title: Pediatric-type high-grade neuroepithelial tumors with CIC gene fusion share a common DNA methylation signature

status: Public on Mar 10 2023

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

summary: Pediatric neoplasms in the central nervous system show an extensive clinical and molecular heterogeneity. Molecular genetic testing contributes to accurate diagnosis and enables an optimal clinical management of affected children. Unsupervised visualization of genome-wide DNA methylation array data revealed a molecularly distinct type of pediatric high-grade neuroepithelial tumor with fusions involving the capicua transcriptional repressor (CIC) gene, with the most common fusion being CIC::LEUTX. Histopathological review demonstrated a morphologically heterogeneous group of high-grade neuroepithelial tumors with positive immunostaining for markers of glial differentiation in combination with weak and focal expression of synaptophysin, CD56 and CD99. In summary, we expand the spectrum of pediatric-type tumors of the CNS by reporting a previously uncharacterized group of rare high-grade neuroepithelial tumors that share a common DNA methylation signature and recurrent gene fusions involving the transcriptional repressor CIC.

overall_design: DNA methylation signature

first: Philipp

last: Sievers


title: Age-related alterations in meningeal immunity drive impaired CNS lymphatic drainage

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

country: USA

institute: Washington University in Saint Louis

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A single-cell transcriptome landscape of the non-human primate placenta across pregnancy.

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

summary: The human placenta, a transient endocrine organ, is vital for successful pregnancy and fetal health, which undergoes dynamic cellular and functional changes during gestation. However, systematic longitudinal analysis of in utero human placenta formation and development across the lifespan is not feasible due to ethical and technical limit. To circumvent those difficulties and reveal the dynamic placentation, we obtain transcriptional snapshots of 217404 single cells from cynomolgus monkey placenta, decidua and embryo tissues spanning ten consecutive but distinct developmental stages across pregnancy. We reveal the development-related changes in the compositions of placental trophoblasts, mesenchymal cells and endothelial cells in different pregnant stage. We pinpoint that the placenta mesenchymal cells are derived from a special extra-embryonic mesoderm. Particularly, we describe the relationship between the embryonic primitive hematopoiesis and the placental endothelial cells, Hofbauer cells and erythrocytes. Besides, we found the cell types and their transcriptome compositions in decidual tissues show insignificant changes during the gestation. Finally, cell-cell interactions between trophoblasts and decidual cells, and between different cell types on villi are performed and suggested the mechanisms in dynamic placentation. Together, the high-resolution atlas we constructed would serve as a valuable resource to extrapolate key events for studies on human placentation and its associated disorders.

overall_design: single cells from cynomolgus monkey placenta, decidua and embryo tissues spanning ten consecutive but distinct developmental stages across pregnancy. RNA libraries were prepared for sequencing using 10x Single Cell 3' Library & Gel Bead Kit v3  protocol

first: Hongmei

last: Wang

first: Jinglei

last: Zhai

first: Zhenyu

last: Xiao

first: Haifeng

last: Wan

first: Yanhong

last: Xu

first: Xulun

last: Wu

first: Dan

last: Zhang


title: Age-related alterations in meningeal immunity drive impaired CNS lymphatic drainage [FACS LECs]

summary: The meningeal lymphatic network—housed within the dural meninges surrounding the brain— is critical for cerebrospinal fluid (CSF) drainage. Through continuous brain interstitial fluid (ISF) mixing with CSF via the glymphatic system, this lymphatic network facilitates the removal of central nervous system (CNS) waste. During aging and in Alzheimer’s disease (AD), attenuated meningeal lymphatic drainage promotes the buildup of toxic misfolded proteins—including amyloid beta—in the CNS. Alleviating this age-related meningeal lymphatic dysfunction represents a promising therapeutic strategy to alleviate AD pathology. However, the mechanisms underlying this lymphatic decline remain elusive. Here we demonstrate that age-related alterations in meningeal immunity contribute to meningeal lymphatic impairment. Single-cell RNA-sequencing of dural lymphatic endothelial cells in aged mice demonstrated a response signature to the cytokine IFNγ, which was elevated in the aged dura due to meningeal T cell accumulation. Chronic elevation of IFNγ in the meninges of young mice via AAV-mediated overexpression altered lymphatic adherans junctions and impaired CSF drainage to deep cervical lymph nodes—comparable to the deficits observed in aged mice. Direct disruption of lymphatic junctions via CSF-delivered VE-Cadherin disrupting antibodies was sufficient to phenocopy impairments in CSF drainage. Therapeutically, IFNγ neutralization in aged mice alleviated age-related impairments in meningeal lymphatic function. These data suggest manipulation of meningeal immunity as a viable therapeutic target to normalize CSF drainage in aged mice and alleviate the pathology in AD mice associated with impaired waste removal.

overall_design: Mice were given a lethal dose of anesthetics via i.p. Euthasol (10% v/v) and transcardial perfusion performed with 0.025% heparin in PBS. Mice were decapitated immediately posterior to the occipital bone, and overlying skin and muscle was removed from the skull. Meninges were peeled from the skull cap using fine forceps, and placed in ice-cold DMEM for the entirety of collection. Meninges were then digested for 15 minutes at 37 °C with constant agitation using 1 mL of pre-warmed digestion buffer (DMEM, with 2% FBS, 1 mg/mL collagenase VIII (Sigma Aldrich), and 0.5 mg/mL DNase I (Sigma Aldrich)), filtered through a 70 μm cell strainer, and neutralized with 1 mL of complete medium (DMEM with 10% FBS). An additional 2 mL of FACS buffer was added, samples were centrifuged at 400 × g for five minutes, and resuspended in FACS buffer and kept on ice. Cells were resuspended in FACS buffer with 1:100 CD16/32 Fc block. They were stained with CD31, CD45, Podoplanin and Lyve1, washed, and resuspended in DAPI-containing FACS buffer. Single meningeal lymphatic endothelial cells were sorted as Live (DAPI-) CD45- CD31+ PDPN+ Lyve1+ cells using a FACS Aria II. Individual cells were sorted into 96-well plates containing 2 µL of 10X RNA lysis buffer (Takara) and 5% RNAse out (Takara) and rapidly frozen over dry ice. Library preparation was performed with 2 μL of single cell lysates arrayed in 96-well PCR  plates.  ds-cDNA was prepared using a protocol adapted from the Takara-Clontech SMARTer methods and scaled to a 5μL reaction volume. This method introduces a unique barcode upstream of the polyA tail using a modified oligo-dT primer. Briefly, 0.5μLof the Takara dilution buffer with 5% RNase inhibitor and 0.25μL of 25μM FACSseq barcode primer was added to the lysate and heated to 72 °C for 3 minutes. Then, 2.25 μL of the reverse transcription master mix was added to each well with 1 μL 5X first strand buffer, 0.125μL 100 mM DTT, 0.25 μL 20mM dNTPs, 0.25 μL, 50μM FACSseq TSO primer, 0.125 μLRNase inhibitor, and 0.5 μL SMARTscribe reverse transcriptase (Takara). The reaction was incubated at 42 °C for 90 minutes, 70 °C for 10minutes, then a 4 °C hold. All wells from the plate were then pooled and purified with Ampure XP beads (Beckman Coulter) with a 1X ratio. cDNA was eluted in 39μLwater. cDNA was amplified using 5 μL10X PCR buffer, 2 μL10mM dNTPs, 2 μL 12μM FACSseq206TSO PCR primer, 2 μL 50X Advantage 2 Polymerase (Takara). PCR conditions were 95 °C for 1 minute, 16 cycles of 95 °C for 15 seconds, 65 °C for 30 seconds, 68 °C for 6 minutes, 1 cycle of 72 °C for 10 minutes, followed by a 4 °C hold. cDNA was purified with 1.2XAmpure bead cleanup, measured with 209 Qubit  dsDNA  assay, and visualized on bioanalyzer. cDNA was fragmented using a Covaris E220 210 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3’ ends, and had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 16 cycles using a standard Illumina i7 primer to introduce an index sequence and FACSseq Lib PCR 1.0 specific to fragments containing the cell barcode added during cDNA synthesis. Fragments were sequenced on an Illumina NextSeq using paired end reads with 25 cycles for read 1, 7 cycles for the i7 index, and 100 cycles for the paired read. The sequencing run was performed with a custom sequencing primer for read 1 to read the 10bp barcode unique to each cell. The i7 index allows for multiple plates to be sequenced together. Read 2 contains the mRNA sequences. Two plates (S1 and S2) for each age time point were sequenced in separate sequencing runs.

first: Justin

last: Rustenhoven

first: Taitea

last: Dykstra


title: Transcriptomic profiling of human bone marrow non-hematopoietic cells

status: Public on Mar 12 2023

city: Lund

first: Stefan

last: Lang

address: Sölvegatan 17

department: Molecular Hematology

country: Sweden

institute: Lund University

summary: To solve the heterogeniety of human bone marrow non-hematopoietic cells, we perfomed transcriptomic profiling of bone marrow non-hematopoietic cells using scRNAseq.

overall_design:
Transcriptomic profiling of human bone marrow CD45-CD235a- cells was performed using single-cell RNA sequencing
>>> Due to Swedish law, the patient consent, and the risk that the sequencing data contains personally-identifiable information and hereditary mutations, we cannot deposit the short sequencing read data in a repository. <<<

first: Hongzhe

last: Li


title: Age-related alterations in meningeal immunity drive impaired CNS lymphatic drainage [bulk LECs]

overall_design: C57BL/6 mouse primary lymphatic endothelial cells were purchased from Cell Biologics. Cells were maintained in T25 tissue culture flasks with gelatin-based coating solution (Cell Biologics) and Complete Human Endothelial Cell Medium (Cell Biologics). Cells were passaged with Trypsin/EDTA 0.25% Solution (Cell Biolgics) and plated at 15,000 cells/cm2 surface area in coated 6 well plates or 6 well chamber slides. Cells were grown ~72-96 hours until a confluent monolayer was formed. At completion, RNA was extracted using the RNAqueous™-Micro Total RNA Isolation Kit and DNAase performed using the Invitrogen Ambion TURBO DNA free Kit. Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.


