title: EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [RNA-seq]

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

institute: University of Geneva

summary: The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. In tetrapods, posterior Hoxd genes transcription in digits is controlled by a well-characterized series of enhancers forming a large regulatory landscape, which has its syntenic counterpart in zebrafish. We show here that the deletion of the orthologous landscape in fishes does not affect the transcription of these genes in fin buds. Instead, it abrogates hoxd expression in the cloaca, an essential structure related to the mammalian uro-genital sinus. We also report that Hoxd gene function in the mammalian uro-genital sinus depends on enhancers located in the same regulatory landscape and thus conclude that an ancestral Hox ‘cloacal’ regulation was co-opted, in tetrapod, as a playground to subsequently accompany the evolution of both external genitals and digits regulatory landscapes, along with the emergence of these developmentally and phylogenetically related structures.

overall_design: RNA-seq experiment in E18.5 male and female urogenital sinus from wild type and mutant embryos.

first: Aurélie

first: Chase

last: Bolt

first: Lucille

last: Lopez-Delisle

first: Sandra

last: Gitto

first: Bénédicte

last: Mascrez

first: Denis

last: Duboule


title: Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [ATAC-seq]

status: Public on Apr 17 2024

city: Philadelphia

first: Mitchell

middle: L

last: Conery

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

country: USA

institute: Children's Hospital of Philadelphia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To nominate identify tissues relevant to the etiology of bone mineral density we generated ATAC-seq in pediatric hMSC-osteoblasts, hFOB 1.19 cells (hFOBs), osteoclasts, and primary chondrocytes. Leveraging the results of this experiment, we designed a CRISPRi screen in hFOBs with scRNA-seq expression read out. The targets selected for the screen were informed by newly generated Capture-C and bulk RNA-seq from hFOBs.

overall_design: ATAC-seq was executed in pediatric hMSC-osteoblasts, hFOB 1.19 cells (hFOBs), osteoclasts, and primary chondrocytes in order to study the heritability enrichment of bone mineral density in regulatory regions of a diverse number of cell types. ATAC-seq in hFOBs was also used for identifying regulatory regions to be targeted in a paired CRISPRi screen in hFOBs.

first: James

middle: A

last: Pippin

first: Matthew

middle: C

last: Pahl

first: Struan

middle: F

last: Grant


title: In vitro reconstitution of epigenetic reprogramming in the human germ line

status: Public on Apr 24 2024

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Systemic comparison of molecular characteristics in different skin fibroblast senescent models

status: Public on Apr 10 2024

city: Nanjing

first: Xiaokai

last: Fang

state: Jiangsu

address: No.12, Jiangwangmiao Street, Xuanwu District, Nanjing City, Jiangsu Province

country: China

institute: Dermatology Hospital of Chinese Academy of Medical Sciences

summary: Each senescent FB model exhibited different characteristics. Besides the upregulated expression of natural senescence features, FB-UVB and FB-ATV expressed high levels of senescence-related genes including SASP, and FB-P30 had the greatest similarity with FB-E. However, D-galactose-stimulated FB did not clearly present aging characteristics. It provides references for choosing senescent FB model in studying aging and related skin disease.

overall_design: To explore and compare their signatures among senescence-induced FB models, human skin primary FBs were obtained from children (FB-C) and elderly healthy individuals (FB-E). Further senescent models were induced by ultraviolet B irradiation (FB-UVB), D-galactose stimulation(FB-D-gal), atazanavir treatment(FB-ATV), and replication exhaustion induction (FB-P30), respectively.


title: EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [ATAC-seq]

country: Switzerland

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design:
To assay chromatin accessibility, we conducted ATAC-seq experiments. We collected different mouse and zebrafish tissues. Samples were processed as described in 10.1038/nmeth.2688.

UPDATE: [08-12-2024] For Samples GSM7976428, GSM7976429, and GSM7976430, the stage was corrected from 16hpf to 30hpf in the titles, stage characteristics, and processed data files. The raw data and processed data associated with these Sample accession numbers did not change.


title: EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [ChIP-seq]

overall_design:
Histone mark ChIP-seq experiments in wild type mouse urogenital sinuses.
Please note that the CTCF ChIP-seq experiments in one mouse sample from GSE194418 and four zebrafish samples from GSE156096 have been re-analyzed:
BioProject accession: PRJNA800459
GEO Sample      SRA Runs        BioSample       Title
==========      ========        =========       =====
GSM5835468   SRR17750150  SAMN25248179  ChIP_CTCF_E105_PT_rep1
BioProject accession: PRJNA656773
GEO Sample      SRA Runs        BioSample       Title
==========      ========        =========       =====
GSM4724551      SRR12435909     SAMN15802273    ChIP-seq in zebrafish wild-type embryos at 24hpf, replicate 1
GSM5344491      SRR14670351     SAMN19371946    ChIP-seq in zebrafish wild-type embryos at 24hpf, replicate 2
GSM5344494      SRR14670354     SAMN19371948    ChIP-seq in zebrafish wild-type embryos at 48hpf, replicate 1
GSM5344495      SRR14670355     SAMN19371947    ChIP-seq in zebrafish wild-type embryos at 48hpf, replicate 2
Please see more details in the 're-analysis_readme.txt'.


title: Analysis of Spatial Transcriptomics for Unveiling the novel molecular characteristics of Recurrent and Non-Recurrent High-Grade Serous Ovarian Cancer

status: Public on Apr 18 2024

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

country: South Korea

institute: Incheon National University

summary: Our study utilized spatial transcriptomics (ST) to interpret the tumor microenvironment to examine spatial characteristics across different sites in eight patients with HGSOC divided into recurrent (R, n = 5) and non-recurrent (NR, n = 3) groups based on a 60-month recurrence criterion. This study identified diagnostic and therapeutic targets for HGSOC, marking a step towards personalized medicine.

overall_design: We obtained ovarian cancer tissues from eight treatment-naïve patients who underwent cytoreductive surgery. Visium spatial transcriptomics analysis was performed on the eight patients with HGSOC: five in recurrent (R) and three in non-recurrent (NR) groups.

first: Hye-Yeon

last: Ju

first: Seo

middle: Y

last: Youn

first: Jun

last: Kang

first: Min

last: Whang

first: Youn

middle: J

last: Choi


title: Increased HIF-2α Activity in the Nucleus Pulposus Causes Mild Degenerative Changes in the Intervertebral Disc in the Aging Mouse Spine

status: Public on Mar 27 2024

first: Makarand

last: Risbud

address: 1015 Walnut Street

institute: Thomas Jefferson University

summary:
Transcriptomic analysis of nucleus pulposus (NP) tissues from intervertebral discs of 14- and 24-month-old mice with the conditional postnatal overexpression of HIF-2α.
Hypoxia-inducible factors (HIFs) are essential for the homeostasis of the hypoxic tissues, and therefore, increased activity of the transcription factor HIF-2α is shown to contribute to the pathogenesis of mild disc degeneration in the spine. We examined the transcriptomic profiles of nucleus pulposus cells in control and K19-HIF-2α-dPA overexpression mice using microarrays.

overall_design: Tissues from the nucleus pulposus (NP) were harvested from the intervertebral discs of four K19-HIF-2αdPA control (HIF-2αdPA/dPA) (WT) and four K19-HIF-2αdPA overexpression mice (K19-HIF-2αdPA/dPA) (MUT) at both 14 and 24 months of age. NP tissues were pooled from caudal discs in each animal for RNA extraction and hybridization using Affymetrix microarrays.

first: Shira

middle: N

last: Johnston

first: Maria

last: Tsingas

middle: V


title: EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS

first: Aurelie

last: Hintermann


title: Clinicopathological and molecular landscape of 5-year IDH-wild-type glioblastoma survivors: a multicentric retrospective study

status: Public on Mar 31 2024

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

summary: Background: Less than 5% of glioblastoma multiforme (GBM) patients survive more than 5-years (long-term survivors, LTS). Nevertheless, the molecular fingerprint of LTS remains uncharted. We aimed to characterize LTS by clinicopathological assessment, DNA methylation (DNAm)/Copy Number Variation (CNV) and mutation profiling.   Methods: This multicentric project proposed by Alliance Against Cancer was coordinated by Fondazione IRCCS Istituto Neurologico Carlo Besta. One-hundred forty-two LTS patients were screened, and samples centrally reviewed; 95 patients were enrolled. DNAm profiles and sequencing were performed on 27 LTS and 24 standard survival GBM (STS).    Results: We focused on 73 IDHwt-LTS. All patients underwent at least partial resection, followed by Stupp protocol (48/70). The median time to progression was 43 months (4-186), and almost all received a second treatment. Morphological and routine diagnostic molecular features of LTS did not deviate from the classic findings. MGMT promoter methylation was detected in 92% of cases.    No significant differences were observed between LTS and STS in terms of prevalence of mutated genes, with TP53 as the most commonly mutated gene (26% of all samples). DNAm showed a more heterogeneous group for LTS, with several cases classified as pediatric high-grade glioma and peculiar CNVs.  We identified 18 differentially methylated regions, 4 associated with survival probability (NR2F2, MME, WDR66 and ENPP4). Methylation levels of individual probes in IGFBP3 gene and corresponding protein expression showed a significant correlation with survival.   Conclusions: We found no significant different morphology nor mutational profile of LTS. DNAm confirmed as a valuable tool for GBM classification. No specific episignature was detected, but methylation levels of specific genes had prognostic value in LTS.

overall_design: 27 LTS (long-term survival) glioblastoma patients were compared to 24 standard survival (control) glioblastoma patients

first: Sara

last: Patrizi

first: Andrea

last: Ciolfi

first: Lucia

last: Pedace

first: Sabina

last: Barresi

first: Angela

last: Mastronuzzi

first: Marco

last: Tartaglia

first: Franco

last: Locatelli


title: Metallothionein 1 (Mt1) Regulates Growth and Survival of DNMT3A;NPM1-Mutant Acute Myeloid Leukemia

status: Public on Mar 26 2024

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Adult de novo acute myeloid leukemia (AML) is a hematologic malignancy with poor prognosis, commonly driven by mutations in genes including the DNA methyltransferase DNMT3A and nucleophosmin NPM1. We previously generated sequentially inducible mouse models of these mutations and observed transformation from clonal hematopoiesis (CH) to myeloproliferative disorder to AML. In transformed AML, leukemia-propagating cells have a myeloid-restricted progenitor cell phenotype (c-Kit+). Here, to identify mechanisms that sustain tumorigenesis, we performed single-cell RNA-seq of c-Kit+ cells from four primary Dnmt3a;Npm1-mutant AML samples. The most primitive subset of c-Kit+ cells, a multipotent progenitor population Multi-Lin-2, had increased expression of the antioxidant and heavy metal chelator metallothionein 1 (Mt1) in all AML samples. Cas9-mediated Mt1 knockout in primary Dnmt3a;Npm1-mutant AML resulted in reduced cell cycling and proliferation and increased pyroptosis in vitro and increased overall survival following transplant into congenic recipient mice.

