title: Immune suppressive activity of myeloid-derived suppressor cells in cancer requires inactivation of the type I interferon pathway

status: Public on Feb 15 2021

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Myeloid-derived suppressor cells (MDSC) are pathologically activated neutrophils and monocytes with potent immune suppressive activity. These cells play an important role in accelerating tumor progression and undermining the efficacy of anti-cancer therapies. The natural mechanisms limiting MDSC activity  are not well understood. Here, we present evidence that type I interferons (IFN1) receptor signaling serves as a universal mechanism that restricts acquisition of suppressive activity by these cells. Downregulation of the IFNAR1 chain of this receptor was found in MDSC from cancer patients and mouse tumor models. The decrease in IFNAR1 depended on the activation of the p38 protein kinase and was required for activation of the immune suppressive phenotype. Whereas deletion of IFNAR1 was not sufficient to convert neutrophils and monocytes to MDSC, genetic stabilization of IFNAR1 in tumor bearing mice undermined suppressive activity of MDSC and had potent antitumor effect. Stabilizing IFNAR1 using inhibitor of p38 combined with the interferon induction therapy elicited a robust anti-tumor effect.  Thus, negative regulatory mechanisms of MDSC function can be exploited therapeutically.

overall_design: RNA-seq in WT and IFRAR1 mutant PMN-MDSCs cells

first: Dmitry

last: Gabrilovich

first: Kevin

last: Alicea-Torres


title: mRNA expression data for human muscle cells from individuals with type 2 diabetes and controls

status: Public on Feb 10 2021

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

country: Sweden

institute: Lund University

summary: mRNA expression data for both proliferating myoblasts and differentiated myotubes from n=13 individuals with type 2 diabetes and n=13 controls

overall_design: Comparison of mRNA expression in either proliferating myoblasts or differentiated myotubes from individuals with type 2 diabetes (n=13) versus controls (n=13). mRNA expression data were obtained using HumanHT-12 Expression BeadChip (Illumina, San Diego, CA, USA) which targets 28,688 well-annotated transcripts.

first: Cajsa

last: Davegårdh

first: Johanna

last: Säll

first: Alexander

last: Perfilyev

first: Emma

last: Nilsson

first: Camilla

last: Scheele


title: RNA Decay in Processing Bodies is Indispensable for Adipogenesis

city: Kyoto

first: Satoshi

last: Gojo

address: 465 Kajii-cho, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

type: Expression profiling by high throughput sequencing

summary: The RNA decay pathway plays key regulatory roles in cell identities and differentiation processes. Although adipogenesis is transcriptionally and epigenetically regulated and has been thoroughly investigated, how RNA metabolism that contributes to the stability of phenotype-shaping transcriptomes participates in differentiation remains elusive. In this study, we investigated Ddx6, an essential component of processing bodies (PBs) that executes RNA decay and translational repression in the cytoplasm and participates in the cellular transition of reprogramming. Upon adipogenic induction, Ddx6 dynamically accumulated to form PBs with a binding partner, 4E-T, at the early phase prior to emergence of intracellular lipid droplets. In contrast, preadipocytes with Ddx6 knockout (KO) or 4E-T knockdown (KD) failed to generate PBs, resulting in significant suppression of adipogenesis. Transcription factors related to preadipocytes and negative regulators of adipogenesis that were not expressed under adipogenic stimulation were maintained in Ddx6-KO and 4E-T-KD preadipocytes under adipogenic induction. Elimination of Dlk1, a major negative regulator of adipogenesis, in 3T3L1 Ddx6-KO cells did not restore adipogenic differentiation capacity to any extent. Similar to murine cells, human primary mesenchymal stem cells, which can differentiate into adipocytes upon stimulation with adipogenic cocktails, required DDX6 to maturate into adipocytes. Therefore, RNA decay of the entire parental transcriptome, rather than removal of a strong negative regulator, could be indispensable for adipogenesis.

overall_design: CR-Ddx6 3T3L1 and CR-tdTomato 3T3L1 preadipocytes were inducted into adipocytes using adipococktail. RNA expressions curing dau0-2 were compared between two groups.


title: Next Generation Sequencing Facilitates Quantitative Analysis of TP53-WT and TP53-KO HCT116 cells transcriptomes [RNA-seq]

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare TP53-WT and TP53-KO HCT116 cells transcriptome profiling (RNA-seq) under 5-FU treatment condition and to evaluate the correlation between transcriptome profileing and chromatin accessibility under 5-FU treatment.
Methods: HCT116 cell profiles of TP53-WT and TP53- KO were generated by deep sequencing, in duplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform levels: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA).
Conclusions: Our study represents the detailed analysis of TP53-WT and TP53-KO HCT116 cell transcriptomes under 5-FU treatment with different timepoint, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that RNA-seq offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a TP53-WT and TP53-KO cells with and without 5-FU treatment in different timepoint. We conclude that NGS based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: 5-FU treated and non-treated mRNA profiles of TP53-WT and TP53-KO cells in different timepoint.

first: Chul

middle: M

last: Yang

first: Woong-Jae

last: Jung


title: p53 influences 5-FU-induced chromatin accessibility [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: 5-Fluorouracil (5-FU) is one of the most common drugs used in chemotherapy because of its efficacy and stability. However, 5-FU has been known to work on only 10~15% of colon cancer patients. Therefore, the study of 5-FU sensitivity study is necessary to increase the survival of colon cancer patients. p53 is one of the factors that effect on drug sensitivity. Main function of p53 has been focused on transcription activity in cell death. Numerous drug related studies show that expression of wild-type p53 increases drug sensitivity in various cancer types through inducing apoptotic signaling pathways. Currently, it has been reported that p53 has both transcriptional and non-transcriptional activities in apoptosis. However, most studies about p53 non-transcriptional activities in apoptosis are mainly focused on p53 induced mitochondrial outer membrane permeabilization, triggering the release of pro-apoptotic factors. The chromatin structure and organization have strongly attracted because of their impacts in cellular phenotypes. Recent studies have been shown that changes in chromatin accessibility affect cell phenotypes for external stimuli. Since p53 plays an important role in drug sensitivity and 5-FU is an external stimulus for cancer cells, we hypothesized that p53 may effect on 5-FU sensitivity through different regulation of chromatin accessible regions between TP53-WT and TP53-KO cells. To determine the effect of p53 on chromatin accessibility modification associated with 5-FU sensitivity, ATAC-seq and RNA-seq were performed under 5-FU treatment on TP53-WT as drug sensitive and TP53-KO as drug resistant HCT116 cells. In this study, we found that 5-FU induces chromatin accessibility in both TP53-WT and TP53-KO cells. Moreover, our results show that 5-FU induced chromatin accessibility increases expression of apoptotic genes in TP53-WT HCT116 cells through p53 non-transcriptional activity in nucleus.

overall_design: Examination of 2 different ATAC-seq in TP53-WT and TP53-KO HCT116 cells

first: Jung-Sik

last: Ju

first: Yong-Jin


title: p53 influences 5-FU-induced chromatin accessibility [ATAC-seq]

overall_design:
Examination of 2 different ATAC-seq in TP53-WT and TP53-KO HCT116 cells
Please note that each processed data file was generated from both rep1 and rep2 samples, and is linked to the corresponding rep1 sample records.

first: Yeeun

last: Choi


title: Transcriptomic signature in patients with systemic lupus erythematosus (SLE) [T cells]

status: Public on Feb 11 2021

city: London

first: Marina

last: Botto

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

summary: T cell abnormalities are well-known features of patients with systemic lupus erythematosus (SLE). The role of CD4 and CD8 T lymphocytes, however, remains poorly understood with data suggesting both protective and deleterious roles. This project aimed to identify a cell-specific transcriptional signature in patients with SLE that could be used as a prognostic disease marker. The overall objective is to correlate the clinical presentation with specific RNA signatures to determine if there are signatures that correlate with disease outcome

overall_design: mRNA extraction from isolated blood CD4+ T cells from 14 SLE with active disease, 16 SLE with less active disease and 14 controls. RNA signatures will be correlated with the clinical presentation.

first: Chengguo

last: Shen


title: B. pseudomallei genes differentially expressed during host cell infection

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

country: USA

institute: University of Hawaii at Manoa

summary: Prokaryotic cell transcriptomics have been limited to mixed or sub-population dynamics and individuality of cells within heterogeneous populations. This significantly hampers further knowledge into spatiotemporal and stage-specific processes of prokaryotic cells within complex environments. Herein, we developed a ‘TRANSITomic’ approach to profile transcriptomes of single Burkholderia pseudomallei (Bp) cells as they transit through host cell infection at defined stages, yielding pathophysiological insights. Bp transits through host cells during infection in three observable stages: i) vacuole entry; ii) cytoplasmic escape and replication; and iii) membrane protrusion, promoting cell-to-cell spread. The Bp ‘TRANSITome’ revealed dynamic gene-expression flux during transit in host cells. Some genes undergoing changes are required for pathogenesis. We discovered several hypothetical proteins and assigned them to virulence mechanisms such as attachment, cytoskeletal modulation, and autophagy evasion. The Bp ‘TRANSITome’ has provided high-resolution understanding of host-pathogen interactions and opens the door for future single-cell transcriptomic analysis of other prokaryotic processes.

platform_organism:
Burkholderia mallei
Burkholderia pseudomallei

overall_design: Single B. pseudomallei cell isolation at different stages during macrophage infection. RFP-YFP-tagged B. pseudomallei strain was used to infect macrophage RAW 264.7 cell line. After infection and fixation, the macrophage plasma membrane and endo-vesicular membrane were stained far red and the actin was stained green. Nine single B. pseudomallei cells were observed and isolated at different stages during macrophage infection, including inside of macrophage vacuoles, in the cytoplasm during actin polymerization, and during protrusion. The in vitro control (nine B. pseudomallei cells) was obtained by incubating B. pseudomallei in the DMEM medium in the absence of macrophages. Single B. pseudomallei cells and pooled control B. pesudomallei cells were processed using previously described methods for single cell transcriptomic analysis.

first: Yun

last: Heacock-Kang


title: RNA-seq for Col-0 WT, ddm1(-/-) and Col-0 X ddm1 (F1) to evaluate transposon expression in F1 Col-0Xddm1 and ddm1

city: Vienna

first: Bhagyshree

middle: Babasaheb

last: Jamge

address: Dr. Bohr Gasse -3

country: Austria

institute: Gregor Mendel Institute

summary:
Silencing of transposons by the chromatin remodeler DDM1 is mediated by the deposition of heterochromatic H2A variants.
Transposon mobility and silencing participates in genome evolution but also threaten genome integrity. DECREASED DNA METHYLATION 1 (DDM1) belongs to a conserved family of chromatin remodelers that are required to silence transposons, yet the underlying molecular mechanism has remained unknown. Here we show that DDM1 binds the histone variant H2A.W through two conserved domains that are required to deposit H2A.W and maintain transposon silencing. The mechanism of transcriptional silencing described here is likely shared among chromatin remodelers of the DDM1 family and heterochromatic H2A variants that have evolved in mammals.

