title: TET3 Promotes Tumor Immune Evasion Through Negative Regulation of Type I Interferon Signaling [RNA-Seq]

overall_design: Examination of the impact of TET3 depletion on the transcriptome in Parental/Control and TET3 KO/KD MCF7/B16F10 cells using mRNA-seq or RiboZero RNA-seq.


title: Effect of knock-down SRSF2

status: Public on Jun 26 2026

city: NANJING

first: XINYU

last: YAN

address: 文苑路1号

country: China

institute: NANJING NORMAL UNIVERSITY

type: Expression profiling by high throughput sequencing

summary: To inestigate the change of alternative splicing events

overall_design: Comparative RNA splicing events analysis of RNA-seq data for MCF-7 cells(shSRSF2 v.s. Control)

first: Xinyu

last: Yan


title: METTL3-dependent m6A methylation in atherogenic endothelial inflammation [RNA]

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

summary: Atherosclerosis is initiated by endothelial inflammation. Using RNA-seq and eCLIP, we identified METTL3 as a mechanosensitive m6A writer that upregulates NLRP1 and downregulates KLF4 through YTHDF readers. Knockdown of METTL3 abrogated these changes and protected against flow-induced atherogenesis in vitro and in vivo.

overall_design: RNA-seq was performed on HUVECs exposed to oscillatory shear (OS) with or without METTL3 knockdown to identify m6A-dependent transcriptomic changes.

first: Shu

last: Chien

first: Chian-Shiu

first: Ping-Hsing


title: METTL3-dependent m6A methylation in atherogenic endothelial inflammation [eCLIP]

overall_design: eCLIP-seq was performed on HUVECs exposed to oscillatory shear (OS) with or without METTL3 knockdown to identify m6A-dependent transcriptomic changes.


title: Single-cell multi-omics reveal coordinated neoplastic and immune remodeling following KRAS inhibition

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

state: California

address: 1120 VETERANS BLVD.

country: USA

institute: AMGEN, INC.

summary: Allele-specific KRAS inhibitors are approved for KRAS-mutant cancers, and efforts to maximize patient responses are ongoing. Previous work suggests that KRAS inhibition can modulate anti-tumor immunity, but the critical cellular players and molecular pathways have not been clearly defined. Here we perform multi-omic profiling using single-cell RNA-seq, spatial transcriptomics, and flow cytometry to profile intratumoral changes after KRASG12C inhibition (KRAS(G12C)i), MEK inhibition (MEKi), and combination therapy with KRAS(G12C)i and PD-1 blockade. Treatment with KRAS(G12C)i but not MEKi drove neoplastic adaptation toward increased oxidative stress, integrin signaling, and upregulation of extracellular matrix remodeling factors. These changes were accompanied by enhanced intercellular communication with classical dendritic cells, leading to robust cDC maturation and CD8 effector T-cell activation. Combination treatment with anti-PD-1 further expands T-cell responses, as well as macrophage states associated with increased cancer survival. Our findings connect KRAS inhibition with the coordination of subsequent immune activation and reveal molecular mechanisms that promote and sustain tumor control.

overall_design: Mice were implanted subcutaneously with CT26-KRAS-G12C tumors, and tumors were allowed to develop for 14 days. Single-cell transcriptomic and TCR sequencing of CD45+ sorted cells that were first isolated from treated CT26 tumors, 5 days before the start of treatment (day 14) and 4 days after treatment (day 24).

first: Daniel

middle: R

last: Lu

middle: M

first: Shining

last: Ma

first: Chi-Ming

last: Li


title: Single-cell multi-omics reveal coordinated neoplastic and immune remodeling following KRAS inhibition [Spatial Transcriptomics]

summary: Allele-specific KRAS inhibitors are approved for KRAS-mutant cancers, and efforts to maximize patient responses are ongoing. Previous work suggests that KRAS inhibition can modulate anti-tumor immunity, but the critical cellular players and molecular pathways have not been clearly defined. Here we perform multi-omic profiling using single-cell RNA-seq, spatial transcriptomics, and flow cytometry to profile intratumoral changes after KRASG12C inhibition (KRAS(G12C)i), MEK inhibition (MEKi), and combination therapy with KRAS(G12C)i and PD-1 blockade. Treatment with KRAS(G12C)i but not MEKi drove neoplastic adaptation toward increased oxidative stress, integrin signaling, and upregulation of extracellular matrix remodeling factors. These changes were accompanied by changes in spatial intercellular communication patterns, leading to robust cDC maturation and CD8 effector T-cell activation. Combination treatment with anti-PD-1 further expands T-cell responses, as well as macrophage states associated with increased cancer survival. Our findings connect KRAS inhibition with the coordination of subsequent immune activation and reveal molecular mechanisms that promote and sustain tumor control.

overall_design: Visium-v1 (poly-A-based) profiling of sections from treated CT26 tumors. Tumors were isolated 4 days after treatment and embedded in OCT. 10 micron sections were generated for Visium spatial profiling.


title: Single-cell multi-omics reveal coordinated neoplastic and immune remodeling following KRAS inhibition [scRNA-Seq 1]

overall_design: CT26 KRAS-G12C cells were implanted into Balb/C mice and treated with KRAS or MEK inhibitor for 4 days. Tumors were then harvested and dissociated for single-cell RNA-seq of all cells in the tumors.


title: TRIM37 interacts with TRIM28 to maintain primordial germ cell identity during migration [bulkRNA-seq, scRNA-seq]

city: Shanghai

first: Qing

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

summary: During embryo development, germ cells segregate from soma to ensure the genome transmission of a species. Although the repression of somatic programs in germline specification is well studied, the molecular mechanisms that protect primordial germ cell (PGC) fate thereafter remain poorly understood. Here, we show that the ubiquitin ligase TRIM37 suppresses the somatic programs during PGC migration. Trim37 mutant embryos exhibit PGC developmental defects from embryonic day 9.5 (E9.5) and depletion at E12.5, with  Trim37-deficient PGCs transdifferentiating into somatic cells. Mechanistically, TRIM37 interacts with TRIM28 through its MATH domain to repress somatic gene expression in the nucleus. Forcing TRIM37 out of the nucleus causes PGC depletion. Additionally, the K27-linked polyubiquitination of TRIM28 catalyzed by TRIM37 augments their interaction and promotes the nucleus location of TRIM37. The impairment of TRIM37 ubiquitin ligase activity and mutations in TRIM28 ubiquitination sites both hinder PGC development. Furthermore, TRIM37 deficiency disrupts the DNA binding of TRIM28, which is mostly guided by AP2γ, leading to enhanced chromatin accessibility and increased H3K27ac levels, resulting in the upregulation of somatic genes. Our results shed light on the TRIM37-mediated epigenetic suppression mechanisms controlling germ cell fate maintenance and are relevant for the infertility of Mulibrey nanism patients.

overall_design: To analyze the effect of Trim37 inactivation on PGCs, we performed scRNA-seq and bulk RNA-seq on control and Trim37ko PGCs. For scRNA-seq, the E8.5 Nanog-EGFP transgenic embryos and E9.5 Oct4-EGFP transgenic embryos were dissected from recipient mice and digested with 0.25% Trypsin-EDTA (Thermo Fisher, Cat#25200072) at 37 °C. After digestion, the embryos were gently pipetted and resuspended in the H-CZB medium. E8.5 Trim37ko embryos were generated by injecting hA3A-eBE3-Y130F mRNA and Trim37-sgRNA-stop into the cytoplasm of zygotes from Nanog-EGFP males mated to BDF1 females. E9.5 Trim37ko embryos were obtained by mating Oct4-EGFP/Trim37ko heterozygous males with Trim37ko heterozygous females. The single PGC from wild-type and Trim37ko embryos were picked by a Piezo-drill micromanipulator and transferred into a 200 µL tube containing 3.5 µL lysis buffer. The lysate was used for cDNA amplification with the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat#N712). For bulk RNA-seq, E9.25 control and Trim37ko embryos carrying Nanog-EGFP transgene were dissected from recipient mice and digested with 0.25% Trypsin-EDTA (Thermo Fisher Scientific, Cat#25200072) at 37 °C. Following digestion, Nanog-EGFP positive PGCs were isolated from the suspension via FACS. Control embryos were produced by injecting hA3A-eBE3-Y130F mRNA into the cytoplasm of zygotes from Nanog-EGFP males mated with BDF1 females. Trim37ko embryos were generated by co-injecting hA3A-eBE3-Y130F mRNA and Trim37-sgRNA-stop. Approximately 80 PGCs per sample were transferred into a 200 µL tube containing 3.5 µL of lysis buffer. The lysate was then subjected to cDNA amplification using the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat#N712).

first: Li

last: Guo

first: Jinsong


title: TRIM37 interacts with TRIM28 to maintain primordial germ cell identity during migration

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To investigate the impact of Trim37 inactivation on the modification of H3K27ac and H3K9me3, as well as the binding of TRIM28 and AP2γ in PGCs, we conducted CUT&Tag and CUT&RUN analyses on E9.25 control and Trim37 knockout PGCs.


title: TRIM37 interacts with TRIM28 to maintain primordial germ cell identity during migration [ATAC-seq]

overall_design: To analyze the effect of Trim37 inactivation on chromatin accessibility of PGCs, we performed ATAC-seq on control and Trim37ko PGCs.


title: Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [CUT&Run]

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Medulloblastoma (MB) is a biologically heterogeneous childhood cerebellar tumor harboring frequent chromatin-modifying gene alterations. How these alterations promote transcriptional programs governing malignancy remains poorly defined. To address this knowledge gap, we evaluated chromatin states across MB subgroups by multi-modal integration of histone modifications with mutational, DNA methylation, and transcriptomic profiles. A bivalent/poised enhancer (EnhBiv) state was specifically enriched at the promoters of neurodevelopmental genes in Groups 3 and 4-MB. Integrative bioinformatics coupled with chromatin occupancy studies identified aberrant KDM2B binding at EnhBiv-enriched promoters. CRISPR-mediated knockout or acute protein degradation of KDM2B selectively suppressed the growth of MB models in vitro and in vivo. Mechanistically, KDM2B promotes sequential recruitment of Polycomb repressive complexes (PRC1/PRC2) and EnhBiv chromatin, thereby repressing neuronal differentiation programs. Collectively, we provide foundational insights into an epigenetic basis of MB, nominating KDM2B as a selective dependency in high-risk subgroups that warrants consideration as a candidate therapeutic target.

overall_design: To investigate the dynamic changes of chromatin modifier recruitment and histone modifications following KDM2B perturbation, we performed CUT&RUN in D283 after KDM2B degradation (dTAG vs DMSO) or CRISPR KO (KO vs Ctrl) for KDM2B, HA (detect KDM2B-HA), BCOR, EZH2, H2AK119ub, H3K4me3, H3K4me1, H3K27me3, and H3K36me2 (TH). To understand subgroup difference, we profiled these marks in MB PDX models featuring SHH MB (Med113FH and MED1712FH), Group 3 MB (Rcmb20, Rcmb28, and Med2312FH), and Group 4 MB (DMB006, Med1512FH, and Rcmb37).

first: Ran

last: Tao

middle: A


title: The effects of the loss of EWSR1 on alternative splicing

city: Boston

first: Huy

last: Nguyen

state: MA

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

summary: EWSR1 belongs to the FET family of proteins and has the ability to bind RNA. However, the role of EWSR1 in alternative RNA splicing remains unclear. Here, we performed an RNA sequencing study in the EWSR1 knockout cells to identify genome-wide changes in alternative splicing following loss of EWSR1.

