title: Cooperation between cGAS and RIG-I sensing pathways enables improved innate recognition of HIV-1 by myeloid dendritic cells in elite controllers

city: Cambridge

first: Ce

last: Gao

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

summary: Spontaneous control of HIV-1 replication in the absence of anti-retroviral therapy (ART) naturally occurs in a small proportion of HIV-1-infected individuals known as elite controllers (EC), likely as a result of improved innate and adaptive immune mechanisms. Previous studies suggest that enhanced cytosolic immune recognition of HIV-1 reverse transcripts in conventional dendritic cells (mDC) from EC enables effective induction of antiviral effector T cell responses. However, the specific molecular circuits responsible for such improved innate recognition of HIV-1 in mDC from these individuals remain unknown. Here, we identified a subpopulation of EC whose mDC displayed higher baseline abilities to respond to intracellular HIV-1 dsDNA stimulation. A computational analysis of transcriptional signatures from such high responder EC, combined with functional studies, suggested cytosolic recognition of HIV-1 dsDNA by cGAS, combined with sensing of viral mRNA by RIG-I after polymerase III-mediated HIV-1 DNA transcription. Together, our work identifies collaborative networks of innate sensing pathways that enhance cell-intrinsic abilities of mDC to induce antiviral innate responses against HIV-1; these observations might be useful for the therapeutic induction of effective antiviral immune responses.

overall_design: Total RNA was extracted from sorted Lin- HLADR+ CD11c+ mDC from the blood of a larger cohort of n=24 EC (85% male, 15% female) characterized by a median plasma viral load of 36 copies/ml (range 5-250 copies/ml) and living with HIV-1 for a median of 17.5 years (range = 3–27 years) and with CD4+ T cell counts median of 821 cells/mL (range: 407-1684 cells/mL) and n=15 HIV-1 positive individuals on antiretroviral therapy (HAART) with undetectable viremia (<20 copies/mL) and diagnosed a median of 11 years (min-max; 1.27 years) and with a median CD4+ T cell counts of 909/mL (min-max; 398-1367) patients using the Qiagen RNeasy Micro Kit. Subsequently, RNA-Seq libraries from mDC were generated as previously described. Briefly, SMART-seq2 (37) was used to prepare whole transcriptome amplification (WTA) and tagmentation-based libraries, and samples were sequenced on a NextSeq 500 Instrument (Illumina). Subsequently, sequences were aligned using the Hg38 human genome database by Bowtie 2 (38), and transcripts per million (TPM) values were obtained for each sample by RNA-Seq using Expectation-Maximization (RSEM) (39). TPM values were then normalized among all samples using the upper quantile normalization method. For a first set of analyses mDC RNA-seq data from all EC and all HAART individuals was compared. In subsequent analyses, RNA-seq data from a total of n=8 EC with known high (n=4) or low (n=4) in vitro response to HIV-1 dsDNA stimulation in mDC were compared. Pathway analyses were performed using Ingenuity Pathway Analysis and DAVID software. Additional gene network images were obtained from selected upstream regulator lists using the NetworkAnalyst software (12).

first: Enrique

last: Martín-Gayo

first: Marta

last: Calvet-Mirabent

first: Zhengyu

last: Ouyang

first: Mathias

last: Lichterfeld

first: Xu

last: Yu


title: Sumoylation-deficient phosphoglycerate mutase 2 impairs myogenic differentiation

status: Public on Jan 11 2023

city: Houston

first: Jun

last: wang

state: Texas

address: 6770 Bertner Ave

country: USA

institute: Texas Heart Institute

type: Expression profiling by high throughput sequencing

summary:
To investigate the importance of functional regulation of PGAM2 by SUMO conjugation in the context of myogenic differentiation.
We performed RNAseq analysis of WT and sumoylation deficient mutant (K176R mutatant) C2C12 cells at different differentiation days, i.e. day 0 and day4, respectively (n=3/group).

overall_design: Comparem gene expression profiling analysis of RNA-seq data for C2C12 WT and its homozygous K176R knockin mutant (KI).

last: Wang


title: Liver-specific FGFR4 knockdown in mice on a HFD increases bile acid synthesis and improves hepatic steatosis II

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease with increased risk in patients with metabolic syndrome. There are no FDA approved treatments, but farnesoid X receptor (FXR) agonists have shown promising results in clinical studies for NAFLD management. In addition to FXR, fibroblast growth factor receptor FGFR4 is a key mediator of hepatic bile acid synthesis. Using N-acetylgalactosamine-conjugated siRNA, we knocked down FGFR4 specifically in the liver of mice on chow or high-fat diet (HFD) and in mouse primary hepatocytes to determine the role of FGFR4 in metabolic processes and hepatic steatosis. Liver-specific FGFR4 silencing increased bile acid production and lowered serum cholesterol. Additionally, we found that HFD-induced liver steatosis and insulin resistance improved following FGFR4 knockdown. These improvements were associated with activation of the FXR-FGF15 axis in intestinal cells, but not in hepatocytes. We conclude that targeting FGFR4 in the liver to activate the intestinal FXR-FGF15 axis may be a promising strategy for the treatment of NAFLD and metabolic dysfunction.

overall_design: C57BL6/J male mice were placed on Chow (Mouse Diet 9F, PharmaServ) or 60% HFD (Research diets, D12492) for 12 weeks. The mice were injected subcutaneously with 3 mg/kg of GalNAc conjugated siRNA targeting FGFR4 or a sterile 0.9% sodium chloride solution (control) every two weeks while on the diets. Total RNA was isolated from small intestines.

first: Softic

last: Samir


title: Transcriptomic changes underlying glucocorticoid-induced suppression of milk production by dairy cows

city: Davis

first: Russell

last: Hovey

state: CA

address: 1 Shields Ave

department: Animal Science

institute: University of California Davis

summary:
In this study we sought to establish changes within the mammary glands of lactating dairy cows (n=3-4) in response to a single dose of exogenous DEX by performing serial biopsies of alternating quarters of the udder
Transcriptomic changes in the mammary glands in response to DEX were identified by RNA sequencing of mammary gland RNA at 0, 12, 24 and 72h post-DEX injection, followed by differential gene expression analysis
Coincident with the milk yield and composition changes was the differential expression of 519 and 320 genes at 12 and 24 h after DEX, respectively, with return of all gene expression to baseline levels by 72 h.

overall_design: Differential gene-expression analysis of 3-TAG RNA-seq data for mammary gland RNA sampled at 0, 12, 24 and 72h post-dexamethasone injection

first: Josephine

last: Trott

first: Anna

last: Sadovnikova


title: Role of aerobic exercise in ameliorating NASH

city: Xiamen

first: Qiuhong

last: Liu

address: The First Affiliated Hospital, Xiamen University. No.55 Zhenhai Road, Xiamen, China

country: China

institute: Xiamen Medical College

summary: To investigate the effect of aerobic exercise on liver injury in nonalcoholic steatohepatitis (NASH), we established a NASH model induced by atherosclerotic (Ath) diet and intervened with aerobic exercise training.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq for each group of mice.
Mice in the NASH+exercise group started to exercise training for 8 weeks at the same time after 12 weeks of Ath diet. Mice in the NASH group were fed Ath diet for a total of 20 weeks. The mice in the control group were fed a normal diet.

first: Xuejun

last: Li


title: Continuous Germinal Center Invasion Contributes to the Diversity of the Immune Response

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Antibody responses are characterized by increasing affinity and diversity over time. Affinity maturation occurs in germinal centers by a mechanism that involves repeated cycles of somatic mutation and selection. How antibody responses diversify while also undergoing affinity maturation is not as well understood. Here, we examined germinal center (GC) dynamics by tracking B cell entry, division, somatic mutation and specificity. Our experiments show that naïve B cells continuously enter GCs where they compete for T cell help and undergo clonal expansion. Consistent with late entry, invaders carry fewer mutations but can contribute up to 30 % or more of the cells in late-stage germinal centers. Notably, cells entering the germinal center at later stages of the reaction diversify the immune response by expressing receptors that show low affinity to the immunogen. Paradoxically, the affinity threshold for late GC entry is lowered in the presence of high affinity antibodies.

overall_design:
RNA-seq profiling of Follicular B cells and Germinal Center B cells.
Cells were sorted directly into a solution of 1% 2-β-mercaptoethanol (Sigma) in TCL Buffer (Qiagen, 1031576) and RNA was isolated using RNAClean XP Beads (Beckman Coulter, A63987). Near full-length mRNA was reverse transcribed as previously described (Islam et al., 2014) (Trombetta et al., 2014). Multiplexed libraries were prepared for sequencing using a Nextera XT DNA Library Preparation Kit (Illumina). Libraries were sequenced on an Illumina instrument at the Rockefeller University Genomics Core.

first: Thomas

last: Hägglöf

first: Melissa

last: Cipolla

first: Maximilian

last: Loewe

first: Spencer

middle: T

last: Chen

first: Luka

last: Mesin

first: Harald

last: Hartweger

first: Mohamed

middle: A

last: ElTanbouly

first: Alice

last: Cho

last: Gazumyan

first: Victor

last: Ramos

first: Leonidas

last: Stamatatos

first: Michel

middle: C

last: Nussenzweig

first: Charlotte

last: Viant


title: GDF15 neutralization restores muscle function and physical performance in a mouse model of cancer cachexia

first: Evanthia

last: Pashos

state: MA

address: 1 Portland St

institute: Pfizer Inc

summary: Cancer cachexia is a disorder characterized by both involuntary weight loss and impaired physical performance. Decline in physical performance of patients with cachexia is associated with poor quality of life, and currently there are no effective pharmacological interventions that restore physical performance. Here we examined the effect of GDF15 neutralization in a mouse model of cancer-induced cachexia (TOV21G) that manifested weight loss and muscle function impairments. With comprehensive assessments, our results demonstrated that cachectic mice treated with the anti-GDF15 antibody mAB2 exhibited body weight gain with near-complete restoration of muscle mass and markedly improved muscle function and physical performance. Mechanistically, the improvements induced by GDF15 neutralization were primarily attributed to increased caloric intake, while altered gene expressions in cachectic muscles were restored in both caloric intake-dependent and -independent manners. The findings implicate the potential of GDF15 neutralization as an effective therapy to enhance physical performance of patients with cachexia.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of gastrocnemius muscle from non-tumor bearing, IgG control or anti-GDF15 antibody mAB2 in the TOV21G model of cancer cachexia


title: Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish

first: Isaac

middle: M

last: Oderberg

state: Massachusetts

address: 77 Avenue Louis Pasteur 4th Floor, Room 458

department: Division of Genetics

institute: Brigham and Women's Hospital

summary: Single cell sequencing was performed on the adult zebrafish liver, on both uninjured animals, and animals regenerating from hepatocyte ablation.

overall_design: Samples were sequenced at 0, 1, 2, 3, and 7 days post ablation. Mock-treated and uninjured animals were also sequenced.

