title: Gene expression changes during the inflammatory phase after enthesis injury

city: Shanghai

first: Haihan

last: Gao

address: Xuhui District

department: Department of Orthopaedic Surgery

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: The repair of injured enthesis remains a challenging clinical issue in sports medicine due to dysregulated inflammation and limited regenerative capability. Nevertheless, the mechanisms through which this dysregulated inflammation deteriorates the regenerative niche of enthesis remain unclear. Here, we found that Nlrp3 inflammasomes were activated in macrophages after enthesis injury and subsequently suppressed the regeneration. Nlrp3 inflammasomes generated a proinflammatory niche through an imbalance between the pro-inflammatory factor IL-1β and anti-inflammatory factors including IL-10 and IL-13. Mechanistically, IL-1β was identified as an inhibitory inflammation signaling in proinflammatory niche, reducing the differentiation and migration of stem cells. Moreover, the P2rx7 receptors were verified as an activation signal for Nlrp3 inflammasome post-injury, and conditional knockout of P2rx7 receptors on myeloid cells promoted enthesis regeneration. Together, these results illustrate that Nlrp3 inflammasome generates a proinflammatory niche to suppress enthesis regeneration, and demonstrate that the P2rx7/Nlrp3 inflammasome axis and IL-1β are promising niche-directed regenerative therapeutic targets for enthesis injury treatment.

overall_design: The aims of this study were to understand the effect of inflammatoy phase on enthesis regeneration. We established rotator cuff enthesis injury and repair model and compared the gene expression changes with sham operation group.

first: Liren

first: Yangbao

last: Lyu


title: Stratification of expression profiles of immune-related genes in the lesion of cutaneous leishmaniasis patients with L. major and L. tropica infection

status: Public on Jul 01 2024

city: Tehran

first: Sima

last: Rafati

state: Tehran

address: Pasteur Ave

department: Immunotherapy and Leishmania Vaccine Research

country: Iran

institute: Pasteur Institute of Iran

summary: There is still no reliable human vaccination against cutaneous leishmaniasis (CL), a serious public health issue in many parts of underdeveloped nations like Morocco and Iran. There are few studies comparing the expression of immune-related genes in the skin lesions of CL patients infected with L. major and L. tropica. In this study, we used dcRT-MLPA to analyze the expression profiles of 144 immune response-related genes in CL patients from Morocco and Iran who had been exposed to L. major and L. tropica, respectively.

overall_design: Using a dual-color reverse-transcription multiplex ligation-dependent probe amplification (dcRT-MLPA) assay, the gene expression profile of innate, adaptive and inflammatory immune response was assessed in CL patients from Morocco and Iran who had been exposed to Leishmania major and Leishmania tropica, respectively. Normal skin samples were taken from four volunteers living in non-endemic areas and with no history of cutaneous leishmaniasis.

first: Nasrin

last: Masoudzadeh

first: Mouad

last: Ait Kbaic

first: Meryem

last: Lemrani

first: Josefine

last: Persson

first: Malin

last: Östensson

first: Björn

last: Andersson

first: Suzanne

last: van Veen

first: Eleonora

last: Vianello

first: T

middle: H

last: Ottenhoff

first: Ali

middle: M

last: Harandi


title: Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation.

status: Public on Jun 28 2024

city: Bath

first: Adele

last: Murrell

address: Claverton Down

department: Life Sciences Department

country: United Kingdom

institute: University of Bath

type: Methylation profiling by high throughput sequencing

summary: Colorectal cancer (CRC) progression from adenoma to adenocarcinoma is associated with global reduction in 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). DNA hypomethylation continues upon liver metastasis. Here we show that 5hmC is increased in metastatic liver tissue relative to the primary colon tumour and that expression of TET2 and TET3 is negatively correlated with risk for metastasis in patients with CRC. Genes associated with increased 5-hydroxymethylcytosine show KEGG enrichment for adherens junctions, cytoskeleton and cell migration around a core cadherin (CDH2) network. Overall, the 5-hydroxymethylcyosine profile in the liver metastasis is similar to normal colon appearing to recover at many loci where it was originally present in normal colon and then spreading to adjacent sites. The underlying sequences at the recover and spread regions are enriched for SALL4, ZNF770, ZNF121 and PAX5 transcription factor binding sites. SALL4 and PAX5 are not expressed during CRC progression, but ZNF770 and ZNF121 transcripts are dynamically regulated by TET2 during CRC progression. Finally, we show in a zebrafish migration assay using SW480 CRISPR-engineered TET knockout and rescue cells that reduced TET expression leads to a reduced migration frequency. Together these results suggest a biphasic trajectory for 5-hydroxymethyation dynamics that has bearing on potential therapeutic interventions aimed at manipulating 5-hydroxymethylcytosine levels.

overall_design: Research using patient tumour samples was conducted under the principles of the World Medical Association Helsinki agreement with ethical approval obtained from the Cambridgeshire Local Research Ethics Committee (LREC references 04/Q0108/ 125 and 06/Q0108/307). From a previously reported cohort of 119 CRC patients, available DNA samples included normal colonic mucosa (n=22), taken from tissue some distance away from the tumour, invasive primary carcinoma (n=65), liver metastatic deposits (n=32) and normal liver (5), taken from a site adjacent to the tumour. Genomic DNA was sonicated (Bioruptor) and pulled down using anti-5hmC (Active Motif, 39769). hMeDIP-seq libraries were prepared using the TruSeq DNA sample preparation kit (Illumina) following manufacturer’s instructions. Adaptor modified genomic DNA was then immunoprecipitated, whole genome amplified, and sequenced on an Illumina Genome Analyzer IIx. Sequence reads were aligned to the human reference genome build 38, filtered to remove greylist regions, and analysed for changes in 5mC/5hmC enrichment according to tissue/disease state.

first: Ben

last: Murcott

first: Floris

last: Honig

first: Dominic

last: Halliwell

first: Tian

last: Yuan

first: James

middle: L

last: Robson

first: Piotr

last: Manasterski

first: Jennifer

last: Pinnell

first: Giuseppina

last: Pisignano

first: Therese

last: Dix-Peeks

first: Santiago

last: Uribe-Lewis

first: Ashraf

last: Ibrahim

first: Julia

last: Sero

first: David

last: Gurovich

first: Nikolas

last: Nikolai


title: Epigenetic mechanisms controlling human leukemia stem cells and therapy resistance [RNA-seq]

city: New York

first: Richard

last: Koche

state: New York

country: USA

institute: Memorial Sloan Kettering Cancer Center

type: Expression profiling by high throughput sequencing

summary: Many human cancers, including acute myeloid leukemia (AML), arise from mutations of stem and progenitor cells. Immunophenotypic profiling has shown that leukemia develops hierarchically, with mutations in leukemia stem cells associated with disease propagation and relapse1,2. Although leukemia initiating cells can be enriched using cell surface markers, their frequency tends to be variable and low, obscuring mechanisms and hindering effective therapies3,4. To define AML stem cells in human patients, we performed functional genomic profiling of diverse leukemias using label tracing techniques designed to preserve hematopoietic stem cell (HSC) function in vivo. We found that propagation of human AML is mediated by a rare but distinct quiescent label-retaining cell (LRC) population that evades detection by currently known immunophenotypic markers. We show that human AML LRC quiescence is reversible, sparing genetic clonal competition that maintains its epigenetic inheritance. LRC quiescence is defined by distinct promoter-centered chromatin and gene expression dynamics, and controlled by a novel AP-1/ETS transcription factor network, which is associated with disease persistence and chemotherapy resistance in diverse patients. These results enable prospective isolation and functional genetic manipulation of immunophenotypically-varied leukemia stem cells in human patient specimens, as well as establish the key functions of epigenetic plasticity in leukemia development and therapy resistance. We anticipate that these findings will lead to the elucidation of essential properties of leukemia stem cell quiescence and the design of therapeutic strategies for their clinical identification and control.

overall_design: Molecular and functional profiling of diverese human patient AML stem cells using label tracing techniques in vivo.

first: Sumiko

last: Takao

first: Alex

last: Kentsis

middle: P


title: Cannabis smoking is associated with advanced epigenetic age

city: Calgary

first: Ana

middle: Isabel

last: Hernandez Cordero

state: Alberta

address: 303 13th Avenue SW, unit 1004

country: Canada

institute: Heart Lung Innovation Centre

type: Non-coding RNA profiling by genome tiling array

summary: Cannabis use has been controversial, largely having been designated a controlled substance over the last century. The link between cannabis smoking and disease pathogenesis may best be explored through DNA methylation, an epigentic mechanism. We investigated the relationship between epigenetic age and cannabis smoking in participants within the Canadian Cohort of Obstructive Lung Disease (CanCOLD) cohort (n=93) (ClinicalTrials.gov identifier NCT00920348). Blood  samples were profiled for DNA methylation using the Illumina MethylationEPIC BeadChipv1 at two separate laboratories and the blood epigenetic age of each sample was calculated using the Clock Foundation tool (https://dnamage.clockfoundation.org). An ANOVA was used to identify differences in the age acceleration residuals associated with cannabis smoking status (never, former, and current), adjusted for chronological age, sex, body mass index (BMI), batch, cigarette smoking status, and the first two principal components of blood cell proportions. Our observations indicated that current cannabis smoking and higher joint-years exposure are associated with epigenetic age acceleration; cessation, however, may help to normalize in part this age acceleration.

overall_design:
93 samples profiles for blood DNA methyaltion
contributor:CanCOLD Collaborative Research Group

first: Qingling

last: Duan

first: Janice

last: Leung


title: Epigenetic mechanisms controlling human leukemia stem cells and therapy resistance [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Molecular and functional profiling of diverse human patient AML stem cells using label tracing techniques in vivo.


title: Epigenetic mechanisms controlling human leukemia stem cells and therapy resistance

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

overall_design: Refer to individual Series


title: Single cell RNAseq of Influenza A replication kinetics in primary human bronchial epithelial cells

status: Public on Jun 25 2024

city: Minneapolis

first: Frances

last: Shepherd

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

summary: Influenza viruses pose a significant burden on global human health. Influenza has a broad cellular tropism in the airway, but how infection of different epithelial cell types impacts replication kinetics and burden in the airways is not fully understood. Using primary human airway cultures, which recapitulate the diverse epithelial cell landscape of the human airways, we investigated the impact of cell type composition on virus tropism and replication kinetics. Cultures were highly diverse across multiple donors and 30 independent differentiation conditions and supported a range of influenza replication. Although many cell types were susceptible to influenza, ciliated and secretory cells were predominantly infected. Despite the strong tropism preference for secretory and ciliated cells, which consistently make up 75% or more of infected cells, only ciliated cells were associated with increased virus production. Surprisingly, infected secretory cells were associated with overall reduced virus output. These data highlight the heterogeneous outcomes of influenza virus infections in primary human airway cultures and the disparate impacts of infected cell identity on burst size, even among preferentially infected cell types.

