title: NFIB dependent and independent mechanisms of metastasis in small cell lung cancer [ATAC-seq]

last: Ko

summary: Molecular characterization of lung tumors and liver metastases from SCLC mouse models with and without Nfib knockout. We performed gene expression profiling analysis using data obtained from ATAC-seq of 7 mouse SCLC cell lines.

overall_design: Chromatin accessibility analysis of ATAC-seq data from 7 cell lines derived from RPR2 and RPR2;Nfibf/f mice, 2 replicates each.

first: Debadrita

last: Bhattacharya

first: Julien

last: Sage


title: Single-cell 3D Genome and Multiome of the Human and Mouse Cerebellum

status: Public on Nov 07 2023

city: Stanford

first: Siavash

last: Moghadami

state: CA

address: 299 Campus Drive, Fairchild Science Building, Room D236

department: Neurobiology

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The cerebellum contains most of the neurons in the human brain and exhibits distinctive modes of development and aging. In this work, by developing our single-cell three-dimensional (3D) genome assay—diploid chromosome conformation capture, or Dip-C—into population-scale (Pop-C) and virus-enriched (vDip-C) modes, we resolved the first 3D genome structures of single cerebellar cells, created life-spanning 3D genome atlases for both humans and mice, and jointly measured transcriptome and chromatin accessibility during development. We found that although the transcriptome and chromatin accessibility of cerebellar granule neurons mature in early postnatal life, 3D genome architecture gradually remodels throughout life, establishing ultra–long-range intrachromosomal contacts and specific interchromosomal contacts that are rarely seen in neurons. These results reveal unexpected evolutionarily conserved molecular processes that underlie distinctive features of neural development and aging across the mammalian life span.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
In this project, we have performed single-cell Dip-C, RNA-seq, and ATAC-seq on human and mouse cerebellum tissues.

Please note that the original 12,004 samples are collapsed to represent as 42 sample records.
The original 12,004 sample annotations are provided in the Series 'README_sample_annotations.txt' supplementary file, including the associated raw and processed data file information.


title: Effect of the NuRD subunit CHD4 on DNA accessibility in Ewing sarcoma cells [ATAC-seq]

city: Boston

first: Joana

middle: Graca

last: Marques

state: MA

address: 360 Longwood Avenue

institute: Dana-Farber Cancer Institute

summary: We established Ewing sarcoma cells (SKNMC) stably expressing two doxycycline-inducible shRNAs targeting the NuRD component CHD4 to study its influence on DNA accessibility.

overall_design: DNA accessibility assessed by ATACseq of SKNMC cells upon 48 hours of CHD4 silencing with two doxycycline-inducible shRNAs.

middle: G

first: Quy

middle: A

last: Ngo

first: Beat

middle: W

last: Schaefer


title: Genome wide localization of the NuRD complex in Ewing sarcoma cells [CHIP-seq]

summary: Chromatin immunoprecipitation followed by DNA sequencing of 4 NuRD complex subunits as well as for the fusion transcription factor EWS-FLI1 and relevant histone marks in Ewing sarcoma cells were performed to characterize the binding sites of the chromatin remodeling complex in relation to the fusion oncoprotein.

overall_design: Chromatin immunoprecipitation followed by DNA sequencing for FLI1, the NuRD subunits: CHD4, HDAC2, MTA2, and RBBP4, as well as for the histone marks H3K27ac, H3K27me3, H3K4me1 and H3K4me3 in Ewing sarcoma cells (SKNMC).


title: Diabetes-associated breast cancer has a distinct transcriptome and metabolome and shows DNA repair deficiency [Xenografts]

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

institute: NCI

summary: Diabetes commonly affects cancer patients. As a comorbidity, it may modify tumor biology and therapy response. Yet, we still lack an understanding of the diabetes-induced molecular changes in human breast tumors and their implication for therapy. The goal of this study was aimed to identify diabetes induced phenotypes and molecular signatures in breast cancer.  Here, we investigated the effect of diabetes on breast cancer biology using a three-pronged approach that included analysis of orthotopic human tumor xenografts, patient tumors, and breast cancer cells exposed to diabetes and hyperglycemia. Diabetes and hyperglycemia induced a mesenchymal and stem cell-like phenotypes. Further Diabetes and hyperglycemia also associated with oxidative stress and both gene expression and mutational signatures of DNA repair deficiency. Breast cancer cells cultured under hyperglycemia acquired increased DNA damage and sensitivity to DNA damage response inhibitors. Based on these observations, diabetes-associated breast tumors may show an increased drug response to DNA repair pathway inhibitors that are cancer therapeutics.

overall_design: We orthotopically injected estrogen receptor (ER)-negative breast cancer cells (MDA-MB-231, MDA-MB-468 and Hs578T) into the mammary fat pad of mice for tumor growth. Eight weeks old diabetic and non-diabetic mice were injected unilaterally with 5×10^6 cells in 100 µL of Matrigel/PBS (50∶50) into the fourth abdominal fat pad by subcutaneous injection. The tumor-growing mice (n=4 from each group) were sacrificed at 5 weeks (for MDA-MB-231 xenografts), 6 weeks (for MDA-MB-468 xenografts), or 8 weeks (for Hs578T xenografts) after the initial inoculation of the breast cancer cells into the fat pads. Tumors were obtained and were immediately frozen in liquid nitrogen for subsequent RNA isolation. mRNA profiles of above xenograft tissues were generated by deep sequencing, with 4 replicates, using Illumina NextSeq.

first: Gatikrushna

last: Panigrahi

first: Julián

last: Candia

first: Tiffany

middle: H

last: Dorsey

first: Wei

last: Tang

first: Byun

last: Jung

first: Tsion

middle: Z

last: Minas

first: Amy

last: Zhang

first: Anuoluwapo

last: Ajao

first: Mayank

last: Tadon

first: Ashley

last: Cellini

first: Harris

last: Yfantis

first: Dean

last: Mann

first: Xin

last: Wang

first: Huaitian

last: Liu

first: Christopher

last: Loffredo

first: Ana

last: Napoles


title: Diabetes-associated breast cancer has a distinct transcriptome and metabolome and shows DNA repair deficiency [MDAMB157 cell lines]

first: Stefan

last: Ambs

overall_design: mRNA profiles of breast cancer cells (MDA-MB-157) grown under low (5mM) and high glucose (25mM) for 48 hrs were generated by deep sequencing, with 4 replicates, using Illumina..


title: ATAC-seq, CHIP-seq and RNA-seq in Ewing sarcoma cells

first: Joana

last: Marques

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

overall_design: Refer to individual Series


title: Diabetes-associated breast cancer has a distinct transcriptome and metabolome and shows DNA repair deficiency [CML exposed MDAMB231 cells]

overall_design: mRNA profiles of breast cancer cells (MDA-MB-231)  exposed with 1micro molar Carboxymethyllysine (CML) for 48 hrs were generated by deep sequencing, with 4 replicates, using Illumina NextSeq.

first: Gatikrushna

last: Panigrahi

first: Julián

last: Candia


title: Diabetes-associated breast cancer has a distinct transcriptome and metabolome and shows DNA repair deficiency [Breast Tumors]

overall_design: RNA was isolated from frozen breast tumors with/without diabetes (n = 36 diabetic and n = 37 non-diabetic) using TRIzol method. The mRNA profiles of the above breast tumors were generated by deep sequencing using Illumina NextSeq.

first: Tiffany

last: Dorsey

first: Wei

last: Tang

first: Tsion Zewdu


title: Diabetes-associated breast cancer has a distinct transcriptome and metabolome and shows DNA repair deficiency [ER positive cell lines]

overall_design: mRNA profiles of breast cancer cells (MDA-MB-175, ZR-75-30 and HCC1500) grown under low (5mM) and high glucose (25mM) for 48 hrs were generated by deep sequencing, with 4 replicates, using Illumina.

first: Byun

last: Jung

last: Minas

first: Amy


title: Effect of CHD4 and EWS-FLI1 knockdown on gene expression of Ewing sarcoma cells.

summary: We established Ewing sarcoma cells (SKNMC) stably expressing doxycycline-inducible shRNAs targeting the NuRD component CHD4 or the fusion transcription factor EWS-FLI1 to study their influence in gene expression regulation.

overall_design: Comparative gene expression profiling of Ewing sarcoma cells (SKNMC) upon 24 and 48 hours of EWS-FLI1 or CHD4 silencing by inducible shRNA expression.

first: Quy

last: Ngo

first: Beat

last: Schaefer


title: YAP-activated metaplasia underlies gastric adenocarcinoma and corpus regenerative mechanisms [RNA-Seq]

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

summary: YAP is a transcriptional co-activator of the hippo signaling pathway and is known for its oncogenic and regenerative activity across numerous tissue types. In particular, high YAP levels in patients with gastric cancer (GC) confer a lower survival rate and poor prognosis for these individuals. Therefore, there is a great need to develop targeted therapies against these aggressive tumors. However, the role of YAP and its underlying molecular mechanisms during gastric tumorigenesis are still poorly understood. Using genetic models, we demonstrate the oncogenic function of YAP in CLU+ gastric cells in vivo. YAP over-expression in CLU+ cells induced atrophy, metaplasia and hyperproliferation in the gastric corpus, while its deletion in a Notch activated gastric tumor model rescued metaplasia. Furthermore, we defined the YAP1 targetome in YAP activated gastric tumors, and showed that YAP1 binds to the active chromatin elements of spasmolytic polypeptide-expressing metaplasia (SPEM) related genes and activates their expressions in gastric tumors and ulcers. Together, these results reveal YAP1 as a critical regulator of metaplasia in the gastric corpus, and highlights YAP signaling as a possible therapeutic target to inhibit the progression of gastric tumors.

overall_design: We performed ChIP-Seq and RNA-Seq in normal stomach tissues and Yap1-activated gastric cancer tissues from genetically-engineered mice.

first: Abilasha

last: Rao-Bhatia

first: Adrian

last: Kwan Loe

first: Zhao

last: Wei

first: Tae-Hee

last: Kim


title: YAP-activated metaplasia underlies gastric adenocarcinoma and corpus regenerative mechanisms


title: YAP-activated metaplasia underlies gastric adenocarcinoma and corpus regenerative mechanisms [ChIP-Seq]


title: Ghrelin deletion and conditional ghrelin-cell ablation increase pancreatic islet size in mice

status: Public on Nov 06 2023

city: Dallas

first: Jeffrey

middle: Marc

last: Zigman

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: We utilized single cell sequencing of FACS sorted cells from pancreatic islets of wildtype and ghrelin knock out mice to understand the effects of ghrelin deletion on gene expression profiles of various islet cells.

overall_design: Single-cell RNA sequencing (10X Genomics) was performed on FACS sorted viable cells from the pancreatic islets of wildtype and ghrelin knockout (homogyous) mice. For each genotype, pancreas from 4 mice were pooled for single-cell dissociation, followed by FACS sorting and 10X single-cell RNA sequencing.

