title: Body weight at weaning is the main predictor for diabetic phenotype in male TallyHo/JngJ mice

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: TallyHo/JngJ (TallyHo) mice are a polygenic mouse model for type 2 diabetes (T2D), first described in 2001 and characterized by obesity due to an increased mass of fat pads. We aimed to discover whether environmental condition(s) during early life time or epigenetic factors across generations could be responsible for the varying penetrance of the metabolic phenotype of male and female TallyHo mice. Therefore, we set up the subsequent study in which we analyzed parameters of glucose homeostasis and environmental factors of individual TallyHo mice rather than relying on group averages.

overall_design: We analysed hypothalamic, muscle, sat, vat, and liver tissue from different groups of TallyHo mice: high (>14 g) or low (<10 g) body weight at weaning, high (>300 mg/dl) or low (<200 mg/dl) blood glucose

first: Sieglinde

last: Hastreiter

first: Martin

last: Irmler

first: Kerstin

last: Richter

first: Sandra

last: Hoffmann

first: Raffaele

last: Gerlini

first: Helmut

last: Fuchs

first: Valérie

last: Gailus-Durner

last: Hrabé de Angelis


title: Depletion of DIS3 from human cell lines

status: Public on Jun 02 2026

city: Paris

first: Antonin

last: Morillon

state: Paris

address: 26 rue d'Ulm

country: France

institute: Institut Curie

type: Expression profiling by high throughput sequencing

summary: DIS3 is a 3’ to 5’ exoribonuclease responsible for degradation of multiple RNA targets. Most reports in human cells focus on its function in RNA surveillance in the nucleus. However, a small fraction of DIS3 can be also found in cytoplasm. Thus, the focus of this experiment was to identify the cytoplasmic targets of DIS3. Using rapid, auxin inducible, degradation of DIS3 protein and subcellular fractionation, we were able to identify RNA accumulated in cytoplasm of human cells upon DIS3 depletion. The raw data and counts for annotated and non-annotated transcripts resulting from this experiment are provided.

overall_design: The total and polyA enriched RNA-seq was performed on technical triplicates for cytoplasmic fraction from a control cell line and CRISPR clone with introduced DIS3-AID without treatement or after 1h with auxin for inducion of DIS3 depletion

first: Dominika

last: Foretek

first: Marina

last: Pinskaya

first: Marc

last: Gabriel


title: Pathologic mitophagy in neurites induces mitochondrial plaques in AD mouse brains

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

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

overall_design: Refer to individual Series


title: Single cell transcriptome of cortical inhibitory neurons from the developing mouse brain

city: La Jolla

first: Jessica

middle: Xinyun

last: Du

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: We used single cell RNA-sequencing (scRNAseq) to assess the maturation of inhibtory neurons in and migrating into the developing cortical plate of E18 mouse embryos, in an effort to understand gene expression programs that are dynamically regulated at this timepoint and to develop gene expression-based measures of "maturity" for this celltype.

overall_design: Inhibitory neurons were labeled with in utero intraventricular injection of AAV for expression of eYFP fused with a control peptide under the mDlx promoter. Cortical tissue from E18 embryos was dissociated and fluorescently labeled inhibitory neurons were sorted and used for single cell sequencing.

first: Jessica Xinyun

first: Giordano

last: Lippi


title: Kluyveromyces marxianus: K. marxianus parental (SLP1) and K. marxianus adapted (P8)

city: Zapopan

first: Lorena

last: Amaya Delgado

state: Jalisco

address: Camino arenero 1227

department: Industrial Biotechnology

country: Mexico

institute: CIATEJ

summary: Kluyveromyces marxianus is a non-conventional yeast with outstanding physiological characteristics and a high potential for lignocellulosic ethanol production. However, achieving high ethanol produc-tivities implies overcoming several biotechnological challenges as the cellular inhibition caused by the inhibitors present in the medium. In this work, the adaptation of K. marxianus SLP1 to increase the tolerance to a mix of inhibitory compounds was carried out using the adaptive laboratory evolution (ALE) strategy. As a result of the ALE adaptation process, an improved K. marxianus strain (P8) was obtained after 8 serial passes. The fermentative and physiological parameters evidenced a better response of the P8 strain against the synergistic effect of multiple inhibitors. The P8 strain reduced the lag phase from 12 to 4 h, increasing 40% the biomass and improving 16-fold the volumetric eth-anol productivity. To test the transcriptional dynamics for the adaptation process, we performed a differential gene expression analysis in control conditions; the results showed that the basal gene expression in P8 changes, suggesting the biological capability of K. marxianus to activate the ad-aptative prediction mechanism. This study demonstrates the rapid adaptability of K. marxianus SLP1 to stressful environments, making this yeast a promising candidate to produce lignocellulosic ethanol.

overall_design: Transcriptional profile of two different strains of Kluyveromyces marxianus, K. marxianus parental (SLP1) and K. marxianus adapted (P8).

last: Amaya-Delgado

first: Dania

last: Sandoval-Nuñez

first: Teresa

last: Romero-Gutiérrez

first: Anne

last: Gschaedler

first: Melchor

last: Arellano-Plaza

first: Carolina

last: Gómez-Márquez


title: Dichlorobenzene Mouse S1500+

status: Public on Jun 01 2026

city: Durham

first: Scott

last: Auerbach

state: NC

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

summary: 1,2‑Dichlorobenzene (1,2‑DCB) is a chlorinated aromatic hydrocarbon that is widely used in industrial applications, including as a solvent for waxes, resins, and paints, and it serves as an ingredient in the production of disinfectants and deodorants. 1,4‑Dichlorobenzene (1,4‑DCB) is a chlorinated aromatic hydrocarbon that is used in various industrial and household applications, including as a fumigant for moth control, a deodorizer in urinal cakes, and an air freshener in domestic and public settings. Short-term in vivo transcriptomic studies were used to assess the biological potency of 1,2‑DCB and 1,4-DCB. The data from these studies are intended to support risk assessment and establishment of acceptable exposure levels of 1,2‑DCB and 1,4‑DCB in environmental and occupational settings.

overall_design: Female mice were exposed to 5 concentrations plus control of two dichlorobenzene compounds. TempO-seq S1500+ was performed on samples from 5 tissues: heart, kidney, liver, lung, and ovary.


title: Dichlorobenzene Rat S1500+

summary: 1,2‑Dichlorobenzene (1,2‑DCB) is a chlorinated aromatic hydrocarbon that is widely used in industrial applications, including as a solvent for waxes, resins, and paints, and it serves as an ingredient in the production of disinfectants and deodorants. 1,4‑Dichlorobenzene (1,4‑DCB) is a chlorinated aromatic hydrocarbon that is used in various industrial and household applications, including as a fumigant for moth control, a deodorizer in urinal cakes, and an air freshener in domestic and public settings. Short-term in vivo transcriptomic studies were used to assess the biological potency of 1,2‑DCB and 1,4-DCB. The data from these studies are intended to support risk assessment and establishment of acceptable exposure levels of 1,2‑DCB and 1,4-DCB in environmental and occupational settings.

overall_design: Female rats were exposed to 6 concentrations plus control of two dichlorobenzene compounds. TempO-seq S1500+ was performed on samples from 5 tissues: heart, kidney, liver, lung, and ovary.


title: Transcriptomic analysis of (S)-1,3-butanediol degradation pathway in Pseudomonas putida KT2440

city: Ulsan

first: Nandakumar

last: Arumugam

address: UNIST-gil 50

department: School of Energy and Chemical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

summary: (S)-1,3-butanediol [(S)-1,3-BDO] is a chiral diol and stereoisomer of (R)-1,3-BDO with potential applications in the chemical and pharmaceutical industries; however, its microbial degradation pathway remains poorly understood. In this study, we performed strand-specific, paired-end RNA-seq transcriptomic analysis of Pseudomonas putida KT2440 grown on (S)-1,3-BDO and (S)-3-hydroxybutyrate [(S)-3-HB] as sole carbon sources to elucidate the underlying degradation pathway. Differential gene expression analysis was performed to identify genes specifically induced during (S)-1,3-BDO and (S)-3-HB metabolism, providing insight into the enzymatic steps and regulatory mechanisms governing their catabolism in P. putida KT2440.

overall_design: To elucidate the degradation pathway of (S)-1,3-BDO in Pseudomonas putida KT2440, genome-wide transcriptome profiling was conducted using strand-specific paired-end RNA sequencing (RNA-seq). The wild-type strain was cultivated in modified M9 minimal medium containing 35 mM of (S)-1,3-BDO, or (S)-3-HB as the sole carbon source at 30°C with continuous shaking at 200 rpm. Cells were harvested at mid-exponential growth phase and total RNA was isolated from biological duplicate cultures.

first: Joon Young

last: Park

first: Minchang

last: Jang

first: Donghyuk

last: Kim

first: Sung Kuk

last: Lee

first: Sunghoon


title: The flame retardant triphenyl phosphate induces varying responses in genetically diverse mouse induced pluripotent stem cells

city: Bar Harbor

first: Madison

last: Armstrong

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Genetic variation impacts the biological response to chemical and environmental exposures, contributing to differences in resistance or susceptibility. Forward genetic screens of genetically diverse cell populations can be used to identify the precise genetic variants that drive response variation, but such screens are limited by the lack of available genetically diverse human derived cell panels. Cell lines from laboratory mouse genetic reference populations like the Diversity Outbred (DO) population are genetically diverse and powered for genetic mapping but also offer the significant advantage of in vitro / in vivo trait correlation and in vivo validation using genetically matched individuals. These diverse cell panels are especially beneficial for studying early developmental effects of chemical exposures. We created a panel of induced pluripotent stem cells (iPSCs) derived from the Diversity Outbred mouse population to enable genetic analysis of cellular phenotypes. Cells were exposed to triphenyl phosphate (TPHP), an organophosphate flame retardant that has been linked to numerous adverse developmental effects, to identify cellular responses associated with developmental exposure risk. Our analysis characterizes interline variation in gene expression in response to TPHP in over 200 DO iPSC lines by RNA-seq and applied expression quantitative trait loci (eQTL) mapping to identify genomic loci that contribute to variation in gene expression following TPHP exposure.

overall_design: This dataset includes RNA-seq data from 218 Diversity Outbred mouse iPSC lines, with paired control and triphenyl phosphate treated samples.

