title: Unraveling the Regulatory Impact of LncRNA HNF1AOS1 on Hepatic Homeostasis in Mice

city: Storrs

first: Beshoy

last: Armanios

state: CT

address: 69 N Eagleville Road

institute: University of Connecticut

summary: Abstract: Long noncoding RNAs (lncRNAs) play significant roles in tissue development and disease progression and have emerged as crucial regulators of gene expression. The hepatocyte nuclear factor alpha antisense RNA 1 (HNF1A-AS1) lncRNA is a particularly intriguing regulatory molecule in liver biology that is involved in the regulation of cytochrome P450 enzymes via epigenetic mechanisms. Despite the growing recognition of lncRNAs in liver disease, the comprehensive role of HNF1A-AS1 in liver function remains unclear. This study aimed to investigate the roles of the mouse homolog of the human HNF1A-AS1 lncRNA HNF1A opposite strand 1 (HNF1AOS1) in liver function, gene expression, and cellular pro-cesses using a mouse model to identify potential therapeutic targets for liver disor-ders. Knockdown of HNF1AOS1 was performed in in vitro mouse liver cell line using siRNA and in vivo livers of AAV-shRNA complexes. Changes in the global expression landscapes of mRNA and proteins were revealed using RNA-seq and proteomics, respectively. Changes in the selected genes were further validated by real-time quantitative polymerase chain reaction (RT-qPCR). Phenotypic changes were assessed by histological and absorbance-based assays.  After the knockdown of HNF1AOS1, RNA-seq and proteomics analysis revealed differential gene expression of mRNAs and proteins involved in the processes of molecular transport, liver regeneration, and immune signaling pathways. Downregulation of ABCA1 and SREBF1 in-dicates its role in cholesterol transport and fatty acid and triglyceride synthesis. Additionally, significant reductions in hepatic triglyceride levels were observed in the HNF1AOS1-knockdown group, underscoring its impact on lipid regulation. Notably, the knockdown of HNF1AOS1 also led to an almost complete depletion of CYP7A1, the rate-limiting enzyme in bile acid synthesis, highlighting its role in cholesterol homeostasis and hepatotoxicity. Histological assessments confirmed these molecular findings, with increased hepatic inflammation, hepatocyte swelling, and disrupted liver architecture observed in the HNF1AOS1-knockdown mice. This study illustrated that HNF1AOS1 is a critical regulator of liver health, influencing both lipid metabolism and immune pathways. It maintains hepatic lipid homeostasis, modulates lipid-induced inflammatory responses, and contributes to viral immunity, indirectly affecting glucose and lipid metabolic balance.

overall_design: RNA sequencing of control (rAAV8-Scramble) vs treated (rAAV8-Hnf1aos1) in normal fed C57BL6 mice

first: Jing

last: Jin

first: Ankit

last: Laddha

first: Holly

last: Kolmel

first: Neha

last: Mishra

first: Jose

last: Manoutou

first: Xiaobo

last: Zhong


title: Transcriptomic investigation of differential cellular reprogramming of infected cells by human adenovirus 5 E1A mutants

status: Public on Apr 24 2025

city: Winnipeg

first: Peter

last: Pelka

state: Manitoba

address: 45 Chancellors Cir

department: Microbiology

country: Canada

institute: University of Manitoba

type: Expression profiling by high throughput sequencing

summary: Induction of S-phase is paramount to the replication of most human DNA viruses. Human adenoviruses have evolved sophisticated mechanisms that drive the infected cells into S-phase to ensure that viral genomes are efficiently replicated. We have identified an E1A mutant, E1A289Rdl2-11/YC, that disrupts the canonical means of S-phase induction by E1A. Specifically, this mutant abrogates binding of E1A to the E2F/DP complex as well as to the retinoblastoma protein. Yet, we show that this mutant can still effectively drive the infected cell into S-phase. We explore potential mechanisms of how this occurs via cellular transcriptomic analysis 16 hours after infection. We show that this mutant induces many cell-cycle specific genes to drive S-phase. Interestingly, MYC mRNA is significantly upregulated by this mutant as compared to other viruses investigated. This MYC upregulation, together with normal expression of E4orf6/7 in this mutant, may contribute to efficient S-phase induction. We also demonstrate that this mutant is unable to effectively suppress innate immune response to infection, likely due to loss of p300/CBP binding caused by deletion of E1A residues 2 to 11.

overall_design: RNA-seq of IMR-90 cells, 16 hours post infection, infected by HAdV-C5 and 3 mutants of HAdV-C5, expressing only E1A 289R, only E1A 243R, and a mutated version of E1A 289R.

first: Helwer

last: Rafe

first: Pelka

last: Peter


title: P53 dependent hypusination of eIF5A affects mitochondrial translation and senescence immune surveillance

city: Heidelberg

first: Andres

last: Elia

state: Baden-Württemberg

address: Im Neuenheimer Feld 223

country: Germany

institute: DKFZ

summary: Cellular senescence is characterized by a permanent growth arrest and is associated with tissue aging and cancer. Senescent cells secrete a number of different cytokines referred to as the senescence-associated secretory phenotype (SASP), which impacts the surrounding tissue and immune response. Here, we found that senescent cells exhibit higher rates of protein synthesis compared to proliferating cells and identified eIF5A as a crucial regulator of this process. Polyamine metabolism and hypusination of eIF5A play a pivotal role in sustaining elevated levels of protein synthesis in senescent cells. Mechanistically, we identified a p53-dependent program in senescent cells that maintains hypusination levels of eIF5A. Finally, we demonstrate that functional eIF5A is required for synthesizing mitochondrial ribosomal proteins and monitoring the immune clearance of premalignant senescent cells in vivo. Our findings establish an important role of protein synthesis during cellular senescence and suggest a link between eIF5A, polyamine metabolism and senescence immune surveillance.

overall_design: We performed ribosome profiling in proliferating and oncogene-induced senescent BJ-Ras-ER cells treated either with DMSO or GC7 (10 μM)

first: Xiangli

last: Jiang

first: Ali

last: Baig

first: Giuliana

last: Palazzo

first: Toman

last: Bortecen

first: Sven

last: Groessl

first: Esther

last: Zaal

first: Celia

last: Berkers

first: Cinthia

middle: A

last: Ramirez

first: Alexander

last: Kowar

first: Daniela

last: Aviles-Huerta

first: Wilhelm

last: Palm

first: Jeroen

last: Krijgsveld

first: Darjus

last: Tscharahganeh

first: Rossella

last: Del Pizzo

first: Fabricio

last: Loayza-Puch


title: PRDM16 functions as a co-repressor in the BMP pathway to suppress neural stem cell proliferation

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: BMP signalling acts as an instructive cue in various developmental processes such as tissue patterning, stem cell proliferation, and differentiation. However, it is not fully understood how this signalling pathway generates different cell-specific outputs. Here we have identified PRDM16 as a key co-factor for BMP signalling. PRDM16 contributes to a repressive role of BMP signalling on neural stem cell (NSC) proliferation. We demonstrate that PRDM16 regulates the genomic distribution of BMP pathway transcription factors, the SMAD4/pSMAD complex, preventing the activation of cell proliferation genes. When Prdm16 is lost, the SMAD complex relocates to nearby genomic regions, leading to abnormal upregulation of BMP target genes. This function of PRDM16 is also required for the specification of choroid plexus (ChP) epithelial cells. Through a single-cell resolution fluorescent in situ approach, we have observed that genes co-repressed by SMAD and PRDM16, such as Wnt7b and several cell cycle regulators, become overexpressed in Prdm16 mutant ChP. Our findings elucidate a mechanism through which SMAD4 and pSMAD1/5/8 repress gene expression. Moreover, our study suggests a regulatory circuit composed of BMP and Wnt signaling, along with PRDM16, in controlling stem cell behaviors.

overall_design: To identify BMP and PRDM16 target genes in primary NSCs, we perfomed ChIP-seq for SMAD4, pSMAD1/5/8 and SMAD3 and cut &tag for PRDM16. Cells treated with BMP4 are controled by cells without BMP4. IgG samples in ChIP-seq serve as negative controls, and Input as normalization controls. To measure transcirptional activation status, we perfomed cut&tag for H3K4me3 in Prdm16_expressing, Prdm16_KO cells as well as those treated with BMP4

first: Qi

last: Dai

first: Li

last: He


title: Innate immunity and Nfkb pathway control prostate stem cell plasticity, reprogramming and tumor initiation

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary: Prostate epithelium develops from multipotent stem cells (SCs) which are replaced in adult life by different lineage-restricted basal and luminal unipotent SCs that sustain the homeostasis in a regionalized manner. Deletion of Pten re-induces multipotency in basal cells (BC). However, the molecular mechanisms regulating cell plasticity and tumor initiation are poorly understood. Here, we showed that Pten deletion in BCs led to distinct cell fate reprograming and tumor initiation in a regionalized manner. In anterior and dorsal prostates, BCs were reprogrammed into a Hillock like state that progressed into a basal-luminal hybrid state, which further transitioned into a proximal-like luminal state before progressing to tumorigenesis. In the ventral prostate, BC expressing Nkx3.1 gave rise to distal-like luminal state that are less plastic and progress more slowly to tumorigenesis. Single-cell sequencing and ATAC-seq analysis showed that the reprograming into hillock and proximal states induced activation of the innate immunity pathway during the cellular reprograming and tumor formation. Targeting Il-1, JAK/STAT and Nfkb inhibits Pten-induced cell plasticity and oncogenic reprograming, opening new opportunities in the prevention and treatment of prostate cancer.

overall_design: To unravel the chromatin remodeling and gene regulatory networks associated with oncogenic hits induced BC multipotency in the prostate, we performed bulk ATAC-seq of FACS isolated BCs and LCs from WT mice and BCs 6 weeks following Pten deletion in BC.

first: Chen

last: Jiang

first: Cédric

last: Blanpain


title: The PURB-HOTAIR complex regulates p53-dependent promoter-specific transcriptional activation [RNA-Seq]

city: MANHATTAN

first: Zhangchuan

last: Xia

state: NY

address: 1130 St. Nicholas Ave, Rm 608

department: Institute for Cancer Genetics

country: USA

institute: Columbia University Medical Center

summary: p53 executes its diverse functions through different transcriptional targets but the precise mechanism of promoter-specific regulation by p53 remains largely unknown. Through biochemical purification, we identify purine-rich element binding protein B (PURB), a dual DNA/RNA-binding protein, which acts as a transcriptional corepressor for p53 in a manner dependent on p53 acetylation status. PURB is overexpressed in human cancers, and its knockdown induces p53-dependent activation of p21 but has no effect on other major promoters such as PUMA and MDM2. In contrast to other p53 corepressors, PURB can recognize a unique DNA element at the p21 promoter, with the loss of this element not affecting p53-mediated transactivation but abrogating the ability of p53 to recruit PURB to the p21 promoter for repression. Mechanistically, PURB requires its sequence-specific binding with long noncoding RNA (lncRNA) HOX transcript antisense RNA (HOTAIR) to exert its repressive role. In turn, HOTAIR interacts directly with EZH2 and, bridged by the PURB-HOTAIR complex, p53 can recruit the EZH2 histone methyltransferase to target promoters for transcriptional repression. Further analysis of p53 targets reveals several promoters that may serve as targets for PURB binding, suggesting that this mechanism of PURB-dependent promoter-specific regulation may not be limited to p21. These data establish a mode of lncRNA-mediated regulation of p53 transcription in a sequence-specific manner and reveal a previously unanticipated mechanism for acetylation-mediated promoter-specific regulation through a cis-regulatory element recognized by the PURB-HOTAIR complex.

