title: Effect of hyperoxic exposure on neonatal lung cDCs expression

status: Public on Feb 02 2023

city: Ann Arbor

first: Antonia

middle: P.

last: Popova

state: Michigan

address: 1150 W. Medical Center Dr., Room 3570, MSRBII, Box 5688

department: Pediatrics

institute: University of Michigan Medical School

summary:
Bronchopulmonary dysplasia (BPD), a chronic pulmonary sequela of preterm birth, increases susceptibility to respiratory viral infection. Exposure to hyperoxia of neontal mice (a model of BPD) increases the number of activated, IL-12 producing lung CD103+ dendritic cells (DCs) and augments the inflammatory response to rhinovirus infection.
We used microarray analysis to detail the effect of hyperoxia on the gene expression of the two main subsets of lung cDC, including CD103+ DCs and CD11bhi DC. We identified distinct up- and down-regulated genes in response to hyperoxia in both cDC subclasses.

overall_design: Immature C57BL/6J mice were exposed to normoxia or hyperoxia (0.75 FiO2) for 14 days. Upon discontinuing the exposure the lungs were perfused, minced, digested to single cell suspension and processed for flow cytometry. Flow cytometry sorted CD103+ DCs and CD11bhi DCs were subjected to microarray analysis. Each sample contains sorted cells from two separate neonatal mouse lungs.

middle: P

first: Tracy

middle: X

last: Cui


title: A Cre-deleter specific for embryo-derived brain macrophages reveals distinct features of microglia and border macrophages

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genetic tools to target microglia specifically and efficiently from the early stages of the embryonic development are missing. Here we present Crybb1-Cre, a new constitutive Cre deleter producing a nearly complete recombination of embryonic brain macrophages (microglia and embryonic BAMs) by the perinatal period, with limited recombination leakage in peripheral myeloid cells. Using this tool, in combination with Flt3-Cre lineage tracer, scRNA-seq analysis and confocal imaging we were able to accurately fate-map embryonic derived versus monocyte derived BAMs in the mouse cortex and identified specific surface markers to resolve either population. Furthermore, we used Crybb1-Cre to delete the transcription factor SMAD4. Using multiomics analysis combining single-cell RNA-seq and ATAC-seq we showed that SMAD4-deficient microglia underwent an arrest of their homeostatic maturation and at the same time acquired a BAMs specification signature. By contrast, BAMs development was unaffected. Therefore, SMAD4 drives a transcriptional and epigenetic program that is indispensable for the commitment of brain macrophages to the microglia fate. This data provides a valuable resource to study molecular underpinnings of microglia development.

overall_design:
Immune cells were isolated from the brains of Smad4 F/F and Smad4 cKO mice and subjected to multi-omic profiling using 10X genomics reagents.
Immune cells were isolated from the brains of WT and 5XFAD mice and subjected to scRNAseq using 10X genomics reagents.

first: Simone

last: Brioschi

first: Vincent

last: Peng


title: Expression data from PBMCs in patients with CHB or SC HBV

status: Public on Feb 03 2023

city: Chengdu

first: Chengxia

last: Xie

address: Wangjiang Campus, Sichuan University, Wuhou District

country: China

institute: Sichuan University

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

summary:
There were 3 patients with CHB and 3 patients with SC HBV in microarray analysis. As for the liver function parameters, the average HBsAg and HBeAg levels of CHB group were obviously higher than SC HBV group.
The obtained RNAs expression profiles were analyzed by microarray analysis. A total of 513 lncRNAs, 256 mRNAs and 48 miRNAs were found to be differentially expressed (DE) in patients with CHB compared with patients with SC HBV (fold change > 1.2 and P < 0.05).

platform_organism:
Homo sapiens
synthetic construct

overall_design: The peripheral blood mononuclear cells (PBMCs) were obtained from three patients with SC HBV and three patients with CHB. Total RNA was isolated using miRNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.

first: Jie

last: Chen

first: Shengjie

last: Wang


title: IFNγ is a central node in cancer immune equilibrium

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

summary: The anti-tumor effects of IFNγ are well-known as IFNγ binding to tumor cells increases antigen presentation and can cause cytostatic growth defects. Indeed, the inability of tumors to respond to IFNγ often renders tumors resistant to checkpoint blockade and other immunotherapies reliant on direct T cell cytotoxicity. We performed single-cell RNA-sequencing during virus therapy to get insight into the immune microenvironment of the tumor during treatment.

overall_design: Mice bearing B16-Nectin1+ tumors were injected 4 times intratumorally with PBS, d106S, or d106S-IL12 starting on day seven of tumor growth and collected on day 16 (PBS) or day 17 (virus). Tumors were sorted for CD45+ live cells.

first: Michael

middle: J

last: Walsh

first: Courtney

middle: T

last: Stump

first: Rakeeb

last: Kureshi

first: Patrick

last: Lenehan

first: Lestat

last: Ali

first: David

middle: M

last: Knipe

middle: K


title: A tick C1q protein alters infectivity of the Lyme disease agent   by modulating interferon γ

status: Public on Feb 01 2023

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

institute: Zhejiang University

summary: To understand the immunomodulation roles of complement C1q-like protein 3 (IsC1ql3), we utilized RNA sequencing (RNA-seq) to investigate the effect of IsC1ql3 on the murine transcriptome.

overall_design: We compared the transcriptome of murine splenocytes stimulated by the Lyme disease agent Borrelia burgdorferi, with or without IsC1ql3, for 6 hours.

first: Erol

last: Fikrig


title: Defects in placental syncytiotrophoblast cells are a common cause of developmental heart disease

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

summary: E14.5 placentas from three mutant mutant mouse lines (Atp11a, Smg9 and Ssr2) with high co-occurance of placental and heart defects were sequenced. Transcriptional changes associated with ventricular septal defects were characterized.

overall_design:
Mutant mouse lines were generated with EUCOMM/KOMP knockout first conditional-ready targeted ES cell resources ((http://www.mousephenotype.org/about-ikmc/eucomm-program/eucomm-targeting-strategies).
Gene expression profiling was comapred at E14.5 between wild-type, and heterozygous and homozygous (KO) mutants (6-11 per genotype) in Atp11a, Smg9 and Ssr2 lines (Tm1a- non functional gene strcuture only)

first: Bethany

middle: N

last: Radford


title: Single-cell and spatial architecture of human tissue granulomas reveals an aberrant immune-regulatory program underlying sarcoidosis

status: Public on Feb 06 2023

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

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

overall_design: Refer to individual Series


title: Comparative analysis of transcriptome profiles reveals organ-dependent (Intestine and Tail) genomic and nongenomic actions of thyroid hormone in Xenopus tropicalis tadpoles

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: To investigate which genes expression are inhibited in TR double knockout tadpoles under over thyroid hormone condition in each tissue.

overall_design: Compare the thyroid hormone target gene expression with or without thyroid hormone receptor in the intestine and tail at stage 54 in anuran amphibian, Xenopus tropicalis.

first: Shouhong

first: Yuki

last: Shibata

first: Yuta

last: Tanizaki

first: Hongen

last: Zhang

first: Yun

middle: B

last: Shi


title: Diverse CMT2 Neuropathies are Linked to Aberrant G3BP Interactions in Stress Granules

first: Ge

last: Bai

state: Zhejiang Province

address: 866 Yuhangtang Rd

institute: Zhejiang university

summary: The formation of stress granules (SGs) is an important anti-stress mechanism in response to environmental insults. SG is a type of discrete cytoplasmic foci composed of translationally silent ribonucleoproteins. To explore the composition of SGs, we use CLIP-Seq to detect the RNAs associated  with G3BP1.

overall_design: Comparative RNA composition of stress granule in HeLa cells expressing GlyRSWT, GlyRSP234KY and GlyRSL42A-P234KY.

first: Hongyun

last: Bi

first: Bokai

last: Gu


title: The SET Oncoprotein Promotes Estrogen-Induced Transcription by Facilitating Establishment of Active Chromatin

city: Mexico City

last: Valle-Garcia

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan

country: Mexico

institute: National Institute of Neurology and Neurosurgery

summary: SET is a multifunctional histone-binding oncoprotein that regulates transcription by an unclear mechanism. Here, we show that SET enhances estrogen-dependent transcription. SET knockdown abrogates transcription of estrogen-responsive genes and their enhancer RNAs (eRNAs). In response to 17β-estradiol (E2), SET binds to the estrogen receptor α (ERα) and is recruited to estrogen receptor α (ERα)-bound enhancers and promoters at estrogen response elements (EREs). SET functions as a histone H2 chaperone that dynamically associates with H2A.Z via its acidic C-terminal domain and promotes H2A.Z incorporation, ERα, MLL1 and KDM3A loading and modulates histone methylation at EREs. SET depletion diminishes recruitment of condensin complexes to EREs and impairs E2-dependent enhancer-promoter looping. Thus, SET boosts E2-induced gene expression by establishing an active chromatin structure at ERα-bound enhancers and promoters, which is essential for transcriptional activation.

overall_design: ChIP-seq of SET in MCF-7 cells. RNA-seq of MCF-7 control or estrogen treated cells with or without SET KD.

first: Changying

last: Guo

first: Karla

middle: F

last: Meza-Sosa

first: Judy

last: Lieberman


title: Time dependent gene expression post SNL in IPSA vs Contralateral DRGs

city: Salt Lake City

first: Christopher

middle: A

last: Reilly

state: UT

address: 30 S 2000 E, Room 201 Skaggs Hall

department: Pharmacology and Toxicology

institute: University of Utah

summary: Chronic pain can be debilitating, and current treatments are neither universally efficacious, nor without risks. New therapeutic options are needed. Transient receptor potential (TRP) ion channels regulate inflammation and pain. Understanding how endogenous TRP ligands regulate inflammation and pain may provide insights for new therapies. Spinal nerve ligation (SNL) injury was used as a model for chronic pain. Transcriptomic and targeted lipidomic analysis of damaged tissue revealed time-dependent increases in Cyp1b1 mRNA and a concurrent accumulation of 8,9-EET and 19,20-EpDPA post injury. Production of 8,9-EET and 19,20-EpDPA by human CYP1B1 and mouse Cyp1b1 was confirmed in vitro. 8,9-EET and 19,20-EpDPA selectively and dose-dependently sensitized and activated TRPA1 in overexpressing HEK-293 cells and Trpa1-expressing/AITC-responsive cultured mouse peptigergic DRG neurons. Activation of TRPA1 was attenuated by the antagonist A967079, and mouse Trpa1 was more responsive to agonists including 8,9-EET and 19,20-EpDPA than human TRPA1. This latter effect was mediated in part by amino acids Y933, G939, and S921. Intra-plantar injection of 19,20-EpDPA induced acute mechanical, but not thermal hypersensitivity in mice, which was blocked by A967079. Similarly, Cyp1b1 knockout mice displayed a reduced chronic pain phenotype, indicating a role for Cyp1b1-derived oxylipins in promoting Trpa1 activation and pain. Manipulation of the CYP1B1-oxylipin-TRPA1 axis following nerve injury could have therapeutic benefit.