overall_design: To investigate the transcriptional differences observed in CRISPR-Cas9 mediated knock-down of Metallothionein 1 (Mt1) in Dnmt3aR878H/+;Npm1cA/+ associated AML in C57BL/6 mice.

first: Patricia

middle: D

last: Colom

first: Nathan

last: Boyer

first: Tim

last: Sterns


title: Dual specificity phosphate 1 (DUSP1) has a key non-invasive predictive marker in preeclampsia

city: Marseille

first: Jonatane

last: Andrieu

address: 14 rue de chanterac

department: Recherche

country: France

institute: ADES EFS CNRS

summary: Preeclampsia (PE) is a multisystem pregnancy complication constituting a major cause of maternal and fetal morbidity and mortality. Factors pointing to a placental origin are the development of the pathology only during pregnancy, and its disappearance in the post-partum period. Our study identified a specific signature of PE including five Gene Ontology clusters including "angiogenesis and differentiation", "cell cycle”, "cell adhesion", "inflammatory response" and "cellular metabolism". Interestingly, we identified DUSP1 as a biomarker of interest in PE. Pregnant women with PE have a higher concentration of DUSP1 in serum in the first trimester of pregnancy compared to healthy donors. Interesting, at a distance from childbirth DUSP1 finds a rate like the control group showing the predictive interest of DUSP1 as a predictive biomarker of PE

overall_design: Here, we aim to identify new early predictive biomarkers based on a transcriptional signature of PE using RNAseq at the time of the event and the disappearance of expression of these markers at a distance from the event in the postpartum

first: Agathe

last: Donet

first: Jean-François

last: Cocallemen

first: Guillaume

last: Charbonnier

first: Noémie

last: Resseguier

first: Julien

last: Paganini

first: Jean-Louis

last: Mège

first: Soraya

last: Mezouar

first: Florence

last: Bretelle


title: Pharmacogenomic synthetic lethal screens reveal hidden vulnerabilities and new therapeutic approaches for treatment of NF1-associated tumor

status: Public on Mar 21 2024

city: Minneapolis

first: David

last: Largaespada

state: MN

address: 515 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

summary: Neurofibromatosis Type 1 (NF1) is a common cancer predisposition syndrome, caused by heterozygous loss of function mutations in the tumor suppressor gene NF1. Individuals with NF1 develop benign tumors of the peripheral nervous system (neurofibromas), originating from the Schwann cell linage after somatic loss of the wild type NF1 allele, some of which progress further to malignant peripheral nerve sheath tumors (MPNST). There is only one FDA approved targeted therapy for symptomatic plexiform neurofibromas and none approved for MPNST. The genetic basis of NF1 syndrome makes associated tumors ideal for using synthetic drug sensitivity approaches to uncover vulnerabilities. We developed a drug discovery pipeline to identify therapeutics for NF1-related tumors using isogeneic pairs of NF1 proficient and deficient immortalized human Schwann cells. We utilized these in a large-scale high throughput screen (HTS) for drugs that preferentially kill NF1 deficient cells, which identified 23 compounds capable of killing NF1 deficient Schwann cells with selectivity. Multiple hits from this screen clustered into classes defined by method of action. Four clinically interesting drugs from these classes were tested in vivo using both a genetically engineered mouse model of high-grade peripheral nerve sheath tumors and human MPNST xenografts. All trugs tested showed single agent efficacy in these models as well as significant synergy when used in combination with the MEK inhibitor selumetinib. This HTS platform has yielded novel therapeutically relevant compounds for the treatment of NF1-associated tumors and can serve as a tool to rapidly evaluate new compounds and combinations in the future.

overall_design: To understand the transcriptional response to a variety of drug treatments in MPNST cells, we treated S462TY cells with a variety of drug treatments and combinations. RNAseq was captured at both 2 hour and 24 hour timepoints for Digoxin, Rigosertib, and Selumetinib, as well as combinations of Digoxin with Selumetinib and Rigosertib with Selumetiinib. DMSO (vehicle) controls were captured for both time points. Untreated cell line controls were captured at 0, 2, and 24 hour timepoints.

first: Kyle

middle: B

last: Williams

first: Tyler

last: Jubenville


title: Differential expression of Pseudomonas fluorescens SBW25 during growth using glucose or MHPP as carbon sources

status: Public on Mar 22 2024

city: Richland

first: Joshua

last: Elmore

state: WA

address: 902 Battelle Blvd

institute: PNNL

summary: Identify genes involved in catabolism of the compound Methyl 3-(4-hydroxyphenyl)propionate

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Pseudomonas fluorescens SBW25 grown on different carbon sources

first: Andrew

last: Wilson


title: Multiomic Single Cell Sequencing Identifies Stemlike Nature of Mixed Phenotype Acute Leukemia and Provides Novel Risk Stratification  [normal bone marrrow PIP-Seq]

status: Public on Mar 13 2024

city: San Francisco

first: Catherine

last: Smith

state: California

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

summary: Mixed phenotype acute leukemia (MPAL) also known as acute leukemia of ambiguous lineage (ALAL), is characterized by leukemic blasts with both lymphoid and myeloid cell surface markers.  Here, we use SC multiomic profiling on newly diagnosed MPAL samples to characterize the immunophenotypic, genetic, and transcriptional landscapes of MPAL. This profiling allows us to definitively contradict the paradigm of MPAL as a disease on a continuum with myeloid and lymphoid lineage acute leukemias, and instead identifies MPAL as a distinct, stem-like disease that, unlike other leukemias, cannot be defined by genetics alone. We further describe a stem cell gene expression signature for MPAL that can predict patient survival. These results broaden our understanding of MPAL biology and suggest a path toward novel risk stratification for MPAL. Importantly, these findings have potential to direct treatment and, hopefully, ultimately improve the prognosis of this disease.

overall_design: Samples from 14 adult patients with de novo MPAL were analyzed for single cell DNA, RNA, protein.

first: Cheryl

last: Peretz

first: Vanessa

middle: E

last: Kennedy

first: Anushka

last: Walia

first: Cyrille

last: Delley

last: Koh

first: Elaine

last: Tran

first: Iain

last: Clark

first: Corey

last: Hayford

first: Chris

last: Amato

first: Kristina

middle: M

last: Fontanez

first: Ritu

last: Roy

first: Aaron

last: Logan

first: Alexander

last: Perl

first: Adam

last: Abate

last: Olshen


title: EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [HiC-seq re-analysis]

first: Aurelie

last: Hintermann

type:
Other
Third-party reanalysis

relation:
SubSeries of: GSE250267
Reanalysis of: GSM4724554
Reanalysis of: GSM4724555
Reanalysis of: GSM5344533
Reanalysis of: GSM5344534
Reanalysis of: GSM4625562

overall_design:
To assay chromatin conformation at the hoxDa locus, we reanalysed published HiC-seq sequencing data conducted on wild type zebrafish collected at either 24 hpf (2 samples from GSE156099 and 1 sample from GSE152741) or 48 hpf (2 samples from GSE156099). All individual samples were aggregated into a single interaction matrix.

BioProject accession: PRJNA656767
GEO Sample SRA Runs  BioSample  Title
========== ========  =========  =====
GSM4724554 SRR12435867  SAMN15802270  HiC in zebrafish wild-type embryos at 48hpf, replicate 1
GSM4724555 SRR12435868  SAMN15802269  HiC in zebrafish wild-type embryos at 48hpf, replicate 2
GSM5344533 SRR14670388  SAMN19372006  HiC in zebrafish wild-type embryos at 24hpf, replicate 1
GSM5344534 SRR14670389  SAMN19372005  HiC in zebrafish wild-type embryos at 24hpf, replicate 2

BioProject accession: PRJNA640313
GEO Sample SRA Runs  BioSample  Title
========== ========  =========  =====
GSM4625562 SRR12044304,SRR12044305,SRR12044306,SRR12044307,SRR12044308,SRR12044309 SAMN15314075  WT_ZF_Embryos_24hpf

Please see more details in the 're-analysis_readme.txt'.

first: Aurélie

first: Chase

last: Bolt

first: Lucille

last: Lopez-Delisle

first: Sandra

last: Gitto

first: Bénédicte

last: Mascrez

first: Denis

last: Duboule


title: A common polymorphism in the Intelectin-1 gene influences mucus plugging in severe asthma

status: Public on Apr 04 2024

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

institute: National Jewish Health

summary: By incompletely understood mechanisms, type 2 (T2) inflammation present in the airways of severe asthmatics drives the formation of pathologic mucus which leads to airway mucus plugging. Here we investigate the molecular role and clinical significance of intelectin-1 (ITLN-1) in the development of pathologic airway mucus in asthma. Through analyses of human airway epithelial cells we find that ITLN1 gene expression is highly induced by interleukin-13 (IL-13) in a subset of metaplastic MUC5AC+ mucus secretory cells, and that ITLN-1 protein is a secreted component of IL-13-induced mucus.  Additionally, we find ITLN-1 protein binds the C-terminus of the MUC5AC mucin and that its deletion in airway epithelial cells partially reverses IL-13-induced mucostasis. Through analysis of nasal airway epithelial brushings, we find that ITLN1 is highly expressed in T2-high asthmatics, when compared to T2-low children.  Furthermore, we demonstrate that ITLN1 gene expression is significantly reduced and ITLN-1  protein expression is lost through a common genetic variant that is associated with protection from the formation of mucus plugs in T2-high asthma. This work identifies one of the first biomarkers and targetable pathways for the treatment of mucus obstruction in asthma.

overall_design: Bronchial cells were dissociated from the bronchial airway brushes from 2 asthmatic children using Bacillus licheniformis cold active protease (10mg/ml), EDTA (0.5mM), and EGTA (0.5mM) at 4°C with vortex mixing, followed by enzyme neutralization with FBS.  Red blood cell lysis was performed and cells were washed twice in 0.04% BSA/PBS prior to targeted capture for scRNA-seq.

