title: Regulation of potassium uptake in Caulobacter crescentus [ChIP-seq]

summary: Potassium (K+) is an essential physiological element determining membrane potential, intracellular pH, osmotic/turgor pressure, and protein synthesis in cells. Here we describe the regulation of potassium uptake systems in the oligotrophic alpha-proteobacterium Caulobacter crescentus known as a model for asymmetric cell division. We show that C. crescentus can grow in concentrations from the micromolar to the millimolar range by mainly using two K+ transporters to maintain potassium homeostasis, the low affinity Kup and the high affinity Kdp uptake systems. When K+ is not limiting, we found that the kup gene is essential while kdp inactivation does not impact the growth. In contrast, kdp becomes critical but not essential and kup dispensable for growth in K+-limited environments. However, in the absence of kdp, mutations in kup were selected to improve growth in K+-depleted conditions, likely by increasing the affinity of Kup for K+. In addition, mutations in the KdpDE two-component system, which regulates kdpABCDE expression, suggest that the inner membrane sensor regulatory component KdpD mainly works as a phosphatase to limit the growth when cells reach late exponential phase. Our data therefore suggest that KdpE is phosphorylated by another non-cognate histidine kinase. On top of this, we determined the KdpE-dependent and independent K+ transcriptome. Together, our work illustrates how an oligotrophic bacterium responds to fluctuation in K+ availability.

overall_design: Examination of KdpE whole genome binding/occupancy (ChIP-Seq) in WT, ∆kdpD and ∆kdpE of Caulobacter crescentus grown in synthetic minimal media M2G-K with 0.025 mM K+ or 0.5 mM K+

last: Aurélie


title: Multiscale mapping of transcriptomic signatures for cardiotoxic drugs

status: Public on Jan 22 2024

city: New York

first: Ravi

last: Iyengar

state: NY

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

type: Expression profiling by high throughput sequencing

summary: Targeted inhibition of cancer-selective tyrosine kinases (TKI) has become a successful strategy in the treatment of multiple different cancer types. A sever side effect can be the induction of cardiomyopathy. We analyzed, if we could identify transcriptomic signatures induced by different tyrosine kinase inhibitiors in human IPSC-derived cardiomyocytes from healthy donors that might be associated with a cardiotoxic resonse. To investigate, if the predicted transcriptomic signatures are modified by other cell types of the human heart, we here stimulated two cardiomyocyte cell lines either in isolation or in coculture with human coronary arterial endothelial cells (HCAECs) with the TKIs pazopanib or dabrafenib.

overall_design: Human iPSC-derived cardiomyocytes were incubated in isolation or in coculture with human coronary arterial endothelial cells (HCAECs) for 48 hrs. HCAECs were separated from cardiomyocytes by a poros membrane. Thereafter, we stimulated isolated and cocultured cardiomyocytes with pazopanib, dabrafenib or vehicle (DMSO). Cardiomyocytes were separately processed for Bulk RNA-seq. HCAEC which were on glass coverslips were fixed with 4%PFA and stained for Actin and DAPI.

first: Jens

last: Hansen

first: Yuguang

last: Xiong

first: Mustafa

last: Siddiq

first: Priyanka

last: Dhanan

first: Bin

last: Hu

first: Bhavana

last: Shewali

first: ArjunS

last: Yadaw

first: Gomathi

last: Jayaraman

first: Rosa

last: Tolentino

first: Yibang

last: Chen

first: Pedro

last: Martinez

first: Kristin

middle: G

last: Beaumont

first: Robert

last: Sebra

first: Dusica

last: Vidovic

first: Stephan

middle: C

last: Schürer

first: Joseph

last: Goldfarb

first: James

last: Gallo

first: Marc

middle: R

last: Birtwistle

first: Eric

middle: A

last: Sobie

first: Evren

middle: U

last: Azeloglu

first: Seth

last: Berger

first: Angel

last: Chan

first: Christoph

last: Schaniel

first: Nicole

last: Dubois


title: IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency

status: Public on Jan 16 2024

city: Philadelphia

first: Naiara

last: Akizu

state: PA

address: 3501 Civic Center Blvd

department: Pathology And Lab Medicine

institute: Children's Hospital of Philadelphia

summary: Metabolic dysregulation is one of the most common causes of pediatric neurodegenerative disorders. However, how the disruption of ubiquitous and essential metabolic pathways predominantly affect neural tissue remains unclear. Here we use a mouse model of AMPD2 deficiency to study cellular and molecular mechanisms that lead to selective neuronal vulnerability to purine metabolism imbalance. We show that AMPD deficiency in mice primarily leads to hippocampal dentate gyrus degeneration despite causing a generalized reduction of brain GTP levels. Remarkably, we uncover that neurodegeneration resistant regions of the hippocampus accumulate micron sized filaments of IMPDH2, the rate limiting enzyme in GTP synthesis. In contrast, IMPDH2 filaments are barely detectable in the dentate gyrus, which show a progressively neuroinflammation and neurodegeneration. Furthermore, using a human AMPD2 neural cell culture model, we show that blocking IMPDH2 polymerization with a dominant negative IMPDH2 variant impairs AMPD2 deficient neural progenitor growth.  Together, our findings suggest that IMPDH2 polymerization prevents detrimental GTP deprivation caused by AMPD2 deficiency, providing resistance to neurodegeneration. This data opens the possibility of exploring the involvement of IMPDH2 assembly as a therapeutic intervention for neurodegeneration.

overall_design: To determine why the hippocampus is more vulnerable to GTP depletion and IMPDH2 assembly in dKO mice, we conducted a mRNA sequencing (RNAseq) analysis of the three brain regions exhibiting different degrees of neurodegeneration and IMPDH2 aggregation: the hippocampus showing neurodegeneration and IMPDH2 filaments, the cerebral cortex with apparently no neurodegeneration and low density of IMPDH2 filaments and the cerebellum with no degeneration or IMPDH2 filaments.

first: Marco

last: Flores-Mendez

first: Laura

last: Ohl

first: Thomas

last: Roule

first: Yijing

last: Zhou

first: Jesus

last: A Tintos-Hernandez

first: Kelsey

last: Walsh

first: Xilma

last: Ortiz-Gonzalez


title: The role of gene duplication in shaping divergent patterns of gene expression across a complex life cycle

status: Public on Jan 21 2024

city: Atlanta

middle: Gabriel Amor

last: DuBose

state: Georgia

address: 1510 East Clifton Road Northeast 2006

department: Biology

institute: Emory Univeristy

summary: The objective of this study was to explore the transcriptional basis of the holometabolous development of Danaus plexippus (the monarch butterfly), which we reasoned would lend insight into how complex life cycles evolve.

overall_design: To investigate the transcriptional basis of the Danaus plexippus (the monarch butterfly) holometabolous development, we used RNA-Seq to profile the gene expression from whole body homogenate of third instar larvae, fifth instar larva, early pupae, late pupae, and adult monarchs.

first: Jacobus

last: de Roode


title: Multifaceted anti-tumor activity of a CDK9 inhibitor in prostate cancer

status: Public on Feb 07 2024

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Dynamic enhancer interactome promotes senescence and aging

status: Public on Jan 18 2024

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene Expression Profiles Induced by RNA interference on NSD1 Δ5Δ7, and NSD1 Δ19–23 isoforms in Fibroblast Cells II.

status: Public on Jan 17 2024

city: Genova

first: Giuseppina

last: Conteduca

state: GE

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale San Martino

summary: NSD1 Δ5Δ7, NSD1 Δ19–23 5’end and canonical NSD1 transcript are involved in cell cycle regulation and in tumoral and neoplastic development. Another NSD1 isoform AT2 target that might mediate the cellular division mechanisms is ARP3 actin-related protein 3 homolog B ACTR3B that may act downstream of the stress fibers and bundle of actin filaments formation

overall_design: Fibroblasts cell obtained from four different healthy donors were screened to confirm the absence of NSD1 mutation

first: Davide

last: Cangelosi

first: Michela

last: Malacarne

first: Chiara

last: Baldo

first: Alessia

last: Arado

first: Barbara

last: Testa

first: Ryan

middle: T

last: Wagner

first: Keith

middle: D

last: Robertson

first: Franck

last: Dequiebedt

first: Gilberto

last: Filaci

first: Domenico

last: Coviello


title: Effect of RANKL inhibition on fibrous dysplasia lesions

status: Public on Jan 15 2024

city: Bethesda

first: Luis

last: Fernandez de Castro Diaz

state: Maryland

address: 30 Convent Drive

department: SDMHS

institute: NIDCR/NIH


title: Endocrine disruptor-induced epimutagenesis in vitro: Insight into molecular mechanisms [EM-Seq]

status: Public on Jan 31 2024

city: San Antonio

first: Jake

middle: Dean

last: Lehle

state: TX

address: 16631 Vance Jackson Rd APT#1220

department: NDRB

institute: The University of Texas at San Antonio

summary: Endocrine disrupting chemicals (EDCs) such as bisphenol S (BPS) are xenobiotic compounds that can disrupt endocrine signaling following exposure due to steric similarities to endogenous hormones within the body. EDCs have been shown to induce disruptions in normal epigenetic programming (epimutations) that accompany dysregulation of normal gene expression patterns that appear to predispose disease states. Most interestingly, the prevalence of epimutations following exposure to many different EDCs often persists over multiple subsequent generations, even with no further exposure to the causative EDC. Many previous studies have described both the direct and prolonged effects of EDC exposure in animal models, but many questions remain about molecular mechanisms by which EDCs initially induce epimutations or contribute to the propagation of EDC-induced epimutations either within the exposed generation or to subsequent generations. Additional questions remain regarding the extent to which there may be differences in cell type-specific susceptibilities to various EDCs, and whether this susceptibility is correlative with expression of relevant hormone receptors and/or the location of relevant hormone response elements (HREs) in the genome. To address these questions, we exposed cultured mouse pluripotent (induced pluripotent stem [iPS]), somatic (Sertoli and granulosa), and germ (primordial germ cell like [PGCLCs]) cells to BPS and measured changes in DNA methylation levels at the epigenomic level and gene expression at the transcriptomic level. We found that there was indeed a difference in cell type-specific susceptibility to EDC-induced epimutagenesis and that this susceptibility correlated with differential expression of relevant hormone receptors and, in many cases, tended to generate epimutations near relevant HREs within the genome. Additionally, however, we also found that BPS can induce epimutations in a cell type that does not express relevant receptors and in genomic regions that do not contain relevant HREs, suggesting that both canonical and non-canonical signaling mechanisms can be disrupted by BPS exposure. Most interestingly, we found that when iPS cells were exposed to BPS and then induced to differentiate into PGCLCs, the prevalence of epimutations and differentially expressed genes (DEGs) initially induced in the iPSCs was largely retained in the resulting PGCLCs, however, >90% of the specific epimutations and DEGs were not conserved but were rather replaced by novel epimutations and DEGs following the iPSC to PGCLC transition. These results suggest a unique mechanism by which an EDC-induced epimutated state may be propagated transgenerationally following a single exposure to the causative EDC.