first: Wolfram

last: Goessling


title: PPARg and C/EBPa response to acute cold stress in brown adipose tissue [ChIP-Seq]

city: Grand Rapids

first: Ning

last: Wu

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Brown adipose tissue (BAT) has the ability to burn calories as heat. BAT thermogenesis is an attractive way to combat obesity pandemic. However, the transcriptional network resulting in lipid synthesis to oxidation shift during thermogenesis is not completely understood. Here, we report the regulation of two master regulators of adipogenesis, PPARγ and C/EBPα, during acute cold stress in BAT. We found PPARγ dissociated from DNA in a third of its binding sites and these included cebpa enhancers leading to decreased C/EBPα. This dissociation required PPARγ binding to activating ligands, thus modulated by diet. Meanwhile PPARα also detached from DNA, and co-activator PGC1α associated with ERR1 as part of transcriptional network regulating lipid metabolism. Subsequent global replacement of C/EBPα by C/EBPβ and its associated transcriptional machinery was required for upregulation of structural lipid synthesis despite general upregulation of fatty acid oxidation.

overall_design: Various ChIPseq of BAT

first: Kin

middle: H

last: Lau

first: Althea

middle: N

last: Waldhart

first: Holly

last: Dykstra

first: Tracey

last: Avequin


title: Depressed protein synthesis and anabolic signaling potentiate ACL tear resultant quadriceps atrophy II

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

institute: University of Kentucky

summary: Background: An anterior cruciate ligament tear (ACLT) leads to protracted quadriceps weakness and atrophy. Protein turnover largely dictates muscle size and is highly responsive to injury and loading. Regulation of the molecular protein synthetic machinery within the quadriceps following ACLT has largely been unexplored, limiting the development of targeted therapies. Purpose: To define the effect of ACLT on 1) activation of protein synthetic and catabolic signaling within quadriceps biopsies from human participants, and 2) the time course of alterations to protein synthesis and its molecular regulation in a mouse model of ACL injury. Study Design: Descriptive laboratory studyMethods: Muscle biopsy specimens were obtained from the ACL-injured and non-injured vastus lateralis of young adults following an overnight fast (n=21, mean ± SD: 19 ± 5 years). Mice had their limbs assigned to ACLT or control, and whole quadriceps were collected 6 hours, 1, 3, or 7 days post-injury with puromycin (0.04µmol/g) injected 30 minutes before tissue collection. Muscle fiber size and expression and phosphorylation of protein anabolic signaling proteins and E3 ubiquitin ligases were assessed at the protein and transcript level. Relative protein synthesis was measured by puromycin incorporation in mice.Results: Human quadriceps showed reduced phosphorylation of ribosomal protein S6 (-41%) in the ACL-injured limb (p<0.05), in addition to elevated phosphorylation of eukaryotic initiation factor 2α (+98%, p<0.05), indicative of depressed protein anabolic signaling in the injured limb. No differences in E3 ubiquitin ligase expression were noted (p>0.05). Protein synthesis was lower at 1 and 3 days post-ACLT in mice (p<0.05 vs. control limb). Conclusions: 1) Global protein synthesis and anabolic signaling deficits occur in the quadriceps in response to ACL injury, without notable changes in measured markers of muscle protein catabolism. 2) Importantly, these deficits occur prior to the onset of significant atrophy, underscoring the need for early intervention.  Clinical Relevance: These findings suggest blunted protein anabolism as opposed to increased catabolism likely mediates the quadriceps atrophy that occurs following ACL injury. Thus, future interventions should aim to restore muscle protein anabolism rapidly following the initial injury.

overall_design: Comparative gene  expression was assessed in human quadricep tissue in non-ACL injured limbs and ACL-injured limbs pre reconstruction surgery

middle: R

first: Camille

last: Brightwell

first: Christine

last: Latham

first: Nicholas

last: Thomas

first: C

middle: B

last: Mobley

first: Kevin

last: Murach

first: Darren

middle: L

last: Johnson

first: Brian

last: Noehren

first: Christopher

middle: S

last: Fry


title: Effect of NUF2 knockdown on gene expression in OVCAR3 cells

city: Jinan

first: Ruobing

last: Leng

state: Shandong

address: 324 JingwuWeiqi Road

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

summary: Ovarian cancer is the fifth most lethal malignancy in women, and epithelial ovarian cancer (EOC) is the most common histological type. Due to the absence of specific symptoms and diagnostic biomarkers, greater than 70% of EOC patients are diagnosed with clinical stage Federation International of Gynecology and Obstetrics (FIGO) III or IV, which has a five-year survival rate of only 20% to 30%. Thus, it is crucial to identify novel molecular biomarkers and therapeutic targets for EOC. NDC80 kinetochore complex component (NUF2) is upregulated and plays an important role in various human cancers. Our results showed that NUF2 was significantly upregulated in EOC tissues. Downregulation of NUF2 decreased cell proliferation, migration, invasion and tumor growth in nude mice. However, the mechanism of NUF2 in EOC remains unclear. The mechanisms by which NUF2 regulates EOC progression were detected by RNA sequencing. Thus, OVCAR3 cells after transfection with shNC (control) and shNUF2 (NUF2i) were added puromycin for establishing stable cell lines. RNA-seq was performed to analyze the differentially expressed genes in OVCAR3 cells after NUF2 knockdown.

overall_design: OVCAR3 cells after transfection with shNC (control) and shNUF2 (NUF2i) were treated with puromycin for establishing stable cell lines. RNA-seq was performed to analyze the differentially expressed genes in OVCAR3 cells after NUF2 knockdown

first: YunFang

last: Meng

first: Xiaomei

last: Sun

first: Yingzi

last: Zhao


title: T cell cellular stress and reticulocyte signatures, but not loss of naïve T lymphocytes, characterize severe COVID-19 in older adults

city: Tucson

first: Janko

middle: Nikolich

last: Zugich

address: 1656 E. Mabel St., MRB225, Tucson, AZ 85724

department: Immunobiology

institute: University of Arizona

summary: In children and younger adults up to 39 years of age, SARS-CoV-2 usually elicits mild symptoms that resemble the common cold. Disease severity increases with age starting at 30 and reaches astounding mortality rates that are ~330 fold higher in persons above 85 years of age compared to those 18-39 years old. To understand age-specific immune pathobiology of COVID-19 we have analyzed soluble mediators, cellular phenotypes, and transcriptome from over 80 COVID-19 patients of varying ages and disease severity, carefully controlling for age as a variable. We found that reticulocyte numbers and peripheral blood transcriptional signatures robustly correlated with disease severity. By contrast, decreased numbers and proportion of naïve T cells, reported previously as a COVID-19 severity risk factor, were found to be general features of aging and not of COVID-19 severity, as they readily occurred in older participants experiencing only mild or no disease at all. Single-cell transcriptional signatures across age and severity groups showed that severe but not moderate/mild COVID-19 causes cell stress response in different T cell populations, and some of that stress was unique to old severe participants, suggesting that in severe disease of older adults, these defenders of the organism may be disabled from performing immune protection. These findings shed new light on interactions between age and disease severity in COVID-19.

overall_design:
Single cell RNA Seq analysis of Covid patients among the following categories: Severe Old, Severe Adult, Mild Old and Mild Adult
Please note that raw data for Patient 7 - Patient 15 samples were lost and thus are not provided.

first: Ruchika

last: Bhat

middle: P

last: Coplen

first: Mladen

last: Jergovic

first: Makiko

last: Watanabe


title: PPARg and C/EBPa response to acute cold stress in brown adipose tissue

first: Ning

last: Wu

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

overall_design: Refer to individual Series


title: PPARg and C/EBPa response to acute cold stress in brown adipose tissue [RNA-seq]

overall_design: Various mRNA-seq of BAT

first: Kin

last: Lau

first: Althea

last: Waldhart

first: Holly

last: Dykstra

first: Tracey

last: Avequin


title: NCI-H460 gene expression analysis after in vivo treatment with anti-PD1 antibody

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Immune checkpoint inhibitors (ICIs) targeting PD-1/PD-L1 axis have made a breakthrough in the treatment of non-small cell lung cancer (NSCLC). However, a paradoxical boost in tumor growth was reported in a fraction of NSCLC patients after ICIs administration: a novel pattern of cancer progression defined “hyperprogressive disease” (HPD). Because the mechanism of HPD onset has not completely elucidated yet, this study aimed at investigating the cellular and molecular bases of this clinical phenomenon. Pre-treatment histological samples obtained from NSCLC patients were evaluated by immunohistochemistry (IHC) for immune cell infiltrate. Tissue samples from all patients with HPD showed tumor-infiltration by M2-like macrophages. To validate these findings in preclinical models, we utilized athymic nude mice that, lacking T-cells that may cloud the results, represent a suitable model to evaluate the role of macrophages in determining HPD. Immunodeficient mice were injected with human NSCLC NCI-H460 cell line, treated with anti-PD-1 antibody and tumor growth was evaluated over time. Anti-PD-1 treated H460 tumor-bearing mice showed HPD-like tumor growth as well as an increase in macrophage infiltration compared to control group. Interestingly, in these in vivo models, HPD-like growth, triggered by anti-PD-1 treatment, was dependent of anti-PD-1 antibody Fc domain. These results suggest that macrophages are the major players in HPD development and that FcR engagement on macrophages may determine a functional reprogramming of these immune cells toward a more aggressive and pro-tumorigenic phenotype, eventually inducing HPD.

overall_design: NCI-H460 cells (2.5x106 cells/mouse) were injected subcutaneously (s.c.) on the mice right flank of 8- to 9-week-old female athymic nude mice. Mice were peritumorally (p.t.) treated with 200 ug of monoclonal antibody anti mouse PD-1 (clone RMP1-14) starting 3 days after tumor injection. Anti-PD-1 antibody was administered twice a week until the end of the experiment. Control group received saline. Tumor growth was monitored over time. At the end of the experiment, tumor-bearing mice were sacrificed and tumors were collected and immediately frozen in liquid nitrogen until RNA extraction.


title: CNTNAP4 signaling regulates osteosarcoma disease progression

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

summary: Improved treatment strategies for sarcoma rely on clarification of the molecular mediators of disease progression. Recently, we identified the secreted glycoprotein NELL1 modulates osteosarcoma (OS) disease progression in part via altering the sarcomatous extracellular matrix and cell-ECM interactions. Of known NELL1 interactor proteins, Contactin-associated protein-like 4 (Cntnap4) encodes a member of the neurexin superfamily of transmembrane molecules best known for its presynaptic functions in the central nervous system. Here, CRISPR/Cas9 gene deletion of CNTNAP4 reduced OS tumor growth, sarcoma-associated angiogenesis, and pulmonary metastases.  CNTNAP4 knockout (KO) in OS tumor cells largely phenocopied the effects of NELL1 KO, including reductions in sarcoma cell attachment, migration, and invasion.  Moreover, CNTNAP4 KO cells were unresponsive to the effects of NELL1 treatment. Transcriptomic analysis combined with protein phosphoarrray demonstrated notable reductions in MAPK signaling with CNTNAP4 deletion, the ERK agonist isoproterenol restored OS cell functions among CNTNAP4 KO tumor cells. Finally, human primary cells and tissues in combination with publicly available sequencing data confirmed the significance of CNTNAP4 signaling in human sarcomas.  In summary, our findings demonstrate the biological importance of NELL-1/CNTNAP4 signaling in disease progression of human sarcomas and suggest that targeting NELL-1/CNTNAP4 signaling represents a strategy with therapeutic benefit in sarcoma patients.

