title: STING regulates aging-related osteoporosis by mediating the Hk2-Vdac1 mitochondrial axis

city: Hangzhou

first: Yani

last: Chen

state: Zhejiang

address: No. 268, Kaixuan Rd.

institute: Zhejiang University

summary: Metabolic abnormalities and mild inflammation are hallmarks of aging and major driving factors for aging-related damage and bone metabolic diseases. Mitochondria are crucial links in energy metabolism and immune homeostasis regulation. Mitochondrial dysfunction is considered one of the pathogenic factors of aging-related osteoporosis, but its mechanism of action needs further research. Here, we demonstrated that the interaction between stimulator of interferon genes (STING)-mediated regulation of hexokinase 2 (Hk2)-voltage-dependent anion channel-1 (Vdac1) is a critical factor contributing to mitochondrial dysfunction and osteogenic abnormalities during aging. As the aging process progresses, factors related to aging cause an increase in STING expression, which disrupts the interaction between Hk2 and Vdac1. Dissociation of Hk2 from Vadc1 triggered the opening of the mitochondrial inner mitochondrial permeability transition pore (mPTP), leading to mitochondrial dysfunction and abnormal osteogenic differentiation, thereby disrupting bone homeostasis. In brief, this study demonstrates that STING acts as an intracellular metabolic Checkpoint, influencing mitochondrial function to promote the development of osteoporosis. These findings significantly enhance the development of STING-targeted treatments for aging-related osteoporosis.

overall_design: RNA-seq profiling of bone marrow-derived mesenchymal stem cells (BM-MSCs) from 4-week-old control (n = 3) and shVdac1 (n = 3) male C57BL/6 mice.

first: Wenjin

last: Cai

first: Jiaying

last: Zhao

first: Ning

last: Gao

first: Zengzhe

last: Liu

first: Tingben

last: Huang

first: Lingling

last: Dong

first: Guoli

last: Yang

first: Ying

last: Wang


title: A Simple and Efficient Method for the Robust Expansion of Human ILC2s to Prevent Acute GvHD

status: Public on Jul 05 2025

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

country: USA

institute: University of North Carolina at Chapel Hill

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: IGF2BP3 increases IL-13/IL-4 signalling in human bronchial epithelial cell

city: London

first: Paniz

last: Khooshemehri

address: Great Maze Pond

department: Infectious diseases

country: United Kingdom

institute: King's college London

summary: To investigate the genome-wide role of RNA binding protein IGF2BP3 in IL13 mechanisms of action in bronchial epithelial cells

overall_design: Constitutive knock down shControl and shIGF2BP3 BEAS-2B cell lines and stimulated with IL-13 overnight. Frac-seq was performed to allow comparison of total mRNA (input) to polyribosomal (polysome) bound mRNAs

first: Rocio

last: Martinez-Nunez


title: High serum LDL promotes ovarian cancer cells metastasis by upregulating FOXQ1

first: Song

last: Tang

address: School of Medicine C233, Zijingang Campus of Zhejiang University, 866 Yuhangtang Road, Hangzhou, P.R. China.

country: China

summary: Ovarian cancer has increasingly been linked with lipid metabolism disturbances, while the association between circulating low-density lipoprotein (LDL) levels and ovarian cancer remains controversial. our study found that high serum LDL promoted migration, invasion, epithelial-mesenchymal transition (EMT) and stemness of ovarian cancer cells. Through high throughput sequencing, we found LDL enhanced the expression of genes related to EMT and stemness pathways in ovarian cancer cells. Besides, the effect might be facilitated by upregulating the critical transcription factor FOXQ1. Overall,  our study uncovers a mechanism underlying metastasis in ovarian cancer cells, and suggests potential clinical strategies controlling serum LDL levels or targeting FOXQ1 to prevent ovarian cancer progression.

overall_design: This experiment was conducted using SKOV3 cells, which were divided into control group (4 samples: C1-4) and treatment group (4 samples: T1-4). Both the control group and the treatment group were cultured in the same cell incubator and the same culture medium. In the treatment group, each sample was treated with LDL at a concentration of 50 μg/mL for 48 hours, and then all the samples were collected together for testing.

first: Kelie

first: Fang

last: Zheng

first: Zhiqin

last: Fu

first: Yuequn

last: Niu

first: Xinxin

first: Heng

last: Ni

first: Xiaoyu

last: Yuan

first: Zhenyan

last: Cui

first: Weiguo

last: Lu

first: Dajing

last: Xia

first: Yihua

last: Wu


title: mRNA profiles of Celf1fl/fl and adipocyte-specific Celf1 deficiency (Celf1fl/fl AKO) in iWAT after acute cold stimulation

city: Chongqing

first: Ting

last: Zeng

address: No. 1 Medical College Road

institute: Chongqing medical university

summary: RNA-seq reveals the critical role of adipocyte Celf1 in cold-responsive thermogenic remodeling in inguinal white adipose tissue (iWAT). The cold-induced thermogenic program in iWAT was severely blunted in Celf1AKO mice, especially the obvious downregulation of Ucp1, Dio2, Elvol3, Tbx1, Cox7a1, and Cidea genes. The GO analysis revealed that the down-regulated genes were primarily involved in adaptive thermogenesis, temperature homeostasis, and mitochondrial-related processes, including lipid oxidation, fatty acid metabolism and so on. KEGG pathway analysis further showed that these down-regulated genes were involved in thermogenesis-related pathways, including thermogenesis, PPAR signaling, metabolic pathways, fatty acid degradation, and AMPK signaling. Together, these results suggest that adipocyte Celf1 deficiency impairs cold-induced iWAT thermogenic program.

overall_design: To explore the role of Celf1 in beiging of iWAT, we exposed fl/fl control mice and Celf1AKO mice to cold stimulation at 4℃ for 6h, and then performed RNA sequencing of iWAT.


title: The Epigenetic Regulator PHF16 Redresses Homeostasis During Intestinal Injury Repair [RNA-seq]

status: Public on Jul 06 2025

city: Incheon

first: Ik Soo

last: Kim

address: Gaetbeol-ro, Yeonsu-gu

country: South Korea

institute: Gachon University college of Medicine

summary: The intestinal stem cells (ISCs) are highly vulnerable to DNA damage, being in a constant state of proliferation1. Reserve crypt stem cells restore homeostatic intestinal epithelium following damage-induced ablation of ISCs2-5. Here, we report that the epigenetic regulator PHD finger protein 16 (PHF16) redresses revival stem cell (revSC) activity after damage repair. Phf16-/Y mice showed defects in exit from the regenerative state of revSCs and failed in intestinal crypt regeneration, while they still induced revSCs in response to tissue damage, as observed using single-cell RNA-sequencing. RNA-sequencing and ATAC-sequencing analyses of Phf16-/Y intestinal organoids revealed that PHF16 controls intestinal epithelial differentiation by promoting HBO1-mediated histone H3K14 acetylation, while PHF16 also counteracts YAP/TAZ activity by ubiquitination of CDC73, faithfully reverting damage-induced revSCs to homeostatic gut epithelial cells. Together, our findings demonstrate the importance of timely suppression of regenerative activity by PHF16 for the restoration of gut homeostasis after acute tissue injury.

overall_design:
ATAC-Seq: Comparative chromatin accessibility profiling analysis of assay for transposase-accessible chromatin using sequencing (ATAC-seq) in WT and Phf16-/Y intestinal organoid cells on Day1-3.
RNA-Seq: Comparative gene expression profiling analysis of RNA-seq data for WT and Phf16-/Y intestinal organoid cells on Day1-3.

first: Sung

middle: H

last: Baek

first: Jun-Yeong

last: Ahn


title: A Simple and Efficient Method for the Robust Expansion of Human ILC2s to Prevent Acute GvHD [ATAC-seq]

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

summary: Reconstitution of stem cells and enhancement of the barrier function of the gastrointestinal (GI) tract is critical to the resolution of intestinal acute graft-versus-host disease (aGvHD). Previously, our group has shown in murine models that type II innate lymphoid cells (ILC2) cells generate proteins in the GI tract that enhanced GI tract barrier function and diminished the expansion and function of pro-inflammatory donor cells when given to allogeneic stem cell transplant recipients. Therefore, the infusion of donor ILC2 cells could treat or prevent GI tract acute GvHD, but for this approach to be clinically applicable, robust expansion of a homogenous population of human ILC2 cells is needed. Here, we describe a method for the rapid expansion of a uniform population of human ILC2 cells which decrease GvHD in (NOD scid gamma mouse) NSG mice. The addition of IL-4 to the culture was critical to prevent the expansion of pro-inflammatory ILC1-like cells. Our approach should allow for the evaluation of human ILC2 cells to treat therapy-resistant GI tract acute GvHD.

overall_design:
Cells were enriched via Rosette separation and expanded in complete a-MEM media with 10-50 ng/ml IL-7, IL-2, IL-4, IL-25, and IL-33 for 21 days.

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

first: Danny

middle: W

last: Bruce

first: Sonia

middle: J

last: Laurie

first: Yan

last: Xing

first: Heather

middle: E

last: Stefanski

first: Keli

middle: L

last: Hippen

first: Alec

middle: D

last: Wilkinson

first: Mark

middle: G

last: Woodcock

first: James

middle: M

last: Coghill Jr

first: Karen

middle: P

last: McKinnon

first: Bruce

middle: R

last: Blazar

first: Jonathan

middle: S

last: Serody


title: A Simple and Efficient Method for the Robust Expansion of Human ILC2s to Prevent Acute GvHD [RNA-seq]


title: Small nucleolar RNA HIDDEN TREASURE 2 decrease drought tolerance through multiple pathways in Arabidopsis thaliana

city: Changchun

first: Liangliang

last: Li

address: 4888 Shengbei Street, Kuancheng District

department: Northeast Institute of Geography and Agroecology

institute: Chinese Academy of Sciences

summary: To understand the role of hid2 in regulating drought tolerance, we performed the comparative transcriptome profiling WT and hid2 mutant seedlings.

overall_design: 12-day-old WT and hid2 mutant seedlings were transferred from 1/2 Murashige and Skoog (MS) plates to soil and grown for 12 additional day. The rosette leaves of this 24-day-old seedlings were harvested after dehydration for 0, 2, and 4 h, and then frozen in liquid nitrogen immediately. Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo (dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530,New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired. A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X).And polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000.

first: Xianpeng

last: Yang

first: Haodong

last: Huang

first: Chenbo

last: Zhu

first: Minghui

first: Kaixin

first: Xiaofan

last: Nie

first: Jiahe

last: Fu

first: Mingming

last: Wang

first: Zhengwei

last: Liang

first: Xianzhong

last: Feng

first: Jiuhai

last: Zhao

first: Xiangnan

first: Shiyou

last: Lü

first: Yong

last: Shi

first: Lam-Son

last: Tran

first: Xiaojian

last: Yin

first: Weiqiang


title: Integrated ChIP-seq and Transcriptomic Profiling of Histone Modifications Across Breast Cancer Progression in MCF10A-Derived Cell Lines [ChIP-Seq]

