title: Nuclear speckles regulate functional programs in cancer (RNA SART1, DDX39A, SARNP, FIBP, TMEM259 kd)

status: Public on Sep 03 2024

city: Cold Spring Harbor

first: Katherine

middle: Ann

last: Alexander

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Nuclear speckles are dynamic nuclear bodies characterized by high local concentrations of RNA binding proteins and specific non-coding RNAs. Although the contents of speckles suggest multifaceted roles in regulating chromatin dynamics and gene expression, the overarching biological function(s) of nuclear speckles remain enigmatic. In this study, we investigate speckle compositional variation in human cancer, finding two main speckle compositional states based on RNA expression of speckle-resident proteins. One cancer speckle state was more similar to normal adjacent tissues, while the other was dissimilar from normal tissue, and thus considered an aberrant cancer speckle state. We link the aberrant speckle state to altered speckle positioning within the nucleus, to elevation of the TREX RNA export complex, and to worse patient outcomes in clear cell renal cell carcinoma (ccRCC). ccRCC is typified by hyperactivation of the HIF-2a transcription factor, and we demonstrate that HIF-2a drives physical association of a select subset of its target genes with nuclear speckles depending on HIF-2a's two speckle targeting motifs (STMs) defined in this study. STMs are highly enriched among transcription factors, suggesting that DNA-speckle targeting may be a general mechanism of gene regulation and providing a resource of candidate speckle-targeting factors. Via integration of tissue culture functional studies with tumor genomic and imaging analysis, we show that HIF-2a gene regulatory programs are impacted by speckle compositional state and by abrogation of speckle targeting abilities of HIF-2a. These findings suggest that, in ccRCC, a key biological function of nuclear speckles is to modulate expression of a specific subset of HIF-2a-regulated target genes that, in turn, influence patient outcomes. Beyond ccRCC, tumor speckle compositional states broadly correlate with altered functional pathways and expression of speckle-associated gene neighborhoods, exposing a general link between nuclear speckles and gene expression dysregulation in human cancer.

overall_design: 786-O ccRCC cells were treated with non-targeting control siRNA or siRNAs against different speckle protein genes and processed for RNA-seq in duplicate.

first: Shelley

last: Berger


title: Nuclear speckles regulate functional programs in cancer (RNA ALYkd)

state: NY

country: USA

type: Expression profiling by high throughput sequencing

overall_design: 786-O ccRCC cells were treated with non-targeting control siRNA or one of two ALYREF siRNAs and processed for RNA-seq in duplicate.

middle: A

middle: L


title: Histone demethylase JMJ4 interacts with transcription factor BLH3 to modulate jasmonate biosynthesis in tomato response to cold stress [ChIP-seq]

status: Public on Aug 27 2024

city: Hangzhou

first: Chenxu

last: Liu

state: Zhejiang

address: Xihu District, No.866 Yuhangtang Road

department: Horticulture

country: China

institute: Zhejiang university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To clarify the specific regulating mechanism of JMJ4 under cold treatment, we performed ChIP-seq assay of jmj4 mutant and wild type plants under control and cold treatment conditions.

overall_design: For ChIP-seq of H3K27me3, jmj4 mutant and wild type plants were both subjected to 25 degree and 4 degree treatment for 12h, then leaf samples were collected for high-throughput sequencing. For ChIP-seq of HA tag, OE-JMJ4 plants were subjected to 4 degree treatment for 12h, then leaf samples were collected for high-throughput sequencing.

first: Tong

last: Xu

first: Jie

last: Zhou


title: Gene expression profile at single cells level of liver tissues in Nek2 conditioned-knock out mice model (Nek2f/f lyz2cre)

status: Public on Aug 31 2024

first: Xiaozhen

last: Zhang

address: 79 QIngchun Road

department: Department of Hepatobiliary and Pancreatic Surgery

institute: the First Affiliated Hospital, School of Medicine, Zhejiang University

summary: Nek2 in macrophages was considered as an important regulator in hepatocarcinogenesis. We used scRNA-seq to analyse immune microenvironment of liver.

overall_design: liver tissues of Nek2f/f lyz2cre was isolated by FACS and analysed by scRNAseq.

first: Xueli

last: Bai

first: Tingbo

last: Liang


title: Nuclear speckles regulate functional programs in cancer (ChIP)

overall_design: 786-O cells were treated with DMSO control or PT2399 HIF-2alpha inhibitor for 3 hours and processed for HIF-2alpha ChIP-seq in duplicate, with input chromatin used for background subtraction


title: Nuclear speckles regulate functional programs in cancer (RNA PT2399)

overall_design: 786-O ccRCC cells were treated with DMSO control for 12 hours or PT2399 HIF-2alpha inhibitor for 3, 6, 9, or 12 hours. RNA-seq was performed in two replicates for each condition


title: A genotype-first approach identifies variants for orofacial clefts and other phenotypes in dogs

status: Public on Oct 02 2024

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
Dog breeding promotes within-group homogeneity through conformation to strict breed standards and also drives between-group heterogeneity in pursuit of distinct morphological forms and characteristic breed traits. In this study, the genotype-first approach was adapted to the dog genome to investigate coding variation from over 2000 dogs, leading to discoveries of new mutations related to craniofacial morphology and stature.
Breed enriched variants were prioritized according to gene constraint, which was calculated using a mutation model derived from trinucleotide substitution probabilities in the dog. Most priority variants were not associated with genomic signatures for breed differentiation, as these regions were enriched for constrained genes intolerant to nonsynonymous variation, suggesting a model of breed phenotype diversification based on regulatory changes to essential genes. Identification of trait-associated variants in dogs informs new biological roles of genes.  Improved collection of breed disease risk data, along with increased breed representation, will drive further discoveries.

overall_design: Dataset containing a total of 1,742 samples of which 1,434 are reanalyzed from GSM series, GSE83160, GSE83225, GSE90441, GSE96736, GSE121027, GSE123368, GSE193384, GSE213053, GSE241367. Remaining 308 samples are of various dog breeds, processed through GenomeStudio into a PLINK format for downstream analyses.

first: Reuben

middle: M

last: Buckley

first: Nüket

last: Bilgen

middle: C

first: Peter

last: Savolainen

first: Cafer

last: Tepeli

first: Metin

last: Erdoğan

first: Aitor

last: Serres Armero

first: Dayna

last: Dreger

first: Frank

middle: G

last: van Steenbeek

first: Marjo

middle: K

last: Hytönen

first: Jessica

last: Hale

first: Hannes

last: Lohi

first: Bengi

last: Çınar Kul

first: Adam

middle: R

last: Boyko

first: Elaine

last: Ostrander


title: Nuclear speckles regulate functional programs in cancer (CnR)

first: Katherine

last: Alexander

overall_design: 786-O ccRCC cells were treated with DMSO control or the PT2399 HIF-2a inhibitor for three hours (two replicates each), then Cut and Run was performed with the SON antibody (for speckles) or an isotype-mached IgG control antibody.

first: Shelley

last: Berger


title: Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration (Hi-C)

status: Public on Aug 26 2024

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

summary: Metastatic cancer cells traverse tight junctions that exert forces on their nucleus and the genomic contents within. Cancerous tumors are highly heterogeneous and not all cells within them can achieve such a feat. Here, we investigated what initial genome architecture characteristics favor the constricted migratory ability of cancer cells and which arise only after passage through multiple constrictions. We identified a cell surface protein (ITGB4) whose expression correlates with increased initial constricted migration ability in human melanoma A375 cells. Sorting out this subpopulation allowed us to identify cellular and nuclear features that pre-exist and favor migration, as well as alterations that only appear after cells have passed through constrictions.  We identified specific genomic regions that experienced altered genome spatial compartment profiles only after constricted migration. Our study reveals 3D genome structure contributions to both selection and induction mechanisms of cell fate change during cancer metastasis.

overall_design: A375 cells from either the original cell line population (Parental) or a population grown from a single cell (Clone3) were FACS sorted according to expression of Integrin Beta 4 (ITGB4).  Cells were then allowed to migrate through 5 rounds of constricted migration.  Genome structure was characterized by Hi-C across all populations and migration conditions.

first: Christopher

last: Playter

first: Rosela

last: Golloshi

first: Joshua

middle: H

last: Garretson

first: Alvaro

last: Gonzalez

first: Taiwo

last: Olajide

first: Ahmed

last: Saad

first: Samuel

middle: J

last: Benson

middle: P


title: Nuclear speckles regulate functional programs in cancer (TSA)

overall_design: 786-O ccRCC cells were treated with DMSO control or the PT2399 HIF-2a inhibitor for three hours (two replicates each), then SON TSA-seq was performed with the SON antibody (for speckles).


title: The Loss of an orphan Nuclear Receptor augments Wnt/β-Catenin signaling via epigenetic dysregulation that promotes Sp1 and Myc interactions in Hepatocellular Carcinoma Development [FAIRE-seq]

city: Little Rock

first: Kyounghyun

last: Kim

state: AR

address: Rm 318 CI.3329 4104 Outpatient Circle

department: Pharmacology & Toxicology

institute: University of Arkansas Medical Sciences

summary:
We previously reported that the nuclear receptor NR2E3 activates the tumor suppressor gene p53 by modulating chromatin accessibility. In this study, we further investigated the impact of NR2E3 deficiency on chromatin accessibility. We used FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements) analysis to find that NR2E3 loss increased chromatin accessibility in genomic regions interacting with various transcription factors, including Sp1. Additionally, NR2E3 loss enhanced chromatin accessibility and expression of crucial genes, such as JAK1 and PPARD, essential for WNT-β-catenin signaling pathway activation by facilitating interactions between Sp1 and Myc transcription factors at their promoters. Gene set enrichment analysis (GSEA) on mouse liver tumor tissues from wild-type and NR2E3 knockout mice confirmed that NR2E3 ablation activated WNT-β-catenin signaling pathways in vivo. Kaplan-Meier survival analysis using liver cancer patient data from two clinical datasets confirmed that patients with low NR2E3 expression exhibited increased WNT-β-catenin signaling activation, associated with adverse clinical outcomes. These findings highlight NR2E3 as a crucial tumor suppressor gene in hepatocellular carcinoma (HCC), primarily restraining WNT-β-catenin signaling pathway activation to maintain epigenetic homeostasis and contribute to HCC development. Our results prove NR2E3's critical role in liver cancer pathogenesis by regulating WNT-β-catenin signaling pathways and epigenetic equilibrium maintenance.
The Formaldehyde Assisted Isolation of Regulatory Elemens (FAIRE)-Seqwas performed using control (shCT) and NR2E3-depleted (shNR2E3) HepG2 cells.

