title: Differential Gene Expression in Bladders of Wild-Type Mice Compared to Mice Lacking miroRNA-29a/b1

city: Madison

first: Dale

last: Bjorling

state: WI

address: 2015 Linden Drive

department: Surgical Sciences

institute: University of Wisconsin School of Veterinary Medicine

summary: Lower urinary tract symptoms (LUTS) refer to a spectrum of urological diseases, and incomplete bladder emptying is common among affected patients. The etiology of LUTS is largely unknown and evidence arising from epidemiologic, clinical, and basic research suggests that bladder fibrosis is an important contributing factor to pathogenesis of LUTS. MicroRNAs (miRNAs) are short (~22 nucleotides), non-coding RNAs that repress target gene expression by a combination of mRNA degradation and translation inhibition. The miR-29 family is best known for its anti-fibrotic role in various organs. Recent studies have reported decreased miR-29 in bladders of patients with outlet obstruction and in a rat model of bladder outlet obstruction, suggesting that miR-29 may be associated with impaired bladder function subsequent to tissue fibrosis. In the present study, we characterized bladder function in male mice lacking expression of MIR29A and MIR29B1 (miR-29a/b1). We found that lack of miR-29a/b1 resulted in severe urinary retention, increased urination duration with reduced flow rate, and these mice failed to void or voided irregularly during anesthetized cytometry.  Collagens and elastin were increased in the bladder walls of mice lacking miR-29a/b1. These findings reveal an important role of mir-29 in bladder homeostasis and suggest therapeutic potential of miR-29 to improve symptoms in patients with LUTS.

overall_design: Total RNA was isolated from bladders of wild-type mice and age matched mice lacking expression of microRNA-29a/b1. Mice lacking expression of microRNA 29-a/b1 were sacrificed when bladder enlargement and dysfunction were observed. RNAseq was performed.

first: Jianghui

last: Hou


title: MLL methyltransferases regulate H3K4 methylation to ensure CENP-A assembly at human centromeres

status: Public on May 15 2023

city: Hyderabad

first: Shweta

last: Tyagi

state: Telangana

address: Opp. to Metro Rail Pillar No.NUP-9, Inner Ring Road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics (CDFD)

type: Expression profiling by high throughput sequencing

summary: To investigate the function of KMT2A and KMT2F in the regulation of gene transcriptiom,siRNA based  knock-down of KMT2A and KMT2F was performed in U2OS cells.

overall_design: Gene expression profiling analysis  was performed using data obtained from RNA-seq of Control- and KMT2A/KMT2F- siRNA treated  cells.

first: Kausika

middle: K

last: Malik

first: Deepshika

last: Pulimamidi


title: Analysis of mRNA-miRNA interaction network reveals the role of CAFs-derived exosomes in the immune regulation of oral squamous cell carcinoma

status: Public on May 16 2023

city: Kunming

first: Weizhou

last: Wang

state: Yunnan

address: Chunrong West Road

country: China

institute: Kunming Medical University

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A multiplexing strategy to create primary and orthotopic endometrial cancer models in mice

city: Xi’an, China

first: lei

last: zhao

state: Shaanxi

address: Youyixi Road 21

department: School of Ecology and Environment

institute: Northwestern Polytechnical University

summary: Endometrial cancer (EC) is the most common female reproductive tract cancer and its incidence is continuously rising recently. The underlying mechanisms of EC tumorigenesis remain unclear and efficient target therapies are lack, both of which require feasible endometrial cancer animal models for translational studies. Here, we report an organoid and genome editing-based strategy to generate primary, orthotopic, and drivers-defined ECs in mice. Bulk RNA sequencing was performed with organoids of various genetics-mediated EC models.

overall_design: Bulk RNA-seq of organoids from endometrial cancer mouse models tissue.

first: Jingyao

last: Chen

first: Siqi

last: Dai

first: Lei

last: Zhao

first: Yu

last: Liu

first: Chong


title: Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden

city: Cambridge

first: Christopher

middle: A

last: Voigt

state: MA

address: 500 Technology Square, NE47-140

department: Biological Engineering

country: USA

institute: Massachusetts Institute of Technology

summary: To build therapeutic strains, Escherichia coli Nissle (EcN) have been engineered to express antibiotics, toxin-degrading enzymes, immunoregulators, and anti-cancer chemotherapies. For efficacy, the recombinant genes need to be highly expressed, but this imposes a burden on the cell, and plasmids are difficult to maintain in the body. To address these problems, we have developed landing pads in the EcN genome and genetic circuits to control therapeutic gene expression. These tools were applied to EcN SYNB1618, undergoing clinical trials as a phenylketonuria treatment. The pathway for converting phenylalanine to trans-cinnamic acid was moved to a landing pad under the control of a circuit that keeps the pathway off during storage. The resulting strain (EcN SYN8784) achieved higher activity than EcN SYNB1618, reaching levels near when the pathway is carried on a plasmid. This work demonstrates a simple system for engineering EcN that aids quantitative strain design for therapeutics.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT E. coli Nissle 1917 cells and engineered derivatives (EcN_SensorArrayOnly EcN_NOTgate_PsrA, EcN_NOTgate_HlyIIR, EcN_NOTgate_BM3R1, EcN_NOTgate_AmtR, EcN_NOTgate_QacR, EcN_NOTgate_LitR, EcN_NOTgate_AmeR, EcN_NOTgate_IcaR, EcN_NOTgate_BetI, EcN_NOTgate_PhlF)

first: Alexander

middle: J

last: Triassi

first: Brandon

middle: D

last: Fields

first: Catherine

middle: E

last: Monahan

first: Jillian

middle: M

last: Means

first: Yongjin

last: Park

first: Hamid

last: Doosthosseini

first: Jai

middle: P

last: Padmakumar

first: Vincent

last: Isabella


title: Reversing Vemurafenib-resistance in primary melanoma cells by combined Romidepsin and Type I IFN treatment through blocking of tumorigenic signals and induction of immunogenic effects

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary:
BRAFV600 mutations are the most common oncogenic alterations in melanoma cells, supporting proliferation, invasion, metastasis, and immune evasion. In patients, these aberrantly activated cellular pathways are inhibited by BRAFi whose potent antitumor effect and therapeutic potential are dampened by the development of resistance. Here, by using primary melanoma cell lines, generated from lymph node lesions of metastatic patients, we show that the combination of two FDA-approved drugs, the histone deacetylate inhibitor (HDCAi) romidepsin and the immunomodulatory agent IFNα-2b, reduces melanoma proliferation, long-term survival and invasiveness, and overcomes acquired resistance to the BRAFi vemurafenib (VEM). Targeted resequencing revealed that each VEM-resistant melanoma cell line and the parental counterpart are characterized by a distinctive and similar genetic fingerprint, shaping the differential and specific antitumor modulation of MAPK/AKT pathways by combined drug treatment. By using RNA-sequencing and functional in vitro assays, we further report that romidepsin-IFNα-2b treatment restores epigenetically silenced immune signals, modulates MITF and AXL expression, and induces both apoptosis and necroptosis in sensitive and VEM-resistant primary melanoma cells.  Moreover, the immunogenic potential of drug-treated VEM-resistant melanoma cells results significantly enhanced, given the increased phagocytosis rate of these cells by dendritic cells, which in turn exhibit also a selective down-modulation of the immune checkpoint TIM-3.
Overall, our results provide evidence that combined epigenetic-immune drugs can overcome VEM resistance of primary melanoma cells by oncogenic and immune pathways reprogramming, and pave the way for rapidly exploiting this combination to improve BRAFi-resistant metastatic melanoma treatment, also via reinforcement of immune checkpoint inhibitor therapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for romidepsin-IFN mestatic melanoma cells and untreated cells.

first: Alessandra

last: Fragale

first: Carlo

last: Presutti

first: Lucia

last: Gabriele


title: Single cell RNAseq data from Dlk1+ and Dlk1- aged murine hematopoietic stem cells

status: Public on May 13 2023

city: Würzburg

first: Reyna Edith

last: Rosales Alvarez

address: Versbacher Str. 9

department: Quantitative Single-Cell Biology of the Immune System

country: Germany

institute: Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg

summary:
Quantification of gene expression noise on young versus aged bone marrow HSCs at single-cell resolution revealed Dlk1 increases both noise and expression levels upon aging. Dlk1, encoding a cell surface non-canonical Notch ligand, is partially expressed in the LT-HSC compartment, without generating clusters of individual subpopulations by conventional clustering analysis. We aimed to characterize the trascriptome of aged LT-HSC with positive and negative expression of Dlk1 cells.

Dataset created as part of the publication: "VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing  hematopoietic stem cells"

overall_design: LT-HSC (Lin-CD150+CD48-CD34-Kit+Sca1+) Dlk1+ and Dlk1- cells from bone marrow of 18 months old mice were sorted into 384-well plates. Cells processed for scRNAseq with a similar mCELseq2 protocol (Herman et al., 2018 Nat Methods, DOI: 10.1038/nmeth.4662)

first: Reyna

last: Rosales-Alvarez

first: Josip

middle: S

last: Herman

first: Jasmin

last: Rettkowski

first: Dominic

last: Grün


title: THP1 cell response to Mycobacterium tuberculosis infection and Mtb PAMP stimulation

first: Amy

middle: K.

last: Barczak

address: The Ragon Institute, 400 Technology Square

department: Medicine/Infectious Diseases

institute: Massachusetts General Hospital

summary: To compare gene expression changes induced by infection with Mycobacterium tuberculosis (Mtb) with changes induced by purified Mtb products, we infected THP-1 cells with Mtb strain H37Rv or treated with purified Mtb products, then performed RNAseq.

overall_design: THP1 cells were stimulated with PMA for 24 hours, then washed 3 times with PBS, and rested in R10 media for an additional 24 hours. For experiment 1, cells were treated with the indicated PAMPs at 10ug/ml for 8 hours. RNA was then harvested and analyzed by RNAseq. For experiment 2, cells were infected with H37Rv-GFP at an MOI of 10:1 for 4 hours of phagocytosis followed by an 8 hour incubation. Cells were then sorted into infected and bystander populations based on GFP signal. RNAseq libraries were prepared from uninfected, infected, and bystander cells.

first: Charul

last: Jani

first: Sydney

middle: L

last: Solomon

first: Joshua

last: Peters

first: Stephanie

middle: C

last: Pringle

first: Amelia

last: Hinman

first: Julie

last: Boucau

first: Bryan

last: Bryson


title: RNAseq of ATDC5 cells with mechanotransductive perturbations

city: Philadelphia

first: Grey

last: Hallstrom

state: Pennsylvania

address: 3450 Hamilton Walk

institute: University of Pennsylvania

summary: Chondrocyte phenotype is preserved when cells are round and the actin cytoskeleton is cortical. Conversely, these cells rapidly dedifferentiate in vitro with increased mechanoactive Rho signaling, which increases cell size and causes large actin stress fiber to form. While the effects of Rho on chondrocyte phenotype are well established, the molecular mechanism is not yet fully elucidated. Yap, a transcriptional co-regulator, is regulated by Rho in a mechanotransductive manner and can suppress chondrogenesis in vivo. Here, we sought to elucidate the relationship between mechanoactive Rho and Yap on chondrogenic gene expression. We first show that decreasing mechanoactive state through Rho inhibition results in a broad increase in chondrogenic gene expression. Next, we show that Yap and its co-regulator Taz, are negative regulators of chondrogenic gene expression, and removal of these factors promotes chondrogenesis even in environments that promote cell spreading. Finally, we establish that Yap/Taz is essential for translating Rho-mediated signals to negatively regulate chondrogenic gene expression, and that its removal negates the effects of increased Rho signaling. Together, these data indicate that Rho is a mechanoregulator of chondrogenic differentiation, and that its impact on chondrogenic expression is exerted principally through mechanically-induced translocation and activity of Yap and Taz.

