title: Inflammaging in aged tissues drives remodeling of the CD8+ T cell compartment

city: St. Louis

first: Maxim

last: Artyomov

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: Aging profoundly reshapes the immune cell landscape, with particularly strong effects on CD8+ T cells, including a marked decline in naïve cells and the emergence of age-associated GZMK+ CD8+ T cells (TAA cells). Although TAA cells make up a significant fraction of the aged CD8+ T cell compartment, the pathway underlying their differentiation remains unknown. In this study, we demonstrate that TAA cell development is cell-extrinsic and requires antigen exposure within aged non-lymphoid tissues. Using a novel TNFΔ69AU/+ mouse model, we show that systemic low-grade inflammation, characteristic of inflammaging, accelerates CD8+ T cell aging and promotes early accumulation of TAA cells. Through detailed analysis of TAA cell heterogeneity, we identified a progenitor subpopulation enriched in the aged adipose tissue. Using heterochronic transplantation, we show that adipose tissue acts as a functional niche, supporting progenitor maintenance and driving the conversion of young CD8+ T cells into the aged phenotype. Taken together, our findings reveal how aging of non-lymphoid tissues orchestrates the reorganization of the CD8+ T cell compartment and highlight adipose tissue as a promising target for therapeutic strategies aimed at modulating immune aging.

overall_design: Splenic CD3e+CD8+ T cells were sorted from young and middle-aged TNFΔ69AU/+, as well as from young, middle-aged, and old WT controls.

first: Irina

last: Shchukina

first: Carlos

last: Rodriguez-Hernandez

first: Maksim

last: Kleverov

first: Heather

last: Ruiz

first: Gwendalyn

last: Randolph


title: RNA sequencing analysis of LN T cells from B6 and 8in4 (CD8 Dual) mice

status: Public on Mar 23 2026

city: Frederick

first: Jack

last: Chen

state: MD

address: 8560 Progress Drive

country: USA

institute: Frederick National Laboratory

type: Expression profiling by high throughput sequencing

summary: We performed genome-wide RNA sequencing to analyze gene expressions in CD8.1 and CD8.2 LN T cells from 8in4 mice.  We found that gene expression pattern of CD8.1 T cells resembled to that of B6 CD4 helper T cells, while gene expression pattern of CD8.2 T cells resembled to that of B6 CD8 cytotoxic T cells.

overall_design: Comparison of mRNA profiles of CD4 and CD8 LN T cells from B6 mice and CD8.1 (8a.1) and CD8.2 (8a.2) LN T cells from 8in4 mice.

first: Alfred

last: Singer

first: Miho

last: Shinzawa


title: Opposing effects of systemic and pancreas-specific inhibition of BCKDK on pancreatic carcinogenesis

city: Philadelphia

first: Michael

last: Noji

address: 421 Curie Blvd., BRB II/III, Room 638

department: Cancer Biology

institute: University of Pennsylvania

summary: Branched-chain amino acid (BCAA) metabolism is perturbed in patients with pancreatic cancer, but the contribution of systemic or pancreas-intrinsic BCAA metabolism to pancreatic carcinogenesis is unclear. We show here that pancreas-specific loss of DBT, the E2 subunit of the branched-chain keto-acid dehydrogenase (BCKDH) complex required for BCAA oxidation, strikingly exacerbates premalignant pancreatic intraepithelial neoplasia (PanIN) lesions in KC (p48-Cre;LSL-KrasG12D/+) mice. However, deletion of upstream enzyme BCAT2 neither phenocopied nor rescued loss of DBT in KC mice, ruling out involvement of both upstream and downstream metabolites as mediators of PanIN promotion. Instead, we observed that DBT deficiency led to loss of the kinase BCKDK, a negative regulator of the BCKDH complex, and that, remarkably, pancreas-specific loss of BCKDK phenocopied DBT deficiency in accelerating PanIN formation. These data thus support a model in which pancreas BCKDK restrains tumorigenesis. In contrast, systemic treatment of KC mice with the BCKDK inhibitor BT2, which inhibits BCKDH phosphorylation across many tissues except the pancreas, reduced PanIN formation and preserved normal acinar area. Together the data reveal the promotion of BCAA catabolism systemically, but not within the pancreas, as a promising intervention strategy to suppress tumor initiation.

overall_design: Bulk RNA-seq profiling of pancreata from 5 1/2 week old male animals of the following genotypes: P48-Cre control, DBTfl/fl control, and DBT-pKO (P48-Cre;DBTfl/fl)

first: Noji

last: Michael

first: Wellen

last: Kathryn

first: Arany

last: Zoltan


title: Multiomics and single-cell sequencing reveal protein aggregation and translation fidelity enhance cross-tolerance of L. bulgaricus

city: qingdao

first: Liang

last: Liu

country: China

institute: Ocean University of China

summary: Microorganisms enter dormancy under sublethal stress through the formation of protein aggregates, thereby acquiring cross-tolerance to environmental challenges. This phenomenon may be exploited to improve the survival ability of microbial products during the processing. In this context, this study involved inducing dormancy using sublethal concentrations of rifampicin to impart cross-tolerance to stress (acid, alkali, and heat) in L. bulgaricus. Suppressing bacterial transcriptional activity forced the bacteria into dormancy while inducing liquid-liquid phase separation (LLPS) -mediated protein aggregation. These aggregates were enriched in transcription/translation-related proteins and DNA repair enzymes, potentially serving as "molecular safe houses" that protected essential biomolecules and increased biochemical reaction efficiency through localised concentrations under stress. The formation of these protein aggregates was driven mainly by disordered proteins, and the expression of disordered proteins was probably regulated by the SOS response. The contribution of molecular chaperones and ion pumps to cross-tolerance were relatively small. Single-cell RNA sequencing revealed that the main resistance subgroups may enhance tolerance by ensuring translation fidelity through acylation and ribosome quality control, which was ambiguous in bulk RNA sequencing. This study advances the understanding of antibiotic-induced dormancy and cross-tolerance mechanisms, offering novel insights for developing engineering stress-resistant bacteria and combating pathogen resistance.

sample_organism: Lactobacillus delbrueckii subsp. bulgaricus

overall_design: The L. bulgaricus solution cultured at 37 degrees Celsius for 13 hours in normal MRS medium was used as the control group, and after 13 hours, 0.64mg/ml rifampicin was added and treated for 3 hours to form the experimental group.Using M20 Genomics VITA series MscRNA seq, prepare a single-cell suspension and immobilize the cells, then add random primers into the single cells. Afterwards, reverse transcription was performed using random primers as the amplification starting point to obtain random RNA segments. Finally, Gel Beads with sequence labels, pre mixed samples and reagents, and oil were loaded into their respective injection channels for cell labeling to obtain a library of single-cell cell markers for microorganisms. Finally, cDNA amplification was performed on the single-cell library to obtain Illumina based library for sequencing.（n=1）


title: A single-cell atlas exposes the transcriptional complexity of algal life cycle transitions

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

summary: Microalgae produce around half of Earth’s oxygen, yet are often considered simple, undifferentiated cells that are at the mercy of their environment. Here, we challenge this view by demonstrating that diatoms, the most species-rich eukaryotic algae, rival multicellular organisms in terms of their life cycle complexity. A single-cell atlas of 8,674 high-quality transcriptomes, enriched with extensive experimental data, uncovered unique mechanisms for meiotic regulation and sex determination and revealed a universal regulatory logic that drives the critical transition from vegetative to reproductive growth, both in cultured and environmental diatom species. Finally, we introduce a molecular model of the remarkable 15-fold expansion of auxospores, supported by reporter lines as developmental timekeepers. Altogether, our work reframes microalgae as attractive models to study eukaryotic life cycles.

overall_design: Two different strains of Cylindrotheca closterium were crossed and cultures were harvested for scRNA-seq analysis at three different timepoints after crossing

first: Gust

last: Bilcke

first: Nadine

last: Rijsdijk

first: Arthur

last: Cleyman

first: Triana

last: Forment

first: Thomas

last: Eekhout

first: Darja

last: Belisova

first: Peter

last: Chaerle

first: Carolin

last: Grones

first: Michiel

last: Van Bel

first: Judith

last: Porters

first: Nicolás

last: Manosalva Pérez

first: Sien

last: Audoor

first: Evelien

last: Mylle

first: Daniël

last: Van Damme

first: Lieven

last: De Veylder

first: Wim

last: Vyverman

first: Klaas

last: Vandepoele


title: Alveolar macrophages inhibit emphysematous pathology via expression of carbonic anhydrase 4.

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: Chronic obstructive pulmonary disease (CODP) including emphysema affects approximately 400 million individuals worldwide. Therapies to treat COPD remain limited and fail to prevent disease progression. Alveolar macrophages (AMs) reside in the alveoli of the lung and are ideally positioned to encounter inhaled particles and pathogens. Despite exposure to these stimuli, AMs exhibit specialized phenotypes that restrict inflammation to prevent alveolar damage. Here we demonstrate that AMs express high levels of the surface bound enzyme carbonic anhydrase 4 (Car4). Deletion of Car4 on AMs results in increased susceptibility to emphysematous pathology and therapeutic treatment with Car4 is sufficient to prevent emphysema-like disease. Consistent with our murine studies, reduced levels of Carbonic anhydrase 4 (CAIV) distinguishes COPD patients with emphysema from those without emphysema. Mechanistically, murine and human Car4 directly inhibit elastase that promotes destruction of alveolar walls. Collectively, these studies reveal an underappreciated function for Car4 in preventing lung pathology.

overall_design: Homozygous Cx3cr1CreERT2-IRES-YFP were crossed with homozygous Rosa26-TdT for 'fate-mapper' mice. Mice were inoculated subcutaneously with a 200µl suspension of 550 Nippostrongylus brasiliensis (Nb) L3. ‘Fate-mapper’ mice, mice were treated i.p. Day -1 and Day +1 of infection with 75mg/kg tamoxifen dissolved in corn oil. This allows labeling of monocyte-derived alveolar macrophages (Mo-AM) from tissue-derived alveolar macrophages (TD-AMs). ‘fate-mapper’ mice, control and infected mice were sort-purified on live CD45+CD64+F4/80+CD11c+SiglecF+ and then sorted based on expression of TdT, with tissue-resident cells being TdT- and monocyte-derived cells TdT+. The purities of all cell populations were ≤ 98%. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). The NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) were utilized to generate Illumina-compatible libraries and sequencing was performed using an Illumina NovaSeq 6000 system using a configuration of paired-end 2x50-base pair (bp) reads. For bulk RNA-seq analysis the output reads were aligned to the GRCm38 (mm10) genome using STAR, followed by gene count generation using feature Counts and StringTie. DESeq2 was used for normalization and comparison of read counts compared between groups for differential gene expression with significance cutoff at false discovery rate-adjusted p<0.05. This was executed in accordance with the nf-core RNA-seq guidelines v.1.4.2. Determination of functional pathways was performed using Ingenuity Pathway Analysis (IPA) on differentially expressed genes, p<0.05.

first: John J.

last: Ponessa

first: Mark C.

