title: Post-transcriptional modifications on tRNA fragments confer functional changes to high-density lipoproteins in atherosclerosis [small RNA-seq]

city: Nashville

first: Kasey

last: Vickers

address: 2220 Pierce Ave, PRB 312

institute: VUMC

type: Non-coding RNA profiling by high throughput sequencing

summary: Epitranscriptomic modifications on RNA play critical roles in stability, processing, and function, partly by influencing interactions with RNA-binding proteins and receptors. The diverse role(s) of post-transcriptional RNA modifications on cell-free small non-coding RNAs (sRNA) remain poorly understood, particularly in disease contexts. Although HDL confer many beneficial properties to health, HDL particles lose these features during atherosclerotic cardiovascular disease (ASCVD). As HDL transport sRNA fragments from classes of RNA known to harbor extensive modifications, we predicted that changes to regulatory modifications on HDL-sRNAs may contribute to HDL functionality changes in ASCVD. To assess HDL-RNA modification levels in ASCVD, total RNA were isolated from HDL of healthy subjects (CAC=0) and those with advanced atherosclerosis, as determined by coronary artery calcium (CAC) scores >21 Agatston units. HDL-RNA were quantified using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and AlkB-facilitated RNA (de)Methylation Sequencing (ARM-seq). LC-MS/MS revealed elevated levels of modified nucleosides in HDL-sRNAs from ASCVD subjects, while ARM-seq detected an enrichment of m1A-modified sRNAs-derived from parent tRNAs (tDR), particularly tDR-ArgACG-1. To assess the impact of disease HDL on immune cells, primary macrophages were treated with HDL isolated from ASCVD (CAC+) and control subjects, and results showed that ASCVD-HDL directly induced expression of genes associated with immune signaling and cell adhesion, including TMEM123, a transmembrane protein linked to immune cell migration, adhesion, and cytoskeletal organization. In addition, recombinant HDL particles loaded with m1A-tDR-ArgACG-1 were found to significantly increase TMEM123 expression in treated primary macrophages. Together, these findings propose a model in which HDL-delivered m1A-HDL-tDRs directly stimulate immune signaling, macrophage activation, and pro-inflammatory sub-phenotypes within the atherosclerotic lesion. This study highlights HDL-associated RNA modifications as previously unrecognized contributors to immune modulation, with direct implications for targeting modified HDL-tDRs as a new approach to therapy for ASCVD.

overall_design: sRNA sequencing of human high density lipoproteins (HDL) from healthy controls and those with a coronary artery calcium score > 21. HDL from both cohorts was either untreated or treated with AlkB-facilitated RNA methylation.

first: Elizabeth M.

last: Semler

first: Danielle L.

last: Michell

first: Kasey C.


title: RXR-Mediated Remodeling of Transcriptional and Chromatin Landscapes in APP Mouse Brain: Insights from Integrated Single-Cell RNA and ATAC Profiling

status: Public on Dec 11 2025

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

country: USA

institute: University of Pittsburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Ligand activation of nuclear receptor has been linked with therapeutic implications in Alzheimer's Disease. In this study, we used AD mouse model treated with Bexarotene, an RXR agonist and performed scRNA-seq and snATAC-seq using the brain tissue. We reavealed changes in chromatin architure in brain of AD-lie mouse model in response to RXR ligand and  link those changes to the initiation of transcriptional programs at a single-cell resolution.

overall_design: We used an AD mouse model treated with Bexarotene, an RXR agonist. scRNA-seq and snATAC-seq were performed using mouse brain 10-day post-treatment to assess brain transcriptome and chromatin accessibility change in response to RXR activation. The results were further validated by ChIP-seq.


title: Integrative transcriptomics and network analysis reveals core genes driving meningioma pathogenesis and clinical outcomes

city: Atlanta

first: Youssef

middle: M

last: Zohdy

state: GA

address: 1365 Clifton Road NE

department: Neurosurgery

institute: Emory University

type: Expression profiling by high throughput sequencing

summary: Meningiomas are the most common primary CNS tumors, often managed conservatively due to their benign histology. Molecular phenotyping is considered the current frontier in meningioma classification to predict progression and guide clinical management of adjuvant therapies. While several biomarkers have been studied, a definitive molecular prognostic panel has yet to be established—a gap this study seeks to address. Using patient-resected meningioma tumor tissues paired with normal meninges, transcriptomic analysis identified a subset of significantly differentially-expressed-genes(DEG) linked to cellular proliferation and immune suppression in the tumor microenvironment. Graph-theory analysis revealed a rich-club organization in the gene networks, with highly connected core nodes. Core gene expression levels significantly correlated with tumor WHO grading, achieving an ROC-AUC of 0.8 for distinguishing low-grade(grade-1) from high-grade(grades-2&3) tumors(P < 0.001). For clinical outcomes, core gene expression achieved an AUC of 0.96 for predicting tumor recurrence(P < 0.001) and 0.74 for patient survival(P = 0.018). This study employs an analytical pipeline integrating transcriptomic analysis of meningiomas with a graph-theory approach to identify core regulators within pathological tumor networks. This refined method facilitated the discovery of phenotype-encoding biomarkers, which accurately predicted histological grade and clinical outcomes. The identified core markers provide insights into meningioma-specific pathophysiological pathways and offer potential targets for therapeutic intervention.

overall_design: RNA-seq profiling of human resected meningiomas and compared to normal meninges.

first: Ali

last: Alawieh

first: Arman

last: Jahangiri

first: Benjamin

last: Siciliano

first: Leonardo

last: Tariciotti

first: Alejandra

last: Rodas

first: Justin

last: Maldonado

first: Kimberly

last: Hoang

first: Edjah

last: Nduom

first: Brian

last: Howard

first: Daniel

middle: L

last: Barrow

first: Aliaksandr

last: Aksionau

first: Stewart

middle: G

last: Neill

first: Zhexing

last: Wen

first: Gustavo

last: Pradilla

first: Tomas

last: Garzon-Muvdi


first: Iliya

last: Lefterov

overall_design: We used an AD mouse model treated with Bexarotene, an RXR agonist. scRNA-seq and snATAC-seq were performed using mouse brain 10-day post-treatment to assess brain transcriptome and chromatin accessibility change in response to RXR activation.


title: Gene expression profile from the bicuspid aortic valve(BAV), tricuspid aortic valve(TAV) and control samples.

city: nanjing

first: yuanyuan

last: wang

address: 818 Tianyuan E Rd, Nanjing, JIANGSU

country: China

institute: nanjing medical university

summary: bulk RNA sequencing was employed to investigate the discrepancies in transcript levels between TAV and BAV in valve tissues of end-stage CAVD.

overall_design: collect aortic valve leaflets of the bicuspid aortic valve(BAV), tricuspid aortic valve(TAV) and control samples.

first: Wei

last: Yuan

first: Xiaojie

last: Zhou

first: Haotian

last: Pan


title: Post-transcriptional modifications on tRNA fragments confer functional changes to high-density lipoproteins in atherosclerosis [RNA-seq]

first: Kasey

last: Vickers

overall_design: Total RNA sequencing of mouse bone marrow derived macrophages treated with lipoproteins (HDL) from healthy controls and subjects with a coronary artery calcium (CAC) score >21

first: Elizabeth M.

last: Semler

first: Danielle L.

last: Michell

first: Kasey C.


title: Mammalian ZAP and KHNYN independently restrict CpG-enriched avian viruses

city: Minneapolis

first: Frances

last: Shepherd

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

summary: Zoonotic viruses are an omnipresent threat to global health. Influenza A virus (IAV) transmits between birds, livestock, and humans. Proviral host factors involved in the cross-species interface are well known, less is known about antiviral mechanisms that suppress IAV zoonoses. We observed CpG dinucleotide depletion in human IAV relative to avian IAV. Notably, human ZAP selectively depletes CpG-enriched viral RNAs with its cofactor KHNYN. ZAP is conserved in tetrapods but we uncovered that avian species lack KHNYN. We found that chicken ZAP does not affect IAV (PR8) or CpG enriched IAV. Human ZAP or KHNYN independently restricted CpG enriched IAV by overexpression in chicken cells or knockout in human cells. Additionally, mammalian ZAP-L and KHNYN also independently restricted an avian retrovirus (ROSV). Curiously, platypus KHNYN, the most divergent from eutherian mammals, was also capable of direct restriction of multiple diverse viruses. We suggest that mammalian KHNYN may be a bona fide restriction factor with cell-autonomous activity. Furthermore, we speculate that through repeated contact between avian viruses and mammalian hosts, protein changes may accompany CpG-biased mutations or reassortment to evade mammalian ZAP and KHNYN.

overall_design: RNAseq profiling of chicken DF-1 cells stably expressed human ZAP-L (long isoform of ZAP), ZAP-S (short isoform of ZAP), KHNYN, or dKHNYN (catalytically inactive form). Influenza A strains were either wild-type PR8 or PR8 with elevated CG dinucleotide frequencies.

first: Jordan

middle: T

last: Becker

first: Clayton

middle: K

last: Mickelson

first: Lauren

last: Pross

first: Autumn

middle: E

last: Sanders

first: Esther

middle: R

last: Vogt

first: Chloe

last: Wick

first: Alison

middle: J

last: Barkhymer

first: Stephanie

last: Aron

first: Elizabeth

last: Fay

first: Reuben

middle: S

last: Harris

first: Ryan

middle: A

last: Langlois


title: Activation of IRF3 impairs mitochondrial function and leads to heart failure. [Rescue]

city: Heidelberg

first: Ashraf

last: Rangrez

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University Hospital

summary: Averting heart failure in ischemic cardiomyopathy is challenging. Heightened inflammatory response and mitochondrial dysfunction drives the pathophysiology of heart failure. However, the transcriptional regulators within cardiomyocytes driving crosstalk between cardiac sterile inflammation and mitochondrial energy metabolism remain ill-defined. Here we identify elevated Ser396/Ser398 phosphorylation of the transcription factor IRF3, a key regulator of type I interferon (IFN) response, in the left ventricular of patients and mice with ischemic cardiomyopathy. Our data show that cardiomyocyte-specific Irf3 deficiency in mice attenuated contractile dysfunction upon myocardial infarction. Conversely, activation of Irf3 in cardiomyocytes through a phosphomimic Irf3 mutant repressed Pgc-1α expression leading to dysfunctional mitochondrial oxidative phosphorylation, impaired NAD metabolism and excessive type I IFN inflammatory milieu, collectively detrimental towards cardiac function. Restoring cardiomyocyte-specific Pgc-1α expression in Irf3-overexpressor mice attenuated the contractile dysfunction by augmenting metabolic flexibility towards fatty acid oxidation and decreasing inflammatory fibrotic responses. We identify Irf3 activation in cardiomyocytes as a potential in vivo model of type I IFN stimulated sterile inflammation that downregulates Pgc-1α and functions as a transcriptional nexus between inflammation and metabolic fuel switch contributing to heart failure.

overall_design: We identified the transcriptomic profile in the left ventricle of CMI3OE mice treated with AAV-PGC-1a or AAV-EGFP for 3 weeks followed by Tamoxifen induction of IRF3-2D gene expression.

first: Manju

last: Kumari

first: Joerg

last: Heeren


title: Advanced paternal age impacts common loci in the sperm and placenta DNA methylomes

