title: Testing biological actions of medicinal plants from Northern Vietnam on zebrafish embryos and larvae: developmental, behavioral, and putative therapeutical effects.

city: Liège

first: Marc

last: Muller

address: B34 Sart Tilman

department: Life Sciences

country: Belgium

institute: Université de Liège

summary: Evaluating the risks and benefits of using traditional medicinal plants is of utmost importance for a huge fraction of the human population, in particular in Northern Vietnam. Zebrafish are increasingly used as a simple vertebrate model for testing toxic and physiological effects of compounds, especially on development. Here, we tested 12 ethanolic extracts from popular medicinal plants collected in Northern Vietnam for their effects on zebrafish survival and development during the first 4 days after fertilization. We characterized more in detail their effects on epiboly, hatching, growth, necrosis, body curvature, angiogenesis, skeletal development and mostly increased movement behavior. Finally, we confirm the effect on epiboly caused by the Mahonia bealei extract by staining the actin filaments and show that this extract also inhibits cell migration of mouse embryo fibroblasts. In conclusion, we show that zebrafish early life stages reveal that traditional medicinal plant extracts are able to affect embryo development to various degrees, prompting caution to apply these medications to pregnant women. In addition, we show that an extract causing delay in epiboly also inhibits mammalian cell migration, suggesting that this effect may serve as a preliminary test for identifying extracts that inhibit cancer metastasis.

overall_design: Zebrafish embryos were treated with an ethanolic extract from stems of Mahonia bealei and RNA extracted from 8 hours post-fertilization for whole larvae RNA-Seq. 4 controls and 4 treated samples were analyzed.

first: My

middle: H

last: Tran

first: Gustavo

last: Guerrero-Limon

first: Hai

middle: T

last: Pham

first: Lai

last: Nguyen

first: Renaud

last: Nivelle


title: Genome wide enhancer loops (HiChIP) and 3-D high order chromatin features associated with EWS-FLI1 in Ewing Sarcoma. [HiC]

status: Public on Mar 16 2023

city: Charlestown

first: Rui

last: Dong

state: MA

address: 149 13th Street

country: USA

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Tumor cell identity is the product of complex interactions between oncogenic drivers and mechanisms regulating normal differentiation pathways. Cell fate transitions observed in embryonic development involve structural changes in genomic organization that provide proper lineage specification, however, whether similar events also occur within tumor cells and contribute to cancer evolution remains largely unexplored. Here we modeled this process in the pediatric bone cancer Ewing sarcoma and investigated high resolution looping and large-scale 3D nuclear conformation changes associated with EWS-FLI1, the oncogenic fusion protein that drives this tumor. We find that chromatin interactions in Ewing sarcoma cells are dominated by highly connected looping hubs centered on EWS-FLI1 binding sites, which directly control the activity of linked enhancers and promoters to establish oncogenic expression programs. Depletion of EWS-FLI1 leads to the loss of looping networks associated with the fusion protein and, strikingly, also results in widespread nuclear reorganization through the establishment of new patterns of looping and large-scale inter-compartment connectivity that resemble the chromatin configuration of mesenchymal stem cells, a candidate cell of origin of this tumor. Our data thus demonstrate that major architectural features of nuclear organization in cancer cells can be linked to a single oncogenic event and readily reversed to re-establish latent differentiation programs.

overall_design:
Using in-situ HiC and H3K27ac Hi-ChIP, we profiled the organization and establishment of EWS-FLI1 mediated enhancer connectome in Ewing sarcoma model cells, A673 and SKNMC. The re-organization of enhancer network is further compared to the MSCs, a potential cell or origin or Ewing Sarcoma. Pooled HiC and Hi-ChIP libraries of each condition, shGFP/shFLI, from Ewing cells and wildtype MSCs were used in the study.
NOTE FROM SUBMITTER: Since the MSC samples (HiC, HiChIP and ChIP-seq) are from patients, we did not include the raw data due to privacy concern.

first: Rajendran

last: Sanalkumar

first: Miguel

middle: N

last: Rivera

first: Nicolò

last: Riggi


title: Genome wide enhancer loops (HiChIP) and 3-D high order chromatin features associated with EWS-FLI1 in Ewing Sarcoma. [HiChIP]


title: Genome wide enhancer loops (HiChIP) and 3-D high order chromatin features associated with EWS-FLI1 in Ewing Sarcoma. [ChIP-seq]

overall_design:
H3K27ac ChIP is carried out to identify the all active chromatin regions marked by the H3K27ac histone modifications.
NOTE FROM SUBMITTER: Since the MSC samples (HiC, HiChIP and ChIP-seq) are from patients, we did not include the raw data due to privacy concern.


title: Single-Cell Map of Dynamic Multicellular Ecosystem of Radiation-Induced Intestinal Injury

status: Public on Mar 06 2023

city: Beijing

first: Yiming

last: Lu

address: Taiping Road

country: China

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

type: Expression profiling by high throughput sequencing

summary: Using single-cell RNA sequencing, we pictured a dynamic landscape of the intestinal microenvironment during RIII and regeneration. We generated transcriptomes of 22,680 single cells in the intestinal microenvironment, trying to profile the dynamics of ISCs and immune cells located in the mucous layer. This large-scale single-cell transcriptome data can be used as a valuable resource for further studying the cellular mechanism of RIII and development of potential therapy strategies.

overall_design: To generate a dynamic single-cell map of the intestinal microenvironment related to RIII, we employed a droplet-based scRNA-seq (10x Genomics) approach to profile the transcriptomes of single cells from the intestinal tissues at day 1 (n = 4), day 3 (n = 3), day 7 (n = 3) and day 14 (n = 3) after irradiation exposure as well as the unexposed healthy intestinal tissues (n = 4). Raw data will be available at European Genome-phenome Archive (EGA) soon.

first: Gangqiao

last: Zhou

first: Yang

last: Li


title: Xinyang Maojian green tea (Camellia sinensis) microRNAs data in different leaf development stages.

status: Public on Mar 05 2023

city: Xinxiang

first: xianyou

last: Wang

state: Henan

address: No.90 Hualan Avenue

institute: Henan Institute of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: The microRNAs reveal the molecular mechanism involved in the regulation of leaf development in Xinyang Maojian green tea.

overall_design:
An integrated analysis of microRNAs and the transcriptome reveals the molecular mechanisms underlying the regulation of leaf development in Xinyang Maojian green tea (Camellia sinensis)
The sBud represents Xinyang Maojian (XYMJ) green tea buds, the sL1 and sL2 represent XYMJ green tea the first and second leaves, and the sS1 represent XYMJ green tea stem.

first: Xianyou

first: Shanshan

last: Zhao


title: Gene expression analysis of lung cancer cells in the presence of lung fibrosis

status: Public on Mar 08 2023

city: Hiroshima

first: Kiyofumi

last: Shimoji

address: 1-2-3, Kasumi, Minami-ku

department: Molecular and Internal Medicine, Graduate School of Biomedical and Health Sciences

country: Japan

institute: Hiroshima University

summary: To investigate the interaction between lung cancer cell and lung fibrosis in vivo, gene expression analysis was performed using orthotopic tumor bearing animal model with C57BL/6 mice and Lewis Lung Carcinoma cells (LC model) and LC model with bleomycin-induced lung fibrosis (IP+LC model).

overall_design: Gene expression analysis of lung cancer cells in the presence of bleomycin-induced lung fibrosis.

first: Taku

last: Nakashima


title: Single cell RNA sequencing unravels the transcriptional network underlying zebrafish retina regeneration

status: Public on Mar 03 2023

city: Dresden

first: Fabian

last: Rost

address: Pfotenhauerstraße 108

country: Germany

institute: MPI-CBG

summary: In the lesioned zebrafish retina, Müller glia produce multipotent retinal progenitors that generate all retinal neurons, replacing lost cell types. To study the molecular mechanisms linking Müller glia reactivity to progenitor production and neuronal differentiation, we used single cell RNA sequencing of Müller glia, progenitors and regenerated progeny from uninjured and light-lesioned retinae. We discover an injury-induced Müller glia differentiation trajectory that leads into a cell population with a hybrid identity expressing marker genes of Müller glia and progenitors. A glial self-renewal and a neurogenic trajectory depart from the hybrid cell population. We further observe that neurogenic progenitors progressively differentiate to generate retinal ganglion cells first and bipolar cells last, similar to the events observed during retinal development. Our work provides a comprehensive description of Müller glia and progenitor transcriptional changes and fate decisions in the regenerating retina, which are key to tailor cell differentiation and replacement therapies for retinal dystrophies in humans.

overall_design: Droplet-based, 10x Genomics scRNAseq was done on four samples. Each sample consists of 15000 cells sorted from a single cell suspension obtained by dissociating 8 retinae pooled from the eyes of 4, adult zebrafish (2 males and 2 females). Samples were collected from light-lesioned animals at 44 hours post-light lesion (hpl) (s2_44_hpl_), 4 and 6 days post-light lesion (dpl) (s3_4_dpl_ and s5_6_dpl_, respectively). Two, separate uninjured control samples included cells dissociated from 8 retinae of 4, uninjured zebrafish (s1_Uninjured_Ch_ and s4_Uninjured_whole_retina_ctrl_, respectively). Sample collection occurred on two, different working days. On the first day, s1_Uninjured_Ch_, s2_44_hpl_ and s3_4_dpl_ were collected. On the second day, s4_Uninjured_whole_retina_ctrl_ and s5_6_dpl_ were collected. Fluorescent Activated Cell Sorting (FACS) was applied to each sample and eventually 15.000 cells per sample were sorted and sent for sequencing.

first: Laura

last: Celotto

first: Anja

last: Machate

first: Juliane

last: Bläsche

first: Andreas

last: Dahl

first: Anke

last: Weber

first: Stefan

last: Hans

first: Michael

last: Brand


title: Neuronal Transcriptome Disruption, Tau Accumulation and Synapse Loss inAlzheimer’s Knock-in Mice Require Cellular Prion Protein

status: Public on Mar 01 2023

city: New Haven

first: Stephen

middle: M

last: Strittmatter.

state: Connecticut

address: 295 Congress Ave, BCMM Rm433

department: Neurology

institute: Yale University

summary: Cellular prion protein (PrPC) is a high-affinity cell-surface receptor for Amyloid-β oligomers(Aßo). In certain overexpression models of Alzheimer’s Disease (AD), pharmacology and genetics demonstrate its essential role for synaptic plasticity impairment, memory deficits and synapse loss. However, PrPC ’s role in AD-related phenotypes with endogenous expression levels, its role in tau accumulation and its effect on imaging biomarkers are unknown. The necessity of PrPC for transcriptomic alterations driven by Aß across cell types is unexplored.

overall_design: The role of PrPC was examined as a function of age in homozygous AppNL-G-F/hMapt double knock-in mice (DKI). Phenotypes of AppNL-G-F /hMapt mice with a deletion of Prnp expression (DKI; Prnp-/- ) were compared with DKI mice with intact Prnp, mice with a targeted deletion of Prnp (Prnp-/- ), and mice with intact Prnp (WT). Phenotypes examined included behavioral deficits, synapse loss by PET imaging, synapse loss by immunohistology, tau pathology, gliosis, inflammatory markers, and snRNA-seqtranscriptomic profiling.