last: Siracusa


title: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 30) [I38]

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: This study is part of the immgenT Open Source Project, specifically from IGT38, which focuses on a pan-organ and time course analysis of T cells in acute LCMV (Armstrong) infection at day 30 post-infection. The dataset includes T cells isolated from multiple organs: spleen, prostate, submandibular gland, bone marrow, mesenteric lymph node, small intestine epithelium, small intestine lamina propria, lung, and mediastinal lymph node. 7-week-old male C57BL/6J mice infected intraperitoneally with 2×10^5 PFU LCMV Armstrong, and T cells were analyzed at 60 days post-infection (dpi). The study includes both endogenous T cells and adoptively transferred P14 and SMARTA TCR transgenic T cells. Mice received IV 100,000 SMARTA (CD45.1.2) and 50,000 P14 (CD45.1) T cells one day before infection.

overall_design: T cells were isolated from individual organs using mechanical dissociation, enzymatic digestion (collagenase I or DTE), and anti-CD45 intravenous labeling to distinguish tissue-resident from circulating cells. Sorted CD3e+ or IV- CD3e+ were profiled using single-cell RNA sequencing (10x Genomics), combined with CITE-seq (TotalSeq C) and paired TCR α/β sequencing. Samples were pooled using hashtags.

first: Giovanni

last: Galletti

first: Sara

last: Quon

first: Nicole

middle: E

last: Scharping

first: Kennidy

last: Takehara

first: Amir

last: Ferry

first: Ananda

last: Goldrath


title: Targeting adipocyte ESRRA alleviates osteoarthritis via interrupting inter-organelle crosstalk of complement C3-CFD-MAC cascade

city: Shenzhen

first: Tongling

last: Huang

address: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences  1068 Xueyuan Avenue,Shenzhen University Town,  Nanshan District, Shenzhen, China

summary: Osteoarthritis is an aging-related systemic disease involving the crosstalk of multiple organs/tissues in metabolism and inflammation, yet little is known about the contribution of liver and marrow adipose tissue (MAT).   Here we show that MAT-derived complement factor D (CFD) and component 3 (C3) derived from steatotic liver coordinately drive excessive alternative complement activation, resulting in cartilage damage in mice during aging and metabolic disorders.   Mechanistically, estrogen-related receptor α (ESRRA) transcriptionally upregulates CFD responding to bone marrow adipocytes (BMAds) expansion.   Inhibition of ESRRA/CFD signaling in BMAds blocks the chondrocyte senescence and catabolism triggered by C3 that is released from steatotic hepatocyte, interrupting C3-CFD-MAC cascade, thereby suppressing ERK1/2 phosphorylation and mitochondrial dysfunction.   Adipocyte-specific ablation or pharmacological inhibition of ESRRA reduces CFD levels particularly in adipocyte-rich bone marrow, attenuating osteoarthritis progression in aged mice.   Our findings highlight a key liver-MAT-cartilage axis bridged by C3-CFD-MAC pathway, raising the potential for adipocyte ESRRA-targeting therapies for aging-related metabolic osteoarthritis.

overall_design: Esrrafl/fl and Adipoq-Cre;Esrrafl/fl mice,which exhibit genetic deletion of Esrra specifically in adipocytes, were maintained on a long-term high-fat high-cholesterol (HFHC) diet for 13 weeks. Total RNA was extracted, and bulk RNA-seq transcriptome analysis was performed on gonadal white adipose tissue from HFHC-fed mice

first: Zihui

last: Wang

first: Lu

last: Gao

first: Jun

first: Zhaocheng

last: Lu

first: Pengda

last: Li

first: Chon Him

last: Choy

first: Zhuolei

last: Yuan

first: Yanting

last: Zhong

first: Min

last: Guan


title: Human pluripotent stem cell-derived atrioventricular node-like pacemaker cells exhibit biological conduction bridge properties [hpsc_scRNAseq]

city: Toronto

first: Stephanie

last: Protze

state: Ontario

address: 101 College Street

department: McEwen Stem Cell Institute

country: Canada

institute: University Health Network

summary: The atrioventricular node (AVN) ensures synchronized heart contractions by establishing the electrical connection between the atria and ventricles. Dysfunction of the pacemaker cells of the AVN leads to atrioventricular block (AV block), a life-threatening condition managed with electronic pacemakers (EPMs). EPMs have drawbacks that could be overcome by a human pluripotent stem cell (hPSC)-derived biological conduction bridge (BioCB). Recent studies demonstrated the differentiation of AVN-like cells from hPSCs, but their conduction properties upon engraftment in vivo remain unexplored. Here we report the generation of AVN-like pacemaker cells (AVNLPCs) from hPSCs using WNT and BMP signaling modulation. These AVNLPCs transcriptionally resemble fetal AVN pacemaker cells, exhibit pacemaker action potentials, and display AVN-like conduction properties. Notably, when transplanted into the guinea pig heart, AVNLPCs electrically integrate and maintain their conduction properties. Our study highlights AVNLPCs as a valuable tool for disease modeling and BioCB development to improve treatment for AV block patients.

overall_design: Examining the transcriptome of the cells in the endogenous fetal atrioventricular node and human pluripotent stem cell derived atrioventricular node-like pacemaker cells.

first: Michelle

last: Lohbihler

first: Amos

middle: A

last: Lim

first: Stéphane

last: Massé

first: Maggie

last: Kwan

first: Omar

last: Mourad

first: Olya

last: Mastikhina

first: Brandon

middle: M

last: Murareanu

first: Malak

last: Elbatarny

first: Renu

last: Sarao

first: Beiping

last: Qiang

first: Wahiba

last: Dhahri

first: Matthew

middle: L

last: Chang

first: Alice

last: Xu

first: Amine

last: Mazine

first: Shahryar

last: Khattak

middle: S

last: Nunes

first: Kumaraswamy

last: Nanthakumar

first: Michael

last: Laflamme


title: N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development [mESC_RNA-seq]

city: Beijing

first: Li

last: Tang

state: Beijing

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: Transcription factors (TFs) have key roles in cell fate determination, and are rapidly upregulated to fulfill developmental functions. During second cell fate decisions in pre-implantation embryonic development, upregulated key TFs, including GATA6 and NANOG, drive the differentiation and functional establishment of primitive endoderm (PrE) and epiblast (EPI) cells. However, how the embryo achieves this swift TF upregulation and the precise molecular mechanisms underlying specific TF initiation remain unclear. In this study, we showed how N6-methyladenosine (m6A) affected embryo and embryoid differentiation. Using two types of extended pluripotent mouse embryonic stem cells with in vivo embryonic and extraembryonic potency-extended pluripotent stem cells (EPSCs) and totipotent blastomere-like cells (TBLCs) alongside mouse embryos, we observed that the m6A writers METTL3 and VIRMA were essential for PrE development. Mechanistically, globally increased mRNA stability occurred during embryo development - mediated by m6A modification. Specifically, m6A enhanced key regulator stability during PrE differentiation, such as Gata6, by interacting with the m6A reader IGF2BP3, thereby promoting protein production and ultimately impacting on cell fate decisions. Our results suggest that post-transcriptional mRNA regulation is a pioneering mechanism governing second cell fate decisions, and highlights the molecular mechanisms underlying mouse embryogenesis.

overall_design: This study characterized the transcriptomic states of mESCs and investigated the RNA stability across different states.

first: Weide

last: Xiao

first: Mingli

last: Ma

first: Kuisheng

last: Liu


title: Resistance to the KRASG12D Inhibitor MRTX1133 is Associated with Aberrant Histone Acetylation and Increased Sensitivity to BET Inhibition

city: Sao Paulo

first: Alexandre

middle: Ferro

last: Aissa

state: SP

address: Rua Botucatu 740

country: Brazil

institute: Universidade Federal de São Paulo

summary: As many as 90% of human pancreatic ductal adenocarcinoma (PDAC) tumors harbor gain-of-function mutations in the KRAS oncogene. Recently, inhibitors of the most common KRAS mutation, KRASG12D, have entered the clinical arena. However, early evidence suggests that as monotherapy, KRASG12D inhibitors such as MRTX1133 at best provide brief periods of disease stabilization. Hence, there is a growing interest in understanding the mechanisms through which tumors acquire resistance to KRAS inhibition. In the present study, we generated in vitro models of MRTX1133 resistance and subjected parental and drug-resistant cell lines to RNA sequencing. This suggested that MRTX1133-resistant tumor cells undergo a global shift toward histone acetylation. Inhibition of the histone acetyltransferase EP300 reversed the drug-resistant phenotype in vitro, which subsequent RNA sequencing experiments determined was associated with the suppression of pro-survival FOSL1 signaling. Accordingly, siFOSL1 reversed the MRTX1133-resistant phenotype with similar effects on pro-survival signaling. Given the lack of clinically useful EP300 or FOSL1 inhibitors, we next explored whether inhibitors of the acetylation scanning BET proteins would be similarly effective. The addition of BET inhibitors re-sensitized several highly resistant cell lines to MRTX1133 and impaired FOSL1-mediated survival signaling in vitro. In murine models of MRTX1133-resistant PDAC, BET inhibition cooperated with MRTX1133 to markedly extend overall survival. As BET inhibitors are currently under clinical testing, the combination of MRTX1133 and BET inhibitors warrants further investigation, particularly in tumors that have developed resistance to KRAS inhibition.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To investigate mechanisms of resistance to the KRAS inhibition, we established two cell lines that are resistant to the KRASG12D inhibitor MRTX1133. These cells were referred to as PANC1K or 2138K. PANC1 and PANC1K or 2138 and 2138K cells were again grown in 3D floating collagen cultures for 48 hours and subjected to RNA sequencing followed by gene set enrichment analysis (GSEA).
Next, to identify the potential resistance mechanisms being regulated by EP300, we reestablished 3D floating collagen cultures using PANC1K cells treated with either a DMSO vehicle or SGC-CBP30. After 48 hours, cells were subjected to RNA sequencing and GSEA. We next repeated these RNA sequencing experiments using 2138K cells.
We next reestablished 3D floating collagen cultures using PANC1K cells, which had been incubated with either siControl or siFOSL1. After 48 hours, cells were subjected to RNA sequencing and GSEA
Finally, to determine potential mechanisms regulated by BET inhibitors, we again established 3D floating collagen cultures using PANC1K cells, which were then incubated with DMSO vehicle, JQ1, or OTX-015. After 48 hours, cells were subjected to RNA sequencing and GSEA.

