title: PTEN, a master driver of nonhealing phenotype in venous leg ulcers, suppresses immune response, angiogenesis and lymphangiogenesis [scRNA]

first: Anthony

last: Griswold

summary: We used single-cell RNA-Seq (scRNA-Seq) and bulk RNA-Seq to identify molecular mechanisms and cellular functions associated with impaired healing in venous leg ulcer (VLU). scRNA-Seq of chronic VLUs revealed impairments in immune, lymph endothelial, and endothelial cells, along with the underlying signaling pathways. Next, patients were treated with the standard of care and wound healing was followed for at least 4 weeks to distinguish healing and non-healing VLU. RNA-Seq was performed on healing and non-healing VLUs, and transcriptomes were compared to those of human acute wounds (AW). A robust suppression of inflammatory response, lymphangiogenesis and angiogenesis was hallmark of non-healing, in contrast to healing VLUs that showed similarity to physiological healing. Diminished inflammatory response in non-healing VLUs was due to impaired leukocyte transmigration and egression, with suppression of kinases’ activity, including AKT, ERK, JNK1/2, SRC, and PDGFR, underlining the non-healing signature. Bioinformatic analyses pinpointed PTEN as a master negative regulator of the processes and signaling pathways suppressed in non-healing VLU. Indeed, increased PTEN was confirmed in non-healing compared to healing VLUs on scRNA-Seq and protein level. Functional in vivo murine studies confirmed that pharmacological PTEN inhibition enhances immune response, and proinflammatory signals, leading to accelerated wound closure. We identify PTEN as a master regulator of non-healing VLU phenotype that orchestrates multiple key processes responsible for impaired healing. Targeting PTEN as a therapeutic approach may shift non-healing VLUs into healing trajectory allowing for progression of wound closure.

overall_design: A single-cell suspension from chronic VLUs and control skin samples was analyzed using  scRNA-Seq

middle: J

first: Jelena

last: Marjanovic

first: Irena

last: Pastar

first: Marjana

last: Tomic-Canic


title: P5CS regulates translation by functioning as non-canonical RBP [Ribo-seq]

status: Public on Jun 09 2026

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

country: China

institute: Southeast University

summary: P5CS is the rate-limiting enzyme in the proline biosynthetic pathway, while whether P5CS mediates function beyond enzyme activity remains completely unknown. Here, we reveal that P5CS functions as a non-canonical RNA-binding protein and inhibits the growth and metastasis of cancer cells by suppressing translation initiation in an enzyme activity-independent manner.  To explore the underlying mechanism of P5CS in translation regulation, Ribo-seq, RIP-seq and LACE-seq were performed to investigate the downstream targets of P5CS.

overall_design: translation analysis of Ribo-seq data for puro and sh-ALDH18A1 in NCI-H1299 cells.

first: Qingqing

last: Zhang

first: shuwen

last: Cheng

first: shan


title: P5CS regulates translation by functioning as non-canonical RBP [RIP-seq]

overall_design: RNA binding-sites analysis of LACE-seq data for Anti-P5CS and Anti-IgG in NCI-H1299 cells.

first: Shuwen


title: P5CS regulates translation by functioning as non-canonical RBP [RNA-seq]

type: Expression profiling by high throughput sequencing

overall_design: translation analysis of RNA-seq data for puro and sh-ALDH18A1 in NCI-H1299 cells.


title: NK Cell Dysregulation May Potentiate Cardiovascular Disease in Adolescents with Perinatally Acquired HIV on Antiretroviral Therapy

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

country: USA

institute: Case Western Reserve University

summary: Perinatally acquired HIV (PHIV) and antiretroviral therapy (ART) can alter innate immune cells, (monocytes and natural killer [NK] cells) which are important in the pathogenesis of cardiovascular disease (CVD). We compared cardiovascular biomarkers and immune signatures between PHIV adolescents on suppressive ART and HIV-unexposed, uninfected adolescents in Uganda. Carotid intima-media thickness (IMT) was increased in PHIV, suggesting a higher CVD risk. Flow cytometry analysis revealed greater activation, memory, and migratory capabilities of NK cells, and increased pro-inflammatory intermediate monocytes in PHIV, and these were supported by transcriptomics. Many of these innate immune cell subsets displayed associations with carotid IMT. Plasma oxidized-LDL (Ox-LDL) was significantly lower among PHIVs, and negatively correlated with pro-inflammatory, memory-like NK subsets. We demonstrated increased uptake of Ox-LDL by macrophages in the presence of activated, memory-like NK cells in vitro, suggesting a possible mechanism for greater CVD risk in PHIV. Collectively, our data demonstrate associations between dysregulated NK cell signatures and increased CVD risk among PHIV adolescents.

overall_design: Cryopreserved peripheral blood mononuclear cells (PBMC) and plasma samples were obtained from two groups: adolescents living with perinatally acquired HIV and a group of age-and sex-matched adolescents unexposed and HIV negative

first: Mario

last: Alles

first: Manuja

last: Gunasena

first: Aaren

last: Kettelhut

first: Kate

last: Ailstock

first: Victor

last: Musiime

first: Cissy

last: Kityo

first: Brian

last: Richardson

first: Will

last: Mulhern

first: Banumathi

last: Tamilselvan

first: Michael

last: Rubsamen

last: Sun

first: Grace

middle: A

last: McComsey

first: Dhanuja

last: Kasturiratna

first: Thorsten

last: Demberg

first: Cheryl

middle: M

first: Nicholas

middle: T

last: Funderburg

first: Sahera

last: Dirajlal-Fargo

first: Namal

last: Liyanage


title: C. difficile's proline reductase harnesses host and commensal factors to drive efficient metabolism and progression to disease. Commensal plus C. difficile.

city: Boston

first: Lynn

last: Bry

state: MA

address: 75 Francis St.

department: Pathology

institute: Brigham and Women's Hospital

summary:
Gnotobiotic mice were colonized with Clostridium sardiniense DSM 599 7 days prior to infection with 10^3 spores of wild-type Clostridioides difficile ATCC 43255 or the proline reductase (ΔprdB) mutant of ATCC43255 strain. Cecal contents were collected and underwent RNASeq at the timepoints indicated below for pathway enrichment and transcritpmic analyses.

Metatranscriptomic sequence processing was carried out as in Girinathan, et al, 2021 (PMID: 34637781)

sample_organism:
Clostridioides difficile
Mus musculus
Clostridium sardiniense

overall_design: Gnotobiotic mice were pre-colonized with a gut commensal bacterial species (Clostridium sardiniense) and then infected with C. difficile.

first: Jay

middle: N

last: Worley

first: Laura

last: Cersosimo

first: Madeline

last: Graham


title: C. difficile's proline reductase harnesses host and commensal factors to drive efficient metabolism and progression to disease. Mono-association.

summary:
Gnotobiotic mice were mono-colonized with either the wild-type Clostridioides difficile ATCC 43255 strain or the proline reductase mutant (ΔprdB) of the ATCC 43255 strain. Cecal contents were collected and underwent RNASeq at the timepoints indicated below for pathway enrichment and transcritpmic analyses.

Metatranscriptomic sequence processing was carried out as in Girinathan, et al, 2021 (PMID: 34637781)

overall_design: Gnotobiotic mice were infected with either the wild-type C. difficile ATCC 43255 strain or the proline reductase mutant of the same strain.


title: ZNHIT1-dependent H2A.Z deposition at meiotic prophase I underlies pachytene gene expression and meiotic progression during male meiosis [RNA-seq]

status: Public on Jun 08 2026

city: Shanghai

first: Jiang

last: Yamei

address: Songhu Road

institute: Fudan University

summary: Accurate meiotic progression is important for gamete formation and the generation of genetic diversity. However, little is known about the identity of chromatin regulators that underlie mammalian meiosis in vivo. Here, we identify the multifaceted functions of the chromatin remodeler ZNHIT1 in governing meiosis. The expression of *Znhit1* gradually increases during the meiotic prophase, and *Znhit1* knockout in spermatocytes results in arrested pachytene development, impaired DNA double-strand break repair, and defective homologous recombination. Single-cell RNA sequencing and transcriptome analysis reveal that *Znhit1* loss dysregulates meiotic transcriptional programs at the pachytene stage. Chromatin immunoprecipitation data show that ZNHIT1 is needed for the incorporation of the histone variant H2A.Z into pachytene chromatin. Moreover, we found that H2A.Z cooperates with the transcription factor A-MYB to co-bind DNA elements and control gene activity. Our findings provide insights into the regulatory mechanisms governing meiotic progression and highlight ZNHIT1 as a critical regulator of meiotic progression.

overall_design: To elucidate the impact of ZNHIT1 on gene expression, we performed RNA-seq profiling using germ cells.

first: Shenfei

first: Yamei

last: Jiang

first: Ning

first: Qiaoli

last: Zhang

first: Hongjie

last: Pan

first: Fujing

last: Huang

first: Xinna

first: Yuxuan

last: Guo

first: Xiaoyu

last: You

first: Kai

last: Gong

first: Wei

last: Wei

first: Hanmin

last: Liu

first: Zhenju

last: Song

first: Yuanlin

first: Xiaofang

last: Tang

first: Miao

last: Yu

first: Runsheng

last: Li

first: Xinhua

last: Lin


title: Cytotoxic CD39+ tumor-associated NK cells respond to NKG2A blockade in lung cancer

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: ZNHIT1-dependent H2A.Z deposition at meiotic prophase I underlies pachytene gene expression and meiotic progression during male meiosis [ATAC-seq]

first: Jiang

overall_design: To investigate the effect of ZNHIT1 on chromatin accessibility, we performed ATAC-seq profiling in pachytene spermatocytes.

first: Shenfei

last: Sun

first: Yamei

first: Ning


title: Spatial transcriptomic data for skin tissue of systemic sclerosis or localized scleroderma

city: Pittsburgh

first: Tianhao

address: F28W+RH Pittsburgh, Pennsylvania

institute: University of Pittsburgh

summary:
Juvenile localized scleroderma (LS) and systemic sclerosis (SSc) are rare autoimmune diseases that can cause substantial morbidity and disability in children. However, the cellular and molecular mechanisms underlying juvenile scleroderma remain poorly understood. To investigate disease pathogenesis, we applied Visium CytAssist spatial transcriptomics (ST), which preserves tissue architecture while enabling whole-transcriptome profiling, to skin lesions from pediatric patients with LS and SSc.
Spatial domains identified from ST data showed strong concordance with pathologist-defined anatomical structures. Integration of paired ST and single-cell RNA sequencing (scRNA-seq) data from the same patients validated the biological consistency of both platforms and enabled estimation of cell-type composition within spatial domains. Moreover, ST analysis accurately delineated pathologist-annotated immune infiltrates, including perivascular inflammatory regions, highlighting the biological relevance of the spatial transcriptomic findings.
To our knowledge, this is the first study to apply spatial transcriptomics to skin lesions from patients with juvenile scleroderma. Integration of ST with scRNA-seq and pathological assessment provided a high-resolution view of tissue organization and immune infiltration, offering new insights into the pathogenesis of juvenile scleroderma.

