title: Unwinding the roles of DEAD-box RNA helicases DDX39A and DDX39B in alternative RNA splicing

city: charlottesville

first: Shefali

last: Banerjee

state: Virginia

address: 622 Noush court

institute: University of Virginia

summary: Dead-box RNA helicases are crucial in mRNA processing, specifically in RNA splicing. Our previous work has shown that DDX39B is responsible for regulating the splicing of IL7R exon 6 and several FOXP3 introns, which rely on DDX39B's helicase and ATPase activities, respectively [this is not accurate since exon 6 also must require the ATPase activity, which is required for helicase activity]. In this study, we aimed to investigate whether DDX39A, a highly homologous paralog of DDX39B, plays a similar role in regulating alternative RNA splicing. We find that DDX39A and DDX39B have significant redundancy in their gene targets, however, DDX39A is incapable of complementing defective splicing of IL7R exon 6 when DDX39B is knockdown. Conversely, overexpressing DDX39A can rescue FOXP3 intron 11 splicing under DDX39B-depleted conditions. In this work we also confirm that introns containing C-rich/U-poor polypyrimidine tract are very sensitive to DDX39B levels. We also observed that cassette exons with C-rich/U-poor py tracts in upstream introns were also sensitive to DDX39B levels and were skipped more upon depletion of DDX39B, but not DDX39A. Among the introns retained more upon DDX39A and DDX39B depletion were DDX39A and DDX39B intron 6, which depend on DDX39A and DDX39B levels, respectively. Therefore, we identified an autoregulatory mechanism through which DDX39A and DDX39B control their respective expression. This study presents evidence that while DDX39A and DDX39B differentially impact certain RNA splicing events, they have many shared targets.

overall_design: HeLa cells were treated with two independent siRNAs targeting DDX39A expression (siD06 and siD09) and two independent siRNAs targeting DDX39B expression (siD11 and siD13). Control siRNA NSC at two different concentrations 5nM and 25 nM as a non-targeting control. The changes in DDX39A expression were compared with NSC-25 samples and changes in DDX39B expression were compared to NSC-5nM samples.

first: Chloe

last: Nagasawa

first: Steven

last: Widen

first: Mariano

last: Garcia-Blanco


title: The transcriptional landscape associated with the deletion of Regnase-1 [RNA-Seq]

status: Public on May 30 2024

city: Osaka

first: Xin

last: Sun

address: 3-1 Yamadaoka, Suita

country: Japan

institute: IFReC, Osaka University

type: Expression profiling by high throughput sequencing

summary: Having identified the crucial role of IFN-γ in anti-tumor immunity of Reg-1ΔNK, we attempted to elucidate the mechanism underlying the regulation of Ifng in the context of Regnase-1 deletion. Despite the notable increase in Ifng mRNA expression in Reg-1ΔNK-NK cells, Ifng was not a direct substrate of Regnase-1. However, the production of the IFN-γ was further enhanced upon stimulation with IL-12/18. We proposed that modifications may have occurred in the transcriptional regulation of Ifng in Reg-1ΔNK-NK cells.

overall_design: To elucidate the transcriptional landscape associated with the deletion of Regnase-1, we performed paired assays for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) using Reg-1fl/fl- and Reg-1ΔNK-NK cells treated with or without IL-12/18.


title: TWEAK/Fn14 signalling in Breast Cancer  (RNA-Seq)

status: Public on May 29 2024

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: This study explores the transcriptiomic and epigenetic roles of TWEAK/Fn14 signalling in Breast Cancer

overall_design: HER2 breast cancer cell lines were treated with TWEAK for 48h then harvested for RNA-seq

first: Nicholas

last: Sim


title: TWEAK/Fn14 signalling in Breast Cancer (TNBC H3K27ac ChIP-seq)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: TNBC cell lines were treated with TWEAK for 48h then washed out for 72h. Cells were then used for H3K27ac ChIP-seq


title: TWEAK/Fn14 signalling in Breast Cancer (ATAC-Seq)

overall_design: SKBR3 cells were treated with TWEAK for 48h then harvested for ATAC-seq


title: TWEAK/Fn14 signalling in Breast Cancer (Fn14 KO TNBC H3K27ac ChIP-seq)

overall_design: Fn14 KO TNBC cell lines were treated with TWEAK for 48h then harvested for H3K27ac ChIP-seq


title: TWEAK/Fn14 signalling in Breast Cancer (MAFG ChIP-seq)

overall_design: Breast cancer cell lines were treated with TWEAK for 48h then harvested for MAFG ChIP-seq


title: The transcriptional landscape associated with the deletion of Regnase-1 [ATAC-Seq]


title: TWEAK/Fn14 signalling in Breast Cancer [patient ATAC-seq]

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) on six Fn14 high triple negative breast cancer tumours and their matched normal samples.


title: GFI1B determines specificity of lung tissue-resident multipotent ILC

city: Brisbane

first: Qiutong

last: Huang

state: QLD

address: 37 Kent Street

country: Australia

institute: The University of Queensland

summary: GFI1B expression identified a multi-lineage ILC subset that retained the capacity for ILC2 development in the lung. We used single cell RNA sequencing (scRNAseq) to analyse the differentially expressed genes in these multipotent lung resident ILC.

overall_design: Lung ILCs of the GFI1BGFP mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of GFP signal and analysed using scRNAseq.

first: Gabrielle

last: Belz


title: TWEAK/Fn14 signalling in Breast Cancer [patient K27 ChIP]

overall_design: Chromatin immunoprecipitation-sequencing (ChIP-seq) for the histone modification H3K27ac in six Fn14 high triple negative breast cancer tumours and their matched normal samples.


title: TWEAK/Fn14 signalling in Breast Cancer [cell line hiChIP]

overall_design: In situ chromatin conformation capture followed by chromatin immunoprecipitation DNA-sequencing for the histone modification H3K27ac (H3K27ac HiChIP) in untreated and TWEAK treated triple negative breast cancer cell line MDA-MB-231.


title: TWEAK/Fn14 signalling in Breast Cancer [cell line ATAC-seq]

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) on untreated and TWEAK treated breast cancer cell lines: MDA-MB-231, Hs578T and MCF7


title: TWEAK/Fn14 signalling in Breast Cancer [cell line RNA-seq]

overall_design: RNA-sequencing (RNA-seq) of untreated and TWEAK treated breast cancer cell lines: MDA-MB-231, Hs578T, MCF7 and CAMA1


title: TWEAK/Fn14 signalling in Breast Cancer [cell line K27 ChIP]

overall_design: Chromatin immunoprecipitation-sequencing (ChIP-seq) for the histone modification H3K27ac in untreated and TWEAK treated breast cancer cell lines: MDA-MB-231, Hs578T, MCF7 and CAMA1.


title: TWEAK/Fn14 signalling in Breast Cancer (HER2 H3K27ac ChIP-seq)

overall_design: HER2 breast cancer cell lines were treated with TWEAK for 48h then harvested for H3K27ac ChIP-seq


title: Deletion of the mRNA endonuclease Regnase-1 promotes NK cell anti-tumor activity via OCT2- dependent transcription of Ifng

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

overall_design: Refer to individual Series


title: TWEAK/Fn14 signalling in Breast Cancer [p52_ChIP]

overall_design: P52 ChIP-seq on TWEAK treated MDA-MB-231 cells


title: Integrated transcriptomics of human blood vessels defines the spatially regulated niche for early mesenchymal progenitors

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

country: USA

institute: Johns Hopkins University

summary: Blood vessel walls are organized into concentric cellular layers, in which the outer layer, or tunica adventitia, represents the major niche for mesenchymal progenitor cells. By profiling large vessels (arteries and veins) using spatial transcriptomics, we found a hierarchy of stem cells based on spatial organization. In addition, we performed scRNaseq on CD34+ adventitial cells and integrated to out spatial transcriptomics where we identified the novel stem cell marker CD201 in the outer layer. This segregation was regulated by the WNT and TGFβ signaling pathways, which was confirmed by total RNAseq of CD201Low/High subsets of adventitial cells.    To investigate the transcriptomic differences between the novel subset of  of adventitial cells (CD34+,CD31-,CD45-) based on CD201 expression, FACTS isolated adventitial cells with low /high CD201 expression were sequenced.

overall_design: subsets of adipose derived adventitial cells (CD34+,CD31-,CD45-) with low or high expression of CD201 were isolated by by Fluorescence-activated cell sorting (FACS) based on their immunophenotype and analyzed using total RNA sequencing. ANOVA comparison was performed between three biologic replicates of each class.

first: Yiyun

last: Wang

first: Neelima

last: Thottappillil

first: Mario

middle: A

last: Gomez-Salazar

middle: W


title: NanoDam Profiling of EGL-43 and FOS-1 in Dopaminergic Neurons

city: Stanford

first: Callista

last: Yee

state: California

address: 327 Campus Drive, Shen lab, Bass Biology 329

institute: Stanford University/HHMI

summary: Activity-dependent mechanisms have been long known to play a critical role in synaptogenesis. Here, we utilize a recently adapted technology, NanoDam, to perform targeted DamID using endogenously tagged GFP transcription factors.

overall_design: A single copy insertion of a dopaminergic promoter driving expression of a GFP nanobody fused to Dam methylase was crossed together with animals carrying endogenous EGL-43::GFP and FOS-1::GFP. Dam methylase permanently methylated DNA in close proximity to regions of TF binding. DNA from L3 worms was extracted, digested with DpnI, amplified, and sequenced using the MinION Nanopore platform

first: Kang

last: Shen


title: NACC2 is a molecular effector of miR-132 regulation at the interface between adult neurogenesis and Alzheimer’s disease

status: Public on May 28 2024

city: Amsterdam

first: Evgenia

last: Salta

state: north holland

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute For Neuroscience

summary: The process of generating new neurons at the hippocampal neurogenic niche, also referred to as adult hippocampal neurogenesis (AHN), is impaired in Alzheimer’s disease (AD). MicroRNA-132 (miR-132), the most consistently downregulated microRNA (miRNA) in AD, was recently identified as a potent regulator of AHN, exerting multilayered proneurogenic effects in adult neural stem cells (NSCs) and their progeny. Supplementing miR-132 in AD mouse brain restores AHN and relevant memory deficits, yet the exact mechanisms involved are still unknown. Here, we identify NACC2 as a novel miR-132 target implicated in both AHN and AD. miR-132 deficiency in mouse hippocampus induces Nacc2 expression and inflammatory signaling in adult NSCs. We show that miR-132-dependent regulation of NACC2 is involved in the initial stages of human NSC differentiation towards astrocytes and neurons. Later, NACC2 function in astrocytic maturation becomes uncoupled from miR-132. We demonstrate that NACC2 is present in reactive astrocytes surrounding amyloid plaques in mouse and human AD hippocampus, and that there is an anticorrelation between miR-132 and NACC2 levels in AD and upon induction of inflammation. Unraveling the molecular mechanisms by which miR-132 regulates neurogenesis and cellular reactivity in AD, will provide valuable insights towards its possible application as a therapeutic target.

