title: Patch-Seq of seven 5-HT neuronal subpopulations in zebrafish whole brain

status: Public on Nov 14 2024

city: Shanghai

first: Chun-Xiao

last: Huang

address: 65 Chifeng Road, Yangpu District

department: School of Medcine, Tongji University

summary: The goals of this study is to compare transcriptome profiles (RNA-seq) of seven 5-HT neuronal subpopulations in zebrafish whole brain. Tg(tph2:GFP) fish at 7 dpf were fixed in a recording chamber containing extracellular solution. The somata of 5-HT neurons from seven subpopulations (PT, SR-R, SR-M, SR-C, IR-R, IR-C, MO) were visualized under a fluorescence microscopy, then targeted and collected separately using glass electrode. For each sample, 10-12 neurons were collected and transferred to lysis buffer solution. Total RNA was extracted for construction of cDNA libraries, involving fragmentation, PCR enrichment, N7 index linking, and purification. A total of 71 QuantSeq libraries (N=9-12 samples for each subpopulation) were prepared using the Lexogen’s QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina according to the manufacturer’s instructions. Sequencing was carried out using Illumina NovaSeq 6000 with 150 bp paired-end reads. Gene expression level analysis was performed using R (Version 4.3.1) package Seurat (Version 5.0.2), and the mean gene expression matrix of all samples was obtained after processing by NormalizeData function. For marker gene analysis of each subpopulation, FindAllMarkers function in Seurat was used, with parameters set as min.pct=0.1 and logfc.threshold=0.25. Differential expression analysis revealed that each subpopulation expressed a set of featured genes, including specific markers for neurotransmitters, axon projection, neuron development, synapse, and ion channels, suggesting that seven 5-HT neuronal subpopulations display distinct genetic profiles.  We demonstrated that seven 5-HT neuronal subpopulations are molecularly discriminative by expressing distinct molecular markers.

overall_design: To compare transcriptome profiles (RNA-seq) of seven 5-HT neuronal subpopulations in zebrafish whole brain, Tg(tph2:GFP) fish at 7 dpf were fixed in a recording chamber containing extracellular solution, and neurons were collected separately with glass pipette. A total of 71 QuantSeq libraries (N=9-12 samples for each subpopulation) were prepared using the Lexogen’s QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina according to the manufacturer’s instructions.

first: Jianren

last: Guan

first: Ziqi

first: Chunxiao


title: Effect of the reduced mTORC1 activity on gene expression in LAM cells

status: Public on Nov 20 2024

city: Higashihiroshima

first: Takafumi

last: Ogawa

state: Hiroshima

address: 1-3-1 Kagamiyama

country: Japan

institute: Hiroshima University

type: Expression profiling by high throughput sequencing

summary: mTORC1 is inhibited by rapamycin or Torin1 in lymphangioleiomyomatosis (LAM) 621-101 (TSC2-deficient) cells, in which mTORC1 activity is elevated, and we compared these effects to inhibition of S6K and its target SRPK2.

overall_design: To investigate the effect of mTORC1 inhibition on gene expression, we assessed the gene expression affected by Rapamycin, Torin1, an S6K inhibitor PF4708671(PF), an SRPK1 inhibitor SRPIN340 (SRPIN), or SRPK2 knockout(SRPK2KO) in LAM cells.

first: Ziyun

last: Wu

first: Meltem

last: Isik

first: T

middle: K

last: Blackwell


title: CRISPR-SaCas9-KKH targeting of miR-21 through a single adeno-associated virus vector prolongs survival of GB-bearing mice

status: Public on Nov 27 2024

city: Charlestow

first: Lisa

last: Nieland

state: Massachusetts

address: 149 13th street

department: Neurology

country: USA

institute: Massachusetts General Hospital

summary: Glioblastoma (GB), the most aggressive tumor of the central nervous system (CNS), has poor patient outcomes with limited effective treatments available. MicroRNA-21 (miR-21) is a known oncogene, abundantly expressed in many cancer types. MiR-21 promotes glioblastoma progression, and lack of miR-21 reduces tumorigenic potential of tumor. Here, we propose a single adeno-associated virus (AAV) vector strategy targeting miR-21 using the Staphylococcus aureus Cas9 ortholog (SaCas9) guided by a single-guide RNA (sgRNA). Our results demonstrate that AAV8 is a well-suited AAV serotype to express SaCas9-KKH/sgRNA at the tumor site in an orthotopic glioblastoma model. The SaCas9-KKH induced a genomic deletion, resulting in lowered miR-21 levels in the brain, leading to reduced tumor growth and improved overall survival. In this study we demonstrated that a single AAV-mediated mir-21 disruption influences glioma development resulting in beneficial anti-tumor outcomes in GB-bearing mice.

overall_design: To investigate the therapeutic effect of targeting microRNA-21 in a glioma context we peformed Next Generation Sequencing analysis to confirm gene-editing of the targeted microRNA-21. A wild-type (WT) non-edited cell line and/or SaCas9 only condition were the controls. 1) Co-transfected in vitro in glioma cell lines (CT2A and GL261) with SaCas9 and sgRNA to knockdown miR-21. 2) Tested a single construct containing both SaCas9 and sgRNA to target miR-21 in vitro cell lines. 3) designed a single AAV vector to CRISPR-edit microRNA-21 in vivo in a glioblastoma mouse model. The AAV was delivered locally by injecting it intratumorally in the mice brain. We then analysed FACS sorted tumor tissue for CRISPR-editing of microRNA-21 by Next Generation Sequencing. 4) We screened 5 potential off-targets in the mouse genome of the specific sgRNA we used in this study by Next Generation Sequencing.

first: Anne

last: B Vrijmoet

first: Isabelle

last: W Jetten

first: David

last: Rufino-Ramos

first: Alexandra

last: J.E.M. de Reus

first: Koen

last: Breyne

first: Benjamin

last: P Kleinstiver

first: Casey

last: A Maguire

first: Marike

last: L.D. Broekman

first: Xandra

last: O Breakefield

first: Erik

last: R Abels


title: Single-nucleus and spatial landscape of the sub-ventricular zone in human glioblastoma

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary: Glioblastoma (GBM) clinical management is challenging due to its heterogeneous nature, invasive potential, and poor response to radio- and chemo-therapy. As a result, GBM inevitably recurs and only a minority of patients survive 5 years post-diagnosis. We were the first to show that in the majority of GBM patients, the sub-ventricular zone (SVZ) of the lateral ventricles is a reservoir of cancer stem-like cells (CSCs) that show distinct patterns of treatment resistance when compared to matched CSCs from the tumor mass and contribute to the seeding of the recurrent tumor. However, the sampling and the characterization of the SVZ in GBM patients pose several challenges, as this area is extremely small and needs to be objectively identified during tumor surgical resection.

overall_design: To overcome this challenge, by using our fluorescence-guided multiple sampling scheme, we built a single-nucleus RNA-sequencing-based microenvironment landscape of the SVZ in GBM patients (T_SVZ). By performing a systematic comparison with tumor mass (T_Mass) samples isolated from the same patients and using two histologically normal SVZ (N_SVZ) samples through a number of computational tools and experimental methods, we identified novel therapeutic vulnerabilities in the T_SVZ of GBM patients.

first: Suganya

last: Subramanian

first: Bryan

last: Granger

first: Yamhilette

last: Licón-Muñoz

first: Vanessa

last: Avalos

first: Sara

middle: G

last: Piccirillo


title: Transcriptomics of A. mexicanum Regeneration: A Comparative Study Reveals Key Proteins And Pathways for Limb Regeneration.

city: Mexico City

first: Ernesto

last: Soto-Reyes

state: Delegación Cuajimalpa de Morelos

address: Av. Vasco de Quiroga 4871

country: Mexico

institute: Universidad Autónoma Metropolitana

summary: The axolotl is an animal with remarkable regenerative abilities, making it an ideal model for studying potential regenerative therapies in mammals, including humans. However, the molecular mechanisms involved in regeneration remain unclear. We conducted a transcriptomic analysis of juvenile axolotls' limbs and their blastema and compared the results with aged axolotls that failed to regenerate after amputation. We identified a set of genes involved in cell differentiation, transcriptional regulation, cartilage development, bone morphogenesis, and extracellular matrix remodeling. Four highly expressed genes (FSTL1, ADAMTS17, GPX7, and CTHRC1) were identified in regenerating tissue, but underexpressed in aged axolotls. Structural and homology analysis showed that these genes are conserved and have important roles in development, bone morphogenesis, and cartilage formation. Our findings propose a novel set of key axolotl genes involved in tissue regeneration that could be a starting point for further studies in other vertebrates.

overall_design: Total RNA from the inferior limbs of five juvenile axolotls, aged 8 months, as well as from two aged axolotls, aged 8 years. Blastema was collected 10 days post-amputation from juvenile axolotls, whereas aged axolotls did not display any development of blastema tissue.

first: Aylin

last: del Moral-Morales

first: Cynthia

last: Sámano

first: José

middle: A

last: Ocampo-Cervantes

first: Maya

last: Topf

first: Jan

last: Baumbach

first: Rodrigo

last: González-Barrios


title: Effect of feeding on gene expression in WT, raga-1, and rsks-1 mutant animals

first: Takafumi

last: Ogawa

summary: After subjecting WT, raga-1, and rsks-1 (S6K) animals to this growth arrest, we compared them by RNA sequencing (RNA-seq) to a group that was released from arrest by feeding for four hours

overall_design: To investigate the nutrient response on gene expression, we treated WT, raga-1, and rsks-1 animals with 4 hours of feeding at the L1 larval stage.

first: Ziyun

last: Wu

first: Meltem

last: Isik

first: T

last: Blackwell


title: Sp140L Is a Herpesvirus Restriction Factor [Day8_WT_vs_LPKO_BulkRNAseq]

city: Durham

first: Jana

last: Cable

state: NC

address: 213 Research Dr.