overall_design: Bulk RNA sequencing of 143B human osteosarcoma cell line with or without CNTNAP4 gene deletion. 3 biological replicates for CNTNAP4 Vector Control (VC) and Knockout (KO) each

first: Qizhi

last: Qin

first: Sowmya

last: Ramesh


title: Applying multi-omics data to study the genetic background of bovine respiratory disease infection in feedlot crossbred cattle

city: Edmonton

first: Graham

last: Plastow

state: Alberta

address: 1400 College Plaza, 8215 - 112 Street

department: Agricultural, Food & Nutritional Science

country: Canada

institute: University of Alberta

summary: Bovine respiratory disease (BRD) is the most common and costly infectious disease affecting the well-being and productivity of beef cattle in North America. BRD is a complex disease whose development is dependent on environmental factors and host genetics. Due to the polymicrobial nature of BRD, our understanding of the genetic and molecular mechanisms underlying the disease is still limited. This knowledge would augment the development of better genetic/genomic selection strategies and more accurate diagnostic tools to reduce BRD prevalence. Therefore, this study utilized multi-omics data (genomics, transcriptomics, and metabolomics) analyses to study the associations between genome, transcriptome, metabolome, and BRD phenotype of feedlot crossbred cattle. The findings may be useful for the development of genomic selection strategies for BRD susceptibility, and for the development of new diagnostic and therapeutic tools.

overall_design: 143 samples were collected from 80 cattle diagnosed with BRD and 63 pen matched controls at one time point. 43 of the samples are a re-analysis from a previous submission (GSE162156).

first: Robert

last: Mukiibi

first: Janelle

last: Jiminez

first: Ziquan

last: Wang

first: Everestus

last: Akanno

first: Edouard

last: Timsit


title: Effect of Non-small cell lung cancer (NSCLC) cell line conditioned medium (CM) on bone marrow-derived macrophages (BMDMs)

summary: Hyperprogressive disease (HPD) is a newly described pattern of tumor progression characterizing a percentage of cancer patients receiving an immunotherapeutic regimen based on immune checkpoint inhibitors (ICIs), such as anti-PD1/PDL1 antibodies. Patients experiencing HPD are characterized by an unpredictable acceleration of tumor growth and a deterioration of the clinical conditions, rapidly leading to death. We have previously reported that macrophages play a pivotal role in contributing to HPD development. By analyzing non-small cell lung cancer (NSCLC) patient tumor samples, we observed that the tumor microenvironment (TME) of HPD-patients was infiltrated by particular clusters of macrophages. These macrophages are present before the initiation of ICI therapy and, therefore, we hypothesized that certain tumor cells may induce the acquisition of an “HPD-related” phenotype in macrophages that upon interaction with anti-PD1 antibody can unleash HPD. Since one of the strategies exploited by cancer cells to educate macrophage is to secrete molecules with immunomodulatory activity in the TME, bone marrow-derived macrophages (BMDMs) were exposed for 24 hours to the conditioned medium (CMs) obtained from five different NSCLC cell lines. We found that macrophages exposed to the CMs obtained from NCI-H460 and PC9 cell lines, reported to undergo a HPD-like growth in immunocompromised mice after anti-PD1 antibody treatment, have a gene expression profile completely different compared to the other experimental groups. Our findings suggest that soluble factors released by tumor cells can reprogram macrophages towards a phenotype potentially able to trigger HPD after interaction with anti-PD1 antibody.

overall_design: RNA was extracted from bone marrow-derived macrophages (BMDMs) after 24 hours exposure to NCI-H460 (n=4), PC-9 (n=3), A549 (n=4), NCI-H1299 (n=4), Calu-1 (n=4) conditioned medium (CMs). Moreover, RNA was also isolated from LPS+IFN- (M1) and IL-4 (M2) stimulated BMDMs (n=3 for each experimental condition) and untreated macrophages (M0, n=4).


title: Transcriptional profiling efficacy to define biological activity similarity for cosmetic ingredients’ safety assessment based on next generation read-across

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

institute: Procter & Gamble

summary: The objective of this work was to use transcriptional profiling to assess the biological activity of structurally related chemicals to define their biological similarity and with that, substantiate the validity of a read-across approach usable in risk assessment. Two case studies are presented, one with 4 short alkyl chain parabens: methyl (MP), ethyl (EP), butyl (BP), and propyl paraben (PP), as well as their main metabolite, p-Hydroxybenzoic acid (pHBA) with the assumption that PP was the target chemical; and a second one with caffeine (CA) and its main metabolites theophylline (TP), theobromine (TB) and paraxanthine (PX), where caffeine was the target chemical. The comprehensive transcriptional response of MCF7, HepG2, A549 and ICell cardyomiocytes was evaluated (TempO-Seq) after exposure to vehicle-control, each paraben or pHBA, caffeine or its metabolites, at 3 non-cytotoxic concentrations, for 6h. Differentially expressed genes (FDR ≥ 0.05, and fold change ±1.2≥) were identified for each chemical, at each dose of exposure, and used to determine similarities between them. Each of the chemicals is able to elicit changes in the expression of a number of genes, as compared to controls, particularly at the highest dose tested. Importantly, the transcriptional profile elicited by each of the parabens shares a high degree of similarities across the category members. The highest number of genes commonly affected by the parabens was found between BP and PP. The transcriptional profile of the parabens is similar to the one elicited by some estrogen receptor agonist, among other actives. Pathway enrichment analysis (MSigDB v7.0) of the transcriptional profile for each paraben indicated a significant overlap in the up- and down-regulated pathways across the four parabens.The highest similarity in biological activity was found between BP and PP. This was indicative of their biological similarity, and thus the validity of the read across among the group, with BT being the closest structural and biological analogue for PP. In the caffeine case and its main metabolites, the transcriptional profile elicited of all four compounds had a high degree of similarity across the cell types, with CA and TP being the most active. The most robust response was obtained in the cardiomyocytes with the highest transcriptional profile similarity between CA and TP. The transcriptional profile of the methylxantines is similar to the one elicited by inhibitors of phosphatidylinositol 3-kinase as well as other actives. Pathway enrichment analysis (MSigDB v7.0) of the transcriptional profile for each compound indicated a significant overlap in the up- and down-regulated pathways across the four methylxanthines. The highest similarity in biological activity was found between CA and TP, supporting the conclusion that from the group of methylxantines evaluated TP is the most appropriate analogue to read-across for CA. Overall, our results support the approach of incorporating transcriptional profiling in well-designed in vitro tests to support biological similarity driven read-across procedures and strengthening the traditional structure-based approaches useful in risk assessment.

overall_design:
Four cell types were used for the transcriptomic experiments: MCF-7 (breast epithelial adenocarcinoma), A549 (lung epithelial carcinoma), HepG2 (hepatocellular carcinoma) and iCell cardiomyocytes (derived from induced pluripotent stem cells, FujiFilm Cellular Dynamics, Madison, WI). MCF-7, A549 and HepG2 cells were purchased from American Type Culture Collection (Manassas, VA) and grown in phenol red-free DMEM media containing 10% serum (Invitrogen, Carlsbad, CA). The iCell cardiomyocytes were grown in a proprietary maintenance medium (FujiFilm Cellular Dynamics, Inc.) for 168 h before chemical treatment. All cell cultures were performed in 96-well plates with 5 vehicle controls on each plate. Cells were seeded on 96 well plates and treated with 3 concentrations of each chemical or vehicle (DMSO) for 6 h. Treatments were randomized across the plate to minimize batch effect and dispensed using an Andrew System 1000G liquid handling robot (Andrew Alliance, Waltham, MA). Following 6 h treatment, cell lysates were harvested according to a protocol provided by Biospyder (TempO-Seq Workflow — BioSpyder) and then stored at −80 °C until analysis. Each experiment was performed in 3 biological replicas. Cell lysate plates were shipped frozen to BioSpyder (BioSpyder Technologies, Inc., Carlsbad, CA) and Tempo-Seq human whole transcriptome (version 2.0) assay was performed at BioSpyder as previously described by Biospyder, Inc. (Yeakley et al., 2017).

***RAW data not provided for A549 and iCAR cell lines***

first: Jorge

last: Naciff

middle: K

first: Xiaohong

first: George

last: Daston


title: Effect of NEAT1 modulation on antiviral immune response

city: Faridabad

first: Abhay

middle: Deep

last: Pandey

address: 3rd Milestone, Faridabad-Gurgaon Expressway

department: Virology

country: India

institute: Regional Centre for Biotechnology

summary:
Reduction of NEAT1 transcript associated with Cell type-specific differential expression. The Knockdown of NEAT1 in Huh7 cells modulated antiviral response and dengue virus replication via the RIG-I pathway.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NEAT1 knock down and wild type Huh7 cells infected with Dengue virus2.

first: Arup

last: Banerjee

first: Jaya

last: Saini

first: Sudhanshu

last: Vrati

middle: D


title: Single-nucleus RNA-sequencing of unaffected control and Huntington's disease GLAST-positive iPSC-derived astrocytes

city: Irvine

first: Leslie

middle: M.

last: Thompson

address: 845 Health Sciences Road

institute: University of California, Irvine

summary: Huntington's disease (HD) and control GLAST-postive induced pluripotent stem cell (iPSC)-derived astrocytes underwent single-nucleus RNA-sequencing to investigate cell state diversity across control and HD patient-derived astrocytes.

overall_design: Single-nucleus RNA-sequencing of control and HD iPSC-derived GLAST-positive astrocytes. Cells were processed using the 10x Genomics single-cell platform. Libraries were sequenced on the Illumina NovaSeq 6000 to obtain paired-end 100 reads at >50K reads per cell. Data were processed using CellRanger and gene-by-cell expression matrices were generated and used as input for Seurat.

first: Andrea

last: Reyes-Ortiz


title: The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities

city: Bethesda

first: Gordon

last: Hager

state: MD

address: 41 Center Dr

department: NCI

institute: NIH

summary: The glucocorticoid receptor (GR) is a ubiquitously expressed transcription factor that controls metabolic and homeostatic processes essential for life. Although numerous crystal structures of the GR ligand-binding domain (GR-LBD) have been reported, the functional oligomeric state of the full-length receptor (FL-GR), which is essential for its transcriptional activity, remains disputed. Here we present five new crystal structures of agonist-bound GR-LBD, along with a thorough analysis of previous structural work. We identify four distinct homodimerization interfaces on the GR-LBD surface, which can associate into 20 topologically different homodimers. Biologically relevant homodimers were identified by studying a battery of GR point mutants including crosslinking assays in solution, quantitative fluorescence microscopy in living cells, and transcriptomic analyses. Our results highlight the relevance of non-canonical dimerization modes for GR, especially of contacts made by loop L1-3 residues such as Tyr545. Our work illustrates the unique flexibility of GR’s LBD and suggest many dimeric conformations can coexist within cells. In addition, we unveil pathophysiologically relevant quaternary assemblies of the receptor with important implications for glucocorticoid action and drug design.

