title: Gene expression profile at single cell level of blood neutrophils  sorted from  young and old mice

city: Shanghai

first: guiheng

last: zhang

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

summary: The differences of neutrophils clusters and genes expression between blood neutrophils sorted from young and old mice

overall_design: To investigate the the features and function of senescent neutrophils during aging, we performed single cell RNA-sequencing analysis by using BD Rhapsody system from blood neutrophils sorted from young and old mice

first: Qingchen

last: Zhu

first: Guiheng

first: Yichuan

last: Xiao


title: Single-cell RNA sequencing of PBMCs from COVID-19 recovered adolescents (n = 3) and adults (n = 3)

status: Public on Feb 25 2025

first: yangdian

last: lai

address: South Chongqing Road 281

country: China

institute: Shanghai Jiaotong University School of Medicine

type: Expression profiling by high throughput sequencing

summary: We performed single-cell RNA sequencing (scRNA-seq) on PBMCs from convalescent COVID-19 adolescents aged 10-15 years old (n=3) and convalescent adults aged over 40 years old (n=3) .We have  observed LDLR+ macrophages displaying heightened IFNI responses in BCG-vaccinated adolescent COVID-19 patients.

overall_design: Freshly isolated PBMCs from 3 recovered COVID-19 adults (aged over 45) and 3 recovered COVID-19 adolescents (aged under 15) were diluted as a single cell suspension with cell viability exceeding 90%.

last: Lai

first: yingying

last: Chen

first: ying

last: Wang


title: Epigenetic priming promotes acquisition of TKI resistance and oncogene amplification in human lung cancer [CUT&RUN]

status: Public on Feb 26 2025

city: New Haven

first: Eric

last: Sun

state: CT

address: 10 Amistad St

department: Genetics

country: USA

institute: Yale University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In mammalian cells, gene copy number is tightly controlled to maintain gene expression and genome stability. However, a near-universal molecular feature across cancer types is oncogene amplification, which promotes cancer progression by dramatically increasing the copy number and expression of tumor-promoting genes. For example, in tyrosine kinase inhibitor (TKI)-resistant lung adenocarcinoma (LUAD), oncogene amplification occurs in over 40% of patients’ tumors. Despite the prevalence of oncogene amplification in TKI-resistant tumors, the mechanisms facilitating oncogene amplification are not fully understood. Here, we find that LUAD tumors exhibit a unique chromatin signature demarcated by strong CTCF and cohesin deposition in drug-naïve tumors, which correlates with the boundaries of oncogene amplicons in TKI-resistant LUAD cells. Throughout the acquisition of TKI resistance, we identified a global chromatin priming effect, marked by a dynamic increase of H3K27Ac, cohesin loading, and inter-TAD interactions, which occurs before the onset of oncogene amplification. Furthermore, we have identified that the protein METTL7A, which was previously reported to localize to the ER and inner nuclear membrane, has a novel chromatin regulatory function in binding to amplified oncogenes and regulating cohesin recruitment and inter-TAD interactions. Surprisingly, we discovered that METTL7A remodels the chromatin landscape prior to any noticeable oncogene copy number gains. Furthermore, while METTL7A depletion has little effect on drug-naïve cells, METTL7A depletion prevents the formation of TKI resistant-clones, highlighting the specific role of METTL7A as cells are acquiring resistance. In summary, we discovered an unexpected mechanism required for the acquisition of TKI resistance regulated by a largely uncharacterized factor, METTL7A. This discovery sheds new light into maintenance of oncogene copy number and paves the way to the development of new therapeutics for preventing TKI resistance in LUAD.

overall_design: CUT&RUN: CUT&RUN was performed in PC9 wild-type, PC9 METTL7A KO (PC9_M7A_KO), and PC9 METTL7A Rescue (overexpression of METTL7A-MYC-tag_FLAG in METTL7A KO cells) against IgG, H2A, PDS5A, RAD21, and H3K27Ac.

first: Rebecca

middle: M

last: Starble

middle: G

first: Rana

last: Gybli

first: Jonathan

last: Radda

first: Jiuwei

last: Lu

first: Tyler

middle: B

last: Jensen

first: Ning

first: Shuai

last: Zhao

first: Nitin

last: Roper

first: Gang

first: Jikui

last: Song

first: Katerina

last: Politi

first: Siyuan

first: Andrew

middle: Z


title: The effect of CTBP dehydrogenase inhibitors MTOB and 4-Cl-HIPP in J774.1 cells

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

summary: C-terminal binding proteins (CTBPs) are conserved transcriptional repressors involved in cancer and inflammation. Uniquely amongst transcriptional coregulators, CTBPs possess a functional dehydrogenase domain. Since multiple malignancies display elevated CTBP levels, CTBP inhibitors targeting this dehydrogenase domain have been developed. While the importance of CTBPs dehydrogenase function for transcriptional regulation remains unclear, multiple studies have relied CTBP inhibitors such as MTOB and 4-Cl-HIPP. In vitro studies have confirmed binding of these compounds to CTBP’s active site, however evidence for specificity is currently lacking. To address this, we treated wildtype or Ctbp1, 2 double knockout J774.1 cells with MTOB or 4-Cl-HIPP and performed RNAseq. We observed that both inhibitors elicit distinct transcriptional changes indicating non-overlapping modes of action. Moreover, the majority of changes induced by either inhibitor are observed in knockout cells indicative of off-target effects. We hypothesize that those CTBP dehydrogenase inhibitors might lack specificity to CTBPs.

overall_design: To investigate whether commonly used inhibitors of C-terminal binding proteins (CTBPs) MTOB (4-methylthio-2-oxybutyrate) and 4-Cl-HIPP (3-(4-Chlorophenyl)-2-(hydroxyimino)propanoic acid) specifically affect CTBPs function, wildtype and Ctbp1-/-, Ctbp2-/- (Ctbp1/2dKO) cells of the macrophage cell line J774.1 were treated with either inhibitor or a vehicle control (n=3 for each combination of genotype and treatment). Following RNA extraction, library preparation and RNA sequencing we assess transcription rates altered between wildtype and knockout and compare alterations by genotype to effects elicited by the inhibitors versus vehicle control. To define specificity we then investigate whether inhibitor effects observed in the wildtype are present in CTBP1/CTBP2 knockout cells.

first: Benjamin

middle: A

last: Strickland

first: Nina Henriette

last: Uhlenhaut


title: 4E-BP1-dependent translation in microglia controls mechanical hypersensitivity

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

summary: Spinal microglia play a pivotal role in the development of neuropathic pain. Peripheral nerve injury induces changes in the transcriptional profile of microglia, including increased expression of components of translational machinery. Whether microglial protein synthesis is stimulated following nerve injury and has a functional role in mediating pain hypersensitivity is unknown. Here, we show that nascent protein synthesis is upregulated in spinal microglia following peripheral nerve injury in both male and female mice. Stimulating mRNA translation in microglia, by selectively ablating the translational repressor eukaryotic initiation factor 4E-binding protein 1 (4E-BP1), promoted the transition of microglia to a reactive state and induced mechanical hypersensitivity in both sexes, whereas spontaneous pain was increased only in males. Conversely, inhibiting microglial translation by expressing a mutant form of 4E-BP1 in microglia attenuated their activation following peripheral nerve injury and alleviated neuropathic pain in both sexes. Thus, stimulating 4E-BP1-dependent translation promotes microglial reactivity and mechanical hypersensitivity, whereas inhibiting it alleviates neuropathic pain.

overall_design: Spinal microglia from WT and 4E-BP1 cKO mice (lacking 4E-BP1 in microglia) were FACS-sorted and sequenced using scRNAseq

first: Kevin

middle: C

last: Lister

first: Calvin

last: Wong

first: Weihua

last: Cai

first: Sonali

last: Uttam

first: Theodore

middle: J

last: Price

first: Jeffrey

middle: S

last: Mogil

first: Arkady

last: Khoutorsky


title: RNA-seq Analysis of Vesicular Stomatitis Virus (VSV)-Infected RAW264.7 Macrophages with and without Prior BCG-lysate  Exposure

first: yangdian

last: lai

summary: Our findings demonstrated that BCG treatment significantly reduced the intracellular viral titers of Vesicular Stomatitis Virus (VSV). To explore the molecular mechanisms responsible for the enhanced antiviral immunity of BCG-trained macrophages, we conducted RNA sequencing analysis on RAW264.7 cells infected with VSV, comparing macrophages pre-exposed to BCG with those without prior exposure.

overall_design: To explore the impact of BCG-induced trained immunity on antiviral responses, we initially established an in vitro cellular model by treating RAW264.7 cells with BCG lysate for 24 hours, followed by a 5-day rest period. Subsequently, both PBS-treated and BCG-trained RAW264.7 cells were infected with Vesicular Stomatitis Virus (VSV) in vitro for 48 hours.

first: ying

last: wang


title: Effects of daridorexant on gene expression in the hypothalamus of LPS-induced mice.

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

summary: Acute inflammatory processes disrupt hypothalamic homeostatic systems, leading to a preference for sleep over wakefulness. Orexin knockout mice exhibit faster recovery from LPS-induced sickness, possibly due to enhanced sleep during inflammation. The reduction in orexin activity limits physical activity and encourages sleep, though it remains uncertain whether these responses are pathological or protective. In this study, to investigate the effects of daridorexant, a dual orexin receptor antagonist, on brain inflammation and sleep quality, we employed a systemic inflammatory model in C57BL/6J mice. LPS treatment resulted in significant decreases in REM sleep and wakefulness, while non-REM sleep increased. Here, we provide gene expression profiling of hypothalamus tissues using the RNA sequencing for identifying changes by daridorexant in gene expression of the LPS-treated mice.

overall_design: mRNA profiles of  hypothalamus were generated by RNA sequencing using the Illumina NextSeq 500  (Illumina).

first: Dai

last: Horiuchi

first: Koichiro

last: Tatsumi


title: Transcriptomic changes after orexin receptor antagonism in P301S/E4 mouse model of tauopathy

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

summary: Our aim was to investigate whether increasing sleep via orexin receptor antagonism can modify tau-mediated neurodegeneration and neuroinflammation.

overall_design: Cortex mRNA profiles of 41 weeks old P301S/E4 mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000.

first: Samira

last: Parhizkar

first: David M

last: Holtzman

first: Xin

last: Bao

first: Wei

last: Chen

first: Nicholas

last: Rensing

first: Yun

first: Michael

last: Kipnis

first: Sihui

last: Song

first: Grace

last: Gent

first: Melissa

last: Manis

first: Choonghee

last: Lee

first: Javier Remolina

last: Serrano

first: Megan E

last: Bosch

first: Emily

last: Franke

first: Carla M

last: Yuede

last: Landsness


title: Sustained epigenetic reactivation in fragile X neurons with an RNA-binding small molecule [RNA-seq]

