title: Spatiotemporal dynamics of molecular expression pattern and intercellular interactions in glial scar responding to spinal cord injury

status: Public on Feb 01 2022

city: nantong

first: songlin

last: zhou

address: 19 qixiu road

institute: Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education

summary: Adult regeneration in spinal cord is poor in mammalian but remarkable in the neonatal mammals and some vertebrates, including fish and salamanders. Increasing evidences basis of this interspecies and ontogeny highlighted the pivotal roles of neuron extrinsic factors-the glial scar, which exert confusing inhibiting or promoting regeneration function, but the spatiotemporal ordering of cellular and molecular events that drive repair processes in scar formation remains poorly understood. Here, we firstly constructed tissue-wide gene expression measurements of mouse spinal cords over the course of scar formation using the spatial transcriptomics (ST) technology in Spinal cord injury (SCI) repair. We analyzed the transcriptomes of nearly 15449 spots from 32 samples and distinguished normal and damage response regions. Compared to histological changes, spatial mapping of differentiation transitions in spinal cord injury site delineated the possible trajectory between subpopulations of fibroblast, glia and immune cell more comprehensively and defined the extent of scar boundary and core more accurately. Locally, we identified gene expression gradients from leading edge to the core of scar areas that allow for re-understanding of the scar microenvironment and found some regulators in special cell types, such as Thbs1 and Col1a2 in macrophage, CD36 and Postn in fibroblast, Plxnb2 and Nxpe3 in microglia, Clu in astrocyte and CD74 in oligodendrocyte. Last, we profiled the bidirectional ligand-receptor interactions at the neighbor cluster boundary, contributing to maintain scar architecture during gliosis and fibrosis, and found GPR37L1_PSAP and GPR37_PSAP were top 2 enriched gene-pairs between microglia and fibroblast or microglia and astrocyte. Together, the establishment of these profiles firstly uncovered scar spatial heterogeneity and lineage trajectory, provide an unbiased view of scar and served as a valuable resource for CNS injury treatment.

overall_design: Examination of 4 different  time points after injury over the course of scar formation inmice spinal cord injury

first: Leilei

last: Gong

first: Yun

first: Xiaosong

first: Songlin

last: Zhou


title: RNA sequencing of splenic CD8+ T cells treated with AAV-IL-27/ctrl in vivo

city: Shanghai

first: Jianmin

last: Zhu

state: Shanghai

address: Dongfang road 1678

country: China

institute: Shanghai Children's Medical Center

type: Expression profiling by high throughput sequencing

summary: Splenic CD8+ T cells of C57BL/6 mice treated with AAV-IL-27/ctrl for a month were sepreated by MACS. Transcriptome profiling (RNA-seq) of these purified CD8+ T cells (>95%) was completed by BGI. Changing in gene express profiling resulted by IL-27 was analyzed in this study.

overall_design: T cells were derived from 4 mice. 2 mice treated with AAV-ctrl and 2 mice teerated with AAV-IL-27.

first: Xue-Feng

last: Bai


title: Transcriptome differences between wild-type and ERF096 transgenic rice before and after cold treatment

city: Da qing

first: Yang

last: shen

state: Heilongjiang Province

address: No. 5 Xinfeng Road, Longfeng District

institute: Heilongjiang Bayi Agricultural University

summary: To reveal the involvement of OsERF096 in response to cold stress, this study performed transcriptome sequencing of WT, OsERF096-OX and OsERF096-RNAi rice before and after cold stress.Based on transcriptome sequencing, this study found that OsERF096 is involved in the regulation of hormone signal transduction.

overall_design: mRNA profiles of WT, OsERF096-OX and OsERF096-RNAi in untreated and 4℃ treated for 12h

first: Mingzhe

last: Sun

last: Shen

first: Yue

last: Chen

first: Xiaoli


title: Change of gene expression for elemene in RBE

city: shanghai

first: yating

last: pan

address: 725 Wanping South Road, Xuhui District, Shanghai

institute: Longhua Hospital

summary: We used cDNA Microarray technology to identify genes to determine changes in gene expression in RBE at 0, 24, and 48 h after elemene induction. It provides some scientific basis for the follow-up experiment and clinical application.

overall_design: Elemene induced gene expression in RBE was measured at 0, 24 and 48 hours after exposure to elemene. Three independent experiments were performed at each time using different donors for each experiment.

first: Guanzhen

last: Yu

first: Yating

last: Pan


title: Integrative and Quantitative Analysis of Tumor Progression Reveals Fundamental Properties of Glioblastoma

status: Public on Feb 02 2022

city: Heidelberg

first: Haikun

last: Liu

address: Im Neuenheimer Feld 581

department: Molecular Neurogenetics

country: Germany

institute: Deutsches Krebsforschungszentrum

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The principle of tumor growth is one of the most fundamental aspects in cancer biology and it remains to be superficially understood. Here we developed a set of genetic and mathematical tools for integrative analysis of mouse glioblastoma (GBM) progression. Quantitative temporal imaging of mouse GBM and mathematical modeling suggest that mouse GBM grows exponentially, which led to the discovery that a sustainable exponential growth requires outward migrating brain tumor stem cells (BTSCs). Quantitative single cell tracing of BTSCs in vivo unravels symmetric expansion of BTSCs, asymmetric differentiation, and a non-reversible differentiation process during tumor progression. Mosaic tracing of BTSCs and non-BTSCs reveals cellular dynamic changes and turnover. These experimentally collected parameters were integrated step by step to a quantitative mathematical model of GBM growth, which faithfully predicts tumor cellular architecture, tumor response to chemotherapy and BTSC therapy. Bulk and single cell RNA-Seq reveals distinct molecular hierarchy and molecular heterogeneity in BTSCs, which was confirmed by analyzing human GBM single-cell RNA-Seq results. This study reveals fundamental developmental principles that govern tumor growth, which provides insights into understanding cancer development, tumor heterogeneity and GBM therapy.

overall_design: We performed Tlx and H3K27ac Chip-seq experiments in Neural stem cells and Brain tumour stem cells cultures.

first: Chunxuan

last: Shao


title: mRNA expression profile in the fluvalinate exposed Apis mellifera ligustica brain tissue

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

summary: A.mellifera ligustica with similar group potential and randomly divided them into two sets (3 replicates in each group). One set as control groups, and the other set as test groups. The test groups were exposed to fluvalinate at a normal dosage for administration to honeybees (according to the instructions for use of the medicine, mite treatment was added every 7 days). The sequencing is performed by the Illumina HiSeq TM 4000.

overall_design: A.mellifera ligustica  brain tissue mRNA  profiles  of before, 10 days after, 20 days after and 30 days after fluvalinate exposure

first: Fan

last: yunhan

first: Wang

last: Guizhi


title: RNA expression data of Tn/mem-iPSC derived T/ CAR T cells,  PBMC derived T/CAR T cells, PBMC derived NK cells and Tn/mem-iPSC cells

city: Duarte

first: wei

last: chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

country: USA

institute: City of Hope National Medical Center

summary: T and CAR T cells were generated from mock or CD19CAR+ Tn/mem-derived induced pluripotent stem cells (Tn/mem-iPS) by 3D-organoid culture system. We performed RNA deep sequencing analysis to better elucidate their phenotype and compare their gene expression profiles among groups of Tn/mem-iPSC derived T/ CAR T cells,  PBMC derived T/CAR T cells, PBMC derived NK cells and T-iPSC cells, as well as CD4 and CD8 subsets of iPSC derived or PBMC derived CAR T cells.

overall_design: RNA was extracted with the Quick-RNA Microprep kit (Zymo Research) and treated with DNase I. RNA deep sequencing was performed by the City of Hope Integrative Genomics Core Facility. Briefly, stranded RNA-seq libraries were prepared using the KAPA mRNA HyperPrep kit (Roche), according to the manufacturer’s recommended protocol. Libraries were quantified using Qubit quantification kit (Thermofisher Scientific) and loaded onto the HiSeq 2500 sequencing platform (Illumina) for single-end 51-bp sequencing. Base calling was done using Illumina Real Time Analysis (RTA) v1.18.64.

first: Christine

last: Brown

first: Zhiqiang

last: Wang


title: Lactate treatment regulates transcriptome of mouse embryonic stem cells (mESCs)

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

summary: We treated mESCs with 50mM lactate to examine its impact on mESC transcriptome. Interestingly, we found that lactate supplementation activated both germline genes and cleavage embryo genes, indicating that lactate supplementation expands transcriptional network in mouse ESCs.

overall_design: We treated mESCs with 50mM lactate, and produced libraries to identify changes of transcriptome.

first: Qing

last: Tian


title: Sex differences in the developmental patterns of the cortical astroglial cell translatome

city: New Haven

first: Gianfilippo

last: Coppola

state: CT

address: 333 Cedar st

department: Pathology

institute: Yale University

summary: Employing translating ribosome affinity purification with RNA sequencing (TRAPseq) on cortical tissue to isolate astroglial-specific translatome from Aldh1l1-L10-GFP mice and examine sex (male + female) and age (postnatal days 1, 4, 7, 14, 35; adults (9 weeks)) dependent changes in the astroglial translatome.

overall_design: Cortical lysate (N=53 independent samples) from male and female Aldh1l1-GFP reporter mice (C57BL/6 background strain) at 6 different postnatal time points was used for translating ribosome affinity purification (TRAP) to extract actively transcribed RNA and then used with Illumina Hi-Seq RNA sequencing. Four of the samples (P7 Female 10, P7 Female 6, P7 Male 2, P7 Male 6) were sequenced twice.

first: Gareth

middle: M

last: Rurak

first: Stephanie

last: Simard

first: Moises

last: Freitas-Andrade

first: Baptiste

last: Lacoste

first: François

last: Charih

first: Amanda

last: VanGeel

first: John

last: Stead

first: Barbara

last: Woodside

first: James

middle: R

last: Green

first: Natalina

last: Salmaso


title: Lactate treatment regulates epigenome of mouse embryonic stem cells (mESCs)

summary: We treated mESCs with 50mM lactate to examine its impact on mESC epigenome. Interestingly, we found that lactate supplementation stimulated H3K18 lactylation accumulation on a subset of genes, which in turn promoted transcriptional elongation. Our results indicate that lactate supplementation expands transcriptional network of mouse ESCs.

overall_design: We treated mESCs with lactate, and produced libraries to identify changes of epigenome.


title: CITE-Seq analysis of total PBMC pre- and post-PfSPZ vaccination in the IMRAS trial

city: Seattle

first: Raphael

last: Gottardo

state: WA

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutch

summary: Immunization with radiation-attenuated sporozoites (RAS) can confer sterilizing protection against malaria, although the mechanisms behind this protection are incompletely understood. We performed a systems biology analysis of samples from the Immunization by Mosquito with Radiation Attenuated Sporozoites IMRAS) trial, which comprised P. falciparum RAS-immunized (PfRAS), malaria-naive participants whose protection from malaria infection was subsequently assessed by controlled human malaria infection (CHMI). Blood samples collected after initial PfRAS immunization were analyzed to compare immune responses between protected and non-protected volunteers leveraging integrative analysis of whole blood RNA-seq, high parameter flow cytometry, and single cell CITE-seq of PBMCs.