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Herpesviruses, including the oncogenic Epstein-Barr Virus (EBV), must bypass host DNA sensing mechanisms to drive infection and pathogenesis. The first viral latency protein expressed, EBNA-LP, is essential for the transformation of naïve B cells, yet its role in evading host defenses remains unclear. Using single-cell RNA sequencing of EBNA-LP-Knockout (LPKO)-infected B cells, we reveal an antiviral response landscape implicating the ‘speckled proteins’ as key restriction factors countered by EBNA-LP. Specifically, loss of SP100 or the primate-specific SP140L reverses the restriction of LPKO, suppresses a subset of canonically interferon-stimulated genes, and restores viral gene transcription and cellular proliferation. Notably, we also identify Sp140L as a restriction target of the herpesvirus saimiri ORF3 protein, implying a role in immunity to other DNA viruses. This study reveals Sp140L as a restriction factor that we propose links sensing and transcriptional suppression of viral DNA to an IFN-independent innate immune response, likely relevant to all nuclear DNA viruses.

overall_design: Bulk RNAseq of B cells 8 days post-infection with LPKO virus or WT virus

last: M Cable

first: Wiyada

last: Wongwiwat

first: Jenna

last: C Grabowski

first: Robert

last: E White

first: Micah

last: A Luftig


title: ESR1 Y537S and D538G mutations drive resistance to CDK4/6 inhibitors in estrogen receptor-positive breast cancer

status: Public on Nov 12 2024

city: Dallas

first: Chang-Ching

last: Lin

state: TX

address: 4554 Glenwick Ln, Apt 2203

department: Harold C. Simmons Comprehensive Cancer Center

institute: UT Southwestern Medical Center

summary: Purpose: Breast cancers with ESR1 mutations are resistant to antiestrogen therapy. We aimed to investigate the association of ESR1 mutations with resistance to CDK4/6 inhibitors (CDK4/6i) using real-world data analysis and experimental validation. Patients and Methods: A total of 3,958 patients with estrogen receptor-positive (ER+) metastatic breast cancer with DNA sequencing data were analyzed. Breast tumor DNA and circulating tumor (ct) DNA were sequenced using the Tempus xT tumor assay and Tempus xF liquid biopsy, respectively. Patients were stratified into either treated with CDK4/6i (breast tumors: 1,070; ctDNA: 1,885) or CDK4/6i naïve (breast tumors: 750; ctDNA: 253). Engineered MCF7 cells carrying ESR1 Y537S or D538G knock-in mutations were used to study antitumor efficacy of the CDK4/6i, palbociclib in vitro and in vivo.  Results: In both xF and xT assays, ESR1 mutations were the only somatic alterations significantly more frequent in those who received CDK4/6i than those who did not. Knock-in of ESR1 Y537S or ESR1 D538G in MCF7 cells resulted in upregulation of cell cycle-related gene signatures upon treatment with CDK4/6i ± antiestrogen compared to cells with non-mutant ESR1. MCF7 xenografts harboring ESR1 Y537S and D538G mutations established in nude mice were resistant to palbociclib. Conclusions: We report herein real-world and preclinical evidence that ESR1 mutations, particularly Y537S and D538G, can drive resistance to CDK4/6 inhibitors.

overall_design: To investigate the effects of ESR1 Y537S and D538G mutations on sensitivity to CDK4/6 inhibitors, we treated MCF7 cells harboring ESR1 wild-type, Y537S, or D538G mutations with palbociclib alone or in combination with estrogen-deprived media or fulvestrant.

first: Lin

last: Chang-Ching

first: Guo

last: Lei


title: Extensive binding of uncharacterized human transcription factors to genomic dark matter

status: Public on Nov 11 2024

city: Toronto

first: Arttu

last: Jolma

state: Ontario

address: 160 College Street, Room 1350

department: Donnelly Centre

country: Canada

institute: University of Toronto

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity of many human transcription factors

summary: A long-standing challenge in human regulatory genomics is that transcription factor (TF) DNA-binding motifs are short and degenerate, while the genome is large. Motif scans therefore produce many false-positive binding site predictions. By surveying TFs across 25 families using >1,500 cyclic in vitro selection experiments with fragmented, naked, and unmodified genomic DNA – a method we term GHT-SELEX (Genomic HT-SELEX) – we find that many human TFs possess much higher sequence specificity than anticipated. Moreover, genomic binding regions from GHT-SELEX are often surprisingly similar to those obtained in vivo (i.e. ChIP-seq peaks). We find that comparable specificity can also be obtained from motif scans, but performance is highly dependent on derivation and use of the motifs, including accounting for multiple local matches in the scans. We also observe alternative engagement of multiple DNA-binding domains within the same protein: long C2H2 zinc finger proteins often utilize modular DNA recognition, engaging different subsets of their DNA binding domain (DBD) arrays to recognize multiple types of distinct target sites, frequently evolving via internal duplication and divergence of one or more DBDs. Thus, contrary to conventional wisdom, it is common for TFs to possess sufficient intrinsic specificity to independently delineate cellular targets.

overall_design:
We used fragmented genomic DNA based in vitro selection method to analyze target locations of putative transcription factors in order to understand how well TFs can define their target sitesd independently of other chromatin proteins. This project was carried out as part of Codebook consortium and the dataset contributes to several other studies in it.

***************************************************************
The table below lists ENA accessions for raw data already submitted to ENA under PRJEB76622.
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first: Aldo

last: Hernandez-Corchado

first: Ally

middle: W

last: Yang

first: Ali

last: Fathi

first: Kaitlin

middle: U

last: Laverty

first: Alexander

last: Brechalov

first: Rozita

last: Razavi

first: Codebook

last: Consortium

first: Ivan

last: Kulakovskiy

first: Hamed

middle: S

last: Najafabadi

first: Timothy

middle: R

last: Hughes


title: Transcriptional profiling of CD4+ T cells with high, intermediate and low PD-1 and ICOS co-expression from HCV infected chimpanzees

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: A sustained CD4+ T cell response is required for resolution of acute HCV infection but remains poorly characterized.  Here, CD4+ T cells with high PD-1 and ICOS co-expression expanded in the blood of chimpanzees during acute HCV infection.  The peak response was comprised primarily of HCV-specific populations and temporally associated with acute hepatitis, seroconversion, and initial control of HCV replication. Circulating PD-1hiICOShi CD4+ T cells differentially expressed genes associated with Tfh, Th1, and cytotoxic signatures.  Co-production of Tfh (CXCL13, IL-21) and Th1 (IFN-) effector molecules was observed after HCV antigen stimulation. HCV-specific Tfh1 CD4+ T cells infiltrated liver, consistent with expression of chemokine receptors that mediate homing to inflamed tissues. Most were CXCR5-negative and therefore resembled Tph/Tfhx13 CD4+ T cells recently described in cancer and autoimmune conditions. Detailed transcriptional, phenotypic, and functional analysis of the protective CD4+ T cell response presented here is expected to aid HCV vaccine development.

overall_design: CD4+ T cells from HCV infected chimpanzees were sorted into 3 sub-populations PD-1/ICOS low (n=4), PD-1/ICOS intermediate (n=4) and PD-1/ICOS high (n=5) and transcriptional profililng was performed

first: Heather

last: Blasczyk

first: Bill

last: Bremer

first: Yan

last: Zhou

first: David

last: Bowen

first: Zhaohui

last: Xu

last: Lanford

first: Naglaa

last: Shoukry

first: Arash

last: Grakoui

first: Nicole

last: Skinner

first: Chris

last: Walker


title: An in vivo repertoire of zebrafish cardiomyocyte-specific cis-regulatory elements [RNA-Seq]

city: Clayton

first: Hieu

middle: Tri

last: Nim

state: VIC

address: Monash University Clayton Campus, Wellington Rd

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

summary: cis-Regulatory elements (cREs) are essential for the spatio-temporal control of gene expression during development and disease. However, cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell-types, predominantly cardiomyocytes. Therefore, cardiomyocytes-specific modelling is required to understand the cis-regulation of the developing heart. Zebrafish are an ideal model to study heart development, as they share a number of physiological features with the human heart during development. Therefore, we present a comprehensive cardiomyocyte-specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling, providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes, validating these genomic regions as cardiac regulatory elements. We share this comprehensive, reproducible cardiomyocyte-specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects.

overall_design: Cardiomyocytes were isolated from the Tg(myl7::GFP) zebrafish transgenic line. Larvae were collected 72 hpf (hours post fertilization). GFP-positive (30,000 cells, n=3 biological replicates) and GFP-negative cells (500,000 cells, n=3 biological replicates) were collected, and RNA-sequencing was performed on these samples.

first: Marcus

last: Tondl

first: Gulrez

last: Chahal

first: Monika

last: Mohenska

middle: T

first: Mirana

last: Ramialison


title: An in vivo repertoire of zebrafish cardiomyocyte-specific cis-regulatory elements


title: Extensive binding of uncharacterized human transcription factors to genomic dark matter [NewChIP_ERP163147]

first: Arttu

last: Jolma

summary: Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized transcription factors (TFs). We determined genomic binding locations of 166 uncharacterized human TFs in living cells. Nearly half of them associated strongly with known regulatory regions such as promoters and enhancers, often at conserved motif matches and co-localizing with each other. Surprisingly, the other half often associated with genomic dark matter, at largely unique sites, via intrinsic sequence recognition. Dozens of these, which we term “Dark TFs” mainly bind within regions of closed chromatin. Dark TF binding sites are rarely under purifying selection, and are enriched for transposable elements. Many Dark TFs are KZNFs, which contain the repressive KRAB domain, but many are not, and may represent potential pioneer TFs: based on compiled literature information, the Dark TFs exert diverse functions ranging from early development to tumor suppression. Thus, a large fraction of previously uncharacterized human TFs may have unappreciated activities within the dark matter genome.

overall_design: Stable cell lines for each TF was established via Flp recombination of EGFP-tagged TF plasmid in HEK293 Flp-In-TRex. Cells were treated with doxycyclin and after 24 hours, ChIP is performed using anti-GFP antibody.

first: Rozita

last: Razavi

first: Ali

last: Fathi

first: Isaac

last: Yellan

first: Alexander

last: Brechalov

first: Kaitlin

last: Laverty

first: Hong

last: Zheng

first: Ally

last: Yang

first: Marjan

last: Barazandeh

first: Chun

last: Hu

first: Ilya

last: Vorontsov

first: Zain

last: Patel

first: Ivan

last: Kulakovskiy

first: Philipp

last: Bucher

first: Hamed

last: Najafabadi

first: Quaid

last: Morris

last: Hughes


title: High efficacy of combined MEK Inhibitor Trametinib and RTK Inhibitor Anlotinib Therapy in KRAS-Mutant Lung Cancer

first: Baohui

last: Han

address: 227 South Chongqing Road

department: Department of Respiratory and Critical Care Medicine

country: China

institute: Shanghai Chest Hospital

summary: Oncogenic KRAS mutations frequently detected in non-small cell lung cancer (NSCLC)1,2, have been considered undruggable until recent development of inhibitors, e.g., sortorasib, adagrasib or divarasib, specifically targeting KRASG12C 3-6. However, it still remains as a big challenge to target all the KRAS mutants besides KRASG12C 2,7,8. We here found that MEK inhibitor trametinib treatment results in the feedback activation of multiple receptor tyrosine kinases (RTKs) in NSCLC, and combined treatments with trametinib and anlotinib, a pan-RTK inhibitor, effectively inhibited KRAS-mutant lung cancer progression.