first: Deepali

last: Gupta

first: Dana

middle: C

last: Schwalbe

first: John

middle: N

last: Campbell

middle: M


title: Functional recovery following traumatic brain injury in rats is enhanced by bovine thymus nuclear extract supplementation

city: Kannapolis

first: Robert

last: Reid

state: NC

address: 150 Research Campus Drive, Suite 3333

department: Bioinformatics and Genomics

institute: UNC Charlotte

summary: Traumatic brain injury (TBI) is one of the leading causes of death worldwide. Due to complex etiology, there are currently no effective treatments for TBI, and trauma survivors suffer from a variety of long-lasting health consequences. One of the pathological manifestations of TBI is neuroinflammation, which is thought to delay tissue repair and patient recovery. With nutritional support recently emerging as a vital step in improving TBI patients’ outcomes, we sought to evaluate the potential therapeutic benefits of nutritional supplements derived from bovine glandular tissues, which can deliver a variety of nutrients and bioactive molecules. We show that bovine thymus-derived extracts contain antigens found in neural tissues and are relevant to neuroinflammation, and supplementation of rats with thymus extracts induces production of IgG antibodies against neuronal and glial antigens. In a rat model of controlled cortical impact (CCI) we determined that animals supplemented with a nuclear extract of bovine thymus (TNF) display greatly improved performance on beam balance and spatial memory tests following CCI. Using RNA-Seq, we identified an array of signaling pathways that are modulated by TNF supplementation in rat hippocampus, including those involved in the process of autophagy. Finally, we demonstrate that TNF supplement-induced increase in blood levels of IgG autoantibodies against nervous system antigens correlates with better animal performance on behavioral tests. Together, our data show, for the first time, that a nutritional supplement containing nuclear fraction of bovine thymus is potent at enhancing the functional recovery from TBI in a rat model, modulates signaling pathways implicated in TBI pathology and recovery at gene and protein levels, and may be beneficial for reducing neuroinflammation and improving tissue repair.

overall_design: Expression profiling by RNA-Seq high throughput sequencing. 3 supplement treatments versus sham controls using adult male Sprague-Dawley (aged 6-7 weeks, from Charles River Laboratories).

first: Bassem

middle: F

last: El-Khodor


title: Multi-omics analysis of zebrafish response to tick saliva reveals biological processes associated with alpha-Gal syndrome

city: Ciudad Real

first: Rita

last: Vaz-Rodrigues

address: Ronda de Toledo 12

department: SaBio

country: Spain

institute: Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM)

summary: This study provides a multi-omics approach to determine the effect on the transcriptome and proteome gut profiles of zebrafish inoculated with tick saliva followed by mammalian meat consumption. With bioinformatics analysis using the R software, we sought for significant biological and metabolic pathway changes, in order to fill up some of the current knowledge gaps associated with the alpha-Gal syndrome (AGS). In addition, ortholog mapping allowed to obtain highly concordant biological 1:1 human ortholog genes for the detection of gene-disease associations (GDAs) and disease enriched pathways. Further data validation was performed using reverse transcriptase quantitative PCR (RT-qPCR) and Western Blot (WB) analysis on target differentially expressed genes (DEGs) and differentially represented proteins (DRPs), respectively. We found that treatment with tick saliva increased mortality and caused significant higher incidence of hemorrhagic type allergic reactions, changes in behavior and feeding patterns. Transcriptomics analysis showed downregulation of biological and metabolic pathways correlated with anti-Gal IgE and allergic reactions to tick saliva such as blood circulation, cardiac and vascular smooth muscle contraction, behavior and sensory perception. Disease enrichment analysis revealed that downregulated orthologous genes were mostly associated with human disorders affecting the nervous, musculoskeletal, and cardiovascular systems. Proteomics analysis predominantly revealed suppression of biological and metabolic pathways associated with the immune system production of reactive oxygen species (ROS) and cardiac muscle contraction. The underrepresented proteins were mainly linked to nervous and nutritional/metabolic human disorders. Furthermore, 12 DEGs were found to have concomitant protein-level representation. Lastly, the integration of transcriptomics and proteomics layers through multi-omics pathway enrichment revealed inhibition of pathways associated with adrenergic signaling in cardiomyocytes, as well as heart and muscle contraction. This research contributed to the discovery of AGS-related biological pathways, reinforcing disease multisystemic organ involvement and linking α-Gal sensitization with other illnesses. Furthermore, our results shed light on novel bioinformatic strategies for the identification of key genes and proteins that may serve as potential disease biomarkers.

overall_design: RNA-seq was performed on a total of 6 pooled zebrafish (Danio rerio) intestinal tissue samples. For the treatment group (tick saliva), 6 independent biological samples were pooled in pairs (2 per pool), while the other 9 control (PBS) samples were pooled in groups of three (3 per pool).

first: Lorena

last: Mazuecos

first: Margarita

last: Villar

first: Marinela

last: Contreras

first: Sara

last: Artigas-Jerónimo

first: Almudena

last: González-García

first: Christian

last: Gortázar

first: José

last: de la Fuente


title: REST and Impaired Neural Stress Resistance in Bipolar Disorder

first: Katharina

last: Meyer

address: 201 Brookline Ave

department: Synthetic Biology

institute: Wyss Institute

summary: Neurodevelopmental changes and impaired stress resistance have been implicated in the pathogenesis of bipolar disorder (BD), but the underlying regulatory mechanisms are unresolved.  Here we describe a cerebral organoid model of BD that exhibits altered early neural development, elevated neural network activity, and a major shift in the transcriptome. These phenotypic changes were reproduced in cerebral organoids generated from iPS cell lines derived in multiple different laboratories. The BD cerebral organoid transcriptome showed highly significant enrichment for gene targets of the transcriptional repressor REST. This was associated with reduced nuclear REST and REST binding to target gene recognition sites.  Reducing the oxygen concentration in organoid cultures to a physiological range ameliorated the developmental phenotype and restored REST expression.  These effects were mimicked by treatment with lithium.  Reduced nuclear REST and derepression of REST targets genes was also observed in the prefrontal cortex of BD patients. Thus, an impaired cellular stress response in BD cerebral organoids leads to altered neural development and transcriptional dysregulation associated with downregulation of REST. These findings provide a new model and conceptual framework for exploring the molecular basis of BD

overall_design: The aim of this study was to establish a cerebral organoid model of BD to identify and study disease relevant phenotypes. We performed unbiased RNA sequencing (RNAseq) analysis and analyzed overall structure and morphology of cerebral organoids. Sample size was not calculated prior to experiments. Initial experiments were performed on 5 control and 7 bipolar disorder iPSC lines and later reproduced in additional 5 controls and 5 bipolar disorder iPSCs from different sources. All experiments were repeated 3-5 times by seeding and growing several batches of cerebral organoids from all available lines. Outliers were determined by first, gross morphological observation of organoids, as some lines randomly do not produce viable organoids in each batch and second, by statistical ROUT analysis.

first: King-Hwa

last: Ling

first: Pei-Ling

last: Yeo

first: Angeliki

last: Spathopoulou

first: Derek

last: Drake

first: Jaejoon

last: Choi

first: Liviu

last: Aron

first: Tak

last: Ko

first: Eunjung

last: Lee

first: Jenny

last: Tam

first: Mariana

last: Garcia-Corral

first: Roy

last: Perlis

first: George

last: Church

first: Li-Huei

last: Tsai

first: Bruce

last: Yankner


title: Cpeb3 knockout cortical neuronal cultures

city: Hamburg

first: Jan Broder

last: Engler

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

summary: Neuroinflammation causes neuronal injury in multiple sclerosis (MS) and other neurological diseases. MicroRNAs (miRNAs) are central modulators of cellular stress responses, but knowledge about miRNA–mRNA interactions that determine neuronal outcome during inflammation is limited. Here, we combined unbiased neuron-specific miRNA with mRNA sequencing to assemble the regulatory network that mediates robustness against neuroinflammation. As a critical miRNA-network hub we defined miR-92a. Genetic deletion of miR-92a exacerbated the disease course of mice undergoing experimental autoimmune encephalomyelitis (EAE), whereas miR-92a overexpression protected neurons against excitotoxicity. As a key miR-92a target transcript, we identified cytoplasmic polyadenylation element-binding protein 3 (Cpeb3) that was suppressed in inflamed neurons in mouse EAE and human MS. Accordingly, Cpeb3 deletion improved neuronal resistance to excitotoxicity and ameliorated EAE. Together, we discovered that the miR-92a–Cpeb3 axis confers neuronal robustness against inflammation and serves as potential target for neuroprotective therapies.

overall_design: Cortical neuronal cultures were generated from E15.5 embryonic cortices of Cpeb3fl/fl;Snap25-Cre animals and Cpeb3fl/fl controls and analysed on DIV16.

first: Iris

last: Winkler

first: Jan

middle: B

first: Manuel

last: Friese


title: A versatile CRISPR/Cas13d platform for multiplexed transcriptomic regulation and metabolic engineering in primary human T cells

first: Victor

last: Tieu

state: CA California

address: 290 Jane Stanford Way

department: Bioengineering

summary: CRISPR technologies have begun to revolutionize T cell therapies; however, conventional CRISPR/Cas9 genome-editing tools are limited in their safety, efficacy, and scope. To address these challenges, we developed MEGA (Multiplexed Effector Guide Arrays), a platform for programmable and scalable regulation of the T cell transcriptome using the RNA-guided, RNA-targeting activity of CRISPR/Cas13d. MEGA enables quantitative, reversible, and massively-multiplexed gene knockdown in primary human T cells without targeting or cutting genomic DNA. Applying MEGA to a model of CAR T cell exhaustion, we robustly suppressed inhibitory receptor upregulation and uncovered paired regulators of T cell function through combinatorial CRISPR screening. We additionally implemented druggable regulation of MEGA to control CAR activation in a receptor-independent manner. Lastly, MEGA enabled multiplexed disruption of immunoregulatory metabolic pathways to enhance CAR T cell fitness and anti-tumor activity in vitro and in vivo. MEGA offers a versatile synthetic toolkit for applications in cancer immunotherapy and beyond.

overall_design: Bulk RNA-seq of in vitro day 10 MEGA HA-28ζ CAR T cells (L vs NT; T vs NT; LT vs NT; GLY vs NT; 4KO vs AAVS1); Bulk RNA-seq of in vitro day 5 MEGA T cells (B2M vs NT)


title: The miR-92a–Cpeb3 axis safeguards neuronal function during neuroinflammation

type: Non-coding RNA profiling by high throughput sequencing

overall_design: miRNA of Chat+ spinal cord motor neurons derived from mice undergoing experimental autoimmune encephalomyelitis (EAE) and healthy control mice was enriched by miRNA tagging and affinity-purification (miRAP) and sequenced by small RNA-seq.


title: Formation and fate of stem-cell like Tcf7+ CD8+ T cells during a primary immune response to viral infection [scRNA-seq]

