title: The effect RARG fusion genes or PML-RARA overexpression in human CD34+ cells on the gene expression.

city: Beijing

first: Feng

last: Wang

address: 1 Tian Tan Xi Li

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences

summary: Currently, AML with RARG rearrangements (RARG AML), including NUP98-RARG, PML-RARG, CPSF6-RARG, NPM1-RARG, and HNRNPC-RARG, has been identified as a novel entity of AML. Overexpression of RARG fusions in human CD34+ cells promoted the expansion of immature myeloid cells, reduced the percentage of mature granulocytes, inhibited the differentiation of myeloid cells, and self-renewal abilities of hCD34+ cells. To understand how RARG fusion proteins regulate their target genes in the hematopoietic system, we first expressed HA-tagged X-RARG fusions or HA-tagged PML-RARA in hCD34+ cells. We then analyzed the differential genes expression in hCD34+ cells with or without RARG fusion genes or PML-RARA overexpression through RNA-seq.

overall_design: To analyzed the differential genes expression in hCD34+ cells with or without RARG fusion genes or PML-RARA overexpression, human CD34+ cells infected with control or RARG fusions retrovirus were sorted for GFP positive cells. Then the mRNA profiles of human CD34+ cells with or without RARG fusion genes or PML-RARA overexpression were generated by deep sequencing, two repeats each group, using Illumina HiSeq 6000.

first: Ke

first: Luyao

last: Zhao

first: Hong-Hu

last: Zhu

first: Kankan

first: Ya-Zhen

last: Qin

first: Yun

last: Tan

first: Xufeng

last: Cen


title: Differential gene expression in immortalised fibroblasts derived two independent Nestor Guillermo Progeria Syndrome (NGPS) patients, compared to immortalised fibroblasts of an healthy individual

status: Public on Oct 18 2024

city: Cambridge

first: Delphine

last: Larrieu

address: CIMR Hills Road

country: United Kingdom

institute: University of Cambridge

type: Expression profiling by high throughput sequencing

summary: Progeria syndromes are very rare, incurable premature aging conditions recapitulating most aging features. Through a whole genome, multiparametric CRISPR anti-aging screen,we identified 43 new genes that can reverse multiple aging phenotypes in progeria. The screen was implemented in fibroblasts from Néstor-Guillermo Progeria Syndrome (NGPS) patients, carrying a homozygous p.Ala12Thr mutation in barrier-to-autointegration factor (BAF A12T). The hits were enriched for genes involved in protein synthesis, protein and RNA transport and osteoclast formation. We further confirmed that BAF A12T drives increased protein translation and translational errors that could directly contribute to premature aging in patients. This RNA seq analysis identified 213 genes as being differentially expressed in NGPS cells compared to WT cells. GO analysis showed enrichment for genes involved in translation, supporting that the BAF A12T mutation modulates the expression of genes regulating translation

overall_design: We extracted RNA from NGPS 1 and 2 fibroblasts, as well as from  wild type cells. We then compared genes that were differentially expressed in NGPS cells compared to WT

first: Jack

last: Houghton


title: DELETED - Replaced by GSE280037

status: Public on Oct 12 2024

city: Kunming

first: meiqi

last: Lin

address: Kunming, Yunnan province

country: China

institute: State Key Laboratory of Primate Biomedical Research

summary: This Series has been replaced by GSE280037.


title: Analysis of the chromatin accessibility in CPSF6-RARG or NUP98-RARG overexpressing hCD34+ cells compared to control hCD34+ cells using ATAC-seq.

status: Public on Oct 16 2024

address: Tian Tan Xi Li 1

institute: Peking Union Medical College

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We found that RARG fusions selectively upregulated BCL2 and ATF3 in HSPCs, driving uncontrolled proliferation and disrupting the differentiation of RARG-AML cells.To investigate the mechanism how RARG fusions mediate activation of their downstream targets such as BCL2 and ATF3, we defined the chromatin accessibility using ATAC-seq assay in human CD34+ (hCD34+) cells with or without CPSF6::RARG or NUP98::RARG overexpression.

overall_design: 10,0000 hCD34+ cells with or without CPSF6::RARG or NUP98::RARG overexpression were harvested and  performed the ATAC-seq assay according to the manufacturer’s protocol using the Hyperactive ATAC-seq Library Prep Kit for Illumina (Vazyme, Nanjing, China, #TD711).

last: Li


title: Targeted delivery of flagellin by nebulization offers optimized respiratory immunity and defense against pneumococcal pneumonia

status: Public on Oct 11 2024

city: Lille

first: Yasmine

last: Zeroual

state: Nord

address: 1 Rue du professeur Calmette, 59000 Lille (Institut pasteur de Lille)

country: France

institute: INSERM

summary: Novel therapeutic approaches for addressing pneumonia caused by Streptococcus pneumoniae, which exhibit resistance to standard-of-care antibiotics are greatly needed. One viable approach involves precisely stimulating innate immune defenses within the lungs. Using murine models of pneumococcal pneumonia, prior studies demonstrated that intranasal administration of the Toll-like receptor 5 agonist, flagellin, results in a 100-fold decrease in lung infection compared to sole antibiotic therapy, when used as an adjunct treatment to the antibiotic. To promote the transfer of this immunotherapy to clinics and mitigate unwanted systemic inflammation, this project assessed whether the direct delivery of flagellin to the airways through nebulization stimulates respiratory defenses against bacterial infection. Similarly to intranasal administration, nebulized flagellin induced a transient activation of lung innate immunity. In contrast, inhalation by nebulization resulted in an attenuated activation of systemic immune responses. We conclude that flagellin aerosol therapy represents a secure and promising approach in addressing bacterial pneumonia within the context of antimicrobial resistance.

overall_design: Six-to-eight weeks-old female mice were treated with recombinant flagellin FLAMOD (intranasally or via nebulization). Lungs were sampled 2 hours post-administration and processed for RNA isolation and sequencing.

first: Mara

last: Baldry

first: Charlotte

last: Costa

first: Beury

last: Delphine

first: Jean-Claude

last: Sirard


title: Lineage-specific genomic imprinting in the ZNF791 locus [BiSulfite-seq]

city: Columbus

first: Jinsoo

last: Ahn

address: 2029 Fyffe Rd

country: USA

institute: Ohio State Univesity

type: Methylation profiling by high throughput sequencing

summary: To identify genomic imprinting in pigs, we generated parthenogenetic porcine embryos alongside biparental normal embryos, and then performed whole-genome bisulfite sequencing and RNA sequencing on these samples. In our analyses, we discovered a maternally methylated differentially methylated region within the orthologous ZNF791 locus in pigs, while identifying both a major imprinted isoform of the ZNF791-like gene and an imprinted antisense transcript that has not been previously annotated. Importantly, our comparative analyses of the orthologous ZNF791 gene in various eutherian mammals, including humans, non-human primates, rodents, artiodactyls, and dogs, revealed that this gene is subjected to genomic imprinting exclusively in domesticated animals, thereby highlighting lineage-specific imprinting.

overall_design: Whole genome bisulfite sequencing was performed on parthenogenetically activated embryos and control pig embryos.

first: Seongsoo

last: Hwang

first: Kichoon

last: Lee


title: 10X Multiome AKSP

status: Public on Oct 17 2024

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: To characterize transcription factors (TFs) that govern the various cellular states in CRC, AKSP tumoroids were subjected to Mutliome analysis combining s.c ATAC-seq and s.c 3' RNA-seq.

overall_design: AKSP tumoroids were collected for s.cRNA-seq before reaching confluency to minimize cell death.

first: Slim

last: Mzoughi

first: Deniz

last: Demircioglu


title: Gene expression profile at single cell level of immune cells from 2153L GEM tumors upon different treatments

city: houston

first: Longyong

last: Xu

state: TX

address: SCRB4, 1901 East Road

department: ET

institute: University of Texas MD Anderson Cancer Center

summary: To understand how the combination of ORIN1001 plus docetaxel promotes anti-tumor immunity, we performed single-cell RNA sequencing (scRNA-seq) of CD45+ cells from 2153L tumors. Our data found that combo induces CD8+ T cells that express high levels of T cell activation, cytotoxicity, and exhaustion genes. combo also increase the cDC1 and MHC-II high macrophages which exhibited higher M1-like macrophages scores.

overall_design: CD45+ immune cells were isolated by fluorescence-activated cell sorting and analyzed using scRNAseq.

first: Fanglue

last: Peng

first: Fei

last: Yuan


title: Impact of SLC15A4, TASL and TASL2(Gm6377) deficiency on endolysosomal TLR7 and TLR9 responses

status: Public on Nov 04 2024

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: Nucleic acid sensing by endolysosomal TLR7-9 results in the induction of antiviral and proinflammatory transcriptional responses. We recently identified TASL as the innate immune adaptor mediating TLR7-9-induced IRF5 activation via the interaction with SLC15A4, but its relevance in primary murine cells remained unexplored. Here we assessed the impact of deficiency in TASL and/or its previously uncharacterized paralogue Gm6377, named here TASL2, on endolysosomal TLR responses in primary bone-marrow-derived pDCs and splenic B cells. Double knockout TASLxTASL2 (TASLDKO) phenocopied the strong impairement observed in cells from SLC15A4-deficient feeble mice, while single TASL or TASL2 deficiency showed partial effect. Altogether, this study demonstrates that the SLC15A4-TASL/TASL2 complex play a critical role for TLR7-9-driven inflammatory responses.

overall_design: To investigate the function of SLC15A4-TASL complex in TLR7-9 induced signaling, we compared transcriptional profile of 5 different genotypes (WT, TASLKO, TASL2KO, TASLDKO, feeble - SLC15A4 deficient) in steady state and upon activation with TLR7 or TLR9 agonists. For this,  bone marrow derived plasmacytoid dendritic cells (BM-pDC) and primary splenic B cells were used in 3-4 biological replicates for each genotype.

first: Ales

last: Drobek

first: Léa

last: Bernaleau

first: Maeva

last: Delacrétaz

last: Calderon Copete

first: Mélissa

last: Longepierre

first: Marta

last: Monguió-Tortajada

first: Jakub

last: Korzenioswski

first: Julien

last: Marquis

first: Manuele

last: Rebsamen


title: Identifying  RARG fusions or PML-RARA binding genes or analysis the epigenetic changes (H3K27ac, H3K4me1, and H3K4me3)  in hCD34+ cells overexpressing CPSF6::RARG and NUP98::RARG.

first: Feng

last: Wang

summary: To understand how RARG fusion proteins regulate their target genes in the hematopoietic system, we overexpressed fusions or PML-RARA in hCD34+ cells and identified target genes that are regulated by RARG fusions. We found that RARG fusions selectively upregulated BCL2 and ATF3 in HSPCs, driving uncontrolled proliferation and disrupting the differentiation of RARG-AML cells.To investigate the mechanism how RARG fusions mediate activation of their downstream targets such as BCL2 and ATF3, we dected the epigenetic changes (H3K27ac, H3K4me1, and H3K4me3) associated with RARG fusions binding in hCD34+ cells overexpressing CPSF6::RARG and NUP98::RARG.

overall_design: 2000,000 hCD34+ cells with  CPSF6-RARG,NUP98-RARG,  HNRNPC-RARG, NPM1-RARG, PML-RARG or PML-RARA overexpression or hCD34+ cells with or without CPSF6::RARG or NUP98::RARG overexpression were harvested and performed ChIP-seq assay.