overall_design:
Children with localized scleroderma (LS) or systemic sclerosis (SSc) with disease onset before 18 years of age were eligible for inclusion. Participants were recruited through the National Registry for Childhood Onset Scleroderma (NRCOS) at the University of Pittsburgh (Principal Investigator: Torok; IRB Protocol #PRO11060222). All participants were enrolled between 2008 and 2023 and fulfilled established diagnostic criteria for LS or SSc. The study included four pediatric participants, comprising three with LS and one with SSc.
Written informed consent and assent, when applicable, were obtained from all participants or their legal guardians in accordance with institutional review board requirements. Skin biopsies were collected using 4-mm punch biopsies from clinically affected sites. For the participant with SSc, biopsies were obtained from the forearm, whereas biopsies from participants with LS were collected from affected areas of the limbs, trunk, or scalp.

first: Theresa

middle: R

last: Hutchins

last: Chen

first: Kathryn

middle: S

last: Torok


title: EIF1 coordinates transcriptomic and splicing networks associated with cell cycle dysregulation in diabetic retinopathy

city: Yinchuan

first: LI

address: The General Hospital of Ningxia Medical University

institute: Ningxia Medical University General Hospital

summary: EIF1, an RNA-binding protein implicated in multiple diseases, remains poorly characterized in diabetic retinopathy (DR). To investigate its role in DR, human retinal pigment epithelial cells (ARPE-19) were exposed to 50 mM glucose to model the condition. Under hyperglycemic conditions, EIF1 was knocked down using siRNA, followed by transcriptome sequencing (RNA-seq) to profile differentially expressed genes (DEGs) and alternative splicing events (ASEs).

overall_design: experimental design：Human retinal pigment epithelial cells (ARPE-19) were exposed to 50 mM glucose to model DR. EIF1 was knocked down using siRNA under hyperglycemic conditions, followed by transcriptome sequencing (RNA-seq) to profile differentially expressed genes (DEGs) and alternative splicing events (ASEs).


title: Single-cell RNA-seq of healthy human epidermal cells from adult abdominal skin

city: Vienna

first: Hannes

last: Kühtreiber

state: Vienna

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University Vienna

summary: Single-cell RNA sequencing was performed on viable epidermal cells isolated from healthy adult human abdominal skin samples obtained during abdominoplasty. Epidermal cell suspensions were generated by enzymatic dissociation, viability sorting, and 10x Genomics Chromium-based single-cell library preparation. Libraries were sequenced on an Illumina HiSeq 3000/4000 platform.

overall_design: Skin samples were obtained from three healthy adult donors undergoing abdominoplasty. Six biopsies were prepared from each skin sample. Epidermis was separated after overnight Dispase II digestion at 4 °C and further dissociated using enzymatic digestion. One portion was processed with the GentleMACS Human Whole Skin dissociation kit for 2.5 hours at 37 °C, and the other portion was digested with 0.05% Trypsin-EDTA and DNase I for 7 minutes at 37 °C. Dissociated cell suspensions were pooled, mechanically processed using the GentleMACS OctoDissociator, filtered through 100 µm and 40 µm cell strainers, stained with DAPI, and sorted for viable cells by fluorescence-activated cell sorting. Viable cells were processed using the 10x Genomics Chromium platform for single-cell RNA-seq library generation and sequenced on an Illumina HiSeq 3000/4000 instrument. Three biological replicates were included, corresponding to three independent healthy adult donors.

first: Polina

last: Kalinina

first: Michael

last: Mildner


title: Paradoxical Phenotype of Fibromyalgia Neutrophils: Elevated Baseline Inflammation but Blunted Response to Stimulation

city: Montreal

first: Sahel

last: Jahangiri Esfahani

address: 3775 University Street

country: Canada

institute: McGill

summary: Fibromyalgia (FM) is a long-term pain condition of unknown etiology. We investigated transcriptomic responses of FM and healthy control neutrophils to inflammatory stimuli. We observed a state of inflammation in neutrophils from FM patients. However, FM neutrophils were unable to efficiently respond to lipopolysaccharide (LPS). This impairment was especially characteristic of FM patients with no improvement after 5 years post-diagnosis in comparison with those who did improve. Further analysis identified NF-κB suppression as a key biological process associated with low grade inflammation and LPS non-responsiveness in FM neutrophils. The clinically used NF-κB activator, bryostatin, alleviated hypersensitivity in mice treated with FM plasma, pointing to controlled inflammation induction through reactivation of the NF-κB pathway as a possible therapeutic target for FM treatment. Our whole blood single-cell RNA sequencing replicated this NF-κB-driven inflammation and revealed that this inflammatory signature is strongly pronounced not only in neutrophils, but across a broad range of immune cells.

overall_design: We recruited 62 patients with clinician-confirmed fibromyalgia (FM) and 64 age-, sex-, and BMI-matched healthy controls (HC). Peripheral blood neutrophils were isolated from all participants and cultured under either unstimulated conditions or following stimulation with lipopolysaccharide (LPS, 10 ng/mL) for 1 hour to assess inflammatory responsiveness. RNA was extracted and subjected to bulk RNA sequencing, and differential gene expression, pathway enrichment, and transcription factor analyses were performed while adjusting for age, sex, and BMI. Participants were followed for approximately five years, and FM patients were stratified into Improvers and Persisters based on Patient Global Impression of Change (PGIC) scores. To evaluate the functional relevance of the identified molecular signatures, pooled plasma from HC, Improvers, and Persisters was transferred into mice to assess mechanical hypersensitivity and sensory neuron activation, and the therapeutic potential of NF-κB reactivation was tested using the NF-κB activator bryostatin. Finally, findings were validated in an independent cohort using whole-blood single-cell RNA sequencing to characterize immune-cell-specific transcriptional changes associated with FM.

first: Mohamad

last: Karaky

first: Marc

last: Parisien

first: Francesca

last: Montagna

first: Carolina

middle: B

last: Meloto

first: Jeffrey

last: Mogil

first: Luda

last: Diatchenko


title: Custom Probe-Based Spatial Transcriptomics Enables Microbiome Detection in FFPE Colorectal Cancer Tissue

city: Duarte

first: David

middle: Wesley

last: Craig

state: CA

address: 1500 East Duarte Road

department: Integrated Translational Sciences

institute: City of Hope

summary: We describe a custom probe design pipeline targeting the variable regions of bacterial 16S rRNA, compatible with the probe-based chemistry of the 10X Genomics Visium CytAssist platform, enabling spatially resolved bacterial profiling in FFPE tissue. Applied to a cohort of six FFPE colorectal cancer tumor and normal adjacent tissue specimens, we demonstrate the feasibility of a probe-based spatial metatranscriptomics for simultanous profiling of host gene expression and the intratumoral bacterial communities.

overall_design: Four colorectal cancer patients contributed six FFPE tissue sections comprising three tumor and three normal adjacent (NAT) specimens, with matched tumor-NAT pairs available for two patients and unmatched samples for the remaining two. Each section was simultaneously profiled for host transcriptome and intratumoral bacterial composition using a custom 16S rRNA probe panel on the 10X Genomics Visium CytAssist platform.

first: Rayyan

last: Aburajab

first: Jennifer

last: Karmouch

first: Robert

last: Jenq

middle: W


title: Enhanced vasoactive intestinal peptide signaling prevents the development of Duchenne muscular dystrophy-associated cardiomyopathy through inhibition of NF-κB signaling

city: Kansas city

first: Jian

last: Huang

state: KS

address: 3901 Rainbow Boulevard

department: Cardiovascular Medicine

institute: KUMC

summary: Duchenne muscular dystrophy (DMD) is an X-linked recessive neuromuscular disorder caused by mutations in the dystrophin gene. Loss of dystrophin in cardiomyocytes leads to cell death, myocardial fibrosis, and ultimately, dilated cardiomyopathy. Vasoactive intestinal peptide (VIP) is a cardioprotective neuropeptide that signals through VPAC1 and VPAC2 receptors to activate cAMP-PKA signaling in cardiomyocytes. Elevated PKA activity in the heart may suppress NF-κB signaling, although the mechanism remains incompletely understood. Using physiological, histological, and molecular approaches, we evaluated whether PB1046, a long-acting VIP polymer developed by PhaseBio Inc., prevents cardiac dysfunction in mdx:Utrn+/- mice. Animals received PB1046 (0.75 or 1.5 mg/kg) or saline every other day from 4 to 12 weeks of age. Cardiac function was assessed weekly by echocardiography, and hearts were collected at 14 weeks of age for histological and molecular analyses. High-dose PB1046 treatment preserved cardiac function and reduced fibrosis in mdx:Utrn+/- mice. Bulk RNA sequencing analysis of cardiomyocytes isolated from mdx:Utrn+/- mice treated with high-dose PB1046 revealed an upregulation of cAMP-associated transcripts and a downregulation of NF-κB pathway genes. The activation of cAMP signaling was confirmed by elevated cardiac cAMP levels and increased phosphorylation of nuclear CREB in mdx:Utrn+/- mice treated with high-dose PB1046. Nuclear phosphorylation of p65 was significantly reduced, suggesting that NF-κB signaling was suppressed. Together, these results indicate that activation of VIP signaling protects against cardiac dysfunction in a murine model of DMD, likely through inhibition of NF-κB signaling pathways.

overall_design: Bulk RNA sequencing was performed for differential transcripts of cAMP-PKA-CREB signaling and NF-kB signaling.

first: Terry

last: Gemelli

first: Xuan

last: Jiang

first: Yunbeen

last: Bae

first: Xiang

last: Luo

first: John

last: Shelton

first: Bret

last: Evers

first: Sue

last: Arnoldf

last: Lee

first: Pradeep P.A.

last: Mammen


title: Host transcriptional responses reveal molecular signatures of immune regulation and blood-brain barrier remodelling in porcine neurocysticercosis

city: Lima

first: Carla

middle: Angelica

last: Apaza-Quiroz

address: Honorio Delgado 430 San Martin de Porres

country: Peru

institute: Universidad Peruana Cayetano Heredia

summary: Neurocysticercosis, caused by the establishment of Taenia solium larvae in the central nervous system, is a leading cause of acquired epilepsy and neurological morbidity in endemic regions. Viable cysticerci can persist in the brain for years with minimal inflammation, whereas parasite degeneration, either spontaneous or induced by antiparasitic treatment, triggers intense inflammatory and vascular responses. Despite the clinical relevance of this transition, the host transcriptional changes associated with viable infection and early post-treatment lesions remain poorly understood. We performed the first bulk RNA sequencing analysis of brain tissue from experimentally infected pigs, a physiologically relevant model of human neurocysticercosis. We compared transcriptional profiles from uninfected controls (n=3), infected untreated pigs with viable clear-capsule cysts (n=6), and infected pigs treated with albendazole plus praziquantel with disrupted blue-capsule lesions (n=3). Differential expression and pathway enrichment analyses were used to characterise host responses associated with infection and treatment. Neurocysticercosis infection was associated with altered expression of genes involved in immune activation, together with reduced vascular- and endothelial-associated signalling. In contrast, anthelmintic treatment was associated with coordinated inflammatory and endothelial activation, including cell adhesion molecule pathways, extracellular matrix remodelling, and transcriptional features consistent with active blood-brain barrier remodelling in a disrupted lesion state. Integrated pathway analysis showed that infection and treatment shared immune activation features but diverged in MAPK, vascular and endothelial programmes. These findings show that viable and post-treatment lesions are associated with distinct host transcriptional programmes involving immune regulation, endothelial activation and barrier-associated tissue remodelling. By defining these lesion-associated signatures, this study provides a framework for understanding parasite persistence, inflammation and disease progression in porcine neurocysticercosis.

