title: Conservation of chromatin states and their association with transcription in land plants

first: Vikas

last: Shukla

state: Vienna

address: Dr.Bohr-Gasse 3

institute: Gregor Mendel Institute

summary: The complexity of varied modifications of chromatin composition is reduced to archetypal combinations called chromatin states that broadly define the local potential for transcription. The degree of conservation of chromatin states has not been established amongst plants, and how they interact with transcription factors is unknown. We have identified and characterized chromatin states in the flowering plant Arabidopsis thaliana and the bryophyte Marchantia polymorpha, showing a large degree of functional conservation over more than 450 million years of land plant evolution. We analyzed the interplay between transcription factors and chromatin states to understand their influence on gene regulation. Combining binding sites with activity of transcription factors, we have shown their preferential association with specific chromatin states in both species. These associations define three main groups of transcription factors that bind in the promoter 5’ of the transcription start site, at the +1 nucleosome or inside the gene body downstream of the transcription start site. These groups broadly associate with distinct functions, such as house-keeping genes, putative pioneer factors, development, and response to the environment, suggesting co-evolution of the chromatin regulatory mechanisms with transcription factors.

overall_design: ChIP-seq for histone H2A variants: H2A.Z, H2A.X.1, H2A.X.2, H2A.M.2 performed in 14 days old thalie of Marchantia polymorpha (wt-Tak1). ChIP-seq for histone modifications H3K27me3, H2AKUb, H3K4me3, H3K27me1, and H3K9me1 in wild type and Mpez1,Mpknox2 double mutant of of Marchantia polymorpha.

first: Tetsuya

last: Hisanaga

first: Frederic

last: Bereger

first: Elin

last: Axelsson


title: Human skeletal muscles in exercise

status: Public on Aug 20 2025

city: Kawasaki

first: Shihori

last: Tanabe

state: Kanagawa

address: 3-25-26, Tonomachi, Kawasaki-ku

department: Division of Risk Assessment

country: Japan

institute: National Institute of Health Sciences

summary:
The exercises such as running alter gene expression in skeletal muscles.
The gene expression profiling in human skeletal musles after running and not exercised were compared.

overall_design: The series of the samples comprises 3 not-exercised and 7 exercised skeletal muscle. Each sample corresponds to each individual.

first: Tetsuo

last: Yamaguchi

first: Hideaki

last: Horikawa


title: RNA-sequencing of endothelial cells and 3D cardiac microtissues from hiPSCs

city: Leiden

first: Valeria

last: Orlova

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

type: Expression profiling by high throughput sequencing

summary: We previously showed that two major cellular components of the human heart, cardiac endothelial cells and cardiomyocytes, could be derived simultaneously from human induced pluripotent stem cells (hiPSCs). In vivo studies in mice have shown these lineages derive from a common MESP1+ mesoderm progenitor. Although this has been investigated using whole transcriptome sequencing, the transcriptional control and dynamics of their segregation from cardiac mesoderm are not yet fully understood. In addition, the same transgenic approach cannot be used in human. Here, we used bulk and single cell RNA sequencing (RNAseq) to investigate EC and cardiomyocytes co-differentiation in hiPSC. We confirmed segregation of these two cardiac lineages from common cardiac mesoderm precursors but more importantly, revealed a critical role of transient expression of the transcription factor ETV2 for endothelial fate specification and showed unexpectedly that functional cardiomyocytes could also originate from ETV2+ progenitors. This dataset contain 10X-based scRNA-seq data human induced pluripotent stem cell derived endothelial cells and 3D cardac microtissues, as well as bulk RNA-seq data of endothelial cells derived from cardiac and paraxial mesoderm.

overall_design: scRNA-seq data: Two batches of  cardiac mesoderm derived endothelial cells (CMEC), two batches of  paraxial mesoderm derived endothelial cells (PMEC),  two batches of  3D cardiac microtissues (MTP) differentiated from hiPSCs. Bulk RNA-seq data:  5-6 batches of CMEC and PMEC on differentiation day 6 and 8 from COUPTF-II reporter hiPSC line, 3 batches of CMECs sorted on differentiation day 6, on day 27 of 2D culture and on 27 of microtissues.

first: Xu

last: Cao


title: CTHRC1 is a new therapeutic target and serum diagnostic biomarker for aortic dissection [Ab_mouse_RNAseq]

status: Public on Aug 19 2025

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

country: China

institute: Tongji University

summary: Aortic dissection (AD) is a cardiovascular disease with rapid onset and extremely high short-term mortality, currently lacking specific peripheral blood-based biomarkers and effective treatments. Here, our analyses of AD samples from animal models and human patients revealed elevated blood levels of CTHRC1, a protein secreted by vascular fibroblasts. Furthermore, CTHRC1 regulates the phenotypic switch of vascular smooth muscle cells (VSMCs) during arterial remodeling by binding to ADAM9 on the VSMC membrane, activating the ERK1/2 signaling pathway, and promoting a contractile-to-synthetic transition. In Ang-II/BAPN induced AD mouse models, genetic ablation or antibody-mediated blockade of CTHRC1 effectively prevented AD formation and development. These findings unveil activated vascular fibroblast derived CTHRC1 as a critical regulator of VSMC phenotype and aortic structural integrity via the ERK1/2 signaling pathway, suggesting its potential as a novel serum diagnostic biomarker for AD diagnostic and a promising therapeutic target. Collectively, our data propose a new and effective strategy for diagnosis and clinical management of patients with AD.

overall_design: RNA seq of aortas from the wt mice under AngII/BAPN infusion treated with anti-CTHRC1 Ab or IgG Isotype


title: CTHRC1 is a new therapeutic target and serum diagnostic biomarker for aortic dissection [MOVAS_rhCTHRC1_RNAseq]

overall_design: RNA seqencing of WT MOVAS cells and knockouting ADAM9 MOVAS cells treated with vehicle and rhCTHRC1 protein. RNA seqencing of MOVAS cells treated with ADAM9 inhibitor(ADAM9i).


title: Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3’UTR isoform diversity

city: Philadelphia

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Biophysics

country: USA

institute: University of Pennsylvania

summary: The 3’ untranslated regions (3’UTRs) of mRNAs play a critical role in controlling gene expression and function because they contain binding sites for microRNAs and RNA binding proteins (RBPs) that alter mRNA stability, localization, and translation. Most mRNA 3’ ends contain multiple polyadenylation sites (PAS) that can be utilized in condition-specific manners, a process known as alternative polyadenylation (APA), however the mechanisms driving the regulation of APA remain poorly characterized. By integrating a large set of over 500 RNA binding protein (RBP) depletion and binding experiments across two cell lines generated by the ENCODE consortium, we uncovered a number of RBPs in each cell type whose depletion leads to widespread alteration of 3’ UTR patterns. These include not only known regulators of APA, but also many putative novel regulators of 3’UTR isoform expression. We focused analysis on the largely unstudied DEAD box RNA helicase, DDX55, and validate its novel role in 3’UTR isoform regulation using molecular assays and targeted 3’ end sequencing experiments (QuantSeq REV V2, Lexogen). Our findings identify DDX55 as a new regulator of APA, particularly at PAS that contain features of RNA secondary structure. Our data also suggest additional previously unrecognized regulators of 3’ UTR processing and differential stability.

overall_design: We preformed targeted 3'end sequencing (QuantSeq REV V2, Lexogen) to determine polyA site usage in HepG2 cells transfected with siRNAs for control non-targeting pool or targeting DDX55, in triplicate. RNA was profiled from whole cell in addition to nuclear and cytoplasmic fractions.

first: Matthew

middle: R

last: Gazzara

first: Michael

middle: J

last: Mallory

first: Yoseph

last: Barash

middle: W


title: CTHRC1 is a new therapeutic target and serum diagnostic biomarker for aortic dissection [Cthrc1_wt_ko_RNAseq]

overall_design: RNA seq of aortas from the wt mice and Cthrc1-/- mice.


title: Transcriptome analysis of hiPSC-CMs carrying MYPN mutations

city: Saint-Petersburg

first: Margarita

last: Sorokina

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Centre

summary: In this study we performed transcriptome analysis of cardiomyocytes (CMs) derived from hiPSC line of patient with hypertrophic cardiomyopathy (HCM) associated with a novel p.N989I (c.2966A>T) variant in MYPN gene. Detailed information about iPSC line characterization can be found in hiPSCreg database: FAMRCi015-A.

overall_design: Mononuclear cells (MNCs) of the HCM patient were reprogrammed into hiPSC using the Epi5™ Episomal iPSC Reprogramming Kit user guide (Thermo Fisher Scientific, Waltham, MA, USA). The hiPSC line (AD3) was generated from human newborn fibroblasts (HNFs) of Healthy Donor using the lentiviral nonintegrating Sendai reprogramming kit (CytoTune-iPS 2.0 Sendai Reprogramming kit (Invitrogen, Paisley, UK) according to the manufacturer’s instructions and was used as control cells. Then hiPSC were differentiated into mature cardiomyocytes (45 days), according to a previously published protocol (https://doi.org/10.1002/cm.21922). RNA-libraries from Donor and HCM cardiomyocytes were prepared with TruSeq Stranded mRNA kit, samples were sequenced on Illumina NextSeq 2000, read length 51 bp.

first: Anna

last: Kostareva


title: In vivo HSC gene therapy enables sustained eCD4-Ig expression predominantly by B-cells for SIV prevention

city: Seattle

first: John

middle: K

last: Bui

state: WA

address: 1100 Fairview Ave. N.

institute: University of Washington

summary: eCD4Ig-Emm06 was delivered using the helper-dependent adenovirus 6/3+ platform to transduce rhesus hematopoietic stem cells in vivo. Animals underwent SIV challenge to assess for protection. Serum SIV was sequenced to evaluate for escape mutations.

overall_design: 3 rhesus macaques received the HDAd-eCD4Ig-Emm06 vector (animals A21138, A21140, A22054) and 3 rhesus macaques received the HDAd-control vector (animals A23051, A21137, A22065). Animals underwent infection with SIVmac239 and had serum virus sequenced at 11 weeks post-infection (with the exception of A21138 that had sequencing performed at 7 weeks post-infection).

first: Chang

last: Li

last: Anderson

first: Anne-Sophie

last: Kuhlmann

middle: D

last: Alpert

first: Nickolas

last: Skamangas

first: Charles

middle: C

last: Bailey

first: Tianling

last: Ou

last: Farzan

first: Keith

last: Jerome

first: Hans-Peter

last: Kiem

first: Andre

last: Lieber


title: Maternal care during early development is necessary for the acquisition of a calming response to back stroking

city: Ota-ku

first: Sachine

last: Yoshida

address: 5-21-16 Omori-Nishi

department: Faculty of Medicine

institute: Toho University

summary: In many mammals, early postnatal interactions between caregivers and offspring involve rich physical contact, including stroking, holding, and grooming. Offspring typically remain calm and close to the caregiver during such stimulation. Although these behaviors are widely believed to support emotional regulation and bonding during infancy, the underlying biological mechanisms and the role of prior experience in eliciting the calming response remain poorly understood. Here, we demonstrate that back stroking induces a conserved calming response in both human infants and mouse pups, characterized by reductions in spontaneous movement and heart rate. In mouse pups, stroking further facilitated sleep onset, increased EEG delta power, and attenuated stress-induced corticosterone elevations. These sleep-promoting and stress-buffering effects were absent in artificially reared pups deprived of postnatal maternal contact, underscoring the importance of early tactile experience. Transcriptomic analysis revealed downregulation of the voltage-gated calcium channel subunit gene Cacna1b in the hypothalamus of artificially reared pups. Moreover, targeted knockdown of hypothalamic Cacna1b in maternally reared pups abolished stroking-induced reductions in movement and heart rate, as well as the increase in delta power. This study identifies a conserved, experience-dependent calming response to affiliative tactile input, biologically embedded through plasticity, that supports physiological regulation and stress resilience during early development. While the developmental plasticity of discriminative tactile sensation has long been recognized, our results highlight that affiliative tactile sensation similarly depends on early experience to organize neural mechanisms regulating internal states.