first: Ke

last: Li

first: Hong-Hu

last: Zhu

first: Kankan

first: Ya-Zhen

last: Qin

first: Luyao

last: Zhao

first: Yun

last: Tan

first: Xufeng

last: Cen


title: Two temperature-responsive RNAs act in concert: The small RNA CyaR and the mRNA ompX

status: Public on Oct 10 2024

city: Bochum

first: Franz

last: Narberhaus

address: Universitätsstraße 150

department: LS Biologie der Mikroorganismen

country: Germany

institute: Ruhr-Universität Bochum

summary: Bacterial pathogens, such as in Yersinia pseudotuberculosis, encounter temperature fluctuations during host infection and upon return to the environment. These temperature shifts impact RNA structures globally. While previous transcriptome-wide studies have focused on RNA thermometers in the 5’-untranslated region of virulence-related mRNAs, our investigation revealed temperature-driven structural rearrangements in the small RNA (sRNA) CyaR. At 25°C, CyaR primarily adopts a conformation that occludes its seed region, but transitions to a liberated state at 37°C. By RNA-sequencing and in-line probing experiments, we identified the Shine-Dalgarno sequence of ompX as a direct target of CyaR. Interestingly, the ompX transcript itself exhibits RNA thermometer-like properties, facilitating CyaR base pairing at elevated temperatures. This interaction impedes ribosome binding to ompX and accelerates degradation of the ompX transcript. Furthermore, we observed induced proteolytic turnover of the OmpX protein at higher temperatures. Collectively, our study uncovered multi-layered posttranscriptional mechanisms governing ompX expression, resulting in lower OmpX levels at 37°C compared to 25°C. We propose that CyaR remains mostly passive at 25°C but becomes primed to repress ompX at 37°C, thereby expediting outer membrane remodelling in anticipation of pathogenesis.

overall_design: Illumina RNA sequencing of the transcriptomes of Yersinia pseudotuberculosis wild type and CyaR deletion mutant (ΔCyaR) at different growth phases (OD600 0.5 & 1.5) and different temperatures (25°C & 37°C)

first: David

middle: A

last: Guanzon

first: Stephan

last: Pienkoss

first: Vivian

middle: B

last: Brandenburg

first: Jennifer

last: Roeder

first: Daniel

last: Scheller

first: Alisa

last: Dietze

first: Andrea

last: Wimbert

first: Christian

last: Twittenhoff


title: Methylated RNA Immunoprecipitation sequencing Quantitative Analysis of HCT116 Wild Type and TTC7B-KO Transcriptomes

first: ren

middle: qian

last: wen

state: Beijing

address: Fu-Cheng-Lu #52, Haidian District

department: Division of Etiology

institute: Peking University Cancer Hospital & Institute

summary: To explore the function of TTC7B on colon cancer，we established HCT116 TTC7B-KO cell lines. The purpose of this study aims to predict possible downstream target genes of TTC7B and to investigate the effects of TTC7B knockout on modification of gene RNA m6A methylated RNA site by MeRIP-seq

overall_design: Comparative gene expression profiling analysis of MeRIP-seq data for HCT116 WT cells and TTC7B-KO cells.


title: Effect of p53 on the expression of combo induced dsRNAs in 2153L GEM tumors

first: Longyong

last: Xu

summary: We analyzed the expression of dsRNAs in control and p53 restored 2153L GEM tumors upon different treatments. Our ChIP-seq and RNA-seq experiments showed that the restored p53 bound to the regulatory regions of dsRNA-containing genes that account for 91% of the total dsRNA abundance in combination therapy–treated 2153L tumors, and suppressed their expression upon combination therapy. The abundance of dsRNA (TPM) was calculated from the dsRIP experiment.

overall_design: 2153L GEM tumors were transduced with empty vector control or tamoxifen inducible p53ERTAM. These tumors were further treated with vehicle control or IRE1⍺ RNase inhibitor ORIN1001 (150 mg/kg, daily) and docetaxel (20 mg/kg, weekly) for 8 days. RNA from these tumors was subjected to RNAseq. The dsRNAs-containing genes whose regulatory regions have p53 binding were flited out first, followed by a second selection for genes that upregulated upon combination compared to vehicle in empty vector control transduced tumors. The expression (TPM) of these genes in p53 restored tumors under vehicle or combination therapy was analyzed.

first: Fei

last: Yuan


title: Comparing Neoantigen Cancer Vaccines and Immune Checkpoint Therapy Unveils an Effective Vaccine and Anti-TREM2 Macrophage-Targeting Dual Therapy [neoAgSpCD8Tcells]

city: Houston

first: Sunita

last: Keshari

state: Texas

address: 7455 Fannin St Rm Scr, The University Of Texas Md Anderson

department: Immunology

institute: UT MD Anderson Cancer Center

summary: The goal of therapeutic cancer vaccines and immune checkpoint therapy (ICT) is to eliminate cancer by expanding and/or sustaining T cells with anti-tumor capabilities. Here, we compared effective therapeutic tumor-specific mutant neoantigen (NeoAg) synthetic long peptide (SLP) cancer vaccines with anti-CTLA-4 and/or anti-PD-1 ICT in preclinical models. Effective NeoAg SLP vaccines and ICT required both CD8 and CD4 T cells. Both NeoAg SLP vaccines and ICT induce expansion of intratumoral NeoAg-specific CD8 T cells, though the degree of expansion and acquisition of effector activity was much more substantial following NeoAg SLP vaccination. Further, we found that NeoAg SLP vaccines are particularly adept at inducing proliferating and stem-like NeoAg-specific CD8 T cells. While NeoAg SLP vaccines and anti-PD-1 affected the CD4 T cell compartment, it was to less of an extent than observed with anti-CTLA-4, which notably induced ICOS+Bhlhe40+ Th1-like CD4 T cells. Although effective NeoAg SLP vaccines or ICT expanded intratumoral M1-like iNOS+ macrophages, NeoAg SLP vaccines maintained, rather than suppressed as observed with ICT, M2-like CX3CR1+CD206+ macrophages expressing the TREM2 receptor. While combining NeoAg SLP vaccination with ICT induced superior efficacy compared to either therapy in isolation, we also assessed a novel combination of NeoAg SLP vaccination and anti-TREM2, demonstrating enhanced efficacy of this combination associated with a decrease in intratumoral CX3CR1+CD206+ macrophages and promotion of IFN-g+ NeoAgspecific CD8 T cells. These findings highlight the utility of combining NeoAg SLP vaccines with ICT, as well as novel combinatorial therapy targeting the myeloid compartment via TREM2 blockade to enhance NeoAg SLP vaccine efficacy.

overall_design: Droplet-based 5′ end massively parallel single-cell RNA sequencing was performed by encapsulating sorted  mLama4 Tetramer positive CD8 T cells (NeoAg-specific CD8 T cells) into droplets and preparing libraries using Chromium Single Cell 5′ Reagent Kits following the manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using a NovaSeq 6000 Sequencing System (Illumina).

first: Alexander

middle: S

last: Shavkunov

first: Qi

last: Miao

first: Akata

last: Saha

first: Tomoyuki

last: Minowa

first: Martina

last: Molgora

first: Charmelle

middle: D

last: Williams

first: Mehdi

last: Chaib

first: Anna

middle: M

last: Highsmith

first: Josué

middle: E

last: Pineda

first: Sayan

last: Alekseev

first: Elise

last: Alspach

first: Kenneth

middle: H

last: Hu

first: Marco

last: Colonna

first: Kristen

last: Pauken

first: Ken

last: Chen

first: Matthew

last: Gubin


title: Next Generation Sequencing Facilitates Quantitative Analysis of HCT116 Wild Type and TTC7B-KO/OE Transcriptomes

first: ren

last: wen

summary: To explore the function of TTC7B on colon cancer，we established HCT116 TTC7B-KO/OE cell lines. The purpose of this study is to utilize next-generation sequencing techniques to investigate the effects of TTC7B knockout or overexpression on the biological behavior of tumor cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 WT cells and TTC7B-KO/OE cells.


title: Gene expression profiling study to identify molecular markers exhibiting distinct characteristics of Pseudomyxoma Peritonei [Fresh Frozen]

status: Public on Oct 09 2024

city: Daejeon

first: sungghwan

last: park

address: Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: The purpose of this study is to evaluate gene expression changes and identify characteristics in patients with Pseudomyxoma Peritonei (PMP). We analyzed RNA-seq data to identify gene signatures associated with PMP development using 19 fresh frozen tissue samples including 12 PMPs (discovery cohort). Through analyzing the differences in gene expression between normal tissues and PMP, we identified statistically significant gene groups, and confirmed the biological functions and pathways associated with these gene groups.

first: Jeong-Hwan

last: Kim

first: Seon-Kyu

first: Seong-Hwan

last: Park

first: Seon-Young

first: Ye

middle: J

last: Ha

first: Jong

middle: L

last: Lee


title: RARG fusion genes

status: Public on Oct 15 2024

first: Feng

last: Wang

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression profile at single cell level from the liver of sham  and sepsis mice

city: Augusta

first: Sergei

last: Bombin

institute: Augusta University

summary: To study the heterogeneity of cell lineages in the liver undergoing sepsis-induced senescence

overall_design: Single cell preparations were made from liver tissues isolated pooled from 3 sham and 4 mice with CLP induced sepsis.

first: Rupa

last: Lavarti

first: Raghavan

middle: P

last: Raju


title: Lineage-specific genomic imprinting in the ZNF791 locus [RNA-seq]

first: Jinsoo

last: Ahn

overall_design: RNA sequencing was performed on parthenogenetically activated embryos and control pig embryos.

first: Seongsoo

last: Hwang

first: Kichoon


title: A gene expression profiling study to identify distinct molecular markers in formalin-fixed, paraffin-embedded samples of Pseudomyxoma Peritonei [FFPE]

summary: The purpose of this study is to evaluate gene expression changes and identify characteristics in patients with Pseudomyxoma Peritonei (PMP). We analyzed RNA-seq data from 34 formalin-fixed paraffin-embedded (FFPE) samples, including 25 PMPs (validation cohort), to identify gene signatures associated with the development of PMP. We confirmed protein expression levels using a tissue microarray (TMA) cohort of PMP patients. Through analyzing the differences in gene expression between normal tissues and PMP, we identified statistically significant gene groups, and confirmed the biological functions and pathways associated with these gene groups.

overall_design: We analyzed RNA-seq data from 34 formalin-fixed paraffin-embedded (FFPE) samples, including 25 PMPs (validation cohort).


title: The gene expression profiles of leukemia cells isolated from spleens of CreMx-1;CPSF6-RARG mice and Wt1F/+CreMx-1;CPSF6-RARG mice

summary: We found that CPSF6-RARG fusion gene drives the aberrant expansion of HSCs and progenitor cells, which may lead to a preleukemic phenotype. Moreover, wt1 haploinsufficiency cooperates with RARG fusions to induce AML. To investigate the mechanism by which Wt1 haploinsufficiency cooperates with RARG fusion overexpression to induce AML in vivo, we analyzed the gene expression profiles of leukemia cells isolated from CreMx-1;CPSF6-RARG mice and Wt1F/+CreMx-1;CPSF6-RARG mice through RNA-seq.

overall_design: To investigate the mechanism by which Wt1 haploinsufficiency cooperates with RARG fusion overexpression to induce AML in vivo,   leukemia cells were isolated from the spleens of Wt1F/+CreMx-1;CPSF6-RARG mice and  CreMx-1;CPSF6-RARG mice and analyzed through RNA-seq .