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

summary: Cancer arises from complex epigenetic mechanisms that drive tumorigenesis. Gene regulatory elements play a pivotal role in reprogramming gene expression patterns, facilitating tumor initiation, progression, and metastasis. However, a comprehensive characterization of epigenetic alterations across cancer development remains incomplete, particularly for the spectrum of post-translational histone modifications in the evolution of breast tumors. In this study, we explored the dynamic landscape of epigenetic changes using a breast cancer progression model based on the MCF10A cell line. We integrated ChIP-seq and transcriptomic profiling to investigate the epigenetic heterogeneity across four MCF10A-derived cancer cell lines: normal (MCF10A), HRAS G12V transformed, ductal carcinoma in situ (DCIS), and metastatic (CA1a). Our analysis revealed significant changes in chromatin patterns at regulatory elements, including stage-specific variability in H3K27me3 and H3K9me3-marked heterochromatin domains.  These profiles underly the epigenomic changes in each of these cell states to provide insights into human breast cancer progression.

overall_design: This study includes an analysis of ChIP-seq data from four MCF10A-derived cell lines representing different stages of breast cancer progression: normal (MCF10A), HRAS G12V transformed, ductal carcinoma in situ (DCIS), and metastatic (CA1a). We investigated the epigenetic changes through ChIP-seq profiling of histone modifications (H3K27me3, H3K9me3, H3K4me1, H3K27ac, H4K5ac, H4K8ac). Biological replicates were included to ensure robustness and reproducibility of the data.

first: Cong

last: Gao


title: Long-term transcriptome-wide therapeutic effects of AAV-hpCas13d

city: Shanghai

first: Zilong

last: Geng

address: 800 Dongchuan Rd, Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

summary: To fully understand  the enduring therapeutic effects of hpCas13d and its potential for clinical translation, comprehensive investigation is needed. In this study, we employed RNA-sequencing to analyze transcriptome alterations in Myh6RH/+ hearts, Myh6RH/RQ hearts, and hpCas13d[RQ]-treated Myh6RH/RQ hearts, aiming to elucidate the molecular mechanisms underlying the regression of cardiac hypertrophy induced by hpCas13d[RQ] treatment.

overall_design: To evaluate the transcriptome-wide therapeutic impact, hearts were harvested from Myh6RH/+, Myh6RH/RQ, and Myh6RH/RQ+AAV-hpCas13d mice 12 months after neonatal administration. Total RNA was extracted and subjected to RNA sequencing analysis.

first: Yingmei

last: Lou

first: Ping

first: Bing

last: Zhang


title: Spatiotemporal multi-omics analysis reveals distinct epigenetic and transcriptional signatures in the hippocampal-amygdala circuit during fear memory consolidation [CFC_Spatial]

city: Blacksburg

first: Timothy

last: Jarome

address: Mail Stop: 0306,ANIMAL SCIENCES  MC0306,LITTON REEVES   STE 3490

institute: Virginia Tech

summary: The consolidation of contextual fear memories requires the crosstalk among multiple brain regions, including the hippocampus and amygdala. Despite the advance in single cell transcriptomic techniques, tracing the dynamic gene expression across the hippocampal-amygdala circuit remain challenging. Here we integrated high resolution spatial transcriptomics with single nuclei multi-omics techniques to systematically investigate the spatiotemporally transcriptional programs across the hippocampal-amygdala circuit during the encoding and retrieval of contextual fear memory. It reveals highly dynamic gene expression in the subregions of hippocampus and amygdala. Our data provide new insights into the transcriptional programs underlying consolidation of memory.

overall_design: Adult C57BL/6 male mice (12~15 weeks) were subjected to contextual fear conditioning (CFC), mice without foot shock were used as context control (CC), and mice stayed in the home cage until sample harvest were used as home cage control (HC). Mice were harvested 1h or 4h after foot shock on the training day (day 0) and 4h after memory retrieval on day 1 to assess fear memory consolidation and reconsolidation. To profile spatial transcriptome, the mouse brains were freshly isolated to prepare FFPE tissue blocks, then coronally sectioned and placed onto the Visium slides for Visium Spatial Gene Expression library preparation. To simultaneously profile the transcriptome and chromatin accessibility at single cell resolution, hippocampus and amygdala were micro-dissected from the freshly isolated mouse brain tissues for single nuclei suspension preparation and subsequently loaded onto the Chromium iX using the single nucleus multiome kit from 10x genomics. Single nucleus RNA-seq (snRNA-seq) and single nucleus ATAC-seq (snATAC-seq) libraries were simultaneously constructed from the same nucleus following the manufactures' instructions.

first: Xiguang

last: Xu

first: Yu

last: Lin

first: Hehuang

last: Xie


title: Effect of complete abroagation of hyaluronan synthesis on osteogenic differentiation of mesenchymal stem cells (MSc) in vitro

city: Leipzig

first: Ulf

last: Anderegg

address: Johannisallee 30

department: Dept. of Dermatology

country: Germany

institute: Leipzig University, Faculty of Medicine

summary: Mesenchymal stem cells (MSc) show diminished osteogenic differentiation upon complete knockout of all known Hyaluronan (HA) synthases (Has). We demonstrated that Has-knockout completely abrogated the release of HA into the culture medium by MSc and that these MSc showed an impaired osteogenic differentiation detected by Alizarin red staining at days 7 and 12 of differentiation compared to wildtype MSc. To gain insight intor the transcriptomic changes due to Has knockout we compared differentiating MSc at day 7 of differentiation.

overall_design: MSc from mouse femurs and tibiae were cultured in vitro and treated twice with 4-hydroxytamoxifen in order to induce cre recombination for Has2-knockout. Two groups were compared: MSc from wildtype mice (C57Bl6/J) and MSc from Has-total knockout mice (constitutive knockout of Has1 and Has3 plus induced knockout of Has2). MSc were isolated from 8 mice (n=4 per genotype) and the RNA from MSc at day 7 of osteogenic differentiation was analyzed.

first: Anderegg

last: Ulf

first: Saalbach

last: Anja

first: Krohn

last: Knut


title: Single cell level characterization of immune cells in 10-week-old C57BL/6 knee joints and femur bone marrow

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

summary: Post-traumatic Osteoarthritis (PTOA) occurs in about half of individuals who sustained articular injuries including tibial plateau fracture, meniscus tear, or an anterior cruciate ligament (ACL) rupture. We utilize a noninvasive tibial compression injury (TCI) model that can closely replicate the anterior cruciate ligament rupture in patients, which reliably initiates PTOA development. In other studies we utilize single-cell RNA sequencing to temporally explore differences in immune cell infiltration following injury. Although extreme care is taken during immune cell isolation to prevent contamination from bone marrow, we also wanted to rule out the possibility of contamination from bone marrow immune cells in our knee joint samples. Therefore, we proceeded to compare the neutrophil populations from uninjured joint (joint) to bone marrow (marrow) to identify the similarities and differences between these populations.

overall_design: Right knee joints and bone marrow obtianed from Femur/Tibial bones of 10-week-old C57BL/6 mice were collected and immune (Cd45+) cells were analyzed using scRNA-seq.

first: Aimy

last: Sebastian

first: Gabriela

last: Loots


title: Single cell level characterization of injury-induced immune changes in 10-week-old and 95-week-old C57BL/6 knee joints

summary: Post-traumatic Osteoarthritis (PTOA) occurs in about half of individuals who sustained articular injuries including tibial plateau fracture, meniscus tear, or an anterior cruciate ligament (ACL) rupture. Damage-associated molecular pattern (DAMP) proteins are typically secreted from injured or dying cells of the synovial joint into the surrounding environment immediately following injury which in turn recruit leukocytes to mediate debris clean-up and repair. Prior bulk RNA-seq experiments exploring organismal age-related differences following ACL rupture found an increased expression of inflammatory-response related genes in 95-week-old mice relative to 10-week-old mice. Using single-cell RNA sequencing technology we temporally explored differences in immune cell infiltration in the synovial joint in 10-week-old and 95-week-old C57BL/6 mice.

overall_design: Right knee joints of 10-week-old and 95-week-old C57BL/6  mice were injured using a tibial compression injury model. Uninjured joints and injured joints from 7-post-injury were collected and immune (Cd45+) cells were analyzed using scRNA-seq.


title: Effect of PLOD3 on the progression of colorectal cancer

city: Bishan

first: Hong

last: Peng

state: ChongQing

address: Shuangxing avenue 9

institute: AffiliatedBishan hospital of Chongqing Medical  University

summary:
To investigate the effect of PLOD3 siRNA on HCT116 cells,
We performed gene expression profiling analysis using data obtained from RNA-seq of 2 groups(NC, PLOD3 siRNA).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells treated with si NC, or PLOD3 siRNA.

first: Zheng

last: Jiang


title: Distinct and overlapping immunological responses to SARS-CoV-2 and Mycobacterium tuberculosis identified by single-cell RNA-seq of co-infected whole blood

city: Melbourne

first: Dylan

last: Sheerin

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: To determine distinct and similar aspects of the human immune responses in the blood to Mycobacterium tuberculosis and SARS-CoV-2 infection or concurrent infection with both pathogens.

overall_design: Human whole blood samples were infected with Mycobacterium tuberculosis and/or SARS-CoV-2, or left uninfected, for 24 or 96 hours. Infected samples were compared against the uninfected sample at each time point and overlapping/distinct responses were examined between infection conditions.


title: Gene expression profiles analasis in chronic salpingitis

city: Harbin

first: Mengke

last: Yuan

state: Heilongjiang

address: 24 heping, xiangfang

institute: Heilongjiang University of Chinese Medicine

summary: Chronic salpingitis (CS) plays an important role in gynecological diseases such as infertility and ectopic pregnancy. In order to explore mechanism of CS at transcriptomics, we conducted microarray analysis of long non-coding RNA (lncRNA), circular RNA (circRNA), and mRNA expression profiles in patients with CS for the first time. The expression of genes in 4 CS and 4 normal tissue samples was detected using Gene chips, asn fold changes and p-value were utilized to filter differentially expressed genes (DEGs). The function of the DEGs was analyzed and their potential role in CS was explored.

overall_design: The expression of genes in 4 CS tissuse samples (N1, N3, N5, N9)and 4 normal (N2, N4, N6, N7) samples was detected using Gene chips, asn fold changes and p-value were utilized to filter differentially expressed genes (DEGs). The function of the DEGs was analyzed and their potential role in CS was explored.

first: Jinzhe

last: Liu

first: Li

last: Li


title: PAR-iCLIP MCMV infection

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

summary: Swiss murine embryonic fibroblasts (NIH-3T3) or murine TCMK-1 epithelial cells were infected with BAC-derived wild-type Smith strain mouse cytomegalovirus (MCMV) at a multiplicity of infection (MOI) of 10. PAR-iCLIP was performed using 4-thiouridine labeling on both uninfected and MCMV-infected cells (72h post infection).