overall_design: Comparative gene expression profiling analyses of RNA-seq data of dexamethasone treated mammary adenocarcinoma 3617-derived GRKO cells stably expressing GFP-tagged versions of mouse GR (WT, Y551A, Y551A-Dim, D647V, D647V-Tetra).

first: Alba

last: Jiménez-Panizo

last: Alegre-Martí

first: Theophilus

middle: T

last: Tettey

first: Gregory

last: Fettweis

first: Montserrat

last: Abella

first: Rosa

last: Antón

first: Thomas

last: Johnson

first: Rodney

last: Schiltz

first: Sohyoung

last: Kim

first: Israel

last: Nuñez-Barrios

first: Joan

last: Font-Díaz

first: Carme

last: Caelles

first: Annabel

middle: F

last: Valledor

first: Paloma

last: Pérez

first: Ana

last: Rojas

first: Juan

last: Fernández-Recio

first: Diego

last: Presman

first: Pablo

last: Fuentes-Prior

first: Eva

last: Estébanez-Perpiñá


title: Circulating cell-free DNA methylation mirrors alterations in cerebral patterns in epilepsy

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

type: Methylation profiling by genome tiling array

summary: DNA methylation progiling of circulaing cell-free DNA isolatated from serum of 12 MTLE patients and 11 healthy controls. The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs.

overall_design: Bisulphite converted DNA from the 23 samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip.

first: Jane

last: Doe

first: Ricardo

last: Martins-Ferreira

first: Bárbara

last: Leal

first: Chaves

last: João

first: Ciudad

last: Laura

first: Samões

last: Raquel

first: MartinsdaSilva

last: António

first: Paulo

last: Costa


title: microRNA (miRNA) expression signatures in patients with thyroid eye disease (TED) and identification of miRNA biomarkers of activity

city: Anyang

first: MIN JOUNG

last: LEE

address: 22 Gwanpyeong-ro

department: Ophthalmology

country: South Korea

institute: Hallym University Sacred Heart Hospital

summary:
Among the 798 miRNAs analyzed, 173 differentially downregulated miRNAs were identified in TED patients compared to HCs.
Ten circulating miRNAs were differentially expressed between active and inactive TED groups and regarded as candidate biomarkers for TED activity

overall_design: Total RNA was isolated from the sera of patients with TED (n=10) and healthy controls (HC, n=5) using the miRNeasy Serum/Plasma Kit. The NanoString assay was used for comprehensive analysis of 798 miRNA expression profiles.

first: Min

middle: J

last: Lee

first: Namju

last: Kim


title: Transient differential expression of transcription factors underlies the trans-differentiation of human monocytes to macrophages.

city: Shanghai

first: Chen

last: Min

address: 800 Dong Chuan Rd

institute: Shanghai Jiao Tong University

summary: To elucidating the time-series transcriptome changes during the trans-differentiation of primary human monocytes activated by surface-adsorption into macrophages via serum addition

overall_design: RNA-seq was performed on several biological replicates at 11 time points (mono, 0 h, 2 h, 4 h, 8 h, 12 h, 1-day, 2-days, 3-days, 4-days and 7-days).

first: Weihang

last: Deng

last: Chen

first: Le

last: Zhang

first: Zeqian

last: Xu

first: Ying

last: Tang

first: Daniel

middle: M

last: Czajkowsky

first: Xinhui

last: Li

first: Zhifeng

last: Shao


title: Transcript shortening through alternative polyadenylation promotes gene expression during fracture healing

city: Winston Salem

first: Ming

last: Leung

state: NC

address: 1 Medical Center Blvd

department: Comprehensive Cancer Center

institute: Atrium Health Wake Forest

type: Non-coding RNA profiling by high throughput sequencing

summary: Maturation of the 3¢ end of almost all eukaryotic messenger RNAs (mRNAs) requires cleavage and polyadenylation. Most mammalian mRNAs are polyadenylated at different sites within the last exon, generating alternative polyadenylation (APA) isoforms that have the same coding region but distinct 3¢ untranslated regions (UTRs). The 3¢UTR contains motifs that regulate mRNA metabolism; thus, changing the 3¢UTR length via APA can significantly impact gene expression. Endochondral ossification is a central process in bone healing, and the impact of APA on gene expression during this process is unknown. Here, we report widespread utilization of APA that impacts multiple pathways with established roles in bone healing. Importantly, progression of endochondral ossification is typified by global 3¢UTR shortening that is coupled with an increased abundance of shortened transcripts as compared to all other transcripts, underscoring the role of APA in promoting gene expression during endochondral bone formation.  Our mechanistic studies of genes that undergo APA in the fracture callus uncover an intricate regulatory network in which APA boosts the expression of collagen, type I, alpha 1 (Col1a1) and Col1a2 genes, which encode the 2 subunits of the abundantly expressed protein collagen 1. APA does so via shortening the 3¢UTRs of Col1a1 and Col1a2 mRNAs, which removes the binding sites of miR-29a-3p that otherwise potently triggered the degradation of both transcripts. Taken together, our study takes the lead in characterizing crucial roles of APA in tailoring the 3¢UTR landscape and regulating gene expression during fracture healing.

overall_design: 16-week-old, male C57BL/6J mice were subjected to mid-diaphyseal tibial fractures. At days 14 and 21 post-fracture, callus tissues were isolated and snap frozen in liquid nitrogen, and RNA was purified and subjected to RNA sequencing. Three biological replicates of each time point were analyzed.

first: Deepak

last: Khajuria

first: Irena

last: Nowak

first: Vengadeshprabhu

last: Karuppagounder

first: Yuka

last: Imamura

first: Christopher

middle: C

last: Norbury

first: Fadia

last: Kamal

first: Reyad

middle: A

last: Elbarbary


title: Effect of GSDMD knockout on hyperoxia-induced lung and retinal injury

city: Miami

first: Augusto

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

summary:
To investigate the role of GSDMD-mediated pyroptosis in neonatal lung and retinal injury induced by hyperoxia
We performed RNA-seq of lung and retina of newborn rats exposed to hyperoxia for 2 weeks

overall_design: Comparative gene expression profile of WT and GSDMD knockout mice exposed to room air or hyperoxia

first: Shu

last: Wu

first: Huijin

last: Yuan

first: Shaoyi

first: Matthew

last: Duncan

first: Kevin

last: Park


title: C42B HiC

city: Los Angeles

first: Suhn

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: We performed Hi-C, Micro-C, and capture Micro-C  in human prostate cancer cells and compared chromatin interactions called using different methods. By integrating Micro-C with NOMe-seq, ChIP-seq, and RNA-seq, we investigated the relationships among nucleosome positioning of regulatory elements, chromatin interactions, and transcription. This work provides a framework for understanding the chromatin interactions among regulatory elements, nucleosome-depleted regions, and transcription.

overall_design: Hi-C in C42B prostate cancer cells

first: Beoung

middle: H

last: Lee

first: Zexun


title: C42B NOMe-seq

type: Methylation profiling by high throughput sequencing

overall_design: NOMe-seq in C42B prostate cancer cells


title: C42B Micro-C

overall_design: Micro-C in C42B prostate cancer cells


title: C42B RNA-seq

overall_design: RNA-seq in C42B prostate cancer cells


title: Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C

overall_design: Refer to individual Series


title: Gene expression of intracellular pathways in the liver and spleen in experimental infection by SARS-CoV-2

city: Athens

first: Spyros

last: Foutadakis

address: Soranou

country: Greece

institute: Biomedical Research Foundation Academy of Athens

summary: A new experimental model of infection by SARS-CoV-2 is presented which is induced after the intravenous challenge of mice with plasma from patients with COVID-19 pneumonia and severe respiratory failure. Results coming from challenged mice are compared to mice challenged with plasma from healthy individuals.

overall_design: Plasma from adults with COVID-19 pneumonia and severe respiratory failure and from healthy individuals is injected intravenously in mice

first: Evangelos

last: Giamarellos-Bourboulis


title: C42B Capture Micro-C

overall_design: Capture Micro-C in C42B prostate cancer cells


title: RNA sequencing of macrophages and monocytes from first-trimester human decidua basalis (decB), decidua parietalis (decP), and placenta

city: Vienna

first: Martin

last: Knoefler

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

summary: Aim of the study was to characterize decidual macrohage populations and to verify the isolation protocol by showing the distinction between macrophages and monocytes

overall_design: Decidual macrophages and monocytes were isolated from donor-matched decB, decP, and placental tissues using enzymatic digestion and FACS, and RNA was extracted directly after cell isolation.

first: Sigrid

last: Vondra

first: Andreas

middle: I

last: Lackner

first: Jürgen

last: Pollheimer


title: CDCA7 promotes TGF-β-induced epithelial-mesenchymal transition via transcriptionally regulating Smad4/Smad7 in ESCC

city: Taiyuan

first: Hongyi

last: Li

address: Xinjian Southroad 56#

institute: Shanxi Medical University

summary:
Purpose：Cell division cycle associated 7 (CDCA7) is a copy number amplification gene that contributes to the metastasis and invasion of tumors, including esophageal squamous cell carcinoma (ESCC). This present study aimed at clarifying whether high expression of CDCA7 promotes the metastasis and invasion of ESCC cell lines and exploring the underlying mechanisms implicated in EMT of ESCC.
Mehtod：We established KYSE150 cell lines in which target gene has been knocked down by shRNA and KYSE180 cell lines in which target gene has been ovexpressed by plasmid.We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells.Each cell has three repetions.
Result：KEGG pathway enrichment analysis on the data of RNA-seq showed that Wnt signaling pathway and TGF-β signaling pathway which are related to EMT process were screened out.
Conclusion：CDCA7 was heavily involved in EMT by regulating the expression of Smad4 and Smad7 in TGF-β signaling pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KYSE150 cells and its knockdown derivatives (shCDCA7) and KYSE180 cells and its overexpression derivatives(CDCA7) .

first: SHaojie

last: Wang

first: Haoyu

last: Zhang

first: Yongjia

last: Weng

first: Dinghe

last: Guo

first: Pengzhou

last: Kong

first: Caixia

last: Cheng

first: Yanqiang

first: Ling

first: Xiaolong

first: Yongping

last: Cui


title: Methylation profiles of B cells subpopulations

city: Szczecin

first: Tomasz

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

summary: Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylationEPIC BeadChip in DNA samples extracted from subpopulations of B cells.

overall_design: This data set contains four profiles of unswitched memory B cells, two of switched memory B cell, and four of true naive B cells subpopulations.

first: Oriane

last: Cédile

first: Dianna

middle: B

last: Hussmann

first: Lise

last: Hansen

first: Christine

first: Jonas

last: Bybjerg-Grauholm

first: Kjell

last: Titlestad

first: Niels

last: Abildgaard

first: Charlotte

middle: G

last: Nyvold


title: ANRIL overexpression globally induces expression and alternative splicing of genes involved in inflammation in HUVECs