overall_design: Sung-Gwon,Lee

first: Chungoo

last: Park


title: Synergistic combination therapies involving regorafenib in experimental glioma based on genome-wide CRISPR-Cas9 functional screens

status: Public on Aug 21 2024

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

country: Germany

institute: Hertie-Institute for Clinical Brain Research

summary: Registered systemic treatment options for glioblastoma patients are limited, particularly for progressive glioblastoma, including bevacizumab in the US and some other countries as well as lomustine. The phase II REGOMA trial suggested an improvement of overall survival in progressive glioblastoma by the multi-tyrosine kinase inhibitor regorafenib. This has not been confirmed by GBM AGILE, however. Of note, regorafenib has been administered as monotherapy in progressive glioblastoma or as an addition to standard of care in newly diagnosed glioblastoma. Rational combination therapies involving regorafenib, instead of entirely discontinuing any consideration of this compound, might be therefore a reasonable strategy. We addressed this research gap and used an innovative discovery and validation approach to identify functionally-instructed combination therapies. We applied a genome-wide CRISPR-Cas9-based functional genomics experimental approach including activation and knockout screens for the discovery of potential molecular targets modifying the therapeutic efficacy of regorafenib in experimental glioma. Selected functionally instructed molecular hits were then validated regarding synergistic interaction in vitro, ex vivo and in two orthotopic mouse models in vivo.This functional genomics approach led to the discovery of several molecular targets. Based on subsequent validation experiments including a customized compound library, we identified novel combination therapies. Particularly, the combination of regorafenib with Bcl-2/Bcl-xL inhibition was among the most promising strategies.

overall_design: Human glioma cell lines were treated with the multi tyrosine kinase inhibitor regorafenib at IC50 concentrations or corresponding DMSO concentrations for 24 hours.

first: Ghazaleh

last: Tabatabai


title: Gut microbiota drives vitiligo-related oxidative stress in skin via the metabolite Hippuric Acid

city: Beijing

first: Qingrong

last: Ni

address: No.30 Fucheng Road

department: Department of dermatology

institute: Air force medical center

summary: Vitiligo is a common autoimmune skin disorder. We constructed an induced vitiligo mouse model and performed bulk-RNA sequencing on the skin and 16S rRNA sequencing of feces from vitiligo mice and uninduced mice. Next, we performed skin bulk-RNA sequencing after treatment using ABX. Lastly, we subjected gut microbe-related metabolite hippuric acid to control mice and performed bulk-RNA sequencing on the skin to observe oxidative stress-related gene expression changes.

overall_design:
To mimic the vitiligo skin state, we constructed a vitiligo mouse model and sequenced the tail skin using bulk RNA-seq.
To detect the effect of gut microbiota on vitiligo skin, we depleted the gut microbes of vitiligo mice using ABX and tested the skin using bulk RNA-seq.
To mimic the effects of elevated concentrations of the gut microbe-derived metabolite hippuric acid on the skin and to rule out other possible factors, we injected hippuric acid intraperitoneally in wild type mice to observe the ROS accumulation phenomenon and sequenced the skin using bulk RNA-seq.

first: Lin

last: Xia

first: Meng

last: Nian

first: Yijin

last: Wang


title: Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration (RNA-Seq)

overall_design: A375 cells from either the original cell line population (Parental) or a population grown from a single cell (Clone3) were FACS sorted according to expression of Integrin Beta 4 (ITGB4).  Cells were then allowed to migrate through 5 rounds of constricted migration.  Different combinations of sorted ITGB4 status and migration were carried out and RNA extracted for polyA mRNA sequencing.


title: Molecular and spatial transcriptomic classification of midbrain dopamine neurons and their alterations in a LRRK2G2019S model of Parkinson’s disease

status: Public on Aug 19 2024

city: Chicago

first: Rajeshwar

last: Awatramani

state: IL

address: 2344 W Charleston, APT 2

department: Neurology

institute: Northwestern University

summary: In this study, we used snRNASeq to identify midbrain DA neuron subtypes in a LRRK2 model of PD, as well as explore subtype-specific alterations to gene expression.

overall_design: Four samples from a total of n=8 DAT-Cre mice with a nuclear GFP reporter and either WT (n=4) or heterozygous G2019S mutant (n=4) alleles for the gene Lrrk2. Samples contain tissue from midbrains after isolation of DAT+ nuclei via microfluidic sorting for GFP.

first: Zachary

last: Gaerner

first: Cameron

last: Oram

first: Amanda

last: Schneeweis

first: Jean-Francois

last: Poulin


title: Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration

first: Rachel

last: McCord

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

overall_design: Refer to individual Series


title: Oral Citrate Supplementation Mitigates Age-Associated Pathological Intervertebral Disc Calcification in LG/J Mice

status: Public on Aug 16 2024

city: Philadelphia

first: Makarand

middle: V

last: Risbud

state: PA

address: 1025 Walnut Street

department: Orthopaedic Surgery

institute: Thomas Jefferson University

summary: Despite the high prevalence of age-dependent intervertebral disc calcification, there is a glaring lack of treatment options for this debilitating pathology. Here, we investigate the efficacy of long-term oral K3Citrate supplementation in ameliorating disc calcification in LG/J mice, a model of spontaneous age-associated disc calcification. K3Citrate successfully reduced the incidence of disc calcification in LG/J mice without deleterious effects on vertebral bone structure, plasma chemistry, and locomotion. Notably, a positive effect on grip strength, a marker of frailty, was evident in treated mice. Spectroscopic investigation of the persisting calcified nodules indicated K3Citrate did not alter the mineral composition, and collagen 10 and aggrecan staining revealed that reactivation of an endochondral differentiation program in endplates may drive LG/J disc calcification. Importantly, K3Citrate reduced calcification incidence without altering the abundance of endplate hypertrophic chondrocytes, suggesting mitigation of disc calcification through Ca2+ chelation. This was further supported by the inability of K3Citrate to inhibit hypertrophic differentiation of chondrogenic ATDC5 cells and minimal effects on their metabolic status. Overall, this study sheds light on the pathogenesis of intervertebral disc calcification in LG/J mice and underscores the therapeutic potential of K3Citrate as a systemic intervention strategy for disc calcification.

overall_design: To investigate the impact of the presence (or absence) of intervertebral disc calcification on nucleus pulposus (NP) tissues, caudal NP tissue was collected from 23-month-old LG/J mice from two treatment cohorts: untreated controls, which received regular drinking water; or K3Citrate mice which received water continuously supplemented with 80mM K3Citrate from the time mice were 17 months of age (prior to developing disc calcification) until euthanasia. RNA-sequencing was then conducted on RNA isolated from NP tissues from control and K3Citrate cohorts. Each cohort contains four samples, each corresponding to a different mouse.

first: Olivia

last: Ottone


title: Degenerative and regenerative peripheral processes are associated with persistent painful chemotherapy-induced neuropathies in males and females

status: Public on Aug 08 2024

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary:
We investigated biological processes associated with persistency of chemotherapy-induced neuropathies in males and females
We then performed gene expression profiling analysis using data obtained from RNA-seq of hind paw and dorsal root ganglion (DRG) of males and females at different time points post-chemotherapy (PTX) treatment.

overall_design: Comparative gene expression profiling analysis of hind paw and DRG RNA-seq data for PTX treated male and female at 1, 16 and 31 days post-PTX.

first: George

middle: T

last: Naratadam

first: Jennifer

last: Mecklenburg

first: Sergey

last: Shein

first: Yi

last: Zou

first: Zhao

last: Lai

first: Alexei

last: Tumanov

first: Armen

middle: N

last: Akopian


title: Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: The maternal-to-zygotic transition is crucial in embryonic development, marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However, the changes occurring at the protein level during this transition remain unclear. Here, we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry, integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes, protein changes are less dynamic. Further, increases in protein levels correlate with mRNA translation, whereas declines in protein levels do not, suggesting active protein degradation processes. Interestingly, proteins from pure zygotic genes are present at fertilization, challenging existing mRNA-based gene classifications. As a proof of concept, we utilized CRISPR-Cas13d to target znf281b mRNA, a gene whose protein significantly accumulates within the first two hours post-fertilization, demonstrating its crucial role in development. Consequently, our protein profiling, coupled with CRISPR-Cas13d, offers a new approach to unravel maternal mRNAs function during embryonic development.

overall_design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ‘‘purge’’ mature eggs and used to establish an oogenesis time-line. Fish were euthanized and ovaries harvested within 1–11 days post-purging (dpp). Stage I and II oocytes were collected at 1–2 dpp, stage III oocytes (germinal vesicle in central position) at 4–7 dpp, and stage IV oocytes (germinal vesicle asymmetrically located) at 8–10 dpp. Oocyte isolations were based on73, and conducted in isolation medium Leibovitz L‐15 (Sigma-Aldrich #L5520) plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I (Sigma-Aldrich C0130) and 3 mg/mL Collagenase II (Gibco 17101015). Stage III was isolated with 3 mg/mL Collagenase I (Sigma-Aldrich C0130). Stage IV was isolated by mechanical stripping with forceps and needle without the use of Collagenases. Isolated oocytes were snap-frozen and RNA was extracted with TRIzol (Invitrogen #15596026) following manufacturer’s protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap-frozen in TRIzol (Invitrogen #15596026). Four time points of embryonic development were included: 1-cell stage (0-hpf, hours post fertilization), 2-hpf, 4-hpf, and 6-hpf. RNA was extracted with Direct-zol RNA MicroPrep kit (Zymo Research #R2062) following manufacturer’s protocols.

first: Gabriel

last: da Silva Pescador


title: ZFP36-family RNA-binding proteins in regulatory T cells reinforce immune homeostasis [bulk RNA-seq]

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

summary: RNA binding proteins (RBP) of the ZFP36 family limit the differentiation and effector functions of CD4 and CD8 T cells, but little is known of their expression or function in regulatory T cells (Treg). By Treg-restricted deletion of Zfp36 family members we identify the essential role of Zfp36l1 and Zfp36l2 in Treg to maintain immune homeostasis. Mice with Tregs deficient in these RBP display an inflammatory phenotype with an expansion in the numbers of type-2 conventional dendritic cells, T effector cells, T follicular helper and germinal center B cells and elevated serum cytokines and immunoglobulins. In the absence of Zfp36l1 and Zfp36l2, the pool of cycling CTLA-4 in naïve Treg was reduced, Tregs were less sensitive to IL-2 and IL-7 but were more sensitive to IFNγ. In mice lacking both RBP in Treg, the deletion of a single allele of Ifng is sufficient to ameliorate the pathology. Thus, ZFP36L1 and ZFP36L2 regulate multiple pathways that enable Tregs to enforce immune homeostasis.

overall_design: RNA-seq in regulatory T cells, comparing naïve Treg from Zfp36l1/Zfp36l2 conditional KO (Foxp3-YFP-Cre) female mice with naïve Treg from Foxp3-YFP-Cre controls. Libraries from male floxed controls were also generated from naïve and effector Treg. 5-7 replicates were included for each cell/genotype.

first: Beatriz

last: Sáenz-Narciso

first: Sarah

middle: E

last: Bell

first: Ram

last: Venigalla

middle: S

first: Martin

last: Turner


title: Trajectory modeling of first trimester placenta highlight differences between cytotrophoblast progenitors and trophoblast stem cells

city: La Jolla

first: Robert

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD


title: Nuclear speckles regulate functional programs in cancer (RNA HIF2A)

first: Katherine

middle: Ann

last: Alexander

overall_design: MCF7 cells, which have low endogenous HIF-2alpha, were treated treated with doxycycline in control cells without dox-inducible HIF-2alpha (two replicates), or in single cell clones (3 separate clones) with proteosome-stabilized HIF-2alpha that has wild type speckle targeting motifs or that has deletion of the two HIF-2alpha speckle targeting motifs.