first: Austin

middle: J

last: Stoner

first: Li

last: Fu

first: LaShae

last: Nicholson

first: Chao

last: Zheng

first: Takuya

last: Toyonaga

first: Joshua

last: Spurrier

first: William

last: Laird

first: Zhengxin

last: Cai

last: Strittmatter


title: Glioma synapses recruit mechanisms of adaptive plasticity: Gene expression changes induced by BDNF treatment in SU-DIPGVI in vitro

city: Stanford

first: Michelle

last: Monje

state: CA

address: 265 Campus Drive, SIM1 G3035

institute: Stanford University

summary: The nervous system plays an increasingly appreciated role in the regulation of cancer. In gliomas, neuronal activity drives tumor progression through paracrine signaling factors such as neuroligin-3 and brain-derived neurotrophic factor (BDNF), and also through electrophysiologically functional neuron-to-glioma synapses mediated by AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors. The consequent glioma cell membrane depolarization drives tumor proliferation. In the healthy brain, activity-regulated secretion of BDNF promotes adaptive plasticity of synaptic connectivity and strength. Here, we show that malignant synapses exhibit similar plasticity regulated by BDNF. Signaling through the receptor TrkB (tropomyosin receptor kinase B), BDNF promotes AMPA receptor trafficking to the glioma cell membrane, resulting in increased amplitude of glutamate-evoked currents in the malignant cells. This potentiation of malignant synaptic strength shares mechanistic features with synaptic plasticity that contributes to memory and learning in the healthy brain. BDNF-TrkB signaling also regulates the number of neuron-to-glioma synapses. Abrogation of activity-regulated BDNF secretion from the brain microenvironment or loss of TrkB in human glioma cells robustly inhibits tumor progression. Blocking TrkB genetically or pharmacologically abrogates these effects of BDNF on glioma synapses and substantially prolongs survival in xenograft models of pediatric glioblastoma and diffuse intrinsic pontine glioma (DIPG). Taken together, these findings indicate that BDNF-TrkB signaling promotes malignant synaptic plasticity and augments tumor progression.

overall_design:
Bulk RNA sequencing was performed in patient-derived SU-DIPGVI cells treated with 100 nM BDNF ("DIPG6_BDNF-treated") or vehicle ("DIPG6_ctrl") for 16 hours. RNA was sequenced on the Illumina NextSeq 500 and subsequently analyzed with DESeq2 in R.  Reported DESeq2 fold changes are all relative to "DIPG6_ctrl" samples. Replicates were performed as indicated in the metadata spreadsheet. Due to patient privacy concerns, we are witholding raw sequencing files at this time.
***Raw data for human samples not available due to patient privacy concerns***

first: Kathryn

middle: R

last: Taylor

first: Rebecca

last: Mancusi


title: Patch-seq of human patient-derived diffuse midline glioma xenografts

address: 265 campus drive, SIM1 G3035

summary: Treatment-resistance of lethal high-grade brain tumors including H3K27M diffuse midline gliomas is thought to arise in part from transcriptional and electrophysiological heterogeneity. These phenotypes are readily studied in isolation using single-cell RNA-seq and whole-cell patch clamping, respectively, but their simultaneous capture is now possible by aspirating a cell's contents into a patch pipet after electrophysiology recordings using a method called 'patch-seq'.  Here, we adapt this method to characterize the gene expression programs and functional responses of patient-derived glioma xenografts to neuronal firing at single-cell resolution.

overall_design:
Xenografted patient-derived diffuse midline glioma cells were analyzed by whole-cell patch clamp with neuronal stimulation and subsequently by single cell RNA-seq
***Raw data not available due to patient privacy concerns***

first: Shawn

last: Gillespie


title: Gene Expression Analysis of Laser Captired Purkinje Cells from the Post-Mortem Essential Tremor Cerebellum

status: Public on Feb 28 2023

city: Dallas

first: Karthigayini

last: Sivaprakasam

state: Texas

address: Forest Road

institute: University of Texas Southwestern Medical Center

summary: RNA-seq evaluation of enriched Purkinje cells from the post-mortem human cerebellum. Purkinje cells were removed via laser capture microdissection and pooled for RNA-extraction and sequencing. 24 ET patients and 16 controls healthy age matched were compared.

overall_design: The Purkinje cell has shown extensive morphological changes in the ET cerebellum, but are less abundant than other cell types (Ex: Granule cells) by a factor of about 1:600. We sought to sequence enriched Purkinje cells from patients diagnosed with Essential Tremor and patients who are neurologicall clear.

first: Regina

last: Martuscello

last: Sivprakasam

first: Whitney

last: Hartstone

first: Sheng-Han

last: Kuo

first: Genevieve

last: Konopka

first: Elan

middle: D

last: Louis

first: Phyllis

middle: L

last: Faust


title: High Capacity Sample Multiplexing for Chromatin Accessibility Profiling Within Single Cells

city: Seattle

first: Gregory

middle: Thomas

last: Booth

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Single-cell chromatin accessibility has emerged as a powerful means of understanding the epigenetic landscape of diverse tissues and cell types, but profiling cells from many independent specimens is challenging and costly. Here we describe a novel approach, sciPlex-ATAC-seq, which uses unmodified DNA oligos as sample-specific nuclear labels, enabling the concurrent profiling of chromatin accessibility within single nuclei from virtually unlimited specimens or experimental conditions. We first demonstrate our method with a chemical epigenomics screen, in which we identify drug-altered distal regulatory sites predictive of compound- and dose-dependent effects on transcription. We then analyze cell type-specific chromatin changes in PBMCs from multiple donors responding to synthetic and allogeneic immune stimulation. We quantify stimulation-altered immune cell compositions and isolate the unique effects of allogeneic stimulation on chromatin accessibility specific to T-lymphocytes. Finally, we observe how various immunosuppressive compounds disrupt canonical allogeneic activation of resting T-cells through chromatin.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell ATAC-seq libraries were produced using two and three level single-cell combinatorial indexing ATAC sequencing (sci-ATAC-seq) from small molecule-inhibited or untreated A549, and NIH-3T3 cells, as well as from cultured human PBMCs.  PBMCs were cultured in the presense of irradiated foreign PBMCs (mixed lymphocyte reactions),  T-cell expansion beads, or otherwise untreated. Irradiated PBMCs were also profiled. For individual experiments, different cells and treatments were hashed and pooled prior to sci-ATAC-seq using a nuclear barcoding strategy. This nuclear barcoding strategy relies on fixation of barcode containing, well-specific oligos that are specific to a given cell type, replicate or treatment condition.

first: Riza

last: Daza

first: Sanjay

last: Srivatsan

first: José

last: McFaline-Figueroa

first: Scott

last: Furlan

first: Jay

last: Shendure

first: Cole

last: Trapnell

first: Rula

last: Green Gladden


title: Type I PRMT inhibitor MS023 promotes SMN2 exon 7 inclusion and synergizes with nusinersen to rescue the phenotype of SMA mice

city: Oxford

first: Anna

middle: Jolanta

last: Kordala

address: Old Road Campus, Roosevelt Dr, Headington

country: United Kingdom

institute: University of Oxford

summary: In our study we have identified MS023, an inhibitor of PRMTs, to increase SMN protein and FL SMN2 transcript levels, and to improve survival and weights of treated SMA mice, alone and in combination with currently approved antisense oligonucleotide. In order to understand the molecular underpinnings of the added benefit provided by the combinatorial treatment, we performed bulk transcriptomic analysis in spinal cords of SMA mice treated with MS023 only, nusinersen only, and MS023 in combination with nusinersen, compared to wild type and SMA littermates.

overall_design: spinal cords of mice, five groups, four biological replicates per group: untreated SMA mice, SMA mice treated with nusinersen, SMA mice treated with MS023, SMA mice treated with nusinersen and MS023, untreated controls

first: Nina

last: Ahlskog

first: Muhammad

last: Hanifi

first: Jessica

last: Stoodley

first: Wooi

middle: F

last: Lim

first: Suzan

last: Hammond

first: Matthew

last: Wood

first: Carlo

last: Rinaldi


title: TimeLapse-seq reveals that ALKBH5 modulates RNA stability of metabolic transcripts

status: Public on Feb 01 2023

city: West Haven

last: Simon

address: 300 Heffernan Dr, 300 Hefferna Dr

summary: N6-methyadenosine (m6A) RNA modification controls numerous cellular processes through regulation of RNA stability and translational efficiency. Whether the RNA m6A modification regulates energy metabolism process by posttranscriptional regulation is unknown. We here show that loss of the m6A demethylase ALKBH5  results in instability of oxogluatarate-dehydrogenase (Ogdh) messenger RNA and transcripts of other metabolic enzymes.

overall_design: RNA isolated from wildtype and Alkbh5-deficient murine lineage-depleted bone marrow cells treated +/- s4U was subjected to oxidative-nucleophilic-aromatic-substitution chemistry. Sequencing libraries were prepared from all RNA.

first: Yimeng

last: Gao

first: Joshua

last: Zimmer

first: Radovan

last: Vasic

first: Chengyang

last: Liu

first: Rana

last: Gbyli

first: Shu-Jian

last: Zheng

first: Amisha

last: Patel

first: Wei

first: Raman

last: Nelakanti

first: Yuanbin

last: Song

first: Giulia

last: Biancon

first: Andrew

middle: Z

last: Xiao

first: Sarah

last: Slavoff

first: Richard

middle: A

last: Flavell

first: Toma

last: Tebaldi

first: Hua-Bing

last: Li

first: Stephanie

last: Halene


title: Redifferentiated cardiomyocytes retain residual dedifferentiation signatures and are protected against ischemic injury

status: Public on Feb 02 2023

city: Atlanta

first: Avraham

last: Shakked

state: GA

address: 1760 Haygood Dr NE

institute: Emory University

summary: To investigate the effects of cardiomyocyte redifferentiation and its cardioprotective effects, we performed gene expression profiling analysis using data obtained from RNA-seq of whole hearts that were either WT, or ERBB2 over-expressing, at 3 different timepoints both for sham injury and MI injury.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hearts either during (T1/Dediff), 2 weeks after (T2/Intermediate) or 4 weeks after (T3/Rediff) transient ERBB2 overexpression in cardiomyocytes, controlled for injury status and transgene presence.

first: Eldad

last: Tzahor


title: In vivo gene expression profile between vermilion and skin

status: Public on Jan 31 2023

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: gene expression profiling of a total of 19,770 genes of human lip tissues obtained from three infant patients

overall_design: The lip tissues that were discarded during cheiloplasty were obtained. The specimens included vermilion with adjacent contiguous skin, depending on the surgical procedure, i.e., the triangular flap technique or straight-line technique with a small triangular flap.

