title: Effects of depletion of Mel18 on genome wide distribtion of H2AK119ub1 in lineage negative hematopoietic stem cells [CUT&RUN]

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

institute: Northwestern University

summary: Polycomb group (PcG) proteins play important roles in hematopoietic stem cell (HSC) self-renewal. Mel18 and Bmi1 are homologs of the PCGF subunit within the Polycomb repressive complex 1 (PRC1). Bmi1 (PCGF4) enhances HSC self-renewal and promotes terminal differentiation. However, the role of Mel18 (PCGF2) in hematopoiesis is not fully understood and how Mel18 regulates gene transcription in HSCs remains elusive. We found that acute deletion of Mel18 in the hematopoietic compartment significantly increased the frequency of functional HSCs in the bone marrow. Furthermore, we demonstrate that Mel18 inhibits HSC self-renewal and proliferation. RNA-seq studies revealed that HSC self-renewal and proliferation gene signatures are enriched in Mel18-/- hematopoietic stem and progenitors (HSPCs) compared to Mel18+/+ HSPCs. Notably, ATAC-seq revealed increased chromatin accessibility at genes important for HSC self-renewal, whereas CUT&RUN showed decreased enrichment of H2AK119ub1 at genes important for proliferation, leading to increased expression of both Hoxb4 and Cdk4 in Mel18-/- HSPCs. Furthermore, leukemia stem cells and several types of acute leukemia gene signatures are enriched in Mel18-/- HSCs compared to WT HSCs. Thus, we demonstrate that Mel18 inhibits hematopoietic stem cell self-renewal through repressing the transcription of genes important for HSC self-renewal and proliferation.

overall_design: To determine whether polycomb group protein Mel18 alters genomic distribution of h2ak119ub1 in HSPCs, we established conditional Mel18 knock out mouse model in hematopoietic system. We then performed differential peak calling analysis using data obtained from CUT&RUN coupled with next generation sequencing in sorted Lin- cells from either wildtype or Mel18-null mouse.

first: Sisi

last: Chen


title: Effects of depletion of Mel18 on chromatin accessibility in lineage negative hematopoietic stem cells [ATAC-seq]

status: Public on May 08 2025

department: Department of Medicine

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To determine whether polycomb group protein Mel18 alters chromatin accessibility in mouse HSPCs, we established conditional Mel18 knock out mouse model in hematopoietic system. We then performed differential peak calling analysis using data obtained from ATAC-seq with sorted Lin- cells from either wildtype or Mel18-null mouse.


title: Effects of depletion of Mel18 on gene expression in lineage negative hematopoietic stem cells [RNAseq_Lin_neg_cell]

type: Expression profiling by high throughput sequencing

overall_design:
To determine whether polycomb group protein Mel18 alters gene transcription in mouse HSPCs, we established constional Mel18 knock out mouse model in hematopoietic system. We then performed gene expression profilling analysis using data obtained from RNA-seq with sorted Lin- cells from either wildtype or Mel18-null mouse.
Comparative gene expression profilling analysis of RNA-seq data was performed between wildtype and Mel18 knouck out HSCs.


title: Gene expression profle at single cell level of lacrimal gland

city: Qingdao

first: xiaoyu

last: li

state: Shandong

address: NO.5 Yanerdao Road

country: China

institute: Qingdao Eye Hospital of Shandong First Medical University

summary: The lacrimal gland (LG) is essential for tear secretion and plays a critical role in dry eye disease (DED). This study utilized single-nucleus RNA sequencing (snRNA-seq) to investigate the cellular diversity of the LG in both normal and DED conditions.

overall_design: Samples were collected from normal control mice, dry eye mice induced by scopolamine (SCOP) and dry stress (DS), and dry eye mice treated with tamsulosin for single-nucleus RNA sequencing (snRNA-seq).


title: Effects of depletion of Mel18 on gene expression in mouse long-term hematopoietic stem cells [RNAseq_LT-HSC]

overall_design:
To determine whether polycomb group protein Mel18 alters gene transcription in mouse HSC self-renewal, we established constional Mel18 knock out mouse model in hematopoietic system. We then performed gene expression profilling analysisng ysing data obtained from RNA-seq using sorted HSCs from either wildtype or Mel18-null mouse.
Cpmparative gene expression profilling analysis of RNA-seq data was performed between wildtype and Mel18 knouck out HSCs.


title: CD163+ cardiac macrophages attenuate pressure overload-induced left ventricular systolic dysfunction via interleukin-10

city: Xiamen

first: Binbin

state: Fujian

address: Jinshan Road

department: Xiamen Cardiovascular Hospital

institute: Xiamen University

summary: Background Chronic sustained pressure overload induces cardiac remodeling, which often leads to heart failure. Cardiac macrophages (cMacs) are heterogeneous cell populations, and their elimination has been shown to exacerbate pressure overload-induced heart failure. CD163, a macrophage-specific scavenger receptor expressed in a subset of cMacs, has been linked to cardiovascular events through its serum soluble form. This study aimed to elucidate the functional role of the CD163+ cMacs subset in pressure overload-induced heart failure. Methods Transverse aortic constriction (TAC) was performed on wild-type and CD163-deficient (Cd163-/-) mice to investigate the role of CD163 in pressure overload-induced cardiac remodeling and heart failure. Echocardiography was used to assess heart structure and function. Transcriptomic analysis and transmission electron microscopy were employed to observe mitochondrial structure in cardiomyocytes. Flow cytometry was used to quantify cMacs and cytokine-expressing cMacs in the heart. Additionally, serum samples from hypertensive patients with and without heart failure were analyzed to explore the relationship between CD163 and heart failure. Results TAC-induced left ventricular systolic dysfunction, including reduced ejection fraction and fractional shortening, was significantly aggravated in Cd163-/- mice post-surgery. Genes differentially expressed due to CD163 deficiency were enriched in pathways related to mitochondrial bioenergetics and homeostasis. Transmission electron microscopy revealed an increase in dysfunctional mitochondria in cardiomyocytes of Cd163-/- mice post-TAC. Additionally, decreased serum interleukin (IL)-10 levels and reduced IL-10 expression in cMacs were observed in Cd163-/- mice post-TAC. IL-10 supplementation significantly reversed TAC-induced reductions in left ventricular systolic function and improved mitochondrial bioenergetics and homeostasis in Cd163-/- mice. Conclusions The protective functions of CD163 in cMacs are associated with IL-10 expression during pressure overload-induced heart failure.

overall_design: TAC was performed as previous report. Briefly, 8-week-old male mice were anesthetized with 2% isoflurane and incubated with 0.5–1 L/min oxygen mixed with 1.5–2% isoflurane during surgery. The transverse aorta was exposed and tied with a 27-gauge blunt needle by 6-0 silk string. The needle was removed later. The chest and skin were closed, and mice were allowed to recover from anesthesia. Sham surgery was carried out as above without aortic ligation. Cd163-/- mice received subcutaneous injections of mouse recombinant IL-10 (50 μg/kg/day) on days 0, 1, 3, 5, 7, 10, 13, 16, 19, 22, 25, and 27 following TAC surgery. Peritoneal macrophages were harvested from the peritoneal cavity three days after stimulation with thioglycolate-containing medium (16). Following centrifugation, the macrophages were cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 5% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S) at 37 °C in a 5% CO₂ environment. The cells were allowed to adhere for 2–3 hours, and non-adherent cells were removed. After overnight culture, the adherent cells were treated with 100 nM dexamethasone for 48 hours.

first: Wei

last: NI


title: Loss of the Endothelial Glycocalyx Component EMCN Leads to Glomerular Impairment

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary: Endomucin (EMCN), an endothelial-specific glycocalyx component, was found to be highly expressed by the endothelium of the renal glomerulus. We reported an anti-inflammatory role of EMCN and its involvement in the regulation of vascular endothelial growth factor (VEGF) activity through modulating VEGF receptor 2 (VEGFR2) endocytosis. The goal of this study is to investigate the phenotypic and functional effects of EMCN deficiency using the first global EMCN knockout mouse model.Global EMCN knockout mice were generated by crossing EMCN-floxed mice with ROSA26-Cre mice. Flow cytometry was employed to analyze infiltrating myeloid cells in the kidneys. The ultrastructure of the glomerular filtration barrier was examined by transmission electron microscopy, while urinary albumin, creatinine, and total protein levels were analyzed from freshly collected urine samples. Expression and localization of EMCN, EGFP, CD45, CD31, CD34, podocin, albumin, and α-smooth muscle actin were examined by immunohistochemistry. Mice were weighed regularly and their systemic blood pressure was measured using a non-invasive tail-cuff system. Glomerular endothelial cells and podocytes were isolated by fluorescence-activated cell sorting for RNA sequencing. Transcriptional profiles were analyzed to identify differentially expressed genes in both endothelium and podocytes, followed by gene ontology analysis of up- and down-regulated genes.  Protein levels of EMCN, albumin, and podocin were quantified by Western blot.EMCN-/- mice were viable with no gross anatomical defects in kidneys. The EMCN-/- mice exhibited increased infiltration of CD45+ cells, with an increased proportion of Ly6GhighLy6Chigh myeloid cells and higher VCAM-1 expression. EMCN-/- mice displayed albuminuria with increased albumin in the Bowman's space compared to the EMCN+/+ littermates. Glomeruli in EMCN-/- mice revealed fused and effaced podocyte foot processes and disorganized endothelial fenestrations. We found no significant difference in blood pressure between EMCN knockout mice and their wild-type littermates. RNA sequencing of glomerular endothelial cells revealed downregulation of cell-cell adhesion and MAPK/ERK pathways, along with glycocalyx and extracellular matrix remodeling. In podocytes, we observed reduced VEGF signaling and alterations in cytoskeletal organization. Notably, there was a significant decrease in both mRNA and protein levels of podocin, a key component of the slit diaphragm.

overall_design: FACS sorted glomeruli endothelium and podocyte from EMCN+/+ and EMCN-/- kidneys from mouse

first: Zhengping

last: Hu

first: Issahy

last: Cano

first: Fengyang

last: Lei

first: Jie

first: Harper

last: Gordon

first: Eleftherios

middle: I

last: Paschalis

first: Magali

last: Saint-Geniez

first: Yin

last: Ng

first: Patricia

middle: A

last: D’Amore


title: ATAC-seq analysis of kidney cortex following KLF6 induction

city: Stony Brook

first: Sandeep

last: Mallipattu

state: NY

address: 101 Nicolls Road

institute: Stony Brook University

summary: The goal of this study was to identify chromatin changes mediated by KLF6 induction 24 hours after aristolochic acid-induced acute kidney injury

overall_design: Four experimental groups were analyzed, one replicate per group.