overall_design: NHBE cells were infected with Cal/04/09 at an MOI of 0.5 or mock infected (one well each). 10 hours post infection cells were washed and trypsinized to generate single cell suspensions. Single cell suspensions were filtered and counted and 10,000 cells per condition were used to generate Gel Bead-in Emulsions (GEMs). The 10X Chromium 3' GEX Capture kit and the 10X Chromium controller were used to generate GEMs and barcoding per manufacturers protocol (10X Genomics, Pleasanton, CA, USA). GEMs generated were used for cDNA synthesis and library preparation using the Chromium Single Cell 3' Library Kit and run on a NovaSeq S2. 2x100 PE Run.

first: Shanley

middle: N

last: Roach

middle: K

first: Clayton

last: Mickelson

first: Jessica

last: Fiege

first: Beth

last: Thielen

first: Lauren

last: Pross

first: Autum

middle: E

last: Sanders

first: Mason

last: Robertson

first: Ryan

middle: A

last: Langlois


title: PACT-mediated regulation of endogenous dsRNA sensing by PKR

status: Public on Jun 16 2024

city: Boston

first: Sun

last: Hur

state: MA

address: 3 Blackfan St,

institute: Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine

summary: Protein kinase R (PKR), an innate immune sensor for double-stranded RNA (dsRNA), is critical for antiviral defense, but its aberrant activation by cellular dsRNA is linked to various diseases. The dsRNA-binding protein PACT plays a crucial and controversial role in the PKR pathway. We demonstrate that PACT is an essential negative regulator of PKR against endogenous dsRNA ligands like inverted repeat Alu RNAs, which satisfy PKR’s selectivity for long dsRNA and robustly activate PKR in the absence of PACT. PACT employs an unusual inhibitory mechanism sensitive to dsRNA length and concentration, inhibiting PKR through low-affinity interactions most effective when both are bound to the same dsRNA molecule. Consequently, PACT’s inhibition of PKR is more robust when dsRNA is longer and less abundant, with minimal effect on abundant or short dsRNA. Thus, PACT functions as a rheostat, setting the PKR activation threshold for long endogenous dsRNA without altering its inherent activity.

overall_design:
To identify the endogenous RNA ligands of PACT, we generated Flag-tagged PACT expressing HCC1806 cells. We then performed fCLIP with Anti-Flag antibody and sequenced the Input and CLIP samples. 2 biological replicates were prepared
To identify the endogenous RNA ligands of PKR, we generated PKR/PACT double knock out cell lines in HCC1806 cells expressing HA-tagged PKR(K296R). We then performed fCLIP with Anti-HA antibody and sequenced the Input and CLIP samples. 3 biological replicates were prepared
To identify the endogenous RNA ligands of PKR in PACT-sufficient and PACT-deificient backgrounds, we generated PKR knockout and PKR/PACT double knock out cell lines in HCC1806 cells expressing HA-tagged PKR(K296R). We then performed fCLIP with Anti-HA antibody and sequenced the Input and CLIP samples. 4 biological replicates were prepared

first: Sadeem

last: Ahmad

first: Xi

last: Wang

first: Tao

last: Zou

first: Matthew

last: Meyerson


title: Gene expression at single cell level of tumor-infiltrating cells from the tumor foci, draining lymph node and peripheral blood of triple-negative breast cancer

status: Public on Jun 12 2024

city: Guangzhou

first: Hao

last: Jin

state: Guangdong

address: No.72 of Second Zhongshan Road

country: China

institute: Sun Yat Sen Memorial Hospital

summary: Tumor-infiltrating cells are considered as a homogeneous populations in the tumor microenvironment. We used single cell RNA sequencing (scRNA-seq)  to analyze the diversity of tumor-infiltrating cells of the tumor foci, draining lymph node and peripheral blood from patients with triple-negative breast cancer who received chemotherapy.

overall_design: Single-cell RNA-seq libraries were generated for two triple-negative breast cancer samples, including pre- and post- chemotherapy treatment samples, using the 10X Genomics Chromium platform and sequenced on the Illumina NovaSeq 6000.

first: Yue

last: Chen

first: Dongbo

last: Zhang

first: Junfan

last: Lin

first: Songyin

last: Huang

first: Xiaohua

last: Wu

first: Wen

last: Deng

first: Jiandong

first: Yandan

last: Yao


title: Gene expression profile at single cell level of injured enthesis at 7 day post repair operation from wild type and Nlrp3 knockout mice

status: Public on Jun 10 2024

first: Haihan

last: Gao

summary: The repair of injured enthesis remains clinically challenging in sports medicine. We have proved that the activation of Nlrp3 inflammasomes suppressed enthesis regeneration. So we used single cell RNA-seq to uncover the  mechanisms by which Nlrp3 inflammasomes modulate enthesis regeneration

overall_design: Enthesis at 7 day post injury and repair from wild type and Nlrp3 -/- mice were carefully harvested under surgical microscope and pooled together. Single-cell RNA sequencing was used to analyze


title: Genes associated with mitogen-activated protein kinase activity in pancreatic cancer cells

status: Public on Jun 05 2024

city: Tokyo

first: Toru

last: Furukawa

address: 8-1 Kawadacho, Shinjuku-ku

department: Institute for Integrated Medical Sciences

country: Japan

institute: Tokyo Women's Medical University

summary: We performed a transcriptome analysis to determine what genes were altered in expression when U0126, MAP2K inhibitor, was administered to cells of human pancreatic cancer cell lines. Five genes including ETV5, ETV4, COL13A1, HIST1H4L/H4C13, and WDR62 were found to be particularly downregulated by the inhibition of MAPK pathway, meaning that these genes were preferentially upregulated by the active MAPK. The expression of ETV5 was most modulated, suggesting that ETV5 is strongly associated with the MAPK activity and may play a role in human pancreatic cancer.

overall_design: Human pancreatic cancer cell lines AsPC-1, MIA PaCa-2, and PCI-35 were used in this study. AsPC-1 and MIA PaCa-2 were obtained from the American Type Culture Collec-tion (Manassas, VA, USA), and PCI-35 was provided by Dr. Hiroshi Ishikura [Int J Cancer 1993;54:972-977]. Unless otherwise stated, AsPC-1 and PCI-35 were cultured with RPMI-1640 with 10% fetal bovine serum, and MIAPaCa-2 was cultured with Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum. Cells of the human pancreatic cancer cell lines were seeded at 5 × 105 cells per dish in 10-cm culture dishes and cultured under 37°C in 5% CO2. After 24 hours, the medium was replaced with medium containing U0126 (Sigma-Aldrich, St. Louis, MO, USA), a MAP2K inhibitor, dissolved in dimethyl sulfoxide (DMSO) to a final concentration of 10 μmol/L, or with medium containing only the same amount of DMSO without U0126 as a control. After incubation for 24 hours, cells were dissociated for RNA isolation. Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instruction. The isolated total RNA was used for construction of a fragment library using TruSeq Stranded Total RNA LT Sample Prep Kit Gold (Illumina, San Diego, CA, USA). Constructed libraries were subjected to total transcriptome enrichment using a NovaSeq 6000 S4 Reagent Kit. The prepared transcriptome libraries were sequenced on an Illumina NovaSeq 6000 platform using the paired-end sequencing method. All procedures were performed according to the manufacturer’s instructions and done by Macrogen Japan Corp. (Tokyo, Japan). Reads were aligned to GRCh38 using HISAT2. Around one hundred million reads were mapped per sample. Known genes and transcripts were assembled with StringTie based on the reference genome model. The FPKM value of known genes obtained through StringTie analysis was used to detect the differentially expressed genes. During data preprocessing, low-quality transcripts were filtered out. Afterward, log2 transformation of FPKM+1 and quantile normalization were performed. Genes showing two-fold or more changes in expression by MAPK attenuation were interpreted as significant.

first: Tomohiko

last: Ishikawa

first: Aya

last: Noguchi


title: In a nutshell: pistachio genome and kernel development

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: 1 Shields Ave.

department: Plant Sciences

institute: University of California, Davis

summary: Pistachio is a sustainable nut crop with exceptional climate resilience and nutritional value. To advance pistachios as a future food source and establish a model system for hard-shelled fruits, we generated essential knowledge and resources for the scientific community. We include a new chromosome-scale reference genome assembly and annotation of the most widely grown pistachio cultivar (Pistacia vera ‘Kerman’) and a spatiotemporal developmental study of the hull, shell, and kernel. Our study defined four distinct stages of pistachio growth and maturation by integrating tissue-level physiological and molecular data from thousands of nuts across twenty-four time points over three growing seasons. Transcriptional and metabolic changes in the kernel elucidate nutritional quality, such as the accumulation of unsaturated fatty acids, vital for shelf life and dietary value. This work yields new knowledge that will inform other woody crops and facilitate further improvement of pistachio as a globally significant, sustainable, and nutritious crop.

overall_design: Gene expression analysis was performed on three pistachio tissues, hull (fruit exocarp), shell (fruit endocarp), and kernel (seed), across 15 weeks of fruit and seed development.

first: Jaclyn

last: Adaskaveg

first: Chaehee

last: Lee

first: Yiduo

last: Wei

first: Fangyi

first: Filipa

last: S Grilo

first: Selina

middle: C

first: Giulia

last: Marino

first: Louise

last: Ferguson

first: Patrick

middle: J

last: Brown

first: Georgia

last: Drakakaki

first: Adela

last: Mena-Morales

first: Annalisa

last: Marchese

first: Antonio

last: Giovino

first: Esaú

last: Martínez

first: Francesco

last: Paolo Marra

first: Lourdes

last: Marchante Cuevas

first: Luigi

last: Cattivelli

first: Paolo

last: Bagnaresi

first: Pablo

last: Carbonell-Bejerano

first: Grey

last: Monroe


title: Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity [scRNAseq-fetal tissue]

status: Public on Jun 04 2024

city: Toronto

first: Amy

last: Wong

state: Ontario

address: 686 Bay Street, Toronto

department: Developmental & Stem Cell Biology

institute: The Hospital for Sick Children

summary: While animal models have provided key insights into conserved mechanisms of how the lung forms during development, human-specific developmental mechanisms are not always captured. To fully appreciate how developmental defects and disease states alter the function of the lungs, studies in human lung models are important. Here, we sequenced >150,000 single single-cells from 19 healthy human fetal lung tissues from gestational weeks 10-19 and identified at least 58 unique cell types/states contributing to the developing lung. We captured novel dynamic developmental trajectories from various progenitor cells that give rise to ciliated, pulmonary neuroendocrine cells, and other specialized cell types. We also identified four CFTR-expressing progenitor cell types and pinpointed the temporal emergence and spatial localization of these cell types. These developmental dynamics reveal broader epithelial cell plasticity and novel lineage hierarchies that were not previously reported. Combined with spatial transcriptomics, we identified both cell autonomous and non-cell autonomous signalling pathways that may dictate the temporal and spatial emergence of cell lineages. Finally, we showed that human pluripotent stem cell (hPSC)-derived fetal lung models capture similar cell lineage trajectories specifically through progenitor cells that express abundant levels of the CFTR gene. Overall, this study provides a comprehensive single-cell atlas of the developing human lung, outlining the temporal and spatial complexities of cell lineage development and benchmarks fetal lung cultures from hPSC differentiations to similar developmental window.

overall_design:
19 fresh fetal lung tissues ranging from GW 10-19 were collected and analyzed through scRNAseq.