overall_design: To investigate the genome-wide effects of EWSR1 loss, we generated EWSR1 knockout cells in the RPE TP53 -/- background and performed RNA sequencing with RPE p53-/- parent and EWSR1 knockout cells.

first: Shuhei

last: Asada

first: Jithma

last: P Abeykoon

first: Guangli

last: Zhu

first: Divya

last: R Iyer

first: Alan

middle: D

last: D’Andrea


title: Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [RNA-Seq]

overall_design: To investigate the mechanisms underlying KDM2B dependency in Group 3 D283 cells or Group 4 DMB006 cells, we examined transcriptomic changes in D283 by RNA-seq following KDM2B degradation with or without rescue by wild-type KDM2B or KDM2B mutants (CXXC deletion, JmjC deletion, JmjC mutation). We also profiled transcriptomic changes in D283 and DMB006 cells following KDM2B CRISPR KO.


title: Specific biological processes associated with T2D-induced left ventricular dysfunction in patients with aortic stenosis pressure overload

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

summary:
Background: Type 2 diabetes (T2D) is increasingly prevalent and increases the risk of developing heart failure. T2D is frequently associated with left ventricular (LV) pressure overload, such as encountered in hypertension and aortic stenosis (AS), and few studies suggested an aggravating effect of T2D. We aimed to explore if the deleterious impact of T2D on LV remodeling and function in patients with AS is associated with specific biological processes.
Methods: We combined a profound clinical and echocardiography phenotype of patients with severe AS+/-T2D (without overt heart disease) referred for a valve replacement with histolog-ical and transcriptomic analyses of an intra-operative myocardial LV biopsy and ELISA measurement of circulating levels of different biomarkers.
Results: 84 patients, including 34 with T2D, were included with median age (67 YO), and 38% were females. Hypertension (p<0.01) and dyslipidemia (p<0.01) coexisted more frequently in T2D patients. T2D patients had greater BMI (p<0.01) and BSA (p=0.034). T2D patients had similar AS severity but displayed worse cardiac remodeling, systolic and diastolic function than non-diabetics. At the tissue level, T2D was associated with worse cardiomyocyte hypertrophy and apoptosis with a structural reticulum-mitochondria Ca2+ uncoupling. Regarding metabolic biomarkers, leptin and FABP3 were significantly increased in T2D patients compared to non-diabetics, correlating respectively with diastolic dysfunction and hypertrophy. Endothelin-1 was also significantly increased in the T2D group and associated with hypertrophy and systolic dysfunction. Importantly, in agreement with the myocardial analyses, inflammatory and fibrotic circulating markers were not different between groups. Regarding the transcriptomic analysis, the upregulated pathways in T2D gathered regulation of inflammation, extracellular matrix organization, endothelial function/angiogenesis, and adaptation to cardiac hypertrophy and remained T2D-specific despite comorbidity adjustment. Gene sets downregulated in T2D patients were related to mitochondrial respiratory chain organization/function, mitochondrial organization, amino acid metabolism, and regulation of muscle contraction. The mitochondrial respiratory chain process and mitochondrial organization were independently associated with T2D, while the other downregulated pathways were no longer significantly associated with T2D after adjusting for covariates.
Conclusion: Increased adverse LV remodeling and dysfunction in T2D with severe AS is associated with specific processes which may lead to potential therapeutic targets.

overall_design: During the aortic valve replacement surgery, a perioperative Left Ventricular myocardial biopsy was collected and snap frozen.

first: Helene

last: Thibault

first: Melanie

last: Paillard

first: Maelle

last: Cherpaz

first: Emmanuelle

last: Meugnier


title: Spatial Transcriptomics of MHC Expression in Mauritian Cynomolgus Macaque Tissues

status: Public on Jun 25 2026

city: Madison

first: David

middle: H

last: O'Connor

state: WI

address: 585 Science Drive

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

summary: A spatial transcriptomics method was developed with the 10X Genomics Visium HD platform and a custom probe panel to study expression of Major Histocompatibility Complex (MHC) genes in tissues from Mauritian-origin cynomolgus macaques. Previous scRNA sequencing studies with these macaque demonstrated a wide range of allele-specific MHC transcript levels in multiple peripheral blood mononuclear cell subsets. The restricted genetic diversity of the Mauritian macaque population made it possible to design a manageable number of custom MHC probes for this pilot study . Tissues examined included kidney, liver, lung and heart that of particular interest for transplant research. The Visium Human Transcriptome Kit v2 performed well with at least 40 different kidney cell types identified based on cell clustering with gene expression definitions in a human kidney cell atlas. In addition, higher overall transcript levels were observed for several major MHC class I alleles compared to minor alleles that tend to be expressed at low levels in peripheral blood mononuclear cells.

overall_design: Formalin-fixed paraffin-embedded blocks of normal liver, lung, kidney and heart tissue from four Mauritian-origin cynomolgus macaques were selected from the archive of the Wisconsin National Primate Research Center Nonhuman Primate Biological Material Distribution Program. The first and second macaques were homozygous for the MHC M1 or M3 haplotypes, respectively while the remaining pair of macaques were heterozygous for these MHC  haplotypes. Gene expression in four normal tissues (liver, lung, kidney and heart) from each of these cynomolgus macaques was evaluated with 10X Genomics Visium HD CytAssist spatial capture technology. Global gene expression was measured with the Visium Human Transcriptome Kit v2. For detection of major histocompatibility complex M1 and M3 allele-specific macaque transcripts, a custom panel of 219 RNA Template Ligation probe pairs were designed and spiked-in with the human transcriptome probes. These custom MHC probes were designed according to 10X Genomics guidelines with the primary exception that they were targeted to contain single nucleotide polymorphisms that lie within four basepairs of the ligations junctions to distinguish highly similar transcripts.

first: Julie

last: Karl

first: Anthony

middle: J

last: Veltri

first: Roger

middle: W

last: Wiseman

first: William

middle: K

last: Gardner

first: Max

middle: C

last: Ertl

first: Miranda

last: Stauss

first: Heather

last: Simmons


title: Integrated Transcriptomic Profiling of Rectal and Adipose HIV-1 Reservoirs Relative to Matched PBMCs in ART-Treated Individuals

city: shenzhen

first: huang

last: peiming

state: Guangdong

address: xinhu

institute: Sun Yat-sen University

summary: HIV-1 persistence in anatomical reservoirs remains a major obstacle to a functional cure under suppressive antiretroviral therapy. This study used bulk RNA-seq to characterize host transcriptomic features across matched peripheral blood mononuclear cells (PBMCs), rectal tissue, and subcutaneous adipose tissue (SAT) from ART-treated people with HIV. Transcriptomic profiling revealed tissue-specific remodeling in rectal and adipose reservoirs relative to matched PBMCs, including extracellular matrix remodeling, immunometabolic alterations, and shared PI3K-Akt-related transcriptional features.

overall_design: Bulk RNA-seq profiling was performed on 14 paired-end samples from ART-treated people with HIV: four matched PBMC-rectum donor pairs (048, 084, 092, 111) and three matched PBMC-SAT donor pairs (095, 097, 104). The analysis compared rectal tissue versus matched PBMC and SAT versus matched PBMC to identify tissue-specific and shared host transcriptomic signatures associated with anatomical HIV-1 reservoirs.

first: Jie

last: Qin

first: Peiming

last: Huang

first: Minghua

last: Chen

first: Hua

last: Zong

first: Jingjing

last: Luo

first: Jianteng

last: Zeng

first: Xu

last: Zhang

first: Shiting

first: Jianqiang

last: Zou

first: Xin

last: He

first: Shuangxin

last: Wu

first: Liqin

last: Sun

first: Ting

last: Pan


title: KRAS inhibition is an effective therapy for appendiceal adenocarcinoma

city: HOUSTON

first: John Paul

last: Shen

state: TX

address: 1515 Holcombe Blvd

department: Gastrointestinal Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: Appendiceal adenocarcinoma (AA) is a rare cancer with limited treatment options. KRAS is the most commonly mutated gene in AA and a promising therapeutic target, but its preclinical and translational relevance in AA remains unclear. We evaluated KRASG12D–specific (MRTX1133) and pan-KRAS inhibitor (RMC-6236) in KRASmut organoid and PDX models of AA. Tumor-intrinsic and microenvironmental responses were characterized using multi-omics profiling. MRTX1133 was highly effective for KRASG12D organoids (IC50 = 4.1 nM); both KRASG12D and KRASG12V organoids were sensitive to RMC-6236 (IC50 = 4.4 nM vs. 0.5 nM, respectively). In PDX models of peritoneal carcinomatosis from AA, MRTX1133 reduced tumor growth in the KRASG12D model TM00351, and RMC-6236 reduced tumor growth in KRASG12V model AAPDX-16. Pathologic evaluation showed dramatically reduced tumor cellularity, proliferation, and pERK expression as well as induction of apoptosis. Gene Set Enrichment Analysis (GSEA) demonstrated consistent downregulation of E2F targets and RAS/ERK signaling across both models, confirming on-target KRAS inhibition, alongside upregulation of EMT (Epithelial-to-Mesenchymal Transition), suggesting a shared resistance-associated transcriptional program. Interferon-alpha and interferon-gamma signaling were significantly upregulated following pan-KRAS inhibition, implicating TME (Tumor Microenvironment) immunomodulation as a downstream consequence of KRAS inhibition in AA. scRNA-seq analysis of the TME showed a dramatic shift from normal to inflammatory cancer-associated fibroblasts (iCAFs) following KRAS inhibition. Upregulation of interferon alpha and gamma pathways was also observed, suggesting that KRAS inhibition can activate innate immune response in the setting of peritoneal metastases. While effective suppression of RAS/ERK signaling by KRAS inhibitors reduces tumor growth, adaptive activation of the EMT pathway may mediate resistance in KRASmut AA. Additionally, KRAS inhibition remodels TME and may enhance innate immune signaling. These findings support the continued clinical development of KRAS inhibitors in AA and provide a rationale for combination strategies targeting resistance pathways and stromal remodeling.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Comprehensive analyses of RNA-seq profiles comparing patient-derived xenograft (PDX) models of appendiceal cancer treated with intraperitoneal injections of (i) MRTX1133 (KRASG12D AA tumors) and (ii) RMC-6236 (KRASG12V AA tumors) versus those treated with vehicle control

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raw data are missing due to patient privacy concerns
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first: Ichiaki

last: Ito

first: Saikat

last: Chowdhury


title: Spatiotemporal Transcriptomic Immune Responses to a Recombinant Hemagglutinin Protein Vaccine [CosMx SMI profiling]

city: Gold Coast

first: Laurelle

last: Jackson

state: Queensland

address: 1 Parklands Dr, Southport

department: Pharmacy and Medical Sciences

country: Australia

institute: Griffith University

summary: Vaccination triggers coordinated immune responses that begin at the injection site and propagate to draining lymph nodes, yet spatially resolved maps linking these events remain limited. Here, we applied high-plex spatial transcriptomics to profile early responses to an adjuvanted recombinant haemagglutinin (rHA) protein vaccine. In mice, early innate activation was observed in non-follicular lymph node regions at Day 1, transitioning to adaptive, germinal centre–associated responses within follicles by Day 7. At the injection site, stromal and muscle cells exhibited strong chemokine and interferon responses, spatially localised to fibroblast-rich regions. These tissue-level dynamics were accompanied by transient systemic cytokine responses and increased antigen-specific IgG. Together, this study links spatially organised local inflammation with lymph node architecture to define early vaccine-induced immune responses.

