title: An RNA ligase shapes transcriptional profiles, neural function, and behaviour in the developing larval zebrafish

city: Konstanz

first: Fiona

middle: Sophie

last: Klusmann

address: Universitätsstrasse 10

institute: University of Konstanz

summary: We report the transcriptomic analysis of zebrafish wild-type and maternal-zygotic rlig1 mutant embryos and larvae using RNA-sequencing to investigate the role of Rlig1 in vertebrate development.

overall_design: Transcriptomes of WT and MZrlig1 embryos were profiled at six developmental stages (4-cell, sphere, shield, bud, 1 dpf, 5 dpf). Pools of 8–10 embryos were collected per replicate, with 2–4 biological replicates per stage. In addition, RNA was extracted from dissected heads of 5 dpf larvae, which were classified as “good” or “bad” responders in a visual motion assay.

first: Onur

last: Önder

first: Patrick

last: Müller


title: Differential m6A methylation between parental and temozolomide resistant U87 MG cells

status: Public on Jun 01 2026

city: New Haven

first: Sigrid

last: Nachtergaele

state: CT

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

country: USA

institute: Yale University

type: Expression profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is a critical regulator of mRNA processing and function, playing roles in mRNA processing, translation, and decay. Changes in m6A status have been implicated in various cancers, including glioblastoma (GBM), where acquired chemoresistance to temozolomide (TMZ) remains a major clinical challenge. We developed cell culture models of acquired TMZ resistance in GBM and analyzed the regulation of resistance-associated genes and pathways by m6A. We find that key resistance-associated genes and pathways are regulated by m6A methylation, including MGMT, the enzyme that repairs primary TMZ-induced DNA damage. Inhibition of METTL3 with STM2457 treatment destabilizes MGMT mRNA. Intriguingly, other TMZ resistance-associated genes are similarly regulated by m6A, suggesting that METTL3 inhibition may represent a promising therapeutic approach for overcoming TMZ resistance.

overall_design: m6A-eCLIP mapping of m6A peaks and single nucleotide sites in U87 MG, U87-R, and U87-R cells with STM2457 treatment (performed by Eclipse Bioinnovations).

first: Emily

last: Dangelmaier

first: Dorthy

last: Fang

first: Kyal Sin

last: Htet

first: Nicole

middle: S

last: Harry

first: Renee

last: Pascoe

first: Je Won

last: Yang

first: Clara

last: Wang


title: Regulation of temozolomide resistance by m6A mRNA methylation in glioma cell lines

overall_design: RNA-seq profiling of parental U87 MG and LN229 cells, and their temozolomide resistant counterparts (U87-R, LN229-R), with and without STM2457 treatment.


title: Dynamic remodeling of the pancreas immune landscape in obesity.

city: NYC

first: Alexey

last: Koshkin

state: New York

department: Department of Pathology and Cell Biology

institute: Columbia University Medical center, department of Pathology and Cell Biology

summary: Obesity is a known risk factor for diseases of the pancreas, including diabetes, pancreatic cancer and pancreatitis, but mechanisms remain unclear. To elucidate how obesity impacts pancreatic immune homeostasis, we performed spatial, transcriptomic and functional profiling of human pancreatic immune cells from obese and non-obese organ donors. Obesity was associated with higher density of tissue resident memory T-cells (TRM) in the exocrine pancreas which display high cytotoxic functions and aggregated around macrophages. Single cell sequencing of pancreatic macrophages revealed two main subsets - FOLR2+ CD11c- fetal-derived macrophages with pro-repair and immunoregulatory function and a FOLR2- CD11c+ monocyte-derived macrophages with greater T-cell interactions and pro-inflammatory function. In obesity, the pancreatic macrophage landscape shifts to lower predominance of FOLR2+ CD11c- macrophages and higher FOLR2- CD11c+ macrophages which interact selectively with the TRM and inflamed exocrine epithelium. Together, these results identify macrophage-T cell circuits and immune epithelial interactions that fuel chronic pancreatic inflammation in obesity – a potential unifying mechanism for obesity-related pancreatic diseases

overall_design: The experimental design consists of two parallel analyses using CITE-seq: 1) A cross-tissue comparison of T cells isolated from pancreas, small intestine, spleen, and pancreatic lymph nodes from 3 human donors. 2) A deep profiling of macrophages isolated from the pancreas of 5 human donors.

first: Kranthi Kiran

middle: K

last: Kishore Tanagala

first: Anna

last: Eichinger

first: Michael

last: Chait

first: Aoife

last: Young

first: Shanila

last: Shakil

first: Junichi

last: Yoshikawa

first: Yosuke

last: Sakamoto

first: Steven

last: B. Wells

first: Xiaojuan

last: Chen

first: Boris

last: Reizis

first: Donna

last: L. Farber

first: Stuart

last: P. Weisberg

first: Ladan

last: Fazlollahi


title: Dynamic remodeling of the pancreas immune landscape in obesity. [CITE-Seq]


title: Dynamic remodeling of the pancreas immune landscape in obesity [bulk RNA-seq]

overall_design: Examination of TRM gene expression profiles from donor-matched pancreas, jejunum, pancreas draining lymph node (PLN) and blood CD8+ TEM from living healthy donors.


title: Conductive and bioactive supramolecular scaffolds promote neuronal maturation

city: Evanston

last: Metlushko

state: IL

address: 2236 Sherman Avenue, Unit K-2

department: Biomedical Engineering

institute: Northwestern University

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

overall_design: Refer to individual Series


title: Conductive and bioactive supramolecular scaffolds promote neuronal maturation [Stupp06_RNA-seq]

city: Chicago

first: Matthew

middle: J.

last: Schipma

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

summary: Traumatic injury in the central nervous system (CNS) results in neuronal damage and death, with chronic symptoms such as damaged cognition and paralysis. While chemically engineered scaffolds can be delivered to provide a substrate to stimulate axon regrowth, many grafts lack efficacy due to inefficient electrical coupling between the material and the conductive in vivo environment. We have incorporated a conductive component, functionalized poly[3,4-(ethelynedioxythiophene)] (PEDOT), into a supramolecular biomaterial scaffold which facilitates neuronal differentiation and maturation. Peptide amphiphiles (PAs) can self-assemble into high-aspect ratio nanostructures that mimic native extracellular matrix and may be functionalized with bioactive epitopes such as (previously described) laminin mimetic (IKVAV).  Interestingly, this synthesized PEDOT:PA enhanced neurite length and branching in murine primary cortical neurons. Furthermore, protein analysis clearly showed PEDOT:PA upregulated maturation and pre-/post-synaptic markers (Map2, PSD 95, Syn). Moreover, human induced pluripotent stem cell (iPSCs) derived spinal cord neuron models showed enhanced differentiation of iPSCs into human spinal cord progenitors through increased expression of TUJ-1. These results strongly suggest that PEDOT:PA promotes CNS maturation in mouse and human systems and shows its potential as a therapeutic in spinal cord injury.

overall_design: Comparative gene expression profiling analysis of cortical neurons and therapy treatment

first: Nozomu

last: Takata


title: Conductive and bioactive supramolecular scaffolds promote neuronal maturation [Stupp05_RNA-seq]


title: Conductive and bioactive supramolecular scaffolds promote neuronal maturation [Stupp08_RNA-seq]


title: Macrophage-Mediated IL1beta/IL23 Signaling Regulates gamma delta (gammadelta) T Cell Immunity Against Non-Tuberculous Mycobacteria [scRNA-seq 3]

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

country: China

institute: Fudan University

summary: Mechanistic Insights. Our study reveals the crucial role of gammadelta T cells in non-tuberculous mycobacteria (NTM) infection. We observed a significant increase and activation of gammadelta T cells in mice infected with MAB or with MAB infection combined with pulmonary fibrosis. Depletion of gammadelta T cells worsened the infection, while transfer of gammadelta T cells reversed this effect. Mechanistically, we found that MAB infection stimulates macrophages to produce IL-1beta and IL-23, which promotes the expansion of gammadelta T17 cells. MAB can also directly activate gammadelta T cells, leading to the clearance of MAB through an IL-17A-dependent pathway. Our findings suggest that gammadelta T cells represent a potential therapeutic target for NTM infections.

overall_design: For single-cell sequencing, the PBMC of NTM-infected patients were collected.


title: ACSS2 modulates endothelial glycolysis in angiogenesis

city: HANGZHOU

first: Yunyun

last: Wang

address: Yuhangtang Road 866

institute: Zhejiang University

summary: Endothelial cells (ECs) sustain high glycolytic flux and display remarkable metabolic plasticity. Although the molecular pathways regulating endothelial glycolysis are well characterized, the metabolic mechanisms underlying hypoxia-induced glycolytic activation during angiogenesis remain poorly understood. Here, we show that acetyl-CoA synthetase 2 (ACSS2) serves as a critical metabolic modulator, coupling acetate utilization with glycolytic flux to control EC function and angiogenesis. The high level of ACSS2-mediated acetate-to-acetyl-CoA conversion in angiogenic front ECs sustains acetyl-CoA levels, which are essential for EC proliferation and retinal vascularization. Conversely, endothelial-specific Acss2 deletion disrupts pathological angiogenesis and normalizes tumor vasculature. Mechanistically, ACSS2 maintains hypoxia-inducible factor 1α transcriptional activity and stabilizes glucose transporter 1, thereby preserving glycolysis. Pyruvate dehydrogenase kinase 4 knockdown rescues metabolic and functional defects in ACSS2-deficient ECs, revealing acetyl-CoA homeostasis as a lynchpin of hypoxic endothelial metabolism. Collectively, our work establishes ACSS2 as a pivotal regulator of vascular development and proposes targeting acetate metabolism as a strategy to modulate pathological angiogenesis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from HUVECs under various conditions: Scramble siRNA treatment, ACSS2 siRNA knockdown treatment, and ACSS2 + PDK4 siRNA double knockdown treatment. Each of the three treatments has three replicates, and all treatments underwent transfection with siRNA for 6 days, followed by 1% oxygen treatment for 30 hours prior to sampling.

first: Luyang

last: Yu

first: Xiaolong

last: Zhu


title: Expression data from Pten, Apc, and Smad4 knockout prostate cancer mouse models

city: Notre Dame

first: Xin

last: Lu

state: IN

address: 109 Galvin Life Science Center

institute: University of Notre Dame

summary:
Prostate-specific deletions of tumor suppressor genes such as Pten, Apc, and Smad4 contribute to diverse molecular programs in prostate cancer. To investigate the transcriptional effects of these alterations, we generated genetically engineered mouse models with prostate-specific knockout of Pten alone or in combination with Apc or Smad4, using PB-Cre.
We used microarrays to profile gene expression in tumors derived from different genotypes, comparing bulk tumor tissues and isolated cancer cells. This dataset enables investigation of gene expression changes driven by distinct oncogenic drivers and tumor cell populations in prostate cancer.

overall_design: For 16–25 week-old PB-Cre⁺ PtenL/L, PB-Cre⁺ PtenL/L ApcL/L, and PB-Cre⁺ PtenL/L Smad4L/L male mice carrying the mTmG reporter allele, prostates were harvested once tumors became detectable. GFP⁺ cancer cells were isolated by FACS from dissociated prostate tissues, while bulk tumor tissues were collected separately without sorting. Total RNA was extracted from both GFP⁺ cells and bulk tumors, and samples were profiled using the Affymetrix Mouse Genome 430 2.0 Array for transcriptome analysis.