UPDATE: [Apr-14-2025] The full_fetal_lung_dataset.rds file was updated.

first: Henry

last: Quach

first: Spencer

last: Farrell

first: Ming

last: Wu

first: Kayshani

last: Kanagarajah

first: Joseph

middle: W

last: Leung

first: Xiaoqiao

last: Xu

first: Prajkta

last: Kallurkar

first: Andrei

last: Turinsky

first: Christine

last: Bear

first: Felix

last: Ratjen

first: Brian

last: Kalish

first: Sidhartha

last: Goyal

first: Theo

last: Moreas


title: A two-step regulatory mechanism dynamically controls histone H3 acetylation by SAGA complex at growth-related promoters

status: Public on Jun 03 2024

city: Geneva

first: Sevil

last: Zencir

address: 30, quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

summary: Acetylation of histone H3 at residue K9 (H3K9ac) is a dynamically regulated mark associated with transcriptionally active promoters in eukaryotes.  However, our understanding of the relation-ship between H3K9ac and gene expression remains largely correlative.  In this study, we identify a large suite of growth-related genes in yeast that undergo a particularly strong down-regulation of both transcription and H3K9ac upon stress, and delineate the roles of transcriptional activa-tors, repressors, SAGA histone acetyltransferase, and RNA-polymerase II in this response.  We demonstrate that H3K9 acetylation states are orchestrated by a two-step mechanism driven by the dynamic binding of transcriptional repressors and activators, that is independent of tran-scription.  In response to stress, promoter release of transcriptional activators at growth-related genes is a prerequisite for rapid reduction of H3K9ac, whereas binding of transcriptional re-pressors is required to establish a hypo-acetylated, strongly repressed state.

overall_design: Histone H3 acetylation level and RNA Polymerase II occupancies were measured by ChIP of H3K9ac and Rbp1, respectively. The ChIP experiments were performed with the samples treated- or non-treated with rapamycin for 20 min in wild type, stb3Δdot6Δtod6Δ, CRF1 expressing strains as well and upon nuclear depletion of TBP, Sfp1 and Ifh1. Stb3 and Rpd3 occupancies were measured by ChIP in Stb3-Flag and Rpd3-Myc tagged wild type and CRF1 expressing strains following 20 min rapamycin stress.

first: Daniel

last: Dilg

first: Maria

last: Bruzzone

first: Françoise

last: Stutz

first: Julien

last: Soudet

first: David

last: Shore

first: Benjamin

last: Albert


title: scRNA-seq reveals transcriptional dynamics of Encephalitozoon intestinalis parasites in human macrophages

status: Public on Jun 26 2024

first: Kacie

middle: Lee

last: McCarty

address: 550 E First Ave

institute: New York University Grossman School of Medicine

summary: Microsporidia are single-celled intracellular parasites that cause opportunistic diseases in humans. Encephalitozoon intestinalis is a prevalent human-infecting species that invades the small intestine. Dissemination to other organ systems is also observed, and is potentially facilitated by macrophages. The macrophage response to infection and the developmental trajectory of the parasite are not well studied. Here we use single cell RNA sequencing to investigate transcriptional changes in both the host and parasite during infection. While a small population of infected macrophages mount a response, most remain transcriptionally unchanged, suggesting that the majority of parasites may avoid host detection. The parasite transcriptome reveals large transcriptional changes throughout the life cycle, providing a blueprint for parasite development. The stealthy microsporidian lifestyle likely allows these parasites to harness macrophages for replication and dissemination. Together, our data provide insights into the host response in primary human macrophages and the E. intestinalis developmental program.

sample_organism:
Homo sapiens
Encephalitozoon intestinalis

overall_design: Monocyte derived macrophages were isolated from four healthy human donors. The macrophages were infected with the human infecting species of microsporidia, Encephalitozoon intestinalis, over 3 hour post infection to 72 hours post infection and anaylzed using scRNAsequencing.

first: Pattana

last: Jaroenlak

first: Bo

last: Xia

first: Cherry

last: Lam

first: Erin

last: Zwack

first: Itai

last: Yani

first: Gira

last: Bhabha

first: Damian

last: Ekiert


title: Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation [CUT&Tag]

status: Public on Jun 01 2024

city: Zhanjiang

first: Yiting

last: Guan

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Guangdong Medical University

summary: Granulosa cells (GCs) are the most dynamically responsive cell lineage to encourage continuous folliculogenesis; however, developmental dynamics and interplay with downstream transcription circuitry remain unclear. Here, we unravel the redistribution of genome-wide chromatin areas that drive broad developmental-related transcriptomic alterations during follicular maturation in murine and porcine GCs. Distinct GC-activated accessibility regions (GAAs) at the ovulatory phase are responsible for augmenting flanking GC-involved developmental gene (GDG) expression, which are essential for transcriptional responses to developmental cues. Mechanistically, the transcription factor (TF) Fosl2 is strongly recruited to GAAs, facilitating chromatin accessibility state transition. Elevated GAA signals driven by Fosl2 loading induce a significant upregulation of adjacent GDG expression. Additionally, GC-specific Fosl2 deletion in mice perturbs GC cellularity, leading to subfertility related to reproductive aging. Together, we highlight a dynamic chromatin accessibility landscape during follicular maturation, revealing the indispensable Fosl2 function not only controls transcriptional activation via a reconfigured chromatin state, but also orchestrates intricate signaling pathways that are fundamental for ovulation and reproduction.

overall_design: CUT&Tag assays in pig GCs to investigate the genome-wide Fosl2, H3K27ac and H3K4me3 occupancy spanning follicular stages.


title: Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation

sample_organism:
Sus scrofa
Mus musculus

platform_organism:
Sus scrofa
Mus musculus


title: Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation [ATAC-seq]

overall_design: Paired-end ATAC-seq of oocytes and GCs in pig and mouse to sought the accessible chromatin spanning follicular stages.


title: Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation [RNA-seq]

overall_design: RNA sequencing  spanning follicular stages to sought the transcriptome developmental changes of oocytes and GCs in pig and mouse.


title: Polarized Dock Activity Drives Shh-Mediated Axon Guidance

status: Public on May 31 2024

city: Montreal

first: Frederic

last: Charron

state: Quebec

address: 110 Avenue des Pins Ouest

institute: IRCM

summary: In the developing spinal cord, Sonic hedgehog (Shh) attracts commissural axons toward the floor plate. How Shh regulates the cytoskeletal remodeling that underlies growth cone turning is unknown. We found that Shh-mediated growth cone turning requires the activity of Docks, which are unconventional GEFs. Knockdown of Dock3 and 4, or their binding partner ELMO1 and 2, abolished commissural axon attraction by Shh in vitro. Dock3/4 and ELMO1/2 were also required for correct commissural axon guidance in vivo. Polarized Dock activity was sufficient to induce axon turning, indicating that Docks are instructive for axon guidance. Mechanistically, we show that Dock and ELMO interact with Boc, the Shh receptor, and that this interaction is reduced upon Shh stimulation. Furthermore, Shh stimulation translocates ELMO to the growth cone periphery and activates Rac1. This identifies Dock/ELMO as an effector complex of non-canonical Shh signaling and demonstrates the instructive role of GEFs in axon guidance.

overall_design: RNA sequencing was performed on commmissural neurons isolated from embryonic day 13 rat embryos cultured for two days in vitro.

first: Shirin

last: Makihara

first: Steves

last: Morin

last: Ferent

first: Patricia

middle: T

last: Yam


title: RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection

status: Public on Jul 04 2024

city: Tampere

first: Reetta

last: Nätkin

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology, Prostate Cancer Research Center

country: Finland

institute: Tampere University and Tays Cancer Center

summary: Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis, as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up- or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA-seq was conducted using a low dose infection (approximately 30 CFU) at 4 weeks post infection, from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria.

overall_design: Identification of the up- and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed, from three to nine biological replicates in each group. Wild type (WT) sibling fish were used as a control. The groups were WT PBS injected, mutant PBS injected, WT M. marinum infected, mutant M. marinum infected.

first: Meri

last: Uusi-Mäkelä

first: Sanna-Kaisa

last: Harjula

first: Alina

last: Sillanpää

first: Mirja

last: Niskanen

first: Matti

last: Nykter

first: Mika

last: Rämet


title: Transcriptome profiling of ANXA4 KO in A498 cells

status: Public on May 28 2024

city: Freiburg

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

country: Germany

institute: University Medical Center Freiburg

summary: ANXA4 WT (control) and ANXA4 KO in A498 kidney cancer cells was generated using CRISPR/Cas9 and two independent gRNAs for control and two independent gRNAs targeting ANXA4. Single cells clones (Ctrl.-1, Crtl.-2, KO-1, KO-2) were selected and validated by western blotting confirming loss of ANXA4 in KO cell lines on protein level. Transcriptome profiling (RNA-Sequencing) and differential gene expression analysis of 2 independent replicates per cell line was performed (resulting in 4 control and 4 ANXA4 KO sequencings). ANXA4 KO cells exhibit transcriptional changes compared to WT cells including upregulation of the ETS transcription factor ELF3 and regulation of Matrisome genes.

overall_design: mRNA sequencing analysis of control and ANXA4 KO in A498 kideny cancer cell line

first: Christoph

last: Schell


title: Platelet Reactivity ExpreSsion Score Predicts Cardiovascular Risk

status: Public on Jun 30 2024

city: New York City

first: Matthew

last: Muller

state: NY

address: 550 First Avenue

department: Department of Medicine

institute: New York University

summary: Platelets are key mediators of atherothrombosis; yet, limited tools exist to identify individuals with a hyperreactive platelet phenotype. Here we derive and validate a Platelet Reactivity ExpreSsion Score (PRESS) integrating platelet aggregation responses and RNA sequencing in multiple cohorts. PRESS performs well in identifying a hyperreactive phenotype in patients with cardiovascular disease (AUC [cross-validation] 0.81, 95% CI 0.68 to 0.94), with similar discrimination in an independent cohort of healthy participants (AUC [validation] 0.77, 95% CI 0.75 to 0.79); accuracy 80%, sensitivity 71%, and specificity 86%. Next, we validate PRESS in multiple cohorts of patients with platelet RNASeq available. Following multivariable adjustment, PRESS was significantly higher in MI (β=1.8, p=0.02), and individuals with a score above the median more frequently develop a future cardiovascular event (adjusted HR 1.90, CI 1.07 to 3.36), p=0.027). Altogether, we provide strong evidence that PRESS is a robust prognostic marker, which could have an essential role in facilitating a personalized approach to cardiovascular risk management.