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: In response to infection, naïve CD8+ T cells (Tn) expand and differentiate into short-lived terminal effector (Tte) cells, which eliminate infected cells, or into central memory (Tcm) cells, which persist following pathogen clearance and mediate protection against re-infection thanks to their stem cell-like properties. The stage-specific signals required for the cell fate changes have remained incompletely understood. Here we find that Tn cells, which express the transcription factor Tcf1 (Tcf7), yield Tcf1+ cells, which retain stem-like potential throughout the primary response and which quantitatively yield Tcf1+ Tcm cells following pathogen clearance. However, only the Tcf1+ cells present during priming are competent to yield Tcf1- Tte cells. Priming commits cells to undergo multiple divisions while maintaining Tcf1 expression. The presence of type I interferon during the division, rather than the priming phase suppresses Tcf1 expression. Tcf1 loss results in the stable loss of stemness, an event that precedes the stable acquisition of a Tte state. Thus, inflammatory cytokines drive Tte differentiation from dividing Tcf1+ cells, which are prone to become Tcm cells.

overall_design: Tcf7gfp P14 cells (CD45.2) purified from the spleen of naive mice were adoptively transferred into C57BL/6 (B6)  mice (CD45.1) one day prior to infection with LCMV Armstrong (Arm). Total P14 cells sorted from the spleen of recipient mice at d2, d3, d4 and d6 post infection (p.i) or from the spleen of naive mice (d0), were subjected to scRNA-Seq analysis.

first: Werner

last: Held

first: Daniela

last: Pais Ferreira


title: Overexpression of BEH2 regulates a much broader range of gene expression than BZR1

city: seoul

first: So-Hee

last: Kim

address: Wangsimni-ro

country: South Korea

institute: Hanyang univ.

summary: Based on the distinct phenotypes of BEH2-overexpressing plants, we compared the functional roles of BZR1 and BEH2. The BEH2 is a stronger transcriptional regulator of BR-responsive gene expression than BZR1. It appears that BEH2 also regulates gene expression in a BR-independent manner.

overall_design: To examine whether BZR1 and BEH2 have different transcriptional regulations in BR signaling, we performed RNA-Seq analysis in Col-0, Col-0 treated with BL, 35S-BZR1-YFP, and 35S-BEH2-YFP.

first: Se-Hwa

first: Tae-Wuk

first: Sung-Jin

last: Cho


title: Formation and fate of stem-cell like Tcf7+ CD8+ T cells during a primary immune response to viral infection [ATAC-seq]

overall_design: Tcf7GFP P14 cells (CD45.2) purified from the spleen of naive mice were adoptively transferred into C57BL/6 (B6)  mice (CD45.1) one day prior to infection with LCMV Armstrong (Arm). At d4 and d8 post infection, Tcf7GFP+, Tcf7GFP- Klrg1- and Tcf7GFP- Klrg1+ P14 cells were flow sorted from the spleens of infected recipient mice. CD8+ CD44- CD62L+ cells were flow sorted from the spleen of naive P14 mice (d0). The sorted cells were subjected to bulk ATACseq analysis.


title: Formation and fate of stem-cell like Tcf7+ CD8+ T cells during a primary immune response to viral infection


title: YH29407 with anti-PD-1 ameliorates anti-tumor effects via increased T cell functionality and antigen presenting machinery in the tumor microenvironment

city: Seoul

first: Dongkwon

address: Yonsei ro 50-1

institute: Yonsei university

summary: Among cancer cells, indoleamine 2,3-dioxygenase1 (IDO1) activity has been implicated in improving the proliferation and growth of cancer cells and suppressing immune cell activity. IDO1 is also responsible for the catabolism of tryptophan to kynurenine. Depletion of tryptophan and an increase in kynurenine exert important immunosuppressive functions by activating regulatory T cells and suppressing CD8+ T and natural killer (NK) cells. In this study, we compared the anti-tumor effects of YH29407, the best-in-class IDO1 inhibitor with improved pharmacodynamics and pharmacokinetics, with first and second-generation IDO1 inhibitors (epacadostat and BMS-986205, respectively). YH29407 treatment alone and anti-PD-1 (aPD-1) combination treatment induced significant tumor suppression compared with competing drugs. In particular, combination treatment showed the best anti-tumor effects, with most tumors reduced and complete responses. Our observations suggest that improved anti-tumor effects were caused by an increase in T cell infiltration and activity after YH29407 treatment. Notably, an immune depletion assay confirmed that YH29407 is closely related to CD8+ T cells. RNA-seq results showed that treatment with YH29407 increased the expression of genes involved in T cell function and antigen presentation in tumors expressing ZAP70, LCK, NFACT2, B2M, and MYD88 genes. Our results suggest that an IDO1 inhibitor, YH29407, has enhanced PK/PD compared to previous IDO1 inhibitors by causing a change in the population of CD8+ T cells including infiltrating T cells into the tumor. Ultimately, YH29407 overcame the limitations of the competing drugs and displayed potential as an immunotherapy strategy in combination with aPD-1

overall_design: bulk-RNAsequencing; We treated YH29407, anti-PD-1 to MC38 tumor bearing mouse and collected tumor and analysis

first: Kyoung-Ho

last: Pyo


title: VEXAS syndrome is characterized by blood and tissues inflammasome pathway activation and monocyte dysregulation

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

summary: Acquired mutations in the UBA1 gene, occurring in myeloid cells and resulting in expression of a catalytically impaired isoform of the enzyme E1, were recently identified in patients with severe adult-onset auto-inflammatory syndrome called VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic). The precise physiological and clinical impact of these mutations remains poorly defined. Here, we studied a unique prospective cohort of individuals with severe autoinflammatory disease with (VEXAS) or without (VEXAS-like) UBA1 somatic mutations and compared with low-risk myelodysplastic syndromes (MDS) and aged gender-matched healthy controls. We performed an integrated immune analysis including multiparameter phenotyping of peripheral blood leukocytes, cytokines profiling, bulk and single-cell gene expression analyses and skin tissue imaging mass cytometry. Focusing on myeloid cells, we show that monocytes from UBA1-mutated individuals were quantitatively and qualitatively impaired and displayed features of exhaustion with aberrant expression of chemokine receptors. Within affected tissues, pathological skin biopsies from VEXAS patients showed an abundant enrichment of CD16 + CD163 + monocytes adjacent to blood vessels and M1 macrophages, possibly promoting local inflammation in part through STAT3 activation. In peripheral blood from VEXAS patients, we identified a significant increase in circulating levels of many proinflammatory cytokines, including IL-1β and IL-18 which reflect inflammasome activation and markers of myeloid cells dysregulation. Gene expression analysis of whole blood confirmed the role of circulating cells in the IL-1β and IL-18 dysregulation in VEXAS patients and revealed a significant enrichment of TNF-a and NFkB signaling pathways that could mediate cell death and inflammation. Single-cell analysis confirmed the inflammatory state of monocytes from VEXAS patients and allowed us to identify specific molecular pathways that could explain monocytopenia, especially the activation of PANoptosis and a deficiency in the TYROBP/DAP12 axis and β-catenin signaling pathway. Together, these findings on monocytes from patients with UBA1 mutations provide important insights into the molecular mechanisms involving the mature myeloid commitment in VEXAS syndrome and suggest that the control of the undescribed inflammasome activation and PANoptosis could be novel therapeutic targets in this condition.

overall_design: Characterisation of the Inflammasome activation and monocyte dysregulation in VEXAS  syndrome

first: Olivier

last: Kosmider

first: Céline

last: Possémé

first: Marie

last: Templé

first: Aurélien

last: Corneau

first: Francesco

last: Carbone

first: Eugénie

last: Duroyon

first: Twinu-Wilson

last: Chirayath

first: Marine

last: Luka

first: Camille

last: Gobeaux

first: Estibaliz

last: Lazaro

first: Roderau

last: Outh

first: Guillaume

last: Le Guenno

first: François

last: Lifermann

last: Berleur

first: Chloé

last: Friedrich

first: Cédric

last: Lenormand

first: Thierry

last: Weitten

first: Vivien

last: Guillotin

first: Barbara

last: Burroni

first: Pierre

last: Sohier

first: Jay

last: Boussier

first: Lise

last: Willems

first: Selim

last: Aractingi

first: Léa

last: Dionet

first: Pierre-Louis

last: Tharaux

first: Béatrice

last: Vergier

last: Raynaud

first: Hang-Korng

last: Ea

last: Ménager

first: Darragh

last: Duffy

first: Benjamin

last: Terrier


title: An epigenetic barrier in neural progenitor cells and early neurons set the timing of human neuronal maturation [RNA-seq]

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: A challenge for understanding the development of brain circuits is to identify the factors that instruct neurons to accomplish each developmental steps at the appropriate stage. Neuronal maturation follows an intrinsic species-specific developmental pace that is extremely protracted in humans and that is retained during human pluripotent stem cells (hPSCs) differentiations. Using a novel platform that synchronized the generation of cortical neurons from hPSC, we established morphological, functional, and molecular roadmaps of maturation. We found that the temporal unfolding of maturation programs proceeds gradually and is limited by the retention of complex epigenetic signatures. Loss-of-function of multiple such epigenetic factors at the neuron stage triggered precocious molecular and functional maturation. Remarkably, transient pharmacological manipulation of a subset of epigenetic factors, including EZH2, EHMT1/2 and DOT1L, at the progenitor cell stage can prime precursors to reach enhanced molecular and functional signatures of maturity as neurons. Our results indicate that the rate at which neurons mature is set well before neurogenesis through the establishment of an “epigenetic barrier” in progenitor cells that gets slowly erased in neurons, allowing the gradual onset of maturation programs.

overall_design: Time-dependent assay of transcriptomes with 3 replicates

first: Gabriele

last: Ciceri

middle: S

first: Meghana

last: Kshirsagar

first: Christina

last: Leslie

first: Lorenz

last: Studer


title: An epigenetic barrier in neural progenitor cells and early neurons set the timing of human neuronal maturation

overall_design: Refer to individual Series


title: An epigenetic barrier in neural progenitor cells and early neurons set the timing of human neuronal maturation [ATAC-seq]

overall_design: Time-dependent assay of open chromatin by ATAC-seq with 3 replicates


title: Docetaxel inhibits epithelial-mesenchymal transition in human mammary cells

status: Public on Nov 05 2023

city: Crawley

first: Jessica

last: King

state: WA

address: 35 Stirling Hwy

department: School of Molecular Sciences

country: Australia

institute: University of Western Australia

summary:
Epithelial–mesenchymal transition (EMT) is a reversible and dynamic biological process in which epithelial cells acquire mesenchymal characteristics including enhanced stemness and migratory ability. EMT can facilitate cancer metastasis and is a known driver of cellular resistance to common chemotherapeutic drugs such as docetaxel. Current chemotherapeutic practices such as docetaxel treatment can promote EMT and increase the chance of tumour recurrence and resistance, calling for new approaches in cancer treatment. Here we show that prolonged docetaxel treatment at a sub-IC50 concentration inhibits EMT in immortalized human mammary epithelial (HMLE) cells.
Using immunofluorescence, flow cytometry, and bulk transcriptomic sequencing to assess EMT progression, we analysed a range of cellular markers of EMT in docetaxel-treated cells and observed an upregulation of epithelial markers and downregulation of mesenchymal markers in the presence of docetaxel. This finding suggests that docetaxel may have clinical applications not only as a cytotoxic drug but also as an inhibitor of EMT-driven metastasis and multidrug resistance, depending on the concentration of its use.