first: Eri

last: Kobayashi

first: Yiwei

last: Ling

first: Ryota

first: Emi

last: Hoshikawa

first: Eriko

last: Itai

first: Osamu

last: Sakata

first: Shujiro

last: Okuda

first: Eiji

last: Naru

first: Kenji

last: Izumi


title: PRO-IP-seq: Pol II CTD code at nt-resolution in human K562 cells

status: Public on Feb 24 2023

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

summary: Active sites of transcription were labelled with biotinylated nucleotide during a run-on reacation, where after an immunoprecipitation with antibodies that target Pol II CTD was conducted. This PRO-IP-seq protocol was conducted in human K562 erythroleukemia cells. The K562 cells were either untreated (NHS) or treated with 30 minutes of heat shock at 42°C (HS).


title: Genome wide enhancer loops (HiChIP) and 3-D high order chromatin features associated with EWS-FLI1 in Ewing Sarcoma.

first: Rui

last: Dong

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

overall_design: Refer to individual Series


title: Induction of CtsR-regulated chaperones improves Xylanase production in Bacillus subtilis

status: Public on Feb 21 2023

city: Amsterdam

first: Biwen

last: Wang

address: Work, Science Park 904,1098 XH,Amsterdam,The Netherlands

department: Swammerdam Institute for Life Science

country: Netherlands

institute: University of Amsterdam

summary: We examined the effect of high-level expression of the commercially important endo-1,4-β-xylanase XynA on the B. subtilis transcriptome using RNA-seq. Rather unexpectedly, we found a reduced expression of several protein chaperones, including ClpC, ClpE and ClpX, was downregulated when XynA was overproduced. Expression of these proteins is controlled by the transcriptional repressor CtsR. CtsR levels are directly controlled by regulated proteolysis, involving ClpC and its cognate protease ClpP. Preventing this downregulation by knocking out the involved transcriptional repressor CtsR resulted in increased XynA production by more than 25 %.

overall_design: We used B. subtilis 168 derivative BSB1, which is prototrophic for tryptophan, and removed the native xynA gene through a marker-free clean deletion procedure. This was to assure that the negative control strain does not produce any XynA. Overexpression of XynA was achieved by cloning xynA in the multicopy expression plasmid pUB110 behind the strong amyQ promoter. As a negative control, we used the same plasmid lacking the xynA gene. The strains were grown in nutrient-rich LB medium at 37 °C in the presence of 50 μg/ml kanamycin to maintain the plasmids. We sampled cells at 3 h (OD~0.8) and 6h growth (OD~4) and performed RNA-seq. We compared the transcriptomes between XynA overproducing cells and non-producing cells. Two independent biological replicates were performed.

first: Frans

last: van der Kloet

first: Leendert

middle: W

last: Hamoen


title: Mitigating the detrimental developmental impact of early fetal alcohol exposure using a maternal methyl donor-enriched diet

status: Public on Jan 23 2023

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

country: Canada

institute: CHU Ste-Justine Research Center/Université de Montréal

type: Methylation profiling by high throughput sequencing

summary: Fetal alcohol exposure at any stage of pregnancy can lead to Fetal Alcohol Spectrum Disorder (FASD), a group of life-long conditions characterized by congenital malformations, as well as cognitive, behavioral, and emotional impairments. The teratogenic effects of alcohol have long been publicized; yet fetal alcohol exposure is one of the most common preventable causes of birth defects. Currently, alcohol abstinence during pregnancy is the best and only way to prevent FASD. However, alcohol consumption remains astoundingly prevalent among pregnant women; therefore, additional measures need to be made available to help protect the developing embryo before irreparable damage is done. Maternal nutritional interventions using methyl donors have been investigated as potential preventative measures to mitigate the adverse effects of fetal alcohol exposure. Here, we show that a single acute preimplantation (E2.5; 8-cell stage) fetal alcohol exposure in mice leads to long-term FASD-like morphological phenotypes (e.g., growth restriction, brain malformations, skeletal delays) in late-gestation embryos (E18.5) and demonstrate that supplementing the maternal diet with a combination of four methyl donor nutrients, folic acid, choline, betaine, and vitamin B12, prior to conception and throughout gestation effectively reduces the incidence and severity of alcohol-induced morphological defects without altering DNA methylation status and regulation of imprinting control regions. This study clearly supports that preimplantation embryos are vulnerable to the teratogenic effects of alcohol, emphasizing the dangers of maternal alcohol consumption during early gestation, and provides a potential proactive maternal nutritional intervention to minimize FASD progression, reinforcing the importance of adequate preconception and prenatal nutrition.

overall_design: DNA methylation levels of imprinted control regions were quantified using the Implicon technique adapted from Klobučar et al. (2020) in forebrain of embryos subjected to either a standard or methyl donor-enriched maternal diet and exposed to either saline (control) or ethanol in utero.

first: Mélanie

last: Breton-Larrivée

first: Elizabeth

last: Elder

first: Alexandra

last: Langford-Avelar


title: Role of human dural fibroblasts in the angiogenic responses of human endothelial cells: an in vitro dural model for EDAS

status: Public on Feb 15 2023

city: Seoul

first: Min-Ho

last: Hwang

address: 8, Gamasan-ro 20-gil, Guro-gu

department: Biomedical Sciences

country: South Korea

institute: Korea University

summary: To determine whether dural fibroblasts (DuF) under IL-1β-mediated wound conditions, release pro-angiogenic factors, and promote angiogenic properties in human endothelial cells (ECs).  DuF were stimulated by pro-inflammatory cytokines interleukin (IL)-1β, and transcriptome sequencing was then used to identify the differentially expressed genes in the DuF with/without IL-1β stimulation (DuFCon/DuFIL1b)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Dura fibroblast with/without IL-1β stimulation.

first: Woo-Keun

last: Kwon


title: Transcriptional analysis of murine cortical astrocytes with adeno-associated viral transduction with and without 4x6T miR cassette, vs transgenically labeled astrocytes

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary:
We generated adeno-associated Cre viral vectors with improved astrocyte-specific expression by including a cassette of miRNA targeting sequences (4x6T) to decrease off-target expression. We delivered these viruses in Ribotag mice using the PHP.eB serotype, either intracortically or systemically. We compared these samples with mice that received intracortical AAV2/5::GfaABC1D-Cre and transgenic Aldh1l1-CreERT2/Ribotag mice.
We sequenced whole-tissue RNA as well as ribosomally-loaded astrocyte-enriched mRNA to assess cell-type specificity of viruses as well as virus-related transcriptomic changes.

overall_design: Four cohorts were generated: Aldh1l1-CreERT2/Ribotag transgenic mice (control mice with highly astrocyte-specific labeled ribosomes); AAV2/5::GfaABC1D-Cre intracortical injection mice (standard astrocyte-enriched virus); PHP.eB::GfaABC1D-Cre-4x6T intracortical injection mice; and PHP.eB::GfaABC1D-Cre-4x6T systemic injection mice. Each cohort included 4 mice, and each mouse had both input (whole-cortex) and immunoprecipitated (ribosomally loaded, astrocyte-enriched) mRNA samples.

first: Amy

last: Gleichman

first: Thomas

middle: S

last: Carmichael


title: Transcriptomic and functional analysis of ANGPTL4 overexpression in pancreatic cancer nominates targets that reverse chemoresistance

status: Public on Jan 19 2023

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: 3'RNAseq FWD with or without gemcitabine treatment in pancreatic cancer cell lines with altered ANGPTL4 expression

overall_design: We performed QuantSeq 3' RNAseq FWD on MIAPaCa2, Panc1, and P10.05 cells whose ANGPTL4 expression had been altered with CRISPR or DsiRNA then treated or not treated with gemcitabine.

first: Emily

last: Gordon


title: Spatial transcriptomics reveals unique gene expression changes in different brain regions after sleep deprivation

status: Public on Jan 12 2023

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 169 Newton Road

department: Neuroscience and Pharmacology

institute: University of Iowa

summary: We report a spatial transcriptomics dataset of mouse brain tissue generated with the 10x Genomics Visium platform to identify gene expression changes after sleep deprivation

overall_design: We performed spatial gene expression profiling analysis using Visium data obtained from coronal mouse brain sections of 2 groups (sleep deprived vs. non sleep deprived).

first: Zeru

last: Peterson

last: Walsh

first: Snehajyoti

last: Chatterjee

first: Li-Chun

last: Lin

first: Lisa

middle: C

last: Lyons

last: Nickl-Jockschat

first: Ted

last: Abel


title: Airway-derived p63+ facultative progenitors contribute to alveolar regeneration after lung injury.

status: Public on Feb 20 2023

city: Shanghai

first: zixin

last: liu

address: 320 Yueyang road, Life Science Research Building A2112

institute: Center for Excellence in Molecular Cell Science

summary: Lung injury activates potential stem cells or progenitors for alveolar repair and regeneration. However, the activation program and source of injury-induced facultative progenitors remain incompletely known. Here, we find that lung injury induces emergence of p63-expressing progenitors, which rapidly proliferate and differentiate into alveolar type-1 (AT1) and type-2 (AT2) cells. scRNA-seq analysis uncovers that a subset of p63+ progenitors exhibit two distinct parallele transient stages before differentiation into mature AT1 and AT2 cells, respectively. Dual recombinases-mediated sequential genetic tracing reveals that facultative p63+ progenitors originate from the distal airway secretory cells and subsequently regenerate alveoli. Functioanlly, secretory cell-specific knockout of p63 significantly impairs their contribution to alveolar epithelium during lung regeneration. Our study identified secretory cell-derived facultative p63+ progenitors that contribute to alveolar regeneration, indicating a potential therapeutic target for lung treatment after injuires.

overall_design: tdT+ and tdT- lung epithelial cell of the p63-CreER; R26-tdT mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Zan

last: Lv

first: Zixin

last: Liu

first: Kuo

first: Wenjuan

last: Pu

first: Yan

last: Li

first: Huan

last: Zhao

first: Ying

last: Xi

first: Astrid

last: Gillich

first: Bin

last: Zhou


title: DNA elements tether canonical Polycomb Repressive Complex 1 to human genes

status: Public on Jan 13 2023

city: Umeå

first: Yuri

last: Schwartz

address: Building 6K, 6L  University Hospital Area

department: Molecular Biology

institute: Umeå University

summary: Development of multicellular animals requires epigenetic repression by Polycomb group proteins. The latter assemble in multi-subunit complexes, of which two kinds, Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2), act together to effect the repression of key developmental genes. How PRC1 and PRC2 recognize specific genes remains an open question. Here we report that small adjustment in the next generation sequencing of the Immunoprecipitated Chromatin (ChIP-seq) allows identification of several hundreds of DNA elements that tether canonical PRC1 to human developmental genes. Their analysis indicates that sequence features associated with canonical PRC1 tethering differ from those that favour the retention of PRC2. Throughout the genome, the two kinds of sequence features mix in different proportions to yield a gamut of DNA elements that range from those tethering predominantly PRC1 to ones capable of tethering both PRC1 and PRC2 or the elements that retain exclusively PRC2. The emerging picture is similar to paradigmatic targeting of Polycomb complexes by Polycomb Response Elements (PREs) of Drosophila but providing for unexpected degree of plasticity.

overall_design: ChIP-seq of the Polycomb group proteins SUZ12, MEL18/BMI1 and RING, and the histone modification H3K27me3, performed on the cell lines NT2-D1, TIG-3, and KBM7-1-55-S2-24 clone F10. Each experiment was done in two replicates. DNA isolated from corresponding chromatins  prior to immunoprecipitation (Input) were sequenced as controls.