first: Jamie

last: Everman

first: Satria

middle: P

last: Sajuthi

first: Maude

last: Liegeois

first: Erik

middle: H

last: Collet

first: Michael

last: Peters

first: Maurizio

last: Chioccioli

first: Camille

last: Moore

first: Bhavika

last: Patel

last: Dyjack

first: Roger

last: Powell

first: Cydney

last: Rios

middle: T

last: Montgomery

first: Celeste

last: Eng

first: Jennifer

middle: R

last: Elhawary

first: Angel

last: Mak

first: Donglei

last: Hu

first: Scott

last: Huntsman

last: Salazar

first: Luigi

last: Feriani

first: Ana

last: Fairbanks-Mahnke

first: Gianna

last: Zinnen

first: Cole

last: Michel

first: Joe

last: Gomez

first: Xing

last: Zhang

first: Vivian

last: Medina

first: Hong

middle: W

last: Chu

first: Pietro

last: Cicuta

first: Victor

last: Ortega

first: Nichole

last: Reisdorph

first: Eleanor

last: Dunican

first: Monica

last: Tang

first: Brett

last: Elicker

first: Travis

last: Henry

first: Eugene

last: Bleecker

first: Mario

last: Castro

first: Serpil

last: Erzurum


title: Transcriptomic and V(D)J profiling at the single cell level of plasmablasts from lymph nodes of mice immunized with bMOG protein

status: Public on Mar 04 2024

city: Quebec

first: Luc

last: Vallières

state: Quebec

address: 2705 Laurier Boulevard

department: Neuroscience

country: Canada

institute: University Hospital Center of Quebec – Laval University

summary: Autoantibodies contribute to many autoimmune diseases, yet there is no therapy to neutralize them selectively. A popular mouse model, experimental autoimmune encephalomyelitis (EAE), could serve to develop such a therapy, provided we can better understand the nature and importance of the autoantibodies involved. In this study, we analyzed autoantibody-secreting extrafollicular plasmablasts in mice with EAE induced by immunization with a mutated myelin oligodendrocyte glycoprotein (MOG) antigen called bMOG. These CD138+ cells were enriched from lymph nodes at day 8 post-immunization and analyzed by single-cell RNA sequencing using 10× Genomics technologies. Here we provide the raw and processed data obtained from the gene expression (GEX) and VDJ cDNA libraries.

overall_design: Single-cell suspensions were prepared from inguinal lymph nodes of mice at day 8 post-immunization with bMOG. CD138+ cells were enriched using the EasySep Mouse CD138 Positive Selection Kit (Stemcell Technologies). Cells were processed with the Chromium Single Cell Chip A and Chromium Controller (10× Genomics) with the goal of analyzing ~6,000 cells per mouse. RNA samples were pooled for reverse transcription and amplification to generate gene expression and V(D)J libraries using the Single Cell 5’ Library Kit and Single Cell V(D)J Enrichment Kit (10× Genomics). Libraries were pooled and sequenced using both Illumina Hiseq 2500 PE100 technology (low pass) at the University Hospital Center of Quebec and Illumina NovaSeq 6000 S4 PE150 technology (high pass) at Genome Quebec. Sequencing results from both technologies were combined for bioinformatics analyses.

first: Catherine

last: Bélanger

first: Juan

last: Dominguez

first: Jacques

last: Corbeil


title: Inheritance of miRNAs via Yolk Promotes Stress Resilience in Progeny [small RNA]

status: Public on Mar 12 2024

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 5eme Etage

department: Development and stem cell biology

institute: Institut Pasteur

type: Non-coding RNA profiling by high throughput sequencing

summary: At the onset of reproduction, oviparous animals synthesize large amounts of yolk in somatic tissues to provide lipids and other nutrients to their progeny. However, whether the yolk transports other types of molecules, such as RNAs with gene regulatory functions, remains largely unexplored. Here, we have biochemically purified the yolk granules in the nematode Caenorhabditis elegans and show they contain microRNAs (miRNAs). We provide evidence that the yolk transports such miRNAs from the mother’s intestine to the embryos via the lipoprotein yolk receptor RME-2. These yolk-enriched miRNAs inherited by the embryos regulate the transcriptomes of developing larvae. Moreover, environmental stresses and maternal age modulate the transfer of yolk-enriched miRNAs, contributing to stress resilience benefits to progeny. This discovery establishes a novel paradigm in intergenerational gene regulation, where the gut-germline axis orchestrates the transmission of environmental cues through yolk-enriched miRNAs. Our work reveals a new mechanism underlying the soma-to-germline transfer of epigenetic information in animals.

overall_design:
small RNA sequencing profiles of sorted yolk by VIT-2::GFP and 2-cell embryos under different conditions of growth and genotypes.
RNA sequencing profiles of 2-cell embryos or freshly hatched L1 larvae.

first: Névé

last: Aupérin

first: Meetali

last: Singh

first: Loan

last: Bourdon

first: Almira

last: Chervova

first: Julie

last: Ovieve

first: Pierre-Henri

last: Commere

first: Hélène

last: Lopez-Maestre

first: Florent

last: Dingli

first: Damarys

last: Loew


title: Inheritance of miRNAs via Yolk Promotes Stress Resilience in Progeny

overall_design: RNA sequencing profiles of 2-cell embryos or freshly hatched L1 larvae.


title: EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [cHiC]

first: Aurelie

last: Hintermann

overall_design: To assay chromatin conformation at the HoxD locus, we conducted capture HiC-seq experiments. We collected urogenital sinuses separately from male and female wild type E18.5 mice. Samples were processed as described in 10.1371/journal.pbio.3000004.

first: Aurélie

first: Chase

last: Bolt

first: Lucille

last: Lopez-Delisle

first: Sandra

last: Gitto

first: Bénédicte

last: Mascrez

first: Denis

last: Duboule


title: Resistance to Naïve and Formative Pluripotency Conversion in RSeT Human Embryonic Stem Cells

status: Public on Mar 07 2024

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 35/GF-127, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: One of the most important properties of human embryonic stem cells (hESCs) is related to their primed and naïve pluripotent states. Our previous meta-analysis indicates the existence of heterogeneous pluripotent states derived from diverse naïve protocols. In this study, we have characterized a commercial medium (RSeT)-based pluripotent state under various growth conditions. Notably, RSeT hESCs can circumvent hypoxic growth conditions as required by naïve hESCs, in which some RSeT cells (e.g., H1 cells) exhibit much lower single cell plating efficiency, having altered or much retarded cell growth under both normoxia and hypoxia. Evidently, hPSCs lack many transcriptomic hallmarks of naïve and formative pluripotency (a phase between naive and primed states). Integrative transcriptome analysis suggests our primed and RSeT hESCs are close to the early stage of post-implantation embryos, similar to the previously reported primary hESCs and early hESC cultures. Moreover, RSeT hESCs did not express naïve surface markers such as CD75, SUSD2, and CD130 at a significant level. Biochemically, RSeT hESCs exhibit a differential dependency of FGF2 and co-independency of both Janus kinase (JAK) and TGFβ signaling in a cell-line-specific manner. Thus, RSeT hESCs represent a previously unrecognized pluripotent state downstream of formative pluripotency. Our data suggest that human naïve pluripotent potentials may be restricted in RSeT medium. Hence, this study provides new insights into pluripotent state transitions in vitro.

overall_design: There were 24 hESC samples, representing three different hESC lines (H1, H7, H9), cultured in hESC medium (Primed) and RSeT medium under normoxia or hypoxic growth condition.

first: Kevin

middle: G

last: Chen

first: Kyeyoon

last: Park

first: Forest

last: Yang

first: Yang

last: Fann

first: Pamela

last: Robey

first: Barbara

middle: S

last: Mallon


title: Sequential transcriptional waves and NFκB-driven chromatin remodeling direct drug-induced dedifferentiation in cancer

status: Public on Feb 13 2024

city: Seattle

first: Wei

last: Wei

address: 401 Terry Ave N

institute: INSTITUTE FOR SYSTEMS BIOLOGY

overall_design: Refer to individual Series


title: The stem cell-type transcriptome of bioenergy sorghum reveals the spatial regulation of secondary cell wall networks

status: Public on Feb 09 2024

city: Urbana

first: Amy

last: Marshall-Colon

state: IL

address: 1201 W Gregory Drive

department: Plant Biology

institute: University of Illinois

summary: Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum’s 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type specific gene regulatory networks (GRNs) revealed that unique TF families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with a stem developmental transcriptome dataset to identify the GRN that differentially activates the secondary cell wall (SCW) formation in stem xylem sclerenchyma and epidermal cells. The cell-type transcriptomic dataset provides a valuable source of information about the function of sorghum stem cell types and GRNs that will enable the engineering of bioenergy sorghum stems.

overall_design: 5 individual tissues isolated using laser capture microscopy (LCM), plus bulk stem, 4 replicates each.

first: Jie

last: Fu

first: Brian

last: McKinley

first: Brandon

last: James

first: William

last: Chrisler

first: Lye

last: Markillie

first: Matthew

last: Gaffrey

first: Hugh

last: Mitchell

first: Ka

last: Yu

first: Galya

last: Orr

first: Kankshita

last: Swaminathan

first: John

last: Mullet


title: Combined Dietary and Pharmacological Depletion of Polyamines Targets Oncogenic Translation in Neuroblastoma

city: Zurich

first: Sarah

last: Cherkaoui

address: August-Forel-Strasse 51

department: Oncology

institute: University Children's Hospital Zurich

summary: Cancer growth is fueled by nutrients obtained from circulation and local biosynthesis. Isolating and exploiting tumoral nutrient dependencies to potentiate current anti-cancer therapies is undergoing active research. We used unbiased metabolomics on patient samples and identified reprogramming of the arginine-proline-glutamine axis in MYCN amplified neuroblastoma. Tumoral acquisition of these non-essential amnio acids, as revealed by stable isotope tracing, was primarily by import, while extra-tumoral deamination of arginine indirectly feeds tumor ornithine via circulation. Dietary depletion of proline and arginine reduced systemic ornithine, the direct precursor of polyamine biosynthesis, and in combination with the clinically approved polyamine biosynthesis inhibitor, difluoromethylornithine, enhanced their depletion to improve survival in a MYCN-driven neuroblastoma mouse model. Mechanistically, ribosome profiling indicated specific translation defects, with ribosomal pausing at adenine-ending codons, to cause reprogramed protein biosynthesis affecting cell cycle and inducing neuronal differentiation. This work provides proof of concept for combined small molecule and nutrient depletion therapy for simultaneous targeting of translation in cancers dependent on external nutrient uptake.

