title: TRPC3 Contributes to Cyclophosphamide-Induced Cystitis Progression by Enhancing Bladder Fibrosis Through Activation of the TGF-β/Smad Pathway

first: Jialiang

last: Chen

address: Tianhe Road 600

department: Urology

institute: Third Affiliated Hospital of Sun Yat-Sen University

summary: The pathogenesis of interstitial cystitis/bladder pain syndrome (IC/BPS) remains incompletely understood. Bladder fibrosis is a significant histopathological feature of IC/BPS, particularly in non-Hunner-type IC (NHIC). Transient receptor potential cation channel subfamily C member 3 (TRPC3) is known to play a crucial role in myocardial and renal fibrosis. This study investigates the involvement of TRPC3 in bladder fibrosis associated with IC/BPS. A rat model of IC/BPS was established using cyclophosphamide (CYP, 50 mg/kg, intraperitoneally, every 3 days for 3 doses). Bulk RNA sequencing was used to identify differentially expressed transient receptor potential (TRP) channel genes in CYP-induced cystitis rats, whereas single-cell RNA sequencing was utilized to pinpoint the cell type predominantly expressing transient receptor potential cation channel subfamily C member 3 (TRPC3) . TRPC3 inhibition was achieved through intraperitoneal injection of Pyrazole 3 (Pyr3, 0.1 mg/kg or 1 mg/kg). Suprapubic mechanical allodynia was assessed using up-down method with von Frey filaments and micturition frequency was assessed by cystometry. The expression of TRPC3 and components of the transforming growth factor beta (TGF-β)/Smad signaling pathway (TGF-β, p-Smad2, and p-Smad3) in the bladder was analyzed by Western blot. Bladder fibrosis was assessed through Masson’s staining and detection of fibrosis markers (Vimentin, Collagen I, and Collagen III) using Western blot.  The RNA and protein expression of TRPC3 was up-regulated in CYP-induced cystitis rats. TRPC3 inhibition led to significant improvements in suprapubic mechanical allodynia and reduced micturition frequency in CYP-induced cystitis rats. Western blot analyses revealed that markers of bladder fibrosis (Vimentin, Collagen I, and Collagen III) were markedly upregulated in CYP-induced cystitis rats. Masson’s staining showed an increased area of collagen fibers. Additionally, inhibition of TRPC3 resulted in significant downregulation of the TGF-β/Smad signaling pathway (TGF-β, p-Smad2, and p-Smad3) in CYP-induced cystitis rats. TRPC3 activation contributes to bladder fibrosis in IC/BPS. Inhibition of TRPC3 ameliorates suprapubic mechanical allodynia and micturition frequency in CYP-induced cystitis rats by downregulating the TGF-β/Smad pathway. TRPC3 represents a potential therapeutic target for managing bladder fibrosis in IC/BPS.

overall_design: Gene expression profiling analysis of RNA-seq data from the bladder of CYP-induced cystitis rats and normal rats. Samples were collected from these groups of the differentiation in duplicate.

first: Ruixiang

last: Luo

first: Wenshuang

first: Junlong

last: Huang

first: Zheng

first: Chi

first: Honglu

last: Ding


title: Multigenerational cell tracking of DNA replication and heritable DNA damage (scRNA)

status: Public on Mar 31 2025

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

type: Expression profiling by high throughput sequencing

summary: The goal of this project was to analyze gene expression changes and gene expression heterogeneity at the single cell level upon DNA damage induced by ionizing radiation (IR). To this end, human U-2 OS cells were left untreated or exposed to 4 Gy of IR. 48 h after IR exposure, single cells were sorted into 384 well plates for scRNA-seq analysis.

overall_design: For SORT-Seq, cells were sorted on a FACS Aria III 3L system. 48 hours prior to sorting, cells were treated with 4 Gy of ionizing radiation.

first: Andreas

last: Panagopoulos

first: Merula

last: Stout

first: Sinan

last: Kilic

first: Peter

last: Leary

first: Julia

last: Vornberger

first: Virginia

last: Pasti

first: Antonio

last: Galarreta

first: Aleksandra

last: Lezaja

first: Kyra

last: Kirschenbühler

first: Ralph

last: Imhof

first: Urs

last: Ziegler

first: Hubert

last: Rehrauer

first: Matthias

last: Altmeyer


title: Multigenerational cell tracking of DNA replication and heritable DNA damage (bulk)

summary: The goal of this project was to analyze gene expression changes upon DNA damage induced by ionizing radiation (IR). To this end, human U-2 OS cells were left untreated or exposed to 4 Gy of IR and 24 h after IR exposure collected for RNA extraction and sequencing.

overall_design: For Bulk RNA Sequencing unsynchronized U-2OS cells were treated for 24 hours with 4 Gy of ionizing radiation, or left untreated. Then cells were lysed and RNA extraction was done using the TRIzol isolation protocol.


title: Neoadjuvant anlotinib combined with PD-1 blockade therapy remodeling the microenvironment in advanced non-small cell lung cancer

city: Tianjin

first: Lili

last: Yang

state: Tianjin

address: Huanhuxi Road, Tiyuanbei, Hexi District

country: China

institute: Tianjin Medical University Cancer Institute and Hospital

summary: Neoadjuvant anlotinib combined with PD-1 blockade therapy can prolong the survival of patients, but the underlying mechanisms for the failure of patients to benefit from combination therapy remain to be explored. To explore the mechanism of drug resistance and predict patient response,  we performed scRNA-seq from 6 NSCLC patients, including 3 post-treatment patients with major pathological response (MPR), and 3 Non-MPR patients to observe and analyze the dynamic changes of immune cells, stromal cells and cancer cells from the NSCLC patients who received neoadjuvant anlotinib combined with PD-1 blockade therapy and verified in an independent cohort.

overall_design: Advanced NSCLC patients received neoadjuvant anlotinib combined with PD-1 blockade therapy, and surgical treatment was performed after reaching the resectable criteria. 6 patients were enrolled in this study from December 2022 to December 2023. Single cells was isolated from 6 tissue samples respectively and analysed using scRNA-seq.


title: Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [CUT&TAG]

city: Hefei

first: Yan

state: Anhui

address: No.373 Huangshan Road

institute: University of Science and Technology of China

type: Genome binding/occupancy profiling by high throughput sequencing

summary: α-satellite RNA has been shown to interact with specific sets of RNA-binding proteins. By forming complexes with centromere proteins CENPA, CENPB, and CENPC, α-satellite RNA demonstrated its essential role in maintaining functional human centromeres. Also, α-satellite RNA has been reported to interact with SUV39H1, which is the histone methyltransferase that is responsible for H3K9me3. Together with the findings in mice and some other eukaryotes that RNA components are required for the recruitment of heterochromatin proteins and the maintenance of pericentric heterochromatin, it has long been suspected that α-satellite RNA might also be involved in the heterochromatin formation and recruitment of HP1 in human cells. In this study, we identified Scaffold Attachment Factor-A (SAF-A) as a novel α-satellite RNA binding protein. SAF-A, also known as hnRNPU, the most abundant member in the hnRNP complex, was initially identified as the major component of the nuclear scaffold. It binds to the nuclear scaffold in AT-rich regions through its DNA-binding domain. In recent years, several studies have suggested that SAF-A may play a more fundamental and general role in nuclear organization in interphase. Depletion of SAF-A will lead to pronounced chromatin condensation of gene-rich regions and global changes in 3D genome architecture.

overall_design: CUT&Tag for SAF-A in both mitotic and  asynchronized RPE cells.

first: Bingbing

last: Ren

first: Yinchun

last: Zhong

first: Ge

last: Shan


title: RNA-seq of human RPE1 cells treated with or without Doxorubicin and Ferrostatin-1

city: Haining

first: Mikael

last: Bjorklund

address: International Campus

institute: Zhejiang University-University of Edinburgh Institute

summary: This experiment compares the transcriptional response of control cells with those treated with Doxorubicin only, or a combination of Doxorubicin and Ferrostatin-1

overall_design: Four replicates each for control, four treated with Doxorubicin and four treated with both Doxorubicin and Ferrostatin-1


title: Meiotic Maturation-associated RNA G-quadruplexes removal is Crucial for Translational Activation in Mouse Oocytes

status: Public on Mar 29 2025

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: Following meiosis resumption, the transcription was silencing; and large number of maternal mRNA was actively translated and degraded during oocyte maturation. However, due to the limitation of sample number and technology, the dynamic distribution of RNA structure and its correlation with RNA dynamic change have never been revealed. RNA G-quadruplex (rG4) was a four-stranded RNA secondary structure related to translation regulation and RNA stability. In this study, we developed a low-input technique of rG4 detection (G4-lace-seq), and found that rG4s were highly abundant in fully grown oocytes and reduced during oocyte maturation. We ingeniously applied rG4 stable ligand BYBX in aim to eliminate the DNA G-quadruplex obstruction, and phenotypic analysis showed that rG4 accumulation severely impaired oocytes maturation. Above all, RBPs proteomic spectra revealed RNA structure change caused by G4 accumulation directly weakened the binding of RBPs to RNA, especially the enrichment of G4s affect the RBP binding associated with RNA metabolism, and G4s on the 5′-UTR hindered 40s ribosome movement and binding of 60s ribosome eukaryotic translation initiation factors to RNA. Combined analysis of G4-Lace-seq with Ribo-lite and RNA-seq, further proved that rG4s accumulation on UTRs disrupted translational efficiency and maternal mRNA degradation during oocyte maturation. Overexpression of DHX36, a G4s helicase, rescued the defects caused by BYBX to oocytes and restored the development rates. Jointly analyzing the function and distribution of rG4s and the metabolic signature of maternal mRNA, we hypothesized that a large amount of rG4s present before meiosis resumption is necessary to protect long-term mRNA stability from degradation in a state of poor efficiency translation. Following meiosis resumption, rG4s were cleaned up, translation efficiency increased, and the mRNA became unstable and was rapidly degraded. Collectively, our results announced for the first time that G4, as a secondary structure, had a hand in in the special dynamic rule of RNA content and translation. rG4s clearance determined the fate of cytoplasmic maturation during oocyte maturation.

overall_design: The 4-week-old female mice were injected with 5 IU of pregnant mare’s serum gonadotropin (PMSG, Ningbo Sansheng Pharmaceutical) and humanely euthanized 44h later. Oocytes were obtained in 37°C pre-warmed M2 medium (M7167; Sigma-Aldrich) at the GV stage and cultured in M16 medium (M7292; Sigma-Aldrich) covered with mineral oil (M5310; Sigma-Aldrich) at 37°C in a 5% CO2 atmosphere. BYBX (5 mM) was diluted to a gradient concentration by DMSO and added to M16 medium. Milrinone (2 μM) was applied with the culture medium to inhibit spontaneous GVBD in some experiments.Ribo-lite experiments were improved according to published procedure. Briefly, 500 oocytes were gathered in 1.5 ml Eppendorf LoBind microcentrifuge tubes and lysed with lab-made cell lysis buffer with CHX added. After digesting by RNase I, the pellet ribosome with ribosome-binding fragments (RPF) were centrifuged by Beckman Optima MAX-IP ultracentrifuge. Then the RPF were purified by electrophoresis, and the cDNA library were constructed with Dplex-Small-RNA-seq Kit (DIAGENODE, c05030001).