overall_design: Total RNA was extracted from the hypothalamus of postnatal day 13 mouse pups that were either maternally reared or artificially reared. Bulk RNA sequencing was performed to obtain comprehensive transcriptomic profiles, and differential gene expression analysis was conducted to identify genes with altered expression between the two rearing conditions.

first: Akiko

last: Harauma

first: Toru

last: Moriguchi

first: Yousuke

last: Tsuneoka

first: Kimiya

last: Narikiyo

first: Kazuya

last: Miyanishi

first: Makoto

last: Kashima

first: Hiromasa

last: Funato


title: Metabolic Adaptation of Regenerative Hematopoiesis Depends on Docking-Independent Mitochondrial Connexin-43

city: BOSTON

first: Jose

last: Cancelas

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Hematopoietic stem cells (HSCs) exhibit a distinctive antioxidant profile during steady-state and stress hematopoiesis. HSCs and multipotential progenitors (MPPs) are metabolically coupled to bone marrow mesenchymal stromal cells through mitochondrial transfer, a process dependent on hematopoietic connexin 43 (Cx43) and low adenosine monophosphate–activated protein kinase (AMPK) activity. However, the mechanism by which Cx43 preserves mitochondrial functionality in HSCs remains elusive. Here, through integrated transcriptomic, proteomic, metabolomic, phenotypic, and functional analyses of HSCs and their isolated mitochondria, we identified that Cx43 is present on the inner and outer mitochondrial membranes of HSCs/MPPs, in which it primarily regulates mitochondrial metabolism and adenosine triphosphate synthesis by preserving the mitochondrial cristae and activating mitochondrial AMPK and 2-oxoglutarate dehydrogenase, a rate-liming enzyme in tricarboxylic acid cycle and electron transfer chain. During replicative stress, Cx43-deficient HSCs/MPPs fail to adapt metabolically and accumulate mitochondrial Ca2+, leading to increased mitochondrial AMPK activity, mitochondrial fission, mitophagy, and production of reactive oxygen species, thereby limiting HSC/MPP regeneration potential. Disruption of hyperfragmentation of mitochondrial and mitophagy by Drp1 dominant-negative mutant (Drp1K38A) or restoration of mitochondrial function through ex vivo heteroplasmy prevents the harmful effects of Cx43 deficiency on mitochondrial metabolism and restore HSC activity in serial transplantation experiments. Re-expression analysis of Cx43 structure-function mutants indicates that Cx43 hemichannels are sufficient to reset HSC mitochondrial metabolism, dynamics, Ca2+ levels, and regeneration capacity. This report defines the cell-autonomous mechanism of action behind the role of Cx43 in HSC activity and opens a venue to translational applications in transplantation.

overall_design: RNA-Seq profiling of WT and Connexin 43 (Cx43) knockout quiescent (0h) and dividing (48h of culture) HSC.

first: Abhishek

last: Singh

first: Angelo

last: D’Alessandro

first: Ashley

middle: M

last: Wellendorf

first: Daniel

last: Gonzalez-Nieto

first: Matthew

last: Kofron

first: Monika

last: Dzieciatkowska

first: Leo

last: Mejia

first: Luis

last: Barrio

first: Marie

last: Filippi

middle: A


title: Pro-inflammatory c-Met+ CD4 T cells in multiple sclerosis

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: Objective Hepatocyte growth factor (HGF) binds exclusively the c-Met surface receptor, and the HGF/c-Met axis regulates T-cell function in autoimmune diseases. We analyzed c-Met expression on human CD4 T cells in the blood and cerebrospinal fluid (CSF) from patients with multiple sclerosis (MS) versus non-inflammatory neurological disease (NIND), to better understand the role of CD4 T cells in MS. Methods We recruited 34 untreated MS patients (aged 28–43 years) and 10 NIND (aged 34–51 years) who underwent paired blood and CSF sampling at the time of diagnosis work-up. Phenotypic and functional CD4 T cells characterization was determined by flow cytometry and bulk RNA sequencing. Adhesion and transmigration capacities were studied to further characterize the function of c-Met+ CD4 T cells. Results c-Met+ memory CD4 T cells were detected at higher levels in both blood (median of 1.98%) and CSF (5.88%) in MS compared to NIND (0.37% and 0.68% respectively) (p<0.0001). Ex vivo c-Met+ CD4 T cells exhibited higher levels of GM-CSF, IL-17, IFN-γ and double positive IL-17+IFN-γ+ expression, compared with c-Met- CD4 T cells. c-Met+ CD4 T cells expressed increased levels of integrins – Itgα4β1 (VLA-4) and ItgαLβ2 (LFA-1) – compared with c-Met- CD4 T cells. Anti-Itgα4 (natalizumab) and anti-ItgαLβ2 (odulimomab) inhibited CD4 T cell transmigration with predominant inhibition of CD4 T cells expressing c-Met. Interpretation These results emphasize c-Met as an immune marker of highly pro-inflammatory and migratory CD4 T lymphocytes in both the periphery and central nervous system of MS patients.

overall_design: FACS-sorted T cell subsets were washed with PBS and resuspended in RNA lysis solution with 1% DTT. Total RNA was extracted using the Nucleospin RNA kit (Macherey-Nagel). Complementary DNA was synthesized from total RNA using a reaction mix containing Tris-aminoMethane (200 mM), KCl (500 mM), MgCl2 (0.2 M; Sigma-Aldrich), DTT (100 mM; Invitrogen), random hexamers (50 mM; Invitrogen), oligo(dT) 15 primer (100 mg/ml; Promega), dNTP mix (10 mM; Promega), RNAsin (40 U/ml; Promega) and SuperScriptTM II (200 U/ml; Invitrogen). After incubation at 42°C for 50 min and inactivation at 99°C for 3 min, cDNA was diluted and stored at -20°C until use. On the FACS-sorted c-Met⁻ and c-Met⁺ CD4 T cells, we performed bulk-RNA sequencing. The SMART-Seq v4 kit from Clontech was used for the reverse transcription and cDNA amplification according to the manufacturer’s specifications, starting with 1 ng of total RNA as input. Two hundred picograms of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High Sensitivity chip (Agilent Technologies). Libraries were sequenced on a NovaSeq 6000 Illumina sequencer for SR100 reads, generating an average of around 35,000,000 reads per sample. We employed GSEA to identify enriched biological themes within our dataset. Initially, differentially expressed genes (DEGs) were identified based on specific criteria (e.g., fold-change and p-value thresholds) and ranked based on their expression levels. Using the ranked list, GSEA was performed to determine whether sets of genes associated with specific biological processes, molecular functions, or cellular components were statistically overrepresented. We utilized the Molecular Signatures Database (MSigDB) for gene set annotations, and enrichment scores, nominal p-values, and false discovery rate (FDR) were calculated to assess the significance of gene set enrichment.

first: Gautier

last: Breville

first: Mahdia

last: Benkhoucha

first: Ayman

last: Rezk

first: Ngoc Lan

last: Tran

first: Isis

last: Senoner

first: Amit

last: Bar-Or

first: Patrice

middle: H

last: Lalive


title: Maintenance of Fibroblast Identity During Cardiac Reprogramming and Heart Repair [RNA-seq]

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

summary: Direct cardiac reprogramming (CR) of fibroblasts into induced cardiomyocytes represents a promising therapeutic avenue to treat heart failure as it would use the injury by-product and transform fibroblasts into new cardiac muscle thereby achieving the unmet medical need of cardiac regeneration. However, low reprogramming efficiency limits its clinical potential. Our lab identified four transcription factors playing a conserved role as barriers to CR. Knock-down of these barriers increase CR five-fold compared to MGT (MEF2C; GATA4; TBX5) overexpression alone. Exploration of direct downstream targets of these barriers identified proteoglycan sulfation as potential pathway regulating cell fate stability.   Proteoglycan sulfation, specifically Carbohydrate Sulfotransferase 7 (CHST7), was identified as a conserved barrier to CR. Knockdown of Chst7 in mouse and human fibroblasts significantly enhances CR, increasing expression of cardiac-specific markers and promoting sarcomeric organization. Functional screening of proteoglycan core proteins identifies CD44 as a conserved barrier to reprogramming. Additionally, Chst7 and Cd44 functionally interact to mediate cell fate stability. RNA sequencing and transcription factor analysis identify Junb as the main TF mediating Chst7-regulated transcription during CR. Mechanistic studies of Chst7-regulated pathway genes demonstrate that Chst7 knockdown reduces Pip4k2c expression, establishing a novel regulatory axis between Chst7/Cd44/Junb and Pip4k2c. In vivo, shRNA-mediated Pip4k2c knockdown significantly enhances MGT-mediated CR, increasing cardiac muscle content and reducing fibrosis after myocardial infarction. These findings establish proteoglycan sulfation as a key regulator of cell fate stability, offering new opportunities to improve CR therapies. Thus, proteoglycan sulfation-associated genes might represent an innovative target space to enhance CR for therapeutic purposes.

overall_design: Expression profiling through bulkRNA-seq of iMGT (Mef2c, Gata4, Tbx5)-Myh6-eGFP-MEF cell line reprogrammed into induced-cardiomyocytes at multiple timepoints (day0, day1, day3) comparing siControl and siChst7 conditions.

first: Michaela

last: Romero

first: Sean

last: Murphy

first: Alexandre

last: Colas


title: Transcriptomic insights and feeder-free culturing of porcine expanded potential stem cells from cloned embryos

city: Cheongju

first: Lian

last: Cai

state: Chungcheongbuk-do

address: 1 Chungdae-ro, Seowon-gu

country: South Korea

institute: Chungbuk national university

summary: Background: Generating expanded potential stem cells from cloned porcine embryos (pEPSCsNT) represents a notable advancement in regenerative medicine and agricultural biotechnology. However, challenges, including low derivation efficiency, limited understanding of transcriptomic features, and unknown feasibility of culturing under feeder-free conditions, remain. This study aimed to generate pEPSCs using blastocysts derived from parthenogenetic activation, in vitro fertilization, and somatic cell nuclear transfer (SCNT) using a modified culture system. Methods: We derived pEPSCNT lines using an optimized culture system. We characterized the pEPSC lines from all three origins by analyzing pluripotent marker expression, performing karyotyping, and assessing their differentiation potential into the three germ layers. Furthermore, we performed a comparative transcriptomic analysis using in vivo and cloned embryo data, with a major focus on cell lines derived from SCNT (pEPSCsNT). We optimized feeder-free culture conditions for the pEPSCNT line and derived the pEPSCNT lines using an optimized culture system with an efficiency of ~14%. Results: The cells were closely correlated with 8-cell to morula-stage embryos and exhibited significant enrichment of EPSC signature genes, suggesting a unique pluripotent state relatively close to the naïve state, specifically within a formative state. The pEPSCsNT possessed broad differentiation capacity, indicative of Hippo signaling pathway enrichment, blastocyst-like structure formation ability, and potential differentiation into trophoblast lineage cells. Conclusions: Our modified culture medium combined with the 2× Matrigel coating system facilitated the transition to feeder-independent culture conditions. These findings facilitate the establishment of a feeder-free culture system while preserving pluripotency and differentiation potential.