overall_design: Bulk RNA-seq profiling of brain tissue samples from a porcine model of neurocysticercosis. The study compared uninfected control brain tissue, infected untreated pigs with viable clear-capsule cyst-associated tissue, and infected pigs treated with albendazole plus praziquantel with disrupted blue-capsule cyst-associated tissue, to characterize host transcriptional responses associated with viable infection and post-treatment inflammatory lesion states.

first: Cielo

middle: C

last: Rojas-Portocarrero

first: Sneider

last: Gutierrez

first: Emily

middle: K

last: Ponce-Nakatahara

first: Javier

last: Bustos

first: Gianfranco

last: Arroyo

middle: H

last: Gilman

first: Héctor

last: García

first: Mirko

last: Zimic


title: Comparative Tnseq of Vibrio cholerae grown without and with tobramycin at 2% MIC for 50 generation

city: paris

first: Zeynep

last: Baharoglu

address: 25 rue du dr roux

country: France

institute: Institut Pasteur

summary: Antibiotics at 2% of the MIC are not lethal for bacteria but cause stress. We studied the contribution of each gene in the fitness of V. cholerae for growth in tobramycin 2%MIC.

overall_design: We constructed transposon insertion library in V. cholerae N16961 8637 and obtained a library of 500 000 clones. We sequenced (TN-seq) the library (time zero) and grew it either in mueller hinton without tobramycin or with tobramycin 0,02 µg/ml, for 50 generations and we seuanced the final population.

first: Didier

last: Mazel


title: ECM1/SQSTM1 Axis Remodels Colorectal Cancer Immune Microenvironment via CXCL1-CXCR2-Dependent Neutrophil Recruitment and NETosis (scRNA-seq)

city: Chongqing

first: Jian

last: Wang

address: No. 725, Jiangzhou Avenue, Dingshan Subdistrict, Jiangjin District

department: Department of Oncology

institute: Chongqing University Affiliated Jiangjin Hospital

summary: Extracellular matrix protein 1 (ECM1) has been implicated in tumorigenesis; however, its precise role in modulating the immunosuppressive tumor microenvironment (ITM) in colorectal cancer (CRC) remains inadequately elucidated.

overall_design: In this study, through single-cell transcriptomic analysis, we revealed that ECM1 regulates neutrophil recruitment and activation within the tumor microenvironment (TME).


title: ECM1/SQSTM1 Axis Remodels Colorectal Cancer Immune Microenvironment via CXCL1-CXCR2-Dependent Neutrophil Recruitment and NETosis (Spatial transcriptomics)

overall_design: Through spatial transcriptomic analyses, we reveal that ECM1 regulates neutrophil recruitment and activation within the tumor microenvironment (TME).


title: Integrative multi-omics analyses reveal that exogenous indole-3-lactic acid enhances growth by modulating various metabolic pathways in Lemna aequinoctialis culture

city: Seoul

first: SoHee

last: Park

address: 84, Heukseok-ro

country: South Korea

institute: Chung-ang university

summary: Background: Lemna aequinoctialis is an aquatic plant with high potential for feed, food, and pharmaceutical resources due to its rapid propagation and rich metabolite profile. In this study, we investigated the effects of various concentrations of indole-3-lactic acid (ILA) on the growth and metabolomic, lipidomic, and transcriptomic profiles of L. aequinoctialis using gas chromatography–mass spectrometry, liquid chromatography–mass spectrometry, and next-generation sequencing-based assays. Results: ILA significantly promoted the growth of the L. aequinoctialis culture and altered the metabolomic, lipidomic, and transcriptomic profiles. It also increased the cellular production of asparagine, fumaric acid, malic acid and tryptophan among metabolites, and diacylglycerols, digalactosyldiacylglycerols, monogalactosyldiacylglycerols and triacylglycerols among lipids. Integrated metabolomic and transcriptomic analyses showed that 100 μM ILA treatment affected the ‘Glycolysis or Gluconeogenesis,’ ‘Glycerophospholipid metabolism,’ ‘Pyruvate metabolism,’ ‘Alanine, aspartate and glutamate metabolism,’ and ‘Glutathione metabolism’ pathways in L. aequinoctialis. Moreover, ILA altered the levels of bioactive metabolites and lipids in L. aequinoctialis. Conclusions: These findings suggest that ILA can be used to enhance the growth and production of useful metabolites and lipids in large-scale cultivation of L. aequinoctialis as feed, food, and pharmaceutical resources.

overall_design: We hypothesized that exogenous ILA treatment would influence the growth and biosynthetic regulation of L. aequinoctialis. The primary objective of this study was to explore the effects of ILA on the growth and metabolomic, lipidomic, and transcriptomic profiles of L. aequinoctialis.

first: Hyung-Kyoon

last: Choi


title: Screening of Cerebral Palsy Biomarkers and Cross-Species Conservative Target Analysis between Human and Mouse Based on Whole Transcriptome Array Chip Sequencing_circRNA-seq

city: Kunming

first: shouyao

last: zhang

state: Yunnan

address: No.1076, yuhua road, chenggong district

institute: Yunnan University of Chinese Medicine

summary:
Cerebral Palsy (CP) is a group of neurodevelopmental disorders characterized by persistent motor and posture impairments. Its molecular mechanisms remain poorly understood, and there is a lack of reliable blood-based biomarkers.
This study employed circRNA-seq technology to analyze the expression profiles of circRNAs in peripheral blood from 3 children with cerebral palsy and 3 healthy controls.

overall_design: Shuang, Wang

first: Shouyao


title: TLR4 governs strain-specific transcriptional responses of bovine mammary epithelial cells challenged by Staphylococcus aureus and its small colony variant

city: Guelph

first: Umesh

middle: K.

last: Shandilya

state: Ontario

address: 50 Stone Rd E

department: Animal Biosciences

institute: University of Guelph

summary: Staphylococcus aureus small colony variants (SCVs) are metabolically adapted, slow-growing subpopulations responsible for chronic, recurrent bovine mastitis through enhanced intracellular persistence and immune evasion. The role of Toll-like receptor 4 (TLR4) in regulating bovine mammary epithelial transcriptional responses to S. aureus SCV challenge remains poorly understood. Using CRISPR-Cas9-generated TLR4-knockout (TLR4-KO) MAC-T cells combined with RNA sequencing, global transcriptional responses of wild-type (WT) and TLR4-KO MAC-T cells infected with S. aureus SCV Heba3231 and its isogenic parental strain (PS) were compared. The WT cells mounted highly divergent S. aureus strain-specific responses, with only 0.5% overlap in differentially expressed genes between PS and SCV conditions. The PS infection induced apoptotic and HIF-1 signalling pathways, whereas SCV infection promoted lipid metabolic reprogramming, accompanied by suppression of epithelial barrier integrity genes. TLR4 disruption dramatically amplified transcriptional dysregulation, with a 192-fold increase for the PS (1,921 DEGs) and a 6.6-fold increase for SCV (2,279 DEGs) relative to WT infected controls. This revealed a large core set of TLR4-regulated genes with approximately 57% shared across S. aureus strains that govern innate immunity, structural homeostasis, and apoptotic coordination. WFDC2, ITGB3, SH3BGRL, and HKDC1 emerged as novel TLR4-dependent candidate genes. Collectively, these findings identify TLR4 as a key determinant of strain-specific transcriptional discrimination and epithelial homeostasis during S. aureus infection, with particular relevance to SCV-mediated persistence in bovine mastitis.

overall_design: Bovine mammary epithelial MAC-T cells were used to investigate the role of TLR4 in host transcriptional responses to Staphylococcus aureus infection. Wild-type MAC-T cells and CRISPR-Cas9-generated TLR4-knockout MAC-T cells were challenged in vitro with either the S. aureus parental strain 3231 or its isogenic small colony variant Heba3231. Uninfected wild-type MAC-T cells treated with sterile carrier medium served as the control. Cells were infected at a multiplicity of infection of 25:1 for 3.5 h at 37°C with 5% CO₂. The experimental groups were: WT-Control, WT-PS, WT-SCV, TLR4-KO-PS, and TLR4-KO-SCV. Total RNA was extracted from infected and control cells and subjected to paired-end RNA sequencing on an Illumina NovaSeq X Plus platform to compare transcriptional responses across genotype and infection conditions.

first: U

first: Y

last: Liang

first: H

last: Atalla

first: B

last: Mallard

first: N

last: Karrow


title: Loss of IL10RA rewires epithelial immune responses to intracellular Staphylococcus aureus 1 small colony variants in bovine mammary epithelial cells

summary: Staphylococcus aureus small colony variants (SCVs) are a persistence-adapted phenotype associated with chronic and recurrent bovine mastitis. The interleukin-10 receptor ⍺ (IL10RA) is a key regulator of anti-inflammatory signalling in the mammary gland, yet its role in governing transcriptional responses to intracellular staphylococcal challenge remains unknown. Using CRISPR/Cas9-generated IL10RA knockout (KO) MAC-T bovine mammary epithelial cells (MECs) and RNA sequencing, we compared transcriptional responses to infection with S. aureus SCV Heba3231 and its isogenic parental strain (PS). The wild-type (WT) MAC-T cells mounted fundamentally divergent responses to the PS (8 DEGs) and the SCV (461 DEGs), with no transcriptional overlap, indicating strain-specific engagement of distinct molecular programmes. SCV infection of WT cells up-regulated lipid and sterol biosynthetic pathways, and suppressed genes associated with epithelial barrier integrity, including S100A8, S100A9, TGM3 and KRTDAP. IL10RA disruption dramatically amplified transcriptional dysregulation. The IL10RA-KO cells infected with the PS yielded 619 DEGs (77.4-fold increase over WT-PS), while IL10RA-KO cells infected with SCV yielded 1,297 DEGs (2.8-fold increase over WT-SCV). A moderate core of IL10RA-regulated genes (~32–36%) was shared across infection conditions. IL10RA loss derepressed pro-inflammatory cytokine pathways (TNF, IL-17), enhanced pro-apoptotic programmes during SCV infection, and suppressed phagosomal maturation and lipid metabolic gene programmes. Novel candidate genes, including CD79B, WFDC2, AMN and LY6E, were identified as potential biomarkers of IL10RA-dependent mammary immune signalling. These findings establish IL10RA as a broad transcriptional homeostasis regulator in bovine mammary epithelial cells during intracellular staphylococcal infection.

overall_design: Bovine mammary epithelial MAC-T cells were used to investigate the role of IL10RA in host transcriptional responses to Staphylococcus aureus infection. Wild-type MAC-T cells and CRISPR-Cas9-generated  IL10RA-knockout MAC-T cells were challenged in vitro with either the S. aureus parental strain 3231 or its isogenic small colony variant Heba3231. Uninfected wild-type MAC-T cells treated with sterile carrier medium served as the control. Cells were infected at a multiplicity of infection of 25:1 for 3.5 h at 37°C with 5% CO₂. The experimental groups were: WT-Control, WT-PS, WT-SCV,  IL10RA-KO-PS, and  IL10RA-KO-SCV. Total RNA was extracted from infected and control cells and subjected to paired-end RNA sequencing on an Illumina NextSeq 1000 platform to compare transcriptional responses across genotype and infection conditions.


