title: RNA binding protein YWHAZ mediates translation of specific mRNA and regulates cell Proliferation and apoptosis in diabetic foot ulcer

city: Urumqi

first: jie

last: wang

address: 152 Longquan Street, Tianshan District, Urumqi, Xinjiang Uygur Autonomous Region, China

institute: People’s Hospital of Xinjiang Uygur Autonomous Region

summary: YWHAZ was a significantly up-regulated and validated RBP in DFU by RT-qPCR and immunohistochemistry. Cellular experiments revealed that Si_YWHAZ facilitated proliferation and migration while inhibiting apoptosis, consistent with its upregulation in DFU. RNA-seq identified 1072 DEGs in Si_YWHAZ cells. Up-regulated genes were significantly enriched in cell proliferation-related processes and included AREG, FOSL1, HAS2 and IL7R, whereas down-regulated genes were associated with cell adhesion, such as LAMB3, SLAMF7, COL12A1 and ITGA5. IRIP-seq results demonstrated that YWHAZ interacts with plentiful of mRNAs and genomic location toward the CD and introns region. As well, ABLIFE algorithm indicated that YWHAZ bound to GC-rich motifs. Integrated iRIP-seq and RNA-seq analyses identified 57 DEGs that were selectively bound by YWHAZ, most of which were down-regulated. Notably, SREBF1, which was positively associated with type 2 diabetes risk. KEGG pathway analysis revealed SREBF1 is enriched in insulin resistance and insulin signaling pathway

overall_design: In our study, we hypothesized that YWHAZ, as a critical RBP, is dysregulated in non-healing DFU and contributes to impaired keratinocyte function under high-glucose conditions via specific post-transcriptional regulatory networks. To verify this, we employed RNA-seq analysis and found that YWHAZ was highly expressed in the ulcerated skin tissues of patients with non-healing DFU. RT-qPCR and immunohistochemistry results showed that YWHAZ was up-regulated in non-healing diabetic foot ulcer tissues. Then, we adopted high-glucose model combined with RNA-seq and improved RNA immunoprecipitation and sequencing (iRIP-seq) to explore the binding mode of YWHAZ in DFU. These findings provide valuable insights into DFU pathogenesis and pave the way for identifying novel diagnostic markers and therapeutic targets.


title: Intermittent Fasting Rewires Tissue-Specific Gene-Transposable Element Regulatory Networks

status: Public on Jul 29 2026

city: Melbourne

first: Xiangru

last: Cheng

state: VIC

address: Plenty Rd

department: LIMS

country: Australia

institute: La Trobe University

type: Expression profiling by high throughput sequencing

summary: Intermittent fasting (IF) is a dietary intervention known to promote systemic health benefits, yet its impact on genome-wide transcriptional regulatory networks, particularly those involving transposable elements (TEs), remains poorly understood. This study investigates the multi-tissue transcriptomic response to chronic IF in mice, focusing on TE regulation and its integration with host gene networks. We subjected C57BL/6 mice to 16 hours of daily fasting for four months and performed RNA sequencing on liver, skeletal muscle, and cortex tissues. Using locus-specific TE quantification, we found that IF induces profound, tissue-specific changes in TE expression, with the liver showing the strongest response (5,359 differentially expressed TEs), followed by skeletal muscle (620), while minimal changes were observed in the cortex. Integrated co-expression network analysis (WGCNA) in liver and muscle revealed IF-responsive TEs that co-vary with nearby genes, forming distinct co-expression modules. Functional enrichment of genes proximal to co-expressed TEs within these modules highlighted clear tissue-specific regulatory programs. In the liver, the enriched terms were predominantly associated with translation and metabolism, whereas in skeletal muscle, the enriched pathways were involved in muscle contraction, mitochondrial organization, and chromatin modification. Furthermore, correlation analysis revealed strong, significant co-expression between TEs and their proximal genes within these modules, suggesting that TEs may exert potential cis-regulatory effects on adjacent genes. Taken together, our results provide a high‑resolution atlas of TE regulation under IF and demonstrate that TEs are integral components of tissue‑specific transcriptional networks reshaped by fasting. These findings offer new insights into how dietary interventions influence gene regulatory systems.

relation:
Reanalysis of: GSM8808701
Reanalysis of: GSM8808702
Reanalysis of: GSM8808703
Reanalysis of: GSM8808704
Reanalysis of: GSM8808705
Reanalysis of: GSM8808706
Reanalysis of: GSM8808707
Reanalysis of: GSM8808708
Reanalysis of: GSM8808709
Reanalysis of: GSM8808710
Reanalysis of: GSM8808711
Reanalysis of: GSM8808712
Reanalysis of: GSM8808713
Reanalysis of: GSM8808714
Reanalysis of: GSM8808715
Reanalysis of: GSM8808716
Reanalysis of: GSM8808733
Reanalysis of: GSM8808734
Reanalysis of: GSM8808735
Reanalysis of: GSM8808736
Reanalysis of: GSM8808737
Reanalysis of: GSM8808738
Reanalysis of: GSM8808739
Reanalysis of: GSM8808740
Reanalysis of: GSM8808741
Reanalysis of: GSM8808742
Reanalysis of: GSM8808743
Reanalysis of: GSM8808744
Reanalysis of: GSM8808745
Reanalysis of: GSM8808746
Reanalysis of: GSM8808747
Reanalysis of: GSM8808748
Reanalysis of: GSM8808765
Reanalysis of: GSM8808766
Reanalysis of: GSM8808767
Reanalysis of: GSM8808768
Reanalysis of: GSM8808769
Reanalysis of: GSM8808770
Reanalysis of: GSM8808771
Reanalysis of: GSM8808772
Reanalysis of: GSM8808773
Reanalysis of: GSM8808774
Reanalysis of: GSM8808775
Reanalysis of: GSM8808776
Reanalysis of: GSM8808777
Reanalysis of: GSM8808778
Reanalysis of: GSM8808779
Reanalysis of: GSM8808780

overall_design:
The 48 GSM accession numbers from GSE290224 were analyzed in this study. These comprise 16 samples per tissue (cortex, liver, and muscle). To profile transposable element expression, we utilized SQuIRE, a pipeline that integrates reference genome retrieval, read alignment, TE annotation, and quantitative TE expression analysis. The resulting count tables are available as Squire_Cortex_gene_TE_counttable.txt, Squire_Liver_gene_TE_counttable.txt, and Squire_Muscle_gene_TE_counttable.txt.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Yibo

last: Fan

first: Xiangyuan

last: Peng

first: Thiruma

middle: V

last: Arumugam


title: Colonic epithelial regeneration shapes susceptibility to Clostridioides difficile infection

city: Boston

first: Carol

middle: A

last: Kumamoto

state: MA

address: 150 Harrison Ave.

department: Department of Molecular Biology and Microbiology

country: USA

institute: Tufts University

summary: Clostridioides difficile infection (CDI) susceptibility and severity are strongly associated with preexisting colonic inflammation. However, chronic inflammatory conditions such as cystic fibrosis rarely progress to symptomatic CDI despite high rates of C. difficile colonization, suggesting that inflammation alone is insufficient to explain disease vulnerability. Notably, populations relatively protected from symptomatic CDI exhibit impaired regenerative capacity within the colon epithelium. Here, we used single cell RNA sequencing of human colonoid monolayers to map markers of CDI susceptibility and severity to cell populations associated with inflammation and epithelial repair. We identified an inducible microfold-like (M-like) population that is largely absent from the healthy colon but emerges during inflammation and regeneration. These cells were enriched for markers of severe CDI, C. difficile toxin interaction genes, and elevated CCL20 and CFTR expression. Spatial imaging localized CCL20-producing cells to wound-like gaps in mock and CDI-treated colonoids, identifying a repair-associated niche active independent of infection. Following exposure to C. difficile, wound-healing transcription within the M-like lineage declined while tuft-like populations expanded and upregulated genes associated with immune cell recruitment. These findings demonstrate that epithelial regeneration shapes host CDI vulnerability.

sample_organism:
Clostridioides difficile
Homo sapiens

platform_organism:
Clostridioides difficile
Homo sapiens

overall_design:
We used antibiotic-treated human colonoid monolayers that recapitulate key features of the mature colonic epithelium to examine early cellular responses to C. difficile infection. To map signatures of CDI vulnerability and severity to epithelial subtypes, we performed single-cell RNA sequencing (scRNA-seq) on monolayers collected 4, 15, and 25 hours following mock-treatment (“Mock”) or C. difficile inoculation (“C. difficile-infected”).GSM9661693, GSM9661694, GSM9661695, GSM9661696, the 15h timepoints were previously published, but reanalyzed here for this scRNA-seq time series study.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Adrianne

middle: D

last: Gladden

first: Paola

last: Zucchi

first: Albert

last: Tai

first: Rebecca

last: Batorsky


title: The immune landscape of the post–cardiac arrest brain in young and aged mice

city: Durham

first: Vaibhav

last: Jain

state: North Carolina

address: 300 N Duke St

department: Duke Molecular Physiology Institute

institute: Duke University

summary: The objective of the current study was to profile immune cells in the post-cardiac arrest brain of young and aged mice at single-cell resolution.

overall_design: Both young (3-6 months old) and aged (18-20 months old) C57Bl/6 mice were subjected to sham or cardiac arrest (CA) and resuscitation. On day 3 after CA, we sorted CD45 positive cells stroke for scRNA-seq analysis. Four samples were analyzed: Young_sham, Young_CA, Aged_sham, and Aged_CA  (Y_Sham, Y_CA, A_Sham, A_CA). Each sample were pooled from 3 mice.

first: Wei

last: Yang

first: Ran

last: Zhang

first: Lihong

last: Dang


title: Integrated Analysis of Granulosa Cells and Extracellular Vesicles Reveals Predictive Biomarkers of Oocyte Maturation in the Southern White Rhinoceros

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

type: Non-coding RNA profiling by high throughput sequencing

summary: Assisted reproductive technologies (ARTs) are an imperative conservation tool to rescue species from extinction. An essential step towards technological advancement and ARTs’ success is identifying optimal in vitro culture conditions to mature oocytes, carry out fertilization, and culture embryos for future transfer. The role of extracellular vesicles (EVs) and granulosa cells (GC) in follicular development, oocyte maturation, and fertilization has been extensively studied for decades in human and domestic species models. This study aimed to characterize transcriptomic differences in GC and evaluate the communication between EVs in the follicular fluid and GC miRNA cargo between oocytes that matured (PB) and those that did not mature (NoPB) after in vitro culture. Overall, in GC, 1,117 transcripts (annotated and unannotated) were differentially expressed between groups. In the miRNA from the GC, 11 were differentially expressed between groups, all higher in the PB group. For the miRNA in follicular fluid EVs, there were 15 miRNA differentially expressed. When comparing targets of the miRNA identified to the differentially expressed genes, multiple genes were being targeted and affected. These miRNA and genes are potential targets for further investigation to be used for support during in vitro maturation or to develop markers for an oocytes potential to mature during in vitro maturation.  In conclusion, extracellular vesicle–mediated molecular signaling during folliculogenesis in the SWR may offer critical insights into physiological and pathological reproductive conditions that contribute to abnormal fertility, ultimately informing the development of novel reproductive strategies to enhance ART outcomes in this species and others.

overall_design: miRNASeq of granulosa cells and extracellular vesicles from follicular fluid. Samples 1-6 are the miRNA isolated from granulosa cells. Samples 7-14 are the miRNA isolated from the extracellular vesicles in the follicular fluid. The GC and EV cames from follicles with ooyctes that did and did not mature by extruding a polar body after in vitro maturation.