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Long non-coding RNAs（LncRNAs）have important cellular functions and some have roles in different mechanisms of gene regulation. LncRNA-antisense noncoding RNA in the INK4 locus (ANRIL) were found to affect cell inflammation,Nevertheless, the potential genes related to the inflammatory response regulated by ANRIL remain unclear. In this study, we investigated the potential function of ANRIL in regulating expression and alternative splicing. ANRIL-regulated human umbilical vein endothelial (HUVEC) cell transcriptome achieved by high-throughput RNA sequencing(RNA-seq) was obtained to investigate the potential role of ANRIL.  Lipofectamine 2000 was used for plasmid transfection.  The gene expression profile and alternative splicing pattern of HUVEC overexpressed by ANRIL were analyzed by RNA-seq and compared with the control group. ANRIL overexpression (ANRIL-OE) widely affects the transcription levels of genes related to inflammatory response, NF-κB pathway, type I interferon-mediated signal transduction pathway, and innate immune response.  ANRIL extensively regulates the alternative splicing of hundreds of genes through functions such as gene expression, translation, DNA repair, RNA processing, and NF-κB pathway.  Many of these genes have an indispensable role in the inflammatory response. ANRIL regulated inflammatory response may be achieved by regulating alternating splicing and potential transcription, which broadens the understanding of ANRIL-mediated gene regulation mechanisms and clarifies the role of ANRIL in mediating inflammatory response mechanisms.

first: Alimu

last: Wufuer

first: Xiemusiye

last: Luohemanjiang

first: Lei

last: Du

first: Jing

last: Lei


title: Clonal dynamics of SARS-CoV-2-specific T cells in children and adults with COVID-19

city: Darlinghurst

first: Peter

last: Croucher

state: New South Wales

address: 384 Victoria St

department: Bone

country: Australia

institute: Garvan Insititute of Medical Research

summary: Children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop less severe coronavirus disease 2019 (COVID-19) than adults. The mechanisms for the age-specific differences and the implications for infection-induced immunity are beginning to be uncovered. We show by longitudinal multimodal analysis that SARS-CoV-2 leaves a small footprint in the circulating T cell compartment in children with mild/asymptomatic COVID-19 compared to adult household contacts with the same disease severity who had more evidence of systemic T cell interferon activation, cytotoxicity and exhaustion. Children harbored diverse polyclonal SARS-CoV-2-specific naive T cells whereas adults harbored clonally expanded SARS-CoV-2-specific memory T cells. More naive interferon-activated CD4+ T cells were recruited into the memory compartment and recovery was associated with the development of robust CD4+ memory T cell responses in adults but not children. These data suggest that rapid clearance of SARS-CoV-2 in children may compromise their cellular immunity and ability to resist reinfection.

overall_design: scRNA seq of 28 samples, 7 children, 5 adults and 2 ICU adults samples collected at acute and convalescent stage.

first: Weng

last: Khoo

first: Katherine

last: Jackson

first: Chansavath

last: Phetsouphanh

first: John

last: Zaunders

first: José

last: Alquicira-Hernandez

first: Seyhan

last: Yazar

first: Stephanie

last: Ruiz-Diaz

first: Mandeep

last: Singh

first: Rama

last: Dhenni

first: Wunna

last: Kyaw

first: Fiona

last: Tea

first: Vera

last: Merheb

middle: X

last: Lee

first: Rebecca

last: Burrell

first: Annaleise

last: Howard-Jones

first: Archana

last: Koirala

first: Li

last: Zhou

first: Aysen

last: Yuksel

first: Daniel

middle: R

last: Catchpoole

first: Catherine

middle: L

last: Lai

first: Tennille

last: Vitagliano

first: Romain

last: Rouet

last: Christ

first: Benjamin

last: Tang

first: Nicholas

last: West

first: Shane

last: George

last: Gerrard

first: Anthony

last: Kelleher

first: Christopher

last: Goodnow

first: Jonathan

last: Sprent

first: Joseph

last: Powell

first: Fabienne

last: Brilot

first: Ralph

last: Nanan

middle: S

last: Hsu

first: Elissa

last: Deenick

first: Philip

middle: N

last: Britton

first: Tri


title: Transcriptome Analysis of the cadiomyoocytes derived from Rett syndrome patent-specific Isogenic induced Pluripotent Stem Cell

city: HK ISLAND

first: KM

last: NG

address: L503, LAB BLOCK,FMB, 21 Sassoon rd

department: Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: Rett syndrome (RTT) is a severe neurodevelopmental disorder caused by MeCP2 mutation. However, the pathophysiological roles of MeCP2 mutation in the aetiology of QT prolongation and sudden death remain unclear. Here, we performed RNA sequencing-based transcriptome analysis in a pair of isogenic RTT female patient-specific induced pluripotent stem cell derived-cardiomyocytes (iPSC-CMs) that expresses either MeCP2wildtype or MeCP2mutant allele, and iPSC-CMs from a non-disease female control. The result revealed up-regulation of various WNT family genes in MeCP2mutant iPSC-CMs.

overall_design: mRNA profiles of isogenic iPSCs-derived cardiomyocytes expressing wildtype or mutant MeCP2 allele. Additional line from normal female was also included for comparison

first: N

last: Kwong-Man

first: T

last: Yiu-Lam


title: Effect of hepatocyte-specific PPARgamma (PPARg)expression and diet-induced NASH in the liver transcriptome of male and female mice with pre-stablished diet-induced obesity

city: Chicago

first: Jose

last: Cordoba-Chacon

state: IL

address: 835 S Wolcott Ave

institute: University of Illinois at Chicago

summary: Adult PPARg floxed male and female mice were fed a high fat diet (HFD) for 16 weeks to induce obesity. Half of these mice were then injected with AAV8-TBG-Cre to knockout PPARg in hepatocytes. The remaining half were injected with AAV8-TBG-Null to generate control mice. After two weeks, mice fed the HFD were either maintained on this diet or switched to a high fat, high cholestrol, high fructose (HFCF) diet for an additional 16 weeks. This study was designed to examine whether the loss of hepatocyte PPARg in mice with established obesity would alter the liver transcriptomics in a PPARg dependent manner when the mice are fed a HFD or a HFCF diet.

overall_design: There are 10 groups of mice which are catagorized by there gender (Male [M], Female [F]), diet (Low fat diet [L], High fat diet [H], High fat, cholesterol and fructose [N], and PPARgamma expression (Control [C], Hepatocyte-specific KO [K]). For MALE mice: Male, HIgh fat diet, control mice [MHC]: 6 mice, MHC876, MHC878, MHC920, MHC922, MHC958, MHC962; Male, HIgh fat diet, PPARgamma knockout mice [MHK]: 6 mice, MHK877, MHK879, MHK923, MHK959, MHK961, MHK963. Male, High fat, cholesterol and fructose diet, control mice [MNC]: 6 HFCF mice: MNC892, MNC894, MNC908, MNC910, MNC948, MNC950;   Male, High fat, cholesterol and fructose diet,  PPARgamma knockout mice mice [MNK]: 6 mice, MNK893, MNK911, MNK949, MNK970, MNK972, MNK974.; For FEMALE; Female, low fat diet, control mice [FLC]: 4 mice, FLC1152, FLC1156, FLC1091, FLC1093; Female, low fat diet,  PPARgamma knockout mice [FLK]: 4 mice, FLK1099, FLK1110, FLK1102, FLK1153; Female, High fat diet, Control mice [FHC]: 4 mice, FHC1137, FHC1151, FHC1136, FHC1158; Female, High fat diet,  PPARgamma knockout mice [FHK]: 4 mice, FHK1134, FHK1157, FHK1135, FHK1160; Female, High fat, cholesterol, fructose, control mice [FNC]: 4 mice, FNC1117, FNC1118, FNC1119, FNC1142; Female, High fat, cholesterol, fructose,  PPARgamma knockout mice [FNK]: 4 mice FNK1084, FNK1085, FNK1116, FNK1140.

first: Samuel

last: Lee

last: Muratalla


title: Targeting tumor-stroma communication by blocking endothelin-1 receptor signaling sensitizes high-grade serous ovarian cancer to PARP inhibitor

city: Torino

first: Ivan

last: Molineris

state: TO

address: Via Nizza 52

department: Life Science and System Biology

institute: University of Turin

summary: High-grade serous ovarian cancer (HG-SOC), characterized  by very frequent mutations in TP53 gene, is a highly lethal cancer and is refractory to therapeutic strategies. In HG-SOC, the reciprocal signal exchange between tumor cells and various types of stromal elements from the tumor microenvironment (TME) shapes the malignant phenotype and limits drug efficacy, suggesting that blunting the HG-SOC/TME interplay may improve the anti-tumor therapy response rate. Here, we unveil how the endothelin-1 (ET-1)/ET-1 receptors (ET-1R) signaling, instructing the mutual inter-regulation between HG-SOC cells, endothelial cells (EC) and activated fibroblasts, regulates malignant progression and PARP inhibitor (PARPi) response. Mechanistically, ET-1 axis, mimicking hypoxia, enhances the mutant p53 (mutp53)/YAP/hypoxia inducible factor-1α (HIF-1α) transcriptional cooperation, that culminates with the release of diffusible mediators, as ET-1 and VEGF, that charting a bilateral HG-SOC/stroma signaling route, regulate the acquisition of pro-metastatic traits and PARPi response. Concurrently, our study establishes that ET-1 signaling its instrumental for the activation of p53/YAP/HIF-1α transcriptional machinery within the EC and the activated fibroblasts, shaping their behaviour and secretome. The dual ET-1R antagonist macitentan, dismantling the ET-1R-mediated mutp53/YAP/HIF-1α network, interferes with the ET-1-guided tumor/stroma communication. In vivo macitentan, sensitizing HG-SOC patient-derived xenografts (PDX) to the PARPi, Olaparib, reduces their metastatic potential. Clinically relevant, ETAR/YAP/HIF-1α gene signature correlates with a dismal prognosis in HG-SOC patients. Our findings recognize in the networking between ET-1R and YAP/mutp53/HIF-1α a tumor/TME shared escaping strategy from DNA damaging agents and support the use of ET-1R antagonists in combinatorial treatments with PARPi for HG-SOC patients.

overall_design: We monitored the global transcriptome in a preclinical relevant model of patient-derived primary cultures of HG-SOC cells (PMOV10), harboring TP53 mutation, isolated from ascitic fluid. PMOV10 cells were stimulated with endothelin-1 (ET-1, 100 nM), or with the ET-1R antagonist macitentan (MAC, 1µM), alone or in combination with ET-1, or with acetic acid (1% in H20), as vehicle (CTR) for 24 hours, by employing 4 biological replicates for each condition.