first: Lu

last: Xin

first: Liu

last: Guoqiang


title: Hepatic Yap1 activates systemic catabolism and muscle loss during organ repair: evidence for a common mechanism with cancer cachexia [eWAT_RNAseq]

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 2730 S Moody Ave

department: CDCB

institute: OHSU

summary: Here, we report the gene expression changes that occur in the mouse epididymal white adipose tissue (eWAT), at 3 day, and day7 following 70% partial hepatectomy (PHx) in mice.

overall_design: Using total RNA-sequencing, we analyzed eWAT from 5 adult C57BL6/J  male mice, 3, and 7days after 70% partial hepatectomy. Control animals received a sham surgery (laparotomy) with no partial hepatectomy. 4 sham control mice and 5 PHx mice (day3), and 3 PHx mice (day7) were used for the RNA-Seq analysis.

first: Leonidas

middle: G

last: Koniaris

middle: A

first: Adrian

middle: M

last: Baris

first: Tewfik

last: Hamidi


title: Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma [DNAseq]

city: Los Angeles

first: Aram

last: Modrek

state: Ca

address: 1441 EastLake Ave

institute: USC

summary: We introduced hundreds of CRISPR–Cas9-mediated DNA double-strand breaks (DSBs) into glioblastoma stem-like cells and tracked chromatin, transcriptional, and structural changes over time. Long after the DSBs were repaired, we found durable reprogramming of chromatin conformation and gene expression, as well as emergence of structural variants. These findings suggest that DNA damage can induce stable non-genetic alterations in cancer cells.

overall_design: DNA pull down of specific regions that have Cas9 breaks using a DNA probe panel was performed in glioblastoma stem-like cells. The cells treated with doxycycline-inducible multi-target gRNAs (mtg142 or mtg483) to introduce widespread DSBs. Samples were collected at 3 hours and 2 weeks post-induction. Vector control cells (wtCas9 expressed with no guide RNA) were also included. Each condition was run in biological duplicate.

first: Keerthivasan

middle: R

last: Chandradoss

first: Catherine

last: Do

first: Ravesanker

last: Ezhilarasan

first: Theodore

last: Sakellaropoulos

first: Jerome

last: Karp

first: Yingwen

last: Ding

first: Ze-Yan

last: Zhang

first: Melanie

last: Graciani

first: Giulia

last: Cova

first: Jennifer

middle: E

last: Phillips-Cremins

first: Erik

middle: P

last: Sulman

first: Jane

last: Skok


title: SARS-CoV-2 Variant Boosters and Breakthrough Infections Drive Functional Differences in the Memory B Cell Repertoire

city: Bethesda

first: Sarah

last: Andrews

address: 40 Convent Drive

institute: NIH

summary: Evolving respiratory viruses such as influenza and COVID-19 cause seasonal respiratory illness and death. Updated vaccines with virus variants are made to increase efficacy, but pre-existing immunity affects the response. To understand if variant boosters modify the memory B cell (MBC) repertoire, we analyzed the human MBC response in the COVAIL vaccine trial where individuals previously vaccinated with COVID-19 prototype spike immunogens were boosted with prototype spike, variant spikes, or both. We analyzed the cross-reactivity, phenotype and functionality of the MBC response and determined that variant vaccine boosters led to greater recall of cross-reactive MBCs compared to a prototype but limited de novo variant-specific MBC responses. Some study participants also experienced breakthrough infections with SARS-CoV-2 Omicron variants after the vaccine boost that primarily expanded cross-reactive MBCs. These MBCs potently neutralized closely related Omicron virus strains, but displayed less breadth toward more distant Omicron subvariants than MBCs from uninfected individuals. Thus, infection can narrow the cross-reactivity of the memory B cell repertoire.

overall_design: B cells  were isolated at various timepoints from PBMCs of individuals undergoing vaccination against COVID-19. Antibody derived tag, whole transcriptome, and VDJ libraries were generated for all samples.


title: HTR2B Enhances the Phagocytosis of Brain Macrophages and Alleviates Brain Injury after Stroke

first: Yueman

address: 160 Pujian Rd

institute: Department of Anesthesiology,  Renji Hospital, School of Medicine Shanghai Jiao Tong University, China

summary: This study employs single-cell RNA sequencing to investigate the dynamic changes in monocytic-macrophage populations in the brain following ischemic stroke. We analyzed brain tissues from mice subjected to middle cerebral artery occlusion (MCAO) for 3 days. Additionally, we compared the macrophage transcriptomes between Htr2bfl/fl and Lyz2creHtr2b mice to elucidate the impact of HTR2B deficiency on macrophage responses 3d-post-stroke. Our findings provide novel insights into the role of HTR2B in regulating macrophage behavior and its potential implications in stroke pathogenesis and recovery.

overall_design: Brain tissues were collected from mice subjected to 3 days of MCAO. Single-cell suspensions were prepared, and single-cell RNA sequencing was performed to profile the transcriptomic landscape of monocytic-macrophage cells in the post-stroke brain. Furthermore, brain tissues from Htr2bfl/fl and Lyz2creHtr2b  mice were processed similarly to investigate the effects of HTR2B knockout on macrophage gene expression and cellular states. The study design enables the identification of HTR2B-dependent regulatory mechanisms in macrophages during ischemic stroke.

first: Peiying

last: Li


title: Single-embryo and single-blastomere RNA-seq analysis of 2-cell and 4-cell mouse embryos

city: Xuhui, Shanghai

first: Jie

state: Shanghai

address: 320 Yueyang Road, Shanghai

institute: Center for Excellence in Brain Science and Intelligence Technology (Institute of Neuroscience), Chinese Academy of Sciences

summary: Understanding how the first cell fate decisions arise in the mammalian embryo remains a central question in developmental biology. While lineage segregation becomes morphologically apparent at the 16-cell stage, increasing evidence suggests that molecular asymmetries emerge much earlier. Here, we systematically profile the transcriptome of  whole embryo and individual blastomere of mouse embryos at 2-cell and 4-cell stage using SMART-Seq2.

overall_design: We conducted RNA sequencing of intact and separated blastomeres of mouse embryos at 2-cell and 4-cell stage.

first: Zhen

last: Liu

first: Wencheng

last: Zhu

first: Shiyu

last: Sun

first: Qingtong

last: Tan

first: Zihong

last: Wang

first: Hongyu

last: Chen


title: Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma [BiSulfite-seq]

first: Aram

last: Modrek

type: Methylation profiling by high throughput sequencing

overall_design: DNA methylation profiling was performed in glioblastoma stem-like cells treated with doxycycline-inducible multi-target gRNAs (mtg142 or mtg483) to introduce widespread DSBs. Samples were collected at 3 hours and 2 weeks post-induction. Vector control cells (wtCas9 expressed with no guide RNA) were also included. Each condition was run in biological duplicate.

first: Keerthivasan

last: Chandradoss

first: Catherine

last: Do

first: Ravesanker

last: Ezhilarasan

first: Theodore

last: Sakellaropoulos

first: Jerome

first: Yingwen


title: Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma [HiC]

overall_design: RNA-seq was performed in glioblastoma stem-like cells treated with doxycycline-inducible multi-target gRNAs (mtg142 or mtg483) to introduce widespread DSBs. Samples were collected at 3 hours and 2 weeks post-induction. Vector control cells (wtCas9 expressed with no guide RNA) were also included. Each condition was run in biological duplicate.

last: Karp

last: Ding

first: Ze-Yan

last: Zhang

first: Melanie

last: Graciani

first: Giulia

last: Cova

first: Jennifer

first: Erik

first: Jane


title: Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma [isBLISS]

overall_design: isBLISS was performed in glioblastoma stem-like cells treated with doxycycline-inducible multi-target gRNAs (mtg142 or mtg483) to introduce widespread DSBs. Samples were collected at 3 hours. Vector control cells (wtCas9 expressed with no guide RNA) were also included. Each condition was run in biological duplicate.

last: Phillips-Cremins

last: Sulman

last: Skok


title: Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: H3K27ac ChIP-seq was performed in glioblastoma stem-like cells treated with doxycycline-inducible multi-target gRNAs (mtg142 or mtg483) to introduce widespread DSBs. Samples were collected at 3 hours and 2 weeks post-induction. Vector control cells (wtCas9 expressed with no guide RNA) were also included. Each condition was run in biological duplicate.


title: Brg1 defect causes aberrent nucleosome landscape and affects totipotency & pluripotency transcriptional factors binding during embryogenesis [RNA-seq]

first: Xinyu

address: Siping Road 1239

institute: Tongji University

summary: Mammalian embryogenesis involves intricate epigenetic reprogramming and chromatin remodeling. In this study, we investigated the role of Brg1, a catalytic ATPase subunit of the SWI/SNF complex, in early embryonic development and mouse embryonic stem cell (mESC) pluripotency. By generating Smarca4 flox/flox Gdf9-Cre female mice to knockout Brg1 in MII oocytes and using CRISPR-Cas9 to knockout Brg1 in mESCs, we found that Brg1 deficiency led to multiple defects. In mouse embryos, maternal knockout of Brg1 caused reduced blastocyst formation, delayed development, elevated nucleosome occupancy at gene promoters, and dysregulation of zygotic genome activation (ZGA) genes, potentially due to disrupted binding of totipotency-related transcription factors (TFs). In mESCs, Brg1 knockout resulted in abnormal clone morphology, decreased pluripotency marker expression, and reduced cell proliferation. Brg1 affected pluripotency mainly by influencing the binding of pluripotency-related TFs such as Oct4 through enhancer accessibility. We identified those TFs as totipotency/pluripotency Brg1-dependent TFs. Overall, this study demonstrates the crucial role of Brg1 in ZGA and mESC identity maintenance in affecting specific TF binding on proximal and distal regulatory elements.

overall_design: RNA-seq, ULI-MNase-seq and ATAC-seq of mouse embryo and ESC.To get MII oocytes for ICSI, B6D2F1 or Smarca4flox/flox Gdf9 Cre C57BL/6 female mice (8–12-weeks old) were superovulated by injection with 7 IU each of pregnant mare serum gonadotropin (PMSG), followed by injection of 5 IU of human chorionic gonadotropin (hCG) (San-Sheng Pharmaceutical) 48 h later. Brg1 knockout R1 ES cell lines are generated by CRISPR-Cas9 technology targeting the exon 4 & 5 of Smarca4.

first: Qi

last: Shi

first: Chong

last: Li

first: Shaorong

last: Gao

first: Xiaoyu

last: Liu


title: Oscillatory shear stress induced extracellular vesicles mediate valvular endothelial-interstitial cell crosstalk exacerbating aortic valve calcification

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

summary: Calcific aortic valve disease (CAVD) involves pathological crosstalk between human valvular endothelial cells (hVECs) and interstitial cells (hVICs), yet the role of this communication in pathogenesis remains poorly defined. Here, we identify a novel extracellular vesicle-derived circRNA, CircILRUN, originating from hVECs and demonstrate its critical function in promoting hVIC osteogenesis and CAVD progression in vitro and in vivo. CircILRUN expression is significantly elevated in extracellular vesicles from hVECs under oscillatory shear stress. Its deletion markedly attenuates aortic valve calcification (AVC) in mice, reducing valve thickness, calcium deposition, and improving echocardiographic parameters, findings corroborated in osteogenic medium-induced hVICs. Through unbiased protein-RNA screening and biochemical validation, we identify N-acetyltransferase 10 (NAT10) as a key target of CircILRUN. Nat10 depletion also effectively reduces AVC in vivo. Mechanistically, CircILRUN acts as a molecular scaffold facilitating the interaction between NAT10 and the deubiquitinase USP11, thereby stabilizing NAT10 protein. Integrated transcriptomic and ac4C epitranscriptomic profiling reveals that CircILRUN promotes NAT10-mediated acetylation of CD36 mRNA, stabilizing CD36 and accelerating AVC progression. Collectively, our findings establish an extracellular vesicle-mediated circILRUN–NAT10–CD36 axis driving CAVD pathogenesis and identify both circILRUN and NAT10 as promising therapeutic targets

overall_design: CircRNAs expression in human valvular endothelial cell-derived exosomes (hVECs-Exos) were measured after exposure to oscillatory shear stress (OSS) and laminar shear stress (LSS), respectively. Three independent experiments were performed at each group (OSS and LSS) using different donors for each experiment.

