title: scMulti-omics of E7.0 mouse embryos

first: Jingjing

last: He

institute: Southeast University

summary: We used single cell Multiome (ATAC + Gene Expression sequencing) sequencing  to analyze E7.0 mouse embryo.

overall_design: E7.0 mouse embryos were dissociated and then subjected to nuclei isolation, library preparation by following the manufacturer’s instruction. The library was sequenced and analyzed using scMulti-omics.

first: Jiang

last: Xu

first: Zhuanzhuan

last: Che


title: A Novel Function of the Branched-Chain Fatty Acid iso15:0 in Suppressing HCC Malignant Progression through GPCR/PI3K/AKT Pathway Inhibition

status: Public on Dec 07 2025

city: Chongqing

first: Juan

address: No. 131 Yubei Road, Shapingba District

country: China

institute: Chongqing University

type: Expression profiling by high throughput sequencing

summary: Despite advances in hepatocellular carcinoma (HCC) treatment, the discovery of novel bioactive molecules with well-defined mechanisms remains a critical need. This study identifies the branched-chain fatty acid iso15:0 as a potent suppressor of HCC progression and delineates its underlying molecular pathway. We demonstrated that iso15:0 significantly inhibits the proliferation and migration of HCC cells in vitro and suppresses tumor growth and metastasis in vivo. Transcriptomic profiling of treated cells revealed widespread alterations in gene expression, with Gene Set Enrichment Analysis (GSEA) pinpointing a significant suppression of the GPCR signaling pathway. Subsequent mechanistic investigations established that iso15:0 executes its function by specifically targeting the Gβγ subunits of heterotrimeric G proteins, thereby disrupting the downstream activation of the PI3K/AKT signaling cascade. This inhibition leads to cell cycle arrest and suppression of epithelial-mesenchymal transition (EMT). Our findings unveil a previously unrecognized tumor-suppressive function of iso15:0 and define a novel mechanism by which it inhibits HCC progression through targeted interference with the Gβγ–PI3K/AKT signaling axis. This work not only provides a mechanistic basis for the anti-tumor activity of iso15:0 but also highlights its potential as a promising lead compound for the development of new molecularly-targeted therapies against HCC.

overall_design: the control group (Control_con-1 to -5) and five to the iso15:0 treatment group (Treat_iso15-1 to -5)


title: Single-nucleus RNA sequencing in the post-mortem thamaus and cortex in bipolar disorder

city: Tokyo

first: Masaki

last: Nishioka

address: Bunkyo-ku Hongo 2-1-1

country: Japan

institute: Juntendo University

summary: We performed high-throughput single-nucleus RNA sequencing (snRNA-seq) using the 10x Genomics Chromium platform on archived postmortem thalamus and frontal cortex (BA10) tissues from patients with bipolar disorder and control subjects to identify cell type–specific differentially expressed genes and compositional changes.

overall_design: Single-nucleus RNA sequencing (snRNA-seq) was performed using the 10x Genomics Chromium platform on cell nuclei extracted from the thalamus and frontal cortex (BA10) of postmortem brain tissue from 20 control subjects and 21 individuals with bipolar disorder. snRNA-seq libraries were prepared with the 10x Genomics Chromium Single Cell 3’ Reagent Kits v3.1 (dual index) and sequenced on the Illumina NextSeq 2000 platform (paired-end). Count matrices were generated with Cell Ranger v7.0.0.

first: Mie

last: Sakashita-Kubota

first: Kouichirou

last: Iijima

first: Naguib

last: Mechawar

first: Gustavo

last: Turecki

first: Tadafumi

last: Kato


title: Translatome and transcriptome sequencing data of 16-day kinetic response in colorectal cancer to 5-FU chemotherapy

city: Montpellier

first: Eric

last: Rivals

address: 161 Rue Ada

department: Montpellier University and CNRS

country: France

institute: Laboratoire d'informatique, de robotique et de microélectronique de Montpellier

summary: Resistance to 5-fluorouracil (5-FU) remains a major challenge in colorectal cancer therapy, often resulting in tumor relapse fueled by drug-tolerant persister (DTP) cells. Unexpectedly, instead of suppressing translation under chemotherapeutic stress, 5-FU by integrating ribosomal RNA of persister cells drives a transient surge in protein synthesis, revealing a distinct adaptive state. This translational reprogramming drives a highly plastic subpopulation that supports survival under drug pressure. Integrated translatome profiling uncovered selective translation of mRNAs linked to survival pathways including epigenetic and metabolic changes, apoptosis resistance, cell cycle arrest and a senescence-like phenotype. Together, our findings uncover active translation as an unrecognized hallmark of the DTP state.

overall_design: Comparison of cytoplasmic transcriptome and polysome profiling fractions (more than 3 linked ribosomes) of HCT116 colorectal cancer cells treated with 5-FU. RNA samples were collected at 6 time points (D0, D1, D2, D7, D14 and D16) after treatment, 3 replicates were used.

first: Mounira

last: Chalabi-Dchar

first: Laura

last: Jentschel

first: Julie

last: Ripoll

first: Anne

last: Vincent

first: Rita

last: Khoueiry

first: Arnaud

last: Vigneron

first: Nicole

last: Dalla Venezia

last: Pannequin

first: Jean-Jacques

last: Diaz


title: Mechanisms of PM2.5 Exposure Impact on the Malignant Progression of Breast Cancer Subtype [MCF-7 RNA-seq]

city: 南充市

first: ziru

last: zhou

state: 四川

address: 顺庆区涪江路234号

institute: 川北医学院

summary: As a major global health threat to women, breast cancer demonstrates significant molecular subtype-specific variations in response to PM2.5 exposure. While epidemiological evidence has confirmed the association between PM2.5 and breast cancer, the molecular mechanisms by which severe PM2.5 pollution drives subtype heterogeneity remain poorly understood and are difficult to characterize using conventional phenotypic approaches. To address this, we apply integrated transcriptomic sequencing and bioinformatics analysis to investigate molecular response mechanisms in three representative breast cancer cell lines—Luminal A (MCF-7), Luminal B (T-47D), and triple-negative (MDA-MB-231)—following severe PM2.5 exposure. Our results reveal that although all three subtypes share a common response to the stress of metal ions and inorganic substances, each exhibits distinct molecular alterations after PM2.5 exposure: the response mechanisms of MCF-7 cells are primarily involved in extracellular matrix remodeling, neuro-lik differentiation, and inflammatory signaling; T-47D cells show significant enrichment in the synaptic membrane, oxidoreductase metabolism, and ferroptosis pathway; and MDA-MB-231 cells exhibit a core response centered on cell cycle progression and mitosis. Furthermore, we identify subtype-specific hub genes and predict the corresponding targeted drugs: Niclosamide targeting BRCA1 in MCF-7, Menadione targeting NQO1 in T-47D, and PHA-793887 targeting CDK1 in MDA-MB-231. This study establishes a comprehensive research framework spanning environmental exposure, cellular response, clinical validation, and drug prediction. The findings provide important insights into the subtype-specific carcinogenic mechanisms of PM2.5 and support the development of individualized prevention strategies for breast cancer.

overall_design: RNA-seq profiling of MCF-7 cells under control (MCF-7_CK1, MCF-7_CK2, MCF-7_CK3) and experimental treatment (MCF-7_CQ1, MCF-7_CQ2, MCF-7_CQ3) conditions. The study includes three biological replicates per condition to investigate transcriptomic changes in response to the experimental treatment.


title: Effect of over expression RGS6e forward and RGS6e Reverse on gene expression of SK-N-SH cells (Human neuroblastoma cell line)

city: Guangzhou

first: Zhongju

last: Wang

state: Guangdong

address: No. 1023-1063, South Sha-tai Road, Baiyun District

institute: Southern Medical University

summary: As fundamental units of transcriptional regulation, enhancers also produce transcriptional products known as enhancer RNAs (eRNAs), whose expression levels reflect their activity. Recently, more studies have demonstrated the function of eRNAs. Therefore, it is important to elucidate the relationship between enhancers and schizophrenia for a deeper understanding of the molecular mechanisms underlying schizophrenia. We here report the enhancer activity and the expression products of RGS6e may contribute to decrease schizophrenia risk. we found that the unregulated genes of over-expression RGS6e  are significantly enriched in psychiatric disorders, suggesting that RGS6e may regulate the expression of nervous system-related genes through trans-acting mechanisms. Taken together, our data supported the notion that RGS6e may impact susceptibility to SZ through trans-acting effects.

overall_design: RNA-seq profiling of over-expression RGS6e Forward and RGS6e Reverse, and their corresponding empty vector in SK-N-SN cells.


title: NANP Targeting Radio-sensitizes Glioblastoma through TNFR1 Sialylation-Driven Mesenchymal Shift

city: New York

first: Erik

last: Sulman

state: NY

address: 522 First Avenue

department: Radiation Oncology

country: USA

institute: NYU Langone

summary: GBM remains a highly devasting brain tumor mainly due to the resistance to radiotherapy (RT), the most impactful first-line treatment for GBM. Our clonal evolution study reveals no dominant RT-resistant clones to target for recurrence prevention, leading us for a genome-wide CRISPR screening for radio-sensitizing targets in GBM. The screening highlighted DNA damage response genes, particularly in the non-homologous end-joining (NHEJ) pathway, such as PRKDC and NHEJ1, as potent radio-sensitizers. Additionally, NANP (N-acylneuraminate-9-phosphatase), a critical enzyme in the sialic acid synthetic pathway, was identified as a novel RT-sensitizing target associated with patient outcomes. NANP knockdown induces increased G2/M arrest and apoptosis following radiation, with γH2AX staining and comet assays indicating greater DNA damage. NANP deficiency impairs DNA repair, favoring error-prone NHEJ over homologous recombination (HR). Mechanistically, NANP modulates the sialylation of TNFR1, thereby influencing NF-kB signaling and the mesenchymal (MES) state of glioma stem cells (GSCs), which consequently affects RT sensitivity. Intracranial orthotopic xenograft experiments validate the function of NANP in vivo. In summary, our findings identify NANP as a novel radio-sensitizing target, dependent on TNFR1 sialylation and MES shift, providing a basis for developing innovative RT sensitizers for GBM.

overall_design:
To investigate the transcriptomic impact on GSCs upon NANP siliencing by shRNAs, we established control and NANP knockdown GSC20 (shCTL,shNANP-1 and shNANP-3)  and GSC11(shCTL and shNANP-1).
We then performed gene expression profiling analysis from RNA-seq of these GSCs.
Comparative analysis of gene expression were then performed using DESeq2.