overall_design: KRAS-mutant NSCLC cells were treated with trametinib (10nM) for 2, 5, and 10 days in 6-well plates. 4 KRAS-mutant NSCLC cell lines (A549, Calu-1, H460 and H23) were used in trametinib adaptive resistance analysis. 3 samples for each timepoint were collected for sequencing and bioinformatic analysis. For the combinational analysis, A549 cells were treated with trametinib (10nM) or anlotinib (1μM) or combination treatments for 24 hours in 6-well plates. 3 samples for each treatment were collected for sequencing and bioinformatic analysis.

first: Yikai

last: Zhao

first: Xinlei

last: Cai


title: Gene expression divergence between locally adapted inland annual and coastal perennial ecotypes of Mimulus guttatus across developmental stages

status: Public on Nov 10 2024

city: EAST LANSING

first: David

middle: Bryant

last: Lowry

state: MI

address: 612 WILSON RD RM 166

department: Plant Biology

institute: Michigan State University

summary: The action of natural selection across heterogeneous natural landscapes drives local adaptation and the formation of plant ecotypes, the precursors to new species. Plant ecotypes typically differ greatly in morphology, physiology, and development, yet we have a poor understanding of the underlying genetic basis of this divergence. Despite their importance, studies of the molecular underpinnings of ecotypic divergence through developmental stages are rare. In this study, we compared gene expression at different developmental time points between two locally adapted populations derived from the coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. We conducted gene co-expression network analyses to identify putative genetic and molecular mechanisms driving ecotypic divergence and evaluated gene ontology enrichment. Overall, we found significant global expression differences between the ecotypes and among developmental stages. We also found evidence to support the hypothesis that interacting hormone pathways, especially the gibberellin and jasmonic acid pathways, may play a key role in annual versus perennial ecotype divergence. Further, genes within known chromosomal inversions were more likely to be differentially expressed than genes in colinear regions, but only in leaves and not for floral buds. Collectively, our results reinforce our existing hypotheses about how ecotype formation has occurred in this system through shifts in hormone biosynthesis/signaling and help advance our understanding of the evolution of annuality versus perenniality in plants.

overall_design: To identify patterns of gene expression divergence between the ecotypes, we compared gene expression for leaves and floral buds collected from one coastal perennial (SWB-4) and one inland annual (LMC-17) accession. Developmentally equivalent leaf pairs and floral buds were collected in a time series manner. Only one tissue was collected per plant to avoid induced responses and repeated measures. For the inland annual plants, we sampled at the two-leaf, four-leaf, and floral bud stages because plants often flowered after producing four true leaves. Because the coastal perennial plants flowered at a later developmental stage, we sampled at the two-leaf, four-leaf, six-leaf, eight-leaf, and floral bud stages. All tissue samples were collected before anthesis. Overall, we collected 10 biological replicates for each developmental stage x ecotype combination (N = 80 total tissue samples).

middle: B

first: Jason

middle: D

last: Olsen

first: Billie

last: Gould

first: Yani

last: Chen


title: An in vivo repertoire of zebrafish cardiomyocyte-specific cis-regulatory elements [ChIP-Seq]

first: Hieu

last: Nim

overall_design: Cardiomyocytes were isolated from the Tg(myl7::GFP) zebrafish transgenic line. Larvae were collected 72 hpf (hours post fertilization). GFP-positive (30,000 cells, n=3 biological replicates) and GFP-negative cells (30,000 cells, n=3 biological replicates) were collected, and ChIP-sequencing was performed on these samples. The raw ChIP-seq FASTQ files are provided in SRA. The supplementary files are: the BED file containing differential peaks only found in GFP-negative samples (GSM7995224_GFP-_only.bed.gz), the BED file containing differential peaks only found in GFP-positive samples (GSM7995227_GFP+_only.bed.gz).

first: Marcus

last: Tondl

first: Gulrez

last: Chahal

first: Michael

last: Eichenlaub

first: Mirana

last: Ramialison


title: In vitro to in vivo extrapolation modeling to facilitate the integration of transcriptomics data into genotoxicity assessment

status: Public on Nov 13 2024

city: Ottawa

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada


title: DNA methylation insulates exons from CTCF loops with nuclear speckles

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University


title: DNA methylation insulates exons from CTCF loops with nuclear speckles (CUT&TAG)

summary: CTCF is necessary for the formation and maintenance of many DNA loops and Topologically Associating Domains, but the genomic features that influence CTCF looping are incompletely understood. We characterized the downstream effects of treating cells with a DNMT1 inhibitor and acute depletion of nuclear speckles to study the factors that influence CTCF looping.

overall_design: SON Cut&Tag for K562 and HCT116 cells treated with a DNA methylation inhibitor (DNMT1i) and DMSO control.

first: Shelby

last: Roseman

first: Allison

middle: P

last: Siegenfeld

first: Ceejay

last: Lee

first: Nicholas

middle: Z

last: Lue


title: Dual targeting CDK4/6 and CDK7 augments tumor response and anti-tumor immunity in breast cancer

status: Public on Nov 07 2024

city: New York

first: Hee Won

last: Yang

state: NY

institute: Columbia University

summary: CDK4/6 inhibitors (CDK4/6i) have significantly improved the prognosis for hormone-positive (HR+) breast cancer patients. However, the emergence of drug resistance severely limits their long-term efficacy, and CDK4/6i monotherapy remains largely ineffective against triple-negative breast cancer (TNBC). Here, we demonstrate that combining CDK4/6i with CDK7 inhibitors (CDK7i) offers a promising therapeutic strategy to overcome resistance in both HR+ breast cancer and TNBC. Kinetic analyses reveal that CDK7i primarily targets RNA polymerase II-mediated transcription, a key driver of CDK4/6i resistance by amplifying E2F activity following the degradation of the retinoblastoma protein. Consequently, the combination of CDK4/6i and CDK7i synergistically suppresses E2F activity and inhibits the growth of drug-resistant tumors. Furthermore, this combination stimulates immune response pathways and cytokine production in cancer cells, enhancing anti-tumor immunity. These findings provide critical insights into evolving CDK inhibition strategies and highlight the therapeutic application of CDK7i in breast cancer management.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bulk RNA-Seq was performed on the MDA-MB-231 cell line, and scRNA-Seq was conducted on tumors extracted from an AT3-OVA syngeneic mouse model.

first: Sungsoo

last: Kim

first: Eugene

last: Son

first: Haram

last: Park

first: Minah

first: HeeWon


title: Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation [scRNA-Seq]

city: Zhanjiang

first: Yiting

last: Guan

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Guangdong Medical University

summary: Granulosa cells (GCs) are the most dynamically responsive cell lineage to encourage continuous folliculogenesis; however, developmental dynamics and interplay with downstream transcription circuitry remain unclear. Here, we unravel the redistribution of genome-wide chromatin areas that drive broad developmental-related transcriptomic alterations during follicular maturation in murine and porcine GCs. Distinct GC-activated accessibility regions (GAAs) at the ovulatory phase are responsible for augmenting flanking GC-involved developmental gene (GDG) expression, which are essential for transcriptional responses to developmental cues. Mechanistically, the transcription factor (TF) Fosl2 is strongly recruited to GAAs, facilitating chromatin accessibility state transition. Elevated GAA signals driven by Fosl2 loading induce a significant upregulation of adjacent GDG expression. Additionally, GC-specific Fosl2 deletion in mice perturbs GC cellularity, leading to subfertility related to reproductive aging. Together, we highlight a dynamic chromatin accessibility landscape during follicular maturation, revealing the indispensable Fosl2 function not only controls transcriptional activation via a reconfigured chromatin state, but also orchestrates intricate signaling pathways that are fundamental for ovulation and reproduction.

overall_design: scRNA-seq of ovaries from 8-week-old Fosl2flox/flox and Cyp19a1-Cre; Fosl2flox/flox female mice to sought the changes of cell trajectories after knockout Folsl2 conditionally within GCs


title: A novel method for characterizing cell-cell interactions at single-cell resolution reveals unique immune signatures in blood T cell-monocyte complexes during infection (Dengue scTCR-Seq)

status: Public on Nov 06 2024

city: La Jolla

first: Ningxin

last: Kang

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: We designed a novel method to study the transcriptome of single cells forming complexes in a high-throughput fashion, without the need for bioinformatic deconvolution. We applied this method to the study of T cells and monocytes forming complexes in blood isolated from individuals with dengue fever, with blood collected at the acute and convalescent phase of infection. We found that the transcriptomic signatures of T cells and monocytes forming complexes significantly overlapped with those identified in T cell-monocyte complexes in active tuberculosis, with upregulation of genes associated with T cell activation, cytotoxicity, cell adhesion and MHC-II. Thus, using our novel method, we identified that T cells and monocyte forming complexes in blood hold unique immune signatures distinct from singlets, and that they may be a previously overlooked valuable biomarker to monitor immune synaptic interactions during infection.

overall_design:
PBMC were isolated, cryopreserved and thawed on the day of the experiment. T cell-monocyte complexes were identified by flow cytometry as live CD3+CD14+CD19- events and sorted in bulk. Cell sorting effectively disrupts the physical connection between cells forming complexes, with the vast majority of resulting cells being singlet CD3+ or singlet CD14+ cells remaining in suspension. The single-cell suspension was then used for droplet single-cell sequencing using the 10X genomics platform.
-----------------------------------
Authors state the following concerning the raw data "privacy concerns".

first: Julie

last: Burel

first: Gregory

last: Seumois

first: Ashu

last: Chawla

first: Bjoern

last: Peters


title: ATR/CHK1/WEE1 dependency in SRSF2-mutated myeloid malignancies

status: Public on Nov 24 2024

city: Charlestown

first: Timothy

last: Graubert

address: 149, 13th Street, Navy Yard

department: Cancer Center

summary: The aim of this experiment is to characterize mRNA splicing in clones derived from the K562 cell line, which have been genetically engineered using CRISPR/Cas9 to carry SRSF2 mutations frequently observed in myeloid malignancies

overall_design:
SRSF2 specific guide RNAs which harbored substitution mutations were used to target the nucleotides that code for Proline at amino acid position 95 (P95).
Mutations that replace amino acid Proline (P) at position 95 (P95) on SRSF2 were introduced individually in different K562 clones. Proline was substituted with arginine (P95R), leucine (P95L) or histidine(P95H).
Subsequently, RNA-sequencing was carried out from individual clones.