overall_design: Comparative gene expression profiling using RNA-seq data for HMLE cells at 0 and 20 d upon exposure to EMT induction either with or without docetaxel.

first: Samuel

middle: J

last: Beerkens

first: Kelly

middle: L

last: Irving

first: Sugandha

last: Bhatia

first: Erik

last: Thompson

first: Nicole

last: Smith

first: K

last: Iyer

first: Cameron

last: Evans


title: LncRNA SNHG5 adversely governs follicular growth in PCOS via miR-92a-3p/CDKN1C axis

city: Shanghai

first: Zuwei

last: Yang

address: No. 419, Fangxie Road

country: China

institute: Obstetrics and Gynecology Hospital, Fudan University

summary: Small nucleolar RNA host genes (SNHGs) have been implicated in various biological processes, yet their involvement in polycystic ovary syndrome (PCOS) remains elusive. Specifically, SNHG5, a long non-coding RNA implicated in several human cancers, shows elevated expression in granulosa cells (GCs) of PCOS women and induces PCOS-like features when overexpressed in mice. In vitro, SNHG5 inhibits GC proliferation and induces apoptosis and cell cycle arrest at G0/G1 phase, with RNA-seq indicating its impact on DNA replication and repair pathways. Mechanistically, SNHG5 acts as a competing endogenous RNA by binding to miR-92a-3p, leading to increased expression of target gene CDKN1C, which further suppresses GC proliferation and promotes apoptosis. These findings elucidate the crucial role of SNHG5 in the pathogenesis of PCOS and suggest a potential therapeutic target for this condition. Additional investigations such as large-scale clinical studies and functional assays are warranted to validate and expand upon these findings.

overall_design: In order to investigate the biological effects of SNHG5, RNA-seq was performed to analyze the gene expression profiles affected by SNHG5 knockdown in KGN cells.

first: Jiexue

last: Pan

first: Chengliang

last: Zhou

first: Hefeng

last: Huang


title: Biosynthesis of the high-value natural products bottromycin and pamamycin from lignin-, plastic- and seaweed-based monomers using engineered Streptomyces lividans

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

institute: Bielefeld University

summary: Background. Transforming waste and non-food materials into bulk biofuels and chemicals represents a major stride in creating a sustainable bioindustry, optimizing the use of resources while reducing environmental footprints. Yet, despite these advancements, the production of high-value natural products often continues to rely on first-generation substrates, underscoring the intricate processes and specific requirements of their biosynthesis. This is also true for Streptomyces lividans, a renowned host organism celebrated for its capacity to produce and uncover a wide array of natural products, attributed to its genetic versatility and potent secondary metabolism. Given this context, it becomes imperative to assess and optimize this microorganism for the synthesis of natural products specifically from waste and non-food substrates.  Results. We metabolically engineered S. lividans TK24 to heterologously produce the ribosomally synthesized and post-translationally modified peptide, bottromycin, as well as the polyketide, pamamycin. The modified strains successfully produced these compounds using waste and non-food model substrates like protocatechuate (derived from lignin), 4-hydroxybenzoate (sourced from plastic waste), and mannitol (from seaweed). Comprehensive transcriptomic and metabolomic analyses offered insights into how these substrates influenced the cellular metabolism of S. lividans. When evaluating production efficiency, S. lividans showcased remarkable tolerance, especially in a fed-batch process using a mineral medium containing the toxic aromatic 4-hydroxybenzoate, leading to enhanced and highly selective bottromycin production. Additionally, it generated a unique spectrum of pamamycins when cultured in mannitol-rich seaweed extract without the need for added nutrients. Conclusion. Our study showcases the successful production of high-value natural products using varied waste and non-food raw materials, thereby circumventing the reliance on costly, food-competing resources. S. lividans exhibited remarkable adaptability and resilience across these diverse substrates. When cultured on aromatic compounds, it displayed a distinct array of intracellular CoA esters, presenting promising avenues for polyketide production. Future research could focus on enhancing S. lividans' substrate utilization pathways to more efficiently process the intricate mixtures commonly found in waste and non-food sources.

overall_design: Whole transcriptomes of a bottromycin production strain derived from cells grown on three different substrates (manitol, 4-hydroxybenzoate, and 3,4-dihydroxybenzoate) using 3 biological replicates each.

first: Seo

last: Kyoyoung

first: Shu

last: Wei

first: Rückert-Reed

last: Christian

first: Gerlinger

last: Patrick

first: Erb

last: Tobias

first: Kalinowski

last: Jörn

first: Wittmann

last: Christoph


title: TGF-β broadly modifies rather than specifically suppresses reactivated memory CD8 T cells in a dose-dependent manner (RNA-Seq)

city: Seattle

first: Martin

last: Prlic

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutchinson Cancer Center

summary: Transforming growth factor β (TGF-β) directly acts on naïve, effector and memory T cells to control cell fate decisions, which was shown using genetic abrogation of TGF-β signaling. TGF-β availability is altered by infections and cancer, however the dose-dependent effects of TGF-β on memory CD8 T cell (Tmem) reactivation are still poorly defined. We examined how activation and TGF-β signals interact to shape the functional outcome of Tmem reactivation. We found that TGF-β could suppress cytotoxicity in a manner that was inversely proportional to the strength of the activating TCR or pro-inflammatory signals. In contrast, even high doses of TGF-β had a comparatively modest effect on IFN-γ expression in the context of weak and strong reactivation signals. Since CD8 Tmem may not always receive TGF-β signals concurrently with reactivation, we also explored whether the temporal order of reactivation versus TGF-β signals is of importance. We found that exposure to TGF-β prior to as well as after an activation event were both sufficient to reduce cytotoxic effector function. Concurrent ATAC-seq and RNA-seq analysis revealed that TGF-β altered ~10% of the regulatory elements induced by reactivation and also elicited transcriptional changes indicative of broadly modulated functional properties. We confirmed some changes on the protein level and found that TGF-β-induced expression of CCR8 was inversely proportional to the strength of the reactivating TCR signal. Together, our data suggest that TGF-β is not simply suppressing CD8 Tmem, but modifies functional and chemotactic properties in context of their reactivation signals and in a dose-dependent manner.

overall_design: OT-1 memory mice were harvested for secondary lymphoid organs (lymph nodes and spleen). A T cell isolation was performed to isolate T cells. T cells were plated for 2 hours with or without TGFb and for 24 hours with SIINFEKL and TGFb or SIINFEKL alone. OT-1 cells (CD45.1 and CD8+) were FACS sorted for downstream analysis by low input bulk RNAseq.

first: Alexis

last: Taber

first: Andrew

last: Konecny

first: Shannon

last: Oda

first: James

last: Scott-Browne


title: TGF-β broadly modifies rather than specifically suppresses reactivated memory CD8 T cells in a dose-dependent manner (ATAC-Seq)

overall_design: OT-1 memory mice were harvested for secondary lymphoid organs (lymph nodes and spleen). A T cell isolation was performed to isolate T cells. T cells were plated for 2 hours with or without TGFb and for 24 hours with SIINFEKL and TGFb or SIINFEKL alone. OT-1 cells (CD45.1 and CD8+) were FACS sorted for downstream analysis by bulk RNAseq and bulk ATACseq.


title: Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity

city: Eugene

first: Chris

last: Doe

address: 1440 Franklin Blvd

institute: University of Oregon

summary: How our brain generates diverse neuron types that assemble into precise neural circuits remains unclear. Using Drosophila lamina neuron types (L1-L5), we show that the primary homeodomain transcription factor (HDTF) Brain-specific homeobox (Bsh) is initiated in progenitors and maintained in L4/L5 neurons to adulthood. Bsh activates secondary HDTFs Ap (L4) and Pdm3 (L5) and specifies L4/L5 neuronal fates while repressing the HDTF Zfh1 to prevent ectopic L1/L3 fates (control: L1-L5; Bsh-knockdown: L1-L3), thereby generating lamina neuronal diversity for normal visual sensitivity. Subsequently, in L4 neurons, Bsh and Ap function in a feed-forward loop to activate the synapse recognition molecule DIP-β, thereby bridging neuronal fate decision to synaptic connectivity. Expression of a Bsh:Dam specifically in L4 reveals Bsh binding to the DIP-β locus and additional candidate L4 functional identity genes. We propose that HDTFs function hierarchically to coordinate neuronal molecular identity, circuit formation, and function. Hierarchical HDTFs may represent a conserved mechanism for linking neuronal diversity to circuit assembly and function.

overall_design: In C. elegans, terminal selectors show non-redundant control of neuronal identity genes and redundant control of pan-neuronal genes. To see if the same mechanism is used by the HDTF Bsh, we profiled Bsh direct targets with precise spatial and temporal control: only in L4 neurons at the time of synapse formation (46-76h APF). To do this, we used Targeted DamID (Aughey et al., 2021), which can be used to identify Bsh DNA-binding sites across the genome.

first: Chundi

last: Xu

first: Tyler

last: Ramos

first: Edward

last: Rogers

first: Michael

last: Reiser

middle: Q


title: TGF-β broadly modifies rather than specifically suppresses reactivated memory CD8 T cells in a dose-dependent manner

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


title: Ataxia-telangiectasia mutated (Atm) disruption sensitizes spatially-directed H3.3K27M/TP53 diffuse midline gliomas to radiation therapy

status: Public on Nov 04 2023

city: Durham

first: Zachary

last: Reitman

address: B227 LSRC, 308 Research Dr

institute: Duke University

summary: Diffuse midline gliomas (DMGs) are lethal brain tumors characterized by inactivating p53 mutations and oncohistone H3.3K27M mutations that rewire the cellular response to genotoxic stress, presenting therapeutic opportunities. We used RCAS/tv-a retroviruses and Cre recombinase to inactivate p53 and induce K27M in the native H3f3a allele in a lineage- and spatially-directed manner, yielding primary mouse DMGs. Disruption of the DNA damage response kinase Ataxia-telangiectasia mutated (Atm) enhanced the efficacy of focal brain irradiation, extending mouse survival. This finding suggests that targeting ATM will enhance the efficacy of radiation therapy for p53-mutant DMG but not p53-wildtype DMG. We used spatial in situ transcriptomics and an allelic series of primary murine DMG models to identify transactivation-independent p53 activity as the key mediator of such radiosensitivity.

overall_design: Primary mouse models of diffuse midline glioma were treated with tumoral Atm loss and/or focal brain irradiation.

first: Simon

middle: G

last: Gregory


title: Inhibition of METTL3 results in a cell-intrinsic interferon response that enhances anti-tumour immunity [CRISPR screen]