first: Kristin

last: Klohonatz

first: Nico

middle: G

last: Menjivar

first: Dawit

last: Tesfaye

first: Elena

last: Ruggeri


title: Transcriptomic Profiling of the Liver during Citrobacter rodentium Infection

first: Yuko

last: Hasegawa

address: 181 Longwood Ave.

institute: Brigham and Women's Hospital

summary: To determine the role of the liver in coordinating systemic immune responses to enteric infection, matched measurements of global gene expression profiles were collected from the murine liver and intestinal epithelium throughout the course of enteric infection and clearance of Citrobacter rodentium, a mouse model of infectious colitis

overall_design: Time-course RNA-seq profiling of mouse liver and colon epithelial after Citrobacter rodentium infection

first: Akina

last: Osaki

first: Masataka

last: Suzuki

first: Ian

last: Campbell

first: Matthew

middle: K

last: Waldor


title: Bulk RNA-seq of mouse brain following closed head injury: role of IL-1R1 signaling

city: Lexington

first: Joshua

middle: M

last: Morganti

state: KY

address: 789 S. Limestone St

department: Sanders-Brown Center on Aging

institute: University of Kentucky

summary: Bulk RNA-seq was performed on brain tissue from mice following closed head injury (CHI) or sham surgery at 9h, 24h, and 72h post-injury. Four genotypes were studied: C57BL/6J wild-type, IL-1R1 global knockout (gKO), IL-1R1 endothelial restore (eRestore), and IL-1R1 neuronal restore (nRestore) to dissect cell-type specific IL-1R1 signaling contributions to the transcriptomic response to traumatic brain injury.

overall_design: 200 samples total. Mouse brain tissue collected from 4 genotypes (C57BL/6J, IL-1R1 gKO, IL-1R1 eRestore, IL-1R1 nRestore) x 2 conditions (CHI, sham) x 3 timepoints (9h, 24h, 72h) x 2 sexes (M, F) with biological replicates. Paired-end 150bp sequencing on Illumina NovaSeq X Plus.

first: Bachstetter

last: Adam

first: Morganti

last: Josh


title: UBTD1 Drives Ovarian Cancer Progression and Chemoresistance via the TNF/AP-1 Signaling Axis

city: Shanghai

first: Cuiping

address: No. 168 Wanghe Road, Fengxian District, Shanghai, China Welfare Association International Peace Maternity and Child Health Hospital, Fengxian Campus

department: Central Laboratory

country: China

summary: The ubiquitin domain-containing protein 1 (UBTD1), a protein involved in degradation and cell cycle regulation, is gaining recognition for its role in tumorigenesis. Ovarian cancer (OC) is the deadliest gynecological cancer, characterized by poor prognosis due to aggressive growth and chemoresistance. This study investigates the role of UBTD1 in OC pathogenesis. UBTD1 expression and prognosis were analyzed using public databases such as the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). UBTD1 was knocked down via Short hairpin RNA (shRNA) in A2780 and SKOV3 cells. Functional impacts on proliferation, migration, cell cycle, and apoptosis were assessed. RNA sequencing and Quantitative reverse transcription polymerase chain reaction (qRT-PCR) were used to investigate downstream pathways. UBTD1 is markedly overexpressed in OC and correlates with reduced survival. Its knockdown suppressed proliferation, migration, and invasion, induced G0/G1 arrest (upregulating p21, downregulating Cyclin D1), and enhanced cisplatin sensitivity. Transcriptome analysis revealed downregulation of the tumor necrosis factor (TNF) pathway and activator protein-1 (AP-1) factors FOS/FOSB. Ectopic FOS expression rescued the malignant phenotypes. UBTD1 drives OC progression and chemoresistance, potentially through the TNF/AP-1 axis, emerging as a prognostic biomarker and therapeutic target.

overall_design: RNA-seq analysis of 9 samples from three experimental groups (Vec, UB-sh1, UB-sh2), with three biological replicates per group.

first: Aixin

last: Liu

first: Yanxia

last: Chen


title: iCLIP3: A streamlined, non-radioactive protocol for mapping protein-RNA interactions in cellular transcripts at single-nucleotide resolution

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt

summary: UV-C crosslinking and immunoprecipitation (CLIP)–based methods are the gold standard for identifying direct RNA binding protein (RBP) interaction sites on cellular RNA in vivo. Here, we describe individual-nucleotide resolution CLIP version 3 (iCLIP3), an optimized protocol for generating transcriptome-wide maps of RBP–RNA interaction sites at single-nucleotide resolution from low-input material. iCLIP3 introduces several key improvements over previous iCLIP variants, including rapid and safe infrared-based visualization of RBP–RNA complexes, silica column-based RNA isolation, and the incorporation of TruSeq adapter sequences with unique dual indexing. These modifications streamline library preparation, facilitate multiplexing, and enable concurrent sequencing of iCLIP3 libraries alongside unrelated RNA-seq libraries. In addition, we provide a detailed bioinformatics workflow for identifying crosslinking events and defining RBP binding sites. The complete protocol can be performed within 4–5 days, offering a robust and efficient approach for high-resolution mapping of RBP–RNA interactions.

overall_design: iCLIP3 of U2AF2 using endogenous antibodies and different protein concentrations from HeLa cells

first: Vladimir

last: Despic

first: Kathi

last: Zarnack

first: Melina

last: Klostermann

first: Anke

last: Busch

first: Julian

last: König


title: Hippocampal small RNAs from patients with schizophrenia induce specific cognitive and neural phenotypes in mice [human]

city: Barcelona

first: Marcos

last: Galán-Ganga

address: C/ Casanova, 143.

department: Biomedicine

country: Spain

institute: University of Barcelona

summary: Schizophrenia is a neuropsychiatric syndrome characterized by the presence of psychotic, negative and cognitive symptoms. Cognitive deficits can appear even before the onset of the first psychotic episode and their severity has been recently associated with altered levels of small RNAs (sRNAs), including microRNAs. Nevertheless, how the dysregulation of sRNAs can lead to cognitive impairments and their role in the onset and pathophysiology of the disorder are still unknown. In our research, we hypothesized that hippocampal sRNAs generated in patients with schizophrenia could contribute to the impairment of specific cognitive domains that are altered in the disease. Through deep sequencing, we identified novel dysregulated sRNAs (including microRNAs and tRNA derived fragments) in the hippocampus of patients with schizophrenia. Furthermore, when injected in the hippocampus of wild-type mice, animals exhibited an impairment in spatial short-term memory accompanied by a reduction in spine density of CA1 pyramidal neurons. RNA-sequencing of the hippocampus of injected mice revealed changes in key pathways related to neurotransmission. Specifically, we found higher levels of the presynaptic marker for Parvalbumin interneurons synaptotagmin II (Syt2), mirroring observations made in the brain of schizophrenia patients. We also detected subtle morphological changes in mouse hippocampal microglia in response to sRNAs from affected individuals. Our results point out that sRNAs can contribute to cognitive symptoms in schizophrenia through synaptic alterations, highlighting these molecules as promising novel therapeutic targets for the disorder.

overall_design: Small RNA-seq profiling of sRNA samples extracted from postmortem human hippocampal tissue. Experimental groups included non-affected control individuals and patients with schizophrenia. sRNAs from patients were pooled to create comparable groups, and all samples passed quality control prior to sequencing.

first: Anna

last: Guisado-Corcoll

last: Sancho-Balsells

first: Marina

last: Herrero-Lorenzo

first: Ivan

last: Ballasch

first: Lisa

last: Patterer

first: Jordi

last: Alberch

first: Belén

last: Arranz

first: Albert

last: Giralt

first: Eulàlia

last: Martí


title: Social hierarchy shapes behavioral and transcriptional responses to chronic stress and ketamine in male mice

city: Solna

first: Serena

last: Gasperoni

address: Solnavägen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Chronic stress is a major risk factor for psychiatric disorders, yet the mechanisms underlying individual variability in stress vulnerability and treatment response remain poorly understood. Here, we combined a novel behavioral phenotyping system with high-throughput gene expression profiling to examine how chronic stress and ketamine treatment interact over time. Bulk RNA sequencing was performed in the medial prefrontal cortex and ventral hippocampus, revealing a hierarchy-dependent transcriptional response with 141 differentially expressed genes in the medial prefrontal cortex of dominant, ketamine-treated mice, enriched in synaptic and postsynaptic compartments. These findings identify synaptic remodeling as a substrate for ketamine’s sustained antidepressant effects and underscore social rank as a critical factor when dissecting molecular responses to stress and treatment.

overall_design: RNA-seq profiling of mPFC and vHipp of male mice following chronic social defeat stress and ketamine administration


title: Post Kala Azar Dermal Leishmaniasis (PKDL) genome wide transcriptional profiling by bulk RNA-sequencing

city: Kolkata

first: Mitali

last: Chatterjee

state: West Bengal

address: 244B, AJC Bose Road

department: Pharmacology

country: India

institute: Institute of Post Graduate Medical Education & Research, Kolkata

summary: Post-kala-azar dermal leishmaniasis (PKDL), a dermal sequel of visceral leishmaniasis (VL), is considered an important reservoir that facilitates the transmission of VL. Although PKDL lesions demonstrate an overwhelming infiltration of CD8⁺ T cells, the molecular mechanisms regulating their recruitment to the skin remain poorly defined. To address this, bulk RNA sequencing was performed on dermal lesions from patients withPKDL and healthy controls to characterize the lesional chemokine and cytokine landscape associated with T-cell homing.Transcriptomic analysis revealed a significant upregulation of genes encoding T-cell chemoattractants, including CCL3, CCL4, CCL5, CCL17, CXCL9, and CXCL10, in PKDL lesions compared to healthy skin. In addition, sequencing data demonstrated increased expression of inflammatory cytokine transcripts such as IFN-γ, IL-5, IL-15, and TNF-α, indicating an activated inflammatory milieu. The transcriptomic profile further showed elevated expression of genes associated with chemokine receptor pathways, particularly CCR4, CCR5, and CXCR3, suggesting enhanced signaling pathways that promote CD8+ T cell migration from circulation and retention within lesional skin. Collectively, the RNA sequencing data highlights a chemokine-driven CD8+T cell recruitment and contributes to  characterise the molecular markers related to the homing of lesional CD8+ T cells.

overall_design: Bulk RNA sequencing of dermal biopsies sourced from four patients with PKDL and three unrelated healthy individuals.

first: Raghunath

first: Shriya

last: Saha

first: Deep

last: Goswami

first: Saikat

last: Karuri

first: Soham


title: KDM8 acts as a co-regulator of transcription factor SOX2 for promoting cell pluripotency [ChIP-Seq]

city: changchun

first: songqin

last: yang

address: No. 5625, Renmin Street

institute: Changchun Institute of Applied Chemistry

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Since their discovery, iPSCs have drawn significant attention for their biomedical potential, yet reprogramming remains inefficient and the underlying mechanisms are incompletely defined. KDM8, a histone demethylase, is known to play critical roles in processes such as cell-cycle regulation and embryonic development; nevertheless, its function in reprogramming has not been reported. Here, we investigate the role of KDM8 in reprogramming. Our results demonstrate that KDM8 significantly enhances the reprogramming efficiency mediated by the canonical Yamanaka factors (OCT4, SOX2, KLF4 and MYC). Remarkably, KDM8, in combination with OCT4 alone, is sufficient to reprogram somatic cells. Further analyses reveal that KDM8 facilitates reprogramming through a dual regulatory mechanism. On the one hand, KDM8 leverages its canonical enzymatic activity to reduce the epigenetic barriers to iPSC formation. More importantly, KDM8 functions as a co-regulator of the transcription factor SOX2, modulating SOX2's DNA-binding affinity and transcriptional regulation of downstream target genes, thereby substantially promoting cellular pluripotency. Accordingly, we propose a novel regulatory framework that uncovers novel mechanisms and functions of KDM8 in cellular reprogramming.