overall_design: Assessment of translation of tumors through ribosome profiling and transcriptomics. Each sample are taken from tumor found from TH-MYCN mice under pharmacological and dietary intervention. Each sample represents a different mouse. Control samples are the mice with a defined control diet (CD) and no pharmacological treatment.

first: George

last: Allen

first: Olesya

middle: O

last: Panasenko

first: Raphael

last: Morscher


title: EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [CUT&RUN]

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

institute: University of Geneva

summary: The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. In tetrapods, posterior Hoxd genes transcription in digits is controlled by a well-characterized series of enhancers forming a large regulatory landscape, which has its syntenic counterpart in zebrafish. We show here that the deletion of the orthologous landscape in fishes does not affect the transcription of these genes in fin buds. Instead, it abrogates hoxd expression in the cloaca, an essential structure related to the mammalian uro-genital sinus. We also report that Hoxd gene function in the mammalian uro-genital sinus depends on enhancers located in the same regulatory landscape and thus conclude that an ancestral Hox ‘cloacal’ regulation was co-opted, in tetrapod, as a playground to subsequently accompany the evolution of both external genitals and digits regulatory landscapes, along with the emergence of these developmentally and phylogenetically related structures.

overall_design: CUT&RUN experiments against histone marks, in wild type 16hpf zebrafish posterior trunk. Samples were processed according to (10.1038/nprot.2018.015)

first: Aurélie

first: Chase

last: Bolt

first: Lucille

last: Lopez-Delisle

first: Sandra

last: Gitto

first: Bénédicte

last: Mascrez

first: Denis

last: Duboule


title: Persistent Neurological Deficits in Mouse PASC Reveal Antiviral Drug Limitations

status: Public on Feb 23 2024

city: IOWA CITY

first: Abhishek

middle: K

last: Verma

state: IA

address: 3-730, Bowen Science Building, 51 Newton Road

department: Department of Microbiology and Immunology

institute: The University of Iowa

summary: PASC (Post-Acute Sequelae of COVID-19) involves many organs, including most prominently the central nervous system. Most studies of PASC in laboratory animals were performed in the context of mild disease, but higher PASC prevalence is observed in patients with severe disease.    Here, to investigate the basis of chronic neurological disease, we infected mice with mouse-adapted SARS-CoV-2 that causes severe respiratory disease but does not infect the brain. We assessed long-term effects on olfactory and substantia nigra (SN) function. While anosmia resolved within a few days, we observed long term loss of tyrosine hydroxylase (TH) expression in the olfactory bulb glomeruli, indicating chronically altered function of olfactory sensory neurons. These changes were accompanied by increased inflammation suggesting the involvement of the host immune response in anosmia-related changes. We also observed decreased neurotransmitter expression in the substantia nigra (SN) accompanied by increased levels of proinflammatory cytokines and neurobehavioral changes. Microglia have been implicated in long term changes in SARS-CoV-2 infected mice and in human neurodegenerative disease. RNAseq analysis of mouse brain microglia isolated several months after infection demonstrated key roles for these cells in ongoing pathogenesis. Finally, we showed that early treatment with antivirals (nirmatrelvir and molnupiravir) reduced virus titer and inflammation in the lung but did not prevent neurological abnormalities. Together these results show that these mice will be useful for probing the role of SARS-CoV-2 in the development of neurodegenerative disease, an aspect of disease not amenable to study in patients and that neurological PASC is not ameliorated by anti-viral therapy.

overall_design: Comparative gene analysis between Mock and 100dpi mouse brain CD11b+ cells

first: Stanley

last: Perlman

first: Juan

last: Abrahante Lloréns


title: 5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma

status: Public on Feb 01 2024

city: Chicago

first: Mark

last: Applebaum

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

institute: University of Chicago

summary:
Purpose: Neuroblastoma is the most common extracranial solid tumor in childhood. We previously showed that circulating cell-free DNA (cfDNA) and tumor biopsy derived 5-hydroxymethylcytosime (5-hmC) profiles identified patients with neuroblastoma who experienced subsequent relapse. Here, we hypothesized that 5-hmC modifications selectively enriched in cfDNA compared with tumor biopsy samples would identify epigenetic changes associated with aggressive tumor behavior and identify novel biomarkers of outcome in patients with high- risk neuroblastoma.

Methods: 5-hmC profiles from cfDNA (n = 64) and tumor biopsies (n = 48) were compared. Two neuroblastoma cell lines underwent chromatin immunopre- cipitation followed by sequencing (ChIP-Seq) for H3K27me3, H3K4me3, and H3K27ac; kethoxal-associated single-stranded DNA sequencing; hmC-Seal for 5-hmC; and RNA-sequencing (RNA-Seq). Genes enriched for both H3K27me3 and H3K4me3 in the included cell lines were defined as bivalent. Using bivalent genes defined in vitro, a bivalent signature was established in three publicly available cohorts of patients with neuroblastoma through gene set variation analysis. Differences between tumors with high or low bivalent signatures were assessed by the Kaplan-Meier method and Cox proportional hazards models.

Results: In cfDNA compared with tumor biopsy derived 5-hmC profiles, we found in- creased 5-hmC deposition on Polycomb Repressive Complex 2 target genes, a finding previously described in the context of bivalent genes. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogeneous neuroblastoma cell lines. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in patients with high-risk neuroblastoma.

Conclusion: Low expression of bivalent genes is a biomarker of worse outcome in patients with high-risk neuroblastoma.

overall_design: This SuperSeries is composed of the SubSeries listed below; refer to individual Series


title: Machine-learning model based on glycosyltransferase expression predicts multiple cancer types, subtypes and survival probability

status: Public on Feb 03 2024

city: Thuwal

first: Jing

last: Kai

address: King Abdullah University of Science and Techonology

department: Biological and Environmental Science and Engineering Division

country: Saudi Arabia

summary: Whereas current tools for diagnosing cancer focus on identifying markers in limited types of the disease, such as the PAM50 kit known primarily for subtyping breast cancer, our research reveals that 27 different cancers have a unique glycosyltransferase (GT) fingerprint that can be detected using a single test, with 93.7% accuracy in external validation. Four models were built on the expression patterns of 71 GTs that are universally influential in inducing the formation of cancer cells and giving them the impetus to metastasize. The first differentiates cancer tissue from normal tissue, the second distinguishes cancer types, and the third and fourth models differentiate between subtypes of cancer, in particular breast cancer and glioma. Data from the Cancer Genome Atlas database were used for deriving the models, while independent publicly available databases and newly collected patient samples were used for validation. Running these models against external databases showed just how powerful they are, producing results that were highly comparable to those achieved in internal testing. Furthermore, the breast cancer classifier differentiated between breast cancer subtypes with an average of 81% accuracy in external testing, far surpassing the industry-standard PAM50’s accuracy ratio of 43%. Meanwhile, a separate prognostic model designed to predict the probability of survival among glioma patients achieved high accuracy by zooming in on four GT genes that are strongly related to prognosis. Taken together, the models demonstrate the revolutionary potential of focusing on GT genes to simplify cancer diagnostics.

overall_design:
To establish the reproducibility and verify the effectiveness of our models, we sought external validation using collected patient tissues.
We isolated the mRNA from 57 fresh and frozen patient tissue samples, both with and without cancer across six different tissue types: breast tissues (23), colon/rectum tissues (10), kidney tissues (8), brain tissues (7), liver tissues (6), and uterine tissues (3).
RNA-seq data of patient samples were used to test the clinical values of our models

first: Jasmeen

last: Merzaban

first: Abdulghani

middle: A

last: Nafisah

first: AlFadel

last: AlShaibani

first: Ali

last: Alzahrani


title: Dynamic changes of macrophage polarization during Salmonella infection in zebrafish

status: Public on Jan 25 2024

city: Montpellier

first: Mai-Eva

last: Nguyen-chi

address: Pl. Eugène Bataillon

institute: CNRS

summary:
To investigate the polarization status of macrophages during salmonella persistent infection we established a model of Salmonella enterica serovar Thyphimurium infection in the zebrafish larva in which salmonella survive long term inside the host. In this model, during initial stages of the infection, macrophages are recruited to the infection site and express tnfa. By contrast, in the late stages of the infection, macrophages form clusters at the infection site and do not express tnfa.
The objective is to characterize the transcriptional profile of macrophages in early stage of infection (4 hours post-infection) and late stage of infection (4 days post-infection).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for macrophages from Salmonella infected larvae at 4 hours post-infection (4 replicates) and 4 days post-infection (4 replicates). Controls are macrophages from non-infected larvae at 4 hours post-infection (4 replicates) and 4 days post-infection (3 replicates).

first: Jade

last: Leiba

first: Christina

last: Begon-Pescia

first: Mai

last: Nguyen-Chi


title: Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils [Hi-C]

status: Public on Jan 30 2024

city: Bunkyo-ku

first: Naoko

last: Yokota

state: Tokyo

address: 1-1-1 yayoi

department: Department of Cell and Molecular Biology

institute: The University of Tokyo

summary: The Structural Maintenance of Chromosome (SMC) protein complexes cohesin, condensin and the Smc5/6 complex (Smc5/6) are essential for chromosome function. At the molecular level, these complexes fold DNA by loop extrusion. Accordingly, cohesin creates chromosome loops in interphase, and condensin compacts mitotic chromosomes. However, the role of Smc5/6’s recently discovered DNA loop extrusion activity is unknown. Here, we uncover that Smc5/6 controls the spatial organization of supercoiled chromosomal regions. The results show that Smc5/6 associates with transcription-induced positively supercoiled chromosomal DNA at cohesin-dependent chromosome loop boundaries. Mechanistically, single-molecule imaging reveals that dimers of Smc5/6 specifically recognize the tip of positively supercoiled DNA plectonemes, and efficiently initiates loop extrusion to gather the supercoiled DNA into a large plectonemic loop. Finally, Hi-C analysis shows that Smc5/6 links chromosomal regions containing transcription-induced positive supercoiling in cis. Altogether, our findings indicate that Smc5/6 controls the three-dimensional organization of chromosomes by recognizing and initiating loop extrusion on positively supercoiled DNA.