first: Daniel

middle: R

last: Principe

first: Jeffrey

middle: H

last: Becker

first: Anastasia

last: Metropulos

first: Alejandra

last: Marinelarena

first: Thao

middle: D

last: Pham

middle: F

first: Hidayatullah

middle: G

last: Munshi


title: NAC promotes co-translational protein folding at the ribosomal tunnel exit

city: Heidelberg

first: Manuel

last: Günnigmann

address: Im Neuenheimer Feld 282

country: Germany

institute: ZMBH

summary: The nascent polypeptide-associated complex (NAC) is crucial for protein biogenesis, coordinating enzymatic modifications and membrane targeting of nascent chains at the ribosomal tunnel exit. However, its role in co-translational folding remains unclear. Here, we report the genome-wide profiling of NAC interactions with nascent chains in human cells, demonstrating that it correlates with emerging segments of folded domains of cytonuclear proteins. Single-molecule and structural analyses revealed that NAC’s b-barrel domain dynamically interacts with the ribosome and emerging chains at the tunnel exit, presumably facilitating initial compaction and early folding, and that NAC binding promotes native folding of proteins. Additionally, we uncovered compartment-specific nascent chain interactions of NAC, supporting it’s role in targeting proteins to the endoplasmic reticulum and in mitochondrial membrane protein biogenesis. Together, these findings establish NAC as a bona fide co-translational chaperone that facilitates early protein folding at the ribosomal tunnel exit, expanding its functional repertoire in protein biogenesis.

overall_design: Selective ribosome profiling (SeRP) of the human nascent polypeptide-associated complex (NAC). NAC subunits (NACA and BTF3) were purified either from a cell lysate or from sucrose cushion purified ribosomes. In addition, soluble ribosome profiling (SolubleRP) was performed in human cells to analyze ribosome engagement with membranes. All experiments were performed in two biological replicates. Ribosome profiling experiments were performed on HEK293T cells containing an NACβ auxin inducible degradation system. Briefly, a GS linker-miniIAA7-GFP11 sequence was inserted at residue 176 of endogenous BTF3 via CRISPR/Cas9-mediated homology-directed repair in cells stably expressing AtAFB2. Cells were seeded on 10 cm dishes 48 hours prior to harvest to ensure an 70-80% confluency at the time of collection. Cells were treated with 100 μg/mL indole-3-acetic acid sodium (Santa Cruz, sc-215171) for 9 hours prior to harvesting. Untreated cells were used as a control. All experiments were performed in two biological replicates.

first: Jaime

last: Santos

first: Radoslaw

middle: J

last: Gora

first: Marija

last: Iljina

first: Masa

last: Predin

first: Ilgin Eser

last: Kotan

first: Pratiman

last: De

first: Dhawal

last: Choudhary

first: Juwon

last: Jang

first: Frank

last: Tippmann

first: Nenad

last: Ban

first: Sander

last: Tans

first: Shu-ou

last: Shan

first: Günter

last: Kramer

first: Bernd

last: Bukau


title: Human pluripotent stem cell-derived atrioventricular node-like pacemaker cells exhibit biological conduction bridge properties [fetal_scRNAseq]

first: Stephanie

last: Protze

first: Michelle

last: Lohbihler

first: Amos

last: Lim

first: Stéphane

last: Massé

first: Maggie

last: Kwan

first: Omar

last: Mourad

first: Olya

last: Mastikhina

first: Brandon

last: Murareanu

first: Malak

last: Elbatarny

first: Renu

last: Sarao

first: Beiping

last: Qiang

first: Wahiba

last: Dhahri

first: Matthew

last: Chang

first: Alice

last: Xu

first: Amine

last: Mazine

first: Shahryar

last: Khattak

first: Sara

last: Nunes

first: Kumaraswamy

last: Nanthakumar

first: Michael

last: Laflamme


title: The role of car4 in alveolar macrophages

first: Alexander

last: Lemenze

summary: To investigate the role carbonic anhydrase IV has in the phenotype and function of alveolar macrophages

overall_design: RNA sequencing of sorted alveolar macrophages from Car4fl/fl-CD11cCre mice (n=3) compared to Car4fl/fl mice (n=3)

first: John

last: Ponessa

first: Mark

last: Siracusa


title: APOE4 expression causes distinct effects on meningeal immunity, brain lipid composition, and cognition in male and female mice

city: Jacksonville

first: Sandro

last: Da Mesquita

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

summary: This experiment was designed to understand the distinct effects of sex and APOE genotype on the transcriptome of meningeal dural vascular and resident immune cells. After transcardiac perfusion with a buffered saline solution containing heparin and actinomycin D, meningeal dural whole mounts were immediately dissected from the skulls of 12-month-old male and female mice expressing APOE3 or APOE4 and digested into a single-cell suspension. After enrichment for CD31+ cells via positive selection using MACS, the cells were counted and approximately 5000 cells per sample were used to obtain single-cell gene expression libraries using 10x Genomics equipment and reagents, namely the Chromium Single Cell 3' Reagent Kits. The generated libraries were sequenced in 2 lanes of a NovaSeq 6000 S4 PE100 flow cell.

overall_design: scRNAseq of MACS-enriched (CD31+), mouse, meningeal dura expressing APOE3 or APOE4, given a control or PLX5622 diet, in males and females


title: Selective targeting of endothelial and perivascular ROCK2 reverses liver fibrosis in  pigs and human patients

city: Chengdu

first: Bi-Sen

last: Ding

state: Sichuan

address: Wuhou District, Renmin three paragraphs

department: The West China Second UniversityHospital of Sichuan University

institute: Sichuan University

summary: Investigation of ROCK2 distribution and expression in NPC subpopulations of fibrotic and healthy human and minipig livers.

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design:
This study was designed to analyze the distribution of different cell types and gene expression in fibrotic and healthy liver tissues obtained through surgical biopsy
We performed single-cell RNA sequencing on liver non-parenchymal cells (NPCs) derived from humans and minipigs to evaluate ROCK2 expression and therapeutic effects.
Human samples: NPCs were isolated from fibrotic liver tissues and healthy controls obtained during surgical resection.
Minipig samples: A MASH model was established using a high-fat, high-sugar diet combined with intraperitoneal injection of carbon tetrachloride for 3 months. Paired liver biopsies were collected at two timepoints: pre-treatment (after 3 months of induction) and post-treatment (after 9 months of ROCK2 inhibitor administration).

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

first: Chengju

last: Xiao

first: Yan

last: Hu


title: The RNA-seq data of root tissue from transgenic poplar

first: Han tian

last: Wei

address: Chinese Academy of Forestry

institute: Chinese Academy of Forestry

summary: The root tissues of WT, bHLH58-OE#20, bhlh58-KO#6, bHLH151-OE#17, bhlh151-KO#40, and bhlh58/151-KO#32 plants were collected for RNA-seq analysis with three biological replicates.

overall_design: To find the upstream and downstream regulatory genes associated with root phenotype, we performed transcriptome sequencing.

first: Han-tian

first: Jian-jun


title: An immune-excluding vascular barrier limits immunotherapy efficacy in neuroendocrine cancers

city: Chengdu, China

first: Ailing

last: Zhong

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

summary: Small cell lung cancer (SCLC), a highly aggressive neuroendocrine malignancy, is among the most immune-desert tumor types and exhibits poor response to immunotherapy. However, the mechanisms underlying this immune resistance remain unclear. Here, we identify a unique immune-excluding vascular (IEV) barrier in SCLC, distinct from non-small cell lung cancer (NSCLC) and other cancers, composed of tightly connected endothelial cells, a thickened basement membrane, and dense pericyte coverage. Functionally, this barrier restricts immune cell infiltration, contributing to SCLC’s immunotherapy resistance. Mechanistically, we show that ASCL1, the master transcription factor of SCLC, is essential for IEV barrier formation. ASCL1 drives expression of insulin-like growth factor-binding protein 5 (IGFBP5), and depletion of IGFBP5 in tumor cells reduces IGF1 signaling in endothelial cells. Endothelial-specific disruption of IGF1R impairs barrier integrity. Importantly, targeting this axis either through IGFBP5 knockout or treatment with the IGF1R inhibitor OSI-906 enhances CD8+ T cell infiltration and synergizes with anti-PD1 therapy in SCLC. Furthermore, we demonstrate that this ASCL1-IGFBP5-IGF1R axis and the IEV barrier are conserved across multiple neuroendocrine cancers (NECs). Our findings reveal a previously unrecognized vascular barrier in NECs and propose novel therapeutic strategies to overcome immune exclusion and enhance immunotherapy efficacy in these recalcitrant cancers.

overall_design: Mouse tumor tissues were dissociated using a digestion buffer containing 1.0 mg/mL collagenase I (Gibco, 17100–017) and 0.5 mg/mL collagenase IV (Gibco, 17104–019) in DMEM/F12 medium (Gibco, C11330500BT). Following dissociation, endothelial cells were sorted as GFP-CD45-CD31+ populations using flow cytometry for bulk RNA-seq.

first: Yiyun

last: Wang


title: B cell derived type I interferon promotes T cell effector function during chronic infection

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

summary: B cells are the most abundant lymphocytes and play a central role in humoral immunity. However, their impact on T cell responses, in particular of CD8+ T cells, remains incompletely understood. Here, we identify a critical role for B cells in promoting CD8+ T cell responses to chronic, but not to acute, viral infections. We identify B cells as key type I interferon (IFN-I) producers and demonstrate that the T cell requirement for B cell-derived IFN-I is cell-intrinsically regulated by T cell receptor (TCR) stimulation, with T cells encountering high antigen loads showing an increased dependency on IFN-I to acquire effector function. In the absence of B cells, exhausted T cells displayed more severe functional impairments in effector differentiation and cytokine production, resembling tolerized T cells. Overall, we uncover a previously unrecognized role for B cells in supporting effective CD8+ T cell in chronic infection responses through the provision of IFN-I.

overall_design: Single cell rna sequencing of P14 T cells primed in spleen or lymph nodes of WT or uMT mice

first: Catarina

last: Gago da Graça

first: Leonie

last: Heyden

first: Anna

last: Lindermann

first: Sining

last: Li

first: Annika

last: Poch

first: Minh-Hanh

middle: T

last: Nguyen

first: Nhat-Truong

last: Huynh

first: Yuxi

last: Cao

first: Danielle

last: Chen

first: Carlson

last: Tsui

first: Zeinab

last: Abdullah

last: Schröder

first: Jayendra

last: Singh

first: Axel

last: Kallies

first: Daniel

last: Utzschneider


title: HER2 Overexpression Drives Drug-Tolerant Persisters to First-Line Amivantamab and Lazertinib in EGFR-Mutant Non-Small Cell Lung Cancer

city: Seoul

first: Byoung Chul

last: Cho

address: 501, ABMRC Bldg., 50-1 Yonsei-ro

department: Division of Medical Oncology

country: South Korea

institute: Yonsei Cancer Center

summary: In 2024, the U.S. FDA approved first-line amivantamab-lazertinib combination therapy for epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC) based on the MARIPOSA trial, which demonstrated superior overall survival (OS) over osimertinib. However, the underlying mechanisms of resistance to this therapy are still poorly understood. Here, we investigated the drug-tolerant state induced by amivantamab-lazertinib in a treatment-naïve NSCLC patient-derived xenograft (PDX) model with EGFR mutations. Single-cell RNA sequencing (scRNA-seq) revealed a distinct drug-tolerant persister (DTP) population characterized by increased HER2 expression. HER2 Immunohistochemistry (IHC) analysis of tumors from the PDX models demonstrated amivantamab-lazertinib therapy induced HER2 overexpression. Strikingly, biopsy samples from patients who had progressive disease (PD) following first-line amivantamab-lazertinib therapy showed increased HER2 protein expression, and in vitro studies confirmed that HER2 overexpression conferred resistance. Notably, a patient who progressed after first-line amivantamab-lazertinib with HER2 overexpression and amplification achieved a stable response with a HER2 targeted tyrosine kinase inhibitor (TKI). These findings suggest that elevated HER2 expression induced by amivantamab-lazertinib in DTPs, followed by HER2 overexpression, may serve as a resistance mechanism to first-line amivantamab-lazertinib therapy.