first: Qiongwen

last: Lu

first: Shaoyuan

last: Liu

first: Yuke

last: Wu

first: Yujing

first: Qianqian

last: Sha


title: Effect of crpPg gene deletion on Porphyromonas gingivalis gene expression

city: Wrocław

first: Michał

last: Śmiga

address: Fryderyka Joliot-Curie 14a

country: Poland

institute: Faculty of Biotechnology, University of Wrocław

summary: Porphyromonas gingivalis is one of the main etiological agents responsible for initiating and progressing periodontal diseases in humans. This bacterium inhabits unfavorable conditions, therefore, to adapt to the changing external environment, e.g. redox conditions, and nutrient limitations, it must respond quickly to these stress factors. For this purpose, it uses transcription regulators. One of them can be the CrpPg protein classified to the CRP/FNR protein superfamily. The goal of this study was to investigate the properties of the CrpPg protein and identify the regulatory pathways it influences related to P. gingivalis virulence. For this, we generated ΔcrpPg mutant strain (A7436ΔcrpPg ) in the A7436 wild-type. Using RNA sequencing (RNA-seq), we examined how the deletion of crpPg affects gene expression in P. gingivalis.

overall_design: Raw data files for the A7436ΔcrpPg mutant strain are provided here, while those for the reference wild-type A7436 strain are available in the Gene Expression Omnibus (GEO; NCBI) under accession number GSE275439.


title: Exploratory pilot study on transcriptome analysis in blood and urine for identifying potential miRNA biomarker candidates to dustinguish of bacterial vs. viral infections in children with fever (blood mRNA)

status: Public on Mar 28 2025

city: Riga

first: Tatjana

last: Kiseļova

address: Dzirciema iela

country: Latvia

institute: Riga Stradins University

summary: There is a lack of fast, reliable and non-invasive methods for distinguishing between bacterial and viral infections in modern clinical practice. It negatively impacts the effectiveness of treatment and increases the risk of unnecessary antibiotic administration and thus antibiotic resistance spread. Using microRNA biomarkers in urine may become the solution to the problems listed. miRNAs in urine are relatively stable and can provide an indirect yet specific insight into systemic infections, thus offering a promising diagnostic tool. Combining urine microRNA analysis with blood transcriptomics allows to explore systemic changes that are not limited to a single biological fluid, improving reliability by cross-verifying findings. In this pilot study, the analysis of urine microRNA and blood full transcriptome sequencing data was carried out in children with bacterial (n = 7), viral infections (n = 7) and controls (n = 8) with the goal of determining microRNA diagnostic signatures that distinguish between the said infections, and connecting differentially expressed urine microRNA with differentially expressed transcripts in blood. Using LASSO regularised regression and ANOVA statistical analysis, microRNA biomarker candidates were prioritised and miRNA:mRNA high-likelihood interactions were analysed using correlation analysis and target prediction to further explore systemic changes in response to infection. The differential expression analysis revealed unique features and common patterns in microRNA expression in infections with bacterial or viral etiology. The resultant five microRNAs chosen by both feature selection methods have shown the ability to cluster bacterial infections patients, viral infections and controls. Subsequent correlation analysis and target prediction revealed the role of microRNA regulation in various immune processes such as the interaction of cytokine and cytokine receptors, as well as the regulation of T-cell activation. Our study suggests that prioritised urine microRNA biomarkers have a strong potential for implementation in clinical diagnostics. This could enable a targeted and timely treatment, potentially reducing the risk of spread of antibiotic resistance.

overall_design: RNA-seq profiling of blood samples from children with confirmed bacterial or viral infections as well as age-matched controls with no signs of infection.

last: Kiselova

first: Baiba

last: Vilne

first: Gunda

last: Zvigule-Neidere

first: Dace

last: Gardovska


title: Type I interferon protects against bone loss in periodontitis by mitigating an interleukin (IL)-17-neutrophil axis [scRNA-seq]

city: Iowa City

first: Shaoping

last: Zhang

address: 801 Newton Rd

department: Periodontics, College of Dentistry

country: USA

institute: University of Iowa

summary: We determined the early inflammatory infiltrates on day 3 after ligature placement, a stage prior to noticeable bone loss, by performing single -cell RNA sequencing (scRNA -seq)

overall_design: We prepared the gingival single -cell suspension pooled from two ligated Ifnar1 -/- mice and two ligated WT mice separately and sorted out live CD45 + immune cells, on which scRNA -seq was perform

first: Jinmei

first: Qiong

last: Ding

first: Angela

middle: X

last: Wang

first: Maoxuan

last: Lin

first: Ning

last: Yu

first: Kevin

last: Moss

first: Megumi

middle: A

last: Williamson

first: Di

last: Mao

first: Julie

middle: T

last: Marchesan

first: Erliang

last: Zeng

first: Wei

last: Shi

first: Hongli

last: Sun

first: Yu Leo

last: Lei


title: The differential impact of HNRNPA1 isoforms on gene expression and their relevance to dsRNA-mediated innate immune response

city: Montreal

first: Christine

last: Vande Velde

state: QC

address: 900, rue Saint-Denis, R09.474

department: Neurosciences

country: Canada

institute: CRCHUM, Universite de Montreal

summary: Heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1) is a highly abundant RNA binding protein alternatively spliced in two main isoforms named, hnRNP A1 and hnRNP A1B. While being ubiquitously expressed, both isoforms have different cellular localizations and are differentially expressed in tissues during development and aging. To improve our understanding of the cellular function of each isoform, we performed RNA sequencing in cells exclusively expressing hnRNP A1 or hnRNP A1B. As expected, some genes were commonly regulated, however >300 genes were differentially regulated by the two isoforms. Functional annotation indicated an enrichment for genes implicate in cellular defense, especially for innate immunity and dsRNA response. Here, we demonstrate that in basal conditions, hnRNP A1, but not hnRNP A1B, represses interferon stimulated genes including the family of dsRNA sensors oligoadenylate synthases (OASs). Thus, the dsRNA-mediated interferon antiviral response can be potentiated by the loss of hnRNP A1-mediated repression.

overall_design: RNA-seq library preparation and sequencing Total RNA was extracted from CB3, CB3 A1 and CB3 A1B cells (in triplicate) using TRIzol™ Reagent (Invitrogen) according to the manufacturer’s instructions. RNA extracts were purified and concentrated using the RNeasy MinElute cleanup kit (Qiagen) following the manufacturer’s instructions. Library preparation and sequencing were performed by the Genome Québec Expertise and Service Center. RNA integrity numbers (RIN), measured on a Bioanalyzer (Agilent), were equal or above 9.7 for all/most samples. For two samples, the Bioanalyzer failed to calculate a RIN number, but manual inspection of the graphs confirmed quality similar to the other samples. An rRNA-depleted stranded (HMR) library was prepared and sequenced via 100 bp paired-end reads on the Illumina NovaSeq 6000 system.

first: Jade-Emmanuelle

last: Deshaies

first: Valérie

last: Triassi

first: Andréanne

last: Lacombe

first: Myriam

last: Gagné

first: Karen

last: Ling

first: Asmita

last: Ghosh

first: Marjorie

last: Labrecque

first: Frank

last: Rigo

first: Paymaan

last: Jafar-nejad

first: Martine

last: Tétreault


title: Impaired ketogenesis in Leydig Cells drives testicular aging

status: Public on Mar 27 2025

city: Guangzhou

first: Jiajie

last: Yu

state: State

address: No.58 Zhongshan Second Road

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Testicular aging commonly leads to testosterone deficiency and impaired spermatogenesis, yet the underlying mechanisms remain elusive. Here, a comprehensive analysis of senescence landscapes in mice testes during aging revealed that the Leydig cells (LCs) are particularly vulnerable to aging processes. Single-cell RNA sequencing identified the expression of Hmgcs2 (3-hydroxy-3-methylglutaryl-CoA synthetase 2), the gene encoding the rate-limiting enzyme of ketogenesis, decreased significantly in LCs from aged mice. Additionally, the concentrations of ketone bodies β-hydroxybutyric acid (BHB) and acetoacetic acid (AcAc) in the young testes were substantially higher than that in serum, but significantly diminished in aged testes. Silencing of Hmgcs2 in young LCs resulted in decreased ketone body production, which in turn drove LCs senescence and accelerated testicular aging. Mechanistically, BHB acted as an endogenous inhibitor of histone deacetylase 1 to upregulate the expression of Foxo3a by promoting histone acetylation, thereby mitigating LCs senescence and promoting testosterone production. Consistently, enhanced ketogenesis by genetic manipulation or oral BHB supplementation alleviated LCs senescence and ameliorated testicular aging in aged mice. These findings highlight defective ketogenesis as a pivotal factor in testicular aging, suggesting novel therapeutic avenues for addressing age-related testicular dysfunction.

overall_design: RNA-seq profiling of MLTC-1 cells treated with DMSO or Hymeglusin and primary Leydig cells isolated from 2- or 24-mon-old mice testes.

first: Congyuan

last: Liu


title: Exploratory pilot study on transcriptome analysis in blood and urine for identifying potential miRNA biomarker candidates to dustinguish of bacterial vs. viral infections in children with fever

first: Tatjana

last: Kiseļova

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Non-coding RNA-seq profiling of urine samples from children with confirmed bacterial or viral infections as well as age-matched controls with no signs of infection.

last: Kiselova

first: Baiba

last: Vilne

first: Gunda

last: Zvigule-Neidere

first: Dace

last: Gardovska


title: Histologic and molecular features shared between antibody-mediated rejection of kidney allografts and chronic histiocytic intervillositis support common pathogenesis

city: PARIS

first: Juliette

last: LEON

address: 149 rue de Sèvres

country: France

institute: APHP

summary: Transcriptomic analyses of placenta with chronic histiocytic intervillositis

overall_design: RNA from FFPE slides from placentas with chronic histiocytic intervillositis or control placentas was extracted and hybrided with the nCounter Banff Human Organ Transplant panel (B-HOT, NanoString Technologies, Seattle, WA, USA)

last: Leon

first: Leonie

last: Albersammer

first: Marion

last: Rabant


title: SARS-CoV-2 induced immune perturbations in infants vary with disease severity and differ from adults’ responses

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

summary: Differences in immune profiles of children and adults with COVID-19 have been previously described. However, no systematic studies have been reported from infants hospitalized with severe disease. We applied a multidimensional approach to decipher the immune responses of SARS-CoV-2 infected infants (n=26; 10 subacute, 11 moderate and 5 severe disease; median age=1.6 months) and matched controls (n=14; median age=2 months). Single cell (scRNA-seq) profiling of PBMCs revealed substantial alterations in cell composition in SARS-CoV-2 infected infants; with most cell-types switching to an interferon-stimulated gene (ISGhi) state including: (i) CD14+ monocytes co-expressing ISGs and inflammasome-related molecules, (ii) ISGhi naïve CD4+ T cells, (iii) ISGhi proliferating cytotoxic CD8+ T cells, and (iv) ISGhi naïve and transitional B cells. We observe increased serum concentrations of both interferons and inflammatory cytokines in infected infants. Antibody responses to SARS-CoV-2 are also consistently detect in the absence of anti-IFN autoantibodies. Compared with infected adults, infants display a similar ISG signature in monocytes but a markedly enhanced ISG signature in T and B cells. These findings provide insights into the distinct immune responses to SARS-CoV-2 in the first year of life and underscore the importance of further defining the unique features of early life immunity.

