title: Schlafen 11 triggers innate immune responses through its ribonuclease activity upon detection of single-stranded DNA

status: Public on May 07 2024

city: Beijing

first: De-Pei

last: Liu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

summary: Nucleic acids are major structures detected by the innate immune system. Although intracellular single-stranded DNA (ssDNA) is accumulated during pathogen infection or pathogenesis, it remains unclear whether and how intracellular ssDNA stimulates the immune system. We report that intracellular ssDNA triggers cytokine expression and cell death in a CGT motif-dependent manner. Through a genome-wide CRISPRLCas9 screen, we identified Schlafen-11 (SLFN11), which is essential for the response to endogenous and pathogen ssDNA. SLFN11 directly binds ssDNA containing CGT motifs and translocates to the cytoplasm upon ssDNA recognition. The mice deficient in SLFN9, the homologue of SLFN11, were resistant to CGT ssDNA-induced inflammation, acute hepatitis and septic shock. This study establishes CGT ssDNA and SLFN11/9 as a novel type of immunostimulatory nucleic acids and pattern recognition receptors, respectively.

overall_design: To investigate and compare the immunostimulatory potential of intracellular single-stranded oligodeoxynucleotides (ODNs), human umbilical vein endothelial cells (HUVECs) and human promyelocytic leukemia cells (HL60) were transfected with either control ODN (ODN60rc), CGT ODN (ODN60), poly(I:C), or poly(dA:dT) at a concentration of 1 μg/mL for 18 hours. Subsequently, RNA was extracted for RNA-Seq analysis.

first: Peng

first: Depei


title: Shared patterns of glial transcriptional dysregulation link Huntington's disease and schizophrenia

status: Public on May 08 2024

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

country: USA

institute: University of Rochester Medical Center

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Huntington’s disease (HD) and juvenile-onset schizophrenia (SCZ) have long been regarded as distinct disorders. However, both manifest cell-intrinsic abnormalities in glial differentiation, with resultant astrocytic dysfunction and hypomyelination. To assess whether a common mechanism might underlie the similar glial pathology of these otherwise disparate conditions, we utilized comparative correlation network approaches to analyze RNA-seq data from human glial progenitor cells (hGPCs) produced from disease-derived pluripotent stem cells. We identified gene sets preserved between HD and SCZ hGPCs yet distinct from normal controls, that included 174 highly-connected genes in the shared disease-associated network, focused on genes involved in synaptic signaling. These synaptic genes were largely suppressed in both SCZ and HD hGPCs, and gene regulatory network analysis identified a core set of upstream regulators of this network, of which OLIG2 and TCF7L2 were prominent. Among their downstream targets, ADGRL3, a modulator of glutamatergic synapses, was notably suppressed in both SCZ and HD hGPCs. ChIP-seq confirmed that OLIG2 and TCF7L2 each bound to the regulatory region of ADGRL3, whose expression was then rescued by lentiviral overexpression of these transcription factors. These data suggest that the disease-associated suppression of OLIG2 and TCF7L2-dependent transcription of glutamate signaling regulators may impair glial receptivity to neuronal glutamate. The consequent loss of activity-dependent mobilization of hGPCs may yield deficient oligodendrocyte production, and hence the hypomyelination noted in these disorders, as well as the disrupted astrocytic differentiation and attendant synaptic dysfunction associated with each. Together, these data highlight the importance of convergent glial molecular pathology in both the pathogenesis and phenotypic similarities of two otherwise unrelated disorders, HD and SCZ.

overall_design: Refer to individual Series

first: Nguyen

middle: P

last: Huynh

first: Mikhail

last: Osipovitch

first: Rossana

last: Foti

first: Janna

last: Bates

first: Benjamin

last: Mansky

first: Jose

middle: C

last: Cano

first: Abdellatif

last: Benraiss

first: Chuntao

last: Zhao

first: Q

middle: R

last: Lu

middle: A


title: Pre-analytical considerations in quantifying circulating miRNAs that predict end-stage kidney disease in diabetes

city: Boston

first: Eiichiro

last: Satake

state: MA

address: One Joslin Place

department: Genetics and Epidemiology

institute: Joslin Diabetes Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Our previous study identified 8 risk and 9 protective plasma miRNAs associated with progression to end-stage kidney disease (ESKD) in diabetes. This study aimed to elucidate pre-analytical factors that influence the quantification of circulating miRNAs. Using the EdgeSeq platform, which quantifies 2,002 miRNAs in plasma, including ESKD-associated miRNAs, we compared miRNA profiles in whole plasma vs. miRNAs profiles in RNA extracted from the same plasma specimens. Less than half of the miRNAs were detected in standard RNA extracted methods from plasma. Detection of individual and concentrations of miRNAs were much lower when RNA extracted from plasma was quantified by RNA sequencing (RNASeq) or RT-qPCR platforms compared to EdgeSeq. Plasma profiles of miRNAs determined by the EdgeSeq platform had excellent reproducibility in assessment, and had no variation with age, sex, HbA1c, BMI, and cryostorage time. The risk ESKD-associated miRNAs were detected and measured accurately only in whole plasma and using the EdgeSeq platform. Protective ESKD-associated miRNAs were detected by all platforms except RT-qPCR, however, correlations among concentrations obtained with different platforms were weak or non-existent.  In conclusion, pre-analytical factors have a profound effect on detection and quantification of circulating miRNAs in ESKD in diabetes. Quantification of miRNAs in whole plasma and using the EdgeSeq platform may be the preferable method to study profiles of circulating cell-free miRNAs associated with ESKD, and possibly other diseases.

overall_design:
To compare circulating miRNA profiles from plasma with RNA extraction or direct isolation, samples from eight individuals were randomly selected from the Josliln Kidney Study.
miRNA expression profilings were performed by the HTG EdgeSeq miRNA sequence, and RNA sequencing of small RNAs, including SeqMatic and LC Sciences platforms.
Comparisons of the miRNA expression profilings between EdgeSeq and RNA sequencings were performed.

***************************************************************
Raw data file not available because the HTG company went bankrupt
***************************************************************

first: Bozena

last: Krolewski

first: Hiroki

last: Kobayashi

first: Zaipul

middle: I

last: Md Dom

first: Joseph

last: Ricca

first: Jonathan

middle: M

last: Wilson

first: Dave

middle: S

last: Hoon

first: Kevin

middle: L

last: Duffin

first: Marcus

middle: G

last: Pezzolesi

first: Andrzej


title: Proteome-scale tagging and functional screening in mammalian cells by ORFtag [ORFtag]

status: Public on May 10 2024

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

summary: Determining protein function in a systematic and comprehensive manner is a key goal in modern molecular biology research but is challenging with current approaches. Here, we introduce ORFtag, a versatile method for the massively parallel protein tagging and interrogation of protein function at the proteome scale with minimal effort and expense. We demonstrate the versatility of ORFtag in mouse and human cells with a series of functional screens for transcriptional activators, repressors and post-transcriptional gene regulatory proteins.

overall_design: 3 different functional proteome-wide screens were performed using ORFtag in mouse cell lines.

first: Filip

last: Nemčko

first: Moritz

last: Himmelsbach

first: Vincent

last: Loubiere

first: Ramesh

last: Yelagandula

first: Michaela

last: Pagani

first: Nina

last: Fasching

first: Julius

last: Brennecke

first: Ulrich

last: Elling

first: Stefan

last: Ameres


title: KAP1 negatively regulates elongation kinetics to activate signal-induced transcription [ChIP-Seq]

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

summary: Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction are still unfolding. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Unexpectedly, acute KAP1 loss triggers an increase in RNA Polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation and dampening IEG transcription. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.

overall_design: Comparative occupancy of factors for control (DMSO-treated) and KAP1 depletion (dTAG-treated) conditions upon serum starvation: 0 min (SS), and serum replenishment for various time points (15 min, 30 min, 3 hr).

first: Usman

last: Hyder

first: Ashwini

last: Challa


title: The Histone Methyltransferase SUV420H2 Regulates Brown and Beige Adipocyte Thermogenesis (ATAC-Seq)

status: Public on May 09 2024

city: Atlanta

first: Bingzhong

last: Xue

state: GA

address: 50 Decatur St. SE

department: Biology

institute: Georgia State University

summary: Activation of brown adipose tissue (BAT) thermogenesis increases energy expenditure and alleviates obesity. Epigenetic regulation has emerged as a key mechanism underlying BAT development and function. To study the epigenetic regulation of BAT thermogenesis, we surveyed the expression of epigenetic enzymes that catalyze histone modifications in developmental beige adipocytes and found a unique expression pattern of suppressor of variegation 4-20 homolog 2 (Drosophila) (Suv420h2), a histone methyltransferase that preferentially catalyzes the tri-methylation at histone H4 lysine 20 (H4K20me3), a hallmark of gene silencing. Here we discovered that Suv420h2 expression parallels that of UCP1 expression in brown and beige adipocytes and that SUV420H2 knockdown significantly reduces, whereas SUV420H2 overexpression significantly increases UCP1 levels in brown adipocytes. Suv420h2 knockout (H2KO mice exhibit impaired cold-induced thermogenesis and are prone to diet-induced obesity. In contrast, mice with specific overexpression of Suv420h2 in adipocytes display enhanced cold-induced thermogenesis and are resistant to diet-induced obesity. Further study showed that Suv420h2 catalyzes H4K20 trimethylation at eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) promoter, leading to down-regulated expression of 4E-BP1, a negative regulator of the translation initiation complex. This in turn up-regulates PGC1α protein levels, which is associated with increased expression of thermogenic program. We conclude that Suv420h2 is a key regulator of brown/beige adipocyte development and thermogenesis.