title: Transcriptome analyses of the cortex and white matter of focal cortical dysplasia type II human samples: novel insights into disease mechanisms and contributions to tissue characterization

city: Campinas

first: Fabio

last: Rogerio

state: Sao Paulo

address: Rua Tessália Vieira de Camargo, 126

department: Department of Pathology,

country: Brazil

institute: University of Campinas – UNICAMP

summary: Focal cortical dysplasia (FCD) is a common cause of pharmacoresistant epilepsy. According to the 2011 International League Against Epilepsy classification, FCD type II is characterized by dysmorphic neurons (IIa and IIb) and may be associated with balloon cells (IIb). We present a multicentric study to evaluate the transcriptomes of the gay and white matters of surgical FCD type II specimens. Our aim was to contribute to pathophysiology and tissue characterization. We investigated FCD II (a and b) and control samples by performing RNA-sequencing followed by immunohistochemical validation by means of digital analyses. We found 342 and 399 transcripts differentially expressed in the gray matter of IIa and IIb lesions compared to controls, respectively. The top enriched cellular pathway in IIa and IIb gray matter was cholesterol biosynthesis, their genes HMGCS1, HMGCR and SQLE being upregulated in both type II groups. We also found 12 differentially expressed genes when comparing transcriptomes of IIa and IIb lesions. Only 1 transcript (MTRNR2L12) was significantly upregulated in FCD IIa. The white matter in IIa and IIb lesions showed 2 and 24 transcripts differentially expressed respectively compared to controls. No enriched cellular pathways were detected. GPNMB, not previously described in FCD samples, was upregulated in IIb compared to IIa and control groups. Upregulations of cholesterol biosynthesis enzymes and GPNMB genes in FCD groups were immunohistochemically validated. Such enzymes were mainly detected in both dysmorphic and normal neurons, whereas GPNMB was observed only in balloon cells. Overall, our study contributed to the identification of cortical enrichment of cholesterol biosynthesis in FCD type II, which may correspond to neuroprotective response to seizures. Moreover, specific analyses in either the gay or the white matter revealed upregulations of MTRNR2L12 and GPNMB, which might be potential neuropathological biomarkers of a cortex chronically exposed to seizures and of balloon cells, respectively.

overall_design: Comparative study of gray and white matter of human frontal lobe tissue surgically obtained from FCD II (a and b) patients and control samples (obtained from adults submitted to autopsy -between 6 and 12 hours post mortem) by performing RNA-sequencing

first: Guilherme

middle: R

last: Assis-Mendonça

first: Maria

middle: C

last: Athié

first: João

middle: V

last: Tamanini

first: Arethusa

last: de Souza

first: André

middle: S

last: Vieira

first: Gabriel

middle: G

last: Zanetti

first: Patrícia

middle: A

last: Araújo

first: Enrico

last: Ghizoni

first: Helder

last: Tedeschi

first: Marina

middle: K

last: Alvim

first: Vanessa

last: de Almeida

first: Welliton

first: Roland

last: Coras

first: Ingmar

last: Blümcke

first: Clarissa

middle: L

last: Yasuda

first: Fernando

last: Cendes

first: Iscia

last: Lopes-Cendes


title: HypoSUMOylation in embryonic stem cells generate head-trunk embryo-like structures [scRNAseq]

status: Public on Mar 17 2023

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

summary: Numerous models of synthetic embryos have recently been established to simulate mammalian development. Two main strategies have been developed to build mouse or human embryo-like structures (ELS): by assembling embryonic and extraembryonic stem cells or by challenging embryonic stem cells (ESCs) with a pulse of WNT agonist. However, both models did not fully recapitulate early organogenesis, particularly the emergence of brain derivatives. SUMOylation was recently identified as a general barrier to cell fate transitions. Here, we show that mouse ESCs exposed to a small-molecule inhibitor of SUMOylation alone generate adherent spheroids which, once in suspension, self-organize in gastrulating structures containing cell types spatially and functionally-related to embryonic and extraembryonic compartments. Alternatively, spheroids cultured in an optimized droplet-microfluidic device form elongated ELS characterized by a multi-axial organization of the body plan reminiscent of natural embryo morphogenesis. Single-cell transcriptomics further revealed various cell types including anterior neuronal cell types, Schwann cell precursors and somites. Mechanistically, transient SUMOylation repression gradually increases the global level of DNA methylation, which in turn represses transcription of Nanog and other pluripotency-associated genes, enhancing cellular plasticity of ESCs. Our morphogen-free protocol constitutes a new facet to study regulative mechanisms of early development by targeting reprogramming roadblocks to shape multicellular architecture.

overall_design: Transcriptomic profiling by MARS-seq (scRNA-seq) of cells at D1, D3, D8 D10, D18, cells from aggreWell gastruloids, µfluidic device-derived gastruloids and cells from embryo-like structures. Control ES cells (D1) were treated with ML-792 for 48h (D3) in serum+Lif medium. Drug was washed and cells were allowed to recover for 5 days (D8), before undergoing another ML-792 treatment for 48h (D10) in serum+Lif medium. Drug was washed and medium was changed to N2B27+Lif for 8 days (D18). ESC_N2B27Lif is a control condition that corresponds to untreated ES cells that underwent the medium switch.  D18 cells were transferred to AggreWell plates and cultured for 3 days in N2B27+Lif (Gastruloid_AgW). ESC_AgW is a control condition that corresponds to untreated ES cells that underwent the medium switch and the plate transfer.  D18 cells were transferred to a droplet-microfluidic device and cultured for 2 days (Gastruloid_F2) or 5 days (Gastruloid_F5) in N2B27+Lif.  D18 cells were transferred to a droplet-microfluidic device and cultured for 4 days then extracted and embedded in 20% Matrigel for 3 additional days of culture in N2B27+Lif (ELS_M7).

first: Jack-Christophe

last: Cossec

first: Tatiana

last: Traboulsi


title: H4K20me1 plays a dual role in transcriptional regulation during regeneration and axis patterning of Hydra

status: Public on Mar 09 2023

city: Pune

first: Sanjeev

last: Galande

state: Maharashtra

address: Dr. Homi bhabha road, Pashan

department: Biology

country: India

institute: IISER Pune

type: Genome binding/occupancy profiling by high throughput sequencing


title: H4K20me1 plays a dual role in transcriptional regulation during regeneration and axis patterning of Hydra [ChIP-seq ALP]

summary: The evolution of the first body axis in the animal kingdom and an extensive ability to regenerate makes Hydra, a Cnidarian, an excellent model system to understand the underlying epigenetic mechanisms. We identify that SETD8 is critical for regeneration, and H4K20me1 colocalizes with transcriptional activation machinery locally at the β-catenin bound TCF/LEF binding sites on the promoters of head-associated genes, marking an epigenetic activation node. Contrastingly, a global genome-wide analysis of the H4K20me1 occupancy revealed a negative correlation with transcriptional activation. We propose H4K20me1 as a general repressive histone mark in Cnidaria and describe its dichotomous role in transcriptional regulation in Hydra.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H4K20me1 in control and ALP treated Hydra polyps.

first: Akhila

last: Gungi


title: Effects of the circulating environment of COVID-19 on platelet and neutrophil behavior

status: Public on Mar 08 2023

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Thromboinflammatory complications are well described sequalae of Coronavirus Disease 2019 (COVID-19), and there is evidence of both hyperreactive platelet and inflammatory neutrophil biology that contributes to the thromoinflammatory milieu. It has been demonstrated in other thromboinflammatory diseases that the circulating environment may affect cellular behavior, but what role this environment exerts on platelets and neutrophils in COVID-19 remains unknown. We tested the hypotheses that 1) plasma from COVID-19 patients can induce a prothrombotic platelet functional phenotype, and 2) contents released from platelets (platelet releasate) from COVID-19 patients can induce a proinflammatory neutrophil phenotype. We treated platelets with COVID-19 patient and disease control plasma and found that COVID-19 patient plasma promoted auto-aggregation, thereby reducing response to further stimulation ex-vivo. Neither disease condition increased the number of platelets adhered to a collagen and thromboplastin coated parallel plate flow chamber, but both markedly reduced platelet size. We treated healthy neutrophils with COVID-19 patient and disease control platelet releasate and found that COVID-19 patient platelet releasate increased myeloperoxidase-deoxyribonucleic acid complexes and induced changes to neutrophil gene expression. Together these results suggest aspects of the soluble environment of COVID-19 stimulate circulating platelets, and that the contents released from those platelets can elicit inflammatory neutrophil behavior independent of direct cellular contact.

overall_design: 5 control (COVID negative) patients and 5 COVID positive patients

first: Alexander

middle: T

last: Fields

first: Elizabeth

last: Andraska

first: Christof

last: Kaltenmeier

first: Zachary

last: Matthay

first: Kimberly

last: Herrera

first: Brenda

last: Nuñez-Garcia

first: Carolyn

middle: M

last: Hendrickson

middle: J

last: Bainton

first: Chayse

last: Jones

first: Katherine

middle: D

last: Wick

first: Michael

first: Tessa

last: Barrett

first: Jeffrey

last: Berger

first: Silvia

first: Yan-Ping

last: Yu

first: Jian-Hua

last: Luo

first: Matthew

last: Neal

first: Lucy

middle: Z

last: Kornblith


title: mRNAs encoding IL-12 and a decoy-resistant variant of IL-18 synergize to engineer T cells for efficacious intratumoral adoptive immunotherapy

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

country: Spain

institute: FIMA

summary: Mixtures of pmel-1 TCR-transgenic T cells electroporated with scIL-12 or DRIL-18 mRNAs exerted powerful therapeutic effects on injected and distant melanoma lesions. These effects are associated with T-cell metabolic fitness, changes in glycosylation of surface proteins gaining adhesiveness to E-selectin and enhanced miR-155 control on immunosuppressive target genes.

overall_design:
Samples are pre-activated pmel-1 T cells with gp100 antigen and electropored with the indicated mRNA. RNA was extracted 24h later for bulk RNAseq analysis.
contributor: Macrogen

first: Irene

last: Olivera

first: Elixabet

last: Bolaños

first: Ignacio

last: Melero


title: Local and systemic multiomics signature of eosinophilic esophagitis (EO) in children

city: Jouy-en-Josas

first: Marco

last: Moroldo

address: Domaine de Vilvert

department: Animal Genetics

institute: INRA

summary: We aimed to provide the most comprehensive description to date of both local and systemic immune constituents characterizing children with EO. For that purpose, we performed comprehensive immunophenotyping and cytokine/antibody measurements on paired biopsies and blood samples collected from children with EoE, in comparison to age-matched controls. EoE status was clinically and histologically characterized and confirmed using transcriptomer analysis. As a second objective, we aimed to identify an EoE signature in the periphery by combining the comprehensive analysis of circulating immune components and non-targeted metabolomics on plasma.

