title: Locally-Directed Morphogenesis Enabling Engineered hPSC Embryoids for Robust Symmetry Breaking

city: Vancouver

first: Marina

last: Bockaj

address: 2222 Health Sciences Mall

institute: University of British Columbia

summary: Controlling the modality of the morphogen BMP4 controls and alters the gene expression and developmental trajectory within hPSC embryoids.

overall_design: Three different modalities of BMP4 (localized, immbolized BMP4 with no BSA, localized, immobilized BMP4 with BSA, and global BMP4 distrubuted in media) were tagged with 3 hashing antibodies (TotalSeq™-B0251,B0252,B0253 anti-human Hashtag 1,2,3) and analyzed using scRNA sequencing using 10X genomics

first: Tiam

last: Heydari

first: Peter

middle: W

last: Zandstra

first: Yale

middle: S

last: Michaels


title: Top2a Differentially Modulates Promoter Activity in Embryonic Stem Cells via Trim28 Recruitment and PRC2 Displacement [ChIP-Seq]

status: Public on Mar 01 2025

city: Guangzhou

first: Mangmang

last: Li

state: Baiyun District

address: 1023 Shatai South Road

country: China

institute: Southern Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: High levels of the type II topoisomerase α (Top2a) play a crucial role in maintaining the stemness of embryonic stem cells (ESCs). However, the mechanisms governing Top2a's ESC-specific function remain largely unknown. Here, using an unbiased proteomic approach, we discovered Trim28, along with subunits of various chromatin remodeling complexes and modifiers, among the top interactors of Top2a on ESC chromatin. We demonstrate that Top2a directly interacts with Trim28 in an ESC-specific manner. Functionally, Trim28 can promote Top2a expression, and synergize with Top2a in maintaining stemness of ESCs as well as promoting induced pluripotent stem cells (iPSCs) generation. Genome-wide approaches reveal that Top2a-Trim28 co-regulated genes contribute to glycolysis and self-renewal, and Top2a fine-tunes promoter activity by recruiting Trim28 to co-activated genes and displacing PRC2 to co-repressed genes. Remarkably, targeting Top2a in combination with Trim28 in breast cancer stem cells shows an extremely synergistic anti-tumorigenic effect. Therefore, Top2a collaborates with Trim28 in ESCs to fulfill its cell type-specific functions, which may highlight the therapeutic strategy of combinational targeting of Top2a and Trim28 to combat cancer stem cells.

overall_design: To invextigate the influence of Trim28 knockdown or Top2a knockdown in mESC (R1/E) cell line, we established R1/E cell lines where Trim28 has been knocked down by shRNA or Top2a has been knocked down by siRNA.

first: Lei

last: Wang

first: Sisi

last: Xu

first: Lu

last: Chen

first: Liu

last: Yang

first: Zeyou

last: Qiu

first: Weiping

last: Huang

first: Yizhou

last: Wu

first: Le

last: Hu

first: Xiaochun

last: Bai

first: Jing

first: Kuangyu

last: Yen


title: Top2a Differentially Modulates Promoter Activity in Embryonic Stem Cells via Trim28 Recruitment and PRC2 Displacement [RNA-Seq]

type: Expression profiling by high throughput sequencing


title: Top2a Differentially Modulates Promoter Activity in Embryonic Stem Cells via Trim28 Recruitment and PRC2 Displacement [ATAC-Seq]


title: Comparison of transcriptional changes in regenerating mice livers at baseline and 24-48 hours post 70% partial hepatectomy with or without etomoxir treatment

city: Beijing

first: Runping

last: Liu

state: Beijing

address: 11 Beisanhuandonglu

institute: Beijing University of Chinese Medicine

summary: To investigate liver transcriptomes in the proliferative stage of early liver regeneration, we here established 70% partial hepatectomy model and performed gene expression profiling analysis using data obtained from RNA-seq of regenerating livers at different time points.

overall_design: To investigate the changes of gene expression in the proliferative stage of early liver regeneration. Wild-type C57/BL6J mice were performed sham operation or 70% hepatectomy. Liver tissue was analyzed at 0, 24 and 48 hours post resection by RNA-seq, respectively. Etomoxir (12.5 mg/kg) was treated intraperitoneally 4 hours before partial hepatectomy (PHx), and an extra dose was administrated 24 hours post-PHx for mice in the 48 hours group.


title: H3K27ac CUT&Tag of regenerating liver after 70% partial hepatectomy

summary: To investigate the chromatin profiling and  transcriptional regulatory mechanism in the preparatory stage of liver regeneration, we here analyzed the genome-wide profiles of H3K27ac by CUT&Tag using control and renewal liver samples at 12 hours after surgery section.

overall_design: Wild-type C57/BL6J mice were performed sham operation or 70% hepatectomy. Liver tissue was analyzed at 0 and 12 hours post resection by CUT&Tag, respectively.


title: SMYD2 overexpression in Neonatal rat ventricular cardiomyocytes

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: From this array we would like to know the role of Smyd2 on hypoxic regulated genes mainly angiogenic pathway. We performed overexpressions of Smyd2 and beta galactosidase by adenoviral approach and knockdown of HIF1 and Smyd2 were performed by lipofectamine RNAiMAX.Cardiomyocytes were isolated from neonatal rats at P3.

overall_design: 2 groups, each with 2 biological replicates

first: Tatyana

last: Novolatyeva

first: Swathi

last: Veeroju


title: Comparison of transcriptional changes in regenerating mice livers at baseline and 3-12 hours post 70% partial hepatectomy

summary: To refine the timeframe of liver regeneration initiation and investigate the temporal characteristics of metabolic reprogramming in the preparatory stage, we here established partial hepatectomy model and performed gene expression profiling analysis using data obtained from RNA-seq of regenerating livers at different time points.

overall_design: To investigate the changes of gene expression in the preparatory phase of liver regeneration. Wild-type C57/BL6J mice were performed sham operation or 70% hepatectomy. Liver tissue was analyzed at 3, 6, 12 hours post resection by RNA-seq, respectively.


title: Heterogeneity of Purkinje cells orchestrates cerebellar development

city: Farmington

first: Nagham

last: Khouri-Farah

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

country: USA

institute: UConn Health

summary: In this study, we performed single-cell RNA sequencing of E16.5 and E18.5 mouse cerebella to analyze diversity in in Purkinje cells during development.

overall_design: Single-cell  or single-nuclei suspensions of embryonic mouse cerebellum were prepared following the protocols recommended by 10x Genomics. Subsequently, samples were processed with the 10X Genomics Chromium Kits.

first: James


title: Dense ion clouds attracted by supercharged supramolecular polymers boost development of neurons

city: Chicago

first: Matias

last: Alvarez-Saavedra

state: IL

address: 303 East Superior Street, Lurie 11-221303 East Superior Street, Lurie 11-221

department: Simpson Querrey Institute for BioNanotechnology

institute: Northwestern University

summary: Neuronal circuitry is critically dependent on the controlled transport of ions in and out of cells. We report here a strategy to supercharge a nanoscale supramolecular assembly that can harbor a huge concentration of monovalent ions which enhances neuronal development. This was accomplished by embedding a small organic cation in a negatively charged peptide amphiphile nanostructure that leads to full ionization of all monomers without destroying the supramolecular polymer. We cultured mouse and human neurons on the supercharged filaments covered by dense ion clouds and observed rapid neurite branching and functional maturation. Furthermore, rat hippocampal brain slices revealed that the dense ion clouds can increase and sustain the frequency of action potential propagation. Our study has provided a vision for the potential use of synthetic systems to boost neurotransmission.

overall_design: To investigate the molecular cascades trigerred by our ion-charged nanostructures (ICNs), we treated embryonic mouse cortical neurons with Na+ ICNs or K+ ICNs and compared their relative gene expression changes to non-charged peptide amphiphiles 72 hrs after treatment.Gene expression profiling was performed using single-end RNA-Seq data obtained from 3 biological replicates per condition.

middle: A

first: Zois

last: Syrgiannis

first: Samuel

middle: I

last: Stupp


title: Commensal myeloid crosstalk in neonatal skin regulates long-term cutaneous type 17 inflammation

city: San Francisco

first: Miqdad

last: Dhariwala

state: California

address: 513 Parnassus

institute: University of Caifornia, San Francisco

summary: Early life microbe-immune interactions at barrier surfaces have lasting impacts on the trajectory towards health versus disease. Monocytes, macrophages and dendritic cells are primary sentinels in barrier tissues, yet the salient contributions of commensal-myeloid crosstalk during tissue development remain poorly understood. Here, we identify that commensal microbes facilitate accumulation of a population of monocytes in neonatal skin. Transient postnatal depletion of these monocytes resulted in heightened IL-17A production by skin T cells, which was particularly sustained among CD4+ T cells into adulthood and sufficient to exacerbate inflammatory skin pathologies. Neonatal skin monocytes were enriched in expression of negative regulators of IL-1 pathway. Functional in vivo experiments confirmed a key role for excessive IL-1R1 signaling in T cells as contributing to the dysregulated type 17 response in neonatal monocyte-depleted mice. Thus, a commensal-driven wave of monocytes into neonatal skin critically facilitates long-term immune homeostasis in this prominent barrier tissue.

overall_design: We performed scRNA sequencing on immune cells in the skin of D15 mice that were either depleted of monocytes by treating with the anti-Gr-1 antibody (aGr1) or with an isotype control. CD45+ cells were FACS sorted from the skin of mice in each condition. Cells from 4-7 mice were pooled for each ocndition.

middle: O

first: Andrea

middle: M

last: DeRogatis

first: Joy

middle: N

last: Okoro

first: Antonin

last: Weckel

first: Victoria

last: tran

first: Irek

last: Habrylo

first: Oluwasunmisola

middle: T

last: Ojewumi

first: Allison

middle: E

last: Tammen

first: John

last: Leech

first: Geil

middle: R

last: Merana

first: Ricardo

last: Carale

first: Rio

last: Barrere-Cain

first: Kamir

middle: J

last: Hiam

first: Matthew

middle: H

last: Spitzer

first: Tiffany

middle: C

last: Scharschmidt


title: Gene expression of Ts93 under copper stress

city: Nanchang

first: kehe

last: Fu

address: RuiXiang road No.889, Nanchang Changbei Economic Development Zone

department: life of science

institute: Nanchang Normal University

summary: To investigate the copper-related genes of Ts93, we estiblished 3 treatments of Ts93.

overall_design: We  performed gene expression profiling analysis using data obtained from RNA-seq of 3 different treatment of Ts93

first: lili

last: fan


title: The underlying mechanism by which SRSF1 exerted carcinogenesis and its potential targets in CRC

city: nanjing

first: xian

last: luo

address: xianlin

institute: NJUCM

summary: An RIP experiment was performed in RKO cells using SRSF1 antibody as bait. The position of peak summit around transcript start sites of genes can predict the interaction sites of protein and gene. We compared the peak summit of  RKO WT and RKO ZCCHC7-OE cells to find the differences between RKO WT cells and RKO ZCCHC7-OE cells.

overall_design: Examination  in RKO cells.

first: Xian

last: Luo

first: Ye

last: Yang

first: Chunyang

last: Gu


title: The underlying mechanism by which ZCCHC7 exerted carcinogenesis and its potential targets in CRC

summary: An RIP experiment was performed in RKO cells using ZCCHC7 antibody as bait. The position of peak summit around transcript start sites of genes can predict the interaction sites of protein and gene. We compared the peak summit of  RKO WT and RKO ZCCHC7-OE cells to find the differences between RKO WT cells and RKO ZCCHC7-OE cells.