first: Tingwen

last: Zhou


title: Brain Mecp2 Genetic Dosage and Gene Therapy Shape Multi-omics Signatures and Biomarkers in Rett Syndrome [2]

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

summary: Rett syndrome is a neurodevelopmental disorder, caused by mutations in the MECP2 gene. Like other genetic disorders of neurodevelopment, it lacks molecular biomarkers to assess disease and therapy outcomes. We present a strategy to identify mechanisms of disease and biomarkers, which is reliant on a library of brain proteins defined by their responsiveness to Mecp2 gene dosage, and correlated with molecular, and clinical outcomes after AAV9-mediated MECP2 gene therapy into Mecp2-KO mouse brain. Gene rescue restored MECP2 brain expression, corrected clinical phenotypes in Mecp2-KO mice, and reverted transcriptome and proteome phenotypes. We identified 327 shared proteins among a total of 1852 proteins in cortex and hippocampus responsive to Mecp2/MECP2. Of these shared proteins, 119 have congruently expressed transcripts. Both the Mecp2-responsive proteome or the congruent 119 transcript-proteins pairs were enriched in synaptic and metabolic pathways including mitochondria carbon and NAD+ metabolism. We used this genetically validated and therapy-responsive library of proteins to inform the selection of putative biomarkers in cerebrospinal fluid of Rett patients. We analyzed cerebrospinal fluid composition of neurotypical and Rett subjects using an ultrasensitive nucleic acid based multiplexed ELISA. We identified 28 proteins altered in Rett patients, 9 of which overlapped with proteins sensitive to gene therapy and dosage. Multivariate regression linked several candidate biomarkers to Mecp2/MECP2 protein abundance and phenotypic improvements in mice. Our paradigm provides a rigorous molecular systems-level framework integrating genetics, preclinical MECP2 gene therapy, and rodent clinical metrics to define robust, cross-species biomarkers and mechanisms in Rett syndrome and other neurodevelopmental disorders.

overall_design: RNA-seq profiling of small RNAs in cortex and hippocampus in response to AAV9-mediated MECP2 gene therapy in Mecp2-KO mice. Genotypes consisted of  Mecp2-WT animals and Mecp2-KO animals. Injection conditions consisted of AAV9-rrt271 therapy (1e11 and 3e11) and also Mecp2 overexpression driven by a Tau promoter.

first: Victor

last: Faundez

first: Stephanie

last: Zlatic


title: Transcriptome analysis of Mac3a3b in Arabidopsis thaliana group to regulate high temperature stress response

city: 昆明

first: 贝贝

last: 邓

address: 云南大学呈贡校区

institute: 云南大学

summary: RNA-seq transcriptome analysis was used to detect the differential expression of heat stress-related genes of WT and mutant mac3a3b after the end of heat stress

overall_design: RNA-seq transcriptome analysis was used to detect the differential expression of genes related to heat stress in WT and mutant mac3a3b at 0 hours and 3 days after the end of heat stress


title: Expanding the genetic code to generate human brain organoids with vasculature and microglia

city: Suzhou

first: Hu

last: Du

state: Jiangsu

address: Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, China.

institute: university of science and technology of china

summary: Genetic code expansion technology (GCE-T) has been applied to precisely manipulate protein structure and function in bacteria, virus, yeast, mammalian cells, and even in animals. It has not been fully explored in 3D tissues or organoids. Here, we presented a new strategy leveraging GCE-T to generate vascularized human cerebral organoids (vhCOs) containing resident microglia. By reassigning a premature termination codon in ETV2, a targeted noncanonical amino acid was incorporated to drive endothelial differentiation in hPSCs at the translational level. Strikingly, the generated vhCOs exhibited coordinated differentiation of functional vasculature, blood brain barrier feature and microglia. single-nucleus transcriptomic analysis revealed multiple brain regional distribution, marked neurogenesis, and neuro-vascular-immune network in vhCOs, resembling human fetal brain. Upon Zika virus infection, vhCOs exhibited impaired vasculature, disrupted neurogenesis and microglial development. This strategy offers a unique platform for producing high-fidelity cerebral organoids integrated with vasculature and immune components, opening a new avenue to advance organoid research and applications.

overall_design: snRNA-seq was performed at development to Day90, where hCO represents human cerebral organoids and vhCO represents vascularized human cerebral organoids, vhCO+Z.V. represents vhCO after Zika virus infection.

first: Haishuang

last: Lin

first: Yaqing

last: Wang

first: Yuxin

last: Qin

first: Jiayue

first: Peng

first: Pengwei

last: Deng

first: Qian

first: Lin

last: Wei

first: Jianhua


title: Brain Mecp2 Genetic Dosage and Gene Therapy Shape Multi-omics Signatures and Biomarkers in Rett Syndrome [1]

overall_design: RNA-seq profiling of cortex and hippocampus in response to AAV9-mediated MECP2 gene therapy in Mecp2-KO mice. Genotypes consisted of  Mecp2-WT animals and Mecp2-KO animals. Injection conditions consisted of AAV9-rrt271 therapy (1e11 and 3e11) and also Mecp2 overexpression driven by a Tau promoter.


title: Migratory astrocyte subset drives CNS regeneration after astrocyte loss

city: Zurich

first: Marina

last: Herwerth

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

summary: Mature astrocytes become activated upon central nervous system (CNS) tissue damage and contribute to glial border formation. Proliferation and migration of reactive astrocytes at the border of destructive CNS lesions are considered very limited. However, the regenerative behavior of individual astrocytes following selective astroglial loss, as seen in astrocytopathies such as neuromyelitis optica spectrum disorder, remains unexplored. Here, we performed longitudinal in vivo imaging and temporospatial transcriptional profiling of cortical astrocytes after focal aquaporin-4 antibody-mediated astrocyte ablation in mice. Our findings define the molecular and cellular principles of astrocyte plasticity upon focal brain injury. A migratory subset of reactive astrocytes is fundamental for the restoration of astrocytic networks in the adult mammalian brain. Promoting this regenerative phenotype bears therapeutic potential for neurological conditions involving glial dysfunction.

overall_design: Somatosensory cortices were collected from Aldh1l1-GFP transgenic mice, each predominantly harboring two NMO lesions. Tissue samples were harvested at three distinct time points following lesion induction: 3 days post-injection (3 dpi, n = 4), 5 days post-injection (5 dpi, n = 2), and 17 days post-injection (17 dpi, n = 2). Spatial transcriptomics was performed on all collected samples to analyze gene expression patterns in the lesioned tissue.

first: Matthias

middle: T

last: Wyss

first: Nicola

middle: B

last: Schmid

first: Anna

last: Lasne

first: Jacqueline

last: Condrau

first: Luca

last: Ravotto

first: José María

last: Mateos Melero

first: Andres

last: Kaech

first: Gustav

last: Bredell

first: Carolina

last: Thomas

first: Kim

last: Rachel

first: Petra

last: Kukanja

first: Vladyslav

middle: L

last: Korobeynyk

first: Christine

last: Stadelmann

first: Thomas

last: Misgeld

first: Jeffrey

last: Bennett

first: Sebastian

last: Jessberger

first: Aiman

last: Saab

first: Shane

last: Liddelow

first: Bruno

last: Weber


title: NSUN2 rewires metabolism to support protein secretion and enhance bioproduction output

city: Nashville

first: John

last: Karijolich

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: The production of bioactive materials such as viral vectors and neutralizing antibodies for research and clinical applications has realized an exponential increase in demand. Stable cell lines, such as HEK-293FT and CHO cells, that support virus-based packaging of genetic material and are readily modified to support protein and antibody production. NSUN2 is an RNA methyltransferase that modifies tRNA and mRNA substrates altering their stability, localization, and function. While NSUN2 has been well-characterized in its role of regulating innate immune activity in response to active infection promoting the virus life cycle, its potential role as a tool in bioproduction has not been explored. In the current study, we have identified NSUN2 as a novel target to aid bioproduction processes. We demonstrated that CHO cells upregulate NSUN2 in high-performing clones and that overexpressing NSUN2 significantly enhanced pembrolizumab production. Further, overexpressing NSUN2 in HEK293FT cells transcriptomically enriched for genes in the unfolded protein response and protein secretion pathways. Functionally, we demonstrated that cells overexpressing NSUN2 generated significantly higher viral titers, improving transduction efficiency and lowering the input requirement. Mechanistically, we observed that NSUN2 activity reprograms metabolism enabling fuel flexibility, resistance to nutrient depletion, and UDP-GlcNAc production. Proteomic analysis of purified viral particles showed a significant enrichment in N-Glycans on particles produced with NSUN2-overexpressing cells. Considering the widespread use of these systems in basic research and production of FDA-approved therapies, overexpressing NSUN2 offers an approach that can optimize producer cells to improve yields, making these tools and therapies more accessible.

overall_design: HEK293FT cells were transduced to stably express an empty vector control or overexpress NSUN2. Following antibiotic selection, the EV and NSUN2 cells were plated and cultured in standard growth media (DMEM, 10% FBS, 1% L-Glutamine, 1% Pen/Strep) for 48 hours. RNA was extracted from biological triplicates of each condition and  a quality control analysis was performed. The samples were then subjected to mRNA enrichment and cDNA library preparation utilizing the stranded mRNA (polyA-selected) library preparation kit. Sequencing was performed at Paired-End 150 bp on the Illumina NovaSeq X Plus targeting an average of 30M reads per sample.

first: Zachary

last: Bacigalupa

first: Xiang

last: Ye

first: Erin

last: Jennings

first: Kimryn

last: Rathmell


title: Pyruvate, lactate, and hypoxia reprogram murine CD8 T cell chromatin landscape

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary: To investigate how metabolic and environmental cues shape gene regulation and chromatin accessibility in T cells, CD8 T cells were isolated from mice, activated in vitro, and exposed to lactate, pyruvate, sodium chloride, or hypoxic conditions. On day 3 post-activation, cells were harvested for RNA-seq and ATAC-seq analyses. This integrative approach enabled the identification of transcriptional and epigenetic changes in response to distinct metabolic and oxygen availability conditions

overall_design: CD8 T cells were isolated from mouse spleens and lymph nodes, activated in vitro for 3 days, and treated with lactate, sodium pyruvate, sodium chloride, or oxyrase from day 2 to day 3 post-activation. Cells were then collected for both RNA-seq and ATAC-seq analyses to assess transcriptional and chromatin accessibility changes in response to metabolic treatments.