overall_design: Groups of three female BALB/c mice per treatment were immunised intramuscularly (quadriceps) with either AF03-adjuvanted recombinant haemagglutinin (rHA) protein or PBS on Days 0 and 21. Blood samples were collected longitudinally (Days 0, 14, and 35) for serum isolation and immunogenicity assessment. For spatial analyses, injection site muscle and draining lymph nodes were harvested at Days 1 and 7 post-vaccination, formalin-fixed, paraffin-embedded, and sectioned for downstream GeoMx™ DSP and CosMx™ SMI profiling with the Whole Ttanscriptome Atlas probe set and the 1000-plex mouse probe set respectively. Matched H&E-stained sections were used for histological evaluation.

first: Sarah

last: Williams

first: James

last: Sinclair

first: Ana

last: Kume

first: Azadeh

last: Bahadoran

first: Ingeborg

last: Langohr

first: Hillary

last: Danz

first: Bin

last: Lu

first: Dinesh

last: Bangari

first: Amanda

last: Cox

first: Laurence

last: Macia

first: Sudha

last: Chivukula

first: Nicholas

middle: P

last: West


title: Effect of intravenous poly(lactide-co-glycolide) nanoparticles on M2-polarized bone-marrow derived macrophages

city: Ann Arbor

first: Hannah

last: Viola

state: Michigan

address: 1600 Huron Parkway

department: Biomedical Engineering

institute: University of Michigan - Ann Arbor

summary: Organ fibrosis presents a substantial disease burden with few therapeutic options. Innate immunity mediates fibrinogenesis, but also plays a major role in fibrinolysis. Here, we show that immunomodulatory nanoparticles (NPs) can harness this endogenous antifibrotic capacity by catalyzing monocyte activation leading to resolution of bleomycin-induced pulmonary fibrosis in vivo. Cargo-free NPs comprised of the degradable biopolymer poly(lactide-co-glycolide) (PLG) induce a transcriptional shift toward antifibrotic immune activation in profibrotic M2 macrophages (MΦs) in vitro. NPs stimulate M2 MΦs toward a glycolytic, rather than fatty acid oxidative, metabolism; suppress canonical M2 markers like arginase-1 (Arg1) and periostin (Postn); and upregulate collagenases, hyaluronidases and immunoregulatory factors. When delivered intravenously in vivo, NPs resolve established bleomycin-induced pulmonary fibrosis and invert the trajectory of over 1,000 genes from pre- to post-treatment according to bulk RNA-sequencing. NPs also suppress profibrotic signaling and increase expression of repair-associated pathways like peroxisome proliferator-activated receptor gamma (PPAR-γ), nuclear retinoic acid receptor (RAR), vascular endothelial growth factor (VEGF), and sphingolipid signaling in fibrotic lungs. Flow cytometry confirms that NPs induce monocyte recruitment to fibrotic lungs via enhanced integrin expression. Altogether, NPs induce a robust pro-regenerative signature comprised of ECM degradation, inflammation resolution, and tissue repair pathways, concomitant with increased NP+ monocyte recruitment to fibrotic lungs. This work demonstrates that monocytes are not intrinsically profibrotic, but rather, their effects are context-dependent, and they retain a capacity for fibrotic resolution under conditions that can be induced by materials with translational potential.

overall_design: Bulk RNA-sequencing was conducted on M2-polarized bone-marrow derived macrophages from 2 conditions: NP-treated (n=3), and Vehicle (n=3).

first: Kate

last: Griffin

first: Bethany

middle: B

last: Moore

first: Lonnie

last: Shea


title: Transcriptome changes driving multiple regulatory pathways involved in TGF-β-induced Anterior Subcapsular Cataract

city: Sydney

first: Frank

last: Lovicu

address: K25 - Medical Foundation Building

department: Molecular and Cellular Biomedicine

institute: University of Sydney

summary: Transforming Growth Factor-beta (TGF-β) promotes lens epithelial-mesenchymal tran-sition (EMT) and fibrosis, contributing to anterior subcapsular cataract (ASC) formation. Transgenic mice overexpressing TGF-β1 in lens have been studied for over three decades, and yet the impact of active TGF-β1-overexpression on the lens epithelial transcriptome is undefined. We have addressed this knowledge gap by examining the gene expression landscape of these unique lens epithelia. High-throughput RNA-sequencing was per-formed on isolated lens epithelia from three-week-old TGF-β1-overexpression trans-genic mice from two independent lines, OVE853 and OVE918, and wild-type mice. Downstream analyses included comparisons with lens datasets (e.g., cataract-surgery model) and investigations using various resources/tools (e.g., Gene Ontology, CompBio, iSyTE). Compared to wild-type murine lens epithelia, 384 differentially expressed genes (DEGs) were commonly identified in lens of both transgenic lines. Candidates involved in EMT, inflammatory response, extracellular matrix organization, and mecha-no-sensation were elevated, while those involved in lipid metabolism, Wnt-suppression, Bmp- and Notch-activation were reduced. Comparative analyses with temporal tran-scriptomes on a mouse cataract-surgery model identified overlapping pathological pathways, and some elevated genes, for example endoplasmic reticulum stress genes, were in agreement with human ASC data. A major discovery was the identification of several novel TGF-β1-targets. All our data is made user-friendly accessible through iSyTE.

overall_design: RNA-seq profiling of isolated lens epithelia from three week-old TGF-β1-overexpression transgenic mice from two independent lines, OVE853 and OVE918 and wild-type mice

middle: Y

last: Coomson

first: Chirag

last: Parsania

first: Charles

middle: G

last: Bailey

first: Cynthia

last: Metierre

first: Mary

last: Flokis

first: Salil

last: Lachke


title: AAV-mediated gene therapy demonstrates phenotypic rescue in a mouse model of Cockayne Syndrome

city: Worcester

first: Ana Rita

last: Batista

address: 366 Plantation St, N8-1099

department: Genetic and Cellular Medicine

institute: UMass Chan Medical School

summary: Cockayne Syndrome (CS) is an autosomal recessive, progressive developmental and neurodegenerative disease. Approximately 30% of cases are caused by mutations in the ERCC8/CSA gene. Patients with CS present with cutaneous photosensitivity, growth failure, shorter life span, and a progressive degeneration of the central nervous system. Loss-of-function mutations in CSA result in deficiencies in the transcription-coupled nucleotide excision repair (TC-NER). Currently, no therapies are available for these patients. Adeno-associated virus (AAV)-mediated gene therapy offers an opportunity to address this unmet need.  We designed a new AAV vector encoding human CSA under a ubiquitous promoter. We tested the therapeutic efficacy of this AAV9-CSA vector by neonatal intracerebroventicular injection in the Csa-/-;Xpa-/- mouse model. Treatment with AAV9-CSA resulted in a significant increase in lifespan, and broad distribution of human CSA in the brain and heart, without evidence of vector‑related toxicity. Despite clear therapeutic benefit, we also observed neuroradiological abnormalities, and neuropathologic alterations, including hypomyelination, astrocytosis, and microgliosis, as well as likely life-limiting transcriptomic alterations in liver at endpoint. Nonetheless, the success of these experiments paves the way for the first clinical translation of an AAV gene therapy for CS patients into humans.

overall_design: RNA-seq profiling of livers of 12 mice: 3 mice per sex per genotype, with genotypes KO = Csa-/-;Xpa+/+ and Het = Csa-/-;Xpa+/-.

first: Aine

last: Scholand

first: William

middle: S

last: Callahan

first: McKenna

last: Watson

first: Cassandra

last: Sion

first: Tyler

last: Mola

first: Kennedy

last: O'Hara

first: Simon

last: Wentworth

last: Sena-Esteves

first: Oliver

last: King

first: Robert

first: Miguel


title: Transcriptomic analyses of PDX tumors (QQX-09) to gain insight into the mechanisms underlying FOLFOXIRI-induced DTP state.

status: Public on Jun 27 2026

city: Jinan

first: Shuohui

last: Dong

address: Qilu Hospital, Shandong University, No.107, Wen Hua Xi Road, Jinan, Shandong, 250012, P.R. China

institute: Qilu Hospital of Shandong University

summary: Chemotherapy resistance remains a significant challenge, often leading to tumor relapse and poor prognosis. While past efforts to overcome treatment resistance have focused primarily on genetic alterations—such as somatic mutations, chromosomal aberrations, and dysregulated signaling pathways—these insights have yet to translate into effective clinical interventions. The recent discovery of drug-tolerant persister (DTP) cells, which survive therapy through reversible, non-genetic adaptations akin to embryonic diapause, has unveiled a novel mechanism of chemotherapy resistance. To investigate this further, we employed treatment-naïve colorectal cancer (CRC) patient-derived xenograft (PDX) models. Upon reaching a tumor volume of 100 mm³, the PDX models were treated with a single maximum-tolerated dose of the FOLFOXIRI regimen. Post-treatment responses varied, including initial tumor shrinkage followed by regrowth, mirroring the "sensitivity-DTP-regrowth" pattern observed in CRC patients. Transcriptomic analyses of these PDX tumors were then conducted to elucidate the mechanisms underlying the FOLFOXIRI-induced DTP state.

overall_design: RNA-seq profiling of QQX-09 models across control (baseline), DTP (residual), and regrowth status.


title: SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs

city: Suita

first: Tetsuro

last: Hirose

state: Osaka

address: 1-3 Yamadaoka

department: Graduate School of Frontier Biosciences

country: Japan

institute: The University of Osaka

summary: Conventional RNA extraction with acid guanidinium thiocyanate–phenol–chloroform (AGPC) reagents incompletely recovers a subset of transcripts, termed semi-extractable RNAs (seRNAs). This underrepresented RNA population includes architectural RNAs (arcRNAs), which scaffold membraneless organelles, as well as stress-induced downstream-of-gene readthrough transcripts (DoGs). Although our previously developed “improved” AGPC protocol incorporating physical disruption enhances seRNA recovery, it also co-extracts abundant, readily extractable RNAs, yielding mixed populations that hinder precise characterization of seRNAs. Here, we present SERIPH (Semi-Extractable RNA Isolation from the InterPHase), a simple two-step protocol that selectively enriches seRNAs by separating them from readily extractable RNA species. By depleting abundant extractable RNAs, SERIPH increases detection sensitivity, enabling the capture of weakly semi-extractable transcripts, including those of low abundance, that were overlooked by previous approaches. This increased sensitivity expands the detectable seRNA repertoire and reveals a broader genomic extent of DoG transcription than previously appreciated. Together, SERIPH provides a robust framework for high-resolution analysis of seRNA populations, advancing studies of RNA processing, transcriptional regulation, and RNA-mediated nuclear organization in stress responses and disease

overall_design: Using RNA-seq, we compared four RNA preparation methods—SERIPH 1st-step fraction (SERIPH1st), SERIPH 2nd-step fraction (SERIPH2nd), conventional RNA extraction, and improved RNA extraction—under two cellular conditions: HEK293 cells under standard culture conditions (control) and HEK293 cells treated with sorbitol and cycloheximide (OS+CHX). This study follows a 2 × 4 experimental design, and RNA-seq was performed in biological replicates (n = 2) for each condition.

first: Naoko

last: Fujiwara

first: Junichi

last: Iwakiri


title: RNA-seq profiling of wildtype Xenorhabdus griffiniae HGB2511 exposed to conventional and axenic Steinernema hermaphroditum nematodes.