overall_design: ATDC5 cells cultured in chemically defined chondrogenic media under the following conditions: Rho inhibition for 3 days with C3 transferase, Rho promotion using LPA for 3 days, siRNA to Yap1/Wwtr1 five days post-transfections, and cells seeded for two days at low density on fibronectin coated glass, 55 kPa polyacrylamide gels and 5 kPa polyacrylamide gels.

middle: F

first: Ryan

last: Locke

first: Dakota

last: Jones

first: Robert

last: Mauck


title: The role of NFATc4 on aldosterone production in NCI-H295R human adrenocortical cell line

status: Public on May 12 2023

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: To investigate the role of NFATc4 in aldosterone production, we created NFATc4 knock-out NCI-H295R cell line and overexpressed active NFATc4 in wild type NCI-H295R cells. We then analyzed the transcriptome of the four cell types.

overall_design: We compared the gene expression profile of NFATc4-KO and control as well as  active-NFATc4 overexpresing cells and their mock overexpression controls.

first: David

last: Ribas

first: Mesut

last: Berber


title: Enhanced DMS-MaP enables superior RNA structural analysis

city: Houston

first: Anthony

middle: McDowell

last: Mustoe

state: TX

address: 1 Baylor Plaza

department: Biochemistry

institute: Baylor College of Medicine

summary: We develop an enhanced MaP protocol based on MarathonRT and bioinformatic optimizations which enables robust DMS probing of all four RNA nucleotides within living cells. We demonstrate this on RNA from E. coli and HEK293 cell lines.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: RNA from HEK293 and E. coli cells were probed in-cell or cell-free with DMS and libraries were generated using Superscript II, MarathonRT, or TGIRT-III MaP protocols.

last: Mitchell III

first: Jennifer

last: Cotter

first: Irfana

last: Saleem


title: IDO1 overexpression significantly affects exosomal miRNA subsets derived from osteosarcoma and ordinary osteoblasts

status: Public on May 14 2023

city: Shanghai

first: Dan

last: Yang

address: 355 Luding Road, Putuo District

institute: Shanghai Children's Hospital

summary: To investigate whether IDO1 participated in OS malignant progression through miRNA, we selected non-metastatic OS cell line (MG63), metastatic OS cell line (143B) and non-tumorigenic immortalized osteoblastic hFOB1.19 cell line as the research object. Over Expression cell lines are contructed and exosomal miRNAs from both control and OE cell lines are sequenced to find out the differences in expression in the exosomes secreted from IDO1 overexpressing and WT cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 143B, MG63and hFOB1.19 cells and their IDO1 OE derivatives.

first: Zhen

middle: N

last: He


title: NBEAL2 deficiency in humans leads to low CTLA-4 expression in  activated conventional T cells

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

summary:
Loss of NBEAL2 function leads to grey platelet syndrome (GPS), a bleeding disorder
characterized by macro-thrombocytopenia and α-granule-deficient platelets. A proportion of
patients with GPS develop autoimmunity through an unknown mechanism,	which might be
related to the proteins NBEAL2 interacts with, specifically in immune cells. Here we show a
comprehensive interactome of NBEAL2 in primary T cells, based on mass spectrometry
identification of altogether 74 protein association partners. These include LRBA, a member of
the same BEACH domain family as NBEAL2, recessive	mutations of which cause
autoimmunity and lymphocytic infiltration through defective CTLA-4 trafficking. Investigating
the potential association between NBEAL2 and CTLA-4 signalling that is suggested by the
mass spectrometry results, we confirm by co-immunoprecipitation that CTLA-4 and NBEAL2
interact with each-other. Interestingly, NBEAL2 deficiency leads to low CTLA-4 expression in
patient-derived effector T cells, while their regulatory T cells appear unaffected. Knocking-
down NBEAL2 in healthy primary T cells recapitulates the low CTLA-4 expression observed
in T cells of GPS patients. Our results thus show that NBEAL2 is involved in the regulation of
CTLA-4 expression in conventional T cells and provide a rationale for considering CTLA-4-
immunoglobulin therapy in patients with GPS and autoimmune disease.

overall_design: scRNAseq on PBMC from 7 healthy donors, 5 patients with mutations in LRBA, 5 patients with mutations in NBEAL2

first: Laure

last: Delage

first: Francesco

last: Carbone

first: Quentin

last: Riller

first: Jean-Luc

last: Zachayus

first: Erwan

last: Kerbellec

first: Armelle

last: Buzy

first: Marie-Claude

last: Stolzenberg

first: Marine

last: Luka

first: Camille

last: de Cevins

first: Georges

last: Kalouche

first: Rémi

last: Favier

first: Alizée

last: Michel

first: Sonia

last: Meynier

first: Aurélien

last: Corneau

first: Caroline

last: Evrard

first: Nathalie

last: Neveux

first: Sébastien

last: Roudières

first: Brieuc

last: Pérot

first: Mathieu

last: Fusaro

first: Christelle

last: Lenoir

first: Olivier

last: Pellé

first: Mélanie

last: Parisot

first: Marc

last: Bras

last: Héritier

first: Guy

last: Leverger

first: Anne-Sophie

last: Korganow

first: Capucine

last: Picard

first: Sylvain

last: Latour

first: Bénédicte

last: Collet

first: Alain

last: Fischer

last: Neven

first: Aude

last: Magérus

first: Mickaël

last: Ménager

first: Benoit

last: Pasquier

first: Frédéric

last: Rieux-Laucat


title: A novel Modulator of Ring Stage Translation (MRST) gene alters artemisinin sensitivity in Plasmodium falciparum

city: Tampa

first: Caroline

last: Simmons

state: Florida

address: 3720 E Spectrum Blvd

institute: University of South Florida

summary: RNAseq data profiling the artemisinin-sensitive P. falciparum piggyBac mutant of the PF3D7_1136600 gene (conserved Plasmodium gene, unknown function)

overall_design: Each run-folder contains paired-end fastq data for two complete bioreps of the two parasite lines (NF54 wild-type control; artemisinin-sensitive mutant referred to in sample-names as PB52) collected after 3 rounds of sortibol synchronization under normal asexual growth conditions. Parasites were at early ring stage (T6), mid ring stage (T12), early trophozoite stage (T24), late trophozoite stage (T36), or schizont stage (T48) as verified by Giemsa-stained microscopy. Each sample was run on an Illumina Nextseq

first: Justin

last: Gibbons

first: Chengqi

last: Wang

first: Camilla

middle: V

last: Pires

first: Min

last: Zhang

first: Jenna

last: Oberstaller

first: Debora

last: Casandra

first: Andreas

last: Seyfang

first: Thomas

last: Otto

first: John

middle: H

last: Adams


title: CXCL8/CXCR2 signaling is Enriched in Fibrotic Myeloproliferative Neoplasms and is Vulnerable to Therapeutic Inhibition [ATAC-Seq]

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pro-inflammatory signaling is a hallmark feature of human cancer, including in myeloproliferative neoplasms (MPNs), most notably myelofibrosis (MF). Dysregulated inflammatory signaling contributes to fibrotic progression in MF; however, the individual cytokine mediators elicited by malignant MPN cells to promote collagen-producing fibrosis and disease evolution remain yet to be fully elucidated. Previously we identified a critical role for combined constitutive JAK/STAT and aberrant NF-kB pro-inflammatory signaling in myelofibrosis development. Using single-cell transcriptional and cytokine-secretion studies of primary MF patient cells and two separate murine models of myelofibrosis, we extend this previous work and delineate the role of CXCL8/CXCR2 signaling in MF pathogenesis and bone marrow fibrosis progression. MF patient hematopoietic stem/progenitor cells are enriched in a CXCL8/CXCR2 gene signature and display dose-dependent proliferation and fitness in response to exogenous CXCL8 ligand in vitro. Genetic deletion of Cxcr2 in the hMPLW515L adoptive transfer model abrogates fibrosis and extends overall survival, and pharmacologic inhibition of the CXCR1/2 pathway improves hematologic parameters, attenuates bone marrow fibrosis, and synergizes with JAK inhibitor therapy. Our mechanistic insights provide a rationale for therapeutic targeting of the CXCL8/CXCR2 pathway in MF patients at risk for continued fibrotic progression.

overall_design: ATAC-seq of CD34+ PBMC samples

first: Andrew

last: Dunbar

first: Ross

last: Levine

first: Ronald

last: Hoffman


title: CXCL8/CXCR2 signaling is Enriched in Fibrotic Myeloproliferative Neoplasms and is Vulnerable to Therapeutic Inhibition [RNA-Seq]

overall_design: RNA-seq of CD34+ PBMC samples


title: A preliminary analysis of the southern white rhinoceros granulosa cell transcriptome (Ceratotherium simum simum)

status: Public on May 11 2023

city: Escondido

first: Elena

last: Ruggeri

state: CA

address: 15600 San Paqual Valley Rd.

institute: San Diego Zoo Wildlife Alliance

summary: In vivo-collected granulosa cells (GC) from the southern white rhinoceros (SWR) provide a non-invasive assessment of the developmental status of oocytes prior to in vitro culture, which will  aid in the development of assisted reproductive technologies (ART). Our study aimed to investigate gene expression in SWR granulosa cells (GC), collected in vivo and gain preliminary insight into the transcriptional activity occurring within the cells during various stages of oocyte development.  It was hypothesized there would be similarities between the SWR GC transcriptome and cattle and humans, two species for which well-annotated genomes are available and ART are commonly used. GC were collected from SWR following ovum pickup (OPU) and pooled from all aspirated follicles. Total RNA was isolated, libraries prepared and sequencing performed using an Illumina NextSeq 500. Reads were aligned and annotated to CerSimCot1.0. Databases for cattle and human were acquired for comparison. This study identified 37,407 transcripts present in GC of SWR. It was determined that cattle and human transcriptomes are valuable resources with a homology of 45% with the SWR. In conclusion, these data provide preliminary, novel insights into the transcriptional activity of GC in the SWR that can be used to enhance ART in this species.

overall_design: Transcriptomic analysis via RNA Seq of Southern White Rhino Granulosa Cells

first: Kristin

last: Klohonatz

first: Marc-Andre

last: Sirard

first: Barbara

last: Durrant

first: Stephen

last: Coleman


title: Expression profile of castration-resistant LY6D+ luminal progenitors during prostate tumourigenesis

city: Manchester

first: Esther

last: Baena

address: The University of Manchester, Wilmslow Road

department: Prostate Oncobiology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary: By using luminal lineage tracing model, here we report the regulatory network underlying intrinsically castration-resistant LY6D+ luminal progenitors during prostate tumourigenesis. The luminal cell-specific PTEN deficient mouse model of PCa (K8-CreERT2;PtenFlox/Flox;R26-StopFlox/Flox-EYFP (K8PY) and the control K8-CreERT2;R26-StopFlox/Flox-EYFP (K8Y) mice) are used in this study.