first: Kathryn

last: Janeczko

first: Hannah

middle: B

last: Dewey

last: Czechanski

first: Qiongyu

last: Chen

first: Emily

last: Swanzey

first: Callan

last: O’Connor

first: Steven

middle: C

last: Munger

first: Laura

middle: G

last: Reinholdt


title: A global view of cell-type-specific temporal dynamics in mammalian aging

city: New York

first: Ziyu

last: Lu

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

type: Genome binding/occupancy profiling by high throughput sequencing


title: Hippocampal CA3 Nex+ neuronal TNFR2 alleviates chronic neuropathic pain by sex-dependently engaging opioid and endocannabinoid pathways

city: Washington

first: John

middle: R

last: Bethea

state: DC

address: 2300 I Street NW

institute: The George Washington University

summary: Chronic neuropathic pain develops due to persistant neuroinflammation and maladaptive synaptic plasticity in the central nervous system following nerve injury. While TNFR2 signaling has been extensively studied in pain resolution, its expression on specific neuronal populations and the molecular pathways involved in spontaneous pain recovery remain unknown. In this, study, we investigated the role of TNFR2 within hippocampal Nex/Neurod6+ pyramidal neurons in promoting recovery from chronic constriction injury (CCI). To achieve neuron-specific deletion of TNFR2, we generated tamoxifen-inducible conditional knockout mice (NexCreERT2:TNFR2F/F). We demonstrate that TNFR2 deletion from Nex/Neurod6+ neurons prevents spontaneous pain recovery in both sexes. Exogenous administration of a TNFR2 agonist significantly improved mechanial withdrawal thresholds in both sexes of wld-type mice but did not alleviate pain in NexCreERT2:TNFR2F/F, indicating that Nex-TNFR2 expression is required for TNFR2-mediated analgesia. Bulk RNA sequencing of hippocampal (Hc) tissue collected six weeks after CCI revealed that TNFR2 activation upregulates genes Pomc and oleoyl-ACP-hydrolase (Olah). Immunostaining also showed that TNFR2 agonism restored cornu ammonis 3 (CA3) region POMC and β-Endorphin protein levels that were suppresed after CCI. A behavioral experiment demonstrated that systemic blockade of the u-opioid receptor with naltrexone prevented TNFR2-mediated pain recovery in males but only partially in females. In contrast, inhibition of cannabinoid 1 receptor (CB1R) signaling abolished TNFR2-driven analgesia in both sexes. Together, these data reveal that Hc TNFR2 signaling in Nex+ neurons is critical for CNP recovery and TNFR2 acivation promotes analgesia by engaging endogenous u-opioid and endocannabinoid pathways in a sex-dependent manner

overall_design: Bulk RNA-seq profiling of C57BL/6 WT mice and NexCreERT2:TNFR2F/F mice compared among Naïve, CCI+PBS and CCI+TNFR2 Agonist of male Hc tissue at the endpoint of the study

first: Sreejita

last: Arnab

first: Payam

last: Fathi

first: Erin

last: Jones

first: Aravind

last: Meyyappan

first: Kayla

middle: L

last: Nguyen

first: Valerie

last: Bracchi-Ricard

first: Shruti

last: Gupta

first: Roman

last: Fischer

first: Veronica

middle: J

last: Tom


title: Endothelial FOXQ1 is required for CNS angiogenesis and blood brain barrier formation

city: Chongqing

first: Yulin

last: Yan

address: No. 83 Shabei Street

country: China

institute: Bioengineering College of Chongqing University

summary: The transcriptional mechanisms coordinating angiogenic sprouting with the acquisition of barrier properties in the developing central nervous system (CNS) remain incompletely defined. Here, we demonstrate that the forkhead box transcription factor Foxq1 is essential for CNS angiogenesis and blood-brain barrier (BBB) formation. Endothelial-specific deletion of Foxq1 in mice resulted in defective angiogenesis in the brain and retina, characterized by impaired tip cell identity, reduced vascular coverage, and diminished proliferation. Moreover, mutant embryos exhibited compromised BBB integrity, evidenced by enhanced leakage of molecular tracers. Single-cell transcriptomics revealed that Foxq1 is enriched in tip cells and barrier-competent capillary populations, and its loss disrupts the transcriptional programs governing both endothelial sprouting and barrier maturation. Mechanistically, Foxq1 couples angiogenic morphogenesis with BBB acquisition by regulating tip cell-enriched transcripts such as Esm1, alongside core barrier determinants including Cdh5 and Mfsd2a.These findings establish Foxq1 as a critical transcriptional link between CNS vascular growth and functional barrier establishment, with implications for understanding neurovascular developmental disorders.

overall_design: At the E12.5 stage of mice, brain tissues from Foxq1flox/flox and Foxq1iECKO mice were collected separately. Endothelial cells were enriched using CD31 magnetic beads, and single-cell RNA-seq analysis was performed on these endothelial cells


title: Integrative multiomic analysis reveals how non-viral delivery system selection shapes CRISPR gene editing outcomes in stem cells.

city: Bethlehem

first: Joshua

last: Graham

state: PA

address: 124 E Morton st

institute: Lehigh University

summary: The clinical translation of CRISPR gene editing is challenged by the lack of delivery systems that are both safe and efficient in therapeutically relevant cell types such as mesenchymal stem cells (MSCs). Non-viral delivery avoids the immunogenicity and genomic integration risks of viral vectors but faces fundamental trade-offs between editing efficiency and cytotoxicity. Here, we present a comprehensive multiomic analysis of four non-viral CRISPR delivery modalities including cell-penetrating peptide- (CPP), lipid-, and polymer-based nanoparticles and electroporation; across mRNA and ribonucleoprotein (RNP) molecular formats. We systematically evaluate each modality, demonstrating that lipid-based delivery achieved the highest editing rates at the cost of genomic instability, interferon pathway activation, and a pro-inflammatory shift in the MSC paracrine activity. Alternatively, CPPs yield moderate editing rates while reducing these unintended side-effects, whereas polymers and electroporation consistently yielded the lowest efficiencies. CRISPR molecular format and delivery method interacted in a stress-dependent manner, with RNP delivery reducing editing rates under high-stress systems while improving them in lower-stress modalities such as CPP and electroporation. These findings establish that editing efficiency alone is an insufficient metric for delivery system selection, and that genomic stability, transcriptomic dysregulation, and inflammatory response must be treated as primary design criteria for CRISPR therapies.

overall_design: Human bone marrow mesenchumal stem cells were transfected with either eGFP mRNA, Cas9 mRNA &  AAVS1 gRNA, or an AAVS1 targeting Cas9 RNP using CPP, lipid, or polymeric nanoparticles or electroporation. Two days after sequencing total RNA was purified using the Trizol reagent and the Purelink RNA minikit (Thermo Fisher). Total RNA was sequenced by Novogene using the NovaSeq X Plus Series platform (PE150) with 6 G of raw data per sample. The resulting .fastq files were processed using kallisto with mapping to the Ensembl human reference transcriptome (GRCh38, release 111, cDNA, all transcripts)

first: Josh

first: Tomas

last: Gonzalez-Fernandez


title: METTL3-mediated m6A modification controls Tcra recombination center formation and thymic T cell development

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is the most prevalent internal modification of RNA, and METTL3 functions as the catalytic core of the methyltransferase complex. While m6A regulates T cell activation and differentiation, whether this RNA modification participates in antigen receptor V(D)J recombination remains unknown. Using conditional Mettl3 knockout mice and multi-omic profiling, we examined m6A function in thymocyte development and Tcra rearrangement. Mettl3 deficiency reduced thymic cellularity by about 20-30%, substantially decreased double-positive (DP) thymocytes, diminished peripheral CD8+ T cells, and selectively impaired Tcra but not Tcrb rearrangement. Mechanistically, m6A specifically decorated TEA germline transcripts and maintained recombination center architecture. METTL3 loss abolished m6A enrichment at TEA, diminished Eα-TEA chromatin looping, and reduced germline transcription. Concurrently, rearranged Tcra translation efficiency fell to about 40% of wild-type levels, significantly reducing TCR-CD3 surface expression on DP, CD4 SP, and CD8 SP cells. Mettl3 knockout further upregulated DNA repair genes  such as Lig4, Fignl1, and Rad51ap1, activated the interferon pathway, and increased γH2A.X DNA double-strand break markers and double-stranded RNA accumulation in DP thymocytes. Collectively, these results establish RNA m6A modification as a previously unrecognized regulatory layer of V(D)J recombination that controls recombination center formation and preserves genomic integrity during Tcra gene rearrangement.

overall_design: scRNA-seq analysis of Mettl3 WT and Mettl3 KO thymocytes(1 replicates); Bulk RNA-seq analysis of Mettl3 WT and Mettl3 KO for DP thymocytes(3 replicates); H3K4me3 and H3K27ac Chip-seq analysis of Mettl3 WT and Mettl3 KO (3 replicates); ATAC-seq analysis of Mettl3 WT and Mettl3 KO for DP thymocytes(3 replicates);RIBO-seq analysis of Mettl3 WT and Mettl3 KO for thymocytes(3 replicates);MERIP-seq analysis of Mettl3 WT and Mettl3 KO for DP thymocytes(3 replicates);5'RACE analysis of Mettl3 WT and Mettl3 KO for Tcra,Tcrb,Tcrd  V(D)J usage, CDR3 length, and repertoire diversity  (3 replicates);

first: Keyi

last: Li

first: Bingtso

last: Hao


title: ATR kinase inhibitors induce mitochondrial fission in CD8+ T cells and impair immune memory in vivo

city: Annandale

first: Thomas

last: Conrads

state: VA

address: 3289 Woodburn Rd, Suite 375

institute: Women’s Health Integrated Research Center

summary: The DNA damage response kinase ATR restrains CDK1 activity during S and G2 phases of the cell cycle, confining CDK1-driven processes to mitosis. ATR kinase inhibitors were originally developed to potentiate chemotherapy-induced DNA damage at stalled replication forks and to disrupt DNA damage-induced cell cycle checkpoints. Recent evidence, however, reveals that these inhibitors also disrupt cell cycle organization in cells that have not sustained any DNA damage. We show that ATR kinase inhibitors potently trigger unscheduled mitochondrial fission, causing loss of mitochondrial mass in actively dividing CD8+ T cells that persists in memory CD8+ T cells. Moreover, ATR inhibition during the peak of CD8+ T cell expansion in a mouse model of LCMV Armstrong infection impairs the formation of immune memory. These findings carry significant clinical implications. ATR kinase inhibitors are currently being evaluated in clinical trials in combination with chemotherapy, radiation, and immune checkpoint inhibitors in patients where anti-tumor immune responses are recognized as a determinant of durable response. Our results identify an unexpected consequence of ATR inhibition that disrupts cellular metabolism with broad implications for both preclinical research and clinical application.

overall_design: RNA-seq profiling of sorted GP33-specific (GP33) CD8+ T cells at 6 weeks post-infection and treated with ATRi on days 5, 6, and 7 post‑infection.

first: Christopher

last: Bakkenist

first: Lawrence P.

last: Kane


title: The GSK3/SHAGGY-Like OsGSK3 Phosphorylates and Inhibits Phase Separation of OsFCA at Ser-43 and Ser-45 to Regulate Brassinosteroid Signaling and Rice Architecture

city: nanjing

first: jiaqi

last: zhang

institute: nanjing agricultural university

summary: Brassinosteroid (BR) signaling plays a critical role in rice (Oryza sativa) grain development. GLYCOGEN SYNTHASE KINASE 3 (OsGSK3), a negative regulator of BR signaling, suppresses the transcriptional activity of OsBZR1 through phosphorylation. In this study, we employed a phosphoproteomic approach to constructed an OsGSK3-mediated regulatory network. Within this network, we identified OsFCA as a positive regulator of BR signaling and grain length, with m-Osfca mutants exhibiting significantly lower sensitivity to brassinolide treatment. Importantly, OsGSK3 interacts with and phosphorylates OsFCA on serine residues S43 and S45, and then forms condensates via liquid-liquid phase separation. Phosphorylated OsFCA promotes the translocation of the OsGSK3-OsFCA complex into the cytoplasm. Within the cytoplasm, OsGSK3 and OsFCA no longer exist in a condensate state. This mechanism provides precise regulation of grain length in rice. Notably, Osfca mutants are late-flowering, with OsFCA promoting heading under long-day conditions by repressing the expression of Ghd7 while activating that of Ehd1, Hd3a, and RFT1, which is potentially modulated by OsGSK3. This study clarifies the BR signaling transduction network by identifying OsFCA as a positive BR signaling component that regulates grain development and heading date, providing theoretical foundations for molecular breeding design in rice.