city: Pasadena

first: Elin

middle: Maria

last: Larsson

state: CA

address: 1200 E California Blvd

institute: California Institute of Technology

summary: Xenorhabdus griffiniae was grown for 24 hours with and without being in close proximity to their host nematode Steinernema hermaphrodtium.

overall_design: Xenorhabdus griffiniae was grown in triplicate for 24 hours in 25C in 24-well transwell plates. The plate inserts were either empty or contained their host nematode Steinernema hermaphroditum. After 24 hours of growth, the bacteria were collected and frozen for RNA extraction and sequencing.

first: Carly

last: Myers

first: Dianne

last: Newman

first: Mengyi

last: Cao


title: Platelet-derived S100A9 contributes to Endotheliopathy in Alcohol-Associated Hepatitis [PBS and Aspirin]

city: New Haven

first: Matthew

last: McConnell

state: Connecticut

address: PO Box 208019, 300 Cedar St

institute: Yale University

summary: Alcohol-associated liver disease (ALD) is a growing global health concern, with alcohol-associated hepatitis (AH) leading to the highest morbidity and mortality. Available therapies are limited and often inadequate. Platelets contribute in a variety of ways to the pathogenesis of liver diseases, but their role in AH remains largely unexplored. In this study we address the hypothesis that platelets contribute to pathological inflammation in AH. Using patient samples and a multi-omics approach, we found that platelets undergo proinflammatory transcriptomic and proteomic changes in AH, with two alarmins, S100A8 and S100A9, being among the top upregulated genes/proteins.  Additionally, the abundance of platelet-derived microparticles containing S100A8 and S100A9 in AH patient plasma was increased (p=0.032) and correlated with disease severity (MELD-Na, r=0.51, p=0.03) and endotheliopathy (ICAM1, r=0.70, p=0.001) (CXCL8, r=0.48, p=0.04) (vWF, r=0.59, p=0.01). We mechanistically linked S100A9 with endotheliopathy via crosstalk between primary human liver sinusoidal endothelial cells and primary human monocytes. We also demonstrate that Interleukin-6 (IL6) upregulates S100A9 in megakaryocytic cells in a JAK/STAT-dependent manner, modeling changes occurring in the bone marrow in patients with AH. Our studies establish proinflammatory platelets as important contributors to AH disease pathology. Moreover,  anti-platelet agents, or more specifically S100A9 targeted drugs, are potential therapeutic strategies in AH.

overall_design: RNAseq of platelets from healthy donors and alcohol-associated hepatitis patients

first: Kirlin

last: Fallyn

first: McConnell

last: Matthew


title: Effect of Ly6d overexpression on the mechanism of MASLD

city: Chongqing

first: Xiaohe

last: Luo

state: Chongqing

address: No. 165, Xincheng Road, Wanzhou District, Chongqing

department: Central lab

institute: Chongqing University Three Gorges Hospital

summary: mRNA expression profiles of genes in the livers of wild-type mice and Ly6d liver-overexpressed mice

overall_design: We then performed gene expression profiling using RNA-seq data from mice fed 2 different genotypes on the same diet.

first: Juanjuan

last: Meng

first: Linxin

last: Chen


title: Regulatory T cells Restrain CD4 T Cell Control of MHC-I-Deficient Metastatic Pancreatic Cancer Emerging After PD-L1 Blockade [ATAC-seq]

city: Minneapolis

first: Ingunn

last: Stromnes

state: Minnesota

address: 2-186 Wallin Medical Biosciences Building, 2101 6th St SE

department: Medical School

institute: University of Minnesota

summary: We investigate mechanisms of immunotherapy resistance in pancreatic cancer. PD-L1 blockade selected for metastatic tumor variants with defective IFN-g–inducible MHC-I due to epigenetic Tap1 silencing. Restoration of MHC-I limited primary tumor growth but failed to prevent metastasis. In contrast, regulatory T cell (TREG) depletion abrogated metastasis by unleashing conventional CD4 T cells. Metastasis was also mitigated by transfer of tumor-reactive CD4 T cells or by CTLA-4 blockade. Tumor-specific CD4 T cells adopt a TCF1⁺SLAMF6⁺ progenitor state in lymph nodes and further differentiate in malignant sites. CTLA4 blockade abrogated metastasis, drove intratumoral accumulation CD4 T cells with stemness and tissue residency features, producing a gene signature correlating with improved patient outcomes. MHC-I restoration with anti-CTLA4 prolonged animal survival. TREG and CD4 T cells co-localized in human tumors and abundance correlated with tumor MHC-I and overall survival. Together, these findings identify actionable mechanisms of immune evasion and metastasis in immunotherapy-resistant cancer.

overall_design: Assay for Transposase Accessible Chromatin sequencing was performed on 50,000 cultured tumor cells per sample. Cells were pelleted, washed once in cold PBS, and lysed in 50 µl ice-cold lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Igepal CA-630) to isolate nuclei. Nuclei were immediately pelleted (500 × g, 10 min, 4°C) and resuspended in a 50 µl transposition reaction containing 25 µl 2× TD buffer, 2.5 µl TDE1 Tn5 transposase (Illumina 20034197), and 22.5 µl nuclease-free water. Transposition was carried out at 37°C for 30 min with gentle shaking (100 rpm). DNA was purified using a Qiagen MinElute PCR Purification Kit and eluted in 10 µl Buffer EB (10 mM Tris-Cl). Libraries were paired-end sequenced at the University of Minnesota Genomics Center.


title: Effect of ER stress on inflammatory response in macrophages

first: Tomohiko

last: Murakami

state: OSAKA

address: 1-8 Yamada-Oka

institute: Osaka University

summary: To understand the effects of ER stress on inflammation, primary bone marrow derived macrophages (BMDMs) were stimulated with tunicamycin (Tm)  and/or LPS. Total RNA was analyzed by RNA-seq.

overall_design: RNA-Seq profiles of primary bone marrow derived macrophages (BMDMs) stimulated with tunicamycin (Tm) and/or LPS


title: Gene expression profiling of NAT10 knockdown in HepG2 hepatocellular carcinoma cells by QuantSeq 3' mRNA-seq

city: Yushima, Bunkyo-ku, Tokyo

first: Ryota

last: Kurimoto

state: Tokyo

department: Systems BioMedicine

institute: Tokyo Medical and Dental University

summary: NAT10 (N-acetyltransferase 10) is an RNA acetyltransferase that catalyzes N4-acetylcytidine (ac4C) modification of mRNA and rRNA. To investigate the transcriptomic consequences of NAT10 depletion, we performed siRNA-mediated knockdown of NAT10 in HepG2 hepatocellular carcinoma cells. Total RNA was extracted using TRI reagent 2 days after siRNA transfection, and 3' mRNA-seq libraries were prepared using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD. Sequencing was performed on Illumina NovaSeq 6000. Four biological replicates per condition were analyzed: samples 1, 2, 5, 6 are negative control siRNA (siCtrl), and samples 3, 4, 7, 8 are siNAT10 knockdown.

overall_design: HepG2 cells were transfected with siRNA targeting NAT10 (siNAT10) or negative control siRNA (siCtrl). Two days post-transfection, total RNA was harvested. Libraries were prepared by Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD and sequenced on Illumina NovaSeq 6000 (paired-end). Gene expression was quantified using STAR v2.7.9a alignment to GRCh38 followed by featureCounts. Samples: siCtrl replicates 1,2,3,4 (library IDs 1,2,5,6) vs siNAT10 replicates 1,2,3,4 (library IDs 3,4,7,8).

first: Kurimoto

last: Ryota

first: Hiroshi

last: Asahara


title: Transcriptional Effects of 6-Shogaol and 6-Gingerol in LPS-Stimulated BV2 Microglial Cells

city: seoul

first: taehyun

last: kim

address: 26-6, Kyungheedae-ro, Dongdaemun-gu

department: regulatory science

country: South Korea

institute: kyunghee univ.

summary: This study investigated the transcriptomic effects of the ginger-derived compounds 6-Shogaol and 6-Gingerol on inflammation-associated gene expression in LPS-stimulated BV2 mouse microglial cells. RNA-seq was performed to compare gene expression profiles among untreated control cells, LPS-treated cells, and cells co-treated with LPS and different concentrations of 6-Shogaol or 6-Gingerol.

overall_design: Comparative gene expression profiling was performed using RNA-seq data from BV2 mouse microglial cells under the following conditions: untreated control, LPS treatment, LPS plus 10 µM 6-Shogaol, LPS plus 10 µM 6-Gingerol, LPS plus 30 µM 6-Shogaol, and LPS plus 30 µM 6-Gingerol.

first: Insung

last: Choi

first: Tae Hyun

last: Kim

first: Yong-jun

last: Jeon

first: Jin Hee

first: Myung Sook

last: Oh

first: Inwha

last: Baek


title: The lung environment in pulmonary Mycobacterium tuberculosis infection influences local monocyte differentiation

city: San Francisco

first: Alexander

last: Mohapatra

department: Medicine

institute: University of California, San Francisco

summary: Infection by Mycobacterium tuberculosis (Mtb) continues to cause significant mortality due to pathogen persistence in lung cells derived from blood monocytes. Since persistent blood monocytosis is a hallmark of tuberculosis and monocyte-derived lung subsets differ in their ability to restrict the growth of intracellular Mtb in mice, the ontogeny of these subsets could inform development of host-directed therapies. Recent literature suggests that circulating monocytes are heterogeneous and derive from mobilization of distinct bone marrow (BM) or spleen progenitors that direct local differentiation. However, the role of the inflamed lung environment on this process has not been addressed. We compared monopoiesis in the BM of Mtb-infected mice and uninfected controls and found that these monocyte pools had similar differentiation within the infected lung. While Mtb infection induced splenic monopoiesis, we found no impact on lung monocyte differentiation in splenectomized mice. However, when monocytes were transferred into Mtb-infected recipients with a distinct lung environment, we observed altered differentiation. We identified monocyte-derived lung subsets with unique gene expression, associated with specific spatial distributions and cell neighborhoods. These findings suggest that the local lung environment has a larger influence on the phenotypic diversity of monocyte-derived lung cells than does the peripheral environment.

overall_design: The left lung lobe was excised from each of 2 C57BL/6 mice infected with aerosolized Mtb strain H37Rv for 27 days. Following embedding in paraffin blocks, 5 mm sections were cut onto one Xenium slide per mouse (0094877 and 0094885), with 3 sections per slide (Regions 1-3). Probes utilized targeted a total of 429 unique genes, including a set specific for a custom 50-gene add-on panel designed by 10X Genomics and those contained in the 10X Mouse Tissue Atlassing Panel (mMulti_v1). Imaging data from 2 regions per slide were analyzed.