first: Sian

middle: E

last: Piret

first: Maanasa

last: Hanubal

first: Merin

last: Davis

first: Jiakang

last: Wang

first: Samaneh

last: DiMartino

first: Nehaben

last: Gujarati

first: Tej

last: Bahadur

first: Asha

last: Rath

first: Robert

last: Bronstein

first: Yiqing

last: Guo

middle: K


title: Transcriptomic analysis of kidney cortex following KLF6 induction

summary: The goal of this study was to identify transcriptomic changes mediated by KLF6 induction 24 hours after aristolochic acid-induced acute kidney injury


title: MEF2D functions as a tumor suppressor in breast cancer

city: Pittsburgh

first: Bowen

last: Dong

state: Pennsylvania

address: 4200 Fifth Ave, Pittsburgh, PA 15260

institute: University of Pittsburgh

summary: The myocyte enhancer factor 2 (MEF2) gene family plays fundamental roles in the genetic programs that control cell differentiation, morphogenesis, proliferation, and survival in a wide range of cell types. The molecular programs they regulate and their role in tumor development and progression remain incompletely understood. The present study evaluated whether the MEF2D transcription factor functions as a tumor suppressor in breast cancer. We found knockout of the MEF2D gene in mouse mammary epithelial cells resulted in phenotypic changes characteristic of neoplastic transformation, including: enhanced cell proliferation, loss of contact inhibition, and anchorage-independent growth in soft agar, as well as capacity for tumor development in mice. Through RNAseq analysis, we found knockout of MEF2D induced the epithelial-to-mesenchymal transition (EMT) and activated several oncogenic signaling pathways. In summary, our study indicates that MEF2D may be a putative tumor suppressor, acting through selective gene regulatory programs that have clinical and therapeutic significance in breast cancer.

overall_design: To determine MEF2D-dependent gene expression programs, we harvested RNA from sgControl and sgMef2d EpH4 cells and performed RNA-seq analysis.

first: Xiaoxia

first: He

last: Shen

first: Yanmin

last: Chen

first: Yali

last: Zhang

first: Jianmin

first: Song

last: Liu

first: Bo

last: Xu

first: Hai

first: Costa

last: Frangou


title: Spatial Transcriptional Landscape of Human Heart Failure

city: Seoul

first: Sang Eun

last: Lee

state: Songpa-gu

address: 88, Olympic-ro 43-gil

department: Department of Cardiology

country: South Korea

institute: Asan Medical Center

summary: Heart failure (HF) poses a major clinical challenge with diverse underlying causes. Despite advances, the intricate molecular alterations specific to distinct cell types and histological patterns during HF progression remain inadequately characterized. Using the GeoMx whole human transcriptome digital spatial profiler, we discerned gene expression dynamics in failing human hearts, integrating cell type, clinical, and histological nuances. We demonstrated the cellular composition of the left ventricle myocardium and validated the GeoMx platform's compartmentalization efficiency, showing high accuracy for cardiomyocytes but limitations for endothelial cells and fibroblasts. Gene regulation in HF was influenced by cellular context, with contrasting patterns across cell types. Differentially expressed genes, such as UCHL1, IGFBP2, CCL14, ACKR1, and PLVAP, were linked to specific histologic features like degeneration and fibrosis. Multiplex immunohistochemistry confirmed the co-localization of PLVAP and ACKR1 in endothelial cells, correlating with fibrosis severity. Furthermore, our data highlight pronounced inflammatory responses in end-stage HF. Integrative analysis, combining histological and clinical perspectives, spotlighted CRIP3, PFKFB2, and TAX1BP3 as potential contributors to HF progression. Our findings underscore the pivotal role of cell enriched and histology-specific transcriptome mapping in understanding the complex pathophysiological landscape of failing hearts, unveiling potential therapeutic targets and molecular insights.

overall_design: Nanostring GeoMx Digital Spatial Profiler sequencing was performed using human heart samples from various cardiomyopathy patients. (e.g. Ischemic cardiomyopathy (ICMP), hypertrophic cardiomyopathy (HCMP), Dilated cardiomyopathy (DCMP))

first: Sang

first: Jeong

middle: H

last: Joo

first: Hee

middle: S

last: Hwang

first: Shang-Fu

first: Douglas

last: Evans

first: Kyoung

middle: Y

first: Kyung-Hee

last: Kim

first: Junho

last: Hyun

first: Min-Seok

first: Sung-Ho

last: Jung

first: Jae-Joong

last: lee

first: Ali

last: Torkamani


title: Human-biased TMEM25 expression promotes expansion of neural progenitor cells to alter cortical structure in the developing brain

city: Higashi-Hiroshima

first: boyang

last: An

state: Hirohsima

address: Kagamiyama 1-3-1

country: Japan

institute: Hiroshima University

summary:
TMEM25 can receive extracellular signals to expand bRGs, a process which occurs specifically in human cortical development
To reveal the molecular mechanism by which TMEM25 regulates neurogenesis, we performed RNA-seq to examine the transcriptome changes after TMEM25 knockdown in human NPCs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AF22 NPCs and its KD derivatives (TMEM25 sh1 and TMEM25 sh2).

first: Boyang

first: Akari

last: Ando

first: Hiroto

last: Akuta

first: Takuya

last: Imamura


title: Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Esophageal Squamous Cell Carcinoma

city: Hong Kong

first: Xin

middle: Yuan

last: Guan

state: -- Country other than USA or Canada --

address: Room L10-56, 10/F, Laboratory Block, 21 Sassoon Road, Hong Kong

department: Department of Clinical Oncology

institute: The University of Hong Kong

summary: We profiled the transcriptome of 85, 263 single cells from ESCC patients with lymph node metastasis (LNM) and clustered 7, 196 myeloid cells into 18 subclusters including nine for macrophage cells, one for neutrophils, two for monocytes, two for mast cells, one for tolerogenic dendritic cells, one for plasmacytoid dendritic cells and two for conventional dendritic cells. In this study, we not only provides a high-resolution landscape of the tumor, immune and stromal compartments in metastatic lymph node, but also highlights metastatic-specific patterns comparing with primary tumor. These findings provide insights that may help to shape the tumor microenvironment and inform the development of new strategies against these pro-metastatic non-tumor components for inhibiting tumor growth and overcoming metastasis.

overall_design: Four patients who were pathologically diagnosed with ESCC were enrolled in this study and no patient received preoperative treatment. Fresh sterile biopsies were collected from normal tissue adjacent to the primary tumor, matched primary tumor site and lymph node site by endoscopy for every patient, and then were all fresh-processed for scRNA-seq using 10X Genomics platform. Three of four patients have lymph node metastasis but the remaining patient not.

first: Baifeng

last: Zhang

first: Yongxu

last: Jia

first: Yanru

last: Qin

first: Xinyuan


title: H3K4me3 occupancy around CYP1B1 TSS in CD133-positive liver cancer stem-like cells compared with CD133-negative cells.

city: Hangzhou

first: Jiaqi

last: Wang

state: Zhejiang

address: Yuhangtang No.866

institute: Zhejiang University

summary: To investigate the contribution of H3K4me3 marks in CYP1B1 activation in CD133-positive liver cancer stem-like cells, cleavage under targets and tagmentation (CUT&Tag) was performed for H3K4me3 profiles in CD133+/- subsets of HCC cell lines and HCC-PDX tumor.

overall_design: Xiaoli,Zheng


title: RAF conformational autoinhibition and 14-3-3 proteins promote paradoxical activation

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: RAF kinase inhibitors can, in some conditions, increase RAF kinase signaling. This process, which is commonly referred to as “paradoxical activation” (PA), is incompletely understood. RAF kinases are regulated by autoinhibitory conformational changes, and the role of these conformational changes in PA is unclear. Our mathematical investigations reveal that a dynamic equilibrium between autoinhibited and non-autoinhibited forms of RAF, along with the RAF inhibitor stabilization of the non-autoinhibited form, can be sufficient to create PA. Using both computational and experimental methods we demonstrate that 14-3-3 proteins, which stabilize both RAF autoinhibition and RAF dimerization, potentiate PA. Our model led us to hypothesize that increased 14-3-3 expression would amplify PA for the third generation RAF inhibitors that normally display minimal to no PA. Our subsequent experiments find that 14-3-3 overexpression increases PA, increases RAF dimerization, and promotes resistance to these inhibitors, effectively “breaking” these “paradox breaker” and pan-RAF inhibitors. Overall, this work reveals a robust mechanism for PA based solely on equilibrium dynamics of canonical interactions in RAF signaling.

overall_design: mRNA profiles of SK-MEL-2 human melanoma cells in media supplemented with vemurafenib, media supplemented with PLX8394, and regular growth media at day 3, 7, 14 and 21.

first: Gaurav

last: Mendiratta

first: Kodye

last: Abbott

first: Yao-Cheng

last: Li

first: Jianfeng

last: Huang

first: Maxim

middle: N

last: Shokhirev

first: Thomas

last: McFall

first: Geoffrey

last: Wahl

first: Edward

middle: C

last: Stites


title: The robust inflammatory responses caused by MjHKU4r-S mediated cell fusion

status: Public on May 07 2025

city: Shanghai

first: Tianyu

last: Lu

address: No.130, Dongan Road

institute: Fudan University

summary: The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) has extremely high virulence and pathogenicity in human, but some MERS-related coronaviruses (bat-CoV HKU4, bat-CoV HKU5-1/2 and MOW15-22/PnNL2018B) showed limited infectivity in human beings. Unlike previously reported MERS-related coronaviruses, the currently identified MERS-related Manis javanica HKU4-related coronavirus (MjHKU4r-CoV-1) exhibited significant infectivity in human cell, organs, and hDPP4-transgenic mice. However, the detailed pathogenic features and underlying mechanisms were unknown. In virological experiments, we found MjHKU4r-CoV-1 triggered extensive syncytia formation by its spike protein (S) and caused significant inflammation responses. Herein, we use RNA sequencing (RNA-Seq) to investigate the transcriptional alterations underlying the robust inflammatory responses caused by S protein mediated syncytia formation.

overall_design: 293T cells were transfected with the pAAV-IRES-EGFP vector plasmid encoding S proteins of MjHKU4r-CoV-1, HKU4 (the negative control), or SARS-CoV-2 KP.2 variant (the positive control) S proteins to serve as effector cells. Caco-2 cells, which naturally express human ACE2 receptors on their membrane surface, were used as target cells. The effector cells were cultured, collected, resuspended, and subsequently co-incubated with the target cells (Caco-2) for 36 hours at 37 °C. Hence, three groups were set in our study: 293T-MjHKU4r-S:Caco2 (the study group); 293T-SARS-CoV-2-S:Caco2 (the positive control); 293T-HKU4-S:Caco2 (the negative control), and each group had four biological replications. Following incubation, cells were lysed, and RNA extraction was performed according to the manufacturer’s instructions. Purified RNA was used for cDNA synthesis and library preparation. RNA sequencing was conducted on the Illumina NovaSeq 6000 PE150 platform.