middle: A

first: Shelley

middle: L

last: Berger


title: Definition of a multi-omics signature for Esophageal Adenocarcinoma prognosis prediction [scRNA-seq]

status: Public on Aug 02 2024

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

summary: Esophageal cancer, a highly lethal tumor, contributes to 5% of all cancer deaths, with its primary subtypes being esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). While most studies focus on ESCC, this study investigates EAC using single-cell RNA sequencing (scRNA-seq) to analyze CD45+ immune cells from tumors and matched non-tumor tissues in therapy-naïve patients. By examining the transcriptional profiles of these immune cells and the entire transcriptome in a cohort of 23 patients, the study identifies distinct transcriptional signatures. These signatures were used to stratify a large cohort of TCGA EAC patients, revealing strong associations with prognosis and clinical outcomes. The findings suggest that these transcriptional profiles can improve prognosis accuracy post-surgery and potentially guide effective therapies, including immunotherapy, for EAC patients.

overall_design: Single Cell and RNA sequencing analysis of CD45+ cells from Tumoral and non-tumoral biopsies of EAC patients to extrapolate immune signature to improve diagnosis and treatments

first: Luca

last: Lambroia

first: Carola

middle: M

last: Conca Dioguardi

first: Simone

last: Puccio

first: Clelia

last: Peano


title: Phosphorylation of PLIN5 is dynamically regulated in mice, required for IRS2 expression in the male mice liver, but dispensable for PGC1a target genes previously associated with PLIN5

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: Perilipin 5 (PLIN5) is a lipid droplet (LD) protein highly expressed in tissues that are active in fatty acid oxidation such as the heart, oxidative muscle, the liver, and brown adipocytes. PLIN5 shares homology with PLIN1: it prevents lipolysis in basal state but promotes lipolysis upon the activation of protein kinase A (PKA). In vitro studies expressing exogenous PLIN5 have shown that PLIN5 is phosphorylated at serine 155 (S155) by PKA. In addition to the regulation of lipolysis, phosphorylation of PLIN5 at S155 has been shown to regulate expression of genes in lipid metabolism, mitochondria, inflammation, and autophagy by traveling to the nucleus and activating peroxisome proliferater-activated-receptor-gamma-coactivator-1-α (PGC1a). However, a role of PLIN5 phosphorylation at S155 has been primarily studied in vitro with exception of a few studies expressing exogenous wild type (WT) and phosphorylation resistant PLIN5 (S155A) in the heart or the liver of mice. Here, we aim to determine the extent of endogenous PLIN5 phosphorylation in vivo and its role in the regulation of lipid metabolism and gene expression in the liver using PLIN5 S155A knock in mice (S155A). First, we enriched LDs from the liver of fed and fasted C57BL6 WT mice to measure non-phosphorylated and S155 phosphorylated PLIN5 by LC-MS/MS. While peak area of non-phosphorylated PLIN5 was similar, S155 phosphorylation was increased in the liver from fasted mice compared with fed mice confirming that endogenous PLIN5 is phosphorylated at S155 when PKA is activated during fasting (3.0-fold increase, p<0.05). Then, we utilized Phos-tag gel as a simple method to assess the extent of PLIN5 phosphorylation. When the heart and the liver from WT and S155A mice were run on Phos-tag gel and immunoblotted for PLIN5, a phosphorylated band was significantly reduced in S155A tissues confirming that S155 is the dominant phosphorylation site in vivo. Next, we assessed phenotypes of S155A mice to gauge the necessity of S155 phosphorylation for metabolism and gene expression in the fasted liver. For the glucose tolerance test, 4-month-old male and female S155A mice showed no differences, but one year-old S115A males had impaired glucose tolerance. There was not a significant difference in weight or blood glucose in fasted young S155A females compared to wild type, but aged male S155A mice had a higher fasted blood glucose (p<0.05) without difference in weight. There was not a significant difference in serum insulin, triglycerides (TG), beta-hydroxybutyrate, or non-esterified fatty acids levels between WT and S155A mice in either males or females. The liver TG contents did not differ between WT and S155A mice of both genders. When qPCR tested the liver of fasted WT and S155A mice, Pgc1a target genes upregulated by fasting and proposed to be regulated by PLIN5 phosphorylation did not show striking difference in expression. Pgc1a, Ppara, Acot1, Pdk4, and Ascl1 expression was similar between WT and S155A liver of fasted mice. Cpt1a and G6pc showed trend of reduction in S155A liver but did not reach statistical significance (n=5 to 7). Inflammation markers such as IL1b and Ccl2 did not differ between WT and S155A liver of fasted mice either. We performed unbiased RNA sequencing of WT and S155A liver from fasted female mice to identify genes differentially regulated by phosphorylation of PLIN5 at S155. There were limited number of genes differentially expressed in S155A female livers with 3 genes < 0.05 for adjusted p value. Interestingly, RNA seq identified insulin receptor substrate 1 (Irs1) as a gene with significantly decreased expression in the liver of female S155A mice (Log2 fold change -0.74, adjusted p value 0.003). The difference was confirmed in qPCR of fasted liver for the female mice (p<0.05), but not for males. Interestingly, insulin receptor substrate 2 (Irs2) measured by qPCR was not different in the liver of female S155A mice but was reduced in male S155A mice (p<0.05). The reduction of IRS2 protein in the liver of S155A male mice was confirmed by Western blot. In conclusion, endogenous PLIN5 in the liver increases phosphorylation at S155 upon fasting in mice. However, the loss of S155 phosphorylation does not affect serum lipids or liver TG. Also, changes in the expression of PGC1a target genes were subtle in the liver of fasted S155A mice compared with WT mice indicating that the loss of PLIN5 S155 phosphorylation can be readily compensated by other mechanisms. Unexpectedly, IRS2 showed decreased expression in the liver of S155A male mice that may explain glucose intolerance in aged male mice. Thus, PLIN5 phosphorylation may impact the insulin signaling in the liver by supporting IRS2 expression in male mice.

overall_design: To investigate the role of PLIN5 S155 phosphorylation in vivo, C57BL/6J were obtained and Crispr Cas9 was used to introduce S155A mutation to these mice. RNAseq was done to compare gene expression in the liver of the WT C57BL/6J and the phosphorylation deficient mice.

first: Yumi

last: Imai

first: Corinne

last: Bovee


title: Host complement C3 promotes malaria transmission by killing symbiotic bacteria in the mosquito midgut

status: Public on Aug 01 2024

city: chongqing

first: Biao

last: He

state: chongqing

address: Gaotanyan street 30, Shapinba district

department: Department of Pathogen Biology

institute: Army medical university

summary: Host-derived factors are sucked into midgut of mosquitoes during natural malaria transmission, but their influence on malaria transmission is largely unknown. We reported that mouse complement C3 taken into mosquitoes significantly promoted malaria transmission either in laboratory or in field. This effect was attributed to the reduction of microbiota abundance in mosquito midgut by host-derived C3 through direct lyses the predominant symbiont bacteria Elizabethkingia anopheles. Elizabethkingia anopheles symbiont bacteria were demonstrated to be detrimental to malaria sexual stages in mosquitoes. Strikingly, the promoted effect of host C3 on malaria transmission was confirmed by laboratory mosquitoes membrane-feeding on Plasmodium falciparum. Therefore, we reveal a novel strategy of malaria parasite to utilize host complement C3 to promote its transmission, and the administration of C3 inhibitor would provide us a novel strategy to control malaria transmission.

overall_design: RNA-seq analysis of anopheles stephensi mosquito fed on P. yoelii-infected C57BL/6 or C3-/- mice after 12h and 24h

first: Wenyue

last: Xu


title: Functional maps of a genomic locus reveal confinement of an enhancer by its target gene [Tagmentation]

city: Amsterdam

first: Christina

last: Moene

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Genes are often activated by enhancers located at large genomic distances. The importance of this positioning is poorly understood. Here, by relocating different promoter-reporter constructs into >1,000 alternative positions within a single locus, we dissected the positional relationship between the mouse Sox2 gene and its distal enhancer. This revealed an intricate, sharply confined activation landscape, in which the native Sox2 gene occupies an optimal position for its activation. Deletion of the gene relaxes this confinement and broadly increases reporter activity. Surprisingly, this confining effect of the Sox2 gene on reporter activity is partially conferred by its ~1 kb coding region. Our local relocation approach provides high-resolution functional maps of a genomic locus and reveals that a gene can strongly constrain its enhancer’s realm of influence.

overall_design: Sleeping Beauty transposon insertions in clonal cell lines and cell pools were mapped genome-wide using tagmentation mapping. For each biological sample, integrations were mapped by sequencing outwards from both transposon inverted terminal repeats (ITRs), resulting in a fw (forward, 3' ITR) and rv (reverse, 5' ITR) mapping library for each sample.

first: Mathias

last: Eder

first: Lise

last: Dauban

first: Christ

last: Leemans

first: Martijn

last: Verkuilen

first: Bas

last: van Steensel


title: Single-Cell and Spatial Transcriptomics Identified Fatty Acid–Binding Proteins Controlling Endothelial Glycolytic and Arterial Programming in Pulmonary Hypertension

city: St. Louis

first: Zhiyu

last: Dai

address: 4960 Childrens Place

institute: Washington University in St. Louis

summary:
Rationale: Pulmonary arterial hypertension (PAH) is a devastating disease characterized by obliterative vascular remodeling and persistent increase of vascular resistance, leading to right heart failure and premature death. Understanding the cellular and molecular mechanisms will help develop novel therapeutic approaches for PAH patients.
Objectives: To determine whether upregulation of fatty-acid binding protein 4 and 5 (FABP4/5) is critical in pathogenesis of PAH.
Methods: FABP4/5 expression was examined in pulmonary arterial endothelial cells (PAECs) and lung tissues from patients with idiopathic PAH and pulmonary hypertension (PH) rat models. Plasma proteome analysis was performed in human PAH samples. Echocardiography, hemodynamics, histology, and immunostaining were performed to evaluate the lung and heart PH phenotypes in Egln1Tie2Cre (CKO) mice and Egln1Tie2Cre/Fabp4-5-/- (TKO) mice.
Measurement and Main Results: Both FABP4 and FABP5 were highly induced in ECs of CKO mice and PAECs from IPAH patients, and in whole lungs of PH rats. Plasma levels of FABP4/5 were upregulated in IPAH patients and directly correlated with severity of hemodynamics and biochemical parameters. Genetic deletion of both Fabp4 and 5 in CKO mice caused a reduction of right ventricular systolic pressure (RVSP) and RV hypertrophy, attenuated pulmonary vascular remodeling and prevented the right heart failure. Fabp4/5 deletion also normalized EC glycolysis, reduced ROS and HIF-2a expression, and decreased aberrant EC proliferation in CKO lungs.
Conclusions: PH causes aberrant expression of FABP4/5 in pulmonary ECs which leads to enhanced EC glycolysis and hyperproliferation, contributing to the accumulation of arterial ECs and vascular remodeling and exacerbating the disease.