overall_design: Analysis of chromosome structure by Hi-C in various mutants in Saccharomyces cerevisiae

first: Kristian

last: Jeppsson

first: Biswajit

last: Pradhan

first: Takashi

last: Sutani

first: Toyonori

last: Sakata

first: Miki

middle: U

last: Igarashi

first: Davide

last: Berta

first: Takaharu

last: Kanno

first: Ryuichiro

last: Nakato

first: Katsuhiko

last: Shirahige

first: Eugene

last: Kim

first: Camilla

last: Björkegren


title: Maternal Undernutrition Results in Transcript Changes in Male Offspring that May Promote Resistance to High Fat Diet Induced Weight Gain

status: Public on Jan 04 2024

city: LITTLE ROCK

first: Melanie

last: MacNicol

state: Arkansas

address: 4301 W Markham St

institute: UAMS

summary: Maternal nutrition during embryonic development and lactation influences multiple aspects of offspring health. Using mice, this study investigates the effects of maternal caloric restriction (CR) during mid-gestation and lactation on offspring neonatal development and on adult metabolic function when challenged by a high fat diet (HFD). The CR maternal model produced male and female offspring that were significantly smaller, in terms of weight and length, and females had delayed puberty. Adult offspring born to CR dams had a sexually dimorphic response to the high fat diet.  Compared to offspring of maternal control dams, adult female, but not male, CR offspring gained more weight in response to high fat diet at 10 weeks. In adipose tissue of male HFD offspring, maternal undernutrition resulted in blunted expression of genes associated with weight gain and increased expression of genes that protect against weight gain.  Regardless of maternal nutrition status, HFD male offspring showed increased expression of genes associated with nonalcoholic liver disease (NAFLD). Furthermore, we observed significant, sexually dimorphic differences in serum TSH. These data reveal tissue- and sex-specific changes in gene and hormone regulation following mild maternal undernutrition, which may offer protection against diet induced weight gain in adult male offspring.

overall_design: Male FVB.129P2 mice were singly housed for at least 24 hours prior to mating. Female FVB.129P2 mice were introduced to males in the evening of proestrus (embryonic day -1), which was determined by vaginal cytology. Vaginal plugs were visualized the next morning to confirm that mating occurred. Embryonic day 0 (E0) was established as the day after mating, when the vaginal plug was visualized. On E0, mated females were singly housed and weighed. At E10, females were again weighed to verify pregnancy with an expected 3 g increase in weight from E0. Pregnant females, or dams, received ~25 g of food daily starting at E12 to visually acclimate to receiving less food. Dams were paired into two feeding groups: ad libitum (FED) and 20% calorie restricted (CR20). At E15, the caloric restriction began, with CR20 dams receiving 80% of the food the paired FED dam consumed from the previous day. Food intake was measured daily around 0930. The undernutrition continued until the offspring were euthanized or weaned. There was one exception to this protocol: The day before parturition, the FED dams consumed less than 3 g of food. To prevent CR20 dams from consuming young at any point in the study, 3 g of food was the minimum made available to CR20 dams. Therefore, if the FED dams consumed less than 3 g of food before parturition, available food to undernourished dams was not reduced below 3 g.  Pups were born around E19, with the average litter size being 8±1 pups.

first: Tiffany

last: Miles

first: Melody

middle: L

last: Allensworth-James

first: Angela

last: Odle

first: Ana

last: Silva Moreira

first: Anessa

middle: C

last: Haney

first: Alexandra

middle: N

last: Lagasse

first: Allen

middle: J

last: Gies

first: Stephanie

last: Byrum

first: Angelica

last: Riojas

first: Angus

first: Gwen

last: Childs


title: Anterior Pituitary Transcriptomics Following a High Fat Diet:  Impact of oxidative stress on organelle pathology

summary: Anterior pituitary cells are highly active with regards to protein synthesis and secretion, processes which depend heavily on mitochondrial ATP production and functional endoplasmic reticula.  It is well known that obesity adds an allostatic overload to tissues, requiring them to adapt to inflammation and oxidative stress.  Therefore, we hypothesized that the pituitary is highly vulnerable to the stress of high fat diet-induced weight gain. In this study, we utilized a 10-15 week high fat diet (HFD, 60%) plus a thermoneutral housing paradigm, testing both male and female FVB.129P mice. We quantified serum hormones and cytokines, characterized the metabolic phenotype, and defined changes in the pituitary transcriptome using single-cell RNA-seq. Weight gain was significant by 3 weeks in HFD mice, and by 10 weeks all HFD groups had gained 20 g.  HFD females (15 weeks) had increased energy expenditure and decreased activity. All HFD groups showed increases in serum leptin, Il-6, resistin, MCP-1, and TNFα. HFD males had increased insulin; both HFD males and females had increased TSH, and HFD females had decreased serum prolactin and growth hormone (GH) pulse amplitude.  Pituitary scRNA-seq revealed modest or no changes in pituitary cell gene expression in the different cell types from HFD males after 10 or 15 weeks or HFD females after 10 weeks.  However, females exposed to a HFD for 15 weeks showed significant numbers of differentially expressed genes in lactotropes and stem cells.  Pathway analyses identified a reduction in pathways that supported protein translation, ribosome biogenesis, and oxidative phosphorylation, indicating mitochondrial dysfunction.  Collectively, these studies reveal that pituitary cells from males are more resilient to the oxidative stress of obesity than females and identify the most vulnerable pituitary cell populations in females.

middle: D

first: Alex

first: Victoria

last: Ortega

first: Cole

last: Bolen

first: Jewel

last: Banik

first: Milla

last: Reddick

first: Ashley

last: Herdman

middle: V


title: Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Insights into Type 2 Diabetes Genetics [RNA-seq]

status: Public on Jan 15 2024

city: Farmington

first: Eishani

middle: Kumar

last: Sokolowski

state: CT

address: 263 Farmington Avenue

institute: University of Connecticut Health Center

summary: Endoplasmic reticulum (ER) and inflammatory stress responses are two pathophysiologic factors contributing to islet dysfunction and failure in Type 2 Diabetes (T2D). However, how human islet cells respond to these stressors and whether T2D-associated genetic variants modulate these responses is unknown. To fill this knowledge gap, we profiled transcriptional (RNA-seq) and epigenetic (ATAC-seq) remodeling in human islets exposed to ex vivo ER (thapsigargin) or inflammatory (IL-1β+IFN-γ) stress. 5,427 genes (~32%) were associated with stress responses; most were stressor-specific, including upregulation of genes mediating unfolded protein response (e.g. DDIT3, ATF4) and NFKB signaling (e.g. NFKB1, NFKBIA) in ER stress and inflammation respectively. Islet single-cell RNA-seq profiling revealed strong but heterogeneous beta cell ER stress responses, including a distinct beta cell subset that highly expressed apoptotic genes. Epigenetic profiling uncovered 14,968 stress-responsive cis-regulatory elements (CREs; ~14%), the majority of which were stressor-specific, and revealed increased accessibility at binding sites of transcription factors that were induced upon stress (e.g. ATF4 for ER stress, IRF8 for inflammation). Seventy-six stress-responsive CREs overlapped known T2D-associated variants, including 20 residing within CREs that were more accessible upon ER stress. Among these, we linked the rs6917676 T2D risk allele (T) to increased in vivo accessibility of an islet ER stress-responsive CRE and allele-specific beta-cell nuclear factor binding in vitro. We showed that MAP3K5, the only ER stress-responsive gene in this locus, promotes beta cell apoptosis. Consistent with its pro-apoptotic and putative diabetogenic roles, MAP3K5 expression inversely correlated with beta cell abundance in human islets and was upregulated in beta cells from T2D donors. Together, this study provides new genome-wide insights into human islet stress responses and putative mechanisms of T2D genetic variants.

overall_design: Primary human pancreatic islets from cadaveric organ donors were exposed for 24 hours to thapsigargin (250 nM; ERS) or 0.025% DMSO solvent control or to 25 U/mL of IL1β + 1000 U/mL of IFNγ (R&D Systems; CYT) vs. untreated control. Islet gene expression in these samples was assessed using RNA-seq.

first: Romy

last: Kursawe

first: Vijay

last: Selvam

first: Redwan

middle: M

last: Bhuiyan

first: Asa

last: Thibodeau

first: Chi

last: Zhao

first: Cassandra

last: Spracklen

first: Duygu

last: Ucar

first: Michael

last: Stitzel


title: Ribosome profiling reveals conserved guanosine residues at ribosome pausing sites in Bacillus subtilis [RNA-seq]

status: Public on Jan 01 2024

city: Amsterdam

first: Yaozu

last: Han

address: Science Park 904

country: Netherlands

institute: Unversity Of Amsterdam

summary: Ribosome pausing slows down translation and can affect protein synthesis. Improving translation efficiency can therefore be of commercial value. Here, we investigated the occurrence of ribosome pausing during amylase secretion by the industrial production organism Bacillus subtilis under semi fed-batch fermentation conditions. We first assessed our ribosome profiling setup by inducing ribosome stalling at isoleucine codons using the antibiotic mupirocin, and found a pause preference for isoleucine codons preceded by E and P site codons with guanosine residues in their first nucleotide position. Interestingly, when we applied standard ribosomal profiling conditions we found again an enrichment of guanosine residues in the E and P site of ribosome pause sites, but this time also upstream of the ribosome pause site. This sequence motif deviates from previously described ribosome pausing motifs. For the highly expressed amylase gene amyM several strong ribosome pausing sites were detected, which remained present during the 64-hour long fermentation, and were neither related to rare codons nor to secondary protein structures. When surveying the genome, an interesting finding was the presence of strong ribosome pausing sites in several toxins genes. These potential ribosome stall sites may function in preventing inadvertent activity in the cytosol.

overall_design: To analyze ribosome pausing in B. subtilis under repeated batch conditions, a simple fermentation setup was established by using rich medium to which 1% glucose was added after 16, 40 and 64 h. The culture was grown at 30 °C under continuous shaking, resulting in an OD600 of around 28 units after 64 h (Fig. 1). B. subtilis strain BY212 was used for amyM expression.

first: Biwen

last: Wang

first: Alberto

last: Agnolin

first: Gaurav

last: Dugar

first: Frans

last: Klis

first: Christopher

last: Sauer

first: Paul

middle: I

last: Costea

first: Max

middle: F

last: Felle

first: Mathis

last: Appelbaum

first: Leendert

last: Hamoen


title: Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils.

