title: Cellular Mg2+ decrease causes a distinctive NF-κB-dependent form of cell death

status: Public on Jan 03 2026

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Mg2+ is an essential cofactor for numerous enzymes, supporting fundamental cellular processes. Phosphatase of regenerating liver (PRL) protein family, inhibits cyclin M (CNNM) Mg2+ efflux transporters. To elucidate the physiological role of PRL in Mg2+ homeostasis at the cellular level, we employed combined genetic knockout and knockdown approaches. Such PRL KO + KD led to marked reduction of intracellular Mg2+ levels and triggered extensive cell death. To investigate the mechanism underlying cell death induced by PRL KO + KD, we next performed transcriptomic analysis to profile the changes in global gene expression, which revealed activation of the NF-κB pathway, and accordingly, genetic deletion of NF-κB p65 subunit abrogated cell death. Similarly, CNNM overexpression triggered intracellular Mg2+ decrease, NF-κB activation and subsequent cell death. Notably, this form of cell death exhibited unique morphological features, including actin-driven fiber-like protrusions, distinguishing it from known cell death modalities. Our findings uncover a previously unrecognized mode of NF-κB-dependent cell death triggered by intracellular Mg2+ decrease.

overall_design: RNA-seq analysis of wild-type or PRL2-/-; PRL1+/- cells transfected with control or PRL1-siRNA

first: Koyuki

last: Kawamura

first: Yosuke

last: Funato

first: Hiroaki

last: Miki


title: Cigarette smoke and biological age induce degenerative heterogeneity in retinal pigment epithelium [scRNA-seq]

city: Baltimore

first: Yang

last: Jin

state: MD

address: 620 Boulton St. Bel Air

country: USA

institute: Johns Hopkins University

type: Expression profiling by high throughput sequencing

summary: Environmental exposure such as cigarette smoke induces epigenetic changes that can induce degenerative heterogeneity and accelerate aging. In early age-related macular degeneration (AMD), the leading worldwide cause of blindness among the elderly, retinal pigment epithelial (RPE) cell heterogeneity is a key change. Since smoking is the strongest environmental risk factor for AMD, we hypothesized that cigarette smoke induces degenerative RPE heterogeneity through epigenetic changes that are distinct from aging, and that with aging, the RPE becomes vulnerable to cigarette smoke insult. We administered cigarette smoke condensate (CSC) intravitreally to young and aged mice and performed snRNA-seq and snATAC-seq on the RPE/choroid. This analysis identified separate cell clusters corresponding to healthy and abnormal, dedifferentiated RPE in both aged vehicletreated and young CSC-treated mice. The dedifferentiated RPE were characterized by a global decrease in chromatin accessibility and decreased expression of genes in functional categories that were linked to hallmarks of aging. Notably, young, dedifferentiated RPE also exhibited a compensatory upregulation of hallmarks of aging-related genes, specifically those related to mitochondrial function and proteostasis. In contrast, aged dedifferentiated RPE did not express these compensatory changes, and did not survive CSC treatment, as experimentally verified with TUNEL labeling. These changes are relevant to early AMD because we identified through scRNA-seq, similar dedifferentiated and healthy macular RPE clusters in a donor who smoked and another with early AMD, but not from a nonsmoker. Degenerative cellular heterogeneity can include an abnormal cluster that jeopardizes cell survival and may represent an additional hallmark of ocular aging.

overall_design: The tenets of the Declaration for Helsinki for research involving human tissue were followed. Human eyes (n=3) were obtained from the Advancing Sight Network (Birmingham, AL). Preliminary experiments were conducted to determine the viability of RPE that was based on death to enucleation (D-E) time. Single cell RNA-seq on normal eyes from two different 86 yr old female donors with D-E of 3.3 and 6 hr with experimentation time of <24 hours and found that the 3.3 hr D-E interval globe exhibited superior viability (>70%), and nearly double the number of genes detected per cell (1301 vs 708 genes/cell). Therefore, globes with D-E times of < 6 hr and death to experimentation of <24 hr. Specifically, human globes from a 79 yr old female nonsmoker without AMD with a death to enucleation (D-E) time of 4.9 hr, a 67 yr old male smoker without AMD with a D-E of 3.8 hr, and a 67 yr old female smoker with early AMD (Minnesota Grade 2) with a D-E of 1.8 hr were immediately preserved on ice for overnight shipping to Hopkins, and dissected no later than 16 hr postmortem. After removing the anterior segment, the fundus was examined both with the retina and with the retina removed and classified using the Minnesota Grading Scale105. A 6 mm sample of the RPE/choroid in the macula was obtained using a 6 mm punch (Integra Lifesciences, Princeton, NJ) that was centered around the fovea. RPE/choroidal cells were dissociated using Papain Dissociation System (Worthington Biochemical, Lakewood, NJ) following the manufacturer’s instructions. Dissociated cells were resuspended in ice-cold PBS, 0.04% BSA and 0.5 U/μl of RNAse inhibitors. Cells were then filtered through a 50μm filter and processed for single-cell RNA-sequencing. Cell viability (>90%) was confirmed by negative staining with trypan blue.