overall_design: Total RNA was isolated from lung tissue from WT, CKO (Egln1Tie2Cre) and TKO (Egln1Tie2Cre/Fabp4-5-/-) mice with Zymo Research Quick-RNA Miniprep Kits with DNase I digestion. RNA sequencing was carried out at the Novogene Corporation Inc. All samples were sequenced with an Illumina Novaseq 6000 platform with a pair end 150-bp read length.


title: Adipogenesis, lipolysis, and extracellular matrix remodeling are early modulated by a triterpene-enriched natural extract in a mouse cell line and primary human adipocytes

status: Public on Jul 31 2024

city: Medellin

first: alejandro

last: mejia

state: Antioquia

address: carrera 56A #61-24

country: Colombia

institute: University of antioquia

summary: Chronic Inflammation has a key role in the development of insulin resistance and type 2 diabetes. Previously, we demonstrated that OBE100, a natural extract from the leaves of Eucalyptus tereticornis, has anti-inflammatory properties. Three pentacyclic triterpenoids, ursolic acid, oleanolic acid, and ursolic acid lactone are the major compounds present in OBE100. These molecules have shown multiple biological activities. In this study we analyzed how the compounds of OBE100 modify adipocyte gene expression using RNA sequencing. Triterpenoids regulate the inflammatory program in differentiated adipocytes,  inhibiting the expression of many cytokines, chemokines, and inflammatory mediators. However, the OBE100 extract has a more powerful immunomodulatory effect than the triterpene mixture increasing the number of genes regulated, both in mouse and human models. Our study shows that OBE100 is a promising extract for the treatment of diabetes that can break the link between inflammation and insulin resistance.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
3T3-L1(CL-173TM) mouse pre-adipocytes were purchased from ATCC (Manassas, VA, USA). Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal bovine serum (FBS), 2mM glutamine, 1% penicillin/streptomycin, and 25 mM glucose (Growth Medium 2 – GM2) at 37°C and 5% CO2. Differentiation was induced two days postconfluence by adding GM2 containing 0.5 mM 3-isobutyl-1-methylxanthine (IBMX), 0.25 μM dexamethasone, 2 μM Rosiglitazone, and 1 μg/ml insulin. After two days of incubation, the medium was replaced with GM2 containing 1 μg/ml insulin. Two days later, the medium was replaced by GM2 and incubated for 24 hours with the different treatments. Human primary adipocyte culture was obtained from the abdominal fat of young women. Pre-adipocytes were induced into adipocytes after 100% confluence cultured in a differentiation medium (DMEM 25 mM glucose, 10% FBS, 0.5 mM IBMX, 5 μM dexamethasone, 10 μM insulin, and 2 μM Rosiglitazone) for 7 days. The cells were incubated with DMEM, 25 mM glucose, 10% SFB, and different treatments for another 24 hours.Crude extract OBE100, M1, UA, OA, and UAL were reconstituted in dimethyl sulfoxide (DMSO) at 25 mg/ml (stock solution). The final concentration of the compounds in the culture medium was OBE100 50 µg/ml, M1 39 µg/ml (UA+OA+UAL mix), UA 23.8 µg/ml, OA 7 µg/ml, and UAL 8.2 µg/ml. The concentration used for the three different triterpenes, both in the mixture called M1 and individually, were those determined in the fraction called OBE100. Three independent experiments were performed, each in triplicate.
We then performed RNA seq profiling using data obtained from RNA-seq. We compared differentiated adipocytes againts each control (OBE100, M1, UA, OA, UAL) and we also included an adipocyte without fat as control, to verify that the differentation was successfull

first: Norman

last: Balcazar

first: Sergio

last: Acin

first: Geysson

last: Fernandez

first: Alejandro

last: Mejia-Garcia


title: Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria

first: Aleksandr

last: Arzamasov

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Bifidobacteria are among the earliest colonizers of the human gut and are widely used as probiotics for their health-promoting properties. However, individual responses to probiotic supplementation may vary with strain type(s), microbiota composition, diet, or lifestyle conditions, highlighting the need for strain-level insight into bifidobacterial carbohydrate metabolism. Here, we systematically reconstructed 68 pathways involved in the utilization of mono-, di-, oligo-, and polysaccharides by analyzing the distribution of 589 curated metabolic functional roles (catabolic enzymes, transporters, transcriptional regulators) in 3083 non-redundant cultured Bifidobacterium isolates and metagenome-assembled genomes (MAGs) of human origin. Our analysis uncovered extensive inter- and intraspecies heterogeneity, including a distinct clade within the Bifidobacterium longum species capable of metabolizing starch. We also identified isolates of Bangladeshi origin that harbor unique gene clusters implicated in the breakdown of xyloglucan and human milk oligosaccharides. Thirty-eight predicted carbohydrate utilization phenotypes were experimentally validated in 30 geographically diverse Bifidobacterium isolates in vitro. Our large-scale genomic compendium expands the knowledge of bifidobacterial carbohydrate metabolism and can inform the rational design of probiotic and synbiotic formulations tailored to strain-specific nutrient preferences.

sample_organism: Bifidobacterium catenulatum subsp. kashiwanohense

overall_design: Three biological replicates were analyzed for each of the four conditions (growth in the medium supplemented with different carbon sources)


title: ZFP36-family RNA-binding proteins in regulatory T cells reinforce immune homeostasis

first: Louise

last: Matheson


title: Bulk RNA-Seq of Wnt signaling activating cardiomyocytes and scRNA-Seq of endothelial cells and atrioventricular canal cells in zebrafish

status: Public on Aug 23 2024

city: Yamagata

first: Ayano

last: Chiba

state: Yamagata

address: 2-2-2 Iida-Nishi

department: Department of Pharmacology

country: Japan

institute: Yamagata University


title: Arid1a-dependent canonical BAF complex suppresses inflammatory programs to drive efficient GC B cell responses [CUT&TAG]

first: Vipul

last: Shukla

state: Illinois

address: 303 E. Superior Street

department: Department of Cell and Developmental Biology

summary: Differentiating B cells in germinal centers (GC) require tightly coordinated transcriptional and epigenetic transitions to generate efficient humoral immune responses. The mammalian BAF (Brg1/Brm-associated factor) complexes are major regulators of nucleosomal remodeling, crucial for cellular differentiation and development, and are commonly mutated in several cancers, including GC-derived B cell lymphomas. However, the specific roles of distinct BAF complexes in GC B cell biology and the generation of functional humoral immune responses are not well-understood. Here, we show that the Arid1a-dependent canonical BAF (cBAF) complex is indispensable for generatingon of fully mature GCs and high affinity humoral immune responses. While Arid1a-deficient B cells undergo activation to initiate GC responses, they fail to sustain the GC program, resulting incausing premature GC collapse. Mechanistically, Arid1a-dependent cBAF activity establishes permissive chromatin landscapes at several thousand genomic regions during B cell activation and isare concomitantly required to suppress inflammatory gene programs to maintain transcriptional fidelity in early GC B cells. Interestingly, the inflammatory signatures instigated by Arid1a- deficiency in early GC B cells recruits neutrophils and inflammatory monocytes, and eventually disrupts GC homeostasis. Remarkably, dampening of inflammatory cues with anti-inflammatory glucocorticoid receptor signaling rescues GC B cell differentiation of Arid1a-deficient B cells, thus highlighting a critical role of inflammation in impeding GC responses. In sum, our work identifies essential functions of Arid1a-dependent BAF activity in promoting efficient GC responses. These findings further support recent paradigms uncovering a deterministic role of unrestrained inflammation in obstructing GC responses, common in patients with severe bacterial and viral infections.

overall_design: To investigate Arid1a binding (CUT and Tag) in WT and Arid1a KO in B cells, using Cg1cre

first: Ajay

last: Abraham

first: Daniela

last: Samaniego-Castruita

first: Isabella

middle: G

last: Han

first: Prathyaya

last: Ramesh

first: Mi

last: Tran

first: Jillian

last: Paladino

first: Heather

last: Kligfeld

first: Roxroy

last: Morgan

first: Rebecca

last: Schmitz

last: Southern

first: Ashima


title: Cpt2 knockout in muscle stem cells

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 270 S Russel St

department: Animal Sciences

institute: Purdue University

summary: Analysis of skeletal muscle satellite cells with specific knockout (KO) of Carnitine Palmitoyltransferase 2 (Cpt2) gene in mouse (named Cpt2PKO). Cpt2 knockout disrupts fatty acid oxidation in satellite cells and causes energy insufficiency and alteration of protein acetylation, which eventually impedes their expansion and differentiation, leading to impairments in muscle regeneration.

overall_design: FACS (fluorescence activated cell sorting)-isolated satellite cells from the experimental Cpt2PKO and wild type control hind limb muscles were cultured for 7 days in growth medium. Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA quality analysis was performed by Agarose Gel Electrophoresis and Agilent 2100 Bioanalyzer. A complementary DNA library was then constructed using poly(A) selected RNA, and sequencing was performed according to the Illumina HiSeq standard protocol (high-throughput, paired-end 150bp fragment sequencing). Raw reads from RNA-seq libraries are filtered to remove reads containing adapters or with low quality. Statistics analysis of data production and quality was performed to confirm the sequencing quality. Reference genome and gene annotation files were downloaded from a genome website browser (NCBI/UCSC/Ensembl). TopHat2 was used for mapping the filtered reads to the reference genome (Mus musculus, GRCm38/mm10). For the quantification of gene expression level, HTSeq V0.6.1 was used to analyze the read numbers mapped for each gene. The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene was calculated based on the gene read counts mapped to genes or exons. A differential expression analysis was performed using the DESeq2 R/EdgeR R package with the threshold of significance set as adjusted P < 0.05.

first: Feng

last: Yue


title: Interpretably deep learning amyloid nucleation by massive experimental quantification of random sequences

status: Public on Jul 17 2024

city: Barcelona

first: Mariano

last: Martín

address: c/ Baldiri Reixac 10-12

country: Spain

institute: IBEC

summary: More than 50 human diseases are characterized by the deposition of specific protein aggregates in the form of insoluble amyloid fibrils.  However, only a very small number of proteins are known to form amyloids with high propensity, limiting our ability to understand, predict and engineer amyloid aggregation from sequence. Here we use a massively parallel assay to quantify the amyloid nucleation propensity of >100,000 random 20 amino acid sequences.  Approximately 5% of assayed random sequences nucleate the formation of aggregates, generating a very large and diverse training dataset from which to train models to predict amyloid nucleation. We use this dataset to train CANYA, a convolution-attention hybrid neural network that predicts the propensity of any primary sequence to form amyloids. CANYA outperforms previous predictors of protein aggregation on additional random sequences and out-of-sample datasets including human disease-causing amyloids, with very stable performance across diverse prediction tasks.  We adapt and extend recent advances in interpretability of genomic neural networks to elucidate CANYA’s decision-making process and learned grammar and to provide mechanistic insights into amyloid formation. Our results demonstrate the power of massive experimental random sequence-space exploration and provide an interpretable and robust neural network model for understanding, predicting and designing amyloid-forming proteins.