first: Naoko

last: Yokota

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


title: Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Insights into Type 2 Diabetes Genetics

first: Eishani

last: Sokolowski


title: Harnessing Bronchoalveolar Lavage Metagenomics for Distinguishing Lung Cancer from Pulmonary Infectious Diseases

status: Public on Jan 08 2024

city: Guangzhou

first: Bin

last: Yang

address: Guangzhou 510700

institute: Vision Medicals Co., Ltd.

summary: Recent progress in unbiased metagenomic next-generation sequencing (mNGS) allows simultaneous examination of microbial and host genetic material in a single test. Leveraging affordable bronchoalveolar lavage fluid (BALF) mNGS data, we employed machine learning to create a diagnostic approach distinguishing lung cancer from pulmonary infections, conditions prone to misdiagnosis in clinical settings. This prospective study analyzed BALF-mNGS data from lung cancer and pulmonary infection patients, delineating differences in DNA/RNA microbial composition, bacteriophage abundances, and host responses, including gene expression, transposable element levels, immune cell composition, and tumor fraction derived from copy number variation (CNV). Integrating these metrics into a host/microbe metagenomics-driven machine learning model (Model VI) demonstrated robustness, achieving an AUC of 0.87 (95% CI = 0.857-0.883), sensitivity = 73.8%, and specificity = 84.5% in the training cohort, and an AUC of 0.831 (95% CI = 0.819-0.843), sensitivity = 67.1%, and specificity = 94.4% in the validation cohort for distinguishing lung cancer from pulmonary infections. The application of a rule-in and rule-out strategy-based composite predictive model significantly enhances accuracy (ACC) in distinguishing between lung cancer and tuberculosis (ACC=0.913), fungal infection (ACC=0.955), and bacterial infection (ACC=0.836). These findings highlight the potential of cost-effective mNGS-based analysis as a valuable tool for early differentiation between lung cancer and pulmonary infections, offering significant benefits through a single comprehensive testing.

overall_design: This observational study assessed adults admitted to the First Affiliated Hospital, Zhejiang University School of Medicine, suspected of lung cancer or pulmonary infections. Enrollment occurred between March 8, 2020, and May 27, 2023, for patients aged ≥18, requiring BALF samples within 72 hours of intubation to establish the etiology. Exclusions involved cases with underlying leukemia, no definitive diagnosis post-extensive follow-up, or lacking matching DNA and RNA mNGS data from BALF samples. A total of 123 lung cancer, 279 pulmonary infections including tuberculosis, fungal, and bacterial infections. The diagnosis of lung cancer relies on clinical suspicion and positive laboratory results from tests cytology, flow cytometry and/or tissue biopsy. The diagnosis of pulmonary infections is based on clinical suspicion and determination of the causative pathogen through standard microbiological diagnostics (cultures, antigen/antibody tests, PCR, sequencing).

first: Dongsheng


title: Ribosome profiling reveals conserved guanosine residues at ribosome pausing sites in Bacillus subtilis [Ribo-seq]

middle: W


title: Bulk RNAseq data for bladder cancer specimens [UC cohort]

city: New York

first: Li

address: 1 Gustave L. Levy Pl

institute: Icahn school of medicine at Mount Sinai

summary:
When applying deconvolution methods to bulk RNAseq data, a limitation of most prior studies is the lack of paired scRNA-seq and bulk RNA-seq data from the same samples to serve as ground truth for deconvolution. Our UC cohort, containing matched scRNA-seq and bulk RNA-seq data therefore provided a unique opportunity. (The scRNAseq datasets have been published before [PMID: 32111252 PMID: 36129800 PMID: 36099881 PMID: 33837006 ]. Please see linked manuscript for details)
We assembled a scRNA-seq dataset of 100,667 cells from 30 UC tissue samples (20 unique patients). Bulk RNA sequencing was performed on a subset of patients(14) in the single-cell RNA sequencing cohort due to tissue availability.

overall_design: Bulk RNAseq data for bladder cancer specimens from 14 patients.

first: Sudeh

last: Izadmehr


title: Ribosome profiling reveals conserved guanosine residues at ribosome pausing sites in Bacillus subtilis


title: Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Insights into Type 2 Diabetes Genetics [ATAC-seq]

overall_design: Primary human pancreatic islets from cadaveric organ donors were exposed for 24 hours to thapsigargin (250 nM; ERS) or 0.025% DMSO solvent control or to 25 U/mL of IL1β + 1000 U/mL of IFNγ (R&D Systems; CYT) vs. untreated control.  Whole islet chromatin accessibility from treated vs. respective control cells was determined using ATAC-seq.

first: Romy

last: Kursawe

first: Vijay

last: Selvam

first: Redwan

last: Bhuiyan

first: Asa

last: Thibodeau

first: Chi

last: Zhao

first: Cassandra

last: Spracklen

first: Duygu

first: Michael


title: Effect of SIgA amplification on epithelial cells of small intestine during anti-PD-L1 immunotherapy treatment [Epithelial_cells_RNAseq]

status: Public on Dec 29 2023

city: Bellinzona

first: Fabio

last: Grassi

address: Via Francesco Chiesa 5

institute: Institute for Research in Biomedicine

summary: The gut microbiota is essential for many aspects of host physiology, and locally generated secretory IgA (SIgA) modulates its function. Microbiota community determines the efficacy of immune checkpoint blockade (ICB) in cancer immunotherapy. Extracellular ATP (eATP) released by the microbiota restricts the SIgA repertoire by limiting T follicular helper (Tfh) cells activity in the Peyer’s Patches (PPs) via stimulation of ionotropic P2X7 receptor. Here we show that SIgA amplification by oral administration of the ATP hydrolysing enzyme apyrase corrects enteropathic features of ICB and improves the therapeutic outcome.

overall_design: Epithelial cells were sorted as Zombie- EPCAM+CD45- from the ileum of MC38 tumor-bearing mice treated with anti-PD-L1 or in combination with apyrase at day 12 after tumor injection


title: Characterization of macrophages influence in human melanoma cells

status: Public on Dec 11 2023

city: Madrid

first: Rafael

last: Samaniego

address: Calle Dr Esquerdo 46

country: Spain

institute: Fundación para la Investigación Biomédica del Hospital Gregorio Marañón

summary: Tumor cells attract and dynamically interact with monocytes/macrophages, one of the more abundant cell types in the tumor microenvironment, to subvert their differentiation into tumor associated macrophages (TAMs), which mainly promote immunosuppression and neoplastic progression, but the mechanisms governing their protumoral activity are not completely understood. Thus, identifying molecular pathways promoted by macrophages that could be responsible for immune evasion and tumor malignicity may provide new therapeutic targets to improve the efficacy of immunotherapy of cancer.

overall_design: BLM human melanoma cell line was coculture for 24h with in vitro differentiated macrophages, obtained from CD14+ monocytes isolated from human PBMCs in the presence of GM-CSF or M-CSF for seven days. All samples have been processed in triplicates.

first: Celia

last: Barrio-Alonso

first: Alicia

last: Nieto-Valle

first: Paloma

last: Sánchez-Mateos

first: Elena

last: García-Martínez


title: Sepsis-associated acute kidney injury in mice and humans elicits heterogeneous renal microvascular microRNA responses

status: Public on Dec 31 2023

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

summary: Microvascular endothelial cells play important roles in sepsis-associated acute kidney injury (SA-AKI). In this study, we focused on microvascular microRNAs changes following SA-AKI to identify microRNAs as novel druggable targets and microvasculature-related early biomarkers of SA-AKI. Using small RNA sequencing we identified 40 differentially expressed microRNAs in the renal microvasculature in response to SA-AKI. While the induction of most microRNAs was restricted to a single microvascular compartment, miR-21-5p levels were increased across the renal microvasculature in both mice and humans following SA-AKI. Functional assessment in vitro revealed that inhibition of hsa-miR-21-5p exacerbated endothelial inflammatory activation, suggesting a protective role of this microRNA in endothelial cells. Furthermore, patients with SA-AKI exhibited elevated hsa-miR-21-5p levels in plasma compared with critically ill sepsis patients without AKI. These results highlight the potential of hsa-miR-21-5p and other microRNAs as therapeutic targets and biomarkers in SA-AKI.

overall_design: MicroRNA analysis in microvascular compartments from mouse kidney cortex (arterioles, glomeruli, peritubular capillaries, post-capillary venules) to reveal altered microRNA transcription in response to sepsis-induced acute kidney injury

first: Matthijs

last: Luxen

first: Tamar

last: van der Aart

first: Rianne

last: Jongman

first: Peter

last: Zwiers

first: Jill

last: Moser

first: Marianne

last: Pultar

first: Susanna

last: Skalicky

first: Hjalmar

middle: R

last: Bouma

first: Jacqueline

last: Koeze

first: Matthias

last: Hackl

first: Grietje

last: Molema

first: Matijs

last: van Meurs


title: Sepsis-Associated Coagulation and Inflammation are Differentially Regulated in Renal Microvascular Beds

overall_design: Refer to individual Series


title: Transcriptomic profiling of human AML cell lines and primary AML samples

status: Public on Jan 14 2024

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

summary:
We sequenced mRNA from both cell lines and primary samples to investigate transcriptomic profiles of human AML cell lines and primary samples.
We then performed gene expression profiling analysis using data obtained from RNA-seq of AML cell lines and primary samples that have sphingolipidomic characterization to identify transcriptional differences between two distinct sphingolipidomic subtypes in AML samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human AML cell lines and primary samples that belonged to two distinct sphingolipidomic subtypes.

first: B

last: Paudel

first: Francine

last: Garrett-Bakelman

first: David

last: Feith


title: Pan-cancer analysis of pyrimidine metabolism using pathway-based approach unravels complex signaling pathways connections with a role in chemoresistance

status: Public on Dec 04 2023

city: Odense

first: Paolo

last: Ceppi

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: To investigate the effect of DHODH inhibitor, Brequinar (BRQ), in inhibiting the pyrimidine metabolism and its associated signaling pathways, lung cancer cell line (A549) was treated with BRQ for 72 hours and performed gene expression profiling using RNA-seq.

overall_design: Differential gene expression analysis for A549 cells treated with BRQ and control cells at 72 hours in replicates.