first: Shua

last: Xia

first: Fanke

last: Jiao

first: Jing

last: Chen

first: Lijue

first: Shibo

last: Jiang

first: Lu


title: The mechanism of gluconeogenic enzyme Pck1 in ulcerative colitis through regulation of Pla2g6-mediated lipid metabolism II

city: Chengdu

first: Ming

state: Sichuan

address: No. 37, GuoXue Xiang, Chengdu, China

institute: West China Hospital of Sichuan University

summary: Metabolic dysregulation may serve as a pivotal driver of inflammatory bowel disease (IBD), with the crosstalk between metabolism and the immune system emerging as a critical research focus. Ulcerative colitis (UC) patients exhibit enhanced glycolysis but suppressed gluconeogenesis in the intestinal mucosa, yet the mechanistic links between these metabolic alterations and mucosal injury remain poorly defined. This study establishes phosphoenolpyruvate carboxykinase 1 (Pck1), a key rate-limiting enzyme in gluconeogenesis, as a central regulator of UC progression. We found Pck1 expression was significantly downregulated in colon tissues of UC patients and mice with DSS‑induced colitis. Utilizing an intestinal epithelial cell (IEC)-specific Pck1 knockout mouse model, we demonstrated for the first time that Pck1 deficiency exacerbates intestinal inflammation. Mechanistically, Pck1 depletion induces metabolic reprogramming that upregulates Pla2g6 expression, driving abnormal hydrolysis of phosphatidylcholine and phosphatidylethanolamine in IECs. Pharmacological inhibition of Pla2g6 ameliorated colitis in Pck1-deficient mice. These findings position Pck1 as a potential early diagnostic biomarker for UC and suggest that therapeutic targeting of the Pck1-Pla2g6 metabolic axis may yield novel strategies for UC management.

overall_design: The RNA extracted from left-sided colonic mucosal biopsy specimens of active UC patients (n=3), remission UC patients (n=3), and healthy controls (n=3) was subjected to RNA-seq.

first: Chengwei

last: Tang

first: Zhiyin


title: Transcriptomic profiling following TRIM28 and PARP1 silencing in 786-O kidney cancer cells

city: Nanchang

first: Xiangpeng

last: Zhan

state: None Selected

institute: Department of Emergency, The First Affiliated Hospital of Nanchang University

summary: lobal gene expression changes by TRIM28 or PARP1 knockdown in 786-O renal cancer cells

overall_design: Parental 786-O renal carcinoma cells, TRIM28 knockdown cells, and PARP1 knockdown cells were subjected to mRNA-seq.

first: Bin

last: fu

first: Songhui

last: Xu


title: CircSHOC2 regulates steroid hormone synthesis in ovarian granulosa cells through the mir-130b-5p/ASH1L pathway

city: Yangling

first: Lutong

last: Zhang

state: shannxi

institute: northwestern A&F university

summary: Estrus is a critical phase in the reproductive cycle of sows and depends on normal ovarian development and steroid hormone secretion. Granulosa cells (GCs) play crucial roles in maintaining normal ovarian physiological functions in sows by secreting estradiol (E2) and progesterone (P4). CircRNAs influence steroid hormone synthesis, but their involvement in regulating gilt estrous remains unclear. In this study, circRNA sequencing was performed on the ovaries of estrus (ES) and nonestrus (NES) gilts, leading to the identification of a novel circRNA, termed circSHOC2, which is highly expressed in ES ovaries. The overexpression of circSHOC2 promoted the synthesis of E2 and P4 and increased the protein levels of key steroidogenic enzymes. Further investigation revealed that circSHOC2 acts as a sponge for miR-130b-5p. Silencing miR-130b-5p significantly enhanced E2 and P4 production, along with the upregulation of steroidogenic proteins. Additionally, miR-130b-5p was found to target ASH1 like histone lysine methyltransferase (ASH1L), with miR-130b-5p overexpression significantly inhibiting ASH1L expression. Cotransfection experiments revealed that ASH1L mitigated the inhibitory effects of miR-130b-5p on E2 and P4 synthesis in GCs. This study, through circRNA sequencing of ovaries from ES and NES gilts, revealed that circSHOC2 regulates steroid hormone synthesis in porcine GCs via the miR-130b-5p/ASH1L axis, shedding light on a potential molecular pathway involved in gilts estrus. Our results will provide molecular targets for the selection of excellent estrus sows, thereby improving the utilization rate of gilts in estrus.

overall_design: At a pig farm in Shaanxi Province, 643 healthy, lineage-verified New French Yorkshire sows with at least three parities, an average litter size of 12.5 or more piglets, and a minimum of seven pairs of teats were selected as the maternal stock to establish the core breeding population (C0 generation) for purebred production. We selected 102 litters (290 gilts) of C1 generation gilts and began estrus detection from 165 days of age. Gilts with two consecutive estrus cycles were recorded as ES, those with only one estrus cycle were recorded as irregular estrus, and those without estrus were recorded as NES. Ultimately, 24 litters were fully estrus, 12 litters were completely nonestrus, 32 litters had irregular estrus, and in 34 litters, oth ES and NES gilts were present. To study the differences between full-sibling individuals with estrus and nonestrus, we excluded 4 litters with inconsistent body condition from the 34 litters that met the experimental requirements, ultimately selecting 30 litters. From the same litter, one ES gilt and one NES gilt were selected, and the ES gilt was slaughtered during its third estrus period. A total of 6 groups were slaughtered, including 6 ES gilts and their corresponding full-sibling NES gilts. The right ovaries were frozen and stored at -80 °C for subsequent sequencing result verification, while the left ovaries were used for circRNA sequencing.

first: Teng

first: Xiangrong

last: Song

first: Madaniyati

last: MieLie

first: Yihao

first: Lei

last: Gao

first: Gongshe

last: Yang

first: Guiyan

last: Chu


title: Urine progenitor renal cells

city: Badalona

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series

first: Josep

middle: M

last: Cruzado

first: Anna

last: Sola

first: Miguel

middle: L

last: Pato

last: Manonelles

first: Cristian

last: Varela

first: Fernando

last: Setien

first: Carlos

last: Quero-Dotor

first: James

last: Herald

first: David

last: Pinyero

first: Ana

last: Amaya-Garrido

first: Nuria

last: Dolade

first: Sergi

last: Codina

last: Couseiro

last: Bolanos

first: Montserrat

last: Goma

first: Fransesc

last: Vigues

first: Angelika

last: Merkel

first: Paola

last: Romagnani

first: Maria

last: Berdasco


title: mTOR signal in mitral valve diseases

city: New Haven

first: Fu

last: Gao

state: CT

address: 55 Prospect Street

institute: Yale University

summary: Mitral valve prolapse (MVP) is often benign but can progress to mitral regurgitation, requiring invasive treatment. In mgR mice with hypomorphic Fbn1 mutations—mimicking Marfan syndrome—myxomatous mitral degeneration and regurgitation develop by 12 weeks. TGF-β and mTOR signaling activation, along with macrophage infiltration, appear by 4 weeks, before histological changes. Short-term rapamycin treatment blocks early TGF-β activation and inflammation, while long-term mTOR or TGF-β inhibition rescues valve degeneration. Transcriptomics revealed integrins as upstream regulators of mTOR. Blocking integrin signaling or altering its pathway prevented mTOR activation. These findings are conserved in human MVP, suggesting that mTOR activation via abnormal integrin-matrix signaling drives disease and that mTOR inhibition may be a potential therapy.

overall_design: Single cell RNA sequence by 10x, mgR/mgR mice, as well as their respective wild type controls Fbn1+/+ (+/+))


title: Combination of HDAC inhibition and cytokine enhances therapeutic HPV vaccine therapy

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: HPV-associated malignancies continue to present a major health concern despite the development of prophylactic vaccines. Standard therapies offer limited benefit to patients with advanced stage disease. Despite improved outcomes with PD-1 targeted therapies, treatment resistance and modest response rates highlight a significant unmet need to develop novel therapies for these patients. PDS0101 (designated HPV vaccine) is a liposomal nanoparticle HPV16-specific therapeutic vaccine that has been shown to generate strong HPV-specific responses in pre-clinical and clinical studies. Here we assess the efficacy of this HPV vaccine in combination with the tumor-targeting immunocytokine NHS-IL12 (PDS01ADC), plus either aPD-1 or the class I histone deacetylase (HDAC) inhibitor Entinostat. Mice bearing HPV16+, aPD-1 refractory TC-1 and mEER tumors were treated with HPV vaccine, NHS-IL12, and either aPD-1 or Entinostat to determine anti-tumor efficacy and survival benefits. A comprehensive analysis of the tumor microenvironment was performed using flow cytometry, multiplex immunofluorescence, chemokine and cytokine assessment, and scRNAseq with TCR enrichment. Combination of HPV vaccine and NHS-IL12 with either Entinostat or aPD-1 yields significant anti-tumor activity and prolonged survival in aPD-1 refractory models of HPV16+ cancer, with superior activity employing Entinostat versus aPD-1 combination. Entinostat triple therapy increased overall and HPV16-specific tumor CD8+ T cell infiltration with heightened cytotoxicity. TCR sequencing revealed a CD8+ T cell clone unique to vaccine-treated cohorts, which displayed an enriched cytotoxic transcriptional profile with triple therapy. These effects were parallelled by strong differentiation of tumor-associated macrophages (TAMs) towards proinflammatory, anti-tumor M1-like cell states.  Single-cell transcriptomic analysis indicated all three agents were required for highest modulation of both CD8+ T cells and TAMs conducive to tumor control. A biomarker signature reflecting the pre-clinical findings was found to be associated with improved survival in patients with HPV-associated malignancies. Together, these findings provide a rationale for the combination of HPV vaccine, NHS-IL12, and Entinostat in the clinical setting for patients with HPV16-associated malignancies.

overall_design: CD45+ cells were isolated from treated TC-1 tumors harvested from C57Bl/6 mice using magentic separation and analyzed for scRNAseq with TCR enrichment

first: Lisa

last: Poppe

first: Caroline

last: Jochems

first: Sofia

last: Gameiro

first: Jeffrey

last: Schlom


title: Profiling Extracellular Vesicle and PBMCS MicroRNA Signatures in Amyotrophic Lateral Sclerosis: Unraveling Disease-Specific Biomarkers

city: Pavia

first: Francesca

last: Dragoni

state: Italy

address: Via Mondino, 2

country: Italy

institute: IRCCS Mondino Foundation

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA-mediated toxicity, which can be controlled by alteration of gene expression, is considered a key event in Amyotrophic Lateral Sclerosis (ALS). Transcriptomic deregulation of miRNAs expression can spread via "horizontal" RNA transfer through extracellular vesicles (EVs) to act in conjunction with proteins, leading to changes in mRNA, which can provide early signals to indicate forthcoming neuropathological changes in the brain. The aim of this work is to compare expression profiles (obtained by miRNA-seq) from different tissues to highlight commonly expressed and tissue-specific miRNAs. miRNA species from plasma EVs were correlated with miRNA profiles obtained from peripheral blood mononuclear cells (PBMCs). Each tissue from ALS patients was compared to controls, revealing 159 deregulated (DE) miRNAs in Exosomes (EXOs), 247 DE miRNAs in PBMCs and 162 DE miRNAs in Microvesicles (MVs). Next, data were filtered to include only miRNAs expressed in disease samples (not in healthy subjects), to reduce the number of tissue- and ALS- specific miRNAs (EXO n=22, MV=11, PBMCs n=8). We identified specific miRNAs and pathways related to each tissue. Interestingly, in PBMCs we found mainly neuro-linked pathways, such as neurotransmitters, brain and neuron development, while in EXOs, we found miRNAs implicated in MAPK and ERB signaling. In contrast, the altered pathways in MVs were not specific. This study shows that the composition of small RNA differs significantly between blood cells and its respective EVs fraction. Differentially expressed miRNAs can target definite transcripts in different cellular and molecular fractions. It is evident that, in terms of miRNAs cargo, MVs are not specific to ALS. Therefore, future studies will focus on the interaction between cells and EXOs.