overall_design: Total RNA was extracted with Spectrum plant total RNA kit (Sigma Aldrich) from 4-5 week old leaves of WT Col-0, F1 DDM1/ddm1 (Col-0Xddm1) and ddm1 2nd generation. For RNA-seq analyses, rRNA was removed by Ribo-Zero rRNA Removal kit (Illumina). After depletion of rRNA, RNA-seq libraries were generated with NEBNext UltraII directional RNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s instructions. The libraries were sequenced with Illumina Hiseq 2500 to generate single-end 50 bp reads. Samples were prepared from three independent biological replicates.

first: Akihisa

last: Osakabe


title: The chromatin remodeler DDM1 silences transposons through deposition of the histone variant H2A.W

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

overall_design: Refer to individual Series


title: Quantitative imaging of RAD51 expression as a marker of platinum resistance in Ovarian Cancer

city: Singapore

first: Michal

middle: Marek

last: Hoppe

address: 14 Medical Dr

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

summary: Early relapse after platinum chemotherapy in epithelial ovarian cancer (EOC) portends poor survival. A-priori identification of platinum-resistance is therefore crucial to improve on standard first-line carboplatin-paclitaxel treatment. The DNA repair pathway Homologous Recombination (HR) repairs platinum-induced damage, and the HR recombinase RAD51 is overexpressed in cancer. We therefore designed a REMARK-compliant study of pre-treatment RAD51 expression in EOC, using fluorescent quantitative immunohistochemistry (qIHC) to overcome challenges in quantitation of protein-expression in-situ. In a discovery cohort (n=284), RAD51-High tumours had shorter progression-free and overall survival compared to RAD51-Low cases in univariate and multivariate analyses. The association of RAD51 with relapse/survival was validated in a carboplatin-monotherapy SCOTROC4 clinical trial cohort (n=264), and was predominantly noted in HR-proficient cancers (Myriad HRDscore<42). Interestingly, overexpression of RAD51 modified expression of immune-regulatory pathways in-vitro, while high-RAD51 tumours showed exclusion of cytotoxic-T-cells in-situ. Our findings highlight RAD51 expression as a determinant of platinum resistance, and suggest possible roles for therapy to overcome immune exclusion in high-RAD51 EOC. The qIHC approach is generalizable to other proteins with a continuum instead of discrete/bimodal expression.

overall_design: This dataset contains RNA-seq data from four high grade serous ovarian carcinoma cell lines - TYK-nu, Caov-3, COV362, FUOV1 - either with stable Flag-RAD51 overexpression from the pMSCV vector or stable integration of an empty control vector.

first: Michał

first: Anand

middle: D

last: Jeyasekharan


title: CAF-1 promotes HIV-1 latency by leading the formation of phase-separated suppressive nuclear bodies.

status: Public on Feb 09 2021

city: Guangzhou

first: Xiancai

last: Ma

state: Guangdong

address: North Campus, Zhongshan Road II, No.74

department: Institute of Human Virology

country: China

institute: Sun Yat-sen University

summary: HIV-1 latency is a major obstacle to achieve a functional cure for AIDS. To eradicate the viral reservoir, one of the strategies is to specifically reactivate HIV-1-infected cells and followed by elimination with potent immune surveillance. However, present latency-reversing agents (LRAs) are quite dissatisfactory because of their high toxicity and low efficiency. New targets need to be identified to develop more promising LRAs. Here, we found that histone chaperone chromatin assembly factor 1 (CAF-1) promotes HIV-1 latency by forming versatile suppressive nuclear bodies. CAF-1 plays a leading role for the formation of bodies recruiting multi-layer suppressive epigenetic modifiers and maintainers, and is of the characteristic of liquid-liquid phase separation (LLPS). Three distinct disordered regions of CHAF1A subunit coalesce CAF-1 body components by forming LLPS and play a key in maintaining HIV-1 latency. Therefore, disruptive induction of phase-separated CAF-1 body could be an important strategy to reactivate latent HIV-1.

overall_design: mRNA profiles of wildtype (WT), TNFα-stimulated (TNFα) and CHAF1A knockout (KO) J-Lat 10.6 cells. Wildtype J-Lat 10.6 cells were treated as control samples. Each group included replicates.

first: Jun

last: Liu

first: Zhonghui

last: Tang

first: Hui

last: Zhang


title: A temporal map of maternal immune activation-induced changes reveals a shift in neurodevelopmental timing and perturbed cortical development in mice

city: Davis

first: Alexander

middle: Star

last: Nord

state: CA

address: 1544 Newton Court

department: Center for Neuroscience

institute: University of California Davis

summary: Background: Environmental insults that activate the maternal immune system are potent primers of developmental neuropathology and maternal immune activation (MIA) has emerged as a risk factor for neurodevelopmental and psychiatric disorders. Animal models of MIA provide an opportunity to identify molecular pathways that initiate disease processes and lead to neuropathology and behavioral deficits in offspring. MIA-induced behaviors are accompanied by anatomical and neurochemical alterations in adult offspring that parallel those seen in affected human populations.  Methods: We performed transcriptional profiling and neuroanatomical characterization in a time course across mouse embryonic cortical development, following MIA via single injection of the viral mimic polyinosinic:polycytidylic acid (polyI:C) at E12.5. Transcriptional changes identified in the cortex of MIA offspring at E17.5 were validated and mapped to cortical neuroanatomy and cell types via protein analysis and immunohistochemistry.  Results: MIA induced strong transcriptomic signatures, including induction of genes associated with hypoxia, immune signaling, and angiogenesis. The acute response identified 6h after the MIA insult was followed by changes in proliferation, neuronal and glial differentiation, and cortical lamination that emerged at E14.5 and peaked at E17.5. Decreased numbers of proliferative cell types in germinal zones and alterations in neuronal and glial cell types across cortical lamina were identified in the MIA-exposed cortex.  Conclusions: MIA-induced transcriptomic signatures in fetal offspring overlap significantly with perturbations identified in neurodevelopmental disorders (NDDs), and provide novel insights into alterations in molecular and developmental timing processes linking MIA and neuropathology, potentially revealing new targets for development of novel approaches for earlier diagnosis and treatment of these disorders.

overall_design: Timecourse transcriptomics signatures in a developing mouse cortex following maternal immune activation (MIA) via polyinosinic:polycytidylic acid (polyI:C) at E12.5, E 14.5, E17.5, and at P0

first: Cesar

middle: P

last: Canales

first: Myka

middle: L

last: Estes

first: Karol

last: Cichewicz

first: Kartik

last: Angara

first: John

last: Aboubechara

first: Scott

last: Cameron

first: Kathryn

last: Prendergast

first: Linda

last: Su-Feher

first: Iva

last: Zdilar

first: Ellie

middle: J

last: Kreun

first: Emma

middle: C

last: Connolly

first: Jin

last: Seo

first: Jack

middle: B

last: Goon

first: Kathleen

last: Farrelly

first: Tyler

last: Stradleigh

first: Deborah

last: van der List

first: Lori

last: Haapanen

first: Judy

last: Van de Water

first: Daniel

last: Vogt

first: Kimberley

last: McAllister

first: Alex

middle: S


title: An inflammatory loop established between spleen-derived myeloid cells and CD4+ T cells leads to accumulation of long-lived plasma cells that exacerbate lupus autoimmunity

first: sungjin

last: pyo

address: Hanyang University, 222 Wangshimni-ro, Seongdong-Gu

department: Dept. of Life Science

institute: Hanyang University

summary: Splenic long-lived plasma cells (PCs) are abnormally numerous and deleterious in systemic autoimmune diseases, yet how they accumulate remains poorly understood. We demonstrate here that a pathological role of spleen-derived CD11b+Gr-1+ myeloid cells (SPMCs) underpins the accumulation of splenic long-lived PCs in a lupus-prone model. SPMCs were a mixture of granulocytic and monocytic myeloid-derived suppressor cells (MDSCs) that were expanded and acquired proinflammatory phenotypes in situ during lupus progression. By promoting the development of IFN--secreting and follicular helper T cells, SPMCs licensed CD4+ T cells to be pathologic activators of SPMCs and PCs. SPMCs also directly promoted the survival of PCs by providing B-cell activating factor of the TNF family. The frequency of SPMCs correlated with that of splenic long-lived PCs. Depletion of CD11b+Gr-1+ cells reduced autoantibody production. Thus, our findings suggest that SPMCs expanded in situ establish a positive feedback loop with CD4+ T cells, leading to accumulation of long-lived PCs which exacerbate lupus autoimmunity.

overall_design: Roquin(san/+) mice on a C57BL/6 background were originally purchased from Mutant Mouse Regional Resource Center at the University of California at Davis and were maintained in a specific pathogen-free barrier facility at Hanyang University. Total RNA was extracted from CD11+Gr-1hi and CD11+Gr-1lo cells from the spleens (SP) and bone marrow (BM) of approximately 20-wk-old sanroque mice. cDNA libraries were prepared using a TruSeq Stranded mRNA LT Sample Prep kit (Illumina) and sequenced on a NovaSeq 6000 platform using 101 bp paired-read strategy. In total, 8 samples (2 SP Gr-1 hi, 2 SP Gr-1 low, 2 BM Gr-1 hi, 2 BM Gr-1 low) were collected.

first: Eunkyeong

last: Jang

first: Somi

last: Cho

first: Sungjin

last: Pyo

middle: W

last: Nam

first: Jeehee

last: Youn


title: Transcriptomic signature in patients with systemic lupus erythematosus (SLE) [CD8 T cells]

first: Marina

last: Botto

overall_design: mRNA extraction from isolated blood CD8+ T cells from 16 SLE with active disease, 18 SLE with less active disease and 14 controls. RNA signatures will be correlated with the clinical presentation

first: Chengguo

last: Shen


title: N4BP1 negatively regulates NF-κB by binding and inhibiting NEMO oligomerization

status: Public on Feb 08 2021

city: Dallas

first: Sara

middle: K

last: Hildebrand

state: TX

address: 5323 Harry Hines blvd

department: Center for the Genetics of Host Defense

institute: UT Southwestern Medical Center

summary: Many immune responses depend upon activation of NF-κB, a key transcription factor in the elicitation of a cytokine response. Here we show that N4BP1 inhibits TLR-dependent activation of NF-κB by interacting with the NF-κB signaling essential modulator (NEMO, also known as IκB kinase γ) to attenuate NEMO-NEMO dimerization or oligomerization. The UBA-like (ubiquitin associated-like) and CUE-like (ubiquitin conjugation to ER degradation) domains in N4BP1 mediate the interaction with the NEMO COZI domain. Both in vitro and in mice, N4bp1 deficiency specifically enhances TRIF-independent (TLR2, TLR7, or TLR9-mediated), but not TRIF-dependent (TLR3 or TLR4-mediated), NF-κB activation leading to increased production of proinflammatory cytokines. In response to TLR4 or TLR3 activation, TRIF causes activation of caspase-8, which cleaves N4BP1 distal to residues D424 and D490 and abolishes its inhibitory effect. N4bp1-/- mice also exhibit diminished numbers of T cells in the peripheral blood. Our work identifies N4BP1 as an inhibitory checkpoint protein that must be overcome to activate NF-κB, and a TRIF-initiated caspase-8-dependent mechanism by which this is accomplished.