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

summary: Fragile X syndrome (FXS) is a disease of pathologic epigenetic silencing induced by RNA. In FXS, an expanded CGG-repeat tract in the FMR1 gene induces epigenetic silencing during embryogenesis.  FMR1 silencing can be reversed with 5-aza-deoxyctidine (5-aza-dC), a nonspecific epigenetic reactivator; however, continuous administration of 5-aza-dC is problematic due to its toxicity.  We describe an approach to restore FMR1 expression in FXS neurons by transient treatment with 5-aza-dC, followed by treatment with 2HE-5NMe, which binds the CGG-repeat expansion in the FMR1 mRNA and blocks the resilencing of the FMR1 gene after withdrawal of 5-aza-dC.  Genome-wide profiling of histone marks shows that 2HE-5Nme maintains FMR1 in a reactivated state. FMR1 reactivation in neurons results in re-expression of FMRP and reversal of FXS-associated dendritic spine defects.  These results demonstrate that an RNA-binding small molecule can achieve gene-specific epigenetic control, and provide an approach for restoration of FMRP in FXS neurons.

overall_design: WCM37 or SI-214 cells were plated on 35 mm dishes and differentiated as described above. The differentiated neurons were next incubated in 5-aza-dC (1 µM) for 7 days. Media was then used to wash out 5-aza-dC and then the neurons were incubated in media with 2HE-5NMe or vehicle (DMSO) for 14 days. Media was removed from cells and then RNA was extracted from the cells using Trizol (Invitrogen, 15596026) following the manufacturer’s instructions. The RNA was precipitated using isopropanol, washed with 70% ethanol and resuspended in water. The RNA (100 ng) was then converted into a cDNA library using the SMART-seq mRNA LP (with UMIs) kit (Takara, 634762) following the manufacturer’s instructions. The quality of the library was assessed using a High Sensitivity D5000 ScreenTape assay (Agilent) and then the cDNAs were sequenced using a NovaSeq 6000 with S1 Flow Cells (paired end, 2x50 bp).

first: Christina

middle: W

last: Kam

first: Jason

last: Dumelie

first: Gabriele

last: Ciceri

first: Wang-Yong

last: Yang

first: Matthew

middle: D

last: Disney

first: Lorenz

last: Studer

middle: R


title: Sustained epigenetic reactivation in fragile X neurons with an RNA-binding small molecule [CUT&RUN]

overall_design: CUT&RUN was performed following the published protocol by Skene et al (2018). On day 21 of neuronal differentiation, WT or FXS patient-derived induced neurons were plated at 150K/cm2. Neurons were treated for 7 days with 5-aza-dC, if indicated, and 14 days with DMSO or 500 nM 2HE-5NMe, if indicated. 300,000 FXS neurons were harvested, washed and bound to beads. Neurons-beads were divided into three aliquots for determining binding locations of IgG control, H3K4me3, and H3K27me3. Neurons were permeabilized and the appropriate primary antibodies were utilized on each aliquot separately. Protein A-MNase fusion protein (gifted by the Henikoff lab) was then added to bind to primary antibody locations. Targeted digestion was activated with addition of calcium and occurred for 5 minutes. Cut fragments were then released from insoluble nuclear chromatin and extracted using NucleoSpin columns (Takara) following manufacturer’s instructions. Size selection was performed using AMPure XP beads (Agencourt) before library preparation with the Kapa Hyper Prep Kit (Roche) following manufacturer’s instructions. End repair and A-tailing were performed before adapter ligation with TruSeq (Illumina) indices. The libraries were amplified and then quality control was performed to ensure that primer dimers were negligible. 150 base pair-end sequencing was performed with HiSeq by the Genomics Core Facility of the WCM Core Laboratories Center. We used an alignment strategy that eliminates reads that align to any mouse transcripts, since some mouse feeder cells may have remained in the sample used for CUT&RUN.  Paired-end reads were aligned to human genome version GRCh38.p13 using Bowtie2. Reads were normalized for sizes of libraries. Reads were then mapped onto a list of all protein-coding gene promoters (-1000 to +1000 of MANE Select transcription start sites from GRCh38.p13).


title: Tissue nanotransfection-based endothelial PLCγ2-targeted epigenetic gene editing in vivo rescues diabetic ischemic wound healing

city: Pittsburgh

first: CHANDAN K

last: SEN

state: PA

address: 221 Republic Street

institute: University of Pittsburgh

summary: Diabetic wounds often suffer from poor perfusion. Reliance on VEGF therapy to improve perfusion makes logical sense, yet clinical study outcomes fall far short of expectations. Our previous work has identified that genetically silenced phospholipase Cγ2 (PLCγ2) hinders VEGF therapy of the diabetic ischemic limb. However, the underlying mechanisms remained unknown. Emerging evidence supports the notion that hyperglycemia leads to DNA methylation-based gene silencing. Given that epigenetic changes are reversible, this work guided by scRNA sequencing of human wound-edge, tests the efficacy of gene-targeted therapeutic demethylation with respect to enabling VEGF therapy. Bipedicle ischemic wounds were placed in diabetic mice. PLCγ2 promoter CpG methylation were analyzed using bisulfite sequencing. To specifically demethylate endothelial PLCγ2 promoter during VEGF therapy, a CRISPR/dCas9-based demethylation cocktail was delivered to the wound-edge using tissue nanotransfection (TNT) technology. The functional outcome of such demethylation was assessed using perfusion imaging. PLCγ2 promoter was hypermethylated at murine diabetic ischemic wound-edge. Demethylation-based upregulation of PLCγ2 during VEGF therapy improved wound tissue blood flow with increased abundance of vWF+/PLCγ2+ vascular tissue elements by activating p42/p44-MAPK→HIF1α pathway. Taken together, TNT-based endothelial demethylation of the PLCγ2 gene promoter improved VEGF therapy on the perfusion of cutaneous diabetic wounds resulting in improved closure.

overall_design: single cell RNA sequeing from chronic wound-edge samples from diabetic and non diabetic subjects

first: Kanhaiya

last: Singh

first: Chandan

middle: K

last: Sen

first: Rajneesh

last: Srivastava

first: Sumit

last: Verma


title: Transcriptomes of BNST brain regions from mouse model of anxiety

city: Nan Jing

first: Yizhou

last: Hong

state: Jiang Su

address: No. 639, Longmian Avenue, Jiangning District, Nanjing City

institute: China Pharmaceutical University

summary: The bed nucleus of the stria terminalis (BNST), as part of the extended amygdala, is a sexually dimorphic and highly complex structure and has become a region of increasing interest regarding its role in numerous human stress-related psychiatric diseases, including post-traumatic stress disorder and generalized anxiety disorder amongst others.  We performed RNA sequencing on the BNST brain region of male and female mice in both the control group and the CRS-induced anxiety-like group.

overall_design: Total RNA of mouse brain were sequenced by deep sequencing using Illumina HiSeq 2500

first: Shiya

last: Zhang

first: Haiyang

last: Hu


title: Gene expression changes in tomato hairy root cultures with pertubations in exodermis-enriched transcription factors.

city: Utrecht

first: Leonardo

last: Jo

email: l.jo@uu.nl, jo.leonardo85@gmail.com

address: Padualaan 8, Z309

department: Institute of Environment Biology

country: Netherlands

institute: Utrecht University

summary: This study provides the overall changes in gene expression in tomato hairy root cultures with CRISPR knockouts (ko) or 35Spro-driven overexpression (OX) of exodermis enriched transcription factors.  The transcription factors investigated in this study are: SlMYB41 (Solyc02g079280.3.1), SlMYB92 (Solyc05g051550.2.1) and SlWRKY71 (Solyc02g071130.3.1).

overall_design: In this study, RNA was extracted and sequenced from 1cm root tips of tomato (Solanum lycopersicum) cultivar M82 hairy-root cultures to investigate the transcriptome impact of transcription factor genes, specifically SlMYB41, SlMYB92, and SlWRKY71. Hairy-root cultures were transformed with different constructs to generate three experimental groups: (1) control lines transformed with an empty vector, (2) knock-out (KO) lines transformed with CRISPR/Cas9 constructs carrying guide RNAs to specifically knock out SlMYB41, SlMYB92, and SlWRKY71, and (3) overexpression (OE) lines transformed with constructs expressing SlMYB41-3xFLAG, SlMYB92-3xFLAG, and SlWRKY71-3xFLAG under the control of the constitutive CaMV 35S promoter. For each group, mRNA was isolated from the hairy-root cultures, and RNA sequencing was performed to profile global gene expression changes associated with the knockout or overexpression of the target transcription factors.

first: Jo

last: Leonardo

first: Buti

last: Sara

first: Rianne

last: Kluck

first: Kajala

last: Kaisa


title: Transcriptomes across seven brain regions from mouse model of anxiety

summary: Anxiety disorders are highly heterogeneous diseases. The molecular mechanisms underlying multi-brain region origin and sex dimorphism remain largely unknown. Herein, by leveraging large-scale transcriptomes across seven brain regions from mouse model of anxiety and extensive experiments at the molecular, synapse activity, and behavior levels, we dissected brain region- and sex-specific gene networks and identified critical sex-specific mediators of anxiety susceptibility.


title: A Study of Allostery Within Liganded RARα:RXR Heterodimers at the Genome Scale [CUT&Run]

status: Public on Feb 24 2025

city: Knoxville

first: Conner

last: Hawkins

state: TN

address: 309 Ken and Blaire Mossman Bldg.

department: BCMB

institute: University of Tennessee

summary: We provide evidence of coordination between heterodimeric nuclear hormone receptor ligands at the genome scale to reveal three unique transcriptional outcomes. First, when stimulated in pancreatic acinar cells, distinct doubly-liganded complexes of the retinoic acid receptor-α (RARα) and retinoid-X-receptor (RXR) bind divergent DNA hormone response elements (HRE). Furthermore, the link between ligand pairs and HRE specificity is correlated with RNA transcript formation.  Second, RXR ligands can function as either silent partners or as cooperative effectors on distinct HREs, also with correlated transcriptional outcomes. Third, the absence of unique binding sites on DNA by unliganded RARα:RXR suggests that productive HRE recognition and binding is an exclusive feature of the agonist-bound heterodimer. To achieve the above, DNA-bound heterodimers of RARα:RXR were isolated separately with an RARα-specific antibody,  RARα-specific and RXR-specific agonists and the pan-ligand, 9-cis retinoic acid, using the CUT&RUN technique. At each liganded state, transcriptional activity was detected by mRNA sequencing.