title: Hereditary spastic paraplegia (HSP) gene 11 (SPG11) attenuates lipid accumulation in myeloid cells and neuroinflammation independent of α-synuclein pathology

city: Stanford

first: Tawaun

middle: Autry

last: Lucas

address: 1201 Welch Rd

institute: Stanford University

summary: Hereditary spastic paraplegia type 11 (HSP-SPG11) is a neurodegenerative disorder caused by mutations in SPG11, which encodes the large scaffolding protein spatacsin, involved in lysosomal and autophagosomal trafficking. A portion of patients with SPG11 mutations show overlapping clinical presentations with Parkinson’s disease (PD) patients. While spatacsin dysfunction is linked to neurodegeneration, the underlying cellular mechanisms remain largely unclear. Here, we demonstrate that loss of Spg11 results in neuroinflammation and lipid accumulation in myeloid cells, independent of α-synuclein aggregation. Bulk RNA sequencing revealed a strong upregulation of microglial genes in Spg11 knockouts, supported by increased CD68 expression and morphological changes consistent with microglial activation. Spg11 depletion in two in vivo models of PD revealed no enhancement of phosphorylated αSyn-positive inclusions or dopaminergic neuron loss; however, the mice did exhibit Spg11-dependent microglial reactivity. Further in vitro studies using primary bone-derived macrophages revealed increased phagocytic capacity and neutral lipid accumulation under basal and stress conditions. These findings support a model where SPG11 is a critical regulator of microglial activation and myeloid lipid metabolism, contributing to neurodegeneration through pathways distinct from classical α-synuclein-mediated pathology.

overall_design: RNAseq profiling of SPG11-/- of normal aged and A53T mice created by inserting early stop codons in exon 32 of SPG11. A53T mice express human α-synuclein with an A53T mutation under the mouse prion protein promoter

first: Margaret

last: Hayne

first: Joanna

last: Lipka

first: Allison

middle: L

last: Soung

first: Max

last: Adrian

first: Soumitra

last: Ghosh

first: Han

last: Lin

first: Sarah

last: Chu

first: Kimberly

last: Stark

first: Hai

last: Ngu

first: Oded

last: Foreman

first: Joshua

last: Kaminker

first: Casper

last: Hoogenraad


title: Circadian screening of neutrophils identifies therapeutic targets in multiple sclerosis

city: Genève

first: Christoph

last: Scheiermann

address: 1, rue Michel Servet

country: Switzerland

institute: UNIGE

summary: Circadian rhythms are intrinsic time-keeping mechanisms that play a critical role in tuning immunity. Here, we investigated the impact of circadian rhythms on the pathogenesis of experimental autoimmune encephalomyelitis (EAE), a mouse model for multiple sclerosis (MS). We demonstrate that circulating neutrophils in blood significantly increase early in EAE, prior to symptoms onset. Importantly, we found that these cells infiltrate the central nervous system (CNS) in a time-of-day (ToD)-dependent manner, with increased infiltration at the onset of the behavioral active phase of the mice (evening). Transcriptomic analysis of CNS-infiltrating neutrophils revealed distinct ToD-dependent gene expression profiles, which identified Formyl peptide receptor 2 (FPR2) as a potential therapeutic candidate, since pharmacological inhibition of FPR2 led to reduced EAE disease severity. Furthermore, combinatorial treatment with a drug that targets VLA-4 (in the clinic used under the trade name Natalizumab to treat MS) led to additive effects, substantially reducing EAE symptoms. Together, these findings highlight the importance of circadian immune cell dynamics during EAE development and provide a first characterization of the circadian immune landscape in an animal model of MS, identifying potentially novel targets for MS therapies

overall_design: Spinal cords were collected from EAE-induced mice and harvested at 2 time points (ZT1 and ZT13).  Spinal cords were digested as described above, and CD45+CD11b+Ly6G+ cells were sorted using an Astrios sorter (Beckman).

first: Francesco

last: De Virgiliis

first: Coline

last: Barnoud

first: Wenyan

last: He

first: Qun

last: Zeng

first: Robert

last: Pick

first: Tianyue

last: Sun

first: Stéphane

last: Jemelin

first: Valeria

last: Maria Oliva

first: Tiphaine

last: Furlan

first: Carmen

last: Picon-Muñoz

first: Doron

last: Merkler


title: Gene expression proﬁling of 22Rv1 cells treated with  a CDK9 degrader, Compound 45 (D45)

city: Shanghai

first: Weisong

last: Tan

state: Shanghai

address: No. 2005 Songhu Road

institute: Fudan University

summary: As one of the serine/threonine protein kinase family members, Cyclin-dependent kinase 9 (CDK9) functions as a critical regulator of transcription. Its overexpression has been observed in various cancers, including prostate cancer, positioning it as a potential therapeutic target. D45, a newly developed small molecular CDK9 degrader, has been shown to significantly inhibit the growth of triple-negative breast cancer cells. Currently, we carried out a study to explore the role of CDK9 in castration-resistant prostate cancer (CRPC). Hence, human CRPC 22Rv1 cells were treated with small molecule compound, D45, targeting CDK9, followed by RNA-sequencing.

overall_design: 22Rv1 cells were treated with the small molecule compound D45 (40 nM) targeting CDK9 and vehicle (DMSO) for 12 hours.

first: Jingya

first: Jiaxuan

last: Li

first: Ruimin

last: Huang

first: Jun

last: Yan


title: CD14 Serves as a Predicted Marker for Coronary Artery Lesions in Kawasaki Disease

city: suzhou

first: xiaoling

last: li

state: State...

address: 100 Chongwen Road, Suzhou Industrial Park, Jiangsu Province, China

institute: suzhou func biotec inc.

summary: Kawasaki Disease (KD) is an acute vasculitis that commonly occurs in younger children, which can lead to coronary artery aneurysm, dilatation and other severe cardiovascular diseases. However, the mechanism of coronary artery lesions remains unclear. In this study, we detected the mRNA expression profile of KD patients in the acute and subacute stages in the coronary artery lesions group (KD-CALs) and the non-coronary artery lesions group (KD-nCALs). 62 differentially expressed genes were found in the CALs group, and the differential genes were enriched in immune-related signaling pathways, significantly in the NF-kappa B signaling pathway. CD14-mRNA was confirmed to be down-regulated in the subacute stage of KD-CALs. Moreover, the downregulation of CD14 caused a decrease in the expression of a series of downstream genes such as IκBα, A20, and A1/Bf1_1. But only the downregulation of IκBα was in sync with CD14. In conclusion, CD14-mRNA was differentially expressed in the KD-CALs group and regulated the expression of IκBα via the NF-kappa B signaling pathway, finally inducing vascular endothelial cell injury. It can be served as a predicted marker for coronary artery lesions in KD. Besides, CD14 could become a potential therapy target for KD, especially in reversing coronary artery lesions (CALs).

overall_design: We enrolled 12 children diagnosed with KD, and studied the transcriptome differences between KD patients in the acute and subacute stages in the coronary artery lesions group (KD-CALs) and the non-coronary artery lesions group (KD-nCALs). Then, qRT-PCR was used to validate the difference. Meanwhile, we enrolled 12 new KD patients (6 of KD-CALs, and 6 of KD-nCALs; Each group collected blood samples from acute and subacute periods, respectively) and investigated the expression of CD14 and a series of downstream genes in NF-Kappa B Signaling Pathway (such as A20, A1/Bf1_1, and IκBα) by qRT-PCR. At last, molecular docking was used to analyze the binding force of the core effective compounds with CD14 in the “herbal medicine-compound-target” network.


title: Nonsense-mediated decay mRNA quality control system is essential for root development and efficient root nodule symbiosis in Medicago truncatula

city: Szeged

first: Peter

last: Kalo

address: Temesvari krt. 62.

department: Institute of Plant Biology

country: Hungary

institute: HUN-REN Biological Research Centre

summary: Quality control systems ensure the fidelity of gene expression by identifying and eliminating aberrant gene products. Nonsense-mediated decay (NMD) mRNA surveillance pathway recognizes and degrades aberrant mRNAs containing premature termination codons. Additionally, NMD regulates the expression of several normal genes, and in Arabidopsis, it also modulates antibacterial defense by controlling the expression of resistance genes. Surprisingly, the role of quality control systems in root nodule symbiosis has remained unexplored. To investigate the function of NMD in nitrogen-fixing symbiosis, we attempted to inactivate the core NMD factors UPF1 and UPF2 in Medicago truncatula. Since the complete knockout of these genes was not achievable, we conclude that NMD is essential for root growth. We therefore generated upf1 and upf2 NMD-deficient RNAi roots and inoculated them with Sinorhizobium medica. Both infection events and nodule formation were significantly reduced in the RNAi roots, indicating that NMD is required for efficient symbiosis; even partial inactivation of NMD impairs infection. In line with the sensitivity of symbiosis to NMD intensity, we identified multiple autoregulatory circuits that stabilize NMD activity in M. truncatula. Finally, RNA-seq revealed pronounced alterations in symbiosis-related pathways, including flavonoid biosynthesis and defense responses, in NMD-deficient roots, likely explaining the defects in rhizobia infection.

overall_design: To identify the NMD regualted genes in the roots of Medicago truncatula, RNA-seq profiling was generated from 3 biological replicates of control and upf1 and upf2 NMD-deficient test roots. In the upf1 and upf2 roots, the UPF1 and UPF2 NMD key factors were inactivated by RNAi, respectively.

first: Daniel

last: Silhavy


title: FlAsH-ID: A short peptide tag for live cell photoproximity labeling

city: Jupiter

first: Wuyue

last: Zhou

address: 110 Scripps Way

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

summary: Methods to determine how biomolecules interact in a cellular context has led to significant advances in our understanding of biology. Of these, proximity labeling has emerged as a valuable tool for the interrogation protein-protein and protein-RNA interactions. Almost all proximity labeling methods are deployed via large fusion proteins, which while powerful in many contexts, can disrupt native biology or obscure important epitopes on the protein under study. This challenge is especially prominent for small transcriptionally active proteins where the protein cistrome is vital for correct localization and function. Here, we have developed a photoproximity labeling method that is localized to a short 6 amino acid peptide sequence that employs the combination of the Tsien tetracysteine tag with FlAsH dye for localized singlet oxygen generation that we term FlAsH-ID. We demonstrate this method is non toxic and can be employed to label several cellular compartments, and generate high quality interactomics data around H3.1. Furthermore, we show that FlAsH-ID can be used to probe dynamic chnages in protein movement in response to immune stimuli, identifying several RNA-binding protiens that are trafficked to the nucleus following poly(I:C) treatment. Finally we demonstrate FlAsH-ID can be used for proximity proteomics in primary CD8+ T cells by focusing on the transcription factor RUNX3. RUNX3-tetracysteine, but not RUNX3-TurboID, recaptiulated the function of wildtype RUNX3 and rescued the phenotype of Runx3-deficeint CD8+ T cells in response to viral infection in vivo. In primary CD8+ T cells, FlAsH-ID identified RUNX3 in proximity to the nucleosome remodeler ARID1A and we show that both factors act concertedly during initial naive CD8+ T cell activation to drive chromatin accessibility in cis-regulatory regions that induce differentiation of effector and long-lived memory CD8+ T cells. Our results suggest this technique will expand the field of proximity labeling to small, functionally sensitive proteins in primary cells without perturbing their function.

overall_design: RNA-seq was performed on ex vivo stimulated CD8+ T cells transduced with 6 RUNX3 fusion constructs (FT, LOV, APEX, ULTRA, MINI, TID) compared against empty vector (EV) and wild-type RUNX3 (WT) controls, with 2 biological replicates per condition (16 samples total).