overall_design: We performed CITE-seq with a panel of 14 antibodies using PBMC samples collected on day 0, day 3 and day 14 after the priming dose of PfSPZ from an IMRAS subject who dropped out of the trial. We obtained single cell RNA seq gene expression and surface protein marker profile data from a total of 12,442 cells.

first: Suzanne

last: McDermott

first: Nina

last: Hertoghs

first: Ying

last: Du

first: Ken

last: Stuart


title: Gastrointestinal B-cells license metabolic T-cell activation in NASH microbiota anigen-independently and contribute to fibrosis by IgA-FcRy signalling

city: Edinburgh

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

summary: Non-alcoholic steatohepatitis (NASH) is a T-cell mediated, auto-aggressive condition that can result in progressive liver disease and hepatocellular carcinoma. Gastrointestinal B-cells are activated and increased in number in mouse and human NASH, licensing metabolic-cell activation to induce NASH antigen- and microbiota-independently. Genetic or therapeutic depletion of B-cells systemically or gastrointestinal B-cells specifically prevented or reverted NASH and fibrosis. Clinical and molecular analyses from NASH patients demonstrated IgA-levels and activated FcRy+ hepatic myeloid cells to correlate with liver fibrosis degree.

overall_design: Single, live cells were isolated from a NAFLD liver explant and FACS-sorted for CD45+ cells, taking a 70-30 HLADR- to HLADR+ split to correct for lymphocyte preponderance.

first: Sebastian

last: Wallace

first: Ross

last: Dobie

first: Neil

middle: C

last: Henderson


title: Transcriptomic profiling of KLB expressing cells in the basolateral amygdala

city: Iowa City

first: Kyle

middle: Harrington

last: Flippo

state: IA

address: 169 Newton Road, 3320 PBDB

department: Neuroscience and Pharmacology

institute: University of Iowa

summary: KLB-Cre mice were crossed to Ai14 mice to label KLB-expressing cells with tdTomato. The basolateral amygdala was then dissected out and tdTomato positive cells were isolated using FACs sorting. FACs sorted cells were then captured for single cell RNA sequencing analysis using the BD Rhapsody Whole Transcriptome Analysis kit.

overall_design: Prior to tissue isolation three mice were treated with vehicle and 3 mice were treated with FGF21 (1mg/kg) for three days (once/day).

middle: H

first: Matthew

middle: J

last: Potthoff


title: A distinct brain-β-cell circuit regulates insulin secretion

city: Bethesda

first: Youngjae

last: Bahn

state: Maryland

address: 10 Center Dr.

institute: NIH

summary: Hypothalamic neurons are multisynaptically connected to pancreatic islet β-cells.

overall_design:
Expression profiling by RNA-Seq in PVNOXT neurons by injecting with AAV-DJ-CMV-DIO-eGFP-2A-TeNT virus (PVNOXT:TeNT mice) or with AAV5-EF1a-DIO-EYFP-WPRE-pA virus (PVNOXT:GFP mice)
Total RNA was extracted from isolated mouse pancreatic islet cells.

first: Papazoglou

last: Ioannis

first: Young

first: Sushil

middle: G

last: Rane


title: An overlooked subset of Cx3cr1wt/wt microglia in the Cx3cr1CreER-Eyfp/wt mouse has a repopulation advantage over Cx3cr1CreER-Eyfp/wt microglia following microglial depletion

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

summary: Cx3cr1CreER-Eyfp/wt mice contain a subset of microglia lacking Cre and EYFP expression. These microglial escape Cre-mediated recombination and gain a repopulation advantage following Cre-driven DTA-mediated microglial depletion.

overall_design: Identify microglia do not carry genetic labels in the widely used Cx3cr1GFP/wt or Cx3cr1CreER-EYFP/wt mouse models

first: Kai

last: Zhou

first: Nageswara

first: Klas

last: Blomgren


title: Multi-omics analyses reveal early metabolic imbalance and mitochondrial stress in neonatal photoreceptors leading to cell death in Pde6b rd1/rd1 mouse model of retinal degeneration

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

summary: Retinal diseases exhibit extensive genetic heterogeneity and complex etiology with varying onset and severity. Mutations in over 200 genes can lead to photoreceptor dysfunction and/or cell death in retinal neurodegeneration. To deduce molecular pathways that initiate and/or drive cell death, we adopted a temporal multi-omics approach and examined molecular and cellular events in newborn and developing photoreceptors before the onset of degeneration in a widely-used Pde6brd1/rd1 (rd1) mouse, a model of autosomal recessive retinitis pigmentosa caused by PDE6B mutations. Transcriptome profiling of neonatal and developing rods from the rd1 retina revealed early downregulation of genes associated with anabolic pathways and energy metabolism. Quantitative proteomics of rd1 retina showed early changes in calcium signaling and oxidative phosphorylation, with specific partial bypass of complex I electron transfer, which precede the onset of cell death. Concurrently, we detected alterations in central carbon metabolism, including dysregulation of components associated with glycolysis, pentose phosphate and purine biosynthesis. Ex vivo assays of oxygen consumption and transmission electron microscopy validated early and progressive mitochondrial stress and abnormalities in mitochondrial structure and function of rd1 rods. These data uncover mitochondrial over-activation and related metabolic alterations as determinants of early pathology and implicate aberrant calcium signaling as an initiator of higher mitochondrial stress. Our studies thus provide a mechanistic framework with mitochondrial damage and metabolic disruptions as early drivers of photoreceptor cell death in retinal degeneration.

overall_design: We generated rd1-GFP mice by mating the Pde6brd1/rd1 mice to TgNrlp-EGFP (WT) (Akimoto et al., 2006) mice, used flow cytometry to purify GFP+ rods at P2, P4, P6, P8 and P10 and performed RNA-seq analysis. Isolated cells were lysis with TRIzol LS and the total RNA were isolated. RNAseq data were generated using TruSeq Stranded mRNA Sample Prep Kit (Illumina) and 125 base pair-end reads were generated on HiSeq 2500 platform (Illumina).

first: Ke

last: Jiang

first: Anupam

middle: K

last: Mondal

first: Yogita

last: Adlakha

first: Jessica

last: Gumerson

first: Angel

last: Aponte

first: Linn

last: Gieser

first: Jung-Woong

last: Kim

first: Alexis

last: Boleda

first: Jacob

last: Nellissery

first: Donald

middle: A

last: Fox

first: Robert

last: Balaban

first: Raul

last: Covian

first: Anand

last: Swaroop


title: Spatial, temporal and molecular dynamics of swine influenza virus-specific CD8 tissue resident memory cells

city: Woking

first: Veonica

last: Martini

state: Scotland

address: Ash Road, Pirbright

institute: The Pirbright Institute

summary: We have defined naïve, central memory, effector memory and terminally differentiated porcine CD8 T cells, using CD45RA and CCR7 mAbs. We analyzed the phenotype of CD8 T cells specific for three influenza nucleoprotein (NP) epitopes using tetramers after influenza infection or immunization in lymphoid and respiratory tissues. The hierarchy of response to the three epitopes changes during the response in different tissues.  Most NP-specific CD8 T cells in broncho-alveolar lavage (BAL) and lung are tissue resident memory cells (TRM), that express CD69 and have an effector memory or terminally differentiated phenotype. NP-specific cells isolated from BAL express genes characteristic of TRM, but gene expression differs at 7, 21 and 63 days post infection. The frequency of NP-specific cells declines over 63 days in all tissues but is best maintained in BAL. The pig is a powerful model for understanding how best to induce and harness local immunity.

overall_design: RNA-seq of influenza specific FAC-sorted T cells

first: Veronica

first: Siddharth

last: Jayaraman

first: Timothy

last: Connelley

first: Elma

last: Tchilian


title: single cell RNA Sequencing of antral follicle cells from xenografted ovarian tissue

city: New York

first: Daylon

last: James

address: 515 East 71st

institute: Weill Cornell Medicine

summary: We isolated cells from antral follicles that grew in the context of superphysiologic AMH and subjected them to 10x Chromium single cell sequencing

overall_design: Sequencing libraries prepared from cell populations that were prospectively isolated from antral follicles grown in xenografts co-transplantation of control or AMH-expressing endothelial cells


title: Large-scale analysis of longitudinal skin gene expression in systemic sclerosis reveals relationships of immune cell and fibroblast activity with skin thickness and a trend towards normalization over time

city: Houston

first: Shervin

last: Assassi

state: TX

address: 6431 Fannin

department: Division of Rheumatology

institute: The University of Texas Health Science Center at Houston

summary:
339 total forearm skin biopsies were obtained from 113 unique SSc patients and 44 matched healthy controls.  105 SSc patients had a 2nd biopsy, 76 patients had a 3rd biopsy, and 1 patient had a 4th biopsy.  Global gene expression profiling was performed, and differentially expressed genes and cell type-specific signatures in SSc were evaluated for relationships to skin thickness and other clinical variables.  Changes in skin gene expression over time were analyzed by mixed effects models and principal component analysis.  Immunohistochemical staining was performed to validate conclusions.
Skin thickness in SSc is related to dysregulated immune cell and fibroblast gene expression.  Skin gene expression changes over time in early diffuse SSc, with a tendency towards normalization.

overall_design: 339 total forearm skin biopsies were obtained from 113 unique SSc patients and 44 matched healthy controls.  105 SSc patients had a 2nd biopsy, 76 patients had a 3rd biopsy, and 1 patient had a 4th biopsy.  Global gene expression profiling was performed.

first: Brian

last: Skaug

first: Marka

last: Lyons

first: William

last: Swindell

first: Gloria

last: Salazar

first: Minghua

last: Wu

first: Tuan

last: Tran

first: Julio

last: Charles

first: Connor

middle: P

last: Vershel

first: Maureen

middle: D

last: Mayes


title: Argonaute protein binding Met-tRNAiMet represses translation initiation

city: beijing

first: Sun

last: Xianhui

state: 北京

address: No 15 Datun Road, Chaoyang District, Beijing

institute: institute of biophysics,chinese academy of sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Initiation factor 2 (eIF2) delivering the initiator methionine transfer RNA (Met-tRNAiMet) to the ribosome is a conserved key step in translation initiation. Argonaute (Ago) proteins were initially identified as eukaryotic translation initiation factor 2C,2 (EIF2C2). In the past 2 decades, Argonaute were extensively studied as a core component of RNA induced gene silencing, although various model raised the exact mechanism of Ago in translation repression remains elusive. Here we found Ago protein directly bind Met- tRNAiMet independent of miRNA binding, which interfere the formation of the ternary complex eIF2–GTP–Met- tRNAiMet. Ago proteins can solely inhibit protein synthesis via competing tRNAiMet with eIF2. Our findings elucidate a physical link between Ago and tRNAiMet and provide mechanistic insight into translation repression by Ago proteins.

overall_design: RNA interactome of Ago2 in light ribonucleoprotein or polysome fractions of sucrose gradient

first: Zhao

last: Qian

first: Zhang

last: Xiaorong


title: Distinct sub-cellular autophagy impairments occur independently of protein aggregation in aged induced neurons from patients with Huntington’s disease

