title: Iron Overload Reprograms Glul+ Hepatocyte Fate to Induce Steatosis and Fibrosis via WNT-signaling pathway in Mice

city: Changchun

first: Peng

last: Chen

address: Xinmin Street 126

department: Department of genetics

institute: Jilin University

summary: Background & Aims Hepatic iron overload is associated with non-alcoholic fatty liver disease (NAFLD) and cirrhosis in lean individuals. We aimed to explore the underlying mechanism through which excessive iron induces fatty liver and cirrhosis at single-cell resolution.  Methods Mouse models were established through feeding a high iron or high fat diet to mimic the condition of iron overload and obesity. Iron overload and obesity induced NAFLD models were confirmed by biochemistry measurements and histological sections. Single-cell RNA-seq (scRNA-seq) and single-nucleus ATAC-seq (snATAC-seq) were conducted to provide insights to the molecular effects of iron overload or obesity on major liver cell types. Pseudo-time analysis and motif activity analysis were performed to gain insight of the differentiation trajectory and the underlying regulatory mechanisms. Cell-cell interaction analysis was utilized to evaluate the hepatic microenvironment in mice with iron overload.  Results Iron overload-induced fatty liver is characterized by down-regulation of PPAR signaling pathway. Ghr+ pericentral hepatocytes, expressing key regulator PPARα, are perturbed by iron, in contrast to the increased population in HFD mice. Iron overload and obesity induced distinctive hepatocyte differentiation trajectories. Differentiation of iron-overloaded hepatocytes mitigates oxidative damage but leads to the downregulation of the PPAR signaling pathway. Glul+ pericentral hepatocytes, serves as transit-amplifying cells (TACs) in liver lobule, lose their differentiation ability under high iron diet. The motif analysis of the transcription factors indicated the role of TCF7L2/LEF1 in governing the differentiation of Glul+ hepatocytes through WNT pathway. Reprogrammed Glul+ pericentral hepatocytes under iron overload also established an inflammatory micro-environment involving increased interactions between hepatocytes and non-parenchymal cells (NPCs), contributing to the formation of liver fibrosis. Conclusions This study offers comprehensive evidence elucidating the distinctive molecular and cellular mechanism of iron overload-induced NAFLD and fibrosis. PPARA and TCF7L2 agonists should be considered in developing effective therapeutic strategies for iron overload-induced lean NAFLD.

overall_design: The primary objective of this investigation was to unravel the unique molecular and cellular mechanisms through which iron overload precipitates lipid accumulation in the liver, particularly in normal weight conditions. To emulate the conditions of interest, we developed 3 diet-induced mouse models, on the basis of normal chow diet. These included a normal chow diet, a high-iron diet (HID) where 30g/kg of carbonyl iron was incorporated into the normal chow, a high-fat diet (HFD) containing 60 kcal% fat relative to the normal chow.

first: Zhengwen

last: An

first: Zewen

last: Sun


title: P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [RNAseq_MASHABT263]

status: Public on Feb 10 2026

city: Los Angeles

first: Ivan

middle: Alexander

last: Salladay-Perez

state: CA

address: 615 Charles E Young Dr S

department: Department of Microbiology Immunology and Molecular Genetics

country: USA

institute: University of California, Los Angeles

type: Expression profiling by high throughput sequencing

summary: Cellular senescence drives chronic sterile inflammation during aging via the senescence-associated secretory phenotype (SASP); however, the cell types responsible for this pathology remain poorly defined. Here, we identify p21⁺Trem2⁺ senescent macrophages as a major source of inflammaging. Using primary mouse and human macrophages, we developed a model of DNA damage and cholesterol-induced senescence and applied multi-omic profiling to fully characterize senescent macrophages. We found that senescent macrophages exhibit a distinctive p21-TREM2 expression profile and SASP, driven in part by type-I interferon signaling via secreted mitochondrial DNA. We also found that senescent macrophage accumulation occurs in aged and MASLD mouse livers and is enriched in human cirrhotic liver tissue. Finally, senolytic treatment targeting senescent macrophages reduced liver inflammation and steatosis in both aged and MASLD mice. Together, these findings establish macrophage senescence as a central driver of chronic inflammation in aging and metabolic liver disease, highlighting a promising, tractable therapeutic target.

overall_design: APOE*Leiden-CETP mice crossed to a C57BL/6J background were placed on a HFHCD. Starting at week 12 of the HFHCD, mice were either treated with vehicle or ABT-263 diluted in 10% ethanol, 30% polyethylene glycol 400 (Sigma, 807485) and 60% Phosal 50 PG (Medchem Express, HY-Y1903). ABT-263 was administered by oral gavage at 50 mg per kg body weight per day (mg kg−1 d−1) for 7 consecutive days with a 2-week break or interval between another 7-day cycle. Tissues were harvested week 17 of the HFHCD, 1-week after the last dose of ABT-263.

first: Anthony

middle: J

last: Covarrubias

middle: A

first: Itzetl

last: Avila


title: Renal cell carcinoma and cysts in a patient affected by von Hippel Lindau disease

status: Public on Feb 11 2026

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

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

overall_design: Refer to individual Series


title: Targeting the lipid metabolism proteins FASN and GPAM in alveolar type II cells decreases lung metastasis

city: London

first: Mariia

last: Yuneva

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Cancer cells that seed in the lung require lipids, which are mostly produced by alveolar type II (AT2) cells. However, whether overt metastases depend on AT2 cell-derived lipids and whether AT2 cells can be targeted to reduce metastasis growth remains unknown. We discovered that metastases stimulate the proliferation of AT2 cells in their vicinity and reprogram them into lipid feeder cells in mice and patients with breast cancer using spatial mass spectrometry imaging combined with immunohistochemistry and spatial transcriptomics. Mechanistically, we find that the secretome of the metastases contains IL-6 and formate, which increase the activity of the transcription factor sterol regulatory element-binding transcription factor 1 (SREBP-1). This in turn enhances the expression of key de novo lipid synthesis genes including fatty acid synthase (FASN) and glycerol-3-phosphate acyltransferase 1 (GPAM). Deleting Fasn selectively in AT2 cells or targeting FASN and GPAM systemically is sufficient to impair breast cancer-derived metastasis growth in mice. In summary, we discovered that overt metastases reprogram AT2 cells and that targeting the lipid metabolism of AT2 cells impairs metastasis growth.

overall_design: 6–8-week-old female Balb/c mice were inoculated with 4T1 (1 x 10^6) cells in the mammary fat pad. Mice were euthanized after 21-23 days. Lungs from either tumour-bearing or control mice were taken for the analysis. Visium spatial transcriptomics analysis was carried out according to the manufacturer’s instructions (10x Genomics) with the following parameters: Fresh-frozen mouse either control or metastatic lung tissues derived from 4T1 m.f.p. injection model was processed for spatial gene expression profiling using the 10x Genomics Visium Spatial Gene Expression platform (Visium Slide PN-2000233, SN: V13J17-305). Tissue sections were mounted on a Visium Spatial Gene Expression Slide with four capture areas, each containing ~5,000 spatially barcoded spots. Following fixation and hematoxylin and eosin (H&E) staining, tissue permeabilization was performed for 18 minutes—a duration determined through prior tissue optimization using the 10x Genomics Tissue Optimization protocol (CG000238). mRNA released from permeabilized tissue was hybridized to oligonucleotides on the slide, and reverse transcription was carried out in situ to generate spatially barcoded cDNA. Subsequent library preparation followed the manufacturer's protocol (Visium Spatial Gene Expression Reagent Kits User Guide, CG000239 Rev F), including second-strand synthesis, cDNA amplification, enzymatic fragmentation, end repair, adaptor ligation, and sample index PCR. Libraries were sequenced on an Illumina platform (NovaSeq 6000) using paired-end sequencing (Read 1: 28 bp, Read 2: 90 bp) at a target depth of (50k reads per cell/spot).

first: Weigang

last: Cai

first: Yulia

last: Panina

first: Jiadong

last: Mao

first: Juan

last: Fernández-García

first: Xiao-Zheng

last: Liu

first: Robert

last: Gunn

first: Marg

last: Crawford

first: Sarah-Maria

last: Fendt


title: Integrated Transcriptomic and Metabolomic Analyses Reveal Distinct Energy Metabolic Signatures and Functional Properties of RPE Cells under Two Culture Conditions

city: Chongqing

first: FAN

last: ZHANG

state: - Select -

address: Building 4, Room 211, 313 Jin Yue Road, Gao Xin District

country: China

institute: Jinfeng Laboratory

summary: Retinal pigment epithelium (RPE) degeneration is a major cause of vision loss in multiple retinal diseases, including age-related macular degeneration, Bietti crystalline dystrophy and Stargardt disease. Induced pluripotent stem cell (iPSC)-derived RPE cells hold promise for regenerative therapies. B27- and KSR-based media are among the most commonly used for RPE culture; however, how these culture conditions shape RPE cell identity and features remain incompletely understood. Here, we performed comprehensive transcriptomic and metabolomic profiling of iPSC-derived RPE cells cultured in B27 or KSR media to systematically compare their gene expression and metabolic features. B27- and KSR-cultured RPE cells exhibited distinct morphologies and barrier properties. Integrated multi-omics analyses revealed that KSR-cultured RPE cells displayed a relative bias toward fatty acid oxidation and oxidative phosphorylation, whereas B27-cultured RPE cells showed a relative bias toward glycolytic metabolism. The glycolytic tendency observed in B27-RPE cells was accompanied by increased expression of extracellular matrix–related genes and higher transepithelial resistance. In contrast, KSR-RPE cells exhibited comparable tricarboxylic acid cycle activity but higher expression of oxidative phosphorylation–related genes compared with B27-RPE cells. Together, these results demonstrate that RPE cells cultured under different conditions adopt distinct but partially overlapping metabolic and transcriptional states, which are associated with differences in RPE-related features and barrier properties. Our findings highlight the importance of metabolic balance between glycolysis and fatty acid oxidation in shaping in vitro RPE phenotypes.

overall_design: RNA-seq profiling of iPSC-deverived RPE maintained in KSR and B27 based culture medium at 4 weeks

first: Fan

last: Zhang

first: Chenlu

last: Wang


title: Repurposing salmon calcitonin for Glioblastoma Treatment: Targeting YAP/TAZ via Hippo pathway activation

city: Bangalore

first: Jayita

last: Goswami

address: CV Raman road

country: India

institute: Indian Institute of Science

summary: The calcitonin receptor (CTR) signaling axis has been implicated in growth regulation in Glioblastoma (GBM). This study examines the molecular and signaling effects of salmon calcitonin (sCT) treatment in GBM using proteomic, cellular, in vivo, and computational approaches. Reverse Phase Protein Array (RPPA) analysis was performed to assess changes in protein expression in glioma cells following sCT treatment and to identify signaling pathways associated with CTR activation. Complementary biochemical and functional assays were used to characterize CTR-mediated regulation of the Hippo pathway. CTR expression was found to be elevated in human and murine glioma stem-like cells in comparison to their differentiated counterparts, and intranasal sCT treatment lead to decrease in the GSC-initiated tumor growth in orthotopic mouse glioma model. In parallel, microsecond-scale all-atom molecular dynamics simulations were conducted to examine structural features of wild-type and patient-derived mutant CTR variants and their interactions with calcitonin and Gα subunits. Together, this work reveals mechanism of CT/CTR axis, therapeutic implications of sCT, and impact of structural alterations in patient-derived CTR variants in GBM.

