title: Titanium with nanotopography attenuates the osteoclast-induced disruption of osteoblast differentiation by regulating histone methylation

city: Ribeirão Preto

first: Rayana

middle: Longo

last: Bighetti-Trevisan

state: São Paulo

address: Avenida do Café s/n.

department: Basic and Oral Biology

country: Brazil

institute: University of São Paulo

summary:
We report the application of RNA sequencing to evaluate the effect of titanium (Ti) with nanotopography, compared to Ti control, on the whole transcriptome of osteoblastic cells in isolated cultures grown on these surfaces and to evaluate the effect of Ti with nanotopography, compared to Ti control, on the whole transcriptome of osteoblastic cells, grown on these surfaces, in co-culture with osteoclastic cells.
MC3T3-E1 osteoblastic cells were plated at the density of 1x10^4 cells/well on the Ti discs with nanotopography and Ti control, in 24-well plates in osteogenic medium and kept isolated for 5 days to allow cell adhesion. Osteoclast cells from the RAW 264.7 lineage were cultured on osteoclastogenic medium on ThinCert™ cell culture inserts (Greiner Bio-One), with 0.4 μm pore, at the density of 1x104 cells/membrane, and was also be kept isolated for 5 days to allow cell adhesion. At the end of this period theThinCert™ cell culture inserts (Greiner Bio-One), containing the osteoclast cells were positioned on the osteoblastic cell cultures, thereby establishing indirect co-culture. The controls were osteoblastic cells of the MC3T3-E1 lineage grown on the Ti discs in the absence of osteoclast cells of the RAW 264.7 lineage, i.e., not maintained in co-culture.

overall_design: All the experiments were performed considering biological triplicates of each group.

first: Luciana

middle: O

last: Almeida

first: Larissa

last: Castro-Raucci

first: Jonathan

middle: A

last: Gordon

first: Coralee

middle: E

last: Tye

first: Gary

last: Stein

first: Jane

middle: B

last: Lian

first: Janet

first: Adalberto

last: Rosa

first: Marcio

last: Beloti


title: 4C-seq analyses of the 3’Igh locus during B cell development

status: Public on Nov 23 2021

city: Chicago

first: Amy

last: Kenter

state: Illinois

address: 835 S Wolcott Ave

country: USA

institute: University of Illinois at Chicago

summary: We report the application of 4C-seq for analysis of the 3’ end of he Igh locus during B cell development. We generated genome-wide 4C maps for BM derived Rag2-/- pro-B cells, resting splenic B cells, LPS+IL4 activated B cells and ConA stimulated splenic T cells using two viewpoints, Em and hs4 located in 3’Ea.  We find that long range interactions are present only on B lineage cells reflecting enhancer activation status.

overall_design: Chromatin templates were isolated from Rag2-deficient B cell progenitors expanded ex vivo in IL7, column purified resting splenic B cells, B cells activated with LPS+IL4 for 40 hours and splenic T cells that were ConA activated.  These samples were were then submitted to 4C-seq analysis, libraries prepared and submitted to NGS studies.  Biological replicates were prepared.

first: Robert

last: Wuerffel

middle: L

first: Xue

last: Lei


title: Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling

city: Wako

first: tomoya

last: fujita

state: Saitama

address: 2-1, Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

type: Non-coding RNA profiling by high throughput sequencing

summary: Ribosome pauses are associated with diverse co-translational events and determine the fate of mRNAs and proteins. Thus the identification of the precise pause sites across transcriptome is a key, however, the landscape in bacterial has remained ambiguous. Here, we harnessed the multiple ribosome profiling strategies (standard, high-salt-wash, and disome) to survey the robust ribosome pause sites in E. coli. The found pause sites showed the correspondence with biochemical validation by integrated nascent chain profiling (iNP), which detects polypeptidyl-tRNA, an elongation intermediate. Among the list, ribosome pause at Asn586 of ycbZ was ensured by biochemical reporter assay, tRNA-seq, and cryo-electron microscopy. Our results provide a useful resource of ribosome stalling sites in bacteria.

overall_design: Ribosome profiling and tRNA

first: Tomoya

last: Fujita

first: Takeshi

last: Yokoyama

first: Mikako

last: Shirouzu

first: Hideki

last: Taguchi

first: Takuhiro

last: Ito

first: Shintaro

last: Iwasaki


title: Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling II

overall_design: Ribosome profiling of monosome is mono-ribosome (we analyzed ribosome footprints derived from one ribosome in the library), and disome is di-ribosome (we analyzed ribosome footprints derived from collied ribosomes in the library). Both samples were frozen in liquid nitrogen.


title: Determine anti-Siglec-F and IL-33 costimulation induced transcriptional changes on murine eosinophils

city: Erlangen

first: David

last: Voehringer

address: Wasserturmstrasse 3-5

department: Department of Infection Biology

country: Germany

institute: University Clinic Erlangen

type: Expression profiling by high throughput sequencing

summary: Eosinophils costimulation with anti-Siglec-F and IL-33 synergistically increases their IL-4 and IL-13 release (Willebrand et al. PLoS One 2016). Here we analyze costimulation induced transcriptional changes involved that potentially enhance effector release.

overall_design: To determine transcriptional changes in primary eosinophils induced by anti-Siglec-F (clone E50-2440) and IL-33 costimulation we performed single and combined treatments with anti-Siglec-F and IL-33. Sorted eosinophils (SSChigh4get+) of IL-5tg_4get/C57BL/6 mice (original IL-5tg: Lee et al. 1997 J Immunol; original 4get: Mohrs et al. Immunity 2001) in which eosinophilia is driven by IL-5 and IL-4 producing cells are labelled with GFP were analyzed. We compare isotype, anti-Siglec-F, IL-33 and Siglec-F + IL-33 costimulated groups.

first: Daniel

last: Radtke

first: Stefanie

last: Westermann


title: CNO stimulated hM3Dq-expressing iPS cell-derived neural cells

city: Shinjuku Tokyo

first: Momotaro

last: Kawai

address: 35 Shinanomachi

department: Department of Orthopaedic Surgery

institute: Keio University School of Medicine

summary: hM3Dq-expressing iPS cell-derived neural cells were stimulated by CNO treatment for two hours. Comparing to the vehicle-treated control, enhanced expressions of immediate early genes were observed.

overall_design: 3 samples for the CNO treatment and the control, each.

first: Kent

last: Imaizumi

first: Morio

last: Matsumoto

first: Hideyuki

last: Okano

first: Masaya

last: Nakamura

first: Narihito

last: Nagoshi


title: Stimulation to human iPS cell derived neural stem/progenitor cells

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Mouse spinal cords transplanted with human iPS cell-derived neural cells with and without chemogenetic stimulations on 14-days and 42-days after spinal cord injury.

summary: hM3Dq-expressing human iPS cell-derived neural cells were transplanted in the injured mouse spinal cord. Thereafter, transplanted cells were selectively stimulated daily by intraperitoneal injection of CNO. The spinal cord 14-days and 42-days after the injury were eviscerated for analyses.

overall_design: 4 samples for the CNO treated spinal cord 14-days after the injury.3 samples for the CNO treated spinal cord 42-days after the injury, and the control spinal cords 14-days and 42-days after the injury, each.


title: An instructive role for IL7RA in the development of human B-cell precursor leukemia

city: Rehovot

first: Dan

last: Ben-Avraham

address: Hertzel 234

department: Grand Israel National Center for Personalized Medicine

country: Israel

institute: Weizmann Institute of Science

summary: 10X single cell analysis of human leukemia, pre-leukemia and normal control. The leukemia was developed in xenograft mice that was serialy transplanted with cells from primary mouse that was transplanted with normal cord blood after transduction with virues encoding hyper activated mutant  IL7RA. The preleukemic cells are from the primary engrafted mouse and the control is the same cord blood that was transduced with backbone virus expressing GFP.

overall_design: human CD10+CD19+ cells from the BM of the leukemic mouse (Leukemic F49), the pre-leukemic mouse (Preleukemic 49_Q2) and the mouse engrafted with matching CB transduced with control BackBone virus (Backbone BB) were sorted. Additionally, the preleukemic mouse sample separately sorted the CD10highCD19low sub-population (preleukemic 1, 49_P2). Cells were subjected to 10X single cell gene expression analysis

first: Ifat

last: Geron

first: Angela

last: Savino

first: Michael

last: Gershovits

first: Shai

last: Izraeli


title: Extracellular matrix targeted mRNA profiles of PKN2 KO/WT mouse pancreatic stellate cell lines (PSCs) treated with TGF-b or vehicle control

status: Public on Nov 22 2021

city: London

first: Angus

last: Cameron

state: Islington

address: John Vane Science Centre, Charterhouse Sq,

department: Tumour Biology

country: United Kingdom

institute: Queen Mary University of London

summary: In pancreatic ductal adenocarcinoma (PDAC), differentiation of pancreatic stellate cells (PSCs) into myofibroblast-like cancer-associated fibroblasts (CAFs) promotes fibrotic,  therapy-resistant tumours. Conversely, suppression of CAFs can result in aggressive metastatic tumours. Here we show that the Rho-effector kinase protein kinase N2 (PKN2) is critical for PSC myofibroblast differentiation. Loss of PKN2 was associated with reduced PSC proliferation and contractility, retention of lipid droplets and decreased a-SMA stress fibres. PKN2 loss was also associated with a myofibroblast CAF to -like inflammatory CAF switch in the PSC matrisome signature both in vitro and in vivo. In spheroid co-cultures with PDAC cells, loss of PKN2 prevented PSC invasion but, counter-intuitively, promoted invasive cancer cell outgrowth. Further, deletion of PKN2 in the pancreatic stroma induced more locally invasive, orthotopic pancreatic tumours. Finally, we demonstrated that a PKN2KO PKN2 KO matrisome signature predicts poor outcome in pancreatic and other solid human cancers. Our data indicate that suppressing PSC myofibroblast differentiation function can limit important stromal tumour suppressive mechanisms, while promoting a switch to a cancer-supporting CAF phenotype.

overall_design: Extracellular matrix targeted mRNA profiles of 3 PKN2 knockout (KO) or 3 PKN2 wild type (WT) mouse pancreatic stellate cell lines (PSCs) treated with TGF-b or a vehicle control.

middle: J

first: Elizabeth

middle: R

last: Murray

first: Shinelle

last: Menezes

first: Jack

last: Henry


title: Fasting enriched metabolic enhancers associate with histone lysine 9 ß-hydroxybutyrylation

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: β-hydroxybutyrate (β-OHB) is an essential metabolic energy source during fasting and functions as a chromatin regulator by lysine β-hydroxybutyrylation (Kbhb) modification of the core histones H3 and H4. We report that Kbhb on histone H3 (H3K9bhb) is enriched at proximal promoters of critical gene subsets associated with lipolytic and ketogenic metabolic pathways in small intestine (SI) crypts during fasting. Similar Kbhb enrichment is observed in Lgr5+ stem cell-enriched epithelial spheroids treated with β-OHB in vitro. Combinatorial chromatin state analysis reveals that H3K9bhb is associated with active chromatin states and that fasting enriches for an H3K9bhb-H3K27ac signature at active metabolic gene promoters and distal enhancer elements. Intestinal knockout of Hmgcs2 results in marked loss of H3K9bhb-associated loci, suggesting that local production of β-OHB is responsible for chromatin reprogramming within the SI crypt. We conclude that modulation of H3K9bhb in SI crypts is a key gene regulatory event in response to fasting.