overall_design: To investigate cell type-specific differential susceptibility to BPS, we exposed cultured mouse pluripotent (induced pluripotent stem [iPS]), somatic (Sertoli and granulosa), and germ (primordial germ cell like [PGCLCs]) cells to BPS or vehicle alone and measured changes in DNA methylation at the epigenomic level via EM-seq.

first: Lehle

last: Jake D.

first: Lin

last: Yu-Huey

first: Gomez

last: Amanda

first: Chavez

last: Laura

first: McCarrey

last: John R.


title: Gene Expression Profiles Induced by RNA interference on NSD1 Δ5Δ7, and NSD1 Δ19–23 isoforms in Fibroblast Cells III.

first: Giuseppina

last: Conteduca

first: Davide

last: Cangelosi


title: Endocrine disruptor-induced epimutagenesis in vitro: Insight into molecular mechanisms [Infinium]

type: Methylation profiling by genome tiling array

overall_design: To investigate cell type-specific differential susceptibility to BPS, we exposed cultured mouse pluripotent (induced pluripotent stem [iPS]), somatic (Sertoli and granulosa), and germ (primordial germ cell like [PGCLCs]) cells to BPS or vehicle alone and measured changes in DNA methylation at the epigenomic level via the Illumina Infinium Mouse Methylation BeadChip Array.

first: Yu-Huey

last: Lin

first: Amanda

last: Gomez

first: Laura

last: Chavez

first: John

last: McCarrey


title: Gene Expression Profiles Induced by RNA interference on NSD1 Δ5Δ7, and NSD1 Δ19–23 isoforms in Fibroblast Cells I.

first: Michela

last: Malacarne

first: Chiara

last: Baldo

first: Alessia

last: Arado

first: Barbara

last: Testa

first: Ryan

last: Wagner

first: Keith

last: Robertson


title: Cholesterol biosynthesis inhibition synergizes with AKT inhibitors in triple-negative breast cancer

status: Public on Jan 14 2024

city: Dundee

first: Ralitsa

middle: Radostinova

last: Madsen

address: Dow Street

department: Medical Research Council Protein Phosphorylation and Ubiquitylation Unit

country: United Kingdom

institute: School of Life Sciences, University of Dundee

summary: Triple-negative breast cancer (TNBC) is responsible for a disproportionate number of breast cancer deaths due to its molecular heterogeneity, high recurrence rate and lack of targeted therapies. Dysregulation of the phosphoinositide 3-kinase (PI3K)/AKT pathway occurs in approximately 50% of TNBC patients. We performed a genome-wide negative selection CRISPR/Cas9 screen with PI3K and AKT inhibitors to identify targetable synthetic lethalities in TNBC. We found that cholesterol homeostasis is a collateral vulnerability with AKT inhibition. Disruption of cholesterol homeostasis with pitavastatin synergized with AKT inhibition to induce TNBC cytotoxicity in vitro, in mouse TNBC xenografts and in patient-derived organoids of estrogen receptor (ER)-negative breast cancer. Neither ER-positive breast cancer cell lines nor ER-positive organoids were sensitive to combined AKT inhibitor and pitavastatin. Mechanistically, TNBCs show dysregulated SREBP-2 activation in response to single agent or combination AKT inhibitor and pitavastatin, and this was rescued by inhibition of the cholesterol trafficking protein Niemann-Pick C1 (NPC1). NPC1 loss promoted lysosomal cholesterol accumulation, decreased endoplasmic reticulum cholesterol levels and promoted SREBP-2 activation. Taken together, these data identify a TNBC-specific vulnerability to the combination of AKT inhibitors and pitavastatin mediated by dysregulated cholesterol trafficking. This work motivates combining AKT inhibitors with pitavastatin as a therapeutic modality in TNBC.

overall_design: We performed comparative mRNA sequencing (RNAseq) in TNBC (MDA-MB-468) and ER+ breast cancer cells (T47D), exposed to the catalytic AKT inhibitor AZD5363, pitavastatin, or the combination of AZD5363 and pitavastatin for 24 or 48 h. To limit the confounding effect of differential potency, we determined the doses of AZD5363 that would result in comparable suppression of downstream signaling in each cell line at these time points (MDA-MB-468: 10 µM, T47D: 0.25 µM). As a control, cells were treated with DMSO. The data are from three independent experiments performed in growth factor-complete medium.

first: Alissandra

last: Hillis

first: Alex

last: Toker


title: Effect of RANKL inhibition on fibrous dysplasia lesions (human)

first: Luis

last: Fernandez de Castro Diaz

summary: we investigated mechanisms underlying RANKL inhibition with the monoclonal antibody denosumab on FD tissue, and its likely indirect effects on osteoprogenitors, by evaluating human FD tissue pre and post-treatment and in murine in vivo pre-clinical models.Results from this study demonstrate that, beyond its expected anti-osteoclastic effects, denosumab reduces FD lesion activity by decreasing FD cell proliferation and increasing osteogenic maturation, leading to increased bone formation within lesions

overall_design: For human analysis :6 pairs of human samples (FD patients) before and after denosumab treatment. For Mouse model: 6 uninduced mice (WT), 6 mice induced for FD and treated with Isotype control and 6 mice induced for FD and treated with αRANKL antibody

middle: F

last: de Castro

first: Jarred

middle: M

last: Whitlock

first: Zachary

last: Michel

first: Kristen

last: Pan

first: Jocelyn

last: Taylor

first: Vivian

last: Szymczuk

first: Brendan

last: Boyce

first: Daniel

last: Martin

first: Vardit

last: Kram

first: Kamran

last: Melikov

first: Rebeca

last: Galisteo

first: Leonid

middle: V

last: Chernomordik

first: Michael

last: Collins

first: Alison


title: The anticancer Ruthenium drug BOLD-100 regulates apoptosis of BRAFMT colorectal cancer cells through modulation of the AhR/ROS/ATR signalling axis.

status: Public on Jan 10 2024

city: Belfast

first: Daryl

last: Griffin

address: 97 Lisburn Road

institute: Queens University, Belfast

summary: The understanding of how oncogenes modulate the mechansim of action of compounds relies on interrogating acute and longer transcriptional changes following treatment. We report here the transcriptional profiles of an isogenic cell line model VACO432 (BRAFMT V600E/WT) and VT1 (BRAFWT/-) following 3H and 24H treatment with a novel ruthenium compound BOLD-100. We compare the two cell line models based on their BRAF status to identify transcriptional changes modulted by oncogenic BRAF.

overall_design: Bulk RNA-sequencing was performed for VACO432 and VT1 cells treated with IC30 dose (24μM) BOLD-100 for 3h and 24h. Three biological replicates for each sample were included in the experiment. Total RNA was extracted as described in the main materials and methods section. Each sample underwent QC, and library preparation was performed with 100ng RNA (Illumina NextSeq 500 kit, Illumina, UK)  according to the manufacturer's instructions. using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, USA).  Paired 91 end sequencing was conducted with a sequencing depth of 50 million reads, resulting in 75-base pair reads. The reads were trimmed based on Phred score from the 3-prime end and then aligned to the human genome (hg38) using TopHat21 (version 2.1.0) with default settings.

first: Sandra

last: Van Schaeybroeck


title: Akt is the main kinase mediating the embryonic specification of artery cells

city: New Haven

first: Joey

middle: J.

last: Ghersi

state: CT

address: 300 George street

department: School of Medicine

institute: Yale University

summary: This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish.

overall_design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.

middle: J

first: Wenping

last: Zhou

first: Emma

last: Ristori

first: Nicole

last: Semanchik

first: Andrew

last: Prendergast

first: Liqun

last: He

first: Paola

last: Carneiro

first: Gabriel

last: Baldissera

first: William

last: Sessa

first: Stefania

last: Nicoli


title: Mural cells interact with macrophages in the dural meninges to regulate CNS immune surveillance

status: Public on Jan 04 2024

city: Durham

first: Shane

middle: Mitchell

last: O'Neil

state: NC

address: 701 W Main St

department: Neuroscience

institute: Duke University

summary: We sought to elucidate the cell-cell communication, primarily between pericytes and macrophages, within the dura mater compared to other relevant tissues (leptomeninges and brain) in pre-symptomatic EAE and at the onset of symptoms.

overall_design: Pdgfrb-CreER/T2::Rosa-DTR mice were treated with tamoxifen to induce expression of diphtheria toxin receptor (DTR) on PDGFRb+ cells. EAE was induced via MOG immunization and dura mater, leptomeninges, and brain (cortex) isolated 7 or 14 days later.

first: Hyunjung

last: Min

first: Li

last: Xu

first: E

last: Moseman

first: Joanne

last: Kurtzberg

first: Anthony

last: Filiano


title: Mitochondrial complex I activity in microglia sustains neuroinflammation [scRNA-seq]

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: Sustained smouldering, or low grade, activation of myeloid cells is a common hallmark of several chronic neurological diseases, including multiple sclerosis (MS). Distinct metabolic and mitochondrial features guide the activation and the diverse functional states of myeloid cells. However, how these metabolic features act to perpetuate neuroinflammation is currently unknown. Using a multiomics approach, we identified a new molecular signature that perpetuates the activation of myeloid cells through mitochondrial complex I (CI) activity driving reverse electron transport (RET) and the production of reactive oxygen species (ROS). Blocking CI activity in pro-inflammatory microglia protected the central nervous system (CNS) against neurotoxic damage and improved functional outcomes in animal disease models in vivo. Our data show that mitochondrial CI in microglia is a potential new therapeutic target to foster neuroprotection in smouldering inflammatory CNS disorders.

overall_design: MOG-EAE induction in Cx3cr1YFPCreERT2:R26tdTomato mice

first: Luca

last: Peruzzotti-Jametti

first: Cory

last: Willis

first: G

last: Krzak

first: Liviu

last: Pirvan

first: Stefano

last: Pluchino


title: Enhancing radiotherapy response via intratumoral injection of the TLR9 agonist CpG to stimulate CD8 T cells in an autochthonous mouse model of sarcoma

status: Public on Jan 01 2024

first: Vincent

middle: Michael

last: Perez

address: 25 Alexandria Wy

department: Translational reasearch

institute: Tempus AI

summary: p53/MCA sarcomas are induced by intramuscular injection of adenovirus expressing Cas9 and sgRNA targeting Trp53 (Adeno-p53-sgRNA; Viraquest) at gastrucnemius muscle site. We used bulk tumor RNAseq to analyze the differences in tumor cells and immune cells after treatment with CpG+RT

overall_design: we performed bulk tumor RNA-seq on an independent cohort of p53/MCA tumors harvested 6 days after RT and 3 days after CpG treatment or their respective controls. Ctl (n=5), CpG alone (n=5), RT alone (n=5), CpG+RT (n=5)

first: Chang

last: Su

first: Collin

last: Kent

first: David

last: Kirsch


title: Studies on AGO1 and AGO2 in mouse embryonic stem cells

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary: We determined the small RNAs associated with AGO1 and AGO2 in mouse embryonic stem cells.