title: Expression data from transgenic mice with conditional deletion of CDKN2A/p16 in esophageal glandular cells

city: Washington

first: Jorge

middle: Lemos

last: Sepulveda

state: DC

address: 2300 M Street NW, Suite 700

department: Pathology

institute: George Washington University

summary:
The tumor suppressor CDKN2A Exon 1a (coding for p16) was removed in esophageal and squmous-columnar junction (SCJ) epithelial cells when tamoxifen was injected in experimental mice. Sections of the SCJ were subjected to laser capture microdissection to retain only the glandular mucosal layer. RNA was extracted and analyzed by Affymetrix Clariom D Pico assay, mouse (Thermo Fisher, Waltham, MA).
We used microarrays to identify transcriptomic changes associated with p16 knockout.

overall_design: We used 4 control mice (P16WT) and 4 experimental mice (p16KO) with p16 knocout in the SCJ.  All mice express human IL1-beta in the esophagus and were treated with bile acids to induce Barrett's-like lesions. P16 conditional knockout results from CRE recombinase (modified with estrogen receptor moieties) expressed from the LGR5 promoter, upon activation by tamoxifen injection. LGR5 derived cells include most SCJ glandular epithelial cells, therefore P16 knockout is restricted to those cells. We microdissected the


title: Human primary AoSMC treated by Y27632 and not to investigate the role of RhoA/ROCK1/YAP/F-actin in aortic dissection formation

city: Shanghai

first: Wei

last: Zhang

address: No.180 Fengling Road, Xuhui

department: Vascular Surgery

institute: Zhongshan Hospital, Fudan University

summary: Rho-kinase signaling and YAP signaling are related to aortic dissection (AD) formation. However, as important biomechanical signaling pathways, their relationships with aortic smooth muscle cell (AoSMC) mechanics have not been investigated in AD formation. This study aims to explore the correlation between RhoA/ROCK1 and YAP, as well as their relationship with intrinsic AoSMC stiffness during AD formation. The expression of RhoA/ROCK1 and YAP as well as F-actin polymerization were analyzed in AoSMCs isolated from normal and AD human aortas. The intrinsic cell stiffness of normal and AD AoSMCs was measured using atomic force microscopy (AFM). The correlations among RhoA/ROCK1, YAP, and intrinsic AoSMC stiffness were explored by manipulating the activity of RhoA and ROCK1, and YAP expression. Finally, the role of RhoA/ROCK1/YAP/F-actin and AoSMC stiffness during AD formation was studied in pharmaceutically induced AD mouse models.Compared to normal human AoSMCs, the expression of RhoA and ROCK1 was downregulated, while the phosphorylation of YAP was increased in AD human AoSMCs, coupled with impaired F-actin polymerization and decreased intrinsic cell stiffness. Pharmaceutical inhibition of RhoA or ROCK1 activities and depletion of YAP all led to impaired F-actin polymerization and decreased intrinsic AoSMC stiffness. Moreover, abnormal collagen deposition and impaired cell-ECM interactions were found when RhoA/ROCK1/YAP/F-actin signaling was inhibited in normal human AoSMCs. We further analyzed the normal human AoSMC treated by Y27632 or not using RNA sequencing to investigate the impact of RhoA/ROCK1/YAP/F-actin on AoSMCs. GO analysis showed that differentially expressed genes (DEGs) related to cAMP-mediated signaling, cytoskeleton organization, cell-matrix adhesion, and extracellular matrix (ECM) organization were affected when ROCK1 activity was inhibited by Y27632 in normal AoSMCs. KEGG analysis showed differences in PI3K-Akt signaling, focal adhesion, MAPK, actin cytoskeleton, and ECM-receptor interaction. Consistently, cAMP, actin cytoskeleton organization, and ECM structural constituents were all downregulated in AoSMCs treated with Y27632 according to GSEA. We also analyzed the downregulated genes in AoSMCs treated with Y27632. Results demonstrated that the downregulated genes were mainly related to the cell-ECM unit, PI3K, MAPK, focal adhesion, and cAMP signaling pathways.

overall_design: Experiement group: Human primary AoSMC treated by Y27632 10uM for 48h; Control: Human primary AoSMC treated by PBS as control

first: Mengxiao

last: Wang

first: Enci

last: Lu

first: Zengxia

last: Li

first: Gaofei

last: Hu

first: Qi

first: Wenxin

last: Shan

first: Yongjun

last: Dang

first: Lemin

last: Zheng

first: Lixin


title: Gene expression profile at  of  motor neurons under simulated microgravity (SMG) and normal gravity(NG)

city: 武汉市

first: yang

last: fei

address: 狮子山街道

institute: 无

summary: We differentiated motor neuron progenitor cells through small molecule combination and put them under microgravity and normal gravity respectively, and then performed gene expression profiling analysis using data obtained from RNA-seq of cells from 2 different group.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SMG cells and NG cell

first: Danxia

last: Huang

first: Fei


title: Single cell transcriptomic analysis of human retina

city: Philadelphia

first: Mingyao

state: PA

address: 423 Guardian Drive

institute: Univerrsity of Pennsylvania

summary: Single-cell gene expression profiling by high throughput sequencing

overall_design: Human retina


title: RNA Sequencing of TA Muscles from Various Mouse Models of Cachexia

city: Charleston

first: Denis

last: Guttridge

state: SC

address: 173 Ashley Ave

department: Pediatrics

institute: Medical University of South Carolina

summary: To study the differentially regulated genes in cachectic mice, we RNA sequenced the TA muscles of different mouse models of cachexia and their respective controls

overall_design: RNA Sequencing in TA muscles after tumor-bearing mice that have reached endpoint

first: Spadafora

last: Victoria

first: Guttridge

last: Denis C


title: Distinctive metabolic remodeling in TYMP deficiency beyond mitochondrial dysfunction

city: Jinan

first: Jixiang

last: Du

state: Shandong

address: Wenhua Xi road

institute: Shandong university

summary:
Purpose: Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE), a rare mitochondrial encephalomyopathy subtype, is caused by mutations of thymidine phosphorylase (TYMP). As a metabolic enzyme localized in the cytoplasm, the biological processes disturbed by TYMP functional defect are supposed to be not limited in the abnormal replication of mitochondrial DNA. This study aimed to elucidate the characteristic biological alterations and associated homeostatic regulation caused by TYMP deficiency.
Methods: Clinical evaluation and genetic analysis were performed on three patients from two independent families carrying heterozygous TYMP variants. Molecular dynamic (MD) simulation and nucleosides detection were used to investigate the pathogenicity of the variants. Plasma from patients with MNGIE and m.A3243G MELAS and healthy volunteers were analyzed by targeted and untargeted metabolomics to characterize the metabolic profiles of MNGIE. Transcriptomics analysis and bioenergetic studies were performed on skin fibroblasts from these three groups of subjects.
Results: Three novel TYMP pathogenic variants were identified in our MNGIE patients. Total 72 plasma metabolites were identified as specific alterations of MNGIE patients through comparing the differentially changed metabolites in MNGIE patients and m.A3243G MELAS patients. Beside pyrimidine metabolism, MNGIE patients showed significant changes in multiple metabolisms, such as bile acids metabolism, caffeine metabolism and steroid hormone metabolism. Despite comparable mitochondrial dysfunction existing in fibroblasts from patients with TYMP deficiency and ones with m.A3243G mutation, a distinct downregulated cholesterol metabolism and fatty acids (FAs) metabolism were revealed in the fibroblasts from MNGIE patients via multiple analysis of metabolites levels, metabolic enzymes expression, mitochondrial substrates dependency and transcription factors expression.
Conclusions: Our findings revealed a more expansive metabolic disturbance may be caused by TYMP deficiency beyond mitochondrial disfunction, extending a comprehensive understanding of the biochemical outcome of TYMP deficiency.

overall_design: mRNA profiles of skin fibroblasts from patients with MNGIE, m.A3243G MELAS and healthy controls


title: HNRNPC RIP-Seq and RNA-Sequence Analysis of si-LY6E-DT and si-HNRNPC in 231 cells

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

summary: RNA-seq was used to analyze the differential expression of mRNAs between si-LY6E-DT and si-NC 231 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for si-LY6E-DT, si-HNRNPC and RIP-HNRNPC in 231 cells.

first: Hai-ting

last: Liu

first: Sen

first: Xiang-yu

last: Guo

first: Guo-hao


title: The PKR/JNK signalling pathway promotes the palmitic acid-induced myocardial ageing phenotype via SIRT1 inactivation

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

summary: This study investigated the role and mechanism of palmitic acid (PA) in ageing phenotype changes in AC16 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AC16 cells and its Experimental group（stimulated by PA）.

first: Wenxi

first: Guoshun

first: Shuijin

first: Tianhai

last: Lin

first: Cheng

last: Peng

first: Feng


title: A pro B cell population forms the apex of the leukemic hierarchy in Hoxa9/Meis1-dependent AML

city: Hannover

first: Tobias

last: Maetzig

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary: In the murine HoxA9/Meis1 (H9M) AML model leukemic stem cell (LSC) potential lies in three different heterogeneous immunophenotypes including Lin-cKit+ progenitor cells (Lin-), Gr1+CD11b+cKit+ myeloid cells and lymphoid cells (Lym+). We performed Bulk-RNA sequencing to reveal differences in the transcriptional program between Lin- and Lym+ cells. Therefore, Lin- and Lym+ cells of secondary AML mouse bone marrow was isolated and sequenced. We could identify potential lymphoid master regulators that correlated with lymphoid cell development and presumably aggressive disease.

overall_design: In total, 6 bone marrow samples from 6 secondary transplanted HoxA9/Meis1 mice were anaylzed. 3 samples contained lymphoid leukemic stem cells (LSCs) from mice that were transplantaed with lymphoid LSCs. The other 3 samples contained Lin- LSCs from mice transplanted with Lin- LSCs

first: Anna

last: Lieske


title: Cancer Associated Histone Mutations

city: Pittsburgh

first: Benjamin

middle: Alexander

last: Nacev

address: 5117 Centre Avenue, Suite 2.6b

department: Medicine

institute: University of Pittsburgh

summary: Analysis of the effect of cancer assocaited histone mutations on gene expresison and chromatin

overall_design: Differential Gene expression between cells expressnig WT histone vs mutant histone was determined by RNA-seq


title: Single-cell RNA-sequencing of angioblasts and endothelial cells from E9.5-E11.5 mouse embryos

city: Oxford

first: Oliver

last: Stone

address: Sherrington Road

country: United Kingdom

institute: University of Oxford

summary:
Background: The formation of the lymphatic system has been a subject of controversy for over a century. Although the accepted view is that lymphatic endothelial cells originate exclusively from veins, there have been reports of non-venous derived lymphatics in multiple tissues.
Methods: We performed single-cell RNA sequencing analyses on ~20000 individual cells isolated from Pax3Cre/+;Rosa26tdTomato mouse embryos at E9.5, E10.5 and E11.5, the temporal window in which lymphatic endothelium initially emerges.
Results: These analyses revealed the existence of populations of lymphangioblasts which arise from paraxial mesoderm and directly incorporate into the lymph sacs. Our findings support the notion that lymphatic endothelial cells also have non-venous origins and explain the discrepancies between previous studies.