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

institute: Peter MacCallum Cancer Centre

summary: Therapies that enhance antitumor immunity have altered the natural history of many cancers. Consequently, leveraging nonoverlapping mechanisms to increase immunogenicity of cancer cells remains a priority. Using a novel enzymatic inhibitor of the RNA methyl-transferase METTL3, we demonstrate a global decrease in N6-methyladenosine (m6A) results in double-stranded RNA (dsRNA) formation and a profound cell-intrinsic interferon response. Through unbiased CRISPR screens, we establish dsRNA-sensing and interferon signaling are primary mediators that potentiate T-cell killing of cancer cells following METTL3 inhibition. We show in a range of immunocompetent mouse models that although METTL3 inhibition is equally efficacious to anti-PD-1 therapy, the combination has far greater preclinical activity. Using SPLINTR barcoding, we demonstrate that anti-PD-1 therapy and METTL3 inhibition target distinct malignant clones, and the combination of these therapies overcomes clones insensitive to the single agents. These data provide the mole-cular and preclinical rationale for employing METTL3 inhibitors to promote antitumor immunity in the clinic.

overall_design: CRISPR screen using the Brie library on B16 cells co-cultured with OT-I cells and in the presence of Mettl3 inhibitors

middle: A

last: Guirguis


title: Quantifying the neuronal and glial composition of the brain using DNA methylation profiles

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

summary: To date, most epigenetic datasets have been generated on DNA samples isolated from bulk tissues. As the proportion of individual cell types within a sample can vary across individuals, systematic differences in cellular proportions that correlate with the phenotype of interest may manifest as differences in the overall epigenetic profile. Deconvolution algorithms calculate a series of continuous variables reflecting the underlying cellular heterogeneity of each sample from the bulk tissue profile that can be used to adjust for confounding in epigenome-wide association analyses. Here we provide novel reference profiles for brain cell types for use with reference based deconvolution algorithms. We used a FANS protocol recently described by our group to purify nuclei populations from prefrontal cortex tissue from 43 adult donors. Our initial gating strategy used an antibody against NeuN  to isolate neuronal nuclei in combination with an antibody against SOX10 to separate oligodendrocyte nuclei from other glial nuclei. Subsequently, in a second gating strategy we additionally included an antibody against IRF8 to enrich microglia from the NeuNNeg/SOX10Neg fraction. Our third gating strategy used an antibody against SATB2 in place of NeuN to isolate excitatory neurons. We generated DNA methylation profiles using the Illumina EPIC array for NeuNPos (neuron-enriched; n = 28), NeuNNeg/SOX10Pos (oligodendrocyte-enriched; n = 24), NeuNNeg/SOX10Neg (microglia- and astrocyte-enriched; n = 21), NeuNNeg/SOX10Neg/IRF8Pos (microglia-enriched; n = 17), NeuNNeg/SOX10Neg/IRF8Neg, (astrocyte-enriched; n = 7), SATB2Pos (excitatory neuron-enriched; n = 9), and SATB2Neg (inhibitory neuron- and glial- enriched; n = 6) nuclei populations. We have demonstrated that these are applicable for use with established deconvolution algorithms to quantify the cellular heterogeneity of the cortex and other regions of the human brain from bulk DNAm data. These variables will be critical covariates to include in future epigenetic studies of brain disorders to minimise the risk of false positive associations and improve our understanding of the changes in the brain that underpin the development of psychiatric disorders and neurodegenerative diseases.

overall_design: Post-mortem prefrontal cortex (PFC) samples  were processed using our optimized FANS protocol to purify nuclei populations  from 42 adult donors. Our initial gating strategy used an antibody against NeuN (a robust marker of post-mitotic neurons) to isolate neuronal nuclei in combination with an antibody against SOX10 (a transcription factor involved in the differentiation of oligodendrocytes) to separate oligodendrocyte nuclei from other glial nuclei. Subsequently, in a second gating strategy we additionally included an antibody against IRF8 (a transcription factor that is upregulated in microglia(30)) to enrich microglia from the NeuNNeg/SOX10Neg fraction. Our third gating strategy used an antibody against SATB2 (a DNA binding protein involved in transcriptional regulation and chromatin remodeling which is expressed in excitatory neurons in the mature central nervous system)  in place of NeuN . We generated DNAm profiles using the Illumina EPIC array for NeuNPos (neuron-enriched; n = 28), NeuNNeg/SOX10Pos (oligodendrocyte-enriched; n = 24), NeuNNeg/SOX10Neg (microglia- and astrocyte-enriched; n = 21), NeuNNeg/SOX10Neg/IRF8Pos (microglia-enriched; n = 17), NeuNNeg/SOX10Neg/IRF8Neg, (astrocyte-enriched; n = 7), SATB2Pos (excitatory neuron-enriched; n = 9), and SATB2Neg (inhibitory neuron- and glial- enriched; n = 6) nuclei populations.

first: E

last: Hannon

first: J


title: Tumor and immune cell types interact to produce heterogeneous phenotypes of pediatric high grade glioma [scRNA-seq]

status: Public on Nov 03 2023

city: Aurora

first: John

last: DeSisto

state: CO

department: Pediatrics

institute: University of Colorado

summary: Single-cell RNA-Seq was conducted on 19 pediatric high-grade glioma patient samples to study tumor heterogeneity and tumor/immune cell interaction.

overall_design: scRNA-Seq on 19 patient samples of pediatric high grade glioma

first: Adam

last: Green


title: Tumor and immune cell types interact to produce heterogeneous phenotypes of pediatric high grade glioma [bulkRNA-seq]

summary: Bulk RNA-Seq of pediatric high-grade glioma patient samples


title: Corticosteroid-binding globulin (SERPINA6) consolidates sexual dimorphism of adult rat liver

city: Vancouver

first: Victor

last: Viau

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: The University of British Columbia

summary: Produced by the liver, corticosteroid-binding globulin (CBG) regulates the plasma distribution and actions of glucocorticoids. A sex difference in pituitary growth hormone secretion patterns established during puberty in rats results in increased hepatic CBG production and two-fold higher plasma corticosterone levels in females. Glucocorticoids control hepatic development and metabolic activities, and we have therefore examined how disrupting the SerpinA6 gene encoding CBG influences plasma corticosterone dynamics, as well as liver gene expression in male and female rats before and after puberty. Comparisons of corticosterone plasma clearance and hepatic uptake in adult rats, with or without CBG, indicated that CBG limits corticosterone clearance by reducing its hepatic uptake. Hepatic transcriptomic profiling revealed minor sex differences (207 differentially expressed genes) and minimal effect of CBG deficiency in 30-day-old rats before puberty. While liver transcriptomes in 60-day-old males lacking CBG remained essentially unchanged, 2,710 genes were differentially expressed in wild-type female versus male livers at this age. Importantly, ~10% of these genes lost their sexually dimorphic expression in adult females lacking CBG, including those related to cholesterol biosynthesis, inflammation, and lipid and amino acid catabolism. Another 203 genes were altered by the loss of CBG specifically in adult females, including those related to xenobiotic metabolism, circadian rhythm, and gluconeogenesis. Our findings reveal that CBG consolidates the sexual dimorphism of the rat liver initiated by sex differences in growth hormone secretion patterns and provide insight into how CBG deficiencies are linked to glucocorticoid-dependent diseases.

overall_design:
To investigate the role of CBG in liver function, we generated CBG-deficient rats using a CRISPR/cas9 strategy to ablate SerpinA6 gene expression.
We then performed gene expression profiling analysis using data obtained from RNA-seq of rat livers at 30 and 60 days of age, under basal conditions. Male and female wild-type (Cbg+/+) and CBG-knockout (Cbg-/-) rats were employed (n=4).

first: Julia

last: Toews

first: Tristan

last: Philippe

first: Matthew

last: Dordevic

first: Lesley

last: Hill

first: Geoffrey

last: Hammond


title: RBPMS regulates cardiomyocyte contraction and cardiac function through RNA alternative splicing

first: Zhaoning

last: Wang

state: New York

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

summary: Background:   Modulation of mRNA splicing acts as an important layer of gene regulation, in addition to transcriptional regulation and epigenetic modifications. RNA binding proteins (RBPs) play essential roles in mediating RNA splicing and are key regulators of heart development and function. Our previous studies demonstrated that RBPMS (RNA-binding protein with multiple splicing) regulates cardiac development through modulating mRNA splicing during embryogenesis. Here we explored the postnatal function of RBPMS in the heart.    Methods:   We ablated Rbpms in the heart by generating a cardiac-specific knockout mouse line (Myh6-Cre, Rbpmsfl/fl), and evaluated its cardiac functions by histology, echocardiography, and gene expression. Paired-end RNA sequencing and RT-PCR were performed to identify and validate splicing targets of RBPMS in adult mouse hearts. Proximity-dependent Biotin Identification (BioID) assay and mass spectrometry analysis were performed to identify RBPMS binding partners. We also measured contractility and calcium fluxes in isolated mouse cardiomyocytes, and contractile forces of cardiac papillary muscle. Human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) were also used as a model to explore the influence of RBPMS on contractility of human cardiomyocytes.   Results:    he absence of Rbpms in the heart led to dilated cardiomyopathy (DCM) and heart failure, causing early death in mice. Mice with cardiac-specific knockout of Rbpms showed myocardium noncompaction with reduced cardiomyocyte number at the neonatal stage and developed DCM with pervasive myocardial fibrosis in adulthood. We found that RBPMS mediates a largely distinct RNA splicing profile in adult mouse hearts compared to neonatal hearts, indicating a stage-specific modulation of alternative RNA splicing by RBPMS. In adult hearts, RBPMS mainly influenced alternative splicing of genes associated with sarcomere structures and cardiomyocyte contraction, such as Ttn, Pdlim5 and Nexn, to generate new protein isoforms. In neonatal hearts, RBPMS influenced the splicing of cytoskeletal genes. RBMPS was associated with spliceosome factors and other RNA binding proteins that play important roles in the heart, such as RBM20 and GATA4. Importantly, we found that the absence of Rbpms caused severe cardiomyocyte contractile defects and reduced calcium sensitivity in both mouse and hiPSC-CMs. Our results demonstrated that Rbpms is crucial for postnatal cardiac function and cardiomyocyte contractility by regulating RNA alternative splicing.   Conclusions:   Loss of Rbpms in the heart causes reduced cardiomyocyte number and impaired cardiomyocyte contraction, leading to DCM and heart failure.

overall_design: RNA from P1 and 2-month-old hearts of Rbpms cardiac-specific KO mice and control mice were extracted and subjected to paired-end RNA sequencing for gene expression profiling and alternative splicing analysis.

first: Peiheng

last: Gan

first: Eric

last: Olson


title: Differential roles of positive and negative supercoiling in organizing the E. coli genome

first: Monica

last: Guo

address: 750 Republican St

department: Microbiology

institute: University of Washington

summary: This study aims to explore whether and how positive and negative supercoiling contribute to the three-dimensional (3D) organization of the bacterial genome. We used recently published Escherichia coli GapR ChIP-seq and TopoI ChIP-seq (also called EcTopoI-seq) data, which marks positive and negative supercoiling sites, respectively, to study how supercoiling correlates with the spatial contact maps obtained from chromosome conformation capture sequencing (Hi-C and 5C). We find that supercoiled chromosomal loci have overall higher Hi-C contact frequencies than sites that are not supercoiled. Surprisingly, positive supercoiling corresponds to higher spatial contact than negative supercoiling. Additionally, positive, but not negative, supercoiling could be identified from Hi-C data with high accuracy. We further find that the majority of positive and negative supercoils coincide with highly active transcription units, with a minor group associated with replication and other genomic processes. Our results show that both positive and negative supercoiling enhance spatial contact, with positive supercoiling playing a larger role in bringing genomic loci closer in space. Based on our results, we propose new physical models of how the E. coli chromosome is organized by positive and negative supercoils.