overall_design: AGO1 and AGO2 were immunoprecipitated from mouse embryonic stem cells, and then RNA isolated from the immunoprecipitated AGO1 and AGO2, followed by library preparation and RNA sequencing


title: Enhancing radiotherapy response via intratumoral injection of the TLR9 agonist CpG to stimulate CD8 T cells in an autochthonous mouse model of sarcoma (single-cell RNA-seq analysis)

summary: A single-cell analysis (10x) of p53/MCA induced sarcomas tumors with and without radiation and CpG treatment. p53/MCA induced sarcomes are induced by intramuscular injection of adenovirus expressing Cas9 and sgRNA targeting Trp53 (Adeno-p53-sgRNA; Viraquest) at gastrucnemius muscle site. We used scRNA-seq to analyze the differences in immune cells after treatment with CpG+RT

overall_design: CD45+ cells were isolated by fluorescence-activated cell sorting (FACS) from four treatment groups. Ctl (n=5), CpG alone (n=5), RT alone (n=5), CpG+RT (n=5)

middle: G


title: Methylation of cg09897064 and Reduced Expression of ZBP1: Innovative Checkpoint Inhibitors in Lung Adenocarcinoma with Implications for Macrophage Polarization and Tumor Growth in Lung Cancer

city: Jinan

first: zhang

last: shi

address: handong First Medical University

country: China

institute: handong First Medical University

summary: Lung cancer, a prevalent and aggressive disease, is characterized by recurrence and drug resistance. Understanding the underlying mechanisms and identifying new therapeutic targets are crucial for improving treatment outcomes. Our research indicates that methylation of cg09897064 and reduced expression of ZBP1 are associated with poor prognosis in lung cancer patients. Furthermore, these factors play a role in macrophage polarization, with ZBP1 upregulated in M1 macrophages compared to both M0 and M2 polarized macrophages. We observed cg09897064 methylation in M2 polarization, but not in M0 and M1 polarized macrophages. ATACseq analysis revealed closed chromatin accessibility of ZBP1 in M0 polarized macrophages, while open accessibility was observed in both M1 and M2 polarized macrophages. Our findings suggest that ZBP1 is downregulated in M0 polarized macrophages due to closed chromatin accessibility and downregulated in M2 polarized macrophages due to cg09897064 methylation. Further investigations manipulating cg09897064 methylation and ZBP1 expression through overexpression plasmids and shRNAs provided evidence for their role in modulating macrophage polarization and tumor growth. ZBP1 inhibits M2 polarization and suppresses tumor growth, while cg09897064 methylation promotes M2 polarization and macrophage-induced tumor growth. In mechanism investigations, we found that cg09897064 methylation impairs CEBPA binding to the ZBP1 promoter, leading to decreased ZBP1 expression. Targeting these factors may hold promise as a strategy for developing innovative checkpoint inhibitors in lung cancer treatment.

overall_design: We performed ATAC-seq experiments with some modifications based on the protocol described by Daniel [16, 17]. M0, M1, and M2 macrophages were isolated and the number of cells was adjusted to 50 cells/ml in phosphate buffer saline (PBS). The nuclei of these macrophages were then isolated using ATAC-LB. Following DNA fragmentation and purification, the DNA was amplified through 14 cycles. To assess the fragment distribution of the libraries, an Agilent Bioanalyzer was used, and the libraries were subsequently sequenced on a HiSeq 2500 platform. We focused on ATAC-seq peaks that were located near the transcription initiation sites (TSSs) of ZBP1. These peaks were extracted and visualized in a plot showing their distribution in the reads. Additionally, motif analysis of the peak regions was conducted using the HOMER tool and the findMotifsGenome.pl function.

first: Shi

last: Zhang


title: Single-nucleus RNA-sequencing of human subcutaneous adipose tissue biopsies from 84 Finnish participants.

status: Public on Jan 12 2024

city: Los Angeles

first: Marcus

last: Alvarez

state: CA

address: 695 Charles E Young Dr South, Gonda 6335

department: Human Genetics

institute: UCLA

summary: We performed single-nucleus RNA-seq using 10X on 84 randomly sampled participants from the METabolic Syndrome In Men (METSIM) cohort. The purpose of the study was to characterize cell type composition changes associated with metabolic diseases such as obesity and type 2 diabetes.

overall_design:
Single cell RNA-seq samples were multiplexed to increase sample size. Fresh-frozen subcutaneous adipose tissue biopsies from 4 donors were pooled immediately prior to isolation. We then isolated nuclei using mincing, washing, and straining. Single nucleus sequencing libraries were prepared using the 10X single cell 3' v3.1 kit and the 10X Chromium platform. The resulting libraries were sequenced on an Illumina NovaSeq targeting 200 million reads per sample. Samples were demultiplexed with Demuxlet.

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Päivi

last: Pajukanta

first: Markku

last: Laakso


title: Second-Hand Melanoma Melanosomes Regulate Diversity Among Tumor-Associated Macrophages

status: Public on Dec 31 2023

city: Jerusalem

first: Yuval

last: Nevo

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University of Jerusalem

summary: Extracellular vesicles (EVs) are a key form of cell-to-cell communication. Here we reveal a new mode of communication involving the large EVs, melanosomes. Unlike small EVs, which are dissolved in the receiver cell, melanosomes stay intact within them, gain a unique protein signature, and can then be further transferred to another cell, a state we term “second-hand EVs”. We found that melanoma-secreted melanosomes uptaken by and then released from epidermal keratinocytes or dermal fibroblasts can be further engulfed by resident macrophages. The respective consequence for macrophages is polarization into pro-tumor or pro-immune-cell-infiltration phenotypes. Fibroblasts load melanosomes with AKT1, which induces VEGF secretion from macrophages in an mTOR-dependent manner, promoting angiogenesis and metastasis in-vivo. In melanoma patients, macrophages co-localized with AKT1, were correlated with disease aggressiveness, and immunotherapy non-responders were enriched in macrophages containing melanosome markers. Thus, the network of interactions via second-hand EVs helps form the metastatic niche. Since macrophage heterogeneity is pivotal in advancement of cancer, our data suggest an opportunity to halt melanoma progression by blocking the melanosome cues of macrophage diversification.

overall_design: To elucidate the fates of primary human monocyte-derived Naive macrophages that have been cultured with melanosomes derived from MNT1 melanoma, keratinocytes, and fibroblast cells, we analyzed their transcriptomes.  As controls, we used naive macrophages polarized towards the classical M1 (pro-inflammatory) or M2 (anti-inflammatory) phenotypes. All experimental conditions were done in triplicates.

first: Oren

last: Kobiler

first: Sharona

last: Elgavish

first: Alon

last: Scope

first: Carmit

last: Levy


title: HNF4A-induced lncRNA MIR194-2HG derived miR-194 and miR-192 coordinatively inhibit gastric cancer progression by targeting BTF3L4

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: LncRNA MIR194-2HG and derived miR-194 and miR-192 were transcriptionally induced by HNF4A. The oncogenic driver BTF3L4 is identified to be a common target gene of miR-194 and miR-192. Our finding highlights that MIR194-2HG inhibits GC progression through activating the expression miR-192 and miR-194 and repressing BTF3L4 expression.

overall_design: To reveal the target genes of miR-194 and miR-192, we transfected two human GC cell lines with miR-194/miR-192 mimics, respectively. The transcriptome sequencing studies were performed by deep sequencing, using Illumina HiSeq 4000. The RNA-seq data of miR-194 was available in GSE134308.

first: Shanshan

last: Qin

first: Dandan

last: Li


title: Transcriptomic signatures of individual cell types in cerebral cavernous malformation

status: Public on Dec 30 2023

city: Chicago

first: Issam

last: Awad

state: IL

address: 5841 S Maryland Avenue MC 3026, J 341 MC 3026, J 341

department: Neurological Surgery

institute: University of Chicago

summary:
Cerebral cavernous malformation (CCM) is a hemorrhagic neurovascular disease with no currently available therapeutics. Prior evidence suggests that different cell types may play a role in CCM pathogenesis. The contribution of each cell type to the dysfunctional cellular crosstalk remains unclear.
Herein, RNA-seq was performed on FACS sorted endothelial cells (ECs), pericytes, neuroglia and microglia from CCM lesions and non-lesional brain tissue controls. Differentially Expressed Gene (DEG), pathway and Ligand-Receptor (LR) analyses were performed to characterize the dysfunctional genes of respective cell types within CCMs.
Common DEGs among all three cell types were related to inflammation and endothelial-to-mesenchymal transition (EndMT). DEG and pathway analyses supported a role of lesional ECs in dysregulated angiogenesis and increased permeability.
In addition, VEGFA was particularly upregulated in pericytes. Further pathway and LR analyses identified VEGFA/VEGFR2 signaling in lesional ECs and pericytes that would result in increased angiogenesis. Moreover, lesional pericytes and neuroglia predominantly showed DEGs and pathways mediating the immune response.
Further analyses of cell specific gene alterations in CCM endorsed  potential contribution to EndMT, coagulation, and a hypoxic microenvironment. Taken together, these findings motivate mechanistic hypotheses regarding non-endothelial contributions to lesion pathobiology and may lead to novel therapeutic targets.

overall_design: 29 total RNA samples from FACS-sorted endotelial cells, pericytes or neuroglia from 6 subjects with human cavernous malformation and 4 healthy controls

first: Ying

first: Romuald

last: Girard

first: Abhinav

last: Srinath

first: Diana

last: Vera Cruz

first: Cezary

last: Ciszewski

first: Chang

last: Chen

first: Rhonda

last: Lightle

first: Sharbel

last: Romanos

first: Je

middle: Y

last: Sone

first: Thomas

last: Moore

first: Dorothy

last: DeBiasse

first: Agnieszka

last: Stadnik

first: Justine

last: Lee

first: Robert

last: Shenkar

first: Janne

last: Koskimäki

first: Miguel

last: Lopez-Ramirez

first: Douglas

last: Marchuk

first: Mark

middle: H

last: Ginsberg

middle: L

last: Kahn

first: Changbin

last: Shi


title: Transcriptome profiles with and without L-cysteine supplementation

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

summary: CyuR (b0447, also known as DecR or YbaO) is a recently characterized transcription regulator responsible for the generation of hydrogen sulfide (H2S) from L-cysteine (Cys), which decreases oxidative stress. Given that mitigation of oxidative stress is an important survival mechanism to achieve antibiotic resistance (AR) in many pathogenic bacteria such as Escherichia coli and Salmonella enterica, detailed studies about its effect and the regulatory network of CyuR are imperative. In this study, we investigated the roles of CyuR and its regulon genes in a Cys-dependent AR mechanism in E. coli in a microaerobic condition. We show that (1) CyuR negatively controls the expression of mdlAB encoding a transporter that may export antibiotics. (2) Cys metabolism has a significant role in AR and its effect is conserved in many E. coli strains including clinical isolates. (3) CyuR binds ‘GAAwAAATTGTxGxxATTTsyCC’ in the absence of Cys found by performing an in vitro binding assay. (4) CyuR may regulate 14 genes, in addition to previously reported 2 genes, as we suggested by in silico motif scanning and transcriptome sequencing. Collectively, our findings confirm the significant roles of CyuR and its relevance to antibiotic resistance associated with Cys.