overall_design: RNA-seq profiling of young panicles of wild-type ZH11, mutant Osfca, and double mutant Osgsk3 Osfca.

first: Jiaqi

last: Zhang

first: Fan

last: Wang

first: Sijia

first: Qian

last: Yu

first: Qimiao

last: Dong

first: Jianbo

first: Xianglei

last: Wei

first: Huaying

last: Du

first: Ye

last: Shen

first: Rong

last: Mu

first: Yanxiao

last: Jia

first: Jinping

last: Cheng

first: Hongsheng

first: Ji

last: Huang

first: Xiuying

last: Gao


title: Single-cell RNA sequencing reveals Reg3g-dependent alteration of alveolar macrophage transcriptomes during LPS-induced acute lung injury

city: hangzhou

first: REN

last: YICHAO

state: zhejiang

address: zhejianghangzhou

institute: zhejiang university

summary: To investigate how Reg3g modulates alveolar macrophage (AM) transcriptional programs during acute lung injury, we performed single-cell RNA sequencing on fluorescence-activated cell sorting (FACS)-purified CD45⁺Ly6G⁻F4/80⁺CD11b/c⁺ lung macrophages from mice treated with PBS, LPS, or LPS + Reg3g for 24 hours. Libraries were generated using the 10x Genomics Chromium GEM-X Single Cell 3′ platform. Following quality control, approximately 29,000 cells were retained. Unsupervised clustering identified 22 distinct cell populations. Reclustering of AMs revealed multiple transcriptional states. LPS exposure shifted AMs toward a pro-inflammatory phenotype, whereas Reg3g treatment attenuated this inflammatory remodeling and restored homeostatic transcriptional signatures. These data identify Reg3g as a modulator of alveolar macrophage functional plasticity during acute lung injury.

overall_design: Single-cell RNA-seq profiling of FACS-sorted, macrophage-enriched lung cells from C57BL/6 mice following 24-hour treatment with PBS (control), LPS (acute lung injury model), or LPS + Reg3g. Lung macrophages were identified as DAPI⁻CD45⁺Ly6G⁻F4/80⁺CD11b/CD11c⁺ cells and purified using a BD FACSAria Fusion flow cytometer. Each biological replicate consisted of pooled cells from three independent mice to ensure sufficient cell yield for downstream 10x Genomics scRNA-seq analysis.

first: Yichao

last: Ren

first: Huifeng

last: Qian

first: Jianguo

last: Xu

first: Qiang

last: Shu


title: Biophysical modeling for accurate T cell specificity prediction of viral and tumor antigens

city: Houston

first: Jeffrey

last: Molldrem

state: United States

address: 7435 Fannin St

department: Hematopoietic Biology & Malignancy

institute: MD Anderson Cancer Center

summary: Accurate predictions of T cell receptor (TCR) specificity remain an important open problem in immunology, with broad implications for vaccine design, optimal immunotherapy, and improved management of autoimmune diseases. However, diversity in peptide antigens and TCR sequences at the level of individual patient repertoires remains a formidable computational challenge. Here, we develop a joint experimental and computational approach for predicting the antigen specificity of clinically-derived TCR sequences. Our model is trained on a combination of experimentally pre-identified and in silico-predicted TCR-pMHC structures using AlphaFold3. We apply our structural model in the clinical setting of hematopoietic stem cell transplant (HSCT) and demonstrate that our model is able to effectively discern the specificity of previously unseen donor and patient-derived TCR sequences against tumor associated and viral antigens. Model performance was further enhanced through the integration of sequence-based clustering and structurally diverse training templates. Our results highlight the predictive capabilities of structurally guided machine learning frameworks, trained on a minority test dataset, for antigen specificity prediction on unseen TCR sequences and their potential impact on a wide range of immunological applications.

overall_design: Single cell tetramer CITE-Seq and TCR-Seq from peripheral blood and bone marrow samples to identify viral and tumor antigens

first: Xizeng

last: Mao

first: Noah

last: Tubo

first: Priya

last: Koppikar

first: Jason

last: George

first: Zahra

last: Ghoreyshi


title: Reverse genetics in humanized mice reveals CARD8-mediated pyroptosis causing pancytopenia in human DPP9 deficiency

city: NEW HAVEN

first: Tianli

last: Xiao

state: Connecticut

address: 1 Gilbert street, TAC S570

department: Immunobiology

institute: Yale University

summary: Loss of function mutation in the human DPP9 gene causes Hatipoglu syndrome leading to severe inflammasomopathy. A key feature of the disease is pancytopenia and patients require bone marrow transplantation, but the mechanism of cell loss is unclear since Dpp9 mutant mice have normal hematopoiesis, suggesting that a distinct mechanism of disease occurs in humans. Here, we present a model of human DPP9 deficiency leveraging reverse genetics in the MISTRG6 humanized mice. We found that CRISPR editing of human CD34+ HSPCs led to very efficient and persistent gene deletion in vivo across human cell lineages. Human DPP9 deletion recapitulated cytopenia in peripheral blood and in the bone marrow, and cell loss was cell-intrinsic. However, DPP9 deletion led to little transcriptional changes suggesting post-transcriptional regulation in human HSPCs. Mechanistically, DPP9 deficiency led to the activation of the CARD8 inflammasome resulting in HSPC pyroptosis, whereas NLRP1 was dispensable for cell death. Thus, our results reveal a unique human mechanism of disease for this inflammasomopathy and offer therapeutic insight for this inflammasomopathy.

overall_design: human CD34+ HSPCs were edited with control or sgRNA against DPP9 to generate control and DPP9KO cells, which were then engrafted into MISTRG6 humanized mice. 4 weeks later, Linage- CD34+ human cells were FACS sorted from the MISTRG6 bone marrow to perform scRNAseq. DPP9KO and control cells are hashtagged separately then pooled.

first: Fengrui

last: Zhang

first: Richard

middle: A

last: Flavell


title: An effector TaCRVP from Tuta absoluta oral secretion impairs H₂O₂-mediated plant defense by targeting tomato SlCAT2

city: fuzhou

first: 竹君

last: 王

address: cangshan street

institute: fujian agriculture and forestry university

summary: The arms race between plants and herbivorous insects involves sophisticated molecular strategies. Tuta absoluta ranks among the most devastating pests of Solanaceous crops. While herbivorous insects commonly secrete effector proteins to modulate plant immunity, how T. absoluta accomplishes this remains largely unknown. This study identifies TaCRVP, a novel salivary effector protein from the T. absoluta. We demonstrate that TaCRVP is delivered into plant cells during feeding and functions as a key factor by targeting the host catalase SlCAT2. We found that TaCRVP promotes SlCAT2 tetramerization, thereby enhancing its enzymatic activity to scavenge H₂O₂. Furthermore, TaCRVP enhances SlCAT2 stability by competitively inhibiting its interaction with the plant E3 ubiquitin ligase SlAdBiL, thereby blocking the SlAdBiL-mediated targeting of SlCAT2 for 26S proteasomal degradation. The consequent increase in both SlCAT2 activity and abundance effectively suppresses H₂O₂ accumulation, a critical defense signal, leading to the downregulation of jasmonic acid-mediated defenses and the biosynthesis of key compounds. Our findings reveal a convergent evolutionary strategy whereby herbivorous insect effector, like pathogen effectors, manipulates host redox homeostasis by targeting catalase. This study advances our understanding of plant-insect interactions and lays the groundwork for developing novel pest management strategies by identifying potential molecular targets.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and OE-TaCRVP groups


title: Green manure enhances reproductive heat resilience by cooling panicles and endosperms at grain filling in a heat-resilient cultivar Nijinokirameki

city: Tsukuba

first: Hirofunmi

last: Fukuda

state: Ibaraki

address: 1-31-1 Kannondai

country: Japan

institute: National Agriculture and Food Research Organization (NARO)

summary: Reproductive-stage heat stress reduces rice yield and grain appearance quality, even in modern heat-resilient cultivars. Although our previous work showed that green manure can lessen ripening heat damage in the widely grown but heat-susceptible Japanese cultivar Koshihikari, it remains unclear whether similar benefits occur in heat-resilient cultivars and how green manure influences source–sink molecular responses during ripening. Here, using the heat-resilient cultivar Nijinokirameki, we tested whether green manure alleviates ripening heat stress by modifying panicle thermal status, nitrogen assimilation, and early endosperm stress responses. Green manure increased flag-leaf size and tiller (panicle) number and enhanced ripening-stage heat resilience by lowering panicle temperature without a meaningful phenological shift. Consistent with reduced heat load at the target organ, endosperm RNA-seq at 5 days after flowering (DAF) revealed weaker induction of heat-responsive programs under green manure, accompanied by increased grain protein content and reduced chalkiness classes (e.g., white milky, and white belly and back kernels). In parallel, shoot nitrogen contents at panicle formation stage were increased and flag-leaf RNA-seq at 5 DAF showed upregulation of ASN1 and NADH-GOGAT2, suggesting contribution to nitrogen assimilation in source organs and nitrogen allocation to grains. Together, these results link a sustainable fertility practice to tissue-scale heat stress mitigation and coordinated source–sink transcriptional responses at ripening that reflects enhanced grain protein accumulation and appearance quality under green manure treatment.

overall_design: RNA-seq on the endosperm at 5 DAF of ‘Nijinokirameki’ grown under chemical fertilizer or hairy vetch–based green manure in 2024.

first: Hirofumi

first: Daisuke

last: Ogawa


title: DICER-Driven Regulation of Lipid Metabolism and Macrophage-Adipocyte Crosstalk in Partial Lipodystrophy

city: Campinas

first: Marcelo

last: Mori

state: São Paulo

address: R. Monteiro Lobato

country: Brazil

institute: UNICAMP

summary: Partial lipodystrophy is characterized by abnormal fat distribution, impaired thermogenesis, systemic inflammation, and diminished DICER expression in adipose tissue. Using adipocyte-specific DICER-deficient models to mimic lipodystrophy, we identified early metabolic and inflammatory alterations that coincide with the onset of partial lipodystrophy. DICER deficiency in adipocytes impaired lipid metabolism, leading to increased release of saturated lipids and triglycerides into the medium while reducing the biosynthesis of anti-inflammatory lipids. These changes promoted a pro-inflammatory environment by reprogramming macrophages to release IL-1beta. Lipidomic analyses revealed reduced levels of docosahexaenoic acid (DHA) and other polyunsaturated fatty acids (PUFAs) in DICER-deficient adipocytes, accompanied by increased expression of CYP450 enzymes linked to lipid degradation and reduced DHA biosynthesis. DHA supplementation mitigated the pro-inflammatory response triggered by conditioned media from DICER-deficient adipocytes.