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

overall_design:
We examined E. coli chromosome conformation during exponential growth in LB with Hi-C.

Grant #MCB1817551
Grant title: Experimental and theoretical investigations of gene regulation by chromosomal topological domains in E. coli
Grantee: Jie Xiao
Funding source: NSF

first: Ziqi

last: Fu

first: Weiqiang

last: Zhou

first: Jie

last: Xiao


title: NFIB dependent and independent mechanisms of metastasis in small cell lung cancer [RNA-seq]

city: Stanford

first: Julie

last: Ko

address: 265 Campus Drive G2065

institute: Stanford University

summary: Molecular characterization of lung tumors and liver metastases from SCLC mouse models with and without Nfib knockout. We performed gene expression profiling analysis using data obtained from RNA-seq of 10 individual tumors dissected from mouse lungs and livers.

overall_design: Gene expression profiling analysis of RNA-seq data from 3 individual lung tumors and 2 liver metastases each from RPR2 mice and RPR2;Nfibf/f mice.

first: Myung

last: Chang Lee

first: Haley

last: Hauser

first: Julien

last: Sage


title: Social isolation-induced transcriptomic changes in mouse hippocampus impact the synapse and show convergence with human genetic risk for neurodevelopmental phenotypes

status: Public on Nov 02 2023

city: Galway

first: Aodan

last: Laighneach

address: University Rd.

country: Ireland

institute: University of Galway

summary: Early life stress (ELS) can impact brain development and is a risk factor for neurodevelopmental disorders such as schizophrenia. Post-weaning social isolation (SI) is used to model ELS in animals, using isolation stress to disrupt a normal developmental trajectory. We aimed to investigate how SI affects the expression of genes in mouse hippocampus and to investigate how these changes related to the genetic basis of neurodevelopmental phenotypes. BL/6J mice were exposed to post-weaning SI (PD21-25) or treated as group-housed controls (n = 7-8 per group). RNA sequencing was performed on tissue samples from the hippocampus of adult male and female mice. Four hundred and 1,215 differentially-expressed genes (DEGs) at a false discovery rate of < 0.05 were detected between SI and control samples for males and females respectively. DEGS for both males and females were significantly overrepresented in gene ontologies related to synaptic structure and function, especially the post-synapse. DEGs were enriched for common variant (SNP) heritability in humans that contributes to risk of neuropsychiatric disorders (schizophrenia, bipolar disorder) and to cognitive function. DEGs were also enriched for genes harbouring rare de novo variants that contribute to autism spectrum disorder and other developmental disorders. Finally, cell type analysis revealed populations of hippocampal astrocytes that were enriched for DEGs, indicating effects in these cell types as well as neurons. Overall, these data suggest a convergence between genes dysregulated by the SI stressor in the mouse and genes associated with neurodevelopmental disorders and cognitive phenotypes in humans.

overall_design: To investigate the effect of post-weaning social isolation on gene expression in the adult male and female mouse hippocampus tissue, we used RNA-seq to measure gene expression changes between socially-isolated (SI) animals and group-housed (GH) controls.

first: Aodán

first: John

middle: P

last: Kelly

first: Lieve

last: Desbonnet

first: Laurena

last: Holleran

first: Daniel

last: Kerr

first: Declan

last: McKernan

first: Gary

last: Donohoe

first: Derek

middle: W

last: Morris


title: Bone marrow adipocytes fuel emergency hematopoiesis

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

summary: Hematopoiesis advances cardiovascular disease by generating inflammatory leukocytes that attack the arteries, heart and brain. While it is well documented that the bone marrow niche regulates hematopoietic stem cell proliferation and hence the systemic leukocyte pool, it is less clear how cardiovascular disease affects the vasculature forming this niche. Here we show that arterial hypertension, atherosclerosis and myocardial infarction alter the anatomy and function of bone marrow vasculature. Hypertension and atherosclerosis instigated vascular fibrosis, leakage and endothelial dysfunction in the bone marrow. Myocardial infarction induced vascular leakage and bone marrow angiogenesis via Vegf signaling. Endothelial cell-specific deletion of the Vegf receptor 2 limited emergency hematopoiesis after myocardial infarction, indicating that new vasculature supports higher blood cell production. RNA-sequencing of bone marrow endothelial cells revealed inflammatory gene expression in mice with cardiovascular disease. Endothelial cell-specific deletion of interleukin 6 or versican, which were highly expressed in mice with atherosclerosis or myocardial infarction, respectively, reduced hematopoiesis and systemic myeloid cells. Taken together, cardiovascular disease affects the vascular bone marrow niche, thus influencing hematopoietic stem cell behavior and expanding innate immune cell supply to atherosclerotic plaque and ischemic myocardium. Interrupting this feed back loop may constrain cardiovascular inflammation.

overall_design: We performed transcriptional profiling using RNA-seq in flow sorted hematopoietic progenitor cells (GMP) isolated from i) naïve control mice (Control), ii) mice 2 days after acute myocardial infarction (Inflammation). n=3 animals per group.

first: Matthias

last: Nahrendorf


title: Single cell transcriptomic analysis of proliferative diabetic retinopathy fibrovascular membranes reveals AEBP1 as fibrogenesis modulator.

city: Chicago

first: Katia

last: Corano Scheri

state: IL

address: 300 E. Superior St.

department: Ophthalmology, Feinberg School of Medicine

institute: Northwestern University

summary: The management of preretinal fibrovascular membranes, a devastating complication of advanced diabetic retinopathy (DR), remains challenging. We characterized the molecular profile of cell populations in these fibrovascular membranes to identify new therapeutic targets. Preretinal fibrovascular membranes were surgically removed from patients and submitted for single cell RNA (scRNA) sequencing. Differential gene expression was implemented to define the transcriptomic profile of these cells and revealed the presence of endothelial, inflammatory, and stromal cells. Endothelial cell re-clustering identified subclusters characterized by non-canonical trascriptomic profile, and active angiogenesis. Deeper investigation of the inflammatory cells showed a subcluster of macrophages expressing pro-angiogenic cytokines, presumably contributing to angiogenesis. The stromal cell cluster included a pericyte-myofibroblast transdifferentiating subcluster, indicating the involvement of pericytes in fibrogenesis. Differentially expressed gene analysis showed that Adipocyte Enhancer-binding Protein 1, AEBP1, was significantly upregulated in myofibroblast clusters, suggesting that this molecule may have a potential role in transformation. Cell culture experiments with human retinal pericytes (HRP) in high glucose condition confirmed the molecular transformation of pericytes towards myofibroblastic lineage. siAEBP1 transfection in HRP reduced the expression of profibrotic markers in high glucose.  In conclusion, AEBP1 signaling modulates pericyte-myofibroblast transformation, suggesting that targeting AEBP1 could prevent scar tissue formation in advanced DR.

first: Jeremy

last: Lavine

first: Thomas

last: Tedeschi

first: Benjamin

middle: R

last: Thomson

first: Amani

last: Fawzi


title: Mammalian oocytes store proteins in cytoplasmic lattices

city: Goettingen

first: Sarah Mae

last: Penir

address: Am Fassberg 11

department: Department of Meiosis

institute: Max Planck Institute for Multidisciplinary Sciences

summary: To investigate the transcriptomic profile of Padi6 -/- and Tle6 -/- oocytes

overall_design: Expression profiling through RNA sequencing

first: Ida

last: Jentoft

first: Sarah

first: Melina

last: Schuh


title: Single-cell RNA-seq of AT2-specific loss of Mdm2-Day8

first: Purushothama Rao

last: Tata

email: pt93@duke.edu, tata.lab@yahoo.com

address: 303 Research Dr., Alexander Sands Building, Room- 451, BOX 3709

department: Department of Cell Biology

institute: Duke University School of Medicine

summary: We performed single-cell RNA-seq analysis  (10X genomics 3'-GEM scRNA-seq kit) of AT2-specific loss of Mdm2 on Day8

overall_design: Three doses of Tamoxifen was administered to Sftpc-creER;MDM2fl/fl ; R26R-tdTomato mice and lungs were collected on day-8 post final dose of tamoxifen.

first: Aleksandra

first: Pankaj

last: Agarwal


title: Repli-seq sample preparation using cell sorting with cell-permeant dyes

city: Minneapolis

first: Juan Carlos

last: Rivera-Mulia

state: MN

address: 420 Washington Ave SE

department: Department of Biochemistry, Molecular Biology and Biophysics

institute: University of Minnesota Medical School

summary: DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we developed a sample preparation method to measure RT genome-wide that does not require fixation.

overall_design: Genome-wide replication timing profiles were constructed from the HepG2 cell line.

first: JuanCarlos


title: Epidermal Growth Factor Receptor Activation is Essential for Kidney Fibrosis Development

city: Nashville

first: Yinqiu

last: Wang

state: TN

address: 313 Harpeth view circle

department: medicine

institute: vumc

summary: We found that EGFR expression increased in interstitial myofibroblasts in human and mouse fibrotic kidneys. Selective EGFR deletion in the fibroblast/pericyte population inhibited interstitial fibrosis in response to unilateral ureteral obstruction, ischemia or nephrotoxins. We used single-nucleus RNA sequencing analysis to demonstrate the role of EGFR activation in UUO model.

overall_design: Kidneys from both WT mice and FibEGFR-/- mice at day 1 and day 3 after UUO were used with kidneys of 3-5 mice from same group being combined for analysis.

