title: Generation of complex human induced pluripotent stem cell-derived bone marrow organoids

city: Munich

first: Stephanie

last: Frenz-Wiessner

address: Lindwurmstr. 4

department: Department of Pediatrics, Dr. von Hauner Children’s Hospital

institute: Ludwig-Maximilians-University Munich

summary: We present a method for generating complex bone marrow-like organoids (BMOs) from human induced pluripotent stem cells (iPSCs) and applied single-cell RNA-seq to study cell commposition and hematopoietic development of BMOs.

overall_design: Dissociated iPSC-derived bone marrow organoids were analysed using single cell RNA sequencing.

first: Christoph

last: Klein


title: SARS-CoV-2 Infection Causes Dopaminergic Neuron Senescence [scRNA-Seq]

status: Public on Dec 04 2023

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

country: USA

institute: Weill Cornell Medical College

type: Expression profiling by high throughput sequencing

summary: COVID-19 patients commonly present with neurological signs of central nervous system (CNS) and/or peripheral nervous system dysfunction. However, which neural cells are permissive to infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been controversial. Here, we show that midbrain dopamine (DA) neurons derived from human pluripotent stem cells (hPSCs) are selectively susceptible and permissive to SARS-CoV-2 infection, and that SARS-CoV-2 infection triggers a DA neuron inflammatory and cellular senescence response. A high-throughput screen in hPSC-derived DA neurons identified several FDA approved drugs, including riluzole, metformin, and imatinib, that can rescue the cellular senescence phenotype by preventing SARS-CoV-2 infection. RNA-seq analysis of human ventral midbrain tissue from COVID-19 patients, using formalin-fixed paraffin-embedded autopsy samples, confirmed the induction of an inflammatory and cellular senescence signature and identified low levels of SARS-CoV-2 transcripts. Our findings demonstrate that hPSC-derived DA neurons can serve as a disease model to study neuronal susceptibility to SARS-CoV-2 and to identify candidate neuroprotective drugs for COVID-19 patients. The susceptibility of hPSC-derived DA neurons to SARS-CoV-2 and the observed inflammatory and senescence transcriptional responses suggest the need for careful, long-term monitoring of neurological problems in COVID-19 patients.

overall_design: 2 total samples

first: Liuliu

last: Yang

first: Yuling

last: Han

first: Tae

middle: W

last: Kim


title: Gut complement induced by the microbiota combats pathogens and spares commensals

city: Boston

first: Meng

last: Wu

state: MA

address: 77 Avenue Louis Pasteur

department: Immunology

institute: Harvard Medical School

summary: Canonically, the complement system is known for its rapid response to remove microbes in the bloodstream. However, relatively little is known about a functioning complement system on intestinal mucosal surfaces. Herein we report the local synthesis of complement component 3 (C3) in the gut, primarily by stromal cells. C3 is expressed upon commensal colonization, is regulated by the composition of the microbiota in healthy humans and mice, leading to an individual host’s specific luminal C3 levels. The absence of membrane attack complex (MAC) components in the gut ensures that C3 deposition does not result in the lysis of commensals. Pathogen infection triggers the immune system to recruit neutrophils to the infection site for pathogen clearance. Basal C3 levels directly correlate with protection against enteric infection. Our study reveals the gut complement system as a novel innate immune mechanism acting as a vigilant sentinel that combats pathogens and spares commensals.

overall_design: To examine the C3 transcriptional levles and other complement gene expression levels in the colon, we used fluorescence-activated cell sorting (FACS) to isolate stromal (EpCAM-CD45-CD31-PDPN+ cells), CD45+, and IEC (EpCAM+) populations from the subepithelial compartment of the colon of WT C57BL/6 mice, then performed bulk RNASeq.


title: A phage-encoded RNA-binding protein inhibits the antiviral activity of a toxin-antitoxin system

city: Cambridge

first: Chantal

middle: K

last: Guegler

address: 31 Ames Street

department: Biology

institute: MIT

summary: Bacteria harbor diverse mechanisms to defend themselves against their viral predators, bacteriophages. In response, phages can evolve counter-defense systems, most of which remain poorly understood. In T4-like phages, the gene tifA prevents bacterial defense by the type III toxin-antitoxin (TA) system toxIN, but the mechanism by which TifA inhibits toxIN remains unclear. Here, we show that TifA directly binds both the endoribonuclease ToxN and RNA, leading to the formation of a high molecular weight ribonucleoprotein complex in which ToxN is inhibited. The RNA binding activity of TifA is necessary for its interaction with and inhibition of ToxN. Thus, we propose that TifA inhibits ToxN during phage infection by trapping ToxN on cellular RNA, particularly the abundant 16S rRNA, preventing cleavage of phage transcripts. Taken together, our results reveal a novel mechanism underlying inhibition of a phage-defensive RNase toxin by a small, phage-encoded protein.

overall_design: E. coli toxI and chitin binding domain-tagged ToxN were overexpressed with bacteriophage RB69 TifA (wild-type or the RNA-binding mutant TifA(K55A R56A R59A) in E. coli T7 express cells (NEB). Lysate was then purified through chitin resin to isolate RNAs and proteins associated with ToxN during the co-expression. RNAs from whole cell lysates and following chitin purification were then deep sequenced to identify the RNA species that co-purify with ToxN when it is co-expressed with TifA.

first: Gabriella

middle: I

last: Teodoro

first: Sriram

last: Srikant

first: Keerthana

last: Chetlapalli

first: Christopher

middle: R

last: Doering

first: Dia

middle: A

last: Ghose

first: Michael

middle: T

last: Laub


title: FANSseq profiling of human striatal cell types

first: Kert

last: Matlik

address: 1230 York Avenue

institute: Rockefeller University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Selective degeneration of striatal projection neurons is one of the main features of Huntington’s disease (HD). The differences between vulnerable and resilient striatal cell types and cell type-specific molecular events associated with HD progression have not been established. Here we employed fluorescence-activated nuclear sorting (FANS) and deep molecular profiling to gain insight into the properties of different cell types of the human striatum in HD and control donors.

overall_design: Populations of cell nuclei from different types of striatal neurons and glia from post-mortem human brain were labeled with cell type-specific probes and separated by FACS, followed by RNAseq-based quantification of nuclear transcript levels.

first: Nathaniel

last: Heintz


title: Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons

city: Trondheim

first: Nathalie

last: Jurisch-Yaksi

address: Erling Skjalgsons gate 1

country: Norway

institute: NTNU

summary: Olfaction plays important roles in food and mate choice, and also in the avoidance of predators, making it a vital sensory modality for preservation and reproduction. In the vertebrates, olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons (OSNs). Although olfactory cilia dysfunction can cause loss of the sense of smell, how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1, a fork head-domain containing transcription factor traditionally linked with motile cilia biogenesis, is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia, we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells, are repressed in the OSNs. Strikingly, we also found that besides ciliogenesis, Foxj1 controls the differentiation of the OSNs by regulating their cell type-specific gene expression, such as that of olfactory marker protein (omp) involved in odour-evoked signal transduction. In line with these requirements, response to bile acid, an odour detected by OMP-positive OSNs, was significantly diminished in the foxj1 mutant zebrafish. Taken together, our findings establish how the canonical Foxj1-mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves.

overall_design: to investigate the role of Foxj1 genes in zebrafish, foxj1a and foxj1b knock-out fish used for RNA isolation at 4 dpf.

first: Dheeraj

last: Rayamajhi

first: Mert

last: Ege

first: Kirill

last: Ukhanov

first: Sudipto

last: Roy


title: Decoupling NAD+ metabolic dependency in chondrosarcoma by targeting the SIRT1–HIF-2α axis

status: Public on Dec 01 2023

city: Seoul

first: Hyeonkyeong

state: Seoul

address: Molecular regenerative medicine lab, 301ho, Building 502, Gwanak_1 Gwanak-ro, Gwanak-gu,

country: South Korea

institute: Seoul National University

summary: Chondrosarcomas represent the second most common primary bone malignancy. Despite the vulnerability of chondrosarcoma cells to nicotinamide adenine dinucleotide (NAD+) depletion, targeting the NAD+ synthesis pathway remains challenging due to broad implications in biological processes. Here, we establish SIRT1 as a central mediator reinforcing the dependency of chondrosarcoma cells on NAD+ metabolism via HIF-2α-mediated transcriptional reprogramming. SIRT1 knockdown abolishes aggressive phenotypes of chondrosarcomas in orthotopically transplanted tumors in mice. Chondrosarcoma cells thrive under glucose starvation by accumulating NAD+ and subsequently activating the SIRT1–HIF-2α axis. Decoupling this link via SIRT1 inhibition unleashes apoptosis and suppresses tumor progression in conjunction with chemotherapy. Unsupervised clustering analysis identifies a high-risk chondrosarcoma patient subgroup characterized by the upregulation of NAD+ biosynthesis genes. Finally, SIRT1 inhibition abolishes HIF-2α transcriptional activity and sensitizes chondrosarcoma cells to doxorubicin-induced cytotoxicity, irrespective of underlying pathways to accumulate intracellular NAD+. We provide system-level guidelines to develop therapeutic strategies for chondrosarcomas.

overall_design:
To investigate association of SIRT1 with HIF-2α-mediated transcription and chondrosarcoma malignancy, we analyzed transcriptome obtained from SW1353 cells with SIRT1 knockdown.
For transcriptomic analysis, SW1353 cells were transduced with the firefly or SIRT1 shRNA. Three biological replicates were used for each group.

first: Jooyeon

last: Suh

first: Jin-Hong

first: Yi-Jun


title: Sustained hyperglycemia specifically targets translation of mRNAs for insulin secretion

first: Jonathan

middle: M

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: Pancreatic beta-cells are specialized for coupling glucose metabolism to insulin peptide production and secretion. Acute glucose exposure robustly and coordinately increases translation of proinsulin and proteins required for secretion of mature insulin peptide. By contrast, chronically elevated glucose levels that occur during diabetes impair beta-cell insulin secretion and have been shown experimentally to suppress insulin translation. Whether translation of other genes critical for insulin secretion are similarly downregulated by chronic high glucose is unknown. Here, we used high-throughput ribosome profiling and nascent proteomics in MIN6 insulinoma cells to elucidate the genome-wide impact of sustained high glucose on beta-cell mRNA translation. Prior to induction of ER stress or suppression of global translation, sustained high glucose suppressed glucose-stimulated insulin secretion and downregulated translation of not only insulin, but also of mRNAs related to insulin secretory granule formation, exocytosis, and metabolism-coupled insulin secretion. Translation of these mRNAs was also downregulated in primary rat and human islets following ex-vivo incubation with sustained high glucose and in an in vivo model of chronic mild hyperglycemia. Furthermore, translational downregulation decreased cellular abundance of these proteins. Our study uncovered a translational regulatory circuit during beta-cell glucose toxicity that impairs expression of proteins with critical roles in beta-cell function.

overall_design: To determine effect of sustained high glucose on mRNA translation of pancreatic beta-cell, ribosome profiling was performed to measure mRNA translation efficiency based on the proportion of mRNA bound by the ribosome compared to total mRNA per gene. MIN6 cells were incubated in media with 5.5 mM or 25 mM glucose for 24 hours prior to ribosome profiling.