first: Ke

last: Li

first: Luyao

last: Zhao

first: Hong-Hu

last: Zhu

first: Kankan

first: Ya-Zhen

last: Qin

first: Yun

last: Tan

first: Xufeng

last: Cen


title: CUT&Tag analysis genome-wide maps of chromatin state in hCD34+ cells with X-RARG fusion genes overexpression.

summary: CUT&Tag technology were used for high-throughput profiling of RARG fusion genes or PML-RARA with core promoters of its target genes in hCD34+ cells with RARG fusion genes or PML-RARA overexpression. We first expressed HA-tagged X-RARG fusions or HA-tagged PML-RARA in hCD34+ cells and then performed CUT&Tag with antibody to RARG fusion genes or PML-RARA and analyzed the binding of RARG fusion genes or PML-RARA with core promoters of its target genes. Common peaks for the binding sites of RARG fusions and PML-RARA and unique peaks for specific targets of RARG fusions that are not targets of PML-RARA were identified.

overall_design: hCD34+ cells with HA-tagged X-RARG fusions or HA-tagged PML-RARA overexpression were harvested, and then the CUT&Tag assay was performed according to the manufacturer’s protocol using Hyperactive Universal CUT&Tag Assay Kit for Illumina.


title: The effects of scar resection in chronic complete spinal cord injury(SCI) and the effects of scar resection combined with decellularized hydrogel (scaffold)

status: Public on Oct 08 2024

city: Shinjuku-ku

first: Keitaro

last: Ito

state: Tokyo

country: Japan

institute: Keio university

summary: This study examines the molecular effects of surgical scar resection in　complete chronic spinal cord injury (SCI) through RNA sequencing. Results show that scar resection alters gene expression, with downregulation of axonal growth inhibitors and upregulation of neuroprotective genes. Additionally, the application of a decellularized extracellular matrix (dECM) hydrogel as a scaffold promoted angiogenesis. Gene Ontology analysis indicated enrichment of immune-related processes, suggesting that scar resection improves the spinal cord microenvironment for neural repair. These findings indicate the potential of combining scar resection with scaffolding to support recovery after chronic complete SCI.

overall_design:
To confirm the treatment effects, we created a rat model of complete transection at the thoracic level 10 of the spinal cord and performed therapeutic intervention six weeks post-injury during the chronic phase.
We created a group that underwent scar resection on the chronically injured spinal cord and another group where a scaffold was implanted after scar resection. The untreated group was used as the control.


title: Single Cell RNA Sequencing Provides Clues for the Developmental Genetic Basis of Syngnathid Fish Evolutionary Adaptations

city: Eugene

first: William

last: Cresko

state: Oregon

address: 1505 Franklin Blvd #131

institute: University of Oregon

summary: Seahorses, pipefishes, and seadragons are fishes from the family Syngnathidae that have evolved extraordinary traits including male pregnancy, elongated snouts, loss of teeth, and dermal bony armor. The developmental genetic and cellular changes that led to the evolution of these traits are largely unknown. Recent syngnathid genomes revealed suggestive gene content differences and provide the opportunity for detailed genetic analyses. We created a single cell RNA sequencing atlas of Gulf pipefish embryos to understand the developmental basis of four traits: derived head shape, toothlessness, dermal armor, and male pregnancy. We completed marker gene analyses, built genetic networks, and examined spatial expression of select genes. We identified osteochondrogenic mesenchymal cells in the elongating face that express regulatory genes bmp4, sfrp1a, and prdm16. We found no evidence for tooth primordia cells, and we observed re-deployment of osteoblast genetic networks in developing dermal armor. Finally, we found that epidermal cells expressed nutrient processing and environmental sensing genes, potentially relevant for the brooding environment. The examined pipefish evolutionary innovations are composed of recognizable cell types, suggesting derived features originate from changes within existing gene networks. Future work addressing syngnathid gene networks across multiple stages and species is essential for understanding how their novelties evolved.

overall_design:
We created scRNAseq atlases from embryos of 2 wild caught Gulf pipefish (Syngnathus scovelli). 20 embryos per pouch were isolated for libraries. Embryos were at the 'frontal jaws' stage whereby they possessed cartilaginous craniofacial skeletons but it has not elongated yet. Embryos were dissociated in 460ul of .25% trypsin and 40ul 100mg/ml collagenase I. Cell concentratoins were quantified with the TC20 Automated Cell Counter then diluted to 800 cells/ul in .04%. The University of Oregon Genomics and Cell Characterization Core prepared single cell libraries for the two samples using the 10X Genomics Single Cell 3' Genome Expression mRNAseq kit with NextGEM v3.1 chemistry.
Grants:
William Cresko, OPP-2015301, National Science Foundation, the evo-devo of male pregnancy and its effects on the brood pouch microbiome
Hope Healey, F31DE032559, National Institute of Health NIDCR, Discovery of craniofacial genes capable of compensation through evolutionary mutant model

first: Hope

last: Healey

first: Hayden

last: Penn

first: Clay

last: Small

first: Vithika

last: Goyal

first: Micah

last: Woods

first: Susan

last: Bassham


title: Macrophages reside in the muscle spindle to control sensorimotor function at millisecond timescale

city: London

first: Franziska

last: Müller

address: Du Cane Road

department: Brain Sciences

institute: Imperial College London

summary: The stretch reflex is a fundamental component of the motor system to orchestrate the coordinated muscle contractions underlying movement. At the heart of this process lie the muscle spindles (MS), specialized receptors finely attuned to fluctuations in tension within intrafusal muscle fibers. The tension variation in the MS triggers a series of neuronal events: an initial depolarization of sensory type Ia afferents that subsequently causes the activation of  motoneurons within the spinal cord. This neuronal cascade culminates in the execution of muscle contraction, underscoring a presumed closed-loop mechanism between the muscular and nervous systems.  In contrast, surprisingly here we report the discovery of a new population of macrophages with exclusive molecular and functional signatures within the muscle spindle that express the machinery for synthesizing and releasing glutamate. Using mouse intersectional genetics with optogenetics and electrophysiology, we show that muscle spindle macrophages (MSMP) activation drives proprioceptive sensory neurons firing at millisecond timescale with subsequent activation of spinal circuitries, motor neurons, and muscles by a glutamate-dependent mechanism. Additionally, we found that MSMP can also respond to the activation of the stretch reflex circuitry by increasing the expression of glutaminase, allowing them to convert the glutamine released by myocytes during muscle contraction into glutamate.  Our results identified a new cellular component, the MSMP, that directly regulates neural activity and muscle contraction. The glutamate-mediated signalling of MSMP and their dynamic response to sensory cues introduces a novel dimension to our understanding of sensation and motor action, potentially offering innovative therapeutic approaches in conditions that affect sensory-motor function.

overall_design: To investigate the distinct molecular and functional signature of muscle spindle and muscle spindle macrophages (MSMP), we sequenced mucle spindle and non-muscle spindle areas; macrophages from muscle, heart and lung.

first: Yuyang

last: Yan

first: Simone

last: Di Giovanni


title: Prenatal Maternal Stress in Rats Alters the Epigenetic and Transcriptomic Landscape of the Maternal-Fetal Interface Across Four Generations [methylation]

status: Public on Oct 07 2024

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

country: Canada

institute: University of Lethbridge

summary: Prenatal maternal stress (PNMS) determines lifetime mental and physical health. Here, we show in rats that PNMS has consequences for placental function and fetal brain development across four generations (F0-F3). Using a systems biology approach, comprehensive DNA methylation (DNAm), miRNA, and mRNA profiling revealed a moderate impact of PNMS in the F1 generation, but drastic changes in F2 and F3 generations, suggesting compounding effects of PNMS with each successive generation. Both maternal and placental miRNA gene targets included de novo DNA methyltransferases, indicating robust PNMS-induced disruption in the complex epigenetic regulatory network between miRNAs and DNAm. Transgenerational programming mainly involved genes and biological pathways associated with neurological and psychiatric diseases which were linked to maternal-fetal crosstalk facilitated by the placenta. The highly correlated placenta-brain profiles support the use of placenta as a noninvasive biomarker resource to predict pathological changes in the neonatal brain. The transgenerational persistence of critical DNAm, miRNA and mRNA signatures may explain familial non-genetic disease risks.

overall_design: Four generations of transgenerational, multigenerational, and control prenatal maternal stress rats were created. Fetal cortex and placenta were extracted at G21 to isolate mRNA, miRNA, and DNA methylation. A total of 24 animals were used with n=3 for each treatment (F0 control, F0 stress, F1-S, F1-N, F2-SN, F2-SS, F2-NN, F3-SNN, F3-SSS, F3-NNN).

first: Stephanie

last: King

first: Nicola

last: Schatz

first: Olena

last: Babenko

first: Igor

last: Kovalchuk

first: Gerlinde

last: Metz


title: Comparing Neoantigen Cancer Vaccines and Immune Checkpoint Therapy Unveils an Effective Vaccine and Anti-TREM2 Macrophage-Targeting Dual Therapy [CD45]

first: Sunita

last: Keshari

overall_design: Droplet-based 5′ end massively parallel single-cell RNA sequencing was performed by encapsulating sorted live intratumoral CD45+ cells into droplets and preparing libraries using Chromium Single Cell 5′ Reagent Kits following the manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using a NovaSeq 6000 Sequencing System (Illumina).

first: Alexander

last: Shavkunov

first: Qi

last: Miao

first: Akata

last: Saha

first: Tomoyuki

last: Minowa

first: Martina

last: Molgora

first: Charmelle

last: Williams

first: Mehdi

last: Chaib

first: Anna

last: Highsmith

first: Josué

last: Pineda

first: Sayan

last: Alekseev

first: Elise

last: Alspach

first: Kenneth

last: Hu

first: Marco

last: Colonna

first: Kristen

last: Pauken

first: Ken

last: Chen

first: Matthew

last: Gubin


title: Macrophages reside in the muscle spindle to control sensorimotor function at millisecond timescale [scRNA-seq]

first: Franziska

last: Müller

overall_design: Muscle spindle macrophages from mouse hindlimb muscles and neurons from mouse L4-6 dorsal root ganglion (DRG) were isolated by fluorescence-activated cell sorting (FACS).

first: Yuyang

last: Yan


title: NGR1 reduces neuronal apoptosis through regulation of ITGA11 following subarachnoid hemorrhage

city: 珠海

first: HOU

last: YU

address: 拱北街道海安园

institute: 澳门科技大学

summary: Subarachnoid hemorrhage (SAH), a prevalent cerebrovascular condition associated with a high mortality rate, frequently results in neuronal apoptosis and an unfavorable prognosis. Recent research has indicated that the adjunctive use of Traditional Chinese medicine (TCM) with surgical interventions exerts a therapeutic impact on SAH. Nevertheless, the mechanism by which TCM mediates apoptosis following SAH remains unclear. In the present study, HT22 mouse neuronal cells were exposed to Oxyhemoglobin (OxyHb) to establish an in vitro model of SAH. The results indicated that treatment with Notoginsenoside R1 (NGR1) alleviated the short-term neurological deficits, reduced the expression of apoptosis-related proteins, and mitigated brain edema in mice. Similarly, it attenuated OxyHb-induced apoptosis of HT22 neurons. Furthermore, RNA-seq analysis was used to examine the transcriptomic changes between HT22 cells stimulated with OxyHb alone and those treated with NGR1 concurrently or independently. The RNA-seq results revealed significant alterations in the expression levels of apoptosis-related genes in OxyHb-stimulated HT22 cells upon administration of NGR1. This study explored the potential mechanism by which NGR1 mitigates neuronal apoptosis, presenting a novel therapeutic approach for treating SAH through the use of a single TCM ingredient.