overall_design:
Single cell RNA-seq profiling (scRNA-seq) of PBMCs  from 26 SARS-CoV-2 infected infants (n=26; 10 subacute, 11 moderate and 5 severe disease; median age=1.6 months) and matched controls (n=14; median age=2 months).

pCoV40_cleaned_12062021.h5ad:
AnnData object containing 40 samples from 26 infants with COVID-19 and 14 healthy controls (i.e. pediatric cohort or pCoV). This object was generated running the scanpy pipeline at:
https://github.com/dnehar/Infants_Cov19
The pipeline includes doublet removal, filtering based on mitochondrial as well as batch effect correction using BBKNN. The number of cells included in the object is 203,402 cells.

paCov_Tsang_harm_withSCs_12072021.h5ad:
AnnData object containing 79 samples from 40 samples from the pediatric cohort (pCoV) and 39 samples from a publicly available adult COVID-19 cohort (aCoV; Tsang lab; GSE161918). The pipeline includes doublet removal, filtering based on mitochondrial as well as batch effect correction using Harmony. The number of cells included in the object is 408,281 cells.
For the re-analysis of GSE161918, the samples of interest (COVID T0 and healthy controls, listed in the 'List_samples_GSE161918.txt') were selected from the seurat object (GSE161918_AllBatches_SeuratObj.rds.gz) at:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161918

Submitter declares that the raw data will be available through dbGAP (phs002655.v1) due to patient privacy concerns.

first: Asunción

last: Mejías

first: Jacques

last: Banchereau

first: Virginia

last: Pascual

first: Octavio

last: Ramilo


title: Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs [RNA-Seq]

status: Public on Apr 01 2025

city: Randwick

first: Julie

last: Thoms

state: NSW

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

department: Adult Cancer Program

country: Australia

institute: UNSW Sydney

summary: Hypomethylating agents are used as frontline therapy for myelodysplastic neoplasms (MDS), but clinical response is unpredictable. To determine whether response was associated with in vivo dynamics of DNA hypomethylation, we conducted a phase 2 trial for MDS using both injection and oral azacitidine (AZA). We established that global DNA methylation levels in peripheral blood and bone marrow mononuclear cells were comparable in AZA responders and non-responders during their course of treatment. However, there were distinct baseline and early drug induced differences in CpG methylation in haematopoietic stem and progenitor cells (HSPCs) in responders compared to non-responders that overlapped with regulatory regions of genes associated with tissue patterning, cell migration and myeloid differentiation. Following six cycles of therapy when clinical response typically manifests, differential hypomethylation in responder HSPCs pointed to marrow adaptation as a driver of enhanced haematopoiesis. Taken together, CpG methylation differences in HSPCs may explain variable response to AZA.

overall_design: Patients were treated with 6 cycles of injected azacitidine, where a cycle consists of 7 days of treatment followed by 21 days rest. Response assessment was done following 6 cycles. Patients then received an additional cycle of oral azacitidine where a cycle consists of 21 days of treatment.

first: Thoms

last: Julie

first: Koch

last: Forrest

first: Pimanda

last: John


title: RNA-seq analysis of human monocytes in patients with and without coronary atherosclerosis

city: Moscow

first: Yegor

middle: S

last: Chegodaev

address: 8, Baltiyskaya st.

department: Ministry of Health of the Russian Federation

country: Russia

institute: Institute Of General Pathology And Pathophysiology, Russian Federation

summary: We conducted RNA-Seq transcriptome profiling on monocytes isolated from patients undergoing coronary angiography. After the procedure, patients were divided into two groups: those without coronary artery stenosis ("w.o. CA", n=11) and those with coronary artery stenosis ("w. CA", n=9). All patients were men, aged 61±6 years. CD14+ monocytes were isolated, and RNA-seq was performed on the Illumina NextSeq 2000 platform. This data was analyzed to identify changes in gene expression profiles associated with coronary atherosclerosis. Transcriptome analysis revealed an upregulation of numerous inflammatory genes. Moreover, we found that the gene expression profile of monocytes from patients with coronary atherosclerosis shifted towards the profile typically observed in minor CD16+ monocyte subsets.

overall_design: After coronary angiography, the patients were divided into two groups: those without coronary artery stenosis ("w.o. CA", n=11) and those with coronary artery stenosis ("w. CA", n=9). All patients were men, aged 61±6 years. CD14+ monocytes were isolated, and RNA-seq was performed using the Illumina NextSeq 2000.

first: Nikita

middle: G

last: Nikiforov

first: Elena

last: Pudova

first: Andrey

middle: V

last: Omelchenko


title: Gene expression profile at single cell level of  testicular cells from young and aged mice

city: guangzhou

first: Liu

last: Congyuan

address: Engineering, Ministry of Education, National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.

institute: Sun Yat-sen University

summary: Testicular aging commonly leads to testosterone deficiency and impaired spermatogenesis, yet the underlying mechanisms remain elusive. Here, we performed a comprehensive scRNA-seq analysis of senescence landscapes in mice testes during aging.

overall_design: We harvested testicular tissue from 2-month-old and 24-month-old mice, isolated the stroma cells, and then performed single-cell sequencing

first: Congyuan

last: Liu

first: Jiajie

last: Yu

first: Hong

last: Chen

first: Peng

last: Luo

first: Yuanchen

last: Ma

first: Wangsheng

last: Ou

first: Suyuan

last: Zhang

first: Hao

last: Peng

first: Cuifeng

last: Yang

first: Kia

last: Xia

first: Andy

middle: P

last: Xiang

first: Chunhua

last: Deng


title: Root growth and branching are enabled by brassinosteroid-regulated growth anisotropy and carbon allocation

city: Haifa

first: Tamar

last: Lahav

address: Zor

department: Biology

country: Israel

institute: Technion

summary: Plants function as an integrated system of interconnected organs, with shoots and roots mutually influencing each other. Brassinosteroid (BR) signaling is essential for whole-plant growth, yet the relative importance of shoot versus root BR function in shaping root system architecture (RSA) remains unclear. Here, we directly tackle this question using micro-grafts between wild-type and BR-null mutants in both Arabidopsis and tomato, assisted by phenotyping, transcriptomics, metabolic profiling, transmission electron microscopy, and modeling approaches. These analyses demonstrate that shoot BR, by determining root carbon availability, allows for a full rescue of mutant root biomass, while loss of shoot BR attenuates root growth. In parallel, root BR dictates the spatial distribution of carbon along the root, through local regulation of growth anisotropy and cell wall thickness, shaping root morphology. A newly developed “grow and branch” simulation model demonstrates that these shoot- and root-derived BR effects are sufficient to explain and predict root growth dynamics and branching phenotype in wild-type, BR-deficient mutants, and micro-graft combinations. Our interdisciplinary approach, applied to two plant species and integrating shoot and root hormonal functions, provides a new understanding of how RSA is modulated at various scales.

overall_design: Whole roots of grafted Col-0 and cpd (combinationations: WT-S/WT-R, WT-S/cpd-R, cpd-S/WT-R and cpd-S/cpd-R), 5 Replicates for each sample, each replicate consists three roots of respective type.

first: Hitaishi

last: Khandal

first: Guy

last: Horev

first: Bas

last: van den Herik

first: Yoram

last: Soroka

last: Avin-Wittenberg

first: Kirsten

last: ten Tusscher

first: Sigal

last: Savaldi-Goldstein


title: ZMYND8 transcriptome in trastuzumab resistant breast tumor cells

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

department: Pathology

institute: UT Southwestern Medical Center

summary: ZMYND8 regulates genes involved in trastuzumab resistance.

overall_design: Isogenic cells were transduced with lentivirus containing ZMYND8 sgRNAs and subjected to mRNA-seq.

first: Yong

last: Wang


title: Multiple sclerosis severity variant in the DYSF–ZNF638 locus associates with increased neuronal loss and inflammation

city: Amsterdam

first: Jeen

last: Engelenburg

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute for Neuroscience

summary: A recent genome-wide association study identified homozygous carriership of the A allele at variant rs10191329 to associate with faster disability accrual in multiple sclerosis (MS). We investigated the impact of rs10191329AA carriership on MS pathology in the Netherlands Brain Bank MS cohort (n=290) and explored its impact on neuro-axonal damage, lymphocyte accumulation, and protein expression of the flanking genes dysferlin (DYSF) and zinc finger protein 638 (ZNF638) by comparing homozygous carriers (n=6) to non-carriers (rs10191329CC; n=12). Homozygous carriership associated with more amyloid precursor protein (APP)+ bulbs/axons, reflecting increased acute axonal stress, in normal-appearing white matter (NAWM) and white matter lesions, as well as with reduced neuronal density in cortical normal-appearing grey matter (NAGM). Further, homozygous carriers showed a higher proportion of active and mixed active/inactive lesions with foamy microglia, which associate with higher cerebrospinal fluid neurofilament light chain levels. DYSF and ZNF638 were expressed by neurons and oligodendrocytes. In homozygous carriers, NAWM was characterized by a higher proportion of ZNF638+ oligodendrocytes, and NAGM showed more DYSF+ cells. Unexpectedly, nuclear RNA sequencing did not show changes in DYSF or ZNF638 expression in oligodendrocytes and neurons but rather an upregulation of mitochondrial genes in homozygous carriers, specifically those associated with Leber’s hereditary optic neuropathy (LHON), a mitochondrial disease that can have a mechanistic interaction with MS. These data suggest that the association between MS severity and rs10191329 may be driven by increased susceptibility to neurodegeneration, demyelination, and chronic inflammatory lesions. Further understanding of the role of DYSF and ZNF638 as well as LHON-associated mitochondrial pathways in MS pathology may reveal new therapeutic targets to attenuate MS progression.

overall_design: To investigate transcriptional differences between MS donors carrying the A:A genotype vs the C:C genotype of rs10191329, we isolated Olig2+ and NeuN+ nuclei from white and grey matter of Netherlands Brain Bank donors. After sorting, we isolated RNA and preformed RNA sequencing.

