title: KMT2D Links TGF-β Signalling to Non-Canonical Activin Pathway and Regulates Pancreatic Cancer Cell Plasticity

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: Although KMT2D, also known as MLL2, is known to play an essential role in development, differentiation, and tumor suppression, its role in pancreatic cancer development is not well understood. Here, we discovered a novel signaling axis mediated by KMT2D, which links TGF-β to the activin A pathway. We found that TGF-β upregulates a microRNA, miR-147b, which in turn leads to post-transcriptional silencing of KMT2D. Loss of KMT2D induces the expression and secretion of activin A, which activates a non-canonical p38 MAPK-mediated pathway to modulate cancer cell plasticity, promote a mesenchymal phenotype, and enhance tumor invasion and metastasis in mice. We observed a decreased KMT2D expression in human primary and metastatic pancreatic cancer. Furthermore, inhibition or knockdown of activin A reversed the pro-tumoral role of KMT2D loss. These findings support a tumor-suppressive role of KMT2D in pancreatic cancer and identify miR-147b and activin A as novel therapeutic targets.

overall_design: For KMT2D knockout experiments, 3 samples were analyzed and a control cell line without gRNA was used as control. For TGF-β treatment study, 8 samples were analyzed and vehicle-treated PANC-1 cells were used as control.

first: Shuang

last: Lu

first: Hong

last: Kim

first: Yubo

last: Cao

first: Karan

last: Bedi

first: Lili

first: Ishwarya

last: Narayanan

first: Brian

last: Magnuson

first: Yumei

last: Gu

last: Yang

first: Zhujun

last: Yi

first: Michelle

last: Paulsen

first: Sivakumar

last: Jeyarajan

first: Ping

last: Qiu

first: Chang

last: Xu

first: Dafydd

last: Thomas

first: Yali

last: Dou

first: Howard

last: Crawford

first: Marina

last: Pasca di Magliano

first: Kai

last: Ge

first: Bo

first: Jiaqi

last: Shi


title: Manufacture of GMP-compliant functional SARS-COV-2 cytotoxic T lymphocytes (CTLs) utilizing the CliniMACS® Cytokine Capture System; Gene expression using NanoString pancancer immune profiling gene expression panel

status: Public on Mar 31 2023

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

country: USA

institute: Nationwide Children's Hospital

summary: SARS-CoV-2 CTLs can be generated from convalescent donors by viral peptide stimulation and enrichment via the CliniMACS® Cytokine Capture System.

overall_design: Here, we report the results of convalescent donor prescreening with SARS-CoV-2 PepTivator viral peptides (Miltenyi Biotec)○R as well as validation and characterization of SARS-CoV-2 vCTLs manufactured utilizing the Cytokine Capture System on the CliniMACS® Prodigy device.

first: Yaya

last: Chu

first: Mitchell

last: Cairo


title: RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific

city: Toronto

first: Timothy

last: Hughes

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: Thousands of RNA-binding proteins (RBPs) crosslink to cellular mRNA. Among these are numerous unconventional RBPs (ucRBPs)—proteins that associate with RNA but lack known RNA-binding domains (RBDs). The vast majority of ucRBPs have uncharacterized RNA-binding specificities. We analyzed 492 human ucRBPs for intrinsic RNA-binding in vitro and identified 23 that bind specific RNA sequences. Most (17/23), including 8 ribosomal proteins, were previously associated with RNA-related function. We identified the RBDs responsible for sequence-specific RNA-binding for several of these 23 ucRBPs and surveyed whether corresponding domains from homologous proteins also display RNA sequence specificity. CCHC-zf domains from seven human proteins recognized specific RNA motifs, indicating that this is a major class of RBD. For Nudix, HABP4, TPR, RanBP2-zf, and L7Ae domains, however, only isolated members or closely related homologs yielded motifs, consistent with RNA-binding as a derived function. The lack of sequence specificity for most ucRBPs is striking, and we suggest that many may function analogously to chromatin factors, which often crosslink efficiently to cellular DNA, presumably via indirect recruitment. Finally, we show that ucRBPs tend to be highly abundant proteins and suggest their identification in RNA interactome capture studies could also result from weak nonspecific interactions with RNA.

overall_design: In the RNAcompete assay, purified GST-tagged RBP is incubated with an excess of RNA pool and bound RNA from individual pulldown experiments are directly labeled with Cy3 or Cy5 and hybridized to a custom Agilent 244K microarray.

first: Debashish

last: Ray

first: Kaitlin

middle: U

last: Laverty

first: Arttu

last: Jolma

first: Kate

last: Nie

first: Reuben

last: Samson

first: Sara

last: Pour

first: Cyrus

middle: L

last: Tam

first: Niklas

last: von Krosigk

first: Syed

last: Nabeel-Shah

first: Mihai

last: Albu

first: Hong

last: Zheng

first: Gabrielle

last: Perron

first: Hyunmin

last: Li

first: Hamed

last: Najafabadi

first: Benjamin

last: Blencowe

first: Jack

last: Greenblatt

first: Quaid

last: Morris

middle: R


title: Single-nucleus resolution of the adult C. elegans and its application to the mapping of inter-generational response to alcohol exposure

city: Los Angeles

first: Yen-Wei

last: Chen

address: 650 Charles E. Young Dr. South  16-035 Center for Health Sciences

department: IDP Molecular Toxicology

institute: University of California, Los Angeles

type: Expression profiling by high throughput sequencing

summary: Single-cell RNA sequencing technologies have significantly contributed to our understanding of tissue heterogeneity as well as developmental and cell differentiation trajectories. They also provide an opportunity to map an organism’s response to environmental cues with high resolution and identify sensitive tissues and cell types. However, the requirement for cellular integrity during extraction has limited the examination of organs that are syncytial or of cell types, such as neurons, that have significant cellular projections. We developed a mechanical method for single nucleus extraction in C. elegans that, combined with snRNA-seq, identifies a remarkable number of cell types in the adult nematode. Clustering analysis recapitulated established morphological and functional categories as well as the differentiation trajectory of the syncytial germline. Our approach also uncovered novel features of C. elegans biology, such as previously uncharacterized intestinal subpopulations and the up-regulation of X-linked transcripts in the somatic compartment of the hermaphrodite spermatheca. We applied this method to identify the impact of intergenerational exposure to a human-relevant dose of alcohol. We show that parental ethanol exposure causes a highly cell type-specific response in the adult F1 with oocytes, motor neurons, mechanosensory neurons, and neuronal support cells displaying the highest number of differentially expressed genes, the majority of which were downregulated. Cluster-level GO analysis revealed pathways previously not known to be altered by ethanol such as sister chromatid dynamics in the oocyte and autophagy in the uterine epithelium. Together, snRNA-seq provides a powerful approach for the detailed examination of an adult organism physiology.

overall_design: 9 single nuclei C. elegans datasets were generated. 5 unexposed samples, 2 water treated F1 samples and 2 0.05% F1 ethanol treated samples.

first: Patrick

last: Allard

first: Lisa

last: Truong

first: Rio

last: Barrere-Cain


title: Low RNA stability signifies increased post-transcriptional regulation of cell identity genes

city: Boston

first: Yanqiang

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

summary: Cell identity genes are distinct from other genes with respect to the epigenetic mechanisms to activate their transcription, e.g., by super-enhancers and Broad H3K4me3 domains. However, it remains unclear whether their post-transcriptional regulation is also unique. We performed a systematic analysis of transcriptome-wide RNA stability in nine cell types and found that unstable transcripts were enriched in cell identity-related pathways while stable transcripts were enriched in housekeeping pathways. Joint analyses of RNA stability and chromatin state revealed that significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Intriguingly, the RNA m6A methyltransferase, METTL3, preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains, and their associated genes. METTL3 binding intensity is positively correlated with RNA m6A methylation and negatively correlated with RNA stability of cell identity genes, likely due to co-transcriptional m6A modifications promoting RNA decay. Nanopore direct RNA-seq showed that METTL3 knockdown has a stronger effect on RNA m6A and mRNA stability for cell identity genes. Our data suggest a run and brake model, where cell identity genes undergo both frequent transcription and fast RNA decay to achieve precise regulation of RNA expression.

overall_design:
For T cell RNA-seq, the T cells were collected from the patient's blood and separated using the apheresis method. The cells were cultured in the complete median and treated with transcription inhibition ActD at 4 different time points, 0-hour, 0.25-hour, 1 hour, and 2 hours. Total mRNA was extracted by the TRIzol reagent (Invitrogen), and the Poly(A) RNA-seq library was performed by using the TruSeq RNA Sample Prep kit, following the manufacturer’s instructions.
Two samples including shCTRL and shMETTL3 of  T cells were used to do nanopore direct RNA-seq to detect the m6A modifications. The RNA-seq reads were mapped to human hg19 and hg38 genome version.

first: Kaifu


title: bulk RNA-seq of E11.5 wild-type, CD1 facial prominences, neural tube, and limb

city: Cincinnati

first: Samantha

last: Brugmann

address: Department of Developmental Biology, DK 1 BLDG R, 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

overall_design: Facial prominence, neural tube, and limb mRNA profiles of E11.5 wild-type, CD1 mice were generated by sequencing using Illumina HiSeq4000

first: Sai

middle: K

last: Balchand

middle: A


title: Overexpression of IκB⍺ modulates NF-κB activation of inflammatory target gene expression

status: Public on Mar 30 2023

city: Manchester

first: Polly

last: Downton

address: Oxford Road

country: United Kingdom

institute: University of Manchester

summary:
Cells respond to inflammatory stimuli such as cytokines by activation of the nuclear factor-κB (NF-κB) signalling pathway, resulting in oscillatory translocation of the transcription factor p65 between nucleus and cytoplasm to mediate immune response.  We investigate the relationship between p65 and inhibitor-κB⍺ (IκBα) protein levels and dynamic properties of the system, and how this interaction impacts on the expression of key inflammatory genes. Using bacterial artificial chromosomes, we developed new cell models of IκB⍺-eGFP protein overexpression in a native genomic context. We find that cells with high levels of the negative regulator IκBα remain responsive to inflammatory stimuli and maintain dynamics for both p65 and IκBα. In contrast, canonical target gene expression is dramatically reduced by overexpression of IκBα, but can be partially rescued by overexpression of p65.  Treatment with leptomycin B to promote nuclear accumulation of IκB⍺ also suppresses canonical target gene expression, suggesting a mechanism in which nuclear IκB⍺ accumulation prevents productive p65 interaction with promoter binding sites.  This causes reduced target promoter binding and gene transcription, which we validate by chromatin immune precipitation and in primary cells.  Overall, we show how inflammatory gene transcription is modulated by the expression levels of both IκB⍺ and p65, and that transcription can be partially decoupled from p65 protein dynamics.  This results in an anti-inflammatory effect on transcription, demonstrating a broad mechanism to modulate the strength of inflammatory response.
https://doi.org/10.1101/2023.03.14.532132

overall_design: 4 cell lines x 6 time points x 2 replicates

first: Antony

middle: D

last: Adamson


title: Gene expression profile at single cell level of CD45+ tumor-infiltrating immune cells in msothelioma-bearing mice

city: Tokushima

first: atsushi

last: mitsuhashi

address: 3-18-15 Kuramoto-cho

department: Department of Respiratory Medicine and Rheumatology

country: Japan

institute: Tokushima university

summary: Fibrocytes are bone marrow-derived cells expressing fibroblast markers. We used single cell RNA sequencing (scRNA-seq) to analyze the tumor-infiltrating fibrocytes in the lung adenocarcinoma patients

overall_design: Tumor-infiltrating immune cells of AB1-HA mesothelioma-bearing mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of PE-Cy7-conjugated CD45 antibody and analyzed using scRNAseq.