overall_design: Examination of 9 different histone modifications in FED and FASTED mice replicates

first: Kristina

last: Stemler

first: Christopher

last: Terranova


title: Petunia ODO1 ChIP-seq and RNA-seq

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

institute: Purdue University

summary: Petunia floral scent production and emission is highly regulated, with a major role for the transcription factor ODORANT1 (ODO1) in directing activation of volatile biosynthesis. Using ChIP-seq of tagged ODO1 protein from petunia flowers, and RNA-seq of wild-type and odo1i RNAi flowers, the ODORANT1-regulated gene network of petunia is described, which extends to branches involved in phenylpropanoid intermediate production and S-adenosyl-methionine biosynthesis to potentiate production and emission of volatiles. Analysis of direct targets of regulation has also enabled the identification of an ODO1 binding motif.

overall_design: RNA-seq and ChIP-seq

middle: M

first: Maaike

last: Boersma

first: Ying

last: Li

first: Robert

middle: C

last: Schuurink


title: Enoxacin shows a broad-spectrum antiviral activity against diverse viruses by enhancing antiviral RNAi in insects

city: Wuhan

first: Yang

last: Qiu

state: Hubei

address: No. 44 Xiaohongshan Central District, Wuchang District,

country: China

institute: Wuhan institue of virology, CAS

summary: RNA interference (RNAi) functions as the major host antiviral defense in insects, while less is understood about how to utilize antiviral RNAi in controlling viral infection in insects. Enoxacin belongs to the family of synthetic antibacterial compounds based on a fluoroquinolone skeleton that has been previously found to enhance RNAi in mammalian cells. In this study, we showed that enoxacin efficiently inhibited viral replication of Drosophila C virus (DCV) and Cricket paralysis virus (CrPV) in cultured Drosophila cells. Enoxacin promoted the loading of Dicer-2-processed virus-derived siRNA into the RNA-induced silencing complex, thereby enhancing antiviral RNAi response in infected cells. Moreover, enoxacin treatment elicited an RNAi-dependent in vivo protective efficacy against DCV or CrPV challenge in adult fruit flies. In addition, enoxacin also inhibited replication of flaviviruses, including Dengue virus and Zika virus, in Aedes mosquito cells in an RNAi-dependent manner. Together, our findings demonstrated that enoxacin can enhance RNAi in insects, and enhancing RNAi by enoxacin is an effective antiviral strategy against diverse viruses in insects, which may be exploited as a broad-spectrum antiviral agent to control vector transmission of arboviruses or viral diseases in insect farming.

sample_organism:
Drosophila melanogaster
Drosophila C virus strain EB

overall_design: Small RNA profile of virus-infected Drosophila S2 cells.

first: Bao

last: Lyu

first: Chang

last: Wang

first: Yuanyuan

last: Bie

first: Jing

last: Kong

first: An

first: Liang

last: Jin

first: Xi

last: Zhou


title: Integrative Clinical and Molecular Characterization of Translocation Renal Cell Carcinoma

city: Boston

first: Ziad

last: Bakouny

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Translocation renal cell carcinoma (tRCC) is a poorly-characterized subtype of kidney cancer driven by MiT/TFE gene fusions. Here, we define the landmarks of tRCC through an integrative analysis of 152 patients with tRCC identified across multiple genomic, clinical trial, and retrospective cohorts. Most tRCCs harbor few somatic alterations apart from MiT/TFE fusions and homozygous deletions at chromosome 9p21.3 (19.2% of cases). Transcriptionally, tRCCs display a heightened NRF2-driven antioxidant response that is associated with resistance to many targeted therapies. Consistently, we find that outcomes for patients with tRCC treated with vascular endothelial growth factor receptor inhibitors (VEGFR-TKI) are worse than those treated with immune checkpoint inhibition (ICI). Multiparametric immunofluorescence confirmed the presence of CD8+ tumor-infiltrating T cells compatible with a clinical benefit from ICI and revealed an exhaustion immunophenotype distinct from that of clear cell RCC. Our findings comprehensively define the clinical and molecular features of tRCC and may inspire new therapeutic hypotheses.

overall_design: 6 cell line conditions, 3 replicates each, including 2 control conditions.  The 4 study conditions are:  ASPS-TFE3  PRCC-TFE3  SFPQ-TFE3  NONO-TFE3    The two control conditions are:  WT TFE3  Mock

first: Eliezer

last: Van Allen

first: Toni

middle: K

last: Choueiri

first: Srinivas

last: Viswanathan


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Dicer LKO Liver mRNA Transcriptomes

city: Suzhou

first: Jianming

address: 199 Renai Road

institute: Soochow University

summary: Liver mRNA profiles of one-month-old wild-type (WT) and Dicer liver-specific knockout (Dicer LKO) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq X.

first: Yao

last: Liu


title: Alternative Splicing Mediated by RNA-binding Protein RBM24 Facilitates Cardiac Myofibrillogenesis in a Differentiation Stage-Specific Manner

city: Miaoli County

first: Paul

middle: Wei-Che

last: Hsu

state: Taiwan

address: Zhunan: 35, Keyan Road, Zhunan Town

department: National Health Research Institutes

country: Taiwan

institute: National Health Research Institutes

summary: We ablated RBM24 from human embryonic stem cells (hESCs) using CRISPR/Cas9 techniques. Although RBM24-/- hESCs still differentiated into sarcomere-hosting cardiomyocytes, they exhibited disrupted sarcomeric structures with punctate Z-lines due to impaired myosin replacement during early myofibrillogenesis. Transcriptomics revealed >4000 genes regulated by RBM24. Among them, core myofibrillogenesis proteins (e.g. ACTN2, TTN, and MYH10) were misspliced. Consequently, MYH6 cannot replace non-muscle myosin MYH10, leading to myofibrillogenesis arrest at the early premyofibril stage and causing disrupted sarcomeres. Intriguingly, we found that the actin-binding domain (ABD; encoded by exon 6) of the Z-line anchor protein ACTN2 is predominantly excluded from early cardiac differentiation, whereas it is consistently included in human adult heart. CRISPR/Cas9-mediated deletion of exon 6 from ACTN2 in hESCs, as well as forced expression of full-length ACTN2 in RBM24-/- hESCs, further corroborated that inclusion of exon 6 is critical for sarcomere assembly. Overall, we have demonstrated that RBM24-facilitated inclusion of exon 6 in ACTN2 at distinct stages of cardiac differentiation is evolutionarily conserved and crucial to sarcomere assembly and integrity.

overall_design: To study the molecular mechanism by which RBM24 regulates cardiogenesis and sarcomere assembly in a temporal-dependent manner.

first: Su-Yi

last: Tsai


title: Loss of skin and mucosal CXCR3+ resident memory T cells causes irreversible tissue-confined immunodeficiency in HIV

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary: Single cell RNA-seq , VDJ DNA sequencing  and Bulk RNA-seq sequencing of human skin and blood CD45+ cells from HIV+ patients and healthy controls

overall_design:
For Bulk RNA-seq, we isolated total RNA from skin biopsies and PBMCs. For single cell RNA seq coupled with VDJ DNA Seq, we isolated CD45+ Skin single cells and CD45+ bloos PBMCs.
Raw data not provided due to patient confidentiality.

first: S

last: Saluzzo

first: R

middle: V

last: Pandey

first: G


title: Spatially resolved transcriptomic analysis of acute kidney injury in a female murine model

city: Saint Louis

first: Eryn

last: Dixon

state: MO

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

summary: We optimized and validated a female bilateral ischemia reperfusion injury model. Using the 10X Genomics Visium Spatial Gene Expression solution, we generated spatial maps of gene expression across the injury and repair time course, and applied two open-source computational tools, Giotto and SPOTlight, to increase resolution and measure cell-cell interaction dynamics. An ischemia time of 34 minutes in a female murine model resulted in comparable injury to males across the time course of injury and repair. We report increased resolution of cell and gene expression with Giotto, a computational toolbox for spatial data analysis. Using a seeded non-negative matrix regression (SPOTlight) to deconvolute the dynamic landscape of cell-cell interactions, we find that injured proximal tubule cells are characterized by increasing macrophage and lymphocyte interactions even at 6 weeks after injury, consistent with a pro-inflammatory role for this cell state. In this transcriptomic atlas, we defined region-specific and injury-induced loss of differentiation markers and their re-expression during repair, as well as region-specific injury and repair transcriptional responses. Lastly, we created a data visualization web application for the scientific community to explore these results (http://humphreyslab.com/SingleCell/).

overall_design: 10X Visium was used to create a transcriptomic atlas of female kidney injury to discover, validate, and define spatial and temporal expression of injury specific genes.

first: Haojia

last: Wu

first: Yoshiharu

last: Muto

first: Parker

last: Wilson

first: Benjamin

middle: D

last: Humphreys


title: 10X single-cell RNASeq profiling of immune infiltrate from mutant IDH1 ICC tumors treated with AG120 (mIDH1 inhibitor) or vehicle

city: Cambridge

first: Kira

middle: Eileen

last: Olander

address: 75 Ames St

department: Cancer Program

institute: Broad Institute

summary: AG120, mIDH1 inhibitor, has an immune-dependent mechanism. Single-cell RNA sequencing was used to profile the tumor microenvironment and the key immune subsets impacted by the inhibitor.

overall_design: Profiling of immune infiltrate from mIDH1 ICC treated with AG120 or Vehicle.

first: Emily

last: Kessler

first: Juan

last: Dubrot


title: BS-seq of Tet-TKD 2-cell embryos

first: Julia

last: Arand

address: Schwarzspanierstr. 16

type: Methylation profiling by high throughput sequencing

summary: whole genome bisulfite sequencing of single control and Tet-TKD 2-cell embryos

overall_design: BS-seq was performed for single  2-cell embryos derived from control-morpholino injected and Tet1-,Tet2- plus Tet3-morpholino injected germical vesicle oocytes

first: Mark

last: Wossidlo


title: Transcriptome profile of mouse Embryonic Stem Cells with different BetaCatenin amount

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: To analyse gene expression differences between ESCs BetaCatenin null and rescued with different amount of an exogenous BetaCatenin

overall_design: Total RNA was extracted from n=4 of biological replicates for each experimental group

first: L

last: Marucci


title: Tet enzymes are essential for embryogenesis and completion of embryonic genome activation

summary: Mammalian embryo development begins in transcriptional silence followed by activation of thousands of genes. Reprogramming of DNA methylation is integral to embryogenesis and linked to Tet enzymes; however, their function in early development is not fully understood. Here, we generated combined deficiencies of all three Tet enzymes in mouse oocytes and observed arrest at 2-cell stage with the most severe phenotype linked to Tet2. Gene expression analysis revealed that Tet enzymes are required for completion of embryonic genome activation. Our results demonstrate that Tet enzymes have non-redundant roles and are key components of EGA in mammalian embryos.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: RNA-Seq of control-morpholino injected, Tet3-morpholino injected, Tet1-, Tet2-, and Tet3-morpholino injected 2-cell embryos (11 replicates each) as well as alpha-amanitin treated 2-cell embryos (12 replicates) and negative controls (3 replicates)

first: HyoJin

last: Chiang

first: Michael

middle: P

last: Snyder

first: Renee

last: Reijo Pera


title: Transcriptional regulator HDP1 regulates expansion of the inner membrane complex during early sexual differentiation of malaria parasites

status: Public on Nov 21 2021

city: New York

first: Bjorn

middle: FC

last: Kafsack

state: NY

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine


title: Transcriptional regulator HDP1 regulates expansion of the inner membrane complex during early sexual differentiation of malaria parasites [RNA-Seq]

summary: In this study, we identify HDP1, a previously uncharacterized DNA-binding protein first expressed during early sexual differentiation. The development of HDP1-deficient gametocytes arrests at the Stage I to Stage II transition and ends in loss of viability. Analysis of gene expression and HDP1-binding shows that this protein functions as a positive transcriptional regulator of genes essential for gametocyte development, including genes that are critical for the expansion of the inner membrane complex (IMC) that gives P. falciparum gametocytes their characteristic shape.