first: Krishna

last: Singh

first: Jiang

last: Qian

first: James

middle: T

last: Handa


title: Spatial single cell transcriptomic analysis of a lineage-traceable mouse model of DICER1 Syndrome informs tumor developmental hierarchy [Xenium]

status: Public on Jan 05 2026

city: Vancouver

first: David

last: Huntsman

state: BC

address: 675 W 10th Ave

department: Molecular Oncology

country: Canada

institute: BC Cancer Research Centre

summary: DICER1 syndrome predisposes children and young adults to tumor development across various organs. Most of these cancers are sarcomas, which uniquely express the RNase IIIb domain-deficient form of DICER1 and exhibit histological and molecular similarities regardless of their anatomical origins. To uncover their cellular origin and developmental hierarchy, we established a lineage-traceable genetically engineered mouse model allowing for controlled activation of Dicer1 mutations in Hic1+ mesenchymal stromal cells. This resulted in the development of renal tumors closely mirroring human DICER1 sarcoma histologically and molecularly. Spatial single-cell transcriptomics analysis revealed that a Hic1+Pdgfra+Mfap4+ fibroblastic progenitor population, corresponding to perivascular universal fibroblasts of steady-state kidneys, exhibits the capability to undergo rhabdomyoblastic differentiation or transition into proliferative sarcomatous cells. Investigation of patient samples identified analogous cell states and developmental trajectories. This study uncovers a fibroblastic origin for DICER1 sarcoma and provides a faithful model for future mechanistic and translational investigation.

overall_design: Control mice and mice bearing a tamoxifen inducible compound heterozygous Dicer1 -/D1693N genotype (HDT) were treated with tamoxifen; both express tdTomato in Hic1+ cells. Control and HDT kidney and renal tumor tissues, respectively, were formalin-fixed and paraffin-embedded (FFPE). For murine tissue microarray (TMA) construction, 1.0 mm cores of formalin-fixed, paraffin-  embedded (FFPE) tissue from control and HDT mice were used. For spatial transcriptomic analyses, 5 μm sections were obtained from FFPE cores of control and HDT mice and visualized via the 10X Genomics Xenium In Situ Gene Expression platform, using the Mouse Tissue Atlassing Panel, PN1000627.

first: Felix

middle: K

last: Kommoss

first: Joyce

last: Zhang

first: Branden

middle: J

last: Lynch

first: Shary

middle: Y

last: Chen

first: Janine

last: Senz

first: Yana

last: Moscovitz

first: Lesley

middle: A

last: Hill

first: Wilder

last: Scott

first: Jonathan

last: Bush

first: Kenneth

middle: S

first: Andrew

last: Roth

first: Andreas

last: von Diemling

first: William

middle: D

last: Foulkes

first: Gregg

middle: B

last: Morin

first: Tully

middle: M

last: Underhill

first: Yemin

last: Wang

middle: G


title: Ultra high-throughput single-cell transcriptome and epitope profiling of healthy human PBMCs using SCITO-seq2

status: Public on Jan 04 2026

city: Seoul

first: Byungjin

last: Hwang

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

summary: This study presents comprehensive single-cell transcriptome and surface protein profiling using SCITO-seq2, an enhanced platform that improves the recovery of unique transcripts while enabling simultaneous detection of surface proteins. The analysis was conducted in two phases: first, using healthy donor PBMCs to validate technical performance, and second, by comparing samples from healthy controls, patients with childhood systemic lupus erythematosus (cSLE), and patients with CTLA4 haploinsufficiency and autoimmune infiltration (CHAI). These results demonstrate the platform’s applicability to both normal and disease states.

overall_design:
The study consisted of two major experimental sets.
PBMC 1: Fresh PBMCs from a healthy donor were divided into four replicate pools, each labeled with pool-specific antibodies and RNA probes. After pooling, 200,000 cells were loaded onto a Chromium Next GEM Chip Q for GEM generation to assess data consistency across pools derived from the same sample.
PBMC 2: Fresh PBMCs were isolated from healthy donors (n=4), childhood systemic lupus erythematosus (cSLE) patients (n=4), and CTLA4 haploinsufficiency with autoimmune infiltration (CHAI) patients (n=2). For sample multiplexing, cells from healthy and cSLE groups were labeled with unique TotalSeq-B hashing antibodies and pooled within their respective groups, while CHAI samples were processed as individual pools.
All samples underwent fixation and RNA probe hybridization following the 10x Genomics protocol. For each experimental set, 200,000 cells were loaded onto a Chromium Next GEM Chip Q for GEM generation. Libraries were prepared using the 10x Genomics Fixed RNA Profiling protocol and sequenced on an Illumina NovaSeq 6000 platform with 2 × 150 bp paired-end reads.