overall_design: The total RNA was extracted through the culture of neuron cell HT22. Each group was divided into three replicates.  There were three groups in total, namely, the experimental group, the control group and the intervention group.  Subsequently, RNA isolation, quantification and quality assessment were carried out. Then, the mRNA sequencing library was prepared, and then the library quality analysis was carried out.  Finally, the high-throughput Transcriptome was sequenced on Illumina NovaSeq.

first: Yu

last: Hou

first: Lihan

last: Zhang

first: Wenzhe

last: Ma

first: Yong

last: Jiang


title: Prenatal Maternal Stress in Rats Alters the Epigenetic and Transcriptomic Landscape of the Maternal-Fetal Interface Across Four Generations [miRNA]

first: Yaroslav

last: Ilnytskyy

type: Non-coding RNA profiling by high throughput sequencing

first: Stephanie

last: King

first: Nicola

last: Schatz

first: Olena

last: Babenko

first: Igor

last: Kovalchuk

first: Gerlinde

last: Metz


title: Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis [Spatial Transcriptomics]

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

institute: Schroeder Arthritis Institute

summary: Objective: To spatially resolve the identified celltypes, subtypes and transcriptomic profiles from single-nuclei RNA-seq with matched 12 infrapatellar fat pad of knee OA patients using spatial transcriptomics sequencing.

overall_design: Spatial transcriptomics sequencing libraries were constructed for 12 infrapatellar fat pad (IFP) of knee OA samples using the 10X Genomics Visium CytAssist Spatial Gene Expression Reagent Kits to spatially resolve the celltypes in the IFP tissue using bioinformatics analysis.

first: Hayley

last: Peters

first: Pratibha

last: Potla

first: Jason

last: Rockel

first: Teodora

last: Tockovska

first: Chiara

last: Pastrello

last: Jurisica

first: Keemo

last: Delos Santos

first: Shabana

last: Vohra

first: Noah

last: Fine

first: Starlee

last: Lively

first: Kim

last: Perry

first: Nikita

last: Looby

first: Sheng

last: Han Li

first: Vinod

last: Chandran

first: Katrina

last: Hueniken

first: Paramvir

last: Kaur

first: Anthony

middle: V

last: Perruccio

first: Nizar

middle: N

last: Mahomed

first: Raja

last: Rampersaud

first: Khalid

last: Syed

first: Eric

last: Gracey

first: Roman

last: Krawetz

last: Buechler

first: Rajiv

last: Gandhi


title: Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis

first: Mohit

last: Kapoor

first: Hayley

last: Peters

first: Pratibha

last: Potla

first: Jason

last: Rockel

first: Teodora

last: Tockovska

first: Chiara

last: Pastrello

first: Igor

last: Jurisica

first: Keemo

last: Delos Santos

last: Vohra

first: Matthew


title: PfNSUN1 protein programs gene expression regulation in Plasmodium falciparum [RIP-seq]

status: Public on Oct 05 2024

city: Changsha

first: Xiaomin

last: Shang

state: Hunan Province

address: 172 Tongzipo Road

department: Department of Parasitology

institute: Central South University

summary: C5 methylation of cytosines is a common RNA modification in eukaryotes, and the NSUN family are essential m5C modification executors. Currently, little is known about this family in Plasmodium spp. Thus, we constructed the pfnsun1 knockdown strain, and the knockdown efficiency was confirmed by growth curves and western blot experiments. The knockdown transcriptome data was acquired to find differentially expressed genes, and target genes of PfNSUN1 protein were identified by RNA immunoprecipitation and high-throughput sequencing experiments. Our data revealed that pfnsun1 is an indispensable RNA post-transcriptional modification regulator in P. falciparum that regulates gene expression.

overall_design: To explore the function of PfNSUN1 protein, we collected ring stage sample of pfnsun1-ty1-glmS strain to identify its direct-binding RNAs by RIP-seq experiments.

first: Yanting

last: Fan


title: Single-cell RNA-seq profiling of Pseudomyxoma Peritonei

first: sungghwan

last: park

summary: Through single-cell transcriptomic profiling of five samples with Pseudomyxoma Peritonei (PMP) , we identified ten distinct cell type-specific clusters, including an epithelial cell community with significantly increased expression of canonical epithelial molecules, and a mesenchymal cell community with notably higher expression of established mesenchymal molecules, supporting the presence of both epithelial and mesenchymal molecular characteristics in PMP disease.

overall_design: Single-cell transcriptomic profiling was performed in a patient group with five PMPs to verify cell type-specific gene expression patterns.

first: Jeong-Hwan

last: Kim

first: Seon-Kyu

first: Seong-Hwan

last: Park

first: Seon-Young

first: Ye

last: Ha

first: Jong

last: Lee


title: Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis [snRNA-seq]

first: Mohit

summary: Objective: To identify and characterize celltypes and distinct transcriptomic signatures present in the infrapatellar fat pad (IFP) of knee OA patients using single-nucleus RNA sequencing.

overall_design: Single-nucleus RNA sequencing was performed on 21 knee OA - IFP samples by using 10X Genomics Chromium NEXT GEM Single cell 3' Reagent kit and Illumina NextSeq550 sequencer.

first: Hayley

first: Shabana

first: Noah

last: Fine

first: Starlee

last: Lively

first: Kim

last: Perry

first: Nikita

last: Looby

first: Sheng

last: Han Li

first: Vinod

last: Chandran

first: Katrina

last: Heuniken

first: Paramvir

last: Kaur

first: Anthony

last: Perruccio

first: Nizar

last: Mahomed

first: Raja

last: Rampersaud

first: Khalid

last: Syed

first: Eric

last: Gracey

first: Roman

last: Krawetz

last: Buechler

first: Rajiv

last: Gandhi


title: RNA helicase MOV10 suppresses fear memory and dendritic arborization and regulates microtubule dynamics in hippocampal neurons [eCLIP-seq]

status: Public on Oct 04 2024

city: Urbana

first: Stephanie

last: Ceman

state: Illinois

address: 506 S Mathews Ave

department: Cell and Developmental Biology

institute: University of Illinois Urbana-Champaign

summary: RNA helicase MOV10 is highly expressed in postnatal brain and associates with FMRP and AGO2, suggesting a role in translation regulation in learning and memory. We generated a brain-specific knockout mouse (Mov10 Deletion) with greatly reduced MOV10 expression in cortex and hippocampus. Behavior testing revealed enhanced fear memory, similar to that observed in a mouse with reduced brain microRNA production, supporting MOV10’s reported role as an AGO2 cofactor. Cultured hippocampal neurons have elongated distal dendrites, a reported feature of augmin/HAUS over-expression in Drosophila da sensory neurons. In mitotic spindle formation, HAUS is antagonized by the microtubule bundling protein NUMA1. Numa1 mRNA is a MOV10 CLIP target and is among the genes significantly decreased in Mov10 Deletion hippocampus. Restoration of NUMA1 expression and knockdown of HAUS rescued microtubule comet formation in dendritic growth cones. This is the first evidence of translation regulation of NUMA1 as a control point in dendritogenesis.

overall_design: To investigate if AGO2 binding to its target mRNAs is affecetd by MOV10's absence, AGO2 and its bound mRNAs were immunoprecipitated from WT and MOV10 Deletion whole brains for sequencing.

first: Temirlan

last: Shilikbay

first: Aatiqa

last: Nawaz

first: Megan

last: Doon


title: RNA-seq of laser-captured dissected endometrium of WT and Thra1 PV/+ mice

status: Public on Oct 03 2024

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: Thyroid hormone receptors (TRs) mediate the genomic actions of the thyroid hormone (T3). Mutations of THRA gene cause a human disease known as resistance to thyroid hormone (RTHa). We created a mouse model expressing a dominant negative mutated TRa1 (Thra1PV/+ mice) that exhibits severely retarded growth, bone abnormalities, constipation, and anemia, as found in RTHa patients. It has been previously observed that female Thra1PV/+ mice exhibit fertility deficiency. In the present study, we aim to understand the molecular basis underlying female infertility caused by TRa1 mutants. The uterus of mutant mice atrophied with 50-60% reduction in weight, as compared with wild-type (WT) mice with reduced proliferation, increased apoptosis, and loss of ~90% of uterine glands. Fibrosis of the endometrium and squamous metaplasia were detected in the uterine epithelium of all Thra1PV/+ mice examined. RNA-seq analysis of laser-captured micro-dissected endometrium to understand the gene expression changes that lead to uterine atrophy, epithelium metaplasia, immune cells infiltration and ectopic expression of IL-33.Analysis of altered gene expression profiles has reveled by RNA-seq analysis provide new insights to understand how thyroid dysfunction could lead to female infertility.

overall_design: To study the altered global gene profiles in Sub-Tissue Distinct Cellular Compartments of WT and Mutant Endometrium.

first: Sheue-yann

last: Cheng

first: Xuquang


title: RNA helicase MOV10 suppresses fear memory and dendritic arborization and regulates microtubule dynamics in hippocampal neurons [RNA-seq]

summary: RNA helicase MOV10 is highly expressed in postnatal brain and associates with FMRP and AGO2, suggesting a role in translation regulation in learning and memory. We generated a brain-specific knockout mouse (Mov10 Deletion) with greatly reduced MOV10 expression in cortex and hippocampus.  Behavior testing revealed enhanced fear memory, similar to that observed in a mouse with reduced brain microRNA production, supporting MOV10’s reported role as an AGO2 cofactor. Cultured hippocampal neurons have elongated distal dendrites, a reported feature of augmin/HAUS over-expression in Drosophila da sensory neurons. In mitotic spindle formation, HAUS is antagonized by the microtubule bundling protein NUMA1. Numa1 mRNA is a MOV10 CLIP target and is among the genes significantly decreased in Mov10 Deletion hippocampus. Restoration of NUMA1 expression and knockdown of HAUS rescued microtubule comet formation in dendritic growth cones. This is the first evidence of translation regulation of NUMA1 as a control point in dendritogenesis.

overall_design: We isolated total RNA from hippocampi WT and Mov10 Deletion P0 mice and performed RNA-seq to look at the steady state expression of mRNAs.


title: Disruption of deoxynucleotide biosynthesis leads to RASproto-oncogene activation and perturbation of mitochondrial metabolism [DNA-seq]

status: Public on Oct 02 2024

city: Paris

first: Kyle

last: Raymond

address: 28 Rue du docteur Roux, Lwoff-22-02-03

department: Department of Virology

institute: Institut Pasteur

summary: Perturbation of the deoxyribonucleotide triphosphate (dNTP) pool is recognized for contributing to the mutagenic processes involved in oncogenesis. The RAS gene family encodes well characterized oncoproteins whose structure and function are among the most frequently altered in several cancers. In this work, we show that fluctuation of the dNTP pool induces CG->TA mutations across the whole genome, including RAS gene at codons for glycine 12 and 13, known hotspots in cancers. Cell culture addition of the ribonucleotide reductase inhibitor thymidine increases the mutation frequency in nuclear DNA and leads to disruption of mitochondrial metabolism. Interestingly, this effect is counteracted by the addition of deoxycytidine. Finally, screening for the loss of hydrogen bonds detecting CG->TA transition in RAS gene of 135 patients with colorectal cancer confirmed the clinical relevance of this process. All together, these data demonstrate that fluctuation of intracellular dNTP pool alters the nuclear DNA and mitochondrial metabolism.

