analysis (ssGSEA). This study identified and validated a novel molecular classification based on fatty acid degradation that predicts clinical response to anti-PD-1 therapy in hepatocellular carcinoma.

overall_design: In total, 69 samples from hepatocellular carcinoma tumors and adjacent non-tumor liver tissue have been obtained from 44 patients who underwent radical resection between January 2019 and June 2021 in Nanjing Drum Tower Hospital. Three samples didn’t pass the quality control for RNA-seq and 6 samples didn’t pass the quality control for lipidomics analysis due to tissue degradation or limited tissue amount, thus being ruled out from the study. Seventeen patients received anti-PD1 therapy and were available with clinical response. The study was approved by the Research Ethics Committee of Drum Tower hospital, and written informed consent was obtained from each patient. Each sample was assigned a new research ID, and the patient’s name or medical record number used during hospitalization was de-identified.

first: Yunzheng

first: Beicheng

last: Sun

first: Decai

last: Yu


title: Transcriptional profiling of Liver tissue from mice with bcatenin and Myc mutations

summary: The effect of combinations Apc, Bcatenin and Myc mutation on mouse liver was examined with RNAseq at two time points.

overall_design: Expression data from liver with the noted mutations at the noted time points.


title: Intravenous BCG induces primed immune signaling that correlates with protection against tuberculosis

status: Public on May 31 2023

city: Cambridge

first: Bryan

middle: B

last: Bryson

address: 77 Massachusetts Avenue

department: Department of Biological Engineering

institute: Massachusetts Institute of Technology

summary: We profiled rested and PPD-stimulated bronchoalveolar lavages to understand immune features of protection.

overall_design: Rested and PPD-stimulated bronchoalveolar lavages (BALs) from vaccinated and naïve rhesus macaques were profiled using Seq-Well

first: Joshua

last: Peters

first: Tricia

last: Darrah


title: High-resolution analysis of mononuclear phagocytes reveals clinically relevant markers in human colo-rectal liver metastasis II

status: Public on May 02 2023

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

summary: Macrophages (Mf) are the most abundant mononuclear phagocytes in tumor tissues and hold promise as therapeutic targets and indicators of disease progression. In this work, we mapped by single-cell analysis the distinct Mf populations infiltrating the invasive margin and normal adjacent regions of human colo-rectal liver metastasis (CLM), and we exploited this information to identify non redundant markers with clinical relevance. Different populations were enriched in the invasive margin, including early-mature, inflammatory Mf (MoMf) expressing the monocytic markers S100A12 and SERPINB2, and a more mature population (TAMs) expressing CD68, GPNMB and TREM2. TAMs were enriched in pathways of matrix degradation, angiogenesis and lipid metabolism, similarly to dysfunctional macrophages described in other tumors. Cell-cell interaction analysis with CD8+ T cells defined opposing roles of MoMf, predicted to interact via IL-15, and TAMs, engaging T cells via IL-20 and IL-10. By multiplex immunofluorescence in CLM sections, we confirmed that SERPINB2 and GPNMB are expressed by different Mf subsets, with distinct topographical distribution and opposite association with patient clinical outcome.

overall_design: A total of six samples. Three invasive margin tissues (IM) and three normal adjacent tissues (NA).

first: R

last: Carriero

first: N

last: Cortese

first: P

last: Kunderfranco

first: F

last: Marchesi

first: A

last: Mantovani


title: Transcriptional profiling of multiple tissues from mice with and without Apc deficiency

first: Kathryn

last: Gilroy

summary: The effect of whole body Apc deficiency on multiple mouse tissues was examined with RNAseq.

overall_design: Expression data from the noted tissues with and without Apc deficiency.

first: Owen

last: Sansom


title: PP2Ac Deficiency Enhances Tumor Immunogenicity by Activating STING-Type I Interferon Signaling in Glioblastoma

first: Beisi

last: Xu

overall_design: Refer to individual Series


title: Serum miRNA as Potential Biomarkers for ovarian cancer

status: Public on Apr 27 2023

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Serum samples were obtained from patients with ovarian cancer (OC; n=64) and noncancerous control (n=4) for microarray. We found that four miRNAs were significantly high-expression level in OC relative to the controls.

overall_design: The aim of this study was to examine whether serum microRNAs is useful as a biomarker for ovarian cancer (OC).

first: Takuma

last: Fujii

first: Rina

last: Kawahara


title: DRMY1 promotes robust morphogenesis by sustaining translation of a hormone signaling protein

status: Public on Apr 24 2023

city: Ithaca

first: Adrienne

last: Roeder

address: 239 Weill Hall, 526 Campus Road

department: Weill Institute of Cell and Molecular Biology and Plant Biology Section, School of Integrative Plant Science

institute: Cornell University

summary: Robustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals initiate at robust positions and times and grow to equal size to enclose and protect the inner floral organs. We previously characterized the mutant development related myb-like1 (drmy1), where 3-5 sepals initiate at irregular positions and variable times and grow to different sizes, compromising their protective function. The molecular mechanism underlying this loss of robustness was unclear. Here, we show that drmy1 has reduced TARGET OF RAPAMYCIN (TOR) activity, ribosomal content, and translation. Translation reduction decreases the protein level of ARABIDOPSIS RESPONSE REGULATOR7 (ARR7), a rapidly synthesized and degraded cytokinin signaling inhibitor. The resultant upregulation of cytokinin signaling disrupts the robust positioning of auxin signaling, causing variable sepal initiation. Our work shows that the homeostasis of translation, a ubiquitous cellular process, is crucial for the robust spatiotemporal patterning of organogenesis.

overall_design: Inflorescences of ap1 cal AP1-GR and drmy1 ap1 cal AP1-GR were induced with dexamethasone for three days and collected on the fourth day since the first induction (when sepals are emerging from the floral meristems). Three biological replicates were collected for each genotype.