first: Atsushi

last: Mitsuhashi

first: Kazuya

last: Koyama

first: Yasuhiko

last: Nishioka


title: Effect of BFD2 (TGME49_311100) knockout on T. gondii gene expression during BFD1 induction

city: Cambridge

first: Sebastian

last: Lourido

state: Massachusetts

address: 455 Main Street, Rm 555

institute: Whitehead Institute

summary:
The acute-to-chronic stage transition in Toxoplasma gondii involes a global restructuring of the parasite transcriptome.
Prior work identified a single transcription factor (BFD1) that is both necessary and sufficient to establish the chronic-stage program, making it the master regulator of this process.
Recently, we found that parasites lacking a CCCH-type zinc finger RNA-binding protein (BFD2) are also unable to produce chronic forms.
To understand how BFD2 aids in establishing the BFD1 transcriptional program, we knocked out BFD2 in a BFD1-conditional expression strain, wherein BFD1 is induced by treatment with the small molecule Shield-1.

overall_design:
Comparative RNA-seq analysis was performed on conditional BFD1 expression strains in the presence (DD-BFD1) and absence of BFD2 (DD-BFD1/∆bfd2), after 48h of treatment with either 3 µM Shield-1 to induce BFD1 expression or an equivalent volume of ethanol (i.e. vehicle).
Experiments were performed in biological triplicate (separate infections) and technical duplicate (i.e. samples split in two at the time of harvest and processed in parallel for all subsequent steps, from RNA isolation through library prepartion and sequencing).

first: M

middle: H

last: Licon


title: Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus

status: Public on Mar 29 2023

city: Stanford

first: Liang-Fu

state: CA

address: 265 Campus Drive, Lokey Stem Cell Research Building/SIM1

department: Chemical and Systems Biology

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Enhancer clusters overlapping disease-associated mutations in Pierre Robin sequence (PRS) patients regulate SOX9 expression at genomic distances over 1.25 Mb. We applied optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS-enhancer activation. We observed pronounced changes in locus topology between cell types. Subsequent analysis of single-chromatin fiber traces revealed that these ensemble-average differences arise through changes in the frequency of commonly sampled topologies. We further identified two CTCF-bound elements, internal to the SOX9 topologically associating domain, which promote stripe formation, are positioned near the domain's 3D geometric center, and bridge enhancer-promoter contacts in a series of chromatin loops. Ablation of these elements results in diminished SOX9 expression and altered domain-wide contacts. Polymer models with uniform loading across the domain and frequent cohesin collisions recapitulate this multi-loop, centrally clustered geometry. Together, we provide mechanistic insights into architectural stripe formation and gene regulation over ultra-long genomic ranges.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CTCF and RAD21 in cranial neural crest cells (CNCCs).

first: Hannah

last: Long

first: Joanna

last: Wysocka


title: Receptor Interacting Protein 140 (Nrip1) Controls Cardiac Fuel Metabolism and Function [CUT&RUN]

city: Philadelphia

first: Daniel

last: Kelly

state: PA

address: 3400 Civic Center Blvd

department: Penn Cardiovascular Institute

institute: University of Pennsylvania

summary: During development of heart failure, capacity for cardiomyocyte fatty acid oxidation (FAO) and ATP production is progressively diminished contributing to pathologic cardiac hypertrophy and contractile dysfunction. Receptor interacting protein 140 (RIP140; Nrip1) has been shown to function as a transcriptional co-repressor of oxidative metabolism. Here we show that mice lacking RIP140 in striated muscle (strRIP140-/-) have increased expression of a broad array of involved in a broad array of mitochondrial energy metabolism and contractile function in heart and skeletal muscle. strRIP140-/- mice were resistant to the development of pressure overload-induced cardiac hypertrophy, and cardiomyocyte-specific RIP140 deficient (csRIP140-/-) mice were defended against development of heart failure caused by pressure overload combined with myocardial infarction. Genomic enhancers activated by RIP140 deficiency in cardiomyocytes were enriched in binding motifs for transcriptional regulators of mitochondrial function (estrogen-related receptor) and cardiac contractile proteins (myocyte enhancer factor 2).  Consistent with a role in the control of cardiac fuel metabolism, loss of RIP140 in heart resulted in augmented triacylglyceride turnover and FA utilization. We conclude that RIP140 functions as a suppressor of a transcriptional regulatory network that controls cardiac fuel metabolism and contractile function, representing a potential therapeutic target for heart failure.

overall_design: CUT&RUN (Cleavage Under Targets & Release Using Nuclease) experiment to identify changes in H3K27Ac chromatin modification patterns due to cardiac-specific RIP140 deficiency in cardiomyocytes. IgG antibody is used in control experiments. 3 biological replicates per condition

first: Tsunehisa

last: Yamamoto

first: Kirill

last: Batmanov

first: Santosh

last: Maurya

first: Elizabeth

last: Pruzinsky

first: Yang

last: Xiao

last: Wang

first: Ling

last: Lai

first: Kendra

middle: S

last: McDaid

first: Swapnil

middle: V

last: Shewale

first: Teresa

middle: C

last: Leone

first: Pieterjan

last: Dierickx

first: Mitchell

last: Lazar

first: Douglas

last: Lewandowski

middle: P


title: Interrogating bromodomain inhibitor resistance in KMT2A-rearranged leukemia through combinatorial CRISPR screens

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

summary: Bromo- and extra-terminal domain inhibitors (BETi) have exhibited therapeutic activities in many cancers, including KMT2A-rearranged (KMT2A-r) leukemia, in preclinical studies. However, the mechanisms controlling BETi response and resistance are poorly understood. We conducted genome-wide loss-of-function CRISPR screens using BETi-treated KMT2A-r cell lines. SPOP gene deficiency caused significant BETi resistance, which was further validated in cell line and xenograft models. In SPOP-knockout KMT2A-r leukemia cells, TRIM24 was identified as a SPOP substrate that mediates resistance to BETi. Additionally, proteomics analysis and a kinase-vulnerability CRISPR screen indicated that resistant cells are sensitive to GSK3 inhibition. Genetically perturbating TRIM24 or pharmaceutical inhibition of its downstream target GSK3 in SPOP-knockout cells reversed the BETi-resistance phenotype. A combination therapy regimen inhibiting both BET and GSK3 impeded leukemia progression in patient-derived xenografts in vivo. Our results revealed not only novel molecular mechanisms underlying BETi resistance but also a promising strategy for treating KMT2A-r leukemia.

overall_design: SEM cells, with or without SPOP KO, were treated with DMSO, CHIR98014, ABBV-744, or a combination thereof.

first: Shaela

last: Wright

first: Jianzhong

last: Hu

first: Hong

first: Judith

last: Hyle

last: Zhang

first: Guoqing

last: Du

first: Marina

middle: Y

last: Konopleva

first: Steven

middle: M

last: Kornblau

first: Mohamed

middle: N

last: Djekidel

first: Xujie

last: Zhao

first: Ying

last: Shao

first: Beisi

last: Xu

first: Rui

last: Lu

first: Jun

middle: J

last: Yang

first: Chunliang

last: Li


title: Effect of BFD2 (TGME49_311100) deletion on gene expression in Toxoplasma gondii

first: Sebastian

last: Lourido

summary:
The acute-to-chronic stage transition in Toxoplasma gondii involes a global restructuring of the parasite transcriptome and is induced under alkaline stress.
We found that parasites lacking the RNA-binding protein BFD2 are unable to produce chronic forms, consistent with a block in this develomental program.
To understand how BFD2 facilitates chronic-stage transcriptional reprogramming in T. gondii, we profiled the transcriptomes of both 'wildtype' and BFD2-knockout parasites under alkaline-stressed and standard culture conditions

overall_design:
Comparative RNA-seq analysis was performed on ∆bfd2 and its parental strain of Toxoplasma (ME49), cultured for 48h under either alkaline-stressed or undstressed conditions.
Experiments were performed in biological triplicate (separate infections) and technical duplicate (i.e. samples split in two at the time of harvest and processed in parallel for all subsequent steps, from RNA isolation through library prepartion and sequencing).

first: M

last: Licon


title: Renal tubular Pck1 knockout mice showed albuminuria.

first: Kazuhiro

last: Hasegawa

department: Department of Nephrology

institute: Tokushima University Graduate School of Biomedical Sciences

summary:
We aim to investigate the role of renal Pck1 on albuminuria. To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish between wild type mice.
To elucidate the molecular mechanisms underlying the increase in albuminuria by our Pck-CKO (Pck1 conditional knockout) mice, we performed DNA microarray analysis using whole kidneys to examine the differences in gene expression between Pck1-CKO and wild-type control mice.

overall_design: Mice in the Pck1-CKO and WT(wild-type control) groups were killed at 32weeks of age. We obtained the whole kidneys to be used for total RNA isolation and subjected to analysis on microarray


title: Encephalitis and poor neuronal death-mediated control of herpes simplex virus in human inherited RIPK3 deficiency

city: New York

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

summary: We hypothesize that human RIPK3 deficiency does not result in impairment of type I IFN mediated antiviral immunity, contrasting with the situation in deficiencies of the TLR3-IFNAR1 circuit. To test the cellular responses to HSV1 at the wide transcriptome level, bulk RNA sequencing was performed with human primary fibroblasts without or with HSV-1 infection for 24 hours, in cells from healthy controls, RIPK3 HSE patient and other patients with recessive TLR3, IFNAR1 or NEMO deficiency.

overall_design: RNA was extracted from primary fibroblasts with the Quick RNA MicroPre Kit. RNA-Seq libraries were prepared with the Illumina RiboZero TruSeq Stranded Total RNA Library Prep Kit and RNA-sequencing was performed on the Illumina NovaSeq platform, with a read length of 100 bp and a read depth of 40 million reads.