overall_design: RNA-seq profiling of the EPSCsNT line, SCNT-derived blastocysts at Day 7, and induced pluripotent cells (iPSCs) line of pig

first: Mirae

last: Kim

first: Hyerin

last: Choi

first: Haneul

first: Sang-Hwan

last: Hyun

first: Eunhye


title: Genitourinary defects, anxiety and aggressive-like behavior and glucose metabolism disorders in Zmym2 mutant mice with inserted piggyBac transposon

city: shanghai

first: Rufeng

last: Dai

address: 399 Wanyuan Road，Minhang District

institute: Children’s Hospital of Fudan University

summary: Mutations in ZMYM2 lead to syndromic congenital anomalies of the kidney and urinary tract (CAKUT) in humans. Tbx18 is co-expressed with Zmym2 in mesenchymal compartment of developing mouse ureter, indicating a potential in vivo relevance of the TBX18–ZMYM2 protein interaction in ureter development. The presence of multiple phenotypes beyond the urinary system in CAKUT patients carrying ZMYM2 mutations suggests that ZMYM2 has extensive roles in various developmental processes.

overall_design: This study aims to comprehensively examine the multi-phenotypic consequence of ZMYM2 mutations, with a particular focus on the roles of ZMYM2 in embryonic development, late metanephros formation, and the reproductive, nervous and endocrine systems, in addition to its role in urinary system. Using a new Zmym2 mutant mouse model with an inserted piggyBac transposon (PB), we found that homozygous Zmym2 mutations resulted in severe growth retardation of embryos by embryonic day 9.5 (E9.5D) and lethality from E10.5D. Heterozygous mutations caused morphogenetic issues in the genitourinary system, including duplex kidneys, vesicoureteral reflux (VUR), and cryptorchidism. And these heterozygous mutants exhibited anxiety and aggressive-like behaviors, and glucose metabolism disorders. Additionally, Zmym2 mutations induced duplicated ureteric bud (UB) eruption and abnormal nephrogenic zone extension, contributing to duplex kidney formation. Reduced apoptosis in the nephric duct might have contributed to abnormal ureter-bladder connections, which could explain the observed cases of VUR. Notably, Tbx18 is co-expressed with Zmym2 in mouse kidney, reduced Tbx18 expression in Zmym2 mutants further supports the hypothesis that Zmym2 interacts with Tbx18 during kidney development. Zmym2 PB mouse is the first model to demonstrate roles of Zmym2 in neuroethology and endocrinology, extending its significant beyond genitourinary defects and embryonic development. Further investigation of these phenotypes in CAKUT patients carrying ZMYM2 mutations will enhance our understanding of their phenotypes and improve strategies for early diagnosis, monitoring, and treatment.

first: Ye

last: Yin

first: Qian

last: Shen

first: Hong

last: Xu


title: RNA-seq of 3xTg-AD and WT brain cortex and hippocampus regions

first: Ying

last: Shao

address: 3500 N Broad St, MERB1083A

institute: Temple University

summary: Background: Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by memory impairment. Neuroinflammatory processes, mediated by glial and immune cells, contribute to neuronal damage. Emerging evidence implicates innate immune mechanisms, including trained immunity and cell trans-differentiation, in AD pathogenesis, though their roles remain unclear. Objective: To investigate transcriptomic changes in the 3xTg-AD mouse model, focusing on trained immunity and cell trans-differentiation in disease mechanisms. Methods: RNA-sequencing was performed on brain tissue (cortex plus hippocampus) from 11-month-old female 3xTg-AD and wild-type mice (n = 3/group). Differentially expressed genes (fold change > 1.5, p < 0.05) were identified and followed by bioinformatics and knowledge-based transcriptomic profiling. Public AD datasets were also analyzed. Results: 3xTg-AD mice exhibited 316 upregulated and 412 downregulated genes. Downregulated genes included those for blood-brain barrier protein, while upregulated genes related to cerebrospinal fluid. Increased expression of proinflammatory markers, as well as genes related to cell differentiation, proliferation, activation, and adhesion. Upregulation of genes associated with cell migration and trans-differentiation suggests a potential role for inflammation and cellular plasticity. Additionally, genes involved in inflammasome pathways, immunometabolism, and trained immunity were upregulated. Mechanistically, these genes were modulated by knockdown of trained immunity promoter SET-7, overexpression of trained immunity inhibitor IL-37, and knockout of inflammasome genes IL-1 receptor, caspase-1, and pattern recognition receptor CD36. Conclusions: The finding underscore the potential role of trained immunity and cell trans_x0002_differentiation in AD, revealing a mechanistic framework in which danger-associated molecular patterns drive innate immune responses, inflammasome activation, and cell plasticity contribute to AD, offering therapeutic targets for neuroinflammation and cellular reprograming.

overall_design: RNA were extracted from brain including cortex and hippocampus that isolated from eleven-month-old female 3xTg-AD and C57BL/6J mice and then sent for sequencing.

first: Saaoud

last: Fatma

first: Yang

last: Xiaofeng


title: Intestinal region-specific functions of AHR in intrinsic enteric neurons during infections

city: Hangzhou

first: Heping

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

summary: Intrinsic enteric neurons (iENs) form a crucial neuronal network within the myenteric and submucosal plexus of the gastrointestinal tract, primarily responsible for regulating gut peristalsis. The mechanisms by which iENs sense and integrate dietary and microbial signals to regulate intestinal homeostasis and inflammation remain unclear. Here we showed that environmental sensor aryl hydrocarbon receptor (AHR) was expressed in different iEN subsets in the ileum and colon, and AHR ligands differentially modulated iEN activity in these regions. Genetic perturbation of Ahr in neurons increased iEN activation in the ileum but conversely decreased it in the colon in response to different intestinal pathogens. Furthermore, neuronal AHR deficiency enhanced the clearance of bacterial pathogens, which was associated with increased proliferation and abundance of group 3 innate lymphoid cells in the ileum. Together, our findings demonstrate the region-specific functions of AHR in neurons in response to infections.

overall_design: For single-nucleus RNA sequencing of iEN nuclei, AhrΔActl6b: Sun1-GFP (CKO) and Ahrflox/flox: Sun1-GFP (CTL) mice were infected with Citrobacter rodentium ( 2×109 CFU in 200 μl of PBS) by oral gavage. The ileum and colon muscularis externa were harvested on day 7 after the infection for nucleus isolation and fluorescence-activated cell sorting (FACS). Flow-sorted GFP-positive iEN nuclei were pooled for gene expression library and Feature Barcode library construction via using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10×Genomics). For single-cell RNA sequencing of  ILCs and T helper cells, AhrΔActl6b (CKO) and Ahrflox/flox (CTL) mice were infected with Citrobacter rodentium ( 2×109 CFU in 200 μl of PBS) by oral gavage. The intestinal immune cells in the lamina propria of the ileum were obtained on day 7 after the infection for fluorescence-activated cell sorting (FACS). The flow-sorted ILCs and T helper cells (Viability-CD45+Lin-(CD11c, CD11b, Gr-1, CD19, NK1.1, FcεRIa, TCRγ/δ, CD8α)CD90.2+) were pooled for gene expression library and Feature Barcode library construction via Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10×Genomics).

first: Zijia

last: Sun

first: Shaorui

last: Liu

first: Yinsheng

last: Wang


title: Disruption of Fibroblast MYD88 Signaling Promotes Antitumor Immunity in Pancreatic Ductal Adenocarcinoma [scRNAseq_col1a1myd88]

city: Stanford

first: Daniel

last: Delitto

address: 257 Campus Dr

institute: Stanford University

summary: Pancreatic ductal adenocarcinoma (PDAC) continues to carry a dismal prognosis. The disease is characterized by a uniquely dense fibrotic matrix generated by cancer-associated fibroblasts (CAFs). We have previously demonstrated that fibroblast-driven chronic inflammation suppresses T cell function through a MYD88-dependent mechanism. While extensively studied in myeloid cells, the role of MYD88 signaling in CAFs and its effects on PDAC remain poorly understood. In this study, we identify a MYD88-driven inflammatory CAF population in PDAC using a combination of bulk, single-cell, and spatial transcriptomic studies. Using an innovative collagen gel implantation model, we demonstrate that loss of MYD88 in CAFs enhances T cell infiltration and suppresses tumor growth. Combining MYD88 inhibition with immune checkpoint blockade significantly reduces tumor size and enhances antitumor immune responses, underscoring its potential as a therapeutic target in PDAC.

overall_design: Following implantation of the KPC-seeded collagen gels into tamoxifen induced Col1a1CreERT2 MyD88fl/fl mice or control mice, tumors were harvested and dissociated into single cells using the Miltenyi Mouse Tumor Dissociation Kit and analyzed using scRNA-seq.

first: Maria

last: Korah

first: Rosyli

middle: F

last: Reveron-Thornton

first: Mahsa

last: Fallah


title: Junctional Epithelial Plakoglobin facilitates intestinal inflammation by p38MAPK-Dependent Activation of the Inflammasome

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

summary: Background and Aims: Desmosomes play an underexplored role in intestinal epithelial homeostasis and have been linked to the pathogenesis of inflammatory bowel diseases. Here, we assessed a novel function of the desmosomal plaque protein plakoglobin (JUP) in initiating the innate immune response that facilitates intestinal inflammation. Methods: Surgical tissue samples of patients with Crohn’s Disease (CD) were collected and characterized for junctional protein changes. Mouse models using an intestinal epithelial-specific and inducible VilCreERT2-mediated conditional knockout of Jup under basal conditions and in acute dextran-sodium sulfate (DSS)-induced colitis were characterized using functional analyses, single cell and bulk sequencing. Intestinal organoids served to determine molecular mechanisms. Results: In patients with CD and in murine DSS colitis, loss of JUP was evident. Intestinal epithelial-specific knockout of Jup in mice resulted in augmented submucosal infiltration of macrophages and neutrophils and in an overall activation of the inflammasome. However, loss of intestinal barrier function, bacterial translocation or altered microbial composition were absent under basal conditions. In DSS-induced colitis, epithelial Jup-deficiency led to increased disease activity and strong activation of interleukin IL23/17-signalling compared to littermate controls with neutrophils representing the major source of IL23 under these conditions. Mechanistically, intestinal epithelial organoids lacking Jup demonstrated robust NLRP1 inflammasome activation due to p38MAPK hyperphosphorylation. This activation was evidenced by increased expression of NLRP1, IL1β, and IL18 in Jup-deficient intestinal epithelial cells, which was mitigated by p38MAPK inhibition.  Conclusion: These findings point to a novel role for JUP in initiating intestinal inflammation. The loss of JUP in tissues from CD patients underscores its potential relevance in disease pathology.

first: Natalie

last: Burkard

first: Panagiota

last: Arampatzi

first: Nicolas

last: Schlegel


title: Aberrant basement membrane production by hepatic stellate cells in MASLD is attenuated by the bile acid analog INT-767