title: Transcriptional Response to WNT-inhibition-induced human cardiomyogenesis (single-cell RNA-seq)

city: Aberdeen

first: Ellen

middle: Elizabeth

last: Smith

address: University of Aberdeen

department: School of Biological Sciences

country: United Kingdom

institute: University of Aberdeen

summary: Since embryonic cardiac development in vivo and in vitro cardiomyocyte differentiation protocols both require WNT inhibition, our study focussed on how inhibition of WNT signalling guides the transcriptional landscape towards human cardiomyocyte differentiation. We uncovered transcriptional responses using single-cell RNA sequencing. with bioinformatics analysis defining cell identities, reconstructing differentiation trajectories, dissecting WNT inhibition-dependent gene expression and inferring Gene Regulatory Networks (GRN) driving cardiomyocyte specification. We found that WNT inhibition (WNTi) redirects early mesoderm precursors towards a cardiomyocyte fate while limiting alternative lineages.

overall_design: Human cardiomyocyte differentiation was modelled with H7 hESCs (WA07; 46,XX; WiCell, cultured feeder-free in growth factor–reduced Matrigel ). The human cardiomyocyte protocol was based on the WNT-ON, WNT-OFF differentiation protocol. Once pluripotent cells reached roughly 70-80% confluency, all cells were then cultured for one day in media containing the WNT agonist CHIR999021 (2 μM) and for one additional day without WNT agonist (Day 2 (D2) sample collected). After Day 2, remaining cells were cultured for another two days (to Day 4 (three different D4 samples collected)): some cells without any WNT inhibitor (0i treated sample), some cells with Wnt inhibitor IWP2 (5 μM) (48i treated sample) and some cells 36 hours in media without any WNT inhibitor and then the remaining 12 hours with Wnt inhibitor IWP2 (5 μM) (12i treated sample). D2, D4-0i, D4-12i and D4-48i were analysed with single-cell RNA-seq.

first: Victor

last: Velecela

first: Antoine

last: Bassil

first: Dimitris

last: Konstantopoulos

first: Fredrik

last: Salmén

first: Andreia

last: Bernardo

first: Stefan

last: Hoppler


title: Mapping immune cellular landscapes and vaccine responses across a spectrum of health and immunodeficiency [TCR-seq]

city: Parkville

first: Davide

last: Vespasiani

state: VIC

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute

summary: Immune responses to infection and vaccination exhibit diversity between individuals that can be shaped by differences in their immune cell landscapes and the signalling, transcriptional, and genetic mechanisms that coordinate immune cell function. Specific antibody deficiency (SAD) and common variable immunodeficiency (CVID) are common forms of predominantly antibody deficiencies that result in poor responses to vaccination. While molecular and cellular causes of the immune dysfunction and poor vaccination responses for individuals with CVID have been reported, immune cell or molecular defects have not yet been identified in SAD. Here, we have used single-cell multi-omics to define the cellular landscapes, transcriptional states, adaptive immune repertoires and protein expression of patients with SAD and CVID before and after polysaccharide vaccination. We discovered that while SAD and CVID exhibit overlapping immune defects, including accumulation of exhausted NK memory cells and dysregulated expression of genes that mediate lipopolysaccharide sensing and clearance by monocytes, individuals with SAD have a unique expansion of cytotoxic CD4+ T cells that correlates with reduced regulatory T cells. In response to vaccination, we observed rapid changes in gene expression associated with lipopolysaccharide responses by monocytes and NF-kB pathway activation in B cells, and an apparent expansion of a CD95+ class-switched memory B cell population that does not occur in patients with lower antigen-specific responses. Together, our findings reveal cellular and molecular factors that underpin variability in vaccine responses and define SAD in a broader spectrum of immune dysfunction.

overall_design: This project contains data from CITE-seq and VDJ-seq of peripheral mononuclear blood cells (PBMC) collected from 10 patients with CVID, 10 SAD and 10 healthy controls before and after vaccination. All 60 PBMC samples were stained with Hash Tag Oligonucleotides (HTOs) and a panel of 130 Antibody-Derived Tags (ADTs) using TotalSeqTM antibodies before pooling and split them into 5 batches (12 samples each). For each batch, GEX, ADT and HTO and VDJ libraries were generated using the 10X Genomics Chromium single-cell 5′ reagent kit v3 and then sequenced on a NovaSeq X Plus (PE150). The resulting dataset includes single-cell expression data (GEX) and single-cell protein expression data (ADT, antibody-derived tags library) for 454,025 human PBMCs (322,174 after quality filtering) and single-cell B/T cell receptor repertoire data for 157,108 human T and 26,873 B cells after quality filtering.

first: James

last: Lancaster

first: Hamish

last: King


title: Mapping immune cellular landscapes and vaccine responses across a spectrum of health and immunodeficiency [BCR-Seq]


title: EHMT1/2 knockout induces a broad interferon signature

city: Boston

first: Teng

last: Teng

address: 201 Brookline Ave Suite 901

institute: Tango Therapeutics

summary: Epigenetic silencing of interferon (IFN) signaling contributes to the profound resistance of “immune-cold” tumors to PD-1/PD-L1 blockade. In this study, we conducted a fluorescence-activated cell sorting (FACS)-based CRISPR-Cas9 screen to identify tumor-intrinsic regulators of PD-L1 surface expression and identified the histone-lysine methyltransferases EHMT1 and EHMT2 as key suppressors of interferon signaling. We then developed TNG917, a histone substrate-competitive dual inhibitor of EHMT1/2 with superior, low-nanomolar potency in cells and high selectivity over other methyl transferases. In cancer cell lines, TNG917 relieved H3K9-mediated repression, restored interferon-stimulated gene expression, and triggered secretion of T-cell chemoattractant cytokines including CXCL10. When dosed orally in both syngeneic and humanized mouse models, TNG917 monotherapy led to marked tumor growth inhibition, while combination with anti-PD1 therapy produced complete, durable regressions and established protective immune memory. Early pharmacokinetic and toxicology assessments revealed favorable exposure profiles and a wide safety margin. These findings establish EHMT1/2 inhibition by TNG917 as a novel strategy to convert immune-cold tumors into T-cell-inflamed lesions and potentiate checkpoint blockade, supporting its advancement into clinical development in combination immunotherapy.

overall_design: In this study, differential gene expression from NanoString analysis of HT29 cells following knockout of EHMT1, EHMT2, or EHMT1/2 double knockout were compared with non-targeting controls in triplicates


title: Time-dependent processing of dengue virus polyprotein yields multiple capsid forms that disrupt cellular homeostasis

city: hyderabad

first: Musturi

last: Venkataramana

state: telagana

address: Prof.C.R. Rao Road

department: department of biotechnology

country: India

institute: University of hyderabad

summary: Dengue virus infections spread to new geographical regions every year, cause significant morbidity and mortality, yet the progress in drug/vaccine development is limited due to an incomplete understanding of its life cycle. While a few of the proteins coded by this virus exist in multiple forms, the sequential events of polyprotein processing to yield them and the consequential effects on host cells are unclear. In this study, the virus infected cell culture data suggest that the polyprotein undergoes a time-dependent processing to yield multiple capsid forms, ie, capsid, capsid-anchor, capsid-anchor-pr, capsid-anchor-prM. Among them, the c-anc and c-anc-pr were found to localize to the mitochondria upon transfection into the HEK cells.  The pulldown experiments indicate that c-anc also interacts with α1-syntrophin (SNTA1), a cytoplasmic protein that plays a role in redox potential, oxidative stress and mitochondrial biogenesis. Importantly, the mitostress analyses suggest that c-anc triggers impaired mitochondrial dysfunctions like potential, respiration and ATP generation. In this study, we also identify ursonic acid (UNA) as a c-anc binding compound that restores mitochondrial functions and suppresses virus multiplication in vitro, ex vivo and in mice. The revealed disrupted mitochondrial homeostasis appears to be common to DENV, ZIKV, JEV, YFV, HCV, ASFV and SARS-CoV-2; hence, UNA or its related compounds could be considered as inhibitors for the above virus infections.Whole-transcriptome sequencing was performed on four samples. High-quality paired-end reads (6.64–9.70 Gb per sample) were generated on the Illumina platform using 2 × 150 bp chemistry. The reads were aligned to the Homo sapiens reference genome (GRCh38) using STAR (v2.7.10a) with default parameters. Mapping rates ranged from 91.09% (pEGFPNI vector-transfected HEK cells, replicate 2) to 94.18% (Capsid Anchor pGFP-transfected cells, replicate 1). Differential expression analysis was carried out using the DESeq2 R package.

overall_design: Whole Transcriptome Sequencing of pEGFPN1 vector and Dengue pEGFP-capsid-anchor transfected HEK cells

first: Preeti

last: Chauhan


title: High-Resolution Lineage Tracing in Native Tissue Contexts

first: Yuemeng

last: Jia

address: 1 Blackfan Circle

institute: Boston Children's Hospital

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

overall_design: Refer to individual Series


title: High-Resolution Lineage Tracing in Native Tissue Contexts [SPACE-seq]

summary: High-resolution lineage tracing has provided essential insights into key biological processes, yet existing methods are limited in tracing diverse cell populations at single-cell resolution while preserving spatial context. Here, we present SPACE-seq (SPatial trAcing enabled by CRISPR-based barcodEs and Slide-seq), a versatile tracing platform that integrates spatial transcriptomics with Cas9 barcoding in mice, to allow simultaneous analysis of cell lineages, transcriptomic states, and spatial organization at near-cellular resolution. Using this approach, we generated lineage maps that reveal novel interactions during liver cancer progression within the tumor microenvironment and uncovered distinct clonal architecture patterns in the developing cerebral cortex. Additionally, we identified a developmentally restricted window for hepatoblast migration and spatially confined compartments involved in liver lobe formation. With its broad applicability and adaptability, SPACE-seq offers new potential to explore previously inaccessible questions in cellular organization and lineage dynamics.

overall_design: SPACE-seq


title: Gene expression profiles for the interaction of Botrytis cinerea Vv3 and Sl3 strains on Vitis vinifera grapes.