first: Su-Hyeon

last: Lee

first: Bo-yeong

last: Jin

first: Murim

last: Choi


title: Cigarette smoke and biological age induce degenerative heterogeneity in retinal pigment epithelium

first: Yang

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: C56BL/6J mice that were free of the Rd8 mutation (Jackson Labs, Bar Harbor, ME) were given water ad libitum and kept in a 12-hr light–12-hr dark cycle. For experiments, an equal number of male and female mice aged either 3- or 12-months old were given an IVT injection of 250 μg/ml CSC in 1 μl (Murty Pharmaceuticals, Inc. Lexington, KY) or an equal volume (1 μl) of vehicle (DMSO) in both eyes using a microinjection pump (Harvard Apparatus, Holliston, MA, USA) on day 1 and day 3.

first: Krishna

last: Singh

first: Jiang

last: Qian

first: James

last: Handa


title: Cellular senescence in human liver under normal aging and cancer

status: Public on Jan 01 2026

city: St Louis

first: Alla

last: Karpova

state: MO

address: 700 Rosedale avenue Campus Box 1000

institute: Washington University St Louis

summary: Cellular senescence, a stress-induced program causing stable cell-cycle arrest, is a hallmark of liver aging, fibrosis, and cancer. However, the cell-type-specific mechanisms, spatial organization, and cancer-associated alterations in the liver remain unclear. We profiled 43 normal human livers spanning ages and fibrosis stages using a single-cell multiome, Xenium spatial transcriptomics, and CODEX, complemented by fibrotic mouse models and 24 colorectal cancer liver metastases. We found CDKN1A+ senescent hepatocytes, fibroblasts, cholangiocytes, and endothelial cells associated with age, liver disease, or cancer. Senescence differed between aged and fibrotic livers, with similar patterns in mice. Spatially, CDKN1A+ hepatocytes localized periportally, while SERPINE1+ aging-associated hepatocytes formed spatial clusters, potentially mediated by Claudins and THBS1. Fibrotic regions contained CXCL12+ senescent fibroblasts interacting with CXCR4+ immune cells. Chemotherapy intensified senescence in hepatocytes by 5-fold relative to aging and led to unique CDKN2A+ populations. Across conditions, senescent cells shared AP-1 activation, pro-inflammatory cytokines, and apoptosis resistance, suggesting therapeutic opportunities.

overall_design: Briefly, 8-week-old male C57BL/6J mice received sham or 75% proximal small bowel (sbr) resection. Mice were randomized into 2-, 10-, 26-, and 52-week cohorts. Each mouse liver was collected at the assigned time point, inspected for tumors and sectioned for H&E and SR staining highlighting fibrotic tissue. Selected mouse liver samples were further subjected to snRNA-Seq.

first: Li

last: Ding

first: Daniel

last: Alligood


title: HNRNPH2 variant linked to intellectual disability disrupts myelination by impairing oligodendrocyte differentiation

city: Zhuhai

first: Bin

state: Zhuhai

address: Room 2007, Building 6, North HuanDao  Road 2515,

country: China

institute: Guangdong institute of intelligence and science technoloty

summary: Mutations in heterogeneous nuclear ribonucleoprotein H2 (HNRNPH2) lead to an X-linked neurodevelopmental disorders (NDDs) characterized by abnormal brain development and cognitive impairments. However, the underlying cellular and molecular mechanisms remain poorly understood. Here, we report that mice carrying the homologous P213L point mutation exhibit cognitive deficits and behavioral abnormalities resembling intellectual disability (ID). Notably, Hnrnph2P213L mice exhibit significant myelination defects, primarily due to impaired differentiation of oligodendrocyte progenitor cells. Mechanistically, the P213L mutation downregulates myelination-related genes by disrupting the interaction between hnRNPH2 and its target transcripts. Moreover, the myelin-enhancing drug benztropine rescues myelination, restores myelin-related gene expression and ameliorates cognitive deficits, highlighting the role of hnRNPH2 P213L-induced myelin abnormalities in the pathogenesis of ID. This study uncovers a crucial mechanistic link between myelin dysfunction and ID, providing potentially therapeutic ways for X-linked NDDs.

overall_design: RNA-seg profiling of cerebral cortex in wildtype and Hnrnph2P213L mice at postnatal day 7

last: Jiao

first: Qiu

first: Xinyu

last: Hu

first: Xiaoyi

last: Liao


title: Cellular senescence in human liver under normal aging and cancer [Xenium]

overall_design: This dataset includes Xenium 5K data for 12 liver samples from SBR and Sham cohort mice. Briefly, 8-week-old male C57BL/6J mice received sham or 75% proximal small bowel (sbr) resection. Mice were randomized into 2-, 10-, 26-, and 52-week cohorts. Each mouse liver was collected at the assigned time point, inspected for tumors and sectioned for H&E and SR staining highlighting fibrotic tissue. Selected mouse liver samples were further subjected to Xenium 5K.