first: Hendrik

middle: J

first: Aletta

middle: M

last: van den Bosch

first: J

last: Chen

first: Cheng-Chih

last: Hsiao

first: Marie-José

last: Melief

first: Adil

last: Harroud

first: Inge

last: Huitinga

first: Jörg

last: Hamann

first: Joost

last: Smolders


title: A secretome atlas of cardiac fibroblasts from healthy and infarcted mouse hearts

city: Düsseldorf

first: Julia

last: Hesse

address: Universitätsstr. 1

department: Molecular Cardiology

country: Germany

institute: Heinrich Heine University Düsseldorf

summary: Cardiac fibroblasts (CF) are key players after myocardial infarction (MI), but their signaling is only incompletely understood. Here we report a first secretome atlas of CF in control (cCF) and post-MI mouse hearts (miCF), combining a rapid cell isolation technique with SILAC and click chemistry. In CF, numerous paracrine factors involved in immune homeostasis are identified. Comparing secretome, transcriptome (SLAMseq), and cellular proteome disclose protein turnover. In miCF at day 5 post-MI, significantly upregulated proteins include SLIT2, FN1, and CRLF1 in mouse and human samples. Comparing the miCF secretome at days 3 and 5 post-MI reveals the dynamic nature of protein secretion. Specific in-vivo labeling of miCF proteins via biotin ligase TurboID using the POSTN promotor mirrors the in-vitro data. In summary, we identify numerous paracrine factors specifically secreted from CF in mice and humans. This secretome atlas may lead to new biomarkers and/or therapeutic targets for the activated CF.

overall_design: Metabolic RNA sequencing (SLAMseq) of cardiac fibroblasts isolated from adult healthy male C57Bl/6J wildtype mice

first: Ria

last: Zalfen

first: Daniel

last: Rickert

first: Thorsten

last: Wachtmeister

first: Jürgen

last: Schrader


title: Placental cytotrophoblast microvillar stabilization is required for cell-cell fusion

status: Public on Mar 26 2025

city: Edmonton

first: Meghan

last: Riddell

state: AB

institute: University of Alberta

summary: The placenta is an essential organ of pregnancy required for maternal-fetal transport and communication. The surface of the placenta facing the maternal blood is formed by a single giant multinucleate cell: the syncytiotrophoblast. The syncytiotrophoblast is formed and maintained via fusion of progenitor cytotrophoblasts. Cell-cell fusion is a tightly regulated process, and in non-trophoblastic cells is accompanied by stereotypical alterations in cell shape by cells that have attained fusion-competence. The most prominent feature is the formation of actin-based membrane protrusions, but whether stereotypic morphological changes occur in fusion-competent cytotrophoblasts has not been characterized. Using a human placental explant model and trophoblast organoids, we identify apical microvilliation as an obligate morphological feature of fusion-competent cytotrophoblasts. Disruption of microvilli using an inhibitor of the actin-membrane cross linker protein ezrin prevented cytotrophoblast fusion and differentiation. We provide evidence that these polarized apical microvillar domains function to regulate polarized endocytosis and to spatially localize and accumulate a key glycoprotein for fusion, CD98. Thus, we propose that the polarized assembly of microvillar domains is critical for mediating efficient syncytiotrophoblast development.

overall_design:
To understand the role of microvili in cytotrophoblast fusion we utilized an ezrin inhibitor to block the stabilization of microvili in both explants and organoids. We performed RNA-seq analysis at 2 different time points and two different conditions for the explants (Ezrin inhibitor vs control). For the organoids, there were 3 different time points across the two conditions.
Model characterization was also performed for both the explants and the organoids. Three replicates were performed for the explants, and two replicates were performed for the organoids.

first: Juan

last: Garcia Rivas

first: Wendy

last: Duan

first: Sumaiyah

last: Shaha

first: Bethan

last: Wilson


title: The role of TIGIT in idiopathic inflammatory myopathies

first: SHI

last: JIA

state: guangdong province

address: nonglin street

institute: SUN Yat-sen university

summary: To investigate the role of Tight in idiopathic inflammatory myopathies.We evaluated global transcriptome changes in the quadriceps muscles of Tight-/- and WT mice with EAE. For EAM induction, 6-week-old female BALB/c mice were immunized with 100 μl of 50% complete Freund’s adjuvant (Sigma, USA) containing 1mg myosin (or with an equal volume of PBS in control group) on bilateral sides of the hind foot pads, the tail base and flanks four times at 1-week intervals as previously described.

overall_design: Total RNA was isolated from the quadriceps muscles of Tigit-/- and WT mice with EAE

first: Yimei

last: Lai

first: Hui

last: Zhang


title: Type I interferon protects against bone loss in periodontitis by mitigating an interleukin (IL)-17-neutrophil axis [RNA-Seq]

first: Shaoping

summary: We assessed the transcriptomic profile at the late stage on day 10 at the end of the ligature-induced periodontitis model through RNA-seq.

overall_design: We used the ligated gingival samples from the Ifnar1-/- mice and WT mice. The gingival tissues approximating the ligature were collected and RNA-seq were performed at the end of ligature model on day 10 post-ligature placement.

first: Jinmei

first: Qiong

last: Ding

first: Angela

last: Wang

first: Maoxuan

last: Lin

first: Ning

last: Yu

first: Kevin

last: Moss

first: Megumi

last: Williamson

first: Di

last: Mao

first: Julie

last: Marchesan

first: Erliang

last: Zeng

first: Wei

last: Shi

first: Hongli

last: Sun

first: Yu Leo

last: Lei


title: Effect of Tigit deficiency on CD4 T cell

first: SHI

summary: To  investigate the role of TIGIT in CD4+ T cell differentiation, Total CD4+ T cells were isolated from WT or Tigit -/- mice. Cells were stimulated with anti-CD3/CD28 for 3 d. Cells were then collected and total RNA was extracted.

overall_design: Total CD4+ T cells were isolated from WT or Tigit -/- mice. There were 3 biological replicates in each group.


title: Hedgehog-interacting protein orchestrates alveologenesis and protects against BPD and emphysema by modulating hedgehog-IGF1 signaling axis

city: Zhongshan

first: Chaoqun

state: Guangdong province

address: Xiangshan Street

institute: Zhongshan Institute for Drug Discovery, Chinese Academy of Sciences

summary: A majority of the gas-exchange surface is generated during alveologenesis, and disruption of this process causes bronchopulmonary dysplasia (BPD) in preterm infants, characterized by alveolar simplification. BPD is a significant risk factor for adult emphysema, marked by alveolar loss. A comprehensive molecular understanding of alveologenesis and effective treatments for BPD and emphysema are still lacking. Here, we show that the cells expressing Hhip, a gene associated with both BPD and emphysema, expand within the alveoli during alveologenesis, followed by hedgehog (Hh) inhibition and myofibroblast transition. Stromal-specific deletion of Hhip leads to aberrant persistence of SMA+ alveolar myofibroblasts, mediated by a hyperactive Hh-IGF1 axis. Conditional knockout animal and 3D stroma-stem cell organoid models demonstrate that loss of Hhip induces alveolar stem/progenitor cell senescence in a non–cell-autonomous manner. Alveolar simplification and BPD phenotypes induced by Hhip deletion can be partially rescued by IGF1 signaling blockade. We also observe the downregulation of Hhip expression and hyperactivation of Hh-IGF1 signaling in hyperoxia-induced BPD animal models. In addition, adult mice deficient in Hhip expression develop emphysema phenotype with abnormal alveolar myofibroblasts. Finally, we develop a therapeutic Fc-fused HHIP recombinant protein that attenuates BPD phenotypes in postnatal mice and emphysema in adult mice. These findings underscore the critical role of HHIP in coordinating alveologenesis and preventing BPD and emphysema by restricting Hh-IGF1 signaling.

overall_design: For mouse scRNA-seq, all live mesenchymal and epithelial cells were sorted from two Gli1creERT/+: Hhipflox/flox 14 days post-birth. Mesenchymal cells were isolated based on forward and side scatter, DAPI, CD31, CD45 and CD326 exclusion. epithelial cells were isolated based on DAPI, CD31 and CD45 exclusion. One mouse was challenged with tamoxifen and one was treated with oil at the same timepoints as a control. The sorted mesenchymal and epithelial cells were resuspended in PBS containing 0.05% BSA in a 3:1 mixture. Cells were loaded onto a single lane per sample into the ChromiumTM Controller to produce gel bead-in emulsions (GEMs). GEMs underwent reverse transcription for RNA barcoding and cDNA amplification, with the library prepped using the Chromium Next GEM Single Cell 5' Kit v2. Each sample was sequenced in 1 lane of the HiSeq2500 (Illumina) in Rapid Run Mode.

first: Datian

last: Ye


title: Concerted epithelial and stromal changes during progression of Barrett’s Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis

first: Lorenzo

last: Ferri

state: Quebec

address: 1650 Cedar Avenue

department: Surgery & Oncology

institute: McGill University

summary: Esophageal adenocarcinoma arises from Barrett’s esophagus, a precancerous metaplastic replacement of squamous by columnar epithelium in response to chronic inflammation. Multi-omics profiling, integrating single-cell transcriptomics, extracellular matrix proteomics, tissue-mechanics and spatial proteomics of the paths of progression from squamous epithelium through metaplasia, dysplasia to adenocarcinoma, in a total of 107 samples from 26 patients in two independent cohorts revealed shared and patient-specific progression characteristics. The metaplastic replacement of epithelial cells was paralleled by changes in stromal cells, ECM and tissue stiffness. Strikingly, this change in metaplasia was already accompanied by appearance of fibroblasts with characteristics of carcinoma-associated fibroblasts and of an NK cell-associated immunosuppressive microenvironment. Thus, Barrett’s esophagus progresses as a coordinated multi-component system, supporting treatment paradigms that go beyond targeting cancerous cells to incorporate stromal reprogramming.

overall_design: scRNAseq of normal, metaplastic, dysplastic and cancerous human esophageal tissue

first: Michael

middle: K

last: Strasser

first: David

middle: L

last: Gibbs

first: Philippe

last: Gascard

first: Joanna

last: Bons

first: John

middle: W

last: Hickey

first: Deng

last: Pan

first: Joseph

last: Caruso

first: Xianhong

first: Chira

last: Chen-Tanyolac

first: Rosemary

last: Bai

first: Christian

last: Schürch

first: Yuqi

last: Tan

first: Sarah

last: Black

first: Pauline

last: Chu

first: Alican

last: Ozkan

first: Nathan

last: Basisty

first: Veena

last: Sangwan

first: Jacob

last: Rose

first: Samah

last: Shah

first: Jordan

middle: B

last: Burton

first: Sophie

last: Camilleri-Broet

first: Pierre-Oliver

last: Fiset

first: Nicolas

last: Bertos

last: Berube

first: Haig

last: Djambazian

first: Rui

last: Li

first: Spyridon

last: Oikonomopoulos

first: Daffolyn

middle: R

last: Fels-Elliott

last: Vernovsky

first: Elee

last: Shimshoni

first: Deborah

last: Collyar

first: Ann

last: Russell

first: Jiannis

last: Ragoussis

first: Matthew

middle: D

last: Stachler

first: James

last: Goldenring

first: Stuart

last: McDonald

first: Donald

middle: E

last: Ingber

first: Birgit

last: Schilling

first: Garry

last: Nolan

first: Thea


title: Tick-borne flavivirus exoribonuclease-resistant RNAs contain a double loop structure

city: Aurora

last: Szucs

state: CO

institute: University of Colorado Denver Anschutz Medical Campus

summary: Viruses from the Flaviviridae family contain human relevant pathogens that generate subgenomic noncoding RNAs during infection using structured exoribonuclease resistant RNAs (xrRNAs). These xrRNAs block progression of host cell’s 5′ to 3′ exoribonucleases. The structures of several xrRNAs from mosquito-borne and insect-specific flaviviruses reveal a conserved fold in which a ring-like motif encircles the 5′ end of the xrRNA. However, the xrRNAs found in tick-borne and no known vector flaviviruses have distinct characteristics and their 3-D fold was unsolved. Here, we verify the presence of xrRNAs in the encephalitis-causing tick-borne Powassan Virus. We characterize their secondary structure and obtain a mid-resolution map of one of these xrRNAs using cryo-EM, revealing a unique double loop ring element. Integrating these results with covariation analysis, biochemical data, and existing high-resolution structural information yields a model in which the core of the fold matches previously solved xrRNA fold, but the expanded double loop ring is remodeled upon encountering the exoribonuclease. These results are representative of a broad class of xrRNAs and reveal a conserved strategy of structure-based exoribonuclease resistance achieved through a unique topology across a viral family of importance to global health.