first: Chang

last: Chih-Hao

first: Wei

last: Jian


title: Efficient LAMA1 gene activation by epigenome editing as a therapeutic 2 approach for LAMA2-CMD

city: Waltham

first: Keith

last: Connolly

state: MA

address: 43 Foundry Ave, Dock #3

institute: Modalis Therapeutics - Cambridge, MA

summary: Epigenome editing technology holds great promise for treating diverse genetic disorders. Here we demonstrate epigenetic activation of the LAMA1 gene for the treatment of LAMA2-CMD, a severe congenital muscular dystrophy (CMD) caused by biallelic mutations in the LAMA2 gene. LAMA1 is a sister homologue that is known to compensate for the function of LAMA2. However, supplementing LAMA1 or LAMA2 gene via viral platform is not feasible due to the large size of their coding sequences. Through a single administration of our Adeno-associated virus (AAV) vector encoding all the necessary elements for epigenetic activation, we observed significant LAMA1 gene upregulation and phenotype improvements in mouse disease models. The muscle-tropic AAV capsid exhibited desired vector biodistribution and promising pharmacodynamics with good safety profiles in 2-year-old juvenile non-human primates (NHPs). Moreover, administration to 8-month-old infant NHPs demonstrated superior pharmacodynamics compared to juveniles, even at half the dose. Our approach holds broad applicability for a range of loss-of-function genetic disorders and could offer a therapeutic breakthrough where active epigenome offers clinical benefit.

overall_design: Adult (7-12 week old) C57BL/6J (Jax#000664) mice were systemically injected with AAV9 packaged GNDM constructs expressing either treatment (m31) or control (non-targeting) guide RNA. Gastrocnemius muscle tissues were isolated 11 weeks post administration and total RNA was isolated.


title: Ginsenoside RK1 Promotes Hepatic Stellate Cell Glycolysis-Mediated Ferroptosis by Activating the HK2/ACSL4/LPCAT3/ALOX5 Signaling Pathway

city: wenzhou

first: Ziqiang

last: Xia

address: First Affiliated Hospital of Wenzhou Medical University

summary: Liver fibrosis (LF) is a pathological condition that if not controlled can progress into liver sclerosis and malignant tumors. Ferroptosis has been comprehensively studied and found to improve LF by exacerbating hepatic cell ferroptosis. Ginsenoside RK1 (GRK1) is an essential component of ginseng with anti-fibrotic effects. However, the anti-LF mechanism of GRK1 remains elusive. The impact of GRK1 on LF was evaluated via RNA-sequence analysis of GRK1-treated hepatic stellate cells (HSC). Furthermore, cellular thermal shift assay, drug affinity responsive target stability, and molecular docking analyses were carried out to verify the interaction between GRK1 and HK2. The fibrosis indicators and histopathology assessment revealed that GRK1 substantially suppressed CCl4-induced LF in mice. Moreover, GRK1 markedly improved MDA, lipid ROS, and liver Fe2+ in CCl4-stimulated mice. This study revealed that GRK1 targets HK2 in HSC-T6 cells to stimulate the ACSL4/LPCAT3/ALOX5 pathway, thereby inducing HSC ferroptosis and alleviating hepatic fibrosis.

overall_design: Perform RNA sequencing analysis on untreated HSC-T6 cells and HSC-T6 cells treated with GRK1.

first: Fujun

last: Yu

first: Yixiao

last: Wang

first: Qian

last: Zhao

first: Jun

last: Xu

first: Min

last: Deng


title: Activation of M3 muscarinic ameliorates experimental autoimmune encephalomyelitis by restoring microglial quiescence

first: Kaichun

address: Yishan Road No.600

institute: Shanghai Jiao Tong University

summary: The cholinergic system serves as a crucial signaling mediator in neuroimmune regulation. Our previous study has shown that muscarinic acetylcholine receptors (mAChRs) contributed to microglial inflammatory response. However, its role in autoimmune neurodegeneration, such as multiple sclerosis (MS) remains unclear. In this study, we investigated the role of microglial mAChRs in MS pathology. For downstream analysis, we employed high-throughput transcriptomic sequencing in lipopolysaccharide (LPS)-stimulated BV2 microglia cells treated with pilocarpine (Pilo), a agonist of mAChRs. LPS+Pilo-treated cells displayed a transcriptional profile with similarity to that of normal cells. Alterations in cell chemotaxis and immune responses, with the activation of multiple GPCR downstream signaling pathways and TNF signaling pathways are also seen in LPS+Pilo-treated cells compared with LPS-stimulated cells, with significantly different expression of Msr1, Cybb, Ccl12, and Nr4a1. The results revealed that activation of mAChRs in microglia significantly upregulates Nr4a1 expression, which subsequently suppresses NF-κB-mediated inflammatory signaling.

overall_design: To explore the mechansims underlying Pilo-dependent modulation of microglia inflammatory response, we performed RNA-seq using BV2 microglia cells stimulated by LPS in the presence of absence of Pilo treatment (n=3, respectively).

first: Jianrong


title: Targeting PRMT5- FOXM1 axis inhibits pyrimidine metabolism to impede the progression of oral leukoplakia and squamous cell carcinoma

city: Guangzhou, Guangdong

first: Siqi

last: Jiang

address: No.56 Lingyuanxi Road

institute: Sun Yat-sen University

summary: Oral leukoplakia (OLK), as one of oral latent malignant diseases (OPMDs), is easily transformed into oral squamous cell carcinoma (OSCC). A critical hallmark of cancer development is the up-regulation of nucleotide metabolism, which fulfills the demands of unchecked cellular proliferation. Protein arginine methyltransferase 5 (PRMT5) has been implicated in the pathogenesis of various diseases, including OSCC. However, the specific regulatory role of PRMT5 in nucleotide metabolism, particularly pyrimidine metabolism, remains inadequately understood. Here, we observed that the targeted inhibition of PRMT5 markedly reduced the proliferation, migration, and invasion of dysplastic oral keratinocyte (DOK) cells. RNA-seq and metabolomics results showed that targeting PRMT5 significantly inhibited pyrimidine metabolism. The mechanism observed in both DOK and OSCC cell lines is that PRMT5 promotes the activation of the transcription factor FOXM1 through H3R2me2s-K4me3, and collaborates with FOXM1 to enhance the expression of TK1, RRM2, TYMS, and CAD, thereby activating the pyrimidine metabolic pathway. Animal experiments corroborate that the inhibition of PRMT5 and FOXM1 suppresses the proliferation of OSCC tumors. Furthermore, supplementing exogenous dNTPs can partially mitigate the suppression of proliferation, invasion, and migration caused by targeting PRMT5. Consequently, our study suggests that PRMT5 augments pyrimidine metabolism through the epigenetic activation of FOXM1, thereby promoting the progression of OLK and OSCC. Targeted interventions against PRMT5 or FOXM1 are considered promising therapeutic strategies for the treatment of OLK and OSCC.

overall_design: This study took DOK cells as the main object of study, supplemented by OSCC cell line verification, to explore the function of PRMT5 in the progression of OPMDs, aiming to provide a theoretical basis for the treatment of OPMDs and the early clinical intervention of OSCC.

first: Zhaona

last: Fan


title: Translational biomarkers of hypoxic brain injury uncovered in CSF secreting human choroid plexus organoids

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

summary: The choroid plexus-cerebrospinal fluid (ChP-CSF) barrier regulates a microenvironment supporting neural stem cell growth, strongly affected by hypoxia through ChP function. From human induced pluripotent stem cells (hiPSCs), here we established and validated in vitro ChP organoid secreting CSF-like fluid (iCSF) and exposed them to low oxygen atmosphere for 24h. Transcriptomic indicated major data on morphological and functional alterations in the ChP cells and shotgun proteomics revealed significant changes in proteins involved in energy metabolism and mitochondrial function. We found that H2AZ and ITM2B, involved in neurogenesis and neurite growth, were the key proteins downregulated in hypoxic iCSF and ChP organoids, respectively. Positive correlation analysis between hypoxia-induced mRNA expression of the neuronal progenitor biomarkers SOX2 and PAX6. Mature neuron MAP2 and H2AZ also confirmed impairment of neurogenesis. The results from this study suggest that ChP-CSF barrier opens new opportunities to characterize hypoxic brain pathophysiology and discover novel biomarkers.

overall_design:
By comparing the metabolic pathways of GMB7-1 organoids in healthy and hypoxia-treated conditions.
RNA were isolated  from GMB7-1 organoids in healthy and hypoxia-treated conditions. Three sample from each group were used. For gene expression analysis, the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit was utilized, enabling the simultaneous measurement of over 20,000 human RefSeq genes.
The identified metabolic pathways of GMB7-1 organoids in healthy and hypoxia-treated conditions were identified and compared.

first: Romane

last: Gaston-Breton

first: Amal

last: Bouzid

first: Ekaterina

last: Antipushina

first: Alaa

last: Altaie

first: Jean

last: Armengaud

first: Narciso

last: Costa

first: Balazs

last: Sarkadi

first: Agota

last: Apati

first: Rania

last: Harati

first: Maxim

last: Sharaev

first: Clémence

last: Disdier

first: Aloïse

last: Mabondzo


title: A molecular atlas of cellular vulnerability and resilience in the parkinsonian striatum. [snRNA_seq]

city: Stockholm

first: Konstantinos

last: Meletis

address: Solnavagen 9

country: Sweden

institute: Karolinska Institutet

summary: The progressive degeneration of dopaminergic projections to the striatum is a key disease mechanism in Parkinson’s disease (PD). To define the cellular landscape in the parkinsonian striatum, we mapped the cellular transcriptome in early and progressive PD mouse models and in human PD stages. Our analyses revealed significant transcriptomic changes across both neuronal and glial populations, with astrocytes and oligodendrocytes exhibiting distinct disease-associated gene expression profiles. Notably, progressive dopamine depletion uncovered differential neuronal vulnerability, identifying eccentric type striatal projection neurons (SPNs) and Chst9-expressing direct pathway SPNs as the most resilient subtypes in mice and humans. This cross-species molecular atlas of the cell-state dynamics in the parkinsonian striatum uncovers the selectively vulnerable and resilient cell types that can inspire new treatment strategies.

overall_design: This dataset includes both single-nucleus RNA sequencing (snRNA-seq) and Spatial Transcriptomics (ST) data derived from mouse models of Parkinson’s disease (PD), designed to capture both cell-type-specific and spatial gene expression changes across different stages and mechanisms of PD-like pathology.  1. Single-nucleus RNA sequencing (snRNA-seq) snRNA-seq was performed on mouse striatal tissue from two distinct PD models:  Mild Neurotoxin Model (6-OHDA): Adult wild-type mice received unilateral injections of 6-hydroxydopamine (6-OHDA) at a low dose (0.6 µg/µL) into the medial forebrain bundle (MFB), selectively damaging nigrostriatal dopaminergic neurons and inducing mild Parkinsonian pathology. Untreated wild-type mice served as controls.  Progressive Genetic Model (MitoPark): The MitoPark model (Slc6a3-cre; Tfam^flx/flx) induces mitochondrial dysfunction specifically in dopaminergic neurons, leading to progressive neurodegeneration. Samples were collected at two timepoints:  10–11 weeks of age: Early stage, pre-symptomatic or mildly affected.  15–18 weeks of age: Late stage, with clear motor deficits and advanced degeneration.  This snRNA-seq dataset enables in-depth analysis of transcriptomic alterations across distinct PD etiologies and stages.

