title: Post-transcriptional regulation of human immunodeficiency virus type-2 (HIV-2) replication by N6-methyladenosine

city: Santiago

first: Daniela

last: Toro Ascuy

state: Region Metropolitana

address: Av. Independencia 1027

department: Virology

country: Chile

institute: University of Chile

summary: Human immunodeficiency virus type-2 (HIV-2) establishes reservoirs at levels comparable to HIV-1, but its infection is associated with lower rates of progression to AIDS. As such, a hallmark of people living with HIV-2 is the very low—usually undetectable—viral loads, which is partially explained by a post-transcriptional repression exerted at the level of protein synthesis and the accumulation of the full-length RNA in cytoplasmic granules. Here, we investigated whether HIV-2 Gag expression was regulated by the presence of the m6A RNA modification. Our results indicate that the HIV-2 full-length RNA contains m6A residues, which are required for Gag synthesis. Interestingly, the YTHDF family of cytoplasmic m6A readers exert different effects on HIV-2 Gag synthesis. As such, while YTHDF1 and YTHDF2 are necessary for Gag synthesis, YTHDF3 negatively regulates Gag expression by promoting full-length RNA localization in cytoplasmic granules. Interestingly, we demonstrate that the cellular m6A machinery including writers, erasers and readers re-localize into cytoplasmic granules together with the full-length RNA in a non-Gag producing cell sub-population. We also observed that FTO overexpression has no effect in Gag synthesis but promotes full-length RNA packaging suggesting a dynamic regulation of the cytoplasmic fate of this viral RNA. Together, these data suggest that the HIV-2 full-length RNA undergoes a complex regulation exerted by the cellular m6A machinery that controls the cytoplasmic localization, ribosome association and particle incorporation of this viral RNA.

overall_design: We are providing RNAseq data from inputs (fragments of polyA RNA) and m6A-immunoprecipitated RNA from both HEK293T cells expressing HIV-2 pROD10. Two biological replicates are included.

first: Ricardo

last: Soto Rifo

first: Sebastian

last: Riquelme


title: RNAseq of bone marrow stromal/stem cells under metabolic stress.

status: Public on Dec 14 2024

city: Goyang-si

first: Seo-Young

last: Park

address: 32, Dongguk-ro, Ilsandong-gu

country: South Korea

institute: Dongguk university

type: Expression profiling by high throughput sequencing

summary: To obtain a global profile of gene expression, we performed RNA sequencing (RNA-seq) using cells cultured under different conditions to determine genes and signaling pathways associated with enhanced osteogenesis and cell survival in hBMSCs

overall_design:
Three replicates were analyzed for three different patient groups
The hBMSCs were established from bone marrow samples from 7 patients (mean age: 70 years, range: 50-90 years). A statement of consent was informed to all donors. All experiments were performed according to the relevant guidelines and regulations


title: RNA-seq data of aortas from WT or PALMD+/- mouse

city: Beijing

first: Jichao

last: Zhang

address: 2 Anzhen Ave

country: China

institute: Beijing Anzhen Hospital, Capital Medical University

summary: Reduced PALMD expression is strongly associated with the development of calcified aortic valve stenosis (CAVS); however, the role of PALMD in vascular calcification remains unknown.

overall_design: mRNA profiles of aortas from 15-week old wild type and  PALMD+/- mice

first: Yingchun

last: Han


title: Mothers with a history of adverse childhood experiences and their emotional states during pregnancy: study of epigenetic components as potential mediators

status: Public on Dec 13 2024

city: Ciudad Autónoma de Buenos Aires

first: Bruno

middle: Gabriel

last: Berardino

state: Buenos Aires

address: Intendente Güiraldes 2160, Ciudad Universitaria

department: Biological Chemistry Department

country: Argentina

institute: University of Buenos Aires

type: Methylation profiling by genome tiling array

summary: Adverse childhood experiences (ACEs) have detrimental intergenerational health consequences; however, mechanisms require elucidation. We test the associations among mothers’ ACEs, mothers’ prenatal anxiety and depression symptoms, and DNA methylation (DNAm) in maternal prenatal blood and infant umbilical cord blood. Maternal ACE score was associated with higher prenatal depression (β= 0.84, p=0.004) and anxiety (β = 1.36, p=0.02) symptoms and lower rates of secure attachment at 3 months (OR= 0.52 p=0.003). Prenatal depression (OR= 0.92, p=0.194) and anxiety (OR= 0.94, p= 0.072) were not correlated with infant attachment. Results from the regression of epigenetic age acceleration in maternal prenatal blood on maternal ACE score were: β =0.49, p= 0.09. Regressing epigenetic age in cord blood on prenatal depression yielded: β = -0.10, p=0.07 and on anxiety yielded β =-0.05, p=0.07. No CMR was associated with maternal ACE score at the FDR-corrected p<.05 level. ACE-associated DNAm variation was enriched for genes related to nervous and reproductive systems development. ACEs may affect the next generation through maternal mental health, infant attachment, and DNAm.

overall_design: Data were analyzed from 67 women in Buenos Aires, Argentina and a subsample of 24 for DNAm data. DNAm was analyzed using Illumina EPIC microarray. Regression analyses were used to assess the associations between maternal ACEs and infant attachment, prenatal depression and anxiety, and DNAm age. ANCOVA assessed differential methylation in co-methylated regions (CMRs) between ACE+ and ACE- dyads. Genes associated with CMRs with unadjusted p-values below 0.05 were used for gene set enrichment analysis and functional annotation using ShinyGO.

middle: G

first: Ariel

middle: A

first: Eduardo

middle: T

last: Cánepa

first: Estefanía

last: Fesser

first: Julia

last: Redondo

first: Pamela

last: Scorza


title: Deubiquitinase USP9X regulates Wnt-signaling to control CNS vascular formation and barrier maintenance [Human]

city: Tianjin

first: Yi

last: Lei

address: Qixiangtai street NO.22

institute: Tianjin Medical University General Hospital

summary: Deubiquitinating enzymes play crucial roles in various cellular activities, yet their involvement in central nervous system (CNS) vascularization and barrier function remains elusive. Canonical Wnt signaling is essential for proper CNS vascularization and barrier maintenance. Using a loss-of-function screening for Wnt signaling activity, we identified ubiquitin-specific peptidase 9 X-linked (USP9X) as a key regulator in brain endothelial cells (BECs). Endothelium-specific Usp9x knockout reduces Wnt-signaling activity, compromising CNS vascularization and barrier function during development. Activation of Wnt signaling rescues these defects. Mechanistically, we uncovered β-catenin as a direct substrate of USP9X, with USP9X catalyzing K48 polyubiquitin chains to stabilize β-catenin. In pathological models of impaired CNS vascular barrier function, including an intracerebral hemorrhage model and an oxygen-induced retinopathy model, loss of Usp9x intensifies barrier disruption, accentuating defects. This finding implicates USP9X as a critical regulator of CNS vascularization and barrier function through Wnt signaling, offering insights into CNS disease implications.

overall_design: HCMECs were transfected with siRNA targeting control (siCtrl) or USP9X (siUSP9X) for 48 h, followed by Wnt3a stimulation for 12h. Total RNA was harvested for subsequent RNA-seq analysis.

first: Jiandong

last: Hu

first: Jiyun

last: Zhao

first: Qiangyun

last: Liu


title: Cardiac reprogramming and Gata4 overexpression reduce fibrosis and improve diastolic dysfunction in heart failure with preserved ejection fraction [RNA-seq]

city: Tsukuba

first: Yu

last: Yamada

state: Ibaraki

address: 1-1-1 Tennoudai

department: Cardiovascular

country: Japan

institute: University of Tsukuba

summary: Fibrosis is important pathogenesis in heart failure with preserved ejection fraction (HFpEF). We previously reported that the overexpression of cardiac transcription factors, Mef2c/Gata4/Tbx5/Hand2 (MGTH) could directly reprogram cardiac fibroblasts (CFs) into induced CMs (iCMs) and reduce fibrosis. Here we show that in vivo cardiac reprogramming generated iCMs from resident CFs, improved cardiac function, and reversed fibrosis in HFpEF model using a novel transgenic mouse system. RNA-seq revealed that the MGTH activated the cardiac program and concomitantly suppressed fibroblast and inflammatory signatures. Thus, cardiac reprogramming improves HFpEF via myocardial regeneration and anti-fibrosis.

overall_design: Hearts were harvested 15 weeks after the start of the experiment from three groups (Ctrl, Ctrl_HF, and TTg_HF) for bulk RNA-seq.

first: Masaki

last: Ieda


title: Transcriptome analysis reveals the effect of STAT3 gene of JAK-STAT signaling pathway on apoptosis of Brucella macrophages

city: china

first: lianmin

last: li

state: changchun

address: No. 2888 Xincheng Street

institute: Jilin Agriculture University

summary: Brucella is a significant intracellular parasitic bacterium that establishes an infection within a host cell to facilitate its proliferation. While the survival of Brucella in cells is an important manifestation of its virulence, the research on this aspect is not yet complete. Transcriptome sequencing techniques were employed for the analysis of transcript levels of various genes in RAW 264.7 macrophages infected with M5 and wild strains. siRNA can be employed to silence differentially expressed genes, with the subsequent validation of their functions conducted through a variety of techniques, including RT-qPCR, Western blot, flow cytometry, and others.In the study, a significant up-regulation of the STAT3 gene was observed in the vaccine strain when compared with the wild strain. The design of the relevant siRNA to silence STAT3 resulted in the promotion of apoptotic gene expression and the inhibition of apoptosis-inhibiting gene expression, thereby facilitating cell apoptosis.The results demonstrated that the discrepancy in STAT3 gene transcription between the vaccine and wild strains resulted in a reduction in cell damage and a decline in the virulence of the vaccine strain M5. This finding offers novel insights into the intracellular survival mechanism of Brucella and the underlying cause of M5 weakness.

overall_design: RNA seq analysis was performed on RAW 264.7 macrophages infected with M5 and wild-type strains.

first: Rui

last: Du

first: Jun-Feng

last: Shi

first: Lian-Min

last: Li

first: Jian-Min

first: Fei


title: Unveiling the modulators of mutable collagenous tissue in the brittle star Ophiomastix wendtii. an RNA-seq analysis

city: Kannapolis

first: Robert

last: Reid

state: NC

address: 150 Research Campus Drive, Suite 3333

department: Bioinformatics and Genomics

country: USA

institute: UNC Charlotte

summary: Collagenous connective tissue is responsible for body integrity in all multicellular organisms and has many biomedical applications within a multibillion-dollar industry. An inspiration for a new generation of collagen-based biomaterials with a wide range of applications may come from echinoderms, a group of marine invertebrates that includes sea stars, sea cucumbers, brittle stars, sea urchins, and sea lilies. Echinoderms are capable of reversibly controlling the pliability of certain connective tissue components (i.e., tendons and ligaments) that are composed of mutable collagenous tissue (MCT). The MCTs variable tensility allows echinoderms to perform unique functions, including energy-saving posture maintenance, autotomy, and asexual reproduction. It is known that neurosecretory juxtaligamental cells in the nervous system control the MCT. These cells release substances that either soften or stiffen the MCT. So far, only a few of these substances have been purified and characterized, and the genomics behind MCT biology are still mostly unknown. Therefore, we propose to identify the putative MCT-related genes in echinoderms and better understand the biology of the juxtaligamental cells. Our research improves our knowledge about the MCT molecular control mechanism, with the ultimate goal of unlocking new biomaterial applications. In this project, we utilize RNA-Seq to identify and annotate differentially expressed genes in the MCT structures of the brittle star Ophiomastix wendtii

overall_design: We employed a transcriptome-wide high-throughput gene expression analysis approach (RNA-Seq) to quantify gene expression in the inner arm core region enriched in juxtaligamental cells (JLC) of the brittle star Ophiomastix wendtii compared to the whole arm (containing the basal level (i.e., neither enriched nor depleted) of the JLCs) and stomach (which is devoid of JLCs).