first: Piera

last: Tocci

first: Celia

last: Roman

first: Rosanna

last: Sestito

first: Valeriana

last: Di Castro

first: Andrea

last: Sacconi

first: Giovanni

last: Tonon

first: Francesca

last: Paolini

last: Blandino

first: Anna

last: Bagnato


title: Alterations in the expression of long noncoding RNAs and mRNAs in extracellular vesicles derived from the murine heart post ischemia-reperfusion injury

first: Xiaohui

last: Zhou

address: No.150 Jimo Road,Pudong district

department: Shanghai Heart Failure Research Center

institute: Shanghai East Hospital, Tongji University School of Medicine, Shanghai

summary: Extracellular vesicles (EVs) play important roles in cardiovascular diseases by delivering multiple RNA molecular, such as lncRNAs and mRNA. However, the features and functional mechanisms of the lncRNAs and mRNA in cardiac EVs during ischemia-reperfusion (IR) remains poorly understood. Therefore, we performed RNA sequencing to profile the expression feature of lncRNAs and mRNAs and predict their potential functions.

overall_design: Cardiac extracellular vesicles (EVs) was isolated from C57BL/6J mice  (10 weeks old, 26±1 g) in the sham and IR groups.

first: Xinyu

last: Ge

first: Qingshu

last: Meng

first: Jing

last: Liu


title: Microarray identifies differentially expressed circRNAs of cartilages between osteoarthritis (OA) patients and control patients

city: nanjing

first: yuxi

last: liu

address: Dingjiaqiao Road 87,Nanjing,China

institute: Southeast university

summary: Chondrocyte apoptosis and aberrant metabolism are involved in the pathogenesis of osteoarthritis. Our study provides potential therapeutic targets to chondrocyte apoptosis and aberrant metabolism in the context of osteoarthritis.

overall_design: CircRNA expression, four patients with osteoarthritis and four paired controls.

first: Yuxi


title: Effects of interferon alpha and intraferon gamma alone or in combination on human monocytes

city: Bethesda

first: Timothy

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: Monocyte cultures stimulated with IFNa or IFNg or IFNa+IFNg

first: Chase

last: Johnson

first: Daniel

last: Green

first: Kathryn

last: Zoon


title: CD4+ T cells mRNA profiles of lean and obese mice

first: Shumeng

last: Hao

address: Yue Yang Road 320

institute: Chinese Academy of Sciences

summary: To figure out how obesity drives glycolysis in CD4+ T cells, we performed RNA-sequencing to analyze the transcriptome of lean and obese-derived splenic CD4+ T cells. Mice were fed with either a normal diet (referred to lean mice) or a high-fat diet (HFD, 60 kcal% fat, referred to obese mice) generally from 6-8 weeks of age, for up to 4 months.

first: Yichuan

last: Xiao


title: Microarray identifies differentially expressed mRNAs of cartilages between osteoarthritis (OA) patients and control patients

summary: Chondrocyte apoptosis and aberrant metabolism are involved in the pathogenesis of osteoarthritis. Our study provides a potential new therapeutic target to chondrocyte apoptosis and aberrant metabolism in the context of osteoarthritis.

overall_design: MRNA expression, four patients with osteoarthritis and four paired controls.


title: Engineering TERT promoter mutation in neural progenitors confers a growth advantage following telomere shortening in vivo

city: La Jolla

first: Frank

last: Furnari

state: California

address: 9500 Gilman Dr, CMME2021

institute: UCSD

summary: We conducted RNA sequencing of engineered TERT promoter mutant and wild type tumors with CDKN2A/B null, PTEN null, EGFRvIII O.E background.

overall_design: RNA sequencing of human iPSC-derived NPC-derived tumor. The tumors have either TERT promoter mutant (C228T/WT) or wild type (WT/WT) in an isogenic background. P stands for the primary tumors derived from NPC (TERT promoter mutatant n=4, TERT promoter WT type n=4). S stands for the secondary tumors generated by serial injection of primary tumors (TERT promoter mutatant n=3, TETR promoter WT type n=3).

first: Alison

last: Parisian

first: Shunichiro

last: Miki


title: Transcriptome of chicken spleens with Escherichia coli infection

city: Beijing

first: Jiahui

last: Shi

address: 38 Life Science Park Road, Changping District, Beijing

institute: National Center for Protein Sciences (Beijing)

summary:
Purpose: the goals of this study was to find the differential genes of spleen in chickens infected with Escherichia coli
Methods: The spleen samples from control group and the spleen samples from infection group were generated by deep sequencing using Illumina system with 9 biological repetitions and 2 technical repetitions, respectively.
Results: Using an optimized data analysis workflow, we mapped about 68-91 million sequence reads per sample to the chicken spleens from the infection and control group by Hisat2. Approximately a quarter of the transcripts showed differential expression between the infection and control group, with a 5x SD fold change and p value <0.05.

overall_design: The one-day-old white leghorn SPF chickens were reared in isolators for 7 days, then these chickens were transferred to fumigated animal houses and reared for another 7 days. All the chickens were proved to be adapted to the breeding environment by 15 days old. After weighing, the chickens were randomly divided into two groups and 48 chickens in each group. The chickens in infection group were injected in the chest muscles with 0.5 mL of E. coli O78 bacterial fluid, while the chickens in control group were injected in the chest muscles with 0.5 mL sterile normal saline. At the time point of 72 h, the chickens for quantitative proteomics experiment were sacrificed, and spleens were dissected out and frozen at -80 ℃ for preservation. and part of the spleens were selected for transcriptomic analysis.

first: Ping

last: Xu


title: Single Cell sequencing analysis of Inflammatory Breast Cancer Samples

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

summary: EGFR Is a Master Switch Between Immunosuppressive and Immunoactive Tumor Microenvironment in Inflammatory Breast Cancer

overall_design: Inflammatory Breast Cancer Samples treated with Panitumumab or control.

first: Wang

last: Xiaoping

first: Hu

last: Min

first: Manyam

last: Ganiraju

first: Ueno

last: Naoto


title: Deep sequencing data from crRNA processing by SuCasΩ

city: Wurzburg

last: Beisel

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-Based Infection Research

summary: In this work we analyzed crRNA processing by SuCasΩ Type V CRISPR-Cas nuclease in E. coli

overall_design: SuCasΩ was expressed with crRNA in E. coli. Total RNA from the culture was extracted and sequenced. After data processing, the reads were mapped to the crRNA-expression locus.

first: Oleg

last: Dmytrenko

first: Dylan

last: Keiser

first: Valerie

last: Crowley

first: Elena

last: Vialetto

first: Ioannis

last: Mougiakos

first: Katharina

last: Wandera

first: Johannes

last: Weber

first: Hannah

last: Domgaard

first: Thom

last: Hallmark

first: Josie

last: Metcalf

first: Matthew

last: Begemann

first: Benjamin

last: Gray


title: RNA-Seq for LIN28A or LIN28A loss of function mutant expressing 293FT cells

city: Tokyo

first: Yutaro

last: Uchida

address: 1-5-45, Yushima, Bunkyo-Ku

country: Japan

institute: Tokyo Medical and Dental University

summary: We report the upregulated genes by the expression of LIN28A or loss of function mutant of LIN28A for 293FTcells..

overall_design: Examination of duplicated sample for 293FT cells expressing negative control or LIN28A or loss of function mutant of LIN28A

first: Hiroto

last: Yamamoto

first: Ryota

last: Kurimoto

first: Hiroshi

last: Asahara


title: Deep sequencing data from PFS screen of SuCas12a2 CRISPR-Cas nuclease

first: Chase

last: Beisel

summary: In this work we analyzed PFS sequence recognized by SuCas12a2 Type V CRISPR-Cas nuclease

overall_design: SuCas12a2 was challanged with a library of randomized flanking sequences. Two biological replicates were prepared and analyzed. Each replicate consisted of a library of flankign sequences challanged by SuCas12a2 (pOD4) and a library processed in the absence of SuCas12a2 (pOD49). Sequences were extracted from the Illumina data and their corresponding depletion scores were calculated.

first: Gina

last: Neumann

first: Thomson

first: Thomas

last: Gaudin

first: Ryan

last: Jackson


title: Gene expressional changes in control or adult reprogramming cardiomyocytes

city: Taipei

first: Yuan-Yuan

last: Cheng

address: Academia road

country: Taiwan

institute: Academia Sinica

summary: To investigate gene expressional changes in adult control or early reprogramming cardiomyocytes.

overall_design: αMHC promoter-driven Yamanaka's OSKM factor mice were established and adult cardiomyocytes can be induced reprogramming in vivo by doxycycline. Adult cardiomyocytes were isolated from αMHC promoter-driven Yamanaka's OSKM factor mice after intraperitoneal injection of doxycycline for 2 days.

first: Patrick

last: Hsieh


title: Single-cell RNA-seq data of human glioma

city: Nanjing

first: Ran

last: Wang

state: Jiangsu

address: Guangzhou street No.264

institute: The Affiliated Brain Hospital of Nanjing Medical University

summary: Six freshly resected recurrent glioma samples were obatined to analyze the diversity of expression states of human gliomas. About 3000 cells from each sample were profiled.

overall_design: One WHO IV grade glioma and five WHO III grade gliomas were collected immediately during operation. Microwell arrays were used as the platform for isolating single cells, and those samples were profiled by Illumina Hiseq 4000.

first: Yong

last: Xiao

first: Kun

last: Yang

first: Hong

first: Hongyi

last: Liu


title: CLIP-Seq for LIN28A or LIN28A loss of function mutant expressing 293FT cells

summary: We report the direct target genes by  LIN28A or loss of function mutant of LIN28A for 293FTcells using CLIP-Seq

overall_design: CLIP-Seq for 293FT cells expressing negative control or LIN28A or loss of function mutant of LIN28A


title: Cas12a2 elicits abortive infection through RNA-triggered destruction of dsDNA

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

overall_design: Refer to individual Series


title: High-precision mapping reveals rare N6-deoxyadenosine methylation in the mammalian genome

city: Guangzhou

first: Zhang

last: Zhang

state: Guangdong

address: Xingangxi Roda 135#

institute: Sun Yat-sen University

summary: DNA modification has been characterized as a critical epigenetic regulator in gene expression. N6-deoxyadenosine methylation (6mA) is the most widespread type in prokaryotes and some unicellular eukaryotes. Nevertheless, the lack of a precise and comprehensive mapping method greatly hinders studying the presence and biological significance of 6mA in mammals. Here, we develop a new method MM-seq (Modification-induced Mismatch Sequencing) for genome-wide 6mA mapping in single-base resolution. This method balances accuracy and sensitivity based on a novel detection principle. We find modified DNA bases are likely to flip out of the DNA duplex, forming a mismatch-like structure that an antibody can capture. The mismatch-like structure can be recognized by endonuclease or exonuclease, which marks the exact modified site for readout via sequencing. Using this method, we examine the genomic positions of 6mA in bacteria, green algae, and mammalian cells. We find that human and mouse genomes contain rare and randomly distributed 6mA sites, with almost no overlap between different cell types. After knock-out of the RNA m6A methyltransferase Mettl3, limited 6mA sites in gDNA are diminished. Our results support the perspective that rare 6mA in the mammalian genome is caused by the misincorporation of N6-methyladenine via the nucleotide-salvage pathway.