overall_design: Examination of mRNA expression in N4bp1 KO and wild-type peritoneal macrophages from two mice of each genotype that were untreated or treated with R848 or LPS.

first: Hexin

last: Shi


title: SARS-CoV-2 Oropharyngeal and Nasopharyngeal samples

status: Public on Feb 06 2021

first: Erle

last: Robertson

state: Pennsylvania

address: 3610 Hamilton Walk Johnson Pavilion

department: Department of Otorhinolaryngology

institute: University of Pennsylvania

summary: Microbiome analysis of oropharyngeal and nasopharyngeal samples of SARS-CoV-2 infected patients

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: Analysis of the the different microbial species detected in the oropharyngeal and nasopharyngeal samples of the SARS-CoV-2 patients We have developed this technology as a potential resource that can be used as a sensitive diagnostic tool for early detection of highly infectious microorganisms in clinical samples, which includes all known respiratory viruses as well as SARS-CoV-2. DNA and RNA were isolated from nasopharyngeal (NP) and oropharyngeal swabs (OP), which were then subjected to whole transcriptome amplification (WTA) where the amplified products were used to hybridize against probes on specifically designed PathoChIPs containing sequences that are unique, conserved and frequently mutated across various regions of the SARS-CoV-2 genome. This PathoChip (V5) contains 60,000 probes and represents all known viruses, including SARS-CoV-2, and pathogenic microbes that comprise 250 helminths, 130 protozoa, 360 fungi, and 320 bacteria, totaling more than 6,000 accessions.

last: Seckar

first: Xiang

last: Lin

first: Dipayan

last: Bose

first: Zhi

last: Wei

first: Joey

last: Rohrbaugh

first: Ronald

middle: G

last: Collman


title: RNA-seq for WT and ddm1(-/-) to evaluate transposon expression in ddm1 1st generation

first: Bhagyshree

last: Jamge

overall_design: Total RNA was extracted with Spectrum plant total RNA kit (Sigma Aldrich) from 4-5 week old leaves of WT Col-0 and ddm1 1st generation. For RNA-seq analyses, rRNA was removed by Ribo-Zero rRNA Removal kit (Illumina). After depletion of rRNA, RNA-seq libraries were generated with NEBNext UltraII directional RNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s instructions. The libraries were sequenced with Illumina Hiseq 2500 to generate single-end 50 bp reads. Samples were prepared from three independent biological replicates.

first: Akihisa

last: Osakabe


title: scRNA-Seq of peripheral CD8 T cells from patients with metastatic melanoma taking ICI therapy.

status: Public on Feb 05 2021

city: Modena

first: Andrea

last: Cossarizza

state: Modena

address: Via Campi 287

country: Italy

institute: University of Modena and Reggio Emilia

summary: Patients with metastatic melanoma have been treated with the new class of drug named immune checkpoint inhibitors. Single-cell RNA-sequencing was performed in circulating CD8+ T cells isolated by cell sorting from 20 patients who were followed for 6 months. Among them, 11 responded to therapy, whilst 9 did not. Overall, the data obtained by sc-RNA seq showed the presence of MAIT cells, that had higher levels in those who showed a better response to treatment.

overall_design: scRNA-Seq of peripheral CD8 T cells obtained from 20 melanoma patients (11 Responders and 9 Non-Responders) before (T0), after first (T1) and second (T2) cycle of ICI therapy. Almost all samples were sequenced in four replicates.

first: Domenico

last: Lo Tartaro

first: Mattia

last: Forcato

first: Silvio

last: Bicciato


title: mRNA expression data throughout human muscle cell differentiation in individuals with type 2 diabetes and controls

first: Charlotte

last: Ling

summary: mRNA expression data throughout human muscle cell differentiation in n=13 individuals with type 2 diabetes and n=13 controls

overall_design: Comparison of mRNA expression in proliferating myoblasts versus differentiated myotubes in either individuals with type 2 diabetes (n=13) or controls (n=13). mRNA expression data were obtained using HumanHT-12 Expression BeadChip (Illumina, San Diego, CA, USA) which targets 28,688 well-annotated transcripts.

first: Cajsa

last: Davegårdh

first: Johanna

last: Säll

first: Alexander

last: Perfilyev

first: Emma

last: Nilsson

first: Camilla

last: Scheele


title: Tumor methionine metabolites reprograms chromatin accessibilities of CD8+ T cells linking to T cell dysfunction.

city: Bethesda

first: Xin Wei

last: Wang

state: Maryland

address: 37 Convent Drive, Bldg 37 Rm 3050

department: Center for Cancer Research

institute: National Institutes of Health

summary: T-cell exhaustion denotes a hypofunctional state of T lymphocytes commonly found in cancer, but how tumor cells drive T-cell exhaustion remains elusive. We found oncogenic reprograming of HCC methionine recycling with elevated 5-methylthioadenosine (MTA) and S-adenosylmethionine (SAM)  to be tightly linked to T-cell exhaustion. We used an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to assay the genome-wide chromatin accessibility of T cells during activation and SAM/MTA treatment.

overall_design: ATAC-sequencing was performed on non-activated CD8+ T cell and activated CD8+ T cells with and without SAM or MTA treatment.

first: X


title: Interleukin-1α mediates innate and acquired resistance to immunotherapy in melanoma

status: Public on Feb 04 2021

city: Houston

first: Richard

middle: Eric

last: Davis

address: 7455 Fannin Street

institute: MD Anderson Cancer Center

summary: In a syngeneic mouse model of melanoma, we found that tumor size was inversely correlated with response to immunotherapy. Large tumors had higher levels of IL-1α, Th2 cytokines, granulocytic myeloid-derived suppressor cells (GMDSCs), and regulatory T cells but lower levels of IL-12, Th1 cytokines, and activated CD4+ and CD8+ T cells. Blocking IL-1 signaling decreased GMDSCs and their associated PD-L1 expression in the tumor microenvironment, and enhanced tumor-specific immunity.

overall_design: C57BL/6 mice were inoculated with the syngeneic B16 melanoma cell line, and after 8 days developed tumors that were either small (10-20 mm2) or large (70-80 mm2). Gene expression analysis was used to compared small vs. large tumors.

first: Shubhra

last: Singh

first: Zhiqiang

middle: E

first: Willem

last: Overwijk

first: Manisha


title: Increased expression of Polδ does not alter the canonical replication program in vivo

city: Brighton

first: Robert

last: Zach

address: Science Park Road, GDSC

department: Genome Damage and Stability Centre

institute: University of Sussex

summary: In vitro experiments utilising the reconstituted Saccharomyces cerevisiae eukaryotic replisome indicated that the efficiency of leading strand replication is impaired by a moderate increase in Polδ concentration. It was hypothesised that the slower rate of the leading strand synthesis characteristic for reactions containing 2-fold and 4-fold increased quantities of Polδ represented a consequence of a rare event, during which Polδ stochastically outcompeted Polε and, in an inefficient manner, temporarily facilitated extension of the leading strand. Inspired by this observation, we aimed to determine whether increased Polδ levels influence replication dynamics in vivo using the fission yeast Schizosaccharomyces pombe as a model system. We provide an evidence that 2-4-fold over-production of Polδ does not significantly alter cell cycle progression and the dynamics of the three replicative polymerases: Polδ, Polε and Polα. Our experiments do not disapprove the existence of opportunistic polymerase switches, however, the data indicate that, if stochastic replacement of Polε for Polδ does occur in vivo, it represents a rare phenomenon that does not significantly influence canonical replication program.

overall_design: Polymerase usage sequencing analysis of S. pombe mutants characterised by increased expression of polymerase delta.

first: Antony

last: Carr


title: Different p53 status controls resistance to 5-fluorouracil via distinct chromatin accessibility dynamics in human colorectal cancer cell line

first: Hyoung-Pyo

last: Kim


title: Role of CxxC-finger Protein 1 in the Establishment of Epigenetic Landscapes in Mouse Oocytes

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

type: Methylation profiling by high throughput sequencing

summary: During oogenesis, oocytes gain competence to accomplish meiotic maturation and prepare for embryonic development following fertilization. Trimethylated histone H3 on lysine-4 (H3K4me3) mediates a wide range of nuclear events during these processes. Oocyte-specific knockout of CxxC-finger protein 1 (CXXC1, also known as CFP1), the chromatin-binding subunit of SETD1 methyltransferase, impairs the H3K4me3 accumulation during murine oogenesis and caused changes in chromatin configurations. This study investigated the changes of genomic H3K4me3 landscapes in oocytes after Cxxc1 knockout, as well as the influences of H3K4me3 changes on other epigenetic marks including DNA methylation, H3K27me3, H2AK119ub1, and H3K36me3. Chromatin immunoprecipitation and sequencing results indicated that H3K4me3 is globally decreased after abolishing Cxxc1, including both the promoter region and the gene body. The results also demonstrate that CXXC1 and another histone H3 methyltransferase MLL2 have nonoverlapping roles in mediating H3K4 trimethylation during oogenesis. In addition, Cxxc1 deletion caused a significant decrease of DNA methylation level in oocytes, and affected H3K27me3 and H2AK119ub1 distributions in the maternal genome, particularly at the regions that have high DNA methylation levels. The changes of epigenetic networks caused by Cxxc1 deletion correlated with transcription changes of the genes in the corresponding genomic regions. Taken together, this study provided mechanistic explanations underlying the phenotypes and molecular defects in Cxxc1 deleted oocytes, and highlighted a role of CXXC1 in orchestrating multiple factors to build up the appropriate epigenetic states of maternal genome during oocyte maturation.

overall_design: WT and Cxxc1 null oocytes are collected to performed high-throughput sequencing.

first: Qianqian

last: Sha

first: Yezhang

last: Zhu

first: Yunlong

last: Xiang

first: Hengyu

last: Fan


title: PGC1/PPAR drive cardiomyocyte maturation at single cell level viaYAP1 and SF2B2

status: Public on Feb 02 2021

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

summary: We wanted to study maturation of cardiomyocytes so we sequenced postnatal mouse cardiomyocytes.

overall_design: We ran single cell RNA seq on mouse cardiomyocyotes at P0, P7, P14, P21, and P28. We included control and PGC1a/b null cardiomyocytes.

first: Sean

last: Murphy

first: Suraj

last: Kannan


title: Comparison of the transcriptome of DNA polymerase zeta deficient and proficient mouse embryonic fibroblasts.

city: Smithville

first: Sara

last: Martin

state: Texas

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: We found changes in the transcriptome due to disruption Rev3l, the catalytic subunit of DNA polymerase zeta. In particular, we found upregulation of interferon-stimulated genes in Rev3l disrupted MEFs.