overall_design: We analyzed the transcriptome of Δhdp1 and parental NF54 on day 2 of gametocytogenesis, in order to identify changes in expression that may be responsible for aberrant development of HDP1-deficient gametocyes. Two biologically independent replicates were evaluated.

first: Xinran

last: Tong

first: Björn

middle: F


title: Transcriptional regulator HDP1 regulates expansion of the inner membrane complex during early sexual differentiation of malaria parasites [ChIP-Seq]

overall_design: We performed chromatin immunoprecipitation sequencing on nuclei from hdp1-gfp and hdp1-Ty1 gametocytes on day 5 of development, with the latter serving as a negative control, in order to evaluate HDP1-genome wide binding. Two biologically independent replicates were evaluated.

first: Riward

last: Campelo Morillo

first: Steven

last: Abel

first: Karine

middle: G

last: Le Roch


title: Next Generation Sequencing (NGS) of brain BRAFV600E/pAkt/Trp53KO- and control-derived tissue

city: Bonn

first: Silvia

last: Cases

address: Venusberg-Campus 1

institute: Uniklinikum Bonn

summary:
Purpose: Usage of next generation sequencing (NGS) to quantify the expression levels of the overall transcriptome from brain BRAFV600E/pAkt/Trp53KO tumors and and compare it with the contralateral brain control derived from mice.
Methods: Tumor tissues and adjacent normal tissues from mouse brains were microdissected, frozen in liquid nitrogen and stored at -80 °C before RNA extraction. RNA was isolated using the RNeasy Micro Kit (Qiagen) following the manufacturer´s instructions and evaluated using a NanoDrop1000 spectrophotometer and a Qubit RNA HS Assay Kit on a Qubit 2.0 Fluorometer (Thermo Fisher Scientific).
Conclusion: Comparison between the transcriptome of tumor and control brain tissue rise the presence of differentially expressed genes related to immune system, inflamation, proliferation, invasion, synaptic processes, etc.

overall_design: Tumor and control mRNA profiles of BRAFV600E/pAkt/Trp53KO and control brain mouse tissue

last: Cases-Cunillera

first: Karen

last: van Loo

first: Sugirthan

last: Sivalingam

first: Albert

last: Becker


title: Genome-wide analysis of human bone marrow-derived MSC cells in comparision with MSC with EGR1 knockdown or EGR1 overexpressing cells

city: Lund

first: Hongzhe

last: Li

address: Klinikgatan 26

department: Lund Stem Cell Center

country: Sweden

institute: Lund University

summary: Analyze and compare the gene expression profile of human bone marrow derived-MSC in comparison with EGR1 knockdown or EGR1 overexpressing cells. The hypothesis was some genes were differentially expressed in these cell populations. Results provided important information regarding the gene expression difference by EGR1.

overall_design: Total RNA obtained from isolated from different groups of cells were amplified and genome wide gene profiling was compared.


title: A virus-derived microRNA targets immune response genes during SARS-CoV-2 infection [sRNA-seq]

status: Public on Nov 20 2021

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 4eme Etage

department: Development and stem cell biology

country: France

institute: Institut Pasteur

summary: SARS-CoV-2 infection results in impaired interferon response in severe COVID-19 patients. However, how SARS-CoV-2 interferes with host immune response is incompletely understood. Here, we sequenced small RNAs from SARS-CoV-2-infected human cells and identified a microRNA (miRNA) derived from a recently evolved region of the viral genome. We show that the virus-derived miRNA produces two miRNA isoforms in infected cells by the enzyme Dicer and they are loaded into Argonaute proteins. Moreover, the predominant miRNA isoform targets the 3´UTR of interferon-stimulated genes and represses their expression in a miRNA-like fashion. Finally, the two viral miRNA isoforms were detected in nasopharyngeal swabs from COVID-19 patients. We propose that SARS-CoV-2 can potentially employ a virus-derived miRNA to hijack the host miRNA machinery which can lead to evasion of the interferon-mediated immune response.

overall_design: 16 samples were analyzed by sRNA-seq, including replicates (sample name contains 'rep').

first: Meetali

last: Singh

first: Maxime

last: Chazal

first: Piergiuseppe

last: Quarato

first: Loan

last: Bourdon

first: Thomas

last: Vallet

first: Marco

last: Vignuzzi

first: Sylvie

last: van der Werf

last: Behillil

first: Flora

last: Donati

first: Nathalie

last: Sauvonnet

first: Giulia

last: Nigro

first: Maryline

last: Bourgine

first: Nolwenn

last: Jouvenet


title: A virus-derived microRNA targets immune response genes during SARS-CoV-2 infection

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

overall_design: Refer to individual Series


title: DamID transcriptional profiling identifies the Snail/Scratch  transcription factor Kahuli as an Alk target in the Drosophila visceral mesoderm

city: Gothenburg

first: Erik

last: Larsson

address: Medicinaregatan 9A

institute: University of Gothenburg

summary: We used targeted DamID (TaDa) to identify Alk targets in embryos overexpressing Jeb versus embryos with abrogated Alk activity, revealing differentially expressed genes, including the Snail/Scratch family transcription factor Kahuli (Kah)

overall_design: Examination of Alk targets via trancriptional profiling with DamID by Alk activation/deactivation using generic and specific promoters

first: Ruth

last: Palmer

last: Lekholm

first: Patricia

last: Mendoza

first: Swaraj

last: Basu


title: piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development [RNA-seq]

first: Germano

last: Cecere

summary: Eukaryotic genomes harbor invading transposable elements silenced by PIWI-interacting RNAs (piRNAs) to maintain genome integrity in animal germ cells. However, whether piRNAs also regulate endogenous gene expression programs remains unclear. Here, we show that C. elegans piRNAs trigger the transcriptional silencing of hundreds of spermatogenic genes during spermatogenesis, promoting sperm differentiation and function. This silencing signal requires the piRNA-dependent small RNA biogenesis and loading into downstream nuclear effectors, which correlates with the dynamic reorganization of two distinct perinuclear biomolecular condensates present in germ cells. In addition, the silencing capacity of piRNAs is temporally counteracted by the Argonaute CSR-1, which targets and licenses spermatogenic gene transcription. The spatial and temporal overlap between these opposing small RNA pathways contributes to setting up the timing of the spermatogenic differentiation program. Thus, our work identifies a prominent role for piRNAs as direct regulators of endogenous transcriptional programs during germline development and gamete differentiation.

overall_design: 11 samples were analyzed by RNA-seq, including replicates (sample name contains 'rep').

first: Eric

last: Cornes

last: Singh

first: Florian

last: Mueller

first: Blaise

last: Li


title: piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development [small RNA-IP-seq]

overall_design: 28 IP-input paired samples were analyzed by sRNA-seq.

first: Meetali

first: Piergiuseppe

last: Quarato

first: Loan

last: Bourdon


title: piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development [GRO-seq]

overall_design: 17 samples were analyzed by GRO-seq, including replicates (sample name contains 'rep').


title: Disruption of pancreatic stellate cell myofibroblast phenotype promotes pancreatic tumour invasion.

status: Public on Nov 19 2021

first: Angus

last: Cameron

address: John Vane Science Centre, Charterhouse Sq,

summary: In pancreatic ductal adenocarcinoma (PDAC), differentiation of pancreatic stellate cells (PSCs) into myofibroblast-like cancer-associated fibroblasts (CAFs) promotes fibrotic,  therapy-resistant tumours. Conversely, suppression of CAFs can result in aggressive metastatic tumours. Here we show that the Rho-effector kinase protein kinase N2 (PKN2) is critical for PSC myofibroblast differentiation. Loss of PKN2 was associated with reduced PSC proliferation and contractility, retention of lipid droplets and decreased a-SMA stress fibres. PKN2 loss was also associated with a myofibroblast CAF to -like inflammatory CAF switch in the PSC matrisome signature both in vitro and in vivo. In spheroid co-cultures with PDAC cells, loss of PKN2 prevented PSC invasion but, counter-intuitively, promoted invasive cancer cell outgrowth. Further, deletion of PKN2 in the pancreatic stroma induced more locally invasive, orthotopic pancreatic tumours. Finally, we demonstrated that a PKN2KO PKN2 KO matrisome signature predicts poor outcome in pancreatic and other solid human cancers. Our data indicate that suppressing PSC myofibroblast differentiation function can limit important stromal tumour suppressive mechanisms, while promoting a switch to a cancer-supporting CAF phenotype.

overall_design: mRNA profiles of 6 stromal-PKN2 knockout (KO) and 5 stromal-PKN2 wild type (WT) mouse orthotopic pancreatic tumours.

first: Elizabeth

last: Murray

first: Shinelle

last: Menezes

first: Jack

last: Henry

first: Faraz

last: Khan

first: Jun

last: Wang


title: Chromosome-scale assembly of hexaploid genome of Ma Bamboo (Dendrocalamus latiflorus Munro)

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

summary: Dendrocalamus latiflorus Munro (D. latiflorus) is a woody clumping bamboo with rapid shoot growth. Both genetic transformation and CRISPR-Cas9 gene editing techniques are available for D. latiflorus, enabling reverse genetic approaches. Thus, D. latiflorus has the potential to be a model bamboo species. However, the genome sequence of D. latiflorus has remained unreported due to its polyploidy and large genome size. Here, we sequenced the D. latiflorus genome and assembled it into three allele-aware subgenomes (AABBCC), representing the largest genome of a major bamboo species. We assembled 70 allelic chromosomes (2,737 Mb) for hexaploid D. latiflorus using both single-molecule sequencing from the Pacific Biosciences (PacBio) Sequel platform and chromosome conformation capture sequencing (Hi-C). Repetitive sequences comprised 52.65% of the D. latiflorus genome. We annotated 135,231 protein-coding genes in the genome based on transcriptomes from eight different tissues. Transcriptome sequencing using RNA-Seq and PacBio single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) revealed highly differential alternative splicing (AS) between non-abortive and abortive shoots, suggesting that AS regulates the abortion rate of bamboo shoots. This high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using D. latiflorus as a model species.

overall_design: RNA-seq of D.latiflorus

first: Yushan

last: Zheng

first: Deming

last: Yang


title: Overloading mesenchymal progenitors (FAPs)

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: Skeletal muscle possesses the ability to adapt its size in response to milieus, which is called plasticity. Resistance training induces the increment of muscle mass called muscle hypertrophy. Muscle stem cells (MuSC; also known as muscle stem cells) function to supply new nuclei for myofiber during the overload in muscle. We found that Yap1 and Taz in mesenchymal progenitors (also called FAPs) are critical for MuSC proliferation in overloaded muscles. We hypothsize that Yap1/Taz-dependent mesenchymal progenitors derived factor induces MuSC proliferation. In order to identify such factors, RNA-seq of overloaded FAPs were performed.