first: Juan

middle: I

last: Barrasa

first: Tatyana

middle: G

last: Kahn

first: Moa

last: Lundkvist

middle: B


title: Chemical-Induced Phase Transition and Global Conformational Reorganization of Chromatin [Hi-C]

status: Public on Jan 11 2023

first: Qinying

last: Ye

address: Haike Road #230

institute: ShanghaiTech University

summary: Chemicals or drugs were demonstrated to accumulate within biomolecule condensates formed through phase separation in cells. Here, we employed super-resolution imaging to search for chemicals that induce phase transition of chromatin at the microscale. We found that adriamycin (doxorubicin), a widely-used chemotherapeutic drug against malignancies, is able to induce local condensation and global conformational change of chromatin in cancer and primary cells. Hi-C and ATAC-seq experiments demonstrated that adriamycin-induced chromatin condensation is accompanied by weakened chromatin interaction within topologically-associated domains, compartment A/B switching, lower chromatin accessibility, and corresponding transcriptomic changes. Mechanistically, adriamycin complexes with histone H1 and induces the phase transition of H1, forming fibrous aggregates in vitro. Our results reveal a new action mechanism of an anti-cancer drug discovered for decades, demonstrate the link between the physical properties of chromatin and gene expression, and suggest that interactions between drugs and biomolecules could exert profound effects on cells.

overall_design: Comparative chromatin feature analysis of HiC data for U2OS cells treated with no treatment or treatment with  adriamycin

first: Shuxiang

last: Shi

first: Tengfei

last: Wang

first: Qian

last: Bian

first: Chao-Po

last: Lin


title: In vivo gene expression profile between vermilion and oral mucosa

first: Satoshi

last: Kondo

first: Eri

last: Kobayashi

first: Yiwei

last: Ling

first: Ryota

first: Emi

last: Hoshikawa

first: Eriko

last: Itai

first: Osamu

last: Sakata

first: Shujiro

last: Okuda

first: Eiji

last: Naru

first: Kenji

last: Izumi


title: ISG induction in ∆7bp IFNAR2 mutant, IFNAR1 KO and wild type THP1.

status: Public on Jan 25 2023

city: 北京

first: Linnan

last: Zhang

state: 北京

address: 15,Datun Road, Chaoyang, Beijing

institute: IBP

summary: ISG induction in IFNAR2 mutant, IFNAR1 KO and wild type THP1

overall_design: IFNß3 hours.(each treatment with two repeats)

first: Xiaoyang

last: Jin

first: Jianping

last: Ma

first: Liguo

first: Liwei


title: Chemical-Induced Phase Transition and Global Conformational Reorganization of Chromatin [ATAC-seq]

first: Qinying

last: Ye

overall_design: Comparative chromatin feature analysis of ATAC-seq data for U2OS cells treated with adriamycin or etopside

first: Shuxiang

first: Tengfei

first: Qian


title: Chemical-Induced Phase Transition and Global Conformational Reorganization of Chromatin [RNA-seq]

overall_design: Comparative gene expression analysis of RNA-seq data for U2OS cells treated with adriamycin or etopside

last: Shi

first: Chao-Po


title: Machine learning analysis of the T cell receptor repertoire identifies sequence features that predict self-reactivity

status: Public on Jan 09 2023

city: Nijmegen

first: Franka

last: Buytenhuijs

state: Please select your county

address: Toernooiveld 200

institute: Radboud University

summary: The T cell receptor (TCR) determines the specificity and affinity for both foreign and self-peptides presented by MHC. It is established that self-pMHC reactivity impacts T cell function, but it has been challenging to identify TCR sequence features that predict T cell fate. To discern patterns distinguishing TCRs from naïve CD4+ T cells with low versus high self-pMHC reactivity, we used data from 42 mice to train a machine learning (ML) algorithm that predicts self-reactivity directly from TCRβ sequences. This approach revealed that n-nucleotide additions and acidic amino acids weaken selfreactivity. We tested our ML predictions of TCRβ sequence self-reactivity using retrogenic mice. Extrapolating our analyses to independent datasets, we found high predicted self-reactivity for regulatory CD4+ T cells and low predicted self-reactivity for T cells responding to chronic infection. Our analyses suggest a potential trade-off between repertoire diversity and self-reactivity intrinsic to the architecture of a TCR repertoire.

overall_design: We generated a dataset of 1.5x10^7 unique CDR3β sequences from a total of 42 mice, investigating patterns among TCRβ chain sequences between mature CD5lo and CD5hi naïve CD4+ T cells, as well as sequences in the double positive (DP, pre-selection) and single positive (SP, post-selection) stage in the thymus.

first: Johannes

last: Textor

first: Dakota

last: Rogers

first: Ève

last: Gauthier

first: Shabaz

last: Sultan

first: Inge

middle: N

last: Wortel

first: Kathrin

last: Kalies

first: Anke

last: Fähnrich

first: René

last: Pagel

first: Heather

last: Melichar

first: Jürgen

last: Westermann

first: Judith

last: Mand


title: Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity [RNA-seq]

status: Public on Jun 14 2023

city: La Jolla

first: Jesse

last: Dixon

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

summary: Chromatin conformation reorganization is emerging as an important layer of regulation for gene expression and lineage specification. Yet, how lineage-specific transcription factors contribute to the establishment of cell type-specific 3D chromatin architecture in the immune cells remains unclear, especially for the late stages of T cell subset differentiation and maturation. Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation of T cells specializing in suppressing excessive immune responses. Here, by comprehensively mapping 3D chromatin organization during Treg cell differentiation, we show that Treg-specific chromatin structures were progressively established during its lineage specification, and highly associated with Treg signature gene expression. Additionally, the binding sites of Foxp3, a Treg lineage specifying transcription factor, were highly enriched at Treg-specific chromatin loop anchors. Further comparison of the chromatin interactions between wide-type Tregs versus Treg cells from Foxp3 knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that Foxp3 was essential for the establishment of Treg-specific 3D chromatin architecture, although it was not dependent on the formation of the Foxp3 domain-swapped dimer. These results highlighted an underappreciated role of Foxp3 in modulating Treg-specific 3D chromatin structure formation.

overall_design: RNA sequencing in T-cell development with a focus on T-reg maturation, and Foxp3 mutant T-regs


title: Spatial transcriptome unveils the heterogeneity between subpopulations of Bacillus subtilis surface-associated communities

status: Public on Jan 05 2023

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE - Université Paris-Saclay

summary:
Bacillus subtilis has been extensively used as a model for molecular studies on biofilm formation.
These studies encompassed the development of complex macro-colonies on agar, the formation of pellicles at the air-liquid interface, and lately the formation of submerged architectural biofilms at the solid-liquid interface.
Beside similarities, these multicellular communities also display considerable heterogeneity at the structural, chemical and biological levels.
Here we use RNA-seq to analyze nine different spatio-physiological conditions, including the three biofilm populations (colony, pellicle, and submerged).

overall_design:
From shaken planktonic cultures, the exponential (EX) and the stationary (ST) phase were collected.
The stationary phase cultures were used to inoculate static liquid cultures and semi-solid agar plates, which were incubated for 24 hours.
From the static liquid culture, three localized compartments were collected separately: the pellicle (PL) formed at the air-liquid interface, the submerged biofilm (SB) formed on the solid-liquid interface, and the free detached cells (DC) between these two compartments were collected separately.
From the semi-solid agar plate, four localized compartments were collected separately: the mother colony (MC), corresponding to the inoculation site from which the swarm has developed as a mature macrocolony; the base (BS) of the dendrites in the early biofilm form; the dendrites (DT), a monolayer of cells ready to form later the biofilm; and the tips (TP) formed of motile and highly dividing cells.
the base (BS) of the dendrites in the early biofilm form; the dendrites (DT), a monolayer of cells ready to form later the biofilm; and the tips (TP) formed of motile and highly dividing cells.
For each compartment, three independent samples were taken as biological replicates and subjected to transcriptome analysis (RNA-Seq).

first: Yasmine

last: DERGHAM

first: Dominique

last: LE COQ

last: NICOLAS

first: Romain

last: BRIANDET


title: A CRISPR/Cas9 library screening identified CARM1 as a critical inhibitor for Sorafenib-induced ferroptosis in hepatocellular carcinoma cells

status: Public on Jan 01 2023

city: Tianjin

first: Chenghao

last: Xuan

address: 22 Qixiangtai Road

institute: Tianjin Medical University

summary: CARM1 inhibits ferroptosis through promoting the transcription of GPX4. HepG2 cells expressing control shRNAs or CARM1 shRNAs were treated with Sorafenib for 24 hours, and then the mRNAs were extracted and subjected to RNA-seq.

overall_design: Examination of gene expression changes in CARM1 knockdown and control HepG2 cells in the presence of Sorafenib.

first: Yiming

last: Cheng


title: Single-nuclei sequencing of Parvalbumin interneurons in mouse visual cortex after optoTrkB activation

status: Public on Jan 06 2023

city: Toyoake

first: Juzoh

last: Umemori

address: 1-98 Kutsukakecho, Dengakugakubo

institute: Fujita Health University

summary: After deep anesthesia by pentobarbital, the mice were perfused with ice-cold NMDG ACSF, and the brains were isolated and sliced by vibratome in NMDG ACSF. Then the slices were exposed by LED blue light, and incubated in a modified HEPES aCSF for one hour. The visual cortex was Isolated from the slices under microscope with red light, and tissues were homogenized, and nuclei were extracted. All procedures were performed with RNase free in the dark condition. The nuclei were stained with Hoechst 33342 and mouse monoclonal anti-NeuN antibody (Sigma-Aldrich, MAB377), and double positive nuclei were sorted by FACS. Then the sorted nuclei were used to make cDNA Library with Chromium Single Cell 3ʹ Gene Expression v3 library preparation kit (10x Genomics), and sequenced with NovaSeq 6000 (Illumina). Data was pre-processed using CellRanger 3.0, and analysed by Chipster version 3.16/Seurat v3.

overall_design: snRNA-seq of neurons in the visual cortex

first: Frederike

last: Winkel

first: Salome

last: Mateo

first: Elias

last: Jetsonen

first: Eero

last: Castren


title: A CRISPR/Cas9 library screening identified CARM1 as a critical inhibitor for Sorafenib-induced ferroptosis in hepatocellular carcinoma cells [CRISPR screen]

summary: To find epigenetic factors potentially involved in Sorafenib resistance in hepatocellular carcinoma cells, an epigenetic factors-targeted CRISPR/Cas9 library was applied to perform the screening.

overall_design: The CRISPR/Cas9 library which contains 5,648 sgRNAs (cloned into the pLentiCRISPRv2 vector) targeting epigenetic factors (containing 131 non-targeting controls) was packaged into lentivirus particles and used to infect HepG2 cells to generate a cell pool. The cell pool was treated with DMSO or 5 μM Sorafenib for 15 days, or not treated. Then, the fragments containing sgRNAs were amplified by PCR, and subjected to high-throughput sequencing.