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

summary: Background: The farnesoid X receptor (FXR) is a leading therapeutic target for MASH-related fibrosis. INT-767, a potent FXR agonist, has shown promise in preclinical models. We aimed to define the mechanisms of INT-767 activity in experimental MASH and dissect cellular and molecular targets of FXR agonism in human disease. Methods: Leptin-deficient ob/ob mice were fed a MASH-inducing diet for 15 weeks prior to study start. After baseline liver biopsy and stratification, mice were allocated to INT-767 (10 mg/kg/day) or vehicle treatment for 8 weeks, either alongside ongoing MASH diet (progression) or following conversion to normal chow (reversal). Effects on extracellular matrix remodelling were analyzed histologically and by RNA-sequencing. Serum fibrosis biomarkers were measured longitudinally. Human liver samples were investigated using bulk and single-cell RNA-sequencing, histology, and cell culture assays.  Results: INT-767 treatment was antifibrotic during MASH progression but not reversal, attenuating accumulation of type I collagen and basement membrane proteins (type IV collagen, laminin). Circulating levels of PRO-C4, a type IV collagen formation marker, were reduced by INT-767 treatment and correlated with fibrosis. Expression of basement membrane constituents also correlated with fibrosis severity and adverse clinical outcomes in human MASH. Single-cell RNA-sequencing analysis of mouse and human livers, and immunofluorescence staining colocalized FXR and basement membrane expression to myofibroblasts within the fibrotic niche. Treatment of culture-activated primary human hepatic stellate cells with INT-767 decreased expression of basement membrane components. Conclusion: These findings highlight the importance of basement membrane remodelling in MASH pathobiology and as a source of circulating biomarkers. Basement membrane deposition by activated hepatic stellate cells is abrogated by INT-767 treatment and measurement of basement membrane molecules should be included when determining the therapeutic efficacy of FXR agonists.

overall_design: RNA-seq of poly A-enriched RNA isolated from AMLN ob/ob-MASH mouse model following treatment with INT-767 (n=4) or vehicle (n=7).

first: Kristoffer

last: Rigbolt

first: Prakash

last: Ramachandran

first: Jonathan

last: Fallowfield


title: Genome-wide occupancy profiling of Foxa2 in iHepC [ChIL-seq]

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We investigated which genomic regions the transcription factor Foxa2, ectopically introduced to induce hepatocyte-like cells (iHepCs) from MEFs through direct reprogramming, binds to in iHepCs.

overall_design: We performed ChIL-seq analysis for Foxa2 in iHepC to determine its binding sites on the genomic sequence.

first: Ryoga

first: Kenichi

last: Horisawa


title: ABCC4 impairs the clearance of plasma LDL cholesterol through suppressing LDLR abundance on hepatic surface

first: Luzhang

last: Ji

summary: Low expression level of low-density lipoprotein receptor (LDLR) on the surface of hepatocytes contributes to hypercholesterolemia and ultimately is the primary determinant of atherosclerotic cardiovascular disease (ASCVD)，which is the leading cause of death in humans globally. Here, we report that inhibition of hepatocyte ABCC4, identified as a top hit from large-scale CRISPR/Cas9 screens, significantly increases hepatic LDLR abundance and LDL cholesterol clearance. As a hepatic transporter for cAMP efflux, ABCC4 silencing alters its intracellular distribution and  activates downstream Epac2/Rap1a signaling pathway, which ultimately downregulates PCSK9 protein expression, thereby blocking lysosomal degradation of LDLR. Furthermore, in both animal and cell models, we demonstrate that liver-specific disruption of ABCC4 and pharmacological inhibition of ABCC4 enhance hepatic plasma membrane LDLR expression and lower plasma LDL cholesterol level through ABCC4-cAMP-PCKS9 pathway. Collectively, genome-wide CRISPR screening offers a valuable resource for identifying LDLR modifiers, providing potential insights for therapeutic strategies in hypercholesterolemia and atherosclerosis.

overall_design:
RNA seqencing of AML12 cells knockouting Abcc4 or Rosa26.
AML12 cells treated with DMSO or Ceefourin-1.


title: Single-Cell RNA Sequencing Defines Developmental Progression and Reproductive Transitions in Pneumocystis carinii

city: Newport

first: Aaron

last: Albee

state: KY

address: 17 Youngs Ct

institute: University of Cincinnati

summary: This study presents the first single-cell RNA sequencing (scRNA-seq) atlas of Pneumocystis carinii, generated from isolated organisms recovered from the bronchoalveolar lavage fluid of infected rats to map the life cycle of P. carinii.

overall_design: scRNA-seq profiling of wildtype P. carinii, The filtrates were centrifuged at 2500 x g to pellet fungal cells, which were resuspended in 0.85% ammonium chloride solution at 37°C.  for 10 minutes to lyse red blood cells. After centrifugation, the resulting pellets were maintained in RPMI 1640 medium (Fisher Scientific, Pittsburgh, PA) supplemented with 20% fetal bovine serum (Cytiva, Sweden AB), MEM Non-Essential Amino Acids (Gibco, Pittsburgh, PA), MEM Vitamin Solution (Gibco, Pittsburgh, PA), penicillin-streptomycin (10,000 µg/mL,10,000 µg/mL; Gibco, Pittsburgh, PA), and vancomycin (5 mg/mL; Fisher Scientific, Pittsburgh, PA). Following extractions, incubation at 37°C for 30 minutes in T25 tissue culture flasks facilitated host cell adherence and enabled the enzymatic degradation of extracellular DNA using DNase I (Thermo Fisher Scientific, Waltham, MA). DNase I was applied at a concentration of 100 U/mL for effective DNA removal in cell culture systems. P. carinii organisms were collected from the supernatant, followed by centrifugation at 2500 x g to pellet and resuspended in 1 mL of 2% Ficoll-Hypaque before placement on a Ficoll gradient (38). We used a Ficoll-Hypaque gradient (Ficoll: Millipore, Billerica, MD; Hypaque: Sigma, St. Louis, MO). The gradient was prepared with Ficoll concentrations diluted in 16% sodium diatrizoate, ranging from 2% to 12% increments. Following centrifugation, each layer was collected, and the cells were rinsed with cold Dulbecco’s Phosphate-Buffered Saline (DPBS; Fisher Scientific, Pittsburgh, PA) and pelleted by centrifugation at 2500 × g. To minimize cell clumping, pellets were gently resuspended using a 20-gauge ball-tip gavage needle (Becton Dickinson & Co., Franklin Lakes, NJ) before final centrifugation at 2500 x g. The resulting samples were reconstituted in Mg²⁺ and Ca²-free RPMI 1640 medium (Fisher Scientific, Pittsburgh, PA) supplemented as described above.

first: Aleksey

last: Porollo

first: Melanie

last: Cushion


title: NGF stimulation alters the transcriptome and surface TrkB expression in axons of dorsal root ganglia neurons

city: Wuerzburg

first: Michael

last: Briese

state: Bavaria

address: Versbacherstr. 5

department: Institute of Clinical Neurobiology

institute: University Hospital Wuerzburg

summary: Nerve growth factor (NGF) is released after injury from macrophages and other cell types and induces an inflammatory response in neurons, characterized by local subcellular reactions and transcriptomic modulation. NGF-induced axonal transcriptome modulation may be crucial for pain initiation and maintenance. To explore these acute modulations, we cultured dorsal root ganglion neurons in microfluidic chambers and stimulated the axons with NGF. We found that axonal levels of the Il7 transcript encoding interleukin-7 (IL-7) are increased after NGF stimulation, followed by IL-7 release from axons. In growth cones of sensory neurons, we also observed a reorganization of the ribosomal subunits 60S and 40S in response to NGF stimulation. In addition, a dynamic change in the spatio-temporal distribution of the Tropomyosin Kinase B (TrkB) receptor occurs at the plasma membrane of sensory neuron growth cones. TrkB is recruited from the endoplasmic reticulum (ER) leading to increased cell surface levels. De-novo synthesis of TrkB seems to be limited to somatic regions of sensory neurons. Thus, cytosolic mechanisms within distal regions of the sensory neurons may autonomously regulate signaling and translation in response to external NGF stimuli.

overall_design: RNA-seq profiling of the somatic and axonal compartment of cultured DRG neurons stimulated with either NGF or CNTF.

first: Maximilian

last: Koch

first: Manas

last: Kshirsagar

first: Ankita

last: Rawat

first: Abdolhossein

last: Zare

first: Felicitas

last: Schlott

first: Thorsten

last: Bischler

last: Sendtner


title: YBX1-interacting small RNAs and RUNX2 can be blocked in primary bone cancer using CADD522

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

summary: Primary bone cancer (PBC) comprises several subtypes each underpinned by distinctive genetic drivers. This driver diversity that produces novel morphological features plus clinical behaviour serendipitously makes an excellent model to study metastasis. Here we report that some transfer RNA-derived small RNAs termed tRNA fragments (tRFs) act as a constitutive tumour suppressor mechanism by blunting potential metastatic protein-RNA interaction, a mechanism lost in PBC progression. We demonstrate a gradual loss of tRNAGlyTCC cleavage into 5’ end tRF-GlyTCC when comparing low-grade, intermediate-grade and high-grade clinical samples. Contrarily, we show recurrent activation of microRNA-140 leading to upregulated RUNX2 in high-grade clinical samples. Mechanistically, loss and gain of function studies using antisense LNA inhibitors plus RNA mimics revealed that ectopic tRF-GlyTCC reduced RUNX2 and dispersed tumour sphere architecture in vitro. This mode of RNA silencing is sequence specific because tRF-GlyTCC and RUNX2 share a motif in their 3’ ends. Rather than perform in an AGO2-dependent complex to achieve gene silencing, this motif matches the YBX1 recognition site known to stabilise metastatic messenger RNAs, which iCLIP experiments revealed includes RUNX2. Discovery of this novel tRF-GlyTCC-RUNX2 axis led to in vivo development of the RUNX2 transcription factor/ATP synthase inhibitor CADD522 as a PBC treatment in mice.

overall_design: Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP-seq) of YBX1 protein done in triplicate

first: Darrell

last: Green

first: Archana

last: Singh

first: Karan

last: Shah

first: Luke

last: Tattersall

first: Victoria

last: Tippett

first: Chileleko

last: Siachisumo

first: Nicole

last: Ward

first: Paul

last: Thomas

first: Simon

last: Carter

first: Lee

last: Jeys

first: Vaiyapuri

last: Sumathi

first: Iain

last: McNamara

first: David

last: Elliott

first: Alison

last: Gartland

first: Tamas

last: Dalmay

first: William

last: Fraser


title: CTHRC1 is a new therapeutic target and serum diagnostic biomarker for aortic dissection