overall_design: KDM8 ChIP-seq conducted on Day 8 post-lentiviral transduction in: Human Dermal Fibroblast (HDF) cells overexpressing OCT4 and KDM8. Human Dermal Fibroblast (HDF) cells overexpressing OCT4 and KDM8 with concomitant SOX2 knockdown (shSOX2).

first: Songqin

last: Yang

first: Zhikai

last: Ye

first: Lu

last: Lin

first: Zhenlong

last: Jiang

first: Erkang

last: Wang

first: Jin


title: KDM8 acts as a co-regulator of transcription factor SOX2 for promoting cell pluripotency

overall_design: RNA-seq of HDF cells overexpressing EGFP and HDF cells overexpressing KDM8 (EGFP and KDM8) on day 5 of lentivirus transduction


title: Novel hydrophobic tag degraders overcome endocrine-resistant breast cancer by recruiting HSP27-mediated E3 ligase complex for ERα proteasomal degradation

city: wuhan

first: song

last: zemin

address: no.185 the road of eastlake

institute: wuhan university

summary: Hydrophobic tag (HyT)-mediated protein degradation has emerged as a pivotal tool for targeted protein degradation (TPD), yet its underlying degradation mechanism remains incompletely elucidated. Herein, we designed structurally optimized HyT-based degraders by covalently conjugating hydrophobic amino acid tags to ERα-targeting ligands via alkane linkers of varying lengths, identifying the lead compound VI-10h. VI-10h exhibited potent antiproliferative activity and efficient ERα degradation in endocrine-resistant breast cancer cells (LCC2, MCF-7D538G, MCF-7Y537S, and MCF-7EGFR) and superior antitumor activity compared to the clinical drug fulvestrant (Ful) in MCF-7 and tamoxifen-resistant LCC2 xenograft models. To elucidate the HyT-mediated degradation mechanism, we synthesized biotin-conjugated HyTs (biotin-Lys and biotin-Trp) and performed pull-down assays combined with mass spectrometry. Our results unveiled that VI-10h selectively recruits HSP27 as a novel atypical E3 ligase adaptor protein, forms an ERα-HSP27-RING1 ternary complex to promote ERα degradation, disrupts estrogen-dependent oncogenic networks, and circumvents the drug resistance associated with conventional CRBN- or VHL-dependent E3 ligase-recruiting degraders. This study validates HyT technology’s degradation mechanism and feasibility in reversing resistance to conventional E3 ligases and overcoming endocrine-resistant breast cancer, establishing a molecular design strategy for next-generation targeted degraders that reverse endocrine resistance.

overall_design: MCF7 cells were treated with DMSO, VI-10H, and VI-10J, followed by RNA sequencing to determine the transcriptional profiles induced by the different drug treatments.


title: Persistence of mucosal CAR-T cells and inflammatory remodeling in enterocolitis associated with BCMA CAR-T cell therapy

city: New York

first: Saurabh

last: Mehandru

state: New York

address: 1425 Madison Avenue

institute: Icahn School of Medicine

summary: B cell-targeted therapies are expanding across oncologic and autoimmune indications, yet their consequences for immunity remain incompletely examined. Here, we define the mucosal pathophysiology of ciltacabtagene autoleucel CAR-T cell-induced enterocolitis (CAR-TEC), a severe complication of B cell maturation antigen (BCMA)-targeted CAR-T cell therapy in multiple myeloma. Using single-cell transcriptomics, flow cytometry, and tissue imaging of intestinal biopsies from patients with CAR-TEC (n=10), CAR-T cell treated controls (CAR-TCTRL) without enterocolitis (n=7), and healthy volunteers (n=26), we identify profound depletion of mucosal B cells and plasma cells (PCs) accompanied by expansion of highly cytotoxic CAR-T cells and inflammatory myeloid, stromal, and glial cell remodeling to be associated with CAR-TEC. Cell-cell communication analyses suggest a compensated mucosal state in CAR-TCTRL, while telocyte-driven stromal niche dysfunction was noted in CAR-TEC. Interferon and JAK-STAT-associated reprogramming was noted across stromal, endothelial, and epithelial compartments, supporting JAK inhibition as a rational, mechanism-based therapeutic strategy. Upadacitinib, an oral selective JAK1 inhibitor resulted in clinical, endoscopic and histologic improvement in 2 individuals with CAR-TEC. Our findings define CAR-TEC as a multi-compartment syndrome of severe mucosal dysregulation with implications for the emerging field of B cell-targeted therapies.

overall_design: Lamina propria (LP) mononuclear cells were isolated from fresh intestinal biopsies (left colon) from 23 patients (NV = 11, CAR-TCTRL = 5, CAR-TEC = 7) by dissociating them to generate single-cell suspensions after epithelial layer removal and enzymatic digestion, and dead cells were removed using a Dead Cell Removal Kit (Miltenyi Biotec, catalog no. 130-090-101). Single-cell suspensions subjected to scRNA-seq and analyzed.

first: Nikhit

last: Kethidi

first: Saumya

last: Pothukuchi

first: Pablo

last: Canales-Herrerias

first: Samir

last: Parekh


title: KDM8 acts as a co-regulator of transcription factor SOX2 for promoting cell pluripotency [RNA-Seq]

overall_design: RNA-seq of HDF cells overexpressing OCT4+EGFP and HDF cells overexpressing OCT4+KDM8 (O-EGFP and O-KDM8) on day 5 of lentivirus transduction


title: Thioredoxin interacting protein (TXNIP), a redox regulator, mediates the EPAC-RAP1 signaling dependency of primary melanoma

city: Madison

first: Sireesh Kumar

last: Teertam

state: WI

address: 1111 Highland Ave

department: Dermatology

institute: UW-Madison

summary: RAP guanine exchange factors EPAC1/2 (Exchange Protein Activated by cyclic AMP) are important signaling proteins. EPACs are important for the growth of cutaneous primary melanoma and loss of dependency on EPACs is associated with melanoma metastatic progression. In this study, employing transformed human melanocytes, we show that activation of EPACs is an early event in malignant transformation, and using chemical inhibition and genetic deletion of EPAC in Braf/Pten mice, we also show that EPACs promote melanoma tumor development and growth.   Query of the Cancer Genome Atlas (TCGA) and immunohistochemical analysis of melanoma tumors showed that low EPAC mRNA and RAP1-GTP protein correlate with better recurrence free survival of patients with primary melanoma. RNAseq analysis of primary and metastatic melanoma cells treated with an EPAC inhibitor showed that TXNIP, an important regulator of redox homeostasis, is a downstream effector of EPAC signaling. We also show that EPACs promote melanoma growth by regulation of redox homeostasis and mitochondrial ROS through activation of mechanistic target of rapamycin complex 1 (mTORC1) that stabilizes hypoxia-inducible factor 1-alpha (HIF-1α), a transcriptional activator of TXNIP and glycolytic enzymes. Our data suggest that targeting mechanisms employed by melanoma cells to bypass EPAC dependency as a potential therapeutic approach for melanoma.

overall_design: Performed bulk RNA-seq analysis on patient-matched primary (WM115) and lymph node-metastatic melanoma (LN-met) cells (WM239, WM266, and WM165) treated with EPACi (ESI-09). Performed differential gene expression (DEG) analysis to show gene expression changes induced by EPACi post 6h & 12h treatment.

first: Mithalesh K

last: Singh

first: Sarah

last: Altameemi

first: Sonia

last: Gude

first: Sushmita

last: Roy

first: Ryan

last: Rossman

first: Michael

last: Newton

first: Daniel

last: Bennett

first: Nihal

last: Ahmad

first: Xiaodong

last: Cheng

first: Vijayasaradhi

last: Setaluri


title: An Integrated Multi-omic Analysis Reveals Novel Gene-Metabolite Relationships in Human Steatohepatitic Hepatocellular Carcinoma

first: Robert

middle: N

last: Helsley

address: 741 S. Limestone St.

department: Intern

summary: Background Metabolic dysfunction-associated steatotic liver disease (MASLD) is the fastest-growing etiology of hepatocellular carcinoma (HCC). A mechanistic understanding of the metabolic heterogeneity of MASLD-driven tumors is crucial to inform strategies for future treatment options.  Methods Paired tumor (n=8) and adjacent non-tumor tissue (n=8) were collected from patients with steatohepatitic HCC at the University of Kentucky Markey Cancer Center. Hematoxylin and eosin (H&E) staining was used for pathological determination of tumor and adjacent nontumor tissue by a board-certified pathologist. Lipidomic, metabolomic, and transcriptomic analyses were performed, and data were integrated across platforms to identify novel relationships across tumor and adjacent nontumor tissue.  Results Histological analysis by H&E showed significant lipid vacuole accumulation and inflammatory foci in HCC tumors relative to nontumor tissue. Across omics platforms, we identified 1,679 genes, 1,696 metabolites, and 292 lipids that were significantly (padj<0.01) increased or decreased in tumors relative to nontumor tissue. We identified significant reductions in total ceramides and increases in fatty acyl chain saturation in tumor tissue. Furthermore, metabolites involved in amino acid and fatty acid metabolism were largely decreased in tumors relative to nontumor tissue. We also identified a total of 303 highly significant and novel transcript-metabolite associations (117 gene-metabolite; 186 gene-lipid) across tumor and nontumor tissue.  Conclusions Taken together, this integrative analysis reveals novel relationships between steady-state gene transcripts and specific metabolites in steatohepatitic tumors, thereby identifying new pharmacological targets that may be exploited for therapeutic benefit.

overall_design: We performed bulk RNA-sequencing on tumor and adjacent nontumor tissue from patients with primary HCC.

first: Garrett B.

last: Anspach

first: Robert M.

last: Flight

first: Sehyung

last: Park

first: Hunter N.B.

last: Moseley

first: Robert N.


title: Lipotoxic fingerprints in clinically relevant postoperative pancreatic fistula

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: This study investigates lipotoxic stress responses induced by postoperative pancreatic fistula (CR-POPF) effluents in non-malignant stromal cell types relevant for anastomotic healing. Postoperative drain effluents from patients undergoing pancreatoduodenectomy were characterized by gas chromatography–mass spectrometry to identify lipolysis-derived lipid species. Based on functional cytotoxicity screening, two CR-POPF effluents with reproducible biological effects were selected for transcriptomic profiling. Primary human peritoneal mesothelial cell preparations and human foreskin fibroblasts were exposed in vitro to patient-derived effluents, a defined lipolysis-derived lipid (monopalmitin), or medium control. RNA sequencing was performed to characterize stimulus-specific transcriptional stress responses. The dataset enables comparative analysis of metabolic, inflammatory, and stress-associated gene expression programs induced by distinct lipolytic stimuli in stromal and mesothelial cells.

overall_design: This is an in vitro transcriptomic study examining cellular responses to lipolysis-derived postoperative pancreatic effluents. Primary human peritoneal mesothelial cell preparations (n = 5) and a human foreskin fibroblast cell line were exposed for 24 hours to one of four conditions: medium control, CR-POPF effluent AES1448, CR-POPF effluent GR1479, or the defined lipolysis-derived lipid monopalmitin (0.2 mM). Effluents were selected based on prior metabolomic profiling and functional viability screening. For each cell type and condition, three biological replicates were generated. RNA was isolated from all samples and subjected to stranded mRNA sequencing. The experimental variables include stimulus type (effluent vs. lipid vs. control) and cell source, enabling comparative analysis of stimulus-specific transcriptional stress and metabolic response programs.