overall_design:
Brown fat genomic DNA ATAC-sequencing of 12-week-old WT and AH2Tg mice after 1-day cold exposure
----------------------------------------
Authors state:
The raw data is missing, because the hard drive used to store the raw data was not working, and the sequencing company has already deleted the original data on their server, we could only provide the processed data

first: Hang

last: Shi


first: Steven

last: Goldman

sample_organism:
Homo sapiens
Rattus norvegicus

overall_design: ChIP-seq of TCF7L2 and OLIG2 in human GPCs and HepG2; ChIP-seq of Tcf7l2 in rat glial cells

first: Nguyen

last: Huynh

first: Mikhail

last: Osipovitch

first: Rossana

last: Foti

first: Janna

last: Bates

first: Benjamin

last: Mansky

first: Jose

last: Cano

first: Abdellatif

last: Benraiss

first: Chuntao

last: Zhao

first: Q Richard

last: Lu


title: lncRNA CDKN2B-AS1 regulates collagen expression

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: The long noncoding RNA CDKN2B-AS1 harbors a major coronary artery disease risk haplotype, which is also associated with progressive forms of the oral inflammatory disease periodontitis as well as myocardial infarction (MI). Despite extensive research, there is currently no broad consensus on the function of CDKN2B-AS1 that would explain a common molecular role of this lncRNA in these diseases. Our aim was to investigate the role of CDKN2B-AS1 in gingival cells to better understand the molecular mechanisms underlying the increased risk of progressive periodontitis. We downregulated CDKN2B-AS1 transcript levels in primary gingival fibroblasts with LNA GapmeRs. Following RNA-sequencing, we performed differential expression, gene set enrichment analyses and Western Blotting. Putative causal alleles were searched by analyzing associated DNA sequence variants for changes of predicted transcription factor binding sites. We functionally characterized putative functional alleles using luciferase-reporter and antibody electrophoretic mobility shift assays in gingival fibroblasts and HeLa cells. Of all gene sets analysed, collagen biosynthesis was most significantly upregulated (Padj=9.7x10-5 (AUC>0.65) with the CAD and MI risk gene COL4A1 showing strongest upregulation of the enriched gene sets (Fold change = 12.13, Padj = 4.9 x 10-25). The inflammatory "TNFA signaling via NFKB" gene set was downregulated the most (Padj=1x10-5 (AUC=0.60). On the single gene level, CAPNS2, involved in extracellular matrix organization, was the top upregulated protein coding gene (Fold change=48.5, P<9x10-24). The risk variant rs10757278 altered a binding site of the pathogen responsive transcription factor STAT1 (P=5.8x10-6). rs10757278-G allele reduced STAT1 binding 14.4% and rs10757278-A decreased luciferase activity in gingival fibroblasts 41.2% (P=0.0056), corresponding with GTEx data. CDKN2B-AS1 represses collagen gene expression in gingival fibroblasts. Dysregulated collagen biosynthesis through allele-specific CDKN2B-AS1 expression in response to inflammatory factors may affect collagen synthesis, and in consequence tissue barrier and atherosclerotic plaque stability.

overall_design:
To establish the molecular function of the lncRNA CDKN2B-AS1, we downregulated CDKN2B-AS1 transcript levels in cultures of primary gingival fibroblasts from 3 different donors with LNA GapmeRs. We then performed gene expression profiling by RNA-Sequencing with RNA extracted 48 hours after LNA GapmeR transfection.  3 control samples were transfected with negative control GapmeRs and  matched with the 3 samples that were transfected with LNA GapmeRs that targeted CDKN2B-AS1.  Additionally, we transfected an immortalized (hTERT) human gingival fibroblast cell line (ihGF; Applied Biological Materials Inc, cat.-no T0026) with LNA GapmeRs that targeted CDKN2B-AS1 and with negative control LNA GapmeRs
-------------------------
Authors state "no file provided due to donor privacy concerns".

first: Weiwei

first: Jiahui

last: Song

first: Avneesh

last: Chopra

first: Henrik

last: Dommisch

first: Dieter

last: Beule

first: Arne

last: Schaefer


title: Mate choice in the brain: Species differ in how male traits ‘turn on’ gene expression in female brains

city: University Park

first: Jason

last: Keagy

state: PA

address: 410 Forest Resources Bldg

department: Ecosystem Science and Management

institute: Penn State University

summary: Mate choice plays a fundamental role in speciation, yet we know little about the molecular mechanisms that underpin this crucial decision-making process. Stickleback fish differentially adapted to limnetic and benthic habitats are reproductively isolated and females of each species use different male traits to evaluate prospective partners and reject heterospecific males. Here, we integrate behavioral data from a mate choice experiment with gene expression profiles from the brains of females actively deciding whether to mate. We find substantial gene expression variation between limnetic and benthic females, regardless of behavioral context, suggesting general divergence in constitutive gene expression patterns, corresponding to their genetic differentiation. Intriguingly, female gene co-expression modules covary with male display traits but in opposing directions for sympatric populations of the two species, suggesting male displays elicit a dynamic neurogenomic response that reflects known differences in female preferences. Furthermore, we confirm the role of numerous candidate genes previously implicated in female mate choice in other species, suggesting that evolutionary tinkering with these conserved molecular processes underlies divergent mate preferences and sexual isolation. Taken together, our study adds important new insights to our understanding of the molecular processes underlying female decision-making critical for generating sexual isolation and speciation.

overall_design: Benthic and limnetic threespine sticklebacks were collected from two lakes on Texada Island, British Columbia and transferred to Michigan State University. Each female subject experienced one of three trial conditions: 1) courtship by a male from their lake and species (conspecific courtship), 2) courtship by a male from their lake and the opposite species (heterospecific courtship), or 3) a control in which female subjects were with another female from her same lake and species (social control). Brains were extracted after 20 min or when spawning occured, whichever occured first. Sample size for each treatment for Paxton limnetic, Paxton benthic, and Priest limnetic populations was n = 5-6; Priest benthic fish brains were not sequenced because of low sample siazes and we expected large indiviual variation in transcriptomes.

first: Hans

last: Hofmann

first: Janette

middle: W

last: Boughman


title: Uncoupling Histone Modification Crosstalk by Engineering Lysine Demethylase LSD1 [RNA-seq]

first: Kwangwoon

last: Lee

address: 77 Avenue Louis Pasteur, NRB 164

department: Medicine

institute: Brigham and Women's Hospital

summary: Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation but its functional significance in cells has been difficult to discern.  Prior enzymatic studies have revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine specific demethylase 1 (LSD1). Here we have engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. Y391K LSD1 knockin cells show increased repression of a set of genes associated with cellular adhesion. Chromatin profiling revealed that the cis-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation than the baseline in unedited, parental cells. Y391K LSD1 knockin cells show diminished H3 mono-methyl Lys4 in the vicinity of these silenced genes, consistent with a role for enhanced LSD1 demethylase activity in these regions. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme in gene and chromatin regulation.

overall_design: We performed RNA-Seq to investigate the transcriptomic changes induced by Y391K LSD1 in K562 cells. Y391K LSD1 is a gain-of-function mutant that can overcome H3K14ac-mediated impediment. Parental K562 cells are homozygously edited to express wtLSD1-GFP (C-terminal GFP-tag). Edited K562 cells 1 and 2 are heterozygously edited with Y391K-LSD1, in which two alleles contain Y391K-LSD1-GFP and one allele contain wtLSD1-GFP.

first: Philip

last: Cole


first: Steven

last: Goldman

overall_design: RNAseq analysis of GPCs ans astrocytes derived from CTR, HD, and SCZ patients.

first: Nguyen

last: Huynh

first: Mikhail

last: Osipovitch

first: Rossana

last: Foti

first: Janna

last: Bates

first: Benjamin

first: Abdelatif


title: Nuclear receptor Nur77 and Yin-Yang 1 synergistically increase mitochondrial abundance and activity in macrophages [RNA-seq]

city: London

first: Duco

middle: Steven

last: Koenis

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Mitochondrial biogenesis requires precise regulation of both mitochondrial-encoded and nuclear-encoded genes. Nuclear receptor Nur77 is known to regulate mitochondrial metabolism in macrophages and skeletal muscle cells. Here, we compared genome-wide Nur77 binding site and target gene expression in these two cell types, which revealed conserved roles for this nuclear receptor in the regulation of nuclear-encoded mitochondrial ribosomal proteins (MRP) and enrichment of motifs for the transcription factor Yin-Yang 1 (YY1). We show that Nur77 and YY1 interact, that YY1 increases Nur77 activity, and that their binding sites are co-enriched at MRP gene loci. Nur77 and YY1 co-expression synergistically increases mitochondrial abundance and activity in macrophages but not skeletal muscle. As such, we identify a macrophage-specific Nur77-YY1 interaction that enhances mitochondrial metabolism.

overall_design: Gene expression profiling by RNA-seq was performed in triplicate in C2C12 mouse myoblast stable cell lines with doxycycline-inducible overexpression of HA-tagged NUR77 or GFP as control.

first: Inkie

last: Evers-van Gogh

first: Wilbert

last: Zwart

first: Carlie

middle: J

last: de Vries

first: Eric

last: Kalkhoven


title: Nuclear receptor Nur77 and Yin-Yang 1 synergistically increase mitochondrial abundance and activity in macrophages.

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


title: Nuclear receptor Nur77 and Yin-Yang 1 synergistically increase mitochondrial abundance and activity in macrophages [ChIP-seq]

overall_design: Nur77 binding site profiling by ChIP-seq was performed in triplicate in C2C12 mouse myoblast stable cell lines with doxycycline-inducible overexpression of HA-tagged NUR77.


title: Brd4::Nutm1 fusion gene initiates NUT carcinoma in vivo [RNA-seq]

city: East Lansing

first: Bin

last: Gu

state: MI

address: 755 Woodlot Drive

department: OBGYN

institute: Michigan State University

summary: NUT carcinoma (NC) is an aggressive cancer with no effective treatment.  About 70% of NUT carcinoma is associated with chromosome translocation events that lead to the formation of a BRD4::NUTM1 fusion gene. Because the BRD4::NUTM1 gene is unequivocally cytotoxic when ectopically expressed in cell lines, questions remain on whether the fusion gene can initiate NC. Here, we report the first genetically engineered mouse model (GEMM) for NUT carcinoma that recapitulates the t(15;19) chromosome translocation in mice. We demonstrated that the mouse t(2;17) syntenic chromosome translocation, forming the Brd4::Nutm1 fusion gene, could induce aggressive carcinomas in mice. The tumors present histopathological and molecular features similar to human NC, with an enrichment of undifferentiated cells. Similar to the reports of human NC incidence, Brd4::Nutm1 can induce NC from a broad range of tissues with a strong phenotypical variability. The consistent induction of poorly differentiated carcinoma demonstrated a strong reprogramming activity of BRD4::NUTM1.  The new mouse model provided a critical preclinical model for NC that will lead to better understanding and therapy development for NC.

overall_design: RNA-seq for six oral mNC tumors and six normal oral mucosa samples from the control mice.

first: Dejin

last: Zheng

first: Chenxiang

last: Luo


title: YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RIP-seq)

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

summary: Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding of its impact on a fully efficient DNA damage response remains limited. Here, through a targeted CRISPR-knockout screen, we identified RNA binding proteins and modifiers that participate in mediating the p53 response. Among the top hits, m6A reader YTHDC1 was identified as a master regulator of p53 expression. YTHDC1 binds to the transcription start sites ofTP53and other genes involved in DNA damage response, promoting their transcriptional elongation. YTHDC1 deficiency leads to reducedTP53expression, and also retention of introns leading to aberrant protein production of key DNA damage factors. While intron retention is dependent on m6A, YTHDC1 favoursTP53transcriptionalpause-release independently of m6A. Depletion of YTHDC1 causes genomic instability and aberrant cancer cell proliferation mediated by genes regulated by YTHDC1. Our results uncover YTHDC1 as an orchestrator of the DNA damage response through distinct mechanisms of co-transcriptional mRNA regulation.