overall_design: Deep Sequencing of the HRAS gene in HeLa cells after treatment with biased dNTP pools at different concentrations and combinations.  A mutation analysis within the HRAS gene was compared to non-treated HeLa cell controls.

first: Raymond

last: Kyle

first: Suspene

last: Rodolphe

first: Vartanian

last: Jean-Pierre


title: Disruption of deoxynucleotide biosynthesis leads to RASproto-oncogene activation and perturbation of mitochondrial metabolism [RNA-seq]

overall_design: Investigation of the effects of dNTP nucleotide pool shifts in HeLa cells by exposing HeLa cells to different nucleotide concentrations compared to a non-treated control using RNA Seq and differential gene expression analysis.


title: Quantitative Analysis of Transcriptional Changes in Atrx Conditional Knockout Mice

status: Public on Oct 01 2024

first: Brendan

middle: H.

last: Lee

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: ATP-dependent chromatin remodeling protein ATRX is an essential regulator involved in maintenance of DNA structure and chromatin state and regulation of gene expression during development. However, the impact of ATRX during early skeletal development has not been examined. To understand the underlying mechanisms that impaired osteoclast differentiation, we performed RNA-seq on the tibias harvested from control and Atrx cKO mice at 8 weeks of age.

overall_design: Paired-end sequencing of polyA-enrichd mRNA harvested from the tibias of control and Atrx condtional knockout mice.

first: Yi-Ting

last: Chen

first: Yangjin

last: Bae


title: Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics

city: San Francisco

first: Brianna

middle: Lynn

last: Bibel

state: CA

department: Cellular and Molecular Pharmacology

institute: Brianna Bibel

summary: The antibiotics chloramphenicol (CHL) and oxazolidinones including linezolid (LZD) are known to inhibit mitochondrial translation. This can result in serious, potentially deadly, side effects when used therapeutically. Although the mechanism by which CHL and LZD inhibit bacterial ribosomes has been elucidated in detail, their mechanism of action against mitochondrial ribosomes has yet to be explored. CHL and oxazolidinones bind to the ribosomal peptidyl transfer center (PTC) of the bacterial ribosome and prevent incorporation of incoming amino acids under specific sequence contexts, causing ribosomes to stall only at certain sequences. Through mitoribosome profiling, we show that inhibition of mitochondrial ribosomes is similarly context-specific – CHL and LZD lead to mitoribosome stalling primarily when there is an alanine, serine, or threonine in the penultimate position of the nascent peptide chain. Our findings could help inform the rational development of future, less mitotoxic, antibiotics, which are critically needed in the current era of increasing antimicrobial resistance.

overall_design: Mitochondrial ribosome profiling in human cells (HEK293) with and without antibiotic (chloramphenicol, linezolid, or retapamulin) treatment

first: Mary

middle: T

last: Couvillion

first: Stirling

last: Churchman

first: Danica

last: Fujimori


title: Single cell transcriptomics in blood of patients with chronic obstructive pulmonary disease

city: Chuncheon

first: HEO

last: YEONJEONG

address: 70, Bangsong-gil

institute: Kangwon National University Hospital

summary:
Background
Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality worldwide. Single-cell RNA sequencing (scRNA-seq) provides gene expression profiles at the single-cell level. Hence, we evaluated gene expression in the peripheral blood of patients with COPD.
Methods
Peripheral blood samples from seven healthy controls and eight patients with COPD were obtained in this study. The 10X Genomics Chromium Instrument and cDNA synthesis kit was utilized to generate a barcoded cDNA library for single cell RNA-sequencing. We compared the scRNA-seq data between the COPD and control groups using computational analysis. Functional analyses were performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses.
Results
scRNA-seq was used to analyze the transcriptome of peripheral blood mononuclear cells from seven normal controls and eight patients with COPD. We found increased numbers of monocyte macrophages in the COPD group compared to those in the normal control group. Among the differentially expressed genes (DEGs) in monocyte-macrophages, we identified five upregulated genes (HLA-DRB5, ITGB2, EGR1, CXCL8, and CCL4) and seven downregulated genes (FOLR3, RPS4Yq, CD52, LY6E, HLA-DQB1, G0S2, and CCL3L1) in the COPD group compared to the normal control group.
Conclusions
Using scRNA-seq, we found differences in cell type distribution, especially in monocyte macrophages. Several upregulated and downregulated genes were found in the monocyte-macrophages of the COPD groups.

overall_design: Data from the Chronic Obstructive Pulmonary Disease in Dusty Areas (CODA) cohort were analyzed. The CODA cohort enrolled participants living in six cities (Gangneung, Donghae, Samcheok, Yeongwol, Danyang, and Jecheon) near cement plants in the Kangwon and Chungbuk provinces of South Korea between 2012 and 2017. Among the COPD group and the heath group who participated in the CODA cohort, patients who agreed to participate in our study were divided into two groups and scRNA sequencing was performed on peripheral blood samples. We obtained data from seven healthy participants and eight participants with COPD from the CODA cohort. Peripheral blood samples were obtained by dividing the patients living in two cities (Samcheok and Yeongwol) into two groups: COPD and normal control. Peripheral blood mononuclear cells (PBMCs) were isolated by density centrifugation and processed directly or after frozen storage, labeled with cell hashing antibodies and loaded on droplet-based (10x) scRNA-seq platforms

first: Yeonjeong

last: Heo

first: Jeeyoung

last: Kim

first: Seok-Ho

last: Hong

first: Woo


title: Disruption of deoxynucleotide biosynthesis leads to RASproto-oncogene activation and perturbation of mitochondrial metabolism.

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

overall_design: Refer to individual Series


title: RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [sRNA-seq]

city: Beijing

first: Ling

middle: Tong

last: Liu

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, Chinese Academy of Sciences

summary: Background: Plant-unique RNA polymerase IV (Pol IV) governs the establishment of small RNA-directed DNA methylation (RdDM) and contributes to the maintenance of transposable element (TE) silencing. Pol IV-dependent RdDM is highly active during embryonic development, and its absence occasionally reduces seed sets in species with high TE content. However, the mechanism underlying embryonic development failure due to the loss of Pol IV-RdDM remains largely unclear. Results: Here, we report that the loss-of-function of SlNRPD1, encoding the largest subunit of the Pol IV complex leads to aberrant embryogenesis in tomato (Solanum lycopersicum). The slnrpd1 mutants show non-CG hypomethylation and a burst of 21/22-nt sRNA from the distal chromatin region. We found that non-CG hypomethylation at the gene body region is generally associated with the activation of transcription, and knocking out DEMETER-like DNA demethylases cannot reverse slnrpd1 embryo lethality. mCHH hypomethylation in slnrpd1 disrupts gene expression related to auxin and WUSCHEL-related homeobox (WOX) signaling. TE reactivation in slnrpd1 mainly affects the expression of a limited number of nearby genes rather than contributing to excessive sRNA. Conclusion: We conclude that Pol IV-mediated RdDM is essential for tomato embryogenesis via non-CG methylation. mCHH hypomethylation in the slnrpd1 embryo leads to abnormal auxin/WOX signaling and TE reactivation which probably disrupts the tissue and organ initiation. This study provides new insights into the epigenetic regulation of gene and TE expression during embryogenesis. Keywords: DNA methylation, RdDM, NRPD1, Embryogenesis, Tomato

overall_design: To investigate the function of NRPD1 in tomato embryogenesis,  we collected 21 days after flowering (DAF) embryos of wild type and slnrpd1 to perform sRNA-sequencing.

first: Lingtong

first: Yixuan

last: Feng


title: High-quality co-expression networks for accurate gene function predictions in the fungal cell factory Aspergillus niger and beyond

city: Berlin

first: Stephan

last: Starke

address: Gustav Meyer Allee 25

department: Microbiology

institute: TU Berlin

summary: Co-expression networks have recently emerged as a useful approach for updating and improving gene annotation at a near-genome level. This is based on the hypothesis that function can be inferred by delineating transcriptional networks in which a gene of interest is embedded. In this study, we generated a co-expression network for the filamentous cell factory Aspergillus niger from 128 RNA-seq experiments. We confirm that over 70% of the >14,000 A. niger genes are represented in this network and show that gene functions can be accurately predicted as evidenced by analysis of various control sub-networks. Our analyses further indicate that this RNA-seq co-expression network has a higher predictive power compared to the microarray co-expression network that we published in 2019. To demonstrate the potential of the new co-expression network to unveil complex and non-intuitive predictions for gene regulation phenomena, we provide here new insights into the temporal, spatial and metabolic expression profile that connects a secreted antifungal peptide with mycelial growth, asexual development, secondary metabolism and pectin degradation in A. niger. To empower biologists to generate or apply co-expression networks in the fungal kingdom and beyond, we also demonstrate that (i) high quality networks can be generated from only 32 transcriptional experiments; (ii) such low numbers of experiments can be safely compensated for by using higher thresholds for defining co-expression pairs; and (iii) a ’safety in numbers’ rule applies, whereby experimental conditions have minimal impact on network content provided a certain number of experiments are included.

overall_design:
This experiment aimed to determine the effect of anafp (A. niger antifungal protein) expression on the mRNA profile of A. niger. The goal was to validate predictions made by the co-expression network. Illumina HiSeq RNA sequencing was performed on Aspergillus niger mRNA, obtained from biomass cultivated in the presence or absence of anafp. To express anafp, the doxycycline (Dox)-responsive Tet-On gene switch ws utilized. RNA was extracted from biomass that had been cultivated in a 4-liter bioreactor (using liquid CM medium, without doxycycline) until the mid-exponential growth phase. The biomass was then transferred to agar plates lacking a carbon source and incubated for 35 hours, in the presence or absence of 5 µg/ml doxycycline before harvesting. The experiment was conducted in biological duplicates.
For differential gene expression analysis, the mRNA profile of A. niger STS4.10 (Tet-On anafp) with 5 µg/ml doxycycline (representing the overexpression phenotype) was compared to that of STS4.10 with 0 µg/ml doxycycline (representing the knockout phenotype). Additionally, differential gene expression was assessed for A. niger VG8.27 (Tet-On-luciferase) in the presence or absence of 5 µg/ml doxycycline, which served as an overexpression control strain.

first: Sascha

last: Jung

first: Vera

last: Meyer


title: Insulin resistance disrupts midbrain metabolic and functional homeostasis and aggravates dopaminergic neuron loss in GBA-PD via FOXO1 overexpression.

city: Esch sur Alzette

first: Alise

last: Zagare

state: Belval

address: 7 Avenue des Hauts-Fourneaux

country: Luxembourg

institute: University of Luxembourg


title: Insulin resistance disrupts midbrain metabolic and functional homeostasis and aggravates dopaminergic neuron loss in GBA-PD via FOXO1 overexpression [WTvsGBA]

summary: Growing evidence indicates that Type 2 diabetes (T2D) is associated with an increased risk of developing PD Parkinson’s disease (PD) through shared disease mechanisms. Studies show that insulin resistance, which is the driving pathophysiological mechanism of T2D plays a major role in neurodegeneration by impairing neuronal functionality, metabolism, and survival. To better understand the importance of insulin signalling in the human midbrain, which is the most affected brain region in PD, we expose IPSC-derived human midbrain organoids from healthy individuals and GBA-N370S mutation-carrying PD patients to either high insulin concentrations, promoting insulin resistance, or to more physiological insulin concentrations restoring normal insulin signalling function. We are able to show that insulin resistance compromises dopaminergic neuron and dopamine levels in the midbrain organoids of healthy donors. Moreover, insulin-resistant organoids display diminished neuronal activity and reduced metabolic efficiency. Furthermore, our findings demonstrate FOXO1 role in GBA-PD phenotype severity and show the potential beneficial effects of the anti-diabetic drug Pioglitazone in GBA-PD treatment. Overall, our results highlight insulin resistance as a significant target in PD prevention and disease-modifying therapy.