first: Mingyuan

last: Zhu


title: Mapping disease-associated regulatory circuits by cell type from single-cell multiomics data (S. aureus scRNA-seq)

first: Elena

last: Zaslavsky

summary: Resolving chromatin remodeling-linked gene expression changes is important for understanding disease states. We describe MAGICAL (Multiome Accessible Gene Integration Calling And Looping), a hierarchical Bayesian approach that leverages paired scRNA-seq and scATAC-seq data from different conditions to map disease-associated transcription factors, regulatory sites and genes as regulatory circuits. By introducing hidden Bayesian variables to allow modeling noise and signal variation across cells and conditions in both transcriptome and chromatin data, in systemic evaluations MAGICAL achieved high accuracy on circuit prediction at cell-type resolution. We applied MAGICAL to study Staphylococcus aureus sepsis from peripheral blood mononuclear single cell data that we generated from infected subjects and healthy uninfected controls. MAGICAL identified sepsis-associated regulatory circuits predominantly in CD14 monocytes, known to be sepsis activated. We addressed the challenging problem of distinguishing methicillin-resistant- (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA) infections, where differential expression analysis failed to show predictive value. MAGICAL, however, identified epigenetic circuit biomarkers that distinguished MRSA from MSSA.

overall_design: scRNA sequencing of PBMCs from 10 samples with MRSAs, 11 samples with MSSAs and 23 healthy controls

first: Xi

last: Chen


title: CPD-capture-seq map of CPD formation in UV-irradiated primary melanocytes, normal human skin fibroblasts and UV-irradiated genomic DNA

status: Public on Apr 12 2023

city: Pullman

first: John

middle: J.

last: Wyrick

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

type: Genome variation profiling by high throughput sequencing

summary: UV-induced CPDs were mapped in primary skin melanocytes or normal human skin fibroblasts following either UVC or UVB irradiation and in isolated human genomic DNA (naked DNA control) that was UVB or UVC irradiated. CPDs were mapped across the human genome using the CPD-capture-seq method and the resulting libraries were captured for ~4000 genomic regions of interest (~3 Mbp) of the human genome by the company Rapid Genomics prior to Illumina sequencing

overall_design: A method known as CPD-capture-seq was used to map the formation of UV-induced CPDs across the genome of primary human melanocytes (NHEM 2) and normal human skin fibroblasts (NHF1) cells after they were irradiated with a UVB or UVC light. As a control experiment, isolated human genomic DNA was irradiated with UVB or UVC light (naked DNA control) and CPDs were mapped using CPD-capture-seq and the resulting libraries were captured for ~4000 genomic regions of interest (~3 Mbp) of the human genome by the company Rapid Genomics prior to Illumina sequencing

first: Kathiresan

last: Selvam


title: Paired single nucleus RNA and ATAC sequencing on the role of diet and aging in hematopoietic stem and progenitor cells

status: Public on Apr 21 2023

city: San Diego

first: Pura

last: Muñoz-Cánoves

state: CA

address: 5510 Morehouse Dr

institute: Altos Labs

summary: We performed joint single-nucleus RNA (snRNA-seq) and ATAC (snATAC-seq) sequencing on hematopoietic stem and progenitor cells (LSK) isolated from mouse bone marrow of mice of different ages and dietary treatments. Mice were either fed ad libitum continually until bone marrow isolation at young (yAL) or old (oAL) age, or underwent a mild dietary restriction (DR; 30% reduction in food intake by weight) for the two weeks prior to bone marrow isolation at young (yDR) or old (oDR) age to investigate early response to nutrient deprivation. Each of these four samples contained pooled cells from two mice.

overall_design: Profiles of single-nucleus transcriptomes and epigenomes, assayed using snRNA-seq and scATAC-seq, across sorted LSK cells from mouse bone marrow for mice of different diets and ages.

first: Marthe

last: Behrends

first: Yulin

first: Martin

last: Bens


title: Gene expression profile of FFPE samples collected with translational purposes from the MITO16/MaNGO-OV2 clinical trial

status: Public on Apr 19 2023

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: MITO16/MaNGO-OV2 (NCT01706120) is a multicenter, phase IV, single arm trial for advanced stage IIIB-IV or recurrent, previously untreated, ovarian cancer patients receiving carboplatin, paclitaxel plus bevacizumab for six 3-weekly cycles followed by bevacizumab single agent until progression or unacceptable toxicity up to a maximum of 22 total cycles. The trial that was specifically designed with a translational primary endpoint to explore if selected clinical and biological factors could identify ovarian cancer patients with better prognosis in terms of progression free survival and overall survival after combined first-line treatment with chemotherapy plus Bevacizumab. The translational study, designed together with the clinical trial, the translational study implicated the collection of patients’ tissue (formalin-fixed paraffin-embedded – FFPE) and blood samples. Gene expression profile was among the molecular analyses proposed on FFPE samples.

overall_design: After pathological revision, two 1 mm-cores of FFPE tissues cores were selected to represent at least a percentage >70% of tumor cells, no significant signs of necrosis and to avoid excessive presence of stromal tissue for RNA extraction. RNA from 195 patients of MITO16/MaNGO-OV2 trial was isolated using Qiagen RNeasy FFPE kit (Qiagen, Hilden, Germany) and quality checked. RNA concentration was assessed by the Nanodrop 2000 UV-Vis Spectrophotometer. Sample purity was assessed by 260/280 and 260/230 ratios and the recorded values ranged from 1.9-2.2. Gene expression profiling was performed using the GeneChip WT Pico kit (Affymetrix, Thermo Fisher Scientific) following the guidelines for FFPE material. EGFR status: M0,negative; MM,100%membrane expression; M,≤ 30%.