overall_design: Ten individuals affected by eosinophilic esophagitis (EO) and ten controls (CT) were studied. The analyses were carried out by comparing EO to CT

first: Karine

last: Adel-Patient

first: Florence

last: Campeotto

first: Marta

last: Grauso

first: Guillaume

last: Lezmi


title: H4K20me1 plays a dual role in transcriptional regulation during regeneration and axis patterning of Hydra [RNA-seq]

first: Sanjeev

last: Galande

overall_design: 3’ mRNA sequencing for differential gene expression on regenerating tips of Hydra with and without treatment with UNC0379 (SETD8 inhibitor)

first: Akhila

last: Gungi


title: DUSP6 is a memory retention feedback regulator of ERK signaling for cellular resilience of human pluripotent stem cells in response to dissociation

status: Public on Mar 07 2023

city: Cheongju

first: Yong-Ou

last: Kim

state: Chungchung buk do

address: Osongsangmyeong 2ro

country: South Korea

institute: Korea National Institute of Health

summary: Cultured human pluripotent stem cells (hPSCs) grow as colonies that require breakdown into small clumps for further propagation. Although cell death mechanism by single-cell dissociation of hPSCs has been well defined, how hPSCs respond to the deadly stimulus and recover the original status remains unclear. Here we show that dissociation of hPSCs immediately activates ERK, which subsequently activates RSK and induces DUSP6, an ERK-specific phosphatase. Although the activation is transient, DUSP6 expression persists days after passaging. DUSP6 depletion using the CRISPR/Cas9 system reveals that DUSP6 suppresses the ERK activity over the long term. Elevated ERK activity by DUSP6 depletion increases both viability of hPSCs after single-cell dissociation and differentiation propensity towards mesoderm and endoderm lineages. These findings provide new insights into how hPSCs respond to dissociation in order to maintain pluripotency.

overall_design: Two biological replicates were analyzed for each point of sampling cells cultured by mechanical or chemical passaging method. For differentiation with 5% FBS-containing differentiation medium, cells were cultured TeSR-E8 medium for 3 weeks with or without inhibitors and then differentiated with 5% FBS-containing medium.

first: Dae Hoon

last: Yoo

first: Young Sam

last: Im

first: Ji Young

last: Oh

first: Dayeon

last: Gil


title: H4K20me1 plays a dual role in transcriptional regulation during regeneration and axis patterning of Hydra [ChIP-seq Reg]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H4K20me1 in regenerating tips of Hydra.


title: Different immunological mechanisms between AQP4-positive and MOG-positive optic neuritis based on RNA-seq analysis of whole blood

city: Wuxi

first: Wenjun

last: Zou

address: NO.68 Zhongshan Road

institute: Wuxi No.2 People’s Hospital

summary: To compare the different immunological mechanisms between aquaporin 4 antibody-associated optic neuritis (AQP4-ON) and myelin oligodendrocyte glycoprotein antibody-associated optic neuritis (MOG-ON) based on RNA sequencing (RNA-seq) of whole blood.

overall_design: Whole blood was collected from seven healthy volunteers, 6 patients with AQP4-ON and 8 patients with MOG-ON, and used for RNA-seq analysis. An examination of immune cell infiltration was performed using the CIBERSORTx algorithm to identify infiltrated immune cells.

first: Ke

last: Wang

first: Xuelian

last: Chen

first: Libo

last: Cheng


title: The molecular consequences of androgen activity in the human breast

city: Los Angeles

first: Simon

last: Knott

state: California

address: 8723 Alden Dr

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center


title: miRNA expresion data from PDAC Tumour, adjacent normal and PDX tissue samples

status: Public on Mar 06 2023

city: Dublin

first: Fiona

last: O'Neill

state: Dublin

address: National Institute for Cellular Biotechnology, Dublin City University

country: Ireland

institute: DCU

summary:
mRNA expression profiling of pancreatic cancer, comparing adjacent normal tissue, patient tumour and first generation patient derived xenograft tumours
Fresh tumour samples for human pancreatic adenocarcinoma patients were implanted in SCID mice. 70% of these pancreatic ductal adenocarcinoma patients grew as PDX tumours, confirmed by histopathology. Frozen samples from F1 PDX tumours could be later successful passaged in SCID mice to F2 PDX tumours. The human origin of the PDX was confirmed using human specific antibodies; however, the stromal component was replaced by murine cells. Cell lines were successfully developed from three PDX tumours. RNA was extracted from 8 PDX tumours and where possible, corresponding primary tumour and adjacent normal tissues. mRNA profiles of tumour vs F1 PDX and normal vs tumour were compared by Affymetric microarray analysis

overall_design: matched patient samples


title: The molecular consequences of androgen activity in the human breast (ATAC-seq data)

summary:
The mammary gland is a hormone responsive organ and has been extensively studied under the influences of estrogen and progesterone. However, the molecular implications of androgen exposure in the normal breast remain elusive and unexplored, partially due to a lack of relevant tissue to study the functional consequences of androgen action. Transgender men are born female but identify as male, and many choose to undergo gender-affirming androgen therapy, which elicits wide-ranging masculinizing effects that help align their physical characteristics and gender identity.
Here we perform single cell resolution profiling of androgen treated breast tissue from transgender men at the transcriptome, chromatin, and spatial level to elucidate the regulatory action of androgen. We show male-biased androgen receptor gene targets are specifically upregulated in androgen receptor expressing cell types, and that other sex-relevant changes are also initiated in cells lacking androgen receptor expression, through paracrine signaling cascades. We observe a functionally and structurally altered epithelium, shifts in immune populations and directed reduction of capillary vasculature. Finally, we discover evidence of the metabolic impact of androgen and demonstrate how the treatment induces fat loss by specifically targeting adipocyte function. This work provides a comprehensive and mechanistic characterization of the mammary tissue responses to androgen activity at single-cell resolution.

overall_design: single nuclei RNA and ATAC sequencing was used to interrogate molecular responses in breast tissue cells of transgender men and cis-gender females.

first: Florian

last: Raths

first: Mehran

last: Karimzadeh

first: Nathan

last: Ing

first: Ying

last: Qu

first: Andrew

last: Martinez

first: Tian-Yu

last: Lee

first: Brianna

last: Mulligan

first: Suzanne

last: Devkota

first: Bo

first: Armando

middle: E

last: Giuliano

first: Hani

last: Goodarzi

first: Ed

last: Ray

first: Xiaoxiang

last: Cui

first: Yoona

last: Yang

first: Wayne

last: Tilley

first: Theresa

last: Hickey


title: RNAseq analysis of wild-type and npf8.4 under normal or 2-day N-depleted condition

city: Taipei

first: Yi-Fang

last: Tsay

address: 128 Academia Rd, Sec. 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: Our study shows that expression of NPF8.4, as well as most photorespiration-associated genes, are up-regulated in response to 2 days of N depletion. Thus, study of NPF8.4 reveals a novel role for photorespiration in N flux to cope with short-term N depletion.

overall_design: The young leaves of Col-0 and npf8.4 mutant plants grown with 5 mM KNO3 for 15 days or that had been transferred to N-free medium for 2 days were obtained. Each treatment has three biological replicates, with each replicate comprising 15 plants.

first: Yi-Chen

last: Lin


title: Ethanol Induced Cerebellar Transcriptomic Changes in a Postnatal Model of Fetal Alcohol Spectrum Disorders: Focus on Disease Onset

city: Little Rock

first: Stephanie

last: Byrum

state: Arkansas

address: 501 Jack Stephens Dr, Jackson T. Stephens Bldg 4th floor

institute: University of Arkansas for Medical Sciences

summary: Fetal alcohol spectrum disorders (FASD) are a group of neurodevelopmental disorders caused by ethanol exposure in utero, which can result in neurocognitive and behavioral impairments, growth defects, and craniofacial anomalies. FASD affects up to 1-5% of school-aged children in the United States, and there is currently no cure. The underlying mechanisms involved in ethanol teratogenesis remain elusive and need greater understanding to develop and implement effective therapies. Using a third trimester human equivalent postnatal mouse model of FASD, we evaluate the transcriptomic changes induced by ethanol exposure in the cerebellum on P5 and P6, after only 1 or 2 days of ethanol exposure, with the goal of shedding light on the transcriptomic changes induced early during the onset and development of FASD. We have highlighted key pathways and cellular functions altered by ethanol exposure, which include pathways related to immune function and cytokine signaling as well as the cell cycle.  Additionally, we found that ethanol exposure resulted in an increase in transcripts associated with a neurodegenerative microglia phenotype, and acute- and pan-injury reactive astrocyte phenotypes. Mixed effects on oligodendrocyte lineage cell associated transcripts and cell cycle associated transcripts were observed. These studies help to elucidate the underlying mechanisms that may be involved with the onset of FASD and provide further insights that may aid in identifying novel targets for interventions and therapeutics.

overall_design: Comparative gene expression profiling analysis of RNAseq data from neonatal mouse cerebellum in Control versus Ethanol treated animals

first: Kalee

middle: N

last: Holloway

first: James

last: Douglas

first: Tonya

last: Rafferty

first: Ania

last: Majewska

first: Cynthia

last: Kane

first: Paul

last: Drew


title: The molecular consequences of androgen activity in the human breast (RNA-seq data)

first: Simon

last: Knott

first: Florian

last: Raths

first: Mehran

last: Karimzadeh

first: Nathan

last: Ing

first: Ying

last: Qu

first: Andrew

last: Martinez

first: Tian-Yu

last: Lee

first: Brianna

last: Mulligan

first: Suzanne

last: Devkota

first: Bo

last: Wang


title: SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites [CUT&Tag]

status: Public on Mar 05 2023

city: shanghai

first: bao

last: wang

address: jin zun road

institute: shanghai jiao tong university school of medicine

summary: Spatial genome organization is critical for precise gene regulation during development. Special AT-rich sequence binding protein 1 (SATB1) has long been proposed to act as a global chromatin loop organizer in T cells. However, the exact functions of SATB1 in genome organization remain elusive. Here we show that the depletion of SATB1 in human and murine T cells led to transcriptional dysregulation for genes involved in T cell activation, as well as alterations of 3D genome architecture at multiple scales, including the A/B compartment, topologically associating domains (TADs), and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 led to increased chromatin contacts among and across the SATB1/CTCF co-occupied sites, thereby affecting the transcription of critical genes involved in T cell activation. The loss of SATB1 did not affect the genome-wide occupancy of CTCF, but significantly reduced the retention of CTCF in the nuclear matrix. Collectively, our data reveal that SATB1 constrains chromatin topology surrounding CTCF-binding sites by tethering CTCF to the nuclear matrix, and suggest that the functional interplay between SATB1 and CTCF contributes to 3D genome organization.

overall_design: We isolated CD4+ T cells from the peripheral blood of healthy individuals and subsequently activated and expanded the cells for 7 days. Finally, CUT&Tag experiments for SATB1 and CTCF were performed.

first: Bao

first: Luzhang

last: Ji

first: Qian

last: Bian


title: SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites

summary: SATB1, a nuclear matrix-associated protein, has long been proposed to function as a global chromatin loop organizer in T cells. However, the precise roles of SATB1 in chromatin organization remain elusive. Here we show that the depletion of SATB1 in immortalized T cells led to pronounced changes in gene expression, particularly for genes involved in cell proliferation and T cell activation, as well as 3D genome architecture at multiple scales, including the A/B compartment, topologically associating domains (TADs), and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 led to increased association among the SATB1/CTCF co-occupied sites, as well as increased chromatin contacts across these sites, thereby altering the genome-wide chromatin loop landscape. SATB1 does not regulate genome architecture by modulating CTCF occupancy. Rather, the topological effects imposed by SATB1 may be attributed to SATB1-dependent anchoring of CTCF to the salt extraction-resistant nuclear matrix. Together, our findings suggest that the functional interplay between nuclear matrix and CTCF plays a critical role in orchestrating 3D genome organization.