overall_design: RNA-seq of purified platelets from patients with cardiovascular disease.

first: Jeffrey

middle: S

last: Berger

first: MacIntosh

middle: G

last: Cornwell

first: Yuhe

last: Xia

first: Nathaniel

middle: R

last: Smilowitz

first: Jonathan

middle: D

last: Newman

first: Caron

middle: B

last: Rockman

first: Kelly

middle: V

last: Ruggles

first: Deepak

last: Voora

first: Judith

last: Hochman

first: Tessa

last: Barrett


title: Comprehensive multi-mark and multi-omic profiling reveals epigenetic and transcriptional reprogramming in lung tumors

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: We present comprehensive epigenomic and transcriptomic mapping of 18 tumor and 20 non-neoplastic tissues from non-small cell lung adenocarcinoma patients. Our profiling covers active marks (H3K4me3, H3K4me1, and H3K27ac), repressive marks (H3K27me3 and H3K9me3) and gene expression using only 20 mg of tissue. Genome-wide differentially modified peaks and differentially expressed genes associated with non-small cell lung cancer were identified. Key pathways related to cancer and cell proliferation were found to be enriched among these regions. 118 differential transcription factors (TF) were identified by Taiji, showing a global impact on TF in tumor. Regulation associated modules (RAM) analysis by findRAM uncovered consensus RAMs (cRAM) specific to non-plastic or tumor samples, most of which were marked with differential histone modification and gene expression. Integrative analysis by EpiSig identified 6 sections of genomic regions with distinct co-modification patterns. These clusters showed a clear distribution pattern over the specific cRAMs and were enriched in key cancer related pathways. Our results demonstrate the power of integrated analysis of multiple epigenomic and transcriptomic marks in patient samples.

overall_design:
Chromatin immunoprecipitation followed by sequencing using a microfluidic platform (MOWChIP-seq) for histone modifications H3K27ac, H3K4me1, H3K4me3, H3K27me3 and H3K9me3, and RNA-seq using Smart-Seq2 in patient derived non-neoplastic lung tissue and non-small cell lung adenocarcinoma samples.
Please note that the raw ChIP-seq and RNA-seq data on the human lung tissues were deposited in dbGaP under accession number phs003113.v1.p1

first: Zhengzhi

last: Liu

first: Lina

last: Zheng

first: Zirui

last: Zhou

first: Wei

last: Wang


title: Complementary Ribo-seq approaches refine the translatome and provide a small protein census in a bacterial pathogen

status: Public on May 23 2024

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

institute: Albert-Ludwigs-University Freiburg

summary: Three translatomic approaches were applied to the foodborne pathogen Campylobacter jejuni to identify translated open reading frames, start codons, and stop codons and reveal novel small proteins

overall_design: Total RNA-seq, ribosome profiling, TIS (translation initiation site) profiling (retapamulin and oncocin), and  TTS (translation termination site) profiling (apidaecin 137; monosomes and disomes) using apidaecin in Campylobacter jejuni NCTC11168

first: Sarah

middle: L

last: Svensson

first: Cynthia

middle: M

last: Sharma


title: Small molecule ML233 is a direct inhibitor of tyrosinase function and reduces melanoma proliferation

status: Public on May 22 2024

city: Portland

first: Thomas

middle: Dexter

last: Morse

state: ME

address: 154 New Island Ave

institute: MDIBL

summary: Melanogenesis is the biological process regulating the synthesis of melanin pigments in melanocytes. Defective melanogenesis is associated with numerous human skin diseases, including, but not limited to, albinism, vitiligo, melasma, hypo- and hyperpigmentation disorders. Tyrosinase is the rate-limiting enzyme controlling melanogenesis, and hence tremendous efforts have been made to identify potent and safe inhibitors of tyrosinase function. Such inhibitors would also have potential as cancer therapies; melanomas are derived via malignant transformation of melanocytes, and inhibition of tyrosinase activity and/or melanogenesis has been suggested as a possible therapeutic strategy. However, despite decades of research, there is currently no effective treatment that inhibits melanogenesis or tyrosinase activity with no adverse side effects. In this study, we report characterization of the ML233 chemical as a potent inhibitor of tyrosinase activity in vivo and in vitro. We demonstrated that ML233 reduces melanin production in the zebrafish model with no observable significant toxic side effects, and in murine melanoma cells. We also showed that these effects are likely mediated through direct tyrosinase-ML233 interaction, i.e., binding of the ML233 molecule to the active site of the protein to inhibit its function. In addition, we showed that ML233 has the capacity to limit melanoma-cell proliferation in patient-derived xenograft organoids. Together, our results reveal that ML233 plays a dual role via inhibition of both melanin production and melanoma proliferation, and that ML233-mediated tyrosinase inhibition is a potentially safe and effective approach to alleviate the symptoms of melanocyte-associated diseases and thereby substantially improve human health.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for zebrafish apelin KO mutants vs wild-type at points 3hr and 24hr  post appiication of drug ML233 at 0.5 µM with associated control

first: Romain

last: Menard

first: Aissette

last: Baanannou

first: Caroline

last: Halluin

first: Dexter

first: Sadie

last: Kuhn

first: Joel

last: Graber

first: James

last: Strickland

last: Madelaine


title: Gene expression data from HeLa cells under high salt condition

city: Hongo, Bunkyo-ku

first: Hiroki

last: Ryuno

state: Tokyo

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

summary:
We examined the role of HES1 in high salt response as a novel regulator of NFAT5.
We analyzed gene expression of HeLa cells under isoosmotic and high salt condition.

overall_design:
HeLa cells were transfected with siControl, siNFAT5 and siHES1. mRNA samples were obtained from the transfected cells 7.5 hours after osmotic stress treatment (isoosmotic or high salt). The samples were amplified, labeled and hybridized to the Clariom S Array human (Thermo Fisher Scientific). The data were analyzed with Affymetrix Expression Console Software 1.4.1 offered SST-RMA using Affymetrix default analysis settings.

* The data files in the submission were replaced on April 15, 2025 *

first: Isao

last: Naguro

first: Hidenori

last: Ichijo


title: scRNA-seq analysis of skin CD45+ cells mice where Tsc2 is deleted in CD11c-expressing cells

city: Vienna

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

summary: Rationale: Chronic sarcoidosis is a complex granulomatous disease with limited treatment options that can progress over time. Understanding the molecular pathways contributing to disease would aid in new therapeutic development.  Objectives: To understand if macrophages from non-resolving chronic sarcoidosis patients are predisposed to macrophage aggregation and granuloma formation, and if modulation of the underlying molecular pathways influence sarcoidosis granuloma formation.  Methods: Macrophages were cultivated in vitro from isolated peripheral blood CD14+ monocytes and evaluated for spontaneous aggregation. Transcriptomics analyses, phenotypic and drug inhibitory experiments were performed on these monocyte-derived macrophages. Human skin biopsies from sarcoidosis patients and a myeloid Tsc2-specific sarcoidosis mouse model were analyzed for validatory experiments. Measurements and Main Results: Monocyte-derived macrophages from chronic sarcoidosis patients spontaneously formed extensive granulomas in vitro compared to healthy controls. Transcriptomic analyses separated healthy and sarcoidosis macrophages and identified an enrichment in lipid metabolic processes. In vitro patient granulomas, sarcoidosis mouse model granulomas, and those directly analyzed from lesional patient skin expressed an aberrant lipid metabolism profile and contained increased neutral lipids. Conversely, a combination of statins and cholesterol-reducing agents reduced granuloma formation both in vitro and in vivo in a sarcoidosis mouse model.  Conclusions: Together, our findings show that altered lipid metabolism in sarcoidosis macrophages is associated with its predisposition to granuloma formation and suggest cholesterol-reducing therapies as a treatment option in patients.

overall_design: Skin CD45+ immune cells

first: Clarice

last: Lim

first: Schuster

last: Michael

first: Weichhart

last: Thomas


title: Immunotherapeutic targeting of surfaceome heterogeneity in AML

status: Public on May 21 2024

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: Immunotherapy remains underexploited in AML compared to other hematological malignancies. Currently, gemtuzumab ozogamicin is the only therapeutic antibody approved for this disease. To identify potential targets for immunotherapeutic intervention, we analyzed the surface proteome of 100 genetically diverse primary human AML specimens for the identification of cell surface proteins and conducted single-cell transcriptome analysis on a subset of these specimens to assess antigen expression at the sub-population level. Through this comprehensive effort, we successfully identified numerous antigens and markers preferentially expressed by primitive AML cells. Many identified antigens are targeted by therapeutic antibodies currently under clinical evaluation for various cancer types, highlighting the potential therapeutic value of the approach. Importantly, this initiative led to the uncovering of AML heterogeneity at the surfaceome level, identifying several antigens and potential LSC markers characterising AML subgroups and positioning immunotherapy as a promising approach to target AML subgroup specificities.

overall_design: Single-cell RNA sequencing of 20 primary human AML specimens for antigen and marker identification

first: Vincent-Philippe

last: Lavallée

first: Véronique

last: Lisi

first: Azer

last: Farah

first: Banafsheh

last: Khakipoor

first: Jalila

last: Chagraoui

first: Nadine

last: Mayotte

first: Isabel

last: Boivin

first: Arnaud

last: Métois

first: Éric

last: Audemard

first: Marie-Eve

last: Bordeleau

first: Louis

last: Theret

first: Jean-François

last: Spinella

first: Léo

last: Aubert

first: Ossama

last: Moujaber

first: Laure

last: Mallinger

first: Azadeh

last: Hajmirza

last: Bonneil

first: François

last: Béliveau

first: Sybille

last: Pfammatter

first: Albert

last: Feghaly

first: Geneviève

last: Boucher

first: Patrick

last: Gendron

first: Pierre

last: Thibault

first: Frédéric

last: Barabé

first: Sébastien

last: Lemieux

first: Guillaume

last: Richard-Carpentier

first: Josée

last: Hébert

first: Philippe

middle: P

last: Roux


title: Genome-scale CRISPRi screen identifies pcnB repression conferring improved physiology for overproduction of free fatty acids in Escherichia coli

city: Tianjin

first: Lixia

last: Fang

address: 135 Yaguan Road, Jinnan District

institute: Tianjin University

summary: Microbial physiology plays a pivotal role in construction of a superior microbial cell factory for efficient production of desired products. Here we identified pcnB repression through genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS), which confers improved physiology for free fatty acids (FFAs) overproduction in Escherichia coli. The repression of pcnB could improve the stability and abundance of the transcripts involved in proton-consuming system, conferring a global improvement on cell membrane, redox state, and energy level. These physiological advantages facilitated further identification of acrD repression enhancing FFAs efflux. The engineered strain pcnBi-acrDi-fadR+ achieved 35.1 g l−1 FFAs production in fed-batch fermentation, which is the maximum titer in E. coli reported to date. This study underscores the significance of hidden genetic determinants in microbial biosynthesis and sheds light on the role of microbial physiologies in boosting microbial biosynthesis.