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

institute: Tongji University

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

overall_design: Refer to individual Series


title: Decidual ESF co-culture with primary EVTs

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

summary: Endometrial Stromal Fibroblasts, Decidualized Endometrial Stromal Fibroblasts (dESF), Extravillious Trophoblasts (EVTs) and co-cultured EVTs and dESFs

overall_design: 3 sample each of ESFs, dESFs, EVTs, dESFs after co-culture with EVT, and EVTs after co-culture with dESFs

first: Kshitiz

last: Gupta

first: Wenqiang

last: Du


title: Therapeutic Efficacy of Oncolytic Adenovirus YSCH-01 in Osteosarcoma: Evaluation Using PDX and CDX Mouse Models

first: Hanqiang

last: Jin

address: Pujian Road No.160

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: Abstract Background: YSCH-01, a recombinant L-IFN adenovirus injection, is an oncolytic virus- based anticancer drug with dual anti-tumor effects. In previous studies, we have confirmed the potential of YSCH-01 in the treatment of malignant gliomas. Additionally, YSCH-01 has emerged as a promising candidate for osteosarcoma treatment, exhibiting significant antitumor properties. However, its specific role in osteosarcoma and the underlying mechanisms remain poorly understood. Methods: We evaluated the infectivity and efficacy of YSCH-01 in osteosarcoma cells by collecting clinical samples of osteosarcoma and conducting experiments using osteosarcoma cell lines both in vitro and in vivo. Additionally, we studies the impact of YSCH-01 on interferon overexpression at the RNA and protein levels to highlight its potential antitumor properties. Furthermore, RNA-seq analysis of tumor samples treated with YSCH-01 provided valuable insights into the altered gene expression profiles and signaling pathways, helping to elucidate the molecular basis of its antitumor effects. Results: Our findings demonstrated the dose-dependent infectivity of YSCH-01 in osteosarcoma cells, with varying effects observed across different cell lines. Both in vitro and in vivo studies showed that YSCH-01 effectively inhibited osteosarcoma cell proliferation. In CDX and PDX animal models, YSCH-01 exhibited potent therapeutic effects, particularly in terms of its distant effects. Additionally, IFN-αsignaling pathway was activated in the tumor tissues with YSCH-01 treatment. Conclusions: The initial findings of this study revealed the complex molecular pathways through which YSCH-01 exerts its antitumor effects in osteosarcoma. By elucidating the correlation between key molecular markers in osteosarcoma and patient outcomes, we have identified potential therapeutic targets, presenting a promising avenue for osteosarcoma treatment. Keywords: Osteosarcoma; Oncolytic Virus; YSCH-01; L-IFN.

first: Ruoyu

last: Chen

first: Jin

last: Huang

first: Xue-ping

last: Cao

first: Xian-long

last: Fang

first: Ning

last: Li

first: Kang-jian

last: Zhang


title: Calcium dysregulation is the critical initiator in high dose chloroquine-induced programmed cell death of Plasmodium falciparum

city: Edinburgh

first: Tianchi

last: Zhou

address: Crewe Rd S

institute: University of Edinburgh

summary: Understanding the mechanism of action of novel antimalarial drugs is a key goal in eradicating malaria. Previously we have explored a possible alternative cell death mechanism that is elicited by micromolar amounts of the antimalarial chloroquine (CQ) against Plasmodium falciparum. The phenotypes assessed were calcium redistribution, mitochondrial depolarization and parasite digestive vacuole membrane permeabilization. Identifying the source or initiator of calcium release in the parasite will reveal a potential new therapeutic target. From timepoint studies we revealed the simultaneous loss of mitochondrial integrity along with intracellular calcium dysregulation, followed by downstream membrane rupture. Using a series of calcium efflux inhibitors and antioxidants, mitochondrial calcium (Ca2+mt) was implicated in initiating this cascade of parasite cell death phenotypes. Having established the mechanism with a high dose concentration of CQ, we expanded the search for similar phenotypic outcomes in a high-content screening of the Medicines for Malaria Venture (MMV) Pathogen Box. Three “hit” compounds were subjected to further characterization assays and the top performing compound (MMV085071) was identified. Ten analogues based on the top hit were assessed with dose-response assays and one lead analogue (MMV1545561) was selected as the top candidate based on its efficacy. Both parent and lead compound were investigated for their ability to redistribute Ca2+mt. While the effects were statistically significant, the lack of complete reversal of compound-induced calcium dysregulation and mitochondrial collapse by inhibitors suggested that Ca2+mt’s role is more limited as compared to that of chloroquine. Furthermore, it is likely that the novel screening compounds are directed at multiple parasite targets and due to their highly efficacious nature, further follow-up work to ascertain their mechanism of action is warranted.

overall_design: P. falciparum 3D7 strain parasites were synchronized with sorbitol and MACS sorting to enrich those in schizont stage. The enriched schizonts were seeded at 1.5-2% parasitemia at 1.25% haematocrit. Further synchronisation by sorbitol was performed 12 hours post seeding to ensure all parasites were synchronised at the ring stage. Drug treatments starts when parasites reach mid-to-late trophozoite stage. The infected RBCs were given fresh MCM and incubated for 4 hours, with 3uM MMV 085071, MMV 1545561, CQ or the same volume of DMSO resuspended in MCM medium.

first: Trang Thi Thu

last: Chu

first: Jie Xin

last: Tong

first: Kevin Shong-Wei

last: Tan


title: Linoleic acid-induced ANGPTL4 inhibits C2C12 skeletal muscle differentiation by suppressing Wnt/β-catenin.

city: Athens

first: Chad

middle: Michael

last: Paton

state: Georgia

address: 100 Cedar St.

department: Nutritional Sciences

institute: University of Georgia

summary: To evaluate the effects of free fatty acids (FFAs) on skeletal muscle differentiation in vitro.

overall_design: Comparative gene expression profiling analysis of RNA-seq data to determine which pathways and targets were differentially regulated in response to LA as well as ANGPTL4.

first: Yura

last: Son

first: Walter

last: Lorenz


title: Disruption of Fibroblast MYD88 Signaling Promotes Antitumor Immunity in Pancreatic Ductal Adenocarcinoma [scRNAseq_ICBCA4948tx]

first: Daniel

last: Delitto

overall_design: Following implantation of the KPC-seeded collagen gels into C57BL/6J mice, mice underwent treatment with ICB alone, ICB with CA-4948, and control. Tumors were harvested and dissociated into single cells using the Miltenyi Mouse Tumor Dissociation Kit and analyzed using scRNA-seq.

first: Maria

last: Korah

first: Rosyli

last: Reveron-Thornton

first: Mahsa

last: Fallah


title: KIF11 and its inhibitor SB-743921 inhibit acute myeloid leukaemia (AML) by blocking the cell cycle

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

summary: Acute myeloid leukaemia (AML) is a highly heterogeneous haematological malignancy with limited prognostic improvement despite evolving therapeutic strategies.KIF11 is a member of the kinesin family and a microtubule-associated motility protein that plays a key role in spindle dynamics during cellular mitosis and is overexpressed in leukaemias including AML. Studies have shown that inhibition of KIF11 leads to spindle pole collapse, which prevents chromosome segregation and leads to cell death; this identifies KIF11 as a potential therapeutic target.SB-743921, a novel selective inhibitor of KIF11, has shown anti-tumour activity in a variety of cancers, including breast, lung, and cholangiocarcinoma. Our study shows that SB-743921 can effectively inhibit the proliferation of AML cells and induce cell cycle arrest, thereby hindering tumour growth. In vitro experiments showed that SB-743921 exhibited significant cytotoxicity against several AML cell lines, and its IC50 value indicated that these cells were very sensitive to SB-743921. Further in vivo studies in AML mouse models treated with SB-743921 showed that the drug significantly delayed tumour progression while prolonging survival with minimal toxic side effects. In addition, RNA sequencing analysis showed that SB-743921 inhibited tumour cell proliferation by down-regulating key signalling pathways, including MYC, E2F and G2M. These findings suggest that KIF11 plays a crucial role in the onset and progression of AML. As its inhibitor, SB-743921 has significant anti-tumour effects and is an innovative targeted agent for the treatment of AML. This discovery provides new insights into potential clinical applications for the treatment of this challenging malignancy.

overall_design: mRNA profiles of CMK cells treated with 4nmol SB-743921 or not for 24 h were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Linbo

last: Cai

first: Jian

last: Pan


title: Disruption of Fibroblast MYD88 Signaling Promotes Antitumor Immunity in Pancreatic Ductal Adenocarcinoma [BulkRNA-seq_LPSstim]

overall_design: Cancer-associated fibroblasts (CAFs) isolated from PDACs were stimulated with LPS and control and underwent bulk RNA sequencing.


title: Sertraline Hydrochloride Exposure Leads to Reactive Oxygen Species Burst in Model Microalgae Species (Raphidocelis subcapitata)

status: Public on Aug 18 2025

city: Duluth

first: Phillip

last: Ankley

state: MN

address: 6201 Congdon Blvd

institute: U.S. EPA

summary:
Microalgae play important ecological roles and serve as useful models for assessing impacts of environmental contaminants on lower trophic aquatic organisms. Sertraline, a commonly prescribed selective serotonin reuptake inhibitor (SSRI) found in urban waters, has been observed to induce chlorosis in Raphidocelis subcapitata close to environmentally relevant concentrations.
This study estimated potentially hazardous concentrations of sertraline hydrochloride by deriving transcriptomic and metabolomic points of departure (tPODs and mPODs) below which chronic adverse effects would not be expected. Additionally, an Adverse Outcome Pathway describing the mechanism by which sertraline hydrochloride impacted R. subcapitata was proposed using a multi-omics approach. The mPOD derived from nontargeted metabolomics was comparable to the tPOD (455 µg/L vs 690 µg/L) and annotated dysregulated metabolites along with reduced photosynthetic capability indicated that uncoupling of the cyclic electron flow required for photosynthesis led to a reactive oxygen species (ROS) burst. This probable ROS burst altered cell membrane composition and downregulated genes associated with protoporphyrinogen IX and heme biosynthesis pathways. This research highlights the molecular mechanisms underlying pharmaceutical-induced chlorosis in a model microalgae species and demonstrates the utility of integrating metabolomics and transcriptomics for assessing the potential ecological risks of SSRIs.

overall_design: R. subcapitata (5 × 106 cells/mL) were exposed to nominal concentrations of 50, 125, 314, 784, 1,960, 4,900, 12,250, and 30,620 µg sertraline hydrochloride/L (CAS #: 79559-97-0; Purity: ≥ 98.0 %, Millipore-Sigma, MA, USA) or solvent control (0.01% DMSO) for 24 h in triplicate plates in 96-deep-well (2.0 mL) plates using 800 µL of solution per well (Catalog # 267007; Beckman Coulter, CA, USA) sealed with gas-permeable, optically clear adhesive covers (BEM-1, Diversified Biotech, MA, USA). There were five replicate wells per treatment (one replicate well per concentration for atrazine), per plate (n = 3), with treatments distributed such that there were equal numbers of interior and exterior (edge) wells for each treatment. Throughout the 24 h exposure period, R. subcapitata were held under constant light and kept in suspension by gentle shaking using a temperature controlled orbital shaker (Titramax 1000, Heidolph Instruments GmbH, Germany). RNA was extracted from pooled homogenates (n = 3) using Plant/Fungi Total RNA Purification kits (Catalog #31900, Norgen Biotek, Ontario, Canada) with a protocol slightly modified from the manufacturer’s instructions. Total RNA was shipped to the Michigan State University Research Technology Support Facility Genomics Core for library preparation using QuantSeq 3’ mRNA-Seq V2 Library Prep Kit (Lexogen GmbH, Austria) and sequenced on NovaSeq SP flow cells (Illumina, Inc, CA, USA).