overall_design: RNA-seq profiling of Control (sh-NC) U2OS cells and U2OS cells with inducible PURB knockdown (sh-PURB) for 72h.

first: Wei

last: Gu

first: Ning

last: Kon

first: Zhenyi

last: Su

first: Jingjie

last: Yi

first: Xu

last: Hua

first: Hui

last: Zhou

first: Zhiguo

last: Zhang


title: Longitudinally stable T cell and innate immune activity distinguish healthy adult immunotypes I

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Using cytometric, proteomic, and transcriptomic longitudinal data derived from whole blood, we identified four robust longitudinally stable immunotypes associated with innate immune activation and T-cell function in healthy adults.

overall_design: We enrolled and comprehensively phenotyped a cohort of 100 healthy adults aged 25-35 and 55-65 years who were longitudinally followed for 10 visits over 2 years. Using mass cytometry features that remain stable within - but differ between – individuals, we identified four stable immunotypes. We characterized these immunotypes using whole blood RNA sequencing, Olink proteomic profiling, and whole blood ex vivo stimulation.

first: Megan

middle: E

last: Smithmyer

first: Alex

last: Hu

first: Matthew

middle: J

last: Dufort

first: Anne

middle: M

last: Hocking

first: Alice

last: Wiedeman

first: Kayla

last: Fasano

first: Troy

middle: R

last: Torgerson

first: Kxiaojun

last: Li

first: Qiuyu

last: Gong

first: S. Alice

last: Long

first: Adam

last: Lacy-Hulbert

first: Claire

last: Gustafson

first: Jane

middle: H

last: Buckner

first: Cate

last: Speake


title: Longitudinally stable T cell and innate immune activity distinguish healthy adult immunotypes [II]


title: Longitudinally stable T cell and innate immune activity distinguish healthy adult immunotypes

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

overall_design: Refer to individual Series


title: Clemastine fumarate accelerates accumulation of disability in progressive multiple sclerosis by enhancing pyroptosis.

city: Bethesda

first: Bibi

last: Bielekova

state: MD

address: 10 Center Dr, Bethesda

institute: NIH

summary:
Multiple sclerosis (MS) is an immune-mediated demyelinating disease of the central nervous system (CNS). Clemastine fumarate, the over-the-counter antihistamine and muscarinic receptor blocker, has remyelinating potential in MS. A clemastine arm was added to an ongoing platform clinical trial TRAP-MS (NCT03109288) to identify a cerebrospinal fluid (CSF) remyelination signature and to collect safety data on clemastine in patients progressing independently of relapse activity (PIRA). The clemastine arm was stopped per protocol-defined criteria when 3/9 patients triggered individual safety stopping criteria (χ2 p=0.00015 compared to remaining TRAP-MS treatments). Clemastine treated patients had significantly higher treatment-induced disability progression slopes compared to remaining TRAP-MS participants (p=0.0075). Quantification of ~7000 proteins in CSF samples collected before and after clemastine treatment showed significant increase in purinergic signaling and pyroptosis. Mechanistic studies showed that clemastine with sub-lytic doses of extracellular ATP activates inflammasome and induces pyroptotic cell death in macrophages. Antagonist of the purinergic channel P2RX7 that is strongly expressed in oligodendrocytes and myeloid cells, blocked these toxic effects of clemastine. To further confirm our results, we performed the bulk RNA-seq analysis of primary human macrophages (MDMs) and THP-1 cells to identify signaling pathways affected by clemastine (+ATP) stimulation. Ingenuity Pathway Analysis (IPA) predicted
inflammasome activation, pyroptosis, and immunogenic cell death as pathways affected by ATP+CLM treatment.

overall_design: For bulk RNA-seq, the cells were primed with 200 ng/mL of LPS overnight and then stimulated either with medium + DMSO (Ctrl) or 2 mM ATP +/- 10 µg/mL CLM for 3 h or 6h. For each drug condition, we sequenced the following samples (n=3): MDMs incubated with drugs for 3h, MDMs incubated with drugs for 6h, THP-1 cells incubated with drugs for 3 h.


first: Yura

last: Song

overall_design: As Rapamycin treatment strongly inhibits the activation of BC multipotency and the initiation of prostate tumorigenesis, we performed bulk-RNAseq in BCs 3 weeks following Pten deletion and PI3K activation to further investigate the mechanisms that lead to the cell fate changes

first: Chen

last: Jiang

first: Cédric

last: Blanpain


overall_design: To define the molecular mechanisms associated with the basal to luminal transition that accompanies prostate tumorigenesis, we performed single-cell RNAseq (scRNA-seq) following Pten deletion. We FACS isolated epithelial cells in WT mice，YFP+ epithelial cells 6 weeks and 10 months following TAM administration in K5CreER/Ptenfl/fl/Rosa-YFP and performed 10x chromium scRNA-seq.


title: RNA-seq analysis in hepatocyte-specific Atg7-knockout mice with different p62 mutations [RNA-seq_T352A]

city: Tokyo

first: Keiko

last: Kan-O

address: Kawadacho 8-1, Shinjuku-ku

department: Department of Respiratory Medicine

country: Japan

institute: Tokyo Women's Medical University

summary: To investigate global proteome changes dependent on on KEAP1-p62 binding in vivo

overall_design: We performed cytoplasmic proteome profiling.

first: Nozomi

last: Shinomiya

first: Masaaki

last: Komatsu

first: Tomoaki

last: Koga


overall_design: To investigate the molecular mechanisms that lead to the cell fate changes upon Pten deletion in BC, we performed bulk RNA-seq of FACS isolated BC and LC in WT mice and 5 weeks following Pten deletion in BC.


title: Effect of EZH2 inhibition and CART19 on gene expression of B-NHL cell lines (OCI-ly18 and SU-DHL-4)

city: Philadelphia

first: Marco

last: Ruella

state: PA

address: 3400 Civic Center Blv

department: Center for Cellular Immunotherapies

institute: University of Pennsylvania

summary: The goas of this experiment were: 1) to assess the effect of tazemetostat on B-NHL tumor cells lines; 2) to assess the effect of CART19 killing on B-NHL tumor cells lines;  3) to assess the effect of combining tazemetostat/CART19 on B-NHL tumor cells lines.

overall_design: OCI-ly18-GFP+ or SU-DHL-4-GFP+ were pre-treated for 3 days with tazemetostat (500 nM); killing assay was performed by adding CART19 vs UTD cells (+/- tazemetostat). After 48 hours, tumor cells were sorted from 4 experimental conditions (UTD-DMSO, UTD-TAZ, CART19-DMSO, CART19-TAZ) and RNA was extracted for bulk RNA sequencing.

first: Patrizia

last: Porazzi

first: Siena

last: Nason

first: Linhui

last: Chen

first: Ruchi

last: Patel

first: Ivan

last: Cohen


title: Isoform characterization of m6A in single cells identifies its role in RNA surveillance [Direct RNA-seq for SMG1i treated]

city: GuangZhou

first: Zhijun

last: Ren

address: Sun Yat-sen University

country: China

institute: Sun Yat-sen University

summary: The distribution of m6A across various RNA isoforms and its heterogeneity within single cells are still not well understood. Here, we develop m6A-isoSC-seq, which employs both Oxford Nanopore long-read and Illumina short-read sequencing on the same 10x Genomics single-cell cDNA library with APOBEC1-YTH induced C-to-U mutations near m6A sites. Through m6A-isoSC-seq on a pooled sample of three cell line origins, we unveil a profound degree of m6A heterogeneity at both the isoform and single-cell levels. Through comparisons across single cells, we identify widespread specific m6A methylation on certain RNA isoforms, usually those mis-processed RNA isoforms. Compared to the coding isoforms of the same genes, the expression of highly methylated misprocessed RNA isoforms is more sensitive to METTL3 depletion. These mis-processed RNAs tend to have excessive m6A sites in coding regions, which are targets of CDS-m6A decay (CMD). This study offers undocumented insights into the role of m6A on RNA surveillance.

overall_design: For NMD pathway inhibition, approximately 1 × 10^7 HEK293T cells were treated with either DMSO (Sigma-Aldrich, #D2650) or 300 nM of the small molecule NMD inhibitor SMG1i (compound 11j, MedChemExpress, #HY-124719) for 4 h prior to cell harvest.

first: Xiang

last: Huang

first: Jinkai

last: Wang


title: Isoform characterization of m6A in single cells identifies its role in RNA surveillance [m6A-isoSC-seq(nanopore)]

overall_design:
The pcDNA3.1-YTH-APOBEC-T2A-EGFP construct was transfected into HEK293T cells, HepG2 cells, and HeLa cells, respectively, using Lipofiter 3.0 (Hanbio) according to the manufacturer's instructions. The medium was refreshed 6 hours after transfection, and the EGFP-positive cells of the three cell lines were isolated, respectively, through cytometry 3 day after transfection.
The EGFP-positive HEK293T, HepG2, and HeLa cells were mixed together in a 1700:1700:1700 ratio and then isolated to create cell suspension. The mixed single-cell suspension was utilized to generate a barcoded single-cell RNA-seq library using the 10x Genomics 3’ gene expression kit (v3) following the recommended protocol provided by the manufacturer. The other half of the full-length cDNA generated from 10x Genomics was amplified by five cycles of PCR with TruSeq read 1 forward primer 5′-NNN CTA CAC GAC GCT CTT CCG ATC T-3′ and 3′ partial TSO reverse primer 5′-NNN AAG CAG TGG TAT CAA CGC AGA GTA CAT-3′ for Nanopore sequencing. After that, amplified full-length cDNA was treated with 0.55x SPRIselect to remove PCR primers and the cDNAs with lengths shorter than 1000bp. The purified cDNA reagent into a final elution of 51 µL in Buffer EB to allow for adequate template/volume for the necessary assessment of quality control (QC) metrics and PromethION library preparation. Single cell nanopore sequencing library was prepared with the Oxford Nanopore LSK-110 kit (PCR free) and sequenced on PromethION following the manufacturer’s instructions to generated 339 million long reads derived from about 5000 cells.


title: Combined therapy with DR5- targeting antibody-drug conjugate and CDK inhibitors as a novel strategy for advanced MSS and MSI-H colorectal cancer

city: Ganzhou

first: zhou

last: dongdong

address: hexie avenue

institute: Gannan Medical University

summary: Targeted therapies for advanced microsatellite stable (MSS) subtypes of colorectal cancer (CRC) continue to present significant clinical challenges. Death receptor 5 (DR5/TRAIL-R2) is an apoptotic receptor frequently overexpressed in various cancers. Evidence suggests that DR5-targeting antibody drug conjugates (ADC) show promising efficacy in several cancers. In this study, we demonstrated DR5 as a clinically significant target for CRC by analyzing tissue microarrays from advanced CRC cohorts (473 MSS cases and 36 MSI-H cases), as well as data from a TCGA cohort comprising 418 cases. Our novel clinical-stage DR5-targeting ADC, Oba01, designed to deliver the microtubule-disrupting agent MMAE, shows superior therapeutic efficacy across various CRC cell lines, patient-derived xenografts (PDXs), and corresponding organoids (PDXOs), regardless of their MSS or MSI-H status. Importantly, our functional RNAseq and proteomic analysis of the impact of Oba01 on global gene expression revealed that the cell cycle pathway and cyclin-dependent kinases (CDKs) are mechanistically synergistic targets of the drug's effects. Supporting this idea, we presented solid evidence to show Oba01 and abemaciclib, a FDA-approved CDK4/6 inhibitor for metastatic breast cancer, substantially synergize across various clinically relevant models derived from advanced CRC patients with both MSS and MSI-H status, in both in vitro and in vivo settings. The fact that this synergy spans multiple CDK inhibitors further highlights the potential of combining DR5-mediated delivery of MMAE with CDK inhibition as a novel therapeutic strategy for advanced CRC patients, especially those with the challenging to treat MSS subtype.