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

overall_design: In this study, we carried out genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS) to identify genetic determinants for FFAs overproduction in Escherichia coli. The pcnBi (AP) strain that repressed the expression of pcnB produced 2992 mg l FFAs, which was 4.0-fold of the CF (A) strain. To analyze the underlying mechanism of FFAs overproduction, the engineered strain pcnBi and the control strain CF were applied to the transcriptomic and proteomic analyses.

first: Yingxiu

last: Cao

first: Xueyan

last: Hao

first: Jie

last: Fan


title: Single-cell transcriptomic analysis identifies infiltrating plasmacytoid dendritic cells in psoriasis epidermis

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary: The study focuses on the cellular composition of the psoriasis epidermis, using single-cell transcriptomics to identify cell subsets and their interactions in both healthy and psoriatic skin. The research uncovers three keratinocyte populations and seven immune cell subsets exclusive to psoriatic lesions. A significant finding is the identification of a previously undetected population of plasmacytoid dendritic cells (pDCs) in the psoriatic epidermis, suggesting their role in the disease's pathogenesis. The study also highlights enhanced keratinocyte-immune cell interactions in psoriatic lesions, contributing to our understanding of psoriasis at the cellular level.

overall_design: Epidermal sheets from biopsies obtained from lesional and nonlesional skin of 5 untreated psoriasis patients and 3 healthy donors were subjected to partial dissociation preserving physical cell-cell interactions, followed by separation of CD45neg and CD45pos subsets by flow cytometry. Single-cell RNA sequencing was performed followed by Cell Interaction by Multiplet Sequencing (CIM-seq) analysis.

first: Longlong

last: Luo

first: Huaitao

last: Cheng

first: Andor

last: Pivarcsi

first: Enikö

last: Sonkoly


title: Liver gene expression analysis of male ApoE-/- mice treated with Isoginkgetin

status: Public on May 15 2024

city: Hefei City

first: ZHIDAN

last: ZHANG

state: Anhui Province

address: No. 96 Jinzhai Road

institute: University of Science and Technology of China

summary: Isoginkgetin (ISOGK) is a biflavone derived from Ginkgo Biloba that inhibits RNA splicing. ISOGK has been reported to have various protective effects, including anti-inflammatory, antioxidant, and anti-tumorigenic properties. The study aimed to investigate the impact of ISOGK treatment on atherosclerosis induced by a Western diet in ApoE-/- mice. After seven weeks of a high-fat diet, ISOGK was administered intraperitoneally for eight weeks. At the endpoint, mice were euthanized for sample collection, and a series of indicators were tested. The study results indicate that the ISOGK treatment group significantly reduced the area of aortic plaques, aortic sinus plaques, and the necrotic core area. Additionally, ISOGK significantly lowered the levels of total cholesterol in the serum. These findings suggest that ISOGK is effective in treating atherosclerosis and reducing blood lipid levels.

overall_design: Liver mRNA profiles were generated for ApoE-/- mice fed a Western diet and administered ISOGK (20mg/kg/day) or vehicle. The drug treatment lasted for 8 weeks.

first: Suowen

last: Xu

first: Zhidan

last: zhang


title: Genome-scale CRISPRi screen identifies pcnB repression conferring improved physiology for overproduction of free fatty acids in Escherichia coli II

status: Public on May 26 2024

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

overall_design: In this study, we carried out genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS) to identify genetic determinants for FFAs overproduction in Escherichia coli. Two rounds of screening were carried out. In the first round, the transformed cell library (named Tra1) carrying the pCF plasmid and the genome-scale sgRNA expression plasmid library was induced by IPTG and then cultivated for 40 h to sample the cell library before sorting (BS) (named Cul2). Then, BS was dyed with Nile red and sorted by FACS, obtaining the cell library after sorting (AS) (named Sor3). In the second round, the cultured cell library before sorting (BS) (named B-cul2) carrying the pCF-pcnBi plasmid and the genome-scale sgRNA expression plasmid library was sorted by FACS, obtaining the cell library after sorting (AS) (named B-sor3-P5). The Tra1, Cul2, Sor3, B-cul2, and B-sor3-P5 were applied for NGS to get the reads of sgRNA sequence.


title: Study of microbial species in extracellular vesicles of sclerosis multiple patients

status: Public on May 07 2024

city: Donostia

first: Alex

middle: Martínez

last: Ascensión

state: Gipuzkoa

address: P/ Doctor Begiristain

country: Spain

institute: Biogipuzkoa HRI

summary: Extracellular vesicles (EVs) are released by most cell types and are implicated in several biological and pathological processes, including multiple sclerosis (MS). In this study we performed RNA sequencing to analyze the diversity of microorganisms by assignment of reads using different taxa profilers. To diminish the risk of false positive biases derived from sample handling, we performed a similar analysis on EVs derived from known cultured bacterial species, as well as artificially-generated samples. Overall, we detect a range of microbial species in MS and healthy control (HC) samples, that are not detected in control samples, as well as species with differential abundance between MS and HC samples. These results reveal the relevance of putative communication of microbial species using EVs as a communication vector.

sample_organism:
Lactobacillus acidophilus
Homo sapiens
synthetic construct
Bifidobacterium animalis subsp. lactis

overall_design:
Peripheral blood from 20 MS patients and 10 HC was collected by venipuncture in EDTA tubes and centrifuged to separate the plasma from the cellular fraction. Additionally, cultured samples of from L. acidophilus and B. lactis were also retrieved.
To isolate EVs, plasma aliquots were double-centrifuged to pellet EVs. The pellet was then resuspended with 100 µL of DPBS, and RNA was isolated using Trizol LS.
Lastly, samples were pooled to fulfil a minimum input of 2 ug of RNA. rRNA was depleted from the total RNA sample and cDNA libraries were built. Paired-end sequencing was performed with Illumina HiSeq X Ten with an average of 40–50 × 10^6 reads obtained per sample.

first: Leire

last: Iparraguirre

first: Ainhoa

last: Alberro

first: Laura

last: Moles Alegre

first: David

last: Otaegui


title: High-throughout sequencing of RAW264.7 cells treated with LPS and Harmine

status: Public on May 20 2024

city: Wenzhou

first: Kejie

last: Chen

state: Zhejiang

address: Chashan

institute: Wenzhou Medical University

summary: After stimulation of RAW264.7 cells with LPS and Harmine, high-throughput sequencing technology was used to explore the changes in the inflammation level of RAW cells and the enrichment of signaling pathways after LPS and Harmine treatment, and to find an interesting target pathway.

overall_design: Mouse macrophage RAW264.7 is pretreated with 10µM Harmine for 0.5 h and then treated with 0.5µg/ml LPS for 6 h.

first: Yihui

last: Zhai

first: Xiaohui

last: Zheng


title: Endothelial Pd1 orchestrates cerebrovasculature homeostasis and oligodendrogenesis during brain development

status: Public on May 13 2024

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose: To explore further into the mechanisms by which endothelial PD1 controls cerebrovascular development and oligodendrogenesis, we employed RNA-seq to examine genome-wide alterations in endothelial cells from P0 conditional PD1 knockout mice, comparing them with their wild-type littermates.
Methods: mRNA was extracted from P0 isolated endothelial cells of Pd1fl/fl and Pd1cKO-Tie2 mice, and the quality and quantity were assessed using the Agilent 2100 Bioanalyzer. Subsequently, the mRNA was converted to cDNA and Libraries were prepared. RNA-sequencing was performed on the Illumina HiSeq 2500 platform at Annoroad Genomics.
Results: Approximately one thousand transcripts showed differential expression between the Pd11fl/fl and Pd1cKO-Tie2 mice brain endothelial cell, with a fold change ≥2 and p value <0.05.Geneontology analysis of the downregulated genes were enriched in terms related to positive regulation of angiogenesis, positive regulation of vascular endothelial growth factor production and positive regulation of inflammatory response.  Concomitantly, upregulated genes were enriched in terms related to endothelial cell migration, sequestering of BMP from receptor via BMP binding and regulation of establishment of blood-brain barrier. These results reflected endothelial PD1  plays vital roles in cortex development.
Conclusions: Endothelial PD1 RNA-seq would provide a overall understanding how endothelium-derived PD1regulates vessel development and oligodendrogenesis during brain development

overall_design: mRNA profiles of P0 Pd1fl/fl and Pd1cKO-Tie2 mice were generated by deep sequencing, in duplicate,  using Illumina HiSeq 2500.

first: Tingting

last: He


title: Mouse MRE11-RAD50-NBS1 is needed to start and extend meiotic DNA end resection [ChIP-seq]

status: Public on May 06 2024

city: New York

first: Soonjoung

last: Kim

email: kims16@mskcc.org, soonjk@yuhs.ac

state: New York

address: 430 East 67th Street

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer C

summary: Nucleolytic resection of DNA ends is critical for homologous recombination, but its mechanism is not fully understood, particularly in mammalian meiosis. Here we examine roles of the conserved MRN complex (MRE11, RAD50, and NBS1) through genome-wide analysis of meiotic resection during spermatogenesis in mice with various MRN mutations, including several that cause chromosomal instability in humans. Meiotic DSBs form at elevated levels but remain unresected if Mre11 is conditionally deleted, thus MRN is required for both resection initiation and regulation of DSB numbers. Resection lengths are reduced to varying degrees in MRN hypomorphs or if MRE11 nuclease activity is attenuated in a conditional nuclease-dead Mre11 model. These findings unexpectedly establish that MRN is needed for longer-range extension of resection beyond that carried out by the orthologous proteins in budding yeast meiosis. Finally, resection defects are additively worsened by combining MRN and Exo1 mutations, and mice that are unable to initiate resection or have greatly curtailed resection lengths experience catastrophic spermatogenic failure. Our results elucidate MRN roles in meiotic DSB end processing and establish the importance of resection for mammalian meiosis.

overall_design: Chromatin immunoprecipication DNA sequencing (ChIP-seq) for MRE11 in mouse testis cells

first: Shintaro

last: Yamada

first: Scott

last: Keeney


title: Mouse MRE11-RAD50-NBS1 is needed to start and extend meiotic DNA end resection [S1_Exo7T-seq]

overall_design: Detection of DNA double-strand-break ends and resection tracts in the genome in mouse testis cells


title: Mouse MRE11-RAD50-NBS1 is needed to start and extend meiotic DNA end resection [SSDS]

overall_design: Chromatin immunoprecipication DNA sequencing (ChIP-seq) for DMC1, RAD51, or RPA2 in mouse testis cells. During the library preparatoin, single-stranded DNAs (ssDNAs) were specifically enriched as described before (ref.1, 2). (ref. 1) Khil, et al., Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA, Genome Res. May; 22(5): 957–965. (2012). (ref. 2) Brick, et al., Analysis of Meiotic Double-Strand Break Initiation in Mammals. Methods Enzymol 601: 391-418. (2018).