overall_design: A CLIP experiment was performed to identify YTHDC1 binding sites

first: Daniel

last: Elvira-Blázquez

first: José

last: Fernández-Justel

first: Aida

last: Arcas

first: Luisa

last: Statello

first: Enrique

last: Goñi

first: Jovanna

last: González

first: Benedetta

last: Ricci

first: Sara

last: Zaccara

first: Ivan

last: Raimondi


title: Selective targeting and modulation of plaque associated microglia via systemic hydroxyl dendrimer administration in an Alzheimer’s disease mouse model.

city: Irvine

first: Kim

last: Green

state: CA

address: 3400 Biological Sciences III

institute: University of California, Irvine

summary: Background: In Alzheimer’s disease (AD), microglia surround extracellular plaques and mount a sustained inflammatory response, contributing to the pathogenesis of the disease. Identifying approaches to specifically target plaque-associated microglia (PAMs) without interfering in the homeostatic functions of non-plaque associated microglia would afford a powerful tool and potential therapeutic avenue. Methods: Here, we demonstrated that a systemically administered nanomedicine, hydroxyl dendrimers (HDs), can cross the blood brain barrier and are preferentially taken up by PAMs in a mouse model of AD. As proof of principle, to demonstrate biological effects in PAM function, we treated the 5xFAD mouse model of amyloidosis for 4 weeks via systemic administration (ip, 2x weekly) of HDs conjugated to a colony stimulating factor-1 receptor (CSF1R) inhibitor (D-45113).  Results: Treatment resulted in significant reductions in amyloid-beta (Aβ) and a stark reduction in the number of microglia and microglia-plaque association in the subiculum and somatosensory cortex, as well as a downregulation in microglial, inflammatory, and synaptic gene expression compared to vehicle treated 5xFAD mice.  Conclusions: This study demonstrates that systemic administration of a dendranib may be utilized to target and modulate PAMs.

overall_design: We took 12-month old WT, WT/D45113, 5xFAD, and 5xFAD/D45113 mice and performed bulk RNA Sequencing on the hippocampi to assess the differences in gene expression between each group


title: Binding Changes in Chromatin Factors Upon Targeted XPO1 Inhibition in T Cells

city: Cleveland

first: Yi Fan

last: Chen

state: OH

address: 2109 Adelbert Road Biomedical Research Building 747A

institute: Case Western Reserve University School of Medicine

summary:
We assessed the chromatin localization of XPO1 and p300 in response to C646 (10 uM), S109 (1 uM), and SP100030 (1 uM).
We used CUT&RUN sequencing as a lower-input (500,000 cells per sample), higher-sensitivity alternative to ChIP-Seq to assess chromatin binding of different factors

overall_design: Differential binding analysis and overlap analysis of XPO1 and p300 at basal conditions (DMSO), activated conditions (50 nM PMA + 1 uM Ionomycin), or activated + small molecule treatment in Jurkat T cells

first: Drew

last: Adams


title: KAP1 regulates elongation kinetics to activate signal-induced transcription

last: D'Orso


title: Single cell discovery of m6A RNA modifications in the hippocampus

first: Magdalena

middle: Justyna

last: Koziol

address: Science Park Road

country: China

institute: Chinese Institute for Brain Researach, CIBR

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is a prevalent and highly regulated RNA modification essential for RNA metabolism and normal brain function. It is particularly important in the hippocampus, where m6A is implicated in neurogenesis and learning. Although extensively studied, its presence and impact in specific cell types remain poorly understood. We investigated m6A in the hippocampus at the single-cell level, revealing a comprehensive landscape of m6A modifications within individual cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We identified m6A RNA sites in bulk RNA sequencing and in single cell data by detecting RNA editing sites that were introduced near m6A sites. We first tested our approach in HEK293T cells, with bulk RNA-seq. We transfected our samples with YTH viruses that caused editing near m6A sites, while YTHmut viruses and APOBEC1 and wild type samples were used as background controls. After we verified this approach in HEK293T cells, we applied it the mouse hippocampus also with bulk RNA-seq. We then performed single cell sequencing to identify m6A sites in single cells by identifying mutations in the sequencing data.  We confirmed our data with m6A-RNA immunoprecipitation and sequencing (m6A-RIP seq).

first: Shuangshuang

last: Feng

first: Maitena

last: Tallaetxe-Abete

first: Yujie

last: Zhang

first: Yan

last: Peng

first: Han

last: Zhou

first: Mingjie

last: Dong

first: Erika

last: Larrea

first: Liang

last: Xue

first: Li


title: A disease similarity approach identifies short-lived Niemann-Pick type C disease mice with accelerated brain aging as a novel mouse model for Alzheimer’s disease and aging research

city: Richmond

first: Vikas

last: Gujjala

state: Virginia

address: 1000 W Cary Street

institute: Virginia Commonwealth University

summary: Since its first description in 1906 by Dr. Alois Alzheimer, Alzheimer’s disease (AD) has been the most common type of dementia. Initially thought to be caused by age-associated accumulation of plaques, in recent years, research has increasingly associated AD with lysosomal storage and metabolic disorders, and the explanation of its pathogenesis has shifted from amyloid and tau accumulation to oxidative stress and impaired lipid and glucose metabolism aggravated by hypoxic conditions. However, the underlying mechanisms linking those cellular processes and conditions to disease progression have yet to be defined. Here, we applied a disease similarity approach to identify unknown molecular targets of AD by using transcriptomic data from congenital diseases known to increase AD risk, namely Down Syndrome, Niemann Pick Disease Type C (NPC), and Mucopolysaccharidoses I. We uncovered common pathways, hub genes, and miRNAs across in vitro and in vivo models of these diseases as potential molecular targets for neuroprotection and amelioration of AD pathology, many of which have never been associated with AD. We then investigated common molecular alterations in brain samples from an NPC disease mouse model by juxtaposing them with brain samples of both human and mouse models of AD. Detailed phenotypic and molecular analyses revealed the NPCmut mouse as a novel, short-lived in vivo model of AD characterized by accelerated brain aging, concluding that the NPCmut mouse model can serve as a potential short-lived in vivo model for AD research and for understanding molecular factors affecting brain aging. This research represents the first comprehensive approach to congenital disease association with neurodegeneration and a new perspective on AD research while highlighting shortcomings and lack of correlation in diverse in vitro models. Considering the lack of an AD mouse model that recapitulates the physiological hallmarks of brain aging, the characterization of a short-lived NPC mouse model will further accelerate the research in these fields and offer a unique model for understanding the molecular mechanisms of AD from a perspective of accelerated brain aging.

overall_design:
To identify novel biomarkers and treatment strategies against AD in the context of congenital disorders with increased AD-risk, we performed commonality analysis on AD and selected congenital disorders (DS, NPC, MPS I) human samples and mice samples from APP/PS1 mice and NPC1KO (NPC model) mice
We compared frontal cortex transcriptomic data from our NPC1KO mice to both APP/PS1 AD mouse frontal cortex transcriptomic data and human AD frontal cortex data

first: Alaattin

last: Kaya


title: Dichotomous transactivation domains contribute to growth inhibitory and promotion functions of TAp73

city: Singapore

first: Kanaga

last: Sabapathy

state: Singapore

address: 60 Nanyang Drive

department: SBS

country: Singapore

institute: Nanyang Technological University Singapore

summary: The transcription factor p73, a member of the p53 tumor-suppressor family, regulates cell death and also supports tumorigenesis, though the mechanistic basis for the dichotomous functions is poorly understood. We report here the identification of an alternate transactivation domain (TAD) located at the extreme carboxyl (C)-terminus of TAp73β, a commonly expressed p73 isoform. Mutational disruption of this TAD significantly reduced TAp73β’s transactivation activity, to a level observed when the amino (N)-TAD that is similar to p53’s TAD is mutated.  Mutation of both TADs almost completely abolished TAp73β’s transactivation activity. Expression profiling highlighted a unique set of targets involved in extracellular matrix-receptor interaction and focal adhesion to be regulated by the C-TAD, resulting in FAK phosphorylation, distinct from the N-TAD targets that are common to p53 and involved in growth inhibition. Interestingly, the C-TAD targets are also regulated by the oncogenic, amino-terminal deficient DNp73β isoform. Consistently, mutation of C-TAD reduces cellular migration and proliferation. Mechanistically, selective binding of TAp73β to DNAJA1 is required for the transactivation of C-TAD target genes, and silencing DNAJA1 expression abrogated all C-TAD-mediated effects. Taken together, our results provide a mechanistic basis for the dichotomous functions of TAp73 in the regulation cellular growth through its distinct TADs.

overall_design: Microarray analysis was performed on 17 samples using [Clariom_S_Human] Affymetrix Clariom S Assay, Human (GPL23159).

first: Dan

last: Li


title: KAP1 negatively regulates elongation kinetics to activate signal-induced transcription [TT-Seq]

first: Ivan

overall_design: Comparative gene expression profiling analysis of TT-seq data for control (DMSO) and KAP1-depletion condition (dTAG).

first: Usman

last: Hyder


title: YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response

first: Maite

last: Huarte

overall_design: Refer to individual Series


title: KAP1 negatively regulates elongation kinetics to activate signal-induced transcription [PRO-Seq]

overall_design: Comparative Active RNA Polymerase II density profiling analysis of PRO-Seq data for control (DMSO) and KAP1 depletion (dTAG) with and without serum (0, 5, 10 min)

first: Tulip

last: Nandu

first: Micah

last: Thornton

first: W

last: Kraus


title: KAP1 negatively regulates elongation kinetics to activate signal-induced transcription [RNA-Seq]

last: D'Orso

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control (DMSO) and KAP1-depletion condition (dTAG) with and without serum (30 min)


title: YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RNAP II ChIP-Seq)

overall_design: A YTHDC1 ChIP was performed in WT A549 cells

first: Daniel

last: Elvira-Blázquez

first: José

last: Fernández-Justel

first: Aida

last: Arcas

first: Luisa

last: Statello

first: Enrique

last: Goñi

first: Jovanna

last: González

first: Benedetta

last: Ricci

first: Sara

last: Zaccara

last: Raimondi


title: YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (Ythdc1 ChIP-Seq)


title: YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (RNA-Seq)

overall_design: Total RNA samples were sequenced from siSCR and siYTHDC1 cells


title: FLT4 causes developmental disorders of the cardiovascular and lymphovascular systems via pleiotropic molecular mechanisms

city: Manchester

first: Simon

last: Williams

address: Oxford Road

institute: The University of Manchester

summary: Genetic variation in FLT4 is associated with the most prevalent cyanotic congenital heart disease,Tetralogy of Fallot (TOF). Distinct genetic variation in FLT4 is an established cause of Milroy disease, the prevailing form of primary hereditary lymphoedema. Phenotypic features of the conditions are non-overlapping, implying pleiotropic mechanisms. Here, TOF-associated FLT4 variants identified in patients,aggregate in the perinuclear/secretory pathway, activating proteostatic/metabolic signalling that lymphoedema-associated FLT4 variants do not. FLT4 TOF variants display characteristic gene expression changes in developmental signalling pathways, when expressed in undifferentiated human endothelial cells, revealing a role for FLT4 in cardiogenesis distinct from its role in lymphatic development. Inhibition of the main pathways of proteostasis abrogates these effects, identifying potential avenues for therapeutic intervention. We show that a gain-of-pathogenic-function mechanism causes TOF, contrasting with the dominant negative mechanism identified for Milroy-causative variants.This is among the first demonstrations that mechanistically elucidates developmental pleiotropy of thevascular system.