sample_organism:
Escherichia coli
Chlamydomonas reinhardtii
Homo sapiens
Mus musculus

overall_design: We develop a new method MM-seq (Modification-induced Mismatch Sequencing) for genome-wide 6mA mapping in single-base resolution, and applied it in Chlamydomonas reinhardtii, E. coli, human and mouse cell lines.

first: Li-Qian

last: Chen

first: Guan-Zheng

last: Luo


title: The Testis-Specific Transcription Factor TCFL5 Responds to A-MYB to Elaborate Male Meiotic Program in Mammals

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

summary: In the mammalian testis, the pool of spermatogonia is amplified by mitosis before these progenitor germ cells undergo meiosis to generate the haploid cells that give rise to sperm. Extensive changes in the transcriptome accompany the onset of the pachytene stage of meiosis, including the transcriptional activation of meiotic genes, the pachytene piRNA pathway, as well as mRNAs required later during spermiogenesis. How transcription is regulated to ensure the precise timing of this major reprogramming of gene expression remains largely uncharacterized. Here, we report that the testis-specific transcription factor TCFL5 is initially activated by the transcription factor A-MYB during meiosis. Subsequently, A-MYB and TCFL5 mutually reinforce their own transcription establishing a central regulatory circuit that regulates meiosis and spermiogenesis, as well as mediates pachytene piRNA production. TCFL5 drives the transcription of 476 genes required for meiosis including genes encoding pachytene piRNA biogenesis proteins, and 796 genes required for spermiogenesis. Tcfl5−/− mutant mice are sterile and spermatogenesis arrests at the mid- or late-pachytene stage of meiosis. Intriguingly, Tcfl5 haploinsufficiency leads to reduced male fertility suggesting germ cells are sensitive to Tcfl5 dosage to develop. Compromised TCFL5 expression underlies the reduced fertility phenotype directly or indirectly through regulating other transcription factors in Tcfl5+/− mutant mice. TCFL5 drives the transcription of evolutionarily younger pachytene piRNAs, while A-MYB regulates older pachytene piRNAs. Older and younger piRNAs mutually initiate their own processing providing evidence how these selfish genetic elements hijack meiotic transcriptional network to amplify themselves. We also demonstrate that TCFL5-mediated regulation of male meiosis and piRNA production is conserved in macaque. Our data establish a direct role of TCFL5 in ensuring the simultaneous activation of genes required for meiosis and spermiogenesis in mammals.

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus

overall_design: CUT&RUN, ChIPseq and RNAseq for adult male mouse germ cells or adult mouse testis

first: Ozata

last: Deniz

first: Yu

last: Tianxiong

first: Weng

last: Zhiping

first: Philip

middle: D

last: Zamore


title: Effect of superovulation treatment on oocyte´s DNA methylation

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: Controlled ovarian stimulation is a necessary step in some assisted reproductive procedures allowing the collection of female gametes at a precise time and at a suitable amount needed for subsequent fertilization steps. However, studies in animals have shown many consequences of hormonal treatments over the oocyte. Several of these studies used comparisons between oocytes from different donors, which is known that may influence the response differently. In this work we propose the use of the bovine model where each animal served as its own control. DNA methylation profile of oocytes from pre-ovulatory unstimulated follicles (NS) was compared to oocytes from stimulated follicles (S), after single-cell whole genome bisulphite sequencing. Results show that global percentage of methylation was similar between groups but percentage of methylation was lower for non-stimulated oocytes in the imprinted genes APEG3, MEG3 and MEG9, and higher in TSSC4 when compared to stimulated oocytes. Differences were also found in CpGi of imprinted genes: higher methylation was found among NS oocytes in MEST (PEG1)), IGF2R, GNAS (SCG6), KvDMR1 ICR UMD and IGF2. In another region around IGF2 the methylation percentage was lower for NS oocytes when compared to S oocytes. Data drawn from this study might help to understand the molecular reasons of the appearance of certain syndromes in assisted reproductive technologies-derived offspring.

first: Jordana

last: Lopes

first: Elena

last: Ivanova

first: Salvador

last: Ruiz

first: Simon

last: Andrews

first: Gavin

last: Kelsey

first: Pilar

last: Coy


title: RALY selectively regulates the alternative splicing of transcription factors and the expression of immune/ inflammatory response genes in HeLa cells

city: Wuhan

first: Dong

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

institute: ABLife, Inc.

summary: We applied a HeLa cell model with enforced expression of RALY and studied the effect of RALY on cancer cell proliferation and apoptosis. We then obtained RNA-seq transcriptomes from the normal cells and those with RALY overexpression, followed by analysis of the deregulation of alternative splicing and gene expression that were mediated by RALY overexpression.

overall_design: We overexpressed RALY in HeLa cells by transfecting Flag with RALY. Negative control was prepared at the same time. Two biological replicates were obtained and prepared for RNA-seq experiments.

first: Liang

last: Zhao


title: Salinomycin induces expression of ER and Golgi apparatus related genes in EMT cell model

city: Zagreb

first: Marko

last: Marjanović

state: Zagreb

address: Bijenička c. 54

department: Division of Molecular Medicine

country: Croatia

institute: Ruđer Bošković Institute

summary: Epithelial-to-mesenchymal transition (EMT) gives rise to cells with properties similar to cancer stem cells (CSCs) that drive tumor metastasis. Recently, a screening of a large compound library on a breast EMT model has identified salinomycin, a K+/H+ ionophore, as a highly selective drug towards CSCs. We used the same EMT model to show that salinomycin targets Golgi apparatus. We have performed RNA-seq analysis on HMLE-Twist and HMLE-pBp cells (EMT and non-EMT) that were either mock treated or treated for 24h with micro molar concentration (0.2uM) of salinomycin. Salinomycin induced expression of genes enriched by known ER and Golgi stressors.

overall_design: Total RNA from biological triplicates from mock and salinomycin treated HMLE-Twist and HMLE-pBp cells was extracted (12 biological samples in total). Library was prepared with TrueSeq Stranded mRNA kit (Illumina) from 750 ng of RNA. Library was sequenced on a NextSeq500 using High output flow-cell in pair-end mode (75+75 cycles). Raw data yielded total over 920 million high-quality reads (Q30 > 75%).

first: Marijeta

last: Kralj


title: LncRNA-mRNA expression profile and functional network of vascular dysfunction in endotoxemic rats

first: Jinghua

last: Yang

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

institute: Beijing Zhiyun data technology co. LTD

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: In our study, we used a rat model of LPS intervention to extract blood vessels. Differentially expressed LncRNA and mRNA were screened in lps rat blood vessels and normal rat blood vessels by microarray analysis. And through CNC and ceRNA analysis, lncRNA, miRNA, and mRNA regulatory network diagrams were constructed using verified lncRNA. This has the potential to highlight specific molecular functions and mechanisms. Later, we performed functional enrichment analysis and annotation to further explore the importance of lncRNA in vascular cell injury in sepsis. This work helps to reveal the underlying mechanism of vascular cell damage caused by sepsis and provides a new therapeutic target for controlling vascular damage in sepsis.

overall_design: We use high-throughput technologies to screen the lncRNAs and mRNAs in the blood vessel tissues from LPS rats (n=5) compared with Ctrl rats (n=5).  Differential expression lncRNAs and mRNAs were confirmed by qRT-PCR. We constructed a CNC and ceRNA network to reveal the core genes in hyposalivation.

first: Hongzhi

last: Xie

first: Zhujun

last: Shen

first: Yechen

last: Han

first: Yining

last: Wang


title: Type 2 immune polarization is associated with cardiopulmonary disease in preterm infants

city: Clayton

first: Jan

last: Schroeder

state: VIC

address: Building 75 Innovation Walk

department: Anatomy & Developmental Biology

institute: Monash University

summary: In order to explore the cell types involved in a murine model of bronchopulmonary dysplasia, we performed single-cell RNA-seq on lungs from 5 day old mice exposed to inflammation and hyperoxia.

overall_design: Endothelial, epithelial and immune cells were obtained by flow-sorting of lung cells from pups subjected to the murine BPD model (inflammation + hyperoxia) for 5d, and subjected to single cell-sequencing. N=4 per group (Air, Hyperoxia)

first: Christine

last: Bui

first: Yu

last: Sun

first: Marcel

last: Nold


title: Expression patterns of white blood cells in response to individual food treatments relative to LPS treatment and untreated in an FPIES subject.

status: Public on Jan 10 2023

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

summary: Total blood white blood cells from a FPIES subject were treated with individual treatmens of 2 foods that were safe for the subject (pear and breast milk), two foods that were triggers (quinoa and sweet potato), and 19 foods of unknown status for the subject. These treatments were compared to LPS treatment and untreated.

overall_design: Blood was drawn from FPIES subject who was on trigger-food avoidance, the WBCs isolated by ACK buffer RBC lysis, and the WBCs plated in 12-well plate wells, and treated with individual food treatments, LPS or untreated.

first: Mohamad

last: El-Zaatari

first: Charles

last: Schuler

first: John

middle: Y

last: Kao


title: Radiogenomics features of tumor dissemination in ABVD treated cHL patients

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

institute: Azienda USL- IRCCS di Reggio Emilia

summary: RNA extracted from diagnostic tumor samples of 126 patients affected by cHL was analyzed on the nCounter system using the PanCancer Immune Profiling Panel.

overall_design: Gene expression profile were linked to tumor dissemination measured by Dmax PET feature in cHL.

first: Alessia

last: Ciarrocchi

first: Stefano

last: Luminari


title: Multivalent state transitions shape the intratumoral composition of small cell carcinoma

city: Chicago

first: Mohamed

last: Abazeed

address: 303 E Superior St Lurie

department: Radiation Oncology

institute: Northwestern University

summary: Analysis of small cell lung carcinoma human-derived xenografts. The hypothesis tested in the present study was that small cell lung carcinomas demonstrate transcriptomic diversity. Results provide important information on the variation and groupings (clustering) of distinct small cell lung carcinomas.

overall_design:
RNA obtained from small cell lung carcinoma tissue derived from a human biospy or surgical specimen then passaged through NSG mice.
***Raw data are being deposited in dbGaP due to patient privacy concerns***

first: Priyanka

last: Gopal

middle: E


title: Modified method for differentiation of myeloid-derived suppressor cells in vitro enhances immunosuppressive ability via glutathione metabolism