overall_design: Nestin:GFP+-niche cells were FACS-sorted from the dentate gyrus of Nestin-GFP mice. Four miR-132 antagomir-injected and four control-injected nestin-GFP male mice were used, and 96 cells were initially plated-sorted per mouse (each sample consisted of 1 full dentate gyrus; right and left hemisphere). We then performed gene expression profiling by high throughput sequencing.

first: Amber

last: Penning

first: Sarah

last: Snoeck

first: Oxana

last: Garritsen

first: Giorgia

last: Tosoni

last: Hof

first: Fleur

last: de Boer

first: Joëlle

last: van Hasenbroek

first: Lin

last: Zhang

first: Nicky

last: Thrupp

first: Katleen

last: Craessaerts

first: Mark

last: Fiers


title: Large-scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific

status: Public on May 27 2024

first: Kevin

last: Emmerich

address: 1800 Orleans St

department: Ophthalmology

summary: Many genes are known to regulate Müller glia (MG)-dependent retinal regeneration following widespread tissue damage. Conversely, genes controlling regeneration following limited retinal cell loss, per degenerative disease, are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here, transgenic zebrafish enabling inducible selective retinal ganglion cell (RGC) ablation were combined with single cell multiomics and CRISPR/Cas9-based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration- seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly, 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration, and seven of these knockouts actually enhanced RGC replacement kinetics, including sox2, olig2, and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e., biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem-like state and context-specificity in how genes function during regeneration. Increased understanding of how disease-relevant cell types can be selectively regenerated will, support the development of disease-tailored regenerative therapeutics.

overall_design: We performed single-cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells (RGCs, 4 timepoints) and ablation of rod photoreceptors, and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.

first: Jeff

middle: S

last: Mumm


title: Role of iRhom2 in Olfaction: Implications for Odorant Receptor Regulation and Activity-dependent Adaptation

city: New York

first: Carl

last: Blobel

state: New York

address: 515 East 71st street

institute: Hospital for Special Surgery, Research Institute

summary: The cell surface metalloprotease ADAM17 and its binding partners iRhom2 and iRhom1 modulate cell-cell interactions by mediating the release of membrane proteins such as TNFa and EGFR-ligands from the cell surface. Most cell types express both iRhoms, though myeloid cells exclusively express iRhom2, and iRhom1 is the main iRhom in the mouse brain. Here we report that iRhom2 is uniquely expressed in olfactory sensory neurons (OSNs), highly specialized cells expressing one olfactory receptor (OR) from a repertoire of over a thousand OR genes in mice. iRhom2-/- mice had no evident morphological defects in the olfactory epithelium (OE), yet RNAseq analysis revealed differential expression of a small subset of ORs. Notably, while the majority of ORs remain unaffected in iRhom2-/- OE, OSNs expressing ORs that are enriched in iRhom2-/- OE showed fewer gene expression changes upon odor environmental changes than the majority of OSNs. Moreover, we discovered an inverse correlation between the expression of iRhom2 compared to OSN activity genes and that odor exposure negatively regulates iRhom2 expression.  Given that ORs are specialized G-protein coupled receptors (GPCRs) and many GPCRs activate iRhom2/ADAM17, we investigated if ORs could activate iRhom2/ADAM17. Activation of OR2AT4 by its agonist sandalore in keratinocytes, where this receptor is ectopically expressed, leads to ERK1/2 phosphorylation, likely via an iRhom2/ADAM17-dependent pathway.  Taken together, these findings point to a mechanism by which odor stimulation of OSNs activates iRhom2/ADAM17 catalytic activity, resulting in downstream transcriptional changes to the OR repertoire and activity genes, and driving a negative feedback loop to downregulate iRhom2 expression.

overall_design: To investigate gene expression differences between iRhom2-/- and WT olfactory epithelium, main olfactory epitheliums were harvested at various ages and bulk sequenced.

first: Stephanie

last: Azzopardi

first: Hsiu-Yi

last: Lu

first: Sebastien

last: Monette

first: Ariana

middle: I

last: Rabinowitsch

first: Jane

middle: E

last: Salmon

first: Hiroaki

last: Matsunami

middle: P


title: Metabolism of plant stem cells under low oxygen tension: metabolic reprogramming by phytoglobin (Pgb1) underlying stem cell functionality

city: Winnipeg

first: Claudio

last: Stasolla

state: MB

address: 66 Dafoe Road

department: Plant Science

country: Canada

institute: University of Manitoba

summary: The quiescent center (QC) stem cells of maize (Zea mays L.) roots are highly hypoxic under normal oxygen tension. Despite this state, they are vulnerable to hypoxic stress which causes their degradation with the subsequent inhibition of root growth. These effects are abolished by over-ever-expression of the nitric oxide (NO) scavenger Phytoglobin 1 (ZmPgb1.1) preserving the functionality of the QC stem cells during the stress. Among the metabolic changes occurring in WT QC stem cells under low oxygen are the depletion of starch and soluble sugars, reliance of glycolytic fermentation, and impairment of the TCA cycle through the depressed activity of several enzymes including pyruvate dehydrogenase (PDH). This suggests that carbohydrate delivery from the shoot is insufficient to meet the metabolic demand of the QC stem cells during the stress. Atypical hypoxic responses related to the induction of alcohol dehydrogenase (ADH) and accumulation of glycolytic metabolites were also identified.  The preservation of QC stem cells by ZmPgb1.1 was underpinned by extensive metabolic rewiring centered around to the activation of the TCA cycle and the retention of carbohydrate storage products, denoting a more efficient production of energy and diminished demand of carbohydrates under conditions where nutrient transport may be limiting. Overall, this study provides an unprecedented overview of metabolic responses occurring in plant stem cells during oxygen deficiency.

overall_design: The roots of 5-day old maize (Zea mays L.) seedlings overexpressing [line ZmPgb1.1(S)] or down-regulating [line ZmPgb1.1(A)] Phytoglobin 1 (ZmPgb1.1) were exposed to normoxic (0h) and hypoxic conditions for 12 hours (12h). The quiescent center (QC) stem cells were isolated from the root tips for multi-omic measurements, including RNA-sequencing.

first: Mohammed

middle: M

last: Mira

first: Robert

middle: D

last: Hill

first: Alexander

last: Hilo

first: Matthias

last: Lange

first: Sean

last: Robertson

first: Abir

middle: U

last: Igamberdiev

first: Olivia

last: Wilkins

first: Hardy

last: Rolletschek


title: Polycomb sustains promoters in a deep OFF-state by limiting PIC formation to counteract transcription

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

summary: The Polycomb system plays fundamental roles in regulating gene expression during mammalian development. However, how it controls transcription to enable gene repression has remained enigmatic. Here we employ rapid degron-based depletion coupled with live-cell transcription imaging and single-particle tracking to uncover how the Polycomb system controls transcription in single cells. We discover that the Polycomb system is not a constitutive block to transcription but instead sustains a long-lived deep promoter OFF-state which limits the frequency with which the promoter can enter into a transcribing state. We demonstrate that Polycomb sustains this deep promoter OFF-state by counteracting the binding of factors that enable early transcription pre-initiation complex formation and show that this is necessary for gene repression. Together these important discoveries provide a new rationale for how the Polycomb system controls transcription and suggests a universal mechanism that could enable the Polycomb system to constrain transcription across diverse cellular contexts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The genomic distribution of TAF1-T7 was profiled in RING1B-miniAID;TAF1-T7-dTAG mESCs, in which RING1B can be conditionally depleted.

first: Aleksander

last: Szczurek

middle: J

last: Klose


title: Transcriptome Analysis Reveals Potential Protective Effects and Biomarkers of Pien Tze Huang on CCl4-induced Liver Cancer (lncRNA and mRNA)

status: Public on May 26 2024

city: Shanghai

first: Yongzhi

last: Wang

state: Shanghai

address: Huashan Road 1954

country: China

institute: Shanghai Jiao Tong University

summary:
Pien Tze Huang (PZH) is a traditional Chinese medicinal formula that has been extensively used in Asia for the treatment of liver diseases. We created two groups of liver cancer mouse models induced by carbon tetrachloride (CCl4): one group received treatment with PZH and the other did not receive any treatment. In the non-PZH treated group, we observed a significant increase in liver function indices including albumin (ALB), alanine aminotransferase (ALT), and aspartate aminotransferase (AST). Histological examination using hematoxylin and eosin (HE) staining revealed inflammation around the hepatic vein in the non-PZH treated group. Furthermore, Masson's trichrome staining demonstrated the presence of blue-stained collagen fibers around the hepatic vein in the non-PZH treated group. These findings suggest that PZH may have therapeutic effects on liver inflammation and cancer.

To further explore the molecular mechanisms of PZH's action, we conducted mRNA, long non-coding RNA (lncRNA), circular RNA (circRNA), and microRNA (miRNA) sequencing to identify potential drug targets at the transcriptome level. We identified 478 differentially expressed protein-coding transcripts and 68 differentially expressed lncRNA transcripts. Our study provides insights into potential transcriptional therapeutic targets for the clinical use of PZH in treating liver diseases.

overall_design: We construct two groups liver cancer mice model using CCl4, one group using PZH treatment, and the other did not receive any treatment. We also did a blank experiment with normal mice using water.In the 22nd week, we selected six mice from each group for lncRNA and mRNA sequencing.

first: Hao

last: Wu

first: Shengying

last: Qin


title: Transcriptomic analysis of HIV-associated nephropathy (Tg26) mouse kidney [bulk RNA-seq]

city: Bethesda

first: Teruhiko

last: Yoshida

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

summary: We analyzed the transcriptomic profiles of Tg26 mouse kidney cortex by bulk mRNA-seq with or without treatment by PKR inhibitor (C16).

overall_design: Transcriptomic profiles of Tg26 mouse kidney cortex by bulk mRNA-seq

first: Khun

middle: Z

last: Latt

first: Avi

last: Rosenberg

first: Yongmei

last: Zhao

first: Shashi

last: Shrivastav

first: Koji

last: Okamoto

first: Cheryl

last: Winkler

first: Jeffrey

middle: B

last: Kopp


title: Ultrasound-responsive theranostic platform for real-time monitoring and efficient thrombolysis in tPA-resistant thrombi

city: Chongqing

first: Wen

last: Zeng

address: Gaotanyan street

department: Department of Cell Biology

institute: Army Medical University

summary: There is no noninvasive solution for tPA-resistant thrombi while endovascular thrombectomy is the last option. Here, we proposed neutrophil extracellular traps (NETs), ε-(γ-glutamyl)lysine isopeptide bonds and fibrin scaffold as keychain in tPA-resistant thrombus, which was confirmed in the thrombi retrieved from stroke patients. A theranostic platform was designed for the combination of sonodynamic and mechanical thrombolysis under the guidance of ultrasonic imaging. Three rounds of 10 min noninvasive treatment led to the breakdown of the keychain, achieving great recanalization rate of 90% in rat occlusion model while tPA only made 10% improvement. RNA sequencing results and endothelium functional tests jointly indicated that the vascular homeostasis can be effectively reconstructed. The noninvasive theranostic capability presented in pig’s lengthy thrombi (>8mm) and thrombosis-susceptible tissue engineered vascular grafts (TEVGs) indicated its clinical transformation prospects. Taken together, this non-invasive theranostic platform provides a new strategy for tPA-resistant thrombi.