overall_design: Systematic measurement of the nucleation of random 20mers peptides

first: Ben

last: Lehner

first: Benedetta

last: Bolognesi

first: Michael

last: Thompson

last: Martìn


title: Cellular origin and clonal evolution of human dedifferentiated liposarcoma

status: Public on Jul 22 2024

city: Paris

first: Fabien

last: Quinquis

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Dedifferentiated liposarcoma (DDLPS) is the most frequent high-grade soft tissue sarcoma subtype. It is characterized by a component of undifferentiated tumor cells coexisting with a component of well-differentiated adipocytic tumor cells. Both dedifferentiated (DD) and well-differentiated (WD) components exhibit MDM2 amplification, however their cellular origin remains elusive. Using single-cell RNA sequencing and functional assays in paired WD and DD components from primary DDLPS tumors, we characterized the cellular heterogeneity of DDLPS tumor and micro-environment. We identified a population of tumor adipocyte stem cells (ASC) showing striking similarities with adipocyte stromal progenitors found in white adipose tissue. We show that tumor ASC harbor the ancestral genomic alterations of WD and DD components, suggesting that both derive from these progenitors following clonal evolution. Last, we show that DD tumor cells keep important biological properties of ASC including pluripotency and that their adipogenic properties are inhibited by a TGF-β high immunosuppressive tumor micro-environment.

overall_design:
Primary DDLPS, WDLPS, liposarcoma and peritumoral fat tissue of untreated patients were isolated and analyzed using scRNAseq.

UPDATE [May-20-2025] The processed data files were updated.

first: Nadège

last: Gruel

first: Chloé

last: Quignot

first: Sophie

last: El Zein

first: Laëtitia

last: Lesage

first: Sylvie

last: Bonvalot

first: Dimitri

last: Tzanis

first: Julien

last: Vibert

first: Nadine

last: El Tannir

first: Didier

last: Decaudin

first: Héloïse

last: Derrien

first: Ahmed

last: Dahmani

first: Odette

last: Mariani

last: Linares

first: Sylvain

last: Baulande

first: Joshua

last: Waterfall

first: Olivier

last: Delattre

first: Sarah

last: Watson


title: Phage-phage competition and biofilms affect interactions between two virulent bacteriophages and Pseudomonas aeruginosa

city: Berlin

first: Magdalena

last: Bürkle

address: Chritéplatz 1

institute: Charité

summary: Virulent bacteriophages (or phages) are viruses that specifically infect and lyse a bacterial host. When multiple phages co-infect a bacterial host, the extent of lysis, dynamics of bacteria-phage and phage-phage interactions are expected to vary. The objective of this study is to identify the factors influencing the interaction of two virulent phages with different Pseudomonas aeruginosa growth states (planktonic, an infected epithelial cell line, and biofilm) by measuring the bacterial time-kill and individual phage replication kinetics. A single administration of phages effectively reduced P. aeruginosa viability in planktonic conditions and infected human lung cell cultures, but phage-resistant variants subsequently emerged. In static biofilms, the phage combination displayed initial inhibition of biofilm dispersal, but sustained control was achieved only by combining phages and meropenem antibiotic. In contrast, adherent biofilms showed tolerance to phage and/or meropenem, suggesting a spatiotemporal variation in the phage-bacterial interaction. The kinetics of adsorption of each phage to P. aeruginosa during single- or co-administration were comparable. However, the phage with the shorter lysis time depleted bacterial resources early and selected a specific nucleotide polymorphism that conferred a competitive disadvantage and cross-resistance to the second phage. The extent and strength of this phage-phage competition and genetic loci conferring phage resistance, are, however, P. aeruginosa genotype dependent. Nevertheless, adding phages sequentially resulted in their unimpeded replication with no significant increase in bacterial host lysis. These results highlight the interrelatedness of phage-phage competition, phage resistance and specific bacterial growth state (planktonic/biofilm) in shaping the interplay among P. aeruginosa and virulent phages.

overall_design:
To investigate the changes in P. aeruginosa PAO1 transcriptome upon infection with JG024 and coinfection with JG024+JG005.
We performed RNA-seq to determine transcriptional changes after 8 and 24 minutes of infection

first: Gopinath

last: Krishnamoorthy

first: Kai

last: Papenfort

first: Anne

last: Lippegaus


title: RNA-seq dataset for "Reelin marks cocaine-activated striatal ensembles, promotes neuronal excitability, and regulates cocaine reward"

status: Public on Jul 10 2024

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

summary: This dataset contains RNA-seq results from rat embryonic striatal neuronal cultures treated with CRISPRi machinery (dCas9-KRAB-MeCP2 fusion) with a CRISPR sgRNA targeting lacZ (a bacterial gene not found in the mammalian genome; used as a non-targeting control) or Reln.

overall_design: This experiment contains 8 biological samples, each of which underwent RNA-seq on an Illumina NovaSeq6000 instrument. Samples were treated with CRISPRi machinery targeting lacZ (lacZ control; samples X1i, X2i, X3i, X4i), or Reln (samples X5i, X6i, X7i, X8i) . Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.

first: Kasey

last: Brida

first: Lara

last: Ianov


title: snRNA-seq dataset for "Reelin marks cocaine-activated striatal ensembles, promotes neuronal excitability, and regulates cocaine reward"

summary: This dataset contains single-nucleus RNA-seq results from rat adult nucleus accumbens tissue treated with CRISPRi machinery (hSyn-driven dCas9-KRAB-MeCP2 fusion) with a CRISPR sgRNA targeting lacZ (a bacterial gene not found in the mammalian genome; used as a non-targeting control) or Reln.

overall_design: This experiment contains 8 biological samples, which represent individual rats (4 male, 4 female). Rats underwent stereotaxic surgery to transduce nucleus accumbens tissue with lentiviruses expressing CRISPRi machinery targeting lacZ (lacZ control; sample names beginning with lacZ), or Reln (sample names beginning with Reln). Two weeks following surgery, animals (4 lacZ, 4 Reln 2M/2F per group) were euthanized prior to rapid decapitation. Brains were blocked in 1mm sections, and NAc punches were obtained, flash frozen, and stored at -80°C prior to nuclei isolation. Following FACS-assisted nuclei isolation and quantification, nuclei from one rat were loaded into one GEM (gel beads in emulsion) well to generate barcoded nuclei (10× Genomics, PN-1000123, PN-1000122) on a Chromium iX instrument. Libraries were prepared according to the 10X Genomics manufacturer's recommendations, and sequenced on a NovaSeq 6000 platform to a depth of 300,000 reads per nuclei. Forward and reverse paired-end reads are denoted as "R1" or "R2" in raw file names.

first: Catherine

last: Newman


title: Effect of DEN-induced liver cancer in wildtype and OTUD3 knockout mice

city: Beijing

first: Hongmiao

last: Dai

address: Changping District

department: National Center for Protein Sciences (Beijing)

institute: State Key Laboratory of Proteomics

summary: To further investigate gene expression in DEN-induced liver cancer in mice with Otud3 gene knockout, we employed RNA-seq profiling as a discovery platform to identify the pathways or biological processes potentially responsible for the occurrence of DEN-induced liver cancer in both wildtype and Otud3 knockout mice. Liver cancer tissues from Otud3 knockout mice and their littermates, with or without a 14-day-old DEN injection, were utilized as samples for analysis.

overall_design: RNA-seq in mice liver cancer tissues was measured at 30 weeks post-DEN-injection. Three independent mice for each group were performed.

first: Lingqiang

last: Zhang

first: Bo

last: Wu

first: Hongchang

last: Li


title: Definition of a multi-omics signature for Esophageal Adenocarcinoma prognosis prediction [totalRNA-seq]

first: Bioinformatics

last: Unit

first: Luca

last: Lambroia

first: Carola

last: Conca Dioguardi

first: Simone

last: Puccio

first: Clelia

last: Peano


title: The life-saving benefit of dexamethasone in severe COVID-19 is linked to a reversal of monocyte dysregulation

status: Public on Jul 04 2024

first: Julia

middle: K

last: Polansky

address: Augustenburger Platz 1

institute: Berlin Institute of Health @ Charité Universitätsmedizin Berlin

type: Methylation profiling by genome tiling array

summary: Dexamethasone is a life-saving treatment for severe COVID-19, yet its mechanism of action is unknown, and many patients deteriorate or die despite timely treatment initiation. Here, we identify dexamethasone treatment-induced cellular and molecular changes associated with improved survival in COVID-19 patients. We observed a reversal of transcriptional hallmark signatures in monocytes associated with severe COVID-19 and the induction of a monocyte substate characterized by the expression of glucocorticoid-response genes. These molecular responses to dexamethasone were detected in circulating and pulmonary monocytes, and they were directly linked to survival. Monocyte single-cell RNA sequencing (scRNA-seq)-derived signatures were enriched in whole blood transcriptomes of patients with fatal outcome in two independent cohorts, highlighting the potential for identifying non-responders refractory to dexamethasone. Our findings link the effects of dexamethasone to specific immunomodulation and reversal of monocyte dysregulation, and they highlight the potential of single-cell omics for monitoring in vivo target engagement of immunomodulatory drugs and for patient stratification for precision medicine approaches.