first: Vignesh

last: Ramesh

first: Luisa

last: Pinna


title: Epigenetics of Yakutia and Central Russia regions

status: Public on Dec 14 2023

city: Nizhny Novgorod

first: Alena

last: Kalyakulina

address: Gagarin avenue, 23

country: Russia

institute: Lobachevsky State University

summary:
Lobachevsky University DNAm dataset. Whole blood DNA Methylation (EPIC) profiles from healthy samples from two regions: central Russia (131 samples) and Yakutia (114 samples) obtained in the Laboratory of System Medicine for Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Russia
Dataset contains DNAm data from 245 healthy control samples from two regions: central Russia (131) and Yakutia (114). The following characteristics are available for all samples: sex, age, region. Healthy participants in the central Russia region were recruited in 2019–2022. Yakutian participants we recruited in 2022. All measurements were performed at the Laboratory of System Medicine for Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Russia.

overall_design: Genome-wide DNA methylation in whole blood from 245 participants was assessed with the HumanMethylationEPIC BeadChip array

first: Igor

last: Yusipov

first: Elena

last: Kondakova

first: Raisa

last: Zakharova

first: Tatiana

last: Sivtseva

first: Claudio

last: Franceschi

first: Maria

last: Vedunova

first: Mikhail

last: Ivanchenko


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [RNA-Seq 3]

status: Public on Nov 20 2023

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

summary: A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific assembly of chromatin that supercedes these constraints is required to configure the genome to support the gene expression changes that guide faithful lineage progression. Using loss-of-function approaches in B cell precursors in vivo we show that IKAROS assembles interactions between sites often separated by megabase distances to configure a significant fraction of the genome in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries and assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains.In vitro deletion provides temporal resolution to changes in chromatin modifications, loops, and compartmental localization. Gain-of-function experiments in epithelial cells confirm IKAROS’ ability to reconfigure chromatin architecture at multiple scales.  While the compaction of the Igk locus required for genome editing represents a function of IKAROS unique to the lymphoid system, the more general function of this lineage-defining DNA binding protein to preconfigure the genome to support lineage specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction.

overall_design: We performed in situ Hi-C in wild-type and IkE5Δ/Δ large pre-B cells to understand IKAROS’ function in the genome organization in early B cell development.

first: Yeguang

last: Hu

first: Daniela

last: Salgado Figueroa

first: Zhihong

last: Zhang

first: Margaret

last: Vaselits

first: Sourya

last: Bhattacharyya

first: Marcus

last: Clark

first: Mariko

last: Kashiwagi

first: Bruce

last: Morgan

first: Ferhat

last: Ay


title: Atlas of subcellular RNA localization in human embryonic stem cells and its flow during differentiation

status: Public on Dec 22 2023

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

summary: The distribution of RNA in human embryonic stem cells (hESC) and the function of RNA localization in maintaining hESC pluripotency and differentiation are currently unknown. Here, by isolating five subcellular components of hESCs and differentiated cells, we uncovered the global subcellular RNA localization in hESC. For protein-coding mRNA, different transcripts of the same gene exhibit an “isoform switch” between subcellular components, which is regulated by localization cis-elements in their variable regions. For noncoding RNA, multiple sequence features such as polyA tail, length, and GC content jointly regulate their subcellular localization. In addition, we found that some developmental genes can be transcribed in advance and confined to chromatin in undifferentiated hESCs. Finally, we revealed significant changes in overall RNA distribution, mapped RNA dynamic localization atlas, and characterized different dynamic RNA localization patterns during hESC differentiation into mesoderm. The multiple RNA localization patterns we revealed will provide some new enlightenment for hESC stemness maintenance and differentiation.

overall_design: RNA localization profiling of RNA-seq data of subcellular components for hESCs and differentiated cells (Day3 and Day5).

first: Fanqi

last: Zhou

first: Puwen

last: Tan

first: Dong

last: Wang

first: Yanni

last: Ma


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [ChIP-Seq 3]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications and transcription factors in wildtype and IkE5Δ/Δ large preB cells


title: ROBO1 deficiency impairs hematopoietic stem progenitor cell self-renewal and erythropoiesis via CDC42 and predicts poor prognosis in MDS

status: Public on Dec 01 2023

city: Shanghai

first: Jiaying

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

summary: We previously identified inactivating mutations in roundabout guidance receptor 1 (ROBO1) in patients with myelodysplastic syndrome (MDS), which was associated with poor prognosis and susceptibility to acute myeloid leukemia (AML) transformation. Nonetheless, the exact role of ROBO1 in hematopoiesis remains poorly delineated. Here we report that the ablation of Robo1 in mice is sufficient to confer MDS-like disease with anemia and multilineage dysplasia. More specifically, Robo1 deficiency impairs the self-renewal and differentiation capacity of hematopoietic stem progenitor cells (HSPCs) and disrupts HSPC pool, especially the reduction of megakaryocyte erythroid progenitors (MEPs), which causes a blockage in the early stages of erythropoiesis in mice. Similarly, Robo1-deficienct HSPCs recapitulated MDS-like disease with anemia and multilineage dysplasia in transplanted mice. Correspondingly, clinical data also reveal that low expression of ROBO1 is associated with shortened survival, severe anemia and a high risk of AML transformation in patients with MDS. Mechanistically, transcriptional profiling indicates that Cdc42, a member of the Rho-GTPase family, serves as a downstream target gene for Robo1 in HSPCs. Overexpression of Cdc42 partially restores the proliferation of erythroid colonies in Robo1 deficient mice. In contrast, Cdc42 inhibitor (CASIN) effectively attenuates the erythroid colony formation of HSPCs. Collectively, our results suggest that Robo1 deficiency may provide a promising therapeutic target against MDS by impairing HSPC self-renewal and erythropoiesis via CDC42, predicting a poor prognosis for severe anemia and a high risk of AML transformation in MDS.

overall_design: Knockout of Robo1 by Mx1-cre in mice after three doses of poly (I:C),

first: Jia-Cheng

last: Jin

first: Bing-yi

last: Chen

first: Lan

first: Ling-yun

last: Wu


title: Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Insights into Type 2 Diabetes Genetics [scRNA-seq]

first: Eishani

last: Sokolowski

summary: Endoplasmic reticulum (ER) and inflammatory stress responses are two pathophysiologic factors contributing to islet dysfunction and failure in Type 2 Diabetes (T2D). However, how human islet cells respond to these stressors and whether T2D-associated genetic variants modulate these responses is unknown. To fill this knowledge gap, we profiled transcriptional (RNA-seq) and epigenetic (ATAC-seq) remodeling in human islets exposed to ex vivo ER (thapsigargin) or inflammatory (IL-1β+IFN-γ) stress. 5,427 genes (~32%) were associated with stress responses; most were stressor-specific, including upregulation of genes mediating unfolded protein response (e.g. DDIT3, ATF4) and NFKB signaling (e.g. NFKB1, NFKBIA) in ER stress and cytokine-induced inflammation respectively. Islet single-cell RNA-seq profiling revealed strong but heterogeneous beta cell ER stress responses, including a distinct beta cell subset that highly expressed apoptotic genes. Epigenetic profiling uncovered 14,968 stress-responsive cis-regulatory elements (CREs; ~14%), the majority of which were stressor-specific, and revealed increased accessibility at binding sites of transcription factors that were induced upon stress (e.g. ATF4 for ER stress, IRF8 for cytokine-induced inflammation). Eighty-six stress-responsive CREs overlapped known T2D-associated variants, including 20 residing within CREs that were more accessible upon ER stress. Among these, we linked the rs6917676 T2D risk allele (T) to increased in vivo accessibility of an islet ER stress-responsive CRE and allele-specific beta cell nuclear factor binding in vitro. We showed that MAP3K5, the only ER stress-responsive gene in this locus, promotes beta cell apoptosis. Consistent with its pro-apoptotic and putative diabetogenic roles, MAP3K5 expression inversely correlated with beta cell abundance in human islets and was induced in beta cells from T2D donors. Together, this study provides new genome-wide insights into human islet stress responses and putative mechanisms of T2D genetic variants.

overall_design: To uncover the transcriptional responses of islets to stress, we procured primary human pancreatic islets from non-diabetic donors and exposed them to a 24-hour treatment with either thapsigargin vs. DMSO (solvent control) or pro-inflammatory cytokines (IL-1β+IFN-γ) vs. untreated (control), respectively.

middle: K

first: Romy

last: Kursawe

first: Vijay

last: Selvam

first: Redwan

last: Bhuiyan

first: Asa

last: Thibodeau

first: Chi

last: Zhao

first: Cassandra

last: Spracklen

first: Duygu

last: Ucar

first: Michael

last: Stitzel


title: Donor regulatory T cells rapidly adapt to recipient tissues to control acute graft-versus-host disease

city: Regensburg

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg


title: Gene expression profile at single cell level of tumor-infiltrating immune cells from mice treated with anti-PD-L1+E.colipBAD28 vs anti-PD-L1+E.colipApyr [CD45positive_TILs_scRNAseq]

first: Fabio

last: Grassi

overall_design: CD45+ cells were immediately sorted from MC38 tumor-bearing mice treated with anti-PD-L1+E.colipBAD28  or anti-PD-L1+E.colipApyr at day 18 from tumor injection and analyzed using scRNA-seq


title: Donor regulatory T cells rapidly adapt to recipient tissues to control acute graft-versus-host disease [scRNA-seq & scTCR-seq]

summary: Adoptive transfer of donor regulatory T cells (Treg) is a promising treatment option for Graft-versus-Host disease (GvHD), but has not yet found its way into routine clinical practice. To map distinctive properties of protective Treg (generated by either polyclonal or allogeneic in vitro expansion), we followed their fate in recipient organs (spleen, liver, colon) in a prophylactic mouse model of MHC-mismatched bone-marrow transplantation (BMT). Using comprehensive gene expression and T cell receptor profiling, we show that both in vitro expansion protocols generated Treg products that preserved hallmark Treg properties,  ameliorated GvHD symptoms, retained their phenotypic plasticity and rapidly acquired organ-specific gene expression profiles after BMT, comparable to their tissue-resident counterparts. When co-transplanted with GvHD-inducing T cells, Treg enabled hallmark suppressive and cytotoxic features, most evidently in the colon. Dominant Treg T cell receptor clonotypes were evenly distributed between organs and across recipients, suggesting a major role of ubiquitous alloantigen-specific Treg in controlling GvHD. Effective protection inversely correlated with the relative abundance of organ-specific Treg, that were transcriptionally distinct, less “activated” and preferentially accumulated in the colon of recipients receiving polyclonally expanded Treg. In summary, we provide a detailed atlas of Treg selection and adaptation in the prophylactic therapy of GvHD.

overall_design: Donor Treg were reisolated from recipient mice in a GvHD model and sequenced (singleCell RNASeq, TCRSeq)

first: David

last: Dittmar

first: Franziska

last: Pielmeier

first: Hanna

last: Stanewsky

first: Nicholas

last: Strieder


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [ChIP-seq LpreB cell]

first: Katia

last: Georgopoulos

first: Yeguang

last: Hu

first: Daniela

last: Salgado Figueroa

first: Zhihong

last: Zhang

first: Margaret

last: Vaselits

first: Sourya

last: Bhattacharyya

first: Marcus

last: Clark

first: Mariko

last: Kashiwagi

first: Bruce

middle: A

last: Morgan

first: Ferhat

last: Ay


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Refer to individual Series

Grant ID:    NIH T32 AI007512
Grant title: Molecular Basis of Allergic and Immunologic Disease
Affiliation: Children's Hospital
Name:        Yeguang Hu


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [RNA-seq HaCaT]

overall_design: We performed RNA-seq in HaCaT keratinocyte cells.  Doxycycline (Dox) was added into the culture medium to a final concentration of 0.1μg/ml to induce the expression of IKAROS (HaCaT_Tet-on_Ik1) or Luciferase (HaCaT_Tet-on_Luc).