overall_design:
NIH-3T3 or TCMK-1 murine epithelial cells from seven 15 cm dishes per condition (for MCMV infection) were trypsinized and resuspended in 1ml cell culture medium per plate. Cells were infected immediately after trypsinization in suspension (7ml) with wild-type MCMV at an MOI of 10. 1 h later, fresh cell culture medium was added (containing 25 µM 4-thiouridine (4sU)) and cells were plated on to ten 15cm dishes. After 24 and 48 h of infection, +25 µM and +50µM 4sU was added to the cell culture medium. For the uninfected samples, cells were plated onto fresh plates. 24h after platting, metabolic RNA labeling was performed for 24h using 100 µM of 4sU. Prior to UV cross-linking at 365 nm on ice, cell culture medium was taken off the plates. Cross-linking was performed at 0.15 J/cm2 of 365 nm UV light using a Spectrolinker XL-1500 (Spectronics Corporation). Cells were harvested and iCLIP libraries were prepared as described in detail (Konig et al., J Vis Exp. 2011).
TCMK-1 murine kidney epithelial cells (ATCC: CCL-139) and M2-10B4 bone marrow stroma cells (ATCC: CRL-1972) were cultured in DMEM containing 10% fetal calf serum and penicillin/streptomycin. NIH-3T3 fibroblasts (ATCC: CRL-1658) were cultured in DMEM medium containing 5% fetal calf serum and penicillin/streptomycin. For MCMV infection, cells from seven 15 cm dishes (80% confluent) per condition (for MCMV infection) were trypsinized 3-4 days after the last split. Cells were resuspended in 1 ml cell culture medium per plate. MCMV virus stock was added at an MOI of 10 (t=0). Similar to centrifugal enhancement, infecting cells in suspension rather than on plates results improves infection by about 10-fold.). 1h later, cells were transfered to a bottle with 195 ml cell culture media containing a final concentration of 25 µM 4sU. Cells were plated to ten 15 cm dishes (20 ml per plate). At 24 and 48 h post infection, an additional 25µM (24hpi) and 50 µM (48hpi) 4sU was added to the cell culture medium. Uninfected cells were split 24h prior to beginn of 4sU labeling (100µM 24h).

first: Anne

last: L'Hernault

first: Andrzej

last: Rutkowski

first: Jernej

last: Ule

first: Lars

last: Dölken


title: Landscape of CD4+Foxp3+ Treg cells in the liver of neonatal mice

city: Beijing

first: Yujia

last: Wang

state: Beijing

address: 38 Xueyuan Road, Haidian District

department: Department of Immunology

institute: Peking university school of basic medical sciences

summary: To study the heterogeneity of regulatory T cells (Tregs) in various organs, we performed single-cell RNA sequencing on liver and splenic Treg cells obtained from 12-day and 7-week old mice. Unique Treg subsets in neonatal liver were found and their impact on liver development and maturation was investigated.

overall_design: To fully characterize liver Treg cells in neonatal mice, we performed scRNA-seq on sorted liver and splenic CD4+Foxp3GFP+ Tregs from 12-day-old Foxp3GFP-Cre Rosa26loxP-Stop-loxP-YFP mice. We also compared it with the scRNA-seq of Tregs purified from the liver and spleen of 7-week-old mice.

first: Lijun

last: Yang

first: Mingyang

first: Jie

last: Hao

first: Xiuyuan

last: Sun

first: Rong

last: Jin

first: Hounan

last: Wu

first: Xuyu

last: Zhou

first: Qing

last: Ge


title: IL-2 and IL-15 drive intrathymic differentiation of functionally distinct regulatory T lymphocyte-clusters

city: Toulouse

first: Joost

last: van Meerwijk

address: CHU Purpan BP 3028

department: CPTP U1043

country: France

institute: INSERM

summary: Intrathymic development of Foxp3-expressing regulatory T lymphocytes (Treg) depends on signals from the TCR, cytokine-receptors, and other cell-surface receptors. The cytokines IL-2 and IL-15 have been suggested to quantitatively modulate Treg-development. However, recent evidence showed that very large proportions of thymic Treg are cells that had migrated from the periphery back to the thymus. It remained therefore unclear if IL-2 and IL-15 quantitatively control the development of Treg. Moreover, these cytokines may also contribute to the differentiation of functionally distinct Treg subsets. Using an experimental setting in which we unambiguously distinguish newly developing from recirculating Treg, we here address the quantitative and qualitative roles of IL-2 and IL-15 in Treg-development, selection, and differentiation. Our results definitively demonstrate that in absence of IL-2 or IL-15 the thymus produces substantially less Treg. Importantly, IL-2 and IL-15 drive the differentiation of transcriptionally and phenotypically distinct Treg clusters, the number of which is substantially higher than previously appreciated. These cytokines also differentially modulate the TCR-repertoire expressed by newly developing Treg. Adoptive transfer of Treg from wt, IL-2- or IL-15-deficient animals into Treg-deficient new-born Scurfy mice, revealed differences in the in vivo function of these cells. Combined, our results indicate that IL-2 and IL-15 drive the development of functionally complementary Treg clusters.

overall_design: We here address the quantitative and qualitative roles of IL-2 and IL-15 in Treg-development, selection, and differentiation

first: Cécile

last: Apert

first: Ariel

last: Galindo-Albarran

first: Sarah

last: Castan

first: Claire

last: Detraves

first: Jérémy

last: Santamaria

first: Nicola

last: McJannett

first: Manuel

last: Lebeurrier

first: Olivier

last: Joffre

first: Simon

last: Fillatreau

first: Bart

last: Haegeman

first: Nathalie

last: Vialaneix

last: Hoede

first: Paola

last: Romagnoli


title: RNA sequencing of neonatal mouse liver

first: Yujia

last: Wang

summary: Liver development in neonatal mice with T-bet+ Tregs deletion was detected by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 12-day-old Foxp3GFP-Cre Rosa26loxP-Stop-loxP-YFP and Tbx21flox/flox Foxp3GFP-CreRosa26loxP-Stop-loxP-YFP mouse liver samples.

first: Lijun

last: Yang

first: Mingyang

last: Li

first: Jie

last: Hao

first: Xiuyuan

last: Sun

first: Rong

last: Jin

last: Wu


title: Identification of Neuritin 1 as a local metabolic regulator of brown adipose tissue

status: Public on Jul 04 2025

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Brown adipose tissue (BAT) plays a key role in metabolic homeostasis through its thermogenic effects and the secretion of regulatory molecules. Here we report that RAP250 haploinsufficiency stimulates BAT in mice, thus contributing to a decrease in fat accumulation. Local in vivo AAV-mediated RAP250 silencing in BAT reduces body weight and fat mass and enhances glucose oxidation, thereby indicating that RAP250 participates in the regulation of BAT metabolic activity.   Analysis of the mechanisms  led to the finding that Neuritin 1 is produced and released by brown adipocytes, it plays a key metabolic role, and it participates in the enhanced BAT metabolic activity under RAP250 deficiency.  Forced overexpression of Neuritin 1 in UCP1-expressing cells markedly decreases fat mass and body weight gain in mice and induces the expression of thermogenic genes in BAT. Neuritin 1-deficient brown adipocytes also shows a reduced b-adrenergic response. We demonstrate a metabolic role of BAT-derived Neuritin 1 acting through an autocrine/paracrine mechanism.  Based on our results, Neuritin-1 emerges as a potential target for the treatment of metabolic disorders.

overall_design: Vector plasmid pAAV-UCP1-m-NRN1 contains the mouse Neuritin 1 (gene ID 68404, RefSeq# BC035531, ORF size 429 bp, protein 142 Aa).

first: Manuela

last: Sánchez-Feutrie

first: Antonio

last: Zorzano

first: Vanessa

last: Hernández

first: Óscar

last: Reina


title: Identification of Neuritin 1 as a local metabolic regulator of brown adipose tissue.

overall_design: RNA-seq profiling of Intescapular brown adipose tissue of WT and RAP250 heterozygous 20 week-old male mice

first: Montserrat

last: Romero


title: The Nhd1–MYB110–MADS15 transcription factor module regulates flowering time in rice

city: Nanjing

first: Yi

address: No. 666, Binjiang Avenue, Jiangbei New District

institute: Nanjing Agricultural University

summary: The precise regulation of flowering time, known as heading date in rice (Oryza sativa L.), is critical for regional adaptation, agricultural productivity, and crop rotation practices. In rice, the florigen activation complex (FAC) and its downstream effectors are well-characterized mediators of the floral transition in the shoot apical meristem (SAM). Here, we characterized OsMYB110 as a SAM-localized transcription factor that promotes flowering, exhibiting functional similarity to the established flowering regulator Nhd1 (N-mediated heading date-1). Through integrated molecular and genetic analyses, we demonstrate that: (1) Nhd1 directly binds to the OsMYB110 promoter to activate its expression, while OsMYB110 in turn binds to and activates the OsMADS15 promoter to control flowering progression, and (2) genetic epistasis places OsMYB110 downstream of Nhd1 but upstream of OsMADS15 in the flowering regulation hierarchy. Furthermore, while elevated phosphate accelerates flowering, this response is abolished in myb110 and mads15 mutants but maintained in nhd1 mutants. These results define a previously unrecognized Nhd1–OsMYB110–OsMADS15 regulatory module that integrates developmental and nutrient signaling pathways to control rice flowering time.

overall_design: Samples from the SAM and the first new blade of the main stem were collected at one month after being transplanted in the field condition. The SAM samples from 20 plants and the blade samples from 5 plants were mixed into one pool. Three individual pools of WT and myb110 mutants were used for RNA-Seq analysis


title: Multi-selective RAS(ON) Inhibition Targets Oncogenic RAS Mutations and Overcomes RAS/MAPK-Mediated Resistance to FLT3 and BCL2 Inhibitors in Acute Myeloid Leukemia

city: San Francisco

first: Catherine

last: Smith

address: 513 Parnassus Ave.

department: Medicine, Hematology/Oncology

institute: UCSF

summary: Aberrant activation of the RAS/MAPK signaling limits the clinical efficacy of several targeted therapies in acute myeloid leukemia (AML). In FLT3-mutant AML, the selection of clones harboring heterogeneous RAS mutations drives resistance to FLT3 inhibitors (FLT3i). RAS activation is also associated with resistance to other AML targeted therapies, including the BCL2 inhibitor venetoclax. Despite the critical need to inhibit RAS/MAPK signaling in AML, no targeted therapies have demonstrated clinical benefit in RAS-driven AML. To address this unmet need, we investigated the preclinical activity of RMC-7977, a multi-selective inhibitor of GTP-bound active [RAS(ON)] isoforms of mutant and wild-type RAS in AML models. RMC-7977 exhibited potent antiproliferative and pro-apoptotic activity across AML cell lines with MAPK-activating signaling mutations. In Molm-14 and OCIAML-3 cell lines, RMC=7977 downregulated expression of genesets involved in RAS/MAPK and PI3K/Akt/mTOR signaling, as well as MYC targets and cell cycle regulators.

overall_design: AML cell lines Molm-14 and OCIAML-3 were treated for 2h and 24 hours with either DMSO or the RAS(ON) inhibitor RMC-7977, then RNA was isolated and RNA sequencing was performed.