overall_design: K8PY and K8Y mice (>8 weeks old) were treated with tamoxifen to induce Pten deletion and/or YFP expression in the K8+ luminal cells, either hormone sensitive mice or one-month post-surgical castration. Four months post-tamoxifen, primary prostate cells were isolated and luminal prostate cells were FACS-sorted by YFP+LY6D+ and YFP+LY6D- from K8Y and K8PY mice.  Total RNA from FACS-purified luminal cells was isolated using an RNA/DNA Purification Micro Kit (Norgen, #50300)

first: Ivana

last: Steiner


title: Transcriptome profiling of m6A mRNA modification in  GES-1 cells infected by Helicobacter pylori

city: Changsha

first: Huan

last: Li

state: Hunan

address: 138 Tongzipo Road, Yuelu district

department: Gastroenterology department

institute: The Third Xiangya Hospital of Central South University

summary: Helicobacter pylori (H.pylori) infection is an important factor in the occurrence of human gastric diseases, but its pathogenic mechanism is not clear. N6-methyladenosine (m6A) is the most prevalent reversible methylation modification in mammalian RNA and it plays a crucial role in controlling many biological processes. We used MeRIP-seq technology to sequence the GES-1 cells  infected with Helicobacter pylori(H. pylori) for 48 h.

overall_design: meRIP-seq, RNA-seq for GES-1 cells infected by H. pylori for 48h

first: Jiahui

last: Lin

first: Xiaoming

last: Liu

first: Canxia

last: Xu


title: CXCL8/CXCR2 signaling is Enriched in Fibrotic Myeloproliferative Neoplasms and is Vulnerable to Therapeutic Inhibition

overall_design: Refer to individual Series


title: Interaction of V. cholerae with human macrophages

city: Basel

first: Lucia

last: Vidakovic

address: Spitalstrasse 41

institute: Biozentrum, University of Basel

summary: In this study we determined the gene expression of the whole genome of V. cholerae during the interaction with THP-1 derived macrophages by RNA-sequencing.

sample_organism:
Vibrio cholerae O1 biovar El Tor
Homo sapiens

overall_design: V. cholerae was exposed to THP-1 derived macrophages in 12-well plates and RNA-samples were taken at different time points after start of the V.cholerae-macrophage interaction. Four independent biological replicates for each sampled time point are provided. As a control, samples containing only bacteria were taken.

first: Valerya

last: Nisnevich

first: Noa

last: Bossel Ben-Moshe

first: Roi

last: Avraham

first: Knut

last: Drescher


title: Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP [dataset 2]

status: Public on May 10 2023

city: Lausanne

first: Christina

last: Ernst

state: Vaud

address: EPFL SV GHI LVG, AI 3147 (Bâtiment AI), Station 19

department: School of Life Science

institute: EPFL

summary: RNA-binding proteins are instrumental for post-transcriptional gene regulation, yet transcriptome-wide methods to profile RNA-protein interactions remain technically challenging. We present an improved library preparation strategy for cross-linking and immunoprecipitation (CLIP) that involves tailing and ligation of cDNA molecules (TLC) for increased sensitivity and efficiency. TLC-CLIP eliminates time-consuming purifications, reduces sample loss, and minimises experimental steps, allowing precise profiling of RNA-protein interactions from limited starting material at nucleotide resolution.

overall_design:
We have generated benchmarking libraries for 4 well-studied RNA-binding proteins from 50.000 293T cells in duplicates, including additional control samples comparing different RNase concentrations, additional adapter removal, omitting PAGE purification and profiling of co-purifying fragments from non-crosslinked samples. We further demonstrate the high sensitivity of our protocol by profiling hnRNPc and RBFOX2 from only 10,000 and 1,000 cells.
To integrate our CLIP data with functionally relevant sites we have performed RNA-Seq in 293T knockout cells for RBFOX2 to identify alternatively spliced exons.

first: Julien

last: Duc

first: Didier

last: Trono


title: Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP

summary:
This SuperSeries is composed of the SubSeries listed below.
GSE200432 - TLC-CLIP data
GSE225357 - RNA-Seq data


title: CFP1 governs uterine epigenetic landscapes to intervene in progesterone responses for uterine physiology and suppression of endometriosis

city: Pangyo

first: Seung Chel

last: Yang

address: Seongnam, Gyeonggi

country: South Korea

institute: CHA University

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


title: CFP1 governs uterine epigenetic landscapes to intervene in progesterone responses for uterine physiology and suppression of endometriosis (RNA-Seq)

summary: Progesterone (P4) is essential to prepare the endometrium for a successful pregnancy. While P4 resistance is a major cause of infertility that leads to endometrial disorders, such as endometriosis, the underlying epigenetic imbalance responsible for P4 resistance in the endometrium remains unclear. We demonstrated that CXXC finger protein 1 (CFP1), a major mediator of histone H3 lysine 4 trimethylation (H3K4m3), is an indispensable factor in the maintenance of epigenetic landscapes of P4-progesterone receptor (PGR) signaling networks in the uterus. Cfp1flox/flox;Pgr-Cre (Cfp1d/d) mice suffered from impaired P4 responses, leading to abnormal uterine cell proliferation and complete failure of embryo implantation and decidualization, albeit regular estrous cycle with normal hormone profiles. mRNA and chromatin immunoprecipitation sequencing analyses showed that CFP1 binding enriches promoter regions to regulate uterine mRNA landscapes not only in H3K4me3-dependent but also in H3K4me3-independent manners. Especially, CFP1 directly regulates subsets of important P4 response genes, including Gata2, Sox17, and Ihh, which mediate the activation of the smoothened signaling pathway in the uterus. P4 cannot interfere with E2 actions on uterine epithelial proliferation in Cfp1d/d mice, which was restored by supplementing a smoothened agonist (SAG). Furthermore, ectopic lesions of Cfp1d/d uterus in an endometriosis model showed P4 resistance, which was rescued by SAG. In human endometriosis, CFP1, GATA2, SOX17, and IHH, were significantly downregulated, and a positive correlation was found in the expression levels between CFP1 and these P4 targets regardless of PGR levels. Collectively, we suggest that CFP1 is an epigenetic modulator of P4-PGR signaling networks to promote uterine receptivity for embryo implantation and suppress endometriosis with P4 resistance. CFP1 is a key epigenetic factor that intervenes in the P4–epigenome–transcriptome networks for uterine function under physiologic and pathophysiologic conditions.

overall_design: To understand the CFP1-dependent epigenetic regulation on transcriptional landscapes in the uterus, we performed mRNA sequencing with the uteri of Cfp1f/f and/or Cfp1d/d mice on day 4 of pregnancy.

first: Seung

first: Mira

last: Park

first: Haengseok

last: Song


title: CFP1 governs uterine epigenetic landscapes to intervene in progesterone responses for uterine physiology and suppression of endometriosis (ChIP-Seq)

overall_design: To understand the CFP1-dependent epigenetic regulation on transcriptional landscapes in the uterus, we performed CFP1 and H3K4me3 ChIP sequencing with the uteri of Cfp1f/f and/or Cfp1d/d mice on day 4 of pregnancy.


title: Identification of Hub Genes and Potential ceRNA Networks of Diabetic Cardiomyopathy [RNA-seq]

city: chongqin

first: Yao

state: chongqin

address: Gaotanyan

institute: TMMU

summary:
To explore the unique pathogenesis of DCM and analyzed the differences in gene expression, associated pathways and immune cell infiltration among different organs that are targeted by high glucose by bioinformatics-based strategy. In order to find the specific factors that trigger DCM, we contrasted the gene profile of DCM to that of other diabetic diseases including diabetic peripheral neuropathy (DPN) and nephropathy (DN).
we performed RNA-seq and miRNA sequencing on heart tissue from db/db mice to explore the transcriptome alterations in DCM pathogenesis including lncRNA, miRNA and mRNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for heart tissue from db/db and db/m mice.

first: Jun

last: Hou

first: Haoyu

last: Deng


title: Identification of Hub Genes and Potential ceRNA Networks of Diabetic Cardiomyopathy [miRNA-seq]


title: Identification of Hub Genes and Potential ceRNA Networks of Diabetic Cardiomyopathy


title: Optimization of Cas12a for multiplexed genome- scale transcriptional activation

status: Public on May 08 2023

city: Cambridge

first: John

last: Doench

address: 75 Ames St

department: Genetic Perturbation Platform

institute: Broad Institute

summary: Cas12a CRISPR technology, unlike Cas9, allows for multiplexing guide RNAs from a single transcript, simplifying combinatorial perturbations. While Cas12a has been implemented for multiplexed knockout genetic screens, it has yet to be optimized for CRISPR activation (CRISPRa) screens in human cells. Here we develop a new Cas12a-based transactivation domain (TAD) recruitment system using the ALFA nanobody and demonstrate simultaneous activation of up to four genes. We screen a genome-wide library to identify modulators of growth and MEK inhibition, and we compare these results to those obtained with open reading frame (ORF) overexpression and Cas9-based CRISPRa. We find that the activity of multiplexed arrays is largely predictable from the best-performing guide and we provide criteria for selecting active guides. We anticipate that these results will greatly accelerate the exploration of gene function and combinatorial phenotypes at scale.

overall_design: Bulk RNA sequencing (RNA-seq) on MelJuSo cells expressing 5x-tag-dCas12a-VP64 and nanobody-p65 or nanobody-VP64 with or without the cassette containing three CD4-targeting guides. There are 5 unique samples in total and each is screened in triplicates.

first: Audrey

last: Griffith

first: Fengyi

last: Zheng

first: Abby

last: McGee

first: Nathan

last: Miller

first: Zsofia

last: Szegletes

first: Ganna

last: Reint

first: Fabian

last: Gademann

first: Ifunanya

last: Nwolah

first: Mudra

last: Hegde

first: Yanjing

first: Amy

last: Goodale


status: Public on May 09 2023

overall_design: Secondary genome-wide CRISPR screen on MelJuSo cells expressing 5x-tag-dCas12a-VP64 and nanobody-p65 or nanobody-VP64. There are 2 droparms: dropout and selumetinib. Each sample is screened in duplicates.

last: Liu


title: RNA Seq comparing HD37 with dSHP2-HD37

city: London

first: Simon

last: Thomas

address: The MediaWorks, 191 Wood Lane

institute: Autolus

summary: Comparison of gene expression by Nanostring of activated and non activated CAR T cells expressing a CD19 CAR in the absence or presence of the dSHP2 module

overall_design: T cells from six individual donors were transduced to express an anti-CD19 CAR alone or alongside the dSHP2 module. CAR T cells were then stimulated through the CD19 CAR or left unstimulated and gene expression assessed 24hours later


title: ChIP-seq of mouse alveolar organoids treated with bleomycin

status: Public on May 07 2023

city: Hamamatsu

first: Yasunori

last: Enomoto

state: Shizuoka

address: 1-20-1 Handayama

department: Department of Regenerative and Infectious Pathology

country: Japan

institute: Hamamatsu University School of Medicine

summary: In fibrotic lung, upregulation of p53 signaling in alveolar epithelium is observed. Then, we performed p53 ChIP-seq using alveolar organoids to investigate genes directly targeted by p53 protein in bleomycin-treated p53-upregulated alveolar epithelial cells.