overall_design: Sham and overloaded mesenchymal progenitors from Control (Pdgfra-CreERT2) or cdKO  (Pdgfra-CreERT2::Yap1 flox/flox ::Taz flox/flox) were used for RNA-seq analysis.

first: Akihiro

last: Kaneshige

first: Takayuki

last: Kaji

first: Ohkawa

last: Yasuyuki

first: So-ichiro

last: Fukada


title: Genome-scale CRISPR screen identifies TMEM41B as a critical host factor required for coronavirus replication

first: Shengsong

last: Xie

address: 1st Shizishan Street, Hongshan

institute: Huazhong Agricultural University


title: Mitochondrial-derived glutamate dictates resistance to pathogen infection through vitamin-dependent metabolic remodeling

city: College Station

first: Jason

last: Karpac

state: Texas

address: Reynolds Medical Building

department: Molecular and Cellular Medicine

institute: Texas A&M University Health Sciences Center

summary: The functional integration of innate immune and metabolic signaling responses represents an ancient strategy to manage infections in metazoans.  Using Drosophila, we uncovered that immune-metabolic sensing in muscle dictates resistance to enteric bacterial infection through vitamins dependent metabolic remodeling. Within muscle, the activation strength of systemic innate immune signaling, integrated with mitochondrial-dependent glutamate dehydrogenase (Gdh) function, conditions lipid mobilization from adipose. Mild intramuscular IMD/innate immune signaling activity allows for infection-mediated increases in mitochondrial biogenesis/function, which further stimulates mitochondria/Gdh-dependent synthesis of glutamate. Intramuscular derived glutamate acts as a systemic metabolite to influence lipid mobilization through altering vitamin metabolism. This lipid mobilization improves bacterial clearance and boost infection resistance. Conversely, elevated activation of IMD/innate immune signaling in muscle impedes infection-mediated increases in mitochondrial biogenesis/function and subsequent metabolic remodeling. Finally, life history traits that fine-tune intramuscular mitochondrial dynamics consequently influence infection resistance and shape phenotypic diversity of infection responses within populations.

overall_design: We wanted to explore the muscle and adipose transcriptional networks in response to enteric bacterial infection. Utilizing transcriptomics (RNA-seq.), we generated genome-wide expression profiles from dissected thoraces/muscle and carcass/fat body of Act88FGal4>UAS-RelishRNAi flies upon Mock (sucrose) or Pseudomonas entomophila (P.e.) oral infection (compared to controls [Act88FGal4>w1118), and also drosocin-GFP (Dro-GFP) flies upon Mock (sucrose) or P.e. oral infection (Dro-GFP Positive and Dro-GFP Negative).

first: Xiao

last: Zhao


title: Adipocyte Precursor Cells from First Degree Relatives of type 2 diabetic patients feature changes of hsa-mir-23a-5p, -193a-5p, and -193b-5p and Insulin-Like Growth Factor 2 expression

city: Napoli

first: Gregory

middle: Alexander

last: Raciti

address: Via S. Pansini 5

institute: Università degli Studi di Napoli Federico II


title: Mapping translation in wild-type and METTL5 knockout (KO) mice

city: Chicago

first: Caraline

last: Sepich

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

summary: We performed ribosome profiling on wild-type and METTL5 KO mice to investigate translation changes due to loss of METTL5.

overall_design: Comparing sequencing of ribosome-protected-fragments (RPFs, normalized to input RNA-seq) from wild type and METTL5 KO mice.

last: Sepich-Poore

first: Sigrid

last: Nachtergaele

first: Chuan

last: He


title: Adipocyte Precursor Cells from First Degree Relatives of type 2 diabetic patients feature changes of hsa-mir-23a-5p, -193a-5p, and -193b-5p and Insulin-Like Growth Factor 2 expression [RNA-Seq]

summary: First-degree relatives (FDRs) of type 2 diabetics (T2D) feature dysfunction of subcutaneous adipose tissue (SAT) long before T2D onset. miRNAs have a role in adipocyte precursor cells (APC) differentiation and in adipocyte identity. Thus, impaired miRNA expression may contribute to SAT dysfunction in FDRs. In the present work, we have explored changes of miRNA expression associated with T2D family history which may affect gene expression in SAT APCs from FDRs. Small RNA-seq was performed in APCs from healthy FDRs and matched controls and omics data were validated by qPCR. Integrative analyses of APC miRNome and transcriptome from FDRs revealed down-regulated hsa-miR-23a-5p, -193a-5p and -193b-5p accompanied by up-regulated Insulin-like Growth Factor 2 (IGF2) gene which proved to be their direct target. The expression changes of these marks were associated with SAT adipocyte hypertrophy in FDRs. APCs from FDRs further demonstrated reduced capability to differentiate into adipocytes. Treatment with IGF2 protein decreased APC adipogenesis, while over-expression of hsa-miR-23a-5p, -193a-5p and -193b-5p enhanced adipogenesis by IGF2 targeting. Indeed, IGF2 increased the Wnt Family Member 10B gene expression in APCs. Down-regulation of the three miRNAs and IGF2 up-regulation were also observed in Peripheral Blood Leukocytes (PBLs) from FDRs. In conclusion, APCs from FDRs feature a specific miRNA/gene profile, which associates with SAT adipocyte hypertrophy and appears to contribute to impaired adipogenesis. PBL detection of this profile may help in identifying adipocyte hypertrophy in individuals at high risk of T2D.

overall_design: The study has been centered around the hypothesis that changes in the expression of specific miRNAs and mRNAs is associated with family history of T2D. To achieve this goal, transcriptome and miRNome profilings of Subcutaneous Adipose Tissue (SAT)-Adipocyte Precursor Cells (APCs) in Healthy individuals with Family history of Type 2 diabetes (FDR) and in Healthy individuals without Family history of Type 2 diabetes (Ctrl) were generated by deep sequencing in pooled samples (n=2 for Ctrl and n=2 for FDRs) using Illumina Hiseq2000 platform. qPCR has been adopted for validation analyses of small RNA- and RNA-seq computational data in all individuals belonging to the FDR (n=8) and Ctrl (n=10) groups.

first: Paola

last: Mirra

first: Antonella

last: Desiderio

first: Rosa

last: Spinelli

first: Cecilia

last: Nigro

first: Michele

last: Longo

first: Luca

last: Parrillo

first: Vittoria

last: D’Esposito

first: Annamaria

last: Carissimo

first: Shahram

last: Hedjazifar

first: Ulf

last: Smith

first: Pietro

last: Formisano

first: Claudia

last: Miele

middle: A

first: Francesco

last: Beguinot


title: A test of the pioneer factor hypothesis using ectopic liver gene activation [0.05dox CUTTag]

status: Public on Nov 18 2021

city: St. Louis

first: Barak

last: Cohen

address: 4515 McKinley Ave

department: Genetics

summary: The Pioneer Factor Hypothesis (PFH) states that pioneer factors (PFs) are a subclass of transcription factors (TFs) that bind to and open inaccessible sites and then recruit non-pioneer factors (nonPFs) that activate batteries of silent genes. We tested the PFH by expressing the endodermal PF FoxA1 and nonPF Hnf4a in K562 lymphoblast cells. While co-expression of FoxA1 and Hnf4a activated a burst of endoderm-specific gene expression, we found no evidence for functional distinction between these two TFs. When expressed independently, both TFs bound and opened inaccessible sites, activated endodermal genes, and “pioneered” for each other, although FoxA1 required fewer copies of its motif to bind at inaccessible sites. A subset of targets required both TFs, but the mode of action at these targets did not conform to the sequential activity predicted by the PFH. From these results we propose an alternative to the PFH where “pioneer activity” depends not on the existence of discrete TF subclasses, but on TF binding affinity and genomic context.

overall_design: To measure binding, we treated clonally derived K562 cell lines that were previously transduced with lentiviral vectors carrying doxycycline-inducible FoxA1 or Hnf4a with +/- 0.05µg/ml doxycycline for 24 hours in duplicate. We then split each uninduced and induced samples and treated with +/- primary antibody followed by a species-specific secondary antibody. Then, we isolated 1e5 cells/sample and followed the CUTANA Direct-to-PCR CUT&Tag protocol from Epicypher. Due to extremely low background in both the uninduced and negative antibody samples and based on recommendation from the lab that developed the technology (Kaya-Okur 2020), we only sequenced +doxycycline +antibody samples. We size selected the libraries with AmpureXP beads and sequenced them on an Illumina NextSeq 500 using 2x150 paired-end reads.

first: Jeffrey

last: Hansen

first: Kaiser

last: Loell


title: A virus-derived microRNA targets immune response genes during SARS-CoV-2 infection [RNA-seq]

first: Germano

last: Cecere

first: Meetali

last: Singh

first: Maxime

last: Chazal

first: Piergiuseppe

last: Quarato

first: Loan

last: Bourdon

first: Thomas

last: Vallet

first: Marco

last: Vignuzzi

first: Sylvie

last: van der Werf

last: Behillil

first: Flora

last: Donati

first: Nathalie

last: Sauvonnet

first: Giulia

first: Maryline

last: Bourgine

first: Nolwenn

last: Jouvenet


title: Alterations of 5-Hydroxymethylcytosines in Circulating Cell-free DNA Reflect Retinopathy in Type 2 Diabetes

first: Issam

last: Awad

address: 5841 S. Maryland Avenue

department: Department of Neurology

institute: The University of Chicago

summary: Diabetic retinopathy (DR) is a common microvascular complication that may cause severe visual impairment and blindness in patients with type 2 diabetes mellitus (T2DM). Early detection of DR will provide opportunities for more treatment options and better control of disease progression. Effective biomarkers, which are not currently available, may improve clinical outcomes through precise diagnosis and prognosis. We sought to develop a non-invasive diagnostic approach for diabetic retinopathy among type 2 diabetes mellitus based on 5-hydroxymethylcytosines (5hmC), an emerging epigenetic marker, in circulating cell-free DNA (cfDNA)

overall_design: We obtained genome-wide 5hmC profiles using the 5hmC-Seal technique in cfDNA samples from 70 prospectively enrolled Chinese patients, within 35 patients diagnosed with DR and 35 age-, gender-, diabetic duration-matched T2DM controls. The 5hmC-based marker genes for DR were developed using the elastic net regularization under a case-control design

first: Wei

last: Zhang

first: Chang

last: Chen

first: Liyuan

last: Han

first: Shiwei

last: Duan


title: piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development

first: Germano

last: Cecere

summary:
Eukaryotic genomes harbor invading transposable elements silenced by PIWI-interacting RNAs (piRNAs) to maintain genome integrity in animal germ cells. However, whether piRNAs also regulate endogenous gene expression programs remains unclear. Here, we show that C. elegans piRNAs trigger the transcriptional silencing of hundreds of spermatogenic genes during spermatogenesis, promoting sperm differentiation and function. This silencing signal requires the piRNA-dependent small RNA biogenesis and loading into downstream nuclear effectors, which correlates with the dynamic reorganization of two distinct perinuclear biomolecular condensates present in germ cells. In addition, the silencing capacity of piRNAs is temporally counteracted by the Argonaute CSR-1, which targets and licenses spermatogenic gene transcription. The spatial and temporal overlap between these opposing small RNA pathways contributes to setting up the timing of the spermatogenic differentiation program. Thus, our work identifies a prominent role for piRNAs as direct regulators of endogenous transcriptional programs during germline development and gamete differentiation.