title: PTEN variant and genetic backgrounds combine to modify cerebellar neuronal differentiation in autism spectrum disorder

city: Cleveland

first: Ya

last: Chen

state: OH

address: 2109 Adelbert Road, Room 747A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Mutations in the PTEN gene have been implicated in autism spectrum disorders (ASD), particularly among individuals with comorbid macrocephaly. In our previous study, we demonstrated that the PTEN p.Ile135Leu variant, in an ASD-related genetic background dependent fashion, disrupts both cortical neurogenesis and gliogenesis. While abnormal cerebellar development is a recognized feature of ASD, the specific cellular targets and timing of disruptions during cerebellar differentiation and development remain poorly understood. To investigate these aspects, we applied our previously established cerebellar organoid protocol and used isogenic human iPSC lines harboring this PTEN-variant. We examined the expression of Purkinje cells, granule cells, interneurons, and glial cells prior to 22 weeks of differentiation, assessed genes expression at 8 weeks, and evaluated spontaneous spikes activity in Purkinje cells after 11 weeks. We observed that cell-type-specific expression patterns differed between the PTEN p.Ile135Leu variant in control versus ASD-genetic backgrounds. However, these background differences were diminished in PTEN knockout lines across both backgrounds. Our single-cell RNA sequencing (scRNA-seq) dataset revealed that the PTEN p.Ile135Leu variant increased the number of interneuron progenitor cells, whereas PTEN knockout led to an expansion of meningeal-like cells in both genetic contexts. Moreover, both the PTEN p.Ile135Leu variant and PTEN knockout abolished spontaneous simple spikes activity in Purkinje cells across both backgrounds, including PTEN-corrected patient-derived lines. Together, these findings provide direct evidence linking PTEN dysfunction and genetic background to altered cerebellar differentiation and neuronal network activity in human cerebellar organoids.

overall_design: For 10X scRNA-seq, we used the Chromium Nest GEM Single Cell 3’ Kit v3.1 (10x Genomics, 1000268) for all scRNA-seq library preparations. Single-cell suspensions from Chap WT/WT, Chap WT/I135L, Chap KO/KO, Apex WT/WT. Apex WT/I135L and Apex KO/KO were loaded onto the chromium Next Chip G Single Cell Kit (10x Genomics, 1000120) and processed with Chromium Controller 10v Genomics (10x Genomics) to generate single-cell gel beads in emulsion. The libraries were sequenced on the NovaSeqX platform using paired-end sequencing, with the first read having a length of 28 bases and the second read having a length of 90 bases.  Raw fastq files were uploaded into the 10x Genomics cloud and reads were aligned to Human (GRCh38) with Cell Ranger. The generated filtered raw matrix including barcodes, features and matrix were uploaded into Seurat v5.

first: Anthony

last: Wynshaw-Boris


title: Single cell sequencing of Stellate Ganglion of mice retrolabeled from interscapular brown adipose tissue and forelimb

city: New York

first: Daniele

last: Neri

state: NY

address: 630 West 168th Street

institute: Columbia University Irving Medical Center

summary: To identify the molecular signature of the sympathetic neurons innervating interscapular brown adipose tissue (iBAT) in mice, we isolated, sorted, and sequenced single cells from the stellate ganglia (SG) of mice three days after injections of CTB-555 in iBAT and CTB-488 in forelimb. Each cell was analyzed for their emission after excitation at 488 and 555nm, and was assigned to either 488-positive, 555-positive, or none.

overall_design: Six C57BL/6J male mice between six and eight weeks of age were injected with CTB-488 in their forelimb and with CTB-555 in their iBAT. Three days later, SGs were harvested, dissociated, and single cells were sorted in 96-well plates. Two mice were used for each set, for a total of three sets. Ganglia were pooled within sets. Four plates per set were collected, except for the third set, where only three plates were collected, for a total of 1039 cells across 11 plates. Finally, plate-based single cell sequencing was performed.

first: Seoeun

first: Lori

last: Zeltser


title: Chemogenetic activation of iBAT-projecting sympathetic neurons

summary: To investigate the activation of sympathetic nerves projecting to brown fat, we injected a neuron-specific, retrograde, AAV in the interscapular brown adipose tissue (iBAT) of Th-Cre mice expressing the excitatory designed receptor exclusively activated by a designer drug (DREADD) hM3Dq under Cre control. Over three weeks later, we anesthetized these mice, stimulated them with DCZ or Saline, and collected their iBAT 30 minutes later to profile their gene expression. In parallel, we performed a similar study on separate set of wild type (WT) mice without virus injection.