overall_design: Comparison of the transcriptome of DNA polymerase zeta deficient (knockout (KO) of Rev3l) and proficient (Rev3l heterozygous (HET)) mouse embryonic fibroblasts. And we also compared Rev3l KO mouse embryonic  fibroblasts expressing a REV3L construct, TR4-2. Three clones were used for each cell type.

last: Wood


title: Non-viral Induction of Transgene-free iPSCs from Somatic Fibroblasts of Multiple Mammalian Species [marmoset_single-cell]

status: Public on Feb 03 2021

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

institute: Keio University School of Medicine

summary: Induced pluripotent stem cells (iPSCs) are capable of providing an unlimited source of cells from all three germ layers as well as germ cells. The derivation and usage of iPSCs from various animal models may facilitate stem-cell-based therapy, generation of gene-modified animals, and evolutionary studies assessing interspecies differences. However, there is a lack of species-wide methods for deriving iPSCs, in particular by means of non-viral and non-transgene-integrating (NTI) approaches. Here, we demonstrated the derivation of iPSCs from somatic fibroblasts of multiple mammalian species from three different taxonomic orders, including the common marmoset (Callithrix jacchus) in Primates, the dog (Canis lupus familiaris) in Carnivora, and the pig (Sus scrofa) in Cetartiodactyla, by combinatorial usage of chemical compounds and NTI episomal vectors. Interestingly, the somatic fibroblasts temporarily acquired a neural stem cell (NSC)-like state during the reprogramming procedure. Collectively, our method, robustly applicable to various species, holds a great potential for facilitating stem-cell-based research using various animals in Mammalia.

overall_design: Single-cell RNA seq of marmoset fibroblasts, iNSLCs, ESCs and iPSCs

first: Tsukasa

last: Sanosaka

first: Mayutaka

last: Nakajima

first: Hideyuki

last: Okano


title: Transcriptomic Analysis of mouse brain after traumatic brain injury reveals that the angiotensin receptor blocker candesartan acts through novel pathways

first: Aviva

middle: Jane

last: Symes

address: 4301 Jones Bridge Road

department: Pharmacology

institute: Uniformed Services University

summary:
Purpose: To gain a better understanding of the molecular mechanisms through which candesartan improves revocery after controlled cortical impact.
Methods: We performed a transcriptomic analysis of the ipsilateral hippocampus, thalamus, and hypothalamus at 3 and 29 days post-injury utilizing bulk mRNA-seq.
Results: A majority of the differentially expressed genes were identified in the hippocampus at 3 days post injury showing alterations in angiogenesis, interferon signaling, extracellular matrix organization, and DNA replication.  At 29 days post injury candesartan treatment reduced genes associated with the inflammatory response.
Conclusion: Our data suggests that candesartan has broad actions in the brain after injury and affects different processes in acute and chronic times after injury.

overall_design: Transcriptomic analysis of ipsilateral mouse hippocampus, thalamus, and hypothalamus at 3 and 29 dpi after sham injury or controlled cortical impact with or without candesartan treatment.

first: Peter

last: Attilio

first: Dustin

last: Snapper

first: Anthony

middle: R

last: Soltis

first: Michael

last: Wilkerson

first: Clifton

last: Dalgard


title: Eradication of donor-dependent variations of mesenchymal stem cells in immunomodulation to enhance their therapeutic values.

status: Public on Feb 01 2021

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

summary: Mesenchymal stem cells (MSC) are one of the most widely clinically trialed stem cells, due to their abilities to secret regenerative/rejuvenating factors, modulate immune functions, among others. In this study, we analyzed human umbilical-cord-derived MSC from 32 donors and revealed donor-dependent variations in two non-correlated properties, 1) cell proliferation, and 2) immune modulatory functions in vitro and in vivo, which might explain inconsistent clinical efficacies of MSC. Through unbiased transcriptomic analyses, we discovered that IFN- γ and NF-κB signaling were positively associated with immune modulatory function of MSC. Activation of these two pathways via IFN-γ and TNF-α treatment eradicated donor-dependent variations. Additional transcriptomic analyses revealed that treatment with these two factors, while abolished donor-dependent variations in immune modulatory function, did not overall made different donor-derived MSC more similar at whole transcriptomic levels, meaning the cells were still different in many other biological perspectives, and might not perform equally for therapeutic purposes other than immune modulation. Pre-selection or pre-treatment to eradicate MSC variations in a disease-treatment-specific manner would therefore be necessary to assure clinical efficacies. Together this study provided novel insights into the quality control perspective of using different-donor-derived MSC to treat inflammation-related clinical conditions and/or autoimmune diseases.

overall_design: In this study, we analyzed human umbilical-cord-derived MSC from 32 donors and revealed donor-dependent variations. We also analyzed 3 MSC strains with 3 replicates in 2 conditions.

first: Yi

last: Sun

first: Chunxue

first: Zhen

last: Wang

first: Wenxia

last: Gao

first: Wei

last: Chen


title: INPP4B protects from metabolic disease and obesity associated prostate neoplasia.

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

summary: A high fat diet and obesity have been linked to the development of metabolic dysfunction and the promotion of multiple cancers in mice and men. The causative cellular signals are multifactorial and not completely understood. Previous studies have shown that metabolic dysfunction leads to activation of the AKT and PKC pathways. Both signaling pathways are inhibited by the dual specificity phosphatase, INPP4B, which dephosphorylates PI(3,4)P2, an activator of AKT, and PI(4,5)P2, an activator of the PLC/PKC pathway. We established that INPP4B signaling protects mice from metabolic dysfunction. Inpp4b-/- male mice had accelerated activation of SREBF1 in liver which, along with the high fat diet, caused increased expression and activity of PPARG and other lipogenic pathways leading  non-alcoholic fatty liver disease (NAFLD), type II diabetes, expansion and inflammation of WAT, and systemic and localized prostate inflammation that drives the development of high-grade prostatic intraepithelial neoplasia (PIN).

overall_design: WT and Inpp4b-/- males were fed with either LFD (LabDiet 5V75, St. Louis, MO) or HFD (TestDiet 58R3, St. Louis, MO). The HFD consisted of 59.4% fat, 25.7% carbohydrate, and 14.9% protein (total 22.8 kJ/g), whereas the regular chow contained 12.9% fat, 63.8% carbohydrate, and 23.2% protein (total 13.6 kJ/g). All LFD WT, LFD Inpp4b-/-, HFD WT, and HFD Inpp4b-/- mice were euthanized and dissected at 12 weeks and their tissues where collected for analysis. RNA was purified  from HFD WT (N=4) and HFD Inpp4b-/- (N = 4) and submitted to Novogene for RNA sequencing.

first: Manqi

first: Elena

middle: Y

last: Kaftanovskaya

first: Judy

last: Vasquez

first: Jean

last: Vacher

first: Alexander

middle: I

last: Agoulnik

middle: M

last: Ittmann

first: Irina

middle: U


title: High throughput sequencing of Siwi associated piRNAs from Bombyx mori BmN4 cells

city: Tokyo

first: Ryo

last: Murakami

address: 2-11-16, Yayoi, Bunkyo-ku

department: Department of biological sciences

institute: The University of Tokyo

type: Non-coding RNA profiling by high throughput sequencing

summary: RNAs associating with PIWI proteins were Immunoisolated from BmN4 cells. Sequence libraries were generated with NEBNext Small RNA Library Prep Set for Illumina(NEB). Libraries were sequenced using Illumina MiSeq (single-end, 51 cycles).

overall_design: Two Small RNA libraries were prepared from Flag-Siwi immuno-precipitate samples of BmN4 cells treated DDX43 siRNA

first: Tetsutaro

last: Sumiyoshi

first: Mikiko

last: Siomi


title: Targeting a Braf/Mapk pathway rescues podocyte lipid peroxidation in CoQ deficiency kidney disease

city: Boston

first: Eriene-Heidi

last: Sidhom

state: MA

address: 4 Blackfan Circle HIM 536

institute: Harvard Medical School

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

overall_design: Refer to individual Series


title: Diet-Dependent Changes of the DNA Methylome Using a Göttingen Minipig Model for Obesity

city: Shenzhen

first: Epigenomics

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

summary: In the present study, we have compared the promoter methylome in liver tissue of a Göttingen minipigs fed a high fat/fructose/cholesterol (FFC) diet with the promotor methylome of GM pigs fed the FFC diet and reverted to standard chow (FFC/SD), and fed standard chow (SD) respectively. Furthermore, we correlated the methylation patterns of key genes with their gene expression profiles in liver. We show that minipigs exhibited extensive, functionally relevant methylome perturbation under FFC diet compared to normal chow group. Also, the methylation levels were highly correlated with gene expression in key genes in the liver. Surprisingly, the diet-induced methylome variation could be only partially reversed to lean stage after replacing the FFC diet to normal chow diet, promotors of several obesity-related genes still remained differential methylated and expression was perturbed even after diet reversion.

overall_design: High-throughput liquid hybridization capture-based bisulfite sequencing (LHC-BS) was used to quantify the promoter regions of liver tissues of twenty-night male castrated minipigs (age 6 to 7 months) with different diet intervention: standard chow (SD, N = 7); FFC diet (FFC, N = 10); a group fed high fat/fructose/cholesterol diet but changed to standard diet after 7 months (FFC/SD, N = 12). Expression profiling of metabolically relevant genes were detected on the Biomark HD system.

first: Yayan

last: Feng

first: Fei


title: Histone demethylases ELF6 and JMJ13 antagonistically regulate self-fertility in Arabidopsis

city: London

first: Charlie

last: Keyzor

address: Imperial College, Kensington

department: Department of Life Sciences

institute: Imperial College London

summary: The chromatin modification H3K27me3 is involved in almost every developmental stage in  Arabidopsis. Much remains unknown about the dynamic regulation of this histone modification in flower development and control of self-fertility. Here we demonstrate that the H3K27me3-specific demethylases ELF6 and JMJ13 antagonistically regulate carpel and stamen growth and thus modulate self-fertility. Transcriptome and epigenome data are used to identify potential targets of ELF6 and JMJ13 responsible for these physiological functions. We find that ELF6 relieves expansin genes of epigenetic silencing to promote cell elongation in the carpel, enhancing carpel growth and therefore encouraging out-crossing. On the other hand, JMJ13 activates genes of the jasmonic acid regulatory network alongside the auxin responsive SAUR26, to inhibit carpel growth, enhance stamen growth, and overall promote self-pollination. Our evidence provides novel mechanisms of self-fertility regulation in A.thaliana demonstrating how chromatin modifying enzymes govern the equilibrium between flower self-pollination and out-crossing.

overall_design: RNA sequencing of the primary inflorescences from elf6, ref6, jmj13 knock-out mutants.

first: Benoit

last: Mermaz

first: Jie

last: Song


title: RNA sequencing of mouse podocytes with and without knockdown of Pdss2

summary: We report trancriptional changes between wildtype mouse immortalized podocytes and compared to podocytes with shRNA-knockdown of Pdss2.