first: Dongdong

last: Zhou

first: Er’jiang

last: Tang

first: Wenjun

first: Youban

last: Xiao


title: Isoform characterization of m6A in single cells identifies its role in RNA surveillance [m6A-isoSC-seq (Illumina)]

overall_design:
The pcDNA3.1-YTH-APOBEC-T2A-EGFP construct was transfected into HEK293T cells, HepG2 cells, and HeLa cells, respectively, using Lipofiter 3.0 (Hanbio) according to the manufacturer's instructions. The medium was refreshed 6 hours after transfection, and the EGFP-positive cells of the three cell lines were isolated, respectively, through cytometry 3 day after transfection.
The EGFP-positive HEK293T, HepG2, and HeLa cells were mixed together in a 1700:1700:1700 ratio and then isolated to create cell suspension. The mixed single-cell suspension was utilized to generate a barcoded single-cell RNA-seq library using the 10x Genomics 3’ gene expression kit (v3) following the recommended protocol provided by the manufacturer. Half of the amplified cDNA was employed for short-read sequence library preparation following the 10x Genomics protocol and sequenced on an Illumina NovaSeq 6000 sequencing system to generate 310 million 150 bp paired-end reads.


title: Isoform characterization of m6A in single cells identifies its role in RNA surveillance [eDART-Seq]

overall_design:
The pcDNA3.1-YTH-APOBEC-T2A-EGFP construct was transfected into HEK293T cells, HepG2 cells, and HeLa cells, respectively, using Lipofiter 3.0 (Hanbio) according to the manufacturer's instructions. The medium was refreshed 6 hours after transfection, and the EGFP-positive cells of the three cell lines were isolated, respectively, through cytometry 3 day after transfection.
Then, the total RNA of pcDNA3.1-YTH-APOBEC-T2A-EGFP transfected HEK293T, HeLa and HepG2 was harvested using Trizol (Invitrogen) followed by treatment with RNase-Free DNase (NEB) to remove possible DNA contamination, respectively. RNA-seq libraries were prepared with Dynabeads mRNA Purification Kit (Ambion) and TruSeq Stranded mRNA Library Prep Kit (Illumina). Sequencing was performed with Illumina HiSeq 2000 to generate about 55 million strand-specific 150 bp paired-end reads for each cell line.


title: Epigenomic disorder and partial EMT impair luminal progenitor integrity in Brca1-associated breast tumorigenesis

status: Public on Apr 23 2025

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

summary: In breast cancer related to the BRCA1 mutation, luminal progenitor cells are believed to be the cells of origin, yet how these cells transform into invasive cancer cells remain poorly understood. Here, we combine single-cell epigenomic and transcriptomic data to reconstitute sequences of events in luminal cells that lead to tumorigenesis. Upon deletion of Trp53 and Brca1, we find that luminal progenitors display an extensive epigenomic disorder associated with a loss of cell identity. These cells then progress to tumor formation through a partial epithelial-to-mesenchymal transition, orchestrated by Snail and the timely activation of immunosuppressive and FGF signaling with their microenvironment. In human samples, pre-tumoral changes can be detected in early stage, basal-like tumors, which rarely recur, as well as in normal-like mammary glands of BRCA1 mutation carriers who have had cancer. Our study fills critical gaps in our understanding of BRCA1-driven tumorigenesis, opening perspectives for the early monitoring of individuals with high cancer risk.

overall_design: snCUT&Tag was adapted from  Cusanovic et al. 2021. All washes were made with 500 µL unless otherwise stated and all centrifugations were done using a swinging bucket centrifuge at 1300g for 4 min at 4°C for nuclei preparation, or 600g for 8 min at 4°C for the subsequent steps. Nuclei were extracted from 1-2 million cells for 10 min on ice in 6 mL ice-cold NE1 buffer (20 mM HEPES pH7.2, KCl 10 mM, spermidine 0.5 mM, glycerol 20%, BSA 1%, NP-40 0.1%, digitonin 0.01%, proteases inhibitor 1x). Nuclei were filtered with a 30 uM cell strainer, washed in 6 mL PBS + BSA 1% and resuspended in Dig-Wash buffer (20 mM HEPES pH7.2, NaCl 150 mM, spermidine 0.5 mM, BSA 1%, NP-40 0.01%, digitonin 0.01%, proteases inhibitor 1x), checked under microscope and counted with 4,6-diamidino-2-phenylindole (DAPI) staining. 50,000 to 100,000 nuclei were resuspended in 50uL antibody buffer (EDTA 2 mM, 20 mM HEPES pH7.2, NaCl 150 mM, spermidine 0.5 mM, BSA 1%, NP-40 0.01%, digitonin 0.01%, proteases inhibitor 1x) with 1:50 antibody (Anti-H3K4me1 #5326 D1A9, Cell Signaling) and incubated overnight at 4°C with rotation. Next day, nuclei were washed with Dig-Wash buffer and resuspended in 100uL Dig-300 buffer (20 mM HEPES pH7.2, NaCl 300 mM, spermidine 0.5 mM, BSA 1%, NP-40 0.01%, digitonin 0.01) with the proteinA-Tn5 fusion (Diagenode, #C01070001, 1:250) and incubated for 1 h at room temperature with rotation. Then, nuclei were washed three times with Dig-300 buffer, resuspended in 300 µL Tag-Buffer (20 mM HEPES pH7.2, NaCl 300mM, spermidine 0.5mM, BSA 1%, NP-40 0.01%, digitonin 0.01%, MgCl2 10 mM) and incubated for 1 h at 37°C. Tagmentation was stopped by addition of one volume of 1x Diluted Nuclei Buffer (DNB, 10X Genomics) supplemented with 2% BSA, 12.5 mM EDTA. The nuclei were then centrifuged at 1300g, 4 min at 4°C and washed twice with 200 µL 1x DNB supplemented with 2% BSA. The nuclei were resuspended in 10-70 µl of DNB + 2% BSA. If the sample did not show nuclei aggregates, nuclei were loaded on a 10x Chromium system using 10x Chromium Single Cell ATAC–Seq kit v2 (10X Genomics) as described16. Final library amplification with 15 PCR cycles was performed according to the Chromium Single Cell ATAC Library kit manual. snCUT&Tag libraries were sequenced on a NovaSeq 6000 (Illumina) in PE50 mode.

first: Camille

last: Landragin

first: Melissa

last: Saichi

first: Marthe

last: Laisné

first: Adeline

last: Durand


title: Isoform characterization of m6A in single cells identifies its role in RNA surveillance


title: Epigenomic Profiling of H3K4me2 and H3K4me3 in Patient-Derived NPCs to Study L2HGDH Deficiency

city: Dallas

first: Wen

last: Gu

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed to investigate the epigenetic landscape in neural progenitor cells (NPCs) derived from L2HGA patient iPSCs with or without correction of the pathogenic L2HGDH variant. We profiled histone modifications H3K4me2 and H3K4me3 as well as input control across four conditions: unedited Patient 1 NPCs, corrected Patient 1 NPCs, corrected NPCs treated with DMSO, and corrected NPCs treated with the KDM5 inhibitor C70. This dataset provides insight into enhancer and promoter activity at the MYC locus and genome-wide effects of L-2HG-associated epigenetic dysregulation.

overall_design: The study includes ChIP-seq analysis of 12 samples: three biological replicates each for input, H3K4me2, and H3K4me3 across four treatment groups—unedited NPCs, corrected NPCs, corrected NPCs + DMSO, and corrected NPCs + KDM5-C70. Immunoprecipitated DNA was sequenced on an Illumina platform. Peaks were called and differential enrichment analysis was performed to identify epigenetically dysregulated loci associated with L-2HG metabolism.

first: Ralph

last: DeBerardinis


title: Overexpressing NEGR1 gene in mice brain induces anxiety or depression-like phenotypes and synaptic dysfunction

city: Kunming

first: Ming

last: Li

state: Yunnan

address: NO 32 Jiao-Chang Donglu

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

summary: Single nucleotide polymorphisms (SNPs) within 1p31.1 region have been identified as significant genetic variations associated with depression, and our prior functional genomics pinpointed a regulatory variant rs3101339 among them. However, its precise roles in depression pathogenesis remains elusive. In this study, we employed series analytical and functional approaches, including regulatory element annotation, brain expression quantitative trait loci (eQTL), reporter gene assay, electrophoretic mobility shift assay (EMSA), and precision gene editing. Our results confirmed that rs3101339 is a causal variant within 1p31.1 with its risk allele C upregulating NEGR1 expression. To further investigate the consequences of NEGR1 upregulation, we overexpressed NEGR1 in specific region of the mouse brain (including medial prefrontal cortex (mPFC) and ventral hippocampus (vHIP)) using stereotaxic injection. Behavioral assessments revealed that elevated NEGR1 levels in the brain, particularly in the vHIP, results in working memory impairing and anxiety- and depression-like behaviors in mice. Neuronal sparse labeling assays and electron microscopy revealed that NEGR1 overexpressing in the vHIP leads to neural spine loss and synaptic ultrastructure abnormality. Immunoprecipitation-mass spectrometry (IP-MS) further identified 67 high-confidence proteins that interact with NEGR1, many of them are involved in neurotransmitter exocytosis and synaptic vesicle endocytosis. Notably, Snap25 emerged as a potential central hub within this protein-protein interaction network. Transcriptomic profiling revealed 94 differentially expressed genes in NEGR1-OE (vHIP) mice compared to control mice (P adj < 0.05). These genes were enriched in myelination-related signaling pathways (such as myelination, ensheathment of neurons, axon ensheathment in central nervous system, etc.). Moreover, several myelination-related genes, such as Itgax, Itgb4, Mag, Mbp, Sox10, Bcas1, Trf, Slc8a3, Myrf, and Plp1, were downregulated in NEGR1-OE (vHIP) mice. Together, our findings implicated that the overexpression of the NEGR1 gene in the mouse brain as a potential driver of anxiety- or depression-like phenotypes potentially through impairing synaptic function and myelination.

overall_design: To investigate the function of NEGR1 in working memory impairing and anxiety- and depression-like behaviors in mice, we procured the ventral hippocampus tissues from three control mice and three NEGR1 overexpression mice. Subsequently, we conducted a comprehensive gene expression profiling analysis, leveraging the data derived from RNA sequencing (RNA-seq) of these tissues. Comparative gene expression profiling analysis of RNA-seq data for control mice and NEGR1 overexpression mice.