title: Dissecting developmental disorders caused by CTCF mutation at R567 [SPARC-seq]

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: In this study, we performed SPARC-seq experiments in brain tissue from E18.5 mouse embryo.

overall_design: SPARC-seq experiments were performed in the brain tissues from E18.5 mouse embryo.

first: Gongcheng

first: Hongjie

last: Yao


title: Dissecting developmental disorders caused by CTCF mutation at R567 [snRNA-seq]

summary: In this study, we performed single nucleus RNA sequencing in heart, lung and cortex tissues from E18.5 mouse embryo.

overall_design: SnRNA-seq was performed using wild type and Ctcf homozygous mutated heart, lung and cortex tissues from E18.5 mouse embryo.


title: Deciphering age-related transcriptomic changes in mouse retinal pigment epithelium

status: Public on May 10 2024

city: Johnson City

first: Mark

middle: Ellsworth

last: Kleinman

state: Tennessee

address: Quillen College of Medicine

department: Department of Surgery

institute: East Tennessee State University

summary: Aging of the retinal pigment epithelium (RPE) leads to a gradual decline in RPE homeostasis over time, significantly impacting retinal health. Understanding the mechanisms underlying RPE aging is crucial for elucidating the background in which many age-related retinal pathologies develop. In this study, we compared the transcriptomes of young and aged mouse RPE and found a marked upregulation of immunogenic and proinflammatory genes in aging RPE. Additionally, aging RPE exhibited dysregulation of pathways associated with visual perception and extracellular matrix production. Research on aging in post-natal quiescent RPE is hindered by the absence of relevant in vitro models. We evaluated an in vitro model of chronologically aged primary human RPE to address this gap, which displayed gene expression patterns comparable to native-aged RPE. Profiling this in vitro aging model highlighted its potential utility in investigating cellular and molecular mechanisms of RPE aging and in preliminary testing of therapeutic compounds. Overall, our findings suggest chronological aging of RPE leads to the acquisition of a proinflammatory phenotype, impacting RPE function and serving as a significant factor in the development of age-related retinal pathologies.

overall_design: We performed transcriptome profiling of ribosomal RNA depleted sequencing data from RPE/choroid of young (2-3 months) and aged (20-24 months) mice (n=4 per group).

first: Sushil

middle: K

last: Dubey

first: Rashmi

first: Kyung

middle: s

last: Jung

middle: E


title: CTCF mutation at R567 causes developmental disorders by 3D genome rearrangement, premature exhaustion of stem cells and abnormal neurodevelopment [scRNA-seq]

summary: In this study, we performed single RNA sequencing in 1-month and 2-month cortical organoids derived from wild-type and Ctcf heterozygous hESCs.

overall_design: ScRNA-seq was performed using cortical organoids derived from wild-type and Ctcf heterozygous hESCs.


title: Deletion of an sRNA primes development in a multicellular bacterium

city: Zurich

first: Marco

last: La Fortezza

state: Zurich

address: Universitätstrasse 16

department: Environmental Systems Science

institute: ETH Zurich

summary: Small non-coding RNAs (sRNAs) regulate gene expression of many biological processes. During growth, some myxobacteria produce an sRNA — Pxr — that blocks fruiting-body development, an aggregative multicellular process typically triggered by starvation. Deleting the pxr gene allows Myxococcus xanthus to develop despite nutrient availability, but Pxr binding targets and the genes regulated by Pxr remain unknown. Here, after showing that Pxr controls the temporal dynamics of development, we compare the transcriptomes of vegetative M. xanthus cells possessing vs lacking pxr. Over half of the genes impacted by pxr deletion are linked to development, including known and previously undiscovered critical regulators. Pxr also positively regulates genes associated with general metabolic processes. Our study discovers phenotypic effects of Pxr regulation with ecological importance, identifies the suite of genes this sRNA controls during vegetative growth and reveals a previously unknown developmental regulator. These findings provide insights into the molecular mechanism controlling myxobacterial development.

overall_design: We generated and contrasted the transcriptional profiles of wild-type M. xanthus cells (GJV1, derived from DK1622) to those of cells lacking the small RNA pxr expression. The RNA was sampled from vegetative cells growing in liquid, allowing us to identify the potential gene targets of the sRNA Pxr in this bacterium.

first: Jasper

last: Verwilt

first: Sarah

last: Cossey

first: Sabrina

middle: A

last: Eisner

first: Gregory

middle: J

last: Velicer

first: Yuen-Tsu Nicco

last: Yu


title: Dissecting developmental disorders caused by CTCF mutation at R567 [RNA-seq]

summary: In this study, we analyzed gene expression change in brain tissues, in vitro cultured neurons and cortical organoids by using RNA-seq.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative gene expression analysis of RNA-seq data for wild-type, Ctcf heterozygous mutated and Ctcf homozygous mutated samples.


title: Optimized methods for mapping DNA double-strand-break ends and resection tracts and application to meiotic recombination in mouse spermatocytes

status: Public on Apr 30 2024

summary: DNA double-strand breaks (DSBs) made by SPO11 protein initiate homologous recombination during meiosis. Subsequent to DNA strand breakage, endo- and exo-nucleases process the DNA ends to resect the strands whose 5' termini are at the DSB, generating long 3'-terminal single-stranded tails that serve as substrates for strand exchange proteins. DSB resection is essential for meiotic recombination, but a detailed understanding of its molecular mechanism is currently lacking. Genomic approaches to mapping DSBs and resection endpoints, e.g., S1-sequencing (S1-seq) and similar methods, play a critical role in studies of meiotic DSB processing. In these methods, nuclease S1 or other enzymes that specifically degrade ssDNA are used to trim resected DSB ends, allowing capture and sequencing of the ends of resection tracts. Here, we present optimization of S1-seq that improves its signal:noise ratio and allows its application to analysis of spermatocyte meiosis in adult mice. Furthermore, quantitative features of meiotic resection are evaluated for reproducibility, and we suggest best practices for analysis and interpretation of S1-seq data. We also compare S1-seq to variants that use exonuclease T and or exonuclease VII from Escherichia coli instead of nuclease S1. Detailed step-by-step protocols and suggestions for troubleshooting are provided.


title: Transcriptome profiling of ovaries in aged mice administered with Samul-tang

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

summary: Samul-tang (SM), a traditional herbal medicine is used to treat menstrual irregularities and infertility. The mechanism underlying the role of SM in ovary function needs elucidation. In this study, the influence of SM administration on the ovarian reserve of aged mice was investigated. Female BALB/c mice (8 and 40 weeks-old) were administered with distilled water (young or old group) or SM for 4 weeks. SM administration prevented age-related ovarian follicle loss in mice. Quality of oocytes and blastocysts were enhanced in SM-administrated mice compared to those of non-treated old mice. Further, SM administration increased the pregnancy rate and number of litters. SM triggered changes in aging-related genes that are linked to the RAS-mediated pathway. Thus, we demonstrate that SM can be used to increase the oocyte yield in aged women, potentially improving age-related cognitive decline in the ovarian reserve.

overall_design: To obtain RNA-seq data of ovaries treated with Samul-tang (Hanpoong, Iksan, Korea), mice were randomly divided into groups of n=6 each. Aged mice(40-week-old) were orally administered either distilled water (OC group)  or SM at a dose of 2.5g/kg (OC+SM group), five times a week for four weeks. Young mice (8-week-old) received distilled water (YC group)

first: Sooseong

last: You

first: Jihyun


title: Dissecting developmental disorders caused by CTCF mutation at R567 [Hi-C]

summary: In this study, we performed BL-Hi-C experiments to investigate the influence of CTCF mutation on higher-order chromatin structures.

overall_design: BL-Hi-C experiments were performed using wild-type and Ctcf homozygous mutated tissues from E18.5 mouse embryo.


title: Dissecting developmental disorders caused by CTCF mutation at R567

status: Public on May 05 2024

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

overall_design: Refer to individual Series


title: Celastrol targets LRP1 to inhibit fibroblast-macrophage crosstalk and ameliorates psoriasis progression

status: Public on Apr 20 2024

city: Nanjing

first: Jiao

last: Qu

address: Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China

institute: Nanjing University

summary:
Purpose: This study aimed to explore the mechanism of Celastrol in improving psoriasis through single-cell transcriptomics
Methods: Supplementation with intragastric administration of celastrol in  C57BL/6 mice to observe its effect on IMQ-induced psoriasis.  Single-cell RNA sequencing were performed to explore the role of celastrol for IMQ-induced psoriasis.
Results: A natural product library was used to screen for a small molecule compound, celastrol, that could interfere with fibroblast-macrophage communication. It was demonstrated that celastrol targeted low-denisity lipoprotein receptor-related protein 1 (LRP1) to inhibit fibroblast secretion of CCL2 and inhibited psoriasis progression by reducing its recruitment to macrophages, thereby blocking communication between the two cells
Conclusion: We report that celastrol targeted low-denisity lipoprotein receptor-related protein 1 (LRP1) to inhibit fibroblast secretion of CCL2 and inhibited psoriasis progression by reducing its recruitment to macrophages. The use of celastrol maybe a noveltherapeuticoption for psoriasis.

overall_design: Molecular mechanism of  celastrol in improving  psoriasis.

first: Yang

last: Sun

first: Yuyu

last: Zhu

first: Chenyang

last: Zhang


title: Loop Stacking Attenuates Chromatin Boundaries in TCR Loci During Thymocyte Development

status: Public on Apr 27 2024

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

summary: Topologically Associating Domains (TADs) partition the genome into self-interacting regions through boundaries. Chromatin configuration plays a crucial role in TCR gene rearrangements, thereby affecting repertoire diversity. To assess the dynamics of chromatin boundaries within TCR genes, we conducted Hi-C assays on double-negative (DN) and double-positive (DP) cells from RAG-deficient mice. A chromatin boundary at the 3' end of the Tcrb locus observed in DN cells dissipated in DP cells, thereby altering interactions between the main Vβ cluster and the recombination center. Additionally, the INTs boundary in the Tcra-Tcrd locus disappeared in DP cells, leading to enhanced interactions between the proximal Vα region and recombination center at the Jα segments. Subsequent analysis revealed that the disappearance of boundaries was not attributable to diminished CTCF binding but rather heightened activity within these regions. This study illuminates the developmental dynamics of TAD boundaries in TCR genes, enriching our understanding of their evolving nature.