first: Abigael

last: Cheruiyot

first: Jennifer

last: Hollister-Lock

first: Brooke

last: Sullivan

first: Hui

last: Pan

first: Susan

last: Bonner-Weir

first: Jean

middle: E

last: Schaffer


title: Diagnostic marker development of tRNA-derived fragments in cerebrospinal fluid and blood serum

city: Galveston

first: Xiaoyong

last: Bao

state: TX

address: 301 University Boulevard

department: Pediatrics

institute: University of Texas Medical Branch

type: Non-coding RNA profiling by high throughput sequencing

summary:
The development of non-invasive diagnostic methods is crucial in early disease detection and thus better treatment options. Small RNAs have been identified as good candidates for such diagnostic markers due to their small size, which allows ease of transport from live cells. Correlating small RNAs in bodily fluid with those in tissue cells of interest may even shed light on disease mechanisms and the development of therapeutic targets. tRNA-derived RNA fragments (tRFs), a family of recently discovered small non-coding RNAs (sncRNAs), have been found to be significantly changed in various disease states, including Alzheimer's disease (AD), the most common type of dementia. Previously, tRFs have been found to be significantly enhanced in human AD hippocampus tissues. However, whether tRFs change in body fluids is unknown.
In this study, we planned to identify baselines for potential usage of tRFs as biomarkers in cerebrospinal fluid and blood serum for future development of AD biomarkers. Towards this goal, we used T4 polynucleotide kinase-RNA-seq, a modified next-generation sequencing technique, to identify detectable tRFs in human cerebrospinal fluid (CSF) and serum samples. Interestingly, we found an abundance of tRFs in both CSF and serum samples in comparison to microRNAs, well-known small RNAs (about 3-10 times higher in read counts). This clearly indicates the significant potential of tRFs as non-invasive biomarkers in CSF and serum.

overall_design: We obtained CSF samples through the National Institutes of Health (NIH) NeuroBioBank (https://neurobiobank.nih.gov/). Serum samples were requested and obtained from the Texas Alzheimer's Research and Care Consortium (TARCC).

first: Wenzhe

last: Wu

first: Audrey

last: Shen

first: Inhan

last: Lee

first: Heidi

last: Spratt

first: Miguel

last: Pappolla

first: Xiang

last: Fang


title: UBTF tandem duplication AMLs are sensitive to menin inhibition

city: UTRECHT

first: Olaf

last: Heidenreich

state: UTRECHT

address: Prinses Máxima Centrum voor kinderoncologie | Postbus 113| 3720 AC BILTHOVEN | Heidelberglaan 25 |  3584CS UTRECHT | Nederland

country: Netherlands

summary: To investigate the effect of Menin inhibitor on UBTF-TD harboring AML. We characterized UBTF-TD interaction with KMT2A and Menin in different leukemia models including KMT2A-r, transduced and normal cbCD34+ cells as well as in primary AML cells with UBTF-TD mutation. We also analized gene expression pattern upon treatment with Menin inhibitor.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for patient-derived UBTF-TD AML cells after treatment with Menin inhibitor (SNDX-5613/Revumenib).

first: Juan

last: Barajas

first: Milad

last: Rasouli

first: Masayuki

last: Umeda

first: Ryan

last: Hiltenbrand

first: Sherif

last: Abdelhamed

first: Rebecca

last: Mohnani

first: Bright

last: Arthur

first: Tamara

last: Westover

first: Melvin

last: Thomas 3rd

first: Ilaria

last: Iacobucci

first: Minoo

last: Ashtiani

first: Beisi

last: Xu

first: Ti-Cheng

last: Chang

first: Wojciech

last: Rosikiewicz

first: Emily

last: Xiong

first: Chandra

last: Rolle

last: Low

first: Reethu

last: Krishan

first: Nicole

last: Michmerhuizen

first: Michael

middle: P

last: Walsh

first: Jing

last: Ma

first: Shilpa

last: Narina

last: Klein

first: Patrick

last: Connelly

first: Shondra

last: Miller

first: Taosheng

last: Chen

first: Anja

last: Krippner-Heidenreich

first: Eva

last: Papachristou

first: Clive

last: D'Santos

first: C

last: Zwaan

first: Jeffery

last: Klco


title: Effect of CD97 knockdown or overexpression in patient-derived GBM cultures (PDGCs)

first: Niklas

last: Ravn-Boess

address: 550 1st Avenue

institute: NYU Langone

summary: To investigate differentially expressed genes upon CD97 manipulation in GBM

overall_design: RNA-seq from four PDGCs following CD97 knockdown or overexpression in one of the PDGCs.

first: Dimitris

last: Placantonakis


title: Single cell data from IDH mutant astroxytoma and IDH wildtype GBM tumor specimen

summary: Glioblastoma (GBM) is the most common and aggressive primary brain malignancy. Adhesion G protein-coupled receptors (aGPCRs) have attracted interest for their functional role in gliomagenesis and their potential as treatment targets. To identify therapeutically targetable opportunities among aGPCR family members in an unbiased fashion, we analyzed expression levels of all aGPCRs in GBM and non-neoplastic brain tissue. Using bulk and single cell transcriptomic and proteomic data, we show that CD97 (ADGRE5), an aGPCR previously implicated in GBM pathogenesis, is the most promising aGPCR target in GBM, by virtue of its abundance in all GBM tumors and its de novo expression profile in GBM compared to normal brain tissue and neural progenitors. CD97 knockdown or knockout significantly reduces the tumor initiation capacity of patient-derived GBM cells (PDGC) in vitro and in vivo. Transcriptomic and metabolomic data from PDGCs suggest that CD97 promotes glycolytic metabolism. The oncogenic and metabolic effects of CD97 are mediated by the MAPK pathway. Activation of MAPK signaling depends on phosphorylation of the cytosolic C-terminus of CD97 and recruitment of    -arrestin. Using single-cell RNA-sequencing and biochemical assays, we demonstrate that THY1/CD90 is the most likely CD97 ligand in GBM. Lastly, we show that targeting of GBM cells with an anti-CD97 antibody-drug conjugate in vitro selectively kills tumor cells but not human astrocytes or neural stem cells. Our studies identify CD97 as an important regulator of tumor metabolism in GBM, elucidate mechanisms of receptor activation and signaling, and provide strong scientific rationale for developing biologics to target CD97 in GBM.

overall_design:
Glioma specimen are flash frozen and single cell RNAsequencing and ATAC sequencing
The sample was then processed as described in the “10X Genomics Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + GEX Sequencing Demonstrated Protocol CG000375 Rev B”


title: Osmolar modulation drives reversible cell cycle exit and human pluripotent cell differentiation via NF-κВ and WNT signaling

city: Leuven

first: Jonathan

middle: Sai-Hong

last: Chui

state: Vlaams Brabant

address: Herestraat 49 PB804

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

summary: Terminally differentiated cells are regarded as the most stable and common cell state in adult organisms as they reside in growth arrest and carry out their cellular function. Improving our understanding of the mechanisms involved in promoting cell cycle exit would facilitate our ability to manipulate pluripotent cells into mature tissues for both pharmacological and therapeutic use. Here, we demonstrated that a hyperosmolar environment enforced a protective p53-independent quiescent state in dedifferentiated and pluripotent stem cells (PSCs)-derived models of human hepatocytes and endothelial cells, depicting the endodermal and mesodermal lineages. Prolonged culture in hyperosmolar conditions stimulated transcriptional and functional cell maturation. Interestingly, hyperosmolar conditions did not only trigger cellular maturation but were also necessary to maintain this maturated state, as switching back to serum osmolarity caused the loss of maturation markers and the gain of proliferative markers. Transcriptome analysis revealed activation of NF-κВ and repression of WNT signaling as the two main pathways downstream of osmolarity-regulated growth arrest and cell maturation, respectively. In pluripotent cell differentiation, blocking NF-κВ signaling under hyperosmolar conditions disrupted cell cycle arrest and cell maturation. In contrast, WNT activation reduced transcriptional maturation without effects on the cell cycle. These studies revealed that increased osmolarity serves as a biochemical signal to promote long-term growth arrest, transcriptional changes, and maturation into different lineages, serving as a practical method to generate differentiated hiPSCs that resemble their mature counterpart more closely.

overall_design: HUH7.5 cells and iPSC-derived HLCs were differentiated under hyperosmolar conditions

middle: S

first: Teresa

last: Izuel Idoype

first: Frederic

last: Lluis


title: B cell-intrinsic STAT3-mediated interferon suppression during murine gammaherpesvirus 68 infection revealed through in vivo competition model.

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

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

overall_design: Refer to individual Series


title: Identification of genes regulated by pri and ken in late Drosophila embryos

city: Toulouse

first: Helene

last: Chanut

address: 118 route de Narbonne

department: CBI

country: France

institute: CNRS

summary:
We aim to identify genes commonly repressed by pri and ken in epidermis of Drosophila embryos.
We performed gene expression profiling analysis using data obtained from RNA-seq of control, pri mutant and ken mutant embryos.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control, ken and pri mutant embryos.

first: Maylis

last: Gallois

first: Delphine

last: Menoret

first: Simon

last: Marques-Prieto

first: Audrey

last: Montigny

first: Philippe

last: Valenti

first: Bernard

last: Moussian

first: Serge

last: Plaza

first: François

last: Payre

first: Hélène

last: Chanut-Delalande


title: Enhanced meningeal lymphatic drainage ameliorates lipopolysaccharide-induced brain injury in aged mice

status: Public on Nov 30 2023

city: Nanjing

first: Hongquan

last: Dong

address: 300 Guangzhou Road

country: China

institute: Nanjing Medical University

summary: Sepsis-associated encephalopathy (SAE) is an acute cerebral dysfunction caused by sepsis. Neuroinflammation induced by sepsis is considered a potential mechanism of SAE; however, very little is known about the role of the meningeal lymphatic system in SAE. The aged mice with SAE showed a significant decrease in the drainage of OVA-647 into the dCLNs and the coverage of the Lyve-1 in the meningeal lymphatic, indicating that sepsis impaired meningeal lymphatic drainage and morphology. The meningeal lymphatic function of aged mice was more vulnerable to sepsis in comparison to young mice. Sepsis also decreased the protein levels of caspase-3 and PSD95, which was accompanied by reductions in the activity of hippocampal neurons. Microglia were significantly activated in the hippocampus of SAE mice, which was accompanied by an increase in neuroinflammation, as indicated by increases in interleukin-1 beta, interleukin-6 and Iba1 expression. Cognitive function was impaired in aged mice with SAE. However, the injection of AAV1-VEGF-C significantly increased coverage in the lymphatic system and tracer dye uptake in dCLNs, suggesting that AAV1-VEGF-C promotes meningeal lymphangiogenesis and drainage. Furthermore, AAV1-VEGF-C reduced microglial activation and neuroinflammation and improved cognitive dysfunction. Improvement of meningeal lymphatics also reduced sepsis-induced expression of disease-associated genes in aged mice. Pre-existing lymphatic dysfunction by ligating bilateral dCLNs aggravated sepsis-induced neuroinflammation and cognitive impairment.

overall_design: Sepsis was established in male C57BL/6J mice by intraperitoneal injection of 5 mg/kg lipopolysaccharide, and the function of meningeal lymphatic drainage was assessed. Adeno-associated virus 1-vascular endothelial growth factor C (AAV1-VEGF-C) was injected into the cisterna magna to induce meningeal lymphangiogenesis. Ligation of deep cervical lymph nodes (dCLNs) was performed to induce pre-existing meningeal lymphatic dysfunction. Cognitive function was evaluated by a fear conditioning test, and inflammatory factors were detected by enzyme-linked immunosorbent assay.