first: Ya-Qi

last: Zhang

first: Qing

first: Yi

last: Yang

first: Li-Li

last: Yu

first: Shi-Wu

first: Yong-Bo

last: Guo


title: Transcriptomic profiling of L2HGDH-deficient and corrected human neural progenitor cells and neurons

summary: L-2-hydroxyglutaric aciduria (L-2HGA) is a neurometabolic disorder caused by mutations in the L2HGDH gene, leading to accumulation of L-2-hydroxyglutarate (L-2HG). To investigate the molecular impact of L2HGDH deficiency, we performed bulk RNA sequencing on neural progenitor cells (NPCs) and neurons derived from patient iPSCs with or without correction of the pathogenic L2HGDH variant. This dataset provides transcriptomic insights into the role of L-2HG in neurodevelopmental processes and offers a resource for exploring gene expression changes associated with L-2HGA.

overall_design: Neural progenitor cells (NPCs) and neurons were derived from induced pluripotent stem cells (iPSCs) of a patient with L2HGDH deficiency, either unedited or corrected by CRISPR/Cas9-mediated genome editing. Bulk RNA-seq was performed on biological triplicates of unedited and corrected NPCs and neurons.


title: A role of Hdac1 in fate decision to exhausted CD8+ T cells in response to chronic viral infection

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

summary: The goal of this study is to determine how an epigenetic regulator, Hdac1, mediates control of exhausted CD8 T cell fate decision and differentiation at the early stage of responses to chronic viral infection.

overall_design: Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) was performed on sort-purified GP33-tetramer+ CD8+ T cells on day 8 post-infection with LCMV clone 13.

first: Hu

last: Wei

last: Sheng'en

first: Zang

last: Chongzhi

first: Xue

last: Hai-Hui


title: A core stemness program in exhausted CD8+ T cells

city: Beijing

first: Min

last: Peng

address: Haidian

institute: Tsinghua university


title: The transcriptome of playfulness is sex-biased in the juvenile rat medial amygdala: a role for inhibitory neurons

city: Baltimore

first: Mahashweta

last: Basu

address: 670 W. Baltimore Street

institute: Institute for Genome Sciences

summary: Social play is a well-conserved, dynamic behavior known to be sexually differentiated. In most species, males play more than females, a sex difference largely driven by the medial amygdala (MeA) yet the full mechanism establishing this bias is unknown. Here, we explore “the transcriptome of playfulness” in both sexes for the first time, demonstrating that the transcriptomic profile in the juvenile rat MeA associated with playfulness is markedly distinct in males and females. Parallel single-cell RNA-sequencing experiments from newborn rats suggest that inhibitory neurons drive this sex difference. Furthermore, we show that inhibitory neurons comprise the majority of play-active cells in the juvenile MeA, with males having more play-active cells than females, of which a greater proportion are GABAergic. Through integrative bioinformatic analyses, we further explore the expression, function, and cell-type specificity of key play-associated gene modules, providing valuable insight into the sex-biased mechanisms underlying this fundamental social behavior.

overall_design: In this study, we generated bulk RNA-seq data from the amygdala of P30 (30 days of age; juvenile) high- and low-playing male and female rats. Playfulness was assessed once daily from P26-29, and animals that exhibited an average play score that was in the top third per sex (n=6 per group) were sacrificed, amygdalas dissected, and sequenced using RNA-seq. MHI = male high-players; MLO = male low-players; FHI = female high-players; FLO = female low-players

first: Ashley

last: Marquardt

first: Jonathan

middle: W

last: VanRyzin

first: Seth

last: Ament

first: Margaret

last: McCarthy


title: Effect of overexpression of Empty or POU2F2 on gene expression in P14 CD8 T cells at single cell level [scRNA-seq II]

summary: In chronic viral infections, sustained CD8+ T cell response relies on TCF1+ precursor exhausted T cells (TPEX) exhibiting stem-like properties. TPEX self-renew and respond to PD-1 blockade, underscoring their paramount importance. However, strategies for effectively augmenting TPEX remain limited. Here, we demonstrate that ZC3H12A deficiency initiates a stemness program in TPEX but also increases cell death, whereas BCOR deficiency predominantly promotes TPEX proliferation. Consequently, co-targeting of both BCOR and ZC3H12A imparts exceptional stemness and functionality to TPEX, thereby enhancing viral control. Mechanistically, BCOR and ZC3H12A collaboratively suppress a core stemness program in TPEX characterized by heightened expression of approximately 216 factors. While TCF1 plays a role, this core stemness program relies on novel factors, including PDZK1IP1, IFIT3, PIM2, LTB, and POU2F2. Crucially, overexpressing POU2F2 robustly boosts TPEX and enhances antiviral immunity. Thus, a core stemness program exists in exhausted T cells, jointly repressed by BCOR and ZC3H12A, robustly controlling TPEX differentiation and providing new targets for addressing T cell exhaustion.

overall_design: scRNA-seq profiling of Empty or POU2F2 OE P14 CD8 T cells isolated from spleen of chronically infected mice on day14 post LCMV Clone 13 infection

first: Jing

last: Xu

first: Zeran

last: Jia

first: Xiaocui

last: Zhao

first: Lixia

last: Wang

first: Gang

last: Jin

first: Zhuoyang

last: Yin

first: Yinqing


title: Effect of depletion of Bcor, Zc3h12a or both on gene expression of P14 CD8 T cells at single cell level [scRNA-seq]

overall_design: scRNA-seq profiling of WT, Bcor KO, Zc3h12a KO and Bcor/Zc3h12a DKO P14 CD8 T cells isolated from spleen of chronically infected mice on day14 post LCMV Clone 13 infection

last: Li


title: Effect of depletion of Bcor, Zc3h12a or both on chromatin accessibility of P14 CD8 T cells at single cell level [scATAC-seq]

overall_design: scATAC-seq profiling of WT, Bcor KO, Zc3h12a KO and Bcor/Zc3h12a DKO P14 CD8 T cells isolated from spleen of chronically infected mice on day14 post LCMV Clone 13 infection


title: Exercise improves age-related osteoporosis and cognitive impairment by regulating osteoblast-to-osteocyte transition

city: Shanghai

first: Kai

last: Yang

address: 197 Ruijin 2nd Road, Shanghai, 200025, China

department: Shanghai Institute of Traumatology and Orthopedics

institute: Shanghai Jiao Tong University School of Medicine

summary: To validate the protection effect of physical exercises on age-related cognitive impairment, aged male C57BL/6J mice (12 months old, 12M) were subjected to treadmill running or standard housing for 4 weeks, and comparing with young (2 months old, 2M) male mice.

overall_design:
For bone tissues, after collagenase A digestion for discarding the periosteum, the long bones are sagittal split apart followed by removing the bone marrow by extremely washing. All the bone species are subjected to mRNA isolation and bulk RNA-seq analysis.
Comparative gene expression profilling analysis of RNA-seq data between 2M mice and 12M mice, or housing 12M mice and exercised 12M mcie.

first: Rong

last: Zhou

first: Wei

last: Yan

first: Yuxin

last: Zhang

first: Jiahui

first: Yichen

first: Ruonan

last: Ning

last: Jiang

first: Lianfu

last: Deng


title: Effect of depletion of Bcor, Zc3h12a or both on chromatin accessibility of P14 CD8 T cells [ATAC-seq]

first: Min

last: Peng

overall_design: ATAC-seq profiling of WT, Bcor KO, Zc3h12a KO and Bcor/Zc3h12a DKO P14 CD8 T cells isolated from spleen of chronically infected mice on day14 post LCMV Clone 13 infection


title: Effect of depletion of Bcor, Zc3h12a or both on gene expression of P14 CD8 T cells [RNA-seq]

overall_design: RNA-seq profiling of WT, Bcor KO, Zc3h12a KO and Bcor/Zc3h12a DKO P14 CD8 T cells isolated from spleen of chronically infected mice on day14 post LCMV Clone 13 infection


title: IκBζ-dependent responses in keratinocytes upon Staphylococcus aureus infection

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: In this study we investigated the transcriptional responses of keratinocyte-derived IκBζ (encoded by NFKBIZ) upon infection with the pathogenic Staphylococcus aureus (S. aureus) USA300 wildtype strain.

overall_design: Primary human keratinocytes were obtained from foreskin. Ctrl and lentiviral NFKBIZ knockdown cells  were either treated with S. aureus or murmamyl-dipeptide (MDP) in vitro. Gene expression profile analysis was conducted using data obtained from n=3 RNA samples of each cell line and treatment condition.

first: Berenice

last: Fischer

first: Daniela

last: Kramer


title: Single-cell sequencing across radiation treatment timepoints in head and neck cancer

city: Milwaukee

first: Joseph

last: Zenga

state: WI

address: 9200 W WISCONSIN AVE

institute: MEDICAL COLLEGE OF WISCONSIN

type: Genome variation profiling by high throughput sequencing

summary: We performed single cell sequencing across treatment timepoints to evaluate the immunological impact of radiation in head and neck cancer.

overall_design: Enrolled patients underwent biopsy followed by 4.6Gy x 10 fractions, immediately followed by a biopsy, and then a third biopsy at approximately 6 weeks later at the time of surgery. All biopsies underwent single-cell RNA and TCR sequencing.

first: Heather

last: Himburg

first: Musaddiq

last: Awan


title: H2A.Z regulates transcription, oocyte maturation and female fertility in mouse [ChIP-seq]

first: Yu

address: 138 Yi Xue Yuan Road

institute: Fudan university

summary: Histone variants differ from canonical histones in their ability to be incorporated into chromatin independently of S-phase. H2A.Z is an evolutionarily conserved histone variant that plays critical roles in transcription regulation. However, its roles during mammalian oogenesis, a unique developmental stage marked by dynamic transcription activity without DNA replication, remain elusive. In this study, we demonstrated that oocyte-specific depletion of H2A.Z results in profound epigenetic and transcriptional alterations, impeding oocyte meiosis II resumption in mice, causing female infertility. Mechanistically, H2A.Z in mouse oocytes is enriched at active promoters and enhancers. Interestingly, H2A.Z is depleted from CG-rich silenced promoters in fully-grown oocytes (FGOs), unlike that in growing oocytes, early embryos and mESCs. In FGOs, the presence of H2A.Z correlates with H3K27ac, except in regions with DNA methylation and H3K36me3. Depletion of H2A.Z leads to partial loss of H3K27ac at both promoters and enhancers, correlated with impaired gene expression. Consistent with a role in gene activation, H2A.Z in FGOs is widely acetylated at the promoters and enhancers. Together, our findings uncover an essential role of H2A.Z in oocyte maturation and activation of cis-regulatory elements.

overall_design: STAR ChIP-seq for H2A.Z, H2A.Zac, H3K4me3, H3K27ac, H3K27me3 were applied on mouse oocytes and cell line

first: Qianhua

last: Xu

first: Chunyi

last: Huang

last: Xie


title: Immuno-metabolic stress responses control longevity from mitochondrial translation inhibition.

city: Amsterdam

first: Man

middle: Iman

last: Hu

address: Meibergdreef 9

department: Laboratory Genetic Metabolic Diseases

country: Netherlands

institute: Amsterdam UMC Location University of Amsterdam

summary: Perturbing mitochondrial translation represents a conserved longevity intervention, with proteostasis processes proposed to mediate the resulting lifespan extension. Apart from the proteostasis response, whether and how other mechanisms contribute to lifespan extension upon mitochondrial translation inhibition is underexplored. Using multi-omics and functional in vivo screening, we identified the ethylmalonyl-CoA decarboxylase orthologue C32E8.9 in C. elegans as essential for mitochondrial translation inhibition-induced longevity. Reducing C32E8.9 completely abolishes lifespan extension from mitochondrial translation inhibition while mitochondrial unfolded protein response activation is unaffected. We show that C32E8.9 mediates immune responses and lipid remodeling, which play crucial roles in the observed lifespan extension. Additionally, we discovered that sma-4 (a TGF-β co-transcription factor) serves as an effector of C32E8.9, responsible for the immune response triggered by mitochondrial translation inhibition. Collectively, these ﬁndings underline the importance of the “immuno-metabolic stress responses” in longevity upon mitochondrial translation inhibition and identify C32E8.9 as a central factor orchestrating these responses.

