title: HSF1 excludes CD8+ T cells from breast tumors via suppression of CCL5 [4T1 tumors]

status: Public on Jul 11 2023

city: Bloomington

first: Richard

middle: L

last: Carpenter

state: IN

department: Biochemistry and Molecular Biology

institute: Indiana University

summary: Breast cancer cells or tumors underwent RNA-sequencing or single cell RNA-sequencing to study the role of HSF1 in tumor-immune interactions.

overall_design: Human MDA-MB-231 and mouse 4T1 cells expressing either control or HSF1-directed shRNA were subjected to RNA sequencing. Tumors derived from 4T1 control or HSF1 shRNA-expressing cells were subjected to single cell RNA-sequencing.

first: Sha

last: Cao


title: HSF1 excludes CD8+ T cells from breast tumors via suppression of CCL5 [4T1]

country: USA

type: Expression profiling by high throughput sequencing


title: HSF1 excludes CD8+ T cells from breast tumors via suppression of CCL5 [MDA-MB-231]


title: Hypoglycosylated FSH enhances oocyte quality via increased cell-to-cell interaction during mouse follicle development

status: Public on Jul 15 2023

city: Aurora

first: T. Rajendra

last: Kumar

state: CO

department: Obstetrics & Gynecology

institute: University of Colorado Anschutz Medical Campus

summary: Differences in follicle-stimulating hormone (FSH) ß-subunit N-glycosylation results in distinct FSH glycoforms. Hypoglycosylated FSH21 is more bioactive and abundant in reproductively young women, whereas fully glycosylated FSH24 shows lower bioactivity and a relative increase with age. To investigate if the coinciding shift in FSH glycoform abundance contributes to the age-dependent decline in oocyte quality, an encapsulated in vitro follicle growth system was utilized to examine the direct effects of FSH glycoforms on folliculogenesis and resulting oocyte quality. Long-term culture (10-12 days) with FSH21 (10 ng/ml) enhanced follicle growth, estradiol secretion, and oocyte quality compared to equivalent FSH24 treatment. FSH21 exhibited enhanced capacity to establish transzonal projections, gap junctions, and cell-to-cell communication within 24 hrs in culture. Transient inhibition of FSH21-mediated bidirectional communication abrogated the positive effects of FSH21 on follicle growth, estradiol secretion and oocyte quality. These findings indicate FSH21 promotes folliculogenesis and oocyte quality in vitro through increasing cell-to-cell communication early in folliculogenesis and that the shift in abundance from FSH21 to FSH24 with reproductive aging could contribute to the age-dependent decline in oocyte quality.

overall_design: To determine how FSH glycoforms modulate the transciptome of early secondary follicles, follicles were treated with 0, 1, or 10 ng/ml FSH21 or FSH24 for 24 hrs. Three biological replicates of each treatment were conducted.

first: Aubrey

last: Converse

first: Zhenghui

last: Liu

first: Jai Chand

last: Patel

first: Chittibabu

last: Guda

first: George

middle: R

last: Bousfield

first: T

first: Francesca

middle: E

last: Duncan


title: HSF1 excludes CD8+ T cells from breast tumors via suppression of CCL5

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Colonic Gene expression of SPF mice fed either a Control Diet or a High Salt Diet

city: Hamilton

first: Zarwa

last: Saqib

state: ON

address: 1280 Main St W

country: Canada

institute: McMaster University

summary: Compositional changes in the microbiota (dysbiosis) may be a basis for Irritable Bowel Syndrome (IBS) but biomarkers are currently unavailable to direct microbiota-directed therapy. We therefore examined whether changes in fecal β-defensin could be a marker of dysbiosis in a murine model.  Experimental dysbiosis was induced using four interventions relevant to IBS: a mix of antimicrobials, westernized diets (high-fat/high-sugar and, high salt diets), or mild restraint stress. Fecal mouse β-defensin-3 and 16S rRNA-based microbiome profiles were assessed at baseline, during and following these interventions. Each intervention, except for mild restraint stress, altered compositional and diversity profiles of the microbiota. Exposure to antimicrobials or a high-fat/high-sugar diet, but not mild restraint stress, resulted in decreased fecal β-defensin-3 compared to baseline. In contrast, exposure to the high salt diet increased β-defensin-3 compared to baseline but this was not accompanied by discernible inflammatory changes in the host.

overall_design: We extracted total RNA from colonic tissues extracted from SPF mice that were fed either a control diet (n=5/sex, total=10) or a high salt diet (n=5/sex, total=10) for a period of one week. After RNA extraction, RNA samples were pooled to form 4 samples representing controls and another 4 samples representing mice on high salt diet intervention. We then ran a total of 8 samples through the NanoString nCounter® Gene Expression CodeSet for mouse immune, gut barrier and neurobiology related genes.


city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

summary: ADNP syndrome, involving the ADNP transcription factor in the SWI/SNF chromatin-remodeling complex, is characterized by developmental delay, intellectual disability, and autism spectrum disorders (ASD). In ASD, ADNP is a highly penetrant risk gene, accounting for ~0.17% cases. Although Adnp-haploinsufficient mice display various phenotypic deficits, the underlying synaptic mechanisms are poorly understood. Here we report age-differential synaptic plasticity deficits associated with cognitive inflexibility and CaMKIIα hyperactivity in Adnp-mutant mice. These mice show impaired and inflexible contextual learning and memory additional to social and anxiety-related deficits in adults long after a marked decrease in ADNP protein levels to ~10% of newborn levels in juveniles. In addition, Adnp-mutant adults show abnormally enhanced long-term potentiation in adults but not in juveniles. This accompanies CaMKIIα hyperactivity involving increased baseline autophosphorylation, as revealed by unbiased proteomic analyses. Therefore, ADNP haploinsufficiency in mice leads to cognitive inflexibility involving altered synaptic plasticity and signaling in adults long after a marked decrease in Adnp expression in juveniles.

overall_design: Transcriptome analysis of Adnp-heterozygous mice in the hippocampus of adults and juveniles.

first: Heejin

last: Cho

first: Taesun

last: Yoo

first: Heera

last: Moon

first: Hyojin

last: Kang


title: Regulation of mitochondrial Ca2+ uniporter expression and calcium signalling by lncRNA Tug1 in cardiomyocytes

status: Public on Jul 22 2023

city: Parkville

first: Adam

middle: James

last: Trewin

state: Victoria

address: Royal Pde

department: Anatomy and Physiology

country: Australia

institute: University of Melbourne

summary: Cardiomyocyte Ca2+ is buffered by mitochondria via the mitochondrial calcium uniporter (MCU) complex. The MCU complex consists of pore-forming proteins including the mitochondrial calcium uniporter (MCU), and regulatory proteins such as mitochondrial calcium uptake proteins 1 and 2 (MICU1/2). The stoichiometry of these proteins influences the sensitivity to Ca2+ and activity of the complex. However, the factors that regulate their gene expression remain incompletely understood. Long non-coding RNAs (lncRNAs) regulate gene expression through various mechanisms, and we recently found that the lncRNA Tug1 affected the expression of MCU-associated genes. To further explore this, we knocked down Tug1 (Tug1 KD) in H9c2 rat cardiomyocytes using antisense LNA oligo. This led to increased MCU protein expression yet this did not enhance a marker of mitochondrial Ca2+ uptake. RNA-seq revealed that Tug1 KD increased Mcu and led to differential expression of genes and pathways related to Ca2+ regulation in the heart. To understand the effect of this on Ca2+ signalling, we measured phosphorylation of Ca2+/calmodulin-dependent protein kinase II (CaMKII) and its downstream target cAMP Response Element-Binding protein (CREB), a transcription factor known to promote Mcu gene expression. Tug1 KD attenuated the increase in CAMKII and CREB phosphorylation in response to ionomycin, a Ca2+ ionophore. Inhibition of CaMKII, but not CREB, partially prevented the Tug1 KD mediated increase in Mcu. Together, these data suggest that Tug1 modulates MCU expression via a mechanism that may involve CAMKII and CREB. The Tug1 mediated regulation of MCU on mitochondrial Ca2+ uptake, may have functional consequences for cellular Ca2+ handling which could have implications for cardiac disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H9c2 cells with or without antisense LNA-mediated knockdown of Tug1

middle: J

first: Kate

last: Weeks

first: Glenn

middle: D

last: Wadley

first: Séverine

last: Lamon


title: Adrenomedullin has a pivotal role in trophoblast differentiation: A promising nanotechnology-based therapeutic target for preeclampsia.

status: Public on Jul 09 2023

city: Hong Kong

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

summary: Preeclampsia (PE) is the leading cause of prenatal morbidity and mortality. It is associated with defective trophoblast functions at implantation, but manifestation of its phenotypes is in late pregnancy. There is no reliable method for early prediction and treatment of PE. Adrenomedullin (ADM) is an abundant placental peptide in early pregnancy. Here, integrated single-cell sequencing and spatial transcriptomics confirm a high ADM expression in the human villous cytotrophoblast. The levels of ADM in chorionic villi and serum were lower in first-trimester pregnant women who later developed PE than those with normotensive pregnancy. ADM stimulates differentiation of trophoblast stem cells and trophoblast organoids in vitro. In pregnant mice, placenta-specific ADM suppression led to PE-like phenotypes. The PE-like phenotypes in a mouse PE model were reduced by a novel placenta-specific nanoparticle-based forced expression of ADM. Our study reveals the roles of trophoblastic ADM in placental development, PE pathogenesis and its potential clinical uses.

overall_design: Control Tsc vs ADM knockout TSC

first: Zhang

last: Qingqing

first: Cheuk-Lun

last: Lee

first: Philip

middle: C

last: CHIU


title: Transcriptome profiles of canonical MED19 LNCaP and control LNCaP cells cultured under androgen deprivation with vehicle or R1881 treatment

status: Public on Jul 06 2023

city: New York

first: Michael

last: Garabedian

state: NY

address: 500 First Ave

institute: NYU School of Medicine

summary: We report the application of RNA sequencing to uncover the process through which sustained overexpression of the canonical MED19 isoform in androgen-dependent LNCaP cells enhances growth under conditions of androgen deprivation. We identified the canonical MED19 transcriptome by comparing control LNCaP cells with those expressing canonical MED19. This research offers significant understanding of the mechanism by which prostate cancer cells grow under low androgen conditions, emphasizing the key role of the canonical MED19 isoform in this process.

overall_design: To examine how the canonical MED19 isoform affects the proliferation of prostate cancer cells, we created LNCaP cells that overexpress canonical MED19 isoform and control LNCaP cells expressing an empty vector. We then performed expression profiling analysis using data obtained from canonical MED19 and control LNCaP cells. We compared the RNA sequencing results to identify differentially expressed genes between the canonical MED19-LNCaP cells and the control cells with the empty vector.

first: Hannah

last: Weber

first: Rachel

last: Ruoff


title: RNA sequencing of human CD8+ T cell subsets [TEX]

status: Public on Jul 01 2023

city: Innsbruck

first: Alexander

last: Kirchmair

address: Innrain 80-82

country: Austria

institute: Medical University of Innsbruck

summary: RNA sequencing of human CD8+ T cell subsets to compare hypofunctional exhausted cells (TEX) to fully activated effector cells (TEFF).

overall_design: Primary human CD8+ T cells from three healthy donors were TCR-transduced and stimulated with cognate antigen (NY-ESO-1) to generate effector cells (TEFF, 1x stimulation) and exhausted cells (TEX, 4x stimulation).