first: Xiaonan

last: Dai

first: Yin

last: Zhou

first: Wenjie

last: Jin


title: B cell-intrinsic STAT3-mediated interferon suppression during murine gammaherpesvirus 68 infection revealed through in vivo competition model.[ccbr1030_Stat3_2021]

summary: RNA-sequencing from sorted B cells of d16 infected mixed bone marrow chimeras. Non-GC, GC uninfected, and GC infected samples of STAT3 WT and STAT3 KO B cells from 3 independent mixed bone marrow chimera experiments.

overall_design: 25,000 STAT3 WT or STAT3 KO non-germinal center and germinal center B cells, of which GC cells were both uninfected and infected with MHV68 (YFP+) were sorted, followed by RNA sequencing. Three independent experiments, infected GC samples had 2x samples per expeirment, for a total of 24 samples (3 of which failed QC).

first: Chad

middle: H

last: Hogan

middle: J

first: Laurie

last: Krug


title: RNA-seq of epithelial cells flow-sorted from PDAC tumors derived from the orthotopic transplantation of PDAC T-LOH KPC organoids with either Egfr WT PSCs or Egfr KO PSCs in NSG mice

city: CAMBRIDGE

first: Giulia

last: Biffi

state: Cambridgeshire

address: Cancer Research UK, Robinson Way

country: United Kingdom

institute: University of Cambridge

summary: We investigated differences in epithelial cells flow-sorted from PDAC tumors derived from the orthotopic transplantation of PDAC T-LOH KPC organoids with either Egfr WT PSCs or Egfr KO PSCs

overall_design: Comparative gene expression of epithelial cells flow-sorted from PDAC tumors derived from the orthotopic transplantation of PDAC T-LOH KPC organoids with Egfr WT PSCs compared to epithelial cells flow-sorted from PDAC tumors derived from the orthotopic transplantation of PDAC T-LOH KPC organoids with Egfr KO PSCs

first: Gianluca

last: Mucciolo

first: Muntadher

last: Jihad


title: RNA-seq analysis of CAFs and epithelial cells flow-sorted from PDAC tumors derived from the orthotopic transplantation of PDAC T-LOH KPC organoids in C57BL/6J mice following 2-week treatment with Neratinib or vehicle

summary: We investigated changes in CAFs and epithelial cells flow-sorted from PDAC tumors derived from the orthotopic transplantation of PDAC T-LOH KPC organoids in C57BL/6J mice following 2-week treatment with Neratinib compared to vehicle

overall_design: We compared CAFs flow-sorted from PDAC tumors following 2-week treatment with Neratinib compared to CAFs flow-sorted from PDAC tumors following 2-week treatment with vehicle. We also compared epithelial cells flow-sorted from PDAC tumors following 2-week treatment with Neratinib compared to epithelial cells flow-sorted from PDAC tumors following 2-week treatment with vehicle


title: RNA-seq comparison of CD90- myCAFs and CD90+ myCAFs flow-sorted from murine PDAC tumors derived from the orthotopic transplantation of PDAC KPC T-LOH organoids

summary: We investigated differences between CD90- myCAFs and CD90+ myCAFs flow-sorted from murine PDAC tumors derived from the orthotopic transplantation of PDAC KPC T-LOH organoids

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD90- myCAFs compared to CD90+ myCAFs from murine PDAC tumors derived from the orthotopic transplantation of PDAC KPC T-LOH organoids. 10 matched samples in total (5 male mice)


title: MAFB-binding sites by ChIP-Seq on human M-CSF derived macrophages

city: Madrid

first: Miguel

last: Vega

address: Ramiro de Maeztu 9

country: Spain

institute: CIB (CSIC)

summary: We report the the genome-wide profiling of MAFB-binding sites by ChIP-Seq on M-MØ from two independent donors

overall_design: Examination of MAFB-binding sites in M-CSF derived macrophages.

first: Miriam

last: Simón-Fuentes

first: Angeles

last: Domínguez-Soto

first: Angel

middle: L

last: Corbí


title: Unraveling the role of sex in endothelial cell dysfunction – Evidence from lineage tracing mice and cultured cells

city: Cleveland

first: Olga

last: Cherepanova

state: OHIO

address: 9620 Carnegie Ave N Bldg

department: Cardiovascular and Metabolic Science

institute: Cleveland Clinic Lerner Research Institute

summary: Background: Biological-sex differences play a vital role in cardiovascular diseases, including atherosclerosis. The endothelium is a critical contributor to cardiovascular pathologies since endothelial cells (EC) regulate vascular tone, redox balance, and inflammatory reactions. Although EC activation and dysfunction play an essential role in the early and late stages of atherosclerosis development, little is known about sex-dependent differences in EC. Methods: We used aortic EC that was isolated from 13-week-old female and male mice as well as EC-lineage tracing (Cdh5-CreERT2 Rosa-YFP) atherosclerotic Apoe‒/‒ mice to investigate the biological sexual dimorphism of the EC functions in vitro and in vivo. RNA sequencing (RNAseq) analyses were performed on male and female mouse aortic EC and human lung EC. Results: In vitro, female mouse aortic EC (F_MAEC) showed more apoptosis and higher cellular ROS levels, lower mitochondrial membrane potential (ΔΨm), and lower levels of mitochondrial transcription factor A (TFAM) than male aortic EC (M_MAEC). Additionally, F_MAEC had decreased angiogenic potential (tube formation, cell viability, and proliferation) compared to M_MAEC. In vivo, female mice had significantly higher lipid accumulation within the aortas, less efficient outward vessel remodeling, and lower endothelial-mediated vasorelaxation than males. Using the EC-lineage tracing approach, we found that female lesions had significantly lower rates of intraplaque neovascularization and Endothelial-to-Mesenchymal (EndoMT) transition within advanced atherosclerotic lesions but higher incidents of missing EC lumen coverage and higher levels of oxidative products and apoptosis. RNAseq analyses revealed that both mouse and human female EC had higher expression of genes associated with inflammation and apoptosis and lower expression of genes related to angiogenesis and oxidative phosphorylation than male EC. Conclusions: Our study delineates critical sex-specific differences in EC relevant to pro-inflammatory, pro-oxidant, and angiogenic characteristics, which are entirely consistent with a vulnerable phenotype in females. Our results provide a biologic basis for sex-specific pro-atherosclerotic mechanisms.

overall_design: To investigate the sexual dimorphism of endothelial cells, we isolated endothelial cells from male and female mouse aortas. We established mouse aortic primary cultured endothelial cells. We then performed gene expression profiling analysis of RNA-seq data for sexual dimorphism of endothelial cells.

first: Junchul

last: Shin


title: Analysis of plasma small RNAs prior to breast cancer diagnosis

city: L'Hospitalet del llobregat

first: Miquel Angel

last: Pujana

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals

department: ProCURE

institute: Catalan Institute of Oncology IDIBELL

summary: Overabundance of circulating RNY transcripts and fragments has been associated with cancer. Here we analyzed the levels of RNYs in plasma collected from women before developing breast cancer and compared the results to matched controls that remained unaffected. Using small RNA-seq, two cohorts were analyzed: a cohort of women carriers of pathogenic variants in BRCA1 and BRCA2, and diagnosed with breast cancer as a first neoplasm within a period of < 12 months after blood test (n = 11), or that provided a blood sample at a similar age and remained unaffected (n = 13); and a cohort from a long-term prospective study, and comprising 8 sporadic breast cancer cases (diagnosed in a period of < 12 months after blood test) and 8 controls matched for individual and epidemiological variables

overall_design:
To investigate the basal levels of RNY transcripts and fragments in plasma of women that developed breast cancer and compare the results to women that remained cancer-free
**RAW data will be uploaded to dbGAP**

first: Joanna

last: Palade

first: Eric

last: Alsop

first: Kendall

last: Jensen

first: Francesca

last: Mateo

first: Rafael

last: de Cid

first: Miquel


title: B cell-intrinsic STAT3-mediated interferon suppression during murine gammaherpesvirus 68 infection revealed through in vivo competition model.[ccbr1030_Stat3_2019]

first: Thomas

last: Meyer

summary: RNA-sequencing from sorted B cells of d16 infected mixed bone marrow chimeras. GC uninfected and GC infected samples of STAT3 WT and STAT3 KO B cells from 3 independent mixed bone marrow chimera experiments.

overall_design: 20,000 STAT3 WT or STAT3 KO germinal center B cells both uninfected and infected with MHV68 (YFP+) were sorted, followed by RNA sequencing. Three independent experiments, for a total of 12 samples.

first: Chad

last: Hogan

first: Laurie


title: Lsr2, a pleiotropic regulator at the core of the infectious strategy of Mycobacterium abscessus

city: Montigny-le-Bretonneux

first: Frédéric

last: Crémazy

address: 2 avenue de la source de la Bièvre

institute: UVSQ/INSERM


title: Lsr2, a pleiotropic regulator at the core of the infectious strategy of Mycobacterium abscessus [ChIP-seq]

summary: Mycobacterium abscessus (Mabs) is a fast-growing, non-tuberculous mycobacterium responsible for serious lung infections in patients with cystic fibrosis. This bacterium evolves during the pulmonary infection between a smooth (S) and a rough morphotype (R). We have previously isolated the lsr2 gene as being differentially expressed during the transition between Mabs-S and Mabs-R. lsr2 encodes a pleiotropic transcription factor belonging to the superfamily of nucleoid-associated proteins (NAPs), which play an essential role in the hierarchical organization of bacterial chromosomes. The present study aims to unravel the molecular role of Lsr2 in regulating expression of gene involved in the adaptation and the pathobiology of Mabs using both RNA-Seq and ChIP-seq.

overall_design: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) performed on Mabs-S and Mabs-R strains both expressing FLAG-tagged Lsr2 proteins, obtained using homologous recombination.

first: Elias

last: Gerges

first: María

last: del Pilar Rodríguez-Ordoñez

first: Nicolas

last: Durand

first: Jean-Louis

last: Herrmann


title: Lsr2, a pleiotropic regulator at the core of the infectious strategy of Mycobacterium abscessus [RNA-seq]

overall_design: We performed RNA-seq on Mabs-S and Mabs-R Lsr2 mutant and WT strains and conduct a differential gene expression analysis using RNA-seq to identify Lsr2-regulated targets.


title: RNA-Seq of flow-sorted Egfr WT or Egfr KO pancreatic stellate cells (PSCs) and flow-sorted pancreatic tumor organoids following co-culture.

first: Giulia

last: Biffi

summary: We investigated changes in transcriptome in Egfr KO PSCs co-cultured with pancreatic tumor organoids compared to Egfr WT PSCs co-cultured with the same pancreatic tumor organoids. We also investigated the changes in transcriptome in pancreatic tumor organoids co-cultured with Egfr WT or Egfr KO PSCs.

overall_design: 23 samples in total. Comparative gene expression profiling analysis of RNA-seq data for flow-sorted Egfr KO PSCs co-cultured with pancreatic tumor organoids compared to flow-sorted Egfr WT PSCs co-cultured with the same pancreatic tumor organoids. 12 samples were analyzed (n=4 WT; n=8 KO). Comparative gene expression profiling analysis of RNA-seq data for flow-sorted pancreatic tumor organoids co-cultured with Egfr WT PSCs or Egfr KO PSCs. 11 samples were analyzed (n=4 WT; n=7 KO).