first: Zhiyong

last: Liu

first: Eduardo

last: Reino

first: Oliver

last: Harschnitz

first: Hongyan

last: Guo

first: Yi

last: Chan

first: Noopur

last: Khobrekar

first: Mary

last: Hasek

first: Kerry

last: Dobbs

first: Darawan

last: Rinchai

first: Marie

last: Materna

first: Daniela

last: Matuozzo

first: Danyel

last: Lee

first: Paul

last: Bastard

first: Jie

last: Chen

first: Yoon

first: Seong

last: Kim

first: Shuxiang

first: Lazaro

last: Lorenzo

first: Yoann

last: Seeleuthner

first: Remi

last: Chevalier

first: Laure

last: Mazzola

first: Claire

last: Gay

first: Jean-Louis

last: Stephan

first: Baptiste

last: Milisavljevic

first: Soraya

last: Boucherit

first: Flore

last: Rozenberg

first: Rebeca

last: de Diego

first: Richard

last: Dix

first: Nico

last: Marr

first: Vivien

last: Béziat

first: Aurelie

last: Cobat

first: Mélodie

last: Aubart

first: Laurent

last: Abel

first: Stephane

last: Chabrier

first: Gregory

last: Smith

first: Luigi

last: Notarangelo

first: Edward

last: Mocarski

first: Lorenz

last: Studer

first: Jean-Laurent

last: Casanova

first: Shen-Ying


title: Effect of topical emollient on the development of atopic dermatitis and atopic march in a mice model

city: shanghai

first: JIE

last: ZHENG

state: shanghai

address: 197 Ruijin Second Road

country: China

institute: Ruijin Hospital, Shanghai jiaotong university

summary: To investigate the effect of emollient on atopic march in a murine model of chronic atopic dermatitis (AD). Mice were divided into 3 groups and treated with topical calcipotriol and ovalbumin alone or with a linoleic acid-ceramide-containing emollient. After 28 days, clinical, histological, and transcriptomic analyses were performed in skin lesions, lung and serum. Calcipotriol combined with ovalbumin induced a typical AD model with concomitant increased expression of Th2 and basophil-related genes in the lung. Compared to AD group, emollient group: 1) Skin: clinical severity and inflammatory cell infiltration were significantly reduced and transcriptomic analysis revealed significant downregulation of AD-related genes (286 of 1450 differentially expressed genes (DEGs)) including those related to innate inflammation (S100a8/a9, Il1b, Defb3/6, Mmp12), chemokines (Cxcl1/3, Ccl3/4) and barrier (Krt2/6b/80, Serpinb12, Lce3e, Sprr2). DEGs down-regulated by emollient were enriched in mitochondrial OXPHOS-related pathways, while up-regulated DEGs were mainly enriched in axon guidance, tight junctions, as shown by KEGG analyses. 2) Serum: total IgE and TSLP levels were significantly decreased, and IL-4 levels showed a decreasing tendency. 3) Lung: 187 of 275 upregulated DEGs were significantly downregulated in lung tissue including genes involved in cytokine and cytokine receptor interaction (Cxcl2/Cxcr2, Ccl2/3, Csf3r, etc.) and basophil activation (Mcpt8, Cd200r3, Ms4a2).  Thus, topical emollient not only reduces skin inflammation and maintain skin barrier homeostasis by inhibiting the mitochondrial respiratory chain, but also limits systemic inflammation by decreasing TSLP and IgE levels. Moreover, it reduces respiratory chemokine production and basophil infiltration and activation, providing a molecular basis for blocking the atopic march.

overall_design: The study samples are from control mice, AD mice and AD mice treated with a linoleic acid-ceramide-containing emollient (3 mice each group). Skin and lung samples are collected. Gene expression profiling analysis of RNA-seq data.

first: Jie

last: Zheng

first: Lihong

last: Chen

first: Li

last: Zhang

first: Xintian

last: Xu

first: Jiayi


title: Comparative transcriptome and metabolomic survey reveal key pathways involved in the control of the chilling injury disorder superficial scald in two apple cultivars, ‘Granny Smith’ and ‘Ladina’

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

summary: The low temperature normally applied to prevent fruit decay during the storage of apples, can also triggers the onset of a chilling injury disorder known as superficial scald. In this work, the etiology of this disorder and the mechanism of action of two preventing strategies, such as the application of 1-MCP and storage at low oxygen concentration in ‘Granny Smith’ and ‘Ladina’ apple cultivars was investigated. The metabolite assessment highlighted a reorganization of specific secondary metabolites, in particular flavan-3-ols (catechin, epicatechin and procyanidin B) and unsaturated fatty acids (oleic acid, linoleic acid and linolenic acid), while the genome-wide transcriptomic analysis grouped the DEGs into four functional clusters. The KEGG pathway, GO enrichment analysis, together with the gene-metabolite profiling interactome, showed as the treatment with 1-MCP prevented the development of superficial scald by actively promoting the production of unsaturated fatty acids, especially in ‘Granny Smith’. ‘Ladina’ was instead more susceptible to superficial scald, and characterized by a higher accumulation of very long chain fatty acids (VLCFAs). Storage at low oxygen concentration stimulated a higher accumulation of ethanol and acetaldehyde together with the expression of genes involved in anaerobic respiration, such as malate and alcohol dehydrogenase and pyruvate decarboxylase in both cultivars. Moreover, in ‘Granny Smith’ apple, the expression of three members of the VII subgroups of ERF genes, encoding for elements coordinating the acclimation process to hypoxia in plants was observed. The global RNA-Seq pattern also elucidated a specific transcriptomic signature between the two cultivars, validating the effect of the different genetic background in the control of this disorder.

overall_design: RNA-Seq analysis of 6 samples (GS_RA, GS_1-MCP, GS_LO, LA_RA, LA_1-MCP, LA_LO). For each sample three replicates were assessed.

first: Lorenzo

last: Vittani

first: Francesca

last: Populin

first: Stefan

last: Stuerz

first: Andreas

last: Buehlamnn

first: Iuliia

last: Khomenko

first: Franco

last: Biasioli

first: Urska

last: Vrhovsek

first: Domenico

last: Masuero

first: Angelo

last: Zanella

first: Nicola

last: Busatto


title: Spt3 and Spt8 are involved in the formation of a silencing boundary by interacting with TATA-binding protein

city: Fukui-city

first: Takahito

last: Ayano

state: Fukui

address: 3-9-1, Bunkyo

department: Graduate school engineering

institute: University of Fukui

summary: In Saccharomyces cerevisiae, a heterochromatin-like chromatin structure called the silencing region is present at the telomere as a complex of Sir2, Sir3, and Sir4. Sir2 is a histone deacetylase, and Sir3 and Sir4 promote spreading of the silencing region at the telomere. Histone acetyltransferases restrict the silencing region. Here, we show that Spt3 and Spt8 block the spread of silencing regions. Spt3 and Spt8 are members of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex, which has histone acetyltransferase activity. Although both Spt3 and Spt8 interact with telomere-binding proteins (TBPs), Spt3 had a greater effect on genome-wide transcription. Mutant analysis showed that TBPs play an important role in boundary formation, in particular the interaction between Spt3 and TBPs.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: All strain cells were grown at 30ºC in 5ml YPD media with shaking. Total RNAs were collected at exponential phase (optimal density of 0.7) using acid phenol-chloroform extraction method and hybridized on Affymetrix microarrays.

first: Kazuma

last: Kamata

first: Masaya

last: Oki


title: Effect of the depletion of ZC3H41 (Tb927.11.1980) on the transcriptome of procyclic Trypanosome brucei

city: Armilla

first: Antonio

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

country: Spain

institute: CSIC

summary: Depletion of ZC3H41 has minor effects on the transcriptome of procyclic trypanosomes. In general, ZC3H41-regulated transcripts seem to be expressed at low abundance, and almost half of them (43%) are probably non-coding, since the corresponding encoded proteins have not been detected in proteomic surveys . A transcript encoding a trans-sialidase (Tb927.11.11410) was clearly upregulated in ZC3H41-depleted cells .

overall_design: Total RNA was obtained from three biological replicates corresponding to ZC3H41-depleted trypanosomes after 48h of RNAi induction.

last: Estévez


title: mRNAseq of primary hepatocytes treated in vitro with Itaconate, Lipid, or Itaconate + Lipid

status: Public on Mar 28 2023

city: Frederick

first: Ian

last: Bettencourt

state: MD

address: 1050 Boyles Street Rm 31-16A

department: CIL

institute: NCI

summary: primary hepatocytes isolated from wildtype mouse livers and treated overnight in complete media with 10mM sodium itaconate in the presence or absence of a 1:10 dilution of sterile, chemically defined lipid mixture 1 (Sigma-Aldrich)

overall_design: Gene expression analysis from four replicates of primary hepatocytes were untreated (control), treated with sodium itaconate alone, lipid mix alone, or itaconate and lipid mix overnight

first: Jonathan

last: Weiss


title: Human iPSC-derived proinflammatory macrophages cause insulin resistance in an isogenic white adipose tissue microphysiological system

city: Berkeley

first: Yuchen

last: He

state: California

address:
344 Morgan Hall, University of California
 Berkeley

department: Department of Nutritional Science and Toxicology

institute: University of California Berkeley

summary: Chronic white adipose tissue (WAT) inflammation has been recognized as a critical early event in the pathogenesis of obesity-related disorders. This process is characterized by the increased residency of proinflammatory M1 macrophages in WAT. However, the lack of an isogenic human macrophage-adipocyte model has limited biological studies and drug discovery efforts, highlighting the need for human stem cell-based approaches. Here, human induced pluripotent stem cell (iPSC) derived macrophages (iMACs) and adipocytes (iADIPOs) are cocultured in a microphysiological system (MPS). iMACs migrate toward and infiltrate into the 3D iADIPOs cluster to form crown-like structures (CLSs)-like morphology around damaged iADIPOs, recreating classic histological features of WAT inflammation seen in obesity. Significantly more CLS-like morphologies formed in aged and palmitic acid-treated iMAC-iADIPO-MPS, showing the ability to mimic inflammatory severity. Importantly, M1 (proinflammatory) but not M2 (tissue repair) iMACs induced insulin resistance and dysregulated lipolysis in iADIPOs. Both RNAseq and cytokines analyses revealed a reciprocal proinflammatory loop in the interactions of M1 iMACs and iADIPOs. Our iMAC-iADIPO-MPS thus successfully recreates pathological conditions of chronically inflamed human WAT, allowing us to study the dynamic inflammatory progression and identify clinically relevant therapies.

overall_design: To study interaction between isogenic macrophages and adipocytes derived from the same iPSC line, these two types of cells were monocultured in 24-well plate or cocultured in trans-well settings with 3 biological replicates per condition for 2 days. Macrophages in trans-wells and adipocytes in 24-well culture plates were respectively lysed and purified for bulk RNA that was RNA-seq analysized by Novogene. Genes of interests were then selected based on the relevance to iMAC-iAdipo interaction, and replotted based on data in DAVID analysis (The Database for Annotation, Visualization, and Integrated Discovery).