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

type: Methylation profiling by genome tiling array

summary:
Background: Epidemiological studies have reported an association between advanced paternal age at conception and an increased risk of neurodevelopmental disorders in offspring, such as autism spectrum disorder. Evidence suggests that DNA methylation alterations in sperm of older men may be transmitted to the feto-placental unit and associated with offspring brain development and behavioral differences later in childhood.
Objective: We aimed to assess the association of advanced paternal age with DNA methylation alterations in the human placenta and compare the results to previous findings in sperm.
Methods: For this study, 64 placenta samples from the 3D (Design, Develop, Discover) prospective birth cohort study were categorized based on paternal age at conception. DNA methylation of the placenta was interrogated using the Illumina 850K array. There were no differentially methylated sites found to be statistically significant after correction for multiple comparisons, therefore sites with significant nominal p-values <0.05 were assessed and used to define differentially methylated regions (DMRs) associated with genes.
Results: Advanced paternal age was associated with DNA methylation alterations in the placenta at up to 688 genes, with a predominance of hypomethylation (65%), including at 8 imprinted loci. About 7% of genes with age-associated DNA methylation changes in placenta overlapped with genes previously reported to show altered DNA methylation in sperm of older men; seven genes common to placenta and sperm had previously been identified in association with susceptibility to autism spectrum disorder. Amongst loci most affected, we found evidence of sex-specific hypermethylation at genes linked to neurodevelopment (GRM7, EBF3, FOXG1).
Conclusion: Our findings suggest that advanced paternal age at conception is associated with altered DNA methylation in the human placenta, including at genes tied to neurodevelopment. This study highlights the use of the placenta DNA methylome as a surrogate marker for the potential impact of advanced paternal age on the child.

overall_design:
For this study, 64 placenta samples from the 3D (Design, Develop, Discover) Study were categorized based on paternal age. DNA methylation of the placenta was interrogated using the Illumina 850K array.
The two samples (P855 and P856) did not pass the QC (poor signal quality) and therefore were omitted in our analysis.

first: Julia

last: Barnwell

first: Sophia

last: Rahimi

first: Sherri

last: L Jones

first: Donovan

last: Chan

first: Josée

last: Martel

first: Sara

last: Abdessamie

first: Catherine

last: Herba

first: Jean

last: Séguin

first: William

middle: D

last: Fraser

first: Celia

last: Greenwood

first: Tuong-Vi

last: Nguyen

first: Tina

last: Montreuil


title: Profiling of terminating ribosomes reveals translational control at stop codons

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

institute: Cornell University

summary: Accurate termination of protein synthesis is paramount for the integrity of cellular proteome. Here we establish profiling of terminating ribosomes in mammalian cells and report a wide range of ribosome pausing at individual stop codons. We identify a sequence motif upstream of stop codons that contributes to termination pausing, which was confirmed by massively paralleled reporter assays. Lack of termination pausing increases the chance of stop codon slippage, generating proteins with mixed C-terminal extensions. We demonstrate that the sequence- dependent termination pausing is a result of post-decoding mRNA scanning by the 3’ end of 18S rRNA. We further uncover tissue-specific termination pausing that correlates with the stoichiometry of Rps26, which constrains mRNA:rRNA interaction. Termination pausing represents a translational signature associated with translational control at stop codons.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Ribo-seq under 18S rRNA mutation, RPS26 knockdown, and RPS26 overexpression; Ribo-seq from mouse liver, testis, kidney, brain, and heart.


title: The transcriptional profile of extracellular vesicles extracted from cerebrospinal flood in patients with multiple system atrophy, Parkinson's disease, amyotrophic lateral sclerosis

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

country: Japan

institute: Hirosaki University Graduate School of Medicine

summary: Extracellular vesicles (EVs) play a role in intercellular communication by transferring proteins and/or transcripts.  The profile of proteins and/or transcripts in EVs may differentiate multiple system atrophy (MSA) from Parkinson's disease. In the present study, we performed transcriptome analysis of EVs extracted from cerebrospinal flood of patients with multiple system atrophy, Parkinson's disease, amyotrophic lateral sclerosis.

overall_design: Exosomes were extracted from the cerebrospinal fluid, collected via spinal tap and frozen at -20°C using the MagCapture Exosome Isolation Kit PS Ver.2(FujiFilm, #290-84103) method. RNA was then purified using the exoRNeasy Midi Kit (77144, Qiagen).

first: Yasuo

last: Miki

first: Eri

last: Shibuya


title: Nuclear Phase Separation drives Acute Myeloid Leukemia

city: HOUSTON

first: Margaret

last: Goodell

state: TX

address: 1 Baylor Plz, Rm N1030

institute: Baylor College of Medicine

summary: To investigate how nuclear condensates formed by NPM1c coordinate protein recruitment and promote chromatin binding in leukemia

overall_design:
We assessed chromatin binding of XPO1. NUP98, KMT2A, and MENIN in the context of NPM1c degradation, XPO1 inhibition, or MENIN inhibition using Cut-and-run sequencing
Using an established OCI-AML3 cell line expressing an inducible degradation platform for NPM1c, we treated cells for 24hrs with dTAG-13, Eltanexor, or VTP50469 and performed Cut-and-run sequencing

first: Gandhar

last: Datar

first: Chun-Wei

last: Chen

first: Joshua

last: Riback


title: Activation of IRF3 impairs mitochondrial function and leads to heart failure. [CMI3OE vs Ctrl]

first: Ashraf

last: Rangrez

overall_design: To determine the downstream transcriptional changes by IRF3 activation in cardiomyocytes, we performed RNA-seq experiments and identified the transcriptional profile in the left ventricle upon cardiomyocyte-specific activation of IRF3 using IRF3-2D phosphomimic mutant transgene crossed to aMHCMCM.

first: Manju

last: Kumari

first: Joerg

last: Heeren


title: Integrated transcriptomic, epigenetic, and TCR clonality analysis of CD4⁺ Tm subsets in liver and lung during chronic GVHD in mice [RNA-seq]

city: Monrovia

first: Xiwei

last: Wu

state: CA

address: 655 HUNTINGTON DR.

institute: City of Hope

summary: Pathogenic CD4+  T cells perpetuate chronic tissue inflammation, but mechanisms remain largely undefined. Here, with transcriptome, epigenome, and clonal analysis, we compared CD4+Tm subsets among the liver and lung  in the No GVHD and cGVHD recipients. Four CD4+Tm subsets identified with Ly108 versus CD69 expression were compared

overall_design: cGVHD mice were established with BALB/c recipients in receiving graft from B6 donors. CD4+T cells from lungs of cGVHD mice were enriched at day 60 after HCT and four Tm subsets were sorted with Ly108 vs CD69 expression among H2Kb+TCRb+CD4+ cells. mRNA were then extracted with commercial mRNA isolation kit and processed for bulk RNA-seq.

first: Defu

last: Zeng

first: Xiaohui

last: Kong

first: Hyejin

last: Cho


title: Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [scRNA-seq]

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

summary: A remarkable transition during murine development is the progression from the 1-cell embryo to the 2-cell stage, accompanied by the activation of a specific set of embryonic genes, epigenome reprogramming, and nuclear architecture reorganization. Some of these characteristics are recapitulated in vitro with the spontaneous emergence of 2-cell-like cells from mouse embryonic stem cells, which exhibit a transcriptomic signature resembling the 2-cell stage, including the expression of genes such as Dux, Zscan4, and the repetitive element MERVL, and a more relaxed chromatin state. Here, we show that inter-and intra-chromosomal interactions, driven by Zscan4 chromatin factors, form during this transition and segregate into a distinct genomic compartment (Z compartment). Mechanistically, the formation of Z-DNA, an alternative DNA conformation regulated by polyamine levels, promotes the emergence of totipotent-like cells and the establishment of the Z compartment. This compartment is characterized by a decrease in active histone marks and a reduced expression of genes associated with differentiation and late developmental processes. Overall, these findings suggest that Z-DNA formation may play a dual role, first in activating ZGA genes and later in guiding genome compartmentalization to safeguard the totipotent-like state by restricting the expression of non-ZGA genes within a permissive chromatin environment.

overall_design: Single cell experiments were performed in mouse ESCs or human iPSCs with or without curaxin treatment

first: Shireen

last: Shajahan

first: Jack-Christophe

last: Cossec


title: Gut Microbiota Metabolite Indole-3-Acetic Acid Maintains Intestinal Epithelial Homeostasis via the transcription factor AHR

city: Tianjin

first: Mengfan

last: Li

address: 154 Anshan Road, Heping District, Tianjin

institute: Tianjin Medical University General Hospital

summary: The incidence and prevalence of inflammatory bowel disease (IBD) is gradually increasing. A high-fat diet (HFD) is known to disrupt intestinal homeostasis and aggravate IBD, yet the underlying mechanisms remain largely undefined. Here, a positive correlation between dietary fat intake and disease severity in both IBD patients and HFD-fed mice is observed. HFD induces a significant decrease in indole-3-acetic acid (IAA) and lead to intestinal barrier damage. Furthermore, IAA supplementation enhances the intestinal mucin sulfation and effectively alleviates colitis. Mechanistically, IAA upregulates key molecules involved in mucin sulfation, including Papss2 and Slc35b3, the synthesis enzyme and the transferase of 3'-phosphoadenosine-5'-phosphosulfate (PAPS), via the Aryl Hydrocarbon Receptor (AHR). More importantly, AHR can directly bind to the transcription start site of Papss2. Oral administration of Lactobacillus reuteri, which can produce IAA, contributes to protecting against colitis and promoting mucin sulfation, while the modified L. reuteri strain lacking the iaaM gene (LactobacillusΔiaaM) and the ability to produce IAA fails to exhibit such effects. Overall, IAA enhances intestinal mucin sulfation through AHR, contributing to the protection of intestinal homeostasis.

overall_design: CUT&Tag was performed in the colonic tissues from mice treated with or without IAA and were incubated with the AHR antibody.


title: Transcriptomic Profiles of Bovine Mammary Epithelial Cells Under Heat Stress and During Subsequent Recovery

first: Guangsheng

state: NY

address: 507 Tower Rd.