title: Neuropilin-1+ vs. Neuropilin-1- CD8+ T cells from Plasmodium berghei ANKA-infected mice

status: Public on Dec 31 2022

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Characterization of Neuropilin-1+ and Neuropilin-1- splenic CD8+ T cells from Plasmodium berghei ANKA-infected C57BL/6 mice

overall_design: To study the role of Nrp-1 on the phenotype of CD8+ T cells during experimental cerebral malaria, gene expression analysis of sort-purified Nrp-1+ and Nrp-1- CD8+ T cells from spleens of PbA-infected C57BL/6 mice was performed.

first: H

last: Abberger

first: W

last: Hansen

first: R


title: The single-cell atlas of the murine intrauterine tissues during preterm labor

status: Public on Jan 04 2023

city: Detroit

first: Roger

last: Pique-Regi

state: Michigan

address: 540 E Canfield (Scott Hall 3309)

institute: Wayne State University

summary: scRNA-seq was utilized to reveal that preterm labor affects the cellularity of the uterus, decidua, and cervix through immune cell infiltration and altered transcriptomic profiles of non-immune cell types.

overall_design: We utilized scRNA-sequencing coupled with an allogeneic murine model of intra-amniotic infection (using E. coli) to investigate the cellular landscape and cell-cell communications in the reproductive tissues (uterus, decidua, and cervix) during the process of preterm labor. In summary: C57BL/6 dams impregnated by BALB/c males were intra-amniotically injected with E. coli (n = 4) or PBS control  (n = 4) under ultrasound guidance, and the cervix, uterus, and decidua were collected 24 hours post-injection to prepare single-cell suspensions. Next, single cells were encapsulated in droplets using 10x Genomics technology and cDNA libraries were generated for sequencing.

first: Nardhy

last: Gomez-Lopez


title: Macrophage-specific alfa5 integrin signaling protects the infarcted heart from adverse remodeling, by stimulating angiogenesis

city: Bronx

first: Silvia

last: Hernandez

state: New York

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

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

overall_design: Refer to individual Series


title: The role of α5 Integrin in regulating macrophage phenotype and function during cardiac remodeling after myocardial infarction

summary: Macrophages infiltrate the infarcted heart and play a critical role in repair, remodeling and fibrosis. Macrophages sense changes in the extracellular matrix (ECM) environment through Integrins, thus activating signaling pathways that regulate their function. Analysis of our previous RNA sequencing data identified integrin α5 (Itgα5) as one of the most upregulated integrin genes in infarct macrophages. Accordingly, we hypothesized that integrin α5 signaling in infarct macrophages transduces ECM-derived signals, regulating  responses critical for repair and remodeling of the infarcted heart.

overall_design:
In order to study the role of ITGA5 in myeloid cells in vivo, we generated mice with myeloid specific loss of ITGA5 in lysozyme M+ cells (Myα5KO). We used a transgenic mouse line in which Cre recombinase is driven by the LyzM promoter (Jackson Laboratory #004781). LyzM-Cre mice were bred with ITGA5 fl/fl mice (Jackson Laboratory #32299) to generate LyzM-Cre;ITGA5fl/fl animals (Myα5KO) and corresponding ITGA5 fl/fl control littermates. A model of non-reperfused myocardial infarction was induced by permanent ligation of left anterior descending coronary artery in 12-weeks-old mice and samples were collected 7 days after coronary occlusion for ITGA5 fl/fl and Myα5KO.
>>> Submitter declares raw data are unavailable and cannot be recovered. <<<

first: Ruoshui

last: Li

first: Bijun

last: Chen

first: Anis

last: Hanna

first: Claudio

last: Humeres

first: Jun

first: Nikolaos

last: Frangogiannis


title: Fear extinction is regulated by the activity of long noncoding RNAs at the synapse

city: St Lucia

first: Qiongyi

last: Zhao

state: Queensland

address: Building 79, QBI, The University of Queensland

department: Queensland Brain Institute

country: Australia

institute: The University of Queensland

summary: Long noncoding RNAs (lncRNAs) represent a multidimensional class of regulatory molecules involved in many aspects of brain function. Emerging evidence indicates that lncRNAs are expressed at the synapse; however, a direct role for their activity in this subcellular compartment in memory formation has yet to be demonstrated. Using lncRNA capture-seq on synaptosomes, we identified a significant number of lncRNAs that accumulate at synapses within the infralimbic prefrontal cortex of adult male C57/Bl6 mice. Among these is a splice variant related to the stress-associated lncRNA, Gas5. RNA immunoprecipitation followed by mass spectrometry and single molecule imaging revealed that this Gas5 isoform, in association with the RNA binding proteins G3bp2 and Caprin1, regulates the activity-dependent trafficking and clustering of RNA granules in dendrites. In addition, we found that cell-type-specific, state-dependent, and synapse-specific knockdown of the Gas5 variant led to impaired fear extinction memory. These findings identify a new mechanism of fear extinction that involves the dynamic interaction between local lncRNA activity and the coordination of RNA condensates in the synaptic compartment.

overall_design: lncRNA capture sequencing in the synaptic compartment

first: Wei-Siang

last: Liau

first: Timothy

last: Bredy


title: Chronic inflammation is a risk factor for gastric carcinogenesis after Helicobacter pylori eradication

city: Chiba-City

first: Ariki

last: Nagashima

address: Inohana 1-8-1

department: Department of gastroenterology

institute: Graduate School of Medicine, Chiba University.


title: Poly(ADP-ribosyl)ating enzymes cooperate to coordinate development

status: Public on Dec 21 2022

city: Grand Forks

first: Alexei

last: Tulin

state: North Dakota

address: 501 N Columbia Rd Stop 9061

department: Epigenetics Department

institute: University of North Dakota

summary: Comparative gene expression profiling analysis of RNA-seq data in Drosophila melanogaster L3 larva puffstage 7-9 between male Parg mutants (parg27.1/Y) and yellow white males as a control (w1118, y1/Y)

overall_design: In total 6 samples: 3 biological replicates of L3 larva puffstage 7-9 w1118, y1/Y male larvae used as control and 3 biological replicates of L3 larva puffstage 7-9 parg27.1/Y male larvae.

first: Guillaume

last: Bordet

first: Iaroslava

last: Karpova


title: Chronic inflammation is a risk factor for gastric carcinogenesis after Helicobacter pylori eradication [miRNA]

summary: Even after endoscopic treatment of early gastric adenocarcinoma (GAC) and eradication of Helicobacter pylori (H. pylori), some patients develop a metachronous recurrence (MR), the mechanism of which is still unknown. To elucidate the mechanism and risk factors for MR, we analyzed gene expression at multiple locations of the gastric mucosa, considering the heterogeneity of gastric mucosal damage caused by H. pylori infection and investigated the mechanism and risk factors for MR.

overall_design: Five patients with MR (MR group) and five patients without MR (control) after early GAC treatment and eradication of H. pylori were included.   In each case, mucosal tissue was collected as biopsy specimens from four sites in the stomach.  In each patient, one specimen was obtained from the lesser curvature of the antrum (LA) and the greater curvature of the antrum (GA), both within 2−3 cm from the pylorus, middle portion of the lesser curvature of the body between the cardia and angle (LB), and middle portion of the greater curvature of the corpus (GB).mRNA sequencing and microRNA(miRNA) sequencing were performed.

first: Kenichiro

last: Okimoto

first: Ryo

last: Nakagawa

first: Ryuta

last: Kojima


title: Chronic inflammation is a risk factor for gastric carcinogenesis after Helicobacter pylori eradication [RNA-seq]


title: Framework humanization increases the affinity and potency of anti-CD72 nanobody-based CAR-T cells for B-cell malignancies

status: Public on Dec 29 2022

city: San Francisco

first: Benjamin

last: Huang

address: 1450 3rd Street

institute: University of California San Francisco

summary: Anti-CD19 CAR T cells can induce remissions in some patients with B-cell malignancies. However, new immunotherapeutic targets are urgently needed for the many who relapse. We recently described CD72 as a promising target in B-cell leukemia and lymphoma, developing fully synthetic nanobody-based CAR-T cells (nanoCARs) against this antigen. Toward clinical translation, here we humanize our previous nanobody framework regions, derived from llama, and surprisingly discover a clone ("H24") with enhanced potency against B-cell tumors both in vitro and in vivo. In vitro, H24 nanoCARs showed improved cytokine secretion and favorable immunophenotypic properties. RNA sequencing before and after tumor exposure reveals humanized H24 CD72 nanoCARs have unique transcriptional programs compared to CD19 CAR T cells. We further find that H24 nanoCARs lead to sustained CD72 downregulation on tumors treated in vivo. Underpinning this improved potency, H24 had higher binding affinity to CD72 compared to a fully llama framework. Further affinity maturation moderately increased cytotoxicity versus antigen-low tumors. This work supports clinical translation of H24 CD72 nanoCARs, reveals potential mechanisms of resistance to this cellular therapy, and unexpectedly demonstrates that nanoCAR potency can be improved by framework alterations alone, without any change to the complementarity determining regions (CDRs) of the nanobody sequence.

overall_design: T cells were isolated from the peripheral blood from healthy blood donors. T cells were transduced with a lentivirus that encoded either H24 CD72 nanoCAR, CD19 CAR, or empty CAR. CAR-T cells were then cultured in the presence of IL-7 and IL-15. Each of the CAR-T constructs was co-cultured with a B cell acute lymphoblastic leukemia (B-ALL) cell line (SEM) for 24 hours, and then CAR-T cells were isolated from residual leukemia cells using magnetic activated cell sorting (MACS) enrichment. In addition, empty, CD19, and H24 CAR-T cells that were never exposed to B-ALL cells were also submitted for RNA-seq. These CAR-T cells are known as pre-tumor CAR-T cells. Cell pellets from all of the CAR-T cell conditions were then submitted to the company BGI for bulk RNA-seq analysis.

first: William

last: Temple

first: Arun

middle: P

last: Wiita


title: Development of a potency test assay for CD34+ cell-based for acute myocardial infarction

status: Public on Dec 16 2022

city: Mulhouse

first: Anne

last: ARIES

address: 87 Av d'Alkirch

institute: IRHT

summary: RNA-seq analysis was performed on RNA samples extracted from human autologous expanded CD34+ cells for 9 days ((ProtheraCytes®) in acute myocardial infarction patients and healthy donors in order to determine the up- and down-regulated genes involved in angiogenesis and vasculogenesis, to explore the mechanism of action of PortheraCytes® and thereby develop a potency assay for CD34+ cell-based therapy

overall_design: RNAseq profiling of ProtheraCytes from AMI patients versus Healthy Donors

last: Aries

first: Christine

last: Vignon

first: Céline

last: Zanetti

first: Aurélien

last: Goubaud

first: Arthur

last: Cormier

last: Diederichs

first: Rachid

last: Lahlil

first: Philippe

last: Hénon

first: Ibon

last: Garitaonandia


title: Interplay of NLRC4/NLRP3 inflammasomes and Fc-ˠ-Receptors on CD1c+ DC Associates with Pathogenic IFNˠ+IL17+ T cells and RA Severity