overall_design: We constructed two lentiviral vectors, shCtrl (shRNA control) and shSATB1. After infecting and knocking down the expression of SATB1 in Jurkat cells, we performed RNA-seq experiment.


title: SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites [Hi-C]

overall_design: We constructed two lentiviral vectors, shCtrl (shRNA control) and shSATB1. After infecting and knocking down the expression of SATB1 in Jurkat cells, we performed Hi-C experiment.


title: Endothelin-1-Endothelin B complex contributes to oligodendrocyte differentiation and myelin deficits during preterm white matter injury

status: Public on Mar 04 2023

city: 杭州市

first: 晓龙

last: 辛

address: 浙江省杭州市西湖区三墩镇浙江大学紫金港校区医学院

institute: 浙江大学

summary: Preterm cerebral white matter injury (WMI), a major form of prenatal brain injury, may potentially be treated by oligodendrocyte (OL) precursor cell (OPC) transplantation. However, the defective differentiation of OPCs during WMI seriously hampers the clinical application of OPC transplantation. Thus, improving the ability of transplanted OPCs to differentiate is critical to OPC transplantation therapy for WMI. Here, we established a hypoxia-ischemia-induced preterm WMI model in mice and screened the molecules affected by WMI using single-cell RNA sequencing. We revealed that endothelin (ET)-1 and endothelin receptor B (ETB) were a pair of signaling molecules for the interaction between neurons and OPCs, and that preterm WMI led to an increase in the number of ETB-positive OPCs and premyelinating OLs. Furthermore, the maturation of OLs was reduced by knocking out ETB, but promoted by stimulating ET-1/ETB signaling. Our work reveals a new signaling module for neuron-OPC interaction and provides new insight for therapy targeting preterm WMI.

overall_design: We revealed that endothelin (ET)-1 and endothelin receptor B (ETB) were a pair of signaling molecules for the interaction between neurons and OPCs, and that preterm WMI led to an increase in the number of ETB-positive OPCs and premyelinating OLs and analyzed using scRNAseq.

first: Mengjie

last: Du

first: Xiaolong

last: Xin

first: Chun-Lan

last: Yan

first: Yan

last: Gu

first: Liang

last: Shen


overall_design: We constructed two lentiviral vectors, shCtrl (shRNA control) and shSATB1. After infecting and knocking down the expression of SATB1 in Jurkat cells, we performed CUT_Tag experiment with 2 or 3 replicates in each group.


title: Transcriptome analysis of the potential mechanism of Longkui Yinxiao soup in the treatment of imiquimod-induced psoriasis-like mice

status: Public on Mar 03 2023

city: Shanghai

first: Congcong

last: Zhu

address: 1278 Baode Road

institute: Shanghai Skin Disease Hospital

summary: Psoriasis is a common inflammatory skin disease in clinic. In order to clarify the mechanism of Longkui Yinxiao soup in treating psoriasis, we used imiquimod-induced psoriasis-like mouse model for sequencing analysis. The results showed that its mechanism of action was mainly related to lipid metabolism.

overall_design: This experiment was divided into three groups, namely blank group, model group and Longkui Yinxiao soup group, with 3 replicates in each group. The blank group did not receive any treatment, the model group was coated with imiquimod, and the drug group was given Longkui Yinxiao soup on the basis of imiquimod.

first: Ya

last: Chen

first: Zongguang

last: Tai


title: CMS classification of the CC-531 cells, CC-531 organoids and CC-531 ex vivo tumor tissue grown in the peritoneum of rats

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary:
To investigate the CMS subtype of the CC-531 cells, CC-531 organoids and CC-531 ex vivo tumor tissue grown in the peritoneum of WAG/Rij rats
We then performed gene expression profiling analysis using data obtained from RNA-seq of CC-531 cells, CC-531 organoids and CC-531 ex vivo tumor tissue grown in the peritoneum of WAG/Rij rats of three different passages per sample type.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CC-531 cells, CC-531 organoids and CC-531 ex vivo tumor tissue

first: Roxan

middle: F

last: Helderman

first: Arlene

last: Oei


title: Truncated KDM6A exhibits differential chromatin occupancy and regulatory interactions

city: İZMİR

first: Serap

last: Erkek Özhan

state: BALÇOVA

address: İzmir Biyotıp ve Genom Merkezi (IBG), Dokuz Eylül Üniversitesi Sağlık Yerleşkesi, Mithatpaşa Caddesi No:58/5

country: Turkey

institute: Izmir Biomedicine and Genome Center

summary: Genome-wide studies characterizing mutational landscape of bladder cancer revealed the exceptionally high rate of chromatin modifier genes in bladder cancer. Thus, epigenetic deregulation is a critical theme which needs further investigation for bladder cancer research. One of the highly mutated genes in bladder cancer is KDM6A, functioning as H3K27 demethylase and part of MLL3/4 complexes. To decipher the role of KDM6A in normal vs tumor setting, we identified the genomic localization profiles of KDM6A in normal, immortalized and cancer bladder cells. Our results showed differential occupancy of KDM6A at the genes involved in cell differentiation, chromatin organization and Notch signaling depending on the cell type and the mutation status of KDM6A. Transcription factor motif analysis revealed an enrichment for HES1 for the KDM6A peaks identified for T24 bladder cancer cell line, which has a truncating mutation in KDM6A and lacking demethylase domain and also for the other clusters showing KDM6A localization. For the first time, using co-immunoprecipitation experiments, we show that KDM6A is in complex with TLE co-repressors and HES1, and illustrate the potential interaction of KDM6A with TLE co-repressors, HES1, RUNX, HHEX transcription factors by computational structural biology models. Our work makes important contributions to the understanding of KDM6A malfunction in bladder cancer and provides models for the functioning of KDM6A independent of its demethylase activity.

overall_design: ChIP-Seq

last: Özhan

first: Gülden

middle: O

last: Yılmaz

first: Gökhan

last: Karakülah


title: Identification of PITX2 as a novel factor in arrhythmogenic cardiomyopathy pathogenesis [patient line]

status: Public on Mar 02 2023

city: Leiden

first: Sebastiaan

middle: Johannes

last: van Kampen

address: Sylviusweg 62

institute: LUMC

summary: In this study, we identified a novel heterozygous variant within DSP (c.3562T>C) in a patient diagnosed with ACM. Using CRISPR/Cas9 we corrected patient-derived human induced pluripotent stem cells (hiPSC) and created a knock-in (KI) hiPSC line with the same mutation. Compared to wildtype cardiomyocytes, we observed a prolonged action potential duration (APD) and reduced expression of desmosomal components, which was paralleled by abnormal levels of essential cardiac ion channels. Strikingly, the transcription factor paired-like homeodomain 2 (PITX2), which acts as a repressor of ion channel-related genes, was induced in these cells. Together, we identified PITX2 as a potential missing link between mutations in DSP and the cardiac conductance abnormalities often seen in these patients.

overall_design: hiPSC-derived cardiomyocyte mRNA profiles for DSP p.Tyr1188His/WT and control cells - Patient line.

first: Eva

last: van Rooij


title: Spontaneously Evolved Progenitor Niches Escape Yap Oncogene Addiction in Advanced Pancreatic Ductal Adenocarcinomas [RNA-Seq]

city: Washington

first: Chunling

last: Yi

state: DC

address: 3700 O St NW

department: Oncology

institute: Georgetown University

summary: Lineage plasticity has been proposed as a major source of intratumoral heterogeneity and therapeutic resistance. Employing an inducible genetic engineered mouse model, we illustrate that lineage plasticity enables advanced Pancreatic Ductal Adenocarcinoma (PDAC) tumors to develop spontaneous relapse following elimination of the central oncogenic driver - Yap. Transcriptomic and immunohistochemistry analysis of a large panel of PDAC tumors reveals that within high-grade tumors, small niches of PDAC cells gradually evolve to re-activate pluripotent transcription factors (PTFs), which lessen their dependency on Yap. Comprehensive Cut&Tag analysis demonstrate that although acquisition of PTF expression is coupled with the process of epithelial-to-mesenchymal transition (EMT), PTFs form a core transcriptional regulatory circuitry (CRC) with Jun to overcome Yap dependency, which is distinct from the classic TGFb-induced EMT-TF network.  A chemical-genetic screen and follow-up functional studies establish Brd4 as an epigenetic gatekeeper for the PTF-Jun CRC, and strong synergy between BET and Yap inhibitors in blocking PDAC growth.

overall_design: RNA-seq of GFP+Yap+ and Tm+Yap- cells from Murine Primary Pancreatic Ductal Carcinoma (PDAC)

first: Shigekazu

last: Murakami

first: Shannon

last: White

first: Alec

last: McIntosh

first: Chan

last: Nguyen


title: Mac-1 marks a quiescent and functionally superior HSC subset during regeneration

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

institute: BMC

summary: Here, we assessed the expression of Mac-1 on mouse HSCs during regeneration following transplantation and observed a transient increase in Mac-1 expression during the early reconstitution phase. Serial transplantation experiments demonstrated that reconstitution potential was highly enriched in the Mac-1+ portion of the HSC pool.

overall_design: RNAseq of steady state HSCs and HSCs isolated 4 weeks after transplantation and sorted based on their expression of Mac-1

first: Anna

last: Rydström

first: Els

last: Mansell

first: Valgardur

last: Sigurdsson

first: Julia

last: Sjöberg

first: Kenichi

last: Miharada

first: Jonas

last: Larsson


title: Identification of PITX2 as a novel factor in arrhythmogenic cardiomyopathy pathogenesis

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

overall_design: Refer to individual Series


title: Genomic methylation patterns in pre-meiotic gynoecia of wild-type and RdDM mutants of Arabidopsis

city: Irapuato

first: Jean-Philippe

last: Vielle-Calzada

state: Guanajuato

address: Libramiento Norte carretera Leon Km 9.6

country: Mexico

institute: CINVESTAV

type: Methylation profiling by high throughput sequencing

summary: Although DNA methylation patterns are generally considered to be faithfully inherited in Arabidopsis thaliana (Arabidopsis), there is evidence of reprogramming during both male and female gametogenesis. The gynoecium is the floral reproductive organ from which the ovules develop and generate meiotically derived cells that give rise to the female gametophyte. It is not known whether the gynoecium can condition genomic methylation in the ovule or the developing female gametophyte. We performed whole genome bisulfite sequencing to characterize the methylation patterns that prevail in the genomic DNA of pre-meiotic gynoecia of wild-type and three mutants defective in genes of the RNA-directed DNA methylation pathway (RdDM): ARGONAUTE4 (AGO4), ARGONAUTE9 (AGO9), and RNA-DEPENDENT RNA POLYMERASE6 (RDR6). By globally analyzing transposable elements (TEs) and genes located across the Arabidopsis genome, we show that DNA methylation levels are similar to those of gametophytic cells rather than those of sporophytic organs such as seedlings and rosette leaves. We show that none of the mutations completely abolishes RdDM, suggesting strong redundancy within the methylation pathways. Among all, ago4 mutation has the strongest effect on RdDM, causing more CHH hypomethylation than ago9 and rdr6. We identify 22 genes whose DNA methylation is significantly reduced in ago4, ago9 and rdr6 mutants, revealing potential targets regulated by the epigenetic landscape in premeiotic gyneocia. Our results indicate that drastic changes in methylation levels in all three contexts occur in female reproductive organs at the sporophytic level, prior to the alternation of generations within the ovule primordium, offering a possibility to start identifying the function of specific genes acting in the establishment of the female gametophytic phase of the Arabidopsis life cycle.