first: Samuli

last: Eldfors

first: Sumit

last: Rai

first: Vineet

last: Sharma


title: A novel method for characterizing cell-cell interactions at single-cell resolution reveals unique immune signatures in blood T cell-monocyte complexes during infection (Dengue scRNA-Seq)


title: Single cell RNA sequencing of CD45+ immune cells from tumor and tumor-adjacent mammary adipose tissue in a postmenopausal breast cancer model of lean, obese, and weight loss Trem2+/+ and Trem2-/- mice

status: Public on Nov 05 2024

city: Nashville

first: Matthew

last: Cottam

state: TN

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

summary: Triggering receptor expressed on myeloid cells 2 (Trem2) has been shown to be immunosuppressive in cancer and increased in obese adipose tissue. We utilized high fat and low fat diet to generate lean, obese, and weight loss mice in Trem2 wild-type (Trem2+/+) and Trem2 deficient (Trem2-/-) conditions. Once obesity and weight loss were established, mice were injected with E0771 breast cancer cells and tumors were allowed to grow for 4 weeks. We wanted to better understand the immune landscape of both the tumor and the surrounding adjacent mammary adipose tissue (mAT). Therefore, the CD45+ immune cells from both the tumor and tumor-adjacent mAT were isolated and sequenced using single-cell RNA sequencing and V(D)J sequencing.

overall_design: Samples include live CD45+ cells from the tumor and tumor-adjacent mammary adipose tissue of lean, obese, and weight loss Trem2+/+ and Trem2-/- C57BL/6J mice. A sample size of 3-4 is included for each group.

first: Elysa

last: Pierro

first: Alyssa

middle: H

last: Hasty

first: Barbara

last: Fingleton

first: Jeffrey

middle: C

last: Rathmell

first: Kathryn

middle: E

last: Wellen

first: Liza

last: Makowski


title: DNA methylation insulates exons from CTCF loops with nuclear speckles (ChiP-Seq)

first: Brian

last: Liau

overall_design: CTCF ChIP-seq for K562 and HCT116 cells treated with a DNA methylation inhibitor (DNMT1i) and DMSO control. Also, CTCF ChIP_seq data for speckle dTAG knockin K562 cells treated with dTAG-13 for speckle depletion and DMSO control. All experiments were performed in biolocial duplicate.

first: Shelby

last: Roseman

first: Allison

last: Siegenfeld

first: Ceejay

last: Lee

first: Nicholas

last: Lue


title: DNA methylation insulates exons from CTCF loops with nuclear speckles (RNA-Seq)

overall_design: Comparative gene expression profiling analysis of full-length RNA-seq data for K562 and HCT116 cells treated with a DNA methylation inhibitor (DNMT1i) and DMSO control. Also, comparative gene expression profiling analysis of full-length RNA-seq data for speckle dTAG knockin K562 cells treated with dTAG-13 for speckle depletion and DMSO control. All experiments were performed in biolocial triplicate.


title: Elucidating human female genital tract resident DC response to HIV-1 exposure.

status: Public on Nov 08 2024

city: Detroit

first: Marta

last: Rodriguez-Garcia

address: 275 E Hancock St

institute: Wayne State University

summary: The female genital tract (FGT) represents a complex and dynamic environment with specialized immune mechanisms uniquely designed to maintain a delicate balance between protection against invading pathogens and accommodating the unique physiological changes associated with reproductive function. Dendritic cells (DCs) are critical in shaping mucosal immunity against pathogens and maintaining tissue homeostasis. The unique ability of DCs to recognize invading pathogens through pattern recognition receptors (PRRs), and prime naive T cell function, make DCs ideal targets for vaccination and therapeutic strategies against cancers and infections. However, in HIV pathogenesis, DCs are considered a double-edged sword due to their ability to secrete anti-viral proteins and resist viral replication but capture and transfer active viral particles to target CD4+ T cells. Understanding the heterogeneity of DC populations in the FGT, along with their unique contribution to HIV pathogenesis is key for targeted interventions.

overall_design: Hysterectomy samples of endometrium, endocervix and ectocervix of female donor, determined to be healthy according to study criteria, (no cancer or active infections) were enzymatically digested to generate single-cell suspensions. To enrich for myeloid immune cells, the single cell suspensions were filtered to remove cells larger than 30mm, followed by depletion of CD3+ T cells, CD19+ B cells, CD235a+ red blood cells and fibroblasts through magnetic bead selection. Purified cells were incubated with HIV-BaL (R5) isolates (MOI=0.5) or media alone for 30 minutes at 37C, after which the cells were washed to remove excess unbound virus. The cells were subsequently stained with CITE-seq antibodies (AbSeq) and sample multiplexing antibodies (hs_SampleTag). Single-cell suspensions were processed on the BD Rhapsody system according to manufacturer’s protocols. cDNA libraires were constructed using BD Rhapsody Whole Transcriptome (WTA) Amplification KIT (BD Biosciences, Catalog# 633801).

first: Ragav Siddharth

last: Parthasarathy


title: A novel method for characterizing cell-cell interactions at single-cell resolution reveals unique immune signatures in blood T cell-monocyte complexes during infection (ATB scRNA-Seq)

first: Ningxin

last: Kang

summary: We designed a novel method to study the transcriptome of single cells forming complexes in a high-throughput fashion, without the need for bioinformatic deconvolution. We applied this method to the study of T cells and monocytes forming complexes in blood isolated from individuals with active tuberculosis, with blood collected at diagnosis and after treatment. We found that the transcriptomic signature of T cells and monocytes forming complexes was associated with TCR/MHC-II immune synaptic features, enrichment for cytotoxic clonally expanded T cells and intermediate monocytes, and - especially at diagnosis - transcriptomic signatures indicating increased immune and metabolic activity. We also found a striking enrichment of “dual-expressing” cells (i.e., co-expressing T cells and monocyte marker genes) in complexes, suggesting RNA exchange occur during T cell-monocyte interactions. Thus, using our novel method, we identified that T cells and monocyte forming complexes in blood hold unique immune signatures distinct from singlets, and that they may be a previously overlooked valuable biomarker to monitor immune synaptic interactions during infection.

first: Julie

last: Burel

first: Gregory

last: Seumois

first: Ashu

last: Chawla

first: Bjoern

last: Peters


title: Effect of Mac1 deletion on copper homoestasis and virulence in Fusarium oxysporum f. sp. lycopersici [RNA-seq]

city: Córdoba

first: Antonio

last: Di Pietro

state: Córdoba

address: Campus Rabanales, Edificio Gregor Mendel, 1

department: Genetics

country: Spain

institute: Universidad de Cordoba

summary: The transcription factor Mac1 is a key regulator of copper homeostasis, controlling the transcriptional response to copper-limiting conditions in fungi. It has been described as a virulence factor in human pathogens such as Candida albicans and Aspergillus fumigatus, but surprisingly its role in plant pathogenesis is poorly understood. Targeted deletion of Mac1 in the soilborne pathogen Fusarium oxisporum results in an inability to grow under copper-limited conditions and kills tomato plants. The aim of this RNA-seq analysis is to elucidate the role of Mac1 in gene regulation under copper starvation and during infection of tomato plants by F. oxysporum.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Fusarium oxysporum f. sp. lycopersici 4287 WT and mac1 knock-out mutant  grown in liquid culture with and witout added copper (Cu) and tomato root tissue after 2 and 6 days post infection (dpi)

first: Rafael

last: Palos-Fernández

first: María

middle: V

last: Aguilar-Pontes

first: Gema

last: Puebla-Planas

first: Harald

last: Berger

first: Lena

last: Studt-Reinhold

first: Joseph

last: Strauss

first: Manuel

last: López-Berges


title: Gene expression at single cell level of cells from genetically modified mouse colon tumors

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

summary: In the colonic epithelium, fetal programming is induced by Yes-associated protein (YAP) signaling, which is associated with tumorigenesis and progression in colorectal cancer (CRC). While CRC was long considered a Wnt driven disease, we showed fetal programmed cells with activated YAP signaling can arise independently of Wnt activation. Fetal programmed cells, in the presence of hyper- or hypo-activated Wnt, have different characteristics and are associated with poor relapse. Furthermore, using various mouse models, we demonstrated the conserved characteristics of two different fetal programmed cell states with different Wnt activation, which can be switched from hyperactivated to hypoactivated Wnt state based on genetic alteration, particularly Kras mutation. Altogether, these data redefine the key determinants of epithelial cell states in colorectal cancer and integrate emerging preclinical biology into a robust landscape of states observed in human and mouse.

overall_design: Colonic tumour cells with combinations of Apc, Braf, Kras, P53, Notch and Tgfbr1 mutations were isolated by fluorescence activated cell sorting (FACS) and analysed using scRNAseq.

first: Tamsin

last: Lannagan

first: Megan

last: Mills

first: Yourae

last: Hong

first: Owen

last: Sansom


title: A novel method for characterizing cell-cell interactions at single-cell resolution reveals unique signatures in blood T cell-monocyte complexes during infection

first: Ningxin

last: Kang

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

overall_design: Refer to individual Series


title: A novel method for characterizing cell-cell interactions at single-cell resolution reveals unique immune signatures in blood T cell-monocyte complexes during infection (ATB scTCR-Seq)

first: Julie

middle: G

last: Burel

first: Gregory

last: Seumois


title: DNA methylation insulates exons from CTCF loops with nuclear speckles  (HiChIP)

first: Brian

last: Liau

overall_design: CTCF HiChIP for K562 and HCT116 cells treated with a DNA methylation inhibitor (DNMT1i) and DMSO control. Also, CTCF HiChIP  for speckle dTAG knockin K562 cells treated with dTAG-13 for speckle depletion and DMSO control. All experiments were performed in biolocial duplicate.

first: Shelby

middle: A

last: Roseman

first: Allison

last: Siegenfeld

first: Ceejay

last: Lee

first: Nicholas

last: Lue


title: Conserved role for spliceosomal component PRPF40A in microexon splicing

city: Riverside

first: Adam

middle: David

last: Norris

state: CA

address: 3401 Watkins Drive

institute: University of California, Riverside

summary: Microexons (exons ≤30 nts) are important features of neuronal transcriptomes, but pose mechanistic challenges to the splicing machinery. We previously showed that PRP-40, a component of the U1 spliceosome, is globally required for microexon splicing in C. elegans. Here we show that the homologous PRPF40A is also globally required for microexon splicing in mouse neuroblastoma cells. We find that PRPF40A co-regulates microexons along with SRRM4, a neuron-specific regulator of microexon splicing. The relationship between exon size and dependence on PRPF40A/SRRM4 is distinct, with SRRM4-dependence exhibiting a size threshold (~30 nts) and PRPF40A-dependence exhibiting a graded decrease as exon size increases. Finally, we show that PRPF40A knockdown causes an increase in productive splicing of its spliceosomal binding partner Luc7l by skipping of a small “poison exon.” Similar homeostatic cross-regulation is often observed across paralogous RNA binding proteins. Here we find this concept likewise applies across evolutionarily unrelated but functionally and physically coupled spliceosomal components.

overall_design: Mouse neuroblastoma N2a cells treated with siRNAs against PRPF40a, or PRPF40b, or SRRM4. Each condition performed in biological triplicate