This SuperSeries is composed of the SubSeries listed below.


title: RNA-sequencing results of five samples across three YMC cycles of both wt and yaf9W89A strains

city: Chapel Hill

first: Brian

middle: David

last: Strahl

state: NC

address: 120 Mason Farm Road 3060 Genetic Medicine

department: Biochemistry

institute: UNC-Chapel Hill

summary: The goal of the experiments is to study how the absence of Yaf9-H3 acyl reading affected metabolic and global gene transcription. We performed RNA-seq for our wt and yaf9W89A cells across three consecutive YMC cycles. We found that HOC genes maintained expression in the LOC phase and that LOC genes were not properly expressed in the LOC phase.

overall_design: 5 time points of YMC samples were collected across three consecutive cycles for both wt and yaf9W89A strains. Samples WT1-WT5 cover one wt YMC cycle. WT6-WT10 and WT11-WT15 are replicates; Samples W89A16-W89A20 cover one yaf9W89A YMC cycle. W89A21-W89A25 and W89A26-W89A30 are replicates. The triplicates were processed with RNA sequencing technology.


title: Genome-scale CRISPR screen identifies TMEM41B as a critical host factor required for coronavirus replication [PigGeCKO]

city: Wuhan

first: Shengsong

last: Xie

summary: We use the a porcine genome-scale CRISPR/Cas9 knockout (PigGeCKO)  library (Zhao et al., 2020)  to identify key host factors facilitating TGEV infection in porcine cells.

overall_design: We generated a PigGeCKO cell collection (in the PK-15 background) as previously described  and performed a genome-wide loss-of-function genetic screen.Briefly, we conducted three rounds of TGEV challenge, employing untreated PK-15-Cas9 cells as a negative control.

first: Guiqing

last: Peng

first: Limeng

last: Sun

first: Changzhi

last: Zhao


title: Exploring the organ specific expression pattern of CD4+iNKT1 cells of C57BL/6 and BALB/c mice.

city: Hannover

first: Hristo

last: Georgiev

address: Carl Neuberg Str. 1

department: Institute of Immunology

institute: Hannover Medical School

summary:
iNKT cells are generated in thymus and settle all organs and tissues in mice. We used RNA high throughput sequencing to identify genes that displayed an organ specific expression by comparing iNKT1 cells of thymus, liver, blood, and spleen origin, respectively.
We observed organ specific expression of a variety of genes that might reflect specialized functional adaptations connected to the unique micro-environments of the investigated organs.

overall_design:
CD4+CXCR3+iNKT1 cells were sorted out of CD3+tetramer+DAPI-B220-CD138- lymphocytes by flow cytometry (blood, liver, spleen).
For thymus, CD122 was used instead of CXCR3 and CD138 was not included as a negative marker in order to obtain CD4+iNKT1 cells.

first: Georgia

last: Papadogianni

first: Günter

last: Bernhardt


title: Genome-scale CRISPR screen identifies TMEM41B as a critical host factor required for coronavirus replication [Focused cell]

summary: We use the Focused-library to identify key host factors facilitating TGEV infection in porcine cells.

overall_design: We generated a Focused cell collection (in the PK-15 background) as previously described and performed a focused loss-of-function genetic screen. Briefly, we conducted five rounds of TGEV challenge, employing untreated PK-15-Cas9 cells as a negative control to confirm the cell death caused by TGEV infection in each round.  The surviving mutant cells were collected and used for subsequent TGEV challenge rounds. Finally, the sgRNA constructs in surviving mutant cells of third and fifth rounds were PCR amplified and deep sequenced.


title: Library-based analysis reveals segment and length dependent characteristics of defective influenza genomes

status: Public on Nov 17 2021

city: San Diego

first: Alistair

middle: Brian

last: Russell

state: CA

address: 9500 Gilman Dr,

department: Biological Sciences

institute: University of California, San Diego

summary: Parasitic elements of the viral population which are unable to replicate on their own yet rise to high frequencies, defective interfering particles are found in a variety of different viruses.  Their presence is associated with a loss of population fitness, both through the depletion of key cellular resources and the stimulation of innate immunity.  For influenza A virus, these particles contain large internal deletions in the genomic segments which encode components of the heterotrimeric polymerase.  Using a library-based approach, we comprehensively profile the growth and replication of defective species, demonstrating they possess an advantage during genome replication, and that exclusion during packaging reshapes population composition in a manner consistent with their final, observed, distribution in natural populations.  We find that innate immunity is not linked to the size of a deletion; however, replication of defective segments can enhance their immunostimulatory properties.  Overall, our results address several key questions in defective influenza A virus biology, and the methods we have developed to answer those questions may be broadly applied to other defective viruses.

overall_design: For each artificial library, three independent experiments, from library generation onwards, are presented. For natural sequencing, two biological replicates are presented, each with two technical replicates.

middle: B

first: Marisa

last: Mendes


title: Adipocyte Precursor Cells from First Degree Relatives of type 2 diabetic patients feature changes of hsa-mir-23a-5p, -193a-5p, and -193b-5p and Insulin-Like Growth Factor 2 expression [smallRNA-seq]

first: Gregory

last: Raciti

first: Paola

last: Mirra

first: Antonella

last: Desiderio

first: Rosa

last: Spinelli

first: Cecilia

last: Nigro

first: Michele

last: Longo

first: Luca

last: Parrillo

first: Vittoria

last: D’Esposito

first: Annamaria

last: Carissimo

first: Shahram

last: Hedjazifar

first: Ulf

last: Smith

first: Pietro

last: Formisano

first: Claudia

last: Miele

first: Francesco

last: Beguinot


title: Liver Transcriptomics from Male and Female Mice of Three Strains on Control, Medium Protein and Low Protein Diets

city: Madison

first: Cara

middle: Leanne

last: Green

state: Wisconsin

address: 2214 Kendall Ave

department: Medicine

institute: University of Wisconsin-Madisin

summary: Mice were put on either a control, medium or low protein diet and their liver transcriptomic expression was measured after 13 weeks on diet after an overnight fast. This was to discover the impact of sex, strain and protein level on the metabolism of the liver.

overall_design: To compare the metabolic effect of a Low and Medium Protein Diets on different sexes and strains, 10-week-old  mice were placed on either a Control, Medium Protein or Low Protein diets for 13 weeks. All mice were maintained at a temperature of approximately 22°C. Mice were euthanized by cervical dislocation and livers were harvested and snap frozen in liquid nitrogen following overnight (16-hr) fasting.

middle: L


title: Dual effect: High NADH levels contribute to efflux-mediated antibiotic resistance but drive ROS lethality

city: Braunschweig

first: Alejandro

last: Arce Rodriguez

address: Inhoffenstraße 7

institute: Helmholtz-HZI

summary: In light of the antibiotic crisis, emerging strategies to sensitize bacteria to available antibiotics should be explored. Several studies on the mechanisms of killing suggest that bactericidal antibiotic activity is enforced through the generation of reactive oxygen species (ROS lethality hypothesis). Here, we artificially manipulated the redox homeostasis of the model opportunistic pathogen Pseudomonas aeruginosa using specific enzymes that catalyze either the formation or oxidation of NADH. Increased NADH levels led to the activation of antibiotic efflux pumps and high levels of antibiotic resistance. However, higher NADH levels also resulted in increased intracellular ROS and amplified antibiotic killing. Our results demonstrate that growth inhibition and killing activity are mediated via different mechanisms. Furthermore, the profound changes in bioenergetics produced low virulence phenotypes characterized by reduced inter-bacterial signaling controlled pathogenicity traits. Our results pave the way for a more effective infection resolution and add an anti-virulence strategy to maximize chances to combat devastating P. aeruginosa infections while reducing the overall use of antibiotics.

overall_design: Differential expression of P. aeruginosa cells expressing either a NADH oxidase or a formate dehydrogenase and compared to a empty plasmid control

first: Matthias

last: Preusse

first: Susanne

last: Häussler


title: A test of the pioneer factor hypothesis using ectopic liver gene activation [0.05dox RNAseq]

first: Barak

last: Cohen

institute: Washington University in St. Louis

overall_design: To measure expression, we treated clonally derived K562 cell lines that were previously transduced with lentiviral vectors carrying doxycycline-inducible FoxA1 or Hnf4a with +/- 0.05µg/ml doxycycline for 24 hours in triplicate. We extracted RNA from 1e6 cells/sample with the PureLink RNA Mini column extraction kit (Invitrogen #12183020) and then treated with on-column DNA digestion with PureLink DNase (Invitrogen #12185010). We then prepared libraries with the NEBNext Ultra II Directional RNA Library Prep Kit, size selected the libraries with AmpureXP beads, and then sequenced them on an Illumina NextSeq 500 using 2x75 paired-end reads.

first: Jeffrey

last: Hansen

first: Kaiser

middle: J

last: Loell


title: NCOR2 controls androgen deprivation therapy failure in advanced prostate cancer through re-wiring of the onco-epigenome [RNA-seq]

city: Buffalo

first: Mark

last: Long

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: NCOR2 is frequently and significantly mutated in late stage androgen deprivation therapy resistant prostate cancer (ADT-RPCa). NCOR2 has been characterized as a transcriptional corepressor and has mechanistic links to DNA methylation, but its global functions and overall contributions to PCa progression remain enigmatic. We mapped the dihydrotestosterone (DHT) dependent and independent effects of NCOR2 on the transcriptome, cistrome and DNA methylome in androgen sensitive (AS) and ADT-RPCa cells using the isogenic LNCaP and LNCaP-C4-2 (C4-2) cell models and the CWR22 xenograft model of ADT-RPCa.

overall_design: total RNA was isolated from  androgen sensitive (LNCaP) and androgen therapy resistant (LNCaP-C42) prostate cancer cell lines after 6hr treatment (EtOH or 10nM DHT) .

first: Dominic

last: Smiraglia

first: Moray

last: Campbell


title: Genome-scale CRISPR screen identifies TMEM41B as a critical host factor required for coronavirus replication [RNA-seq]

first: Shengsong

last: Xie

summary: Explore the potential downstream signaling pathways that inhibit TGEV replication after knocking out TMEM41B by RNA-seq analysis.

overall_design: For RNA high-throughput sequencing (RNA-seq), RNA libraries were created from each group, for example, TMEM41B KO cells (TMEM41B_KO_MOCK, TMEM41B_KO_TGEV) and WT cells (WT_MOCK, WT_TGEV). Three  replicates were conducted for each sample.

first: Guiqing

last: Peng

first: Limeng

last: Sun

first: Changzhi

last: Zhao


title: Overloading mesenchymal progenitors (FAPs)

city: suita

first: so-ichiro

last: fukada

address: 1-6 yamadaoka

institute: osaka University

summary: Skeletal muscle possesses the ability to adapt its size in response to milieus, which is called plasticity. Resistance training induces the increment of muscle mass called muscle hypertrophy. Muscle stem cells (MuSC; also known as muscle stem cells) function to supply new nuclei for myofiber during the overload in muscle. We hypothesize that mesenchymal progenitors (also called FAPs) -derived factor induces MuSC proliferation. In order to identify such factors, RNA-seq of overloaded FAPs were performed.

overall_design: Control and overloaded mesenchymal progenitors from C57BL/6 were used for RNA-seq analysis.

first: Akihiro

last: Kaneshige

first: Takayuki

last: Kaji

first: Ohkawa

last: Yasuyuki

first: So-ichiro

last: Fukada


title: Transcriptomic Taxonomy and Neurogenic Trajectories of Adult Human, Macaque and Pig Hippocampal and Entorhinal Cells

