title: A chronic, low-dose treatment with methamphetamine modulates genes implicated in neurodegeneration in a transgenic model of NeuroHIV

status: Public on Apr 01 2024

city: Riverside

first: Marcus

last: Kaul

state: California

address: 900 University Ave, SOM RB Room 311

department: Biomedical Sciences

institute: University of California, Riverside

summary: Methamphetamine (METH) is a frequently abused addictive psychostimulant. METH use is highly prevalent in people living with HIV (PLWH). The HIV and drug interaction may promote progression of HAND, as PLWH who uses METH reportedly have increased neuronal injury, cognitive impairment and viral load. However, low concentration of METH has an approved clinical use as a treatment for patients diagnosed with attention-deficit/hyperactivity disorder (ADHD). Recent studies have also reported potential non-injurious effects via low-dose METH exposure, that improved learning and memory, and limited neuronal injury. This suggests that the specific dosage of METH plays a key role in determining whether the psychostimulant effects will be associated with apparent neurotoxicity or not. This study explored in vivo the effects of a long-term, low-dose METH regimen (12 weeks) in the HAND animal model with inducible expression of HIV-1 transactivator of transcription (Tat). In our observation, low dose of METH has a modulatory effect on learning and memory in the presence of the pathology-inducing HIV regulatory protein Tat. The observations from this study create the framework for future identification of potential targets for the treatment of neuroHIV/HAND in the context of psychostimulant use.

overall_design: To investigate the effects of a long-term, low-dose treatment of METH in a transgenic model of NeuroHIV. Four groups of animals were analyzed (Ctl, Tat, METH, Tat+METH). Animals receiving METH were given low-dose injections for 12 weeks between 4-mo and 7-mo. All animals were harvested at 12-mo. Brain tissue from the hippocampus were used for RNA-seq.

first: Indira

last: Harahap-Carrillo

first: Dominic

last: Fok

first: Gabriel

last: Malik

first: Ricky

last: Maung

first: Xinru

last: Qiu

first: Daniel

last: Ojeda-Juárez

first: Victoria

last: Thaney

first: Ana

middle: B

last: Sanchez

first: Adam

last: Godzik

first: Amanda

last: Roberts


title: Defective flow space limits the scaling up of turbulence bioreactors for platelet generation

status: Public on Mar 26 2024

city: Chiba

first: Naoya

last: Takayama

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Graduate School of Medicine

country: Japan

institute: Chiba University

type: Expression profiling by high throughput sequencing

summary: To complement donor-dependent platelet supplies, we previously developed an ex vivo manufacturing system using iPSC-derived expandable megakaryocytes, imMKCLs, and a turbulent flow bioreactor, VerMES, to generate iPSC-derived platelet products (iPSC-PLTs). However, the tank size of VerMES was limited to 10 L (VerMES10). Here we examined the feasibility of scaling up to 50 L (VerMES50) with reciprocal motion by two impellers. Under optimized turbulence parameters corresponding to VerMES10, VerMES50 elicited iPSC-PLTs with intact in vivo hemostatic function but with less production efficiency. This insufficiency was caused by increased defective turbulent flow space. A computer simulation proposed that designing VerMES50 with three impellers or a new bioreactor with a modified rotating impeller and unique structure reduces this space. These findings indicate that large-scale PLT manufacturing from cultured imMKCLs requires optimization of the tank structure in addition to optimal turbulent energy and shear stress.

overall_design: RNA-sequencing (RNA-Seq)

first: Sou

last: Nakamura

first: Atsushi

last: Kaneda


title: Development of a ß-Globin Gene Replacement Strategy as a Therapeutic Approach for ß-Hemoglobinopathies

city: San Francisco

first: Kristen

last: Seim

state: CA

address: 201 Haskins Way

country: USA

institute: GraphiteBio

type: Genome variation profiling by high throughput sequencing

summary: β-hemoglobinopathies are the most common genetic disorders worldwide. In sickle cell disease (SCD) a single mutation (E6V) in the b-globin (HBB) gene results in dysfunctional hemoglobin protein, while in β-thalassemia, over 300 mutations distributed across the HBB gene are known to reduce the production of β-globin and cause severe anemia. A genetic engineering approach that replaces the whole HBB gene is an ideal strategy to rescue HBB expression for most genotypes but is technically challenging as the insert cannot be homologous to the endogenous gene and codon-optimized, intron-less sequences may not reconstitute adequate HBB levels. Here, we developed a novel approach for a “one-size-fits-all" HBB gene repair strategy using CRISPR-Cas9 which successfully addresses these problems.  First, our DNA donor design avoids sequence homology through a diverged HBB coding sequence and second, incorporates heterologous introns from the fetal g-globin gene, further reducing homology to endogenous HBB while mimicking its intron composition. Screening DNA donors with various heterologous globin introns, polyadenylation signals and truncated sequences, identified a heterologous intron DNA donor that highly expresses β-globin and rescued β-globin expression in two in vitro hemoglobinopathy models in hematopoietic stem and progenitor cells (HSPCs). Furthermore, healthy donor HSPCs modified with this HBB gene replacement approach showed successful engraftment in immunodeficient mice at 16 weeks. In summary, we developed a universal HBB gene replacement strategy that results in physiological b-globin production, offering a potential differentiated approach for treating patients with β-thalassemia, SCD or compound heterozygous individuals.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: HBB gene repair strategy using CRISPR-Cas9 which includes: RNAseq on donors 1125 and 3404; mouse engraftment study, and long read sequencing data.

first: Kirby

middle: A

last: Wallace

first: Beeke

last: Wienert


title: Effect of stroke on the transcriptome in the small intestines

status: Public on Mar 24 2024

city: Melbourne

first: Deanna

middle: S

last: Deveson Lucas

state: Victoria

address: 15 Innovation walk, Monash University, Clayton

country: Australia

institute: Monash University

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

overall_design: Refer to individual Series


title: Combination therapy strategy to overcome resistance to EGFR inhibitors in NSCLC with Paeoniae Radix

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: Epidermal growth factor receptor (EGFR) inhibitors, as targeted therapies for non-small-cell lung cancer (NSCLC), have significantly enhanced patient survival and quality of life. However, despite these advancements, a significant proportion of patients exhibit resistance to EGFR inhibitors, limiting their overall treatment effectiveness. This study investigates the synergistic effects of combining Paeoniae Radix (PR) with the EGFR inhibitors erlotinib and gefitinib to overcome this resistance. The transcriptomic analysis of PR treatment revealed its potential to reverse the gene signature associated with resistance to EGFR inhibitors, as identified through analysis of a cell line database in EGFR mutant NSCLC. Combination treatment experiments validated that PR increased responsiveness to erlotinib and gefitinib in H1650 and H1975 NSCLC cells. By combining molecular experiments and transcriptome analysis, we found that PR may suppress resistance by modulating the Aurora B and apoptosis pathways. Notably, the combination therapy upregulated the apoptosis pathway and downregulated the Aurora B pathway more than single drug treatments. These results may contribute to the development of natural product-based combination therapeutic strategies to inhibit drug resistance in NSCLC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H1650 cells by Erlotinib, Gefitinib and/or Paeoniea Radix (PR) treatment

first: Heerim

last: Yeo

first: Han

middle: N

last: Kang

first: Sang-Min

last: Park


title: Circular RNA circRERE2 knockdown in rat primary cortical neurons

status: Public on Mar 18 2024

city: Zürich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: D-HEST

country: Switzerland

institute: ETH Zürich

type: Non-coding RNA profiling by high throughput sequencing


title: A prognostic neural epigenetic signature in high-grade glioma

status: Public on Mar 20 2024

city: Hamburg

first: Richard

last: Drexler

address: Martinistraße 52

department: Neurosurgery

country: Germany

institute: Medical Center Hamburg-Eppendorf

summary: Neural-tumor interactions drive glioma growth as evidenced in preclinical models, but clinical validation is limited. We present an epigenetically defined neural signature of glioblastoma that independently predicts patients’ survival. We use reference signatures of neural cells to deconvolve tumor DNA and classify samples into low- or high-neural tumors. High-neural glioblastomas exhibit hypomethylated CpG sites and upregulation of genes associated with synaptic integration. Single-cell transcriptomic analysis reveals a high abundance of stem cell-like malignant cells in high-neural glioblastoma, primarily of the neural lineage. These cells are further classified as neural precursor cell-like, astrocyte cell-like, and oligodendrocyte precursor-like, alongside oligodendrocytes and neurons. In line with these findings, high-neural glioblastoma cells engender neuron-to-glioma synapse formation in vitro and in vivo and show an unfavorable survival after xenografting. In patients, a high-neural signature associated with decreased survival. High-neural tumors also exhibit increased functional connectivity in magnetencephalography and resting-state magnet resonance imaging and can be detected via DNA analytes and brain-derived neurotrophic factor in patients’ plasma. The prognostic importance of the neural signature was further validated in patients diagnosed with diffuse midline glioma. Our study presents an epigenetically defined malignant neural signature in high-grade gliomas that is prognostically relevant. High-neural gliomas likely require a maximized surgical resection approach for improved outcomes.

overall_design: DNA was extracted from glioblastomas of 363 patients and analyzed for genome-wide DNA methylation patterns using the Illumina EPIC (850k) array.

first: Franz

middle: L

last: Ricklefs

first: Ulrich

last: Schüller


title: Transcriptomic profile of Lin negative, LEPR positive cells of murine peri-implant fibrous tissue and peri-implant bone

status: Public on Mar 21 2024

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: To investigate the transcriptomic profile difference between LEPR cells in peri-implant fibrous tissue and peri-implant bone

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LEPR cells isolated from murine peri-implant fibrous tissue and peri-implant bone tissue.

first: Suhardi

last: Vincentius

first: Oliver

last: David

first: Chinenov

last: Yurii


title: Exosomal miR-92a-3p as a diagnostic biomarker for adenomyosis and its pathological mechanism

city: Jiaxing

first: Wanqi

last: Shao

address: 2468 Central Road East

department: Jiaxing University Master Degree Cultivation Base

country: China

institute: Zhejiang Chinese Medical University

summary: This study aimed to elucidate the role of microRNA miR-92a-3p in the pathogenesis of adenomyosis. We focused on understanding how miR-92a-3p in exosomes derived from ectopic lesions influences the behavior of endometrial cells, DRG neurons, and Human Umbilical Vein Endothelial Cells (HUVECs), and its potential as a non-invasive diagnostic biomarker. Our findings revealed that MiR-92a-3p is significantly upregulated in exosomes derived from ectopic lesions of adenomyosis. This upregulation was associated with enhanced migration and invasion capabilities in eutopic endometrial cells, DRG neurons, and HUVECs. Furthermore, the study demonstrated a significant correlation between the levels of MiR-92a-3p in urinary exosomes and the clinical symptoms of adenomyosis, suggesting its potential as a non-invasive biomarker for the disease. This study elucidates an exosomal signaling process via miR-92a-3p that drives pathological infiltration and angiogenesis to promote adenomyosis progression. Upregulated miR-92a-3p in biofluid exosomes shows promising non-invasive biomarker potential for diagnosis and monitoring of this disease. Our findings unveil novel targets and tools for improved clinical management.