first: Joaquín

last: Araos Henriquez

first: Gianluca

last: Mucciolo

first: Muntadher

last: Jihad


title: Gene expression profile at single nucleus level of the generated neural concentroids with or without vascularization

first: Yoke Chin

last: Chai

state: Leuven

address: Herestraat 49, ON5

department: Development & Regeneration

summary: We generated homogeneous neural constructs called neural concentroids. We used single nucleus RNA sequencing (snRNA-seq) to analyze the diversity of brain cell types in the neural concentroids with or without the incorporation of hiPSC-derived endothelial cells as an effect of vascularization

overall_design: Cell nuclei were isolated by in-house protocols and analyzed using snRNAseq.

first: Yoke

middle: C

first: San

last: To

first: Susan

last: Simorgh

first: Samantha

last: Zaunz

first: YingLi

last: Zhu

first: Karan

last: Ahuja

first: Alix

last: Lemaitre

first: Roya

last: Ramezankhani

first: Bernard

last: van der Veer

first: Keimpe

last: Wierda

first: Stefaan

last: Verhulst

first: Leo

last: van Grunsven

first: Vincent

last: Pasque

first: Catherine

last: Verfaillie


title: Phosphorylation of RPT6 controls its ability to bind DNA and regulate gene expression in the hippocampus during memory formation

city: Blacksburg

first: Timothy

last: Jarome

state: VA

address: 175 W Campus Dr

institute: Virginia Polytechnic Institute and State University

summary: We used RNA-sequencing along with novel genetic approaches and biochemical, molecular, and behavioral assays to test the hypothesis that pRPT6-S120 functions independently of the proteasome to bind DNA and regulate gene expression during memory formation. RNA-sequencing following siRNA-mediated knockdown of free RPT6 revealed 46 gene targets  in the dorsal hippocampus of male rats following fear conditioning, where RPT6 was involved in transcriptional activation and repression. Through CRISPR-dCas9-mediated artificial placement of RPT6 at a target gene promoter, we found that RPT6 DNA binding alone was sufficient for altering gene expression following learning. Further, CRISPR-dCas13-mediated conversion of S120 to glycine on RPT6 revealed that phosphorylation at S120 is necessary for RPT6 to bind DNA and properly regulate transcription during memory formation. Together, we reveal a novel function for phosphorylation of RPT6 in controlling gene transcription during memory formation.

overall_design: Male Sprague-Dawley rats were injected into the dorsal hippocampus CA1 region with Accell siRNA against Psmc5 or control (Scr-siRNA). Five days later animals were trained to contextual fear conditioning and the CA1 region (dorsal) was dissected, RNA collected via columns and used for RNA-seq analysis

first: Kayla

last: Farrell

first: Aubrey

last: Auerbach

first: Madeline

last: Musaus

first: Shaghayegh

last: Navabpour

first: Yu

last: Lin

first: Hehunag

last: Xie


title: Cotton (Gossypium barbadense) root transcriptional response to Fusarium oxysporum f.sp. vasinfectum (FOV) race 4 (FOV4) infection

city: Lubbock

first: Mauricio

last: Ulloa

state: Texas

address: 3810 4th Street

department: PA, CSRL

institute: USDA-ARS

summary: We performed RNA-seq analysis of the root transcriptional response to Fusarium oxysporum f.sp. vasinfectum (FOV) race 4 (FOV4) infection in Gossypium barbadense, also known as Pima cotton. Susceptible Gossypium barbadense inbred lines Pima S-7 (PI 560140) and Pima 3-79 susceptible to Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV)] race 4 (FOV4), and Pima S-6 (PI 608346) which is resistant to FOV4 infection, were used for the preparation of cDNA libraries and further RNA-seq analyses. An isolate of FOV4 (FOV CA-14) from a naturally infested field in Fresno County in the San Joaquin Valley, California was used in this study.

overall_design: Susceptible Gossypium barbadense inbred lines Pima S-7 (PS7) and Pima 3-79 (P379) susceptible to FOV4 and Pima-S6 (PS6), resistant to FOV4, were used for the preparation of cDNA libraries/RNAseq analyses. An isolate of FOV4 (FOV CA-14) from a naturally infested field in Fresno County in the San Joaquin Valley, California was used in this study. We used no inoculation for control plants, three replicates for FOV4-inoculated and non-inoculated control, respectively. Cultures from single spores were stored on filter paper at -20oC. To produce inoculum, the isolate was grown in 9-cm-diameter Petri dishes containing 20 ml potato dextrose agar (PDA) with 3 mM streptomycin per liter at room temperature for 1 week. Then a few patches of 2-3-mm-squre of fresh grown culture were cut and put into 500 ml flasks containing potato dextrose liquid medium with 3 mM streptomycin at 28 C with rotation for 3-4 days.  The conidial suspension was then filtered through eight layers of cheesecloth to remove hyphae, quantified with the aid of a hemacytometer, and diluted with water to obtain 1 x 10^6 conidia per ml. Cultivars or genotypes were germinated in seedling trays for one week and then seedlings were uprooted. Roots were rinsed with tap water and immediately dipped for 3 min into an aqueous suspension of FOV4 inoculum containing 1 x 10^6 conidia per ml. The non-inoculated control plants were processed the same way except they were dipped into water without FOV4. Seedlings were then transplanted into steam-sterilized U.C. Mix #2 (Baker, 1957) soil in new pots with five plants in each pot and placed in a warm greenhouse maintained between 24-28 degrees Celcius. At 11 days after inoculation (dai), the plant and soil ball were removed from the pots, and the soil removed gently from roots by washing under continuous water flow. The washed roots were placed immediately in 50ml screw-top plastic vials, liquid nitrogen was added, and the vials placed in a -80o C freezer with the tops off to allow vaporization of the liquid N.

first: Damar

last: López-Arredondo

first: Jonathan

middle: O

last: Ojeda-Rivera

first: Luis

last: Herrera-Estrella


title: Effect of  homoharringtonine and Rocaglamide A on synchronized AC16 cells

city: Lille

first: Alexandre

last: Berthier

address: U1011, Bâtiment J&K, Bd du Pr Leclerc

institute: Inserm

summary:
Transcriptomic analysis of synchonized AC16 cells treated with homoharringtonine 1 µM or Rocaglamide A 100 nM for 4h (20h after synchronization)
We used microarrays to detail the global programme of gene expression

overall_design: control (DMSO) was analysed in triplicats. Numbers of Replicats for treatment were n=4 for homoharringtonine and n=3 for Rocaglamide A

first: Céline

last: Gheeraert

first: Philippe

last: Lefebvre


title: Transcriptomic profiles of synchronized AC16 cells after a kinetic  exposition to digoxin

summary:
Transcriptomic analysis of synchonized AC16 cells after 0-6-12-18 or 24 h of digoxin treatment (5µM)
We used microarrays to detail the global programme of gene expression

overall_design: All conditions were analyzed in triplicats


title: RNA-Seq comparison of pancreatic stellate cells (PSCs) cultured with control media, TGF-beta, pancreatic tumor organoid conditioned media or pancreatic tumor organoid conditioned media in the presence of ERBBi (neratinib)

first: Giulia

last: Biffi

summary: We investigated the role of ERBB signaling in PSCs cultured with TGF-beta (myCAFs) or pancreatic tumor organoid conditioned media (with or without ERBBi) compared to PSCs cultured with control media (quiescent PSCs)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  in PSCs cultured with TGF-beta (myCAFs) or pancreatic tumor organoid conditioned media (with or without ERBBi) compared to PSCs cultured with control media (quiescent PSCs). 17 samples total (4-5 replicates per condition) were analyzed.

first: Joaquín

last: Henriquez

first: Gianluca

last: Mucciolo

first: Muntadher

last: Jihad


title: Variants in ZFX Cause an X-linked Neurodevelopmental Disorder with Recurrent Facial Gestalt

city: Los Angeles

first: Peggy

last: Farnham

state: California

address: 1450 Biggy St

department: Biochemistry and Molecular Biology

institute: USC Keck School of Medicine

summary: Pathogenic variants in multiple X-linked genes have been implicated in syndromic and non- syndromic intellectual disability disorders. The gene ZFX on Xp22.11 encodes a transcription factor that has been linked to diverse processes including oncogenesis and development, but germline variants have not previously been reported in association with disease. Here, we present clinical and molecular characterization of 18 patients with germline ZFX variants. Exome or genome sequencing revealed 11 variants in 18 subjects (14 males and 4 females) from 16 unrelated families. Four missense variants were identified in 11 subjects, with seven frameshift variants in the remaining individuals. Clinical findings included developmental delay/intellectual disability, behavioral abnormalities, hypotonia, and congenital anomalies. Overlapping and recurrent facial features were identified in all subjects, including thickening and medial broadening of eyebrows, variations in the shape of the face, external eye abnormalities, smooth and/or long philtrum and ear abnormalities. Hyperparathyroidism was found in 4 families with missense variants and enrichment of different types of tumors was also observed. In molecular studies, variants in the DNA-binding domain demonstrated differential expression of target genes relative to wild-type ZFX in cultured cells, suggesting a gain or loss of transcriptional activity. Additionally, a zebrafish model of ZFX loss displayed an altered behavioral phenotype, supporting the pathogenicity of predicted loss- of-function frameshift variants. Our clinical and experimental data support that variants in ZFX cause a novel X-linked intellectual disability syndrome characterized by a recurrent facial gestalt, neurocognitive and behavioral abnormalities, and an increased risk for congenital anomalies and hyperparathyroidism.

overall_design: RNA-seq and ChIP-seq in HEK293T Kidney Cells and ZFX/ZNF711 Knockout HEK293T Kidney Cells

first: Charles

last: Nicolet

first: Shannon

last: Schreiner

first: Marwan

last: Shinawi

first: James

last: Shepherdson

first: Katherine

last: Hutchison


first: Cheol-Hee

last: Kim


title: Non-Canonical Hedgehog Signaling Mediates Profibrotic Hematopoiesis-Stroma Crosstalk in Myeloproliferative Neoplasms

city: Rotterdam

first: Jessica

last: Pritchard

address: Dr. Molewaterplein 40

institute: Erasmus MC

summary: We sorted lineage negative hematopoietic cells from mice previously transplanted with WT or Gli1 knockout bone marrow in both control and fibrosis settings. Cells were  via magnetic depletion and facs sorting and performed scRNAseq on them. We identified 13 hematopoetic cells clusters across all lineages and one non-hematopoietic stromal cell cluster

overall_design: We used scRNA 3' RNA sequencing product from 10x Genomics to investigate the role of hematopoietic Gli1 in Jak2V617F-induced myelofibrosis

first: Juliette

last: Pearce

first: Fabian

last: Peisker

last: Nagai

first: Vanessa

last: Krämer

first: Monica

last: Hannani

first: Ivan

middle: G

last: Costa

first: Rafael

last: Kramann

first: Rebekka

last: Schneider


title: Single-cell reconstruction of molecular architecture in myocardial ischemia-reperfusion injury by multiplexed in situ protein profiling [RNA]

city: Beijing

first: Wang

last: Li

address: 167 Beilishi Rd

department: State Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences

summary: Rationale: Reperfusion therapy is critical to myocardial salvage in the event of a myocardial infarction, but is complicated by ischemia-reperfusion injury (IRI). Limited understanding of the spatial organization of cardiac cells, which governs cellular interaction and function, has hindered the search for targeted intervention minimizing the deleterious effects of IRI.  Methods: We used imaging mass cytometry (IMC) to characterize the spatial distribution and dynamics of cell phenotypes and communities in the mouse left ventricle following IRI. Heart sections were collected from 12 cardiac segments (basal, mid-cavity, apical and apex of the anterior, lateral and inferior wall) and 8 time points (prior to ischemia (I-0h, and post reperfusion (R-0h, -2h, -6h, -12h, -1d, -3d, -7d)), and stained with 29 metal-isotope-tagged antibodies. Cell community analysis was performed on reconstructed images, and the most disease-relevant cell type and target protein was selected for intervention of IRI.  Results: We obtained a total of 251 multiplexed images, and identified 197,063 single cells, which were grouped into 23 distinct cell communities based on the structure of cellular neighborhoods. The cellular architecture was heterogeneous throughout the ventricular wall, and exhibited swift changes following IRI. Analysis of proteins with post-translational modifications (PTMs) in single cells unveiled 13 PTM intensity clusters, and highlighted increased H3K9me3 as a key regulatory response in endothelial cells during the middle stage of IRI. Erasing H3K9 methylation, by silencing its methyltransferase Suv39h1 or overexpressing its demethylase Kdm4d, in isolated endothelial cells (EC) attenuated cardiac dysfunction and pathological remodeling, compared to PBS and unmodified EC control, when injected into the infarcted area of the myocardium.