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

institute: INRAE

summary: Full transcriptomes of the infection of Vitis vinifera grapes  with the Botrytis cinerea wild-type Vv3 and Sl3 strains, at 24h and 48h, were studied.

overall_design: Vitis grapes were infected with Botrytis cinerea Vv3 and Sl3 strains and incubated for 24h or 48h. 3 replicates were performed. The 12 total-RNA samples were used for RNA-SEQ sequencing.

last: Simon

first: Muriel

last: Viaud


title: Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome [ChIP-Seq ZTA]

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

summary: We systematically investigate interactions between Epstein-Barr virus (EBV) transcriptional regulators (vTRs) and the human genome. Starting with 16 known and candidate vTRs, we identify nine whose introduction into human cells results in substantial alterations to host gene expression. Genome-scale determination of vTR genomic binding events and alterations to chromatin accessibility reveals a detailed map of EBV's functional interactions with the human genome, including >100,000 vTR binding events impacting almost a quarter of all human genes. BMRF1 emerges as a potent regulator, impacting >7,000 genes and altering >37,000 chromatin regions. Our results provide new evidence that EBV RTA interacts with and stabilizes the binding of human RBPJ. Network analysis reveals that many human genes are targeted by multiple EBV vTRs, highlighting the vast coordinated impact of EBV on human gene expression. This study provides a valuable, extensive resource for examining EBV-induced alterations to human gene regulation, with data available on multiple platforms.

overall_design: We performed anti-GFP ChIP-seq on Akata cell lines that had been transfected either with the Epstein-Barr virus transcriptional regulator ZTA or a control. The experiments were performed in triplicate.

first: Leah

last: Kottyan


title: Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome [ChIP-seq YY1]

overall_design: We performed anti-GFP ChIP-seq on a Flp-In-293 cell line that had been transfected with a GFP-tagged YY1 construct. The experiment was performed twice.


title: Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome [ChIP-Seq EBNA2]

overall_design: We performed anti-EBNA2 ChIP-seq in 2 biological replicates from EBNA2+ EBV (B95.8) infected Ramos B cells.


title: High-Resolution Lineage Tracing in Native Tissue Contexts [I]

overall_design: Different liver lobes were collected, and RNA was extracted and reverse transcribed using DARLIN-specific primers containing UMIs. The DARLIN array at the Col1a1 locus was subsequently amplified by nested PCR, followed by indexing and sequencing on a NextSeq 1000.


title: Human Colitis-on-Chip Model Reveals Dual Roles of Butyrate in Epithelial and Macrophage Defense Against Candida albicans Tissue Invasion

city: Jena

first: Marc Thilo

last: Figge

state: Thuringen

address: Adolf-Reichwein-Straße 23

department: Applied System Biology

country: Germany

institute: HKI-Leibniz

summary: Microbial dysbiosis in inflammatory bowel disease (IBD) reduces intestinal butyrate levels, compromising epithelial barrier integrity and enabling overgrowth of opportunistic pathogens such as Candida albicans. Here, we present a human immunocompetent colitis-on-chip model (CooC) that mimics key features of inflamed gut mucosa, including DSS-induced epithelial damage and C. albicans tissue invasion. Using this model, we uncover dual protective roles of microbiota-derived butyrate: (i) stabilization of epithelial adherens junctions and promotion of epithelial renewal, thereby restricting fungal penetration; and (ii) modulation of macrophage function to enhance antifungal activity while attenuating inflammasome-mediated inflammation. Butyrate pretreatment preserves barrier function, limits fungal translocation, and promotes macrophage viability through the inhibition of histone deacetylase (HDAC) and the suppression of NLRP3 inflammasome activation. These findings position butyrate as a key metabolite in orchestrating epithelial-immune defense against fungal exacerbation in colitis, supporting its therapeutic and preventive potential in restoring mucosal resilience in IBD.

overall_design: RNA-seq analysis of flow treated intestine-on-chips vs static treated intestine-on-chips including enterocytes, vascular cells and myeloid cells after 120h of growth and 48h after LPS-treatment.

first: Manuel

last: Allwang

first: Maximilian

last: Wipplinger

first: Parastoo

last: Akbarimoghaddam

first: Raquel

last: Alonso-Roman

first: Zoltan

last: Cseresnyes

first: Axel

last: Dietschmann

first: Valentin

last: Wegner

first: Adrian

last: Feile

first: Yann

last: Bachelot

first: Mohamed

last: Hassan

first: Maria

last: Warschinke

first: Sonnhild

last: Mittag

first: Otmar

last: Huber

first: Bernhard

last: Hube

first: Mark

last: Gresnigt

first: Alexander

last: Mosig


title: Pleiotropic effects of the milk somatic cell transcriptome associated with feed efficiency and immunity in Holstein dairy cows

first: Victoria

last: Asselstine

address: 553 Gordon St #501

summary: In the livestock industry, feed is the largest expense, driving interest in breeding more feed-efficient animals. Residual feed intake (RFI) is a widely used measure of feed efficiency, accounting for actual feed intake versus expected requirements for maintenance and production. Because feed efficiency is highly polygenic, associated genes may have pleiotropic effects on traits such as immunity, complicating breeding strategies. One way to study pleiotropy is through -OMICs technologies, including transcriptomics, which uses RNA-Sequencing (RNA-Seq) to analyze the transcriptome at specific tissue levels and time points. This study used RNA-Seq to identify differentially expressed (DE) genes between Low RFI (n = 22) and High RFI (n = 17) Holstein cows. A total of 36 genes were DE between groups, enriched in 28 metabolic pathways (FDR < 0.01), most of which were immune-related, including the RIG-I-like receptor signaling pathway. QTL annotation and enrichment analyses were also performed for the DE genes. Within these gene regions, 646 previously annotated QTL were identified, of which 26.7% were related to milk traits. Notably, 10 QTL were associated with feed efficiency, while 4 were linked to host immunity. QTL enrichment further revealed 387 significantly enriched QTL, with the majority of the top associations related to health. In summary, this research identified candidate genes and QTL regions suggesting potential pleiotropic relationships between feed efficiency and immunity in Holstein dairy cows. These findings highlight the need for further investigation to balance productivity and health in genetic improvement programs.

overall_design: RNA-Sequencing was performed on 39 Holstein dairy cows ranked with either High or Low feed efficiency to identify differentially expressed genes between the two extreme groups.

first: Flavio

last: Schenkel

first: Filippo

last: Miglior

first: Christine

last: Baes

first: Paul

last: Stothard

first: Angela

last: Cánovas


title: Histone H3 availability is more important for development than H3.2 versus H3.3 subtype identity

city: Chapel Hill

first: Jeanne-Marie

middle: E.

last: McPherson

state: North Carolina

address: 3344 Genome Sciences Building, 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

summary: The distinct contributions of replication-dependent (RD) and replication-independent (RI) histones to development and genome function remain unclear. We investigate how the RI expression and distinct protein identities of the histone H3.2 and H3.3 subtypes influence Drosophila development and gene regulation. Replacing RI H3.3 genes with RD H3.2 revealed that RI H3.3 is essential for fertility, adult locomotor behavior, and normal lifespan. However, development to adulthood does not depend on which RI H3 subtype is expressed. RI H3 is dispensable for establishing or maintaining global chromatin accessibility or gene expression in the adult brain. H3.2 expression becomes essential in post-mitotic cells lacking RI H3.3, and the HIRA histone chaperone complex in critical for preserving genome function when RI H3.3 is deleted. We conclude that an available pool of H3 is more critical than the specific identity of H3 in the pool.

overall_design: Comparative gene expression profiling analysis of total RNA-seq data from OreR (H33WT), H3.3H3.2 (H33H32), H3.3Δ (H33null), H3.3H3.2 (H33H32), H3.3S31A (H33S31) and H3.3WT 3LW (wt_3LW) Drosophila melanogaster cells. H33WT, H33Δ, H33H32, and H33S31A samples are 1 day after eclosion (1dAE) and 10 days after eclosion (10dAE) brains. wt_3LW samples are wandering third instar larvae. Total RNA-seq PE100.

first: McPherson

last: Jeanne-Marie

first: McKay

last: Daniel

first: Duronio

last: Robert


title: Pediatric and AYA meningiomas constitute a molecularly distinct entity not captured by adult-based risk strategies

city: Heidelberg

first: Philipp

last: Sievers

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

type: Methylation profiling by genome tiling array

summary: Meningiomas in pediatric and adolescent/young adult patients are poorly characterized biologically and clinically, and risk stratification is largely extrapolated from adult tumors. We analyzed 293 tumors from patients aged 0–39 years using integrated histopathological and molecular profiling. Youth-onset meningiomas were enriched for NF2 and SMARCE1 alterations and exhibited a gain-dominated copy-number landscape, including recurrent chr17q gain, whereas canonical adult high-risk features, such as chr1p loss, lacked prognostic significance. Adult-derived prognostic frameworks—including WHO grade, methylation-based stratification, and integrated risk scores—failed to predict progression in patients ≤21 years. Tumors segregated into age-enriched epigenetic clusters defined by SMARCE1, NF2, and BAP1 alterations. Among NF2-altered tumors, patterns of Merlin inactivation shaped by germline status and co-occurring copy-number variations delineated biologically divergent subsets. Across all groups, extent of resection remained the strongest predictor of outcome. These findings define pediatric and young adult meningiomas as a distinct molecular entity requiring age-adapted risk stratification.

overall_design: Molecular profiling

first: Felix

last: Sahm


title: Sulfotransferase Signaling Sustains Fibroblast Identity and Antagonizes Therapeutic Cardiac Reprogramming

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: Maintenance of cell identity requires regulatory mechanisms that preserve lineage-specific gene expression programs and chromatin states. To investigate the role of JUNB in fibroblast fate stability during cardiac reprogramming, we performed CUTandRUN profiling of JUNB binding in mouse embryonic fibroblasts undergoing Mef2c, Gata4, and Tbx5 (MGT)-mediated cardiac reprogramming. JUNB occupancy was examined under control conditions and following perturbation of the fibroblast identity barrier gene Chst7. These datasets were generated to define genome-wide JUNB chromatin binding patterns and to investigate how extracellular signaling pathways influence JUNB-mediated regulation of chromatin accessibility and transcriptional programs during cell fate conversion. The resulting data provide a resource for studying transcription factor occupancy, chromatin regulation, and mechanisms of cell identity maintenance during direct cardiac reprogramming.

overall_design: CUTandRUN of iMGT (Mef2c, Gata4, Tbx5)-Myh6-eGFP-MEF cell line reprogrammed into induced-cardiomyocytes at day 1 post-MGT overexpression comparing siControl, siChst7 conditions. Antibody target to JUNB

first: Michaela

last: Romero

first: Yu-Ling

last: Chang

first: Sean

last: Murphy

first: Alexandre

last: Colas


overall_design: Comparative chromatin accessibility profiling analysis of ATAC-seq data from OreR (H33WT), H3.3H3.2 (H33H32), H3.3Δ (H33null), H3.3H3.2 (H33H32), and H3.3S31A (H33S31) Drosophila melanogaster cells. Samples are 1 day after eclosion (1dAE) and 10 days after eclosion (10dAE) brains.


title: Macrophages drive inguinal fat pad and lymph node remodelling in response to peripheral inflammation.

city: Glasgow

first: Heather

last: Mathie

state: --None--

address: Sir Graeme Davies Building, 126 University Place

institute: University of Glasgow

summary: Adaptive immune responses are intensely energy-dependent and rely on a local source of fuel-producing molecules which have been proposed to be derived from fat pads in which mammalian lymph nodes are embedded. However, the trigger for their release has not been identified. Here we demonstrate that cutaneous inflammation is directly correlated with rapid atrophy of perinodal fat pads and increase in embedded lymph node size. We further demonstrate that the fat pad atrophy is associated with influx of a CCR2-independent, lipid metabolising, macrophage population and that macrophage depletion ameliorates fat pad atrophy, and lymph node expansion, downstream of inflamed sites. Our data therefore identify peripheral inflammation as an antigen-independent trigger of downstream fat pad and lymph node remodelling and contributes to the release of essential nutrients to drive the energetic requirements of the adaptive immune response.