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

department: Neuroscience

institute: Yale University

summary: The hippocampal-entorhinal system supports cognitive functions, has lifelong neurogenic capabilities in many species, and is selectively vulnerable to Alzheimer’s disease. To investigate neurogenic potential and cellular diversity, we profiled single-nucleus transcriptomes in five hippocampal-entorhinal subregions in human, macaque, and pig.  Integrated cross-species analysis revealed robust transcriptomic and histologic signatures of neurogenesis in adult mouse, pig and macaque, but not humans. Doublecortin (DCX), a widely accepted marker of newly generated granule cells, was detected in diverse human neurons, but it did not define immature neuron populations. To explore species differences in cellular diversity and implications for disease, we characterized subregion-specific transcriptomically-defined cell types and transitional changes from the three-layered archicortex to the six-layered neocortex. Notably, METTL7B defined subregion-specific excitatory neurons and astrocytes in primates, associated with endoplasmic reticulum and lipid droplet proteins, including Alzheimer's disease-related proteins. Together this resource reveals cell-type- and species-specific properties shaping hippocampal-entorhinal neurogenesis and function.

sample_organism:
Macaca mulatta
Homo sapiens
Sus scrofa

platform_organism:
Macaca mulatta
Homo sapiens
Sus scrofa

overall_design: snRNA-seq of hippocampal-entorhinal system in 6 human donors, dentate gyrus in 3 rhesus macaque donors, and adult hippocampus in 9 pig donors with different postmortem intervals (30 minutes, 1 hour, 7 hour)

first: Daniel

last: Franjic

first: Mario

last: Skarica

first: Shaojie

last: Ma

first: Jon

middle: I

last: Arellano

first: Andrew

middle: T

last: Tebbenkamp

first: Jinmyung

last: Choi

first: Chuan

last: Xu

first: Qian

last: Li

first: Yury

middle: M

last: Morozov

first: David

last: Andrijevic

first: Zvonimir

last: Vrselja

first: Ana

last: Spajic

first: Gabriel

last: Santpere

first: Mingfeng

first: Shupei

last: Zhang

first: Yang

last: Liu

first: Joshua

last: Spurrier

first: Le

first: Ivan

last: Gudelj

first: Lucija

last: Rapan

first: Hideyuki

last: Takahashi

first: Anita

last: Huttner

first: Rong

last: Fan

first: Stephen

last: Strittmatter

first: Andre

last: Sousa

first: Pasko

last: Rakic


title: NCOR2 controls androgen deprivation therapy failure in advanced prostate cancer through re-wiring of the onco-epigenome [CWR22_EPIC]

first: Mark

middle: D

last: Long

type: Methylation profiling by genome tiling array

overall_design: Bisulphite converted DNA from CWR22 xenograft samples were hybridised to the Illumina Infinium HumanMethylation850 BeadChip

first: Dominic

last: Smiraglia

first: Moray

last: Campbell


title: Protection against autoimmunity is driven by thymic epithelial cell-mediated regulation of Treg development

city: Zürich

first: Claudia

last: Haftmann

address: Winterthurerstr. 190

department: Experimental Immunology

country: Switzerland

institute: University of Zurich

summary: Thymic education of Tregs is superior to negative selection in the prevention of autoimmunity. To address this hypothesis, TCR repertoires of thymic and peripheral Tcells (including Tregs) from conditional NIK KO and WT mice have been sequenced and compared.

overall_design: Tregs cells have been sorted from spleen of 5 WT and 5 Foxn1CrexNIKflfl mice.

first: Florian

last: Ingelfinger

first: Pascale

last: Zwicky

last: Mair

first: Stefan

last: Flöss

first: Rene

last: Riedel

first: Pawel

last: Durek

first: Marianne

last: Spalinger

first: Ekatarina

last: Friebel

first: Brian

last: Leung

first: Jan

last: Kieslow

first: Ari

last: Waisman

first: Mir-Farzin

last: Mashreghi

first: Jochen

last: Hühn

first: Burkhard

last: Becher


title: Transcriptional profile of human memory B cells isolated from lung, lung-draining lymph node and PBMCs

city: Melbourne

first: Hyon Xhi

last: Tan

state: Victoria

address: 792 Elizabeth St

department: Department of Microbiology and Immunology

country: Australia

institute: The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity

summary: RNAseq was performed on human memory B cells isolated from lung, lung-draining lymph nodes and PBMCs to identify differentially expressed genes underpinning tissue localisation.

overall_design: Cells from human tissues were stained and sorted for memory B cells (CD20+ CD19+ IgD- IgG+). Transcriptional profiling and differential gene expression was performed using RNA sequencing.

first: Hyon-Xhi

first: Jennifer

last: Juno

first: Robyn

last: Esterbauer

first: Hannah

last: Kelly

first: Kathleen

last: Wragg

first: Penny

last: Konstandopoulos

first: Sheilajen

last: Alcantara

first: Carolina

last: Alvarado

first: Robert

last: Jones

first: Graham

last: Starkey

first: Boa

middle: Z

last: Wang

first: Osamu

last: Yoshino

first: Thomas

last: Tiang

first: M

last: Grayson

first: Helen

last: Opdam

first: Rohit

last: D'Costa

first: Angela

last: Vago

first: Laura

middle: K

last: Mackay

first: Claire

last: Gordon

first: David

last: Masopust

first: Joanna

middle: R

last: Groom

first: Stephen

last: Kent

first: Adam

last: Wheatley


title: A novel diagnostic approach for the classification of small B-cell lymphoid neoplasms based on the NanoString platform

first: Wei

last: Zhang

address: Jiefang Avenue

department: Hematology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Small B-cell lymphoid neoplasms (SBCLNs) are a heterogeneous group of diseases characterized by malignant clonal proliferation of mature B-cells. However, the classification of SBCLNs remains a challenge, especially in cases where histopathological analysis is unavailable or those with atypical laboratory findings or equivocal pathologic data. In this study, gene expression profiling of 1,039 samples from 27 GEO datasets was first investigated to select highly and differentially expressed genes among SBCLNs. Samples from 57 SBCLN cases and 102 nonmalignant control samples were used to train a classifier using the NanoString platform. The classifier was built by employing a cascade binary classification method based on the random forest algorithm with 35 refined gene signatures. Cases were successively classified as chronic lymphocytic leukemia/small lymphocytic lymphoma, conventional mantle cell lymphoma, follicular lymphoma, leukemic non-nodal mantle cell lymphoma, marginal zone lymphoma, lymphoplasmacytic lymphoma/Waldenström’s macroglobulinemia, and other undetermined. The classifier algorithm was then validated using an independent cohort of 197 patients with SBCLNs. Under the distribution of our validation cohort, the overall sensitivity and specificity of proposed algorithm model were >95% respectively for all the cases with tumor cell content greater than 0.72. Combined with additional genetic aberrations including IGH-BCL2 translocation, MYD88 L265P mutation, and BRAF V600E mutation, the optimal sensitivity and specificity were respectively found at 0.88 and 0.98. In conclusion, the established algorithm demonstrated to be an effective and valuable ancillary diagnostic approach for the sub-classification and pathologic investigation of SBCLN in daily practice.

overall_design: Using the NanoString platform, we developed the assay which may help classify small B-cell lymphoid neoplasms.

first: Qilin

last: Ao

first: Yuqi

last: Guan

first: Zhoujie

last: Zhu

first: Dong

last: Kuang

first: Monica

last: Li

first: Kefeng

last: Shen

first: Meilan

first: Jiachen

first: Li

last: Yang

first: Haodong

last: Cai

first: Ying

first: Ken

middle: H

last: Young

first: Jianfeng

last: Zhou

first: Min

last: Xiao


title: NCOR2 controls androgen deprivation therapy failure in advanced prostate cancer through re-wiring of the onco-epigenome [CellLine_EPIC]

first: Mark

last: Long

overall_design: Bisulphite converted DNA from LNCaP and LNCaP-C42 cell lines were hybridised to the Illumina Infinium HumanMethylation850 BeadChip

first: Dominic

last: Smiraglia

first: Moray

last: Campbell


title: NCOR2 controls androgen deprivation therapy failure in advanced prostate cancer through re-wiring of the onco-epigenome [CWR22 xenograft]

overall_design: Total RNA was isolated from CWR22 xenograft tissue at point of androgen withdrawal (PRE-ADT), 1 week post androgen withdrawal (POST-ADT), or upon recurrence (RT).


title: Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Illumina)

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

summary: Pseudouridine (Ψ) is an abundant mRNA modification in the mammalian transcriptome, but its function has remained elusive due to the difficulty of transcriptome-wide mapping. We develop nanopore native RNA sequencing for quantitative Ψ analysis that utilizes native content training, machine learning model prediction, and single read coordination. We find interferon inducible Ψ modifications in the interferon stimulated gene transcripts, consistent with a role of Ψ in the efficacy of mRNA vaccines.

sample_organism:
Saccharomyces cerevisiae
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens
human feces metagenome

overall_design: Illumina seq of rRNA mixture from human, yeast, C.elegans, Drosophila and stool microbiome

first: Sihao

last: Huang

first: Christopher

last: Katanski

first: Devin

last: Dersh

first: Wen

first: Qing

last: Dai

first: Jonathan

last: Yewdell

first: A

last: Eren


title: Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Nanopore)

platform_organism:
Saccharomyces cerevisiae
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens
human feces metagenome

overall_design: Nanopore seq of two biological replicates of untreated, IFN gamma treated and IFN beta treated HeLa cells. Nanopore seq of rRNA mixture from human, yeast, C.elegans, Drosophila and stool microbiome

last: Zhang


title: Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling

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

overall_design: Refer to individual Series


title: Transcriptional and phenotypic profile of lung-resident memory B cells induced by influenza infection

first: Hyon Xhi

last: Tan

summary: Long-lived, tissue-resident memory B cells (BRM) are established in the lungs of mice after pulmonary influenza infection. Influenza-specific BRM were localised within inducible bronchus-associated lymphoid tissues (iBALT) and displayed phenotypic and transcriptional signatures reminiscent of tissue-resident T cells, distinct from classical memory B cells in the blood or secondary lymphoid sites.

overall_design:
Mice were infected intranasally with 50pfu of PR8 influenza virus. Memory (Bmem) or germinal centre (GC) B cells in lung, spleen, mediastinal lymph node and blood were bulk-sorted and transcriptional gene expression profiles generated by RNAseq.
contributor:  The Austin Liver Transplant Perfusionist Group

first: Hyon-Xhi

first: Jennifer

last: Juno

first: Robyn

last: Esterbauer

first: Hannah

middle: G

last: Kelly

first: Kathleen

last: Wragg

first: Penny

last: Konstandopoulos

first: Sheilajen

last: Alcantara

first: Carolina

last: Alvarado

first: Robert

last: Jones

first: Graham

last: Starkey

first: Boa

last: Wang

first: Osamu

last: Yoshino

first: Thomas

last: Tiang

first: M

last: Grayson

first: Helen

last: Opdam

first: Rohit

last: D’Costa

first: Angela

last: Vago

first: Laura

last: Mackay

first: Claire

last: Gordon

first: David

last: Masopust

first: Joanna

last: Groom

first: Stephen

last: Kent

first: Adam

last: Wheatley


title: Effect of Environmental Enrichment on Transcriptomic Profile and Chromatin Accessibility of Cortical Neurons

city: Cambridge

first: Ravikiran

last: Raju

address: 15A Maple Ave

department: Picower Institute

institute: MIT

summary: Wildtype Swiss webster mice were exposed to four weeks of either standard housing (SH) or environmental enrichment (EE) starting at one month of age. EE chambers were large mouse cages containing two nesting/burrowing materials, a running wheel, and toys that were changed every 3-4 days for novelty and exploration. By contrast, SH control mice were housed with an equal number of littermates in smaller, standard cages containing only one nesting material and no toys or running wheel. We used an antibody for Rbfox3 (NeuN) to sort neuronal nuclei from the dissociated frontal cortices of male mice reared in EE and SH conditions. Isolated neuronal nuclei were then subjected to ATAC-seq or nuclear RNA isolation (random hexamer priming) as per published protocols.