overall_design: Ribosomal RNA removed RNA prepared from cell cultures of E. coli W at the exponential phase.

first: Irina

middle: A

last: Rodionova

first: Hyun

last: Lim

middle: O


title: Effect of VEGF-C treatment on sorted meningeal CD45+ cells

status: Public on Dec 29 2023

city: Paris

first: Ruchith

last: Singhabahu

address: 47 bd de l'Hôpital

country: France

institute: Institut du Cerveau

summary: Transcriptional profiling of mouse dural CD45+ cells in comparing AAV-Controls with AAV-VEGFC treaded mice. Objective was to determine the effect of the VEGFC treatment on global gene expression of meningeal immune cells.

overall_design: Total RNA was obtained from sorted dural immune cells of 10 to 12 pooled meningeal samples for each condition (AAV-CTRL vs AAV-VEGFC pre-treated mice). The experiment was repeated 2 times for each condition.

first: Marie-Renée

last: El Kamouh

last: Guégan


title: Characterizing Local Extension of Retinoblastoma by Single-cell Transcriptomics

status: Public on Dec 19 2023

city: Shanghai

first: wei

last: hu

address: No. 650 Songjiang Road

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

summary: Retinoblastoma (RB) is the most prevalent ocular tumor of childhood whose extraocular invasion largely increase metastasis risk. Nevertheless, a single-cell characterization of RB local extension has been lacking. Here, we perform single-cell RNA sequencing (scRNA-seq) 4 RB samples (2 from intraocular and 2 from extraocular RB patients), and integrate public scRNA-seq datasets  to characterize the local extension of RB at single-cell level.

overall_design: Human eye samples were collected immediately following eye enucleation, tissue was dissected to isolate the tumor region for single-cell dissociation. we applied scRNA-seq on 4 RB samples (2 from intraocular RB patients and 2 from extraocular RB patients

first: Yaoming

last: Liu

first: Rong

last: Lu


title: Mitochondrial RNA-seq and total RNA-seq of 293T, HeLa, and N2a cells; RIP-seq of SUPV3L1, ceSUPV3L1, ATP5B, and TRAP1; Small RNA-seq of 293T mitochondrial fractions

city: Hefei,

first: Xu

state: Anhui Province

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

type: Non-coding RNA profiling by high throughput sequencing

summary: The mechanism of mecciRNA degradation remains unknown. To investigate the degradation of mecciRNAs, we performed mitochondrial RNA sequencing and total RNA sequencing of 293T, HeLa, and N2a cells. To investigate the degradation mechanism of mecciRNAs, RIP-seq was conducted in 293T, HL-1 cells, and C. elegans. Small RNA sequencing of mitochondrial sucrose gradient fractions was performed to identify mecciRNA degradation fragments.

sample_organism:
Caenorhabditis elegans
Homo sapiens
Mus musculus

overall_design: 293T, HeLa, and N2a cells were treated with Actinomycin D (ActD) for the indicated time. Mitochondria were isolated from ActD-treated cells and control (DMSO) cells. Mitochondrial RNAs and total RNAs were isolated for ribosomal RNA (rRNA) depleted RNA sequencing (RNA-seq). SUPV3L1 RIP-seq was performed using 293T whole cell and 293T mitochondrial materials. TRAP1 RIP-seq was performed using mitochodnrial fractions of 293T and HL-1 cells. ATP5B RIP-seq was performed using 293T mitochondrial materials. Mitochondria of C. elegans (young adult) were isolated for ceSUPV3L1 and ceELAC2 RNA-seq. RNA of mitochondrial fractions from a 5%–18% sucrose gradient were separated in a 5% urea PAGE gel, and the small RNA bands in fractions were cut off and purified for small RNA sequencing.

first: Qinwei

last: Wang


title: The transcription factor AP2XI-2 is a key negative regulator of Toxoplasma gondii merogony

city: Lanzhou

first: JinLei

address: yanchangbao

institute: LVRI

summary: Commitment to and completion of sexual development are essential for Toxoplasma gondii to produce oocysts in the intestine of the feline host. Understanding of the molecular mechanism responsible for sexual commitment is extremely limited due to the lack of model systems. Here, we show that the transcription factors AP2XI-2 and AP2XII-1 associated with the epigenetic repressors MORC/HDAC3 complex are constitutively expressed in both tachyzoite and bradyzoite stages but not in the merozoite stage. Depletion of AP2XI-2 or AP2XII-1 elicits the expression of genes specific to merozoites, but they play different roles in the merogony process. Depletion of AP2XI-2 in type II Pru strain induced parasites to undergo merogony and produce mature merozoites in alkaline medium but not in neutral medium, whereas the AP2XII-1 depleted Pru strain underwent several rounds of schizogony and produced merozoites in neutral medium and more markedly under alkaline conditions. Furthermore, we show that two AP2XI-2 interacting proteins are also involved in repressing merozoite programming. Overall, these findings indicate that the merozoite primed pre-sexual commitment is controlled by an intricate regulatory network and that AP2XI-2 or AP2XII-1 depleted parasites can be used as a model to study the merogony in vitro.

overall_design: We report genome-wide AP2XI-2 and AP2XII-1 profiles in Toxoplasma gondii using CUT&TAG

first: Jin-Lei

first: Ting-Ting

last: Li

first: Nian-Zhang

last: Zhang

first: Meng

first: Li-Xiu

last: Sun

first: Zhi-Wei

first: Bao-Quan

last: Fu

first: Hany

last: Elsheikha

first: Xing-Quan

last: Zhu


title: Effect of RANKL inhibition on fibrous dysplasia lesions (mouse)

city: Bethesda

first: Luis

last: Fernandez de Castro Diaz

address: 30 Convent Drive

institute: NIDCR/NIH

summary: we investigated mechanisms underlying RANKL inhibition with the monoclonal antibody denosumab on FD tissue, and its likely indirect effects on osteoprogenitors, by evaluating human FD tissue pre and post-treatment and in murine in vivo pre-clinical models. Results from this study demonstrate that, beyond its expected anti-osteoclastic effects, denosumab reduces FD lesion activity by decreasing FD cell proliferation and increasing osteogenic maturation, leading to increased bone formation within lesions

overall_design: For human analysis :6 pairs of human samples (FD patients) before and after denosumab treatment. For Mouse model: 6 uninduced mice (WT), 5 mice induced for FD and treated with Isotype control and 6 mice induced for FD and treated with αRANKL antibody

last: de Castro

first: Jarred

last: Whitlock

first: Zachary

last: Michel

first: Kristen

last: Pan

first: Jocelyn

last: Taylor

first: Vivian

last: Szymczuk

first: Brendan

last: Boyce

first: Daniel

last: Martin

first: Vardit

last: Kram

first: Kamran

last: Melikov

first: Rebeca

last: Galisteo

first: Leonid

last: Chernomordik

first: Michael

middle: T

last: Collins

first: Alison


title: Glucose stress causes mRNA retention in nuclear Nab2 condensates

city: Zürich

first: Mostafa

last: Zedan

address: Otto-Stern-Weg 3

country: Switzerland

institute: ETH-Zurich

summary: Nuclear mRNA export via nuclear pore complexes is an essential step in eukaryotic gene expression. Although factors involved in mRNA transport have been characterized, a comprehensive mechanistic understanding of this process and its regulation is lacking. Here, we use single-RNA imaging in yeast to show that cells use mRNA retention to control mRNA export during stress. We demonstrate that upon glucose withdrawal the essential RNA-binding factor Nab2 forms RNA-dependent condensate-like structures in the nucleus. This coincides with a reduced abundance of the DEAD-box ATPase Dbp5 at the nuclear pore. Depleting Dbp5, and consequently blocking mRNA export, is necessary and sufficient to trigger Nab2 condensation. The state of Nab2 condensation influences the extent of nuclear mRNA accumulation and can be recapitulated in vitro, where Nab2 forms RNA-dependent liquid droplets. We hypothesize that cells use condensation to regulate mRNA export and to control gene expression during stress.

overall_design: To investigate differences in RNA expression in non-stress and stress conditions in wild type Nab2 and two Nab2 mutants (IDR mutant and interface mutant), we obtained mRNA from whole cell extracts and nuclear extracts and performed RNAseq.

first: Stephanie

last: Heinrich

first: Maria

last: Hondele

first: Désirée

last: Marchand

first: Carina

middle: P

last: Derrer

first: Alexandra

last: Oswald

first: Liliana

last: Malinovska

first: Federico

last: Uliana

first: Sarah

last: Khawaja

first: Roberta

last: Mancini

first: David

last: Grunwald

first: Karsten

last: Weis


title: TRPS1 mutant (R544Q) regulates epithelial to mesenchymal transition through binding to ZEB1 promoter region

status: Public on Dec 15 2023

city: beijing

first: wenjie

last: liu

address: No. 17 Nanli, Panjiayuan, Chaoyang District

institute: National Cancer Center/National Clinical  Research Center for Cancer/Cancer  Hospital

summary:
TRPS1 was selected as a candidate for further exploring the molecular mechanism of CRC distant metastasis according to single cell seq results.
As TRPS1 is a transcriptional factor mainly located in cellular nucleus , we performed Cleavage Under Targets and Tagmentation (CUT&Tag) Sequencing assay on TRPS1-WT and TRPS1-MT cells respectively to explore the whole-genome binding site of TRPS1.

overall_design: Hong,  Zhao

first: Wenjie

last: Liu

first: Yalan

last: Lu

first: Wei

last: Zhang

last: Song


title: ABBV-319: A First-In-Class CD19-targeting Glucocorticoid Receptor Modulator (GRM) Agonist Antibody-Drug Conjugate (ADC) for the Treatment of B-cell Malignancies [RNA-seq]

city: South San Francisco

first: Weilong

last: Zhao

address: 1000 Gateway Blvd

institute: AbbVie Inc.

summary: Glucocorticoids are key component of the immuno-chemotherapy regimens (e.g., R-CHOP, EPOCH-R, Hyper-CVAD) for the treatment of B-cell non-Hodgkin lymphoma (NHL). However, prolonged systemic glucocorticoid treatment is associated with several adverse events. ABBV-319 is a CD19-targeting antibody-drug conjugate (ADC) engineered to reduce glucocorticoid-associated toxicity while possessing three distinct mechanisms of action (MOA) to increase therapeutic efficacy: (1) antibody-mediated delivery of glucocorticoid receptor modulator (GRM) payload to activate apoptosis, (2) inhibition of CD19 signaling, and (3) enhanced Fc-mediated effector function via afucosylation of the antibody backbone. ABBV-319 elicited potent GRM-driven anti-tumor activity against multiple B-cell NHL cell lines in vitro as well as in cell line-derived xenografts (CDXs) and patient-derived xenografts (PDXs) in vivo. Remarkably, a single-dose of ABBV-319 induced sustained tumor regression and enhanced anti-tumor activity compared to repeat dosing of systemic prednisolone at the maximum tolerated dose (MTD) in mice. The unconjugated CD19 monoclonal antibody (mAb) also displayed anti-proliferative activity on a subset of B-cell lymphoma cell lines through the inhibition of PI3K signaling. Moreover, afucosylation of the CD19 mAb enhanced Fc-mediated antibody-dependent cellular cytotoxicity (ADCC), and this activity was maintained after conjugation with GRM payloads. Notably, ABBV-319 displayed superior efficacy compared to afucosylated CD19 mAb in human CD34+ PBMC-engrafted NSG-Tg(Hu-IL15) transgenic mice, demonstrating enhanced anti-tumor activity when different MOAs are combined. ABBV-319 also showed durable anti-tumor activity across multiple preclinical B-cell lymphoma models, including non-germinal center B-cell (GCB) DLBCL and relapsed lymphoma after R-CHOP treatment. Collectively, these data support the ongoing testing of ABBV-319 in Phase I clinical trial (NCT05512390)

overall_design: PBMC samples from two different donors were collected and treated with ABBV-319, CD19 mAb, or DMSO. Genomic materials were collected at 24hr post treatment and profiled for CITE-seq to investigate treatment effect of ABBV-319 on different myeloid and lymphoid cell lineages.