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

institute: Lund University

type: Methylation profiling by genome tiling array

summary:
Huntington’s disease (HD) is an inherited neurodegenerative disorder caused by CAG expansions in the huntingtin (HTT) gene. Modelling HD in the lab has proven challenging as rodent models poorly reproduce the disease process and cellular models fail to include age-dependent processes crucial to the disease. Here we generated induced neurons (iNs) that retained age-dependent epigenetic characteristics of the donors through direct reprogramming of skin fibroblasts.
HD-iNs displayed a transcriptionally regulated, distinct neurite specific alteration in autophagy, characterized by reduced transport of late autophagic structures and subsequent cargo degradation. In addition, HD-iNs displayed shorter, smaller and fewer neurites. CRISPRi-mediated silencing of both HTT alleles did not rescue the morphology nor the autophagic defect in HD-iNs. Strikingly, it resulted in additional autophagy alterations when done using ctrl-iNs, highlighting the importance of wt HTT in neuronal autophagy. In summary, our results have identified a distinct subcellular autophagy impairment in aged patient derived HD-neurons. In addition, we have shown a role for normal wt HTT in autophagy. Together this work provides a new rational for future development of autophagy activation therapies while also highlighting problems that may arise using non allele specific HTT silencing approaches, some of which are now in clinical trials.

overall_design: Examination of DNA methylation of directly reprogrammed induced neurons from healthy donors and Huntington’s disease patients.

first: Karolina

last: Pircs

first: Janelle

last: Drouin-Ouellet

first: Jeovanis

last: Valdés

first: Melinda

last: Rezeli

first: Daniela

last: Grassi

first: Raquel

last: Garza

first: Yogita

last: Sharma

first: Isabelle

last: St-Amour

first: Marie

middle: E

last: Jönsson

first: Pia

last: Johansson

first: Kate

last: Harris

first: Romina

last: Vuono

first: Tom

last: Stoker

first: Bob

last: Hersbach

first: Kritika

first: Jessica

last: Lagerwall

first: Stina

last: Lagerström

first: Vivien

last: Horváth

first: Elena

last: Cattaneo

first: Sébastien

middle: S

last: Hébert

first: György

last: Marko-Varga

first: Malin

last: Parmar

first: Roger

last: Barker

first: Johan

last: Jakobsson


title: Comparative expression analysis of the Arabidopsis karrikin up regulated F-box 1 (kuf1) under dehydration conditions

city: Kaifeng

first: Weiqiang

last: Li

state: China

address: No.85 Minglun Street

department: School of Life Sciences

institute: Henan University

summary: To understand the role of KUF1 in water stress response, we have carried out comparative expression analysis of the kuf1-1 mutant and WT plants under dehydration and well-watered (control) conditions. Aligent’s whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Two-week-old WT and kuf1-1 mutant plants were transferred from GM plates to soil and grown for 10 additional day. The aerial parts of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 4 h. All rosette leaves of independent 24-d-old plants were collected. Total RNA was prepared and used for the microarray hybridization. Three independent biological replicates were used for each plant sample.

first: Cuong

last: Tran

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Lam-Son


title: Glucose regulates cotton fiber elongation by interacting with brassinosteroid

city: Zhengzhou

first: Xinyang

address: Science Avenue

institute: Institute of Cotton Research, Chinese Academy of Agricultural Sciences

summary: Our study provides evidence for the mechanism of Glc regulation of cotton fiber elongation, indicating that Glc not only serves as a nutrient, but also serves as a signal to regulate cotton fiber elongation. We also provided evidence that there is crosstalk between Glc and BR, and that the BR signal is located downstream of the Glc signal in the regulation of cotton fiber elongation

overall_design: The ovule mRNAs were cultured with glucose of 50 mM, 150 mM and 300 mM for five days.

first: Xiongfeng

last: Ma

first: Daigang

last: Yang

first: Wei


title: Novel Peripheral Blood Allergen Stimulation Test for Non-IgE-mediated Gastrointestinal Food Allergies in Neonates and Infants.

city: Maebashi

first: Yag

last: Hisako

address: 3-39-22 Showa-machi

country: Japan

institute: Department of Pediatrics, Gunma University Graduate School of Medicine

summary:
The lymphocyte stimulation test (LST) helps with the diagnosis of non-IgE-mediated gastrointestinal food allergies. However, The LST requires large volumes of fresh peripheral blood and long culture times.The purpose of this study was to develop a novel LST. we obtained whole blood from patients with non-IgE-GI-FAs to cow’s milk and disease control children. And, we stimulated it with α-casein and Pmix, which is a mixture of four milk protein components (α-casein, κ-casein, α-lactalbumin, or β-lactoglobulin for 24 hours.   Then we analyzed genome-wide gene expression using microarray and selected up- or down-regulated genes
Nine putative marker genes, including those known to be involved in allergic inflammation, such as IL2RA, CCL17 and CISH were specific to patient group after stimulation with α-casein. On the other hand, 232 marker genes were specific to patient group after stimulation with Pmix.

overall_design: Whole blood samples from  non-IgE-mediated gastrointestinal food allergie patients and disease control children were stimulated with α-casein and Pmix for 24 hours and subjected to genome-wide gene expression profiling analysis using microarray chips.

first: Hisako

last: Yagi

first: Takumi

last: Takizawa


title: RNA Seq analysis of E9.5 embryonic vagal regions in Rdh10 mutants of mouse

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: The enteric nervous system (ENS) is formed from vagal neural crest cells (NCC), which generate the neurons and glia that regulate gastrointestinal function. Defects in the migration, colonization or differentiation of NCC in the gut can result in gastrointestinal disorders such as Hirschsprung disease (HSCR). Although mutations in many genes have been associated with the etiology of HSCR, a significant proportion of affected individuals have an unknown genetic diagnosis. Therefore, it’s important to identify new genes, modifiers and environmental factors that regulate ENS development and HSCR. We discovered that retinol dehydrogenase 10 (Rdh10) loss-of-function mouse embryos exhibit total intestinal aganglionosis, the most severe form of HSCR. Rdh10 catalyzes the first oxidative step in the metabolism of vitamin A to its active metabolite, RA, and is therefore a central regulator of vitamin A metabolism and retinoic acid (RA) synthesis during embryogenesis. Rdh10 is highly expressed in the mesenchyme surrounding the entrance to the foregut and we demonstrate that paracrine retinoid signaling is essential between E7.5-E9.5 for NCC entry into the gut. Vagal NCC form and migrate in Rdh10 mutant embryos but fail to enter the foregut. Comparative RNA-sequencing revealed Ret-Gdnf-Gfra1-signaling which is critical for vagal NCC chemotaxis is downregulated in Rdh10 mutants and furthermore that the composition of the extracellular matrix through which NCC migrate is altered, particularly by increased collagen deposition. Collectively this restricts NCC entry into the gut, demonstrating that Rdh10-mediated vitamin A metabolism and RA signaling pleiotropically regulates the NCC microenvironment during ENS formation and in the pathogenesis of HSCR.

overall_design: The vagal (somite 1-7) regions of Rdh10 mutant or wt E9.5 mouse embryos were isolated in quadruplicate and compared for gene expression using RNA Seq.

first: Paul

last: Trainor

first: Naomi

last: Tjaden


title: Next Generation RNA Sequencing of LSD1 knockdown samples in human osteoclast differentiation.

city: Kyoto

first: Kohei

last: Doi

state: Kyoto

address: 54, Kawahara-cho, Shogoin, Sakyo-ku

department: Orthopaedics

institute: Kyoto University

summary: Human CD14-positive monocytes were nucleofected with scrambled control or LSD1-specific siRNAs, and cultured with M-CSF (20 ng/ml) and RANKL (40 ng/ml) stimulation for 0, 24, or 48 hours.

overall_design: mRNA were obtained from two independent donors.

first: Koichi

last: Murata


title: RNA Seq analysis of GCNF mutant and wt in anterior and posterior cranial regions of E9.25 embryos in Mus musculus

summary: Neural crest cells are migratory progenitor cells that contribute to nearly all tissues and organs throughout the body. Their formation, migration and differentiation are regulated by a multitude of signaling pathways, that when disrupted can lead to disorders termed neurocristopathies. While work in avian and amphibian species has revealed essential factors governing the specification and induction of neural crest cells during gastrulation and neurulation in non-mammalian species, their functions do not appear to be conserved in mice, leaving major gaps in our understanding of neural crest cell formation in mammals. Here we describe Germ Cell Nuclear Factor (GCNF/Nr6a1), an orphan nuclear receptor, as a critical regulator of neural crest cell formation in mice. Gcnf null mutant mice, exhibit a major disruption of neural crest cell formation. The purpose of this experiment is to examine gene expression changes in response to Gcnf mutation in anterior and posterior cranial regions of E9.25 mouse embryos.

overall_design: Mouse embryos were collected at E9.25 corresponding to 9-11 somite stage separating the cranial regions (1st pharyngeal arch and anterior) and posterior regions (2nd pharyngeal arch and posterior) for comparison of gene expression between homozygous GCNF mutant and wt.

first: Annita

last: Achilleos


title: Expression data of sham and p21-overexpressed MLE-12 cells

city: Beijing

first: Chang

last: Liu

address: 1 Xian Nong Tan Street, Xicheng District

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: We report that p21 expression was increased in the alveolar epithelial type 2 cells (AEC2s) in a time dependent manner following multiple bleomycin induced pulmonary fibrosis (PF). The AEC2s with the elevated expression of p21 exhibited cell senescence and lost the ability of self-renewal and differentiation. Evaluation of mRNA profiles in sham and p21-adenovirus treated MLE-12 cells is helpful to analyze the changes of lung alveolar epithelial cells after p21 deposition.

overall_design: we treated MLE-12 cells with the  p21-overexpressed and control adenovirus in triplicates. The stably transfected cells were collected for RNA extraction.

first: Xiao-xi

last: Lv


title: The developmental impacts of natural selection on human pelvic morphology

city: Cambridge

first: Mariel

last: Young

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

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

overall_design: Refer to individual Series


title: The developmental impacts of natural selection on human pelvic morphology [RNA-seq]

summary: We investigate the genetic architecture of pelvis development at the regulatory and transcriptomic level.

overall_design: Examination of open chromatin regions (ATAC-seq) and differentially expressed genes (RNA-seq) in the developing pelvis.