overall_design: Patient-Derived Xenograft (PDX) Models and Treatment Design The PDX model was generated under IRB approval number 4-2016-0788. Treatment-naïve patient-derived xenograft (PDX) models YHIM-1024 (EGFR L858R mutation) and YHIM-1003 (EGFR exon 19 deletion) were established as previously described40. Upon reaching a tumor volume of approximately 500 mm², mice were randomized into treatment groups: vehicle control, lazertinib (10 mg/kg, orally administered daily), amivantamab (10 mg/kg, orally administered three times per week), and combination treatment with lazertinib (10 mg/kg, oral daily) + amivantamab (10 mg/kg, oral thrice weekly). In the combination treatment Internal group, treatments were administered for 7 days, followed by mouse sacrifice. Tumor tissues were harvested for bulk RNA sequencing (RNA-seq), immunohistochemistry (IHC), and snap-freezing. For the YHIM-1003 model, an additional sample was collected for single-cell RNA sequencing (scRNA-seq). In the combination treatment regrowth group, treatments were administered for 28 days, followed by drug withdrawal. Tumor progression was monitored until the tumor volume reached 500 mm², at which point tumors were harvested and processed as described above. Positive control groups receiving monotherapy with lazertinib or amivantamab were included in the experimental setup but were excluded from subsequent analyses. scRNA-seq data were obtained from the Ex19del PDX model (n=3 per treatment group), while bulk RNA-seq data were obtained from both the Ex19del and L858R PDX models (n=5 per treatment group, except for the regrowth group, where YHIM-1024 had n=4 and YHIM-1003 had n=6).  Single cell RNA sequencing and analysis For tumor dissociation, gentle MACS Human Tumor Dissociation Kit (Miltenyi Biotec) was used, and single-cell library preparation was conducted according to the manufacturer’s guidelines (10X Genomics). Gene expression libraries were generated using the Chromium Single Cell 5′ Reagent Kits (10X Genomics), targeting a capture of 8000 to 10,000 cells. Sequencing results were aligned to the mm10 and hg19 reference genomes to distinguish human from murine genomic reads. Read quantification and sample merging were performed using Cell Ranger v7.1.0. Mouse and human gene expression data were separated as previously described41. Quality control, normalization, batch correction (using Harmony and BBKNN) and clustering were performed using Scanpy42. Quality control procedures were conducted as previously described41. Pseudotime analysis was conducted using CellOracle30.  Bulk RNA sequencing and analysis The TruSeq Stranded Total RNA Library Prep Globin Kit (Illumina) was used for RNA sequencing libraries construction and sequenced on the NovaSeq X platform (Illumina). Sequencing reads were performed for quality assessment using FastQC v0.11.7, and adaptor trimming and low-quality read removal were performed using Trimmomatic v0.38. Filtered reads were aligned to the GRCh38 (human) and mm10 (mouse) reference genomes using HISAT2. BAMCMP was utilized to separate human and murine reads, retaining only human-derived reads (GRCh38) for downstream analysis. DESeq2 was used for the identification of differentially expressed genes43, and GSEA software was used for gene set enrichment analysis (GSEA)44.

first: Joo sung

last: Shim

first: Youwon

last: Lee

first: Su-jin

last: Choi


title: RNF25 confers tolerance to azacytidine-induced mRNA damage by curbing activation of the integrated stress response

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

summary: Excessive RNA damage activates cellular stress responses, triggering cell death. However, pathways that negatively regulate RNA damage responses are largely uncharacterized. Using genetic screens, we here find that the ubiquitin ligase RNF25 provides tolerance to RNA damage caused by the nucleoside analogue azacytidine, a chemotherapeutic agent used to treat acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Mechanistically, azacytidine is incorporated into mRNA, where it causes lesions that stall elongating ribosomes, leading to cytotoxic activation of the GCN2-dependent integrated stress response (ISR). RNF25 prevents ISR hyperactivation by ubiquitylation of ribosomal protein eS31, suppresses cell death upon azacytidine treatment. Our study reveals an mRNA damage tolerance mechanism that determines cellular survival in response to azacytidine, highlighting RNA damage-induced stress response as a potentially critical component of chemosensitivity in AML and MDS.

overall_design: Ribosome profiling of HAP1 cells treated or not with 20 uM azacytidine for 4 hours.

first: Selay

last: Kaya

first: Carla

last: Engel

first: Julian

last: Stingele


title: Complement C3aR deletion does not attenuate neurodegeneration in a tauopathy model or alter acute inflammation-induced gene expression changes in the brain

city: Mississauga

first: Justin

middle: JM

last: Wong

address: 7070 Mississauga Road

institute: Hoffmann-La Roche Limited

summary: C3aR is highly expressed in microglia in the mouse brain and has been shown to play a role in neuroinflammation. This study examines single cell RNA expression profiles and cellularity changes in mouse hippocampi from WT or C3aRKO mice injected with PBS or LPS. The results from this study potentially provides a useful ScRNAseq dataset for LPS induced effects, critical insights for future C3aR inhibition efficacy readouts.

overall_design: 4~5-month-old WT or C3aRKO mice will be injected with PBS vehicle control or LPS (1mg/kg). After 48 hrs, mice will be perfused with PBS and single cell suspension will be obtained by FACS from one mouse hippocampus.

first: Yuanyuan

last: Wang

first: Shristi

last: Pandey

first: Martin

last: Weber

first: Jesse

last: Hanson


title: Chromatin regulator KDM6B is required for the establishment and maintenance of neural stem cells in mouse hippocampus

city: San Francisco

first: Eugene

last: Gil

state: CA

address: 1585 5th Avenue, , Apt 301

institute: University of California, San Francisco

summary: Neural stem cells in the mouse hippocampal dentate gyrus generate new neurons postnatally and throughout adult life. Here we show that the chromatin regulator KDM6B is required for both the establishment and maintenance of NSCs in the mouse DG. Conditional deletion of Kdm6b in embryonic DG precursors results in an adult hippocampus that is essentially devoid of NSCs, and hippocampal-dependent behaviors are defective.  Kdm6b-deletion causes precocious neuronal differentiation, and the NSC population fails to become established in the postnatal DG.  Using single cell RNA sequencing (scRNA-seq), we observed that Kdm6b-deletion disrupts the transcriptomic signature of NSC maintenance.  Furthermore, deleting Kdm6b in adult DG NSCs induces early neuronal differentiation, and the NSC population is not properly maintained.

overall_design: Dentate gyri were microdissected from P2 hGFAP-Cre;Kdm6bF/F mice and littermate controls, dissociated into single cells, and analyzed using scRNAseq.

first: Sung Jun

last: Jong

first: David

last: Wu

first: Dae Hwi

last: Park

first: Ryan

middle: N

last: Delgado

first: Martina

last: Malatesta

first: Sajad Hamid

last: Ahanger

first: Karin

last: Lin

first: Saul

last: Villeda

last: Lim


title: Endothelial GATA6 deficiency suppresses intracellular TLR3-interferon signaling in HPAECs and promotes interferon response in HPASMCs

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: GATA6 is a key transcription factor crucial for maintaining endothelial cell (EC) homeostasis. The dysregulation of endothelial immune function is a central feature in diseases such as pulmonary arterial hypertension (PAH). In this study, we explored the consequences of GATA6 deficiency in human pulmonary arterial endothelial cells (HPAECs) and its impact on immune response pathways. We report that siRNA-induced GATA6 deficiency or the GATA inhibitor led to significant downregulation of interferon response genes and a marked reduction in toll-like receptor 3 (TLR3) expression. GATA6 overexpression enhanced the expression of these genes, and TLR3 inhibition abrogated this response. Furthermore, conditioned medium from GATA6-deficient HPAECs upregulated interferon genes in pulmonary artery smooth muscle cells (HPASMCs), indicating a paracrine effect. Overall, these findings highlight the critical role of GATA6 in modulating TLR3 signaling and immune responses in endothelial cells and suggest its involvement in endothelial-smooth muscle cell interactions in vascular inflammation.

overall_design: Bulk-RNA seq of control PASMCs treated with conditioned medium from siScr and siGATA6 treated HPAECs for 24hrs.

first: Vrinda

last: Dambal

first: Maria

last: Trojanowska


title: N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development  [TBLC_RNAseq]

first: Li

last: Tang

overall_design: This study characterized the transcriptomic states of TBLCs and investigated the RNA stability across different states.

first: Weide

last: Xiao

first: Mingli

last: Ma

first: Kuisheng

last: Liu


title: Typical plasticisers DEHP, DBP treatment of human liver-like organs

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

summary: Phthalates are widely used as industrial plasticisers in the manufacture of plastics, resins, rubbers, paints, emulsifiers, medical devices, personal care products, and so on. Diethylhexyl phthalate (DEHP) and dibutyl phthalate (DBP) are the most common members of the phthalate group. As typical peroxisome proliferators, plasticisers and their derivatives have been shown to induce fatty liver in rodents by interfering with peroxisome proliferator-activated receptors (PPARa) (Feige et al. 2010; Issemann and Green 1990). In this study, the effects of plasticisers on hepatic glycolipid metabolism were investigated using a human liver organoid to explore the endocrine-disrupting effects of plasticisers and their mechanisms in a state more closely resembling that of a real human organ.

overall_design: Using human liver-like organs from Elephant Technologies source, differentiation was carried out after 5 days of incubation using the proliferation medium (changing the medium every 2 days) and 5 days of incubation using the differentiation medium (changing the medium every 2 days) followed by treatment with typical plastocyanin metabolite substances: MEHP (100 μM), MBP (100 μM), and a control group was treated for 2 days using 1‰ of DMSO as a solvent control. transcriptome receiving samples.

first: Yaru

last: Tian

first: Lijuan

last: You

first: Xiaoning

last: Ji

first: Jing

first: Zhisen

last: Zhuang


title: Hippocampal single cell transcriptomic changes and cellular remodeling is associated with chronic neurobehavioral outcomes following alphavirus infection

city: Blacksburg

first: Hehuang

last: Xie

state: VA

address: 1015 Life Science Circle

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

summary: Viral infections, including Venezuelan equine encephalitis virus (VEEV), have been likened to neurological diseases such as Parkinson’s and Alzheimer’s, though mechanisms remain unclear. VEEV, a neuroinvasive alphavirus, can cause significant neurological deficits in humans. Chronic effects of VEEV are poorly understood, with no antivirals or neuroprotective treatments available. This study examines longitudinal neuropathological, behavioral, and single-cell transcriptomic changes in C57BL/6 mice intranasally infected with VEEV TC-83. Acute infection significantly altered inflammatory and innate immune signaling and induced astrocyte and microglia activation and loss of neurons in the hippocampus. Persistent motor dysfunction, memory impairment, and reduced anxiety-like behavior were observed up to 106 days post-infection (DPI). These changes correlated with alterations in synaptogenic signaling gene expression, neuron loss, and persistent glia cell activation at 106 DPI. Collectively, this study demonstrates that infection with VEEV induces chronic alterations in the hippocampus that may correlate with neurological sequalae observed in human patients.