overall_design: We performed miRNA-seq profiling of 26 sALS patients and 11 healthy controls. We used RNA extracted from PBMCs, EXOs and MVs comparing their cargo.

first: Rosalinda

last: Di Gerlando

first: Luca

last: Diamanti

first: Bartolo

last: Rizzo

first: Matteo

last: Bordoni

first: Eveljn

last: Scarian

first: Camilla

last: Viola

first: Giovanni

last: Cerchia

first: Susanna

last: Zucca

first: Orietta

last: Pansarasa

first: Stella

last: Gagliardi


title: Autophagy related 14 regulates liver homeostasis and function

city: Indianapolis

first: Xiaocheng

middle: Charlie

last: Dong

state: IN

address: 635 Barnhill Dr, MS 1021D

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: Autophagy regulated 14 (ATG14) is a key regulator of autophagy; however, its role in the liver remains poorly understood. This study aimed to investigate the hepatocyte-specific function of ATG14 in vivo. We generated Atg14 hepatocyte-specific knockout (HepKO) mice using adeno-associated virus (AAV) to deliver thyroxine-binding globulin (TBG) gene promoter-driven Cre into Atg14 floxed mice at an adult age and fed control and knockout mice with a Western diet for 4 weeks.

overall_design: RNA-seq analysis of liver tissue samples from control and Atg14 HepKO mice

first: X


title: Anti-TGF-β treatment shows increased bone mass and strength in a novel mouse model for osteogenesis imperfecta type I

city: Houston

first: Ellen

last: Busschers

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Anti-Transforming growth factor beta (TGF-β) is a promising approach for the treatment of osteogenesis imperfecta (OI). To date, preclinical and clinical studies for the use of anti-TGF-β therapy have focused on moderate to severe OI caused by qualitative defects in collagen. However, the majority of OI patients are represented by type I OI. Haploinsufficiency of type I collagen causes OI type I. To study the effect of anti-TGF-β therapy in type I OI, we generated novel mouse model for OI type I. CMV-CRE mice were crossed to mice where Col1a1 was floxed between exon 2 and 5 to create a full body heterozygous deletion of Col1a1. Haploinsufficiency in the tibia was confirmed by decreased Col1a1 mRNA and protein expression. Comparable to OI patients, we observed reduced bone mass by μCT in these Col1a1+/- mice. Biomechanical measurements showed a decrease in bone strength and an increase in bone brittleness. Histomorphometric analysis showed an increase in osteoclast number and a trend towards increased osteoblasts. Overall suggesting this mouse shows a phenotype overlapping with OI type I. Upon treatment with a pan anti-TGF-β antibody, 1D11, this mouse model of OI type I showed increased bone mass. anti-TGF-β treatment further improved ultimate strength in the Col1a1+/- mice, but measures of ductility did not show improvement. Overall, our findings support expanding research on anti-TGFβ treatment for OI to OI caused by haploinsufficiency for type I collagen.

overall_design: tibias from 12 week old female Col1a1+/- and WT mice were used for RNA isolation. 3 samples for each group.  Library prep was performed by poly-A selection

first: Yuqing

last: Chen-Everson

first: Oscar

last: Ruiz

first: Brendan

last: Lee


title: Synthesis of a Novel Mitochondrial Fluorescent Probe - Killing Cancer Cells in Vitro and in Vivo

city: Jining

first: Wenzhi

last: Shen

address: No. 133 Hehua Road

institute: Jining Medical University

summary: To investigate the function and mechanism of mitochondrial probe molecule 4 (WT4, named MPM-1 in the manuscript) in inhibiting colorectal and lung cancers, we utilized SW480 cells treated with DMSO and mitochondrial probe molecule 4 (WT4, named MPM-1 in the manuscript), respectively.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of SW480-DMSO and SW480-WT4 cells.
Comparative gene expression profiling analysis of RNA-seq data for SW480-DMSO and SW480-4 cells.

first: Xiaowen

last: Yang


title: Blimp-1 protects the transcriptional identity of group 2 innate lymphocytes in lung inflammation [ATAC-seq]

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

summary: Type 2 inflammation in the lung underlies allergic asthma and promotes tumor metastasis. Type 2 innate lymphoid cells (ILC2s) respond to tissue damage signals including IL-33 and IL-25 and are implicated in type 2 inflammatory diseases of the lung, but the factors that maintain ILC2s ability to produce type 2 cytokines are not known. We show Blimp-1 is a key transcriptional repressor of type 1 genes induced by the type 2 cytokine IL-9 in ILC2s in response to tissue damage signals. Loss of Blimp-1 in ILC2s altered inflammation in response to allergens, but also limited metastatic melanoma in the lung by limiting type 2 cytokines in favor of type I cytokines including IFNg and TNF. Thus, Blimp-1 protects the type 2 identity of ILC2s during lung inflammatory diseases.

overall_design: 2 female Blimp-1IL7RaCre and 2 female ControlIL7RaCre mice match with age were used. Whole lung was harvested and ILC2s were sorted from lung by the following markers: live, lineage-, CD90.2+, CD3-. After sorting, ~15,000 ILC2s cells from each sample were cultured in complete RPMI in 96-well plate with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours. After 72 hours, ILC2s were collected passed down for sequencing.

first: Yibo

last: Zheng

first: Aaron


title: Type-I interferon priming signal balances anti-bacterial and anti-tumor trained immunity in alveolar macrophages [ATAC-seq]

first: Yushi

last: Yao

address: 866 Yu Hang Tang Road

summary: Tissue-resident macrophages may be trained to confer enhanced response to heterologous re-stimulation, and thus foster versatile trained immunity (TI) against both infections and tumors. However, key priming signals that contribute to such functional versatility in trained macrophages remain not fully understood. Here we show that influenza A virus (IAV) infection in mice induces lasting transcriptional imprints of acute type-I interferon (IFN-I) signaling in lung-resident alveolar macrophages (AMs) that confer balanced anti-bacterial and anti-tumor TI responses. In both IAV-infected mice and an ex vivo cytokine-mediated training system, IFN-I signaling is found to be critical to developing anti-tumor TI functions, although it limits anti-bacterial TI functions in AMs. Moreover, human AMs carrying transcriptional imprints of IFN-I signaling are associated with anti-tumor immunity and immune activation in lung cancer tissues. Our findings highlight IFN-I as a key priming signal required to developing versatile TI functions in AMs with balanced anti-bacterial and anti-tumor potential.

overall_design: AMs from different groups  were isolated from mouse lung BAL, and processed with standard ATAC-seq protocol

first: Tao

last: Wang

first: Jinjing

last: zhang

first: Yuxuan

last: Miao

first: Yanling

first: Ying

last: Li

first: Lu

first: Yuanyuan

last: Liu

first: Chia-Wei

last: Chang

first: Enguo

last: Chen


title: Blimp-1 protects the transcriptional identity of group 2 innate lymphocytes in lung inflammation [RNA-seq]

overall_design: For bulk RNA sequencing evaluating Blimp-1 deficiency (including library WT_1, WT_2, WT_3, KO_1, KO_2 and KO_3), 3 female Blimp-1IL7RaCre and 3 female ControlIL7RaCre mice match with age were used. Whole lung was harvested and ILC2s were sorted from these individual mice by the following markers: live, lineage-, CD90.2+, CD3-. After sorting, ~15,000 ILC2s cells from each sample were cultured in complete RPMI in 96-well plate with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours. After 72 hours, ILC2s were collected and RNA was isolated with RNeasy Plus Micro Kit (74034, Qiagen). RNA quality was assessed by RIN score and passed down to library preparation.  For bulk RNA sequencing comparing unstimulated ILC2s ex vivo from lung with stimulated ILC2s (including library 1_unstim, 2_unstim, 3_unstim, 4_unstim, 1_stim, 2_stim, 3_stim and 4_stim), 8 female B6 mice were separated into two groups. Whole lung was harvested and ILC2s were sorted from these individual mice lung by the following markers: live, lineage-, CD90.2+, CD3-. After sorting, ~15,000 ILC2s cells from each sample were cultured in complete RPMI in 96-well plate with or without IL-33 (20ng/mL) according to their group for 24 hours. After 24 hours, ILC2s were collected and RNA was isolated with RNeasy Plus Micro Kit (74034, Qiagen). RNA quality was assessed by RIN score and passed down to library preparation.


title: Engineering an in vivo charging station for CAR-redirected invariant natural killer T cells to enhance cancer therapy

city: Los Angeles

first: Youcheng

state: California

address: 430 Westwood Plaza, 5121 Engineering V, Box 951600, Attn (PI NAME): Li Lab

department: Bioengineering

institute: UCLA

summary: Invariant natural killer T (iNKT) cells are a distinct subset of T lymphocytes that possess unique properties making them highly suitable for addressing the challenges of solid tumor immunotherapy. Unlike conventional T cells, which are restricted by polymorphic major histocompatibility complex (MHC) molecules and recognize peptide antigens, iNKT cells are restricted by the non-polymorphic CD1d molecule and respond to lipid antigens. Chimeric antigen receptor (CAR)-redirected iNKT (CAR-iNKT) cells represent a significant advancement in cancer immunotherapy. However, optimizing sustained activation and long-term persistence of CAR-iNKT cells remains a critical need for effective solid tumor treatment. To address these limitations, we develop the iNKT cell-targeted microparticle recruitment and activation system (iMRAS), a biomimetic platform designed to enhance iNKT cell functionality through localized immunostimulation in vivo. This biomimetic platform is designed to function as an in vivo “charging station” containing chemotactic and activation signals for the recruitment, activation, and expansion of CAR-iNKT cells, leading to more effective tumor killing and longer persistence of CAR-iNKT cells, as demonstrated in the therapy of lymphoma and melanoma. Through its biomimetic design and localized immunostimulatory effects, iMRAS helps overcome the limitations of current therapies for solid tumors, establishing a robust platform for enhancing systemic CAR-iNKT cell-mediated immunotherapy.

overall_design: Human CAR-iNKT cell samples were FACS sorted (identified as iNKT TCR+CD3+ cells) and delivered to the UCLA TCGB Core for library construction and scRNA-seq. Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina). For cell clustering and annotation, the merged digital expression matrix generated by Cellranger was analyzed using an R package Seurat (v.4.0.0) following the official website guidelines. Briefly, after filtering the low-quality cells, the expression matrix was normalized using NormalizeData function, followed by selecting top 2,000 most variable genes across datasets using FindVariableFeatures and SelectIntegrationFeatures functions. To correct the batch effect, FindIntegrrationAnchors and IntegrateData functions were used based on the selected feature genes. The corrected dataset was subjected to standard Seurat workflow for dimension reduction and clustering. In this study, clusters of therapeutic cells were manually merged and annotated based on gene signatures reported from Human Protein Atlas (proteinatlas.org) and previous studies, and clusters of mouse immune cells were merged and annotated based on the immune lineage markers. AddModuleScore was used to calculate module scores of each list of gene signatures, and FeaturePlot function was used to visualize the expression of each signature in the UMAP plots. For gene set enrichment analysis (GSEA), clusterProfiler packages were used to calculate the enrichment scores of each cluster in the signature gene list.