first: Marcel

last: Trefny

first: Giorgia

last: Lamberti

first: Anne

last: Krogsdam


title: FGF19-FGFR4 promotes the progression of gallbladder carcinoma in a biliary autocrine pathway dependent on GPBAR1-EGR1 axis

status: Public on Jul 07 2023

city: Jinan

first: Tianli

last: Chen

state: Shandong

address: 107 West Wenhua Road

department: Department of General Surgery

country: China

institute: Qilu Hospital of Shandong University

summary: GBC is the most common type of biliary tract cancers and the seventh most common gastrointestinal cancer. Most patients are diagnosed as GBC in an unresectable stage because of the silent symptoms. Even after curative surgery, most patients undergo recurrence due to the early metastasis and limited adjuvant therapies. All these reasons lead to an extremely dismal prognosis of advanced GBC, with a 5-year survival rate approximately 5%-10%. Cholestasis has been shown to be an important factor in the malignant progression of gallbladder cancer. In this study, we stimulate GBC-SD cells with high concentration of CDCA to simulate cholestasis and analyzed the DEGs in the stimulation of CDCA.

overall_design: GBC-SD cells were stimulated with CDCA(100μM) for 72 hours and subjected to differential gene expression studies by RNA-seq

first: Yunfei

last: Xu


title: Bulk RNA-seq of mouse heart tissue for analyzing  gene expression of myocardial infarction progression

status: Public on Jul 04 2023

city: Shanghai

first: Peng

last: Yu

state: Shanghai

address: 2205 Songhu Road, Yangpu District,Shanghai, China

institute: Fudan University

summary: Myocardial infarction (MI) is a leading cause of heart failure (HF), which is associated with morbidity and mortality worldwide. Understanding the molecular characteristics of  of MI is of significance for treating post-MI HF. In this study, RNA-seq was performed on heart tissue from mouse models at multiple time points (sham, 7d and 28d) to explore genetic features that influence MI progression.

overall_design: Nine 8-week-old male C57BL/6JR mice were included in the experiment. The experiment was divided into 3 groups. Each group contained 3 mice, 2 groups of which required surgery to make models, called the operation group, and the other group was the sham operation group. The operation group was divided into 7d and 28d subgroups after MI. The mice were anaesthetized with  isoflurane (1%-2%) and placed on the operating table. After anesthetizing mouse and left thoracotomy, the heart was exposed and the left anterior descending coronary artery was ligated with a 6-0 silk suture. The suture was passed 2-3 mm below the tip of the left auricle. And the sham group was subjected to the same procedures without LAD ligation.

first: S

last: Song

first: P

first: X

last: Zhang

first: A

last: Sun


title: RNA sequencing of human CD8+ T cell subsets [MEM]

summary: RNA sequencing of human CD8+ T cells at different stages of in vitro differentiation.

overall_design: Primary human naive CD8+ T cells from the blood of three healthy donors were activated in vitro and sampled at various differentiation stages before and after activation with anti-CD3/CD28 beads and IL-2.

first: Zlatko

last: Trajanoski


title: Replication dynamics identifies the folding principles of the inactive X chromosome

city: Tsu-shi

first: Rawin

last: Poonperm

state: Mie

address: 1577 Kurimamachiya

department: Graduate School of Bioresources

country: Japan

institute: Mie University

summary:
Chromosome-wide late replication is an enigmatic hallmark of the inactive X chromosome (Xi). How it is established and what it represents remains obscure. By single-cell DNA replication sequencing, here we show that the entire Xi is reorganized to replicate rapidly and uniformly in late S-phase upon X-chromosome inactivation (XCI), reflecting its relatively uniform structure revealed by 4C-seq. Despite this uniformity, only a subset of the Xi became earlier replicating in SmcHD1-mutant cells. In the mutant, these domains protruded out of the Xi core, contacted each other, and became transcriptionally reactivated. 4C-seq suggested that they constituted the outermost layer of the Xi even before XCI and were rich in escape genes. We propose that this default positioning forms the basis for their inherent heterochromatin instability in cells lacking the Xi-binding protein SmcHD1 or exhibiting XCI escape. These observations underscore the importance of 3D genome organization on heterochromatin stability and gene regulation.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
BrdUIP Repli-seq, RNA-seq, and 4C-seq experiments were performed in wild-type and SmcHD1 mutant female JB4/EI7HZ2 mouse embryonic stem cells, day-9 differentiated cells, and neural stem cells (NSCs). Single-cell Repli-seq (scRepli-seq) was performed in wild-type and SmcHD1 mutant NSCs. We only deposited single-cell data sets which passed our filtering steps.

Refer to individual Series


title: Prior antibiotic administration disrupts outcomes of PD-1 blockade in advanced gastric cancer by altering gut microbiome and systemic immune response

city: Seocho-gu

first: June-Young

last: Koh

state: Seoul

address: 2575 Nambusunhwan-ro,

institute: GENOME INSIGHT

summary: We thoroughly uncovered clinical and translational evidence that pATB use can influence treatment outcomes of ICI treatment, highlighting the significance of such practice among patients with AGC.

overall_design: We analyzed circulating immune cells and gut microbiota via single-cell (sc) RNA and TCR sequencing

first: Chang Gon

last: Kim

first: Su-Jin

last: Shin

first: Ji-Hee

first: Hei-Cheul

last: Jeung

first: Jeong Seok

last: Lee

first: Young-Do

last: Nam

first: Minkyu

last: Jung


title: RNA-seq analysis of transcriptomes of WT and Foxp3∆2 Treg cells in spleen and LNs

city: Beijing

first: Gu

last: Qianchong

address: No. 3, yard 1, Beichen West Road

institute: Institute of Microbiology, Chinese Academy of Sicences

summary:
We performed RNA-seq analysis of Tregs isolated from Foxp3RFP/∆2Foxp3∆CNS1-cre-Thy1.1Rosa26LSL-YFP female mice. CD4+YFP+RFP+ (WT Tregs) and CD4+YFP+RFP- (Foxp3∆2 Tregs) cells were sorted from lymph nodes and spleen to a typical purity of >95%
We detected 638 differentially expressed genes (DEGs, FDR < 0.05) between Foxp3∆2 and WT Tregs

overall_design: Transcriptional profiles of WT and Foxp3∆2 Treg cells in spleen and LNs

first: Qianchong

last: Gu

first: Xuyu

last: Zhou


title: Nontarget-site resistance due to rapid physiological response in 2,4-D resistant Conyza sumatrensis: Reduced 2,4-D translocation and auxin-induced gene expression

status: Public on Jun 30 2023

city: Fort Collins

first: Todd

last: Gaines

address: 1177 Campus Delivery

department: Agricultural Biology

institute: Colorado State University

summary: We used RNAseq to quantify trascript expression from three populations of Conyza sumatrensis before and 5 hours after treatment with 2,4-D. This study investigates different responses between a 2,4-D resistant biotype compared to a 2,4-D sensitive biotype.

overall_design: Comparative transcript expression profiling analysis of RNA-seq data for a herbicide resistant population (r) compared to two sensitive populations (S and T) before and 5 hours after treatment.

first: Amanda

last: Souzaa

first: Jessica

middle: F

last: Leal

first: Jacob

middle: S

last: Montgomery

first: Mirella

last: Ortiz

first: André

last: Araujo

first: Sarah

last: Morran

first: Marcelo

last: Figueiredo

first: Ana

last: Langaro

first: Luiz

middle: H

last: Zobiole

first: Scott

last: Nissen

middle: A

first: Camila

last: Pinho


title: JIA vs HD PBMC

city: Prague

first: Zuzana

last: Parackova

address: V Uvalu

country: Czech Republic

institute: Charles University

summary: To compare expression profile of JIA in active disease (JADAS>1) PBMCs vs HD PBMCs

overall_design: 10 samples from JIA active patients, 4 HD samples

first: Irena

last: Zentsova


title: High-throughput identification of Toxoplasma gondii effector proteins that target host cell transcription

city: London

first: Simon

last: Butterworth

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Intracellular pathogens and other endosymbionts reprogram host cell transcription to suppress immune responses and recalibrate biosynthetic pathways. This reprogramming is critical in determining the outcome of infection or colonization. We combine pooled CRISPR knockout screening with dual host-microbe single-cell RNA sequencing, a method we term dual perturb-seq, to identify the molecular mediators of these transcriptional interactions. Applying dual perturb-seq to the intracellular pathogen Toxoplasma gondii, we are able to identify previously uncharacterized effector proteins and directly infer their function from the transcriptomic data. We show that TgGRA59 contributes to the export of other effector proteins from the parasite into the host cell and identify an effector, TgSOS1, that is necessary for sustained host STAT6 signaling and thereby contributes to parasite immune evasion and persistence. Together, this work demonstrates a tool that can be broadly adapted to interrogate host-microbe transcriptional interactions and reveal mechanisms of infection and immune evasion.

sample_organism:
Toxoplasma gondii
Homo sapiens

platform_organism:
Toxoplasma gondii
Homo sapiens

overall_design: Human foreskin fibroblasts (HFFs) were infected with a pool of Toxoplasma gondii CRISPR mutants for 24 h. Direct-capture perturb-seq using 10x Genomics 3' Gene Expression with Feature Barcoding was carried out on infected cells to identify perturbations in the intracellular Toxoplasma gondii parasites that alter the transcriptome of the host cell. Three experiments were carried out: (1) A pilot experiment in which the Toxoplasma gondii parasites were transfected with two different perturb-seq plasmid vectors. (2) A pilot experiment in which the parasites were transfected with a panel of 24 plasmids. (3) A screen in which the parasites were transfected with a pool of 1,312 plasmids with sgRNAs targeting 256 genes. This screen was carried out in both unstimulated and interferon-gamma-stimulated HFFs. Three replicates were carried out for unstimulated HFFs and two for interferon-gamma-stimulated HFFs, with 2-4 Chromium Controller channels per replicate.

first: Moritz

last: Treeck


title: Essential Signaling Function of Cytoplasmic NELFB Independent of RNA Polymerase II Pausing

city: Washington

first: Haihui

last: Pan

state: DC

address: 2121 I St NW

department: Biochemistry and Molecular Medicine

institute: George Washington University

summary: Biochemical studies have established that the four-subunit negative elongation factor (NELF) complex mediates RNA polymerase II (Pol II) pausing at promoter proximal regions. Genetic ablation of individual NELF subunits destabilizes the entire NELF complex and causes lethality of cultured cells, leading to the prevailing concept that NELF-mediated Pol II pausing is essential for cell survival. Using separation-of-function mutations, we show here that NELFB’s effects on cell proliferation can be uncoupled from its function in Pol II pausing. NELFB mutants localized in the cytoplasm and incapacitated in the NELF complex assembly still retain their ability to support cell proliferation and at least part of NELFB-dependent transcriptome. Furthermore, we demonstrate that cytoplasmic NELFB physically and functionally interacts with multiple pro-survival signaling kinases, most notably PI3K/AKT. Enforced activation of PI3K/AKT-related kinases largely rescues deficiency of NELFB-depleted cells in proliferation, but not Pol II pausing. Together, these data revise the current understanding of the growth impact of Pol II pausing and underscore multiplicity of the biological function of individual NELF subunits.

overall_design: RNA libraries were prepared following the Illumina TruSeq stranded mRNA-seq sample preparation guide.