overall_design: Endothelial progenitors and endothelial cells were isolated from Pax3Cre/+;Rosa26tdTomato embryos at ~E9.5, ~E10.5 and ~E11.5, to define transcriptional differences between  paraxial mesoderm-derived and and non-paraxial mesoderm-derived endothelium.  Single cell gene expression was profiled using the 10x Genomics Chromium Next GEM Single Cell 3' GEM, Library and Gel Bead Kit v3.1.

first: Irina-Elena

last: Lupu


title: Mesenchymal stromal cells-derived small extracellular vesicles affect T-lymphocytes mRNA expression

city: Nes ziona

first: Batia

last: Avni

state: State*

address: 1 lotus st

country: Israel

institute: Hadassah medical center

summary: In the current research, we further study the immune-modulatory effect of bmMSCs on T cells, by mRNA sequencing of activated T cells co-cultured with bmMSC-sEVs. Methods: activated T lymphocytes were cocultured with and without bmMSC derived sEVs. mRNA profiling was performed using the QIAGEN Illumina sequencing platform. IPA® software, KEGG pathway, GSEA and STRING database were applied to analyze pathway networks and biological functions of the differentially expressed genes.

overall_design: Three batches of sEVs were isolated from three different bmMSC donor. Activated lymphocytes were isolated from one sample of buffy coat. The study evaluates acticated lymphocytes versus activated lymphocytes cocultured with three different batches of sEVs

first: Andrea

last: Fracchia

first: Drirh

last: Khare

first: Reuven

last: Or

first: Amnon

last: Buxboim

first: Boaz

last: Nachmias

first: Claudine

last: Barkatz

first: Osnat

last: Almogi-Hazan

first: Swasti

last: Tiwari

first: Polina

last: Stepensky

first: Yuval

last: Nevo

first: Hadar

last: Benyamini

first: Sharona

last: Elgavish


title: Gene changes associated with deletion of Esrrg in fast-spiking cortical neurons in mice [1735-192]

city: Birmingham

first: Rita

last: Cowell

state: AL

address: 2000 9th Avenue South

department: Neuroscience

institute: Southern Research

summary:
Purpose: The goal of this study is to understand what gene changes are associated with removal of Esrrg in parvalbumin-positive neurons from the mouse cortex using BAC-TRAP
Methods: Cortex from mice expressing the L10a transgene used for BAC-TRAP method of RNA isolation and PVcre on either WT or ESRRG flox backgrounds, 3-4 monts of age; two hemispheres/mouse were then extracted and flash frozen on dry ice. RNA was isolated using the BAC-TRAP method and samples were sent for sequencing.

overall_design: Cortical fast-spiking interneuron mRNA profiles of wildtype mice compared to mice with Esrrg deletion. All mice were expressing the L10a transgene Pvcre to enable for BAC-TRAP method of RNA-isolation.

first: David

last: Crossman


title: BioID-Esrrg Overexpresssion in SH-SY5Ys [H202SC21031899]

summary: SH-SY5Y cells were transfected with either BioID-GFP-NLS control or BioID-Flag-ERRg expressing adenoviruses and isolated with Trizol after 48 hours to compare gene expression and find potential ERRg targets specific to neuron-like cells.

overall_design: Examination of gene expression resulting from BioID-ERRg expression in SH-SY5Y cells.

first: Kathlene

last: Joyce


title: Plasma miRNA Differential Expression Analysis and miRNA-mRNA Network Construction in Patients with Acute Pancreatitis

city: TIANJIN

first: JIYU

last: SHI

address: Heping District,No.22 Qixiangtai Road

institute: Tianjin Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: In the early stages of acute pancreatitis, diagnostic sensitivity is limited and prognosis is difficult to determine. We provide a new idea for the diagnosis and prognosis of AP by studying the expression of plasma miRNAs in patients. Plasma samples from 22 normal subjects and AP patients at different stages were screened for miRNAs sequencing. A total of 27 miRNAs were found to be differentially expressed. Then we performed downstream target gene prediction for differentially expressed miRNAs. Analysising of KEGG, GO, GSEA and network interaction, it was found that its therapeutic effect was closely related to apoptosis, inflammatory response and autophagy process.

overall_design: By setting strict inclusion and exclusion criteria, plasma of 6 normal subjects and 16 patients with AP at different stages were screened. After RNA extraction from plasma samples, miRNAs were sequenced for the samples to find the differentially expressed miRNAs in AP patients, and bioinformatics analysis of differentially expressed miRNAs was performed.

first: Jiyu

last: Shi

first: Zhenwei

last: Yang

first: Ao

last: Jia

first: Xiayu

last: Wang

first: Yunfeng

last: Cui


title: Effect of Qingyi Decoction on the Treatment of Acute Pancreatitis Mice via mRNA Sequencing Analysis

summary: Acute pancreatitis (AP) is an inflammatory disease of pancreatic tissue caused by pancreatic acinar cell injury. AP treatment of Qingyi Decoction(QYD) is a widely and commonly used traditional Chinese medicine prescription. A mice model of acute pancreatitis was established and treated with Qingyi Decoction, and mRNA high-throughput sequencing was performed on the pancreatic tissue of mice treated with Qingyi Decoction for the first time. There were 4477 and 4359 differentially expressed genes in the control group compared with the model group and the Qingyi Decoction group, while there were 8 differentially expressed genes in the model group compared with the Qingyi Decoction group by analyzing the mRNA expression profiles. Analysising of KEGG, GO, GSEA and network interaction, it was found that its therapeutic effect was closely related to apoptosis, inflammatory response and autophagy process.

overall_design: Wild-type C57BL/6 mice were randomly divided into three groups. Each mouse was given once per hour for 7 intraperitoneal injections.Model group and Qingyi Decoction group were injected 50 mg/kg caerulein,and LPS was added for the last time. Control group was injected with the same amount of normal saline. Qingyi Decoction group was given medication at 0 and 8 hours after modeling，while control group and model group were treated with saline. Pancreatic tissue was taken for high throughput sequencing of mRNA 24 hours after the start of modeling.


title: Gene regulatory consequecnes of loss of Kdm1a in the kidney [RRBS]

status: Public on Feb 28 2025

city: BOSTON

first: Satya keerthi

last: Kota

state: MA

address: 188 LONGWOOD AVE HSDM REB 406

institute: HARVARD UNIV

type: Methylation profiling by high throughput sequencing

summary: Histone methyltransferases and demethylases play crucial roles in gene regulation and are vital for the proper functioning of multiple tissues. In this study, we investigated the functions of Kdm1a by employing a renal progenitor-specific deletion during kidney development and evaluated global differences in DNA methylation between control and Kdm1a conditional knockout kidneys using Reduced representation bisulfite sequencing (RRBS-seq).

overall_design: Reduced representation bisulfite sequencing for DNA methylation in Kdm1a control and conditional knockout kidneys.

first: Satya

first: Savithri

last: Balasubramanian


title: Impaired vitamin D signaling causes LMNA mutation-related cardiomyopathy

city: Tokyo

first: Shintaro

last: Yamada

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

summary: Mutations of the lamin A/C gene (LMNA) cause a variety of diseases including dilated cardiomyopathy (DCM). LMNA-related DCM often leads to severe heart failure, but the underlying pathophysiology is unknown. Here we show that vitamin D receptor (VDR) signaling is critically involved in LMNA-related DCM. We established iPS cells from DCM patients with an LMNA mutation and found that the iPS cell-derived cardiomyocytes (iPSCMs) showed remarkable DNA damage and reduced contractility compared with the isogenic control. Screening of a chemical library revealed that vitamin D2 reduced DNA damage of the mutant iPSCMs. RNA sequencing analysis showed that expression levels of putative downstream genes of VDR including DNA repair factors were downregulated in the mutant iPSCMs, which were upregulated by vitamin D2. Protein-protein interaction screening revealed that the binding of VDR to mutant LMNA was more robust than to wild-type LMNA, resulting in attenuated VDR signaling in the mutant iPSCMs. Vitamin D2 administration reduced DNA damage and improved cardiac function in pressure overload-induced heart failure mice. These results indicate that impaired DNA repair caused by reduced transcriptional activity of VDR induces cardiac dysfunction of LMNA-related DCM and suggest that VDR signaling is a potential therapeutic target for patients with DCM and heart failure.

overall_design: Bulk RNA-seq analysis in LMNA mutant iPS cell-derived cardiomyocytes.

first: Masamichi

last: Ito

first: Manami

last: Katoh

first: Tatsuro

last: Sassa

first: Mikako

last: Katagiri

first: Issei

last: Komuro


title: Second harmonic generation microscopy reveals the spatial orientation of glutamine-potentiated liver regeneration after hepatectomy

city: Tainan

first: Chih Chieh

last: Yen

address: No. 138, ShengLi Rd., North Dist.

department: Department of Oncology

country: Taiwan

institute: National Cheng Kung University Hospital

summary: Eight-week-old C57BL/6 mice underwent either 70% partial hepatectomy (PHx) or sham surgery in the absence of hepatic resection via midline laparotomy. L-glutamic acid 5-amide (Gln) was obtained from MilliporeSigma, MA, US, and mice were fed 0.6% Gln versus PBS in the drinking water starting at 7 days prior to PHx and another 6 days after Phx. Mice were randomized into four groups: 1) sham with Gln supplementation (sham + Gln), 2) sham without Gln supplementation (sham – Gln), 3) PHx with Gln supplementation (PHx + Gln), and 4) PHx without Gln supplementation (PHx – Gln).

overall_design: Liver samples were prepared for mRNA expression microarray from day 1 to day 7 post-PHx. Briefly, microarray analyses were performed using the SurePrint G3 GeneChip Mouse Gene Express V2 Array Kit (Agilent, Santa Clara, CA, US; Design ID:074809) according to the manufacturer’s protocols.


title: Transcriptional change in intestinal crypts by TLR4 activation upon radiation exposure

city: Beijing

first: Zebin

last: Liao

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine

summary:
Purpose: The activation of TLR4 was reported to effectively alleviate intestinal injury induced by irradiation (IR). The goals of this study are to investigate the transcriptome profiling (RNA-seq) of intestinal crypts thereby clarifying the underlying mechanism mediating the radio-protective activity of TLR4 on intestinal stem cells.
Methods: Intestinal crypts mRNA profiles of mice treated or untreated with TLR4 low-toxic agonist monophosphyal lipid A (MPLA) upon abdominal body irradiation (AIR) exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500 sequencer. To pre-treated the data, adaptor and low-grade reads removal, low-quality bases elimination from 3' or 5' ends, original and effective sequencing quantity analysis, as well as guanine and cytosine statistics were subjected, in turns. Differential expression genes were selected via correlation test, principal component analysis and cluster analysis, in which the fold change (FC) was greater than 2 and p value was less than 0.05 could be regarded significance. Different expressed genes (DEGs) were clustered into pathways of intestinal crypts through KEGG.
Results: As compared to the nonirradiated group, 2733 DEGs were identified in intestinal crypts after AIR damage, while there were 2168 DEGs between irradiated group and irradiated plus MPLA treatment group. Among the DEGs, a series of genes involving intestinal stem cells regeneration, which mainly falls into three stem cell related pathway according to Gene ontology analysis and KEGG enrichment: Hippo, Wnt and Notch signaling pathway. Based on these DEGs, we focused on a group of genes which was suppressed by IR, while could be restored by TLR4 activation. Based on the criteria, 8 DEGs (SOX9, cMyc, MSI1, Lgr5, Notch1, Wnt5b, Axin2, DLL4) involving intestinal stem cell regulation were further selected for validation, from which the mRNA levels of 4 genes (SOX9, YAP1, cMyc) were confirmed to be up-regulated by MPLA treatment.
Conclusions: Our study represents the first detailed analysis of intestinal crypts transcriptomes by TLR4 activation upon IR damage, with biologic replicates, generated by RNA-seq technology. And the confirmation of DEGs will facilitate the development of novel targets and techniques to efficiently stimulate the regeneration of intestinal stem cells to reconstruct the intestine after radiation injury.