first: Lin

last: Qi

first: Koji

last: Matsuo

first: Ashley

last: Pereira

first: Yue

middle: T

last: Lee

first: Fenmiao

last: Zhong

first: Peter-James

last: Zushin

first: Marko

last: Gröger

first: Aditi

last: Sharma

first: Holger

last: Willenbring

first: Edward

last: Hsiao

last: Stahl


title: Identification of  mRNAs associated with the protein complex ZC3H41/Z41AP (Tb927.11.1980/Tb927.7.7460) in Trypanosoma brucei

summary: Data were analyzed with the peak caller MACS2, which gave us a list of 104 mRNAs highly likely to be associated with the complex. There was a notable abundance of mRNAs encoding ribosomal proteins among these top-ranked transcripts (72 of 104 transcripts).

overall_design: Tandem-affinity purification (TAP) was used to identify mRNAs associated with the complex. Input RNA vs affinity-purified RNA were compared.


title: scRNAseq studies of pMHCII-NP-induced Tet+ cells with different insulin-epitopes

city: Barcelona

first: Pere

last: Santamaria

address: C/Rosselló 149-153

institute: IDIBAPS

summary: SMARTseq2 scRNAseq analysis was performed on Tet+ and Tet- (Tconv) induced with 3 different insulin epitopes specificities (InsB12-20-CT-R1/IAg7, InsB13-21-R2/IAg7 and InsB10-23-CT_R3/IAg7) to study transcriptional reprogramming to different registers of the same epitope

overall_design: Treatment of NOD mice with InsB12-20-CT-R1/IAg7, InsB13-21-R2/IAg7 and InsB10-23-CT_R3/IAg7 to induce Tet+ cells and perform scRNAseq studies

first: Santamaria

last: Pere

first: Solé

last: Patricia

first: Josep

last: Garnica


title: LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis [Hi-C]

city: Milano

first: gabriele

last: bucci

state: MI

address: via olgettina 58

department: CTGB

institute: IRCCS Ospedale San Raffaele

summary: We have previously shown that EPR favors the interaction between Mettl7a1 promoter and a distal enhancer element. To comprehensively map long-range interactions between promoters and distal regulatory elements that are affected by EPR KO in large intestine, we preformed Promoter capture Hi-C experiments. Crypts were purified from proximal colon of two EPR fl/fl control and two EPR cKO mice. Hi-C libraries were constructed and hybridized with biotinylated RNA probes from the Arima mouse promoter panel designed to hybridize the promoters of 25752 mouse genes. Captured libraries were sequenced and bioinformatically analyzed. Our results indicate that EPR knockout leads to a rewiring of a number of promoter-enhancer interactions.

overall_design: Crypts from proximal colon were isolated from three distinct EPR fl/fl and three EPR cKO mice, snap-frozen and shipped to Arima Genomics (San Diego, CA) where the experiments were conducted. Briefly, chromatin from crypts was crosslinked and digested using a restriction enzyme cocktail. The 5’-overhangs are then filled in, causing the digested ends to be labeled with a biotinylated nucleotide. Next, spatially proximal digested ends of DNA are ligated, capturing the sequence and structure of the genome. The ligated DNA is then purified, producing pure proximally-ligated DNA. The proximally-ligated DNA is then fragmented, and the biotinylated fragments are enriched. The enriched fragments are then subjected to a custom library preparation protocol utilizing the Arima Library Prep Module . Following Library prep we perform shallow sequencing (500k-2M paired-end reads) to assess the libraries’ quality in terms of library complexity and long-range interaction information prior to proceeding with the capture. Once Hi-C is complete, the sample is pre-cleared to remove carry over biotinylated Hi-C molecules. The interactions of interest are then enriched using biotinylated RNA probes from the Arima Mouse Promoter Panel .

first: P

last: Briata

first: E

last: Zapparoli

first: G

last: Bucci

first: A

last: Inga

first: F

last: Chiacchiera

first: L

last: Caputo

first: R

last: Gherzi


title: LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis

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

overall_design: Refer to individual Series


title: Receptor Interacting Protein 140 (Nrip1) Controls Cardiac Fuel Metabolism and Function

first: Daniel

last: Kelly


title: Comparative analysis of cell-cell communication at single-cell resolution

first: Aaron

middle: James

last: Wilk

address: 300 Pasteur Dr Bldg S131, Grant

summary: Inference of cell-cell communication from single-cell RNA-sequencing data is a powerful technique to uncover intercellular communication pathways, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell level information. Here we present Scriabin, a flexible and scalable framework for comparative analysis of cell-cell communication at single-cell resolution that is performed without cell aggregation or downsampling. We use multiple published atlas-scale datasets, genetic perturbation screens, and direct experimental validation to show that Scriabin accurately recovers expected cell-cell communication edges and identifies communication networks that can be obscured by agglomerative methods. Additionally, we use spatial transcriptomic data to show that Scriabin can uncover spatial features of interaction from dissociated data alone. Finally, we demonstrate applications to longitudinal datasets to follow communication pathways operating between timepoints. Our approach represents a broadly applicable strategy to reveal the full structure of niche-phenotype relationships in health and disease.

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated from a single donor. NK cells and B cells were isolated from these PBMCs and mRNAs encoding either GFP, CD40, or CD40L were transfected via CARTs. NK and B cells were co-cultured and subjected to single-cell RNA sequencing via the Seq-Well platform.

first: Catherine

last: Blish


title: Gene expression profile at single cell level of CD45+ cells from human skin

city: Charleston

first: Heehwa

last: Son

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

summary: We used single cell RNA sequencing (scRNA-seq) to analyze and characterize cytotoxic CD4 T cells in the normal human skin

overall_design: Using enzymatic dissociation, cell suspension was isolated from normal human skin. Then cells were FACS sorted to get CD45+ propidium iodide- cells and analyzed using scRNA seq.

first: Tomonori

last: Oka

first: Shadmehr

last: Demehri


title: Receptor Interacting Protein 140 (Nrip1) Controls Cardiac Fuel Metabolism and Function [RNA-seq]

summary: During development of heart failure, capacity for cardiomyocyte fatty acid oxidation (FAO) and ATP production is progressively diminished contributing to pathologic cardiac hypertrophy and contractile dysfunction. Receptor interacting protein 140 (RIP140; Nrip1) has been shown to function as a transcriptional co-repressor of oxidative metabolism. Here we show that mice lacking RIP140 in striated muscle (strRIP140-/-) have increased expression of a broad array of involved in a broad array of mitochondrial energy metabolism and contractile function in heart and skeletal muscle. strRIP140-/- mice were resistant to the development of pressure overload-induced cardiac hypertrophy, and cardiomyocyte-specific RIP140 deficient (csRIP140-/-) mice were defended against development of heart failure caused by pressure overload combined with myocardial infarction. Genomic enhancers activated by RIP140 deficiency in cardiomyocytes were enriched in binding motifs for transcriptional regulators of mitochondrial function (estrogen-related receptor) and cardiac contractile proteins (myocyte enhancer factor 2).  Consistent with a role in the control of cardiac fuel metabolism, loss of RIP140 in heart resulted in augmented triacylglyceride turnover and FA utilization. We conclude that RIP140 functions as a suppressor of a transcriptional regulatory network that controls cardiac fuel metabolism and contractile function, representing a potential therapeutic target for heart failure.

overall_design: Differential gene expression analysis of RNA-Seq data from cardiac ventricles of mice lacking RIP140 in striated muscle and control mice

first: Tsunehisa

last: Yamamoto

first: Kirill

last: Batmanov

first: Santosh

last: Maurya

first: Elizabeth

last: Pruzinsky

first: Yang

last: Xiao

last: Wang

first: Ling

last: Lai

first: Kendra

last: McDaid

first: Swapnil

last: Shewale

first: Teresa

last: Leone

first: Pieterjan

last: Dierickx

first: Mitchell

last: Lazar

first: Douglas

middle: E

last: Lewandowski


title: A pilot study of ex vivo human prefrontal RNA transcriptomics in Parkinson’s disease

status: Public on Mar 27 2023

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: Parkinson’s disease (PD) can dramatically change cortical neurophysiology. The molecular basis for PD-related cortical changes is unclear because gene expression data are usually derived from postmortem tissue collected at the end of a complex disease and they profoundly change in the minutes after death. Here, we studied cortical changes in tissue from the prefrontal cortex of living PD patients undergoing deep-brain stimulation implantation surgery. We examined 780 genes using the NanoString nCounter platform and found that 40 genes were differentially expressed between PD (n = 12) and essential tremor (ET; n = 9) patients. One of these 40 genes, STAT1, correlated with intraoperative 4-Hz rhythms and intraoperative performance of an oddball reaction-time task. Using a pre-designed custom panel of 780 targets, we compared these intraoperative data with those from a separate cohort of fresh-frozen tissue from the same frontal region in postmortem human PD donors (n = 6) and age-matched neurotypical controls (n = 6). This cohort revealed 279 differentially expressed genes. Fifteen of the 40 intraoperative PD-specific genes overlapped with postmortem PD-specific genes, including CALB2 and FOXP2. Transcriptomic analyses identified pathway changes in PD that had not been previously observed in postmortem cases. These molecular signatures of cortical function and dysfunction may help us better understand cognitive and neuropsychiatric aspects of PD.

overall_design: We had two cohorts - intraoperative and postmortem.

first: Queena

last: Lin

first: Nandakumar

last: Narayanan


title: Single cell transcriptomic profiling of human brain organoids reveals developmental timing- and cell-type-specific vulnerabilities induced by NRXN1 CNVs in schizophrenia

city: CINCINNATI

first: Kang

last: Jin

address: 3333 Burnet Ave, Cincinnati

institute: Cincinnati Children's Hospital Medical Center

summary: De novomutations and copy number variations (CNVs) inNRXN1(2p16.3) pose a significant risk for schizophrenia (SCZ). HowNRXN1CNVs impact cortical development in a cell type-specific manner and how disease genetic background modulates these phenotypes are unclear. Here, we leveraged human pluripotent stem cell-derived brain organoid models carryingNRXN1heterozygous deletions in isogenic and SCZ patient genetic backgrounds and conducted single cell transcriptomic analysis over the course of cortical brain organoid development from 3 weeks to 3.5 months. We identified maturing glutamatergic and GABAergic neurons as being consistently impacted due toNRXN1CNVs irrespective of genetic background, contributed in part by altered gene modules in ubiquitin-mediated pathways, splicing, and synaptic signaling. Moreover, while isogenicNRXN1CNVs impact differentiation and maturation of neurons and astroglia, cell composition and developmental trajectories of early neural progenitors are affected in SCZ-NRXN1CNVs. Our study reveals developmental timing dependentNRXN1CNV-induced cellular mechanisms in SCZ at single cell resolution and highlights the emergence of disease-specific transcriptomic signatures and cellular vulnerabilities, which can arise from interaction between genetic variants and disease background.

overall_design: Developing forebrain organoid samples generated from a cohort of human pluripotent stem cells including 4 donor derived healthy control iPSC lines, 4 schizophrenia patient derived iPSC lines, and 1 NRXN1 cKO hESC line. NRXN1 cKO hESC line samples include 2 replicates of d50 and d100 time points. All other samples are single replicate across time points (from d22/23 to d100/101).