middle: W

first: Denis

middle: J

last: Machado

first: Vladimir

last: Mashanov


title: Deubiquitinase USP9X regulates Wnt-signaling to control CNS vascular formation and barrier maintenance


title: Regulation of Sex-biased Gene Expression by the X-Y Chromosomal Gene Pair Kdm5c-Kdm5d in Pluripotent Cells

city: Ann Arbor

first: Sundeep

last: Kalantry

state: MI

address: 3710 Med Sci II 1241 Catherine St

department: Human Genetics

institute: University of Michigan

summary: Mammalian sex differences are determined by the X and Y chromosomes.  Ancestral homologous genes on the sex chromosomes, termed X-Y gene pairs, have been predicted to drive sex differences.  However, among the five X-Y gene pairs conserved across eutherians, which pairs drive sex-biased gene expression have remained undefined.  Here, we investigate the roles of the X-Y gene pair Kdm5c-Kdm5d in regulating sex-biased gene expression independently of sex hormones using pluripotent mouse embryonic stem cells (ESCs) as a model.  Wild-type (WT) XX female and WT XY male ESCs significantly differ in the expression of approximately 4% of all expressed genes, classified as female- or male-biased.  Loss of Kdm5c in female ESCs results in the downregulation of female-biased genes.  In contrast, loss of either Kdm5c or Kdm5d in male ESCs results in the upregulation of female-biased genes and downregulation of male-biased genes, effectively neutralizing sex-biased gene expression.  In male ESCs, most sex-biased genes change in expression in a similar direction upon loss of Kdm5c or Kdm5d.  However, Kdm5c loss dysregulates a greater number of sex-biased genes relative to Kdm5d loss in male ESCs.  Remarkably, in female ESCs ectopic Kdm5d expression is sufficient to drive a sex-biased gene expression pattern similar to that of WT male ESCs.  Taken together, these results establish Kdm5c-Kdm5d as a critical X-Y gene pair in driving sex-biased gene expression in pluripotent cells.

overall_design: To test the contributions of X-linked Kdm5c and Y-linked Kdm5d to sex-biased gene expression, we derived and analyzed all combinations of WT and mutant female and male mouse embryonic stem cells. Three biological replicates were analyzed per genotype.

first: Rebecca

middle: M

last: Malcore

first: Milan

middle: K

last: Samanta

first: Shigeki

last: Iwase


title: The Dlk1-Dio3 noncoding RNA cluster coordinately regulates mitochondrial respiration and chromatin structure to establish proper cell state for muscle differentiation [ATAC-Seq]

city: Boston

first: Frank

last: Naya

state: MA

address: 24 Cummington Mall

institute: Boston University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate the collective role of the Dlk1-Dio3 ncRNA cluster in myogenesis, we developed two stable CRISPR-Cas9 gene-edited C2C12 skeletal muscle cell lines, Meg3-proximal cis-acting sequence (Meg3-CAS or 2-4) to over-express and Meg3-transcription start site (Meg3-TSS or 2-7) to under-express the entire mega-cluster of Dlk1-Dio3 ncRNAs. Mutations affecting the dosage of all ncRNAs expressed from the Dlk1-Dio3 locus cause profound changes in myoblast fusion and differentiation. To evaluate  genome-wide perturbations in chromatin accessibility we evaluated specific histone lysine modifications, inducing the repressive histone mark, H3K27me3, and the activating mark, H3K4me3

overall_design: ATAC-seq in gene-edited (Dlk1-Dio3 ncRNA locus) C2C12 cells compared to C2C12 control cells

first: Amanda

last: Pinheiro

first: Kevin

last: Cabrera

first: Jawahar

last: Mahendran

first: Payton M.

last: Bock

first: Francisco J.

first: Eric

last: Palanques-Tost


title: Evolutionary pressures shape undifferentiated pleomorphic sarcoma development and radiotherapy response.

city: Stanford

first: Ajay

last: Subramanian

state: CA

address: 450 Serra Mall

department: Radiation Oncology

institute: Stanford University School of Medicine

summary: Although radiotherapy plays a crucial role in treating many cancers, the effect of radiation on tumor evolution remains unclear. We integrated temporal genomic profiling of 120 spatially distinct tumor regions from 20 patients with undifferentiated pleomorphic sarcomas (UPS), longitudinal circulating tumor DNA (ctDNA) analysis, and evolutionary biology computational pipelines to study UPS evolution during tumorigenesis and in response to radiotherapy. Most unirradiated UPS displayed initial linear evolution followed by subsequent branching evolution with distinct mutational processes during early and late development. Using metrics of genetic divergence between regions, we demonstrated evidence of strong selection pressures during UPS development that further increased during radiotherapy. We observed changes in subclone abundance following radiotherapy with subclone contraction tied to alterations in calcium signaling and demonstrated that inhibiting calcium transporters can radiosensitize sarcoma cells. Finally, ctDNA analysis accurately measured subclone abundance and enabled non-invasive monitoring of subclonal changes. These results demonstrate that radiation exerts selective pressures on UPS and suggest that targeting radioresistant subclonal populations could improve outcomes after radiotherapy.

overall_design: Bulk RNA-sequencing was performed on a total of 13 pre-treatment and 25 post-treatment soft tissue sarcoma specimens from 12 patients treated with chemoradiation therapy.

first: Everett

last: Moding

first: Marius

last: Fried

first: Matthias

last: Gaida


title: Single-cell transcriptome landscape in colorectal cancer

city: Shanghai

first: Xueliang

last: Zhou

state: --- Select One ---

address: Shanghai

institute: Ruijin hospital, Shanghai Jiao Tong university School of medicine

summary: One tumor tissue specimen pathologically diagnosed as adenocarcinoma undergoing radical colorectal surgery without any preoperative treatment at our center was collected, and the single cell transcriptome sequencing was performed, which was consistent with the inclusion and exclusion criteria for the prospective observational clinical study.The detailed procedures of pre-processing and quality control were as follows: (1) Raw data quality control; (2) Data comparison and mapping; (3) Cell Barcode Correction; (4) UMI disaggregation; (5) Count matrix generation; (6) Quality control indicators; (7) Data standardization and normalization; (8) Identification of highly variable genes (HVGs); (9) Filtering condition settings: nCount_RNA > 1000 & nFeature_RNA < 3000 & percent.mt < 10 & nFeature_RNA > 200. The t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm was used for downscaling and cell clustering, and the "SingleR" R package was used for cell annotation. The "CellChat" and "NicheNet" R packages were used for cell communication. The "monocle2" was used for cell trajectory analysis.

overall_design: One tumor tissue specimen pathologically diagnosed as adenocarcinoma undergoing radical colorectal surgery without any preoperative treatment at our center was collected, and the single cell transcriptome sequencing was performed, which was consistent with the inclusion and exclusion criteria for the prospective observational clinical study.The following inclusion criteria must all be met for eligibility: (1) Age ≥18 years and ≤70 years；(2) ECOG performance status of 0 or 1; (3) Pathologically proven colorectal adenocarcinoma; (4) No family history of hereditary cancer; (5) Treated with standardized radical resection of colorectal cancer satisfying R0 resection and removal of at least 12 lymph nodes; (6) Adequate primary tumor tissues from surgery or biopsy in compliance with the sample criteria; (7) Adequate peripheral blood sample in compliance with the sample criteria; (8) Patient able and voluntary to provide legitimate informed consent for the study. The exclusion criteria included the following : (1) Currently participating in clinical trials that might interfere with treatment judgments or receiving experimental treatments; (2) Patients who present abnormalities involving heart, lung, liver, kidney, hematopoiesis, and bone marrow reserve that cannot tolerate surgical treatments and chemotherapy; (3) Any other progressive malignant disease or malignancy requiring treatment within the preceding 5 years with the exception of curative basal cell carcinoma and squamous cell carcinoma; (4) Mental illness or serious cardiovascular disease; (5) Pregnancy, breastfeeding, or planning for pregnancy within 1 year; (6) Emergency surgery for perforation, bleeding, bowel obstruction, etc. Postoperative follow-up time points for CRC patients were based on specific time points after surgery, including scheduled follow-up visits at the first, third, and sixth months after surgery and subsequent six-month or annual follow-up visits. At each follow-up visit, high-quality clinical assessment, appropriate imaging and laboratory tests, and detailed data recording and analysis played important roles in evaluating treatment outcomes, monitoring survival, and guiding subsequent treatment decisions.

first: Jing

last: Sun


title: DIS3 ablation in spermatocytes causes defective spermatogenesis in mice

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

summary: Conditional inactivation of DIS3 in spermatocytes impairs meiotic progression and causes defective spermatogenesis in mice. scRNA-seq analysis indicates that DIS3 mutation significantly impairs spermatocytes meiotic progression and dysregulates transcriptome in spermatocytes. We show that DIS3 ribonuclease plays critical roles in male meiotic progression and spermatogenesis in mice.

overall_design: scRNA-seq was performed using P20 testicular cells from control and DIS3 knockout mice to identify different subpopulations. Re-clustering of spermatocytes was performed to determine the germ cell distribution and differentially expressed genes in knockout mice.

first: Zhengpin

last: Wang


title: YTHDF2 contributes to psoriasis by promoting proliferation and inflammatory response through regulation of Wnt signaling pathway

city: harbin

first: youlin

last: wang

address: the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China.

institute: The Second Affiliated Hospital of Harbin Medical University,

summary: YT521-B homology domain family 2 (YTHDF2), an m6A-binding protein, plays a crucial role in various biological processes, including cell migration, proliferation, differentiation, and inflammation. It is also involved in mRNA decay and pre-rRNA processing. This study investigates the specific impact of YTHDF2 on the pathogenesis of psoriasis and its underlying mechanisms. Initially, increased expression of YTHDF2 was observed in psoriasis. Subsequent silencing of YTHDF2 in psoriatic cell model led to a decrease in mRNA expression of IL-17A, S100A8, and S100A9, as well as a reduction in cell proliferation. Conversely, overexpression of YTHDF2 resulted in the opposite effects. Treatment with the YTHDF2 inhibitor DC-Y27-13 demonstrated a therapeutic effect on psoriasis mice. mRNA sequencing analysis revealed enrichment of differentially expressed genes in the Wnt signaling pathway. Further investigation indicated that deletion of YTHDF2 increased the half-life and expression of Dickkopf homolog 3 (DKK3), which in turn inhibited the Wnt signaling pathway, ultimately attenuating the inflammatory response and inhibiting cell proliferation.