overall_design: Comparative gene expression analysis of insulin-resistant and insulin-sensitive midbrain organoids derived from iPSCs of healthy individuals and GBA-N370S mutation-carrying PD patients.

first: Janis

last: Kurlovics

first: Catarina

last: Almeida

first: Daniele

last: Ferrante

first: Daniela

last: Frangenberg

first: Ahmed

last: Hemedan

first: Armelle

last: Vitali

first: Gemma

last: Gomez-Giro

first: Reijko

last: Krüger

first: Enrico

last: Glaab

first: Christian

last: Jäger

first: Paul

last: Antony

first: Rashi

last: Halder

first: Egils

last: Stalidzans

first: Marek

last: Ostaszewski

first: Giuseppe

last: Arena

first: Jens

middle: C

last: Schwamborn


title: RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [RNA-Seq]

first: Ling

last: Liu

overall_design: To investigate the function of NRPD1 in tomato embryogenesis,  we collected 21 days after flowering (DAF) embryos of wild type and slnrpd1 to perform RNA-sequencing.

first: Lingtong

first: Yixuan

last: Feng


title: Insulin resistance disrupts midbrain metabolic and functional homeostasis and aggravates dopaminergic neuron loss in GBA-PD via FOXO1 overexpression [WTs]

first: Alise

last: Zagare

overall_design: Comparative gene expression analysis of insulin-resistant and insulin-sensitive midbrain organoids derived from iPSCs of healthy individuals.

first: Janis

last: Kurlovics

first: Catarina

last: Almeida

first: Daniele

last: C Schwamborn


title: DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts

status: Public on Sep 30 2024

city: OXFORD

first: Krzysztof

last: Kus

state: Oxfordshire

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: RNA polymerase II (Pol II) termination is a crucial step in the transcriptional cycle, ensuring the recycling of Pol II and preventing interference with neighboring gene transcription. Xrn2 is an enzyme with 5'-3'- exonuclease activity, responsible for degrading RNA that is still being transcribed by Pol II after cleavage at the poly(A) site, ultimately leading to Pol II termination. We have confirmed that Xrn2's catalytic activity is essential for timely transcription termination. Furthermore, we have discovered a link between Xrn2 and the conserved, multifunctional transcription factor Spt5. Importantly, our research demonstrates that Xrn2 interacts with Pol II/Spt5 complexes. Additionally, when Spt5 is depleted, it not only impairs global transcription but also results in defective transcription termination. On the other hand, absence of Spt5 leads to the derepression of non-coding transcription and premature termination/attenuation at the 5'-end of coding genes. We propose that Spt5 acts as a "licensing" factor, ensuring that Pol II complexes are properly assembled for efficient transcription and co-transcriptional pre-mRNA processing.

overall_design: Nascent transcriptome (TT-seq) was used to study how Spt5 and Xrn2 impact transcription. Spt5 was depleted using auxin degron and compared to DMSO-treated strain. Three Xrn2 degron strains were created: one without Xrn2 rescue, one with WT rescue, and one with MUT rescue (containing a catalytic D235A mutation). The rescue Xrn2 (or its mutant) under the native promoter was placed in the ura4 locus. The experiments were performed twice and spike-in normalized.

last: Kuś

first: Loic

last: Carrique

first: Tea

last: Kecman

first: Marjorie

last: Fournier

first: Sarah

last: Hassanein

first: Ebru

last: Aydin

first: Cornelia

last: Kilchert

first: Jonathan

last: Grimes

first: Lidia

last: Vasiljeva


title: Single-cell Multiomic profiling of soybean cotyledon-stage seeds

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: To understand the processes governing soybean seed development, we profiled the mRNA transcriptome and chromatin accessibility of cotyledon-stage seeds at the single-nucleus level.

overall_design: snRNA-Seq and snATAC-seq data from cotyledon-stage seed single-nuclei, using 10X Genomics Chromium Single Cell MultiOme ATAC + Gene Expression

first: Julie

last: Pelletier

first: Min

last: Chen

first: Robert

middle: B

last: Golberg


title: Novel integrated multiomics analysis reveals Itgbl1-mediated regulation of fibrogenesis through antagonism of Tgfβ1 and IL1β signaling. (single cell RNA-Seq)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: To understand the molecular mechanism of minority cell population in skin would healing process, we performed single cell RNA sequencing (scRNA-seq) of murine skin wound tissues at 3 different time points after injury (3d, 7d, 14d).

overall_design: scRNA-seq analysis data were obtained by using murine skin wound tissues which includes on day 3, 7, and 14 post incisional injury.

first: Sang-Eun

last: Kim

first: Ryota

last: Noda

first: Yu-Chen

last: Liu

first: Shoichiro

last: Kameoka

last: Okuzaki

first: Ryoichi

last: Mori


title: Novel integrated multiomics analysis reveals Itgbl1-mediated regulation of fibrogenesis through antagonism of Tgfβ1 and IL1β signaling. (mRNA-Seq)

summary: To elucidate the molecular mechanisms underlying the roles of inflammatory cells in scar formation, we performed RNA-seq of inflammation-related mRNAs and miRNAs from both wild-type mice and PU.1 knock-out mice (PU.1 KO). This approach allowed us to comprehensively investigate how inflammation-related gene expression influences the skin wound healing process.

overall_design: Comparative gene expression profiling analysis was performed using RNA-sequencing data obtained from murine skin wound tissue samples. These samples were collected from both wild-type and PU.1 knockout (PU.1 KO) mice, harvested 24 hours post-excisional wounding.


title: Intratumor heterogeneity of EGFR expression mediates targeted therapy resistance and formation of drug tolerant microenvironment

city: Helsinki

first: Heidi

last: Haikala

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors are commonly used to treat non-small cell lung cancers with EGFR mutations, but drug resistance often emerges. Intratumor heterogeneity is a known cause of targeted therapy resistance and is considered a major factor in treatment failure. This study identified clones of EGFR-mutant non-small cell lung tumors expressing low levels of both wild-type and mutant EGFR protein. These EGFR-low cells were found to be intrinsically more tolerant to EGFR inhibitors, more invasive, and exhibited an epithelial-to-mesenchymal-like phenotype compared to their EGFR-high counterparts. The EGFR-low cells secrete TGFβ-family cytokines, leading to increased recruitment of cancer-associated fibroblasts and immune suppression, thus contributing to the drug-tolerant tumor microenvironment. Notably, pharmacological induction of EGFR using epigenetic inhibitors sensitized the resistant cells to EGFR inhibition. These findings suggest that intrinsic drug resistance could be prevented or reversed using combination therapies.

overall_design: PC-9 cells were stained with EGFR antibody and sorted 6 sequential rounds for 5-10% highest("EGFR-high") and 5-10% lowest ("EGFR-low") expressing cells. Bulk mRNA sequencing was conducted for PC-9 Parental cells, PC-9 EGFR-high cells and PC-9 EGFR-low cells.

first: Jänne

last: Pasi


title: PfNSUN1 protein programs gene expression regulation in Plasmodium falciparum [RNA-seq]

first: Xiaomin

last: Shang

summary: C5 methylation of cytosines is a common RNA modification in eukaryotes, and the NSUN family are essential m5C modification executors. Currently, little is known about this family in Plasmodium spp. Thus, we constructed the pfnsun1 knockdown strain, and the knockdown efficiency was confirmed by growth curves and western blot experiments. The knockdown transcriptome data was acquired to find differentially expressed genes, and target genes of PfNSUN1 protein were identified by RNA immunoprecipitation and high-throughput sequencing experiments. Our data revealed that pfnsun1 is an indispensable RNA post-transcriptional modification regulator in P. falciparum that regulates gene expression.

overall_design: To explore the function of PfNSUN1 protein as an epigenetic regulator, we performed strict synchronization and divided the samples into drug-added and non-drug-added groups, then collected the transcriptome samples in the next growth cycle at ring, trophozoite and schizont stages, respectively.

first: Yanting

last: Fan


title: Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survival [CUT&Tag]

status: Public on Sep 27 2024

first: Satoshi

last: Namekawa

department: Department of Molecular and Cellular Biology

institute: University of California, Davis

summary: To understand the functional role of CHD4, a member of the Nucleosome Remodeling and Deacetylase (NuRD) complex, in establishing chromatin states in the formation and maintenance of ovarian reserve and the maintenance of female and male germ cells, we eliminated CHD4 function in germ cells using Ddx4-Cre and Gdf9-iCre to generate CHD4 conditional knockout (Chd4 DcKO and GcKO) mice. We discover that CHD4 defines the chromatin state that ensures germ cell survival, thereby enabling the long-term maintenance of female and male germ cells. We then performed CUT&Tag for CHD4 in Chd4 f/f  P1 oocytes.

overall_design: Comparative chromatin profiling analysis of CUT&Tag data for Chd4 f/f P1 non-growing oocytes.

first: Yasuhisa

last: Munakata


title: Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survival [RNA-seq]

summary: To understand the functional role of CHD4, a member of the Nucleosome Remodeling and Deacetylase (NuRD) complex, in establishing chromatin states in the formation and maintenance of ovarian reserve and the maintenance of female and male germ cells, we eliminated CHD4 function in germ cells using Ddx4-Cre and Gdf9-iCre to generate CHD4 conditional knockout (Chd4 DcKO and GcKO) mice. We discover that CHD4 defines the chromatin state that ensures germ cell survival, thereby enabling the long-term maintenance of female and male germ cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of Chd4 Dctrl and Chd4 DcKO non-growing oocytes and undifferentiated spermatogonia, and Chd4 Gctrl and Chd4 GcKO non-growing and growing oocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for (1) Chd4 Dctrl and DcKO P1 and P5 non-growing oocytes; (2) Chd4 Gctrl and GcKO  P10 non-growing and growing oocytes; (3) Chd4 Dctrl and DcKO P3 undifferentiated spermatogonia.


title: Novel integrated multiomics analysis reveals Itgbl1-mediated regulation of fibrogenesis through antagonism of Tgfβ1 and IL1β signaling.