first: Bogdan

last: Popescu


title: RNAseq analysis of Lactuca sativa leaf under UV treatment

city: Bari

first: Vitantonio

last: Pantaleo

address: Via Amendola 165/a

country: Italy

institute: Institute for Sustainable Plant Protection

summary: Baby leaves of lettuce (Lactuca sativa L.) are widely used to produce ready-to-eat salads all around the year. For this purpose, lettuce plants are cultivated under plastic tunnels and harvested at a very early growth stage, between 30-45 days after sowing depending on the season, cultivar and site of cultivation. Usually, the plastic film covering the cultivation tunnels transmits only a very small amount of the solar UVB radiation and partially attenuates UVA radiation. We used UV treatment post-harvest of fresh-cut lettuce baby leaves to compare the efficiency of two UV emission wavebands centred at 306 and 366 nm (achieved by employing narrow-band UV LEDs sources) to identify putative transcriptomic signatures. The analyses have been carried out supported by and in the frame of Project @CNR 2021, Title "EnhAncement of Natural anTIviral Compounds in ready- to-eat Vegetables", Acronym: ANTI-CoV to Dr. G. Agati. IDP-NAHEP, ICAR, Govt of India to A.R.B.

overall_design: RNA-seq analysis and profiling of Lactuca satica L., variety "Luna bionda" and "Falstaff" baby leaves under UV treatments. Emission spectrum of the LED lamp used for the UV treatments. The visible part of the spectrum is the combination of the warm white and cold white LEDs. Irradiance was measured at a 50 cm distance from the lamp. The warm and cold white LEDs as well as the UVA (365 nm) LED emissions were set at 10% of the maximal intensity. The UVB (306 nm) LED emission was set at the 100% intensity.

first: Giovanni

last: Agati

first: Akhil Ranjan

last: Baruah

last: Leonetti


title: H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells [ChIP-Seq]

city: Cleveland

first: Kaixiang

last: Cao

state: Ohio

address: 10900 Euclid Avenue

institute: Case Western Reserve University

summary: In metazoans, nucleosomes harboring H3K79 methylation (H3K79me) deposited by the histone methyltransferase DOT1L decorate actively transcribed genes. Although DOT1L is implicated in transcription regulation and pathogenesis of human diseases such as leukemia and neurological disorders, the role of H3K79me in these biological processes remains elusive. Here, we reveal a novel functional synergism between H3K79me and H3K36 tri-methylation (H3K36me3), another histone modification enriched at active genes, in regulating gene expression and neural cell fate transition. Simultaneous catalytic inactivation of DOT1L and the H3K36 methyltransferase SETD2 via gene editing leads to the global loss of H3K79me and H3K36me3, hyperactive transcription, and failures in neural differentiation. Interestingly, the loss of H3K79me and H3K36me3 causes increased transcription elongation, gained chromatin accessibility at a group of enhancers, and increased binding of TEAD4 transcription factor and its co-activator YAP1 at these enhancers. Furthermore, YAP-TEAD inhibition partially restores the expression levels of hyperactivated genes upon H3K79me/H3K36me3 loss. Taken together, our study demonstrates a synergistic role of H3K79me and H3K36me3 in regulating transcription and cell fate transition, unveils novel mechanisms underlying such synergism, and provides insight into designing therapies that target diseases driven by misregulation or mutations of DOT1L and/or SETD2.

overall_design: Identify the role of H3K79me and H3K36me2 in regulating the chromatin landscape.


title: Drought inhibits thermomorphogenesis via salicylic acid-mediated suppression of ELF3 phase separation

first: Xiaoyi

last: Li

address: west beichen

department: Chinese Academy of Sciences

institute: Institute of Genetics and Developmental Biology

summary: Plants are constantly exposed to environmental changes and must respond carefully to ensure survival and growth. Under high temperatures, many plants exhibit a series of morphological and developmental adjustments, including increased hypocotyl and petiole elongation. These adaptations, collectively termed thermomorphogenesis, promote transpiration and water loss, thereby enhancing evaporative cooling. However, this phenomenon has primarily been described under well-watered conditions, whereas in nature, heat often coincides with other environmental challenges, such as drought. How thermomorphogenesis integrates with water shortage conditions, where excess water loss can be detrimental, remains unclear. Here, we demonstrate that restricting water availability and mimicking drought stress with mannitol inhibit thermomorphogenesis. Mechanistically, mannitol treatment reduces high temperature-induced transcriptional activation of PHYTOCHROME INTERACTING FACTOR4 (PIF4), a central regulator of thermomorphogenesis . This suppression is contributed by the enhanced production of plant phytohormone salicylic acid (SA), which disrupts phase separation and prevents the deactivation of EARLY FLOWERING 3 (ELF3), a repressor of PIF4, at high temperatures, thereby inhibiting PIF4 activation. Our study highlights the trade-off between cooling at high temperatures and minimizing excessive water loss under water-limited conditions, providing insights into plant responses to complex environmental challenges.

overall_design: For RNA extraction, 7-day-old seedlings grown at 21°C were shifted to 27°C or kept at 21°C with or without mannitol treatment at ZT1, and seedlings were collected at ZT13. The extracted RNA was used for library preparation and sequencing

first: Danhua

last: Jiang

first: Ruitian

last: Song


title: H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells [ATAC-Seq]

overall_design: Identify the role of H3K79me and H3K36me2 in regulating chromatin accessibility.


title: H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells [RNA-Seq]

overall_design: Identify the role of H3K79me and H3K36me2 in regulating gene expression.


title: Dysregulated microRNAs in blood correlate with central nervous system neuropathology of prion disease

city: Zaragoza

first: Sonia

last: Pérez-Lázaro

address: Miguel Servet 177

institute: Universidad de Zaragoza

type: Non-coding RNA profiling by high throughput sequencing

summary: The role of microRNAs (miRNAs) in neurodegenerative diseases has gained significant attention due to their involvement in gene regulation and potential as biomarkers. In prion diseases, including scrapie, miRNAs may modulate pathogenesis and disease progression. This study investigated circulating miRNA profiles in blood of sheep naturally affected by scrapie at preclinical and clinical stages using small RNA sequencing and RT-qPCR validation. While only one novel miRNA was dysregulated in preclinical blood samples, 66 previously identified miRNAs were significantly dysregulated in clinical sheep compared to healthy ones. These miRNAs were associated with pathways commonly altered in neurodegenerative diseases, such as autophagy, ubiquitin-mediated proteolysis, and endoplasmic reticulum protein processing. Notably, miR-1271-5p, let-7f-5p, miR-186-5p, and miR-425-5p showed consistent upregulation in the central nervous system of clinical animals, replicating the results observed in blood, with an increasing trend already in the preclinical stage and a strong correlation with neuropathological prion features. Additionally, predicted target genes such as UBQLN2, PGK1, KRAS, and CLTC were inversely expressed relative to these miRNAs, supporting their regulatory roles. These findings highlight the relevance of circulating miRNAs in prion neuropathology and support further research into the specific functional roles of these miRNAs and their predictive capacity for disease progression.

overall_design: Small RNA sequencing profiling of blood from naturally scrapie-affected sheep in the preclinical stage (n=5) and clinical stage (n=10) of the disease, compared to healthy control sheep (n=10), using the Illumina HiSeq 2500 platform.

first: Inmaculada

last: Martín-Burriel

first: Luca

last: Cozzuto

first: Julia

last: Ponomarenko

first: Juan

last: Badiola

first: Rosa

last: Bolea

first: Janne

last: Toivonen


title: H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells

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

overall_design: Refer to individual Series


title: single-cell multiomics data for the developing human pelvic girdle [Multiomics]

city: Cambridge

first: Gayani

last: Senevirathne

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

summary: Human pelvic girdle, especially the ilium is considered an evolutionary novelty. To understand the genetic architecute behind the formation of this structure, we conducted single cell multiomics across developmental stages.

overall_design: Fresh ilium samples were dissected out (along with the soft tissues surrounding them) and were processed using 10X Genomics multiomics protocol. Each 10X genomics multiomics run has raw fatq files for RNA and ATAC, along with the same processed files.

first: G


title: A genome-wide in vivo CRISPR activation screen identifies BACE1 as a therapeutic vulnerability of lung cancer brain metastasis

city: Hamilton

first: Sheila

middle: K

last: Singh

state: ON

address: 1280 Main St. West

department: Surgery

country: Canada

institute: McMaster University

summary: Brain metastasis occurs in up to 40% of patients with non-small cell lung cancer (NSCLC).  Considerable genomic heterogeneity exists between the primary lung tumor and respective brain metastasis; however, the identity of the genes capable of driving brain metastasis is incompletely understood.  Here, we carried out an in vivo genome-wide CRISPR activation (CRISPRa) screen to identify molecular drivers of brain metastasis from a NSCLC patient-derived xenograft model.  We discovered activation of the Alzheimer’s disease associated -site amyloid precursor protein cleaving enzyme 1 (BACE1) led to a significant increase in brain metastasis.   Furthermore, BACE1 knockout or inhibition with MK-8931 treatment blocked NSCLC brain metastasis.  Mechanistically, we identified BACE1 cleaves an N-terminal fragment of EGFR to activate downstream signalling through MEK and ERK and drive this metastatic phenotype.  Together our data highlights the power of in vivo CRISPR screening to unveil novel molecular drivers and potential therapeutic targets of NSCLC brain metastasis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Samples include 13 NSG mouse lungs and 12 NSG mouse brains and a T0 cell pellet

first: Shawn

middle: C

last: Chafe

first: Kui

last: Zhai


title: RNA-Seq sequencing of Aspergillus fumigatus strain CEA10 at 37°C and 42°C

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology


title: single-cell multiomics data for the developing human pelvic girdle [spatial]

overall_design: Fresh ilium samples were dissected out (along with the soft tissues surrounding them), flash frozen in OCT, and were processed using 10X Genomics visium spatial transcriptomics protocol. Each 10X genomics visium run has raw fatq files and input files


title: TET1 modulates trophoblast function by regulation of ODC1 in preeclampsia

status: Public on Jul 03 2025

city: Jinan

first: Chao

last: Fan

address: No. 9-7, Jiang Shui Quan Road, Lixia District

institute: Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University

summary: Analysis of trophoblast cell line HTR8/SVneo knocking down the DNA hydroxymethylase TET1. The results provide insights into genes that undergo expression changes in trophoblast cells due to DNA hydroxymethylation.

overall_design: RNA-seq profiling of wildtype HTR8/SVneo cells and their knockdown derivatives (siTET1).

first: Yan

last: Kang

first: Zhenya

last: Fang

first: Lixia

last: Liu

first: Chunying

last: Wang

first: Man

last: Zhao

first: Li

last: Xiao

first: Changqing

last: Zhang


title: Single-cell RNA-sequencing data of human medial ganglionic eminence organoids

city: Ann Arbor

first: Jeyoon

last: Bok

state: MI

address: 2350 Hayward Street

department: Mechanical Engineering Department

institute: University of Michigan

summary: We analysed scRNA-seq data in human pluripotent stem cell-derived medial ganglionic eminence (MGE) organoids. This in vitro system recapitulates some key aspects of humam MGE development including inhibitory cortical interneuron diversification.