overall_design: MiRNA deep sequence analysis was performed to identify significantly different miRNAs between adenomyosis and controls (8 adenomyosis patients and 8 non-adenomyosis controls).

first: Xuan

last: Che

first: Yayuan

last: Yu

first: Jianzhang

last: Wang


title: Circular RNA circRERE2 knockdown in rat primary cortical neurons [polyA RNA-seq]

summary: Circular RNAs (circRNAs), a diverse class of ncRNAs highly enriched in developing neurons, play roles in local protein synthesis and synaptic plasticity. However, distinguishing functional from non-functional circRNAs is challenged by their abundance, tissue specificity and splicing variability. To address this, we conducted a RNAi knockdown screen targeting 32 highly expressed, conserved circRNAs enriched in dendritic processes. circRERE isoforms emerged as regulators of dendritic synapse density and electrophysiological characteristics. mRNA-seq supports the dysregulation of synaptic genes, particularly miR-128-3p-sensitive transcripts. MiR-128-3p activity and expression are reduced, with circRERE possessing multiple miR-128-3p binding sites, suggesting a protective interaction supported by a rescue of the synaptic phenotype upon miR-128-3p overexpression. Conversely, circRERE overexpression with intact miR-128-3p sites rescued the synaptic phenotype and independently increased miR-128-3p levels. These findings demonstrate the necessity for the broad characterization of circRNAs in the nervous system to comprehensively understand their influence on essential non-coding RNA regulatory networks.

overall_design: We performed highly penetrant electroporation of primary cortical neurons. We utilised an empty vector control (pSUPER), a ScramSh control (Pum2MM, a mismatched scrambled shRNA) and a shRNA expressing plasmid knocking down circRERE2 (RERE2). There were four biological replicates gathered (N1-N4) of each of the 3 conditions. The same input RNA was used for both miRNA- and polyA-RNA-seq.

first: Darren

last: Kelly

first: Pierre-Luc

last: Germain


title: TET activity propagates transcriptional memory through embryonic dormancy

status: Public on Mar 19 2024

city: Berlin

first: Maximilian

last: Stötzel

state: Berlin

address: Ihnestraße 65

department: Meissner

institute: Max-Planck-Institute for molecular genetics

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing


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

status: Public on Apr 16 2024

first: Frederik

middle: Richard

last: Heinrich

address: Chariteplatz 1

department: Bioinformatics

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 a longitudinal study of peripheral blood plasmablasts upon vaccination with different vaccines and vaccination schemes. To do so, single cell transcriptomes and BCR/TCR sequencing of sorted plasmablasts, memory B cells and activated T cells from peripheral blood samples of 36 individuals taken at different time points after first, second or third dose of COVID-19 (Comirnaty or Vaxzevria) or dipheteria/tetanus/pertussis vaccines were prepared.  In addition, cells were also incubated with DNA barcoded antibodies for Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq). Some 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 v1.1 (single index) and Illumina NextSeq2000.

first: Marta

last: Ferreira-Gomes

first: Gabriela

middle: M

last: Guerra

first: Katrin

last: Lehmann

first: Pawel

last: Durek

first: Mir-Farzin

last: Mashreghi


title: Acinar to β-like cell conversion through inhibition of focal adhesion kinase

status: Public on Mar 12 2024

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

summary: Insufficient functional β-cell mass causes diabetes; however, an effective cell replacement therapy for curing diabetes is currently not available. Reprogramming of acinar cells toward functional insulin-producing cells would offer an abundant and autologous source of insulin-producing cells. Our lineage tracing studies along with transcriptomic characterization demonstrate that treatment of adult mice with a small molecule that specifically inhibits kinase activity of focal adhesion kinase results in trans-differentiation of acinar cells into insulin producing β-like cells. The acinar-derived insulin-producing cells infiltrate the pre-existing endocrine islets, partially restore β-cell mass, and significantly improve glucose homeostasis in diabetic mice. Importantly, this treatment can substantially reduce the exogenous insulin requirements in streptozotocin-induced diabetic non-human primates. These findings provide evidence that inhibition of the kinase activity of focal adhesion kinase can convert acinar cells into insulin-producing cells and could offer a promising strategy for treating diabetes.

overall_design: To better characterize these newly formed insulin-producing cells, we conducted single cell RNA sequencing (scRNA-seq) analysis on islets isolated from wild type mice ten days after cessation of vehicle- or FAKi treatment. Approximately 8500 cells were sequenced at 225,000 reads per cell.

first: Farzad

last: Esni

first: Shakti

last: Dahiya


title: Identification of unique gene expression and splicing events in early-onset colorectal cancer

status: Public on Apr 11 2024

city: Hershey

first: Gregory

last: Yochum

address: 700 HMC Crescent Road

department: Biochemistry, Colorectal Surgery

institute: Penn State College of Medicine

summary:
Background: The incidence of colorectal cancer (CRC) has been steadily increasing in younger individuals over the past several decades for reasons that are incompletely defined. Identifying differences in gene expression profiles, or transcriptomes, in early-onset colorectal cancer (EOCRC, < 50 years old) patients versus later-onset colorectal cancer (LOCRC, > 50 years old) patients is one approach to understanding molecular and genetic features that distinguish EOCRC.
Methods: We performed RNA-sequencing (RNA-seq) to characterize the transcriptomes of patient-matched tumors and adjacent, uninvolved (normal) colonic segments from EOCRC (n=21) and LOCRC (n=22) patients. The EOCRC and LOCRC cohorts were matched for demographic and clinical characteristics. We used The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) database for validation. We used a series of computational and bioinformatic tools to identify EOCRC-specific differentially expressed genes, molecular pathways, predicted cell populations, differential gene splicing events, and predicted neoantigens.
Results: We identified an eight-gene signature in EOCRC comprised of ALDOB, FBXL16, IL1RN, MSLN, RAC3, SLC38A11, WBSCR27 and WNT11, from which we developed a score predictive of overall CRC patient survival. On the entire set of genes identified in normal tissues and tumors, cell type deconvolution analysis predicted a differential abundance of immune and non-immune populations in EOCRC versus LOCRC. Gene set enrichment analysis identified increased expression of splicing machinery in EOCRC. We further found differences in alternative splicing (AS) events, including one within the long non-coding RNA, HOTAIRM1. Additional analysis of AS found seven events specific to EOCRC that encode potential neoantigens.
Conclusion: Our transcriptome analyses identified genetic and molecular features specific to EOCRC which may inform future screening, development of prognostic indicators, and novel drug targets.

overall_design: Gene expression profiles of 22 surgically resected tumors and patient-matched adjacent colonic segments from colorectal cancer patients were generated with RNA-sequencing.

first: Olivia

last: Marx

first: Walter

last: Koltun

first: Mark

last: Mankarious


title: Whole organism snRNA-seq reveals systemic peripheral changes in Alzheimer’s Disease fly models

status: Public on Mar 14 2024

city: Houston

first: Hongjie

last: Li

state: TX

address: One Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

summary: Alzheimer's Disease (AD) is known for its profound impact on the brain, yet its systemic effects, particularly on peripheral tissues, remain underexplored. To address this gap, we utilized Drosophila, an established model for aging and neurodegeneration studies, to create the Alzheimer's Disease Fly Cell Atlas (AD-FCA). This comprehensive atlas comprises whole-organism single-nucleus transcriptomes from 219 cell types in two AD models, where adult flies express human Aβ42 or Tau exclusively in neurons. Our in-depth analyses reveal that Aβ42 prominently affects peripheral sensory neurons, whereas Tau expression leads to notable alterations in several non-neuronal tissues, including the gut, fat body, and reproductive system. The AD-FCA uncovers the nuanced interplay between neuronal pathology and peripheral tissue responses, offering novel insights into potential biomarkers and the systemic nature of AD.

overall_design: To know how Aβ42 and hTau impact brain neurons and periphery cells during aging, we collected 10d, 20d, and 30d flies from control, Aβ42, and hTau flies to perform snRNA-seq. Head and body were separated. Female and male were also profiled separately.

first: Tzu-Chiao

last: Lu

first: Ye-Jin

last: Park


title: TET activity propagates transcriptional memory through embryonic dormancy [RNA-Seq]

first: Maximilian

last: Stötzel

summary: Dormancy is an essential biological process for the propagation of many life forms through generations and stressful conditions. Early embryos of many mammals are preservable for weeks to months within the uterus under dormancy, which can be induced in vitro through mTOR inhibition. Dormancy features silencing of the genome and abundant heterochromatin formation, which conflicts with the permissive and uncommitted genomic profile of pluripotent cells. Cellular strategies to maintain pluripotency in the fate of this conflict are not known.  Here we probed chromatin regulation during embryonic stem cells’ (ESC) entry into dormancy to identify mechanisms that ensure nsure faithful propagation of cellular identity through dormancy. We show a global increase in DNA methylation and loss of chromatin accessibility in dormant ESCs and find that TET DNA demethylases are essential to counteract this trend at key pluripotency regulatory elements. Perturbation of TET activity compromises transcriptional programs and embryo survival through dormancy; whereas its enhancement improves survival rates. We propose that key regulatory elements are bookmarked coordinately by TETs and transcription factors in dormancy for maintenance of cellular identity. Our results reveal the first essential chromatin regulator in establishing mammalian dormancy and paves the way to building its temporal regulatory code in embryonic and adult tissues.

overall_design: Either wild-type or TET1/2 double-knock out embryonic stem were cultured with or without mTOR inhibition using Ink128

first: Aydan

last: Bulut-Karslioglu


title: Circular RNA circRERE2 knockdown in rat primary cortical neurons [miRNA-seq]

first: Gerhard

last: Schratt

overall_design: We performed highly penetrant electroporation of primary cortical neurons. We utilised an empty vector control (pSUPER), a ScramSh control (Pum2MM, a mismatched scrambled shRNA) and a shRNA expressing plasmid knocking down circRERE2 (RERE2). There were four biological replicates gathered (N1-N4), but one sample (pSUPER_N2) did not pass QC for small-RNA seq and was thus not sequenced. Otherwise the same input RNA was used for both miRNA- and polyA-RNA-seq.