department: Animal Science

institute: Cornell

summary: Heat stress (HS) poses a significant challenge to the dairy industry as it negatively affects milk production. However, the molecular mechanism behind mammary gland responses to HS and recovery remains poorly understood. This study aimed to determine the transcriptomic profile and uncover the underlying mechanism using RNA-sequencing and functional analysis in bovine mammary epithelial (MAC-T) cells. MAC-T cells were cultured in 6 groups: 1) basal (undifferentiated, unDiff) medium or 2) lactogenic (differentiated, Diff) medium for four days. Differentiated cells were subject to either 3) non-HS (37℃) or 4) HS (42℃) for 1hr. Two HS groups were further allowed to recover at 37℃ for 2 hr (D2R) and 6 hr (D6R).  Among six group comparisons, 1,668 differentially expressed genes (DEGs) were identified. HS vs. D6R groups yielded the highest number of DEGs, followed by HS vs. non-HS, and Diff vs. unDiff groups. Functional analysis suggested that differentiated cells exhibited upregulated genes associated with milk lipid synthesis, indicating their lactogenic state. Moreover, HS suppressed cellular differentiation and activated several heat shock protein (HSP) genes. Additionally, several transcription factors were identified as potential positive or negative regulators of HS response. During recovery, chaperon-mediated protein folding remained elevated and apoptosis regulation was induced after 2 hr. After 6 hrs, response to oxidative stress and cellular homeostasis regulation were enriched.  Overall, differentiated MAC-T cells enriched genes in lipid synthesis activities. HS triggered heat shock response and protein misfolding while impaired cellular differentiation in differentiated MAC-T cells. Furthermore, MAC-T cells demonstrated dynamic recovery responses, including regulations on apoptosis and hypoxia

overall_design: RNA-seq and functional analyses were used to detect the differentially expressed genes and pathways in MAC-T cells under differentiation, heat stress, and during recovery

first: Xingtan

last: Yu

first: Rebecca

last: Harman

first: Nikola

last: Danev

first: Yifei

last: Fang

first: Gerlinde

last: Van de Walle

first: Jingyue

last: Duan


title: Integrated transcriptomic, epigenetic, and TCR clonality analysis of CD4⁺ Tm subsets in liver and lung during chronic GVHD in mice [ATAC-seq]

summary: Pathogenic CD4+  T cells perpetuate chronic tissue inflammation, but mechanisms remain largely undefined. Here, with transcriptome, epigenome, and clonal analysis, we compared CD4+Tm subsets among the liver and lung  in the No GVHD and cGVHD recipients. Four CD4+Tm subsets identified with Ly108 versus CD69 expression were compared.

overall_design: cGVHD mice were established with BALB/c recipients in receiving graft from B6 donors. CD4+T cells from lungs of cGVHD mice were enriched at day 60 after HCT and four Tm subsets were sorted with Ly108 vs CD69 expression among H2Kb+TCRb+CD4+ cells. Cell quality were checked and processed for ATAC-seq.


title: Integrated transcriptomic, epigenetic, and TCR clonality analysis of CD4⁺ Tm subsets in liver and lung during chronic GVHD in mice [scTCR-seq]

overall_design: cGVHD mice were established with BALB/c recipients in receiving graft from B6 donors. Livers were harvested at day 60 after HCT. H2Kb+TCR+CD4+T cells from livers of cGVHD mice were sorted for scRNA-seq and scTCR-seq.


title: Genome-wide DNA methylation mediates alternative transcripts

city: Guangzhou

first: Huichuan

state: Guangdong

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

summary: We demonstrate that DNA m5C methylation may present alternative transcription starting positions on a genome-wide scale by showing widespread effect on alternative transcripts in response to the demethylation agents 5aza.

overall_design: Examination of transcripts following 5aza treatment in HCT116 cells.

first: Xiaolin

last: Wang

first: Yanxin

last: Luo


title: Whole genome bisulfite sequencing of peach fruits

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

type: Methylation profiling by high throughput sequencing

summary: Using whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in peach fruits (Prunus persica) in six different stages.

overall_design: 6 samples examined: Pp1, Pp2, Pp3, Pp4, Pp5, and Pp6 (each sample has two replicates).

first: Kai

last: Tang

first: Zhaobo

last: Lang


title: Whole genome bisulfite sequencing of pear fruits

summary: Using whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in pear fruits ( "Suli", Pyrus bretschneideri Rdhd. ) in four different stages.

overall_design: 4 samples examined: Pb1 (130 DAB); Pb2 (157 DAB); Pb3 (184 DAB); Pb4 (200 DAB). [DAB: days after bloom]

first: Huan

last: Huang

first: Ruie

last: Liu

first: Qingfeng

last: Niu


title: Whole genome bisulfite sequencing of apple fruits

summary: Using whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in apple fruits ( Malus x domestica Borkh. ) in four different stages.

overall_design: 4 samples examined: Md1 (120 DAB); Md2 (145 DAB); Md3 (166 DAB); Md4 (190 DAB). [DAB: days after bloom]


title: GATA6 coordinates cross‑talk between BMP10 and oxidative stress axis in pulmonary arterial hypertension

status: Public on Dec 10 2025

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Pulmonary arterial hypertension (PAH) is a life-threatening condition characterized by a progressive increase in pulmonary vascular resistance leading to right ventricular failure and often death. Here we report that deficiency of transcription factor GATA6 is a shared pathological feature of PA endothelial (PAEC) and smooth muscle cells (PASMC) in human PAH and experimental PH, which is responsible for maintenance of hyper-proliferative cellular phenotypes, pulmonary vascular remodeling and pulmonary hypertension. We further show that GATA6 acts as a transcription factor and direct positive regulator of anti-oxidant enzymes, and its deficiency in PAH/PH pulmonary vascular cells induces oxidative stress and mitochondrial dysfunction. We demonstrate that GATA6 is regulated by the BMP10/BMP receptors axis and its loss in PAECs and PASMC in PAH supports BMPR deficiency. In addition, we have established that GATA6-deficient PAEC, acting in a paracrine manner, increase proliferation and induce other pathological changes in PASMC, supporting the importance of GATA6 in pulmonary vascular cell communication. Treatment with dimethyl fumarate resolved oxidative stress and BMPR deficiency, reversed hemodynamic changes caused by endothelial Gata6 loss in mice, and inhibited proliferation and induced apoptosis in human PAH PASMC, strongly suggesting that targeting GATA6 deficiency may provide a therapeutic advance for patients with PAH.

overall_design: Human pulmonary arterial endothelial cells (HPAECs) were treated with scrambled siRNA control or siRNA directed against GATA6 to profile changes in gene expression resulting from GATA6 depletion.

first: Tetsuo

last: Toyama

first: Maria

last: Trojanowska


title: Apoe3 Enhances Acetylcholine Receptor Clustering via Lrp4

city: Richmond

first: Michael

last: McClure

state: VA

address: 601 W. Main St.

institute: Virginia Commonwealth University

summary: C2C12 myoblasts were co-cultured with NSC-34 motor neurons. Both muscle cells and motor neurons were isolated and RNA collected for sequencing.

overall_design: C2C12 myoblasts were co-cultured with NSC-34 motor neurons for 3 days. At endpoint, cells were collected in Trizol and sequenced using Nanopore Oxford minION sequencing.

first: James T

last: Redden

first: Sophie

last: Kothe

first: David J

last: Cohen

first: Zvi

last: Schwartz

first: Michael J


title: Global transcriptome analysis of IL-33, IL-25, IL-13, TSLP, IL-4, and IL-9 overexpression in mouse spleen

city: Tarrytown

first: Kaitlyn

last: Gayvert

address: 777 Old Saw Mill River Rd

department: Molecular Profiling & Data Science

institute: Regeneron Pharmaceuticals

summary: IL-33 is an inflammatory cytokine contributing to asthma, Chronic Obstructive Pulmonary Disease (COPD), and autoimmune diseases. Although recent studies suggest that IL-33 can induce the generation of autoantibodies, the role of IL-33 on B cell maturation and tolerance is poorly understood. Here, by inducing systemic overexpression of IL-33 in mice, we show that this cytokine induces the IL-5 and CD4 T cell-dependent accumulation of plasmablasts and plasma cells of all isotypes in the spleen, and leads to an increased antibody production. IL-33 also disrupts splenic architecture and elevates autoantibody production, indicating a break in peripheral tolerance. Consistently, elevated levels of IL-33 exacerbate autoantibody production, kidney damage, and decrease survival in a mouse model of lupus. Additionally, intranasal delivery of IL-33 in mice exposed to house dust mite extract (HDM) increases autoantibodies in the lung. Notably, blocking IL-33 reduced the autoantibodies generated during HDM exposure, indicating that HDM-induced autoantibody production is IL-33 dependent.  Thus, our findings implicate IL-33 in the break of peripheral B cell tolerance, opening new therapeutic avenues for the treatment of infection, COPD and autoimmune conditions.

overall_design: To evaluate the overall impact of IL-33 overexpression in spleen, we performed unbiased global transcriptome analysis following IL-33 HDD and analyzed cell type enrichment. These effects were compared to overexpression of other cytokines (L-25, IL-13, TSLP, IL-4, and IL-9).

first: Wei Keat

last: Lim

first: Eva

last: Conde Garcia


title: Müller cell glutamine metabolism links photoreceptor and endothelial injury in diabetic retinopathy

city: Chicago

first: Katia

last: Corano Scheri

state: IL

address: 300 E. Superior St.

department: Ophthalmology, Feinberg School of Medicine

institute: Northwestern University

summary: We characterized the timeline of molecular dysfunction in diabetic retinopathy (DR) and diabetic retinal disease (DRD) by studying the streptozotocin (STZ)-induced mouse retina over the course of 6 months of diabetes. We performed bulk RNA-Seq on endothelial and retinal cells, separately, at 1, 3 and 6 months of diabetes and single-cell RNA-Seq (scRNA-Seq) at 3 months. Transcriptomic changes were validated by in vitro, and ex vivo assays and immunohistochemistry of mouse and human tissue. Bulk RNA-Seq revealed inflammation in endothelial cells at 1 month. At 3 months, scRNA-Seq identified glutamine-driven anaplerotic dysfunction in Müller cells, confirmed by retinal culture. We posited this glutamine deficiency would impact the photoreceptors and endothelial cells. We validated this hypothesis using endothelial cells in vitro, and immunohistochemistry of disrupted photoreceptor ribbon synapses in mouse and human diabetic retinas. Additionally, glutamine deprivation increased expression of apoptotic genes in endothelial cells. At 6 months, we observed significant downregulation of angiogenic pathways and elevated profibrotic markers. Our results suggest that dysfunction of the metabolic ecosystem linking the Müller-photoreceptor-endothelial cells is central to the early stages of DRD pathogenesis, impacting photoreceptor synapses and endothelial cells, before the appearance of the classic microvascular features of DR.

overall_design: Bulk RNA-seq on endothelial and retinal cells (analyzed separately) from sham and STZ-diabetic mice at 1, 3, and 6 months of diabetes, and single-cell RNA-seq at 3 months of diabetes (sham vs. STZ)

first: Yi-Wen

last: Hsieh

first: Thomas

last: Tedeschi

first: James

middle: B

last: Hurley

first: Amani

last: Fawzi


title: Single-cell RNA sequencing of a lung metastasis and normal lung tissue from a breast cancer patient.

city: Darlinghurst

first: Leila

last: Eshraghi

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary: The estrogen receptor (ER) drives growth in most breast cancers. Endocrine therapy reduces recurrence, however around 30% of cancers relapse. Many recurrences occur years later, with slowly proliferating, hard-to-treat disease. To study this, we generated slow-growing resistant cells that form small primary tumours but readily metastasize. Single-cell RNA sequencing (scRNAseq) revealed that endocrine therapy reprograms these cells, notably upregulating the Rac1 signalling component P-Rex1. We found in clinical cohorts that P-Rex1 is high in ER+ breast cancer, including in late recurrent disease.