overall_design: Mice were used as their own controls to compare injured vs uninjured DRG gene expression

first: Cassandra

last: Rice

first: Alan

last: Light

first: Toto

last: Olivera


title: mRNA transcription profiles of livers and tumors from C57BL/6J mice treated with or without diethylnitrosamine (DEN) and fed either a Western-style diet (WD) or Control diet (CD)

city: London

first: Dimitrios

last: Anastasiou

address: 1 Midland Road

department: Cancer Metabolism Laboratory

country: United Kingdom

institute: The Francis Crick Institute

summary: We used RNA-seq to measure mRNA levels of livers and liver tumors from mice treated with or without the chemical carcinogen diethylnitrosamine (DEN) and fed CD or obesogenic WD, with the aim to explore how metabolism in hepatic tissues and tumors (where present) is affected by diet, carcinogen treatment and tumor development. We used the RNA-seq data for differential gene expression analysis, and for the reconstruction and constraining of genome-scale metabolic models in order to estimate metabolic changes across tissues under the various treatment conditions.

overall_design:
Four experimental groups: [1]: nonDEN-CD (mice not injected with DEN, fed CD); [2]: nonDEN-WD (mice not injected with DEN, fed WD); [3]: DEN-CD (mice injected with DEN, fed CD); [4] DEN-WD (mice injected with DEN, fed WD and bearing liver tumors)
Five types of tissues (i-v) analyzed from groups 1-4: (i) Group [1] liver; (ii) Group [2] liver; (iii) Group [3] liver; (iv) Group [4]-Peritumoral tissue; (v) Group [4] tumor

first: Frederick

last: Clasen

first: Patricia

last: Nunes

first: Saeed

last: Shoaie


title: Induction of primordial germ cell-like cells from common marmoset embryonic stem cells by inhibition of WNT and retinoic acid signaling

city: Fukuoka city

first: Mayumi

last: Shono

state: Japan

address: 3-1-1, Maidashi, Higashi-ku, Fukuoka city

country: Japan

institute: Kyushu university

summary: Reconstitution of germ cell lineage using pluripotent stem cells provides a unique platform to deepen our understanding of the mechanisms underlying germ cell development and to produce functional gametes for reproduction. Here, we report a robust induction of primordial germ cell-like cells (PGCLCs) from common marmoset (Callithrix jacchus) embryonic stem cells. The robust induction was achieved by not only activation of the conserved PGC-inducing signals, WNT and BMP4, but also temporal inhibitions of WNT and retinoic acid signals, which prevent mesodermal and neural differentiation, respectively, during PGCLC differentiation. Many of the gene expression and differentiation properties of common marmoset PGCLCs were similar to those of human PGCLCs, making this culture system a reliable and useful primate model. Finally, we identified PDPN and KIT as surface marker proteins by which PGCLCs can be isolated from embryonic stem cells without genetic manipulation. This study will expand the opportunities for research on germ cell development and production of functional gametes to the common marmoset.

overall_design: RNA-seq analysis of common marmoset embryonic stem cells (cjESC), pre-induced cells, differentiated cells to common marmoset primordial germ cell-like cells (cjPGCLC) or others in multiple conditions, and cjPGCLCs aggregated with mouse gonadal somatic cells

first: Keiko

last: Kishimoto

first: Orie

last: Hikabe

first: Masafumi

last: Hayashi

first: Katsunori

last: Semi

first: Yasuhiro

last: Takashima

first: Erika

last: Sasaki

first: Kiyoko

last: Kato

first: Katsuhiko


title: ICOS costimulation is indispensable for the differentiation of T follicular regulatory cells

city: Montreal

first: Woong-Kyung

last: Suh

state: QC

address: 110 Pine avenue, SuhLab

institute: institut de Recherche Clinique de Montreal (IRCM)

summary: ICOS is a T cell costimulatory receptor critical for Tfh cell generation and function. However, the role of ICOS in Tfr cell differentiation remains unclear. Using Foxp3-Cre-mediated ICOS knockout (ICOS FC) mice, we show that ICOS deficiency in Treg-lineage cells drastically reduces the number of Tfr cells during GC reactions but has a minimal impact on conventional Treg cells. Single-cell transcriptome analysis of Foxp3+ cells at an early stage of the GC reaction suggests that ICOS normally inhibits Klf2 expression to promote follicular features including Bcl6 upregulation. Further, ICOS costimulation promotes nuclear localization of NFAT2, a known driver of CXCR5 expression.  Notably, ICOS FC mice had an unaltered overall GC B cell output but showed signs of expanded autoreactive B cells along with elevated autoantibody titers. Thus, our study demonstrates that ICOS costimulation is critical for Tfr cell differentiation and highlights the importance of Tfr cells in maintaining humoral immune tolerance during GC reactions.

overall_design: Splenocytes from Foxp3YFP-creIcos+/+(ICOS WT) and Foxp3YFP-creIcosfl/fl(ICOS FC) male mice were isolated 6 dpi with NP-OVA/alum and stained with anti-CD4 alexa fluor 647 (GK1.5, BioLegend), anti-TCRβ PeCy7 (H57-597, BioLegend) and propidium iodide (ThermoFisher). Live (PI-) conventional (YFP-) and regulatory (YFP+) CD4+TCRβ+ T cells were sorted with a BD FACSAria (BD Biosciences) and mixed in a 1:10 ratio. A total of 13500 cells from ICOS WT and ICOS FC mice were sent for library preparation. Libraries were generated using the following components from 10x Genomics: Chromium Next GEM Chip G Single Cell kit, Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead kit v3.1, Chromium i7 Multiplex kit. Sequencing was performed by Genome Québecusing a NovaSeq 6000 (Illumina) with a flow cell S1 PE28*91.

first: Vincent

last: Panneton

first: Barbara

last: Mindt

first: Yasser

last: Bouklouch

first: Antoine

last: Bouchard

first: Saba

last: Mohammaei

first: Jinsam

last: Chang

first: Nikoletta

last: Diamantopoulos

first: Mariko

last: Witalis

first: Joanna

last: Li

first: Albert

last: Stancescu

first: John

last: Bradley

first: Troy

last: Randall

first: Jörg

last: Fritz


title: Distinct roles for canonical and variant histone H3 lysine 36 in polycomb silencing

city: Chapel Hill

first: Gregory

last: Matera

state: North Carolina

address: Genome Science Building

institute: University of North Carolina at Chapel Hill

summary: Polycomb complexes regulate cell-type specific gene expression programs through heritable silencing of target genes. Trimethylation of histone H3 lysine 27 (H3K27me3) is essential for this process. Perturbation of H3K36 is thought to interfere with H3K27me3. We show that mutants of Drosophila replication-dependent (H3.2K36R) or -independent (H3.3K36R) histone H3 genes generally maintain Polycomb silencing and reach later stages of development. In contrast, combined (H3.3K36RH3.2K36R) mutants display widespread Hox gene misexpression and fail to develop past the first larval instar. Chromatin profiling showed that the H3.2K36R mutation disrupts H3K27me3 levels broadly and significantly throughout silenced domains, whereas these regions are mostly unaffected in H3.3K36R animals. Analysis of H3.3 distributions showed that this histone is enriched at presumptive PREs (Polycomb Response Elements) located outside of silenced domains but relatively depleted from those inside. We conclude that H3.2 and H3.3 K36 residues collaborate to repress Hox genes via distinct genomic subcompartments and mechanisms.

overall_design: H3K27me3 CUT&RUN of Drosophila melanogaster. Three replicates of pellet and supernatant fractions for each genotype. Genotypes: H3.3Adelta, HWT, H3.2K36R, and H3.3BK36R.

first: Harmony

middle: R

last: Salzler

first: Vasudha

last: Vandadi

first: Benjamin

middle: D

last: McMichael

middle: C

last: Brown

first: Sally

last: Boerma

first: Mary

last: Leatham-Jensen

first: Kirsten

last: Adams

first: Michael

last: Meers

first: Jeremy

last: Simon

first: Robert

last: Duronio

first: Daniel

last: McKay

first: A

middle: G


title: Effect of knocking down HOXB9 in gastric cancer cells

status: Public on Jan 31 2023

city: Hong Kong

first: Bonan

last: Chen

address: The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, The People's Republic of China

country: Hong Kong

institute: the Chinese University of Hong Kong

summary: HOX proteins play fundamental roles during ontogenesis by interacting with other non-HOX gene-encoded partners and performing transcriptional functions, while aberrant activation of HOX members drives tumorigenesis. In this study, gastric cancer (GC) expression microarray data indicates that HOXB9 is a prominent upregulated HOX member in GC samples and is significantly associated with clinical outcomes and advanced TNM stages. However, the functional role of HOXB9 in GC remains contradictory in previous reports, and the regulatory mechanisms are elusive. By in silico and experimental analyses, we found HOXB9 was upregulated by a vital cell cycle-related transcription factor E2F1. Depleting HOXB9 causes G1 phase cell cycle arrest by downregulating CDK6 and a subset of cell cycle-related genes. Meanwhile, HOXB9 contributes to cell division and maintains the cytoskeleton in GC cells. PBX2 is a potential transcription factor for CDK6. We verified that HOXB9 interacts with PBX2 to form a heterodimer and upregulates CDK6. Knocking down CDK6 can phenocopy the tumor-suppressive effects of HOXB9 depletion. Inhibiting HOXB9 can enhance the anti-tumor effect of CDK6 inhibitors on GC growth. In conclusion, we elucidate the oncogenic role of HOXB9 and reveal CDK6 as its potent downstream modulator in GC.

overall_design: The potent target genes of HOXB9 were identified by deep sequencing, using Illumina NovaSeq 6000.

first: Jinglin

last: Zhang


title: Heat shock protein 90 inhibition attenuates inflammation elicited by 12-O-tetradecanoylphorbol-13-acetate

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Pre-clinical models for prediction of immunotherapy outcomes and immune evasion mechanisms in genetically heterogeneous multiple myeloma

city: Pamplona

first: Cristina

last: Perez

address: Av. Pio XII 55

country: Spain

institute: Cima Universidad de Navarra

type: Genome variation profiling by high throughput sequencing

summary: Multiple myeloma (MM) is a neoplasia of bone marrow (BM) plasma cells that remains largely incurable with current treatment. Advancing therapeutic discoveries has been hampered by the lack of genetically heterogeneous models of MM. To circumvent this limitation, we engineered fifteen mouse models carrying combinations of eight MM genetic drivers, which fulfilled the pathogenesis of human disease including progression from premalignant states under immune surveillance. Integrative analyses of ⁓500 mice and ⁓1,000 patients revealed a MAPK-MYC genetic pathway that regulates time to progression and immune escape mechanisms across genetically heterogeneous tumors. During progression, MYC-dependent and independent remodeling of the BM microenvironment divided MM into immune categories with predominance of selected T-cell subpopulations, which dictated immunotherapy responses. Experimental targeting of the cytotoxic or immunosuppressive T-cell states observed in refractory MM patients enhanced immunotherapy effectiveness. Our resource enabled characterization of MM cell-intrinsic and immunological traits at unprecedented levels, which will accelerate the translation of personalized immunotherapy.