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia [etp82a_RNA-seq]

status: Public on Nov 04 2024

first: Javier

last: Rodriguez Hernaez

state: New York

address: East 30th Street. 8th Floor

institute: NYU Langone Health

summary: Cancer progression is associated with genetic and epigenetic aberrations that affect chromatin 3D organization in the nucleus. Changes in loop extrusion or phase separation alter the relationships between enhancer and promoter elements, defining novel gene expression programs that are selected to promote growth and survival. Here, we provide an integrative approach based on chromatin conformation, accessibility and transcription, further validated by CRISPR interference screenings in order to identify chromatin topologies relevant to different subtypes of T-cell leukemia, namely T-ALL and ETP-ALL. By focusing on highly interconnected elements, we characterized 3D hubs as headquarters of leukemia progression and identity, demonstrating that oncogenes and disease markers are regulated by multiple cis-regulatory regions.

overall_design: Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) and early T cell precursor leukemia (ETP-ALL) were collected and analyzed. To enrich for blast representation, samples were sorted based on clinical immune-phenotype, for CD2 and/or CD7 surface expression

first: Boccalatte

last: Francesco

first: Rodriguez-Hernaez

last: Javier

first: Gambi

last: Giovanni

first: Nadorp

last: Bettina

first: Aifantis

last: Ioannis

first: Tsirigos

last: Aristotelis


title: TE-Seq: A Transposable Element Annotation and RNA-Seq Pipeline

city: Providence

first: Maxfield

last: Kelsey

address: 225 Dyer St.

institute: Brown University

summary: The TE-Seq pipeline conducts an end-to-end analysis of RNA sequencing data, examining both genes and TEs. It implements the most current computational methods tailor-made for TEs, and produces a comprehensive analysis of TE expression at both the level of the individual element and at the TE clade level. Furthermore, if supplied with long-read DNA sequencing data, it is able to assess TE expression from non-reference (polymorphic) loci. As a demonstration, we analyzed proliferating, early senescent, and late senescent lung fibroblast RNA-Seq data, and created a custom reference genome and annotations for this cell strain using Nanopore sequencing data. We found that several retrotransposable element (RTE) clades were upregulated in senescence, which included non-reference, intact, and potentially active elements.

overall_design: We applied our pipeline to RNA-Seq data from our laboratory on LF1 cells spanning three biological conditions: LF1 cells were passaged to replicative senescence, and were harvested 4 and 16 weeks later, yielding early senescence (ESEN) and late senescence (LSEN) conditions. Early passage proliferating LF1 cells (PRO) were used as a control. Poly-A selected, stranded, 150bp paired-end libraries were sequenced in quadruplicate.

middle: M

first: Radha

middle: L

last: Kalekar

first: John

last: Sedivy


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia [HiChIP]

overall_design: Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) and early T cell precursor leukemia (ETP-ALL) were collected and analyzed for H3K27ac HiChIP. To enrich for blast representation, samples were sorted based on clinical immune-phenotype, for CD2 and/or CD7 surface expression


title: Trans-generational adaptation to maternal climate through hormone transport in plants [scRNA-seq]

city: Norwich

first: William

last: Bezodis

address: Norwich Research Park, Colney Lane

department: Crop Genetics

institute: John Innes Centre

summary: Whether and how organisms can inherit environmental information from their parents is a major question in evolutionary theory. Plants have evolved to link reproductive development to seasonal environmental cues and seed dormancy is highly contingent on the environmental temperature during seed set, although the mechanism by which seeds acquire seasonal timing information is unclear. Here we show that loss of maternal like heterochromatin protein 1 (LHP1) causes an inability of progeny seeds to sense temperature and that this is linked mechanistically to reduced ABA levels in seeds and hyperaccumulation of free nitrate. Remarkably, single cell transcriptomics reveals that in both maternal fruit and seed tissues, the effect of small changes in temperature closely phenocopies the lhp1 mutant phenotype and ABA biosensor imaging reveal large fluxes of maternal ABA into seeds is modulated by temperature cues. We show that temperature activates ABA production in leaves and that maternal ABA is necessary and sufficient for progeny seeds to acquire seed dormancy. Thus, we reveal that the climate experience of mother plants causes adaptation of progeny behaviour via hormone transport during seed set.

overall_design: single nucleus RNA-seq was performed on whole developing siliques including seeds at the bend cotyledon stage of embryo development. Plants were grown in controlled long day conditions at 16°C D/14°C N. with a single day transfer to 22°C for the relevant samples to match developmental stage. Plants are WT Col-0 or homozygous lhp1-6 in the Col-0 background.

first: Xiaochao

last: Chen

first: Steven

last: Penfield


title: The contribution of foam cells to angiogenesis and inflammation after spinal cord injury

status: Public on Nov 01 2024

city: Shanghai

first: Yersen

last: Mulat

state: Shanghai

address: No. 650 Xin Songjiang Road

department: School of Medicine

institute: Shanghai Jiao Tong University

summary: After spinal cord injury (SCI), macrophages engage in the phagocytosis of myelin debris and dead cells, transforming into foam cells. Nevertheless, the ultimate fate and functional role of these foam cells remain unclear, while their inflammatory phenotype elicits ongoing controversy. We discovered that macrophages transform into foam cells through 3 stages, which were phagocytosis, digestion, and lipid overload. Macrophages possess a certain degree of antioxidant capacity. When confronted with excessive lipid pressure, they undergo lipid droplets formation and metabolic reprogramming to alleviate lipotoxicity, also promoting angiogenesis. The anti-inflammatory phenotype of macrophages gradually diminished after SCI, phagocytosing debris could assist in maintaining this phenotype. Moreover, most genes expression patterns were conserved both in the SCI mice and rats. Our study provides a detailed description of the changes in gene expression and function during foam cell formation and long-term fate after SCI, which provides a theoretical basis for further research.

overall_design: To investigate whether the genetic profile of bone marrow-derived macrophages (BMDM) changes when they engulf myelin debris (MD) under different conditions, we conducted RNA-seq sequencing, including genetic profiling of BMDM in different polarized states (M1, M2), MD ingested at different concentrations (50ug/ml, 1mg/ml) and at different times (6h, 24h, 72h), as well as genetic profiling of BMDM after they have been treated with two possible drugs that may reduce lipid content within BMDM: badoxifene and bafometrin.

first: Haodong

last: Lin

first: Ying

last: Peng

first: yersen

last: mulat

first: Zhenwu

last: Yang


title: Single cell sequencing and retrograde barcode tracing reveal human DA neuron identities based on projection patterns in stem cell-derived grafts

status: Public on Nov 03 2024

city: Lund

first: Petter

last: Storm

state: Select...

address: Sölvegatan 19, BMC A11

country: Sweden

institute: Lund University

summary: Groundbreaking research in the last decade has definitively established human pluripotent stem cells (hPSCs) as a powerful source for the unlimited generation of dopamine (DA) neurons used in cell-based therapy in Parkinson’s disease (PD). However, DA neurons constitute a heterogeneous group of cells with different molecular identities and, consequently, different functions and innervation targets. Moreover, the inaccessibility of the human brain has so far hindered our understanding of the highly complex human DA system and, therefore, the design of DA neuron subtype-specific differentiation protocols for more effective cell replacement therapies. Currently, DA neurons – located in human ventral midbrain – can only be reliably distinguished based on their projection patterns. Here, we used hPSCs to derive and then transplant DA neurons into a rat model of PD. After one year of transplantation, we performed single nucleus RNA sequencing (snRNAseq) of ~80,000 human nuclei to transcriptionally define cell type composition and obtained a comprehensive map of DA neuron molecular identities. Exploiting the fact that transplanted DA neurons innervated and integrated within the host circuitry, we then combined snRNAseq with axonal retrograde AAV barcoding to trace the projection patterns of molecularly distinct human DA neuron subtypes in the grafts. We thus defined human DA neuron transcriptional profiles based on their target-specific outgrowth in the host brain. The resulting datasets provide an unprecedented resource both for elucidating the molecular basis of human DA neuron diversity as well as for developing more targeted cell-based therapies, with major implications for outcomes of PD patients.

overall_design:
Single-nuclei RNA-seq of stem cell derived midbrain grafts
NOTE FROM SUBMITTER: Due to privacy concerns we are unable to submit raw data and has hence only uploaded count matrices.

first: Malin

last: Parmar

first: Alessandro

last: Fiorenzano


title: Single nuclei sequencing of the nodose ganglia

city: Richardson

first: Catherine

last: Thorn

address: 800 W Campbell Rd

department: Neuroscience

institute: The University of Texas at Dallas

summary: The vagus nerves are important carriers of sensory information from the viscera to the brain. Emerging evidence suggests that sensory signaling through the right, but not the left, vagus nerve evokes striatal dopamine release and reinforces appetitive behaviors. However, the extent to which differential gene expression within vagal sensory neurons may underlie this asymmetric reward-related signaling is unknown. Here, we use single-nucleus RNA sequencing, in situ hybridization, and calcium imaging to identify a single cluster of neurons, defined by co-expression of Chrna3 (nicotinic acetylcholine receptor subunit 3) and Cckar (cholecystokinin 1 receptor), that is preferentially expressed in the right nodose ganglia of rats. This neuronal population also expresses several genes implicated in digestive signaling, including Glp1r and Sctr, consistent with a gut-innervating subtype. Our results suggest that right-biased expression of this unique chemosensing vagal cell type may contribute to asymmetric encoding of interoceptive rewards by the vagus nerves.

overall_design: The right and left NG of experimentally naïve, 8-week-old male and female rats were dissected, and single-nuclei RNA sequencing (snRNA-Seq) was performed.

first: Hailey

middle: F

last: Welch

first: Ishwarya

last: Sankaranarayanan

first: Khadijah

last: Mazhar

first: Theodore

middle: J

last: Price


title: Transcriptomic study on the effect of Igf1r deficiency in control and bleomycin-challenged mouse lungs.

city: Logroño

first: Jose

middle: Garcia

last: pichel

state: La Rioja

address: Piqueras 98

department: Oncology

institute: FUNDACIÓN RIOJA SALUD - CIBIR

summary: Acute lung injury (ALI), ARDS and COVID-19 usually involve a “cytokine storm”. IGF1R (Insulin-like growth factor receptor 1) maintains lung homeostasis and is implicated in these pulmonary inflammatory diseases. In mice, widespread IGF1R  deficiency was reported to counteract respiratory inflammation and alveolar damage after bleomycin (BLM)-induced ALI. To explore the molecular mechanisms mediated by Igf1r signaling after BLM challenge, we performed RNA-sequencing in lungs of IGF1R-deficient mice after BLM or saline (SAL) instillation. Transcriptomic analysis identified differentially expressed genes between BLM-challenged and SAL-treated control lungs, detecting biological processes and signaling pathways involved in ALI pathobiology. Igf1r depletion in BLM-challenged mice reversed large part of the transcriptional changes triggered by BLM, counteracting the transcriptomic profile of the inflammatory "cytokine storm". Data mining also identified changes in the expression of gene clusters with key roles in DNA damage, metabolic reprogramming, mitochondrial homeostasis, and epigenetics. Exploration of these functional groups, together with validation studies, provide new insights into the molecular mechanisms underlying the attenuating effect of Igf1r deficiency on ALI. These findings allow a more comprehensive view of IGF1R signaling at the transcriptional level, reinforcing its important role in promoting ALI and postulating it as a global epigenetic regulator in ARDS.