overall_design: WT female mice were given a ~62.5 mg dose of Aldara™ (Meda AB) cream containing 5% Imiquimod or an equivalent volume of control cream (Boots Aqueous Cream/10% Vaseline Lanette Cream) by application to shaved dorsal skin near the base of the tail. Cream was applied for 3 consecutive days (day 1, day 2 and day 3) and the mice culled 24h after the final application. Excised inguinal fat pads were digested for 1 hour using Liberase (0.44 Wunch units/sample) at 37’C on a 1000rpm shaker, and filtered through a 70um filter.  Macrophages were magnetically isolated from resulting cell suspension using Anti-F480 MicroBeads Ultrapure (Miltenyi Biotech). Purity of the samples were tested using flow cytometry and RNA extraction was performed on samples with >90% F4/80+CD64+ cells. After F480-magnetic positive selection, the eluted cell suspensions from 6 inguinal fat pads were pooled together to obtain enough ATMs (around 30,000 cells) for low-input RNA sequencing. Cells were spun down at 1000g for 10 minutes, lysed, and spun again to remove bound magnetic beads before proceeding with RNA extraction. RNA was extracted using the RNeasy Microkit with on-column DNAse I digestion (Qiagen), following manufacturer’s instructions, obtaining samples of around 100-150ng of total RNA in water.  RNA samples were then sent to a commercial sequencing provider (Novogene), for RNA QC, mRNA library preparation (poly-A enrichment) and Illumina Sequencing

first: Robin

last: Bartolini

first: Deepika

last: Sharma

first: Gillian

middle: J

last: Wilson

last: Dunphy

first: Jonathan

last: Cavanagh

first: Heba

last: Halawa

first: John

last: Cole

first: Stefan

last: Weidt

first: Jennifer

last: Barrie

first: Kirstyn

last: Gardner-Stephen

first: Gerard

last: Graham


title: Transcriptomic profiling of NNMT knockdown in MKN-45 gastric cancer cells

city: Nanning

first: Lingzhang

last: Meng

state: Guangxi

address: Qingxiu District

institute: Guangxi Academy of Medical Sciences

summary: MKN-45 gastric cancer cells were subjected to NNMT knockdown or negative control treatment and cultured in three independent biological replicates per group. Total RNA was extracted using TRIzol reagent, and RNA integrity was confirmed with RIN > 8.0. RNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit and sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads. Differential gene expression analysis was performed to identify transcriptomic changes induced by NNMT knockdown.

overall_design: 3 samples untouched as control, and another 3 sample was NNMT knockdown


title: Mitochondrially Transcribed dsRNA Mediates Manganese-induced Neuroinflammation

city: Atlanta

first: Maureen

last: Sampson

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

summary: Manganese (Mn) is an essential trace element required for various biological functions, but excessive Mn levels are neurotoxic and lead to significant health concerns. The mechanisms underlying Mn-induced neurotoxicity remain poorly understood. Neuropathological studies of affected brain regions reveal astrogliosis, and neuronal loss, along with evidence of neuroinflammation. Here, we present a novel Mn-dependent mechanism linking mitochondrial dysfunction to neuroinflammation. We found that Mn disrupts mitochondrial transcriptome processing, resulting in the accumulation of complementary RNAs that form double-stranded RNA (dsRNA). This dsRNA is released to the cytoplasm, where it activates cytosolic sensor pathways, triggering type I interferon responses and inflammatory cytokine production. This mechanism is evident in 100-day human cerebral organoids, where Mn-induced inflammatory responses are observed predominantly in mature astrocytes. Similar effects were observed in the transcriptome and cytokine profile of female and male mouse brains carrying mutations in the SLC30A10 gene, a model of hypermanganesemia with dystonia1 disorder. These findings highlight a previously unrecognized role for mitochondrial dsRNA in Mn-induced neuroinflammation and provide insights into the molecular pathogenesis of manganism. We propose that this mitochondrial dsRNA-induced inflammatory pathway could be active in other diseases caused by environmental or genetic factors.

overall_design: Cerebral organoids were generated from human iPSCS (line TMOi001-A) and cultured for 100 days. Organoids were untreated or exposed to 250μM manganese for 48h. Immediately following treatment, organoids were dissociated for 10x single-cell sequencing.

first: Anson

middle: D

last: Sing

first: Erica

last: Werner


title: Assessment of the effect of CLDN1 knockdown in cholangiocarcinoma patient-derived organoids

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

summary: Cholangiocarcinoma (CCA) is an adenocarcinoma of the hepatobiliary system showing an alarming rise in incidence and mortality with unsatisfactory treatment options. Claudin-1 (CLDN1) is a transmembrane protein expressed in tight junctions and exposed on the cell surface in liver fibrosis and cancer. Using single cell RNA-sequencing (scRNA-Seq) and spatial transcriptomics of CCA patient tissues, we show that CLDN1 expression is highly upregulated in cancer cells and is associated with stemness and cell fate. Gain-of-function studies in CCA orthotopic in vivo mouse models showed decreased survival and enhanced tumor growth, unraveling a functional role of CLDN1 as an oncogenic driver. Targeting exposed CLDN1 using highly specific CLDN1 monoclonal antibodies (mAbs) robustly inhibited tumor growth across CCA CDX and PDX mouse models and patient-derived CCA organoids including tumors with medium or low CLDN1 expression. Moreover, antibody treatment markedly inhibited tumor cell migration, invasion, and extrahepatic metastasis. Mechanistically, targeting exposed CLDN1 on CCA tumors inhibited Notch1, and Hippo-YAP signaling, resulting in decreased cancer cell stemness, EMT and extracellular matrix remodeling. In conclusion, these results uncover CLDN1 as a previously undiscovered CCA driver and therapeutic target, paving the way for the clinical development of CLDN1 mAbs to improve the dismal outcome of patients with advanced CCA.

overall_design: To investigate the role of CLDN1 in cholangiocarcinoma, CLDN1 was knocked-down in patient-derived organoids, and organoids were harvested and analyzed using RNA-Seq .

first: Zeina

last: Nehme

first: Jade

last: Brochon

first: Thomas

middle: F

last: Baumert


title: Assessment of the effect of CLDN1 knockout in cholangiocarcinoma cells in vitro

summary: Cholangiocarcinoma (CCA) is an adenocarcinoma of the hepatobiliary system showing an alarming rise in incidence and mortality with unsatisfactory treatment options. Claudin-1 (CLDN1) is a transmembrane protein expressed in tight junctions and exposed on the cell surface in liver fibrosis and cancer. Using single cell RNA-sequencing (scRNA-Seq) and spatial transcriptomics of CCA patient tissues, we show that CLDN1 expression is highly upregulated in cancer cells and is associated with stemness and cell fate. Gain-of-function studies in CCA orthotopic in vivo mouse models showed decreased survival and enhanced tumor growth, unraveling a functional role of CLDN1 as an oncogenic driver. Targeting exposed CLDN1 using highly specific CLDN1 monoclonal antibodies (mAbs) robustly inhibited tumor growth across CCA CDX and PDX mouse models and patient-derived CCA organoids including tumors with medium or low CLDN1 expression. Moreover, antibody treatment markedly inhibited tumor cell migration, invasion, and extrahepatic metastasis. Mechanistically, targeting exposed CLDN1 on CCA tumors inhibited Notch1  and Hippo-YAP signaling, resulting in decreased cancer cell stemness, EMT and extracellular matrix remodeling. In conclusion, these results uncover CLDN1 as a previously undiscovered CCA driver and therapeutic target, paving the way for the clinical development of CLDN1 mAbs to improve the dismal outcome of patients with advanced CCA.

overall_design: To investigate the role of CLDN1 in cholangiocarcinoma, CLDN1 was knockedout in CCA cells, and cells were harvested and analyzed using RNA-Seq .


title: Assessment of the effect of CLDN1 knockout in cholangiocarcinoma cells in vivo

summary: Cholangiocarcinoma (CCA) is an adenocarcinoma of the hepatobiliary system showing an alarming rise in incidence and mortality with unsatisfactory treatment options. Claudin-1 (CLDN1) is a transmembrane protein expressed in tight junctions and exposed on the cell surface in liver fibrosis and cancer. Using single cell RNA-sequencing (scRNA-Seq) and spatial transcriptomics of CCA patient tissues, we show that CLDN1 expression is highly upregulated in cancer cells and is associated with stemness and cell fate. Gain-of-function studies in CCA orthotopic in vivo mouse models showed decreased survival and enhanced tumor growth, unraveling a functional role of CLDN1 as an oncogenic driver. Targeting exposed CLDN1 using highly specific CLDN1 monoclonal antibodies (mAbs) robustly inhibited tumor growth across CCA CDX and PDX mouse models and patient-derived CCA organoids including tumors with medium or low CLDN1 expression. Moreover, antibody treatment markedly inhibited tumor cell migration, invasion, and extrahepatic metastasis. Mechanistically, targeting exposed CLDN1 on CCA tumors inhibited Notch1 and Hippo-YAP signaling, resulting in decreased cancer cell stemness, EMT and extracellular matrix remodeling. In conclusion, these results uncover CLDN1 as a previously undiscovered CCA driver and therapeutic target, paving the way for the clinical development of CLDN1 mAbs to improve the dismal outcome of patients with advanced CCA.

overall_design: To investigate the role of CLDN1 in cholangiocarcinoma, fresh tumor tissues from mice bearing HuCC-A1-xenograft tumors established from HuCC-A1 CLDN1 knockout cells or control cells were harvested and analyzed using RNA-Seq .

first: Marine

middle: A

last: Oudot


title: Using Rhodopseudomonas palustris as a model bacterium to study fungal-bacterial interactions in wood decayed by the brown rot fungus Rhodonia placenta

city: Saint Paul

first: Nathan

last: Lewis

email: nalewis159@gmail.com, lewi1449@umn.edu

state: MN

address: 1445 Gortner Ave

department: Plant & Microbial Biology

institute: University of Minnesota

summary: Brown rot fungi play an essential role in carbon cycling by decomposing lignocellulose into substrates usable by themselves and other microbes. Interactions between bacteria and fungi can be competitive or beneficial, but these relationships are not well understood because of a lack of good model systems. To model cross-feeding between fungi and bacteria, wood decayed by the brown rot fungus Rhodonia placenta was used as a carbon source for the phototrophic bacterium Rhodopseudomonas palustris. We found that fungal decay products generated by Rda. placenta could be used by R. palustris for growth, and later decay stages contained more usable substrates than early stages. Mass spectrometry identified a range of aromatic and non-aromatic acids, but after 95 days of bacterial growth, R. palustris only consumed non-aromatic acids over the aromatic lignin monomers. Genes involved with aromatic compound degradation were unimportant for growth and RNA sequencing revealed that aromatic compound degradation genes were repressed on decayed wood extract. Randomly barcoded transposon sequencing failed to identify a solitary catabolic pathway used by R. palustris, suggestive of substrate co-utilization, and surprisingly showed that genes involved with copper toxicity were essential. Finally, we found genes involved with biosynthesis of certain cofactors were non-essential on decayed wood extract, suggesting these nutrients were scavenged, and implicating these resources in supporting microbial communities in the environment. This study helps lay the foundation for a model fungal-bacterial system to study interactions that govern these relationships which will be valuable for understanding ecological interactions and industrially relevant co-culture systems.