overall_design:
scRNA-seq + scTCR-seq were performed in 13 bone marrow aspirates from 2 healthy (Ycɣ1), 3 MGUS (BIcɣ1), 3 MM (BIcɣ1), 3 MGUS (MIC) and 2 MM (MIC) bearing mice. Cells were FACS sorted (a mix of 0.8x10^5 T cells + 0.8x10^5 NK cells + 0.25x10^5 monocytes + 0.15x10^5 B cells) in 100 µL of PBS+0.05% BSA. Samples with at least 90% viability were processed using the 10X Genomics (CA, USA) scRNA/TCRseq kit, following the manufacturer’s instructions (Chromium Next GEM Single Cell V(D)J v1.1 protocol rev F for human samples and Chromium Next GEM Single Cell 5’ v2 Dual Index protocol rev B for mice samples). Quality control was performed with Qubit Fluorometric Quantification (ThermoFisher Scientific, MA, USA) using the double-stranded DNA high-sensitivity assay kit, and with TapeStation (Agilent, Santa Clara, CA) using high-sensitivity screentapes. Libraries were sequenced on a NextSeq 550 (Illumina, San Diego, CA).
WES was performed in 71 BM samples isolated from GFP+ CD138+B220− PCs (purity, >99%), including 62 samples from the MM stage, 3 samples of pooled PCs from nine mice at the MGUS stage (3 mice with similar genotype were included on each pooled sample), and 6 samples from MM-derived cell lines. As MM reference controls, 5TGM1 and 12598Vk*Myc cell lines were also characterized.

first: Marta

last: Larrayoz

first: Jose

last: Martinez-Climent


title: Cardiomyocyte Pdk4 response is associated with metabolic maladaptation in aging

city: Tampa

first: Ji

last: Li

state: FL

address: 12901 Bruce B. Downs Blvd

department: Surgery

institute: University of South Florida

summary: Pyruvate Dehydrogenase Kinase 4 (Pdk4) is a pyruvate dehydrogenase inhibiton gene that strongly regulates metabolism. We studied the expression of Pdk4 in the young and aged mouse heart in both healthy conditions and after  ischemic insult.

overall_design: Left ventricle tissue samples from healthy (sham) mice and mice after ischemic insult (I/R), collecting both young and aged tissue.

first: Mohammad

last: Fatmi

first: Di

last: Ren


title: NanoString nCounter Gene Expression of keratinocytes pretreated with HSP90 inhibitor and challenged with 12-O-tetradecanoylphorbol-13-acetate (TPA)

summary: The mRNA levels of 579 inflammatory genes were analyzed with Nanostring nCounter Human Immunology Panel in primary  human keratinocytes pretreated with RGRN-305 (HSP90 inhibitor) and challenged with TPA

overall_design: The keratinocytes were grouped into 4 different groups receiving; Vehicle; RGRN-305; TPA; or TPA + RGRN-305. Six different donors were used. In total 24 samples.

first: Sabine

last: Seeler


title: Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

summary: Comparison of overall tRNA level and fraction of charged tRNAs upon treatment with auxin to deplete Not1 in the degron strain and compared to untreated cells.

overall_design: Control cells used for tRNA charging and abundance - 3 replicates

first: Christine

last: Polte

first: Martine

last: Collart


title: Characterisation of the genetic mutation driving enhanced superantigen SpeA expression in Streptococcus pyogenes M1UK

status: Public on Jan 30 2023

city: Parkville

first: Magnus

middle: Ganer

last: Jespersen

state: Victoria

address: 792 Elizabeth street

country: Australia

institute: The University of Melbourne


title: Effect of RGRN-305 on TPA-induced skin inflammation in mice 4 hours post-TPA challenge

summary: The aim was to demonstrate that pretreatment with RGRN-305 suppresses 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced alterations in gene expression.

overall_design: Mice were pretreated with RGRN-305 or vehicle before challenge with TPA or vehicle on ears of mice. Four hours post TPA-challenge ear biopsies were collected and RNA sequenced ( gene expression analysis). Number of mice in treatment groups: vehicle = 4, RGRN-305 = 4, TPA = 10, TPA+RGRN-305 = 10.


title: Characterisation of the genetic mutation driving enhanced superantigen SpeA expression in Streptococcus pyogenes M1UK (second 5448)

summary: A new variant of group A Streptococcus (GAS) serotype M1 (designated ‘M1UK’) has been reported in the United Kingdom, linked with seasonal scarlet fever surges, marked increase in invasive infections, and exhibiting enhanced expression of the superantigen SpeA. The progenitor GAS ‘M1global’ and M1UK clones can be differentiated by 27 SNPs and 4 indels, yet the mechanism for speA upregulation is unknown. Here we investigate the previously unappreciated expansion of M1UK in Australia, now isolated from the majority of serious infections caused by serotype M1 GAS. M1UK sub-lineages circulating in Australia also contain a novel toxin repertoire associated with epidemic scarlet fever causing GAS in Asia. A single SNP in the M1UK tmRNA gene ssrA drives enhanced SpeA superantigen expression as a result of ssrA terminator readthrough in the M1UK lineage. This represents a new paradigm of toxin expression and urges enhanced international surveillance.

overall_design: RNA-seq

first: Mark

last: Davies

first: Nadia

last: Keller

first: Stephan

last: Brouwer

first: Amanda

last: Cork

first: Andrew

last: Hayes

first: Miranda

middle: E

last: Pitt

first: David

last: De Oliveira

first: Nichaela

middle: H

last: Price

first: Olivia

last: Bertolla

last: Mediati

first: Bodie

last: Curren

first: George

last: Taiaroa

first: Jake

last: Lacey

first: Helen

middle: V

last: Smith

first: Ning-Xia

last: Fang

first: Lachlan

last: Coin

first: Kerrie

last: Stevens

first: Steven

last: Tong

first: Martina

last: Sanderson-Smith

first: Jai

last: Tree

first: Adam

last: Irwin

first: Keith

last: Grimwood

first: Benjamin

last: Howden

first: Amy

last: Jennison

last: Walker


title: Characterisation of the genetic mutation driving enhanced superantigen SpeA expression in Streptococcus pyogenes M1UK (initial)

first: Magnus

last: Jespersen

first: Mark

last: Davies

first: Nadia

last: Keller

first: Stephan

last: Brouwer

first: Amanda

last: Cork

first: Andrew

last: Hayes

first: Miranda

last: Pitt

first: David

middle: P

last: De Oliveira

last: Price

last: Bertolla

first: Daniel


title: Next-generation mRNA sequencing of MKL-1 Merkel cell carcinoma cells expressing wild-type or mutant YAP or TAZ

status: Public on Jan 29 2023

city: Boston

first: Ashley

middle: K.

last: Gartin

address: 450 Brookline Ave. Mayer 444

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: The overarching goal of this study was to characterize TEAD-dependent transcriptional effects of YAP and TAZ in Merkel cell carcinoma cells. To that end, transcriptional profiling was performed on MKL-1 cells induced to express GFP, wild-type YAP or TAZ, or YAP S94A or TAZ F52A for 3 days.

overall_design: MKL-1 cells with doxycycline-inducible GFP, YAP, TAZ, YAP S94A, or TAZ F52A were treated in triplicate with 2 µg/mL doxycycline for 3 days. 15 samples are analyzed.

first: Thomas

last: Frost


title: Single Cell Cortical Bone Transcriptomics from Sost-Cre

status: Public on Jan 24 2023

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: Single cell cortical bone transcriptomics from Sost-Cre enriched cell population.

overall_design: Long bone pieces were digested and the Sost-cre cell population was enriched to obtain osteoblast and osteocytes.

first: Rafiou

last: Agoro

first: Kenneth

last: White


title: Characterisation of the genetic mutation driving enhanced superantigen SpeA expression in Streptococcus pyogenes M1UK (second SP1380)

middle: J

first: Nichaela

first: Olivia

last: Mediati

first: Bodie

last: Curren

first: George

last: Taiaroa

first: Jake

last: Lacey

first: Helen

last: Smith

first: Ning-Xia

last: Fang

first: Lachlan

last: Coin

first: Kerrie

last: Stevens

first: Steven

last: Tong

first: Martina

last: Sanderson-Smith

first: Jai

last: Tree

first: Adam

last: Irwin

first: Keith

last: Grimwood

last: Howden

last: Jennison


title: Cardiomyocyte infection by Trypanosoma cruzi promotes innate immune response and glycolysis activation

status: Public on Jan 28 2023

first: Gabriela

middle: Venturini

last: Venturini da Silva

state: Massachusetts

address: 77 Avenue Louis Pasteur, New Research Bu

department: Department of Genetics

institute: Harvard Medical School

summary:
To investigate the effects of T. cruzi on human cardiomyocytes during infection, we infected induced pluripotent stem cell_x0002_derived cardiomyocytes (iPSC-CM) with the parasite and analyzed responses at 24 hours and 48 hours post infection (hpi) em compared to basal (0hpi - Control) using transcriptomics (RNAseq)
We also validated our finds using RNA-seq data from HIF-1alpha mutated iPSC-CM treated with LPS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iPSC-CM at day 30 after T. cruzi infection


title: Single-cell transcriptomic atlas reveals the evolution of immune cells and molecules across multiple vertebrate species

city: xian

first: Cangang

last: Zhang

state: State...

address: Yanta district, xi 'an city, shaanxi province

institute: xian jiaotong university

summary: We utilized single-cell RNA sequencing (scRNA-seq) to carry out comparative transcriptome analysis in various immune cells from the spleens across seven vertebrate species.

sample_organism:
Danio rerio
Xenopus tropicalis
Macaca mulatta
Homo sapiens
Sus scrofa
Mus musculus
Rattus norvegicus

overall_design: High-dimensional single-cell RNA sequencing (10X Genomics) was used to profile the transcriptomes of total immune cells isolated from seven organism  spleens.

first: Baojun

first: Anjun

last: Jiao

first: Xin

last: Wang


title: Nanostring analysis of medulloblastoma samples using the PanCancer Immune Profile Nanostring Panel

city: Braga

first: Rui

middle: Pedro

last: Ferreira Marques

address: Campus de Gualtar

department: Life and Health Sciences Institute

country: Portugal

institute: School of Medicine, University of Minho

summary: The present study aimed to characterize the immune checkpoint profile in medulloblastomas, assess whether there is a distinct profile among molecular subgroups, and evaluate its prognostic outcome.

overall_design: We included 88 formalin-fixed paraffin-embedded (FFPE) medulloblastoma specimens from patients diagnosed at Barretos Cancer Hospital (BCH), Barretos, and Ribeirão Preto Medical School, Brazil, from 1986 to 2018. Experienced pathologists reviewed the histology, and the tumors were previously molecularly characterized by a 22-gene nCounter assay into WNT (n=14), SHH (n=43), Group 3 (n=12), and Group 4 (n=19). Additionally, three non-tumoral samples derived from non-tumor tissue surrounding brain tumor metastasis were included in the study. Gene expression assays were performed in the nCounter® FLEX Analysis System, using the PanCancer Immune Profiling Panel (NanoString Technologies, Inc., Seattle, WA). This panel comprises 730 immuno-oncology-related targets, including 109 cell surface markers for 14 immune cell types and 40 reference genes (https://nanostring.com/products/ncounter-assays-panels/oncology/pancancer-immune-profiling/).