overall_design: ChIP-seq using an antibody for p53 in bleomycin-treated alveolar organoids

first: Mitsuru

last: Morimoto

first: Mitsutaka

last: Kadota

first: Osamu

last: Nishimura


title: SARS-CoV-2 Viral Genes Compromise Survival and Functions of Human Cardiomyocytes via Reducing Cellular ATP Level

city: Indianapolis

first: Lei

last: Yang

state: Indiana

address: 1044 W Walnut Street, R4 272

department: Department of Pediatrics

institute: Indiana University School of Medicine

summary: We uncovered the global responses of host human heart muscle cells to SARS-CoV-2 genes Nsp6, Nsp8 and M, defined the molecular mechanisms underlying SARS-CoV-2 genes-induced cardiac abnormalities, and explored the potentially therapeutic approaches to ameliorate cardiac dysfunctions in COVID-19 patients.

overall_design: Human pluripotent stem cell-derived cardiomyocytes.

first: Juli


title: Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP [dataset 1]

first: Christina

last: Ernst

overall_design:
We have generated benchmarking libraries for 4 well-studied RNA-binding proteins from 50.000 293T cells in duplicates, including additional control samples comparing different RNase concentrations, additional adapter removal, omitting PAGE purification and profiling of co-purifying fragments from non-crosslinked samples. We further demonstrate the high sensitivity of our protocol by profiling hnRNPc and RBFOX2 from only 10,000 and 1,000 cells.
To integrate our CLIP data with functionally relevant site we have performed RNA-Seq in 293T knockout cells for RBFOX2 to identify alternatively spliced exons.

first: Julien

last: Duc

first: Didier

last: Trono


title: RNAseq analyses of WT MDCKII cells

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

institute: University of Geneva

summary: To determine the level expression of genes coding for junctional proteins

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of MDCKII WT cells.

first: Marine

last: Mauperin

first: Sandra

last: Citi


title: Role of gut microbiota in modulation of dendritic cell mediated immune tolerance with age

city: CHANDIGARH

first: Rashmi

last: Kumar

state: Punjab

address: CSIR-Institute of microbial technology,sector 39A chandigarh, IMTECH, housing, Type 1 A6, IMTECH, housing, Type 1 A6

institute: CSIR-Institute of microbial technology

summary: With our experiments we have shown LP(Lactobacillus plantarum) mediated modification of immunogenic bone marrow derived dendritic cells (BMDCs) to acquire tolerogenic phenotype, to unravel the molecular mechanism of LP mediated immunomodulation we performed global transcriptomic  Gut of old mice was reconstituted with LP, and RNA was extracted from LPS stimulated BMDCs from young, young treated with antibiotic cocktail, old and old-LP groups for gene array profiling by Agilent GeneChips.

overall_design: TRIzol reagent was used to isolate total RNA from DCs after LPS stimulation (1μg/ml) for 24 hours according to the manufacturer's protocol (Invitrogen, CA, USA). Later, DNase1 enzyme was added to digest and remove genomic DNA. Concentrations of RNA were measured with the NanoDrop ND-100 Spectrophotometer


title: Regulation of endothelial DNA methylation by the sustained response to IL-6

status: Public on May 05 2023

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

type: Methylation profiling by genome tiling array

summary: Endothelial dysfunction is a critical factor in promoting organ failure during septic shock. Organ dysfunction during shock increases the risk of long-term sequelae in survivors through mechanisms that remain unknown. We postulated that vascular dysfunction during shock contributes to long-term morbidity post-shock through transcriptional and epigenetic changes within the endothelium. We performed cross-omics analyses on kidney endothelium from acute endotoxin-challenged mice lacking or not the JAK/STAT3 inhibitor SOCS3. This analysis revealed significant DNA methylation changes upon proinflammatory signaling associated with transcriptional activity through AP1, STAT, and IRF families, suggesting a mechanism driving transcription-induced gene-specific methylation changes. In vitro, we demonstrated that IL-6 induces similar changes in DNA methylation. Specific genes showed DNA methylation changes in response to an IL-6+R and consistently changes in their expression levels within 72 hours of IL-6+R treatment. Further, changes in the endothelial methylome remain in place for prolonged periods without IL-6, suggesting that this cytokine may elicit transcriptional changes long after the resolution of inflammation. Also, demonstrated that DNA methylation changes could directly alter the expression of these genes and that STAT3 activation had a causal role in this transcriptional response. Our findings provide evidence for a critical role of IL-6 signaling in regulating shock-induced epigenetic changes and sustained endothelial activation, offering a new therapeutic target to limit vascular dysfunction.

overall_design: Severe, acute inflammation was induced by a single IP injection of a bolus of 250 μg/250 μl LPS. Control mice were given 250 μl of sterile saline via IP injection. Disease severity was scored 14 hours after the LPS challenge as described before17. Immediately after scoring, body weight and temperature were measured. Mice were then euthanized with an overdose of pentobarbital. No mice were excluded from the studies. Assignment to the saline or LPS groups was performed through randomization of mice within each genotype and sex for each litter. All handling, measurements, and scoring were performed by a researcher masked to treatment and genotype groups and based on mouse ID (ear tags). Experimental groups were unmasked at the end of each experiment. After euthanasia, the animals were cannulated on the left ventricle, and the right atrium was nicked to allow perfusion with 5 ml/min PBS for 3 min. Kidneys were collected and minced into small pieces (~1 mm3). The tissues were transferred to 50 ml conical tubes containing 5 ml of PBS containing calcium and magnesium plus 100 mg of type 1 collagenase and 100 mg dispase II for 10 minutes at 37°C. The slurry of tissue and buffer was triturated by passage through a 14-gauge cannula attached to a 10 ml syringe approximately 10 times, followed by a 20-gauge cannula attached to a 10 ml syringe. The cell suspensions were filtered through a 70 µm cell strainer, resulting in single cell suspensions prior to centrifugation at 400×g for 8 min at 4 °C. Pellets were resuspended with 1.5ml of ice-cold PBS + 0.1% BSA.   Cell suspensions were transferred to RNAse free polystyrene tubes containing 60 µl of streptavidin-conjugated dynabeads bound to biotinylated EpCAM and biotinylated CD45 antibodies. The cell suspensions were incubated with these beads for 10 min at RT with rotation. Following this, tubes were placed on a Dynal MPC-S magnet for 5 minutes. The supernatants were transferred to RNAse free polystyrene tubes containing 45ul of streptavidin-conjugated dynabeads bound to biotinylated CD31 antibodies and incubated for 10 min at RT with rotation. Following this, tubes were placed on a Dynal MPC-S magnet for 5 minutes and the supernatant was discarded. The remaining cells bound to the beads were washed six times with PBS containing 0.1% BSA to remove any contaminating cells. After removal of the final wash, the cells were resuspended in 200 µl PBS. 200 µl were transferred to an RNAse-free tube and proceeded to DNA isolation using the DNeasy Blood & Tissue Kits (Qiagen, USA).   The concentration of DNA was measured by the Qubit dsDNA BR Assay Kit (Molecular Probes). The DNA samples were stored at -80°C. Bisulfite conversion of 500 ng of genomic DNA was performed using an EZ DNA Methylation-Gold™ Kit (Zymo Research) following manufacturer’s instructions. Analysis of DNA methylation was carried out using Infinium Mouse Methylation BeadChip arrays for mouse genomes (>285K sites) by the Epigenomic Services from Diagenode.

middle: B

last: Ramos

first: Alejandro

last: Adam


title: Gene expression analysis of mouse pancreatic islets from Ggcxff; Pdx1-Cre and Ggcxff mice by RNA-sequencing.

city: Montréal

first: Mathieu

last: Ferron

state: Quebec

address: 110 Ave des Pins O

country: Canada

institute: IRCM

summary: Vitamin K-dependent carboxylation is necessary to the acquisition of an adequate beta-cell mass and for insulin secretion in mice. To better understand how this pathway affect pancreatic beta-cell function, we analysed the expression profile of pancreatic islets from Ggcxff; Pdx1-Cre and Ggcxff mice by RNA-sequencing.

overall_design: Total RNA from freshly isolated islets was extracted. Islets from 2 mice were pooled before the extraction, therefore each replicate represents 2 mice.

first: Julie

last: Lacombe


title: Different biological roles of embryonic- and monocyte-derived macrophages in ovarian cancer ascites ecosystem.

city: Shanghai

first: Xipeng

last: Wang

state: Shanghai

address: No. 1665, Kongjiang Road, Yangpu District, Shanghai

institute: Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: To investigate the dichotomous ontogeny of ascites-enriched macrophages and the contribution of embryonic-derived macrophages to the ascites microenvironment and tumor progression.

overall_design: We employed Ms4a3Cre-RosaTdT monocyte fate-mapping mouse models to precisely quantify the different ontogeny of macrophages in malignant ascites of ovarian tumour bearing mouse. We then performed gene expression profiling analysis using data obtained from bulk RNA-seq of 2 subpopulations of ascites-enriched macrophages with different origins.Comparative gene expression profiling analysis of RNA-seq data for embryonic- and monocyte-derived macrophages.

first: Xiaocui

last: Zheng


title: Transcriptional profiling of long bone skeletal stem cells and vertebral counterparts

city: New York

first: Genomics-core-facility

last: WCM

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: To identify specific markers for vertebral skeletal stem cells (vSSCs), we isolated vSSC candidates and lbSSCs by FACS from p10 mice long bone (tibia and femur) and vertebrae.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for four lbSSC samples and four candidates vSSC samples.

first: Jun

last: Sun

first: Matthew

last: Greenblatt


title: Shock drives a highly coordinated transcriptional and DNA methylation response in the endothelium


title: Clearance of defective muscle stem cells by senolytics reduces the expression of senescence-associated secretory phenotype and restores myogenesis in myotonic dystrophy type 1

city: Montreal

first: Gilberto

last: Duran Bishop

address: 110 Pine Avenue West

department: stem cells and cellular reprogramming

institute: Montreal Clinical Research Institute (IRCM)

summary: Muscle weakness and atrophy are clinical hallmarks of myotonic dystrophy type 1 (DM1). Muscle stem cells, which contribute to skeletal muscle growth and repair, are also affected in this disease. However, the molecular mechanisms leading to this defective activity and the impact on the disease severity are still elusive. Here, we explored through an unbiased approach the molecular signature leading to myogenic cell defects in DM1. Single cell RNAseq data revealed the presence of a specific subset of DM1 myogenic cells expressing a senescence signature, characterized by the high expression of genes related to senescence-associated secretory phenotype (SASP). This profile was confirmed using different senescence markers in vitro and in situ. Accumulation of intranuclear RNA foci in senescent cells, suggest that RNA-mediated toxicity contribute to senescence induction. High expression of IL-6, a prominent SASP cytokine, in the serum of DM1 patients was identified as a biomarker correlating with muscle weakness and functional capacity limitations. Drug screening revealed that the BCL-XL inhibitor (A1155463), a senolytic drug, can specifically target senescent DM1 myoblasts to induce their apoptosis and reduce their SASP. Removal of senescent cells re-established the myogenic function of the non-senescent DM1 myoblasts, which displayed improved proliferation and differentiation capacity in vitro; and enhanced engraftment following transplantation in vivo. Altogether this study presents a well-defined senescent molecular signature in DM1 untangling part of the pathological mechanisms observed in the disease; additionally, we demonstrate the therapeutic potential of targeting these defective cells with senolytics to restore myogenesis.