overall_design: RNA-Seq profiling of iBAT collected from Th-Cre and WT mice, 30 minutes after being stimulated with either DCZ or Saline

first: Dominique

last: Bozec

first: Lucas

last: Castro e Souza

first: Alexis

last: Fohn

first: Natalie

last: Lopatinski


title: miRNA expression reveals a differential profile with moderate beer consumption in whole blood of healthy subjects

city: Barcelona

first: Teresa

last: Padro

state: BARCELONA

address: C/ de Sant Quintí, 77-79

department: IR BCVD

country: Spain

institute: IR Sant pau

summary:
Affymetrix microarray (GeneChip microRNA 4.0) profilling of whole blood.
We used miRNA arrays to profile miRNAs isolated from whole blood samples of healthy subjects with or without moderate consumption of traditional beer

overall_design: We isolated miRNAs from whole blood samples of healthy subjects and profiled them to determine miRNA signature

first: Escate

last: Rafael

first: Camino

last: Sandra

first: Padró

last: Teresa

first: Badimon

last: Lina


title: Nucleosome Positioning Shapes Cryptic Antisense Transcription.

city: Vienna

first: Jian Yi

last: Kok

address: Dr.-Bohr-Gasse 3

country: Austria

institute: GMI - Gregor Mendel Institute of Molecular Plant Biology

summary: Maintaining transcriptional fidelity is essential for precise gene regulation and genome stability. Despite this, cryptic antisense transcription, occurring opposite to canonical coding sequences, is a pervasive feature across all domains of life. How such potentially harmful cryptic sites are regulated remains incompletely understood. Here, we show that nucleosome arrays within gene bodies play a key role in suppressing cryptic transcription. Using the fission yeast Schizosaccharomyces pombe as a model, we demonstrate that CHD1-family chromatin remodelers coordinate with the transcription elongation machinery, specifically the PAF complex, to position nucleosomes at sites of cryptic transcription initiation within gene bodies. In the absence of CHD1, AT-rich sequences within gene bodies lose nucleosome occupancy, exposing promoter-like sequences that drive cryptic initiation. While cryptic transcription is generally detrimental, we identify a subset of antisense transcripts that encode critical meiotic genes, suggesting that cryptic transcription can also serve as a source of regulatory innovation. These findings underscore the essential role of nucleosome remodelers in maintaining transcriptional fidelity and reveal their broader contributions to cellular homeostasis and evolutionary adaptability.

overall_design: We aimed to characterize the diversity of antisense transcripts present in Schizosaccharomyces pombe (S. pombe). To achieve this, we employed Iso-Seq long-read sequencing to capture full-length transcripts. Our experimental design included two genetic backgrounds: wild-type (WT) S. pombe and an hrp1Δ hrp3Δ double mutant, which is known to exhibit increased levels of antisense transcription. Both genotypes were grown under standard laboratory conditions and subjected to two distinct stress treatments: caffeine and clotrimazole. This resulted in the following sample conditions for each genotype: untreated (control), caffeine-treated, and clotrimazole-treated. For sequencing, we multiplexed our samples in two separate runs. The first run included only the wild-type, untreated sample. The second run comprised all remaining conditions: both genotypes (WT and hrp1Δ hrp3Δ), each with and without the two stress treatments (caffeine and clotrimazole). This multiplexing strategy was chosen due to technical constraints.

first: Elin

last: Axelsson


title: Effect of circ72309 overexpression on gene expression related to gemcitabine sensitivity in pancreatic cancer cell lines

first: Daisuke

last: Motooka

country: Japan

summary: Understanding the molecular characteristics of gemcitabine sensitivity in pancreatic cancer is essential for advancing individualized treatment strategies. This study identifies circ72309 as a potential contributor to improve gemcitabine sensitivity. circ72309 decreased cytidine deaminase, a nucleoside enzyme which transforms gemcitabine into an inactive form, via reactive oxygen species activity, and increased solute carrier family 29 member 1 (SLC29A1), a nucleoside transporter which imports gemcitabine into cells, by regulating targeted miRNAs.

overall_design: To identify the  changes of mRNA expression, gemcitabine-resistance pancreatic cancer cell line (GR3) was established and transfected with either circ72309 vector or negative control (scramble) oligonucleotides. Gene expression profiling was performed using RNA-seq data obtained from these two cell lines. A comparative analysis of the RNA-seq data was conducted to evaluate gene expression profiles between circ72309-transfected cells and scramble controls.

first: Naoko

last: Sekiguchi

first: Yoshito

last: Tomimaru

first: Hidenori

last: Takahashi

first: Hidetoshi

last: Eguchi


title: Asrij/OCIAD1 expression delineates functionally distinct hematopoietic stem cells in the bone marrow