overall_design: SHAPE-MaP and DMS-MaP probing of the class 2 xrRNA from the liniage II Powassan Virus (DTV) spooner isolate in the context of the  in vitro transcribed full 3'UTR, sfRNA1, and sfRNA2 .

first: Conner

last: Langeberg

first: Madeline

last: Sherlock

first: Quentin

last: Vicens

first: Jeffrey

last: Kieft


title: Effects of overexpression of PTPN21 on gene expression of Jurkat cells

city: Hangzhou

first: Ni

last: Zhu

address: 54 Youdian Road

department: Hematology

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

summary: Acute Lymphoblastic Leukemia (ALL) is a malignant disease characterized by the abnormal growth of immature lymphocytes. The high resistance to chemotherapy drugs and frequent recurrence contribute to low long-term survival in ALL patients. Presently, PTPN21 is associated with cancer development. Our research revealed that elevated PTPN21 levels hindered the apoptosis of ALL cells triggered by chemotherapy drugs like vincristine and daunorubicin. Through a series of laboratory experiments, we established that PTPN21 regulates ALL drug resistance to vincristine via GADD45A and the JNK signaling pathway. Additionally, the over-expression of PTPN21 reversed the cell cycle arrest in the G2/M phase induced by vincristine. As a phosphatase, targeting PTPN21 inhibition may offer a new approach for addressing drug resistance in recurrent and refractory ALL in the future.

overall_design: To investigate the key molecules involved in PTPN21-mediated apoptosis inhibition, we conducted transcriptome sequencing in Jurkat cells after 48h of incubation with VCR. Jurkat cells in both control and PTPN21 overexpressed groups were treated with VCR for 48 hours. Subsequently, cells from both groups were harvested for RNA sequencing (RNA-seq) with three replicates per group. The sequencing of Digital Gene Expression Tag Profiling and data analysis were outsourced to a commercial company (Pinggu Biotechnology Co., Wuhan, China).


title: Expression profile of gemcitabine resistant pancreatic cancer cells

status: Public on Mar 25 2025

city: Pittsburgh

first: Song

last: Li

state: Pennsylvania

address: 335 Sutherland Dr, Pittsburgh, PA 15213, Salk Pavilion room 223

institute: University of Pittsburgh

summary: To investigate the expression profile in gemcitabine resistant cells, we generated gemcitabien resistant KPC2 cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type and gemcitabine resistant KPC2 cell line

first: Haozhe

last: Huang

first: Yiqing

last: Mu


title: RNA Transcripts Serve as a Template for Double-Strand Break Repair in Human Cells

city: New York

first: Hina

last: Shah

state: NY

address: 430 East 67th Street

department: Molecular Biology

institute: Sloan Kettering Institute

summary: Double-strand breaks (DSBs) are toxic lesions that lead to genome instability. While canonical DSB repair pathways typically operate independently of RNA, emerging evidence suggests that RNA:DNA hybrids and transcripts near damaged sites can influence repair outcomes. However, a direct role for transcript RNA as a template during DSB repair in human cells is yet to be established. In this study, we designed fluorescent- and sequencing-based assays, which demonstrated that RNA-containing oligonucleotides and messenger RNA serve as templates to promote DSB repair. We conducted a CRISPR/Cas9-based genetic screen to identify factors that promote RNA-templated DSB repair (RT- DSBR), and of the candidate polymerases, we identified DNA polymerase-zeta (Polζ) as the potential reverse transcriptase that facilitates RT-DSBR. Furthermore, by analyzing sequencing data from cancer genomes, we identified the presence of whole intron deletions, a unique genomic scar reflective of RT- DSBR activity generated when spliced mRNA serves as the repair template. These findings highlight RT- DSBR as an alternative pathway for repairing DSBs in transcribed genes, with potential mutagenic consequences.

overall_design: Amplicon sequencing of adjacent exons to identify if the intron they flank is removed from the genomic sequence. This whole intron deletion serves to measure repair templated by the endogenous spliced mRNA after a DSB within the intron. 293T TP53BP1-/- cells were analyzed at: introns of highly transcribed loci CALR intron 2 and GNAS intron 11, nontranscribed loci IL3 intron 4, adjacent introns, and in a REV3L knockdown derivative.


title: Proteome-wide determinants of co-translational chaperone binding in bacteria

city: SEVILLA

first: Carla

middle: Veronica

last: Galmozzi

state: SEVILLA

address: Avda. Manuel Siurot s/n

department: Genetics

country: Spain

institute: Instituto de Biomedicina de Sevilla

summary: Chaperones are essential to the co-translational folding of most proteins. However, the principles of co-translational chaperone interaction throughout the proteome are poorly understood, as current methods are restricted to few substrates and cannot capture nascent protein folding or chaperone binding sites, precluding a comprehensive understanding of productive and erroneous protein biosynthesis. Here, by integrating genome-wide selective ribosome profiling, single-molecule tools, and computational predictions using AlphaFold we show that the binding of the main E. coli chaperones involved in co-translational folding, Trigger Factor (TF) and DnaK correlates with “unsatisfied residues” exposed on nascent partial folds – residues that have begun to form tertiary structure but cannot yet form all native contacts due to ongoing translation. This general principle allows us to predict their co-translational binding across the proteome based on sequence only, which we verify experimentally. The results show that TF and DnaK stably bind partially folded rather than unfolded conformers. They also indicate a synergistic action of TF guiding intra-domain folding and DnaK preventing premature inter-domain contacts, and reveal robustness in the larger chaperone network (TF, DnaK, GroEL). Given the complexity of translation, folding, and chaperone functions, our predictions based on general chaperone binding rules indicate an unexpected underlying simplicity.

overall_design: In this study, we employed selective ribosome profiling of key chaperones across various Escherichia coli strains to elucidate the co-translational chaperone network throughout the proteome.

first: Frank

last: Tippmann

first: Florian

last: Wruck

first: Josef

last: Auburger

first: Ilia

last: Kats

first: Manuel

last: Guennigmann

first: Katharina

last: Till

first: Edward

last: O´Brien

first: Sander

last: Tans

first: Günter

last: Kramer

first: Bernd

last: Bukau


title: Exploration of conserved human adipose subpopulations using targeted single cell nuclei RNAseq datasets

city: Scarborough

first: Lucy

last: Liaw

state: ME

address: 81 Research Drive

department: Center for Molecular Medicine

institute: MaineHealth Institute for Research

summary: Smooth muscle cells and pericytes are mural cells. Pericytes can differentiate into myofibroblasts, chondrocytes, vascular smooth muscle cells, and adipocytes, marking them as a distinct progenitor population. Our goal was to molecularly define the progenitor cell populations in human adipose tissues and test the adipogenic potential of human mural cells. Single-cell transcriptomic profiling of primary human cultured vascular smooth muscle cells (VSMCs) treated with either lipogenic media or VSMC differentiation media was conducted to elucidate signals associated with the lipogenic phenotype observed in these primary vascular cells.

overall_design: VSMCs were obtained from two sources. Either derived from a surgically removed aortic wall of an abdominal aortic aneurysm patient, or purchased from ATCC (cat# PCS-100-012TM). Group one (DM) underwent VSMC differentiation, cultured with VSMC differentiation medium (DM, SmBM2 containing 2% FBS and 1mg/ml heparin). Group two (Adipo-B) underwent lipogenesis treatment, cultured with lipogenic induction medium (Lipo-T). Cells were harvested and fixed. Fixed cells were subjected probe-targeted scRNAseq.

first: Christian

last: Potts

first: Xuehui

last: Yang

first: Matthew

last: Lynes

first: Kimberly

last: Malka


title: Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [RNA-seq]

city: Hefei

first: Yan

address: No.373 Huangshan Road

institute: University of Science and Technology of China

summary: α-satellite RNA has been shown to interact with specific sets of RNA-binding proteins. By forming complexes with centromere proteins CENPA, CENPB, and CENPC, α-satellite RNA demonstrated its essential role in maintaining functional human centromeres. Also, α-satellite RNA has been reported to interact with SUV39H1, which is the histone methyltransferase that is responsible for H3K9me3. Together with the findings in mice and some other eukaryotes that RNA components are required for the recruitment of heterochromatin proteins and the maintenance of pericentric heterochromatin, it has long been suspected that α-satellite RNA might also be involved in the heterochromatin formation and recruitment of HP1 in human cells. In this study, we identified Scaffold Attachment Factor-A (SAF-A) as a novel α-satellite RNA binding protein. SAF-A, also known as hnRNPU, the most abundant member in the hnRNP complex, was initially identified as the major component of the nuclear scaffold. It binds to the nuclear scaffold in AT-rich regions through its DNA-binding domain. In recent years, several studies have suggested that SAF-A may play a more fundamental and general role in nuclear organization in interphase. Depletion of SAF-A will lead to pronounced chromatin condensation of gene-rich regions and global changes in 3D genome architecture.

overall_design: RPE1 cells were synchronized to four distinct cell cycle stages: G1, S, G2, and M phase. EU-RNA-seq was conducted on cells at these stages, as well as on asynchronous RPE1 cells.

first: Bingbing

last: Ren

first: Yinchun

last: Zhong

first: Ge

last: Shan


title: Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [ChIRP-seq]

summary: RNA components seem to be required for the localization of SAF-A on chromatin. A SAF-A/RNA mesh model has been proposed and supported by super-resolved images, in which SAF-A forms a homogeneous mesh together with nuclear scaffolding RNA species to regulate chromatin structure. As an evolutionarily conserved RNA-binding protein, SAF-A has been reported to interact with a wide variety of RNAs in different cell types. Particularly, a recent study points out that repetitive non-coding sequences of pre-mRNAs and lncRNAs can serve as scaffold RNAs to counter chromatin compaction and maintain chromosome territory architecture together with SAF-A. At this moment, most studies have demonstrated the role of SAF-A/RNA in regulating interphase chromatin structure, and very few works have covered the role of SAF-A/RNA in mitosis. A recent study showed that SAF-A, together with most of its interacting RNAs, needs to be evicted from the condensing chromosomes during mitosis. This brings out an open question of how the SAF-A/RNA scaffold is disassembled and rebuilt when the cell enters and exits mitosis. Here, we showed that α-satellite RNA is dynamically expressed and stays associated with the centromeric chromatin throughout the mitotic cell cycle. Specific interactions between α-satellite RNA and SAF-A were observed both in vitro and in vivo. Depletion of either α-satellite RNA or SAF-A would lead to chromosome missegregation phenotypes during mitosis. More importantly, interfering with α-satellite RNA showed an evident effect on the chromatin relocalization of SAF-A, and further LAP2 upon mitosis exit. Therefore, we proposed that α-satellite RNA may act as a foundation stone for recruiting SAF-A scaffold upon mitosis exit.