overall_design: Myoblasts were extracted from muscle biopsies provided by 3 different DM1 patients and 3 different age and sex-matched healthy individuals. After expansion in vitro, cells were purified by Fluorescence-activated cell sorting (FACS) based on the expression of the myogenic marker CD56, pooled together and analized using scRNA-seq.

first: Talita

last: Conte

last: Duran-Bishop

first: Zakaria

last: Orfi

first: Inès

last: Mokhtari

first: Alyson

last: Deprez

first: Marie-Pier

last: Roussel

first: Isabelle

last: Côté

first: Ornella

last: Pellerito

first: Damien

last: Maggiorani

first: Basma

last: Benabdallah

first: Severine

last: Leclerc

first: Lara

last: Feulner

first: Jean

last: Mathieu

first: Cynthia

last: Gagnon

first: Gregor

last: Andelfinger

first: Christian

last: Beauséjour

first: Serge

last: McGraw

first: Elise

last: Duchesne

first: Nicolas

middle: A

last: Dumont


title: Genome-wide gene expression analysis in RAS-mutated cells with EZH2 inactivation

city: Graz

first: Armin

last: Zebisch

state: Styria

address: Auenbruggerplatz 38

department: Division of Hematology

country: Austria

institute: Medical University of Graz

summary: EZH2 was inactivated by shRNA in the RAS-mutated HL-60 acute myeloid leukemia cell line. RNA-seq genome wide expression profiling was used to screen for genes deregulated by EZH2 inactivation within this setting.

overall_design: Differential expression analysis of three EZH2 shRNA knock-out cell lines and three scrambled control shRNA cell lines in a HL-60 background.


first: Ramon

last: Bossardi Ramos

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUVEC cells treated with a combination of IL-6+R or saline for 72h prior to the RNA-seq.

first: Alejandro

last: Adam


title: Optimisation of trace mineral supplementation in diets for Atlantic salmon smolt with reference to holistic fish performance in terms of growth, health, welfare, and potential environmental impacts

status: Public on May 04 2023

city: Ås

first: Aleksei

last: Krasnov

state: Viken

address: Øreveien, 47B

country: Norway

institute: Nofima AS

summary: Responsible aquaculture growth requires practices adjusted to higher knowledge based industrial standards that can secure good fish welfare, health, and low environmental impacts, alongside with the production of safe and nutritious consumer products and the economic sustainability of the business. The fish feed ingredient pallet is ever changing, from marine to plant based, and recently evolving to incorporate increasing amounts of low trophic, side stream and circular economy based raw materials, each one contributing with variable amounts and qualities of macro- and micronutrients. Meeting the micronutrient requirement of farmed fish for healthy and efficient growth under normal and challenging conditions is of paramount importance. Trace minerals are essential for critical life processes, including respiration, protein and lipid metabolism, immune responses, and cell REDOX balance. The study results bring new knowledge on Atlantic salmon physiology, growth, welfare status and utilization efficiency of trace minerals of different origin and dietary inclusion levels revealing differential effects on fillet yield, fillet technical and nutritional quality, bone strength, skin morphology, organ mineralization, midgut transcriptome, trace mineral apparent digestibility and retention efficiency, and growth.

overall_design: A feeding trial was based on a 2x4 factorial design with 3 replications for each dietary treatment, where Atlantic salmon smolt were fed one of 8 experimental diets supplemented with either organic or inorganic mineral premixes (copper, iron, manganese, selenium, and zinc) at 4 dietary inclusion levels. High and low levels were analysed with microarray.

first: Krasnov

last: Aleksei

first: Katerina

last: Kousoulaki

first: Marialena

last: Kokkali


title: RNA sequencing of the stomachs of H. pylori-infected  mice after 8 weeks

city: Changsha

first: Huan

last: Li

address: 138 Tongzipo Road, Yuelu district

institute: The Third Xiangya Hospital of Central South University

summary: The aim of this study is to identify alterations induced in gastric mucosa of mice  infected with Helicobacter pylori, in order to identify genes that  associated to the infection on gastric lesions.

overall_design: RNAseq analysis was performed by using RNA extracted from the stomachs of H. pylori-infected mice after 8 weeks in duplicate.

first: Jiahui

last: Lin

first: Xiaoming

last: Liu

first: Canxia

last: Xu


title: Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin

status: Public on May 06 2023

city: Shinjuku-ku

first: Akihiko

last: Sakashita

state: Tokyo

address: 35 Shinanomachi

department: Department of Molecular Biology,

institute: Keio University School of Medicine

summary: Sperm chromatin retains small amounts of histones, and the chromatin states of sperm mirror gene expression programs of the next generation. It remains largely unknown how paternal epigenetic information is transmitted through sperm chromatin. Here we developed a novel mouse model of paternal epigenetic inheritance in which deposition of Polycomb repressive complex 2 (PRC2) mediated-repressive H3K27me3 is attenuated in the paternal germline. By applying modified methods of assisted reproductive technology, we rescued infertility of mice absent of Polycomb protein SCML2, which is the regulator of germline gene expression through the establishment of H3K27me3 on bivalent promoters with other active marks H3K4me2/3. In F1 males of Scml2-knockout mice, which has wild-type genotype, gene expression is dysregulated in the male germline during spermiogenesis. These dysregulated genes are targets of SCML2-mediated H3K27me3 in mature sperm. Thus, SCML2 mediates intergenerational inheritance of paternal epigenetic information through the regulation of sperm chromatin.

overall_design:
RNA-seq analysis of livers and spermatozoa from Ctrl-F1, Scml2-KO-F1 and Scml2-KO-F2 male mice.

Native ChIP-seq analysis for H3K27me3 and H3K4me3 in testicular and cauda-epididymal sperm from Crtl and Scml2-KO male mice.

first: Satoshi

last: Namekawa


title: miRNAs signature as potential biomarkers for cervical precancerous lesions in Human Papillomavirus Positive women

city: Medellín

first: Gloria

middle: I.

last: Sanchez

state: Antioquia

address: Carrera 51D No 62-29 Lab 219

department: Facultad de Medicina

country: Colombia

institute: Universidad de Antioquia

summary: Cervical cancer ranks as the first in cancer mortality among women of low-middle income countries, where 80% of the 570,000 cases and 311,000 worldwide deaths estimated for 2018 occurred (Ferlay et al. 2018  ). Persistent infections with high-risk HPV (hrHPV) genotypes can lead to high-grade cervical intraepithelial (CIN) grade 2 (CIN2) or higher, (CIN2+), if untreated, a high percentage of these lesions may progress to cancer. Despite its high sensitivity, the hrHPV test has low specificity to detect CIN2+ lesions given that a high percentage of women (80 %) infected with hrHPV genotypes will resolve the infection spontaneously. microRNAs (miRNAs) are small non-coding RNAs and their differential expression patterns seen to be associated with cervical intraepithelial lesions. Our work aimed to identify miRNAs differentially expressed in CIN2+ respect with <CIN1 and to evaluate their potential use as biomarkers to distinguish low- from high-grade lesions within hrHPV positive women. For our discovery set we used  small RNA sequencing (miRNA-seq) to compare the miRNA expression patterns in 20 Formalin-Fixed Paraffin-Embedded (FFPE) tissues from hrHPV-positive women from Medellin, Colombia presenting low- (n=10) and high-grade lesions (n=10). Top five miRNAs presenting high fold change and low coefficient of variation were  used validated by RT-PCR in our validation set composed 210 age-matched independent hrHPV-positive FFPE tissues, and  an in-silico approach was used to understand the function of the differentially expressed miRNAs in the context of HPV infection.

overall_design:
We did smallRNA-seq in 20 preneoplastic cervical lesion and non lesion tissue samples from women hr-HPV positive (10 high-grade cervical lesion and 10 low grade cervical lesion). RNA was extracted, qualified by Agilent 2100, quanitfied by qubit. Librarires were prepared using the QIAseq miRNA Library Kit from Qiagen and sequenced at 1 x 75bp (2,5M reads/sample)

Case samples =  high-grade cervical lesion samples
Control samples = low-grade cervical lesion or no lesion samples

first: Martha

middle: I

last: González-Ramírez

first: Yurley

middle: T

last: Cardona

first: Carlos

last: Orozco-Castaño

first: María

last: Agudelo

first: Carolina

last: López

first: Li

first: Jone

last: Garai

first: Jovanny

last: Zabaleta

last: Sánchez

first: Samuel

first: Juan

middle: J

last: Florez


title: Genome-wide CRISPR screens decode cancer cell pathways that trigger gamma-delta T cell detection and killing

city: San Francisco

first: Alexander

last: Marson

address: 1650 Owens St

institute: UCSF Gladstone Institutes

summary: Gamma-delta T cells are potent anti-cancer effectors with the potential to target tumours broadly, independent of patient-specific neoantigens or HLA background. Gamma-delta T cells can sense conserved cell stress signals prevalent in transformed cells, although the mechanisms behind the targeting of stressed target cells remain poorly characterized. Vg9Vd2 T cells – the most abundant subset of human gamma-delta T cells – recognize a protein complex containing butyrophilin 2A1 (BTN2A1) and BTN3A1, a widely expressed cell surface protein that is activated by phosphoantigens abundantly produced by tumour cells. Here, we layered genome-wide CRISPR screens in target cancer cells to identify pathways that regulate: (1) killing by gamma-delta T cells during co-culture, and (2) BTN3A cell surface expression. In addition to confirming the importance of the phosphoantigen-producing mevalonate pathway, the screens revealed previously unappreciated multilayered regulation of BTN3A abundance on the cell surface and triggering of gamma-delta T cells through transcription, post-translational modifications, membrane trafficking. Notably, IRF1 and ZNF217 were discovered to be positive and negative transcriptional regulators that directly occupy the promoters of BTN3A1/2/3 genes. In addition, diverse genetic perturbations and inhibitors disrupting metabolic pathways in the cancer cells, particularly ATP-producing processes, were found to alter BTN3A levels. This induction of  BTN3A, as well as BTN2A1, during metabolic crises was dependent on AMP-activated protein kinase (AMPK). Finally, small molecule activation of AMPK in a cell line model and in patient-derived tumour organoids led to increased expression of the BTN2A1-BTN3A complex and increased Vg9Vd2 TCR-mediated killing. This AMPK-dependent mechanism of metabolic stress-induced ligand upregulation deepens our understanding of gamma-delta T cell stress surveillance and suggests new avenues to enhance gamma-delta T cell anti-cancer activity.