first: Rong

last: Li

first: Xiaolong

last: Cheng


title: Essential Signaling Function of Cytoplasmic NELFB Independent of RNA Polymerase II Pausing [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA Polymerase II or flag (to detect WT and NELFB mutants)


title: A transcriptional activator effector of Ustilago maydis regulates hyperplasia in maize during pathogen-induced tumor formation

city: Cologne

first: Gunther

last: Doehlemann

address: Zuelpicher Str. 47a

country: Germany

institute: University of Cologne

summary: Ustilago maydis causes common smut in maize, which is characterized by tumor formation in aerial parts of maize. Tumors result from the de novo cell division of highly developed bundle sheath and subsequent cell enlargement. However, the molecular mechanisms underlying tumorigenesis are still largely unknown. Here, we characterize the U. maydis effector Sts2 (Small tumor on seedlings 2), which promotes the division of hyperplasia tumor cells. Upon infection, Sts2 is translocated into the maize cell nucleus, where it acts as a transcriptional activator, and the transactivation activity is crucial for its virulence function. Sts2 interacts with ZmNECAP1, a yet undescribed plant transcriptional activator, and it activates the expression of several leaf developmental regulators to potentiate tumor formation. On the contrary, fusion of a suppressive SRDX-motif to Sts2 causes dominant negative inhibition of tumor formation, underpinning the central role of Sts2 for tumorigenesis. Our results not only disclose the virulence mechanism of a tumorigenic effector, but also reveal the essential role of leaf developmental regulators in pathogen-induced tumor formation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from leaves of maize seedlings treated with the CRISPR knock-out mutant of Ustilago maydis Sts2, as well as the Ustilago maydis solopathogenic strain SG200, or water as controls. Three biological replicates were generated.

first: Weiliang

last: Zuo

first: Jasper

last: Depotter

first: Sara

last: Stolze

first: Hirofumi

last: Nakagami


title: Transcriptomic Analyses Reveal Proinflammatory Activation of Human Brain Microvascular Endothelial Cells by Aging-Associated Peptide Medin and Reversal by Nanoliposomes

status: Public on Jun 27 2023

city: Phoenix

first: Raymond

last: Migrino

state: Arizona

address: 650 E Indian School Rd

institute: Phoenix Veterans Affairs Health Care System

summary: Medin is a common vascular amyloidogenic peptide recently implicated in Alzheimer’s disease (AD) and vascular dementia and its pathology remains unknown. We aim to identify changes in transcriptomic profiles and pathways in human brain microvascular endothelial cells (HBMVECs) exposed to medin, compare that to exposure to β-amyloid (Aβ) and evaluate protection by monosialoganglioside-containing nanoliposomes (NL). HBMVECs were exposed for 20 hours to medin (5 µM) without or with Aβ(1-42) (2 µM) or NL (300 µg/mL), and RNA-seq was performed. Pathway analysis on differentially expressed genes revealed multiple pro-inflammatory signaling pathways, such as the tumor necrosis factor (TNF) and the nuclear factor-κB (NFkB) signaling pathways, were affected specifically by medin treatment. Reverse transcription polymerase chain reaction of select identified genes was done in HBMVECs treated with medin (5µM) without or with NFκB inhibitor RO106-9920 (10 µM) or NL (300 µg/mL). Medin caused upregulation of pro-inflammatory genes associated with TNF and NFκB signaling that was not aggravated by Aβ42 co-treatment but reversed by NL.  RO106-9920 and NL reduced medin-induced pro-inflammatory activation. Medin induced endothelial cell pro-inflammatory signaling in part via NFκB that was reversed by NL. This has potential implications in the pathogenesis and treatment of vascular aging, AD and vascular dementia.

overall_design: We conducted transcriptomic profiling using RNA-Seq on human brain microvascular endothelial cells (HBMVECs) treated with various combinations of medin, Aβ(1-42), and NL.

first: Yining

last: Zhang

first: Nina

last: Karamanova

first: Jillian

last: Madine

first: Seth

last: Truran

first: Kaleb

last: Morrow

first: Volkmar

last: Weissig

first: Ming

first: Mehdi

last: Nikkhah

first: Jin

middle: G

last: Park

middle: Q


title: Unlocking the Potential of Allogeneic Vδ2 T Cells for Ovarian Cancer Therapy through CD16 Biomarker Selection and CAR/IL-15 Engineering

status: Public on Jun 29 2023

city: Los Angeles

first: Wenbin

last: Guo

state: CA

address: 610 Charles E. Young Drive, TLSB 5000

institute: UCLA

summary: Allogeneic Vγ9Vδ2 (Vδ2) T cells are attractive candidates in the development of cancer therapies due to their demonstrated safety in allogeneic settings and innate ability to fight tumors. However, the limited clinical success of Vδ2 T cell-based treatments may be attributed to donor variability, short-lived persistence, and tumor evasion. To address these limitations, we have generated Vδ2 T cells with improved properties. By utilizing CD16 as a donor selection biomarker, we have generated Vδ2 T cells with high levels of cytotoxicity and potent antibody-dependent cell-mediated cytotoxicity (ADCC) function, and RNA sequencing characterization supports the increased effector function of Vδ2 T cells obtained from CD16 high (CD16Hi) donors. Further improvement was achieved through CAR and IL-15 engineering techniques. Preclinical studies in two ovarian cancer models showed that engineered CD16Hi Vδ2 T cells are both effective and safe, targeting tumors through multiple mechanisms, exhibiting long-term persistence in vivo, and not causing graft-versus-host disease. These findings support the potential of engineered CD16Hi Vδ2 T cells as a viable cancer therapy option.

overall_design:
To assess the differences between Vδ2 T cells that carry different CD16 expression levels, we performed bulk RNA-Seq on Vδ2 T cells expanded from 13 PBMC donors (all Vδ2 T cells were cultured and expanded in the same way). In this study, 7 new Vδ2 T cell samples were sequenced, and 6 Vδ2 T cell samples were sequenced in our previous study (GEO Accession: GSE164425), thus we downloaded the raw sequencing data and reanalyzed them. Besides the Vδ2 T cell samples, we also sequenced 4 new NK cell samples and retrieved 3 abT cell samples from our previous study (GEO Accession: GSE164425) as a reference. All the samples were subject to the same processing and analysis procedure as denoted in the PROTOCOLS section.
Re-analysed Samples PRJNA690603/GSE164425:
GSM5009488 SRR13381427/SRX9804343 SAMN17255257
GSM5009489 SRR13381428/SRX9804344 SAMN17255248
GSM5009490 SRR13381429/SRX9804345 SAMN17255241
GSM5009491 SRR13381430/SRX9804346 SAMN17255231
GSM5009492 SRR13381431/SRX9804347 SAMN17255222
GSM5009493 SRR13381432/SRX9804348 SAMN17255214
GSM5009496 SRR13381435/SRX9804351 SAMN17255123
GSM5009497 SRR13381436/SRX9804352 SAMN17255122
GSM5009499 SRR13381438/SRX9804354 SAMN17255120

first: Derek

last: Lee

first: Zachary

last: Dunn

first: Lili

last: Yang


title: Multiparity increases the risk of diabetes by impairing proliferative capacity of beta cells I

status: Public on Jun 16 2023

city: Seoul

first: Joonyub

address: 222, Banpo-daero, Seocho-gu

institute: Seoul St. Mary's hospital

summary: Pregnancy poses significant metabolic challenges for women, yet the impact of repeated deliveries on overall glucose metabolism in females remains inadequately explored. In this study, we investigate alterations in female glucose metabolism following multiple deliveries using a comprehensive phenotyping mouse model that closely resembles humans. To establish a multiparty mouse model, a 9-week-old female mouse underwent three consecutive pregnancies. Three weeks post-pregnancy, multiparous mice exhibited improved glucose tolerance and enhanced glucose-stimulated insulin secretion (GSIS), without changes in insulin sensitivity compared to virgin mice. Histological analysis revealed an increased beta cell mass in multiparous mice at this stage of life. Intriguingly, 16 weeks after the last delivery, multiparous mice demonstrated impaired glucose tolerance, accompanied by compromised GSIS and increased basal insulin secretion both in vivo and ex vivo. These mice also developed insulin resistance at 16 weeks post-delivery, with no discernible difference in beta cell mass. To assess whether multiparous islets were impaired in their compensatory ability to meet increased insulin demand, multiparous and virgin islets (3 weeks after the last delivery) were transplanted to opposite sides of the kidney capsule in a single recipient mouse. Upon S-961 injection, multiparous mice were reduced in Ki-67 expressing cells compared with virgin mice. Bulk RNA sequencing (RNA-seq) analysis of S-961-injected multiparous islet genes revealed downregulation of cell cycle-related genes (Cenpi and Cenpf, Cdk1, Cdk2, and Cdkn2d). Single-cell RNA-seq analysis identified multiparous-specific beta cell clusters that displayed upregulation of stress-related genes (Ddit3, Fkbp11, Sdf2l1, Nupr1, Atf5, Atf3, Hspa1a, Hspa1b, and Dnajb1). Furthermore, multiparous mice beta cells exhibited shortened telomere lengths and increased expression of Cdkn2a, indicating an accelerated aging phenotype. In humans, women with higher parities (parity > 3 times) exhibited greater impairment in glucose tolerance and increased obesity compared to women with lower parities (parity < 3 times) at 2 months postpartum. Women with higher parity who experienced weight gain after delivery also demonstrated a greater decline in beta cell function (disposition index). Overall, our findings indicate that multiparty increases the risk of diabetes by impairing beta cells ability to compensate for the increased insulin demand.

overall_design:
Nine weeks aged C57BL/6J female mice underwent 3 consecutive pregnancies to establish multipara mice model. Aged matched virgin mice were used as control.
To examine whether multipara islets are impaired in their compensatory ability to increased insulin demand, bulk RNAsequencing was performed in islets isolated from virgin and multipara mice (3 weeks after the last delivery) injected with S-961.
Bulk RNAsequencing in virgin and multipara islets (3 weeks after the last delivery) without injection of S-961 was also performed.

first: Joon

last: Moon

first: Kyun

last: Kim

first: Hail


title: Gene expression profile at single cell level of bone marrow derived CD133+ endothelial like cells from young and aged mice bone marrow

status: Public on Jun 15 2023

city: Shenzhen

first: yuan

last: meng

address: College avenue 1066#

department: Department of Medicine

institute: Shenzhen University

summary: bone marrow derived ELCs We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of CD133+ ELCs between young and old.

overall_design: Intestinal CD133+ ELCs (approximately 8,000-10,000 cells) of the  young (3-month-old, n=3) and old (18.5-month-old, n=3) mice were isolated by Fluorescence-activated cell sorting (FACS)  and analyzed using scRNAseq.