overall_design:
To assess the possible influence of patient’s DNA-methylation status on responsiveness to dexamethasone treatment, we performed comparative analysis of the included patients from the Pa-COVID-19 study cohort with stable (Responder, n = 10) versus progressive disease (Non_Responder, n = 10) under treatment, i.e. which progressed from moderate to severe disease or death after having received at least 2 days of treatment with a sample collected within the first 4 days of treatment. Control patients without disease progression under treatment were matched for sex, age and available early samples after initiation of dexamethasone treatment. If more than one equivalent match was available, data was reviewed by at least two clinically experienced physicians for pre-existing comorbidities to find the most appropriate match.
CAPNETZ Study Group
Pa-COVID-19 Study Group

first: Rainer

last: Knoll

first: Elisa

last: Helbig

first: Kilian

last: Dahm

first: Olufemi

last: Bolaji

first: Frederik

last: Hamm

first: Martina

last: van Uelft

first: Sophie

last: Müller

first: Lorenzo

last: Bonaguro

first: Jonas

last: Schulte-Schrepping

first: Lev

last: Petrov

first: Benjamin

last: Krämer

first: Michael

last: Kraut

first: Paula

last: Stubbemann

first: Charlotte

last: Thibeault

first: Heidi

last: Theis

first: Gudrun

last: Hack

first: Elena

last: De Domenico

first: Jacob

last: Nattermann

first: Matthias

last: Becker

first: Marc

middle: D

last: Beyer

first: David

last: Hillus

first: Philipp

last: Georg

first: Pinkus

last: Tober-Lau

first: Lena

last: Lippert

first: Belén

last: Millet Pascual-Leone

first: Frank

last: Tacke

first: Gernot

last: Rohde

first: Norbert

last: Suttorp

first: Martin

last: Witzenrath

first: Thomas

last: Ulas

first: Birgit

last: Sawitzki

first: Leif

last: Sander

first: Joachim

last: Schultze

first: Anna

middle: C

last: Aschenbrenner

first: Florian

last: Kurth


title: ZFP36-family RNA-binding proteins in regulatory T cells reinforce immune homeostasis [single cell RNA-seq]

first: Louise

last: Matheson

address: Babraham Research Campus

institute: The Babraham Institute

summary: RNA binding proteins (RBP) of the ZFP36 family limit the differentiation and effector functions of CD4 and CD8 T cells, but little is known of their expression or function in regulatory T cells (Treg). By Treg-restricted deletion of Zfp36 family members we identify the essential role of Zfp36l1 and Zfp36l2 in Treg to maintain immune homeostasis. Mice with Tregs deficient in these RBP display an inflammatory phenotype with an expansion in the numbers of type-2 conventional dendritic cells, T effector cells, T follicular helper and germinal center B cells and elevated serum cytokines and immunoglobulins. In the absence of Zfp36l1 and Zfp36l2, the pool of cycling CTLA-4 in naïve Treg was reduced, Tregs were less sensitive to IL-2 and IL-7 but were more sensitive to IFNγ. In mice lacking both RBP in Treg, the deletion of a single allele of Ifng is sufficient to ameliorate the pathology. Thus, ZFP36L1 and ZFP36L2 regulate multiple pathways that enable Tregs to enforce immune homeostasis.

overall_design: Single cell RNA-sequencing of control and Zfp36l1/Zfp36l2-deficient regulatory T cells (Treg) from 14-week-old mice, with one replicate per genotype. Deletion was driven by the Foxp3-YFP-Cre allele. Treg from the two genotypes were labelled using Totalseq oligo-conjugated antibodies (BioLegend), before pooling, such that library generation and sequencing was performed within a single sample.

first: Beatriz

last: Sáenz-Narciso

first: Sarah

last: Bell

last: Turner


title: Genetic analysis of cis-enhancers associated with bone mineral density and periodontitis in the gene SOST

status: Public on Jun 27 2024

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

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

summary: A haplotype block at the sclerostin (SOST) gene correlates with bone mineral density (BMD) and increased periodontitis risk in smokers. Investigating the putative causal variants within this block, our study aimed to elucidate the impact of linked enhancer elements on gene expression and to evaluate their role on transcription factor (TF) binding. Using CRISPR/dCas9 activation (CRISPRa) screening in SaOS-2 cells, we quantified disease-related enhancer activities regulating SOST expression. Additionally, in SaOs2-cells, we investigated the influence of the candidate TFs CCAAT/enhancer-binding protein beta (CEBPB) on gene expression by antisense (GapmeR) knockdown, followed by RNA sequencing. The periodontitis-linked SNP rs9783823 displayed a significant cis-activating effect (25-fold change in SOST expression), with the C-allele containing a CEBPB binding motif (position weight matrix (PWM) = 0.98, Pcorrected = 7.7 x 10-7). CEBPB knockdown induced genome-wide upregulation but decreased epithelial-mesenchymal transition genes (P= 0.71, AUC = 2.2 x 10-11). This study identifies a robust SOST cis-activating element linked to BMD and periodontitis, carrying CEBPB binding sites and highlights CEBPB's impact on epithelial-mesenchymal transition.

overall_design: To establish the regulatory role of CEBPB, we downregulated CEBPB transcript levels in cultures of SaOs2 cells in 3 cell cultures 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 CEBPB.

first: Avneesh

last: Chopra

first: Jiahui

last: Song

last: Mikolaj Weiner 3rd

first: Dieter

last: Beule

first: Arne

last: Schaefer


title: Deoxypodophyllotoxin suppresses Malignant pleural mesothelioma growth via mitotic dependent necroptosis

status: Public on Jun 26 2024

city: Shanghai

first: Cheng

last: Zhong

state: Shanghai

address: Yishan road 600, Xuhui District, Shanghai, China

department: Department of Respiratory Medicine

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University

summary: Malignant pleural mesothelioma (MPM) is a highly aggressive tumor with a poor prognosis. Patients are typically diagnosed at an advanced stage due to the disease's long incubation period. Limited therapeutic advancements in the last two decades have prompted further investigation into alternative treatments. Previous studies have identified significant dysregulation in the mitotic spindle assembly checkpoint pathway and microtubule network of MPM, underscoring the potential of targeting microtubules in managing MPM. Deoxypodophyllotoxin (DPT) is a novel microtubule-targeting drug that has demonstrated promising therapeutic efficacy in various cancers. While the precise mechanism of DPT's anti-MPM effect remains undisclosed, our research indicates that DPT inhibits MPM growth in a dose-dependent manner both in vitro and in vivo. Moreover, it exhibits a favorable safety profile and shows lower toxicity towards normal cells and mice at therapeutic doses. Mechanistic studies involving three MPM cell lines (MSTO-211H, H2452, and H28) revealed that DPT induces multinucleated and micronucleated cells, disrupts spindle formation, and triggers Mitosis cell cycle arrest and necroptosis in tumor cells. In conclusion, our findings suggest that DPT holds promise as a safe and effective therapeutic option for MPM.

overall_design: Extract total RNA from MPM H2452 cells treated with DPT (20nM) or DMSO (control) 48h. We analyzed the differentially expressed genes between the treatment group and the control group using RNA. Both groups were treated in four biological replicates.

first: Rong

last: Sun

first: Tao

last: Ren


title: Cellular fitness of MYC-driven cancer cells to genetic and pharmacologic perturbations in normoxia, hypoxia and 3D

city: Memphis

first: Hongjian

last: Jin

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: MYC and hypoxia gene clusters are the two most commonly recurring transcriptional programs in heterogenous tumors. Understanding the cellular fitness of MYC-driven cancer cells in normoxia and hypoxia may lead to identification of distinct cancer cell vulnerabilities. Using genome-wide CRISPR screenings of MYC-driven liver cancer cells cultured over 4 weeks in 21% and 1% oxygen in monolayer, and 21% oxygen in 3D spheroid, we not only identify over 600 essential genes under all three conditions but also context-specific fitness genes and pathways. Knockout of VHL-HIF1 pathway results in incompatible fitness defects under 21% oxygen versus 1% oxygen or 3D.  Genetic deletion of each of the mitochondrial respiratory complex I-V has distinct cellular fitness outcomes. Notably, the organogenesis signaling pathways such as TGF-SMAD specifically limits the uncontrolled cell proliferation of 3D spheroids while inactivation of epigenetic modifiers (Bcor, Kmt2d, Mettl3 and Mettl14) has opposite outcomes in monolayer versus 3D. We also discover distinct metabolic requirement for fatty acid and cholesterol synthesis in three conditions. Chemical perturbations using 125 FDA approved oncology drugs reveal that MYC-driven liver cancer cells have different sensitivity to inhibition of tyrosine kinase receptors under hypoxia and 3D. Our resource study highlights unique epigenetic and metabolic dependency of MYC-driven cancer cells in different tumor environmental settings.

overall_design: To understand the gene transcription differences in normoxia vs hypoxia, monolayer vs 3D,, we performed we performed RNA-seq after NEJF10 cells were cultured in 21% and 1% oxygen in monolayer, or 21% oxygen in 3D spheroid.

first: Jie

last: Fang

first: Shibiao

last: Wan

first: Jun

last: Yang


overall_design: To explore chromatin accessibility in normoxia vs hypoxia 2D vs 3D, we performed we performed ATAC-seq after NEJF10 cells were cultured in 21% and 1% oxygen in monolayer, or 21% oxygen in 3D spheroid.

first: Fang

last: Jie

first: Jin

last: Hongjian

first: Yang

last: Jun


title: Esculetin promotes HDL-driven cholesterol excretion involved in CD36-mediated phagocytosis of adipose tissue macrophages and CEBPbeta

status: Public on Jun 12 2024

city: Xiamen

first: Binbin

last: Liu

state: Fujian

address: Jinshan Road

department: Xiamen Cardiovascular Hospital

institute: Xiamen University

summary: Postprandial dyslipidemia is a recognized risk factor for atherosclerosis. High-density lipoprotein (HDL)-mediated reverse cholesterol transport plays a crucial role in mitigating this risk by clearing postprandial lipids. This study aimed to investigate the impact of esculetin, a 4-Hydroxycoumarin, on postprandial cholesterol metabolism and excretion after a high-fat meal. Esculetin significantly elevated postprandial HDL cholesterol levels in serum and postprandial bile acid levels in bile, and altered serum metabolomics in mice fed a high-fat meal, indicating esculetin promotes HDL-driven cholesterol excretion after a high-fat meal. Furthermore, esculetin administration in mice led to an increase in the ratio and phagocytic activity of a subset of adipose tissue macrophages (ATMs) expressing high levels of CD36 and Tim4. Inhibition of CD36 by Sulfo-N-succinimidyl oleate (SSO) blocked esculetin-induced elevation of postprandial serum HDL and bile acid levels in bile. Additionally, esculetin demonstrated the ability to increase the uptake of oxidized LDL (ox-LDL) via CD36 in a macrophage cell line, which might involve alteration of the epigenetic landscape controlled by CCAAT enhancer-binding protein beta (C/EBPβ). Esculetin-induced increased uptake of ox-LDL and elevation of CD36 was inhibited in C/EBPβ-deficient cells. A relatively higher expression of C/EBPβ was observed in CD36+ ATMs, and esculetin increased the ratio of C/EBPβ+ CD36+ ATMs in mice fed a lipid-rich meal. Moreover, the direct interaction between esculetin and C/EBPβ were observed by Terahertz chemical microscope. Overall, these findings suggest esculetin promotes HDL-mediated postprandial cholesterol excretion by directly binding to C/EBPβ and enhancing CD36-dependent phagocytosis in ATMs.

overall_design: To study the transcriptomic alterations induced by esculetin in the liver, esculetin (0 or 90mg/kg/d) was daily administered to the mice by oral gavage for 7 days. In the first 4 days, the mice were fed with a control diet (CD) containing 10% kcal from fat. Then the mice were fed with a high- fat diet (HFD) containing 60% kcal from fat for additional 3 days to understand lipid-rich meals-induced postprandial lipid circulation. The transcriptomic alterations induced by esculetin were further analyzed in ox-LDL-treated RAW264.7 cells.  RAW264. 7 cells were treated with 25 ug/mL DIL-oxLDL and esculetin (0 or 40 ug/mL) for 24 hr.