overall_design: Bulk RNA sequencing of control and knockdown, n=3 biological replicates per condition, at day 14 of differentiation, 7 days following knockdown with scrambled- or Pdss2-targeted shRNAs. Two different validated Pdss2-targeted shRNAs were used.

first: Anna

last: Greka


title: De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 maize inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes in maize exceeds 103,000 and that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres further revealed the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that correlate with known QTLs and changes in gene expression.

overall_design: Genotype pooling of NAM founder leaf tissues across three biological replicates and two technical replicates of single-cell ATAC-seq libraries. Individual cells were genotyped and reads from cells from the same founder were aggregated.

first: Alexandre

last: Marand

first: Bob


title: Identification of transcripts bound to and regulated by the PuREBP1/2 complex in Trypanosoma brucei

city: Armilla

first: Antonio

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

country: Spain

institute: CSIC


title: Effect of the depletion of PuREBP1 (Tb927.4.4550) on the transcriptome of Trypanosoma brucei [RNAi]

summary:
We have previously characterized a short RNA stem-loop cis-element within the 3'-UTR of the NT8 nucleobase transporter mRNA (PuRE, Purine Responsive Element) that is necessary and sufficient to confer a strong repression of gene expression in response to purines in the human parasite Trypanosoma brucei (PMID: 24813448). In this study, we have identified a protein complex composed of two RNA-binding proteins (Tb927.4.4550 and Tb927.3.3060, named here as PuREBP1 and PuREBP2 respectively) that binds to the PuRE in vitro and to NT8 mRNA in vivo. Depletion of PuREBP1 by RNAi results in the upregulation of just NT8 and the mRNAs encoding the amino acid transporter AATP6 paralogues. Moreover, we found that the PuREBP1/2 complex is associated with only a handful of mRNAs, and that it is responsible for the observed purine-dependent regulation of NT8 expression.
Depletion of PuRBP1 results in the upregulation of just two mRNAs (encoding membrane transporters NT8 and AATP6) and downregulation of four other mRNAs (including the one encoding PuREBP1, as expected)

overall_design: Total RNA was obtained from non-induced (control) vs PuREBP1-depleted trypanosomes after 48h of RNAi induction. Two biological replicates = 4 samples in total

first: Miriam

last: Rico

last: Estévez


title: Identification of the mRNAs associated with the protein complex PuREBP1/PuREBP2 (Tb927.4.4550/Tb927.3.3060) in Trypanosoma brucei [RIP-seq]

summary:
We have previously characterized a short RNA stem-loop cis-element within the 3'-UTR of the NT8 nucleobase transporter mRNA (PuRE, Purine Responsive Element) that is necessary and sufficient to confer a strong repression of gene expression in response to purines in the human parasite Trypanosoma brucei (PMID: 24813448). In this study, we have identified a protein complex composed of two RNA-binding proteins (Tb927.4.4550 and Tb927.3.3060, named here as PuREBP1 and PuREBP2 respectively) that binds to the PuRE in vitro and to NT8 mRNA in vivo. Depletion of PuREBP1 by RNAi results in the upregulation of just NT8 and the mRNAs encoding the amino acid transporter AATP6 paralogues. Moreover, we found that the PuREBP1/2 complex is associated with only a handful of mRNAs, and that it is responsible for the observed purine-dependent regulation of NT8 expression.
Just a handful of mRNAs are associated with the PuREBP1/2 complex: NT8, AATP6, mCUd and other mRNAs encoding proteins of unknown function, mainly membrane proteins

overall_design: Tandem-affinity purification (TAP) was used to identify mRNAs associated with the complex. Input RNA vs affinity-purified RNA were compared. As a control, TAP was performed with a functionally-inactive PuREBP1/2 complex


title: Localized EMT reprograms glial progenitors to promote spinal cord repair

status: Public on Jan 31 2021

city: St. Louis

first: Mayssa

last: Mokalled

state: MO

address: 4523 Clayton Ave CB 8103

department: Developmental Biology

institute: Washington University


title: Localized EMT reprograms glial progenitors to promote spinal cord repair [single-cell RNA-seq]

summary: Single nuclear RNA-sequencing was performed on spinal cord tissues from Tg(gfap:EGFP) zebrafish at 1 week post injury using the 10x Genomics platform.

overall_design: Single nuclear RNA-sequencing of spinal cord tissue.

first: Dana

last: Shaw

first: Vishnu

last: Saraswathy

first: Lili

last: Zhou


title: Transcriptome analysis of plaque and pWAT immune cells of 16 weeks fed high fat high cholesterol diet LXRa WT and S196A mice.

city: New York

first: Michael

last: Garabedian

state: NY

address: 550 First Avenue

department: Microbiology

institute: NYU School of Medicine

summary:
Purpose: The goals of this study is to evaluate the impact of LXRa phosphorylation at S196 in immune cells on atherosclerosi and obesity, on gene expression via RNA-seq.
Lab Methods: Bone marrow from LXRa WT and S196A mice was transplanted into Ldlr-/- mice, which were fed a high fat, high cholesterol diet for 16 weeks prior to evaluation of atherosclerosis and obesity. Plaque CD68+ and T cells, and pWAT macrophages and T cells mRNA profiles of LXRa WT and S196A mice were generated by RNA-seq using Illumina HiSeq 2500 (plaque CD68+ samples) or HiSeq 4000 (Plaque T cells and pWAT FBC, FB and T cells samples).
Bioinformatics Methods: Quality control and Illumina adapter removal was performed on the raw sequencing output, followed by mapping of each read pair to the GRCm38.96 transcriptome in order to generate  the mRNA profile of each sample. Sample groups from different tissues as well as groups from wild-type or mutant samples were compared against each other for differential gene expression.
Results:  we analyzed genes differentially expressed in plaque LXRa S196A and found that LXRa S196A induced 365 and repressed 205 genes in CD68+ (LogFC > 0.6, p-value < 0.05), and induced 1,578 genes and repressed 2,392 genes in plaque T cells compared to LXRa WT (LogFC > 1, FDR < 0.05). In pWAT, LXRa S196A vs WT analysis showed that LXRa S196A repressed 419 genes and induced 379 genes in FBC, induced 182 genes and repressed 228 genes in FB, and 624 genes were induced and 622 genes were repressed in LXRa WT (LogFC > 1, FDR < 0.05).
Conclusions: This study is the first detailed analysis of plaque and pWAT immune cells transcriptomes from LXRa S196A in bone marrow cells of LDLR-/- mice under high fat and high cholesterol diet, generated by RNA-seq. We demonstrated that LXRa S196A is largely affecting transcriptome of immune cells in atherosclerotic plaque and pWAT. The transcriptome remodeling observed is tissue and cell specific, and controls atherosclerosis and obesity progression.

overall_design: Plaque and pWAT immune cells transcriptomic profiles of LXRa WT and S196A

first: Maud

last: Voisin

first: Chris

last: Zoumadakis


title: Transcriptomic analysis of Pot1a/b knockout in a native mouse model of glioma

first: Ali

last: Jalali

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Please see the cited publication below for further details. This study found that Pot1a/b knockout in a native mouse model of glioma confers sexual dimorphism of survival and discovered sex-dependent changes in telomere content as well as signatures of immune infiltration and cell cycle in these tumors.

overall_design: The native mouse model of glioma used in this study (C3 model) was generated via embryonic CRISPR/Cas9 knockout of Trp53, Nf1, and Pten. Additional CRISPR/Cas9 knockout of Pot1a and Pot1b resulted in the C5 model.

first: Kwanha

last: Yu

first: Vivek

last: Beechar

first: Brittney

last: Lozzi

first: Melissa

last: Bondy

first: Benjamin

last: Deneen


title: Copper Availability Influences the Transcriptomic Response of C. albicans to Fluconazole Stress

city: Durham

first: Katherine

middle: J.

last: Franz

state: NC

address: 2103 French Science Center, 124 Science Dr., Box 90346

department: Chemistry

institute: Duke University

summary: We used whole transcriptome profiling (RNA-seq) to analyze the effects of Cu availability on the transcriptomic response of Candida albicans to the azole antifungal drug fluconazole. This study provides a framework for understanding how two treatments work in concert to generate unique impacts on stress response mechanisms of pathogenic fungi.

overall_design: Examination of Candida albicans cells treated with fluconazole under basal and elevated (10 µM) Cu conditions.

first: Elizabeth

last: Hunsaker

first: Chen-Hsin


title: Transcriptomic analysis of the trade-off between endurance and burst-performance in the frog Xenopus allofraseri

city: Paris

first: Valerie

last: Ducret

address: 55 rue buffon

country: France

institute: MNHN

summary:
Background: Variation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and performance trade-offs remains poorly understood. In this study we identify the genes, signaling pathways, and regulatory processes responsible for the trade-off between burst performance and endurance observed in Xenopus allofraseri, using a transcriptomic approach.
Results: We obtained a total of about 121 million paired-end reads from Illumina RNA sequencing and analyzed 218,541 transcripts obtained from a de novo assembly. We identified 109 transcripts with a significant differential expression between endurant and burst performant individuals (FDR ≤ 0.05 and logFC ≥ 2), and blast searches resulted in 103 protein-coding genes. We found major differences between endurant and burst-performant individuals in the expression of genes involved in the polymerization of actin filaments, cellular trafficking, proteoglycans and extracellular proteins secreted, lipid metabolism, mitochondrial activity and regulators of signaling cascade. Remarkably, we revealed transcripts isoforms of key genes with function in metabolism, apoptosis, nuclear export and as transcriptional corepressor, expressed in either burst-performant or endurant individuals. Lastly, we find two up-regulated transcripts in burst-performant individuals that correspond to the expression of myosin-binding protein C fast-type (mybpc2). This suggests the presence of mybpc2 homoeologs and may have been favored by selection to permit fast and powerful locomotion.
Conclusion: Locomotor performance trade-off in Xenopus allofraseri can be attributed to the differential expression of genes belonging to the different pathways of calcium signaling, endoplasmic reticulum stress response and striated muscle contraction, but also attributed to the use of alternative splicing and regulatory processes. Ultimately, our transcriptomic analysis offers new perspectives for future analyses of the role of single nucleotide variants, homoeology and alternative splicing in the evolution of locomotor performance trade-offs.