first: Daniel

last: Moreno

first: Luciane

last: Silva

first: Leticia

last: Leal

first: Flávia

last: de Paula

first: Iara

last: Santana

first: Gustava

last: Teixeira

first: Fabiano

last: Saggioro

first: Luciano

last: Neder

first: Bruna

last: Mançano

middle: M

last: Reis

first: Carlos

last: Junior


title: Osteocyte Egln1/Phd2 links oxygen sensing and biomineralization via FGF23

city: Indianapolis

first: Kenneth

last: White

state: IN

address: 635 Barnhill Drive

institute: Indiana University School of Medicine

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

overall_design: Refer to individual Series


title: Osteocyte Egln1/Phd2 links oxygen sensing and biomineralization via FGF23 [RNA-seq]

summary: Genome-wide gene expression changes in response to mimicked hypoxia in undifferentiated MPC2 cells (mesenchymal stem cell-like) or 3-week osteogenic differentiated MPC2 cells (osteocyte-like)

overall_design: Undifferentiated MPC2 cells (MSC-like cells) and 3-week differentiated MPC2 cells (osteocyte-like cells) were treated with vehicle (DMSO) or 50 uM of the hypoxia mimetic FG-4592 (Roxadustat) for 48 hours

first: Megan

middle: L

last: Noonan


title: Characterisation of the genetic mutation driving enhanced superantigen SpeA expression in Streptococcus pyogenes M1UK (second SP1448)

first: Magnus

last: Jespersen

first: Mark

last: Davies

first: Nadia

last: Keller

first: Stephan

last: Brouwer

first: Amanda

last: Cork

first: Andrew

last: Hayes

first: Miranda

last: Pitt

first: David

last: De Oliveira

first: Nichaela

last: Price

first: Olivia

last: Bertolla

last: Mediati

first: Bodie

last: Curren

first: George

last: Taiaroa

first: Jake

last: Lacey

first: Helen

last: Smith

first: Ning-Xia

last: Fang

first: Lachlan

last: Coin

first: Kerrie

last: Stevens

first: Steven

last: Tong

first: Martina

last: Sanderson-Smith

first: Jai

last: Tree

first: Adam

last: Irwin

first: Keith

last: Grimwood

first: Benjamin

last: Howden

first: Amy

last: Jennison

last: Walker


title: The SHAPE-MaP experiment to identify RNA structures of pri-mir-142 variants

status: Public on Jan 23 2023

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

institute: The Hong Kong University of Science and Technology

summary: MicroRNAs (miRNAs) are short non-coding RNAs that play essential roles in RNA silencing and gene regulation. The human Microprocessor (MP) is the key factor to initiate miRNA biogenesis by cleaving primary microRNAs (pri-miRNAs). However, the Microprocessor alone cannot precisely and efficiently cleave all pri-miRNAs; thus, it requires cofactors to assist its cleavage. SRSF3 interacts with CNNC in pri-miRNAs, enhancing the MP cleavage. However, it is unknown if SRSF3 can function with other non-CNNC motifs and if secondary structure might influce CNNC function. In addition, function of SRSF7, a paralog of SRSF3, in the SR proteins family, in miRNA biogenesis is largely unknown. In this study, by conducting the high-throughput pri-miRNA cleavage assays for the MP with SRSF3 or SRSF7 and randomized pri-miRNAs, we discovered that SRSF7 also stimulate MP clevage. Futhermore, we found that both SRSF3 and SRSF7 can function with some non-CNNC motifs and with CNNC motifs with certain secondary structures. Furthermore, we also demonstrated that SRSF7 and SRSF3 governed the cleavage sites of the Microprocessor in human cells. Our findings disclose the roles SRSF7 in miRNA biogenesis, demonstrate a compresenhive moleucalr mechanism of SFSF3 and SRSF7 in enhancing cleavage of MP and described in more detail the RNA-binding features of SRSF7 and SRSF3.

first: Anh

middle: T

first: Ngoc

last: Le


title: EGFR pathway expression persists in recurrent glioblastoma independent of amplification status

status: Public on Jan 25 2023

city: Cleveland

first: Andrew

last: Dhawan

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: Background: Glioblastoma mortality is driven by tumour progression or recurrence despite administering a therapeutic arsenal consisting of surgical resection, radiation, and alkylating chemotherapy. The genetic changes underlying tumour progression and chemotherapy resistance are poorly understood. Methods: In this work, we sought to define the relationship between EGFR amplification status, EGFR mRNA expression, and EGFR pathway activity. We compared RNA-sequencing data from matched primary and recurrent tumour samples (N = 40 patients, 20 with EGFR amplification). Results: In the setting of glioblastoma recurrence, the EGFR pathway was overexpressed regardless of EGFR amplification status, suggesting a common genomic endpoint in recurrent glioblastoma, although EGFR amplification did associate with higher EGFR mRNA expression. Three of forty patients in the study cohort had EGFR-amplified tumours and received targeted EGFR therapy. Their molecular subtypes and clinical outcomes did not significantly differ from patients who received conventional chemotherapy. Conclusion: Our findings suggest that while the EGFR amplification may confer a unique molecular profile in primary glioblastoma, pathway analysis reveals upregulation of the EGFR pathway in recurrence, regardless of amplification status. As such, the EGFR pathway may be a key mediator of glioblastoma progression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for glioblastoma patient samples at time of diagnosis and recurrence.

first: Venkata

middle: S

last: Manem

first: Gabrielle

last: Yeaney

first: Justin

last: Lathia

first: Manmeet

last: Ahluwalia


title: Single cell sequencing of the E13.5 mouse anterior palate reveals mesenchymal heterogeneity

city: Aurora

first: Emily

middle: Anne

last: Bates

state: CO

institute: University of Colorado Anschutz Medical Campus

summary: Cleft palate is one of the most prevalent birth defects. Mice are useful for studying palate development because of their morphological and genetic similarities to humans. In mice, palate development occurs between embryonic days (E)11.5 to 15.5. Single cell transcriptional profiles of palate cell populations have been a valuable resource for the craniofacial research community, but we lack a single cell transcriptional profile for anterior palate at E13.5, at the transition from proliferation to shelf elevation. Here, a detailed single cell RNA sequencing analysis reveals heterogeneity in expression profiles of the cell populations of the E13.5 anterior palate. Mesenchymal populations spatially segregate into four domains. One of these mesenchymal populations expresses ligands and receptors distinct from the rest of the mesenchyme, suggesting that these cells have a unique function. RNAVelocity analysis shows two terminal cell states that contribute to either the proximal or distal palatal regions emerge from a single progenitor pool. This single cell resolution expression data and detailed analysis from E13.5 anterior palate provides a powerful resource for mechanistic insight into secondary palate morphogenesis for the craniofacial research community.

overall_design: The E13.5 anterior palate represents an important period in palate development just prior to palatal elevation. We used scRNA seq to characterize heterogeneity within this tissue characterizing mesenchymal, epithelial, proliferating, immune, endothelial, and schwann cell populations.

middle: A

first: Yunus

last: Ozekin

first: Rebecca

last: O'Rourke


summary: Human Microprocessor cleaves pri-miRNAs to initiate miRNA biogenesis. The accuracy and efficiency of Microprocessor cleavage ensure appropriate miRNA sequence and expression and thus its proper gene regulation. However, Microprocessor cleaves many pri-miRNAs incorrectly, so it requires assistance from its many cofactors. For example, SRSF3 enhances Microprocessor cleavage by interacting with the CNNC motif in pri-miRNAs. However, whether SRSF3 can function with other motifs and/or requires the motifs in a certain secondary structure is unknown. In addition, the function of SRSF7 (a paralog of SRSF3) in miRNA biogenesis still needs to be discovered. Here, we demonstrated that SRSF7 could stimulate Microprocessor cleavage. In addition, by conducting high-throughput pri-miRNA cleavage assays for Microprocessor and SRSF7 or SRSF3, we demonstrated that SRSF7 and SRSF3 function with the CRC and CNNC motifs, adopting certain secondary structures. In addition, SRSF7 and SRSF3 affect the Microprocessor cleavage sites in human cells. Our findings demonstrate the roles of SRSF7 in miRNA biogenesis and provide a comprehensive view of the molecular mechanism of SRSF7 and SRSF3 in enhancing Microprocessor cleavage.

overall_design: The high-throughput human pri-miRNA processing assays for MP, MP and SRSF3, MP and SRSF7


title: Gene expression profiling of cancer cells purified from prostate cancer bone metastasis mouse model

city: Edinburgh

first: Cigdem

last: Selli

address: Little France Crescent

department: Centre for Reproductive Health

institute: Queen's Medical Research Institute

summary: The study aimed to determine mechanisms of macrophage promotion of anti-androgen resistance of prostate cancer bone disease. For this purpose, we  developed a novel prostate cancer bone metastasis mouse model, MycCaP-Bo, via multiple rounds of in vivo selection of bone homing cells following intra-cardiac inoculation of a murine prostate cancer cell line, MycCaP cells. Cancer cells were purified from bone metastasis using fluoresent accelerated-cell sorting (FACS) based on their iRFP expression. Cancer cells were purified from treatment- naïve tumours, resistant tumours and resistant tumours with short-term depletion of macrophages. RNA was extracted from purified cancer cells and profiled using next-generation sequencing.

overall_design: Gene expression profiles of cancer cells purified from different stages of prostate cancer bone metastasis mouse model; naïve tumours (vehicle-treated), naïve tumours (vehicle-treated plus macrophage depleted by liposome clodronate treatment for four days), resistant tumours (18-day Enzalutamide treated), and resistant tumours with short-term depletion of macrophages  (18-day Enzalutamide treated plus macrophage depleted by liposome clodronate treatment in the last four days).

first: Xue-Feng

last: Li

first: Bin-Zhi

last: Qian


title: Engraftment of allogeneic iPS cell-derived cartilage organoid in a primate model of articular cartilage defect

city: Suita

first: Noriyuki

last: Tsumaki

state: Select One

address: 2-2 Yamadaoka

department: Department of Biochemistry and Molecular Biology

institute: Osaka University, Graduate School of Medicine

summary: Induced pluripotent stem cells (iPSCs) are a promising resource for allogeneic cartilage transplantation to treat articular cartilage defects that do not heal spontaneously and often progress to debilitating conditions, such as osteoarthritis. However, to the best of our knowledge, allogeneic cartilage transplantation into primate models has never been assessed. Here, we show that allogeneic iPSC-derived cartilage organoids survive and integrate as well as function as articular cartilage in a primate model of chondral defects in the knee joints. Histological analysis revealed that allogeneic iPSC-derived cartilage organoids in chondral defects elicited no immune reaction and directly contributed to the tissue repair for at least four months. iPSC-derived cartilage organoids integrated with the host native articular cartilage and prevented degeneration of the surrounding cartilage. Single-cell RNA-sequence analysis indicated that iPSC-derived cartilage organoids differentiated after transplantation, acquiring expression of PRG4 that is crucial for joint lubrication. Pathway analysis suggested the involvement of SIK3 inactivation, verified through molecular experiments. Our study outcomes suggest that allogeneic transplantation of iPSC-derived cartilage organoids may be clinically applicable for the treatment of patients with chondral defects of the articular cartilage.

overall_design: We performed a single cell (sc)RNA-seq transcriptome analysis of cynomolgus monkey iPS cells (cyiPSC) and cyiPSC-derived cartilage (pre-transplant cyiPS-Cart). We created chondral defects in articular cartilage in knee joints of cynomolgus monkeys. We transplanted allogeneic cyiPS-Cart or nothing. Four months after transplantation, articular cartilage (AC), transplanted cyiPS-Cart (post-transplanted cyiPS-Cart) and fibrous tissue (cyFT) formed in the chondral defects where nothing had been transplanted were harvested and subjected to scRNA-seq analysis.