overall_design: Examination of ATAC-seq and nuclear RNA-seq signal from cortical neurons after enrichment

first: Li-Huei

last: Tsai

first: Scarlett

last: Barker


title: Polycomb repressive complex 2 (PRC2) function in adult hair follicle stem cells is dispensable for hair regenration

city: Bronx

first: Deyou

last: Zheng

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Polycomb repressive complexes 2 mediated gene regulation in adult HFSCs is non-instructive for hair regenration

overall_design: Hair follicle stem cells (HFSCs)  were purified from P70 control , P70 Eed KO, P28-30 (for anagen) and P50-52 (for telogen) back skin by FACS sorting. RNA from the sorted cells was analyzed by RNA-seq.

first: Pooja

last: Flora

first: Meng

middle: Y

last: Li

first: Phillip

last: Galbo

first: Maider

last: Astorkia

first: Elena

last: Ezhkova


title: RNA-seq analysis of Vy9Vd2 T cells expanded in the presence or absence of TGFbeta1

city: London

first: John

last: Maher

address: Great Maze Pond

institute: King's College London

summary: Matched Vy9Vd2 T cells expanded from healthy PBMCs with zoledronate + IL2 versus Vy9Vd2 T cells expanded from healthy PBMCs with zoledronate + IL2 + TGFbeta1

overall_design: PolyA RNA analysis of matched Vy9Vd2 cells expanded from healthy PBMCs with zoledronate + IL2 versus Vy9Vd2 cells expanded from healthy PBMCs with zoledronate + IL2 + TGFbeta1, in serum-free media. Samples run on Illumina 1.9 for 25 cycles

first: Ana

last: Parente-Pereira

first: Jinger

last: Xie

first: Fred

last: Aswad

first: Domenico

last: Cozzetto


title: Abcc6 null mice a model mineralization disorder PXE show vertebral osteopenia without enhanced intervertebral disc calcification with aging

city: Philadelphia

first: Makarand

last: Risbud

address: 1025 Walnut Street

institute: Thomas Jefferson University

summary:
Transcriptomic analysis of annulus fibrosus (AF) tissues from intervertebral discs of 7-month-old mice with the global deletion of ABCC6.
ABCC6 is an efflux transporter of ATP in hepatic cells and loss of function results in metabolic ectopic mineralization disorder pseudoxanthoma elsaticum. To understand the role of ABCC6 and ectopic mineralization in the disc, we examined the transcriptomic profiles of annulus fibrosus cells in control and ABCC6 knock-out mice using microarrays.

overall_design: Tissue from the annulus fibrosus (AF) was harvested from the intervertebral discs of four ABCC6 control (ABCC6WT) and four ABCC6 knock-out mice (ABCC6KO) at 7 months of age. AF tissue was pooled from lumbar discs in each animal for RNA extraction and hybridization using Affymetrix microarrays.

first: Paige

last: Boneski

first: Vedavathi

last: Madhu

first: Ryan

last: Tomlinson

first: Koen

last: Van de Wetering

first: Irving

last: Shapiro

middle: V


title: Typhoidal Salmonella Dendritic Cell Survival Mechanism Revealed by Dual RNA sequencing

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Salmonella enterica represent a major disease burden worldwide. While non-typhoidal Salmonella (NTS) serovars trigger self-limiting diarrhoea, leading to occasional secondary bacteraemia, S. enterica serovar Typhi is responsible for potentially life-threatening Typhoid fever. Dendritic cells (DCs) are key professional antigen presenting cells of the human immune system. The ability of pathogenic bacteria to subvert DC functions and prevent T cell recognition contributes to their survival and dissemination within the host. Here, we adapted Dual RNA-sequencing to define how different Salmonella pathovariants remodel their gene expression in tandem with that of infected DCs. We find DCs harness iron handling pathways to defend against invading Salmonellas, which, the human pathogen S. Typhi is able to circumvent. We show that S. Typhi mounts a robust response to host oxidative stress to avoid host iron-mediated defence mechanisms. In parallel, we provide evidence that invasive non-typhoidal Salmonella employs several strategies to impair DC functions and undertake alternative nutrient scavenging strategies to survive in the hostile intracellular environment.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

sample_organism: Salmonella enterica subsp. enterica serovar Typhi str. Ty2

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

overall_design: Dual RNA-seq of mini-bulks (20'000 cells) of human monocyte derived dendritic cells infected with S. Typhimurium strain LT2 or D23580 or S. Typhi strain Ty2 or left uninfected

first: Anna

last: Aulicino

first: Agne

last: Antanaviciute

first: Joe

last: Frost

last: Sousa-Geros

first: Esther

last: Mellado

first: Moustafa

last: Atttar

first: Marta

last: Jagielowicz

first: Julia

last: Sinz

first: Lorena

last: Preciado-Llanes

first: Giorgio

last: Napolitani

first: Rory

last: Bowden

first: Hashem

last: Koohy

first: Hal

last: Drakesmith


title: Subtype-Independent ANP32E Reduction During Breast Cancer Progression in Accordance with Chromatin Relaxation.

status: Public on Nov 16 2021

city: Rochester

first: Garrett

last: Ruff

address: 601 Elmwood Ave

institute: University of Rochester

summary: We report the enrichment of ANP32E in MCF-7 cells assayed with CUT&Tag sequencing.

overall_design: CUT&Tag of MCF-7 cells with ANP32E antibody probe

first: Ruff

last: Garrett

first: Murphy

last: Patrick

first: Vertino

last: Paula


title: The N-terminal Region of Middle East Respiratory Syndrome Coronavirus Accessory Protein 8b is Essential for Enhanced Virulence of an Attenuated Murine Coronavirus

city: taian

first: yuming

last: li

state: shandong

address: 2 Yingsheng Dong Road

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

summary: Middle East respiratory syndrome coronavirus (MERS-CoV) is a beta coronavirus that emerged in 2012, causing severe pneumonia and renal failure. MERS-CoV encodes five accessory proteins. Some of them have been shown to interfere with host antiviral immune response. However, the roles of protein 8b in innate immunity and viral virulence was rarely studied. Here, we introduced individual MERS-CoV accessory protein genes into the genome of an attenuated murine coronavirus (Mouse hepatitis virus, MHV), respectively and found accessory protein 8b could enhance viral replication in vivo and in vitro, and increase the lethality of infected mice. RNA-seq analysis revealed that protein 8b could significantly inhibit type I interferon production (IFN-I) and innate immune response in mice infected with MHV expressing protein 8b. We also found that MERS-CoV protein 8b could initiate from multiple internal methionine sites and at least three protein variants were identified. Residues 1-23 of protein 8b was demonstrated to be responsible for increased virulence in vivo. In addition, the inhibitory effect on IFN-I of protein 8b might not contribute to its virulence enhancement as aa1-23 deletion did not affect IFN-I production in vitro and in vivo. Next, we also found that protein 8b was localized to the endoplasmic reticulum (ER)/Golgi membrane in infected cells, which was disrupted by C-terminal region aa 88-112 deletion. This study will provide new insight into the pathogenesis of MERS-CoV infection.

overall_design: Transcriptome of brain obtained from mice infected with rJ2.2.8b and rJ2.2.8b-KO virus

first: Yuming

last: Li

first: Yingkang

last: Jin

first: Lijun

last: Kuang

first: Zhenhua

last: Luo

first: Fang

first: Jing

last: Sun

first: Airu

last: Zhu

first: Zhen

last: Zhuang

first: Yanqun

last: Wang

first: Liyan

last: We

first: Donglan

last: Liu

first: Chunke

last: Chen

first: Mian

last: Gan

first: Jingxian

last: Zhao

first: Jincun


title: Sex and mutation specific p53 gain-of-function activity in gliomagenesis [RNA-seq]

city: St Louis

first: Joshua

last: Rubin

state: Missouri

address: 660 South Euclid Ave

department: Pediatrics

institute: Washington University In St Louis

summary: The goal of this study is to compare the sex specific effects of the expression of p53 missense mutations on the transcriptomes of male and female primary astrocytes. Primary cortical astrocytes harboring a single floxed Trp53 allele were harvested from male and female postnatal day one pups, and transduced with mutant p53;IRES GFP followed by CRE recombinase. mRNA was collected from male and female astrocytes transduce with mouse Trp53:R172H, Trp53:Y202C, or Trp53:Y217C. This study revealed sex specific gain-of-function effects on the transcriptomes of each cell line that correlated with cancer pathways.

overall_design: Comparison of mRNA expression profiles between three p53 mutations and p53 KO in male and female primary mouse astroyctes.

first: Nathan

last: Rockwell


title: Analysis of the antiviral activity of TIP against SARS-CoV2 in Mesocricetus auratus

city: San Francisco

first: Xinyue

state: California

address: 1650 Owens St

institute: Gladstone Institutes

summary: Syrian golden hamsters were treated with TIP or control RNA and infected with SARS-CoV2, at 5 days post infection, RNA was extracted and RNAseq was performed, uninfected hamsters treated with TIP or Control RNA were used as controls.

overall_design: Samples 1-10: 8-week old syrian golden hamsters were infected through intranasal installation of 10^6 total PFU per animal of SARS-CoV-2 (USA-WA1/2020) 100 ml of DMEM, as described (Rogers et al., 2020).  6 hours pre-infection and 18 hours post infection animals were given an intranasal dose of 100 ml  of LNP solution containing 60 mg of either TIP RNA (hamsters n=5; samples 1-5) or control RNA (hamsters n=5; samples 6-10). For uninfected samples; 8-week old syrian golden hamsters were intranasally treated with TIP (hamsters n=3; samples 11-13) or control RNA LNPs (hamsters n=3; samples 14-16). At day-5 post-infection, animals were sacrificed and lungs were harvested for gene expression analysis.

first: Sonali

last: Chaturvedi

last: Beutler


title: NCOR2 controls androgen deprivation therapy failure in advanced prostate cancer through re-wiring of the onco-epigenome [ChIP-seq]

first: Mark

last: Long

summary: NCOR2 is frequently and significantly mutated in late stage androgen deprivation therapy resistant prostate cancer (ADT-RPCa). NCOR2 has been characterized as a transcriptional corepressor and has mechanistic links to DNA methylation, but its global functions and overall contributions to PCa progression remain enigmatic. We mapped the dihydrotestosterone (DHT) dependent and independent effects of NCOR2 on the transcriptome, cistrome and DNA methylome in androgen sensitive (AS) and ADT-RPCa cells using the isogenic LNCaP and LNCaP-C4-2 (C4-2) cell models and the CWR22 xenograft model of ADT-RPCa.