overall_design: Aspen wafers were decayed by the brown rot fungus Rhodonia placenta to depolymerize and partially catabolize the lignocellulose. The decayed wood was infused into bacterial growth medium and used as a carbon source to support growth of the phototrophic bacterium Rhodopseudomonas palustris. In this experiment, we compared transcript counts for Rhodopseudomonas palustris grown in this decayed wood extract to transcript counts in medium containing a single carbon source, acetate, to identify what genes are upregulated during growth on fungal decayed wood.

middle: M

first: Irshad

middle: U

last: Haq

last: Schilling

first: Kathryn

last: Fixen


title: NEMO lysine mutant mice reveal ROS-RelA signaling required for optimal CD40-induced humoral immunity [NEMODK_CUTTAG]

city: Milwaukee

first: Demin

last: Wang

state: WI

address: 8727 W Watertown Plank Rd

institute: 1Versiti Blood Research Institute

summary: Oxidative and genotoxic stresses activate NF-κB signaling through intracellular pathways distinct from those initiated by membrane receptors, but their physiological roles remain incompletely defined. We created the NEMODK mouse model with germline arginine substitutions at NEMO (NF-κB essential modulator) lysines 270 and 302, key sites for post-translational modifications selectively induced by these intracellular stresses to enable NF-κB signaling in vitro. NEMODK mice exhibited B cell-intrinsic defects in the generation of germinal center B cells and humoral responses. Mechanistically, NEMODK B cells displayed a CD40-specific NF-κB signaling defect, unrelated to acute canonical and delayed noncanonical NF-κB activity, which was accompanied by the lack of sustained NEMO monoubiquitination downstream of mitochondrial reactive oxygen species generation without relying on nuclear DNA damage. This specifically reduced persistent RelA activity and a failure to mount transcriptomic and epigenetic changes critical for homotypic B cell aggregation, cell proliferation, class switch recombination and antibody secreting cell generation. Thus, CD40 induces a uniquely sustained NEMO modification and persistent RelA transcriptional activity to efficiently generate class-switched antibodies.

overall_design: Splenic B cells were isolated from WT and NEMODK mice, stimulated with anti-CD40 and IL-4 for two days, then washed and resuspended in wash buffer. Cells were bound to ConA-coated beads, incubated overnight with anti-RelA (Cell Signaling, 8242), anti-H3K4me3 (Active Motif, 39159), anti-H3K27ac (Active Motif, 39034), and anti-H3K27me3 (Cell Signaling, 9733) antibodies, followed by secondary incubation with anti-rabbit IgG antibodies (Antibodies Online). After washing, the cells were incubated with the pA-Tn5 adapter complex (Epicypher) at room temperature for 1 hour. Tagmentation was performed at 37°C, after which DNA was extracted and PCR-amplified to generate sequencing libraries. Libraries were sequenced on an Illumina NovaSeq platform to produce paired-end 150 bp reads.


title: Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

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

overall_design: Refer to individual Series


title: Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency - CUT&RUN

summary: In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associated H3K27me3 histone modifications. In contrast, these poised enhancers (PEs) are scarce in naive hPSCs that model pre-implantation epiblast. PEs form abundant chromosomal contacts with developmental genes, but when these contacts emerge, how their formation relates to enhancer poising and their functional significance remains incompletely understood. Here, we devise high-resolution, PE-targeted Capture Hi-C to generate a comprehensive atlas of PE chromosomal contacts in the time course of hPSC transition from the naive to primed state. We find that enhancer poising emerges early in the transition, while the contacts show diverse dynamics that is only partially coupled to poising. PROTAC-induced degradation of Polycomb Repressive Complex 2 (PRC2) early in the transition weakens PE connectivity, while inhibition of its H3K27 methyltransferase activity does not, suggesting a non-catalytic role of Polycomb in supporting PE contacts. Notably, PE contacts persist after developmental activation or ectopic CRISPRa targeting and can mediate long-range gene induction. Together, these findings reveal the temporal and mechanistic principles of PE connectivity, highlighting a potential role of PE contacts in establishing gene expression patterns in human development.

overall_design: The genomic location of H3K27me3 was profiled using CUT&RUN in primed human pluripotent cells. The experiment was independently performed two times.

first: Marina

last: Nocente

first: Monica

last: Della Rosa

first: Andrew

last: Malcom

first: George

last: Lister

first: Isabella

last: Savin

first: Helen

last: Ray-Jones

first: Sarah

last: Elderkin

first: Ruilin

last: Tian

first: Adam

last: Bendall

first: Claudia

last: Semprich

first: Martin

last: Kampmann

first: Valeriya

last: Malysheva

first: Maria

last: Rostovskaya

first: Peter

last: Rugg-Gunn

first: Mikhail

last: Spivakov


title: Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency - CUT&Tag

overall_design: Naïve human pluripotent stem cells were transitioned rowards a primed-like state in the presence of EED PROTAC or EZH2 inhibitor or DMSO control. On day 5 of the transition, cells were harvested and CUT&Tag was used to profile the genomic location of H3K27me3 and H2AK119ub. The experiment was independently performed two times.


title: Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency - RNA-seq

overall_design: Naïve human pluripotent stem cells were transitioned rowards a primed-like state in the presence of EED PROTAC or EZH2 inhibitor or DMSO control. On day 5 of the transition, cells were harvested and RNA-seq was used to profile their transcriptomes. The experiment was independently performed three times.


title: Intestinal FXR deficiency uncouples steatosis protection from liver inflammation and fibrosis in MASH-diet fed mice

city: Lille

last: Peschard

address: 1, rue du professeur Calmette BP245

institute: INSERM UMR 1011

summary:
The bile-acid receptor FXR is known to be expressed in both intestine and liver, and FXR agonists are currently Under clinical evaluation for Metabolic Associated SteatoHepatitis (MASH) treatment. However, the specific question about activate or de-activate FXR specifically in the intestine in MASH is still unlear, protective results being available for both case.
We used micro-arrays to identify both liver and intestine transcriptome alterations led by intestinal FXR deletion in the context of MASH

overall_design: Mouse samples were selected from the whole cohort after RNA quality control on an Agilent 2100 BioAnalyzer. The RNA integrity being >7, 5 mouse per genotype were selected. We sought to obtain liver and intestinal transcriptome of these MASH mice to decipher the effect of intestinal FXR deletion on the progression and development of MASH.

first: Margaux

last: Nawrot

first: Morgane

last: Thibaut

first: Kévin

last: Ory

first: Emmanuelle

last: Vallez

first: Emilie

last: Dorchies

first: Véronique

last: Touche

first: Amandine

last: Descats

first: Julie

last: Dubois-Chevalier

first: Céline

last: Gheeraert

first: Sandrine

last: Caron

first: Kadiombo

last: Bantubungi

first: Philippe

last: Lefebvre

first: Anne

last: Tailleux

first: Joel

middle: T

last: Haas

first: Laure

middle: B

last: Bindels

first: Isabelle

last: Leclercq

first: Davic

last: Dombrowicz

first: Sophie

last: Lestavel

first: Bart

last: Staels


title: Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency - ChIP-seq

first: Simon

last: Andrews

overall_design: The genomic location of p300 was profiled using ChIP-seq in naïve and primed human pluripotent stem cells. The experiment was independently performed once for primed cells and twice for naïve cells.

first: Marina

last: Nocente

first: Monica

last: Della Rosa

first: Andrew

last: Malcom

first: George

last: Lister

first: Isabella

last: Savin

first: Helen

last: Ray-Jones

first: Sarah

last: Elderkin

first: Ruilin

last: Tian

first: Adam

last: Bendall

first: Claudia

last: Semprich

first: Martin

last: Kampmann

first: Valeriya

last: Malysheva

first: Maria

last: Rostovskaya

first: Peter

last: Rugg-Gunn

first: Mikhail

last: Spivakov


title: Identification of a novel deeply quiescent neural stem cell population in the subventricular zone

city: OXFORD

first: Liliana

last: Minichiello

address: Department of Pharmacology, University of Oxford, Mansfield Road, University of Oxford

institute: University of Oxford

summary: This study shows that a novel genetic tool, the Penk-CreAi9 line, expressing Cre recombinase under the Proenkephalin promoter and combined with the Ai9-tdTomato line, labels a distinct group of stem cells in the SVZ together with previously identified subgroups of B-cells and neuroblasts. Single-cell RNA sequencing (scRNA-seq) demonstrates that these cells represent a previously unappreciated population of qNSCs with a unique transcriptional profile and a less differentiated state than the canonically accepted GLAST+ NSCs. In particular, the analysis further reveals expression of 5-hydroxytryptamine receptor 2C (5-HT2C receptor) and prolactin receptor (PRLR), which were previously functionally correlated with qNSCs but not captured or profiled in RNAseq experiments. This study also identifies novel markers, including Kcnj13, a gene that encodes the potassium channel KiR7.1, that define the identity of these cells.

overall_design: RNA-seq profiling of FACS-sorted tdTomato+ or tdTomato+/Cd11b- cells from the SVZ/striatal tissue of Penk-Cre Ai9 line.

first: Claus

last: Nerlov

first: Arup

middle: R

last: Nath

first: Roy

last: Drissen


title: Cancer immunotherapy targeting myeloid cells requires endosomal pattern recognition

city: Solna

first: Mikael

last: Karlsson

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

summary: Immunotherapy is now an established and efficient treatment option for many cancer patients, but unfortunately, a proportion of the patients still experience poor outcomes due to resistance to treatment. Thus, there is a need to both understand key mechanisms of resistance as well as to develop new treatments. Herein, we explore an immunotherapeutic approach that targets tumor associated macrophages (TAMs) as an alternative to direct T cell targeting. We demonstrate that TAMs need to have a functional endosomal pattern recognition machinery for immunotherapy to be efficient. This is true for TAM targeting using both anti-PD-L1 (αPD-L1) or anti-MARCO (αMARCO) antibodies, and we determine that the absence of endosomal Toll-like receptors (TLRs) makes the TAMs unresponsive to treatment while retaining an immunosuppressive phenotype. For αMARCO treatment, we also find that TLR9 activation to express components of the inflammasome is specifically needed to render TAMs responsive to treatment. This key feature of immunotherapy efficacy, with TAMs being sensitized by the tumor microenvironment via endosomal TLRs, could be exploited to improve immunotherapeutic outcomes.

overall_design:
Bulk RNA Sequencing of TAMs from wild-type and Unc93b1 3d/3d mice was performed at day 21 after inoculation of EO771 tumors and treated every 3 days with isotype or αMARCO antibodies.
Single cell RNA Sequencing of CD45+ immune cells from wild-type and Unc93b1 3d/3d mice was performed at day 21 after inoculation of EO771 tumors and treated every 3 days with isotype or αMARCO antibodies.

first: Yueyun

last: Pan

first: Shengduo

last: Pei

first: Heng

last: Liang


title: RNA-seq and acRIP-seq in NAT10 overexpression HaCaT cells [RNA-seq]

city: hangzhou

first: zhiqi

last: xie

address: huzhou street 51

institute: Hangzhou city university

summary: To elucidate the function of the RNA acetyltransferase NAT10 in keratinocytes and its regulatory impact on atopic dermatitis pathogenesis, we conducted RNA-seq and acRIP-seq of HaCaT cells overexpressing NAT10 versus empty-vector controls.