overall_design: Differential expression analysis between four endurant and four burst-performant males

first: Adam

last: Richards

first: Mathieu

last: Videlier

first: Thibault

last: Scalvenzi

first: Karen

middle: A

last: Moore

first: Konrad

last: Paszkiewicz

first: Camille

last: Bonneaud

first: Nicolas

last: Pollet

first: Anthony

last: Herrel


title: Global discovery of SLE genetic risk variant allelic enhancer activity

city: Cincinnati

first: Xiaoming

last: Lu

state: Ohio

address: 3333 Burnet Ave

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

summary: Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3,073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we constructed a massively parallel reporter assays (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into Epstein-Barr virus-transformed B cell line GM12878 revealed 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. Combined with allelic enhancer activity analyses in Jurkat cell line, we identified shared and unique allelic transcriptional regulatory mechanisms at SLE risk loci. In-depth analysis of allelic transcription factor (TF) binding at and around 51 allelic variants identified one class of TFs whose DNA-binding motif tends to be directly altered by the risk variant and a second, larger class of TFs that also bind allelically but do not have their motifs directly altered by the variant. Collectively, our approach provides a blueprint for the discovery of allelic gene regulation at risk loci for any disease and offers insight into the transcriptional regulatory mechanisms underlying SLE.

sample_organism:
Homo sapiens
unidentified plasmid

platform_organism:
Homo sapiens
unidentified plasmid

overall_design: Massively parallel reporter assays to study SLE associated variants for risk allele-dependent transcriptional enhancer activity, 3-5 replicates, 2 conditions, 2 cell types

first: Xiaoting

last: Chen


title: Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA-seq]

first: Mayssa

last: Mokalled

summary: mCherry/EGFP double positive cells were isolated from the spinal cords of Tg(ctgfa:mCherry; gfap:EGFP) zebrafish  at 5 days post injury. Bulk spinal cord tissue at 5, 10, and 21 days post-injury were also sequenced.

overall_design: Whole RNA-sequencing of FACS-sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.

first: Dana

last: Shaw

first: Vishnu

last: Saraswathy

first: Lili

last: Zhou


title: Ectopic expression of the oncogene TLX3 in DN-like stage

city: Marseille

first: Mohamed

last: BELHOCINE

address: 163, Avenue de Luminy

institute: INSERM

summary: It is now well established that members of the homeobox gene family play a critical role in normal hematopoietic cell development and that their unbalanced or ectopic expression can lead to characteristic perturbations in haemopoiesis and the onset of leukaemia. TLX3 expression in human haematologic malignancies is exclusive to T-ALL, where it is almost universally associated with transformation of early cortical CD4+CD8+ DP thymocytes. investigated the impact of ectopic TLX3 expression on T cell development, and the initiating mechanisms of T-cell transformation leading to leukemia onset. Forced expression of TLX3 disrupted the thymic develoment at DN-like stage giving rise to immortalized preleukemic clones.

overall_design: Gene expression data from 2 culture conditions was performed for the following cells: DN thymocytes from Rag2-/-  mice and    sorted DN thymocytes from wild-type mice transduced with TLX3 and cultured on OP9-DL1 . All conditions are performed in three replicates.

last: Belhocine

last: Simonin

first: Agata

last: Cieslak

first: Lydie

last: Pradel

first: Charlotte

last: Smith

first: Eve-Lyne

last: Mathieu

first: Guillaume

last: Charbonnier

first: José

last: Flores

first: Iris

last: Manosalva

first: Joost

last: Martens

first: Hendrik

last: Stunnenberg

first: Denis

last: Puthier

first: Pierre

last: Ferrier

first: Vahid

last: Asnafi

first: Salvatore

last: Spicuglia


title: Transcriptomic analysis of the influence of arachidonic acid on polymicrobial biofilms of Candida albicans and Pseudomonas aeruginosa

city: Bloemfontein

first: Carolina

middle: H

last: Pohl

state: Free State

address: 205 Nelson Mandela avenue, Park West

department: Department of Microbial, Biochemical and Food Biotechnology

country: South Africa

institute: University of the Free State

summary: The interaction of clinically relevant microorganisms is the focus of various studies, e.g. the interaction between the pathogenic yeast, Candida albicans, and the bacterium, Pseudomonas aeruginosa and these interactions can alter the outcome of infection, growth dynamics of each species and antimicrobial resistance of pathogens. During infection, both C. albicans and P. aeruginosa can elicit the release arachidonic acid (AA) from host cells membranes through the action of phospholipases. This polyunsaturated fatty acid can be transformed into immune-modulating compounds, termed eicosanoids, by both host-derived and microbial-derived enzymatic reactions. In its free form, AA can affect the growth of both C. albicans and P. aeruginosa, inhibiting the morphogenesis of C. albicans as well as reducing resistance towards antifungal agents. However, the mechanism of this is unknown. Previous studies on the effect of polyunsaturated fatty acids have indicated a possible alteration in plasma membrane organisation and permeability. Our group aimed to address how AA affects C. albicans in both single species biofilms, as well as in polymicrobial biofilms with P. aeruginosa. RNAseq was performed on single and polymicrobial biofilms in the presence and absence of a sub-inhibitory (100 µM) concentration of AA. Differential expression was determined between C. albicans single species biofilms in the presence and absence of AA. Secondly, the influence of co-incubation of C. albicans with P. aeruginosa in the absence of AA was evaluated to identify novel facets of interaction not previously identified, and to establish a baseline to determine the effect of AA on C. albicans in polymicrobial biofilms. Lastly, the effect of AA on C. albicans in polymicrobial biofilms was determined through comparison with polymicrobial biofilms in the absence of AA. This study provides a comprehensive analysis of the effect of AA and both co-incubation of C. albicans with P. aeruginosa focused on the transcriptome.

sample_organism:
Pseudomonas aeruginosa
Candida albicans

platform_organism:
Pseudomonas aeruginosa
Candida albicans

overall_design: Four sets of samples in triplicate (n = 3) were analysed consisting of single species or polymicrobial biofilms prepared in 20 mL RPMI-1640 medium and incubated at 37ºC for 6 hours to allow biofilm formation. These include single species biofilms of C. albicans exposed to 100 µM arachidonic acid (CAA; arachidonic acid dissolved in ethanol) compared to single species biofilms of C. albicans exposed to ethanol control (CET; ethanol equivalent to amount arachidonic acid added - final concentration of 0,076% ethanol v/v). Secondly, polymicrobial biofilms consisting of C. albicans and P. aeruginosa (exposed to 0,076% ethanol; CPET) were compared to CET. Lastly, polymicrobial biofilms exposed to 100 µM AA (CPAA) were compared to CPET. Total RNA extraction was performed and subjected to sequencing on the Illumina NextSeq 500. Resultant FastQ files were subjected to a relevant bioinformatics pipeline to determine differential expression.

first: Ruan

last: Fourie


title: Transcriptomic analysis of Treg and Tconv cells from inflamed tissues of mice that are deficient for TNFR2 in Treg cells

status: Public on Jan 30 2021

first: Benoit

middle: L

last: Salomon

address: 91 Bd de l'hopital

institute: Inserm

summary:
Methods: Foxp3Cre-ERT2 x Tnfrsf1bFlox/Flox (icKO) and Foxp3Cre-ERT2 control (Ctrl) mice were immunized with MOG35-55 peptide to induce active EAE. From day 7 to 14, they were treated with Tamoxifen to delete TNFR2 only in Tregs. At day 14, Tregs and Tconvs were purified by flow cytometry from the inflamed central nervous system (CNS) or draining lymph nodes (dLN) for RNA extraction
Results: In the CNS, TNFR2-deficient Tregs have lower expression of several Treg cell-signature genes and increased expression of genes normally expressed by Tconvs. The expression of 185 and 229 genes was respectively down- and up-regulated in Tconvs isolated from the CNS of mutant animals, compared to controls. Tconvs from icKO mice displayed a highly activated phenotype.

overall_design: RNA-Seq of total mRNA of Tregs and Tconvs from the CNS or dLN at day 14 of EAE from mice that have TNFR2-deficient Tregs or control mice

first: Emilie

last: Ronin

first: Maryam

last: Khosravi

first: Yenkel

last: Grinberg-Bleyer


title: Transcriptomic analyses of Lysinibacillus varians GY32 respiring with electrode or oxygen

status: Public on Jan 29 2021

city: Guang zhou

first: kong

last: guannan

address: 100 Martyrs Central Road

institute: Guangdong Institute of Microbiology

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

overall_design: Refer to individual Series


title: Transcriptomic analyses of Lysinibacillus varians GY32 respiring with electrode or oxygen [RNA-seq G]

summary: Lysinibacillus varians GY32 is a filamentous bacteria that can generate electricity in microbial fuel cells. To find potential genes participating in the electron transfer to electrode of Lysinibacillus varians GY32, we compared the gene expression profiles of this bacteria with yeast extract as electron donor and two electron acceptors, i.e. oxygen and electrode in microbial fuel cells. The results showed that several cytochrome c genes might play specific roles in the extracellular electron transfer to electrode in this strain.

overall_design: Six samples are included, three aerobic samples (control replicates, CK) and three microbial fuel cell samples (Treatment replicates, MFC).

first: Guannan

last: Kong

first: Chunjie

last: Zhu

first: Yonggang

last: Yang


title: Transcriptomic analyses of Lysinibacillus varians GY32 respiring with electrode or oxygen [RNA-seq K]

summary: Lysinibacillus varians GY32 is a filamentous bacteria that can generate electricity in microbial fuel cells. To find potential genes participating in the electron transfer to electrode of Lysinibacillus varians GY32, we compared the gene expression profiles of this bacteria with acetate as electron donor and two electron acceptors, i.e. oxygen and electrode in microbial fuel cells. The results showed that several cytochrome c genes might play specific roles in the extracellular electron transfer to electrode in this strain.

overall_design: Six samples are included: three aerobic samples (control replicates, O2) and three microbial fuel cell samples (Treatment replicates, MFC).


title: Clinical Utility of Targeted Next-Generation Sequencing Assay to Detect Copy Number Variants in Myeloid Malignancies: Is It Ready for Prime Time?

city: Baltimore

first: Ying

last: Zou

address: 1812 Ashland Ave, Suite 221

department: Department of Pathology

institute: Johns Hopkins University

type: Genome variation profiling by high throughput sequencing

summary: Genetic abnormalities including copy number variants (CNVs, such as gains and losses), and gene mutations are important for diagnosis and treatment of myeloid malignances. In a routine clinical setting, somatic gene mutations are detected by targeted next generation sequencing (NGS), but CNVs are commonly detected by conventional chromosome analysis and fluorescence in situ hybridization (FISH). The aim of this proof-of-principle study was to investigate the feasibility of using a targeted NGS assay to simultaneously detect not only somatic mutations, but also CNVs. Here, we sequenced 406 consecutive patients with myeloid malignancies and performed a head-to-head comparison with the results from conventional clinical assays including conventional chromosome analysis and myeloid FISH to detect CNVs. The targeted NGS assay revealed all 120 CNVs detected by myeloid FISH panel including monosomy 5/5q deletions, monosomy 7/7q deletions, trisomy 8, and 20q deletions. Furthermore, the targeted NGS assay also detected 605 CNVs outsides targeted regions of the myeloid FISH panel, which were revealed by conventional cytogenetic testing. The targeted NGS assay achieved 100% concordance with the myeloid FISH for detection of these common myeloid CNVs, with a high clinical sensitivity (> 99%) and specificity (>99%). The lower limit of detection by the myeloid FISH and the targeted NGS assay was similar and was generally 5% variant allele fraction for DNA. This proof-of-principle study demonstrated that the targeted NGS assay can simultaneously detect both common myeloid CNVs and somatic mutations, which can provide more comprehensive genetic profiling for patients with myeloid malignancies using a single assay.