overall_design: RNA sequencing of isoproterenol-stimulated DICER knockout (DICERKO) and control white adipocytes differentiated from immortalized tamoxifen-inducible Dicer1 flox/Cre-ERT2 preadipocytes. Cells were treated with 4-hydroxytamoxifen (4-OHT) for 48 hours to induce DICER knockout, followed by 6 hours of stimulation with 10 uM isoproterenol to mimic cold/thermogenic activation. Total RNA was extracted using Trizol and libraries prepared with NEBNext Ultra II kit. Sequencing was performed on Illumina NovaSeq 6000 (paired-end 150 bp). Differential expression analysis was conducted using edgeR with TMM normalization (FDR < 0.05).

first: Andréa L.

last: Rocha

first: Rhaissa

last: Godoi

first: Tanes

last: Imamura de Lima

first: Diogo

last: de Moraes

first: Bruna Brasil

last: Brandao

first: Alan

last: Saghatelian

first: Marcelo A.


title: Neuronal oversight of germline small RNAs prevents heat-induced sterility in lab-domesticated Caenorhabditis elegans

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

type: Non-coding RNA profiling by high throughput sequencing

summary: Thermal pollution, whether local or driven by global warming, threatens biodiversity in part through its detrimental effects on reproduction. Non-coding small RNAs (sRNAs) are crucial for maintaining germline developmental robustness under heat stress. Remarkably, we uncovered that neuronal sRNAs regulate germ cells’ thermotolerance, affecting both spermatogenic and oogenic germline in a cell non-autonomous manner. Furthermore, we demonstrate that an oxygen-sensing neural circuit antagonizes germline maintenance, likely reflecting the nematode’s innate association of reduced oxygen levels with food availability and reproductive permissive environments. Finally, we provide evidence that sRNAs buffer the negative consequences of laboratory domestication, which otherwise cause the laboratory strain to lose germline integrity and become sterile at elevated temperatures. Hence, our findings reveal that mere sensory perception, independent of direct environmental change, modulates germline integrity through sRNA pathways, highlighting a novel mechanism by which neural circuits integrate environmental information to safeguard reproductive fitness in fluctuating environments.

overall_design: Total RNA was isolated from day 1 adults using standard phenol-chloroform method using TRIzol or Qiagen RNeasy Kits per manufacture instruction. Libraries for RNA-seq were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® coupled with NEBNext® Poly(A) mRNA Magnetic Isolation Module. The sample quality was accessed on Agilent BioAnalyzer instrument and High Sensitivity RNA ScreenTapes. The resulting cDNA libraries were pooled and paired-end sequencing was performed on the Nextseq 2000 platform. For small RNA-seq, the total RNA was first treated with RNA 5′ Polyphosphatase (epicentre) followed by library preparation using TruSeq Small RNA Library Prep Kit (Illumina). Size selection on E-gel (Invitrogen, Life Technologies) was performed to enrich for 140-160 nt long cDNA. The sample quality was then accessed on BioAnalyzer instrument and High Sensitivity RNA ScreenTapes. The sampled were pooled and sequenced on Illumina Hiseq 2500.

first: Chee Kiang

last: Ewe

first: Hanna

last: Achache

first: Shir

last: Weiss

first: Anna

last: Mogilevskaya

first: Myriam

last: Valenski

first: Guy

last: Teichman

first: Sarit

last: Anava

first: Rachel

last: Posner

first: Olga

last: Antonova

first: Yonatan

last: Tzur

first: Oded

last: Rechavi


title: Breast carcinoma amplified sequence 2 rescues adult hippocampal neurogenesis and cognitive deficits in Alzheimer’s disease via regulating BDNF/TrkB signaling [Bcas2_KD_hippo_snRNA_seq]

city: Beijing

first: Hai

middle: xia

last: Ma

address: Changchun street NO.45

institute: Xuanwu Hospital

summary: Adult hippocampal neurogenesis (AHN) occurs throughout lifespan of humans and rodents and is correlated with memory performance and cognitive plasticity. In Alzheimer’s disease (AD), AHN is impeded, while the molecular basis behind this impairment remains to be elucidated. Here we identified Breast carcinoma amplified sequence 2 (BCAS2), a core component of the CDC5L/Prp19 spliceosome complex, regulating AHN in AD. Using Bcas2 conditional knockout mice, AD mouse model APP/PS1 mice, established mouse primary adult neural stem cells and single cell sequencing, we demonstrate that BCAS2 replacement in adult mouse hippocampus promotes NSC activation and differentiation to neuron, restore AHN and relevant memory deficits through BDNF/TrkB signaling. Our findings corroborate the significance of AHN in AD and reveal the possible therapeutic potential of targeting BCAS2 in neurodegeneration.

overall_design: snRNA-seq profiling of hippocampal tissues of AAV-vehicle or AAV2/9-Syn-cre injected Bcas2F/F mice

first: Haixia

first: Congcong

last: Liu

first: Wenbo

first: Jing

first: Yuli

last: Hou

first: Qiao

last: Song

first: Yaqi

last: Wang

first: Peichang


title: Breast carcinoma amplified sequence 2 rescues adult hippocampal neurogenesis and cognitive deficits in Alzheimer’s disease via regulating BDNF/TrkB signaling

overall_design: RNA-seq profiling of hippocampal tissues of AAV-vehicle or AAV2/9-Syn-cre injected Bcas2F/F mice


title: The Intrinsic Cardiac Nervous System is Essential for Cardiac Function and Survival Across Conditions

city: New Haven

first: Qian

last: Xu

address: 100 College

institute: Yale university

summary: The intrinsic cardiac nervous system (ICNS) is a key node in heart-brain communication and an emerging target for cardiac therapy, yet its physiological importance and functional organization remain poorly understood. Here we show that the ICNS is essential for cardiac performance and survival across conditions. Using integrated genetic and imaging approaches in mice, we identify two molecularly distinct intrinsic cardiac neuron (ICN) subtypes  that differ in extrinsic inputs, projection architectures, and functional roles. Npy⁺ ICNs preferentially receive vagal input and mediate parasympathetic control of heart rate and coronary perfusion, and their ablation leads to fatal cardiac failure. In contrast, Ddah1⁺ ICNs receive sympathetic input and are required to preserve electrical stability and prevent sudden cardiac arrest under extreme physiological  or psychological stress, with their activation providing cardioprotection. Together, these findings establish the ICNS as a critical determinant of cardiac function, providing a framework for precise, cell type–targeted neuromodulatory therapies.

overall_design: Intrinsic cardiac neurons acutely isolated from anterior, posterior, and mixed regions of adult Baf53bL10-GFP mice were purified using Fluorescence-Activated Cell Sorting (FACS) and subjected to single-cell RNA sequencing using the 10x Genomics platform

first: Le

last: Zhang

first: Rui

last: Chang


title: The transcription factor AFF3 is necessary to maintain metabolic quiescence in naïve CD8 T cells and prevent premature immune aging

city: Indianapolis

first: Martin

last: Richer

state: IN

address: R2 Rm 366 950W Walnut St

department: Microbiology and Immunology

institute: Indiana University School of Medicine

summary: Naïve CD8 T cells must be maintained in a quiescent metabolic state in order to respond robustly to infection while avoiding inappropriate activation and causing immunopathology. With age this quiescent state is lost and the CD8 T cell response to infection decreases. The factors regulating metabolic quiescence of CD8 T cells and how this regulation is lost during aging are not completely understood. Herein, we identify the transcription factor AFF3 as a novel regulator of metabolic quiescence in naïve CD8 T cells. While naïve AFF3 deficient CD8 T cells are more metabolically active prior to infection, they have reduced accumulation in response to viral infection and this is correlated with a poor capacity to engage glycolysis. During aging in both murine and human CD8 T cells, AFF3 expression is reducing, correlating with to a loss of quiescent metabolism without the cells entering an activated state. Our data highlights the role of the metabolism in CD8 T cell quiescence and identifies a novel transcription factor that may be a target to reinvigorate CD8 T cell responses during aging.

overall_design: RNA-seq proflie of WT and AFF3 KO CD8 T cells at Day 0, 6 and 24 hours after ex vivo activation, 5 and 8 days after LCMV infection.

first: Molly

middle: E

last: Lumnitzer

first: Stefanie

middle: F

last: Valbon

first: Stephanie

last: Condotta

first: Allison

last: Norlander

first: Sheng

first: Jun

last: Wan


title: The CD49b (ITGA2) Collagen Receptor Excludes CD8+ T Cell Infiltration in Pancreatic Ductal Adenocarcinoma (PDAC)

city: BOSTON

first: Ibrahim

last: Eissa

state: MASSACHUSETTS

address: 55 Fruit St.,

department: Surgical Oncology

institute: Massachusetts general hospital

summary: PDAC is characterized by a dense desmoplastic stroma, contributing to tumor progression and immune evasion. This study investigates the functional role of CD49b in modulating anti-tumor immune responses and collagen architecture in PDAC. CD49b demonstrated a high tumor-specific expression compared to normal pancreatic tissues and peripheral blood mononuclear cells. Loss of CD49b impaired PDAC cell adhesion to collagen, suppressed and delayed the tumor growth, and enhanced CD8+ T cell infiltration. In vivo depletion of CD8 T cells rescued the tumor growth in CD49b knock-out tumors. CD49b-knockout tumors showed increased secretion of CXCL10 chemokine, which drives T cell chemotaxis, while FAK signaling was downregulated. FAK overexpression restored tumor growth. CD49b knockout changed alignment of collagen fibers which was associated with a microenvironment permissive to immune infiltration. Targeting of CD49b with Vatelizumab disrupted PDAC cell adhesion and reduced tumor progression while increasing CD8+ T cells infiltration. CD49b is a key regulator of collagen-mediated immune interactions in PDAC, and these results support its potential as a therapeutic target.

overall_design: Bulk RNA-seq (Illumina HiSeq, PE 2x150) was performed on KPCWT and KPC49bKO pancreatic cancer cell lines grown in vitro (2 biological replicates each) and as subcutaneous tumors in vivo (KPCWT: 3 replicates; KPC49bKO: 2 replicates) to identify transcriptomic differences associated with loss of CD49b (ITGA2).

first: Eissa

last: Ibrahim


title: Expression data from OT-I CD8 T cells that are either naïve or isolated on day 5 following immunization with DC-OVA or with DC-OVA + LCMV

summary: Inflamatory cytokines have a number of effects on the differentiation and function of CD8 T cells. To separate the effects of TCR/co-stimulation from the effects of inflammatory cytokines, we took an immunization approach. We transferred 1 x 10^4 OT-I CD8 T cells to naive C57BL/6 mice on day -1. On day 0 mice were immunized with either 5 x 10^5 OVA peptide loaded, LPS-matured dendritic cells (DC-OVA) injected ip or 5 x 10^5 DC-OVA and 2 x 10^5 pfu of LCMV injected ip. On day 5 following the indicated treatment, OT-I CD8 T cells were enriched via AutoMACS and sorted via flow cytometry prior to RNA extraction from 1 x 10^6 cells using an RNeasy kit (Qiagen). Naive OT-I CD8 T cells were enriched and sorted for RNA extraction to serve as a control. Each group had 3 biological replicates.