first: Yingwen

last: Ding

first: Ze-Yan

last: Zhang


title: Exacerbation of influenza virus induced lung injury by alveolar macrophages and its suppression by pyroptosis blockade in a human lung alveolus chip

city: Boston

first: Yuncheng

last: Man

state: MA

address: 201 Brookline Ave

institute: Wyss Institute, Harvard University

summary: Alveolar macrophages (AMs) are the major sentinel immune cells in human alveoli and play a central role in eliciting host inflammatory responses upon distal lung viral infection. Here, we incorporated peripheral human monocyte-derived macrophages within a microfluidic human Lung Alveolus Chip that recreates the human alveolar-capillary interface under an air-liquid interface along with vascular flow to study how residential AMs contribute to the human pulmonary response to viral infection. When Lung Alveolus Chips that were cultured with macrophages were infected with influenza H3N2, there was a major reduction in viral titers compared to chips without macrophages; however, there was significantly greater inflammation and tissue injury. Pro-inflammatory cytokine levels, recruitment of immune cells circulating through the vascular channel, and expression of genes involved in myelocyte activation were all increased, and this was accompanied by reduced epithelial and endothelial cell viability and compromise of the alveolar tissue barrier. These effects were partially mediated through activation of pyroptosis in macrophages and release of pro-inflammatory mediators, such as interleukin (IL)-1β, and blocking pyroptosis via caspase-1 inhibition suppressed lung inflammation and injury on-chip. These findings demonstrate how integrating tissue resident immune cells within human Lung Alveolus Chip can identify potential new therapeutic targets and uncover cell and molecular mechanisms that contribute to the development of viral pneumonia and acute respiratory distress syndrome (ARDS).

overall_design: To investigate the role of blood monocyte-derived macrophages on exacerbating influenza-induced lung injury, we cultured human lung alveolus chips with or without macrophages in the epithelial channels, infected or mock infected chips with influenza H3N2, and compared the global gene expression of these chips.


title: Gene expression profiling of parental and EGFR inhibitor resistant EGFR-mutant NSCLC cell lines treated with MCB-613

city: Durham

first: Kris

last: Wood

state: NC

address: 450 Research Drive, LSRC C259, PO Box 3813

department: Department of Pharmacology and Cancer Biology

institute: Duke University

summary: RNA-seq analysis in PC9, GR4, and WZR12 cells treated with DMSO or MCB-613 for 24 hours.

overall_design: PC9, GR4, and WZR12 cells were treated with DMSO or 2 µM MCB-613 for 24 hours in biologically independent triplicate. RNA was isolated using the Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions and sent for paired-end RNA sequencing by the Duke Sequencing and Genomic Technologies core facility. Mapped reads were using DESeq2 and assessed for differential expression in vehicle- and MCB-613-treated parental (PC9) and EGFR inhibitor resistant (GR4, WZR12) cells.

first: Christopher

middle: F

last: Bassil

middle: C

first: Jacob

middle: P

last: Hoj


title: Ascl5 variant disrupts gene expression in developing mandibular teeth and dental arch structures

city: Bangkok

first: Thanakorn

last: Theerapanon

address: 34 Henri-Dunant Road, Wangmai, Patumwan

country: Thailand

institute: Faculty of Dentistry, Chulalongkorn university

summary: Lobodontia, a rare dental anomaly marked by supernumerary cusps and a single pyramid-shaped molar root resembling carnivorous teeth, is s linked to variants in the CACNA1S gene. However, the underlying molecular mechanisms remain unclear. Here, we identified a novel heterozygous missense variant in ASCL5 (c.274G>A, p.Glu92Lys) as the primary genetic determinant for lobodontia. Through microsatellite linkage and genome sequencing analysis of six families affected by lobodontia, we identified the ASCL5 c.274G>A variant, located upstream of the previously reported CACNA1S variant, completely segregating with the phenotype. To validate this finding, we generated Ascl5 knock-in mutant mice using CRISPR/Cas9. Ascl5Mut/WT exhibited dental anomalies resembling human lobodontia, while Ascl5Mut/Mut displayed significant defects in tooth and jaw development, underscoring the essential role of ASCL5 in craniofacial patterning. Transcriptomic analysis of E17.5 mandibular teeth and arches revealed a significant differential expression of forty-two genes in Ascl5mut/mut compared to Ascl5WT/WT, including reduced expression of key developmental genes Dlx1as, Dlx2, and Shh. Functional assays showed that ASCL5 promotes transcriptional activity of DLX2, a key regulator of craniofacial development. However, the p.Glu92Lys ASCL5 significantly impaired this activation, providing a mechanistic explanation for the observed phenotype. This study establishes ASCL5 as the primary gene responsible for lobodontia, revising the previously understood genetic basis of this rare condition. Our findings highlight the crucial role of ASCL5 in craniofacial development, opening new avenues for understanding craniofacial anomalies.

overall_design:
Mandibular dental arches from Ascl5Mut/Mut, and Ascl5WT/WT mice at embryonic day 17.5 (E17.5) were dissected for subsequent RNA extraction. The total RNA libraries were constructed using Illumina TruSeq Stranded mRNA LT Sample Prep Kit and sequenced using Illumina NovaSeq platform.
The RNA differential expression compared between Ascl5WT/WT mice as a control group and the Ascl5Mut/Mut mice as a comparison group was analyzed using RNA-Seq Differential Expression program (Illumina Inc., San Diego, CA, USA).

first: Theerapanon

last: Thanakorn

first: Thaweesapphithak

last: Sermporn


title: CRISPR screen of genes encoding protein interactors of MCB-613 in parental and EGFR inhibitor resistant EGFR-mutant NSCLC cell lines

summary: CRISPR screen of genes encoding protein interactors of MCB-613 in PC9, GR4, and WZR12 cells

overall_design: PC9, GR4, and WZR12 cells were infected with a CRISPR library targeting genes encoding protein interactors of MCB-613 and carried forward in triplicate for 14 population doublings at 1000X coverage. Genomic DNA was extracted using the QIAamp Blood Maxi Kit (Qiagen). Extracted DNA was amplified using a two-step protocol involving staggered barcode sequences for pooled sequencing. Sequencing was performed on an Illumina NextSeq 500 with 75bp paired-end sequencing and analysis was performed using the Models-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) software analysis pipeline under default conditions.

first: Christian

last: Cerda-Smith


title: Ascl5 variant alters gene expression in postnatal maxillary molars through potential gain-of-function effect

summary: Lobodontia is a rare dental anomaly characterized by supernumerary cusps and a single, pyramid-shaped molar root resembling those of carnivorous mammals. Through genetic analysis of six unrelated families, we identified a novel heterozygous missense variant in the ASCL5 gene (c.274G>A; p.Glu92Lys) that segregates fully with the phenotype. To investigate the functional impact of this variant, we generated Ascl5 knock-in mutant mice using CRISPR/Cas9. Heterozygous (Ascl5Mut/WT) mice displayed dental anomalies consistent with human lobodontia, whereas homozygous (Ascl5Mut/Mut) mice exhibited more severe craniofacial abnormalities, highlighting the essential role of ASCL5 in tooth and jaw development. To explore the molecular basis of the dental phenotype, we performed transcriptomic analysis of maxillary first molars from postnatal day 1 (P1) Ascl5Mut/WT and Ascl5Mut/Mut mice, each compared to wild-type controls. Based on a gain-of-function hypothesis for the p.Glu89Lys variant, we focused on genes upregulated in both mutant genotypes. This analysis identified 87 commonly upregulated genes. Pathway enrichment analysis using Metascape revealed 11 significantly enriched biological pathways, including Dmp1, Phex, and Atg4b genes associated with biomineral tissue development. Notably, the regulatory region of Phex contains a conserved E-box motif, a known binding site for bHLH transcription factors such as ASCL5, suggesting it may be a direct transcriptional target.

overall_design: To investigate the impact of the Ascl5 mutation on gene expression, we compared mRNA profiles from maxillary first molars of three mouse genotypes harvested at postnatal day 1 (P1): Ascl5Mut/WT, Ascl5Mut/Mut, and Ascl5WT/WT (control). Total RNA was extracted, and Illumina SMARTer Stranded RNA-Seq Kit was used to construct RNA libraries, which were then sequenced on a NovaSeq platform. Differential gene expression analysis was performed using the RNA-Seq Differential Expression program (Illumina Inc., San Diego, CA, USA) to identify genes whose expression was significantly altered in the mutant genotypes compared to the wild-type control.


title: Single-cell and spatial omics reveal progressive loss of xylem developmental complexity across seed plants

city: Taipei

first: Ying-Chung Jimmy

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Life Science

country: Taiwan

institute: National Taiwan University

summary: Secondary growth is a key characteristic evolved from seed plants and generates secondary xylem—the most abundant tissue on Earth. Recent studies have uncovered xylem developmental lineages in eudicots and magnoliids of angiosperms. However, xylem development in gymnosperms, the other representative clade of seed plants, remained elusive. We performed single-cell transcriptomics for xylem cells of conifers (Cunninghamia lanceolata), the major clade in gymnosperms. Using Seurat and scVI-based cross-species integration, we reconstructed the xylem differentiation trajectories and revealed that the radial system is conserved across seed plants, while the axial system in C. lanceolata exhibits a composite lineage architecture resembling both eudicots and magnoliids. To validate these trajectories, we established a multi-modal spatial framework incorporating spatial transcriptomics, spatial proteomics, and spatial metabolomics. These three spatial layers provided orthogonal evidence confirming cell-type identities and trajectory inference. Additionally, we identified a xylem cell population unique to gymnosperms, suggesting a lineage-specific specialization. Together, our findings uncover a more complex ancestral xylem architecture in gymnosperms and propose a progressive simplification of axial developmental programs from gymnosperms to angiosperms, highlighting a trajectory of reductive evolution in seed plant vascular development.

overall_design: Single-cell RNA sequencing of stem differentiating xylem (SDX) of C. lanceolata.

first: Peng

last: Shuai

first: Jo-Wei

middle: A

last: Hsieh

first: Chung-Ting

last: Kao

first: Chen-Wei

last: Hu

first: Ray

first: Shang-Che

last: Kuo

first: Ming-Ren

last: Yen

first: Pin-Chien

last: Liu

first: Yi-Chi

last: Ho

first: Chia-Chen

last: Chu

first: Shuotian

last: Huang

first: Jiao

first: Lixia

last: Wu

first: Yi-Jyun

last: Luo

first: Quanzi

last: Li

first: Chuan-Chih

last: Hsu

first: Chao-Li

first: Jung-Chen

last: Su

first: Mei-Chun

last: Tseng

first: Ying-Lan

last: Chen

first: Te-Lun

last: Mai

first: Ying-Chung

middle: J


title: SETD1A is required for intestinal homeostasis and prevention of DNA damage

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

country: Germany

institute: BIOTEChnology Center TU Dresden

summary: The impact of SETD1A on the small intestine was evaluated in sorted intestinal stem, transit amplifying (TA) and Paneth cells  from Setd1aFC/+; Lgr5-eGFP-CreERT2/+ (control) and  Setd1aFC/FC; Lgr5-eGFP-CreERT2/+ (knockout) mice, 4 days after  tamoxifen-induced mutagenesis. Using 100-base-pair reads, over 35 million  reads per sample with comparable unique mapped reads were obtained. To analyze differentially  expressed genes, we applied DESeq2 analysis to the RNA-seq dataset.  Analysis by DAVID and GSEA at a false discovery rate (FDR) of 5% was  conducted.The stem and TA cell transcriptome revealed that Setd1a knockout  cells exhibited a decreased expression of several DNA damage repair genes.

overall_design: mRNA profiles of sorted stem, TA and Paneth cells from Setd1aFC/+;  Lgr5-eGFP-CreERT2 (control) and Setd1aFC/FC; Lgr5-eGFP-CreERT2 (knockout)  mice, 4 after tamoxifen were generated by deep sequencing.