overall_design: The human glioblastoma cell line LN229 was treated with salmon calcitonin (sCT; 300 nM) for 60 minutes. Treatments were performed in biological duplicates. Following treatment, cells were harvested and subjected to Reverse Phase Protein Array (RPPA) analysis to quantify changes in protein expression of 441 proteins. Differentially regulated proteins were identified by comparison with untreated LN229 control samples.

first: J

first: P

last: Uttarasili

first: L

last: Garg

first: KR

last: Prasasvi

first: A

last: Chowdhury

first: S

last: Saha

last: Chatterjee

last: Srivastava

first: K

last: Somasundaram


title: Single-cell analysis of human kidney biopsy tissue reveals epithelial and immune cell responses to BK polyomavirus infection

city: Ann Arbor

first: Phillip

middle: John

last: McCown

state: MI

address: 1500 E. Medical Center Drive

department: Internal Medicine - Nephrology

institute: University of Michigan Medicine

summary: BK polyomavirus (BKV) infection is associated with injury and subsequent graft loss due to the extent of injury or rejection. However, the molecular mechanisms driving injury and subsequent adverse outcomes remain poorly understood. In a cross-sectional study, single-cell RNA sequencing from kidney allograft biopsies was used to assess cell type-specific responses between uninfected controls and two distinct phases of BKV infection: peaking (increasing viral blood titers) and resolving (decreasing viral titers following immunosuppression reduction). Genes upregulated in BK viral nephropathy (BKVN) were enriched for polyomavirus infection hallmarks, including ribosome biogenesis, translation, and energy restructuring. Additionally enriched pathways included wound healing, cellular stress, antigen presentation and immune signaling. Even without BKVN (peaking BK viremia alone), epithelial cells expressed signatures for wound healing, cellular stress, and extracellular matrix remodeling. In vivo tubular cell responses at single-cell resolution were validated against single cell transcriptomic data of BKV infected cells in a cell culture model. Despite similarities, in vivo tubular cells underwent metabolic adaptation favoring fatty acid oxidation and proinflammatory responses not observed in culture models likely from an absent innate and adaptive immune system. Despite lymphopenia and immunosuppressive therapies, the proportion of recipient derived intrarenal adaptive immune cells was expanded in biopsies associated with peaking viremia alongside activation of innate immune responses. Adaptive immune cells continued to have persistent inflammatory signaling and remodeling of energy metabolism during the resolving phase of infection. These novel insights into BKV-associated injury could have implications for clinical management and improved allograft outcomes

overall_design: Kidney biopsies post transplantation were collected from allografts at time of transplant, 3 months post transplantation, and 12 months post transplantation. If a patient developed BK infection, additional kidney biopsies were collected during the course of infection. Due to the rarity of kidney transplants and to respect the confidentiality of patients' sequencing data, raw data is not deposited.

first: Tess

last: Marvin

first: Rachel

last: Sealfon

first: Olga

middle: G

last: Troyanskaya

first: Matthias

last: Kretzler

first: Chandra

middle: L

last: Theesfeld

first: Abhijit

middle: S

last: Naik


title: Investigation of tumor heterogeneity using single cell transcriptomics in Von Hippel-Lindau related renal cancer

first: Giulia

last: Scotti

summary: Von Hippel-Lindau (VHL) dìsease is a rare inherited disorder caused by the loss of the VHL gene and characterized by benign and malignant tumors in several organs. Patients with VHL disease have risk of developing multiple primary clear cell renal carcinomas (ccRCC). Patients are managed with multiple sessions of renal surgery causing renal failure and complication of dialysis or systemic progression and cancer-specific mortality. Our hypothesis states that multiple independent tumors from one VHL patient may display inter-tumoral heterogeneity characterized by differences in tumor grade, metabolic, stromal, and immune cell features that may cause different response to systemic therapy. We took advantage of a nephrectomy from one VHL patient to investigate molecular and microenvironmental factors in five independent primary tumors.

overall_design: To assess the cellular and molecular landscape of multiple tumors within the index VHL patient, five independent tumors (i.e., L1, L2, L4, L5.1 and L7) and one sample of normal parenchyma (i.e. LN) were selected and processed with single-cell RNA sequencing (scRNAseq).

first: Isaline

last: Rowe

first: Giovanni

last: Pipitone

first: Andrea

last: Salonia


title: HOW(S) RIP-seq in D. melanogaster testes

city: Leeds

first: Michaela

last: Agapiou

address: Woodhouse Lane

institute: University of Leeds

summary: Held out wings (HOW) is an RNA-binding protein essential for spermatogenesis in Drosophila melanogaster. HOW is a signal transduction and activation of RNA (STAR) protein, these proteins are important post-transcriptional regulators of RNAs. The characteristics of RNA-binding by the conserved short cytoplasmic isoform, HOW(S), are unknown. In vivo RIP-seq identified 121 novel transcripts bound by HOW(S) in spermatogonia, many with signal transduction functions. (A/G/U)CUAAC motifs were enriched in 3'-UTRs and GCG(A/U)G in 5'-UTRs. HOW binds with high-affinity to sites containing the CUAAC motif from lola and hipk mRNAs, but not to GCG(A/U)G 5’-UTR motifs. Overall, this study provides new insight into STAR protein-RNA interactions and potential importance to spermatogenesis.

overall_design: In vivo RIP-seq with anti-HA beads from two different genotypes of D. melanogaster testes: 1) nanos-GAL4>UAS-HOW(S)-HA and 2) nanos-GAL4.

first: Agapiou

last: Michaela

first: Hopes

last: Tayah

first: Bretman

last: Amanda

first: Edwards

last: Thomas

first: Aspden

last: Julie


title: Role of Cancer-Associated Fibroblasts in Prognostic Stratification of Advanced-Stage Gastric Cancer through Interacting with Endothelial and Malignant Epithelial Cells [AGC scRNA-seq]

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

summary: Patients with advanced gastric cancers (AGCs) would experience poor prognosis, lacking investigation on comprehensive ecosystem profile and specific prognostic factors. Here, we conducted patient stratification based on unsupervised clustering of transcriptomic profile of 108 normal/tumor AGC pairs and integrated single-cell RNA transcriptome profile of 116 gastric cancer/normal samples, revealing the heterogeneity of AGC, which can be stratified into distinct AGC-related signature (AGCRS)-based patient groups with different prognosis. AGCRS scores are over-presented in cancer-associated fibroblasts (CAF) and increase in metastasis-enriched subtypes (e.g., myofibroblastic CAF). More prolific cell-cell communications were observed between CAF and metastasis-enriched epithelial/endothelial through collagen-related interactions. Experimentally, CAF conditional-medium can enhance the tube formation of endothelial cells and HOXC-AS2-related migration ability of gastric cancer cells. Particularly, HOX-AS2 can facilitate the nucleus translocation of YBX1 through direct binding in cytoplasm and induce the epithelial-mesenchymal transition. Our findings highlight the potential prognostic role of AGC heterogeneity induced by CAF-related communications.

overall_design:
Upload data contains 11 in-house samples and 105 samples that have been submitted by others to GEO (We do the re-analysis and annotated these data by geo_accession).

***************************************************************
Submitter states that missing raw data are being made available in the Genome Sequence Archive (GSA) for human.
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***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
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title: Prostaglandin D2 synthase controls Schwann cells metabolism

city: Milano

first: Luca

last: Massimino

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: We previously reported that in the absence of Prostaglandin D2 synthase (L–PGDS) peripheral nerves are hypomyelinated in development and that with aging they present aberrant myelin sheaths. We now demonstrate that L–PGDS is part of a coordinated program aiming at preserving myelin integrity. In vivo and in vitro lipidomic, metabolomic and transcriptomic analyses confirmed that myelin lipids composition, Schwann cells energetic metabolism and key enzymes controlling these processes are altered in the absence of L–PGDS. Moreover, Schwann cells undergo a metabolic rewiring and turn to acetate as the main energetic source. Further, they produce ketone bodies to ensure glial cell and neuronal survival. Importantly, we demonstrate that all these changes correlate with morphological myelin alterations and describe the first physiological pathway implicated in preserving PNS myelin. Collectively, we posit that myelin lipids serve as a reservoir to provide ketone bodies, which together with acetate represent the adaptive substrates Schwann cells can rely on to sustain the axo-glial unit and preserve the integrity of the PNS.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Gene espression profiles of rat Schwann cells -mouse dorsal root ganglia myelinated cocultures treated with AT-56, an L-PGDS specific inhibitor for 7 days or with the DMSO control vehicle

first: Amelia

last: Trimarco

first: Carla

last: Taveggia


title: The interplay between RNA sequestration in P-bodies and chromatin architecture sustains myeloid leukemia

city: Houston

first: Eric

last: Van Nostrand

state: Tx

address: 1 Baylor Plaza

department: Biochemistry and Molecular Pharmacology

institute: Baylor College of Medicine

summary: To identify direct DDX6 mRNA targets in AML cells, we performed eCLIP-seq in the MOLM-13 cell line.

overall_design: DDX6 eCLIP-seq of MOLM-13 cells

first: Srikanth

last: Kodali

first: Mason

middle: D

last: Bartels

first: Anne

middle: C

last: Starner

first: Bruno

last: Di Stefano


title: P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [RNAseq_sgCMPK2]

first: Ivan

last: Salladay-Perez

overall_design:
Primary bone marrow derived macrophages edited with CRISPR/Cas9 RNP complex for Rosa26 and Cmpk2 locus. Data represents .csv and .fastq.gz files of 2x100 bp mRNA sequencing.