overall_design: Intestinal crypts of mice treated or untreated with MPLA upon IR were collected 3 days post IR.

first: Yanyong


title: Gene changes associated with deletion of Esrrg in spiny projection neurons in mice using RNA sequencing

first: Rita

last: Cowell

summary:
Purpose: The goal of this study is to understand what gene changes are associated with removal of Esrrg in spiny projection neurons from the mouse striatum using injection of AAV for CamKcre
Methods: Striatum from mice with or without deletion of Esrrg using AAV:CamKCre were aged to 1 month, striata were extracted and flash frozen on dry ice. RNA was  isolated using the trizol method and samples were sent for sequencing.

overall_design: Striatal mRNA profiles of mice 1 month post deletion of Esrrg in the striatum compared to mice with no Esrrg deletion.

first: David

last: Crossman

first: Stephanie

last: Fox


title: The 2',3' cyclic phosphatase Angel1 facilitates mRNA degradation during human ribosome-associated quality control

city: La Jolla

first: Timothy

middle: Luis Cabrera

last: Nicholson-Shaw

address: 9500 Gilman Dr.

department: Biological Sciences

institute: University of California San Diego

summary: The Ribosome-associated Quality Control (RQC) pathway serves to resolve ribosomes stalled during the translation process and degrade the associated mRNA and nascent polypeptide. Here we identify the 2',3' cyclic phosphatase Angel1 as a rate-limiting factor in this process in human cells. Angel1 associates with proteins of the RQC pathway and with mRNA coding regions, consistent with a factor that monitors the translation process. Depletion of Angel1 causes stabilization of reporter mRNAs that are targeted for RQC by the absence of stop codons, but not an mRNA targeted for nonsense-mediated decay. Angel1 catalytic activity is critical for its function in RQC, as a catalytic inactivating mutation causes loss of RQC function. We also identify N4BP2 as the human RQC endonuclease. Given the biochemical activity of Angel1 as a 2',3' cyclic phosphatase, our observations suggest that a rate-limiting step in RQC-mediated mRNA decay is the resolution of a cyclic phosphate, possibly one generated upon N4BP2 cleavage.

overall_design: Identification of RNA sequences bound by Angel1 using enhanced cross-linking and immunoprecipitation (eCLIP) in HEK293 expressing FLAG-Angel1.

first: Tim

first: Yasmeen

last: Ajaj

first: Amit

last: Fulzele

first: Gene

last: Yeo

first: Eric

last: Bennet

first: Jens

last: Lykke-Andersen


title: Chromatin immunoprecipitation sequencing to identify KDM4A regulating signaling pathway in CRC

city: Guangzhou

first: Tanxing

last: Cai

state: Guangdong

address: 26 Erheng Road, Yuancun, Tianhe District

department: Department of General Surgery

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

summary: To explore the underlying mechanism of KDM4A mediated H3K9me3 modification in CRC. We performed Chromatin immunoprecipitation sequencing(CHIP-seq) between control CRC cells and CRC cells with KDM4A overexpression to identify KDM4A regulating signaling pathway.

overall_design: CHIP-seq profiling of control group and KDM4A overexpression group using HCT8 cells

first: Liang

last: Kang

first: Li

last: Xiong

first: Zhenxing

last: Liang


title: Epigenome-wide analysis identifies pollution-sensitive loci in fibrotic interstitial lung disease

city: Vancouver

first: Gillian

middle: Catherine

last: Goobie

state: British Columbia

address: Centre for Heart Lung Innovation, St. Paul's Hospital, 1081 Burrard Street

department: Division of Respiratory Medicine

country: Canada

institute: University of British Columbia

type: Methylation profiling by genome tiling array

summary: Rationale: Particulate matter <=2.5um (PM2.5) adversely impacts patients with fibrotic interstitial lung disease (fILD). Objective: To determine whether PM2.5-associated epigenetic alterations contribute to the environmental pathogenesis of fILD.Methods: Retrospective two-cohort study applying satellite-derived PM2.5 and constituent exposure matching to the residential location of patients with fILD. Robust linear regressions evaluated cohort-specific epigenome-wide differential blood DNA methylation with increasing pollutant exposures (Illumina MethylationEPIC BeadChip). Cox and linear regressions evaluated associations of cytosine-phosphate-guanine (CpG) loci with transplant-free survival and lung function. Wilcoxon test evaluated cartilage-associated protein (CRTAP) levels in fILD and control lungs.Results: The University of Pittsburgh (UPitt) cohort (n=306) had 5-year median PM2.5 exposures of 12.1ug/m3 compared with 5.1ug/m3 in the University of British Columbia (UBC) cohort (n=170).  Higher pollutant exposures in the UPitt cohort were associated with lower methylation at cg25354716, annotated to CRTAP, a critical extracellular matrix remodeling enzyme. Higher exposures in the UBC cohort were associated with higher methylation at cg01019301, annotated to TLN2 (talin-2), a cytoskeletal protein involved in fibroblast migration. A 10% increase in cg25354716 methylation was associated with a hazard ratio (HR) of 0.81 for death or lung transplantation in the meta-analyzed cohorts (95%CI 0.69-0.96, p=0.01), whereas the same change in cg01019301 was associated with a HR of 1.36  (95%CI 1.07-1.74, p=0.01). CRTAP protein was overexpressed more abundant in lungs tissue from patients with fILD compared with donor controls (p<0.001). Conclusions: PM2.5 is associated with altered blood DNA methylation in fILD. This work identifies novel pollution-sensitive targets that hold potential for therapeutic modulation in fILD.

overall_design: We aimed to profile the blood DNA methylation profile (Illumina MethylationEPIC BeadChip Array) from patients with various forms of fibrotic interstitial lung disease and match that with satellite-derived hybrid model estimates of PM2.5 and constituent components (pollutant data accessed from the Atmospheric Composition Analysis Group online repository: https://sites.wustl.edu/acag/datasets/surface-pm2-5/) to the residential location of these patients. Epigenome-wide association of PM2.5 and constituent exposures with differential methylation was then performed. The analysis cohort included 306 patients with fILD from the University of Pittsburgh Simmons Center for Interstitial Lung Disease cohort and 170 from the University of British Columbia ILD Registry. There was one duplicate sample removed from this dataset (patient 199) and three samples that were excluded from the analysis due to quality issues.

first: Goobie

last: Gillian C.


title: Mitochondrial calcium uniporter links acetyl-CoA metabolism and H3K27 acetylation to maintain glioblastoma stem cells [ChIP-Seq]

city: Shanghai

first: Gguangqin

last: Liu

address: No. 130 Dong-An Road

institute: Fudan university

summary: Glioblastoma stem cells (GSCs) exhibit remarkable metabolic and epigenetic adaptability, contributing to therapeutic resistance and tumor recurrence. However, the mechanisms underlying this plasticity remain incompletely understood. Here, we identify a novel metabolic-epigenetic axis centered on the mitochondrial calcium uniporter (MCU) that governs GSC fate and tumor initiation. MCU is preferentially expressed in GSCs, and its knockdown significantly impairs GSC self-renewal and viability. Mechanistically, MCU enhances mitochondrial calcium uptake, promoting acetyl-CoA production via pyruvate dehydrogenase activation, which drives histone H3K27 acetylation at the TRIB3 locus to sustain stemness programs. In glioblastoma patients, higher MCU expression is correlated with increased acetyl-CoA levels, elevated H3K27 acetylation, enhanced TRIB3 expression, higher tumor grade, and poorer survival. Pharmacological inhibition of MCU with Berberine suppresses GSC growth and extends survival in mice. These findings establish MCU as a critical link between mitochondrial metabolism and epigenetic regulation, highlighting its potential as a therapeutic target for glioblastoma.

overall_design: ChIP-seq of H3K27ac in glioblastoma stem cells with shRNA-induced silencing of MCU.

first: Guangqin

first: Haoqian

last: Zhang

first: Siqi

last: Chen

first: Jiayi

first: Xin

last: Pan


title: Effect of depletion of Olfml3 on macrophage function

first: Qijun

last: Yu

state: Shanghai

address: 227 South Chongqing Road

institute: Shanghai Jiaotong University School of Medicine

summary: To inveestigate the role of Olfml3 knockout in two different macrophage cell lines (RAW264.7 and BMDM)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Olfml3+/+ and Olfml3-/- cells

first: Hong

last: Mei

first: Qian

last: Gu

first: Ran

last: Zeng

first: Yanan

last: Li

first: Junjie

first: Chenxu

last: Gao

first: Hai

last: Fang

first: Jieming

last: Qu

first: Jia


title: Epithelial Muscarinic Receptor 3 Ablation Induces Sex-Specific Modulation of Colonic Intestinal Progenitor Cells and Response to Intestinal Injury [586CW]

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Klinikum rechts der Isar

summary: In this study, we investigated regional and sex differences in the cholinergic modulation of intestinal epithelial cells in homeostasis and regeneration. Genetic intestinal epithelial ablation of the M3R employing Vil-Cre x M3R fl/fl mice interestingly resulted in the prominent reduction in Lgr5-expressing progenitor cells in male tissues, contrasting an expansion of these cells in the female intestinal epithelium. This prominent difference showed abrogated in young female mice with reduced circulating sex hormone levels. M3R ablation further induced the expansion of pEGFR+ tuft cells and induced the activation of the PI3K/Akt pathway. Importantly, sex-specific differences in Lgr5-expressing progenitor cells translated into the development of severe inflammation in male Vil-Cre x M3R fl/fl mice subjected to an acute colitis model, which did almost not affect female Vil-Cre x M3R fl/fl mice. In addition, sex-specific effects of modulations of cholinergic signaling on epithelial cells could be corroborated in murine and human colonoids. Collectively, our data reveal regional and sex differences in the cholinergic, muscarinic modulation of intestinal epithelial cells.

overall_design: Bulk gene expression data are presented for epithelial cells following treatment with Bethanechol (n=8) or no treatment (n=8) grown in female (n=4) and male (n=4) human colonic organoids.

first: Mohab

last: Ragab

first: Caroline

last: Waldherr Ávila de Melo

first: H. Carlo

first: Moritz

last: Middelhoff


title: Epithelial Muscarinic Receptor 3 Ablation Induces Sex-Specific Modulation of Colonic Intestinal Progenitor Cells and Response to Intestinal Injury [JW468]

overall_design: Bulk gene expression data are presented for sorted Lgr5-EGFP+ cells following treatment with Bethanechol (n=8) or no treatment (n=8) grown in female (n=4) and male (n=4) murine colonic organoids from Lgr5-IRES-eGFP-CreERT2 mice.