first: Terence

last: Capellini

first: Daniel

last: Richard

first: Pushpanathan

last: Muthuirulan


title: γδT cell Interactions within the Tissue Ecosystem Network [bulk RNAseq]

city: London

first: Miguel

last: Muñoz-Ruiz

address: 1 Midland Rd, Somers Town

institute: The Francis Crick institute

summary: Numerous lymphocytes seed the body surfaces of metazoans promoting tissue protection and integrity. These tissue-resident populations differ substantially from circulating lymphocytes, as they adopt a unique phenotype and do not recirculate. They span the innate-adaptive continuum, ranging from innate lymphoid cells (ILCs) to unconventional T cells (NKT, MAIT, γδT cells and IELs) and tissue-resident memory (TRM) T cells, and while differ in the particulars of their biology, all contribute to barrier immunity, tissue homeostasis, and immune regulation. Although they share the same microenvironment, little is known about how these tissue-resident lymphocyte populations interact with each other and with the non-lymphoid cellular environment. As such, there is an emerging view of tissues as varied ‘‘ ecosystems ’’, whereby protection against inflammatory challenges is orchestrated through the interplay between tissue-resident and infiltrating-lymphocyte subtypes. In mice, barrier tissues are populated during early life by innate-like γδT lymphocytes. These cells provide tissue protection, including limiting conventional T cell-driven inflammation. Therefore, elucidating the contributions of tissue-resident T cells, particularly γδT cells, to the basic pathophysiology of tissue function and protection against infection, inflammation, and cancer is a priority. To this aim, we have induced allergic contact dermatitis in the back skin of different strains and we analyzed the behavior of γδT cells

overall_design: Examination of  γδT cells in challenged and unchallanged mice in WT and IFNgRIKO

first: Adrian

last: Hayday


title: Tissue-resident memory T cells (TRM) Interactions within the Tissue Ecosystem Network


title: Tissue-resident memory T cells (TRM) Interactions within the Tissue Ecosystem Network [scRNA-seq]

summary: We aim to understand here, the influence of TCR-Vγ5+ γδT cells in the recruitment of TRM population. Along these lines we will analyse the populations of TRM recruited to the Skin after the challenge process (induction of allergic contact dermatitis), in the presence of TCR-Vγ5+ or TCR-Vγ5− (replacement population).

overall_design: Examination of  TRM in challenged in WT and FVB/NTac (FVB.Tac) mice carrying a mutation in Skint1 gene.


title: Macrophage Scavenger Receptor 1 mediates lipid-induced inflammation in non-alcoholic fatty liver disease

city: Newcastle upon Tyne

first: Olivier

last: Govaere

address: Framlington Place

institute: Newcastle University

summary: In this study, we explored the role of macrophage scavenger receptor 1 (MSR1) in the progression of non-alcoholic fatty liver disease. Mice lacking Msr1 proved to be protected against high fat-cholesterol diet (HFD)-induced metabolic disorder, showing fewer hepatic lipid-laden foamy macrophages, less hepatic inflammation and changed lipid metabolism.

overall_design: To understand the role of Msr1 during NAFLD, 5 male Msr1-/- and 4 male Wt mice were fed a high fat-cholesterol diet (HFD) for 16 weeks.


title: BRD4-directed Super-enhancer Organization of Transcription Repression Programs Links to Chemotherapeutic Efficacy in Breast Cancer

first: Beibei

address: NO. 10 Xitoutiao Road

institute: Capital Medical University

summary: BRD4 is well known for its role in super-enhancer organization and transcription activation of several prominent oncogenes including c-MYC and BCL2. As such, BRD4 inhibitors have being pursued as promising therapeutics for cancer treatment. However, drug resistance also occurs for BRD4-targeted therapies. Here we report that BRD4, unexpectedly, interacts with the LSD1/NuRD complex and co-localizes with this repressive complex on super-enhancers. Integrative genomic and epigenomic analyses indicate that the BRD4/LSD1/NuRD complex restricts the hyperactivation of a cluster of genes that are functionally linked to drug resistance. Intriguingly, treatment of breast cancer cells with a small molecule inhibitor of BRD4, JQ1, results in no immediate activation of the drug-resistant genes, but long-time treatment or destabilization of LSD1 by PELI1 decommissions the BRD4/LSD1/NuRD complex, leading to resistance to JQ1 as well as to a broad spectrum of therapeutic compounds. Consistently, PELI1 is up-regulated in breast carcinomas, its level is negatively correlated with that of LSD1, and the expression level of the BRD4/LSD1/NuRD complex-restricted genes is strongly correlated with a worse overall survival of breast cancer patients. Together, our study uncovers a functional duality of BRD4 in super-enhancer organization of transcription activation and repression linking to oncogenesis and chemoresistance, respectively, supporting the pursuit of a combined targeting of BRD4 and PELI1 in effective treatment of breast cancer.

overall_design: RNA-seq and ChIP-seq was used for the analysis of genes influenced by BRD4 and genome-wide binding signals of specific proteins.

first: Xinhua

first: Yongfeng

last: Shang


title: Gene expression profiling of Fischer rat thyroid (FRT) cells

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: The purpose of the study was to define the global expression profile of FRT cells, with a particular focus on genes involved in ion transport

overall_design: Total RNA was extracted from four separate preparations of FRT cells

first: R


title: Maternal cadmium exposure during pregnancy changes DNA methylation patterns in adult F1 rats ovarian granulosa cells.

city: Fuzhou

first: Lingfeng

last: Zeng

address: No. 1 Xuefu North Road, University Town

institute: Fujian Medical University

summary: Cadmium is a heavy metal pollutant and environmental endocrine disruptor. Studies have shown that cadmium exposure, whether it occurs in adulthood, in puberty or during the period from weaning to sexual maturity, can produce notable toxic effects on ovarian cells, especially ovarian granulosa cells. However, the effects of prenatal cadmium exposure on the morphology, function and its epigenetic mechanism of ovarian granulosa cells in offspring during adulthood have not been reported.In this study,the promoter methylation was assessed using MeDIP-Chip and Several methods were used to analyze the scanned genes, including the Gene Ontology Consortium tools, hierarchical clustering and KEGG pathway analysis.The results indicated that multiple signaling pathways, including apoptosis and hormone synthesis related pathways were affected,besides, some genes DNA methylation status of apoptosis and hormone synthesis pathways were changed.In summary, our results provide a scientific basis for subsequent analyses of cadmium-induced ovarian granulosa cell damage and its epigenetic mechanism.

overall_design: Pregnant rats in the control group (0mg/kg) received water by gavage and in the experimental groups received cadmium chloride solution (8.0mg/kg body weight) by gavage during gestation periods (from gestation day 1 to 21). At postnatal day 56, vaginal smears were conducted to evaluate the stage of the estrous cycle, all female offspring were sacrificed after anesthesia and and ovarian granulosa cells were isolated from the F1 SD rats.The DNA samples from the ovarian granulosa cells in the control and 8.0mg/kg CdCl2 groups were sequenced,three biological replicates were sequenced for each group.

first: Wenchang

last: Zhang


title: Cohesin Regulates 3D Accessible Genome Organization and Function

city: Berkeley

first: Robert

last: Tjian

address: LKS

institute: UC Berkeley/HHMI

summary: we combined Assay for Transposase-Accessible Chromatin and lattice light-sheet PALM microscopy (3D ATAC-PALM) to selectively image key features of the 3D accessible genome in single cells. We found that accessible chromatin domains (ACDs) form spatially segregated clusters in the nucleus. Rapid depletion of CTCF or Cohesin (RAD21 subunit) induced extensive 3D spatial mixing of ACD clusters and reduced physical separation between ACDs within chromosomes. Experimental perturbations and modeling suggest that both weak, multivalent, dynamic protein-protein interactions together with loop extrusion influence ACD organization. Live-cell studies suggest that ACD clustering regulates transcription factor binding site distribution, target search kinetics and binding dynamics. Here we report the ATAC-seq results from Tn5 PA549 and nextera Tn5 upon various chemical and genetic perturbations.

overall_design: Examine accessible chromatin landscape in mouse embryonic stem cells under a variety of chemical/genetic purturbations. We performed at least two biological replicates for each condition.

first: Liangqi

last: Xie


title: Regulation of retinal development by a Casz1 chromatin remodelling complex

city: Ottawa

first: Pierre

last: Mattar

state: ON

address: CCW6109, Box 511, 501 Smyth Rd.

country: Canada

institute: OHRI

summary: Analysis of chromatin accessibility and histone marks on control or Casz1 conditional mutant retinal cells

overall_design: Control or Casz1 conditional mutant retinal cells

first: Christine

last: Jolicoeur

first: Michel

last: Cayouette


title: The genomic landscape of colitis-associated colorectal carcinomas is dominated by TP53 mutations, aneuploidy and gains of chromosome arm 5p

city: Bethesda

first: Daniela

last: Hirsch

address: 50 South Drive

department: National Cancer Institute

institute: National Institutes of Health

type: Genome variation profiling by genome tiling array

summary: Ulcerative colitis associated colorectal tumors were characterized by array-based comparative genomic hybridization to elucidate chromosomal aneuploidy patterns.

overall_design: n = 23 tumors

first: Timo

last: Gaiser


title: Identification of exosomal miRNAs specifically derived from intrafollicular cells involved in polycystic ovary syndrome

first: Chenchen

last: Cui

state: Henan

address: Weiwu Road #7

department: Department of Reproductive Medicine Center

institute: Henan Provincial People’s Hospital

summary:
Exosomes have recently been shown to play a key role in cell-to-cell communication through delivery of various functional content, including microRNAs (miRNAs). We investigated the potential roles of exosomal miRNA derived intrafollicular cells in polycystic ovary syndrome (PCOS). Using microarray profiling, a total of 492 miRNAs and 220 miRNAs were found in follicular fluid-derived exosomes and serum-derived exosomes, respectively, in PCOS and non-PCOS females. By excluding miRNAs existing in serum-derived exosomes, we found 179 miRNAs which were specifically expressed in follicular fluid-derived exosomes both in PCOS and non-PCOS females.
Using microarray profiling, a total of 492 miRNAs and 220 miRNAs were found in follicular fluid-derived exosomes and serum-derived exosomes, respectively, in PCOS and non-PCOS females. By excluding miRNAs existing in serum-derived exosomes, we found 179 miRNAs which were specifically expressed in follicular fluid-derived exosomes both in PCOS and non-PCOS females.

overall_design: Exosomes were isolated from pooled follicular fluid of PCOS and non-PCOS females, respectively. Serum-derived exosomes were isolated from pooled serum of  PCOS and non-PCOS females, respectively. miRNA profiles were generated using microarray. Comparison of miRNAs expression in fluid-derived exosomes and serum-derived exosomes were preformed to identify the exosomal miRNAs specifically derived from intrafollicular cells

first: Jie

last: Wang

first: Cuilian


title: mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana [nuclear fraction]

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

summary: RNA-IP was performed on nuclear fraction of chemically cross linked MTA-GFP and GFP (control) plant tissues followed by sequencing of NGS libraries

overall_design: Immunoprecipitation mediated by anti-GFP antibodies was followed by RNA extraction and NGS library preparation

first: Dawid

last: Bielewicz

first: Artur

last: Jarmolowski


title: miR-21 is critical in stress response and facilitates breast cancer development and metastasis [miRNA array]

city: Philadelphia

first: Anuradha

last: Shastri

state: Pennsylvania

address: 233 S 10th Street

institute: Thomas Jefferson University

summary: miR-21 is upregulated in advanced tumor stages, distal metastasis, and poor survival and in response to cytotoxic stress, but is also known to confer resistance to radiation and chemotherapy. We discovered that global ablation of miR-21 significantly decreased tumorigenesis and metastatic spread of breast cancer, while sensitizing breast carcinomas to cytotoxic agents by evoking Fas/FasL-dependent apoptosis. Targeting miR-21 may represent a novel and efficacious therapeutic modality either alone or in combination with standard oncologic treatments.