first: Yan-Ruide

first: Haochen

first: Zeyang

first: Youchen

first: Lili

first: Song


title: Type-I interferon priming signal balances anti-bacterial and anti-tumor trained immunity in alveolar macrophages [RNA-seq]

first: Yushi

overall_design: AMs from different groups  were isolated from mouse lung BAL, and processed with standard RNA-seq protocol


title: Higher expression of HPV16 derived E7_LI Transcript Observed in Men with HIV and Recurrent Anal Cancer

city: Birmingham

first: Kevin

middle: James

last: Maroney

state: Alabama

address: 1001 20th Street S, 1501, Ascend Apartments

institute: University of Alabama at Birmingham

summary: Squamous cell carcinoma of the anus (SCCA) or anal cancer (AC) is an understudied cancer with a high occurrence rate in people with HIV (PWH), especially men having sex with men (MSM). Furthermore, AC recurs in approximately one fourth of patients who undergo standard care with chemoradiation therapy (CRT). Using bulk RNA sequencing data of AC obtained from 12 patients with non-recurrent (NR, N=9) or recurrent (R, N=3) cancer, we previously showed upregulated expression of key immune genes in the NR compared to the R group. Although the main causative agent of anal cancer is high-risk human papillomavirus (HPV), association of host and viral RNA transcript expression contributing to AC recurrence has not been extensively studied. The objective of the current study was to determine whether enrichment of specific HPV genotypes and/or HPV gene expression patterns differentiate the two groups and if any specific viral (HPV) and host (human) immune mediators correlate with each other. Using bulk RNA sequencing data and VIRTUS 2, we detected viral RNA reads mapping to 7 high-risk and 6 low-risk HPV types of which the high-risk HPV16 observed in 83% (10/12) AC tumors (7/9 non-recurrent and 3/3 recurrent). Rate of all HPV genomes trended towards a decrease in non-recurrent anal cancer isolates and correlation between HPV types was more commonly observed in low-risk ones. Analysis of HPV 16 gene expression profile showed a significantly lower positivity rate for a polycistronic transcript encoding for E7^L1 in the non-recurrent group (1/9, NR versus 3/3, R, p value <0.05). An unbiased correlation analysis of HPV-human transcript expression showed a direct correlation between HPV transcripts and human genes involved in cell growth. The data also identified human transcripts showing an inverse correlation with HPV gene expression. These included genes involved in negative regulation of growth, proliferation and immune response.  Taken together, these data indicate that concurrent analyses of viral and host factors in the same tumor can identify potential new therapeutic targets to ameliorate cancer recurrence post treatment.

overall_design: 12 FFPE primary tissues from patients with confirmed anal cancer (AC) diagnosis prior to chemoradiation therapy (CRT), 3 who went on to have recurrent AC post CRT and 9 who did not recur (non-recurrent). RNA was purified with Quick-DNA/RNA FFPE kit (R1009, Zymo) and developed into cDNA libraries using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara). Pooled libraries were then sequenced on a NovaSeq 6000 (Illumna) to a depth of > 40 million paired-end 150 bp reads per sample. Phred quality was > 30 for all samples.

first: Yuanfan

last: Ye

first: Staci

last: Sudenga

first: Sameer

last: Diffalha

first: Nilam

last: Banerjee

first: Sadeep

last: Shreshta

first: Anju

last: Bansal


title: Roles of chromosomal and gonadal sex in the fetal and placental responses to maternal food restriction in mice [junctional zone/decidua]

city: Burnaby

first: Julian

last: Christians

state: BC

address: 8888 University Drive

department: Biological Sciences

country: Canada

institute: Simon Fraser University

summary: It is hypothesized that male fetuses are more vulnerable to in utero insults than female fetuses due to different growth strategies, and that the placenta contributes to these sex differences. Using the Four Core Genotypes mouse model, we examined sex differences in the fetal and placental responses to maternal food restriction (~60% of ad libitum) beginning mid-gestation (day 11.5), including the independent roles of chromosomal and gonadal sex. Food restriction reduced fetal and placental weights, but had no effect on the number of viable conceptuses. However, the effect of food restriction did not differ between gonadal male and female conceptuses, or between XX and XY conceptuses. Sex differences in gene expression in both the labyrinth and the combined junctional zone/ decidua, as assessed by RNA sequencing, were due entirely to chromosomal sex, and not to gonadal sex. Food restriction affected the expression of 525 and 665 genes in the labyrinth and the combined junctional zone/ decidua, respectively. However, these effects of food restriction did not differ by gonadal sex or chromosomal sex when assessed for statistical interactions. In contrast, when analysing XX and XY placentas separately, we found hundreds of genes that were affected by food restriction in one sex but not the other, including hundreds of genes not found to be significant in the combined analyses. However, estimated effect sizes were generally similar for XX and XY placentas, suggesting that these sex-stratified analyses greatly exaggerated the extent of sex-dependent responses. Overall, we did not find evidence of the hypothesized sex differences in fetal growth strategy, and found that sex differences in placental gene expression were largely due to chromosomal sex.

overall_design: To investigate sex differences in the placental response to maternal food restriction, we mated C57BL/6J females with either wildtype C57BL/6J males of Four Core Genotypes (FCG) males, the latter matings producing pregnancies with XX males, XX females, XY males and XY females. On gestational day 11.5, pregnant females were single-housed, and randomly allocated to either the ad libitum diet (control) group, or the food restriction group, which received ~ 60% of ad libitum. At gestational day 17.5, placentas were collected and dissected to separate the labyrinth from the junctional zone and decidua (i.e., junctional zone and decidua were combined). This series includes the junctional zone/decidua samples.

first: J


title: Cardiovascular Mettl3 Deficiency Causes Congenital Cardiac Defects and Postnatal Lethality in Mice

city: Beijing

first: Qianqian

last: Feng

address: 38 Xueyuan Road, Haidian District

institute: Peking University

summary: N6-methyladenosine (m6A) is the most common epigenetic modification of RNA, but whether m6A RNA methylation modulates cardiovascular development or congenital heart diseases (CHDs) has not been determined. The published high-throughput sequencing data suggested that transcripts of genes related to CHDs were prone to m6A modification, while the expression of methyltransferase-like 3 (METTL3)-involved methyltransferase complex was downregulated in mouse embryonic hearts following prenatal alcohol exposure as a critical CHD risk factor, indicating the association of insufficient m6A RNA methylation with CHDs. Using cardiovascular-specific Mettl3 knockout mice (Tagln-Cre; Mettl3flox/flox), we observed that cardiovascular Mettl3 deficiency resulted in postnatal lethality and profound congenital cardiac defects, including left pulmonary stenosis, ventricular septal defects and right ventricular hypoplasia. The m6A-specific methylated RNA-immunoprecipitation sequencing identified Sox4, Sox11 and Mef2a, the critical transcription factors involved in right ventricle and outflow tract development, were the regulatory targets of METTL3-catalyzed m6A RNA methylation. Mettl3 deficiency-caused insufficient m6A RNA methylation downregulated the expression of SOX4, SOX11 and MEF2A in mouse embryonic hearts. In conclusion, cardiovascular Mettl3 deficiency directly led to congenital cardiac defects by downregulating the m6A-dependent expression of Mef2a, Sox4 and Sox11. METTL3-catalyzed m6A RNA methylation may become a potential target for the prevention and treatment of CHDs.

overall_design: MeRIP (m6A immunoprecipitation) for right ventricle and outflow tract tissues of Tagln-Cre; Mettl3flox/flox mice and Mettl3flox/flox mice on embryonic day 10.5 to 11.5

first: Lihua

last: Qi

first: Jiaqi

last: Huang

first: Yuan

last: Zhou

first: Yi

last: Fu


title: Investigating therapy-induced senescence as a reversible escape mechanism of drug resistance in breast cancer cells using high-dose doxorubicin treatment [RNA-seq]

city: Budapest

first: Andras

last: Furedi

state: HU

address: Magyar tudosok krt 2

department: Molecular Life Sciences

country: Hungary

institute: HUN-REN RCNS

summary: The emergence of drug resistance remains a critical challenge in cancer treatment, significantly contributing to high mortality rates. Here, we investigate therapy-induced senescence (TIS) as a reversible escape mechanism of drug resistance in breast cancer cells. Using high-dose doxorubicin, we induced TIS in MCF7, T47D, MDA-MB-231 and Hs578T breast cancer cell lines. Bulk RNA sequencing revealed a unique transcriptomic profile in TIS cells, distinct from both parental and repopulated cells in every cell line, exposing a small subpopulation of TIS cells with the potential to escape senescence. Gene set enrichment analysis indicated significant downregulation of proliferation-related genes, downregulation of DNA repair pathways, and the upregulation of immune response related genes.

overall_design: MCF7, T47D, MDA-MB-231 and Hs578T control, therapy-induced senescent (TIS) and repopulated cells and also HFF control and therapy-induced senescent cells were analyzed using RNAseq

first: Eszter

last: Bajtai

first: Csaba

last: Kiss

first: Sandor

last: Spisak


title: Differential expression of transcriptional genes in paclitaxel-resistant mouse gastric adenocarcinoma cell lines

city: Shanghai

first: Wenshuai

last: Liu

state: Shanghai

address: Fenglin road 180

department: General Surgery

institute: Zhongshan Hospital Fudan University

summary: Paclitaxel is commonly used as a second-line treatment for gastric cancer, but the mechanisms underlying paclitaxel resistance remain to be further investigated. To address this, we successfully established a mouse gastric adenocarcinoma cell line (MPC) from murine gastric adenocarcinoma organoids. Subsequently, a paclitaxel-resistant cell line (MPC-PTX) was generated through multi-cycle drug stimulation. This model provides a valuable tool for studying the mechanisms of paclitaxel resistance in gastric cancer.

overall_design: The increasing drug concentration method was employed in this study to induce drug resistance in the cell line. Initially, the primary IC50 (pIC50) of the parent cell line was determined. When the cells reached 50% confluence, the MPC cells were exposed to the IC50 dose of paclitaxel (PTX). After 2 days of treatment, the medium was changed to fresh medium for culture for the next 5 days. Every 4 cycles of treatment, the treated PTX IC50 (tIC50) level of MTC was reassessed. MTC cells were treated with a new cycle of PTX at the tIC50 concentration. After ~30 cycles of PTX treatment, the drug resistance index (RI), defined as RI = tIC50/pIC50, exceeded 5, indicating successful establishment of a PTX-resistant cell line, which was named MPC-PTX. According to the methods mentioned above, MTC-R cells also underwent monoclonal selection, and the IC50 of PTX was remeasured.


title: Mir-494-3p enhances an aggressive phenotype of non-small cell lung cancer cells by regulating SET/I2PP2A

city: Aichi

first: Hisanori

last: Isomura

address: 1, Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya

institute: Nagoyacityuniversity

summary: High expression of miR-494-3p have been associated with poor prognosis in non-small cell lung cancer (NSCLC). However, the role of miR-494-3p in the development and progression of NSCLC remains elusive. In this study, we found that miR-494-3p was overexpressed in both lung adenocarcinoma and lung squamous cell carcinoma in the Clinical Proteomic Tumor Analysis Consortium and Cancer Genome Atlas databases. A bioinformatic analysis revealed that representative pathways associated with cancer metastasis were enriched in the genes positively correlated with miR-494-3p expression levels, suggesting the potential involvement of miR-494-3p in aggressive properties of NSCLC. To identify potential targets of miR-494-3p, we explored genes inversely correlated with miR-494-3p in the mRNA expression datasets of NSCLC cell lines obtained from the Cancer Dependency Map. Integration of RNA sequencing analysis of NSCLC cells with miR-494-3p inhibition and a bioinformatic search of miRNA target prediction algorithms resulted in identification of SET/I2PP2A as a direct target of miR-494-3p. We found that suppression of SET/I2PP2A by miR-494-3p promoted cell migration and invasion, but not cell viability, in NSCLC cells, indicative of miR-494-3p and its downstream molecules as potential therapeutic targets in NSCLC with aggressive phenotypes.

overall_design: RNA-seq profilling of NCI-H2030 cells treated with miR-494-3p AS or SC.

first: Yuwen

last: Du

first: Taisuke

last: Kajino

first: Yukako

last: Shimada

first: Takashi

last: Takahashi

first: Ayumu

last: Taguchi


title: Single cell transcriptomic analysis of nephron and UB lineages in recombinant hPSC-derived kidney organoids grown under various conditions.