overall_design: Samples were collected from a patient with ER+ metastatic breast cancer. Samples were collected through the MonARC Program, approved human ethics protocol SVH17/173 with informed consent, and analysed under the Personalized Medicine for Breast Cancer study, protocol x19-0496. Normal and tumour single-cell suspensions from patient's lungs were prepared, captured on 10X Genomics platform and sequenced on Illumina NextSeq 500. Raw sequencing data were demultiplexed and aligned to GRCh38 genome with Cell Ranger software (version 3.1.0), normalised with Seurat (v.3.1.2) in R (v.3.6.1), and visualised with Loupe Browser 5.1.0.  ***Raw Data Disclaimer: Raw human data files are deposited to the EGA (EGAS00001008353) to adhere to ethics.***

first: C

last: Caldon


title: Integrated transcriptomic, epigenetic, and TCR clonality analysis of CD4⁺ Tm subsets in liver and lung during chronic GVHD in mice [scRNA-seq]

first: Xiwei

last: Wu

first: Defu

last: Zeng

first: Xiaohui

last: Kong

first: Hyejin

last: Cho


title: E. coli Pathobionts and Crohn’s Disease:  Varied genetic paths leading to similar phenotypes

city: Bethesda

first: Melissa

last: Arroyo-Mendoza

state: MD

address: 8 CENTER DR RM 2A11

department: LBG

institute: NIDDK

summary: Crohn’s disease (CD), an inflammatory bowel disease that arises from an immune attack of the GI tract, affects roughly 1.6 million Americans. The etiology of CD and the other major irritable bowel disease, ulcerative colitis, is not known, but host genetics and immunology, the gut microbiome, and environmental factors are all thought to be involved.  In addition, Adherent Invasive Escherichia coli (AIEC) strains are frequently found to be associated with CD.  Key features distinguish AIEC from commensal E. coli, including adherence/invasion of the intestinal epithelium, increased biofilm formation, increased antibiotic resistance, and survival/replication within macrophages. However, these pathobionts lack genetic features typical of frank pathogens.  Thus, the potential role AIEC play in CD pathogenesis is not clear.  The E. coli pathobiont LF82, isolated from ileum of a patient with CD, has been a well-studied, prototypic AIEC. Dozens of single nucleotide polymorphisms (SNPs) distinguish LF82 and other AIEC from commensal E. coli, suggesting that some of these genetic features might account for particular LF82 phenotypes. In this review, we summarize changes in the CD gut, the association of AIEC with CD, genes and SNPs associated with AIEC, and recent work connecting a specific SNP within a bacterial RNA polymerase gene to the expression of genes associated with the LF82 lifestyle.

overall_design:
To investigate the effect of a rare mutation found in the rpoB of E. coli LF82, isogenic LF82 WT and rpoB E1263A mutant were created.
Gene expresion profilling analysis was performed using the data that was obtained from the RNA-seq of the isogenic pairs that were grown in triplicate. Comparative gene expression profilling analysis of the RNA-seq data for the LF82 isogenic pairs and E.coli MG1655 isogenic pairs (WT and rpoB E1263A mutant) grown at 37o C was performed
Comparative gene expression profilling analysis of the RNA-seq data for the LF82 isogenic pairs (WT RNA-Seq has already been submited GEO: GSE253924, Bioproject: PRJNA1067676) grown at 37o C was performed.

first: Hernan

last: Lorenzi

first: Gregory

last: Phillips

first: Deborah

last: Hinton


title: Grassystatin G, a new cathepsin D inhibitor from marine cyanobacteria: discovery, synthesis, and biological characterization

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

institute: UNIVERSITY OF FLORIDA

summary: Through ongoing investigations of marine cyanobacteria, a prolific source of structurally diverse secondary metabolites, we isolated grassystatin G (1), a new statine-containing linear peptide, closely related to the cathepsin E (CatE) inhibitors grassystatins A–F, some of which may function as CatE probes. The planar structure of 1 was determined by analysis of 1D, 2D NMR and MS/MS fragmentation data, and is structurally distinct from its analogs by being shorter and containing a hydrophobic residue (Val) adjacent to the statine unit instead of a polar residue (Asn, Gln). We employed chiral HPLC analysis and modified Marfey's method to assign the absolute configuration of constituent amino acids, suggesting the presence of N-Me-L-Phe instead of N-Me-D-Phe in other grassystatins. To prove the structure and overcome the lack of material for further biological studies and mechanistic characterization, we developed a 3 + 3 convergent synthesis and have accessed the peptide with an overall yield of 19% using standard peptide coupling. As the statine moiety is a known pharmacophore with an inhibitory effect against aspartic proteases, we screened grassystatin G against a panel of human and virus aspartic proteases. In contrast to grassystatins A–F, preferentially targeting CatE over CatD with 18–66-fold selectivity, grassystatin G displayed 2-fold selectivity for CatD over CatE, suggesting that the key structural differences may be exploited for CatD probe design. Docking and molecular dynamics provided insights into the structural features responsible for the selectivity towards CatD. CatD is well-documented to play a role in cancer proliferation and metastasis, particularly in the context of breast cancer. We tested grassystatin G against MDA-MB-231 triple-negative breast cancer cells and demonstrated its cooperative effects with TRAIL. RNA-seq highlighted the potential pathways and molecular mechanisms governed by grassystatin G alone and in combination with TRAIL.

overall_design: RNA-seq of MDA-MB-231 treated with grassystatin G (40 μM), TRAIL (25 ng mL−1) and the combination of both at 6 h and 12 h.

first: Lobna

last: Elsadek

first: Hendrik

last: Luesch


title: Rat sperm small RNA following exposure to ethylene glycol monomethyl ether

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

summary: RNA-seq analysis was conducted as part of an experiment investigating the effects of ethylene glycol monomethyl ether (EGME), on rat sperm RNA. EGME is a testicular germ cell toxicant that selectively targets spermatocytes. This experiment used an established model in which rats are treated with EGME by daily oral gavage for 5 days, with no additional treatment for 5 weeks, which is the time required for spermatocytes to become mature spermatozoa. The goal of the study was to test which small RNAs in rat sperm are altered following EGME exposure at doses below those that cause testicular histopathology. Testicular histopathology is observed at doses of 100 mg EGME/kg/d and above; this experiment included a dose range of 0 (vehicle), 50, 60, and 75 mg EGME/kg/d.

overall_design: Adult male Fischer rats were treated with 0 (water vehicle), 50, 60, or 75 mg EGME/kg/d in water vehicle, by oral gavage from for five days. Treatment was discontinued, and cauda epidiymal sperm was collected five weeks after cessation of exposure. Each biological replicate consists of total RNA extrated from cauda epidiymal sperm of a single male.

first: Angela

last: Stermer

first: August

last: Guang

first: Yuan

last: Pu


title: HIV-1 Infection Regulates Gene Expression by Altering Alternative Polyadenylation Through CPSF6 and CPSF5 Delocalization

city: Rochester

first: Eric

middle: John

last: Wagner

address: 575 Elmwood Avenue

department: Biochemistry and Biophysics

institute: University of Rochester Medical Center

summary: HIV-1 viral core transport to the nucleus, an early infection event, triggers cleavage and polyadenylation specificity factor (CPSF)5 and CPSF6 to translocate from paraspeckles to nuclear speckles, forming puncta-like structures. CPSF5 and CPSF6 regulate alternative polyadenylation (APA), which governs approximately 70% of gene expression. APA alters the lengths of mRNA 3’-untranslated regions (3’-UTRs), which contain regulatory signals influencing RNA stability, localization, and function. We investigated whether HIV-1 infection–induced changes in CPSF5 and CPSF6 subcellular localization are accompanied by changes in cellular function. Using two independent methodologies to assess APA in human primary CD4+ T cells and cell lines, we found that HIV-1 infection regulates APA, dependent on the interaction of CPSF6 with the viral capsid, recapitulating the APA phenotype observed in CPSF6 knockout cells. Our study demonstrates that HIV-1 infection leverages the interaction between the viral capsid and CPSF6 to co-opt cellular processes, alter gene expression, and drive pathogenesis.

overall_design: PAC-Seq profiling was employed to map global mRNA 3’-end changes in HIV-1–infected and mock-infected A549 cells

first: Charlotte

last: Luchsinger

first: Annie

last: Dai

first: Aiswarya

last: Balakrishnan

first: Cinzia

last: Bertelli

first: Bin

last: Cui

first: Ramon

last: Redondo

first: Felipe

last: Diaz-Griffero


title: The Dichotomy of Tumor Control by Recruited and Resident Tumor-Associated Macrophages

city: Denver

first: Sonia

last: Leach

state: Colorado

address: 1400 Jackson St

institute: National Jewish Health

summary: Macrophages are among the most abundant immune cells in solid tumors, yet how their diverse origins and spatial organization shape anti-tumor immunity remains unclear. Here, we uncover a fundamental division of labor between tissue-resident interstitial macrophage (IM) subsets and recruited macrophages (recMacs) in lung cancer. Using single-cell and spatial transcriptomics, we identify chemokine-defined IM subsets with opposing functions: Cxcl13-, Cxcl9-, and Cxcl10-producing CD206hi IMs positioned along bronchovascular regions drive tertiary lymphoid structure formation, lymphocyte recruitment, and tumor control, whereas Ccl2-expressing IMs localize within tumor regions and recruit pro-tumorigenic recMacs. We further show that recMac-derived moDCs function as immunosuppressive antigen-presenting cells in draining lymph nodes. During neoantigen vaccination, CCR5 inhibition with Maraviroc selectively blocks antigen-bearing monocyte but not dendritic cell migration, thereby enhancing dendritic cell-mediated tumor immunity. These findings reveal how macrophage ontogeny and spatial compartmentalization govern tumor immunity and point to therapeutic strategies that preserve protective IM functions while disrupting recMac-driven immunosuppression.

overall_design: Spatial transcriptomics were performed on four tumor-bearing lungs (two B16F10 melanoma, two KPAR1.3 adenocarcinoma) using the 10x Xenium platform and a targeted gene panel enriched for pan leukocytes, myeloid cells, chemokines, and stromal transcripts.

first: Soubhik

last: Ghosh

first: Xin

last: Li

first: Claudia

middle: V

last: Jakubzick


title: Sentinel flaps recapitulate key inflammatory aspects of human face transplant rejection

first: William

last: Crisler

state: Massachusetts

address: 221 Longwood Ave

department: Dermatology

institute: Brigham & Women's Hospital

summary: Sentinel flaps are used for remote-site monitoring in vascularized composite allotransplantation (VCA), but their molecular relationship to facial allografts during rejection has not been defined. We analyzed gene expression in formalin-fixed paraffin-embedded (FFPE) skin biopsies from facial allografts (FA) and sentinel flaps (SF) obtained from five face transplant recipients at Brigham and Women’s Hospital. Simultaneous 4-mm punch biopsies were collected from FA and SF sites during grade 0 (non-rejection) and grade 3 (acute rejection) episodes, yielding 14 matched pairs. RNA was extracted and profiled using the NanoString nCounter PanCancer Immune Profiling Panel (730 immune-related genes). Data were normalized to positive controls and housekeeping genes using NanoString nSolver v4.0. Differentially expressed genes were identified by comparing grade 3 versus grade 0 samples in FA and SF separately. These datasets provide transcriptional profiles of acute rejection in human face transplants and sentinel flaps for use in comparative and mechanistic studies.

overall_design: This study uses NanoString transcriptional profiling with the PanCancer Immune Profiling Panel (Accession #: GPL35924). Samples include formalin-fixed paraffin-embedded (FFPE) skin biopsies from facial allografts (n=14) and sentinel flaps (n=14) collected from five face transplant recipients. Simultaneous 4-mm punch biopsies were obtained from both sites during grade 0 (non-rejection) and grade 3 (acute rejection) episodes. Data were analyzed using nSolver v4.0 to compare grade 3 versus grade 0 samples within each tissue type.