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

summary: Deregulated myeloid cells infiltrating to the joints likely contribute to rheumatoid arthritis (RA) pathogenesis through multiple mechanisms, including the secretion of proinflammatory cytokines and the induction of pathogenic adaptive Th17 cells, that mediate joint damage. However, the individual contribution of specific myeloid subsets such as CD1c+ and CD141+ conventional dendritic cells (cDC) to RA development and progression has been poorly studied and remains unclear. In particular, the potential molecular mechanisms specifically affecting CD1c+ cDCs in RA patients and their functional implications have not been characterized. Using RNA-seq, multiparametric flow cytometry and in vitro functional assays, we compared in parallel transcriptional, phenotypical and functional characteristics of monocytes, CD1c+ and CD141+ cDCs from the blood and synovial fluid of RA patients.

overall_design: We performed RNA sequencing using RNA from Monocytes, Dendritic Cd1c+ and Dendritic Cd141 cells obtained from blood/sinovial fluid of Rheumatoid Arthritis versus healthy/CPPD matched controls.

first: Cristina

last: Delgado-Arévalo

first: Marta

last: Calvet-Mirabent

first: Ana

last: Triguero-Martinez

last: Vázquez de Luis

first: Alberto

last: Benguría

first: Diego

last: Calzada-Fraile

first: Idelfonso

last: Sánchez-Cerrillo

first: Roberto

last: Moreno-Vellisca

first: Hortensia

last: de la Fuente

first: Almudena

last: Ramiro

first: Francisco

last: Sánchez-Madrid

first: Santos

last: Castañeda

last: Dopazo

first: Isidoro

last: Gonzalez-Álvaro

last: Martín-Gayo


title: Integrin α5 neutralization in Bone Marrow Macrophages to examine its signaling role in macrophage responses relevant following myocardial infarction

first: Silvia

last: Hernandez

overall_design:
In order to study the role of integrin α5 in mmacrophages in vitro, we isolated bone marrow macrophages from WT mice and grow them  in fibronectic coated and normal culture dishes, and treated them with a anti-integrin α5 neutralizing antibody and its control (IgG).
>>> Submitter declares raw data are unavailable and cannot be recovered. <<<

first: Ruoshui

last: Li

first: Bijun

last: Chen

first: Anis

last: Hanna

first: Claudio

last: Humeres

first: Jun

first: Nikolaos

last: Frangogiannis


title: Early microbial exposure shapes adult immunity by altering CD8+ T cell development [RNA-seq]

status: Public on Dec 04 2022

city: Ithaca

first: David

last: Iu

state: NY

address: 427 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

summary: Microbial exposure during development can elicit long-lasting effects on the health of an individual. However, how microbial exposure in early life leads to permanent changes in the immune system is unknown. Here, we show that the microbial environment alters the setpoint for immune susceptibility by altering the developmental architecture of the CD8+ T cell compartment.  In particular, early microbial exposure results in the preferential expansion of highly responsive fetal-derived CD8+ T cells that persist into adulthood and provide the host with enhanced immune protection against intracellular pathogens.  Interestingly, microbial education of fetal-derived CD8+ T cells occurs during thymic development rather than in the periphery and involves the acquisition of a more effector-like epigenetic program. Collectively, our results provide a new conceptual framework for understanding how microbial colonization in early life leads to lifelong, and potentially irreversible, changes in the immune system.

overall_design: Gene profile analysis was performed on FACS purified naive fetal- and adult-derived CD8+ T cells with a CD49dlo phenotype, CD8+ T cells with a CD49dlo CD44hi phenotype, or CD49dloCD44lo phenotype

first: Cybelle

last: Tabilas

first: Ciarán

last: Daly

first: Kristel

middle: J

last: Yee Mon

first: Arnold

last: Reynaldi

first: Samantha

last: Wesnak

first: Jennifer

middle: K

last: Grenier

first: Miles

last: Davenport

first: Norah

last: Smith

first: Brian

last: Rudd

first: Andrew

last: Grimson


title: Developing & Optimizing Acute Myeloid Leukemia Specific Therapeutic Antibodies [CITE-seq]

status: Public on Dec 08 2022

city: South San Francisco

first: Simon

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

summary: Following nearly five decades with few approved therapies for acute myeloid leukemia (AML), the last three years have brought stellar progress with the U.S. Food and Drug Administration approving a number of new therapies for AML patients. Despite these advances, there are several high-risk patient AML populations with dismal survival on the order of months including those with primary refractory disease, those whose AML developed from an antecedent hematologic disorder, and those with high risk cytogenetic or mutational profiles (such as TP53 mutations or a complex karyotype). Furthermore, therapeutic options are limited for those unfit to receive cytotoxic chemotherapy due to age or co-morbidities. These treatment challenges clearly illustrate the need for improved therapeutic approaches in AML. Here we identify that antibody therapies for AML can be enhanced via optimization of (1) Fab target selection, and (2) engineering the Fc portion of the antibody to maximally engage receptors on immune effector cells. We demonstrate that antibodies targeting a novel AML-specific cell surface marker known as U5 snRNP200 have therapeutic efficacy in AML. Finally, we performed a whole-genome CRISPR screen to identify mechanisms by which U5 snRNP200 traffic to the cell surface. This revealed a requirement for cell-surface CD32a to enable U5 snRNP200 cell membrane localization.

overall_design: We employed Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) to simultaneously capture surface proteomes and gene expression. A panel of 131 oligo-tagged antibodies, including a custom antibody-derived tagged (ADT) anti-U5 snRNP200 antibody, was applied to eleven bone marrow samples including three age matched normal donors and eight newly diagnosed AML patients.

first: Kate

last: Knorr

first: Jahan

last: Rahman

first: Omar

last: Abdel-Wahab


title: Developing & Optimizing Acute Myeloid Leukemia Specific Therapeutic Antibodies

status: Public on Dec 07 2022


title: Developing & Optimizing Acute Myeloid Leukemia Specific Therapeutic Antibodies [CRISPR Screen]

status: Public on Dec 02 2022

summary: Following nearly five decades with few approved therapies for acute myeloid leukemia (AML), the last three years have brought stellar progress with the U.S. Food and Drug Administration approving a number of new therapies for AML patients. Despite these advances, there are several high-risk patient AML populations with dismal survival on the order of months including those with primary refractory disease, those whose AML developed from an antecedent hematologic disorder, and those with high risk cytogenetic or mutational profiles (such as TP53 mutations or a complex karyotype). Furthermore, therapeutic options are limited for those unfit to receive cytotoxic chemotherapy due to age or co-morbidities. These treatment challenges clearly illustrate the need for improved therapeutic approaches in AML.  Here we identify that antibody therapies for AML can be enhanced via optimization of (1) Fab target selection, and (2) engineering the Fc portion of the antibody to maximally engage receptors on immune effector cells. We demonstrate that antibodies targeting a novel AML-specific cell surface marker known as U5 snRNP200 have therapeutic efficacy in AML. Finally, we performed a whole-genome CRISPR screen to identify mechanisms by which U5 snRNP200 traffic to the cell surface. This revealed a requirement for cell-surface CD32a to enable U5 snRNP200 cell membrane localization.

overall_design: K-562 and U-937 cancer cell lines were transduced with cDNA encoding the Cas9 endonuclease and a genome-scale sgRNA library to genetically deplete each gene in the genome, then sorted by flow cytometry for increased (higher than baseline) or decreased (lower than baseline) expression of cell surface SNRNP200. Single replicate samples for high and low SNRNP200 expression or a bulk unsorted population, respectively, were sequenced from each cell line and the distribution of sgRNAs was determined to infer genes/biological pathways involved in the regulation of cell surgface SNRNP200.


title: Comparison of gene expression profiles of RNA-seq data from lungs of wild-type mice and RBM47KI mice

status: Public on Nov 29 2022

city: Wuhan

first: Yiqi

last: Wang

state: State...

address: Shizishan Street

institute: Huazhong Agricultural University, China

summary:
To investigate the function of RBM47-ISGylation in mouse lungs, we generated an RBM47 knock-in mouse in which K329 and K332 were mutated to ISGylation-deficient arginine (K329R;K332R).
We then performed gene expression analysis using data obtained from RNA-seq of lung tissues from wild-type and pure mice from the same litter.

overall_design: Gene expression profile of RBM47 K329R;K332R KI mouse lung RNA-seq data.

first: Min

last: Zhang

first: Shihui

last: Ding


title: Early microbial exposure shapes adult immunity by altering CD8+ T cell development [ATAC-seq]

first: David

last: Iu

overall_design: ATAC-seq analysis was performed on FACS purified naive fetal- and adult-derived CD8+ T cells with a CD49dlo phenotype, CD8+ T cells with a CD49dlo CD44hi phenotype, or CD49dloCD44lo phenotype

first: Cybelle

last: Tabilas

middle: D


title: Lung response to oil vapor exposure in rats

city: Morgantown

first: Christina

middle: M

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

summary: The lung response to inhalation exposure to oil vapor particles was investigated in a rat model.  Adult male Sprague-Dawley rats were exposed by whole-body inhalation to air or an aerosol containing oil vapor particles at concentrations of 300 ppm, 6 hours/day for 1 day (shot-term) or 300 ppm, 6 hours/day, 4 days/week for 4 weeks (long-term).  The control and oil vapor exposed rats were euthanized at post-exposure time intervals of 1 and 28 days and lung toxicity determined.  Analysis of bronchoalveolar lavage parameters of toxicity such as lactate dehydrogenase activity, oxidant generation, and inflammation did not reveal any significant lung toxicity in the oil vapor exposed rats.  Approximately 50 genes each were found significantly differentially expressed in both the short- and long-term exposure groups of the rats at the one-day post-exposure time interval. The data obtained from the present study demonstrated that oil vapor inhalation exposure, under the exposure conditions employed in the present study, did not result in any significant lung toxicity in the rats despite the gene expression changes detected.

overall_design: The rats were exposed by whole-body inhalation to filtered air or oil vapor particles (300 ppm, 6 hours/day for 1 day or 300 ppm, 6 hours/day, 4 days/week for 4 weeks). At post exposure time intervals of 1 and 28 days, the air and oil vapor exposed rats were euthanized and lung samples (n=6) were used to determine gene expression profiles by RNA sequencing.

first: Tina

last: Sager

first: Pius

last: Joseph


title: RNA-sequencing of renal cells from Setd2-wildtype PKD and Setd2-knlckout ccRCC mice.

status: Public on Dec 26 2022

city: Shanghai

first: Rao

last: hanyu

address: Huashan Road NO.1954

institute: Shanghai Jiao Tong University

summary: To explore potential role of SETD2 in PKD-ccRCC transition in vivo, we generated a PKD mouse model by overexpressing oncogene c-MYC under the control of the Ksp promoter (KM mice), and knockout Setd2 gene using the same Ksp promoter in this PKD mice (KMs mice) to establish a ccRCC mouse model. To further characterize biological responses trigered by SETD2 deletion during PKD-ccRCC transition at the mRNA level, we next conducted global transcriptomics studies.

overall_design: Renal primary tubular epithelial cells mRNA profiles of five Kmmice and five KMS mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Hanyu

last: Rao

first: Changwei

last: Liu

first: Li

last: Li


title: PD-L1 regulates inflammatory programs of macrophages from human pluripotent stem cells.