overall_design: CUT&RUN against retinoic acid receptor alpha in mouse acinar pancreatic tissue (266-6) with differing agonistic treatment

first: William

last: Blaner

first: Elias

last: Fernandez


title: Circulating monocytes from patients promote calcific aortic valve disease development

city: Rouen

first: Sylvain

last: Fraineau

address: 22 Boulevard Gambetta

country: France

institute: Unversity of Rouen Normandy

summary: Calcific Aortic Valve Disease (CAVD) is the most frequent valvular heart disease in developed countries. It is characterized by a progressive calcification of aortic valve leaflets mediated by myeloid cells, such as monocytes and macrophages. However, the molecular mechanisms involved in their recruitment and activity are still poorly understood and limit the development of a pharmacological treatments. Previous studies have already demonstrated the role of macrophages in CAVD development. However, little is known about the implication of their precursors, monocytes. Thus, we hypothesized that circulating monocytes from CAVD patients have higher pro-calcific and pro-inflammatory capacities. We aimed first to assess the pro-calcifying potential of circulating monocytes from patients with CAVD and second to better understand the molecular mechanisms of this pro-calcific effect through a whole transcriptomic study.  Methods : We first characterized monocytes sub-population, from PBMCs isolated from peripheral blood of healthy volunteers (Vol) and patients with CAVD or without CAVD (NCAVD), with flow cytometry. Then we analyzed the whole transcriptome of these monocytes by RNA sequencing (RNAseq) to identify dysregulated genes expression, further confirmed by RT-qPCR. Finally, after evaluation of monocytes secretome with multiplex analysis, we evaluated CAVD monocytes capacities to induce myofibroblastic transdifferenciation and osteoblastic differencitation of human valvular interstitial cells (hVIC) with immunocytochemistry (ICC) and O-cresolphtalein assay.  Results : In CAVD (calcific aortic valve disease) monocytes, we observe a shift in their sub-populations, with an increased frequency of classical monocytes (CD14+CD16-) and a decreased frequency of non-classical monocytes (CD14+CD16++). Interestingly, we found specific upregulation of genes linked to both inflammation (PDK4) and calcification (ATP2B1), alongside the downregulation of immunomodulatory genes (DDR1, IKBKE) in monocytes from CAVD patients. Additionally, CAVD monocytes produce lower levels of immunomodulatory and anti-osteoblastogenic cytokines (IL3, CCL3), which promote myofibroblastic transdifferentiation (TIMP1, TNC) and osteoblastic differentiation (ALPL, OPG). This correlates with an increase in αsma+ and opn+ cells and a doubling of hVIC calcifications.  Conclusions : We demonstrated for the first time that circulating monocytes from CAVD patients have higher pro-inflammatory and pro-calcific capacities that might promote CAVD development. Likewise, we identify dysregulated genes, which could be used as new therapeutic targets.

overall_design: used total RNA extracted from healthy volunteer (n=5), NCAVD (n=5) and CAVD (n=5) human patient monocytes. Poly-A mRNA-seq, sequencing length of 150 nt paired end (PE150) with the Illumina NovaSeq 6000 was performed.

first: Léa

last: Di Maria

first: Hugues

last: Boël

first: Nicolas

last: Perzo

first: Sylvanie

last: Renet

first: Bryan

last: Marais

first: Zina

last: Badji

first: Chloé

last: Valentin

first: Théo

last: Lemarcis

first: Thomas

last: Levesque

first: Delphine

last: Béziau-Gasnier

first: Hélène

last: Eltchaninoff

first: Ebba

last: Brakenhielm

first: Eric

last: Durand


title: Multimodal single cell profiling of bone fracture microenvironment

city: Berlin

first: Christian

middle: H

last: Bucher

address: Augustenburger Platz 1

institute: Charité - Universitätsmedizin Berlin

summary: Age-specific alterations of the adaptive immune system include low-grade chronic inflammation, which contributes to the unfavorable outcome of the bone healing process in the elderly. In this work, we aimed to characterize the effect of immune experience and age on cellular phenotype during the early inflammatory phase after bone fracture by using a mouse model which included young, aged, and immune-aged mice 2- and 5-days post osteotomy. Single-cell proteo-genomics quantified thousands of transcriptomes of cells isolated from three different bone regions (fracture hematoma, proximal and distal bone marrow). The fracture hematoma is a very distinct tissue consisting of coagulated blood caused by rupture of adjacent blood vessels, bone marrow influx and cells attracted from the surrounding tissue. The hematoma matures with the healing process and the adjacent bone marrow (proximal and distal to the fracture gap) supports the healing process.

overall_design: We compared young, aged (non-experienced immune system) and immune-aged (experienced immune system) animals during the immediate-to-early response to bone fracture, whereby mice (three mice per group) were sacrificed 2- or 5-days post osteotomy. We dissected 3 anatomical regions from each bone (fracture hematoma, adjacent proximal and distal bone marrow). After cell dissociation, enrichment sorting and labeling, cell encapsulation and library preparation were performed, followed by single-cell proteo-genomics, which included transcriptome quantifications and surface protein detection using the CITE-seq approach.

first: Katharina

last: Schmidt-Bleek

first: Ann-Kathrin

last: Mess


title: Immunological characteristics of non-tuberculous mycobacterial pulmonary disease

city: Daejeon

first: In Soo

last: Kim

address: Mun-hwa ro 266

country: South Korea

institute: Chungnam National University

summary: This study aims to comprehensively investigate the immunological responses associated with non-tuberculous mycobacterial pulmonary disease (NTM-PD). We evaluated immune-related gene expression profiles using nCounter assays on peripheral blood mononuclear cell samples from 18 patients diagnosed with NTM-PD, comparing them with samples from 6 healthy controls.

overall_design: nCounter assays on PBMCs from 18 NTM-PDs and 6 HCs

first: Eun-Kyeong

last: Jo


title: Comparative Methylome Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety [Bisulfite-seq]

city: yangzhou

first: Liu

middle: zi

last: yu

address: shuangqiao

institute: Yangzhou University

type: Methylation profiling by high throughput sequencing

summary: We carried out genomewide DNA methylation analysis by whole genome bisulfite sequencing to identify candidate genes involved in pear fruit semi-russet formation, by comparing the CK (russet) and bagging treated (green) ‘Cuiguan’ pear fruit skin 115 DAFB.

overall_design: Genomewide DNA methylation analysis of untreated and fruit bagging treated ‘Cuiguan’ pear fruit skin, insights into pear fruit semi-russet formation

first: Chunlei

last: Wang

first: Jing

last: Zhang


title: ScRNA-seq trajectory analysis of Th17, Tfh17, and exTh17-Tfh cells

city: Columbus

first: Hsin-Jung Joyce

last: Wu

state: Ohio

address: 480 Medical Center Drive

department: Department of Internal Medicine

institute: The Ohio State University

summary: This experiment was designed to study the functional differences between the Th17-derived Tfh and regular Tfh cells. To achieve these goals, we performed flow sorting and enriched CD4+ T cells from Current-Ex Th17 fate-mapping mice. We then performed scRNA seq analysis to compare the transcriptomic profiles of Tfh cells.

overall_design: CD4+ T cells from Peyer's patches (PP) of Th17 Current-Ex fate-mapping mice were sorted and then single-cell RNA sequencing (scRNA-seq) analysis was performed.

first: Tingting

last: Fan

first: Chi

last: Tai


title: Unveiling the Cellular and Molecular Mechanisms of Diabetic Retinopathy with Human Retinal Organoids

city: Brno

first: Tomas

last: Barta

address: Kamenice 3

department: Faculty of Medicine

country: Czech Republic

institute: Masaryk University

summary: Diabetic retinopathy (DR) is a leading cause of vision impairment worldwide, driven by chronic hyperglycaemia and its complex metabolic consequences. While animal models have been widely used to study DR, they often fail to replicate human retinal physiology. To address this limitation, we utilized human retinal organoids as a model to investigate hyperglycaemia-induced changes, focusing on late-stage organoids (D150+28), where we performed next-generation sequencing (NGS). Transcriptomic analysis revealed significant disruptions in photoreceptor maturation, with a marked downregulation of genes associated with phototransduction and sensory perception. Oxidative stress-related pathways were upregulated, suggesting an enhanced reactive oxygen species (ROS) response. While photoreceptors were particularly vulnerable to hyperglycaemia, other retinal cell types, including bipolar cells, ganglion cells, and Müller glia, exhibited greater resilience. Additionally, glial activation, evidenced by increased expression of astrocyte markers (CD44, GFAP, TGFBR2), suggested a reactive gliosis response.

overall_design: Human-induced pluripotent stem cells (hiPSCs) were differentiated into retinal organoids following an established protocol. Retinal organoids were cultured for 150 days (D150) to achieve an advanced stage of differentiation. To investigate the effects of hyperglycaemia, organoids were exposed for 28 days to one of the following conditions: 1) Control: Standard maintenance medium containing 17.5 mM D-Glucose. 2) Hyperglycaemia (D-Glucose): Maintenance medium supplemented with additional 7.5 mM D-Glucose for a final concentration of 25 mM D-Glucose.

first: Lada

last: Polesovska


title: A Study of Allostery Within Liganded RARα:RXR Heterodimers at the Genome Scale [RNA-seq]

first: Conner

last: Hawkins

overall_design: RNA-seq Profiling in mouse acinar pancreatic tissue (266-6) with differing agonistic treatment of the retinoic acid receptor alpha

first: William

last: Blaner

first: Elias

last: Fernandez


title: Overexpression of miR-23b-3b+miR-218-5p+miR-124-3p differentially modifies the transcriptome of C-33A and CaSki cells and the regulation of cellular processes involved in the progression of cervical cancer

city: Chilpancingo

first: Gloria

last: Fernández Tilapa

state: Guerrero

address: Ciudad Universitaria Sur, Av. Lázaro Cárdenas S/N

country: Mexico

institute: Autonomous University of Guerrero

summary: Dysregulation of tumor suppressor miRNAs (tsmiRs) is associated with tumor progression in cancer. miR-23b-3p, miR-218-5p and miR-124-3p are tsmiRs in cervical cancer (CC) and regulate the translation of genes involved in metastasis-related biological processes. Objective. To analyze transcriptome changes in cervical cancer cell lines (C-33A HPV-negative and CaSki HPV-positive) overexpressing miR-23b-3b+miR-218-5p+miR-124-3p, to identify specific target transcripts common to all three miRNAs, as well as signaling pathways and cellular processes related to tumor progression. Methods. The transcriptome of C-33A and CaSki cells transfected with miR-23b-3b+miR-218-5p+miR-124-3p was analyzed by RNA-seq. Differentially expressed genes (DEGs) were subjected to Gene Ontology analysis on the DAVID platform. The function of under-regulated genes was analyzed on the GEPIA 2.0, Kaplan-Meier plotter and STRING platforms. On the TargetScanHuman platform it was determined which transcripts have MREs for miR-23b-3p, miR-218-5p and/or miR-124-3p in their 3`UTR region. Results. Simultaneous overexpression of miR-218-5p, miR-124-3p and miR-23b-3p induced changes in global gene expression in C-33A and CaSki cells. In C-33A cells, DEGs included 45 over- and 172 under-regulated transcripts; in CaSki, 125 transcripts were over- and 84 under-regulated. The under-regulated transcripts enrich proliferation, migration, apoptosis and angiogenesis; 20 of these genes are associated with overall survival (OS) in women with CC, and 18 of the 20 mRNAs have MREs for one, two or all three miRNAs. Conclusions. miR-23b-3b+miR-218-5p+miR-124-3p, differentially modify global gene expression in C-33A and CaSki cells. The results indicate that these miRNAs act synergistically and modulate CC progression through individual and shared targets by two or all three miRNAs.

overall_design: We analyzed the effect of miR-23b-3b+miR-218-5p+miR-124-3p overexpression on the transcriptome of C-33A and CaSki cells, with the aim of identifying differential expression profiles between cell lines, recognizing specific target transcripts shared by the three miRNAs, as well as gene sets involved in signaling pathways and cellular processes related to cervical cancer progression. C-33A and CaSki cells were transfected with mimic miRNAs: hsa-miR-23b-3p; hsa-miR-124-3p; and hsa-miR-218-5p. As a negative control mirVana™ miRNA Mimic, Negative Control #1 (scramble). To analyze changes in the transcriptome of C-33A and CaSki cells overexpressing miR-23b-3b+miR-218-5p+miR-124-3p, to identify specific target transcripts common to all three miRNAs, the transcriptome of C-33A and CaSki cells was analyzed by RNA-seq. Three independent experiments were performed for each condition to ensure reproducibility.