overall_design: We performed gene expression analysis using data obtained from RNA-seq of FLT4 WT and FLT4 genes containing variants associated with both TOF and Milroy disease (MD).

first: Richard

last: Monaghan

last: Naylor

first: Daisy

last: Flatman

first: Paul

last: Kasher

first: Bernard

middle: D

last: Keavney


title: PIP-seq identifies novel heterogeneous lung innate lymphocyte population activation after combustion product exposure

status: Public on May 06 2024

city: La Jolla

first: Yung-An

last: Huang

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Innate lymphoid cells (ILCs) are a heterogeneous population that play diverse roles in airway inflammation after exposure to allergens and infections. However, how ILCs respond after exposure to environmental toxins is not well understood. Here we show a novel method for studying the heterogeneity of rare lung ILC populations by magnetic enrichment for lung ILCs followed by particle-templated instant partition sequencing (PIP-seq). Using this method, we were able to identify novel group 1 and group 2 ILC subsets that exist after exposure to both fungal allergen and burn pit-related constituents (BPC) that include dioxin, aromatic hydrocarbon, and particulate matter. Toxin exposure in combination with fungal allergen induced activation of specific ILC1/NK and ILC2 populations as well as promoted neutrophilic lung inflammation. Oxidative stress pathways and downregulation of specific ribosomal protein genes (Rpl41 and Rps19) implicated in anti-inflammatory responses were present after BPC exposure. Increased IFNγ expression and other pro-neutrophilic mediator transcripts were increased in BPC-stimulated lung innate lymphoid cells. Further, the addition of BPC induced Hspa8 (encodes HSC70) and aryl hydrocarbon transcription factor activity across multiple lung ILC subsets. Overall, using an airway disease model that develops after occupational and environmental exposures, we demonstrate an effective method to better understand heterogenous ILC subset activation.

overall_design: The mice received intranasal Alternaria alternata challange without or with the supplement of the environmental toxin cocktail (TCDD, BaP, and PM4) for continous 3 days. The next day, mouse lung ILCs were negatively enriched by Mouse Pan-ILC Enrichment Kit. The transcriptome was analyzed by scRNA-seq.

first: Allyssa

middle: N

last: Strohm

first: Taylor

last: Doherty


title: Deep clinical responses and limited inflammatory toxicity in patients with relapsed/refractory T-cell lymphomas receiving Duvelisib and Romidepsin

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

summary: PI3K-d inhibitors have shown impressive activity in lymphoid malignancies but have been hampered by autoimmune and infectious toxicities leading to market withdrawals.  We previously demonstrated single-agent activity of the PI3K-dg duvelisib in T-cell lymphomas that was associated with inflammatory adverse events. We conducted a phase Ib/IIa study of duvelisib in combination with either romidepsin or bortezomib in patients with relapsed/refractory TCL and found that the addition of romidepsin, but not bortezomib, appeared to increase efficacy while attenuating PI3K inhibitor-driven toxicity. The primary endpoint of the study was to determine the maximum tolerated dose of duvelisib, which was 75 mg twice daily when combined with romidepsin versus 25 mg twice daily when combined with bortezomib. Among those with peripheral T-cell lymphomas (PTCL), secondary endpoings of overall and complete response rates of duvelisib and romidepsin were 56% and 44% respectively with less grade 3/4 hepatotoxicity (14%) compared to the 40% rate of grade 3/4 transaminase elevation seen in our prior study with duvelisib monotherapy. Correlative analyses demonstrated enhanced response rates in patients with a follicular helper T-cell subtype.  Finally, the attenuated hepatotoxicity seen in this study was associated with reductions in circulating inflammatory mediators and myeloid cell inflammatory gene expression. These findings support further development of combined PI3K and HDAC inhibition in T-cell lymphomas and suggest a unique strategy to enable PI3K inhibitor-based combinations for additional patient populations.

overall_design: We employed combined single-cell surface epitope identification, transcriptome sequencing, and VDJ sequencing using the 10x Genomics Single Cell Immune Profiling Platform on paired viable CD45+ peripheral blood mononuclear cells (PBMCs) from 10 patients with T-cell lymphomas receiving treatment with romidepsin and duvelisib.

first: Steven

last: Horwitz

first: Ajit

last: Nirmal

first: Ran

last: Xu

first: Esther

last: Drill

first: Natasha

last: Galasso

first: Nivetha

last: Ganesan

first: Theresa

last: Davey

first: Helen

last: Hancock

first: Leslie

last: Perez

first: Catherine

last: Maccaro

first: Alexandra

last: Bahgat

first: Evan

last: Marzouk

first: Elizabeth

last: Cathcart

first: Alison

last: Moskowitz

first: Ariela

last: Noy

first: Anita

last: Kumar

first: Eric

last: Jacobsen

first: David

last: Fisher

first: Neha

last: Mehta-Shah

first: Youn

middle: H

last: Kim

first: Michael

last: Khodadoust

first: Nikita

last: Kotlov

first: Anastasia

last: Nikitina

first: Olga

last: Kudryashova

first: Valeria

last: Zubareva

first: Ksenia

last: Zornikova

first: Nara

last: Shin

first: Maria

last: Sorokina

first: Sandrine

last: Degryse

first: Ekaterina

last: Postovalova

first: Aleksander

last: Bagaev

first: Kinga

last: Hosszu

first: Devin

last: McAvoy

first: Jaap

last: Boelens

first: Wenchao

last: Wu

first: Zoe

last: Ciantra

first: Jackson

last: Appelt

first: Christopher

last: Trevisani

first: Sam

last: Amaka

last: Weinstock

first: Santosha


title: Construction of human 3D striato nigral circuitoids to recapitulate medium spiny neuronal projection defects in Huntington disease

city: Nanjing

first: Yan

last: Liu

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

department: School of Pharmacy

institute: Nanjing Medical University

summary: Striato nigral circuit is composed of medium spiny neuronal projections that were mainly sent from striatum to midbrain substantial nigra (SN), which is essential for regulating motor behaviors. Dysfunction of striato-nigral circuitry may cause a series of motor disabilities which are associated with neurodegenerative disorders, such as Huntington disease (HD). Although the etiology of HD is known as abnormally expanded CAG repeats of the huntingtin gene (HTT), treatment of HD remains tremendous challenges. One possible reason is lack of effective HD model which resembles striato nigral circuitry deficits for the pharmacology studies. Here we first differentiate striatum-like organoids from human pluripotent stem cells, containing functional medium spiny neurons (MSN). We then generated 3D striato nigral circuitoids by assembling striatum-like organoids with midbrain substantial nigra like organoids. With AVV hSYN GFP viral tracing, the extensive MSN projections from striatum to SN are established, which form synaptic connection with dopaminergic neurons and showed the electronic field potentials by labeling striatum like organoids with optogenetic virus. Furthermore, this striato nigral circuitoids exhibited improved calcium activity than individual striatal organoids. Importantly, we further demonstrated the reciprocal projection defects of the HD iPSC derived circuitoids, which could be reversed with the treatment of brain derived nerve factors. Altogether, the striato nigral circuitoids could be used for identifying MSN projection defects, which would be applied as a potential drug test platform for HD.

overall_design: For the scRNA-seq,  striatal organoids and striato-nigral circuitoids  were dissociated by 1 ml of trypLE (Life Technology Inc) for 30 min in the condition of 37°C and 5% CO2 into single cell when differentiated in vitro for 80 days. The cell debris and other aggregates were removed by additional low-speed centrifugation. Droplet-based single-cell RNA sequencing was performed using the 10X Genomics Chromium Single Cell platform, version 3. Approximately 5,000 cells were captured for each sample onto a Chromium Single Cell 3’ Chip (10X Genomics, PN-120236), and the released RNA in each cell was barcoded through reverse transcription in individual gel beads in emulsions (GEMs).

first: Hong

last: Yuan


title: A network-based trans-omics approach for predicting synergistic drug combinations

city: Iizuka

first: Midori

last: Iida

address: Kawazu 680-4

country: Japan

institute: Kyushu Institute of Technology

summary:
We examined the mode-of-action of synergistic drug combinations by microarray analysis. We focused on the drug combination of capsaicin and mitoxantrone, which were the top predicted drug pair identified by SyndrumNET.
Combination therapy can offer greater efficacy on medical treatments. However, the discovery of synergistic drug combinations is challenging. We propose a novel computational method, SyndrumNET, to predict synergistic drug combinations by network propagation with trans-omics analyses. The prediction is based on the topological relationship, network-based proximity, and transcriptional correlation between diseases and drugs. SyndrumNET was applied to analyzing six diseases including asthma, diabetes, hypertension, colorectal cancer, acute myeloid leukemia (AML), and chronic myeloid leukemia (CML), and it outperformed the previous methods in terms of high accuracy. We performed in vitro cell survival assays to validate our prediction for CML. Of the top 17 predicted drug pairs, 14 drug pairs successfully exhibited synergistic anticancer effects. Our mode-of-action analysis also revealed that the drug synergy of the top predicted combination of capsaicin and mitoxantrone was due to the complementary regulation of 12 pathways, including the Rap1 signaling pathway. The proposed method is expected to be useful for various complex diseases.

overall_design: Gene expression was measured when capsaicin 50 μM, mitoxantrone 30 nM, and capsaicin 50 μM + mitoxantrone 30 nM were exposed to K562 human CML cells for 24 hours.

first: Yurika

last: Kuniki

first: Kenta

last: Yagi

first: Mitsuhiro

last: Goda

first: Satoko

last: Namba

first: Jun-ichi

last: Takeshita

first: Ryusuke

last: Sawada

first: Michio

last: Iwata

first: Yoshito

last: Zamami

first: Keisuke

last: Ishizawa

first: Yoshihiro

last: Yamanishi


title: mWGS analysis of the fecal microbiota of WT and TCRb-/- mice

city: Shanghai

first: Xiaofei

last: Yu

address: 2005 Songhu Rd

institute: Fudan University

summary: The gut microbiota plays an important role in host health. Microbiota dysbiosis has been implicated in the global epidemic of Metabolic Syndrome (MetS) and could impair host metabolism by noxious metabolites. It has been well established that the gut microbiota is shaped by host immune factors. However, the effect of T cells on the gut microbiota is yet unknown. Here, we performed a metagenomic whole-genome shotgun sequencing (mWGS) study of the microbiota of TCRb-/- mice, which lack alpha/beta T cells.