first: Baohua

last: Liu

first: Yuan

last: Meng


title: Global transcriptional analysis of Geobacter sulfurreducens gsu1771-mutant in response to biofilm development in different supports

status: Public on Jun 19 2023

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: The formation of electroactive biofilms is a crucial process for the generation of bioelectricity and bioremediation. G. sulfurreducens is a dissimilatory metal-reducing microorganism that can couple oxidation of organic matter with extracellular electron transfer to different insoluble electron acceptors. It has the capability to form biofilms in insoluble metal oxides and electroconductive biofilms in electrodes in bioelectrochemical systems. The formation of electroactive biofilms in this microorganism is a process that has been studied from a physiological, genetic, physical, and electrochemical approach. In G. sulfurreducens, we found that the transcriptional regulator GSU1771 participates in the gene expression of essential genes involved in electron transfer and biofilm formation. Strains deficient in GSU1771 increases Fe(III) reduction, produces more c-type cytochromes and exopolysaccharides. Furthermore, the biofilms produced are thicker and more electroactive than wild-type. In this work, we investigate the global gene expression profile performing RNA-seq comparing Δgsu1771 mutant biofilm grown in non-conductive support (glass) and respiring-graphite electrode. RNA-seq analysis of Δgsu1771 biofilm grown in glass support revealed a total of 467 (167 upregulated and 300 downregulated) differentially expressed genes versus the wild-type biofilm. Meanwhile, in Δgsu1771 biofilm developed in respiring-electrode graphite, we detect 119 (79 upregulated and 40 downregulated) differentially expressed genes with respect to wild-type biofilm. Moreover, transcriptional changes of 67 (56 with the same regulation and in 11 counterregulation) genes were shared in Δgsu1771 biofilm developed in glass and graphite electrodes. We locate upregulated in Δgsu1771 biofilms potential target genes, involved in exopolysaccharide synthesis (gsu1961-63, gsu1959, gsu1972-73, gsu1976-77). We confirmed the upregulation of gsu1979, gsu0972, gsu0783, pgcA, omcM, aroG, panC gnfK, gsu2507, and the downregulation of asnA, ato-1, gsu0810, pilA, csrA, ppcD, and gsu3356 genes by RT-qPCR. DNA-protein binding assay shows direct binding of the GSU1771 regulator to the promoter region of pgcA, pulF, relA, and gsu3356. Also, heme-staining and western blotting revealed an increase of c-type cytochromes in Δgsu1771 biofilms such as OmcS and OmcZ. In general, our data shows that GSU1771 is a global regulator involved in controlling the extracellular electron transfer and exopolysaccharide synthesis, processes required for electroconductive biofilm development.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Geobacter sulfurreducens biofilm from wild type and gsu1771-mutant strains grown on a glass support and graphite electrode. From each sample, experimental duplicates were used.

first: Bernardo

last: Jaramillo-Rodriguez

last: Vega-Alvarado

first: Luis

middle: M

last: Rodriguez-Torres

first: Guillermo

last: Huerta-Miranda

first: Alberto

last: Hernández-Eligio

first: Katy

last: Juárez


title: Cellular profiling of a recently-evolved social behavior [spatial transcriptomics]

status: Public on Jun 14 2023

city: Atlanta

first: Larry

last: Young

state: GA

address: 954 Gatewood Rd NE

department: Department of Psychiatry

institute: Emory University

summary: Social behaviors are essential for survival and reproduction and vary strongly among individuals, species, and heritable brain diseases. The molecular and cellular bases of this variation are poorly resolved, and discovering them is necessary to understand how neural circuit and behavioral functions—and dysfunctions—vary in social contexts. Here we integrate single nucleus RNA-sequencing (snRNA-seq) with comparative genomics and automated behavior analysis to investigate the neurobiology of castle-building, a recently-evolved social, spatial, goal-directed, and repetitive construction behavior in Lake Malawi cichlid fishes. We simultaneously control for and analyze two biological variables correlated with castle-building behavior: quivering, a courtship “dance” behavior, and relative gonadal mass. We find signatures of building-, quivering-, and gonadal-associated neuronal excitation, gene expression, and neurogenesis in distinct cell populations. Converging lines of evidence support the involvement of estrogen, TrkB, and CCK signaling systems, and specific pallial excitatory neuronal subpopulations, in castle-building behavior. We show additional evidence that castle-building has evolved in part through genomic divergence in a gene module that is selectively expressed in stem-like quiescent radial glial cells (RGCs) lining the ventricular zone of the pallium. This RGC subpopulation exhibits signatures of a building-associated departure from quiescence, which in turn is associated with neuronal rebalancing in the putative fish homologue of the hippocampus. Our work supports an unexpected role for glia and neurogenesis in the evolution of social behavior, and more broadly shows how snRNA-seq can be used to systematically profile the cellular bases of previously unstudied social behaviors in new species systems.

overall_design: Spatial transcriptomics analysis was performed on coronal telencephalic sections sampled from Mchenga conophoros during bower-building behavior and ‘control’ fish that were not building.

first: Johnson

last: Zachary

first: Hegarty

last: Brianna

first: Gruenhagen

last: George

first: Lancaster

last: Tucker

first: McGrath

last: Patrick

first: Streelman

last: Jeffrey


title: Cellular profiling of a recently-evolved social behavior

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

overall_design: Refer to individual Series


title: Multiparity increases the risk of diabetes by impairing proliferative capacity of beta cells II

first: Joonyub

last: Lee

overall_design:
Nine weeks aged C57BL/6J female mice underwent 3 consecutive pregnancies to establish multipara mice model. Aged matched virgin mice were used as control.
Single cell RNAsequencing in virgin and multipara islets (3 weeks after the last delivery) was performed.

first: Joon

last: Moon

first: Kyun

last: Kim

first: Hail


title: Transcriptomic analysis of the effects of long-term menopause on vaginal wall tissue in rats

city: chengdu

first: Xia

last: Yu

address: No.1617 Ri Yue Street, Chengdu, Sichuan

institute: Chengdu women and Children's hospital

summary: Long-term menopause is considered to be one of the risk factors for pelvic organ prolapse. In the case of long-term menopause, the supporting function of the pelvic floor tissue is weakened, but the effect on the vaginal wall tissue is not fully elaborated. This study intends to use transcriptomics to further clarify.

overall_design: The postmenopausal rat model was constructed by ovariectomization method. After 7 months of breeding, the vaginal wall tissues of the rats were collected and the expression of genes in the vaginal wall was analyzed by transcriptomics

first: Yu

last: Xia


title: Next Generation Sequencing of human trophoblast stem cells expressing a doxycycline-inducible dominant-negative MAML1 construct.

city: Vienna

first: Bianca

last: Dietrich

address: Waehringer Guertel 18-20

institute: Medical University of Vienna

summary: Mastermind-like 1 (MAML1) functions as a co-activator in the NOTCH signaling pathway. A truncated version of its wild type form, the so-called dominant-negative MAML1 (DN-MAML1) , lacks the transactivation domains that are needed for stimulation of gene expression. The aim of the study was to characterize the effects of NOTCH signaling pathway inhibition in human trophoblast stem cells (TSCs) by overexpression of DN-MAML1.

overall_design: To examine gene expression patterns of human TSCs with wild-type or inhibited NOTCH signaling, TSCs were genetically modified by piggyBac-transposase-dependent transfection, that stably integrated a doxycyclin-inducible DN-MAML1 construct into the genome. The transfection was performed using lipofection. Three clonal TSC lines expressing DN-MAML1 were cultured further on fibronectin-coated cell culture dishes in a culture medium promoting trophoblast stemness. The transcriptomes of TSCs overexpressing DN-MAML1 by 6 days of doxycycline stimulation were compared with non-stimulated TSCs, that still have wild-type NOTCH signaling activity. As a control for possible off-target-effects, three TSC lines were also cultured with or without doxycycline for 6 days. The analysis comprise in total 12 samples: three genetically modified TSC lines and three wild-type TSC lines, cultured with and without doxycycline, respectively.

first: Andreas

middle: I

last: Lackner

first: Martin

last: Knöfler


title: Milk microRNA variations in different milk compartments during feed restrictions of different intensities in dairy cows

status: Public on May 31 2023

city: Jouy-en-Josas

first: Sandrine

last: Le Guillou

address: Domaine de Vilvert Bat.440

department: Animal Genetics

country: France

institute: INRAE

type: Non-coding RNA profiling by high throughput sequencing

summary: In dairy cows, milk production and composition are affected by numerous factors, including diet. Milk is the body fluid with the highest RNA concentration, including numerous microRNA. These microRNA presence in the different milk compartments is still poorly documented and the effect of feed restriction on milk miRNome has not been described yet. The aim of this study was to describe the effects of feed restrictions of different intensitizes on milk compartment miRNome composition. Two feed restriction trials were performed on lactating dairy cows, one of high intensity and one of moderate intensity. 2 896 mature microRNA were identified in milk, including 1 493 that were already known in bovine specie. Among the 1 095 miRNA that were abundant enough to be informative, 10% were exclusive to one milk compartment and the abundance of 155 varied between compartments, revealing a specific miRNome for each milk fraction. Feed restriction affected differently these miRNome, with microRNA in whole milk and milk extracellular vesicles being the most affected and microRNA in fat globules and exfoliated mammary epithelial cells being relatively or completely unaffected. Target prediction of known microRNA that varied under feed restriction reflected modification of some key pathways for lactation related to milk fat and protein metabolisms, cell cycle and stress responses. These findings open up opportunities for future research on the use of milk miRNA as biomarkers of energy status in dairy cows.

overall_design: microRNA profiles of whole milk samples, purified milk fat globules, milk extracellular vesicles and exfoliated mammary epithelial cells in milk, sampled the week before the initiation of a feed restriction and after 5 days of feed restriction, from 16 multiparous mid-lactation Holstein cows, generated by deep sequencing, using Illumina HiSeq 4000

first: Antoine

last: Leduc

first: Denis

last: Laloe

first: Andrea

last: Rau

first: Yannick

last: Faulconnier

first: Patrice

last: Martin

first: Marine

last: Gelé

first: José

last: Pires

first: Christine

last: Leroux

first: Marion

last: Boutinaud

first: Fabienne

last: Le Provost


title: Real-time quantitative PCR analysis of mouse ameloblasts

status: Public on Jun 01 2023

city: Fukuoka

first: Masashi

last: Shin

state: Fukuoka

address: 2-15-1 Tamura, Sawara-ku

institute: Fukuoka Dental College

summary:
Incisor enamel organ epithelial cells were isolated and enzymatically processed from postnatal day 4 mice transgenic for Amelx-promoter driven tdTomato. Single cell suspensions were subjected to fluorescence-activated cell sorting (FACS) to isolate tdTomato positive ameloblasts. tdTomato-positive cells were isolated from enamel organ epithelial from the incisors of three mouse lines, which were Mmp20+/+ -AT4 (WT), Mmp20-/--AT4 (KO), Mmp20+/+ Tg-AT4 (Tg, overexpress MMP20).
We used Fukuoka Dental College mouse ameloblast PCR array panel to quantitate gene expression of genes associated with enamel formation, cell migration and cell adhesion from ameloblasts.

overall_design: qPCR gene expression profiling.  Ameloblasts from three mice were used  as indicated in the summary. Equal amount total RNA from each cell was pooled prior to gene expression analysis.