overall_design: immunoprecipitated (IgG or NCOR2) DNA was isolated from  androgen sensitive (LNCaP) and androgen therapy resistant (LNCaP-C42) prostate cancer cell lines after 1hr treatment (EtOH or 10nM DHT) .

first: Dominic

last: Smiraglia

first: Moray

last: Campbell


title: Expression Profile of Relapsed/Refractory Aggressive B-cell Non Hodgkin Lymphoma Tumors

first: Daniel

last: Landsburg

state: PA

address: 3400 Civic Center Boulevard, #12-182

department: Perelman School of Medicine

institute: University of Pennsylvania

summary: Fimepinostat (formerly known as CUDC-907) is a synthetic, orally-available, small molecule that potently inhibits the activity of histone deacetylase, or HDAC, and phosphotidyl-inositol 3 kinase, or PI3 kinase enzymes.  Subjects were aggregated from Phase I and II clinical trials (ClinicalTrials.gov Identifier: NCT01742988, NCT02674750) to evaluate efficacy and safety in Lymphoma(s).   RNA Seq expression profiles were developed from 34 samples from trial subjects with FFPE tissue samples available and who had been on treatment for at least 42 days.

overall_design: 34 FFPE tissue samples from relapsed-refractory diffuse large B-cell lymphoma (RR DLBCL) patients treated with Fimepinostat for at least 42 days were analyzed.  DNA and RNA were isolated and assayed for concentration by fluorescence assay.  Extracted RNA quality was assayed by Agilent Bioanalyzer 28S/18S (0.8 – 3.0) or Agilent Bioanalyzer RIN score >= 6.0.  Hi quality RNA Samples were processed by Illumina TruSeq RNA Exome library preparation for RNA Seq profiling (Illumina).  For each sample, 20 – 30 million 50 bp paired end reads were sequenced on Illumina HiSeq2500 platform.  RNA Seq reads were mapped to the Homo sapiens reference human_g1k_v37_decoy genome via STAR/GATK workflow and the Gencode v19 annotation.


title: The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity [RNA-Seq]

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

summary: PARP does have an essential role in the regulation of global EBV episome chromatin structure. We have functionally characterized the effect of PARP enzymatic inhibition on total episomal structure and we mapped intragenomic contact changes after PARP inhibition to global binding of the chromatin looping factors CTCF and cohesin across the EBV genome. The altered expression profile after the structural rearrangement induced by PARP inhibition supports the model where PARP1 helps maintain EBV latency programs.

overall_design: Two biological replicates of both LCL and Mutu control cell and olaparib [2.5 uM] treated cells. For RNAseq total RNA was extracted and depleted of the ribosomal RNA component using RiboZero (Epicentre).

first: Sarah

last: Johnson

first: Italo

last: Tempera


title: Sex and mutation specific p53 gain-of-function activity in gliomagenesis


title: NCOR2 controls androgen deprivation therapy failure in advanced prostate cancer through re-wiring of the onco-epigenome

address: Elm & Carlton Streets

institute: Roswell Park Comprehensive Cancer Center


title: The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity [ChIP-Seq]

overall_design: Two biological replicates of both LCL and Mutu control cell and olaparib [2.5 uM] treated cells. Chromatin immunoprecipitation (ChIP) was performed using RAD21 antibody or sonicate chromatin (input) were used to make ChIP-seq libraries. For peak calling we compare the RAD21 enrichment to the input signal


title: Robust RNA editing via recruitment of endogenous ADARs using circular guide RNAs

status: Public on Nov 15 2021

city: La Jolla

first: Dario

last: Meluzzi

address: 9500 Gilman Drive #0648

department: School of Medicine

institute: UC San Diego

summary: We engineered circular ADAR recruiting guide RNAs (cadRNAs) that efficiently recruit endogenous ADARs to edit specific sites on target RNA

overall_design: We tested two Circular ADAR recruiting guide RNAs (cadRNAs). "Circular 100,50" refers to a cadRNA targeting the RAB7A transcript with an antisense domain of length 100 bp and containing a centrally located C-mismatch (position 50). Similarly, "Circular 200,100" refers to a cadRNA targeting the RAB7A transcript with an antisense domain of length 200 bp and containing a centrally located C-mismatch (position 100). "293FT" refers to the control sample, i.e., HEK-293FT cells that were not treated with any cadRNA.

first: Dhruva

last: Katrekar

first: Prashant

last: Mali


title: Transcriptional changes in response to OXA-23 overexpression in Acinetobacter baumannii ATCC 17978

city: Decatur

first: Philip

middle: N

last: Rather

state: Georgia

address: 1670 Clairmont Rd, Room 5A-183

department: Microbiology & Immunology

institute: Emory University

summary:
Purpose:
The goal of this study was to elucidate the collateral effects associated with OXA-23 overexpression on the Acinetobacter baumannii global transcriptome.

Results:
Besides the 99.73-fold increase in blaOXA-23 transcript upon IPTG induction, no other transcripts showed more than a 2-fold change compared to the wildtype control. This suggests that OXA-23 over expression to levels similarly observed in multi drug resistant A. baumannii clinical isolates does not effect the transcriptome.

overall_design: Global mRNA profiles of A. baumannii ATCC 17978 wildtype and IPTG-induced OXA-23 overexpression

first: Jennifer

last: Colquhoun


title: CblX disease is both an inborn error of cobalamin metabolism and a ribosomopathy

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: CblX is a recently described X-linked variant of combined methylmalonic acidemia and homocystinuria, cblC type, which is the most common inborn error of intracellular cobalamin metabolism. While cblC is due to mutations in MMACHC, which is in the cobalamin metabolic pathway, cblX is caused by mutations in the transcriptional cofactor HCFC1 and its obligate transcription factor partner RONIN . Since HCFC1 and RONIN jointly regulate MMACHC transcription, cblX patients suffer from low levels of MMACHC during development and thus develop a disease highly similar to cblC. Beyond this finding, there is little else known about the other genes de-regulated in cblX and the resulting pathophysiology. Therefore, we have generated the first mouse models of this disease (Hcfc1A115V/Y and RoninF80L/F80L). We show that our cblX models exhibit the expected metabolic perturbations, along with CNS, hematopoietic and cardiac developmental defects, typically observed in cblC patients. We also uncovered a large cohort of target genes that encode ribosome protein subunits as well as unexpected phenotypes that we ascribe to deregulation of ribosome biogenesis impacting normal translation during development. In addition to identifying RONIN and HCFC1 as new transcriptional regulators of ribosome biogenesis, we establish cblX as a complex syndrome exhibiting aspects of cblC and a ribosomopathy.

overall_design: RNA was extracted from the brains of control and mutant Ronin (F80L/F80L) animals for RNA-seq library preparation. And the brains of control animals were used as input for Ronin ChIP-seq.

first: Ross

middle: A

last: Poche


title: Leveraging cell-type specific regulatory networks to interpret genetic variations in abdominal aortic aneurysm

city: Stanford

first: Shining

last: Ma

address: 318 Campus Drive

department: Statistics

institute: Stanford University

summary: Abdominal aortic aneurysm (AAA) is a common degenerative cardiovascular disease without clear understanding of its pathobiology. To detect AAA associated variants that may affect gene regulation, we generated H3K27ac HiChIP data for aortic smooth muscle cells (AoSMC) and aortic endothelia cells (HAEC), the two cell types most relevant to the AAA disease. We further implemented cell type-specific REs defined from HiChIP experiments, and observed the consistency between the chromatin accessibility of REs and the expression levels of their target genes. Moreover, the cell type-specific REs contributed to detect the AAA most relevant cell type, AoSMC, and locate the important AAA-related TFs, ERG and KLF family.

overall_design: H3K27ac HiChIP profiles for human aortic smooth muscle cells (AoSMC) and aortic endothelia cells (HAEC)

first: Xi

last: Chen

first: Xiang

last: Zhu

middle: S

last: Tsao

first: Wing

last: Wong


title: A transcriptome atlas of the mouse iris at single cell resolution defines cell types and the genomic response to pupil dilation

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

summary: Single nuclei RNAseq, in situ hybridization, and immunohistochemistry were used to study the cells comprising the mouse iris in its different functional states.

overall_design: single nuclei RNA-seq were preformed on control, dilated, and constricted, adult mice irises.

first: Jie

last: Wang

first: Jeremy

last: Nathans


title: Resolving the Difference Between Left-sided and Right-sided Colorectal Cancer by Single-cell Sequencing

city: jinan

first: Jingxin

last: Li

address: wenhuaxi road

institute: Shandong university

summary: Colorectal cancers (CRCs) exhibit differences in incidence, pathogenesis, molecular pathways and outcome depending on the location of the tumor. The transcriptomes of 27,927 single human CRC cells, from three left-sided and three right-sided CRC patients were profiled by scRNA-seq. Right-sided CRC harbors a significant proportion of exhausted CD8 T cells of a highly migratory nature. One cluster of cells from left-sided CRC exhibiting states preceding exhaustion and a high ratio of “pre-exhausted” to exhausted T cells were favorable prognostic markers. Notably, we identified a novel RBP4+ NTS+ subpopulation of cancer cells that exclusively expands in left-sided CRC. Tregs from left-sided CRC showed higher levels of immunotherapy-related genes than those from right-sided CRC, indicating that left-sided CRC may have increased responsiveness to immunotherapy. Antibody-dependent cellular phagocytosis (ADCP) and antibody-dependent cellular cytotoxicity (ADCC) induced by M2-like macrophages were more pronounced in left-sided CRC and correlated with a good prognosis in CRC.

overall_design: Single-cell RNA sequencing profiles of left-sided and right-sided colorectal cancer.

first: Wei

last: Guo

first: Cuiyu

last: Zhang

first: Xia

first: Dandan

last: Dou

first: Dawei


title: Dependence on Bcl6 and Blimp1 identifies distinct mechanisms driving memory and follicular helper CD4+ T cell differentiation [scATAC-Seq]

status: Public on Nov 14 2021

city: Bethesda

first: Remy

last: Bosselut

state: Maryland

address: 9000 Rockville Pike, Building 37

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

summary: During the immune response, CD4+ T cells differentiate into distinct effector subtypes, including follicular helper T (Tfh) cells that help B cells, and into memory cells. Tfh and memory cells are required for long-term immunity; both depend on the transcription factor Bcl6, raising the question of whether they differentiate through similar mechanisms. Here, using notably single-cell RNA and ATAC sequencing, we show that virus-responding CD4+ T cells lacking both Bcl6 and Blimp1 can differentiate into cells with transcriptomic, chromatin accessibility and function attributes of memory cells, but not of Tfh cells. Thus, Bcl6 promotes memory cell differentiation primarily through its repression of Blimp1.  These findings demonstrate that distinct mechanisms underpin the differentiation of memory and Tfh CD4+ cell and define the Bcl6-Blimp1 axis as a potential target for promoting long-term memory T cell differentiation.

overall_design: Single cell epigenomic analysis of d7, >=d30 p.i. WT and dKO GP66-I-Ab+ CD4+ T cells and d7 p.i. WT and dKO Smarta T cells

first: Melanie

last: Vacchio

first: Laura

last: Chopp


title: Dependence on Bcl6 and Blimp1 identifies distinct mechanisms driving memory and follicular helper CD4+ T cell differentiation [scRNA-Seq]

overall_design: Single cell transcriptomic analysis of d7, >=d30 p.i. WT and dKO GP66-I-Ab+ CD4+ T cells and d7 p.i. WT and dKO Smarta T cells

first: Jia

last: Nie