first: Kengo

last: Abe

first: Saeko

last: Koyamatsu


title: Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: The goal is to compare role of Not1,4,5 in co-translational decay and solubility of RNAs from soluble and total RNA pools using degron strains

overall_design: The cells are grown exponentially and total RNA is prepared by acid phenol extraction from cell pellets or from cell lysates prepared as for polysome profiling

first: Benjamin

last: Weiss

first: Susanne

last: Huch

first: Vicent

last: Pelechano

first: Martine

last: Collart


title: Single-cell and spatial architecture of human tissue granulomas reveals an aberrant immune-regulatory program underlying sarcoidosis [single-cell sequencing]

status: Public on Feb 07 2023

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary:
Purpose: Granulomas are lumps of immune cells that can form in various organs, causing chronic inflammation and tissue destruction. While most granulomas appear histologically heterogeneous and unstructured, they have a certain resemblance of lymphoid organ formation. We thus pursued the hypothesis that granuloma formation is a highly orchestrated process that mixes and repurposes various regulatory mechanisms of normal development
Methods: We performed single-cell sequencing and spatial transcriptomics on granulomas from patients diagnosed with cutaneous sarcoidosis, and we bioinformatically reconstructed their gene-regulatory networks and cell-cell interactions
Results: We observed regulatory processes underlying granuloma formation that were highly conserved across individuals and followed characteristic spatial patterns. We identified metabolically reprogrammed macrophages, various T cells subsets and structural cells including fibroblasts and endothelial cells as key players in granulomas. Specifically, exhausted interferon-gamma-producing Th17.1 cells with cytotoxic potential and inflammatory fibroblasts were identified as drivers of granuloma formation by attracting various immune cell types.
Summary: we found that granuloma formation in sarcoidosis is a molecular and cellular process that adopts specific aspects of normal lymphoid organ development in aberrant combinations. Our study frames human granuloma formation as a developmental pathology and raises the future perspective of therapeutic targeting of granuloma-specific regulatory programs.

overall_design:
single-cell sequencing on granulomas and healthy skin from patients diagnosed with cutaneous sarcoidosis, enriched in the immune compartment
NOTE FROM SUBMITTER: Raw data will be uploaded to the European Genome-phenome Archive since it contains patient genetic data.

first: Thomas

last: Krausgruber

first: Anna

last: Redl

first: Daniele

last: Barreca

first: Georg

last: Stary


title: BG4 RIP-seq using mouse forebrain tissues

status: Public on Jan 21 2023

city: Yokohama

first: Sefan

last: Asamitsu

state: Kanagawa

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

institute: RIKEN Center for Integrative Medical Sciences

summary: To identify G4-enriched mRNAs expressed in the mouse brain, RNA immunoprecipitation by BG4 antibody (G4-specific antibody) was performed.

overall_design: Mouse forebrain tissues were lysed and precleared using the Protein G HP SpinTrap Kit (GE healthcare). The precleared samples were incubated at 4°C overnight in a Protein G HP SpinTrap column that had been treated with His-tagged BG4 (or normal rabbit IgG for control) and anti-6×His. The resultant solution was washed three times and eluted with elution buffer. The BG4-bound RNA fraction was purified using the RNeasy Mini Kit (Qiagen) and subjected to RNA-sequencing library preparation.

first: Yasushi

last: Yabuki

first: Kazuya

last: Matsuo

first: Moe

last: Kawasaki

first: Yuki

last: Hirose

first: Gengo

last: Kashiwazaki

first: Anandhakumar

last: Chandran

first: Toshikazu

last: Bando

first: Dan

middle: W

last: Ohtan

first: Hiroshi

last: Sugiyama

first: Norifumi

last: Shioda


title: Osteocyte Egln1/Phd2 links oxygen sensing and biomineralization via FGF23 [ATAC-seq]

first: Kenneth

last: White

summary: Genome-wide chromatin accessiblity changes in response to mimicked hypoxia in undifferentiated MPC2 cells (mesenchymal stem cell-like) or 3-week osteogenic differentiated MPC2 cells (osteocyte-like)

first: Megan

last: Noonan


title: Breast cancer cell lines treated with mebedazole (an FDA-approved anti-parasitic) under 20% or 1% oxygen conditions.

city: Baltimore

first: Ines

last: Godet

state: MD

address: 1650 Orleans Street, CRB1, room 128

department: Oncology

institute: Johns Hopkins University

summary: The main purpose of this project is to identify gene expression changes between treated breast cancer cells (w/ MBZ) vs. non-treated cells (w/o MBZ) under normal (20% O2) or hypoxic (1% O2) conditions. Preliminary analysis using iclue revealed that MBZ might behave similarly to HIF inhbitors so we hypothesize that MBZ might repress HIF-response under hypoxia. We have submitted three different cell lines: SUM159 (SM), MDA-MB-231 (MDA) and MCF7; MBZ treatment: 0uM of MBZ (0M or 0); 1uM MBZ (1M or 1); Oxygen conditions: 1% O2 - hypoxia (H); 20% O2 - normoxia (N).

overall_design: Breast cancer cell lines were treated either with 1 uM or 0 uM of MBZ under 20% or 1% oxygen

last: Gilkes


title: Thyroid Hormone Action Controls Multiple Components of Cell Junctions at the Ventricular Zone in the Newborn Rat Brain

city: Research Triangle Park

first: Katherine

middle: Lynn

last: O'Shaughnessy

state: NC

address: 109 TW Alexander Drive

institute: United States Environmental Protection Agency

summary:
We investigated if developmental hypothyroidism controlled cell signaling in the ventricular zone of the rat brain on postnatal day 2.
We performed laser capture microdissection to isolate the ventricular zone in euthyroid (control) and hypothyroid rats. Hypothyroidism was induced by a maternal exposure to the goitrogen propylthiourail (PTU) during pregnancy and lactation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of the posterior ventricular zone from euthyroid (control) and hypothyroid (PTU) rat pups collected on postnatal day 2.


title: Ilime-seq of pre-miR-142 from DICER-KO HCT116 cells

city: Hong Kong

first: Duc

last: Nguyen

summary: The experiments were conducted to examine the effects of SRSF3 or SRSF7 on DROSHA cleavage of pri-mir-142_WT in human cells.

overall_design: DICER-KO HCT116 cells were transfected with pXG, pXG-SRSF3 or pXG-SRSF7 and pri-mir-142_WT. Pre-mir-142 sequencing libraries of the transfected DICER-KO cells were generated using Ilime-seq (Le et al., 2022).

first: Anh

first: Ngoc

last: Le


title: Quant-seq on COMPASS-degron cells

status: Public on Jan 20 2023

city: Beijing

first: Hua

last: Wang

address: 38 Xueyuan Rd

institute: Peking University

summary: Here, we showed that acute lost H3K4me3 induces rapid reduction in global transcription with progressively increase in magnitude over the time-course cooccurrence with lost all H3K4 methylations,

overall_design: To define the primary effects of rapid H3K4me3 removal on transcription, we measured the synthesis of newly transcribed RNAs using a Thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) with a 0, 2, 8 and 24 hour time-course in the degron cells. DPY30mAID, DPY30-mAID degron cell; DPY30mAID_Kdm5dKO, Kdm5a and Kdm5b double knock out based on DPY30-mAID degron cell; RBBP5FKBP, RBBP5-FKBP degron cell. For all trans-retinoic acid (RA, Sigma-Aldrich, R2625-50MG) treatment, cells were induced with 1 μM RA and without LIF for the indicated time.


title: mNET-seq on COMPASS-degron cells

summary: We measured the the dwell time of existed paused RNAPII at the promoter by mammalian native elongating transcript sequencing (mNET-seq). We found a median RNAPII half-life of 5.3 min at protein-coding genes in DMSO pre-treated control mESCs, whereas the RNAPII half-life at these genes significantly slowdown to 8.96 min when pre-treated with Auxin in the DPY30-mAID degron cell. The data suggested that loss H3K4me3 directly slows down the release of paused RNAPII throughout genes.

overall_design: To directly investigate the temporal stability and half-life of promoter RNAPII, we used Triptolide, a potent inhibitor of transcription initiation, coupled with mammalian native elongating transcript sequencing (mNET-seq) to measure the dwell time of existed paused RNAPII at the promoter. Unlike previous measurements, the single-nucleotide resolution of the mNET-seq data allowed us to specifically direct measure the RNAPII engaged RNA signal at protomer-proximal region.


title: A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: DNA methylation has been utilized for target gene silencing in plants, however it’s not well-understood whether other silencing pathways can be also used to manipulate gene expression. Here we performed a gain-of-function screen for proteins that could silence a target gene when fused to an artificial zinc finger. We uncovered many proteins that suppressed gene expression through DNA methylation, histone H3K27me3 deposition, H3K4me3 demethylation, histone deacetylation, inhibition of RNA Polymerase II transcription elongation or Ser-5 dephosphorylation. These proteins also silenced many other genes with different efficacy, and a machine learning model could accurately predict the efficacy of each silencer based on various chromatin features of the target loci. Furthermore, some proteins were also able to target gene silencing when used in a dCas9-SunTag system. These results provide a more comprehensive understanding of epigenetic regulatory pathways in plants and provide an armament of tools for targeted gene manipulation.

overall_design: This dataset includes ChIP-seq, RNA-seq and BS-PCR to understand the molecular mechanism of Arabidopsis ZF targeting proteins.

first: Wang

last: Ming

first: Zhong

last: Zhenhui


title: Identification of a CD106+ pericyte stem cell leading to Ly6G+ cell accumulation responsible for resistance to immunotherapy in pancreatic cancer

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary: We report the identification of a cell population that shares pericyte, stromal and stemness features, does not harbour the KrasG12D mutation and drives tumoral growth in vitro and in vivo. We termed these cells pericyte stem cells (PeSCs) and defined them as CD45-EPCAM-CD29+CD106+CD24+CD44+ cells. Our data reveals the existence of a cell population that instruct immunosuppressive myeloid cell responses to bypass PD-1 targeting and thus suggest potential new approaches for overcoming resistance to immunotherapy in clinical settings.

overall_design: Single cell RNA sequencing was performed in FACS purified ductal tumor cells from a pool of five KC or 4KC mice (LSL-KrasG12D/+;Ptf1a-Cre mice).

first: Pia

last: Gamradt

first: Zhichong

last: Wu

first: Ana

last: Hennino


title: Muscle RNAseq in SBMA mice

status: Public on Jan 19 2023

city: padova

first: Maria

last: Pennuto

state: Padova

address: via ugo bassi 58b

country: Italy

institute: University of Padua

summary: The pattern of gene expression changes was analyzed in the skeletal muscle of transgenic mouse models of Spinal and bulbar muscular atrophy (SBMA) at 1 and 2 month of age.