overall_design: Feces were collected from of Tcrb-/- and WT mice. Genomic DNA was extracted and sequenced by a metagenomic whole-genome shotgun sequencing (mWGS).

first: Zheyu

last: Jin


title: Transcriptome analysis of the extremophile tardigrade Hypsibius exemplaris exposed to the DNA-damaging agent bleomycin

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

institute: NARO

overall_design: 0-24 hours after 24 hour exposure to 100µM bleomycin and non exposed controls, all in three biological replicates

first: Kazuharu

last: Arakawa


title: Human Amniotic membrane modulates collagen production and deposition in vitro

city: Marietta

first: Isioma

last: Enwerem-Lackland

address: 1775 W Oak Commons Ct

department: Research and Development

institute: Mimedx

summary: Pathological fibrosis, an excessive accumulation of collagen, compromises tissue architecture, impedes its function and represents a medical complication. Properties of the amniotic membrane have demonstrated potential to regulate fibrotic processes. RNA sequencing analysis evaluated the effects of dehydrated human amnion/chorion membrane (DHACM) on fibrotic events using in vitro macromolecular crowding to mimic a physiologically relevant microenvironment. Functional enrichment with Reactome pathway analysis indicated that the function of a subset of these dysregulated genes was associated with the composition and function of the extracellular matrix. Further use of macromolecular crowding in vitro was used to evaluate the effects of DHACM and a lyophilized human amnion/chorion membrane (LHACM) on type 1 collagen production and deposition under profibrotic conditions (addition of TGFβ1). In the continued presence of TGFβ1, LHACM and DHACM regulated the intracellular production and extracellular deposition of type 1 collagen. In addition, results suggest that the effect on collagen deposition could in part be modulated through the regulation of proteins responsible for the extracellular post-translational modifications of collagen. These observations may support the use of DHACM and LHACM in the regulation collagen production/deposition in profibrotic environments.

overall_design: To investigate the effects of DHACM on fibrosis in a human dermal fibroblast (HDF) in vitro macromolecular crowding model

first: Sarah

last: Moreno


title: The evolutionarily conserved zebrafish choroid plexus maintains the size of brain ventricles

city: Trondheim

first: Nathalie

last: Jurisch-Yaksi

address: Erling Skjalgsons gate 1

country: Norway

institute: NTNU

summary: The choroid plexus produces cerebrospinal fluid (CSF) by transport of electrolytes and water from the vasculature to the brain ventricles. The choroid plexus plays additional roles in brain development and homeostasis by secreting neurotrophic molecules, and by serving as a CSF-blood barrier and immune interface. Prior studies have identified transporters on the epithelial cells that transport water and ions into the ventricles and tight junctions involved in the CSF-blood barrier. Yet, how the choroid plexus epithelial cells maintain the brain ventricle system and control brain physiology remain unresolved. To provide novel insights into the physiological roles of the choroid plexus, we use juvenile and adult zebrafish as model systems. Upon histological and transcriptomic analyses, we first identified that the zebrafish choroid plexus is highly conserved with the mammalian choroid plexus and that it expresses all transporters necessary for CSF secretion. Using novel genetic lines, we also identified that the choroid plexus secretes proteins into the CSF. Next, we generated a transgenic line allowing us to ablate specifically the epithelial cells in the choroid plexus. Using the ablation system, we identified a reduction of the ventricular sizes, but no alterations of the CSF-blood barrier. Altogether, our findings identified that the zebrafish choroid plexus is evolutionarily conserved and critical for maintaining the size and homeostasis of the brain ventricles.

overall_design: We performed RNA sequencing on adult zebrafish forebrain choroid plexus. We extracted total RNA from adult zebrafish forebrain choroid plexus (Nacre and AB, 6 - 8-month-old, >3 cm) after removing the pineal gland. RNAsequencing was performed on 2 different batches. Each batch was collected from 12-19 pooled forebrain choroid plexus tissues.

first: Jeong

last: Inyoung

first: Jurisch-Yaksi

last: Nathalie


title: Identification of unique cell type responses in pancreatic islets to stress

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 Euclid

institute: Washington University in St. Louis

summary: We single cell sequenced multiplexed primary human islets treated ex vivo with ER and inflammatory chemicals, indexed cell type specific stress responses, found genes to regulate in SC-islets to reduce apoptosis. We conducted multiomic ATAC+RNA sequencing on human islets treated with BFA, DMSO, IL1B+IFNG+TNFa, or PBS

overall_design: Single cell RNA sequencing of primary human islets treated with Brefeldin A, Thapsigargin, and a variety of cytokines

first: Marlie

last: Maestas


title: RNA-seq of Muscle stem cells (WT and Nedd4L-cKO) and Myoblasts (WT)

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

country: Canada

institute: McGill University

summary: Muscle stem cell quiescence is a complex and dynamic state.  In this study we examined the role of the Ubiquitin Protease System in muscle stem cell function and quiescence.  Using a genetic mouse model where Nedd4L is selectively deleted in myogenic cells, we characterized the effect of the loss of Nedd4L on muscle stem cells.  With RNA-Seq we determined that the genetic deletion of Nedd4L resulted in the transition of the muscle stem cells out of deep quiescence and into Galert. Characterized by the upregulation of cell cycle genes and differentiation genes and loss of expression in numerous known quiescence genes.  Nedd4L-cKO muscle stem cells are more prone to differentiation and fail to expand properly in vitro.

overall_design: To determine the effect of the genetic deletion of Nedd4L on the transcriptome of MuSCs, RNA-Seq was performed on 1000 freshly isolated MuSCs from Nedd4L-WT and Nedd4L-cKO mice.  For the comparison of the transcriptome between MuSCs and myoblasts, 1000 freshly isolated MuSCs from WT mice were used for RNA-Seq and from the same mice cells were allowed to grow in culture for 3 days and then 1000 cells were collected to prepare RNA-Seq libraries


title: The E3 Ubiquitin Ligase Nedd4L Acts as a Checkpoint Against Activation in Quiescent Muscle Stem Cells

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


title: RNA-DNA hybrids formed in the absence of Senataxin  drive non-coding RNA expression and protein aggregation in the nucleolus

city: Austin

first: Tanya

middle: T.

last: Paull

address: 2500 Speedway MBB 2.448

department: Molecular Biosciences

institute: Univ. of Texas at Austin

summary: Neurodegeneration in the human population is often associated with loss of protein homeostasis that is driven by accumulation of specific aggregated proteins. Here we investigate whether deficiency in Senataxin, an RNA-DNA helicase associated with cerebellar ataxia and ALS, induces destabilization of intrinsically disordered proteins as we previously found with Ataxia-telangiectasia (A-T) cells and tissue. We find that Senataxin loss does generate protein aggregates but, unlike in A-T, these are associated with the nucleolus and are independent of oxidative stress and PARP activity. Non-coding RNA expression from the intergenic spacer region of ribosomal DNA is induced in the absence of Senataxin and drives the association and aggregation of many proteins known to be prone to aggregation in neurodegenerative disease. Both non-coding RNAs and protein aggregates are eliminated by overexpression of RNaseH1, implicating RNA-DNA hybrids as the key driver of these outcomes. We find that hybrids are high in the absence of Senataxin at intergenic sites, not at annotated protein-coding genes; these include sites of Senataxin binding in the genome, ribosomal DNA, and peri-centromeric regions. These findings suggest that destabilization of the proteome is driven by Senataxin loss and that RNA-DNA hybrids and non-coding RNAs play a critical role in this process.

overall_design: R-ChIP (catalytically inactive human RNase) in wild-type and Senataxin knock out U2OS cells; RNAseq (TGIRT) in control, shSETX, and SETX knock out U2OS cells

first: Xuemei

last: Wen

first: Hengxi

last: Xu

first: Phillip

last: Woolley

first: Olivia

last: Conway

first: Andreas

last: Matouschek

first: Alan

last: Lambowitz


title: Hydrogen sulfide produced by the microbiota suppresses GLP-1 production

first: Xiaofei

last: Yu

sample_organism:
Mus musculus
feces metagenome

platform_organism:
Mus musculus
feces metagenome

overall_design: Refer to individual Series

first: Zheyu

last: Jin

first: Qingqing

last: Qi


title: Single cell RNA-seq of intestinal L cells in antibiotic-treated and Desulfovibrio-colonized mice

summary: To examine the effects of Desulfovibrio on L cells, L cells from antibiotic-treated and Desulfovibrio-colonized B6.Cg-Gcgtm1.1(cre/GFP)Rpa/J (Gcg-Cre:GFP) mice were isolated and subjected to scRNA-seq.

overall_design:
Gcg-Cre:GFP mice were treated with an antibiotic cocktail, followed by Desulfovibrio colonization. After 2 weeks, L cells (GFP+) were isolated by FACS sorting, stained with Hashtag antibodies and subjected to single cell (sc)RNA sequencing with the 10x Genomics platform.
L cells in this analysis represent cells from two different treatment conditions:
Cells from mice treated with an antibiotic cocktail
Cells from mice colonized with Desulfovibrio


title: Csk restrains BCR-mediated ROS production and contributes to germinal center selection and affinity maturation

city: Suita-shi

first: Takeshi

last: Inoue

state: Osaka

address: 3-1 Yamadaoka

institute: Osaka University

summary: Compared with naïve B cells, the B cell receptor (BCR) signal in germinal center (GC) B cells is attenuated; however, the significance of this signaling attenuation has not been well defined. Here, to investigate the role of attenuation of BCR signaling, we employed a Csk mutant mouse model in which Csk-deficiency in GC B cells resulted in augmentation of net BCR signaling with no apparent effect on antigen presentation. We found that Csk is required for GC maintenance and efficient antibody affinity maturation. Mechanistically, ROS-induced apoptosis was exacerbated concomitantly with mitochondrial dysfunction in Csk-deficient GC B cells. Hence, our data suggest that attenuation of the BCR signal restrains hyper-ROS production, thereby protecting GC B cells from apoptosis and contributing to efficient affinity maturation.

overall_design: Germinal centers (GCs) are the primary site where B cells undergo affinity maturation, the process whereby the average affinity of antibodies increases with time after immunization. To investigate the role of B cell receptor signaling in GC B cell selection, we analyzed the transcriptome of Csk-deficient GC light zone B cells by RNA-seq. Samples consist of 3 Csk(+/+) and 2 Csk(f/f) biological replicates.

first: Yuma

last: Matsumoto

first: Chie

last: Kawai

first: Osamu

last: Ohara


title: 16S-seq analysis of the microbiota of WT and TCRb-/- mice

summary: To examine the microbiota abundance difference, we performed fecal 16s sequencing of wild type, TCRb-/-, TCRb-/- co-housed with WT and TCRb-/- receiving WT T cells.