title: Genome-wide activation of a glioma cancerous transcription program and super-enhancers by a single enhancer HOXDeRNA [ChiRP-Seq]

status: Public on Mar 31 2023

city: Boston

first: Evgeny

last: Deforzh

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

institute: Brigham and Women's Hospital

summary: A growing number of studies describe multiple functions of lncRNAs in chromatin that support their active roles in normal and disease-specific gene expression. We identified a specific enhancer-associated LINC01116 (named HOXDeRNA), which targeted activation transformed human astrocytes into glioma-like cells. Using a combination of RNA-Seq, ChIRP-Seq, and ChIP-Seq, we defined the transcriptomic and epigenetic changes underlying the transformation. We demonstrate that HOXDeRNA binds in trans to the promoters of 44 glioma-specific transcription factors distributed throughout the genome and derepresses them by removing the Polycomb 2 complex. This process is mediated by the RNA G-quadruplex structure of HOXDeRNA. Moreover, HOXDeRNA-induced astrocyte transformation is accompanied by the activation of glioma-specific super-enhancers enriched for binding sites of glioma master transcription factors SOX2 and OLIG2, and multiple oncogenes such as EGFR, PDGFR, BRAF, and miR-21. Our results help reconstruct the sequence of events underlying the process of astrocyte transformation and suggest a driving role of HOXDeRNA eRNA in gliomagenesis.

overall_design: ChiRP-Seq were performed on Glioma Stem Cells (GBM4, GBM6, GBM8)  and HOXDeRNA-activated astrocytes to capture all direct interactions between the HOXDeRNA and genomic DNA


title: Genome-wide activation of a glioma cancerous transcription program and super-enhancers by a single enhancer HOXDeRNA

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


title: Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis

status: Public on May 04 2023

city: St. Louis

first: Christopher

last: Maher

state: Missouri

address: 1 Brookings Dr

institute: Washington University in St. Louis

summary: Colorectal cancer (CRC) is the most common gastrointestinal malignancy in the U.S.A. and approximately 50% of CRC patients develop metastatic disease (mCRC) with an average 5-year survival rate of 13%. Despite our understanding of circular RNAs (circRNAs) in primary cancer, their role throughout mCRC remains poorly characterized. Further, despite the availability of bulk RNA-Seq data for monitoring circRNA expression little is known about their cell-type specific expression profiles to fully understand their functions between tumor cells and the microenvironment. To evaluate circRNAs in mCRC progression, total RNA-Seq was performed on 30 matched normal, primary, and distant metastatic samples from 14 mCRC patients. Additionally, the transcriptome of five CRC cell lines were sequenced to construct a circRNA catalog in CRC. Differential expression (DE) analysis identified circRNAs dysregulated between normal, primary, and metastatic tissues. Differential backsplicing (DS) analysis was used to highlight circRNAs with an altered tendency in backsplicing as compared to their linear counterparts. Cell-type deconvolution was performed using published CRC single-cell RNA-Seq datasets as signature matrices. The cell-type specific expression of circRNAs was then estimated through a non-negative least squares statistical model.

overall_design: Comparative gene & circRNA expression profiling analysis of RNA-seq data between matched normal, primary, metastasis tissue in colorectal cancer patients. Cell lines serve as a reference catalog or circRNAs.

first: Sidi

last: Zhao

first: Amy

last: Ly

first: Ryan

middle: C

last: Fields

middle: A


title: Skeletal Muscle Transcriptomic Responses to Chronic Concurrent Exercise Training

status: Public on Apr 01 2023

city: Melbourne

first: Baubak

last: Shamim

state: VIC

address: Level 5, 215 Spring Street

department: Mary MacKillop Institute for Health Research

country: Australia

institute: Australian Catholic University

summary: Combining resistance and endurance exercises in a training regime (concurrent training) can impair improvements in muscle hypertrophy, strength, and power compared to resistance training alone. Here we aimed to characterize skeletal muscle transcriptomic changes following chronic concurrent training to determine whether contraction-induced gene expression may reveal molecular underpinnings explaining impaired adaptations. Eighteen young, healthy male participants underwent 12 weeks of resistance, endurance, or concurrent training. Maximal strength, aerobic capacity, and anaerobic power were assessed. Transcriptomics were performed on skeletal muscle biopsies obtained pre and post-intervention. Improvements to maximal anaerobic power are impaired with concurrent and endurance training. Gene expression related to plasma membrane structures was enriched while gene expression related to regulation of mRNA processing and protein degradation was suppressed with concurrent training. Considerable overlap of gene expression related to extracellular matrix remodeling was observed between concurrent and endurance training. Our results provide the first comprehensive comparison of unique and overlapping gene sets enriched following chronic resistance, endurance, and concurrent training, and reveals pathways that may have implications in relation to impaired adaptations when undertaking concurrent training.

overall_design: The study employed a parallel-groups design where participants were stratified according to lean body mass (LBM) and allocated to either a resistance only (RES), endurance only (END) or concurrent resistance and endurance exercise training (CET) group for 12 weeks. Measures of maximal strength, aerobic capacity, and anaerobic power, as well as body composition were performed pre- and post-intervention. Resting biopsies were obtained from the vastus lateralis muscle pre-intervention, after weeks 2 and 8 of exercise training, and post-intervention. For the duration of the intervention, all participants consumed a high-protein diet (2 g·kg-1·d-1). The study was approved by the Australian Catholic University Human Research Ethics Committee and was carried out in accordance with the latest revision of the Declaration of Helsinki. This trial was registered with the Australian New Zealand Clinical Trials Registry (ACTRN12617001229369).