first: Raymond

last: Harris

first: Ming-Zhi

last: Zhang

first: Shirong

last: Cao


title: Single-cell RNA-seq in AT1 cell-ablated mouse lungs

summary: We performed single-cell RNA-seq analysis using Drop-seq S3 method in mouse lungs following AT1 cell ablation

overall_design: Single-cell RNA-seq at day 3, 6 and 10 following AT1 cell ablation

first: Yoshihiko

last: Kobayashi


title: BCG induces CX3CR1hi effector memory T cells to provide cross-protection via IFN-y mediated trained immunity

status: Public on Nov 01 2023

city: Montreal

first: Maziar

last: Divangahi

state: QC

address: 1001 Decarie Bvld

institute: McGill University

summary: After a century of the Bacillus Calmette-Guérin (BCG) vaccine, our understanding of its protection against homologous (Mycobacterium tuberculosis) or heterologous (e.g. influenza virus) infections is still limited. Here we show that systemic (intravenous) BCG vaccination (BCG-iv) provides significant protection against subsequent influenza A virus (IAV) infection in mice. We further demonstrate that the BCG-mediated cross-protection against IAV is largely due to the enrichment of conventional CD4+ αβ effector memory T cells that express high levels of CX3CR1hi in circulation trafficking into the lung parenchyma. Importantly, pulmonary CX3CR1hi T cells limit early viral infection in an antigen-independent manner via potent IFNγ production, which subsequently enhances long-term antimicrobial activity of the innate immune system like alveolar macrophages. Similarly, we uncover a prominent IFNγ signature in which its increased basal production was associated with enhanced BCG-mediated heterologous innate memory responses in BCG-vaccinated humans. These results offer insight into the unknown mechanism by which BCG has persistently displayed broad protection against non-tuberculous infections via a crosstalk between adaptive and innate memory responses.

overall_design: BCG vaccination administered intravenously generated a significant enrichment of effector memory T cells chracterized by their CX3CR1hi surface marker expression. Our data provides evidence that the expansion of these cells is key in the subsequent cross-protection between BCG vaccination and influenza infection. The increase in numbers of these cells in BCG-iv mice is evident, however asssessing the transcriptional profile of these cells can reveal any functional signature of the induction of memory T cells by BCG. We thus vaccinated mice with BCG-iv in paralell with PBS controls and after 28 days, purified CX3CR1lo and CX3CR1hi splenic T cells. We subjected the cells to Bulk-RNAseq and assessed the transcriptional landscape.

first: Divangahi

last: Maziar

first: Ding

last: Jun


title: Expression data from young and old vascular smooth muscle cells

city: Brooklyn

first: Ngoc

last: Luu

address: 6 Metrotech Center

institute: New York University

summary:
The allostatic adaption VSMCs to a mechanical perturbation relies on the interaction of the CSK contractile components to generate cellular force, as well as the engagement of the mechanosensitive signaling elements, i.e. the interplay among mechanosensitive ion channels, integrin-focal adhesion-actin axis, and calcium signal that convert the mechanical input into cellular contractile response
We used miroarray to analyze the biophysical mechanisms underlying aging-associated decline in mechanosensation and VSMC functions

overall_design: Vascular smooth muscle cells were isolated from mice of Young (12 weeks) and Old (58-78 weeks) age.

first: Weiqiang

last: Chen

first: Apratim

last: Bajpai


title: HIV-1 latent infection triggers broader transcriptional changes in protein-coding and long non-coding RNAs than active infection of SupT1 cells (RNA-Seq)

city: Ithaca

first: Gabrielle

last: Lê-Bury

address: 930 campus road

institute: Cornell University

summary: Latent HIV-1 infection poses a major challenge in complete viral remission and cure. HIV-1 latency is a multi-dimensional, dynamic process and many aspects of how the viral latency is established and maintained still remains incompletely characterized. Here, we have investigated the host chromatin organization and transcriptomic changes in active- and latently-infected SupT1 cells. We employed an in vitro model of HIV-1 latency in SupT1 cells using a dual-reporter virus, HIVGKO, which enables high purity sorting and characterization of active- and latently-infected cells. We found a significant divergence in chromatin organization and gene expression pattern between active and latent infection compared to uninfected cells. Latent infection results in a repressive reorganization of the host chromatin, while active infection leads to an overall increase in chromatin accessibility. A stronger correlation was also observed between chromatin accessibility and gene expression in latent infection, which was manifested in a greater alteration of the cellular transcriptome in latent than active infection, for both proteincoding and long-non-coding RNAs (lncRNAs). We identified a number of novel lncRNAs associated with either active and latent infection. A reversal in expression pattern of latency-associated lncRNAs following PMA-induced reactivation indicated their infection state-specific expression and potential roles in HIV-1 latency. Taken together, this integrated, comparative study revealed that latent HIV-1 infection requires a substantially greater alteration in cellular epigenome and transcriptome. Understanding of the distinct cellular states conducive to active and latent infection may support devising strategies for specific modulation of host cellular functions as a curative intervention for HIV-1.

overall_design: Four days post-infection (dpi), HIV GKO-infected SupT1 cells were flow sorted into the two populations: active (mKO2+GFP+) and latent (mKO2+GFP-) HIV-1- infected cells. RNA-sequencing was performed with total cellular RNA extracted from the flow-sorted uninfected, active- and latently infected SupT1 cells from two independent experiments.

first: Yao

first: Jordan

last: Rhen

first: Jennifer

middle: K

last: Grenier

first: Amit

last: Singhal

first: David

last: Russell

first: Saikat

last: Boliar


title: HIV-1 latent infection triggers broader transcriptional changes in protein-coding and long non-coding RNAs than active infection of SupT1 cells

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

overall_design: Refer to individual Series


title: FMRP deficiency leads to multifactorial dysregulation of splicing and mislocalization of MBNL1 to the cytoplasm

city: Worcester

first: Suna

last: Jung

address: 373 Plantation street. Suit 204

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: Fragile X syndrome (FXS) is a neurodevelopmental disorder that is often modeled in Fmr1 knockout mice where the RNA-binding protein FMRP is absent. Here, we show that in Fmr1-deficient mice, RNA mis-splicing occurs in several brain regions and peripheral tissues. To assess molecular mechanisms of splicing mis-regulation, we employed N2A cells depleted of Fmr1. In the absence of FMRP, RNA-specific exon skipping events are linked to the splicing factors hnRNPF, PTBP1, and MBNL1. FMRP regulates the translation of Mbnl1 mRNA as well as Mbnl1 RNA auto-splicing. Elevated Mbnl1 auto-splicing in FMRP-deficient cells results in the loss of a nuclear localization signal (NLS)-containing exon. This in turn alters the nucleus-to-cytoplasm ratio of MBNL1. This redistribution of MBNL1 isoforms in Fmr1-deficient cells could result in downstream splicing changes in other RNAs. Indeed, further investigation revealed that splicing disruptions resulting from Fmr1 depletion could be rescued by overexpression of nuclear MBNL1. Altered Mbnl1 auto-splicing also occurs in human FXS postmortem brain. These data suggest that FMRP-controlled translation and RNA processing may cascade into a general dys-regulation of splicing in Fmr1-deficient cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and Fmr1 KO brain (Cortex, Hippocampus, Cerebellm), peripheral tissues (Liver, Muscle, Testis) and N2a cell line (siNT control and siFmr1 knockdown)

first: Sneha

last: Shah

first: Geongoo

last: Han

first: Joel

middle: D

last: Richter


title: Inhibition of SWI/SNF broadly disrupts enhancers and reveals remodeler redundancy at promoters

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Appropriate gene expression requires the establishment of accessible chromatin at promoters and enhancers. These patterns are maintained thorugh the action of, such as the SWI/SNF family. Despite this critical role, previous studies have remained inconclusive regarding the direct role of SWI/SNF. Herein, we employ BRM014, a fast-acting small-molecule inhibitor of the SWI/SNF ATPase subunit, to probe the direct response of mouse embryonic stem cells to disruption of appropriate SWI/SNF chromatin remodeling activity. We demonstrate that the immediate role of SWI/SNF inhibition is a broad loss of chromatin accessibility at both promoter and enhancer loci, and this is reflected in an associated reduction in nascent transcription. We determine that this initial perturbation can be compensated for at a majority of gene promoters, such that these elements regain accessibilty and gene expression under prolonged treatment. However, a subset of gene promoters, as well as most enhancers, fail to recover under these conditions. Finally, we identify EP400 as a putative factor driving compensation ability, as the loss of this factor impedes promoter recovery.

overall_design:
ATAC-seq, PRO-seq, ChIP-seq, RNA-seq. For all experiments, at least two replicates were generated for each condition.

Comparative gene expression profiling analysis of RNA-seq data for A548 and H1299 cells following 12 h treatment with 5 uM BRM014 or DMSO control.

first: Eileen

last: Ablondi

first: Benjamin

middle: E

last: Martin


title: Identification of a Therapeutically Targetable JAK-STAT Enriched Androgen Receptor (AR) and AR Splice Variant Positive Triple Negative Breast Cancer Subtype [Spacial]

status: Public on Oct 31 2023

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with no targeted therapeutics. The luminal androgen receptor (LAR), one of the six TNBC subtypes, constitutes 15% of TNBC and is enriched for AR and AR-target genes. Here, we show that a cohort of TNBC not only expresses full-length AR (AR-FL) at a much higher rate (~80%) than previously reported, but also expresses AR splice variants (AR-SVs) (~20%), subclassifying the LAR-TNBC subtype into LAR-FL, LAR-AR-SV, or dual positive. Higher AR and AR-SV expression and corresponding aggressive phenotypes were observed predominantly in specimens obtained from African American women. RNA sequencing of LAR TNBC specimens indicates an enrichment of hallmark interferon, JAK-STAT, and androgen signaling pathways, which were exclusive to AR-expressing epithelial cancer cells as demonstrated by spatial genomics. LAR and LAR-AR-SV TNBC cell proliferation, orthotopic cell line and patient-derived xenograft, and patient-derived tumor explants growth were inhibited by AR N-terminal domain (NTD)-binding selective AR degrader (SARD) that irreversibly inhibits AR or by the JAK inhibitor ruxolitinib. Subsequent biochemical analysis suggests that STAT1 is an AR coactivator, and SARD or ruxolitinib blocks this coactivation. Collectively, our work identifies and characterizes a pharmacologically targetable and previously unreported TNBC subtype predominantly in African American women and identifies a growth-promoting interaction between AR and JAK-STAT signaling.

overall_design: To determine the difference between AR-expressing cells and AR-negative cells, tissue microarray was constructed with 12 TNBC specimens. Tissues were stained for AR, panCK (epithelial marker), and DNA. PanCK-positive cells from region that stained high and low for AR were captured and sequenced.

first: Sarah

last: Asemota

first: Ramesh

last: Narayanan


title: HNF1αmaintains pancreaticα and β cell functionsin primary human islets [RNA-seq]

status: Public on Oct 30 2023

first: Mollie

middle: F

last: Qian

state: CA

address: 279 Campus Drive W

department: Developmental Biology

summary: Transcriptomic profiling by high-throughput sequencing of primary human alpha and beta cells following HNF1A loss of function.

overall_design: Profiling of FACS-purified human pancreatic HNF1A shRNA-mediated knockdown GFP+ alpha or beta cells by RNA-Seq, compared to a non-targeting shRNA control for each donor.

first: Seung

last: Kim


title: Transcriptomic profiles of MCF7-derived tamoxifen resistant cell lines

status: Public on Oct 25 2023

city: HOUSTON

first: Benny

middle: Abrhaam

last: Kaipparettu

address: 1 Baylor Plaza T832

department: Department of Molecular and Human Genetics

institute: Baylor College Of Medicine

summary: We report mRNA profiles of human breast cancer cell lines, MCF7 parental, and MCF7-derived tamoxifen resistant cell lines MCF7-TR1 and MCF7-TR2.