overall_design: Rat common carotid artery thrombosis was induced by ferric chloride, vascular recanalization was achieved under the combination of sonodynamic therapy and physical-explosion therapy, and the recanalized common carotid arteries were collected after one day and one week. Normal rat common carotid artery was taken as control.

first: Lin

last: Lin


title: Transcriptome Analysis Reveals Potential Protective Effects and Biomarkers of Pien Tze Huang on CCl4-induced Liver Cancer

type: Non-coding RNA profiling by high throughput sequencing


title: The OTX2-regulated alternative splicing landscape controls differentiation and reconstitutes the developmental origins of Group 3 medulloblastoma

status: Public on May 24 2024

city: Toronto

first: Liam

last: Hendrikse

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

institute: University Health Network

summary: RNA sequencing was performed on Group 3 medulloblastoma tumorspheres following PPHLN Morpholino treatment or scramble control.

overall_design: A custom splice-blocking morpholino to induce exon skipping was designed for PPHLN1 (ENSG00000134283.13, exon 6, 5’-AGAGTCTAGCTCAAAACTCACCTCT-3’).  A concentration of 1 µM in ddH20 was added to HDMB03 single cell suspensions cultured in ultra-low-attachment plates for 5 days prior to RNA extraction.

first: Tamra

last: Werbowetski-Ogilvie


title: Terminal nucleotidyl transferases govern secondary siRNA production at distinct steps in plants

status: Public on May 22 2024

city: København N

first: Peter

last: Brodersen

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

summary: In this study, we aim at understanding the contributions from TUTases, HESO1 and URT1, in miRNA-targeted secondary siRNA production in Arabidopsis thaliana. We have sequenced small RNAs from various T-DNA insertation single/double/triple mutants and compared their capability of producing ectopic secondary siRNAs from endogenous miRNA targets. The DESeq analysis is also included.

overall_design: small RNA seq data from mutant lines (ski2-5, rrp4-2, urt1-1, heso1-4, heso1-1/urt1-1, rrp4-2/urt1-1/heso1-4, rrp4-2/urt1-1/dcl2CRISPR) and a wild type line. All lines are ecotype Col-0. There are three biological triplicates of each sample. The tissue that has been sequences is inflorescences.

first: Maria

middle: L

last: Vigh

first: Axel

last: Thieffry

first: Laura

last: Arribas-Hernández


title: Anti-tumor effects of the eIF4A Inhibitor didesmethylrocaglamide and its derivatives in human and canine osteosarcomas

status: Public on May 23 2024

city: Columbus

first: Long-Sheng

last: Chang

state: Ohio

address: 575 Children's Crossroad, WC-5574, Ctr for Childhood Cancer & Dept of Pediatrics, Nationwide Children's Hosp & The Ohio State U

department: Center for Childhood Cancer

institute: Research Institute at Nationwide Children's Hospital

summary: Inhibition of translation initiation using eIF4A inhibitors like (-)-didesmethylrocaglamide [(-)-DDR] and (-)-rocaglamide [(-)-Roc] is a potential cancer treatment strategy as they simultaneously diminish multiple oncogenic drivers. We showed that human and dog osteosarcoma cells expressed high levels of eIF4A1/2, which are important for cell growth. To advance preclinical development of eIF4A inhibitors, the importance of (-)-chirality in DDR for growth-inhibitory activity was demonstrated. Bromination of DDR at carbon-5 abolished growth-inhibitory activity, while acetylating DDR at carbon-1 was tolerated. Like DDR and Roc, DDR-acetate increased the γH2A.X levels and induced G2/M arrest and apoptosis. These rocaglates decreased the levels of several mitogenic kinases, the STAT3 transcription factor, and the stress-activated protein kinase p38. However, phosphorylated p38 was greatly enhanced, implying activation of stress response pathways. Importantly, these rocaglates potently suppressed canine osteosarcoma patient-derived xenografts. These results suggest that these eIF4A inhibitors can be leveraged to treat both human and dog osteosarcomas.

overall_design: RNA sequencing of MG-63 and Saos2 human osteosarcoma cells treated for 24 hours with DMSO or 1x growth-inhibitory IC50 of the eIF4A1/2 inhibitors rocaglamide (Roc) or didesmethylrocaglamide. MG-63 treatment was conducted as two biological replicates and Saos2 cells as three biological replicates.

first: Janet

last: Oblinger


title: CCR3 knockdown attenuates prolonged underwater operation-induced cognitive impairment via alleviating microglia-mediated neuroinflammation

status: Public on May 20 2024

first: Houyu

state: Yangpu

address: No. 5, Panshan Road, Yangpu District, Shanghai

institute: Naval medical university

summary: It is important to maintain cognitive integrity during underwater operations, which may also trigger cognitive alterations. Cognitive effect of underwater operations and the underlying mechanism remain elusive. Here, we found a single underwater operation affects cognition in a time-dependent model. Prolonged exposure elicits significant cognitive impairment and hippocampal dysfunction, which was accompanied by activation of microglia and upregulation of pro-inflammatory cytokines. RNA-sequencing supported the involvement of neuroinflammation and indicated the critical role of CCR3. Knockdown of CCR3 significantly rescued cognitive impairment and hippocampal dysfunction. Furthermore, the upregulation of pro-inflammatory cytokines was also reversed. Mechanistically, CCR3 knockdown switched the activated microglia from a pro-inflammatory to neuroprotective phenotype. Taken together, these results highlighted the time-dependent effects of a single underwater operation on cognitive function. Knocking down CCR3 can attenuate neuroinflammation by regulating polarization of activated microglia, thereby alleviating prolonged underwater operation-induced cognitive impairment.

overall_design: To  uncover the underlying molecular mechanisms of prolonged underwater operation-induced cognitive impairment, we performed gene expression profiling analysis using data obtained from RNA-seq of hippocampal tissues of the NC group and the AS3h group.


title: Disrupting TSLP - TSLP receptor interactions via small molecule inhibitors yields a novel and efficient treatment option for atopic diseases

status: Public on May 17 2024

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

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

summary: Thymic stromal lymphopoietin (TSLP) is a key player in the pathogenesis of atopic diseases. Its pathophysiological relevance has sparked great interest in therapeutically targeting TSLP. Yet, so far, no small-mo lecule TSLP inhibitors exist due to the challenging nature of disrupting the protein-protein interaction between TSLP and its receptor. Here, we report the development of small-molecule TSLP receptor inhibitors  using structure- based virtual screening and docking of >1,000,000 compounds followed by iterative chemical synthesis. BP79 emerged as our lead compound that effectively abrogates TSLP-triggered cytokine release  at low micromolar concentrations. Topical application of BP79 yields efficient skin absorption followed by significant downregulation of atopy-relevant proinflammatory cytokines in immunocompetent skin disease  models. For further analysis, we developed a human atopic disease drug discovery platform using microfluidic multi-organ chips. Here, topical application of BP79 onto atopic-like skin disease models that were co -cultivated with lung models in the presence of Th2 cells effectively suppressed immune cell infiltration and key atopy mediators including IL-13, IL-4, TSLP, and periostin, while upregulating skin barrier prote ins such as filaggrin. RNA-Seq analysis corroborated these findings and also indicated protective downstream effects on the lung epithelium. To the best of our knowledge, this represents the first report of a po tent and safe small molecule TSLPR inhibitor which has the potential to expand the therapeutic and preventive options in atopic diseases. Further, it serves as a starting point for further developments in target ing TSLP as a central player of inflammation.

overall_design: Two tissues (skin and lung) were divided between two 3D model conditions ("atopic-like" and normal) and then treated with BP79 compound or left untreated. Differential gene expression was used to infer regulated genes in either condition, and gene set enrichment analysis was used for discerning of relevant biological pathways

first: Partho

last: Protim Adhikary

first: Dieter

last: Beule

first: Sarah

last: Hedtrich


title: Increased activity of protein kinase A, even without DNAJB1, is sufficient to cause Fibrolamellar hepatocellular carcinoma

first: David

last: Requena

state: NY

address: 1230 York Avenue

institute: Rockefeller University

summary: Most fibrolamellar carcinoma (FLC) is driven by a fusion of DNAJB1 and PRKACA, the catalytic subunit of protein kinase A (PKA). Overexpression of DNAJB1::PRKACA, ATP1B1::PRKACA or PRKACA, but not catalytically inactive kinase, caused similar transcriptomic changes of primary human hepatocytes; these recapitulated most changes observed in FLC. This is consistent with the observation that FLC is found in patients missing a regulatory subunit or with a ATP1B1::PRKACA fusion. Thus, the DNAJB1 domain is not required for FLC.

overall_design: Primary Human Hepatocytes were transduced with either DNAJB1::PRKACA, ATP1B1::PRKACA, PRKACA or kinase inactive DNAJB1::PRKACA or dsRED.

first: Mahsa

last: Shirani

first: Ype

last: deJong

first: Sanford

last: Simon


title: ATP-citrate lyase regulates chromatin-dependent activation and maintenance of the myofibroblast gene program and cardiac fibrosis

status: Public on May 16 2024

city: Philadelphia

first: Michael

middle: Panagiotis

last: Lazaropoulos

state: PA

address: 3500 North Broad Street

department: Department of Cardiovascular Sciences

institute: Temple University

summary:
Differentiation of cardiac fibroblasts (CFs) to myofibroblasts is necessary for matrix remodeling and fibrosis in heart failure. We previously reported mitochondrial calcium signaling drives α-ketoglutarate-dependent histone demethylation, promoting the myofibroblast gene program. Here, we investigated the role of ATP-citrate lyase (ACLY), a key enzyme for acetyl-CoA biosynthesis, in histone acetylation regulating myofibroblast formation and persistence in cardiac fibrosis. Inactivation of ACLY prevented, and importantly reversed, myofibroblasts towards quiescence. Genetic deletion of Acly in activated myofibroblasts prevented fibrosis and preserved cardiac function in murine pressure-overload. TGFβ stimulation enhanced ACLY nuclear localization and increased H3K27ac at fibrotic gene loci. Pharmacological inhibition of ACLY or forced nuclear expression of dominant-negative ACLY mutant prevented myofibroblast formation and H3K27ac. Our data indicate nuclear ACLY activity is necessary for myofibroblast differentiation and persistence by maintaining histone acetylation at TGFβ-induced myofibroblast genes. These findings provide novel clinical rational to prevent and reverse pathological fibrosis.
CUT&RUN Sequencing for H3K27ac on the role of ACLY in myofibroblast differentiaton.

overall_design: H3K27ac-enriched DNA using CUT&RUN from cardiac fiborblasts stimulated with or without TGFβ and treated with and without ACLY inhibitor.

first: Andrew

last: Gibb

first: Douglas

last: Chapski

first: Thomas

last: Vondriska

first: John

last: Elrod


title: Periprostatic adipose tissue inhibits tumor progression by secreting apoptotic factors: A natural barrier induced by the immune response during the early stages of prostate cancer

status: Public on May 15 2024

city: Taoyuan City

first: I-Hung

last: Shao

address: No. 5, Fuxing St., Guishan Dist.