first: Marta

last: Graziano

first: Ioannis

last: Mantas

first: Yuvarani

last: Masaprapu

first: Solène

last: Frapard

first: Raquel

last: Garza

first: Anita

last: Adami

first: Shaline

last: Fazal

first: Annelies

last: Quaegebeur

first: Roger

last: Barker

first: Johan

last: Jakobsson

first: Stefania

last: Giacomello


title: Innate immunocompetent iNSpheroids:A hiPSC-derived 3D model to study the central nervous system captures an early CNS response to rAAV

city: Oeiras

first: Catarina

middle: Monteiro

last: Gomes

state: Lisboa

address: Av. República, Qta. do Marquês

country: Portugal

institute: iBET

summary: Gene therapies using adeno-associated viruses (AAVs) for central nervous system (CNS) disorders face challenges due to host immune responses not represented in classical preclinical models. Here, we present a human-induced pluripotent stem cell (hiPSC)-derived innate immunocompetent 3D CNS model that recapitulates neuroinflammatory hallmarks, serving as a platform for preclinical gene therapy development. Utilizing various scales of stirred-tank bioreactor systems, we produced iNSpheroids composed of neurons, astrocytes, and oligodendrocytes, alongside microglial cells (iMGL) to mimic the neuro-immune axis. These systems enabled large-scale production of iNSpheroids and subsequent miniaturization for co-culture experiments and screening of inflammatory stimuli, while maintaining a highly controlled environment. The iMGL-iNSpheroids demonstrated active neuron-microglia crosstalk and exhibited distinct inflammatory responses to a series of neuroinflammatory factors. iMGL-iNSpheroids mounted a mild and transient response to rAAV9, mediated by the activation of inflammatory pathways (e.g., TNF-via NF-κB activation) in glial cell populations.. This model offers a valuable tool to dissect neuroinflammatory mechanisms, accelerating gene therapy development.

sample_organism:
Homo sapiens
Dependoparvovirus

platform_organism:
Homo sapiens
Dependoparvovirus

overall_design: iNSpheroid and iMGL were co-culture and subsquently transduced with rAAV9. Samples before and after transduction were collected and processed for snRNA-seq.

first: Gabriela

last: Silva

first: Mafalda

last: Aleixo

first: Daniel

last: Simão

first: Stephan

last: Holtkamp

first: Diana

middle: D

last: Lobo

first: Pradeep

last: Harish

first: Lekh

last: Dahal

first: Rui

middle: J

last: Nobre

first: Luís

last: Almeida

first: Mark

last: Trautwein

first: Paula

last: Alves

last: Brito


title: PKP2 orchestrates OXPHOS expression in cardiomyocytes via a PGC-1a dependent mechanism

city: Utrecht

first: Su Ji

last: Han

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We performed single cell RNA sequencing (scRNAseq) on cardiomyocytes generated from human induced pluripotent stem cells (hiPSCs) derived from a patient with arrhythmogenic cardiomyopathy harboring a PKP2 variant and its isogenic control. The goal of this experiment was to compare the cellular transcirptomes of PKP2 mutant and control cells and look at PKP2 correlated genes.

overall_design: scRNAseq of PKP2 mutant and reverted hiPSC-derived cardiomyocytes 1 month after the start of the differentiation


title: A molecular atlas of cellular vulnerability and resilience in the parkinsonian striatum.

first: Konstantinos

last: Meletis

overall_design: This dataset includes Spatial Transcriptomics (ST) data derived from mouse models of Parkinson’s disease (PD), designed to capture both cell-type-specific and spatial gene expression changes across different stages and mechanisms of PD-like pathology. The Mild Neurotoxin Model (6-OHDA): Adult wild-type mice received unilateral injections of 6-hydroxydopamine (6-OHDA) at a low dose (0.6 µg/µL) into the medial forebrain bundle (MFB), selectively damaging nigrostriatal dopaminergic neurons and inducing mild Parkinsonian pathology. Untreated wild-type mice served as controls. Spatial gene expression profiling was conducted on the striata of mice from the mild 6-OHDA model to preserve anatomical context. Tissue sections were collected from six adult mice — three 6-OHDA-treated and three untreated controls. For each animal, four rostro-caudal levels of the striatum were analyzed, capturing regional heterogeneity in response to dopaminergic denervation. The 10X Genomics Visium platform was used to generate spatially resolved transcriptomic maps. This ST dataset allows for the visualization and quantification of spatial patterns in gene expression following mild dopaminergic injury, complementing the cell-type-specific insights gained from the snRNA-seq data.

first: Marta

last: Graziano

first: Ioannis

last: Mantas

first: Yuvarani

last: Masaprapu

first: Solène

last: Frapard

first: Raquel

last: Garza

first: Anita

last: Adami

first: Shaline

last: Fazal

first: Annelies

last: Quaegebeur

last: Barker


title: Metabolic surgery reduces CRC disease progression mediated by circulating bile acid diversion

city: Freiburg

first: Rebecca

last: Kesselring

address: Breisacher Straße 115

department: General and Visceral Surgery

country: Germany

institute: Medical Center University Freiburg

summary: Tumor organoids of a patient with microsatellite stable (MSS) colorectal cancer were co-incubated with primary bile acids (CA, GCA, TCA; 100 µM) to analyze the effect of bile acids on tumorigenesis of colorectal cancer.

overall_design: RNA-seq profiling of human tumor organoids from primary tumor of a MSS colorectal carcinoma co-incubated with primary bile acids (CA, TCA, GCA; 100 µM) for 24 hours

first: Bernhard

last: Mauerer

first: Christopher

last: Berlin


title: Youth-associated protein TIMP2 regulates microglial state and function in healthy and aged mice [Bulk RNA-seq]

city: New York

first: Joseph

middle: Michael

last: Castellano

state: NY

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: There is little understanding of how aging serves as the strongest risk factor for several neurodegenerative diseases. Microglia, undergo age-related maladaptive changes, including increased inflammation, impaired debris clearance, and cellular senescence, yet specific mediators that regulate these processes remain unclear. The aged brain is rejuvenated by youth-associated plasma factors, including tissue inhibitor of metalloproteinases 2 (TIMP2), which we have shown acts on the extracellular matrix (ECM) to regulate synaptic plasticity. Given emerging roles for microglia in these processes, we examined the impact of TIMP2 on microglial function. We show that TIMP2 deletion in mice exacerbates microglial phenotypes associated with aging, including transcriptomic changes in cell activation, changes in lysosomal-associated markers and phagocytosis, and elevated levels of stress and inflammatory proteins in the brain extracellular space measured by in vivo microdialysis. Deleting specific cellular pools of TIMP2 in vivo increases microglial CD68 and alters myelin phagocytosis. Treating aged mice with TIMP2 reverses several phenotypes observed in our deletion models, resulting in decreased microglial activation, reduced proportions of proinflammatory microglia, and enhanced phagocytosis of physiological substrates. Our results identify TIMP2 as a modulator of age-associated microglia dysfunction. Harnessing its activity may mitigate detrimental effects of age-associated insults on microglia function.

overall_design: Primary microglia from TIMP2 WT and TIMP2 KO mice (N = 7 samples per genotype, each sample represents a a pool of 5 pups (P6-P7), sex-matched) were analyzed using bulk RNA-seq.

first: Brittany

last: Hemmer

first: Ana Catarina

last: Ferreira

first: Sarah

last: Philippi

first: Samuele

middle: F

last: Petridis

first: Annie

last: Phan


title: Youth-associated protein TIMP2 regulates microglial state and function in healthy and aged mice [snRNA-seq]

overall_design: Hippocampal were dissected  from 20-month-old wild-type male mice following systemic treatment with TIMP2 or vehicle and nuclei were isolated and processed using single nuclei RNA sequencing.


title: Reduced inflammatory and Th1 transcriptional profiles in adult and geriatric cotton rats infected with respiratory syncytial virus

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

summary: Human respiratory syncytial virus (RSV) is a leading cause of severe respiratory disease in elderly populations. RSV clearance is delayed in individuals over 65 years of age, a finding that is recapitulated in the geriatric cotton rat model. Altered inflammatory responses in elderly populations have been implicated with impaired clearance of several pathogens but remain poorly described for RSV. We performed RNA sequencing (RNA-seq) and pathway analysis on lung tissue of RSV-infected adult and geriatric cotton rats to characterize differential host immune responses between these age groups. No differences in inflammatory gene expression were observed between uninfected adult and geriatric cotton rats. At day 1 post-infection, adult cotton rats expressed higher levels of several cytokines and transcription factors associated with acute inflammation and initiation of a Th1 response, including IFN-β, IL12, and Tbet, compared to geriatric cotton rats. By day 4 post-infection, adult cotton rats additionally expressed higher levels of effector molecules associated with Th1 responses, including IFN-γ. Pathway analysis showed significantly increased activation of several pro-inflammatory pathways in adults, including the Th1 pathway, macrophage classical (M1) activation, and pathogen-induced cytokine signaling. To evaluate lymphocyte Th1/Th2 polarization resulting from RSV infection in both age groups, we stimulated splenocytes with RSV peptides at day 28 post-infection and measured IFN-γ and IL-4 production by ELISA. Splenocytes of all adult cotton rats produced detectable IFN-γ and no IL-4, indicating Th1 polarization. Splenocytes of all geriatric cotton rats produced detectable IL-4, indicating Th2 polarization. Collectively, these results indicate that geriatric cotton rats exhibit impaired generation of a Th1 response and a decreased inflammatory response overall to RSV.

overall_design: RNA-seq of whole-lung homogenates from adult and geriatric cotton rats at days 0 (uninfected), 1, and 4 post-RSV infection.

first: Jonathan

last: Miller

first: Cameron

last: Leedale

middle: S

first: Jèssica

last: Garrido

first: Tyler

last: Alioto

first: Lianbo

last: Yu

first: David

last: Symer

first: Stefan

last: Niewiesk


title: Expression profile of cells overexpressing genetic variants encoding XIAP with distinct subcellular localization.

city: Rio de Janeiro

first: Gabriela

last: Nestal de Moraes

state: Rio de Janeiro

address: venida Carlos Chagas Filho, 373, Sala H2-003,  Cidade Universitária

department: Instituto de Bioquímoca Médica Leopoldo de Meis

country: Brazil

institute: Universidade Federal do Rio de Janeiro

summary: Messenger RNA (mRNA) samples from MCF-7 breast cancer cells transfected with the plasmid vectors: pEBB (empty vector), pEBB-HA-XIAPwild type (cytoplasmic XIAP expression), pEBB-HA-XIAPH467A (lack of ubiquitin ligase activity; cytoplasmic XIAP expression), pEBB-HA-XIAPΔRING (deletion of the RING domain; nuclear and cytoplasmic XIAP expression) and XIAPNLS (insertion of a nuclear localization signal; nuclear and cytoplasmic XIAP expression) were amplified, labeled and hybridized to the ClariomTM S Array human (Thermo Scientific, USA). Normalization and analysis of microarray data was performed using the Transcriptome Analysis Console (TAC) software (Affymetrix, USA).

overall_design: We analyzed gene expression from MCF-7 breast cancer cells overespressing empy vector (pEBB) and XIAP genetic variants (XIAPwild type, XIAPH467A, XIAPΔRING and XIAPNLS) using the ClariomTM S Array human (Thermo Scientific, USA). Array data was processed and analyzed using Transcriptome Analysis Console (TAC) software (Affymetrix, USA).

