summary: We profiled total small RNA from wild-type and aar2-1 mutant

overall_design: Total small RNA from wild-type and aar2-1 mutant seedling were examined. Three biological replicates were included.


title: Identification of new TCF21 targets in adrenocortical carcinoma cells

status: Public on Jun 30 2022

city: Sao Paulo

first: Barbara

last: Passaia

address: Prof Lineu Prestes Avenue

country: Brazil

institute: University of Sao Paulo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcription factor 21 (TCF21) directly binds and regulates SF1 in tumor and normal adrenocortical cells, and both are involved in the development and steroidogenesis of the adrenal cortex. TCF21 is a tumor suppressor gene and its expression is reduced in malignant tumors. In adrenocortical tumors, it is less expressed in adrenocortical carcinomas (ACC) than in adrenocortical adenomas (ACA) and normal tissue. However, a comprehensive analysis to identify TCF21 targets have not yet been conducted in any type of cancer. In this study, we performed Chromatin Immunoprecipitation and Sequencing (ChIP-Seq) in adrenocortical carcinoma cell line (NCI-H295R) overexpressing TCF21, with the aim of identifying TCF21 new targets. The five most frequently identified sequences corresponded to the PRDM7, CNTNAP2, CACNA1B, PTPRN2 and KCNE1B genes. Validation experiments showed that, in NCI-H295R cells, TCF21 regulates gene expression positively in PRDM7 and negatively in CACNA1B. Recently, it was observed that the N-type calcium channel v2.2 (Cav2.2) encoded by CACNA1B gene is important in Angiotensin II signal transduction for corticosteroid biosynthesis in NCI-H295R adrenocortical carcinoma cells. Indeed, TCF21 inhibits CACNA1B and Cav2.2 expression in NCI-H295R. In addition, in a cohort of 55 adult patients with adrenocortical tumor, CACNA1B expression was higher in ACC than ACA, and was related to poor disease-free survival in ACC patients. These results suggest a mechanism of steroidogenesis control by TCF21 in adrenocortical tumor cells, in addition to the control observed through SF1 inhibition. Importantly, steroid production could impair tumor immunogenicity, contributing to the immune resistance described in adrenal cancer.

overall_design: Fragmented DNA without immunoprecipitation was used as a positive control, and two replicates of NCI-H295R pCMVMycPOD1 cells were sequenced. Reads were mapped using GRCh38 Homo sapiens (human) genome assembly. The Phred Quality Score (Q>30) of the bases was verified, low-quality and duplicate readings were removed, and Peak calling was performed using MACS2 (v2.1.1) (p<0.01) wrapped in AQUAS ChIP-Seq pipeline (https://github.com/NHLBI-BCB/TF_chipseq_pipeline, accessed on 22/Nov/2020) (Zhang et al., 2008). The IDR <0.05 (Irreproducible Discovery Rate) was calculated to identify consistent peaks, which guarantees the reproducibility of the experiment (Li et al., 2011). All readings considered as noise by the blacklist of the Encyclopedia of DNA Elements (ENCODE) were excluded (Amemiya et al., 2019).

middle: S

first: Jean

middle: L

last: Kremer

first: Maria

middle: C

last: Fragoso

first: Claudimara

middle: F

last: Lotfi


title: DEG of panicle primordia in ZH11 and OsGATA6-AM lines at the In2 and In3 stages

status: Public on Jun 29 2022

city: Shanghai

first: Yan-Jie

last: Zhang

address: 800 Dongchuan RD. Minhang District

country: China

institute: Shanghai Jiao Tong University

summary: To investigate how OsGATA6 regulates heading date, grain number per panicle, and grain phenotypes, we collected panicle primordia of ZH11 and OsGATA6-AM lines at the In2 and In3 stages. We analyzed gene expression using a rice expression profiling chip. Compared with ZH11, OsGATA6-AM lines had 818 up-regulated genes and 284 down-regulated genes

overall_design: According to SEM observations of panicle primordia, we selected panicle primordia at the In2–In3 stages from wild-type ZH11 and OsGATA6-AM lines and analyzed differentially expressed genes using a rice expression profile chip (Agilent Technologies, Santa Clara, CA, USA).Each sample had three biological replicates.

first: Wen-Hui

last: Lin


title: PSMG2-controlled proteasome-autophagy balance mediates the tolerance for MEK targeted therapy in TNBC

status: Public on Jun 28 2022

city: Chengdu

first: Jing

last: Yu

state: Sichuan

address: No.17, Section 3, Renmin South Road

institute: Sichuan university

summary: We performed an unbiased genome-wide CRISPR/Cas9 knockout screening to identify synergistic drug targets in TNBC cells with MEK inhibitor. PSMG2 was found as a critical synthetically lethal gene with MEK inhibition. Mechanism investigation unraveled that PSMG2 knockdown inhibited proteasome function, which in turn activated cell autophagy. Autophagy, unlike its function in chemoresistance, inhibited PI3K/AKT pathway by specific degradation of PDPK1. Co-targeting MAPK pathway and proteasome pathway synergistically suppressed TNBC cells proliferation in vitro and in vivo.

overall_design: BT549 cells pre-expressing Cas9 were infected with a lentiviral sgRNA library (GeCKO V2) consisting of six single guide ribonucleic acids (sgRNAs) per gene  targeting 19050 human genes. The titer of virus added to cells was carefully  manipulated to get a multiplicity of infection (MOI) as low as 0.3, ensuring only one sgRNA  per cell. Cells were subsequently applied to a puromycin selection to remove the cells  without infection. The cells were then split into three parts. One group was directly applied  to sgRNA sequencing and labeled as DMSO-Day0. The other two groups, which were  labeled as DMSO-Day7 and AZD-Day7, were treated with DMSO and AZD6244 (MEK inhibitor),  respectively. After 7 days, the cells were collected and subjected to next-generation sequencing (NGS) of the sgRNA sequences

first: Xueyan

last: Wang

first: Xiaowei

last: Liu


title: Understanding how IL-2 cytokine synergizes with PD-1 directed immunotherapy during chronic viral infection [ATAC-Seq]

status: Public on Jun 27 2022

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

country: USA

institute: Emory University

summary: This work aimed to understand how different IL2 varients

overall_design: Mice were treated with IL2, IL2+antiPDL1 or PDL1 alone. Antigen specific CD8 T-cells were sorted from mice 2 weeks after treatment and analyzed by RNAseq

first: Masao

last: Hashimoto

first: Rafi

last: Ahmed


title: Effects of Cyclic Acute and Chronic Hypoxia on Expression Level of Metabolism Related Genes in a Pancreatic Cancer Cell Line

city: Amman

first: Hamzeh

middle: J.

last: Al-Ameer

address: Madaba

department: Biology and Biotechnology

country: Jordan

institute: American University of Madaba

summary: This work aims to characterize cycling hypoxia induced changes in metabolism related genes expression in pancreatic cancer cell line. PANC1were exposed to either 7 hours cycles of hypoxia every other day for 20 cycles cyclic acute hypoxia, or to 72 hours cycles of hypoxia once a week for 5 cycles cyclic chronic hypoxia. Gene expression changes were profiled using RT PCR  and compared to cells under normoxia. Western blotting analysis confirmed upregulation of hypoxia inducible factor 1 α, glucose 6 phosphate isomerase gene, and ribokinase gene. Genes encoding glycolysis enzymes were upregulated under cyclic acute more than chronic hypoxia including hexokinase2 and phosphoglycerate kinase1. Genes encoding pentose phosphate pathway enzymes transketolase and transaldolase were upregulated similarly. Genes encoding pyruvate dehydrogenases that block pyruvate flow to TCA cycle were significantly upregulated. Exposure of PANC1 cells to acute hypoxia results in upregulation of genes that shift cells metabolism toward glycolysis and pentose phosphate pathways in adaptation to hypoxic stress

overall_design: The present study was designed to mimic short term and long-term cycling hypoxic conditions in tumors, and to characterize metabolism related gene changes that may occur in pancreatic cancer cells in response to cyclic acute or chronic hypoxia using PANC1 cell line which represents a pancreatic ductal adenosarcoma

first: Nour

middle: M

last: Obeidat

first: Malek

middle: A

last: Zihlif

first: Dana

last: Alqudah

first: Walhan

last: Alshaer

first: Moath

last: Alqaraleh

first: Shtaywy

last: Abdalla


title: Understanding how IL-2 cytokine synergizes with PD-1 directed immunotherapy during chronic viral infection [scRNA-seq]

type: Expression profiling by high throughput sequencing

summary: In this study we have examined how the cytokine interleukin-2 (IL-2) synergizes with programmed cell death-1 (PD-1) directed immunotherapy during chronic lymphocytic choriomeningitis virus (LCMV) infection. PD-1 blockade in combination with IL-2 is one of the most effective combination therapies in this very stringent LCMV mouse model of life-long chronic infection with irreversible T-cell exhaustion. Our paper makes the following points: First, we show that the more effective viral control seen after PD-1/IL-2 combination therapy compared to PD-1 monotherapy is mediated by the CD8+T-cell response. Then we identify the virus-specific CD8+T cells that proliferate and respond to the combination therapy and show that these are the same lymphoid resident PD-1+TCF-1+stem-like CD8+T cells that act as resource cells to maintain the CD8+T-cell response during chronic infection and also respond to PD-1 blockade. However, the combination therapy dramatically changes the differentiation program of these chronic resource CD8+T cells and results in the generation of transcriptionally and epigenetically distinct effector CD8+T cells that resemble highly functional effector CD8+T cells seen after an acute viral infection. In contrast, PD-1 monotherapy doesnot modify the differentiation program and one gets more virus-specific CD8+T cells but they are transcriptionally and epigenetically similar to what is seen in untreated chronically infected mice. This epigenetic inflexibility of exhausted CD8+T cells is a potential barrier to PD-1 therapy and the ability of this combination therapy to modify the epigenetic signature of virus-specific CD8+T cells during chronic infection could be an important determinant of the striking synergy seen between IL-2 therapy and PD-1 blockade. We also highlight the importance of blocking the PD-1/PD-L1 inhibitory pathway at the target site for effective viral control. Expanding the CD8+ Tcell population and generating better effector cells is important but it is also critical to block PD-1 inhibitory signals at the target site for optimal immunotherapy. Finally, we show that CD25 engagement with IL-2 plays an important and essential role in the observed synergy between IL-2 cytokine and PD-1 blockade. Either blocking CD25 with an antibody or using a mutated version of IL-2 that does not bind CD25 but still binds CD122/132 almost completely abrogated the synergistic effects seen after PD-1/IL-2 combination therapy. There is currently considerable interest in PD-1/IL-2 combination therapy for cancer patients and our fundamental studies defining the underlying mechanisms of how IL-2 synergizes with PD-1 blockade should inform these human translational studies.

overall_design: Cell sorting was performed byFACS Aria II (BD Biosciences).For scRNA-seq (10X Genomics), LCMV chronically infectedmice (> day 40 p.i.) were untreated or treated with various therapeutic modalities for 2 weeks, and DbGP33+CD8+T cells in spleens were sorted from pooled spleens. Naïve (CD44lo) CD8+T cells were sorted from pooled spleens from uninfected mice (n=2).