city: Bengaluru

first: Maneesha

last: Inamdar

state: Karnataka

address: JNCASR, Jakkur

department: MBGU

country: India

institute: JNCASR

summary: Hematopoietic stem cells (HSCs) within the bone marrow (BM) display significant molecular and functional heterogeneity. Deciphering intrinsic factors that govern HSC diversity is key to enriching specific HSC subtypes for predictable and clinically relevant differentiation outcomes. Here, we show that the mitochondrial protein Asrij/OCIAD1, a conserved regulator of hematopoietic homeostasis, contributes to HSC heterogeneity. Asrij depletion is known to cause loss of quiescence, myeloid bias, and aging-like changes in mouse BM HSCs. Interestingly, Asrij expression is inherently heterogeneous and enriched in only 47% of the HSC population. To investigate whether Asrij expression levels influence HSC fate, we generated a novel Asrij-mNeonGreen (mNG) knock-in reporter mouse using CRISPR-Cas9 technology. We show that the Asrij reporter faithfully recapitulates its heterogeneous expression in the BM HSCs, allowing isolation of live cells based on Asrij expression levels. Ex vivo culture of HSCs demonstrated that Asrijlow HSCs exhibit enhanced self-renewal capacity, whereas Asrijhigh HSCs are primed for differentiation. Transplantation assays further revealed that Asrijlow HSCs have enhanced reconstitution in the BM hematopoietic stem and progenitor cell (HSPC) and myeloid cell compartments. Transcriptomic analysis uncovered signatures of quiescence in Asrijlow HSCs, whereas Asrijhigh HSCs exhibit hallmarks of HSC activation. In summary, we show that Asrij levels impact the quiescence, self-renewal, and differentiation potential of HSCs, thereby contributing to the functional diversity of the HSC pool. Furthermore, the Asrij-mNG reporter mouse provides a powerful and versatile model for investigating the molecular underpinnings of functional diversity within the HSC compartment.

overall_design: Bulk RNA sequencing analysis of bone marrow long term (LT) hematopoietic stem cells expressing low and high levels of Asrij. Experiment was performed using 4 month old mice.

first: Aishwarya

last: Prakash

first: Souvik

last: Halder


title: Piezo1 dictates K⁺ homeostasis through coordinated regulation of the ubiquitin ligase Kelch-like 3 in RBCs and the kidney

city: Itabashi

first: Shigeru

last: Shibata

institute: Teikyo University

summary: The maintenance of potassium (K+) balance is a fundamental biological process involving multiple organs. However, mechanisms by which inter-organ communication regulates K+ homeostasis remain largely unexplored. By combining human genetics and mouse model generation using CRIPSR/Cas9, we demonstrate that the ubiquitin ligase Kelch-like 3 (KLHL3) orchestrates K⁺ transport across K⁺-storing erythrocytes and K⁺-excreting kidneys by interacting with the mechanosensitive Ca2+ channel Piezo1.

overall_design: We compared RNA profiles obtained from the spleen between wild-type and KLHL3 knock-in mice.

first: Kenichi

last: Ishizawa


title: Lineage plasticity of the integrated stress response is a hallmark of lung cancer evolution.

city: Montréal

first: Antonis

last: Koromilas

state: QC

address: 3755 Chem. de la Côte-Sainte-Catherine

institute: Lady Davis Institute - McGill University

summary: Lung adenocarcinoma (LUAD) progresses from a single alveolar type 2 (AT2) cell to a complex, malignant tissue through a multi-step process involving acquisition of high plasticity and stem cell-like traits in a subset of cancer cells. Oncogenic transformation and signals from the tumor microenvironment (TME) activate the integrated stress response (ISR), a key survival mechanism that allows tumor cells to adapt and thrive under stress. Using single-cell transcriptomics, we identified high stemness and plasticity cell clusters in mouse LUAD tumors expressing mutant KRAS and lacking TP53 (KP model), which displayed elevated ISR program expression. Disrupting ISR via the genetic loss of phosphorylated eIF2a (p-eIF2a) or the transcription factor ATF4 hindered LUAD growth and the emergence of high-plasticity, stemness-associated lineages, resulting in the formation of a distinct cell state characterized by mitochondrial dysfunction. Additionally, treatment with ISRIB - a small-molecule ISR inhibitor with low toxicity and cognitive benefits - led to an accumulation of AT2-like LUAD cells, blocking developmental progression and tumorigenesis. In human LUAD, the ISR program is similarly elevated in KRAS-mutant tumors with high plasticity and stemness features and correlates with poor patient outcomes. These findings suggest that ISR is a key driver of LUAD progression and targeting ISR could provide a promising approach to slow LUAD progression and improve lung cancer treatment outcomes.

overall_design: To investigate the role of integrated stress response, specifically p-eIF2, in LUAD evolution, we conducted scRNA-seq on GFP+/CD45- lung tumor cells isolated by Fluorescence-Activated Cell Sorting (FACS).

first: Shiqi

last: Diao

first: Jia Yi

last: Zou


title: Nascent transcript sequencing visualizes mouse preimplantation embryonic genome activation

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: Embryonic genome activation (EGA), a pivotal transcriptional event during preimplantation development, is accompanied by post-transcriptional regulation of maternal mRNAs. Disentangling the transcriptional output of the newly activated embryonic genome from concomitant post-transcriptional processing is important for decoding EGA dynamics.Here, using optimized low-input SLAM-seq (thiol(SH)-linked alkylation for the metabolic sequencing) in mouse embryos, we delineates the temporal hierarchy of EGA nascent transcription during mouse preimplantation embryogenesis and uncovers a mechanistic link between EGA and the first lineage specification, providing new insights into the regulatory architecture of early mammalian development.