overall_design: N2 worms were synchronized and treated with RNAi bacteria ( HT115, mrps-5, C32E8.9, mrps-5 + C32E8.9 ) from the L1 stage. Day 5 adult animals were harvested by washing three times with M9 buffer and two times with water before being snap-frozen in liquid nitrogen. ~1000 worms for each sample. 6 replicates per condition.

first: Iman

first: Marte

last: Molenaars

first: Yorrick

last: Jaspers

first: Bauke

middle: V

last: Schomakers

first: Michel

last: van Weeghel

first: Amber

last: Bakker

first: Melanie

last: Modder

middle: P

last: Dewulf

first: Guido

middle: T

last: Bommer

first: Arwen

last: Gao

first: Georges

last: Janssens

first: Riekelt

last: Houtkooper


title: DNA methylation in frontal cortex of Setd1a haploinsufficient mice

status: Public on Apr 22 2025

city: Exeter

first: Nicholas

last: Clifton

address: RILD Building

country: United Kingdom

institute: University of Exeter

type: Methylation profiling by genome tiling array

summary: SETD1A, a histone methyltransferase, is implicated in schizophrenia through rare loss-of-function mutations. While SETD1A regulates gene expression via histone H3K4 methylation, its influence on broader epigenetic dysregulation remains incompletely understood. We explored the hypothesis that SETD1A haploinsufficiency contributes to neurodevelopmental disruptions associated with schizophrenia risk via alterations in DNA methylation. We profiled DNA methylation in the frontal cortex of Setd1a+/- mice across prenatal and postnatal development using Illumina Mouse Methylation arrays. Differentially methylated positions and regions were identified, and their functional relevance examined through gene and biological annotation. We integrated these findings with transcriptomic and proteomics datasets, and assessed mitochondrial complex I activity to explore potential downstream functional effects. Setd1a haploinsufficiency resulted in widespread hypomethylation of genes related to ribosomal function and RNA processing that persisted across all developmental stages. Setd1a-targeted promoter regions and noncoding small nucleolar RNAs (snoRNAs) were also enriched for differentially methylated sites. Despite the downregulation of mitochondrial gene expression, the same genes were not differentially methylated and complex I activity in Setd1a+/- mice did not differ significantly from controls. Genes overlapping hypomethylated regions were enriched for common genetic associations with schizophrenia. Our findings suggest that SETD1A haploinsufficiency disrupts the epigenetic regulation of ribosomal pathways. These results provide insight into an alternative mechanism through which genetic variation in SETD1A influences developmental and synaptic plasticity, contributing to schizophrenia pathophysiology.

overall_design: We used the Illumina Infinium Mouse Methylation Array to quantify DNA methylation in heterozygous Setd1a mutant mouse frontal cortex compared to wildtype control.


title: H2A.Z regulates transcription, oocyte maturation and female fertility in mouse [RNA-seq]

last: Zhang

overall_design: RNA-seq

first: Wei


title: Epigenomic disorder and partial EMT impair luminal progenitor integrity in Brca1-associated breast tumorigenesis

first: Céline

last: Vallot

overall_design: Refer to individual Series

first: Camille

last: Landragin

first: Melissa

last: Saichi

first: Marthe

last: Laisné

first: Adeline

last: Durand


summary: Defects in double-strand repair mechanisms - both through germline or somatic inactivation of repair genes - is a hallmark of basal-like breast cancers. In this genetically-unstable context, a recurrent major shift in cell identity occurs within the mammary epithelium. Basal-like BRCA1 tumors have indeed been proposed to originate from luminal progenitor cells yet tumor-initiating events remain poorly understood. Here, we map the state transitions leading luminal progenitors to tumor formation, using a mouse model launching tumorigenesis in multiple LP cells. We identify a population of cycling p16-expressing cells, emerging from the luminal progenitor compartment, undergoing partial epithelial-to-mesenchymal transition and losing luminal identity. Pseudo-temporal analyses position these cells as a transitory state between aberrant Brca1-deficient luminal progenitors and growing tumor cells. Concomitant to p16 activation, we show that LP cells undergo an epigenomic crisis attested by the general re-organization of their heterochromatin. They accumulate multiple H3K27me3 micro-foci - reminiscent of the formation of senescence-associated heterochromatin foci (SAHFs) - and lose their inactive X (Xi). Both p16 activation and heterochromatin reorganization are hallmarks of human basal-like breast tumors, we propose that these events occur during initial LP transformation and are scars of an initial transitory senescent-like state.

overall_design: Single-cell RNA-seq was performed mammary gland samples from n=3 Cre Negative (Brca1+/+ Tp53 +/+) and n= 8 Cre Positive (Brca1-/- Tp53 -/-) samples at different histological stages : young mice (2-3 months old), mice with millimitric tumors (5-5.4 months) and tumor samples at different sizes (6 months).

first: Pacôme

last: Prompsy

first: Celine


title: Diversification of Dentate Gyrus Granule Cell Subtypes is Regulated by Nrg1 Nuclear Back-Signaling

first: David

last: Talmage

address: 35 Convent Dr, Room 3B-101

department: NINDS

institute: National Institutes of Health

summary: Neuronal heterogeneity is a defining feature of the developing mammalian brain, but the mechanisms regulating the diversification of closely related cell types remain elusive. In this study, we investigated the heterogeneity of dentate gyrus (DG) granule cells (GCs) and the influence of a psychosis associated V321L mutation in Neuregulin1 (Nrg1) on GC subtype composition. Using morpho-electric characterization, single-nucleus gene expression, and chromatin accessibility profiling, we identified distinct morphological and molecular features of typical GCs and a rare subtype known as semilunar granule cells (SGCs). The V321L mutation disrupts Nrg1 nuclear back-signaling, resulting in an overabundance of SGC-like cells. We discovered pseudotime gene expression trajectories suggesting the potential for GC-to-SGC transitions, supported by the accessibility of SGC-specific genes in other GCs. Intriguingly, we found an increase in SGC-marker expression over the adolescence to adulthood transition window in wild-type mice, coinciding with a decline in Nrg1 nuclear back-signaling capacity. This suggests that intact Nrg1 signaling suppresses SGC-like fate acquisition, and that its natural downregulation may underlie the emergence of SGC-like cells during postnatal development. Similarly, a pathological block of nuclear back signaling by the V321L mutation in Nrg1, may result in acquisition of the SGC-like fate due to loss of the repressive mechanisms maintained by intact nuclear back signaling. Our findings reveal a novel role for Nrg1 in maintaining DG cell-type composition and suggest that disrupted subtype regulation may contribute to disease-associated changes in DG GC morphology and function. Understanding these mechanisms provides new insights into mechanisms of cell-type diversity and its potential role in psychiatric pathology.

overall_design: To investigate the heterogeniety of DG GC subtypes and influence of the V321L mutation in Nrg1, we prepared single nucleus suspensions from 4 WT and 4 mutant mouse (2M/2F) microdissected DGs. Nuclei were processed according to the 10x Genomics multiome kit to obtain single nucleus RNA and ATAC Seq libraries which were sequenced.

first: Prithviraj

last: Rajebhosale

first: Kory

last: Johnson


title: Toxoplasma gondii infection of neurons alters the production and content of extracellular vesicles directing astrocyte phenotype and contributing to the loss of GLT-1 in the infected brain

city: Riverside

first: Emma

last: Wilson

state: California

address: 3401 Watkins Dr

department: Biomedical Sciences

institute: University of California, Riverside

summary: Toxoplasma gondii (T. gondii), a prolific protozoan parasite, forms cysts within neurons of the central nervous system that maintain infection for the lifetime of the host. Astrocytes are fundamental to neuronal health by providing nutrients and structural support and help regulate neurotransmitters by continuous communication with neurons. It is not yet known how infection and the presence of intracellular cysts, disrupts the crucial relationship between these cells. Extracellular vesicles (EVs) function in intracellular communication and can contain proteins, lipids, DNA, miRNA, and other RNA subtypes. EVs are produced by all cells and play an important role in neuronal-astrocyte interactions, including the regulation of glutamate receptors on astrocytes. Previous work has demonstrated that Toxoplasma infection reduces astrocytic expression of the primary glutamate transporter, GLT-1. Here we tested if cyst infection of neurons alters the production and content of EVs. EVs were isolated from uninfected and infected primary murine cortical neurons and their size, concentration, and characterization were confirmed with nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), ELISA, western blot, liquid chromatography (LC)-mass spectrometry (MS)/MS, and microRNA sequencing. Analysis reveals that infection of neurons reduced neuronal production of EVs and altered their protein and miRNA content. In addition to changes in host protein content, EVs from infected neurons contained the Toxoplasma proteins GRA1, GRA2, GRA7, MAG1 and MAG2. Following incubation of neuronal EVs with primary astrocytes, GRA7 protein could be observed within intracellular EVs and the nuclei of GRA7+EV-containing cells. EVs from infected neurons altered gene expression of astrocytes resulting in an increase in pro-inflammatory transcriptional signatures, along with a downregulation of GLT-1 protein expression with similar transcriptional changes found in astrocytes in vivo. These results demonstrate the ability of a parasitic infection in the brain to alter EV production and the fundamental communication between neurons and astrocytes.

overall_design:
To determine if infection alters astrocyte and neuron communication EVs from T. gondii infected primary cortical murine neurons were isolated and added onto primary murine astrocyte cultures for 24 hours prior to bulk RNA-Sequencing. The addition of LPS/IFNy was used as a positive control, media without Dexamethasone (Dex) as a negative control, and media as an experimental control.
Primary murine cortical astrocytes were grown and treated with 100nM of Dexamethasone one day prior to the addition of the four different conditions. Samples were incubated for 24 hours prior to RNA extraction and bulk RNA Sequencing. Each sample was done in triplicate. For the negative control Dexamethasone was never added.

first: Emily

middle: Z

last: Tabaie


title: Single-cell RNA Sequencing of Pig Lung Transplantation Reveals Macrophage Ferroptosis in Lung Ischemia‒Reperfusion Injury

city: shanghai

first: Junqi

last: Wu

state: shanghai

address: No. 507 Zhengmin Road, Shanghai 200443, China.

institute: Shanghai Pulmonary Hospital

summary: Primary graft dysfunction (PGD), which is caused primarily by ischemia–reperfusion injury (IRI), is a major obstacle in lung transplantation. Here, we developed an orthotopic, single-lung transplant pig model to simulate prolonged cold IRI. After 24 hours of cold ischemia and 8 hours of warm reperfusion, the transplanted lung exhibited severe allograft injury. Subsequent single-cell RNA sequencing (scRNA-seq) revealed significant changes in alveolar macrophages after IRI, with prominently enriched ferroptosis pathways. Transmission electron microscopy (TEM) confirmed characteristic ferroptosis changes in lung macrophages, and decreased GPX4 expression in macrophages indicated increased susceptibility to ferroptosis. Overall, our pig orthotopic left lung transplant model effectively simulates IRI after transplantation, which offers a valuable platform for more detailed investigations of early reperfusion injury to pulmonary grafts. Moreover, we preliminarily demonstrated the importance of macrophage ferroptosis in IRI, suggesting that inhibiting macrophage ferroptosis may be a promising therapeutic strategy for lung IRI.