first: John

last: Bartlett


title: The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development [RNA-seq]

status: Public on Jun 07 2023

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: Caulobacter species are dimorphic Gram-negative bacteria that inhabit diverse terrestrial and aquatic ecosystems. A suite of molecular sensory systems enables these microbes to control growth, development, and reproduction in response to levels of essential elements, including carbon, nitrogen, and phosphorus. Although the enhancer binding protein NtrC and its cognate sensor histidine kinase NtrB are well-established regulators of bacterial nitrogen assimilation, their precise functions in Caulobacter metabolism and cell development remained largely undefined. Deletion of C. crescentus ntrC slowed cell growth in complex medium, while ntrB and ntrC were essential for growth when ammonium was the sole nitrogen source due to their requirement for glutamine synthase (glnA) expression. Random transposition of a conserved IS3-family mobile genetic element frequently rescued the growth defect of ntrC mutant strains by restoring glnBA transcription, revealing a possible role for IS3 transposition in shaping the evolution of Caulobacter populations during nitrogen limitation. We further defined the NtrC regulon through transcriptomic and ChIP-seq analyses, which demonstrated the role of NtrC as both a transcriptional activator and repressor. The chromosome of C. crescentus harbors dozens of direct binding sites for NtrC, with a significant proportion located near genes involved in polysaccharide biosynthesis. Numerous NtrC binding sites align with those of GapR, an essential protein involved in chromosome organization, and MucR1, a cell cycle regulator. This observation suggests that NtrC participates in the regulation of cell cycle and cell development. Indeed, loss of NtrC function led to elongated polar stalks and elevated synthesis of cell envelope polysaccharides. These developmental defects were restored by supplementing media with glutamine or by ectopic expression of the glnBA operon. This study establishes a regulatory connection between NtrC, nitrogen metabolism, polar morphogenesis, and envelope polysaccharide synthesis in Caulobacter.

overall_design:
To investigate the NtrC regulon in Caulobacter by creating an in-frame knockout of ntrC
To investigate effects of glutamine supplementation on global expression in both WT and ∆ntrC  by growing  these Caulobacter strains in peptone yeast extract (PYE) complex medium supplemented with 9.3 mM (final concentration) glutamine
We performed gene expression analysis from RNA-seq data of WT and ∆ntrC Caulobacter strains were grown in PYE or PYE supplemented with 9.3 mM (final concentration) glutamine to log phase
Gene expression profiles across strains (i.e., WT, ∆ntrC) and/or across medium condidtions (i.e., PYE, PYE supplemented with 9.3 mM glutamine) were compared

first: Hunter

last: North

first: Maeve

last: McLaughlin

first: Aretha

last: Fiebig


title: Transcriptional pausing induced by ionizing radiation enables the acquisition of radioresistance in nasopharyngeal carcinoma [ChIP-seq]

status: Public on May 25 2023

city: Changsha

first: Honglu

last: Liu

state: Hunan

address: Kaifu district, Xiangya road

department: Xiangya hospital

institute: Central South University

summary: Lesions on the DNA template can impact transcription via distinct regulatory pathways. Ionizing radiation (IR) as the mainstay modality for many malignancies elicits most of the cytotoxicity by inducing a variety of DNA damages in the genome. How the IR treatment alters transcription cycle and whether it contributes to the development of radioresistance remain poorly understood. Here, we report an increase in the paused RNA polymerase II (RNAPII), as indicated by the phosphorylation at serine 5 residue of its C-terminal domain, in recurrent nasopharyngeal carcinoma (NPC) patient samples after IR treatment and cultured NPC cells developing IR resistance. Reducing the pool of paused RNAPII by either inhibiting TFIIH-associated CDK7 or stimulating the transcription elongation factor P-TEFb, a CDK9-CycT1 heterodimer, attenuates IR resistance of NPC cells. Interestingly, the poly(ADP-ribosyl)ation of CycT1, which disrupts its phase separation, is elevated in the IR-resistant cells. Mutation of major poly(ADP-ribosyl)ation sites of CycT1 decreases RNAPII pausing and restores IR sensitivity. Genome-wide chromatin immunoprecipitation followed by sequencing analyses reveal that several genes involved in radiation response and cell cycle control are subject to the regulation imposed by the paused RNAPII. Particularly, we identify the NIMA-related kinase NEK7 under such regulation as a new radioresistance factor, whose downregulation results in the increased chromosome instability, enabling the development of IR resistance. Overall, our results highlight a novel link between the alteration in transcription cycle and the acquisition of IR resistance, opening up new opportunities to increase the efficacy of radiotherapy and thwart radioresistance in NPC.

overall_design: Examination of RNA Pol II pausing and its CTD phosphorylation modifications in nasopharyngeal carcinoma cell.

first: Kai

last: Yuan


title: Hippocampus RNA-seq in Egr1cKO mice

city: Blacksburg

first: Hehuang

last: Xie

state: VA

address: 1015 Life Science Cir

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

summary: Sex difference in hippocampus gene expression of Egr1cKO mice and controls

overall_design: 24 Samples, 12 males and 12 females

first: Cody

last: Swilley

first: Yuze

last: Zheng

first: Yu

last: Lin


title: The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development [ChIP-seq]

overall_design:
To investigate the NtrC direct regulon/DNA binding sites in Caulobacter by creating a 3xFLAG-tagged ntrC allele, which resulted in a 3xFLAG tag at the N-terminus of NtrC
We performed NtrC DNA-binding analysis from ChIP-seq data of Caulobacter harboring 3xFLAG-ntrC grown in PYE to log phase


title: Gene expression profile at single cell level of virus-specific CD8+ T cells in subjects with past or current HCV infection.

status: Public on Jun 08 2023

first: Ana

last: Maretti-Mira

address: 1450 Biggy Street, NRT 3514

department: Medicine

institute: USC

summary: CD8+ T cells play a central role in antiviral control. We used single cell RNA sequencing (scRNA-seq) to analyze the differences of HCV-specific CD8+ T cells isolated from subjects that are chronically infected by HCV, individuals that spontaneously resolved an acute HCV infection, and chronic HCV patients in treatment with direct-acting antiviral (DAA). We also profiled non-HCV virus-specific cells (CMV and FLU) to analyze the impact of HCV infection on the adaptive immune response.

overall_design: We selected our cohort from our biobank. We included 4 subjects with chronic HCV, 4 subjects with self-limiting HCV infection, 3 non-HCV-exposed non-diseased controls. We also evaluated 3 patients that went through 12 weeks of DAA therapy in 4 different time points: pre-treatment (Pre-tx), 2-4 weeks into the treatment (Early-tx), 8 weeks of therapy (Late-tx), and 12 weeks after therapy completion (Post-tx). We used the stored PBMCs to isolate virus-specific CD8+ T cells by sorting cells CD8+ CD3+ CD4- CD56- that were positive for barcoded-dextramers (dCODE Dextramers, Immudex). The sorted cells were partitioned for scRNAseq (10x Genomics), and gene expression and surface protein libraries were prepared using Chromium Next GEM Single Cell 5' Kit v1.1 (10x Genomics, Pleasanton, CA).

first: Matthew

middle: P

last: Salomon

first: Lucy

last: Golden-Mason


title: Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development

status: Public on May 26 2023

city: Seattle

first: Chengxiang

last: Qiu

state: WA

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

department: Genome Sciences

institute: University of Washington

summary: Mouse models represent a critical tool to study human diseases, particularly developmental disorders, as well as for advancing our general understanding of mammalian biology. However, it has long been suspected that conventional approaches for phenotyping are insufficiently sensitive to detect subtle defects throughout the developing mouse. Here we set out to establish single cell RNA sequencing (scRNA-seq) of the whole embryo as a scalable platform for the systematic molecular and cellular phenotyping of mouse genetic models. We applied combinatorial indexing-based scRNA-seq to profile 101 embryos of 26 genotypes at embryonic stage E13.5, altogether profiling over 1.6M nuclei. The 26 genotypes included 22 mouse mutants representing a range of anticipated severities, from established multisystem disorders to deletions of individual enhancers, as well as the 4 wildtype backgrounds on which these mutants reside. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibited changes in dozens of trajectories (e.g., the pleiotropic consequences of altering the Sox9 regulatory landscape) whereas the impact of others was considerably more restricted. We further identified differences between widely used wildtype strains, compared phenotyping of gain vs. loss of function mutants, and characterized deletions of topological associating domain (TAD) boundaries. Intriguingly, even among these 22 mutants, some changes are shared by heretofore unrelated models, suggesting that developmental pleiotropy might be “decomposable” through further scaling of this approach. Overall, our findings show how single cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution.

overall_design: We applied sci-RNA-seq3 to profile 1.6M single cell transcriptomes from 103 individual E13.5 embryos, derived from 22 mutants and four wildtype strains, in one experiment.

first: Xingfan

last: Huang

first: Jana

last: Henck

first: Varun

last: Sreenivasan

first: Uwe

last: Kornak

first: Ingo

last: Kurth

first: David

last: Beier

first: Diane

last: Dickel

first: Axel

last: Visel

first: Len

last: Pennacchio

first: Junyue

last: Cao

first: Malte

last: Spielmann

first: Jay

last: Shendure


title: Transcriptome changes in response to dDAVP stimulation in CRISPR/Cas9 mediated Camk2d knock-out mpkCCD cells

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary: The Ca2+/CaM-dependent protein kinase 2-delta (CAMK2D) has been proposed to be involved in vasopressin signaling in the renal collecting duct, which controls water and salt excretion by the kidney. RNA sequancing  and quantitative proteomics analyses identified the expression of multiple CAMK2 isoforms, with CAMK2D being the most abundant in collecting duct cells. To investigate the role of CAMK2D in regulating RNA expression in response to vasopressin signaling, the transcriptome of CRISPR/Cas9-mediated Camk2d knock-out mpkCCD cells was profiled using RNA-Seq in the presence of vasopressin analogue dDAVP.

overall_design: Five intact and five Camk2d knockout cell lines generated from mouse cortical collecting duct mpkCCD cell lines were cultured on a membrane filter system for 7 days in the presence of dDAVP. Total RNA profiling was carried out using standard RNA-seq protocols.

first: Euijung

last: Park

first: Mark

last: Knepper


title: Transcriptional pausing induced by ionizing radiation enables the acquisition of radioresistance in nasopharyngeal carcinoma

status: Public on May 23 2023

first: Honglu

last: Liu


title: Nm-Mut-seq: The base-resolution quantitative method for mapping transcriptome-wide 2’-O-methylations

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

summary: 2’-O-methylation (Nm) is a prevalent post-transcriptional RNA modification present in many cellular RNAs and plays a critical role in modulating both the physical properties and regulation of eukaryotic RNAs. Studies of Nm modifications in RNA have long been hampered by a lack of effective mapping methods. Previously reported approaches can work well for detecting Nm modifications on abundant RNAs, but face challenges when applied to low-abundant RNAs, such as mRNA, lack stoichiometric information, and are challenged by issues of RNA sample degradation due to chemical treatment. Here, we present Nm-Mut-seq, a mutation signature-based Nm mapping method, which uses a custom reverse transcriptase (RT) that installs mutations at Am, Cm, and Gm-modified sites (Um is undetectable by this method). Our work provides a much-needed approach to detect Nm at base resolution in low abundant RNAs and to estimate the stoichiometry of each modified site transcriptome-wide.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
[dataset1] 15 samples (Sample 1-15): Duplicates or Triplicates for "Input" and "Treated" samples in Nm-Mut-seq to detect Nm in total RNA and polyA+ RNA from wild-type HeLa and HepG2 cells. Note that RNA 3'-adaptor sequence is 5’rApp-NNNNN ATCACG AGATCGGAAGAGCACACGTCT-3SpC3; RNA 5'-adaptor sequence is 5’-GUUCAGAGUUCUACAGUCCGACGAUC NNNNN-3'.

[datase2] 20 samples (Sample 16-35): Duplicates for "Input" and "Treated" samples in Nm-Mut-seq to depict Nm calibration curves for estimating Nm methylation fractions.