overall_design: 4 Control mice were compared to 4 AR100Q mice at 1 month of age; 3 Control mice were compared to 4 AR100Q mice at 2 M

first: Paolo

last: Martini

first: Caterina

last: Marchioretti

first: Marco

last: Pirazzini

first: Giulia

last: Zanetti


title: Ocean warming and acidification affect the transitional C:N:P ratio and macromolecular accumulation in the harmful raphidophyte Heterosigma akashiwo

city: Wuhan

first: Satheeswaran

last: Thanagraj

state: Hubei

address: Lumo Road

department: Marine Science

institute: China University of Geosciences

summary: We used single cell RNA-seq to comprehensively map raphidophyte Heterosigma akashiwo to grow under present and future ocean conditions. We unveiled several unique types of metabolic changes, signaling pathways, and regulons associated with these cells.

overall_design: Comparative gene expression analysis have been performed from Heterosigma akashiwo incubated in different culture conditions (low-temperature; low-carbon-dioxide [LTLC] 21 ℃; pCO2 400 ppm) and (high-temperature; high-carbon-dioxide [HTHC] 25 ℃; pCO2 1000 ppm)

last: Thanagaraj

first: Jun

last: Sun


title: Muscle-specific gene expression changes in spinal and bulbar muscular atrophy (SBMA) at presymptomatic timepoint

summary: The pattern of gene expression changes were analyzed in the skeletal muscle of knock-in mouse models of SBMA at 3 month of age.

overall_design: Microarray analysis was performed in 90-day-old mice (wild type, and AR113Q-NCD).

first: M

first: P

first: C

last: Chivet

first: G


title: ChIP-seq on COMPASS-degron cells

first: Hua

last: Wang

summary: Here, we showed that acute lost H3K4me3 induces rapid reduction in global transcription with progressively increase in magnitude over the time-course cooccurrence with lost all H3K4 methylations. To further determine the effects of COMPASS subunits degradation on H3K4 methylations occupancies genome-wide, we performed time-course spike-in chromatin immunoprecipitation and sequencing (ChIP-seq, also known as ChIP-Rx) analysis in both degron systems.

overall_design: DPY30-mAID and RBBP5-FKBP degron tag into the 3’ end of both alleles of endogenous Dpy30 and Rbbp5 locus of the E14 mESC cell line, respectively. The endogenous Dpy30 gene was edited to encode Auxin inducible degradation (miniAID)-BFP at the C terminus of Dpy30 in OsTir1 E14 mESCs. The endogenous Rbbp5 gene was edited to encode FKBP12 tag-Neomycin that enables targeted degradation upon dTAG-13 treatment. DPY30mAID, DPY30-mAID degron cell; DPY30mAID_Kdm5dKO, Kdm5a and Kdm5b double knock out based on DPY30-mAID degron cell; RBBP5FKBP, RBBP5-FKBP degron cell.


title: Time-restricted feeding mediated transcriptomic changes in the indirect flight muscle tissue in Drosophila obesity models

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: The goal of the study was to investigate the mechanistic basis for Time-restricted feeding (TRF) improvement in skeletal muscle by assessing transcriptomic data of wild type (WT),  WT under High-fat diet (HFD), and genetic obesity linked mutant sphingosine kinase 2 (Sk2) under ad libitum feeding (ALF) and time-restricted feeding (TRF) conditions. Next generation sequencing was used to assess the changes along a diurnal cycle in the transcriptome of Drosophila indirect flight muscle (IFM) tissue at 3-week of age under ad libitum feeding (ALF) or time-restricted feeding (TRF).

overall_design: After 3 weeks of age on the assigned diet (normal and HFD) and feeding regimen (ALF & TRF), indirect flight muscle (IFM) was collected from 10 female flies every 4 h over 24 h and samples were flash frozen. Total RNA were prepared using the RNeasy kit (QIAGEN). Libraries were prepared according to Illumina protocols for single-end 50 bp mRNA sequencing and sequenced on an Illumina machine. Reads were aligned to the Drosophila melanogaster genome (BDGP r5) using STAR (v2.3.0e).

first: Christopher

last: Livelo

first: Yiming

last: Guo

first: Hiep

middle: D

last: Le

first: Satchidananda

last: Panda

first: Girish

middle: C

last: Melkani

first: Max

last: Chang


title: TT-seq on COMPASS-degron cells

summary: Here, we use elongation velocity analysis showed that acute loss H3K4me3 caused a general transcriptome-wide attenuation of elongation velocity in cells.

overall_design: In order to examine and monitor the effects of H3K4me3 on newly synthesized RNA rates genome-wide from actively transcribing RNAPII, we performed the modified transient transcriptome sequencing (TTchem-seq) and DRB/TTchem-seq with spike-in strategy on degron cells.


title: Whole human genome expression microarray for circSTK3-related genes

status: Public on Jan 18 2023

city: Harbin

first: boyang

last: fan

address: 246 Xuefu Road, Nangang District

department: Department of Colorectal Cancer Surgery

institute: The Second Affiliated Hospital of Harbin Medical University

summary: Whole genome expression microarray identified potential downstream targets and the regulatory networks of circSTK3; Gene Ontology analysis confirmed circSTK3 involvement in the CRC metastasis phenotype.

overall_design: To further explore the gene expression changes related to circSTK3 in CRC, we analyzed three pairs of HCT116 cells transduced with si-NC and si-circSTK3 using microarrays.

first: B

last: Fan


title: GM-free immortalization and high yield production of cultured chicken

city: Jerusalem

first: Avner

last: Ehrlich

address: Silberman 3-512, Edmond J. Safra Campus (Givat Ram)

department: Bioengineering

country: Israel

institute: The Hebrew University of Jerusalem

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

overall_design: Refer to individual Series


title: Eomes is sufficient to regulate IL-10 expression and cytotoxic effector molecules in murine CD4+ T cells

city: Freiburg

first: Vincent

last: Schipperges

address: Breisacher Str. 153

department: Institut für Medizinische Bioinformatik und Systemmedizin

institute: Universitätsklinikum Freiburg

summary: The T-box transcription factors T-bet and Eomesodermin regulate type 1 immune responses in innate and adaptive lymphocytes. T-bet is widely expressed in the immune system but was initially identified as the lineage-specifying transcription factor of Th1 CD4+ T cells, where it governs expression of the signature cytokine IFN-g and represses alternative cell fates like Th2 and Th17. T-bet’s paralog Eomes is less abundantly expressed and Eomes+ CD4+ T cells can mostly be found in the context of persistent antigen exposure, like bone marrow transplantation, chronic infection or inflammation as well as malignant disorders. However, it has remained unresolved whether Eomes executes similar transcriptional activities as T-bet in CD4+ T cells. Here we show in a novel genetic model that the expression of Eomes in CD4+ T cells drives a distinct transcriptional program that shows only partial overlap with T-bet. We found that Eomes was sufficient to induce the expression of the immunoregulatory cytokine IL-10 and, together with T-bet, promoted a cytotoxic effector profile, including Prf1, Gzmb, Gzmk, Nkg7 and Ccl5, while repressing alternative cell fates. Our results demonstrate that Eomes+ CD4+ T cells, which are often found in the context of chronic antigen stimulation, are likely to be a unique CD4+ T cell subset with the potential to limit inflammation and immunopathology as well as to eliminate antigen-presenting and malignant cells.

overall_design: Gene expression analysis of RNA-seq data

first: Benedikt

last: Thelen

first: Paulina

last: Knörlein

first: Jonas

middle: F

last: Hummel

first: Frederic

last: Arnold

first: Laurence

last: Kupferschmid

first: Christoph

last: Klose

first: Sebastian

first: Melanie

last: Börries

first: Yakup

last: Tanriver


title: MiRNA Differences Related to Treatment Resistant Schizophrenia

city: Santiago de Compostela

first: Roberto Carlos

middle: Agís

last: Balboa

state: Coruña

address: Travesía da Choupana s/n

department: Movement Disorders Group (AC22)

institute: Health Research Institute of Santiago de Compostela (IDIS)

type: Non-coding RNA profiling by high throughput sequencing

summary: Schizophrenia (SZ) is a serious mental disorder that is typically treated with antipsychotic medication. Treatment-resistant schizophrenia (TRS) is the condition where symptoms remain after pharmacological intervention, resulting in long-lasting functional and social impairments. As the identification and treatment of a TRS patient requires previous failed treatments, early mechanisms of detection are needed in order to quicken the access to effective therapy, as well as improve treatment adherence. In this study, we aim to find a microRNA (miRNA) signature for TRS, as well as to shed some light on the molecular pathways potentially involved in this severe condition. To do this, we compared the blood miRNAs of schizophrenia patients that respond to medication and TRS patients, thus obtaining a 16-miRNA TRS profile. Then, we assessed the ability of this signature to separate responders and TRS patients using hierarchical clustering, observing that most of them are grouped correctly (~70% accuracy). We also conducted a network, pathway analysis, and bibliography search to spot molecular pathways potentially altered in TRS. We found that the response to stress seems to be a key factor in TRS and that proteins p53, SIRT1, MDM2, and TRIM28 could be the potential mediators of such responses. Finally, we suggest a molecular pathway potentially regulated by the miRNAs of the TRS profile.

overall_design: We recruited schizophrenia patients with a normal antipsychotic response (MR; n = 19), schizophrenia patients with antipsychotic resistance (MNR; n = 21), patients with a first psychotic episode (P; n = 13), and 43 healthy individuals (C; n = 43). Two blood samples were collected per patient, the first one at the hospital arrival (MRA, MNRA, PA) and the second one at the hospital discharge (MRD, MNRD, PD). To find a miRNA signature of the antipsychotic response, we looked for differences in miRNA expression between the MR and MNR groups.

first: Daniel

last: Pérez-Rodríguez

first: Maria

last: Penedo

first: Tania

last: Rivera-Baltanás

first: Tonatiuh

last: Peña-Centeno

first: Susanne

last: Burkhardt

first: Andre

last: Fischer

first: José

last: Prieto-González

last: Olivares

first: Hugo

last: López-Fernández

first: Roberto

last: Agís-Balboa


title: Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen

status: Public on Jan 13 2023

city: Harpenden

last: Smith

state: Hertfordshire

address: West Common

department: IDE

institute: Rothamsted Research

summary: Background: Studying genomic variation in rapidly evolving pathogens potentially enables definition of genes supporting  their “core biology” present, functional and expressed by all strains or “flexible biology”,  varying between strains. Genes supporting flexible biology may be  considered to be “accessory”, whilst the “core” gene set is likely to be important for common features of a pathogen species biology, including virulence on all host genotypes.  The wheat-pathogenic fungus Zymoseptoria tritici represents one of the most rapidly evolving threats to global food security and was the focus of this study. Results:We constructed a pangenome of 18 European field isolates, with 12 also subjected to RNAseq transcription profiling during infection. Combining this data, we predicted a “core” gene set comprising 9807 sequences which were; (1) present in all isolates; (2) lacking inactivating polymorphisms ; and (3) expressed by all isolates. A large accessory genome, consisting of 45% of the total genes was also defined. We classified genetic and genomic polymorphism  at both chromosomal and individual gene scales. Proteins required for essential functions including virulence, had lower-than average sequence variability amongst core genes. Both core and accessory genomes encoded many small, secreted candidate effector proteins that likely interact with plant immunity. Viral vector-mediated transient in planta overexpression of 88 candidates failed to identify any which induced leaf necrosis characteristic of disease. However, functional complementation of a non-pathogenic deletion mutant lacking five core genes, demonstrated that full virulence was restored by re-introduction of the single gene exhibiting least sequence polymorphism and highest expression. Conclusions:These data support the combined use of pangenomics and transcriptomics for defining genes which represent core, and potentially exploitable, weaknesses in rapidly evolving pathogens.