overall_design: To investigate the genomic regions associated with α-satellite, we targeted α-satellite by antisense biotin-tagged probes and performed ChIRP experiments in both mitotic and  asynchronized RPE cells.


title: Histone Methyltransferase ASH1L Primes Metastases and Metabolic Reprogramming of Macrophages in the Bone Niche

city: Houston

first: Chenling

last: Meng

state: TX

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

summary: ASH1L promotes cancer metastasis, we performed single-cell RNA sequencing (scRNA-seq) to investigate the impact of ASH1L on  the crosstalk of  invading cancer cells and immune cells in metastatic bone niches

overall_design: To generate a syngeneic bone metastasis model,DX1 cells with or without ASH1L KD were injected into the tibia of 6-week-old male C57BL/6 mice. 3wk ater injection, control and ASH1L-knockout metastatic bone tumors were dissected, minced, and digested for scRNA-seq

first: Di

last: Zhao


title: CUT&RUN of NFKB1 and JUN in TNF treated RPTEC cells

city: Ediburgh

first: Maximilian

last: Reck

address: 47 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

summary: Analysis of snATAC-seq data suggests increased motif of NFKB and AP-1 motifs of renal epithelia in kidney injury. To confirm binding sites we performed CUT&RUN of JUN and NFKB1 transcription factors in TNF-alpha treated cultured primary human renal proximal tubule cells.

overall_design: Primary human renal proximal tubule cells were cultured and treated with 20ng/ml of TNF-alpha 24hours before harvest. Cells were detached and nuclei isolated. The CUT&RUN assay was then performed using the ChIC/CUT&RUN kit (EpiCypher). Positive reactions were performed using JUN and NFKB1 antibodies. Background signal was assessed using an IgG antibody.

first: Bryan

last: Conway


title: Nanostring CosMx 980-plex RNA profiling of human kidney biopsy and nephrectomy

summary:
The human kidneys are comprised of multiple different cell types in a complex anatomical arragemnt that is optimal for their key functions such as waste removal, regulation of fluid and electrolyte homeostasis and production of hormones. In chronic kidney disease (CKD) this arrangement is disrupted with de-differentiation and atrophy of epithelial cells, recruitment of immune cells and activation of myofibroblasts to produce excess scarring. A better understanding of cellular phenotypes, complex intercellular communication and intracellular signaling pathways that promote CKD could lead to development of novel therapies.
We applied single-cell spatial transcriptomics (CosMx Spatial molecular imaging) to human kidney biopy and nephrectomy samples from patients with IgA nephropathy (n=6), minimal change disease (n=3) and advanced pyelonephritis (n=4).

overall_design:
FFPE biopsy or nephrectomy samples with IgA nephropathy (n=6), minimal change disease (n=3) and advanced pyelonephritis (n=4) were profiled using the Nanostring CosMx.
A total of 980 transcripts were targeted. PanCK, CD45 and CD3 and DAPI were used for cell visualisation.
3 biopsy or 4 nephrectomy samples were adhered to the same microscope slide and profiled in the same run. Slides were prepared and imaged according to manufacturer protocols.


title: Bulk RNA-seq of irradiated RPTEC cells

summary: RPTEC cells were cultured and irradiated to induce cellular senescence. Bulk RNA-seq was performed to observe the transcriptional response.

overall_design: RPTEC/TERT1 cells were cultured under standard conditions and plated into six well plates. Two groups of 5 replices were studied. The irradiated group either irradiated (10Gy)  or not irradiated (Control). After 7 days RNA was extracted, polyA-enriched libraries for RNA-seq prepared and sequenced.


title: Interferon gamma suppresses T follicular helper cells and antibody responses upon viral infection

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

summary: Humoral and cellular immunity upon viral infections usually co-exist; however, sometimes, one of the two responses emerges as dominant and is responsible for most of the antiviral activity. For example, infection with lymphocytic choriomeningitis virus (LCMV) induces very strong cellular responses, but weak and inefficient neutralizing Ab (nAb) responses. Lack of nAb responses is an important issue for complete clearance of LCMV and other similar viruses, which in some instances tend to establish chronic infections. Recent work from our group has shown that this unbalance is observed also at the level of CD4 T cells responses, with subcutaneous LCMV infection leading almost exclusively to TH1 but no TFH differentiation.  Here, we report that LCMV-induced TH1 cells are heterogeneous and comprise a Tcf-1+ subset and a GzmB+ subset. We found that none of the subsets is dependent on the major TH1-polarizing cytokine IL-12. Instead, IFN-gamma (IFN-g) was found to promote the development of GzmB+ cells and to suppress the commitment of the Tcf-1+ population into fully differentiated TFH. As a result, blockade of IFN-g led to a rescue in the TFH population, germinal center B cells and antibody responses. Our results shed light on new mechanisms underlying the inefficient nAbs production in response to non-cytopathic viruses such as LCMV and are promising for the design of new vaccination strategies.

overall_design: scRNA-seq was performed on SMARTA CD4+ T cells which are specific for the MHC-II-restricted GP61-80 epitope of the LCMV glycoprotein. Naïve SMARTA CD4+ T cells were adoptively transferred into WT mice one day prior to s.c. intrafootpad infection with rLCMV and sorted from footpad-draining popliteal LNs (dLNs) five days after infection. To be able to compare transcriptional profiles of TH1 to those of TFH cells, we also sorted total SMARTA CD4+ T cells from dLNs of mice infected with rVSV, a recombinant VSV strain expressing the LCMV WE glycoprotein. Control SMARTA CD4+ T cells were isolated from naïve mice.

first: Eleonora

last: Sala

first: Chiara

last: Laura

first: Eyal

last: David

first: Matteo

last: Iannacone

first: Mirela

last: Kuka


title: Plasmid DNA or mRNA formulated in lipid nanoparticles drive unique innate immune activation to promote adaptive immunity

status: Public on Mar 24 2025

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Gene-vectored vaccines grew in importance over the past several years. However, understanding the differences between of lipid nanoparticle (LNP) formulations for delivering DNA and mRNA in particular has not been studied. Characterization of LNP-formulated DNA compared with mRNA could build upon current genetic delivery approaches. Here, we study a four-component ionizable LNP33 plasmid DNA formulation (DNA-LNPs) which we demonstrate induces potent innate and adaptive immunity at low doses with similar potency to mRNA-LNPs and adjuvanted protein. Using an influenza virus hemagglutinin-encoding construct (HA), we show that these DNA-LNPs drive potent inflammation dependent on the cGAS-STING-TBK1 pathway but independent of TLR9. Priming with HA DNA-LNP demonstrated robust activation in migratory DC (mDC) subpopulations and significant upregulation of mDCs and neutrophils. Transcriptomics elucidated activation and upregulation of pro39 migration factors among multiple innate immune populations after priming with DNA-LNP. HA DNALNP uniquely induced superior HA-specific CD8+ 40 T cell responses relative to other platforms. HA DNA41 LNP additionally induced robust germinal center responses attenuated in frequency to mRNA-LNPs and adjuvanted protein, but with equivalent functional serum antibodies. Extending these findings to an additional pathogen antigen, SARS-CoV-2 spike-encoding DNA-LNP elicited protective efficacy comparable to spike mRNA-LNPs. Thus, this study identifies priming mechanisms and characterizes immune phenotypes after DNA-LNP immunization, suggesting additional avenues for vaccine development.

overall_design: Single Cell RNA-Seq of cells from lymph nodes of mice left naïve, or treated with DNA vaccine, mRNA vaccine, or adjuvanted protein vaccine

first: Nicholas

last: Tursi

first: David

last: Weiner


title: Single-nuclei RNA/ATAC-seq of healthy and injured human kidney nephrectomy tissue

summary: Improved understanding of the renal cell phenotypes and intercellular signaling pathways that mediate chronic kidney disease is required to develop novel therapeutics. To this end, we performed simultaneous single nuclear RNA and ATAC-sequencing on kidney tissue from patients undergoing tumour nephrectomy, where the ureter was either obstructed by tumour or remained unobstructed. In obstructed kidneys a discrete subset of proximal and ascending thin limb of loop of Henle tubular cells acquired a pro-inflammatory phenotype enriched in senescence markers.

overall_design: We performed single-nuclei RNA and ATAC sequencing using the 10x Genomics Multiome kit to profile gene expression and chromatin changes during kidney injury. Nuclei were isolated from human kidney nephrectomy tissue and 3-5 samples were pooled and processed simultaneously.


title: A high-quality transcriptome of Chinese local pig

city: Yunnan Kunming

first: Huo

last: Jinlong

address: Jinhei Road 95

institute: Yunnan Agricultural University

summary: PacBio SMRTseq long reads and Illumina short reads of pig heart, kidney, liver, lung, and spleen

overall_design: Use PacBio IsoSeq to sequence pig heart, kidney, liver, lung, and spleen RNAs

first: Guiying

first: Jinlong

last: Huo


title: Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and 3D genome alterations to stimulate oncogene expression [ChIP-seq_ECa_patients]

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

institute: Netherlands Cancer Institute

summary:
The incidence and mortality of Endometrial Cancer (EC) is on the rise. 85% of ECs depend on Estrogen Receptor alpha (ERα) for proliferation, but little is known about its transcriptional regulation in these tumors. We generated epigenomics and Hi-C data streams in healthy and tumor endometrial tissues, identifying robust ERa reprogramming and profound alterations in 3D genome organization that lead to a gain of tumor-specific enhancer activity during EC development. Integration with WGS data from metastatic samples revealed a striking enrichment of non-coding somatic mutations at tumor-enriched ERa sites. Through machine learning-based predictions and interaction proteomics analyses, we identified an enhancer mutation which alters 3D genome organization, impairing recruitment of the transcriptional repressor EHMT2/G9a/KMT1C, thereby alleviating transcriptional repression of ESR1 in EC. In summary, we identified a complex genomic-epigenomic interplay in EC development and progression, altering 3D genome organization to enhance expression of the critical driver ERα.