overall_design: CUT&RUN was performed on Daudi-Cas9 cells using IRF1, ZNF217, IgG, and H3K4me3 antibodies. Samples were processed in technical triplicates or duplicates

first: Murad

middle: R

last: Mamedov

first: Shane

last: Vedova

first: Jacob

middle: W

last: Freimer

first: Avinash

last: Das Sahu

first: Amrita

last: Ramesh

first: Maya

middle: M

last: Arce

first: Angelo

middle: D

last: Meringa

first: Mineto

last: Ota

first: Peixin

last: Chen

first: Kristina

last: Hanspers

first: Vinh

middle: Q

last: Nguyen

first: Kirsten

last: Takeshima

first: Jonathan

middle: K

last: Pritchard

first: Jürgen

last: Kuball

first: Zsolt

last: Sebestyen

first: Erin

last: Adams


title: Shock drives a highly coordinated transcriptional and DNA methylation response in the endothelium_DNA methylation

first: Ramon

last: Bossardi Ramos

overall_design: Human Umbilical Vein Endothelial Cells (HUVECs) were isolated in-house. The identity and purity of the HUVEC isolations were confirmed for each isolation by more than 99% positive immunostaining with endothelial cell markers (FITC-Ulex europaeus lectin, VE-cadherin) and more than 99.9% negative for α–smooth muscle actin. Cells were assayed between passages 3 and 8. To induce IL-6 signaling, cells were plated at full confluence at a density of 8 × 104 cells/cm2 on plates precoated for 30 min with 0.1% gelatin and incubated at least 48 h prior to the start of experiments. Cells were then treated with a combination of 200 ng/mL recombinant human IL-6 and 100 ng/mL sIL-6Rα (IL-6+R) or PBS (control) for 72 hours. After 72 hours, a subset of control and IL-6+R-treated cells were washed and incubated for 96 hours in EGM-2 Growth Medium. Treated HUVECs and controls were immediately centrifuged and stored until DNA extraction. DNA was isolated using the DNeasy Blood & Tissue Kit (Qiagen, USA) according to the manufacturer's instructions, including optional treatment with 100 mg/ml RNase A. The concentration of DNA was measured by the Qubit dsDNA BR Assay Kit (Molecular Probes). The DNA samples were stored at -80°C. Bisulfite conversion of 500 ng of genomic DNA was performed using an EZ DNA Methylation-Gold™ Kit (Zymo Research) following manufacturer’s instructions. Analysis of DNA methylation was carried out using Illumina Infinium MethylationEPIC BeadChip arrays33  for human genomes (>850K sites)

last: Ramos

first: Alejandro

middle: P

last: Adam


first: Alexander

last: Marson

institute: Gladstone-UCSF Institute of Genomic Immunology

summary: Gamma-delta T cells are potent anti-cancer effectors with the potential to target tumours broadly, independent of patient-specific neoantigens or HLA background. Gamma-delta T cells can sense conserved cell stress signals prevalent in transformed cells, although the mechanisms behind the targeting of stressed target cells remain poorly characterized. Vg9Vd2 T cells – the most abundant subset of human gamma-delta T cells – recognize a protein complex containing butyrophilin 2A1 (BTN2A1) and BTN3A1, a widely expressed cell surface protein that is activated by phosphoantigens abundantly produced by tumour cells. Here, we layered genome-wide CRISPR screens in target cancer cells to identify pathways that regulate: (1) killing by gamma-delta T cells during co-culture, and (2) BTN3A cell surface expression. In addition to confirming the importance of the phosphoantigen-producing mevalonate pathway, the screens revealed previously unappreciated multilayered regulation of BTN3A abundance on the cell surface and triggering of gamma-delta T cells through transcription, post-translational modifications, membrane trafficking. Notably, IRF1 and ZNF217 were discovered to be positive and negative transcriptional regulators that directly occupy the promoters of BTN3A1/2/3 genes. In addition, diverse genetic perturbations and inhibitors disrupting metabolic pathways in the cancer cells, particularly ATP-producing processes, were found to alter BTN3A levels. This induction of BTN3A, as well as BTN2A1, during metabolic crises was dependent on AMP-activated protein kinase (AMPK). Finally, small molecule activation of AMPK in a cell line model and in patient-derived tumour organoids led to increased expression of the BTN2A1-BTN3A complex and increased Vg9Vd2 TCR-mediated killing. This AMPK-dependent mechanism of metabolic stress-induced ligand upregulation deepens our understanding of gamma-delta T cell stress surveillance and suggests new avenues to enhance gamma-delta T cell anti-cancer activity.

overall_design: Genome-wide CRISPR KO in Daudi-Cas9 cells, followed by co-culturing with primaryhuman Vg9Vd2 T cells

first: Murad

last: Mamedov

first: Shane

last: Vedova

last: Freimer

last: Sahu


title: Expression data from food colorants treated C. elegans

city: Murcia

first: Fernando

last: Gandía-Herrero

state: Murcia

address: Universidad de Murcia, Campus Espinardo - Edificio Veterinaria

department: Biochemistry and Moleular Biology

country: Spain

institute: University of Murcia

summary:
Effects of food colorants in C. elegans gene expression is studied.
Microarrays were used to analyze the global programme of gene expression underlying the lifespan change and identified distinct classes of up/down-regulated genes in animals treated with food colorants.

overall_design: C. elegans young adults treated with Tartrazine and Ponceau Red from L1 stage were selected for RNA extraction and hybridization on Affymetrix microarray chips.

first: M

last: Guerrero-Rubio

last: Lopez-Andreo

first: S

last: Hernandez-Garcia

first: F

last: Garcia-Carmona

last: Gandia-Herrero


summary: target tumours broadly, independent of patient-specific neoantigens or HLA background. Gamma-delta T cells can sense conserved cell stress signals prevalent in transformed cells, although the mechanisms behind the targeting of stressed target cells remain poorly characterized. Vg9Vd2 T cells – the most abundant subset of human gamma-delta T cells – recognize a protein complex containing butyrophilin 2A1 (BTN2A1) and BTN3A1, a widely expressed cell surface protein that is activated by phosphoantigens abundantly produced by tumour cells. Here, we layered genome-wide CRISPR screens in target cancer cells to identify pathways that regulate: (1) killing by gamma-delta T cells during co-culture, and (2) BTN3A cell surface expression. In addition to confirming the importance of the phosphoantigen-producing mevalonate pathway, the screens revealed previously unappreciated multilayered regulation of BTN3A abundance on the cell surface and triggering of gamma-delta T cells through transcription, post-translational modifications, membrane trafficking. Notably, IRF1 and ZNF217 were discovered to be positive and negative transcriptional regulators that directly occupy the promoters of BTN3A1/2/3 genes. In addition, diverse genetic perturbations and inhibitors disrupting metabolic pathways in the cancer cells, particularly ATP-producing processes, were found to alter BTN3A levels. This induction of BTN3A, as well as BTN2A1, during metabolic crises was dependent on AMP-activated protein kinase (AMPK). Finally, small molecule activation of AMPK in a cell line model and in patient-derived tumour organoids led to increased expression of the BTN2A1-BTN3A complex and increased Vg9Vd2 TCR-mediated killing. This AMPK-dependent mechanism of metabolic stress-induced ligand upregulation deepens our understanding of gamma-delta T cell stress surveillance and suggests new avenues to enhance gamma-delta T cell anti-cancer activity.

overall_design: Genome-wide CRISPR KO in Daudi-Cas9 cells, followed by FACS sorting the top (high) and bottom (low) 25% of cells according to BTN3A expression.

first: Jacob

first: Avinash

first: Amrita

last: Ramesh

first: Maya

last: Arce

first: Angelo

last: Meringa

first: Mineto

last: Ota

first: Peixin

last: Chen

last: Hanspers

last: Nguyen

first: Kristen

last: Takeshima

last: Pritchard

first: Jurgen

last: Kuball


title: Distinct lactation-associated macrophages exist in murine mammary tissue and human milk [RNA-seq: human]

status: Public on May 03 2023

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

institute: ETH ZURICH / University of Zurich

summary: Macrophages are involved in immune defense, organogenesis and tissue homeostasis. They also contribute to the different phases of mammary gland remodeling during development, pregnancy and involution post-lactation. Yet, less is known about the dynamics of mammary gland macrophages in the lactation stage. Here, we describe a macrophage population present during lactation in mice. By multi-parameter flow cytometry and single-cell RNA sequencing we reveal this population as distinct from the two resident macrophage subsets present pregestationally. These lactation-induced macrophages (LiMacs) are predominantly monocyte-derived and expand by proliferation in situ concomitant with nursing. LiMacs develop independently of IL-34 but require CSF-1 signaling and are partly microbiota-dependent. Locally, they reside adjacent to the basal cells of the alveoli and extravasate into the milk. Moreover, we also found several macrophage subsets in human milk, resembling LiMacs. Collectively, these findings reveal the emergence of unique macrophages in the mammary gland and milk during lactation.

overall_design: 10 000 of CD45+ human milk cells (8 - 63 dpp, n=6, barcoded) were included in the analysis.

first: Dilay

last: Cansever

first: Ekaterina

last: Petrova

first: Hubert

last: Rehrauer

first: Greter

last: Melanie


title: Distinct lactation-associated macrophages exist in murine mammary tissue and human milk [RNA-seq: mouse]

overall_design: 10 000 cells (for 7 dpp, n=1 for virgin mammary gland and n=2 for lactating mammary gland) and 18 000 cells (for 8 dpp, 11 dpp, 14 dpp, n=3 for each time point, time points barcoded) were included in the analysis.


title: Genome-wide gene expression profiling post PCCB knockdown in human forebrain organoids

status: Public on May 02 2023

city: Chang sha

first: Wendiao

last: Zhang

address: No. 932, Lushan South Road

institute: School of Life  Sciences, Central South University

summary: We established PCCB knockdown human induced pluripotent stem cell (hiPSC) line using CRISPR interference (CRISPRi). The established PCCB knockdown and control hiPSCs were then used to generate human forebrain organoids (hFOs). On day 60 of organoid culture, PCCB knockdown and control hFOs were randomly selected for RNA-sequencing (RNA-seq). We found that differentially expressed genes (DEGs) affected by PCCB knockdown were enriched with GABAergic synapse, synaptic vesicle cycle, neurotransmitter transport, forebrain development, axon development, synaptic organization, and calcium signaling pathways. The DEGs were also significantly overlapped with schizophrenia (SCZ)-associated genes, including genes dysregulated in brains or organoids derived from SCZ patients, and genes reported in SCZ GWAS.

overall_design: We established PCCB knockdown hiPSC lines (U2F) using CRISPRi. For hiPSC line, two guidance RNA sequences (G1 and G2) were designed in CRISPRi to minimize the off-target effects. The established PCCB knockdown (PCCB-G1 and PCCB-G2) and control (PCCB-NC) hiPSCs were used to generate hFOs. On day 60 of organoid culture, two hFOs in PCCB knockdown or control group were randomly pooled together as one mixed sample. Three to five mixed samples in each group were then used for RNA-seq (150 bp, paired-end) on the Illumina NovaSeq 6000 system. DEseq2 was used to identify DEGs between PCCB knockdown and control hFOs. DEGs (adjusted P value < 0.05) were used for Gene Ontology and KEGG pathway analysis.

first: Qingtuan

last: Meng

first: Ming


title: Transcriptional regulation of quinolones and cephalosporins resistance formation by PhoPQ in Salmonella enterica serovar Enteritidis.

first: mengjun

last: Hu

address: Shanghai Jiao Tong University，School of Agriculture & Biology, Dongchuan road 800

institute: Shanghai Jiao Tong University

summary:
To elucidated the global profile of genes regulated by PhoPQ under quinolones/cephalosporins stresses in S. Enteritidis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 group bacterial samples.