sample_organism:
Triticum aestivum
Zymoseptoria tritici

platform_organism:
Triticum aestivum
Zymoseptoria tritici

overall_design: Z.tritici expression in vitro and in planta (at 6 and 9 days post infection)

first: Hongxin

last: Chen

first: Robert

last: King

first: Dan

first: Carlos

last: Bayon

first: Tom

last: Ashfield

first: Stephano

last: Torriani

first: Kostya

last: Kanyuka

first: Kim

last: Hammond-Kosack

first: Stephane

last: Bieri

first: Jason

last: Rudd


title: Effect of Cold Atmospheric Microwave Plasma (CAMP) on wound healing in canine keratinocytes

status: Public on Jan 17 2023

city: Gwanak

first: Pattawika

last: Lertpatipanpong

state: Seoul

department: College of Veterinary Medicine

country: South Korea

institute: Seoul National University

summary: CAMP treatment provided beneficial effects for the curative wound process through induction of genes involved in wound healing, promotion of EMT, and increase of the molecular targets in the hippo signaling pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CPEK cells with or without treatment of CAMP

first: Chanin

last: Sillapachaiyaporn

first: Garam

last: Oh

first: Yeong-Hun

last: Kang

first: Cheol-Yong

last: Hwang

first: Seung

middle: J

last: Baek


title: Short-Term Treatment with Rho-Associated Kinase Inhibitor Preserves Keratinocyte Stem Cell Characteristics In Vitro

city: London

first: George

middle: Thomas

last: Hall

address: Zayed Centre for Research, 20 Guilford Street

department: UCL Great Ormond Street Institute of Child Health

institute: University College London

summary: Primary keratinocytes including keratinocyte stem cells (KSCs) can be cultured as epidermal sheets in vitro and are attractive for cell and gene therapies for genetic skin disorders. However, the initial slow growth of freshly isolated keratinocytes hinders clinical applications. Rho-associated kinase inhibitor (ROCKi) has been used to overcome this obstacle, but its influence on the characteristics of KSC and its safety for clinical application remains unknown. In this study, primary keratinocytes were treated with ROCKi Y-27632 for six days (short-term). Significant increases in colony formation and cell proliferation during the six-day ROCKi treatment were observed and confirmed by related protein markers and single-cell transcriptomic analysis. In addition, short-term ROCKi-treated cells maintained their differentiation ability as examined by 3D-organotypic culture. However, these changes could be reversed and became indistinguishable between treated and untreated cells once ROCKi treatment was withdrawn. Further, the short-term ROCKi treatment did not reduce the number of KSCs. In addition, AKT and ERK pathways were rapidly activated upon ROCKi treatment. In conclusion, short-term ROCKi treatment can transiently and reversibly accelerate initial primary keratinocyte expansion while preserving the holoclone-forming cell population (KSCs), providing a safe avenue for clinical applications.

overall_design: Human keratinocytes were treated with Rho-associated kinase inhibitor and compared against untreated cells (both during and following treatment) using scRNAseq.

first: Vignesh

last: Jayarajan


title: Whole genome doubling drives oncogenic loss of chromatin segregation [WGS]

status: Public on Jan 12 2023

city: Lausanne

first: Luca

last: Nanni

state: Vaud

address: Quartier Sorge

department: Computational Biology

institute: Université de Lausanne

summary: Whole genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies. However, the 3D organization of the chromatin in WGD cells and its contribution to oncogenic phenotypes are currently unknown. Here, we show that in p53 deficient cells WGD induces loss of chromatin segregation (LCS), characterized by reduced segregation between short and long chromosomes, A and B sub-compartments, and adjacent chromatin domains. LCS is driven by downregulation of CTCF and H3K9me3 in cells that bypassed activation of the tetraploid checkpoint. Longitudinal analyses revealed that LCS primed genomic regions for sub-compartment repositioning in WGD cells, which resulted in chromatin and epigenetic changes associated with oncogene activation in tumours ensuing from WGD cells. Importantly, sub-compartment repositioning events were largely independent of chromosomal alterations, indicating that these were complementary mechanisms contributing to tumour development and progression. Overall, LCS initiates chromatin conformation changes that ultimately result in oncogenic epigenetic and transcriptional modifications, suggesting that chromatin evolution is a hallmark of WGD-driven cancer.

overall_design: For mutational and copy number change analyses in post-WGD cells in RPE TP53-/- line, whole genome sequencing was performed in RPE TP53-/- control, WGD, and 6w and 20w pWGD cells grown in vitro and in vivo. Biological replicates for 6w pWGD were considered and are denoted as experiment 1-4 based on multiple WGD inductions. RPE cells with a TP53 wild type background were considered as reference for calling mutations and copy number changes.

first: Ruxandra

last: Lambuta

first: Yuanlong

last: Liu

first: Juan

last: Diaz-Miyar

first: Arvind

last: Iyer

first: Daniele

last: Tavernari

first: Natalya

last: Katanayeva

first: Giovanni

last: Ciriello

first: Elisa

last: Oricchio


title: Whole genome doubling drives oncogenic loss of chromatin segregation [RNA-seq]

overall_design: Comparative gene expression analysis between pre- and post-WGD RPE TP53-/- cells. Three biological replicates were included for each of the two conditions.


title: Hippo pathway and Bonus control developmental cell fate decisions in the Drosophila eye

city: Boston

first: Alexey

last: Veraksa

state: MA

address: 100 William T. Morrissey Blvd.

department: Biology Department

country: USA

institute: University of Massachusetts Boston

summary: The canonical function of the Hippo signaling pathway is the regulation of organ growth. How this pathway controls cell fate determination is less well understood. Here, we identify a function of the Hippo pathway in cell fate decisions in the developing Drosophila eye, exerted through the interaction of Yorkie (Yki) with the transcriptional regulator Bonus (Bon), an ortholog of mammalian Transcriptional Intermediary Factor 1/tripartite motif (TIF1/TRIM) family proteins. Instead of controlling tissue growth, Yki and Bon promote epidermal and antennal fates at the expense of the eye fate. Proteomic, transcriptomic, and genetic analyses reveal that Yki and Bon control these cell fate decisions by recruiting transcriptional and post-transcriptional co-regulators, and by repressing Notch target genes and activating epidermal differentiation genes. Our work expands the range of functions and regulatory mechanisms under Hippo pathway control.

overall_design: To identify the transcriptional output of Yki and Bon in the eye vs. epidermis cell fate determination, we performed RNA sequencing to examine the transcriptome of pupal eyes at 40-41 hrs after puparium formation (APF), when the ectopic epidermal trichomes in the eye initiate, upon Bon overexpression, with or without simultaneous knockdown of Yki using RNAi, under the eye-specific driver GMR-GAL4. Three biological replicates were analyzed for each condition: mCherry (WT control), Bon-mCherry, and Bon-mCherry + yki-RNAi.

first: Heya

last: Zhao

first: Kenneth

middle: H

last: Moberg


title: Deep phenotypin heart-specific Tregs

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary:
Myocardial infarction (MI) is a sterile inflammatory condition that results in the activation of T- cells targeting cardiac antigens. T-cells have been shown to contribute to reparative and maladaptive remodeling post-MI. However, the differentiation trajectories and in situ activity of heart-specific CD4+T cells and the effect of distinct T-cell phenotypes on MI repair remains poorly understood.  Herein, we combined T-cell receptor transgenic models and tetramer staining targeting myocardial protein with single-cell transcriptomics (scRNAseq) and functional phenotyping to elucidate how the myosin-specific CD4+ T cells (TCR-M) differentiate in the murine infarcted myocardium and influence tissue repair. Furthermore, we transferred pro-inflammatory versus regulatory pre-differentiated heart-specific T-cells to dissect how they differentially regulate post-myocardial infarction (MI) inflammation.
Flow cytometry and scRNAseq findings reveled that transferred TCR-M cells acquired an induced regulatory phenotype (iTreg) in the infarcted myocardium and blunt local inflammation. Myocardial TCR-M cells differentiated into two main lineages enriched with cell activation and pro-fibrotic transcripts (e.g. Tgfb1) or with suppressor immune checkpoints (e.g. Pdcd1), which we also found in human myocardial tissue. These cells produced high levels of latency-associated peptide (LAP) and inhibited interleukine-17 (IL-17) responses. Tetramer staining further  identified endogenous myosin-specific T-cells that acquired a regulatory phenotype in the heart post-MI. Notably, TCR-M cells that were pre-differentiated in vitro towards a regulatory phenotype maintained a stable in vivo FOXP3 expression and anti-inflammatory activity whereas  TH17 partially converted towards a regulatory phenotype in the injured myocardium, which was associated to blunted myocardial inflammation. Moreover, myocardial scar of Treg TCR-M transferred mice showed blunted inflammatory transcripts and enrichment for growth factors supporting fibroblasts and endothelial cells.

overall_design:
Digested hearts and MedLNs were obtained from pooled TCR-M transferred mice at 5 and 7 days after sham or MI operation (n: 5-7 mice per group). Cell suspension was obtained as previously described and following surface staining, heart CD4+ T-cells were enriched by magnetic cell sorting, using anti-PE microbeads (Miltenyi Biotec, Bergisch-Gladbach, Germany). Before sorting, samples were separately labeled with an anti-CD45/H2-K hashtag antibody (Biolegend TotalSeqC antibodies, San Diego, CA, USA, 1:150 dilution). Additionally, all samples were labeled with anti-Thy1.1 (clone OX-7) and anti-CD25 (clone PC61) Cite-Seq antibodies (Biolegend TotalSeqC antibodies, San Diego, CA, USA, 1:100). Sodium azide was omitted in the buffers used for sorting purposes. After staining, heart and MedLN samples were separately pooled and CD4+ T-cells were sorted using a FACS Aria III instrument (BD, Heidelberg, Germany). Following a washing step, all samples were pooled and suspended in 65 µL of PBS/0.04% BSA and loaded in the 10x Genomics Chromium system as one multiplexed sample. A total of two libraries from the same experiment were generated and merged for analysis.