overall_design: miRNA microarray analysis was performed on RNA extracted from primary and metastatic tumor samples treated with sham radiation or 10 Gy radiation.

first: Ajay

last: Palagani

first: Tu

last: Dan

first: Simone

last: Buraschi

first: Thomas

last: Neill

first: Jason

last: Savage

first: Aastha

last: Kapoor

first: Tiziana

last: DeAngelis

first: Sankar

last: Addya

first: Kevin

last: Camphausen

first: Renato

last: Iozzo

first: Nicole

middle: L

last: Simone


title: Contribution of Age, Brain Region, Mood Disorder Pathology, and Interindividual Factors on the Methylome of Human Microglia

status: Public on Jan 31 2022

city: New York

first: Fatemeh

last: Haghighi

state: NY

address: 1425 Madison Ave, 9-20D

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Total of 56 microglia samples from postmortem brain tissue of four different brain regions, medial frontal gyrus (MFG), superior temporal gyrus (STG), subventricular zone (SVZ) and thalamus (THA), of 22 donors, encompassing 1 patient with schizophrenia, 13 patients with mood disorder pathology, and 8 control subjects, were isolated and assayed using a genome-wide methylation array to characterize the DNA methylation landscape of human microglia and the factors that contribute to variations in the microglia methylome

overall_design: Genomic DNA from 59 subjects (28 with only pre-blast exposure sample, 31 with both pre- and post- blast exposure samples) was bisulfite converted and CpG methylation determined using Illumina Infinium MethylationEPIC BeadChip microarrays

first: Lot

last: de Witte

first: Zhaoyu


title: Single cell sequencing of Tri-PyMT cells

first: Dingcheng

last: Gao

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

summary:
To study the contribution of epithelial-to-mesenchymal transition (EMT) in tumor metastasis, we established an EMT lineage tracing model in a multiple-transgenic mouse (MMTV-PyMT/Fsp1-Cre/Rosa26mT/mG, Tri-PyMT). In this model, breast tumor cells that underwent EMT would irreversibly switch their expression of the fluorescent marker from RFP+ to GFP+ due to the mesenchymal specific Cre expression. Surprisingly, we found that metastatic tumor cells did not convert from RFP+ to GFP+. Lung metastases were predominantly composed of RFP+ tumor cells persistently exhibiting epithelial phenotypes. These findings challenge the concept that EMT is required for metastasis, and have attracted vigorous discussion about its true contributions to metastasis. One of the major concerns with the EMT lineage tracing model is that expression of GFP only indicates the complete EMT transition. The partial-EMT programming, a novel concept describing tumor cells exhibiting both epithelial and mesenchymal features, could possibly fail to launch the Fsp1-Cre-mediated fluorescent marker switch. To address this concern, we evaluated the EMT status of Tri-PyMT cells on the single cell level by performing single cell RNA-sequencing (scRNA-seq). We found that the expression of epithelial markers (i.e. Epcam and Krt18) and mesenchymal markers (i.e. Vim and S110a4) were largely confined to RFP+ and GFP+ subpopulations, respectively. Based on the differentially expressed EMT related genes, we observed an EMT spectrum in which the low EMT score end was enriched with RFP+ cells, whereas the high EMT score end was enriched with GFP+ cells. Indeed, the fluorescent marker switch in Tri-PyMT cells predicted their EMT status with high specificity and sensitivity.
Tri-PyMT cells which were derived from the primary breast tumor of triple transgenic mouse (MMTV-PyMT:Fsp1-cre:Rosa26mT/mG) were sorted into RFP+ or GFP+  populations by FACS and subjected for Drop-seq analysis.

overall_design: Single cells of RFP+ and GFP+ populations (4 samples each) were sequenced seperately by Drop-seq in two lanes


title: Analysis of gene expression in uniparental mouse blastocysts produced in different culture media

city: Muenster

first: Michele

last: Boiani

address: Roentgenstrasse 20

institute: Max Planck Institute Muenster

summary:
In the field of in vitro embryo production it is generally thought that the culture media are not as good as the oviductal fluid, resulting in detrimental changes of embryonic gene expression. Yet in vitro embryo culture (IVC) is one of the pillars of the assisted reproductive technologies. Therefore, unintended effects on gene expression may impact on the health of ART babies (PMID 27554442). Granted, human ART has many more components than just the culture media, but, the practice of embryo culture superimposes with the phase of life when cellular totipotency is present - that's why embryo culture media receive special attention. Discerning what culture media do is difficult because several confounders are present, including but not limited to oocyte heterogeneity, sperm heterogeneity as well as time of fertilization. We propose to take advantage of experimentally produced parthenogenetic embryos, and thereby remove two confounders (sperm variability, time of fertilization), in order to assess the effects of specific culture media of embryonic gene expression, in the mouse model of human reproduction.
After synchronous parthenogenetic activation of MII oocytes,  pronuclear oocytes were cultured in parallel in ART medium vs KSOM(aa) medium. Resultant blastocysts were compared and contrasted for gene expression among the parthenotes, as well as against zygotic blastocysts.

overall_design: High embryo uniformity ensured by the time of activation (same for all, chemical parthenogenesis) and by the chromosomal sex (same for all parthenotes, XX) allows to ascribe gene expression differences to the culture media applied from the pronuclear stage onward. After superovulation and collection of oocytes from oviduct, MII oocytes were activated using SrCl2 (10 mM) and latrunculin B (5 microM) in Ca-free alpha-MEM medium, so as to generate diploid parthenotes. These were cultured individually in 75 microliters Continuous Single Culture®Complete, Global®total®LP, GM501 CULT, G-TLTM, SAGE 1-StepTM, or KSOM(aa), using 96-well plates. At the blastocyst stage, samples of 5 parthenogenetic embryos were collected in duplicate from each medium (except for zygotic embryos, 3 samples from KSOM(aa) only), and lysed in lysis buffer. Samples were subjected to Affymetrix microarray analysis, performed by Anika Witten c/o Institut fuer Humangenetik, Universitaetsklinikum Muenster.

first: Verena

last: Nordhoff


title: Characterizing cell interactions at scale with made-to-order droplet ensembles (MODEs)

city: San Francisco

first: Russell

last: Cole

state: CA

address: 953 Indiana Street

institute: Scribe Biosciences

summary: Cell-cell interactions are important to numerous biological systems, including tissue microenvironments, the immune system, and cancer. However, current methods for studying cell combinations and interactions are limited in scalability, allowing just hundreds to thousands of multi-cell assays per experiment; this limited throughput makes it difficult to characterize interactions at biologically relevant scales. Here, we describe a new paradigm in cell interaction profiling that allows accurate grouping of cells and characterization of their interactions for tens to hundreds of thousands of combinations. Our approach leverages high throughput droplet microfluidics to construct multicellular combinations in a deterministic process that allows inclusion of programmed reagent mixtures and beads. The combination droplets are compatible with common manipulation and measurement techniques, including imaging, barcode-based genomics, and sorting. We demonstrate the approach by using it to enrich for CAR-T cells that activate upon incubation with target cells, a bottleneck in the therapeutic T cell engineering pipeline. The speed and control of our approach should enable valuable cell interaction studies.

overall_design: Comparison of sorted and unsorted CAR-T cells paired in droplets with Raji cells

first: Justin

last: Madrigal

first: Nathan

last: Schoepp


title: LIF-responsive genes in monocytes from healthy donors

city: Barcelona

first: Joan

last: Seoane

address: Vall d'Hebron 119-129

country: Spain

institute: VHIO

summary:
LIF has an important role in immunosupression in different scenarios, such as in embryo implantation in the uterus, autoimmune disease or organ transplantation. In tumor progression it has been largely demonstrated the importance of immune system. The fact that LIF is highly expressed in certain tumor types, in addition to its immunomodulatory properties, led us to hypothesize that tumors expressing high levels of LIF might be promoting an immune-tolerant microenvironment precluding the anti-tumor immune response.
To establish whether the effect of LIF was relevant in the context of human monocytes, we isolated CD14+ cells (monocytes) from peripheral blood mononuclear cells (PBMCs) from healthy donors and analyzed the effect of LIF blockade. Instead of using recombinant LIF, we studied the effect of the endogenous LIF secreted by U251 cell line. RNA was extracted from the CD14+ cells and the transcriptomic analysis was performed.

overall_design: We selected the GBM cell line U251 that secreted high levels of LIF. Those cells were engineered by us to express shRNAs targeting LIF, in order to knock down LIF expression and secretion. We collected the conditioned media from control and shLIF U251 cells, and incubated human monocytes (CD14+ cells isolated from peripheral blood mononuclear cells from healthy volunteers) with the conditioned media. After 5 day treatment, cells were lysed for RNA extraction and hybridized on Affymetrix microarrays to determine how the specific blockade of LIF impacted on the gene expression of monocytes.

first: Ada

last: Sala-Hojman


title: Genome-wide DNA methylation profiling in anorexia nervosa discordant identical twins

city: VALENCIA

first: JUAN

middle: SANDOVAL

last: DEL AMOR

state: COMUNIDAD VALENCIANA

address: FERNANDO ABRIL MARTORELL 106

institute: INSTITUTO INVESTIGACION SANITARIA LA FE

summary: Up until now, no study has looked specifically at epigenomic landscapes throughout twin samples, discordant for Anorexia nervosa (AN). Our goal was to find evidence to confirm the hypothesis that epigenetic variations play a key role in the aetiology of AN. In this study, we quantified genome-wide patterns of DNA methylation using the Infinium Human DNA Methylation EPIC BeadChip array (850K) in DNA samples isolated from whole blood collected from a group of 7 monozygotic twin pairs discordant for AN. Results were then validated performing a genome-wide DNA methylation profiling using DNA extracted from whole blood of a group of non-family related AN patients and a group of healthy controls. Our first analysis using the twin sample revealed 9 CpGs associated to a gene. The validation analysis showed two statistically significant CpGs with the rank regression method related to two genes associated to metabolic traits, PPP2R2C and CHST1. When doing beta regression, 6 of them showed statistically significant differences, including 3 CpGs associated to genes JAM3, UBAP2L and SYNJ2.Finally, the overall pattern of results shows genetic links to phenotypes which the literature has constantly related to AN, including metabolic and psychological traits.  The genes PPP2R2C and CHST1 have both been linked to the metabolic traits type 2 diabetes through GWAS studies. The genes UBAP2L and SYNJ2 have been related to other psychiatric comorbidity.

overall_design: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.