title: TRPS1 mutant (R544Q) regulates epithelial to mesenchymal transition

summary:
TRPS1 was selected as a candidate for further exploring the molecular mechanism of CRC distant metastasis according to single cell seq results.
We next performed bulk RNA sequencing to explore the underlying mechanism by which TRPS1 R544Q mutation contributes to CRC metastasis.Comparative gene expression profiling analysis of RNA-seq data for HCT116 (control,TRPS1,R544Q）and  SW480 (control,TRPS1,R544Q）

overall_design: Hong,Zhao

first: YaLan


title: ABBV-319: A First-In-Class CD19-targeting Glucocorticoid Receptor Modulator (GRM) Agonist Antibody-Drug Conjugate (ADC) for the Treatment of B-cell Malignancies [CITE-seq]


title: ABBV-319: A First-In-Class CD19-targeting Glucocorticoid Receptor Modulator (GRM) Agonist Antibody-Drug Conjugate (ADC) for the Treatment of B-cell Malignancies

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

overall_design: Refer to individual Series


title: Transcriptome profiling of human cytomegalovirus-infected trophoblasts

status: Public on Dec 14 2023

city: Minneapolis

first: Craig

middle: John

last: Bierle

address: 2001 6th Street SE

department: Pediatrics

institute: University of Minnesota

summary: Placental infection plays a central role in the pathogenesis of congenital human cytomegalovirus (HCMV) infections and is a cause of fetal growth restriction and pregnancy loss. HCMV can replicate in some trophoblast cell types, but it remains unclear how the virus evades antiviral immunity in the placenta and how infection compromises placental development and function. Human trophoblast stem cells (TSCs) can be differentiated into extravillous trophoblasts (EVTs) and syncytiotrophoblasts (STBs). This study assessed the utility of TSCs as a model of HCMV infection in the first trimester placenta. TSCs and TSC-derived EVTs and STBs were infected with HCMV (TB40/Ewt-mCherry). RNA was isolated from infected cells at 24, 48, and 72 hours post-infection and Illumina RNA-Sequencing was used to measure viral and host gene expression. Viral gene expression in TSCs does not follow the kinetic patterns observed during lytic infection in fibroblasts. Canonical antiviral responses were largely not observed in HCMV-infected TSCs and TSC-derived trophoblasts. Rather, infection dysregulated factors involved in cell identity, differentiation, and WNT signaling.

overall_design:
CT27 and CT29 TSCs were grown in self-renewal media or differentiated into EVT and STBs for 3 days. Cells were infected with HCMV (TB40/Ewt-mCherry) at a MOI of 1 (2  replicates per cell type and time point).  RNA was extracted from mock- and CMV-infected cells at 24, 48, and 72 hours post-infection.
Infected TSCs were flow sorted based on mCherry flourescense into three populations: mock-infected, infected cells that expressed high levels of mCherry, and infected cells that expressed low levels of mCherry. RNA was extracted from these cells and Illumina sequencing libraries were prepared using the SMARTer Pico Mammalian V2 kit (Takara) and sequenced using and Illumina NovaSeq (S4 Flow Cell, 2x150-bp PE reads).
RNA was extracted directly from EVTs and STBs and used to prepare TruSeq Stranded mRNA (Illumina) sequencing libraries. These samples were sequenced using and Illumina NovaSeq (S4 Flow Cell, 2x150-bp PE reads).

first: Micah

last: Gearhart


title: The transcription factor Sfp1 imprints specific classes of mRNAs and links their synthesis and cytoplasmic decay

status: Public on Dec 13 2023

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

summary: To function as a system, transcription and post-transcriptional stages must communicate - the underlying mechanism of which is still little studied. Here we focus on S. cerevisiae genes, transcription of which is regulated by Sfp1 that binds their promoters. We show that Sfp1 also binds downstream chromatin regions, thereby changing Pol II configuration, resulting in enhanced Pol II backtracking and possibly Rpb4 dissociation. Unexpectedly, this transcription factor binds >264 transcripts of these genes - near their 3’ ends – and regulates their deadenylation and stability. The interaction of Sfp1 with these mRNAs is controlled by the promoter and it occurs concomitantly with its dissociation from the chromatin. Collectively, we propose that Sfp1 accompanies Pol II and binds the RNA co-transcriptionally. It then accompanies these mRNAs to the cytoplasm and regulates their stability. Thus, Sfp1 co-transcriptional binding imprints the mRNA fate and serves as a paradigm for posttranscriptional regulation of specific mRNAs by the transcription apparatus.

overall_design: UV Cross-linking and cDNA analyses of N-termally HTP tagged Sfp1 in the presence or absence of Rbp4. Independent replicate experiments were performed with each strain.

first: Mordechai

last: Choder

first: José

middle: E

last: Pérez-Ortín

first: Sebastian

last: Chávez

last: Jordán-Pla

first: Sander

last: Granneman


title: Cortical organoids in Huntington’s disease reveal a chaotic premature corticogenesis cascade and precede HD subcortical projections

status: Public on Dec 11 2023

first: Lixiang

last: Ma

address: Dong'an road No.130

department: School of Basic Medical Sciences

institute: Fudan University

summary: Bulk RNA-seq characterization of human cortical organoids derived from two HD patients (CAG55 and 59)  and one healthy (CAG19) sibling's induced pluripotent stemm cells (iPSCs) and human embryonic stemm cells H9 .

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control group (CAG19 and H9) and HD group (CAG55 and 59)

first: Yang

first: Xinyu

last: Chen

first: Hexige

last: Saiyin


title: RNA Targets and Function of Topoisomerase 3β in Reducing Stress in Neuronal Physiology

status: Public on Dec 07 2023

city: Bern

first: Shohreh

last: Teimuri

address: Baltzerstrasse

institute: Bern University

summary: Topoisomerase 3β (Top3β) relaxes DNA and RNA and its dysregulation is implicated in various neurodevelopmental and cognitive disorders. We developed a novel protocol to isolate RNA targets of the topoisomerase without artificial cross-linking and used it to identify the RNA targets of Top3β. Lack of the enzymatic activity of Top3β affects gene expression of (pre)mRNAs with the characteristics described for the Top3β targets and we found evidence that this might also apply to several neurological diseases and cancers with which human Top3β was associated.

overall_design: To test if the lack of the enzymatic activity of Top3β stresses neurons, affecting the morphology of the neuromuscular junction (NMJ) in adult flies, and it causes premature aging and loss of coordinated movement.

first: Beat

last: Suter


title: GTP-dependent regulation of heterochromatin fluctuations at subtelomeric regions in S. cerevisiae

status: Public on Dec 28 2023

city: Fukui-city

first: Takahito

last: Ayano

state: Fukui

address: 3-9-1, Bunkyo

department: Graduate school engineering

country: Japan

institute: University of Fukui

summary:
Analysis of gene expression changes following deletion of SIR genes at subtelomeric region.
A total of 4 samples were analyzed : Wild type (BY4742) strain, SIR2 deletion strain, SIR3 deletion strain, SIR4 deletion strain.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Genes repressed by the Sir2/3/4 complex were identified.

first: Takuma

last: Yokosawa

first: Masaya

last: Oki


title: Cancer-Associated Fibroblast Secreted Collagen is associated with Immune Suppressive LAIR-1 in Gliomas

status: Public on Dec 09 2023

first: Shashwat

last: Tripathi

state: Illinois

address: 302 e Huron St

department: Neurosurgery

institute: Northwestern

summary: This is for a research letter in which we use peds glioma data to show collagen expression and CAFs are more abundant in the high grade glioma over low grade gliomas and additionally report the presence of LAIR1 in close proximity with these collagen rich areas.

overall_design: To investigate the presence of CAFs, collagen and related immune suppression markers.

first: Amy

last: Heimberger

first: Michael

last: DeCuypere


title: RNA-seq of human PDAC cell lines PANC-1 and BxPC3 treated with Gemcitabine compared to untreated controls

status: Public on Dec 05 2023

city: Leuven

first: Vincent

last: de Laat

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: Gemcitabine is commonly used for the treatment of PDAC, here we assess the effect of gene expression in human PDAC cell lines.

overall_design: We performed RNAseq on 2 PDAC cell lines treated with Gemcitabine or control.


title: ESR1 fusions invoke breast cancer subtype-dependent enrichment of ligand independent oncogenic signatures and phenotypes [RNA-seq]

city: Pittsburgh

first: Megan

middle: E.

last: Yates

address: 5051 Centre Ave

institute: University of Pittsburgh

summary: Breast cancer is a leading cause of female mortality and despite advancements in personalized therapeutics, metastatic disease largely remains incurable due to drug resistance. The estrogen receptor (ER, ESR1) is expressed in two-thirds of all breast cancer, and under endocrine stress, somatic ESR1 mutations arise in ~30% of cases that result in endocrine resistance. We and others reported ESR1 fusions as a mechanism of ER mediated endocrine resistance. ER fusions, which retain the AF1 and DNA binding domains, harbor ESR1 exons 1-6 fused to an in-frame gene partner resulting in loss of the ER ligand binding domain (LBD). We demonstrate that in a no-special type (invasive ductal carcinoma (IDC)- NST) and an invasive lobular carcinoma (ILC) cell line, ER fusions exhibit robust hyperactivation of canonical ER signaling pathways independent of estradiol or anti-endocrine therapies. We employ cell line models stably overexpressing ER fusions with concurrent endogenous ER knockdown to minimize endogenous ER influence. Cell lines exhibited shared transcriptomic enrichment in pathways known to be drivers of metastatic disease, notably MYC signaling. Cells expressing the 3’ fusion partners SOX9 and YAP1 consistently demonstrated enhanced growth and cell survival. ILC cells expressing the DAB2 fusion led to enhanced growth, survival, and migration; phenotypes not appreciated in the IDC- NST DAB2 model. Herein, we report that cell line activity is subtype-, fusion-, and assay-specific suggesting that LBD loss, the fusion partner, and the cellular landscape all influence fusion activities. Therefore, it will be critical to assess fusion frequency, in the context of the tumor clinicopathology.