first: Darren

last: Kelly

first: Pierre-Luc

last: Germain


title: Exercise activates AMPK in mouse pancreatic islet leading to decreased senescence

status: Public on Mar 16 2024

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Increased beta-cell senescence contributes to the development of type 2 diabetes (T2D). Exercise is critical in the treatment of T2D and can attenuate aging-associated cellular changes, but its effects on beta-cell senescence are unknown. Using two mouse models of insulin resistance, we showed that exercise prevented and reversed beta-cell senescence. Mechanistic studies revealed that these effects were mediated by exercise-induced increases in serum glucagon leading to AMPK activation in beta-cells. Nuclear translocation of NRF2 in mouse islets after exercise and its inversely proportional regulation of p16Ink4a, suggested its role as a molecular mediator between AMPK activation and cellular senescence.

overall_design: C57Bl/6 retired breeder male mice were subjected to a structured running protocol of a single-bout/day of acute treadmill running protocol. After a 3-day acclimatization protocol, animals were trained for 1 hour/day, 5 times per week, for 2 weeks, at 17 cm/s and 5 degree incline. Under anesthesia, mice were injected with collagenase into the pancreatic duct before pancreatectomy. After digestion and centrifugation, islets were hand-picked under a microscope and plated in a petri dish with islet media. Islet media was composed of RPMI medium (11 mM glucose), 10% FBS and 1% Penicillin-Streptomycin. Islets from trained and sedentary C57Bl6 mice were isolated for RNA sequencing.

first: Priscila

last: Carapeto

first: Kanako

last: Iwasaki

first: Francesko

last: Hela

first: Jiho

last: Kahng

first: Ana

last: Alves-Wagner

first: Roeland JW

last: Middelbeek

first: Michael

middle: F

last: Hirshman

first: Guy

last: Rutter

first: Laurie

middle: J

last: Goodyear

first: Cristina

last: Aguayo-Mazzucato


title: Possible involvement of transient receptor potential channels in adenomyosis

city: Suzhou

first: zhixing

last: jin

address: 889 Pinghai Road

institute: Soochow University Affiliated No 1 People\'s Hospital: First Affiliated Hospital of Soochow University

summary:
To investigate the role and mechanism of the TRPM3 antagonist, primidone in tamoxifen-induced adenomyosis mouse.
The neonatal female mice were randomly divided into three groups: control group, adenomyosis group and primidone treatment group. We then performed gene expression profiling analysis using data obtained from RNA-seq of uterus from different groups

overall_design: The neonatal female mice were randomly divided into three groups: control group, adenomyosis group and primidone treatment group. From day 1 to day 5 after birth, female neonatal mice in the ADE group (n=3) and primidone treatment group (n=3) received 1 mg/kg tamoxifen suspended in a peanut oil/lecithin/condensed milk mixture (2:0.2:3, by volume) at a dose volume of 5 μl/g body weight, while the control neonatal mice (n=3) were fed similarly with the same amount of solvent without tamoxifen. All mice were weaned and separated from the dams upon reaching 3 weeks of age, where the dams were sacrificed using cervical dislocation. From 10 weeks after birth, mice in primidone treatment group were administered by intraperitoneal injection with either primidone (2mg/kg/d) for 3 weeks, while the mice in the control and ADE groups were administered similarly with corresponding quantities of the vehicle.  Uterine samples from the mice in different group were harvested at 13 weeks of age for RNA-seq.

first: Zhixing

last: Jin

first: Yaoming

last: Peng

first: He

last: Zhang

first: Xiaoping

last: He

first: Yi

first: Xinwei

last: Zou

first: Xin

first: Min

last: Li

first: Qianqian

last: Yang


title: Transcriptomic profile of Lin negative, LEPR positive cells of human peri-implant fibrous tissue and peri-implant bone

status: Public on Mar 10 2024

first: HSS Genomics

last: Research Center

summary: Peri-implant fibrosis is one of the most common reasons for implant failure and surgical revision after prosthetic joint replacement. This type of surgical revisionis associated with substantial additional morbidity and healthcare costs. However, the cellular and molecular mediators of peri-implant fibrosis remain unclear. Here, we show that peri-implant fibrotic tissue in mice and humans is largely composed of a specific population of leptin receptor-expressing(LEPR+) cells and that these LEPR+cells are necessary and sufficient to both generate and maintain peri-implant fibrotic tissue. Genetic ablation of LEPR+cells prevents peri-implant fibrosis, and implantation of LEPR+cells from peri-implant fibrotic tissue is sufficient to induce fibrosis in secondary hosts. We further identify adhesion G protein-coupled receptorF5 (ADGRF5) as a crucial mediator of the fibrotic response by LEPR+cells, as conditional deletion of ADGRF5 in LEPR+cells attenuates peri-implant fibrosis while augmenting peri-implant bone formation. Finally, we demonstrate that inhibition of ADGRF5 by intra articular or systemic administration of neutralizing anti-ADGRF5prevents and reverses peri-implant fibrosis. Thus, pharmaceutical agents that inhibit the ADGRF5 pathway inLEPR+cells may represent a new approach to prevent and treat peri-implant fibrosis.

overall_design: Bulk RNA sequencing was performed on FACS-sorted LEPR+ and LEPR- cell populations isolated from human trabecular bone and fibrotic tissues from patients underwent primary total knee or total hip arthroplasty and human peri-implant fibrous tissue from patients underwent revision surgery for aseptic loosening

first: Vincentius

last: Suhardi

first: David

last: Oliver

first: Yurii

last: Chinenov


title: Transcriptome of vitamin D3 bolus supplementation in a cohort of 25 individuals

status: Public on Mar 11 2024

city: Olsztyn

first: Carsten

last: Carlberg

state: Warmia-Mazury

address: Tuwima 10

department: Food Technology

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

summary: In this study, we analyse the in-vivo modulation of the transcriptome of human PBMCs by a bolus of vitamin D3 (80,000 IU) after 24 hours.

overall_design: PBMCs of 25 healthy individuals were collected before and after an in-vivo intake of a single large bolus of 80,000 IU of vitamin D3. Analysis was performed on the cohort to find plausible vitamin D target genes.

first: Ranjini

last: Ghosh Dastidar


title: A smooth muscle cell gene-regulatory network critical for the development of advanced-stage and symptomatic atherosclerosis [human]

status: Public on Mar 05 2024

city: Stockholm

first: Michael

last: Vanlandewijck

address: Blickagången 6

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

summary: While our understanding of the single-cell gene expression patterns underlying the transformation of vascular cell types during the progression of atherosclerosis is rapidly improving, the clinical and pathophysiological relevance of these changes remain poorly understood.  Single cell RNA sequencing (scRNAseq) data generated with SmartSeq2 (~8000 genes/cell) in nearly 19,000 single cells isolated during atherosclerosis progression in mice with human-like plasma lipoproteins and from humans with asymptomatic and symptomatic carotid plaques was clustered into multiple subtypes. For clinical and pathophysiological context, the advanced-stage and symptomatic subtype clusters were integrated with 135 tissue-specific (atherosclerotic aortic wall, mammary artery, liver, skeletal muscle, and visceral and subcutaneous, fat) gene-regulatory networks (GRNs) inferred from 600 coronary artery disease (CAD) patients in the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) study.Advanced stages of atherosclerosis progression and symptomatic carotid plaques were largely characterized by three smooth-muscle cells (SMC), and three macrophage (MP) subtype clusters with extracellular matrix organization/osteogenic (SMC), and M1-type pro-inflammatory/Trem2-high lipid-associated (MP) phenotypes. Integrative analysis of these 6 clusters with STARNET revealed significant enrichments of three arterial wall GRNs: GRN33 (MP), GRN39 (SMC) and GRN122(MP) with major contributions to CAD heritability and strong associations with clinical scores of coronary atherosclerosis severity (SYNTAX/Duke scores). The presence and pathophysiological relevance of GRN39 was verified in five independent RNAseq datasets obtained from the human coronary and aortic artery, and primary SMCs and by targeting its top-key drivers, FRZB and ALCAM, in cultured human vascular SMCs.By identifying and integrating the most gene-rich single-cell subclusters of atherosclerosis to date with a CAD framework of GRNs, GRN39 was identified and independently validated as being critical for the transformation of contractile SMCs into an osteogenic phenotype promoting advanced-stage, symptomatic atherosclerosis.

overall_design:
single-cell transcriptomes were generated of individual cells captured from atherosclerotic plaque biopsies from carotid Endarterectomy
Please note that each sample records  represents multiple cells.


title: De Novo Design of Adaptive Hydrogels with Solubilized Flavonoids for Whole Layer Regeneration of Diabetic Wound

status: Public on Mar 08 2024

city: Beijing

first: sa

last: du

institute: Peking University School of Stomatology

summary: A whole layer functional regeneration can be achieved by Gel-Fla, which ensures an improved healing effect than commercial dressing approaches. The multi-level and stereo regeneration Gel-Fla system provides a promising strategy in diabetic wound healing.

overall_design: Comparative gene expression profiling analysis of Gel, Gel-Myr, Gel-2H myr, Gel-Cat, Gel-Que with RAW264.7.

first: Qiang

last: Zeng

first: Sa

last: Du

first: Rui

last: Yuan

first: Yuwei

last: Wu

first: Lei

last: Tao

first: Zhihui

last: Tang


title: Increased homing of immune cells by orexigenic catecholaminergic neurons alleviates autoimmune disorder

status: Public on Mar 01 2024

city: Hefei

first: Liang

last: Wang

state: Anhui

address: 96 Jinzhai Road

institute: University of Science and Technology of China

summary: Whole-body energy status significantly impacts the immune system. Both feeding behavior and energy metabolism are controlled by the central nerve system, but it is unknown whether the brain can regulate the immune system in response to fluctuations of the energy status. Here, we show that catecholaminergic (CA) neurons in the nucleus of the solitary tract (NTS) and ventrolateral medulla (VLM) were activated by fasting, and demonstrate that chemogenetic activation of these hindbrain CA neurons both increased food intake and drove homing of CD45+ cells, T cells, and B cells from blood to bone marrow, which was mediated by enhanced HPA axis and upregulation of the chemokine receptor CXCR4. This activation of CA neurons also prevented immune cell infiltration to the brain in the experimental autoimmune encephalomyelitis (EAE) mouse model, and ameliorated the disease outcome. Our study demonstrates the neuronal control of immune function in response to host energy scarcity and sheds light on communications between the nervous and immune systems.

overall_design: 1. mRNA expression of CD45+ immune cells in the bone marrow of DbhVLM-hM3Dq and DbhVLM-mCherrry mice 4 hour after CNO injections.   2. mRNA expression of CD45+ immune cells in spleen of DbhVLM-hM3Dq and DbhVLM-mCherrry mice 4 hour after CNO injections. .   Four biological replicates were prepared for mRNA profiles.