first: Rachael

last: Clark


title: Functional Validation and Mechanistic Insights into Cadmium Removal by the Green Microalgae Coelastrella tenuitheca S93-3

city: Chengdu

first: xiumei

last: luo

address: Shuangliu

department: Institute of Urban Agriculture

institute: Chinese Academy of Agricultural Sciences

summary: Coelastrella tenuitheca strain S93-3 is a green microalga that demonstrates remarkable tolerance to heavy metal stress. It is a promising candidate for bioremediation applications, strongly resistant to cadmium, and an essential organism for phytoremediation studies. However, the molecular mechanism of the response of C. tenuitheca S93-3 to cadmium stress, and the key regulatory genes for specific detoxification processes are poorly understood.

overall_design: The isolated microalgal strain S93-3 cultured in modified BG-11 liquid media, containing a gradient of cadmium chloride (CdCl₂) concentrations: 5, 10, 15, 20, 25, 30, and 50 mg/L. All cultures were incubated under controlled conditions at 28°C with constant shaking at 150 rpm for a duration of 7 days. Growth was monitored daily by measuring OD₆₈₀ and assessing overall culture status. Dry biomass was quantified at the endpoint of the experiment. The half-maximal inhibitory concentration (IC₅₀)—the cadmium concentration required to reduce the dry biomass by 50% compared to the control—was calculated from this data.

first: Xiumei

last: Luo

first: Sawera

last: Akram


title: Engineering ATP Import in Yeast Uncovers a Synthetic Route to Extend Cellular Lifespan

city: Charlottesville

first: Alaattin

last: Kaya

state: Virginia

address: 1340 Jefferson Park Ave

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: Aging results from the gradual accumulation of molecular damage as a result of cellular processes and is characterized by impaired functions, most notably an age-related decline in ATP production. However, the causal relationship between cellular ATP homeostasis and aging has not been established. In this study, we used a novel approach by harnessing a nucleotide transporter from a eukaryotic intracellular parasite to facilitate the direct import of extracellular ATP into budding yeast cells, enabling us to effectively manipulate their intracellular ATP levels. We found that depletion of ATP significantly reduces lifespan, while the supplementation of ATP in the growth medium fully restores it thereby extending lifespan. Moreover, gene expression analysis revealed that elevated ATP levels inhibit catabolic processes, indicating a suppression of glucose metabolism. Overall, our study revealed the direct impact of cellular ATP homeostasis on lifespan regulation that has never been directly tested before. This work offers new insights into the bioenergetic control of aging and positions energy metabolism as a promising target for longevity interventions.

overall_design: Yeast strains expressing the Encephalitozoon cuniculi nucleotide transporter NTT1 or empty-vector controls were grown in complete synthetic medium to mid-log phase. Cells were either left untreated or treated with 5 mM extracellular ATP for 1 hour, and total RNA was extracted for RNA-seq analysis. Three independent biological replicates were collected per strain and treatment condition.

first: Naci

last: Oz

first: Hetian

last: Su

first: Vedat

last: Sari

first: Praveen

last: Patnaik

first: Rohil

last: Hameed

first: Jong

middle: H

last: Song

first: Derek

middle: C

last: Prosser

first: Vyacheslav

last: Labunskyy

first: Vadim

middle: N

last: Gladyshev

last: Hao


title: Up-regulation of an epithelial miRNA is associated with immune evasion in progressive bronchial premalignant lesions [PCGA_miRNA_BR]

first: Adam

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: Bronchial premalignant lesions (PMLs), precursors of lung squamous cell carcinoma, have distinct molecular subtypes. The proliferative subtype, enriched with bronchial dysplasia, had decreased expression of an antigen processing/presentation gene co-expression module in progressive/persistent versus regressive PMLs, suggesting a functional impact of these genes on immune evasion. Here, we performed miRNA sequencing, miRNA in situ hybridization (ISH), and spatial proteomics of bronchial biopsies from patients at high risk for lung cancer. A miRNA-gene network analysis identified hsa-miR-149-5p as a potential regulator of the antigen presentation gene module. Staining on adjacent biopsy tissue showed that hsa-miR-149-5p was predominantly expressed in the epithelium and up-regulated in progressive/persistent proliferative lesions.  Targets of this miRNA, the transcriptional coactivator of MHC-I gene expression, NLRC5, and the genes it regulates were down-regulated in these lesions. Decreased NLRC5 expression reduced both IFN-gamma induced MHC-I surface expression and CD8 T cell cytotoxicity in lung squamous cancer cells.  In PMLs, basal cells with high levels of NLRC5 were in close spatial proximity to CD8 T cells, suggesting that these cells exhibit increased functional MHC-I gene expression in vivo. These findings indicate a functional role for hsa-miR-149-5p in PML progression/persistence and suggest this axis as a potential therapeutic target for PML immunomodulation.

overall_design: microRNA sequencing (miRNA-seq) was performed in bronchial brushings obtained from patients at high risk of lung cancer.

first: Boting

last: Ning

first: Darren

last: Chiu

first: Jennifer

last: Beane


title: Sox11 overexpression restores embryonic pro-growth transcription in mature corticospinal tract neurons [snRNA-Seq]

city: Milwaukee

first: Murray

last: Blackmore

state: WI

address: 561 N 16th St

department: Biomedical Sciences

institute: Marquette University

summary: Neurons in the central nervous system (CNS) display a high capacity for axon growth during early development but mostly lose this ability during a key stage of differentiation marked by synaptic maturation, circuit integration, and a profound shift in gene transcription. Once mature, neurons largely fail to reverse this transcriptional switch after axon injury, fundamentally constraining their intrinsic capacity for repair. Here, we show with single-nucleus RNA sequencing that forced expression of the transcription factor Sox11 in adult corticospinal tract neurons produces large-scale and stable changes in gene expression that are highly enriched for growth-relevant processes, and which strongly resemble those of pre-synaptic embryonic stages. Moreover, Sox11 is equally effective when delivered to chronically injured CST neurons. These data reveal Sox11’s ability to reverse a critical step of neuronal maturation even in otherwise unperturbed neurons, clarifying the transcriptional underpinnings and highlighting Sox11’s potential as a pro-regenerative stimulus.

overall_design: In adult mouse samples, corticospinal tract (CST) neurons were transduced with a retrograde, nuclear-localized fluorophore (mGl) and control or Sox11-expressing virus by retrograde transduction from cervical spinal cord. Animals recevied either no injury or a cervical contusion injury six weeks prior to tissue collection. Animals that received Sox11 and no injury were collected at four time points: 1 week, 2 weeks, 4 weeks, or 6 weeks after viral delivery, with each time point uniquely barcoded and pooled in the same sequencing reaction. Embryonic cortex was collected at embryonic day 18. For all samples, single nucleus RNA sequencing was performed. Adult samples were pre-purified using fluorescent activated nuclei sorting prior to library preparation. E18 embryonic libraries were prepared from ixed cortical tissue.

first: Elizabeth

last: Batsel

first: Zimei

last: Wang

last: Otten

first: Rabia

last: Mohammad

first: Paula

last: Pascal

first: Darby

last: O'Shea

first: Jose

last: Rosas

first: Pantelis

last: Tsoulfas


title: Up-regulation of an epithelial miRNA is associated with immune evasion in progressive bronchial premalignant lesions [PCGA_miRNA_BX]

overall_design: microRNA sequencing (miRNA-seq) was performed in bronchial biopsies obtained from patients at high risk of lung cancer.


title: Up-regulation of an epithelial miRNA is associated with immune evasion in progressive bronchial premalignant lesions.

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

overall_design: Refer to individual Series


title: Single-cell transcriptomic analysis demonstrates decreased TNF signaling in patients receiving BAF312 during intracerebral hemorrhage

city: New Haven

first: Jonathan

middle: Howard

last: DeLong

state: CT

address: 300 George St Ste 353

department: Neurology

institute: Yale University

summary: Single cell RNA sequencing of PBMC collected at days 1, 3, and 7 after intracerebral hemorrhage from 5 patients treated with the immunomodulatory drug BAF312 (Siponimod) and 2 patients treated with a placebo control.

overall_design: Patient blood was shipped overnight, then PBMC were isolated and frozen. Samples were thawed and live cells were sorted by flow cytometry. Single cell RNA sequencing was performed utilizing the 10X Genomics platform.

first: Sebastian

last: Díaz-Pérez

first: Kevin

last: Sheth

first: Jang-Ho

last: Cha

first: CJ

last: Malanga

first: Patricia

last: Wagner

first: Nicole

last: Pezous

first: Aurelie

last: Hanin

first: Kyle

last: Walsh

first: H

last: Hinson

first: Lauren

last: Sansing


title: CAD-C reveals the near-perfect alignment of sister chromatids

city: New York

first: Axel

last: Delamarre

address: 411 E 67th st

institute: MSKCC

summary: Three-dimensional (3D) genome organization plays a central role in gene regulation, chromatin folding, and genome stability. Although chromosome-conformation capture (3C)–derived methods have revolutionized our understanding of genome architecture, most remain limited in resolution, in their capacity to detect multiway interactions and in their ability to distinguish sister chromatids. Here, we present CAD-C, a new chromatin-conformation capture strategy that uses Caspase-Activated DNase (CAD) chromatin fragmentation. The fragmentation of chromatin to the nucleosome level by CAD digestion substantially enhance the proximity ligation efficiency, enabling formation of multi-nucleosome ligation products. Nanopore sequencing of these long DNA molecules allows reconstruction of chromatin fiber connectivity and 3D contact maps at nucleosome-level resolution. CAD-C furthermore captures multiway interactions. Importantly, CAD-C is also able to identify sister-chromatid interactions at the nucleosome resolution which reveals a surprisingly tight, nucleosome-scale register of cohesion in G2 in S. cerevisiae. Together CAD-C overcome several limitations of 3C approaches and is the first assay to distinguish sister chromatids interactions at the nucleosome level.

overall_design: CAD-C of yeast cells synchronized in G1 or G2, and with inducible depletion of the Scc1 subunit of Cohesin using the AID system. Datasets includes high-resolution interaction maps. And Bigwig profile of sister nucleosome overlap.

first: Maurane

last: Reveil

first: David

last: Pintor Pichon

first: Neeman

last: Mohibullah

first: Michael

last: Boemo

first: Iestyn

last: Whitehouse


title: Single-cell transcriptome uncovers heterogeneity and distinct states of ileum between suckling and early-weaning piglets

city: Hangzhou

first: Wenjie

last: Tang

address: Yuhangtang Road

institute: Zhejiang university

summary:
We set out to better understand the cellular heterogeneity and niche cues of the remodeling porcine intestine after weaning by performing single-cell mRNA sequencing (scRNA-seq) survey of 42,149 cells from ileum tissue in piglets. Substantial heterogeneity among diverse epithelial, stromal, and immune cell subsets was observed. We map the various cell committed state within ileum tissue, and connect them through cell-cell interactions. We delineated a new classification of different epithelium secretory cells. Apart from goblet cell and enteroendocrine cell, we found that few pH-sensing BEST4/OTOP2 cells also exist in the ileum13. The immune component of early-weaned piglet was shifted as reduction of Th17 and abundance of CTL. Th17 cells harbor features of classical phonotype in normal suckling piglet (NSP) and pathogenicity in early weaning piglet (EWP), which may be induced by special cytokine milieu suggested as previous stduy14,15. We conclusively showed enrichment of the pathogenic effector CD8+ GZMB+ CTL cells may be a critical factor exacerbating ileal inflammation via mitochondrial dysfunction inducing epithelia cell apoptosis in EWP.