overall_design: The endothelial cells  were isolated from mouse heart tissues and then were treated with low oxygen (hypoxia), and untreated cells as contol (normoxia). The hyoxia treated cells were then split into two addtional groups to overexpress Kdm4d or supress Suv29h1 via lentivius infection. Th H3K9me3 ChIPseq  were performed and input as contol.

first: Luyan

last: Yao

first: Funan

last: He

first: Quanyi

last: Zhao

first: Dandan

first: Shufang

last: Fu

first: Mingzhi

last: Zhang

first: Xingzhong

first: Bingying

last: Zhou

first: Li

last: Wang


title: Single-cell reconstruction of molecular architecture in myocardial ischemia-reperfusion injury by multiplexed in situ protein profiling [ChIP]


title: Identification of direct connections between the dura and the brain [young + aged]

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: The arachnoid barrier delineates the border between the central nervous system and dura mater. Although the arachnoid barrier creates a partition, communication between the central nervous system and the dura mater is crucial for waste clearance and immune surveillance. How the arachnoid barrier balances separation and communication is poorly understood. Leveraging transcriptomic data, we developed novel transgenic mice to examine specific anatomical structures that serve as routes across the arachnoid barrier. Bridging veins create discontinuities where they cross the arachnoid barrier, forming structures that we termed arachnoid cuff exit (ACE) points. The openings that ACE points create allow the exchange of fluids and molecules between the subarachnoid space and the dura, enabling the drainage of cerebrospinal fluid and limited entry of molecules from the dura to the subarachnoid space. In healthy human volunteers, MRI tracers transit along bridging veins in a similar fashion to access the subarachnoid space. Interestingly, in neuroinflammatory conditions such as experimental autoimmune encephalomyelitis, ACE points also allow cellular trafficking, representing a previously unknown route for immune cells to directly enter the subarachnoid space from the dura mater. Collectively, our results indicate that ACE points are a critical part of the anatomy of neuroimmune communication in both mice and humans that links the central nervous system with the dura and its immunological diversity and waste clearance systems.

overall_design: Young (2-3 months) and aged (20 months) cranial leptomeninges were microdissected and placed into 50 uL nuclei isolation medium (NIM: 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, 1 mM DTT, 1 U/mL RNase inhibitor (Takara, 2313B), protease inhibitor (1 tablet/10 mL; Thermo, A32955). Leptomeninges were chopped on ice for 10 minutes, before the volume was increased to 1 mL with NIM. Samples were then passed 10 times through a 2 mL dounce homogenizer with pestle A, then 10 times with pestle B. Nuclei were passed through a 20 um strainer, mashed with a glass pestle, and washed through two times with 0.5 mL NIM. Nuclei were spun at 1000 x g for 5 minutes at 4 oC, and resuspended in 1 % ultrapure nuclease-free BSA (Invitrogen, AM2616) in PBS with RNase inhibitor (1 U/mL) and DAPI (100 nM). Fluorescence-activated cell sorting was performed on nuclei based on forward and side scatter, and DAPI signal. Nuclei were then spun at 1500 x g for 5 minutes at 4 oC, and resuspended in 1 % ultrapure nuclease-free BSA (Invitrogen, AM2616) in PBS with RNase inhibitor (1 U/mL) to a concentration of 1500 nuclei/uL. The sorted nuclei were loaded onto a 10X Genomics Chromium platform for GEM and cDNA generation carrying cell- and transcript-specific barcodes and sequencing libraries constructed using the Chromium Single Cell 3′ Library & Gel Bead Kit v3. Libraries were sequenced on the Illumina NovaSeq6000, targeting a depth of 100,000 reads per cell.

first: Leon

last: Smyth

first: Taitea

last: Dykstra


title: Single-cell reconstruction of molecular architecture in myocardial ischemia-reperfusion injury by multiplexed in situ protein profiling

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

overall_design: Refer to individual Series


title: Identification of direct connections between the dura and the brain


title: Identification of direct connections between the dura and the brain [EAE]

overall_design: EAE was induced in mice by subcutaneous injection of MOG35–55 peptide (200 μg, CSBio) emulsified in Freund’s adjuvant (Sigma Aldrich) supplemented with 4 mg/mL of Mycobacterium tuberculosis (BD) into each flank. Pertussis toxin (200 ng, List Biologicals) was injected i.p. on day 0 and day 2 after MOG immunization. Controls were treated similarly, but MOG peptide was excluded. At peak disease (day 16), cranial leptomeninges were microdissected and placed into 50 uL nuclei isolation medium (NIM: 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, 1 mM DTT, 1 U/mL RNase inhibitor (Takara, 2313B), protease inhibitor (1 tablet/10 mL; Thermo, A32955). Leptomeninges were chopped on ice for 10 minutes, before the volume was increased to 1 mL with NIM. Samples were then passed 10 times through a 2 mL dounce homogenizer with pestle A, then 10 times with pestle B. Nuclei were passed through a 20 um strainer, mashed with a glass pestle, and washed through two times with 0.5 mL NIM. Nuclei were spun at 1000 x g for 5 minutes at 4 oC, and resuspended in 1 % ultrapure nuclease-free BSA (Invitrogen, AM2616) in PBS with RNase inhibitor (1 U/mL) and DAPI (100 nM). Fluorescence-activated cell sorting was performed on nuclei based on forward and side scatter, and DAPI signal. Nuclei were then spun at 1500 x g for 5 minutes at 4 oC, and resuspended in 1 % ultrapure nuclease-free BSA (Invitrogen, AM2616) in PBS with RNase inhibitor (1 U/mL) to a concentration of 1500 nuclei/uL. The sorted nuclei were loaded onto a 10X Genomics Chromium platform for GEM and cDNA generation carrying cell- and transcript-specific barcodes and sequencing libraries constructed using the Chromium Single Cell 3′ Library & Gel Bead Kit v3. Libraries were sequenced on the Illumina NovaSeq6000, targeting a depth of 100,000 reads per cell.


title: OCA-B/Pou2af1 is sufficient to promote CD4 memory and prospectively identifies memory precursors

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

institute: University of Utah


first: Peggy

last: Farnham


title: HEXIM1 Overexpression Alters GATA1 Activity and Promotes Fetal Globin Expression

city: Rochester

first: Laurie

last: Steiner

state: New York

address: 601 Elmwood Ave

institute: University of Rochester

summary: Erythropoiesis is a highly organized process whereby multipotent HSCs become committed to the erythroid linage and mature into enucleate erythrocytes. Recent work from our lab demonstrated that HEXIM1 is essential in the regulation of erythroid proliferation, viability and gene expression, and also promotes the expression of GATA1 target genes. New analyses of HEXIM1 overexpression (OE) in HUDEP2 cells revealed a significant increase of gamma globin production, with a higher proportion of cells expressing fetal hemoglobin. To gain insights into the mechanisms underlying the increased fetal globin expression, we performed CUT&RUN assays for Ser5 phosphorylated and total RNPII in HEXIM1 OE and control cells. Surprisingly, OE of HEXIM1 had only modest impacts on RNPII pausing, but instead lead to changes in the genes occupied by RNPII. Our results support a model where elevated HEXIM1 levels promote the pioneer activity of GATA1, and facilitate the expression of a fetal transcriptional program in adult cells in a pTEFb-dependent manner.

overall_design: CUT&RUN assays for total and Ser5 phophorylated RNA Polymerase II, and GATA1 in HUDEP-2 cells. CUT&RUN assays for HEXIM1 and ATAC-seq in HUDEP-2 cells.

first: Xiurui

last: Lv

first: Kristin

last: Murphy

first: Zachary

first: Getman

last: Michael


title: Interleukin-17-Mediated Protective Cytokine Signaling Against Degeneration of the Retinal Pigment Epithelium

status: Public on Nov 29 2023

city: OKLAHOMA CITY

first: Jiyang

last: Cai

state: OK

address: 940 STANTON L YOUNG BLVD OUHSC

department: Physiology

institute: UNIVERSITY OF OKLAHOMA HEALTH SCIENCES CENTER

summary: Injuries to the retinal pigment epithelium (RPE) and outer retina often result in the accumulation of retinal microglia within the subretinal space. These subretinal microglia play crucial roles in inflammation and resolution, but the mechanisms governing their functions are still largely unknown. Our previous research highlighted the protective functions of choroidal gd T cells in response to RPE injury. In the current study, we employed single-cell RNA sequencing approach to delve deeper into the mechanisms involved. We found that gd T cells were the primary producer of interleukin-17 (IL-17) in the choroid. IL-17 signaled through its receptor on the RPE, subsequently triggering the production of interleukin-6 (IL-6). This cascade of cytokines initiated a metabolic reprogramming of subretinal microglia, enhancing their capacity for lipid metabolism. RPE-specific knockout of IL-17 receptor A led to the dysfunction of subretinal microglia and RPE pathology. Collectively, our findings suggest that responding to RPE injury, the choroidal gd T cells can initiate a protective signaling cascade that ensures the proper functioning of subretinal microglia.

overall_design: CD45+ cells from mouse choroid were sorted by flow cytometry and analyzed by scRNA-seq

first: Chen

last: Yan

first: Bounds

last: Sarah E

first: Ma

last: Xiang

first: Karmoker

last: Jame Regun

first: Liu

last: Yin

last: Jian-Xing

first: Cai

last: Jiyang


title: Ten-eleven translocation (Tet) methylcytosine dioxygenases dependent viral DNA demethylation mediates in vivo hepatitis B virus (HBV) biosynthesis

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

type: Methylation profiling by high throughput sequencing

summary: Liver-specific ten-eleven translocation methylcytosine dioxygenases 2 and 3 (Tet2 plus Tet3)-deficient hepatitis B virus (HBV) transgenic mice fail to support viral biosynthesis.  The levels of viral transcription and replication intermediates are dramatically reduced.  Hepatitis B core antigen (HBcAg) is only observed in a very limited number of pericentral hepatocytes in a pattern that is similar to glutamate-ammonia ligase (Glul), a -catenin target gene.  HBV transcript abundance in Tet-deficient mice resembles that observed in wild-type neonatal mice.  Furthermore, the RNA levels of several -catenin target genes including Glul, Lhpp, Notun, Oat, Slc1a2 and Tbx3, in Tet-deficient mice was also similar to that observed in wild-type neonatal mice.  As HBV transcription is regulated by -catenin, these finding support the suggestion that neonatal Tet-deficiency might limit -catenin target gene expression, limiting viral biosynthesis.  Additionally, HBV transgene DNA displays increased 5-methylcytosine (5mC) frequency at CpG sequences consistent with neonatal Tet-deficiency being responsible for decreased developmental viral DNA demethylation mediated by 5mC oxidation to 5-hydroxymethylcytosine (5hmC), a process that might be responsible for the reduction in cellular -catenin target gene expression and viral transcription and replication.