overall_design: Here, we developed an orthotopic, single-lung transplant pig model to simulate prolonged cold IRI. After 24 hours of cold ischemia and 8 hours of warm reperfusion, the transplanted lung exhibited severe allograft injury. To further investigate the pathological changes associated with lung IRI, we performed scRNA-seq of CD45+ cells (n=2) and CD45- cells (n=1) generated from allograft tissues, and total cell suspensions isolated from right donor lung tissues (n=3).

first: Fenghui

last: Zhuang

first: Ye

last: Ning

first: Chongwu

last: Li

first: Yunzhe

last: Luo

first: Peigen

first: Tao

last: Wang

first: Chenyang

last: Dai

first: Huikang

last: Xie

first: Wenxin

last: He

first: Chang

last: Chen


title: Oleic Acid Promotes Lipid Accumulation in Bovine Adipocytes: The Role of PPARα Activity

city: East Lansing

first: G. Andres

last: Contreras

state: MI

address: 736 Wilson Road Room D202, Michigan State University

department: Large Animal Clinical Sciences

institute: Michigan State University

summary: Background: Excessive lipid mobilization due to negative energy balance (NEB) in periparturient dairy cows increases their risk for diseases and decreases their productivity. Improving energy intake during the immediate postpartum limits NEB. One way to enhance energy density of the diet is through fatty acid (FA) supplementation. In periparturient cows, oleic acid (OA) limits lipolysis and improves adipose tissue (AT) insulin sensitivity. However, the mechanisms behind OA effect are still unknown. Our objective was to characterize the effect of OA, alone and in combination with palmitic acid (PA), on lipid accumulation, and identify a mechanism of action in bovine adipocytes. Results: Compared with CON, FA treatments had no effect on preadipocyte differentiation (P = 0.65). The treatments 300PA, 200OA, 300OA, 60-40, 50-50, and 40-60 increased lipid accumulation compared with CON (P < 0.0001). At d 7, 300PA and 300OA increased PPARα protein expression compared with CON (P = 0.04). PPARα inhibition decreased triglyceride levels of OA and 60-40 (P<0.05) but not for PA (P=0.26).

overall_design: Pre-adipocytes were isolated from subcutaneous AT explants (Holstein cows) and induced to differentiate into adipocytes. Mature adipocytes were cultured with standard differentiation media (CON) supplemented with PA or OA (100, 200, and 300 µM), and mixtures of PA-OA (60-40, 50-50, and 40-60 at 300 µM) for 4 or 7 d. To evaluate the effect of PPARα signaling, adipocytes were treated with or without a PPARα specific antagonist (GW6471; 10 µM) for 7 d after induction.

first: Ursula

last: Abou-Rjeileh

first: Adam

last: Lock

first: Andres


title: Toxoplasma gondii infection of neurons alters the production and content of extracellular vesicles directing astrocyte phenotype and contributing to the loss of GLT-1 in the infected brain [miRNA-Seq]

first: Emma

type: Non-coding RNA profiling by high throughput sequencing

overall_design: To determine if infection alters neuronal extracellular vesicle content EVs were isolated form T. gondii infected and uninfected neurons prior to miRNA Sequencing. EVs from uninfected neurons were used as an experimental control.


title: DC-T Cell Immunity

first: Xiaozhe

last: Yin

address: Room A305, Building Zhengyutong, Tsinghua University

institute: Tsinghua University

summary: Understanding and harnessing intratumoral DC-T cell dynamics and provide new therapeutics for improving treatment outcomes.

overall_design:
To investigate the influence of radiotherapy-activated prodrug treatment (namely X-Ray+O-IMDQ) to tumor infiltrated DCs and T cells, MC38 tumor-bearing mice were treated with or without radiotherapy-activated prodrug, then DCs and TILs were isolated 72 h after the second treatment.
We then performed gene expression profiling analysis using data obtained from RNA-seq of DC and T cells at control and radiotherapy-activated prodrug treatment group.

first: Li

last: Yu


title: Insect hormone prothoracicotropic hormone (PTTH) regulates lifespan through temporal and spatial activation of NF-κB signaling during Drosophila metamorphosis [2]

city: Ames

first: Ping

last: Kang

state: Iowa

address: 3266 Molecular Biology Building 2437 Pammel Drive

department: GDCB

institute: Iowa State University

summary: The prothoracicotropic hormone (PTTH) is a well-known neuropeptide that regulates insect metamorphosis (the juvenile-to-adult transition) by inducing the biosynthesis of steroid hormones, similar to the hypothalamic-pituitary-gonadal control of mammalian puberty. However, the role of Ptth in adult physiology and longevity is largely unexplored. Here, we show that Ptth loss-of-function mutants are long-lived and exhibit increased resistance to oxidative stress in Drosophila. Intriguingly, we find that loss of Ptth blunt age-dependent upregulation of NF-κB signaling specifically in fly oenocytes, the homolog of mammalian hepatocytes. We further show that oenocyte-specific overexpression of NF-κB/Relish blocks the lifespan extension of Ptth mutants, suggesting that Ptth regulates lifespan through oenocyte-specific NF-κB signaling. Surprisingly, adult-specific knockdown of Ptth did not prolong lifespan, indicating that Ptth might control longevity through developmental programs. Our developmental transcriptomic analysis reveals an interesting activation of NF-κB signaling during fly metamorphosis, which is attenuated in Ptth mutants. Intriguingly, the knockdown of NF-κB/Relish, specifically in oenocytes during metamorphosis, significantly prolongs the lifespan of adult flies. Thus, our findings uncover an unexpected role of insect hormone PTTH in controlling adult lifespan through temporal and spatial activation of NF-κB signaling in developing hepatocytes.

overall_design: Comparing gene expression of wild type and Ptth mutant third instar larvae, white pupa and P1, P2, P3, P4, A0(newly emerged adults). White pupa was marked on the wall of the vials. P1, P2, P3 and P4 pupa were collected every 24 hours afterwards for RNA extraction.

first: Peiduo

last: Liu

first: Jinoh

last: Kim

first: Marie

last: Bolton

first: Wren

last: Murzyna

first: Ankur

last: Kumar

first: Ting

last: Miao

first: MaryJane

last: Shimell

first: Weihang

first: Yanhui

last: Hu

first: JoAnne

last: Powell-Coffman

first: Michael

middle: B

last: O’Connor

first: Norbert

last: Perrimon

first: Hua

last: Bai


title: The Condensin II Complex Subunit NCAPH2 Regulates Patterns of H4K20me1 Occupancy and Erythroid Gene Expression [RNA-Seq]

city: Rochester

first: Laurie

last: Steiner

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

summary: To gain insight into the mechanisms underlying the NCAPH2 mutant phenotype, we assessed the global expression in murine primitive erythroblasts isolated from E11.5 NCAPH2 Δ/Δ and littermate control embryos.

overall_design: RNA-seq was used to compare the global expression in murine primitive erythroblasts isolated from E11.5 NCAPH2 Δ/Δ and littermate control embryos.

first: Kristin

last: Murphy

first: Deanna

last: Abid

first: Zachary

last: Getman


title: The Condensin II Complex Subunit NCAPH2 Regulates Patterns of H4K20me1 Occupancy and Erythroid Gene Expression [CUT&RUN]

summary: To gain insights into the mechanisms underlying the NCAPH2 mutant phenotype, we assessed the genomic targets of NCAPH2 in E11.5 erythroblasts and changes in H4K20me1 occuapncy in E11.5 NCAPH2 Δ/Δ erythroblasts compared to littermate control.

overall_design: CUT&RUN was used to identify genomic targets of NCAPH2 in E11.5 erythroblasts and changes in H4K20me1 occuapncy in E11.5 NCAPH2 Δ/Δ erythroblasts compared to littermate control.


title: Characterization of a stripe rust resistance gene YR86 in wheat chromosome 2AL

first: Qiang

last: Cao

address: 12 Zhongguancun South Street, Haidian District, Beijing

institute: Chinese Academy of Agricultural Sciences

summary: Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), significantly affects wheat production worldwide. The most economical and effective way to control this disease is breeding resistant cultivars. Wheat cultivar Zhongmai 895 was earlier found to carry YR86 in an 11.6 Mb recombination-suppressed region in chromosome 2AL when crossed with Yangmai 16. To fine-map the YR86 locus, we developed two large F2 populations from crosses Emai 580/Zhongmai 895 and Avocet S/Zhongmai 895. Remarkably, both populations exhibited suppressed recombination in the same 2AL region. Collinearity analysis across Chinese Spring, Aikang 58, and 10+ wheat genomes revealed a 4.1 Mb chromosomal inversion spanning 708.5–712.6 Mb in the Chinese Spring reference genome. Molecular markers were developed in the breakpoint and used to assess a wheat cultivar panel, revealing that Chinese Spring, Zhongmai 895, and Jimai 22 shared a common sequence named InvCS, whereas Aikang 58, Yangmai 16, Emai 580, and Avocet S shared the sequence named InvAK58. The inverted configuration explained the suppressed recombination observed in all three bi-parental populations. Normal recombination was observed in a Jimai 22/Zhongmai 895 F2 population, facilitating mapping of YR86 to a genetic interval of 0.15 cM corresponding to 710.27–712.56 Mb falling within the inverted region. Thirty-three high-confidence genes were annotated in the interval using the Chinese Spring reference genome, with six identified as potential candidates for YR86 based on genome and transcriptome analyses. These results will accelerate map-based cloning of YR86 and its deployment in wheat breeding.

overall_design: Flag leaves from field plants of ZM895 (R) and stripe rust susceptible cultivars JM22 (S) and Mingxian 169 (MX169, CK) were collected for RNA-Seq analysis

first: Zhonghu

last: He

first: Yuanfeng

last: Hao


title: HDAC1 regulates effector CD8+ T cell differentiation during chronic viral infection

city: washington dc

first: Shaoqi

last: Zhu

state: WASHINGTON

address: 725 21st st nw

institute: the george washington university

summary: Hdac1 is a known epigenetic regulator of gene expression. The aim of this study is to investigate whether Hdac1 influences CD8+ T cell fate during chronic infection. We demonstrate that the genetic ablation of Hdac1 reduces the generation of Tex-Int cells

overall_design: Gzmb-Cre; Rosa26-lsl-GFP; Hdac1 wild-type or floxed mice were directly infected with LCMV Clone 13. On day 8 post-infection, Gp33 tetramer-positive cells were sorted into three populations based on surface markers Cx3cr1 and Slamf6 for ATAC-seq analysis.

first: Hai-Hui

last: Xue

first: Weiqun

last: Peng

first: Wei


title: Potential Epigenetic Biomarkers for Preeclampsia Preterm Birth and Preventative Medicine

city: Pullman

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: Preterm birth has dramatically increased within the population (i.e., >10%) and preeclampsia is one of the most unanticipated sub-categories of preterm birth. No clinical parameter or biomarkers exists for preeclampsia preterm birth, except for high blood pressure toward the end of pregnancy. The current study investigates the potential use of epigenetic (DNA methylation) alterations as a preeclampsia biomarker. Non-preeclampsia term births were compared to preeclampsia preterm births to identify methylation differences. Buccal cell cheek swabs were used as a marker cell for systemic epigenetic alterations in the individuals. A total of 389 differential DNA methylation regions (DMRs) were identified and associated with the presence of preeclampsia. The DMRs were genome-wide and were predominantly low CpG density (<2 CpG/100 bp). In comparison with a previous preterm birth epigenetic biomarker there was a 15% (60 DMR) overlap, indicating the majority of the DMRs are unique for preeclampsia.