first: Bruna

last: dos Santos Mendonça

first: Renata

last: Binato

first: Eliana

last: Abdelhay


title: Targeting NAT10 to surpress ferroptosis and attenuate skin fibrosis progression

city: Beijing

first: Xuan

last: Ma

address: No.33 Badachu Road,Shijingshan District

institute: Plastic Surgery Hospital,Chinese Academy of Medical Science and Peking Union Medical College

summary:
Abstract
Background: N-acetyltransferase 10 (NAT10) is a unique RNA acetyltransferase responsible for catalyzing N4-acetylcytidine (ac4C) modifications on mRNA, influencing RNA stability and translation. While NAT10 has been implicated in fibrosis of other organs, its role in skin fibrosis and ferroptosis regulation remains poorly understood. This study aimed to investigate the involvement of NAT10 in fibroblast activation and skin fibrotic remodeling via modulation of ferroptosis.
Methods: The expression of NAT10 was assessed in bleomycin-induced fibrotic mouse skin tissues and TGF-β1-stimulated fibroblasts. Functional experiments, including wound healing, transwell migration, and EdU staining, were performed following NAT10 knockdown. The impact of NAT10 on ferroptosis was evaluated by measuring lipid ROS, GSH, and MDA levels, along with key ferroptosis markers such as GPX4, SLC7A11, and TFR1. RNA-seq and bioinformatic analyses identified MAP1LC3A as a downstream target. The effects of NAT10 inhibition were further validated in vivo using Remodelin and Erastin interventions.
Results: NAT10 expression and ac4C RNA modification were upregulated in fibrotic skin tissues and activated fibroblasts. Silencing NAT10 impaired fibroblast proliferation and migration, alleviated fibrosis, and reduced ferroptosis-related oxidative stress both in vitro and in vivo. Mechanistically, NAT10 knockdown decreased MAP1LC3A stability, leading to suppressed ferroptosis. Pharmacological modulation with Erastin partially reversed the antifibrotic effects of NAT10 inhibition, underscoring the involvement of ferroptosis in this process.
Conclusions: Our findings demonstrate that NAT10 contributes to skin fibrosis by promoting ferroptosis through the regulation of MAP1LC3A stability. Targeting NAT10 may offer a promising therapeutic approach for fibrotic skin diseases.
Keywords: Skin Fibrosis, Ferroptosis, NAT10, Fibroblast


title: Spatial mapping of telocytes along the crypt-villus axis reveals their role in intestinal homeostasis

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: We employed a single-cell RNA sequencing approach using the 10X Genomics platform to study the diversity of telocyte populations in the mouse jejunum. Telocytes are a unique mesenchymal cell type expressing the transcription factor Foxl1 and forming a subepithelial network along the entire crypt-villus axis. This study characterizes the gene expression profiles and spatial distribution of telocytes along the crypt-villus axis of the mouse jejunum.

overall_design: Using the Foxl1Cre; Rosa-mTmG reporter mouse model, single GFP+ cells were sorted and subjected to single-cell RNA sequencing on the 10X Genomics platform to characterize the gene expression profiles of Foxl1+ telocyte subpopulations. We mapped these subpopulations along the crypt-villus axis of the jejunum using single-molecule RNA FISH and immunostaining for uniquely expressed landmark genes.

first: Amal

last: Gharbi

first: Noa

last: Corem

first: Sharona

last: Elgavish

last: Plachkes

first: Marco

last: Canella

first: Moriya

last: Shmuel

first: Hadar

last: Horowitz

first: Jianmei

last: Tan

first: Hongqian

last: Chen

first: Bing

last: Su

first: Mahmud

last: Abu-Gazala

first: Noam

last: Shussman

first: Michal

last: Shoshkes-Carmel


title: Early Candida–Oral Tumor Interactions Suggest miRNA-Mediated Regulation of Inflammatory and Tumor-associated processes

city: Szeged

first: Marton

last: Horvath

state: Csongrád

address: Közép fasor 52.

department: Microbiology

country: Hungary

institute: University of Szeged

type: Non-coding RNA profiling by high throughput sequencing

summary: When simultaneously present, oral cancer and oral candidiasis are associated with high mortality. Recently, fungi-driven OSCC has emerged as a recognized phenomenon, that is triggered by Candida and sustained by several pro-tumor mechanisms. This study aimed to deepen our understanding and investigate how these mechanisms are regulated at the early stages of fungi-tumor interactions. Post-transcriptional regulation was examined through the analysis of miRNA (miR) responses in a metastatic cell line. We characterized early tumor responses to two common oral yeasts, C. albicans, frequently responsible for oral infections, and C. parapsilosis, a yeast with mostly commensal behavior in this niche. Exposed to C. albicans, tumor cells exhibited overexpression of inflammatory and pro-tumor pathways. This was also mirrored at the miR-level. Intriguingly, this species induced upregulation of oncogenic miRs, while simultaneously downregulated tumor-suppressive miRs. miR-target analyses revealed targets primarily to be involved in inflammation (TNFa signaling via NFKB), albeit tumor progression was also heavily influenced based on the targets identified within the PanCancer Progression Panel. Several miR-target pairs were identified with TRIB1-miR-30c-1-3p highlighted at the route of inflammation, and MMP3-miR-374a-3p and JUN-miR-1268b/miR-16-1-3p/miR-30c-1-3p at the route of OSCC progression. These findings highlight that C. albicans drives OSCC progression, in part, through miR regulation. Contrarily, C. parapsilosis elicited tumor responses predominantly related to hypoxia and metabolic regulation, followed by a mild activation of inflammatory and tumorigenic processes. No significant miR-regulatory responses were identified.

overall_design: RNA-Seq and miRNA-Seq profiling of the oral metastatic cell line, HSC-2, in response to C. albicans SC5314 and C. parapsilosis CLIB 214 stimuli, the latter in different doses, for 1 and 6 hours at 37C, in the presence of 5% CO2.

first: Attila

last: Gacser

last: Toth


title: Transcriptomic Profiling of NSUN2-KO Murine BMM Cells Post-M1 Polarization

city: Wuhan

first: Yaoting

last: Ji

state: Hubei

address: No.237 Luoyu Road

institute: Wuhan University

summary: NSUN2, a C-type lectin receptor, has been implicated in macrophage-mediated immunity, but its role in M1 polarization remains unclear. Here, we performed RNA sequencing on bone marrow-derived macrophages (BMMs) from NSUN2-knockout (KO) and wild-type (NC) mice following M1 stimulation.

overall_design: Bone marrow-derived macrophages (BMMs) from NSUN2-KO and NC mice (3 biological replicates per group) were polarized to M1 phenotype (LPS/IFN-γ stimulation) and subjected to RNA sequencing. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).


title: The gene expression of primitive macrophage derived from human induced pluripotent stem cells treated by PNU282987

city: Kyoto

first: Keiichi

last: Ishihara

state: Kyoto

address: 5 Misasagi Nakauchi-cho, Yanashina-ku

country: Japan

institute: Kyoto Pharmaceutical University

summary: Microglia are immune cells in the brain originating from primitive macrophages, which developed in the yolk sac during embryonic development. We have previously found that stimulation of the nicotinic acetylcholine receptor α7 subtype (α7 nAChR) in rodent microglia promotes the phagocytosis. In this study, we performed a comprehensive gene expression analysis of human induced pluripotent stem cell-derived primitive macrophages treated with a full agonist of α7 nAChR, PNU282987, to evaluate gene expression changes human microglia model system.

overall_design: As a human microglia model, human induced pluripotent stem cells were differentiated into primitive macrophages. These cells were treated with a full agonist of α7 nAChR, PNU282987, to evaluate gene expression changes human microglia model system. The comparative gene expression profiling analysis of RNA-seq data for primitive macrophages derived from human induced pluripotent stem cells.

first: Koki

last: Harada

first: Kazuyuki

last: Takata


title: Sensory neurons drive pancreatic cancer progression through glutamatergic cancer-neuron pseudo-synapses.

city: Munich

first: Rouzanna

last: Istvánffy

address: Ismaningerstr. 22

department: Department of Surgery

institute: Klinikum rechts der Isar

summary: The results provide significant insights into the role of Grin2D in regulating the secretion of neurotrophic factors that promote neuritogenesis. Transcriptomic analysis of orthotopically transplanted PDAC cancer cells with a knockout of the NMDA receptor subunit Grin2D, along with dorsal root ganglia (T8–T12) innervating the pancreas, strongly supports this conclusion. Furthermore, RNA-Seq analysis of tumor and ganglion biopsies from PDAC patients was performed to validate the identified gene candidates in a human context. This study tested the hypothesis that neuronal glutamate drives pancreatic cancer progression via glutamate-mediated GluN2D signaling at the cancer-neuron pseudo-synapses.

first: Lei

last: Ren

first: Ekin

last: Demir


title: Transcriptome profiling of SKHEP1 cells and differentiated SKHEP1 cells induced by forced expresssion of PPARG using RNA-sequencing.

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

summary: The core proeprty of cancer cells is neural stemness, which determines tumorigenicity and pluripotency. Therefore, cancer cells can supposedly be induced to differentiate along different lineages. SKHEP1 is a human hepatocellular carcinoma cell line. We found that SKHEP1 cells differentiated into adipocytes upon induction by adipocyte differentiation factor PPARG.

overall_design: Forced expression of human PPARG (SKHEP1_PPARG) in SKHEP1 cells was perfomed with lentiviral transfection. In paralell, cells transfected with lentivirus carrying only the empty vector were used as control (SKHEP1_Ctrl). All cells were cultured in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% FBS at 37°C in 5% CO2 for 12 days when significant phenotypic change occurred in cells with forced PPARG expression. Control and differentiated cells were then collected and subjected to RNA-sequencing.

first: Yang

last: Liu


title: Transcriptome profiling of SKHEP1 cells and differentiated SKHEP1 cells induced by knockdown of SETDB1 using RNA-sequencing

summary: The core proeprty of cancer cells is neural stemness, which determines tumorigenicity and pluripotency. Therefore, cancer cells can supposedly be induced to differentiate along different lineages. SKHEP1 is a human hepatocellular carcinoma cell line. SETDB1 is an epigenetic modification factor responsible for catalyzing the histone modification H3K9me3. Transcription of SETDB1 gene is enriched in embryonic neural cells during vertebrate embryogenesis. SETDB1 is upregulated in cancer cells and promotes cancers. We found that knockdown of SETDB1 in SKHEP1 cells led to a neuronal-like differentiation phenotype.

overall_design: SETDB1 was knocked down with specific short-hairpin RNA (shSETDB1) in SKHEP1 cells using lentiviral infection (SKHEP1_shSETDB1), while cells infected with virus carrying only the empty vector was used as control (SKHEP1_shCtrl). Cells were cultured in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% FBS at 37°C in 5% CO2 for 9 days when knockdown cells underwent significant phenotypic change. Control cells and knockdown cells were then collected and subjected to RNA-sequencing.


title: Transcriptome profiling of SKHEP1 cells and differentiated SKHEP1 cells induced by forced expresssion of MYOD1 using RNA-sequencing.

summary: The core proeprty of cancer cells is neural stemness, which determines tumorigenicity and pluripotency. Therefore, cancer cells can supposedly be induced to differentiate along different lineages. SKHEP1 is a human hepatocellular carcinoma cell line. We found that SKHEP1 cells differentiated into muscle cells upon induction by muscle differentiation factor MYOD1.

overall_design: Forced expression of human MYOD1 (SKHEP1_OEMYOD) in SKHEP1 cells was perfomed with lentiviral transfection. In paralell, cells transfected with lentivirus carrying only the empty vector were used as control (SKHEP1_OECTRL). All cells were cultured in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% FBS at 37°C in 5% CO2 for 12 days when significant phenotypic change occurred in cells with forced MYOD1 expression. Control and differentiated cells were then collected and subjected to RNA-sequencing.