overall_design: 12-13 week old male C57BL/6 mice were intranasally infected with Venezuelan equine encephalitis virus (VEEV) or saline (Mock/Uninfected). At 7 and 106 days post infection mice were euthanized, perfused with PBS, and the right hemisphere hippocampus was dissected and pooled in n=5 for sequencing. At 7 DPI, mice were classified as Mock 7 DPI (uninfected, or mock-infected) and VEEV 7 DPI. At 106 DPI mice, groups were classified as Mock 106 DPI, VEEV 106 DPI, and VEEV + neuro 106 DPI which are a group of mice which displayed neurological  symptoms (i.e. >2 days of circling, head tild, head pressing, recumbency, altered gait, imbalance) resulting from VEEV infection

first: Morgen

last: VanderGiessen

first: Liduo

last: Yin

first: Kylene

last: Kehn-Hall


title: N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development [EPSC_RNA-seq]

overall_design: This study characterized the transcriptomic states of EPSCs and investigated the RNA stability across different states.


title: Remodeling p38 signaling in muscle controls locomotor activity via IL-15

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Exercise activation of muscle p38γ raises blood IL-15, which signal in the brain for a boost on locomotor activity.

overall_design: Three pairwise contrasts were performed: p38αMCK-KO vs. control, p38α/γMCK-KO vs. control, and p38αMCK-KO vs. p38α/γMCK-KO

first: L

last: Herrera

first: G

last: Sabio

first: C

last: Folgueira

first: A

last: Mora


title: Bortezomib increases immunotherapy efficacy through enhancement of  STING and IFN-γ signaling in lung adenocarcinoma

city: 湖北省 / 武汉市 / 硚口区

first: Yu

last: Xi

state: hubei province

address: 同济医学院附属同济医院

department: Department of Thoracic Surgery

institute: huazhong University of science and technology

summary: BTZ has been reported to block cell proliferation and promote apoptosis of NSCLC cells. However,  the clinical trails of BTZ alnoe or BTZ combinated with other chemotherapy have failed. Here,  we reported that BTZ enhanced the anti-tumor efficacy of PD1/PDL1 blockade therapy in a Lewis lung carcinoma (LLC) tumor model. In both in vitro and in vivo assay, our data showed that BTZ activated STING pathway and increased the responsiveness of tumor cells to IFN-γ through the upregulation of surface IFN-γ receptor I (IFNGR1), which contributed to the superior anti-tumor efficacy of BTZ in combination with PD1/PDL1 inhibitors in lung adenocarcinoma.

overall_design: Subcutaneous LLC tumors in triplicates that grew in C57BL/6 mice were uesd. The mice were divided into 3 groups: isotype; anti-PDL1 alone; BTZ+anti-PDL1

first: Kelin

last: Meng

first: Taiyan

last: Yu

first: Congjian

last: Wang


title: Retrospective analysis reveals the early origin and development of pulmonary perivascular cells [scRNA-seq]

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

summary: Emerging evidence suggests pericytes play a significant role in various lung diseases. However, characterizing pericytes remains challenging, impeding our understanding of their role in lung development and disease. Using single-cell RNA sequencing and DCM-time machine technology, we tracked the development of mouse pulmonary pericytes. Our study revealed the differentiation of perivascular progenitors into pericytes and vascular smooth muscle cells. Temporal analysis uncovered dynamic gene expression profiles during pericyte differentiation, highlighting pathways crucial for pulmonary vascular development. Further analysis showed intricate signaling interactions between pericyte progenitors and mature pericytes, and we validated Mcam as a bona fide pulmonary pericyte marker. These findings challenge conventional views on pericyte origin and underscore the importance of accurate pericyte identification in developmental and disease contexts. Overall, this study enhances our understanding of pulmonary pericyte ontogeny and differentiation, offering insights into their potential as therapeutic targets in pericyte-associated lung diseases.

overall_design: We performed scRNA-seq and MeD-seq on DCM-time machine mice to track the development of mouse pulmonary pericytes.

first: Isabel

last: Sreeram

first: Ruben

last: Boers

first: Joachim

middle: B

first: Robbert

last: Rottier


title: Retrospective analysis reveals the early origin and development of pulmonary perivascular cells [MeD-seq]

type: Methylation profiling by high throughput sequencing


title: Retrospective analysis reveals the early origin and development of pulmonary perivascular cells

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

overall_design: Refer to individual Series


title: Expression Data from murine follicular B cells with or without Kindlin-3 knockout

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Integrin-mediated interactions between hematopoietic cells and their microenvironment are important for the development and function of immune cells. Here, we studied the role of the integrin adaptor Kindlin-3 in B cell homeostasis. To this end, we compared B cell development in B cell specific knockout mice for Kindlin-3 with that in wt littermates. In the spleen, constitutive B cell specific Kindlin-3 knockout caused a loss of marginal zone B cells but expansion of follicular B cells. To gain further insight on the mechanisms behind this expansion we performed microarray analysis.

overall_design: Splenocytes from Kindlin3 fl/fl mice with and without mb1-Cre (control and Kindlin-3 deficient B cells; 4 of each group) were sorted for follicular B cells and analyzed by whole transcriptome array

first: Melanie

last: Boerries

first: Dietmar

last: Pfeifer

first: Andrea

last: Härzschel

first: Tanja

last: Hartmann


title: Selective nucleophagy removes cytotoxic trapped PARP1

city: Oxford

first: Gwendoline

last: Hoslett

address: MRC Weatherall Institute of Molecular Medicine (Oxford University & John Radcliffe Hospital)

department: Oncology

country: United Kingdom

summary: Poly (ADP-ribose) polymerase inhibitors (PARPi) induce cytotoxicity in homologous recombination deficient cancers by causing PARP1 to become trapped on chromatin, resulting in irreparable replication-associated DNA damage. Cancer cells commonly develop resistance to PARPi, with a recently proposed mechanism being the clearance of trapped PARP1 from chromatin, yet details surrounding this process remain unclear. PARPi treatment causes increased autophagy flux, whilst autophagy inhibition can hypersensitise cells to PARPi. With selective autophagy of nuclear substrates (nucleophagy) shown, we wanted to explore if this occurs during DNA damage repair by clearance of trapped PARP1. We used various biochemical, cell biological and live imaging-based assays, demonstrating that trapped PARP1 is processed by selective nucleophagy. We identified that nucleophagy of trapped PARP1 is orchestrated by selective autophagy receptor TEX264 and its partner protein p97/VCP. TEX264 directly interacts with trapped PARP1, then bridges PARP1 to autophagosomal resident protein LC3 for processing via autophagy. Impeding this process, either chemically or genetically, heightened PARP1 trapping, leading to replication-associated DNA damage and cell lethality, re-sensitising PARPi-resistant cells to various PARPi. In conclusion, we show that selective nucleophagy acts in a cytoprotective manner to directly target PARPi-induced trapped PARP1 for degradation.

overall_design: To investigate the role of TEX264 in PARP inhibitor response, we developed TEX264 knockout cell lines in HeLa and CAL51. We then performed gene exression profiling by RNA-seq after 24 hours of talazoparib treatment with 2 repeats for CAL51 and 3 repeas for HeLa. We performed comparative gene expression profiling to compare wild type cells with and without treament and TEX264-KO cells to wild type with treatment.


title: N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development  [GLORI]

first: Li

last: Tang

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: Transcription factors (TFs) have key roles in cell fate determination, and are rapidly upregulated to fulfill developmental functions. During second cell fate decisions in pre-implantation embryonic development, upregulated key TFs, including GATA6 and NANOG, drive the differentiation and functional establishment of primitive endoderm (PrE) and epiblast (EPI) cells. However, how the embryo achieves this swift TF upregulation and the precise molecular mechanisms underlying specific TF initiation remain unclear. In this study, we showed how N6-methyladenosine (m6A) affected embryo and embryoid differentiation. Using two types of extended pluripotent mouse embryonic stem cells with in vivo embryonic and extraembryonic potency-extended pluripotent stem cells (EPSCs) and totipotent blastomere-like cells (TBLCs) alongside mouse embryos, we observed that the m6A writers METTL3 and VIRMA were essential for PrE development. Mechanistically, globally increased mRNA stability occurred during embryo development - mediated by m6A modification. Specifically, m6A enhanced key regulator stability during PrE differentiation, such as Gata6, by interacting with the m6A reader IGF2BP3, thereby promoting protein production and ultimately impacting on cell fate decisions. Our results suggest that post-transcriptional mRNA regulation is a pioneering mechanism governing second cell fate decisions, and highlights the molecular mechanisms underlying mouse embryogenesis.

overall_design:
The study was designed to investigate the impact of Virma on the m6A methylation profile in TBLC. To achieve this, we employed a gene knockdown approach using siRNA to specifically deplete Virma within TBLC . Following the knockdown, we utilized the GLORI to comprehensively assess the changes in the m6A methylation landscape.
This experiment was designed to validate the m⁶A demethylation efficiency of the dCas13b-FTO-sgRNA targeting system.

first: Weide

last: Xiao

first: Mingli

last: Ma

first: Kuisheng

last: Liu


title: Transcriptional characterization of Mycobacterium tuberculosis-specific memory T cell subset response

city: Newark

first: Padmini

last: Salgame

state: NJ

address: 185 South Orange Ave

department: Medicine

institute: Rutgers New Jersey Medical School

summary: We provide transcriptional profiles of CD4+ memory T cell subsets in response to M. tuberculosis antigen stimulation of cells obtained from donors with confirmed latent TB infection (LTBI) to interrogate the memory recall response.  We observe that different memory T cell subsets exhibit unique responses to Mtb stimulation.

overall_design: Transcriptome profiles via RNAseq of sort-purified CD4+ stem cell memory, central memory, transitional memory, and effector memory T cells [4 cell types], under conditions of co-stimulation plus Mtb antigen stimulation or co-stimulation only [2 treatment conditions], obtained from five LTBI donors [5 subjects].