Keywords: Expression profiling by high throughput sequencing

overall_design:
Three litters (Landrace x Yorkshire, 12 piglets per litter) were selected. At 21 d of age (pre-weaning stage), piglets of each litter were randomly allotted to two groups (n = 6) as follows: the EWP group was moved in farrowing barn without sow; the NSP group was continuously nursed by sows during full-trial period.

>>>Submitter reports that the included samples of droplet-based single cell RNA-seq experiments also captured ambient mRNA present in the input solution.<<<

first: Haifeng

last: Wang


title: Extracellular vesicle-based targeted protein degradation platform for multiple extracellular proteins

city: Wuhan

first: Bide

last: Tong

state: Hubei

address: Jiefang Avenve 1277, Jianghan District, wuhan

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Targeted protein degradation (TPD) is an emerging therapeutic approach that enables the degradation of undruggable targets via intracellular degradation systems. Extracellular vesicles (EVs) have shown potential to act as next-generation TPD platforms. However, the molecular mechanism underlying their degradation remains unknown, which restricts their application in TPD. In this study, we found that the autophagy-mediated lysosomal pathway was the major route by which EVs were degraded. MAP1LC3B recognized the LIR motifs of SQSTM1 and induced the degradation of EVs in the autophagy pathway. Based on the EV degradation mode, we developed an EV-based targeted protein degradation platform (EVTPD) using EVs loaded with the LIR motif of SQSTM1 as a degradation signal. Additionally, target protein-binding domains were integrated into the EVTPD to capture target proteins. EVTPD selectively degraded extracellular proteins without requiring receptors on target cells. Furthermore, dual-targeting EVTPD effectively degraded both TNF-α and IL-1β and exhibited potent anti-inflammatory effects in a rat and goat models of intervertebral disc degeneration. This study has established a modular EV-based TPD strategy with multi-targeting potential.

overall_design: We used RNA-seq to elucidate the remodeling of transcription patterns in NPCs following T/I-EVTPD administration.

first: Cao

last: Yang


title: Time-series RNA-seq analysis reveals dynamic transcriptional responses and crosstalk in chronic lymphocytic leukaemia (CLL) autologous and monoculture in vitro models

city: Toulouse

first: Vera

last: Pancaldi

address: 2 Avenue Hubert Curien

institute: Toulouse Cancer Research Center (CRCT)

summary: Chronic lymphocytic leukaemia (CLL) cells were cultured either within autologous peripheral blood mononuclear cells (PBMCs) or as purified monocultures and sampled at five time points (days 1, 4, 8, 11 and 14) to capture dynamic transcriptional programs during ex vivo activation and survival. Time-series RNA-seq was performed on 60 samples derived from three patients (DAR, SAS, PRG), enabling the reconstruction of gene expression trajectories and identification of signalling pathways contributing to CLL activation, immune crosstalk and prolonged viability.

overall_design: RNA-seq profiling of autologous PBMC cultures and purified B-CLL cell monocultures from 3 CLL patients over a 14-day time course (days 1, 4, 8, 11, 14).

first: Hugo

last: Chenel

first: Malvina

last: Marku


title: M1 and M2 myeloid cells behave differently in classical immune type contexts

first: Sonia

middle: M

last: Leach

summary: Macrophages maintain tissue homeostasis and act as first responders to immune threats. A central question is whether these cells exhibit transcriptional plasticity in vivo. We tested macrophage polarization across classical type 4 immunity using a B16F10 melanoma model.

overall_design: Single-cell RNA sequencing data were obtained from mouse pulmonary cells 16 days post-iv injection of 400,000 B16F10 melanoma cells. Three samples were loaded on separate lanes, where each loaded sample contained 3 pooled lungs.

first: Soubhik

last: Ghosh

first: Xin

last: Li

first: Claudia

last: Jakubzick


title: Gene Expression in Submandibular Glands of Sjögren's Syndrome Mouse Models

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Mesenchymal stem cells (MSCs) demonstrate significant therapeutic potential for Sjögren's syndrome (SS) owing to their remarkable immunomodulatory properties. However, the underlying molecular mechanisms governing their therapeutic effects remain incompletely understood. In this study, we employed  DNA microarray-based transcriptomic profiling and comprehensive bioinformatic analyses to systematically elucidate the molecular basis of BM-MSC-mediated therapeutic effects in SS. Our investigation specifically focused on identifying critical signaling pathways and hub regulatory genes involved in this process.

overall_design: The SMGs were collected from BMSC and PBS-treated mice. Total RNA was extracted using TRIzol Reagent (15596026, Invitrogen, CA, USA) and purified with the RNeasy MinElute kit (74204, Qiagen, Hilden, Germany). RNA quality was verified via UV absorption and denaturing agarose gel electrophoresis. Gene expression was then assessed using GeneChip Mouse Gene 1.0 ST Array (Thermo Fisher Scientific, 901169, CA, USA), following standard procedures for cDNA synthesis, fragmentation, biotin labeling, hybridization, and signal scanning. Differential gene expression was determined using fold-change (FC) analysis to identify significantly up/downregulated genes.

first: Zhifang

last: Wu


title: Gene expression analysis of non-clear-cell renal cell carcinoma and clear-cell renal cell carcinoma kidney cancers

city: Tokyo

first: Yu-Yu

last: Liu

address: 5-1-1 Tsukiji, Chūō district

institute: National Cancer Center Research Institute

summary: Data regarding the clinical outcomes of immune checkpoint inhibitor (ICI) therapy and profiles of the tumor immune microenvironment (TIME) in non-clear-cell renal cell carcinoma (nccRCC) remain limited. Here, we retrospectively compared the effectiveness profiles of first-line ICI combination therapy between patients with clear-cell RCC (ccRCC) and those with nccRCC.

overall_design:
RNA-seq of non-clear-cell renal cell carcinoma and clear-cell renal cell carcinoma kidney cancers
Please note that cancer subtype information is provided in the "tissue" field. The  treatment details and clinical outcomes of ICI therapy are presented in the associated publication.

first: Hiroki

last: Ishihara

first: Hironori

last: Fukuda


title: Metabolomic Profiling Reveals the Potential of Fatty Acids as Regulators of Exhausted CD8 T Cells During Chronic Viral Infection

city: La Jolla

first: Katelynn

middle: Rose

last: Kazane

state: CA

address: 9500 Gilman Drive, #0329

department: Biological Sciences

institute: University of California San Diego

summary: Chronic infections induce CD8 T cell exhaustion, marked by impaired effector function. While intrinsic drivers are well studied, the role of the surrounding metabolic environment in shaping exhausted CD8 T cells (Tex) is less understood. Using untargeted metabolomics and the murine lymphocytic choriomeningitis virus infection model we investigated systemic metabolite changes following acute versus chronic viral infections. We identified distinct short-term and persistent metabolite shifts, with the most significant differences occurring transiently during the early phase of the sustained infection. This included nutrient changes that were partially associated with CD8 T cell-induced anorexia and lipolysis. One remarkable observation was the elevation of medium- and long-chain fatty acid (FA) and acylcarnitines during the first week after chronic infection. Consistently, virus-specific CD8 T cells from chronic infection exhibited increased lipid accumulation and uptake compared to their counterparts from acute infection, particularly the stem-like Tex (TexSTEM), which generates TexINT that directly limit viral replication. Notably, only TexSTEM increased oxidative metabolism upon ex-vivo FA exposure, while short-term administration of FA during late chronic infection exclusively increased TexSTEM and their mitochondrial potential. The last-mentioned treatment also led to reduced TexINT and enhanced PD-1 across all Tex subsets, which coincided with compromised viral control. Our study offers a valuable resource for investigating the regulatory role of specific metabolites during acute and chronic viral infections and highlights the potential of FA to fine-tune Tex subsets during protracted infections.

overall_design: RNA-seq profiling of splenic T cell subsets isolated from female C57BL/6 mice infected with  LCMV Clone 13. Ex vivo samples were isolated at day 8 post-infection and incubated in BSA (Untr) or BSA-palmitate (FA) for 8 hours. In vivo samples were isolated at day 21 post-infection after treatment with PBS (Untr) or a 1:1 mix of palmitic and lauric acid (FA).


title: Effects of neuron-derived a-synuclein in oligodendrocytes [RNA-Seq]

city: Seoul

first: Eun-Jin

last: Bae

address: 103 Daehak-ro

country: South Korea

institute: Seoul National University

summary: Synucleinopathies, including multiple system atrophy (MSA) and Parkinson's disease (PD), are characterized by intracellular accumulation of α-synuclein (αSyn) aggregates. Despite oligodendrocytes' low expression of αSyn, αSyn aggregates in MSA cause glial cytoplasmic inclusions (GCIs). Here, we show that GCI development is facilitated by αSyn propagation from neurons to oligodendrocytes via Toll-like receptor 2 (TLR2). Demyelination-related characteristics in MSA oligodendrocytes and experimental models were identified by transcriptome studies. NM-101 treatment reversed the demyelination phenotype in the transgenic mouse model. These results point to anti-TLR2 immunotherapy as a possible MSA disease-modifying strategy.

overall_design: RNA sequencing profiling cells from mice brain

first: Yeonwoo William

last: Jeong

first: Seung-Jae

last: Lee


title: Effects of neuron-derived a-synuclein in oligodendrocytes [scRNA-Seq]


title: Single cell transcriptomics analysis of the effect of S100a4 knockout on psoriasis

city: Xinjiang Uygur Autonomous Region

first: Huiqin

last: Wang

address: No. 91 Tianchi Road, Tianshan District, Urumqi, Xinjiang Uygur Autonomous Region

institute: People's Hospital of Xinjiang Uygur Autonomous Region

summary: We employed single-cell RNA sequencing to investigate the pathophysiology of psoriasis and the molecular mechanisms of S100a4 by analyzing alterations in cellular heterogeneity and composition in dorsal skin tissue from differentially treated mice.

overall_design: We generated a global S100a4 knockout mouse model and designed three experimental groups to evaluate the effect of S100a4 knockout on psoriasis: 1) sham-control group with Vaseline application (non-lesional); 2) imiquimod (IMQ)-induced psoriasis group (lesional wild-type); and 3) S100a4 knockout group with IMQ application post-knockout (lesional S100a4 knockout). We selected three independent biological replicates from each of three separete groups to isolate the dorsal skins, and then prepared single-cell suspensions for single-cell transcriptomic sequencing.