first: Juan

last: Sandoval

first: Luis

last: Rojo


title: RNA-seq of human adipose tissue macrophage subtypes in obesity

city: Ann Arbor

first: Lindsey

last: Muir

state: MI

address: 1600 Huron Parkway B520

institute: University of Michigan

summary: We profiled three prominent ATM subtypes from human visceral omental adipose tissue in obesity by RNA-seq. In the related manuscript, we evaluated differences in their signatures and their relationship to type 2 diabetes:  Visceral (VAT) and subcutaneous (SAT) adipose tissue samples were collected from diabetic and non-diabetic obese subjects to evaluate cellular content and gene expression. VAT CD206+CD11c− ATMs were increased in diabetic subjects, scavenger receptor-rich with low intracellular lipids, secreted proinflammatory cytokines, and diverged significantly from two CD11c+ ATM subtypes, which were lipid-laden, lipid antigen presenting, and overlapped with monocyte signatures. Furthermore, diabetic VAT was enriched for CD206+CD11c− ATM and inflammatory signatures, scavenger receptors, and MHC II antigen presentation genes. VAT immunostaining found CD206+CD11c⁻ ATMs concentrated in vascularized lymphoid clusters adjacent to CD206⁻CD11c+ ATMs, while CD206+CD11c+ were distributed between adipocytes. Our results suggest ATM subtype-specific profiles that uniquely contribute to the phenotypic variation in obesity.

overall_design: RNA-sequencing was performed on 9 sorted human ATM subtype samples from 3 subjects. Each subject contributed one replicate of three ATM subtypes based on expression of surface markers CD206 and CD11c.

first: Lynn

last: Geletka

first: Kae

last: Cho

first: Nicki

last: Baker

first: Carmen

last: Flesher

first: Anne

last: Ehlers

first: Niko

last: Kaciroti

first: Stephen

last: Lindsly

first: Scott

last: Ronquist

first: Indika

last: Rajapakse

first: Robert

last: O'Rourke

first: Carey

middle: N

last: Lumeng


title: ADP-ribosylation of mitochondrial proteins is mediated by Neuralized-like protein 4 (NEURL4)

city: Boston

first: Joseph

last: Orofino

address: 72 E. Concord St.

institute: Boston University

summary: We profiled the transcriptomic changes in Hela N4-KO cells vs. WT cells

overall_design: RNAseq on N4-KO and WT Hela Cells

first: Dafne

last: Cardamone


title: Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: diagnostic and mechanistic relevance

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

summary:
Background & Aims:  Serum microRNAs (miRNAs) levels are known to change in non-alcoholic fatty liver disease (NAFLD) and may serve as useful biomarkers. This study aimed to profile miRNAs comprehensively at all NAFLD stages.
Methods:We profiled 2,083 serum miRNAs in a discovery cohort (183 NAFLD cases representing the complete NAFLD spectrum and 10 population controls). MiRNA libraries generated by HTG EdgeSeq were sequenced by Illumina NextSeq. Selected serum miRNAs were profiled in 372 additional NAFLD cases and 15 population controls by quantitative reverse transcriptase-polymerase chain reaction.
Results: Levels of 275 miRNAs differed between cases and population controls. Fewer differences were seen within individual NAFLD stages but miR-193a-5p consistently the showed increased levels in all comparisons.  Relative to NAFL/NASH with mild fibrosis (stage 0/1), three miRNAs (miR-193a-5p, miR-378d and miR378d) were increased in cases with NASH and clinically significant fibrosis (stage 2-4), seven (miR193a-5p, miR-378d, miR-378e, miR-320b, c, d & e) increased in cases with NAFLD Activity Score (NAS) 5-8 compared with lower NAS, and three (miR-193a-5p, miR-378d, miR-378e) increased but one (miR-19b-3p) decreased in steatosis, activity, and fibrosis "activity" (SAF-A) score 2-4 compared with lower SAF-A.  The significant findings for miR-193a-5p were replicated in the additional NAFLD cohort. Studies in Hep G2 cells showed that following palmitic acid treatment, miR-193a-5p expression decreased significantly.  Gene targets for miR-193a-5p were investigated in liver RNAseq data for a case subgroup (n=80); liver GPX8 levels correlated positively with serum miR-193a-5p.
Conclusions: Serum miR-193a-5p levels correlate strongly with NAFLD activity grade and fibrosis stage. MiR-193a-5p may have a role in the hepatic response to oxidative stress and is a potential clinically tractable circulating biomarker for progressive NAFLD.

overall_design: 2,083 serum miRNAs were profiled in 183 NAFLD cases representing the complete NAFLD spectrum and 10 population controls. miRNA libraries were generated by HTG EdgeSeq and sequenced by Illumina NextSeq 500.

first: Quentin

middle: M

last: Anstee

first: Ann

last: Daly

first: Katherine

last: Johnson


title: Variation of UCB CD34+ in erythroid differentiation potential

city: Lund

first: Kenichi

last: Miharada

address: Klinikgatan 17

institute: Lund University

summary: Ex vivo manufactured red blood cells (RBC) generated from immortalized erythroid cell lines which can semi-infinitely grow are expected to become a significant alternative in future transfusion therapies. To establish those cell lines, ectopic expression of human papilloma virus (HPV) E6/E7 gene has successfully been employed. In order to induce differentiation and maturation of the immortalized cell lines, terminating the HPV-E6/E7 expression through a gene induction system has been believed to be essential. Here we report that erythroid cell lines established from human bone marrow using simple overexpression of HPV-E6/E7 is capable of normal erythroid differentiation without turning the gene expression off. Newly established cell lines, Erythroid Lines from Lund University (ELLU), are able to differentiate towards mature cells including enucleated reticulocytes upon changing the culture condition but without terminating HPV-E6/E7 gene expression. ELLU cells are heterogeneous, and unexpectedly, clones expressing adult hemoglobin rapidly differentiate but produced cells are fragile while other clones with fetal hemoglobin start expressing adult hemoglobin upon differentiation and give rise to more mature cells. Our findings propose an alternative method to establish immortalized human erythroid cell lines and describe novel cellular characteristics for desired functionally competent clones.

overall_design:
13 healthy donor samples were sequenced in addition to testing their capacity for erythroid differentiation

To group A, belong CD34+ cells from human umbilical cord blood, which gave rise to the lower frequency of glycophorin-A+ cells (0-30%) after cultured for 6 days in erythroid differentiation media.
To group B, CD34+cells from human umbilical cord blood gave rise to the higher frequency of glycophorin-A+ cells (60-67% ) after being cultured for 6 days in erythroid differentiation media.

first: Svetlana

last: Soboleva

first: Per

last: Brattås


title: Transcription factor-dependent differences in cluster composition and transition states of oligodendrocyte differentiation from human stem cells

city: Munich

first: Moritz

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

summary: Oligodendrocytes (OLs) are critical for myelination and are implicated in several brain disorders. Directed differentiation of human induced OLs (iOLs) from pluripotent stem cells can be achieved by forced expression of different combinations of the transcription factors SOX10 (S), OLIG2 (O) and NKX6.2 (N). Here, we applied quantitative image analysis and single-cell transcriptomics to compare different transcription factor combinations for their efficacy towards robust OL lineage conversion. Compared with S alone, the combination of SON significantly increases the number of myelin basic protein-positive iOLs and generates iOLs with a more complex morphology and higher expression levels of myelin-marker genes . The analysis of RNA velocity of individual cells reveals that S generates a population of volatile oligodendrocyte-precursor cells (OPCs) that appear to be more immature than those generated by SON  and to display distinct molecular properties. Our analysis suggests that protocols for generating iOPCs or iOLs should be chosen depending on the intended application.

overall_design: 3 scRNAseq samples in total: 1 hiPSC-derived NPC sample before induction of exogenous TF expression and 2 hiPSC-derived OL samples with different TF combinations after two weeks of differentiation

first: Florian

last: Raabe

first: Marius

last: Stephan

first: Jan

middle: B

last: Waldeck

first: Verena

last: Huber

first: Damianos

last: Demetriou

first: Nirmal

last: Kannaiyan

first: Sabrina

last: Galinski

first: Laura

middle: V

last: Glaser

first: Michael

last: Wehr

last: Ziller

first: Andrea

last: Schmitt

first: Peter

last: Falkai


title: A Study of Predictive Ability of the Epigenetic Patterns in Peripheral Tissue for the Cortical Thickness

city: Houston

first: Oxana

middle: Yu.

last: Naumova

address: 4849 Calhoun Rd, TIMES, Rm 373

department: Psychology

institute: University of Houston

summary: Genome wide DNA methylation profiling of whole blood, saliva, and T-cells derived from blood. The Illumina Infinium MethylationEPIC microarray was used.

overall_design: Bisulphite converted DNA from the 57 samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip.

middle: Y

first: Elena

last: Grigorenko


title: Target Directed miRNA degradation is pervasive in human cancer

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

institute: Istituto Italiano di Tecnologia

summary: How many RNA transcripts can induce degradation of microRNAs (miRNA) via the mechanism known as target-directed miRNA degradation (TDMD) is currently unknown. We developed TDMDfinder, a bioinformatics pipeline and webtool, which is based on combined sequence alignment and feature selection approaches to identify ‘high confidence’ TDMD interactions either in Human or Mouse transcriptomes. Predictions suggest that TDMD is widespread, and every miRNA is possibly under the control of endogenous targets. Experimental validations support the validity of TDMDfinder predictions with 49% accuracy, revealing novel endogenous TDMDs for miR-17, miR-19, miR-30, miR-221, miR-26 and miR-23 families. TDMD can selectively target specific miRNA family/cluster members. Features like complementarity to the miRNA 3’ region, bulge size and hybridization energy can explain the different sensitivity. A set of computational analyses performed using the multiomic TCGA platform support the involvement of TDMD in human cancer. Many TDMD transcripts showed significant anti-correlations with both miRNA levels and miRNA activity in multiple tumors and 36 highly significant Pan-cancer interactions were highlighted. A proof-of-principle TDMD-pair was experimentally dissected in breast cancer, showing that fully-functioning TDMD could impact on cancer phenotypes, such as mammosphere growth and resistance to drug treatment. Our tool unveils TDMD as a widespread mechanism and pinpoints it as new potential oncogenic mechanism.

overall_design: Examination of miRNA levels  upon over-expression of putative microRNA degradation elements (MDEs). Analysis should be conducted considering paired samples (i.e. those indicated with the same Experiment_number).

first: Matteo

middle: J

last: Marzi

first: Ines

last: Simeone

first: Carmela

last: Rubolino


title: Comparative assessment of the physiological and transcriptomic response of Escherichia coli to disinfectants: Ferrate versus hypochlorite

city: Ames

first: Andrew

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

summary: Disinfection is very critical for the removal of pathogens that constitute public health concerns. However, a rounded understanding of the antimicrobial action of different classes of disinfectants is still lacking. In this work, the physiological and transcriptomic responses of Escherichia coli to two different disinfectants namely: potassium ferrate (K2FeO4) and more conventional disinfectant, sodium hypochlorite (NaOCl), were examined. The study aimed to examine E. coli genetic response to ferrate and compare and contrast it to the genetic response of E. coli to hypochlorite.

overall_design: Three replicate E. coli cultures were used: A, B and C. The first letter in the sample name codes for the culture replicate. The second letter corresponds to the treatment type. ‘W’ codes for water treatment (control), ‘F’ codes for potassium ferrate treatment and ‘H’ codes for sodium hypochlorite treatment. ‘bef’ and ‘aft’ codes for before or after exposure. All E. coli cultures were grown for 48 hours in lake water media supplemented with 100 mg/L yeast extract and 1 mM phosphate buffer prior to exposure

first: Kaoru

last: Ikuma


title: Bulk RNAseq analysis of control and Carm1 KO CD8 T cells

first: Matthew

last: Booker

address: 21-27 Burlington Ave.