overall_design: The sequencing samples were divided into two groups (si-NC group and si-YTHDF2 group), three samples in each group.

first: Youlin

last: Liu

first: Yongchen


title: Lipolysis Engages CD36 to Promote ZBP1-Mediated Necrosis Impairing Lung Regeneration in COPD

city: Zhengzhou

first: Jiazhen

address: 156 Jinshui East Road

institute: Henan University of Chinese Medicine

summary: Lung parenchyma destruction represents a severe condition commonly found in chronic obstructive pulmonary disease (COPD), the leading cause of morbidity and mortality worldwide. Promoting lung regeneration is crucial for achieving clinical improvement. However, no therapeutic drugs are approved to improve the regeneration capacity due to incomplete understanding of the underlying pathogenic mechanisms. Here, we identify a positive feedback loop formed between adipose triglyceride lipase (ATGL)-mediated lipolysis and overexpression of CD36 specific to lung epithelial cells, contributing to disease progression. Genetic deletion of CD36 in lung epithelial cells and pharmacological inhibition of either ATGL or CD36 effectively reduce COPD pathogenesis and promote lung regeneration in mice. Mechanistically, disruption of the ATGL-CD36 loop rescued Z-DNA binding protein 1 (ZBP1)-induced cell necroptosis and restored WNT/β-catenin signaling. Thus, we uncover a previously unrecognized crosstalk between lipolysis and lung epithelial cells, suggesting the regenerative potential for therapeutic intervention by targeting the ATGL-CD36-ZBP1 axis in COPD.

overall_design: To investigate the impact of cigarette smoke extract (CSE) on murine lung epithelial cells (MLE-12 cell line), we treated MLE-12 cells with PBS or CSE. We performed RNA-seq on control and treatment group cells and then analyzed the differential genes and pathways.

first: Ru

first: Yicun

last: Li

first: Haojian

last: Zhang

first: Jiansheng


title: The neuronal homeobox transcription factor HMX3 is a crucial vulnerability in MECOM-negative KMT2A::MLLT3 acute myelomonocytic leukemia [RNAseq_MOLM13_HMX3_KD]

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: The KMT2A::MLLT3 fusion protein causes acute myeloid leukemia (AML) by activating the oncogenic transcription factor MECOM. However, MECOM expression occurs only in half of the cases. By integrating gene expression and enhancer activity data from patient cells, we identified neuronal homeobox transcription factor HMX3 as cell fate determining factor in MECOM-negative KMT2A::MLLT3 AML. HMX3 expression associated with younger age and KMT2A-rearranged leukemia in large AML cohorts (p<0.002). It was absent in other major genetic risk groups and healthy blood cells. Transcriptomic analyses revealed that HMX3 drives cancer-associated E2F, MYC, and cell cycle gene programs. Ectopic HMX3 expression completely inhibited monocytic but not granulocytic colony formation of healthy CD34+ cord blood cells. Its silencing in KMT2A::MLLT3 AML cell lines and patient cells resulted in cell cycle arrest, monocytic differentiation, and apoptosis. Thus, HMX3 is a leukemia-specific vulnerability that enhances proliferation and blocks differentiation of MECOM-negative KMT2A::MLLT3 leukemia.

overall_design: RNA sequencing of primary HMX3-positive KMT2A::MLLT3 AML (P7, 4297) (WT), non-targeting control (1418), HMX3 KD (1) (shRNA, 2355), and HMX3 KD (2) (shRNA, 2416).

first: Saioa

last: Arza-Apalategi

first: Branco

last: Heuts

first: Saskia

last: Bergevoet

first: Roos

last: Meering

first: Daan

last: Gilissen

first: Pascal

last: Jansen

first: Anja

last: Krippner-Heidenreich

first: Peter

last: Valk

first: Michiel

last: Vermeulen

first: Olaf

last: Heidenreich

first: Torsten

last: Haferlach

first: Joop

middle: H

first: Bert

last: van der Reijden


title: The neuronal homeobox transcription factor HMX3 is a crucial vulnerability in MECOM-negative KMT2A::MLLT3 acute myelomonocytic leukemia [RNAseq_CD34_HSPC_ectopic_HMX3]


title: The neuronal homeobox transcription factor HMX3 is a crucial vulnerability in MECOM-negative KMT2A::MLLT3 acute myelomonocytic leukemia [RNAseq_primary_HMX3_KMT2A-MLLT3_AML]


title: Androgens protect murine ILC2 cells from functional suppression during influenza virus infection

city: OKLAHOMA CITY

first: Susan

middle: E

last: Kovats

state: OK

address: 825 NE 13TH ST.

institute: OKLAHOMA MEDICAL RESEARCH FOUNDATION

summary: Lung-resident group 2 innate lymphoid cells (ILC2s) produce type 2 cytokines and facilitate tissue repair in response to alarmins such as IL-33 released during respiratory virus infection, but they also may be functionally suppressed by type 1 cytokines. Compared to females, males harbor significantly fewer lung ILC2s, which express notably high levels of androgen receptor (AR) compared to other lymphocytes. Here we tested the hypothesis that females and males show differential ILC2 responses upon influenza virus (IAV) infection of mice. Over the course of sublethal infection, lungs of female mice contained greater numbers of ILC2s and ILC1s compared to males. However, the female ILC2s were preferentially suppressed at the peak of infection, with a dampened type 2 program manifest as attenuated proliferation, decreased propensity to produce IL-5 and amphiregulin, and reduced expression of GATA3 and IL-33R. Naïve female ILC2s showed higher expression of IFNGR and higher phospho-STAT1 levels following stimulation by IFN, and lymphocyte-restricted STAT1 deficiency reversed suppression of female ILC2s during infection. ILC2s in naive male mice with lymphocyte-restricted AR deficiency displayed levels of IFNGR comparable to female mice, suggesting AR activity underlies sex differences in intrinsic IFNGR expression. Early life orchiectomy or lymphocyte-restricted loss of AR revealed that endogenous androgens decreased ILC2 numbers but protected males from suppression of ILC2s in IAV infection. In sum, intrinsic AR activity preserves canonical ILC2 function in males during IAV infection, which may contribute to the sex differences in morbidity secondary to IAV observed in mice and humans.

overall_design: Female and male mice were infected with PR8 virus intranasally, and lungs were harvested at day 7 p.i.  Lung ILCs were pooled from 4-5 female or male mice and sorted as lineage-negative (CD3, CD5, TCRβ, B220, CD11b, CD11c, TER119, Gr-1, CD19) CD90+IL-7Rα+ cells using a BD FACS Aria II instrument. Female and male ILCs were tagged with distinct Totalseq anti-mouse Hashtag (1 and 2) mAbs (anti-CD45 and MHCI) (Biolegend) to facilitate separation of the ILCs by sex in the sequencing analysis.

first: Sapana

last: Kadel

first: Richard

middle: C

last: Pelikan


title: Dynamic Immune-mesenchymal interplay within the tertiary lymphoid structures promotes autoimmune pathogenesis in Hidradenitis Suppurativa

city: New York

first: Catherine

last: Lu

state: NY

address: 540 1st Avenue

department: Plastic Surgery

institute: NYU School of Medicine

summary: Tertiary lymphoid structures (TLS) play a pivotal role in sustaining chronic inflammation within autoimmune diseases and tumors by fostering crucial immune cell interactions. While much is known about TLS linked to mucosal epithelium, their formation in the skin epithelium and the supporting microenvironment remains unclear. Using multiomics, we uncovered the presence of TLSs in a severe chronic inflammatory skin disease, Hidradenitis Suppurativa (HS), and showed that lymphocyte proliferation exclusively occurs in TLSs, predominantly located in adjacent to the unique epithelialized tunnels in lesional skin. Notably, we found extensive clonal expansion of plasma cells generating antibodies specific to HS lesional keratinocytes across different patients, alongside the proliferation of Tfh, Treg, and pathogenic T cells (IL17A+ and IFNG+). Additionally, we identified two distinct skin fibroblast populations with transcriptional signatures resembling stromal cells in secondary lymphoid organs (SLO), expressing CXCL13 or CCL19, in response to immune cytokines. Employing a microfluidic system to mimic TLSs-on-a-chip, we demonstrated that HS lesional fibroblasts are critical in orchestrating lymphocyte aggregation and proliferation, which involve TNFα-CXCL13 and TNFα-CCL19 feedback loops with B and T cells, respectively. Furthermore, our study revealed that early TNFα blockade effectively suppresses lymphocyte aggregation, but not after aggregates are formed, underscoring the critical role of TNFα during the initiation of the lymphoid aggregation. Through dissecting the intricate network interactions between immune and mesenchymal cells within the HS lesion, our work revealed the crucial mechanism sustaining chronicity in Hidradenitis Suppurativa and potentially other autoimmune diseases.

overall_design:
Single cell RNA sequencing was performed for a total of 29 samples collected from 8 HS patients and 2 healthy control donors. Lesional and perilesional skin samples from axillae, groin or thigh were included.
Single cell VDJ sequencing for both T and B lymphocytes were performed in 4 of the HS patients. This study allows us to acquire better understanding of changes in transcriptome and lymphocyte clonality within the inflammatory landscape of HS.

first: Wei-wen

last: Yu

first: Joy

last: Barrett

first: Jie

last: Tong

first: Meaghan

last: Marohn

first: Meng-ju

last: Lin

first: Ernest

last: Chiu

middle: P


title: Differential expression profile of rat H9C2 cardiac cells following Hypoxia/reoxygenation (H/R)

city: Nantong

first: Baoying

last: Hu

state: JIANGSU

address: No.9 Seyuan road

institute: Nantong University

summary: Acute myocardial infarction is a leading cause of death among adults globally. Hypoxia/reoxygenation (H/R) injury plays a causal role in myocardial damage and death, whose molecular mechanisms remain largely elusive. Our present work employed rat H9C2 cardiomyocytes to establish an H/R injury model and investigated differential expression profiles following H/R treatment using RNA-seq. Normal cultured H9C2 cardiomyocytes were used as the control group.

overall_design: H/R injury was established by culturing H9C2 cells in 1% oxygen, 5% CO2, and 94% nitrogen in a tri-gas incubator for 12 h and then reoxygenated in 5% CO2 normal oxygen conditions for 6 h. Thereafter, H9C2 cells (n=3) with or without H/R treatment were subjected to RNA isolation using the Trizol reagent (Life Technologies) and submitted to BGI for reverse transcription, library preparation, and sequencing using the BGI500 sequencer.