overall_design: 3 biological replicates per group. Group included naïve OT-I CD8 T cells and OT-I CD8 T cells isolated on day 5 following immunization with either DC-OVA or DC-OVA-LCMV

first: Mary

middle: K

last: Boes


title: Transcriptomics Analysis of bulk liver RNA from 129/Sv-Cyp2e1tm1Gonz/J (CYP2E1-KO) and 129S1/SvImJ (WT) mice [RNA-Seq]

city: Charleston

first: Jessica

middle: H

last: Hartman

state: South Carolina

address: 70 President St., Drug Discovery Bldg/Rm DD220

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary: To establish the consequences of whole-animal deletion of CYP2E1, we isolated RNA from bulk liver tissue of 12-13-week male and female WT and KO mice. Mice were maintained on a normal chow diet and were euthanized using CO2 and cervical dislocation prior to liver dissection.

overall_design: Samples include WT and KO groups, with males and females in 5-6 biological replicates

first: Kristina

middle: M

last: Stayer

first: Zaria

last: Killingsworth

first: Kubra

last: Calisir

first: Madison

last: Thornton

first: Kylie

last: Driggers

first: Tsultrim

middle: T

last: Mendenhall

first: Alexandra

last: Tomasevich

first: Joe

last: Delaney

first: Ozgur

last: Sahin

first: Kristi

last: Helke

first: Melinda

last: Engevik


title: Early Developmental Neuronal Activity Impacts Oligodendrocyte Differentiation Through AMPA Receptors

city: Aurora

first: Tessa

last: Allen

state: CO

department: Cell and Developmental Biology

institute: University of Colorado, Anschutz

summary: Oligodendrocytes produce myelin, a lipid-rich membrane that wraps neuronal axons in the central nervous system to provide metabolic and trophic support and allow for saltatory conduction. Developmental myelination requires precisely timed and localized neuron-oligodendrocyte communication. In the mature brain, neuronal activity promotes oligodendrocyte precursor cell (OPC) proliferation and differentiation, but how OPCs respond to neuronal activity in early brain development, before the onset of myelination, is less well characterized. Here, we investigate how glutamatergic neuronal activity regulates early developmental oligodendrocyte maturation in the olfactory system, somatosensory cortex, and corpus callosum in mice. We find that decreased neuronal activity increases oligodendrocyte differentiation in early development, both in a sensory deprivation model and when using in vivo chemogenetics. Conversely, enhanced neuronal activity in early development reduces oligodendrocyte differentiation. Additionally, single-cell RNA sequencing revealed transcriptional changes in oligodendrocytes when neuronal activity was reduced, including upregulation of glutamate receptor gene expression and pathways relating to synapse development. Finally, using ex vivo cortical slice culture, we identify AMPAR signaling as a critical regulator of the later steps of oligodendrocyte maturation, but not the initiation of differentiation.

overall_design: NexCre+/- or WT mice were injected with pAAV-hSyn-DIO-hM4D(Gi)-mCherry(Gi-DREADD) at P0. All animals were orally administered clozapine-N-oxide (CNO) twice daily from P2-P8. On the morning of P8, the cortex and corpus callosum were dissected and pooled from three NexCre+/- and two WT pups. Oligodendrocytes were isolated using magnetic bead separation and scRNA sequencing was performed.

first: Graham

last: Peet

first: Luis

last: Gomez Wulschner

first: Won Chan

last: Oh

first: Wendy

last: Macklin


title: Hepatic Microarray Analysis Reveals the Deodorizing Potential of Ecklonia cava in Trimethylamine-Treated ICR Mice

city: Kumjeong-ku

first: Dae Youn

last: Hwang

state: --- Select One ---

address: Samnangjin-ro, 1268-50

institute: Pusan National University

summary:
To pinpoint genes associated with trimethylamine-induced malodor modulation by Ecklonia cava, we conducted microarray hybridization using total RNA extracted from the liver of trimethylamine-treated ICR mice following oral administration of Ecklonia cava.
Identification of genes associated with deodorizing effects through comparison of hepatic gene expression levels in trimethylamine-treated ICR mice following oral administration of Ecklonia cava.

overall_design: Eight-week-old ICR mice were divided into three groups: no treatment (NO), distilled water for 2 weeks plus TMA (VE), and Ecklonia cava for 2 weeks plus TMA.

last: Hwnag

first: Ji Eun

last: Kim


title: miR-146a is a pleiotropic regulator of motor neuron degeneration

city: St. Louis

first: Dylan

last: Galloway

state: MO

address: 4370 Duncan Ave

department: Neurology

institute: Washington University in St. Louis

summary: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease affecting motor neurons. Here, we have profiled motor neuron microRNAs (miRNAs) during motor neuron degeneration in vivo to gain a better understanding of ALS pathophysiology. We demonstrate that one miRNA, miR-146a, is downregulated in diseased motor neurons despite upregulation in bulk tissue. Genetic deletion of miR-146a significantly extended survival in SOD1G93A mice with heterozygous animals demonstrating the largest benefit. A corresponding reduction in spinal cord gliosis but not motor neuron loss was observed. Finally, we observed that a proportion of miR-146a knockout animals develop spontaneous paralysis, motor neuron loss and chronic neuroinflammation with advanced age. Together these findings demonstrate that a single miRNA influences multiple aspects of motor neuron disease and highlights the complex role for neuroinflammation in ALS pathogenesis.

overall_design: Spinal cords were collected from control and miR-146a knockout animals and snap-frozen. RNA was extracted from snap-frozen spinal cords using the Norgen Plus RNA extraction kit with genomic DNA removal. Cell culture RNA was isolated in a similar fashion. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). Fragmented mRNA was reverse transcribed using SuperScript III RT enzyme (Life Technologies) and random hexamers, followed by a second strand reaction. Fragments were dual indexed and sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases. Reads were aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.

first: Hunter

last: Patterson

first: Mariah

last: Hoye

first: Tao

last: Shen

first: Mark

last: Shabsovich

first: Kathleen

last: Schoch

first: Cindy

last: Ly

first: Timothy

last: Miller


title: Transcriptomics Analysis of bulk liver RNA from 129/Sv-Cyp2e1tm1Gonz/J (CYP2E1-KO) and 129S1/SvImJ (WT) mice

first: Jessica

last: Hartman

summary: To establish the consequences of whole-animal deletion of CYP2E1, we isolated RNA from bulk liver tissue of 16-week male and female WT and KO mice. Mice were maintained on a normal chow diet and were euthanized using CO2 and cervical dislocation prior to liver dissection.

overall_design: Samples include WT and KO groups, with males and females in three biological replicates (1,2, and 3)

first: Kristina

last: Stayer

first: Zaria

last: Killingsworth

first: Kubra

last: Calisir

first: Madison

last: Thornton

first: Kylie

last: Driggers

first: Tsultrim

last: Mendenhall

first: Alexandra

last: Tomasevich

first: Joe

last: Delaney

first: Ozgur

last: Sahin

first: Kristi

last: Helke

last: Engevik


title: RNA-seq profiling of L4-stage Caenorhabditis elegans exposed to AO168=O at environmentally relevant concentrations

city: Shanghai

first: Yanbin

last: Zhao

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong university

summary: Tris(2,4-di-tert-butylphenyl) phosphate (AO168=O) is an emerging organophosphate contaminant derived from plastic antioxidants and widely detected in soils. To investigate its chronic biological effects, synchronized Caenorhabditis elegans were exposed to AO168=O in agar-based NGM medium and sampled at the L4 stage for transcriptomic analysis. Bulk RNA-seq was performed on control and AO168=O-treated worms at 400, 2000, and 10000 ng/g, with three biological replicates per group. The dataset was generated to characterize transcriptional responses associated with developmental restriction and IIS/DAF-16-related stress-responsive pathways.

overall_design: Bulk RNA-seq was performed on whole-organism L4-stage C. elegans collected after approximately 46 h exposure to AO168=O at 0, 400, 2000, and 10000 ng/g in NGM agar, with three independent biological replicates per group.

first: Kaihang

last: Deng

first: Haochun

last: Shi

first: Peng

last: Wang

first: Keqi

last: Dong

first: Congcong

first: Yu

last: Li

first: Kun

last: Zhang

first: Dayong

first: Jiayin

last: Dai

first: Fujin

last: Ma


title: Genome-wide CpG methylation in Hydra viridissima by ONT nanopore sequencing

city: Baltimore

first: Alex

last: Bortvin

state: MD

address: 3520 San Martin Dr

department: Embryology

institute: Carnegie Institution

summary: Genome-wide 5-methylcytosine (5mC) profiling at CpG dinucleotides in Hydra viridissima using Oxford Nanopore long-read sequencing with Dorado base modification detection. Five ONT runs (one symbiotic, four aposymbiotic clone 2) were basecalled with Dorado sup,5mCG_5hmCG, aligned to Carnegie v1 genome assembly (JBWVZK000000000), and methylation quantified with modkit. Global CpG methylation is ~9-10%, bimodal (88% unmethylated, 7% fully methylated). Unique genomic regions show higher methylation (12%) than repetitive regions (7.5%).

overall_design: Five ONT sequencing runs from two conditions: one symbiotic run (SD8) and four aposymbiotic clone 2 runs (SD9-SD12, ~120x combined coverage). Methylation detected directly from native DNA without bisulfite conversion.

first: Alexander

last: Gimelbrant


title: Deletion of P311 enhances regeneration in aged skeletal muscle

city: Durham

first: James

last: White

state: nc

address: 300 N Duke Street

institute: Duke University SOM

summary: While aging results in marked decreases in the capacity of skeletal muscle to repair following injury, as well as increases in fibrosis, the pathways and factors that regulate these processes are poorly defined. P311/Nrep (P311) is a highly conserved protein known to promote fibrosis through TGF-beta production in non-muscle tissues. Considering the over-production of TGF-beta in aged muscle, especially in the context of regeneration, we aimed to determine if the loss of P311 would enhance aged muscle regeneration.  To test this hypothesis, we utilized a chemical injury (BaCl2) model to injure the tibialis anterior (TA) muscle in young (4-7 months) and old (24 months) wild-type and global P311 knockout mice (P311-/-).  In wild-type mice, P311 expression increased in response to injury in young muscle and to an even greater extent in aged muscle. P311-deficiency decreased TGF-β production, particularly in old muscle tissue. P311-deficiency also decreased fibrosis in old mice, including improved histology and reductions in fibrotic gene markers.  Regeneration as assessed by fiber regrowth and force generation was increased in old mice with P311-deficiency, and genetic programs that drive skeletal muscle regeneration were enriched in old P311-/- mice relative to old wild-type mice. Single-cell transcriptomic analysis revealed P311 was found to be highly expressed in skeletal muscle fibroblast and fibroadipogenic progenitor (FAP) populations. The loss of P311 in aged muscle FAPs was sufficient to reduce their fibrogenic capacity. These findings establish P311 as a therapeutic target to enhance aged muscle regeneration through reductions in fibrosis and related fibrogenic pathways.

overall_design: Muscle tissue RNA was extracted following muscle injury in mouse tibialis anterior muscles. The mouse groups were young (4-6 months age), old (24 months age) and old P311-/-.

first: Taylor

last: Gregory

first: Lee

last: David

first: Fee

last: Brian

first: Affeldt

last: Bethann

first: Bouini

last: Amina

first: Sprouse

last: Aemilia

first: Abad

last: Paola

first: Rodriguiz

last: Romana

first: Wetsel

last: William

first: Li

last: Yongwu

first: Khodabukus

last: Alastair

first: Bursac

last: Nenad

first: White

last: James


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

first: Xiaoqian

last: Hu

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

institute: Fudan University

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

overall_design: Splenic γδ T cells were isolated from naïve mice and mice infected with Mycobacterium abscessus  at day 7 post infection. Bulk RNA sequencing and targeted TCR repertoire sequencing were performed to characterize transcriptional changes and TCR clonotype diversity associated with infection-induced γδ T-cell responses.