**Raw data were uploaded to SRA under BioProject PRJNA1416426. SRA Accessions are listed in Series supplementary file (SRA_Run_accessions.xlsx, SRR contains raw data for three replicates).

first: Anthony

last: Covarrubias

first: Cristian

last: Ponce


title: Nucleolar migration regulates meiotic sex chromosome inactivation via phase separation during mammalian spermatogenesis

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

summary: During spermatogenesis, the unsynapsed XY chromosomes undergo meiotic sex chromosome inactivation (MSCI) and form a heterochromatic XY body. Defects in MSCI lead to meiotic arrest and male infertility. Although DNA damage response (DDR) factors are established as key initiators of MSCI, how transcriptional silencing is subsequently achieved remains elusive. Here, we identify the nucleolar components NPM1, SENP3, and rRNA as essential downstream effectors of DDR signaling in MSCI. During pachytene, these components migrate to and transiently cover the XY body during MSCI establishment, before becoming restricted to a corner of the XY body. Genetic deletion of Npm1 or Senp3, or inhibition of rRNA transcription severely impairs MSCI. Mechanistically, SENP3-mediated deSUMOylation of NPM1 promotes its interaction with rRNA, enabling liquid-liquid phase separation, via which they exclude Pol II from the XY body. Together, these data reveal a previously unrecognized role of nucleolar components in the transcriptional regulation of MSCI in mammalian spermatogenesis.

overall_design: Small scale in situ high throughput chromatin conformation capture (sisHi-C) or RNA-seq for WT and mutant zygotene, pachytene, or diplotene spermatocytes

first: Wei

last: Xie


title: Oncogenic mechanisms of DIS3 mutations in Multiple Myeloma

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

summary: DIS3 is mutated in multiple myeloma (MM), but the mechanism by which oncogenesis occurs specifically in B cell lineage remains to be established. Somatic DIS3 variants have substitutions enriched around its RNB domain, which in a dominant negative way, inactivate or reduce the exoribonucleolytic activity of this enzyme responsible for nuclear RNA degradation. Here using knock-in mice with a clinical Dis3 G766R variant, we demonstrate a B cell-specific mutagenic effect that induces aberrant chromosomal translocations, increasing the incidence of plasmacytoma, a mouse model of early-stage MM. Dis3 G766R -dependent translocations display characteristics typical to aberrant activation-induced deaminase (AID) activity sites. Indeed, analysis of MM clinical samples revealed that in MM driver genes, DIS3 alleles lead to increased AID-dependent DNA lesions. Mechanistically, mutated DIS3 accumulates on chromatin-associated RNA substrates, including aberrant AID action sites, fostering oncogenic chromosomal rearrangements. Translocations occur during immunoglobulin class switch recombination, which otherwise proceeds unaffected both MM and the mouse model. In conclusion, MM DIS3 mutations lead to a gain-of-function phenotype and drive MM development, enhancing driver translocations.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of total transcriptome by RNA-seq in Human Multiple Myeloma PE2 (DIS3 A507P/A507P) with lentiviral reconstitution of DIS3 WT expression and in primary mouse embryonic fibroblast cells and B-cells isolated from DIS3 G766R/+ heterozygous mice and their litter counterparts. Examination of genomic structural variants in pristan induced plasmocytoma cells from DIS3 G766R/+ and DIS3 WT mice. Examination of the global chromatin architecture in B-cells isolated from DIS3 G766R/+ heterozygous mice and their WT litter counterparts by MicroC.  Examination of RNA/DNA hybrid accumulation in B-cells isolated from DIS3 G766R/+ heterozygous mice and their WT, litter counterparts by DRIPc-seq.

middle: M

first: Andrzej

last: Dziembowski


title: Ribo-ITP coupled ribosome profiling identifies non-canonical translational events in low input samples

city: Austin

first: Vighnesh

last: Ghatpande

state: Texas

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: In the last decade,  an unexpectedly large number of translated regions (translons) have been discovered using ribosome profiling and proteomics. Translons can regulate mRNA translation and encode micropeptides that contribute to multiprotein complex formation, Ca2+ regulation in muscle, and signaling during embryonic development. However, identification of translons has been limited to cell lines or large organs due to high input requirements for conventional ribosome profiling and mass spectrometry. Here, we employed Ribo-ITP, a low input ribosome profiling technique on difficult to collect samples like microdissected hippocampal tissues and single pre-implantation embryos. We detected thousands of translons across these samples, most of which initiated at non-canonical start sites, were less than 100 amino long with significantly altered amino acid composition. Comparative analysis of more than a thousand ribosome profiling datasets across a wide range of cell types revealed pervasive expression of most of the detected translons. To test the translational capacity of the detected translons, we engineered a translon dependent GFP reporter system, and detected robust expression of translons initiating at near-cognate start codons in mouse embryonic stem cells (mESCs). Mutating the translons in mESCs identified a small proportion that negatively impacted growth. Taken together, we present a proof-of-concept study to identify non-canonical translation events from ultra-low input samples which can be applied to cell and tissue types inaccessible to conventional methods.

overall_design: To identify non-canonical translation events, ribosome profiling from low input samples - microdissected mouse hippocampal acute slices and mouse preimplantation embryos was performed followed by pooled Crispr-Cas9 screen to calidate the identified events.

first: Ghatpande

last: Vighnesh

first: Paul

last: Uma

first: Howard

last: Mackenzie

first: Cenik

last: Can


title: CITE-seq of cardiac CD45+ leukocytes in mice with myocardial infarction and NK cell depletion

city: Würzburg

first: Alexander

last: Leipold

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

summary: Myocardial infarction triggers an inflammatory response which plays a crucial role in repair and remodelling of the infarcted heart. In this study we examined the role of Natural Killer cells (NK cells), a specific type of inflammatory cells, in controlling the inflammatory response and cardiac repair after myocardial infarction. To assess effects on local inflammation, we used single-cell RNA-seq and CITE-seq to profile cardiac CD45+ leukocytes in infarcted mice with or without NK cell depletion. Biological replicates from the different experimental conditions were pooled using cell hashing as follows:  hashtag 1 to 5 control mice; hashtags 6 to 10: NK-depleted mice.

overall_design: 8-12 week old male C57BL6J mice underwent permanent coronary ligation to induce myocardial infarction and were injected i.p. with a depleting mouse anti-mouse NK1.1 monoclonal antibody or with and isotype control antibody 1 hour after coronary artery ligation. Five days after the induction of myocardial infarction, CD45+ cells were extracted from the infarcted heart and processed for single-cell RNA-seq with CITE-seq and cell hashing.

first: Hafid

last: Ait-Oufella

first: Giuseppe

last: Rizzo

first: Clément

last: Cochain

first: Tobias

last: Krammer

first: Antoine-Emmanuel

last: Saliba


title: Single-cell transcriptional patterns impairment in an adult neurogenesis model of Alzheimer´s disease

city: Thuwal

first: Xabier

last: Martinez de Morentin

address: Kaust

country: Saudi Arabia

institute: KAUST

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Alzheimer’s disease (AD) disrupts neurogenesis and neuronal differentiation, processes critical for cognitive function. This study investigates transcriptional and regulatory changes during neuronal differentiation under the influence of amyloid-beta (Aβ) peptide using scRNA-seq and scATAC-seq approaches. Neuronal differentiation trajectories showed three distinct groups of differentially expressed genes (DEGs). Notably, while some neurogenesis-related genes like VIM, MAPT, STMN2, and SLC17A6 were unaffected by Aβ, others, such as PAX6, NEFL, NEFM, and CALB1, displayed significant alterations, particularly in transitions to mature neuronal states. Functional enrichment analysis highlighted disruptions in ATP synthesis, oxidative phosphorylation, synaptic signaling, and cytoplasmic translation. Regulatory transcription factors (TFs) such as EGR1, GATA2, PAX6, and SOX2 were also implicated in these changes.  Translational characterization revealed that the gene expression changes observed in the Aβ condition partially aligned with dysregulated gene patterns in hippocampal tissue from AD patients. Differential analysis across stages indicated that mature neuronal differentiation stages exhibited stronger concordance with AD-related gene expression.  To understand the role of chromatin accessibility, scATAC-seq analysis identified dysregulation in gene regulatory networks (GRNs) driven by key TFs such as ASCL1, HOXB2, POU2F2, and ONECUT2. Notably, regulons promoting neurogenesis in control conditions were impaired or delayed under Aβ exposure, with regulons specific to mature neuronal transitions emerging only in the presence of Aβ. Functional analysis of these regulons revealed enrichment for pathways associated with differentiation, neuron migration, and synaptic regulation, suggesting Aβ-mediated disruption of neurogenesis-associated regulatory programs.  In summary, this study highlights Aβ-induced transcriptional and regulatory disruptions during neuronal differentiation, linking these changes to AD pathology. It underscores the importance of transcriptional and epigenetic regulation in understanding AD and provides insights into how Aβ interferes with neurogenic processes critical for neuronal maturation and function.

overall_design: Neural progenitor cells (NPCs) derived from XCL1 DCXpGFP (ACS5005™, ATCC, Manassas, VA, USA) were cultured and differentiated to neurons following standardized protocols. NPCs were seeded at 0.30 × 10⁶ cells per well in CellMatrix Basement Membrane Gel-coated 12-well plates and maintained in NPC expansion medium, consisting of DMEM/F-12 supplemented with the Growth Kit for Neural Progenitor Cell Expansion. Cultures were incubated in a humidified chamber at 37°C with 5% CO₂.  For neuronal differentiation, NPCs were seeded at 80,000 cells/cm² in 6-well plates. On Day 0, NPCs were cultured in expansion medium, transitioning to a differentiation medium from Day 1 onward, with half-medium changes every 2–3 days. The differentiation medium was BrainPhys™ Neuronal Medium, supplemented with NeuroCult™ SM1 (1:50), N2 Supplement-A (1:100), BDNF (20 ng/mL), GDNF (20 ng/mL), dibutyryl-cAMP (1 mM), and ascorbic acid (200 nM). Amyloid-β peptide (Aβ₁₋₄₂; 50 nM) or DMSO (vehicle control) was added weekly.  Cells were harvested on Days 0, 7, 13, and 20 for both Aβ-treated and control conditions. Detachment was performed using Accutase, followed by washing in Dulbecco's phosphate-buffered saline (DPBS) and centrifugation at 13,000 rpm. Cell pellets were resuspended in a filtered buffer (0.05% BSA in PBS).  Prior to single-cell RNA sequencing (scRNA-seq), viable cells were enriched using TO-PRO-3 dye and sorted using a MoFlo Astrios EQs Sorter. Dead cells were excluded, and single, viable cells were gated based on FSC/SSC and FSC width/area criteria. Between 20,000 and 70,000 viable cells were collected and processed immediately for scRNA-seq analysis.

first: Idoia

last: Blanco-Luquin

first: David

last: Gómez Cabrero

first: Maite

last: Mendioroz


title: Identification of specific binding sites of ADR-1 in vivo

city: Bloomington

first: Boyoon

last: Yang

address: 1001 E 3rd St

institute: Indiana University

summary: We used eCLIP to identify in vivo binding sites of ADR-1, a member of the adenosine deaminase acting on RNA (ADAR) family of dsRBPs in Caenorhabditis elegans, using 3xFLAG ADR-1 animals.

overall_design: CLIP-seq was performed to identify in vivo binding sites of ADR-1 using 3xFLAG ADR-1 animals (HAH59).

first: Douglas

middle: B

last: Rusch

first: Heather

last: Hundley


title: Studying the role of humanized-TLR8 on immune cell dynamics in the placental microenvironment in a spontaneous mouse model of aPL-induced pregnancy loss

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: Antiphospholipid antibodies (aPL) confer a high risk for adverse pregnancy outcomes, especially in women with SLE. aPLs can induce pro-inflammatory signaling via TLR8 receptors, but mouse models to study the role of TLR8 are limited due to the attenuated ssRNA-binding capacity of mouse TLR8. We generated a spontaneous model of aPL-induced pregnancy loss by crossing Sle1 mice with mice expressing a human TLR8 transgene (Sle1.huTLR8tg). Sle1.huTLR8tg mice, but not Sle1 or C57BL6.huTLR8tg mice, have a high frequency of pregnancy loss, demonstrating the requirement for both autoantibodies and TLR8 in fetal-placental injury.  Term placentas from Sle1.huTLR8tg mice displayed multiple abnormalities, including attenuation of vessels in the labyrinth, thinning of the junctional zone, thickened arterial walls, placental infarcts and inflammation. Resorptions were observed in Sle1.huTLR8tg mice at embryonic day (E)13.5, and Sle1.huTLR8tg feto-placental units were decreased in size as early as E8.5, suggesting early developmental defects. The goal of this study was to investigate transcriptional changes in early placental development that could be playing a role in the subsequent adverse pregnancy outcomes.