first: Neha

last: Goveas

first: Sethuraman

last: Subramanian

first: Lea

last: Juznic

first: Mathias

last: Lesche

first: Andreas

last: Dahl

first: Sebastian

last: Zeißig

first: Konstantinos

last: Anastassiadis

first: A

first: Andrea

last: Kranz


title: Streptococcus pneumoniae drives specific and long-lasting memory in NK cells

city: Paris

first: Claudia

last: Chica

address: 25-28 Rue du Dr Roux

institute: Institut Pasteur

summary: Following lung infection with S. pneumoniae, naive (D21PBSpi NKs) and pre-infected NK cells (D21SPNpi NKs) were sorted and used for scRNAseq. We compared their transcriptional program to identify and characterize a new population of NK cells that acquired memory to  bacteria

overall_design: Comparison of naive (D21PBSpi NKs) and memory NK cells (D21SPNpi NKs) mRNA profiles upon secondary S. pneumoniae infection

first: Tipahine

last: Camarasa

first: Julia

middle: T

last: Cortada

first: Sébastien

last: Mella

first: Mélamie

last: Hamon


title: Single-cell transcriptomic comparison of young and aged dermal macrophages

city: Osaka

first: Yu-Tung

last: Li

address: 2-2 Yamada-oka, Suita

institute: Osaka University

summary: Previously, in a meta-analysis of public single-cell transcriptomes profiling various healthy and disease tissues, we demonstrated that macrophage heterogeneity in skin, as well as in other mouse tissues, could be described into 5 distinct identities (S1-5) with a defined transcriptomic fingerprint, regardless of tissue origins. We established a general identity scheme for tissue macrophages, MIKA (Macrophage Identity Kinetics Archive) as an alternative to the conventional M1/M2 scheme which shows limitations in annotating in vivo tissue macrophages. (PMID: 39720957) MIKA was recently updated to finetune identity definition, and to include more tissues and pathophysiological conditions. (PMID: 41342690) Under the current MIKA framework, tissue macrophages are classified to 6 core identities (S1-S6, common to various tissues) and/or tissue-specific macrophages. This dataset is a part of the raw data sources of the latest version of MIKA profiling single-cell transcriptomes of F4/80+MHCII-hi macrophages FACS-isolated from dorsal skin of young (9 week-old) and old (108 week-old) C57BL/6 male mice.

overall_design: Dorsal skins were dissected from male mice of indicated ages, pooled and digested for single cell isolation. Male mice were analysed to avoid drastic menopausal endocrine changes. Macrophages were sorted as F4/80+MHCII-hi cells by BD FACSAria III and transcriptomes were analysed by single-cell RNA-seq.

first: Saki

last: Ishino


title: Acutely denervated muscle EVs reshape neuronal mitochondrial metabolism via retrograde signaling to rescue peripheral nerve injury

status: Public on Dec 06 2025

city: Xi'an

first: Qi

last: Liu

address: No.127, Changle West Road

institute: Air Force Medical University

summary: Peripheral nerve injury causes muscle atrophy due to slow axonal regeneration, highlighting an unmet therapeutic need. Although neuromuscular interactions are classically viewed as unidirectionally nerve-dominated, we show that acutely denervated muscle (adMu) regulates nerve regeneration via a retrograde signaling pathway. adMu initiates a trans-tissue regulatory mechanism through extracellular vesicles (EVsadMu) that orchestrate neural energy homeostasis to accelerate regeneration. Functional profiling identifies IDH2 and CS as key metabolic enzymes within EVsadMu. Neurons treated with EVsadMu exhibit a 1.39-fold increase in NADPH/NADP+ ratio via IDH2, along with a 1.18- and 1.27-fold increase in NADH/NAD+ and FADH2/FAD ratios via CS, fueling the TCA cycle to enhance mitochondrial bioenergetics. This restores redox balance and energy supply, driving axonal regeneration. In sciatic nerve injury models, EVadMu-microneedle conduits significantly promote energy metabolism and functional recovery. Together, our findings position adMu as a metabolic signaling center enabling retrograde regulation for nerve regeneration, offering potential for clinical translation.

overall_design: RNA sequencing of DRG neurons treated with extracellular vesicles from acutely denervated muscle or innervated muscle


title: Mechanisms of PM2.5 Exposure Impact on the Malignant Progression of Breast Cancer Subtype

first: ziru

last: zhou

overall_design: RNA-seq profiling of T47D cells under control (T47D_CK1, T47D_CK2, T47D_CK3) and experimental treatment (T47D_CQ1, T47D_CQ2, T47D_CQ3) conditions. The study includes three biological replicates per condition to investigate transcriptomic changes in response to the experimental treatment.


title: Phenotypic expansion of CALM1/2-associated disorders to include neurologic phenotypes without arrhythmia

city: St Louis

first: Hieu

last: Hoang

state: MO

address: 660 South Euclid Avenue, 4th floor entry 1

department: Pediatrics

institute: Washington University in St Louis

summary: Calmodulin is an intracellular Ca2+ sensor that regulates numerous cellular processes through binding effector proteins and changing their activity. Humans have three calmodulin paralogs, CALM1, CALM2 and CALM3, encoding identical proteins, and missense variants in all three are included in the ACMG recommendations for reporting of secondary findings related to early onset sudden cardiac death caused by arrhythmias long QT syndrome and CPVT.  Recently, a subset of individuals with de novo variants in calmodulin genes were described who also presented with neurologic phenotypes. Here we report two individuals with the same de novo variant c.419A>T in CALM1 or CALM2 that may generate a 5’ splice donor gain and/or a missense change p.E140V.  These individuals share hypotonia, motor delay, intellectual disability, and abnormal electroencephalograms but lack cardiac arrhythmia/electrocardiogram abnormalities of previously described CALM-associated disease, suggesting the variant causes phenotypic expansion beyond the known Mendelian phenotypes. RNA-seq of the CALM1 proband blood’s sample revealed that most transcripts from the variant allele showed usage of the new splice site or intron retention, without NMD, resulting in frameshifted C-terminal truncations, while a minority resulted in production of the p.E140V missense protein.  We modeled the CALM1/2 p.E140V variant as well as a known arrhythmia variant, CALM1 p.E141G, using the C. elegans ortholog cmd-1.  We found that cmd-1 E140V displayed both qualitative and quantitative differences in phenotype from E141G, indicating distinct genetic mechanisms. Together, these findings support CALM1/2 phenotypic expansion, with c.419A>T p.E140V resulting in neurologic, but not arrhythmia phenotypes.

overall_design: RNA seq of WT and cmd-1 (p. E140V) and cmd-1 (p. E141G) homozygotes under grown at 20oC in standard culture condition on NGM plates

first: Schedl

last: Tim

first: Pak

last: Stephen

first: Hoang

last: Hieu

first: Tycksen

last: Eric


title: Light-Responsive Oxygen Generation from Chlorella Hydrogels for Facial Nerve Injury Recovery: Crosstalk between M1/M2 Macrophages and Schwann Cells

city: Chengdu

first: Guihua

last: Wei

address: No.111, North 1st Section, 2nd Ring Rd

institute: Southwest Jiaotong University

summary: Facial nerve injury (FNI), hindered by hypoxic microenvironments limiting Schwann cell (SCs) repair potential, remains a therapeutic challenge. We developed light-responsive Chlorella hydrogels (C-Gel) to modulate oxygen release and inflammation. In vitro, light-activated C-Gel enhanced RSC96 SC proliferation, migration, and secretion while reducing reactive oxygen species (ROS), hypoxia-inducible factor-1α (HIF-1α), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6). It also shifted macrophage polarization from pro-inflammatory M1 (inducible nitric oxide synthase (iNOS)+/TNF-α+) to anti-inflammatory M2 (arginase-1 (Arg-1)+/IL-10+), with M2-conditioned mediumboosting SCs production of neurotrophic factors (nerve growth factor, NGF; glial cell line-derived neurotrophic factor, GDNF), adhesion molecules (neural cell adhesion molecule-1, NCAM-1), regeneration-associated proteins (c-JUN), and myelin components (myelin basic protein, MBP; myelin-associated glycoprotein, MAG). In vivo, C-Gel-light therapy improved behavioral recovery in FNI rats, suppressed inflammation (ROS/HIF-1α/TNF-α), and enhanced SC-mediated remyelination (S100 calcium-binding protein, S100; neurofilament 200, NF200). RNA sequencing identified upregulated phosphoinositide 3-kinase-protein kinase (PI3K-Akt) and calcium ion (Ca²+) signaling pathways. This oxygen-regulating, immunomodulatory biomaterial offers a dual-action strategy to advance FNI rehabilitation by synergistically optimizing the regenerative microenvironment.

overall_design:
Transcriptomic profiling of rat facial nerve tissue at day 14 post-injury, comparing the injury model (FNI) with a C-Gel-light treatment group to elucidate repair mechanisms.
To elucidate the molecular mechanism by which C-Gel-light promotes facial nerve repair, a comparative transcriptomic analysis was conducted. Facial nerve tissues were harvested on day 14 post-injury from two groups: the facial nerve injury (FNI) model group and the C-Gel-light treatment group. Total RNA was extracted from the tissues using TRIzol reagent (Invitrogen). After quality assessment, sequencing libraries were prepared, and paired-end (150 bp) sequencing was performed on an Illumina NovaSeq 6000 platform (Illumina, USA) by Heyuan Biotechnology Co., Ltd. (Shanghai, China). Differential gene expression analysis identified 682 upregulated and 803 downregulated genes in the C-Gel-light group compared to the FNI group. Subsequent bioinformatic analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, were performed to interpret the functional implications of the differentially expressed genes in the context of nerve regeneration.

first: Xi

first: Mengqi

last: Huang

first: Haoyan

last: Wang

first: Zaiqi

first: Shuxin

last: Qu


title: Dual-transcriptomic analysis of human nasal transcriptome and microbiome reveals host-bacteria interactions associated with symptomatic respiratory infection (16S validation)

city: PITTSBURGH

first: Xiangyu

last: Ye

state: Pennsylvania

address: 4401 Penn Ave

institute: UPMC

summary: The human nasopharynx is colonized by a diverse community of commensal microbiota linked to many respiratory diseases, yet their interactions with the host remain unclear. In this study, we introduced a dual-transcriptomics analysis strategy, which can characterize the host transcriptome and microbiome from nasal samples simultaneously. RNA sequencing reads from human nasal swab samples were pre-processed and aligned to the human genome for host gene expression counting, while unmapped reads were further aligned to microbiota genome. After taxonomic classification, microbial abundance matrix was derived at each taxonomic level for differential and host-microbiota interaction analysis. We applied this workflow to a local SARS-CoV-2 cohort with 76 infected patients, among whom 55 (72.37%) were symptomatic at enrollment. Nasal swabs were collected from all 76 patients at enrollment and from 73 patients at one-week later follow-up. We detected a median of 4.81% reads unmapped from the human genome across all 149 samples, among which around half (median 48.63%) were successfully mapped to microbiome genome. Meta-transcriptomic analysis detected significantly higher SARS-related coronavirus loads in samples from the symptomatic group at enrollment, and both groups showed decreased loads one week later. Compared with benchmarking 16S rRNA sequencing on 53 samples, our computational strategy showed high correlation of relative abundance in all top 20 genus. A total of 685 bacteria species were identified to show a relative abundance >= 0.01% in at least 10% samples. Differential abundance analysis identified 66 species (DASs) from 6 phyla with significantly decreased abundance in samples from the symptomatic group compared to the asymptomatic group at enrollment. Integrating these symptom-associated DASs with host’s gene expression using an expression quantitative trait bacteria (eQTB) model, we found 58 symptom-associated DASs identified at enrollment were significantly associated with one to 16 genes. GSEA showed a series of symptom-associated DASs were significantly correlated with pathways related to the activation of olfactory, keratinocyte differentiation, and DNA methylation. In summary, our dual-transcriptomic analysis strategy effectively characterized host-microbiome interactions, offering insights into microbial contributions to respiratory diseases.