overall_design: scRNA-seq was performed on dissociated cells from MGE organoids derived from 3 different human pluripotent stem cell lines at day 30 and day 90. Each condition had 2 replicates.

first: Maria

last: Varela

first: Miranda

last: Walker


title: Collecting Duct Gene Expression in a Mouse Vasopressin-Excess Model without Hyponatremia

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary: Introduction. States of vasopressin excess can exist either with or without hyponatremia, depending on water intake. Here, we set up a mouse model of vasopressin-excess without hyponatremia to address the consequences of vasopressin excess that are independent of serum sodium. Methods. A mouse vasopressin-excess model was created by infusing desmopressin for 5 days without a forced water load. Control mice were infused with vehicle. Results. RNA-seq in microdissected cortical collecting ducts (CCDs) from vasopressin-excess mice showed significant changes in 153 transcripts including the expected increases in aquaporin-2 (AQP2) and AQP3 along with increases in several other targets of V2-receptor-mediated signaling in principal cells. In addition, there were decreases in abundances of many transcripts known to be targets of regulation by the Wnt/frizzled/β-catenin pathway. The vasopressin-excess model also manifested marked increases in phosphorylation of β-catenin at a known protein kinase A (PKA) site, viz. Ser552. CRISPR-mediated mutation of this PKA-target site in mice resulted in extensive changes in the transcriptomes of microdissected CCDs after desmopressin-infusion, heavily weighted toward increases in known transcriptional targets of the Wnt/β-catenin pathway. ATAC-seq in microdissected CCDs from DDAVP-infused mice revealed decreases in chromatin accessibility at promoters of many genes regulated in the Wnt/β-catenin pathway. Conclusion. We conclude that vasopressin-excess is associated with vasopressin/PKA-dependent repression of Wnt/Frizzled/β-catenin target gene expression, mediated in part by PKA-dependent phosphorylation of Ser552 of β-catenin. The repression is associated with decreasing chromatin accessibility in the promoter-TSS regions of target genes. The findings suggest that normonatremic vasopressin-excess is not necessarily benign.

overall_design:
Hyponatremia is quite common in hospitalized patients. A frequent cause is the syndrome of inappropriate antidiuresis (SIAD), originally described by William Schwartz and colleagues in 1957, in two patients with bronchogenic carcinoma. Studies in animals have demonstrated that in SIAD, hyponatremia requires two causal elements: an unregulated source of antidiuretic hormone (either arginine vasopressin or some other antidiuretic substance) and excess water intake. Consistent with the latter element, restriction of water intake has been found to be an effective means of treatment in many SIAD patients. Other therapeutic approaches include treatment with vaptans or urea, which alter water balance by increasing free water excretion. Such therapies can eliminate or reduce the hyponatremia, but do not likely eliminate the source of excess antidiuretic hormone. A relevant question in this context is, “Does antidiuretic hormone excess without hyponatremia have physiological consequences?” If so, mere correction of the hyponatremia in SIAD may not restore normality. To begin to address the question, we have set up a vasopressin-excess model without hyponatremia in mice by continuous infusion of the vasopressin analog, dDAVP (desmopressin). We focus on changes in gene expression in the cortical collecting duct (CCD), employing RNA-seq in microdissected CCD segments.
WT and MT ("PKA-target-site β-catenin S552 mutation").

first: Hiroaki

last: Kikuchi

first: Adrian

last: Rafael Murillo-de-Ozores

first: Shuo-Ming

last: Ou

first: Euijung

last: Park

first: Chin-Rang

last: Yang

first: Viswanathan

last: Raghuram

first: Shaza

last: Khan

first: Chung-Lin

last: Chou

first: Mark

middle: A

last: Knepper


title: Diverse roles of SERPINE1 in regulating cellular proliferation and invasion

city: Tianjin

first: Jing

last: Mo

state: Tianjin

address: 22 Qixiangtai Road, Heping District

department: Pathology

institute: Tianjin medical university

summary: SERPINE1 is involved in various biological processes, but its roles in promoting or suppressing tumorigenesis remain controversial. To understand the underlying mechanisms, we focused on the effects of SERPINE1 downregulation on cell phenotypes, particularly proliferation and invasion, across three types of tumors. High SERPINE1 levels in breast cancer (BRCA) and low-grade glioma (LGG) were associated with poor prognosis. In contrast, elevated SERPINE1 levels in skin cutaneous melanoma (SKCM) correlated with better outcomes. SERPINE1 knockdown resulted in increased xenograft growth in the melanoma cell line C918. This was characterized by the promotion of the cell cycle through the modulation of minichromosome maintenance protein expression and the activity of p53 and SMAD3. In breast cancer cells (MDA-MB-231) with SERPINE1 knockdown, there was decreased xenograft growth and cell proliferation, attributed to a reduction in the uPAR-mediated ERK/p38 activity ratio. With SERPINE1 knockdown, both C918 and MDA-MB-231 cells demonstrated reduced invasion capabilities, decreased matrix metalloproteinase (MMP) activity, and reduced lung metastasis. In low-grade glioma cells (H4), SERPINE1 knockdown led to decreased cell proliferation due to a reduction in the HSP90-mediated ERK/p38 activity ratio. However, it increased invasion and MMP activity, particularly of MMP-1, regulated by the HSP90-p38 axis. Collectively, our findings reveal that SERPINE1 exerts diverse effects on cell proliferation and invasion through context-dependent mechanisms. These results suggest that targeting SERPINE1 may offer personalized therapeutic strategies to enhance treatment precision and reduce adverse effects.

overall_design: RNA-seq profiling of  MDA-MB-231, H4 and C918 cells and their stably knockdown derivatives (shSE1)

first: Wei

last: Wang

first: Pengfei

first: Qiang

last: Huang


title: Chromosomal tethering and mitotic transcription promote ecDNA nuclear inheritance

city: New York

first: John

last: Maciejowski

state: NY

department: Molecular Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: Extrachromosomal DNA (ecDNA) are circular DNA bodies that play critical roles in tumor progression and treatment resistance by amplifying oncogenes across a wide range of cancer types. ecDNA lack centromeres and are thus not constrained by typical Mendelian segregation, enabling their unequal accumulation within daughter cells and associated increases in copy number. Despite intrinsic links to their oncogenic potential, the fidelity and mechanisms of ecDNA inheritance are poorly understood. Here, we show that ecDNA are protected against cytosolic mis-segregation through mitotic clustering and by tethering to mitotic chromosome ends. High fidelity nuclear segregation of MYC-amplifying ecDNA depends on BRD4 transcriptional co-activation and mitotic transcription of the long non-coding RNA PVT1, which is co-amplified with MYC in colorectal and prostate cancer cell lines. Disruption of ecDNA mitotic clustering through BRD4 inhibition, PVT1 depletion, or inhibiting mitotic transcription results in cytosolic mis-segregation, ecDNA chromosomal reintegration, and the formation of homogeneously staining regions (HSRs). We propose that nuclear inheritance of ecDNA is facilitated by an RNA-based mechanism that clusters ecDNA during mitosis and protects against cytosolic missegregation and chromosomal reintegration.

overall_design: HiC-sequencing data of asynchronous or mitotic COLO320-DM, COLO320-HSR, or HCT116 cells.

first: Ashley

last: Nichols

first: Yujin

last: Choi

first: Roshan

last: Norman

first: Yanyang

first: Josefine

last: Striepen

first: Eralda

last: Salataj

first: Eleonore

last: Toufektchan

first: Richard

last: Koche


title: Multiple long-range cis interactions generate CTCF insulator-dependent viral chromatin domains in quiescent HSV-1 genomes

city: Burlington

first: Seth

last: Frietze

address: 149 Beaumont Avenue

institute: University of Vermont

summary: In cellular genomes, CTCF insulators impact transcription over small distances in a one-dimensional manner and over much longer distances in a three-dimensional manner by maintaining chromatin loops.  We have previously shown that the latent HSV-1 genome contains CTCF insulators that function to regulate lytic transcription of adjacent genes in a one-dimensional manner.  Here, we test the hypothesis that HSV-1 CTCF insulators nucleate chromatin loops to regulate the expression of distance separated gene regions through three-dimensional organization of viral genomes. We used 4C-seq methods to identify multiple long-range cis interactions in HSV-1 genomes that generate viral chromatin domains, including those nucleated by the viral CTCF insulator CTRL2.  Deletion of the CTRL2 insulator disrupted these viral chromatin domains. Loop-nucleating interactions were quantitated with a novel approach (UMI-4C-seq) that utilizes unique molecular identifiers to label and count chromatin interactions associated with specific viewpoint primers.  Cis-interaction peaks across four different viewpoints were quantified. Viral genomes lacking CTRL2 displayed more cis-interaction peaks and wider ranges of interaction lengths compared to wt virus, suggesting altered chromatin organization.  Furthermore, differential looping analysis showed viral genomes lacking CTRL2 displayed a more transcriptionally permissive chromatin environment. Thus, the CTRL2 insulator functions as a critical regulator of long-range chromatin interactions and its deletion reshapes the viral chromatin landscape, leading to a more accessible and dynamic regulatory environment that may influence HSV-1 transcriptional programs and latency-associated chromatin states.

overall_design:
4C-seq analysis using bait sequences designed to target different regions of the HSV-1 genome.
UMI-4C analysis using bait sequences designed to target different regions of the HSV-1 genome.

first: Frietze

last: Seth


title: Cataloging the potential functional diversity of Cacna1e splice variants using long-read sequencing

city: Boston

first: Shamsuddin

last: Bhuiyan

address: 60 Fenwood Rd, 7006, Hale

institute: Harvard Medical School and Brigham & Women's Hospital

summary: The degree to which alternative RNA splicing influences the function and structure of voltage gated calcium channel (VGCC) splice variants is poorly understood. Here we used long-read RNA-sequencing to catalog rat Cacna1e (Cav2.3) splice variants, and computationally prioritize which are likely to impact channel function. We sequenced Cacna1e transcripts from rat thalamus using Oxford Nanopore sequencing yielding the structure of 2,110 Cacna1e splice variants. Of these, up to 154 had the potential encode for a functional channel based on predicted amino acid sequences. Our analysis revealed a total of 31 cassette splicing events (in various combinations) potentially affecting channel function, with three cassette exons appreciably expressed and conserved.