overall_design: Liver-specific Tet2-delete, Tet3-deleted and Tet2 plus Tet3-deleted HBV transgenic mice were generated and characterized to determine the role for Tet enzymes in the liver-specific demethylation of HBV transgene DNA which is associated with viral biosynthesis in this model of chronic infection.

first: Rachel

last: Matrenec

first: Claudia

last: Oropeza

first: Eddie

last: Dekoven

first: Grant

last: Tarnow

first: Cecilia

last: Chau

first: Stefan

last: Green

first: Alan

last: McLachlan


title: OCA-B/Pou2af1 is sufficient to promote CD4+ T cell memory and prospectively identifies memory precursors [bulk RNA-Seq]

first: Dean

last: Tantin

summary: Sun et al. use T cell conditional knockout and ectopic expression to show that OCA-B is required for, and sufficient to promote, CD4+ memory T cell formation in vivo, and can be used to prospectively identify effector T cells with enhanced memory potential.

overall_design: CD4+ T cells were purified from female Ly5.1 SMARTA and Ly5.1/5.2 SMARTA mice, and separately transduced with pMIG-OCA-B or empty vector (EV), respectively. On the following day, transduced GFP+ cells were sorted, 20K of each combined 1:1, and injected intravenously into  C57BL/6J recipients mice. 24h later, each recipient mouse was injected intraperitoneally with 2x10^5 pfu LCMVArm. After eight days,CD4+GFP+Ly5.1+Ly5.2+ (EV) and GFP+Ly5.1+ (OCA-B-expressing) cells were sorted and used for RNA purification. Then RNA samples are applied for bulk RNAseq.

first: Wenxiang

last: Sun

first: Heejoo

last: Kim

first: Jelena

last: Perovanovic

first: Erik

last: Hughes


title: An Erratic Gene Expression Signature in Primary Hematopoietic Stem Cells: Implications for Interpretations of Aging

city: Lund

first: Anna

last: Konturek-Ciesla

address: Box 188

department: Department of Molecular Hematology

country: Sweden

institute: Lund University

summary: A decline in hematopoietic stem cell (HSC) function is believed to underlie hematological shortcomings with age, but a comprehensive molecular understanding of these changes is currently lacking. Here, we provide evidence that a transcriptional signature reported in several prior studies on HSC aging is linked to stress-induced changes in gene expression rather than aging. Our findings have strong implications for the design and interpretation of HSC aging studies.

overall_design: Single cell RNA-sequencing was performed to determine the immediate early response signature among hematopoietic stem and progenitor cells in response to different cell isolation protocols. The technology was coupled to cell hashing in order to measure the data simultaneously in samples treated with different conditions.

first: Rasmus

last: Olofzon

first: Shabnam

last: Kharazi

first: David

last: Bryder


title: Combined absence of Trp53 target genes Zmat3, Puma and p21 cause a high incidence of cancer in mice

status: Public on Nov 28 2023

city: Barcelona

first: Gerard

last: Romero

state: Catalonia

address: Doctor Aiguader, 88

department: Dpt of Medicine and Life Sciences, Universitat Pompeu Fabra (MELIS/UPF)

institute: Universitat Pompeu Fabra

summary: Transcriptional activation of target genes is essential for TP53-mediated tumour suppression, though the roles of the diverse TP53-activated target genes in tumour suppression remains poorly understood. Knockdown of Zmat3, an RNA-binding zinc-finger protein involved in regulating alternative splicing, in haematopoietic cells by shRNA caused leukaemia only with the concomitant absence of the Puma and p21, the critical effectors of Trp53-mediated apoptosis and cell cycle arrest respectively. We were interested to further investigate the role of ZMAT3 in tumour suppression beyond the haematopoietic system. Therefore, we generated Zmat3 knockout and compound gene knockout mice, lacking Zmat3 and p21, Zmat3 and Puma or all three genes. Puma-/-p21-/-Zmat3-/- triple knockout mice developed tumours at a significantly higher frequency compared to wild-type, Puma-/-Zmat3-/- or p21-/-Zmat3-/-deficient mice. Interestingly, we observed that the triple knockout and Puma-/-Zmat3-/- double deficient animals succumbed to lymphoma, while p21-/-Zmat3-/- animals developed mainly solid cancers.  This analysis suggests that in addition to ZMAT3 loss, additional TRP53-regulated processes must be disabled simultaneously for TRP53-mediated tumour suppression to fail. Our findings reveal that the absence of different TRP53 regulated tumour suppressive processes changes the tumour spectrum, indicating that different TRP53 tumour suppressive pathways are more critical in different tissues.

overall_design:
To investigate the impact of combined loss of Zmat3, Puma and p21 in Trp53-mediated tumour suppression we crossed Zmat3 -/- (ZKO) with Puma -/- p21 -/- mice to obtain Puma -/- p21 -/- Zmat3 -/- animals /TKOs).
Whole thymus from 8-12 week old mice were isolated and single cell suspension made by gentle mashing with a 70uL filter. 5 million cells were used for RNA extraction.
We then performed gene expression profiling using RNA-seq data
We were interested in the expression differences between Zmat3 KO mice and those with a triple KO (Zmat3, p21 & Puma). We also compared each of them to wild-type samples.

first: Margs

last: Brennan

first: Kerstin

last: Brinkmann

last: Sola

first: Geraldine

last: Healey

first: Leonie

last: Gibson

first: Lahiru

last: Gangoda

first: Maggie

last: Potts

first: Elizabeth

last: Lieschke

first: Stephen

last: Wilcox

first: Andreas

last: Strasser

first: Marco

last: Herold

first: Ana

last: Janic


title: OCA-B/Pou2af1 is sufficient to promote CD4+ T cell memory and prospectively identifies memory precursors [single cell RNA-Seq]

first: Dean

last: Tantin

overall_design: CD4+ T cells were purified from female Ly5.1 SMARTA and Ly5.1/5.2 SMARTA mice, and separately transduced with pMIG-OCA-B or empty vector (EV), respectively. On the following day, transduced GFP+ cells were sorted, 20K of each combined 1:1, and injected intravenously into  C57BL/6J recipients mice. 24h later, each recipient mouse was injected intraperitoneally with 2x105 pfu LCMVArm. After eight days,CD4+GFP+Ly5.1+Ly5.2+ (EV) and GFP+Ly5.1+ (OCA-B-expressing) cells were sorted and used for RNA purification. Then RNA samples are applied for bulk RNAseq.

first: Wenxiang

last: Sun

first: Heejoo

last: Kim

first: Jelena

last: Perovanovic

first: Erik

last: Hughes


title: N -acetyltransferase 10 Regulates Alphavirus Replication via the N4-acetylcytidine (ac4C) modiﬁcation of lymphocyte antigen six family member E (LY6E)

city: Xi'an

first: Yamei

last: Dang

state: Shaanxi

address: No.169 Changle West Road, Xincheng District,

institute: Fourth Military Medical University

summary: To investigate whether NAT10 manipulates SINV replication by regulating downstream mRNAs, we established a Huh7 cell line in which NAT10 was knocked down by shRNA.

overall_design: We performed gene expression profiling using data obtained from RNA-seq of normal cells infected with SINV as well as NAT10 knockdown cells.

first: Wei

last: Ye

first: Fanglin

last: Zhang


title: Single-cell transcriptomics reveals glial cells integrate homeostatic and circadian processes to drive sleep-wake cycle

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

institute: Vlaams Instituut voor Biotechnologie

summary: The sleep-wake cycle is determined by a circadian and a sleep homeostatic process. However, the molecular impact of these two processes and their interaction on different cell populations in the brain remain unknown. To fill this gap, we have profiled the single-cell transcriptome of adult fruit fly brains across the sleep-wake cycle and different circadian times. We show cell type-specific transcriptomic changes between sleep/wakefulness states, different levels of sleep drive, and varying circadian times, with glial cells displaying the largest variations. Furthermore, the cell types whose transcriptomic dynamics correlate with the sleep homeostat or circadian clock are largely non-overlapping, with the exception of glial cells. Diminishing the circadian clock only in glial cells impairs the homeostatic sleep rebound after sleep deprivation. These findings reveal a comprehensive picture of different effects of sleep homeostatic and circadian processes on different cell types and define glial cells as the interaction sites of these two processes to determine sleep-wake dynamics.

overall_design: Single-cell RNA-seq (10X Genomics) on adult Drosophila brain at different sleep, wake, sleep deprivation and Zeitgeber (ZT) times

first: Joana

last: Dopp

first: Antonio

last: Ortega

first: Suresh

last: Poovathingal

first: El-Sayed

last: Baz

first: Sha

last: Liu


title: Smith-specific regulatory T cells halt the progression of lupus nephritis

city: Clayton

first: Peter

last: Eggenhuizen

state: VIC

address: Monash Medical Centre, 246 Clayton Road

department: Medicine

country: Australia

institute: Monash University

summary: Antigen-specific regulatory T cells (Tregs) suppress pathogenic autoreactivity and are potential therapeutic candidates for autoimmune diseases such as systemic lupus erythematosus (SLE). Lupus nephritis is associated with autoreactivity to the Smith (Sm) autoantigen and the human leucocyte antigen (HLA)-DR15 haplotype; hence, we investigated the potential of Sm-specific Tregs (Sm-Tregs) to suppress disease. We identified a novel HLA-DR15 restricted immunodominant Sm T cell epitope using biophysical affinity binding assays, then identified high-affinity Sm-specific T cell receptors (TCRs) using high-throughput single-cell sequencing. Using lentiviral vectors, we transduced our lead Sm-specific TCR onto Tregs derived from patients with SLE who were anti-Sm and HLA-DR15 positive. Compared with polyclonal mock-transduced Tregs, Sm-Tregs potently suppressed Sm-specific pro-inflammatory responses in vitro and suppressed disease progression in a humanized mouse model of lupus nephritis. These results show that Sm-Tregs are a promising therapy for SLE.

overall_design: Co-cultures of human CD4+ T cells and mature dendritic cells pulsed with SmB/B'58-72 were FACS sorted based on CD4+ and CellTrace dye dilution to sort the proliferated T cells. After FACS sorting cells underwent 10x scRNASeq

first: Rachel

last: Cheong

first: Sarah

last: Snelgrove

first: Boaz

last: Ng

first: Janet

last: Chang

first: Yi

last: Ting

first: Julie

last: Monk

first: Khai

last: Loh

first: Cecilia

last: Lo

first: Ashraf

last: Broury

first: Elean

last: Tay

first: Chanjuan

last: Shen

first: Yong

last: Zhong

first: Jia

last: Chung

first: Rangi

last: Kandane-Rathnayake

last: Koelmeyer

first: Alberta

last: Hoi

first: Paolo

last: Manzanillo

first: Ashutosh

last: Chaudhry

first: Eric

middle: F

last: Morand

first: Joshua

middle: D

last: Ooi


title: RNA-seq analysis dataset: Cerebellum tissues from wild type and Dscam del17/del17 mice at P21

city: Okazaki

first: SHOJI

last: TATSUMOTO

address: Myodaiji

country: Japan

institute: The National Institutes of Natural Sciences NINS

summary: The cytoplasmic domain of DSCAM has been reported to exhibit transcriptional activity on genes involved in neuronal wiring in HEK293 cells. Thus, we addressed the possibility that deregulation of the CF synapse in Dscamdel17/del17 mice is caused by the reduced expression of CF synaptogenesis-related genes, by using RNA-seq analyses using the P21 whole cerebellum of WT and Dscamdel17/del17 mice. Expression levels of most of the genes, except for Nefl, Mal, Fat2, and Fat1, were not significantly different between the WT and Dscamdel17/del17 mice, probably because depletion of Dscam in the cerebellum affects only a few cell types, including Purkinje cells. We also confirmed the unchanged expression of Purkinje cell-specific genes (and their encoded proteins), such as Cacna1a (Cav2.1), Sema7a and Sema3a, Grm1 (mGluR1) and Prkcg (protein kinase Cγ [PKCγ]), Grid2 (GluD2), and Adgrb3 (Bai3) between the WT and Dscamdel17/del17 mice. These results raise the possibility that DSCAM in Purkinje cells regulates synapse formation and function, independently of the regulation of gene expression of known CF synaptogenesis-related genes.