overall_design: Participants in this study were household SARS-CoV-2 contactor. Specifically, index cases were COVID-19 patients identified through pediatric outpatient sites, urgent care centers emergency departments and via an online research recruitment program. The infection was diagnosed based on rapid antigen or PCR test. Household contacts of index cases were then enrolled as participants while index cases themselves were not enrolled. Valid household contacts were defined as those that had been exposed for at least 24 hours to a confirmed index case. Household contacts with the following symptoms either on the day before or the day of enrollment were defined as symptomatic infection: (1) fever plus cough or difficulty breathing; or (2) fever or cough plus loss of taste or smell.


title: Dual-transcriptomic analysis of human nasal transcriptome and microbiome reveals host-bacteria interactions associated with symptomatic respiratory infection

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

overall_design: Refer to individual Series


title: Metabolic Engineering of Doxorubicin Biosynthesis: Advancing P450 Catalysis through Redox Partner Optimization and Structural Analysis of DoxA

city: Turku

first: Mikko

last: Metsä-Ketelä

address: Tykistökatu 6A

department: Department of Life Technologies

country: Finland

institute: University of Turku

summary: Doxorubicin is a widely used chemotherapy agent produced by Streptomyces peucetius ATCC27952. Key to the biosynthesis is the cytochrome P450 monoxygenase DoxA that catalyzes three consecutive late-stage hydroxylations. However, the final conversion from daunorubicin to doxorubicin is rate-limiting and industrial manufacturing occurs through semi-synthesis from daunorubicin. Here we have discovered three factors that limit catalysis by DoxA. We performed comparative transcriptome analysis to identify the natural redox partners, the ferredoxin FDX4 and ferredoxin reductase FDR3, preferred by DoxA. We show that the vicinal oxygen chelate (VOC) family protein DnrV is a drug-binding protein aiding catalysis by binding doxorubicin and preventing product inhibition of DoxA. Ternary structures of DoxA in complex with ligands and density functional theory calculations revealed that 14-hydroxylation is limited by the preferred anti conformation of the daunorubicin substrate. We employed these findings to convert a daunorubicin over-producing industrial strain to produce 300 mg / L doxorubicin.

overall_design: RNA-Seq profiling of Streptomyces peucetius ATCC 27952 and their mutant derivatives GOO1 and X121 at Day1-6

first: Arina

last: Koroleva

first: Erika

last: Artukka

first: Keith

last: Yamada

first: Sean

last: Newmister

first: Ralph

last: Harte

first: Hannah

last: Boesger

first: Mikael

last: Londen

first: Jacob

middle: N

last: Sanders

first: Heli

last: Tirkkonen

first: Matti

last: Kannisto

first: Rosan

last: Kuin

first: Mandy

last: Hulst

first: Rongbin

first: Ester

last: Leskinen

first: Morgane

last: Barillec

first: Jarmo

last: Niemi

first: Gilles

last: van Wezel

first: Jacques

last: Neefjes

first: S

middle: E

last: Nybo

first: K

last: Houk

first: David

middle: H

last: Sherman

first: Robbert

middle: Q

last: Kim


title: Spatial Transcriptomics Uncovers the Hybrid Molecular Identity, Ciliated Phenotype, and Immune Signature of Adenomyosis Lesions

city: Liverpool

first: Alison

last: Maclean

state: Merseyside

address: Crown Street

department: Department of Women's and Children's Health

country: United Kingdom

institute: University of Liverpool, Institute of Life Course and Medical Sciences

summary: Adenomyosis is a common gynaecological condition characterised by ectopic endometrial tissue within the myometrium, causing debilitating symptoms with limited treatment options. Despite its prevalence, the pathogenesis of adenomyosis remains poorly understood, hindering the development of targeted therapies for true disease modification rather than symptom management. The objective of this study was to elucidate the spatial transcriptomic profile of adenomyosis lesions with matched eutopic endometrial subregions, with a focus on specific cell types and tissue compartments. The study was designed to identify differentially expressed genes, functionally enriched pathways, and cell-cell communication networks within adenomyosis lesions compared to matched endometrial subregions, and to nominate potential drug targets for future therapeutic development.  We show that adenomyosis lesions exhibit a distinct transcriptome intermediate between matched endometrium and myometrium, with enhanced epithelial ciliation and altered biological pathways. We reveal that lesion transcriptome is more like the endometrial basalis than the functionalis, displaying increased olfactory signalling, altered oxidative phosphorylation and ATP synthesis, and an altered immune microenvironment suggestive of chronic inflammation. In silico drug screening identified potential compounds that can reverse the adenomyosis lesion transcriptome. These findings provide insights into the molecular landscape of adenomyosis lesions and pave the way for developing novel, lesion-specific treatments that could potentially spare the eutopic endometrium and offer alternatives to hysterectomy.

overall_design: Full-thickness endometrial biopsies and matched myometrium containing adenomyosis lesions were prospectively collected from ten premenopausal women undergoing hysterectomy for pelvic pain and/or heavy menstrual bleeding. Paraffin-embedded human uterine biopsies underwent NanoString GeoMx digital spatial profiling. NanoString GeoMx DSP uses a pool of ~20,000 transcript-specific RNA probes, links each of the probes to a unique, probe specific barcode through a UV cleavable linker. The probe pool was hybridized to target mRNAs on tissue slides (overnight), and slides were then stained using fluorophore-labelled antibodies (“morphology markers”; here panCK, CD45, CD31) and imaged on the GeoMx profiler platform. A total of 6 regions of interest (ROIs) were selected per tissue sample (luminal epithelium, endometrial functionalis, endometrial basalis, adenomyosis lesions, and two myometrial regions), and UV light was applied to release and collect the DSP barcodes from selected ROIs. Photocleaved oligonucleotides from ROI aspirates, containing target-specific readout tags and unique molecular identifiers (UMIs), were used for library preparation. Libraries were quality-checked using a Bioanalyzer system (Agilent) and quantified with a Qubit high-sensitivity DNA kit. Sequencing was conducted on an Illumina NovaSeq system using NovaSeq S1 flow cells with paired-end 2 x 50 bp reads, generating approximately 1300 million clusters per cell. Digital count conversion (DCC) files were produced for each target probe.

first: Emily

last: Johnson

first: Corie

last: Rushworth

first: Christopher

last: Hill

first: Eva

last: Caamano-Gutierrez

first: Dharani

middle: K

last: Hapangama


title: Integrated Spatial Analysis Reveals the Molecular Landscape of Ovarian Precancerous Lesions

city: Baltimore

first: Ie-Ming

last: Shih

state: Maryland

address: 1550 Orleans Street, room 305

department: Department of Gynecology and Obstetrics

institute: Johns Hopkins Medical Institutions

summary: Studying precancerous lesions is essential for improving early detection and prevention, particularly in aggressive cancers such as ovarian carcinoma. Here, we conducted integrated and spatial analyses of transcriptomes, aneuploidy, and clinicopathological features in 166 ovarian precancerous lesions. Four pre-cancerous transcriptomic subtypes were identified: proliferative, immunoreactive, dormant, and mixed. These subtypes varied in their frequency of germline-BRCA1/2 mutations, aneuploidy, CCNE1/MYC amplification, proliferative activity, immune-regulatory gene expression, and histological features. Notably, the immunoreactive subtype upregulated immune-regulatory genes, exhibited chronic inflammation, and was enriched in cases with germline-BRCA1/2 mutations, deletions of chromosomes 17 (harboring TP53 and BRCA1) and 13 (harboring BRCA2), leading to a double “two-hit” involving TP53 and BRCA1/2. Tumor invasion was associated with the activation of interferon response pathways, epithelial-mesenchymal transition, and extracellular matrix remodeling. In summary, these results elucidate the earliest molecular landscape of ovarian precancerous lesions, serving as the foundation for future risk stratification to identify aggressive pre-cancerous lesions.

overall_design: Fallopian tube tissues diagnosed with STICs, STILs, and p53 signatures were collocted. A total of 68 patients with 294 epithelial samples consisting of 162 STIC/STIL and four p53 signatures, along with 29 concurrent carcinoma lesions, 99 paired histologically unremarkable or normal fallopian tube epithelia (NFT), and 144 diagnosis-paired stromal samples, were included in this study.

first: Tu-Yung

last: Chang

first: Tian-Li

last: Wang


title: The energetic consequences of oxygen fluxes in a coral reef fish

city: Abu Dhabi

first: Daniel

middle: Michael

last: Ripley

address: NYUAD

country: United Arab Emirates

institute: New York University Abu Dhabi

summary:
Abstract

Ocean warming elevates metabolic rates in marine ectotherms but often constrains energetic resources, causing an imbalance between supply and demand. Transient hypoxia is near-ubiquitous across the world’s coral reefs and may exacerbate this imbalance, yet its effects on the energetics of reef fishes remain poorly understood. In this study, we assess the metabolic costs incurred by a cryptobenthic reef fish exposed to oxygen fluxes measured on the world’s hottest coral reefs in the Arabian/Persian Gulf. Hypoxia-exposure induced an 8.67% increase in aerobic metabolic rate over the six hours following reoxygenation, and resulted in an estimated 2.87% increase in total daily metabolic rate (mg O2 kg -1 day-1). This energetic cost did not coincide with detectable changes in anaerobic metabolism but was accompanied by increased activity during reoxygenation and a strong, acute transcriptomic response in genes related to oxygen-sensing. Oxygen availability on the reefs declined below the threshold for inducing such energetic costs on over half (56.04%) of the days throughout the summer, potentially leading to substantial cumulative costs. Such energetic costs represent an additional and previously under-appreciated consequence of hypoxia in coral reef environments that may exacerbate the temperature-induced mismatches between energy supply and demand, a key balance affecting growth and fitness.

overall_design: 24 samples in total, split into 4 groups of 6 replicates. Each replicate is a cross section from the anterior tail of an Ecsenius pulcher. The sections were trimmed of skin prior to homogenisation. Fish are from either the 'hypoxic' group (N = 12), or the time-matched 'control' group (N = 12). Within each group, samples were taken either during hypoxia, or following reoxygenation and recovery from hypoxia. Hypoxia exposures followed the profiles measured on local reefs.