city: Hong Kong

last: ZHANG

address: Science and Technology W Ave

institute: Centre for Translational Stem Cell Biology Limited

summary: CRISPR knock-out combined with flow cytometry and scRNA-seq show that PD-L1 ablation compromises macrophage development from human pluripotent stem cells

overall_design: PD-L1 is detected  to be sharply expressed in only macrophages, and through PD-L1 knock-out by CRISPR, we found a surge decrease of macrophage population developed from human pluripotent stem cells, by flow cytometry. ScRNA-seq of wild-type and PD-L1 knock-out sample was used to characterize the difference of macrophages between them.

first: Rio

last: Sugimura

first: Handi

last: Cao

last: Xiang


title: Transcriptome changes after curcumin analog treatment in HER2+ breast cancer cells

status: Public on Nov 26 2022

city: Yogyakarta

first: Adam

last: Hermawan

state: DI Yogyakarta

address: Sekip Utara II

department: Pharmacy

country: Indonesia

institute: Universitas Gadjah Mada

summary: HER2+ breast cancer cells were treated with curcumin analog PGB-0-ol and analyzed mRNA expression through mRNA sequencing

overall_design: We performed mRNA sequencing to find differentially expressed genes in PGB-0-ol treated HER2+ breast cancer cells cells.

first: Rohmad

middle: Y

last: Utomo

first: Febri

last: Wulandari

first: Ratna

last: Susidarti

first: Mitsunori

last: Kirihata

first: Edy

last: Meiyanto


title: Early microbial exposure shapes adult immunity by altering CD8+ T cell development

first: David

last: Iu

overall_design: Refer to individual Series


title: Gene expression signatures of MDCK-pTR GFP-RasV12 mCherry-β-catenin Δ131 cells cultured alone or mixed with MDCK mCherry-β-catenin Δ131 cells

status: Public on Nov 16 2022

city: Noda-shi

first: Shunsuke

last: Kon

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

institute: Tokyo University of Science

summary: Normal epithelial cells exert their competitive advantage over RasV12-transformed cells and eliminate them into apical lumen via cell competition. However, it remains elusive which internal or external factors compromise cell competition and provoke oncogenesis. Here, we examine the effect of sequential accumulation of gene mutations mimicking multi-sequential carcinogenesis on RasV12-induced cell competition. Consequently, we find that directionality of cell extrusion of RasV12 cells mosaically produced within Wnt-activated epithelia is reversed, and transformed cells are delaminated into basal lamina via non-cell autonomous MMP21 upregulation. Elevated production of MMP21 is elicited partly through NF-κB signaling, which blockage restores apical elimination of RasV12 cells. Collectively, this study demonstrates that cells with high mutational burdens exploit cell competition for their benefit by behaving as unfit cells and are endowed with an invasion advantage. We performed microarray analysis to search for molecules whose expression is changed in β-catenin Δ131/RasV12 cells surrounded by β-catenin Δ131 cells.

overall_design: 1.2×10^7 cells  of 10:1 mix culture of MDCK mCherry-β-catenin Δ131 and MDCK-pTR GFP-RasV12 mCherry-β-catenin Δ131 cells or a single culture of MDCK-pTR GFP-RasV12 mCherry-β-catenin Δ131 cells were cultured in collagen type I-coated dishes. After incubation with tetracycline for 24 h, GFP-positive cells were collected by an analytical flow cytometer, and total RNA was extracted from the isolated cells.

first: Kazuki

last: Nakai


title: Transcriptomic changes induced by allosteric inhibitor RMC-4550 in FLT3 and KIT mutant human AML cell lines

status: Public on Nov 08 2022

first: Bogdan

last: Popescu

state: CA

address: 513 Parnassus Ave.

institute: UCSF

summary: Targeting the MAPK signaling is an effective therapeutic approach in acute myeloid leukemia (AML) with mutations in FLT3 and KIT tyrosine kinase receptors. SHP2 is a central node in the MAPK signaling pathway and SHP2 inhibition was shown to supress leukemia proliferation in vitro and in vivo. In order to investigate the gene expression alterations induced by allosteric SHP2 inhibition and identify potential co-targets for pharmacological inhibition, we treated three human FLT3 and KIT mutant AML cell lines with RMC-4550 and performed RNAseq.

overall_design: Differential gene expression analysis from RNA-seq in Molm-14, MV4-11 and SKNO-1 treated with RMC-4550 vs treated with vehicle

first: Catherine

last: Smith


title: COPD and non-diseased nasopharyngeal and bronchial organoids characterization by single cell RNA-seq

status: Public on Nov 10 2022

city: Singapore

first: Fransiskus

middle: Xaverius

last: Ivan

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

summary: Clinical COPD, characterised by intermittent and infective exacerbations, lacks cellular model systems for the study of host-pathogen relationships. We establish nasopharyngeal and bronchial organoids from COPD patients and healthy individuals. In contrast to healthy organoids, COPD organoids demonstrate the hallmark goblet cell hyperplasia phenotype with reduced ciliary beat frequency, leading to impaired mucociliary clearance. By single-cell transcriptome analysis, smooth trajectory of cellular differentiation is disrupted in COPD organoids when compared to non-diseased, and functional pathways involved in the development and progression of COPD including mitochondrial dysfunction and sirtuin signalling are activated in the COPD model.

overall_design: Characterization of lung organoids derived from healthy and COPD donors for cell population, differentiation process and pathway analysis

first: Louisa

middle: L

last: Chan

middle: X

first: Hong

last: Cheng

first: Nguan

last: Tan

first: Sanjay

middle: H

last: Chotirmall


title: Gene expression in COPD and non-diseased nasopharyngeal organoids following Pseudomonas aeruginosa infection

summary: Pseudomonas aeruginosa is a common bacteria leading to exacerbations of chronic obstructive pulmonary disease (COPD) patients while this bacteria can be easily eradicated by the immune systems of healthy individuals. Human airway organoids derived from healthy individuals and COPD patients were infected with pseudomonas aeruginosa. This project aims (1) to understand the differences in gene expressions in healthy and COPD airway organoids during stable condition, without infection and (2) to investigate differential pathogenic mechanism (i.e. antimicrobial defense) of pseudomonoas aeruginosa infection in healthy and COPD populations. Three healthy donors and three COPD patients were included in this study and samples were collected with and without pseudomonas aeruginosa infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for COPD and non-diseased nasopharyngeal organoids, with or without infection of Pseudomonas aeruginosa


title: Transcriptomes of normal human mature B cells and REH B-cell acute lymphoblastic leukemia cells: effect of FBXW7 isoform knockdown or knockout followed by reconstitution

status: Public on Oct 31 2022

city: Philadelphia

first: Andrei

last: Thomas-Tikhonenko

state: PA

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Noncanonical exon usage plays many important roles in cellular phenotypes, but its contribution to human B-cell development remains sketchily understood. To fill this gap, we collected various B-cell fractions from bone marrow (BM) and tonsil donors, performed RNA sequencing, and examined transcript variants. We identified 150 genes that harbor local splicing variations in all pairwise comparisons. One of them encodes FBXW7, an E3 ubiquitin ligase implicated as a driver in several blood cancers. Surprisingly, we discovered that in normal human pro-B cells, the predominant transcript used an alternative first exon to produce the poorly characterized FBXW7β isoform, previously thought to be restricted to neural tissues. The FBXW7β transcript was also abundant in cell lines and primary samples of pediatric B-cell acute lymphoblastic leukemia (B-ALL), which originates in the BM. When overexpressed in a heterologous cell system, this transcript yielded the expected protein product, as judged by anti-FLAG immunoblotting and mass spectrometry. Furthermore, in REH B-ALL cells, FBXW7β mRNA was the only FBXW7 isoform enriched in the polyribosome fraction. To shed light on possible functions of FBXW7β, we used gain- and loss-of-function approaches and identified an FBXW7-dependent inflammatory gene signature, apparent in a subset of B-ALL with high FBXW7β expression. This signature contained several members of the tumor necrosis factor superfamily, including those comprising the HLA Class III cluster (LTB, LST1, NCR3, LTA, and NFKBIL1). Our findings suggest that FBXW7β expression drives proinflammatory responses, which could contribute to normal B-cell development, leukemogenesis, and responses to anticancer therapies. For normal bone marrow cell subset data, please go to GEO Series GSE115655.

overall_design: The sample groups are as follows. 1. LN: We performed fluorescence activated cell sorting to isolate primary normal B-cell subsets from human tonsil donors. 2. SYY53 + 54: To investigate functions of individual FBXW7 isoforms, we performed transient knockdown with Morpholinos in REH cell line. SYY53 and SYY54 are biological replicates from two independent experiments. 3. SYY123 + 141: We established REH cell lines where all FBXW7 isoforms were knocked out (pan-FBXW7 CRISPR KO clone 5 = cl5) and stably reconstituted with each FBXW7 isoform via the MIGR1 retroviral vector. SYY123 and SYY141 are biological replicates from two independent retroviral transduction experiments. 4. REH_ctrl: REH parental cell line.

first: Scarlett

last: Yang

first: Kathryn

last: Black


title: CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation

status: Public on Jan 01 2023

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

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


title: Single-cell RNA-sequencing measurements of in vitro activated and differentiated CD8+ T cells cultured in physiological media

status: Public on Nov 15 2022

city: Leuven

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

institute: VIB/KU Leuven

summary: Cytotoxic (CD8+) T cells dynamically rewire their metabolism during the course of an immune response. While T-cell metabolism has been extensively studied at phenotypic endpoints of activation and differentiation, the underlying dynamics remain largely elusive. To resolve these metabolic dynamics, we performed single-cell RNA-sequencing (scRNA-seq) measurements on in vitro activated and differentiated CD8+ T cells cultured in physiological media.

overall_design: Naïve CD8+ T cells were either (a) activated in vitro for 24h (Activated sample), or (b) activated in vitro for 54h and further differentiated in vitro for an extra 144h under either (b.1) IL-2 (Effector-polarized sample) or (b.2) IL-15 (Memory-polarized sample). CD8+ T-cell samples collected for each of the above three conditions/time points were analyzed by scRNA-seq.

first: Sarah

last: Fendt


title: Genome-wide maps of Dot1l associated epigenetic modifications during pluripotency acquistion

status: Public on Nov 01 2022

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

summary: Two independent, scaled, chromatin immunoprecipitation experiments were performed to uncover how Dot1l affects epigenetic modification (1) and RNA polymerase II (RNAPII) (2) localization. Mouse embryonic fibroblasts (MEFs), embryonic stem cells (ESCs), and reprogramming MEFs on day 4 treated with control (DMSO) or Dot1l inhibitor (Dot1li -SGC0946) were profiled. 1) Although ESCs have less global enrichment of H3K79me2 by mass spectrometry than MEFs, H3K79me2 is largely localized on the same shared genes in both cells, yet with reduced levels in pluripotent cells. All degrees of H3K79me (1/2/3) are predominately enriched on the same genes across cell types. Treatment with Dot1li evicts H3K79me1/2/3 from MEF specific, ESC specific, and shared genes with H3K79me2 peaks and enables gain of H3K9ac during reprogramming. 2) To understand how genebody epigenetic modifications affect transcription, RNAPII was analyzed. ESCs have less RNAPII enrichment at the transcriptional start site (TSS), but have similar genebody enrichment as somatic cells indicative of more relative elongation. Dot1li treatment during reprogramming reduces RNAPII at the TSS compared to control.