overall_design: RNA-Seq expression profiling of six transgenic breast cancer cell lines derived from the T47D parental cell line. Cells stably express wildtype ER, truncated ER, or an ER fusion protein (ESR1-DAB2, ESR1-LPP, ESR1-SOX9, ESR1-YAP1), with concurrent endogenous ER knockdown. Each cell type is treated with vehicle or selective estrogen receptor degrader fulvestrant (ICI182,780) for 24 hours prior to RNA extraction and sequencing.

first: Hunter

last: Waltermire

first: Kanako

last: Mori

first: Zheqi

last: Li

first: Yiting

first: Hannah

last: Guzolik

first: Xiaosong

last: Wang

first: Tiantong

last: Liu

first: Jennifer

middle: M

last: Atkinson

first: Jagmohan

last: Hooda

first: Adrian

last: Lee

first: Steffi

last: Oesterreich


title: Characterization of regeneration initiating cells during Xenopus laevis tail regeneration [bulk RNA-Seq 1]

status: Public on Nov 30 2023

city: Vestec by Prague

first: Radek

last: Sindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

summary: In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. Absence or deregulation of RICs leads to excessive extracellular matrix deposition and regeneration defects.

overall_design: Bulk RNA-Seq analysis was done to analyze the temporal changes in gene expression during the regeneration periods of 0, 0.5, 1.5, 3, 6 hpa and 1, 3, 7 dpa.

first: Pavel

last: Abaffy

first: Ravindra

last: Naraine


title: Characterization of regeneration initiating cells during Xenopus laevis tail regeneration [spatial transcriptomics]

overall_design: X. laevis tadpoles at stage 40 (regenerative) and stage 46 (refractory) were analysed. Amputation was performed manually (removal of ~30% of tail tissue) using tricaine anesthetized tadpoles, with 6 replicates for refractory and 8 for regenerating embryos. Together we analyzed: 1) regenerative 6 hours post amputation (hpa) and 1 days post amputation (dpa), 2) refractory 6 hpa and 1 dpa, 3) regenerative and refractory 3 dpa. Dissected tissues were embedded and oriented in 50% optimal cutting temperature (OCT) medium, rapidly frozen using dry ice and then transferred to -80°C for a maximum of six weeks of storage. Samples were sectioned sagitally (20 µm thickness) using Leica CM1950 cryostat (Leica Microsystems). Sections collected for the 10X Visium Spatial Gene Expression processing were then stored at -80°C.

first: Daniel

last: Zucha

first: Sarka

last: Chytilova

last: Kraus


title: NG2/CSPG4 regulates the transcriptional profile of mandibular fibrochondrocytes during serum starvation

status: Public on Dec 02 2023

city: Chicago

first: David

last: Reed

address: 801 South Paulina Street

department: Department of Oral Biology

institute: University of Illinois at Chicago


title: VGLL1 drives therapy resistance in estrogen receptor positive breast cancer

city: London

first: Carolina

last: Gemma

state: Greater London

address: Du Cane Road, Hammersmith Campus

department: Department of Surgery and Cancer

institute: Imperial College London


title: Characterization of regeneration initiating cells during Xenopus laevis tail regeneration [bulk RNA-Seq 2]

overall_design: Bulk RNA-Seq analysis was done to analyze the temporal changes in gene expression during the regeneration and refractory periods of 0, 0.5, 6 hpa and 3 dpa.


title: Characterization of regeneration initiating cells during Xenopus laevis tail regeneration [scRNA-Seq]

overall_design: Single cell experiment was performed using 0, 1, 3, 12 hours post amputation (hpa) of Xenopus laevis tail at stage 40. Embryos were anesthetized and the regenerating part was dissected and collected. Tail pieces from 50 embryos were collected per one sample.


title: Characterization of regeneration initiating cells during Xenopus laevis tail regeneration


title: CTR9 affects virulence of Candida albicans by regulating methionine metabolism

city: Chuncheon-si

first: Shinae

last: Park

address: Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

summary: Project Abstract : Paf1C is a general transcription regulator and is associated with various human diseases. One of its subunits, CTR9, is known as a structurally and functionally core component of Paf1C. While its role in higher eukaryotes have been researched, the association between the core component and human fungal pathogen is not fully understood yet. During pre-infection process, Candida albicans adheres to the surface of hosts and sufficiently grows as the circular form. Under immune deficiency condition, C. albicans enters into the infection process and forms hyphae. Here, we performed virulence tests and transcriptome analysis to identify the role of CTR9 in two infection stages. In pre-infection process, CTR9 regulates basic cellular processes and metabolism, affecting cell growth. Of metabolic processes, methionine biosynthetic genes are significantly dependent on CTR9. This pathway hardly affects cell abundance for pre-infection stage, but has considerable effect on hyphal formation during infection stage. Therefore, it shows that methionine biosynthetic pathway mediated by CTR9 is essential for pathogenesis of C. albicans.

overall_design: Sample number (1-12): We performed RNA-seq with WT, Δctr9, Δleo1, and Δcdc73 strains. Experiments were performed in duplicates. RNA-seq using WT and Δctr9 was performed under yeast and hyphae inducing conditions, whereas RNA-seq using Δleo1 and Δcdc73 was performed only under hyphae inducing conditions. Yeast condition; WT (1,2) and Δctr9 (3,4). Hyphae induction condition: WT (5,6), Δctr9 (7,8), Δleo1 (9,10), and Δcdc73 (11,12)

first: Jung-Shin

first: Jiyeon

first: Jueun

last: Kim


title: Identification of salsolinol as an RNA m6A methylation inducer that mediates dopaminergic neuronal death by regulating YAP1 and autophagy

status: Public on Dec 04 2023

city: Beijing

first: Xuechai

last: Chen

address: 100 Ping Le Yuan, Chaoyang District

institute: Beijing University of Technology

summary: Salsolinol (1-methyl-6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline, Sal) is a catechol isoquinoline that can cause neurotoxicity because of its structural similarity with MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), an environmental toxin that causes Parkinson’s disease (PD). However, the mechanism by which Sal mediates dopaminergic neuronal death remains unclear. In this study, we found that Sal can significantly enhance the global level of N6-methyladenosine (m6A) mRNA methylation in PC12 cells, mainly by inducing the downregulation of the expression of m6A demethylase FTO (fat mass and obesity-associated protein) and ALKBH5 (alkB homolog 5). The results of the RNA-Seq analysis showed that Sal can exert a neurotoxic effect by regulating the Hippo signaling pathway through RNA methylation. We found that m6A reader YTHDF2 (YTH domain-containing family protein 2) promoted the degradation of m6A-containing YAP1 (Yes-associated protein 1) mRNA, which is a downstream key effector in the Hippo pathway. Additionally, the downregulation of YAP1 can also promote autophagy, indicating that the inter-regulation of YAP1 and autophagy can lead to neurotoxicity. Our findings showed the effect of Sal on m6A RNA methylation and revealed that Sal can act as an RNA modification inducer mediating dopaminergic neuronal death through YAP1 and autophagy. Our results provided greater insights into the neurotoxic effects of catechol isoquinolines and might be used as a reference for further assessing the involvement of RNA methylation in the pathogenesis of PD.

overall_design: 200 μM Sal-treated PC12 cells and controls were collected for RNA extraction


title: Diet supplemented with polyphenol- and glucuronoxylan-rich fiber extract regulates colonic barrier function and cell proliferation in healthy rats

status: Public on Dec 01 2023

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: A diet rich in dietary fiber and polyphenols supports the normal intestinal barrier function crucial for intestinal and overall health. Birch wood-derived fiber containing glucuronoxylans (GX)- and polyphenols have the potential in multiple food technological applications and have favorable effects on gut microbiota and colonic metabolism. However, their impact on intestinal barrier function is unknown. To elucidate their potential as new intestinal health-supporting food ingredients, we investigated the effect of GX- and polyphenol-rich extract (GXpoly ) and highly purified GX-rich extract (pureGX) on the gene expression of the colon mucosa.

overall_design:
Four-week-old female and male Wistar rats were acclimatized for 12 days and then fed diets supplemented with 10% w/w of polyphenol-and glucoronoxylan-rich extract (GXpoly), highly purified glucoronoxylan (pureGX), or cellulose (control) for four weeks. Gene expression of the mucosa of the colon mid-segment was investigated using Agilent gene expression microarrays with a two-colour design. Samples were carefully randomized for the microarray experiment to control batch effects arising from the experimental set up. Each experimental group contains samples from 10-11 rats (both male and female).
Please note that each raw data file contains raw data for two samples as indicated in the corresponding sample description field and thus is linked to the Series records.

first: Emma

last: Kynkäänniemi

first: Jere

last: Linden

first: Suchaya

last: Ngambundit

first: Laura

last: Saarimäki

first: Hana

last: Slaba

first: Maarit

last: Lahtinen

first: Kirsi

middle: S

last: Mikkonen

first: Anne-Maria

last: Pajari


title: Decoding the gene regulatory network of endosperm differentiation in maize [scRNA-seq]

status: Public on Nov 29 2023

first: Qiang

last: Huo

address: Yuanmingyuan West Road

institute: China Agricultural University

summary: The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. We delineate the temporal gene expression pattern from 6 to 7 days after pollination. We profile the genomic DNA binding sites of 161 transcription factors differentially expressed between cell clusters and constructed a gene regulatory network by combining the single-cell transcriptomic data with the direct DNA-binding profiles, identifying 181 regulons containing genes encoding transcription factors along with their high-confidence targets, Furthermore, we map the regulons to endosperm cell clusters, identify cell-cluster-specific essential regulators, and experimentally validated three predicted key regulators. This study provides a framework for understanding cereal endosperm development and function at single-cell resolution.

overall_design: Construction of gene regulatory networks in maize endosperm using scRNA-seq and DAP-seq


title: Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization

status: Public on Nov 17 2023

city: Villeneuve d'ascq

first: Tristan

last: Cardon

state: haut de france

address: Bât SN3, 1er étage, porte 109

institute: INSERM U1192 Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM)

summary: Proteogenomics is becoming a powerful tool in personalized medicine by linking genomics, transcriptomics and mass spectrometry (MS)-based proteomics. Due to increasing evidence of alternative open reading frame-encoded proteins (AltProts), proteogenomics has a high potential to unravel the characteristics, variants and expression levels of the alternative proteome, in addition to already annotated proteins (RefProts). To obtain a broader view of the proteome of ovarian cancer cells compared to ovarian epithelial cells, cell-specific total RNA-sequencing profiles and customized protein databases were generated. In total, 128 RefProts and 30 AltProts were identified exclusively in SKOV-3 and PEO-4 cells. Among them, an AltProt variant of IP_715944, translated from DHX8, was found mutated (p.Leu44Pro). We show high variation in protein expression levels of RefProts and AltProts in different subcellular compartments. The presence of 117 RefProt and two AltProt variants was described, along with their possible implications in the different physiological/pathological characteristics. To identify the possible involvement of AltProts in cellular processes, crosslinking-MS (XL-MS) was performed in each cell line to identify AltProt-RefProt interactions. This approach revealed an interaction between POLD3 and the AltProt IP_183088, which after molecular docking, was placed between POLD3-POLD2 binding sites, highlighting its possibility of the involvement in DNA replication and repair.