title: Effect of adenosine treatment on HAP1 cells with a knockout of MTHFD1

status: Public on Apr 26 2023

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Folate metabolism provides the building blocks of many classes of biomolecules including purine nucleotides, thymidylate, serine and methionine and is an important target of antimetabolite drugs. A central enzyme in the pathway is the trifunctional MTHFD1, that catalyzes the interconversion of folates by its formyltetrahydrofolate synthetase and methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase domains. Here, we employ large-scale chemical and genome-wide genetic screens to investigate the chemical and genetic dependencies caused by MTHFD1 loss-of-function and uncover a central role of the enzyme in balancing the response to extracellular adenosine. We show that adenosine is essential in MTHFD1KO cells, where adenine-containing compounds counter AMPK activation and increase proliferation in a PARP8, ATF7 and PML-dependent manner. In contrast, adenosine supplementation causes strong toxicity in patient-derived MTHFD1-derived cells harboring dehydrogenase/cyclohydrolase domain mutations. This response, mediated by replication stress and activation of the DNA damage response, is dependent on the nucleotide salvage enzyme HRPT1 and on NUDT5, an enzyme involved in nuclear ATP generation. Our findings suggest an evolutionary rationale for integrating three distinct enzymatic activities within the single MTHFD1 protein and propose the application of dehydrogenase/cyclohydrolase inhibitors in tumors located in an adenosine-rich microenvironment.

overall_design: RNAseq samples were performed in at least duplicates. All experiments contain respective control samples.

first: Jung

last: Lin

first: Luna

middle: D

last: di Durazzo

first: Pisanu

last: Buphamalai

first: Marton

last: Siklos

first: Jakob

last: Genger

first: Gerald

last: Hofstaetter

first: Anna

last: Koren

first: Kathrin

last: Runggatscher

first: Bettina

last: Guertl

first: D

middle: S

last: Froese

first: David

last: Rosenblatt

first: J

middle: T

last: Hannich

first: Kristaps

last: Klavins

first: Andreas

last: Bregthaler

first: Joerg

last: Menche

first: Sara

last: Sdelci


title: Genome-wide activation of a glioma cancerous transcription program and super-enhancers by a single enhancer HOXDeRNA [ChIP-seq]

first: Evgeny

last: Deforzh

overall_design: We investigated the epigenetic status of HOXDeRNA-occupied genes in control or HOXDeRNA-active astrocytes, using H3K27Ac (#4353, Cell Signaling) as the mark of active chromatin state, and H3K27Me3 (#9733, Cell Signaling) and EZH2 (Cat. 39002, Active Motif) as the marks associated with repressed chromatin.


title: Cancer-specific CD8 T cell frequency at baseline in blood correlates with response to PD-1 blockade in Merkel cell carcinoma.

first: Thomas

middle: Heyward

last: Pulliam

address: 850 Republican St.

institute: University of Washington

summary: Understanding immunotherapy resistance is challenging due to difficulty identifying cancer-specific T cells. Merkel cell carcinoma (MCC) is typically driven by Merkel cell polyomavirus (MCPyV), facilitating identification of cancer-specific T cells across patients. We characterized cancer-specific T cells in 35 MCC patients, including participants in a neoadjuvant anti-PD-1 trial. Higher MCPyV-specific CD8 T-cell frequency in pre-treatment blood (but not tumors) correlated with response (p=0.005). Single-cell transcriptomics revealed MCPyV-specific CD8 T cells in blood had increased stem/memory signatures and decreased exhaustion signatures relative to their intratumoral counterparts. While frequency of peripheral cancer-specific T cells was associated with response to initial PD-(L)1 blockade, longitudinal study of acquired resistance revealed immune evasion by tumor-cell MHC-I downregulation despite cancer-specific T cell expansion to 0.5% in blood. Blood thus appears to be an important reservoir of cancer-specific CD8 T cells and adoptive cell therapies may be particularly effective in patients without such cells.

overall_design:
We used 10x Genomic's Chromium Single Cell 5' Reagent Kits (v1.1 Chemistry Dual Index) with Feature Barcoding technology for Cell Surface Protein and Immune Receptor to identify antigen specific T cell V(D)J sequences. This was performed on tumor and blood specimen taken from 7 pateints. Due to patient privacy concerns, only processed and not raw sequencing reads were deposited.
***raw data were not included due to patient privacy regulations***

first: Saumya

last: Jani

first: Paul

last: Nghiem


title: Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing

status: Public on Mar 21 2023

city: Shanghai

first: Peng

last: Zhang

address: No. 507 Zhengmin Road

institute: Department of Thoracic Surgery, Shanghai Pulmonary Hospital

summary: To address the potential therapy-resistant mechanisms and underly the changes of tumor microenvironment (TME) after immunotherapy, we performed scRNA-seq  and bulk RNA-seq from the patients with resectable non-small cell lung cancer (NSCLC) before and after PD-1 blockade combined with chemotherapy. We found that the combined therapy significantly remodeled the immune cell compartments in the TME. Patients with different pathologic responses had distinct characteristics of malignant cells and immune cell compositions. Our study provided several potential biomarkers for future immunotherapy and novel strategies to improve response.

overall_design:
Transcriptomic dynamics of NSCLC during anti-PD-1 + chemotherapy
Submitter statement concerning raw data: The raw data files have been deposited to Genome Sequence Archive of the BIG Data Center at the Beijing Institute of Genomics, Chinese Academy of Science, under accession number HRA001033.