title: Transcriptome profiling of HCT116 cells and differentiated HCT116 cells induced by forced expresssion of MYOD1 or PPARG using RNA-sequencing.

summary: The core proeprty of cancer cells is neural stemness, which determines tumorigenicity and pluripotency. Therefore, cancer cells can supposedly be induced to differentiate along different lineages. HCT116 is a human colon cancer cell line. We found that HCT116 cells differentiated into muscle- or adipocyte-like cells upon induction by muscle or adipocyte differentiation factor MYOD1 or PPARG, respectively.

overall_design: Forced expression of human MYOD1 (HCT116_MYOD1) or PPARG (HCT116_PPARG) in HCT116 cells was perfomed with lentiviral transfection, respectively. In paralell, cells transfected with lentivirus carrying only the empty vector were used as control (HCT116_Ctrl). All cells were cultured in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% FBS at 37°C in 5% CO2 for 11 days when significant phenotypic change occurred in cells with forced MYOD1 or PPARG expression. Control and differentiated cells were then collected and subjected to RNA-sequencing.


title: Transcriptome profiling of CT26 cells and differentiated CT26 cells induced by knockdown of Setdb1 using RNA-sequencing.

summary: The core proeprty of cancer cells is neural stemness, which determines tumorigenicity and pluripotency. Therefore, cancer cells can supposedly be induced to differentiate along different lineages. CT26 is a mouse colon cancer cell line. Setdb1 is an epigenetic modification factor responsible for catalyzing the histone modification H3K9me3. Transcription of Setdb1 gene is enriched in embryonic neural cells during vertebrate embryogenesis. Setdb1 is upregulated in cancer cells and promotes cancers. We found that knockdown of Setdb1 in CT26 cells led to a neuronal-like differentiation phenotype.

overall_design: Setdb1 was knocked down with specific short-hairpin RNA (shSetdb1) in CT26 cells using lentiviral infection (CT26shSetdb1), while cells infected with virus carrying only the empty knockdown vector was used as control (CT26shCtrl). Cells were cultured in Roswell Park Memorial Institute 1640 (RPMI 1640) supplemented with 10% FBS at 37°C in 5% CO2 for 6 days when knockdown cells underwent significant phenotypic change. Control cells and knockdown cells were then collected and subjected to RNA-sequencing.


title: Low oxygen environment alters transcripts related to energy metabolism without altering the pluripotency core of bovine embryonic stem cells

status: Public on Jun 10 2026

city: Davis

first: Anna

last: Denicol

state: CA

address: 2251 Meyer Hall, One Shields Ave

department: Animal Science Department

institute: University of California Davis

summary: Here we evaluated effects of the adapation of bovine embryonic stem cells (bESC) previously derived on mouse embryonic fibroblasts (MEF) under high  oxygen (21%) conditions in low oxygen environment (5%) and their their molecular profile. Primed bESC established on MEF were adapted to 5% O2 conditions after 5-6 passages. Following culture in low oxygen for 5 passages, bESC were transitioned to feeder-free conditions. Comparing the transcriptomes of bESC cultured in , we found that adaptation to feeder-free conditions triggered commitment towards cell differentiation. Transition of bESC on MEF to a low oxygen environment did not result in changes in morphology or growth. Furthermore, we noted fewer changes in the transcriptome of cells grown on MEF compared to those grown in feeder-free conditions when maintained in low oxygen, compared to cells maintained in atmospheric oxygen. Lastly, while low oxygen tension did not alter the pluripotency profile of bESC, it did promote changes in transcripts related to energetic metabolism. These findings enhance our understanding about the optimal conditions for bESC culture and emphasize the importance of oxygen tension for derivation, maintenance, and performance of embryonic stem cells.

overall_design: Bovine embryonic stem cells were derived from early and full blastocysts using the same methods and medium (Guiltinan et al 2025; DOI: 10.1242/bio.061819). After adaption in low oxygen, and subsequently into feeder free conditions RNA sequencing was performed at passage 15-17 (cells adapted in low oxygen and maintained on MEF feeders) and passage 20-22 (after transtion to feeder-free in low oxygen conditions).

first: Botigelli

last: Ramon

first: Arcanjo

last: Rachel

first: Guiltinan

last: Carly

first: Morton

last: Amanda

first: Smith

last: Justin

first: Denicol

last: Anna


title: Dynamics of poised enhancer connectivity

city: London

first: Mikhail

last: Spivakov

address: Du Cane Road

country: United Kingdom

institute: MRC Laboratory of Medical Sciences (LMS)

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

overall_design: Refer to individual Series


title: AMPK signaling is dysregulated in human tendinopathy and loss of AMPKα1 leads to cell, matrix and mechanical dysfunction in mouse Achilles tendon II

city: Ann Arbor

first: Adam

last: Abraham

state: MI

address: 2800 Plymouth Rd

department: Orthopaedic Surgery

institute: University of Michigan

summary: Tendinopathy is a tendon disorder that is caused by the failure to self-repair and has many pathological characteristics such as disorganized ECM and decreased cell viability. We have identified a possible target to combat these changes, AMPK, an energy stress sensor that was shown to maintain intracellular homeostasis. Through bulk RNA sequencing of healthy and tendinopathic tendons from humans we have identified a novel finding of downregulation of AMPK signaling in the tendinopathic samples which suggests AMPK plays a role in tendon homeostasis. Our studies utilizing a conditional knock-out of Prkaa1 in tendon in mice showed that loss of AMPK results in degenerative ECM, impaired biomechanical properties and increased cellular senescence in Achilles tendon through the lifespan. Additionally, we found that exercise can delay senescence onset independent of AMPK. These findings highlight the importance of energy metabolism in tendon health which will assist in understanding the onset and progression of tendinopathy.

overall_design: RNA-Seq profiling of  Healthy hamstring tendon (H) and chronic tendinopathy (T) rotator cuff biopsy.

first: LeeAnn

last: Hold

first: Nicole

last: Migotsky

first: Jessica

last: Chen

first: Steph

last: Steltzer

first: Paige

last: Cordts

first: Seung-Ho

last: Bae

first: Sydney

last: Grossman

first: Syeda

last: Lamia

first: Tessa

last: Phillips

first: Matthew

last: O'Meara

first: Carol

last: Davis

first: Susan

middle: V

last: Brooks

first: Moeed

last: Akbar

first: Neal

last: Millar

first: Megan

last: Killian

middle: C


title: Cellular mechanisms of early brain overgrowth in autistic children: elevated levels of GPX4 and resistance to ferroptosis

first: Carlos

last: Aguilar

address: 2800 Plymouth Rd.,

institute: University of Michigan - Ann Arbor

summary: Autistic individuals with disproportionate megalencephaly (ASD-DM), characterized by enlarged brains relative to body height, have higher rates of intellectual disability and face more severe cognitive challenges than autistic children with average brain sizes. The cellular and molecular mechanisms underlying this neurophenotype remain poorly understood. To investigate these mechanisms, we generated human induced pluripotent stem cells from non-autistic typically developing children and autistic children with and without disproportionate megalencephaly. We assessed these children longitudinally from ages two to twelve years using magnetic resonance imaging and comprehensive cognitive and medical evaluations. We show that neural progenitor cells (NPCs) derived from ASD-DM children exhibit increased rates of cell survival and suppressed cell death, accompanied by heightened oxidative stress and ferrous iron accumulation. Despite these stressors, ASD-DM NPCs actively suppress apoptosis and ferroptosis by regulating proteins such as caspase-3 (CASP3), poly(ADP-ribose) polymerase 1 (PARP1), and glutathione peroxidase 4 (GPX4). Cellular ferroptotic signatures are further supported by elevated expression of selenocysteine genes, including GPX4, in the blood of ASD-DM children and their mothers, suggesting potential hereditary or environmental influences. Furthermore, we show that peripheral expression of GPX4 and other selenocysteine genes correlate with cognitive outcomes (IQ). These findings underscore the role of ferroptosis in autism, pointing to potential diagnostic biomarkers and targets for intervention.

overall_design: RNA-seq profiling of neural progenitor cells (NPCs) differentiated from induced pluripotent stem cells (iPSCs) at Day 12, derived from three groups: typically developing individuals with normal brain sizes (TD-N), autistic individuals with normal brain sizes (ASD-N), and autistic individuals with disproportionate megalencephaly (ASD-DM), with biological replicates.

first: Siwei

first: Anna

last: Shcherbina

first: Simon

last: Schafer

first: Zoe

middle: A

last: Mattingly

first: Janani

last: Ramesh

first: Cyndhavi

last: Narayanan

first: Sravani

last: Banerjee

first: Brianna

last: Heath

first: Melissa

last: Regester

first: Ivette

first: Sudhir

last: Thakurela

first: Joachim

last: Hallmayer

first: Ruth

last: O’Hara

first: Marjorie

last: Solomon

first: Christine

middle: W

last: Nordahl

first: David

middle: G

last: Amaral

first: Sundari

last: Chetty


title: AMPK signaling is dysregulated in human tendinopathy and loss of AMPKα1 leads to cell, matrix and mechanical dysfunction in mouse Achilles tendon

first: Adam

last: Abraham

overall_design: RNA-Seq profiling of  Wildtype (W) and AMPKcKO (A) Achilles tendons at both 1 and 3 months of age.

first: LeeAnn

last: Hold

first: Nicole

last: Migotsky

first: Jessica

last: Chen

first: Steph

last: Steltzer

first: Paige

last: Cordts

first: Seung-Ho

last: Bae

first: Sydney

last: Grossman

first: Syeda

last: Lamia

first: Tessa

last: Phillips

first: Matthew

last: O'Meara

first: Carol

last: Davis

first: Susan

last: Brooks

first: Moeed

last: Akbar

first: Neal

last: Millar

first: Megan

last: Killian


title: A Scalable Micropatterned Organoid Platform for Quantitative Modeling of Human Forebrain Development and Disease

city: Berlin

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

summary: Brain organoids derived from human pluripotent stem cells have revolutionized the modeling of neurodevelopment and associated disorders. However, challenges of morphological variability and limited scalability restrict their use for high-throughput disease phenotyping and drug-screens. Here, we introduce a micropatterned organoid platform enabling reproducible and scalable generation of forebrain-like structures. By integrating micropatterning with established cortical differentiation protocols, we generate reproducible, miniaturized brain organoids that are suitable for AI-based, quantitative phenotypic analysis. As a proof-of-concept, we model DYRK1A syndrome, a neurodevelopmental disorder characterized by microcephaly and autism spectrum disorder, using genetically engineered isogenic embryonic stem cells (hESCs) and patient-derived induced pluripotent stem cells (iPSCs). Multi-omics and high-content imaging reveal that DYRK1A haploinsufficiency disrupts progenitor proliferation, delays neuronal differentiation, and impairs cortical organization. Our platform provides an efficient tool for early disease detection and analysis, and opens avenues toward phenotypic, genetic and pharmacological screens.

overall_design: Single-cell RNA sequencing (scRNAseq) of  human forebrain micropatterned organoids - Micropatterned Brain Organoids (MIBOs). For scRNAseq, we used (day in vitro) DIV 30 MIBOs of WT and isogenic lines with introduced DYRK1A variant: n=750 MIBOs per sample in n=2 replicates per condition, n=3000 MIBOs in total.