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

overall_design: For mouse single-cell TCR sequencing, the lung of infected and uninfected mice were harvested and converted into single-cell suspension.


title: Distinct HPO axis responses to chronic unpredictable stress in young versus adult female mice

first: Tiannuo

last: Yang

address: Meilong Road 130

institute: East China University of Science and Technology

summary: Environmental and psychosocial stressors constitute major external determinants that accelerate the decline of ovarian function. As a classical paradigm for modeling chronic psychological stress, chronic unpredictable mild stress (CUMS) has been extensively employed to elucidate stress-induced perturbations in reproductive and endocrine homeostasis, as well as their contribution to the development of premature ovarian insufficiency (POI). Nevertheless, CUMS exposure initiated at different ages or administered for varying durations yields markedly heterogeneous physiological responses, and the extent to which these experimental conditions recapitulate the characteristics of long-term stress experienced by women in clinical settings remains insufficiently defined.Female C57BL/6 mice at 2 or 6 months of age were subjected to CUMS for 8 or 12 weeks. Endocrine profiling, hypothalamic–pituitary–ovarian (HPO) axis feedback responses, ovarian histology, and HPO axis transcriptomes were systematically analyzed.

overall_design: RNA-seq profiling of 2-month-old and 6-month-old C57BL/6 mice following 8-week or 12-week chronic unpredictable mild stress (CUMS) exposure, respectively, to characterize the transcriptomic features of the ovary and pituitary gland.

first: Jian

last: Li

first: Zelan


title: Quantum Molecular Resonance attenuates an oxidative stress-induced chimeric transcriptome program in human retinal pigment epithelial cells, preserving RNA structural fidelity

city: Messina

first: Luigi

last: Donato

state: Italy

address: via Consolare Valeria, 1

department: BIOMORF

country: Italy

institute: University of Messina

summary: Chimeric and fusion-like transcripts are increasingly recognized as dynamic, non-genomic responses to acute environmental stress. Elevated reactive oxygen species (ROS) compromise RNA Polymerase II (RNAPII) termination and splicing fidelity, generating a potentially proteotoxic burden of structurally aberrant RNAs. However, robust quantification of these stress-induced chimeras in non-tumor perturbation models remains technically challenging. We profiled the structural fidelity of the transcriptome across a large-scale RNA-seq cohort (n=72 samples) centered on Quantum Molecular Resonance (QMR) therapy and oxidative stress (H2O2 400 µM) in ARPE-19 human retinal pigment epithelial cells, across four treatment groups (Control, QMR Rescue, Secretome, QMR+Secretome Rescue) at 8h, 24h, and 72h post-challenge. Using a stringently uniform bioinformatic pipeline (CLC Genomics Workbench v25.0.3, Detect and Refine Fusion Genes v1.6; hg38/Ensembl v113), chimeric events were stratified into three escalating confidence tiers: Tier 1 (PASS), Tier 2 (PASS + in-frame CDS), and Tier 3 (high-confidence: PASS + in-frame + spanning reads > 0). Ubiquitous background chimeras constitutively expressed across all conditions (e.g., NBPF14--NOTCH2, FBXL5--ENSG00000305512, RAB27A--PIGBOS1) were explicitly identified and partitioned from the dynamic, treatment-responsive fraction. Oxidative stress significantly exacerbated the global Chimeric Burden at 72 hours, with mean aggregate read support surging to 575.5 (SD 55.1) in the Control-OX group. QMR Rescue and QMR+Secretome treatment profoundly attenuated this structural derailment (525.5 ± 139.3 and 449.0 ± 33.9, respectively). A robust 25-event QMR-Rescued Signature was derived, mapping OX-induced chimeras to four discrete biological modules: (I) Lipid/Steroidogenic pathway integrity (CTDNEP1--ENSG00000262526, HSD17B7P2--HSD17B7); (II) Extracellular matrix structural integrity (COL7A1--UCN2, COP1-DT--PAPPA2); (III) Nuclear architecture and mitochondrial coupling (COX17--POPDC2); and (IV) Zinc-finger transcriptional networks (ZNF721--ABCA11P, ZNF782--ZNF510). Top events were orthogonally validated by Arriba and STAR-Fusion (93.3% concordance, 14/15 events), and physically confirmed by junction-spanning RT-qPCR and Sanger sequencing. These findings unveil structural transcriptomic fidelity as a third, unprecedented hierarchical layer of QMR-mediated cellular protection—complementing previously described lncRNA-mediated abundance regulation and miRNA-mediated stability control—and establish a rigorous analytical framework for non-oncological chimeric RNA profiling.

overall_design: Large-scale perturbational RNA-seq study in ARPE-19 (H-RPE) human retinal pigment epithelial cells. Full cohort: n=72 samples across four treatment groups (Control, QMR Rescue [Quantum Molecular Resonance electromagnetic stimulation], Secretome [conditioned medium], QMR+Secretome Rescue), two oxidative stress conditions (OX: H2O2 400 µM; NOX: untreated), three timepoints (8h, 24h, 72h), and three biological replicates (Rep1, Rep2, Rep3). Core differential cohort for chimeric burden analysis: n=32 samples (Rep2 and Rep3, 24h and 72h). Total RNA-seq libraries, paired-end 150 bp, distributed across four sequencing batches (HN00243773, HN00244139, HN00249696, HN00249698). Chimeric transcript detection with CLC Genomics Workbench; orthogonal validation with Arriba v2.4 and STAR-Fusion v1.13; wet-lab validation by RT-qPCR and Sanger sequencing.

first: Alibrandi

last: Simona

first: Mordà

last: Domenico

first: Scimone

last: Concetta

first: Dascola

last: Angela

first: Aliquò

last: Federica

first: Abate

last: Giorgia

first: Pozzato

last: Gianantonio

first: Scalinci

last: Sergio Zaccaria

first: D'Angelo

last: Rosalia

first: Sidoti

last: Antonina

first: Donato

last: Luigi


title: Multiomic profiling of vascular endothelial cell differentiation from human embryonic stem cells [EC diff RNA-Seq]

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: KAIST

summary: To investigate gene regulatory dynamics of normal endothelial cell (EC) differentiation at high resolution, an in vitro differentiation system was employed to derive functional vascular ECs from human embryonic stem cells. Human embryonic stem cells, mesodermal cells, and differentiating cells following VEGF-A stimulation at eight time points (1–48 hours), along with internal controls without VEGF-A treatment (referred to as non-ECs), were collected to profile global RNA expression and H3K27ac signals. In addition, in situ Hi-C data were generated for ECs and non-ECs at 24 hours after VEGF-A treatment to characterize global chromatin contact profiles associated with the EC progenitor state.

overall_design: mRNA-seq profile of hESC-EC differentiation stages

first: Andrew

last: Lee

first: Sunwoo

last: Min

first: Mei-Yu

last: Qiu

first: Gou Young

last: Koh


title: Multiomic profiling of vascular endothelial cell differentiation from human embryonic stem cells [Hi-C]

overall_design: Hi-C 3D chromatin contact profile of endothelial cell progenitors


title: Adipose Derived Reprogrammed iMSCs Exhibit Enhanced Therapeutic Potential for Treating Skin Fibrosis

first: liquan

last: wang

address: Peking Union Medical College Hospital

institute: 北京协和医院

summary: Localized scleroderma (LoS) is a fibrotic skin disorder characterized by excessive collagen deposition, leading to functional and cosmetic impairments. Mesenchymal stromal cells (MSCs) offer therapeutic potential through immunomodulation and tissue repair, but their clinical use is limited by donor variability and replicative senescence. Induced pluripotent stem cell (iPSC)-derived MSCs (iMSCs) present a promising alternative owing to their scalable production and rejuvenated phenotype.

overall_design: We generated adipose-derived iMSCs (AD-iMSCs) from reprogrammed adipose-derived stem cells (ADSCs) and compared their therapeutic efficacy to primary ADSCs in vitro and in vivo. Functional assays including transcriptomic profiling, conditioned media effects on fibrosis markers (α-SMA, TGF-β/Smad), and angiogenesis were conducted. A bleomycin-induced murine LoS model was employed to assess AD-iMSC engraftment, collagen deposition, and microvascularization.

first: Liquan

last: Wang

first: Mingfei

last: Lu


title: Multiomic profiling of vascular endothelial cell differentiation from human embryonic stem cells [ChIP-seq]

overall_design: H3K27ac ChIP-seq profile of hESC-EC differentiation stages


title: IL-6-induced C/EBPα drives follicular regulatory T cell differentiation to regulate humoral immunity in mice

city: Pohang-si

first: Dahun

last: Um

address: 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673

department: Life science

institute: Pohang University of Science and Technology(POSTECH)

summary: Follicular regulatory T (Tfr) cells suppress Tfh-mediated B cell responses to regulate humoral immunity, yet the signaling pathway governing their differentiation remain largely undefined. In this study, we reveal that IL-6-induced C/EBPa is essential for Tfr cell differentiation and function in mice. To investigate whether C/EBPa directly regulates Tfr-related genes and identify endogenous C/EBPa binding targets in Tfr cells, we performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing in Tfr and CXCR5- Treg cells. Collectively, we identify the IL-6-C/EBPa-Bcl6/Cxcr5 axis as a central mechanism to promote Treg-to-Tfr differentiation to control pathogenic humoral immune responses.

overall_design: Tfr (live CD4+Foxp3+CXCR5+PD-1+ICOS+) and CXCR5- Treg (live CD4+Foxp3+CXCR5-) cells were isolated from the spleens of Foxp3-GFP reporter mice by FACS (CytoFLEX SRT sorter) on day 12 after OVA/alum immunization. To obtain sufficient cell numbers for CUT&RUN sequencing, splenocytes from approximately seven mice were pooled to generate a single biological replicate. C/EBPa CUT&RUN sequencing was then performed on the sorted Tfr and CXCR5- Treg populations using an anti-C/EBPa antibody (8178S; Cell Signaling Technology).

first: Haena

first: Hyung-Seok

last: Choi

first: Sin-hyeog

last: Im


title: Single-cell transcriptome reveals keratinocyte subclusters that contribute to altered differentiation and inflammatory responses in atopic dermatitis