first: Rebecca

last: Sebastian

first: Bruce

last: Aronow

first: ChangHui

last: Pak


title: Characterize osteocyte transcriptome under control of PPARa

city: Jupiter, FL 33458

first: Gogce

middle: Ceren

last: Crynen

state: Florida

address: 130 Scripps Way

department: Bioinformatics and Statistics Core

institute: UF Scripps Biomedical Research

summary: RNA-seq analysis of transcriptome of osteocytes isolated from femora cortical bone of 5 mo old C57BL6 mice with WT or PPARa KO genotype. Conclusion: In osteocytes, PPARα controls large number of transcripts coding for signaling proteins and osteocyte secretome which regulates development of bone marrow adipose tissue and peripheral fat metabolism.

overall_design: Cell fraction enriched in osteocytes was isolated by sequential collagenase digestion of femora bone according to previously described protocol. In brief, isolated femurs were cleaned and scrapped to remove soft tissues and periosteum, respectively. Bone marrow was spun down and epiphysis were removed. Bone diaphysis were sequentially digested in buffers supplemented with collagenase or EDTA. Fraction number 3 which is an osteoblastic fraction and fraction number 6, osteocytic fractions were lysed with Tri Reagent and stored at -80°C. Total RNA was extracted from the samples according to the manufacturer’s protocol.

first: Beata

last: Lecka-Czernik

first: Amit

last: Chougule

first: Mi Ra

last: Chang

first: Patrick

last: Griffin

first: Emily

last: Crowe

first: Piotr

last: Czernik


title: LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis SW480 [RNA-Seq]

first: gabriele

last: bucci

summary: The lncRNA EPR (a.k.a BC030870) is highly enriched in the gastrointestinal tract in mice and, more specifically, in the large intestine. We generated conditional EPR knock-out in large intestine e and analyzed genome-wide the gene expression changes by RNA-Seq. Total RNA was extracted from the proximal colon of six control (EPR fl/fl) and six knock-out (EPR cKO) mice. Libraries were constructed and sequenced. Results indicate that EPR knock-out predominantly leads to down-regulation of genes implicated in mucus biogenesis. These results help in explaining the phenotype displayed by EPR cKO mice that is characterized by higher susceptibility to intestinal inflammation and cancer formation.

overall_design: To verify the impact of the peptide in colon cancer cells and we  transfected SW480 with an EPR mutant in which the start codon of the peptide has been mutagenized to a STOP codon SW480-EPRSTOPM. High-quality RNA was extracted from either mock or EPR-overexpressing SW480 cells (biological triplicates for each experimental condition), and a total of six libraries were prepared using standard Illumina Stranded Total RNA Prep with Ribo-Zero Plus protocol and sequenced on Illumina NovaSeq 6000.

first: P

last: Briata

first: E

last: Zapparoli

first: G

last: Bucci

first: A

last: Inga

first: F

last: Chiacchiera

first: L

last: Caputo

first: R

last: Gherzi


title: Expression data from human primary monocyte derived immature dendritic cells (iDC)

city: Heidelberg

first: Lara

last: Gallucci

address: Neuenheimer Feld

department: Department of Infectious Diseases, Integrative Virology

country: Germany

institute: University Hospital Heidelberg

summary:
During HIV-1 infection, iDCs contribute to mounting an immune response and to viral dissemination, however most of the studies addressing iDCs-HIV-1interactions have been performed in standard 2D suspension cultures which do not reflect the 3D architecture of tissues in vivo. To overcome this limitation and to understand the role that the 3D environemt has we studied iDC biology as well as iDC-HIV-1 functional interactions in 3D collagen matrix comparing 3D collagen cultures to standard 2D suspension cultures.
We used microarray data to analyze how the 3D environment affects the expression profile of monocyte derived iDCs under basal condition, LPS stimulation and in response to HIV-1 infection

overall_design: iDCs were either stimulated with LPS as positive control, infected with HIV-1 or left untreated and cultured in 2D suspension or 3D collagen for two days. Two days after RNA was exctracted and transcriptomes were determined by Clariom™ S Pico assay

first: Raffaele

last: Fronza

first: Oliver

last: Fackler


title: Extrahepatic tumors induce inflammation causing liver depletion of HNF4a and driving a systemic metabolic rewiring

city: Rehovot

first: Ayelet

last: Erez

state: Please Select

address: CANDIOTTI 214

country: Israel

institute: WEIZMANN INSTITUTE

summary: To evaluate whether liver metabolic pathways are affected by non-hepatic cancer in-vivo, we performed RNA sequencing of hepatocytes isolated from perfused livers of WT and 4T1 breast cancer-bearing mice on days 4 and 21 following cancer cells injection.

overall_design: At 2 time points, day 4 and day 21 following PBS or 4T1 BC cells injection, 3 mice from each group were sacrificed and their hepatocytes were sent for RNA Seq analysis.

first: Goldman

last: Omer

first: Hajaj

last: Emma

first: Erez

last: Ayelet


title: Extrahepatic tumors induce inflammation causing liver depletion of HNF4a and driving a systemic metabolic rewiring II

summary: To identify which immune cells infiltrate the liver during exra-hepatic carcinogenesis , we performed single-cell RNA sequencing (scRNA) analysis of the non-hepatic parenchyma cells in the liver

overall_design: At 2 time points, day 4 and 21  following 4T1 BC cells injection and wt-pbs injection,  mice were sacrificed and their non parenchimal cells were sent for RNA Seq analysis.

first: Omer

last: Goldman

first: Eyal

last: David

first: Emma

last: Hajaj


title: Monocytes differentiate into macrophages or dendritic cells along two alternative paths controlled by distinct regulatory networks

city: Paris

first: Javiera

last: Villar

address: 25 rue d'Ulm

country: France

institute: Institut Curie

summary: During inflammation, monocytes differentiate within tissues into macrophages (mo-Mac) or dendritic cells (mo-DC). Whether these two progenies derive from alternative differentiation pathways or represent different stages along a continuum remains unclear. Here we addressed this question using temporal single-cell RNA sequencing in an in vitro model allowing the simultaneous differentiation of human mo-Mac and mo-DC. We evidenced divergent differentiation paths, with a fate decision occurring within the first 24 hours. We confirmed this result in vivo using a mouse model of peritonitis. Using a computational approach, we identified candidate transcription factors potentially involved in monocyte fate commitment. We demonstrated that IRF1 is necessary for mo-Mac differentiation, independently of its transcriptional control of interferon-stimulated genes. In addition, we validated the transcription factors ZNF366 and MAFF as regulators of mo-DC development. Our results indicate that mo-Mac and mo-DC represent two alternative cell fates requiring distinct transcription factors for their differentiation.

overall_design: Kinetic of monocyte differentiation by scRNAseq. We performed scRNAseq of monocytes cultured with a cytokine cocktail that yields to the differentiation of monocytes-derived macrophages and dendritic cells. We combined this technology to HASH-sequencing in order to measure these data simultaneously in two healthy human donors and at different time points.

first: Elodie

last: Segura


title: Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin

city: Boston

first: Peter

last: van Galen

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

summary: Tumours most often arise from progression of precursor clones within a single anatomical niche. In the bone marrow, clonal progenitors can undergo malignant transformation to acute leukaemia, or differentiate into immune cells that contribute to disease pathology in peripheral tissues. Outside the marrow, these clones are potentially exposed to a variety of tissue-specific mutational processes, although the consequences of this are unclear. Here we investigate the development of blastic plasmacytoid dendritic cell neoplasm (BPDCN)-an unusual form of acute leukaemia that often presents with malignant cells isolated to the skin. Using tumour phylogenomics and single-cell transcriptomics with genotyping, we find that BPDCN arises from clonal (premalignant) haematopoietic precursors in the bone marrow. We observe that BPDCN skin tumours first develop at sun-exposed anatomical sites and are distinguished by clonally expanded mutations induced by ultraviolet (UV) radiation. A reconstruction of tumour phylogenies reveals that UV damage can precede the acquisition of alterations associated with malignant transformation, implicating sun exposure of plasmacytoid dendritic cells or committed precursors during BPDCN pathogenesis. Functionally, we find that loss-of-function mutations in Tet2, the most common premalignant alteration in BPDCN, confer resistance to UV-induced cell death in plasmacytoid, but not conventional, dendritic cells, suggesting a context-dependent tumour-suppressive role for TET2. These findings demonstrate how tissue-specific environmental exposures at distant anatomical sites can shape the evolution of premalignant clones to disseminated cancer.

overall_design: This GEO repository contains single-cell sequencing data on the bone marrow of six healthy donors, five BPDCN patients without overt bone marrow involvement, and six BPDCN patients with bone marrow involvement. Whole genome and whole exome sequencing data for this study can be found on dbGaP.

first: Gabriel

last: Griffin

first: Christopher

last: Booth

first: Katsuhiro

last: Togami

first: Sun

last: Chung

first: Daniel

last: Ssozi

first: Julia

last: Verga

first: Juliette

last: Bouyssou

first: Yoke

last: Lee

first: Vignesh

last: Shanmugam

first: Jason

middle: L

last: Hornick

first: Nicole

middle: R

last: LeBoeuf

first: Elizabeth

last: Morgan

first: Bradley

last: Bernstein

first: Volker

last: Hovestadt

first: Andrew

last: Lane


title: Single-cell RNA sequencing analysis of a COVID-19– associated maculopapular rash in a patient with psoriasis treated with ustekinumab

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary: Coronavirus disease 2019 (COVID-19) primarily affects the respiratory system but extrapulmonary manifestations, including the skin, have been well documented. However, transcriptomic profiles of skin lesions have not been performed thus far. Here, we present a single-cell RNA sequencing analysis in a patient with COVID-19 infection with a maculopapular skin rash while on treatment with the interleukin (IL)-12/IL-23 blocker ustekinumab for underlying psoriasis. Results were compared with healthy controls and untreated psoriasis. We found the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral entry receptors ACE2 and TMPRSS2 in keratinocytes of the patient with COVID-19, while ACE2 expression was low to undetectable in psoriasis lesions and healthy skin. Among all cell types, ACE2+ keratinocyte clusters showed the highest levels of transcriptomic dysregulation in COVID-19, expressing type 1–associated immune markers such as CXCL9 and CXCL10. In line with a generally type 1–skewed immune microenvironment, cytotoxic lymphocytes showed increased expression of the IFNG gene and other T-cell effector genes, while type 2, type 17, or type 22 T-cell activation was largely absent. Conversely, downregulation of several anti-inflammatory mediators was observed. This first transcriptomic description of a COVID-19-associated rash identifies ACE2+ keratinocytes displaying profound transcriptional changes, and inflammatory immune cells that might help to improve the understanding of SARS-CoV-2-associated skin conditions.