title: Understanding how IL-2 cytokine synergizes with PD-1 directed immunotherapy during chronic viral infection [Bulk RNA-seq]

overall_design: Mice infected with LCMV-clone13 were treated with various immunotherapies. Antigen specific CD8 T-cells were sorted from mice 2 weeks after treatment and analyzed by RNAseq


title: Understanding how IL-2 cytokine synergizes with PD-1 directed immunotherapy during chronic viral infection [RNA-seq]


title: Comparison of gene expression between islets from NOD-Rag and NOD-Idd22 mice

city: GAINESVILLE

first: Clayton

middle: E

last: Mathews

state: Florida

address: 1275 Center DRive

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

summary: NOD-Idd22 mice are congenic mice of NOD background with a piece of chromosome 8 being substituted with ALR genetic material.  These mice are resistant to spontaneous autoimmune diabetes as well as chemically induced in vivo islet beta cell destructions.  The goal of this project is to come pare gene expressions in islets between NOD-Idd22 and NOD mice.  NOD-Rag1 was used instead of NOD to avoid lymphocyte infiltrtation in isltes.

overall_design: Each sample of RNA was extracted from about 200 islets that were isoleated and pooled from 2 mice. Four replicates from NOD-Idd22 and 3 replicates from NOD.Rag1 were analyzed.

first: Robert

last: Whitener


title: Does an immune response at the Ileum contribute to severity and development of helminth-diarrhoea in Merino sheep (ileum)?

city: Perth

first: Shamshad

middle: Ul

last: Hassan

state: Western Australia

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

summary:
Purpose: To investigaet whether an inflammatory immune response at the Ileum can contribute to development and severity of diarrhoea in Merino sheep that are prone and not prone to develop diarrhoea.
Methods:Transcriptomes in the Ileum (third part of small intestine) of Merino sheep were analyzed using RNASeq. Functional enrichment of DEGs using GO terms in biological processes and KEGG pathways were studied. PPI (protein-protein interaction) network and sub-network were studied using clusterONE plugin in Cytoscape.
Result and conclusion: Although Ileum in not a primary site of helminth (species under study in our experiment), the results indicated that an inflammatory immune response can contribute to development and severity of diarrhoea. The low-diarrhoea animals did not show any signs of immune/inflammatory response. The genes with important roles in the responses to helminth infection could be targeted in breeding programs to prevent diarrhoea.

overall_design: Four biological replicates in each of High-diarrhoea (HD) and Low-diarrhoea (LD) group were used. LD group was used as a control group.

middle: U

first: Eng

middle: G

last: Chua

first: Parwinder

last: Kaur

first: Erwin

last: Paz

first: Chin

middle: Y

last: Tay

first: Johan

last: Greeff

first: Shimin

first: Graeme

middle: B

last: Martin


title: The dynamic response to hypoosmotic stress reveals distinct stages of freshwater acclimation by a euryhaline diatom

status: Public on Jun 23 2022

city: Fayetteville

first: Jeffrey

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

department: Biological Sciences

institute: University of Arkansas

summary: The salinity gradient separating marine and freshwater environments is a major ecological divide, and the mechanisms by which most organisms adapt to new salinity environments are poorly understood. Diatoms are a lineage of ancestrally marine microalgae that have repeatedly colonized and diversified in freshwaters. Cyclotella cryptica is a euryhaline diatom that naturally tolerates a broad range of salinities, thus providing a powerful system for understanding the genomic mechanisms for mitigating and acclimating to low salinity. To understand how diatoms mitigate acute hypoosmotic stress, we abruptly shifted C. cryptica from seawater to freshwater and performed transcriptional profiling at 8 time points across 10 hours. We found substantial remodeling of the transcriptome, with over half of the genome differentially expressed in at least one time point. The peak response occurred within 1 hour, with strong repression of genes involved in functions related to cell growth and osmolyte production, and strong induction of genes implicated in stress defense such as scavenging reactive oxygen species and maintaining osmotic balance. Notably, transcripts largely returned to baseline levels within 4–10 hours, with growth resuming shortly thereafter, suggesting that gene expression dynamics may be useful for predicting acclimation. Moreover, comparison to a study of expression profiling following months-long acclimation of C. cryptica to freshwater revealed little overlap between the genes and processes differentially expressed in cells exposed to acute stress versus fully acclimated conditions. Altogether, this study highlights the power of time-resolved transcriptomics to reveal fundamental insights into how cells dynamically respond to an acute environmental shift and provides new insights into how diatoms mitigate natural salinity fluctuations and have successfully diversified across freshwater habitats worldwide.

overall_design: We performed RNA-seq on the diatom Cyclotella cryptica responding to acute freshwater (hypoosmotic) stress across eight time points.

first: Kala

last: Downey

first: Kathryn

middle: J

last: Judy

first: Eveline

last: Pinseel

first: Andrew

last: Alverson


title: Understanding how IL-2 cytokine synergizes with PD-1 directed immunotherapy during chronic viral infection

first: Haydn

last: Kissick

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

overall_design: Refer to individual Series


title: Increased Type I Interferon Signaling and Brain Endothelial Barrier Dysfunction in an Experimental Model of Alzheimer’s Disease

status: Public on Jun 25 2022

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 909 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

summary: Blood-brain barrier (BBB) dysfunction is emerging as a key pathogenic factor in the progression  of Alzheimer’s disease (AD), where increased microvascular endothelial permeability has been  proposed to play an important role. However, the molecular mechanisms leading to increased  brain microvascular permeability in AD are not fully understood. We observed that brain  endothelial permeability in the APPswe/PS1DE9 (APP/PS1) transgenic mouse model of  amyloid-beta (Ab) amyloidosis increases with aging in the areas with the greatest amyloid  plaque deposition. We performed an unbiased bulk RNA-sequencing analysis of brain  endothelial cells (BECs) in APP/PS1 transgenic mice. We observed that upregulation of  interferon signaling gene expression pathways in BECs were among the most prominent  transcriptomic signatures in the brain endothelium of APP/PS1 mice. Immunofluorescence  analysis of isolated BECs from APP/PS1 mice demonstrated higher levels of the Type I  interferon-stimulated gene IFIT2. Immunoblotting of APP/PS1 BECs showed downregulation of  the adherens junction protein VE-cadherin. Stimulation of human brain endothelial cells with  interferon-β decreased the levels of the adherens junction protein VE-cadherin as well as tight  junction proteins Occludin and Claudin-5 and increased barrier leakiness. Depletion of the Type  I interferon receptor in human brain endothelial cells prevented interferon-β-induced VE-  cadherin downregulation and restored endothelial barrier integrity. Our study suggests that Type  I interferon signaling contributes to brain endothelial dysfunction in AD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for brain endothelial cells of Alzheimer's disease.

first: Arundhati

last: Jana

first: Xinge

last: Wang

first: Joseph

middle: W

last: Leasure

first: Lissette

last: Magana

first: Li

first: Young-Mee

last: Kim

first: Hemraj

last: Dodiya

first: Peter

middle: T

last: Toth

first: Sangram

last: Sisodia


title: miR-515-5p suppresses trophoblast cell invasion and proliferation through XIAP regulation in preeclampsia

status: Public on Jun 26 2022

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: MicroRNAs (miRNAs) are non-coding small RNA molecules that can be secreted into the circulation and which exist in remarkably stable forms. Circulating miRNAs regulates numerous regulations of biological process and aberrantly expressed in pathological status. Differentially expressed circulating miRNAs have received attention as potential biomarkers for many diseases. In this study, we revealed that miR-515-5p was significantly upregulated in maternal serum from preeclampsia (PE) patients in comparison to normal pregnant women. Bioinformatics prediction and a dual-luciferase reporter gene assay revealed that miR-515-5p directly targets the X-linked inhibitor of apoptosis protein (XIAP) 3’-untranslated region (UTR). Furthermore, the XIAP mRNA expression was decreased in the preeclamptic placenta in comparison to that in normal pregnancy. The overexpression of miR-515-5p inhibited the proliferation and invasion of HTR-8/SVneo trophoblast cells. Collectively, miR-515-5p may play critical roles in the pathogenesis of PE through suppression of the expression of XIAP and serum miR-515-5p may act as a potential biomarker for PE

overall_design: normal placenta 3, preeclampsia 3

first: Masami

last: Hayashi

first: Misa

last: Nunode


title: Single-cell RNA sequencing of zebrafish pancreatic cells during beta-cell regeneration

status: Public on Jun 21 2022

city: Dresden

first: Prateek

last: Chawla

state: Saxony

address: Fetscherstrasse 105

department: CRTD

country: Germany

institute: TU Dresden

summary: To better understand the underlying mechanism of beta-cell regeneration in adult zebrafish, we performed single-cell transcriptomic profiling of the pancreatic tissue (using 10X Genomics) at various stages post beta-cell ablation.

overall_design: The adult fish (expressing NTR gene under the insulin promoter) were treated with Mtz (Sigma-Aldrich, M3761), dissolved at 10mM concentration in fish water. The animals were treated for 24 hours, protected from light. After 24h, Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz-treated animals were euthanized by an overdose of tricaine. Samples for each time-point comprised of 6 animals (3 males and 3 females). Single-cell suspension was prepared and 15000 live-cells/per condition were FACS sorted for 10X Genomics.

first: Nikolay

last: Ninov

first: Alisa

last: Hnatiuk

first: Margrit

last: Kamel


title: High temporal resolution RNA-seq time series of serum-starved T98G human glioblastoma cells responding to serum stimulation

city: Sydney

first: Walter

last: Muskovic

state: New South Wales

address: Level 1, C25 Lowy Cancer Research Centre, Gate 9 High St, UNSW

institute: Children's Cancer Institute Australia

summary: The advent of next-generation sequencing revealed extensive transcription outside the boundaries of annotated protein-coding genes, giving rise to tens of thousands of long non-coding RNAs (lncRNAs). The functional relevance of these transcripts remains unclear. Compellingly, lncRNA expression is strongly linked with adjacent protein-coding gene expression, suggesting potential cis-regulatory roles. To investigate whether these regulatory roles exist, we examine in detail the timing of lncRNA expression relative to transcripts of known function. If a causal cis-regulatory relationship exists, lncRNA activation must necessarily precede changes in adjacent target gene expression. Here, we report a high temporal resolution RNA-seq time course of synchronized T98G human glioblastoma cells responding to serum stimulation. Detailed profiling of the expression dynamics of lncRNAs and protein-coding genes in these synchronized transitioning human cells provides insight into the feasibility of broad-scale cis-regulatory roles for lncRNAs.

overall_design: Serum-starved T98G human glioblastoma cells were stimulated with serum-rich media and harvested at ten minute intervals, producing 41 total RNA samples (0 min – 400 min) that were subsequently sequenced using an Illumina HiSeq 2500 v4.0 sequencing system to provide a mean sequencing depth of 37.2 million 125 bp paired-end reads per time point sample.