overall_design: NAT10 overexpression or vector control HaCaT cells were used to investigate the different expression genes which were correlated to NAT10.

first: Zhiqi

last: Xie

first: Jinjin

last: Shao


title: Altered expression profile of miRNAs in canine inguinal testes

city: Poznań

first: Arkadiusz

last: Kajdasz

state: wielkopolskie

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

type: Non-coding RNA profiling by high throughput sequencing

summary: Cryptorchidism is a major disorder of sex development (DSD) in dogs, with a complex, polygenic background. It is known that in canine undescended testes expression of protein coding genes is massively up- or down-regulated and it is associated with certain epigenetic modifications.  In the present study we aimed to compare expression profile of small non-coding RNAs (sncRNAs) in undescended (UD) and descended (D) testes. Undescended (UD) and descended (D) testes of unilateral, inguinal cryptorchid dogs (n=9), as well as scrotal testes of control dogs (C, n=8) were analyzed by small non-coding RNA sequencing (sncRNA-seq) approach. Comparison of UD and D testes revealed 224 differentially expressed miRNA (DEGs), with 118 meeting the criteria of FDR < 0.05 and |log2FC| > 1.5 (8 up- and 110 downregulated). Similarly, comparison of UD and C testes identified 200 DEGs, with 102 meeting the same criteria (9 up- and 93 downregulated).

overall_design: small RNA-Seq profiling of undescended (UD) and descended (D) testicles of unilateral cryptorchid dogs (n = 9) and scrotal testicles (C) of control dogs (n = 8)

first: Joanna

last: Nowacka-Woszuk

first: Izabela

last: Szczerbal

first: Monika

last: Stachowiak

first: Marek

last: Switonski


title: Progranulin insufficiency and TDP-43 overexpression interact to worsen FTD-related phenotypes in mice.

city: Birmingham

first: Andrew

last: Arrant

state: AL

address: 1825 University Blvd SHEL 1106

institute: University of Alabama at Birmingham

summary: Progranulin (GRN) mutations, which typically cause progranulin haploinsufficiency, cause frontotemporal dementia with TDP-43 pathology (FTD-TDP). It is not clear how progranulin insufficiency may cause FTD-TDP. Progranulin-insufficient mice develop FTD-related phenotypes without robust TDP-43 pathology, so we crossed crossed Grn+/- mice (RRID:MMRRC_036771-JAX) with transgenic mice expressing wild-type human TDP-43 (RRID:IMSR_JAX:012836) to investigate the effect of progranulin insufficiency on TDP-43 aggregation and TDP-43–related phenotypes.

overall_design: Grn+/- mice and hTDP transgenic mice were crossed to generate littermates of four genotypes: Grn+/+:hTDP-, Grn+/+:hTDP+, Grn+/-:hTDP-, and Grn+/-:hTDP+. At around 10 months of age, we collected frontal cortex of n = 6 mice per genotype and analyzed by bulk RNA sequencing to assess differential gene expression and alternative splicing.

first: Anna

last: Cook

first: Benjamin

last: Lin

first: C

last: Miller

middle: E


title: Rbm5 is required for sustaining leukemia stem cells by modulating a leukemic transcriptional program in concert with the Myc network [ChIP-Seq]

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

institute: Soochow University

summary: Acute myeloid leukemia (AML) represents a type of malignant hematological disease that is caused by the dysregulated developmental program of leukemia stem cells (LSCs). Compared to other hematological malignancies, AML often predicts poor prognosis and unfavorable treatment outcomes in the clinic, urging the need for complex mechanism studies. Rbm5 was recently reported as a key regulator in maintaining the survival of human AML cell lines via non-canonical transcriptional activation of Hoxa9. However, its function in LSCs and the broad genome-wide transcriptional targets remain elusive. Here, using genetic mouse models, ex vivo AML culture, and patient-derived xenografts, we report that Rbm5 is required for murine leukemogenesis and maintains self-renewal of LSCs in vivo but is dispensable for normal hematopoiesis. Rbm5 is highly expressed in LSCs, and its deficiency results in specifically defective LSC function, along with the inhibition of self-renewal gene expression and the induction of a myeloid differentiation program. Multi-disciplinary mechanistic investigations targeting gene expression at both the single-cell level and in bulk populations, together with an acute RBM5 degradation system, further identified the direct transcriptional targets of Rbm5 in primary leukemia cells, including stemness genes, such as Hoxa9 and Myc. Moreover, RBM5 not only interacts with MYC but also maintains its protein levels, thereby sustaining the Myc downstream transcriptional network through its proper genome-wide occupancy. Forced expression of Myc sufficiently rescued the Rbm5-depleted defects both in vitro and in vivo. Thus, our study demonstrates that Rbm5 regulates the AML LSC program through non-canonical transcriptional mechanisms, providing a strong rationale for therapeutically targeting Rbm5 in the treatment of myeloid leukemia.

overall_design: MYC Halotag ChIP-seq were used to identify MYC Targets

first: Fields

last: Shaela

first: Qiong

last: Zhang

first: Beisi

first: Chunliang

last: Li


title: Rbm5 Sustains Leukemia Stem Cells Through a Myc-driven Transcriptional Circuitry

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A Pathogenic CD8⁺ TRM–Chemokine Axis Orchestrates Liver Fibrosis and Provides Circulating Biomarkers during Chronic Clonorchis sinensis Infection

city: Shanghai

first: Jiashun

address: 280 S. Chongqing Rd

department: Department of Immunology and Microbiology

institute: Shanghai Jiao Tong University School of Medicine

summary: Clonorchis sinensis, a carcinogenic hepatobiliary trematode, drives severe pathological sequelae in humans. However, the immunological mechanisms underlying its chronic persistence remain incompletely elucidated. We systematically characterized the spatiotemporal dynamics of host immune responses during long-term C. sinensis infection. Systemically, immunity evolved from an early mixed Th1/Th2/Th17 response toward eventual immune resolution. In contrast, hepatic immunity shifted from an initial Th2 bias to sustained pro-inflammatory activation, paralleling progressive liver pathology. Mechanistically, this hepatic immunopathology was driven by the expansion of CD8⁺ tissue-resident memory T (TRM) cells, which secreted high levels of CCL3, CCL4, CCL5, granzyme B, and granzyme K. Functional analyses demonstrated that CD8⁺ TRM cells orchestrated immune cell recruitment and fibroblast activation, with CD8⁺ T cell depletion significantly ameliorating liver damage. Notably, CCL4 was predominantly produced by CD8⁺ TRM cells and its serum levels correlated with hepatic pathology in both murine models and human patients with clonorchiasis. Our findings identify CD8⁺ TRM cells and CCL-mediated signaling as key drivers of chronic C. sinensis-induced liver immunopathology, highlighting promising targets for therapeutic intervention.

overall_design: Following Clonorchis sinensis infection, liver non-parenchymal cells (NPCs) were isolated from murine livers by differential centrifugation and analyzed using single-cell RNA sequencing (scRNA-seq).

first: Xinyue

last: Du

first: Tingjun

last: Zhu

first: Guangjie

last: Chen

first: Menbao

last: Qian

first: Zhaojun

last: Wang


title: The sodium channel SCN2A regulates cortical excitatory and inhibitory neurogenesis

city: Toronto

first: Jarryll

middle: Anthony

last: Uy

state: ON

address: 60 Leonard Ave

department: Laboratory Medicine and Pathobiology

institute: University of Toronto

summary: Voltage-gated sodium channels regulate neuronal excitability and fast synaptic transmission in the postnatal and adult brain. The gene SCN2A, encoding the sodium channel Nav1.2, regulates synaptic development and variants in SCN2A are associated with autism spectrum disorders (ASD). The expression pattern of SCN2A begins during fetal cortical development, prior to the onset of synaptic transmission, but it is unknown whether SCN2A regulates early cortical development through mechanisms independent of synaptic transmission. Here we reveal that isogenic and ASD patient-derived human forebrain organoids modelling a loss of SCN2A function display impaired excitatory and inhibitory neurogenesis, leading to a developmental imbalance. Unexpectedly, we find precocious generation of cortical inhibitory neurons is driven by elevated sonic hedgehog (SHH) signaling and is reversible through pharmacological inhibition. Functionally, these developmental phenotypes arise due to sodium channel dysfunction and lead to abnormal neuronal network activity. Our results identify a new mechanisim for cortical excitatory and inhibitory neurogenesis involving SCN2A, and reveal that early neurogenesis deficits precedes postnatal neural circuit dysfunction in SCN2A-associated disorders.

overall_design: Cerebral organoids were generated and matured to day 90 from H1 hESC Control, SCN2A-/- and SCN2A +/G1744X genotypes. 3 organoids per genotype were pooled per batch and submitted for fixed scRNAseq. A total of 3 independent differentiation batches were submitted.

first: Karun

last: Singh


title: Engineering a Lipid Nanoparticle with Atypical Calcium Crystal Structure for Enhanced IFNβ-mediated Immunotherapy

city: Beijing

first: yujie

last: luo

state: Beijing

address: xueyuan road 38

institute: peking university

summary: We have employed a single cell sequencing approach using 10x Genomics scRNAseq to study the anti-tumoral effects of NanoCa. Our results have shown that NanoCa activates the innate immune response by inducing IFNβ, to investigate which types of cells are involved in the anti-tumor effect, CT26 tumor and Tumor-draining lymph nodes were isolated and analyzed using scRNA-seq.

overall_design: CT 26 tumor samples treated by NanoCa were isolated by Fluorescence- activated cell sorting (FACS) and analyzed using scRNA-seq. Tumor-draining lymph nodes were isolated and analyzed using scRNA-seq

first: Yujie

last: Luo

first: Chuanda

first: Yu

last: Sun

first: Dan

last: Lu

first: Yufei

last: Xia

first: Zhiqiang

first: Fuping

last: You


title: Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome [ATAC-seq]

city: Cincinnati

first: Matthew

last: Weirauch

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: We systematically investigate interactions between Epstein-Barr virus (EBV) transcriptional regulators (vTRs) and the human genome. Starting with 16 known and candidate vTRs, we identify nine whose introduction into human cells results in substantial alterations to host gene expression. Genome-scale determination of vTR genomic binding events and alterations to chromatin accessibility reveals a detailed map of EBV's functional interactions with the human genome, including >100,000 vTR binding events impacting almost a quarter of all human genes. BMRF1 emerges as a potent regulator, impacting >7,000 genes and altering >37,000 chromatin regions. Our results provide new evidence that EBV RTA interacts with and stabilizes the binding of human RBPJ. Network analysis reveals that many human genes are targeted by multiple EBV vTRs, highlighting the vast coordinated impact of EBV on human gene expression. This study provides a valuable, extensive resource for examining EBV-induced alterations to human gene regulation, with data available on multiple platforms.

overall_design: We performed ATAC-seq on Flp-In-293 cell lines that had been transfected with one of nine Epstein-Barr virus transcriptional regulators or a control. Experiments were performed in triplicate.

first: Leah

last: Kottyan