first: Manuel

last: Romero López

first: Hilda

last: Jiménez Wences

first: Hober

middle: N

last: Núñez Martínez

first: Merlin

middle: I

last: Cruz De la Rosa

first: Judit

last: Alarcón Millán


title: Endocytosis sculpts distinct cAMP signal transduction by endogenously coexpressed GPCRs

city: Minneapolis

first: Emily

last: Blythe

state: MN

address: 420 Washington Avenue SE

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: Many G protein-coupled receptors (GPCRs) trigger a second phase of G protein-dependent signaling from internal membranes after agonist-induced endocytosis. However, individual GPCRs differ significantly in their ability to internalize after activation, and it remains unclear if this confers selectivity on cellular signaling through natively coexpressed GPCRs. We addressed this question by examining the activation of the cyclic AMP (cAMP) / cAMP-dependent protein kinase (PKA) pathway by three ligands that stimulate three distinct, endogenously coexpressed GPCRs in HEK293 cells: isoproterenol (Iso) which primarily activates the β2-adrenergic receptor (β2AR), vasoactive intestinal peptide (VIP) which primarily activates the vasoactive intestinal peptide receptor 1 (VIPR1/VPAC1), and 5'-N-ethylcarboxamidoadenosine (NECA) which primarily activates the adenosine 2B receptor (A2BR). Using location-targeted biosensors and a transcriptional reporter, we demonstrate that each ligand triggers a unique cellular signaling profile and that these responses are differentially sensitive to endocytic inhibition. VIP elicited a response that was endocytosis-dependent at every level in the pathway tested, from upstream global cAMP elevation to downstream activation of nuclear PKA, while Iso elicited a response that was dependent on endocytosis selectively at downstream steps. In contrast, NECA robustly activated the entire cAMP signaling cascade independently of endocytosis, consistent with our observation that human A2BR does not robustly internalize after activation. We conclude that endocytosis indeed sculpts downstream cAMP signaling by GPCRs in a receptor-specific manner. Our results add to the evolving view of compartmentalized signaling in the cAMP / PKA pathway and suggest that differences in GPCR trafficking can encode receptor-specific signaling profiles through a shared signal transduction pathway.

overall_design: To compare the effects of distinct GPCR agonists on transcriptional activation, we carried out 3'-Tag RNA-seq-based differential gene expression analysis. Cultured HEK293 cells were treated with agonist (100 nM Iso, 20 μM NECA, or 500 nM VIP) or their corresponding vehicles (1 μM ascorbic acid, 0.05% DMSO, or water, respectively) for 90 minutes. Experiment was carried out in biological triplicate.

middle: E

first: Mark

last: von Zastrow


title: Gene expression differences between LPS, anti-CD36 Abs, or LPS plus anti-CD36 Abs treated RAW264.7 cells.

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

summary: To comprehensively analyze the transcriptome of macrophages treated with LPS, anti-CD36 Abs, or LPS plus anti-CD36 Abs, respectively, we employed RNA sequencing (RNA-seq) assay

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of LPS (50ng/mL), anti-CD36 Abs (1:100 dilution), or LPS plus anti-CD36 Abs treated RAW264.7 cells.

first: Sun

last: Xin

first: Dan

last: Lu


title: Mechanistic Insights into Targeting APLN/APJ for Ameliorating Testosterone and Reproductive Disorders in Type 2 Diabetes (ATAC-seq)

city: Guangzhou

first: Ke

last: Song

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

institute: Southern Medical University

summary: About 10% of couples of reproductive age worldwide suffer from infertility, with male factors accounting for about 50%, and testosterone is essential for male fertility, but the mechanisms behind the poor sperm quality and abnormally low blood testosterone levels in diabetic patients are unclear. In this study, we found that the peptide Apelin (APLN) significantly inhibited testosterone secretion from Leydig cells (LCs), which in turn led to decreased sperm quality. APLN was found to be localized to leydig cells in the testes of several diabetic mice, and its expression was significantly increased. The addition of APLN to mouse leydig cells decreased testosterone content and decreased the expression of genes related to testosterone synthesis, but the addition of ML221, an APLN receptor inhibitor, significantly increased the expression of testosterone synthesis genes. Injecting ML221 into diabetic mice significantly increased testosterone levels in the blood, increased sperm count as well as enhanced sperm motility and ultimately increased live birth rate of mice after in vitro fertilization. Proteomics revealed that ML221 significantly increased the expression of NR2F2 and further activated the transcription of testosterone synthesis genes. This study will further use mouse and cellular models to completely unravel the specific mechanisms by which APLN inhibits testosterone secretion and elucidate the causes of decreased sperm quality in diabetic patients. This study provides a new clinical target for the development of drugs to improve fertility in diabetic patients.

overall_design: To demonstrate changes in chromatin accessibility under different conditions, we performed ATAC-seq analysis in mouse primary Leydig cells in control and high glucose treatment groups.

first: Xinyan

last: Yang


title: Dual targeting PPARα and NPC1L1 metabolic vulnerabilities blocks tumorigenesis

city: Jinan

first: Fabao

last: Liu

state: Shandong

address: #44 wenhua xi road

institute: Shandong university

summary: Herein we identified Niemann–Pick C1-like 1 (NPC1L1) as a downstream effector of PKM2. Knockout of PKM2 enhanced NPC1L1 expression in breast cancer cells, while reducing the peroxisome proliferator-activated receptor α (PPARα) signaling pathway. Fenofibrate, a PPARα agonist, promoted NPC1L1 expression. Combined administration of fenofibrate and ezetimibe, a NPC1L1 inhibitor, significantly induced cytoplasmic vacuolation and cell apoptosis. Mechanistically, combined administration activated the inositol required enzyme 1α(IRE1α)- x box binding protein spliced (XBP1s) and lysine demethylase 6B (KDM6B). XBP1s interacted with KDM6B to activate genes involved in unfold protein response through demethylating di- and tri-methylated lysine 27 of histone H3 (H3K27) and consequentially increasing the level of H3K27 acetylation in breast cancer cell lines. Fenofibrate and ezetimibe synergistically inhibited tumor growth and lung metastasis in vivo. Together, our findings reveal that dual targeting PPARα and NPC1L1 may be developed as a new regimen for breast cancer therapy.

overall_design: RNAseq profiling of wt and PKM2 KO Cal51 cells; RNAseq profiling of Cal51 cells treated with DMSO, fenofibrate, ezetimibe and fenofibrate plus ezetimibe for 8 hours

first: Xi

last: Hu


title: The NEXT complex regulates H3K27me3 levels to affect cancer progression by degrading G4/U-Rich lncRNAs

city: Shanghai

first: Jianxiu

last: Yu

address: No. 280, Chongqing South Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Polycomb repressive complex 2 (PRC2) is responsible for depositing H3K27me3 and plays essential roles in gene silencing during development and cancer. Meanwhile, the nuclear exosome targeting (NEXT) complex facilitates the degradation of numerous non-coding RNAs in the nucleoplasm. Here find that the functional deficiency of the NEXT complex leads to an overall decrease in H3K27me3 levels. Specifically, ZCCHC8 depletion results in significant upregulation of nascent lncRNAs containing G-quadruplex and U-Rich motifs (G4/U-Rich lncRNAs). The G-quadruplex motif binds to EZH2, blocking the chromatin recruitment of PRC2, while the U-Rich motif is specifically recognized by the NEXT complex for RNA exosome-mediated degradation. In tumor tissues with high ZCCHC8 expression in clear cell renal cell carcinoma (ccRCC) and lung adenocarcinoma (LUAD) patients, the NEXT complex excessively degrades nascent G4/U-Rich lncRNAs. Consequently, PRC2 core subunits are released and recruited to neighboring genomic loci, resulting in increased H3K27me3 levels and downregulation of adjacent genes, including tumor suppressors like SEMA5A and ARID1A. Notably, the EZH2 inhibitor Tazemetostat (EPZ-6438) exhibits greater sensitivity in cells with higher ZCCHC8 expression. Altogether, our findings demonstrate a novel mechanism that the NEXT complex regulates H3K27me3 levels by degrading G4/U-Rich lncRNAs in cancer cells.

overall_design: Thiol(SH)-linked Alkylation for the Metabolic sequencing of RNA (SLAM-seq) was performed using S4U labeling to depict Newly synthesized mRNA profiles and newly synthesized  lncRNA profiles in ACHN cells

first: Qianqian


title: Mechanistic Insights into Targeting APLN/APJ for Ameliorating Testosterone and Reproductive Disorders in Type 2 Diabetes (CUT&Tag)

overall_design: In order to study the distribution of NR2F2 in LC cells, we performed CUT&Tag sequencing analysis on the high-glucose treatment group and the high-glucose + ML221 treatment group in mouse primary Leydig cells.


title: Loss of IL13RA2 promotes metastatic tumour growth in triple-negative breast cancer via increased AKT signalling

city: Nashville

first: Wendy

last: Bindeman

address: Preston Research Building 738 2220 Pierce Ave

department: Cancer Biology

institute: Vanderbilt University

summary: Triple-negative breast cancer is characterized by absence of oestrogen receptor, progesterone receptor, and a lack of HER2 amplification and is associated with poor patient prognosis and high rates of distant metastasis. These patients are at elevated risk of brain metastasis, which remains a major therapeutic challenge. IL13RA2, a high-affinity receptor for IL13, is highly expressed in primary brain cancers, many extracranial solid tumours, and in lung- and brain-seeking metastatic variant cell lines. However, the relationship between IL13RA2 and patient prognosis is variable, and the biological function of this receptor in cancer remains controversial. We sought to define the role of IL13RA2 in TNBC growth and metastasis, with an emphasis on breast-to-brain metastasis. We identified a positive correlation between elevated IL13RA2 mRNA expression and overall survival in a publicly available dataset of basal-like breast cancer patients. We generated IL13RA2-CRISPR knockout derivatives of the human brain-seeking breast cancer cell line MDA231BrM2 as well as murine 4T1 cells and evaluated changes in gene expression, proliferation, survival, and metastatic growth in vivo. We find that both IL13RA2-deficient models demonstrate enhanced survival and proliferation in vitro, as well as augmented metastatic tumour growth and worsened survival in intracardiac models of brain metastasis. Mechanistically, we observe increased AKT and NF-κB signalling in IL13RA2-deficient cells, which renders these cells highly sensitive to inhibition of AKT. We conclude that, in triple negative breast cancer, loss of IL13RA2 in tumour cells is strongly pro-metastatic, antiapoptotic, and pro-proliferative. These phenotypes are mediated through the AKT and NF-κB pathways. IL13RA2-deficient cells are highly vulnerable to AKT inhibition, which may represent a clinically useful vulnerability for patients with IL13RA2-low tumours. However, our data suggest that inhibition of IL13RA2, though promising in other tumour contexts, may be deleterious in metastatic triple-negative breast cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-Seq profiling of wild type 4T1, 4T1 IL13RA1 CRISPR knockouts, 4T1 IL13RA2 CRISPR knockouts, wild type MDA 231 BrM2-831, and MDA 231 BrM2-831 IL13RA2 CRISPR knockouts without cytokine stimulation and of wild type 4T1 and 4T1 IL13RA2 CRISPR knockouts following stimulation with IL13.