title: Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing

status: Public on Jun 22 2022

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas the substrate for Q-modification in tRNA in mammals is queuine, the catabolic product of the Q-base of gut bacteria. This gut microbiome dependent tRNA modification may play pivotal roles in translational regulation in different cellular contexts, but extensive studies of Q-modification biology are hindered by the lack of high throughput sequencing methods for its detection and quantitation. Here, we describe a periodate-treatment method of biological RNA samples that enables single base resolution profiling of Q-modification in tRNAs by Nextgen sequencing. Periodate oxidizes the Q-base, which results in specific deletion signatures in the RNA-seq data. Unexpectedly, we found that periodate-treatment also enables the detection of several 2-thio-modifications including τm5s2U, mcm5s2U, cmnm5s2U, and s2C by sequencing in human and E. coli tRNA. We term this method Periodate-dependent analysis of queuosine and thio modification sequencing (PAQS-seq). We assess Q- and 2-thio-modifications at the tRNA isodecoder level, and 2-thio modification changes in stress response. PAQS-seq should be widely applicable in the biological studies of Q- and 2-thio-modifications in mammalian and microbial tRNAs.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: HEK293T cells were grown with and without queuine in duplicate. Extracted RNA was used to prepare libraries with and without periodate treatment : 8 libraries total. Next, RNA from HEK293T cells with and without queuine was mixed at a ratio of 0% from cells with Q, 10%, 20%... 100% cells with Q. This calibration curve involves 11 libraries in total. Next, RNA extracted from E. coli cells was used to prepare libraries with and without periodate treatment: 2 libraries. Finally, E. coli were grown in duplicate. Each culture was split into 4, and subjected to 1 of 3 stresses or a control. RNA was extracted from these culutures, treated with periodate, and used to prepare libraries: 8 samples. In total this  project involves 29 librarires.

first: Christopher

middle: D

last: Katanski

middle: P

last: Watkins

first: Wen

last: Zhang

first: Matthew

last: Reyer

first: Sammuel

last: Miller


title: Dietary Protein Restriction Reverses Metabolic Dysfunction in Patients with Metabolic Syndrome: a Randomized, Controlled Trial

status: Public on Jun 20 2022

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary:
Aims/hypothesis: Dietary restriction (DR) reduces adiposity and improves metabolism in patients with one or more symptoms of the metabolic syndrome. Nonetheless, it remains elusive whether the benefits of DR in humans are mediated by calorie or nutrient restriction. This study was conducted to identify whether isocaloric dietary protein restriction is sufficient to confer the beneficial effects of dietary restriction in patients with metabolic syndrome.
Methods: We performed a prospective, randomized controlled dietary intervention under constant nutritional and medical supervision. A total of 21 individuals diagnosed with the metabolic syndrome was randomly assigned for caloric restriction (CR; n = 11, mean age 49 ± 8.5 years, female 63%; diet of 5,941 ± 686 KJ per day) or isocaloric dietary protein restriction (PR; n = 10, mean age 51.6 ± 8.9 years, female 50%; diet of 8,409 ± 2,360 KJ per day) and followed for 27 days.
Results: Like CR, PR promoted weight loss (-6.6%, P= 0.0041) due to reduction in adiposity (-9.9%, P= 0.0007), associated with reductions in blood glucose (-52.7%, P= 0.0002), lipid levels (cholesterol, -35.4%, P= 0.0010; triglycerides, -39.5% P= 0.0022) and blood pressure (systolic, -37.7 P< 0.0001; diastolic, -73.2% P< 0.0001). PR resulted in enrichment of metabolic pathways related to the immune system such as B cell proliferation, lymphocyte proliferation and leukocyte proliferation in subcutaneous adipose tissue. Hence, a reduction in calorie intake or changes in the gut microbiome are not necessary to confer the metabolic benefits of DR. Instead, a reduction in protein intake with a mild increase in carbohydrate intake to maintain the isocaloric balance of the diet is sufficient to improve metabolic control.
Conclusions/interpretation: Protein restriction is sufficient to confer almost the same clinical outcomes as calorie restriction without the need for a reduction in calorie intake. The isocaloric characteristic of the PR intervention makes this approach a more attractive and less drastic dietary strategy in clinical settings and has greater potential to be used as adjuvant therapy for people with the metabolic syndrome.

overall_design: RNA seq analysis of participants before and after either a protein restricted diet or a calorie restricted diet.

first: Rafael

last: Ferraz-Bannitz

first: Rebeca

last: Beraldo

first: A

last: Peluso

first: Morten

last: Dall

first: Parizad

last: Babaei

first: Rayana

last: Foglietti

first: Larissa

last: Martins

first: Patricia

last: Gomes

first: Julio

middle: S

last: Marchini

first: Vivian

last: Suen

first: Luiz

middle: C

last: de Freitas

last: Navegantes

first: Marco

last: Pretti

first: Mariana

last: Boroni

first: Jonas

last: Treebak

first: Marcelo

last: Mori

first: Milton

last: Foss

first: Maria

last: Foss-Freitas


title: CTLA-4-Ig internalizes CD80 in fibroblast-like synoviocytes from chronic inflammatory arthritis mouse modelinflammatory arthritis mouse model

status: Public on Jun 19 2022

first: Satoshi

last: Kondo

summary:
In this study, the therapeutic effect of CTLA-4-Ig in a mouse model of rheumtaoid arthritis, in which CD80 is expressed in chondrocytes and the synovial cells of joints.
The therapeutic effect of CTLA-4-Ig appears to extend beyond the lymph nodes into the inflamed synovial compartment through the synergistic inactivation of T cells by the CD80 and PD-L1 axes.

overall_design:
Isolated synovial cells were cultured in DMEM with 10% FBS and cultured at 37°C containing 5% CO2 for overnight.
Abatacept (100 mg/ml), human IgG (100 mg/ml), and vehicle (DMEM with 10% FBS as a control) added and incubated at 37°C with 5% CO2 for 48 h.

first: Yoko

last: Miura

last: Kanazawa


title: A Drosophila proto-oncogene homolog controls aggression via aminergic neurons

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Modulation of action choices according to the environmental context is crucial for animal survival and reproductive success1. Aggression, despite its general importance as a social behavior2, can become detrimental if uncontrolled3,4. However, the genetic and neural basis for aggression control through active suppression remains largely unknown. Here we found nvy, a Drosophila homolog of vertebrate myeloid translocation gene (MTG)5 involved in transcriptional regulation6-8, suppresses aggression through a specific subset of neurons. Mutation of the nvy gene resulted in hyper-aggressiveness, which was rescued by neuronal expression of human MTGs as well as Drosophila nvy. The mutant exhibited persistent aggression under various contexts in which wild-type flies switch their behavioral patterns. Knockdown of nvy in octopaminergic/tyraminergic (OA/TA) neurons increased aggression, phenocopying the nvy deletion. Cell-type specific transcriptomics on OA/TA neurons derived from the nvy mutants revealed aggression-controlling genes that are likely downstream of nvy. Moreover, we found that the nvy-expressing OA/TA neuronal subpopulations specifically suppress aggression. Our results presents a powerful genetic model to unravel not only the neuronal systems that modulate aggression in a social context-dependent manner, but also the conserved molecular mechanism underlying the tumorigenesis caused by the MTG mutations.

overall_design: Transcriptional profiles of octopaminergic/tyraminergic neurons of wild-type and nervy-mutant fruit flies using single-cell RNA-sequencing technology.

first: Kenichi

last: Ishii

first: Matteo

last: Cortese

first: Xubo

last: Leng

first: Margot

last: Wohl

first: Maxim

middle: N

last: Shokhirev

first: Antonio

middle: M

last: Pinto

first: Kenta

last: Asahina


title: Transcriptomic responses of caddisfly Dicosmoecus gilvipes to temperature.

city: Berkeley

first: Jonathon

last: Stillman

state: ca

address: 3040 Valley Life Sciences Building #3140

department: Integrative Biology

institute: University of California Berkeley

summary: These samples are from RNA collected from specimens held at 4 temperatures (15.5, 20.0, 25.0 and 28.6degC).  Specimens were ramped to one of those temperatures over 4 days following a common garden at 11degC for two weeks.  RNA was extracted from thorax tissue and used for RNA-seq.  Genes with statistically different expression levels among temperatures were identified.

overall_design: Exposure of specimens to 4 different temperatures followed by RNA-seq to identify thermally-responsive transcripts

middle: H


title: Developing High-Affinity Decoy Receptor Optimized for Multiple Myeloma and Diffuse Large B Cell Lymphoma Treatment [RNA-seq]

status: Public on Jun 18 2022

city: Houston

first: Dadi

last: Jiang

state: TX

address: 6565 MD Anderson Blvd, Unit 1052

department: Radiation Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: This study demonstrates the dichotomous activities of APRIL and BAFF in MM and DLBCL, which can be safely targeted by an engineered fusion protein designed to trap both ligands with ultrahigh binding affinity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U266 multiple myeloma cells and its knockdown derivatives (siBCMA).

first: Yu

middle: R

last: Miao

first: Can

last: Cenik

first: Albert

last: Koong

first: Amato

last: Giaccia


title: Targeting ESR1 mutation-induced transcriptional addiction with BET inhibition

city: Dallas

first: SM

last: Udden

address: 2201 Inwood Road

institute: UT Southwestern Medical Center

summary: We investigated the therapeutic potential of BET inhibition to target ESR1 mutation-induced “transcriptional addiction” in ER-positive breast cancer. Our studies show that ESR1 mutant (Y537S and D538G) cells activate unique transcriptional programs that are targeted by OTX015, a BET inhibitor

overall_design: We performed gene expression profiling analysis (using RNA-seq) of MCF7 WT, Y537S and D538G cells treated with vehicle, b-estradiol and/or OTX-015 in hormone-deprived conditions to define transcriptional changes.

first: Prasanna

last: Alluri

first: S

first: Venkat

last: Malladi


title: Tsc2 shapes olfactory bulb granule cell molecular and morphological characteristics

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

institute: Clemson University

summary: Tuberous Sclerosis Complex (TSC) is a neurodevelopmental disorder caused by mutations that inactivate TSC1 or TSC2. Hamartin and tuberin are encoded by TSC1 and TSC2 which form a GTPase activating protein heteromer that inhibits the Rheb GTPase from activating a growth promoting protein kinase called mammalian target of rapamycin (mTOR). Growths and lesions occur in the ventricular-subventricular zone (V-SVZ), cortex, olfactory tract, and olfactory bulbs (OB) in TSC. Here, nestin-CRE-ERT2 mice were injected with tamoxifen at postnatal days 2 and 3 and brains harvested at postnatal day 60. OBs were subsequently subjected to RNA sequencing.

overall_design: nestin-CRE-ERT2 mice were injected with tamoxifen at postnatal days 2 and 3 and brains harvested at postnatal day 60. OBs from three mice per condition were subsequently subjected to RNA sequencing.

first: Victoria

middle: A

last: Riley


title: Developing High-Affinity Decoy Receptor Optimized for Multiple Myeloma and Diffuse Large B Cell Lymphoma Treatment [Ribo-seq]

overall_design: Comparative ribosome and gene expression profiling analysis of RNA-seq data for U266 multiple myeloma cells and its knockdown derivatives (siBCMA).