first: Justin

last: Stewart

first: Mackenzie

last: Nash

first: Peter

last: Schumann

first: Kevin

last: Flynn

last: Villeneuve


title: RNA sequencing analysis of embryos exposed to nanoplastics: effects on developmental and transcriptomic alteration

city: Jeongeup-si

first: Hyeongju

last: you

state: Jeongeup-si

address: Primate resource center

institute: KRIBB

summary: The increasing prevalence of nanoplastics (NPs) in the environment has raised concerns regarding their potential risks to ecosystems and human health. NP exposure has been shown to interfere with cellular processes; however, their effects on preimplantation embryonic development remain unclear. Given the critical role of zygotic genome activation and early cell cycle progression, disruption during this period can significantly affect embryonic viability. To investigate the molecular effects of polymethylmethacrylate (PMMA)-NPs on early embryonic development, mouse zygotes were exposed to 0.1 or 1 mg/mL PMMA-NPs, and RNA sequencing was performed on four-cell stage embryos. Differential gene expression analysis revealed that 0.1 mg/mL NP exposure affected genes related to DNA damage repair, transcriptional regulation, and cellular homeostasis while 1 mg/mL NP exposure altered the expression of genes associated with apoptotic signaling, cell cycle arrest, and failure of blastocyst formation, suggesting a concentration-dependent effect on developmental progression. Thus, PMMA-NP exposure disrupts early embryonic development by inducing specific transcriptomic changes that potentially affect genome integrity and developmental competency. This study provides new insights into the molecular mechanisms underlying NP-induced embryo toxicity and elucidate the effect of NPs on preimplantation embryo development.

overall_design: RNA sequencing profiling on mouse 4-cell embryos sampled after treatment with nanoplastics at concentrations of 0, 0.1, and 1 mg/mL.

first: Hyeong-Ju

last: You

first: Yu-Jin

last: Jo

first: Jeongwoo

last: Kwon

first: Seung-Bin

last: Yoon

first: Changsic

last: Youn

first: Yejin

last: Kim

first: Man-Jong

last: Kang

first: Ji-Su


title: Synergistic effects of Ret coding and enhancer loss-of-function alleles cause progressive loss of inhibitory motor neurons in the enteric nervous system

city: New York

first: Sumantra

last: Chatterjee

state: NY

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Grossman School of Medicine

summary: Hirschsprung disease (HSCR) is a congenital enteric neuropathy caused by disrupted migration, proliferation, or differentiation of enteric neural crest-derived cells (ENCDCs), with pathogenic variants at the RET locus accounting for a major fraction of cases. While coding variants in RET are known to impair enteric nervous system (ENS) development, the contribution of non-coding regulatory elements remains incompletely understood. The greatest contribution of this risk is from a common variant (rs2435357) in an ENS-active, SOX10-bound RET enhancer (MCS+9.7) that reduces RET expression in vivo and triggers expression changes in other ENS genes in the human fetal gut. Here, we investigate the role of this enhancer during ENS development using a targeted mouse model by deleting mcs9.7. Single-cell RNA-seq profiling of wildtype and homozygous delmcs9.7/ delmcs9.7 embryos revealed an ~8% decrease in RET expression within ENS clusters, with no gross shifts in ENS cell type composition. Ret expression loss was limited to early differentiating neurons and inhibitory motor neurons, indicating cell-type-specific enhancer control. To identify the Ret functional threshold for normal ENS development, we also generated a compound heterozygous mouse (+/delmcs9.7/;+/CFP) that showed additive reductions in Ret expression in these same cell types and bidirectional feedback between Ret and its upstream transcription factor Sox10. We observed reduced expression of 19 cell cycle genes and significant loss of nNOS+ and VIP+ neurons, consistent with decreased inhibitory neuron network driven by loss of proliferation, a hallmark of HSCR. These findings establish a biphasic, cell-type-specific role for the mcs9.7 enhancer in modulating Ret dosage and reveal how subtle enhancer perturbations alter neural subtype specification without overt aganglionosis. Together, our work uncovers the functional consequences of a common RET enhancer variant offering new insights into gene regulatory mechanisms driving HSCR.

overall_design: single cell RNA seq of dissociated GI tract of E14.5 mouse embryos using 10X genomics platform. This included wildype, dleetion of a partiuclar Hirschsprung disease asscoaited enhancer for the gene Ret ((mcs+9.7) and a double heterzygous mice where both the gene Ret and the enhnacer have been deleted (+/delmcs+9.7;+/CFP). These cells were dissocoaited from teh embryonic gut with accumax and single cell sequencing libraries using Chromium Single Cell technology platform's 3'' RT-based assays


title: Molecular Pathogenesis of Alzheimer's Disease Onset in a Mouse Model: Effects of Cannabidiol Treatment

city: Loma Linda

first: Erik

last: Behringer

state: CA

address: 11041 Campus St.

department: Basic Sciences

institute: Loma Linda University

summary: Alzheimer’s disease (AD) is a common neurodegenerative condition involving a complex blend of disturbances in synaptic development and maintenance, neurovascular cross-talk, ionic and nutrient transport, and mitochondrial metabolism. The precise molecular profile of AD onset with insight for major pathological contributors remains unclear with corresponding impedances in therapeutic development. The current study sought two objectives, as (i) to resolve the molecular pathogenesis from cognitive impairment to the onset of AD-like neuropathology and (ii) whether the novel agent cannabidiol (CBD), noted for its neuroprotective effects, influences the molecular transition associated with AD onset. Dietary CBD was administered daily (80-100 mg/kg/day) in male 3xTg-AD mice and wild-type B6129SF2/J animals from 4.5 to 6.5 mo of age with inclusion of vehicle controls. RNA sequencing encompassed longitudinal and cross-sectional blood and brain samples respectively. Metabolomics and behavioral analyses examined brain regions (cortex, hippocampus) and associated integrated neurocircuitry. There were >1,000 differentially expressed markers of AD onset, whereby >75% were either eliminated or reversed in the direction of expression in response to CBD. Signaling pathways encompassed synaptic development and plasticity (e.g., Foxp2), neurovascular interactions (Smad9, Angptl6), receptors and ion channels (Gria4, Chrna2, Rgs7/Rgs7bp), mitochondrial genes (Ndufa7, Cox7a2), immunity (Ncr1), oxidation-reduction (Esr1), lipid synthesis (Fasn, ApoE), and carbohydrate metabolism (Mafa, Mlxipl). As potentially addressable with CBD treatment, AD onset represents molecular integration of neurovascular interactions, channelopathies, metabolic disturbances, and aberrations in developmental genes with involvement of major pathological contributors such as inflammation, oxidative signaling, dyslipidemia, and insulin resistance.

overall_design: RNAseq profiling of whole blood of male B6129SF2/J and 3xTg-AD mice at 4.5 and 6.5 months of age with cannabidiol-treated and vehicle control groups using a longitudinal analysis design. Note that RNAseq profiling was also conducted for isolated brain samples of all study groups at 6.5 mo of age for cross-sectional analyses. In addition, note that this study also performed a cross-sectional analysis among blood and brain samples at 6.5 mo of age across study groups as well.

first: Phoebe

middle: P

last: Chum


title: Computationally resolved neuroprogenitor cell biomarkers   associate with human disorders

city: Houston

first: Gerarda

last: Cappuccio

address: 1250 Morsund street

institute: Baylor College of Medicine

summary: Adult hippocampal neurogenesis, relies on a rare population of neural stem and progenitor cells (NPCs) within the dentate gyrus complex microenvironment. Discovering the specific genes that define these cells is vital yet challenging due to overlapping expression patterns, limiting detection of rare cell populations using traditional approaches. By employing the computational Digital Sorting Algorithm (DSA) on microarray data we identified 129 genes enriched in murine NPCs.

overall_design: Dentate gyri of mice aged between 4 and 12 weeks (five time points for our study, namely 4, 6, 8, 10 and 12 week-of-age)

first: William

last: Choi


title: Role of CRY1 in DNA end resection

city: Sevilla

first: Pablo

last: Huertas

address: Av.Americo Vespucio 24

country: Spain

institute: University of Sevilla

summary: CRY1 is a circadian clock core component. Data in our laboratory has linked this factor with controlling the activity of the DNA double strand break repair protein CtIP, affecting the process of DNA end resection.  By using ChIP-seq approaches in the DiVA cell system, we can show that the absence of CRY1 increases DNA end resection, measured as the accumulation of RPA at the sites of cleavage of the enzyme AsiSI. Furthermore, this is due to an increase in the accumulation of the resection factor CtIP.

overall_design: Chromatin inmunoprecipitation (ChIP-seq) of RPA, CRY1, CRY2 and CtIP in AsiSI-ER U2OS cells

first: Amador

last: Romero-Franco

first: Sonia

last: Jimeno

first: Silvia

last: Jimeno-González


title: Distinct transcriptional profiles in rat thyroid glands after developmental exposure to three in vitro thyroperoxidase inhibiting chemicals

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary: Thyroperoxidase (TPO) is a key enzyme in thyroid hormone (TH) synthesis in the thyroid gland. TPO inhibition can thus disrupt the TH system and cause deleterious effects associated with hypothyroidism. Many industrial chemicals can inhibit TPO activity in vitro, but it remains unclear how this manifest in the thyroid gland at the molecular level during development. Here, we characterized the transcriptome of rat thyroid glands developmentally exposed to either of three in vitro TPO-inhibitors including amitrole, 2-mercaptobenzimidazole (MBI) and cyanamide.

overall_design: Pregnant Sprague-Dawley rat dams were exposed to 10 mg/kg bw/day MBI, 50 mg/kg bw/day amitrole or 15/11.25 mg/kg bw/day cyanamide from gestation day 7 to postnatal day 16. BRB-seq was performed on thyroid glands from 16-days old male pups (n = 7-8, max 2 pups from each of 4 litters).

first: Anna

last: Rosenmai

first: Terje

last: Svingen

first: Bertrand

last: Evrard

first: Louise

last: Ramhøj


title: Desciption of the transcriptome profiles of mouse heart innervating DRG and Nodose Ganglia-derived sensory neurons

city: Istanbul

first: Tuba

last: Akgül Çağlar

address: Kavacik Neighborhood, Ekinciler Street No:19

department: SABITA

country: Turkey

institute: Istanbul Medipol University

summary: To obtain the mRNA expression profiles of vagal and spinal cardiac sensory neurons,  mouse Dorsal Root Ganglia (DRG) and Nodose Ganglia (NG) neurons innervating the heart were labelled by retrograde Di-8-ANEPPQ dye which was injected to the heart. Then bilateral NGs and DRGs between C-T segments were dissected and Di-8-ANEPPQ-labelled DRG and NG neurons were FACS sorted. Finally, Di-8-ANEPPQ+ DRG and NG neurons were subjected to total RNA extraction and library preparation protocols for RNA-seq experiment. For control samples, total NG and DRG (C-T) neurons were dissected from the wt mice and same RNA extraction and library preparation protocols were applied. Finally, mRNA profiles of heart-spesific DRG and NG neurons were compared to those of total DRG and NG populations, respectively.