first: Xiao

last: Han

first: Zhicheng

last: Jiang

first: Xiaorong

last: Zhou


title: Dimethyl Fumarate Restores Functional Vitamin-D3 Tolerogenic Dendritic Cells differentiated from Multiple Sclerosis Patients [Methylation_array]

city: Badalona

first: eva

last: martinez caceres

address: Cami des escoles s/n

country: Spain

institute: Institut Germans Trias i Pujol

summary: Multiple Sclerosis (MS) is a chronic disease characterised by dysregulated self-reactive immune responses damaging neurons’ myelin sheath, causing disability. The primary therapeutic option, immunosuppressants, inhibit pathogenic anti-myelin responses but depresses the entire immune system. Antigen-specific autologous tolerogenic dendritic cell (tolDC) therapies offer an approach to restore tolerance to auto-antigens without causing generalised immunosuppression. However, immune dysregulation in MS could impact the phenotype and functionality of the starting material for cell therapy. In this study, we defined the immune signature of CD14+ monocytes, mature dendritic cells (mDCs) and Vitamin D3 tolDCs (VitD3-tolDCs) isolated from MS patients and healthy donors (HD). By using a multi-omic approach, we identified a shift in these cell types toward a proinflammatory profile dominated by alterations in the AhR pathway and increased NFkB signalling. Moreover, tolDCs isolated from MS patients showed reduced tolerogenic properties compared to those from HD, which were fully restored through AhR agonism and NFkB downregulation through in vivo or in vitro supplementation with Dimethyl Fumarate (DMF). Remarkably, a combined therapy of DMF and VitD3-tolDC was more efficient to reduce the clinical score of experimental autoimmune encephalomyelitis mice than monotherapies. In summary, we demonstrate that DMF restores the functionality of VitD3-tolDCs derived from MS patients. Moreover, a combined therapy with DMF and VitD3-tolDCs could offer enhanced therapeutic potential in treating MS.

overall_design: Monocytes from 18 active, treatment-naïve RRMS patients and HD, 6 mDCs from HD and 8 mDCs from MS patients, 6 tolDCs from HD and 8 tolDCs from MS patients were isolated and DNA methylation analysis was performed.

first: Federico

last: Fondelli

first: Jana

last: Willemyns

first: Roger

last: Domenech-Garcia

first: Maria

last: Mansilla

first: Gerard

last: Godoy-Tena

first: Anna

last: G Ferreté-Bonastre

first: Silvia

last: Presas-Rodriguez

first: Cristina

last: Ramo-Tello

first: Esteban

last: Ballestar

first: Eva

last: Martínez-Cáceres


title: Dimethyl Fumarate Restores Functional Vitamin-D3 Tolerogenic Dendritic Cells differentiated from Multiple Sclerosis Patients

overall_design: Monocytes from 19 active, treatment-naïve RRMS patients and 19 HD, 6 mDCs from HD and 8 mDCs from MS patients, 6 tolDCs from HD and 8 tolDCs from MS patients were isolated and bulk RNAseq was performed.


title: The neuronal homeobox transcription factor HMX3 is a crucial vulnerability in MECOM-negative KMT2A::MLLT3 acute myelomonocytic leukemia

first: Joost

last: Martens

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

overall_design: Refer to individual Series


title: Effect of overexpressing HNRNPK in glioblastoma stem cell

city: Jinan

first: Anjing

last: Chen

address: 107 Wenhua Xi Road

institute: Shandong University

summary: The mechanisms underlys GBM cellular transitions remain unclear.In our study, we overexpressed HNRNPK in three different types of GSCs. HNRNPK (WT) leads to high expression of core markers in GSCs, and its characteristics are similar to those of the MES subtype, exhibiting stronger invasive abilities and tumorigenic potential. We mutated 422 site from lysine(K) to argnine(R) to study the function of SUMOylation in HNRNPK. Sequencing of GSCs with overexpression of HNRNPK (K422R) mutation confirmed the upregulation of infiltrating markers within the GSCs. The changes in GSC subtypes driven by overexpression of HNRNPK (WT or K422R) were not restricted by GSC mutation features.

overall_design: To investigate the endogenous driving factors of GSC heterogeneity, we overexpressed wild-type HNRNPK or K422-mutated HNRNPK in three different types of GSCs.


title: Inhibition of SF3A2 acetylation at lysine 10 mediated by p300/SIRT7 promotes Fscn1 alternative splicing against myocardial ischemic/reperfusion injury

city: Changchun

first: Qingxia

last: Huang

state: Jilin

address: Boshuo Road No.1035

department: Notheast Asia Research nstitute of Traditional Chinese Medicine

institute: 长春中医药大学


title: Inhibition of SF3A2 acetylation at lysine 10 mediated by p300/SIRT7 promotes Fscn1 alternative splicing against myocardial ischemic/reperfusion injury [RNA-Seq I]

summary:
The 4D-lable free proteomic and acetylomic study were employed to gain the targets of GS. The co-immunoprecipitation, co-localization, and specific acetylation site antibody were used to verify the acetylation. Based on the mass spectrometry analysis, the active monomers in GS were screened by phenotypes of acetylation and mitochondrial function. The mechanism was studied through RNA-seq, qPCR, cellular thermal shift assay, surface plasmon resonance, acetyltransferase activity combined with pharmacological inhibitor, RNA interference and site-specific mutation.
These findings provide a novel mechanism underlying cardiomyocyte protection of ginsenoside Rb2 through p300/SIRT7-SF3A2-Fscn1 signaling and opens new opportunities for pharmacological prevention and treatment of ischemic and associated sequelae.

overall_design: H9C2 cells were pretreated with ginsenoside Rb2 for 48h, and then treated with glucose-oxygen deprivation in a three-gas incubator for 4-6 h, and reoxygenated with glucose-reoxygenation for 12 h.

first: Xiangyan

last: Li


title: Targeted  intragenic demethylation initiates chromatin rewiring for gene  activation

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

type: Methylation profiling by high throughput sequencing

summary: Aberrant Transcription Start Site (TSS) surrounding region DNA methylation is a hallmark of gene silencing in cancer. Currently approved demethylating agents lack specificity and exhibit high toxicity. Herein we show, using  the p16 gene locus as an example, that targeted demethylation of the exon 1-intron 1 region initiates an epigenetic wave of local chromatin remodeling and distal long-range interactions, culminating in gene-locus specific activation. Through development of CRISPR-DiR (DNMT1-interacting RNA), an innovative technology wherein ad-hoc edited guides block methyltransferase activity in a locus-specific fashion, we demonstrate that demethylation is coupled to epigenetic and topological changes. These results suggest the existence of a specialized “demethylation firing center (DFC)” which can be switched on by an adaptable and selective RNA-mediated approach for locus-specific transcriptional activation.

overall_design: Wild type SNU-398 and Decitabine (DAC 2.5uM) treated 3 days SNU-398 cells DNA methylation were profiled through WGBS.  The long range chromatine interactions in SNU-398 CRISPR-DiR Day 13 Control (GN2) sample and D1+D3 targeted (G19, G36, G110, G111) sample were profiled by 4C-seq.

first: Y

last: Liu

first: M

first: Q

middle: X

last: Lin

first: C

last: Wu

first: J

last: Kwon

first: H

last: Tan

first: A

last: Ebralidze

first: L

last: Chai

first: T

last: Benoukraf

last: Di Ruscio

first: D

last: Tenen


title: Pro-survival roles for p21(Cip1/Waf1 in Non-Small cell Lung Cancer

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Quiescence is a reversible state of proliferative arrest, distinct from senescence. While cancer is a disease of dysregulated proliferation, cancer cells can retain the ability to enter quiescence which confers advantages to tumour cells by protecting cells from chemotherapy or by allowing cells to metastasise to distant sites. Multiple mechanisms exist to induce and maintain quiescence that are not yet fully understood. Here, we show that high expression of the CDK inhibitor p21Cip1/Waf1 correlates with a poor prognosis in TP53 wild-type, but not TP53 mutant, non-small cell lung cancer (NSCLC) patients. Using quantitative single-cell imaging of genetically-engineered NSCLC reporter cell lines, we show that TP53 wild-type NSCLC cells can enter a p21-dependent spontaneous quiescent state, downstream of replication stress. Furthermore, p21 expression confers survival advantages to TP53 wild-type NSCLC cells, both under normal proliferation and in response to chemotherapy. We also show that p21 can promote tumour relapse by allowing cells to recover from both G1 and G2 arrest states after drug removal. Together, our data suggest that targeting p21 function in TP53 wild-type tumours could lead to better outcomes for chemotherapy treatment in NSCLC patients.

overall_design: NSCLC lung cancer cell lines (NCI-H1944 mRuby-PCNA p21-mVenus) were FACS sorted into two populations - p21High (quiescent) or p21Low (proliferating) and profiled by RNA-seq. Four biological repeats were performed.

first: Steve

last: Cutty

first: Alexis

last: Barr


title: The heterogeneity of demal mesenchymal cells reproduced in skin equivalents regulate barrier function and elasticity.

status: Public on Dec 12 2024

city: Kizugawa

first: Sawa

last: Yamashiro

address: 6-5-4 Kunimidai

institute: Rohto Pharmaceutical Co., Ltd.

summary: This study aims to advance our understanding of skin physiology and aging through the development of human skin equivalents (HSEs) that replicate the natural heterogeneity of dermal mesenchymal cells, including papillary and reticular fibroblasts and pericytes. By integrating single-cell RNA sequencing (scRNA-seq) and innovative three-dimensional culture techniques, the research emphasizes the pivotal role of cell-to-cell communication in maintaining skin homeostasis. The findings highlight the potential of these HSEs as a robust in vitro platform for evaluating therapeutic interventions, modeling aging-related phenotypes, and mitigating the reliance on animal testing.

overall_design: scRNA-seq profiling of human skin equivalents constructed under three (2D, 3D_ED, 3D_EDV) conditions.

first: Shun

last: Kimura

first: Sachiko

last: Sekiya

first: Tetsuhiro

last: Kikuchi

first: Masatoshi

last: Haga

first: Tatsuya

last: Shimizu


title: The Drosophila Hypoxia-inducible factor 1-alpha is required to establish the larval glycolytic program

city: Bloomington

first: Jason

last: Tennessen

state: Indiana

address: 1001 E 3rd St

institute: Indiana University

summary: The rapid growth that occurs during Drosophila larval development requires a dramatic rewiring of central carbon metabolism to support biosynthesis. Larvae achieve this metabolic state, in part, by coordinately up-regulating the expression of genes encoding enzymes in carbohydrate metabolism. The resulting metabolic program exhibits hallmark characteristics of aerobic glycolysis and establishes a physiological state that supports growth. To date, the only factor known to activate the larval glycolytic program is the Drosophila Estrogen-Related Receptor (dERR). However, dERR is dynamically regulated during the onset of this metabolic switch, indicating that other factors must be involved. Here we discover that Sima, the Drosophila ortholog of Hif1α, is also essential for establishing the larval glycolytic program. Using a multi-omics approach, we demonstrate that Sima mutants fail to properly activate aerobic glycolysis and die during larval development with metabolic defects that mimic those observed in dERR mutants. Moreover, we demonstrate that dERR and Sima/Hif1α stabilize one another, as loss either transcription factor results in loss of the other. Considering that the mammalian homologs of ERR and Hif1α also stabilize one another through heterodimer formation, our findings establish the fly as a powerful genetic model for studying the interaction between these two key metabolic regulators.