title: Gene expression in human keratinocytes from psoriatic skin (directly into the lesion or in area without lesion) or healthy person (control) used for human tissue-engineered skin substitutes and co-cultured with T-lymphocyte

status: Public on Jun 17 2022

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

country: Canada

institute: CUO-Recherche

summary:
The objective of this study was to find deregulated genes between healthy and psoriatic T cell-enriched tissue-engineered models to develop a new therapeutic pathway in psoriasis treatment.
In this study, we used a tissue-engineered, two-layers (dermis and epidermis) human skin substitute enriched in T cells as a biomaterial to study both the cellular and molecular mechanisms involved in psoriasis’ pathogenesis.

overall_design: 3 human healthy keratinocytes population (at passage 3) from 3 healthy donors (18-, 46- and 49-years old), 4 human psoriatic keratinocytes population (at passage 3) from directly into the lesion of 4 psoriatic patients (36-, 46-, 49- and 64- years old) and 3 human psoriatic keratinocytes population (at passage 3) from area without lesion of three psoriatic patients (46-, 49- and 64- years old) co-cultured or not with T-lymphocyte from human tissue-engineered skin substitutes are analyzed by gene profiling.

first: Geneviève

last: Rioux

first: Florence

last: Turgeon

first: Camille

last: Grenier

first: Sylvain

last: Guérin

first: Roxane

last: Pouliot


title: Next generation sequencing of transcripts associated to four selected RNA-binding proteins in Tripanosoma brucei

city: Recife

first: MARIA

middle: JOSE RIBEIRO

last: BEZERRA

state: PE

department: Microbiologia

institute: Fiocruz-PE

summary: We report the sequencing of mRNAs associated with four Trypanosoma brucei translation intiation proteins EIF4E3, EIF4E4, EIF4G3 and EIF4G4. To investigate if the proteins have redundant functions, we analyzed mRNAs subpopulations in cells submitted to RNAi of EIF4E3 and EIF4E4. The reduction of EIF4E3 protein levels did not change the profile of mRNA populations associated to EIF4E4.

overall_design: mRNAs co-precipitated with rabbit polyclonal-antibodies against translation initiation target proteins from cytoplasmic extracts of Trypanosoma brucei cells, CLIP-Seq.

first: Maria

last: Bezerra

first: Talita

last: Monteiro

first: Antônio

last: Rezende

first: Osvaldo

last: de Melo Neto


title: Developing High-Affinity Decoy Receptor Optimized for Multiple Myeloma and Diffuse Large B Cell Lymphoma Treatment

first: Dadi

last: Jiang


title: Microbiota-instructed regulatory T cell differentiation is mediated by a distinct RORgt+ antigen presenting cell subset

city: New York

first: Peter

last: Smibert

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: The mutualistic relationship of gut-resident microbiota and cells of the host immune system promotes homeostasis that ensures maintenance of the microbial community and of a poised, but largely non-aggressive, immune cell compartment1. Consequences of disturbing this balance, by environmental or genetic factors, include proximal inflammatory conditions, like Crohn’s disease, and systemic illnesses, both metabolic and autoimmune. One of the means by which this equilibrium is achieved is through induction of both effector and suppressor or regulatory arms of the adaptive immune system. In mice, Helicobacter species induce regulatory (iTreg) and follicular helper (Tfh) T cells in the colon-draining mesenteric lymph nodes under homeostatic conditions, but can instead induce inflammatory Th17 cells when iTreg cells are compromised3,4. How Helicobacter hepaticus and other gut bacteria direct T cells to adopt distinct functions remains poorly understood. Here, we investigated which cells and molecular components are required to convey the microbial instruction for the iTreg differentiation program. We found that antigen presentation by cells expressing RORgt, rather than by classical dendritic cells, was both required and sufficient for iTreg induction. These RORgt+ cells, likely to be type 3 innate lymphoid cells (ILC3) or a recently-described population of Aire+ cells termed Janus cells5, require the MHC class II antigen presentation machinery, the chemokine receptor CCR7, and av integrin, which activates TGF-β, for iTreg cell differentiation. In the absence of any of these, instead of iTreg cells there was expansion of microbiota-specific pathogenic Th17 cells, which were induced by other antigen presenting cells (APCs) that did not require CCR7. Thus, intestinal commensal microbes and their products target multiple APCs with pre-determined features suited to directing appropriate T cell differentiation programs, rather than a common APC that they endow with appropriate functions.

overall_design: Four week-old Adig mouse lymph nodes (cervical, brachial, axillary, inguinal, and mesenteric) were pooled (n=3 mice) and cells were enriched/depleted using the strategies noted below, persample.

first: Jessica

last: Wang

first: Caleb

last: Lareau

first: Jay

last: Gardner


title: mRNA profiling in Ustilago maydis under RUS (repopulation/regrowth under starvation)

status: Public on Jun 16 2022

city: Belgrade

first: Stefan

last: Stanovčić

state: Serbia

address: Vojvode Stepe 444a

country: Serbia

institute: IMGGE

summary: mRNAs comparison between Ustilago maydis wild type grown in diluted YEPS (control) and in cell-free supernatants of Ustilago maydis wild type treated with H202 in two different concentrations (0.4% and 0.7%).

overall_design: In order to identify genes differentailly expressed under RUS (repopulation/regrowth under starvation) Ustilago maydis wild type was grown for 16h in YEPS (1% (w/v) yeast extract, 2% (w/v) peptone, 2% (w/v) saccharose). The same amount of 2x107 cells of U.maydis wild type overnight culture was transfered to 10% YEPS (as control) as well as to cell-free supernatants of U.maydis wild type treated with H202 in two different concentrations (0.4% and 0.7%) (as two separate conditions). RNAseq analysis of all three type of samples (each analyzed in triplicates) focused on mRNA differentially expressed in two conditions vs. control.

first: Milorad

last: Kojic

first: Mira

last: Milisavljevic

first: Jelena

last: Malesevic

last: Stanovcic


title: Isotype-specific plasma cells express divergent transcriptional programs

status: Public on Jun 15 2022

first: Michael

last: McHeyzer-Williams

address: 10550 N Torrey Pines Rd

institute: Scripps Research Institute

summary: We utilized single cell-indexed custom RNA-sequencing to interogate the transcriptomes of isotype specific plasma cells at homeostasis and following immunization with a model antigen

overall_design: Murine plasma cells were sorted as (Gr1-, CD3-, IgD-, CD138+) with additional sorting gates by isotype (either IgG1, IgG2b, IgG2a, IgA or IgM). Antigen specific plasma cells (NP+ Lambda1+) were isolated from draining lymph nodes before and 5 and 14 days after primary immunization with NP-KLH. Steady steady plasma cells were isolated from the spleen.

first: Brett

last: Higgins

first: Andrew

middle: G

last: Shuparski

first: Karen

middle: B

last: Miller

first: Amanda

last: Robinson

first: Louise


title: Suppression of Ca2+ Signaling Enhances Melanoma Progression

city: Sugar Land

first: Kumaraswamy Naidu

last: Chitrala

address: 13850 University Blvd, SAB1 Room No: 214

department: Engineering Technology

institute: College of Technology, University of Houston

summary:
To investigate the effect of UV on SOCE suppression in melanoma progression
We performed gene expression analysis of cells exhibiting SOCE suppression and cells not exhibiting SOCE suppression compared to control

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WM983 and UACC257 human melanoma cells, UV exposed cells (WM983 Control, WM983 UV2, UACC257 Control, UACC257 UV2).

first: Scott

last: Gross

first: Kumaraswamy

first: Jonathan

last: Soboloff


title: Impact of RXEG1 mutations in Nicotiana benthamiana response to XEG1

city: Nanjing

first: Yan

address: No.1 Weigang Road

department: Plant Pathology

institute: Nanjing Agricultural University

summary: To investigate whether the key residues in RXEG1 determines it function in XEG1 recogntion, we make mutations on these residues and generated stable transformants expressing RXEG1 mutants dirven by the native promoter in rxeg1 knockout mutants. We then treated these mutants using XEG1 and mock, and compare expression of responsive genes in wild typle N. benthamiana and different mutants.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type N. benthamiana and derived mutants

first: Yuanchao


title: The long non-coding RNA mimi scaffolds neuronal granules to maintain nervous system maturity

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

institute: MPI of Immunobiology and Epigenetics

summary: RNA-binding proteins and messenger RNAs assemble into ribonucleoprotein granules that regulate mRNA trafficking, local translation, and turnover. The dysregulation of RNA-protein condensation disturbs synaptic plasticity and neuron survival, and has been widely associated with human neurological disease. Neuronal granules are thought to condense around particular proteins that dictate the identity and composition of each granule type. Here, we show in Drosophila that a previously uncharacterized long non-coding RNA, mimi, is required to scaffold large neuronal granules in the adult nervous system. Neuronal ELAV-like proteins directly bind mimi and mediate granule assembly, while Staufen maintains condensate integrity. mimi granules contain mRNAs and proteins involved in synaptic processes; granule loss in mimi mutant flies impairs nervous system maturity, neuropeptide-mediated signaling and causes phenotypes of neurodegeneration. Our work reports the first architectural RNA for a neuronal granule and provides a handle to interrogate functions of a condensate independently from those of its constituent proteins.

overall_design: mRNA seq of wild-type (CantonS) flies

first: Dominika

last: Grzejda

first: Jana

last: Mach

first: Johanna

last: Schweizer

first: Barbara

last: Hummel

last: Rezansoff

first: Florian

last: Eggenhofer

first: Amol

last: Panhale

first: Maria-Eleni

last: Lalioti

first: Nina

last: Cabezas Wallscheid

first: Rolf

last: Backofen

first: Johannes

last: Felsenberg


overall_design: total RNA seq of  Δmimi and wild type fly heads + respective granule fractions; 3 replicates of tissue lysate per genotype, 2 replicates of granules fraction per each corresponding tissue lysate (6 replicates in total), per genotype; 2 genotypes: wild type (w1118) and Δmimi

first: Andrew


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

overall_design: Refer to individual Series


overall_design: 3' mRNA seq of 4 replicates of four independent wild-type lines


overall_design: totalRNAseq of FNE, RBP9 mutants and wild-type control. 5 replicates per genotype; 4 different genotypes: wild type (w1118), Δfne (fneΔ/fneKOZ2 (females) and fneΔ or fneKOZ2 (males)), Δrbp9 (rbp9P2690/Df(2L)ED206 (males and females)) and ΔfneΔrbp9 (fneΔ/fneKOZ2; rbp9P2690/Df(2L)ED206 (females) and fneΔ; rbp9P2690/ Df(2L)ED206 or fneKOZ2; rbp9P2690/Df(2L)ED206 (males))


title: Pronounced specificity of the TET enzyme catalytic domain guides cellular function

status: Public on Jun 13 2022

city: Dunedin

first: Oscar

middle: Javier

last: Ortega-Recalde

state: Otago

address: 60 Hanover Street

department: Anatomy

country: New Zealand

institute: University of Otago

type: Methylation profiling by high throughput sequencing

summary: TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic domain of mammalian TET enzymes favor CGs embedded within bHLH and bZIP transcription factor binding sites, with up to 250-fold preference in vitro. Crystal structures and molecular dynamics calculations show that sequence preference is caused by intrasubstrate interactions and CG flanking sequence indirectly affecting enzyme conformation. TET sequence preferences are physiologically relevant as they explain the rates of DNA demethylation in TET-rescue experiments in culture and in vivo within the zygote and germline. Most and least favorable TET motifs represent DNA sites that are bound by methylation-sensitive immediate-early transcription factors and OCT4, respectively, illuminating TET function in transcriptional responses and pluripotency support.