overall_design: All samples were obtained from female Balb-C mice at 8-12 weeks. The following samples were used for RNA-sequence analysis: The heart-specific DRG (DRG-HS, three samples, each sample was obtained from three or four animals (n=3/4)), the heart-specific NG (NG-HS; two samples, each sample was obtained from two animals), sham DRG (DRG-T; two samples, each sample was obtained from one animal (n=1)), and sham NG (NG-T; two samples, each sample was obtained from one animal (n=2)). By using the RNeasy micro kit (Qiagen), RNA was extracted from each sample. Before further progress, RNA concentrations were measured using Qubit (Thermo Fisher Scientific) and RNA integrities were assessed on Agilent 2100 Bioanalyzer. In RNA Seq, only the samples with the an average of 7.5 RNA integrity number (RIN) were included. RNA libraries were prepared using Truseq Total RNA Sample Preparation Kit v2. 500 ng/µl and 200 ng/µl of RNA were used for each DRG and NG sample, respectively. Fragments were sequenced as paired-end reads (2 x 75 bp) on the Illumina NextSeq 500 platform in İstanbul Medipol University, Center of Genomics.

last: Akgul Caglar

first: Yusuf

last: Enes Kazci


title: Isoformic PD-1 impedes B cell activation and function in HIV-1 infection

city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

summary: The interaction between PD-1 and PD-L1 inhibits activation of HIV-1-specific CD8+ T cells, yet mechanisms underlying B cell dysfunction in HIV-1 infection remain unclear. Here, we identify a key role for Δ42PD-1, an isoform of PD-1, in human B cells. Chronic HIV-1 infection selectively upregulates Δ42PD-1, but not PD-1, on up to 28% of B cells. BCR stimulation induces Δ42PD-1 expression, resulting in B cell cycle arrest and apoptosis. Mechanistically, Δ42PD-1 recruits SHP1 via its intracellular immunoreceptor tyrosine-based switch motif, leading to AKT1 inhibition and suppression of the AKT1/FOXO1 pathway, thus promoting B cell apoptosis. Notably, targeting Δ42PD-1 with a specific antibody or gene knock-down reduces SHP1 recruitment, restores AKT1/FOXO1 activation, and enhances B cell proliferation and function, including in HIV-1 ENV-specific memory B cells. These findings reveal a novel inhibitory Δ42PD-1-SHP1 axis and support Δ42PD-1 as a therapeutic target to restore B cell responses in HIV-1 infection.

overall_design: Sorted Δ42PD-1+, PD-1+ and double negative B cells at 48 hours after the treatment with α-IgM/G F(ab’)2 and CH34 or isotype control IgG2b.

first: Li

last: Liu

first: Zhiwei

last: Chen


title: Comparative transcriptomics of lateral hypothalamic cell types reveals conserved growth hormone-tachykinin dynamics in feeding

city: South San Francisco

first: Kimberle

last: Shen

address: 1 Dna way

institute: Genentech

summary: The lateral hypothalamus (LH) is a highly heterogenous brain region regulating hunger and motivated behaviours. In zebrafish, the LH exhibits distinct neural activity across hunger, feeding and satiety staes. In this study, we have generated a zebrafish LH transcriptomic dataset to profile cellular diversity and molecular signatures underlying feeding behaviour.

overall_design: High throuput single cell RNAsequencing dataset of lateral hypothalamus from 7dpf larval zebrafish from two treatment groups (50 fish per group): "Food deprived" (for four hours) and "Voracious feeding" (food-deprived for four hours and then supplied with paramecia, which correlates with enhanced hunting and feeding.

first: Vindhya

last: Chaganty

first: Caroline Lei

last: Wee


title: Intronic miRNA–directed regulation of mitochondrial RNA editing enhances plant stress tolerance in Arabidopsis

city: Taian

first: Yan

last: kang

state: Shandong

address: No.61, Daizong Street

department: College of Life Sciences

institute: Shandong Agricultural University

summary: MicroRNAs (miRNAs) have emerged as key regulators in plant development and stress responses. Increasing evidence points to the crucial role of intronic miRNA that derived from the introns of other genes in animals, whereas few reports have explored this topic in plants. We report here an RNA splicing–mediated mechanism involved in stress responses, whereby intronic miR400 modulates mitochondrial RNA editing by targeting the PPR1 mRNA. An intronic miR400 splicing–dependent luciferase transgenic line was generated to monitor the intron splicing events. We determined that luciferase activity decreases upon cadmium (Cd) treatment due to the retention of the intron containing miR400, which inhibits the production of mature miR400. Overexpression of MIR400 rendered plants more sensitive to Cd stress, whereas impaired miR400 expression enhanced their tolerance. Genetic and molecular experiments identified the PENTATRICOPEPTIDE REPEAT PROTEIN 1 (PPR1) as the miR400 target responsible for the plant Cd response. In addition, we demonstrate that PPR1 affects RNA editing of the mitochondrial gene ccb206 to control reactive oxygen species accumulation and improve plant tolerance. Our study illustrates intron splicing as a key step in intronic miR400 regulation and highlights the function of intronic miRNA as a “signal transducer” to enhance plant stress tolerance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild–type, OXmiR400 lines and OXrPPR1 lines.

first: Weibo

last: Xu

first: Lei

last: Zhao

first: Kang

last: Yan

first: Gang

last: Wang


title: Mesenchymal Stromal Cells Play an Analgesic Role through a Npy2r Sensory Neuron-Mediated Lung-to-Brain Axis

city: Guangzhou

first: Yueming

last: Sun

state: Guangdong

address: 74th Zhong Shan two street

department: basic medicine

institute: Sun Yat-sen University

summary: Mesenchymal stromal cells (MSC) have emerged as a promising therapeutic option for neuropathic pain (NP), but the mechanisms remain elusive. Using murine pain models, we demonstrated that MSC effectively alleviate pain, with efficacy comparable to dexmedetomidine, a moderate analgesic. Mechanistically, peripheral delivery of MSC activated pulmonary Npy2r-expressing vagal sensory neurons, which project to the nucleus tractus solitarius and ventral lateral periaqueductal gray area, driving analgesia via the vagal lung-to-brain pathway. Chemogenetic activation of Npy2r sensory neurons similarly ameliorated spared nerve injury (SNI)-induced mechanical allodynia and thermal hyperalgesia. Furthermore, we found that MSC-derived extracellular ATP, released via pannexin1, activated Npy2r sensory neurons through purinergic receptor P2X2 (P2rx2). Strikingly, inhalation of a P2rx2 agonist produced significant therapeutic effects in SNI mice. Together, our findings reveal that Npy2r sensory neuron-mediated lung-brain axis underlies MSC-induced analgesia and highlight the potential of targeting body-brain pathways for novel NP treatments.

overall_design: To investigate the biological characteristics of MSCs and HDFs, we performed RNA-seq experiments to compare the transcriptional profiles between cultured MSCs and HDFs.

first: Jing

last: Huang

first: XiaoRan

last: Zhang

first: Andy

last: Peng


title: Dads matter, too: The behavioural and neurogenomic effects of receiving paternal care [ATAC-Seq]

city: University Park

first: Jason

last: Keagy

state: PA

address: 410 Forest Resources Bldg

department: Ecosystem Science and Management

institute: Penn State University

summary: Offspring are often influenced by the care they receive from their parents. However, we know little about the underlying neurogenomic mechanisms. Using a half-sib design, threespine stickleback fish were either raised by their fathers or hand-reared (“orphaned”). As offspring developed, they were tested in one of three behavioural assays: an open field assay with a simulated predator attack, a social behaviour assay with a simulated predator attack, and a scototaxis assay. Offspring that received parental care were bolder, more social, and less anxious. Fish in the open field assay had their brains sampled one hour following the simulated attack; brains were sampled at the same time from full-sib controls. These brains were processed for gene expression (via Tag-seq) and chromatin accessibility (via ATAC-seq). Experiencing paternal care affected brain gene expression, but sex was also a major factor, despite the fish being reproductively immature. The predator attack in the open field assay affected expression of fewer genes. Sex, and to lesser extent, paternal care, also influenced chromatin accessibility at a whole genome scale. Our findings further our understanding of the mechanistic basis for offspring response to variation in the care they receive from their parents.

overall_design: Using a half-sib design, threespine stickleback fish were either raised by their wild-caught fathers (from Putah Creek, CA = Day 10) or hand-reared (“orphaned” = Day 0). Prior to sexual maturity, when these offspring were 6-8 months old, a subset were individually introduced to an open field assay and allowed to explore for 10 minutes. At 10 minutes, a model sculpin was moved through the pool in one complete circuit simulating a predatory attack. The subsequent behaviour of the juvenile fish was observed for an additional 10 minutes. Following this observation, the fish was left in the open field assay without any more disturbance. Sixty minutes after the attack, the juvenile fish was gently captured, euthanized via decapitation and its brain quickly dissected. Half of the brain was placed in RNAlater for subsequent RNA extraction for 3'TagSeq and the other half was placed in cold PBS and Roche cOmplete Mini Protease Inhibitor Cocktail (PIC) for processing for ATAC-seq. Fish were sexed with a DNA marker.

first: Alison

last: Bell


title: Bacterial ADP-Heptose triggers stem cell regeneration in the intestinal epithelium following injury [scRNA-seq]

city: TORONTO

first: Shawn

last: Goyal

state: ON

address: 1 King's College CirToronto, ON M5S 1A8

country: Canada

institute: University of Toronto

summary: ADP-Heptose (ADP-Hep), a metabolite produced by Gram-negative bacteria as an intermediate of lipopolysaccharide biosynthesis, is detected in the host cytosol by the kinase ALPK1, which engages TIFA-dependent innate immune responses. However, the functional role of the ALPK1-TIFA pathway in the intestinal epithelium remains poorly understood.  Here, we use bulk RNA sequencing of murine derived ileal organoids to study the role of ADP-Hep in initiating stem cell regeneration in the intestinal epithelium.

overall_design: Expression profiling of murine derived ileal organoids by highthroughput sequencing

first: Stephen

middle: E

last: Girardin


title: Bacterial ADP-Heptose triggers stem cell regeneration in the intestinal epithelium following injury [RNA-seq]


title: LENG8 Functions as a Quality Control Checkpoint for Nuclear Retention and Degradation of Misprocessed RNAs

city: Irvine

first: Yongsheng

last: Shi

state: California

address: 811 Health Sciences Road, Medical Sciences B Room 262

department: Microbiology & Molecular Genetics

institute: UC Irvine

summary: Quality control is essential for maintaining proper gene expression. For example, aberrantly processed RNAs are retained and degraded in the nucleus, and defects in this process have been linked to various diseases, including cancer and neurodegeneration. However, the underlying mechanisms of RNA nuclear retention and degradation remain poorly understood. Through a genome wide CRISPR screen, we identified not only known factors involved in nuclear RNA degradation but also candidate proteins mediating RNA nuclear retention, including the poorly characterized protein LENG8. Our findings reveal that LENG8 is recruited to pre-mRNAs by splicing factors, including components of the U1 snRNP. Once RNA-bound, LENG8 is both necessary and sufficient to sequester RNA in the nucleus. Depletion of LENG8 leads to the leakage of intron containing RNAs and numerous nuclear noncoding RNAs into the cytoplasm, demonstrating its crucial role in RNA retention. Mechanistically, we further discovered that LENG8 lacks a specific region required for forming an intact TREX2 complex, unlike its paralog GANP. As a result, LENG8 retains misprocessed RNAs in the nucleus through a dominant-negative mechanism of TREX2/GANP, despite its ability to recruit TREX and the PCID2-SEM1 complex. Additionally, LENG8 interacts with the ZFC3H1-MTR4-exosome complex to degrade nuclear-retained RNAs, linking it to both RNA retention and degradation pathways. In conclusion, our study uncovers a novel mechanism of gene expression quality control, highlighting LENG8 as a key regulator of RNA nuclear retention and degradation, with potential implications for human disease.