overall_design: Male WT and TCRb-/- mice were either self-maintained or co-housed for 4 weeks. Fecal pellets were collected for 16S sequencing targeting the V3-V4 region.


summary: To investigate the effect of H2S on GLP-1 production, GLUTag cells were treated with NaHS, a quick-releasing H2S donor. GSH was used as a redox control.

overall_design:
Transcriptome profiling of GLUTag cells with NaHS and GSH treatment.
Twelve-well cell culture plates were coated with 10 μg/mL poly-D-lysine overnight at 37°C. GLUTag cells were seeded at the density of 5 x 105 cells/well and cultured in DMEM containing 10% FBS and 1x penicillin-streptomycin solution for 48 hrs. Cells were then washed once with DPBS and incubated with 1mM NaHS or 0.33 mM GSH in DMEM for 2 hrs. Cells were harvested for RNA extraction and RNA-sequencing.


title: B cell directed CAR-T cell therapy results in activation of CD8+ cytotoxic CAR-negative bystander T cells in both non-human primates and patients (human)

status: Public on May 05 2024

city: Boston

first: Jim

last: Kaminski

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: There is growing appreciation for the emergence of CARneg bystander T cells after CAR-T cell infusion. However, their phenotypic and transcriptomic hallmarks and mechanisms of activation remain uncertain. We performed single-cell RNA-Seq (scRNA-Seq) on non-human primate (NHP) and patient-derived T cells to interrogate CARneg T cells following B cell targeted CAR-T cell therapy. In a NHP model, we observed a distinct population of activated CD8+ CARneg T cells emerging during CAR-T cell expansion. These bystander CD8+ CARneg T cells exhibited a unique transcriptional signature with upregulation of NK-cell markers (KIR3DL2, CD160, KLRD1), chemokines and chemokine receptors (CCL5, XCL1, CCR9), and downregulation of naive T cell-associated genes (SELL, CD28). A transcriptionally similar population was identified in patients following Tisangelecleucel infusion. Mechanistic studies revealed that IL-2 and IL-15 exposure induced bystander-like CD8+ T cells. These T cells efficiently killed leukemic cells through a TCR-independent mechanism. Together, these data identify bystander CD8+ T cells as a novel mechanism by which CAR-T cell infusion can induce further anti-leukemic activity, measurable in both NHP and in patients.

overall_design:
Examination of scTCR-Seq and scRNA-Seq of T cells in patients receiving CAR-T Therapy
-------------------------------
Authors state "the raw data is in the process of being submitted to dbGaP".

first: Ulrike

last: Gerdemann

first: Ryan

last: Fleming


title: ATAC-Seq of WT and Nedd4L-cKO Muscle stem cells

first: Vahab

last: Soleimani

overall_design: To determine the effect of the genetic deletion of Nedd4L on the chromatin accessibility, ATAC-Seq was performed on 5000 freshly isolated MuSCs from WT and Nedd4L-cKO mice.


title: Spatiotemporal landscape of kidney tubular responses to glomerular proteinuria

city: Lugano

first: Anna

last: Rinaldi

state: Ticino

address: Tesserete

department: Nephrology

country: Switzerland

institute: Ente Ospedaliero Cantonale

summary: Proteinuria is a cardinal feature of glomerular diseases and an important risk factor for tubulo-interstitial damage, progressive decline in kidney function, and cardiovascular complications, but the precise effects of proteinuria on tubules were previously unclear. Here, using an established mouse model of glomerulopathy, single cell sequencing, in vivo imaging and other complementary methods, we investigate in detail the spatiotemporal landscape of genetic responses to increased protein filtration along the nephron. We show that proteinuria is a potent modulator of cell signaling in tubules, and triggers extensive genetic reprogramming in distal segments, with activation of numerous developmental pathways, and a generalized convergence and loss of differentiation markers. Meanwhile, in the proximal tubule - where filtered proteins are normally endocytosed and degraded - we find that encroachment of protein uptake from early (S1) into later (S2) segments causes substantial remodeling of the latter, with dramatic downregulation of canonical processes such as organic anion/uremic toxin secretion and lipid metabolism, and a concomitant increase in reabsorptive markers. Thus, we demonstrate that the tubular effects of proteinuria are extensive, pleotropic and segment specific. Moreover, we identify protein exposure as an important environmental cue that shapes the axial topography of the nephron. Taken together, these findings could explain some well recognized phenomena in humans with chronic kidney disease (CKD).

overall_design: We characterized by single nucleus RNA sequencing (snRNAseq) kidney specimens obtained from 7 transgenic POD-ATTAC mouse model, 2 WT, and 1 transgenic POD-ATTAC mouse treated with saline as control.

last: Faivre

first: Milica

last: Bugarski

first: Thomas

last: Verissimo

first: Imene

middle: B

last: Sakhi

first: David

last: Legouis

first: Sara

last: Correia

first: Monika

last: Kaminska

first: Delal

last: Dalga

first: Pietro

middle: E

last: Cippà

first: Sophie

last: de Seigneux

first: Andrew

last: Hall


title: Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19

city: San Francisco

first: Ravi

last: Patel

address: 513 Parnassus Ave

department: CoLabs

institute: University of California San Francisco

summary: Dexamethasone is the standard of care for critically ill patients with COVID-19, but its immunological effects in this setting and the mechanisms by which it decreases mortality are not understood. We performed bulk and single-cell RNA sequencing of the lower respiratory tract and blood, and plasma cytokine profiling to study the effect of dexamethasone on systemic and pulmonary immune cells. We find signatures of decreased viral injury, antigen presentation, and T cell recruitment in patients treated with dexamethasone. We identify compartment- and cell- specific differences in the effect of dexamethasone in patients with severe COVID that are reproducible in publicly available datasets. Our results highlight the importance of studying compartmentalized inflammation in critically ill patients.

overall_design: PBMCs of severely ill COVID-19 patients that were or were not treated with dexamethasone were analyzed using bulk RNA sequencing

first: Lucile

middle: P

last: Neyton

first: Gabriela

middle: K

last: Fragiadakis


overall_design: Cells from whole-blood and tracheal aspirate of severely ill COVID-19 patients that were or were not treated with dexamethasone were analyzed using single-cell RNA sequencing


title: A myeloid maturation program initiated by nucleotide depletion during S phase [ery_scrnaseq]

city: Cambridge

first: Brian

last: Do

state: MA

address: 500 Main St

institute: MIT

summary: Certain cancers, such as acute myeloid leukemia (AML), are caused by malignant stem cells that fail maturation. We sought to mechanistically understand how metabolism might regulate cell fate decisions and to identify metabolic differentiation agents that might be leveraged therapeutically. We find that nucleotide – purine, pyrimidine, and deoxynucleotide – depletion leads to AML differentiation by way of replication stress. Modulation of nucleotide pools leads to transcriptional reprogramming, epigenetic remodeling, and initiation of differentiation which is dependent on the myeloid regulating transcription-factor PU.1. By single-cell RNA sequencing and microscopy, we find that reprogramming downstream of nucleotide depletion occurs as cells undergo replication stress and that the cell fate decision is initiated prior to completion of the cell cycle. Together, these findings suggest that nucleotide metabolism is a critical determinant of hematopoietic progenitor cell fate, clarify the coordination of the fate decision with the cell cycle, and expand upon the class of inhibitors that can be developed or repurposed as novel differentiation therapy.

overall_design: scRNAseq was performed on erythroid progenitors differentiated from human CD34+ HSPCs at day 11 and 14; they were treated with DMSO, HU, or APH starting at day 7.

middle: T

first: Sidney

middle: Y

last: Vermeulen

first: Matthew

last: Vander Heiden


title: A myeloid maturation program initiated by nucleotide depletion during S phase [CRISPRi screen]

summary: Certain cancers, such as acute myeloid leukemia (AML), are caused by malignant stem cells that fail maturation. We sought to mechanistically understand how metabolism might regulate cell fate decisions and to identify metabolic differentiation agents that might be leveraged therapeutically.  We find that nucleotide – purine, pyrimidine, and deoxynucleotide – depletion leads to AML differentiation by way of replication stress. Modulation of nucleotide pools leads to transcriptional reprogramming, epigenetic remodeling, and initiation of differentiation which is dependent on the myeloid regulating transcription-factor PU.1. By single-cell RNA sequencing and microscopy, we find that reprogramming downstream of nucleotide depletion occurs as cells undergo replication stress and that the cell fate decision is initiated prior to completion of the cell cycle. Together, these findings suggest that nucleotide metabolism is a critical determinant of hematopoietic progenitor cell fate, clarify the coordination of the fate decision with the cell cycle, and expand upon the class of inhibitors that can be developed or repurposed as novel differentiation therapy.

overall_design: Genome-wide and sublibrary CRISPRi screens were performed in ER-Hoxa9, THP-1, and K562 cells with and without BRQ treatment.


title: A myeloid maturation program initiated by nucleotide depletion during S phase [scRNA-seq]

overall_design: Cell lines were treated with vehicle or drug for the indicated times and barcoded with MULTI-seq, and single-cell transcriptomes were sequenced on the 10X Genomics platform.

first: Peggy

last: Hsu

last: Sykes


title: Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19.


title: A myeloid maturation program initiated by nucleotide depletion during S phase [RNA-Seq]

overall_design: Cell lines were treated with vehicle or drug for the indicated times, RNA was extracted, and RNA sequencing was performed.


title: AAV-mediated genome editing is influenced by the formation of R-loops.

city: Stanford

first: Mark

last: Kay

state: California

address: 269 Campus Drive CCSR Building, Room 2110

department: Pediatrics and Genetics

institute: Stanford University School of Medicine

summary: Recombinant adeno-associated viral vectors (rAAV) hold a natural ability to stimulate homologous recombination (AAV-HR). Moreover, they are also reported to randomly integrate into numerous locations throughout the genome. Here, we describe DNA/RNA immune precipitation sequencing (DRIP-seq) studies in HEPA1-6 cells and whole murine liver to detect genomic r-loops. Through genetic and pharmacological manipulation of r-loops formation, we showed a significant enhancement of AAV-HR. Notably, we were able to detect different levels of r-loops along the Albumin locus. Both in vitro and in vivo experiments showed that the 3’ end of Albumin (high r-loops) is efficiently edited by AAV-HR, whereas the upstream region (low r-loops) did not result in any detectable vector integration. In addition, we were also able to find an interesting correlation between previously reported off-target rAAV integration and r-loop enriched genomic regions. Thus, we conclude that highly transcribed genes accumulate high levels of r-loops, and this could lead to rAAV vector genome integration. These findings may shed light on mechanisms for improving the safety and efficacy of genome editing and may enhance our ability to predict regions most susceptible to insertional mutagenesis with canonical rAAV vectors.