title: KCTD20 suppression mitigates excitotoxicity in tauopathy patient organoids

city: Los Angeles

first: Joshua

last: Berlind

address: 1425 San Pablo St

institute: University of Southern California

summary: Excitotoxicity is a major pathologic mechanism in patients with tauopathy and other neurodegenerative diseases. However, the key neurotoxic drivers and most effective strategies for mitigating these degenerative processes are unclear. Here, we show that glutamate treatment of induced pluripotent stem cell (iPSC)-derived cerebral organoids induces tau oligomerization and neurodegeneration, and that these phenotypes are enhanced in organoids derived from tauopathy patients. Using a genome-wide CRISPR interference (CRISPRi) screen, we find that suppression of KCTD20 potently ameliorates tau pathology and neurodegeneration in glutamate-treated organoids and mice, as well as in transgenic mice overexpressing mutant human tau. KCTD20 suppression reduces oligomeric tau and improves neuron survival by activating lysosomal exocytosis, which clears pathological tau. Our results show that glutamate signaling can induce neuronal tau pathology and identify KCTD20 suppression and lysosomal exocytosis as effective strategies for clearing neurotoxic tau species.

overall_design:
ASO-treated wildtype, isogenic, and MAPT V337M mutant organoids were collected 3 or 6 days after glutamate treatment for scRNA seq. Conditions were multiplexed to save on cost.
Please note that processed data generated from both replicate (e.g. *A*B*.gz files) are linked to the corresponding first replicate '*glut 1' sample record.

first: Justin

middle: K

last: Ichida


title: Gene regulatory consequecnes of loss of Kdm1a in the kidney [ChIP-Seq]

first: Satya keerthi

last: Kota

summary: Histone methyltransferases and demethylases play crucial roles in gene regulation and are vital for the proper functioning of multiple tissues. In this study, we investigated the functions of Kdm1a by employing a renal progenitor-specific deletion during kidney development and evaluated global differences in H3K9 trimethylation between control and Kdm1a conditional knockout kidneys using Chromatin Immunoprecipitation DNA sequencing (ChIP-seq).

overall_design: Chromatin immunoprecipitation DNA sequencing for H3K9me3 in Kdm1a control and conditional knockout kidneys.

first: Satya Keerthi

first: Savithri

last: Balasubramanian


title: Targeting PLK1-CBX8-GPX4 axis overcomes BRAF/EGFR inhibitor resistance in BRAFV600E colorectal cancer via ferroptosis

first: zhan

last: zhao

address: 613 West Huangpu Avenue, Tianhe District

department: department of general surgery

institute: The First Affiliated Hospital of Jinan University

summary: Metastatic BRAFV600E colorectal cancer (CRC) confers poor prognosis and represents a therapeutic bottleneck. To identify resistance mechanisms of the mitogen-activated protein kinase (MAPK) pathway in BRAFV600E CRC, we perform genome-wide CRISPR-Cas9 screening and discover that targeting glutathione peroxidase 4 (GPX4) overcomes resistance to BRAF inhibitor (BRAFi) combined with or without epidermal growth factor receptor inhibitor (EGFRi) in BRAFV600E CRC. Specifically, BRAFi ± EGFRi upregulates GPX4 expression, which antagonizes therapy-induced ferroptosis. Moreover, polo-like kinase 1 (PLK1) substrate activation promotes PLK1 translocation to the nucleus, activating chromobox protein homolog 8 (CBX8) phosphorylation at Ser265 to drives GPX4 expression. Targeting PLK1 enhances BRAFi ± EGFRi inhibition and triggers ferroptosis in vitro, vivo, organoid, and patient-derived xenograft model. Collectively, we demonstrate a PLK1–CBX8–GPX4 signaling axis that relays the ferroptosis mechanism of therapeutic resistance and propose a clinically actionable strategy to overcome BRAFi ± EGFRi resistance in BRAFV600E CRC.

overall_design: To identify targets involved in response to BRAFi ± EGFRi, the genome-wide CRISPR knockout screening in BRAF V600E cell line HT-29 were performed

first: Zhan

last: Zhao

first: Jiashuai

last: He

first: Shenghui

last: Qiu

first: Lu

last: Wang

first: Shuchen

last: Huangfu


title: Using transcriptomics data and Adverse Outcome Pathway networks to explore endocrine disrupting properties of Cadmium and PCB-126

city: Stockholm

first: Linus

last: Wiklund

address: Nobels väg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

summary: Omics-technologies such as transcriptomics offer valuable insights into toxicity mechanisms. However, integrating this type of data into regulatory frameworks remains challenging due to uncertainties regarding toxicological relevance and links to adverse outcomes. Current assessments of endocrine disruptors (EDs) relevant for human health require substantial amounts of data and primarily rely on standardized animal studies. Identifying EDs is a high priority in the EU, and so are efforts to replace and reduce animal testing. Alternative methods to investigate EDs are needed, but there is also a lack of health risk assessment methodology that supports regulatory uptake of novel mechanistic information. This study aims to utilize Adverse Outcome Pathways (AOPs) to integrate transcriptomics data for identifying EDs, by establishing a link between molecular data and adverse outcomes. Cadmium (Cd) and 3,3',4,4',5-pentachlorobiphenyl (PCB126) were used as model compounds due to their observed effects on the endocrine system, but not yet being identified as EDs in the EU regulatory setting. Estrogen, androgen, thyroid and steroidogenesis (EATS)-related AOPs were extracted from AOPWiki to generate an AOP network. RNA sequencing (RNA-Seq) was conducted on zebrafish (Danio rerio) embryos exposed to Cd or PCB126 for 4 days. RNA-Seq data were then linked to the AOP network by connecting Gene Ontology biological process (GO BP) terms from the experimental data to key events in the network. Enrichment Maps in Cytoscape and the QIAGEN Ingenuity Pathway Analysis (IPA) software were also used to identify potential ED properties and support the assessment. Potentially EATS-related GO BP terms were identified for both compounds. A lack of accurate standardized terms in KEs of the AOP network hindered a data-driven mapping approach. Instead, manual mapping of GO BP terms onto the AOP network revealed more connections, underscoring the need for harmonizing AOP development for regulatory use. IPA results further supported potentially EATS-related effects of both compounds. Evidence from the Enrichment Maps revealed perturbations of several biological functions, which may be related to either EATS or non-EATS endocrine mechanisms. While AOP networks show promise in integrating RNA-Seq data, several challenges remain. Future research should focus on further developing this methodology to improve the use of mechanistic data in risk assessments. Standardizing AOP development to include accurate GO terms is crucial for enabling automatic integration of transcriptomics data through AOPs.

overall_design: To investigate the effects of cadmium or 3,3',4,4',5-pentachlorobiphenyl (PCB126) on zebrafish embryos. The embryos were exposed to cadmium or PCB126 at three different doses each, from 1dpf to 5 dpf. At 5 dpf, RNA-seq was performed.

first: Emma

last: Wincent

first: Anna

last: Beronius


title: The transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activation

first: Clara

last: Hermant

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells (IES)

institute: Helmholtz Zentrum Munich

summary: The regulatory circuitry of cell-specific transcriptional programmes is thought to be influenced by transposable elements (TEs) whereby TEs serve as raw material for the diversification and genome-wide distribution of genetic elements that contain cis-regulatory elements. However, the transcriptional activators of TEs in relevant physiological contexts are largely unknown. Here, we undertook an evolutionary approach to identify regulators of two main families of MERVL, a major regulator of transcription during early mouse development. Using a combination of phyloregulatory, transcriptomics and loss-of-function approaches we demonstrate that SRF is a novel regulator of MERVL and of embryonic transcription during zygotic genome activation. By resolving the phylogenetic history of two major MERVL families, we delineate the evolutionary acquisition of SRF and DUX binding sites and show that the acquisition of the SRF site precedes that of DUX. SRF contributes to embryonic transcription through the regulation of MERVLs, which in turn serves as promoter for host genes. Our work identifies new transcriptional regulators and TEs that shape the gene expression programmes in early embryos and highlights the process of TE domestication via the sequential acquisition of transcription factor binding sites and co- evolution with the host.

overall_design: Mouse embryos (zygotes) were microinjected with a dominant negative construct of SRF (SRF-LOF), antisense oligos against DUX (DUX-LOF) or in combination (DOUBLE LOF), cultured until the late 2-cell stage and collected for Smart-Seq+5' an adapation protocol of Smart-Seq2

first: Carlos

last: Mourra-Díaz

first: Maria-Elena

last: Torres-Padilla


title: Gene expression profile at single cell level of kidneys from RGMb flox/flox Lyz2 cre (RGMb mKO) & Lyz2 cre (Ctrl) mice with or with cisplatin (20mg/KG body weight for 72h)

city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

summary: Macrophages are considered as an important cell population during kidney injury. We used single cell RNA sequencing (scRNA-seq) to analyze the different population of macrophage in the injury kidney.

overall_design: Whole kidney single cell suspension from the Ctrl and mKO mice with or without indicated cisplation treatment analyzed using scRNA-seq

first: Yin

last: Xia

first: Yonglun

last: Kong


title: miRNA differential expression and miRNA-mRNA network construction in mice with acute pancreatitis

first: JIYU

last: SHI

summary: Acute pancreatitis (AP) is an inflammatory disease of pancreatic tissue caused by pancreatic acinar cell injury. However，its miRNA expression is not clear.A mouse model of acute pancreatitis was established by the establishment of Caerulein and LPS, high throughput miRNA sequencing was performed on the pancreatic tissues of mice in the normal group and model group. We found 25 miRNAs with relatively significant differential expression by analyzing the miRNA expression profile. Then we performed downstream target gene prediction for differentially expressed miRNAs. Analysising of KEGG, GO, GSEA and network interaction, it was found that its therapeutic effect was closely related to apoptosis, inflammatory response and autophagy process.

overall_design: Wild-type C57BL/6 mice were randomly divided into two groups. Each mouse was given once per hour for 7 intraperitoneal injections.Model group  were injected 50 mg/kg caerulein,and LPS was added for the last time. Control group was injected with the same amount of normal saline.Pancreatic tissue was taken for high throughput sequencing of mRNA 24 hours after the start of modeling.

first: Jiyu

last: Shi

first: Ao

last: Jia

first: Zhenwei

last: Yang

first: Xiayu

first: Yunfeng

last: Cui


title: The role of phagocyte NADPH Oxidase (NOX2) in modulating the antimicrobial and inflammatory functions of mouse neutrophils

city: Columbus

first: Xin

state: OH

address: 700 Children's Dr,

department: The Kidney and Urinary Tract Center

institute: Nationwide Children's hosptial

summary: Urinary tract infections (UTI) stand as one of the most prevalent infections worldwide. Uropathogenic Escherichia coli (UPEC) is the primary cause of UTI, instigating 75% of uncomplicated and 65% of complicated UTIs. Innate immune cells play pivotal roles in eliminating invading uropathogens and represent a potential therapeutic target for UTI prevention and treatment. Previous studies in our laboratory demonstrated that selective depletion of neutrophils during experimental UTI, results in an uncontrolled infection and augmented bladder and kidney pathologies. However, the exact antimicrobial mechanisms employed by neutrophils to eliminate multi-drug resistant uropathogens, such as UPEC, and resolve UTI remain poorly understood. Our dataset provides insight of the multifaceted role of neutrophil NOX2 in UPEC elimination and regulation of inflammatory and effector functions of these innate immune cells. Our transcriptome analyses revealed a heightened pro-inflammatory profile in NOX2-deficient neutrophils compared to WT neutrophils after UPEC stimulation.