overall_design: For the SLAM-seq profiling of mouse preimplantation embryos from nine stages, we adopted the criteria of 2 mM 4SU, 6-hour interval labeling and 10 embryos per sample for profiling; For the ATAC-seq, we selected the embryos from seven stages across the preimplantation development; For the function validation of KLF17, we collected contrl (ctrl), KO, mKO, pKO embryos at the M2C stage to perform SLAM-seq.

first: Yuxiang

last: Wang

first: Yue

last: Hu

first: Ran

last: Huo


title: Synergistic Mn-MOF Activation of Pistol Ribozymes for Cancer Immunotherapy

city: Tianjin

first: Yijin

last: Liu

address: Haihe Education Park, 38 Tongyan Road, Tianjin 300071, China

institute: Nankai University

summary: Checkpoint blockade therapies targeting PD-L1 have revolutionized cancer immunotherapy, yet their efficacy is constrained by systemic immune toxicity and inadequate immune infiltration in certain tumor types. Here, we introduce a synergistic gene-silencing nanosystem based on a target-selective Pistol ribozyme (PS473) encapsulated within a manganese-based, pH-responsive metal-organic framework (NKMOF-101-[Mn]). The engineered PS473 exhibited high cleavage efficiency toward GU-rich PD-L1 mRNA motifs and was further activated by Mn2 + cofactors. NKMOF-101-[Mn] not only protects the ribozyme from nuclease degradation but also enables localized Mn2 + release to increase catalytic activity and innate immune signaling under the acidic tumor microenvironment. In vitro, PS473@NKMOF-101-[Mn] markedly suppressed PD-L1 expression and promoted macrophage activation. In the B16F10 melanoma model, this system achieved over 90% tumor inhibition, enhanced immune cell infiltration and activation, and exhibited minimal systemic toxicity. Transcriptomic profiling further revealed the upregulation of immune-related pathways, supporting a synergistic mechanism of gene silencing and immune activation. Overall, this study established a ribozyme-directed immunotherapeutic platform with strong potential for precision cancer therapy via checkpoint modulation and immune reprogramming.

overall_design: Tumor tissues were obtained at 48 h after the last intratumoral injection dministration, and RNA-seq analysis was performed on the tumor tissues of the blank control roup and multiple treatment groups (FreePS473, PS473@CPs, NKMOF-101-[Mn], M5@NKMOF-101-[Mn], PS473@NKMOF-101-[Mn]).

first: Ming

last: Zhao


title: Hand and Arm Dysfunction is Prevalent Following Hemodialysis Access Placement and Associated with Higher Rate of Access Failure

city: Gainesville

first: Terence

last: Ryan

address: 1864 Stadium Rd

institute: University of Florida

summary: This project aimed to map transcriptome changes in the forearm skeletal muscle of patients with chronic kidney disease undergoing hemodialysis access placement surgery. Muscle biopsies were obtained from the brachioradialis muscle pre- and at several timepoints post-operatively.

overall_design: bulk RNA sequencing was performed on brachioradialis muscle specimens obtained from CKD patients undergoing hemodialysis access placement surgery

first: Kim

last: Kyoungrae

first: Ryan

last: Terence E.

first: Scali

last: Salvatore T.


title: Targeting Tumor-associated CCR2+ Macrophages with Proteolipid Nanovesicles to Inhibit Pancreatic Cancer Recurrence Following Irreversible Electroporation

city: Shanghai

first: Weichen

last: Xu

state: Shanghai

address: No. 301, Middle Yanchang Road, Shanghai, 200072

department: Medical ultrasound

institute: Shanghai Tenth People’s Hospital, School of Medicine, Tongji University

summary: Irreversible electroporation (IRE) has emerged as a promising radical ablative therapy for PDAC; however, its clinical efficacy is hindered by the high recurrence rate. Herein, using a preclinical orthotopic PDAC tumor model, we comprehensively characterized the tumor immune microenvironment following IRE treatment through scRNA-seq. Our findings provide direct evidence that IRE treatment induces a CCR2+ tumor-associated macrophages (CCR2+ TAMs)-mediated immunosuppressive microenvironment in the residual tumor, ultimately accelerating tumor recurrence. Targeting CCR2+ TAMs enhances antitumor immunity and improves the chemotherapeutic response in PDAC.

overall_design: Following the establishment of orthotopic pancreatic tumors in mice, tumors were treated with irreversible electroporation (IRE) or subjected to sham surgery once they reached a certain size. Three days post-treatment, tumor samples were collected and analyzed using 10x Genomics scRNA-seq analysis.