overall_design: Buccal samples were collected from mother-infant pairs following delivery. Methylated DNA immunoprecipitation (MeDIP) was performed on the buccal cell DNA samples. The MeDIP was followed by DNA sequencing (MeDIP-Seq). Differential DNA methylation regions (DMRs) were identified between preeclampsia and control samples. The samples used in this study are a combination of newly acquired samples and samples from a previous related study (PMID: 35232984).

first: Eric

last: Nilsson

first: Paul

last: Winchester

first: Cathy

last: Proctor

first: Daniel

last: Beck


title: The effect of acute knockout of Nr2e3 on mouse photoreceptor cells

city: Saint Louis

state: MO

address: 660 S. Euclid

institute: Washington University School of Medicine

summary: Acute knockout of the rod photoreceptor transcription factor Nrl delays retinal degeneration in multiple mouse models of blindness1-3, but the downstream transcriptomic changes that mediate these therapeutic effects are unknown. Here, we show that acute Nrl knockout causes upregulation of a subset of cone genes in rods as well as downregulation of rod genes, including the rod-specific transcriptional repressor Nr2e3. We hypothesized that Nr2e3 downregulation might mediate some of the therapeutic effects of Nrl knockout. Indeed, acute knockout of Nr2e3 prevents photoreceptor degeneration and preserves visual function in mice with mutations in the catalytic subunit of the rod-specific phosphodiesterase (Pde6brd10/rd10). Upregulation of Pde6c, the cone-specific homolog of Pde6b, in Nr2e3-knockout rods is required to prevent degeneration in Pde6brd10/rd10 mice, suggesting that this therapeutic effect is mediated by a gene-replacement mechanism. In contrast, acute Nr2e3 knockout fails to prevent degeneration caused by loss- or gain-of-function mutations in Rhodopsin (Rho-/- and RhoP23H/P23H), whereas acute Nrl knockout delays degeneration in both models. These results suggest that acute Nrl knockout may rescue Pde6brd10/rd10 mice via downregulation of Nr2e3 and consequent upregulation of Pde6c, while rescuing Rho mutants via a distinct mechanism, possibly by downregulating rod genes. These findings indicate that acute NRL knockout may be a promising gene-independent strategy for preventing photoreceptor degeneration in human patients.

overall_design: To determine the transcriptomic effects of acute Nr2e3 knockout we subretinally injected an AAV harboring a guide RNA targeting Nr2e3, or control, into Rosa26-Cas9 mice (Jackson labs strain #024858), which express SpCas9 in all cells. The AAV also harbors an mCherry reporter driven by a photoreceptor specific promoter, allowing us to isolate AAV-transduced photoreceptors by Flourescence Activated Cell (FAC) Sorting. Mice were injected at postnatal day 21 and mCherry expressing cells were sorted for RNA isolation 6 months later.

first: Joseph

middle: C

last: Corbo


title: Expression data from whole mouse retina comparing acute Nrl knockout and control

summary:
Nrl acts as a molecular toggle switch during retinal development: if a photoreceptor precursor turns on Nrl, it differentiates as a rod, otherwise it differentiates as a cone. In contrast, acute Nrl knockout transforms mature rods into cells with features intermediate between those of normal rods and cones (‘cods’).
We used microarray to comprehensively evaluate the transcriptomic changes that occur upon acute knockout of Nrl in mouse retina.

overall_design: Control (Nrlflox/+; CAG-CreERTM), and experimental (Nrlflox/flox; CAG-CreERTM) mice were injected intraperitoneally on a daily basis from P42 to P44 with 4-hydroxytamoxifen to induce recombination of the Nrlflox alleles. RNA was then isolated from two biological replicates (each consisting of total RNA from four retinas) per genotype.

first: Cynthia

middle: L

last: Montana

first: Yu

last: Liu


title: Insect hormone prothoracicotropic hormone (PTTH) regulates lifespan through temporal and spatial activation of NF-κB signaling during Drosophila metamorphosis [1]

first: Ping

last: Kang

overall_design: For all groups, total RNA was collected from ~15 female wholebody flies(1 week old and 5 weeks old, wild type and Ptth mutants), three biological replicates each condition.

first: Peiduo

first: Jinoh

last: Kim

first: Marie

last: Bolton

first: Wren

last: Murzyna

first: Ankur

last: Kumar

first: Ting

last: Miao

first: MaryJane

last: Shimell

first: Weihang

last: Chen

first: Yanhui

last: Hu

first: JoAnne

last: Powell-Coffman

first: Michael

last: O’Connor

first: Norbert

last: Perrimon

first: Hua

last: Bai


title: Spatially Resolved Transcriptomics Exploration in 3D Desktop and Virtual Reality Environments with VR-Omics

city: Clayton

first: Hieu

middle: Tri

last: Nim

state: VIC

address: Monash University Clayton Campus, Wellington Rd

department: Australian Regenerative Medicine Institute

institute: Monash University

summary: Spatially resolved transcriptomics (SRT) produces complex, multi-dimensional gene expression data sets at up to subcellular spatial resolution. While SRT provides powerful datasets to probe biological processes, well-designed computational tools provide the key to extracting value from SRT technology. Currently, no single piece of software facilitates the combined automated analysis, visualisation, and subsequent interaction of single or multi-section SRT data as a desktop application or in an immersive environment. Here we present VR-Omics, a freely available, SRT platform agnostic, stand-alone programme that incorporates an in-built, automated workflow to pre-process and spatially mine SRT data within a user-friendly graphical interface. Benchmarking demonstrates VR-Omics has superior capabilities for seamless end-to-end analyses of SRT data, hence making SRT data processing and mining accessible to users regardless of computational and data handling skills. Importantly, VR-Omics supports comparison between datasets generated using different spatial technologies alongside processing and analysis of multiple 2D or 3D SRT datasets provides a unique environment for biological discovery. Finally, we utilise VR-Omics to uncover the molecular mechanisms that drive the growth of rare paediatric cardiac rhabdomyomas.

overall_design: Samples from 3 patients, comprising a total of 4 cardiac rhabdomyomas, were sequencing using the 10x Visium platform for FFPE Tissue

first: Denis

last: Bienroth

first: Natalie

last: Charitakis

first: Dillon

last: Wong

first: Sabrina

last: Jaeger-Honz

first: Dimitar

last: Garkov

first: Kevin

middle: I

last: Watt

first: Julian

last: Stolper

first: Hazel

last: Chambers-Smith

first: Duncan

last: MacGregor

first: Bronwyn

last: Christiansen

first: Adam

last: Piers

first: Enzo

last: Porrello

first: David

last: Elliott

first: Karsten

last: Klein

first: Falk

last: Schreiber

first: Mirana

last: Ramialison


title: Regulation of translation elongation and integrated stress response in heat-shocked neurons

first: Seth

last: Margolis

address: 725 N. Wolfe St.

department: Department of Biological Chemistry

institute: The Johns Hopkins University School of Medicine

summary: Neurons in the mammalian central nervous system adapt to changes in temperature through molecular mechanisms that are poorly understood. Here, in response to elevated temperatures, we show that primary mouse neurons isolated from the cortex experience a global downregulation of polysome-dependent translation and a concomitant activation of a unique transcriptional program. These new transcripts were found associated with ribosomes during initial stages of this heat-induced stress response, during which time there was little global protein production. Returning neurons to baseline temperature within a defined window of time (<60 minutes) was necessary for translation to return to control levels and ultimately for neuronal survival. Neurons placed at baseline temperature beyond this time window did not recover translation and died. Among the many transcripts upregulated during heat stress, we observed a ~350-fold increase in Hspa1a and yet no detectable translation of Hsp70 protein until recovery at baseline temperature. We considered that this heat stress response was relevant to neuronal resilience and survival following recovery. To begin to test this idea, we chose to use orthogonal approaches to suppress Hsp70 expression or function. We found, in neurons which had experienced heat stress, that Hsp70 was critical for preventing activation of cell death pathways during recovery. Taken together, our findings suggest that neurons are unique in their response to heat stress in that during a finite window they poise ribosomes on new transcripts, such as Hspa1a, thus preparing for exclusive expression of these factors in the event that recovery is an option.

overall_design: Primary mouse neuronal cells isolated from the cortex of embryonic day 14.5 C57Bl6 mice. The cells were heat stressed at 42 °C for 15 and 60 minutes and compared to a control that was maintained at 37 °C for one hour. Total RNA and ribosome-associated RNA was isolated and submitted for RNA-sequencing.

first: Caitlin

last: Seluzicki


title: Single-cell RNA sequencing on TILs from 4T1 mouse model treated with STING agonist deliveredy by PEG biopsy marker shows activation of antigen presenting cells and macrophages but does not show T cell clonality.

status: Public on Apr 21 2025

city: New York

first: Eric Minwei

last: Liu

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: To better characterize the TME effects of ADU-S100 delivered by the PEG, we performed single cell RNA sequencing (scRNA-seq) on CD45+ immune cells from 4T1 tumors 14 days after treatment. We found that antigen presenting cell (APC) and macrophage clusters exhibited robust upregulation of IFN-induced genes by ADU-S100, as well as significant enrichment for hallmark IFN gene signatures. To explore whether immune escape could be secondary to a failure of STING agonist to induce T-cell clonality and expansion, we further performed T-cell receptor sequencing (TCR-seq) on these CD45+ immune cells from animals treated with PEG markers with PBS or 100 µg ADU-S100. We then analyzed the frequency of unique clonotypes that were expanded following PBS versus ADU-S100 treatment. In both groups, there was no evidence for clonotype expansion.

overall_design: Balb/c mice were inoculated with 100K 4T1 cells followed by PEG with PBS or 100 µg ADU-S100 implantation on Day 6 when tumor volumes reached 75 mm3. On Day 14 after PEG implantation, tumors were harvested and pooled (n=4 per group). We then sorted CD45+ cells by Fluorescence-activated cell sorting (FACS) and performed scRNAseq/TCRseq.

first: Yuqing

last: Zhang

first: Zehua

last: Li

first: Patrick

last: Lizotte

first: Sung-Rye

last: Park

first: Michael

middle: Y

last: Tolstorukov

first: Cloud

last: Paweletz

middle: A

last: Barbie

first: Thanh

middle: U


title: Single-cell RNA sequencing on peripheral blood PBMCs from 4T1 mouse model treated with STING agonist deliveredy by PEG biopsy marker does not reveal peripheral T cell clonal expansion.

summary: To explore whether immune escape could be secondary to a failure of STING agonist to induce T-cell clonality and expansion, we performed single-cell RNA sequencing (scRNAseq) and T-cell receptor sequencing (TCR-seq) on peripheral PBMCs from animals treated with PEG markers with PBS or 100 µg ADU-S100, using the low tumor burden model of 4T1. Cell types were clustered based on gene signature analysis with 9 resultant clusters. We then analyzed the frequency of unique clonotypes that were expanded following PBS versus ADU-S100 treatment. In both groups, most of the cells that had a unique clonotype did not expand, showing a frequency of 1. There were no specific clonotypes that had a frequency over 5, indicating that ADU-S100 treatment of 4T1 mice does not result in peripheral T cell clonal expansion.