first: Mingxiu

last: Cheng

first: Jing

last: Chen

first: Jiesi

last: Feng

first: Yulong

first: Famin

last: Xie

first: Li-Hao

last: Huang

first: Jiawen

first: Tao

last: Cai

first: Cheng

last: Zhan


title: A smooth muscle cell gene-regulatory network critical for the development of advanced-stage and symptomatic atherosclerosis

first: Michael

overall_design:
single-cell transcriptomes were generated of individual cells captured from adult mice (10-60 weeks of age) by single-cell RNA-sequencing
Please note that each sample records  represents multiple cells.


title: Gene signature from lung tissue of e-cigarette users

status: Public on Feb 29 2024

city: Winnipeg

first: Christopher

last: Pascoe

state: MB

address: 602-715 McDermot Avenue, Children's Hospital Research Institute of Manitoba

department: Physiology & Pathophysiology

country: Canada

institute: University of Manitoba

summary:
Background: E-cigarette popularity is on the rise in youth and young adults, with mounting concerns regarding the long-term safety of these devices. Cell culture and animal models have highlighted the damaging potential of e-cigarettes, but to date there is a lack of data from human lung tissue to corroborate these findings.
Methods: Using human lung tissue obtained during a bullectomy in young adults, we performed RNA-sequencing to uncover e-cigarette related changes to the human lung transcriptome. Information on e-cigarette use habits was collected via questionnaire.
Samples included in study: S1, S2, S3, S4, S5, S7, S9, S10, S12, S13, S14, S16, S17, S18, S19, S21

overall_design:
Lung tissue collected from people undergoing surgery to repair a spontaneous pneumothorax.

February 2025:  Submitter indicated there was an error in the labelling of some of the samples.  The error has been amended.


title: Tomato Shade Avoidance: Unraveling Internode Elongation and Hormonal Harmony

city: Dalian

first: Changqing

last: Tong

state: Liaoning

address: Heishijiao Str.

department: College of Food science and Engineering

institute: Dalian Ocean University

summary: This study provides a comparison of gene expression in two tomato cultivars, Moneymaker and M82, focusing on first internode and its innermost cell type pith—under two light conditions: white light with far-red supplementation (WL+FR) and the control condition of white light (WL). The samples were harvested at four time points leading to the point where internode elongation could be measured in response to WL+FR. The timepoints were 6, 24, 30, and 48 hours after treatment initiation.

overall_design: The experimental setup was coded for efficient tracking and comparison: "M" was used to denote Moneymaker and "2" for M82 as the initial digit of the sample code. "F" indicated far-red light treatment (FR), and "W" designated white light (WL). The third digit was reserved for the replicate number, representing the plants grown in the same batch. The fourth and final digit identified the sample sequence, with "1" corresponding to the internode sampled at 6h, "2" for the internode at 24h, "3" for the internode at 30h, and "4" for the internode at 48h. Similarly, "5" represented pith samples at 30h, and "6" for pith at 48h. This coding system streamlined the process of data collection and analysis, allowing for a clear distinction between the variables being studied.

first: Li

last: Linge

first: Kajala

last: Kaisa

first: Pierik

last: Ronald


title: Fumarate hydratase orchestrates hepatic steatosis via ULK1 mediated lipophagy

status: Public on Feb 26 2024

city: Hangzhou

first: Sike

last: Yu

address: No.1 Xiangshan Branch Lane, Xihu District

institute: Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences

summary: Hepatic lipid homeostasis is coordinated by various metabolic pathways, such as lipogenesis, lipid uptake, storage, and oxidation. However, the underlying mechanism that orchestrates metabolic crosstalk remains unclarified. Herein, we demonstrated that fumarate hydratase (FH) functioned as an indispensable adaptor governing mitochondria metabolism and lipid droplets (LDs) degradation. Hepatic FH overexpression prevented hepatic steatosis in normal mice and ob/ob mice without interfering mitochondrial lipid oxidation and lipogenesis. Strikingly, we found that FH selectively activated lipophagy-mediated LDs lipidolysis. Mechanistically, FH interacted with ULK1 and stabilized ULK1 through preventing its ubiquitination and degradation, resulting in lipophagy activation and the elimination of hepatic lipid accumulation. Meanwhile, hepatic ULK1 deficiency abrogated the protective effects in FH-overexpressing mice. Also, we clarified that the interaction between FH and ULK1 occurred in cytoplasm, but not in mitochondria. Cytoplasmic FH was sensitive to lipids and downregulated without affecting mitochondrial FH in vivo. Moreover, the FH-ULK1 axis was identified closely associated with hepatic steatosis in human patients. Taken together, our research demonstrates a “two-side” insight of FH on hepatic lipid metabolism and provides a promising strategy for fatty liver treatment.

overall_design: To investigate the role of FH in the protection of fatty liver, we used liver-specific adenovirus AAV8 to administer tail vein injections to 6-8 week old C57BL/6 mice, which were fasted for 24h after one month. And for another model we used liver-specific adenovirus AAV8 to inject 6-8 week old ob/ob mice into the tail vein and then continued to feed them a high-fat diet for one month.

first: Xiaotong

last: Guan


title: Comparing 10x Visium spatial transcriptomic technologies

city: Parkville

first: Matthew

last: Ritchie

address: 1G Royal Parade

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Spatial transcriptomics facilitates the understanding of gene expression within complex tissue contexts. Among the array of spatial capture technologies available is 10x Genomics’ Visium which provides whole tissue section profiling, enabling whole transcriptome spatial analysis. Our dataset comprises spleen tissue from mice infected with malaria, spanning multiple experiments and sample preparation protocols for tissue preservation, either as fresh frozen at optimal cutting temperature (OCT) or formalin-fixed paraffin-embedded (FFPE). Tissue placement was also considered, comparing direct tissue placement on the slide with the use of CytAssist (CA), which expands the Visium platform’s capabilities by allowing for the pre-selection of tissue sections and genes through a set of probes. We also include a matching scRNA-seq dataset that can be integrated with the spatial data.

overall_design: Samples were captured over 5 10x Genomics Visium fresh-frozen (FF) slides and 3 formalin-fixed paraffin-embedded (FFPE) slides and sequenced over 6 Illumina runs. A matching scRNA-seq sample of the 3 mouse spleens (708, 709, 713): 10x scRNA-seq with the large BioLegend panel of antibody derived tags (ADTs) was captured over 1 GEM wells and GEX, ADT, and HTO were sequenced over 1 Illumina run.

first: Mei

middle: R

last: Du

first: Charity

middle: W

last: Law

first: Daniela

last: Amann-Zalcenstein

first: Casey

last: Anttila

first: Ling

last: Ling

first: Callum

last: Sargeant

first: Peter

last: Hickey

first: Yunshun

first: Lisa

last: Ioannidis

first: Diana

last: Hansen

first: Rory

last: Bowden

middle: E


title: Effect of IFN-α and IFN-γ on gene expression of 3D organoids derived from telomerase-immortalized normal human esophageal keratinocyte cell line, EPC2-hTERT.

city: Philadelphia

first: Megha

last: Lal

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: Eosinophilic esophagitis (EoE) is a chronic, allergic inflammatory disease of the esophageal mucosa. While type 2 cytokines are predominant, targeting type 2 inflammation alone is not always effective for all patients. In EoE patients, the transcriptional profiling of  esophageal biopsy reveal upregulation of type I and II interferon (IFN) response, dysregulated immune signaling and downregulation of esophageal-specific genes in EoE patients. However, the role of interferon signaling during EoE is not fully understood. This study aims to investigate the impact of IFN signaling on esophageal epithelium and elucidate its role in EoE. IFN-γ stimulation of esophageal epithelial cells triggered disruption of tissue differentiation, epithelial barrier integrity and cytotoxicity, which are relevant features of EoE immunopathology. Beyond EoE, our findings offer insights into esophageal disorders which may involve increased IFN-γ signaling, including infections, gastrophageal reflux disease, and Barrett's esophagus.

overall_design: Comparative transcriptomic profiling of 3D organoids derived from telomerase-immortalized normal human esophageal keratinocyte cell line, EPC2-hTERT

first: Melanie

last: Ruffner


title: Transcriptome U87MG TMZ resistant

status: Public on Feb 13 2024

city: Lille

first: Mohamed

last: Elati

address: Bd du Professeur Jules Leclercq

country: France

institute: University of Lille

summary: Differential transcriptome analysis between control cells (U87MG), TMZ-resistant cells with continuous TMZ treatment (U87MG R50) and TMZ-resistant cells with interrupted treatment (U87MG OFF R50).

overall_design: The U87MG GBM cell line was obtained from the American Type Culture Collection (LGC Standards Sarl, Molsheim, France).  Two TMZ-resistant clonal lines were established in our laboratory by exposing the U87MG parent line to 50 μM TMZ for an extended period: U87MG R50 and U87MG R50 OFF. U87MG R50 cells were continuously cultured in a medium supplemented with 50 μM TMZ while U87MG R50 OFF were relieved of TMZ pressure after a two-month treatment period. TMZ (cat #T2577; Sigma Aldrich) was prepared as a 100mM stock solution in DMSO and stored at 4°C until use. These cell lines were routinely cultured in Eagle's Minimum Essential Medium (EMEM) with 10% heat-inactivated foetal bovine serum (FBS), 1% sodium pyruvate, and 1% non-essential amino acids at 37°C with 5% CO2. Glioma stem-like cells, NCH644 and NCH421k, were provided by Dr. Christel Herold-Mende (ref).  Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with Nutrient Mixture F-12 and GlutaMAXTM (DMEMF12+GlutaMAXTM, GibcoTM). These cells were cultured under serum-free conditions as neurospheres (NS) to maintain a stem-like state using the medium further enhanced with Bovine Serum Albumin (BSA) Insulin Transferrin (BIT-100, 20%) (Provitro), along with Epidermal Growth Factor (EGF, 20 ng/mL) and Fibroblast Growth Factor (β-FGF, 20 ng/mL) (Reliatech). Induction of differentiation was achieved by culturing the cells in DMEM/F12 + GlutaMAXTM medium (GibcoTM) supplemented with 10% (vol/vol) FBS (GibcoTM) or all-trans retinoic acid (ATRA).  The cultures were maintained at 37°C within a humidified atmosphere comprising of 5% CO2. Periodic authentication of all cell lines was conducted by Multiplexion GmbH, coupled with regular testing for mycoplasma contamination to ensure culture integrity

first: Sophie

last: Foppolo

first: Christelle

last: Thibault

first: Monique

last: Dontenwill


title: Integrative genomics sheds light on the immunogenetics of tuberculosis in cattle

city: Dublin

first: John Francis

last: O'Grady

state: Leinster

address: Belfield, Dublin4

department: UCD School of Agriculture and Food Science

country: Ireland

institute: University College Dublin

summary: Mycobacterium bovis causes bovine tuberculosis (bTB), an infectious disease of cattle that represents a zoonotic threat to humans. Research has shown that the peripheral blood (PB) transcriptome is perturbed during bTB disease but the genomic architecture underpinning this transcriptional response remains poorly understood. Here, we analyse PB transcriptomics data from 63 control and 60 confirmed M. bovis infected animals and detect 2,592 differently expressed genes perturbing multiple immune response pathways. Leveraging imputed genome-wide SNP data, we characterise thousands of cis¬-expression quantitative trait loci (eQTLs) and show that the PB transcriptome is substantially impacted by intrapopulation genomic variation during M. bovis infection. Integrating our cis-eQTL data with bTB susceptibility GWAS summary statistics, we perform a transcriptome-wide association study and identify 132 functionally relevant genes (including RGS10, GBP4, TREML2, and RELT) and provide important new omics data for understanding the host response to mycobacterial infections that cause tuberculosis in mammals.