overall_design: An ESC line with TET1-3 genetically inactivated (TET-TKO) was rescued using an inducible PiggyBAC transposon based vector containing the catalytic domain from mouse TET3 induced by doxicycline and transcriptionally linked to an mCherry reporter gene. Cells without doxycicline treatment were used as control. APOBEC-coupled epigenetic sequencing (ACE-seq) was used to quantitate 5-Hydroxymethylcytosine (5hmC) levels.

first: Timothy

last: Hore

first: Claudia

last: Davies

first: Rosie

last: Glanfield


title: Expression profile of PBMCs from human healthy volunteers in 36-hours-fasting conditions versus basal conditions (12-hours-fasting).

status: Public on Jun 12 2022

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

country: Spain

institute: IMDEA ALIMENTACION

summary: Short-term fasting elicits beneficial effects in mice and humans, including protection from chemotherapy toxicity, but the involved mechanisms are not well understood. We collected blood samples from healthy human volunteers and mice before and after 36 or 24 hours of fasting, respectively, to measure fatty acid composition of erythrocyte membranes, circulating miRNAs, and RNA expression at PBMCs. In both mice and humans, fasting affected the proportion of polyunsaturated versus saturated and monounsaturated fatty acids at the erythrocyte membrane. Also, fasting significantly reduced the expression at PBMCs of insulin signaling-related genes, including the SREBP lipid-metabolizing pathway, in correlation with changes in membrane fatty acids. We tested the relevance of these fatty acid homeostasis parameters using a complete platform to monitor chemotherapy toxicity in mice. When fasted for 24 hours before and 24 hours after administration of the chemotherapeutic drug oxaliplatin, mice showed a strong protection from kidney, liver, heart and bone marrow toxicity. Importantly, the newly discovered fasting parameters defined two clearly separated groups of individuals that accurately predicted a differential protection from chemotherapy toxicity. Our results reveal a novel mechanism of fasting associated with fatty acids homeostasis, and provide novel biomarkers of fasting to predict fasting-mediated protection from chemotherapy toxicity.

overall_design: Human PBMCs from healthy volunteers in basal (12h fasting) and fasting conditions (36h fasting).

first: Pablo

middle: J

last: Fernandez-Marcos

first: Roberto

last: Martin-Hernández

first: Alejo

last: Efeyan


title: Regulation of chromatin accessibility in early embryos of the common house spider Parasteatoda tepidariorum

status: Public on Jun 10 2022

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

institute: JT Biohistory Research Hall

summary: We identified a lineage-specific GATA-like gene named fuchi nashi (fuchi) as a gene required for establishing a germ disc in the early embryo of the common house spider Parasteatoda tepidariorum. To investigate possible involvement of the early fuchi activity in regulation of chromatin accessibility, we used an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Whole embryos at stage 3 that were untreated (wild-type) or treated for fuchi or hedgehog (hh) parental RNAi (pRNAi), as well as wild-type whole embryos at stages 1 and 2, were analyzed by ATAC-seq. We found that chromatin accesibilities were specifically altered by fuchi pRNAi at many regions of the genome, whereas chromatin accessibilities were little affected by Pt-hh pRNAi, which served as negative control.

overall_design: We analyzed by ATAC-seq the nuclei that were extracted from wild-type whole embryos at stage 1 (st1, 9 h after egg laying [AEL]), stage 2 (st2, 12 h AEL), and stage 3 (st3, 18 h AEL) and from fuchi and Pt-hh pRNAi whole embryos at stage 3 (st3, 18 h AEL). Two biological replicates were obtained for each sample type. The tagmented genomic DNAs were amplified to produce indexed libraries, which were paired-end sequenced using the Illumina HiSeq X Ten system (2 x 151 bp reads) . Differential accessibilities between the wild-type and fuchi or Pt-hh pRNAi stage 3 samples were statistically evaluated.

first: Ryota

last: Nanjo

first: Sawa

last: Iwasaki-Yokozawa

first: Yasuko

last: Akiyama-Oda


title: Identification of genes whose expression is affected by fuchi nashi pRNAi in early embryos of the spider Parasteatoda tepidariorum

summary: We identified a GATA-like gene named fuchi nashi (fuchi) as a gene required for establishing a germ disc in the early embryo of the spider Parasteatoda tepidariorum. fuchi transcript is initially expressed in cells at both polar regions of the embryo and later in endodermal and extraembryonic cells. To genome-widely identify genes whose expressions are regulated by fuchi, we conducted RNA-sequencing of whole embryos at three different early stages (stages 2 and 3 and early stage 5) that were untreated (control) or treated for fuchi parental RNA interference (pRNAi).

overall_design: We extracted poly(A) mRNA from whole embryos at stage 2 (st2, 11 h after egg laying [AEL]), stage 3 (st3, 20 h AEL), and early stage 5 (st5e, 31 h AEL) that were prepared from the same mated females before and after treatment for fuchi pRNAi. The mRNAs were sequenced using the Illumina Miseq platform to identify differentiallly epxressed genes (DEGs) between the untreated and treated embryos for each stage.  Two biological replicates were obtained for each sample type. We confirmed that the fuchi gene (aug3.g26874) itself was expectedly included in the detected DEGs for all the stages.


title: C9orf72 deficiency promotes microglial mediated synaptic loss in aging and amyloid accumulation

city: Los Angeles

first: Shaughn

last: Bell

state: CA

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center


title: C9orf72 deficiency promotes microglial mediated synaptic loss in aging and amyloid accumulation [scRNA-seq]

summary: C9orf72 repeat expansions cause inherited amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) and result in both loss of C9orf72 protein expression and production of potentially toxic RNA and dipeptide repeat proteins. In addition to ALS/FTD, C9orf72 repeat expansions have been reported in a broad array of neurodegenerative syndromes including Alzheimer’s disease.  Here we show that C9orf72 deficiency promotes loss of homeostatic signatures in microglia and transition to an inflammatory state characterized by an enhanced type I IFN signature. Furthermore, C9orf72-depleted microglia trigger age-dependent neuronal defects, in particular enhanced cortical synaptic pruning, leading to altered learning and memory behaviors in mice.  Interestingly, C9orf72 deficient microglia also promote enhanced synapse loss and neuronal deficits in a mouse model of amyloid accumulation, while paradoxically improving plaque clearance.  These findings suggest that altered microglial function due to decreased C9orf72 expression directly contributes to neurodegeneration in repeat expansion carriers independent of gain of function toxicities.

overall_design: Mouse microglia single cell RNA-seq:  3 samples per genotype (WT, C9KO-HET, C9KO-HOMO); 1 age (12 months)

first: Deepti

last: Lall

first: Ileana

last: Lorenzini

first: Thomas

last: Mota

middle: E

last: Mahan

first: Jason

middle: D

last: Ulrich

first: Hayk

last: Davytan

first: Jessica

last: Rexach

first: AKM

last: Muhammad

first: Oksana

last: Shelest

first: Jesse

last: Landeros

first: Michael

last: Vazquez

first: Junwon

last: Kim

first: Layla

last: Ghaffar

first: Jacqueline

last: O’Rourke

first: Daniel

last: Geschwind

first: Mathew

last: Blurton-Jones

first: David

last: Holtzman

first: Rita

last: Sattler

first: Robert

last: Baloh


title: C9orf72 deficiency promotes microglial mediated synaptic loss in aging and amyloid accumulation [bulk RNA-seq]

first: Shaughn

last: Bell

overall_design: Mouse bulk RNA-seq:  4 samples per genotype (WT, C9KO-HET, C9KO-HOMO); 2 ages (3 months and 17 months)

first: Deepti

last: Lall

first: Ileana

last: Lorenzini

last: Mota


title: Genome-wide identification of candidate genes whose transcripts are locally expressed in early embryos of the spider Parasteatoda tepidariorum

first: Hiroki

last: Oda

summary: The early embryo of the spider Parasteatoda tepidariorum initially shows spherical symmetry in morphology. Following a symmetry breaking event, it forms a radially symmetric germ disc in the hemisphere of the egg. In this work, we conducted RNA-sequencing of cells isolated from small different regions of radially symmetric forming/formed germ discs, aming to identify candidate genes whose transcripts are locally expressed in early spider embryos.

overall_design: We isolated cells from small regions (central [c], peripheral [p], and intermediate [i]) of radially symmetric forming/formed germ discs at stage 3 (approximately 20 h after egg laying [AEL]), stage 4 (approximately 28-29 h AEL) and early stage 5 (approximately 31-32 h AEL) using glass capillary. We then conducted RNA-sequencing of the isolated cells to obtain transcriptomic data for comparison between different regions of the germ discs. Two or three biological replicates were obtained for each region for each stage. The RNAs were sequenced using the Illumina Miseq platform, and differentially expressed genes (DEGs) were evaluated in each comparison using EdgeR. The comparisons based on the early stage 5 samples allowed us to detect expected differences in gene expression between the central and peripheral regions of the germ disc (e.g., Pt-hh [aug3.g4322], Pt-lab [aug3.g7954], and Pt-opa [aug3.g12202]), which provided technical validation.

first: Sawa

last: Iwasaki-Yokozawa

first: Yasuko

last: Akiyama-Oda


title: Dynamic plasticity of prostate cancer intermediate cells during androgen receptor targeted therapy

status: Public on Jun 09 2022

first: XIANXIAO

last: ZHOU

address: 1470 Madison AVE

department: Department of Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

summary: The prevalence of treatment induced small cell neuroendocrine 1 prostate cancer (t-SCNC) has increased due to the use of potent AR signaling inhibitors. Understanding the kinetics and potential for reversibility of the t-SCNC lineage switch has been hampered by the lack of model systems suitable for studying intermediate tumor cell states. We define a reporter model amenable for measuring acute and dynamic transcriptional changes in response to castration or AR targeting agents. Using this approach, we have identified discreet, transcriptionally defined tumor subpopulations present in hormone intact conditions including the presence of intermediate subpopulations that are coordinately high for PSA and NSE promoter activity. In the presence of castration or AR targeting agents, intermediate cells serve a necessary and sufficient function during therapy induced conversion of human PC cells to an NE transcriptional high status. Castration can also induce greater amounts of secreted NSE suggesting a potential biomarker role. Further, we show that early treatment induced PSA-NSE transcriptional plasticity is reversible in PTEN deficient prostate cancer cells but not in context of secondary genetic driver genes such as MYCN.