overall_design: To investigated the role of NOX2 in modulating neutrophil functions against uropathogenic E coli (UPEC). We harvested neutrophils from wilde-type (WT) and NOX2 KO (Cybb-/-) mice. Isolated neutrophils were stimulated with UPEC or PBS (vehicle) and total RNA was extracted from these cells to perform gene expression analysis.

first: Israel

last: Cotzomi

first: Juan

last: de Dios Ruiz Rosado


title: 4D marmoset brain map reveals MRI and molecular signatures for onset of multiple sclerosis–like lesions [spatial transcriptomes]

city: Bethesda

first: Daniel

middle: S

last: Reich

state: Maryland

address: 10 Center Drive Bldg 10 Rm 5C103

department: NINDS

institute: NIH

summary: Abstract: The cellular and molecular dynamics of multiple sclerosis (MS) lesion development and repair cannot be inferred through study of postmortem tissue harvested decades after lesion onset. Employing MRI-informed spatiotemporal RNA profiling and experimental autoimmune encephalitis (EAE) in the common marmoset — a faithful model for these processes — we identified five microenvironmental groups pertinent to neural function, immune and glial responses, tissue destruction and repair, and regulatory networks at brain borders during lesion evolution. Before visible demyelination, astrocytic and ependymal secretory signals delineated perivascular and periventricular regions, later becoming demyelination hotspots where MS-like lesions frequently grow. An MRI biomarker, the ratio of proton density-weighted signal to T1 relaxation time, captured the hypercellularity phase before apparent myelin destruction. At lesion onset, there was a global shift in cellular connectivity, especially in extracellular matrix-mediated signaling. Early responses included microglia and oligodendrocyte precursor cell proliferation and diversification, replaced by monocyte derivatives and lingering lymphocytes as lesions aged. Concurrent with demyelination, reparative signaling modules were found at the lesion edge as early as 10 days post-lesion establishment. Over-representation of senescence-associated secretory phenotype at the brain borders and the formation of concentric glial barriers at the lesion edge prompted model-based identification of potential treatments to reverse EAE-associated molecular pathology. Our study highlights the marmoset platform's potential for assessing MS treatment outcomes.

overall_design: From 11 marmosets, we derived a transcriptomic map with spatial and single-nucleus resolution and studied the heterogeneity of tissue damage at an individual lesion level. We developed a 10x Visium-compatible staining protocol to quantitatively integrate 16 regions of interest (ROI) and spatiotemporally dissect the significance of focal and global molecular changes as lesions evolve. Mapping the temporal sequence of cellular and molecular changes during lesion evolution, we retrospectively estimated lesion age through serial MRI (Methods). To pinpoint the cellular source of spatially resolved signals, we integrated single-nucleus RNA-seq (snRNA-seq) libraries (n = 43) from 8 animals with spatial transcriptomes (ST) (n = 16 ROI) from 6 animals. WM from healthy control (n = 13) and WM with T2-hyperintense demyelinated MRI features from EAE animals (n = 14) were the most extensively sampled groups. We used additional categories, including normal-appearing WM from EAE animals (n = 2), Gd-enhancing demyelinating WM lesions (n = 2), and resolved WM lesions that were no longer T2-hyperintense on the terminal MRI (n = 3), to group the remaining WM samples. In parallel, we included leukocortical T2-hyperintense lesions (n = 2) along with matching healthy (n = 2) and normal-appearing (n = 1) control tissue, and abnormal-appearing lateral geniculate nucleus tissue on MRI (n = 2) along with matching healthy control tissue (n = 2), to explore tissue-specific and shared responses. We implemented a hierarchical workflow comparing across cell classes (Level 1 analysis, L1) and cell clusters within a class (Level 2 analysis, L2) to better realize the source of each profile change.

first: Jing-Ping

last: Lin

first: Alexis

last: Brake

first: Maxime

last: Donadieu

first: Amanda

last: Lee

first: Ginger

last: Smith

first: Kevin

last: Hu

first: Govind

last: Nair

first: Riki

last: Kawaguchi

first: Pascal

last: Sati

last: Geschwind

first: Steven

last: Jacobson

first: Dorothy

middle: P

last: Schafer


title: Gene regulatory consequecnes of loss of Kdm1a in the kidney [RNA-Seq]

first: Satya keerthi

last: Kota

address: 188 LONGWOOD AVE HSDM REB 406

institute: HARVARD UNIV

summary: Histone methyltransferases and demethylases play crucial roles in gene regulation and are vital for the proper functioning of multiple tissues. In this study, we investigated the functions of Kdm1a by employing a renal progenitor-specific deletion during kidney development and evaluated global differences in gene expression between control and Kdm1a conditional knockout kidneys using RNA sequencing (RNA-seq).

overall_design: Bulk RNA sequencing for H3K9me3 in Kdm1a control and conditional knockout kidneys.

first: Satya

first: Savithri

last: Balasubramanian


title: Genome-wide methylation profiles of semen samples (human)

city: Seoul

first: Hwan Young

address: 103, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University College of Medicine

summary: In this study, 56 semen samples were collected from healthy Korean males aged 18 to 70 and data was obtained utilizing the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA) at Macrogen Inc. (Macrogen, Seoul, Korea).

overall_design: DNA methylation profiling of 56 semen samples was conducted using the Infinium MethylationEPIC

first: Ji Eun


title: Effect of overexpression of cleavage/polyadenylation factor CFIm25 on monocyte-macrophage differentiation

city: Boston

first: Srimoyee

last: Mukherjee

address: 150 Harrison Ave., Jaharis Bldg., Room #401A

department: Department of Developmental, Molecular & Chemical Biology

institute: Tufts University

summary: Macrophages play a crucial role in our body’s development and tissue repair and protect against microbial attacks via cytokine secretion or phagocytosis. A previous study in our lab revealed a crucial role for regulation of mRNA 3' end cleavage and polyadenylation (C/P) in monocyte to macrophage differentiation. Among the various C/P factors involved, the subunit CFIm25 showed a striking increase at an early time point upon treatment of monocytes with the differentiating agent Phorbol Myristate Acetate (PMA), suggesting that CFIm25 may promote this process. To study its role in macrophage differentiation, CFIm25 was overexpressed in the HL-60 and THP-1 monocytic cells, followed by PMA-mediated differentiation. Both cell lines showed a significant increase in macrophagic characteristics and a decrease in monocytic features. Cell cycle was slowed down, accompanied by a greater decrease in the proliferation markers PCNA and cyclin D1 coupled with increased 3’UTR lengthening of cyclin D1 mRNA. Since alternative polyadenylation (APA) could be greatly affected by manipulating CFIm25, we performed mRNA 3' end-focused sequencing to reveal changes in the global APA landscape during differentiation and after CFIm25 overexpression. Among the genes whose 3’UTRs were shortened, TAB2 and TBL1XR1 which are known positive regulators of the NF-κβ signaling pathway, underwent shortening followed by increased protein expression compared to the control. Examination of other components of the NF-κβ pathway showed an increase at earlier time in NF-κβ-p50 and phosphorylated NF-κβ-p65 and in the NF-κβ, targets p21, Bcl-XL, ICAM1 and TNF-α upon CFIm25 overexpression There was also an increase in the shorter isoforms of NF-κB1 mRNA that encodes the NF-κβ p50 precursor. Depletion of CFIm25 suppressed the NF-κβ pathway, as evident by lengthening of TAB2, TBL1XR1, and NF-κB1 mRNAs accompanied by decreased expression of TAB2, TBLXR1, and the NF-κβ proteins. In conclusion, our study supports a model in which CFIm25 accelerates the monocyte to macrophage transition by promoting APA events which lead to activation of the NF-κβ pathway.

overall_design: To determine the effects of CFIm25 on global PAS usage during macrophage differentiation, we used the QuantSeq 3' mRNA-sequencing method which can provide information on differential APA events. PolyA+-selected RNA samples from HL-60 cells overexpressing CFIm25 and control cells after 6 h of PMA treatment were sequenced and analyzed to identify changes in isoform usage.

first: Luyang

last: Wang

first: Bin

last: Tian


title: Tissue-Specific Determinants of Adaptive NK Cell Responses - Spleen vs Liver NK

city: New York

first: Endi

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary:
Natural killer (NK) cells are circulating lymphocytes that possess both innate and adaptive features, the latter including antigen-specific clonal expansion and long-lived memory responses. Unlike other adaptive lymphocytes like T and B cells, NK cells are not thought to require priming in lymphoid organs during activation. However, although NK cells respond in multiple tissue sites during cytomegalovirus (CMV) infection, here we observed that early activation and virus-specific expansion occurs predominantly in the spleen. These splenic NK cells exhibited heightened TNF-a signaling, which we identify as a novel and critical regulator of both innate and adaptive responses through engagement of distinct NF-kB signaling arms downstream of TNFR2. These findings highlight the central role of the spleen as a lymphoid organ in facilitating the innate-to-adaptive transition NK cells undergo during viral infection, and provide insight into how we can better generate innate and adaptive NK cell immunity across diverse settings.
Bulk RNA-Seq data of WT Ly49H+ NK from spleen or liver on day 0 and day 1 post MCMV infection.

overall_design: Ly49H+ NK cells (Ly49H+ CD49b+ TCRb- CD3- CD19- F480-) were sorted from the spleen and livers of wildtype mice that were uninfected or 24 hours p.i with MCMV.

first: Adriana

last: Mujal

first: Mark

last: Owyong

first: Claire

last: Wingert

first: Simon

last: Grassmann

first: Colleen

last: Lau

first: Joseph

last: Sun


title: Tissue-Specific Determinants of Adaptive NK Cell Responses

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

overall_design: Refer to individual Series


title: Tissue-Specific Determinants of Adaptive NK Cell Responses - Myeloid Cells

summary:
Natural killer (NK) cells are circulating lymphocytes that possess both innate and adaptive features, the latter including antigen-specific clonal expansion and long-lived memory responses. Unlike other adaptive lymphocytes like T and B cells, NK cells are not thought to require priming in lymphoid organs during activation. However, although NK cells respond in multiple tissue sites during cytomegalovirus (CMV) infection, here we observed that early activation and virus-specific expansion occurs predominantly in the spleen. These splenic NK cells exhibited heightened TNF-a signaling, which we identify as a novel and critical regulator of both innate and adaptive responses through engagement of distinct NF-kB signaling arms downstream of TNFR2. These findings highlight the central role of the spleen as a lymphoid organ in facilitating the innate-to-adaptive transition NK cells undergo during viral infection, and provide insight into how we can better generate innate and adaptive NK cell immunity across diverse settings.
Bulk RNA-Seq data of cDC1, pDC, red pulp macrophages from spleen at different time points post MCMV infection

overall_design: cDC1s (Lineage- XCR1+ CD11c+), red-pulp macrophages (Lineage- F4/80+ CD64+), and pDCs (Lineage- F4/80- B220+ BST2+ Ly6C+) were sorted from the spleens of uninfected wildtype mice, or those that were d1 or d2 p.i with MCMV. where Lineage refers to CD3, TCRb, CD19, NK1.1, Ly6G. In each independent experiment, RNA was isolated from sorted cells using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher) in accordance with the manufacturer instructions.