overall_design: Hi-C analysis of EACBE+/+Rag1-/- and EACBE-/-Rag1-/- DN thymocytes;Hi-C analysis of EACBE+/+Rag1-/-  DP thymocytes;3C-HTGTS analysis of EACBE+/+Rag1-/- DN and/or DP thymocytesusing different baites(Trbv12-2,Trbv5，Eb,Trav21,Trdv2-2);3C-HTGTS analysis of EACBE+/+Rag1-/- and/or EACBE-/-Rag1-/- DN thymocytes using different baites(Ea,INT2,Trdv2-2,Trdd2,Trdv5,TEA);HTGTS-VDJ analysis of EACBE+/+Rag1-/- and EACBE-/-Rag1-/- DN or DP thymocytes at the baits from Trdj1 or Traj61;ATAC-seq analysis of EACBE+/+Rag1-/- and EACBE-/-Rag1-/- DN thymocytes;ATAC-seq analysis of EACBE+/+Rag1-/- DP thymocytes.

first: Yongchang

first: Ranran

last: Dai

first: Bingtao

last: Hao


title: Dissecting developmental disorders caused by CTCF mutation at R567 [ChIP-seq]

first: gongcheng

last: Hu

summary: In this study, CTCF ChIP experiments were performed to investigate the influence of CTCF mutation on its binding in mouse tissues.

overall_design: ChIP-seq for CTCF in tissues from wild-type and Ctcf homozygous mutated E18.5 mouse embryos.

first: Gongcheng

first: Hongjie

last: Yao


title: A Novel Assessment of Metabolic Pathways in Peritoneal Metastases from Low-Grade Appendiceal Mucinous Neoplasms

status: Public on May 01 2024

city: Irvine

first: Eric

last: Hanse

state: CA

address: 3119 McGaugh Hall

institute: University of California Irvine

summary: Background: There is a paucity of targeted therapies for patients with pseudomyxoma peritonei (PMP) secondary to low-grade appendiceal mucinous neoplasms (LAMNs). Dysregulated metabolism has emerged as a hallmark of cancer, and the relationship of metabolomics and cancer is an area of active scientific exploration. We sought to characterize phenotypic differences found in peritoneal metastases (PM) derived from LAMN versus adenocarcinoma. Methods: Tumors were washed with phosphate-buffered saline (PBS), microdissected, then dissociated in ice-cold methanol dried and reconstituted in pyridine. Samples were derivatized in tert-butyldimethylsilyl (TBDMS) and subjected to gas chromatography-coupled mass spectrometry. Metabolites were assessed based on a standard library. RNA sequencing was performed, with pathway and network analyses on differentially expressed genes.Results: Eight peritoneal tumor samples were obtained and analyzed: LAMNs (4), and moderate to poorly differentiated adenocarcinoma (colon [1], appendix [3]). Decreases in pyroglutamate, fumarate, and cysteine in PM from LAMNs were found compared with adenocarcinoma. Analyses showed the differential gene expression was dominated by the prevalence of metabolic pathways, particularly lipid metabolism. The gene retinol saturase (RETSAT), downregulated by LAMN, was involved in the multiple metabolic pathways that involve lipids. Using network mapping, we found IL1B signaling to be a potential top-level modulation candidate. Conclusions: Distinct metabolic signatures may exist for PM from LAMN versus adenocarcinoma. A multitude of genes are differentially regulated, many of which are involved in metabolic pathways. Additional research is needed to identify the significance and applicability of targeting metabolic pathways in the potential development of novel therapeutics for these challenging tumors.

overall_design: Human patient samples of peritoneal metastatic cancer. Compared are the RNASeq profiles from resected peritoneal metastatic tumors from adenocarcinoma to those derived from low grade appendecial malignancies


title: Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan (RNA-Seq)

status: Public on Apr 17 2024

city: Daegu

first: Hong-Yeoul

last: Ryu

state: Buk-Gu

address: Daehak-ro 80

department: Biotechnology

institute: Kyungpook National University

summary: Yeast has proven to be a useful model system for aging studies, including CR effects. We report here that yeast adapted through in vitro evolution to the severe cellular stress caused by loss of the Ulp2 SUMO-specific protease exhibit both enhanced growth rates and replicative lifespan, and they have altered gene expression profiles similar to those observed in CR. Notably, in certain evolved ulp2Δ lines, a dramatic increase in the auto-sumoylation of Ubc9 E2 SUMO-conjugating enzyme results in altered regulation of multiple targets involved in energy metabolism and translation at both transcriptional and post-translational levels. This increase is essential for the survival of aged cells and CR-mediated lifespan extension

overall_design: RNA-seq of WT, ulp2D and evolved ulp2D S.cerevisiae strains

first: Mark

last: Hochstrasser

first: Dejian

last: Zhao


title: Heterogeneity of immune cells and their communications unveiled by transcriptome profiling in acute inflammatory lung injury

city: hangzhou

first: kang

last: zhiying

address: 浙江省杭州市西湖区余杭塘路866号

institute: zhejiang universty

summary: Background: Acute Respiratory Distress Syndrome (ARDS) or its earlier stage Acute lung injury (ALI), is a worldwide health concern that jeopardizes human well-being. Currently, the treatment strategies to mitigate the incidence and mortality of ARDS are severely restricted. This limitation can be attributed, at least in part, to the substantial variations in immunity observed in individuals with this syndrome. Methods: Bulk and single cell RNA sequencing from ALI mice and single cell RNA sequencing from ARDS patients were analyzed. We utilized the Seurat program package in R and cellmarker 2.0 to cluster and annotate the data. The differential, enrichment, protein interaction, and cell-cell communication analysis were conducted. Results: The mice with ALI caused by pulmonary and extrapulmonary factors demonstrated differential expression including Clec4e, Retnlg, S100a9, Coro1a, and Lars2. We have determined that inflammatory factors have a greater significance in extrapulmonary ALI, while multiple pathways collaborate in the development of pulmonary ALI. Clustering analysis revealed significant heterogeneity in the relative abundance of immune cells in different ALI models. The autocrine action of neutrophils plays a crucial role in pulmonary ALI. Additionally, there was a significant increase in signaling intensity between B cells and M1 macrophages, NKT cells and M1 macrophages in extrapulmonary ALI. The CXCL, CSF3 and MIF, TGFb signaling pathways play a vital role in pulmonary and extrapulmonary ALI, respectively. Moreover, the analysis of human single-cell revealed DCs signaling to monocytes and neutrophils in COVID-19-associated ARDS is stronger compared to sepsis-related ARDS. In sepsis-related ARDS, CD8+ T and Th cells exhibit more prominent signaling to B cell nucleated DCs. Meanwhile, both MIF and CXCL signaling pathways are specific to sepsis-related ARDS. Conclusion: This study has identified specific gene signatures and signaling pathways in animal models and human samples that facilitate the interaction between immune cells, which could be targeted therapeutically in ARDS patients of various etiologies.

overall_design: Six to eight weeks old male C57BL/6 mice of SPF grade were fed in the standard animal laboratory at 25 ± 1°C with humidity of 60 ± 5% and 12-hous light/dark cycle, adequate food and water were supplied. The mice were allowed to acclimated to the environment for 1 week prior to the experiment. The mice were randomly divided into control, pulmonary ALI, and extra-pulmonary ALI group. Pulmonary ALI was induced by intratracheal injection of Lipopolysaccharide (LPS) (10 mg/kg, from Pseudomonas aeruginosa 27316, Sigma-Aldrich, USA, L9143) dissolved in 50 ml sterile PBS. Additionally, we used intraperitoneal injection of LPS (25 mg/kg) to construct sepsisrelated ARDS, known as extra-pulmonary ALI.

first: Zhi-ying

last: Kang

first: Qian-yu

last: Huang

first: Ning-xin

last: Zhen

first: Bao-ping

last: Tian


title: Recruitment of plasma cells from follicular and extrafollicular immune reactions to the bone marrow

status: Public on Apr 16 2024

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics


title: Nano-encapsulated senolytics cocktail ameliorates germ cell senescence in female mice

status: Public on Apr 23 2024

city: Zhanjiang

first: Yiting

last: Guan

address: 236 Yuanzhu Road

institute: Guangdong Medical University

summary: Low-quality oocytes directly affect fertilization and embryo developmental ability, and further contributes to infertility in women. Dasatinib and quercetin, as a senolytics, has been explored extensively in various age-related diseases. Here, we report that nano-encapsulated senolytics cocktail (D+Q) efficaciously ameliorates the the quantity and quality of follicles and oocytes in vitro and in vivo. D+Q cocktail supplementation reduces the level of ROS in aged oocytes, decreases the frequency of fragmentation, maintains the spindle integrity, rescues mislocalized cortical granules, rescues mitochondrial membrane potential and alleviates DNA damage and apoptosis in vitro. Nano-encapsulated D+Q cocktail effectively ameliorates the fertility deficits in the cyclophosphamide-induced primary ovarian failure (POF) mice model. Moreover, RNA sequencing analysis shows that D+Q cocktail improves the fecundity of POF mice by increasing development gene expression and reduces the senescence-associated secretory phenotype (SASP) accumulation. Taken together, our data show that the D+Q cocktail helps to improve assisted reproductive technology and reproductive outcomes in POF.

overall_design: gene expression profiling analysis of RNA-seq data

first: Hongyong


title: Transcriptome profiling of ovaries in aged mice administered with individual ingredients of Samul-tang

first: Haeseung

last: Lee

summary: Samul-tang (SM) is a traditional multi-ingredient treatment widely used in clinical practice for improving ovarian function in women with diminished ovarian reserve. Despite its therapeutic benefits, the complexity of its mechanisms of action due to the combination of multiple compounds has limited its research integration into modern pharmacological science. To address this challenge, we identified 39 herbal compounds as major ingredients in SM and generated transcriptome data from the mice ovaries after administrating with individual ingredients. This dataset aims to provide insights into the mechanisms of action of SM and to aid in the identification of effective ingredient combinations.

overall_design: To obtain RNA-seq data of ovaries treated with compounds of Samul-tang, mice were randomly divided into groups of n=3 each. Aged mice(38-week-old) were orally administered either vehicle (distilled water containing 0.5% Dimethyl sulfoxide) or each of the 39 single compounds at a dose of 5mg/kg, five times a week for four weeks.

first: Sooseong

last: You

first: Hyejin

last: Shin

first: Jihyun

last: Kim


title: Dissecting developmental disorders caused by CTCF mutation at R567 [4C]

first: gongcheng

last: Hu

summary: In this study, we performed 4C sequencing experiments to investigate the change of chromatin interactions between the promoters of Pcdh genes and enhancers across cPcdh locus.

overall_design: 4C-seq experiments were performed using wild-type and Ctcf homozygous mutated brain tissues from E18.5 mouse embryo. Two enhancers at cPcdh locus were used as viewpoints.