overall_design:
Single-cell RNA-seq investigation of skin rash in COVID-19 patient
*** Raw data is not pvovided due to patient privacy concerns ***

first: Philipp

last: Tschandl

first: Jasmine

last: Levine

first: Lisa

last: Shaw

first: Wolfgang

last: Weninger

first: Matthias

last: Farlik

first: Constanze

last: Jonak

first: Patrick

last: Brunner


title: Bacteriophage antidefense genes that neutralize TIR and STING immune responses

city: Los Angeles

first: Douglas

middle: Edmund

last: Feldman

address: 2011 Zonal Avenue

department: Pathology

institute: USC Keck School of Medicine

summary: Programmed cell suicide of infected bacteria, known as abortive infection (Abi), serves as a central immune defense strategy to prevent the spread of bacteriophage viruses and other invasive genetic elements across a population. Many Abi systems utilize bespoke cyclic nucleotide immune messengers generated upon infection to rapidly mobilize cognate death effectors. Here, we identify a large family of bacteriophage nucleotidyltransferases (NTases) which synthesize competitor cyclic dinucleotide (CDN) ligands and inhibit NAD-depleting TIR effectors activated through a linked STING CDN sensor domain (TIR-STING). Through a functional screen of NTase-adjacent phage genes, we uncover candidate inhibitors of host TIR-STING suicide signaling. Among these, we demonstrate that a virus MazG-like nucleotide pyrophosphatase, Atd1, depletes the starvation alarmone (p)ppGpp, revealing a role for the alarmone-activated host toxin MazF as a key executioner of TIR-driven abortive infection. Phage NTases and counter-defenses like Atd1 preserve host viability to ensure virus propagation, and may be exploited as tools to modulate TIR and STING immune responses.

overall_design:
The pooled phage ORF library was transformed into BL21 (DE3) Rosetta 2 competent cells (MilliporeSigma) together with pET30a encoding Flag-TIR-STING or empty vector (EV) control.
100 ml of overnight cultures were diluted 1:20 and grown in M9 media supplemented with 0.25% CAA and 1% glycerol, and induced at A600=0.3-0.4 through the addition of 0.5mM IPTG. Samples were taken immediately prior to induction and at 18 h post-induction.
Reads were obtained from DNA isolated from cultures containing EV or TIR-STING, at either time 0 or after 18 hr induction.

first: Peiyin

last: Ho

first: Yibu

last: Chen

first: Subarna

last: Biswas

first: Ethan

last: Canfield

first: Alireza

last: Abdolvahabi


title: Tumor eradication by hetIL-15 locoregional administration is related to intratumoral accumulation of a novel CD103intCD11b+dendritic cell population

city: Bethesda

first: Katherine

last: Goldfarbmuren

address: 41 Center Dr

department: Advanced Biomedical Computational Science

institute: NCI, Frederick National Laboratory for Cancer Research

summary: Locoregional monotherapy with heterodimeric IL-15 (hetIL-15) in a triple-negative breast cancer (TNBC) orthotopic mouse model resulted in tumor eradication in 40% of treated mice, reduction of metastasis and induction of immunological memory against breast cancer cells. hetIL-15 re-shaped the tumor microenvironment by promoting the intratumoral accumulation of cytotoxic lymphocytes, conventional type 1 dendritic cells (cDC1s) and a novel DC population expressing both CD103 and CD11b markers. These CD103intCD11b+DCs share phenotypic and gene expression characteristics with both cDC1s and cDC2s, have transcriptomic profiles more similar to monocyte derived DCs (moDCs) and correlate with tumor regression. Therefore, hetIL-15, a cytokine directly affecting lymphocytes and inducing cytotoxic cells, has also an indirect rapid and significant effect on the recruitment of myeloid cells, initiating a cascade for tumor elimination though innate and adoptive immune mechanisms. The intratumoral CD103intCD11b+DC population induced by hetIL-15 may be targeted for the development of additional cancer immunotherapy approaches.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for sorted DC subpopulations (CD103+cDC1, CD11b+cDC2 and CD103intCD11b+DC) and macrophages from EO771 tumors in mouse

first: Dimitris

last: Stellas

first: Sevasti

last: Karaliota

first: Vasiliki

last: Stravokefalou

first: Matthew

last: Angel

first: Bethany

middle: A

last: Nagy

first: Christina

last: Bergamschi

first: Barbara

middle: K

last: Felber

first: George

last: Pavlakis


title: Lipid droplets are a metabolic vulnerability in melanoma

status: Public on Mar 26 2023

city: New York

first: Dianne

last: Lumaquin

state: NY

address: 417 E 68th ST

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Melanoma exhibits numerous transcriptional cell states including neural crest-like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here, we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets, the specialized organelle responsible for lipid storage. Single-cell RNA-sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake, an increased number of lipid droplets, and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients, these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle.

overall_design: Expression profiling by high throughput sequencing of zebrafish melanoma

last: Lumaquin-Yin

first: Richard

last: White


title: Individual transcriptomic response to strength-training for myotonic dystrophy type 1 patients

city: Albany

first: J

middle: Andrew

last: Berglund

address: 1400 Washington Avenue

department: RNA Institute, Life Sciences

institute: University at Albany

summary:
Myotonic dystrophy type 1 (DM1), the most common form of adult-onset muscular dystrophy, is caused by a CTG expansion resulting in significant transcriptomic dysregulation that leads to muscle weakness and wasting. While strength training is clinically beneficial in DM1, molecular effects had not been studied. To determine whether training rescued transcriptomic defects, RNA-sequencing was performed on vastus lateralis samples from nine male DM1 patients before and after a 12-week strength training program and six male controls who did not undergo training. Differential gene expression and alternative splicing analysis were correlated with the one-repetition maximum strength evaluation method (leg extension, leg press, hip abduction, and squat). While training program-induced improvements in splicing were similar among most individuals, rescued splicing events varied considerably between individuals. Gene expression improvements were highly varied between individuals with the percentage of differentially
expressed genes rescued after training strongly correlated with strength improvements. Evaluating transcriptome changes individually revealed responses to the training not evident from grouped analysis, likely due to disease heterogeneity and individual exercise response differences. Our analyses indicate
that transcriptomic changes are associated with clinical outcomes in DM1 patients undergoing training and these changes are often specific to the individual and should be analyzed accordingly.

overall_design: 9 male DM1 patients had quadriceps muscle biopsies taken before and after a 12-week strength training program, as well as 6 unaffected controls who did not undergo the exercise program. RNA was extracted from these biopsies and RNA-Seq was performed.

first: Emily

last: Davey

first: Cécilia

last: Légaré

first: Lori

last: Planco

first: Sharon

last: Shaughnessy

first: Claudia

middle: D

last: Lennon

first: Marie-Pier

last: Roussel

first: Hannah

last: Shorrock

first: Man

last: Hung

first: John

last: Cleary

first: Elise

last: Duchesne


title: Single-cell RNA-seq reveals the difference between Schwann cells in dorsal root ganglion and sciatic nerve

city: Nantong

first: Sheng

last: Yi

state: Jiangsu, China

address: 19 Qixiu Road

institute: Nantong University

summary: Schwann cells are important glial cells in peripheral nervous system. In this study, we performed single cell RNA-sequencing (scRNA-seq) analysis of Schwann cells exist in both dorsal root ganglion(DRG) and sciatic nerve.We categorized DRG and sciatic nerve Schwann cells into  different subtypes,and found common subtypes and different subtypes.In addition, we discovered  the proliferation and migration ability of Schwann cells were distinct in different tissues.Our current study revealed the distinctive characteristics of Schwann cells in DRG and sciatic nerve.

overall_design: The Schwann cell mRNA profiles of DRG and sciatic nerve at 1-day-old and 8-week-old SD rats were established by 10x genomic analysis.

first: Ruirui

last: Zhang


title: Single cell RNA-seq analysis of IDH-mutant gliomas

status: Public on Mar 25 2023

city: Beijing

first: Xiaolong

last: Fan

address: No.19, Xinjiekouwai St, Haidian District

institute: Beijing Normal University

summary: To analyze the gene expression proflies of oligodendrocyte lineage in IDH-mutant glioma cells, we profiled more than 70000 cells from 16 IDH-mutant glioma samples by single cell RNA-seq.

overall_design:
Here we analyzed more than 70000 single cell transcriptome of 16 IDH-mutant glioma samples.
NOTE FROM SUBMITTER: Due to patient privacy protection, the raw scRNA-seq data will be made available upon request. The data deposited and made public are compliant with the regulations of the Ministry of Science and Technology of China.

first: Yanfei

last: Wei

first: Tao

last: Jiang


title: Effect of depletion of succinate receptor 1 (SUCNR1) on the gene expression of mouse adipose tissue

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: The concept of “signaling metabolites” in the control of metabolic homeostasis is gaining traction. The Krebs cycle substrate succinate, a pleiotropic metabolite that acts akin to hormones and cytokines through succinate receptor 1 (SUCNR1, also known as GPR91), is one example of this new class of metabolites. SUCNR1 has a broad expression and is highly abundant in white adipose tissue. It was a general assumption that SUCNR1 is functionally inactive in healthy tissues, and for many years, SUCNR1 was explored from an immune perspective, mainly in inflammatory-related conditions, particularly those associated with chronic hypersuccinemia. Recent studies, however, indicate that extracellular levels of succinate transiently increase in response to physiological changes such as exercise, cold exposure, or food ingestion. Succinate thus emerges as a reporter of both tissue stress and metabolism, raising the possibility of its involvement in additional metabolic functions as a hormone-like metabolite. Indeed, it is conceivable that "succinate sensing" by SUCNR1 may be part of the metabolite-sensing machinery that governs energy homeostasis. To better understand the effect of the adipocyte Sucnr1 deletion on adipose tissue, we selectively inactivated Sucnr1 in murine adipocytes and profiled the transcription state of epididymal white adipose tissue from adipocyte cell-specific Sucnr1 knockout mice (Ad-Sucnr1 KO) and control Sucnr1fl/fl mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  epididymal white adipose tissue from Ad-Sucnr1 KO (n=5) and  Sucnr1fl/fl (n=5) mice.

first: Sonia

last: Fernandez-Veledo


title: Tomato prf3 and tft3 mutants response to Pseudomonas syringae pv. tomato (Pst) DC3000

city: Coventry

first: Andrew

last: Bowman

state: West Midlands

address: Gibbet Hill, Gibbet Hill Campus, The University of Warwick

department: Warwick Medical School

institute: University of Warwick

summary: Comparative transcriptomics between prf3, Prf-SBP-FLAG complemented lines as controls and tft3 2-2 line (CRISPR/Cas9 tomato mutant line in Rio Grande-prf3 Prf-SBP-FLAG complemented background), treated with either buffer (as control) or P. syringae DC3000 6 hours post infiltration.