overall_design: Bulk RNA-sequencing was conducted on feto-placental units from Sle1 and Sle1.huTLR8tg mice at Day E8.5 (day of peak decidualization and spiral artery remodeling) and on formed placentas from Day E13.5 (at which time the placenta has been fully formed). Sle1 feto-placental units and placentas acted as the control group for both timepoints, while feto-placental units and placentas from Sle1.huTLR8tg mice were further divided into 2 categories: resorbed and non-resorbed.

first: Zhengzi

last: Yi

first: Anne

last: Davidson


title: Single cell analysis highlights the significance of malignant cell IFN/MHC-II for immunotherapy response in head and neck squamous cell carcinoma

city: Saint Louis

first: Sidharth

last: Puram

address: 660 Euclid Ave

institute: Washington University in St Louis

summary: For many cancers, including head and neck squamous cell carcinoma (HNSCC), response rates to immunotherapy remain modest, with limited ability to predict responders. Previous studies that characterized cellular changes associated with immunotherapy in HNSCC focused on immune cells, providing limited insight into malignant cell responses. Motivated by this gap, we performed single cell RNA-sequencing on 16 HNSCC patients pre- and post-neoadjuvant pembrolizumab treatment. We identified a malignant-interferon (IFN)/MHC-II program in malignant cells, characterized by expression of MHC-II and interferon response genes, which was associated with tumor response to pembrolizumab. We validated malignant cell MHC-II expression at the protein level and characterized its relationship with surrounding immune subsets via multiplexed immunofluorescence. In a murine HNSCC model, IFN-γ-induced malignant cell MHC-II expression marked tumors with favorable immune microenvironments and sensitivity to immunotherapy. Finally, we confirmed pre-treatment expression of the malignant-IFN/MHC-II program as marker of response through deconvolution of bulk RNA-seq data from an independent cohort of 25 pembrolizumab-treated HNSCC patients. Beyond identifying malignant cell MHC-II expression and the malignant-IFN/MHC-II program as potential biomarkers for immunotherapy response in HNSCC, our work provides additional insights into the specific and important role of malignant cells in immunotherapy.

overall_design: We performed single cell RNA-sequencing and T-cell receptor sequencing from fresh primary tumor single-cell suspensions collected from 16 patients with locally-advanced HPV-negative HNSCC, both before and after treatment with neoadjuvant pembrolizumab. We characterized 137,020 high quality cells. Our goal was to capture both immune and malignant cell populations to comprehensively characterize the landscape of cellular and expression heterogeneity and change with immune checkpoint inhibition.

first: Michael

last: Mints

first: Reilly

last: Sample

first: Anuraag

last: Parikh

first: Jesse

last: Zaretsky

first: Itay

last: Tirosh

middle: V


title: CD27 Agonism Enhances Long-Lived CD4⁺ T Cell Vaccine Responses Critical for 2 Anti-Tumor Immunity

city: Durham

last: Severson

state: North Carolina

address: 2301 Erwin Road

department: Department of Surgery

institute: Duke University Health System

summary: Patients with metastatic breast cancer were vaccinated with dendritic cell (DC) vaccine targeting HER2, and all seven survived >18 years. PBMC analysis revealed HER2-specific CD27⁺ memory CD4⁺ and CD8⁺ T cells, suggesting that CD27 signaling supports durable immune memory. We tested this by combining an anti-CD27 agonist antibody (Varlilumab) with a HER2 vaccine, which enhanced HER2-specific responses, particularly long-lived CD4⁺  memory T cells detectable up to 300 days post-vaccination. CD27 agonism improved tumor control (~40% regression) compared to vaccine alone (~6%), and synergy with PD-1 blockade led to complete tumor rejection in ~90% of mice. CD4⁺ T cells were essential for this effect, as shown by depletion and adoptive transfer experiments, while CD8⁺ T cells played a less critical role. We utilized combined scRNA-seq and TCR sequencing to identify expanded clonotypes and increased CD8+ and CD4+ functional subsets with combined CD27 agonism and vaccination as well as vaccination alone. These findings demonstrate that antigen-specific huCD27⁺ CD4⁺ T cells are key effectors of vaccine-induced immunity and support CD27 agonism as a promising strategy to enhance therapeutic cancer vaccination.

overall_design: MM3MG-HER2del16 cells were orthotopically implanted into the mammary fat pad of female 8-12 weeks old F1 offspring mice, by crossing between HuCD27-Tg with regular Balb/C or Jh-Balb/C (1x106 cells/animal). Four arms of these tumors were harvested for combined TCR and scRNA-seq sequencing by 10X: control IgG treated mice, anti-human CD27 antibotdy treated alone, vaccination with AdHER2, and combined vaccination with anti-human CD27 antibody treatment.  Mice were sacrificed and tumor collected at 14 days post vaccination.

first: Zachary

last: Hartman

first: Bin-Jin

last: Hwang

middle: T

first: Erika

last: Crosby


title: The regulatory landscape of optic fissure closure in the vertebrate eye

city: Midlothian

first: Joe

last: Rainger

address: Roslin Institute, Easter Bush Campus

institute: Roslin Institute

summary: The process of optic fissure closure (OFC) is a critical tissue fusion event in eye development. Failure of OFC results in coloboma, a persistent gap in the eye that can significantly affect vision. Most coloboma cases do not have a genetic diagnosis, reflecting poor understanding of the genes required for OFC and how these are regulated and their impact on cell behaviours. The chicken is a good model for interrogating developmental gene expression and regulatory networks, and the embryonic chicken eye develops similarly to humans.  Results: Here we performed integrated profiling of accessible chromatin and gene expression during OFC in the chicken embryonic eye. This revealed domains of accessible chromatin during active fusion and in the broader ventral retina that were distinct from the dorsal retina, implicating these as active during fusion of the optic fissure and important for gene regulation in this distinct region of the developing vertebrate eye. Open chromatin elements could be linked by proximity and TAD boundaries to adjacent genes that have distinct spatial and temporal expression profiles during optic fissure closure. Using a combination of de novo motif enrichment and transcription factor (TF) foot-printing occupancy analyses in silico, we found evidence for TEAD/ZIC/SOX activity during OFC, and retinoic-acid related TF activity in the developing dorsal eye. We were able to map a sub-set of chicken OFC specific peaks to cis-regulatory elements in the human genome and identified loci proximity to known human coloboma genes or in coloboma candidate genes identified by our analyses in chicken. Conclusions: This study leverages eye development in the chicken embryo to deliver the first evidence for dynamic cis-regulatory activity of gene expression during OFC and identifies candidate loci for future mutational and activity analyses, providing the first genetic clues to identify non-coding loci as candidates for coloboma.

overall_design: ATAC-seq samples of bulk-dissected fissure and dorsal retina tissue from Hamburger-Hamilton (HH) stage 30 and 34 chicken embryos respectively. There are three biological replicates per condition, and each replicate is prepared from pooled dissected retinal tissues of 10 embyos.

first: Brian Ho Ching

last: Chan

first: Mariya

last: Moosajee

first: Holly

last: Hardy

first: James

last: Prendergast


title: Single-cell RNA-Seq profiling to characterize mammary tumor infiltrated immune cells with iron supplement during anti-PD-1 immunotherapy

city: Indianapolis

first: Qingfei

last: Wang

state: IN

address: Walther Hall-R3 C243

department: Division of Hematology/Oncology, Department of Medicine

institute: Indiana University School of Medicine

summary: In previous study, we demonstrated that iron supplementation augmented the antitumor effect of PD-1 based immunotherapy in triple-negative breast cancer models. To gain a more profound understanding into whether and how iron plus PD-1 antibody combination influences tumor immune microenvironment to exert better therapeutic activity, in this study, we performed single cell RNA-sequencing with PIP-seq to profile and compare tumor infiltrated CD45+ cells derived from control, iron or PD-1 antibody alone, and combination treated E0771 tumors.

overall_design: Tumor infiltrated CD45+ cells derived from control, iron or PD-1 antibody alone, and combination treated E0771 tumors were flow sorted and analyzed by single cell RNA-sequencing using PIP-seq pipelines. Cells from three or four tumors of each treatment group were pooled for PIP-seq.

first: Mateusz

last: Opyrchal


title: BET inhibition targets pathogenic interstitial macrophages to limit antibody mediated fibrosis in bronchiolitis obliterans chronic GVHD

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

summary: Chronic graft-versus-host disease (cGVHD) is a major cause of late mortality in allogeneic-hematopoietic stem cell transplantation with bronchiolitis obliterans syndrome (BOS) among the most lethal treatment-resistant complications. Despite approval of 4 second-line therapies, clinical response in moderate and severe BOS patients remains poor. Bromodomain and Extra terminal (BET) proteins are epigenetic readers driving oncogenic and inflammatory transcriptional programs in multiple cell types. We hypothesized that BET inhibition would be a feasible therapeutic option by restraining the direct inflammatory T cells as well as macrophage polarization to profibrotic phenotype known. We used an established BOS cGVHD model wherein we treated cGVHD mice with the translatable BET inhibitor: OPN-51107 (BETi). We found that under BETi, T and B cells had reduced germinal center (GC) trafficking ability, and GC activation resulting in reduced IgG1+ class switched B cells. Mice with cGVHD had elevated pathogenic IgM and IgG1 both in circulation and deposited onto lung tissue, which was attenuated under BET inhibition. Furthermore, antibodies produced in cGVHD were both allo- and auto-reactive. Single-cell RNA sequencing analysis revealed 22 distinct cell types in the BOS lung. In cGVHD mice, GSEA analysis revealed upregulation of anti-inflammatory Arginase1 and profibrotic Tgfb1 expression in alveolar macrophages (AM) and interstitial macrophages (IM), which was significantly reduced in BETi treated mice. Spectral flow cytometry confirmed that BETi targeted lung-infiltrating M2 macs, through diminishment of CD206+FcgR+ M2 IMs and AMs. Ultimately, this concluded in reduced collagen deposition and improved lung function in mice treated with BETi. We identify BET proteins as a key regulator of inflammation in BOS. BETi suppresses Tfh and GC B cells, thereby reducing Ab production and deposition. Within the lung, BETi selectively targets M2 IM macs to reduce FcgR and TGF-b expression, thereby regulating collagen deposition and fibrosis. These findings reveal a previously unrecognized mechanistic axis driving cGVHD and highlight BET inhibition as a promising therapeutic strategy.

overall_design: Single cell RNA-sequencing of isolated lung cells via the 10X Genomics NextGem Fixed RNA Profiling kit.