title: Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B [PAR-CLIP]

status: Public on Mar 17 2023

city: Bethesda

first: Ashish

last: Lal

state: MD

address: 37 Convent Drive, Bldg 3, Room 6134

department: Genetics Branch

institute: NCI, NIH

summary:
Purpose: Matrin3 (MATR3) is a DNA and RNA-binding protein and one of the major components of the nuclear matrix. Matrin3 is upregulated in colorectal cancer (CRC) compared to normal tissues, indicating potential oncogenic function in CRC. We found that depletion of Matrin3 results in decreased proliferation and colony formation in two CRC cell lines. To understand the molecular mechanism(s) by which Matrin3 mediates these effects, we aimed to find Matrin3 direct RNA targets and the effects of Matrin3 on them.
Methods: We performed PAR-CLIP for endogenous Matrin3 and RNA-seq after Matrin3 silencing in HCT116 cells, a colorectal cancer cell line.
Results: We uncovered Matrin3-mediated regulation of spindle dynamics in colorectal cancer (CRC) cells. We identified bound and regulated Matrin3 target RNAs transcriptome-wide in CRC cells, and found that Matrin3 broadly regulates alternative splicing. Among the top Matrin3 targets, we focused on CDC14B and found that Matrin3 loss resulted in misprocessing of the CDC14B transcript that has a premature termination codon and simultaneous down-regulation of the standard CDC14B transcript in our model. Selective knockdown of the CDC14B standard variant phenocopied the loss of Matrin3 and resulted in reduced CRC cell proliferation, stabilized microtubules, and defects in mitotic spindle formation with tumbled mitotic spindles, suggesting that CDC14B is a key downstream effector of Matrin3.
Conclusions: Our data show that by regulating the abundance of CDC14B standard variant, Matrin3 contributes to maintenance of microtubules dynamics, spindle morphology and proper mitotic spindle orientation and suggest that defects in this pathway may contribute to the reduced proliferation of cells after depletion of Matrin3.

overall_design: RNA binding profile of Matrin3

first: Bruna

last: Muys

first: Roshan

last: Shrestha

first: Dimitrios

last: Anastasakis

first: Lorinc

last: Pongor

first: Xiao

last: Li

first: Ioannis

last: Grammatikakis

first: Ahsan

last: Polash

first: Raj

last: Chari

first: Myriam

last: Gorospe

first: Curtis

last: Harris

first: Mirit

last: Aladjem

first: Munira

last: Basrai

first: Markus

last: Hafner


title: Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B [Iso-Seq]

overall_design: Iso-seq of HCT116 cell line


title: Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [smallRNAseq]

status: Public on Mar 15 2023

first: Aleksandra

last: Kornienko

state: Vienna

address: Dr. Bohrgasse 3

institute: Gregor Mendel Institute

summary:
Background
Long non-coding RNAs (lncRNAs) are under-studied and under-annotated in plants. In mammals, lncRNA expression has been shown to be reaching the extent of protein-coding expression and be highly variable between individuals of the same species. Using A. thaliana as a model plant organism, we aimed to understand the true scope of lncRNA transcription across plants from different regions, characterize lncRNA natural expression variability, and study the causes of this variability.
Results
Using RNA-seq data spanning 499 natural lines and 4 different developmental stages to create a more comprehensive annotation of lncRNAs in A. thaliana, we found over 10,000 novel loci — three times as many as in the current public annotation. We showed that, while lncRNA loci are ubiquitous in the genome, most appear to be actively silenced and their expression and repressive chromatin levels are extremely variable between natural lines. It was particularly prominent in intergenic lncRNAs, where TE-like sequences present in 50% of the loci are associated with increased silencing and variation and such lincRNAs tend to be targeted by TE silencing machinery.
Conclusion
lncRNAs are ubiquitous in the A. thaliana genome, but their expression is highly variable between different lines and tissues. This high expression variability is largely caused by high structural and epigenetic variability of non-coding loci, especially those containing pieces of transposable elements. We create the most comprehensive A. thaliana lncRNA annotation to date and improve our understanding of plant lncRNA biology.

overall_design: The smallRNA-seq data was obtained to investigate determinants of expression variation in natural accessions of A.thaliana and TE-like silencing of lncRNAs. Plants from 14 different A.thaliana natural accessions (https://1001genomes.org/accessions.html) were grown at the growth chambers of GMI, Vienna, Austria. The growing conditions were 21 degrees Celcius, long-day (16-hour light, 8-hour dark). Accessions 1741, 6024, 6244, 9888 and 9905 were cold-treated at 10 degrees for ~ 4 weeks to induce flowering. Flowers and flower buds from 5-10 individual plants were collected for each accession and snap frozen in liquid nitrogen. Frozen tissue was ground with a Retsch machine using 2 steel beads. RNA was isolated from the whole sample using NucleoSpin miRNA kit from Macherey-Nagel following the manufacturer's protocol.

middle: E

first: Viktoria

last: Nizhynska

first: Almudena

last: Molla Morales


title: mitochondria-encoded circRNA in Hepatocellular Carcinoma

status: Public on Mar 06 2023

city: Hefei,

first: Xu

last: Liu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

summary: To identify mitochondria-encoded circRNA in HCC, we isolated mitochondria and performed RNA sequencing of HCC tissues

overall_design: RNA-seq of Mitochondria. The corresponding adjacent tissues are control samples for analyze.


title: Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing

type: Methylation profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Effect of sub-MIC tobramycin treatment on E. coli MG1655 WT and NCM3416

status: Public on Mar 01 2023

city: Paris

first: Zeynep

last: Baharoglu

address: 28 Rue du Docteur Roux

department: Génomes et Génétique

country: France

institute: Institut Pasteur

summary: Effect of sub-MIC tobramycin treatment on E. coli MG1655 WT (strain classically used as WT strain) and NCM3416 (corrected rph strain). Comparison of genes expression without treatment (MH) in E. coli MG1655 WT and NCM3416.