[datase3] 18 samples (Sample 36-53): Triplicates for Nm-Mut-seq samples to reveal Nm methylation level change in total RNA and polyA+ RNA from siFBL or siFTSJ3 HepG2 cells versus siControl. Note that 5’rApp-NNNNN ATCACG AGATCGGAAGAGCACACGTCT-3SpC3 is for siFBL polyA+ RNA samples (Sample 48, 49, and 50); 5’rApp-NNNNN TTAGGC AGATCGGAAGAGCACACGTCT-3SpC3 is for all the rest samples in dataset3 (Sample 36-47, and Sample 51-53). RNA 5'-adaptor sequence is always 5’-GUUCAGAGUUCUACAGUCCGACGAUC NNNNN-3' for Sample 36-53.

first: Li

first: Chang

last: Ye

first: Bryan

last: Dickinson

first: Chuan

last: He


title: Transcriptome-wide probing of RNA in Bacillus subtilis identified RNA thermometers that regulate translation of two glycerol permease genes

city: University Park

first: Elizabeth

last: Jolley

state: PA

address: 239 Chemistry Bldg, Pennsylvania State University

institute: Pennsylvania State University

summary: Here we use Structure-seq2 to probe the in vivo RNA structurome of B. subtilis grown at four different temperatures. We show that increases in reactivity with increasing temperature follow non-monotonic trends. Focusing on subregions of the transcriptome led to the discovery of two novel RNA thermometers that control expression of glpF and glpT.

overall_design: Structure-seq2 libraries prepared from RNA extracted from Bacillus subtilis grown to mid-exponential phase at four different temperatures. Control samples and DMS-treated samples were prepared from three biological replicates. Libraries were sequenced on an Illumina NextSeq in single-end mode.

first: Helen

last: Yakhnin

last: Tack

first: Paul

last: Babitzke

first: Philip

last: Bevilacqua


title: Transcriptional pausing induced by ionizing radiation enables the acquisition of radioresistance in nasopharyngeal carcinoma [RNA-seq]

overall_design: mRNA profiles of radiosensitive cell line CNE2 and radioresistant cell line CNE2-IR.

first: Kai

last: Yuan


title: Systematic benchmarking of single-cell ATAC sequencing protocols

status: Public on May 22 2023

city: Leuven

first: Stein

last: Aerts

state: Vlaams-Brabant

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

summary: We systematically benchmarked 8 single-cell ATAC sequencing technologies for their capacity to generate high-quality single-cell open chromatin profiles, and to elucidate the regulatory landscape of complex samples. Our study contains 47 individual human PBMC scATAC-seq experiments from a reference male and female donor. To streamline data analysis, we devised PUMATAC (https://github.com/aertslab/PUMATAC), a flexible and universal data analysis pipeline and best practices repository for scATAC-seq. Systematic technology-specific differences in sequencing library complexity and biases in tagmentation specificity were found to impact the accuracy of cell type annotation, genotype demultiplexing, peak calling, differential region accessibility, and motif enrichment. Together, our data forms a new scATAC-seq reference of more than 169, 000 PBMC cells with matched single-cell multiome and RNA-seq data.

overall_design:
We performed a systematic benchmark of 8 different scATAC-seq methods on human PBMC across 47 samples.

Please note that the CellRanger output files have been added to the GSM7102992-GSM7103000 sample records on Nov 16, 2023, as the existing scRNA-seq upload format (a .h5ad file) is dependent on specific software to read.

first: Florian

last: De Rop

first: Gert

last: Hulselmans

first: Chris

last: Flerin

first: Paula

last: Soler-Vila

first: Albert

last: Rafels

first: Valerie

last: Christiaens

first: Carmen

middle: B

last: González-Blas

first: Domenica

last: Marchese

first: Ginevra

last: Caratù

first: Suresh

last: Poovathingal

first: Orit

last: Rozenblatt-Rosen

first: Michael

last: Slyper

first: Wendy

last: Luo

first: Christoph

last: Muus

first: Fabiana

last: Duarte

first: Rojesh

last: Shrestha

first: Tansu

last: Bagdatli

first: Ryan

last: Corces

first: Lira

last: Mamanova

first: Andrew

last: Knights

first: Kerstin

last: Meyer

last: Mulqueen

first: Patrick

last: Maschmeyer

first: Akram

last: Taherinasab

first: Jörn

last: Pezoldt

first: Camille

last: Lambert

first: Marta

last: Iglesias

first: Sebastián

last: Najle

first: Zain

middle: Y

last: Dossani

first: Luciano

last: Martelotto

first: Zach

last: Burkett

first: Ronald

last: Lebofsky

first: José

last: Martin-Subero

first: Satish

last: Pillai

first: Arnau

last: Sebé-Pedrós

first: Bart

last: Deplancke

first: Sarah

last: Teichmann

first: Leif

last: Ludwig

first: Theodore

last: Braun

last: Adey

first: William


title: Single cell transcriptomics reveals cell type specific features of developmentally regulated responses to lipopolysaccharide between birth and 5 years

status: Public on May 18 2023

city: Tucson

first: James

last: Read

state: AZ

address: 1501 N. Campbell Avenue

institute: University of Arizona

summary: Perinatal life is a period of extraordinary change in which newborns transition into a new world abundant in environmental stimuli and pathogens.  To meet this challenge, the neonatal immune system is equipped with unique functional characteristics and is subject to ongoing development across the early childhood years. To investigate differences in innate immune transcriptional responses, we applied scRNA-Seq to analyze blood collected at birth and 5 years of age following stimulation with two well-characterized model antigens - Lipoloysaccharide (LPS) and Polyinosinic:polycytidylic acid (Poly(I:C))

overall_design:
Matched birth (CBMC) and 5 years (PBMC) blood samples from two donors were treated with LPS and Poly(I:C) treatment, along with matched untreated controls, for 18 hours. Post-culture single cell suspensions were profiled with scRNA-Seq (10X Genomics).
----------------------------
Authors state "The raw sequence data (.fastq) will be made available with controlled access (dbGaP)."

first: Anthony

last: Bosco


title: An integrated organoid omics map extends modeling potential of kidney disease

city: Ann Arbor

first: Jennifer

last: Harder

state: MI

address: 1301 Catherine St.

department: Internal Medicine, Division of Nephrology

institute: University of Michigan Medical School

summary: We performed gene expression profiling analysis using data obtained from RNA-seq of isolated kidney organoid spheroids collected at days 21, 25 and 29 in culture.

overall_design:
Bulk RNA Design: All bulk RNA samples start with 'Sample_' in their title. Kidney organoids were generated from human embryonic stem cells (UM77-2, NIH registry #0278) according to published protocol (Harder et al., JCI Insight 2019).  Organoid spheroids were collected at day 21, day 25 and day 29, then lysed. RNA was extracted, and cDNA generated.  Library prep and next-generation sequencing of total RNA on a NovaSeq4000 (150 bp, paired end) were carried out in the Advanced Genomics Core at the University of Michigan.

Single Cell Design: All single cell RNAseq samples start with 'D2' in their title.
Whole well organoids were treated at D23 with TNFα 5ng/ml for 24h and collected at D24. Cells were dissociated using cold active protease into single cells and 10x Genomics sequencing was performed in the Advanced Genomics Core at the University of Michigan.

first: Sean

last: Eddy

first: Fadhl

last: Alakwaa


title: Phase II for N6-methyladenosine RNA modification-based biodosimeters for absorbed ionizing radiation dose estimation

status: Public on May 11 2023

city: Beijing

first: Yiming

last: Lu

address: Taiping Road

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

summary:
We conducted a two-phase mouse total-body irradiation (TBI) experiment and measured the RNA m6A levels in peripheral blood mononuclear cells (PBMCs).
Phase II

overall_design: In the phase I experiment, we focused on screening the RNA transcripts with constantly altered m6A levels during a relatively long period of time post irradiation (TPI) in mouse PBMCs. In this phase, a total of 25 mice exposed to a dose of 6.5 Gy gamma rays were randomly divided into 5 groups for a time-course measurement of the physiological and molecular phenotypes of mice, and 5 sham-exposed mice were used as the control group. The phase II experiment focused on identifying the RNA transcripts that still exhibit significantly altered m6A sites even with a lower dose TBI. In this phase, a total of 10 mice exposed to a dose of 2 Gy gamma rays were randomly divided into 2 groups, and 5 sham-exposed mice were used as the control group.

first: Hongxia

last: Chen

first: Gangqiao

last: Zhou


title: RNA-seq analysis of inferior alveolar nerve after its injury

status: Public on May 16 2023

city: Chiyoda-ku, Tokyo

first: Yoshinori

last: Hayashi

address: 1-8-13, Kandasurugadai

department: Physiology

institute: Nihon University

summary: Differences in gene expression patterns between the inferior alveolar nerve (IAN) 14 days after IAN transection and the intact IAN in sham rats were analyzed by RNA-seq.

overall_design: To analyze changes in gene expression after IAN injury, IANs were collected from three rats 14 days after IAN injury and 14 days after sham surgery, respectively.

first: Eri

last: Oshima

first: Yoshinor


title: Argonaute 2 associated miRNAs in CA1, CA3 and Dentate Gyrus hippocampal subfields from the rat perforant pathway stimulation (PPS) epilepsy model

status: Public on Jun 02 2023

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

summary: MicroRNAs (miRNAs) are short noncoding RNAs that shape the gene expression landscape, including during the pathogenesis of temporal lobe epilepsy (TLE). In order to provide a full catalog of the miRNA changes that happen during experimental TLE, we sequenced Argonaute 2-loaded miRNAs in CA1, CA3 and Dentate Gyrus hippocampal subfields from the rat perforant pathway stimulation (PPS) model at regular intervals between the time of the initial precipitating insult to the establishment of spontaneous recurrent seizures.

overall_design: small RNA sequencing of Ago2-loaded miRNAs from rat perforant pathway stimulation (PPS) model of epilepsy development. Sequenced in timepoints during epileptogenesis and at chronic phase. Each group is in triplicate.

first: Jorgen

last: Kjems

first: David

last: Henshall


title: The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development

last: Crosson

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

overall_design: Refer to individual Series


title: Phase I for N6-methyladenosine RNA modification-based biodosimeters for absorbed ionizing radiation dose estimation

summary:
We conducted a two-phase mouse total-body irradiation (TBI) experiment and measured the RNA m6A levels in peripheral blood mononuclear cells (PBMCs).
Phase I


title: Long non-coding RNA and mRNA expression profiles in rats with LPS-induced myocardial dysfunction

status: Public on May 17 2023

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

summary: Sepsis is a life-threatening disease that often causes multiple organ dysfunctions. Long noncoding RNAs (lncRNAs) are involved in the pathogenesis and development of sepsis. However, there is little known about the function of lncRNAs in sepsis-induced myocardial dysfunction.To test the hypothesis that dysregulating lncRNAs may be involved in sepsis-induced myocardial dysfunction, we identified differentially expressed (DE) lncRNAs and mRNAs in cardiac tissue by high-throughput sequencing. We constructed coding and non-coding co-expression (CNC) and lncRNA-micro RNA (miRNA)-mRNA competing endogenous networks. The findings will provide useful information for exploring therapeutic candidate targets and new molecular biomarkers of septic myocardial injury.