overall_design: R-loops detection by S9.6 immunoprecipitation extracts  HEPA1-6 cells and mouse liver

first: Kay

last: Mark

first: Puzzo

last: Francesco

first: Crossley

last: Magdalena

first: Goswami

last: Aranyak


title: Temporary Alleviation of MAPK by Arbutin Alleviates Oxidative Damage in the Retina and ARPE-19 Cells

city: Tianji

first: Ling

last: Wang

address: No. 22 Qixiang Tai Road, Heping District

institute: Clinical College of Ophthalmology, Tianjin Medical University

summary: Dry age-related macular degeneration (AMD) is one of the main diseases that causes blindness in humans and the number of  cases is increasing every year, but effective treatments are not available,  arbutin (ARB) has been reported to have antioxidant, anti-inflammatory,  and anti-aging effects in other age-related diseases. However,  whether it can help treat dry AMD remains unknown.in this study,  we found 10-100 μM ARB concentration-dependently reversed the H2O2-induced viability decline in HRPECs, and ARB inhibited H2O2-induced HRPEC ROS production and apoptosis by changing the expression of antioxidant and  apoptosis-related genes and proteins. Transcriptome sequencing and western blotting showed that ARB reduced ERK1/2 and  P-38 phosphorylation to prevent H2O2-induced oxidation damage. We concluded ARB reversed the H2O2-induced decline in  HRPEC activity,  which was related to inhibition of ROS production and apoptosis. The ERK1/2 and P38 MAPK signaling pathways may have  mediated this process.

overall_design: To explore the signaling pathway of arbutin against H2O2-induced human RPECs oxidative damage,Cells were pretreated for 24 h with or without 100 µM ARB and then treated with 600 µM H2O2 for 24 h

first: Xiaoyong

last: Yuan


title: Methylation of the epigenetic regulator KMT2D by SMYD2 contributes to therapeutic response in hormone-dependent breast cancer [KMT2D_KI_RNA]

status: Public on May 04 2024

city: Baltimore

first: Eneda

last: Toska

state: MD

address: 1650 Orleans Street, CRB1

institute: Johns Hopkins University

summary: Activating mutations in PIK3CA, the gene encoding PI3Kα, are frequently found in estrogen receptor (ER+) breast cancer and the combination of the PI3K inhibitor alpelisib with the anti-ER agent fulvestrant is approved for therapy. We have uncovered a key role for the chromatin modifier KMT2D in regulating the ER-PI3K crosstalk. PI3Kα effectors, AKT and SGK, negatively regulate KMT2D through S1331 phosphorylation. When PI3K is inhibited, this regulatory event is lost, leading to increased chromatin recruitment of KMT2D and an upregulation of ER-dependent transcription. Here we discovered a previously undescribed methylation site on KMT2D, at K1330 directly adjacent to S1331, catalyzed by the lysine methyltransferase SMYD2. SMYD2 loss attenuates alpelisib-induced KMT2D chromatin binding. Accordingly, loss of SMYD2 abrogates alpelisib-induced changes in gene expression, including ER-dependent transcription. Knockdown or pharmacological inhibition of SMYD2 sensitizes breast cancer cells, patient-derived organoids, and tumors to PI3K/AKT inhibition and endocrine therapy in part through KMT2D K1330 methylation. Methyl dead knock-in clones of KMT2D phenocopy many of the effects of SMYD2 inhibition on cell and tumor growth, drug response, and transcriptional output. Together, our findings uncover a regulatory cross-talk between posttranslational modifications that plays an important role in fine-tuning the functions of KMT2D at the chromatin. This provides a rationale for epigenetic therapy using SMYD2 inhibitors in combination with PI3Kα/AKT inhibitors for the treatment of ER+/PIK3CA mutant breast cancer.

overall_design: RNA-seq was performed in MCF7 cells with a CRISPR knock-in mutation of the SMYD2 methylation site in KMT2D (K1330A), in the presence of DMSO or the PI3K⍺ inhibitor alpelisib

first: Toska

last: Eneda

first: Blawski

last: Ryan

first: Guo

last: Xinyu


title: Transcription factor OsWRKY11 induces rice heading at low concentrations but inhibits rice heading at high concentrations

city: Kunming

first: Lirong

last: Zhao

state: Yunnan

address: No.88 Xuefu Road

department: Xishuangbanna Tropical Botanical Garden

institute: Chinese Academy of Sciences

summary: To identify direct targets of OsWRKY11 in vivo, we performed chromatin immunoprecipitation sequencing (ChIP-seq).

overall_design: The ChIP assays were conducted on shoots obtained from 3-week-old OsWRKY11-OE plants. A total of 2 g of seedling shoots from transgenic pUbi:OsWRKY11-Myc plants were harvested and fixed in a crosslinking solution containing 1% (w/v) formaldehyde under vacuum for 30 min on ice. Subsequently, crosslinking was terminated by treating with 0.125 mM glycine under vacuum for 5 min.

first: Yunwei

last: Liu

first: Houping

first: Diqiu

last: Yu


title: Methylation of the epigenetic regulator KMT2D by SMYD2 contributes to therapeutic response in hormone-dependent breast cancer [KMT2D_ChIP_seq]

overall_design:
ChIP-seq for KMT2D was performed in MCF7 cells with doxycycline-inducible knockdown of SMYD2 to determine the effect of SMYD2 on KMT2D chromatin binding

FLAG-SMYD2 CUT & RUN was performed in MCF7 breast cancer cells with overexpression of FLAG-SMYD2 or empty vector in order to assess SMYD2 chromatin binding genome-wide.

first: Ryan

last: Blawski

first: Wanlu

last: Chen

first: Xinyu

last: Guo


title: A myeloid maturation program initiated by nucleotide depletion during S phase [ATAC-Seq]

first: Brian

last: Do

department: Biology

overall_design: Cell lines were treated with vehicle or drug for the indicated times and ATACseq was performed.

first: Peggy

last: Hsu

first: Sidney

last: Vermeulen

first: David

last: Sykes

first: Matthew

last: Vander Heiden


title: Methylation of the epigenetic regulator KMT2D by SMYD2 contributes to therapeutic response in hormone-dependent breast cancer [SMYD2_KD_RNA]

overall_design: RNA-seq was performed in MCF7 breast cancer cells with doxycycline-inducible knockdown of SMYD2 in the presence of DMSO or the PI3K⍺ inhibitor alpelisib


title: Comparing transcriptional profiles of type 2 innate lymphoid cells from WT and Rag1 knockout mice

first: Aaron

last: Ver Heul

address: 660 S Euclid Ave.

institute: Washington University School of Medicine

summary: Type 2 inflammation contributes to the pathology of skin diseases such as atopic dermatitis and urticaria. Type 2 innate lymphoid cells are key mediators of skin inflammation by releasing type 2 cytokines in response to certain environmental stimuli. We recently found that Rag1 knockout mice exhibit more pronounced skin inflammation in a mouse model of atopic-dermatitis-like disease, despite lacking adaptive immune cells like T helper 2 cells, implicating a critical role of type 2 innate lymphoid cells in this condition. The goal of this study was to characterize transcriptional differences between WT and Rag KO type 2 innate lymphoid cells to determine if Rag knockout leads to cell-intrinsic alterations in innate lymphoid cell function.

overall_design: To directly compare the transcriptional profiles of ILC2s that developed with (WT) or without (Rag1-/-) Rag1 expression, we transplanted bone marrow from the corresponding mice into congenic WT recipients and then sorted ILC2s either 8 weeks or 12 weeks after transplant for RNA-sequencing.

first: Madison

last: Mack

last: Kim


title: A set of circulating microRNAs belonging to the 14q32 chromosomic locus identifies two different subgroups of individuals with recent onset Stage 3 type 1 diabetes [second cohort, untargeted]

status: Public on May 03 2024

city: Siena

first: Francesco

last: Dotta

state: Si

address: Viale Bracci 16

department: Department of Medicine, surgery and neuroscience

country: Italy

institute: University of Siena

summary: Circulating microRNAs are linked to the onset and progression of type 1 diabetes mellitus (T1DM), making them potential biomarkers for the disease. In this study, we employ a multiplatform sequencing approach to analyze circulating microRNAs in an extended cohort of individuals with T1DM from the INNODIA consortium. Our findings reveal that a set of microRNAs located within the T1DM susceptibility chromosomal locus 14q32 distinguishes two subgroups of individuals. To validate our results, we conduct additional analyses on a second cohort of T1DM individuals, confirming the identification of these subgroups, which we have named Cluster A and Cluster B. Remarkably, Cluster B T1DM individuals, who exhibit increased expression of a set of 14q32 miRNAs, show better glycaemic control and display a different blood immunomics profile. Our findings suggest that this set of circulating microRNAs can identify two different T1DM subgroups with distinct blood immunomics at baseline and clinical outcomes during follow-up.

overall_design: The study design involved the analysis of two cohorts of Type 1 Diabetes (T1DM) subjects: an initial screening cohort, the INNODIA first cohort, consisting of n=115 T1DM individuals, and a validation cohort, the INNODIA second cohort, consisting of n=147 T1DM individuals. All subjects were followed-up with programmed visits at 3 (visit 2), 6 (visit 3) and 12 months (visit 4) after clinical diagnosis of T1DM. In both cohorts, blood samples were collected at baseline (visit 1) and processed within 2 hours from blood draw. The collected blood samples underwent centrifugation to separate plasma from contaminant cells and platelets. The plasma samples were then aliquoted (200 μL) and stored at -80°C in a centralized biobank. For the INNODIA first cohort, the plasma samples were subjected to miRNA profiling using two different sequencing platforms: HTG-miRNA Edge Seq and Small RNA-seq. The profiling was followed by validation using droplet digital PCR. For the validation cohort, the plasma samples were analyzed using small RNA-seq, and subsequently validated using droplet digital PCR.


title: Brain-wide AAV-mediated silencing of prion protein by a compact epigenetic editor

first: Tessa

last: Bertozzi

address: 455 Main St

institute: Whitehead Institute

summary: Prion disease is caused by misfolding of the prion protein (PrP) into pathogenic self-propagating conformations, leading to rapid onset dementia and death. However, elimination of endogenous PrP can halt prion disease progression. Here, we describe CHARM, a compact, enzyme-free epigenetic editor capable of silencing transcription through programmable targeted DNA methylation. Using a histone H3 tail-Dnmt3l fusion, CHARM recruits and activates the endogenous DNA methyltransferases, thereby reducing transgene size and bystander effects. When delivered to the mouse brain by an adeno-associated viral (AAV) vector, PRNP-targeted CHARM ablates PrP expression across the brain. We temporally limit editor expression by implementing a kinetically-tuned self-silencing approach. CHARM represents a broadly applicable strategy to programmably prevent expression of pathogenic proteins, including those implicated in other neurodegenerative diseases.