overall_design: We characterized the splicing profile for Cacna1e using ONT RNA-seq data from the rat thalamus

last: Tyson

first: Terrance

last: Snutch

first: Paul

last: Pavlidis


title: NSD1 heterozygosity disrupts fetal growth and neonatal survival and placental abnormalities in mice

city: saga

first: Musashi

last: Kubiura-Ichimaru

country: Japan

institute: Saga university

summary: This study investigates the developmental consequences of Nsd1 haploinsufficiency in mice. NSD1 is a histone methyltransferase that catalyzes H3K36me2 and plays a key role in transcriptional regulation during development. Although homozygous deletion of Nsd1 results in embryonic lethality, the phenotypic impact of heterozygosity has remained unclear. We demonstrate that Nsd1+/- embryos are present at Mendelian ratios during gestation but exhibit significantly reduced survival within 48 hours after birth. Nsd1+/- fetuses display reduced body weight, increased placental weight, and decreased global H3K36me2 levels in the brain and placenta. Histological analysis reveals expansion of the placental junctional zone, and transcriptomic profiling indicates broad gene expression changes without enrichment of specific gene ontologies. These findings suggest that Nsd1 heterozygosity leads to subtle epigenetic and structural abnormalities during late gestation that impair neonatal adaptation and viability

overall_design: To examine the role of NSD1 in late fetal development and perinatal viability, we performed transcriptomic analyses of Nsd1+/- and wild-type (Nsd1+/+) mouse embryos at embryonic day 19.5 (E19.5).


title: Dual roles of fibroblast-epithelial crosstalk in acute and chronic lung injury

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

summary: Dysfunctional interactions between fibroblasts and epithelial cells contribute to the progression of chronic lung diseases, including idiopathic pulmonary fibrosis. Our findings showed that chronic epithelial damage initiates a bidirectional fibrotic cascade between the epithelium and lung fibroblasts, leading to further epithelial damage and the release of pro-fibrotic mediators. Conversely, our transcriptomic and proteomic analyses highlighted that, in the context of acute epithelial injury, a protective signaling environment merges that mitigates further damage. We observed that epithelial cells shift their metabolism towards increased aerobic fatty acid metabolism, promoting healing and repair. By delineating secreted regulators responsible for inducing these positive responses, we identified pentraxin 3 (PTX3) as a top hit harboring antifibrotic characteristics.

overall_design: To explore the interplay between epithelial cells and fibroblasts in the human lung following injury, we developed a coculture system utilizing mature, differentiated primary small airway epithelial cells (SAECs) in an air-liquid interface and primary human lung fibroblasts (LFs). We investigated in two distinct scenarios that mimic chronic and acute injuries. In the chronic injury model, SAECs pre-treated with TGF-β1 for 14 days (tSAECs) were employed, which were subsequently co-cultured with LFs or as monocultures for an additional 3 days in the presence of the stimulus. Conversely, no prior injury was induced in the acute model (nSAECs), but cells were cultivated, before the initiation of the coculture and TGF-β1 treatment.

first: Marie-Therese

last: Bammert

first: Ines

last: Kollak

first: Coralie

last: Viollet

first: Huy

middle: Q

last: Le


title: The Epigenetic Regulator PHF16 Redresses Homeostasis During Intestinal Injury Repair

city: Incheon

first: Ik Soo

last: Kim

address: Gaetbeol-ro, Yeonsu-gu

institute: Gachon University college of Medicine

summary: The intestinal stem cells (ISCs) are highly vulnerable to DNA damage, being in a constant state of proliferation1. Reserve crypt stem cells restore homeostatic intestinal epithelium following damage-induced ablation of ISCs2-5. Here, we report that the epigenetic regulator PHD finger protein 16 (PHF16) redresses revival stem cell (revSC) activity after damage repair. Phf16-/Y mice showed defects in exit from the regenerative state of revSCs and failed in intestinal crypt regeneration, while they still induced revSCs in response to tissue damage, as observed using single-cell RNA-sequencing. RNA-sequencing and ATAC-sequencing analyses of Phf16-/Y intestinal organoids revealed that PHF16 controls intestinal epithelial differentiation by promoting HBO1-mediated histone H3K14 acetylation, while PHF16 also counteracts YAP/TAZ activity by ubiquitination of CDC73, faithfully reverting damage-induced revSCs to homeostatic gut epithelial cells. Together, our findings demonstrate the importance of timely suppression of regenerative activity by PHF16 for the restoration of gut homeostasis after acute tissue injury.

overall_design:
ATAC-Seq: Comparative chromatin accessibility profiling analysis of assay for transposase-accessible chromatin using sequencing (ATAC-seq) in WT and Phf16-/Y intestinal organoid cells on Day1-3.
RNA-Seq: Comparative gene expression profiling analysis of RNA-seq data for WT and Phf16-/Y intestinal organoid cells on Day1-3.

first: Ik

first: Sung

last: Baek

first: Jun-Yeong

last: Ahn


title: Meiotic cohesin Rec8 imposes fitness costs on fission yeast gametes to drive evolution of parental bias in gene expression

city: Lausanne

first: Aleksandar

last: Vjestica

state: Vaud

address: Genopode Building, University of Lausanne

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: Differences between partner gametes, which evolved repeatedly in unicellular and multicellular eukaryotes, are central to biological phenomena such as non-Mendelian inheritance and sexual selection1–4. How functional asymmetries first emerge between equivalent partners is poorly understood due to limited experimental evidence. Here, we report that in the isogamous fission yeast Schizosaccharomyces pombe, partner P- and M-gametes differentially invest into zygotic development by making unequal amounts of the conserved meiotic cohesin Rec85. Driven by asymmetric partner communication, P-gametes produce Rec8 before fertilization to promote meiotic fidelity and production of viable spores in zygotes. However, this early Rec8 expression also causes genomic instabilities6 and imposes a fitness cost on P-gametes, revealing a trade-off between sexual success and gamete survival. Using biologically parametrized model and experimental evolution, we show that the Rec8 costs and benefits drive selection for biased parental investment and evolution of mating populations. Our work dissects a molecular mechanism that selects for functional gamete asymmetries in an isogamous species, providing rare experimental evidence for an early step in the evolution of gamete dimorphism.

overall_design: Heterothallic wild-type strains that produce only one gamete type and thus arrest as unmated cells (NMWT) or homothallic fus1Δ mutants, which arrested as mated pairs (F1), were grown exponentially in liquid MSL+N media and then diluted to density of O.D.600 = 1 and incubated at 30°C with 200 rpm agitation for 5 hours. The starved cells were collected by centrifugation, ~2·107 cells concentrated into 20 μL of media and spotted onto MSL-N solid media. After 10 hours of incubation at 25°C, mating efficiency reached approximately 80% and 6 mating spots (~1.2·108 cells) were harvested using inoculation loops, per biological replica (triplicates), for RNA extraction.

first: Celso

last: Martins

first: Harry

last: Booth

first: Clàudia

last: Salat-Canela

first: Zena

last: Hadjivasiliou

last: Vještica


title: Synovial Dysregulation in Ankle Osteoarthritis: Molecular Insights and Pathogenetic Pathways [RNA-Seq 1]

city: Aurora

first: Julia

last: Matthias

state: Colorado

department: Orthopedic Surgery

institute: University of Colorado - Anschutz Medical Campus

summary: Osteoarthritis (OA) of the ankle is a debilitating condition that impacts almost 20% of adults in the United States. Little is known about the tissue, cellular and molecular basis of the disease, nor is the contribution of the synovium to the disease process understood. Here, we aimed to examine the gene expression profile of the synovium in ankle OA to uncover unique biological pathways altered in this condition.

overall_design: Patients undergoing joint replacement surgery of the ankle OA (n=26) and patients suffering an ankle fracture with either no evidence of OA or early-stage disease (n=8) were recruited, and provided synovial biopsies. Bulk RNA sequencing was performed on these tissues to identify differentially expressed genes.

first: Sara

last: Buckley

first: Michael

last: David

first: Cheryl

last: Ackert-Bicknell

first: Joshua

last: Metzl

first: Daniel

last: Moon

first: Courtney

last: Grimsrud

last: Zuscik

first: Kenneth

last: Hunt


title: Co-Conservation of Synaptic Gene Expression and Circuitry in Collicular Neurons

city: Charlottesville

first: Yuanming

last: Liu

state: Virginia

address: Gilmer Hall

department: Biology Department

institute: University of Virginia

summary: we compared the molecular and cellular organization of superior colliculus in mice, tree shrews, and humans. Our findings reveal that the SC has evolved by conserving neuron subtypes, synaptic genes, and circuitry, while diversifying ciliary gene expression and an inhibitory neuron subtype

sample_organism:
Mus musculus
Tupaia belangeri

platform_organism:
Mus musculus
Tupaia belangeri

overall_design: The sSC was micro-dissected approximately by knife cuts, processed into a single-nuclei suspension and prepared for sequencing with 10X Chromium Next GEM 3’ reagent kit v3.1 according to the manufacturer’s protocol

first: John

last: McDaniel

first: Chen

last: Chen

first: Lu

last: Yang

first: Arda

last: Kipcak

first: Elise

last: Savier

first: Alev

last: Erisir

first: Jianhua

last: Cang

middle: N

last: Campbell


title: Molecular signatures of hyperexcitability and lithium responsiveness in bipolar disorder patient neurons provides alternative therapeutic strategies

city: Montreal

first: Guy

last: Rouleau

state: Quebec

address: 3801 Rue University

department: Neurology

institute: McGill University

summary: Bipolar Disorder (BD) is a chronic psychiatric illness affecting ~3% of the global population. It is one of the top 10 causes of disability and mortality worldwide, largely due to high suicide, cardiovascular, and metabolic comorbidity. Typically, BD has life-long presentation characterized by alternations of extreme mania and depression, associated with psychosis and self-harm. Given the complex heritability and symptoms of BD, long term clinical management of some patients remains unsatisfactory. Thus, there is a major unmet need for new clinical treatment strategies and drug options to help these patients. Lithium (Li) remains the gold standard mood stabilizer and first-line treatment for manic/depressive episodes, reducing suicide and overall mortality rates. Two major questions stand out i) how Li is effective, and ii) why for only a subset of patients? To address this, we studied the biology and lithium effects in iPSC-derived neurons from people with a known clinical and genetic profile, comparing healthy individuals, BD Li-responders, and BD Li-non responders. We combined cell imaging, electrophysiology, biochemistry, , phosphoproteomic and whole transcriptome sequencing approaches to provide mechanistic insights and guide the search for BD biomarkers and Li responsiveness.

overall_design:
To identify cellular processes underlying hyperexcitability in BD neurons, and effects of Li that are general or specific to BD LR neurons.
we performed whole transcriptome sequencing from all patient lines. iPSC-derived neurons of Ctl vs. BD, and BD LR vs. BD LNR -/+ Li were compared. Data from 4-5 lines per group/condition.

first: Anouar

last: Khayachi

first: Malak

last: Abuzgaya

first: Yumin

first: Chuan

last: Jiao

first: Kurt

last: Dejgaard

first: Lenka

last: Schorova

first: Anusha

last: Kamesh

first: Yuting

last: Cousineau

first: Nargess

last: Farangdoost

first: Charle-Etienne

last: Castonguay

first: Boris

last: Chaumette

first: Martin

last: Alda

last: A Rouleau

first: Austen

last: Milnerwood


title: Effect of chronic social defeat stress (CSDS) on gene expression in wild-type mice and in Neurensin-2 knockout mice.