middle: M

first: Daniele

last: D'Agostino

first: Daniela

last: Denk

first: John

last: Burt


title: Screening of differentially expressed genes and microRNAs in rabbits with traumatic proliferative vitreoretinopathy based on high-throughput sequencing

city: nanchang

first: shengxiang

last: zhang

state: Jiangxi Province

address: 463 Bayi Avenue, Donghu District, Nanchang City, Jiangxi Province, China

institute: nanchang university

summary: The retinas of rabbits in the experimental and control groups of traumatic proliferative vitreoretinopathy (PVR) were sequenced by high-throughput sequencing technology, and differentially expressed genes (DEGs) and differentially expressed microRNAs (DEMs) were identified to provide new ideas for the diagnosis and treatment of PVR. Differentially expressed genes (DEGs) and differentially expressed microRNAs (DEMs) were screened to provide new ideas for the diagnosis and treatment of PVR.

overall_design: To investigate the changes in gene expression levels in a rabbit model of proliferative vitreoretinopathy, we performed high-throughput sequencing of retinal tissue from a rabbit model of proliferative vitreoretinopathy

first: Qihua

last: Xu

first: Yujie

last: Tang

first: Shengxiang

last: Zhang


title: Dietary methionine deprivation enhances renal resilience against ischemia-reperfusion injury through modulation of glucose oxidation

city: Hangzhou

first: Xiaofeng

last: Peng

address: Yuhangtang Road 866,Hangzhou,Zhejiang

institute: Zhejiang University

summary: Renal ischemia-reperfusion injury (IRI) is a leading cause of acute kidney injury (AKI) and presents significant challenges during kidney transplantation. Due to the detrimental effects of IRI on kidney function and the lack of effective intervention strategies, we conduct a multi-omics study on surgically induced mouse IRI, revealing a modulatory role for the metabolite S-adenosylmethionine (SAM) in AKI development. Our metabolic analysis of clinical samples establishes a link between various AKI conditions and marked elevations in serum SAM, underlying its potential as a biomarker for diagnosis. Furthermore, we find that short-term dietary methionine deprivation, which reduces circulating methionine and kidney SAM levels, effectively enhances renal resilience against IRI. In vivo isotopic tracing demonstrates that this diet preconditions kidney metabolic programs, enhancing glucose and fatty acid oxidation in preparation for IRI. Particularly, the activation of pyruvate dehydrogenase, which produces acetyl-CoA to fuel the tricarboxylic acid (TCA) cycle, highlights an energy-efficient strategy of glucose metabolism that is essential for the protective effects of dietary methionine deprivation.

overall_design: The experimental design includes transcriptomic sequencing data of kidney tissues from male mice subjected to 30 minutes of ischemia followed by 24 hours of reperfusion (IRI group) and from control mice undergoing sham surgery (Sham group).

first: Xiao feng

first: Hong

last: Jiang

first: Cunqi

last: Ye


title: Autosomal recessive RDH12-Leber congenital amaurosis retinal organoids display reduced photoreceptor length and phospholipid dysregulation

city: LONDON

first: Mariya

last: Moosajee

address: 1 Midland Rd

institute: The Francis Crick Institute

summary: NADPH-dependent retinol dehydrogenase 12 (RDH12) reduces all-trans-retinal in photoreceptor inner segments to regulate the phototransduction cascade and control the concentration of retinoids in the retina. Biallelic variants in RDH12 have been reported to cause autosomal recessive (AR) Leber congenital amaurosis (LCA), a severe cause of childhood blindness. Animal models have failed to recapitulate the clinical phenotype, hence, we generated human induced pluripotent stem cell (hiPSC) derived retinal organoids (RO) from the dermal fibroblasts of a female patient with homozygous missense variant c.619A>G p.(Asn207Asp) in RDH12 (RDH12-AR), and an unrelated healthy control (WT). RDH12-AR RO develop shortened rod and cone photoreceptors (from the outer limiting membrane to the tip of the outer segment), which lack RDH12 localisation in the inner segment. Bulk transcriptomic analysis revealed cone marker and apoptosis dysregulation in RDH12-AR RO compared to WT; but phospholipid transport is perturbed in RDH12-AR RO compared to an autosomal dominant hiPSC-derived RDH12-retinitis pigmentosa RO model. Our study helps to decipher the distinct disease pathways involved in RDH12 retinopathies, however, further modelling from additional patients with isogenic controls will strengthen the findings and aid identification of targets for therapeutic approaches.

overall_design: Inherited eye diseases is a clinically and genetically heterogenous group of stationary and progressive diseases, with limited treatment options. To understand these pathologies, we developed retinal organoids derived from human induced pluripotent stem cells, obtained from skin biopsies of patients affected with inherited eye diseases. We would like to identify transcriptomic signatures for any intracellular and molecular pathophysiology associated with the different forms of RDH12 retinopathy (autosomal recessive [AR] early onset retinal dystrophy versus autosomal dominant [AD] retinitis pigmentosa).

first: Cécile

last: Méjécase

first: Pablo

last: Soro-Barrio


title: Single-cell RNA-seq analysis of immune cells isolated by FACS from zebrafish embryos after acute muscle injury using a novel irg1 knock-in reporter

city: Chapel Hill

first: Celia

last: Shiau

address: 2159 Genome Sciences Building

institute: UNC Chapel Hill

summary: The objective of this experiment was to analyze the single-cell transcriptomes of macrophages for molecular profiling of subtypes that emerge during acute muscle injury in zebrafish. This transcriptomic data was used in conjunction with high-resolution live-cell microscopy, in which individual macrophages were tracked to examine both cellular and population-level dynamics. Comparisons were made between baseline (stage-matched, uninjured controls) and distinct phases of injury: the initial inflammatory response at 24 hours post-amputation (hpa) and the resolution phase beginning at 48 hpa of two genotypes, control/wild-type and chronic inflammation mutant (nlrc3l deletion). Single-cell sequencing revealed significant differences in immune cell transcriptome post injury between control and chronic inflammation nlrc3l mutants, and that most irg1 positive cells were macrophages with a fraction of them being altered neutrophils also expressing irg1 after injury particularly in the mutants.

overall_design: Transgenic zebrafish carrying the novel GFP knock-in reporter irg1-KI:GFP were used to isolate macrophages at distinct phases of acute muscle injury response. Specifically, samples were collected at 24 hours post-amputation (hpa), representing the initial inflammatory phase, and at 48 hpa, marking the onset of tissue repair following debris clearance. Uninjured ("uncut") animals served as baseline controls. Responses were compared between wild-type (or control sibling) zebrafish and mutants with a deleterious nlrc3l mutation that causes chronic macrophage activation. To induce acute muscle injury, large tail amputations were performed on 2 days post-fertilization (dpf) zebrafish embryos. This procedure causes significant muscle damage, which fully regenerates within four days, forming a new tail tip. Activated macrophages upregulate irg1, displaying strong GFP fluorescence, while steady-state macrophages express minimal irg1, resulting in faint GFP signal. All irg1-KI:GFP+ cells expressing any detectable level of GFP were isolated using fluorescence-activated cell sorting (FACS) on a BD FACSMelody across four conditions: control uncut, control 24 hpa, control 48 hpa, and nlrc3l mutant 24 hpa. Two biological replicates were collected per condition, each consisting of pooled cells from 90 embryos, resulting in a total of eight samples. To maintain cell viability and quality, embryos were dissociated and sorted in batches of 30, with three such batches pooled to constitute a single sample. Sample collection was interleaved to evenly distribute conditions across the processing timeline. Embryo dissociation was performed in a buffer containing ROCK inhibitor, protease, DNase with gentle mechanical grinding, and a holding solution composed of HBSS (without phenol red), 1% BSA, and ROCK inhibitor. Cells were kept on ice until 10x genomics downstream processing and library preparation.

first: Matthew

last: Hamilton

first: Ethan

last: Bedsole


title: Bulk RNA-sequencing on sorted zebrafish macrophages based on novel irg1-knock-in reporter comparing control versus nlrc3l mutation under baseline and injury conditions

summary: Using a GFP knock-in zebrafish targeting the irg1/acod1 locus, a gene highly induced in activated macrophages, we isolated macrophages based on high and low GFP levels by FACS to conduct bulk RNA-sequencing. Transcriptome analysis of macrophages showed nlrc3l mutants had constitutively activated macrophages that sustained elevated expression of pro-inflammatory genes, including irg1 and tnfa, and canonical and non-canonical NF-κB pathways genes. Furthermore, transcriptome analysis suggested that wild-type/control macrophages exhibited hybrid M1-like and M2-like characteristics during initial injury response, while nlrc3l mutant macrophages remained locked in a pro-inflammatory state. This analysis supports the rest of the functional experiments to demonstrate that chronic macrophage activation restricts functional plasticity associated with mrc1b deficiency and thereby hinders skeletal muscle repair.

overall_design: Two independent RNA-seq datasets were generated in this study. One dataset (Samples 1-12) corresponds to RNA-seq profiling of macrophages sorted from 3dpf zebrafish embryos that were of either sibling or mutant nlrc3l/st73 genotype based on low or high GFP levels indicating endogenous irg1 transcriptional levels using a GFP knock-in reporter at the irg1 locus. Second dataset (Samples 13-19) corresponds to RNA-seq profiling of macrophages that were similarly isolated based on relative expression of the GFP knock-in reporter for endogenous irg1 from injured (24-hour-post major tail amputation) and non-injured 3dpf zebrafish embryos from control and nlrc3l mutant genotypes.

first: Andrew

last: Burciu


title: Dual-transcriptomic analysis of human nasal transcriptome and microbiome reveals host-bacteria interactions associated with symptomatic respiratory infection [RNA-Seq]

first: Xiangyu


title: Spatial and single-cell transcriptomics reveal the reorganization of cerebellar microglia with aging

city: Stanford

first: Andy

last: Tsai

state: California

address: 290 Jane Stanford Way E365

institute: Stanford University

summary: Aging induces region-specific functional decline across the brain. The cerebellum, critical for motor coordination and cognitive function, undergoes significant structural and functional changes with age. The molecular mechanisms driving cerebellar aging—particularly the role of cerebellar glia, including microglia—remain poorly understood. Here, we used single-nuclei RNA sequencing (snRNA-seq), microglial bulk RNA-seq, and multiplexed error-robust fluorescence in situ hybridization (MERFISH) to characterize transcriptional changes associated with cellular aging in the mouse cerebellum. We discovered that microglia exhibited the most pronounced age-related changes of all cell types and that their transcriptional signatures pointed to enhanced neuroprotective immune activation and reduced lipid-droplet accumulation compared to hippocampal microglia. Furthermore, cerebellar microglia in aged mice, compared to young mice, were found in closer proximity to granule cells. This relationship was characterized using the newly defined neuron-associated microglia score, which captures proximity-dependent transcriptional changes and suggests a novel microglial responsiveness. These findings underscore the unique adaptations of the cerebellum during aging and its potential resilience to Alzheimer’s disease (AD) related pathology, providing crucial insight into region-specific mechanisms that may shape disease susceptibility.

overall_design: Nuclei from the cerebellum of two female and two male mice, aged 3, 12, 18, and 24 months, were isolated using Fluorescence-Activated Cell Sorting (FACS) based on NeuN expression status and subsequently analyzed via single-nucleus RNA sequencing (snRNA-seq).