first: Gang

last: Wang

first: Heng

last: Ye


title: A T cell-IL-3 axis controls the responsiveness of sensory neurons to allergens

status: Public on Jun 11 2024

city: Boston

first: Isabela

middle: J

last: Kernin

state: MA

address: 55 Fruit St

department: Center for Immunology and Inflammatory Diseases

institute: Massachusetts General Hospital

summary:
In naïve individuals, sensory neurons directly detect and respond to allergens, leading
both to the sensation of itch and the activation of local innate immune cells, which
initiate the allergic immune response1,2. In the setting of chronic allergic
inflammation, immune factors prime sensory neurons, causing pathologic itch3-7.
While these bidirectional neuroimmune circuits drive responses to allergens, whether
immune cells regulate the set-point for neuronal activation by allergens in the naïve
state is unknown. Here we describe a T cell-IL-3 signaling axis that controls the
allergen responsiveness of cutaneous sensory neurons. We define a poorly
characterized epidermal T cell subset8, termed GD3 cells, that produces its
hallmark cytokine IL-3 to promote allergic itch and the initiation of the allergic
immune response. Mechanistically, IL-3 acts on Il3ra-expressing sensory neurons in a
JAK2-dependent manner to lower their threshold for allergen activation without
independently eliciting itch. This T cell-IL-3 signaling axis further acts via STAT5 to
promote neuropeptide production and the initiation of allergic immunity. These
results reveal an endogenous immune rheostat that sits upstream of and governs
sensory neuronal responses to allergens upon first exposure. This pathway may
explain individual differences in allergic susceptibility and opens novel therapeutic
avenues for treating allergic diseases.

overall_design: scRNA-seq of gamma-delta T-cells from mouse tissue

first: Cameron

middle: H

last: Flayer

first: Neal

middle: P

last: Smith

first: Alexandra-Chloe

last: Villani

first: Caroline

last: Sokol


title: Alzheimer’s Disease Protective Allele of CLU Promotes Neuron Excitability, Neuron-glia Lipid Transfer and Astrocytic Lipid Droplets via neuronal CLU

status: Public on Jun 10 2024

city: Evanston

first: Jubao

last: Duan

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: Disease causal mechanism remains largely unknown for most Alzheimer’s disease (AD) genome-wide association studies (GWAS) risk loci, including the Clusterin (CLU) locus. Here, leveraging our approach to identify functional GWAS risk variants that show allele-specific open chromatin (ASoC), we nominated a putative AD causal SNP rs1532278 (T/C) of CLU that showed strong ASoC specifically in iPSC-derived excitatory neurons (iGlut). We found the AD protective allele T of rs1532278 elevated neuronal CLU and promoted neuron excitability. Transcriptomic analysis of iGlut (T/T vs. C/C) co-cultured with mouse astrocytes surprisingly showed allele T upregulated lipid synthesis and astrocytic lipid metabolism pathways. Further corroborative functional studies mechanistically tied allele T to CLU-facilitated neuron-glia lipid transfer and astrocytic lipid droplet (LD) formation. Interestingly, astrocytes with more LD were found to uptake less glutamate likely due to reactive oxygen species (ROS), which may contribute to CLU-promoted neuron excitability. Our study uncovered a previously unappreciated protective role of neuronal CLU in maintaining proper neuronal excitability through lipid-mediated neuron-glia communication.

overall_design: We co-cultured CRISPR-cas 9 engneered and iPS-derived glutamatergic neurons and  primary mouse astrocytes to investigate SNP rs1532278 dominated interactive effect between these two cell types.

first: Xiaojie

last: Zhao

first: Yan

last: Li

first: Siwei

last: Zhang


title: O-GlcNAcylation of NONO is Critical for Paraspeckle Component Assembly and Contributes to Tumorigenesis

status: Public on Jun 01 2024

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

summary: Non-POU domain-containing octamer-binding protein (NONO) is a multifunctional member of the Drosophila behavior/human splicing (DBHS) protein family with DNA- and RNA-binding activity. Recent studies revealed that NONO is O-GlcNAcylated and dysregulated in various types of cancer. Excessive O-GlcNAcylation of target proteins has also been implicated in tumorigenesis. However, it is not known whether O-GlcNAcylation of NONO promotes cancer cell growth, and little is known about the effect of O-GlcNAcylation on the biological properties of NONO. This study identifies Thr440 as the primary NONO O-GlcNAcylation site and demonstrates its crucial role in the assembly of paraspeckles, an important subnuclear compartment that facilitates NONO-dependent transcriptional regulation in mammalian cells. We demonstrated that O-GlcNAcylation of NONO is required to maintain the expression of genes related to GO category “microtubule cytoskeleton organization involved in mitosis” and to suppress the expression of genes related to GO category “cellular response to type I interferon”. Moreover, stable depletion of NONO O-GlcNAcylation or NONO knockout significantly inhibited the growth of colon cancer cells. These findings highlight the importance of NONO and its O-GlcNAcylation status in modulating cell cycle progression, immune response, and tumorigenesis.

overall_design: To investigate the function of NONO in HCT116 colorectal cancer cell line, we knocked-down NONO expression by treating siRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different types of cells with 3 biological replication.

first: Yeolhoe

last: Kim

first: Kyung-Tae

last: Lee


title: Phase 1 trial of durvalumab (anti-PD-L1) in combination with lenalidomide in relapsed/refractory cutaneous T cell lymphoma

status: Public on Jul 11 2024

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: T cells in cutaneous T-cell lymphoma (CTCL) are functionally exhausted, expressing immune inhibitory molecules such as PD1 and PD-L1. Durvalumab selectively targets PD-L1 on exhausted T cells and distinct cells within the CTCL tumor microenvironment (TME) and may restore an anti-tumor immune response. The oral immunomodulator lenalidomide, which has shown activity in CTCL, may enhance immune checkpoint blockade by durvalumab. We initiated a phase 1/2 clinical trial of lenalidomide and durvalumab in patients with refractory/advanced CTCL (NCT03011814). Primary objectives were to assess safety and tolerability and identify the maximum tolerated dose/recommended phase 2 dose. Secondary and tertiary objectives were to investigate efficacy and the effects on the TME. Thirteen patients enrolled in sequential cohorts received fixed dose durvalumab and dose escalation of lenalidomide. Thirteen patients were evaluable for toxicities and 12 for response in phase 1. No serious adverse events (AEs) or dose-limiting toxicities (DLTs) were observed during cycles 1-3 (DLT evaluation period). The most frequent AEs were tumor flare, fatigue, neutropenia and leukopenia. Three patients developed grade 1/2 autoimmune thyroiditis that resolved with treatment. Median cycles of treatment were 11 (range, 3-42+). Median duration of response was 25.5 (range 8-36.5) months. Anti-PD-L1/lenalidomide showed clinical activity; there were 7 partial responses, 4 stable disease and 1 progressive disease. Adaptive and innate immune signatures potentially predictive of response seen in gene expression profiling of serial skin samples were downregulation of TNF-alpha signaling via NFκB, IFN-gamma, and PI3-AKT-mTOR signaling pathways in responders vs up-regulation of MYC targets and pro-inflammatory pathways in non-responders. Profiling of immune cell compositions revealed changes in individual immune cell clusters based on treatment status and response.

overall_design:
Formalin-fixed paraffin-embedded (FFPE) tissue blocks from skin biopsies of cutaneous T cell lymphoma, baseline and on-treatment samples from patients treated with durvalumab (anti-PD-L1) and lenalidomide
Gene expression profiling  was performed , RNAseq data are from 2 time points (baseline and on-treatment)

first: Christiane

last: Querfeld

first: Joycelynne

last: Palmer

first: Zhen

last: Han

first: Xiwei

last: Wu

first: Yate-Chin

last: Yuan

first: Min-Hsuan

last: Chen

first: Ching-Yu

last: Sun

first: Ni-Chun

last: Tsai

first: D

first: Samantha

last: Hammond

first: Liliana

last: Crisan

first: Joo

last: Song

first: Raju

last: Pillai

first: Steven

middle: T

last: Rosen

first: Jasmine

last: Zain


title: Decipher immune response in early recovery phase of respiratory virus-induced disorder [BAL scRNA-seq]

status: Public on May 30 2024

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

summary: Appropriate lung repair responses are essential to restore functional integrity and prevent severe disease phenotypes after injury. While macrophages are thought to contribute to repair, whether distinct subsets occupy particular niches and assume dedicated tasks to mediate host recovery post- injury remains unknown. Using an in vivo model of influenza A virus (IAV) infection in combination with single-cell and spatial transcriptomic analyses, bone marrow chimeras and monocyte fate-mapping, we found the transitional appearance of Ccr2-dependent monocyte-derived Ly6G+ macrophages (Ly6G Macs) after viral clearance. Ly6G Macs inhabited the alveolar spaces of regenerating perilesional areas, exhibited a unique ultrastructural morphology as well as a high metabolic potential. Using in vivo gene targeting and ex vivo wound healing assays, we found that Ly6G Macs could limit disease severity and promote alveolar regeneration via interleukin-4 receptor- and arginase-1-dependent mechanisms acting on type 2 alveolar epithelial cells. We also found evidence that similar macrophages existed in other models of lung injury and in the airways of virally-infected humans. Our study thus identifies perilesional alveolar Ly6G Macs as a spatially-restricted short-lived macrophage subset engaging a crosstalk with type 2 alveolar epithelial cells to promote alveolar regeneration and recovery post-injury, thus representing an attractive therapeutic target.

overall_design: 8 BAL samples obtained from routine diagnostic procedures were processed in a pooled single-cell sequencing.

first: Pierre

last: Janssen

first: Cecilia

last: Ruscitti


title: Decipher immune response in early recovery phase of respiratory virus-induced disorder

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

overall_design: Refer to individual Series


title: Vestigial like family protein

status: Public on May 22 2024

city: WORCESTER

first: Susu

last: Guo

address: 7 Pocono Road

institute: UMASS Chan Medical School


title: Transcriptomic analysis of transgenic mouse kidney glomeruli with human APOL1 variants expression [scRNA-seq]

city: Bethesda

first: Teruhiko

last: Yoshida

state: Maryland

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

summary: We analyzed the transcriptomic profiles of transgenic mouse kidney glomeruli by single-nuclear RNA-seq.

overall_design: Transcriptomic profiles of glomeruli from BAC/APOL1xTg26 mouse kidney and BAC/APOL1 mouse kidney treated with interferon-g by single-nuclear RNA-seq

first: Khun

last: Zaw Latt

first: Yongmei

last: Zhao

first: Shashi

last: Shrivastav

first: Cheryl

last: Winkler

first: Jeffrey

middle: B

last: Kopp


title: Gene expression profiling of CTCL patient-derived cell lines after GTSF1 knockdown

status: Public on Jul 02 2024

city: Montreal

first: Amelia

last: Martinez Villarreal

state: Quebec

address: 1001 Boulevard Decarie

country: Canada

institute: McGill University

summary: In CTCL, the ectopic expression of Gametocyte Specific Factor 1 (GTSF1) has emerged as a potential prognostic biomarker. High expression of GTSF1 has been associated with a worse overall prognosis for patients. However, the contribution of GTSF1 to CTCL carcinogenesis remains unknown. We performed a shRNA mediated silencing of GTSF1 in three cell lines representing the most common variants of CTCL: Mac2A, representative of primary cutaneous Anaplastic Large Cell Lymphoma; MyLa 2000, representative of Mycosis Fungoides; and SZ4, representative of Sézary Syndrome. The three cell lines showed different gene expression profiles, signaling the different clinical behaviors of each variant. In Mac2A, silencing of GTSF1 in CTCL led to T cell activation and production of IFNγ and TNFα. This suugests that GTSF1 contributes to carcinogenesis by partially modifying the effector-memory phenotype of the malignant T cells.