title: Unravelling the Transcriptomic Symphony of Muscle Ageing: Key Pathways and Hub Genes Altered by Ageing and Caloric Restriction in Rat Muscle Revealed by RNA Sequencing

city: Liverpool

first: Gulam

last: Altab

address: 6 West Derby Street

institute: University of Liverpool

summary: Sarcopenia is a disease involving extensive loss of muscle mass and strength with age and is a major cause of disability and accidents in the elderly. Mechanisms purported to be involved in muscle ageing and sarcopenia are numerous but poorly understood, necessitating deeper study. Hence, we employed high-throughput RNA sequencing to explicate the global changes in protein-coding gene expression occurring in skeletal muscle with age. Caloric restriction (CR) is a proven prophylactic intervention against sarcopenia. Therefore, total RNA was isolated from the muscle tissue of both rats fed ad libitum and CR rats. Collected data were subjected to Gene Ontology, pathway, co-expression, and interaction network analyses. This revealed the functional pathways most activated by both ageing and CR, as well as the key “hub” proteins involved in their activation. RNA-seq revealed 442 protein-coding genes to be upregulated and 377 to be downregulated in aged muscle, compared to young muscle. Upregulated genes were commonly involved in protein folding and the immune response; meanwhile, downregulated genes were often related to developmental biology. CR was found to suppress 69.7% and rescue 57.8% of the genes found to be upregulated and downregulated in aged muscle, respectively. In addition, CR uniquely upregulated 291 and downregulated 304 protein-coding genes. Hub genes implicated in both ageing and CR included Gc, Plg, Irf7, Ifit3, Usp18, Rsad2, Blm and RT1-A2, whilst those exclusively implicated in CR responses included Alb, Apoa1, Ambp, F2, Apoh, Orm1, Mx1, Oasl2 and Rtp4. Hub genes involved in ageing but unaffected by CR included Fgg, Fga, Fgb and Serpinc1. In conclusion, this comprehensive RNA sequencing study highlighted gene expression patterns, hub genes and signalling pathways most affected by ageing in skeletal muscle. This data may provide the initial evidence for several targets for therapeutic interventions against sarcopenia.

overall_design: Using rat tissue, using rna-sequencing we aimed to identify the key changes in protein-coding gene expression observed in muscle ageing of rats between young (6 months), old (28 months) and old CR (28 months). In addition, we endeavoured to assess to what extent these changes could be reversed using CR.

first: Gulum

first: Brian

last: Merry

first: Charles

middle: W

last: Beckett

first: Priyanka

last: Raina

first: Inês

last: Lopes

first: Katarzyna

last: Goljanek-Whysall

first: Joao

last: Pedro De Magalhaes


title: Sex differences in Non-Alcoholic Steatohepatitis (NASH) in mice evoked by a fructose-palmitate-cholesterol (FPC)-enriched diet [spatial transcriptomics]

status: Public on Sep 24 2024

city: New York

first: Sofie

last: Delbare

state: NY

address: 435 East 30th Street

institute: NYU Langone

summary: To study sex differences in the response to NASH in mice, single nucleus RNA sequencing of livers was performed. Single nucleus RNAseq demonstrated enrichment of differentially-expressed genes particularly in hepatocytes and stellate cells in females versus males fed FPC-NASH. Multiple regulons (transcription factors and target genes) implicated in lipid and other metabolic processes and hormone signaling (hepatocytes) and cell-cell communication and cell adhesion (stellate cells) were noted, which were enriched in female versus male FPC-NASH diet. Bulk liver RNAseq, RNAseq of isolated hepatocytes and hepatic stellate cells, and spatial transcriptomics, were analyzed as validation experiments.

overall_design: Spatial transcriptomics was performed on the top left lobe of livers from FPC-NASH diet fed male mice.

first: Lakshmi

last: Arivazhagan

first: Robin

middle: A

last: Wilson

first: Boyan

last: Zhou

first: Henry

last: Ruiz

first: Kaamashri

last: Mangar

first: Ryoko

last: Higa

first: Emily

last: Brown

first: Huilin

last: Li

first: Michael

last: Garabedian

first: Ravichandran

last: Ramasamy

first: Kathryn

last: Moore

first: Edward

last: Fisher

first: Neil

middle: D

last: Theise

first: Ann

last: Schmidt


title: Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survival

first: Satoshi

last: Namekawa


title: RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation

first: Ling

last: Liu


title: RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [Bisulfite_seq]

first: Lingtong

first: Yixuan

last: Feng


title: DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts.

first: Krzysztof

last: Kus

summary: RNA polymerase II (Pol II) termination is a crucial step in the transcriptional cycle, ensuring the recycling of Pol II and preventing interference with neighbouring gene transcription. Xrn2 is an enzyme with 5'-3'- exonuclease activity, responsible for degrading RNA that is still being transcribed by Pol II after cleavage at the poly(A) site, ultimately leading to Pol II termination. We have confirmed that Xrn2's catalytic activity is essential for timely transcription termination. Furthermore, we have discovered a link between Xrn2 and the conserved, multifunctional transcription factor Spt5. Importantly, our research demonstrates that Xrn2 interacts with Pol II/Spt5 complexes. Additionally, when Spt5 is depleted, it not only impairs global transcription but also results in defective transcription termination. On the other hand, absence of Spt5 leads to the derepression of non-coding transcription and premature termination/attenuation at the 5'-end of coding genes. We propose that Spt5 acts as a "licensing" factor, ensuring that Pol II complexes are properly assembled for efficient transcription and co-transcriptional pre-mRNA processing.

overall_design: Xrn2 and Pol II occupancy were evaluated in a strain with Spt5 depleted using auxin and compared to DMSO-treated cells, with library depth normalization. The chromatin association of Xrn2, or its mutant missing the region between amino acids 444-555, was assessed in DMSO-treated cells using spike-in normalization. The experimental technique used was ChIP-seq

last: Kuś

first: Loic

last: Carrique

first: Tea

last: Kecman

first: Marjorie

last: Fournier

first: Sarah

last: Hassanein

first: Ebru

last: Aydin

first: Cornelia

last: Kilchert

first: Jonathan

middle: M

last: Grimes

first: Lidia

last: Vasiljeva


title: Novel integrated multiomics analysis reveals Itgbl1-mediated regulation of fibrogenesis through antagonism of Tgfβ1 and IL1β signaling. (Spatial Gene Expression)

first: Daisuke

last: Motooka

summary: Spatial transcriptome analysis (Visium, 10x Genomics) was performed to define the spatial topography of inflammation-related gene expressions in microenvironments of wound tissues.

overall_design: Fresh frozen skin wound tissues were isolated on day 3, 7, and 14 post skin injury.

first: Sang-Eun

last: Kim

first: Ryota

last: Noda

first: Yu-Chen

first: Shoichiro

last: Kameoka

last: Okuzaki

first: Ryoichi

last: Mori


title: KMT2A oncoproteins induce epigenetic resistance to targeted therapies.

city: Grand Rapids

first: Derek

middle: H

last: Janssens

state: MI

address: 333 Bostwick Ave. NE

department: Epigenetics

institute: Van Andel Institute

summary: Chromosomal translocations involving the Lysine-Methyl-Tansferase-2A (KMT2A) locus generate potent oncogenes that cause highly aggressive acute leukemias KMT2A and the most frequent translocation partners encode proteins that interact with DNA to regulate developmental gene expression. KMT2A-oncogenic fusion proteins (oncoproteins) contribute to the epigenetic mechanisms that allow KMT2A-rearranged leukemias to evade targeted therapies. By profiling the oncoprotein-target sites of 34 KMT2A-rearranged leukemia samples, we find that the genomic enrichment of oncoprotein binding is highly variable between samples. At high levels of expression, the oncoproteins preferentially activate either the lymphoid or myeloid lineage program depending on the fusion partner. These fusion-partner-dependent binding sites correspond to the frequencies of each mutation in acute lymphoid leukemia versus acute myeloid leukemia. By profiling a sample that underwent a lymphoid-to-myeloid lineage switching event in response to lymphoid-directed treatment, we find the global oncoprotein levels are reduced and the oncoprotein-target gene network changes. At lower levels of expression, the oncoprotein shifts to a non-canonical regulatory program that favors the myeloid lineage, and in a subset of resistant patients, the Menin inhibitor Revumenib induces a similar response. The dynamic shifts in KMT2A oncoproteins we describe likely contribute to epigenetic resistance of KMT2A-rearranged leukemias to targeted therapies.

overall_design:
We used Cleavage under targets and Release using nuclease (Cut-and-Run), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing.

***Raw data for 51 Samples are not provided due to donor privacy concerns***

first: Melodie

last: Duran

first: Dominik

last: Otto

first: Danielle

last: Kirkey

first: Joanna

middle: S

last: Yi

first: Charles

middle: G

last: Mullighan

first: Soheil

last: Meshinchi

first: Jay

middle: F

last: Sarthy

first: Kami

last: Ahmad

first: Steven

last: Henikoff


title: RNA-seq data of the Amphotericin (AmB)-resistant Aspergillus strain 211 and its AmB-susceptible sectorized derivative with and without AmB treatment

status: Public on Sep 25 2024

city: Innsbruck

first: David

last: Eisele

address: Schöpfstraße 41

country: Austria

institute: Medical University of Innsbruck

summary: Summary taken from our paper “Aspergillus terreus Sectorization: A Morphological Phenomenon Shedding Light on Amphotericin B Resistance Mechanism”: WT and ATSec strains were grown in AMM broth for 30 h at 30 °C. Afterwards, the cultures were subjected to either DMSO (control) or 1 µg/ml AmB treatment for 1 h/4 h. Triplicates of each combination of these factors were made, resulting in a total of 24 samples. RNA was extracted with a Promega GmbH kit (Madison, Wisconsin, USA) following the manufacturer’s instructions. The RNA-seq experiment was conducted by BGI, generating a total of around 20 million 100bp paired-end reads with the DNBSEQ platform. BGI employed SOAPnuke (51) to remove rRNA, adaptor-containing sequences, low quality reads, and reads with high unknown nucleotide content, producing "clean reads" datasets that were used in the analysis. On average, clean read datasets contain 45.1 Mb of reads, while the raw read datasets contain 48.7 Mb. For clean reads, the mean Q20 value is 98.3%, and the mean Q30 value is 92.5%.

overall_design: RNA-seq data from Aspergillus strain 211 and its sectorized derivative were analyzed in their gene expression pattern difference in the presence and absence of AmB. Each condition was analyzed in triplicates

first: Roya

last: Vahedi-Shahandashti

first: Anna Maria

last: Dietl

first: Michael

last: Blatzer

first: Cornelia

last: Lass-Flörl


title: Alterations in cellular metabolic pathway and epithelial cell maturation induced by MYO5B defects are partially reversible by LPAR5 activation

city: Nashville

first: Izumi

last: Kaji

state: TN

address: Rm 10465H, MRB IV

department: Surgery

institute: Vanderbilt University Medical Center

summary: Functional loss of the motor protein, Myosin Vb (MYO5B), induces various defects in intestinal epithelial function and causes a congenital diarrheal disorder, microvillus inclusion disease (MVID). Utilizing the MVID model mice, Vil1-CreERT2;Myo5bflox/flox (MYO5B∆IEC) and Vil1-CreERT2;Myo5bflox/G519R (MYO5B(G519R)), we previously reported that functional MYO5B loss disrupts progenitor cell differentiation and enterocyte maturation that result in villus blunting and deadly malabsorption symptoms. In this study, we determined that both absence and a point mutation of MYO5B impair lipid metabolism and alter mitochondrial structure, which may underlie the progenitor cell malfunction observed in MVID intestine. Along with a decrease in fatty acid oxidation, the lipogenesis pathway was enhanced in the MYO5B∆IEC small intestine. Consistent with these observations in vivo, RNA-sequencing of enteroids generated from the two MVID mouse strains showed similar downregulation of energy metabolic enzymes, including mitochondrial oxidative phosphorylation genes. In our previous studies, lysophosphatidic acid (LPA) signaling ameliorates epithelial cell defects in MYO5B∆IEC tissues and enteroids. The present study demonstrated that the highly soluble LPAR5-preferred agonist, Compound-1, improved sodium transporter localization and absorptive function, and tuft cell differentiation in patient-modeled MVID animals that carry independent mutations in MYO5B. Body weight loss in male MYO5B(G519R) mice was ameliorated by Compound-1. These observations suggest that Compound-1 treatment has a trophic effect on intestine with MYO5B functional loss through epithelial cell-autonomous pathways that can accelerate the differentiation of progenitor cells and the maturation of enterocytes. Targeting LPAR5 may represent an effective therapeutic approach for treatment of MVID symptoms induced by different point mutations in MYO5B.