first: Shashank

last: Nagaraja

first: Jihye

last: Kim

first: Thomas

last: Venables

first: Madison

middle: T

last: Jones

first: Sojeong

last: Lee

first: Jinyoung

last: Kang

first: Ezgi

last: Hacisuleyman

first: Matthew

middle: E

last: Pipkin

first: Ciaran

last: Seath


title: Regulatory T cells Restrain CD4 T Cell Control of MHC-I-Deficient Metastatic Pancreatic Cancer Emerging After PD-L1 Blockade [scRNA-seq]

first: Ingunn

last: Stromnes

summary: We investigate mechanisms of immunotherapy resistance in pancreatic cancer. PD-L1 blockade selects for metastatic tumor variants with defective IFNγ-inducible MHC-I due to epigenetic silencing of Tap1. Restoring MHC-I limits primary tumor growth but fails to prevent metastasis. In contrast, regulatory T cell (TREG) depletion suppresses metastasis by unleashing CD4 T helper cells. Adoptive transfer of tumor-specific CD4 T cells impairs metastatic progression. Tumor-specific CD4 T cells in lymph nodes preferentially adopt a TCF1⁺SLAMF6⁺ precursor state. Intratumoral TREG targeting with anti–CTLA-4 abrogates metastasis, drives accumulation of stem-like, tissue-resident helper CD4 T cells, producing a gene signature associated with improved patient outcomes. Combined CTLA-4 blockade and MHC-I restoration eliminates metastasis and prolongs animal survival. In human tumors, TREG and CD4 helper T cells co-localize and correlate with both tumor MHC-I expression and overall survival. Together, these findings identify actionable mechanisms of immune evasion and metastasis in immunotherapy-resistant cancer.

overall_design: Mice were orthotopically implanted with 1 x 10^5 KPC2 tumors immersed in 60% matrigel. On day 7, cohorts were untreated or treated with agonistic anti-CD40 (100 ug  ip) + anti-PD-L1 (200 ug  ip on days 7, 9, and 12) + anti-TNF (200 ug  ip on days 6, 7, 9, 12). On day 14, mice were euthanized, and intratumoral mononuclear cells were isolated and prepared for scRNA-seq using the 10X Genomics platform.  On day 14 post tumor implantation, immune cells were were isolated and samples were pooled by treatment group. Spleen and tumor single cell suspensions were prepared. Immune cells were enriched from the tumor single cell suspensions using a 44/67% percoll density gradient. Briefly, samples were resuspended in 3 mL of 44% percoll in a 15 mL conical tube and then underlaid with 3 mL of 67% percoll using a glass Pasteur pipette. Samples were centrifuged for 20 minutes at 600 x g at 22°C with an acceleration of 1 and brake of 0. After spinning, cells at the density interface were isolated with a P100 pipette and transferred to 20 ml of complete media for washing. T cells were enriched from the percoll sample using a mouse pan T cell negative selection kit (Miltenyi Biotec 130-095-130). For each tissue (tumor or spleen) and each treatment group, samples were stained with unique hashtags (TotalSeq C, Biolegend) at a concentration of 0.2 mg per 1 x 10^6 cells. Next, samples were pooled by tissue containing the 4 treatment groups for proceeding with 2 independent captures. Cells were submitted to University of Minnesota Genomics Core for single cell 10X Chromium 5’ GEX and V(D)J capture targeting 20,000 cells and NovaSeq X series 150 PE sequencing on an S1 flow chip targeting 50,000 reads per cell for GEX.

middle: M


title: Regulatory T cells Restrain CD4 T Cell Control of MHC-I-Deficient Metastatic Pancreatic Cancer Emerging After PD-L1 Blockade [EM-Seq]

type: Methylation profiling by high throughput sequencing

overall_design: EM-seq profiling of methylation changes in EscV2 and KPC2a cells following treatment with DMSO vehicle, interferon gamma, or interferon gamma with decitabine.

first: Audrey

last: Hilk


title: Studying the effect of sarcomeric MYH7R663H and non-sarcomeric BRAFT599R hypertrophic cardimyopathy mutations in human induced pluripotent stemm cell-derived cardiomyocytes

city: Paris

first: Jean-Sébastien

last: Hulot

address: Rue Leblanc

institute: Paris Centre de Recherche Cardiovasculaire

summary: Activating mutations in the RAS-MAPK pathway account for ~20% of cases of paediatric hypertrophic cardiomyopathy (HCM) and are associated with poor outcomes. Mavacamten is approved for obstructive HCM; however, patients with RAS-associated HCM have not been included in the clinical trials so far. We aimed to characterize the functional and energetic disturbances in an in vitro RAS-HCM model and evaluate the therapeutic effects of mavacamten.  Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) carrying a CRISPR-induced BRAF (p.Thr599Arg) mutation and their isogenic control were studied. Cell size, contractility, and transcriptomics were assessed, while energetics were determined using MitoStress assays, live ATP imaging, and NAD(P)H/FAD autofluorescence.  BRAF-mutant hiPSC-CMs showed hypertrophy, hypercontractility, increased mitochondrial cofactor pools, and enhanced maximal respiratory capacity. Despite this, they developed ATP deficiency in response to rapid pacing, suggesting mitochondrial inefficiencies or an overwhelming ATP demand. Mavacamten normalized mitochondrial respiration and excessive ATP consumption, partially restoring energetic balance and highlighting hypercontractility as a major burden in RAS-HCM.  BRAF-mutant cardiomyocytes recapitulate the characteristics of HCM in vitro. Mavacamten mitigates dysfunctions and restores energetic balance under stress conditions, indicating it holds potential as a therapeutic option for RASopathy-associated HCM.

overall_design: RNA-seq profiling of human induced pluripotent stem cell-derived cardiomyocytes from a healthy control patient and two HCM-mutated cell lines generated with CRISPR-Cas9, sarcomeric MYH7R663H and non-sarcomeric BRAFT599R.

first: Ruiz-Velasco

last: Andrea

first: Jouve

last: Charlène

first: Hulot

last: Jean-Sébastien


title: Notch Signaling Reprograms Glial Lipid Metabolism to Promote Hypoxia Resistance

city: La Jolla

first: Dan

address: 9500 Gilman Drive

institute: UCSD

summary: To understand the transcriptional basis of Notch activation-conferred hypoxia tolerance, we performed single-nucleus RNA sequencing (snRNA-seq) of the developing Drosophila central nervous system and generated a comprehensive cellular atlas at single-cell resolution. Analysis of Eaat1-expressing cells revealed that Notch activation reshaped hypoxia-induced transcriptional responses and counteracted metabolic suppression caused by low oxygen. Together, our findings identify Eaat1 glia as a metabolically adaptive glial population and reveal a conserved Notch-regulated mechanism that rewires lipid metabolism to support hypoxia tolerance in the developing brain.

overall_design: Notch-ICD was expressed in the Eaat1-positive glial cells using the Gal4/UAS system. The control and NICD-OE flies were treated with hypoxia (3.5% Oxygen balanced with Nitrogen) for 24 hours. The cell nuclei were isolated from 3rd instar larval brain and subjected to snRNA-seq. The samples from normoxia reared larvae were included as room-air controls.

first: Yajuan

last: Li

first: Charlene

last: Miciano

first: Allen

last: Wang

first: Lingyan

last: Shi

first: Gabriel

last: Haddad


title: The effect of SUD2core overexpression on gene expression in response to SARS-CoV-2 trVLP of dHL-60 cells

city: Chengdu

first: Ying

address: No. 17 Gaopeng Dadao

institute: Sichuan University

summary: To determine whether SUD2core influences the cellular response to SARS-CoV-2 trVLP, bulk RNA sequencing on control (empty vector expressed) and SUD2core-expression of dHL-60 cells following SARS-CoV-2 trVLP infection were performed.

overall_design: The recombinant transcription and replication competent virus like particles trVLPs were added at an MOI of 1 for 24 h in control (empty vector expressed) and SUD2core-expression of dHL-60 cells.


title: The effect of HEBP2-knockout on gene expression in response to SARS-CoV-2 trVLP of dHL-60 cells

summary: To determine whether HEBP2 influences the cellular response to SARS-CoV-2 trVLP, bulk RNA sequencing (RNA-seq) on control (scramble gRNA-transfected) and HEBP2-knockout of dHL-60 cells following SARS-CoV-2 trVLP infection were performed.

overall_design: The recombinant transcription and replication competent virus like particles trVLPs were added at an MOI of 1 for 24 h in control and HEBP2-knockout of dHL-60 cells.


title: Sedanolide alleviates LPS-induced depressive-like behaviors by modulating the C3a/C3aR signaling axis and microglial glycolysis

city: hangzhou

first: fangla

last: luo

address: zhejiang university zijingang campus

institute: zhejiang university

summary: Depression is associated with neuroinflammation and microglial activation. This study investigated the effects of sedanolide in an LPS-induced mouse model of depressive-like behaviors. RNA sequencing of medial prefrontal cortex (mPFC) tissues was performed to identify transcriptomic changes associated with sedanolide treatment. Differential expression analysis revealed candidate genes involved in inflammatory pathways, including C3 and MMP9. Further validation demonstrated that sedanolide regulates neuroinflammation and microglial metabolic reprogramming through the C3a/C3aR signaling axis.

overall_design: RNA-seq was performed to identify differentially expressed genes in mPFC tissues from control, LPS-treated, and sedanolide-treated mice.

first: Shaocong

last: Lu

first: Fangla

last: Luo

first: Niqi

last: Chen

first: Gongde

first: Yeru


title: A Cationic Nanoemulsion Preserves Corneal Barrier Function and Meibomian Gland Integrity in Contact Lens–Related Dry Eye

city: tianjin

first: Zhihui

last: Zhang

address: No. 251 Fukang Road, Xiqing District, Tianjin

institute: tianjin medical university eye hospital

summary: Purpose: To establish a clinically relevant mouse model of contact lens–related dry eye (CLDE) and evaluate the therapeutic effects and potential mechanisms of the cationic nanoemulsion Cationorm®. Methods: CLDE was induced by combined benzalkonium chloride (BAC) exposure and daily contact lens wear. After model establishment, mice were treated with normal saline, hyaluronic acid (HA), or Cationorm®. Tear film stability, tear secretion, and corneal epithelial damage were assessed using tear breakup time, phenol red thread test, and corneal fluorescein staining. Corneal and meibomian gland morphology were evaluated by histology, apoptosis was assessed by TUNEL staining, and barrier- and inflammation-related gene expression was analyzed by RT-qPCR. RNA sequencing was performed to explore treatment-associated molecular pathways. Results: The BAC+CL model induced tear film instability, reduced tear secretion, corneal epithelial damage, barrier-related gene dysregulation, and ocular surface inflammation. Cationorm® significantly prolonged tear breakup time compared with saline and HA and partially improved tear secretion. Cationorm® reduced corneal epithelial damage, improved corneal epithelial morphology, and increased the expression of barrier-related genes, including Zo1 and Occludin. Inflammatory markers, including Il1b, Tnfa, and Mmp9, were reduced after Cationorm® treatment. Cationorm® also reduced apoptosis in the cornea and meibomian gland and preserved meibomian gland structure. Transcriptomic analysis revealed enrichment of epithelial junction–related and immune-related pathways associated with Cationorm® treatment. Conclusions: Cationorm® improves ocular surface abnormalities in a dual-hit CLDE mouse model through coordinated effects on tear film stability, corneal epithelial integrity, inflammation, apoptosis, and meibomian gland structure. These findings support its potential as a multi-target therapeutic strategy for CLDE.

overall_design: Male C57BL/6J mice (6–8 weeks old) were randomly assigned to Control, benzalkonium chloride (BAC), and contact lens–related dry eye (CLDE) groups. A dual-hit CLDE model was established by combining topical BAC exposure (0.1%, 5 μL/eye, twice daily) with daily contact lens wear (6 h/day) to mimic chemical and mechanical stress on the ocular surface. After model induction, CLDE mice were further randomized to receive normal saline (NS), hyaluronic acid (HA), or Cationorm® (5 μL/eye, twice daily) for 14 days. Tear film function (tear breakup time and phenol red thread test), corneal epithelial integrity (fluorescein staining and histology), apoptosis (TUNEL assay), inflammatory and barrier-related gene expression (RT-qPCR), and transcriptomic changes (RNA sequencing) were evaluated. All outcome assessments were performed by investigators blinded to group allocation, and data were analyzed using one-way ANOVA with Tukey’s post hoc test.