overall_design: Leaves of four-week-old tomato prf3, Prf-SBP-FLAG and tft3 2-2 lines leaves were vacuum infiltrated with P. syringae DC3000 (OD=0.1) for 6 h; 10 mM MgCl2 infiltration served as control. All infiltrations were carried out in biological triplicate and three technical replicates were used for each. After tissue harvesting and grinding in liquid nitrogen, RNA extraction was performed using a RNeasy kit (QIAGEN) and quality checked using Bioanalyzer analysis. First-strand cDNA synthesis was performed from 2 µg of total RNA using RevertAid reverse transcriptase (Invitrogen). 200 ng of RNA was used for cDNA synthesis and Cy3-labelling using the Low Input Quick Amp Labeling Kit for One-Color Microarray-Based Gene Expression Agilent analysis. 1.65 µg of linearly amplified and labelled cDNA was hybridized for 17 h at 65oC on 4 x180k format 60-mer oligonucleotide probes designed against the S. lycopersicum cv. Heinz 1706 build 2.4 (annotation 2.5) genome (Agilent design ID = 069672; GEO record GPL21602). Each array contained ~5 probes for 34,619 transcripts. Arrays were imaged using an MS200 microarray scanner with only the 480 nm laser and using the autogain feature of the NimbleScan software.

first: A

middle: H

last: Sheikh

last: Pardal

first: M

last: Gifford

first: V

last: Ntoukakis


title: hMeDIP-Seq of Tet2 knockout hippocampal neurons

city: San Francisco

first: Jeremy

middle: Michael

last: Shea

state: CA

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California, San Francisco

summary: Tet2 regulates gene expression by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine. Profiling the genomic locations of 5-hydroxymethylcytosine after Tet2 manipulation can inform us of the targets of Tet2 regulation. We profiled hydroxymethylcytosine in Tet2 knockout neurons to determine the targets of Tet2 in neurons.

overall_design: hMeDIP-Seq of Tet2 knockout or wildtype hippocampal neurons

first: Karishma

last: Pratt

first: Saul

last: Villeda


title: ZNF469 plays a critical role in regulating synthesis of ECM

status: Public on Mar 24 2023

city: Hangzhou

first: Jing

last: Bao

state: Zhejiang

address: 88 Jiefang Road

institute: The Second Affiliated Hospital of Zhejiang University

summary:
Purpose: In recent years, the mutation of ZNF469 is considered to be one of the pathogenesis of brittle cornea syndrome（BCS）. We establish a znf469 mutant zebrafish line to explore its phenotype and the possible molecular mechanism.
Methods: We generated the znf469 mutant zebrafish by using the CRISPR/Cas9 system. TEM  is applied to examine the phenotype of the cornea in different development stage. RNA sequencing and quantitative RT-PCR are used to reveal the molecular mechanism.
Results: Macroscopically, the homozygous znf469-4del zebrafish larva exhibited a curved body from 72 hpf similar to kyphoscoliosis and a noninflated swimbladder at 7 dpf. TEM reveals the extreme reduction of corneal stroma in homozygous znf469-4del zebrafish in both central and peripheral cornea since the early development stage. RNA-seq analysis demonstrates that the znf469 mutation leads to the decreased synthesis of various ECM component like collagens and proteoglycans but increased synthesis of 26S proteasome families.
Conclusion: Our work indicates that znf469 is a critical gene that encoding a transcription factor, regulating the synthesis and degradation of a large number of ECM components which is also the pathologic basis of the ocular and extraocular phenotypes in the znf469 mutant zebrafish model.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and znf469-4del zebrafish larvae at 7dpf.

first: Xiaoning

last: Yu

first: Xiyuan

last: Ping

first: Xingchao

last: Shentu

first: Jian

last: Zou


title: Changes in gene expression within the skin caused by antigen-specific memory CD4+ T cells during Vaccinia virus infection.

city: Portland

first: Jeffrey

last: Nolz

state: OR

address: 3181 SW Sam Jackson Park Road

institute: Oregon Health & Science University

summary:
To investigate the mechanisms used by memory CD4+ T cells to protect the skin from poxvirus infection, we infected LCMV immune mice with VacV on the right ear skin and VacV expressing the dominant MHC-II restricted epitope from LCMV (VacV-Ii-GP61) on the left ear skin.
On day 3 after the co-infection, RNA from whole skin was isolated and gene expression was analyzed using RNA sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from VacV-infected skin compared to VacV-Ii-GP61 infected skin.

first: Harbour

last: Jake

first: Nolz

last: Jeffrey


title: LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis [RNA-seq]

city: Milano

first: gabriele

last: bucci

address: via olgettina 58

institute: IRCCS Ospedale San Raffaele

summary: The lncRNA EPR (a.k.a BC030870) is highly enriched in the gastrointestinal tract in mice and, more specifically, in the large intestine. We generated conditional EPR knock-out in large intestine e and analyzed genome-wide the gene expression changes by RNA-Seq. Total RNA was extracted from the proximal colon of six control (EPR fl/fl) and six knock-out (EPR cKO) mice. Libraries were constructed and sequenced. Results indicate that EPR knock-out predominantly leads to down-regulation of genes implicated in mucus biogenesis. These results help in explaining the phenotype displayed by EPR cKO mice that is characterized by higher susceptibility to intestinal inflammation and cancer formation.

first: P

last: Briata

first: E

last: Zapparoli

first: G

last: Bucci

last: Inga

first: F

last: Chiacchiera

first: L

last: Caputo

first: R

last: Gherzi


title: Type I interferon signaling in malignant blasts contributes to treatment efficacy in AML patients

city: Prague

first: Michal

last: Hensler

state: Prague 7

address: Jankovcova 1518/2

country: Czech Republic

institute: Sotio Biotech a.s.

summary: While type I interferon (IFN) is best known for its key role against viral infection, accumulating preclinical and clinical data indicate that robust type I IFN production in the tumor microenvironment promotes cancer immunosurveillance and contributes to the efficacy of various antineoplastic agents, notably immunogenic cell death inducers. Here, we report that malignant blasts from patients with acute myeloid leukemia (AML) release type I IFN via a Toll-like receptor (TLR3)-dependent mechanism that is not influenced by treatment. While in these patients the ability of type I IFN to stimulate anticancer immune responses was abolished by immunosuppressive mechanisms driven by malignant blasts, type I IFN turned out to exert direct cytostatic, cytotoxic and chemosensitizing activity in primary AML blasts, leukemic stem cells from AML patients and AML xenograft models. Finally, a genetic signature of type I IFN signaling has independent prognostic value on relapse-free survival and overall survival in cohort of 132 AML patients. These findings delineate a clinically relevant, therapeutically actionable and prognostically informative mechanism through which type I IFN mediates beneficial effects in patients with AML.

overall_design: A total of 24 patient PBMC were sequenced. Peripheral blood from treatment naïve patients were used.

first: Petr

last: Holicek

first: Iva

last: Truxova

first: Jana

last: Rakova

first: Lorenzo

last: Galluzzi

first: Jitka

last: Fucikova


title: U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [PRO-seq]

first: Claudia

last: Mimoso

state: MA

address: 45 Shattuck St. LHRRB

institute: Harvard Medical School

summary: The expansion of introns within mammalian genomes poses a challenge for the production of full-length messenger RNAs (mRNA)s, with increasing evidence that these long AT-rich sequences present obstacles to transcription. Here, we investigate RNAPII elongation in mammalian cells at high resolution and demonstrate that RNAPII transcribes faster across introns. Moreover, we find that this acceleration is mediated by the association of U1 snRNP (U1) with the elongation complex at 5’ splice sites. The direct stimulation of elongation rate through introns by U1 reduces the occurrence of both premature termination and transcriptional arrest, thereby dramatically increasing RNA production. We further show that changes in RNAPII elongation rate due to AT-content and U1 binding explain previous reports of pausing or termination at splice junctions and the edge of CpG islands. We propose that this role for U1 has evolved to mitigate the risks that long, AT-rich intronic sequences pose to transcript completion.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of 10 samples by PRO-seq: 3 biological replicate sets of AMO-treated cells (SCR and U1 AMO) and 4 biological replicates of WT HEK293Ts

first: Karen

last: Adelman


title: U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [ChIP-Seq]

overall_design: Examination of 3 samples by ChIP-seq: 3 biological replicates of RNAPII ChIP-seq in F121-9 cells


title: U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [PAC-seq]

overall_design: Examination of 17 samples by PAC-seq: 3 biological replicate sets of AMO-treated cells (SCR and U1 AMO), 4 biological replicate sets of siRNA-treated cells (siNT and siRRP40), and 3 biological replicates of WT F121-9 cells


title: U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes

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

overall_design: Refer to individual Series


title: U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [RNA-Seq]

overall_design: Examination of 12 samples by RNA-seq: 4 biological replicate sets of siRNA-treated cells (siNT and siRRP40) and 4 biological replicates of WT HEK293Ts


title: RNA N6-methyladenosine reader YTHDC1 is essential for TGF-beta-mediated metastasis of triple negative breast cancer [RIP-Seq]

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: RNA N6-methyladenosine (m6A) modification and its regulators fine tune gene expression and contribute to tumorigenesis. Here, we uncover the oncogenic role and mechanism of YTHDC1, an m6A reader positively correlated to poor prognosis in breast cancer patients. In a mammary fat pad mouse model, YTHDC1 significantly promoted lung metastasis of triple negative breast cancer (TNBC) cells. Using transcriptome-wide sequencing techniques, we found dysregulation of metastasis-related pathways following YTHDC1 depletion and demonstrated that YTHDC1 is critical for nuclear export of SMAD3 mRNA. YTHDC1 depletion desensitizes TNBC cells to TGF-β, resulting in impaired TGF-β-induced gene signature and inhibition on epithelial-mesenchymal transition (EMT) and cell migration/invasion, which could be at least partially restored by SMAD3 overexpression. Furthermore, we show that the ability of YTHDC1 to recognize m6A on SMAD3 RNA is important for its oncogenic role. Collectively, our study unravels YTHDC1 as vital for distant TNBC metastasis by promoting TGF-β-mediated EMT via SMAD3.

overall_design: 4 samples analyzed in two groups (IP and input) containing two biological replicates each. IP group consists of RNA isolated from immunoprecipitation of flag-tagged YTHDC1 overexpressed in MDA-MB-231 cells. Input group consists of total RNA isolated from flag-tagged YTHDC1 overexpressing MDA-MB-231 cells.

first: Brandon

last: Tan

first: Keren

last: Zhou


title: RNA-seq analysis of human tonsil macrophage subsets

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

institute: INSERM

summary: Numerous studies have shown in mouse that identity and function of macrophage populations are imprinted by their tissue of residence. By contrast, the properties of human tissue macrophages remain poorly understood. Here, we characterized human tonsil macrophages and identified 3 macrophage subsets with distinct phenotype, ontogeny and function. Using RNA-seq analysis, we found that CD36hi macrophages were transcriptionally related to monocytes, while CD36lo macrophages showed features of embryonic origin and CD36int macrophages had a mixed profile. Using scRNA-seq profiling of naïve and inflamed tonsils from non-human primates, we showed that monocyte engraftment did not pre-exist an immune challenge.