first: Johannes

last: Lettner

first: Melanie

last: Boerries

first: Dietrich

last: Ruess


title: ZNF469 promotes human lung fibrosis via transcriptionally regulating extracellular matrix genes

city: Bangkok

first: Thammachanok

last: Boonto

address: 254 Phaya Thai Rd, Khwaeng Wang Mai, Pathum Wan

department: Biochemistry

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

summary: Pulmonary fibrosis (PF) is a chronic lung disease defined by excessive deposition of extracellular matrix (ECM) components, leading to remodeling of lung structural architerture and impaired repiratory function. Chronically activated resident fibroblasts are considered one of major cellular source of aberrant ECM accumulation; however, their precise cellular origins and the initiating events that drive their persistent activation remain incompletely understood. Emerging evidence has identified zinc finger protein 469 (ZNF469) as a novel pro-fibrotic transcription factor in hepatic stellate cells and dermal fibroblasts, where it drives ECM gene expression and fibrogenic remodeling, suggesting a potentially conserved role across fibrotic tissues. With short hairpin-mediated doxycycline inducible system, ZNF469 knockdown LFs are employed to explore its ficbrotic potential in LFs. Depletion of ZNF469 resulted in marked impairment of LF proliferation and migratory capacity, accompanied by reduced collagen production and secretion. Transcriptomic profiling further revealed significant downregulation of ECM-associated pathways following ZNF469 knockdown, supporting a conserved role for ZNF469 in fibroblast-driven fibrogenesis. Consistently, CUT&RUN analysis demonstrated direct binding of ZNF469 to the promoters of a broad spectrum of ECM-related genes in LFs. Collectively, these findings uncover a previously unrecognized regulatory role of ZNF469 as a key pro-fibrotic transcription factor in lung fibroblasts and highlight its potential as a promising therapeutic target for pulmonary fibrosis.

overall_design: To examine the contribution of ZNF469 to biological pathway regulation in human lung fibroblasts (LFs), we generated ZNF469-deficient LFs using a doxycycline-inducible shRNA knockdown system. RNA sequencing was conducted on three technical replicates for each experimental group (control and ZNF469 knockdown) to obtain comprehensive gene expression profiles for subsequent transcriptomic analyses.

first: Chaiyaboot

last: Ariyachet


title: Profiling the early transcriptional response of Svevo spikes to Fusarium head blight infection

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

summary: Durum wheat (Triticum turgidum L. ssp. durum) is a major cereal and staple in the semi-arid regions of the Mediterranean Basin. After assembling the Platinum-quality reference genome for Svevo durum wheat cultivar, coupling PACBIO HiFi long read 35X sequencing with BIONANO Optical Mapping and Hi-C conformation capture, a complete and accurate gene annotation was then obtained by coupling Illumina RNASeq and Nanopore Isoseq sequencing from multiple tissues. Gene expression was investigated in spikelets inoculated with Fusarium graminearum and in not infected controls to profile the transcriptional regulation of Fusarium head blight infection.

overall_design: Durum wheat (Triticum turgidum L. ssp. durum) cv. Svevo spikelets and spike internodes were sampled 2 and 4 days after point inoculation with the Fusarium graminearum strain CS3005. Samples were collected in three biological replicates.

first: Elisabetta

last: Mazzucotelli

first: Rachel

last: Rusholme-Pilcher

first: Matteo

last: Bozzoli

first: Tiziana Maria

last: Sirangelo

first: Salvatore

last: Esposito

first: Antoni

last: Prodi

first: Anthony

last: Hall

first: Roberto

last: Tuberosa

first: Luigi

last: Cattivelli

first: Marco

last: Maccaferri


title: CRISPR activation of DLX5 drives neural progenitors to the GnRH cell fate

city: Helsinki

first: Shrinidhi

last: Madhusudan

state: Uusimaa

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Gonadotropin-releasing hormone (GnRH) neurons regulate the hypothalamic pituitary-gonadal axis and are required for puberty onset and reproductive competence. However, the transcriptional regulators governing GnRH neuron specification and migration remain poorly defined. The homeodomain transcription factor DLX5 is expressed in fetal human GnRH neurons, its expression precedes that of GNRH1 in human pluripotent stem cell (hPSC)-derived GnRH neurons, and in mice it serves as a guidance cue for GnRH neuron migration. We hypothesized that DLX5 may act as an upstream regulator of human GnRH neuron fate specification and migratory capacity. Using CRISPR activation, we upregulated DLX5 during FGF8b-directed differentiation of hPSCs to GnRH neurons via dual SMAD inhibition and Notch inhibition, as previously described. DLX5 activation increased neural progenitor motility (p<0.001), upregulated FGF8 (p<0.05), and induced GABAergic markers including GAD1 and GAD2. Notably, DLX5 activation induced GNRH1 in the absence of exogenous FGF8b (p<0.05), suggesting that, in GnRH neurons, DLX5 regulates FGF8. When combined with exogenous FGF8b, DLX5 activation produced distinct neuronal patterning accompanied by upregulation of extracellular matrix genes such as SPARC, which has been implicated in neurite outgrowth. Collectively, these data indicate that activation of DLX5 promotes GnRH neurogenesis from hPSCs by driving GABAergic fate, inducing FGF8, and remodelling the extracellular matrix.

overall_design: RNA-seq profiling of WA09 neural progenitors and GnRH neurons were done. All cells were differentiated with the GnRH protocol (PMID: 27426041). Sample timepoints include Day20 (neural progenitors) and Day25 (GnRH neurons). Variables include DLX5 activation/not activated and 100 ng/ml FGF8b treatment/no FGF8b treatment. Activation treatment and FGF8b treatments all between day10-day20. Samples with labels A,B, J and K include 5 biological replicates per sample. Samples N#_A, F#_A and F#_C were all FACS sorted TdT positive neurons on Day25, and had 3 biological replicates per sample.

first: Nazli

last: Eskici

first: Celia

last: Gomez-Sanchez

first: Kristiina

last: Pulli

first: Kirsi

last: Vaaralahti

first: Venkatram

last: Yellapragada

first: James

last: Conway

first: Yafei

last: Wang

first: Taneli

last: Raivio


title: Cancer-Associated Fibroblast-Derived CCL11 Promotes Prostate Cancer Malignancy by Inducing Epithelial-Mesenchymal Transition via CDK5

city: Bengbu

first: xingyu

last: chen

state: Anhui Province

address: Bengbu Medical University, 2600 Donghai Avenue, Longzihu District, Bengbu City, Anhui Province, P.R. China, 233030

institute: BBMC

summary: To elucidate the key role and underlying mechanisms of C-C motif chemokine ligand 11 (CCL11) in cancer-associated fibroblasts (CAFs)-mediated prostate cancer (PCa) progression. In this study, we analyzed the dataset GSE85606 and validated the upregulation of CCL11 in CAFs using ELISA and qRT-PCR, demonstrating its strong correlation with established CAF biomarkers. Using CAFs-conditioned medium, recombinant human CCL11, specific siRNA, and CDK5 plasmid or siRNA in PCa cell lines (C42 and 22RV1), we investigated the functional role of CCL11. RNA-seq and TCGA database analyses predicted a CCL11’s downstream target (CDK5). Transwell, wound healing, and flow cytometry assays, along with Western blot, were employed to assess the effects of CCL11 on migration, invasion, apoptosis, and epithelial-mesenchymal transition (EMT) pathways. The results indicate that CCL11, predominantly secreted by PCa-derived CAFs, significantly enhances the migration and invasion of PCa cells, suppresses their apoptosis, and activates the EMT pathway, largely through regulating CDK5 expression. Collectively, our findings suggest that CAFs-derived CCL11 may represent a potential therapeutic target for PCa.

overall_design: RNA-seq analysis was performed in prostate cancer cell lines with CCL11 upregulation and matched control cells to identify CCL11-regulated transcriptomic changes and potential downstream target genes involved in prostate cancer progression.

first: Yu

last: Wu

first: Xingyu

last: Chen

first: Xinwei

last: Yuan

first: Zhijun

first: Xiaolin

last: Guo


title: Transcriptomic atlas of the durum wheat plant development

first: Cristian

last: Forestan

summary: Durum wheat (Triticum turgidum L. ssp. durum) is a major cereal and staple in the semi-arid regions of the Mediterranean Basin. It originates from BBAA wild tetraploid domesticated in Neolithic era, later evolving to domesticated emmer and then to up to 11 T. turgidum subspecies, including durum wheat landraces and modern cultivars. Tetraploid wheat is the donor of the A and B genomes of hexaploid bread wheat (DDAABB), representing therefore a valuable source of genetic variability and beneficial alleles for both durum and bread wheat breeding. After assembling the Platinum-quality reference genome for Svevo durum wheat cultivar coupling PACBIO HiFi long read 35X sequencing with BIONANO Optical Mapping and Hi-C conformation capture, a complete and accurate gene annotation was then obtained by coupling Illumina RNASeq and Nanopore Isoseq sequencing from multiple tissues. The expression of 68,154 high confidence genes together with more than 100,000 low confidence, TE-related or long non-coding genes was investigated on 30 diverse tissues from grain, root, leaf, and spike samples across multiple developmental time points to create a transcriptional atlas of durum wheat development.

overall_design: Durum wheat (Triticum turgidum L. ssp. durum) cv. Svevo tissues and organs were sampled at several developmental times across the growth cycle, in three biological replicates to produce a transcriptional atlas of durum wheat development from germinating seed to mature grains.

first: Elisabetta

last: Mazzucotelli

first: Rachel

last: Rusholme-Pilcher

first: Matteo

last: Bozzoli

first: Gabriella

last: Sonnante

first: Francesco

last: Sestili

first: Filippo

last: Bassi

first: Julio Isidro

last: Sanchez

first: Giovanni

last: Giuliano

first: Curtis

last: Pozniak

first: Agata

last: Gadaleta

first: Steven

last: Xu

first: Justin

last: Faris

first: Raul

last: Pirona

first: Alessandra

last: Stella

first: Enrico

last: Pe

last: Dell'Acqua

last: Silvestri

first: Tiziana Maria

last: Sirangelo

first: Salvatore

last: Esposito

first: Anthony

last: Hall

first: Roberto

last: Tuberosa

first: Luigi


title: The quantification comparison of A-to-I RNA editing between NGS and LRS

city: Guangzhou

first: Yulong

last: Song

address: No.1, Xinzao Road, Xinzao Town, Panyu District

institute: Guangzhou Medical University

summary: We performed paired NGS and LRS cDNA RNA-seq of both HEK293T and U2OS cells.

overall_design: First, HEK293T or U2OS cells were collected. Total RNAs were then extracted using the FastPure® Cell/Tissue Total RNA Isolation Kit V2 (Vazyme Biotech Co., Ltd., RC112-01). For the polyA-based mRNA enrichment, mRNAs were captured using VAHTS mRNA Capture Beads (Vazyme Biotech Co., Ltd., N401). For each cell line, the polyA-selected and rRNA-depleted stranded RNA-seq were performed with three replicates.

first: Yuling

last: Qi

first: Jiaxing

last: Zhang


title: CDK12 as an entry point for combination therapy in high-risk neuroblastoma [WES]