first: Gongcheng

first: Hongjie


title: Recruitment of plasma cells from follicular and extrafollicular immune reactions to the bone marrow II

summary: Bone marrow plasma cells (BMPC) are the correlate of humoral immunity, consistently releasing antibodies into the bloodstream. It remains unclear if BMPC reflect different activation environments or maturation of their precursors. Here we define human BMPC heterogeneity and track the recruitment of antibody-secreting cells (ASC) from SARS-CoV-2 vaccine immune reactions to the bone marrow (BM). Trajectories based on single-cell transcriptomes and repertoires of peripheral and BM ASC reveal sequential colonisation of BMPC compartments. In activated B cells, IL-21 suppresses CD19 expression, indicating that CD19low-BMPC are derived from follicular, while CD19high-BMPC originate from extrafollicular immune reactions. In primary immune reactions, both CD19low- and CD19high-BMPC compartments are populated. In secondary immune reactions, most BMPC are recruited to CD19high-BMPC compartments, reflecting their origin from extrafollicular reactivations of memory B cells. A pattern also observed in vaccinated-convalescent individuals and upon diphtheria/tetanus/pertussis recall-vaccination. Thus, BMPC diversity reflects the evolution of a given humoral immune response.

overall_design: This experiment was designed for an in-depth analysis of human bone marrow plasma cells. To do so, single cell transcriptomes and BCR sequencing of sorted plasma cells and memory B cells from 8 human bone marrow samples obtained from patients undergoing hip replacement surgery were prepared.  In addition, cells were also incubated with DNA barcoded antibodies for Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq). When available, plasma cells and memory B cells from paired blood samples were likewise sorted and sequenced. Some bone marrow and blood samples were additionally incubated with fluorophore-coupled tetanus toxoid and SARS-CoV-2 Spike Protein tetramers for antigen-specific cell sorting and sequencing. Sequencing was performed using the 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit v2 (dual index) and Illumina NextSeq2000.

first: Marta

last: Ferreira-Gomes

first: Gabriela

last: Guerra

first: Katrin

last: Lehmann

first: Pawel

last: Durek

first: Mir-Farzin

last: Mashreghi


title: Tissue-specific inflammation induced by constitutively active STING is mediated by enhanced TNF signaling

city: Bonn

first: Rayk

last: Behrendt

state: North Rhine-Westphalia

address: Venusberg-Campus 1

department: Nucleic Acid Immunity & Genome Defense

institute: Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn

summary: Constitutive activation of STING by gain-of-function mutations triggers manifestation of the systemic autoinflammatory disease STING-associated vasculopathy with onset in infancy (SAVI) in humans and in mice. Murine SAVI is characterized by T cell lymphopenia, severe inflammatory interstitial lung disease, neuroinflammation and neurodegeneration with only limited contribution of type I interferon signaling. Here, we show that pharmacologic inhibition of TNF signaling in SAVI mice improved T cell lymphopenia, but had no effect on interstitial lung disease. However, complete blocking of TNF receptor signaling by knocking out TNFR1 and TNFR2 in SAVI mice rescued both, loss of thymocytes as well as interstitial lung disease. Furthermore, chronic STING signaling in lung endothelial cells of diseased mice enhanced transcription of cytokines, chemokines and adhesions proteins resulting in increased transendothelial migration of neutrophils across the endothelial barrier that could be reverted by genetic inactivation of TNFR1 and 2. Thus, our results demonstrate a pivotal role of TNFR-signaling in the development of SAVI-associated lung disease and suggest this pathway as promising target to ameliorate human SAVI

overall_design: Murine lung endothelial cells were isolated from perfused (10 U/ml heparin diluted in PBS) lung tissue. Single cell suspension was obtained after digestion with 1 mg/ml Collagenase (Sigma-Aldrich), 3.5 mg/ml Dispase (Roche) and 25 µg/ml DNaseI (Roche) in native IMDM (Thermo fisher scientific) over 45 min at 37°C. Collected cells were washed with PBS and passed through a 30 µm cell strainer. Lung endothelial cells were enriched by positive selection of CD31+ cells with microbeads (Miltenyi Biotec), according to the manufacturer’s protocol. All selected cells were stained with antibodies (all from BioLegend) against CD45.2 (1:300), CD11b (1:500), Ter-119 (1:500), CD326 (1:500), CD31 (1:300) and separated by FACS Aria. Dead cells and cellular debris were excluded by PI staining.

first: Hella

last: Luksch

first: Angela

last: Rösen-Wolff


title: Microbial infection instigates tau-related pathology in Alzheimer's disease via activating neuroimmune cGAS-STING pathway

status: Public on Apr 11 2024

city: Shanghai

first: Erlin

last: Wang

state: Shanghai

address: 748 Zhongshan Middle Road, Songjiang District, Shanghai

department: Songjiang Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: Microbial infection, the strong trigger to directly induce inflammation in brain, is long considered a risk factor of Alzheimer's disease (AD), but how these infections contribute to neurodegeneration remains underexplored. To examine the effect of herpes simplex virus type 1 (HSV-1) infection on tauopathy in local hippocampus of P301S mice, we utilized a modified HSV-1 strain (mHSV-1) potentially relevant to AD, we found that its infection promotes tau-related pathology in part via activating neuroimmune cGAS-STING pathway in the tau mouse model. Specifically, Sting ablation causes the detectable improvement of neuronal dysfunction and loss in P301S mice, which is causally linked to lowered proinflammatory status in the brain. Administration of STING inhibitor H-151 alleviates neuroinflammation and tau-related pathology in P301S mice. These results jointly suggest that herpesviral infection, as the vital environmental risk factor, could induce tau-related pathology in AD pathogenesis partially via neuroinflammatory cGAS-STING pathway.

overall_design: Comparison of transcriptomic profiling in hippocampal tissue between STING knockout and wild-type Tau mice (P301S) .

first: Xiaoxu

last: Yan

first: Meng

last: Zhao

first: Guanqin

last: Ma

first: Xiang-Xiong

last: Xu

first: Jie-Bin

first: Xiaohong

last: Li

first: Xueling

first: Jianxiong

last: Zeng


status: Public on Mar 31 2024

first: zhang

last: zhang chenyang

address: 163 Xianlin Avenue

summary: In the present study, we analyzed single-cell multi-omics data from psoriasis patients and healthy individuals and found that more fibroblast-macrophage communication was present in the dermis of psoriasis lesions, exacerbating psoriasis progression. A natural product library was used to screen for a small molecule compound, celastrol, that could interfere with fibroblast-macrophage communication. It was demonstrated that celastrol targeted low-denisity lipoprotein receptor-related protein 1 (LRP1) to inhibit fibroblast secretion of CCL2 and inhibited psoriasis progression by reducing its recruitment to macrophages, thereby blocking communication between the two cells. Moreover, conditional knockdown of LRP1 by fibroblasts significantly improved psoriasis in mice, suggesting that LRP1 may be an important target for the treatment of psoriasis.

overall_design: scRNA-seq of  skin from normal(3); scRNA-seq of skin from psoriasis (3); scATAC-seq of skin from normal (1); scATAC-seq of skin from psoriasis (1)

first: Yang

last: Sun

first: Zhu

last: Yuyu

first: Jiao

last: Qu

first: Zhang

last: Chenyang


title: Progressive Senescence Programs Elicit Intrinsic Vulnerability to Ageing-related Cancer

status: Public on Apr 02 2024

city: HangZhou

first: Xiaoqin

last: Liu

state: ZheJiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

institute: Westlake University

summary: Cancer incidence escalates exponentially with advancing age, the mechanism of which remains obscure. Here we built up a chronological molecular clock at the single cell level for the mammary stem cell enriched population to depict the physiological ageing dynamics. We found the mammary ageing process was asynchronous and progressive, determined by the relative proportions of four distinct cellular states. The mammary ageing was initiated by a light senescence state with elevated NFkb, P53 signals, followed by a deep senescence state with reduced NFkb, P53 and enhanced PI3K-Akt-mTOR, Wnt, Notch and pluripotency activities succumb to cancer predisposition. Both of these senescence programs were regulated by a master mammary stem cell factor Bcl11b through modulation of multiple stress, longevity and pluripotency associated pathways. Depletion of Bcl11b triggered morphological, functional and molecular ageing-like phenotypes, and drastically enhanced DMBA-induced tumor formation. We further screened out a drug TPCA-1 that can elevate Bcl11b activity, rejuvenate mammary cells transcriptomically and significantly reduce the ageing-related cancer incidence. Our findings established a molecular portrait of progressive mammary cell ageing and elucidated the regulatory network bridging mammary ageing and cancer predisposition that can be modulated to control the cancer initiation, which has potential implications in management of cancer prevalence.

overall_design: Single cell RNA profiles of mammary gland basal cells from different age, Bcl11b ko mice and mammary gland tumor

first: Huiru

last: Bai

first: Meizhen

last: Lin

first: Yuan

last: Meng

first: Ruolan

last: Tang

first: Yajing

last: Guo

first: Michael

first: Shang

last: Cai


title: Metabolic modeling reveals the aging-associated decline of host–microbiome metabolic interactions in mice

status: Public on Mar 27 2024

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

institute: Christian-Albrechts-University Kiel

summary: Aging is the predominant cause of morbidity and mortality in industrialized countries. The specific molecular mechanisms that drive aging are poorly understood, especially the contribution of the microbiota in these processes. Here, we combined multi-omics with metabolic modeling in mice to comprehensively characterize host–microbiome interactions and how they are affected by aging. Our findings reveal a complex dependency of host metabolism on microbial functions, including previously known as well as novel interactions. We observed a pronounced reduction in metabolic activity within the aging microbiome, which we attribute to reduced beneficial interactions in the microbial community and a reduction in the metabolic output of the microbiome. These microbial changes coincided with a corresponding downregulation of key host pathways predicted by our model that are crucial for maintaining intestinal barrier function, cellular replication, and homeostasis. Our results elucidate potential microbiome–host interactions that may influence host aging processes, focusing on microbial nucleotide metabolism as a pivotal factor in aging dynamics.

overall_design: total-RNA with Illumina’s TruSeq stranded kit, with polyA enrichment, 100bp or 75bp paired end sequencing of 52 samples each from male mice’s (C57BL/6J/Ukj) colons, livers, brains at different ages: 2 (n = 10), 9 (n = 10), 15 (n = 10), 24 (n = 10), and 30 (n = 12) months.

first: Thomas

last: Dost

first: Daniela

last: Esser

first: Stefano

last: Flor

first: Madlen

last: Haase

first: A

middle: S

last: Kadibalban

first: Georgios

last: Marinos

first: Alesia

last: Walker

first: Johannes

last: Zimmermann

first: Rowena

last: Simon

first: Silvio

last: Schmidt

first: Jan

last: Taubenheim

first: Sven

last: Künzel

first: Robert

last: Häsler

first: Marco

last: Groth

last: Waschina

first: Otto

middle: W

last: Witte

first: Philippe

last: Schmitt-Kopplin

first: John

middle: F

last: Baines

first: Christiane

last: Frahm

first: Christoph

last: Kaleta