overall_design:
We analyzed methylomes that prevail in pre-meiotic gynoecia of wild-type and three mutants defective in genes of AGO4, AGO9 and RDR6. All the genotypes are in Col-0 background. Two biological replicates per genotype were sequenced. Once its biological reproducibility was ensured by means of a PCA that took into account the CG methylation in windows of 1 nucleotide, the mapped reads were collapsed by genotype for subsequent analyzes that gave rise to our results.
Please note that the processed data generated from both replicates is linked to the corresponding *replicate #1 sample records.

first: Quetzely

last: Ortiz-Vasquez

first: Gloria

last: León-Martínez

first: Carlos

last: Barragán-Rosillo

first: Eduardo

last: González-Orozco

first: Samuel

last: Deans

first: Billy

last: Aldridge

first: Martin

last: Vickers

first: Xiaoqi

last: Feng


title: From a cells model to a fish trial: Characterization of the immunomodulatory effects of Heat-killed Lactiplantibacillus plantarum as a functional ingredient in aquafeeds for salmonids

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

summary: RNA-seq analysis showed that HK L-137 was able to modulate the gene expression of pathways related to molecular function, biological process and cellular component in DI, without compromising fish performance and gut microbiota. Considering these data, our study has shown that HK L-137 can modulate the physiological response of Atlantic salmon, making fish more robust and possibly more able to cope better under stress factors during production.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for distal intestine from Atlantic salmon fed HK L-137

first: B

last: Morales-Lange

first: S

last: Rocha

first: M

last: Øverland


title: Bitter taste cells in the ventricular walls of the murine brain regulate glucose homeostasis

status: Public on Mar 01 2023

city: Saarbrücken

first: Kathrin

last: Kattler-Lackes

state: non-US Resident

address: Campus A2.4 Raum 0.13

department: Epigenetics

country: Germany

institute: Saarland University

summary: The median eminence (ME) is a circumventricular organ at the base of the brain that controls body homeostasis. Tanycytes are its specialized glial cells that constitute the ventricular walls and regulate different physiological states, however individual signaling pathways in these cells are incompletely understood. Here, we identify a functional tanycyte subpopulation that expresses key taste transduction genes including bitter taste receptors, the G protein gustducin and the gustatory ion channel TRPM5 (M5). M5 tanycytes have access to blood-borne cues via processes extended towards diaphragmed endothelial fenestrations in the ME and mediate bidirectional communication between the cerebrospinal fluid and blood. This subpopulation responds to metabolic signals including leptin and other hormonal cues and is transcriptionally reprogrammed upon fasting. Acute M5 tanycyte activation induces insulin secretion and acute diphtheria toxin-mediated M5 tanycyte depletion results in impaired glucose tolerance in diet-induced obese mice. We provide a cellular and molecular framework that defines how bitter taste cells in the ME integrate chemosensation with metabolism.

overall_design: M5-GFP and M5-DREADD-GFP mice were i.c.v. injected with 2 ml AAV2/1+2-CAGS-mCherry virus three weeks before cell sorting. The basal hypothalamus from adult male M5-GFP mice, which either underwent 14 hours of fasting (8 mice) or normal diet feeding (6 mice) or from 6 adult male M5-DREADD-GFP mice (M5-GFP mice were used as control (6 mice), animals were injected with 2 µg CNO i.c.v. and sacrificed after 3 hours) were dissected and pooled from 2 mice. Dissociation was performed using a Papain dissociation system (Worthington) as described previously73. The dissociated cells were then sorted using FACS (Sony SH800). Cells were sorted by fluorescence (endogenously expressed GFP and virally expressed mCherry) with excitation at 488 nm and 560 nm and emission detected at 508 nm and 600/60 nm. Approximately 1000 sorted M5 tanycytes for each condition were used to build RNA-seq libraries using the Smart-seq2 method.

first: Qiang

last: Yu

first: Igor

last: Gamayun

first: Philipp

last: Wartenberg

first: Qian

last: Zhang

first: Sen

last: Qiao

first: Soumya

last: Kusumakshi

first: Sarah

last: Candlish

first: Viktoria

last: Götz

first: Shuping

last: Wen

first: Debajyoti

last: Das

first: Amanda

last: Wyatt

first: Vanessa

last: Wahl

first: Fabien

last: Ectors

last: Kattler

first: Daniela

last: Yildiz

first: Vincent

last: Prevot

first: Markus

last: Schwaninger

first: Gaetan

last: Ternier

first: Paolo

last: Giacobini

first: Philippe

last: Ciofi

first: Timo

last: Müller

first: Ulrich

last: Boehm


title: Knocking down CDKN2A in 3D hiPSC-derived brown adipose progenitors potentiates differentiation, oxydative metabolism and browning process

city: LILLE

first: souhila

last: amanzougarene

address: 1 place de Verdun

institute: CNRS

summary: Human induced pluripotent stem cells (hiPSCs) have the potential to be differentiated into any cell type, making these cells a relevant tool for therapeutic purposes such as cell-based therapies. In particular, they show great promise for obesity treatment as they represent an unlimited source of brown/brite adipose progenitors (hiPSC-BAPs), although the low brown/brite adipocyte differen-tiation potential in 2D culture represents a strong limitation for clinical use. In adipose tissue, be-sides to its cell cycle regulator functions, the cyclin-dependent kinase inhibitor 2A (CDKN2A) lo-cus modulates the commitment of stem cells to the brown-like type fate, mature adipocyte energy metabolism and browning of adipose tissue. Here, using a new method of hiPSC-BAPs 3D culture, via the formation of an organoid-like structure, we silenced CDKN2A expression during hiPSC-BAP adipogenic differentiation and observed that knocking down CDKN2A potentiates adipogenesis, oxidative metabolism and browning process, resulting in brown-like adipocytes by promoting UCP1 expression and beiging markers. Our results suggest that modulating CDKN2A levels could be relevant for hiPSC-BAPs cell-based therapies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  triplicats sample of hiPSC-BAP 3D at two time points during differentiation and effect of CDKN2A deficiency (siCtrl D0, siCtrl D10, siCDKN2A D0,siCDKN2A D10).

first: Yasmina

last: Kahoul

first: Xi

last: Yao

first: Frédérik

last: Oger

first: Maeva

last: Moreno

first: Souhila

last: Amanzougarene

first: Mehdi

last: Derhourhi

first: Emmanuelle

last: Durand

first: Raphael

last: Boutry

first: Amélie

last: Bonnefond

last: Froguel

first: Christian

last: Dani

first: Jean-Sébastien

last: Annicotte

first: Christophe

last: Breton


title: Identification of PITX2 as a novel factor in arrhythmogenic cardiomyopathy pathogenesis [KI]

first: Sebastiaan

last: van Kampen

overall_design: hiPSC-derived cardiomyocyte mRNA profiles for DSP p.Tyr11988His/WT and control cells - KI line.

first: Eva

last: van Rooij


title: Alterations in oligodendrocyte transcriptional networks reveal region-specific vulnerabilities to neurological disease

first: Brent

last: Fogel

state: CA

address: 710 Westwood Plaza

department: Neurology

institute: UCLA

summary: We identified region-specific co-expression networks representing distinct molecular pathways in oligodendrocytes associated with human neurological disease. Bioinformatic analyses reveal molecular regulators of these networks and, in this data, we confirmed modulation of network expression in vitro in a human cell line. This work supports identification of targetable region-specific vulnerabilities to neurological disease mediated by oligodendrocytes.

overall_design: To validate the results of our systems-level analysis in mouse OLs and connect our observations to human biology and disease, we performed validation experiments using a human OL cell line (HOG) followed by RNA-seq and WGCNA to independently confirm the effects observed in the mouse models.

first: Dario

last: Tommasini

first: Rachel

last: Fox

first: Kathie

last: Ngo

first: Jason

last: Hinman


title: Porcine anti-human lymphocyte immunoglobulin depletes the lymphocyte population to promote successful kidney transplantation

city: Wuhan

first: Kuanhong

last: Xu

address: 1 Zhengdian Gold Industrial Park Road, Jiangxia District, Wuhan, China.

institute: Wuhan Institute of Biological Products

summary: Porcine anti-human lymphocyte immunoglobulin (pALG) has been used in kidney transplantation, but its impacts on the lymphocyte cell pool remain unclear. We retrospectively analyzed 12 kidney transplant recipients receiving pALG, and additional recipients receiving rabbit anti-human thymocyte immunoglobulin (rATG), basiliximab, or no induction therapy as a comparison group. pALG showed high binding affinity to peripheral blood mononuclear cells (PBMCs) after administration, immediately depleting blood lymphocytes; an effect that was weaker than rATG but stronger than basiliximab. Single-cell sequencing analysis showed that pALG mainly influenced T cells and innate immune cells (mononuclear phagocytes and neutrophils). By analyzing immune cell subsets, we found that pALG moderately depleted CD4+T cells, CD8+T cells, regulatory T cells and NKT cells and mildly inhibited dendritic cells. Serum inflammatory cytokines (IL-2, IL-6) were only moderately increased compared with rATG, which might be beneficial in terms of reducing the risk of untoward immune activation. During 3 months of follow-up, we found that all recipients and transplanted kidneys survived and showed good organ function recovery; there were no cases of rejection and a low rate of complications. In conclusion, pALG acts mainly by moderately depleting T cells and is thus a good candidate for induction therapy for kidney transplant recipients. The immunological features of pALG should be exploited for the development of individually-optimized induction therapies based on the needs of the transplant and the immune status of the patient, which is appropriate for non-high-risk recipients.

overall_design: We performed single-cell sequencing on PBMCs obtained from one recipient preoperatively(ZZH20220826-0) and on POD7 (ZZH20220901-7).

first: Limin

last: Zhang

first: Haoyong

last: Zou


title: Integrated Gut/Liver-on-a-Chip platform as in vitro human model of non-alcoholic fatty liver disease