overall_design: Balb/c mice were inoculated with 10K 4T1 cells followed by PEG with PBS or 100 µg ADU-S100 implantation on Day 4. On Day 30, another PEG marker with PBS or 100 µg ADU-S100 was implanted. We then collected peripheral blood from one mouse in each group on Day 50 and performed scRNAseq/TCRseq.

first: Sophie

last: KivLehan

first: Kara

middle: M

last: Soroko

first: Prafulla

last: Gokhale


title: Transcriptomic comparison of hepatocytes derived from a panel of human induced pluripotent stem cells with different ethnicities

city: Laurel

first: Xiugong

last: Gao

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

summary: In the current study, we attempted to establish an in vitro model for assessing population variability in hepatotoxicity testing using a panel of hepatocytes derived from nine human induced pluripotent stem cell (iPSC) lines belonging to three different ethnic groups, Black or African American (BAA), Latino or Hispanic (LOH), and Non-Hispanic White (NHW). The panel of iPSC-derived hepatocytes were exposed to diglycolic acid (DGA) and usnic acid (UA), and transcriptomic changes were characterized and compared.

overall_design: Hepatocytes were differentiated from nine iPSC lines belonging to three ethnicities. Cells were exposed to 3.0 mM DGA or 10.0 μM UA for 24 h. Transcriptomic gene expression was characterizecd using RNA-seq. Two replicates (n = 2) were included for each treatment group including the controls.

first: Miranda

middle: R

last: Yourick


title: Spatial transcriptomics analysis of urticarial rash skin from patients with Schnitzler syndrome

city: Kyoto

first: Naotomo

last: Kambe

state: Kyoto

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Dermatology

institute: Kyoto University

summary: We conducted a multicenter, open-label, single-arm phase II trial (SCan Study) to evaluate the efficacy and safety of canakinumab in 5 Japanese patients with Schnitzler syndrome (SchS), based on a similar study conducted in Germany. As part of this study, spatial transcriptomics of urticarial rash skin lesions were performed before treatment in 2 cases to identify IL1B-expressing cells. The spatial transcriptomics analysis was conducted using the 10x Genomics Xenium platform.

overall_design: This study investigated the spatial transcriptomic profiles of urticarial rash skin lesions in two active Schnitzler syndrome (SchS) patients (a 68-year-old male and a 55-year-old male) with fever, rash, and IgM-kappa type monoclonal gammopathy. Skin tissue samples were collected before canakinumab administration as part of a multicenter, open-label, single-arm phase II trial (SCan Study). Spatial transcriptomics was performed using the 10x Genomics Xenium platform to identify IL1B-expressing cells within the tissue microenvironment.

first: Kosuke

last: Katsuo

first: Satoshi

last: Nakamizo


title: Single-cell RNA sequencing of peripheral blood from Schnitzler syndrome patients before and after canakinumab treatment

summary: We conducted a multicenter, open-label, single-arm phase II trial (SCan Study) to evaluate the efficacy and safety of canakinumab in 5 Japanese patients with Schnitzler syndrome (SchS), based on a similar study conducted in Germany. In this trial, single-cell RNA sequencing (scRNA-seq) of peripheral blood were performed in 2 cases to identify IL1B-expressing cells, using 10x Genomics scRNA-seq.

overall_design:
Peripheral blood samples were collected from 2 active SchS patients (a 68-year-old male and a 55-year-old male) who presented with fever, rash, and IgM-kappa type monoclonal gammopathy, both before and 14 days after canakinumab administration.

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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: Yuyi

last: Zhou

first: Satoru

last: Yonekura


title: Lymphoid subsets in the AML bone marrow microenvironment following chemotherapy induction

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

summary: Using scRNA-seq, bone marrow (BM) aspirates, collected post-induction, from 12 complete responders (CR) and 10 refractory patients were compared for lymphoid cells subpopulations.

overall_design: AML patients’ bone marrow (BM) samples and information were collected after obtaining consent in accordance with institutional review board-approved studies at Fred Hutchinson Cancer Research Center (FHCRC). One vial of BM from each of the 22 patients was thawed with standard protocol. Then, cells were counted, and viability was evaluated with Trypan blue staining. 50,000 cells were directly sent to the Center for Medical Genomics of the Indiana University School of Medicine to be processed on the 10x Genomics while the leftover cells were stained for multicolor flow cytometry.

first: Suganya

last: Subramanian

last: Paczesny


title: E-cadherin regulates female tumor aggressiveness by controlling estrogen-sensitivity [ChIP-seq]

city: Orsay

first: Lionel

last: Larue

address: Centre universitaire Bat 101B-110-111-112 Rue Henri Becquerel CS 90030

department: CNRS UMR3347, INSERM  U1021

institute: Institut Curie

summary: Sex disparities in cancer have been documented, but understanding of the underlying mechanisms is still limited, restricting precision medicine and the discovery of new therapeutic options. By analyzing overall cancer frequency, we found that women, between puberty and menopause, are more prone to develop cancer than men. We identified the cell adhesion molecule, E-cadherin, as a central node of the estrogen response in multiple cancers. Using original mouse melanoma model, a cancer with a higher incidence of women than in men during this period, we identify a previously unknown estrogen-sensitizing signaling pathway linking E-cadherin to the Estrogen Receptor  and to the Gastrin Releasing Peptide Receptor (GRPR), promoting melanoma aggressiveness in female only. Inhibition of this axis through GRPR targeting suppress metastasis in mice, representing a very promising therapeutic approach. Our results demonstrate that E-cadherin prevents carcinoma sensitivity to estrogens and identify a new therapeutic avenue to treat women suffering from multiple E-cadherin-dependent cancers.

overall_design: Chromatin immunoprecipitation DNA-sequencing for histone modification H3K27ac in female and male mouse melanoma cell lines knocked-out or not for Cdh1 (E-cadherin)

first: Jeremy

last: Raymond

first: Valerie

last: Petit

first: Veronique

last: Delmas


title: Tetralone-ABA enhances winter cold acclimation, reduces deacclimation, and delays budbreak in V. vinifera and V. hybrid grapevines

city: Geneva

first: Hongrui

last: Wang

state: NY

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

institute: Cornell University

summary: Cold stress during the dormant season significantly constrains the expansion of grape and wine industries in cool climate viticulture regions of North America and Eurasia. In this study, we systematically evaluated a novel product, tetralone-ABA, for its efficacy in enhancing cold hardiness and delaying budbreak. Our approach included year-round physiological monitoring, transcriptome examination using 3'RNA-seq, and in silico simulation.

overall_design: For the RNA-seq data collection, bud samples were gathered during each deacclimation assay conducted in the 2022-2023 dormant season. The first assay was conducted on early winter buds with 581.5 chilling hours (Utah model). The second assay was conducted on mid-winter buds with 978.5 chilling hours. The third assay was conducted on late winter buds with 1339.9 chilling hours. During each deacclimation assay, control buds and tetralone-ABA treated buds were collected on days 0, 3, 5, 7, and 14 for RNA-seq analysis. Three biological replicates were used for each deacclimation assay, timepoint, and treatment combination.

first: Yue

last: Pan

first: Jason

last: Londo


title: Inflammation-induced epigenetic erosion drives stem cell ferroptosis during aging (PRO-Seq)

city: Madiosn

first: Romeo

middle: S

last: Blanc

address: 1111 Highland Ave, WIMR II, 4th floor, Blanc Lab

department: CRB

institute: University of Wisconsin-Madison

summary: Aging is a complex process associated with multiple events that lead to the decline in stem cell number and function. However, the relationship between these events and their initiation in biological systems remains ambiguous. Here, we investigate the effects of sustained, low-grade systemic inflammation on muscle stem cells (MuSCs) during aging. We show that the slow rise in inflammation during aging causes long-lasting epigenetic remodeling in MuSCs, leading to premature exit of quiescence followed by rapid ferroptotic cell death. The elevation of circulating cytokines results in erosion of histone H4 lysine 20 methylation, fine-tuning of the MuSC transcriptome for future injury response that resembles the Galert state. Prolonged exposure to inflammatory signals during aging results in the loss of H4K20me1 maintenance by lysine methyltransferase 5a (Kmt5a), leading to a disruption of key transcriptional programs required to preserve MuSC quiescence and survival. Mechanistically, we established that Kmt5a genetic deletion prematurely activates MuSC through Notch signaling. Activated cells cannot cycle properly as they display aberrant iron metabolism and repressed Gpx4, resulting in the accumulation of reactive oxygen species, genomic instability, lipid peroxidation, and ultimately, cell death by ferroptosis. Notably, a lifelong reduction in inflammation restores the MuSC number and function and rejuvenates MuSC iron homeostasis. Our findings demonstrates that chronic systemic inflammatory signals reprogram the MuSC epigenome into a primed state, which drives premature cell cycle re-entry and ferroptosis during aging.

overall_design: Comparative gene expression profiling analysis of PRO-seq data for muscle stem cells derived from 3 WT mice (C57) and 3 Kmt5aKO mice, 6 weeks post-induction.

first: Seth

last: Goldman


title: RNA-Seq of Ewing sarcoma shA673-1c cells after knockdown of EWS::FLI1

city: Liège

first: Franck

last: Dequiedt

state: Liège

address: Avenue de l'hôpital, 1

department: Molecular Biology of Diseases

institute: GIGA Institute

summary: Ewing sarcoma shA673-1c cells were cultivated with doxycyclin, treated with ActD and RNA sequenced to examine RNA stability

overall_design: Three biological replicates of Ewing sarcoma shA673-1c cells were cultivated with doxycyclin (dox) for 4 days to knockdown EWS::FLI1, treated with ActD and RNA sequenced at 0h, 1h, 2h and 4h post-treatment

first: Bartimée

last: Galvan


title: Effect of the loss of Cdh1 on gene expression in mouse melanoma tumors.

summary: Loss of E-cadherin molecular consequences on gene expression was assessed by RNA-seq in NRASQ61K;Cdkn2a-/+ female and male mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from 8 male Ecad tumors, 8 female Ecad tumors, 8 males ΔEcad tumors and 8 females ΔEcad tumors.

first: Jérémy

middle: H

first: Véronique


title: Spatial transcriptomics of human dorsal root ganglia from subjects with a history of diabetes

city: Richardson

first: Theodore

last: Price

state: Texas

address: 800 W. Campbell Road

institute: The University of Texas at Dallas

summary: Visium spatial RNA sequencing was performed on 16 human dorsal root ganglia (DRG) tissue sections collected from 7 different DRGs, from 6 human subjects with a history of diabetes.

overall_design:
Human DRGs were recovered from organ donors and tissue samples were processed with 10X VISIUM. Raw seq files were run with 10X SpaceRanger to determine gene counts per barcode. Nageotte nodule and surrounding neuron barcodes were selected in Loupe Browser. Seurat was used for clustering analysis and SONAR for spatial deconvolution.

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Raw files for human/patient samples are available in dbGaP (https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001158.v4.p2) for controlled access to the personally identifiable sequence data.
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first: Stephanie

last: Shiers

first: Khadijah

last: Mazhar

first: Andi

last: Wangzhou

first: Ishwarya

last: Sankaranarayanan

first: Diana

last: Tavares-Ferreira

middle: J