Keywords: Genome binding/occupancy profiling by high throughput sequencing

overall_design:
4 healthy and 5 tumor endometrial tissues derived from Endometrial Cancer patients.
Antibodies against ERα (SantaCruz #sc-543, 5µg/IP) and H3K27ac (ActiveMotif #39133, 5µg/IP)

Raw data are available with restricted access at the EGA under accession number EGAS00001007240.

first: Sebastian

last: Gregoricchio

first: Aleksandar

last: Kojic

first: Marlous

last: Hoogstraat

first: Karianne

last: Schuurman

first: Suzan

last: Stelloo

first: Tesa

last: Severson.

first: Tracy

last: O’Mara

first: Marjolein

last: Droog

first: Abhishek

last: Singh

first: Dylan

last: Glubb

first: Lodewyk

middle: F

last: Wessels

first: Michiel

last: Vermeulen

first: Flora

last: van Leeuwen


title: Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and 3D genome alterations to stimulate oncogene expression [RNA-seq_ECa_patients]

summary: The incidence and mortality of Endometrial Cancer (EC) is on the rise. 85% of ECs depend on Estrogen Receptor alpha (ERα) for proliferation, but little is known about its transcriptional regulation in these tumors. We generated epigenomics and Hi-C data streams in healthy and tumor endometrial tissues, identifying robust ERa reprogramming and profound alterations in 3D genome organization that lead to a gain of tumor-specific enhancer activity during EC development. Integration with WGS data from metastatic samples revealed a striking enrichment of non-coding somatic mutations at tumor-enriched ERa sites. Through machine learning-based predictions and interaction proteomics analyses, we identified an enhancer mutation which alters 3D genome organization, impairing recruitment of the transcriptional repressor EHMT2/G9a/KMT1C, thereby alleviating transcriptional repression of ESR1 in EC. In summary, we identified a complex genomic-epigenomic interplay in EC development and progression, altering 3D genome organization to enhance expression of the critical driver ERα.

overall_design: RNA has been extracted by RNeasy mini kit from around 30mg of flash frozen tissue derived from 3 healthy and 3 tumor endometrial tissues of post-menopausal patients. Raw data are available at EGA under restricted access: EGAS00001007240


title: RNA seq in sensitive A2780 epithelial ovarian cancer cell with FLYWCH1 knockdown and resistant cells with FLYWCH1 overexpression.

status: Public on Mar 21 2025

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

institute: University Stuttgart

summary: RNAseq in sensitive A2780 cells with shRNA induced knockdown of FLYWCH1 and resistant A2780cis cells with induced overexpression of FLYWCH1.

overall_design: For FLYWCH1 KD RNAseq, cells were transduced with control shRNAs and shRNAs targeting FLYWCH1. Treatment with 1 µM cPt was started 7 days after knockdown induction. After completion of the experiment (week 7) cells were sorted for shRNA expressing cells. For FLYWCH1 overexpression RNAseq, cells were transduced with constructs for the overexpression of 3xFLAG or FLYWCH1-3xFLAG. After seven days of overexpression induction, cells were sorted for 3xFLAG/FLYWCH1-3xFLAG expressing cells. RNAseq was performed for all samples.

first: Tabea

last: Fullstone

first: Helene

last: Rohm


title: Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and 3D genome alterations to stimulate oncogene expression [ChIP-seq_Ishikawa]

city: Amsterdam

first: Wilbert

last: Zwart

overall_design: Ishikawa cell lines have been cultered for 3 days in 5%DCC and phenol-red-free media. Upon 6 hours treatment with 10nM estradiol (E2) ChIP was performed using G9a/EHMT2 antibody (Abcam #ab133482, lot # GR154986-1; 5µg/IP). Two biological replicates are provided.


title: Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and 3D genome alterations to stimulate oncogene expression

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

overall_design: Refer to individual Series

first: Sebastian

last: Gregoricchio

middle: A


title: Hydrogen sulfide preserves intestinal barrier repair function through sulfhydration of RPS20 in experimental colitis

city: Beijing

first: Xuan

last: He

address: Xishiku street, Xicheng, Beijing

department: Department of Gastrointestinal Surgery

institute: Peking University First Hospital

summary: Patients with ulcerative colitis (UC) have a significantly impaired intestinal barrier. Hydrogen Sulfide (H2S) is a gaseous mediator that makes notable contributions in a variety of diseases, such as reducing inflammatory response in colitis. The experimental content includes the establishment of a mouse DSS-induced colitis model, mouse colon epithelial organoids culture, H&E staining and mass spectrometry analysis. We recognized that exogenous H2S donor-GYY4137 significantly alleviated the symptoms in UC mice models and maintained Minichromosome Maintenance Complex Component 2 (MCM2) expression. CBS knockdown reduced the expression of sulfhydrated Ribosomal protein S20 (RPS20-ssh) and MCM2 in the mouse colon. Cell experiments indicated that the expression of RPS20-ssh, rather than total expression of RPS20, is responsible.

overall_design: The CRISPR/Cas9 system was used to achieve stable knockout of the CBS gene in Caco-2 cells. In short, the interference target sgRNA was designed according to the sequence of the CBS gene as follows: CTGATGAGATCCTGCAGCAG. We phosphorylated, annealed, and cloned the guide oligonucleotide into the BsmBI site of the pHBLV-U6-gRNA-EF1-CAS9-PURO vector (Hanheng Biotechnology, China), and then verified the constructed vector by sequencing. The transferred plasmid with the guide oligonucleotide was then transformed into E. coli DH5a, and was isolated from the bacteria using a plasmid DNA purification kit (Tiangen, China). The transferable lenti-CAS-puro plasmid, packaging plasmids psPAX2 and pMD2G (Hanheng Biotechnology, China) were transfected into 293 T cells to produce lentivirus. 48 and 72 hours after transfection, the virus-containing supernatant was collected and then used to transfect Caco-2 cells. After 24 h of infection, the medium in each plate was replaced with fresh medium containing puromycin (30 mg/L) for 24 h, and then with fresh medium for 24 h. Three times of repetition were done. Finally, puromycin-resistant Caco-2 cells were collected and western blot was used to detect the CBS knockout efficiency.

first: Pengyuan

last: Wang

first: Shanwen

last: Chen

first: Jichang

last: Li


title: Maternal immune activation elicits rapid and sex-dependent changes in gene expression and vascular dysfunction in the rat placenta

city: London

first: Stephen

last: Renaud

state: Ontario

address: 1151 Richmond St, MSB428

institute: University of Western Ontario

summary: Introduction: Maternal immune activation (MIA), characterized by increased circulating inflammatory mediators during pregnancy, is associated with adverse pregnancy outcomes and neurodevelopmental deficits in offspring. These health outcomes often manifest differently depending on fetal-placental sex. A well-established model of MIA involves administration of a viral mimetic, polyinosinic:polycytidilic acid (PolyI:C), to pregnant rodents. Placental responses to PolyI:C contribute to the detrimental effects of MIA on offspring, but these responses have not yet been well characterized. In the present study, we profiled acute gene expression changes in male and female placentas following PolyI:C administration to pregnant rats. Methods: Pregnant rats received 4 mg/kg PolyI:C or saline intravenously on gestational day 18.5, and tissues were harvested 4-5 hours later. Gene expression profiling on placental tissue was performed. Enzyme immunoassays and immunohistochemistry were conducted to determine levels of select proteins in maternal blood and placental tissue, respectively. Results: Maternal PolyI:C exposure caused a robust increase in levels of inflammatory markers in maternal blood and placental tissue. There were more genes differentially expressed in female placentas after PolyI:C exposure (765) than male placentas (221), including reduced expression of genes associated with maternal-fetal communication. Placentas also had increased expression of genes linked with vascular dysfunction after PolyI:C-induced MIA. Discussion: PolyI:C elicited a powerful inflammatory response in the placenta along with vascular dysfunction, likely contributing to the adverse pregnancy outcomes triggered by MIA. Female placentas responded to PolyI:C more vigorously than male placentas, which could underlie the differential outcomes of MIA depending on sex.

overall_design:
Pregnant Sprague-Dawley rats (4 rats per group) were injected with sterile saline or 4 mg/kg PolyI:C sodium salts on gestational day 18.5. Placentas were collected 5 h later.
Placentas were collected 5 h after injections. Based on genotyping fetuses, one male and one female placenta were used for downstream analyses (therefore 8 placentas per treatment group).
RNA was extracted by homogenizing in TRIzol. After adding chloroform, the aqueous phase was collected and diluted 1:1 with 70% ethanol, placed on RNeasy columns (Qiagen Inc), treated with DNase I, and RNA purified.
Libraries were generated using the NEBNext directional library prep kit for Illumina (New England Biolabs). Indexed libraries were sequenced on a NovaSeq 6000 system (Illumina) at Génome Québec (Montréal, QC, Canada) using a 100 bp, paired-end read format.

first: Erin

last: Biggar

first: Ruth

last: Thomas


title: Premature thymic involution in young Foxn1lacz mutant mice causes peripheral T cell phenotypes similar to aging-induced immunosenescence

city: Nashville

first: Seung Woo

last: Kang

state: TN

address: MRBIV 10475, 2215 Garland Avenue

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

summary: The thymus is a primary lymphoid organ generating self-restricted and self-tolerant naïve T-cells. Early in life the thymus starts to involute, resulting in decreased naïve T-cell output which may be more self-reactive, leading to an increased prevalence of autoimmunity. A decrease in the transcription factor FOXN1 is an early event in thymic involution. Using the Foxn1lacz model, we studied how premature thymic involution affects the thymic microenvironment, thymocytes, and peripheral T cell immunity. We found that early thymic involution led to aged-like thymic epithelial cells that resulted in aged-like thymocyte phenotypes, with a significant decrease in CD4+ single-positive T-cells. We also observed severe lymphopenia in Foxn1lacz mice caused by the premature decrease in T-cell production, resulting in a peripheral T-cell phenotype similar to de novo aged peripheral T-cells. Moreover, following T cell receptor stimulation, Foxn1lacz peripheral T cells had reduced IL-2 secretion and strong initial IFN-g responses, resembling aged wild-type peripheral T-cell responses. Lastly, influenza response in Foxn1lacz had a reduction in some aspects of T cell responses to influenza infection, similar to thymectomized mice. Our study shows an independent and direct impact of premature thymic involution on both thymopoiesis and peripheral immune niches likely contributing to immunosenescence and inflammaging as observed in the elderly population.

overall_design: 1. Total thymic stroma (CD45-) of 1-month-old (30-day-old) male Foxn1+/+ and Foxn1lacZ/lacZ. 2. Total splenocyte of 1-month-old (30-day-old) female Foxn1+/+ and Foxn1lacZ/lacZ and 18-month-old female Foxn1+/+.


title: Meningeal lymphatics-microglia axis regulates synaptic physiology [ligation]

city: St. Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

summary: Meningeal lymphatics serve as the primary outlet for cerebrospinal fluid, and their dysfunction is associated with various neurodegenerative conditions. Previous studies have demonstrated that dysfunctional meningeal lymphatics evoke behavioral deficits, but the neural mechanisms underlying those behavioral changes remained elusive. Here, we show that prolonged impairment of meningeal lymphatics alters the balance of cortical excitatory and inhibitory synaptic inputs by reducing inhibitory synapses, accompanied by deficits in novelty recognition tasks. These synaptic and behavioral alterations are mediated by microglia, which exhibit transcriptomic, morphological, and functional alterations as a result of lymphatic dysfunction. Notably, microglial expression of Il6 increases, thereby mediating the reduction in inhibitory synapses via neuronal signaling. Interestingly, improving the function of meningeal lymphatics in aged mice restores the numbers of functional inhibitory synapses and cortical network activity. Our findings suggest that dysfunctional meningeal lymphatics adversely impact cortical circuitry through a microglia−IL-6-dependent mechanism, providing a potential target for the treatment of aging-associated cognitive decline.