country: Taiwan

institute: Chang Gung Memorial Hospital

summary:
Prostate cancer (PCa) is the second most prevalent malignancy in Western countries and the fifth leading cause of cancer-related death in men. The risk factors for PCa include obesity, age, and family history. Visceral fat has been linked to PCa risk, which has prompted researchers to investigate the influence of body composition and fat distribution on PCa prognosis.
This study investigated the correlation between the composition of pelvic adipose tissue (PAT) and PCa aggressiveness to understand the role played by this tissue in PCa progression. Moreover, we prepared a periprostatic adipose tissue (PPAT)-conditioned medium (CM) to determine the influence of the PPAT secretome on the pathophysiology of PCa. This study included 60 patients with localized PCa who received robot-assisted radical prostatectomy. Medical records were collected, and magnetic resonance imaging scans were analyzed, and body compositions were calculated to identify the correlations between adipose tissue volume and clinical PCa aggressiveness. CM was prepared using PPAT and perivesical adipose tissue (PVAT) collected from 25 patients during surgery, and its influence was investigated using the PCa cell lines C4-2 and LNCaP and the prostate epithelial cell line PZ-HPV-7. Cell proliferation assays and RNA sequencing were performed.
The initial prostate-specific antigen level was significantly correlated with pelvic and perirectal adipose tissue volumes. PPAT volume was significantly higher in patients with extracapsular tumor extension. PCa cells proliferated was significantly slower when cultured in PPAT-CM compared with when cultured in control- and PVAT-CM. RNA sequencing revealed that immune responses and the cell death and apoptosis pathways were enriched in PPAT-CM-cultured cells. The cytokines or other secreted factors in PPAT-CM induced PCa cell apoptosis.
This in vitro study revealed that the PPAT secretome inhibits PCa cells proliferation by activating immune responses and promoting cancer cell apoptosis. This mechanism may act as a first-line defense during the early stages of PCa.

overall_design: RNA-Seq was performed to enable a comparison of the RNA expression between cells cultured in control-CM, PPAT-CM, or PVAT-CM.

first: Tzu-Hsuan

first: Ying-Hsu

first: Yu-Hsin

last: Hsieh

first: Ting-Wen

last: Sheng

first: Li-Jen

last: Wang

first: Yu-Hsuan

last: Chien

first: Liang-Kang

last: Huang

first: Yuan-Cheng

last: Chu

first: Hung-Cheng

last: Kan

first: Po-Hung

last: Lin

first: Kai-Jie

last: Yu

first: Ming-Li

first: Cheng-Keng

last: Chuang

first: Chun-Te

last: Wu

first: Chin-Hsuan

first: See-Tong

last: Pang


title: The oocyte microenvironment is altered in adolescents compared to oocyte donors.

city: Chicago

first: Elnur

last: Babayev

state: IL

address: 303 E Superior St 10-220

department: Obstetrics and Gynecology

institute: Northwestern University

summary:
Study question: Are the molecular signatures of cumulus cells (CCs) and follicular fluid (FF) of adolescents undergoing fertility preservation differ from that of reproductively adult oocyte donors?
Summary answer: The microenvironment immediately surrounding the oocyte, including the CCs and FF, is altered in adolescents undergoing fertility preservation compared to oocyte donors.
What is known already: Adolescents experience a period of subfecundity following menarche. Recent evidence suggests that this may be at least partially due to increased oocyte aneuploidy. Reproductive juvenescence in mammals is associated with suboptimal oocyte quality.
Study design, size, duration: This was a prospective cohort study. Adolescents (10-19 years old, N=23) and oocyte donors (22-30 years old, N=31) undergoing ovarian stimulation and oocyte retrieval at the Northwestern Fertility and Reproductive Medicine Center between November 1, 2020 and May 1, 2023 were enrolled in this study.
Participants/materials, setting, method:  Patient demographics, ovarian stimulation, and oocyte retrieval outcomes were collected for all participants. The transcriptome of CCs associated with mature oocytes was compared between adolescents (10-19 years old, n=19), and oocyte donors (22-30 years old, n=19) using bulk RNA-sequencing. FF cytokine profiles (10-19 years old, n=18 vs. 25-30 years old, n=16) were compared using cytokine arrays.
Main results and the role of chance: RNA-seq analysis revealed 581 differentially expressed genes (DEGs) in cumulus cells of adolescents relative to oocyte donors, with 361 genes downregulated and 220 upregulated. Genes enriched in pathways involved in cell cycle and cell division (e.g., GO:1903047, p= 3.5 x 10-43; GO:0051983, p= 4.1 x 10- 30; GO:0000281, p= 7.7 x 10-15; GO:0044839, p= 5.3 x 10-13) were significantly downregulated, while genes enriched in several pathways involved in cellular and vesicle organization (e.g., GO:0010256, p= 1.2 x 10-8; GO:0051129, p= 6.8 x 10-7; GO:0016050, p= 7.4 x 10-7; GO:0051640, p= 8.1 x 10-7) were upregulated in CCs of adolescents compared to oocyte donors. The levels of 9 cytokines were significantly increased in FF of adolescents compared to oocyte donors: IL-1 alpha (2-fold), IL-1 beta (1.7-fold), I-309 (2-fold), IL-15 (1.6-fold), TARC (1.9-fold), TPO (2.1-fold), IGFBP-4 (2-fold), IL-12-p40 (1.7-fold) and ENA-78 (1.4-fold). Interestingly, 7 of these cytokines have known pro-inflammatory roles. Importantly, neither the CC transcriptomes or FF cytokine profiles were different in adolescents with or without cancer.
Large scale data: Original high-throughput sequencing data will be deposited in Gene Expression Omnibus (GEO) before publication, and the GEO accession number will be provided here.
Limitations, reasons for caution: This study aims to gain insights into the associated gamete quality by studying the immediate oocyte microenvironment. The direct study of oocytes is more challenging due to sample scarcity, as they are cryopreserved for future use, but will provide a more accurate assessment of oocyte reproductive potential.
Wider implications of the findings: Understanding the underpinnings of altered immediate oocyte microenvironment of adolescent patients may provide insights into the reproductive potential of the associated gametes in the younger end of the age spectrum. This has implications for the fertility preservation cycles for very young patients.

overall_design: mRNA-seq on human primary cumulus cells microdissected from MII-oocyte associated cumulus-oocyte complexes (COCs) retrieved from adolescents compared to oocyte donors.

first: Dilan

last: Gokyer


title: Hydroxycitrate delays early mortality in mice and promotes muscle regeneration while inducing a rich hepatic energetic status.

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

country: Spain

institute: CABIMER

summary: ATP citrate lyase (ACLY) inhibitors have the potential of modulating central processes in protein, carbohydrate, and lipid metabolism, which can have relevant physiological consequences in aging and age-related diseases. Here, we show that hepatic phospho-active ACLY correlates with overweight and Model for End-stage Liver Disease score in humans. Wild-type mice treated chronically with the ACLY inhibitor potassium hydroxycitrate exhibited delayed early mortality. In AML12 hepatocyte cultures, the ACLY inhibitors potassium hydroxycitrate, SB-204990, and bempedoic acid fostered lipid accumulation, which was also observed in the liver of healthy-fed mice treated with potassium hydroxycitrate. Analysis of soleus tissue indicated that potassium hydroxycitrate produced the modulation of wound healing processes. In vivo, potassium hydroxycitrate modulated locomotor function toward increased wire hang performance and reduced rotarod performance in healthy-fed mice, and improved locomotion in mice exposed to cardiotoxin-induced muscle atrophy. Our findings implicate ACLY and ACLY inhibitors in different aspects of aging and muscle regeneration.

overall_design: C57BL/6 male mice were divided in different groups with a standard diet or standard diet supplemented with hydroxycitrate. AML12 cells were siRNA interfered for Acly expression and were treated with hydroxycitrate, SB-204990 or Bempedoic acid. RNAseq was performed from AML12 cells, liver, soleo and gastrocnemius.

first: Isabel

last: Espadas

first: María Ángeles

last: Cáliz-Molina

first: Raúl

last: López-Fernández-Sobrino

first: Concepción

last: Panadero-Morón

last: Sola-García

first: Mario

last: Soriano-Navarro

first: Enrique

last: Martínez-Force

first: Monica

last: Venegas-Calderón

first: Joaquin

last: Salas

first: Franz

last: Martín

first: Benoit

middle: R

last: Gauthier

first: Clara

last: Alfaro-Cerbelló

first: David

last: Martí-Aguado

first: Vivian

last: Capilla-González

last: Martín-Montalvo


title: Expression of the membrane tetraspanin claudin 18 on cancer cells promotes T lymphocyte infiltration and antitumor immunity in pancreatic cancer

status: Public on May 14 2024

city: Verona

first: Francesco

last: De Sanctis

address: Piazzale L.A. Scuro, 10

department: Department of Medicine

country: Italy

institute: University and Hospital Trust of Verona

summary: Tumors weakly infiltrated by T lymphocytes poorly respond to immunotherapy. We aimed to unveil malignancy-associated programs regulating T cell entrance, arrest, and activation in the tumor environment. Differential expression of cell adhesion and tissue architecture programs, particularly the presence of the membrane tetraspanin claudin (CLDN)18 as a signature gene, demarcated immune-infiltrated from immune-depleted mouse pancreatic tumors. In human pancreatic ductal adenocarcinoma (PDAC) and non-small cell lung cancer, CLDN18 expression positively correlated with more differentiated histology and favorable prognosis. CLDN18 on the cell surface promoted accrual of cytotoxic T lymphocytes (CTLs), facilitating direct CTL contacts with tumor cells by driving the mobilization of the adhesion protein ALCAM to the lipid rafts of the tumor cell membrane through actin. This process favored the formation of robust immunological synapses (ISs) between CTLs and CLDN18-positive cancer cells, resulting in increased T cell activation. Our data reveal an immune role for CLDN18 in orchestrating T cell infiltration and shaping the tumor immune contexture.

overall_design: Three biological replicates of FC1199-OVA and FC1242-OVA KPC-derived cell lines infected with ovalbumin and GFP-econding lentivirus

first: Silvia

last: Dusi

first: Simone

last: Caligola

first: Cristina

last: Anselmi

first: Varvara

last: Petrova

first: Barbara

last: Rossi

first: Gabriele

last: Angelini

first: Michael

last: Erdeljan

first: Stefan

last: Wöll

first: Melissa

last: Schlitter

first: Thomas

last: Metzler

first: Katja

last: Steiger

first: Zea

last: Borok

first: Peter

last: Bailey

first: Aline

last: Bauer

first: Cornelia

last: Halin

first: Federico

last: Boschi

first: Rosalba

last: Giugno

first: Stefania

last: Canè

first: Rita

last: Lawlor

first: Vincenzo

last: Corbo

first: Aldo

last: Scarpa

first: Gabriela

last: Constantin

first: Stefano

last: Ugel

first: Fulvia

last: Vascotto

first: Ugur

last: Sahin

first: Özlem

last: Tureci

last: Bronte


title: Real-time quantitative PCR analysis of human CRC patients tumor tissues and compared normal tissues

status: Public on May 13 2024

city: Beijing

first: Zhidong

last: Wang

address: Yard 27, Taiping Road, Haidian district

institute: Graduate Collaborative Training Base of Academy of Military Sciences, Hengyang Medical School, University of South China

summary: Tumor tissues and compared normal tissues were collected from 3 CRC patients. The nrStar™ Human snoRNA PCR Array was used to analyze the differentially expressed snoRNAs associated with colorectal cancer.