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: To model tissue interactions in kidney development, a protocol was devised to combine human pluripotent stem cell (hPSC)-derived ureteric bud progenitors with nephrogenic mesenchyme to form kidney organoids. The resulting organoids had a complex composition including the nephron, ureteric, stromal, and endothelial lineages. scRNA-seq was performed to catalog and analyze the populations and developmental trajectories of the different lineages.

overall_design: Kidney organoids were generated by combining induced ureteric bud (UB) and nephrogenic mesenchyme (NM) progenitor cells. Organoids were sampled at days 0, 3, 7, 10, and 14 under standard baseline conditions. Control organoids comprising only NM or UB were also analyzed. Additional conditions were also including: organoids with NOTCH inhibition (DAPT) from days 4-6 and organoids grown in collecting duct (CD) medium +/- A83, U0126, and XAV939 from days 10-14.

first: McCracken

last: Kyle

first: Shi

last: Min


title: Size-dependent temporal decoupling of morphogenesis and transcriptional programs in pseudo-embryos [scRNA-seq]

city: LAUSANNE

first: ALEXANDRE

last: MAYRAN

state: Waadt

address: Station 19

country: Switzerland

institute: EPFL

summary: Understanding the interplay between cell fate specification and morphogenetic changes remains a central challenge in developmental biology. Gastruloids, self-organizing pseudo-embryos that mimic post-implantation mammalian development, provide a powerful platform to address this question. Here, we show that physical parameters, particularly system size, critically influence the timing and outcomes of morphogenetic processes. Larger gastruloids exhibit delayed symmetry breaking, increased multipolarity, and prolonged axial elongation, with morphogenesis driven by system size. Despite these variations, transcriptional programs and cell fate composition remain remarkably stable across a broad size range. Notably, extreme sizes show distinct transcriptional modules and clear shifts in gene expression patterns. Intriguingly, size perturbation experiments rescued the morphogenetic and pattern phenotypes observed in extreme sizes, demonstrating the remarkable adaptability of gastruloids to their effective system size. These findings establish gastruloids as versatile models for studying spatiotemporal dynamics in mammalian embryogenesis and reveal how physical constraints decouple transcriptional from morphogenetic programs.

overall_design: scRNA-seq on gastruloids grown from various initial cell seeding number

first: Alexandre

last: Mayran

first: Lucille

last: Lopez-Delisle

first: Isma

last: Bennabi

first: Pauline

last: Hansen

first: Thomas

last: Gregor


title: Effects of PD-L1 silencing on global transcriptomic changes in tumor

city: Boston

first: Marco

last: Mineo

state: MA

address: 60 Fenwood Rd, BTM 8016N

institute: Brigham and Women's Hospital

summary: Cancers evade anti-tumor immunity by up-regulation of immune checkpoint molecules, such as programmed cell death 1 ligand 1 (PD-L1), in response to stimuli, such as interferon-gamma (IFNγ). Expression of PD-L1 within the tumor microenvironment inhibits the anti-tumor immune response by binding the immune checkpoint receptor PD-1 expressed on T cells. Immune checkpoint inhibitors that target the PD-1/PD-L1 pathway are less toxic than standard chemotherapy and produce durable tumor regression and overall survival benefits in several tumors. However, only a small group of patients respond to these therapies, and some of the responders develop acquired resistance.  Understanding the effects of PD-L1 silencing on global gene expression is critical to identifying potential immune evasive mechanisms. In this study, we performed transcriptome analysis of PD-L1 knockdown cells and showed that silencing PD-L1 reduced the expression of only a few immunosuppressive genes. Our findings suggest that the identification of novel targets that can control a larger number of immunosuppressive molecules could lead to the development of more effective immunotherapies.

overall_design: Tumor cell lines were transfected with an siRNA control or two different siRNAs targeting PD-L1. 48 hours after transfection, cells were stimulated with interferon gamma for 24 hours. RNA expression profiles were generated by RNA-seq, in duplicate, using Illumina NovaSeq6000.

first: Shikha

last: Saini

first: Antonio

last: Chiocca


title: Size-dependent temporal decoupling of morphogenesis and transcriptional programs in pseudo-embryos [BRB-seq]

overall_design: bulk RNA-seq on gastruloids grown from various initial cell seeding number (BRB-seq)

first: Melody

last: Merle


title: Panoramic Elucidation of the Molecular Mechanisms Underpinning the Epigenetic Impact of Gestational Diabetes Mellitus on Offspring

city: Shanghai, China

first: Yang

last: Lily

address: No.1239, Siping Road, Yangpu District, Shanghai

institute: Tongji University

summary: Background: Gestational diabetes mellitus (GDM), a common pregnancy complication with profound effects on maternal and offspring health, involves epigenetic modifications, particularly DNA methylation, but the molecular mechanisms elevating metabolic disease risk in offspring remain elusive. Methods: Integrating public data with whole-genome methylation data from umbilical cord blood of GDM fetuses as the validation cohort, this study characterizes GDM-associated epigenetic features and develops a predictive model validated across external datasets to assess potential long-term health risks in offspring. Results:We identified consistent patterns of differential methylation in the offspring of GDM, with key DMPs associated with glucose homeostasis and insulin sensitivity genes. Pathway analysis revealed enrichment in insulin signaling, AMPK activation, and adipocytokine signaling pathways. Our predictive model demonstrated robust performance across different sample sizes (AUC=0.89 in public data, AUC=0.82 in validation cohort). CpG sites associated with PPARG and INS genes showed persistent predictive significance across datasets. Conclusions:This study provides a comprehensive characterization of the epigenetic landscape in the offspring of GDM, revealing consistent methylation patterns and pathway enrichments across diverse datasets. The developed predictive model holds potential for assessing health risks of GDM in offspring, advancing understanding of GDM pathophysiology and offering epigenetic biomarkers for future diagnostic, therapeutic, and preventive strategies.

overall_design: To confirm the reliability of the methylation pattern and its association with GDM, we conducted a clinical cohort validation experiment: whole genome methylation sequencing was performed on 5 cord blood samples and 5 control samples of newborns born to mothers with GDM, and large-scale epigenome findings were linked to a clinical cohort to analyze the effect of GDM on subrepresentative inheritance.


title: Size-dependent temporal decoupling of morphogenesis and transcriptional programs in pseudo-embryos

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

overall_design: Refer to individual Series


title: Roles of chromosomal and gonadal sex in the fetal and placental responses to maternal food restriction in mice

first: Julian

last: Christians

overall_design: To investigate sex differences in the placental response to maternal food restriction, we mated C57BL/6J females with either wildtype C57BL/6J males of Four Core Genotypes (FCG) males, the latter matings producing pregnancies with XX males, XX females, XY males and XY females. On gestational day 11.5, pregnant females were single-housed, and randomly allocated to either the ad libitum diet (control) group, or the food restriction group, which received ~ 60% of ad libitum. At gestational day 17.5, placentas were collected and dissected to separate the labyrinth from the junctional zone and decidua (i.e., junctional zone and decidua were combined). This series includes the labyrinth samples.

first: J


title: Assessing the role of RIPK1 and TRIF proteins in RIPK3-transcription in MEFs

city: Seattle

first: Sigal

middle: B

last: Kofman

email: sigalk@uw.edu, Kofmansb@gmail.com

state: Washington

address: 750 Republican St

department: Immunology

institute: University of Washington

summary: We previously have found that RIPK3 induces robust anti-viral and inflammatory transcriptional signaling in death-resistant MEFs, however the molecular mechanism that governs this transcription is not well understood. Here we found that RIPK3-depedent transcription is RIPK1 and TRIF dependent in MEFs.

overall_design: Ripk3-2xFv immortalized mouse embryonic fibroblasts (MEFs) lacking MLKL,  were treated with siRNA targeting both TRIF and RIPK1 and a scramble encoded control. Activatable Ripk3-MEFs were then treated with BB homodimerizer for 4hrs. MEF RNA lysates were then submitted for bulk RNAsequencing. NOTES: AP1 = BB, qVD= pan caspase inhibitor, RXMM = ripk3-2xFVfl/fl:ubcERT2cre+MLKL-/-


title: Assessing the contribution of RIPK1 in ZIKV-induced inflammatory transcription in neuorns

summary: We previously have found that RIPK3 induces robust anti-viral and inflammatory transcriptional signaling in primary cortical neurons, however the complete molecular mechanism governing this pathway is incompletely understood. Here we show RIPK1 is required to induce RIPK3-dependent transcription in ZIKV-infected neurons.

overall_design: Primary cortical neurons that were heterozygous (WT-RHIM) or homozygous (RHIM-RHIM) for a mutation in the RHIM domain of RIPK1 were infected with Zika virus (ZIKV) for 24hrs (n=4/group). Neuronal RNA lysates were then submitted for bulk RNAsequencing.


title: Bioinformation and deep-learning based model reveals norepinephrine inhibiting PRDX1 aggravates atherosclerosis

city: shanghai

first: yang

last: xiaobo

address: 上海市浦东新区松涛路647弄四孵产业园

summary: The regulation of metabolites comprises the fundamental biological processes of human. More new phenotypes of classic metabolites were revealed, while the devolution of functional targets and mechanisms of them still have many gaps due to diversity in structures and functions. Here, we report a bioinformation and attention mechanism based deep learning model leveraging abundant bioinformation of metabolites for functional target prediction of specific phenotypes. Taking advantage of this model, the potential target database of 3,382 common human metabolites were resourced publicly. Norepinephrine was identified as a selective peroxidase inhibitor of peroxiredoxin 1 (PRDX1) for atherosclerosis aggravation in model validation experiments. Salvianolic acid A (SAA) was screened out as PRDX1 exogenous stabilization compound for rescuing norepinephrine’s aggravation effects in vivo. Besides, bulk RNA-Sequencing analysis indicated norepinephrine aggravates atherosclerosis through activating transcriptional activity of SREBP2 in a ROS dependent manner. Overall, our research provides a new computational regime for metabolites target identification besides experimental chemical proteomics and PRDX1 stabilization was validated a potential druggable target for cardiovascular diseases intervention.