sample_organism: Escherichia coli str. K-12 substr. MG1655

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

first: Manon

last: Lang

first: Elodie

last: Turc

first: Laure

last: Lemée

first: Thomas

last: Cokelaer


title: Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [RNA-Seq]

summary: Background  Long non-coding RNAs (lncRNAs) are under-studied and under-annotated in plants. In mammals, lncRNA expression has been shown to be reaching the extent of protein-coding expression and be highly variable between individuals of the same species. Using A. thaliana as a model plant organism, we aimed to understand the true scope of lncRNA transcription across plants from different regions, characterize lncRNA natural expression variability, and study the causes of this variability.  Results  Using RNA-seq data spanning 499 natural lines and 4 different developmental stages to create a more comprehensive annotation of lncRNAs in A. thaliana, we found over 10,000 novel loci — three times as many as in the current public annotation. We showed that, while lncRNA loci are ubiquitous in the genome, most appear to be actively silenced and their expression and repressive chromatin levels are extremely variable between natural lines. It was particularly prominent in intergenic lncRNAs, where TE-like sequences present in 50% of the loci are associated with increased silencing and variation and such lincRNAs tend to be targeted by TE silencing machinery.   Conclusion  lncRNAs are ubiquitous in the A. thaliana genome, but their expression is highly variable between different lines and tissues. This high expression variability is largely caused by high structural and epigenetic variability of non-coding loci, especially those containing pieces of transposable elements. We create the most comprehensive A. thaliana lncRNA annotation to date and improve our understanding of plant lncRNA biology.

overall_design: We performed this RNA-seq to map lncRNAs and study their inter- and intra-accession expression variation in Arabidopsis thaliana. Plants from 27 different A.thaliana natural accessions were grown at the growth chambers of GMI, Vienna, Austria. The growing conditions were 21 degrees Celcius, long-day (16-hour light, 8-hour dark). For the “9-leaf rosette” samples we collected the full rosette at the 9-leaf stage with one plant harvested per sample. Seedlings were collected at 7 days post sowing (~5 days post germination). The full seedling with the root was collected with approximately 10 individuals/seedlings harvested per sample. For the “flower” samples we collected flowers and flower buds from approximately 5 individuals per sample. Accessions 1741, 6024, 6244, 9075, 9543, 9638, 9728, 9764, 9888, 9905, 22003, 22004, 22005, 22006, 22007 were cold-treated by placing them into 10oC growth chambers (long-day conditions) for ~ 4 weeks to induce flowering. Pollen was collected using the method described in (Johnson-Brousseau and McCormick, 2004) that uses vacuum suction and a series of filters to harvest dry pollen from flowering plants. We used polyester mesh filters of 3 sizes - 150mm, 60mm and 10mm - for the collection. Collected pollen was snap-frozen in liquid nitrogen, stored at -70oC and ground for RNA-sequencing using ~0.5ml of 0.5mm glass beads (Scientific Industries, Inc.). Frozen tissue was ground with a Retsch machine using steel beads. RNA was isolated using an in-house RNA isolation kit (magnetic beads based) and DNAse treated with DNAse I (New England Biolabs). We did not manage to get accessions 6069 and 6124 to flower, so for these two accessions we only have rosette and seedling samples.

middle: M

last: Morales

first: Dejan

last: Dukic


title: Genome-wide activation of a glioma cancerous transcription program and super-enhancers by a single enhancer HOXDeRNA [RNA-seq]

first: Evgeny

last: Deforzh

overall_design: mRNA-Seq was performed on fetal human astrocytes, Immortalized dCas9 expressing astrocytes (NHA) transduced with sgRNA non-targeting control and custom-made Edit-R CRISPRa human HOXDeRNA lentiviral sgRNAs


title: MYC regulates chromatin interactions in prostate cancer

status: Public on Mar 05 2023

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK


title: MYC regulates chromatin interactions in prostate cancer [RNA]

summary: We used RNA-Seq, ChIP-Seq and HiChIP to assess the role of MYC in the chromatin interactions of prostate cancer

overall_design: RNA-Seq, ChIP-Seq and HiChIP in 22Rv1 cells with or without MYC overexpression

first: Zhao

last: Wei

first: Housheng

middle: H

last: He


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

status: Public on Mar 02 2023

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


title: Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B [polyA capture]

first: Ashish

last: Lal

overall_design: mRNA profiles from HCT116 upon siCTRL, or siMatrin3 after 72 + 48 hours of transfection

first: Bruna

middle: R

last: Muys

first: Roshan

last: Shrestha

first: Dimitrios

middle: G

last: Anastasakis

first: Lorinc

last: Pongor

first: Xiao

last: Li

first: Ioannis

last: Grammatikakis

first: Ahsan

last: Polash

first: Raj

last: Chari

first: Myriam

last: Gorospe

first: Curtis

last: Harris

first: Mirit

middle: I

last: Aladjem

first: Munira

last: Basrai

first: Markus

last: Hafner


title: Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B


title: Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer

status: Public on Feb 22 2023

city: Guangzhou

first: Jie

last: Long

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

summary: In this study, we comprehensively charted the cellular landscape of colorectal cancer (CRC) and well-matched liver metastatic CRC using single-cell and spatial transcriptome RNA sequencing. We generated 41892 CD45- non-immune cells and 196473 CD45+ immune cells from 27 samples of 6 CRC patients, and found that CD8_CXCL13 and CD4_CXCL13 subsets increased significantly in liver metastatic samples that exhibited high proliferation ability and tumor-activating characterization, contributing to better prognosis of patients. Distinct fibroblast profiles were observed in primary and liver metastatic tumors. The F3+ fibroblasts enriched in primary tumors contributed to worse overall survival by expressing pro-tumor factors. However, the MCAM+ fibroblasts enriched in liver metastatic tumors might promote generation of CD8_CXCL13 cells through Notch signaling. In summary, we extensively analyzed the transcriptional differences of cell atlas between primary and liver metastatic tumors of CRC by single-cell and spatial transcriptome RNA sequencing, providing different dimensions of the development of liver metastasis in CRC

overall_design:
For single-cell RNA sequencing, 6 CRC patients with liver metastasis were enrolled after written informed consent was obtained. Primary CC, CN (at least 2 cm from matched tumors), LM, LN (at least 2 cm from matched tumors) and PB of the enrolled patients were collected following resection. All the patients received preoperative chemotherapy and/or radiotherapy. For spatial transcriptome sequencing, formalin-fixed paraffin embedded (FFPE) tissues of 6 CRC patients were prepared.