overall_design: Peripheral blood RNA-seq was extracted from a cohort of control and bovine tuberculosis (bTB) reactor animals to conduct a differential expression, expression quantitative trait loci and transcriptome wide association study to identify differentially expressed genes between the two groups, to characterise genomic variants associated with variability in mRNA transcript abundance and to identify genes with expression patterns correlated with bTB infection

first: John

first: Gillian

middle: P

last: McHugo

first: James

last: Ward

first: Thomas

last: Hall

first: Sarah

last: Faherty O'Donnell

first: Carolina

last: Correia

last: Browne

first: Michael

last: McDonald

first: Eamonn

last: Gormley

first: Valentina

last: Riggio

middle: G

last: Prendergast

first: Emily

last: Clark

first: Hubert

last: Pausch

first: Kieran

last: Meade

first: Isobel

middle: C

first: Stephen

middle: V

last: Gordon

first: David

last: MacHugh


title: Radiation and anti-PD-L1 synergize by stimulating a stem-like T cell population in the tumor-draining lymph node [scRNA-Seq]

status: Public on Feb 22 2024

city: atlanta

first: zach

last: Buchwald

state: ga

address: 1365 Clifton Rd NE Building C

institute: Winship Cancer Institute of Emory University

summary: Radiotherapy (RT) and anti-PD-L1 synergize to enhance local and distant (abscopal) tumor control. However, clinical results in humans have been variable. With the goal of improving clinical outcomes, we investigated the underlying synergistic mechanism focusing on a TCF-1+ PD-1+ CD8+ stem-like T cell subset in the tumor-draining lymph node (TdLN). We found that RT + anti-PD-L1 induces a novel differentiation program in the TdLN stem-like population which leads to their expansion and differentiation into effector cells within the tumor. We also found that optimal synergy between RT + anti-PD-L1 is dependent on the TdLN stem-like T cell population as either blockade of TdLN egress or specific stem-like T cell depletion reduced tumor control. Together, these data demonstrate a multistep stimulation of stem-like T cells following combination therapy which is initiated in the TdLN and completed in the tumor.

overall_design: single cell RNA seq on sorted CD8+ PD-1+ T cells 7 days after treatment with anti-PD-L1, RT alone or combination therapy

first: Zach

first: Yang

last: Shen

first: Erin

last: Connolly


title: Transcriptomic profiling of esophageal epithelium reveals enrichment of IFN-γ response gene signature during active EoE.

first: Megha

last: Lal

summary: Eosinophilic esophagitis (EoE) is a chronic, allergic inflammatory disease of the esophageal mucosa. Although type 2 cytokines are predominant, targeting type 2 inflammation alone is not always effective for all patients. In EoE patients, the transcriptional profiling of esophageal biopsy reveals upregulation of type I and II interferon (IFN) response, dysregulated immune signaling, and downregulation of esophageal-specific genes. However, further investigation is needed to examine the gene expression changes in esophageal epithelium because it plays an important role in EoE. To investigate the upregulation of Interferon Stimulated Genes (ISGs) in EoE esophageal epithelium, we isolated epithelial cells from active EoE patients and non-EoE controls. We performed bulk RNA sequencing to analyze the epithelial-specific transcriptome in EoE. Unsupervised hierarchical clustering of the most variable genes differentiated the active EoE biopsies from non-EoE controls. Gene set enrichment analysis identified IFN-γ response as the most significant upregulated pathway.

overall_design: Comparative profiling of epithelial-specific transcriptome in EoE active and non-EoE controls.

first: Melanie

last: Ruffner


title: Removing an acid residue is necessary and sufficient to turn SOX17 into a pluripotency factor

status: Public on Feb 10 2024

city: Hong Kong

first: Sik Yin

last: Ho

address: Laboratory Block, 21 Sassoon Block

country: Hong Kong

institute: The University of Hong Kong

summary: SOX17 directs the differentiation of the extraembryonic endoderm and acts as a human germline specifier. The replacement of an acidic residue at position 57 with a basic residue found in SOX2 turns SOX17 into a pluripotency factor. Here we systematically interrogated how mutations at this critical position affect the cellular reprogramming activity of SOX17. We found that most mutations turn SOX17 into a pluripotency factor regardless of their biophysical properties. The mutation to an aspartate allows the SOX17E57D protein to maintain a self-renewing endodermal state. Only the glutamate found in the wild-type protein can effectively block a SOX17/OCT4 dimer from binding composite DNA elements found in pluripotency enhancers. Insights into how modifications of an ultra-conserved residue affect functions of developmental transcription factor provide avenues to advance cell fate engineering.

overall_design: To investigate the effects SOX17E57 variants have on maintaining pluripotency, SOX2 or the SOX17E57 variants were introduced into engineered Tet-Off Sox2 mESCs (also known as the 2TS22C cell line) using lentiviruses. Cells were cultured in mouse serum/LIF/2i medium for ten passages prior to analysis.

first: SikYin

first: Ralf

last: Jauch


title: Sf3b4 mutation in Xenopus tropicalis causes RNA splicing defects and gene dysregulation across development and disrupts cranial neural crest cell migration and survival

city: New York

first: Ziyan

last: Lin

state: NY

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

summary: Nager syndrome is a rare craniofacial and limb disorder characterized by midface retrusion, micrognathia, absent thumbs, and radial hypoplasia. This disorder results from haploinsufficiency of SF3B4 (splicing factor 3b, subunit 4) a component of the pre-mRNA spliceosomal machinery. The spliceosome is a complex of RNA and proteins that function together to remove introns and join exons from transcribed pre-mRNA. While the spliceosome is present and functions in all cells of the body, most spliceosomopathies – including Nager syndrome – are cell/tissue-specific in their pathology. In Nager syndrome patients, it is the neural crest (NC)-derived craniofacial skeletal structures that are primarily affected. To understand the pathomechanism underlying this condition, we generated a Xenopus tropicalis sf3b4 mutant line using the CRISPR/Cas9 gene editing technology. Here we describe the sf3b4 mutant phenotype at neurula, tail bud, and tadpole stages, and performed temporal RNA-sequencing analysis to characterize the splicing events and transcriptional changes underlying this phenotype. Our data show that while loss of one copy of sf3b4 is largely inconsequential in Xenopus tropicalis, homozygous deletion of sf3b4 causes major splicing defects and gene dysregulation, which disrupt cranial NC cell migration and survival, thereby pointing at an essential role of Sf3b4 in craniofacial development.

overall_design: Bulk RNA seq analysis of wildtype, heterozygous, and homozygous null sf3b4 mutant Xenopus tropicali embryos from stages 15, 25, and 35.

first: Casey

last: Griffin

first: Kelsey

last: Coppenrath

first: Doha

last: Khan

first: Hugo

last: Juraver-Geslin

first: Marko

last: Horb

first: Jean-Pierre

last: Saint-Jeannet


title: Notochord and axial progenitor generation by timely BMP and NODAL inhibition during vertebrate trunk formation (human 3D)

status: Public on Feb 14 2024

city: London

first: Tiago

last: Rito

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

summary: The formation of the vertebrate body is driven by the progressive and coordinated production of trunk tissues from pools of progenitors located in the posterior of the embryo. Aspects of this process are recapitulated by in vitro models based on pluripotent stem cells (PSCs). However, these models lack several tissue components normally found in the vertebrate trunk. Most strikingly, the notochord, a hallmark of chordates and the source of midline signals that pattern surrounding tissues, is absent from current models of human trunk formation. To investigate how trunk tissue is formed, we performed single-cell transcriptomic analysis of chick embryos. This delineated molecularly discrete progenitor populations, which we spatially locate in the embryo and relate to signalling activity. Guided by this map, we determined how a stereotypical spatial organization of tissue types arises in differentiating human PSCs. This involved LATS1/2 mediated repression of YAP activity facilitating WNT signalling, that, together with FGF mediated ERK1/2 activation, induces the transcription factor Bra/TBXT. In addition, timely inhibition of a WNT-induced NODAL and BMP signalling cascade regulates the proportions of different tissue types produced, including notochordal cells. We exploit this to develop an integrated 3D model of human notochord and neural tissue formation. Together the data provide insight into the mechanisms responsible for the formation of the tissues that comprise the vertebrate trunk and pave the way for future studies of patterning in a tissue-like environment.

overall_design: To investigate trunk tissue formation, we developed a 3D in vitro assay using the human embryonic stem cell line H9 on low-bind 96 well plates. The protocol employs WNT(CHIR) + FGF together with timed BMP and NODAL inhibition (at 18h, 24h, 30h post-induction) for the first 3 days following four days with a RA precursor. Samples represent different days and inhibition delays. Cells of all conditions were dissociated and the transcriptome of single cells analysed using the 10X Genomics platform (Single Cell 3′ v3.1).