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for phoP deletion mutant (ΔphoP) and its parent S. Enteritidis (Wild-type, WT) under nalidixic acid/ceftazidime pressure.

first: Mengjun

first: Xianming

last: Shi


title: Euo is a developmental regulator that represses late genes and activates midcycle genes in C. trachomatis

city: Irvine

first: Syed

middle: Meraj Azhar

last: Rizvi

address: University of California Irvine

department: Microbiology and Molecular Genetics

institute: University of California Irvine

summary: The pathogenic bacterium Chlamydia reproduces via an unusual intracellular developmental cycle in which it converts from a dividing form (reticulate body or RB) to an infectious form (elementary body or EB). The transcription factor Euo has been proposed as a developmental regulator in C. trachomatis because it repressed a number of late chlamydial promoters, which are transcribed during RB-to-EB conversion. To define the Euo regulon, we performed a genome-wide study that combined Euo DNA Immunoprecipitation-seq (DIP-seq) studies with RNA-seq analysis of HeLa cells infected with an Euo-overexpressing C. trachomatis strain. We demonstrate that Euo directly regulates ~7% of C. trachomatis genes. However, only about half were downregulated (28/61; 45.9%) by Euo overexpression while paradoxically the other half were upregulated (33/61; 54.1%). Intriguingly, all downregulated genes were late genes, while the majority of upregulated genes were midcycle genes, which are transcribed during RB replication. DIP analysis showed that Euo occupancy sites were restricted to the core promoter region for downregulated genes, but were located over a wider region immediately upstream of the promoter for upregulated genes. We also found that Euo controls its own expression through a negative feedback mechanism. Electron microscopy analysis of cells infected with the Euo-overexpressing strain showed fewer EBs, consistent with a block in RB-to-EB conversion, as well as fewer and larger RBs. Together, these findings broaden the role of Euo as a developmental regulator that functions as both a transcriptional repressor of late genes and a transcriptional activator of midcycle genes in C. trachomatis.

overall_design: Sheared chromatin (150 bp average size) from C. trachomatis infected HeLa cells incubated with 10-50ng of purified C. trachomatis Euo protein, immunoprecipated, purified

first: Owais

last: Rashid

last: Tan

first: Cuper

last: Ramirez


title: Species-specific roles for the MAFA and MAFB transcription factors in regulating islet β cell identity

status: Public on May 01 2023

city: Nashville

first: Jeeyeon

last: Cha

state: Tennessee

address: 300A 54th Avenue North

institute: Vanderbilt University Medical Center

summary: Type 2 diabetes (T2D) is associated with compromised identity of insulin-producing pancreatic islet beta (β) cells, characterized by inappropriate production of other islet cell-enriched hormones. Here we examined how hormone misexpression was influenced by the MAFA and MAFB transcription factors, closely related proteins that maintain islet cell function. Mice specifically lacking MafA in β cells demonstrated broad, population-wide changes in hormone gene expression with an overall gene signature closely resembling islet gastrin (Gast)-positive cells generated under conditions of chronic hyperglycemia and obesity.  A human b cell line deficient in MAFB, but not one lacking MAFA, also produced a gastrin (GAST)-positive gene expression pattern.  In addition, GAST was detected in human T2D β cells with low levels of MAFB. Moreover, evidence is provided that human MAFB can directly repress GAST gene transcription. These results support a novel, species-specific role for MafA and MAFB in maintaining adult mouse and human β cell identity, respectively, by repressing expression of Gast/GAST and other non-b cell hormones.

overall_design: Bulk RNASeq was performed on 4 groups of isolated mouse islets: Male Wildtype, Male MafADb, Female Wildtype and Female MafADb. Each group includes 4 replicates

first: Xin

last: Tong

first: Mark

last: Magnuson

first: Roland

last: Stein


title: Immune profile associated to vitiligo onset in melanoma patients undergoing treatment with checkpoint inhibitors gives insight into the raising of the adverse event and of the effective anti-tumor response

city: Rome

first: Marika

last: Guercio

state: RM

address: Viale di San Paolo, 15

department: Oncohematology

institute: Ospedale Pediatrico Bambino Gesù

summary: Immunotherapy with checkpoint inhibitors is an efficient treatment for metastatic melanoma. Development of vitiligo upon immunotherapy represents a specific immune-related adverse event (irAE) diagnosed in 15% of patients and associated with a positive clinical response. Therefore, a detailed characterization of immune cells during vitiligo onset in melanoma patients would give insight into the immune mechanisms mediating both this irAE and the anti-tumor response. To better understand these aspects, we analyzed T cell subsets from peripheral blood of metastatic melanoma patients undergoing treatment with anti-programmed cell death protein (PD)-1 antibodies. Stratification of patients for developing or not developing vitiligo during therapy revealed an association between blood reduction of mucosal associated invariant T (MAIT), T helper (h) 17, natural killer (NK) CD56bright, and T regulatory (T-reg) cells and vitiligo onset. To deeply characterize the tumoral T cell response concomitant to vitiligo onset, we analyzed T cell content in skin biopsies collected from melanoma patients who developed vitiligo. Consistently with the observed blood reduction of Th17 cells in melanoma patients developing vitiligo during immunotherapy, we found an enrichment of Th17 cells in the vitiligo skin biopsy, suggesting a migration of Th17 cells from the blood into the autoimmune lesion. To further characterize T cells in vitiligo skin lesion of melanoma patients, we sequenced T cell receptor (TCR) of cells derived from biopsies of vitiligo and primary melanoma of the same patient. Interestingly, we found different TCR sequences between vitiligo and primary melanoma lesions, except for a few cases showing the same TCR sequences. In contrast, shared TCR sequences were identified between vitiligo and metastatic tissues of the same patient. These data indicate that T cell response against normal melanocytes, which is involved in vitiligo onset, is not mainly mediated by the reactivation of specific T cell clones infiltrating primary melanoma but may be elicited by T cell clones targeting metastatic tissues. Altogether, our data indicate that anti-PD-1 therapy induces a de novo immune response, composed of different T cell subtypes, whose role may be related to the development of vitiligo and the response against metastatic tumor.

overall_design:
In this study we performed TCR-Seq of PBMC (10 biological replicateas), primary melanoma (15 biological replicates), metastasis (5 biological replicates) and vitiligo (10 biological replicates) samples deriving from patients affected by metastatic melanoma, who were treated with anti-PD1 immunotherapy at IDI-IRCCS.
***Submitter states that Adaptive Biotechnologies does not release raw data***

first: Maria

middle: L

last: Carbone

first: Alessia

last: Capone

first: Sofia

last: Reddel

first: Domenico

last: Silvestris

first: Daniela

last: Lulli

first: Carmela

last: Ramondino

first: Concetta

last: Quintarelli

first: Elisabetta

last: Volpe

first: Cristina

last: Failla


title: Effet of novel anti-Gal-3 mAb inhibitors in the mouse model of HOCl-induced SSc

city: Suresnes

first: Perrine

last: Soret

address: 52 rue Carnot

institute: Servier

summary: To investigate treatment effect in the mouse model of HOCL-induced SSc

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 anti-Gal-3 specific monoclonal antibody.

first: Frédéric

last: De Ceuninck

first: Sahar

last: Elouej


title: Reduced proliferation capacity of native bone marrow MSC after allogenic stem cell transplantation is associated with clinical outcome

city: Halle

first: Edith

last: Willscher

state: Deutschland

address: Ernst-Grube-Straße 40

department: Internal Medicine IV

institute: Martin Luther University of Halle-Wittenberg

summary:
Engraftment and differentiation of donor hematopoietic stem cells is decisive for the clinical success of allogeneic stem cell transplantation (alloSCT) and depends on the recipient’s bone marrow (BM) niche. Presumably, a damaged niche contributes to poor graft function post-alloSCT, but the underlying mechanisms and specifically the role of BM multipotent mesenchymal stroma cells (MSC) are ill defined.
Upon multivariate analysis in a cohort of 732 individuals, we observed a reduced presence of proliferation-capable MSC in BM-aspirates from patients (N=196) who had undergone alloSCT (OR 0.61, p=.028). This was confirmed by paired analysis in 30 patients showing a higher frequency of samples with a lack of MSC presence post-alloSCT compared to pre-alloSCT. This reduced MSC presence was associated with reduced survival of patients following alloSCT and specifically with impaired graft function. Post-alloSCT MSC showed diminished in vitro proliferation along with a transcriptional antiproliferative signature, upregulation of epithelial-mesenchymal transition and extracellular matrix pathways and abnormal cytokine release in coculture with hematopoietic cells. In order to avoid in-vitro-culture bias we isolated the CD146+/CD45-/HLA-DR- BM cell fraction, which comprised the entire MSC population. The post-alloSCT isolated native CD146+MSC showed a similar reduction in proliferation capacity and shared the same antiproliferative transcriptomic signature as for post-alloSCT adherence-isolated MSC.
Taken together, our data show that alloSCT confers damage to the proliferative capacity of native MSC, which is associated with reduced patient survival after alloSCT and impaired engraftment of allogeneic hematopoiesis. These data represent the basis to elucidate mechanisms of BM-niche reconstitution post-alloSCT and its therapeutic manipulation.

overall_design: Comparative gene expression profiling of RNAseq data from 5 paired human samples of MSC derived pre- and post-allogenic stem cell transplantation by bulk RNA sequencing.

first: Christiane

last: Katzerke

first: Judith

last: Schaffrath

first: Jana

last: Lützkendorf

first: Maike

last: Janssen

first: Anne-Kathrin

last: Meerbach

first: Katrin

last: Nerger

first: Mascha

last: Binder

first: Christian

last: Rohde

first: Carsten

last: Müller-Tidow

first: Lutz

last: Müller


title: Transcriptional profiling of EMB+ cells and EMB- cells across long bone and vertebrae

status: Public on Apr 30 2023

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: To compare gene expression profiling of EMB+ cells and EMB- cells whin CD45-Ter119-CD31--Thy1-6C3-CD200+CD105- population across long bone and vertebrae, we isolated related cells form long bone or vertebrae of zic1 -cre mtmg mice by FACS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for (1)long bone zic1-cre negative CD45-Ter119-CD31--Thy1-6C3-CD200+CD105-EMB+, (2)long bone zic1-cre negative CD45-Ter119-CD31--Thy1-6C3-CD200+CD105-EMB-, (3) vertebrae zic1-cre negative CD45-Ter119-CD31--Thy1-6C3-CD200+CD105-EMB+, (4)vertebrae zic1-cre negative CD45-Ter119-CD31--Thy1-6C3-CD200+CD105-EMB-, (5) vertebrae zic1-cre positive CD45-Ter119-CD31--Thy1-6C3-CD200+CD105-EMB+, (6)vertebrae zic1-cre positive CD45-Ter119-CD31--Thy1-6C3-CD200+CD105-EMB-.  Each population has four replicates.