overall_design: RNAseq profiling of Sima1/20 mutant Drosophila embryos compared to heterozygous Sima 1/+ controls at 8-12, 12-16, and 16-20 hours post egglay and RNAseq profiling of Sima1/20 mutant Drosophila larvae 60HPE compared to heterozygous Sima 1/+ controls.

first: Yasaman

last: Heidarian

first: Tess

middle: D

last: Fasteen

first: Liam

last: Mungcal

first: Kasun

last: Buddika

first: Nader

last: Mahmoudzadeh


title: Endogenous patterned activity-regulated genes specifically regulate different phases of synaptogenesis in the auditory system

city: NanJING

first: CHEN

last: XIN

state: JiangSu

address: N0.2 SiPai Road

institute: Southeast University

summary: In the auditory system, spatiotemporal patterning of correlated activity that originates in immature hair cells (HC) instructs refinement of synaptic connections and tonotopy. Patterned activity-dependent synaptic pruning requires the interplay between Hebbian plasticity and activity-regulated genes (ARGs). However, the genetic basis of this process is incompletely understood. Here we demonstrate that developing spiral ganglion neurons (SGNs) transiently generate discrete bursts of spikes and that blocking burst activity in this critical window causes profound deafness in mice. Using RNA sequencing, we profile ARG programs by genetically disrupting endogenous activity patterns of SGNs without changing spontaneous firing of inner HCs. Gene knockdown reveals that Nptx2 mediates initial synaptic formations at early stage, whereas Them5, which is important for cardiolipin remodeling that enhances mitochondrial function, specifically regulates synaptic pruning at later stage of development. These results suggest that ARGs dictate different phases of synaptogenesis and that Them5-depedent mitochondrial function might underlie synaptic pruning.

overall_design: Gene expression profiling analysis of RNA-seq data from postnatal days 7 mouse auditory spiral ganglion neurons. Approximately 50 spiral ganglion neurons as one biological replicate. Neurons are captured and collected by micro-pipette. Samples were collected from three conditions: control group ( aav-carried EGFP), dominant negtive SK3 channel group (aav-carried truncated SK3 channel), and dominant-negative HCN2 goup (aav-carried site-mutated HCN2 channel). Each condition also include two different regions (apex and base) in mouse cochlea.

first: Xin

last: Chen

first: Danning

last: Zheng

first: Guisheng

last: Zhong

first: Shuijin

last: He


title: Plasma microRNAs as prognostic biomarkers for development of severe epilepsy after experimental traumatic brain injury - EpiBioS4Rx Project 1 study

city: Kuopio

first: Mette

last: Heiskanen

address: Neulaniementie 2, P.O.B. 1627

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose: Post-traumatic epilepsy (PTE) is an epilepsy that develops after traumatic brain injury (TBI), and it comprises 10-20% of structural epilepsies and 5% of all epilepsies. The lack of prognostic biomarkers for PTE hinders the development of anti-epileptogenic treatments. In this preclinical multicenter study, plasma samples collected from a rat model of PTE were analyzed by small RNA sequencing to reveal the post-TBI expression profile of circulating microRNAs and to identify potential miRNA biomarkers for PTE development. Methods: The animal experiments were conducted at 3 different study sites: University of Eastern Finland (Finland), Monash University (Australia), and University of California, Los Angeles (USA). Severe TBI was induced in adult male Sprague-Dawley rats by the lateral fluid-percussion injury (LFPI) method. Rats that developed PTE were identified by video-EEG monitoring during the 7th post-injury month (TBI rats with epilepsy, TBIE; TBI rats without epilepsy, TBIN). Small RNA sequencing was conducted with plasma samples collected 48 hours after TBI or sham operation (craniotomy). Following the primary quantification, DESeq2 (v. 1.42.0) was used to identify differentially expressed miRNAs between the experiment groups. Results were further validated in a larger sample cohort by droplet digital PCR (ddPCR). Results: Small RNA sequencing detected a total of 754 miRNAs that were expressed in at least one sample. DESeq2 detected 23 differentially expressed (DE) miRNAs between the TBI and sham groups, 12 between the TBIE and sham groups, and 5 between the TBIN and sham groups. In contrast, no DE miRNAs were detected between the TBIE and TBIN groups. From the list of 23 DE miRNAs between the TBI and sham groups, 3 upregulated miRNAs (rno-miR-183-5p, rno-miR-323-3p, and miR-434-3p) were selected for further ddPCR validation. The list of miRNAs for validation was further complemented by 4 miRNAs (rno-miR-9a-3p, rno-miR-124-3p, rno-miR-132-3p, and rno-miR-212-3p), which were not differentially expressed in the DESeq2 analysis, but which we have previously detected to be acutely upregulated in TBI rat plasma. The validation was conducted with samples from the entire EpiBioS4Rx cohort [26 baseline samples, 45 sham, 164 TBI (32 TBIE, 132 TBIN)]. DdPCR analysis revealed that all 7 investigated miRNAs were upregulated in the TBI rats compared with the sham controls. No differences were detected between the rats with (TBIE) or without epilepsy (TBIN). In contrast, TBIE rats that had seizure clusters (severe PTE) had lower levels of plasma miR-212-3p compared with other TBI rats. Furthermore, elastic net regularized logistic regression (glmnet) analysis identified miR-212-3p and miR-132-3p as the optimal set to differentiate TBIE rats with seizure clusters from other TBI rats. Conclusions: The profile of circulating plasma microRNAs differed between TBI rats and sham controls. MiR-212-3p alone or in combination with miR-132-3p showed potential as prognostic biomarkers for development of severe PTE.

overall_design: Small RNA sequencing of rat plasma samples collected 48 h after lateral fluid-percussion injury (TBI, n=19) or sham operation (n=10). The plasma samples were collected at three different study sites: UEF, Monash, and UCLA. The TBI group contains 9 rats with epilepsy (TBIE) and 10 rats without epilepsy (TBIN), which was defined by a 4-week continuous video-EEG monitoring during the 7th month after injury.

first: Xavier

last: Ndode-Ekane

first: Idrish

last: Ali

first: Cesar

last: Santana-Gomez

first: Noora

last: Puhakka

first: Shalini

last: Das Gupta

first: Pedro

last: Andrade

first: Riikka

last: Immonen

first: Pablo

last: Casillas-Espinosa

first: Eppu

last: Manninen

first: Gregory

last: Smith

first: Rhys

last: Brady

first: Juliana

last: Silva

first: Emma

last: Braine

first: Matt

last: Hudson

first: Glenn

middle: R

last: Yamakawa

first: Nigel

last: Jones

first: Sandy

last: Shultz

first: Neil

last: Harris

first: David

last: Wright

first: Olli

last: Gröhn

first: Richard

last: Staba

first: Terence

last: O'Brien

first: Asla

last: Pitkänen


title: Spatial Transcriptomics Sequencing of Mouse Liver at 2µm Resolution Using a Novel Spatial DNA Chip

city: Palo Alto

first: Xun

last: Ding

address: 2500 Faber Pl

institute: Centrillion Technologies

summary: Spatial transcriptomics enables deep exploration of cellular gene expression, making it possible to elucidate the relationship between individual cells and tissues, thus enabling researchers to better understand development and disease. In this study, we present spatial transcriptomics data using a novel high-resolution DNA chip with a capture region size of 6.5 x 6.5 mm containing 2 x 2 µm features for spatial barcoding with no gaps between them, thereby maximizing the capture area. These chips are manufactured at wafer scale using photolithography and are transferred to hydrogels, making them compatible with existing workflows for fresh frozen or paraffin-embedded samples. Herein, we examined a fresh frozen sample from an adult mouse liver. Using a bin size of 10, representing a 20 µm x 20 µm capture area, and at 68.78%, sequencing saturation, we obtained over 1.3 billion unique mapped reads, with a median of 16,967 unique reads per region, indicating the potential for more unique reads with deeper sequencing. This high-resolution mapping of liver cell types and the visualization of gene expression patterns illustrate significant advancements in spatial sequencing technology.

overall_design: A spatial transcriptomics assay was performed on a fresh frozen adult mouse liver sample to investigate spatially resolved gene expression. A high-resolution DNA chip with 2 µm × 2 µm features was used for spatial barcoding. The tissue section was processed through a spatial transcriptomics workflow, including RNA hybridization, reverse transcription, and cDNA synthesis. Sequencing was conducted on an Illumina NovaSeq 6000 platform, providing detailed insights into liver cell type zonation and spatial gene expression patterns.

first: Kendall

last: Hoff

first: Radha

last: Swaminathan

first: Scott

last: Pollom

first: Tianlong

last: Huang

first: Xiaochi

last: Li

first: Guoqiang

last: Zhou

first: Zhicong

last: Bai

first: Shizhe

last: Yu

first: Zongping

last: Xia

first: Mikaela

last: Koutrouli

first: Lars Juhl

last: Jensen

first: Filip

last: Crnogorac

first: Su

last: McGall

first: Jeremy

last: Edwards

first: Wei


title: Senescent cells cluster CTCF on nuclear speckles to sustain their splicing program  [APEX-seq]

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str. 40

department: Institute of Pathology

country: Germany

institute: University Medical Center Göttingen

summary: Senescence —the endpoint of replicative lifespan for normal cells— is established via a complex sequence of molecular events. One such event is the dramatic reorganization of CTCF into senescence-induced clusters (SICCs). However, the molecular determinants, genomic consequences, and functional purpose of SICCs remained unknown. Here, we combine functional assays, super-resolution imaging, and 3D genomics with computational modelling to dissect SICC emergence. We establish that the competition between CTCF-bound and non-bound loci dictates clustering propensity. Upon senescence entry, cells repurpose SRRM2 —a key component of nuclear speckles— and BANF1 —a ‘molecular glue’ for chromosomes— to cluster CTCF and rewire genome architecture. This CTCF-centric reorganization in reference to nuclear speckles functionally sustains the senescence splicing program, as SICC disruption fully reverts alternative splicing patterns. We therefore uncover a new paradigm, whereby cells translate changes in nuclear biochemistry into architectural changes directing splicing choices so as to commit to the fate of senescence.

overall_design: Human lung fibroblasts (IMR90S) were cultured under two distinct conditions. One group was maintained in confluency (2*106 cells per 15 cm plate) using standard medium (MEM supplemented with 5% FBS, 1% NEAA, and 1% Pen/Strep). The other group was also grown in confluency (2*106 cells per 15 cm plate), in the same medium further supplemented with ICM to induce senescent phenotype. After mild fixation with 1% paraformaldehyde (PFA), the cells were scraped, centrifuged, and counted. Aliquots containing pellet of 1×106 cells per sample were  then prepared and froze at -80°C. Pellets were then processed for RNA And DNA Interacting Complexes Ligation and Sequencing (RADICL-seq) to investigate possible changes between proliferating and ICM-treated IMR90S in terms of the interactions between RNA molecules and the genomic regions with which they associate.