first: Rathan

last: Kumar

first: Lotus

last: Neidemire-Colley

first: Elizabeth

last: Garfinkle

first: Parvathi

last: Ranganathan


title: The Arp5-Ies6 module is essential for INO80-mediated nucleosome organization

city: Paris

first: Ashish

middle: Kumar

last: Singh

state: Ile-de-France

address: 25-28 Rue du Dr Roux

department: Development and Stem Cell Biology

country: France

institute: Institute Pasteur

summary: ATP-dependent nucleosome remodelers of the INO80 family regulate chromatin by sliding, spacing and positioning nucleosomes. The INO80 remodeler is organized into structural modules that regulate its remodeling activity. Here, we investigate the role of the essential Arp5-Ies6 module towards nucleosome positioning and spacing in S. cerevisiae. We show that the Arp5-Ies6 module is critical for establishing genome-wide nucleosome organization. Deletion of IES6 reduces nucleosome spacing by 3 bp and disrupts regular nucleosome arrays across most genes. Surprisingly, deletion of IES6 is synthetic lethal with the deletion of ISW2, a remodeler from the ISWI family, indicating functional redundancy in nucleosome organization. Notably, INO80 binding directly predicts the role of Arp5-Ies6 in nucleosome organization, whereas changes in gene expression do not correlate with altered nucleosome spacing or array regularity. Together, our results highlight the essential role of the Arp5-Ies6 module in INO80-mediated chromatin organization.

middle: K

first: Felix

last: Mueller-Planitz


title: Clonal biases dictate availability of colonic cancer driver mutations for transformation

city: Cambridge

first: Matthew

last: Eldridge

address: Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

summary: Aged normal tissues harbour cancer mutations predisposing to transformation. However, previous studies of human colon have not allowed a comparison of the prevalence and behaviours of different pro-oncogenic events. Here, having detected cancer driver mutations in histologically normal FFPE tissue using targeted amplicon sequencing, we perform spatial transcriptomics to investigate whether monoallelic cancer driver clones can be phenotypically profiled in normal tissue. We found that KRAS mutant clones are associated with a profound shift in their transcriptome and were able to create a signature of 628 genes. The results highlighted phenotypic heterogeneity in KRAS mutant clones of the same genotype, with mixed lineage presentation seen in a proportion of them, a state that has been linked with increased risk of transformation in other organs. REG4 was also identified as a surrogate protein marker of KRAS mutant clones, the use of which could be further validated in a clinical setting for patient stratification.

overall_design: Human FFPE samples of normal colon tissue with previously identified cancer driver mutations (based on targeted-amplicon sequencing) were subjected to 10X Visium. Targeted-amplicon sequecing had allowed the spatial localisation of the mutant areas, so only these parts of the tissue, togetther with some adjacent normal, were subjected to sequencing.

first: Nefeli

last: Skoufou

first: Doug

last: Winton

first: David

last: Tourigny


title: Bulk RNA-seq profiling of mouse livers with Themis ablation under MASH diet feeding condition

city: Ann Arbor

first: You

last: Lu

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is a severe chronic liver condition characterized by hepatocyte steatosis, inflammation and fibrosis, with a rising prevalence globally, posing significant health risks and potentially leading to complications such as cirrhosis, liver failure, and increased mortality. Previous study in our lab has identified Themis as a highly up-regulated gene in hepatocytes during MASH progression using a diet-induced mouse model. Genetic ablation of Themis exacerbated MASH symptoms, including more severe steatosis, liver injury, fibrosis and more immune cell infiltration.

overall_design: To gain further insights of how Themis regulates how liver responds to MASH diet feeding, liver samples from wild-type or wholebody Themis knockout mice that had been fed on MASH diet were subject to bulk RNA-seq profiling.

first: Xiaoxue

last: Qiu

first: Jiandie

last: Lin


title: Single cell sequencing of bladder cancer patients

city: Chongqing

first: Li

middle: qiu

last: Liu

address: No. 10, Changjiang Road, Daping, Yuzhong District, Chongqing

institute: Chongqing Daping Hospital

summary: To achieve a more profound comprehension of the bladder tumor microenvironment, we have meticulously curated single-cell samples from 11 patients diagnosed with bladder cancer. Our comprehensive analysis not only elucidates the intricate heterogeneity among distinct cellular subpopulations within the tumor but also uncovers the underlying cellular interactions. These findings collectively serve as an invaluable asset, paving the way for the development of innovative and targeted therapeutic strategies for bladder cancer.

overall_design: We performed single-cell sequencing on samples derived from five patients. Initial data processing involved stringent quality control to exclude low-quality cells. This included filtering based on thresholds for unique molecular identifiers (nUMI), expressed genes (nGene), and mitochondrial gene content. We also applied a doublet removal step. The resulting high-quality gene expression matrix is provided to facilitate studies on tumor microenvironment heterogeneity, immune cell composition in bladder cancer.

first: Qiuli

first: Weihua

last: Lan

first: Jun

last: Jiang

first: Weiming

last: Luo


title: Single-nucleus RNA-seq profiling of mouse livers with hepatocyte-specific ablation of Themis under MASH diet feeding

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is a severe chronic liver condition characterized by hepatocyte steatosis, inflammation and fibrosis, with a rising prevalence globally, posing significant health risks and potentially leading to complications such as cirrhosis, liver failure, and increased mortality. Previous study in our lab has identified Themis as a highly up-regulated gene in hepatocytes during MASH progression using a diet-induced mouse model. To gain further insights into the roles of Themis in regulating hepatic responses to MASH diet, we generated mice with hepatocyte-specific ablation of Themis (HKO). The HKO mice exhibited worse MASH symptoms, including more severe steatosis, liver injury, fibrosis and more immune cell infiltration, relative to their Themis flox/flox control littermates.

overall_design: C57BL6/J mice with hepatocytes-specific ablation of Themis (HKO) were established by crossing Themis flox/flox mice with a line carrying Albumin promoter-driven Cre (Alb-Cre). Male mice were fed on a MASH diet for five months. Liver tissues were collected for snRNA-seq experiment.


title: Research on the Resistance Mechanism of Prostate Cancer to BL-B01D1

city: shanghai

first: Yao

last: Zhu

state: shanghai

address: dongan road 270

department: urology

institute: Fudan University

summary: Metastatic castration-resistant prostate cancer (mCRPC) remains a lethal disease with limited treatment options following resistance to AR signaling inhibitors. Despite the known roles of EGFR and HER3 in prostate cancer progression, prior therapies targeting this pathway have failed clinically. In this study, we evaluate the therapeutic potential of BL-B01D1, a bispecific antibody–drug conjugate (ADC) targeting EGFR and HER3, in prostate cancer models.  BL-B01D1 exhibited potent, target-dependent cytotoxicity across prostate cancer cell lines, xenografts, and patient-derived organoids. Mechanistically, we identified ABCG2 upregulation as a driver of acquired resistance, and pharmacological inhibition of ABCG2 restored drug sensitivity. These findings establish BL-B01D1 as a promising therapeutic strategy in mCRPC and nominate ABCG2 as a potential combination target to overcome resistance.

overall_design: 22Rv1 cells were cultured with gradually increasing concentrations of BL-B01D1 or with vehicle as a control.

first: Bangwei

last: Fang


title: UVDE-HS-seq map of 6-4PP and atypical TA photoproducts in UV-irradiated normal human skin fibroblasts and UV-irradiated genomic DNA

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: UV-induced pyrimidine-pyrimidone (6-4) photoproducts (6-4PPs) and atypical thymine-adenine (TA) photoproducts were mapped in normal human skin fibroblasts following 500J/m2 of UVC irradiation and in isolated human genomic DNA (naked DNA control) irradiated with 400J/m2 of UVC irradiation. 6-4PPs and TA-PPs were mapped across the human genome using the UVDE-HS-seq method

overall_design: A method known as UVDE-HS-seq was used to map the formation of UV-induced pyrimidine-pyrimidone (6-4) photoproducts (6-4PPs) and atypical thymine-adenine (TA) photoproducts across the genome of normal human skin fibroblasts (NHF1) cells after they were irradiated with a UV dose of 500 J/m2 of UVC light. As a control experiment, isolated human genomic DNA was irradiated with 400 J/m2 of UV (naked DNA control) and 6-4PPs and TA-PPs were mapped using UVDE-HS-seq.

middle: J

first: Kaitlynne

middle: A

last: Bohm


title: Comparative analysis of the transcriptomic response to cisplatin in drug-sensitive and drug-resistant testicular germ cell tumors.

city: Urbana

first: Mehwish

middle: Wahid

last: Khan

state: Illinois

address: 2001 S Lincoln Ave

department: Department of Comparative BioSciences

institute: University of Illinois Urbana-Champaign

summary: Testicular germ cell tumors (TGCTs) are uniquely curable with cisplatin-based therapies even when widely metastatic, however cisplatin resistance does occur resulting in very poor prognosis. The mechanisms to explain TGCT hypersensitivity to cisplatin and mechanisms of resistance are not well understood. The global transcriptional response to acute cisplatin treatment (24 hours after a 6-hour pulse of cisplatin) was assessed in three parental embryonal carcinoma TGCT cells lines compared to multiple isogenic, stable, cisplatin-resistant clonal lines from these pa-rental cells.  Cisplatin treatment of parental cells consistently showed a more robust overall transcriptional response to cisplatin compared to their cisplatin-resistant cellular counterparts for a common set of genes and pathways including the upregulation of genes associated with histone modifications and p53, EMT, and KRAS signaling and the downregulation of genes normally upregulated by MYC. Focusing on genes exclusively altered in parental cells revealed upregulated genes known to be induced by p53 and downregulated by MYC and the transferrin receptor, TFRC1. Several of these p53/MYC/TFRC1 targets were associated with a higher instance of disease free survival in a cohort of TGCT patients. Cisplatin resistance in TGCT cells is associated with a diminished alteration of cisplatin responsive genes especially genes known the be regulated by p53, MYC and TFRC1 that may be linked to cisplatin hypersensitivity and survival in TGCTs.

overall_design:
This study represents a reanalysis of RNA-seq data combining newly generated cisplatin treated testicular germ cell tumor(TGCT) samples with the previously submitted untreated control samples. Newly submitted samples correspond to cisplatin sensitive TGCT cells and their derived resistant cells treated with Cisplatin. Untreated control samples (GSM3720309 - GSM3720311,GSM3720315-GSM3720320 and GSM3720333-GSM3720350) were obtained from the existing GEO Series GSE129696  and are not resubmitted. All FASTQ files were aligned to human genome assembly NCBI GRCh38 using STAR aligner, the resulting BAM files were summarized to genes using the featureCounts algorithm. The processed files contains the TMM normalized log counts per million (log CPM) values for each Sample,(treated and untreated both).