first: Barbara

last: Fingleton


title: Gene expression profile at single cell level of tumoral immune cells sorted from MB49 tumor tissues of wt and Lcn2 ko chimeric mice

first: zhu

last: Qingchen

address: 320 Yue Yang Rd, Xuhui District

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: Lcn2 was found as a marker of senescent neutrophils and to affect the tumor growth in our research. We used single cell RNA sequencing (scRNA-seq) to analyze the immune cells diversity and function change with Lcn2 knock-out

overall_design: To investigate the the importance of Lcn2 to the neutrophils diversity and  function, we performed single cell RNA-sequencing analysis by using BD Rhapsody system from immune cells sorted from MB49 tumor tissues of wt and Lcn2 ko chimeric mice

first: Qingchen

last: Zhu

first: Guiheng

last: Zhang

first: Yichuan

last: Xiao


title: Spatial transcriptomics profiling of endometrial tissue from recurrent implanation failure patients.

city: Liverpool

first: Jamie

last: Soul

address: Crown St

department: ISMIB

country: United Kingdom

institute: University of Liverpool

summary: Spatial transcriptomics allows the identification of disease- and cell-specific molecular signatures that may inform advance the biomarker development and future treatments. This study used the GeoMX platform to identify shared and disease-specific transcriptional signatures in  CD45, CD56, stromal and epithelial cell populations from patients with recurrent implantation failure

overall_design: Paraffin-embedded human endometrial biopsies from recurrent implanation faiure (n=8) and fertile controls (n=8) were sectioned and mounted on slides. Slides were stained with CD56, CD45, and PanCk antibodies to allow identification of cell type enriched regions. ROIs were selected based on marker staining and AOIs were collected from each ROI for RNA purification and transcriptome analysis using Digital Spatial Profiling (DSP) on the NanoString GeoMx platform.

first: Nicola

last: Tempest


title: TRIM15 drives chondrocyte senescence and osteoarthritis progression

city: Nanjing

first: Zhuang

last: Li

state: Jiangsu

address: 87 DingjiaQaio, Nanjing, P.R. China

institute: Zhongda Hospital, Southeast University

summary: Chondrocyte senescence underlies osteoarthritis (OA). However, the pathogenesis of chondrocyte senescence remains largely unclear. Here we report that TRIM15 is a critical regulator in chondrocyte senescence. TIRM15 is highly expressed in chondrocytes of senescent cartilage from human OA patients and aged mice. Using gain- and loss-of-function studies, we further identify that TRIM15 facilitates chondrocyte senescence. Notably, conditional deletion of TRIM15 in chondrocytes severely impairs skeletal growth, partially due to the fact that embryonic chondrocyte senescence is disturbed. Compared with Col2a1-CreERT2/TRIM15flox/flox mice, TRIM15flox/flox mice exhibits accelerated OA phenotype, increased senescence markers and senescence-associated secretory phenotype (SASP) during aging. Mechanistically, TRIM15 binds with YAP and directly mediates K48-linked YAP ubiquitination at K254, which interrupts the interaction between YAP and AMOT, leading to enhanced YAP nuclear translocation. Intra-articular injection of AAV5-Trim15 shRNA decelerates OA progression in mice. Collectively, these findings indicate that targeting TRIM15 reshapes aging cartilage microenvironment and protects against OA.

overall_design: In order to identify key genes that contribute to chondrocyte senescence and OA progression, we first performed RNA-sequencing using cartilage tissues from 3 OA individuals and 3 healthy control individuals


title: Single cell RNA-Sequencing of adipose innate T cells for investigation of circadian rhythm.

city: Dublin

first: Aaron

last: Douglas

state: Leinster

address: 152-160 Pearse Street

department: School of Biochemistry and Immunology

country: Ireland

institute: Trinity College Dublin

summary: The circadian rhythm of the immune system helps to protect against pathogens; however, the role of circadian rhythms in immune homeostasis is less well understood. Innate T cells are tissue-resident lymphocytes with key roles in tissue homeostasis4–7. Here we use single-cell RNA sequencing, a molecular-clock reporter and genetic manipulations to show that innate IL-17-producing T cells—including γδ T cells, invariant natural killer T cells and mucosal-associated invariant T cells—are enriched for molecular-clock genes, compared with their IFNγ-producing counterparts. We reveal that IL-17-producing γδ T (γδ17 T) cells, in particular, rely on the molecular clock to maintain adipose tissue homeostasis, and exhibit a robust circadian rhythm for RORγt and IL-17A across adipose depots, which peaks at night. In mice, loss of the molecular clock in the CD45 compartment (Bmal1∆Vav1) affects the production of IL-17 by adipose γδ17 T cells, but not that of cytokines by αβ T or by IFNγ-producing γδ T (γδIFNγ T) cells. Circadian IL-17 is essential for de novo lipogenesis in adipose tissue, and mice with an adipocyte-specific deficiency in IL-17 receptor C (IL-17RC) have defects in de novo lipogenesis. Whole-body metabolic analysis in vivo shows that Il17a/f−/− mice (which lack the expression of IL-17A and IL-17F) have defects in their circadian rhythm for de novo lipogenesis, which results in disruptions to their whole-body metabolic rhythm and core-body temperature rhythm. This study identifies a crucial role for IL-17 in whole-body metabolic homeostasis, and shows that de novo lipogenesis is a major target of IL-17.

overall_design: We performed 10x single cell RNA-Sequencing of γδ T cells and iNKT cells from murine epididymal white adipose tissue. Both innate T cell populations were sorted using FACS and then combined and sequenced as sample. A total of five visceral adipose tissue deposits from five independent biological replicates were pooled for sequencing.

first: Harry

last: Kane

first: Hannah

last: Prendeville

first: Amanda

last: Garza

first: Lydia

last: Lynch


title: IGF2BP2 induces subchondral bone loss of the temporomandibular joint via enhancing FOS-PPARγ-NFATC1 network

city: wuhan

first: Ziyan

last: Jiang

address: 237 luoyu Rd

institute: wuhan university

summary: Overactivated osteoclastogenesis leading to abnormal subchondral bone loss is the main feature of temporomandibular joint osteoarthritis (TMJOA). The role of N6-methyladenosine (m6A) in osteoclast differentiation in TMJOA remains unknown. Here, we found that an m6A reader IGF2BP2 was essential for mature osteoclasts induction. In TMJ tissues of TMJOA patients, the expression of IGF2BP2 was increased. Moreover, IGF2BP2 was augmented in subchondral bone of monosodium iodoacetate (MIA)–induced TMJOA mice. Igf2bp2 deficiency attenuated MIA-induced subchondral bone loss and suppressed osteoclast differentiation. Mechanistically, IGF2BP2 directly stabilized PPARγ and C-FOS mRNA to enhance the NFATC1 signaling, thereby inducing osteoclast maturation. Moreover, the stabilized PPARγ promoted the transcription of C-FOS, resulting in a further amplified signaling of NFATC1. In Igf2bp2-deficient cells, overexpression of PPARγ and C-FOS rescued the function of osteoclasts through restoring reduced levels of NFATC1. On the other hand, IGF2BP2/PPARγ/C-FOS axis facilitated the formation of osteoclasts by restoring the inhibited autophagy levels through the downregulation of ATG16L2. Using an IGF2BP2 inhibitor CWI1-2 hindered osteoclast formation and represented therapeutic effects for TMJOA. In summary, IGF2BP2 is essential in differentiation and maturation of osteoclasts and aggravates TMJOA via stabilizing PPARγ and C-FOS, which promoting NFATC1-mediated osteoclast signaling and ATG16L2-mediated autophagy.

overall_design: RNA-Seq profiling of TMJ tissues from 10-week-old littermates WT and Igf2bp2-/- mice

first: Jie

last: Zhao

first: Zhao

last: Gao

first: Yanan

last: Sun

first: Yaying

first: Junchen

last: Pan

first: Jiali


title: RNA Sequencing Analysis of NCAPD2 Knockdown in Lung Adenocarcinoma Cell Line PC9

city: Fuzhou

first: Yun

last: Wu

state: Fujian

address: 134 Dong Street, Gulou District

institute: Fujian Provincial Hospital

summary: This study investigates the effect of NCAPD2 knockdown on lung adenocarcinoma (LUAD) by performing RNA sequencing on PC9 cell lines. The experiment included three control PC9 cells and three PC9 cells in which NCAPD2 was knocked down using shRNA. This RNA sequencing experiment aims to elucidate the role of NCAPD2 in regulating gene expression associated with tumor proliferation, migration, and survival in LUAD. Analysis of differential gene expression provides insights into the pathways affected by NCAPD2 knockdown, with an emphasis on signaling pathways critical to LUAD progression, such as the PI3K/AKT pathway.

overall_design: The experimental design involved RNA sequencing of the lung adenocarcinoma cell line PC9, with the following groups: (1) three control PC9 cell replicates (shNC) and (2) three PC9 cell replicates with NCAPD2 knockdown (shRNA). Total RNA was extracted from each sample, and the quality was verified before sequencing library preparation. Sequencing was conducted using an Illumina platform to generate high-quality reads for transcriptome analysis. Differential expression analysis was performed to compare gene expression between the control and knockdown groups. The objective was to assess the impact of NCAPD2 knockdown on the transcriptional landscape of PC9 cells and identify affected pathways.

first: Ying

last: Lin


title: Gene expression profiling by RNA-seq in the roots of wild-type, mctp4-1 single mutant (M6), mctp3-2 single mutant (M8) and mctp3-2/mctp4-1 double mutant (C2) Arabidopsis thaliana seedlings.