overall_design: mRNA profiles of human breast cancer cell lines after inducing Tamoxifen resistance

first: Cristian

last: Coarfa

first: Suzanne

last: Fuqua


title: CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model [EC4 RNA-seq]

first: Dean

last: Felsher

address: 269 Campus Drive

department: Medicine

summary: The MYC oncogene is often dysregulated in human cancer, including hepatocellular carcinoma (HCC). However, MYC is considered undruggable to date. Here, we comprehensively identify genes essential for the survival of MYC-high but not MYC-low cells by performing a CRISPR/Cas9 genome-wide screen in a MYC-conditional HCC model. Our screen identifies novel MYC-synthetic lethal interactions, as well as most previously identified MYC-synthetic lethal genes. In particular, we found genes involved in nuclear to cytoplasmic transport to be MYC-synthetic lethal in HCC, and we show that many of these genes are transcriptionally upregulated in MYC-high murine HCC.

overall_design: RNA sequencing was performed on conditional MYC-HCC-derived mouse cells (EC4 cells) with MYC expression conditionally controlled by doxycycline.

first: Anja

last: Deutzmann

first: Yulin

last: Li

first: Renumathy

last: Dhanasekaran

first: Delaney

last: Sullivan


title: Metabolomic Rewiring in Endocrine Therapy-Resistant Estrogen Receptor Positive Breast Cancer

summary: We report mRNA profiles of human breast cancer cell lines, SUM159 and SUM149,which are modulated fatty acid beta oxidation (FAO) pathway either pharmacologically using Etomoxir (ETX) or genetically (shRNA).  The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

overall_design: mRNA profiles of human breast cancer cell lines after modifying fatty acid beta oxidation (FAO)


title: Pro-inflammatory activity of SARS-CoV-2 viral peptide-dsRNA complex on human dermal microvascular endothelial cells (HDMVEC)

city: Los Angeles

first: Gerard

last: Wong

address: 410 Westwood Plaza

department: Bioengineering

institute: University of California Los Angles

summary:
To investigate how SARS-CoV-2 viral peptides alter the immune sensing program in HDMVEC, we treated HDMVEC with SARS-CoV-2 viral peptide-dsRNA complex (xenoAMP(S)-dsRNA), Control(S)-dsRNA, dsRNA only or their associated controls.
Control(S) was the homolog sequence of xenoAMP(S) from low pathogenic human coronavirus-OC43(HCoV-OC43).
The gene expression profiles in the stimulated HDMVEC were analyzed with RNA sequencing.

overall_design: HDMVECs were treated with SARS-CoV-2 viral peptide-dsRNA complex (xenoAMP(S)-dsRNA), Control(S)-dsRNA, dsRNA only or their associated controls for 24 hours. Poly(I:C) was used as the synthetic analog of dsRNA. The Poly(I:C) concentration in corresponding groups was 2.5µg/mL. The mRNA was extracted and counted. Differential gene expression profile of xenoAMP(S)-dsRNA complex-treated cells were compared with dsRNA only-treated cells.

first: Yue

last: Zhang

first: Tatsuya

last: Dokoshi

first: Jonathan

last: Chen


title: Various tomato cultivars display contrasting morphological and molecular responses to a chronic heat stress

city: Toulouse

first: Anis

last: Djari

address: 6 All. Emile Monso

institute: INPT

summary: Climate change is one of the biggest threats that human society currently needs to face. Heat waves associated with global warming negatively affect plant growth and development and will increase in intensity and frequency in the coming years. Tomato is one of the most produced and consumed fruit in the world but remarkable yield losses occur every year due to the sensitivity of many cultivars to heat stress. New insights into how tomato plants are responding to heat stress will contribute to the development of cultivars with high yields under harsh temperature conditions. In this study, the analysis of microsporogenesis and pollen germination rate of eleven tomato cultivars after exposure to a chronic heat stress revealed differences between genotypes. The transcriptome of floral buds at two developmental stages of five cultivars revealed common and specific molecular responses implemented by tomato cultivars to cope with chronic heat stress. These data provide valuable insights into the diversity of the genetic response of floral buds from different cultivars to heat stress and may contribute to the development of future climate resilient tomato varieties.

overall_design:
To identify the molecular pathways differentially regulated in the floral buds of five  tomato cultivars (WVA106, DRK7024, M82, Monemaker, JAG8810) under HS, we carried out a genome-wide transcriptomic analysis by RNAseq on the five previously studied cultivars.
RNA was extracted from floral buds of each tomato cultivar grown under NS or HS conditions (3 weeks at 35°C during the day (16h) and 25°C during the night (8h)). Based on the previous histological analysis, floral buds were harvested at the tetrad stage (tetrad floral bud, TFB) and at the pollen mature stage (pollen floral bud, PFB) based on their size,

first: Norbert

last: Bollier

first: Rosa

last: Micol-Ponce

first: Adrien

last: Dakdaki

first: Ellie

last: Maza

first: Mohamed

last: Zouine

first: Mondher

last: Bouzayen

first: Christian

last: Chevalier

first: Frédérick

last: Delmas

first: Nathalie

last: Gonzalez

first: Michel

last: Hernould


title: Discovery of natural small-molecules to combat kidney fibrosis

status: Public on Oct 20 2023

city: Guangzhou

first: Xinrong

last: Hu

state: Guangdong

address: Zhong shan Road II

institute: Nephrology, The First Affiliated Hospital, Sun Yat-sen University

summary: Chronic kidney disease (CKD) has become one of the greatest threats to public health, characterized by renal fibrosis. However, no treatment targeting renal fibrosis is available so far. Several natural diterpene compounds exhibit extraordinary inhibitory effects on TGF-β1-induced renal fibroblast activation and renal fibrosis in UUO mouse model. RNA-sequencing reveals the signaling pathways affected by these compounds. The direct target of the compounds are explored via quantitative mass spectrometry.  Besides, the efficacies of the compounds are compared with pirfenidone, an FDA-approved drug for idiopathic pulmonary fibrosis, which is under clinical trials for treating CKD patients. Moreover, these compounds exhibit more potent anti-fibrotic activities than conventional CKD medications such as valsartan and enalapril.  Taken together, our study discovered that these diterpeniods alleviate kidney fibrosis by blocking the pro-fibrotic signaling pathway, which has great potential for the treatment of CKD.

overall_design: Comparative gene expression profiling analysis of RNA-seq for rat renal fibroblast (NRK-49F) treated with TGF-β1 or TGF-β1+compound.  There are 3 biological replicates per sample.


title: Diurnal RNA-Seq for Petunia hybrida

status: Public on Oct 24 2023

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

institute: Purdue University

summary: To better understand how diurnal transcriptional regulation contributes to day/night cycles of volatile emission from the petunia flower, RNA extracted from corolla in the morning (7AM) and evening (7PM) was sequenced to determine genes differentially expressed at the two time points.

overall_design: Three replicates of RNA were sequenced and aligned to the Petunia axillaris reference genome to determine transcript levels at 7AM and 7PM.

middle: M

first: Ying

last: Li

first: Natalia

last: Dudareva


title: TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome

status: Public on Oct 17 2023

city: Ann Arbor

first: Elizabeth

middle: Anne

last: Werren

state: MI

address: 1137 Catherine St.

institute: University of Michigan

summary: THOC6 is the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 is critical for mammalian Transcription Export complex (TREX) tetramer formation, which is composed of four six-subunit THO monomers. The TREX tetramer facilitates mammalian RNA processing, in addition to the nuclear mRNA export functions of the TREX dimer conserved through yeast. Human and mouse TIDS model systems revealed novel THOC6-dependent, species-specific TREX tetramer functions. Germline biallelic Thoc6 loss-of-function (LOF) variants result in mouse embryonic lethality. Biallelic THOC6 LOF variants do not alter the expression of TREX dimer component proteins in human cells, but reduced binding affinity to ALYREF implicates impaired TREX tetramer formation. Defects in RNA nuclear export functions were not detected in biallelic THOC6 LOF human neural cells. Instead, mis-splicing was detected in human and mouse neural tissue, revealing novel THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for regulation of key signaling pathways in human corticogenesis that dictate the transition from proliferative to neurogenic divisions, developmental biology implicated in TIDS neuropathology.

overall_design: To investigate the transcriptomic and splicing effects due to pathogenic THOC6 variants in human and mouse neural tissue, we differentiated neural progenitors cells from patient-derived induced pluripotent stem cells and control lines, as well as established a Thoc6 knockout mouse model.

first: Stephanie

last: Bielas

first: Ashleigh

last: Schaffer

first: Geneva

last: LaForce


title: HNF1αmaintains pancreaticα and β cell functionsin primary human islets [CUT&RUN]

city: Stanford

first: Mollie

last: Qian

institute: Stanford University

summary: HNF1α genome-binding profiling by CUT&RUN and high-throughput sequencing.

overall_design: We analyzed the genomic targets of HNF1α by HNF1A-FLAG overexpression in primary human pseudoislets and CUT&RUN, comparing anti-Flag antibody to anti-IgG control for each donor.

first: Seung

last: Kim


title: HNF1αmaintains pancreaticα and β cell functionsin primary human islets


title: RNA-seq and anti-LMO2 ChIP-seq data in primary T cells in different stages from LMO2 over-expressing C57BL/6J transgenic mice

city: Tianjin

first: Wei

last: Sun

address: No.94 Weijin Road

department: School of Medicine

institute: Nankai University

summary: In this study, to investigate the pathogenic role of transcriptional regulator LMO2 during T lineage development, we isolated DN1, DN3, DP, CD4SP, CD8SP thymocytes, splenic CD4+ T cells and splenic CD8+ T cells from wild type and LMO2 over-expressing C57BL/6J mice for RNA-seq, and DN3 (CD25+), DP thymocytes, splenic CD4+/CD8+ T cells from transgenic mice and wild type DN3 (CD25+) thymocytes for ChIP-seq.

overall_design: paired samples in same stages (DN1, DN3, DP…) from WT and TG mice were subjected to RNA-seq to dected the difference of transcriptome and  DN3 (CD25+), DP thymocytes, splenic CD4+/CD8+ T cells from transgenic mice and wild type DN3 (CD25+) thymocytes were subjected to ChIP-seq to detect the DNA-binding feature of LMO2.

first: Wenhao

last: Wang

first: Yaxin

last: Chen

first: Yingying

last: Meng


title: CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model

first: Dean

last: Felsher


title: HIV-1 latent infection triggers broader epigenomic changes in protein-coding and long non-coding RNAs than active infection of SupT1 cells (ATAC-Seq)

first: Gabrielle

last: Lê-Bury

first: Yao

first: Jordan

last: Rhen

first: Jennifer

last: Grenier

first: Amit

last: Singhal

first: David

last: Russell

first: Saikat

last: Boliar