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Myeloid-derived suppressor cells (MDSCs), which accumulate in tumor bearers, are known to suppress anti-tumor immunity and thus promote tumor progression. MDSCs are considered a major cause of resistance against immune checkpoint inhibitors in patients with cancer. Therefore, MDSCs are potential targets in cancer immunotherapy. In this study, we modified an in vitro method of MDSC differentiation. Upon stimulating bone marrow (BM) cells with granulocyte-macrophage colony-stimulating factor in vitro, we obtained both lymphocyte antigen 6G positive (Ly-6G+) and negative (Ly-6G−) MDSCs (collectively, hereafter referred to as conventional MDSCs), which were non-immunosuppressive and immunosuppressive, respectively. We then found that MDSCs differentiated from Ly-6G− BM (hereafter called 6G− BM-MDSC) suppressed T-cell proliferation more strongly than conventional MDSCs, whereas the cells differentiated from Ly-6G+ BM (hereafter called 6G+ BM-MDSC) were non-immunosuppressive. In line with this, conventional MDSCs or 6G− BM-MDSC, but not 6G+ BM-MDSC, promoted tumor progression in tumor-bearing mice. Moreover, we identified that activated glutathione metabolism was responsible for the enhanced immunosuppressive ability of 6G− BM-MDSC. Finally, we showed that Ly-6G+ cells in 6G− BM-MDSC, which exhibited weak immunosuppression, expressed higher levels of Cybb mRNA, an immunosuppressive gene of MDSCs, than 6G+ BM-MDSC. Together, these data suggest that the depletion of Ly-6G+ cells from the BM cells leads to differentiation of immunosuppressive Ly-6G+ MDSCs. In summary, we propose a better method for MDSC differentiation in vitro. Moreover, our findings contribute to the understanding of MDSC subpopulations and provide a basis for further research on MDSCs.

overall_design: MDSC (conv.), 6G- BM-MDSC, and DCs were assayed in duplicates as single color experiment.

first: Masashi

last: Tachibana


city: Gaithersburg

first: Atsushi

last: Sakamoto

state: MD

address: 19 Firstfield Road

institute: CVPath Institute

summary:
Vasclar calcification (VC) is concomitant with atherosclerosis. CD163+ M(Hb) macrophages at the site of intraplaque hemorrhage of advanced atherosclerosis provoke angiogenesis and microvascular permeability contributing plaque destabilazation.
We investigated the role of CD163+ macrophage on the process of VC, and found CD163+ macrohpages inhibit VC through NFκB-induced hyaluronan synthase augmentation and subsequently promote the high-risk plaque development.

overall_design: Transcriptomic profiles of human aortic smooth muscle cell (HASMC) which exposed to M(con) or M(Hb) macrophage supernatant with osteogenic conponents supplementation for 6 hours were examined by ClariomTM S microarray.

first: Rika

last: Kawakami

first: Aloke

middle: V

last: Finn


title: Comparison of RNA responses to fentanyl in two mouse strains

city: Charlottesville

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

summary: An increase in opioid-overdose deaths was evident before the COVID-19 pandemic, and has escalated since its onset. Fentanyl, a highly potent synthetic opioid, is the primary driver of these recent trends. The current study used two inbred mouse strains, C57BL/6 J and A/J, to investigate the genetics of behavioral responses to fentanyl. Mice were tested for conditioned place preference and fentanyl-induced locomotor activity. C57BL/6J mice formed a conditioned place preference to fentanyl injections and fentanyl increased their activity. Neither effect was noted in A/J mice. We conducted RNA-sequencing on the nucleus accumbens of mice used for fentanyl-induced locomotor activity. Surprisingly, we noted few differentially expressed genes using treatment as the main factor. However many genes differed between strains. We validated differences in two genes: suppressor APC domain containing 1 (Sapcd1) and Glyoxalase 1 (Glo1), with quantitative PCR on RNA from the nucleus accumbens and prefrontal cortex. In both regions A/J mice had significantly higher expression of both genes than did C57BL/6 J. In prefrontal cortex, fentanyl treatment decreased Glo1 mRNA. Glyoxalase 1 catalyzes the detoxification of reactive alpha-oxoaldehydes such as glyoxal and methylglyoxal, is associated with anxiety and activity levels, and its inhibition reduces alcohol intake. We suggest that future studies assess the ability of Glo1 and related metabolites to modify opioid intake.

overall_design: Comparison of RNA responses of the nucleus accumbens (brain) across both sexes in two strains (A/J and C57BL/6J) in response to intraperitoneal administration of fentanyl HCL at a dose of 0.2 mg/kg or saline (N=4/sex/strain/treatment)

first: Emilie

middle: F

last: Rissman


title: Two weeks of high-intensity interval training increases skeletal muscle mitochondrial respiration via complex-specific remodeling in sedentary humans

city: Corvallis

first: Matthew

middle: M

last: Robinson

state: OR

address: Milam Hall 003

institute: Oregon State University

summary: Aerobic training remodels the quantity and quality (function per unit) of skeletal muscle mitochondria to promote substrate oxidation, however, there remain key gaps in understanding the underlying mechanisms during initial training adaptations. We used short-term high-intensity interval training (HIIT) to determine changes to mitochondrial respiration and regulatory pathways that occur early in remodeling. Fifteen normal-weight sedentary adults started seven sessions of HIIT over fourteen days and fourteen participants completed the intervention. We collected vastus lateralis biopsies before and 48-hours after HIIT to determine mitochondrial respiration, RNA sequencing, and western blotting for proteins of mitochondrial respiration and degradation via autophagy. HIIT increased respiration per mitochondrial protein for lipid (+23% P=0.020), complex I (+18%, P=0.0015), complex I+II (+14%, P<0.0001) and complex II (+24% P<0.0001). Transcripts that increased with HIIT identified several gene sets of mitochondrial respiration, particularly for complex I, while transcripts that decreased identified pathways of DNA and chromatin remodeling. HIIT lowered protein abundance of autophagy markers for p62 (-19%, P=0.012) and LC3 II/I (-20%, P=0.004) in whole-tissue lysates but not isolated mitochondria. Meal tolerance testing revealed HIIT increased the change in whole-body respiratory exchange ratio and lowered cumulative plasma insulin concentrations. Gene transcripts and respiratory function indicate remodeling of mitochondria within 2 weeks of HIIT. Overall changes are consistent with increased protein quality driving rapid improvements in substrate oxidation.

overall_design: 15 normal-weight, sedentary humans, age 18-45 years, completed 2 weeks of high intensity interval training (HIIT). HIIT was completed every other day for 7 sessions and included 10 1-minute bouts of exercise (~90% VO2max) followed by 1 minute rest. Muscle biopsies were acquired before, and 48 hours after, exercise training. Muscle biopsies were subjected to RNA-sequencing.

first: Philip

last: Batterson

first: Erin

last: McGowan

first: Harrison

last: Stierwalt

first: Sarah

last: Ehrlicher

first: Sean

last: Newsom


title: Screening and identification of miR-181a-5p in oral squamous cell carcinoma and functional verification in vivo and in vitro

city: Taiyuan

first: Guohua

last: Song

state: Shanxi

address: Road Xinjian 56, Taiyuan 030001, China

department: Laboratory Animal Center

country: China

institute: Shanxi Medical University

summary: Background: Oral squamous cell carcinoma (OSCC) is a common malignant tumor associated with poor prognosis. MicroRNAs (miRNAs) play crucial regulatory roles in the cancer development. However, the role of miRNAs in OSCC development and progression is not well understood. Methods: We sought to establish a dynamic Chinese hamster OSCC animal model, construct miRNA differential expression profiles of its occurrence and development, predict its targets, and perform functional analysis and validation in vitro. Results: Using expression and functional analyses, the key candidate miRNA (miR-181a-5p) was selected for further functional research, and the expression of miR-181a-5p in OSCC tissues and cell lines was detected. Subsequently, transfection technology and a nude mouse tumorigenic model were used to explore potential molecular mechanisms. miR-181a-5p was significantly downregulated in human OSCC specimens and cell lines, and decreased miR-181a-5p expression was observed in multiple stages of the Chinese hamster OSCC animal model. Moreover, upregulated miR-181a-5p significantly inhibited OSCC cell proliferation, colony formation, invasion, and migration; blocked the cell cycle; and promoted apoptosis. BCL2 was identified as a target of miR-181a-5p. BCL2 may interact with apoptosis- (BAX), invasion- and migration- (TIMP1, MMP2, and MMP9), and cell cycle-related genes (KI67, E2F1, CYCLIND1, and CDK6) to further regulate biological behavior. Tumor xenograft analysis indicated that tumor growth was significantly inhibited in the high miR-181a-5p expression group. Conclusions: Our findings indicate that miR-181a-5p can be used as a potential biomarker and provide a novel animal model for mechanistic research on oral cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the Chinese hamster oral cancer animal model (Use DMBA to induce oral cancer in the animal model)

first: Guoqiang

last: Xu


title: Expression profile of  mRNAs regulated by KNTC1 in HeLa cell

city: jinan

first: shi

middle: qi

last: wang

state: shandong

address: Baotu Spring street

institute: shandong Univercity

summary: To elucidate the molecular mechanisms of KNTC1 functions in cervical cancer, HeLa cells were transfected with KNTC1 siRNA and subjected to human gene expression microarray assays. The mRNA levels of 58,351 genes were examined in cells transfected with siKNTC1 or negative control. Among them, 3428 DEGs were identified with 833 upregulated genes and 2595 downregulated genes after silencing KNTC1 gene expression.

overall_design: HeLa cells were transfected with KNTC1 siRNA or negative control for 48h, and then detected by a human gene expression microarray

first: Wei

last: Pan

first: Shiqi

last: Wang

first: Xiao


title: The acetabular labrum tissue shows unique transcriptome signatures compared to cartilage and responds to combined cyclic compression and surface shearing

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Purpose: Knowledge about labrum specific features is scarce. However, labrum specific cell and tissue markers such as extracellular matrix gene expression markers may be required during the development of labrum tissue engineering approaches. The study aimed to compare the basal gene expression of acetabular labrum tissue and articular cartilage tissue. Methods: Bovine hip joints were collected from a local slaughterhouse (food industry). From each of the five hip joints, one tissue specimen of labrum tissue was collected from the thickest labrum region and one tissue specimen of articular cartilage tissue was collected from the adjacent cartilage tissue. RNA was extracted by chloroform phenol extraction and purified using the RNeasy Mini Kit from Qiagen. RNA sequencing and functional analysis was performed at the Functional Genomics Center Zurich (FGCZ). Results: More than 6'000 differentially expressed genes were identified. In hierarchical clustering the GO term extracellular matrix organization was enriched and in gene set enrichment analysis the GO term extracellular matrix was enriched. Specifically, COL1A1 and COL3A1 were highly expressed in the labrum tissue and significantly higher expressed than in the articular cartilage tissue. Conclusion: Labrum tissue shows substantial differences in basal gene expression compared to articular cartilage. The here presented expression profile and list of differentially expressed genes may contribute to the development of labrum specific markers.

overall_design: Comparison of baseline RNA expression (transcriptome) of articular cartilage tissue and acetabular labrum tissue.

first: Stephen

middle: J

last: Ferguson

first: Stephanie

last: Huber


title: Determination of molecular factor involved in Pseudomonas persistence in human plasma by Tn-seq

city: Grenoble

first: Manon

last: Janet-Maitre

address: 71 Avenue des Martyrs

country: France

institute: IBS

summary: Gain of function screen in a plasma sensitive strain

overall_design: Tn-seq analysis of transposon insertion mutants enriched in plasma compared to heat inactivated plasma in Pseudomonas aeruginosa IHMA87, in duplicates

first: Ina

last: Attrée