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

summary: Membrane contact sites (MCS) are fundamental for intracellular communication, but their role in intercellular communication remains unexplored. We show that in plants, plasmodesmata communication bridges function as atypical endoplasmic reticulum (ER)-plasma membrane (PM) tubular MCS, operating at cell-cell interfaces. Similar to other MCS, ER-PM apposition is controlled by a protein-lipid tethering complex, but uniquely, this serves intercellular communication. Combining high-resolution microscopy, molecular dynamics, pharmacological and genetic approaches, we show that cell-cell trafficking is modulated through the combined action of Multiple C2 domains and transmembrane domain proteins (MCTP) 3, 4, and 6 ER-PM tethers, and phosphatidylinositol-4-phosphate (PI4P) lipid. Graded PI4P amounts regulate MCTP docking to the PM, their plasmodesmata localization and cell-cell permeability. SAC7, an ER-localized PI4P-phosphatase, regulates MCTP4 accumulation at plasmodesmata and modulates cell-cell trafficking capacity in a cell-type specific manner. Our findings expand MCS's functions in information transmission, from intracellular to intercellular cellular activities.

overall_design: mRNA profiles in the roots of 5-day old seedlings from wild-type (Col0), mctp4-1 single mutant (M6), mctp3-2 single mutant (M8) and mctp3-2/mctp4-1 double mutant (C2) Arabidopsis thaliana were generated by deep sequencing, in quadruplicates, on Illumina NovaSeq 6000 platform

first: Emmanuelle

last: Bayer

first: Jessica

last: Perez-Sanchez

first: Marija

last: Smokvarska

first: Yvon

last: Jaillais

first: Pepe

last: Cana-Quijada


title: Arcuate nucleus of the hypothalamus cells are sensitive to nutritional state in a sex dependent manner.

city: Houston

first: Jonathan

middle: Carter

last: Bean

state: TX

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

summary: Obesity has reached epidemic levels and obesity increases the risk for negative health outcomes including type 2 diabetes. Sex differences are evident in metabolic homeostasis with differences seen both in amount and location of adipose stores. Males store more adipose viscerally whereas females store adipose subcutaneously. Interestingly, this can be affected by the brain. The arcuate nucleus of the hypothalamus is a key brain region that exerts control over feeding behavior and metabolism. The cells of the arcuate are heterogeneous in their transcriptomic expression and in their functions. Here we perform single nuclei RNA-sequencing of the arcuate in females and males under varying nutritional states. We found that Agrp neurons were the most sensitive to nutritional state and this was more pronounced in females than in males. KNDy neurons were also sensitive to nutritional state and major sex differences were observed. Dopamine neurons of the arcuate had major sex differences. Ghrh neurons saw moderate nutritional regulation and sexual dimorphism. Both microglia and oligodendrocytes had moderate differences observed between nutritional states. This study represents the first major effort to characterize sex differences across nutritional states in the arcuate.

overall_design: Female and male mice were either ad. Libitum fed or fasted for 28 hours, had their arcuate nucleus of the hypothalamus collected and processed for snRNA-seq.

first: Yong

last: Xu


title: ScRNA-seq Analysis of peripheral blood Tfh cells from rheumatoid arthritis patients

first: Hsin-Jung Joyce

address: 480 Medical Center Drive

institute: The Ohio State University

summary: This experiment was designed to study the functional differences of Tfh cells between the rheumatoid arthritis patients and healthy control participants. To achieve these goals, we performed flow sorting and enriched Tfh cells from peripheral blood mononuclear cell (PBMC). We then performed scRNA seq analysis to compare the transcriptomic profiles of Tfh cells from different patient conditions.

overall_design: Tfh cells from peripheral blood mononuclear cell (PBMC) were sorted and then single-cell RNA sequencing (scRNA-seq) analysis was performed.

first: Chi

last: Tai

first: Tingting

last: Fan


title: Gene expression profile of thalamus based on RNA-seq

city: Yangzhou

first: Tianfeng

last: Huang

address: 98 Nantong West Road

institute: Northern Jiangsu People's Hospital

summary: The impact of neurons on the pathogenesis of central poststroke pain (CPSP) after thalamic hemorrhage is currently unknown. The aim of this study was to identify the key genes in neurons and investigate their roles in pain after thalamic hemorrhage based on  RNA-sequencing (RNA-seq) data from model mice.

overall_design: The differentially expressed genes (DEGs) in neurons between the model and control groups were identified. A protein‒protein interaction (PPI) network of the DEGs was constructed. CytoNCA was utilized to analyze the connectivity of the nodes in the PPI network, and the top 5 genes were identified as key genes in the network. Afterward, an miRNA‒mRNA network and TF-mRNA network were established.

first: Ju

first: Yang

last: Zhang


title: Enteric neuronal GPR41-DHX9 signaling senses microbial metabolites to mediate the crosstalk between serotonergic neurons and intestinal stem cells [RNA-seq]

first: Chenbo

last: Ding

state: None Selected

address: 280 Chongqing South Rd

summary: We show that enteric neuronal Dhx9 is important for proper bowel motility and nutrient absorption which are required for intestine development.

overall_design: To systematically explore the molecular events underlying the intestine developmental defects, we performed bulk RNA sequencing analysis on the total duodenum.


title: Enteric neuronal GPR41-DHX9 signaling senses microbial metabolites to mediate the crosstalk between serotonergic neurons and intestinal stem cells

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

overall_design: Refer to individual Series


title: Enteric neuronal GPR41-DHX9 signaling senses microbial metabolites to mediate the crosstalk between serotonergic neurons and intestinal stem cells [Ribo-seq]

summary: We show that Dhx9 deficiency restricts the development and homeostasis of enteric neuron, and specifically suppresses the early development of serotonergic neurons.

overall_design: To investigate potential mechanisms whereby Dhx9 regulates the development and maturation of serotonin neuron,we performed Ribo-IP-seq analysis.


title: Molecular mechanisms of NEXT complexes regulating H3K27me3 levels and affecting tumor progression (ChIP-Seq)

first: Jianxiu

last: Yu

summary: H3K27me3 is an important post-translational modification of histones and is responsible for establishing and maintaining transcriptional repression in heterochromatin regions. The PRC2 complex is the only complex identified with catalytic activity of H3K27me3, and its functional activity is subjected to a wide range of regulation, in which non-coding RNAs play a key regulatory role. The NEXT complex is an RNA exosome-targeting complex localized in the nucleoplasm and is responsible for the degradation of a large number of non-coding RNAs in the nucleus. However, the functional relationship between the NEXT complex and the PRC2 complex or the regulation of H3K27me3 levels has not been reported. In this study, we found that the NEXT complex promotes the recruitment of the PRC2 complex, especially EZH2, to chromatin by degrading nascent RNAs containing the G4 structure, which in turn promotes the level of H3K27me3 modification and cancer progression.

overall_design: Chromatin immunoprecipitation DNA sequencing for EZH2 as well as the histone modification H3K27me3 in ACHN cells.

first: Qianqian

last: Yang


title: Large-scale analysis of the chicken transcriptomes

city: Jingzhou

first: Tinghua

address: Jingmi Road #266

institute: Yangtze University

summary: We analyzed the gene transcription levels for 251 white leghorn chicken samples spanning 65 normal tissues groups.

overall_design: These RNA isolated from samples were reversed transcribed to labeled cDNA and hybridized, to Affymetrix GeneChip® Chicken Genome Array (900590)

first: Min

last: Yao


title: Molecular mechanisms of NEXT complexes regulating H3K27me3 levels and affecting tumor progression (RNA-Seq)

type: Non-coding RNA profiling by high throughput sequencing

overall_design: mRNA expression profiles and lncRNA expression profiles in ACHN cells


title: PEP444c encoded within MIR444c gene regulates microRNA444c accumulation in barley

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

summary: Mutations in the PEP444c coding region have an impact on the accumulation of corresponding microRNA. The level of microRNA444c is decreased in roots of pep444c-332.10 mutant plants compared to WT plants, whereas the level of microRNA444c in shoots was unchanged. Results indicate a significant effect of PEP444c on the accumulation of microRNA444c in roots.

overall_design: small RNA sequencing of wild type and mutant 33210 plants

first: Dawid

last: Bielewicz

first: Aleksandra

last: Chojnacka


title: Molecular mechanisms of NEXT complexes regulating H3K27me3 levels and affecting tumor progression


title: RpdD and RpoS ChIP-exo in Klebsiella pneumoniae

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

summary: With increasingly concerning strains of antimicrobial resistant strains of the commensal, gram-negative bacteria Klebsiella pneumoniae emerging, there is a pressing need to better understand the pathogen and mechanisms behind its pathogenicity. This study investigated the regulatory mechanisms in strain MGH 78578 of two major sigma factors, the house-keeping sigma factor RpoD, and the general stress response sigma factor RpoS, in mid-exponential and early stationary phase using chromatin immunoprecipitation with exonuclease treatment (ChIP-exo) followed by deep sequencing. Combining ChIP-exo and transcriptome analysis allowed for the determination of sigma factor binding sites, binding motifs, and genes included in the phase-specific sigmulons. The number  of genes included in the RpoS sigmulon was greater than in the RpoD sigmulon, with 1,833 and 1,690 genes included, respectively; however, a majority of sigmulon genes were found in all phase-specific sigmulons. Focussing on pathogenicity  genes, 20 antimicrobial resistance genes (ARGs) and 155 virulence genes, only two ARGs were found exclusively in one phase-specific sigmulon, an oxacillin-hydrolysing class D beta-lactamase and chloramphenicol efflux MFS transporter CmlA5, which were found in the RpoD sigmulon in early stationary phase. Notably, six unnamed proteins that are or pertain to fimbrial proteins were found uniquely in the RpoS sigmulon in early stationary phase. From this, it can be hypothesised that early stationary phase might be an important phase for pathogenicity gene regulation. While there is little conservation in RpoS sigmulons from strain to strain, RpoS appears to have a consistent overarching role across strains, including a role as a regulator of pathogenicity genes.

overall_design: [ChIP-exo] Klebsiella pneumoniae MGH 78578 cells were cultured in M9 minimal media with 0/2% glucose to etiher mid-exponential or stationary phase in biological duplicate or triplicate

first: Zoe

last: Scott-Nevros


title: Host cell gene expression profile in Human respiratory syncytial virus (HRSV) infected HEp2 cells at 20 hours post infection

city: Singapore

first: Richard

last: Sugrue

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: We used the microarray data to analyze host cells response on HEp2 cells infected with HRSV

overall_design: The HRSV infected Hep2 cells were harvested at 20 hpi and RNA extraction was performed using standard protocol as described by Affymetrix. The aim of this experiment is to analyze host cell response to HRSV infection. HRSV UV:  Virus was inactivated by irradiation at λ256nm

first: Myaing

last: MZ

first: Hui

last: Chen

first: Boon

last: Tan


title: scRNA-seq data of spleen immune cells from Vehicle- and Glutoborin-treated mice

status: Public on Feb 23 2025

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

summary: To determine whether Glutoborin exerts its immunomodulatory effects by disrupting interactions between MZMs and MZBs, we performed scRNA-seq to analyze the immune microenvironment of spleens from Pb-infected mice treated with Vehicle or  Glutoborin.

overall_design: Mice were intraperitoneally injected with 1 × 10⁴ iRBCs, and on days 2 and 4 post-infection Vehicle and Glutoborin were administered. On day 5 post-infection spleens from both group were collected to isolate lymphocytes. CD45+ cells were then sorted by flow cytometry for subsequent single-cell sequencing analysis.

first: Sun

last: Xin

first: Dan

last: Lu


title: ScRNA-seq Analysis of ZsGreen+ Tfh, ZsGreen– Tfh and B cells disassociated from ZsGreen–/+ Tfh and B conjugates

city: Columbus

first: Hsin-Jung Joyce

last: Wu

summary: This experiment was designed to study the functional differences between the Th17-derived Tfh and regular Tfh cells. We were also interested in studying how B cells might display functional differences upon receiving help from Th17-derived Tfh cells vs. regular Tfh cells. To achieve these goals, we performed flow sorting and enriched T-B cell doublets with either Th17-derived Tfh or regular Tfh cells to catch the T-B cell interaction “in action”. We then broke the doublets apart with ETDA before scRNA seq analysis to compare the transcriptomic profiles from both T cell side and B cells side.

overall_design: Splenic ZsGreen+ and ZsGreen– Tfh cells conjugated with B cells from K/BxN Th17 fate-mapping mice were both sorted as doublets and then dissociated with EDTA for single-cell RNA sequencing (scRNA-seq) analysis.