overall_design: Male Wistar rats (8–10 weeks old, 150–200 g) were randomly divided into the following two groups: rats in the LPS group (n = 5) received an intraperitoneal injection of 10mg/kg LPS (5 mg LPS dissolved in 1 mL 0.9% saline), and those in the control group (n = 5) were intraperitoneally injected with 0.9% saline (2 ml/kg). we analyzed the lncRNAs, miRNAs and mRNAs expression profiles using RNA-seq. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were carried out and coding and non-coding co-expression and competing endogenous RNA networks were constructed to investigate the mechanisms.

first: Ye-Chen

last: Han

first: Hong-Zhi

last: Xie

first: Zhu-Jun

last: Shen

first: Ruo-Lan

last: Xiang

first: Hao

last: Qian

first: Jing-Yi

last: Li

first: Shu-Yang

last: Zhang


title: Metastasis Ingesting Macrophages

status: Public on May 01 2023

first: Mark

last: Headley

address: 1100 Fairview Ave N

department: TST

institute: Fred Hutch Cancer Center

summary: Comparison of Macrophages from lungs 24hrs post-injection with B16-F10 Melanoma Cells expressing the Fluoresence Protein ZsGreen. ZsGreen+ and ZsGreen- macrophages were sorted and transcriptome compared.

overall_design: Samples are Metastasis Associated Macrophages sorted based on the following surface phenotype. Live, CD45+, CD3-, CD90.2-, CD19-, B220-, Ly6g-, NK1.1-, Siglec F-, CD11c+, MHCII+, CD24-, and either ZsGreen+ or ZsGreen- as an index of tumor ingestion. 4 samples per condition.


title: Mammalian Genomic Manipulation with Orthogonal Bxb1 DNA Recombinase Sites for the Functional Characterization of Protein Variants

status: Public on May 05 2023

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

summary: The Bxb1 bacteriophage serine DNA recombinase is an efficient tool for engineering recombinant DNA into the genomes of cultured cells. Generally, a single engineered “landing pad” site is introduced into the cell genome, permitting the integration of transgenic circuits or libraries of transgene variants. While sufficient for many studies, the extent of genetic manipulation possible with a single recombinase site is limiting, and insufficient for more complex cell-based assays for protein function. Here, we harnessed two orthogonal Bxb1 recombinase sites to enable new avenues for mammalian synthetic biology. By designing plasmids with two recombinase sites, we demonstrate that we can avoid genomic integration of undesirable bacterial DNA elements. We also created “double landing pad” cells simultaneously harboring two orthogonal Bxb1 recombinase sites. These cells allow transgenic protein variant libraries to be readily paired with assay-specific protein partners or biosensors, opening up new functional readouts for large-scale functional assays.

overall_design: Genomically engineered HEK293T cells with amplicons derived from exogenous DNA that has recombined using the Bxb1 bacteriophage integrase and various complementary Bxb1 attP and attB sites

first: Sarah

last: Roelle


title: Stress-induced splicing activation of immediate early genes by nuclear speckle reorganization [HLs]

status: Public on May 04 2023

city: Göttingen

first: Hsu-Min

last: Sung

state: Niedersachsen

address: Humboldtallee 23

institute: Heart Centre Göttingen

summary: Current models posit that nuclear speckles (NSs) serve as reservoirs of splicing factors and facilitate post-transcriptional processing of mRNA. Here, we discovered that ribotoxic stress leads to a profound reorganization of NSs with enhanced recruitment of factors required for 5' and 3' splice site recognition including the RNA-binding protein TIAR, U1 snRNP proteins and U2-associated factor 65, as well as serine 2 phosphorylated RNA polymerase II. NS reorganization is dependent on the stress-activated p38 mitogen activated protein kinase (MAPK), and goes along with splicing activation of both pre-existing and nascent pre-mRNAs. In particular, ribotoxic stress causes targeted excision of retained introns from pre-mRNAs of immediate early genes (IEGs), whose transcription is induced during the stress response. Importantly, enhanced splicing of the IEGs ZFP36 and FOS is accompanied by re-localization of the corresponding mRNAs to NSs. Our study reveals NSs as a dynamic compartment that is remodeled under stress conditions to promote the excision of retained introns and thereby enhance the expression and processing of IEG mRNAs.

overall_design: Transcriptional shut-off with actinomycin D for 0, 1, 2, and 4 h in HeLa cells after treatment with DMSO or Anisomycin (ANI) for 2 h, performed in two biological replicates

first: Johanna

last: Schott

first: Marius

last: Hardt

first: Doris

last: Lindner

first: Georg

last: Stoecklin


title: Electrical stimulation accelerate Wallerian degeneration and promote peripheral nerve regeneration.

first: Xiangling

state: Beijing

address: Fuxing

department: orthopedics

institute: PLA General Hospital

summary:
To investigate the mechamism of electrical stimulation in the regulation of wallerian degeneration after peripheral nerve injury, we prepaired 3 samples for each group to ensure these data's quality.
We then performed gene expression profiling analysis using data obtained from RNA-seq of each group.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for electrical stimulation and non-electrical stimulation for injured nerve.


title: Stress-induced splicing activation of immediate early genes by nuclear speckle reorganization [ThioU]

overall_design: Metabolic labeling of RNA with 4sU in HeLa cells for the last 30 min or for the entire time frame of a 2 h treatment with DMSO or Anisomycin (ANI), performed in two biological replicates, to distinguish nascent and pre-existing RNA.

first: Janina

last: Lehmann


title: Stress-induced splicing activation of immediate early genes by nuclear speckle reorganization


title: Effect of Lacticaseibacillus rhamnosus 0030 on nucleus accumbens gene expression in high-fat diet fed mice

status: Public on Apr 28 2023

city: Nuthetal

first: Andre

last: Kleinridders

state: Brandenburg

address: Arthur-Scheunert-Allee 155

department: Molecular and Experimental Nutritional Medicine

institute: University of Potsdam

summary:
To investigate the effect of Lacticaseibacillus rhamnosus 0030 (LR) on nucleus accumbens gene expression in a mouse model of established diet-induced obesity, we treated high-fat diet fed male mice with 1x10^8 CFU LR using daily peroral gavage. Vehicle (here: PBS)-treated mice fed with a low-fat diet or high-fat diet served as controls.
We then performed gene expression profiling analysis using data obtained from RNA-seq of those three groups (LFD vehicle, HFD vehicle, HFD LR).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for nucleus accumbens from LFD vehicle, HFD vehicle, and HFD LR.

first: Mareike

last: Schell


title: Mycolic acid nanoparticle vaccination leads to lipid antigen persistence and unique differentiation of mycobacterial-specific T cells

status: Public on Apr 25 2023

first: Chyung-Ru

last: Wang

address: 320 E Superior Street

department: Microbiology and Immunology

institute: Northwestern University

summary: Mycobacterium tuberculosis (Mtb) infection elicits both protein and lipid antigen-specific T cell responses. However, the incorporation of lipid antigens into subunit vaccine strategies and formulations has been underexplored, and the properties of vaccine-induced Mtb lipid-specific memory T cells remained elusive. Mycolic acid (MA), a major lipid component of the Mtb cell wall, is presented by human CD1b molecules to T cells.  MA-specific CD1b-restricted T cells have been detected in the blood and disease sites of Mtb-infected individuals, suggesting MA is a promising lipid antigen for incorporation into multicomponent subunit vaccines. In this study, we utilized bicontinuous nanospheres (BCN) to efficiently encapsulate MA and deliver it to MA-specific T cells both alone and in combination with an immunodominant Mtb protein antigen (Ag85B). Pulmonary delivery of MA-loaded BCN (MA-BCN) elicited MA-specific T cell responses in humanized CD1 transgenic mice. Simultaneous delivery of MA and Ag85B within BCN activated both MA- and Ag85B-specific T cells. Interestingly, pulmonary vaccination with MA-Ag85B-BCN led to the persistence of MA, but not Ag85B, within alveolar macrophages in the lung. Vaccination of MA-BCN through intravenous or subcutaneous route, or with attenuated Mtb likewise reproduced MA persistence. Moreover, MA-specific T cells in MA-BCN-vaccinated mice differentiated to have a T follicular helper-like phenotype. Overall, BCN platform allows for the dual encapsulation of lipid and protein antigen and leads to persistent lipid depots that could offer long-lasting immune response and protection.

overall_design: Bone marrow cells from DN1Tg/hCD1Tg/Rag-/- (CD45.2) and hCD1Tg mice (CD45.1) were depleted of mature T cells using anti-Thy-1.2 (AT83.A-6) plus rabbit complement (Cedarlane Laboratories). Equal numbers of cells (5x106) were adoptively transferred into hCD1Tg (CD45.1) mice irradiated with 900 rads. After 6 weeks, mixed BM chimeric mice were intratracheally vaccinated with either 2.5 micrograms of MA in MA-BCN or equivalent volume of PBS. CD44+CD62L+ and CD44-CD62L+ DN1 T cells were sorted from lymph nodes of DN1-hCD1Tg BM chimera mice vaccinated with MA-BCN at 6 weeks post vaccination by BD FACS Aria.

first: Eva

last: Morgun

first: Jennifer

last: Zhu

first: Sultan

last: Almunif

first: Sharan

last: Bobbala

first: Melissa

last: Aguilar

first: Junzhong

first: Yongyong

last: Cui

first: Liang

last: Cao

first: Chetan

last: Seshadri

first: Evan

last: Scott


title: Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis [Tissue_RNA-seq]

status: Public on Apr 23 2023

city: New York

first: Dr. Chiara

last: Giannarelli

state: NY

address: 435 E 30th St

department: Cardiology

institute: NYU Langone Health

summary:
we present a novel path to drug repurposing to identify new immunotherapies for ASCVD. The integration of time
of-flight mass cytometry (CyTOF) and RNA-sequencing identified unique inflammatory
signatures in peripheral blood mononuclear cells (PBMCs) stimulated with ASCVD plasma. By
comparing these inflammatory signatures to large-scale gene expression data from the LINCS
L1000 dataset, we identified drugs that could reverse this inflammatory response.
In conclusion, a systems immunology-driven drug repurposing with pre-
clinical validation strategy can aid the development of new cardiovascular immunotherapies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for atherosclerotic patient tissue stimulated with autologous plasma -/+ saracatinib was performed.

first: Letizia

last: Amadori

first: Chiara


title: Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis [RNA-seq_PBMC]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for healthy donors pbmcs stimulated with patient plasma or healthy donors plasma was performed.

first: Simon

last: Koplev


title: Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis

status: Public on Apr 22 2023


title: MAPT expression is mediated by long-range interactions with cis-regulatory elements [scMultiomics]

status: Public on Apr 12 2023

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Tau is encoded by MAPT and abnormal aggregates of tau are a hallmark of a group of neurodegenerative diseases called tauopathies. MAPT is lowly expressed in neural progenitor cells (NPCs), but it is more highly expressed in oligodendrocytes, astrocytes, and neurons that derive from NPCs. This expression switch at differentiation suggests that MAPT expression is controlled by transcription factors and cis-regulatory elements specific to these differentiated cell types, including neurons.

overall_design: We performed HiC and three-dimensional chromatin conformation capture (Capture-C), single-nucleus multiomics (RNA-seq and ATAC-seq), bulk ATAC-seq, and ChIP-seq for H3K27Ac and CTCF in neurons differentiated from human iPSC cultures. From these methods, we nominated candidate cis-regulatory elements (cCREs) for MAPT in human NPCs, NPCs differentiated to neurons, and pure inhibitory or excitatory neuron cultures. We then functionally assessed nominated regions using luciferase assays and CRISPR dCas9-KRAB inhibition experiments to assess the effect of nominated regions on MAPT expression.