first: Samantha

last: Leong


title: Identification of senescent cell subpopulations by CITE-seq analysis

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Cellular senescence, a state of indefinite growth arrest, is closely associated with aging and age-related diseases.  Deciphering the heterogeneity within senescent cell populations and identifying therapeutic targets are paramount for mitigating senescence-related pathologies.  In this study, proteins on the surface of senescent cells were identified using mass spectrometry, and a subset of them was used for single-cell CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) analysis.  Among seven clusters of senescent cells identified, cluster 1 was characterized by high levels of CD109 and CD112 on the plasma membrane, and cluster 2 by high levels of CD44, CD73, CD49a, and CD54 on the plasma membrane.  The transcriptomes of cluster 1 revealed cells in which translation was reduced, proteolysis was increased, and SASP factors including IL1B, GDF15, CCL13, and CCL2 were expressed.  The transcriptomes of cluster 2 revealed cells that expressed a different subset of SASP factors such as VEGFA, IL13, IL15, FGF2, and FGF7, as well as extracellular matrix remodeling factors.  Our study highlights the heterogeneity of senescent cells and represents the first attempt to explore the potential of cell surface proteins as tools for differentiating senescent cell programs and subclasses, paving the way for targeted therapeutic strategies in disorders exacerbated by senescence.

overall_design: We identified cell surface proteins associated with senescence, and then utilized a selection of available barcoded antibodies recognizing these proteins for subsequent CITE-seq analysis using WI-38 cells that were either left untreated (Proliferating, ‘P’) or were treated with IR (10 Gy) to induce senescence.

first: Kotb

last: Abdelmohsen

first: Krystyna

last: Mazan-Mamczarz

first: Qiong

last: Meng

first: Dimitrios

last: Tsitsipatis

first: Rachel

last: Munk

first: Martina

last: Rossi

first: Jennifer

last: L Martindale

first: Yulan

last: Piao

first: Jinshui

last: Fan

first: Yanai

last: Hagai

last: Beerman

first: Myriam

last: Gorospe


title: Targeted DNA methylation editing in vivo [mouse spleen]

status: Public on Mar 22 2026

city: Stockholm

first: Maja

last: Jagodic

address: Visionsgatan 18

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: The number of epigenome-wide association studies linking CpG DNA methylation with disease, traits and exposures, continues to rise. Establishing the causation of these associations, despite the rapid development of epigenome editing tools, remains challenging, particularly in vivo. In this study, we developed and characterized three Cre-dependent CRISPR-based mouse lines that enable locus-specific DNA methylation deposition by either constitutive or inducible dCas9-DNMT3A expression. We demonstrate robust locus-specific DNA methylation deposition of MHC class II (H2-Ab1) and interleukin 6 (Il6) genes in bone marrow-derived myeloid cells ex vivo. Moreover, neuron-specific targeting results in decreased cannabinoid receptor 1 (Cnr1) expression in striatal neurons in vivo. Notably, we demonstrate that the causal effect of DNA methylation on gene expression is locus-dependent, reinforcing the necessity of such editing tools for detailed understanding of the role of DNA methylation and for addressing the causality of disease-associated CpGs.

overall_design: We generated some new mouse lines that carry the deactivated form of Cas9 tethered with the catalytic domain of the human methylatransferase DNMT3A, named dCas9+/-. Crossing of the original line with another mouse line, led to the generation of an Tamoxifen inducible mouse strain, called CAG+/-; dCas9+/-. After the generation of the new mouse lines, we wanted to characterize the off-target methylation of the cassette in the spleen of the different mouse strains. We collected samples from 3 WT, 3 floxed dCas9+/- animals from the original strain, as well as 3 CAG-/-; dCas9+/- and 3 CAG+/-; dCas9+/- animals treated with Tamoxifen for the induction of the cassette. In total, 12 spleen samples were bisulfide converted and processed with the mouse EPIC methylation array.

first: Maria

last: Kalomoiri

first: Chiara

last: Sorini

first: Sebastiaan

last: Vos

first: Anderson

last: Camargo

first: Chandana

last: Rao Prakash

first: Per

last: Svenningsson

first: Majid

last: Pahlevan Kakhki

first: Lara

last: Kular


title: Targeted DNA methylation editing in vivo [mouse brain]

overall_design: We generated some new mouse lines that carry the deactivated form of Cas9 tethered with the catalytic domain of the human methylatransferase DNMT3A, named dCas9+/-. Crossing of the original line with another mouse line, led to the generation of an Tamoxifen inducible mouse strain, called CAG+/-; dCas9+/-. Afetr the genration of the new mouse lines, we wanted to characterize the off-target methylation of the cassette in the brain of the different mouse strains. We collected samples from 3 WT, 3 floxed dCas9+/- animals from the original strain, as well as 3 CAG-/-; dCas9+/- and 3 CAG+/-; dCas9+/- animals treated with Tamoxifen for the induction of the cassette. In total, 12 brain samples were bisulfide converted and processed with the mouse EPIC methylation array.


title: VLA-4 Agonist Promote Engraftment and Cell Immune Reconstitution of Allogeneic Hematopoietic Stem Cells

city: Shanghai

first: Qiaomei

last: He

address: No. 100 Haining Road, Hongkou District, Shanghai

department: Hematology

institute: Shanghai General Hospital Affiliated to  Shanghai Jiao Tong University

summary: Successful engraftment and early immune reconstitution of donor hematopoietic stem cells (HSCs) are crucial for allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, little is known about how to promote implantation and early immune reconstitution of HSCs through regulating its own functions. Here, we identified very-late antigen (VLA-4) as a pivotal target in regulating HSC implantation. Critically, we screened out a VLA-4 agonist, which could promote the implantation and long-term hematopoietic reconstitution of donor HSCs in a mixed donor chimerism (MDC) mouse model and serial xenotransplantation model of human CD34+ cells from umbilical cord blood (UCB). Competitive transplantation mouse model and limited dilution assay for UCB CD34+ cells revealed that VLA-4 agonist could enhance the self-renewal capacity of HSCs and increase the number of severe combined immunodeficient (SCID)-repopulating cells (SRCs) to five-fold in vivo. Furthermore, the VLA-4 agonist could facilitate early post-transplant cell immune reconstitution by enhancing T cell output of HSCs. VLA-4 agonist regulates HSC functions and lymphoid progenitor differentiation through affecting the ERK1/2 phosphorylation pathway, whereas may not increase the risk of leukemia transformation. These findings indicate that the VLA-4 agonist holds a great clinical translational potential in enhancing engraftment of HSCs and early cellular immune reconstitution following allo-HSCT.

overall_design: Single-cell transcriptome sequencing analysis on bone marrow cells from clinical samples and mouse models in two states, from mixed donor chimerism (MDC) to full-donor chimerism (FDC), was performed to explore the key regulatory target affecting HSC implantation after allo-HSCT. The effects of the agonists that modulate this target on HSC implantation and function after transplantation were investigated in a novel MDC mouse model, competitive transplantation mouse model and serial umbilical cord blood (UCB) xenograft transplantation model. To gain further insight into the effects of VLA-4 A2 on the process of HSC implantation after allo-BMT, we conducted scRNA-seq on BM lineage negative cells from VLA-4 A2- and vehicle-treated MDC mice at 2Ws and 5Ws after transplantation.

first: Xi

last: Sun

first: Lin

last: Chen

first: Jun

last: Yang

first: Huixian

last: Wu

first: Shixuan

last: Tang

first: Liping

last: Wan

first: Yan

last: Zhang

first: Bo

last: Zhou

first: Fang

first: Xianmin

last: Song


title: Single-cell transcriptomic analysis of hepatic immune cells from untreated and ConA-treated mice

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

summary: Hepatic immune tolerance is essential for maintaining liver homeostasis, but its underlying cellular and molecular mechanisms remain poorly defined. In this study, we established a low-dose concanavalin A (ConA)-induced immune tolerance model in mice and performed single-cell RNA sequencing (scRNA-seq) on hepatic immune cells isolated from untreated (UT) and ConA-treated groups. Transcriptomic profiling revealed substantial remodeling of the hepatic immune microenvironment following low-dose ConA stimulation. Notably, we observed a pronounced activation of type II immune responses, characterized by enrichment of Th2-associated cytokine signatures and expansion of Th2, Tfh subsets. Further analysis identified B cells as potential key contributors to this process, exhibiting distinct transcriptional programs associated with humoral immunity that may play a role in the establishment of immune tolerance.

overall_design: C57BL/6J mice were treated with low-dose concanavalin A (ConA) (10 mg/kg, i.v.) for three weeks to establish an immune tolerance model, with untreated (UT) mice as controls. Hepatic CD45⁺ immune cells were isolated by Ficoll density gradient centrifugation and subjected to single-cell RNA sequencing (10x Genomics) to profile the immune microenvironment and investigate mechanisms of hepatic immune tolerance.

first: Wenyu

last: Tian

first: Dan

last: Lv


title: Sprayable Nanozyme Hydrogel Epigenetically Reprograms Inflammation for Diabetic Wound Regeneration [GeoMX spatial transcriptomics]

city: Cheonan-si

first: Amal

middle: George

last: Kurian

state: Chungcheongnam-do

address: Pharmacy Bldg, Dankook University

department: Department of Nanobiomedical Science and Tissue regeneration Engineering

institute: Institute of Tissue Regeneration Engineering

summary: Chronic diabetic wounds present a critical clinical challenge due to persistent inflammation and compromised healing. Here we report a novel sprayable nanozyme hydrogel that epigenetically reprograms macrophages to suppress inflammation and coordinate regeneration. Ultrasmall copper-based nanozymes (CuNZ, ~4 nm) synthesized via an eco-friendly one-pot method demonstrated potent multi-radical scavenging activity. When integrated into gelatin methacryloyl (Gel), CuNZ@Gel exhibited excellent sprayability, conformal skin coverage, and long-term storage stability, offering substantial translatable potential. Notably, the nanozyme hydrogel induced distinct epigenetic modifications in macrophages by remodeling chromatin accessibility, effectively shifting gene expression from pro-inflammatory to anti-inflammatory profiles. This epigenetic modulation persisted under oxidative stress, actively suppressing inflammatory while facilitating regenerative responses. In diabetic wound models, CuNZ@Gel significantly accelerated healing through its coordinated antioxidant, anti-inflammatory, and pro-regenerative actions. Unlike conventional passive dressings, our sprayable nanozyme hydrogel proactively reprograms the wound microenvironment via epigenetic antioxidant mechanisms, offering novel insights and strategy for managing chronic diabetic wounds and inflammatory skin complications.

overall_design: GeoMX spatial transcriptome profiling of rat skin tissues at day 7 post-wounding

first: Amal George

first: Jeong-Hui

last: Park

first: Shanika

last: Karunasagara

first: Archita

last: Gupta

first: Shreyas Kumar

last: Jain

first: Tanza

last: Baby

first: Ueon Sang

last: Shin

first: Sak

last: Lee

first: Rajendra

middle: K

last: Singh

first: Jung-Hwan

first: Kam

middle: W

last: Leong

first: Hae-Won

last: Kim


title: Sprayable Nanozyme Hydrogel Epigenetically Reprograms Inflammation for Diabetic Wound Regeneration [Chip-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chip-Seq

first: Buuvee

last: Bayarkhangai


title: Transcriptomic analyses of human islets

city: LILLE

first: JULIE

last: KERR-CONTE

address: PLACE DE VERDUN

department: University of Lille-Faculty of Medicine

country: France

institute: INSERM U1190

summary: 58 human clinical islet preparations were selected from the frozen biobank of the Cell Therapy Unit of Lille University Hospital. Total RNA was extracted and subjected to high-throughput sequencing on an Illumina platform. Transcriptomic profiles were subsequently analyzed and used for 2 studies : Type 2 diabetic vs. normoglycemic donors and NKX6.1-high vs. NKX6.1-low islets.