city: Jerusalem

first: Hadas

last: Hovav

address: Hadassah Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

summary: CSDS is a robust model of depression with a detective behavioral effect. In prior studies, we established  that the deletion of Neurensin-2, a vesicular protein, confers resilience in this model. The distinctive behavioral effect of CSDS stems from underlying molecular stress-induced changes, including changes in gene expression. To understand the mechanism in which deletion of Neurensin-2 confers resilience, we analysed the stress-induced changes in gene expression within each genotype.

overall_design:
To investigate the stress-induced gene expression changes, we harvested hippocampi from wild-type and Neurensin2 -knockout mice, at base line and after CSDS. 5 for control and 6-7 after CSDS
On the RNA, which was extracted from the hippocampi lysates,  we preformed sequencing, gene expression profiling and pathway analysis.

first: Gali

last: Umschweif


title: The m6A demethylase FTO regulates TNF-α expression in human macrophages following Toxoplasma gondii infection

city: Nanjing

last: gao

state: Jiangsu

address: Longmian Street num101

institute: Nanjingmedicaluniversity

type: Methylation profiling by high throughput sequencing

summary: Toxoplasma gondii (T. gondii) is an opportunistic parasite. After infection, macrophages finely regulate the immune response to restrict parasite proliferation. It is well-known that N6-methyladenosine (m6A) plays a critical role in fine-tuning gene expression. To investigate whether m6A modification is involved in regulating the anti-infection immune response in macrophages against T. gondii, this study utilized T. gondii tachyzoites from the RH strain to infect human THP-1 macrophages. qPCR and ELISA results showed that T. gondii infection mounted the expression of TNF-α. RNA-seq profiling showed that T. gondii infection was associated with difference in genes from pathway associated with TNF signaling. Expression of m6A regulators were evaluated using qPCR and Western blotting. T. gondii infection increased the abundance of m6A methyltransferase WTAP and demethylase FTO. Joint analysis of RNA-seq and m6A-seq data was utilized for enriching differentially expressed genes with significantly altered m6A modifications. After T. gondii infection, the m6A levels of genes associated with TNF signaling were significantly altered. In this study, we found that m6A methylation involved in T. gondii infection induced TNF-α expression.

overall_design: In this study, T. gondii RH strain tachyzoites were utilized to infect THP-1 macrophages, forming the infected group, while untreated macrophages served as the control group. Following the extraction of RNA from both groups of cells, a portion was retained as the input sample. The IP assay was then employed to isolate the m6A fragment from both the control and infected groups. These RNA fractions containing m6A fragments were then employed as IP samples for the control and infected groups.

first: Min

last: Qin

last: Gao

first: Jierui

last: Sun

first: Shuqing

last: Lin

first: Tingting

last: Hu

first: Xinjian

last: Liu

first: Rong

last: Zhang

first: Yong

last: Wang

first: Jingfan

last: Qiu


title: Nucleation-dependent propagation of Polycomb modifications emerges during the Drosophila maternal to zygotic transition

city: Evanston

first: Shelby

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

summary: The manuscript associated with these datasets seeks to address the timing of acquisition of chromatin modifications associated with Polycomb group (PcG) function during the maternal-to-zygotic transition of Drosophila melanogaster. PcG modifications including mono- and tri-methylation of Histone H3 at Lysine 27 (H3K27me1, me3) and ubiquitylation of H2A at lysine 118 (H2Aub) were measured by ChIP-seq in precisely staged embryo collections spanning large scale zygotic genome activation (ZGA), over nuclear divisions NC13 and three timepoints in NC14 (NC14-early, -mid, and -late). Additionally, marks associated with active transcription, including mono- di- and tri-methylation of Histone H3 at Lysine 4 (H3K4me1, me2, me3), RNA Pol2 phosphorylated at serine 5 of the C-terminal domain heptapeptide repeats, and acetylation of Histone H3 at Lysine 27 (H3K27ac) were measured at NC14. We additionally measured genomic localization of the H3K27me3 methyltransferase, Enhancer of zeste (E(z)), and of three factors known to bind Polycomb Response Elements, Pho, Combgap, and GAGA-Factor (GAF), by generating GFP chimeras to these proteins using CRISPR/Cas9 and performing ChIP against the GFP tagged proteins. Data for these GFP-ChIP-seq localization experiments is from embryos collected during NC14. To test for the contribution of DNA binding factors to the establishment of PcG modifications, we additionally measured deposition of H3K27me3 in embryos where GAF was sequestered from nuclei using Jabba Trap (JT-GAF), and measured H3K27me3, H2Aub, E(z), and RNA Pol2 in embryos from zelda mutant germline clones staged at mid-NC14.  Negative control ChIP-seq datasets are provided in the form of anti-GFP ChIP in wild-type embryos that express no GFP tagged protein.

overall_design: The samples deposited here break down into three general experimental groups. 1) Developmental Timecourse Data for wild-type embryos staged from NC13 through three timepoints of NC14 (E = early, M = mid, L = late), for H3K27me1, H3K27me3, and H2Aub. These experiments are supported as well by measurements for H3K4me1, H3K4me2, H3K4me3, RNAPol2, and H3K27ac measurements collected only at NC14. 2) Localization experiments for GFP-tagged E(z), Pho, Cg, and GAF, all staged at NC14. 3) Measurement of GAF localization and H3K27me3 deposition comparing GFP-GAF and Jabba-trap sequestered GFP-GAF (JT-GAF). 4) Measurement of H3K27me3, H2Aub, RNA Pol2, and E(z) localization in zelda germline clone embryos staged at mid-NC14. The negative control experiment is a ChIP using the anti-GFP antibody in wild-type embryos. Data are provided as original paired-end FastQ files (PE75 or PE150). Peaks lists for E(z), Pho, GAF, and Cg, plus computed Polycomb Domains are provided as well as counts-per-million normalized coverage plots (bigwig) for merged replicates for all key comparisons. Two or more independent biological replicates were measured for each condition. Several genotypes represent wild-type embryos in this study. For the negative control experiment, w[1118] embryos were used. Fluorescent markers were included to help stage embryos, and these are otherwise wild-type strains. The fluorescent markers are RpA70-EGFP and His2Av-RFP. RpA-70-EGFP was favored in all cases except when the desired ChIP target was also EGFP tagged, in which case His2Av-RFP was used instead.

first: Natalie

last: Gonzaga-Saavedra

first: Eleanor

last: Degen

first: Isabella

middle: V

last: Soluri

first: Corinne

last: Croslyn


title: The impact of cancer cachexia on skeletal muscle gene expression in mice.

first: Zhiqiang

last: Huang

address: Hankou 22

department: Medical School

institute: Nanjing University

summary: Here, we investigate the systematic impact of tumor cachexia on muscle function. From a nutritional supplementation perspective, we examine the influence of fatty acid metabolism on the cachectic state, revealing that dietary supplementation with high-fat diet does not alleviate the muscle and fat dysfunction induced by tumors but instead accelerates muscle degradation. Utilizing RNA-seq transcriptome data from muscle tissue, we identify metabolic abnormalities in muscle during cachexia, with the PDK4 gene being activated initially and showing significant enrichment of PPARδ targets. We find that inhibiting PDK4 can mitigate the cachectic state and observe a relationship between the activation of muscle PDK4 and PPARδ during cachexia. This is supported by epigenomic data revealing that PDK4 is a transcriptional target gene of PPARδ in muscle. Activation and mechanical modulation of PPARδ in vivo significantly impact muscle atrophy caused by cachexia. Our research suggests that targeting PPARδ could serve as a therapeutic drug target for tumor cachexia.

overall_design: Utilize RNA-seq to investigate the transcriptome profile in muscle mediated by C26 cells.

first: Li

last: Li

first: Hongwei


title: RNA-seq of small intestinal tuft cells from naïve or H. polygyrus-infected mice

city: Beijing

first: Jiali

address: Hai Dian

institute: Tsinghua University

summary: We explored the tuft cell transcriptomics  based on their temporal expression patterns during helminth infection, and identified candidate transcriptional factors associated with the regulation of type 2 immunity.

overall_design: EpCAM+ SiglecF+ small intestinal tuft cells were sorted  at time points 0, 6, 14 days post H. polygyrus infection, and were sent our for RNA-seq library construction.


title: Enrichment of ornithine decarboxylase degron transduced colorectal cancer cells for extended application of cancer stem cell models

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Cancer stem cells (CSCs) are present in small quantities in tumor populations. To permit various analyses of CSCs, we attempted to enrich and expand ornithine decarboxylase (ODC) degron-transduced colorectal cancer (CRC) cells, which retain low proteasome activity. ZsGreen fluorescence-positive (ZsGreen+) cells were collected by sorting the ODC degron-transduced HCT116, DLD1, and SW480 cells, which were defined as enriched ZsGreen+ cells. ZsGreen+ cells still maintained CSC properties. These cells had higher stem cell marker expression and increased resistance to chemotherapy with 5-fluorouracil and oxaliplatin. ZsGreen+ HCT116 and DLD1 cells had greater sphere-forming ability and enhanced tumorigenicity compared to ZsGreen- control cells. Time-lapse microscopy showed that a single enriched ZsGreen+ HCT116 cell had asymmetric cell division. Thus, model CSCs were acquired in sufficient quantity. Using these cells, we performed a comprehensive microRNA analysis; miR-491-3p was a candidate to suppress cancer stemness. Finally, we found that up-regulated genes in the enriched HCT116 ZsGreen+ cells correlated with those up-regulated in human clinical spheroid samples established from patient-derived xenografts derived from CRC tissue samples, further supporting the acquisition of enriched model CSCs. These cells would be useful in identifying novel CSC markers and developing medicine for anti-CSC therapy.

overall_design: RNA-sequencing analyses were performed in two types of cell lines (ZsGreen- HCT116 cells and ZsGreen+ HCT116 cells).

first: Ryo

last: Ikeshima

last: Okuzaki

first: Hirofumi

last: Yamamoto


title: Defining an NK cell-enriched rejection-like phenotype in liver transplant biopsies from the INTERLIVER study

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

institute: University of Alberta

summary:
Background: Initial analysis of liver transplant biopsies in the INTERLIVER study (#NCT03193151) using rejection-associated transcripts failed to find an antibody-mediated rejection state (i.e. rich in NK cells and with interferon-gamma effects). We recently developed an optimization strategy in lung transplants that isolated an NK cell-enriched rejection-like state (NKRL) that was molecularly distinct from T cell-mediated rejection (TCMR). Here we apply the same strategy to a liver transplant biopsy population.
Results: The full model classified 765 biopsies into the following molecular phenotypes, characterized by their gene expression: No-rejection (NR) 54%; TCMR 16%; NKRL 13%; and Injury 16%. Top TCMR transcripts were expressed in effector T cells; top NKRL transcripts were almost exclusively expressed in NK cells; and both had increased IFNG-inducible transcripts, which were more pronounced in TCMR. Most TCMR biopsies had significant parenchymal injury, molecular fibrosis, and abnormal biochemistry. NKRL biopsies had no excess of injury, fibrosis, or biochemistry abnormalities.
Conclusions: Optimized rejection algorithms indicate that some liver transplants manifest an NKRL state that is well-tolerated in the short-term postbiopsy and with minimal injury and relatively normal biochemistry, while also underscoring the potential of TCMR to produce extensive parenchymal injury.