Submitter states: Raw data are not included due to patient privacy concerns, which are deposited in the CNGB Nucleotide Sequence Archive (CNSA: https://db.cngb.org/cnsa; accession number: CNP0002540 for single cell RNA sequencing data, and CNP0003321 for spatial transcriptome RNA sequencing data)

first: Fei

last: Wang


title: Genome-wide H3K4me3 analysis in Arabidopsis

status: Public on Feb 28 2023

city: shanghai

first: li

last: peng

institute: PSC

summary: To explore the bivalent histone modifications in the Arabidopsis genome, we examined genome-wide histone 3 lysine-27 trimethylation (H3K27me3) and histone 3 lysine-4 trimethylation (H3K4me3) in 5-day-old seedlings (Col-0) by ChIP-seq. We found that more than 1300 genes loci contain both H3K27me3 and H3K4me3.

overall_design: Nuclei were extracted from 5-day-old WT (Col-0) seedlings as previously described (Louwers et al., 2009), followed by chromatin immunoprecipitation with Magna ChIP A/G kit (Millipore). DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), and subsequently were sequenced on X Ten (Illumina). Three biologically independent samples have been analyzed.

first: Yang

last: Ou

first: Yuehui

last: He


first: Laura

last: Kerosuo-Pahlberg


title: MYC regulates chromatin interactions in prostate cancer [HiChIP]

first: Haiyang

last: Guo

first: Zhao

last: Wei

first: Housheng


title: A druggable signaling hub of choroid plexus immune-secretory function

status: Public on Feb 17 2023

first: Kris

last: Kahle

address: 55 Fruit Street

institute: MGH

summary: Integrated multi-omics investigation of novel rat models of acquired hydrocephalus, Blood or bacteria in CSF trigger similar choroid plexus (ChP) immune-secretory responses, Crosstalk between ChP immune and epithelial cells drives CSF hypersecretion and ventriculomegaly, Repurposed systemic immunomodulators ameliorate acquired hydrocephalus, Identification of a druggable hub of ChP function relevant for multiple neurological diseases.

overall_design: Examine the effect of IVH and LPS on ChP

first: Kristopher

first: Emre

last: Kiziltug

first: Stephanie

last: Robert

first: Ben

last: Reeves


title: TET2 regulates genes expressed in the differentiated corneal epithelium through 5hmC modification

status: Public on Feb 15 2023

first: Natasha

last: Frank

address: 77 Avenue Louis Pasteur

department: Medicine

summary: We performed RNA-seq to identify the genes regulated by TET2 using human cultured corneal epithelial cells. Also, we performed RNA-seq to identify the genes expressed in MUC16-positive differentiated corneal epithelial cells.

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

***************************************************************
Raw files for human/patient samples are not included due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Yuzuru

last: Sasamoto

first: Siyuan

last: Wu

first: Jiang

last: Yusheng


title: Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B [Ribo-deplete]

first: Ashish

last: Lal

overall_design: RNA total profiles from HCT116 upon siCTRL, or siMatrin3 after 48 hours of transfection

first: Bruna

last: Muys

first: Roshan

middle: L

last: Shrestha

first: Dimitrios

last: Anastasakis

first: Lorinc

last: Pongor

first: Xiao

last: Li

first: Ioannis

last: Grammatikakis

first: Ahsan

last: Polash

first: Raj

last: Chari

first: Myriam

last: Gorospe

first: Curtis

last: Harris

first: Mirit

last: Aladjem

first: Munira

last: Basrai

first: Markus

last: Hafner


title: MYC regulates chromatin interactions in prostate cancer [ChIP-seq]

first: Haiyang

last: Guo

first: Zhao

last: Wei

first: Housheng

last: He


title: Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development.

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

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


title: Gene regulatory dynamics during craniofacial development in a carnivorous marsupial

city: Berkeley

first: Laura

last: Cook

state: California

address: 1 Cyclotron Road

department: Biosciences

institute: Lawrence Berkeley National Laboratory

summary: Marsupials and placental mammals exhibit significant differences in reproductive and life history strategies. Marsupials are born highly underdeveloped after an extremely short period of gestation, leading to prioritization of the development of structures critical for post-birth survival in the pouch. Critically, they must undergo accelerated development of the oro-facial region compared to placentals. Previously we described the accelerated development of the oro-facial region in the carnivorous Australian marsupial, the fat-tailed dunnart Sminthopsis crassicaudata that has one of the shortest gestations of any mammal. By combining genome comparisons of the mouse and dunnart with functional data for the enhancer-associated chromatin modifications, H3K4me3 and H3K27ac, we investigated divergence of craniofacial regulatory landscapes between these species. While genes involved in regulating facial development were largely conserved in mouse and dunnart, the regulatory landscape varied significantly. Additionally, a subset of dunnart-specific enhancers were associated with genes highly expressed only in dunnart relating to cranial neural crest proliferation, embryonic myogenesis and epidermis development. Comparative RNA-seq analyses of facial tissue revealed dunnart-specific expression of genes involved in the development of the mechanosensory system. Accelerated development of the dunnart sensory system likely relates to the sensory cues received by the nasal-oral region during the postnatal journey to the pouch. Together these data suggest that accelerated development in the dunnart can be driven by dunnart-specific enhancer activity. Our study highlights the power of marsupial-placental comparative genomics for understanding the role of enhancers in driving temporal shifts in development.