title: Neural Network-Assisted Humanization of COVID-19 Hamster scRNAseq Data Reveals Matching Severity States in Human Disease

city: Leipzig

first: Vincent

last: Friedrich

address: Härtelstraße 16-18

department: Institute for Medical Informatics, Statistics, and Epidemiology

institute: University of Leipzig

summary: Translating findings from animal models to human disease is essential for dissecting disease mechanisms, developing and testing precise therapeutic strategies. The coronavirus disease 2019 (COVID-19) pandemic has highlighted this need, particularly for models showing disease severity-dependent immune responses. Single-cell transcriptomics (scRNAseq) is well poised to reveal similarities and differences between species at the molecular and cellular level with unprecedented resolution. However, computational methods enabling detailed matching are still scarce. Here, we provide a structured scRNAseq-based approach that we applied to scRNAseq from blood leukocytes originating from humans and hamsters affected with moderate or severe COVID-19. Integration of COVID-19 patient data with two hamster models that develop moderate (Syrian hamster, Mesocricetus auratus) or severe (Roborovski hamster, Phodopus roborovskii) disease revealed that most cellular states are shared across species. A neural network-based analysis using variational autoencoders quantified the overall transcriptomic similarity across species and severity levels, showing highest similarity between neutrophils of Roborovski hamsters and severe COVID-19 patients, while Syrian hamsters better matched patients with moderate disease, particularly in classical monocytes. We further used transcriptome-wide differential expression analysis to identify which disease stages and cell types display strongest transcriptional changes. Consistently, hamster’s response to COVID-19 was most similar to humans in monocytes and neutrophils. Disease-linked pathways found in all species specifically related to interferon response or inhibition of viral replication. Analysis of candidate genes and signatures supported the results. Our structured neural network-supported workflow could be applied to other diseases, allowing better identification of suitable animal models with similar pathomechanisms across species.

overall_design: Whole blood of control and SARS-CoV-2-infected Phodopus roborovskii was analyzed using scRNAseq. Phodopus roborovskii were infected with either 1 × 10^5 (high-dose) or 1 × 10^4 (low-dose) plaque-forming units (pfu) SARS-CoV-2 (variant B1, isolate BetaCoV /Germany)/BavPat1/ 2020). Samples were taken at day 0 (control) as well as 2 and 3 days post infection (dpi).

first: Peter

last: Pennitz

first: Emanuel

last: Wyler

first: Julia

last: Adler

first: Dylan

last: Postmus

first: Luiz

last: Alves

last: Prigann

first: Fabian

last: Pott

first: Daria

last: Vladimirova

first: Thomas

last: Hoefler

first: Cengiz

last: Goekeri

first: Markus

last: Landthaler

first: Christine

last: Goffinet

first: Antoine-Emmanuel

last: Saliba

last: Scholz

first: Martin

last: Witzenrath

first: Jakob

last: Trimpert

first: Holger

last: Kirsten

first: Geraldine

last: Nouailles


title: Epigenome analysis of neonatal blood spots

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

summary: Changes in DNA methylation, is one mechanism by which genes are regulated. Aberrant methylation can lead to gene dysregulation, such as inactivation of tumour suppressor genes, and is observed in all cancers.  Gene dysregulation via aberrant DNA methylation may be an important contributor to disease outcomes. Importantly, these marks are malleable in response to environmental exposures and contribute to phenotypic plasticity in the context of a fixed genotype. Many studies suggest maternal exposures during pregnancy can have a profound impact on the epigenome and so determine gene expression patterns and health throughout the life-course. Studies of altered epigenetic marking are of profound importance for mechanistic understanding of the role of exposures on health but especially for studies of the developmental origins of health.    Historically collected neonatal blood spot samples represent a rich resource in which methylation at birth could be measured decades after being sampled and methylation patterns associated with recorded disease outcomes. Here we aimed to test the feasibility that methylation could be assessed in historically collected blood spot samples and assess if the time since sample collection affected methylation patterns.   The Newcastle Haematology biobank houses blood spots collected routinely from neonates 5-8 days after birth between the years 1984-1994 in the local region. Samples were selected from across the collection period and cross referenced with the Northern region Children's malignant disease registry in an aim to exclude samples from children who had gone on to have a malignancy during childhood. Genome-wide DNA methylation profiling of neonatal blood spots was assessed using the Illumina Infinium® MethylationEPIC BeadChip platform. Extraction yield DNA of sufficient quality and quantity for successful analysis of DNA methylation. Time since collection was not found to significantly influence methylation in this sample. Data from this study could be utilised in future case-controls studies to investigate the relationship between methylation patterns and birth and disease outcomes.

overall_design:
Genome-wide DNA methylation profiling of neonatal blood spot sample taken from heel pricks 2-7 days after birth were assessed
Bisulphite converted DNA extracted from neonatal blood samples were hybridized to Illumina Infinium MethylationEPIC BeadChips

first: Jill

last: McKay

first: Gordon

last: Strathdee

first: Mark

last: Pearce


title: Intrauterine Fetal Growth Restriction Leads to Sexually Dimorphic Programming of Preadipocytes’ Differentiation Potential

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

institute: University of Arizona

summary: Fetal growth restriction (FGR) is a risk factor for obesity in adult life. Importantly, growth-restricted females are more prone to obesity than males. The mechanisms involved in this sexually dimorphic programming are not known. Previously, we have demonstrated that ambient hyperthermia (40° C) led to placental insufficiency and significant FGR, and the perirenal adipose tissue undergoes sexually dimorphic gene expression. We demonstrated that males undergo significant changes in gene expression with growth restriction. This was not the case in females. We have also demonstrated that the isolated preadipocytes from male FGR (MFGR) have reduced differentiation potential compared to control males & females and female FGR (FFGR). Thus, we hypothesized that growth restriction differentially programs gene expression and genetic pathways in perirenal preadipocytes, which reduces their differentiation potential in male fetuses in a sexually dimorphic manner. We created fetal growth restriction by exposing pregnant sheep to ambient hyperthermia. After isolating preadipocytes from perirenal adipose tissue, we differentiated them following published protocols. We examined the gene expression before and after differentiation from control male, control female, MFGR, and FFGR female. We also compared our data with other published studies in mouse and human preadipocytes. Our results demonstrate that a set of 21 genes altered with preadipocyte differentiation to mature adipocytes is common in adipose tissue from both sexes, humans, mice, and sheep, at different organismal ages (embryonic, fetal, and adult) and different sites (subcutaneous inguinal, pancreatic, perirenal). We also demonstrate that female FFGR fetuses demonstrate all these 21 genes altered similar to control males and females; however, MFGR fetuses have six genes (Dgat2, Fabp4, Lipe, Lrrfip1, Spred3, and Thrsp) that are not changed with preadipocyte differentiation to mature adipocyte. These genes may be responsible for reduced differentiation potential and obesity in FGR males compared to FGR females. Another important finding of the present study is that Lrrfip1, known to be associated with obesity, was upregulated with FGR and requires further investigation.  Overall, our studies provide several target genes that may play a crucial role in reducing the risk of MFGR for obesity.

overall_design: Comparative gene expression analysis of perirenal preadipoyctes from four groups - control male, control female, growth restricted male, and growth restricted female before and following differentiation.


title: Quantitative design of microRNA-responsive mRNA from expression data

city: Seattle

first: Lukas

last: Oesinghaus

state: WA

address: 3946 W Stevens Wy NE

institute: University of Washington

summary: Limiting expression to target cell types is a longstanding goal in gene therapy, which could be met by sensing endogenous microRNA. However, an unclear association between microRNA expression and activity currently hampers such an approach. Here, we probe this relationship by measuring the stability of synthetic microRNA-responsive 3'UTRs across 10 cell lines in a library format. By systematically addressing biases in microRNA expression data and confounding factors such as microRNA crosstalk, we demonstrate that a straightforward model can quantitatively predict reporter stability purely from expression data. We use this model to design constructs with previously unattainable response patterns across our cell lines. The rules we derive for microRNA expression data selection and processing should apply to microRNA-responsive devices for any environment with available expression data.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Plasmid libraries containing reporters with microRNA target sequences in their 3'UTR were transiently transfected into either 4 (library 1) or 10 (library 2) cell lines for n=2 replicates. After two days, poly(A) RNA was extracted, reverse transcribed, and sequenced. The original plasmid libraries were also sequenced.

first: Sebastian

last: Castillo-Hair

first: Nicole

last: Ludwig

first: Andreas

last: Keller

first: Georg

last: Seelig


title: In vitro Examination of Piezo1-TRPV4 Dynamics: Implications for Placental Endothelial Function in Normal and Preeclamptic Pregnancies

city: Graz

first: Hanna

middle: Helene

last: Allerkamp

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

summary: Mechanosensation is essential for endothelial cell (EC) function, which is compromised in early-onset preeclampsia (EPE) impacting offspring health. The ion channels Piezo1 and TRPV4 are co-regulated mechanosensors in ECs. Here we show functional co-expression of both channels in feto-placental ECs (fpECs) and that calcium influx and membrane depolarization in response to chemical channel activation is reduced in EPE fpECs. Downstream of channel activation, Piezo1 alone can induce phosphorylation of endothelial nitric oxide synthase (eNOS) in fpECs, while combined activation of Piezo1 and TRPV4 only affects eNOS phosphorylation in EPE fpECs. Additionally, combined activation reduces the barrier integrity of fpECs, also with a stronger effect in EPE fpECs. This implies altered Piezo1-TRPV4 co-regulation in EPE. Mechanistically, we suggest this to be driven by changes in the arachidonic acid metabolism in EPE fpECs as identified by RNA-Seq. Targeting of Piezo1 and TRPV4 might hold potential for EPE treatment options in the future.

overall_design: Placentae were obtained immediately after delivery of singleton pregnancies at the Department of Obstetrics and Gynecology, Medical University of Graz, Austria. Collection and sample processing were approved by the ethics committee of the Medical University of Graz, Austria (29-319 ex 16/17) and voluntary detailed consent was taken from all study participants. Exclusion criteria were maternal systemic disease, other pregnancy complications, nicotine use during pregnancy, and a body mass index of <18 or >27 before pregnancy. The control samples were divided into two control groups: those delivered at ≥38 weeks of gestation called term controls (TC) and those delivered at <38 weeks of gestation called early controls (EC), the latter being age-matched to the early-onset PE group (EPE). EPE was diagnosed by a qualified clinician according to ACOG guidelines (new–onset hypertension with a blood pressure of ≥140/90 mmHg plus organ manifestation with onset of maternal symptoms <34 weeks of gestation). Clinical characteristics can be found in Table 1 of the repsective publication. For the study gene expression was compared between the groups.