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The table below lists GEO accessions reused/reanalyzed for this study.
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middle: W

first: Michael

last: Spinella


title: Single-nucleus RNA-seq profiling of healthy and MASH mouse livers reveals hepatocyte heterogeneity under MASH condition

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is a severe chronic liver condition characterized by hepatocyte steatosis, inflammation and fibrosis, with a rising prevalence globally, posing significant health risks and potentially leading to complications such as cirrhosis, liver failure, and increased mortality. To obtain a deeper understanding of transcriptomic responses to MASH diet feeding, we conducted a single-nucleus RNA-seq (snRNA-seq) experiment on livers from mice fed on regular chow or a MASH diet. Our snRNA-seq analysis revealed expansion of cholangiocytes and activated hepatic stellate cells population, as well as infiltration of macrophages in the MASH livers. In addition, we identified a cluster of hepatocytes, termed disease-associated hepatocytes, that are unique to the MASH livers and are distinct from the hepatocytes from the three liver zonations.

overall_design: Wildtype C57BL6/J male mice were fed either on regular chow or with a MASH diet for five months. Liver tissues were collected for snRNA-seq experiment.


title: DNA Methylation in the Placenta and Maternal Socioeconomic Status: The SPAH Study

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

type: Methylation profiling by genome tiling array

summary:
Background: Disparities in socioeconomic status have been associated with adverse pregnancy outcomes, including preterm birth and fetal growth restriction. As the barrier between maternal exposures and the fetus, the placenta has been proposed to play a role in the mechanisms leading to poor health outcomes seen with socioeconomic disadvantage. We hypothesized that exposure to lower SES during pregnancy may lead to altered placental DNA methylation (DNAme) that is in turn associated with other pregnancy outcomes.
Methods: Placental samples from the Stress, Pregnancy, and Health Study (SPAH) study (n=493) were processed for DNAme analysis using the Illumina Infinium MethylationEPIC BeadChip array. Linear modelling was used to assess whether placental DNAme was associated with Socioeconomic Position, Financial Resources, and/or Disadvantage.
Results: At FDR <0.05 and |∆β| >0.05, we observed only 2 CpGs associated with Socioeconomic Position after correcting for gestational age and ancestry, while at a less stringent |∆β| >0.02 threshold there were 77 and 22 CpG associations with Socioeconomic Position and Disadvantage respectively. However, these changes seemed to be explained by genetic variation influencing DNAme in combination with population stratification by socioeconomic status. We did observe associations between socioeconomic status and DNAme-inferred cell composition and epigenetic age acceleration, with intrinsic (p=0.047) and extrinsic (p=0.050) age acceleration being slightly accelerated with lower levels of Socioeconomic Position. Financial Resources and Disadvantage SES trended in the same direction as Social Position, with lower socioeconomic status seen with higher levels of age acceleration, though not reaching significance. No meaningful associations in sex stratified analyses were identified, although XX placentas showed higher cytotrophoblast:syncytiotrophoblast ratio than XY placentas (p=0.00013).
Conclusions: Our results emphasize the importance in placental studies involving diverse cohorts to account for genetic variation in order to avoid false findings. This study also demonstrates the challenges with elucidating mechanisms underlying socioeconomic associated outcomes, given the complex nature of correlated variables. Further investigation is required to elucidate whether epigenetic age acceleration is an adverse effect of exposure to prenatal maternal stress associated with socioeconomic disparities, or alternatively, if placental epigenetic aging is a potential healthy adaption to pregnancy complications that increase the risk of preterm delivery.

overall_design:
The SPAH study was initially focused on understanding the social and lifestyle factors that affect birthing parents’ and infants’ health during pregnancy (https://sites.northwestern.edu/spah/). We aimed to identify placental DNAme associated with socio economic status using DNAme data from 493 unique human chorionic villi samples profiled with the Infinium MethylationEPIC v1.0 array in Evanston, Illinois, USA.

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IDAT files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable SNP genotyping data for open access.
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first: Ella

middle: O

last: Beraldo

first: Hannah

middle: I

last: Illing

first: Ann

last: Borders

first: Linda

last: Ernst

first: Alexa

last: Freedman

first: Lauren

middle: S

last: Keenan-Devlin

first: Amy

last: Inkster

first: Jungwon

last: Kim

first: Maria

last: Penaherrera

first: Gregory

last: Miller

middle: P


title: Fli1 inhibits proteostasis during nutrient stress to limit NK cell persistence in solid tumors [CUT&Tag_FLI1_Human]

city: Los Angeles

first: Jeong Hyun

last: Ji

state: CA

address: 615 Charles E Young Dr S, Rm 247

institute: University of California, Los Angeles

summary: Natural killer (NK) cells are critical for the immune response to cancer. However, solid tumor-infiltrating NK cells display reduced persistence and effector functions, limiting their clinical efficacy. To understand the mechanisms that induce human NK cell dysfunction in solid tumors, we compared single-cell gene expression in patient-matched tumor-infiltrating compared to tumor-adjacent NK cells to identify unfolded protein response (UPR) genes associated with worse cancer patient survival. Primary human NK cells accumulated unfolded proteins and induced a chronic UPR response to nutrient stress from the tumor microenvironment metabolome (TMM), sufficient to cause pronounced dysfunction and decreased persistence. Mechanistically, the transcription factor Fli1 epigenetically repressed UPR genes to limit human NK cell proteostasis in the presence of the TMM. CRISPR-mediated Fli1 deletion enhanced unfolded protein clearance, persistence, and tumor control in vivo. Thus, our results suggest that the TMM is sufficient to induce human NK cell dysfunction in solid tumors through the regulation of proteostasis.

overall_design: FLI1 CUT&Tag analysis of human NK cells following CRISPR knockout of FLI1 or IgG.

first: Joey

middle: H

last: Li

first: Wesley

last: Armstrong

first: Areeba

last: Lalani

first: Varchas

last: Bharadwaj

first: Kenneth

last: Ho

first: Jingtong

last: Liang

first: Cassidy

middle: D

last: Lee

first: Alexander

last: Muir

first: Timothy

last: O'Sullivan


title: Reprogramming-driven drug discovery uncovers sildenafil as a candidate drug for mitochondrial disease

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

summary: Mitochondrial diseases are a group of rare inherited disorders that affect mitochondrial function. A severe untreatable form of mitochondrial disease is Leigh syndrome (LS), which is characterized by psychomotor regression and acute metabolic crises during which patients quickly deteriorate. To accelerate drug discovery for mitochondrial diseases, we focused on drug repurposing and used induced pluripotent stem cell (iPSC)-derived neuronal precursor cells (NPCs) from LS patients to screen a library of 5,632 repurposable compounds. We identified phosphodiesterase 5 inhibitors (PDE5i) as leads capable of normalizing mitochondrial polarization in NPCs of LS patients. Among the PDE5i, we prioritized Sildenafil due to its established safety profile in children and adults. Sildenafil restored key pathways regulating nervous system development, enhanced neurite outgrowth in LS neurons, and mitigated abnormal calcium responses in LS brain organoids under metabolic stress. Chronic off-label compassionate treatment of six LS patients with Sildenafil showed good tolerability and clear clinical improvements. Our findings highlight the potential of iPSC-driven drug discovery for rare diseases and position Sildenafil as a promising drug candidate for patients with mitochondrial diseases.

overall_design: RNA-profiling of Neuronal Precursor Cells (NPC) generated from iPSCs from control individuals and from patients with Maternally Inherited Leigh Syndrome (MILS) carrying mutations in the MT-ATP6 gene in the presence and absence of 10 µM Sildenafil.

first: Annika

last: Zink

first: Alessandro

last: Prigione


title: The nonsense-mediated mRNA decay (NMD) pathway safeguards telomeres in pluripotent stem cells

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

summary: Telomeres are repetitive DNA sequences that cap chromosome ends and are bound by the Shelterin complex to prevent aberrant activation of DNA damage signaling. While TRF2, a core Shelterin component, is essential for repressing non-homologous end joining (NHEJ) in somatic cells, it is dispensable for telomere protection in mouse embryonic stem cells (mESCs). To uncover compensatory pathways, we performed a synthetic lethal genome-wide CRISPR/Cas9 screen in TRF2-deficient mESCs and identified multiple components of the nonsense-mediated mRNA decay (NMD) pathway as essential for cell viability. We show that NMD promotes telomere protection by regulating the abundance of TRF1, another Shelterin component, at telomeres.  Specifically, NMD limits the accumulation of a TRF1 mRNA isoform that encodes a dominant-negative protein variant. These findings reveal a previously unrecognized role for mRNA surveillance in maintaining telomere integrity in pluripotent cells.

overall_design: RNA-seq profiling of control Trf2f/f mouse embryonic stem cells and sub-lines containing Smg5-/-, Smg6-/-, and Upf1HM alleles.

first: Marta

last: Markiewicz-Potoczny

first: Si Young

first: Soniya

last: Chatterjee

first: Justin

last: Mabin

first: Anna

last: Zinsser

first: Ranjodh

last: Sandhu

first: Gianna

last: Tricola

first: J

middle: R

first: Eros

last: Lazzerini Denchi


title: Fli1 inhibits proteostasis during nutrient stress to limit NK cell persistence in solid tumors [ATAC-Seq_Mouse]

first: Jeong Hyun

last: Ji

overall_design: ATACseq analysis of splenic mouse NK cells following CRISPR knockout of Fli1 or NTC.

first: Joey

last: Li

first: Wesley

last: Armstrong

first: Areeba

last: Lalani

first: Varchas

last: Bharadwaj

first: Kenneth

first: Jingtong


title: Fli1 inhibits proteostasis during nutrient stress to limit NK cell persistence in solid tumors [CUT&Tag_Fli1_Mouse]

summary: Natural killer (NK) cells are critical for the immune response to cancer. However, solid tumor-infiltrating NK cells display reduced persistence and effector functions, limiting their clinical efficacy. To understand the mechanisms that induce Mouse NK cell dysfunction in solid tumors, we compared single-cell gene expression in patient-matched tumor-infiltrating compared to tumor-adjacent NK cells to identify unfolded protein response (UPR) genes associated with worse cancer patient survival. Primary Mouse NK cells accumulated unfolded proteins and induced a chronic UPR response to nutrient stress from the tumor microenvironment metabolome (TMM), sufficient to cause pronounced dysfunction and decreased persistence. Mechanistically, the transcription factor Fli1 epigenetically repressed UPR genes to limit Mouse NK cell proteostasis in the presence of the TMM. CRISPR-mediated Fli1 deletion enhanced unfolded protein clearance, persistence, and tumor control in vivo. Thus, our results suggest that the TMM is sufficient to induce Mouse NK cell dysfunction in solid tumors through the regulation of proteostasis.

overall_design: Fli1 CUT&Tag analysis of mouse NK cells following CRISPR knockout of Fli1 or NTC.

last: Ho

last: Liang

first: Cassidy

last: Lee

first: Alexander

last: Muir

first: Timothy

last: O'Sullivan


title: Neuronal SEL1L-HRD1 ERAD regulates one-carbon metabolism and is essential for motor function and survival

first: You

last: Lu

state: MI

summary: SEL1L-HRD1 endoplasmic reticulum-associated degradation (ERAD) is essential for protein folding quality control and maintaining homeostasis in the ER. Defects in SEL1L-HRD1 ERAD complex has been linked to early onset of severe neurological syndromes. However, its physiological importance and underlying mechanisms in neurons remain poorly understood. This study established a mouse model with neuron-specific deletion of Sel1L and revealed that neuronal SEL1L-HRD1 ERAD is essential for maintaining one-carbon metabolism, motor function, and overall viability.