overall_design: We transduced cell lines with lentiviral vectors. For each of the three cell lines we produced two conditions: (1) Non-silencing control (SCR) and (2) GTSF1 silencing (shGTSF1). Then, we performed RNA-Sequencing with three biological replicates for each condition and each cell line.

first: Danny

last: Bergeron

first: Ivan

last: Litvinov


title: Effect of VGLL2-NCOA2, TEAD1-NCOA2 and YAP5SA overexpression on mRNA expression in HEK293T cells (RNA-Seq)

summary: The vestigial like family proteins (VGLL) are thought to regulate transcription by interacting with the TEA domain transcription factors (TEAD), the primary mediators of the Hippo pathway. However, the functional regulation of VGLL proteins remains poorly characterized. Here, we explored the molecular mechanism of two VGLL2 and TEAD1 fusion proteins generated by recurrent translocations in spindle cell rhabdomyosarcoma. We demonstrated that, compared to VGLL2 and TEAD1 alone, VGLL2-NCOA2 and TEAD1-NCOA2 act as strong transcriptional activators of TEAD-mediated transcription. Although VGLL2-NCOA2 and Yes1 associated transcriptional regulator (YAP) control overlapping transcriptional programs and chromatin landscapes, the downstream transcription induced by the fusion proteins does not require YAP and WW domain containing transcription regulator 1 (TAZ). Furthermore, VGLL2-NCOA2 and TEAD1-NCOA2 fusions engage distinct epigenetic regulation by recruiting E1A binding protein p300 (p300) to drive TEAD-dependent transcription. We showed that small molecule p300 inhibition can suppress VGLL2-NCOA2 and TEAD1-NCOA2-induced oncogenic transformation both in vitro and in vivo. Overall, our data reveal a tumorigenic mechanism of VGLL and TEAD fusion proteins that is related to the Hippo pathway but independent of YAP/TAZ, suggesting potential therapeutic strategies for tumors carrying VGLL, TEAD, or nuclear receptor coactivator (NCOA) gene rearrangements.

overall_design: To investigate the effect of VGLL2-NCOA2 fusion protein, TEAD1-NCOA2 fusion protein and YAP5SA protein on gene transcription, plasmids were transfected into HEK293T cells and mRNA were detected by RNA-seq. HEK293T cells transfected pcDNA3.1 plasmids were used as control group. HEK293T cells with transient transfection of VGLL2-NCOA2, TEAD1-NCOA2 or YAP5SA were used as experimental group. The mRNA expression level was detected by RNA-seq.

first: Junhao

last: Mao

first: Xiaodi

last: Hu

first: Lifang

last: Ma


title: Immune profiling-based targeting of pathogenic T cells with ustekinumab in ANCA-associated glomerulonephritis

status: Public on Jun 28 2024

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

summary: Antineutrophil cytoplasmic antibody (ANCA)–associated vasculitis is a life-threatening autoimmune disease that often results in kidney failure caused by crescentic glomerulonephritis  (ANCA-GN).  To date, treatment of most patients with ANCA-GN relies on unspecific immunosuppressive agents that harbor serious adverse effects and limited efficiency. Using spatial and single-cell transcriptome analysis we characterized inflammatory niches in the kidneys of 34 patients with ANCA-GN and idenjpgied proinflammatory cytokine  producing  CD4+ and CD8+ T cells as a key pathogenic tissue signature. By employing digital pharmacology we then idenjpgied ustekinumab, a monoclonal antibody targeting IL-12 and IL-23 in these T cells, as promising therapeutic avenue. Based on these findings, four patients with relapsing ANCA-GN were treated with ustekinumab in combination with low-dose cyclophosphamide. Ustekinumab was given subcutaneously (90 mg) at weeks 0, 4, 12, and 24 and clinical and renal response were evaluated at week 26. Treatment induced substantial clinical response in all ANCA-GN patients, with improvements in kidney function, and Birmingham Vasculitis Activity Score, and was well tolerated.  Our findings suggest that the pathogenesis-based treatment of ANCA-GN patients with ustekinumab is efficacious and warrants further investigation in clinical trials.

overall_design: For spatial transcriptomics, formalin-fixed paraffin-embedded (FFPE) kidney tissue sections from patients with ANCA-associated glomerulenephritis (biopsies) and controls (healthy tissue from tumornephrectomies) were transferred on Visium (10x Genomics) slides (spatial for FFPE gene expression human transcriptome) and processed according to the manufacturer's instructions.

first: Jonas

last: Engesser

first: Darius

last: Schaub

first: Stefan

last: Bonn

first: Christian

middle: F

last: Krebs

first: Ulf

last: Panzer


title: A surgical mouse model of neonatal right ventricular outflow tract obstruction by pulmonary artery banding

status: Public on May 09 2024

first: Debao

last: Li

address: No. 1678 Dongfang Road, Tangqiao Street

institute: Shanghai Children's Medical Center

summary:
Disease animal models play an extremely important role in preclinical research. Lack of corresponding animal models, many basic research cannot be carried out, and the conclusions obtained are incomplete or even incorrect. Right ventricular (RV) outflow tract (RVOT) obstruction leads to RV pressure overload (PO) and reduced pulmonary blood flow (RPF), which are two of the most important pathophysiological characteristics in pediatric cardiovascular diseases, and seriously affect the survival rate and long-term life quality of many children. Due to the lack of a neonatal mouse model for RVOT obstruction, it is largely unknown how RV PO and RPF regulate postnatal RV and pulmonary development. Thus, many treatment are directly applied from adults despite significant differences in cardiovascular physiology between infants and adults, with limited or even harmful results. Here we firstly introduced a neonatal mouse model of RVOT obstruction by pulmonary artery banding (PAB) on postnatal day 1. PAB induced neonatal RVOT obstruction, RV PO, and RPF. Neonatal RV PO induced cardiomyocyte proliferation, and neonatal RPF induced pulmonary dysplasia, the two features that can not be observed in adult RVOT obstruction. As a result, PAB pups exhibited overall developmental dysplasia, a sign similar to that of children with RVOT obstruction. Since many pediatric cardiovascular diseases are associated with RV PO and RPF, the introduction of neonatal mouse model of RVOT obstruction may greatly enhance our understanding of those diseases, and eventually save or improve the lives of many children.
We used C57 mice in this study and divided them into sham and PAB group, each group contain 3 replicates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the right ventricular tissue of mouse pups on postnatal day 7.

last: li

first: Lincai

last: ye


title: Spatial transcriptomics of colorectal cancer tissues

status: Public on May 17 2024

city: Bangkok

first: Thanawat

last: Suwatthanarak

address: 2 Wanglang Road, Bangkok-Noi

country: Thailand

institute: Mahidol University

type: Expression profiling by genome tiling array

summary: We study and report the whole transcriptome spatial profiling insights in colorectal cancer using the Visium spatial technique (Visium CytAssist, 10x genomics).

overall_design: Formalin-fixed, paraffin-embedded (FFPE) samples were derived from coloractal cancer patients and applied for whole transcriptome spatial profiling (Visium CytAssist, 10x genomics).

first: Pariyada

last: Tanjak

first: Amphun

last: Chaiboonchoe

first: Vitoon

last: Chinswangwatanakul


title: A single cell atlas of the mouse seminal vesicle

status: Public on May 16 2024

city: Worcester

first: Oliver

last: Rando

state: Massachusetts

address: 364 Plantation Street

department: BMB

institute: Umass Chan Medical School

summary: During mammalian reproduction, sperm are delivered to the female reproductive tract bathed in a complex medium known as seminal fluid, which plays key roles in signaling to the female reproductive tract and in nourishing sperm for their onwards journey. The majority of seminal fluid is produced by a somewhat understudied organ known as the seminal vesicle. Here, we report a single-cell RNA-Seq atlas of the mouse seminal vesicle, generated using tissues obtained from 23 mice of varying ages, exposed to a range of dietary challenges. We define the transcriptome of the secretory epithelial cells in this tissue, identifying a relative homogeneous population of the epithelial cells responsible for producing the majority of seminal fluid. We also define the immune cell populations – including large populations of macrophages, dendritic cells, T cells, and NKT cells – which have the potential to play roles in producing various immune mediators present in seminal plasma. Together, our data provide a resource for understanding the composition of an understudied reproductive tissue with potential implications for paternal control of offspring development and metabolism.

overall_design: Seminal vesicles were collected from FVB/NJ and C57BL/6J mice at age of about 12 weeks to 28 months. The animals were maintained under controlled temperature and humidity conditions on a 12 hr light/dark cycle with different diets and water ad libitum. The diets used included Chow diet, High Fat diet. Low Protein diet or AIN-93G (Control diet, CD). The mice on HFD and CD were fed for 9 weeks after weaning. Chromium Single Cell 3’ Reagent Kit V2 (10X Genomics) was used for single-cell sequencing libraries.

first: Fengyun

last: Sun

first: Kathleen

last: Desevin

first: Yu

last: Fu


title: Transcriptome landscape of the adrenal gland and superior cervical ganglion from hypertension-induced left ventricular hypertrophy rat model

status: Public on Jun 17 2024

city: Chongqing

first: Chaohong

address: Yuzhong Road

institute: Chongqing Medical University

summary: Hypertension-induced left ventricular hypertrophy (LVH) is a cardiac structural remodeling and dysfunction resulting from chronic hypertension and is an independent risk factor for cardiovascular morbidity and mortality. Studies have implicated the involvement of the adrenal gland (AG) and superior cervical ganglion (SCG) in hypertension regulation. However, the molecular mechanisms of AG and SCG during hypertension-induced LVH remain unclear. In this study, we investigated the transcriptome characteristics of the left ventricle, AG, and SCG in 24-week-old spontaneously hypertensive rats (SHR) and Wistar-Kyoto (WKY) rats using transcriptome sequencing (RNA-seq) technology. We identified 671 differentially expressed genes (DEGs) in the left ventricle, 1596 DEGs in the AG, and 343 DEGs in the SCG between SHR and WKY rats. Functional analysis revealed that these DEGs were involved in pathways related to immune inflammation, metabolic responses, and synaptic transmission. Further analysis demonstrated the presence of crosstalk among DEGs across these three organs, including 63 overlapping DEGs among these three organs, of which 59 DEGs exhibited consistent changes. In summary, we elucidates the transcriptome features of AG and SCG during hypertension-induced LVH in SHR, highlighting the complex molecular interactions across multiple organs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the left ventricle, AG, and SCG in 24-week-old spontaneously hypertensive rats (SHR) and Wistar-Kyoto (WKY) rats.

first: Fengting

last: Liu

first: Xingyu

first: Xiaohua

last: Yang

first: Qiaoqiao

first: Jing

last: Huang