overall_design: In order to evaluate the effect of generalized Igf1r deficiency in the context of BLM-mediated ALI on the transcriptome, lung RNA samples from the following four groups of mice were sequenced, (3 samples per group, 12 samples in total): 1) SAL-treated Igf1rfl/fl 2) SAL-treated UBC-CreERT2; Igf1rΔ/Δ (Igf1r-deficient; CreERT2) 3) BLM-challenged Igf1rfl/fl (Igf1rfl/fl-BLM)4) BLM-challenged CreERT2 (CreERT2-BLM)  Three differential gene expression comparisons were established between experimental groups: i) CreERT2 vs Igf1rfl/fl ("mutation") ii) Igf1rfl/fl-BLM vs Igf1rfl/fl ("injury") iii) CreERT2-BLM vs Igf1rfl/fl-BLM lungs ("attenuation")  Analysis of differenial gene expression, gene set enrichment analysis (GSEA) and intensive data mining were performed to thoroughly explore transcriptomic data. Additional experimental techniques were used to further investigate transcriptomic results.

first: Alfredo

last: Urtubia

first: María

last: De Toro

first: Sergio

last: Piñeiro-Hermida

first: Elvira

last: Alfaro-Arnedo

first: Marta

last: Canalejo

first: José

last: Pichel

first: Icíar

last: López


title: Human microRNA-122b-5p regulates chikungunya virus replication in macrophages by directly targeting viral 3'-UTR and cellular histone deacetylase 4

status: Public on Oct 31 2024

city: New Delhi

first: Sujatha

last: Sunil

state: Delhi

address: Aruna Asaf Ali Road

department: Vector Borne Disease Group

country: India

institute: International Centre for genetic engineering and Biotechnology

summary: We found that Histone Deacetylase 4 is the target of human miR-122b-5p using transcriptome approach and report thst HDAC4 is downregulated in CHIKV infected human macrophages through global transcriptome profiling

overall_design: 6 samples (each contains 3 triplicates) = 18 samples

first: Priyanshu

last: Srivastava

first: Sakshi

last: Chaudhary


title: Differential transcriptome analysis of mid-logarithmic and early stationary growth phases of hyperacidophilic archaea Oxiplasma meridianum M1

city: Bangor

first: Rafael María

last: Bargiela Bargiela

state: Gwynedd

address: Deniol Road

department: Center for Environmental Biotechnology

institute: Bangor University

summary: Comparative gene expression analysis was employed for deciphering the major metabolic pathways in actively growing and stationary-phase cultures of Oxiplasma meridianum M1. The analysis of data revealed differences in expression profiles that could not be investigated otherwise, e.g. through the shotgun proteome studies. This transcriptome study accompanies physiological and metabolic studies to pinpoint the key  niche adaptation mechanisms and disentangle evolutionary trajectories within Thermoplasmata.

overall_design: After cultivation of Oxiplasma meridianum M1 and samples have been collected after 3 days, corresponding to its mid-log growing phase, and afer 5 days, corresponding to its early stationary phase. The goal is to compare both samples and check when and which proteins are expressed regarding its surface (archeaellum, pili, etc), production of carotenoids and metabolism. RNA-seq experiments were performed to compare the differential expresion of genes among the two growing phases.

first: Olga

last: Golyshina

first: Peter

last: Golyshin

first: Rafael

last: Bargiela


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia [scATAC-Seq]

city: New York

first: Javier

last: Rodriguez Hernaez

overall_design: Primary samples of T cell acute lymphoblastic leukemia (T-ALL) and early T cell precursor leukemia (ETP-ALL) were collected and analyzed by single-cell ATAC sequencing

first: Boccalatte

last: Francesco

first: Lin

last: Ziyan

first: Rodriguez-Hernaez

last: Javier

first: Gambi

last: Giovanni


title: ESRP2-miR122 axis regulates postnatal onset of polyploidization

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

summary: Postnatal period of development is critical for mammalian tissues and is coordinated through precise activation of genetic programs that govern differentiation, growth and maturation. Here, we describe a cell type- and developmental stage-specific program of alternative splicing that drives sequential replacement of fetal-to-adult protein isoforms in the mouse liver. Using deep transcriptome analysis of loss- & gain-of-function models we identified Epithelial Splicing regulatory protein 2 (ESRP2) as the major regulator for these developmental splicing decisions. Targeted deletion of ESRP2 in mice resulted in the failure of fetal-to-adult switch in splicing for hundreds of RNA transcripts that encode proteins involved in functional competence of hepatocytes. To delineate its role in activation of adult splicing program, we generated transgenic mice with tetracycline-inducible and hepatocyte-specific expression of ESRP2. Remarkably, premature expression of ESRP2 in the livers of newborn pups forced an earlier-than-normal onset of adult splicing program. To determine the in vivo ESRP2 RNA binding landscape within hepatocytes, we used CRISPR-Cas9 technology to FLAG-tag the endogenous locus of ESRP2 in mice and performed FLAG-eCLIP to identify genomewide binding sites. We identified ESRP2 as a regulator of miR-122 levels in hepatocytes, wherein this axis balances the polyploidization and proliferation states in postnatal hepatocytes.

overall_design: gene expression and alternative splicing analysis between WT and ESRP2 KO hepatocytes

first: Auinash

last: Kalsotra


title: Single cell analysis of SW620/SW620-TET2CD with long time clone culturing

city: Guangzhou

first: Hao

last: Sun

address: 190 Kaiyuan Avenue

institute: Chinese Academy of Sciences

summary: In order to understand the single cell nature of SW620/SW620-TET2CD, we used the SW620/SW620-TET2CD clone from Day6/Day9/Day12/Day15 to start our single cell sequencing and analysis the diffference of single cell gene expression from different samples.

overall_design: SW620/SW620-TET2CD clones were cultred with different time,ie 6 days, 9 days, 12 days and 15 days. Clones were dissociated to single cell and sequneced. Gene expression difference were analyized between diffferent time points.

first: Zheng

last: Hui

first: Sun

last: Hao

first: Li

last: Changpeng


title: Distinct modes of non-canonical initiation regulate selective host versus viral mRNA translation during poxvirus-induced shutoff

status: Public on Oct 30 2024

city: Chicago

first: Chorong

last: Park

address: 303 E Chicago Ave

institute: Northwestern Univeristy

summary: Many viruses potently inhibit host protein synthesis while employing unconventional strategies to sustain their own translation, but how and why certain cellular mRNAs continue to be translated remains unclear. Here, we show that during shutoff by Vaccinia Virus (VacV) several host mRNAs increase in polysome occupancy but few, topped by JUN, result in increased protein abundance. Translation of viral mRNAs depended on the small ribosomal protein, Receptor for Activated C Kinase 1 (RACK1) and the eukaryotic Initiation Factor, eIF3. Cryo-electron microscopy (cryo-EM) further showed that eIF3 bound to virus-modified RACK1-containing 40S subunits that exhibit altered head rotation during infection. By contrast, RACK1 and eIF3 were dispensable for JUN translation. Moreover, structurally distinct 5’ untranslated regions (5’UTRs) in viral versus JUN mRNAs conferred differential eIF3 dependencies. Altogether, we reveal how distinct modes of non-canonical initiation support the production of both host and viral proteins that facilitate poxvirus replication despite infection-induced shutoff.

overall_design: To investigate how vaccinia virus infection alters host mRNA expression, we used HAP1 cell lines and RACK1 knock out cell lines with or without VacV infection then, performed ribosome profiling and subsequently samples were subjected for polyA selected RNA sequencing.

first: Aaron

last: Ferrell

middle: S

last: Shen

first: Derek

last: Walsh

first: Nathan

last: Meade


title: Identification of LRP1 and CD13 expressing human periosteal cells for stem cell-mediated bone repair

city: Houston

first: Dongsu

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Human periosteal skeletal stem cells (P-SSCs) are critical for cortical bone maintenance and repair. However, their in vivo identity, molecular characteristics, and specific markers remain unknown. Here, single-cell sequencing revealed human periosteum contains SSC clusters  expressing known SSC markers, PDPN and PDGFRA. Notably, human P-SSCs, but not bone marrow SSCs (BM-SSCs), selectively expressed newly identified markers, LRP1 and CD13. Single-cell analysis of mouse periosteum further supported the preferential expression of LRP1 and CD13 in Prx1 P-SSCs. These LRP1CD13 human P-SSCs were perivascular cells with high osteochondrogenic but minimal adipogenic potential. In addition, LRP1CD13 human P-SSCs are maintained in vitro and self-renew in vivo upon transplantation into bone injuries in mice. When Lrp1 was conditionally deleted in Prx1-lineage cells, it led to severe bone deformity, short statue, and periosteal defects. By contrast, local treatment with a LRP1 agonist at the injury sites induced early P-SSC proliferation and bone healing. Thus, human periosteum contains unique osteochondrogenic stem cell subsets, and these P-SSCs express specific markers, LRP1 and CD13, with regulatory mechanism through LRP1 that enhances P-SSC function and bone repair.

overall_design: Non-hematopoietic and non-endothelial cells from mouse long bone periosteum were isolated by Fluorescence-activated cell sorting and analyzed by 10x scRNA-seq

first: Youngjae

last: Jeong


title: Fetal programming by the maternal microbiome of offspring behavior, and DNA methylation and gene expression within the hippocampus

city: Columbia

first: Rene

middle: Gabriel

last: Cortese

state: MO

address: 1 Hospital Dr. MA104E

department: Child health Research Institute

institute: University of Missouri

summary: The microorganisms colonizing the gastrointestinal tract of animals, collectively referred to as the gut microbiome, affect numerous host behaviors dependent on the central nervous system (CNS). Studies comparing germ-free mice to normally colonized mice have demonstrated influences of the microbiome on anxiety-related behaviors, voluntary activity, and gene expression in the CNS. Additionally, there is epidemiologic evidence supporting an intergenerational influence of the maternal microbiome on neurodevelopment of offspring and behavior later in life. There is limited experimental evidence however directly linking the maternal microbiome to long-term neurodevelopmental outcomes, or knowledge regarding mechanisms responsible for such effects.  Here we show that that the maternal microbiome has a dominant influence on several offspring phenotypes including anxiety-related behavior, voluntary activity, and body weight. Adverse outcomes in offspring were associated with features of the maternal microbiome including bile salt hydrolase (Bsh) expression, abundance of certain bile acids, and hepatic expression of S1pr2. In cross-foster experiments, offspring resembled their birth dam phenotypically, despite faithful colonization in the postnatal period with the surrogate dam microbiome. Genome-wide methylation analysis of hippocampal DNA identified microbiome-associated differences in methylation of 196 loci in total, 176 of which were imprinted by the maternal microbiome. Further, single-cell transcriptional analysis revealed accompanying differences in expression of several differentially methylated genes within certain hippocampal cell clusters, and vascular expression of genes associated with bile acid transport. Inferred cell-to-cell communication in the hippocampus based on coordinated ligand-receptor expression revealed differences in expression of neuropeptides associated with satiety. Collectively, these data provide proof-of-principle that the maternal gut microbiome has a dominant influence on the neurodevelopment underlying certain offspring behaviors and activities, and selectively affects genome methylation and gene expression in the offspring CNS in conjunction with that neurodevelopment.