overall_design: 3 cell line (PEO4, SKOV3 and T1074) of ovarian cancer have been analysed by RNAseq to generate a proteomique databased link to the sample, as a proteogenomique analysis

first: Diego

middle: F

last: Garcia-del Rio

first: Mehdi

last: Derhourhi

first: Amelie

last: Bonnefond

first: Sébastien

last: Leblanc

first: Noé

last: Guilloy

first: Xavier

last: Roucou

first: Sven

last: Eyckerman

first: Kris

last: Gevaert

first: Michel

last: Salzet


title: Reanalysis of TSA-Seq mapping to determine genomic coordinates for speckles-associated domains.

city: Boston

first: Parmit

middle: Kumar

last: Singh

state: MA

address: 450 Brookline Avenue

department: Department of Cancer Immunology and Virology

institute: Dana-Farber Cancer Institute

type:
Third-party reanalysis
Other

summary: In this reanalysis, 9 GSM series were reanalyzed to obtain the genomic coordinates of speckles-associated domains.

relation:
Reanalysis of: GSM2157129
Reanalysis of: GSM2157131
Reanalysis of: GSM2157132
Reanalysis of: GSM2157134
Reanalysis of: GSM2157136
Reanalysis of: GSM2157138
Reanalysis of: GSM2157140
Reanalysis of: GSM2157142
Reanalysis of: GSM2157144

overall_design:
Reanalysis of the following samples in GSE81553:
BioProject accession: PRJNA321975
GEO Sample      SRA Runs        BioSample       Title
==========      ========        =========       =====
GSM2157129      SRR3538915      SAMN05007004    No Primary Control_for_SON TSA-Seq
GSM2157131      SRR3538917      SAMN05007006    SON TSA-Seq Condition 1 (TSA only)
GSM2157132      SRR3538918      SAMN05007007    SON TSA-Seq Condition 1 (TSA only) Second pull down
GSM2157134      SRR3538920      SAMN05007009    SON TSA-Seq Condition 2 (TSA+Sucrose)
GSM2157136      SRR3538922      SAMN05007011    SON TSA-Seq Condition 1 (TSA only) Replicate
GSM2157138      SRR3538924      SAMN05007013    SON TSA-Seq Condition 2 (TSA+Sucrose) Replicate
GSM2157140      SRR3538926      SAMN05007015    SON TSA-Seq Condition 3 (TSA+Sucrose+DTT)
GSM2157142      SRR3538928      SAMN05007017    Lamin A/C TSA-Seq Condition 2 (TSA+Sucrose)
GSM2157144      SRR3538930      SAMN05007019    Lamin B TSA-Seq Condition 2 (TSA+Sucrose)
*data processing step
Raw files were downloaded from NCBI, and reanalysis was done using the method described in the original article (PMID: 30154186). The raw sequence reads were aligned against the UCSC hg19 human genome by bowtie2 version 2.3.4.3. Aligned files were sorted in BAM format, and SAMtools version 1.3.1 removed duplicates without any parameter except input. The number of TSA mapped reads was normalized in 20 kb to the total number of mapped reads for a sample. The TSA enrichment score was calculated as the fold change (log2 ratio) between the pulldown sample and the corresponding input for a sliding window of 100 bp in size. For normalization, the parameters were: N =20000, r=100 and l=100. The Python script tsatools_normalisation was used. The SRR3538919 was used as control for SRR3538917 and SRR3538918; SRR3538916, SRR3538921, SRR3538923, SRR3538925, SRR3538927, SRR3538929, SRR3538931 were used as input for the SRR3538920, SRR3538922, SRR3538924, SRR3538926, SRR3538928, and SRR3538930 respectively. UCSC tool wig2bed was used to make bedfile. TSA-Seq score of top 5% percentile as speckles-associated domain.
wig and bed data. The SRR3538917_95P.txt contains coordinates of Speckles-associated domains or SPADs and was used in publications ( PMIDs:32665593 and 35203306).

middle: K


title: Single cell insights into development of the bovine placenta

status: Public on Nov 08 2023

city: Pullman

first: Kimberly

last: Davenport

state: WA

address: 100 Dairy Rd

department: Animal Science

institute: Washington State University

summary: A central determinant of pregnancy success is proper development of the conceptus (embryo/fetus and associated extraembryonic membranes including the placenta). Although the gross morphology and histology of the bovine placenta has been well studied, the cellular and molecular mechanisms regulating placenta development and trophoblast differentiation and function remain essentially undefined. Here single cell RNA-seq analysis was performed on the day 17 bovine conceptus and chorion of day 24, 30 and 50 conceptuses (n = 3-4 samples per day) using the 10X Genomics platform. Bioinformatic analyses identified cell types and their ontogeny including trophoblast, mesenchyme, and immune cells. Loss of IFNT-expressing trophoblast uninucleate cells (UNC) occurred between days 17 and 30, whereas binucleate cells (BNC), identified based on expression of placental lactogen (CSH2) and pregnancy-associated glycoproteins (PAGs) marker genes, first appeared on day 24. Several different types of UNC were present in day 24, 30 and 50 samples, but only one (day 24) or two types of BNC (days 30 and 50). Cell trajectory analyses provided a conceptual framework for UNC development and BNC differentiation, and upstream transcription factor binding enrichment analyses identified candidate transcription factors governing differentiation and function of the trophoblasts. The digital atlas of cell types in the developing bovine conceptus reported here serves as a resource to discover key genes and biological pathways regulating its development during the critical periods of implantation and placentation.

overall_design: Nuclei were isolated and libraries prepared following the 10X Genomics platform protocols

first: Eleanore

middle: V

last: O'Neil

first: M Sofia

last: Ortega

first: Amanda

last: Patterson

first: Andrew

last: Kelleher

first: Wesley

middle: C

last: Warren

first: Thomas

last: Spencer


title: Investigation of cis-regulation of metabolic insecticide resistance related gene expression in Anopheles gambiae using allelic imbalance

status: Public on Nov 22 2023

city: Liverpool

first: Naomi

middle: Anne

last: Dyer

state: Merseyside

address: Pembroke Place

department: Department of Vector Biology

institute: Liverpool School of Tropical Medicine

type: Genome variation profiling by high throughput sequencing

summary: Malaria control relies on insecticides targeting the mosquito vector, but is being increasingly compromised by insecticide resistance. Elevated expression of metabolic enzymes frequently drives resistance. In diploids, gene expression is regulated both in cis, by regulatory sequences on the same chromosome, and by trans acting factors, affecting both alleles equally. Differing levels of transcription can be caused by mutations in cis-regulatory modules, but few cis-regulatory modules controlling the expression of genes that determine insecticide resistance have been identified. Genes potentially under differential cis-regulation between bendiocarb resistant and susceptible Anopheles gambiae strains were identified by counting transcripts produced from maternal and paternal alleles in F1 hybrids of these strains (allelic specific expression). Cis regulatory module sequences controlling gene expression in insecticide resistance relevant tissues such as midgut, Malpighian tubules and legs were predicted using a previously established machine learning method. These predictions included CRM proximal to both genes under differential cis regulation and genes that show consistent differential expression patterns in multiple resistant Anopheles strains.

overall_design:
Crosses were performed between Anopheles gambiae  insecticide susceptible Kisumu strain (origin Kisumu, Kenya, 1970) and bendiocarb and pyrethroid resistant Anopheles gambiae Nagongera strain (origin Tororo, Uganda, 2013). In three crosses the mother was from Nagongera strain (3 biological replicates Wilding_1, Wilding_2 and Wilding_3) and in the other three then mother was from Kisumu strain (3 biological replicates Wilding_4, Wilding_5 and Wilding_6). RNA was extracted from a pool of 10 whole sugar fed adult F1 female progeny from each cross, 3-5 days after eclosion. All mosquitoes were raised in an insectary with temparature 26˚C and 70% relative humidity.
We first compared the gene expression between the reciprocal crosses (mother from Kisumu strain  vs mother from Nagongera strain). We then analyzed expression of genes from each parental allele within each sample (allele specific expression)

first: Eric

middle: R

last: Lucas

first: Sanjay

last: Nagi

first: Jon

middle: H

last: Brenas

first: Alistair

last: Miles

first: Henry

middle: D

last: Mawejje

first: Chris

last: Clarkson

first: Craig

last: Wilding

first: Daniel

last: McDermott

first: Marc

last: Halfon

first: Hasiba

last: Asma

first: Eva

last: Heinz

first: Martin

middle: J

last: Donnelly


title: Decoding the gene regulatory network of endosperm differentiation in maize

status: Public on Nov 28 2023

first: Qiang

last: Huo

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

overall_design: Refer to individual Series


title: FGF independent MEK1/2 signalling is essential for male germline development in mice [somatic cell]

status: Public on Nov 21 2023

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Germline development provides the founding cells for spermatogenesis and oogenesis in males and females, respectively. Disrupted germline differentiation or compromised testis development can lead to subfertility or infertility and are strongly associated with testis cancer in humans. In mice, SRY and SOX9 induce expression of a range of genes, including Fgf9, that promote Sertoli cell differentiation and testis development. FGF9 is also thought to promote male germline differentiation but the pathway through which it signals is unknown. As FGFs signal through Mitogen-Activated Protein Kinases (MAPKs) in other tissues, we explored whether FGF9 regulates male germline development through MAPK by inhibiting either FGF or MEK1/2 signalling in fetal testis cultures from embryonic day (E)12.5, immediately after gonadal sex determination and testis cord formation, but prior to male germline commitment. Inhibition of MEK1/2 disrupted mitotic arrest, dysregulated a broad range of male germline development genes and prevented the upregulation of key male germline markers DPPA4 and DNMT3L. In contrast, when FGF signalling was inhibited, the male germline specific transcriptional program and the expression of male germline markers DPPA4 and DNMT3L were unaffected, and the germ cells entered mitotic arrest normally. While male germline development was not disrupted by FGF inhibition, a significant number of genes were commonly altered after 24h of FGF or MEK1/2 inhibition including genes involved in maintenance germline stem cells, Nodal signalling, proliferation, and germline cancer. Together, these data demonstrate a novel and essential role for MEK1/2 signalling in male germline differentiation, but a surprisingly limited role for FGF signalling. Our data strongly indicate that additional ligands act through MEK1/2 to promote male germline differentiation and highlight a need for further mechanistic understanding of male germline development.

overall_design: E12.5 testes or ovaries were cultured for 0, 24 or 72h with DMSO (vehicle control), BGJ398 (FGFRi) or PD0325901 (MEKi). Several gonads were pooled for 1 biological replicate and somatic cell populations were isolated via FACS. 4 biological replicates were analysed for each treatment.