department: Informatics

institute: Dana Farber Cancer Institute

summary:
The overall goal of this study was to understand the change in antigen-stimulated gene expression in CD8 T cells upon ablation of a transcriptional coactivator Carm1 by CRISPR-Cas9 method.
Seven days following editing, OT-I CD8 T cells were co-cultured for 24 hours with B16F10-Ova tumor cells.  RNA-seq analysis demonstrated changes in gene expression, including upregulation of 1,143 genes and downregulation of 1,199 genes in Carm1 KO compared to control T cells.  Upregulated genes encoded chemokine receptors that mediate T cell recruitment into tumors (Cxcr3) and key genes required for maintenance of memory T cell populations (transcription factor genes Tcf7, Myb, Bcl6; surface receptor Cd27).  Downregulated genes included those associated with terminal differentiation (Klrg1), inhibition of cytokine signaling (Socs1, Socs3) and T cell dysfunction within tumors (Egr2, Eomes).

overall_design:
Examination of transcripts  associated with  control and Carm1 KO OT-I  cells:
SK0*-A*: WT OT-I CD8 T cells co-cultured with B16F10-Ova tumor cells
SK0*-B*: Carm1 KO OT-I CD8 T cells co-cultured with B16F10-Ova tumor cells

first: Sushil

last: Kumar

first: Kai

last: Wucherpfennig


title: Targeting TIGIT Molecule Inhibits the Metastasis of Bladder Cancer through Suppressing IL-32

city: Shen Zhen

first: Kang

last: Wu

state: Guang Dong

address: 47 Youyi Road, Luohu District

department: Urology

institute: The Third Affiliated Hospital of Shenzhen University (LuoHu Hospital Group)

summary: Bladder cancer is a highly metastatic tumor and one of the most common malignant tumors originating in the urinary system. Although the application of immune checkpoint, including programmed cell death-1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), achieved definite efficacy, the effect of immunotherapy for bladder cancer is still not very satisfactory. Therefore, it is very urgent to develop new targets to expand the options of immunotherapies. In this study, we utilized single cell sequencing to explore the cell composition and detected a subset of Treg cells with high expression of T cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) and interleukin (IL)-32 molecules. Certainly, anti-tumor immune response was suppressed by this subset of Treg cells and IL-32 promoted the bladder cancer metastasis. Nevertheless, targeting TIGIT not only could reverse immunosuppression through restoring anti-tumor immune response mediated by T cells but suppressed the secretion of IL-32 and inhibited the metastasis of bladder cancer cells. Thus, our study provided a novel insight into the immunosuppression in bladder cancer and developed the TIGIT as the novel target for immunotherapy of bladder cancer. Furthermore, we also illustrated mechanism of the dual effect of targeting TIGIT in bladder cancer and revealed the metastasis-promoting effect of IL-32 in bladder cancer. Taken together, the discovery raises the possibility of TIGIT targets against bladder cancer from the bench to the bedside.

overall_design: single cell mRNA sequence of bladders from S13N;S13T,S21N or S21T,in triplicate

first: Song


title: Expression of a miRNA targeting mutated SOD1 in astrocytes induces motoneuron plasticity and improves neuromuscular function in ALS mice

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary: In familial forms of amyotrophic lateral sclerosis (ALS) caused by mutations in superoxide dismutase-1 (SOD1) gene, both cell-autonomous and non-cell-autonomous mechanisms lead to the selective degeneration of motoneurons. Gene-targeted deletion of mutated SOD1 in mature astrocytes has been shown to slow down disease progression. However, the potential therapeutic application of targeting astrocytes has not been evaluated yet. Here, an AAV vector encoding an artificial microRNA is used to deliver RNA interference against mutated SOD1 by targeting astrocytes in ALS mice. In mice expressing the mutated SOD1G93A protein, we found that the treatment leads to the progressive rescue of neuromuscular junction occupancy, to the recovery of the compound muscle action potential in the gastrocnemius muscle, and significantly improves neuromuscular function. In the spinal cord, gene therapy targeting astrocytes protects a small pool of fast-fatigable motoneurons until disease end stage. In the gastrocnemius muscle of the treated SOD1G93A mice, the fast-twitch type IIb muscle fibers are preserved from atrophy. Axon collateral sprouting is observed together with muscle fiber type grouping indicative of denervation/re-innervation events. The transcriptome profiling of spinal cord motoneurons shows changes in the expression levels of factors regulating the dynamics of microtubules. Gene therapy delivering RNA interference against mutated SOD1 in astrocytes provides therapeutic effects enhancing motoneuron plasticity and improving neuromuscular function in ALS mice.

overall_design: SOD1-G93A mutant mice were ICV injected at P2 either with the AAV-miR SOD1 vector which drives expression of an artificial anti-human SOD1 miR in astrocytes or with AAV-miR ctrl. An additional group of non-injected SOD1-G93A littermate mice was included in the experiment. At day 65, a transcriptomic analysis was performed on motoneurons captured by laser microdissection in the ventral horn.

first: Cylia

last: Rochat

first: Florence

last: Perrin

first: Patrick

last: Aebischer

first: Bernard

last: Schneider


title: A population of CD4+ T cells with a naïve phenotype stably polarized to the Th1 lineage

city: London

first: Maria

last: Vila de Mucha

address: 72 Huntley Street

institute: UCL Cancer Institute

summary: T-bet is the lineage-specifying transcription factor for CD4+ T helper type 1 (TH1) cells. T-bet has also been found in other CD4+ T cell subsets, including TH17 cells and TREG, where it modulates their functional characteristics. However, we lack information on when and where T-bet is expressed during T cell differentiation and how this impacts the T cell function. To address this, we traced the ontogeny of T-bet-expressing cells using a fluorescent fate-mapping mouse line. We demonstrate that T-bet is expressed in a subset of naïve CD4+ T cells and that this novel cell population is phenotypically and functionally distinct from conventional naïve CD4+ T cells. These cells are also distinct from previously described populations of memory phenotype or stem cell-like T cells. Naïve T-bet-experienced cells are polarised to the TH1 lineage, predisposed to produce IFN upon cell activation, and resist repolarisation to other lineages in vitro and in vivo. These results demonstrate that lineage-specifying factors can function to polarise naïve T cells prior to T cell activation and that this has an impact on the subsequent T helper response.

overall_design: RNA sequencing data comparing YFP+ and YFP-  Naïve (CD62L+ CD44-) and Memory (CD62L-CD44+) CD4+ T cells purified from T-bet cre/+ Rosa26 YFP/+ mice.

first: Jonathan

last: Lo

first: Luke

last: Roberts

first: Natividad

last: Garrido-Mesa

first: Arnulf

last: Hertweck

first: Joana

middle: F

last: Neves

first: Emilie

last: Stolarczyk

first: Ian

last: Jackson

first: Jane

last: Howard

first: Richard

middle: G

last: Jenner

first: Graham

last: Lord


title: Expression data from muscle tissue in children with obesity and normal weight

city: Granada

first: Julio

middle: Ramon

last: Plaza Diaz

state: Granada

address: Avda. del Conocimiento s/n

department: Biochemistry and Molecular Biology II

institute: University of Granada

summary: Analysis of rectus femoris samples from chidren with obesity and normal weight. Obese children display insulin resistance (IR) and other metabolic abnormalities at higher rates than do normal weight children. Results provide insight into the molecular mechanisms underlying the pathogenesis of childhood obesity.

overall_design: We recruited Caucasian children, aged 6–12 years, undergoing abdominal surgery in the Pediatric Surgery Unit of the Hospital Reina Sofía (Cordoba, Spain) with a diagnosis of hernia or false positive diagnosis of acute appendicitis. Children with obesity and normal-weight were categorized according to Cole et al. (BMJ 2000, 320, 1240–1243). All children were in the prepubertal period based on the Tanner criteria (Tanner I) (Tanner et al. Archives of disease in childhood. 1976;51(3):170-9.) and as validated by plasma sex hormone concentrations. The inclusion criteria were a good state of health, age between 5 and 14 years and the absence of endogenous obesity. Exclusion criteria were disease or malnutrition and the use of a medication that alters blood pressure or glucose or lipid metabolism.  The children’s parents or guardians were informed about the purpose and procedures of the study before written consent was obtained, and all children agreed to participate. The protocol was performed in accordance with the Revised Declaration of Helsinki and following the recommendations of the Good Clinical Practice of the European Union (document 111/3976/88 July 1990) and legal in-force Spanish regulations, which regulate clinical investigation in human beings (RD 223/04 about Clinical Assay), as approved by the Ethics Committees of all participants’ institutions.

first: Concepcion

last: Aguilera Garcia

first: Ines

last: Tofe

first: Ramon

last: Cañete


title: The long non-coding RNA Falcor regulates Foxa2 expression to maintain lung epithelial homeostasis and promote regeneration (array)

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: One month following airway injury with naphthalene (275mg/kg IP x1 in corn oil), total RNA was isolated from one lobe of the right lung (whole lung) from either Falcor-/- (null) or injured wild-type control mice.

overall_design: Falcor-/- (null) or  wild-type lung treated with naphthalene

first: Dan

last: Swarr

middle: P

first: Edward

last: Morrisey


title: Treg cell by tumor-associated macrophage ROS and inflammatory signaling through T-cell NF-κB c-Rel drives pathogenesis of lung adenocarcinomas

city: Frederick

first: Yinling

last: Hu

state: MARYLAND

address: NCI/CIP, Building 567, 1050 Boyles  St.

department: NCI

institute: NIH

summary: IKKα, one subunit of the IKK complex composed of IKKα, IKKβ, and IKKγ (NEMO), is essential for canonical and noncanonical NF-κB pathways involved in the development of lymphoid organs, leukocytes, immunity, and epithelial organs. Deletions of the CHUK locus that encodes IKKα significantly reduce survival for both KRAS-mutation lung adenocarcinoma (ADC) patients and mice, but the question of whether IKKα regulates immune responses remains unanswered. Here, we show that tumor-IKKα reduction elicits an immunosuppressive tumor-microenvironment associated with macrophage and Treg cell induction, which are maintained through elevated reactive oxygen species (ROS) and cytokines important for macrophage and Treg cell development in human and mouse lung ADCs. Enhanced macrophage-ROS and inflammatory cytokine signaling, mediated by tumor-cell IKKα reduction, enforces Treg cell differentiation via a ROS/TNFα/TNFR2/c-Rel pathway in CD4 T-cells. The blockage of each crucial step, including ROS, macrophages, Treg cells, and TNFα/c-Rel, impairs lung ADC development. To explore the molecular mechanism, we performed ChIP-Seq to check some important immunoregulatory genes including TNF, IL-23A CSF1, and CCL22 were regulated transcriptionally by IKKα. Therefore, IKKα serves as a specific surveillant that suppresses immunosuppressive responses and antagonizes lung carcinogenesis in humans and mice.