overall_design: Mice carrying the Sel1L flox/flox allele (WT) were crossed with a Synapsin I promoter-driven Cre line, resulting in Sel1L-SynCre (KO) mice with neuron-specific deletion of Sel1L. The cortex and hippocampus were dissected from the brain of 5-week-old WT (n = 2) and KO (n = 2) mice for neuclei prep. The neuclei suspension was subject to fluorescence-activated cell sorting (FACS) and the resulting single-nuclei prep was used for input onto 10x Genomics Chromium system for generating Chromium Single Cell 3′ Libraries.

first: Mauricio

last: Torres

first: Alan

middle: C

last: Rupp

first: Abigail

last: Tomlinson

first: Martin

middle: G

last: Myers Jr

first: Ling

last: Qi


title: Adjuvant personalized multivalent neoantigen DNA vaccination for MGMT unmethylated glioblastoma: a phase I trial [scRNA-seq]

first: Katherine

middle: E

last: Miller

summary: Glioblastoma is a devastating disease with a prognosis of less than 24 months. Recent studies have shown encouraging results using neoantigen-based vaccines to stimulate glioblastoma-directed immune responses, but overall immunogenicity has been low. Here, we report the results of a phase 1 clinical trial (NCT04015700) to assess the safety and efficacy of GNOS-PV01, a personalized DNA vaccine platform, in patients with newly diagnosed MGMT unmethylated glioblastoma following surgery and radiation. Results show GNOS-PV01 is able to safely immunize against up to 40 neoantigens per patient (range 17-40) with neoantigen-specific T cell responses detectable in all evaluated subjects post-vaccination (7 of 7). Furthermore, we developed a novel T cell enrichment method for single nuclei RNA-sequencing to transcriptionally characterize tumor-infiltrating T cells after vaccination. Survival outcomes were encouraging with one-third of vaccinated patients (3 of 9) alive beyond 24 months. Moreover, induction of neoantigen-specific responses was associated with subsequent reactivity to PD-1 blockade therapy.

overall_design: We applied our novel T cell enrichment method to perform 5' single nuclei RNA-sequencing (10X Genomics Chromium Next GEM Single Cell 5' v2 dual index) on pre- and post-vaccination tumor samples in replicate pairs from subjects 2 and 9.

first: Elizabeth

last: Garfinkle

first: Jaye

middle: B

last: Navarro

first: Sophia

last: Paxton

first: Gavin

last: Dunn

first: Tanner

middle: M

last: Johanns


title: Prussian blue nanoparticles targeting multiple PANoptosome-mediated PANoptosis for myocardial ischemia-reperfusion injury therapy

first: ling

middle: ling

last: xu

address: tianlin street

institute: shanghai jiaotong university

summary: The extensive crosstalk between pyroptosis, apoptosis, and necroptosis suggests that inhibiting one of them can lead to compensating for the other, thereby reducing therapeutic efficacy. Here, we identify Prussian blue (PB) nanoparticle as an effective PANoptosis inhibitor that binds to key proteins (RIPK1, ZBP1, and AIM2) to regulate multiple PANoptosomes, thereby comprehensively inhibiting pyroptosis, apoptosis, and necroptosis and blocking their crosstalk in myocardial ischemia-reperfusion injury (MIRI) therapy. This PANoptosis inhibitor significantly alleviated MIRI-induced cardiac functional impairment and adverse ventricular remodeling, promoted extracellular matrix repair and neovascularization, and prevented cardiomyocyte hypertrophy. Furthermore, it modulated mitochondrial metabolism and immune-inflammatory homeostasis, helping to block the crosstalk within PANoptosis. Specifically, single-nuclear transcriptome sequencing of human heart samples, molecular dynamics simulations, transcriptome sequencing analysis, medical imaging technology, and molecular biological methods comprehensively elucidated the role of PB as a PANoptosis inhibitor in MIRI therapy. This study provides a reference paradigm for exploring the role of PANoptosis in other diseases and a framework for studying nanobiological interactions to uncover broader nanomaterial mechanisms.

overall_design: RNA-seq profiles of mouse myocardial tissues in the same treatment groups (control group, MIRI group, PB group, PB@PM group).

first: Lingling

last: Xu


title: Pre-adaptation of Stem Cell-Derived Islet Organoids to Hypoxia via Zinc Transportation Inhibition Drives Rapid Neo-vascularization

city: Shanghai

first: Xiangyi

last: Chen

address: No. 1239, Siping Road, Shanghai, China

institute: Weida Li

summary: Human stem cell-derived islet organoids (SC-islets) hold great potential for diabetes treatment, but their clinical application is hindered by immaturity and ischemia-induced dysfunction post transplantation. Hypoxia-driven angiogenesis via the HIF1A-VEGFA axis is a common adaptation, but the metabolic fragility of SC-islet β cell leads to early functional damage and suppressed VEGFA release, thereby delaying vascularization and causing graft loss. The key challenge in SC-islet transplantation is how to prevent hypoxia-induced stress and promote rapid neo-vascularization. To reconcile this discrepancy, we targeted zinc transportation using a chemical inhibitor to enhance SC-islet maturation, hypoxia resistance and vascularization. We found that excessive zinc in SC-islet β-cells induces oxidative modification that inhibits AMPK activity. Chemical inhibition of zinc transportation activates AMPK, simultaneously enhances functional maturation, improves hypoxia resistance and increases VEGFA expression to facilitate endothelial cell integration. In diabetic animal models, this approach significantly improved hypoxia resistance, accelerated neo-vascularization, and enhanced glycemic control. Our findings demonstrate that chemical inhibition of zinc transportation boosts SC-islet functional competence, offering a potential strategy to advance the paradigm of functional pre-adaptation to stress in regenerative medicine.

overall_design: We generated hESCs reporter cell line (MEL1 Nkx6.1:linker2a:mCherry; INSGFP/w) that enable to precisely and dynamically trace SC-islets during differentiated stages. SC-islets by sorting out GFP and mCherry double-positive SC-β cells with high INS and NKX6.1 expression

first: Zhaoyue

last: Wang

first: Weida

last: Li


title: Fli1 inhibits proteostasis during nutrient stress to limit NK cell persistence in solid tumors [RNA-Seq_Mouse]

first: Jeong Hyun

last: Ji

overall_design: RNAseq analysis of splenic mouse NK cells following CRISPR knockout of Fli1 or NTC.

first: Joey

first: Wesley

last: Armstrong

first: Areeba

last: Lalani

first: Varchas

last: Bharadwaj

first: Kenneth

last: Ho

first: Jingtong

last: Liang

first: Cassidy

last: Lee

first: Alexander

last: Muir

first: Timothy

last: O'Sullivan


title: Fli1 inhibits proteostasis during nutrient stress to limit NK cell persistence in solid tumors [ATAC-Seq_Human]

overall_design: ATACseq analysis of human NK cells following CRISPR knockout of FLI1 or NTC.


title: DLEU2 promotes cell motility and immune infiltration in cervical squamous cell carcinoma through reciprocal feed-forward activation of E2F1

first: Chuntao

last: Tao

state: State...

address: China

institute: Chongqing Medical University

summary: Cancer metastasis is the primary cause of high mortality in patients with cervical squamous cell carcinoma (CESC). The invasive ability of cancer cells is enhanced by increased cell motility, which contributes to their distant metastasis. The oncogenic lncRNA DLEU2, implicated in tumor progression and prognosis, remains understudied in CESC. This study investigated how DLEU2 enhances cell motility and regulates immune infiltration in CESC. We found that DLEU2 was upregulated in CESC tissues and correlated with poor prognosis in advanced-stage patients. Functionally, DLEU2 knockdown suppressed cell migration and invasion, while its overexpression enhanced motility. Mechanistically, DLEU2 knockdown altered the expression of downstream genes related to cell motility and adhesion. An interaction between DLEU2 and E2F1 protein was confirmed by RNA pulldown assay. E2F1 expression was downregulated or upregulated after DLEU2 knockdown or overexpression, respectively, while DLEU2 expression was also upregulated after E2F1 overexpression. Therefore, DLEU2 may form a regulatory loop with E2F1 to activate the transcription of downstream genes related to cell motility and adhesion. Additionally, E2F1 expression strongly correlated with immune infiltration levels (e.g., T cells, Tregs, monocytes, mast cells), and DLEU2 exhibited a parallel immune cell abundance pattern,  suggesting indirect immunomodulatory effects via E2F1. These findings propose that the DLEU2-E2F1 axis promotes CESC metastasis by dual mechanisms: enhancing tumor cell motility and reshaping the immune microenvironment. The study highlights DLEU2 as a potential therapeutic target to disrupt metastatic pathways and immune evasion in CESC. Further validation is needed to explore clinical applications of targeting this regulatory network.

overall_design: 7 unique pairs of biopsy and surgical resection specimens and 1 pairs of cell lines samples were sequenced and profiled.

first: Min

last: He


title: Fli1 inhibits proteostasis during nutrient stress to limit NK cell persistence in solid tumors [RNA-Seq_Human]

overall_design: RNAseq analysis of human NK cells following CRISPR knockout of FLI1 or NTC.


title: A sympathetic-basophil axis promotes skin inflammation [Basophil RNA-seq]

city: Guangzhou

first: xie

last: xinyang

address: 58 Zhongshan Second Road, Yuexiu District, Guangzhou City, Guangdong Province

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: As the largest barrier organ of the body, the skin integrates immune and peripheral sensory nervous systems to respond to environmental stimuli. While sensory neuroimmune interactions in the skin are extensively studied, the role of the sympathetic nervous system (SNS) in skin immunity remains unclear. We show that stress exacerbates atopic dermatitis (AD)-like inflammation in murine models by driving basophil infiltration through SNS activation, independent of the hypothalamic-pituitary-adrenal axis.  By elucidating the crosstalk between SNS and inflammation pathways, our study underscores the critical role of autonomic responses in chronic inflammatory skin diseases.

overall_design: Following the induction of atopic dermatitis by daily application of MC903, all live CD45+Lin-CD49b+FcεRIα/IgE+ basophils of the ear skin of WT mice were sorted by fluorescence-activated cell sorting (FACS) and conducted for the transcriptome sequencing using the Smart-seq2 protocol.

first: Fang

first: Xinyang

last: Xie

first: Xiaobao

last: Huang


title: Impact of ATEVs and EV-DNA on transcriptional profile of DC2.4 cells

city: New Ypok

first: Mengying

last: Hu

state: New York

address: 413 E 69th St, New York, NY 10021

institute: Weill Cornell Medical College

summary: Antigen processing and presentation (APP) is essential for adaptive immunosurveillance in all nucleated cells. Here we describe a novel mechanism through which secreted factors other than cytokines, specifically extracellular vesicles (EVs) released from activated T cells (ATEVs) drive a positive feedback loop that enhances antigen presentation and immune responses in normal physiology and cancer. ATEV-induced immunogenicity relies on extravesicular double-stranded DNA (EVDNA) and granzyme B (Gzmb). ATEV-DNA is notably abundant, primarily consisting of genomic DNA enriched in copies of specific genes, including numerous APP machinery genes. Mechanistically, ATEV transfer of APP machinery genes to recipient dendritic or tumor cells is facilitated by Gzmb disruption of recipient cell nuclear integrity. DNAse treatment of ATEVs removed the majority of EVDNA, preventing APP machinery upregulation in recipient cells, which in turn failed to recruit T lymphocytes into tumors. Notably, ATEVs hold promise as an immune-boosting therapeutic, particularly in restoring MHC-I antigen processing and presentation, and synergize with checkpoint blockade therapy in several immunotherapy-refractory tumors. Collectively, our findings uncover a novel mechanism through which ATEVs boost APP and anti-tumor immunity. Gzmb-mediated nuclear transfer opens new avenues for non-viral gene delivery, offering potential for enhanced intranuclear gene transport and expression efficiency.