overall_design: Methods: We used this strategy to search for a molecular NKRL state in 765 consented liver transplant biopsies collected at participating international centers for both gold-standard histology and molecular assessment by genome-wide microarrays. Validation through a training set-test set approach of an optimized selection of variables as inputs into unsupervised rejection classification identified an NKRL state in livers. 326 out of 763 samples are from GSE193135.


title: RNA-seq of sorted small intestinal tuft cells from naïve and Spib-deficient mice

summary: Genes significantly unregulated in Spib-deficient tuft cells included those associated with type 2 immune responses or induced by type 2 immune stimuli.

overall_design: EpCAM+ SiglecF+ small intestinal tuft cells were sorted  from naïve WT and Spib-deficient mice, and were sent our for RNA-seq library construction.


title: Gene expression profile at single embryo level of 0-3h old hybrid Drosophila embryos

city: Grand Rapids

first: Adelheid

last: Lempradl

state: Michigan

address: 333 Bostwick Ave NE

department: Metabolism and Nutritional Programing

institute: Van Andel Institute

summary: We used single-embryo RNA-sequencing (RNA-seq) to characterize early zygotic gene expression in Drosophila. To assess the accurate transcriptional activation for zygotic genes, we analyze the paternal allele expression as embryos initially contain trace amounts of paternal mRNAs delivered by the sperm. For this purpose, we used two genetically different lines from the Drosophila Genetic Reference Panel (DGRP) with known genetic variations in our crosses (males/DGRP_352, females/DGRP_737). The data provide a continuous timeline of transcript levels and allele-specific gene expression during early development (≤ 3 hours) in Drosophila melanogaster. Deposited RNA-seq data is part of a multi-'omics approach and prior metabolite extraction was performed in each sample.

overall_design: RNA from single Drosophila embryos was isolated and used for library preparation by a modified CelSeq2 single-cell RNA-seq protocol. Next, we performed pseudo-temporal analysis on the single-embryo RNA-seq data to get a high-resolution, time-resolved picture of transcriptional events during early embryonic development. To get allele-specific gene expression, we performed variant calling on the hybrid offspring by a modified GATK’s workflow retaining only known and biallelic SNPs annotated to a single gene. Finally, we match our pseudo-time analysis with the allele-specific gene expression in each embryo. Note: the normalized reads in pseudo-time order that are provided as supplementary file include 8 unfertilized eggs (prefix U) which should be excluded when exclusively analyzing  embryo development (n=245 embryos, prefix E).

first: J

last: Perez-Mojica

first: Kin

middle: H

last: Lau


title: RAPID-SELEX identifies high-affinity RNA targets for chromatin binding proteins PARP1 and MeCP2

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Recent studies showed that some chromatin-binding proteins also interact with RNA to regulate gene expression. Poly (ADP-ribose) polymerase 1 (PARP1) and Methyl-CpG Binding Protein 2 (MeCP2) are two chromatin-associated, DNA-binding proteins with central roles in gene expression, DNA damage response, and epigenetic regulation. PARP1 and MeCP2 both have RNA binding properties, but it is still unclear how PARP1 and MeCP2 are recruited to or recognize RNA binding sites. Here, we used a RAPID-SELEX procedure, a random 70-mer RNA library, and 12 rounds of selection to identify high-affinity PARP1 and MeCP2 RNA targets. PARP1 prefers RNA targets enriched in guanine, while MeCP2 shows a preference for targets enriched in cytosine. However, neither protein seems to have a consensus (linear) RNA sequence motif. Instead, high-affinity PARP1 targets contain intrinsic secondary structures characterized by a relatively long stem and small loop. High affinity MeCP2 targets are also intrinsically structured, characterized by a large loop (or bulge) and multiple stems. These data suggest that both proteins target RNAs based on (unique) structural features rather than nucleotide sequence, and that many different RNA sequences can adopt similar structures.

overall_design: Two replicate groups were obtained for PARP1 and MECP2 each. RNA sequences were obtained for 3 RAPID-SELEX rounds (R3, R8, R12) per replicate group for each protein.

first: Manana

last: Melikishvili

first: Kalpani

last: De Silva

first: Darrell

last: Chandler

first: Hejer

last: Dhahri

first: Kalina

last: Andreeva

first: Yvonne

last: Fondufe-Mittendorf


title: Prenatal benzene exposure in mice alters offspring hypothalamic development predisposing to metabolic disease in later life

summary: Maternal exposure to environmental contaminants during pregnancy poses a significant threat to a developing fetus, as these substances can easily cross the placenta and disrupt the neurodevelopment of offspring. Specifically, the hypothalamus is essential in the regulation of metabolism, notably during critical windows of development.An abnormal hormonal and inflammatory milieu during development can trigger persistent changes in the function of hypothalamic circuits, leading to long-lasting effects on the body’s energy homeostasis and metabolism. We recently demonstrated that gestational exposure to clinically relevant levels of benzene induces severe metabolic dysregulation in the offspring. Given the central role of the hypothalamus in metabolic control, we hypothesized that prenatal exposure to benzene impacts hypothalamic development, contributing to the adverse metabolic effects in the offspring. C57BL/6JB dams were exposed to benzene at 50 ppm in the inhalation chambers exclusively during pregnancy (from E0.5 to E19). Transcriptomic analysis of the exposed offspring at postnatal day 21 (P21) revealed hypothalamic changes in genes related to metabolic regulation, inflammation, and neurodevelopment exclusively in males. Moreover, the hypothalamus of prenatally benzene-exposed male offspring displayed alterations in orexigenic and anorexigenic projections, impairments in leptin signaling, and increased microgliosis. Additional exposure to benzene during lactation did not promote further microgliosis or astrogliosis in the offspring, while the high-fat diet (HFD) challenge in adulthood exacerbated glucose metabolism and hypothalamic inflammation in benzene-exposed offspring of both sexes. These findings reveal the persistent adverse effects of prenatal benzene exposure on hypothalamic circuits and neuroinflammation, predisposing the offspring to long-lasting metabolic health conditions.

overall_design: C57BL/6JB pregnant dams were exposed to benzene (50 ppm) or filtered air (control) for 6 hours per day (6h/day) from E0.5 to E19. The data contain samples from litters of 3 different dams per condition. We determined the sex at P21 before sacrificing the offspring, however the sex of two male (OBMH20, OBMH4) and two female (OBFH14, OBFH5) mice had been misassigned. Ultimately, we used expression of Xist RNA to assign the biological sex to each of the samples.

first: Lisa

last: Koshko

first: Marianna

last: Sadagurski


title: Tafazzin-Deficient Zebrafish Display Mitochondrial Dysfunction and Metabolic Defects Without Myopathy

city: Cleveland

first: Usua

last: Oyarbide

address: Cleveland Clinic, Lerner Research Institute NE6-205

institute: Cleveland Clinic

summary: Barth syndrome is a rare X-linked syndrome characterized by cardiomyopathy, skeletal myopathy, and neutropenia. This life-threatening disorder results from loss of function mutations in TAFAZZIN, which encodes a phospholipid-lysophospholipid transacylase located in the mitochondria inner membrane. Decreased cardiolipin levels and increased monolysocardiolipin levels perturb mitochondrial function. However, the mechanism(s) leading to myopathies and neutropenia are unknown, and there is currently no effective therapy for Barth syndrome. To address these knowledge gaps, we generated tafazzin-deficient zebrafish. Neutropenia developed as early as 5 days post-fertilization, but surprisingly no cardiac or skeletal myopathies were detected into adulthood. Yet, mitochondrial dysfunction in tafazzin mutants led to decreased ATP production. Metabolomic analysis revealed notable changes, including increased levels of lactic acid, decreased glucose, and widespread effects on amino acid and unsaturated fatty acid synthesis. Despite these metabolic disturbances, the zebrafish displayed a normal lifespan and fertility. Cardiolipin abnormalities were detected in both larvae and adult tissues, specifically in the heart and whole kidney marrow. Surprisingly, adult tafazzin mutants exhibited a higher number of neutrophils compared to wildtype fish. Further investigation revealed signs of inflammation as evidenced by elevated levels of il6 in the whole kidney marrows and hearts of adult fish. Our comprehensive studies demonstrated that while mitochondrial dysfunction and metabolic defects were evident in tafazzin-deficient zebrafish, these disturbances did not significantly affect their development nor survival. These findings suggest that zebrafish may possess salvage pathways which compensate for Tafazzin loss or that humans have a unique vulnerability to the loss of TAFAZZIN.

overall_design: RNA was extracted from pools of 25 larvae at 5 dpf using TRIzol reagent. Three pools of maternal zygotic tafazzin mutants and 3 pools of wild-type from the same clutch were compared. RNA quality was determined by Bioanalyzer (Agilent)

first: Seth J

last: Corey


title: 3'UTR-dependent activity of transcription factors and chromatin regulators [RNA-seq]

status: Public on Jul 02 2025

city: New York

first: Yang

last: Luo

address: 408 E 69th St

department: Cancer Biology and Genetics

institute: Sloan Kettering Institute

summary: Over 2700 human mRNAs have highly conserved 3'UTRs, but their biological functions are unknown. These mRNAs enrich for transcriptional regulators. Therefore, we performed RNA-seq to determine the roles of 3'UTRs in controlling the cellular activity of selected transcriptional regulators, here MYC and UTX.

overall_design: RNA-seq profiling of U2OS or MCF7 cell lines transfected with cDNA vectors encoding the transcription factor MYC or the histone demethylase UTX. Gene expression profiles were compared to control, after each protein was expressed from an mRNA template that only contained the coding sequence (-NU) or that contained the coding sequence and its full-length 3'UTR (-U).

first: Mervin

last: Fansler

first: Christine

last: Mayr


title: scRNAseq analysis of kidney treated with GLS1 inhibitor [scRNA-seq Kid_BPTES]

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

institute: IMSUT

summary: We employed the Chromium GEM-X single-cell RNA sequencing platform by 10x Genomics to investigate the effects of the GLS1 inhibitor, BPTES, on the kidney single-cell transcriptome of 19- to 20-month-old wild-type male mice. Previous studies have identified GLS1 as a potential senolytic reagent capable of eliminating senescent cells. Our aim was to determine which cell populations are selectively removed by GLS1 inhibition in aged mice and to assess how this intervention alters intercellular interactions across different cell types.

overall_design: After administering BPTES or DMSO (vehicle control) to 19-month-old male mice for one month, we harvested the kidneys and dissociated the tissue using a Liberase-based enzymatic digestion protocol. The resulting single-cell suspension was then subjected to fluorescence-activated cell sorting (FACS) for cell collection prior to library preparation.

first: Yuki

middle: T

last: Okamura

first: Makoto

last: Nakanishi