overall_design: The purpose is to elucidate the impact of SAA on cholesterol metabolism and atherosclerosis-related pathways by comparing gene expression profiles between the SAA treatment group and the control group.


title: IL-2Rα is Dispensable for Murine B Cell Development and Humoral Response

city: New York

first: Ryan

last: Smolkin

state: NY

address: 408 E 69th St

institute: MSKCC

summary: The cytokine IL-2 plays a pivotal role in the immune system, specifically in the proliferation of T, B, and NK cells. The alpha subunit of the IL-2 receptor, IL-2Rα (CD25), is known to regulate the expansion and differentiation of T lymphocytes. CD25 is also expressed in developing B cells; however, its B cell intrinsic role remains undefined. We generated a mouse model with a B cell-specific deletion of CD25 to ascertain its role in B cell development and function. Unexpectedly, we found that the loss of CD25 had no impact on B cell development, homeostasis, or immune response to model antigens. Additionally, while CD25 expression was upregulated in activated splenic B cells, its absence did not affect class switch recombination in vitro or in vivo. We conclude that in contrast to its critical role in T cell differentiation and function, and despite its expression in developing and activated B cells, CD25 does not have any significant role in B cell development and adaptive immune functions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD25-sufficient and -deficient Pro-B cells.

first: Smolkin

last: Ryan

first: Chowdhury

last: Priyanka

first: Belcheva

last: Kalina

first: Chaudhuri

last: Jayanta


title: Transcriptome aequencing of Antheraea pernyi antennae

city: Weifang

first: Wang

last: Guobao

address: No.5147 Dongfeng East Street

institute: Weifang University

overall_design: The antennae serving as the most important olfactory organ from the adult Antheraea pernyi were used for transcriptome sequencing

first: Guobao

last: Wang


title: Assessing the role of RHIM proteins in ZIKV-induced inflammatory transcription in neurons

summary: We previously have found that RIPK3 induces robust anti-viral and inflammatory transcriptional signaling in death-resistant MEFs in a RIPK1-and TRIF-dependent manner. We nexted wanted to assess whether this mechanism was conserved in neurons during Zika virus infection.

overall_design: WT (B6J) primary cortical neurons were treated with siRNA targeting RIPK3, ZBP1, TRIF, RIPK1 and a scramble encoded control. Neurons were then infected with ZIKV for 24hrs. Neuronal RNA lysates were then submitted for bulk RNAsequencing.


title: Transcriptional Control of C. elegans Male Tail Tip Morphogenesis by DMD-3

first: Porfirio

last: Fernandez

address: 29 Washington Place

department: Biology

institute: New York University

summary: How transcriptional regulators are linked to cell biological effectors of morphogenesis is not fully understood. To elucidate this linkage, we use the C. elegans male tail-tip as a model. The tail-tip is made of four cells that, in males, undergo changes in shape and position during the L4 stage. The transcription factor DMD-3 is the master regulator of this Tail-Tip Morphogenesis (TTM). To identify other genes involved in TTM, the lab has previously performed a genome-wide RNAi screen and conducted an RNA-seq differential expression (DE) analysis using tail tips isolated from L4 wild-type and dmd-3 mutant males. This yielded candidates for genes downstream of and regulated by DMD-3 directly or indirectly. To identify the direct targets of DMD-3, we conducted male-specific DMD-3 ChIP-seq on whole worms during TTM. We identified 1755 DMD-3 binding peaks representing 6061 genes and a de novo DMD-3-associated binding motif, sharing similarity to the chromatin binding factor, EOR-1. Integrating this data with the previous RNAi screen and the DE analysis, we found 270 candidates for direct DMD-3 targets in tail-tip cells. To validate these candidates, we inserted GFP into the endogenous loci using CRISPR and evaluated the expression of the fusion proteins. We then deleted the sequences associated with DMD-3 ChIP peaks or the DMD-3-associated binding motif and assessed if this resulted in a protein expression change or defective TTM. We found four genes where deletion of a peak had an effect: The transcription factor FOS-1 is expressed in nuclei of male tail tips during TTM and in the vulva. Deletion of a DMD-3 peak or DMD-3-associated motif sites abolishes expression in male tail-tip nuclei. NMY-2 is localized as a “cap” at the tip of the tail during TTM. Removal of the peak reduces the level of tail tip NMY-2 expression. The pan-1 locus has two peaks. PAN-1::GFP is first seen in puncta at the cell surface, then at basal lateral membranes. Removal of the distal peak causes TTM defects in 10% of screened males, while removal of both peaks leads to global, previously reported,  pan-1 phenotypes. HMR-1 is expressed at adherens junctions at the onset of TTM and later forms puncta at the cell surface. Deleting the peak has little effect on expression but results in epidermal bulges in both sexes, including the mail tail region. Because of the global phenotypes observed in peak mutants, we hypothesize the peak regions contain binding sites for other factors. Additionally, using extrachromosomal arrays, we tested and confirmed the DMD-3-associated motif’s contribution to wild-type TTM.

overall_design: ChIP-seq of GFP::DMD-3 in C. elegans L4-stage males using a GFP antibody non-antibody treated input DNA samples were used as a control

first: Karin

last: Kiontke

first: Sevinc

last: Ercan

first: David

last: Fitch


title: Assessing RIPK3 dependent genes in death-resistant and death-susceptible MEFs encoding activatable RIPK3-system

summary: The full transcriptional RIPK3-dependent transcriptional potential in MEFs is unknown. Here, we found that RIPK3 is a dominant driver of anti-viral and inflammatory transcription in MEFs.

overall_design: Ripk3-2xFV immortalized mouse embryonic fibroblasts (MEFs) lacking MLKL, were treated with BB homodimerizer or BB homodimerizer and qVD (pan-caspase inhibitor) for 4 or 24hrs (n=3-6/group). MEF RNA lysates were then submitted for bulk RNA sequencing. NOTES: AP1 = BB, qVD= pan caspase inhibitor, RXMM = ripk3-2xFVfl/fl:ubcERT2cre+MLKL-/-


title: Comparison of transcriptional response in ZIKV-infected wildtype (B6J) and RIPK3 KO neurons

summary: The full transcriptional RIPK3-dependent transcriptional potential is unknown. Here, we found that RIPK3 is a dominant driver of anti-viral transcription in neurons following Zika virus infection.

overall_design: B6J and RIPK3 KO primary cortical neurons were infected with Zika virus (ZIKV) for 24hrs (n=3/group). Neuronal RNA lysates were then submitted for bulk RNAsequencing.


title: Idenitifying RIPK3 dependent genes in neurons expressing RIPK3-activatable system

summary: The transcriptional potential of RIPK3 in a non-infectious system in neurons is unclear. Here we found that RIPK3 activation, independent of any upstream signals is sufficient to induce anti-viral transcription in neurons.

overall_design: Ripk3-2xFV primary cortical neurons were treated with BB homodimerizer for 4 and 24hrs (n=6/group). Neuronal RNA lysates were then submitted for bulk RNAsequencing.


title: Investigating therapy-induced senescence as a reversible escape mechanism of drug resistance in breast cancer cells using high-dose doxorubicin treatment

first: Andras

last: Furedi

summary: The emergence of drug resistance remains a critical challenge in cancer treatment, significantly contributing to high mortality rates. Here, we investigate therapy-induced senescence (TIS) as a reversible escape mechanism of drug resistance in breast cancer cells. Using high-dose doxorubicin, we induced TIS in MCF7 and T47D breast cancer cell lines. scRNA sequencing revealed a unique transcriptomic profile for TIS cells, distinct from both parental and repopulated cells in every cell line, exposing a small subpopulation of TIS cells with the potential to escape senescence. Gene set enrichment analysis indicated significant downregulation of proliferation-related genes, downregulation of DNA repair pathways, and the upregulation of immune response related genes.

overall_design: MCF7 and T47D control, therapy-induced senescent (TIS) and repopulated cells were analyzed using scRNAseq

first: Eszter

last: Bajtai

first: Csaba

last: Kiss

first: Sandor

last: Spisak


title: SSEA-1+ and SSEA-1- endometrial epithelial cells

city: Liverpool

first: Jamie

last: Soul

address: Crown St

department: ISMIB

country: United Kingdom

institute: University of Liverpool

summary: SSEA-1+ endometrial epithelial cells (EECs) assume the postulated stem progenitor cell niche within the human endometrium. Previous studies have demonstrated isolated SSEA-1+ cells to have a higher capacity to generate organoids in a 3D matrix, have lower steroid hormone expression and higher telomerase activity with longer telomere lengths. To further explore this we conducted transcriptional profiling comparing human SSEA-1 enriched and depleted endometrial epithelial cells from eight individuals.

overall_design: SSEA-1+ versus SSEA-1- endometrial epithelial cells from eight paired endometrial samples

first: Hannan

last: Al-Lamee


title: Engineering Fibroblast with Reprogramming and Spheronization for Bone Defect Repair

city: Kunming

first: Yanjiao

last: Li

address: Puxin Road 2

institute: Kunming University

summary: Bone diseases profoundly affect patients, particularly the elderly, leading to severe health complications and disabilities. Osteoblasts play a crucial role in bone formation and are ideal candidates for treating bone diseases and engineering living materials. However, the stem and progenitor cells that give rise to osteoblasts, as well as osteoblasts themselves, exhibit dysfunction with aging. Although chemical reprogramming of fibroblasts into osteoblasts has been achieved, effective cell-based therapies or living materials have not been established in clinical practice. Here, we present a method using small molecules to achieve complete osteoblastic specification from human fibroblasts across all age groups. By targeting Wnt signaling pathways and modularizing small molecules and their combinations based on their effects on stage-specific genes, we optimized the temporal regulation of small molecules in reprogramming, achieving healthy induced osteoblasts(iOBs). The iOBs with traits of young native osteoblasts are ideal for forming transplantable tissue spheroids with improved survival, self-bone formation, and accelerated local angiogenesis in vivo, promoting effective bone defect repair. The material-free spheroids function as living, self-scaffolding building blocks for biofunctional constructs that reproduce tissue composition, maintain high cell density, and support matrix remodeling, offering a promising avenue for clinical autologous bone defect repair.

overall_design: 17 samples were analysed by RNA-seq (12 skin + 5 bone)

first: Bin

last: Jiang

first: Zhen

last: Wu

first: Zhaoxia

last: Ma

first: Lihua

last: Qiu

first: Wen

last: Cui

first: Yunhui

last: Zhao

first: Jinghe

last: Yan

first: Daiping

first: Xingfei

first: Shu

last: Liang

first: Sitao

first: Yanqun

first: Mengting

first: Min

last: Hu


overall_design: 12 samples were analysed by RNA-seq.