overall_design: Human islets isolated from the pancreata of brain-dead donors were cultured at 37°C, pelleted by centrifugation, and stored at −80°C in a frozen biobank. 58 preparations were subsequently thawed, resuspended in lysis buffer, and processed for total RNA extraction. : 50 samples were used to compare type 2 diabetic (n=7) and normoglycemic (n=43) patients, and 14 samples were used to compare islets with NKX6.1-high expression (n=7) and NKX6.1-low expression (n=7).

first: G

last: Pasquetti

first: J

last: Kerr-Conte

first: F

last: Pattou

last: Vandel

first: C

last: Amayene Amassogo


title: Defining Chicken Host Responses to Spotty Liver Disease

city: Gainesville

first: Lekshmi

last: Edison

address: 1945 SW 16th Ave

institute: University of Florida

summary: Spotty Liver Disease (SLD) is an acute bacterial infection of layer hens, caused by Campylobacter hepaticus, and occurs most frequently in barn-housed and free-range production systems. The disease is characterized by a sharp decline in egg production and increased mortality.The characteristic  feature is the presence of 1-2 mm white to grey necrotic foci distributed across the liver surface.Despise its impact,the molecular mechanisms underlying host responses to C. hepaticus infection remain poorly understood.To address this gap, we performed a comprehensive analysis using RNA sequencing of liver tissue from naturally infected chickens compared to uninfected controls.

overall_design: To investigate the differential gene expression profiles between healthy (control) chicken liver tissue and liver tissue  infected with Campylobacter hepaticus

first: Varsha

last: Bommineni

first: Chaitanya

last: Gottapu

first: Gary

last: Butcher

first: Subhashinie

last: Kariyawasam


title: 2P-NucTag: on-demand phototagging for molecular analysis of functionally identified cortical neurons [day 0 vs recurring place cells]

city: New York

first: Jingcheng

last: Shi

state: NY

address: 3227 Broadway

department: Neuroscience

institute: Columbia University

summary: Neural circuits are characterized by genetically and functionally diverse cell types. A mechanistic understanding of circuit function is predicated on linking the genetic and physiological properties of individual neurons. However, it remains highly challenging to map the molecular properties onto functionally heterogeneous neuronal subtypes in mammalian cortical circuits in vivo. Here, we introduce a high-throughput two-photon nuclear phototagging (2P-NucTag) approach for on-demand and indelible labeling of single neurons via a photoactivatable red fluorescent protein following in vivo functional characterization in behaving mice. Using this optimized function-forward pipeline to selectively label and transcriptionally profile previously inaccessible ‘place’ and ‘silent’ cells in the hippocampus of behaving mice, we identify unexpected differences in gene expression between these hippocampal pyramidal neurons with distinct spatial coding properties. Furthermore, we demonstrate multiple downstream experimental directions that 2P-NucTag enables including ex vivo slice electrophysiology and histology. Thus, 2P-NucTag opens a new way to uncover the molecular principles that govern the functional organization of neural circuits.

overall_design: Gene expression profiling analysis of RNA-seq data of mouse hippocampal pyramidal neurons functionally identified as 'Day 0' place cells and 'Recurring' place cells during spatial navigation. Nuclei were collected following functional in vivo two photo imaging and phototagging.

first: Bovey

last: Rao

first: Attila

last: Losonczy

first: Ivo

last: Spiegel


title: HDAC3 Regulates Transcriptional Networks Governing Decidualization

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

summary: Hdac3d/d mice showed defective decidualization as early as day 3, establishing this as a key time point for molecular assessment. To identify the signaling pathways regulated by Hdac3 during decidualization, RNA-seq was performed on the stimulated uterine horns of Hdac3f/f and Hdac3d/d mice on day 3

overall_design: We used RNA-sequencing to determine the differences in uterine gene expression resulting from Hdac3f/f and Hdac3d/d mice  at decidualization day 3

first: Jeong

last: Jae Wook

first: Kim

last: Tae Hoon


title: Single-cell transcriptomic profiling of NRasG12V/myrAKT-driven hepatocellular carcinoma with Sepp1 knockdown and selenium supplementation

first: Jiazheng

last: Jiao

state: Shanghai

address: 319 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary:
The immune microenvironment of hepatocellular carcinoma (HCC) is strongly influenced by tumor-infiltrating neutrophils, whose functional heterogeneity and regulatory mechanisms remain incompletely defined. Selenium metabolism, mediated by selenoprotein P (Sepp1), plays an important role in redox homeostasis and immune regulation in the liver.

In this study, Ras/AKT-driven murine HCC models with Sepp1 knockdown were generated under control or selenium-supplemented conditions. Single-cell RNA sequencing was performed using the 10x Genomics Chromium platform to profile tumor tissues and the associated tumor microenvironment, with a particular focus on neutrophil populations.

This dataset enables systematic analysis of neutrophil transcriptional states associated with selenium metabolism and immunoregulatory pathways in HCC. The data provide a resource for investigating how alterations in Sepp1 expression and selenium availability shape tumor-immune interactions at single-cell resolution.

overall_design: Single-cell RNA sequencing was performed using the 10x Genomics Chromium platform to profile the tumor immune microenvironment in a Ras-AKT driven mouse hepatocellular carcinoma model. Tumors were collected from control (CT), selenium supplemented (SE), shRNA negative control (shNC), and Sepp1 knockdown (shSEPP1) groups. Single-cell suspensions were prepared from tumor tissues, and libraries were generated following the 10x Genomics standard protocol. Processed gene expression matrices were generated using Cell Ranger.

first: Lixing

last: Zhan


title: 2P-NucTag: on-demand phototagging for molecular analysis of functionally identified cortical neurons

overall_design: Gene expression profiling analysis of RNA-seq data of mouse hippocampal pyramidal neurons functionally identified as 'place' and 'silent' cells during spatial navigation. Nuclei were collected following functional in vivo two photo imaging and phototagging.


title: Sprayable Nanozyme Hydrogel Epigenetically Reprograms Inflammation for Diabetic Wound Regeneration [mRNA-seq]

first: Amal

last: Kurian

overall_design: mRNA seq profiling of RAW 264.7 macrophage cells treated with hydrogels for 48 hours

first: Amal George

first: Jeong-Hui

last: Park

first: Shanika

last: Karunasagara

first: Archita

last: Gupta

first: Shreyas Kumar

last: Jain

first: Tanza

last: Baby

first: Ueon Sang

last: Shin

first: Sak

last: Lee

first: Rajendra

last: Singh

first: Jung-Hwan

first: Kam

last: Leong

first: Hae-Won

last: Kim


title: Protective role of early Tnfsf15 upregulation in limiting glomerular injury and proteinuria in experimental Alport Syndrome

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

summary: Alport syndrome is a progressive kidney disease caused by pathogenic variants in genes encoding type IV collagen, a major structural component of the glomerular basement membrane (GBM). Abnormal GBM architecture impairs filtration and triggers inflammation, fibrosis, and eventual kidney failure. Because disease progression is irreversible, identifying early molecular changes is essential for understanding disease onset. We performed glomerular single-cell RNA sequencing (scRNA-seq) in a Col4a5 G5X Alport mouse model at 5 weeks of age, prior to detectable proteinuria or GBM/podocyte abnormalities (pre-onset), and at 8 weeks, when mild proteinuria and structural defects emerged. Despite the early stage, scRNA-seq revealed widespread transcriptional alterations, most prominently in podocytes. Among genes upregulated at both time points, we identified Tumor Necrosis Factor Superfamily Member 15 (Tnfsf15), previously associated with kidney disease susceptibility but with unclear function. To determine its role in Alport syndrome, we generated Tnfsf15-deficient Alport mice. Tnfsf15 homozygous knockout mice exhibited increased proteinuria and exacerbated glomerular injury compared with Tnfsf15(+/+) Alport mice during early disease. These findings support a protective role for Tnfsf15 in the early stages of Alport syndrome, mitigating proteinuria and limiting glomerular injury.

overall_design: We performed glomerular single-cell RNA sequencing (scRNA-seq) analysis in a 5-week-old Alport mouse model (Col4a5 G5X), which did not yet exhibit proteinuria or structural changes in the GBM and podocyte (Pre-onset), and in 8-week-old Alport mice, which exhibited mild proteinuria and abnormal structure of the GBM and podocyte.

first: Aimi

last: Owaki

first: Mary Ann

last: Suico

first: Koichiro

last: Miike

first: Ryuichi

last: Nishinakamura

first: Hirofumi

last: Kai


title: Sprayable Nanozyme Hydrogel Epigenetically Reprograms Inflammation for Diabetic Wound Regeneration [ATAC-seq]

first: Amal

last: Kurian

overall_design: ATAC seq profiling of RAW 264.7 macrophage cells treated with hydrogels for 48 hours

first: Amal George

first: Jeong-Hui


title: Gene expression in Meckel's and condylar cartilages from WT and FGFR3 mutant mice

city: Paris

first: Martin

last: Biosse Duplan

address: 24 Boulevard du Montparnasse

institute: Institut Imagine INSERM Université Paris Cité

summary: Meckel's and condylar cartilages are key to mandible development. In achondroplasia, the most common form of genetic dwarfism, abnormalities of these cartilages lead to micrognathia, with significant functional repercussions for affected individuals. Using cartilage laser-microdissection and RNA-seq analyses, we analyzed the genes expressed in these cartilages in a mouse model mimicking achondroplasia and compared the transcriptome of Meckel’s and condylar cartilages from E16.5 embryos of control and Fgfr3Y367C/+ mice. Over 600 genes were differentially expressed. Our data suggest that dysregulation of several pathways due to Fgfr3 gain-of function mutation constitutes an important underlying mechanism in craniofacial defects observed in achondroplasia.

overall_design: RNA-seq profiling of laser-microdissected Meckel's and condylar cartilages from E16.5 embryos of control and Fgfr3Y367C/+ mice

first: Valentin

last: Estibals

first: Mohammed

last: Zarhrate

first: Laurence

last: Legeai Mallet


title: Correcting the immune microenvironment disturbed by the overactivation of the neutrophil-driven microglia positive feedback loop efficiently suppressed pathological retinal angiogenesis

city: Xian

first: Ziyi

last: Zhou

address: Xijing Hospital, No.127, Changle W. Road, Xincheng District

institute: Xijing Hospital

summary: Disrupting Galectin-3/NET-mediated microglia-neutrophil crosstalk suppresses retinal angiogenesis, revealing self-reinforcing immune mechanisms in advanced disease.