overall_design: Castrate and  FBS control single-cell samples of LNCaP cells

first: Zhou

last: Xianxiao

first: Mulholland

last: David


title: Genomics analysis of Drosophila sechellia response to Morinda citrifolia fruit diet

status: Public on Jun 08 2022

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Ave.

department: Biology

institute: Wesleyan University

summary: Drosophila sechellia is an island endemic host specialist that has evolved to consume the toxic fruit of Morinda citrifolia, also known as noni fruit. Recent studies by our group and others have examined genome-wide gene expression responses of fruit flies to individual highly abundant compounds found in noni responsible for the fruit’s unique chemistry and toxicity. In order to relate these reductionist experiments to the gene expression responses to feeding on noni fruit itself, we fed rotten noni fruit to adult female D. sechellia and performed RNA-sequencing. Combining the reductionist and more wholistic approaches, we have identified candidate genes that may contribute to each individual compound and those that play a more general role in response to the fruit as a whole. Using the compound specific and general responses, we used transcription factor prediction analyses to identify the regulatory networks and specific regulators involved in the responses to each compound and the fruit itself. The identified genes and regulators represent the possible genetic mechanisms and biochemical pathways that contribute to toxin resistance and noni specialization in D. sechellia.

overall_design: Differential gene expression analysis of D. sechellia exposed to control food and food supplemented with rotten noni using RNA-sequencing.

first: Zachary

last: Drum

first: Stephen

last: Lanno

first: Sara

last: Gregory

first: Serena

last: Shimshak

first: Will

last: Barr

first: Austin

last: Gatesman

first: Mark

last: Schadt

first: Jack

last: Sanford

first: Aaron

last: Arkin

first: Brynn

last: Assignon

first: Sofia

last: Colorado

first: Carol

last: Dalgarno

first: Trevor

last: Devanny

first: Tara

last: Ghandour

first: Rose

last: Griffin

first: Mia

last: Hogan

first: Erica

last: Horowitz

first: Emily

last: McGhie

first: Jake

last: Multer

first: Hannah

last: O'Halloran

first: Kofi

last: Ofori-Darko

first: Dmitry

last: Pokushalov

first: Nick

last: Richards

first: Kathleen

last: Sagarin

first: Nicholas

last: Taylor

first: Acadia

last: Thielking

first: Phie

last: Towle


title: Improvement in Drinking Behavior after Fecal Transplant in Patients with Alcohol Use Disorder is Transmissible to Germ-free Mice

status: Public on Jun 04 2022

city: Richmond

first: JENNIFER

last: WOLSTENHOLME

state: VA

address: 1217 E Marshall Street, KMSB Rm 536

institute: Virginia Commonwealth University

summary:
Purpose: To determine whether previously observed behavioral differences in alcoholic human patients after fecal microbiota transplantation (FMT) could be transferred to mice.
Methods: Fecal microbiota samples from a previously published phase 1, double-blind, randomized clinical trial of AUD-related cirrhosis patients were used to colonize germ-free mice. Fecal material was transferred to 10-15-week-old GF C57BL/6 male mice by daily gavage for 3 day. The mice were housed in sterile individually filtered cages for 15 days after which stool was collected and then they underwent the alcohol preference experiment using 2-bottle choice drinking (water and 20% ethanol v/v). Microbial DNA was isolated from stool samples by sequencing the V1 and V2 variable regions of the bacterial 16S rRNA gene were sequenced using Multitag fusion primers and sequenced on an Ion Torrent PGM next-generation sequencer. Intestinal mucosa, liver, and prefrontal cortex tissue was collected from mice at time of sacrifice. RNAseq was used to measure gene expression in pre-FMT and post-FMT samples. RNAseq data were aligned to the mouse genome (GRCm39) using STAR (version 2.7.9a) and counts were generated with HTSeq (version 0.13.5). Genes with very low counts across the study (defined as fewer than 10 counts in more than 2 samples) were eliminated before differential expression analysis. Low count genes were determined separately for each tissue type. The DESeq2 package for R was then used to measure differential expression between pre-FMT and post-FMT mice in the intestine, liver, and PFC. Benjamini and Hochberg False Discovery Rate (FDR) was used to correct for multiple testing with FDR ≤ 0.2 considered significant.
Results: Mice colonized with post-FMT stool significantly reduced ethanol acceptance, intake and preference versus pre-FMT colonized mice. Microbial taxa that were higher in post-FMT humans were also associated with lower alcohol intake and preference in mice. RNAseq further showed that differential gene expression, post-FMT, occurred in the intestine rather than the liver and prefrontal cortex.
Conclusions: FMT leads to significant change in gut microbiome population, which in turn alters gene expression in the intestine. FMT also significantly affects alcohol consumption. The microbiotal-intestinal interface may alter gut-liver-brain axis and reduce alcohol consumption in humans.

overall_design: mRNA expression profiles generated by RNAseq in the intestine, liver, and prefrontal cortex of mice before and after FMT

first: Jennifer

middle: T

last: Wolstenholme

first: Justin

last: Saunders

first: Maren

middle: L

last: Smith

first: Jason

last: Kang

first: Philip

last: Hylemon

first: Javier

last: Gonzalez-Maeso

first: Andrew

last: Fagan

first: Derrick

last: Zhao

first: Masoumeh

last: Sikaroodi

first: Jeremy

last: Herzog

first: Amirhossein

last: Shamsaddini

first: Marcela

last: Pena

first: R

last: artor

first: Patrick

last: Gillevet

first: Huiping

last: Zhou

first: Jasmohan

last: Bajaj


title: Signatures of recent activation identify a circulating T cell compartment containing tumor-specific antigen receptors with high avidity

status: Public on Jun 03 2022

city: Munich

first: Sebastian

last: Jarosch

state: Bavaria

address: Trogerstr. 30

department: institut für Medizinische Mikrobiologie, Immunologie und Hygiene

institute: TU Munich

summary: T cell receptor (TCR) avidity is assumed to be a major determinant of the spatiotemporal fate and protective capacity of tumor-specific T cells. However, monitoring polyclonal T cell responses with known TCR avidities in vivo over space and time remains challenging. Here, we investigated the fate and functionality of tumor neoantigen-specific T cells with TCRs of distinct avidities in a well-established, reductionist preclinical tumor model and human melanoma patients. Surprisingly, we found that both high- and low-avidity T cells are similarly abundant within the tumor and adopt concordant phenotypic signs of exhaustion. Outside the tumor, high-avidity TCR T cells were also not generally overrepresented, but instead selectively enriched in T cell populations with intermediate PD-1 protein expression or corresponding RNA and surface protein signatures of recent activation. Tumor-reactive TCRs with high protective capacity circulating in peripheral blood are therefore characterized by a signature of recent activation.

overall_design: scRNA sequencing data for antigen specific cells before and after TIL infusion and from the infusion product of melanoma patients

first: Anna

last: Purcarea

first: Jack

last: Barton

first: Simon

last: Grassmann

first: Ludwig

last: Pachmayr

first: Elvira

last: D’Ippolito

first: Monika

last: Hammel

last: Hochholzer

first: Karolin

middle: I

last: Wagner

first: Joost

last: van den Berg

first: Veit

last: Buchholz

first: John

last: Haanen

first: Dirk

last: Busch

first: Kilian

last: Schober


title: Genome wide effects of vitamin C on in bone and during osteogenesis

city: rochester

first: Roman

last: Thaler

state: MINNESOTA

address: 200 First street SW

institute: Mayo Clinic

summary: Epigenetic effects of vitamin C on bone and osteogenic differentiation by analyzed  RNA-seq, hMeDIP-seq and ChIP-Seq analysis

overall_design: Femurs from 20 week old Gulo-/- mice or 11 week old Prrx1-Cre driven Tet1fl/fl, Tet2fl/fl or Tet1fl/fl and Tet2 fl/fl mice were dissected, bone marrow was flushed, periost was removed and remaining bone tissue was thorogly washed in ice cold PBS. MC3T3-E1 cells were collected at day 7 or day 28 of osteogenic differentiation. For all samples RNA, DNA or chromatin was extracted using commercially available extraction kits and/or standard protocols.

first: Andre

last: van Wijnen


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Skeletal Muscle-Specific Akt Knockout Mice

status: Public on Jun 02 2022

city: Bunkyo-ku

first: Hiroshi

last: Asahara

state: Tokyo

address: 1-5-45 Yushima

department: Department of Systems BioMedicine

institute: Institute of Science Tokyo

summary: Impact of knocking out of Akt in fast-twitch muscle on the transcritome was characterized by down-regulation of genes involved in mitochondria and electron transport chain.

overall_design: Fast-twitch muscle mRNA profiles of 50-week-old skeletal muscle-specific Akt knockout mice and the control floxed mice

first: Takayoshi

last: Sasako

first: Kohjiro

last: Ueki

first: Tomoki

last: Chiba


title: CB1 regualtes genes related TNBC cells development and growth

status: Public on Jun 01 2022

city: Beijing

first: Penyun

last: Li

address: 27 Taiping Road, Haidian District

institute: Beijing Institute of Pharmacology and Toxicology

summary: To investigate the corelation of genes regualted by CB1

overall_design: MDA-MB-231 cells with vehicle treatment and CB1 overexpressed


title: Homo sapiens Raw sequence reads-ferroptosis resistance

summary: To     study pathways associated with ferroptosis sensitivity

overall_design: MDA-MB-231 cells resistant to erastin or RSL3


title: PLK3 amplification and tumor immune microenvironment of metastatic tumors are linked to adjuvant treatment outcomes in uterine serous cancer

city: Durham

first: Wendell

last: Jones

state: NC

address: 2400 Ellis Rd

institute: Q2 Solutions

summary:
Uterine serous carcinoma (USC), an aggressive variant of endometrial cancer representing approximately 10% of endometrial cancer diagnoses, accounts for ~39% of endometrial cancer-related deaths.  We examined the role of genomic alterations in advanced-stage USC associated with outcome using paired primary-metastatic tumors (n=29) treated with adjuvant platinum and taxane chemotherapy.  Comparative genomic analysis of paired primary-metastatic patient tumors included whole exome sequencing and targeted gene expression.
Both PLK3 amplification and the tumor immune microenvironment (TIME) in metastatic tumors were linked to time-to-recurrence (TTR) risk without any such association observed with primary tumors.  TP53 loss was significantly more frequent in metastatic tumors of platinum-resistant versus platinum-sensitive patient and was also associated with increased TTR and mortality risk. Increased levels of chr1 breakpoints in USC metastatic versus primary tumors co-occur with PLK3 amplification.  PLK3 and the TIME are potential targets for improving outcomes in USC adjuvant therapy.

overall_design: 60 samples of matched metastatic and primary uterine serous cancer (USC) were processed to measure both GEX via NanoString IO360 and by WES. The samples were from 29 distinct subjects and included 2 subjects with more than one metastatic tumor.