overall_design: This study consists of n=48 microarrays divided in six experimental groups: i) DamGM1: GM1 dams, ii) DamGM4: GM4 dams, iii) GM1 offspring, iv) GM4 offspring, v) GM1CF: GM1 ofsspring crossfostered in GM4 dams, and iv) GM4CF: GM4 offspring crossforstered in GM1 dams. Microarray data was analyzed using Illumina Genome Studio v2011.1.  Data was processed with background normalization.

last: Ericsson

first: Kevin

last: Gustafson


title: Single cell transcriptomics reveals obesity-induced endothelial and neurovascular dysfunction in brain: implications for cognitive decline

city: Davis

first: Saivageethi

last: Nuthikattu

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

summary: Obesity is a global pandemic and a key risk factor for several neurodegenerative diseases including Alzheimer’s disease (AD), Parkinson’s disease, or dementia. The neurovascular unit (NVU), essential for blood-brain barrier (BBB) integrity and comprised of endothelial cells, glial cells (microglia and astrocytes), and neurons, plays an important role in the pathogenesis of neurodegenerative diseases. However, molecular mechanisms underlying the effects of obesity on endothelial and other cells of and its contribution to neurodegeneration remains largely unknown. In this study we aimed to decipher in-dept molecular modifications induced by obesity in cells of neurovascular unit by integrative multiomics analysis of endothelial cells, neurons, microglial cells, and astrocytes from the hippocampus of ob/ob mice. Hippocampus were isolated from ob/ob and C57BL/6J male mice at 17-18 weeks of age. Gene expression profiles of cells of hippocampus were obtained using single nuclei RNA sequencing (snRNAseq) and data analyzed using in-dept bioinformatic analyses. snRNAseq and UMAP analysis revealed 19 cell types in hippocampus. Comparisons of global gene expression profiles identified different global profiles between ob/ob and WT for each of the cell types of the NVU. Statistical analyses revealed 4463 DEGs in neuronal cells, 1386 DEGs in astrocytes, 125DEGs in endothelial cells, and 155 DEGs in microglia cells, suggesting that obesity significantly impacts the expression profiles of NUV cells. Enrichment analyses revealed that these genes are involved in cellular processing like focal adhesion, cell interactions, inflammation, and metabolism. Changes in the expression in endothelial cells were positively correlated with genomic changes in other cell types, changes that we correlated with tendency in increase in BBB observed using functional MRI. Taken together, obesity exert significant cell-specific changes in global gene expression, genes that are associated with development of Alzheimer’s disease or dementia.

overall_design:
Wild type (C57BL/6J) and ob/ob male mice were fed a standard purified diet AIN-93M, for 8 wks. Mice were sacrificed at 18 weeks of age and hippocampus was dissected from left hemisphere and then stored at -80 degree celcius. Hippocampal nuclei was isolated and single nuclei RNA sequencing was performed. Brain hippocampal endothelial cells, microglial cells, astrocytes, and neuronal cells gene expression was analyzed using a multiomic approach for differential expression of protein and non-protein coding genes, gene networks, functional pathways, and transcription factors. Blood brain barrier permeability was assessed.
The Wild type data described in this study are avalilable in GSM7717249 [Samples 5,11,17, and 21].

first: Dragan

last: Milenkovic

first: Jennifer

last: Norman

first: Amparo

last: Villablanca


title: Cytotoxic and Molecular Effects of Soil Extracts from the Agbogbloshie Electronic-Waste Site on Fish and Human Cell Lines.

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

institute: McGill University

summary: Effect-based methods (EBM) are of growing interest in environmental monitoring programs. Few EBM have incorporated transcriptomics even though these provide a wealth of biological information and can be modeled to yield transcriptomic points of departure (tPODs). The study objectives were to: A) characterize cytotoxic effects of soil extracts on the rainbow trout RTgill-W1 and the human Caco-2 cell lines; B) measure gene expression changes and calculate tPODs; and C) compare in vitro responses to available measures of plastic-related compounds and metals. Extracts were prepared from 35 soil samples collected at the Agbogbloshie E-waste site (Accra, Ghana). Cells were exposed to six soil concentrations (0.3 to 9.4 mg dry weight of extract (eQsed)/ml). Many samples caused cytotoxicity with RTgill cells being more sensitive than Caco-2 cells. Eleven samples were analyzed for transcriptomics in both cell lines, with responses measured in all samples (52 to 5925 differentially expressed genes) even in the absence of cytotoxicity. In RTgill cells there was concordance between cytotoxic measures in tPOD values (spearman = 0.85). Though trends between in vitro measures and contaminant data were observed, more work is needed in this area before definitive conclusions are drawn. Nonetheless, this study helps support ongoing efforts in establishing alternative testing strategies (e.g., alternative to animal methods; toxicogenomics) for the assessment of complex environmental samples.

sample_organism:
Oncorhynchus mykiss
Homo sapiens

platform_organism:
Oncorhynchus mykiss
Homo sapiens

overall_design: Caco-2 and RTgill-W1 cell lines were exposed to extracts prepared from soil samples collected at various e-waste sites, at various concentrations. Endpoints examined were cytotoxicity and transcriptomics

first: Krittika

last: Mittal

first: Ke

last: Xu

first: Jingyun

last: Zheng

first: Stephane

last: Bayen

first: Julius

last: Fobil


title: Differential transcriptome analysis of mid-logarithmic and early stationary growth phases of hyperacidophilic archaea Cuniculiplasma divulgatum S5

first: Rafael María

last: Bargiela Bargiela

summary: Comparative gene expression analysis was employed for deciphering the major metabolic pathways in actively growing and stationary-phase cultures of Cuniculiplasma divulgatum S5. The analysis of data revealed differences in expression profiles that could not be investigated otherwise, e.g. through the shotgun proteome studies. This transcriptome study accompanies physiological and metabolic studies to pinpoint the key  niche adaptation mechanisms and disentangle evolutionary trajectories within Thermoplasmata.

overall_design: After cultivation of Cuniculiplasma divulgatum and samples have been collected after 3 days, corresponding to its mid-log growing phase, and afer 5 days, corresponding to its early stationary phase. The goal is to compare both samples and check when and which proteins are expressed regarding its surface (archeaellum, pili, etc), production of carotenoids and metabolism. RNA-seq experiments were performed to compare the differential expresion of genes among the two growing phases.

first: Olga

last: Golyshina

first: Peter

last: Golyshin

first: Rafael

last: Bargiela


title: Effects of BT-11 treatment on hippocampal gene expression in Female Fisher transgenic 344-AD rats. [Female RNAseq]

status: Public on Oct 29 2024

city: NY

first: Emily

last: Birnbaum

address: 200 West 93rd Street, 6J

institute: CUNY Graduate Center

summary: 5 month old Female Fisher transgenic 344-AD (Tg-AD) rats expressing human Swedish amyloid precursor protein (APPsw) and Δ exon 9 presenelin-1 (PS1ΔE9) were treated with BT-11  (cat. no. HY-102013, MCE) at 8.5 mg/kg body weight administered in rodent chow. Following 6 months of BT-11  treatment, rats (11 months of age) were tested for cognitive behavior prior to sacrificing. Hippocampal Brain region were dissected and  RNA sequencing (RNAseq) analyses was done on the Isolated sample. Taken together we showed that BT-11  treatment enriched pathways for females included passive transmembrane transporter activity, G protein-coupled receptor activity, G protein-coupled peptide receptor activity.

overall_design: To show the effects of BT-11-treatment on gene expression levels, Hippocampi of 5 BT-11 -treated and 5 untreated transgenic rats of male rats were analysed for gene expression by RNAseq. At 11 months of age, the rats were anaesthetized intraperitoneally with ketamine (100 mg/kg) and xylazine (10 mg/kg) and transcardially perfused with cold RNAse-free 1× PBS. Left hippocampi were removed and snap frozen for RNAseq analysis. Left hemisphere of the hippocampus.  F1 – F5 (untreated female transgenic rats), FBT1 – FBT5 (transgenic female AD rats treated with the drug BT-11). Female Rats started BT-11 treatment at 5-months of age and were treated for 6 months untli they were 11 months old.  For this experiment, the gene expression for the drug treated transgenic rats will be compared to that of the untreated transgenic group  (FBT/F)

first: Birnbaum

last: Emily

first: Patricia

last: Rockwell

last: Serrano

first: Maria

last: Figueiredo-Pereira

first: Lei

last: Xie


title: Effects of BT-11 treatment on hippocampal gene expression in Male Fisher transgenic 344-AD rats. [Male RNAseq]

summary: 5 month old Male Fisher transgenic 344-AD (Tg-AD) rats expressing human Swedish amyloid precursor protein (APPsw) and Δ exon 9 presenelin-1 (PS1ΔE9) were treated with BT-11  (cat. no. HY-102013, MCE) at 8.5 mg/kg body weight administered in rodent chow. Following 6 months of BT-11  treatment, rats (11 months of age) were tested for cognitive behaviour prior to sacrificing. Hippocampal Brain region were dissected and  RNA sequencing (RNAseq) analyses was done on the Isolated sample. Taken together we showed that BT-11  treatment enriched pathways in males including salt transmembrane transporter activity, signaling receptor regulator receptor ligand activity, signaling receptor activator activity, and transmembrane transporter activity.