title: MTOR-dependent expression of SP1 promotes the tolerogenic function of dendritic cells by inducing IL10 expression

city: Heraklion

first: Prodromos

last: Sidiripoulos

address: Andrea Kalokerinou 13

country: Greece

institute: University of Crete

summary: Dendritic cells (DCs) are central regulators of immune responses and tolerance. Although CTLA4-Ig has been reported to promote tolerogenic properties in DCs, the molecular mechanisms underlying this process remain incompletely understood. The aim of this study was to characterize the transcriptional programs associated with CTLA4-Ig-induced tolerogenic DCs. Human monocyte-derived DCs from healthy donors were stimulated with LPS in the presence of either control IgG or CTLA4-Ig and subjected to RNA sequencing. Comparative transcriptomic analysis was performed to identify differentially expressed genes and pathways associated with CTLA4-Ig-mediated tolerogenic reprogramming.

overall_design: PBMCs were isolated by density-gradient centrifugation from heparinized peripheral blood obtained from four healthy donors. CD14+ monocytes were purified by magnetic positive selection and differentiated into monocyte-derived dendritic cells (DCs). On day 6 of differentiation, DCs were stimulated with LPS (100 ng/mL) in the presence of either control IgG or CTLA4-Ig (50 μg/mL) for 18 hours. Total RNA was isolated and subjected to bulk RNA sequencing. The study included eight samples in total, comprising four biological replicates per condition. A paired experimental design was used, with each donor contributing one sample to each treatment group.

first: Panagiota

last: Goutakoli

first: Sofia

last: Papanikolaou

first: Elpida

last: Neofotistou-Themeli

first: Giannis

last: Vatsellas

first: George

last: Bertsias

first: Maria

last: Semitekolou

first: Panayotis

last: Verginis

last: Sidiropoulos


title: Early immune cell development precedes gastrulation in annual killifish

city: Seattle

first: Sydney

middle: Marie

last: Sattler

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Native to ephemeral pools in southeastern Africa that evaporate each dry season, the annual killifish, Nothobranchius furzeri (N. furzeri), evolved under intense selective pressure, producing a highly derived mode of early development. Following cleavage, deep blastomeres disperse as individual cells across the yolk surface, remaining independent until undergoing self-organized aggregation and germ layer formation. This dispersed phase lacks the tissue-level organization characteristic of other vertebrate embryos, providing an opporunity to investigate how lineage-specifying GRNs function in an altered morphogenetic environment. To investigate this question, we performed single cell RNA-sequencing on killifish embryos using PIP-seq technology, thereby producing the first coarse-grained atlas of early killifish embryogenesis. Here we show that primitive myelopoiesis, which in most studied vertebrates invariably develops from ventral mesodermal progenitor domains, is uncoupled from this tissue source in N. furzeri. Instead, neutrophils emerge prior to gastrulation. This rearrangement equips the African killifish with functional neutrophils before organogenesis begins, making it a striking example of developmental heterochrony.

sample_organism:
Danio rerio
Nothobranchius furzeri

platform_organism:
Danio rerio
Nothobranchius furzeri

overall_design: Killifish embryos from the dispersed (52 hours post fertilization (hpf)), incipient aggregate (72 hpf), bud (96 hpf), and 8-somite (115 hpf) and zebrafish embryos from 8-somite (~12 hpf) developmental stages were dissociated and 40,000 cells were loaded onto the V4 T20 PIP-seq kit (now the Illumina Single Cell 3’RNA Prep Kit) for each timepoint except for the killifish 115hpf timepoint which consisted of a 1:1 mix of killifish and stage-matched zebrafish cells used to initially assess the efficacy of the PIP-seq kit which, at that time, had not yet been used on teleosts.

first: Philip

last: Abitua


title: Targeting JAK1/3-STAT1 signaling attenuates cytotoxic T lymphocytes activation for the treatment in Stevens-Johnson syndrome and toxic epidermal necrolysis

city: Taoyuan

first: Chuang-Wei

last: Wang

address: No. 5, Fusing St

institute: cgmh

summary: Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are life-threatening severe cutaneous adverse reactions (SCARs). We integrate single-cell and spatial transcriptomic analyses on blood, blisters, and lesional skin from SJS/TEN patients, revealing IFN-γ and JAK/STAT signaling as the key pathways responsible for driving epidermal necrolysis. We identify JAK1/3–STAT1 signaling as a primary driver of the activation of CD8+ cytotoxic T lymphocytes (CTLs), natural killer (NK)/NKT cells, macrophages and conventional dendritic cells in skin lesions. The high proportion of cytotoxic protein (granulysin and granzyme B)–expressing CD8+ CTLs in SJS/TEN blisters is associated with STAT1 phosphorylation. Immunostaining and ex vivo blocking assays further confirm the potential for the JAK1/3 inhibitor to attenuate CD8+ CTL activation in SJS/TEN. We conduct a proof-of-concept clinical trial in 20 patients with SJS/TEN (ClinicalTrials.gov: NCT06474078), and find that the JAK1/3 inhibitor tofacitinib improves clinical outcomes by reducing skin-healing time with no observed mortality. Our study provides an effective and alternative mechanism-based therapeutic approach for SJS/TEN.

overall_design: This study performed single-cell RNA sequencing (scRNA-seq) on blister-derived cells and peripheral blood mononuclear cells (PBMCs) from acute-phase SJS/TEN patients, together with PBMCs from healthy donors (HD). We also performed 10x Visium spatial transcriptomics on lesional skin from patients and on skin from healthy donors.

first: Chun-Bing

first: Wen-Hung

last: Chung


title: Identifying PRMT1 target genes in human primary cytotrophoblasts

city: Kansas city

first: Soumen

last: Paul

state: Kansas

address: Rainbow Blvd

department: Pathology

institute: University of Kansas Medical center

summary: To identify PRMT1 targets in primary cytotrophoblast (CTBs) cells, we performed CUT&RUN-sequencing. CTBs were freshly isolated from 1st trimester human placenta tissues (5.4 to 9wk).

overall_design: For primary CTB  isolation, placental villous tissues were minced and carefully dissected for the villous portion of the placental tissue. These were processed by immunomagnetic separation using EasySepTM  Human PE selection kit with a PE-conjugated anti-ITGA6 antibody. Specific selected CTBs were used for CUT&RUN experiments using anti-PRMT1 and anti-IgG antibodies using CUT&RUN assay kit from Cell Signaling Technology (86652). Isolated DNA was then used for library preparation and sequencing using Novoseq 6000 platform.

first: Purbasa

last: Dasgupta

first: Rajnish

last: Kumar


title: The GPR17 agonist galinex restores oligodendrocyte maturation under inflammatory conditions

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: Chronic neuroinflammation disrupts oligodendrocyte differentiation and limits effective remyelination across multiple neurological disorders. Among the molecular regulators integrating inflammatory cues with oligodendrocyte maturation, G protein-coupled receptor 17 (GPR17) has emerged as a critical checkpoint. Physiologically, GPR17 expression is low in early oligodendrocyte precursors (OPCs) and peaks in immature oligodendrocytes, after which it must be downregulated to allow cells’ terminal maturation. Under neuroinflammatory conditions, GPR17 is permanently upregulated, suggesting a role in blockade of oligodendrocyte (OL) maturation and in defective myelination. Here, we tested whether receptor modulation by the specific agonist Galinex (GAL) can restore proper OL maturation under neuroinflammatory conditions. We first showed that subtoxic inflammatory stress, defined as cytokine exposure that did not cause overt loss of cell viability, consistently impaired oligodendrocyte morphological maturation, reduced the expression of myelin-associated markers, and was accompanied by increased GPR17 expression. Transcriptomics analysis revealed that CTK (Cytokines) induced coordinated transcriptional remodelling involving protein synthesis/proteostasis, mitochondrial metabolism, and lipid-related pathways, together with a shift towards an immunogenic-like, senescence/DNA-damage–associated phenotype. Cross-comparison with publicly available transcriptomic signatures of neuroinflammatory patterns from both mouse models and Alzheimer’s and multiple sclerosis human brains, revealed significant overlap with disease-associated modules, supporting the relevance of the inflammatory pathways engaged in our model. We then showed that treatment of OLs with GAL restored cells’ terminal maturation and morphological features. Moreover, in a synthetic nanofiber myelination assay, GAL significantly increased the length of myelinated segments compared to CTK-treated cells, suggesting an improvement of OL myelinating capacity after inflammatory damage. Together, this study establishes a controlled in vitro model linking alteration of disease-relevant transcriptional pathways to impaired OL differentiation and highlights GPR17 pharmacological modulation as a feasible strategy to promote OL maturation under non permissive inflammatory contexts.

overall_design: Primary rat oligodendrocyte precursor cells (OPCs) where treated for 6 hours with a pro-inflammatory cytokine cocktail containing 2 ng/mL of IL-1beta, TNF-alpha and IFN-gamma or kept in control conditions (pro-differentiating medium). After that, cells received 10 nM of the GPR17 agonist galinex (GAL) or vehicle (DMSO). RNA-sequencing was performed 24 hours after Galinex treatment. N=3 samples were analyzed by RNA-Seq for each condition.

first: Juliana Helena

last: Castro e Silva

first: Davide

last: Marangon

first: Marta

last: Bocazzi

first: Stefano

last: Raffaele

first: Nicolò

last: Cignitti

first: Martina

last: Bavetta

last: Fumagalli

first: Maria Pia

last: Abbracchio

last: Lecca


title: Growth arrest of thoracic aortic aneurysms in aging Marfan mice

city: New Haven

first: Jay

last: Humphrey

state: CT

address: 55 Prospect St

department: Department of Biomedical Engineering

institute: Yale University

summary: There remains a pressing need to identify pathologic mechanisms that render a thoracic aortic aneurysm susceptible to continued enlargement, dissection, or rupture, yet additional insight can be gleaned by understanding compensatory mechanisms that limit disease progression and thereby stabilize a lesion. Our biomechanical data suggest that the ascending aorta within a common mouse model of Marfan syndrome, Fbn1C1041G/+, exhibits progressive disease from 12 weeks to 1 year of age but near growth arrest from 1 to 2 years of age. Comparison of the biomechanical phenotype, histological characteristics, and proteomic signature from 12 weeks to 1 year to 2 years plus the transcriptional profile from 12 weeks to 2 years suggests that multiple differentially expressed genes (including downregulated Ltbp3 and Rictor) and associated proteins may contribute to late-term growth arrest. Although there is a need to understand better the interconnected roles of temporal changes in differential gene expression and protein abundance, modulating TGFβ signaling and reducing mTOR signaling appears to merit increased attention in limiting aneurysmal expansion in Marfan syndrome.

overall_design: We compared gene expression and biological processes using transcriptional analyses of aortic tissue harvested from male marfan mice (Fbn1C1041G/+) at 12 weeks (n=4) and 2 years (n=4) to look at phenotypical changes of growing vs growth arrested aneurysms.