overall_design: 91 specimen were sequecned by Hiseq or Novaseq usingTargeted NGS assay to cover 640 cancer genes

first: Liqun

last: Jiang

first: Aparna

last: Pallavajjala

first: Jialing

last: Huang

first: Emily

last: Adams

first: Kirstin

last: Smith

first: Christopher

last: Gocke


title: RNA expression profile in animal models of neurodevelopmental disorders treated with TAK-418

city: Fujusawa

first: Satoru

last: Matsuda

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

institute: Takeda Pharmaceutical Company Limited

summary: We report the RNA expression profiles in the brain cortex of animal models of neurodevelopmental disorders (rat with prenatal exposure to valproate and mouse with prenatal exposure to poly I:C) treated with TAK-418.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Brain mRNA profiles in vehicle- or TAK-418-treated animal models and respective healthy control animals.

first: Tatsuya

last: Ando

first: Rina

last: Baba


title: Histone modification profile in animal models of neurodevelopmental disorders treated with TAK-418

summary: We report the histone modification profiles in the brain cortex of animal models of neurodevelopmental disorders (rat with prenatal exposure to valproate and mouse with prenatal exposure to poly I:C) treated with TAK-418.

overall_design: Histone modification profiles in the brains of vehicle- or TAK-418-treated animal models and respective healthy control animals.


title: FlyORF-TaDa allows rapid generation of new lines for in vivo cell-type specific profiling of protein-DNA interactions in Drosophila melanogaster

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

country: Australia

institute: Menzies Institute for Medical Research

summary: Targeted DamID (TaDa) is an increasingly popular method of generating cell-type specific DNA binding profiles in vivo. Although sensitive and versatile, TaDa requires the generation of new transgenic fly lines for every protein that is profiled, which is both time-consuming and costly. Here, we describe the FlyORF-TaDa system for converting an existing FlyORF library of inducible open reading frames (ORFs) to TaDa lines via a genetic cross, with recombinant progeny easily identifiable by eye colour. Profiling the binding of the H3K36me3-associated chromatin protein MRG15 in larval neural stem cells using both FlyORF-TaDa and conventional TaDa demonstrates that new lines generated using this system provide accurate and highly-reproducible DamID binding profiles. Our data further show that MRG15 binds to a subset of active chromatin domains in vivo. Courtesy of the large coverage of the FlyORF library, the FlyORF-TaDa system enables the easy creation of TaDa lines for 74% of all transcription factors and chromatin modifying proteins within the Drosophila genome.

overall_design: Targeted DamID.  Two biological replicates for wor-GAL4 driving each of TaDaG2-MRG15, TaDaG2-Dam, FlyORF-TaDa-MRG15, FlyORF-TaDa-Dam.

first: Gabriel

middle: N

last: Aughey

first: Caroline

last: Delandre

first: John

middle: P

last: McMullen

first: Tony

middle: D

last: Southall

middle: J


title: H2AK119ub1 guides maternal inheritance and zygotic deposition of H3K27me3 in mouse embryos

city: Yokohama

first: Azusa

last: Inoue

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Parental epigenomes are established during gametogenesis. While they are largely reset soon after fertilization in mammals, maternal histone H3 tri-methylation at lysine 27 (H3K27me3) is inherited by the next generation embryos. How H3K27me3 is properly established in oocytes and passed on to the embryos remains elusive. Furthermore, although polycomb repressive complex 2 (PRC2)-mediated H3K27me3 is known to interplay with PRC1-mediated mono-ubiquitination of histone H2A at lysine 119 (H2AK119ub1) to coordinate repressive polycomb domains in embryonic stem cells (ESCs), how they act in vivo remains unknown. To address these questions, here we profiled H2AK119ub1 dynamics during mouse oogenesis and preimplantation development, and investigated its functions in maternal inheritance of H3K27me3. Integrative analyses with H3K27me3 dynamics revealed that an unusually broad and distal-rich distribution of H2AK119ub1 is established during oogenesis and co-transmitted to embryos together with H3K27me3. On the other hand, an ESC-like canonical distribution of H2AK119ub1 is newly established at the 2-cell stage, a few days earlier than that of H3K27me3. Deficiency in polycomb group ring finger 1 (PCGF1) and PCGF6, essential components of variant PRC1 (vPRC1), leads to massive reduction of H2AK119ub1 and gene-selective loss of H3K27me3 in oocytes. The gene-selective deficient state of H3K27me3 is irreversibly inherited by embryos, which causes bi-allelic expression of H3K27me3-dependent imprinted genes, including Xist, embryonic sublethality, and placental enlargement at term. Collectively, our study not only revealed instructive in vivo dynamics of H2AK119ub1 for H3K27me3 establishment at the maternal-to-embryonic transition, but also identified PCGF1/6-PRC1 as an essential player for intergenerational epigenetic inheritance.

overall_design: H2AK119ub1 CUT&RUN was performed in WT mouse oocytes and B6/PWK F1 hybrid preimplantation embryos. H2AK119ub1 and H3K27me3 CUT&RUN and RNAseq were performed in Pcgf1, Pcgf6, Pcgf1/6 CTR and KO oocytes. H3K27me3 CUT&RUN and RNAseq were performed in xPWK F1 hybrid Pcgf1/6 CTR and maternal KO late 2-cell, morula embryos. RNA-seq was performed in xPWK F1 hybrid Pcgff1/6 CTR and maternal KO extra-embryonic ectoderm.

first: Hailiang

last: Mei

first: Chisayo

last: Kozuka

first: Ryoya

last: Hayashi

first: Mami

last: Kumon

first: Haruhiko

last: Koseki


title: DNA methylation profile in animal models of neurodevelopmental disorders treated with TAK-418

summary: We report the DNA methylation profiles in the brain cortex of animal models of neurodevelopmental disorders (rat with prenatal exposure to valproate and mouse with prenatal exposure to poly I:C) treated with TAK-418.

overall_design: DNA methylation profiles in the brains of vehicle- or TAK-418-treated animal models and respective healthy control animals.


title: ILT3 (LILRB4) Promotes the Immunosuppressive Function of Tumor-Educated Human Monocytic Myeloid-Derived Suppressor Cells

city: Boston

first: Eric

last: Muise

address: 33 Ave. Louis Pasteur

department: GPGX

institute: Merck

summary: Myeloid-derived suppressor cells (MDSCs) are immature myeloid cells that accumulate in the tumor microenvironment (TME). MDSCs have been shown to dampen anti-tumor immune responses and promote tumor growth; however, the mechanisms of MDSC induction and their role in promoting immune suppression in cancer remain poorly understood. Here, we characterized the phenotype and function of monocytic MDSCs (M-MDSCs) generated by co-culture of human peripheral blood mononuclear cells with SK-MEL-5 cancer cells in vitro. We selected the SK-MEL-5 human melanoma cell line to generate M-MDSCs because these cells form subcutaneous tumors rich in myeloid cells in humanized mice. M-MDSCs generated via SK-MEL-5 co-culture expressed low levels of human leukocyte antigen (HLA)-DR, high levels of CD33 and CD11b and suppressed both CD8+ T cell proliferation and IFN-γ secretion. M-MDSCs also expressed higher levels of immunoglobulin-like transcript 3 (ILT3, also known as LILRB4) and immunoglobulin-like transcript 4 (ILT4, also known as LILRB2) on the cell surface compared to monocytes. We, therefore, investigated how ILT3 targeting could modulate M-MDSC cell function. Treatment with an anti-ILT3 antibody impaired the acquisition of the M-MDSC suppressor phenotype and reduced the capacity of M-MDSCs to cause T cell suppression. Finally, in combination with anti-programmed cell death protein 1 (PD1), ILT3 blockade enhanced T cell activation as assessed by IFN-γ secretion. These results suggest that ILT3 expressed on M-MDSCs has a role in inducing immunosuppression in cancer and that antagonism of ILT3 may be useful to reverse the immunosuppressive function of M-MDSCs and enhance the efficacy of immune checkpoint inhibitors.

overall_design: Total RNA from SK-MEL-5–educated live CD45+ CD14+ CD33+ cells treated with either isotype control hIgG4 or anti-ILT3 antibody c52B8, was sequenced.

middle: S

first: Latika

last: Singh


title: iPSC-derived 2D and 3D models of mitochondrial disease reveal early defects in neuronal morphogenesis and identify intervention strategies

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: Our understanding of the mechanisms underlying the human neuronal pathology associated with impaired oxidative phosphorylation (OXPHOS) is hampered by a lack of effective model systems. Using patient-derived induced pluripotent stem cells (iPSCs) and CRISPR/Cas9 engineering, we developed a human model of Leigh syndrome (LS) caused by mutations in the gene SURF1, which is the most frequent and severe manifestation of mitochondrial disease in children. Single-cell RNA-sequencing and multi-omics analysis revealed compromised neuronal differentiation and morphogenesis of two-dimensional (2D) neuronal cultures and of three-dimensional (3D) cerebral organoids. The phenotypes emerged at the level of neural progenitor cells (NPCs). Mutant NPCs could not shift to OXPHOS and retained a glycolytic proliferative state that failed to support neuronal morphogenesis. Improving NPC bioenergetics by increasing mitochondrial biogenesis via bezafibrate treatment restored early morphogenesis. SURF1 gene augmentation also counteracted the phenotypes, while exposure to hypoxia did not lead to amelioration. Our findings provide mechanistic insights and suggest therapeutic avenues for mitochondrial disease, a rare disease with major unmet medical need.

overall_design: analysis of iPSCs, neuronal culture and brain organoids derived from Leigh Syndrome patients and controls

first: Gizem

last: Inak

first: Agnieszka

last: Rybak-Wolf

first: Pawel

last: Lisowski

first: Tancredi

last: M. Pentimalli

first: Nikolaus

last: Rajewsky

first: Markus

last: Shuelke

first: Alessandro

last: Prigione


title: Animal models of neurodevelopmental disorders treated with TAK-418

first: Satoru

last: Matsuda


title: Circadian clock dysfunction in human omental fat links obesity to metabolic inflammation

city: Brussels

first: Eleonore

last: Maury

address: Avenue Hippocrate, 55

country: Belgium

institute: UCLouvain

summary: In this study we employed unbiased, genome-wide techniques to investigate how obesity impacts BMAL1 occupancy in omental preadipocytes  (OPAs) from non-obese and obese patients. Obesity relocalized BMAL1 occupancy genome-wide in omental preadipocytes. Several thousand BMAL1 binding sites were identified, some of which could be involved in pathological processes.

overall_design: We performed ChIP-seq with antibodies directed against the clock activator BMAL1  in preadipocytes from non-obese or obese (Class III) patients.


title: Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome [rRNA-depleted organoids]