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [RNA-seq LpreB]

overall_design: We performed RNA-seq in wild-type and IkE5Δ/Δ large pre-B cells to understand IKAROS’ function in the genome organization in early B cell development.


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [HiChIP_LpreB steady state]

overall_design: We performed HiChIPs for H3K27ac, CTCF, SMC1a and IKAROS in wild-type and IkE5Δ/Δ large pre-B cells to understand IKAROS’ function in the regulatory and structural genomic interactions in early B cell development.


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [HiChIP_HaCaT]

overall_design: We induced ectopic IKAROS expression in HaCaT cells using a Tet-on strategy and performed HiChIPs for H3K27ac and CTCF at different time points to investigate the impact of IKAROS on regulatory and structural chromatin interactions in human skin epithelial cells which normally do not express IKAROS.


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [HiChIP_LpreB_Inducible]

overall_design: We induced IkE5 deletion in established large pre-B cell culture and performed HiChIPs for H3K27ac, SMC1a and CTCF at different time points to investigate the temporal change in regulatory and structural interactions upon IkE5 deletion.


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [ChIP-seq HaCaT]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications and transcription factors in HaCaT cells that express IKAROS or Luciferase


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [HiC_LpreB_Inducible_deletion]

overall_design: We induced IkE5 deletion in established large pre-B cell culture and performed in situ Hi-C at different time points to investigate the temporal changes in genome organization upon IkE5 deletion.


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [Hi-C_HaCaT]

overall_design: We induced IKAROS expression in HaCaT cells using a Tet-on strategy and performed in situ Hi-C at different time points to investigate the impact of IKAROS on genome organization in human skin epithelial cells which normally do not express IKAROS.


title: CD23+IgG1+ memory B cells are poised to switch to pathogenic IgE production in food allergy

status: Public on Nov 16 2023

city: New Haven

first: Hailong

last: Meng

address: 300 George Str

institute: Yale University

summary: Food allergy is caused by allergen-specific IgE but little is known about the B cell memory of persistent responses. Here we describe in pediatric peanut allergy a population of CD23+IgG1 memory B cells that contains peanut-specific clones and generates IgE plasma cells on activation. Through single cell transcriptomics and B cell receptor (BCR) sequencing, we characterized FCER2/CD23+ IgG1 memory B cells co-expressing IL4R, IL13RA1, IGHE and carrying highly mutated BCRs. Further we found that peanut allergen (Ara h 2)-specific B cells were mostly IgG1 memory cells, carried highly mutated BCRs compared to diphtheria toxin-specific B cells, and expressed FCER2 and germlin IGHE. Our findings suggest that CD23+IgG1+ memory B cells transcribing IGHE are a unique memory population containing precursors for pathogenic IgE in food allergy.

overall_design:
Sampling of peanut allergic (PA) and non-allergic, non-atopic (non-PA) subjects

UPDATE: [09-26-2024] The following supplementary files were updated:
GSE208235_bcr_gex.tsv
GSE208235_data_integrated_annotated_clusters_over.rds
GSE208235_filtered_sequences.tsv

first: Maria

last: Lafaille

first: Miyo

last: Ota

first: Kenneth

last: Hoehn


title: An integrative single-cell multiomics profiling of human pancreatic islets identifies T1D associated genes, regulatory regions, and single nucleotide polymorphism [bulk RNA-seq]

status: Public on Nov 13 2023

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: To investigate the mechanism of DLK1 and RASGRP1 knockout in inducing beta cell apoptosis, we performed gene expression profiling analysis using data obtained from RNA-seq of DLK1 WT vs DLK1-/- and RASGRP1 WT VS RASGRP1-/- hPSCs differentiated beta cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DLK1 WT vs DLK1-/- and RASGRP1 WT VS RASGRP1-/- hPSCs differentiated beta cells.

first: Zeping

last: Zhao

first: Tuo


title: An integrative single-cell multiomics profiling of human pancreatic islets identifies T1D associated genes, regulatory regions, and single nucleotide polymorphism

overall_design: Refer to individual Series


title: An integrative single-cell multiomics profiling of human pancreatic islets identifies T1D associated genes, regulatory regions, and single nucleotide polymorphism [ATAC-seq]

summary: To investigate the mechanism of DLK1 and RASGRP1 knockout in inducing beta cell apoptosis, we performed chromatin access profiling analysis using data obtained from ATAC-seq of DLK1 WT vs DLK1-/- and RASGRP1 WT VS RASGRP1-/- hPSCs differentiated beta cells.

overall_design: Comparative chromatin accessibility profiling analysis of ATAC-seq data for DLK1 WT vs DLK1-/- and RASGRP1 WT VS RASGRP1-/- hPSCs differentiated beta cells.


title: CircRNA profile of renal cortex from mice subjected to cecal ligation and punture compared to control mice

status: Public on Nov 09 2023

city: Zhanjiang

first: Tongtong

last: Ma

state: Guangdong

address: No. 57 South Renmin Avenue

department: Affiliated hospital of Guangdong Medical University

institute: Guangdong Medical University

summary: Sepsis is a complex syndrome characterized by organ dysfunction triggered by dysregulated host response to infection, and the kidney is the most commonly injured organ. To model septic-induced AKI in animal, a well-established mouse model induced by caecal ligation and puncture (CLP) was established.

overall_design: To reveal the dysregulated circRNAs in renal cortex from Sham and CLP mice, we carried out circRNA expression profiling by using circRNA microarray. We collected the renal cortex fom mice subjected to CLP treatment (n=3) and control mice (n=3).


title: Single Cell Transcriptomics of human carotid artery plaques

status: Public on Nov 08 2023

city: München

first: Jessica

last: Pauli

state: Bayern

address: Biedersteiner Str. 29

department: Molecular Vascular Medicine

institute: TUM Universitätsklinikum (Klinikum rechts der Isar)

summary: To profile single-cell transcriptome and analyze the diversity of cell types present in human atherosclerotic tissue specimens (carotid artery, CAR), we carried out scRNA-seq from 10 different patients.

overall_design: scRNA-Seq

first: Lars

last: Maegdefessel

first: Sara

last: Schanda


title: Transcriptome analysis of renal cortex from mice subjected to cecal ligation and puncture compared to control mice [RNA-seq]

overall_design:
To reveal the dysregulated mRNAs in renal cortex from Sham and CLP mice, we carried out global gene expression profiling by using RNA sequencing technology. We collected the renal cortex fom mice subjected to CLP treatment (n=3) and control mice (n=3).
Comparative gene expression profiling analysis of RNA-seq data for CLP mice and control mice.


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [RNA-seq]

status: Public on Nov 04 2023

first: Yi

last: Hu

address: No. 28 Fuxing Rd， Haidian district，Beijing

institute: Chinese PLA General Hospital

summary: we generated ATAC-seq, RNA-seq and high-resolution Hi-C datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells.

overall_design: The mRNA profiles of normal human bronchial epithelial cells and radiation induced lung cancer cells

first: Zhou

last: pingkun

first: Liu

last: qiaowei


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [ATAC-seq]

overall_design: ATAC-Seq profiles of normal human bronchial epithelial cells and radiation induced lung cancer cells


title: RNA-seq data of 5D4- or Calcein AM-treated MDA-MB-468

status: Public on Oct 23 2023

city: Houston

first: Weei-Chin

last: Lin

state: TX

address: R410, One Baylor Plaza

department: Medicine and Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Investigate the transcriptomic profiles of 5D4 treatment, Calcein AM treatment, and TopBP1 depletion.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDA-MB-468 cells after 5D4 or Calcein AM treatment or after TopBP1 knockdown. Each condition has four biological replicates.

first: Fang-Tsyr


title: The Essential Role of O-GlcNAcylation in Hepatic Differentiation

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

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


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells.


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [Hi-C]

overall_design: The Hi-C profiles of normal human bronchial epithelial cells and radiation induced lung cancer cells


title: Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus

status: Public on Nov 03 2023

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

institute: Institute of Science and Technology Austria (IST Austria)


title: Genome-wide methylation profiles of post-mortem tissue samples (human) 2

status: Public on Oct 22 2023

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

institute: Seoul National University College of Medicine

type: Methylation profiling by genome tiling array

summary: In this study, 60 post-mortem tissue samples comprising four tissue types (kidney, liver, and lung) were collected from autopsies of 20 Koreans aged 18 to 78. 250 ng of genomic DNA (gDNA) was employed to generate DNA methylation profiles utilizing the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA) at Macrogen Inc. (Macrogen, Seoul, Korea).

overall_design: DNA methylation profiling of sixty post-mortem tissue samples was conducted using the Infinium MethylationEPIC Beadchip array.

first: Jeong Min


title: Genome-wide methylation profiles of post-mortem tissue samples (human) 3

summary: In this study, 60 post-mortem tissue samples comprising four tissue types (dermis, epidermis, and muscle) were collected from autopsies of 20 Koreans aged 18 to 78. 250 ng of genomic DNA (gDNA) was employed to generate DNA methylation profiles utilizing the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA) at Macrogen Inc. (Macrogen, Seoul, Korea).