first: Douglas

last: Henze

first: Eduardo

last: Ramirez Lopez

first: James

last: Haberberger

first: Chuanpeng

last: Dong

first: Nannan

last: Lu

first: Micaiah

last: Atkins

first: Emma

last: Costa

first: Amelia

last: Farinas

first: Hamilton

last: Oh

first: Patricia

last: Moran-Losada

first: Yann

last: Le Guen

first: Alina

last: Isakova

first: Stephen

last: Quake

first: Tony

last: Wyss-Coray


title: Restoring the potency of neutralizing antibody via guided hypermutation with hyper-antibody editor

city: 北京

first: yuhong

last: wang

state: 北京市

address: 北京大学吕志和楼106

institute: Peking university

summary: Somatic hypermutation (SHM) drives antibody affinity maturation in B cells, and mimicking this process has advanced therapeutic antibody development. Unlike conventional base editing, antibody diversification requires diverse mutations within the antibody complementary determining region (CDR) loops. Here, we engineered a hyper-antibody editor, HAE1, by integrating cytosine and adenine deaminases with a nicked, PAMless Cas9 variant, SpRY. HAE1 enables broad-spectrum mutagenesis with unrestricted targeting, fully covering mutation types observed in nature. Moreover, we developed a dual-expression system in mammalian cells that allows simultaneous expression of both transmembrane and secreted full-length antibodies, streamlining mutation, selection, and validation within the same cells. Using this platform, we rejuvenated the SARS-CoV-2 antibody CV07-209, restoring potency against Omicron variants. These results demonstrate the effectiveness of HAE1 as a powerful tool for antibody engineering, offering a practical strategy for evolving antibodies to address rapidly mutating pathogens and other therapeutic challenges.

overall_design: We introduced Amplicon sequencing to detect the editing products of different antibody editor. eGFP gene was targeted by different sgRNAs and then cloned with specific primers for high-throughput sequencing.

first: Jiazhi

last: Hu

first: Yuhong

last: Wang

first: Xinyi

last: Liu

first: Yuefeng

last: Guo


title: Distinct genomic identities and transformation trajectories of thymomas

city: Daejeon

first: Young Seok

last: Ju

address: 291 Daehakro

country: South Korea

institute: KAIST

summary: Thymoma is a rare tumor originating from epithelial cells of thymus. Despite previous studies, molecular trajectories underlying thymic tumorigenesis remain largely unknown. In this study, we conducted an integrated analysis of genomes and transcriptomes from 124 thymomas and 13 thymic carcinomas. Additionally, we incorporated single-cell transcriptomes of normal thymic tissues collected at different developmental stages. The efforts identify two mutually exclusive molecular types of thymomas: GTF2I-mutant (GTF2I-type) and copy number-altered type (CN-type). The GTF2I-type has a stable copy number profile with cellular identities of transcription similar to thymic progenitor cells. In contrast, CN-type tumors show cellular identities resembling differentiated thymic epithelium with distinct metabolic and immune features and activation of oncogene IRS4. Genome-wide timing analyses on CN-type reveal that tumorigenic courses of the two types were partitioned from the early stage in the lifetime. Our findings provide deep insights into the origin and tumorigenic processes of thymic epithelial cells.

overall_design: We produced single-cell RNA-seq data from 11-week-old mice (FVB). Thymi of seven mice were dissected to generate the dataset. Leukocytes were stained with CD45 antibody and depleted with autoMACS Pro Separator. The single-cell RNA sequencing library was generated using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics).


title: Dextran sulfate sodium (DSS)-induced colitis in WT and NAPRT KO mice [scWT2]

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

summary: NAPRT-mediated deamidated biosynthesis of nicotinamide adenine dinucleotide (NAD), an essential electron carrier for hundreds of biochemical reactions in all living cells, mediates the diet-microbe-host NAD metabolic interaction in mice. To study the function of this metabolic pathway in vivo, we recently generated a mutant mouse strain (NAPRT KO) in which a 21-nt fragment that encodes 7 amino acids in the catalytic domain of NAPRT was deleted in all cells using the CRISPR/Cas9-mediated gene editing technology. Our data showed that NAPRT KO mice are hypersensitive to DSS-induced colitis. To better understand this hypersensitivity at the molecular level, we analyzed transcriptomes of colon tissues from DSS-treated WT and NAPRT KO mice.

overall_design: Eight-week-old WT  female mice were treated  without 2.5% DSS in drinking water together with 3 g/L nicotinamide (NAM) for 7 days.

first: Xiaoling

last: Li

first: Xiaoyue

last: Wu

first: Igor

last: Shats


title: RNA-Seq analysis revealed the expression of terpenes in different parts of Chimonocalamus delicatus at different culm ages

city: kunming

first: Jiangbonan

last: jiang

state: Yunnan

address: panlongqu

institute: Southwest Forestry University

summary: Chimonocalamus is the only bamboo species known to secrete aromatic oils. The species is named after the distinctive aromatic oil found within the cavity of its bamboo stem. This study employed sensory analysis, headspace-gas chromatography-mass spectrometry (HS-SPME-GC-MS), and transcriptome sequencing to investigate the volatile component composition and formation mechanisms in Chimonocalamus delicatus, an endemic bamboo species of Yunnan Province. The bamboo samples analyzed included stems at different stem ages, as well as various parts. The aroma components of Chimonocalamus delicatus primarily consist of sesquiterpenes, including Humulene and Caryophyllene, which are terpenoid compounds. Principal component analysis (PCA) revealed significant differences in the volatile compounds across various stem ages and plant parts. This may constitute a key source of the characteristic aroma of Chimonocalamus delicatus at different stem ages and plant parts. Transcriptome analysis revealed that the aroma of Chimonocalamus delicatus was predominantly enriched in the secondary metabolite pathways, including the MVA and MEP pathways. The enzyme activities of key enzymes in its metabolic pathway were also determined. A comprehensive analysis of differential aroma metabolites and differentially expressed genes (DEGs) in Chimonocalamus delicatus led to the identification of key genes (DXR, FPS, TPS6, TPS7) involved in the regulation of aroma compound biosynthesis. In this study, the volatile components and regulatory network of Chimonocalamus delicatus essential oil were analyzed, which provided a solid theoretical basis for the development of bioactive compounds in Chimonocalamus delicatus.

overall_design: In order to study the difference of aroma composition and gene expression in different culm ages and parts of Chimonocalamus delicatus, a bamboo species endemic to Yunnan, China, we studied the samples of Chimonocalamus delicatus. Differences in the expression of terpene genes in different culm ages and in different sites were assessed. We also used RNA-seq to investigate the molecular basis of terpenoid genes in different parts of Chimonocalamus delicatus at the transcriptional level.

first: Juan

first: Shuguang

first: Bonan

last: Jiang

first: Yongmei


title: Hormonal rewiring of immunity upholds pathogen control and systemic nutrient homeostasis during dietary restriction

status: Public on Dec 05 2025

city: New York

first: Charles

last: Carr

department: Medicine

institute: Weill Cornell

summary: Food shortages and infectious diseases were constant threats throughout mammalian evolution and often occurred simultaneously. When food availability is reduced, it is unclear how the host adapts to fuel energy-demanding immune processes while preventing malnutrition. In the context of dietary restriction (DR), we found that glucocorticoids (GCs) are increased and promoted naïve T cell homing to the bone marrow niche, a site that supported their survival at steady-state. In response to a primary infection, DR-induced GCs dramatically rewired innate and adaptive immunity to simultaneously promote pathogen control and prevent hypoglycemia. This was achieved by dampening neutrophil glycolytic metabolism, which paradoxically enhanced their survival, function, and capacity to control pathogens. In parallel to enhancing neutrophils, DR-induced GCs restrained the generation of pathogen-specific effector T cells. This was essential for preventing hypoglycemia while combating a primary infection during DR. Although effector T cell responses were dampened, DR-induced GCs enriched for memory precursor effector cells to optimize memory T cell formation. Altogether, our work reveals a fundamental host adaptation strategy that upholds immediate and long-term pathogen control while maintaining systemic nutrient homeostasis in the setting of reduced food availability. These results redefine GCs as dominant optimizers of organismal fitness that align immunity and metabolic physiology with the nutritional status of the host.

overall_design: Examination of naive and effector CD8+ T cells and whole blood neutrophils of dietary restriction versus normal controls with bulk RNA-seq. Total CD8+ naive (CD44low CD62L+) T cells were sorted from the bone marrow of mice fed ad libitum or on DR for 3 weeks. For effector T cells, effector YopE69-77-specific CD8+ effector T cells were sorted at day 8 post-infection with WT Yptb from the spleen of mice fed ad libitum or on DR for 3 weeks. For neutrophils, cells were sorted from peripheral blood 8 days post-Yptb infection.

first: Luisa

last: Menezes-Silva

first: Mingeum

last: Jeong

first: Seong-Ji

last: Han

first: Nicholas

last: Collins


title: Preclinical assessment of pan-influenza A virus CRISPR RNA therapeutics in a human lung alveolus chip

city: Boston

first: Yuncheng

last: Man

address: 201 Brookline Ave

institute: Wyss Institute, Harvard University

summary: CRISPR technology offers an entirely new approach to therapeutic development because it can target specific nucleotide sequences with high specificity, however, preclinical animal models are not useful for evaluation of their efficacy and potential off-target effects because of high gene sequence variations between animals and humans. Here, we explored the potential of using the CRISPR effector Cas13 to develop new therapeutic approach for influenza A virus (IAV) infections based on its ability to specifically and robustly cleave single-strand viral RNA using a complementary CRISPR RNA (crRNA). We engineered crRNAs to target highly conserved regions in the IAV genome to create a potential pan-viral treatment strategy. A human lung alveolus chip (Lung Chip) lined by human primary alveolar epithelial cells interfaced with human primary pulmonary microvascular endothelial cells and infected with a pandemic IAV H3N2 strain was used to evaluate the on-target and off-target effects of these antiviral crRNA therapeutics. Our data show that the crRNAs targeting highly conserved regions in the IAV genome potently reduced viral replication in the alveolar airspace in the Lung Chip, and this was accompanied by suppression of the human host inflammatory response as indicated by a significant reduction in cytokine production and recruitment of immune cells. Importantly, only minimal off-target effects were observed based on transcriptomic analyses. As these crRNAs inhibit replication of influenza H1N1 and H3N2 in A549 cells as well as H3N2 in Lung Chips, these findings support use of CRISPR-Cas13 as a potentially viable approach to develop pan-IAV therapeutics or combating future influenza pandemics. The results also demonstrate that human Organ Chips be useful as more clinically relevant preclinical models for testing the efficacy and safety of crRNA therapeutics.

overall_design: To investigate the potential off-target effect of the crRNA, we infected the epithelial cells with H3N2 on-chip, transfected them with Cas13d mRNA and crRNAs, and lysed the cells for transcriptomic analysis.


title: Transcriptomic response of erythrocytes to hypoxia in temperature- acclimated Atlantic salmon

first: Miriam

last: Goetting

address: Yliopistonmäki

department: Dept of Biology

summary: Hypoxia and temperature stresses are often encountered by fishes and their interaction is well documented for a wide range of species. We aimed to characterize how temperature acclimation affects the global gene expression in erythrocytes during hypoxia and reoxygenation. We acclimated Atlantic salmon (Salmo salar) to 8 °C and 15 °C for 3 weeks and exposed them to acute hypoxia and reoxygenation. RNA was extracted at different times (1, 6, 12 hours, and 12 hours of reoxygenation) and RNA-seq analysis performed.