first: Ashley

last: Libby

first: Maddy

last: Demuth

first: Marie-Charlotte

last: Domart

first: Jake

last: Cornwall-Scoones

first: James

last: Briscoe


title: rna-seq snap33-1 vs wt -Description of Arabidopsis thaliana t-SNARE SNAP33

status: Public on Jan 29 2024

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

institute: INRAE

summary: ngs2021_03_snap33-rna-seq snap33-1 vs wt -What molecular pathways (transcripts) contribute to the phenotype of the snap33 loss-of-function mutant-comparing snap33 mutant to the WT out-segregating line in normal growth conditions at 5 and 12 days (before and after the appearance of the phenotype of the mutant snap33

overall_design: 12 samples with 3 biological replicats. gene knock out,genotype comparison,time course

first: José

last: Caius

first: Jean

last: Bigeard

first: Houda

last: Henchiri


title: Differential unfolded protein response regulation in KRAS silencing sensitive versus innately resistant colorectal cancer cells [LS174T]

status: Public on Feb 06 2024

city: Porto

first: Flávia

middle: Oliveira

last: Martins

address: Rua Alfredo Allen, 208

country: Portugal

summary: Colorectal cancer (CRC) responses to mutant-selective KRAS inhibitors remain modest, with stable disease and rapid recurrence as the most common outcomes. The molecular mechanisms enabling CRC cells to tolerate KRAS inhibition and ultimately develop resistance remain poorly understood. Here, we investigated early transcriptional and proteomic responses to KRAS silencing in 3D CRC cell line spheroid models, aiming to identify pathways associated with sensitivity or resistance to KRAS blockade. Cell lines were stratified into KRAS silencing-sensitive (HCT116 and SW480) and -resistant (LS174T and SW837) groups based on spheroid growth, cell cycle progression, and apoptosis induction. Transcriptional profiling revealed the unfolded protein response (UPR) and WNT/β-catenin signaling as pathways specifically upregulated in KRAS silencing-sensitive cells and downregulated in resistant cells. Proteomic analysis of membrane-enriched fractions further supported UPR deregulation, showing a pronounced downregulation of translation-related proteins in sensitive cells. Functional assays validated that the sensitive cell line HCT116 exhibits reduced protein aggregation and lower translational capacity upon KRAS knockdown, consistent with UPR activation. Pharmacological inhibition of IRE1α-mediated UPR signaling did not revert KRAS silencing-induced cell cycle arrest or apoptosis in this cell line. Collectively, our results highlight the UPR activation as an early adaptive response of KRAS-dependent CRC cells tolerant to KRAS silencing.

overall_design: To investigate the effect of KRAS inhibition in colorectal cancer cell lines, we used 4 different KRAS mutant colorectal cancer cell lines (HCT116, LS174T, SW480 and SW837). We then silenced cells using siRNA and performed gene expression profilling analysis using data obtained from RNA-seq of the different cell lines from silenced cells (siKRAS) or its control (siControl).

first: Ana

last: Machado

first: Catarina

last: Almeida

first: Joana

last: Carvalho

first: Hans

last: Beck

first: Vadim

last: Backman

first: Rune

last: Matthiesen

first: Sérgia

last: Velho


title: Transcriptomic profile of bulk C. elegans population over time

city: St. Louis

first: Matthew

last: Mosley

state: MO

address: 660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University in St. Louis School of Medicine

summary: In order to understand age-associated changes in the transcriptome, we quantified the average gene expression profile of C. elegans nematodes at days 1-12 of life. Because of the high temporal resolution at which data was collected, these data can be used as a ground truth measurement for the transcriptomic determination of physiological age.

overall_design: C. elegans were synchronized by hypochlorite treatment aftter which synchronized L1 larvae were distributed across 12 NGM plates seeded with a standard E. coli OP50 lawn. RNA was then collected from one plate every 24 hours through day 12. This was repeated 3 times for a total of 2-3 replicates per time point. To prevent the appearance of progeny, we used a strain of C. elegans carrying a temperature sensative mutation in the spermatogenesis gene spe-9 (hc88), and animals were kept at the restrictive temperature of 25 degrees C.

first: Mosley

last: Matthew

first: Pincus

last: Zachary


title: High-content phenotypic analysis defines generalizable genetic and molecular regulators of lifespan in a C. elegans recombinant inbred population

status: Public on Feb 07 2024

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

institute: École polytechnique fédérale de Lausanne

summary: Background and Aims: Lifespan is influenced by complex interactions between genetic and environmental factors. Limitations in studying those factors in model organisms of a single genetic background hinder translational value. Here, we mapped genetic determinants of lifespans in 85 C. elegans recombinant intercross advanced inbred lines (RIAILs). We assessed molecular profiles – transcriptome, proteome, and lipidome – and life-history traits (lifespan), development, growth dynamics, and reproduction.

overall_design: Total RNA samples were extracted from 85 RIAILs and two parental strains (N2 and CB4856) and subjected to RNA seq.

first: Arwen

last: Gao

first: Johan

last: Auwerx


title: Cryptochrome 1 attenuates plant heat stress response by light-heat stress response signal pathways crosstalk in Arabidopsis

city: FuZhou

first: Jing

last: Zhang

state: Fujian Province

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

summary: Plants regulate growth and development in different  ambient environments through light signaling pathways and heat stress signaling pathways, both of which are very important for plant adaptation to the environment, but whether there is an interaction between the two is still unclear. In this article, we reported that the blue light receptor Cryptochrome CRY1 phosphorylation will be inhibited under high temperature stress, and CRY1 activity will decrease; at this time, CRY1 could not interact with E3 ubiquitin ligase COP1(CONSTITUTIVELY PHOTOMORPHOGENIC 1) and COP1 activity increased. Its substrate HY5(ELONGATED HYPOCOTYL 5）is continuously degraded under heat stress. Through further transcriptome analysis, we found that the substrates of HY5 have a class of HSFAs（HEAT SHOCK FACTOR）HSFA2/HSFA7As/HSFA7Bs transcription factors, which are rapidly induced under heat stress conditions and activate downstream HSPs (HEAT SHOCK PROTEIN)expression.Under normal conditions, HY5 protein inhibits HSFA2/HSFA7As/HSFA7Bs. Under heat stress, HY5 protein is degraded, which releases the expression of HSFAs, thereby enhancing plant heat tolerance. In this paper, we put forward the hypothesis that the phosphorylation of CRY1 seems to be a switch in the ambient environment , and through the regulation of phosphorylation level, the light and heat stress signal are transmitted downward, forming an light-heat signal interactive regulation pathway to regulate the growth and development of plants.

overall_design: WT and cry1 mutant were grown under continuous light at 22°C for 7 days and then transferred to blue light for 1 day. Then part of them was transferred to 44°C blue light for heat treatment, and part continued to grow at 22°C. Samples were taken for RNA-seq after 2 hours.

first: Siyuan

last: Liu

first: Guifang

last: Lin

first: Qin

last: Wang


title: Single-cell transcriptional landscape of human knee cartilage in patients with OA and non-OA controls

status: Public on Feb 25 2024

city: Xi'an

first: Yue

last: Fan

address: Yanta West Road No.76

institute: Xi'an Jiaotong University

summary: Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations.

overall_design: 19 cartilage samples from 8 OA donors, and 3 non-OA control donors

first: Xuzhao

last: Bian

first: Shiquan

last: Sun


title: TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors

city: Freiburg im Breisgau

first: Tanja

last: Bhuiyan

address: Albertstrasse 25

department: Institute of Experimental and Clinical Pharmacology and Toxicology

institute: University of Freiburg

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

overall_design: Refer to individual Series

first: Niccolò

last: Arecco

first: Paulina

middle: K

last: Mendoza Sanchez

first: Juhyeong

last: Kim

first: Carsten

last: Schwan

first: Sophie

last: Weyrauch

first: Sheikh

last: Nizamuddin

first: Andrea

last: Prunotto

first: Mehmet

last: Tekman

first: Martin

last: Biniossek

first: Bettina

last: Knapp

first: Stefanie

last: Koidl

first: Friedel

last: Drepper

first: Pitter

last: Huesgen

first: Robert

last: Grosse

first: Thorsten

last: Hugel

first: Sebastian

last: Arnold


title: Differential unfolded protein response regulation in KRAS silencing sensitive versus innately resistant colorectal cancer cells [HCT116]

first: Flávia

last: Martins

first: Ana

last: Machado

first: Catarina

last: Almeida

first: Joana

last: Carvalho

first: Hans

last: Beck

first: Vadim

last: Backman

first: Rune

last: Matthiesen

first: Sérgia

last: Velho


title: Integrative Transcriptomic Analysis Identifies Emetine as A Promising Drug Candidate for Overcoming Acquired Resistance to ALK Inhibitors in Lung Cancer

status: Public on Jan 09 2024

city: Busan

first: Haeseung

last: Lee

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

department: College of Pharmacy

institute: Pusan National University

summary: Anaplastic lymphoma kinase (ALK) inhibitors (ALKi) are effective in treating lung cancer patients with chromosomal rearrangement of ALK. However, continuous treatment with ALKi invariably leads to acquired resistance in cancer cells. In this study, we propose an efficient strategy to suppress ALKi resistance through a meta-analysis of transcriptome data from various cell models of acquired resistance to ALKi. We systematically identified gene signatures that consistently showed altered expression during the development of resistance and conducted computational drug screening using these signatures. We identified emetine as a promising candidate compound to inhibit the growth of ALKi-resistant cells. We demonstrated that this drug exhibited effectiveness in inhibiting the growth of ALKi-resistant cells, and further elucidated its mode of action through drug-induced RNA-seq data. Our transcriptome-guided systematic approach paves the way for efficient drug discovery to overcome acquired resistance to cancer therapy.

overall_design: To investigate whether the inhibitory effects of emetine on H3122-LR cell growth are associated with the resistant signature, we generated RNA-seq data of H3122-LR cells treated with DMSO or emetine.

first: Mirang

last: Kim

first: Keeok

last: Haam


title: scRNAseq of mouse CD45- C3 positive and negative cells at peak of EAE

status: Public on Feb 01 2024

city: Baltimore

first: Matthew

middle: D

last: Smith

state: MD

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

summary: We performed scRNAseq analysis of CD45- cells sorted from murine brains on the presence or absence of a fluorescent reporter for complement component C3 at peak of experimental autoimmune encephalomyelitis to study the non-immune cellular sources of C3

overall_design: 3' scRNAseq of CD45-;C3-reporter+ (Pos) and CD45-;C3-reporter- (Neg) of mouse brains at peak EAE (D19 post-immunization). Both positive and negative are from same pool of mice.

first: Thomas

last: Garton

first: Elia

last: Afanasiev

first: Adam

last: Groh

first: Jo Ann

last: Stratton

first: Peter

middle: A

last: Calabresi


title: Znf687 recruits Brd4-Smrt complex  to regulate gfi1aa expression   during neutrophil development

city: Shanghai

first: Shuiyi

last: Tan

address: 197 Rui-Jin Road II, Shanghai, China

institute: CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics

summary: Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well-coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia, neutrophilia, and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage-specific transcription factor, whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically, Znf687 functions as a negative regulator of gfi1aa, a pivotal modulator in terminal granulopoiesis, to regulate neutrophil maturation. Moreover, we found BRD4, an important epigenetic regulator, interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator, Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene’s promoter to exert transcription repression. Overall, our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis, but also provides new insights into the role of the two crucial regulators in transcriptional repression.