overall_design: Neuro-2a cells were transduced with ZFcharm Kv1 and CRISPRcharm Kv1 lentiviral constructs. CISPRcharm Kv1 was introduced into cells already expressing either a non-targeting sgRNA or a sgRNA targeting Prnp. An empty lentiviral vector was used as a no-editor control. Each transduction was done in triplicate. Cells were dislodged from 6-well plates using Trizol and total RNA was extracted using the Direct-zol RNA Miniprep Kit (Zymo, R2051). Libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, KK8560) and sequenced as 50 bp single-end reads on a NovaSeq 6000 (Illumina). Raw sequencing reads were aligned to the mouse genome (mm39) using STAR 2.7.1a and quantified using featureCounts. Differential expression analysis was carried out using DESeq2.

first: Edwin

last: Neumann

first: Jonathan

last: Weissman


title: Investigation of parenteral nutrition-induced hepatotoxicity using human liver spheroid co-cultures

city: Brussels

first: Milos

last: Mihajlovic

address: Laarbeeklaan 103

country: Belgium

institute: Vrije Universiteit Brussel

summary: Parenteral nutrition (PN) is typically administered to individuals with gastrointestinal dysfunction, a contraindication for enteral feeding and a need for nutritional therapy. When PN is the only energy source in patients, it is defined as total parenteral nutrition (TPN). TPN is a life-saving approach for different patient populations, both in infants and adults. However, despite numerous benefits, TPN can cause adverse effects, including metabolic disorders and liver injury. TPN-associated liver injury, known as intestinal failure-associated liver disease (IFALD), represents a significant problem affecting up to 90% of individuals receiving TPN. IFALD pathogenesis is complex, depending on the TPN components as well as on the patient’s medical conditions. Despite numerous animal studies and clinical observations, the molecular mechanisms driving IFALD remain largely unknown. The present study was set up to elucidate the mechanisms underlying IFALD. For this purpose, human liver spheroid co-cultures were treated with TPN mixture followed by RNA sequencing analysis. It was found that prolonged exposure to TPN substantially changes the transcriptome profile of liver spheroids and affects multiple metabolic and signaling pathways contributing to liver injury.

overall_design: To evaluate gene expression profiles of liver cells after exposure to total parenteral nutrition (TPN) over time, human liver co-culture spheroids consisting of HepG2/C3A and LX-2 cells were treated with TPN 1% for either 24 hours or 144 hours, using untreated cells as control (n=3).

first: Mathieu

last: Vinken


title: A myeloid maturation program initiated by nucleotide depletion during S phase [Cut & Run]

overall_design: Cell lines were treated with vehicle or drug for the indicated time, and CUT&RUN was performed with the indicated antibodies.


title: A set of circulating microRNAs belonging to the 14q32 chromosomic locus identifies two different subgroups of individuals with recent onset Stage 3 type 1 diabetes [first cohort, untargeted]


title: A Transcriptomic Dataset of Embryonic Murine Telencephalon

city: Sendai

first: Shohei

last: Ochi

state: Miyagi

address: 2-1, Seiryo-machi, Aoba-ku

department: Developmental Neuroscience

institute: Tohoku University Graduate School of Medicine

summary: Sex bias is known in the prevalence/pathology of neurodevelopmental disorders. Sex-dependent differences of the certain brain areas are known to emerge perinatally through the exposure to sex hormones, while gene expression patterns in the rodent embryonic brain does not seem to be completely the same between male and female. To investigate potential sex differences in gene expression and cortical organization during the embryonic period in mice, we conducted a comprehensive analysis of gene expression for the telencephalon at embryonic day (E) 11.5 (a peak of neural stem cell expansion) and E14.5 (a peak of neurogenesis) using bulk RNA-seq data. As a result, our data showed the existence of notable sex differences in gene expression patterns not obviously at E11.5, but clearly at E14.5 when neurogenesis has become its peak. These data can be useful for exploring potential contribution of genes exhibiting sex differences to the divergence in brain development. Additionally, our data underscore the significance of studying the embryonic period to gain a deeper understanding of sex differences in brain development.

overall_design: To investigate potential sex differences in gene expression and cortical organization during the embryonic period in mice, we conducted a comprehensive analysis of gene expression for the telencephalon at E11.5 (a peak of neural stem cell expansion) and E14.5 (a peak of neurogenesis).

first: Shyu

last: Manabe

first: Kikkawa

last: Takako

first: Sara

last: Ebrahimiazar

first: Ryuichi

last: Kimura

first: Kaichi

last: Yoshizaki

first: Noriko

last: Osumi


title: Combination of a SOS1-KRAS interaction inhibitor with a KRASG12C inhibitor combination can address intrinsic and acquired resistance leading to stronger and more durable response [Tru-seq]

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary: To investigate the transcriptomic changes associated with KRAS G12C inhibitor Adagrasib resistance and Adagrasib + SOS1 inhibitor (BI-3406) or Adagrasib + EGFR inhibitor (Cetuximab) combination treatment to overcome resistance. We performed differential gene expression analysis using RNA-seq generated from cell line derived xenograft (CDX) in vivo models. We compared different treatment conditions with DMSO treated condition.

overall_design: CDX models were generated using NSCLC cell line NCI-H2122. For each CDX category, expression data with Natrosol treated and either single agent and combination treatment was generated.

first: Venu

last: Thatikonda

first: Oliver

last: Bergner

first: Donat

last: Alpar

first: Marco

last: Hofmann

first: Malgorzata

last: Kamuda


title: Persistent organic pollutants dysregulate energy homeostasis in human ovaries in vitro

city: Solna

first: Tianyi

last: Li

address: Bioclinicum NKS J5:20, Solnavägen 30

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary: Exposure to persistent organic pollutants (POPs), such as dichlorodiphenyltrichloroethane (DDT) and polychlorinated biphenyls (PCBs), has historically been linked to population collapses in wildlife. Despite international regulations, these legacy chemicals are still currently detected in women of reproductive age, and their levels correlate with reduced ovarian reserve, longer time-to-pregnancy, and higher risk of infertility. However, the specific modes of action underlying these associations remain unclear. Here, we examined the effects of five commonly occurring POPs − hexachlorobenzene (HCB), p,p'-dichlorodiphenyldichloroethylene (DDE), 2,3,3′,4,4′,5-hexachlorobiphenyl (PCB156), 2,2′,3,4,4′,5,5′-heptachlorobiphenyl (PCB180), perfluorooctane sulfonate (PFOS) − and their mixture on human ovaries in vitro. We exposed human ovarian cancer cell lines COV434, KGN, and PA1 as well as primary ovarian cells for 24 h, and ovarian tissue containing unilaminar follicles for 6 days. RNA-sequencing of samples exposed to concentrations covering epidemiologically relevant levels revealed significant gene expression changes related to central energy metabolism in the exposed cells, indicating glycolysis, oxidative phosphorylation, fatty acid metabolism, and reactive oxygen species as potential shared targets of POP exposures in ovarian cells. Alpha-enolase (ENO1), lactate dehydrogenase A (LDHA), cytochrome C oxidase subunit 4I1 (COX4I1), ATP synthase F1 subunit alpha (ATP5A), and glutathione peroxidase 4 (GPX4) were validated as targets through qPCR in additional cell culture experiments in KGN. In ovarian tissue cultures, we observed significant effects of exposure on follicle growth and atresia as well as protein expression. All POP exposures, except PCB180, decreased unilaminar follicle proportion and increased follicle atresia. Immunostaining confirmed altered expression of LDHA, ATP5A, and GPX4 in the exposed tissues. Moreover, POP exposures modified ATP production in KGN and tissue culture. In conclusion, our results demonstrate the disruption of cellular energy metabolism as a novel mode of action underlying POP-mediated interference of follicle growth in human ovaries.

overall_design: 242 samples from 3 passages of 4 cell lines (COV434, KGN, PA1, primary ovarian cells), 20 groups in total (MEDIA, DMSO, HCB 1X, HCB 10X, HCB 100X, DDE 1X, DDE 10X, DDE 100X, PCB156 1X, PCB156 10X, PCB156 100X, PCB180 1X, PCB180, 10X, PCB180 100X, PFOS 1X, PFOS 10X, PFOS 100X, MIX 1X, MIX 10X, MIX 100X)

first: Richelle

last: Björvang

first: Jie

last: Hao

first: Valentina

last: Di Nisio

first: Anastasios

last: Damdimopoulos

first: Cecilia

last: Lindskog

first: Kiriaki

last: Papaikonomou

first: Pauliina

last: Damdimopoulou


title: A set of circulating microRNAs belonging to the 14q32 chromosomic locus identifies two different subgroups of individuals with recent onset Stage 3 type 1 diabetes [first cohort, targeted]

first: Francesco

last: Dotta


title: miRNA-mediated inhibition of an actomyosin network in hippocampal pyramidal neurons restricts sociability in adult male mice

city: Zürich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: D-HEST

institute: ETH Zürich

summary: We recently reported that the loss of the microRNA cluster miR-379-410 leads to hypersocial behavior and anxiety in mice. With this study, we show that ablating miR-379-410 in excitatory neurons of the postnatal mouse hippocampus recapitulates hypersociability, but not anxiety. At the cellular level, miR-379-410 loss in excitatory neurons leads to increased excitatory synaptic transmission and upregulation of an actomyosin gene network. Re-expression of three cluster miRNAs, as well as pharmacological inhibition of the actomyosin activator ROCK, was sufficient to reinstate normal sociability in miR-379-410 knockout mice. Our results unveil a novel microRNA-actomyosin pathway involved in the control of sociability.

overall_design: To investigate whether the knockout of miR379-410 miRNA cluster in glutamatergic neurons of the hippocampus drives differential gene expression, we established genetically modified mice with Cre-driven conditional knockout (cKO) of this cluster in Emx1 positive cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different animals per genotype (6 wild type and 6 cKO mice).

first: Ramanathan

last: Narayanan

first: Pierre-Luc

last: Germain


title: Combination of a SOS1-KRAS interaction inhibitor with a KRASG12C inhibitor combination can address intrinsic and acquired resistance leading to stronger and more durable response (Quant-Seq 2)

first: Daniel

last: Gerlach

summary:
To investigate the transcriptomic changes associated with KRAS G12C inhibitor Adagrasib resistance and Adagrasib + SOS1 inhibitor (BI-3406) or Adagrasib + EGFR inhibitor (Cetuximab) combination treatment to overcome resistance.
We performed differential gene expression analysis using RNA-seq generated from cell line derived xenograft (CDX) in vivo models. We compared different treatment conditions with DMSO treated condition.

overall_design:
CDX models were generated using NSCLC cell line NCI-H2122 and CRC cell line SW837. For each CDX category, expression data with DMSO treated and either single agent and combination treatment was generated.
Repetition of the original experiment. Includes technical replicates for samples previously included and new samples for additional time points

first: Venu

last: Thatikonda