overall_design: qPCR gene expression profiling.  Tumor tissues and compared normal tissues from three CRC patients were used and treated separately as indicated in the summary. Equal amount total RNA from each patients was pooled prior to gene expression analysis.


title: Effect of over-expression of SNORA28 on gene expression in HCT116 cells

summary: SNORA28 is highly expressed in CRC and associated with poor prognosis of patients. HCT116 cells were transfected with lentivirus overexpressing SNROA28 and then performed RNA-seq analysis to provide a molecular basis for further exploring the SNORA28 function in CRC.

overall_design: To explore the molecular basis of SNORA28 function in CRC, we established HCT116 cell lines in which SNORA28 has been ovexpressed by lentivirus.


title: High-throughput characterization of functional variants highlights heterogeneity and polygenicity underlying lung cancer susceptibility

city: Rockville

first: Jiyeon

last: Choi

address: 9615 Medical Center Drive, Rm 3116

institute: NCI

summary: Genome-wide association studies (GWAS) have identified multiple lung cancer risk loci including those that are distinct in the major histological types. However, most of these loci have not been functionally characterized. Here we employed massively parallel reporter assays (MPRA) to assess allelic transcriptional activity of risk-associated variants en masse. We tested 2,245 variants in 42 loci from 3 recent GWASs of East Asian and European populations in the context of lung adenocarcinoma and squamous cell carcinoma cells while incorporating exposure to a tobacco-smoke carcinogen, benzo[a]pyrene. At FDR < 0.01, we identified 844 MPRA-significant variants with allelic transcriptional activity across 88% of lung cancer loci. Further variant scoring using lung-specific epigenomic annotation demonstrated that 63% of the loci harbored multiple equally functional variants in linkage disequilibrium. Cell-type-specific variants were observed in 72% of the loci, a subset of which aligned with histology-specific association in the GWAS. Distinct subsets of transcription factors were predicted to bind to cell-type-specific variants and those affecting multiple GWAS loci in trans. Linking MPRA-significant variants to target genes based on four different approaches identified candidate susceptibility genes including essential genes for lung cancer cell growth. CRISPR-interference of a high-scoring MPRA-significant variant validated multiple variant-gene connections from different datasets, including RTEL1, SOX18, and ARFRP1. Our data provide a comprehensive catalog of functional characterization of lung cancer GWAS loci and the molecular basis of heterogeneity and polygenicity of lung cancer susceptibility.

overall_design: Targeted amplicon RNA-sequencing of ectopic luciferase constructs with sequence tags transfected into A549 human lung adenocarcinoma cell line and H520 human lung squamous cell carcinoma cell line with or without exposure to benzo(a)pyrene (n = 5 transfections for each condition) together with amplicon DNA sequncing of input luciferase constructs for normalization control

first: Harsh

last: Patel

first: Erping

last: Long

first: Alyxandra

last: Golden

first: Karen

last: Funderburk


title: Small molecule inhibitors of fungal ∆(9) fatty acid desaturase as antifungal agent against Candida auris

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

institute: Universite de Montreal

summary: Candida auris has emerged as a significant healthcare-associated pathogen, posing a serious challenge due to its multidrug-resistant nature. Given the pre-existing constraints in the discovery and provision of new antifungals, there is thus an urgent imperative to design effective strategies to tackle this pressing global concern. Here, we screened a chemical library and identified phenyl-carbohydrazide derivatives with potent activity against both C. auris and the most prevalent human fungal pathogen, C. albicans. SPB00525 (N'-(2,6-Dichlorophenyl)-5-nitro-2-furohydrazide) exhibited potent activity against different strains that were resistant to standard antifungals. Using drug-induced haploinsufficient profiling, transcriptomics and metabolomic analysis, we uncovered that Ole1, a ∆(9) fatty acid desaturase, is most likely the target of SPB00525. We also found that another SPB00525 analog, HTS06170 (N'-(2,6-Dichlorophenyl)-4-methyl-1,2,3-thiadiazole-5-carbohydrazide) had a superior antifungal activity against both C. auris and C. albicans. Both SPB00525 and HTS06170 act as antivirulence agents and inhibited the invasive hyphal growth and biofilm formation of C. albicans. SPB00525 and HTS06170 attenuated fungal damage to human enterocytes and ameliorate survival of Galleria mellonella larvae used as a model of systemic candidiasis. These data, suggest that inhibiting ∆(9) fatty acid desaturase activity represents a potential therapeutic approach for treating fungal infection caused by the superbug C. auris and the most prevalent human fungal pathogen, C. albicans.

sample_organism:
Candida albicans SC5314
Candidozyma auris

overall_design: In this study, we used RNA-seq to identify transcripts modulated by exposure to a novel antifungal molecule (SPB00525) in two human fungal pathogens: Candida auris and C. albicans.  We also used drug-induced haploinsufficient profiling to capture the potential target(s) of SPB00525.

first: Faiza

last: Tebbji

first: Anagha

middle: C

last: Menon

first: Inès

last: Khemiri

first: Daniel

last: St-Cyr

first: Antony

middle: T

last: Vincent


title: RNA-sequencing identifies the activation of IFN-dependent and IFN-independent pathways in the lungs of hamsters treated with NanoSTING

city: Houston

first: Navin

last: Varadarajan

state: TX

address: 4722 Calhoun Rd

department: Chemical and Biomolecular Engineering

institute: University of Houston

summary: To investigate the impact of intranasal NanoSTING administration on the lungs of Syrian Golden hamsters (Mesocricetus auratus)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cells isolated from lungs of 4 hamsters treated with NanoSTING and 4 naive hamsters (controls)

first: Ankita

last: Leekha

first: Arash

last: Saeedi

first: Monish

last: Kumar

first: Samiur

last: Sefat

first: Melisa

last: Martinez-Paniagua

first: Hui

last: Meng

first: Mohsen

last: Fathi

first: Rohan

last: Kulkarni

first: Kate

last: Reichel

first: Sujit

last: Biswas

first: Daphne

last: Tsitoura

first: Xinli

last: Liu

first: Laurence

last: Cooper

first: Courtney

last: Sands

first: Vallabh

last: Das

first: Manu

last: Sebastian

first: Brett

last: Hurst


title: Macrophages enhance contractile force in iPSC-derived human engineered cardiac tissue

status: Public on May 10 2024

city: NEW YORK

first: Gordana

last: Vunjak-Novakovic

department: Biomedical Engineering

institute: Columbia University

summary: Resident cardiac macrophages are critical mediators of cardiac function. Despite their known importance to cardiac electrophysiology and tissue maintenance, there are currently no stem-cell derived models of human engineered cardiac tissues (hECT) that include resident macrophages. In this study, we made an iPSC-derived hECT model with a resident population of macrophages (iM0) to better recapitulate the native myocardium, and characterized their impact on tissue function. Macrophage retention within the hECTs was confirmed via immunofluorescence after 28 days of cultivation. Inclusion of iM0 significantly impacted hECT function, increasing contractile force production. A potential mechanism underlying these changes was revealed by interrogation of calcium signaling, which demonstrated modulation of β-adrenergic signaling in +iM0 hECTs. Collectively, these findings demonstrate that macrophages significantly enhance cardiac function in iPSC-derived hECT models, emphasizing the need to further explore their contributions not only in healthy hECT models, but also in the contexts of disease and injury.

overall_design: To investigate the impact of iPSC-derived macrophages (iM0) on human engineered cardiac tissues, iM0 were added to the tissue composition at formation. Tissues with iM0 (+iM0) were compared to control tissues without iM0 (-iM0), which only contained iPSC-derived cardiomyocytes and iPSC-derived cardiac fibroblasts. We performed comparative gene expression profiling analysis of bulk RNA-seq data from n=3 +iM0 tissues and n=3 -iM0 tissues collected at one timepoint of 28 days of culture.

first: Roberta

last: Lock

first: Pamela

last: Graney

first: Daniel

last: Tavakol

first: Trevor

last: Nash

first: Youngbin

last: Kim

first: Eloy

last: Sanchez Jr

first: Margaretha

last: Morsink

first: Derek

last: Ning

first: Connie

last: Chen

first: Sharon

last: Fleischer

first: Ilaria

last: Baldassarri


title: Tyrosine phosphorylation of both STAT5A and STAT5B is necessary for maximal IL-2 signaling and its mitogenic action

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: STAT5 proteins are vital for lymphocyte development and function. Cytokine activation of STAT5A and STAT5B involves the tyrosine phosphorylation of a C-terminal tyrosine in each protein; however, the importance of STAT5 tyrosine phosphorylation in vivo has not been assessed. Here we generated Stat5a and Stat5b tyrosine mutant knockin mice and found they had greatly reduced CD8+ T-cell numbers. Morever, these cells exhibited profoundly diminished IL-2-induced proliferation, correlating with reduced IL-2- mediated induction of Myc, pRB, a range of cyclins and CDKs, and a G1àS phase- transition block. The mutant CD8+ T cells also exhibited decreased IL-2-mediated activation of pERK and pAKT, which can in part be attributed to diminished IL-2-induced expression of IL-2Rb and IL-2Rg. Our findings demonstrate that tyrosine phosphorylation of both STAT5A and STAT5B is essential for maximal IL-2 signaling, and our transcriptomic and proteomic analyses elucidate the molecular basis for the mitogenic effects of IL-2 on CD8+ T cells.

overall_design: ChIP-Seq and RNA-Seq analyses using freshly isolated mouse CD8+ T cells that were expanded with either no cytokine, or with IL-2 at various time points.

first: Jian-Xin

last: Lin

first: Meili

last: Ge

first: Cheng-yu

last: Liu

first: Ronald

last: Holewinski

first: Thorkell

last: Andresson

first: Tesfay

last: Gebregiorgis

first: Warren

last: Leonard


title: A novel tsRNA, m7G-3' tiRNA LysTTT, promotes bladder cancer malignancy via regulating ANXA2 phosphorylation

status: Public on May 11 2024

city: Guangzhou

first: Ying

last: Xiaoling

address: 250 Changgang east road, Guangzhou

institute: The second affiliated Hospital of Guangzhou Medical University

type: Methylation profiling by genome tiling array

summary: Emerging evidence indicates that tRNA-derived small RNAs (tsRNAs) with the most abundant RNA modifications play an important role in many complex physiological and pathological processes. However, the biological function and regulation mechanism of modified tsRNA in cancer are still poorly understood. Here, we screened and confirmed a novel m7G modified tsRNA, m7G-3'tiRNA LysTTT (mtiRL) in a variety of chemical carcinogenic models by combined small RNA sequencing with m7G small RNA modified Chip. Moreover, we found that mtiRL catalyzed by tRNA m7G modifying enzyme mettl1 promoted bladder cancer malignancy in vitro and in vivo. Mechanistically, mtiRL specifically bound to oncoprotein Annexin A2 (ANXA2) to promote Tyr24 phosphorylation of ANXA2 by enhancing interactions between ANXA2 and YES1, leading to ANXA2 activation and increased ANXA2 nuclear distribution in bladder cancer cells. Together, these findings define a critical role for mtiRL, targeting this novel m7G modified tsRNA would be an efficient way for the treatment of BC.