overall_design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing (RNA-seq) analyses were conducted in the remaining mpx+ cells isolated from Tg(mpx:eGFP) and znf687a MO injected Tg(mpx:eGFP) larvae at 48 hpf.

first: Lin

last: Yan


title: TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors [RNA-Seq]

first: Tanja

last: Bhuiyan

summary: TFIID is an essential basal transcription factor, crucial for RNA polymerase II (pol II) promoter recognition and transcription initiation. The TFIID complex consists of the TATA binding protein (TBP) and 13 TBP-associated factors (TAFs) that contain intrinsically disordered regions (IDRs) with currently unknown functions. Here, we show that a conserved IDR drives TAF2 to nuclear speckle condensates independently of other TFIID subunits. Quantitative mass spectrometry analyses reveal TAF2 proximity to RNA splicing factors including specific interactions of the TAF2 IDR with SRRM2 in nuclear speckles. Deleting the IDR from TAF2 does not majorly impact global gene expression but results in changes of alternative splicing events. Further, genome-wide binding analyses suggest that the TAF2 IDR impedes TAF2 promoter association by guiding TAF2 to nuclear speckles. This study demonstrates that an IDR within the large multiprotein complex TFIID controls nuclear compartmentalization and thus links distinct molecular processes, namely transcription initiation and RNA splicing.

overall_design: To investigate gene expression changes and alternative splicing events of GFP-NLS-TAF2deltaIDR and GFP-TAF2 expressing cells, we performed RNA sequencing (RNA-seq). HeLa Flp-In T-Rex cells harboring a transgene under the control of a doxycycline-inducible promoter were used to express GFP-NLS-TAF2deltaIDR and GFP-TAF2 with 1 ug/mL doxycycline for 17.5 h. Control cells without transgene were also induced with 1 ug/mL doxycycline. The experiment was performed as technical triplicate.

first: Niccolò

last: Arecco

first: Paulina

last: Mendoza Sanchez

first: Juhyeong

first: Carsten

last: Schwan

first: Sophie

last: Weyrauch

first: Sheikh

last: Nizamuddin

first: Andrea

last: Prunotto

first: Mehmet

last: Tekman

first: Martin

last: Biniossek

first: Bettina

last: Knapp

first: Stefanie

last: Koidl

first: Friedel

last: Drepper

first: Pitter

last: Huesgen

first: Robert

last: Grosse

first: Thorsten

last: Hugel

first: Sebastian

last: Arnold


title: Comparative analysis of gene expression in control and Zic3 knockdown mESCs differentiated to neurons

status: Public on Jan 05 2024

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To determine the effct of Zic3 knockdown on the neural differentiation profile of mESCs

overall_design: Agilent one-color experiment,Organism: Mouse Agilent Microarray Gene Expression 8x60K Arrays AMADID: 028005

first: Smitha

last: Bhaskar

first: Anujith

last: Kumar


title: TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors [CUT&RUN]

first: Tanja

last: Bhuiyan

overall_design: Cleavage under targets and release using nuclease (CUT&RUN) and greenCUT&RUN followed by DNA sequencing for TFIID subunits TAF1, TAF2, TAF7, TBP and RNA polymerase II subunit RPB1 (CUT&RUN) and for GFP-TAF2, GFP-NLS-TAF2, GFP-NLS-TAF2delta1009-1199 (2 replicates), GFP-NLS-TAF2delta1142-1171 (2 replicates) (greenCUT&RUN). Each CUT&RUN sample has a respective IgG control sample. Each greenCUT&RUN sample has a respective control sample (-Ca2+). All libraries contain spike-in DNA from Drosophila melanogaster. HeLa Flp-In T-Rex cells harboring a transgene under the control of a doxycycline-inducible promoter were used. Protein expression was induced with 1 ug/mL doxycycline where appropriate.

first: Niccolò

last: Arecco

first: Paulina

last: Mendoza Sanchez

first: Juhyeong

last: Kim


title: Universal STING Mimic Boosts Antitumour Immunity via Preferential Activation of Tumour Control Signalling Pathways

status: Public on Jan 22 2024

city: Chapel Hill

first: Ying

last: Wang

state: NC

address: 125 Mason Farm Road, 3118G Marsico Hall, Marsico Hall/3118G/3nd

institute: University of North Carolina at Chapel Hill

summary: The efficacy of stimulator of interferon genes (STING) agonists is compromised by various factors, primarily inefficient intracellular delivery, low/lack of endogenous STING expression in many tumours and a complex balance between tumour control and progression. Here, we report a universal STING mimic (uniSTING) based on a polymeric architecture. The uniSTING activates STING signalling in a range of mouse and human cell types, independent of endogenous STING expression, and selectively stimulates tumour control IRF3/IFN-I pathways, but not tumour progression NF-κB pathways. Intratumoural or systemic injection of uniSTING-mRNA via lipid nanoparticles (LNP) results in potent anti-tumour efficacy across established and advanced metastatic tumour models, including triple negative breast cancer, lung cancer, melanoma and orthotopic/metastatic liver malignancies. Furthermore, uniSTING displays an effective antitumour response superior to 2’3’-cGAMP and ADU-S100. By favouring IRF3/IFN-I activity over the pro-inflammatory NF-κB signalling pathway, uniSTING promotes dendritic cell maturation and antigen specific CD8+ T cell responses. Extracellular vesicles released from uniSTING-treated tumour cells further sensitise dendritic cells via exosome containing miRNAs that reduced the immunosuppressive Wnt2b and a combination of LNP-uniSTING-mRNA with α-Wnt2b antibodies synergistically inhibit tumour growth and prolong animal survival. Collectively, these results demonstrate the LNP-mediated delivery of uniSTING-mRNA as a strategy to overcome the current STING therapeutic barriers, particularly for the treatment of multiple cancer types in which STING is downregulated or absent.

overall_design: To investigate the function of uniSTING in the regulation of Type I IFN signaling pathways, we performed RNA-seq on DC2.4 cells and 4T1 tumor cells post treatments with either uniSTING mRNA or Mock (EGFP) mRNA. Moreover, the uniSTING’s effect on downstream pathways in an unbiased fashion was also examined on 4T1 tumor cells. The gene expression profiling analysis was performed using the RNA-seq data of DC2.4 cells and 4T1 tumor cells after indicated treatments above. To further delineate the genes in DC2.4 cells that were regulated by the miRNAs in EXOuniSTING, we conducted RNA-seq of EXOuniSTING or EXOmock-treated DC2.4 cells.

first: Sirui

last: Li

first: Mengying

last: Hu

first: Yuchen

last: Yang

first: Jenny

last: Ting

first: Rihe

last: Liu


title: Super-enhancers require enhancers and facilitators to fully activate gene expression [Tiled-C]

status: Public on Dec 31 2023

city: Oxford

first: Mira

last: Kassouf

state: Oxfordshire

address: John Radcliffe Hospital

institute: Weatherall Institute of Molecular Medicine

summary: Super-enhancers are compound regulatory elements which control expression of key cell-identity genes. They recruit high levels of tissue-specific transcription factors, co-activators such as the mediator complex, and they contact their target gene promoters with high frequency. Most super-enhancers contain multiple constituent regulatory elements, but it is unclear whether these elements have distinct roles in activating expression of their cognate genes. Here, through comprehensively rebuilding the endogenous α-globin super-enhancer, we show that super-enhancers comprise bioinformatically equivalent but functionally distinct element types: classical enhancers and facilitator elements. Facilitators have no intrinsic enhancer activity, yet in their absence, classical enhancers are unable to fully up-regulate their target genes. Without facilitators, classical enhancers exhibit reduced mediator recruitment, enhancer RNA transcription and enhancer-promoter interactions. Facilitators are interchangeable, but display functional hierarchy based on their position within a super-enhancer. Facilitators thus play an important role in potentiating super-enhancer activity and ensuring robust activation of target genes.

overall_design: Characterisation of a mouse model lacking four out of the five alpha-globin super-enhancer constituents demonstrates that super-enhancer constituents rely on each other to achieve maximal target gene activation. Furthermore, the strongest alpha-globin super-enhancer constituent requires the other four constituents (or a subset thereof) for maximal enhancer-promoter interaction frequency, coactivator recruitment and eRNA expression. Rebuilding the alpha-globin super-enhancer further demonstrates the cooperation between its constituents. The super-enhancer is made up of two functionally distinct element types: active enhancers, and facilitators. Facilitators have little or no ability to activate gene expression directly, but they potentiate the activity of enhancers within the same cluster.

first: Joseph

last: Blayney


title: Super-enhancers require enhancers and facilitators to fully activate gene expression [ChIP-seq]

first: Rosa

last: Stolper


title: responses of maize to the arbuscular fungus rhizophagus irregularis mitigate n deficiency stress-Physiological and molecular responses of maize to the arbuscular mycorrhizla fungus 5AMF) Rhizophagus irregularis mitigate nitrogen deficiency stress.

status: Public on Dec 13 2023

first: Véronique

last: BRUNAUD

summary: ngs2021_19_rhizophagus-responses of maize to the arbuscular fungus rhizophagus irregularis mitigate n deficiency stress-What is the impact of Rhizophagus irregularis on maize transcriptome under different N nutrition conditions, what is the impact of N on R. irregularis transcriptome in maize roots.-After 4 days of germination, maize seeds were sown in pots filled with sterile mix 1:1 clay beads:unfertilized peat. Inoculation performed in 3 times with Rhizohphagus irregularis spores purchased at Agronutrition. First inoculation perfomed with 500 spores/plant at sowing. Two other incoulations performed the following week and 2 weeks later with 100 spore per plant each.

overall_design: 48 samples with 3 biological replicats. fungal gene expression in roots,dose response,genotype comparison

first: Alia

last: Dellagi

first: Alexandra

last: Avon-Launay

first: Etienne

last: Delannoy


title: The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction [WGS]

status: Public on Dec 12 2023

city: Cold Spring Harbor

first: Robert

last: Martienssen

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

summary: The Lemnaceae (duckweeds) are the world’s smallest but fastest growing flowering plants, with a drastically reduced morphology and predominant clonal reproductive habit capable of continuous exponential growth. Here, we present assemblies of 10 Lemna chromosome sets by single molecule nanopore sequencing and chromosome conformation capture. Dynamics of genome evolution in the family are revealed by syntenic comparisons with Wolffia and Spirodela, and diversification of these genera was found to coincide with the “Azolla event”, in which blooms of aquatic macrophytes reduced atmospheric CO2 from greenhouse levels found in the Eocene to those of the current ice age. Orthologous gene comparisons with other aquatic and terrestrial plants uncovered candidate genes for the unique metabolic and developmental features of the family, such as frequent hybrid polyploidy, lack of stomatal closure in high CO2, and accumulation of calcium oxalate, a promising candidate for carbon sequestration. Loss of a spermine-triggered gene network accounts for drastic reduction in stature and preferentially adaxial stomata, a feature of floating aquatic plants. Strikingly, Lemnaceae genomes have selectively lost some of the genes required for RNA interference, including Argonaute genes required for post-zygotic reproductive isolation (the triploid block) and reduced gamete formation. Triploid hybrids arise commonly among Lemna, presumably by hybridization with unreduced gametes, and we have found mutations in highly-conserved ZMM crossover pathway genes that could support polyploid meiosis. Rapid but stable clonal propagation makes Lemna an ideal platform for protein and starch micro-cropping, and for sequestration of dissolved nutrients and atmospheric CO2. Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makes Lemna a powerful biotechnological platform, as exemplified by our recent engineering of high-oil Lemna lines that out-perform with oil seed crops.