overall_design: Examination of IKKα-bound DNA in lung ADC cell line A549

first: NaYoung

last: Song

first: Xin

last: Li


title: CARM1 Inhibition Enhances Cytotoxic T-cell Function and Sensitizes Resistant Cancers to Immune Attack

city: Davis

first: Frederic

last: Chedin

address: 1 Shields Avenue

department: MCB

institute: UC Davis

summary: Several cancer drugs activate innate immune pathways in tumor cells but unfortunately compromise anti-tumor immune function.  We discovered that inhibition of Carm1, an epigenetic enzyme, elicited beneficial effects in both cytotoxic T cells and tumor cells.  Carm1 inactivation in cytotoxic T cells enhanced their activation state and anti-tumor function.  In contrast, Carm1 inhibition in tumor cells resulted in genomic damage and activation of the cGAS-STING pathway.  Inactivation of Med12, a regulatory component of the Mediator complex, elicited the same tumor cell phenotype, thereby connecting Carm1 to regulation of transcription.  Inhibition of Carm1 induced potent T cell mediated tumor immunity and sensitized resistant, highly aggressive tumor cells to checkpoint blockade.  The Carm1 – Med12 pathway thus offers an opportunity to enhance anti-tumor immunity while simultaneously sensitizing resistant tumor cells to immune attack.

overall_design: Characterization of mRNA and RNA:DNA hybrid structures in wild-type and carm1 knockout B16-F10 cells using polyA RNA-seq and sDRIP-seq.

first: Sushil

last: Kumar

first: Lionel

middle: A

last: Sanz

first: Stella

middle: R

last: Hartono

first: Kai

last: Wucherpfennig


title: Glucose infusion into dairy goat mammary gland

city: Hangzhou

first: Jie

last: Cai

address: Yuhangtang Rd

institute: Zhejiang University

summary: Different doses of glucose were inused into dairy goat mammary gland. The mammary gland tissues were biopsied to analyze the changes of transcriptome responding to glucose infusion.

overall_design: Three doses (high, middle, low) of glucose were infused into dairy mammary gland. The mammary gland tissues were biopsied to analyze the changes of transcriptome responding to glucose infusion.


title: Target Gene Diversity of the Nrf1-MafG Transcription Factor Revealed by a Tethered Heterodimer

status: Public on Jan 30 2022

city: Aoba-ku, Sendai

first: Fumiki

last: Katsuoka

state: Miyagi

address: 2-1 Seiryo-cho

institute: Tohoku University

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

overall_design: Refer to individual Series


title: The long non-coding RNA Falcor regulates Foxa2 expression to maintain lung epithelial homeostasis and promote regeneration (RNA-Seq)

summary: EpCAM+ lung epithelial cells were isolated by magnetic bead sorting from either wild-type animals 10-12 weeks of age, or with the genotypes Falcor-/-, Foxa2+/-, or Double-Het (Falcor+/-;Foxa2+/-) animals

overall_design: Wild-type animals 10-12 weeks of age, or with the genotypes Falcor-/-, Foxa2+/-, or Double-Het (Falcor+/-;Foxa2+/-) animals

middle: E


title: Genome wide-binding profile of tethered Nrf1-MafG (T-N1G) heterodimers in the small Maf-deficient cells [ChIP-seq]

summary: To elucidate the function of Nrf1-small Maf heterodimer, we constructed a tethered Nrf1-MafG (T-N1G) heterodimer using a flexible linker peptide and examined its function in the small Maf-deficient mouse embryonic fibroblast (MEF).

overall_design: ChIP-seq was performed using anti-MafG antibody on chromatin prepared from  the T-N1G-expressing F0G0K0 MEFs, treated with 1.0 µM  Proteasome Inhibitor (MG132)  for 4hr.

first: Akihito

last: Ohtsuki

first: Nozomi

last: Hatanaka

first: Haruna

last: Okuyama

first: Masayuki

last: Yamamoto


title: The long non-coding RNA Falcor regulates Foxa2 expression to maintain lung epithelial homeostasis and promote regeneration

first: Michael

last: Morley


title: Germinal centre-driven maturation of B cell response to SARS-CoV-2 mRNA vaccination

city: St. Louis

first: Julian

last: Zhou

address: 425 S. Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

summary: We used ultrasound-guided fine needle aspiration of the draining ipsilateral axillary lymph nodes to interrogate SARS-CoV-2 mRNA vaccine-induced GC responses in humans.

overall_design:
Examination of 56 single-cell RNA-seq samples from PBMC and lymph node taken at multiple time points post-vaccination across multiple participants.

Data processing steps:

1) Single cell feature counts for a single library were generated using `cellranger count` from Cell Ranger v6.0.1.

2) Single cell feature counts for multiple libraries were then pooled by subsampling to the same effective sequencing depth using `cellranger aggr`.

Genome build: GRCh38

Processed data files format and content:

1) matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices

2) features.tsv.gz contains feature information that corresponds to the row index of matrix.mtx.gz

3) barcodes.tsv.gz contains cellular barcodes that correspond to column indices of matrix.mtx.gz. The trailing dash and number (e.g. -12) indicate the sample from which the cell originated and correspond to the row number for that sample in aggregation.csv.

4) aggregation.csv contains sample information. The order of the samples represented as rows in aggregation.csv corresponds to the numbers after the dash (e.g. -12) in barcodes.tsv.gz.

first: Wooseob

last: Kim

middle: Q

first: Stephen

middle: C

last: Horvath

first: Aaron

last: Schmitz

first: Alexandria

last: Sturtz

first: Tingting

last: Lei

first: Zhuoming

last: Liu

first: Elizaveta

last: Kalaidina

first: Mhima

last: Thapa

first: Wafaa

last: Alsoussi

first: Alem

last: Haile

middle: K

last: Klebert

first: Teresa

last: Suessen

first: Luis

last: Parra-Rodriguez

first: Philip

last: Mudd

first: Sean

last: Whelan

first: William

middle: D

last: Middleton

first: Sharlene

last: Teefey

first: Iskra

last: Pusic

first: Jane

last: O'Halloran

first: Rachel

last: Presti

first: Jackson

middle: S

last: Turner

first: Ali

middle: H

last: Ellebedy


title: Conformation and dynamic interactions of the multipartite genome in Agrobacterium tumefaciens

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

summary: Bacterial species from diverse phyla contain multiple replicons, yet how these multipartite genomes are organized and segregated during the cell cycle remains poorly understood. Agrobacterium tumefaciens has a 2.8 Mb circular chromosome (Ch1), a 2.1 Mb linear chromosome (Ch2), and two large plasmids (pAt and pTi). We used this alpha proteobacterium as a model to investigate the global organization and temporal segregation of a multipartite genome. Using Chromosome Conformation Capture (Hi-C) assays, we demonstrate that both the circular and the linear chromosomes but neither of the plasmids have their left and right arms juxtaposed from their origins to their termini, generating inter-arm interactions that require the broadly conserved structural maintenance of chromosomes (SMC) complex. Moreover, our studies revealed two types of inter-replicon interactions: “ori-ori clustering” in which the replication origins of all four replicons interact, and “Ch1-Ch2 alignment” in which the arms of Ch1 and Ch2 interact linearly along their lengths. We show that the centromeric proteins (ParB1 for Ch1 and RepBCh2 for Ch2) are required for both types of inter-replicon contacts. Finally, using fluorescence microscopy, we validated the clustering of the origins and observed their frequent colocalization during segregation. Altogether, our findings provide a high-resolution view of the conformation of a multipartite genome. We hypothesize that inter-centromeric contacts promote the organization and maintenance of diverse replicons.

overall_design:
Hi-C and ChIP-seq experiments were performed on wild type and mutant cells of Agrobacterium tumefaciens C58 and Agrobacterium tumefaciens 15955 growing in LB, ATGN or virulence inducing medium.
Hi-C, ChIP-seq and WGS experiments were performed on wild type and mutant cells of Agrobacterium tumefaciens C58 growing in LB, ATGN.

first: X


title: Rhesus monkey whole genome expression microarray of endometrium obtained on days 2, 4 and 6 after ovulation in mated, proven conception cycles and non-mated, normo-ovulatory cycles in rhesus monkeys

city: New Delhi

first: Debabrata

middle: Government

last: Ghosh

state: DELHI

address: Ansari Nagar, New Delhi

department: Physiology

country: India

institute: All India Institute of Medical Sciences-Delhi

summary:
Several lines of evidence indicate that there exists differential display of biochemical characteristics in endometrium during receptivity in the proven conception cycle as compared to corresponding secretory phases endometrium of non-conception cycles of fertile rhesus monkeys. In the present study, we examined the differential display in the whole genome expression of endometrium during days 2, 4 and 6 post-ovuation in proven conception cycles and normo-ovulatory, non-conception cycles in proven fertile rhesus monkeys. Female monkeys showing at least two consecutive ovulatory menstrual cycles of normal length were allocated to either of the two groups: group 1 in which females were allowed to cohabit with proven fertile males during days 8 to 16 of their menstrual cycles, and group 2 in which females were not allowed to cohabit. Vaginal smears were checked daily and the days of ovulation were assessed from immunopositive profiles of estradiol-17β and progesterone in peripheral serum samples. Endometrial samples were collected on days 2, 4 and 6 after ovulation from both groups of animals following laparotomy and fundal hysterectomy under ketamine anaesthesia. In group 1, only endometrial samples obtained from mated females who yielded viable, preimplantation-stage matched embyos on uterine flushing were used. In group 2, endometrial samples were obtained from females who showed normal ovulatory cycles. Tissue samples from both groups were washed in ice-cold PBS and were used for RNA extraction to run rhesus monkey whole genome expression array.
On average, ~60% and ~68% genes of total number of hybridized genes were expressed in endometrial samples of groups 1 and 2, respectively. Group-wise hierarchical cluster analysis (HCA) yielded highest segregation between peri-implantation stage (groups 1b and 1c) and other (groups 2a-c and group 1a) samples with cluster distance (cd) 0.9, when cd=1.0 denotes complete segregation. On the other hand, least segregation was seen between groups 1a and 2a with cd 0.2, when cd=0 denotes complete aggregation. The number of common genes were less with the progress in days in group 1 (that is in proven conception cycle) unlike that in group 2 (that is in non-mated, normo-ovulatory group). Also, the number of common genes between groups for a given day after ovulation displayed a clear declining trend with increasing number of uncommon genes. Differential dipslay of regulated common genes among all the subgroups based on statistical analyses of variances in data sets obtained from whole genome expression arrays identified a total of fifteen (15) genes that displayed differential (>2-fold, p< 0.05) expression: ADCY5, ADIPOR1, AVEN, CHRND, FOXD3, GJD4, MAPK8IP3, MKS1, NNMT, NUP50,  PALT1, PIGV, TGFBR2, TOX2, VWA5B1.

overall_design: Whole genome expression arrays of endometrial total RNA obtained on days 2, 4 and 6 after ovulation from conception cycles were compared with those from non-mated, normo-ovulatory cycles of proven fertile rhesus monkeys.

first: Muzaffer

last: Ahmed Bhat