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

type: Genome variation profiling by high throughput sequencing

summary: High-risk neuroblastoma (HR-NB) patients undergo aggressive treatments, yet more than half succumb to the disease. HR-NB cells are marked by chronic replicative stress, partly driven by MYCN amplification, and targeting DNA damage response (DDR) pathways presents a promising therapeutic approach. BRCA1 and CDK12, located on the recurrently gained 17q region in HR-NB, play essential roles in maintaining genomic stability. In this study, we hypothesized that pharmacological inactivation of CDK12 could induce a BRCAness phenotype, making NB cells vulnerable to synthetic lethal targets. We evaluated the efficacy of CDK12 inhibitors and protein degraders in a panel of NB cell lines and organoids. Molecular effects of CDK12 inactivation were investigated through immunoblotting and RNA-sequencing. A high-throughput compound screen combining CDK12-targeting agents with a library of ~200 drugs revealed that single-agent treatment with CDK12 inhibitors or degraders induced significant NB cell death in vitro. This was accompanied by a BRCAness signature, including decreased BRCA1 and RAD51 levels, increased DNA damage, and downregulation of DNA repair genes. Additionally, we observed upregulation of immune pathways, suggesting potential for enhancing immunogenicity in HR-NB. The combinatorial drug screen revealed strong synergy with DNA-damaging agents, PARP inhibitors, Ras/MAPK inhibitors, and other compounds. These findings confirm CDK12 as a novel therapeutic target, and the induction of a BRCAness phenotype provides a basis for combination treatments.

overall_design: Whole-exome sequencing (WES) was performed on harvested MYCN-amplified neuroblastoma (NB) patient-derived xenograft (PDX) tumors (MSK cohort). Tumors were collected from mice treated for 21 consecutive days with either vehicle or the OKIMer combination (10 mg/kg OKI-1546 and 24 mg/kg merestinib). Only subjects achieving >40-day survival were included, or, for the vehicle group, the longest-surviving animals.

first: Joshua

last: Goulding

first: Stijn

last: Couwenbergh

first: Kaat

last: Durinck

first: Jan

last: Molenaar


title: TLR7 - ITGAM: A NOVEL INNATE IMMUNE PATHWAY IN CARDIAC ISCHEMIC INJURY [snRNA-Seq]

city: Baltimore

first: Yijia

last: Li

state: MD

address: HSF2 G-S003, 20 Penn street

department: Anesthesiology

institute: University of Maryland, Baltimore

summary: We utilized single-nucleus RNA sequencing (sn-RNAseq) with the 10X Genomics platform to investigate the mechanisms underlying cardiac ischemia/reperfusion (I/R) injury. Cardiovascular disease (CVD), particularly ischemic myocardial infarction (MI), remains the leading cause of death in the U.S. Although percutaneous coronary intervention (PCI) reduces infarct size and preserves cardiac function, reperfusion itself induces I/R injury, exacerbating myocardial damage. Our prior studies demonstrate that I/R injury triggers the release of cellular RNA, and attenuating extracellular RNA (exRNA) reduces myocardial inflammation, conferring cardioprotection against I/R injury. This study elucidates the role of TLR7, an exRNA sensor, and its downstream signaling pathways in myocardial I/R injury, offering new insights into potential therapeutic strategies for cardiac I/R treatment.

overall_design: Myocardial ischemia was induced in mice via left anterior descending (LAD) artery occlusion for 45 minutes, followed by 24 hours of reperfusion. Sham mice underwent thoracotomy only. Mice were administered either normal saline (NS) or the TLR7 antagonist enpatoran (Enpa, 5 mg/kg, i.p.) 1 hour prior to ischemia, with a second dose given 2 hours later. Cardiac nuclei were isolated from the NS-Sham, NS-I/R, and Enpa-I/R groups for single-nucleus RNA sequencing.

first: Amol

middle: C

last: Shetty

first: Wei

last: Chao


title: Gene expression profiling of insulinoma tissues

city: Kobe

first: Kenji

last: Sugawara

state: Please Select

address: 7-5-1 Kusunoki-cho, Chuo-ku

country: Japan

institute: Kobe university graduate school of medicine

summary: This dataset contains gene expression profiles of surgically resected human insulinoma tissues analyzed using an Agilent one-color gene expression microarray platform.

overall_design: Four human insulinoma tissue samples were analyzed by Agilent one-color gene expression microarray. Raw Agilent Feature Extraction output files and a normalized probe-level expression matrix are provided.


title: Impact of Mettl1 on the transcriptional landscape of mouse bone marrow cells at single-cell resolution [scRNA-seq]

city: Duarte

first: Rui

last: Su

state: CA

address: 1500 E Duarte Rd

institute: City of Hope

summary: This study investigates the impact of Mettl1 deletion on the transcriptional landscape of bone marrow cells at single-cell resolution. Bone marrow mononuclear cells (BM MNCs) were collected from Mettl1+/+ Mx1-Cre and Mettl1fl/fl Mx1-Cre mice following poly(I:C)-induced recombination. Single-cell RNA sequencing (scRNA-seq) was performed using the 10x Genomics Chromium platform. The resulting data were used to identify distinct cell populations, and assess transcriptional changes associated with Mettl1 loss. This dataset provides a valuable resource for understanding the role of Mettl1 in normal hematopoiesis.

overall_design: Bone marrow cells were isolated from three female Mettl1+/+ Mx1-Cre mice and three female Mettl1fl/fl Mx1-Cre mice (6 weeks old) from the same litter. All mice were treated with poly(I:C) (4287, R&D systems) via intraperitoneal injection (10 mg/kg, every other day for a total of seven injections) to induce Cre-mediated recombination. Four weeks after the final injection, BM MNCs were harvested. Cells from three mice were pooled into one sample per group. Single-cell suspensions were prepared and subjected to single-cell RNA sequencing using the 10x Genomics Chromium platform. Libraries were constructed using the Chromium GEM-X Single Cell 3′ Reagent Kits v4 and sequenced on the Illumina NovaSeq X platform. Downstream analyses included cell clustering, annotation, and comparative transcriptional profiling between genotypes.

first: Lei

last: Dong

first: Lili

last: Ren


title: Impact of METTL1 on global gene expression in AML [RNA-Seq]

summary: Methyltransferase 1 (METTL1) is an enzyme responsible for the m7G modification of tRNAs. Our studies indicated that METTL1 is highly expressed in AML samples and its elevated level predicts poor prognosis of AML patients. Knockout (KO) of METTL1 in AML cells significantly suppressed their growth in vitro, and substantially delayed leukemogenesis in vivo. Additional rescue assays demonstrated the functions of METTL1 in AML primarily depended on its enzymatic activity. To delineate the molecular mechanism through which METTL1 exerts its biological functions in AML, we conducted transcriptome-wide RNA sequencing with U-937 AML cells following METTL1 KO.

overall_design: We introduced the single-guide RNAs (sgRNAs) targeting METTL1 (sgMETTL1.3) or the control sgRNA (sgNS) into Cas9 single-clone of U-937 AML cells via lentivirus transduction. The transduction-positive AML cells were selected with blasticidin (10 μg/ml; Cat #: ant-bl-1, InvivoGen) and hygromycin B (200 μg/ml; Cat #: ant-hg-5, InvivoGen) for 1-2 weeks. METTL1 KO efficacy was confirmed by Western blot. Then, the total RNAs were extracted from each group with QIAzol and the poly(A)+ RNAs were enriched from total RNAs for library construction and sequencing. For each group, we included 3 replicates.


title: Distinct immunometabolic signatures in peripheral blood mononuclear cells are linked to systemic inflammation in type 2 diabetes and diabetic kidney disease

city: Burjassot

first: José

middle: F.

last: Català-Senent

state: Valencia

address: Dr. Moliner, 50

department: Microbiología y Ecología

institute: Universitat de Valencia

summary: Diabetic kidney disease (DKD) is a frequent complication of type 2 diabetes and is closely linked to systemic inflammation. Peripheral blood mononuclear cells (PBMCs) are markers of systemic inflammatory and metabolic stress. It is unknown if metabolism-related transcriptomic alterations in these cells is associated with DKD.  Using the nCounter® Human Metabolic Pathways Panel we profiled PBMC metabolic transcripts in individuals with type 2 diabetes or DKD and in controls (n = 12/group), and integrated transcriptomic data with clinical, inflammatory, and mitochondrial parameters. Patients with DKD showed increased inflammatory biomarkers and reduced PBMC mitochondrial membrane potential and mass, consistent with mitochondrial dysfunction. Metabolism-related transcriptomic profiling identified 13 differentially expressed genes across groups. DKD subjects displayed downregulation of SLC7A11 versus controls and HLA-DQA1 versus type 2 diabetes, and upregulation of CPT1A and GBA1 versus controls. CPT1A upregulation was confirmed by RT-qPCR and supported by external GEO datasets, though ROC analyses indicated a limited discriminatory performance. Pathway analyses revealed enrichment of immune-related, fatty acid oxidation, and fructose-6-phosphate pathways and reduced cell proliferation pathways in DKD patients. Inflammatory markers correlated positively with energy-regulating pathways and negatively with anabolic processes. In conclusion, these findings suggest that PBMCs reflect immunometabolic remodeling in response to DKD, thus highlighting an association between systemic inflammation, mitochondrial dysfunction, and altered energy metabolism in circulating immune cells.

overall_design: 36 samples in total were analyzed from three groups of participants: healthy controls (C), patients with type 2 diabetes (D) and patients with type 2 diabetes and diabetic kidneydisease (DN) (12 samples per group)

first: Clara

last: Luna-Marco

first: Jose

middle: F

first: Julia

last: Cacace

first: Alberto

last: Hermo-Argibay

first: Omar

last: Hernández-López

first: María

last: Pelechá-Salvador

first: Jonay

last: Pantoja

first: Asunción

last: Sancho

last: Vila

first: Carlos

last: Morillas

first: Celia

last: Bañuls

first: Milagros

last: Rocha

first: Víctor

last: Víctor

first: Susana

last: Rovira-Llopis


title: IFRD1 orchestrates hepatocyte metabolism and macrophage interactions to facilitate liver regeneration [scRNA-Seq]

city: Hefei

first: Taofei

last: Zeng

state: Anhui

address: 17 Lujiang Road

institute: The First Affiliated Hospital of USTC

summary: Background & Aims Liver regeneration is a tightly regulated process requiring coordinated interactions between hepatocytes and non-parenchymal cells; however, its molecular mechanisms remain incompletely defined. Here, we aimed to investigate the role of interferon-related developmental regulator 1 (IFRD1) in regulating metabolic–immune crosstalk during liver regeneration. Methods We integrated public transcriptomic datasets, human liver disease samples, and multiple in-house–generated experimental models to characterize the dynamic expression of IFRD1 during liver regeneration. Genetic loss-of-function approaches, including global and cell type–specific knockout mice, together with adeno-associated virus–mediated gain-of-function strategies, were combined with single-nucleus RNA-seq, ATAC-seq, metabolic and biochemical assays, protein interaction analyses, and in vivo rescue experiments to elucidate the underlying mechanisms and clinical relevance. Results Hepatocyte IFRD1 was rapidly induced during the early phase of liver regeneration in mice but markedly diminished in human chronic liver disease. Hepatocyte-specific loss of IFRD1 impaired liver repair and regeneration, whereas IFRD1 overexpression enhanced regenerative responses across multiple models, including partial hepatectomy, toxic liver injury, and hepatic ischemia–reperfusion injury. Mechanistically, IFRD1 was required to sustain hepatocyte β-oxidation and mitochondrial ATP production by stabilizing SLC25A5 through competition with the E3 ubiquitin ligase TRIM21. This ATP boost enables chromatin remodeling in hepatocytes, promoting CCL/CXC chemokine expression to recruit CCR2+ monocytes and expand the regenerative GPNMB+ macrophage pool. Notably, IFRD1 overexpression restored liver regenerative capacity after partial hepatectomy in mice with metabolic dysfunction–associated steatohepatitis or DEN-induced liver fibrosis. Conclusions Our findings define IFRD1 as a key immunometabolic regulator of liver regeneration, mediating hepatocyte metabolic control to macrophage-driven regenerative responses, and support the therapeutic potential of targeting IFRD1 to enhance regenerative capacity in liver disease.