overall_design: RNAseq profiling of DC2.4 cells after being treated with PBS, ATEVs, NTEVs (non-activated T cell-derived EVs), and DNAse-pretreated ATEVs in vitro


title: Thalassiosira pseudonana growth phase determines gene expression and algicidal behavior of a new Alteromonas macleodii strain

city: Seattle

first: David

last: Wiener

state: Washington

department: School of Oceanography

institute: University of Washington

summary: Phytoplankton-bacteria interactions are pivotal in marine ecosystems, influencing primary production and biogeochemical cycles. Diatoms engage in diverse relationships with bacteria, ranging from mutualism to pathogenicity. This study explores the interaction between a novel Alteromonas macleodii strain from the Equatorial Pacific and the model Thalassiosira pseudonana across the diatom different growth phases. We demonstrate that A. macleodii’s algicidal activity depends on the diatom’s growth phase, defensive capacity, and nutrient availability. The algicidal effect manifests during the diatom’s stationary phase or with external nutrient supplementation, implicating organic matter availability as a key driver. Transcriptomic analysis reveals that A. macleodii shifts from motility-associated to growth-associated gene expression based on the diatom’s physiology and coculture duration. Filtrate assays and fluorescence microscopy suggest a two-stage infection model: initial bacterial motility and exudate secretion induce diatom death, followed by bacterial aggregation around debris. Comparative transcriptomics with other algal hosts highlights host-specific bacterial responses, underscoring the context-dependent nature of these interactions. Our findings provide a deeper understanding of the molecular mechanisms driving diatom-bacteria interactions, shedding light on their role in marine microbial ecology and ecosystem functioning.

sample_organism:
Alteromonas macleodii
Thalassiosira pseudonana

overall_design: T. pseudonana cultures, in either Exponential or Stationary phases, were cocultured with a novel A. macleodii strain isolated from the North Pacific. RNA was extracted at three time points: T1 (30 minutes), T2 (36 hours), and T3 (8 days) for each coculture condition. All experiments were conducted in triplicates (labeled A, B, and C). For Ribodepletion calibration, RNA was extracted from exponentially growing T. pseudonana once and subsequently divided for Ribodepletion, poly(A) selection, and Total RNA sequencing.

first: Zinka

last: Bartolek

first: Riley

last: Dunklin

first: E. Virginia

last: Armbrust


title: A sympathetic-basophil axis promotes skin inflammation [blood]

overall_design: Human basophils from patients with atopic dermatitis and healthy controls were isolated from 10 mL of peripheral blood using the EasySep™ Direct Human Basophil Isolation Kit. The isolated basophils were then analyzed using scRNA-seq.

last: Wang


title: Fli1 inhibits proteostasis during nutrient stress to limit NK cell persistence in solid tumors [CUT&Tag_H3K27ac_Mouse]

first: Jeong Hyun

last: Ji

overall_design: H3K27ac CUT&Tag analysis of mouse NK cells following CRISPR knockout of Fli1 or WT.

first: Joey

last: Li

first: Wesley

last: Armstrong

first: Areeba

last: Lalani

first: Varchas

last: Bharadwaj


title: Adjuvant personalized multivalent neoantigen DNA vaccination for MGMT unmethylated glioblastoma: a phase I trial [RNA-seq]

first: Katherine

last: Miller

address: 700 Children's Dr.

institute: Nationwide Children's Hospital

overall_design: We performed bulk RNA-sequencing on multiple tumor regions from nine patients.

first: Elizabeth

last: Garfinkle

first: Gavin

last: Dunn

first: Tanner

last: Johanns


title: Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR

first: J. Robert

last: Hogg

summary: Gene expression is a product of RNA synthesis and degradation kinetics, which can vary among transcript isoforms of the same gene. Some isoforms contain premature termination codons (PTCs) and are degraded via nonsense mediated mRNA decay (NMD), while others lack these features and are more stable. However, probing the stability of individual isoforms remains challenging. Methods like nucleotide-recoding RNA-seq (NR-seq) enable insights into RNA kinetics, but existing bioinformatic tools are unable to provide robust, isoform-specific degradation rate constant estimates. We present a strategy to infer isoform-level kinetics from short-read NR-seq data, implemented in the EZbakR-suite, which allows us to identify high confidence NMD targets. We also show how custom annotations improve these analyses. We uncovered unexpected stability variability in transcripts with conserved PTC-containing exons and found that other decay pathways can supersede NMD. Our findings provide mechanistic insights into established NMD efficiency correlates and highlight transcript features promoting efficient decay.

overall_design: HEK-293 cells were treated with DMSO or 1 µM SMG1i for 8 hours. For TimeLapse-Seq, indicated samples were treated with 100 µM 4-thiouridine for 2 hours. Total RNA was subjected to TimeLapse chemistry and used for library preparation and short-read sequencing. Unlabeled total RNA samples were also used for long-read sequencing (Iso-seq).

first: Justin

last: Mabin

first: Isaac

last: Vock

first: Matthew

last: Simon

first: Robert


title: R-loop-induced DNA replication defects drive neuropathy in Koolen-de Vries syndrome

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Koolen-de Vries syndrome (KdVS) is a neurodevelopmental disorder caused by KANSL1 haploinsufficiency. KANSL1 encodes a scaffold protein of the non-specific lethal (NSL) complex, which regulates transcription of constitutively expressed genes via acetylation of H4K5 and H4K8 around transcription start sites (TSS). How loss of KANSL1/NSL contributes to the neurodevelopmental defects in KdVS is unknown. Here, we find that KANSL1/NSL prevents the accumulation of R-loops (three-stranded DNA-RNA hybrid structures) at transcription start sites (TSSs) with low basal transcription and H4K5/H4K8 acetylation, where R-loops are typically not detected. If not suppressed, these R-loops delay DNA replication in early S-phase by stalling of the replisome. KdVS neural organoids also suffered from perturbed DNA replication concomitantly with neurodevelopmental defects, while KdVS neuronal cells showed reduced synaptic activity in a manner-dependent on R-loop accumulation. Our study offers insights into how KANSL1/NSL controls R-loop homeostasis to ensure faithful DNA replication during neuronal development, preventing neuropathy in KdVS patients.

overall_design: U2OS WT cells treated with siLuciferase, siKANSL1 and siKANSL3 to a double pulse of EdU (10uM for 15 min, 60 minutes washout  and 10uM for 15 min,). Next, cells were sorted in 384 well plates and subjected to scEdU-seq (van den Berg et al., 2024) .

first: Jolanthe

last: Lingeman

first: Haico

last: van Attikum


title: KLF5 modulates epigenetic modifications driving human pancreatic ductal adenocarcinoma metastasis [RNA-Seq]

city: Baltimore

first: Weiqiang

last: Zhou

address: 615 N. Wolfe Street

department: Department of Biostatistics

institute: Johns Hopkins University Bloomberg School of Public Health

summary: We previously showed that distant metastases of human pancreatic ductal adenocarcinoma (PDAC) are driven by epigenetic alterations in the primary tumor rather than by additional mutations1. However, the specific epigenetic driver genes responsible have not been identified. To identify genes modulating these changes, we performed a pooled CRISPR genetic screen and single-cell multiomics analysis using patient-derived xenograft cell lines established from a primary PDAC tumor and a distant metastasis from the same patient. We identified KLF5 as the leading epigenetic modulator regulating progression in distant metastasis. Knockdown of KLF5 selectively reduced the growth of the distant metastasis and caused a large-scale increase in heterochromatin. Single-cell multiome ATAC and gene expression analysis revealed two clusters with high KLF5 expression and increased expression and chromatin accessibility of stem cell markers and genes related to migration and epithelial to mesenchymal transition. Further, we identified two epigenetic modifiers, NCAPD2 and MTHFD1, which are regulated by KLF5 and result in these increases in heterochromatin when knocked down. These data provide a sequence of epigenetic modulators, modifiers and mediators which shape the metastatic landscape of pancreatic cancer.

overall_design: RNA-seq samples of A13Lg with KLF5 knockdown and scrambles shRNA controls. Single-cell multiomics samples (ATAC+Gene Expression) on A13Pr2 and A13Lg parental cells and with KLF5 knockdown and scrambled controls.

first: Masahiro

last: Maeda

first: Weqiang

first: Kenna

last: Sherman

first: Andrew

last: Feinberg


title: Impact of ATEVs and EV-DNA on transcriptional profile of a pancreatic cancer cell line with poor immunogenicity

first: Mengying

last: Hu

overall_design: RNAseq profiling of a low immunogenic pancreatic cancer cell clone isolated from KPCY (KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre; Rosa26YFP/YFP) mice, after being treated with PBS, ATEVs, NTEVs (non-activated T cell-derived EVs), and DNAse-pretreated ATEVs in vitro


title: Single nuclei transcriptomics of Cryptocercus cockroach

city: Sydney

first: Fabio

last: Zanini

state: NSW

address: Lowy L2

country: Australia

institute: UNSW Sydney

summary: Cryptocercus punctulatus was dissociated into single nuclei and prepared with 10X Genomics 3’ scRNA-Seq libraries.

overall_design: Cryptocercus punctulatus was dissociated into single nuclei, prepared with 10X Genomics 3’ scRNA-Seq libraries, and sequenced on a NovaSeq X.

first: Catherine

last: Gatt

first: Esra

last: Kaymak

first: Thomas

last: Bourguignon


title: In vivo co-cultures of colitis-associated cancer epithelial organoids alone or with matched proximal colon fibroblasts or with matched colitis-associated cancer fibroblasts

city: Cleveland

first: Oliver

last: Wessely

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

summary: The pathogenosis of colitis-associated cancer is unclear. These studies use single nuclear RNA-sequencing on human samples to understand the dominant contributions of cell types to the pathogenesis from histologically normal colon, to colitis, to colitis-associated cancer.

overall_design: Single nuclear RNA-sequencing on optimum cutting tissue preserved human colon samples spanning normal colon, proximal and distal colitc colon, and colitis-associated cancer was conducted. Cell types were annotated based on the dominant categories of epithelia, immune, and non-immune stroma. To further interrogate the interactions between the epithelia and non-immune stromal fibroblasts, both in vitro and in vivo co-cultures were conducted, then subjected to single nuclear RNA-sequencing.

first: Emina

last: Huang

first: R

last: Schweickart

first: Reece

middle: K

last: DeHaan

first: Sarvestani

last: Samaneh


title: KLF5 modulates epigenetic modifications driving human pancreatic ductal adenocarcinoma metastasis [Multiome]