first: Alexander

middle: I

last: Bondarenko

first: Ines

last: Tawfik

first: Nilüfer

last: Kamali-Simsek

first: Monika

last: Horvat Mercnik

first: Corina

last: Madreiter-Sokolowski

first: Christian

last: Wadsack


title: Striga hermonthica kibos ecotype microRNA annotations

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

summary: The purpose of this study was to annotate microRNAs in the parasitic plant Striga hermonthica and investigate any haustorial specific expression of novel microRNAs.

overall_design: Haustorial and leaf tissue were collected from Striga hermonthica kibos ecotype grown on roots of Oryza sativa japonica cultivar KitaakeX. Small RNA libraries were prepared from total RNA and sequenced using Illumina HiSeq 2000.

first: Allison

last: Vanek

first: Saima

last: Shahid


title: The microRNAome of Strongylus vulgaris larvae and their excretory/secretory products with identification of parasite-derived miRNAs in horse arterial tissue

city: Viborg

first: Maibritt

last: Mardahl

address: Blichers Alle 20

department: Department of Animal and Veterinary Research

country: Denmark

institute: Aarhus University

summary: The equine bloodworm, Strongylus vulgaris, is a highly pathogenic parasite causing potentially fatal vascular and intestinal damage. Parasites express and release microRNAs (miRNAs) for internal regulation and to modulate host immunity. The microRNAome (miRNAome) of S. vulgaris remains unannotated and the aim of this study was to annotate the miRNAome of 4th (L4) and 5th (L5) stage larvae of S. vulgaris and to examine differences in miRNA abundance between larval stages and sexes. Furthermore, we aimed to determine if miRNAs were detectable in excretory/secretory products (ESP) from larvae and in arterial tissue from their predilection site, the Cranial Mesenteric Artery (CMA). Larvae were collected from naturally infected foals, and categorized by sex and stage. A subset of larvae was snap-frozen, while the remaining were incubated and the excretory/secretory products (ESP) collected. Arterial tissue samples were collected from the CMA. Small RNA sequencing followed by a custom bioinformatic pipeline was used for annotation. We identified 142 S. vulgaris miRNAs in larvae and 136 in ESP. Significant differences in miRNA abundance were observed between larvae and ESP, and between L5 females (L5Fs) and L5 males (L5Ms), L4s and L5Fs and L4s and L5Ms. No differences were found between L4s and L5s overall. In ESP, several miRNAs were differentially abundant across all groups. Validation through quantitative real-time PCR (qPCR) detected selected miRNAs and their differential abundance in larvae and ESP. One parasite-derived miRNA was detected in some of the horse arterial tissue samples but at very low levels. This study provided the first annotation of the S. vulgaris miRNAome. Most of the annotated  larvae miRNAs were also detectable in ESP and differences in miRNA abundance between sexes were found for larvae, and between sexes and stages for ESP. Parasite-derived miRNAs were, however, not consistently detectable in the surrounding host arterial tissue.

sample_organism:
Equus caballus
Strongylus vulgaris

platform_organism:
Equus caballus
Strongylus vulgaris

overall_design: Exploratory study, including annotation of the Strongylus vulgaris microRNAome by small RNA sequencing and exploration of differences in miRNA abundance between different larval stages and sexes. Additionally, miRNAs in excretory/secretory products from S. vulgaris were profiled and differences between stages and sexes explored, followed by qPCR validation for a panel of selected miRNAs in both larvae and ES. Finally, qPCR was used to detect parasite-derived miRNAs in the larvaes prediliction site the Cranial Mesenteric Artery.

first: Katrine

last: Toft

first: Tina

last: Pihl

first: Cirera

last: Susanna

first: Stig

last: Thamsborg

first: Fromm

last: Bastian

first: Peter

last: Nejsum

first: Marie

middle: L

last: Honoré

first: Lise

last: Nikolic

first: Nichol

last: Ripley

first: Martin

last: Nielsen


title: Senescent cells cluster CTCF on nuclear speckles to sustain their splicing program

first: Argyris

last: Papantonis

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

overall_design: Refer to individual Series


title: Sex and social status influence DNA methylation dynamics in a polygynous bat

city: College Park

first: Gerald

last: Wilkinson

state: MD

address: Biology-Psychology Building

department: Department of Biology

institute: University of Maryland

summary: DNA methylation (DNAm) influences when and where genes are expressed or repressed during growth and development. Recently, patterns of DNAm at conserved genomic sites have been discovered that predict chronological age in all mammals. Deviations from these ‘epigenetic clocks’ have been used to identify factors that alter the aging process. In this study, we profile DNAm with a custom microarray for over 330 wild Phyllostomus hastatus, a highly polygynous bat in which unrelated females form long-lasting associations and larger males compete aggressively to control mating access to female groups. DNAm age estimates reveal that females can live more than 1.5 times as long as males. After fitting linear models for age, sex and their interaction we find that DNAm changes 1.4 times faster in males than females at thousands of sites. Therefore, even though age of either sex can be predicted by a common set of sites, the methylome of males is more dynamic than that of females. Sites associated with differences in the rate of change between males and females are sensitive to androgens and enriched on the X chromosome. Those that gain methylation with age in both sexes are associated with active and repressive chromatin states in blood and are enriched in promoters of genes involved in regulation of metabolic processes. In contrast, few sites differ in DNAm rate between males of different reproductive status, though subordinate males exhibit faster DNAm change than dominant males. Thus, males have accelerated physiological processes  in comparison to females that likely increase mating success but reduce survival.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We aimed to identify sex and age-associated methylation sites using DNA extracted from skin samples of wild-caught greater spear-nosed bats, Phyllostomus hastatus. We used the HorvathMammalMethylChip40, and estimated ages using existing methylation clocks from Wilkinson et al. 2021 (PMC7955057)

first: Danielle

last: Adams

first: Jack

middle: G

last: Rayner

middle: S


title: Expression data from PrimeView human gene expression array

city: SHANGHAI

first: CAIYUN

last: ZHANG

address: CHANGHAI ROAD NO. 168

institute: CHANGHAI HOSPITAL

summary:
Gene expression in CAL-27 cells infected with shCtrl and shSCUBE3 was detected with a PrimeView human gene expression array.
We performed Affymetrix Human Gene Chip Prime View analysis on  shCtrl and shSCUBE3 CAL-27 cells. Of the 931 differentially expressed genes (DEGs) found in shCtrl and shSCUBE3 CAL-27 cells, 353 were up-regulated and 578 were down-regulated based on the threshold of absolute fold change ≥ 1.3 and FDR < 0.05

overall_design: The total RNA of CAL-27 cells infected with shCtrl and shSCUBE3 was extracted. The RNA sequencing was performed with Affymetrix human GeneChip PrimeView and the outcomes were scanned by Affymetrix Scanner 3000. The statistical significance of raw data was completed by a Welch t-test with Benjamini-Hochberg FDR (|Fold Change| ≥ 1.3 and FDR < 0.05 as significant).

first: Minhui

last: Zhu

first: Yi

last: Ma

first: Wei

last: Wang

first: Meng

last: Li

first: Shicai

last: Chen


title: Pulmonary gain-of-function toxicity in alpha-1 antitrypsin deficiency

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Overall, we found that AAT is expressed in alveolar type 2 cells in addition to alveolar macrophages in primary human lung tissue. AT2s and alveolar macrophages in ZZ-AATD exhibit a distinct transcriptomic signature including inflammatory pathway and unfolded protein response gene set enrichment. AT2s in ZZ-AATD additionally exhibit evidence of cell stress including ATF4 regulon enrichment and expression of cleaved caspase 3. Together, these findings extend the prevailing paradigm of emphysema pathogenesis in ZZ-AATD and suggest AAT-expressing resident lung cells as logical therapeutic targets for future study.

overall_design: Survey of human adult lung from AATD diseased  tissue using single cell RNA sequencing.

first: Maria

last: Basil

first: Edward

last: Morrisey


title: 4DNESOLVRKBM - Replicate experiments of in situ Hi-C on CyT49 differentiated to pancreatic endoderm with MboI

city: Boston

last: DCIC

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

summary: Replicates of Hi-C on CyT49 cells differentiated to pancreatic endoderm

overall_design:
**Data Use Guidelines:** This is a data set generated by the 4DN Network and made freely available to the scientific community. If you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication. In your manuscript, please cite the 4DN White Paper ([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) and the 4DN Data Portal paper ([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), and please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).
lab: Bing Ren, UCSD
award: 1U54DK107977-01
accession: 4DNESOLVRKBM
condition: pancreatic endoderm
submitted_by: Bin Li
dataset_label: Hi-C on hESC differentiated to pancreatic endoderm
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESOLVRKBM/
number_of_experiments: 2

experiment: 4DNEXON87MIM; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXJH3AAC8; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f81352af-bd42-44c5-86b6-b04de82c4014/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIELSHHII.pairs.gz, 4DNFITKCX2DO.pairs.gz, 4DNFI823L812.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFISAJ77X3.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f81352af-bd42-44c5-86b6-b04de82c4014/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIELSHHII.pairs.gz, 4DNFITKCX2DO.pairs.gz, 4DNFI823L812.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFIK3NF6R2.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2e9ab254-25fa-4f6b-8eee-51cbce38bed4/
genome_assembly: GRCh38
derived_from: 4DNFIK3NF6R2.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFI7SHVNYK.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2e9ab254-25fa-4f6b-8eee-51cbce38bed4/
genome_assembly: GRCh38
derived_from: 4DNFIK3NF6R2.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFI9EBDZ2I.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f2d06a88-2eee-4fe7-bf8f-ab9342d97557/
genome_assembly: GRCh38
derived_from: 4DNFIK3NF6R2.mcool, 4DNFI7MCA4R6.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFI32O4LL2.bw


title: Ceramide regulated intracellular FGF13 impairs adipose nutrient sensing and glucose metabolism

city: Iowa City

first: Bhagirath

last: Chaurasia

address: 431 Newton Road

institute: University of Iowa

summary: Although, ectopic ceramide accumulation impairs nutrient sensing in adipocytes, leading to deterioration in energy and glucose homeostasis, the underlying mechanisms remain poorly defined. Using, comparative screen to identify ceramide regulated effector molecule in adipose tissue, we found fibroblast growth factor 13 (FGF13) as one of the critical ceramide-effector molecules that impair nutrient sensing in adipocytes. FGF13 is a cytosolic, non-secreted FGF belonging to a non-canonical FGF family member that comprises of FGF11-FGF14 and do not activate FGF receptors. FGF13 has been implicated in numerous physiological process such as development, cardiac arrythmias, neurological disease and cancer.  We demonstrate that FGF13 expression is highly induced in adipose tissue in response to a high fat diet, and its expression is negated by pharmacological and genetic interventions that inhibit ceramide biosynthesis. Inhibition of FGF13 in adipocytes (white, brown and beige), alters adipocyte morphology, prevents the development of obesity, improves glucose homeostasis, insulin sensitivity and resolves hepatic steatosis

overall_design: Epididymal white adipose tissues isolated from lean-vehicle, Obese-vehicle and Obese-myriocin treated animals fed either a normal chow or high fat diet


title: Fibroblast SPP1 mediates ECM deposition and inhibits SMC contractility in MFS aortic aneurysm

city: Tianjin

first: Mei

last: Zhou

address: Heping district，qixiangtai road 22

institute: Tianjin Medicial University

summary: Mutations in the Fbn1 gene cause Marfan Syndrome (MFS) and are associated with excessive transforming growth factor beta (TGF-β) signalling activation, which contributes to extracellular matrix (ECM) homeostasis disruption, thoracic aortic aneurysm (TAA) and dissection development. In this study, we aimed to explore the underlying events contributing to ECM metabolism imbalance and TAA and dissection formation in MFS. We performed sequencing analysis and investigated differentially expressed genes as well as cellular communication using CellChat. Fourteen ECM-related differentially expressed genes (DEGs) were identified. Among the 14 genes, secreted phosphoprotein 1 (Spp1) was involved in multiple pathological processes. We then stimulated primary mouse perivascular fibroblasts and aortic SMCs with recombinant Spp1 and recorded increased collagen expression in fibroblasts and decreased expression of Acta2 and Tagln in SMCs. We also investigated SPP1 levels in healthy controls and patients with TAA and found that elevated SPP1 levels were associated with an increased risk of TAA. Our results have indicated that Spp1 regulates ECM changes in fibroblasts and SMCs contractility during TAA. We believe that our study makes a significant contribution to the literature because our results suggest that Spp1 may serve as a potential target for TAA treatment.