overall_design: Single-cell nuclear RNA sequencing (snRNA-seq) was performed on liver tissues from wild-type (WT) and Ifrd1 knockout (Ifrd1-/-) mice at different time points after partial hepatectomy (PHx). The data were analyzed to identify gene expression changes in response to PHx, with a focus on the role of Ifrd1 in liver regeneration.

first: Dalong

last: Yin


title: IFRD1 orchestrates hepatocyte metabolism and macrophage interactions to facilitate liver regeneration

overall_design: Bulk RNA-seq was performed on liver tissues from wild-type (WT) and Ifrd1 knockout  mice, 12 hours after partial hepatectomy (PHx). The goal was to analyze gene expression changes in response to liver regeneration and to explore the role of Ifrd1 in this process.


title: IFRD1 orchestrates hepatocyte metabolism and macrophage interactions to facilitate liver regeneration [ATAC-Seq liver]

overall_design: ATAC-seq was performed on liver tissues  from wild-type (WT) and Ifrd1 knockout  mice, 12 hours after partial hepatectomy.


title: High salt supplementation of a MASH-inducing diet causes lean MASH phenotype with increased hepatic urea cycle activity and EIF5A hypusination

city: Singapore

first: Jin

last: Zhou

address: 8 College Road Singapore

country: Singapore

institute: Duke-NUS Medical School

summary: MASLD/MASH can occur in lean individuals; however, the environmental triggers and molecular mechanisms of lean MASH are unclear, and suitable animal models are lacking. Western diet + fructose (WDF) causes obesity and MASH. Surprisingly, high salt supplementation of WDF (HSWDF) produced a lean MASH phenotype with significant inflammation and fibrosis, and reduced steatosis. Interestingly, we observed decreased urea cycle activity leading to reduced eukaryotic translation initiation factor 5A hypusination (Eif5aH) and impaired mitochondrial protein synthesis in mice fed WDF.  High saltsupplementation unexpectedly improved these changes to improve hepatic fatty acid oxidation and steatosis. Additionally, single-cell sequencing revealed that high salt induced pro-inflammatory responses in hepatic immune cell subpopulations. In summary, we have established a dietary mouse model of lean MASH with key effects on the hepatic urea cycle, mitochondrial protein synthesis, and immune cell activation. Our findings suggest salt restriction may be beneficial in some patients with lean MASH.

overall_design: Four dietary conditions were included in the studies: (1) NCD group, mice were fed a normal chow diet (Specialty Feeds, SF00-100) and supplied with tap water; (2) HSD group, mice were fed a normal chow diet containing 8% salt (D05011703, Research Diets Inc.) and supplied with tap water; (3) WDF group, mice were fed RD Western Diet (D12079B, Research Diets Inc.) and supplied with 15% fructose in drinking water; (4) HSWDF group, mice were fed with RD Western Diet containing 8% salt (D06111701, Research Diets Inc.) and supplied with 15% fructose in drinking water. Male C57BL/6J mice (8 to 10-week-old) were fed the NCD (n=5), HSD (n=5), WDF (n=6), or HSWDF (n=7) diets for 16 weeks. The animal work was repeated with NCD (n=8), HSD (n=8), WDF (n=10), or HSWDF (n=16). Freshly harvested liver tissues from mice feeding on NCD, HSD, WDF and HSWDF were dissociated into single cell suspensions followed by 1 min spin at 100g to enrich immune cells by Singleron Biotechnologies. Then the enriched cells were analyzed using scRNA-seq.

first: Shaopeiwen

last: Luo

first: Paul

last: Yen


title: Shear Preconditioning Restores Endothelial Function of HLHS Patient-Derived iPSC-ECs for Successful Conduit Implantation

city: New Haven

first: Yibing

last: Qyang

address: 300 George St

institute: Yale University

summary: Thrombosis, stenosis, and unsatisfied remodeling remain major challenges limiting the success of tissue engineered vascular grafts (TEVGs) in clinical application requiring vascular reconstruction. A key contributing factor is the Patients with single ventricle congenital heart defects (SVCHDs) urgently require TEVGs for cardiopulmonary reconstruction during Fontan procedure. However, endothelial dysfunction has been reported in both primary and hiPSC-derived endothelial cells (ECs) from this patient population, especially in the subgroup with hypoplastic left heart syndrome (HLHS), one severe form of SVCHD. Building on our prior work demonstrating that shear preconditioning enhances the antithrombotic and remodeling capacity of endothelialized conduits, we extended this approach to HLHS patient-derived iPSC-ECs. Compared with healthy controls, HLHS iPSC-ECs seeded on the luminal surface of decellularized human umbilical artery (dHUA) scaffolds and subjected to physiological shear preconditioning maintained patency and supported remodeling following implantation into the rat inferior vena cava (IVC), modeling Fontan circulation. In vitro, shear-preconditioned HLHS iPSC-ECs exhibited enhanced resistance to hemodynamic stress, improved anti-inflammatory and antithrombotic function, and partial restoration of mechanosensitive NOTCH1 signaling. These findings demonstrate that shear preconditioning can restore critical endothelial functions in HLHS iPSC-ECs and support the translational potential of autologous, patient-derived endothelialized TEVGs as future therapeutic solutions for SVCHDs. absence of a functional endothelium. We aim to establish a “ready-to-use” endothelial layer on TEVGs suitable for diverse clinical settings. The primary barriers to clinical translation include source fo endothelia and achieving a mature, stable endothelial layer. Human induced pluripotent stem cells (hiPSCs) provide an renewable source capable of generating patient-specific endothelial cells (iPSC-ECs) for TEVG endothelialization.

overall_design: Human iPSCs from three HLHS patients and their related healthy family controls were differentiated into endothelial cells (iPSC-ECs), with endothelial identity confirmed by CD31 and VE-cadherin expression. HLHS iPSC-ECs and control iPSC-ECs were then seeded onto decellularized human umbilical arteries (dHUAs) and subjected to two hemodynamic conditions: (1) a shear preconditioning protocol designed to mimic IVC hemodynamics (ramping from 1 to 15 dynes/cm² over 36 h, maintaining 15 dynes/cm² for 48 h, then reducing to 5 dynes/cm² for 12 h), and (2) a static condition followed by abrupt exposure to 5 dynes/cm² for 6 h (static + abrupt flow). Bulk RNA-seq was performed on iPSC-EC–seeded dHUAs from the preconditioned (flow) and static + abrupt flow groups to identify differentially expressed genes associated with hemodynamic conditioning and endothelial resilience.

first: Wei

last: Zhang

first: Saba

last: Fooladi


title: Macrophage Senescence Links ACL Injury to Posttraumatic Osteoarthritis and Muscle Atrophy [scRNA-seq]

city: Lexington

first: Alexander

middle: Romano

last: Keeble

address: 900 S Limestone st

institute: Northwestern University

summary: Traumatic knee injury often leads to posttraumatic osteoarthritis (PTOA) and significant skeletal muscle atrophy and weakness, resulting in chronic disability. The current standard of care frequently fails to prevent musculoskeletal dysfunction, underscoring the need to identify therapeutically targetable mechanisms of PTOA. Using an established preclinical anterior cruciate ligament (ACL) transection model of PTOA and leveraging an innovative SPiDER-senescence associated β-galactosidase stain to discern senescent cells, we investigated cellular senescence at single-cell resolution and identified Cd163+ anti-inflammatory macrophages as a predominant contributor to the senescent cell burden in both quadriceps muscle and knee joint capsule after ligament injury. Furthermore, conditioned media from senescent macrophages induced senescence- and osteoarthritis-related transcriptional programs in mesenchymal progenitors. Clearance of senescent cells using the senolytic cocktail dasatinib + quercetin (D+Q) mitigated ligament injury-induced muscle atrophy and cartilage degradation. Of note, D+Q demonstrated greater senescent cell clearance within muscle compared to cartilage. We also provide clinical evidence of elevated senescent cell burden in quadriceps muscle of patients following ACL injury and with knee PTOA, which is obstinate to standard of care, highlighting cellular senescence as a therapeutic target with strong potential to improve functional recovery after traumatic joint injury.

overall_design: Mouse quadriceps and joint tissues were dissected and pooled from n = 8 mice at 14 days following ACLT. Tissues were mechanically and enzymatically processed prior to incubation using SPiDER Senescence Cell Detection Kit (Dojindo Molecular Technologies Inc, SG04) and subsequent fluorescence activated cell sorting. Single-cell RNAseq libraries were prepared using the Chromium Single Cell 3′ reagent kit version 3.1 (10x Genomics, PN-1000075; Pleasanton, CA) following manufacturer’s guidelines.

middle: R

first: Allison

last: Owen

first: Sara

last: Gonzalez-Velez

first: Nicholas

middle: T

last: Thomas

first: Camille

last: Brightwell

first: Peyton

middle: J

last: Balawender

first: Madeline

last: O'Daniel

first: Helena

last: Weiss

first: Haley

last: Noehren

first: Heather

last: Thompson

first: Karen

middle: S

last: Zuluaga-Osorio

first: Zane

last: Bates

first: Lauren

last: Gottlieb

first: Douglas

middle: E

last: Long

last: Harrison

first: Philip

last: Kern

first: Caitlin

last: Conley

first: Michael

last: Samaan

first: Stephen

last: Duncan

first: Jeffrey

middle: B

last: Selby

first: Austin

last: Stone

first: Darren

middle: L

last: Johnson

first: Yuan

last: Wen

first: Brian

first: Cory

last: Dungan

first: Christopher

last: Fry


title: Tumor Antigen–Independent Targeting of Solid Tumors by Armored 1 Macrophage-Directed anti-TREM2-CAR T Cells [human scRNA-seq]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Chimeric antigen receptor (CAR) T cell therapy has shown remarkable clinical efficacy in  hematological malignancies and, more recently, in autoimmune diseases. However, its application in solid tumors has been limited by tumor antigen heterogeneity, antigen escape, and the immunosuppressive tumor microenvironment (TME), which is particularly shaped by tumor associated macrophages (TAMs). To overcome these barriers, we developed a novel CAR T cell strategy targeting human TREM2⁺ immunosuppressive TAMs. Macrophage-directed anti- TREM2-CAR T cells demonstrated potent anti-TREM2 activity in both in vitro assays and in solid tumor models in vivo. To further enhance intratumoral T cell function, we incorporated a CAR T cell responsive synthetic DNA biosensor comprising NFAT motifs that enable localized secretion of interleukin-12 upon CAR activation. In murine tumor models, this “armored” TREM2-targeted CAR-T cell approach led to robust remodeling of the TME and tumor-draining lymph nodes, characterized by TREM2⁺ TAM depletion, enhanced T and NK cell infiltration and activation, and complete tumor eradication, independent of tumor antigen expression.

overall_design: To validate the TAM-like phenotype of human macrophages differentiated in vitro,  we characterized CD14+ cells isolated from healthy donors. Cells were cultured with different cytokines cocktails, and their cell state was analyzed based on dominating gene programs using scRNAseq.