overall_design: The mRNA profiles of the cerebellum tissues from five Dscamdel17/del17 homozygous mutant mice and five control mice at P21 were generated using the Illumina NovaSeq platform.

first: Mikio

last: Hoshino

first: Nariko

last: Arimura

first: Kenichi

last: Dewa

first: Yasuhiro

last: Go


title: Gene expression profile at single cell level of pre-cDCs from the bone marrow, spleen and lung of mice

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

institute: Francis Crick Institute

summary: Type 2 pre-cDCs are considered as a homogeneous population in the bone marrow. We used single cell RNA sequencing to show that  the bone marrow contains two subsets of pre-cDC2s that are commited  to give rise to different different cDC2 subsets in peripheral tissues.

overall_design: pre-cDCs from the bone marrow, spleen and lung of WT C57BL6 mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Carlos

last: Minutti

first: Caetano

last: Reis e Sousa


title: Single nucleus RNA-seq of the rhesus macaque nucleus accumbens after chronic morphine exposure

city: Pittsburgh

first: BaDoi

middle: Nguyen

last: Phan

state: PA

address: 5000 Forbes Ave

department: Computational Biology

institute: Carnegie Mellon University

summary: Chronic morphine exposure to rhesus macaque

overall_design: Four subjects (3 male, 1 female; mean age: 12 years, range: 9-18 years) received daily morphine treatment for 5 months (see below); four additional subjects, matched for age, weight, and sex, served as experimental controls (3 male, 1 female; mean age: 14 years, range: 11-21 years). Control subjects had a history of nicotine or cocaine exposure but were drug free for ~1 year prior to tissue collection.

middle: N

first: Ryan

middle: W

last: Logan

first: Andreas

middle: R

last: Pfenning

first: Robert

last: Fenster

first: Kerry

last: Ressler

first: Jack

last: Bergman


title: Gene expression profile of HBV-positive hepatocellular carcinoma.

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: Investigate the intrinsic molecular mechanisms of HBV-related HCCs by RNA-seq.

overall_design: Examination of RNA expression in HBV-positive HCCs.

first: S

last: Yeh

first: P

last: Chen


title: Functional Genomics of human pancreatic acinar and ductal cells

city: San Antonio

first: Pei

last: Wang

state: TX

address: 7703 Floyd Curl Dr

department: Cell Systems & Anatomy

institute: University of Texas Health San Antonio


title: Treatment of MM cells with non-targeting (NT) or ILF2 targeting oligonucleotide antisenses (ASOs)

city: Indianapolis

first: Caleb

middle: A

last: Class

state: IN

address: 4600 Sunset Ave

department: Pharmaceutical Sciences

institute: Butler University

summary: To gain insights into the molecular mechanisms by which myeloma cells overcome ILF2 ASO-induced DNA damage activation, we performed bulk RNA sequencing (RNA-seq) analysis of ASO-treated KMS11 and JJN3 cells at early (1 week) and late (3 weeks) treatment time points.

overall_design: MM cells were treated with NT (control) or ILF2 ASOs for 1 or 3 weeks to evaluate whether they could overcome ILF2 ASO-induced DNA damage. Three replicates were included for each.

first: Nat

last: Thongon

first: Simona

last: Colla


title: Transcriptional responses of the human dorsal striatum in opioid use disorder implicates cell type-specifc programs

summary: Gene expression profile at single cell level of striatal cells from the caudate nucleus and putamen in postmortem human brains of unaffected individuals or those with opioid use disorder.

overall_design: Case-cohort matched postmortem human brain single nucleus RNA-seq of the caudate nucleus and putamen of individuals with and without opioid use disorder

first: Madelyn

last: Ray


title: Single nuclei transcriptomics of human and monkey striatum implicates DNA damage, neuroinflammation, and neurodegeneration signaling in opioid use disorder

summary: The striatum in the brain is involved in various behavioral functions, including reward, and disease processes, such as opioid use disorder (OUD). Further understanding of the role of striatal subregions in reward behaviors and their potential associations with OUD requires molecular identification of specific striatal cell types in human brain. The human striatum contains subregions based on different anatomical, functional, and physiological properties, with the dorsal striatum further divided into caudate and putamen. Both caudate and putamen are associated with alterations in reward processing, formation of habits, and development of negative affect states in OUD. Using single nuclei RNA-sequencing of human postmortem caudate and putamen, we identified canonical neuronal cell types in striatum (e.g., dopamine receptor 1 or 2 expressing neurons, D1 or D2) and less abundant subpopulations, including D1/D2 hybrid neurons and multiple classes of interneurons. By comparing unaffected subjects to subjects with OUD, we found neuronal-specific differences in pathways related to neurodegeneration, interferon response, and DNA damage. DNA damage markers were also elevated in striatal neurons of rhesus macaques following chronic opioid administration. We identified sex-dependent differences in the expression of stress-induced transcripts (e.g., FKBP5) among astrocytes and oligodendrocytes from female subjects with OUD. Thus, we describe striatal cell types and leverage these data to gain insights into molecular alterations in human striatum associated with opioid addiction.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Refer to individual Series


title: Assaying  effector  cell-to-cell  mobility  in  plant  tissues  identifies  hypermobility  and indirect manipulation of plasmodesmata

status: Public on Nov 27 2023

city: Norwich

first: Hannah

middle: Rae

last: Thomas

address: Norwich Research Park, Colney Lane

department: Cell and Developmental Biology

institute: John Innes Centre

summary: In   plants,   plasmodesmata   establish   cytoplasmic   continuity   between   cells   to   allow   for communication  and  resource  exchange  across  the  cell  wall.  While  plant  pathogens  use plasmodesmata  as  a  pathway  for  both  molecular  and  physical  invasion,  the  benefits  of molecular  invasion  (cell-to-cell  movement  of  pathogen  effectors)  are  poorly  understood.  To establish a methodology for identification and characterization of the cell-to-cell mobility of effectors, we performed a quantitative live imaging-based screen of candidate effectors of the fungal  pathogen Colletotrichum  higginsianum.  We  predicted C.  higginsianum  effectors  by their expression profiles, the presence of a secretion signal, and their predicted and in planta localization  when  fused  to  GFP.  We  assayed  for  cell-to-cell  mobility  of  nucleo-cytosolic effectors and identified 14 that are cell-to-cell mobile. We identified that 3 of these effectors are “hypermobile”, showing cell-to-cell mobility greater than expected for a protein of its size. To explore the mechanism of hypermobility we chose two hypermobile effectors and measured their  impact  on  plasmodesmata  function  and  found  that  even  though  they  show  no  direct association with plasmodesmata, each increases the transport capacity of plasmodesmata. Thus, our  methods  for  quantitative  analysis  of  cell-to-cell  mobility  of  candidate  microbe-derived36effectors, or any suite of host proteins, can identify cell-to-cell hypermobility and offer greater understanding of how proteins affect plasmodesmal function and intercellular connectivity.

overall_design: Leaves 7 and 8 from three 4-week old Arabidopsis thaliana plants were collected from Col-0, 35S:ChEC127-GFP, and 35S:ChEC132-GFP plants for RNA-sequencing. Each samples contains 6 leaves and there are 3 bioreplicate for each genotype.

first: Mina

last: Ohtsu

first: Joanna

last: Jennings

first: Matthew

last: Johnston

first: Andrew

last: Breakspear

first: Xiaokun

last: Liu

first: Kara

last: Stark

first: Richard

last: Morris

first: Jeroen

last: de Keijzer

first: Christine

last: Faulkner


title: Next Generation Sequencing to identify the expression of transcripts and abnormal events in 3D skin exposed to blue wavelength and full spectrum of visible light

city: Cajamar

first: Juliana

last: Lago

state: SP

address: Via de Acesso, KM30,5, Prédio C

department: R&D

country: Brazil

institute: Natura Cosméticos S/A

summary: Samples of 3D skin, irradiated using LED light and compared with un-exposed control, regarding one- and four-days of incubation. Three groups were simulating acute exposure: 1h, 2h and 4 hours whereas the 3D skin samples irradiated for 1 hour over four sequential days were simulating repeated exposure, for both blue wavelength and the full visible spectrum of digital light.

overall_design: Eight groups of 3D skin samples were irradiated using LED light, three replicates for each condition pooled, to identify the influence of digital blue light on skin biological mechanisms, compared with un-exposed control. Differential gene expression analysis was normalized using un-exposed 3D skin as a control, regarding one-day of incubation.

first: Melissa

last: Ganzerla

first: Ana-Luisa

last: Dias

first: Joice

middle: P

last: Savietto


title: Runx1+ vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo

city: Edinburgh

first: Mihaela

last: Crisan

address: 5 Little France Drive

institute: The University of Edinburgh

summary: Hematopoietic stem cells (HSCs) produce all essential cellular components of the blood. Stromal cell lines supporting HSCs follow a vascular smooth muscle cell (vSMC) differentiation pathway, suggesting that some hematopoiesis-supporting cells originate from vSMC precursors. These pericyte-like precursors were recently identified in the aorta-gonad-mesonephros (AGM) region; however, their role in in vivo hematopoietic development remains unknown. Here, we identify a subpopulation of NG2+Runx1+ perivascular cells that display a sclerotome-derived vSMC transcriptomic profile. We show that deleting Runx1 in NG2+ cells impairs in vivo hematopoietic development and causes transcriptional changes in pericytes/vSMCs, endothelial cells and hematopoietic cells in the murine AGM. Importantly, this deletion leads also to a signification reduction of HSC reconstitution potential in the bone marrow in vivo. This defect is developmental, as NG2+Runx1+ cells were not detected in the adult bone marrow, demonstrating the existence of a specialised pericyte population in the HSC-generating niche, unique to the embryo.

overall_design: Single-cell transcriptome profiling of E11 AGM samples from NG2 +/+; Runx1 fl/fl (WT) (n=1) and NG2-Cre; Runx1 fl/fl (cKO) (n=1) mice

first: Zaniah

last: Gonzalez

first: Alastair

middle: M

last: Kilpatrick

first: Madalena

last: Marques

first: Diana

last: Sá da Bandeira

first: Telma

last: Ventura

first: Mario

last: Gomez-Salazar

first: Lea

last: Bouilleau

first: Yvan

last: Marc

first: Ana

last: Barbosa

first: Fiona

last: Rossi

first: Mariana

last: Beltran

first: Harmen

last: van de Werken

first: Wilfred

last: van IJcken

first: Neil

last: Henderson

first: Stuart

last: Forbes


title: DNA methylation sequencing of human pancreatic acinar and ductal cells [Bisulfite-seq]

first: Pei

last: Wang

summary: Flow-sorted pancreatic acinar and ductal cells from fresh human pancreatic exocrine tissue were subjected to molecular characterization to identify lineage-specific expression and epigenetic properties. Cells of both lineages were cultured and transformed via lentiviral mutation to form pancreatic ductal adenocarcinoma.