overall_design: To show the effects of BT-11-treatment on gene expression levels, Hippocampi of 5 BT-11 -treated and 5 untreated transgenic rats of male rats were analysed for gene expression by RNAseq. At 11 months of age, the rats were anaesthetized intraperitoneally with ketamine (100 mg/kg) and xylazine (10 mg/kg) and transcardially perfused with cold RNAse-free 1× PBS. Left hippocampi were removed and snap frozen for RNAseq analysis. Left hemisphere of the hippocampus. M1 – M5 (untreated male transgenic rats), MBT1 – MBT5 (transgenic male AD rats treated with the drug BT-11). Male  Rats started BT-11 treatment at 5-months of age and were treated for 6 months untli they were 11 months old. For this experiment, the gene expression for the drug treated transgenic rats will be compared to that of the untreated transgenic group (MBT/M)


title: A Fast Chemical Reprogramming System to Generate Human Pluripotent Stem Cells

status: Public on Oct 28 2024

city: Beijing

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

institute: Peking University

summary: Chemical reprogramming enables the generation of human pluripotent stem cells (hCiPSCs) from somatic cells using small molecules, providing a novel and promising strategy for regenerative medicine. However, the current method for generating hCiPSCs is time consuming, and some cell lines from different donors are resistant to chemical induction, significantly limiting the utility of these cells for personalized medicine. Here, we developed a fast-reprogramming system capable of generating hCiPSCs in as few as 10 days. This accelerated method enables efficient generation of hCiPSCs with a consistent 100% success rate across 15 different donors. In particular, the efficiency of reprogramming within 16 days for cells refractory to previously reported protocols increased more than 30-fold. Mechanistically, we identified KAT3A/B and KAT6A as key epigenetic obstacles, as suppression of these factors facilitated the transition of somatic cells to a poised state by triggering switches in the epigenome, a process essential for this fast-reprogramming system. These results highlight the superiority of this novel system for generating hCiPSCs, which represents a next-generation approach for manufacturing cells for clinical applications. This work also advances our understanding of human cell reprogramming and paves the way for broader applications of chemical reprogramming in regenerative medicine.

overall_design:
To characterize human chemically induced pluripotent stem cells (hCiPSCs), human somatic cells, cells induced from hADSC by CUT&TAG.
To characterize human chemically induced pluripotent stem cells (hCiPSCs by scATAC-seq.


title: Effect of depletion of TRIM47 on gene expression in human brain microvascular endothelial cells (HBMEC)

city: Pessac

first: Claire

last: Peghaire

address: 1 avenue de Magellan

country: France

institute: University of Bordeaux-INSERM 1034

summary: To investigate the transcriptional programme regulated by TRIM47 in HBMEC, we treated these cells with a siRNA targeted TRIM47 or a control siRNA for 72h.We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different conditions (siRNA control or siRNA TRIM47).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HBMEC treated with siControl or siTRIM47 for 72h

first: Juliette

last: Vaurs

first: Carole

last: Proust

first: Béatrice

last: Jaspard Vinassa

first: Thierry

last: Couffinhal

first: Cécile

last: Duplàa


title: High-resolution Hi-C reveals increased chromatin looping with senescence associated with hypomethylation and retrotransposon derepression [Long Read DNA-seq]

city: Providence

first: Nicola

last: Neretti

state: RI

address: 225 Dyer St.

institute: Brown University

summary: This study presents the highest-resolution chromatin map of cellular senescence to date, shedding light on how genomic architecture is altered with this damaging phenotype. Senescence, a driver of aging, is a pro-inflammatory state of proliferative arrest caused by DNA damage; it is associated with epigenetic changes, including those to chromatin organization. We created ~3kb Hi-C contact maps of proliferating, quiescent, and replicative senescent lung fibroblasts, and also compared these to oncogene-induced senescence. Our findings confirm a loss of heterochromatin, with a shift towards the A compartment and A subcompartments. We establish a novel loop analysis framework, revealing the ~six times more unique loops with senescence, which lose methylation at their anchors. Additionally, we present a custom long-read reference genome highlighting structural changes supporting retrotransposon derepression, particularly at a defined ‘hotspot’. These architectural changes contribute to senescence, as they promote cell cycle arrest and inflammation, as well as epigenetic drift.

overall_design: To investigate the role of genomic structure in cellular senescence we generated Hi-C data, total RNA-seq, and long-read DNA sequencing for proliferating and late replicative senescent human diploid lung fibroblasts (LF1). We also generated Hi-C and total RNA-seq for quiescent cells. We compared the proliferating, quiescent, and senescent cell data to determine characteristic architectural features of senescence.

first: Audrey

last: Dalgarno

first: Shane

last: Evans

first: Maxfield

last: Kelsey

first: Thomas

last: Nunez

first: Azucena

last: Rocha

first: Kelly

last: Clark

first: John

last: Sedivy


title: Transcriptomics of C. chinensis and E. ulmoides treated aged C. elegans

city: Berlin

first: Nadine

last: Saul

address: Philippstr. 13, House 22

department: Department of Biology

country: Germany

institute: Humboldt-Universitaet zu Berlin

summary: The nematode Caenorhabditis elegans was treated with extracts of the Traditional Chinese Medicine plants Cuscuta chinensis and Eucommia ulmoides from the L4 stage. In aged worms (on the 7th and 12th day of adulthood) different health parameters were determined. Besides the prolongation of lifespan, we found that C. chinensis improved the swimming behavior, pharyngeal pumping rate, stress resistance, mechanosensation and memory of aged C. elegans. Furthermore, the extract treatment reduced the autofluorescence, which is a known biomarker of ageing. Thus, we concluded that C. chinensis is an overall healthspan enhancer. In contrast, the E. ulmoides extract specifically enhanced the lifespan and stress resistance of aged C. elegans, but did not improve any other health aspect. To reveal the mechanism behind the healthspan enhancing effects of C. chinensis, the transcriptome of treated and untreated C. elegans on the 12th day of adulthood was analysed. For comparison purposes, E. ulmoides treated nematodes were included in the analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C. elegans treated with C. chinensis or E. ulmoides. DMSO treated nematodes were used as control. The treatment of nematodes took place from L4 until the 12th day of adulthood. Five biological repeats were prepared per treatment group.

first: Shimaa

last: Sayed

first: Anna

last: Pitas

first: Christian

last: Schmitz-Linneweber


title: scRNAseq and CITEseq of aged HSPCs derived from FlkSwitch mouse model

city: Santa Cruz

first: Paloma

last: Medina

address: 1156 High St.

institute: University of California Santa Cruz

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

overall_design: Refer to individual Series


title: A Fast Chemical Reprogramming System to Generate Human Pluripotent Stem Cells [RNA-seq]

status: Public on Oct 27 2024

first: Jingxiao

last: Cao

overall_design:
To characterize human chemically induced pluripotent stem cells (hCiPSCs), hCiPSCs, human somatic cells and human embryonic stem cells (hES) by RNA-seq.
To characterize human chemically induced pluripotent stem cells (hCiPSCs) by scRNA-seq.


title: Method of moments approach for generalized differential gene expression analysis (Perturb-seq)

status: Public on Oct 24 2024

city: San Francisco

first: Min Cheol

last: Kim

address: 505 Parnassus Ave

institute: University of California, San Francisco

summary: Differential expression analysis of scRNA-seq data is central for characterizing how experimental factors affect the distribution of gene expression. However, distinguishing between biological and technical sources of cell-cell variability and assessing the statistical significance of quantitative comparisons between cell groups remains challenging. Here, we introduce memento, a tool designed to address these limitations by providing statistically robust and computationally efficient differential expression analysis of the mean, variability, and gene correlation from scRNA-seq. We applied memento to analyze 70,000 tracheal epithelial cells to identify interferon response genes with distinct variability and correlation patterns, 160,000 T cells perturbed with CRISPR-Cas9 to reconstruct gene-regulatory networks that control T cell activation, 1.2 million PMBCs to map cell-type-specific cis expression quantitative trait loci (eQTLs), and arbitrary cell groups within the entire 50 million cell CELLxGENE Discover data corpus. In all cases, memento identified more significant and reproducible differences in mean expression but also identified differences in variability and gene correlation that suggest distinct transcriptional regulation mechanisms imparted by cytokines, genetic perturbations, and natural genetic variation. These results demonstrate that memento is a first-in-class method for the quantitative analysis of scRNA-seq data, scalable to millions of cells and thousands of samples.

overall_design:
CD4+ T cells were isolated Primary human CD4+ T cells were isolated from peripheral blood mononuclear cells, edited using SLICE protocol and analyzed by scRNA-seq.
Human tracheal epithelial cells were harvested from deceased organ donors according to established protocols (PMID: 1616056), stimulated by 4 different interferons followed by scRNA-seq.


title: Single-cell sequencing of pancreatic tissues of mice with acute pancreatitis under the background of normal diet and high-fat diet was compared

status: Public on Oct 22 2024

city: jinan

first: wang

last: qiang

address: West Wenhua Road.

institute: Qilu Hospital.

summary: Background: Acute pancreatitis (AP) is a common severe digestive disorder, with severity linked to high-fat diets (HFD). HFD may exacerbate AP by promoting inflammation and altering gut microbiota. Astragalus polysaccharides (APS) possess anti-inflammatory properties, but it is unclear if APS supplementation can mitigate HFD's detrimental effects on AP by modulating gut microbiota. This study investigates the mechanisms by which APS improves HFD-induced AP exacerbation. In this study, C57BL/6 mice were fed HFD or a standard diet, with or without APS, for 12 weeks. AP was induced via intraperitoneal caerulein injection. Analyses included ELISA, Western blotting, histology, immunohistochemistry, immunofluorescence, single-cell RNA sequencing (scRNA-seq), 16S rRNA sequencing of gut microbiota, and short-chain fatty acid (SCFA) analysis to evaluate inflammation and cellular changes. Results: HFD significantly increased AP severity, indicated by elevated serum enzyme and pro-inflammatory cytokine levels, along with extensive pancreatic damage. Single-cell RNA sequencing (scRNA-seq) showed a notable rise in ICAM1+ neutrophils and activation of the NF-κB/necroptosis pathway in HAP mice. APS alleviated these effects by decreasing ICAM1+ neutrophil infiltration, downregulating the NF-κB pathway, and reducing necroptosis. Moreover, APS restored gut microbiota balance, significantly boosting Lactobacillus reuteri (L. reuteri) abundance and propionate (PA) levels. Treatments with L. reuteri and PA independently mitigated HFD-induced AP severity, indicating that APS's protective effects are microbiota-dependent. Conclusion: APS improves HFD-induced gut dysbiosis and intestinal barrier dysfunction by enriching L. reuteri and PA, effectively reducing AP exacerbation. Our findings highlight the gut-pancreas axis as a promising target for addressing AP severity.

overall_design: C57BL/6 mice were fed a high-fat diet or a standard diet with or without APS for 12 weeks. Acute pancreatitis was induced by intraperitoneal injection of caerulein (50 ug/kg), once per hour for a total of 12 times. Then, pancreatic tissues from each group were taken out and subjected to 10x single-cell sequencing. The groups included normal control group (NC), acute pancreatitis group induced by normal diet (AP), high-fat diet group (HFD), and acute pancreatitis group induced by high-fat diet (HAP). Astragalus polysaccharides were added or not added to AP mice on a high-fat diet to observe the therapeutic effect of astragalus polysaccharides.

first: Dongbo

last: Xue

first: Qiang

last: Wang