overall_design: T24: Bladder cancer cells; T24-KO-M1: METTL1-knockout bladder cancer cells

first: Xiaoling

last: Ying

first: Yapeng

last: Huang

first: Cong

first: Weidong

last: Ji


title: Blockade of Endothelin Receptors Mitigates SARS-CoV-2-induced Osteochondral Damage

status: Public on May 08 2024

city: Hung Hom, Kowloon

first: Lanlan

last: Zhang

address: 11 Yuk Choi Road

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: Previous studies have detected the presence of SARS-CoV-2 viral proteins in bronchial cartilage chondrocytes. We hypothesised that the leakage of viral proteins to local joint tissue was due to virus-induced endothelial dysfunction. Studies have also shown upregulation of endothelin-1 (ET-1), the most potent vasoconstrictor, in COVID patients. We are investigating the direct effect of SARS-CoV-2 spike protein (SP) and the host response to chondrocytes. Human mesenchymal stem cells (hMSCs)-differentiated chondrocytes were treated with either full-length SARS-CoV-2 spike protein (SP) only or a combination of spike protein, neutralising antibody to S1 and endothelin-1 (SAE) to mimic viral insult and host response respectively. RNA sequencing was performed to compared the change in transcriptome in control, SP and SAE. All samples were processed in the same batch. Default quality control parameters were used.

overall_design: Treatment (SP: 5 ug/mL SP, 24h; SAE: 5 ug/mL SP, 5 ug/mL neutralising antibody to S1 and 100nM ET-1, 24h) and control hMSCs-differentiated chondrocytes. Three replicates for each group. Samples are collected for bulk RNA seq.

first: Man Ting

last: AU

first: Junguo

last: Ni


title: Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [HiChIP]

city: Singapore

first: KAIJING

last: CHEN

address: 60 Nanyang Drive

department: school of biological science

institute: Nanyang Technological University

summary: Human silencers have been shown to exist and regulate developmental gene expression. However, the functional importance of human silencers need to be elucidated such as the working mode and whether they can form “super-silencers”. Here, through interrogating two putative silencer components of FGF18 gene, we found that two silencers can cooperate via compensated chromatin interactions to form the “super-silencer”. Furthermore, double knock-out of two silencers exhibited synergistic upregulation of FGF18 expression and changes of cell identity. To disturb the “super-silencers”, we applied the combinational treatment of GSK343 and X5050 (“GR”). We found that GR led to severe loss of TADs and loops, while any single treatment only had mild changes. Such changes of TADs and loops may due to the decreased CTCF proteins upon the GR treatment. Moreover, GSK343 and X5050 can work synergistically to upregulated the super-silencer controlled apoptotic genes, thus gave rise to antitumor effects including apoptosis, cell cycle arrest and tumor growth inhibition. Overall, our data demonstrated the first example of “super-silencer” and showed that combinational usage of GSK343 and X5050 maybe the potential drug to curing cancers through disruption of “super-silencers”.

overall_design: Silencer knockout (KO) Hi-C data has two biological replicates for each condition including EV, S1KO, S2KO, and DKO. Drug treatment Hi-C data has two biological replicates for each drug-treated condition, including DMSO, GSK343, X5050, GR 8h, GR 24h, and GR 72h. Drug treatment Hi-C data has two biological replicates for each DMSO- and etoposide-treated K562 cells (72 hr). siRNA Hi-C data has two biological replicates for each siScramble- and siCTCF-treated K562 cells (48 h). Silencer KO 4C has two biological replicates for each condition (EV, S1KO, and DKO). Silencer KO RNA-seq has two biological replicates for different KO cells (EV, S1KO S2KO, and DKO). H3K27me3 and H3K27ac ChIP-seq for silencer KO cells (EV, S1KO, and DKO) have two biological replicates. H3K27me3 HiChIP in wild-type K562 cells has one biological replicate. Cut and Run CTCF has two biological replicates for CTCF antibodies in EV, S1KO, S2KO, and DKO cells. Cut and Run H3K27me3 has two biological replicates for H3K27me3  antibodies (24 h) in THP1 and K562 cells. ATAC-seq has two biological replicates for each EV, S1KO, S2KO, and DKO cells. ATAC-seq has two biological replicates for each DMSO- and GR-treated K562 cells (72 h). Drug-treated K562 cells RNA-seq has two biological replicates including DMSO, GSK343, X5050, GR 8 h, GR 24 h, and GR 72 h.

first: Kaijing

last: Chen

first: Seng Chuan

last: Tang

first: Yichao

last: Cai

first: Melissa

last: Fullwood


title: Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [4C-seq]


title: Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [ATAC-seq]

summary: Human silencers have been shown to exist and regulate developmental gene expression. However, the functional importance of human silencers needs to be elucidated, such as whether they can form “super-silencers” and whether they are linked to cancer progression. Here, through interrogating two putative silencer components of FGF18 gene, we found that two nearby silencers can cooperate via compensatory chromatin interactions to form a “super-silencer”. Furthermore, double knockout of two silencers exhibited synergistic upregulation of FGF18 expression and changes of cell identity. To perturb the “super-silencers”, we applied combinational treatment of an EZH2 inhibitor GSK343, and a REST inhibitor, X5050 (“GR”). We found that GR led to severe loss of TADs and loops, while the use of one inhibitor by itself only showed mild changes. Such changes in TADs and loops were associated with reduced CTCF and TOP2A mRNA levels. Moreover, GSK343 and X5050 synergistically upregulated super-silencer-controlled genes related to cell cycle, apoptosis and DNA damage, leading to anticancer effects both in vitro and in vivo. Overall, our data demonstrated the first example of a “super-silencer” and showed that combinational usage of GSK343 and X5050 to disrupt “super-silencers” could potentially lead to cancer ablation.

first: SengChuan

first: Zixun

last: Ling


title: Ubiquitylation of Pol II controls early stages of the transcription cycle.

city: Cambridge

first: Ana

last: Tufegdzic Vidakovic

state: Cambridge

address: Cambridge Biomedical Campus, Francis Crick Ave

institute: MRC-LMB

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

overall_design: Refer to individual Series


title: Egr1 regulates regenerative senescence and cardiac repair

status: Public on May 07 2024

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary: Senescence plays a key role in various physiological and pathological processes. We reported that injury-induced transient senescence correlates with heart regeneration, yet the multi-omics profile and molecular underpinnings of regenerative senescence remain obscure. Using proteomics and single-cell RNA-sequencing, here we report the regenerative senescence multi-omic signature in the adult mouse heart and establish its role in neonatal heart regeneration and Agrin-mediated cardiac repair in adult mice. We identified early growth response protein 1 (Egr1) as a regulator of regenerative senescence in both models. In the neonatal heart, Egr1 facilitates angiogenesis and cardiomyocyte proliferation. In adult hearts, Agrin-induced senescence and repair require Egr1, activated by the integrin/FAK-ERK/Akt1 axis in cardiac fibroblasts. We also identified cathepsins as injury-induced senescence-associated secretory phenotype (SASP) components that promote ECM degradation and potentially assist in reducing fibrosis. Altogether, we uncovered the molecular signature and functional benefits of regenerative senescence during heart regeneration, with Egr1 orchestrating the process.

overall_design: Hearts from postnatal day 1 mice were subjected to cryoinjury and were harvested at 1,4,7 and 14 day after injury. The hearts were harvested and flesh frozen for spatial transcriptomics. Hearts were  sectioned until injured area was apparant and then prepd for downstream pipeline.

first: Lingling

first: Jacob

last: Elkahal

first: Tianzhen

first: Racheli

last: Rimmer

first: Alexander

last: Genzelinakh

first: Elad

last: Bassat

first: Dahlia

last: Perez

first: David

last: Kain

first: Daria

last: Lendengolts

first: Roni

last: Winkler

first: Hanna

last: Bueno-levy

first: Kfir

last: Umansky

last: Mishaly

first: Avraham

last: Shakked

first: Shoval

last: Miyara

first: Naomi

last: Goldfinger

first: Amir

last: Prior

last: Morgenstern

first: Yishai

last: Levin

first: Yoseph

last: Addadi

first: Baoguo

last: Li

first: Varda

last: Rotter

first: Valery

last: Krizhanovsky

first: Uriel

last: Katz

first: Elly

last: Tanaka

first: Rachel

last: Sarig

first: Eldad

last: Tzahor


title: Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [ChIP-seq]

first: KAIJING

last: CHEN

first: Ying

last: Zhang

first: Kaijing

last: Chen

first: Seng Chuan

last: Tang

first: Yichao

last: Cai

first: Melissa

last: Fullwood


title: Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [Cut&Run]

first: SengChuan

first: Zixun

last: Ling


title: Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [RNA-seq]


title: Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth

summary: Human silencers have been shown to regulate developmental gene expression. However, the functional importance of human silencers needs to be elucidated, such as whether they can form ‘super-silencers’ and whether they are linked to cancer progression. Here, we show two silencer components of the FGF18 gene can cooperate through compensatory chromatin interactions to form a super-silencer. Double knockout of two silencers exhibited synergistic upregulation of FGF18 expression and changes in cell identity. To perturb the super-silencers, we applied combinational treatment of an enhancer of zeste homolog 2 inhibitor GSK343, and a repressor element 1-silencing transcription factor inhibitor, X5050 (‘GR’). Interestingly, GR led to severe loss of topologically associated domains and loops, which were associated with reduced CTCF and TOP2A mRNA levels. Moreover, GR synergistically upregulated super-silencer-controlled genes related to cell cycle, apoptosis and DNA damage, leading to anticancer effects in vivo. Overall, our data demonstrated a super-silencer example and showed that GR can disrupt super-silencers, potentially leading to cancer ablation.


title: TEAD4 role in trophectoderm commitment and development is not conserved in non-rodent mammals

status: Public on May 05 2024

city: Madrid

first: Leopoldo

last: González-Brusi

state: Madrid

address: Avda Puerta de Hierro, 12

department: Animal Reproduction

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

summary: The first lineage differentiation in mammals gives rise to the inner cell mass (ICM) and the trophectoderm (TE). In mice, TEAD4 is a master regulator of TE commitment, as it regulates the expression of other TE-specific genes and its ablation prevents blastocyst formation, but its role in other mammals remains unclear. TEAD4 ablation in bovine embryos did not impede TE differentiation or blastocyst formation, but a transcriptomic analysis was performed to see if there were any transcriptomic anomalies in knockout embryos.

overall_design: RNAseq analysis was performed on five D8 in vitro produced wild type (WT) and four TEAD4 -/- (KO) bovine embryos generated by conventional CRISPR/Cas9 system.