first: Gal

last: Yagel

first: Dana

last: Rimini

first: Michelle

last: von Locquenghien

first: Roberto

last: Avellino

first: Pascale

last: Zwicky

first: Oren

last: Barboy

first: Gaya

last: Granot

first: Ken

last: Xie

first: Shir

last: Shlomi-Loubaton

first: Eyal

last: David

first: Kfir

last: Mazuz


title: Macrophage Senescence Links ACL Injury to Posttraumatic Osteoarthritis and Muscle Atrophy

first: Alexander

last: Keeble

overall_design: Bone marrow cells were harvested and differentiated as we have previously described. Briefly, femurs were harvested from naïve wild type mice, flushed with cold RPMI media supplemented with glutamine, 25 mM HEPES, 10% fetal bovine serum, 1% antibiotic-antimycotic, and 10 ng/mL mouse recombinant M-CSF (R&D Systems). Cells were plated at 4X104 cells/mL which were differentiated for 7 days to yield mature macrophages. BMDMs were replated in 6-well plates, and senescence was induced by hydrogen peroxide-induced oxidative stress as we previously reported. Briefly, BMDMs were treated with 300 µm H2O2 for 3 hours which was washed off and cells were cultured for 3 days and treated again with 300 µm H2O2 for 3 hours. BMDMs were then cultured an additional 14 days with regular media changes. Control non-senescent BMDMs and senescent BMDMs were incubated for 48h and conditioned media was collected; this was repeated and the conditioned media was pooled from the two collections and frozen (-20 °C) until future use. Mesenchymal stem cells were identified as Col1a1+ Ly6a (i.e. Sca-1)+ cells. Accordingly, we leveraged our Collagen 1-enhanced green fluorescent protein (Col1-eGFP) mice from which we harvested quadriceps muscle tissue from naïve male Col1-eGFP+ mice (n=6) which was mechanically minced under sterile conditions, and a single cell suspension was obtained through enzymatic digestion and cell straining. The cell suspension was incubated with Sca-1 (APC-conjugated, 1:100, Biolegend #122512) for 1 hour at 4°C with gentle agitation followed by co-staining with DAPI as a viability marker. This cell suspension was then sorted using an iCyt FACS machine (Sony Biotechnology, Champaign, IL, USA) along with appropriate negative controls for gaiting. GFP+APC+DAPI- cells were sorted directly into sterile culture media (RPMI supplemented with supplemented with 20% FBS 1% penicillin streptavidin) and immediately plated for cell culture. Col1-eGFP+Sca-1+ cells (MSCs) were expanded and replated (passage 4) in 6-well Primaria plates (Corning, #353846) for the conditioned media experiment. The conditioned media was thawed overnight at 4 °C, and the MSC culture media was replaced with conditioned medium from control macrophages or from senescent macrophages (n=3 replicates, each) and incubated for 72 hours (having changed media with conditioned media at 24h and 48h to ensure nutrient availability).

first: Allison

last: Owen

first: Sara

last: Gonzalez-Velez

first: Nicholas

last: Thomas

first: Camille

last: Brightwell

first: Peyton

last: Balawender

first: Madeline

last: O'Daniel

first: Helena

last: Weiss

first: Haley

last: Noehren

first: Heather

last: Thompson

first: Karen

last: Zuluaga-Osorio

first: Zane

last: Bates

first: Lauren

last: Gottlieb

first: Douglas

last: Long

middle: A

last: Harrison

first: Philip

last: Kern

first: Caitlin

last: Conley

first: Michael

last: Samaan

first: Stephen

last: Duncan

first: Jeffrey

last: Selby

first: Austin

middle: V

last: Stone

first: Darren


title: Peroxisomes in maintenance and neural differentiation of mESCs

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Peroxisomes are single-membrane bound organelles playing important roles in cellular lipid and reactive oxygen species (ROS) metabolism. Defective peroxisome biosynthesis, assembly or biochemical functions leads to a group of autosomal recessive disorders called peroxisome biogenesis disorders (PBDs).  PBDs can affect most organs of the body, with common findings of visual, auditory and neurological deterioration. In this study, we disrupted peroxisome assembly by deleting PEX5 or PEX19, two essential peroxisome biogenesis factors, in mouse embryonic stem cells (mESCs), and analyzed the impacts of peroxisome deficiency on mESC maintenance and neural differentiation in vitro.  Our results reveal that peroxisome deficiency impaired mouse stem cell self-renewal for enhanced cell death and loss of pluripotency. Increased ROS and defective synthesis of plasmalogens at least partially account for the phenotypes. Finally, the peroxisome deficient cells fail to differentiate to neuron stem cells, confirming that peroxisomes are important for ES cell maintenance and neural differentiation.

overall_design: WT, Pex5 KO and Pex19 KO 46C mESCs generated by Crispr/Cas9 gene editing technology cultured in ESGRO maintenance medium were induced for neural differentiation in the NDiff 227 neural differentiation medium (Takaba Y40002) for 4 (D4) or 7 (D7) days. Total RNA was extracted and RNA-seq libraries were prepared with the TruSeq Stranded/Ribo kit (Illumina, San Diego, CA) and sequenced using the single-end 75bp protocol using the Next-Seq 500 platform (Illumina) per the manufacturer’s protocol.

first: Wei

last: Fan

first: Xiaoling


title: Splicing inhibition hampers pancreatic cancer cell viability by disrupting DNA repair proficiency and mitotic checkpoint integrity

city: Rome

first: Marco

last: Pieraccioli

address: Largo Francesco Vito 1

institute: Catholic University of the Sacred Heart rome

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with a remarkably poor prognosis. Splicing dysregulation is emerging as a hallmark of cancer, influencing multiple aspects of tumor development. To evaluate the impact of its dysregulation we employed three splicing-targeting drugs: Pladienolide B (PdB), Thailanstatin A (Th.A) and Indisulam (Ind.), all involved in the recognition of 3’ splice site. Transcriptome analyses in PDAC cell lines and PDOs revealed that splicing inhibition negatively affects the DDR pathway (BRCA1, CHEK1, CHEK2) in homologous recombination-proficient (HRP) PDAC models, representing a promising strategy to enhance their sensitivity to PARP inhibitor (Talazoparib) treatment. Moreover, among the genes that are altered by all three drugs, we observe an enrichment of genes involved in the mitotic checkpoint genes (AURKA, AURKB, CDC25B, KIF21, EZH2). Indeed, splicing inhibitors induced severe mitotic defects with a strong enrichment in the G2/M phase of the cycle, leading to the accumulation of condensed chromosomes on monopolar spindles and misaligned chromosomes on bipolar spindles; which lead to the formation of multinucleated cells. The high expression of AURKA, AURKB and CHEK1 were correlated with poor prognosis in PDAC; furthermore, CHEK1 expression was also significantly correlated with AURKA and AURKB. Indeed, combined treatments with CHEK1i (AZD7762) and AURKAi (Alisertib) have an additive effect on both PDAC cell lines and PDOs, suggesting promising new therapeutic strategies that may be used in PDAC patients.

overall_design: RNA-seq profiling of PANC-1 PDAC cells treated for 6 hours with 3.3 nM Pladienolide B (PdB), for 8 hours with 500 nM Thailastatin A (ThA) or for 12 hours with 3.3 mM Indisulam (Ind) to reveal DEGs and alternative splicing events upon splicing inhibitors treatment.

first: Valentina

last: Panzeri

first: Veronica

last: Ruta

first: Maria Vittoria

last: Manno

first: Sette

last: Claudio


title: GDF5 modulation of MuSC pool as a potential therapeutic benefit for DMD

city: Paris

first: Aly

last: BOURGUIBA

state: France

address: 105 bd de l'hôpital

country: France

institute: Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie,

summary: Duchenne muscular dystrophy (DMD) is a fatal disease characterized by the absence of dystrophin, leading to degeneration of the entire musculature. With the aim of improving muscle pathophysiology and gene therapy for DMD, we investigated the potential of growth differentiation factor 5 (GDF5) in the DMD mdx mouse model. We showed that the overexpression of GDF5 in the muscle improved its histology, reduced inflammation, modulated regeneration and induced the appearance of de novo fibers. We demonstrated that muscle satellite cells (MuSCs) are targeted by GDF5 which enhanced their proliferation and slowed down their myogenic commitment and finally their fusion. Next, we combined GDF5 overexpression with AAV-mediated microdystrophin gene therapy, the most promising treatment for DMD, and showed an increased number of microdystrophin-positive myofibers compared with gene therapy alone. Overall, we reveal here the potential role of GDF5 in improving DMD pathophysiology and provide a first proof of concept of a synergistic effect of the combination of GDF5-based treatment and AAV-microdystrophin.

overall_design: AAV2/9-Scramble (Scr) or -GDF5 (GDF5) were injected into 1-week-old mdx Tibialis Anterior (TA) for 2 weeks or 8 weeks (2 and 8p.i.). Nuclei isolation was performed following the Chromium Nuclei Isolation Kit (10x Genomics). Nuclei were encapsulated in barcoded beads and then sequenced.

last: Bourguiba

first: Lorenzo

last: Giordani


title: Mannose-Modified Tobacco Mosaic Virus-Mediated Macrophage Regulation Inhibits Pulmonary Fibrosis Progression

city: Beijing

first: Jiaodan

last: Jin

address: 29  Zhongguancun East  Road,  Haidian District, Beijing, 100190,  China

institute: Technical Institute of Physics and Chemistry

summary: Idiopathic pulmonary fibrosis (IPF) is a chronic disease, causing irreversible lung scarring and respiratory failure. CD206+ M2 macrophages play a key role in its progression. In this study, we utilize the pro-inflammatory properties of plant viruses to develop a mannose-modified tobacco mosaic virus nanoparticle (TMV-OEG8-Man), which targets and reprograms profibrotic macrophages to inhibit IPF. TMV-OEG8-Man alters the CD206+ M2 macrophage phenotype in vitro, suppressing profibrotic genes (Mrc1, Spp1, Ccr2) and signaling pathways (MAPK, TGF-beta, PI3K-Akt, mTOR, Wnt), thereby reducing the transition of fibroblasts to myofibroblasts. When administered via aerosol, TMV-OEG8-Man achieves prolonged lung retention with minimal systemic exposure. In mice with bleomycin-induced pulmonary fibrosis, a single dose during fibroproliferation attenuated fibrosis progression, increasing survival rate from 50% to 100%, and preserving lung architecture. This study establishes plant viral nanoparticles as a macrophage reprogramming strategy with therapeutic potential for organ fibrosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mature bone marrow derived macrophages (BMDMs) , IL-4 treated BMDMs, and IL-4 and TMV-OEG8-Man treated BMDMs.

first: Ren

last: Xu

first: Huaixiu

last: Fu

last: Qian

first: Yu

last: Liu

first: Jinzhao

last: Ou

first: Meng

last: Zhu

first: Yunzhi

last: Zhou

first: Ye

last: Tian

first: Zhongwei

last: Niu


title: Structure-guided discovery and engineering of miniature CRISPR-Cas12m for epigenome editing

first: Kailong

last: Li

institute: Peking University

summary: Expression profiling by high throughput sequencing

overall_design: RNA-seq was performed to determine the transcriptomic changes.