first: Weidong


title: Inhibition of PAK2 in endothelial cells suppresses tumor angiogenesis and promotes immune sensitization through CXCL10

city: Montreal

first: Jean-Philippe

last: Gratton

address: 2900 Bd Edouard-Montpetit

institute: Université de Montréal

summary: Tumor angiogenesis is driven by pro-angiogenic factors and results in a disorganized tumor vasculature that limits effective perfusion and immune infiltration. The p21-activated kinase 2 (PAK2) regulates endothelial cell (EC) migration, an essential step of angiogenesis, yet its role in tumor angiogenesis remains ill-defined. Here, we show that endothelial-specific deletion of PAK2 in orthotopic tumor mouse models markedly reduces tumor size and angiogenesis. Loss of endothelial PAK2 also normalizes the remaining tumor vasculature and promotes infiltration of dendritic and NK cells. Mechanistically, PAK2 regulates chemokine expression, notably CXCL10. PAK2 depletion enhances CXCL10 secretion from ECs, and CXCL10 expression is required for the inhibitory effects of PAK2 silencing on EC spouting. Moreover, CXCL10 neutralization in mice reverses the vascular and immune changes induced by endothelial PAK2 deletion. Together, these findings identify endothelial PAK2 as a potential target to limit tumor angiogenesis and reprogram ECs to promote immune infiltration through CXCL10 signaling.

overall_design: RNA-seq of CT-PAK2EC and KO-PAK2EC LLC tumors in mice at day 18 of tumor growth. RNA-seq of siCT and siPAK2-transfected HUVEC, and RNA-seq of siCT, siPAK2, siCXCL10 and siPAK2-siCXCL10 transfected HUVEC

first: Corriveau

last: Jeanne

first: Monot

last: Pascale

first: Delisle

last: Chantal

first: Goyette

last: Marie-Anne

first: Gasse

last: Camille

first: El Bakkouri

last: Yassine

first: Hoang

last: Trang

first: Côté

last: Jean-François

first: Gratton

last: Jean-Philippe


title: Effect of Drs2 gene knockout on gene expression in Candida glabrata

city: shanghai

first: Geng

last: Lv

address: huangpuqu

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: To estiamte the role lipid flippase gene Drs2 plays in Candida glabrata, a ΔDrs2 null mutant was constructed based on standard strain ATCC2001 (wild type, WT) through homologous recombination. Then, gene expression profiling analysis was performed using data obtained from RNA-seq of WT and ΔDrs2 mutant.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ATCC2001 yeasts and ΔDrs2 strain yeasts

first: Ke-Zhi

last: Chen

first: Jun-Tao

last: Zhao

first: Si-Jia

last: Huang

first: Lu-Ling

first: Jin-Yan

last: Liu


title: Autologous cell therapy with CD133+ bone marrow-derived stem cells for Asherman Syndrome: a phase 1/2 trial [biopsies]

city: Paterna

first: Carlos

last: Simon

state: Valencia

address: Rda Narcis Monturial, parc. 118 Parque Tecnologico

country: Spain

institute: Carlos Simon Foundation

summary: Asherman Syndrome (AS) is an acquired pathological condition affecting women’s reproductive health, triggered by the substitution of a bona fide endometrium with intrauterine adhesions that cause the uterine walls to adhere to each other. Clinically, AS results in menstrual abnormalities (amenorrhea or oligomenorrhea), pelvic pain, infertility, recurrent miscarriage and abnormal placentation.  Autologous CD133+ bone marrow-derived stem cell (BMDSC) therapy has been designated as an Orphan Drug by the EMA and FDA for the treatment of AS. This phase 1/2, non-randomized, open-label, single-arm trial (EudraCT: 2016-003975-23) assessed the safety and efficacy of this novel therapy in 20 infertile women with moderate to severe AS, unresponsive to prior hysteroscopic treatments.  Single-cell RNA sequencing of endometrium and organoids revealed partial reversion of AS-related changes, and mitochondrial variant tracking offered insights of CD133+ BMDSCs engraftment. These findings suggest that autologous CD133+ BMDSC therapy is a safe and effective treatment for AS.

overall_design:
Patients with moderate-to-severe Asherman syndrome were treated with autologous CD133⁺ bone marrow–derived stem cells, and endometrial responses were evaluated using single-cell RNA-seq of endometrium.

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

first: Xavier

last: Santamaria

first: Maria

last: Pardo-Figuerez

first: Javier

last: Gonzalez-Fernandez

first: Sergi

last: Querol

first: Luciano

last: Rodriguez

first: David

last: Varcárcel

first: Carla

last: Gonzalez

first: Estefanía

last: Fernandez

first: Diego

last: Amorós

first: Michael

last: Robles

first: Sofia

last: Granados-Aparici

first: Sheila

last: Zúñiga

first: Francisco

last: Martínez

first: Diana

last: Valbuena

last: Gómez

first: Julio

last: Herrero

first: Ramón

last: Aurell

first: Juan

last: Torrent

first: Felipe

last: Vilella

first: Petr

last: Volkov

last: Raga

first: Rosa

last: Noguera

first: Hugh

last: Taylor


title: Autologous cell therapy with CD133+ bone marrow-derived stem cells for Asherman Syndrome: a phase 1/2 trial [organoids]

first: Carlos

last: Simon

overall_design:
Patients with moderate-to-severe Asherman syndrome were treated with autologous CD133⁺ bone marrow–derived stem cells, and endometrial responses were evaluated using single-cell RNA-seq of epithelial cell–derived organoids generated from endometrial biopsies collected before and after treatment, as well as from healthy controls.

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

first: Xavier

last: Santamaria

first: Maria

last: Pardo-Figuerez

first: Javier

last: Gonzalez-Fernandez

first: Sergi

last: Querol

first: Luciano

last: Rodriguez

last: Varcárcel

last: Gonzalez


title: Spatio-controlled Sialic Acid Polymer Molecular Patterns for Selective Siglecs Modulation and Cytokine Storm Abrogation

city: Changchun

first: Yusong

last: Cao

address: Renmin Street 5625

institute: Changchun Institute of Applied Chemistry

summary: Cytokine storm is a leading cause of mortality in severe infections and adverse responses to adoptive cell therapiesy. Leveraging multivalent sialic acids (SAs) and the specificity of the SA-Siglec (SA-binding immunoglobulin-type lectins) axis to direct immune cell responses openss a compelling route to efficiently mitigate cytokine storms. However, the optimal configuration of multivalent SAs to maximize Siglec binding affinity and immune-directing activity has yet to be elucidated. Herein, we report Molecular-Patterned Sialic Acid Polymers (MPSPs) Sialic Polymer Molecular Patterns (SPMPMPSPs) , a class of synthetic macromolecular immunomodulators engineered with precise control over polymer backbone conformation, pendant SA densityspacing, and branching topology. This molecular pattern recreates the hierarchical By mimicking the multivalency t architectures of natural glycans while exploiting the modularity of polymer chemistry, and to introduce tunablemolecular controlled SA patterning patterns. Super-resolution fluorescence microscopy and single-molecule spectroscopy confirm structure-specific sialic acid patterns promoteat the molecular scale, SPMPs achieve  Siglec-E clustering and high-affinity engagement with Siglec-E, triggering potent inhibitory signaling . The SPMPs robustly and reshape reshaping innate immune cell functions and effectivelyto abrogated cytokine storms. This pattern-encoded macromolecular strategy es establishes a new paradigm for precise immune modulation and offering a framework for materials-based interventions in inflammatory disorders.

overall_design: To compare the change of gene expression of RAW264.7 cells after treated by LPS  and sialic polymers


title: Identification of a Lipid Oxygen Radical Defense pathway and its epigenetic control

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

overall_design: Refer to individual Series


title: Germ cell motility clock

city: Münster

first: Katsiaryna

last: Tarbashevich

state: NRW

address: Von-Esmarch-Str. 56

department: Institute of Cell Biology

institute: University Münster

summary: Organ development relies on interactions among different cell types that form three-dimensional structures to carry out specific tasks. This process often involves active migration of progenitor cells toward specific positions within the embryo, where the cells then become immotile and form stable connections among each other and with neighboring cell types. Yet, surprisingly little is known about processes of motility loss and the emerging organization of the cells at the site where the organ forms. In this work, we study these the process of motility loss processes using zebrafish primordial germ cells as an in vivo model. We show that changes in embryonic tissues as well as cell-autonomous events regulate germ cells’ behavior as they arrive at their target region. Importantly, we find that reduction in germ cell motility is correlated with the decay of RNA encoding for Dead end 1 (Dnd1), a conserved vertebrate RNA-binding protein that is essential for PGC migration. Indeed, decreasing or increasing the level of Dnd1 results in a premature or delayed stop to motility, respectively. These findings represent a novel RNA decay-based mechanism for timing the duration of cell migration in vivo.

overall_design: RNA-seq profiling of the zebrafish primordial germ cells (PGCs) positioned at the gonad region (wild-type condition) and at ectopic sites (ody mutant condition) at 2 developmental stages (24 and 36 hpf)

first: Zahra

last: Labbaf

first: Jan

last: Schick

first: Lucas

last: Kühl

first: Sargon

last: Gross-Thebing

first: Moritz

last: Ophaus

first: Michal

last: Reichman-Fried

first: Dennis

last: Hoffmann

first: Martin

last: Stehling

first: Jochen

last: Seggewiss

first: Jan Philipp

last: Junker

first: Erez

last: Raz


title: A Complete Spatial Map of Mouse Retinal Ganglion Cells Reveals Density and Gene Expression Specializations [En face Retina]

city: Aurora

first: Samuel

middle: Alexander

last: Budoff

state: co

address: RC1 North Tower, P18-7101 Mail Stop

department: Physiology & Biophysics

institute: Colorado University Anschutz Medica

summary:
Retinal ganglion cells (RGCs) transmit visual information from the eye to the brain. In mice, several RGC subtypes show nonuniform spatial distributions, potentially mediating specific visual functions. However, the full extent of RGC specialization remains unknown. Here, we used en-face cryosectioning, spatial transcriptomics, and machine learning to map the spatial distribution of all RGC subtypes identified in previous single-cell studies. While two-thirds of RGC subtypes were evenly distributed, others showed strong biases toward ventral or dorso-temporal regions associated with sky vision and the area retinae temporalis (ART), the predicted homolog of the area centralis. Additionally, we observed unexpected spatial variation in gene expression within several subtypes along the dorso-ventral axis or within vs. outside the ART, independent of RGC density profiles. Finally, we found limited correlations between the gene profiles of the ART and the primate macula, suggesting divergent specialization between the mouse and primate central vision.
Five wild-type mouse retinas sectioned en face at 20 μm followed by 10x Xenium spatial transcriptomics with a custom panel of 300 genes chosen by the GraSP algorithm. Data processed with Baysor segmentation and CuttleNet cell type prediction as detailed in github.com/sbudoff/MappingAllMurineRGCs

overall_design: Five wild-type C57BL/6 mouse retinas sectioned en face at 20 μm and analyzed with custom 300-gene Xenium panel to map spatial distribution of all RGC subtypes

first: Alon

last: Poleg-Polsky


title: A Complete Spatial Map of Mouse Retinal Ganglion Cells Reveals Density and Gene Expression Specializations [RGC_CrossSection]

summary:
Retinal ganglion cells (RGCs) transmit visual information from the eye to the brain. In mice, several RGC subtypes show nonuniform spatial distributions, potentially mediating specific visual functions. However, the full extent of RGC specialization remains unknown. Here, we used en-face cryosectioning, spatial transcriptomics, and machine learning to map the spatial distribution of all RGC subtypes identified in previous single-cell studies. While two-thirds of RGC subtypes were evenly distributed, others showed strong biases toward ventral or dorso-temporal regions associated with sky vision and the area retinae temporalis (ART), the predicted homolog of the area centralis. Additionally, we observed unexpected spatial variation in gene expression within several subtypes along the dorso-ventral axis or within vs. outside the ART, independent of RGC density profiles. Finally, we found limited correlations between the gene profiles of the ART and the primate macula, suggesting divergent specialization between the mouse and primate central vision.
Pre-dissected regional samples from wild-type mouse retinas cross-sectioned at 20 μm followed by 10x Xenium spatial transcriptomics with the 5000-gene pan-tissue panel. Data processed with Baysor segmentation and CuttleNet cell type prediction as detailed in github.com/sbudoff/MappingAllMurineRGCs

overall_design: Pre-dissected retinal regions from wild-type C57BL/6 mice cross-sectioned at 20 μm and analyzed with Xenium 5k gene panel for regional expression profiling


title: The gene expression of human adipose-derived stem cells treated with butyrate

city: Kyoto

first: Kazuyuki

last: Takata

state: Kyoto

address: 5 Nakauchi-cho, Misasagi, Yamashina-ku

institute: Kyoto Pharmaceutical University

summary: Adipose-derived stem cell (ASC)-conditioned medium shows therapeutic promise for cardiac repair via paracrine mechanisms. Moreover, in our previous report, cellular priming with butyrate (BA) is a promising approach for modulating the secretory phenotype of ASCs. Therefore, the comprehensive gene expression analysis was conducted on human ASC preconditioned with butyrate.