first: A

last: Pérez-Gómez

first: L

first: I

last: Flores-Borobia

first: B

last: Galiano-Cogolludo

last: Lamas-Toranzo

first: J

middle: G

last: Hamze

last: Toledano-Díaz

last: Santiago-Moreno

first: P

last: Ramos-Ibeas

last: Bermejo-Álvarez


title: Transcriptome analysis of repopulated microglia after 7 days of PLX5622 treatment and 10 days of PLX5622 withdrawal

status: Public on May 06 2024

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

summary: Microglia are suspected to be a key player in several neurological diseases. Here, we investigated whether microglia depletion affects dendritic spine density after short-term microglia depletion with subsequent repopulation in the adult mouse brain.

overall_design: 4 samples representing one analysis group: microglia isolation after 7 days of PLX5622 treatment and 10 days of PLX5622 withdrawal

first: Marco

last: Groth

first: Ha-Yeun

last: Chung

first: Christian

last: Geis


title: Specification of a rostro-caudal axis in cortical assembloids through a polarized source of FGF8

status: Public on May 03 2024

city: wien

first: Camilla

last: Bosone

state: Austria

address: Dr Bohr gasse 3

institute: IMBA


title: Expression data from Human gastric cancer cells (BGC‐823)

status: Public on May 04 2024

city: Weifang

first: Panpan

last: Li

address: No.7166 Baotong West Street

institute: Shandong Second Medical University

summary: The goal of this study is to analyze the expression data from Human gastric cancer cells (BGC‐823) followed by PGRN-downregulation and search potential therapeutic targets of diseases associated with Helicobacter pylori infection

overall_design: Total RNA of three siNC and three si-PGRN samples were extracted using Trizol. Biotinylated cRNA were prepared according to the standard Affymetrix protocol.  Following fragmentation, cRNA were hybridized on PrimeView Human Gene Expression Array.  GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000. Finally, the data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

first: Linlin

last: Liu

first: Zongjiao

last: Ren

first: Hongyan

last: Wang


title: Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [Hi-C]

first: KAIJING

last: CHEN

first: Ying

last: Zhang

first: Kaijing

last: Chen

first: Seng Chuan

last: Tang

first: Yichao

last: Cai

first: Melissa

last: Fullwood


title: Human Airway and Alveolar Organoids from Bronchoalveolar Lavage Fluid

status: Public on May 01 2024

city: Boston

first: Carla

last: Kim

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: Many lung diseases remain understudied due to a lack of experimental models. Lung organoids, which consist of self-organizing epithelial cells, provide versatile in vitro models for normal and abnormal biology, drug screening, gene editing, and personalized therapeutics. However, human organoids are generally derived from lung tissue, which is not commonly obtained and represents only a small fraction of lung pathologies. Induced pluripotent stem cells have provided an important alternative but require complex manipulation. Recently, one study reported airway organoids from bronchoalveolar lavage (BAL) fluid, though sample sizes and characterization were limited. Here, we demonstrate robust establishment of airway organoids from a variety of human BAL samples and show that these organoids consist predominantly of basal cells plus differentiated airway cell types including secretory, ciliated, KRT13+ “hillock,” and ionocyte cells. Furthermore, we report the development of BAL-derived alveolar organoids comprised of alveolar type 2 (AT2) cells. These techniques significantly expand the scope of lung diseases that can be studied using safely accessible primary human cells.

overall_design:
Airway and alveolar organoids grown from human BAL fluid were analyzed by scRNA-seq and compared with organoids from human lung tissue.

***************************************************************
Submitter states that missing raw files are due to patient privacy concerns.
***************************************************************

first: MonicaYun

first: Belinda

first: Mehdi

last: Borji

first: Carolina

last: Garcia de Alba Rivas

first: Antonella

middle: F

last: Dost

first: Aaron

last: Moye

first: Nusrath

last: Movval Abdulla

first: Lynn

last: Schnapp

first: Hassan

middle: A

last: Khalil

first: Catherine

last: Wu

first: Nirmal

last: Sharma


title: Specification of a rostro-caudal axis in cortical assembloids through a polarized source of FGF8 (bulk RNA-Seq)

first: Camilla

last: Bosone

summary: Current organoid protocols are widely used to mechanistically study cortical development, evolution and brain pathologies. While these systems generate all major cortical cell types in histologically distinct compartments, they lack cortical area topography, which is initiated by gradients of signaling molecules released by signaling organizers that establish transcriptionally distinct domains along the rostro-caudal axis of the developing cortex. Here, we engineer human cortical assembloids that combine an organizer-like structure expressing FGF8 with an elongated organoid design to enable the controlled modulation of FGF8 signaling along the longitudinal organoid axis. We demonstrate that individual polarized cortical assembloids (polCA) mount a position-dependent transcriptional program that matches the in vivo rostro-caudal gene expression patterns. Importantly, positional identity is lost in polCA carrying a mutation in the FGFR3 gene associated with temporal lobe malformations and intellectual disability in humans. Similar to in vivo, this program is accompanied by transcriptional divergence of radial glia cells and excitatory neurons and their segregation along the longitudinal axis of individual organoids. Thus, this method reproduces in vivo cortical topography in individual organoids and enables the analysis of area-related phenotypes underlying human disorders.

overall_design: In order to explore the position-dependent transcriptional changes in polar cortical asembloids (polCAs), we performed bulk RNA-sequencing analysis on consecutive tissue segments of D60 polCAs (7 replica, 1 is an outlier) and compared to unpatterned controls without FGF8 OrEB. We defined these sections based on their relative distance from the OrEB (when present) as proximal (P), medial (M) and distal (D) to the source. 3 Elongated organoids without OrEB were used to generate three control segments (C1, C2 and C3). Further, FGF3 mutant polCAs (3 replica) were sequenced. To further discern cell type composition, we performed additiona scRNAseq analysis on P-M-D segments from 3 polCAs and C segments from 3 controls at D60

first: Davide

last: Castaldi

first: Thomas

last: Burkard

first: Segundo

last: Guzman

first: Tom

last: Wyatt

first: Cristina

last: Cheroni

first: Nicolo

last: Caporale

first: Sunanjay

last: Bajaj

first: Joshua

last: Bagley

first: Chong

last: Li

first: Benoit

last: Sorre

first: Emanuele

last: Villa

first: Giuseppe

last: Testa

first: Veronica

last: Krenn

first: Juergen

last: Knloblich


title: Pre-existed senescent fibroblasts in aged bladder create tumor-permissive niche via CXCL12 secretion

city: Fukushima

first: Satoru

last: Meguro

state: Fukushima

institute: Fukushima Medical University

summary: We used scRNA-seq analysis to investigate the characteristics of p16high cells in the bladdder cancer microenvironment.

overall_design: We performed scRNA-seq using the aged p16CreERT2-tdTomato mouse bladder. The tdTomato-positive and negative stromal cells were collected through FACS and processed for library preparation.

first: Yoshikazu

last: Johmura

first: Yoshiyuki

last: Kojima

first: Makoto

last: Nakanishi


title: Local source of FGF8 specifies a fronto-temporal axis in engineered human brain organoids (PolarOids)

first: Camilla

last: Bosone

summary: The establishment of the fronto-temporal axis in the developing human cortex is achieved by temporary signaling activity coming from secondary organizers. However, studying this process remains challenging due to the limited access to fetal material and inaccuracy of animal models in mimicking human-specific aspects. Although human brain organoids provide a potential solution to study this, their lack of axial organization does not supply the appropriate positional information needed to recapitulate detailed patterning processes in situ. Here, we develop a method that combines a cell line expressing the morphogen FGF8 fused to organoids engineered with PDMS moulds representing the exact length of the developing brain, resulting in the formation of polarized cortical organoids, or PolarOids. Thanks to a dose-sensitive reporter for anterior cortical differentiation, we carefully titrate and time the fusion dynamics to elicit a gradient in the patterned tissue while preserving neural activity as assessed through electrophysiology. We show that our localized FGF8 source is sufficient to trigger a distance-dependent transcriptional signature that matches fronto-temporal cortical fates in vivo. Lastly, we use these PolarOids to model a disease-relevant FGFR3 mutation and describe the transcriptional loss of axial gradient formation underlying a dramatic cortical phenotype observed in patients. As such, Polaroids provide a powerful tool to model hitherto neglected human diseases caused by defects in antero-posterior patterning in the brain

overall_design: In order to explore the position-dependent transcriptional changes in PolarOids, we performed bulk RNA-sequencing analysis on consecutive tissue segments of D60 PolarOids (3 replica, 1 is an outlier) and compared to unpatterned controls without fgf8 OrEB. We defined these sections based on their relative distance from the OrEB (when present) as proximal (P), medial (M) and distal (D) to the source. Elongated organoids without OrEB were used to generate three control segments (C1, C2 and C3). Further, FGF3 mutant PolarOids (3 replica) were sequenced.

first: Thomas

last: Burkard

first: Jürgen

last: Knoblich


title: Transcriptome profiling of Artemia cyst in in diapause stage and 5 hours after embryonic diapause termination

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

institute: College of Life Sciences, Tianjin Normal University

summary: Embryonic diapause is a widely occurring evolutionary adaptation phenomenon in animals. Artemia is one of the classic animal models for diapause research. The current studies of Artemia diapause mainly focus on the induction and maintenance of the embryonic diapause, but there is little research on the molecular regulatory mechanism of Artemia embryonic diapause termination (EDT) and embryonic reactivation. Here the gene expression of Artemia cyst in diapause stage and 5 hours after embryonic diapause termination (EDT), which is in post-diapause stage were tested by RNA-seq to analyze the mechanism of signal regulation involved in Artemia EDT at the molecular level.

overall_design: The mRNA expression of Artemia cyst in diapause stage and 5 hours after embryonic diapause termination (EDT) with the Illumina high-throughput sequencing technology by Novogene Inc.The DEGs were analyzed especially the DEGs related to signaling transduction.

first: Anqi


title: ATAC-sequencing of Artemia cyst in in diapause stage and 5 hours after embryonic diapause termination

summary: Embryonic diapause is a widely occurring evolutionary adaptation phenomenon in animals. Artemia is one of the classic animal models for diapause research. The current studies of Artemia diapause mainly focus on the induction and maintenance of the embryonic diapause, but there is little research on the molecular regulatory mechanism of Artemia embryonic diapause termination (EDT) and embryonic reactivation. Here the gene expression of Artemia cyst in diapause stage and 5 hours after embryonic diapause termination (EDT), which is in post-diapause stage were tested by ATAC-seq to analyze the mechanism of signal regulation involved in Artemia EDT at the molecular level.