first: Philipp

last: Roth

first: Jacob

last: Metzger


title: AMPK signaling is dysregulated in human tendinopathy and loss of AMPKα1 leads to cell, matrix and mechanical dysfunction in mouse Achilles tendon [RNAseq_AMPK_WheelRunning]

first: Adam

last: Abraham

overall_design: RNA-Seq profiling of  Wildtype (W) and AMPKcKO (A) Achilles tendons at both 3 months of age with either cage activity (C)  or wheel running (R) conditions

first: LeeAnn

last: Hold

first: Nicole

last: Migotsky


title: Unraveling Diabetic Cardiomyopathy (DCM): The Critical Role of the Yap–miR-22-3p–Sirt1 axis in the Pathogenesis of DCM [miRNA-seq]

city: Guangzhou

first: Ning

last: Hou

address: Xinzao Street

institute: Guangzhou Medical University

summary: Background: Diabetic cardiomyopathy (DCM), characterized by myocardial hypertrophy and myocardial fibrosis, is a severe complication of diabetes. Yes-associated protein (Yap) activation contributes to myocardial remodeling and cardiac dysfunction. This study investigated the role of Yap and its molecular mechanism in DCM. Methods: Yap expression was assessed in mice with type 2 diabetes mellitus (T2DM) and high glucose (HG) + insulin-treated neonatal rat cardiomyocytes (NRCMs). Adeno-associated virus transfection, siRNA transfection, and a transgenic mouse model were used to manipulate Yap and sirtuin 1 (Sirt1) expression in vivo and in vitro. RNA sequencing, differential gene analysis, and miRNA sequencing were used to identify downstream targets of Yap and the underlying mechanisms. Functional assays were used to evaluate cardiomyocyte hypertrophy and fibrosis through molecular markers, cell morphology, and echocardiography. Results: Yap expression was increased in HG + insulin-treated NRCMs and in the hearts of mice with T2DM, thereby promoting myocardial hypertrophy and fibrosis. Yap inhibition reduced the cardiomyocyte cross-sectional area, collagen deposition, and the levels of the hypertrophy markers atrial natriuretic peptide and β-myosin heavy chain. RNA sequencing identified Sirt1 as a downstream target of Yap. Bioinformatic analysis suggested that Yap positively regulates miR-22-3p, which inhibits Sirt1. Yap inhibition increased Sirt1 expression, mitigating myocardial remodeling. Conversely, Sirt1 knockdown reversed the protective effects of Yap inhibition, restoring hypertrophy and fibrosis. Conclusion: Yap promotes DCM progression by increasing miR-22-3p expression and suppressing Sirt1 expression. Targeting the Yap–miR-22-3p–Sirt1 axis might represent a novel therapeutic strategy for DCM, thereby improving myocardial structure and function.

overall_design: Primary neonatal rat cardiomyocytes (NRCMs) were isolated from 1–2-day-old neonatal SD rats. In brief, hearts collected from anesthetized neonatal rats were digested with pancreatic enzymes and type II collagenase The .NRCMs were initially cultured in DMEM supplemented with  10% fetal bovine serum and 1% penicillin-streptomycin. Yap expression in these cells was manipulated using adenovirus. The cells were categorized into the Ad-Yap shRNA or Ad-Yap WT group under normal glucose conditions. The group transfected with Ad-GFP  served as the CON group. Total RNA was extracted from NRCMs using a Trizol reagent kit. We then performed gene expression profiling analysis using data obtained from miRNA-seq of adenovirus infected cardiomyocytes.

first: Yilang

last: Li

first: Yuling

last: Lian


title: Low-dose total body irradiation (LD-TBI) primes CD19-directed CAR T cells against large B-cell lymphoman (LBCL)

first: Monica

middle: Liliana

last: Guzman

state: New York

address: 1300 York Ave

department: Medicine

institute: Weill Cornell Medicine

summary: Administering (LD-TBI) before CART19 infusion significantly accelerates tumor elimination and improves overall survival in LBCL.

overall_design: Two cohorts of mice bearing LBCL (A20 GFP-LUC) received Cy/mCART19 and Cy/LD-TBI/mCART19 treatments. 1 Gy LD-TBI was given 4 hours before mCART19 treatment (1.6x106 cells/mouse). Three days after mCART19 administration, cells from the spleen were sorted and analyzed using scRNA-seq approach.

first: Mohammad

last: Alhomoud

first: Michelle

last: Foley

first: Mayumi

last: Sugita

first: Takahiro

last: Yamazaki

first: Joshua A

last: Fein

first: Samuel

last: Yamshon

first: Leandro

last: Martinez

first: Alexandra

last: Gomez-Arteaga

first: Kai

last: Rejeski

first: Roni

last: Shouval

first: Paul

last: Pagnini

first: Maider

last: Astorkia

first: Doron

last: Betel

first: Tsiporah

last: Shore

first: Juliet

middle: N

last: Barker

first: Olivier

last: Boyer

first: Renier

last: Brentjens

first: Koen

last: van Besien

first: Lorenzo

last: Galluzzi

first: Silvia

last: Formenti

first: Jeremie

last: Martinet


title: Mesenchymal Stem Cells relieved Systemic Lupus Erythematosus via CCL2 dependent macrophage polarization

first: xin

last: wen

address: 321 Zhongshan Road, Gulou District

department: Department of Rheumatology and Immunology

summary: Systemic lupus erythematosus (SLE) was an autoimmune disease leading to high morbidity and mortality without effective and low-side effect conventional drugs. Our previous clinical studies demonstrated umbilical cord derived mesenchymal stem cells (MSCs) were a safe and effective treatment, but its therapeutic mechanism is still unclear. In this study, we first detected the MSCs used for clinical therapy showed increased CCL2 expression than primary and aged MSCs or abnormal MSCs from SLE patients. Then, we constructed CCL2 deficient MSCs, and found the immunosuppressive activity of CCL2 deficient MSCs was impaired in the PBMC inhibitory assay in vitro. CCL2 deficient MSCs also failed to relieve SLE in MRL/lpr and pristine-induced mice. To further explore the role of CCL2 in MSCs therapy, we conducted transcriptome of CCL2 deficient MSCs and MSCs, and identified the differential expressed genes were related to chemotaxis, including monocyte chemotaxis. Subsequently, we found that MSCs restored the imbalanced macrophage polarization via CCL2 in vitro. These findings provided valuable insight for investigating the therapeutic mechanism of MSC on SLE.

overall_design: we performed PloyA enriched RNA sequencing of CCL2 deficient MSCs and MSCs

first: Xin

last: Wen

first: Shanshan

last: Liu


title: Macroscopic mechanostress-induced nuclear envelop rupture reorganizes tumor-stromal interactions (scRNA-seq)

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Macroscopic mechanostress can disrupt nuclear envelop integrity of cancer cell. However, the impact of this stimuli on the tumor microenvironment remians unclear. Here, by constructing a single-cell RNA sequencing data of hindpaw-engrafted B16F10 melanoma with/without forced wheel running, we show that reorganization of fibroblast and macrophage subtypes. Fibroblasts from running group showed upregulated Acta2 and Lrrc15 expression with increased ECM production. IL-1b expressing macrophage subtype proportion was increased in running group. Collectively, these data elucidate the changes within the tumor microenvironment upon macroscopic mechanostress.

overall_design: We performed single cell RNA sequencing on the hindpaw engrafted B16F10 melanomas with/without forced wheel running.

first: HyunSeok

last: Kim

first: Wooseok

first: Joon


title: Transcriptional profiles of the Hodgkin lymphoma tumor-associated macrophage in vitro models

city: Warszawa

first: Michal

last: Pawlak

address: Indiry Gandhi 14

department: Department of Experimental Hematology

country: Poland

institute: Institute of Hematology

summary: Tumor-associated macrophages (TAMs) of classic Hodgkin Lymphoma (cHL) contribute to the development of immunosuppressive tumor microenvironment (TME) and are associated with worse treatment outcome. However, detailed features and functions of cHL TAMs and their therapeutic vulnerabilities remain largely unknown. To gain deeper insight into the biology of TAMs in cHL, we analyzed diagnostic biopsies by Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and assessed transcriptional, proteomic and metabolic profiles of the in vitro TAM models. We show that Reed-Sternberg (RS) cells of cHL induce disease-specific TAM phenotype, characterized by elevated expression of factors involved in chemotaxis, angiogenesis, extracellular matrix remodeling and tumor immune escape. Importantly, RS cell-conditioned TAMs expressed TGFβ, CCL17 and tryptophan catabolizing enzymes, IDO1 and IL4I1, facilitating induction or and/or recruitment of Tregs. In addition, we identified PIM1/2/3 kinases in cHL TAMs. We characterized PIMs as important hubs orchestrating RS-macrophage interactions. Pharmacological PIM blockade attenuated development of TAM transcriptional  profile and phenotype induced by RS cells. In established TAMs, PIM inhibition or PROTAC-mediated degradation decreased expression of multiple factors associated with pro-tumoral TAM functions, including IL8, MMP9, CHI3L1/2, CD206, CD209, PD-L1, CCL17, TGFβ, IL4I1 and IDO1. PIM blockade attenuated TAM-dependent eosinophil chemoattraction, extracellular matrix remodelling, angiogenesis and regulatory T cell development. Taken together, our study highlights the role of PIMs in regulation of TAM activities involved in cHL pathogenesis and potentially relevant for response of cHL patients to immunotherapies.

overall_design: To characterize cHL TAMs, we generetated in vitro TAM models of RS-educated macrophages (RS-M) by culturing unpolarized (M0) macrophages differentiated from primary monocytes (MdM) or THP-1 monocytic cells with RS cells (L1236 and/or L428) under conditions prohibiting direct cell-to-cell contacts. Established RS-M and control (M0) macrophages were subjected to gene expression profiling by RNA-seq. To assess transcriptional consequences of pharmacological PIM blockade, RS-M were treated with DMSO or 3umol/L MEN1703 (MEN) for 24 hours, followed by RNA-seq.

first: Maciej

last: Szydlowski


title: Histone chaperone HIRA regulates adiponectin expression and obesity-associated adipose expansion by facilitating Pol II pause release

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

summary: Adipose tissue is essential for maintaining glucose and lipid homeostasis in mammals. However, epigenomic mechanisms underlying adipose tissue function remain largely unclear. Here, we identify the histone chaperon HIRA as a novel epigenomic regulator of adipose tissue function. Adipose tissue-specific knockout of Hira in mice impairs insulin sensitivity and restrains adipose tissue expansion during high-fat diet-induced obesity. Mechanistically, HIRA is required for the expression of Adipoq, encoding the adipokine adiponectin, and lipid metabolism genes in adipose tissue. Genomic mapping reveals that HIRA binds to promoters and enhancers of Adipoq and lipid metabolism genes in adipocytes. Acute HIRA depletion using the dTAG system, followed by nascent RNA-Seq and ChIP-Seq, demonstrates that while HIRA is largely dispensable for enhancer activation and coactivator binding, it promotes transcription of target genes by facilitating RNA polymerase II pause release and subsequent elongation likely independently of H3.3 deposition. Our findings uncover a novel mechanism by which HIRA regulates transcription and establish HIRA's critical role in insulin sensitivity and lipid metabolism, providing a potential therapeutic target for obesity and insulin resistance.

overall_design: Expression profiling by RNA-Seq in control and HIRA knockout adipose tissues, and ChIP-Seq profiling of HIRA, elongation factors (S2P-Pol II, CDK9, SPT6) histone modifications (H3K4me1 and H3K27ac) in 3T3-L1 cultures

first: Danyang

last: Wan

first: Ji-Eun

last: Lee