overall_design: Fraction mRNA-seq to study if misprocessed RNAs are exported into cytoplasm after depletion of LENG8; PAS-seq to study if  IPAs are degraded by LENG8 and if IPAs are exported into cytoplasm after depletion of LENG8

first: Lusong

last: Tian


title: Disrupting tRNA modifications to target mitochondrial vulnerabilities in drug-resistant leukemia cells

city: Heidelberg

first: Fu

address: INF 280

institute: DKFZ

summary: To comprehensively identify cancer-relevant RNA modifications and their regulators, we screened all 150 known human RNA modifying proteins across 18 different normal and cancer lines using a CRISPR-based genetic knockout system.

overall_design: Gene expression profiling of 2 primary human healthy lines (normal human epidermal keratinocytes and normal human epidermal melanocytes) and 16 different cancer cell lines including acute myeloid leukemia, head and neck squamous cell carcinoma, non-small-cell lung carcinoma, melanoma, and multiple myeloma.

first: Cornelius

last: Pauli

first: Michael

last: Kienhöfer

first: Michaela

last: Frye


title: Circulating cell-free RNA signatures for the characterization and diagnosis of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS)

city: Ithaca

first: Anne

last: Gardella

address: 237 Tower Rd

department: Molecular Biology and Genetics

institute: Cornell University

summary: People living with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) experience heterogeneous and debilitating symptoms that lack sufficient biological explanation, compounded by the absence of accurate, noninvasive diagnostic tools. To address these challenges, we explored circulating cell-free RNA (cfRNA) as a blood-borne bioanalyte to monitor ME/CFS. cfRNA is released into the bloodstream during cellular turnover and reflects dynamic changes in gene expression, cellular signaling, and tissue-specific processes. We profiled cfRNA in plasma by RNA sequencing for 93 ME/CFS cases and 75 healthy sedentary controls, then applied machine learning to develop diagnostic models and advance our understanding of ME/CFS pathobiology. A generalized linear model with least absolute shrinkage selector operator regression trained on condition-specific signatures achieved a test-set AUC of 0.81 and an accuracy of 77%. Immune cfRNA deconvolution revealed differences in platelet-derived cfRNA between cases and controls, as well as elevated levels of plasmacytoid dendritic, monocyte, and T cell–derived cfRNA in ME/CFS. Biological network analysis further implicated immune dysfunction in ME/CFS, with signatures of cytokine signaling and T cell exhaustion. These findings demonstrate the utility of RNA liquid biopsy as a minimally invasive tool for unraveling the complex biology behind chronic illnesses.

overall_design: Blood-plasma derived cell-free RNA was isolated and sequenced from 93 patients diagnosed with ME/CFS and 75 healthy sedentary control individuals. The sequencing data was then analyzed to identify blood biomarkers for machine learning diagnostic classifiers and to deepen our biological understanding of ME/CFS.

first: Daniel

last: Eweis-LaBolle

first: Conor

last: Loy

first: Emma

last: Belcher

first: Joan

middle: S

last: Lenz

first: Carl

last: Franconi

first: Sally

middle: Y

last: Scofield

first: Andrew

last: Grimson

first: Maureen

last: Hanson

first: Iwijn

last: De Vlaminck


title: Spatial crosstalk modeling of the tumor microenvironment uncovers CCR5-mediated glia-to-glia signaling as a key regulator of brain metastases

city: HOUSTON

first: HONG

last: ZHAO

state: Texas

address: 6670 Bertner Ave

institute: HOUSTON METHODIST HOSPITAL

summary: Glial cells play a critical role in shaping the tumor microenvironment in brain metastases, facilitating disease progression through complex tumor-glial and distinct glia-to-glia signaling pathways. To investigate these interactions, we conducted RNA sequencing of astrocytes, microglia, and oligodendrocytes at various stages of brain metastasis progression, combined with spatial transcriptomics and crosstalk analysis using the CCCExplorer tool. Our analysis uncovered that while glial cells converge on tumor-promoting pathways such as Ras and Gap junction signaling in tumor cells, they also engage in distinct autocrine and paracrine signaling critical for their own communication. Unique ligand-receptor pairs including OSM-OSMR, CCL4-CCR5, CXCL16-CXCR6, IL1A/B-IL1R, and TNF-TNFR were identified as drivers of glial crosstalk, which sustains the tumor-supportive niche. Targeting CCL4-CCR5-mediated glial signaling with maraviroc, an FDA-approved antiviral drug, reduced brain metastasis progression by 62% (p=0.004) without direct cytotoxicity to tumor cells. These findings highlight the novelty of targeting distinct glial autocrine and paracrine signaling as a therapeutic approach, shifting the focus from tumor cells to disrupting the glial niche that supports brain metastasis growth.

overall_design: 9 pairs of patients primary breast tumor and brain metastasis bulk RNAseq

first: JIANTING

last: SHENG

first: STEPHEN

last: WONG


title: Epigenetic determinants of an immune-evasive phenotype in HER2-low triple-negative breast cancer

city: Durham

first: Maggie

middle: L

last: DiNome

state: NC

address: 308 Research Dr, RM 215B

department: Department of Surgery

institute: Duke University

summary: Identifying molecular drivers of aggressive biology is crucial for patients with triple-negative breast cancer (TNBC). While HER2-low expression predicts response to novel antibody-drug conjugates, its impact on TNBC biology remains unclear. To address this, we generated genome-wide DNA methylation profiles of 58 patients from a multi-institutional TNBC cohort treated at Duke, UCLA, and Scripps Health, integrating our data with three independent cohorts: The Cancer Genome Atlas, the Sweden Cancerome Analysis Network – Breast, and the I-SPY2 clinical trial. TNBC cases were classified as HER2-zero (IHC 0) or HER2-low (IHC 1+ or 2+, ISH non-amplified), and their genomic, epigenomic, transcriptomic, and proteomic landscapes were compared.   Among the 506 patients analyzed (n=288 HER2-low; n=218 HER2-zero), HER2-low TNBC exhibited a significantly lower tumor mutational burden (P = 0.02) and consistent hypermethylation of immune-related genes, particularly HLA. Transcriptomic analyses revealed significant downregulation of immune response pathways, including leukocyte activation, T-cell signaling, and adaptive immunity (adjusted P < 0.001), alongside reduced immune cell infiltration in the tumor microenvironment (P = 0.002). Notably, higher expression of five immune-related genes most downregulated in HER2-low TNBC correlated with improved relapse-free (HR = 0.52; P < 0.001) and overall survival (HR = 0.36; P < 0.001). These findings highlight distinct molecular features of HER2-low TNBC, suggesting an immune-evasive phenotype that should be considered when selecting therapies for this challenging subtype.

overall_design: We aimed to profile genome-wide DNA methylation of 58 patients from a multi-institutional TNBC cohort treated at Duke, UCLA, and Scripps Health. DNA methylome was analyzed using the Infinium Methylation EPIC v2.0 BeadChip (Illumina, Inc) following the manufacturer’s protocol.

first: Maggie L

first: Andrés F

last: Bedoya López

first: Miquel

last: Ensenyat Mendez

first: Diego M

last: Marzese


title: Decoding cellular stress states for toxicology using single-cell transcriptomics

city: Research Triangle Park

first: Brian

last: Chorley

address: US EPA, 109 TW Alexander Dr

institute: US EPA

summary: Single-cell transcriptomics (SCTr) offers a powerful platform for decoding the complexities of cellular stress responses to chemical exposures, capturing rare and transient subpopulations that can be obscured in bulk measurements. This study employs SCTr to profile the responses of HepaRG liver cells to various stress-inducing chemicals, providing detailed insights into adaptive stress response pathways (SRPs), encompassing the response to unfolded proteins, oxidative stress, heat shock, and DNA damage. By leveraging SCTr, we identify distinct cellular subpopulations and elucidate their transcriptomic profiles, linking specific gene expression patterns to biological mechanisms underlying stress responses. Our findings demonstrate the utility of SCTr in discerning the dose-dependent effects of chemicals at a granular level, highlighted by key differences between pseudo-bulk and single-cell analysis. Chemicals such as troglitazone, brefeldin A, rotenone, and tunicamycin induced unique transcriptional signatures associated with specific stress response pathways. Single-cell connectivity mapping with signatures of SRPs and cell fates, including autophagy and apoptosis, revealed clusters of cells with adaptive and potentially adverse phenotypes. These SCTr data have implications for identifying toxicological and disease mechanisms involving adaptive stress pathways. The data can also provide unique insights into toxicological processes by beginning to resolve adaptive chemical exposures, where cells recover, from those that are adverse from which cells do not recover, offering potentially new approaches for chemical safety assessments.

overall_design: We profiled reference perturbagens known to induce stress responses, including the unfolded protein response (UPR), oxidative stress response (OSR), heat-shock response (HSR), response to hypoxia (HPX), and DNA damage response (DDR), in the differentiated HepaRG human liver cell model at three different concentrations. HepaRG cells were dissociated and fixed for single-cell transcriptomic (SCTr) assessments. Here, vehicle (DMSO) treated cells were profiled with 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1.

first: Brian N.

first: Imran

last: Shah

first: Dennis J.

last: Eastburn


title: Conservation of cis-regulatory codes over half a billion years of evolution [Iso-Seq]

city: Saint Louis

first: Joseph

middle: C.

last: Corbo

state: MO

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: The identification of homologous cell types across species represents a crucial step in understanding cell type evolution. The retina is particularly amenable to comparative analysis because the basic morphology, connectivity, and function of its six major cell classes have remained largely invariant since the earliest stages of vertebrate evolution. We used comparative single-nucleus chromatin accessibility analysis of lamprey, fish, bird, and mammalian retinas, which began to diverge over half a billion years ago, to demonstrate cross-species conservation of cis-regulatory codes in all six retinal cell classes. In this study, we acquired retinal single-cell gene expression profiling (scRNA-seq) and single-nucleus chromatin accessibility (snATAC-seq) from sea lamprey (Petromyzon marinus), a jawless species. We also acquired long-read sequence data from lamprey retina and single-nucleus chromatin accessibility from chicken (Gallus gallus).

overall_design: A publicly available sea lamprey transcriptome assembly was updated using newly generated long-read sequencing data. Subsequently, single nuclei multiome profiles (comprising RNA and ATAC) of the downstream migrant lamprey retina were generated with the updated assembly. Furthermore, a single-nuclei chromatin accessibility profile was generated from the newly hatched (P0) chicken, which serves as a comparison of cis-regulatory features across diverse vertebrate species.

first: Yohei

last: Ogawa


title: GM-CSF production by immune cells in steady state and autoimmune neuroinflammation mapped using fate-reporting mice

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

summary: The current study tracked ongoing and past GM-CSF expression in various immune cells from multiple organs, both under steady-state conditions and during autoimmune inflammation of the central nervous system (CNS). RNA sequencing (RNA-Seq) was used to identify differences between naïve and effector memory CD4⁺ T cells with (YFP+) or without (YFP-) a history of GM-CSF expression.

overall_design: Transcriptional analysis for YFP+, YFP− naïve (CD62L+CD44−), and TEM (CD62L−CD44hi) CD4+ T cells from the spleens of Gr/fr mice (n = 3)

first: Javad

last: Rasouli

first: Gholamreza

last: Azizi