title: Specification of a rostro-caudal axis in cortical assembloids through a polarized source of FGF8 (scRNA-Seq)

first: Davide

last: Castaldi

first: Segundo

last: Guzman

first: Tom

last: Wyatt

first: Cristina

last: Cheroni

first: Nicolo

last: Caporale

first: Sunanjay


title: Loss of SELENOW aggravates muscle loss with regulation of protein synthesis and ubiquitin-proteasome system

city: wuhan

first: JiaCheng

last: Yang

address: Huazhong agriculture university

department: State Key Laboratory of Agricultural Microbiology

institute: HuaZhong Agricultre university

summary: To investigate the effect of SELENOW KO in TA muscle of aging mice

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq in TA muscle between WT and SELENOW KO aging mice
Comparative gene expression profiling analysis of RNA-seq data in TA muscle between  WT and SELENOW KO aging mice


title: Interleukin-15-armored GPC3-CAR T cells for patients with solid cancers

first: Antonino

last: Montalbano

address: 1102 Bates Ave

institute: Baylor School of Medicine

summary: Interleukin-15 (IL15) enhances the antitumor properties of CAR T cells in preclinical solid tumor models but its effects on CAR T cells in humans are not known. Here, we report the first-in-human evaluation of IL15 co-expression in CAR T cells in two cohorts of a total of 24 patients with glypican-3 (GPC3) expressing solid neoplasms. In cohort 1, GPC3-CAR T cells were safe, no objective antitumor responses were detected. In cohort 2, co-expression of IL15 in GPC3-CAR T cells was associated with increased peak expansion in blood and measurable antitumor responses. Cytokine release syndrome was controlled with immunomodulation or with the inducible caspase 9 safety switch. Single cell transcriptomic analyses identified gene expression of tumor infiltrating CAR T cells associated with antitumor responses.

overall_design: scRNA-seq from patients' samples.

first: David

last: Steffin

first: Nishta

last: Ghatwai

first: Purva

last: Rathi

first: Amy

last: Courtney

first: Azlann

last: Arnett

first: Ramy

last: Sweidan

first: Tao

last: Wang

first: Huimin

last: Zhang

first: Prakash

last: Masand

first: John

last: Maris

first: Daniel

last: Martinez

first: Jennifer

last: Pogoriler

first: Navin

last: Varadarajan

first: Sachin

last: Thakkar

first: Deborah

last: Lyon

first: Natasha

last: Lapteva

first: Zhuyong

last: Mei

first: Kalyani

last: Patel

first: Dolores

last: Lopez-Terrada

first: Carlos

last: Ramos

first: Premal

last: Lulla

first: Tannaz

last: Armaghany

first: Bambi

last: Grilley

first: Gianpietro

last: Dotti

first: Leonid

middle: S

last: Metelitsa

first: Helen

last: Heslop

first: Malcolm

last: Brenner

first: Pavel

last: Sumazin

first: Andras

last: Heczey


title: Limb reduction in an Esco2 cohesinopathy mouse model is mediated by p53-dependent apoptosis and vascular disruption [scRNA-Seq]

city: New York

first: Arielle

last: Strasser

state: New York

address: 1425 Madison Ave

department: Genetics and Genomics Sciences

institute: Icahn School of Medicine

summary: Roberts syndrome (RBS) is an autosomal recessive disorder with profound growth deficiency and limb reduction caused by ESCO2 loss-of-function mutations. We elucidate the pathogenesis of limb reduction in an Esco2fl/fl;Prrx1-CreTg/0 mouse model using bulk- and single cell-RNA-seq and gene co-expression network analyses during embryogenesis. Our results reveal morphological and vascular defects culminating in hemorrhage of mutant limbs at E12.5. Underlying this abnormal developmental progression is a pre-apoptotic, mesenchymal cell population specific to mutant limb buds enriched for p53-related signaling beginning at E9.5. We then characterize these p53-related processes of cell cycle arrest, DNA damage, cell death, and the inflammatory leukotriene signaling pathway in vivo. In utero treatment with the p53 inhibitor pifithrin-α, identified using a drug repositioning approach, rescued the hemorrhage in mutant limbs. Lastly, significant enrichments were identified among genes associated with RBS, thalidomide embryopathy, and human limb reduction disorders, suggesting etiological commonalities of cell death and vascular defects.

overall_design: Libraries were generated based on three replicates of each genotype (Esco2fl/fl;Prrx1-CreTg/0 and Esco2fl/fl). Each replicate consisted of 3 pooled samples (2 limb buds per sample, comprising a total of 6 limb buds per replicate). Samples were genotyped by PCR and each replicate was sex balanced with two male samples and one female sample.

first: Strasser

last: Arielle


title: Limb reduction in an Esco2 cohesinopathy mouse model is mediated by p53-dependent apoptosis and vascular disruption


title: Limb reduction in an Esco2 cohesinopathy mouse model is mediated by p53-dependent apoptosis and vascular disruption [RNA-Seq]

overall_design: A total of 18 libraries were generated based on triplicate samples of each genotype at each stage (three replicates of Esco2fl/fl;Prrx1-CreTg/0 and Esco2fl/fl at E9.5, E10.5 and E11.5). Libraries were then sequenced on the Illumina NovaSeq 6000 (300 cycle paired-end sequencing with a read length of 150 bp). For each genotype at each age, pairwise comparisons were performed to identify differentially expressed genes between mutant and control limb buds.


title: Clonal evolution of the 3D chromatin landscape of relapsed ALL [H3K27ac HiChIP]

first: Sonali

last: Narang

address: 435 east 30th street

institute: NYU Langone

summary: Relapsed pediatric B-cell acute lymphoblastic leukemia (B-ALL) remains one of the leading causes of cancer mortality in children. Up to 20% of children will suffer relapse and face a poor prognosis. Our recent work on the evolution of the epigenetic landscape from diagnosis to relapse demonstrates both substantial diversity in the chromatin landscape as well as shared relapse-specific superenhancer activation, highlighting the importance of chromatin changes in disease progression.  However, there is a gap in our understanding of B-ALL progression through the lens of three-dimensional (3D) chromosome topology. To uncover 3D chromatin architecture-related mechanisms underlying drug resistance in B-ALL, we performed Hi-C, ATAC-seq, and RNA-seq on 12 matched primary pediatric leukemia specimens at diagnosis and relapse. Mapping of structural variations (SVs) using Hi-C data revealed previously unidentified stable, diagnosis-specific, and relapse-specific SVs providing further evidence for clonal evolution as a mechanism for drug resistance. Moreover, Hi-C analysis revealed genome wide chromatin remodeling specifically in terms of A/B compartments, TAD interactivity, and chromatin loops. Integration with ATAC-seq and RNA-seq datasets revealed strong correlation with both gene expression and chromatin accessibility. Additionally, we identified recurrent A/B compartments and TAD interactivity changes across the patient cohort for which we were able to demonstrate a crucial role in the clonal evolution of B-ALL. Shared changes in 3D genome organization drive the expression of genes/pathways previously implicated in drug resistance as well. Lastly, enrichment analysis revealed key upstream regulators of 3D genome architecture in B-ALL disease progression. These results extend the landscape of genetic alterations in relapsed B-ALL through the addition of the 3D genomic landscape and identify a breadth of novel therapeutic targets.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from 12 matched primary pediatric leukemia specimens at diagnosis and relapse.

first: Yohana

last: Ghebrechristos

first: Nikki

last: Evensen

first: Sylwia

last: Jasinski

first: Talia

middle: H

last: Ostrow

first: Matthew

last: Witkowski

first: Iannis

last: Aifantis

first: Aristotelis

last: Tsirigos

first: William

last: Carroll


title: Opposing tumor cell-intrinsic and -extrinsic roles  of the IRF1 transcription factor in anti-tumor immunity

city: los angeles

first: Prabhat

middle: Kumar

last: Purbey

state: California

address: 675 Charles E. Young Drive South

department: MIMG

institute: UCLA

summary: Type I interferons (IFN-I) and IFN- foster antitumor immunity by facilitating T cell responses. Paradoxically, IFNs may promote T cell exhaustion by activating immune checkpoints. The downstream regulators of these responses are incompletely understood. Herein, we describe how Interferon Regulatory Factor 1 (IRF1) orchestrates these opposing effects of IFNs. IRF1 expression in tumors blocked Toll-like receptor and IFN-I-dependent host antitumor immunity by preventing IFN stimulated gene (ISG) programs and effector programs in dendritic cells and T cells. In contrast, expression of IRF1 in the host, but not IRF3 or IFN-, was also required for antitumor immunity to wildtype and Irf1-/- tumors. Mechanistically, tumor cell IRF1 regulated major histocompatibility class I expression and bound uniquely or together with STAT1 at many ISGs, contributing to expression of immunosuppressive but not immunostimulatory ISGs. Overexpression of PD-L1 in Irf1-/- tumors only partially restored tumor growth, suggesting that the negative effects of tumor IRF1 on antitumor immunity are multifactorial. Thus, we identify tumor cell IRF1 expression as a previously unrecognized selective inhibitor of host IFN-I dependent antitumor immunity, while host IRF1 and IFN-I are critical drivers of antitumor immune responses.

overall_design:
Wildtype and IRF1-/- MC 38 cells were stimulated with IFN-y for 2h. Chromatin from 0, and 2h stimlated samples was immunoprecipitated with antibodies against IRF1 or STAT1 followed by NGS library prep and sequencing in Illumina.

Wildtype and IRF1-/- MC 38 cells (mouse colon cancer line) or M238 cells (human melanoma line)  were stimulated with IFN-y  for 2h or 6h. mRNA from 0, and 2h stimlated samples for MC38 and 0h and 6h stimulated samples for M238 cells were used for RNA-Seq library generation followed by NGS library prep and sequencing in Illumina instrument.

WT and Irf1-/- MC38 tumors (pooled 4-6) from WT and Ifnar-/- mice on day12 were chopped into small pieces (2-4 mm size) before dissociation with Miltenyi's gentle MACS enzyme mix (# 130-096-730) in a Miltenyi GentleMACS Octo Dissociator (Miltenyi Biotec Inc., San Diego, CA) with pre- set 37C_mTDK_1 protocol. After digestion, cells were filtered through 70 uM MACS smart stainer, counted and appropriate number of cells were loaded to target 10,000 cells. Single cell gene expression libraries were created using Chromium Next GEM Single Cell 3' (v3.1 Chemistry) (10x Genomics), Chromium Next GEM Chip G Single Cell Kit (10x Genomics), and Single Index Kit T Set A (10x Genomics) according to the manufacturer's instructions. Sequencing was performed in Illumina Novaseq-6000 instrument at 100 cycle.

middle: K

first: Philip

middle: O

last: Scumpia

first: Stephen

last: Smale


title: Expression data from ovarian cancer with CHSY1 knockdown

city: Wuhan

first: Jinling

last: Huang

state: Hubei

address: Jiefang Road 238

department: Obstetrics & Gynecology,

institute: Renmin Hospital of Wuhan University

summary:
CHSY1 has high expression in malignant tumor cells, such as colorectal cancer and ovarian cancer, and is associated with poor prognosis.The proliferation and invasion of ovarian cancer cells are weakened after knocking down CHSY1 with shRNA transfected
We used microarrays to detail the global programme of gene expression underlying CHSY1 knockdown and identified distinct classes of up-regulated and down-regulated genes.

overall_design: Ovarian cancer cells were transfected with shRNA to knockdown CHSY1  for RNA extraction and hybridization on Affymetrix microarrays. Then we got ovarian cancer cells with different CHSY1 expression:shCHSY1(CHSY1 knockdown group) and shCtrl(control group )

first: Liangbin

last: Xia


title: Clonal evolution of the 3D chromatin landscape of relapsed ALL

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

overall_design: Refer to individual Series


title: Clonal evolution of the 3D chromatin landscape of relapsed ALL [RNA-seq]


title: Clonal evolution of the 3D chromatin landscape of relapsed ALL [Hi-C]