overall_design: H3K79me1, H3K79me2, H3K79me3, H3K9ac, and RNA polymerase II ChIP-Seq in MEFs, ESCs, and reprogramming cells

first: Coral

last: Wille


title: Skeletal Muscle Transcriptome in DMD rats fed MCTKD

status: Public on Nov 04 2022

city: Tsukuba

first: Yuri

last: Fujikura

state: Ibaraki

address: 1-1-1 Higashi

institute: National Institute of Advanced Industrial Science and Technology

summary: The global transcriptome of skeletal muscle from DMD model and wild-type rats was analyzed. The effects of MCTKD on transcriptional changes in DMD model rats were also analyzed.

overall_design: mRNA-seq of skeletal muscle (tibialis anterior) from DMD rats fed ND, DMD rats fed MCTKD, and wild-type rats  fed ND

first: Keitaro

last: Yamanouchi

first: Hidetoshi

last: Sugihara

first: Masaki

last: Hatakeyama

first: Tomoki

last: Abe

first: Satoru

last: Ato

first: Katsutaka

last: Oishi


title: A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation [scRNA-seq high fat diet]

status: Public on Oct 28 2022

summary: Cancer cells outgrowing in distant organs of metastasis rewire their metabolism to fuel on the available nutrients. While this is often considered an adaptive pressure limiting metastasis formation, some nutrients available at the metastatic site naturally or through changes in organ physiology may inherently promote metastatic growth. We find that the lung, a frequent site of metastasis, is a lipid-rich environment. Moreover, we observe that pathological conditions such as pre-metastatic niche formation and obesity further increase the availability of the fatty acid palmitate in the lung. We find that targeting palmitate processing inhibits spheroid growth in vitro and metastasis formation in lean and obese mice. Mechanistically, we discover that breast cancer cells use palmitate to synthesize acetyl-CoA in a carnitine palmitoyltransferase 1a (CPT1a)-dependent manner. Lysine acetyltransferase 2a (KAT2a), whose expression is promoted by palmitate availability, relies on the available acetyl-CoA to acetylate the NF-κB subunit p65. This favors nuclear location of p65 and activates a pro-metastatic transcriptional program. Accordingly, deletion of KAT2a phenocopies CPT1a silencing in vitro as well as in vivo and patients with breast cancer show co-expression of both proteins in metastases across palmitate-rich metastatic sites. In conclusion, we find that palmitate-rich environments foster metastasis growth by increasing p65 acetylation resulting in elevated NF-κB signaling.

overall_design: scRNA-seq from lungs of female BALB/c mice fed with control diet (CD) or high-fat diet (HFD) for 16 weeks.

first: Patricia

last: Altea-Manzano

first: Sofie

last: Demeyer


title: Single-nucleus RNA-seq reveals that MBD5, MBD6, and SILENZIO maintain silencing in the vegetative cell of developing pollen

status: Public on Oct 27 2022

city: Los Angeles

first: Lucia

last: Ichino

address: 610 Charles E Young Dr East

department: MCDB

institute: University of California, Los Angeles

summary: Silencing of transposable elements (TEs) drove the evolution of numerous redundant mechanisms of transcriptional regulation. Arabidopsis MBD5, MBD6, and SILENZIO act as TE repressors downstream of DNA methylation. Here we show via single-nucleus RNA-seq of developing male gametophytes that these repressors are critical for TE silencing in the pollen vegetative cell, which undergoes epigenetic reprogramming causing chromatin decompaction to support fertilization by sperm cells. Instead, other silencing mutants (met1, ddm1, mom1, morc) show loss of silencing in all pollen nucleus types and somatic cells. We found that TEs repressed by MBD5/6 gain accessibility in wild-type vegetative nuclei despite remaining silent, suggesting that loss of DNA compaction makes them sensitive to loss of MBD5/6. Consistently, crossing mbd5/6 to histone 1 mutants, which have decondensed chromatin in leaves, reveals derepression of MBD5/6-dependent TEs in leaves. MBD5/6 and SILENZIO thus act as a silencing system especially important when chromatin compaction is compromised.

overall_design: This study includes bulk RNA-seq data and single nucleus RNA-seq of developing male gametophytes generated with the 10X platform

first: Colette

last: Picard

first: Jaewon

last: Yun

first: Meera

last: Chotai

first: Ranjith

last: Papareddy

first: Yan

last: Xue

first: Steven

middle: E

last: Jacobsen

first: Shuya

last: Wang

first: Evan

last: Lin


title: Fragment-sequencing unveils local tissue microenvironments at single cell resolution

city: Zürich

first: Kristina

last: Handler

address: Winterthurerstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zürich

summary: The spatial organization of cells within tissues is tightly linked to their biological function. Yet, methods to probe the entire transcriptome of multiple native tissue microenvironments at single cell resolution are lacking. Here, we introduce fragment-sequencing, a method that enables the transcriptomic characterization of single cells within spatially distinct tissue niches. Fragment-sequencing of the mouse metastatic liver revealed previously uncharacterized zonated genes and ligand-receptor interactions enriched in the different hepatic microenvironments and the metastatic niche.

overall_design:
Method development of fragment-sequencing (based on single cell RNA sequencing and cell hashing) and its application to metastatic mouse liver (9 replicates), untreated mouse liver (1 replicate), untreated mouse spleen (2 replicates), Crohn?s disease biopsies (2 replicates) and a mix of human and mouse colorectal cancer organoids (1 replicate). To compare Visium of metastatic mouse livers (2 replicates) and conventional scRNAseq of metastatic mouse livers (2 replicates) were performed.

Please note that the records have been updated with two additional samples on Feb 6th, 2023.
Human samples were uploaded August 7th, 2023 and raw data were not provided due to patient privacy concerns.

first: Karsten

last: Bach

first: Costanza

last: Borrelli

first: Xenia

last: Ficht

first: Ilhan

last: Acar

first: Andreas

last: Moor


title: Effect of chronic restraint stress or repeated activation of PVN neurons responding to restraint stress on gene expression of white adipose tissues (iWAT and eWAT) during adipogenesis of mice

status: Public on Oct 29 2022

city: Binzhou

first: Bin

last: Liu

state: Shandong

address: No. 661 Huanghe 2nd Road, Binzhou City, Shandong

institute: Binzhou Medical University Hospital

summary: Comorbid depression and type 2 diabetes (T2D) is associated with more severe symptoms, higher suicide risk and poorer prognosis than those with either disease alone. However, the mechanisms underlying this comorbidity remain unclear. Here, we describe a brain–sympathetic nerve–adipose circuit originating in the hypothalamic paraventricular nucleus (PVN) that is crucial for the depressive-like behaviours and insulin resistance induced by chronic restraint stress. A subset of PVN neurons that were traced from WAT and activated under restraint stress, and chemogenetic manipulations demonstrated the sufficiency and necessity of those PVN neurons for changes in sympathetic innervation of adipose tissue and subsequent depression and insulin resistance induced by chronic stress. We further identify candidate adipokines for the development of depression and insulin resistance, and clarify the molecular mechanism by which the dynamics of sympathetic tone are translated into changes in the expression of candidate adipokines.

overall_design: Adipose tissue (iWAT and eWAT) mRNA profiles of control group mice and the restraint  group mice as well as mcherry group mice and hM3D group mice

first: Wei

last: Li


title: DUSP6 mediates resistance to JAK2 inhibition and drives leukemic progression (single-cell RNA-seq)

status: Public on Oct 25 2022

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

institute: Washington University School of Medicine

summary: Chronic myeloproliferative neoplasms (MPNs) exhibit a propensity for transformation to secondary acute myeloid leukemia (sAML), for which the underlying mechanisms remain poorly understood, resulting in limited treatment options and dismal clinical outcomes. Here, we performed bulk transcriptome profiling accompanied by single cell RNA-sequencing on CD34+ stem/progenitor cells from serial patient samples obtained at the chronic MPN and sAML phases, identifying aberrantly increased expression of dual-specificity phosphatase 6 (DUSP6) underlying disease transformation. Genetic and pharmacologic targeting of DUSP6 led to inhibition of S6 and JAK/STAT signaling, resulting in potent suppression of cell proliferation, while also reducing inflammatory cytokine production in primary samples. Furthermore, ectopic DUSP6 expression augmented proliferation and mediated JAK2 inhibitor resistance, while DUSP6 inhibition reduced colony-forming potential of JAK2 inhibitor-persistent patient cells. Mechanistically, DUSP6 perturbation dampened S6 signaling via inhibition of RSK1, which we identified as a second indispensable candidate associated with poor clinical outcome. Ectopic expression of DUSP6 in patient-derived xenograft (PDX) models exacerbated disease severity and led to early lethality, whereas DUSP6 knockdown suppressed leukemic engraftment. Finally, pharmacological inhibition of DUSP6 potently and specifically suppressed disease development across Jak2 V617F and MPL W515L MPN mouse models, as well as sAML PDXs, without inducing toxicity in healthy controls. These findings underscore DUSP6 in driving disease transformation and therapeutic resistance, and highlight the DUSP6-RSK1 axis as a novel, druggable pathway in myeloid malignancies.

overall_design: Single cell RNA-sequencing of serial MPN and sAML samples from patients, and healthy donor control

first: Stephen

middle: T

last: Oh


title: Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses (scRNA-seq)

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

summary: In vivo differentiation of human pluripotent stem cells (hPSCs) has unique advantages such as multilineage differentiation, angiogenesis, and close cell‒cell interactions. To systematically investigate the multilineage differentiation mechanisms of hPSCs, we constructed the in vivo hPSC differentiation landscape containing 239,670 cells using teratoma models. We inferred 18 cell differentiation trajectories and characterized common and specific gene regulation patterns during hPSC differentiation at both transcriptional and epigenetic levels. The results of developing single cell Basic Local Alignment Search Tool (dscBLAST), our self-developed tool for cell identification and developmental stage speculation, further confirmed the differentiated cell identity and suggested that cells in the teratoma are largely at immature developmental stages. Overall, our study offers new insights into stem cell fate decisions and embryonic development; dscBLAST shows favorable cell identification performance, providing both developmental and adult cells with a powerful tool for cell annotation and stage speculation.

overall_design: To construct the landscape of teratoma, 18 teratomas were used for single-cell RNA sequencing (scRNA-seq) based on Microwell-seq. Among them, six were generated from H9 embryonic stem cells (ESCs), and 12 were from H1 ESCs. To conduct joint analysis of multi-omics data, additional three teratomas from H9 ESCs were utilized for scRNA-seq and scATAC-seq simultaneously. For each teratoma sample, there are human-derived cells differentiated from ESCs and mouse-derived cells infiltrating from the thigh muscles of NOD/SCID mice, where the ESCs were injected.

first: Guoji

last: Guo

first: Daiyuan

first: Yuting

last: Fu

first: Xinru

first: Xueyi