first: Tao

last: Yu

first: Donglin


title: HDAC4 regulates hASCs osteogenesis and bone regeneration by mediating SMAD4 via histone acetylation

city: shanghai

first: liyuan

last: yu

address: 639 Zhizaoju Road, Huangpu District, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

summary: Bone defects in the craniofacial region, such as mandibular critical-sized defects (CSDs), represent a significant clinical challenge due to the limited self-healing capacity and shortcomings of current therapeutic options. Bone tissue engineering using human adipose-derived stem cells (hASCs) offers a promising alternative. This study investigates the role of histone deacetylase 4 (HDAC4) and its inhibition as a therapeutic strategy in regulating hASCs osteogenic differentiation via histone acetylation. Using CUT&Tag sequencing, we identified HDAC4-regulated histone acetylation sites that modulate the expression of osteogenesis-related factors, including the key transcription factor SMAD4. HDAC4 knockdown enhanced histone acetylation, promoted SMAD4 expression, and significantly improved osteogenic differentiation of hASCs. These findings were further validated in vivo using calvarial and mandibular defect models in nude mice. As an alternative inhibition strategy, the selective HDAC4 inhibitor Tasquinimod (Tasq) was evaluated. At 1 µM, Tasq enhanced hASCs proliferation, promoted histone acetylation, upregulated SMAD4, and stimulated osteogenic differentiation markers (ALP, OSX, COL1A1), mimicking the effects of HDAC4 knockdown. To enable localized delivery, a Tasq-loaded GelMA-F127 composite hydrogel was developed. This hydrogel exhibited excellent mechanical properties, biocompatibility, and sustained release. Applied to mandibular defects, GelMA-F127-Tasq significantly enhanced bone regeneration. In conclusion, this study elucidates the epigenetic mechanisms of HDAC4 in hASCs osteogenesis and highlights the potential of Tasq-loaded hydrogels as a therapeutic strategy for bone defect repair.

overall_design: CUT&Tag sequencing of hASCs with siRNA induced scilencing of HDAC4

first: Liyuan

first: Kai

last: Xia

first: Jianwei

last: Chen


title: Combined Targeting of de novo Pyrimidine Synthesis and ATR Promotes ATF4-Mediated Cell Death in TP53-Deficient ALL

city: Utrecht

first: Frank

middle: van

last: Leeuwen

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

summary: Mutations or deletions affecting the TP53 gene predict a dismal outcome in relapsed acute lymphoblastic leukemia (ALL), with limited curative treatment options available. Due to their highly proliferative state, ALL cells are strongly dependent on nucleotide synthesis. Inhibitors of dihydroorotate dehydrogenase (DHODH), a pivotal enzyme in de novo pyrimidine biosynthesis, have demonstrated promising single-agent efficacy in some ALL and acute myeloid leukemia (AML) preclinical models. Using both isogenic TP53 cell line models and patient-derived xenografts (PDX), we show that dual inhibition of DHODH and Ataxia telangiectasia and Rad3 related (ATR) produces pronounced anti-leukemic effects, irrespective of the TP53 status. Through integrated transcriptomic and metabolomic analyses, we show that combined inhibition of DHODH and ATR leads to a reduced flux of glucose to the TCA cycle, accompanied by an increase in oxidative stress. This metabolic phenotype triggers cell death through a mechanism converging on Activating Transcription Factor 4 (ATF4), a key integrator of cellular responses to metabolic and oxidative stress, which operates largely independent of p53.  Taken together, our findings identify ATF4-mediated cell death as a previously unrecognized vulnerability in TP53-deficient ALL.

overall_design: For bulk mRNA sequencing of RCH-ACV TP53KO and TP53WT upon 24-hour treatment with DMSO, 100 nM berzosertib, 4 nM orludodstat, or the combination thereof, cells were seeded in triplicate. After 24 hours of treatment, mRNA was extracted from the cells using a NucleoSpin RNA isolation kit  (Macherey-Nagel, 740955).The NEBNext® UltraTM Directional RNA Library Prep Kit (New England Biolabs) was used to prepare sequencing libraries. Paired-end sequencing (PE150) was performed on the Illumina NovaSeq X Plus and preliminary data processing was performed by Novogene (Germany).

first: Kari

last: J.T. Grunewald

first: Marjolein

last: M.M.G Kes

first: Gawin

last: Stoll

first: Laurens

last: van der Meer

last: van Leeuwen


title: Integration of the naïve pluripotency gene network with the response to Gsk3 inhibition by Tcf7l1-driven enhancer decommissioning (Microarray)

city: Chicago

first: Bradley

last: Merrill

address: 900 S Ashland Ave

institute: University of Illinois at Chicago

summary: The transition out of naïve pluripotency requires the simultaneous dissolution of the naïve gene   regulatory network as well as a redirection of transcriptional response to Wnt/β-catenin signaling.   Here, we show that Tcf7l1 functions as a linchpin factor that connects the two outcomes via effects   at Tcf7l1-bound cis-regulatory elements in mouse pluripotent stem cells. A combination of gene   knockout and inducible expression lines of ESC were generated to experimentally isolate effects   of Tcf/Lef factors on pluripotency.  Naïve cis-regulatory elements were specifically bound by and   rapidly decommissioned by Tcf7l1 upon releasing cells from Gsk3 inhibition. These findings   suggest that Tcf7l1-mediated enhancer decommissioning serves as a critical mechanism by which   pluripotent cells rapidly alter the response to signaling pathways in preparation for gastrulation,   and it may be a mechanism used in diverse cell types for modulating effects of Wnt/β-catenin   signaling pathway on cell fate decisions.

overall_design: Expression profiling by microarray of wild-type and Tcf/Lef knockout cells across ESC, EpiLC and other conditions.

first: Brian

last: Shy


title: Calcium oxalate crystals with a bipyramidal morphology and a high tendency to aggregate attach directly to breast cancer cells and affect their phenotype

city: Beer Sheva

first: Shiran

last: Dror

address: Ben-Gurion blvd. 1, Building 39, room 205

institute: Ben-Gurion University of the Negev

summary: Various types of crystal can form in our bodies under normal and pathological conditions, with the more harmful of these crystals being studied intensively. However, much less is known about calcium oxalate dihydrate (COD) crystals, which are commonly associated with benign conditions. In general, calcium oxalates are pathological biominerals found in kidney stones and as microcalcifications (MCs) in breast and thyroid cancers. In breast cancer MCs, COD crystals are exclusively associated with benign lesions, and we have recently shown that they suppress breast precancer progression in vitro. Here, we studied the influence of synthetic calcium oxalate crystals – both COD and calcium oxalate monohydrate (COM) – with different morphologies and properties on crystal-cell interactions. We found that the less negatively charged crystals exhibited a greater tendency to aggregate and, as aggregates, attached better to cells, particularly to the cells of an invasive breast cancer cell line. We did not find any association between crystallinity, surface area, and solubilities of the crystals and attachment to cells. The crystal types that did attach efficiently to the cells, namely, COD with a thin or thick bipyramidal morphology, had the greatest impact on cell phenotype and functionally delayed cell growth, most probably through contact inhibition. Notably, in terms of morphology and size, these crystals resembled COD MCs found in benign breast tissues, suggesting that they are involved in a mechanism of tumor suppression.

overall_design: MCF10DCIS.com were treated with different CaOx crystals forms

first: Gabriel

last: Yazbek Grobman

first: Yarden

last: Nahmias

first: Dina

last: Aranovich

first: Omri

last: Sharabi

first: Noa

last: Ofir

first: Roi

last: Gazit

first: Netta

last: Vidavskya


title: Cdk7 regulates peripheral myelin sheath extension and lipid content.

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

institute: University of Liège

summary: Myelin allows saltatory transmission of action potentials along axons and functionally relies on its unique constitution. Schwann cells (SC) are the glial cells responsible for myelination in the peripheral nervous system (PNS), and their differentiation constitutes a stepwise process involving accurate coordination of proliferation and fine-tuned gene expression.We previously reported that Cdk7, a regulator of cell cycle progression and transcription, regulates myelin gene expression in oligodendrocytes and contributes to myelin maintenance in the adult central nervous system. Using conditional Cdk7 knock-out mice, we provide evidence that Cdk7 is not required for myelin initiation but is needed for the correct rate of myelination of larger calibre fibres, as well as for myelin elongation and rapid nerve conduction. We show that Cdk7 loss results in significant dysregulation of lipid-related genes in SCs in addition to a reduction in myelin protein zero, leading to disturbed myelin stoichiometry. Finally, we show that Rxrγ, a nuclear receptor involved in lipid metabolism, is downregulated in the absence of Cdk7 and that Cdk7 is required for the myelination-promoting effect of Rxrγ in myelinating dorsal root ganglion explants.

overall_design: Bulk RNA-seq profiling of Ctrl and CNP-Cdk7cKO sciatic nerves at postnatal day 6 (P6), a period where Schwann cells (SCs) proliferate, differentiate and actively myelinate within the developing nerve (n=4 Ctrl: "CNP+/+Cdk7lox/lox"; n=4 CNP-Cdk7cKO: "CNPcre/+Cdk7lox/lox"). CNP-cre transgenic mice (cre-lox system) were used to conditionally invalidate Cdk7 in SCs (CNP-Cdk7cKO).

first: Nathalie

last: Schumacher

first: Alexandra

last: Pieltain

first: Pierre

last: Tocquin

first: Nicolas

last: Thelen

last: Masar

first: Giulio

last: Mucciolli

first: Philippe

last: Gailly

first: Peter

last: Arthur-Farraj

first: Renaud

last: Vandenbosch

first: Rachelle

last: Franzen


title: Anti-CD19 CAR-NK cells coexpressing GITRL to enhance antitumor activity for the treatment of leukemias and lymphomas.

city: Ribeirão Preto

first: Matheus

middle: Henrique

last: dos Santos

state: SP

address: R. Ten. Catão Roxo, 2501

department: Oncology

country: Brazil

institute: University of Sao Paulo

summary: CAR-T cell therapy has transformed the treatment of hematological malignancies; however, its broad application is limited due to toxicities and high cost. As an alternative, NK cells offer advantages, including allogeneic use and intrinsic antitumoral activity. Nevertheless, efficacy can be compromised by the immunosuppressive microenvironment, especially through the action of Treg cells. To overcome this obstacle, we proposed the coexpression of GITRL in CAR19-NK cells, aiming to enhance cytotoxicity against CD19⁺ cells and modulate the tumor microenvironment. CAR19-NK-92 and CAR19-GITRL-NK-92 cells, as well as peripheral blood-derived NK cells (PB-NK), were generated. These cells were evaluated regarding their expansion, expression stability, immunophenotype, metabolism, cytotoxicity, cytokine secretion, degranulation, and effects on Tregs. In vivo assay in a murine leukemia model was performed to evaluate tumor burden and survival. CAR19-GITRL-NK-92 cells exhibited greater expansion capacity, a more active metabolic profile (glycolysis and ATP production), in addition to increased expression of NKp44 and NKp46. Both CAR cells exhibited cytotoxicity nearly 40% higher than that of NK-92 cells, accompanied by increased cytokine secretion (TNF-α and IFN-γ) and degranulation. Although the presence of GITRL did not directly enhance tumor cell lysis in vitro, its expression was upregulated following CAR activation by target cells. RNA-Seq analyses revealed activation of pro-effector pathways (KIT, IRF5) and downregulation of inhibitory signals (IL1RN). For the in vivo assay, CAR19-GITRL-NK-92 cells exhibited enhanced tumor control and prolonged survival. In primary NK cells, coexpression of GITRL increased in vitro cytotoxicity and conferred partial resistance to Treg-mediated suppression, with a 43% reduction in growth, compared to 79% observed in CAR19-PB-NK cells. In conclusion, GITRL coexpression in CAR19-NK cells led to a more active metabolism, enhanced activation of pro-cytotoxic pathways, and superior tumor control in a murine model, as well as partial resistance to Treg-mediated immunosuppression in primary cells. Future studies, particularly in vivo, will be essential to validate and extend these findings. These results emphasize the translational potential of CAR19-GITRL-NK cells as an innovative strategy for the treatment of B-cell leukemias and lymphomas.

overall_design: The CAR-NK cells were co-culture against CD19+ positive Nalm-6 cells for 24 hours. After co-culture, the RNA of CAR-NK cells was purified for differencial gene expression analysis.

first: Dayane

last: Schmidt

first: Virginia

middle: P

last: Castro