overall_design: Examination of gene expression in erythrocytes of warm and cold acclimated Atlantic salmon (Salmo salar) during hypoxia and reoxygenation

first: Mikko

last: Nikinmaa


title: Dextran sulfate sodium (DSS)-induced colitis in WT and NAPRT KO mice [NAPRTKODSS]

first: Xiaojiang

overall_design: Eight to twelve-week-old WT or NAPRT KO female mice were treated with or without 2.5% DSS in drinking water together with 3 g/L nicotinamide (NAM) for 7 days.


title: Restoring the potency of neutralizing antibody via guided hypermutation with hyper-antibody editor [Antibody_sequencing]

first: yuhong

last: wang

overall_design: We introduced Amplicon sequencing to detect the editing products of antibodies with different round of evolution. Antibody (CV07-209) VH gene was cloned with specific primers and subjected to high-throughput sequencing.

first: Jiazhi

last: Hu

first: Yuhong

last: Wang

first: Xinyi

last: Liu

first: Yuefeng


title: Comparison of extracellular vesicles isolation methods reveals method-dependent protein and miRNA profiles in saliva

city: Montpellier CEDEX 4

first: Malik

last: Kahli

address: Parc Euromédecine - CAP DELTA - 1682 Rue de la Valsière

institute: Sys2Diag UMR9005 CNRS - ALCEN

summary: Salivary extracellular vesicles (EVs) represent a powerful, non-invasive source of biomarkers for disease diagnosis and monitoring. Their molecular cargo reflects systemic and local physiological states, offering a window into neurological and inflammatory disorders. However, the diversity of EV isolation protocols and the possibility that each enriches distinct EV subpopulations remains a major barrier to reproducibility and data comparability. We conducted a comprehensive comparison of three EV isolation methods: ultracentrifugation (UC), PEG-based precipitation (Q), and immunoaffinity capture (M) to evaluate their impact on EV yield, purity, and molecular composition. Salivary EVs from healthy volunteers were analysed using proteomic and small-RNA sequencing approaches. Principal component analysis revealed clear isolation method-dependent clustering, where M-derived EVs displayed the most distinct profile. UC and Q produced broader proteomic repertoires with higher total protein content, whereas M-isolated EVs exhibited greater purity and enrichment of trafficking- and lysosome-associated proteins. Over 731 miRNAs selected, 28 were consistently altered across methods and 65 uniquely enriched in M isolates. RT-qPCR confirmed key directional trends. These 93 method-dependent miRNAs have predicted targets associated with synaptic structure and neurodegenerative pathways. These findings show that isolation methodology deeply shapes salivary EV cargo and suggest that immunoaffinity capture can isolate specific EV populations meeting diagnostic requirements.

overall_design: Unstimulated whole saliva was collected from healthy male volunteers and processed immediately. After sequential low-speed centrifugation, 500 µL of clarified saliva (whole saliva, WS) was retained for direct analysis, while 1 mL aliquots were subjected to EV isolation by ultracentrifugation (UC), PEG-based precipitation (Q), or immunoaffinity capture (M). EV preparations were either analysed fresh or stored at −80 °C. Samples were analyzed using small RNA sequencing.

first: Elodie

last: Simphor

first: Jérémy

last: Boulestreau

first: Romane

last: Marchal

first: Franck

last: Molina


title: Pharmacokinetics and tissue distribution of dual PPARα/γ agonist gigantol in mice

city: hefei

first: Yajun

last: Chen

state: anhui

address: No.1688, Lianhua Road, Hefei 230601, Anhui, China.

institute: Hefei Normal University

summary: Gigantol is a bioactive compound in Dendrobium officinale with a wide range of pharmacological properties. This study developed an ultrahigh-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF/MS) method for quantifying gigantol, which was subsequently applied to assess its pharmacokinetics and tissue distribution in Kunming mice. Additionally, the effects of gigantol on peroxisome proliferator-activated receptors (PPARs) were investigated. The UHPLC-Q-TOF/MS method was validated following the guidelines provided by the FDA and EMA for bioanalytical methods. Pharmacokinetic analysis revealed that gigantol exhibits a non-linear kinetic profile. Tissue distribution studies demonstrated high concentrations of gigantol in the liver and lungs. RNA sequencing (RNA-seq) indicated significant enrichment of PPAR signaling pathways in the KEGG database during gigantol-induced gene expression changes in the liver of Kunming mice. Molecular fingerprinting, docking studies and dual luciferase reporter assays confirmed that gigantol is a dual PPARα/γ agonist. These findings provide valuable insights for preclinical research on gigantol.

overall_design: Six male Kunming mice (6–8 weeks old, 20–28 g) were randomly divided into two groups (Administration group (ADMG) and normal group (NG)). ADMG group received gigantol (10 mg/kg) via p.o., while NG group received an equivalent volume of vehicle as a control. Four hours post-administration, the mice were euthanized, and fresh liver tissues were collected. Total RNA was extracted according to the manufacturer's instructions. The purity and integrity of the RNA were assessed using a NanoDrop ND-100 (Wilmington, DE, USA) and an Agilent Bioanalyzer 2100 (Agilent, CA, USA), respectively.

first: Xiaozhong

last: Cheng

first: Jing

first: Jianrong

last: Zhang

first: Lili

last: Lei

first: Yaping

first: Weizhu

first: Minrui

first: Xuan

last: Lu

first: Jianli

first: Wei


title: Transcriptomic changes in the colon of WT and NAPRT KO mice after AOM injection [NAPRTKOAOM]

first: Xiaojiang

last: Xu

summary: NAPRT-mediated deamidated biosynthesis of nicotinamide adenine dinucleotide (NAD), an essential electron carrier for hundreds of biochemical reactions in all living cells, mediates the diet-microbe-host NAD metabolic interaction in mice. To study the function of this metabolic pathway in vivo, we recently generated a mutant mouse strain (NAPRT KO) in which  a 21-nt fragment that encodes 7 amino acids in the catalytic domain of NAPRT was deleted in all cells using the CRISPR/Cas9-mediated gene editing technology. Our results showed that NAPRT is highly expressed in the gut epithelial cells, where it functions to maintain the cellular NAD pool for an efficient response to stress-induced acute NAD depletion. Consistently, NAPRT deficiency impairs DNA repair, sensitizes mice to AOM-induced gut DNA damage. Here we profiled transcriptomic changes in the colon of WT and NAPRT KO mice at different time points after injection of AOM.

overall_design: Female WT and NAPRT KO mice supplemented with nicotinic acid at 3 g/L in drinking water were i.p. injected with 10 mg/Kg AOM, colons were then harvested at 0 (control) , 12, 48 hr after AOM injection (n=7-9 mice/genotype in each tme point)

first: Xiaoling

last: Li

first: Xiaoyue

last: Wu

first: Igor

last: Shats


title: Corticosterone drives behavioral inflexibility via plasticity-related gene expression in the dorsal striatum

city: Philadelphia

first: Keegan

middle: Scott

last: Krick

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Behavioral flexibility allows organisms to modify actions based on new information, such as shifts in reward value or availability, and is promoted by the dorsomedial striatum (DMS). In contrast, behavioral inflexibility provides efficiency and automaticity in familiar contexts, and is promoted by the dorsolateral striatum (DLS). Importantly, chronic elevation of the primary stress hormone, corticosterone (CORT) in rodents or cortisol in humans, impairs behavioral flexibility through dendritic atrophy in the DMS, and promotes inflexible behavioral response strategies through dendritic outgrowth in the DLS. However, understanding of changes in gene expression underlying behavioral inflexibility is lacking. We used a food-motivated operant task in male and female mice to define gene changes that accompany the shift to inflexible behavior with CORT. We discovered that CORT-accelerated loss of behavioral flexibility is accompanied by decreased DMS- and increased DLS-specific synaptic plasticity gene expression, and that distinct genes are either differentially expressed or spliced in the transition to inflexible behavior. Splicing analysis suggests that repressed activity in the DMS during the transition to inflexible behavior may reflect both reduced expression and increased degradation of plasticity-related mRNA transcripts. Finally, given the ability of CORT to influence histone acetylation, we defined CORT-mediated H3K9ac enrichment profiles associated with synaptic plasticity gene regulation stratified by sex and striatal subregion. This study is the first to define CORT-driven epigenetic regulation in the DMS and DLS during the CORT-accelerated transition from flexible to inflexible behavior in male and female mice.

overall_design: RNA sequencing of C57BL/6 mouse dorsal medial striatum and dorsal lateral striatum after chronic corticosterone treatment following limited and extended training paradigms.

first: Michael

middle: D

last: Murphy

middle: S

first: Shuo

first: Elizabeth

last: Heller


title: Programmatic design and editing of cis-regulatory elements

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary: The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Ledidi, a computational method that rephrases the discrete design task of choosing which edits to make as an easily solvable continuous optimization problem. Ledidi can use any pre-trained deep learning model to guide the optimization, yielding an edited sequence that exhibits the desired outcome while explicitly minimizing the number of edits. When applied in dozens of settings, we find that Ledidi's designs can precisely control transcription factor binding, chromatin accessibility, transcription, and enhancer activity in silico. By using several deep learning models simultaneously, we design cell type-specific enhancers and experimentally validate them in cellulo. Finally, we introduce the concept of an "affinity catalog'', where the design task is repeated multiple times across continuous variants of the design target.  We demonstrate how these catalogs can be used to interpret deep learning models and the impact of starting template sequences, and also to design regulatory elements that control transcriptional dosage in a cell type-specific fashion.

overall_design: The activity of developmental enhancer in S2 and ovarian somatic cells were measured using the STARR-seq method.

first: Jacob

last: Schreiber

first: Franziska

last: Lorbeer

first: Monika

last: Heinzl

last: Reiter

first: Baptiste

last: Rafanel

first: Yang Young

first: William

last: Stafford Noble


title: Evaluation of clonality in lentigo maligna

city: Melbourne

first: Mark

last: Shackleton

state: VIC

address: Level 4, Paula Fox Melanoma and Cancer Centre 545 St Kilda Rd

department: School of Translational Medicine

country: Australia

institute: Monash University

type: Genome variation profiling by high throughput sequencing

summary: Lentigo maligna (LM), a type of in situ melanoma, has a high rate of local recurrence following curative-intent surgical resection. Although recurrences might represent inadequately excised incident LMs, apparent recurrences could be new primary LMs developing from distinct melanocytic clones in the same ultraviolet radiation (UVR)-damaged anatomical region. As distinguishing these possibilities has implications for patient management, we tested genetic relationships between incident and recurrent LMs. Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.

overall_design:
Incident LMs with histologically clear margins, and their recurrent LMs and invasive lentigo maligna melanomas (LMMs) were laser microdissected for DNA extraction. Tumour and matched germline DNA underwent whole exome sequencing (WES). Clonal relationships between incident and recurrent LMs were tested by elucidating and tracking clones within and across samples.*Raw sequencing reads for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.