Myosin-specific T-cells (TCR-M cells) were transferred to WT Balb/C mice one day prior to the induction of experimental myocardial infarction (MI). CD4+ T-cells and transferred TCR-M cells were isolated from heart and mediastinal lymph nodes at 5 and 7 days post sham or MI operation by fluorescence activated cell sorting according to the congenical marker Thy1.1 expressed on TCR-M cells. In addition, CD4+ T-cells from sham and MI operated animals which have not received TCR-M cells were obtained at 5 days post-surgery. Pooled CD4+ T-cells and TCR-M cells stained with different hashtag and CITE-seq antibodies were analyzed using scRNAseq. Comparative gene expression profiling analysis of RNA-seq data from infarcted myocardial tissue of control non-T-cell transferred mice versus myocardial tissue from mice receiving adoptive transfer of Treg-polarized myosin-specific T-cells. Samples were collected at 5 days post-surgery and a total of 8 control samples and 6 Treg-transferred samples were analyzed.

first: Murilo

last: Delgobo

first: Emil

last: Weiß

first: Diyaa

middle: E

last: Ashour

first: Leon

last: Richter

first: Lisa

last: Popiolkowski

first: Panagiota

last: Arampatzi

first: Verena

last: Stangl

first: Paula

last: Arias-Loza

first: Encarnita

last: Mariotti-Ferrandiz

first: Peter

middle: P

last: Reiner

first: Burkhard

last: Ludewig

first: Ulrich

last: Hofmann

first: Stefan

last: Frantz

first: Gustavo

last: Ramos


title: Whole genome doubling drives oncogenic loss of chromatin segregation [scRNA-seq]

first: Luca

last: Nanni

overall_design: To assess the transcriptional profile and capture transcriptional and kayotypic heterogeneity of cells post-WGD cells, scRNAseq was performed for RPE TP53-/-  control cells, as well as cells which were kept in vitro after WGD induction for 6 (6w pWGD) and 20 weeks (20w pWGD), and tumours derived from 20w pWGD grown in NSG mice (T1, T2, T3).

first: Ruxandra

last: Lambuta

first: Yuanlong

last: Liu

first: Juan

last: Diaz-Miyar

first: Arvind

last: Iyer

first: Daniele

last: Tavernari

first: Natalya

last: Katanayeva

first: Giovanni

last: Ciriello

first: Elisa

last: Oricchio


title: Spatiotemporal local and abscopal cell death and immune responses to histotripsy focused ultrasound tumor ablation

city: Ann Arbor

first: Clifford

last: Cho

address: 2215 Fuller Road

institute: University of Michigan Ann Arbor

summary: Histotripsy is a novel focused ultrasound tumor ablation modality with potent immunostimulatory effects. To measure the spatiotemporal kinetics of local and abscopal responses to histotripsy, C57BL/6 mice bearing bilateral flank B16 melanoma or Hepa1-6 hepatocellular carcinoma tumors were treated with unilateral sham or partial histotripsy. Treated and Controltralateral untreated (abscopal) tumors were analyzed using multicolor immunofluorescence, digital spatial profiling, RNA sequencing (RNASeq), and flow cytometry.

overall_design: Flow-sorted CD45+ and CD45- cells were lysed and RNA was extracted per manufacturer instructions using the Qiagen RNeasy Mini Kit.  RNA was  submitted to the University of Michigan Advanced Genomics Core for library preparation and QuantSeq analysis.  Pooled libraries were subjected to 101 bp single-end sequencing with Illumina NovaSeq following manufacturer protocols .  Bcl2fastq2 Controlversion Software (Illumina) was used to generate de-multiplexed Fastq files.  Reads were trimmed using Trim Galore (v0.5.0) using default settings.  Reads were aligned using STAR (v 2.6.0) using default settings .  Unique molecular identifiers were collapsed using Lexogen Quantseq (v2.3.6). Reads were mapped to the mouse genome GRCm38 from the Ensembl genome database.  Reads were counted using BioControlductor R package Rsubread and featureCounts function .  RNASeq data analysis and visualizations were performed using BioJupies.

first: Ashley

middle: L

last: Pepple

first: Joe

last: Guy

first: Reliza

last: McGinnis

first: Amy

last: Felsted

first: Brian

last: Song

first: Ryan

last: Hubbard

first: Tejaswi

last: Worlikar

first: Hannah

last: Garavaglia

first: Joseph

last: Dib

last: Chao

first: Nicoleen

last: Boyle

first: Michal

last: Olszewski

first: Zhen

last: Xu

first: Anutosh

last: Ganguly


title: The Aryl Hydrocarbon Receptor Cell-Intrinsically Promotes Resident Memory CD8+ T Cell Differentiation and Function

status: Public on Jan 11 2023

city: Gainesville

first: Liang

last: Zhou

state: FL

address: 2015 SW 16th Ave

department: IDI

institute: University of Florida

summary: The Aryl hydrocarbon receptor (Ahr) regulates the differentiation and function of CD4+ T cells; however, the cell-intrinsic role of Ahr in CD8+ T cells, remains elusive. Herein we show that Ahr acts as a promoter of resident memory CD8+ T cell (TRM) differentiation and function. Under steady state conditions or in an oral infection model, genetic ablation of Ahr in CD8+ T cells leads to an increase in CD127–KLRG1+ short lived effector cells (TSLE) and CD44+CD62L+ T central memory (TCM) cells, but a reduction in Granzyme B-producing CD69+CD103+ T resident memory (TRM) cells. Genome-wide transcriptome and cistrome analyses reveal that Ahr suppresses the circulating while promoting the resident memory core gene program. A tumor resident polyfunctional CD8+ T cell population dependent on Ahr is revealed by single cell RNA-Seq, and deletion of Ahr in CD8+ T cells compromises anti-tumor immunity. Consistent with mouse, human IEL CD8+ T cells highly express AHR that regulates in vitro TRM differentiation and Granzyme B production. Collectively, these data suggest that Ahr is an important cell-intrinsic factor for CD8+ T cell immunity.

overall_design: RNA-seq (2 replicates) analysis of CD8+ T cells isolated from small intestine IEL of Ahrf/fCd8cre (Ahr_CD8cre) mice vs Ahrf/f (CTRL) mice, RNA-seq (2 replicates) analysis of Ahr+/+ vs Ahr –/– antigen specific (OTI) CD8+ T cells isolated from the small intestine IEL of CD45.1/1 mice on day 9 post L.m.-OVA infection, ChIP-seq analysis of CD8+ T cells isolated from spleen of  Ahr+/+ vs Ahr –/–  mice and cultured in vitro under TRM-like skewing conditions, scRNA-seq (2 replicates) analysis of CD45+ cells isolated from B16F10 tumors from Ahr+/+ vs Ahr –/–  mice.

last: Dean

first: Eric

last: Helm


title: scRNA-seq reveals differences in cell states and cell types between human hip, palm, and sole skin

city: Irvine

first: Julie

last: Wiedemann

address: Sprague Hall

institute: UCI

summary:
Palmoplantar skin is structurally and functionally unique, but the transcriptional programs driving this specialization are unknown. Here, we exploit single-cell RNA-sequencing of human palm, sole, and hip skin to describe the distinguishing characteristics of palmoplantar and non-palmoplantar skin while also uncovering previously unappreciated differences between palmar and plantar sites. Our approach reveals downregulation of diverse immunological processes and decreased immune cell populations in palmoplantar skin, highlighting an altered immune environment in the skin of the palms and soles.
Further, we identify specific palmoplantar and non-palmoplantar fibroblast populations that appear to orchestrate key differences in cell-cell communication in palm, sole, and hip. Dedicated analysis of epidermal keratinocytes highlights major differences in basal cell fraction among the three sites and validates the presence of a more differentiated, cycling basal population. Finally, our data demonstrate the existence of two spinous keratinocyte populations that constitute two parallel, site-selective epidermal differentiation trajectories. Together, these results provide a deep characterization of the highly adapted palmoplantar skin and contribute new insights into the fundamental biology of human skin.

overall_design: scRNA-seq of skin biopsies from 4 healthy adult subjects; Subjects 1 and 2 were hip and sole matched, Subjects 3 and 4 were hip and palm matched


title: The impact of Mmu17 non-Hsa21 orthologous genes in the Ts65Dn mouse model of Down syndrome: the “gold standard” refuted

status: Public on Jan 16 2023

city: Bethesda

first: Faycal

last: Guedj

state: Maryland

address: 35A Convent DR

department: NHGRI

institute: National Institute of Health

summary: Background: Despite successful preclinical treatment studies to improve neurocognition in the Ts65Dn mouse model of Down syndrome (DS), translation to humans has failed. This raises questions about the appropriateness of the Ts65Dn mouse as the “gold standard” for DS research. Here we used the novel Ts66Yah mouse that carries both an extra chromosome and the identical segmental Mmu16 trisomy as Ts65Dn without the Mmu17 non-orthologous region.    Methods: Forebrains from embryonic day 18.5 Ts66Yah and Ts65Dn mice, along with euploid littermate controls, were used for gene expression and pathway analyses. Behavioral experiments were performed in neonatal and adult mice. Since male Ts66Yah mice are fertile, parent of origin transmission of the extra chromosome was studied.  Results: We mapped 45 protein coding genes to the Ts65Dn Mmu17 non-orthologous, among which 71-82 % are expressed during forebrain development. Several of these genes were uniquely overexpressed in Ts65Dn embryonic forebrain; this produced major differences in dysregulated genes and pathways. Despite these genome-wide differences, the primary Mmu16 trisomic effects were highly conserved in both models, resulting in several commonly dysregulated disomic genes and pathways. Delays in motor development, communication and olfactory spatial memory were present in Ts66Yah but more pronounced in Ts65Dn neonates. Adult Ts66Yah mice showed working memory deficits and sex-specific effects in exploratory behavior and spatial hippocampal memory, while long-term memory was preserved. These deficits were milder when compared to Ts65Dn mice.   Conclusions: Our findings suggest that triplication of the non-orthologous Mmu17 genes significantly contributes to the phenotype of the Ts65Dn mouse and may explain why preclinical trials that used this model have unsuccessfully translated to human therapies.

overall_design: Total RNA was isolated from the developing E18.5 forebrain using the NuceloMag® RNA/DNA high throughput extraction kit following the manufacturer’s instructions (Macherey-Nagel, Bethlehem, PA). RNA was processed and hybridized on the Clariom S high throughput arrays. Eighty nine arrays were used (18 EupTs65Dn, 23 Ts65Dn, 24 EupTs66Yah and 25 Ts66Yah) and each array corresponded to labeled cDNA from one sample. Balanced numbers of male and female embryos were used in these studies. Analyses were performed using unpaired t-tests. A Benjamini-Hochberg false discovery rate (FDR) of 10% was used for multiple comparison correction of differently expressed (DEX) genes. The marginally expressed genes (MEX) (expression ratios <0.8 and >1.2 and raw p-values <0.01) were used for pathway analyses. Pathway analysis was performed using Ingenuity Pathway Analysis (IPA) database and the Database for Annotation, Visualization, and Integrated Discovery (DAVID).

first: Elise

last: Kane

first: Lauren

last: Bishop

first: Jeroen

last: Pennings

first: Yann

last: Herault

first: Diana

last: Bianchi


title: CircRNA microarray for human colorectal adenocarcinoma and normal mucosa

first: boyang

last: fan

country: China

summary: To determine the circRNA expression profile in CRC and matched non-tumor tissues, we uesed circRNA microArray analysis form Arraystar to examine the expression of circRNAs in CRC and matched non-tumor tissues.

overall_design: Total RNAs were digested with RNase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

first: B

last: Fan


title: Whole genome doubling drives oncogenic loss of chromatin segregation [scHi-C]

first: Luca

last: Nanni

overall_design: To disentangle whether LCS after WGD was detected in single cells, scHi-C was performed in RPE TP53-/- control and WGD cells by isolating individual nuclei from the two populations. scHi-C libraries were prepared from 73 individual nuclei, and, after sequencing, 33 control cells and 25 WGD cells were kept based on sequencing quality.

first: Ruxandra

last: Lambuta

first: Yuanlong

last: Liu

first: Juan

last: Diaz-Miyar

first: Arvind

last: Iyer

first: Daniele

last: Tavernari

first: Natalya

last: Katanayeva

first: Giovanni

last: Ciriello

first: Elisa

last: Oricchio