overall_design: To assess the epithelial cell-autonomous effects of MYO5B inactivation, bulk RNA-sequencing analysis was performed in enteroids that were generated from MYO5B∆IEC and MYO5B(G519R) mouse jejunum. Enteroids were generated from jejunal crypts of adult Vil1-CreERT2; Myo5bflox/flox (for in vitro induced KO (iKO) and control) and Vil1-CreERT2; Myo5bflox/G519R (G519R) mice without tamoxifen treatment and passaged twice with mechanical breakdown by P200 pipette. One day after the second passage, 1 μM 4-OH-tamoxifen (SML1666, Sigma) or vehicle (EtOH) was added into the Mouse Organoid Growth Medium (IntestiCult; Stem Cell Technology) and incubated for 24 hours to induce Cre recombinase. Following day, the medium was replaced with the differentiation medium, which contains 5% Noggin conditioned medium and 5% R-spondin conditioned medium (generated in Vanderbilt Organoid Core) to withdraw Wnt ligands and EGF for enhancing cell differentiation. Some iKO enteroids were incubated with 100 nM Compound-1 for 2 days in the differentiation conditions.

first: Andreanna

last: Burman

first: Francisca

last: Adeniran


title: Effect of SMARCA4 knockdown on repeat elements in senescent IMR90 ER:RAS cells

status: Public on Sep 19 2024

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: We report the analysis of RNA sequencing aimed at understanding the effects induced by the knockdown of SMARCA4 on the expression of repeat and transposable elements in senescent cells. SMARCA4 was initially identified as a target through a genetic screening process designed to locate regulators responsible for upregulating SASP. SMARCA4 is a constituent of the SWI/SNF complex subunit. The findings will help characterise he expression of repeat elements to elucidate the pathway by which SMARCA4 knockdown can promote cytokine expression and Natural Killer cell recruitment.

overall_design: IMR90 ER:RAS cells were transfected with siRNAs against target genes and non-targeting scramble controls (by reverse transfection) one day prior to senescence induction. Oncogene-induced senescence was induced following the administration of 4OHT (tamoxifin) treatment. RNA from the cells was extracted seven days following senescence induction.

first: Virinder

last: Reen

first: Mariantonietta

last: D'Ambrosio

first: Jesus

last: Gil

first: Sanjay

last: Khadayate


title: Bulk RNA-Seq gene expression data for 289 primary and metastatic pancreatic ductal adenocarcinoma (PDAC) tumor samples from FFPE blocks.

city: Portland

first: Rosalie

last: Sears

state: OR

address: 2730 SW Moody Ave, CL4RS

department: Molecular and Medical Genetics

institute: Oregon Health & Science University

summary: Pancreatic Ductal Adenocarcinoma (PDAC) is a deadly disease with a 5 year overall survival rate of 11%. In order to better understand and characterized PDAC we have performed RNAseq on 289 primary and metastatic PDAC tumors collected at our center. Nucleic acids (RNA and DNA) were extracted from formalin fixed paraffin embeded FFPE tumor tissue with tumor enriched regions identified by pathologic analysis. RNA sequencing and resulting gene expression data was then used to study biologic differences in primary PDAC tumors that metastasized to either the liver or to the lung but not liver based on clinical data review. A novel gene expression signature was identified for liver vs lung avid metastatic properties. Samples in the entire cohort were then scored based on this gene signature.  Pathway analysis revealed that samples high for this signature (as well as liver cohort patient samples) were enriched for pathways involved in ongoing replication stress response, and this was associated with poorer patient outcome.

overall_design:
Primary and metastatic PDAC samples obtained from our center that were formalin fixed and paraffin embedded were pathologically reviewed and regions of high tumor content were scraped from slides for nucleic acid extraction and RNA seuencing. The pathologic review was performed at OHSU and at Tempus, where the extraction and sequencing was performed. Raw sequencing data was returned to OHSU where it was pseudoaligned with kallisto

***Raw data have been deposited in dbGaP (phs003597.v1.p1)***

first: Brett

last: Sheppard

first: Jonathan

middle: R

last: Brody

first: Jason

last: Link

first: Dove

middle: J

last: Keith

first: Carl

last: Pelz


title: Effect of SMARCA4 knockdown on senescent IMR90 ER:RAS cells

summary: We report the analysis of RNA sequencing aimed at understanding the effects induced by the knockdown of various target genes on senescent cells. These genes were initially identified through a genetic screening process designed to locate regulators responsible for upregulating SASP. Specifically, we focus on exploring the repercussions of SMARCA4 knockdown, a constituent of the SWI/SNF complex subunit, on the SASP and immune responses within senescent cells. The findings will help characterise the role of SMARCA4 inhibition on senescence surveillance by Natural Killer cells.


title: Sex differences in Non-Alcoholic Steatohepatitis (NASH) in mice evoked by a fructose-palmitate-cholesterol (FPC)-enriched diet [bulk_isolated_cells]

first: Sofie

last: Delbare

summary: To study sex differences in the response to NASH in mice, single nucleus RNA sequencing of livers was performed. Single nucleus RNAseq demonstrated enrichment of differentially-expressed genes particularly in hepatocytes and stellate cells in females versus males fed FPC-NASH. Multiple regulons (transcription factors and target genes) implicated in lipid and other metabolic processes and hormone signaling (hepatocytes) and cell-cell communication and cell adhesion (stellate cells) were noted, which were enriched in female versus male FPC-NASH diet. Bulk liver RNAseq and RNAseq of isolated hepatocytes and hepatic stellate cells were analyzed as validation experiments.

overall_design: Male and female C57BL/6J mice were fed fructose-palmitate-cholesterol (FPC-NASH) diet or standard chow (SC) for 16 weeks. Hepatocytes and hepatic stellate cells were isolated from from control and FPC diet fed male and female mice (N = 4 independent mice/group) and processed for bulk RNAseq.

first: Lakshmi

last: Arivazhagan

first: Robin

last: Wilson

first: Boyan

last: Zhou

first: Henry

last: Ruiz

first: Kaamashri

last: Mangar

first: Ryoko

last: Higa

first: Emily

last: Brown

first: Huilin

last: Li

last: Garabedian

first: Ravichandran

last: Ramasamy

first: Kathryn

last: Moore

first: Edward

last: Fisher

first: Neil

last: Theise

first: Ann

last: Schmidt


title: Transcriptome analysis of the aortic coarctation area

city: Linköping

first: CecilIa

last: Gunnarsson

address: Linköping University Hospital

country: Sweden

institute: Linköping University Hospital

summary: Coarctation of the aorta (CoA) is a relatively common congenital heart defect that affects males more often than females. The underlying causes are not known, but a combination of genetic factors and abnormalities linked to embryonic development is suspected. There are only a few studies of the underlying molecular mechanisms in CoA. The aim of the current study was to expand our understanding of the pathogenesis of CoA by characterizing the transcriptome of the coarctation area.

overall_design:
Tissue samples from 21 pediatric patients operated for CoA were dissected into separate biopsies consisting of the localized coarctation itself, proximal/distal tissue and ductus. RNA was extracted and sequenced to evaluate gene expression in the different biopsies.

***************************************************************
Raw data not provided due to Swedish GDPR law
***************************************************************

first: Rada

last: Ellegård

first: Torsten

last: Malm

first: Constance

last: Weismann

first: Eva

last: Fernlund

first: Anneli

middle: N

last: Björnlert

first: Hanna

middle: K

last: Årstrand

first: Katarina

last: Ellnebo-Svedlund

first: Gunnarsson

last: Cecilia


title: Sex differences in Non-Alcoholic Steatohepatitis (NASH) in mice evoked by a fructose-palmitate-cholesterol (FPC)-enriched diet [bulk_liver]

first: Sofie

last: Delbare

overall_design: Male and female C57BL/6J mice were fed fructose-palmitate-cholesterol (FPC-NASH) diet or standard chow (SC) for 16 weeks. Bulk RNAseq was performed on the top left lobe of livers from control and FPC diet fed male and female mic (N = 3 independent mice/group).

first: Lakshmi

last: Arivazhagan

first: Robin

last: Wilson

first: Boyan

last: Zhou

first: Henry

last: Ruiz

first: Kaamashri

last: Mangar

first: Ryoko

last: Higa

last: Brown

first: Michael


title: Effect of SMARCA4 degradation on ID8 ovarian cancer cells senescent and not senescent.

first: LMS

last: Bioinformatics Core

summary: We report the analysis of RNA sequencing aimed at understanding the effects induced by AU-15330 (SMARCA4 PROTAC)-mediated degradation of SMARCA4 in P53-deficient senescent ID8 ovarian tumour cells. Specifically, we focus on exploring the repercussions of inhibiting SMARCA4, a constituent of the SWI/SNF complex subunit, on the SASP and immune activity within cisplatin-treated senescent cancer cells. The findings will help characterise the role of SMARCA4 inhibition on senescence surveillance by Natural Killer cells.

overall_design: ID8 cells were treated with either  cisplatin alone, SMARCA4 PROTAC alone, or in combination for up 6 days.

first: Mariantonietta

last: D'Ambrosio

first: Virinder

last: Reen

first: Gil

last: Jesus

first: Khadayate

last: Sanjay


title: Kras loss of heterozygosity promotes MAPK dependent pancreatic ductal adenocarcinoma and induces therapeutic sensitivity

status: Public on Sep 22 2024

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

institute: Cancer Research UK Scotland Institute

summary: Pancreatic cancer is characterised by the prevalence of oncogenic mutations in KRAS. Previous studies have reported that altered Kras gene dosage drives progression and metastatic incidence in pancreatic cancer. While the role of oncogenic KRAS mutation is well characterised, the relevance of the partnering wild-type KRAS allele in pancreatic cancer is less well understood and controversial. Using in vivo mouse modelling of pancreatic cancer, we demonstrate that wild-type Kras restrains the oncogenic impact of mutant Kras, and drastically impacts both Kras-mediated tumourigenesis and therapeutic response. Mechanistically, deletion of wild-type Kras increases oncogenic Kras signalling through the downstream MAPK effector pathway, driving pancreatic intraepithelial neoplasia (PanIN) initiation. In addition, in the KPC mouse model, a more aggressive model of pancreatic cancer, loss of wild-type KRAS leads to accelerated initiation but delayed tumour progression. These tumours had altered stroma, downregulated Myc levels and an enrichment for immunogenic gene signatures. Importantly, loss of wild-type Kras sensitises Kras mutant tumours to MEK1/2 inhibition though tumours eventually become resistant and then rapidly progress. This study demonstrates the repressive role of wild-type Kras during pancreatic tumourigenesis and highlights the critical impact of the presence of wild-type KRAS on tumourigenesis and therapeutic response in pancreatic cancer.

overall_design: Gene expression analysis of murine KPC pancreatic tissues and tumours, with and without loss of the second Kras allele, in the presence and absence of MEK inhibitor.

first: Sigrid

last: Fey

middle: L

first: Andrew

last: Campbell

first: Owen

last: Sansom