overall_design: Examination of 2 different histone modifications and gene expression in craniofacial tissue from newborn fat-tailed dunnart pouch young.

first: Irene

last: Gallego Romero

first: Andrew

middle: J

last: Pask


title: Epigenetic function during heroin self-administration controls future relapse-like behaviors in a cell type-specific manner

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary:
Opioid abuse produces enduring associations between the drug euphoria and features of the drug-taking experience, and these powerful associations can trigger relapse in individuals recovering from opioid use disorder. We show here that the epigenetic enzyme, histone deacetylase 5 (HDAC5), functions in the nucleus accumbens (NAc) during active heroin use to limit future relapse-like behavior. Moreover, enhancing HDAC5 function in NAc dramatically suppresses context-associated and reinstated heroin seeking behaviors, but it does not impact sucrose seeking. We also find that HDAC5 functions within dopamine D1 receptor-expressing medium spiny neurons (MSNs) to suppress cue-induced heroin seeking, but within dopamine D2 receptor-expressing MSNs to suppress drug-primed heroin seeking. Using cell type-specific transcriptomics analysis, we found that HDAC5 reduces expression of numerous genes linked to ion transport, and it decreases intrinsic excitability of NAc MSNs, suggesting that HDAC5 limits relapse vulnerability by suppressing NAc MSN firing rates during active heroin use.
We used microarrays to define genes differentially expressed in the presence or absence of AAV2-DIO-HDAC5-3SA in both D1 and D2 cell-types derived from Nucleus accumbens following vTRAP.

overall_design: Testing the transcriptomic effects of overexpressing a nuclear form of HDAC5 in the nucleus accumbens selectively in medium spiny neurons that expressed either dopamine receptor D1R or D2R.

first: Ethan

last: Anderson

first: Christopher

last: Cowan


title: Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [RNA-seq]

summary: Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential expressions and the proportion of distal ACRs were increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages, and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed lights on the improvement of wheat yields and qualities.

overall_design: It is reported that the CRE variants are associated with many important agronomic traits. In this study, we unravelling the transcriptional network underlying wheat grain development by combing ATAC-seq (Assay for Transposase Accessible Chromatin sequencing) and RNA-seq with samples from a series of time points.


title: Genome-wide H3K27me3 and H3K4me3 analyses in Arabidopsis

first: li

last: peng


title: Plasminogen Activator Inhibitor-1 Regulates the Cytoskeleton and Intrinsic Stiffness of Vascular Smooth Muscle Cells

status: Public on Feb 23 2023

city: Columbia

first: Trupti

last: Joshi

address: 103 Math Science Building

department: Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

institute: University of Missouri-Columbia

summary: SMCs express plasminogen activator inhibitor-1 (PAI-1), which regulates SMC function and vascular remodeling. However, whether PAI-1 controls SMC cytoskeletal dynamics and stiffness is unknown, and the causal role of PAI-1 in arterial stiffening is undefined.  SMCs from human coronary arteries and aortae of wild-type vs. PAI-1-deficient mice were cultured with or without PAI-039, a specific PAI-1 inhibitor, after which cell stiffness was measured by atomic force microscopy, filamentous actin structures were assessed by confocal microscopy, and the activities cofilin, LIM domain kinase 1 (LIMK), slingshot homolog 1 (SSH), and AMP-activated protein kinase (AMPK) were measured. RNA sequencing was performed to determine the effects of PAI-039 on SMC gene expression. Effects of PAI-039 on aortic stiffness were assessed by pulse wave velocity.   PAI-039 significantly reduced intrinsic stiffness of human SMCs, which was accompanied by significant decreases in cytoplasmic actin filaments. Similar effects were observed in wild-type, but not in PAI-1-deficient SMCs. Mechanistically, PAI-039 significantly increased the activity of cofilin, an actin depolymerase, in SMCs expressing PAI-1, but not in PAI-1-deficient cells.  PAI-039 had no significant effects on LIMK or SSH activity. RNA-sequencing analysis suggested that PAI-039 up-regulates AMPK signaling in SMCs, which was confirmed by western blotting. Inhibition of AMPK prevented activation of cofilin by PAI-039. In mice, PAI-039 significantly decreased aortic stiffness without significantly altering peri-aortic fibrosis.   PAI-039 decreases intrinsic SMC stiffness by reducing cytoplasmic stress fiber content. These effects are mediated by AMPK-dependent activation of cofilin. PAI-039 also decreases aortic stiffness in vivo. These findings suggest that PAI-1 is an important regulator of the SMC cytoskeleton and that pharmacologic inhibition of PAI-1 has potential to treat cardiovascular diseases mediated by accelerated arterial stiffening.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Human coronary artery smooth muscle cells treated with an inhibitor of plasminogen activator inhibitor (PAI-1), PAI-039 vs. vehicle control. Each group had 3 replicates.

first: Hekmat

last: Khoukaz

first: Manisha

last: Vadali

first: Alex

last: Schoenherr

first: Francisco

last: Ramirez-Perez

first: Mariana

last: Morales-Quinones

first: Zhe

last: Sun

first: Shumpei

last: Fujie

last: Foote

first: Zhen

last: Lyu

first: Shuai

last: Zeng

first: Yan

last: Ji

first: Shi

middle: Y

last: Chen

first: Michael

last: Hill

first: Luis

last: Martinez-Lemus

first: William

middle: P

last: Fay