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

summary: Non-alcoholic fatty liver disease (NAFLD) influence one of third population around the world. Until now, no effective treatments have been established due to the improper in vitro assays and experimental animal models. By co-culturing human gut and liver cell lines (CaCO2 and HepG2 cells, respectively) interconnected via the microfluidic closed medium circulation loop, we created a gut-liver-on-a-chip (iGLC) platform as an in vitro human model of the gut-liver axis (GLA) in initiation and progression of NAFLD.

overall_design: We analyzed cDNA profiles amplified with PCR-cDNA Barcoding Kit generated from RNAs in CaCO2 human gut cells and HepG2 human hpatocellular carcinoma cells with mono- or co-cultured conditions treated with 1 mM of free fatty acids using Oxford Nanopore MiniON.

first: Jiandong

last: Yang

first: Yoshikazu

last: Hirai

first: Iida

last: Kei

first: Ken-ichiro

last: Kamei


title: Toll-like receptor 4 signaling in osteoblasts is required for load-induced bone formation in mice

city: Philadelphia

first: Ryan

last: Tomlinson

address: 1015 Walnut Street

department: Orthopaedic Surgery

institute: Thomas Jefferson University

summary: In this study, we aimed to determine the function of toll-like receptor 4 (TLR4), a key receptor in the NF-κB signaling pathway expressed in osteoblasts. Specifically, we hypothesized that the loss of TLR4 signaling in osteoblasts would result in diminished load-induced bone formation due to decreased NGF expression following loading.

overall_design: RNA sequencing from loaded and non-loaded bones from wildtype and CKO mice


title: Spatial transcriptome uncovers rich coordination of metabolism and signaling in bacterial community (data 2)

first: Tianmin

last: Wang

address: Huaxia Middle Road, 393

department: School of Life Science and Technology

institute: ShanghaiTech University

overall_design: RNA-seq data, using miniBac-seq method to generate RNA-seq data

first: Ping

last: Shen


title: Restraint of IFN-γ expression through a distal silencer CNS–28 for tissue homeostasis

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

summary: Interferon-gamma (IFN-gamma) is a key cytokine in response to viral or intracellular bacterial infection in mammals. While a number of enhancers are described to promote IFN-gamma responses, no silencers for the Ifng gene have been identified. By examining H3K4me1 histone modification in naïve CD4+ T cells within Ifng locus, we identified an unrecognized silencer (CNS–28) that is responsible for restraining Ifng expression. Mechanistic study further demonstrates that CNS–28 maintains Ifng silence by diminishing enhancer-promoter interactions within Ifng locus in a T-bet independent manner. Functionally, CNS–28 restrains Ifng transcription in Th1, Tc1, and NK cells during both innate and adaptive immune responses. Moreover, CNS–28 deficiency resulted in repressed type 2 responses due to elevated IFN-gamma expression, shifting Th1 and Th2 paradigm. Thus, CNS–28 activity ensures immune cell quiescence by cooperating with other regulatory cis elements within the Ifng gene locus to minimize autoimmunity.

overall_design: ChIP-seq, RNA-seq, and Hi-TrAC were used to study the function of a cis-regulatory element of IFN-g in wild type and knockout mice.

first: Kairong

last: Cui

first: Zuojia

last: Chen

first: Shuai

last: Liu

first: Gang

last: Ren

first: Gangqing

last: Hu

first: Difeng

last: Fang

first: Chengyu

first: Jinfang

last: Zhu

first: Chuan

last: Wu

first: Keji

last: Zhao


first: Kei

last: IIDA

overall_design: We analyzed cDNA profiles amplified with SMART-seq v4 generated from RNAs in CaCO2 human gut cells and HepG2 human hpatocellular carcinoma cells with mono- or co-cultured conditions treated with 1 mM of free fatty acids using NovaSeq 6000.

first: Yang

last: Jiandong

first: Hirai

last: Yoshikazu

last: Iida

first: Kamei

last: Ken-ichiro


title: Hoxa1 LoF RNA-seq

status: Public on Feb 28 2023

city: Marseille

first: Stéphane

last: Zaffran

address: 27 Bd Jean Moulin

department: U1251 INSERM

institute: Aix Marseille Univ

summary: Transcriptomic profiling of Hoxa1 null mouse embryos

overall_design: Microdissection of the anterior region in E9.5 embryos.

first: Gaëlle

last: Odelin


title: Impact of media culture and PBMCs signaling on in vitro CD4+ T cells cultures to an optional HIV reactivation assay design.

city: Roma

first: Giuseppe

middle: Rubens

last: Pascucci

state: RM

address: Sant'Onofrio square, 4

department: University Hospital Pediatric Department (DPUO)

country: Italy

institute: Bambino Gesù Children's Hospital

summary: Most of the current assays directed at the investigation of HIV reactivation are based on cultures of infected cells stimulated in vitro with different activatory molecules (i.e.TILDA and QVOA test). The RPMI culture media developed for these tests often include animal components (i.e. Fetal bovine serum, FBS) for their practicality and affordability, but nonetheless lack many age- and donor-specific immunomodulatory components normally found within the autologous plasma. This triggered our interest in understanding the possible impact that different matrices (RPMI or autologous plasma) and the other PBMCs could have on T cell expression profiles, collected from people living with HIV, when cultured/stimulated in vitro. Transcriptional profiles of CD4+ T cells isolated before or after in vitro cell culture from three ART-treated young adults with HIV perinatal infection, highlighted a mitigatory action of plasma on CD4 lymphocytes upon stimulation.

overall_design: We explored the full transcriptome of CD4+ T cells from 3 HIV donors evaluating the impact of isolating the CD4 pre-culture (PREc) or post-culture (POSTc), using autologous plasma (PLSM) or RPMI as culture matrix. Cells were stimulated for 18 h with PMA/IONO and IL-2 together with AZT, or left unstimulated for both matrices (Fig.1). Taking into account all these variables, we analyzed 8 different experimental condition combinations for each donor, plus a sample of un-cultured CD4+ T cells (T0). Overall, a total of 27 samples were sequenced using the MiniION Oxford Nanopore platform.

middle: R

first: Elena

last: Morrocchi

first: Nicola

last: Cotugno

first: Paolo

last: Palma


title: Validation of the upgraded EPIC DNA methylation microarray (900K EPIC v2.0) for high-throughput profiling of the human DNA methylome

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: Technical and biological validation of the new Illumina Infinium HumanMethylationEPIC version 2.0 microarray. Primary normal and tumor tissues and cancer cell lines from different sources were hybridized with the Illumina Infinium HumanMethylationEPIC version 1.0 and version 2.0 to test the robustness of the new version.

overall_design: Bisulphite converted DNA from 48 samples were hybridized to the Illumina Infinium HumanMethylationEPIC version 2.0 microarray

first: Aleix

last: Noguera-Castells

first: Carlos

last: García-Prieto

first: Damiana

last: Álvarez-Errico


title: Generation of stable epithelial-mesenchymal hybrid cancer cells with tumorigenic potential

city: Detroit

first: Gil

middle: G.

last: Mor

state: Michigan

address: 275 E. Hancock

department: C.S. Mott Center for Human Growth and Development

country: USA

institute: Wayne State University School of Medicine

summary: This study was conducted to dissect and characterize the different steps during the transition of cancer cells into the E/M hybrid state

overall_design: Gene expression profiles were compared between non-treated (NT) human ovarian cancer cell line (R182) and treated with hepatocyte growth factor (HGF)

first: Roslyn

last: Tedja

first: Ayesha

middle: B

last: Alvero

first: Alexandra

last: Fox

last: Cardenas

first: Mary

last: Pitruzzello

first: Hussein

last: Chehade

first: Tejeswhar

last: Bawa

first: Nicholas

last: Adzibolosu

first: Radhika

last: Gogoi


title: A cis-element at the Rorc locus regulates the development of type 3 innate lymphoid cells

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

country: China

institute: Tsinghua University

summary: As an important early source of IL-17A and IL-22 in immune responses, type 3 innate lymphoid cells (ILC3s) are critically regulated by the transcription factor retinoic-acid-receptor-related orphan receptor gamma t (RORγt). Previously, we have identified a crucial role of the conserved non-coding sequence 9 (CNS9), located at +5,802 to +7,963 bp of the Rorc gene, in directing T helper 17 differentiation and related autoimmune disease. However, whether cis-acting elements regulate RORγt expression in ILC3s is unknown. Here we show that CNS9 deficiency in mice not only decreases ILC3 signature gene expression and increases ILC1-gene expression features in total ILC3s, but also leads to generation of a distinct CD4+NKp46+ ILC3 population, though the overall numbers and frequencies of RORγt+ ILC3s are not affected. Mechanistically, CNS9 deficiency selectively decreases RORγt expression in ILC3s, which thus alters ILC3 gene expression features and promotes cell-intrinsic generation of CD4+NKp46+ ILC3 subset. Our study thus identifies CNS9 as an essential cis-regulatory element controlling the lineage stability and plasticity of ILC3s through modulating expression levels of RORγt protein.

overall_design: scRNA-seq of small intestinal LPL ILC3s from B6 background WT and CNS9KO mice

first: Dehui

last: Chang

first: Xiaohong

last: Zhao


title: Serum microRNA expression prior to motion sickness stimulus

city: Dayton

first: Michael

last: Markey

state: OH

address: 3640 Colonel Glenn Hwy.

department: Biochemistry and Molecular Biology

institute: Wright State Unviersity

summary: Motion Sickness increases risk of performance deficits and safety of flight concerns. The etiology of motion sickness is poorly understood. Here, we attempted to quantify the physiological effects of motion sickness on static balance and determine the genetic predictors associated with these effects.

overall_design: 16 subjects underwent a disorientation stimulus to induce motion sickness. Motion sickness susceptibility was identified empirically. Postural balance outcomes were measured using two tasks, and small ribonucleic acid profiles were assessed with blood draws before motion sickness stimulus (in 15 subjects). Differences in postural sway before and after the stimulus as well as effect modification of susceptibility were assessed. A random forest followed by regression tree analysis was constructed for each postural sway variable to determine top genetic and covariate predictors.


title: A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum

city: Memphis

first: John

last: Easton

state: TN

address: 1383 Island Town Dr

department: Computational Biology

institute: St.Jude Children's Research Hospital

summary: To acquire an enhanced understanding of the molecular processes that mediate cerebellar development, we performed single-cell RNA-sequencing of 39,245 murine cerebellar cells at twelve critical developmental time points. Using recognized lineage markers, we confirmed that the single-cell data accurately recapitulate cerebellar development

overall_design: scRNA-Seq

first: Robert

middle: A

last: Carter

first: Laure

last: Bihannic

first: Celeste

last: Rosencrance

first: Sivaraman

last: Natarajan

first: Charles

last: Gawad

first: Jennifer

last: Hadley

first: Paul

last: Northcott


title: Human umbilical cord mesenchymal stem cell-derived exosomes promote murine skin wound healing by neutrophil and macrophage modulations revealed by single-cell RNA sequencing

status: Public on Feb 27 2023

first: Yuanyuan

last: Liu

address: Medical School of Chinese People's Liberation Army, 100039 Beijing, China.