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: Atopic dermatitis (AD) is a common chronic inflammatory skin disease with complex, poorly understood pathogenesis due to its mechanistic heterogeneity. To investigate underlying mechanisms, we performed single-cell RNA sequencing (scRNA-seq) on lesional (LAD) and non-lesional (NAD) skin from 42 AD patients and skin from 23 healthy controls (HC). Keratinocytes (KCs) were the most abundant cell type identified. In healthy skin, KC differentiation followed a linear trajectory from basal KCs (BKs) through seven differentiated stages (DK1–DK7) to terminal keratinized cells (KK1 and KK2). In LAD, this process was disrupted, showing a reversed transition from KK2 to KK1, mainly driven by DK7. APOD and LYZ were identified as LAD-specific regulators of this aberrant keratinization, linked to IL-13- and IL-22-driven responses involving endoplasmic reticulum (ER) stress and oxidative damage. Mitochondrial and ER dysfunction were specifically enriched in LAD DK6 cells, suggesting this subcluster as a key pathogenic compartment associated with cytokine activation. Further, cell-cell interaction analysis (validated through Xenium spatial transcriptomics and immunohistochemistry) highlighted TWEAK, derived from IL13+ Th2 and cycling T cells acting on FN14+ basal and differentiated KCs, as a key contributor to AD-associated epidermal responses. These findings reveal how disrupted KC differentiation and specific immune pathways contribute to AD pathogenesis, identifying distinct cellular compartments and inflammatory circuits as potential therapeutic targets.

overall_design: Biopsies were bisected and half of each was processed for scRNA-seq as follows. Samples were incubated in 0.4% dispase (Life Technologies, Thermo Fisher Scientific) in Hank’s Balanced Saline Solution (Gibco, Thermo Fisher Scientific) at 4°C overnight. The epidermis and dermis of the samples were separated and processed. Epidermis was digested in 0.25% Trypsin-EDTA (Gibco) with 10U/mL Dnase I (Thermo Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals), and strained through a 70μM mesh; dermis was minced, digested in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) in plain medium for 1.5 h at 37°C, and strained through a 70 μM mesh. Epidermal and dermal cells were recombined in a 1:3 ratio. The University of Michigan Advanced Genomics Core constructed the single-cell libraries using the 10X Chromium system with chemistry Single cell 5’ and 5’-paired-end sequencing was performed on the Illumina 6000 platform to generate 150bp paired end reads.

first: Johann

last: Gudjonsson

first: Lam

last: Tsoi


title: Multiomic profiling of vascular endothelial cell differentiation from human embryonic stem cells [HUVEC RNA-Seq]

overall_design: mRNA-seq profile of ligand-stiumulated HUVECs to investigate the effects of integrin alphaV inhibition and reduced ITGAV expression


title: Cognitive and Synaptic Impairment Induced by Deficiency of Autism Risk Gene Smarcc2 and its Rescue by Histone Deacetylase Inhibition

city: Buffalo

first: Zhen

last: Yan

state: NY

address: 955 Main St

department: Physiology and Biophysics

institute: University at Buffalo

summary: SMARCC2, which encodes BAF170, a core subunit of chromatin remodeling BAF complex, is one of the top-ranking risk genes for autism spectrum disorder (ASD). However, the mechanisms linking SMARCC2 haploinsufficiency to ASD remain poorly understood. SMARCC2 binds to many other ASD risk genes involved in transcriptional regulation. Knockdown (KD) of Smarcc2 in prefrontal cortex (PFC) of adolescent mice led to impaired working memory, with largely intact social and anxiety-like behaviors. Genome-wide RNA-seq analysis revealed that the downregulated genes by Smarcc2 KD were enriched in synaptic transmission. Significant reduction of GABA and glutamate-related genes was also found in PFC of Smarcc2-deficient mice by qPCR profiling. In parallel, electrophysiological recordings uncovered the significant impairment of GABAergic and glutamatergic synaptic currents in PFC pyramidal neurons by Smarcc2 KD. Smarcc2 binds to HDAC2, and Smarcc2 KD reduced global histone acetylation and H3K9ac enrichment at synaptic gene Slc1a3 (EAAT1), Slc6a1 (GAT1), and Slc32a1 (VGAT) promoters. Treatment of Smarcc2-deficient mice with romidepsin, a class I histone deacetylase (HDAC) inhibitor, restored H3K9ac level, working memory and synaptic gene expression. These findings highlight the critical role of Smarcc2 in regulating cognitive and synaptic function, suggesting that targeting HDAC could alleviate deficits in Smarcc2-associated neurodevelopmental disorders.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

first: Pei

last: Li

first: Siqi

last: Men

first: Prachetas

last: Patel

first: Komal

last: Saleem

first: Ping

last: Zhong

first: Kin

middle: W

last: Tam

first: Jian

last: Feng


title: Spatial proteogenomics reveals S100-RAGE axis as a druggable mediator of trastuzumab deruxtecan resistance in metastatic breast cancer.

city: Houston

first: Stephen

last: Wong

address: 6565 Fannin St

institute: Houston Methodist

summary: Trastuzumab deruxtecan (T-DXd) has substantially improved outcomes for HER2-positive metastatic breast cancer, yet up to 30 percent of patients with high HER2 expression exhibit de novo resistance. Mechanisms underlying this intrinsic resistance, particularly across different metastatic sites, remain poorly understood.

overall_design:
We performed spatial transcriptomic and proteomic profiling using NanoString GeoMx on bone, brain and soft-tissue metastases collected from HER2-positive breast cancer patients prior to T-DXd therapy. Responding and resistant lesions were compared to identify conserved molecular and microenvironmental determinants of treatment outcome.

Spatial proteogenomics workflow:
The GeoMx spatial proteogenomics assay was performed following the manufacturer's two-day protocol. On day one, tissue sections were incubated overnight with a cocktail of DNA-barcoded RNA in-situ hybridization (ISH) probes targeting the whole transcriptome atlas (WTA). On day two, sections underwent overnight incubation with DNA-barcoded antibodies for simultaneous protein detection. Following completion of the assay protocol, slides were imaged using the GeoMx DSP instrument.

Region selection and segmentation:
Regions of interest (ROIs) were manually selected based on tissue morphology and tumor architecture as visualized by the fluorescent morphological markers. Selected ROIs were computationally segmented into distinct areas of interest (AOIs) based on marker expression: tumor compartments were defined as PanCK-positive areas, immune compartments as CD45-positive areas, and nuclear regions by Syto13 staining. This segmentation approach enabled independent molecular profiling of spatially distinct tissue microenvironments within the same histological section.

The library name (included in the correponding sample description field) with '-A-' and '-B-' are both RNA, and the one with '-Y-' is protein.

Please note that the patients information is provided in RNA_METADATA.xlsx, WTAONLY_metadata.xlsx files.  The RowNames column aligns with the name in the corresponding dcc file (e.g.  DSP-1001660022159-B-A02.dcc etc.).

first: Wenjuan

last: Dong

first: Shiruo

first: Bill

last: Chen

first: Matthew

last: Vasquez

first: Wei

last: Yang

first: Xiaoxian

first: Hong

last: Zhao


title: TRIM68 exacerbates sepsis-induced liver injury by inhibiting TIP60-dependent autophagy

city: hefei

first: Yousong

last: Xu

address: huaihe road

department: Department of Critical Care Medicine

institute: The First Affiliated Hospital of Anhui Medical University

summary: Background: Sepsis-induced liver injury (SILI) is a major contributor to mortality in critically ill patients, yet the temporal regulation and functional significance of autophagy in SILI remain poorly defined. Defining the dynamic changes in autophagy and the underlying molecular mechanisms is therefore essential for the development of effective therapies. Methods: We integrated public transcriptomic datasets from human and murine SILI with in vivo and in vitro experimental models to characterize the dynamic regulation of autophagy and identify key regulatory factors. Genetic gain- and loss-of-function approaches targeting tripartite motif containing 68 (TRIM68) were combined with cecal ligation and puncture (CLP) mouse models and LPS-stimulated hepatocytes. These methods were coupled with molecular, biochemical, and imaging analyses, including qRT‒PCR, Western blotting, immunofluorescence, transmission electron microscopy, ELISA, CUT-Tag, coimmunoprecipitation, and ubiquitination assays, to elucidate the underlying mechanisms. Results: Autophagy was dynamically regulated during SILI, with early activation followed by a decrease that coincided with aggravated liver injury and inflammation. Enhancing autophagy significantly alleviated hepatic injury and inflammatory responses. Integrative analyses identified TRIM68 as a conserved autophagy-associated regulator across human and murine SILI. Loss of TRIM68 expression enhanced autophagic flux and reduced proinflammatory cytokine production. Mechanistically, TRIM68 loss stabilized TIP60 by reducing its ubiquitination and proteasomal degradation, thereby enhancing the histone H4 acetylation–dependent transcription of autophagy-related genes. Conclusion: Our findings identify TRIM68 as a key epigenetic regulator of autophagy in sepsis-induced liver injury, mediating TIP60-dependent histone H4 acetylation to drive autophagy gene transcription, and support the therapeutic potential of targeting the TRIM68–TIP60 axis.

overall_design: H4ac CUT&Tag profiling of wildtype HepG2 cells and TRIM68 knockdown derivatives (shTRIM68)


title: Natural Flavonoids Genistein and Baicalein as Well-Tolerated Radiosensitizers to Enhance the Efficacy of 177Lu-PSMA617 in Prostate Cancer: In Vitro and In Vivo Studies

city: Nanjing

first: Congjie

last: He

state: Jiangsu

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine

summary: The efficacy of prostate-specific membrane antigen (PSMA)-targeted radioligand therapy in metastatic castration-resistant prostate cancer (mCRPC) is limited by tumor heterogeneity and intrinsic radioresistance. This study investigates two natural flavonoids, genistein and baicalein, as potential radiosensitizers to improve the therapeutic effectiveness of 177Lu-PSMA617 therapy. In vitro, combined treatment with low-toxicity concentrations (5-15 μM, based on cellular IC50 of either flavonoid dose-dependently enhanced the cytotoxicity of 177Lu-PSMA617 against the human prostate cancer cell line LNCaP, reducing its IC50 to 14.2%-45.1% of that with monotherapy. All combination regimens demonstrated synergistic interaction, with combination indices (CI) below 0.82. Mechanistically, the combinations (particularly at 10 μM) induced a pro oxidant shift (increasing ROS by 78%-144%), amplified DNA damage (γ-H2AX increased by 85-115%), and promoted apoptosis (Caspase-3 activity increased by 325-389%) while suppressing pro-survival p-AKT. Transcriptomic profiling further revealed that both flavonoids induced a pro apoptotic gene signature and significantly modulated multiple cancer-related pathways, particularly inhibiting key DNA double-strand break repair pathways such as non-homologous end-joining (NHEJ) . In vivo, combination therapies  profoundly inhibited tumor growth (50.2-78.1% reduction vs. monotherapy) and extended survival, with no overt systemic toxicity observed in this preliminary assessment. This work establishes genistein and baicalein as effective, multi-targeted radiosensitizers that enhance 177Lu-PSMA617 efficacy by cooperatively amplifying DNA damage, inhibiting repair mechanisms, and activating the apoptotic cascade. Their natural origin and established safety profile, coupled with their natural origin and established safety profile, underscore their translational potential. Thus, genistein and baicalein represent promising novel adjuvants for prostate cancer radioligand therapy.

overall_design: Factorial design: Cell line (LNCaP, PC-3) vs Drug (Genistein, Baicalein) vs Concentration (10uM, 20uM)


title: Epigenomic Profiling of Multiple Myeloma using two different Low-Input platforms with overlapping results.