overall_design: This study aims to investigate the regulatory effects of neutrophils and neutrophil extracellular traps (NETs) on microglia. To achieve this, we performed transcriptome sequencing (RNA-seq) on three groups of mouse BV2 microglial cells: (1) BV2 cells cultured alone (control group); (2) BV2 cells co-cultured with primary mouse neutrophils; and (3) BV2 cells co-cultured with primary mouse neutrophils stimulated by phorbol 12-myristate 13-acetate (PMA) to induce NETosis and NET release. By comparing the gene expression profiles of these groups, we seek to identify key signaling pathways and transcriptional changes in microglia triggered by neutrophil interactions and, more specifically, by NETs. The data generated from this project will provide insights into the crosstalk between innate immune cells and contribute to the understanding of neuroinflammatory mechanisms.

first: Tianhao

last: Yuan

first: Guorui

last: Dou


title: Plasma Olink Explore HT of primary glomerular disease patients

city: Seoul

first: Jae-ik

last: Oh

address: 101, Daehak-ro, Jongno-gu

department: Translational Medicine

institute: Seoul National University College of Medicine

summary: This study utilized large-scale systemic proteome profiling to identify distinct protein signatures that can non-invasively differentiate major subtypes of primary glomerular disease and provide insights into their underlying mechanisms.

overall_design: Plasma proteome profiling was performed using the Olink Explore HT platform, which quantified 5,416 proteins from 147 discovery samples and 85 validation samples encompassing major subtypes of primary glomerular disease (FSGS, IgAN, MCD, MN) and healthy controls.

first: Kyeonghun

last: Jeong

first: Jung Hun

last: Koh

first: Jin Gyeong

last: Kwon

first: Semin

last: Cho

first: Jeong Min

first: Yaerim

first: Hajeong

last: Lee

first: Hyun Je

first: Jeonghwan

first: Jung Pyo

first: Ji In

last: Park

first: Jung Tak

first: Kwangsoo

first: Sehoon

first: Dong Ki


title: Constitutive activation of canonical Wnt signaling in hem progenitors suppresses the fate of hem-derived Cajal-Retzius cells

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: B304 TIFR Homi Bhabha road

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

summary: Cajal-Retzius cells (CR cells) are the earliest born neurons in the cerebral cortex, and have been implicated in neuronal migration and development of cortical circuitry. One of the sources of CR cells is the cortical hem, which is rich in morphogens of the canonical WNT signaling family. In this study we examine the effect of stabilization of β-CATENIN (gain of function, GOF) in the mouse cortical hem and show that although neurons are still produced, they do not acquire a CR cell identity. The trajectory of differentiation examined using single-cell transcriptomics revealed that upon β-CATENIN GOF, hem-derived CR cells do not display a TBR2+ stage characteristic of immature CR cells. This effect is only seen when β-CATENIN GOF is driven in hem progenitors and is not seen upon β-CATENIN GOF in postmitotic CR cells. These data suggest that a TBR2+ stage may be important for hem-derived CR cell development and that this step appears to be sensitive to levels of stabilized β-CATENIN in hem progenitors.

overall_design: This database contains transriptomes from the telencephalic midline of E11.5 and E14.5 mouse embryos, from Lmx1aCre::Ai9 and Lmx1aCre::Ai9::b-cat gof backgrounds. A subdissected region around the cortical hem, including Cajal-Retzius cells and parts of the hippocampal primordium, were used as input. 5 male embryos were dissected (both hemispheres) for the E11.5 libraries, and 3 male embryos were dissected (both hemispheres) for the E14.5 libraries.


title: 10X Visium Spatial transcriptomics of small intestine from mice fed stearic acid-rich high fat diet (HFD)

city: Chuo-ku

first: Keisuke

last: Sekine

state: Tokyo

address: 5-1-1 Tsukiji

department: Graduate School of Medicine

institute: National Cancer Center Research Institute, Japan

summary: We obtained transcriptome profiling of small intestine from mice fed control diet (CD) or stearic acid-rich HFD by using 10X Visium.

overall_design: Comparison of expression pfofiles between mice fed CD and stearic acid-rich HFD.

first: Kazuaki

last: Nakata

first: Yuki

middle: I

last: Kawamura


title: Cancer Stem Cells Induce Proline Synthesis through FAM3C-Mediated SPIN1 Stabilization to Attenuate ROS Stress

city: Chapel Hill

first: Donghai

last: Wang

state: North Carolina

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill (UNC)

summary: Tumors reprogram amino acid metabolism to dysregulate cellular growth through multiple mechanisms. Here, we find that glioblastoma (GBM) stem cells (GSCs) contain increased proline levels relative to differentiated GBM cells (DGCs) through increased proline synthesis. We identified FAM3C (FAM3 Metabolism Regulating Signaling Molecule C) as an upstream driver of proline synthetic enzyme expression. The core stem cell transcription factor, SOX2, drove GSC-specific expression of FAM3C. FAM3C is secreted, but, in GSCs, intracellular FAM3C directly bound histone 3 lysine 4 trimethyl lysine 9 trimethyl (H3K4me3K9me3) reader, SPIN1 (Spindlin1), to prevent SPIN1 lysosomal degradation and promote epigenetic regulation of proline synthesis. Proline synthesis depletes reactive oxygen species (ROS); genetic targeting of FAM3C attenuated ROS scavenging, while SPIN1 overexpression restored ROS levels. Molecular docking screening identified tucatinib as a brain penetrant pharmacologic disruptor of FAM3C-SPIN1 interactions, promoting SPIN1 degradation and reducing intracellular proline levels. Thus, the SOX2-FAM3C-SPIN1 axis activates proline metabolism in GBM and targeted through repurposing of tucatinib.

overall_design: FAM3C was knocked down using shRNA, and total RNA was extracted with Trizol reagent, followed by next-generation sequencing to investigate the molecular mechanism of FAM3C regulation in GSC23 cells.

first: Weichi

last: Wu

first: Jeremy

last: Rich


title: GmMYB21a improves male fertility of CMS-based restorer line under high-temperature stress in soybean

status: Public on Mar 21 2026

city: Nanjing

first: Jilei

last: Gan

address: No. 666, Binjiang Avenue, Jiangbei New District, Nanjing, Jiangsu Province

institute: Nanjing Agricultural University

summary: High-temperature (HT) stress during flowering causes male sterility and yield loss in soybean. MYB transcription factors are key regulators under abiotic stress, yet their function and mechanism in regulating male fertility under HT stress in soybean are not fully understood. In this study, a MYB transcription factor GmMYB21a in soybean was identified. GmMYB21a was induced by HT stress in soybean restorer line and was specifically expressed in pollen. Through overexpression and knockout experiments, we demonstrated that GmMYB21a positively regulates pollen fertility and germination under HT stress. Overexpression of GmMYB21a significantly enhanced these traits in restorer line, whereas knockout plants exhibited the opposite effect. Transcriptome sequencing revealed that GmMYB21a overexpression upregulated numerous stress-responsive genes, particularly those involved in flavonoid biosynthesis and sugar metabolism. In addition, molecular experiments confirmed that GmMYB21a bound to the flavonoid synthesis gene GmCHI2-A and promoted its expression. In summary, our research indicated GmMYB21a enhanced the HT-tolerance of male fertility in soybean restorer line through reactive oxygen species scavenging and flavonoid synthesis. This study aims to elucidate the thermotolerance mechanism in soybean male fertility and identify genetic resources for breeding HT-tolerant restorer lines.

overall_design: RNA-seq profiling of wildtype TL and  overexpression line GmMYB21a-OE2 at normal temperature and high temperature treatment.

first: Hongjie

first: Yujuan

last: Gu

first: Xianlong

last: Ding

first: Shouping

last: Yang


title: Microfluidic technology for low-input mapping of genome-wide lncRNA-chromatin interactions using tissue samples

city: Blacksburg

first: Chang

last: Lu

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: Long noncoding RNAs (lncRNAs) regulate gene expression through binding to DNA, various RNAs, and proteins, playing potentially important but poorly understood roles in development and diseases. Existing approaches for profiling lncRNA–chromatin interactions at the genome scale require large quantities of input material (e.g., 100 million cells per assay). Applying these technologies to tissue samples has been challenging especially when examination of a specific cell type is desired. Here we demonstrate a low-input microfluidic technology based on Chromatin Isolation by RNA purification (ChIRP) process for mapping lncRNA–chromatin interactions using as few as 50,000 cells. We validate our technology on two lncRNAs of different sizes in human and mouse cell lines and brain tissue. We apply our technology muChIRP-seq to neuronal nuclei from postmortem human brain tissues and integrate our data with histone and RNA-seq data to understand the role of lncRNA in the epigenomic and transcriptomic landscape of schizophrenia. MuChIRP-seq enables the mapping of lncRNA–chromatin interactions in tissue samples and in a cell-type-specific fashion, unlocking new opportunities to study lncRNA-mediated gene regulations.

overall_design: To test the capabilities of muChIRP-seq, bulk ChIRP-seq (Chu et al. Molecular Cell 44 (2011) 667-678) was performed for the lncRNA TERC in HeLa cells and was compared to data collected with muChIRP-seq using 1 million, 500K, 250K, 100K, and 50K cells of input. To further test the method, muChIRP-seq data was collected for the lncRNA Gomafu in NE-4C for 500K, 250K, 100K, and 50K cells of input and in HeLa for 100K cells of input. To test performance in cell-type specific tissue, muChIRP-seq was performed for the lncRNA TERC in FACS-sorted NeuN+ and NeuN- nuclei from mouse cortex tissue from 80-week old mice. As a proof-of-concept study, muChIRP-seq for the lncRNAs TERC and Gomafu was performed on NeuN+ nuclei from prefrontal cortex (PFC) tissue of 7 schizophrenia patients (SCZ) and their matched controls (CNTRL).

first: Jenna

middle: A

last: Catalano


title: 10X VisiumHD Spatial transcriptomics of small intestine from mice fed stearic acid-rich high fat diet (HFD).

summary: We obtained transcriptome profiling of small intestine from mice fed control diet (CD) or stearic acid-rich HFD by using 10X VisiumHD.


title: 10X Visium Spatial transcriptomics of pancreatic caner patient tissue.

summary: We obtained transcriptome profiling of pancreatic cancer tissue specimen by using 10X Visium FFPE version2.

overall_design: We performed spatial transcriptomic analysis of pancreatic cancer tissues to investigate the spatial organization and interaction of cancer cells, CAFs, and immune components within the tumor microenvironment.

first: Nobuyoshi

last: Hiraoka

first: Kosuke

last: Arai

first: Kazunori

last: Aoki


title: Gene expresson profile at single cell level of  myeloid cells from pancreatic cancer tissue.

summary: Myeloid cells (CD33+ cells) are heterogenous population and are considered to be immune suppressive in pancreatic cancer tissue. We conducted single-cell RNA sequencing of myeloid cells from pancreatic cancer to analyze the diversity of myeloid cells and their molecular characterisitcs in pancratic cancer.

overall_design: Human myeloid cells were isolated by Fluorescence activated cell sorting (FACS) according to staining with the CD45 and CD33 antibodies, and analyzed using scRNA-seq.

first: Hironori

last: Fukuda