summary: Full-thickness skin wound healing remains a serious undertaking for patients. While stem cell exosomes have been proposed as a potential therapeutic approach, the underlying mechanism of action has yet to be fully elucidated. The current study aimed to investigate the impact of exosomes derived from human umbilical cord mesenchymal stem cells (hucMSC-Exosomes) on the single-cell transcriptome of neutrophils and macrophages in the context of wound healing. Utilizing single-cell RNA sequencing, the transcriptomic diversity of neutrophils and macrophages was analyzed in order to predict the cellular fate of these immune cells under the influence of hucMSC-Exosomes and to identify alterations of ligand-receptor interactions that may influence the wound microenvironment. The validity of the findings obtained from this analysis was subsequently corroborated by immunofluorescence, ELISA, and QPCR. Neutrophil origins were characterized based on RNA velocity profiles. The expression of RETNLG and SLC2A3 was associated with migrating neutrophils, while BCL2A1B was linked to proliferating neutrophils. The hucMSC-Exosomes group exhibited significantly higher levels of M1 macrophages (215 vs 76, p < 0.00001), M2 macrophages (1231 vs 670, p < 0.00001), and neutrophils (930 vs 157, p < 0.00001) when compared to control group. Additionally, it was observed that hucMSC-Exosomes elicit alterations in the differentiation trajectories of macrophages towards more anti-inflammatory phenotypes, concomitant with changes in ligand-receptor interactions, thereby facilitating healing. This study has revealed the transcriptomic heterogeneity of neutrophils and macrophages in the context of skin wound repair following hucMSC-Exosomes interventions, providing a deeper understanding of cellular responses to hucMSC-Exosomes, a rising target of wound healing intervention.

overall_design: C57/BL6j mice skin wound treated with hucMSC-Exosomes were analyzed using scRNAseq.

first: Mingwang

last: Zhang

first: Rongya

last: Yang


title: Transcriptome profiling from peripheral white blood cells in fertile and subfertile beef heifers at weaning

city: Auburn

middle: W

last: Dyce

state: Alabama

address: 559 Devall Dr,

department: Animal Science

institute: Auburn University

summary: The gene expression profiles were measured using RNA-Seq beef heifers sampled at weaning and retrospectively classified as pregnant through artificial insemination (AI-P, n = 8) or non-pregnant (NP, n = 7). In brief, crossbred heifers (Angus-Simmental) were used in this study. At the time of weaning (~238 days after birth), blood samples (10 mL) were collected from the jugular vein into vacutainers containing EDTA. The blood was processed to extract PWBC and was stored at -80 until further processing. During the breeding season, all the heifers followed the same breeding protocol, estrus synchronization, and fixed-time artificial insemination (AI). Fourteen days following the fixed-time AI, the non-pregnant heifers were exposed to fertile bulls for 60 days. Depending on the presence or absence of conceptus at 75 days following AI, heifers were classified as pregnant to AI (AI-P), pregnant to natural breeding (P-NB) or non-pregnant (NP). Heifers that were pregnant to AI (N = 8) and non-pregnant (N = 7) were considered for the study. Total RNA was extracted from peripheral white blood cells of 15 samples (AI-P and NP) and was subjected to sequencing. The RNA-Seq data were subjected to quality control and mapped with STAR aligner to Ensemble’s ARS UCD1.2 Bos taurus reference genome. Read quantification was performed using a STAR aligner to obtain raw counts per gene. Genes with low counts were filtered out. After filtering, the read counts were analyzed using DESeq2 v 1.26.0 to identify differentially expressed genes (DEGs). The DEGs with padj < 0.05 and absolute (log2 fold change) > 0.5 were considered significant. The NP heifers were considered as the reference group, and the DEGs up or downregulated were classified based on the log2 fold change direction. We identified 92 DEGs between AI-P and NP groups. The top pathways identified with DEGs were the immune system, cytokine production and defense response, hematopoietic cell lineage, positive regulation of reactive oxygen species metabolic process, and negative regulation of cysteine-type endopeptidase activity involved in the apoptotic process.

overall_design: Peripheral white blood cell mRNA profiles from 15 Angus-Simmental crossbred heifers (AI-P = 8; NP = 7) were generated using the Illumina Nova-Seq platform. Paired-end 100 bp reads were generated for each sample.

first: Priyanka

last: Banerjee

first: Wellison

last: Diniz

first: Soren

last: Rodning


title: Molecular determinants of mouse adaptation of rat hepacivirus

city: Copenhagen N

first: Troels

middle: K H

last: Scheel

state: Copenhagen

address: Blegdamsvej 3

department: Institute for Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

summary: Lack of immunocompetent animal models for hepatitis C virus (HCV) impedes vaccine development and studies of  immune responses. Norway rat hepacivirus (NrHV) infection in rats shares HCV-defining characteristics, including hepatotropism, chronicity, immune responses, and aspects of pathology. To exploit genetic variants and research tools, we previously adapted NrHV to prolonged infection in laboratory mice. Through intrahepatic RNA inoculation of molecular clones of identified variants, we here characterized four mutations in the envelope proteins responsible for mouse adaptation, including one disrupting a glycosylation site. These mutations led to high titer viremia, similar to that observed in rats. In 4-week-old mice, infection was cleared after around 5 weeks compared to 2-3 weeks for non-adapted virus. In contrast, the mutations led to persistent but attenuated infection in rats, and they partially reverted accompanied by an increase in viremia. Attenuated infection in rat but not mouse hepatoma cells demonstrated that the characterized mutations were indeed mouse adaptive rather than generally enhancing fitness in both cell lines, and that species determinants and not immune interactions were responsible for attenuation in rats. Unlike persistent NrHV infection in rats, acute resolving infection in mice was not associated with development of neutralizing antibodies. Finally, infection of scavenger receptor B-I (SR-BI) knockout mice suggested that adaptation to mouse SR-BI was not a primary function of the identified mutations. Rather, the virus may have adapted to lower dependency on SR-BI, thereby potentially surpassing species-specific differences. In conclusion, we identified specific determinants of NrHV mouse adaptation, suggesting species-specific interactions during entry.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Mice and rats were infected by intrahepatic inoculation of 10 µg in vitro-transcribed viral genomic RNA. Blood samples were collected at the indicated timepoints and viral RNA was extracted form blood sera using TRIzol. The whole viral ORF was reverse-transcribed by RT-PCR using the Maxima H Minus Reverse Transcriptase. The resulting cDNA was purified and libraries were prepared using the NebNext Ultra II FS DNA Library Prep Kit for Illumina. Libraries were quantified using Qubit and pooled at equimolar concentration. Deep sequencing was performed on an Illumina MiSeq instrument.

first: Raphael

last: Wolfisberg

first: Kenn

last: Holmbeck

first: Eva

last: Billerbeck

first: Caroline

last: Thorselius

first: Marina

last: Batista

first: Ulrik

last: Fahnoe

first: Emma

last: Lundsgaard

first: Matthew

last: Kennedy

first: Louise

last: Nielsen

last: Rice

first: Jens

last: Bukh

middle: K


title: Adenosine deaminase augments SARS-CoV-2 specific cellular and humoral responses in aged mouse models of immunization and challenge

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Aged patients suffer disproportionately increased morbidity and mortality associated with SARS-CoV-2 infection. Despite numerous clinically available vaccines and therapeutics, aged patients remain at increased risk for COVID-19 morbidity. Furthermore, the aged patient population has suboptimal responses to SARS-CoV-2 vaccine antigens. Here, we characterize vaccine-induced responses to SARS-CoV-2 synthetic DNA vaccine antigens in 18-month-old mice and interrogate protection. Aged mice have altered cellular responses, including decreased IFNγ secretion and increased TNFα secretion as compared to young mice. Aged mice had significantly decreased binding and neutralizing antibodies in their serum compared to their young counterparts. Co-immunization with the plasmid-encoded molecular adjuvant adenosine deaminase-1 (pADA) enhanced cellular responses and expanded the breadth of humoral responses in aged mice. pADA co-delivery also altered the gene expression profiles of lymph node lymphocytes in aged animals. Upon challenge pADA co-immunization modestly decreased age-associated morbidity and mortality in ACE2 transgenic and mouse-adapted SARS-CoV-2 challenge models. These data support the use of aged mice as a model for age-associated decreased vaccine immunogenicity and infection-mediated morbidity and mortality in the context of SARS-CoV-2 and provide further support of the use of adenosine deaminase as a molecular adjuvant.

overall_design: single cell RNA-seq in young and aged treated and naïve mice

first: Ebony

last: Gary

first: David

last: Weiner


title: CCN3 administration after surgically induced myocardial infarction

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

overall_design: After surgically ligating the left anterior descending artery, mice were administered recombinant human CCN3 at a concentration of 6 µg/kg or PBS as a control by intraperitoneal injection daily for four days. Left ventricles of were collected after four days and total RNA was extracted by via Trizol. Three biological replicates were assessed per group.

first: Jenny

last: Drnevich

first: Catilin

middle: C

last: O'Meara


title: Aging-related changes of facial skin microbiome in healthy women.

status: Public on Feb 24 2023

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary: Profiling the skin microbiota composition from the face of healthy women. Exploring the differences between three age groups and between dry skin and not dry.

overall_design: Total DNA was extracted from the face skin swabs, amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x250bp) Illumina platform.

first: Amedeo

last: Amedei

first: Edda

last: Russo

first: Leandro

last: Di Gloria


title: Intronic natural antisense transcripts in glioma patient biopsies

city: Kaunas

first: Dovydas

last: Širvinskas

address: Eivenių st. 4

country: Lithuania

institute: Lithuanian University of Health Sciences

summary: Natural non-coding antisense transcripts (ncNATs) are long non-coding RNAs (lncRNA) transcribed from the opposite strand of a separate protein coding or non-coding gene and can affect the overlapped gene expression through epigenetic, transcriptional, post-transcriptional and/or translational modulations. ncNATs can influence cancerous cell proliferation, migration and therapeutic resistance. Recently, growing numbers of ncNATs were shown to be dysregulated in cancerous cells, however, actual impact of ncNATs on cancer progression remains largely unknown. We performed RNA-seq on post-surgical tumor samples from 26 glioma patients, and normal brain tissue.

overall_design: Post-surgical tumor samples were used in the experiment. A commercially sourced healthy brain sample was used as control.

first: Giedrius

last: Steponaitis

first: Rytis

last: Stakaitis

first: Arimantas

last: Tamašauskas

first: Paulina

last: Vaitkienė

first: Daina

last: Skiriutė


title: Assessing the effect of myofibroblast depletion for Yap and Wwtr1 by single Cell RNAsequencing within ventricular interstitial cells 6 days post surgical MI.