first: Rheannon

middle: O

last: Blücher

first: Rachel

last: Lim

first: Ellen

middle: G

last: Jarred

first: Patrick

last: Western


title: TREX1 is required for microglial cholesterol homeostasis and subsequent oligodendrocyte maturation during brain development

status: Public on Nov 23 2023

city: La Jolla

first: Alysson

last: Muotri

address: 2880 Torrey Pines Scenic Drive, Room 3005

institute: University of California - San Diego


title: FGF independent MEK1/2 signalling is essential for male germline development in mice [germ cell]

status: Public on Nov 02 2023

overall_design: E12.5 testes or ovaries were cultured for 0, 24 or 72h with DMSO (vehicle control), BGJ398 (FGFRi) or PD0325901 (MEKi). Several gonads were pooled for 1 biological replicate and germ cell populations were isolated via FACS. 4 biological replicates were analysed for each treatment.


title: The cullin Rtt101 promotes ubiquitin-dependent DNA-Protein Crosslink repair across the cell cycle

status: Public on Nov 10 2023

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

institute: Université de Genève

summary: DNA‒protein crosslinks (DPCs) challenge faithful DNA replication and fluid passage of genomic information. Our study unveils the cullin ubiquitin ligase Rtt101 as a novel DPC repair factor. Genetic analyses demonstrate that Rtt101 is essential for resistance to a wide range of DPC types. Using an inducible in vivo DPC system, we reveal the significant impact of Rtt101 on DPC removal, including topoisomerase 1 crosslinks. ChIP-sequencing and ChEC-sequencing specifically highlight the association of Rtt101 with replisomes as well as colocalization with DPCs. Our findings establish Rtt101 as a novel main contributor to DPC repair throughout the yeast cell cycle.

overall_design: Rtt101 ChEC-seq in absence (Raff) or presence (Gal) of a single Flp-Covalent Crosslink and colocalization of Rtt101 and the replication fork during S-phase by ChIP-seq.

first: Audrey

last: Noireterre

first: Ivona

last: Bagdiul

first: Françoise

last: Stutz


title: Genomic maps of lnc-HLX-2-7 occupancy in human medulloblastoma cell line.

status: Public on Nov 01 2023

city: Saint Petersburg

first: Ranjan

last: Perera

state: FL

address: 600 5th St S

department: Oncology Center

institute: Johns Hopkins All Childrens Hospital

summary: To gain more insights into the functional significance of lnc-HLX-2-7  in human medulloblastoma, genomic mapping of lnc-HLX-2-7 occupancy were analyzied by ChIRP DNA sequencing.

overall_design: Genomic maps of lnc-HLX-2-7 occupancy by ChIRP sequencing.

first: Keisuke

last: Katsushma

first: Rabi

last: Murad

first: Kandarp

last: Joshi

first: Menglang

last: Yuan


title: RNA sequencing analysis of intracranial D425 xenografts treated with ASO-CTRL and ASO-lnc-HLX 2-7

city: St. Petersburg

first: Rudrmani

last: Pokhrel

state: United States

address: 600 Fifth Street S.

department: Oncology

institute: Johns Hopkins All Children’s Hospital

summary: To gain more insights into the functional significance of lnc-HLX-2-7, gene expression profiles were measured using  D425 (sh-CTRL), D425 (sh-HLX) and intracranial D425 xenografts treated with ASO-CTRL and ASO-lnc-HLX 2-7 by RNA sequencing.

overall_design: Medulloblastoma mRNA profiles of D425 (sh-CTRL), D425 (sh-HLX) and intracranial D425 xenografts treated with ASO-CTRL and ASO-lnc-HLX 2-7.

first: Rudramani

first: Bongyong

last: Lee


title: MRTF-SRF signalling in the T cell IL2 response

status: Public on Oct 23 2023

first: Philip

last: East

address: Midland Road

institute: The Francis Crick Institute

summary: The transcription factor SRF is a master regulator of growth factor inducible and cytoskeletal gene expression. Two transcription cofactor families, the TCFs & the MRTFs, are responsible for SRF's activity to direct transcriptional programme in response to extracellular signalling through the Ras-ERK and Rho-actin pathways respectively.  We are investigating the role of the SRF network in the response to infection, using the Listeria monocytogenes model. We find that inactivation of the network impairs the ability of CD8 T cells to proliferate in response to listeria and to generate memory cells. Surprisingly, the defect reflects impaired MRTF-SRF signalling rather than the TCF-SRF signalling pathway usually associated with proliferation. Moreover, the defec doesn'tt lie downstream of the initial activation of the TCR, appearing instead to arise from an inability of CD8 T cells to present IL-2 to each other in paracrine fashion.  Consistent with these observations, we find that while cultured CD8 MRTF-null T cells can be effectively activated by TCR crosslinking invitro, their ability to form clusters, which is IL-2-dependent, is impaired. Moreover, as expected, pilot experiments indicate that these cells exhibit deficits both in the basal levels of MRTF-SRF target gene expression, and in their ability to induce these genes in response to IL-2 stimulation:

overall_design:
T cells are activated by TCR crosslinking, then maintained in IL-12 before stimulation with IL-2 for various times.
CD8+ T cells are sorted from pooled LN from 5 mice, each reconstituted with WT or MRTFf/f bone marrow (the latter rendered MRTF-null by a 15-day tamoxifen treatment). Cells are rested in full media for 90 min in incubator at 2x10^6 cells/ml before stimulation with plate-bound antiCD3+antiCD28 (5ug/ml) in a 6-well plate for 24h (6x10^6 cells per well). Cells were washed and transferred to a new plate containing 20ng/ml IL-12 (1x10^6 cells per well) for 12h before stimulation with 20ng/ml IL-2 for various times.IL-2R expression was analyzed by FACS and RNA was prepared for analysis from the following samples in triplicate:
1 Primary cells   t = 0
2 TCR-activated cells   t = 24h
3 Rested cells + IL-12  t = 36h
4 IL-2-stimulated cells   +30min
5 IL-2-stimulated cells   +60min
6 IL-2-stimulated cells   +120min
sequence total RNA (rRNA-depleted) in order to capture intronic sequences - see below.
TOTAL samples 36

first: Diane

last: Maurice

first: Francesco

last: Gualdrini

first: Jimena

last: Perez-Lloret

first: Phil


title: CD38+ Alveolar Macrophages mediate early control of M.tuberculosis proliferation in the lung [CITE-seq]

status: Public on Oct 31 2023

city: Ithaca

first: Davide

last: Pisu

state: NY

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

summary:
Tuberculosis, caused by M.tuberculosis (Mtb), remains an enduring global health challenge, especially given the limited efficacy of current therapeutic interventions. Much of existing research has focused on immune failure as a driver of tuberculosis. However, the crucial role of host macrophage biology in controlling the disease remains underexplored. While we have gained deeper insights into how alveolar macrophages (AMs) interact with Mtb, the precise AM subsets that mediate protection and potentially prevent tuberculosis progression have yet to be identified. In this study, by integrating the use of weighted gene correlation network analysis (WGCNA) modules with our multi-modal scRNA-seq protocol, we were able to evaluate the functional roles of diverse macrophage subpopulations across different infection timepoints, allowing us to delineate the dynamic landscape of controller and permissive AM populations throughout the infection timeline.
Our analyses during specific post-Mtb challenge intervals revealed macrophage populations transitioning between distinct anti- and pro-inflammatory states. Notably, CD38- AMs showed a muted response to early Mtb infection. As infection progressed, we observed a phenotypic shift in AMs, with CD38+ monocyte-derived AMs (moAMs) and a subset of tissue-resident AMs (TR-AMs) emerging as significant controllers of bacterial growth. Interestingly, scATAC-seq analysis of naïve lungs demonstrated that CD38+ TR-AMs possessed a distinct chromatin signature prior to infection, indicative of epigenetic priming, and predisposed them to a pro-inflammatory response. BCG intranasal immunization increased the numbers of CD38+ macrophages, substantially enhancing their capability to restrict Mtb growth.
Collectively, our findings emphasize the pivotal, dynamic roles of different macrophage subsets in TB infection and reveal rational pathways for the development of improved vaccines and immunotherapeutic strategies, with implications for the broader field of infectious diseases.

overall_design:
Mice were intranasally inoculated with 1500 CFUs of the Erdman strains (smyc′::mCherry, hspx′::GFP/smyc′::mCherry, or hsp60′::GFP). At 2, 4, and 6 weeks post-infection (w.p.i.), mice were euthanized. Cells from infected mice were then sorted. Sorted cells were  resuspended in cell staining buffer and an ADT plus HTO antibody cocktail mix. The samples were then fixed in methanol overnight, rehydrated and then processed for scRNA-seq.
Infected samples: M.tuberculosis-infected cells from the lungs of BL/6 mice.
Bystander samples: Uninfected cells from the lungs of M.tuberculosis-infected BL/6 mice.

first: Joshua

middle: T

last: Mattila

first: David

last: Russell


title: Pachytene piRNAs govern male meiosis I by spatial restriction of gene expression (piRNA)

status: Public on Oct 14 2023

city: Houston

first: Jacob

middle: Manuel

last: Ortega

state: Texas

address: 6550 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

summary: Pachytene piRNAs control male fertility across metazoans, yet mechanisms through which they govern meiosis I in pachytene remain unclear. We demonstrate, in C. elegans, that homolog pairing, and crossover formation are compromised in the absence of piRNA function. We identify several protein coding genes as targets of piRNAs including Polo like kinase 3 (PLK-). Pachytene piRNAs spatially restrict and exclude PLK-3 expression from meiosis I. Expansion of PLK-3 expression into the pachytene region, upon loss of piRNAs, is reflected in meiotic defects, which are partially rescued by removal of ectopic PLK-3. Pachytene piRNAs regulate PLK-3 through both translational repression and post-transcriptional degradation establishing the spatiotemporal control of gene expression. Given the conserved role of pachytene piRNAs, we propose that these mechanisms may be applicable to mammals.

overall_design: To measure differences in piRNA levels between wild type and prg-1 mutant adult male C. elegans, we profiled small RNA samples for piRNAs derived from animals of the following genotypes [replicates]: Wild Type [x3], prg-1(null) [x4], prg-1(RNase dead) [x3], and prg-1(∆PAZ-domain) [x3]. Average total piRNA reads between genotypes were normalized to total reads mapping to the C. elegans genome and their abundance was compared.

first: Lamia

last: Wahba

last: Seemann

first: Andrew

last: Fire

first: Swathi

last: Arur


title: Pachytene piRNAs govern male meiosis I by spatial restriction of gene expression


title: CD38+ Alveolar Macrophages mediate early control of M.tuberculosis proliferation in the lung [scATAC-seq]

overall_design: BL/6 naive mice were euthanized, the lungs aseptically removed and a single cell suspension of lung tissue generated. CD45+ cells were sorted, and sorted cells were lysed for nuclei isolation. Isolatad nuclei were then used as an input for the 10X ATAC-sec protocol.


title: Tropomyosin 1 deficiency facilitates cell state transitions and enhances hemogenic endothelial cell specification during hematopoiesis

status: Public on Oct 02 2023

city: Philadelphia

first: Christopher

last: Thom

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: The goal of this study was to determine the developmental stage(s) and mechanisms by which Tropomyosin 1 impacts hematopoiesis.

overall_design: Genome-edited induced pluripotent stem cells were analyzed at the indicated time points during hematopoietic differentiation and compared to isogenic wild type controls. We analyzed 4 replicates at each time point.