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

last: Szeto

first: Peinan

last: Zhao

first: Sophie

last: Lim


title: Differential transcriptional effects of mycobacterial nucleomodulins MgdE and MmpE in THP-1 macrophages

city: Wuhan

first: Liu

last: Chen

address: No.1 Shizishan Street, Hongshan District

department: College of Animal Science & Technology

institute: Huazhong Agricultural University

summary: This study uses RNA-seq to quantitatively compare the gene expression profiles of THP-1 macrophages infected with the wild-type (WT), mgdE-deleted (ΔmgdE), and mmpE-deleted (ΔmmpE) strains of Mycobacterium bovis BCG, in order to investigate the roles of two conserved nucleomodulins, MgdE (Rv1075c) and MmpE (Rv2577), in host-pathogen interactions.

overall_design: RNA-seq profiling was performed on THP-1 macrophages infected for 24 h with wild-type (WT), ΔmgdE, and ΔmmpE strains of M. bovis BCG. Each condition included three biological replicates, with the WT group serving as a shared control for both mutants

first: Chen

last: Liu

first: Baojie

last: Duan

first: Qiang

last: Jiang

first: Yifan

last: Wang

first: Yingyu

first: Changmin

last: Hu

first: Lei

last: Zhang

first: Aizhen

last: Guo


title: Maternal Western-Style Diet alters Kupffer Cell proportion leading to Metabolic Dysfunction-Associated Steatotic Liver Disease when challenged with western diet in adulthood

city: OKC

first: Sarah

middle: Jane

last: Miller

state: OK

address: 940 Stanton L. Young Blvd

institute: University of Oklahoma Health Sciences Center

summary: Exposure to maternal western-style diet (mWD) is associated with early development of metabolic dysfunction-associated fatty liver disease (MAFLD) in offspring. Kupffer cells (KCs), the main resident macrophage population in the liver, are known to promote MAFLD progression, however, the effects of mWD on KC subtypes, ontogeny, and gene expression in offspring are not fully understood. In this manuscript, we used two different models of mWD exposure and challenge in adulthood to understand the impact of mWD on KC proportion, ontogeny, and gene expression in adult offspring. Our data indicate that in the absence of challenge in adulthood, mWD results in increased KC proportion in offspring, with limited changes in KC ontogeny or liver phenotype. In contrast, mWD mice challenged with WD in adulthood had increased expression of inflammatory (Nlrp3) and fibrosis (Tgfb1) related genes compared to chow (CH)-WD fed mice. Although KC proportion and ontogeny were similar when comparing CH-WD and WD-WD fed mice, we found that WD-WD mice had a greater reduction in KC proportion and TdT labelling than CH-WD fed mice when normalized to their respective maternal diet controls. Similar results were found when mice were weaned onto normal chow and re-challenged with WD later on in adulthood. Bulk RNA sequencing data indicate that KCs from mWD mice re-challenged with WD in adulthood had increased expression of inflammatory and antigen presenting genes compared to KCs isolated from WD fed mice lacking mWD exposure. These findings highlight the intergenerational repercussions of mWD on liver phenotype as well as KC proportion and ontogeny and provide novel insight into the mechanisms dictating MAFLD.

overall_design: Bulk RNA seq profiling of the offspring from WD of CH fed dams, with and without WD challenge in adulthood.

first: Rachel

last: Janssen

first: Wanke

first: Karen

middle: R

last: Jonscher

first: Hua

last: Zhong

first: Christa

middle: I

last: DeVette

first: Jacob

last: Friedman

first: Kurt

last: Zimmerman


title: Modeling Mowat-Wilson Syndrome with patient iPSCs reveals transcriptional and phenotypic defects in neural progenitors

city: Genova

first: Paolo

last: Scudieri

state: Genova

address: Largo Daneo 3

department: DINOGMI

country: Italy

institute: University of Genoa

summary: Zinc finger E-box-binding homeobox 2 (ZEB2) is a key transcription factor involved in multiple aspects of nervous system development, including neuronal specification, migration, and differentiation. Loss-of-function variants in ZEB2 cause Mowat-Wilson syndrome (MWS), a severe neurodevelopmental disorder characterized by intellectual disability, epilepsy, and brain structural abnormalities. In this study, we generated and characterized induced pluripotent stem cell (iPSC) lines from MWS patients carrying pathogenic ZEB2 variants. Patient-derived iPSCs retained full pluripotency and were capable of differentiating into all three germ layers, including neural lineages. Upon directed differentiation into neural progenitor cells (NPCs) and early neurons, we identified distinct transcriptional alterations affecting neuroepithelial-to-radial glia transition, glial lineage specification, and neuronal subtype identity. RNA-seq analysis revealed dysregulation of genes involved in cytoskeletal remodeling, extracellular matrix organization, and cell motility. Functional holographic live imaging confirmed a significant increase in motility behavior in MWS NPCs and early neurons, suggesting that altered cell dynamics may underlie aberrant neural circuit formation. Despite these changes, early neuronal markers such as MAP2 were expressed at comparable levels in MWS and control cells. Together, these findings uncover novel cellular and molecular phenotypes associated with ZEB2 deficiency and provide insight into how disrupted progenitor behavior and transcriptional misregulation may contribute to the neurodevelopmental features of MWS.

overall_design: RNA-seq profiling of iPSC-derived neural progenitors generated from two control individuals and four Mowat-Wilson Sindrome patients. Four replicates for each samples

first: Ilaria

last: Musante

first: Giulia

last: Gorrieri

first: Serena

last: Tamburro

first: Giovanni

last: Fiorito

first: Federico

last: Zara

first: Emilia

last: Ricci


title: Effect of SAFB1/SAFB2 knockou or ERH knockout on the miRNA transcriptome of murine Baf3 cells

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

institute: Medical University of Innsbruck, Biocenter

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs are small non-coding RNAs that mediate post-transcriptional silencing of most mammalian genes. They are generated in a multi-step process initiated by the Microprocessor, a protein complex composed of DROSHA and DGCR8. Recent studies have described the phenomenon of “cluster assistance”, in which a prototypic primary miRNA hairpin can license the Microprocessor-mediated processing of a clustered suboptimal hairpin in cis. Mechanistic analyses led to the identification of two critical factors for this process, SAFB2 (scaffold attachment factor B2) and ERH (enhancer of rudimentary homolog), but it remains unclear to which extent these factors contribute to and are required for cluster assistance. Here, we have used a previously established dual fluorescence reporter system (doi: 10.1016/j.molcel.2020.05.011) to generate loss-of-function clones for SAFB2 and its closely related family member SAFB1 as well as for ERH.Our data indicate that loss of SAFB1/2 and of ERH results in overlapping, but not identical defects in primary miRNA biogenesis.

overall_design: Small RNAseq data of Baf3 cell expressing fluorescent reporters for the activity of mutated forms of miR-15a and miR-16 (see doi: 10.1016/j.molcel.2020.05.011 for details) that were transduced with vectors encoding Cas9 and sgRNAs targeting Safb1/2, Erh or murine Rag1 (as a control gene not involved in miRNA biogenesis). The polyclonal population of cells that lost the capability to perform cluster assistance in response to SAFB or ERH gene disruption was identified and sorted out based on the derepression of the dsRed-based miR-15a reporter. Total RNA of the respective cell populations was prepared with Trizol, mixed with defined amounts of spike-in control RNAs and subjected to small RNA library preparation.

first: Aschenwald

last: Simon


title: Effect of the deletion of the reported ERH binding site embedded in the DGCR8 N-terminus and/or global ERH knockdown on the expression of mature miRNAs

summary: MicroRNAs are small non-coding RNAs that mediate post-transcriptional silencing of most mammalian genes. They are generated in a multi-step process initiated by the Microprocessor, a protein complex composed of DROSHA and DGCR8. Recent studies have described the phenomenon of “cluster assistance”, in which a prototypic primary miRNA hairpin can license the Microprocessor-mediated processing of a clustered suboptimal hairpin in cis. Mechanistic analyses led to the identification of ERH (enhancer of rudimentary homolog) as a critical factor in this process. Notably, ERH has been demonstrated to associate with the N-terminus of DGCR8, but it has not been demonstrated that this complex is required for cluster assistance.  Here, we have used prime editing to generate alleles that encode a DGCR8 Δ103-126Q mutant that cannot bind ERH anymore. In contrast to global ERH knockdown, disruption of the ERH binding motif in DGCR8 affects processing of only a subset of cluster assistance-unrelated pri-miRNAs. Thus, ERH-mediated cluster assistance is independent of its described association with DGCR8, indicating that ERH confers two distinct roles in primary miRNA biogenesis: One driven by its direct binding to the Microprocessor via DGCR8 and the other as a DGCR8/ERH complex-independent factor in cluster assistance.

overall_design: Wild-type 293T cell clones and clones in which the DGCR8 locus had been modified by prime editing to delete the reported ERH binding site were transiently transfected with vectors encoding non-targeting shRNA 1 or 2 as well as with shRNAs targeting ERH. Transfected cells were sorted on day 5 based on expression of a fluorescent marker and directly subjected to total RNA isolation. Total RNA of the respective cell populations was prepared with Trizol, mixed with defined amounts of spike-in control RNAs and subjected to small RNA library preparation.

first: Simon

last: Aschenwald


title: Spatial Transcriptomics of Human Fetal Lungs

city: Rochester

first: Soumyaroop

last: Bhattacharya

state: NY

address: 601 Elmwood Ave Box 703

institute: University of Rochester

summary: Spatial transcriptomic profiles were generated using lung tissue sections obtained from twelve prenatal human lung samples ranging in gestational age from 13 – 20 weeks, of which four were diagnosed with Trisomy 21, with defined hypoplasia.

overall_design: Lung tissue sections were assessed for quality using DV200 criteria, and those with DV200 values greater than 50% were selected for spatial transcriptomics. 5-micron tissue sections from individual samples were placed onto Visium Gene Expression Slides (10X Genomics), stained with H&E using Visium chemistry (v1) and scanned, in two batches. Subsequently, the tissue samples were permeabilized to release ligated probe pairs from the cells, that are bound to the spatially barcoded oligonucleotides present on the spots. The resulting barcoded libraries were sequenced on a NovaSeq 6000 sequencer (Illumina) and aligned to GRCh38-2020-A and quantified using the standard Spaceranger workflow (v2.0.1).

first: Bhattacharya

last: Soumyaroop


title: Single-cell transcriptomic profiling of the developing human brain (GW 13, 15, and 19)

city: San Francisco

first: Tianzhi

last: Wu

state: CA

address: 500 Parnassus Ave

institute: University of California, San Francisco

summary: This dataset provides single-cell RNA profiles of the developing human brain. Samples were collected from fresh prenatal human brain tissue at gestational weeks (GW) 13, 15, and 19. For GW15 and GW19, cortical tissues were microdissected into the germinal zone (GZ) and cortical plate (CP) regions. At the earlier developmental stage (GW13), the entire frontal telencephalon, including the ganglionic eminence, was profiled. Single-cell gene expression libraries were prepared using the 10x Genomics Chromium Single Cell Gene Expression Flex Kit.

overall_design: Samples were dissociated using the Papain Dissociation System, fixed with the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics).  Single-cell gene expression libraries were prepared with the 10x Genomics Chromium Single Cell Gene Expression Flex Kit (PN-1000414) following the manufacturer’s protocol (CG000527 Rev E).

first: Li

last: Wang

first: Tanzila

last: Mukhtar

first: Jingjing

last: Li