first: David

last: Tait

first: Chad

last: Livasy

first: Mahrukh

last: Ganapathi

first: Ram


title: Transcriptomic analysis of pre-ovipositional embryonic arrest in the green sea turtle (Chelonia mydas)

status: Public on May 31 2022

city: Melbourne

first: Deanna

middle: S

last: Deveson Lucas

state: Victoria

address: 15 Innovation walk, Monash University, Clayton

institute: Monash University

summary:
After gastrulation, oviductal hypoxia maintains turtle embryos in an arrested state prior to oviposition. Subsequent exposure to atmospheric oxygen upon oviposition initiates recommencement of embryonic development. Arrest can be artificially extended for several days after oviposition by incubation of the egg under hypoxic conditions, with development recommencing in an apparently normal fashion after subsequent exposure to normoxia.  To examine the transcriptomic events associated with embryonic arrestAfter gastrulation, oviductal hypoxia maintains turtle embryos in an arrested state prior to oviposition. Subsequent exposure to atmospheric oxygen upon oviposition initiates recommencement of embryonic development. Arrest can be artificially extended for several days after oviposition by incubation of the egg under hypoxic conditions, with development recommencing in an apparently normal fashion after subsequent exposure to normoxia.  To examine the transcriptomic events associated with embryonic arrest, RNA-sequencing analysis was performed on embryos from freshly laid eggs and eggs incubated in either normoxia (oxygen tension ~159 mmHg) or hypoxia (<8 mmHg) for 36 hours (h) after oviposition (n = 5 per group). The patterns of gene expression differed markedly among the three experimental groups. Normal embryonic development in normoxia was associated with up-regulation of genes involved in DNA replication, the cell cycle, and mitosis, but these genes were commonly down-regulated after incubation in hypoxia. Many target genes of hypoxia inducible factors, including insulin-like growth factor binding protein 1, were down-regulated by normoxic incubation but upregulated by incubation in hypoxia. Notably, some of the transcriptomic effects of hypoxia in green turtle embryos resembled those reported by others to be associated with hypoxia-induced embryonic arrest in diverse taxa, including budding yeast (Saccharomyces cerevisiae), the annelid Caenorhabditis elegans, and zebrafish (Danio rerio). Thus, while among oviparous species, hypoxia-induced pre-ovipositional embryonic arrest appears to be a unique adaptation of turtles, mechanisms underlying hypoxia-induced embryonic arrest per se may be highly conserved across the diverse taxa in which this mechanism operates.
We report the transciptional changes in Chelonia mydas embryos incubated in either normoxia or hypoxia comapred to freshly laid eggs.

first: Richard

last: Reina

first: Roger

last: Evans

first: Angela

last: Gárriz

first: Anup

last: Shah

last: Powell


title: Knockdown of serine protease PRSS23 decreased FGF2 expression in gastric cancer

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: Serine proteases dysregulation has been considered to be closely associated with the inflammatory response and tumor progression. As a novel serine protease, the biological function of PRSS23 is rarely studied in cancers. In this study, we explored the biological function of PRSS23 in GC by RNA sequencing. Our data highlights that PRSS23 promotes GC progression by promoting macrophage infiltration via regulating FGF2 expression.

overall_design: The potent target genes of PRSS23 were identified by deep sequencing, using Illumina HiSeq 4000.

first: Shanshan

last: Qin

first: Dandan


title: Cucurbitacin B-induced G2/M cell cycle arrest of conjunctival melanoma cells mediated by GRP78-FOXM1-KIF20A pathway

city: Shanghai

first: Jinlian

last: Wei

state: Shanghai

address: Meilong Road 130

institute: EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY

summary: Conjunctival melanoma (CM) is a rare and fatal malignant eye tumor, it is life-threatening, mainly because of the lack of diagnostic biomarkers or drug access. In this study, we deciphered a novel anti-CM mechanism of a natural tetracyclic compound isolated from a Cucurbitaceae family plant and named as Cucurbitacin B (CuB). We found that CuB remarkably inhibited the proliferation of CRMM2 cells at a submicromolar level (IC50=0.15 μM) without toxicity to normal cells via G2/M cell cycle arrest and subsequent cell apoptosis. RNA-seq screening identified the Kinesin family member 20A (KIF20A) as a key gene which was abolished by the CuB treatment and proved to be a downstream effector of FOXM1 pathway. Further target identification by the activity-based protein profiling (ABPP) chemoproteomic approach revealed that 78 KDa Glucose-Regulated Protein (GRP78) is a potential target of CuB. Several lines of evidence demonstrated that CuB interacted with GRP78 and bound with a Kd value of 0.11 μM. Furthermore, functional experiments showed that CuB suppressed the ATPase activity of GRP78 both in human recombinant GRP78 and cellular lysates. Knockdown of the GRP78 gene significantly induced the downregulation of FOXM1 and related pathway genes including KIF20A, underlying an interesting therapeutic perspective. Taken together, our current work proved a substantial therapeutic potential of the traditional medicine CuB, and it needs to be explored further for future CM therapies.

overall_design: Examination of CuB (0.1 μM & 0.2 μM) treatment and control samples in CRMM2 cells by RNA-seq, in triplicate.

first: Xin

last: Chen

first: Yongyun

first: Ruoxi

first: Jian

first: Xiaofang

last: Xu


title: Isorhamnetin Inhibits Proliferation and Invasion and Induces Apoptosis Through the Mitochondria‑Dependent Apoptosis in Human Gastric Cancer Cells

status: Public on May 30 2022

city: Lanzhou

first: Yehua

state: Gansu

address: 967-Anning Road

department: College of Life Science

institute: Northwest Normal University

summary: The major treatment strategies for gastric cancer (GC) including surgery, chemotherapy, and molecular-targeted therapy are limited by tumor recurrence and chemoresistance. Isorhamnetin (ISO) derives from the total flavones of Hippophae rhamnoides L. and has been used as potential antitumor medicine in several types of cancer. However, the antitumor effect of ISO on GC cells remains unclear. Here, we investigated the effects of ISO on two types of GC cells and explored its apoptotic mechanisms underlying such effects. The transcriptomic analysis of ISO-treated GC cells enriched multiple targets on cell growth and apoptosis. The CCK-8, colony formation and morphology observation assays demonstrated that ISO treatment significantly inhibited the growth and proliferation of GC cells in time- and dose-dependent manners. In addition, we also found that ISO treatment inhibited cell migration and invasion. Furthermore, ISO increased TUNEL positive apoptotic bodies as well as severe cell apoptosis. Intriguingly, ISO treatment significantly increased the expression of mitochondria-associated Bax/Bcl-2, cytosolic Cytochrome c and activated the cleavage of Caspase-3 and PARP, followed by severe reduction of mitochondrial potential. Moreover, the apoptosis of ISO-treated GC cells was blocked by the specific inhibitor of Caspase-3. Therefore, we demonstrated that ISO could induce apoptosis of GC cells through mitochondria-dependent apoptotic pathway. In summary, we reported for the first time the antitumor function of ISO in GC via intervening apoptosis, indicating a potential application in GC therapy.

overall_design: two types of GC cells (AGS-1 and HGC-27) were treated with 50 μM Isorhamnetin(ISO)

first: Baoqiang

last: Fan

first: Ning

last: Pu

first: Xue

last: Ran

first: Tiancheng

last: Lian

first: Yifan

last: Cai

first: Kun

last: Sun


title: Effect of LPS or IFN-beta activation on gene expression of bone marrow-derived dendritic cells

status: Public on May 29 2022

city: Grand Rapoids

first: Connie

last: Krawczyk

state: MI

address: 333 Bostwick Ave

institute: Van Andel Institute

summary: To examine the changes in genes encoding proteins of metabolic pathways induced by LPS or IFN-beta in bone marrow-derived dendritic cells.

overall_design: RNA-seq of bone marrow-derived dendritic cells activated with LPS or IFN-beta.

first: Hannah

last: Guak


title: Effect of PGC-1beta deficiency, or LPS or IFN-beta activation, on gene expression of bone marrow-derived dendritic cells

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

overall_design: Refer to individual Series


title: Effect of PGC-1beta deficiency on gene expression of bone marrow-derived dendritic cells

summary: To determine the changes in gene expression regulated by PGC-1beta, we knocked down PGC-1beta in bone marrow-derived dendritic cells by shRNA.

overall_design: RNA-seq of bone marrow-derived dendritic cells retrovirally transduced either with control shRNA or shRNA targeting PGC-1beta, then left unstimulated or treated with IFN-beta for 6 hours.


title: A quantitative metric of pioneer activity reveals that HNF4A has stronger in vivo pioneer activity than FOXA1

status: Public on May 27 2022

city: St. Louis

first: Barak

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

summary: We and others have suggested that pioneer activity–a transcription factor’s (TF’s) ability to bind and open inaccessible loci–is not a qualitative trait limited to a select class of pioneer TFs. We hypothesize that most TFs display pioneering activity that depends on the TF concentration and the motif content at their target loci. Here we present a quantitative measure of pioneer activity that captures the relative difference in a TF’s ability to bind accessible versus inaccessible DNA. The metric is based on experiments that use CUT&Tag to measure binding of doxycycline (dox) inducible TFs. For each location across the genome we determine a “dox50,” the concentration of dox required for a TF to reach half-maximal occupancy. We propose that the ratio of a TF’s average dox50 between ATAC-seq labeled inaccessible and accessible binding sites, its Δdox50, is a measure of its pioneer activity. We measured Δdox50’s for the endodermal TFs FOXA1 and HNF4A and show that HNF4A has a smaller Δdox50 than FOXA1, suggesting that HNF4A has stronger pioneer activity than FOXA1. We further show that FOXA1 binding sites with more copies of its motif have a lower Δdox50, suggesting that strong motif content may compensate for weak pioneer activity. Our results suggest that Δdox50s, or other similar measures that assess the difference in TF affinity for inaccessible and accessible DNA, are reasonable measures of pioneer activity.

overall_design: We performed these experiments with clonal K562 lines that express either doxycycline-inducible FOXA1 or HNF4A. We split cells into two replicate flasks, treated each replicate with either 0ug/ml (uninduced), 0.005ug/ml, 0.05ug/ml, 0.1ug/ml, 0.25ug/ml, 0.5ug/ml, or 5ug/ml doxycycline for 24 hours, and then used the CUTANA Direct-to-PCR CUT&Tag protocol from Epicypher to measure binding. We input 1e5 cells from each replicate into either a plus- or minus-primary antibody and then used species-matched secondary antibodies. Due to extremely low background in both the uninduced and minus antibody samples and based on recommendation from the lab that developed the technology (Kaya-Okur 2020), we only sequenced the induced and plus-antibody samples. We size selected the libraries with AmpureXP beads and sequenced them on an Illumina NextSeq 500 using 2x150 paired-end reads.

first: Jeffrey

last: Hansen


title: Human Preadipocyte Response to PCB126

status: Public on May 24 2022

city: Iowa City

first: Aloysius

middle: John

last: Klingelhutz

state: IA

address: 3-604 BSB, 51 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

summary: Purpose: The goal of this study was to perform an expression transcript profile over a timecourse of human preadipocytes that were treated with PCB126; Methods: Immortal human preadipocytes (NPAD) were treated with 10 uM PCB126 for 9 hrs, 1 day, or 3 days. RNA was extracted with TriZol, DNase treated, and purified using a Qiagen column. RNAseq was used to assess gene expression. Bioinformatic analyses were used to determine differential gene expression between PCB126 treated and vehicle-treated at the same timepoint.