overall_design: To elucidate the gene expression patterns in human ASC following BA treatment, we used HAdpc-29-E7-TERT cells obtained from the Japanese Collection of Research Bioresources Cell Bank. The human ASC was divided into four experimental groups with three biological replicates each (vehicle control, 1.0 mM BA, 3.0 pg/mL TNF-α and 10.0 pg/mL IFN-γ, and 1.0 mM BA combined with 3.0 pg/mL TNF-α and 10.0 pg/mL IFN-γ). Following culture under these conditions for 72 h, comprehensive gene expression analysis was performed on each sample.

first: Shinji

last: Kobuchi

first: Koki

last: Harada


title: Single-cell analysis results of pituitary tissue from normal diet (ND) mice and high-fat diet (HFD) mice

city: changchun

first: Haixiang

last: Guo

address: Xi’an Road 5333#, Changchun

institute: Jilin University

summary: Obesity induces spermatogenic disorders in male mice by affecting pituitary gonadotropin levels. Here, using diet-induced obese (DIO) mice, we found that IP3R1 and 9 ZDHHC family members are highly expressed in pituitary gonadotrophs. Mechanistically, we demonstrated that protein palmitoylation and mitochondria-associated endoplasmic reticulum membrane (MAM) are essential for preventing pituitary endocrine defects and spermatogenic disorders in obesity. Overall design: Collect pituitary tissues from normal diet (ND) and high-fat diet (HFD) male mice.

overall_design: Male mice aged 4 weeks were selected. After 12 weeks of high-fat diet (HFD) feeding, pituitary tissues were collected from normal diet (ND) and HFD male mice for single-cell RNA sequencing (scRNA-seq).


title: Cross-Species Single-Cell Analysis Reveals Sex Differences in Mitochondrial Dysfunction as a Conserved Feature of Tau Pathology

city: Esch-Sur-Alzette

first: Mohamed

last: Soudy

address: 2 Avenue de l'Universite

country: Luxembourg

institute: University of Luxembourg

summary: Tau pathology represents one of the main hallmarks of Alzheimer's disease (AD), with previous studies reporting significant sex differences in tau accumulation and disease progression. While the Tau P301L zebrafish model has emerged as a promising tool for studying tauopathy, it has not been systematically compared to human AD at the single-cell level, particularly regarding sex-dependent molecular alterations that could validate its translational relevance. This study aimed to characterize the molecular and cellular pathogenesis of the Tau P301L zebrafish model using single-cell transcriptomics to reveal cell-type-specific and sex-dimorphic responses to tau pathology and confirm its relevance through comparison to human AD and the THY-Tau22 mouse model. We performed single-nucleus RNA sequencing on brain tissue from 6-month-old Tau P301L transgenic and wild-type zebrafish, analyzing differential gene expression across major brain cell types with sex-specific resolution. Cross-species comparisons with single-cell mouse and human AD datasets were performed through gene, pathway, and network-level analyses. Our analysis revealed sex-dimorphic patterns of mitochondrial dysfunction, where electron transport chain genes showed opposite tau-associated expression alterations between males and females across multiple cell types.  The comprehensive single-cell characterization of the Tau P301L zebrafish supports the utility of this model for translational AD research and demonstrates that sex-specific mitochondrial responses represent cross-species conserved pathological mechanisms with important implications for personalized therapeutic strategies.

overall_design: We used the Tg(TauP301L-dsRed) transgenic zebrafish line, which expresses human mutant tau (P301L) under the control of the HuC/D promoter, ensuring neuron-specific expression. This model recapitulates key features of human tauopathy, including tau hyperphosphorylation, neurofibrillary tangle formation, and progressive neurodegeneration. Wild-type AB zebrafish served as controls. We used two biological replicates for each condition (transgenic and wildtype control), with two technical replicates for each biological replicate. All zebrafish procedures were conducted under authorization from Luxembourg's Grand-Ducal Decrees (20 January 2016 and 26 January 2023) and adhered to European regulations (Directive 2010/63/EU). Wild-type AB and Tg(TauP301L-dsRed) zebrafish were maintained under standard conditions at 28.5 ± 0.5°C with a 14h light/10h dark cycle. Adult fish (6 months old) were housed at 4-6 fish per liter in 3.5L tanks with controlled water parameters (pH 7.5, conductivity 700-900 μS/cm). Fish were euthanized using buffered tricaine methanesulfonate (MS-222; 250 mg/L) for 15 minutes, and brains were dissected under stereomicroscopic guidance using sterilized tools, immediately flash-frozen in liquid nitrogen, and stored at -80°C until processing. Nuclei isolation was performed using the Minute Single Nucleus Isolation Kit (BN-020, Invent Biotechnologies) with modifications including addition of Protector RNase Inhibitor (3335399001, Roche) at 0.4U/μl before homogenization. Isolated nuclei from two zebrafish brains were pooled per condition, resuspended in PBS with 4% BSA and 0.2U/μl RNase inhibitor, filtered through 20μm filters (04-004-2335, CellTrics), centrifuged, and resuspended in PBS with 2% BSA and 0.2U/μl RNase inhibitor to achieve 1300-1700 nuclei/μl. Single-nuclei RNA sequencing libraries were prepared using the Chromium GEM-X Single Cell 3' Kit v4 (1000686, 10X Genomics) following the manufacturer's protocols with approximately 17,000 nuclei loaded per sample for GEM generation. Libraries were quantified using Qubit Fluorometer 4.0 (ThermoFisher Scientific), size distribution was assessed on Fragment Analyzer 5200 (Agilent), and equimolar pooled libraries were sequenced on NextSeq2000 (Illumina) in the Luxembourg Centre for Systems Biomedicine (LCSB) Genomics platform (RRID: SCR_021931).

first: Varsha

last: Murthy

first: Maria

middle: L

last: Cordero-Maldonado

first: Rashi

last: Halder

first: Enrico

last: Glaab


title: ATAC-seq of colorectal cancer patient-derived xenograft (PDX) tumors treated with FAP-CAR mRNA-LNP therapy

city: Suita

first: Sikun

last: Meng

state: Osaka

address: Yamadaoka 2-2

institute: the Universiy of Osaka

summary: This study investigates the therapeutic potential of an mRNA–lipid nanoparticle (LNP)-based strategy to deliver fibroblast activation protein (FAP)-specific chimeric antigen receptor (CAR) mRNA in colorectal cancer. Patient-derived xenograft (PDX) tumor models (PDX-1 and PDX-2) were treated by splenocytes (7SL1 knock-in) with FAP-CAR mRNA-LNPs, in comparison with PBS controls. ATAC sequencing of the tumor tissues was performed to profile transcriptional responses associated with treatment efficacy or resistance. Analysis revealed distinct chromatin accessibility programs, including activation of HOX gene clusters in resistant tumors, highlighting potential epigenetic mechanisms of therapeutic escape.

overall_design: Tumor tissues were harvested from colorectal cancer PDX models following treatment with different regimens: PDX-1: PBS control vs. splenocytes (7SL1 knock-in)  + FAP-CAR mRNA-LNPs. PDX-2: splenocytes (7SL1 knock-in) + FAP-CAR mRNA-LNPs.

first: Tomoaki

last: Hara

first: Tetsuya

last: Sato

first: Shotaro

last: Tatekawa

first: Yasuko

last: Arao

first: Yoshiko

last: Saito

first: Toshiro

last: Hirai

first: Daisuke

last: Motooka

first: Sarah

last: Rennie

first: Taroh

last: Satoh

first: Kazuhiko

last: Ogawa

first: Yutaka

last: Miura

first: Masaki

last: Mori

first: Yuichiro

last: Doki

first: Hidetoshi

last: Eguchi

first: Hideshi

last: Ishii


title: RNA-seq of colorectal cancer patient-derived xenograft (PDX) tumors treated with FAP-CAR mRNA-LNP therapy

summary: This study investigates the therapeutic potential of an mRNA–lipid nanoparticle (LNP)-based strategy to deliver fibroblast activation protein (FAP)-specific chimeric antigen receptor (CAR) mRNA in colorectal cancer. Patient-derived xenograft (PDX) tumor models (PDX-1 and PDX-2) were treated by splenocytes with FAP-CAR mRNA-LNPs, including wild-type or 7SL1 knock-in splenocytes, in comparison with PBS controls. RNA sequencing of the tumor tissues was performed to profile transcriptional responses associated with treatment efficacy or resistance. Differential expression and pathway enrichment analyses revealed distinct immune and stromal gene programs, including HOX family transcription factor activation in resistant tumors.

overall_design: Tumor tissues were harvested from colorectal cancer PDX models following treatment with different regimens: PDX-1: PBS control vs. splenocytes + FAP-CAR mRNA-LNPs (with 7SL1 knock-in splenocytes). PDX-2: PBS control vs. splenocytes + FAP-CAR mRNA-LNPs (with wild-type splenocytes or 7SL1 knock-in splenocytes).


title: Effect of oscillating and non-oscillating Ca2+ signal on gene expression in RBL-2H3 cells

city: Durham

first: Anant

last: Parekh

state: NORTH CAROLINA

address: 111 TW Alexander Drive

institute: NIH

summary: Oscillations of Ca2+ signal are generated in all cell types, seen throughout the life of a cell, and are indispensable for diverse biological processes ranging from fertilization to cell death.  Here we report that Ca2+ nanodomains near Ca2+ channels at the cell surface and not cytosolic Ca2+ oscillations are central to gene expression.  Ca2+ nanodomains activate Ca2+-dependent transcription factors to the same extent as Ca2+ oscillations, at the same average cytosolic Ca2+, leading to equivalent activation of a range of intracellular pathways.  Our results establish that the fundamental unit of excitation-transcription coupling is the Ca2+ channel nanodomain at the cell surface.

overall_design: RNAseq transcriptomic profiling of RBL-2H3 cells after treatment with IgE, 2uM thapsigargin, or 20nM thapsigargin.

first: Yu-Ping

last: Lin