sample_organism:
Lemna gibba
Lemna minor
Lemna japonica
Lemna turionifera
Wolffia australiana

overall_design: Whole genome sequencing of 8 Lemnaceae accessions.

first: Evan

last: Ernst

first: Kenneth

last: Acosta

first: Nolan

last: Hartwick

first: Cristian

last: Mateo-Elizalde

first: Buntora

last: Pasaribu

first: Bradley

last: Abramson

first: Kelly

last: Colt

first: Anthony

last: Aylward

first: Umamaheswari

last: Ramu

first: James

last: Birchler

first: Eric

last: Lam

first: Todd

last: Michael


title: Super-enhancers require enhancers and facilitators to fully activate gene expression [ATAC-seq]

first: Mira

last: Kassouf

first: Joseph

last: Blayney

first: Helena

last: Francis

first: Rosa

last: Stolper


title: Super-enhancers require enhancers and facilitators to fully activate gene expression


title: Super-enhancers require enhancers and facilitators to fully activate gene expression [RNA-seq]


title: Consequences of chromatin replication on RNAPII activity and transcriptional outcome

status: Public on Dec 26 2023

city: Seville

first: Cristina

last: González-Aguilera

state: Seville

address: Avenida Américo Vespucio, 24

country: Spain

institute: CABIMER - CSIC


title: The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction

first: Robert

last: Martienssen

sample_organism:
Lemna gibba
Lemna minor
Spirodela polyrhiza
Lemna japonica
Lemna turionifera
Wolffia australiana


title: The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction [RNA-Seq]

sample_organism:
Lemna gibba
Lemna japonica

platform_organism:
Lemna gibba
Lemna japonica

overall_design: Small RNA-seq of 4 Lemnaceae accessions

first: Evan

last: Ernst

first: Kenneth

last: Acosta


title: Systems-based identification of the Hippo pathway for promoting fibrotic mesenchymal differentiation in systemic sclerosis

status: Public on Dec 06 2023

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Systemic sclerosis (SSc) is a devastating autoimmune disease characterized by excessive production and accumulation of extracellular matrix, leading to fibrosis of skin and other internal organs. However, the main cellular participants in SSc skin fibrosis remain incompletely understood. Here using differentiation trajectories at a single cell level, we demonstrate a dual source of extracellular matrix deposition in SSc skin from both myofibroblasts and endothelial-to-mesenchymal-transitioning cells (EndoMT).  We further define a central role of Hippo pathway effectors in differentiation and homeostasis of myofibroblast and EndoMT, respectively, and show that myofibroblasts and EndoMTs act as central communication hubs that drive key pro-fibrotic signaling pathways in SSc. Together, our data help characterize myofibroblast differentiation and EndoMT phenotypes in SSc skin, and hint that modulation of the Hippo pathway may contribute in reversing the pro-fibrotic phenotypes in myofibroblasts and EndoMTs.

overall_design: Single cell RNA sequencing and spatial sequencing on human scleroderma skin tissues

first: Johann

last: Gudjonsson


title: The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction [smallRNA-Seq]

sample_organism:
Lemna gibba
Spirodela polyrhiza
Lemna japonica
Wolffia australiana

first: Nolan

last: Hartwick

first: Cristian

last: Mateo-Elizalde

first: Buntora

last: Pasaribu

first: Bradley

last: Abramson


title: The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction [WGBS]

platform_organism:
Lemna gibba
Spirodela polyrhiza
Lemna japonica
Wolffia australiana

overall_design: Whole genome bisulfite sequencing of 4 Lemnaceae accessions

first: Kelly

last: Colt

first: Anthony

last: Aylward

first: Umamaheswari

last: Ramu

first: James

last: Birchler


title: Temporally-coordinated bivalent histone modifications of BCG1 enable fungal invasion and immune evasion

status: Public on Dec 04 2023

city: Hefei

first: zhao

middle: xiao

last: zhen

address: Anhui Agricultural University, 130 Changjiangxilu, Shushan District, Hefei, Anhui Province, China

institute: Anhui Agricultural University

summary:
Bivalent histone modifications, including functionally opposite H3K4me3 and H3K27me3 marks simultaneously on the same nucleosome, control various cellular processes by fine-tuning the gene expression in eukaryotes. However, the role of bivalent histone modifications in fungal virulence remains elusive. Here, we report that bivalent chromatin modification of BCG1 (bivalent chromatin-marked gene1) is critical for Fusarium graminearum (Fg) successfully invading the host plant. By mapping the genome-wide landscape of H3K4me3 and H3K27me3 dynamic modifications in Fg during invasion, we identified the infection-related bivalent chromatin-marked genes (BCGs). BCG1, which encodes a xylanase containing a novel G/Q-rich motif, possessed the highest bivalent modification. We showed that the G/Q-rich motif of BCG1 is required for its xylanase activity and is essential for the full virulence of Fg. Intriguingly, this G/Q-rich motif can be recognized by pattern-recognition receptors (PRRs) to trigger plant immunity. Therefore, Fg tightly regulates BCG1 expression during different infection stages. During initial infection stages, Fg employs H3K4me3 modification to induce BCG1 expression required for host cell wall degradation. Upon breaching the cell wall barrier, this active chromatin state was reset to bivalency by co-modifying with H3K27me3, which enables epigenetic silencing of BCG1 to escape from host immune surveillance. Collectively, our study highlights how fungal pathogens deploy bivalent epigenetic modification to achieve temporally-coordinated activation and suppression of a critical fungal gene, thereby facilitating successful infection and host immunity evasion.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Triticum aestivum
Fusarium graminearum PH-1

overall_design:
It was proved by ChIP-seq data and sequential ChIPd ata that modulation of BCG1 expression dynamics by bivalent histone methylations enables fungal pathogen to evade host immunity.

Refer to individual Series


title: ideas-IDEAS project on nitrogen starvation

status: Public on Dec 01 2023

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

summary: ngs2020_20_ideas-ideas- whole genome (nuclear and organellar) transcriptomic response to a moderate nitrogen starvation-In the IDEAS project, Arabidopsis thaliana Col0 plants were grown on soil from seed for 19 days on the Phenoscope (IJPB, Versailles). The plants were watered with nitrogen-sufficient or nitrogen-limiting solutions. 10 biological replicates were produced. For each sample, 3 rosettes were pooled to extract RNA. The libraries were generated with the Illumina Truseq stranded with ribozero plant leaf and sequenced on a NextSeq500 in single-end 75 bases.

overall_design: 20 samples with 5 biological replicats. treated vs untreated comparison

first: Alex-avon

last: Alaunay

first: Etienne

last: Delannoy

first: Catherine

last: Rameau

first: GUILLEM

last: Rigaill


title: The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction [Hi-C]

first: Robert

last: Martienssen

platform_organism:
Lemna gibba
Lemna minor
Lemna japonica
Lemna turionifera
Wolffia australiana

overall_design: Hi-C sequencing of 5 Lemnaceae accessions

first: Evan

last: Ernst

first: Kenneth

last: Acosta

first: Eric

last: Lam

first: Todd

last: Michael


title: Bivalent histone modification of BCG1 enables fungal pathogen to evade host immunity (RNA-Seq)

summary: Bivalent chromatin modification containing opposing H3K4me3 and H3K27me3 marks controls various biological processes by fine-tuning gene expression in animals and plants, however how this bivalent modification regulates pathogenicity of fungal pathogen remains exclusive. Here, we provided a genome-wide landscape of H3K4me3 and H3K27me3 of wheat head blight fungus Fusarium graminearum (Fg), leading to the identification of infection-induced bivalent chromatin-marked genes (BCGs). Among those, BCG1, which encodes a novel xylanase with a G/Q rich motif, is required for the full virulence of Fg pathogenicity through degradation of host cell wall. However, the G/Q rich motif is recognized by pattern-recognition receptors and triggers plant innate immunity. Further data illustrates that Fg employs H3K4me3 modification to induce BCG1 expression rapidly during the early infection, and then switches to bivalent H3K4me3-H3K27me3 chromatin state that renders rapid epigenetic silencing of BCG1 for escaping from host immune monitor, therefore leading to the successful invasion. Collectively, our study highlights the molecular mechanism of how fungal pathogen employs bivalent epigenetic modification to facilitate the successful infection by escaping of host immunity, which provides conceptual insights into plant-microbe interaction.

platform_organism:
Triticum aestivum
Fusarium graminearum PH-1

overall_design: Comparative gene expression of RNA-seq data for Wild type PH-1at different hour post-infection .

first: Qin

last: Gu

first: Xiaozhen

last: Zhao


title: Association of Molecular Subtypes with Pathologic Response, PFS and OS in a Phase II Study of Coexpression Extrapolation (COXEN) with Neoadjuvant Chemotherapy (NAC) for Localized, Muscle-Invasive Bladder Cancer (SWOG S1314; NCT02177695)

status: Public on Nov 28 2023

city: Seattle

first: Cathy

last: Tangen

state: WA

address: 1100 Fairview Avenue N, J6-311

institute: Fred Hutchinson Cancer Center

summary: Investigation of RNA-based molecular subtypes as additional predictive biomarkers for neoadjuvant chemotherapy response, progression-free survival and survival in patients treated in S1314.

overall_design: randomized 2-arm phase II trial of neoadjuvant chemotherapy in muscle-invasive bladder cancer, translational analysis of tissue

first: S

last: Lerner

first: D

last: McConkey

first: C

first: J

last: Meeks

last: Daneshmand

first: A

middle: S

last: Alva

first: M

last: Lucia

last: Theodorescu

last: Goldkorn

middle: I

last: Milowsky

first: W

last: Choi

first: R

last: Bangs

middle: L

last: Gustafson

last: Plets

first: I

last: Thompson