overall_design: Flow-sorted pancreatic acinar and ductal cells from fresh human pancreatic exocrine tissue were subjected to reduced-representation bisulfite sequencing, before and after cell culture, for differential analysis of DNA methylation by lineage

first: Yi

last: Xu

first: Michael

middle: H

last: Nipper

first: Zhengqing

last: Ye

first: Naoki

last: Akanuma

first: Kevin

last: Lopez

first: Janice

last: Deng

first: Aatur

last: Singhi

first: Francis

middle: E

last: Sharkey

first: Huamin

first: Luzhe

last: Sun

first: Yidong

last: Chen

first: Jun

last: Liu


title: Suppression of IL-1β promotes beneficial accumulation of fibroblast-like cells in atherosclerotic plaques in clonal hematopoiesis [CITE-seq]

status: Public on Nov 25 2023

city: New York

first: Eunyoung

last: Kim

state: NY

institute: Columbia University

summary: Clonal hematopoiesis (CH) is an independent risk factor for atherosclerotic cardiovascular disease. Murine models of CH suggest a central role of inflammasomes and IL-1β in accelerated atherosclerosis and plaque destabilization. Here we show using scRNAseq in human carotid plaques that inflammasome components are enriched in macrophages, while the receptor for IL-1β is enriched in fibroblasts and smooth muscle cells (SMCs). To address the role of inflammatory crosstalk in features of plaque destabilization, we conducted SMC fate mapping in mice modeling Jak2VF or Tet2 CH treated with IL-1β antibodies. Unexpectedly, this treatment minimally affected SMC differentiation, leading instead to a prominent expansion of fibroblast-like cells. Depletion of fibroblasts from mice treated with IL-1β antibody resulted in thinner fibrous caps. Conversely, genetic inactivation of Jak2VF during plaque regression promoted fibroblasts accumulation and fibrous cap thickening. Our studies suggest that suppression of inflammasomes promotes plaque stabilization by recruiting fibroblast-like cells to the fibrous cap.

overall_design: Bone marrow tranplantation of Dre-Jak2 bone marrow into Ldlr-/- coupled to either cholesterol lowering or not

first: Trevor

last: Fidler

first: Alan

last: Tall


overall_design: Bone marrow transplantation of Dre-Jak2 bone marrow into Ldlr-/- and subjected to Western type diet feeding.


title: Cellular responses toatmospheric-pressure plasma in fission yeast

status: Public on Nov 24 2023

first: Akira

last: Yamashita

state: Aichi

address: Nishigonaka 38, Myodaiji

institute: National Institute for Basic Biology

summary: We characterized fission yeast cellular responses to a novel stress inducer, non-thermal atmospheric-pressure plasma.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq at three time points after plasma irradiation and at one time point after hydrogen peroxide treatment with three biological replicates.

first: Yoko

last: Otsubo

first: Katsuki

last: Johzuka

first: Shinji

last: Yoshimura


title: Effects of BLT1 inhibition in a mouse model of liver fibrosis

city: Riverside

first: Brendan

last: Gongol

state: Ca

address: 900 University Ave

institute: University of California, Riverside

summary: Nonalcoholic steatohepatitis (NASH) is a prevalent disease that can ultimately progress to more severe forms of disease including liver fibrosis, cirrhosis, hepatocellular carcinoma (HCC), and ultimately death. A key feature of NASH is lobular inflammation, which is a major driver of disease progression, and both innate and adaptive immune mechanisms support and perpetuate hepatic inflammation in NASH.  Previous studies have demonstrated that the pro-inflammatory leukotriene B4 (LTB4) is a potent chemoattractant that drives macrophage and neutrophil chemotaxis, and genetic loss or inhibition of its high affinity receptor, leukotriene B4 receptor 1 (BLT1), results in improved insulin sensitivity and decreased lipid accumulation in the liver. Accordingly, the LTB4-BLT1 axis is a potential therapeutic target for the treatment of liver steatosis and insulin resistance by modulating inflammation.The goal of this study is to validate the therapeutic efficacy of BLT1 inhibition in a NASH mouse model.

overall_design: 8 Week old male C57BL/6J mice were fed a choline-deficient L-amino acid defined high fat diet (CDAA-HFD) with 60 kcal% fat with 0.1% methionine and no added choline (Research Diets, A06071302). After 4 weeks, one group remained on CDAA-HFD and the other was started on CDAA-HFD with a 90 mg/kg dose of BLT1i for 8 weeks.

first: Saswata

last: Talukdar

first: Erin

middle: S

last: Coyne

first: Yilin

last: Nie

first: Desiree

last: Abdurrachim

first: Yongqi

last: Zhou

first: Asad

last: Abu Bakar Ali

first: Stacey

last: Meyers

first: Jeff

last: Grein

first: Wendy

last: Blumenschein

first: Yang

first: Cedric

last: Hugelshofer

first: Ester

last: Caraballo-Jane


title: Transcriptome of Magnaporthe oryzae treated with SA, ABA and sakuranetin

city: Hangzhou

first: Chi

last: Zhang

address: Deshengzhong Road No.298

institute: Zhejiang Academy of Agricultural Sciences

summary: To study the effect of plant metabolites on M. oryzae, we selected salicylic acid (SA), abscisic acid (ABA), and sakuranetin to treat M. oryzae grown on the medium with the concentration of 100μM. After 10 days' treatment, the total RNA were extracted and detected the transcriptome.

overall_design: Comparative gene expression profilling analysis of RNA-seq for Magnaporthe oryzae. The contrul group was treated with DMSO, the experiment groups were treated with 100μM SA, ABA or sakuranetin. Each group has 3 repeats.

first: Jitao

last: Hu

first: Gaojie

last: Hong


title: Sleeping Beauty transposon mutagenesis in mouse intestinal organoids identifies genes involved in tumor progression and metastasis [Atxn1]

city: Chuo-ku

first: Haruna

last: Takeda

state: Tokyo

address: 5-1-1 Tsukiji,

institute: National Cancer Center Japan

summary: To identify genes important for colorectal cancer (CRC) development and metastasis, we established a new metastatic mouse organoid model using Sleeping Beauty (SB) transposon mutagenesis. Intestinal organoids derived from mice carrying actively mobilizing SB transposons, an activating KrasG12D, and an inactivating ApcΔ716 allele, were transplanted to immunodeficient mice. Analysis of SB insertion sites in tumors identified numerous candidate cancer genes (CCGs) identified previously in intestinal SB screens performed in vivo, in addition to new CCGs, such as Atxn1. To provide functional validation, we knocked out Atxn1 in mouse tumor organoids carrying an activating KrasG12D, and an inactivating ApcΔ716 allele, and transplanted to mice. Tumor development was promoted when these gene were knocked out, demonstrating that these are potent tumor suppressors.

overall_design: Atxn1 was knocked out by CRISPR-Cas9 in mouse colon tumor organoids carrying an activating KrasG12D, and an inactivating ApcΔ716 allele, and RNA was collected to perform RNA-seq.

first: Yukari

last: Muranaka

first: Daichi

last: Narushima

first: Mamoru

last: Kato


title: Analysis of alternative exon-dependent interactome remodelling reveals multitasking functions of gene regulatory factors

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

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


title: Type 2-polarized memory B cells hold allergen-specific IgE memory

city: Hoerholm

first: Niels Peter

last: Hell Knudsen

address: Bøge Alle 3

country: Denmark

institute: ALK-Abello

summary: Allergen-specific IgE antibodies mediate allergic pathology in diseases such as allergic rhinitis and food allergy. Memory B cells (MBCs) contribute to circulating IgE by regenerating IgE-producing plasma cells upon allergen encounter. We report a population of type 2 polarized MBCs defined as CD23hi, IL-4Rαhi, CD32low at the transcriptional and surface protein levels.

overall_design: Memory B cells were negatvely selected from PBMC's from allergics and non-allergics using magnetic coloumns and antibody labelled beads. The MBC enriched fractions were analysed using the 10X Genomics Chromium Instrument and cDNA synthesis kit (10x Genomics) to generate a barcoded cDNA library for single cell RNA-sequencing from approximately 10,000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library, we performed pair end sequencing on an Illumina NovaSeq6000. 10X Genomics Chromium v2 chemistry

first: J

last: Koenig

first: N

last: Knudsen

first: A

last: Phelps

first: K

last: Bruton

first: I

last: Hoof

last: Lund

first: D

last: Libera

first: L

last: Christensen

last: Glass

first: T

last: Walker

last: Fang

first: S

last: Waserman

first: M

last: Jordana

first: P

last: Andersen


title: Spatial transcriptomics of the achilles tendon harvested from the injury site with and without TrkA neuronal inhibition

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

summary: Peripheral afferent neurons terminate at the surfaces of tendons, yet their role after injury beyond nociceptive functions remain unclear.  Using transgenic animal models, sensory neurons were found to sprout after Achilles tendon injury in domains of Nerve growth factor (NGF) expression. Conditional deletion of Ngf in either myeloid or mesenchymal cell types led to tendon repair defects – findings phenocopied by inactivation of TrkA (Tropomyosin receptor kinase A) using a knockin mouse model. We sought to identify the signals modulated with neural TrkA inhibition. A combination of single cell and spatial transcriptomic analysis was performed on the Achilles injury site of TrkA^F592A animals and compared them to TrkA^WT.

overall_design: The injury site was dissected from TrkAWT and TrkAF592A animals at 14 d post-operative for Spatial transcriptomics. Pooled N=4 mice per genotype

first: Jiajia

last: Xu

first: Zhao

last: Li

first: Robert

middle: J

last: Tower


title: Effect of DRG conditioned media on Tppp3+ tendon cells

summary: Here, we investigated the effect of conditioned media (CM) obtained from cultured mouse DRG neurons on Tppp3+ cells, mainly on proliferation and differentiation potential.  Peripheral afferent neurons terminate at the surfaces of tendons, yet their role after injury beyond nociceptive functions remain unclear.  Using transgenic animal models, sensory neurons were found to sprout after Achilles tendon injury in domains of Nerve growth factor (NGF) expression.  Conditional deletion of Ngf in either myeloid or mesenchymal cell types led to tendon repair defects – findings phenocopied by inactivation of TrkA (Tropomyosin receptor kinase A) using a knockin mouse model.  A combination of spatial and single cell transcriptomics revealed dysregulated inflammatory and TGF signaling upon lack of neural input.  Utilizing sural nerve transection in reporter animals, we identified that neural input is required for proper expansion of Tppp3+ tendon sheath progenitor cells (TSPCs) after injury, and in vitro approaches implicated TGF signaling activation in Tppp3+ TSPC neural response.  Finally, in a translational approach, activation of TrkA+ sensory neurons using a partial agonist led to a significant increase in TGF signaling, TSPC expansion, and improved tendon repair.   Collectively, these data implicate peripheral afferent neural networks in the coordinated acute tendon injury response, and identify candidate molecules to speed the reparative process.

overall_design: Bulk RNA sequencing of mice achiles tendon Tppp3+ cells with DRG CM or 1% FBS media at 24 h. Three biological replicates for experimental Tppp3+ cells with DRG CM were compared with  three biological replicates  Tppp3+ cells with 1% FBS media controls.

first: Masnsen

last: Cherief