first: Jun

last: Sun

first: Matthew

last: Greenblatt


title: Transcriptional analysis and transposable element analysis of livers, lungs and brains from E18.5 mouse embryos (Daxx Y130A  vs Daxx WT and Daxx S226A vs Daxx WT)

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: Objective: Daxx is a protein with multiple functions and is essential for embryonic development. Daxx knockout embryos fail to develop properly and exhibit lethal phenotype around E6.5. One of the important functions is as a histone chaperone for the histone H3 variant, H3.3. Daxx interacts with Atrx to form a protein complex that deposits H3.3 into heterochromatic regions of the genome, including centromeres, telomeres and repeat loci. Here, we investigated how histone chaperone function of Daxx contributes to the embryonic development. Methods: We developed two Daxx mutant alleles in the mouse germline which abolish the interactions between Daxx and Atrx (DaxxY130A), Daxx and H3.3 (DaxxS226A). We set up mating between either heterozygous DaxxY130A or heterozygous DaxxS226A individually and looked for the viability of homozygous mutants at different development stages. We also performed bulk RNA-seq on tissues from the two mutant embryos and analyzed the changes in gene expression and transposable elements (TE).  Results: We found that the interaction between Daxx and Atrx is dispensable for viability in both the pre- and post-natal setting as homozygous Daxx-Y130A mutants are both viable and fertile. The loss of the Atrx interaction, however, does cause dysregulated expression of both endogenous retroviruses and nearby protein coding genes. On the contrary, the interaction between Daxx and H3.3 is not required for embryonic development but is essential for postnatal viability. Transcriptome analysis of embryonic tissues demonstrates that this interaction is important for silencing endogenous retroviruses and for maintaining proper hematopoiesis. Conclusions: The histone chaperone function of Daxx is dispensable for embryonic development but important for hematopoiesis, which is independent of the interaction with Atrx. Moreover, both the interactions with Atrx and with H3.3 is important for regulation of ERV expression. Overall, these results clearly demonstrate that Daxx and H3.3 have both Atrx-dependent and independent functions, advancing our understanding of this epigenetic regulatory complex.

overall_design: Examination of transcriptional and transposable elements changes in the embryos bearing Daxx Y130A or S226A mutations by bulk RNA-seq of livers, lungs and brains from E18.5 embryos. Replication number is 4 with the exception of comparison in Y130A lung vs WT lung where 3 WT lungs are included

first: Chang

first: Amanda

last: Wasylishen


title: Nicotinamide regulates LPS-induced HIF-1alpha responses through post-translational modifications in human macrophages

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

institute: nih

summary: Mechanisms to control the immune response are important to pathogen evasion and host defense. Gram-negative bacteria are common pathogens that can activate host immune responses through their outer membrane component, lipopolysaccharide (LPS). Macrophages activated by LPS induce cell signals that promote hypoxic metabolism, phagocytosis, and antigen presentation. Nicotinamide (NAM) is a vitamin B3 derivative and precursor in the formation of nicotinamide adenine dinucleotide (NAD), which is a required co-factor in cellular function. In this study, treatment of human monocyte derived macrophages with NAM antagonized LPS-induced responses by altering the expression of ubiquitin genes, increasing HIF-1alpha and p65/RelA ubiquitination, decreasing p65/RelA acetylation and promoting the formation of the proteasome. NAM also elevated intracellular NAD levels and altered the genetic expression of sirtuins and poly(ADP-ribose) polymerases. These NAM responses highlight post-translational events in regulating the host response to pathogens and identify the ubiquitome as a target in pathogen evasion and host defense.

overall_design: Each of the four male donor human monocyte-derived macrophages (HMDMs) were treated with four conditions for four hours. The conditions included vehicle control, 10ng/ml lipopolysaccharide (LPS), 10mM nicotinamide (NAM), or LPS plus NAM. There were 16 total samples: 4 control, 4 LPS, 4 NAM, and 4 LPS+NAM.

first: Colleen

middle: S

last: Curran

first: Edward

last: Dougherty

first: Cumhur

middle: Y

last: Demirkale

first: Parizad

last: Torabi-Parizi


title: Distinct lactation-associated macrophages exist in murine mammary tissue and human milk

first: Genome

last: Informatics

department: Functional Genomics Center Zurich (FGCZ)

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptomic analysis of emergency granulopoiesis-generated neutrophils compared to steady state (control) neutrophils

city: Auckland

first: Hannah

last: Darroch

address: Grafton

department: FMHS

country: New Zealand

institute: University of Auckland

summary:
Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control (steady state) neutrophils.
To determine if transcriptomic changes support these functional adaptations, we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and after infection.

overall_design: Differential gene expression analysis of RNA-seq data from neutrophils generated by steady state (control) granulopoiesis or emergency granulopoiesis either before or after infection in biological quadruplet.

first: Christopher

last: Hall


title: Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis [scData]

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

summary: Primary sclerosing cholangitis (PSC) is an autoimmune-like disease of the bile ducts that co-occurs with inflammatory bowel disease (IBD) in almost 90% of cases. Colorectal cancer is a major complication of patients with both PSC and IBD, and these patients are at a much greater risk compared to patients with IBD without concomitant PSC. Combining flow cytometry, bulk and single cell transcriptomics, and T- and B-cell receptor repertoire analysis of right colon tissue from PSC, IBD, and healthy controls we identified a unique adaptive inflammatory transcriptional signature associated with greater risk and shorter time to dysplasia specifically in patients with PSC. This inflammatory signature is characterized by antigen-driven IL-17A+ Foxp3+ CD4 T-cell and an expansion of IgG-secreting B-cell responses. These data results suggest that the mechanisms that drive the emergence of dysplasia in of PSC and IBD dysplasia are distinct and provide molecular insights to guide prevention of colorectal cancer in PSC.

overall_design: Colon biopsy  gene expression profiles from PSC

first: Dustin

middle: G

last: Shaw


title: Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis


title: Metabolic profiling stratifies colorectal cancer and reveals adenosylhomocysteinase as a therapeutic target

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute


title: Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis [bulk RNASeq]

overall_design: Colon biopsy  gene expression profiles from PSC, IBD and healthy controls


title: Transcriptional profiling of small intestinal tissue from Apc-deficient mice, with and without DZNeP treatment

summary: The effect of EZH2 inhibitor DZNeP on the small intestine of mice deificient in Apc was examined with RNAseq.

overall_design: Expression data from small intestinal tissue with the noted treatments

first: Joha

last: n Vande Voorde

first: Owen

last: Sansom


title: Gene expression profile at single cell level of cells from the murine small intestine (SI) lacking functional Apc.

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of cells within the murine small intestine in the absence of functional Apc.

overall_design: Cells from a 5-15cm portion of small intestine were isolated from mice with short term Apc inactivation, before analysis with scRNAseq

first: Johan

last: Vande Voorde

first: Alexander

last: Raven

first: Megan

last: Mills


title: Single-cell sequencing of human intestnal organoids with and without enteroendocrine cells (EECs)

city: Cincinnati

first: Heather

last: McCauley

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: We generated pluripotent stem cell-derived human intestinal organoids with (n=2) and without (n=1) EECs and performed single-cell sequencing after their transplantation under the mouse kidney capsule to evaluate similarities and differences in the absence of enteroendocrine cells.

overall_design: Transplanted human intestinal organoids were dissociated to single cells, sorted by flow cytometry to enrich for live cells, then subjected to 10X sequencing.

first: James

last: Wells


title: Epigenetic-based regulation of transcriptome in Escherichia coli adaptive antibiotic resistance

city: Rende

first: Dina

last: Bellizzi

state: Cosenza

address: Ponte P. Bucci Cubo 4C

department: Biology, Ecology and Earth Science

institute: University of Calabria

summary: To investigate the transcriptome and global methylation patterns of cytosines and adenines in cells selected for adaptive resistance to ampicillin, gentamicin, and ciprofloxacin

overall_design: Comparative gene expression levels evaluated by RNA-sequencing in Escherichia coli JM109 cells (control) and in  ampicillin-, gentamicin-, and ciprofloxain resistant cells selected at sub-MIC concentrations and subsequent growth at increasing concentrations of the three antibotics

first: Patrizia

last: D'Aquila

first: Francesco

last: De Rango

first: Ersilia

last: Paparazzo

first: Giuseppe

last: Passarino


title: Molecular Consequences of Peripheral Influenza A Infection on Cell Populations in the Murine Hypothalamus

city: København N

first: Birgitte

last: Rahbek Kornum

address: Blegdamsvej 3B

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

summary: Infection with Influenza A virus (IAV) causes the well-known symptoms of the flu, including fever, loss of appetite and excessive sleepiness. These responses, mediated by the brain, will normally disappear once the virus is cleared from the system, but a severe respiratory virus infection may cause long-lasting neurological disturbances. These include encephalitis lethargica and narcolepsy. The mechanisms behind such long lasting changes are unknown. The hypothalamus is a central regulator of the homeostatic response during a viral challenge. To gain insight into the neuronal and non-neuronal molecular changes during an IAV infection, we intranasally infected mice with an H1N1 virus and extracted the brain at different time points. Using single-nucleus RNA sequencing (snRNA-seq) of the hypothalamus, we identify transcriptional effects in all identified cell populations. The snRNA-seq data showed the most pronounced transcriptional response at 3 days past infection, with a strong downregulation of genes across all cell types. General immune processes were mainly impacted in microglia, the brain resident immune cells, where we found increased numbers of cells expressing pro-inflammatory gene networks. In addition, we showed that most neuronal cell populations are downregulating their transcriptional landscape including genes contributing to the energy homeostasis in the mitochondria and protein translation in the cytosol. Our data suggest that a preventive mechanism might exist in neuronal cells to avoid intracellular viral replication and attack by phagocytosing cells. This is complemented by increased activity of microglia monitoring their surroundings.

overall_design: single-nucleus RNA sequencing of the murine hypothalmus of female mice. Sampled at 3, 7 and 23 days post infection. Intranasally infected with h


title: The differential expressed mRNAs in spleen B cells between control(normal)，PBS treated or SJMHE1(Schistosoma japonicum-derived peptide) treated OVA-induced allergic rhinitis mice.

city: Zhenjiang

first: Xuerong

last: Gao

address: No.438, Jiefang Road, Jingkou District, Zhenjiang City, Jiangsu Province

institute: Jiangsu Univercity

summary:
In order to explore the molecular mechanism of SJMHE1 intervention in allergic rhinitis, an OVA-induced allergic rhinitis model was established and intervened by subcutaneous injection of PBS and SJMHE1.
Then a global RNA sequencing of mouse spleen B cells from the control, PBS, and SJMHE1 groups were performed.

overall_design: Comparative gene expression profiling analysis of of mouse spleen B cells from the control, PBS, and SJMHE1 groups.

first: Chaoming

last: Mao

first: Liyang

last: Dong