first: Colin

last: Means

first: Gavin

last: Mays

first: Nicola

last: Yeung

first: Cristina

last: Cavinato

first: Edward

last: Manning

first: TuKiet

last: Lam

middle: D

first: Dar

last: Weiss


title: The mutational landscape of STING-induced immunity

city: Lausanne

first: Andrea

last: Ablasser

address: Rte Cantonale

institute: EPFL

summary: Stimulator of interferon genes (STING) is an evolutionary conserved immune signalling protein with key roles in host defence, cancer, senescence and inflammation.STING activation leads to type I interferon (IFN), NF-κB pathway and non-canonical autophagy responses. Despite its central role in immunity and relevance as therapeutic target, the sequence elements that govern STING (in)activation in cells remain poorly understood. Here we developed a massively parallel assay to systematically chart the sequence-function landscape of STING. Profiling thousands of single amino-acid variants, we reconstructed structural and functional determinants that moderate or enable, respectively, STING’s immunostimulatory capacity and its ability to translate ligand recognition into cellular effector responses. Cryo-electron microscopy structures of distinct STING hyperactive variants revealed novel regulatory principles dictating conformational transition from inactive to signalling-competent states of STING. Collectively, these findings define the molecular principles that tune STING activity and chart the full landscape of its functional potential across immune contexts.

overall_design: We identified two noval STING gain-of-function variants, W119K/M120K and D319K/D320K. To monitor the full spectrum of transcriptional activities induced by constitutively active STING proteins in immune cell-relevant contexts, we reconstituted STING1-deficient THP-1 monocytes with WT, W119K/M120K or D319K/D320K variants and performed bulk RNA sequencing.

first: Bing

last: Zhang

first: Yu

last: Meng


title: A Conserved Natural Killer Cell Transcriptional Fingerprint in Rhesus Macaque Models of Acute Viral Infections [RNA-seq_SIVmac239]

city: Durham

first: Andrew

last: Hudson

state: NC

address: 1328 Campus Drive

department: Surgery

institute: Duke University

summary: In this study, we utilize a rhesus macaque (RM) model to define the transcriptomic profile of NK cells during acute lentiviral infection and to map the changes in this profile as infection progresses to the early chronic phase. Using a novel summary gene set for NK cell cytokine stimulation, we report synchronous metabolic and signaling transcriptional patterns that underlie established features of NK cell dysfunction. We further identify a set of core conserved gene pathways central to RM NK cell activation across diverse acute viral contexts.

overall_design: RNA-seq was performed on bulk-sorted peripheral NK cells from rhesus macaques (N=6) infected with SIVmac239 intravenously. Blood was sampled between days 0 and 14 post-infection.

first: Kyle

last: Kroll

first: Benjamin

last: Bimber

first: Brady

last: Hueber

first: Griffin

last: Woolley

first: Keith

last: Reeves


title: Ecological specialization and constrained evolution shape virulence diversity in zoonotic pathogen L. interrogans

first: Alexandre

last: Giraud-Gatineau

address: 25-28 rue du docteur roux

department: Microbiology

institute: Institut Pasteur

summary: Host specialization is central to the emergence of zoonotic pathogens, yet mechanisms shaping bacterial adaptation across diverse hosts remain poorly understood. Leptospira interrogans circulates among an exceptionally broad range of reservoirs, but only serogroup Icterohaemorrhagiae dominates the global burden of human leptospirosis, raising fundamental questions about its ecological and pathogenic success. Here, we integrate a global genomic dataset to dissect host adaptation in L. interrogans. Population genomic analyses reveal that serogroups Icterohaemorrhagiae and Pomona dominate worldwide and display signatures of ecological specialization. These serogroups have followed distinct evolutionary trajectories that are central to host specialization, characterized by extensive divergence in membrane and signaling genes, together with the acquisition of specialized functional repertoires linked to host adaptation. Transcriptomic and proteomic profiling demonstrate that these genomic differences are coupled to distinct regulatory programs, predominantly affecting virulence and stress response. Altogether, these findings demonstrate that intraspecies heterogeneity in L. interrogans emerges from the convergence of genomic constraint, membrane remodeling and regulatory divergence, shaping host specialization and zoonotic pathogenicity.

overall_design: Assessment of host responses to infection with Leptospira interrogans (serogroups Icterohaemorrhagiae or Pomona) in human and murine macrophages.

first: Mathieu

last: Picardeau


title: Response of B. thetaiotaomicron to treatment with cell-penetrating peptide (CPP) fused peptide nucleic acid (PNA) probes

city: Wuerzburg

first: Thomas

last: Guest

address: Am Hubland

country: Germany

institute: University of Wuerzburg

summary: Gram-negative, obligate anaerobic Bacteroides thetaiotaomicron is emerging as the model organism for gut microbiota research. One therapeutic aim may be to enhance its properities that are beneficial to the host. Here, we  performed conventional RNA-seq to capture changes in gene expression in response to exposure to the carrier Mk2i.

overall_design: Bacteroides thetaiotaomicron VPI-5482 (wild type) was grown in minimal medium + glucose until stationary phase and then subcultured until early exponential phase. 3 biological replicates for each untreated (H2O), and treated with 1.2 mM Mk2i. RNA was harvested 4 hours after intervention.

first: Taís

last: Franco de Carvalho


title: SARS-CoV-2 nucleocapsid induces hyperinflammation and vascular leakage through the Toll-like receptor signaling axis in macrophages

city: Los Angeles

first: Pablo

middle: Aldair

last: Alvarez

address: 615 Charles E Young Dr S

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

summary: Nearly 20% of SARS-CoV-2 infections result in ICU admission, often driven by an imbalance between antiviral responses and inflammatory signaling, leading to uncontrolled cytokine secretion. The SARS-CoV-2 nucleocapsid (N) protein is a known immune antagonist, but its role in macrophage-driven cytokine storms is unclear. We demonstrate that N functions in a stimulus-specific manner, specifically amplifying extracellular and dampening intracellular RNA sensing. Moreover, we show that this is a conserved feature of pathogenic betacoronaviruses through distinct mechanisms. Our interaction networks with SARS-CoV-2 variant N proteins suggest the Delta variant N drives inflammation through interactions with several proteins, most notably, cGAS. Profiling of secreted cytokines revealed that the N proteins disrupt the secretome in a variant-specific manner. Most notably, we found that supernatants from the Delta variant N-expressing macrophages dramatically disrupt heart endothelial barriers, implicating N in COVID-19-associated cardiac complications. Our findings highlight N-mediated immune imbalance as a driver of severe COVID-19 and identify N as a promising therapeutic target to mitigate hyperinflammation.

overall_design: There are duplicate samples of each condition. Overall there are two cell lines, with four conditions each. The two cell lines are parental THP-1 derived macrophage-like cells and THP-1 macrophage-like cells expressing the SARS-CoV-2 Wuhan-Hu-1 nucleocapsid protein. These cells were either left untreated, or treated with CL097 (to stimulate TLR7/8), poly I:C (to stimulate TLR3), or transfected with poly I:C (to stimulate RIG-I/MDA5). All cells were treated for 4 hours.

middle: A

first: Zhenlan

last: Yao

first: Melody

last: Li


title: Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [Xenium]

city: Stanford

first: Paul

last: Khavari

address: 269 Campus Dr

department: Dermatology

institute: Stanford University

summary: Stratified epithelial differentiation involves incompletely understood transcriptional and proteomic remodeling. Multi-omic profiling implicated ubiquitin and related networks in differentiation dynamics. Systematic perturbation of ubiquitin-like machinery uncovered opposite functions of NEDD8 and SUMO2. Knockout mice established essential roles for NEDD8 in progenitor maintenance, skin regeneration, and inflammation, whereas SUMO2 was required for differentiation.

overall_design: Nedd8fl/fl, Sumo2fl/fl and Nedd8fl/fl, Nrf2-/-  with or without K14-Cre (littermate controls) were treated with tamoxifen, and post recombination samples either directly or 14 days post wounding were freshly fixed and paraffin embedded. Xenium Prime spatial transcriptomics of FFPE sections

first: Carl Gustaf Marten

last: Winge

first: Leandra

middle: V

last: Jackrazi

last: Pham

first: Dayan


title: WDR82 suppresses breast cancer progression by inhibiting ERK-driven chemokine expression and neutrophil infiltration

city: Tianjin

first: qinyi

last: yu

address: 94 Weijin Road, Nankai District

institute: Nankai University, Tianjin, China

summary: Elucidating tumor-intrinsic mechanisms that drive immune evasion and shape an immunosuppressive tumor microenvironment (TME) is essential for overcoming resistance to cancer immunotherapy and developing novel therapeutic strategies. WDR82, a member of the WD-40 protein family, exhibits context-dependent regulation of cancer, yet its role in breast cancer and its influence on the immunosuppressive TME remain undefined. Here we identify WDR82 as a critical tumor suppressor that governs immune surveillance by restraining the ERK–chemokine–neutrophil axis. WDR82 expression is downregulated in human breast cancer and correlates with poor prognosis.Using orthotopic models, we uncover a functional paradox: while Wdr82 deficiency suppresses tumor cell proliferation in vitro, it accelerates tumor growth in vivo exclusively in immunocompetent hosts, driving enhanced neutrophil infiltration and CD8⁺ T cell exhaustion. Mechanistically, WDR82 directly binds MEK1/2, disrupting c-RAF-MEK assembly and restraining ERK activation. Loss of Wdr82 relieves this inhibition, driving ERK-dependent production of CXCL2 and CXCL7, the key neutrophil chemoattractants that promote CXCR2-mediated recruitment. Neutrophil depletion abolishes the tumor-promoting effect of Wdr82 deficiency, confirming the functional dependency on this axis. Importantly, intratumoral delivery of WDR82-expressing adenovirus reverses neutrophil accumulation, alleviates T cell exhaustion, and suppresses tumor progression. Our findings uncover a previously unrecognized mechanism by which WDR82 links tumor-intrinsic signaling to TME remodeling, establishing a promising therapeutic strategy for breast cancer through targeting the ERK–chemokine–neutrophil axis.

overall_design: WDR82 knockout 4T1 cells or Control 4T1 cells were collected and washed with cooled PBS, the cells were then suspended in TRIZOL and ready for process.


title: Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [RNA-Seq]

summary: Stratified epithelial differentiation involves incompletely understood transcriptional and proteomic remodeling. Multi-omic profiling implicated ubiquitin and related networks in differentiation dynamics. Systematic perturbation of ubiquitin-like machinery uncovered opposite functions of NEDD8 and SUMO2. Knockout mice established essential roles for NEDD8 in progenitor maintenance, skin regeneration, and inflammation, whereas SUMO2 was required for differentiation. Beyond ubiquitin-proteasome-concordant changes, NEDD8 directed proteomic regulation correlated with RNA abundance. Integration of IP-MS with genome-wide suppressor screening revealed context-specific NEDDylated dependencies. Among effectors, HNRNPU emerged as a post-transcriptional regulator of epithelial cell state, whose binding repertoire was modulated by NEDDylation, linking NEDD8 induced proteomic remodeling to RNA regulation. Together, these findings define opposite roles for NEDD8 and SUMO2 in orchestrating epithelial homeostasis, regeneration, and inflammation, underscoring how ubiquitin-like networks govern tissue fate.

overall_design: SCC cell lines (CAL27, A431) were treated with DMSO or NEDD8i for 16hrs


title: Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [RNA-Seq mouse]

overall_design: Wild type mice were treated with topical NEDD8i or DMSO on the dorsal skin for 3 days


title: Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation

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

overall_design: Refer to individual Series