summary: To assess the pathophysiological of genetic depletion of Yap and Wwtr1 in myofibroblasts following myocardial infarction, we utilized a Cre-lox system whereby the inducible Periostin promoter is leveraged to deplete both Yap and Wwtr1 from myofibroblasts in mice. Following myocardial infarction, myofibroblast depletion of  both Yap and Wwtr1 significantly improves cardiac function after injury as compared to injured controls. Here, we have performed single cell RNA sequencing of interstitial cardiac cells 7 days post myocardial infarction to assess differentially express genes within cardiac fibroblasts and immune cell populations.

overall_design: After surgically ligating the left anterior descending artery, mice were adminstered tamoxifen containing chow to excise Yap and a singel copy of Wwtr1 from Periostin expressing myofibroblasts (Yapfl/fl;Wwtr1fl/+;PostnMCM) or control for Cre toxicity (PostnMCM). Both strains carried the R26-eGFP transgene.

first: Santiago

last: Alvarez-Argote


title: TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration

city: Ulm

middle: Karl

last: Melzer

address: Albert-Einstein-Allee 23

institute: Ulm University Hospital

summary: We investigated transcriptional profiles of Ptf1a-Cre driven homozygous Tbx3-KO and wildtype pancreata 72h and 168h after onset of acute pancreatitis.

overall_design: Pancreata were isolated from 3 mice per genotype (Ptf1a-Cre driven homozygous Tbx3-KO, wildtype) at two distinct timepoints (72h and 168h) after onset of acute caerulein-induced pancreatitis.


title: Treatment effects of soluble guanylate cyclase modulation on diabetic kidney disease at single-cell resolution

city: Berlin

middle: S

last: Balzer

address: Charitéplatz 1

department: Dpt. of Nephrology and Medical Intensive Care

institute: Charité - Universitätsmedizin Berlin

summary: Diabetic kidney disease (DKD) is the most common cause of renal failure. Therapeutics development is hampered by our incomplete understanding of animal models on a cellular level. We show that ZSF1 rats recapitulate human DKD on a phenotypic and transcriptomic level. Tensor decomposition prioritizes proximal tubule (PT) and stroma as phenotype-relevant cell types exhibiting a continuous lineage relationship. As DKD features endothelial dysfunction, oxidative stress, and nitric oxide depletion, soluble guanylate cyclase (sGC) is a promising DKD drug target. sGC expression is specifically enriched in PT and stroma. In ZSF1 rats, pharmacological sGC activation confers considerable benefits over stimulation and is mechanistically related to improved oxidative stress regulation, resulting in enhanced downstream cGMP effects. Finally, we define sGC gene co-expression modules, which allow stratification of human kidney samples by DKD prevalence and disease-relevant measures such as kidney function, proteinuria, and fibrosis, underscoring the relevance of the sGC pathway to patients.

overall_design: Single nuclei were isolated from ZSF1 rat kidneys. N=3 Lean, n=3 Obese, n=3 Obese+sGCact, n=3 Obese+sGCstim

first: Julia

last: Frederick

first: Amin

last: Abedini

first: Katalin

last: Susztak


title: Digits in a Dish: An in vitro system to assess the molecular genetics of hand/foot development at single-cell resolution

status: Public on Feb 23 2023

city: Portland

first: H.

middle: Scott

last: Stadler

state: OR

address: 3101 SW Sam Jackson Park Rd

department: Research Center

institute: Shriners Children's Portland

summary: In vitro models allow for the study of developmental processes outside of the embryo. To gain access to the cells mediating digit and joint development, we identified a unique property of undifferentiated mesenchyme isolated from the distal early autopod to autonomously re-assemble forming multiple autopod structures including: digits, interdigital tissues, joints, muscles and tendons. Single cell transcriptomic analysis of these developing structures revealed distinct cell clusters that express canonical markers of distal limb development including: Col2a1, Col10a1, and Sp7 (phalanx formation) Thbs2 and Col1a1, (perichondrium), Gdf5, Wnt5a, and Jun (joint interzone), Aldh1a2 and Msx1 (interdigital tissues), Myod1 (muscle progenitors), Prg4 (articular perichondrium/articular cartilage), and Scx and Tnmd (tenocytes/tendons).  Analysis of the gene expression patterns for these signature genes indicates that developmental timing and tissue-specific localization were also recapitulated in a manner similar to the initiation and maturation of the developing murine autopod.  Finally, the in vitro digit system also recapitulates congenital malformations associated with genetic mutations as in vitro cultures of Hoxa13 mutant mesenchyme produced defects present in Hoxa13 mutant autopods including digit fusions, reduced phalangeal segment numbers, and poor mesenchymal condensation. These findings demonstrate the robustness of the in vitro digit system to recapitulate digit and joint development.  As an in vitro model of murine digit and joint development, this innovative system will provide access to developing limb tissues facilitating studies to discern how digit and articular joint formation is initiated and how undifferentiated mesenchyme is patterned to establish individual digit morphologies. The in vitro digit system also provides a platform to rapidly evaluate treatments aimed at stimulating the repair or regeneration of mammalian digits impacted by congenital malformation, injury, or disease.

overall_design: Dissected distal forelimb mesenchyme cells of E11.5 CD-1 mice were used to seed tissue cultures. Two independent cultures were processed as separate replicates for scRNAseq analysis of Day 2, 7 and 10 timepoints following the cell dissociation and library preparation protocols as described by the manufacturer (10X Genomics).

first: Allison

middle: M

last: Fuiten

first: Yuki

last: Yoshimoto

first: Chisa

last: Shukunami

first: H


title: RNAseq of the effect of selenite and coated selenium nanoparticles against spheroids of SKOV-3 and OVCAR-3 ovarian cancer cell lines

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

country: United Kingdom

institute: Cardiff University

summary: Analysis of transcriptome changes in SKOV-3 and OVCAR-3 spheroids following selenite or coated selenium nanoparticles treatment at sublethal doses for 24 hrs

overall_design: Total RNA was obtained from extraction of 96 spheroids in each condition.The effects of selenite or coated selenium nanoparticles treatment against SKOV-3/OVCAR-3 spheroids were compared to untreated controls.

first: Benoit

last: Toubhans


title: Enteroendocrine cell lineages that differentially control feeding and gut motility

status: Public on Feb 21 2023

city: Boston

first: Judith

last: Kaye

state: Massachusetts

address: 240 Longwood Ave, LHRRB 6th floor

department: Cell Biology

institute: Harvard University

summary: Enteroendocrine cells (EECs) are specialized sensory cells of the gut-brain axis that are sparsely distributed along the intestinal epithelium.

overall_design: Intestinal EECs of  Ngn3-Cre;tdTom and NeuroD1-Cre;tdTom mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of tdTomato signal and analyzed using scRNAseq.

first: Hayashi

last: Marito

first: Ella

last: Douglas

first: Narendra

last: Joshi

first: Gribble

last: Fiona

first: Reimann

last: Frank

first: Stephen

middle: D

last: Liberles


title: Transcriptomic analysis of pea plant responses to chitooligosaccharides’ treatment revealed stimulation of calcium-regulated reactions and mitogen-activated protein kinase cascade

city: Pushkin

first: Polina

last: Kozyulina

address: Podbelsky chausse 3

country: Russia

institute: ARRIAM

summary:
Since chitooligosaccharides are water-soluble, biodegradable and nontoxic compounds, their application may be considered as a promising plant-protecting agent. However, the molecular and cellular modes of action of COs are not yet understood.
Transcriptional changes in pea roots treated with COs were investigated via RNA sequencing. Pea roots treated with the deacetylated CO8-DA at low concentration (10-5 М) were harvested 24 h after treatment and their expression profiles were compared against medium-treated control plants. We observed 886  differentially expressed genes (fold change ≥ 1; p-value ˂ 0.05) 24 h after treatment with CO8-DA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CO8-DA-treated pea Pisum sativum L. plants with plants incubated in medium without elicitors.

first: Olga

last: Pavlova

first: Elizaveta

last: Kantsurova

first: Andrey

last: Bovin

first: Svetlana

last: Shirobokova

first: Aleksandra

last: Dolgikh

first: Alina

last: Dymo

first: Elena


title: Transmission of stimulus-induced epigentic changes through cell division are coupled to changes in transcription factor activity

status: Public on Feb 22 2023

city: Chicago

first: Sarah

middle: J

last: Sun

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

summary: The goal of this study was to investigate whether histone modifcations and gene expression changes in mouse macrophages induced by beta glucan could persist over the course of many cell divisions following stimulus removal

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K4me1, H3K4me3, and H3K27Ac, and RNA-sequencing of LM1 cells (immortalized mouse BMDMs) at 7 timepoints during beta glucan stimulation and 7 timepoints after stimlus removal

first: Raul

last: Aguirre-Gamboa

first: Luis

last: Barreiro


title: Transcriptome changes upon Cas13-based knockdown

city: New York

first: Xuebing

last: Wu

state: NY

address: 630 West 168th Street

department: Medicine/Systems Biology

institute: Columbia University

summary: We used RNA-seq to detect genome-wide gene expression change when a reporter RNA was targeted by Cas13

overall_design:
Examination of two gRNAs and two target RNA concentrations in HEK293T cells
Transfection in HEK293T cells with RfxCas13d (CasRx with NLS), target reporter (DsRed), control reporter (BFP), and gRNA (g3: targeting, g11: control).

first: Peiguo

last: Shi


title: RNA-seq in cadmium resistant breast cancer MDA-MB-231 cells

status: Public on Feb 20 2023

city: Aurora

first: Gregory

last: Wright

state: CO

address: 12800 East 19th Ave

institute: University of Colorado Anschutz Medical Campus

summary: In this study, we compared RNA-seq of cadmium resistant MDA-MB-231 cells vs untreated controls.

overall_design: In this study, we compared RNA-seq for MDA-MB-231 cells treated long term with 10uM cadmium compared to control cells. Cells were passaged in the presence of cadmium to induce heavy metal resistance, generating cadmium resistant cell lines. Parental control cells were serially passaged in normal media as a control.

first: G

first: J

last: Black


title: CUT&RUN in cadmium resistant breast cancer MDA-MB-231 cells

summary: In this study, we compared MTF-1 CUT&RUN of cadmium resistant MDA-MB-231 cells vs untreated controls.

overall_design: In this study, we compared MTF-1 CUT&RUN for MDA-MB-231 cells treated long term with 10uM cadmium compared to control cells. Cells were passaged in the presence of cadmium to induce heavy metal resistance, generating cadmium resistant cell lines. Control cells were serially passaged in normal media as a control.


title: ATAC-seq in cadmium resistant breast cancer MDA-MB-231 cells

summary: In this study, we compared ATAC-seq of cadmium resistant MDA-MB-231 cells vs untreated controls.

overall_design: In this study, we compared ATAC-seq for MDA-MB-231 cells treated long term with 10uM cadmium compared to control cells. Cells were passaged in the presence of cadmium to induce heavy metal resistance, generating cadmium resistant cell lines. Parental control cells were serially passaged in normal media as a control.