first: Brianne

last: Rogers

first: Ashlyn

last: Anderson

first: J

middle: N


title: Involvement of cardiac glycosides targeting Na/K-ATPase in their inhibitory effects on c-Myc expression via its transcription, translation, and proteasomal degradation

status: Public on Apr 07 2023

city: Nagoya city

first: Muneshige

last: Tokugawa

address: 3-1 Tanabe-dori, Mizuhoku

institute: Nagoya City University

summary: Cardiac glycosides (CGs) have been used for decades to treat heart failure and arrhythmic diseases. Recent non-clinical and epidemiological findings have suggested that CGs exhibit anti-tumor activities. Therefore, CGs may be repositioned as drugs for the treatment of cancer. A detailed understanding of the anticancer mechanisms of CGs is essential for their application to the treatment of targetable cancer types. To elucidate the factors associated with the anti-tumor effects of CGs, we performed transcriptome profiling on human multiple myeloma AMO1 cells treated with periplocin, one of CGs. Periplocin significantly down-regulated the transcription of MYC (c-Myc), a well-established oncogene. Periplocin also suppressed c-Myc expression at the protein levels. This repression of c-Myc was also observed in several cell lines. To identify target proteins for the inhibition of c-Myc, we generated CG-resistant (C9) cells using a sustained treatment with digoxin. We confirmed that C9 cells acquired resistance to the inhibition of c-Myc expression and cell proliferation by CGs. Moreover, the sequencing of genomic DNA in C9 cells revealed the mutation of D128N in α1-Na/K-ATPase, indicating the target protein. These results suggest that CGs suppress c-Myc expression in cancer cells via α1-Na/K-ATPase, which provides further support for the anti-tumor activities of CGs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human multiple myeloma AMO1 cells treated with DMSO and those of treated with periplocin.

first: Yasumichi

last: Inoue

first: Hiromasa

last: Aoki

first: Chiharu

last: Miyajima

first: Kan'ichiro

last: Ishiuchi

first: Kento

last: Tsurumi

first: Chisane

last: Kujirai

first: Daisuke

last: Morishita

first: Michiyo

last: Matsuno

first: Hajime

last: Mizukami

first: Masaki

last: Ri

first: Shinsuke

last: Iida

first: Toshiaki

last: Makino

first: Mineyoshi

last: Aoyama

first: Hidetoshi

last: Hayashi


title: Senescent melanocytes driven by glycolytic changes are characterized by melanosome transfer dysfunction [scRNA-seq]

status: Public on Apr 03 2023

city: Suwon

first: Jin Cheol

last: Kim

address: 206, World cup-ro, Yeongtong-gu

institute: Ajou University School of Medicine

summary:
To investigated the functional characteristics and molecular mechanisms underlying senescence in UV irradiated melanocytes.
We performed gene expression profiling analysis using data obtained from scRNA-seq of UV-irradiated senescent melanocytes.

overall_design: Gene expression profiling analysis of scRNA-seq data for UV-irradiated primary normal human melanocytes (HEMn-MP, Gibco, C1025C)

first: Jin

first: Young

middle: J

last: Park

first: Tae

first: Hee

last: Kang


title: Senescent melanocytes driven by glycolytic changes are characterized by melanosome transfer dysfunction [RNA-seq]

summary:
To investigated the functional characteristics and molecular mechanisms underlying senescence in UV irradiated melanocytes.
We performed gene expression profiling analysis using data obtained from RNA-seq of 3 normal melanocytes and 3 UV-irradiated senescent melanocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary normal human melanocytes (HEMn-MP, Gibco, C1025C)  and its UV-irradiated model.


title: TGF-β1 alter the SARS-CoV2 pathogenesis and modulates ACE2 expression by miRNA dependent mechanism

status: Public on Apr 01 2023

city: Charlottesville

first: Agnieszka

last: Swiatecka-Urban

address: 409 Lane Road

department: Pediatrics

institute: University of Virginia School of Medicine

summary: We studied miRNAs and their gene targets affecting SARS-CoV-2 pathogenesis in CF airway epithelial cell models in response to TGF-β1. Small RNAseq in CF human bronchial epithelial cell line treated with TGF-β1 and miRNA profiling characterized TGF-β1 effects on the SARS-CoV-2 pathogenesis pathways. Among the effectors, we identified and validated two miRNAs targeting ACE2 mRNA using different CF and non-CF human bronchial epithelial cell models. We have shown that TGF-β1 inhibits ACE2 expression by miR-136-3p and miR-369-5p. ACE2 levels were higher in cells expressing F508del-CFTR, compared to wild-type(WT)-CFTR and TGF-β1 inhibited ACE2 in both cell types. The ACE2 protein levels were still higher in CF, compared to non-CF cells after TGF-β1 treatment. TGF-β1 prevented the functional rescue of F508del-CFTR by ETI in primary human bronchial epithelial cells while ETI did not prevent the TGF-β1 inhibition of ACE2 protein. Finally, TGF-β1 reduced binding of ACE2 to the recombinant monomeric spike RBD. Our results may help to explain, at least in part, the role of TGF-β1 on the SARS-CoV-2 entry via ACE2 in the CF and non-CF airway.

overall_design: Parental human bronchial epithelial CFBE41o- cells, were maintained in Minimum Eagle's Medium (MEM; Thermo Fisher Scientific, Walthman, MA, USA) supplemented with 50 units/ml penicillin, 50 μg/ml streptomycin and 2mM L-glutamine (Thermo Fisher Scientific), and 10% fetal bovine serum (FBS; Corning, NY) in a 5% CO2, 95% air incubator at 37°C. To establish polarized monolayers, cells were seeded on 24 mm diameter Transwell filters (Corning, New York, NY) at 2×106 and grown in air-liquid interface (ALI) culture at 37 °C for 6-9 days. Human TGF-β1 (Sigma-Aldrich, St. Louis, MO, USA)(n=3), or vehicle control (4 mM HCl + 1 mg/mL Bovine Serum Albumin; BSA, R&D Systems)(n=3) was used at concentration 15 ng/mL

first: NILAY

last: Mitash

first: FANGPIN

last: Mu

first: AGNIESZKA


title: Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis [DRUG_RNA-seq]

first: Dr. Chiara

last: Giannarelli

overall_design: Comparative gene expression profiling analysis of RNA-seq data for healthy donors pbmcs stimulated with patient plasma -/+ selected compounds.

first: Letizia

last: Amadori

first: Chiara

first: Ravneet

last: Kaur


title: Transfer of small RNA from extracellular vesicles secreted by primary human airway epithelial cells to Pseudomonas aeruginosa

status: Public on Apr 11 2023

city: Hanover

first: Thomas

middle: H.

last: Hampton

state: NH

address: Dewey Field Road, HB 7550

institute: Geisel School of Medicine at Dartmouth

summary: P. aeruginosa were exposed to extracellular vesicles (EVs) secreted by primary human airway epithelial cells from 3 donors or PBS vehicle control for 6 h. Total RNA was isolated, small RNA libraries were prepared with the QIAseq smRNA kit (Qiagen) and 75-bp single-end reads were generated using Illumina MiniSeq. To assess transfer of human EV small RNAs to P. aeruginosa, sequences that did not map to the PA14 reference genome were aligned to the human genome.

sample_organism:
Pseudomonas aeruginosa
Homo sapiens

platform_organism:
Pseudomonas aeruginosa
Homo sapiens

overall_design: P. aeruginosa (1.5*E+07 CFU) were exposed to PBS vehicle control or EVs (5E+09 EV/ml) for 6 h. To avoid possible carry-over of EVs (and miRNA) attached to the outside of the bacteria, the bacteria were washed with PBS and the bacterial outer membrane was lysed with EDTA to release periplasmic contents and factors associated with the bacterial outer membrane and periplasm (77-79). The cells were then washed again in PBS, and cytoplasmic RNA was harvested after lysis of bacterial cell wall and inner membrane. Total RNA was isolated with the miRNeasy Mini Kit (Qiagen, Germantown, MD, Cat. # 217004), including the on-column DNA digestion. Sequencing libraries were prepared with the QIAseq smRNA kit (Qiagen) and 75-bp single-end reads were generated using an Illumina MiniSeq. Sequences that did not map to the PA14 reference genome were aligned to the human genome using CLC Genomics Workbench software (Qiagen).

first: Katja

last: Koeppen

first: Fred

middle: W

last: Kolling


title: CUT&RUN analysis of murine wt NPCs grown in alone and in co-culture with primary brain microvascular endothelial cells

status: Public on Mar 27 2023

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: We previously established co-culture assay in which NPCs acquire phenotypic hallmarks of quiescence upon direct cell-cell contact with primary brain microvascular endothelial cells (bmvEC). Here, we used this in vitro assay to identify the mechanisms by which p53 enforces quiescence

overall_design: The experiment was conducted to identify the direct binding sites of p53 at response elements upon co-culture-induced quiescence in mouse NPCs

first: Simona

last: Parrinello

first: Samuel

last: Marguerat


title: RNA-seq analysis of in vitro p53+/+ and p53-/- neural progenitor cells (NPCs) upon direct cell-cell contact with primary brain microvascular endothelial cells (bmvEC)

summary: To investigate the mechanisms that govern neural stem cells quiescence, we performed transcriptomic analysis of mouse NPCs grown in a co-culture assay with primary brain microvascular endothelial cells (bmvEC).

overall_design: 3 independent biological repeats were sequenced for analysis


title: Targeted transcriptome analysis of isolated intestinal epithelial cells from mice with constitutive Ptpn2-deficiency [ILEUM]

status: Public on Apr 06 2023

city: RIVERSIDE

first: Declan

last: McCole

state: CA

address: 3401 Watkins Drive

department: Biomedical Sciences

institute: University of California Riverside

summary: Loss-of-function variants in the protein tyrosine phosphatase non-receptor type 2 (PTPN2) gene are associated with increased risk of inflammatory bowel disease (IBD). PTPN2 encodes T cell protein tyrosine phosphatase (TCPTP), a negative regulator of several intracellular signaling pathways including JAK-STAT. It has been shown that Ptpn2 is critical for intestinal epithelial cell (IEC) barrier maintenance, IEC-macrophage communication, and modulation of the gut microbiome in mice. However, the mechanisms by which Ptpn2 influences the intestinal flora are unknown. In this study, we aimed to identify how Ptpn2-loss affects the expression of genes associated with function/differentiation of IECs in the small and large intestines that could contribute to higher susceptibility to infection.

overall_design: Intestinal epithelial cells were isolated from 21 days old mice (littermates) as Ptpn2-KO mice are normal at birth but die within 3-5 weeks of age. Total RNA was used. Results of two separate panels with a predefined set of targets ('AutoImmune Profiling’ and ‘PanCancer Pathways') from the same intestinal segment were combined for analysis, with the addition of 30 customized targets to each panel comprising of IEC markers, function and differentiation factors, host-bacteria interaction, autophagy, immune response and iron transport, totaling >1500 targets. Data from each panel was normalized separately and then consolidated using the MultiRLF function in the nSolver Analysis Software 4.0.

first: Vinicius

last: Canale

first: Ali

last: Shawki

first: Marianne

middle: R

last: Spalinger

middle: F