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

summary: Mutations in the mitochondrial complex IV assembly factor SURF1 represent a major cause of Leigh syndrome (LS), a fatal neurological disorder. SURF1-deficient animals failed to recapitulate the neuronal failure of LS, which is considered an early-onset neurodegeneration. Using patient induced pluripotent stem cells (iPSCs) and genetically corrected cells, we discovered aberrant bioenergetics initiating in neural progenitor cells (NPCs) leading to impaired neuronal differentiation and maturation. iPSC-derived cerebral organoids recapitulated the neurogenesis defects and appeared smaller with reduced cortical thickness. We suggest defective neurogenesis as a central mechanism in LS pathogenesis and propose NPC function as an interventional target, which allowed us to identify SURF1 gene augmentation as a strategy for restoring neural function in this fatal disease.

overall_design: rRNA-depleted total RNA sequencing of cerebral organoids derived from patient and corrected iPSC lines, in two biological replicates.

last: Glažar

last: Schuelke


title: PolyA RNA-seq from RKO, A549, and H460 cells in normoxia and hypoxia

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: Analysis of steady-state mRNA levels during normoxia and hypoxia in multiple cell lines.

overall_design: Two independent biological replicates each of RKO, A549, and H460 cells exposed to normoxia or hypoxia for 24 hours.

first: Zdenek

last: Andrysik

first: Joaquin

last: Espinosa


title: PRO-seq from HCT116 cells in normoxia and hypoxia

summary: PRO-seq analysis was used to examine rapid transcriptional changes in response to short-term hypoxia in WT and HIF1A-/- HCT116 cells

overall_design: Two independent biological replicates each of WT and HIF1A-/- HCT116 cells exposed to normoxia or hypoxia for 90 minutes.

first: Heather

last: Bender


title: Global transcriptome profiling of SETD2 and hnRNP L depleted cells and H3K36me3 profile of WT 293T cells

city: Kansas City

first: Ning

last: Zhang

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

summary:
We performed RNA-seq of 293T cells post depletion and SETD2 or hnRNP L to compare their global transcriptome profile. We also looked at the distribution of the histone mark H3K36me3 in wild type 293T to correlate it with the observed transcriptome changes upon SETD2 and hnRNP L depletion.
We rescued SETD2 knock out 293T cells with SETD2 FL (Full Length), FLΔSRI (FLwoSRI) and FLΔSHI (FLwoSHI) and performed H3K36me3 ChIP-Seq.

overall_design:
Wild type 293T cells were used in these studies. For transcriptome analysis, the WT cells were treated with scramble siRNA pool or siRNA pool targetting SETD2 or hnRNP L. The validated siRNAs were procurred from Dharmacon. Cells were treated for 72 hours with the siRNAs before proceeding for RNA extraction.
SETD2 knock out 293T cells were used in these studies. The cells were transfected with SETD2 FL, FLΔSRI (FLwoSRI) and FLΔSHI (FLwoSHI) expressing constrcust under the control of CMV promoter. 72 hours post-transfection cells were fixed and processed for ChIP.

first: Saikat

last: Bhattacharya

first: Jerry

last: Workman


title: Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome


title: Identification of an acute transcriptional response to hypoxia driven by HIF1A


title: HIF1A ChIP-seq from HCT116, RKO, A549, and H460 cells in normoxia and hypoxia

summary: ChIP-seq analysis was used to identify HIF1A binding sites in normoxia and hypoxia in HCT116, RKO, A549, and H460 cells

overall_design: Two independent biological replicates each of HCT116, RKO, A549, and H460 cells exposed to normoxia or hypoxia for 24 hours.


title: Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome [polyA RNA-seq]

overall_design: polyA-selected RNA sequencing of neuronal cultures enriched for dopaminergic neurons, derived from two control and two patient-derived hESC/iPSC cell lines, each in three replicates at two time points (4 and 8 weeks of differentiation)

first: Gizem

last: Inak

last: Rybak-Wolf

last: Lisowski


title: LIN28B induces a differentiation program through CDX2 in colon cancer

status: Public on Jan 28 2021

first: Anil

middle: K.

last: Rustgi

state: New York

address: 1130 St. Nicholas Avenue

institute: Columbia University

summary: Most colorectal cancers (CRCs) are moderately-differentiated or well-differentiated, a status that is preserved even in metastatic tumors. However, the molecular mechanisms underlying CRC differentiation remain to be elucidated. Herein, we unravel a novel post-transcriptional regulation mechanism via a previously unappreciated LIN28B-CDX2 signaling axis that plays a critical role in mediating CRC differentiation. Owing to a large number of mRNA targets, the mRNA-binding protein LIN28B has diverse functions in development, metabolism, tissue regeneration and tumorigenesis. Our RNA-binding protein immunoprecipitation (RIP) assay revealed LIN28B directly binds CDX2 mRNA, which is a pivotal homeobox transcription factor in normal intestinal epithelial cell identity and differentiation. Furthermore, LIN28B overexpression results in enhanced CDX2 expression to promote differentiation in subcutaneous xenograft tumors generated from CRC cells and metastatic tumor colonization through mesenchymal-epithelial transition. Chromatin immunoprecipitation (ChIP) sequence for CDX2 identified Alpha-Methylacyl-CoA racemase (AMACR) as a novel transcriptional target of CDX2 in the context of LIN28B overexpression. Overall, we demonstrate that LIN28B promotes CRC differentiation through CDX2-AMACR axis.

overall_design: Examination of CDX2 binding site in Caco-2 cell, a colon cancer cell line, with/without LIN28B knockdown

first: Kensuke

last: Suzuki

first: Kathryn

last: Sun

middle: K


title: Nanostring analysis of macrophage subsets following zymosan-induced peritonitis

city: Edinburgh

first: Pieter

middle: Adriaan

last: Louwe

state: Scotland

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

summary: Resident macrophages from naïve mice or resident/inflammatory macrophages from mice treated with zymosan(10ug) 3 days prior were purified from C57BL/6 CD45.2+ donor mice. Purified populations were transferred into mirroring CD45.1/2+ recipient mice or clodronate pre-treated recipient mice. Donor populations were purified 8 weeks following transfer for Nanostring analysis.

overall_design: Nanostring transcriptomic data are presented from Single Live CD11b+ SiglecF-, CD19-, CD3-, Ly6G- F4/80HiMHCIILo/Int CD45.1- donor macrophages, 8 weeks after adoptive transfer.

first: Stephen

last: Jenkins


title: A genome-wide CRISPR/Cas9 screen reveals KDM2B as a modifier of protein binding to heparan sulfate

city: San Diego

first: Nathan

middle: E.

last: Lewis

state: CA

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

summary: Heparan sulfate proteoglycans (HSPGs) are expressed on virtually all animal cells and are involved in many important biological processes. Each HSPG consists of a core protein with one or more covalently attached linear heparan sulfate (HS) chains composed of alternating glucosamine and uronic acids that are heterogeneously N- and O-sulfated. The arrangement and orientation of the sulfated sugar residues of HS specify the location of distinct ligand binding sites on the cell surface, and these modifications can vary temporally during development and spatially across tissues. While most of the enzymes involved in HS biosynthesis have been studied extensively, much less information exists regarding the specific mechanisms that give rise to the variable composition and binding properties of HS.

overall_design: We conducted genome-wide CRISPR/Cas9 screens in a human melanoma cell line (A375) using guanidinylated neomycin (GNeo), a low molecular weight HS-dependent ligand. We implemented two complimentary screening strategies where GNeo was either conjugated to a cytotoxin or a fluorescent probe, and we screened for cell populations with increased survival or reduced binding to HS, respectively. Top hits from the screens were characterized and categorized based on their predicted gene functions and were examined for their involvement in the regulation of HS composition. Among the resulting targets, we identified many well-known HS biosynthesis enzymes as well as candidate genes with a previously unrecognized link to HS biosynthesis. The top hit shared between both screens was KDM2B, a histone lysine demethylase, for which we found a novel regulatory role in HS biosynthesis.

middle: E

first: Jeffrey

last: Esko

first: Marten

last: Hoeksema


title: Steroid-resistant human inflammatory ILC2s are marked by CD45RO and elevated in type 2 respiratory diseases

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

country: Netherlands

institute: Utrecht University

summary: Group 2 innate lymphoid cells (ILC2s) orchestrate protective type 2 immunity and tissue homeostatis, but have also been implicated in major human type 2 immunopathologies. However, our understanding of the mechanisms that control human ILC2 activity and phenotypic heterogeneity under inflammatory conditions remains limited. We integrated transcriptome profiling, flowcytometry characterization and functional assays to characterize human ILC2s from non-inflamed and inflamed microenvironments. We show that the transition from a resting to an activated inflammatory state in ILC2s is accompanied by a CD45RA-to-CD45RO isoform switch. CD45RA phosphatase activity suppresses ILC2 activation in resting cells, while exposure to activating cytokines induces IRF4/BATF transcription factors to promote a switch to the enzymatically restrained CD45RO isoform. Importantly, CD45RO+ ILC2 levels are increased in nasal polyps but also in the circulation of patients with chronic rhinosinusitis and asthma, which correlates with disease severity and resistance to steroid therapy. CD45RA-to-CD45RO conversion in ILC2s is sensitive to suppression by glucocorticosteroids, a mainstay therapy for patients with type-2 inflammatory disease. However, once converted, CD45RO+ ILC2s are resistant to steroids, likely via unique intrinsic metabolic reprogramming. In summary, we identify an inflammatory ILC2 subset in humans that is marked by CD45RO and is linked to severe type-2 inflammatory disease and steroid resistance.

overall_design: 9 samples of 1 celltype, 3 conditions with 3 replicates

first: Esmee

last: van der Ploeg

first: Korneliusz

last: Golebski

first: Menno

last: van Nimwegen

first: Joannah

middle: R

last: Fergusson

first: Itziar

last: Martinez-Gonzalez

first: Chantal

last: Kradolfer

first: Sophie

last: van Tol

first: Marjolein

last: de Bruijn

first: Geertje

last: de Boer

first: Gerdien

last: Tramper-Stranders

first: Gert-Jan

last: Braunstahl

first: Wilfred

last: van IJcken

first: A

last: Nagtegaal

first: Cornelis

last: van Drunen

first: Wytske

last: Fokkens

first: Danny

last: Huylebroeck

first: Hergen

last: Spits

first: Rudi

middle: W

last: Hendriks

first: Ralph

last: Stadhouders

first: Suzanne

last: Bal


title: Steroid-resistant human inflammatory ILC2s are marked by CD45RO and elevated in type 2 respiratory disease

city: Rotterdam

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

institute: Erasmus Medical Center

summary: Transcriptome analyses of human peripheral blood ILC2, fresh after sort or after culture with activating cytokines +/- dexamethasone

overall_design: biological replicate (n=4) RNA-Seq experiments

first: Esmee

last: van der Ploeg


first: Nathan

last: Lewis

first: Jeffrey

last: Esko