overall_design: Analyze the genetic changes between Fbn1 mice and wild mice

first: Yan

last: Liu


title: Transposable element exonization by non-canonical splicing generates a diversity reservoir of functional protein isoforms

city: Paris

first: Yago

middle: A

last: Arribas

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: mRNA splicing enlarges the diversity of the protein repertoire, mainly through alternative exon retention or skipping. Although non-canonical splicing variants that exonize intronic regions were recently identified at the mRNA level, their contribution to the cellular proteome remains unclear. Here, we describe a population of 1300 unannotated protein isoforms generated by non-canonical splicing between exons and transposable elements (TE) using a combination of transcriptome assembly, ribosome profiling, and mass spectrometry. Despite being shorter and expressed at lower levels, their translation efficiency is similar to that of canonical isoforms, and they are shared between individuals. Functional analyses of 5 different non-canonical isoforms show stable expression, specific intracellular localization, and modified functions, as compared to the corresponding canonical isoforms. Non-canonical isoforms derive mainly from evolutionarily ancient genes and are a preferential source of alternative splicing upon which natural selection can act. We conclude that recently exonized TE isoforms are potentially functional and represent a diversity reservoir of novel protein isoforms.

overall_design: RNA-seq from from human cancer cell lines (treated or untreated with puromycin) used for transcriptome assembly. Differential expression analysis on cell lines overexpressing PTEN and WWOX non-canonical isoforms. Ribosome profiling in lung cancer cell lines. Differential expression analysis on cell lines for the study of non-canonical isoforms.

first: Sebastian

last: Amigorena


title: Copy number variation analysis of a fetus with Silver-Russell syndrome in China

status: Public on Dec 11 2024

city: Zhangzhou

first: Shurong

last: Hong

department: Department of molecular genetic center

institute: Zhangzhou Municipal Hospital of Fujian Province and Zhangzhou Affiliated Hospital of Fujian Medical University

summary: The Affymetrix CytoScan 750K Array chip contains 200000 SNP markers and 550000 CNV markers, distributed across the entire human genome at an average density of approximately 1 marker/4kb (not covering all loci of the entire chromosome genome). It is used to detect clinically significant chromosomal microdeletions/microduplications, chromosomal subtelomer deletion syndrome, and other abnormal chromosomal copy number variations (CNVs) as well as loss of heterozygosity (LOH). In a case study of Zhangzhou Municipal Hospital of Fujian Province, copy number variation detection was performed on a fetus with Silver-Russell syndrome using CytoScan 750K Array chip, and variations in the corresponding region were identified.

overall_design: Affymetrix CytoScan 750K Array was performed according to the manufacturer's directions on DNA extracted from amniotic fluid samples. Copy number analysis of Affymetrix CytoScan 750K Array was performed for a fetus with Silver-Russell syndrome


title: Transcription factor IRF4 deficiency in NK precursors pre-determines epigenetic changes in mature NK cells

city: HOUSTON

first: Xiaolong

last: Zhang

state: Texas

address: 6670 Bertner Avenue, R7-211

department: Immunobiology & Transplant Research Center

institute: Houston Methodist Research Institute

summary: To explore whether IRF4 deficiency determine the epigenetic changes of mature NK cells is at the NKP cell stage, ATAC-seq was performed to analyze chromatin accessibility of NK cells from spleen WT, Irf4-/-, Irf4flox/flox and Ncr1cre+/-Irf4flox/flox mice.

overall_design: We sorted CD3-NK1.1+ NK cells from the spleen of Wilde type C57BL/6 (B6), Irf4–/–, Irf4flox/flox, Ncr1cre+/-Irf4flox/flox mice. These sorted NK cells were subjected to ATAC sequencing

first: Zheng

last: Yin

first: Wenhao

first: Dawei

last: Zou

first: Xiang

last: Xiao


title: Nonuple atg8 mutant provides genetic evidence for functional specialization of ATG8 isoforms in Arabidopsis thaliana

city: Vienna

first: Yasin

last: Dagdas

address: Dr. Bohr-Gasse 3

institute: Gregor Mendel Institute

summary: Autophagy is a vital cellular process that maintains organismal health by recycling damaged or superfluous cellular components within autophagosomes. This process is mediated by conserved ATG proteins, which coordinate autophagosome biogenesis and selective cargo degradation. Among these, the ubiquitin-like ATG8 protein plays a central role by linking cargo to the growing autophagosomes through interactions with selective autophagy receptors. Unlike most ATG proteins, which are represented by single or few isoforms, the ATG8 gene family is expanded in vascular plants, yet the extent of functional specialization within ATG8 isoforms remains largely unknown. Using transcriptional and translational reporters in Arabidopsis thaliana, we revealed that ATG8 isoforms are differentially expressed across tissues and form distinct autophagosomes within the same cell. To explore ATG8 specialization, we generated the nonuple Δatg8mutant lacking all nine ATG8 isoforms. The mutant displayed hypersensitivity to carbon and nitrogen starvation, coupled with defects in bulk and selective autophagy as shown by biochemical and ultrastructural analyses. Complementation experiments demonstrated that ATG8A could rescue both carbon and nitrogen starvation phenotypes, whereas ATG8H could only complement carbon starvation. Proximity labeling proteomics further identified isoform-specific interactors under nitrogen starvation, underscoring their functional divergence. These findings provide genetic evidence for the specialization of ATG8 isoforms in plants and lay a foundation for investigating their roles in diverse cell types and stress conditions.

overall_design: For standard plant growth, Arabidopsis seeds were gas sterilized with sodium hypochlorite + HCl (10:1 v/v), sown on water-saturated soil and grown in 16h light/8h dark photoperiod with 165 μmol m^-2 s^-1 light intensity. For in vitrogrowth, Arabidopsis seeds were surface sterilized in 70% ethanol for 10 minutes twice, then rinsed in absolute ethanol and dried on sterile paper. Seeds were sown in ½ MS liquid medium (Murashige and Skoog salt + Gamborg B5 vitamin mixture [Duchefa] supplemented with 0.5 g/liter MES and 1% sucrose, pH 5.7), vernalized at 4 °C in the dark for 2 days, and then grown under LEDs with 85μM/m²/s with a 14 h light/10 h dark photoperiod.High-quality DNA was extracted using the cetyltrimethylammonium bromide (CTAB) method and used to construct Illumina-compatible libraries with the Nextera XT DNA Library Preparation Kit, following the manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq instrument in paired-end 150 bp mode. Raw FASTQ files obtained from sequencing were quality-checked and adapter-trimmed using TrimGalore (https://github.com/FelixKrueger/TrimGalore) with default settings. The trimmed FASTQ files were aligned to the TAIR10 genome using Bowtie2 (Langmead & Salzberg, 2012) with the parameters -D 15 -R 2 -N 0 -L 22 -i S,1,1.15. The resulting aligned BAM files were sorted and indexed using SAMtools (Danecek et al., 2021) and manually inspected for insertions or deletions using the Integrative Genomics Viewer (IGV).


title: Human intraepithelial mast cell differentiation and effector function are directed by TGF-b signaling

first: Daniel

last: Dwyer

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

summary: Mast cells (MCs) expressing a distinctive protease phenotype (MCTs) selectively expand within the epithelium of human mucosal tissues during type 2 (T2) inflammation. While MCTs are phenotypically distinct from subepithelial MCs (MCTCs), signals driving human MCT differentiation and this subset’s contribution to inflammation remain unexplored. Here, we identify TGF-b as a key driver of the MCT transcriptome in nasal polyps. We find that short-term TGF-b signaling alters MC cell surface receptor expression and partially recapitulates the in vivo MCT transcriptome, while TGF-β signaling during MC differentiation upregulates a larger number of MCT-associated transcripts and inhibits the hallmark MCTC proteases chymase and cathepsin G at both the transcript and protein level, allowing selective in vitro differentiation of MCTs for functional study. We identify discrete differences in effector phenotype between in vitro-derived MCTs and MCTCs, with MCTs greatly enhancing pro-inflammatory lipid mediator generation while selectively modifying cytokine, chemokine, and growth factor production in response to both innate and adaptive stimuli, recapitulating functional features of their tissue-associated counterpart MC subsets. Thus, our findings support a role for TGF-β in promoting human MCT differentiation and identify a discrete contribution of this cell type to T2 inflammation.

overall_design: This study tests the effects of TGF-b1 treatment on mature human peripheral blood-derived mast cells at two timepoints (24h, 6d) versus the effects of differentiating mast cells in the presence or absence of TGF-b1.

middle: F

first: Tahereh

last: Derakhshan


title: The interplay between oxytocin receptor and YAP in regulating gastric cancer progression

city: Shenyang

first: Xin

last: Li

state: China/Liaoning province

address: Puhe road

institute: China Medical University

summary: Gastric cancer (GC) is one of the most lethal malignancies worldwide, but the effective therapeutic targets for GC is still limited. Accumulated evidence implicates the over-activation of Hippo/YAP axis in GC, while pharmaceutical targeting YAP could be a plausible strategy for GC treatment. Thus, it is of great clinical significance to identify novel hits for Hippo/YAP axis in GC. In our study, we identified oxytocin receptor (OXTR) as an important regulator of Hippo/YAP axis. RNA sequence analysis revealed the OXTR depletion inhibited the expression of Hippo target genes in whole genomic scale.

overall_design: SNU216 cell mRNA samples were summarized in six samples, divided into two groups, siControl and siOXTR. Comparative gene expression profiling analysis of RNA-seq data for SNU216 cells treated with siControl and siOXTR.

first: Jian

last: Zhu

first: Kai

first: Yinlu

last: Ding

first: Ziping