title: Tissue-Specific Determinants of Adaptive NK Cell Responses - WT vs TNFR2ko NK

summary:
Natural killer (NK) cells are circulating lymphocytes that possess both innate and adaptive features, the latter including antigen-specific clonal expansion and long-lived memory responses. Unlike other adaptive lymphocytes like T and B cells, NK cells are not thought to require priming in lymphoid organs during activation. However, although NK cells respond in multiple tissue sites during cytomegalovirus (CMV) infection, here we observed that early activation and virus-specific expansion occurs predominantly in the spleen. These splenic NK cells exhibited heightened TNF-a signaling, which we identify as a novel and critical regulator of both innate and adaptive responses through engagement of distinct NF-kB signaling arms downstream of TNFR2. These findings highlight the central role of the spleen as a lymphoid organ in facilitating the innate-to-adaptive transition NK cells undergo during viral infection, and provide insight into how we can better generate innate and adaptive NK cell immunity across diverse settings.
Bulk RNA-Seq data of WT or TNFR2-/- Ly49H+ NK from spleen at different time points post MCMV infection.

overall_design: Wildtype or TNFR2-/- Ly49H+ NK cells (Ly49H+ CD49b+ TCRb- CD3- CD19- F480-) were sorted from the spleens of mixed bone marrow chimera mice 1, 2, or 4 days p.i. In each independent experiment, RNA was isolated from sorted cells using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher) in accordance with the manufacturer instructions.


title: Transcriptomic effects of culturing leukaemia cells in osteoclast-derived conditioned media

city: Crawley

first: Benjamin

last: Mullin

state: WA

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

summary: In order to investigate mechanisms of crosstalk between osteoclasts and leukaemia cells, we performed sequencing on RNA extracted from mouse leukaemia PER-M60 cells cultured in osteoclast-derived conditioned media and control media.

overall_design: Differential gene expression analysis of RNA-seq data from 4 test cultures grown in osteoclast-conditioned media and 4 control cultures grown in control media.

first: Laurence

last: Cheung

first: Anastasia

last: Hughes

first: Sarah

last: Rashid

first: Jinbo

last: Yuan

first: Jiake

last: Xu

first: Richard

last: Lock

first: Sebastian

last: Malinge

first: Vincent

last: Kuek

first: Rishi

last: Kotecha


title: Proteasome inhibition induces alteration of DNA methylation profile by attenuating the synthesis of DNA methyltransferase 1 and 3B in colorectal cancer

status: Public on Feb 27 2025

city: Shenzhen

first: Kun

address: Rm A1921, Guangming International Innovation Center,

institute: Shenzhen Bay Laboratory

summary: Proteasome is an essential organelle in guarding cellular protein homeostasis. Here, we report that inhibition of proteasome alters the profile of DNA methylation in colorectal cancer (CRC) by blocking the synthesis of DNA methyltransferases (DNMTs). We found that treating CRC cells with proteasome inhibitors (PIs) suppress the translation of DNMT1 and DNMT3B by inactivating AKT and mammalian target of rapamycin (mTOR), dependent on the accumulation of p300, an acetyltransferase inactivating AKT by mediating its acetylation modification. Furthermore, we demonstrated downregulation of DNMT1 and DNMT3B protects cancer cells against PI treatment, potentially by reprogramming the transcriptome of CRC cells; highlighting the key role of DNMTs in response to proteostasis disturbance

overall_design: To identify the role of proteasome inhibitor (PI)-induced DNMT1/3B downregulation, we knocked down DNMT1 (shDNMT1) and DNMT3B (shDNMT3B) respectively, and performed RNA sequencing to analyze the transcriptome alteration following depleting DNMT1 or DNMT3B

first: Yuling

last: Sheng

first: Mengqi

last: Yang

first: Changzheng

last: Du


title: Physiological and transcriptional reprogramming in adaptation to salinity stress in endangered mangrove associate Hernandia nymphaeifolia

first: Yuchen

address: Xingangxi Road 135

institute: Sun Yat-sen University

summary: Hernandia nymphaeifolia is an endangered mangrove associate with high ecological, ornamental, and medicinal values. Its special combination of glycophytic and halophytic characteristics provides an ideal system for investigating salt-responsive mechanisms that may be easily extended to genetic improvement of crops with high salt tolerance. However, little is known regarding salt-responsive mechanisms in H. nymphaeifolia. In this study, we posed gradient salt treatments on H. nymphaeifolia seedlings and investigated their physiological and transcriptional reprogramming in response to salinity stress. The results revealed that hyper-salinity stress posed more adverse impacts on leaf growth, cell integrity and photosynthetic performance of H. nymphaeifolia seedlings compared to those in growing in fresh water or low salt condition, mirroring its nature as a mangrove associate. Genes associated with osmolarity sensor and regulator, ROS scavenging and ion homeostasis were differentially expressed accordingly to alleviate the destructive effects. Furthermore, our results unraveled some pivotal kinases and proteins that regulate the synergistic expression of salt-responsive genes, which may act a key role in regulating the transcriptional remodeling upon salinity stress. These findings enrich our knowledge on the molecular mechanisms underlying the phenotypic plasticity of mangrove associates, and also provide valuable genetic resources for mangrove’s conservation and potential bioengineering application in agricultural field.

overall_design: We posed gradient salt treatments on H. nymphaeifolia seedlings and investigated their physiological and transcriptional reprogramming in response to salinity stress

first: Fang

last: Zanshan

first: Zhang

last: Ying

first: Yang

last: Yuchen


title: Differential gene expressions of cancer cells cultured in an oxygen-limiting, micro-metabolic rewiring (μMeRe) device over their normoxia control

first: JEONG MIN

last: OH

state: California

address: 1042 Downey Way DRB 140

department: Biomedical Engineering

summary: Cancer metabolism plays an essential role in therapeutic resistance, where significant inter- and intra-tumoral heterogeneity exists. Hypoxia is a prominent driver of metabolic rewiring behaviors and drug responses. Recapitulating the hypoxic landscape in tumor microenvironment thus offers unique insights into heterogeneity in metabolic rewiring and therapeutic responses, to inform better treatment strategies. We developed a micro-metabolic rewiring (μMeRe) device that provides the scalability and resolution needed to characterize the metabolic rewiring behaviors of different cancer cells in the context of hypoxic solid tumors. Our device generates hypoxia through cellular metabolism without external gas controls, enabling the characterization of cell-specific intrinsic ability to drive hypoxia and undergo metabolic rewiring. We assessed the changes in the transcriptomic profile of different cancer cells in the μMeRe device compared to their normoxia counterpart through bulk RNA-seq. Our data confirms heterogeneity and commonality of rewiring behaviors of diverse cancer cell types.

overall_design: To examine the heterogeneous metabolic rewiring characteristics of different types of cancer cells, we cultured 8 human cancer cell lines originating from 4 different organs (ovary: OAW42, SKOV3, prostate: LNCaP, PC3, lung: A549, PC9, Breast: MCF7, T47D) in μMeRe devices and their normoxia counterparts (serving as control). Cancer cells were injected into the μMeRe device, where they formed a 2D circular micropattern sandwiched between two oxygen diffusion barriers (polycarbonate at the top and glass at the bottom). A natural oxygen gradient was established across the cancer micropattern due to cell-specific consumption and limited lateral diffusion of oxygen across the monolayer. Cancer cells were also injected into the normoxia device sharing the the same dimensions as the µMeRe device except without the PC oxygen diffusion barrier, thus with unobstructed oxygen supply. All µMeRe and corresponding normoxia devices were disassembled after 24 hours of culture to expose the micropatterns for cancer cell extraction, RNA isolation, and RNA-seq. Transcriptome-wide pairwise gene expression analysis was performed between the µMeRe device and its normoxia counterpart for each cancer cell line to identify differentially expressed genes (DEGs) in the oxygen limited microenvironment.

first: Jeong Min

last: Oh

first: Hydari

last: Begum

first: Keyue

last: Shen


title: Human Skeletal Development and Regenerative Capacity is Shaped by Skeletal Stem Cell Diversity

status: Public on Feb 25 2025

city: Sacramento

first: Thomas

last: Ambrosi

address: 2700 Stockton Blvd

institute: UC Davis

summary: This SuperSeries is composed of the SubSeries listed below. The skeleton is one of the most structurally and compositionally diverse organ systems in the human body, depending on unique cellular dynamisms. Here, we integrate prospective isolation of human skeletal stem cells (hSSCs; CD45−CD235a−TIE2−CD31−CD146−PDPN+CD73+CD164+) from ten skeletal sites with functional assays and single-cell RNA sequencing (scRNA-seq) analysis to identify chondrogenic, osteogenic, stromal, and fibrogenic subtypes of hSSCs during development and their linkage to skeletal phenotypes. We map the distinct composition of hSSC subtypes across multiple skeletal sites and demonstrate their unique in vivo clonal dynamics. We find that age-related changes in bone formation and regeneration disorders stem from a pathological fibroblastic shift in the hSSC pool. Utilizing a Boolean algorithm, we uncover gene regulatory networks that dictate differences in the ability of hSSCs to generate specific skeletal tissues. Importantly, hSSC lineage dynamics are pharmacologically malleable, providing a new strategy to treat aberrant hSSC diversity central to aging and skeletal maladies.

first: Rahul

last: Sinha

first: Charles

last: Chan

first: Debashis

last: Sahoo

first: Sahar

last: Taheri


title: Differentiation of T-regulatory type 1 cells into an immunoregulatory Foxp3+ subset distinct from conventional FoxP3+ T-regulatory cells

status: Public on Feb 26 2025

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

country: Spain

institute: IDIBAPS

summary: T-regulatory type-1 (TR1) cells are a subset of interleukin-10-producing but FoxP3-negative Treg cells that arise in vivo in response to chronic antigenic stimulation. We have shown that repetitive systemic delivery of autoimmune disease-relevant peptide-major histocompatibility complex class II (pMHCII)-coated nanoparticles (pMHCII-NP) triggers the formation of large pools of disease-suppressing Foxp3– TR1 cells from cognate T-follicular helper (TFH) cell precursors. Here we show that these Foxp3– TR1 cells spontaneously differentiate into a novel immunoregulatory Foxp3+ TR1 subset that inherits transcriptional and epigenetic hallmarks of their precursors and is distinct from other Foxp3+ Treg cell subsets described to date. Development of this novel Foxp3+ Treg cell subset, as is also the case for Foxp3– TR1 cells but not conventional Foxp3+ Treg cells, is BLIMP1-dependent. In a model of central nervous system autoimmunity, deletion of Il10 in the Foxp3+ TR1 subset, but not its FoxP3+ counterpart, reduces the therapeutic activity of pMHCII-NPs without impairing their pharmacodynamic activity. T cell-specific deletion of Prdm1 and deletion of Il10 in both the FoxP3– and FoxP3+ TR1 subsets almost completely abrogate the therapeutic activity of these compounds. Thus, the TFH-TR1 transdifferentiation pathway evolves through 4 distinct cellular states that culminate in the generation of IL-10-producing FoxP3– and FoxP3+ TR1 subsets in a BLIMP1-dependent manner. This transdifferentiation pathway represents a new target for therapeutic intervention in immunity and autoimmunity.