first: Chi

last: Tai

first: Tingting

last: Fan


title: Gene expression profile at single cell level of CD45 positive and CD45 negative cells sorted from MB49 tumor tissues of male and female mice

first: zhu

last: Qingchen

summary: Sex disparities is epidemiologically linked to non-reproductive cancer and is particularly prominent in bladder cancer. In the past, great attention has been paid to the effectors of sex chromosome associated genes and hormones, yet how the  immune system to influence the sex differences of tumor progression remains unclear. Here, we developed single-cell RNA sequencing (scRNA-seq) data of mouse bladder tumor-infiltrating immune cells and identified a lipocalin-2+ (LCN2+) senescence-like neutrophil (LSLN) subpopulation that exclusively present in the male tumor microenvironment, and importantly predict a poor prognosis for male patients with bladder cancer.

overall_design: To investigate the the function of immune system to the sex difference of tumor progression, we performed single cell RNA-sequencing analysis by using BD Rhapsody system from CD45 positive and CD45 negative cells sorted from MB49 tumor tissues of male and female mice

first: Qingchen

last: Zhu

first: Guiheng

last: Zhang

first: Yichuan

last: Xiao


title: Next-generation sequencing profiling of miRNAs in individuals with 22q11.2 deletion syndrome revealed altered expression of miR-185-5p

city: Sao Paulo

first: Vanessa

middle: Kiyomi

last: Ota

state: SP

address: Rua Botucatu, 740, Ed. Leitao da Cunha, 1o andar

department: Morphology and Genetics

country: Brazil

institute: Universidade Federal de Sao Paulo

summary: Background: The 22q11.2 deletion syndrome (22q11.2DS) is a microdeletion syndrome with highly variable phenotypic manifestations, even though most patients present the typical 3 Mb microdeletion, usually affecting the same ~ 106 genes. One of the genes affected by this deletion is DGCR8, which plays a crucial role in miRNA biogenesis. Therefore, the haploinsufficiency of DGCR8 due to this microdeletion can alter the modulation of the expression of several miRNAs involved in a range of biological processes.  Results: In this study, we used next-generation sequencing to evaluate the miRNAs profiles in the peripheral blood of 12 individuals with typical 22q11DS compared to 12 healthy matched controls. We used the DESeq2 package for differential gene expression analysis and the DIANA-miTED dataset to verify the expression of differentially expressed miRNAs in other tissues. We used miRWalk to predict the target genes of differentially expressed miRNAs. Here, we described two differentially expressed miRNAs in patients compared to controls: hsa-miR-1304-3p, located outside the 22q11.2 region, upregulated in patients, and hsa-miR-185-5p, located in the 22q11.2 region, which showed downregulation. Expression of miR-185-5p is observed in tissues frequently affected in patients with 22q11DS, and previous studies have reported its downregulation in individuals with 22q11DS. hsa-miR-1304-3p has low expression in blood and, thus, needs more validation, though using a sensitive technology allowed us to identify differences in expression between patients and controls.  Conclusions: Thus, lower expression of miR-185-5p can be related to the 22q11.2 deletion and DGCR8 haploinsufficiency, leading to phenotypic consequences in 22q11.2DS patients, while higher expression of hsa-miR-1304-3p might be related to individual genomic variances due to the heterogeneous background of the Brazilian population. Background: The 22q11.2 deletion syndrome (22q11.2DS) is a microdeletion syndrome with highly variable phenotypic manifestations, even though most patients present the typical 3 Mb microdeletion, usually affecting the same ~ 106 genes. One of the genes affected by this deletion is DGCR8, which plays a crucial role in miRNA biogenesis. Therefore, the haploinsufficiency of DGCR8 due to this microdeletion can alter the modulation of the expression of several miRNAs involved in a range of biological processes.  Results: In this study, we used next-generation sequencing to evaluate the miRNAs profiles in the peripheral blood of 12 individuals with typical 22q11DS compared to 12 healthy matched controls. We used the DESeq2 package for differential gene expression analysis and the DIANA-miTED dataset to verify the expression of differentially expressed miRNAs in other tissues. We used miRWalk to predict the target genes of differentially expressed miRNAs. Here, we described two differentially expressed miRNAs in patients compared to controls: hsa-miR-1304-3p, located outside the 22q11.2 region, upregulated in patients, and hsa-miR-185-5p, located in the 22q11.2 region, which showed downregulation. Expression of miR-185-5p is observed in tissues frequently affected in patients with 22q11DS, and previous studies have reported its downregulation in individuals with 22q11DS. hsa-miR-1304-3p has low expression in blood and, thus, needs more validation, though using a sensitive technology allowed us to identify differences in expression between patients and controls.  Conclusions: Thus, lower expression of miR-185-5p can be related to the 22q11.2 deletion and DGCR8 haploinsufficiency, leading to phenotypic consequences in 22q11.2DS patients, while higher expression of hsa-miR-1304-3p might be related to individual genomic variances due to the heterogeneous background of the Brazilian population. Background: The 22q11.2 deletion syndrome (22q11.2DS) is a microdeletion syndrome with highly variable phenotypic manifestations, even though most patients present the typical 3 Mb microdeletion, usually affecting the same ~ 106 genes. One of the genes affected by this deletion is DGCR8, which plays a crucial role in miRNA biogenesis. Therefore, the haploinsufficiency of DGCR8 due to this microdeletion can alter the modulation of the expression of several miRNAs involved in a range of biological processes.  Results: In this study, we used next-generation sequencing to evaluate the miRNAs profiles in the peripheral blood of 12 individuals with typical 22q11DS compared to 12 healthy matched controls. We used the DESeq2 package for differential gene expression analysis and the DIANA-miTED dataset to verify the expression of differentially expressed miRNAs in other tissues. We used miRWalk to predict the target genes of differentially expressed miRNAs. Here, we described two differentially expressed miRNAs in patients compared to controls: hsa-miR-1304-3p, located outside the 22q11.2 region, upregulated in patients, and hsa-miR-185-5p, located in the 22q11.2 region, which showed downregulation. Expression of miR-185-5p is observed in tissues frequently affected in patients with 22q11DS, and previous studies have reported its downregulation in individuals with 22q11DS. hsa-miR-1304-3p has low expression in blood and, thus, needs more validation, though using a sensitive technology allowed us to identify differences in expression between patients and controls.  Conclusions: Thus, lower expression of miR-185-5p can be related to the 22q11.2 deletion and DGCR8 haploinsufficiency, leading to phenotypic consequences in 22q11.2DS patients, while higher expression of hsa-miR-1304-3p might be related to individual genomic variances due to the heterogeneous background of the Brazilian population.

overall_design: We used next-generation sequencing to evaluate the miRNAs profiles in the peripheral blood of 12 individuals with typical 22q11DS compared to 12 healthy matched controls.

first: Anelisa

middle: G

last: Dantas

first: Beatriz

last: Nunes

first: Natália

first: Pedro

last: Galante

first: Paula

middle: F

last: Asprino

first: Maria

last: Melaragno


title: BPTF cooperates with MYCN/MYC to link neuroblastoma cell cycle control with epigenetic cell states

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

summary: The nucleosome remodeling factor BPTF is required for the deployment of the MYC-driven transcriptional program. Deletion of oneBptfallele delays tumor progression in mouse models of pancreatic cancer and lymphoma. In neuroblastoma, MYCN cooperates with the transcriptional core regulatory circuitry (CRC). HighBPTFlevels are associated with high-risk features and decreased survival. BPTFdepletion results in a dramatic decrease of cell proliferation. Bulk RNA-seq, single-cell sequencing, and tissue microarrays reveal a positive correlation ofBPTFand CRCtranscription factor expression. Immunoprecipitation/mass spectrometry shows that BPTF interacts with MYCN and the CRC. Genome-wide distribution analysis of BPTF and CRC in neuroblastoma reveals a dual role forBPTF: 1) it co-localizes with MYCN/MYC at the promoter of genes involved in cell cycle and 2) it co-localizes withthe CRC at super-enhancers to regulate cell identity. The critical role of BPTF across neuroblastoma subtypes supports its relevance as a therapeutic target.

overall_design: To assess the functional effects of BPTF loss-of-function, we generated an inducible lentiviral system and performed RNA-seq after 48h of the induction doxycycline (1µg/mL) in KELLY cells.  Two biological replicates were performed.

first: Irene

last: Felipe

last: Martínez-de-Villarreal

first: Francisco

middle: X

last: Real


title: Gene signature of regulatory T cells isolated from children with Selective IgA Deficiency and Common Variable Immunodeficiency.

city: Krakow

first: Magdalena

last: Rutkowska-Zapala

address: Wielicka 265

institute: Jagiellonian University Medical College

summary:
In our study we aimed to analyze the gene expression profile of Treg cells in CVID and SIgAD patients, compared to age-matched healthy controls.
Selective IgA deficiency (SIgAD) is the most common and common variable immunodeficiency (CVID) is the most symptomatic form of predominant antibody deficiency. Despite differences in the clinical picture, a similar genetic background is suggested. A common feature of both disorders is the occurrence of autoimmune conditions. Regulatory T cells (Tregs) are the major immune cell type that maintains autoimmune tolerance. As the different types of abnormalities of Treg cells were associated with autoimmune disorders in primary immunodeficiency (PID) patients, in our study we aimed to analyze the gene expression profile of Treg cells in CVID and SIgAD patients, compared to age-matched healthy controls. The transcriptome-wide gene profiling was performed using microarray technology. As a results, we analyzed and visualized global expression patterns of genes and pathways of isolated population of Treg cells. We showed the differences at gene-level between patients with and without autoimmunizations. Our finding suggest that gene signature of Treg cells isolated from SIgAD and CVID patients differ from age-matched healthy controls and form each other, while the occurrence of autoimmunity in both PID is associated with IFN signaling pathway. In sum, our findings improve our understanding of Treg dysfunctions in patients with common PIDs and associated autoimmunity.

last: Rutkowska-Zapała

first: Agnieszka

last: Grabowska-Gurgul

first: Marzena

last: Lenart

first: Anna

last: Szaflarska

last: Kluczewska

first: Monika

last: Mach-Tomalska

last: Baj-Krzyworzeka

first: Maciej

last: Siedlar


title: Histone H4 is increased in SARS-CoV-2-infected lung epithelial cells and linked to COVID-19 severity

city: New York

first: David

last: Redmond

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: We found that histone H4 is a potential biomarker of COVID-19 pathogenesis. Bulk RNA-sequencing of endothelial cell samples from idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) patients as well as controls was used in addition to published sequencing data from peripheral blood mononuclear cells or bronchoalveolar lavage fluid cells from COVID-19 and IPF patients as well as controls.

overall_design: Transcriptome sequencing of control, IPF, and COPD endothelial cells

first: José

last: Durán

first: Alexandra

middle: C

last: Racanelli

first: Sean

last: Houghton

first: Raphaël

last: Lis


title: Dissecting PADI6 function defines oocyte cytoplasmic lattices as regulatory hubs for fundamental cellular processes

city: London

first: Louise

last: Walport

address: 82 Wood Lane

institute: Imperial College London

summary: Transcriptome profiling of MII oocytes, zygote and 2-cell embryos (processed as individual blastomeres) from wild-type females, females with a single point mutation in Padi6 resulting in the amino acid substitution C663A (Padi6-C663A), and females with a Padi6 null mutation (Padi6-KO).