last: Wang


title: GRB2 promotes malignant behaviors of breast cancer by modulating the global expression and alternative splicing profiles in SK-BR-3 cells through binding mRNA [RNA-seq]

city: Urumqi

first: hongyu

last: li

state: xinjiang

address: Affiliated Cancer Hospital of Xinjiang Medical University

institute: xinjiang medical university

summary: The flexible protein GRB2 interacts with HER1~4 on the cell surface and regulates the angiogenesis, differentiation, and proliferation of tumor cells. It is an essential component of the intricate signaling cascade of tyrosine kinase receptors. Meanwhile, GRB2 is an RBP that plays an important role in post-transcriptional regulation in eukaryotes, which affects every stage of mRNA synthesis, modification, splicing, stabilization. Research on breast cancer is limited, but one study found a connection between GRB2 and HER2-positive breast cancer, highlighting the potential of GRB2 as a novel biomarker that stimulates tumor growth. In this research endeavor, we will investigate the impact of GRB2's regulatory mechanism on metastasis in HER2-positive breast cancer.

overall_design: SK-BR3 cells were transfected with a plasmid overexpressing GRB2, and RNA-seq sequencing was performed on the cells before and after transfection. The transcriptome sequencing data before and after GRB2 overexpression were compared, and the differentially expressed genes and alternative splicing events influenced by GRB2 were identified. The fRIP-seg data of GRB2 in SK-BR3 were obtained experimentally, the target mRNA and non-coding RNA bound by GRB2 were compared, the RNA-seg and fRIP-seg data were integrated and analyzed, and the cancer-related pathways and related gene expression/alternative splicing events regulated by GRB2 in SK-BR3 cells were obtained, and the potential functions of GRB2 in HER2+ breast cancer transcription and posttranscription were speculated.

first: Hongyu

first: Wei

last: Liu

first: Yumian

last: Huang

first: Lei

last: Qiao


title: DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies I

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

summary: Primary myelofibrosis (PMF) is a clonal blood disorder linked to mutually exclusive mutations in JAK2, CALR, or MPL genes. To understand the epigenetic effects of these mutations, we analyzed DNA methylation (DNAm) profiles of PMF patients. Notably, no differences were found between JAK2 and CALR mutated cases, whereas MPL mutations showed distinct DNAm patterns. Further investigation in induced pluripotent stem cell (iPSC) models with JAK2 mutations revealed only a moderate link to PMF-related epigenetic changes, suggesting these alterations are not directly caused by the mutations. Additionally, PMF-associated epigenetic changes showed minimal correlation with allele burden and were largely evoked by changes in the cellular composition. When comparing PMF DNAm profiles with those from other myeloid malignancies, such as acute myeloid leukemia, juvenile myelomonocytic leukemia, and myelodysplastic syndrome, many overlapping changes were found, making it difficult to distinguish PMF based on individual CpGs. However, a PMF score created by combining five CpGs successfully differentiated PMF from other diseases in training and validation datasets. These findings demonstrate that PMF driver mutations do not directly evoke epigenetic changes. While PMF shares epigenetic changes with other myeloid malignancies, epigenetic signatures can effectively differentiate PMF from related diseases.

overall_design: We analyzed genome-wide DNA methylation changes in PBMCs from 28 PMF patients with different driver mutations (CALR, JAK2, MPL), 2 ET patients, and 10 healthy donors  using the Illumina EPIC v2 microarray.

first: Esra

last: Dursun Torlak

first: Vithurithra

last: Tharmapalan

first: Kim

last: Kricheldorf

first: Joelle

last: Schifflers

first: Madeline

last: Caduc

first: Martin

last: Zenke

first: Steffen

last: Koschmieder


title: Assessing the role of RHIM proteins in RIPK3-transcription in MEFs

first: Sigal

last: Kofman

overall_design: Ripk3-2xFv immortalized mouse embryonic fibroblasts (MEFs) lacking MLKL,  were treated with siRNA targeting ZBP1, TRIF, RIPK1 and a scramble encoded control. Activatable Ripk3-MEFs were then treated with BB homodimerizer for 4hrs. MEF RNA lysates were then submitted for bulk RNAsequencing. NOTES: AP1 = BB, qVD= pan caspase inhibitor, RXMM = ripk3-2xFVfl/fl:ubcERT2cre+MLKL-/-


title: DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies

overall_design: Refer to individual Series


title: DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies II

overall_design: We analyzed genome-wide DNA methylation changes in PBMCs from 4 PV, 4 MF and 4 healthy control samples using the Illumina 450k BeadChip microarray.


title: GRB2 promotes malignant behaviors of breast cancer by modulating the global expression and alternative splicing profiles in SK-BR-3 cells through binding mRNA [fRIP-seq]

last: Li


title: INNATE IMMUNE TRAINING IN THE NEONATAL RESPONSE TO SEPSIS

city: Gainesville

first: Philip

last: Efron

state: FL

address: 1600 SW Archer Road

department: Departament of Surgery

institute: University of Florida

summary: Neonates, especially those born prematurely, are highly vulnerable to infection-induced mortality.  Numerous observational and immunological studies in newborns have shown that live attenuated vaccines have beneficial, non-specific effects (NSEs) against secondary infections to unrelated pathogens.  These beneficial effects have been attributed to trained immunity, and emergency granulopoiesis plays an essential role.  However, trained immunity has been shown to affect multiple myeloid subsets and the diversity by which trained immunity influences the host protective response is still undefined.  Here we show that Bacillus-Calmette-Guérin (BCG) vaccination improves mortality to polymicrobial sepsis by simultaneously reprogramming broad aspects of myelopoiesis.  Specifically, BCG results in the expansion of multiple myeloid subsets, including LSKs and GMPs, and increases CD11b+GR1+ cell number, as well as their oxidative metabolism and capacity to stimulate T-cell proliferation in response to sepsis.  Single-cell RNA sequencing (scRNA-seq) of cells contained in the neonatal spleen suggests that BCG-vaccination changes the broad transcriptional landscape of multiple myeloid subsets promoting the maturation of various neutrophil and monocyte subsets and stimulating antimicrobial processes, while suppressing inflammatory pathways and myeloid-derived suppressor cell (MDSC) transcription.  These findings reveal that BCG administration early after birth fundamentally reorganizes the myeloid landscape to benefit the subsequent response to polymicrobial infection.

overall_design: Neonatal mice received 10E6 CFUs of the BCG vaccine (TICE® strain, Merck) subcutaneously at birth. Polymicrobial intra-abdominal sepsis was induced in neonatal mice at day 7 of life using the cecal slurry model. Briefly, cecal contents were harvested from a B6 adult mouse and an 80 mg/ml of fresh CS solution was prepared using 5% dextrose. CS (1.1 – 1.3 mg/g BW) was administered intraperitoneally to achieve the desire lethality (LD30-70). Eighteen-hours after sepsis-induction, neonatal mice were euthanized following approved IACUC guidelines and spleens were collected. Gene expression and feature-barcoding data at single cell level were generated using 10X Genomics v1.1 3’ chemistry and were sequenced on an Illumina HiSeq® with a target of 10,000 cells/sample. Data were processed using CellRanger followed by applying Seurat as an R package for quality control and visualization. n=4-7 per group: Naive (N), BCG-vaccinated (B),  Sepsis (CS18h), BCG plus sepsis (BCG-CS18h)

first: Jaimar

last: Rincon

first: Dayuan

first: Valerie

last: Polcz

first: Evan

last: Barrios

first: Marvin

last: Dirain

first: Ricardo

middle: F

last: Ungaro

first: Dina

last: Nacionales

first: Leilani

last: Zeumer

first: Feifei

last: Xiao

first: Lyle

last: Moldawer

first: Guoshuai

last: Cai

first: Shawn

middle: D

last: Larson


title: DNA methylation profiles of JAK2-derived induced pluripotent stem cells (iPSC)

first: Wolfgang

last: Wagner

summary: Myeloproliferative neoplasms (MPN) are a clonal hematological disease which harbors different driver mutations, including JAK2 V617F, and there is clear evidence that MPN is associated with aberrant DNA methylation (DNAm). However, it is unclear whether the driver mutation alone is sufficient to recapitulate the MPN phenotype and the global DNA methylation changes observed in patients. For this purpose, we utilized three established induced pluripotent stem cell (iPSC) clones carrying the JAK2 V617F mutation, both heterozygous and homozygous genotypes along with their wild type (WT) counterparts. These iPSCs were differentiated towards hematopoietic stem and progenitor differentiation (iHPCs) to capture the mutant phenotype. Genome wide methylation analysis of JAK2 mutated iPSCs and iHPCs showed no significant methylation differences compared to wild type cells. The iPSC model only partially recapitulated the DNAm changes observed in patients with JAK2 mutation, suggesting that epigenetic changes are not directly evoked by the driver mutation, but rather accumulate over the course of disease development.

overall_design: We analyzed genome-wide DNA-methylation changes in JAK2 V617F in an iPSC model. Three patient derived iPSCs, each with three genotypes (wild type, JAK2 V617F heterozygous and homozygous mutation) were utilized. iPSC cells were differentiated towards hematopoietic stem and progenitor cells (iHPCs) and collected for DNA isolation.

first: Vithurithra

last: Tharmapalan

first: Esra

last: Dursun Torlak


title: Activin A activation of Smad3 confers a natural brake to innate inflammation

city: Bethesda

first: Thierry

last: Gauthier

state: MD

address: 30 convent drive (NIH)

institute: NIH/NIDCR

summary: Phosphorylation of Smad3 is a critical mediator of TGF-b signaling, which plays an important role in regulating innate immune responses. However, whether Smad3 activation can be regulated in innate immune cells in TGF-β-independent contexts remains unknown. Here, we show that Smad3 is activated through the phosphorylation of its C-terminal residues (pSmad3C) in murine and human macrophages in response to bacterial and viral antigens, which is mediated by Activin A in a TGF-b independent manner. Specifically, infectious ligands, such as LPS, induced secretion of Activin A through the transcription factor STAT5 in macrophages, and Activin A signaling in turn activated pSmad3C. This Activin A-Smad3 axis controlled the mitochondrial ATP production and ATP conversion into adenosine by CD73 in macrophages, enforcing an anti-inflammatory mechanism. Consequently, mice with a deletion of Activin A receptor 1b specifically in macrophages (Acvr1bf/f-Lyz2cre) succumbed more to sepsis due to uncontrolled inflammation and exhibited exacerbated skin disease in a mouse model of imiquimod-induced psoriasis. Thus, we have revealed a previously unrecognized natural brake to inflammation in macrophages that occurs through the activation of Smad3 in an Activin A-dependent manner.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for peritoneal elicited macrophages cultured in vitro with or without LPS and isolated from WT or Smad3 KO mice

first: Yun-Ji

last: Lim

first: Wenwen

last: Jin

last: Liu

first: Liliana

last: Patiño

first: Weiwei

last: Chen

first: Daniel

last: Martin

first: Robert

middle: J

last: Morell

first: Gloria

last: Su

first: Wanjun