overall_design: RNAseq profile of differential gene expression over a timecourse caused by treatment of human preadipocytes with PCB126


title: Developmental heterogeneity of embryonic neuroendocrine chromaffin cells and their maturation dynamics

city: New York

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

summary: During embryonic development, nerve-associated Schwann cell precursors (SCPs) give rise to chromaffin cells of the adrenal gland via the “bridge” transient stage, according to recent functional experiments and single cell data from humans and mice. However, currently existing data do not resolve the finest heterogeneity of developing chromaffin populations. Here we took advantage of deep SmartSeq2 transcriptomic sequencing to expand our collection of individual cells from developing murine sympatho-adrenal anlage and uncover the microheterogeneity of embryonic chromaffin cells and corresponding developmental paths. After improving our atlas of sympatho-adrenal development and performing experimental validations, we discovered that SCPs in the local nerve show high degree of microheterogeneity corresponding to early biases towards either Schwann or chromaffin terminal fates. Furthermore, we found that a post-“bridge” population of developing chromaffin cells gives rise to persisting immature chromaffin cells and the two terminal populations (adrenergic and noradrenergic) via diverging differentiation paths. Taken together, we provide a thorough identification of novel markers of adrenergic and noradrenergic populations in developing adrenal glands and report novel differentiation micro-paths leading to them.

overall_design: Smart-Seq2 protocol was performed on single isolated cells by Eukaryotic Single Cell Genomics Facility at SciLifeLab, Stockholm. Single TOMATO+ cells were sorted into 384-well plates prefilled with lysis buffer according to the previously published SmartSeq2 protocol (Picelli, Faridani et al. 2014) using a BD FACSAria Fusion Cell Sorter B5/R3/V3 system with a three-laser configuration (488nm, 633nm, and 405nm) and 16 fluorescence detectors. Single-cell transcriptomic sequencing was performed as previously described (Picelli, Faridani et al. 2014).

first: Natalia

last: Akkuratova

first: Maria

last: Kastriti

first: Polina

last: Kameneva

first: Igor

last: Adameyko


title: HDAC1/2 is indispensable for mouse and bovine ZGA via regulating distribution of H3K27ac and H3K4me3

status: Public on May 21 2022

city: Hangzhou

last: Zhang

address: 866 Yuhangtang Rd

institute: Zhejiang University

sample_organism:
Bos taurus
Mus musculus

platform_organism:
Bos taurus
Mus musculus


title: HDAC1/2 is indispensable for mouse and bovine ZGA via regulating distribution of H3K27ac and H3K4me3 [RNA-seq]

summary: Zygotic genome activation (ZGA) is an impressed biological event following fertilization during early embryo development. Precise reprogramming of epigenetic modifications (e.g. histone H3 lysine 27 acetylation, H3K27ac) have been found contribute to safeguard ZGA in zebrafish and Drosophila, but the dynamic of H3K27ac and the underlying regulation mechanism in mammal embryos are still enigmatic yet. As the main erasers for histone acetylation, histone deacetylase 1 and 2 (HDAC1 and HDAC2) are reported essential for mouse oogenesis and embryo lineage development, while it is unclear if they are functional for ZGA. Here, we observed significant global decrease of H3K27ac during ZGA in both mouse and bovine embryos, and accumulation of HDAC1/2 is responsible for the decline of H3K27ac. Repression of HDAC1/2 by dominant negative mutation led to arrested development at late 2-cell stage in mouse embryos, accompanied by downregulation of genes supposed to be expressed during ZGA. ChIP-seq revealed abnormal distribution of H3K27ac, and DUX participates in H3K27ac aberrant hyper-acetylation in embryos overexpressed mutant HDAC1/2. Moreover, suppression of HDAC1/2 also restrains H3K4me3 removal at gene body regions via impeding expression of KDM5s during mouse ZGA, and compensatory exogenous Kdm5b mRNA can fix the exceeding H3K4me3 and failed ZGA. Intriguingly, function of HDAC1/2 seems to be conservative between mouse and bovine embryos. Together, this study reveals that HDAC1/2 is indispensable for mouse and bovine ZGA via regulating distribution of H3K27ac and H3K4me3.

overall_design: PolyA RNA profiles of mouse and bovine embryos.

first: Yanna

last: Dang


title: Heterologous ChAdOx1-BNT162b2 vaccination in a Korean cohort induces a robust genetic immune and antibody response that includes Omicron [scRNA-seq]

status: Public on May 20 2022

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Heterologous ChAdOx1-BNT162b2 vaccination induces a stronger immune response than two doses of BNT162b2. Yet, the molecular transcriptome, the germline allelic variants of immunoglobulin loci and anti-Omicron antibody levels induced by the heterologous vaccination have not been formally investigated. Moreover, there is a paucity of COVID-19 vaccine studies including diverse genetic populations. Here, we show a robust molecular immune transcriptome and antibody repertoire in 46 office and lab workers from the Republic of Korea after heterologous vaccination, ChAdOx1 followed by BNT162b2. Anti-spike-specific IgG antibody levels against the ancestral SARS-CoV-2 strain increased from 70 AU/ml immediately following the first vaccination to 14,000 U/ml within three days after the second vaccination and 142,000 AU/ml after seven days. Antibody titers against more recent variants, including Omicron, were two- to three-fold lower, yet higher than those obtained after the second dose of a BNT162b2-BNT162b2 homologous vaccination. RNA-seq conducted on peripheral immune cells demonstrated a strong activation of interferon-induced genetic programs in the heterologous cohort and an increase of specific IGHV clonal transcripts encoding neutralizing antibodies was detected. Enrichment of B cell and CD4+ T cell responses was observed following both ChAdOx1-BNT162b2 heterologous and BNT162b2-BNT162b2 homologous vaccination using scRNA-seq, but clonally expanded memory B cells were relatively stronger in the heterologous cohort. In summary, a heterologous vaccination with ChAdOx1 followed by BNT162b2 provides an innate and adaptive immune response exceeding that seen in homologous BNT162b2 vaccination.

overall_design: scRNA-seq were performed with peripheral blood mononuclear cells (PBMCs) from individuals who had received the 2 doses of ChAdOx1 (N=2), 2 doses of BNT162b2 (N=2), and heterologous ChAdOx1 and BNT162b2 vaccination (N=2).

first: Hye-Kyung


title: Study of the DNA methylation in the stroke outcome: an Epigenome-Wide Association Study

city: terrassa

first: NATALIA

last: CULLELL

address: sant antoni 19

institute: fundació mutuaterrassa

summary:
Background and Purpose  The neurological course after stroke is highly variable and is determined by demographic, clinical, and genetic factors. However, other heritable factors such as epigenetic DNA methylation could play a role in neurological changes after stroke.  Methods  We performed a three-stage epigenome-wide association study (EWAS) to evaluate DNA methylation associated with the difference between the National Institutes of Health Stroke Scale (NIHSS) at baseline and at discharge (ΔNIHSS) in ischemic stroke patients. DNA methylation data in the Discovery (n = 643) and Replication (n = 62) Cohorts were interrogated with the 450K and EPIC BeadChip. Nominal CpG-sites from the Discovery (p-value < 10-06) were also evaluated in a meta-analysis of the Discovery and Replication cohorts, using a random-fixed effect model. Specific cell type methylation was assessed using EpiDISH. We integrated the methylation data with 1305 plasma protein expression levels measured by SOMAscan and measured RNA expression with RT-PCR in a subgroup of 13 subjects.   Results   The meta-analysis revealed an epigenome-wide significant association in EXOC4 (p-value = 8.4x10-08) and in MERTK (p-value = 1.56x10-07). Only the methylation in EXOC4 was also associated in the Discovery and in the Replication cohort (p-value = 1.14x10-06 and p-value = 1.3x10-02, respectively). EXOC4 methylation negatively correlated with the long-term outcome (coefficient  = -5.89) and showed a tendency towards a decrease in EXOC4 expression (rho = -0.469, p-value = 0.091). Pathway enrichment from the meta-analysis revealed significant associations related with the exocytic process. Seventy-nine plasma proteins were differentially expressed in association with EXOC4 methylation. Pathway analysis of these proteins showed an enrichment in Natural Killer cell activation.  Conclusions  DNA methylation of EXOC4 is associated with a worse neurological course after stroke. Pathway analysis suggests that the exocytic pathway could be a potential biological mechanism underlying this association.
Background and Purpose  The neurological course after stroke is highly variable and is determined by demographic, clinical, and genetic factors. However, other heritable factors such as epigenetic DNA methylation could play a role in neurological changes after stroke.  Methods  We performed a three-stage epigenome-wide association study (EWAS) to evaluate DNA methylation associated with the difference between the National Institutes of Health Stroke Scale (NIHSS) at baseline and at discharge (ΔNIHSS) in ischemic stroke patients. DNA methylation data in the Discovery (n = 643) and Replication (n = 62) Cohorts were interrogated with the 450K and EPIC BeadChip. Nominal CpG-sites from the Discovery (p-value < 10-06) were also evaluated in a meta-analysis of the Discovery and Replication cohorts, using a random-fixed effect model. Specific cell type methylation was assessed using EpiDISH. We integrated the methylation data with 1305 plasma protein expression levels measured by SOMAscan and measured RNA expression with RT-PCR in a subgroup of 13 subjects.   Results   The meta-analysis revealed an epigenome-wide significant association in EXOC4 (p-value = 8.4x10-08) and in MERTK (p-value = 1.56x10-07). Only the methylation in EXOC4 was also associated in the Discovery and in the Replication cohort (p-value = 1.14x10-06 and p-value = 1.3x10-02, respectively). EXOC4 methylation negatively correlated with the long-term outcome (coefficient  = -5.89) and showed a tendency towards a decrease in EXOC4 expression (rho = -0.469, p-value = 0.091). Pathway enrichment from the meta-analysis revealed significant associations related with the exocytic process. Seventy-nine plasma proteins were differentially expressed in association with EXOC4 methylation. Pathway analysis of these proteins showed an enrichment in Natural Killer cell activation.  Conclusions  DNA methylation of EXOC4 is associated with a worse neurological course after stroke. Pathway analysis suggests that the exocytic pathway could be a potential biological mechanism underlying this association.

overall_design: 59 samples [discovery cohort] and 32 samples [replication cohort1] from stroke were analyzed with the Illumina HumanMethylation450 BeadChip array   30 samples from stroke patients [replication cohort2] were analyzed with the Illumina HumanMethylation EPIC BeadChip array                                                                                Please note that, for the discovery cohort the “Matrix processed file” is provided in the betas_normalized & pval_detection_discovery.txt and the raw matrix signal intensities' data is provided in meth_raw_discovery.txt, and idat files.  Additionally, note that replication cohort1 and replication cohort2 were analyzed together. The “Matrix processed file” for both replication cohorts together is provided in the betas_normalized&pval_detection_replication.txt and the ‘raw matrix signal intensities' data is provided in meth_raw_replication.txt, and idat files.

first: Israel

last: Fernández-Cadenas

first: Joan

last: Montaner

last: Cullell