overall_design: pMHCII-NP-induced Tet+ CD4+ T cells generated in type 1 diabetes (NOD mice) and multiple sclerosis (EAE, MOG-immunized B6 mice) models at different time points and in different conditional-KO strains were processed for 10X single-cell RNA-seq.

first: Joel

last: Moro

first: Pere

last: Santamaria


title: The difference of whole transcriptome genes in pulmonary artery(PA) and mesenteric artery(MA) of adult offspring in HS group and CON group

city: Jining

first: Hongwei

last: Fu

address: No. 45 Jianshe South Road, Rencheng District

country: Singapore

institute: Jining Medical University

summary: In HS group pulmonary artery, The up-regulated mRNA: GHRHR, TRH, MT1R, MT2AR, GPRC5D. The down-regulated mRNA: ANKEF1, DNAJB1, MFSD4A. Among them, the most obvious difference is MT1R and MT2AR.In HS group mesenteric  artery, The up-regulated mRNA: CRYAB and HSPEL. The down-regulated mRNA: APCDD1.

overall_design: Pregnant female rats were fed standard diet, the CON group was given ordinary water, and the HS group was given 20% sucrose water.  The offspring aged 3-5 months were obtained, pulmonary arteries and mesenteric arteries were isolated under the microscope, and the whole transcriptome was sequenced to see whether there were statistical differences in gene expression between the two groups.


title: ATR licenses PINK1-mediated mitophagy

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

summary: Mitochondria are the central metabolic hub of the cell and their function is vital for cellular activities. Mitochondrial autophagy, or mitophagy, is a quality control mechanism to surveille the fitness and functionality of mitochondria and is therefore essential for life. Both mitochondrial dysfunction and malfunctional DNA damage response (DDR) are a major etiology for tissue impairment and aging. ATR has been shown mainly as a nuclear factor to conduct DNA damage response under DNA replication stress. Paradoxically, the human Seckel syndrome caused by ATR mutations is characterized by premature aging and neuropathies, suggesting a role of ATR in non-replicating tissues. Here we report a previously unknown yet direct role of ATR at mitochondria. We find that HSP90 chaperones ATR and PINK1 to mitochondria, where ATR interacts with and thereby stabilizes PINK1 docking at the mitochondrial translocase TOM/TIM complex as well as with the electron transport chain (ETC). ATR mutant cells are refractory to mitophagy initiation, which can be reverted by an ectopic expression of full length, but not ATR-interaction mutant, PINK1. ATR deletion alters mitochondrial dynamics and OXPHOS functions producing aberrantly high reactive oxygen species (ROS) that attack cytosolic macromolecules prior to damaging nuclear DNA. Intriguingly, pharmacological intervention of mitochondrial metabolism to prevent ROS overproduction can mute ATR-mediated nuclear DDR. This study demonstrates that ATR is an integrated component of the mitochondrial membrane to ensure mitochondrial fitness as a primary physiological function, which, together with its essential DDR function, safeguards the cell fate under physiological and genotoxic conditions.

overall_design: Primary mouse embryonic fibroblasts (pMEFs) carrying the floxed ATR fl/fl allele and the CreERT2 transgene. Addition of 4-hydroxytamoxifen (4-OHT) enables an inducible deletion of ATR in these cells (designated as ATR-iKO). RNA-seq was performed on 5 biological replicates with 4-OHT treatment and on 5 biological replicates without treatment. These two groups were contrasted to see gene expression changes in ATR deficient cells.

first: Christian

last: Marx

first: Marco

last: Groth

first: Zhao-Qi

last: Wang


title: Immune-mediated regeneration of cell-free vascular grafts in an ovine model

city: Buffalo

first: Stelios

middle: T.

last: Andreadis

state: NY

address: 908 Furnas Hall

department: Chemical and Biological Engineering

institute: University at Buffalo

summary: We have employed single cell RNA sequencing transcriptomics to characterize the cellular sub-types populating the H2R5 ATEV (Grafts) explanted at 12 weeks, from an Ovine (Sheep) model. The ATEVs were primarily reconstructed by the infiltrating myeloid-precursor cells/monocytes that differentiate under different physiological and mechanosensitive cues into macrophages, smooth muscle cells and endothelial cells. Cell specific markers (CSF1R, CD14, CD163, C1QA, PTPRC) for monocytes, (MYH11, ACTA2, MYL9, TAGLN) for Smooth muscle cells, (PECAM1, VWF, NOS3, CDH5, CLDN5) for endothelial cells were employed to determine the major cell populations in the ATEVs. Characterization of the immune-cell types populating the ATEVs hold immense potential in developing future generation grafts for cardiovascular applications.

overall_design: The ATEVs and the native carotid artery were explanted from the sheep after 12 weeks of implantation. The isolated tissues, maintained in EBM2 medium containing FBS, were first washed with PBS, then clamped with metal clippings and then perfused with Digestion buffer containing collagenase, Neutral protease, Elastase and DNAse1. Following incubation at 37°C for 20 minutes, the enzymatically digested cells were neutralized with FBS, passed through a 40 µ cell strainer and resuspended as single cells and analyzed using scRNA seq.

first: Sai Harsha

last: Bhamidipati

first: Karthik

last: Ramachandran

first: Bita

last: Nasiri


title: Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility

first: Yi

last: Yin

state: CA

address: 695 Charles E. Young Dr. S.

department: Human Genetics

institute: University of California, Los Angeles

summary: Single-cell combinatorial indexing (sci-) methods have addressed major limitations of throughput and cost for many single cell modalities. With the incorporation of linear amplification and 3-level barcoding in our suite of methods called sci-L3, we further addressed the limitations of uniformity in single cell genome amplification. Here, we build on the generalizability of sci-L3 by extending it to template strand sequencing (sci-L3-Strand-seq), genome conformation capture (sci-L3-Hi-C), and the joint profiling of RNA and chromatin accessibility (sci-L3-RNA/ATAC). We demonstrate the ease of adapting sci-L3 to these new modalities by only requiring a single-step modification of the original protocol. As a proof-of-principle, we show our ability to detect sister chromatid exchanges, genome compartmentalization, and cell state specific features in thousands of single cells. We anticipate sci-L3 to be compatible with additional modalities, including DNA methylation (sci-MET) and chromatin associated factors (CUT&Tag), and ultimately enable a multi-omics readout of them.

overall_design: We performed three extensions of the sci-L3 methodology. Profiling replication template strand in single cells using sci-L3-Strand-seq was performed on mouse diploid Patski cells and human haploid HAP1 cells. Single cell genome conformation capture was performed with the GM12878 cell line. The joint profiling of RNA and chromatin accessibility using sci-L3-RNA/ATAC was performed on HEK293T, BJ-5ta, NIH/3T3 cell lines in parallel with sci-L3-RNA/DNA.

first: Peter

last: Chovanec


title: Myelin-reactive CD8+ T cells influence conventional dendritic cell subsets towards a mature and regulatory phenotype in experimental autoimmune encephalomyelitis

status: Public on Feb 24 2025

city: North Liberty

first: Kai

middle: Jordan

last: Rogers

state: IA

address: 2205 Oak Terrace Avenue

department: Pathology

institute: University of Iowa

summary: We performed single cell sequencing using the Parse Biosciences WT kit to evaluate changes in dendritic cell populations following induction of experimental autoimmune encephalomyelitis. Mice in this experiment previously received CD8+ T cells from donor mice that had been immunized with PLP178-191 or OVA323-339. Thus we ask what the effect of these CD8s is on DC populations in the context of EAE.

overall_design: Dendritic cells were harvested from the spleens and inguinal lymph nodes of mice that received CD8+ T cells from mice immunized with either OVA323-339 or PLP178-191. DC harvest was performed 12 days following induction of experimental auotoimmune encephalomyelitis. Cells were fixed using the Cell Fixation Kit and processed with the Evercode Whole Transcriptome Mini Kit from Parse Biosciences. Sequencing was performed on the Illumina NovaSeq 6000 using 100bp paired-end reads.

first: Mohit

last: Upadhye

first: Nitin

last: Karandikar


title: Transcriptomic and Proteomic Analyses of Sclera in Lens-Induced Myopic Guinea Pigs

city: beijing

first: heyan

last: li

state: beijing

address: 1 Beijing Legation Quarter Road, Dongcheng District

institute: Beijing Tongren Hospital

summary: To explore the potential biomarkers and signal pathways in the process of axial elongation, namely in the scleral remodeling and thinning.

overall_design: A myopia guinea pig model was established using male guinea pigs aged 2–3 weeks, which underwent bilateral lens-induced myopization (LIM) (study group) or were left untreated (control group). Five eyes from both the control group and the LIM group were selected for RNA sequencing.

first: Heyan

last: Li

first: Xuhan

last: Shi

first: Wenbin

last: Wei


title: KAT6B overexpression rescues embryonic lethality in homozygous null KAT6A mice restoring vitality and normal lifespan [CUT&TAG]

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

summary: Closely related genes typically display common essential functions but also functional diversification, ensuring retention of both genes throughout evolution. The histone lysine acetyltransferases KAT6A (MOZ) and KAT6B (QKF/MORF), sharing identical protein domain structure, are mutually exclusive catalytic subunits of a multiprotein complex. Mutations in either KAT6A or KAT6B result in congenital intellectual disability disorders in human patients. In mice, loss of function of either gene results in distinct, severe phenotypic consequences. In this dataset, we investigate the effects of overexpression of KAT6B on the histone acetylation changes caused by loss of KAT6A in mouse embryonic fibroblasts. We show that Kat6b overexpression restores acetylation at histone H3 lysines 23 in Kat6a mutant mouse primary embryonic fibroblasts.

overall_design: CUT&Tag results detecting histone H3 lysine 23 acetylation in (H3K23ac) in primary mouse embryonic fibroblasts isolated from E14.5 Kat6a+/+Kat6b+/+, Kat6a–/–Kat6b+/+, Kat6a–/–Tg(Kat6b) and Kat6a+/+Tg(Kat6b)  foetuses. N = 4 foetuses per genotype.

middle: L

first: Anne

last: Voss

first: Tim

last: Thomas


title: Immunization Induces Inflammation in the Mouse Heart during Spaceflight

city: Loma Linda

first: Lorelei

last: Hughes

address: 11021 Campus

department: Pathology and Human Anatomy

institute: Loma Linda University

summary: Space travel is a growing area of interest and includes initiatives such as NASA's Moon-to-Mars Mission. Studies conducted on the cardiovascular effects of space travel reveal changes in morphology, metabolism, and function. In this study, the cardiovascular response to immunization in space was studied in mice which were housed and immunized while on the International Space Station (ISS).  Mice were immunized with tetanus toxoid combined with the adjuvant CpG (TT+CpG) and the effects of vaccination in space were studied using transcriptomics. Analysis of the murine heart transcriptome was performed on ground, flight-control, and flight-immunized mice. Results showed that immunization aboard the ISS stimulates heightened inflammation in the heart via induction of the NF-κB signaling pathway.

overall_design: Determine changes in differential expression of transcripts in the heart of mice immunized aboard the ISS.

first: Alicia

last: Veliz

first: Delia

last: Carrillo

first: Michael

last: Pecuat

first: Mary

last: Kearns-Jonker