overall_design: A total of 6 replicates, three from two different litters were processed for each genotype and stage, resulting in a total of six MII oocytes and six zygotes per genotype. The 2-cell embryos were dissociated into individual blastomeres and processed separately resulting in 12 single 2-cell blastomeres per genotype. Samples are numbered by the litter and given a letter indicating the sample from that litter, e.g. C663A_Zygote_1b = Zygote number 2 from the first C663A Zygote litter. 2-cell blastomeres are further differentiated by _b1 or _b2 indicating which blastomere, e.g. WT_2C_1a_b2 = the second blastomere from the first 2-cell embryo from the first wild-type 2-cell embryo litter.

first: Jack

middle: P

last: Williams

first: Dan

last: Leonce

middle: J


title: Transcriptome Analysis of Kidneys in a Mouse Model of Sepsis-Induced Acute Kidney Injury

city: Harbin

first: Jiannan

last: Zhang

address: No. 23, Youzheng Street

department: Department of Critical Care Medicine

institute: The First Affiliated Hospital of Harbin Medical University

summary: This study delves into the pathophysiological underpinnings of sepsis-associated acute kidney injury (SA-AKI), a critical and often fatal complication arising from the systemic inflammatory response and immune dysregulation triggered by sepsis. By employing the cecal ligation and puncture (CLP) method to simulate sepsis-induced AKI in mice, we conducted comprehensive transcriptome profiling using RNA sequencing (RNA-seq) to explore the molecular dynamics and identify potential new mechanisms underlying SA-AKI. The comparative analysis between the CLP-induced AKI model and control subjects aims to unravel the complex interplay of genes and signaling pathways involved in kidney damage and failure during sepsis. Through this approach, our research seeks to contribute to the broader understanding of SA-AKI's molecular basis.

overall_design: In this experiment, a total of six C57BL/6 mice were equally divided into two groups: a Cecal Ligation and Puncture (CLP) group and a Sham (control) group, each containing three mice. The objective was to investigate the transcriptomic changes in the kidneys of mice subjected to sepsis-induced acute kidney injury (AKI) compared to a control condition. For the induction of sepsis, the mice in the CLP group underwent a surgical procedure under aseptic conditions, where they were first anesthetized with 2% to 4% isoflurane. A midline incision of approximately 2 cm was made below the diaphragm to expose the cecum, which was then partially ligated (two-thirds) using a 5-0 silk suture and punctured twice with a 22-gauge needle to simulate sepsis. A gentle squeeze was applied to the cecum to ensure a small amount of feces was expelled through the puncture sites, effectively mimicking a sepsis condition. Following the procedure, the mice received 1 mL of saline subcutaneously for resuscitation. The Sham group underwent identical surgical procedures, with the exception of the cecal ligation and puncture, to serve as a control for surgical stress without inducing sepsis. This design allowed for the isolation of transcriptomic changes attributable to sepsis-induced AKI from those due to surgical intervention alone. Twenty-four hours post-operation, all mice were euthanized, and their kidneys were harvested for RNA sequencing analysis.

first: Jian-nan

first: Yang

last: Chong

first: Quan-kuan

last: Gu

first: Yi-Qi

last: Wang


title: Effect of  EGCG to multiple myeloma MM.1S cells on gene expression

city: Jinan

first: xunqi

last: zhang

address: Bei yuan street N0.247

department: hematology

institute: Shandong University

summary: Epigallocatechin-3-gallate (EGCG) is the most plentiful polyphenol in green tea and has antiviral, antioxidant, anti-aging, anti-inflammatory, and neuroprotective effects . Studies have shown that EGCG can inhibit a diversity of biological processes of tumor progression, including cell proliferation, invasion, metastasis, and angiogenesis, and can also induce apoptosis and cell cycle arrest. In order to investigate the role of EGCG in multiple myeloma (MM), we carried out this study. We found that EGCG could inhibit myeloma cell activity and promote myeloma cell apoptosis. To further explore the mechanism of EGCG promoting apoptosis in myeloma cells, cells were treated with EGCG and subjected to RNA sequencing.

overall_design: To further explore the mechanism of EGCG promoting apoptosis in myeloma cells, MM.1S cells were treated with EGCG and subjected to RNA sequencing.

first: yang

last: jiang

first: wen


title: ChIP-seq data were used to analyze ASR3 target genes

city: Wuhan

first: Ying

address: No.1 Shizishan Street

institute: Huazhong Agricultural University

summary: Through performing ChIP-seq on ASR3 overexpressing transgenic plants, we analyzed the binding sites of ASR3 on the whole genome.

overall_design: 4 ChIP-seq libraries were sequenced.


title: Single-Cell 5-Hydroxymethylcytosine Landscapes of Mammalian Early Embryos at Single-Base Resolution

first: Jinmin

last: Yang

address: Yiheyuan Road 5

department: School of life science

summary: DNA methylation and hydroxymethylation are extensively reprogrammed in mammalian early embryogenesis. However, a comprehensive picture of DNA hydroxymethylation map across early embryo stages is lacking. Here, we develop “schmC-CATCH” (single-cell 5hmC chemical-assisted C-to-T conversion-enabled sequencing) to obtain quantitative, genome-wide landscape of the base-resolution DNA hydroxymethylome in mouse gametes and pre-implantation embryos from one-cell (PN1-PN5) to blastocyst stages. We revealed the dynamics of DNA hydroxymethylation and observed dramatically different 5hmC patterns on the paternal and maternal genomes. We found hotspots of DNA hydroxymethylation during mouse early embryo development, which are highly associated with young retroelements including LINE1. 5hmC is also associated with regulatory elements, indicating a potential epigenetic function during early embryogenesis. In addition, 5hmC is asymmetrically distributed at the chromosome level and can be used to track the cell and strand lineages during the first two embryo cleavages. Collectively, our work reveals the dynamics of active DNA demethylation during mouse pre-implantation development and provides an important resource for functional studies of epigenetic reprogramming in single cells.

overall_design: We sought to address challenges in dissecting single-cell 5hmC patterns using a quantitative and genome-wide profiling method. We developed schmC-CATCH, an assay combining bisulfite-free chemical labelling with improved library construction for high sensitivity and precision.We adapted our previous chemical strategy to reproducibly label 5hmC in single cells for subtraction-free 5hmC readout, which avoid unacceptable noise signal and templates degradation. We collected gametes and early embryos including zygote, 2-cell, 4-cell, 8-cell, 16-cell and blastocytes by crossing C57BL/6J female mice with the DBA/2N male mice. All samples were extensively washed or purified to remove any somatic, gametic or polar body contaminants. In total, we performed 5hmC analysis of 456 individual cells from sperms, MII oocytes and preimplantation embryos.

first: Dongsheng

last: Bai

first: Xiaohui

last: Xue

first: Yun

last: Gao

first: Fouchou

last: Tang

first: Chengqi

last: Yi


title: Effect of p53 on cardiac hypertrophy and its mechanism

status: Public on Feb 22 2025

city: Nanjing

first: Hao

address: Dingjiaqiao 87#, Southeast University, Gulou District, Nanjing, Jiangsu Province, China

institute: Southeast University

summary: This study aims to investigate the role of p53 in cardiac hypertrophy. We constructed a cardiac hypertrophy model using both wild-type (WT) and p53 knockout (KO) mice subjected to transverse aortic constriction (TAC). After six weeks, cardiac tissues from the hypertrophied left ventricle were collected from both mouse groups. These tissues were analyzed using single-cell RNA sequencing to observe differential gene expression in hypertrophied cardiomyocytes and identify the key pathways enriched in these cells.

overall_design: We performed transverse aortic constriction (TAC) surgeries on both wild-type (WT) and p53 knockout (KO) mice. After six weeks, hypertrophied left ventricle tissues were collected from each group. Each sample consisted of a mixture of three different individual heart tissues from the same group. Single-cell RNA sequencing was then conducted to observe differential gene expression and pathway enrichment in the hypertrophied cardiomyocytes.


title: Identification of circRBM39 as a tumor suppressor in breast cancer

city: Hefei City

first: Dun

last: Liu

state: Anhui Province

address: Division of Life Sciences and Medicine, 443 Huangshan Road

institute: University of Science and Technology of China

summary: Circular RNAs (circRNAs) have emerged as pivotal players in both physiology and human cancers. However, their modes of action in breast cancer remain elusive. Herein, we have identified a significantly downregulated circRNA, termed circRBM39, in breast cancer specimen compared with adjacent non-tumor tissues. Gain- and loss-of-function assays demonstrate that circRBM39 inhibits breast tumorigenesis through the impairment of DNA damage response in vitro and in vivo. Mechanistically, circRBM39 directly interacts with replication protein A2 (RPA2) and decreases the RPA2 protein level via facilitating the HERC2-mediated ubiquitination, thereby disrupting homologous recombination repair. Importantly, administration of in vitro synthesized circRBM39 exhibits substantially repressive effects on breast cancer progression, sensitizes breast cancer cells to PARP inhibition, and renders them susceptible to synthetic lethality in a subcutaneous breast tumorigenesis model. Collectively, our findings demonstrate the tumor-suppressive roles of circRBM39 in breast cancer, and highlight the interplay between circRNA and genome stability in cancers.

overall_design:
In an effort to investigate functional roles of circRNAs in breast cancer, we performed RNA sequencing (RNA-seq) of two-paired breast cancer specimen and adjacent non-tumor (NT) tissues to identify promising circRNA candidates.
To further explore the functional mechanism of circRBM39 in breast cancer, we also performed polyadenylated RNA-seq in control and circRBM39 OE MDA-231 cells.

first: Xing

last: Bian


title: Lamin A/C restrains replication domain activity through higher-order chromatin structures and PCNA interaction [CUT&Tag]

first: Wenxue

last: Zhao

address: Yiheyuan Road

summary: Lamin A/C, a critical nuclear lamina protein, is essential for maintaining nuclear architecture, organizing chromatin and preserving genomic stability. However, its role in directly regulating DNA replication remains unclear. This study investigates how Lamin A/C orchestrates replication initiation by modulating chromatin structure and interacting with proliferating cell nuclear antigen (PCNA). Utilizing high-resolution imaging, chromatin accessibility assays, and sequencing, we demonstrate that Lamin A/C stabilizes replication domains (RDs) by restricting chromatin mobility, preserving spatial organization, and maintaining accessibility. Furthermore, Lamin A/C interacts with PCNA via its Ig-fold domain, regulating PCNA availability by sequestering a pool of PCNA and modulating its expression, and thereby controlling its recruitment to replication machinery. The loss of Lamin A/C results in chromatin architecture reorganization and elevated PCNA availability at RDs, which coordinately trigger excessive activation of replication origins, leading to replication stress and DNA damage. These disruptions prolong the S phase and compromise genome stability, highlighting Lamin A/C as a critical gatekeeper of balanced replication initiation. Our findings reveal Lamin A/C’s dual role in chromatin organization and replication machinery regulation, offering valuable insights into its involvement in replication-associated diseases such as cancer and viral infections and highlighting potential therapeutic opportunities through targeting replication dynamics.

overall_design: CUT&Tag of PCNA in wild-type (WT) and Lamin A/C knockout Hela cells during G1/S phase.


title: Lamin A/C restrains replication domain activity through higher-order chromatin structures and PCNA interaction [ATAC-Seq]

overall_design: ATAC-seq of wild-type (WT) and Lamin A/C knockout Hela cells during G1/S phase.