overall_design: The subject sham/dCLN-ligated 8-weeks-old C57BL/6J male mice were cardio-perfused with 30 ml of 5 U/ml Heparin-PBS after 4-weeks from dCLN-ligation/sham operation. Brains were harvested, located in heparin-PBS and cut through the sharp razor roughly at the AP=+1.00 mm. The anterior part of the brain faces down to the bottom at the section point and is cut horizontally half and half to remove the olfactory tract and striatum; only the upper chunk was used as a PFC sample.  5 PFC samples were pulled per group, and minced with the sharp razor in RPMI 1640 medium with 2% FBS and digested by collagenase VIII and DNase (in 5 ml RPMI 1640 + 2 % FBS) for 45 minutes and titrated with P1000 pipettes once at 30 minutes after digestion starts, and one more at 45 minutes after.  Samples were strained through a 70-um strainer, and 5 ml RPMI 1640 + 10% FBS medium was added to stop digestion and spun down in 450g for 5 minutes. Pellets were resuspended in 14% BSA and spun down in 800 g for 10 minutes with slow acceleration/declaration. Supernatnace was removed carefully, and the pellet was resuspended in MACS buffer (0.5% BSA, 2 mM EDTA containing PBS), followed by spinning down (450g, 5 mins). 50 ul of CD45-bead (Miltenyi, 130-052-301) was added with 450 ul MACS buffer, and CD45+ cells were prepared according to the manufacturer's protocol.

first: Kyungdeok

last: Kim

first: Daviti

last: Abramishvili

first: Siling

last: Du

first: Zachary

last: Papadopoulos

first: Jay

last: Cao

first: Igor

last: Smirnov

first: Jean-Leon

first: Marco

last: Colonna


title: The olfactory receptor OR51E2 regulates prostate cancer aggressiveness and modulates STAT3 in prostate cancer cells and in xenograft tumors

city: Aarhus N

first: Mikkel

middle: Thy

last: Thomsen

state: Midtjylland

address: Palle Juul-Jensens Boulevard 99

department: Department of Clinical Medicine

country: Denmark

institute: Aarhus University

summary: Despite significant advancements in prostate cancer detection and treatment, the molecular mechanisms driving its progression remain elusive. This study aimed to explore the role of the receptor OR51E2, which is frequently upregulated in prostate cancer, in the disease's progression. Using CRISPR-Cas9 technology, we generated monoclonal OR51E2 knockout cells to investigate the receptor's physiological effects. We assessed the tumorigenic potential of these cells both in vitro and in vivo, and conducted transcriptomic and proteomic analyses on xenograft tumors derived from the knockout cells. Additionally, we examined how varying levels of OR51E2 expression in patients from a TCGA cohort impacted disease outcomes. The OR51E2-knockout cells displayed increased proliferation, migration, adhesion, anchorage-independent colony formation, and tumor growth, leading to a more aggressive cancer phenotype. Omics analyses identified several pathways associated with significant molecular changes, particularly an aberration in the STAT3 pathway linked to IL-6 signaling, underscoring a connection to inflammatory pathways. Analysis of the TCGA cohort further revealed that prostate cancer patients with lower OR51E2 expression had worse prognoses and higher average Gleason grades compared to those with higher expression levels. This analysis also supported a role for OR51E2 in modulating the STAT3 pathway within the cohort. Overall, our findings suggest that OR51E2 plays a critical role in regulating prostate cancer progression by influencing cancer cell physiology and aggressiveness. Reduced OR51E2 expression may lead to poorer patient outcomes, potentially through disruptions in the STAT3 pathway that alter cellular responses to inflammatory signaling.

overall_design: To investigate the effects of OR51E2 on in vivo prostate cancer tumor growth, we designed a stable, monoclonal OR51E2-knockout LNCaP-derived cell line. LNCaP WT or OR51E2-KO cells were injected subcutaneously in male CIEA NOG mice and were allowed to grow to a size og 1000 mm3, where the tumors were harvested and snap frozen. Total RNA was extracted from these tumors, sequenced, and the expression data was analyzed (mouse reads removed prior to analysis). 9 WT tumors and 8 KO tumors were analyzed.

middle: T

first: Morten

last: Busk

first: Dalin

last: Zhang

first: Chun-Lung

last: Chiu

first: Hongjuan

last: Zhao

first: Fernando

last: Garcia-Marques

first: Abel

last: Bermudez

first: Sharon

last: Pitteri

first: Michael

last: Borre

first: James

last: Brooks

first: Jens

last: Nyengaard


title: Next Generation Sequencing facilitates to identify the differential expression genes of sorted conventional CD8+ T cells and MAIT cells

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

summary: We obtained conventional CD8+T cells and MAIT cells  to rperforme next-generation sequencing (NGS).  Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2000 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results，we performed the GO and KEGG pathway enrichment analysis. That might suggest the different status of HBV-infected liver from liver surgery(AST<40) and liver transplantation(AST>40).

overall_design: Differential gene expression between MAIT cells  from different patients

first: Xiufang

last: Weng


title: MANF relieves cerebral infarction injury by enhancing the pyroptosis inhibition of BMSCs

city: Harbin

first: Pan

last: yujun

state: Heilongjiang Province

address: No. 23, Youzheng Street, Nangang District

institute: the First Clinical College of Harbin Medical University

summary: Cerebral infarction is a common disease characterized by high mortality, narrow therapeutic window and limited therapeutic avenue.We constructed animal model of Middle Cerebral Artery Occlusion (MCAO), compared different expression genes (DEGs) between Sham and MCAO group by single-cell RNA sequencing (scRNA-seq) to explore the potential cell death-related pathways involved in cerebral infarction.We found that the DEGs up-regulated in four major cellclusters after MCAO were enriched for not only apoptosis, ferroptosis and necroptosis, but also pyroptosis-related pathways and functions. Surprisingly, our protein-protein interaction (PPI) networks analysis showed indirect correlation between MANF and pyroptosis-related proteins.

overall_design: Examination of 2 groups of Sham and MCAO, we mixed 5 samples per group into one cell suspension pools.

first: Yujun

last: Pan

first: Qi

first: Shanshan

last: Shi

first: Yushi

last: Tang


title: Transcriptional effect of SPARCL1 treatment on lung alveolar organoids

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

summary: Lung endothelial cells (ECs) and pericytes are closely juxtaposed with the respiratory epithelium before birth and thus may have instructive roles during development.  To test this hypothesis, we screened EC-secreted proteins for their ability to alter cell differentiation in alveolar organoids.  We identified SPARCL1 as an extracellular matrix molecule that can promote AT2 cell differentiation in vitro.  SPARCL1-treated organoids display lysozyme upregulation and a doubling in the number of differentiated AT2 cells at the expense of intermediate progenitors.  SPARCL1 also induces the upregulation of NF-κB target genes, and suppression of NF-κB activation in lung organoids blocked SPARCL1 effects.  NF-κB activation by LPS was sufficient to induce AT2 cell differentiation; however, pharmacological inhibition of the pathway alone did not prevent it.  These data support a role for SPARCL1 and NF-κB in alveolar cell differentiation and suggest a potential value in targeting this signaling axis to promote alveolar maturation and regeneration.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from lung alveolar organoids treated with recombiant SPARCL1 (2 µg/ml for 24h) versus controls.

first: Paolo

last: Panza

first: Stefan

last: Günther


title: Nanostring CosMx 6,000-plex RNA profiling of human kidney nephrectomy specimens

status: Public on Mar 20 2025

first: Maximilian

last: Reck

type:
Expression profiling by array
Other

summary:
The human kidneys are comprised of multiple different cell types in a complex anatomical arragemnt that is optimal for their key functions such as waste removal,
regulation of fluid and electrolyte homeostasis and production of hormones. In chronic kidney disease (CKD) this arrangement is disrupted with de-differentiation
and atrophy of epithelial cells, recruitment of immune cells and activation of myofibroblasts to produce excess scarring. A better understanding of cellular phenotypes, complex intercellular communication and intracellular signaling pathways that promote CKD could lead to development of novel therapies.
We applied single-cell spatial transcriptomics (CosMx Spatial molecular imaging) to human kidney neprectomy speciemens with unilateral ureteral obstruction (UUO, n=5) and healthy kidneys (n=2).

overall_design:
A total of 6,000 transcripts were targeted. PanCK, CD45 and CD3 and DAPI were used for cell visualisation.
All three nephrectomy specimens were adhered to the same microscope slide and profiled in the same imaging run. Slides were prepared and imaged according to manufacturer protocols.


title: Paramutation-like behaviour of genic piRNA-producing loci in Drosophila virilis

city: Moscow

first: Alina

last: Bespalova

address: Vavilova, 32

department: Russian Academy of Sciences

institute: Engelhardt Molecular Biology Institute

summary: Piwi-interacting RNAs (piRNAs) play a crucial role in silencing transposable elements (TEs) in the germ cells of Metazoa by acting as sequence-specific guides. Originating from distinct genomic loci, called piRNA clusters, piRNA can trigger an epigenetic conversion of TE insertions into piRNA clusters by means of paramutation-like process. However, the variability in piRNA clusters' capacity to induce such conversion remains poorly understood. Here, we investigated two Drosophila virilis strains with differing capacities to produce piRNAs from the RhoGEF3 and Adar gene loci. We found that active piRNA generation correlates with high levels of the heterochromatic mark H3K9me3 over genomic regions that give rise to piRNAs. Importantly, maternal transmission of piRNAs drives their production in the progeny, even from homologous loci previously inactive in piRNA biogenesis. The subtelomeric RhoGEF3 locus, once epigenetically converted, maintained enhanced piRNA production in subsequent generations lacking the original allele carrying the active piRNA cluster. In contrast, piRNA expression from the converted Adar locus was lost in offspring lacking the inducer allele. Our findings highlight that the paramutation-like behavior of piRNA clusters is influenced not only by piRNAs but also by structural features of chromosomal regions, providing new insights into epigenetic regulation in Drosophila.

overall_design: The submission includes samples from chromatin immunoprecipitation sequencing (ChIP-seq), RNA-seq and small RNA-seq from ovaries of female Drosophila virilis. The research focuses on two distinct Drosophila virilis strains: strain 9, collected from Batumi, Georgia, and the laboratory strain 140 (eb, va).

first: Dina

last: Kulikova

first: Elena

last: Zelentsova

first: Alexander

last: Rezvykh

first: Julia

last: Guseva

first: Ana

last: Dorador

first: Justin

last: Blumenstiel

first: Mikhail

last: Evgen’ev

first: Sergei

last: Funikov


title: Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and 3D genome alterations to stimulate oncogene expression [Hi-C_ECa_patients]

first: Wilbert

last: Zwart

overall_design:
For Hi-C libraries preparation we used 3x10 50um-thick slices of flash frozen tissue derived from 3 healthy and 3 tumor endometrial tissues of post-menopausal patients.

***************************************************************
Raw data are available at EGA under restricted access: EGAS00001007240
***************************************************************

first: Sebastian

last: Gregoricchio