overall_design:
Tonsil macrophages were separated into 3 subsets based on the expression of CD36 and CD81. RNA-seq analysis was performed on each subset separately after cell sorting.
Tonsil macrophages were selected after tissue digestion by density gradient, enriched by negative selection, and isolated by cell sorting.

first: Lamine

last: Alaoui


title: Single-cell RNA-seq analysis of macaque tonsil antigen presenting cells

overall_design: We compared a naïve animal with macaques infected intra-nasally with Influenza A virus (H3N2 strain). Tonsils were sampled at day 5 or 14 post-infection. We profiled tonsil mononuclear phagocytes using scRNA-seq after cell enrichment for antigen presenting cells.

first: Benoit

last: Favier


title: Effects of ferroptosis inducer FIN56 in HSC-3 HNSCC cells

city: Taipei

first: Chih-Hung

last: Chung

address: No.155, Sec.2, Linong Street, Taipei, 112 Taiwan (ROC)

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: We treated ferroptosis inducer FIN56 (1uM,48hrs) in HSC-3 HNSCC cells. DMSO treatment as control cells group.

overall_design: RNA sequencing of FIN56 (1uM,48hrs) treated HSC-3 HNSCC cells. DMSO treatment as control cells group.

first: Muh-Hwa

last: Yang


title: Functional specialization of human tonsil macrophages is controlled by both ontogeny and niche-derived signals

sample_organism:
Macaca fascicularis
Homo sapiens

platform_organism:
Macaca fascicularis
Homo sapiens


title: U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes [TT-Seq]

city: Boston

overall_design: Examination of 10 samples by TT-seq: 3 biological replicate sets of AMO-treated cells (SCR and U1 AMO) and 4 biological replicates of WT HEK293Ts


title: Single cell RNA  sequencing of head and neck squamous carcinoma (HNSCC) patient sample

summary: We collected HNSCC primary tumor from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH) for single cell RNA seq analysis.

overall_design: Single cell RNA Sequencing of HNSCC pateint tumor

first: Shyh-Kuan

last: Tai


title: Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity

city: Shanghai

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Using a combination of single-cell multi-omics, lineage tracing and functional assays, we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells (HECs) during zebrafish embryogenesis.

overall_design: Hematopoietic stem and progenitor cells (HSPCs) are considered as a heterogeneous population, but where and how HSPC heterogeneity occurs remain unclear. Here, we performed scRNA-seq and scATAC-seq with zebrafish 36 hpf VDA-derived kdrl+runx1-, kdrl+runx1+, and kdrl-runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish, we performed STRT-seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry- hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency, we performed scRNA-seq with the sorted ECs (kdrl+runx1-), HECs (kdrl+runx1+) and hematopoietic cells (kdrl-runx1+) from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC, we examined genome-wide spi2 binding by cut-tag assay in fli1a-flag-spi2-EGFP+ cells sorted from trunk region of Tg (fli1a-flag-spi2-GFP) embryos at 36 hpf.


title: Expression data of young Arabidopsis root plants experiencing either phosphate deficiency, iron deficiency or both, for 3hours, 6 hours and 9 hours in comparison to plants fully supply with nutrients

city: Montpellier

first: Sandrine

last: Ruffel

address: 2 Place Viala

department: Montpellier University

institute: INRA

summary:
Plants could sense and respond very rapidly to a change in nutrient availability. At a developmental level, phosphate deficiency leads to a rapid repression of the primary root growth. This response is alleviated when iron is also absent from the medium.
We used microarrays to detail the global programme of gene expression during phosphate and/or iron deficiency and to identify gene regulatory network involved in the control of the primary root growth in response to phosphate deficiency.

overall_design: Col-0 wild-type plants were grown in full nutrient medium including Pi at 1mM  for 10 days (Control). One part of the plants was transferred to a nutrient medium not containing Pi (0Pi)  for 3, 6 and 9 h. One part of the plants was transferred to a nutrient medium not containing Fe (0Fe)  for 3, 6 and 9 h and one part was tranferred to a nutrient medium not containing Pi (0Pi) and Fe (0Fe)  for 3, 6 and 9 h.

first: Hatem

last: Rouached

first: Sue

last: Rhee


title: Increased mitochondrial metabolism in neutrophils revealed by single-cell RNA sequencing (scRNAseq) of bronchoalveolar lavage fluid (BALF) predicts remission in a fatal case of neutrophilic asthma

status: Public on Mar 23 2023

first: Longxiang

last: Su

state: Beijing

address: 1 Shuaifu Yuan

department: Department of Critical Care Medicine

institute: Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science

summary: We present a case of lethal neutrophilic asthma, in which the patient required mechanical ventilation due to hypoxia and hypercapnia. After receiving high-dose steroid treatment, the patient eventually recovered and was successfully weaned off mechanical ventilation. To investigate the underlying mechanisms, we performed single-cell RNA sequencing (scRNAseq) analysis on the patient's bronchoalveolar lavage fluid (BALF) both before and during the remission phase. During the remission phase, we discovered a cluster of hybrid recovery-specific neutrophils (rs-Neus) that exhibited significantly higher levels of oxidative phosphorylation (OxPhos) and Tricarboxylic Acid Cycle (TCA) compared to pathological neutrophils (pNeus). Moreover, we observed a significant decrease in the inflammatory response in rs-Neus, which was found to be negatively correlated with their mitochondrial metabolic activity. Pathway analysis suggested that the hypoxia signaling pathway played a key role in the observed metabolic changes. Our fins highlight the changes in the metabolic landscape of neutrophils in BALF during the development of severe neutrophilic asthma. Furthermore, our study suggests that neutrophil mitochondrial metabolism may serve as an essential indicator of remission and underscores the potential of targeting neutrophil metabolism as a therapeutic strategy for severe neutrophilic asthma.

overall_design: We collected bronchoalveolar lavage fluid (BALF) of a patient with lethal neutrophilic asthma both before and during the remission phase, then analyzed the two BALF samples using scRNA-seq.

first: Yingying

first: Haochen

last: Li

first: Peng

last: Liu

first: Xingwu

last: Zhang

first: Qianlin

last: Wang

first: Huaiwu

last: He

last: Cui

first: Xinlun

last: Tian

first: Yun

last: Long


title: RNA degradation analysis reveals ribosome dynamics in complex microbiome samples

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

summary: The microbiome has revealed itself as a key player in health and disease. To better understand its role, in addition to microbial diversity, it is important to understand species-specific activity and gene expression. While metatranscriptomics investigates mRNA abundance2, it does not inform about faster post-transcriptional regulation3. Although prokaryotic translation is a common target for antibiotics, a direct measurement of microbiome ribosome dynamics remains inaccessible. Here we demonstrate that, contrary to expectation, co-translational mRNA degradation is common in prokaryotes, and that in vivo ribosome protection generates widespread 3-nt periodicity in 5´P mRNA decay intermediates. Consequently, 5´P sequencing allows the study of codon and gene specific ribosome stalling in response to stress and drug treatment at single nucleotide resolution. We validate its wide applicability by investigating in vivo species-specific ribosome footprints of clinical and environmental microbiomes and show that amino acid-specific ribosome protection patterns can be used to phenotype microbiome perturbations. Furthermore, we show that multiple RNase activities collaborate to generate in vivo ribosome footprints and that co-translational degradation is phylogenetically conserved across prokaryotes. This strategy opens the way for the study of the metatranslatome, and allows to investigate fast species-specific post-transcriptional responses to environmental and chemical perturbations in unculturable microbial communities.

sample_organism:
Escherichia coli
Synechocystis sp. PCC 6803
Staphylococcus aureus
Enterococcus faecalis
Bacillus amyloliquefaciens
Bacillus subtilis
Lactiplantibacillus plantarum
Limosilactobacillus reuteri
Limosilactobacillus fermentum
Listeria monocytogenes
Saccharomyces cerevisiae
Cryptococcus neoformans
Salmonella enterica
Parabacteroides merdae
Caulobacter vibrioides
Segatella copri
Alistipes finegoldii
Hoylesella timonensis
compost metagenome
human feces metagenome

overall_design:
We performed 2 to 5 biologically independent experiment (_rX) for individually grown bacteria, mock community or compost microbiomes using either 5PSeq (PMID: 26046441) or HT-5PSeq (doi: https://doi.org/10.1101/2020.06.22.165134). Majority of analyzed samples are from total RNA, with the exception of Bacillus subtilis RNA that was extracted from monosome/polyribosome fractions. Samples analyzed in this study include: Bacillus amyloliquefaciens (bamy), Escherichia coli (ecol), Lactobacillus plantarum (lpla), Lactobacillus reuteri (lreu), Bacillus subtilis (bsub-str168 or bsub), Caulobacter vibrioides (cvib), Synechocystis sp. PCC 6803 (spcc-6803), Alistipes finegoldii (afin), Prevotella copri (pcop), Parabacter merdae (pmer), Prevotella timonesis (ptim), Bacillus subtilis 168 trpC2 rnjA::spc (bsub_del-rnjA), ZymoBIOMICS Microbial Community Standard, cat-no D6300 (zymo), Compost microbiome (comp) and Fecal-cultures (fc). Samples were untreated (ctr), randomly fragmented and re-phosphorylated (frag), and treated with Chloramphenicol (cam), Mupirocin (mup), Erythromycin (ery), Doxycycline (dox), heat shock (hs), NaCL salt stress (saltstress), grown to stationary phase (stat) or exposed to low nutrients (starv). We use 2 different rRNA depletion strategies, either commercial RiBo-zero depletion and PAN-Prokaryote Ribopool (sitoolsbiotech REF dp-K024-000003) using biotinylated probes, or a DSN based rRNA depletion as described in the HT-5PSeq approach. See manuscript for use of specific oligonucleotides and sample specific information regarding treatment condition.

Please note that the *mixed sample records were created to include the original mixed fastq files in the records, since the unique molecular identifier information might be lost from the headers of the adapter-trimmed split fastq files (generated for each individual sample).

first: Susanne

last: Huch

first: Lilit

last: Nersisyan

first: Maria

last: Ropat

first: Donal

last: Barret

first: Jing

first: Valerie

last: Valeriano

first: Nelly

last: Vardazaryan

first: Jaime

last: Huerta-Cepas

first: Wu

last: Wei

first: Juan

last: Du

first: Lars

last: Steinmetz

last: Engstrand


title: HIF1a inhibition overcomes castration resistance

city: Illkirch

first: Julie

last: Terzic

address: 1 rue Laurent Fries

department: Génomique fonctionnelle et cancer

institute: IGBMC

summary: We used single-cell RNA sequencing to understand castration resistance in a murine model of prostate cancer

overall_design: Pten(i)pe-/- mice were sham-operated or castrated at 3 months after gene inactivation and sacrificed one month after surgery

first: Terzic

last: Julie

first: Mohamed

last: Abu el Maaty

first: Daniel

last: Metzger

first: Céline

last: Keime

first: Matthieu

last: Jung

first: Régis

last: Lutzing

first: Alexandre

last: Vincent