city: Rome

first: Giacomo

last: Corleone

address: via chianesi 43

institute: IRCCS Regina Elena National Cancer Institute

summary: This study compares two CUT&Tag workflows for profiling histone modifications in multiple myeloma using low cell numbers. Both methods produced high-quality, reproducible data with similar performance, demonstrating their suitability for epigenomic analysis in limited patient samples.

overall_design: Multiple Myeloma Primary cells isolated from patientes were subjected to cut and tag H3K27 analysys with two different platform demonstrating that both protocols yield high-quality and overlapping genomic profiles

first: Maria Chiara

last: Cappelletto

first: Tiziana

last: Bruno

first: Francesca

last: De Nicola

first: Maurizio

last: Fanciulli


title: The influence of IL1B overexpression on the transcriptional level of PTC cell lines.

city: Fuzhou

first: tenghong

last: liu

address: Jiaotong Street

institute: Fujian Medical University

summary: To explore the effect of IL1B on the transcriptional level of PTC cells, we constructed a PTC cell line with overexpression of the IL1B gene through lentiviral stabilization technology. Subsequently, transcriptome sequencing (RNA-seq) analysis was performed on the cells of the control group and the IL1B overexpression group.

overall_design: Transcriptome sequencing (RNA-seq) analysis was performed on five control group cell lines and five IL1B overexpression group cell lines.

first: Tenghong

last: Liu


title: Seasonal changes in the transcriptome of bat eyes reveal adaptive changes to exploit summer twilight

city: College Station

first: Michael

last: Smotherman

state: Texas

address: 3258 TAMU

department: Biology

institute: Texas A&M University

summary: Sensory systems of many organisms display periodic adjustments to accommodate cyclical changes in the local environmental conditions. Seasonal fluctuations in visual perception are documented in many species, including humans, but the mechanisms and ecological significance of these adaptations often remain obscure. Depsite limited knowledge of bat visual ecology relative to hearing, the diversity of bat species makes them useful models for studying sensory adaptation mechanisms. Here we analyze daily and seasonal changes in gene expression in the eyes of a temperate echolocating bat, the Mexican free-tailed bat (Tadarida brasiliensis). A total of 44 wild-caught bats were sampled from the same location across all four seasons, with whole eyes sequenced for total mRNA expression. Expression patterns were analyzed using differential expression analysis and clustering techniques for identifying correlation networks and evidence of cyclical enrichment. Additionally, a target gene list representing key physiological processes was applies to assess which biological pathways displayed the most robust seasonal or daily changes. 17.8% of genes showed significant differential expression based on season, compared to 11.5% of genes for daily expression. Several gene networks related to the circadian clock, phototransduction, and metabolic function displayed significant rhythmic seasonal effects. Quantum catch modeling indicates higher photon capture potential in summer based on weighted opsin expression, consistent with an adaptive response to lower twilight irradiance. Seasonal remodeling of the ocular transcriptome is consistent with enhanced phototransduction in summer, suggesting vision may play a greater role during this period.

overall_design: RNAseq of eye samples from T. brasilieneis taken at different time points: four seasons (fall, winter, spring, summer) and four daily time points (10 PM, 4 AM, 10 AM, 4 PM). Biological replicates vary by time point

first: Cara

last: Webster


title: A regulatory TRIF/IL-1R1 axis controls T-dependent IgA production in the intestines

city: New Brunswick

first: Gaetan

last: Barbet

state: NJ

address: 89 French Street

department: Department of Pediatrics

institute: Rutgers University

summary: This study investigates the innate signals that constrain intestinal IgA induction. Using single-cell RNA sequencing (scRNA-seq), we profiled the Peyer's patch immune landscape in wild-type, Trif-/-, and Il1r1-/- mice. Our analysis reveals that TRIF and IL-1R1 act as molecular "brakes" on mucosal humoral immunity. The dataset provides a high-resolution map of how TRIF and IL-1R1 modulate the B cell microenvironment and intrinsic differentiation pathways to limit mucosal IgA responses.

overall_design: Live cells (ZombieNIR-negative cells) from excised Peyer's patches of wild-type, Trif-/-, and Il1r1-/- mice (4 mice per group; 16 mice total) were sorted by Cytek Aurora CS. One million cells from each sample were fixed with the ScaleBio Sample Fixation Kit and used to prepare one multiplexed ScaleBio Single Cell RNA Sequencing Kit v1.1 library. The same library was sequenced twice on an Illumina NovaSeq X Plus (Run1 and Run2, where Run2 is additional sequencing of the same library).

first: Sung

last: Chi-Chang

first: Chiou

last: Shin-Heng

first: Yang

last: Qi

first: Barbet

last: Gaetan


title: Single-cell Transcriptomic Profiling of Mouse Alcam-Positive Sca-1-Negative Bone Lining Cells

city: Fukuoka

first: Hisayuki

last: Yao

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

summary: Single-cell RNA-seq of FACS-sorted Alcam⁺Sca-1⁻ bone lining cells (BLCs) was performed using the 10x Genomics Chromium system.

overall_design: Alcam⁺Sca-1⁻ BLCs were isolated using a FACS Aria Fusion cell sorter (BD Biosciences). Single-cell RNA-seq libraries were generated with the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics, Pleasanton) following the manufacturer’s protocol. Approximately 10,000 cells were loaded per channel of a Chromium Next GEM Chip G, targeting a recovery of 7,000–8,000 single cells per sample. Sequencing was conducted on the Illumina NovaSeq 6000 platform to produce paired-end reads (28 bp for read 1 and 91 bp for read 2), generating approximately 20,000 paired-end reads per sample. Dual-index barcoding with 10-bp i7 and i5 indices was employed for accurate sample demultiplexing.

first: Ryosuke

last: Yuta

first: Kentaro

last: Hosokawa

first: Fumio

last: Arai


title: Transcriptomics of S3 segment in mice: response to type 1 diabetes, SGLT1/2 inhibition, or GLP1 receptor agonism response to type 1 diabetes, SGLT1/2 inhibition or GLP1 receptor agonism

city: San Diego

first: Young Chul

last: Kim

address: 3350 La Jolla Village Dr

institute: University of California-San Diego

summary: Inhibitors of SGLT2 (SGLT2i) and diabetes enhance glucose delivery and reabsorption in late proximal tubule S3 segments. However, the molecular consequences remain poorly understood. Here we determined transcriptomic changes in S3 segments of male adult DBA wildtype (WT) and littermate diabetic Akita mice ± Sglt1 knockout (Sglt1-KO) given vehicle or SGLT2i dapagliflozin for 2 weeks, and in Akita mice receiving GLP1R agonist (GLP1RA) semaglutide. RNA sequencing was performed in S3 segments isolated by immunostaining-guided laser-capture-microdissection in deep cortex/outer medulla. Among 19,068 detected annotated genes, 838 genes were differentially expressed by SGLT2i in WT (DEGs; p<0.05) and 1,410 genes in Akita vs. WT. ~34% of SGLT2i-sensitive genes changed in same direction in Akita. Both maneuvers upregulated pathways of cellular proliferation (confirmed by phospho-Ser10 Histone H3 staining) and cellular response to stress, while downregulating pathways of immune/inflammatory response, cytokine production/receptor signaling, and cell adhesion/migration. Both maneuvers also induced unique responses. Unique pathway responses to SGLT2i in WT included increase in DNA dealkylation/demethylation and lysosomal acidification, and reduced valine biosynthesis. Differences in Sglt1-dependency of responses to Akita versus SGLT2i in WT suggested different initiating mechanisms. In Akita mice, inhibition of SGLT2, Sglt1-KO and GLP1R agonism restored 12, 18 and 25% of DEGs, respectively. Akita downregulated whole kidney SGLT1 membrane expression, potentially to limit glucose-induced stress. GLP1RA reduced/restored cellular stress response and proliferation in Akita in S3 segments, associated with enhanced/restored kidney membrane expression of SGLT1. Finally, Akita-sensitive genes unresponsive to any of the 3 maneuvers were identified that may indicate new therapeutic avenues.

overall_design: Fourteen week old non-diabetic DBA male mice (Ins2+/+) with Sgl1+/+ or Sglt1-/- were treated with vehicle or dapagliflozin (10mg/kg diet) for 2 weeks, and littermate diabetic DBA male mice (Ins2 Akita/+) with Sglt1+/+ or Sglt1-/- were treated with vehicle, dapagliflozin (10mg/kg idet) or semaglutide (3nmol/kg body weight per day), subcutaneous injection) for 2 weeks. SGLT2-negative LTL-positive late proximal tubules were isolated by laser capture microdissection for RNA sequencing.

first: Chen

last: Meng

first: Sadhana

last: Kanoo

first: Scott

last: Thomson

first: Anil

last: Karihaloo

first: Volker

last: Vallon


title: Murine Dorsal Root Ganglion Single Cell Sequencing of Sham Intrafemoral Inoculation

city: Winston Salem

first: Yusuke

last: Shiozawa

address: 1 Medical Center Blvd

institute: Wake Forest University School of Medicine

summary: We have employed a single cell sequencing approach using 10x Genomics scRNAseq to study murine dorsal root ganglion (DRG) sensory neurons contribution to cancer-induced bone pain. DRG are the hub of sensory neurons and pain signaling. These findings establish a  non-tumor-bearing reference dataset.

overall_design: Mice were intrafemorally inoculated with saline, and after 15 days post-inoculation the lumbar 2-5 ipsilateral DRGs were collected. DRGs were then subjected to enzymatic digestion and density centrifugation to form a single cell suspension. The cells were then processed on a 10X Genomics Chromium controller to generate a cDNA library, which was sequenced on an Illumina NextSeq 500.

first: Shiozawa

last: Yusuke

first: Miller

last: Lance


title: Restoring age-related loss of the lactate receptor GPR81 improves mitochondrial function and mitigates skeletal muscle aging

first: Stelios

middle: T.

last: Andreadis

address: 908 Furnas Hall

department: Chemical and Biological Engineering

summary: Skeletal muscle aging is associated with increased lipid accumulation, or myosteatosis, leading to lipotoxicity and loss of muscle function. Here, we report that loss of the novel lactate receptor GPR81 in aged muscle is associated with impaired lipid oxidation and enhanced lipid accumulation. Knockdown of GPR81 in young healthy myoblasts led to an increase in senescence hallmarks such as DNA damage, accumulation of reactive oxygen species (ROS), mitochondrial dysfunction and impaired autophagy. Conversely, treatment of senescent myoblasts with GPR81 agonists enhanced lipid oxidation in senescent myoblasts leading to a decrease in lipid accumulation, ultimately resulting in decreased DNA damage, ROS accumulation and enhanced ability to form myotubes. In agreement with our in vitro findings, we observed significant improvement in muscle regeneration and overall health of aged or progeric mice that were treated with GPR81 agonists. Our findings suggest that GPR81 plays a key role in skeletal muscle lipid metabolism, and agonists of GPR81 might play a promising role in reversing age-associated lipid accumulation and loss of muscle function.

overall_design: Bulk RNA-seq profiling of Young wildtype mice, LAKI control mice and LAKI mice treated with CHBA.

first: Sai Harsha

last: Bhamidipati

first: Pihu

last: Mehrotra

first: Stylianos