first: Liping

last: Sun


title: Gene expression profile at single cell level of genetically defined organoid models in neoplastic evolution of head and heck squamous cell carcinoma

city: Los Angeles

first: De-Chen

last: Lin

state: CA

address: CSA 210, 2250 Alcazar Street

department: Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center

institute: University of Southern California

summary: To investigate the molecular mechanisms driving neoplastic evolution in head and neck squamous cell carcinoma, we established genetically defined mouse tongue organoid models harboring key driver mutations: control (Ctrl), Trp53/Cdkn2a dual-knockout with a control vector (DKOC), and Trp53/Cdkn2a dual-knockout with the PIK3CA E545K mutation (DKOP), and performed single-cell RNA sequencing (scRNA-seq) using the 10x Genomics platform on these organoid lines.

overall_design: Wild-type mouse tongue organoids were first generated from wild-type C57BL/6 mice and subsequently genetically engineered into three lines: Ctrl, DKOC, DKOP. ScRNA-seq was performed to assess the impact of the dual-knockout of Trp53/Cdkn2a and the additional PIK3CA E545K mutation on gene expression profiles and cellular states within these organoid models.

first: Hua

first: Young-Min

last: Park

first: Yueyuan

last: Zheng

first: Qiong

last: Mao

first: Casey

last: Collet

first: Boyan

first: Tianming

last: Zhou

first: Luda

first: Stephanie

last: Wong

first: Yuhao

last: Pan

first: Anette

middle: V

last: Monreal

first: Uttam

last: Sinha

first: Parish

last: Sedghizadeh

first: Alice

last: Soragni


title: Targeting Notch Signaling to Restore Neural Development and Behavior in Autism

city: Isehara

first: Takatoshi

last: Iijima

state: Kanagawa

address: 143 Shimokasuya

department: School of Medicine

institute: Tokai University

summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social deficits and repetitive behaviors, influenced by both genetic and environmental factors. However, the molecular mechanisms underlying this heterogeneity remain unclear. This study highlights dysregulation of the Notch signaling pathway as a shared molecular mechanism in inherited and non-hereditary ASD models in mice and humans. Aberrant HDAC3-mediated epigenetic activation of Notch signaling during embryonic forebrain development disrupts the specification of caudal ganglionic eminence (CGE) precursors into VIP+ GABAergic interneuron subtypes (VIP-INs). CGE-specific ablation of Notch1/2 genes in ASD models rescues the VIP-IN loss, E/I balance, and selectively improves social behaviors. Remarkably, a single antenatal dose of a γ-secretase inhibitor, previously used in the clinical trials for cancer treatment, effectively ameliorates multiple ASD-associated neuronal, behavioral, and transcriptomic levels in adult models. Thus, the study confers a critical convergence of ASD risk factors on Notch signaling dysregulation and establishes this pathway as a promising therapeutic target for developmental and behavioral deficits in ASD.

overall_design: Pregnant mice received intraperitoneal (i.p.) injections of VPA at E13, E15, or E18. To assess rescue effects, Ro4929097 was administered at E17. Offspring were analyzed at P2.

last: Iijima (corresponding)

first: Yoko

last: Hanno (first)(corresponding)

first: Hiroyuki

last: Hosokawa

first: Moe

last: Nakanishi

first: Akinori

last: Takase

first: Jun

last: Nomura

first: Masami

last: Tanaka

first: Masayuki

first: Masatoshi

last: Ito

first: Katsunaka

last: Mikami

first: Katsuto

last: Hozumi

first: Goichi

last: Miyoshi

first: Toru

last: Takumi


title: c-MET inhibition is synthetic lethal with ARID1A loss via targeting GPX4 and promoting ferroptosis

city: Guangzhou

first: Changjie

last: Wu

state: Guangdong

address: 1838 Guangzhou Avenue North, 510515 Guangzhou, Guangdong, China

institute: Southern Medical University

summary: ARID1A, a subunit of the SWI/SNF chromatin-remodeling complex, functions as a tumor suppressor in various cancer types. Owing to its high frequency of inactivating mutations, ARID1A has emerged as a promising target for the development of anticancer drugs. In this study, we report that ARID1A-deficient colorectal cancer (CRC) cells induce synthetic lethality when treated with inhibitors of c-MET receptor tyrosine kinase. c-MET specific inhibitor PHA-665752 as well as two other FDA-approved drugs, crizotinib and cabozantinib, selectively inhibited the growth of ARID1A-deficient CRC cells in vitro and in xenograft tumor models. Mechanistically, we identified triple genetic interactions between ARID1A, c-MET, and GPX4 in CRC cells, where GPX4, a key regulator of ferroptosis, is a common transcription target of ARID1A and c-MET signaling. ARID1A inactivation significantly downregulated both c-MET and GPX4 levels, and the c-MET inhibitor further diminished GPX4 levels in ARID1A-deficient CRC cells, leading to increased lipid peroxidation and glutathione depletion, ultimately inducing ferroptosis. This study reveals a novel synthetic lethal relationship between ARID1A and c-MET signaling in promoting ferroptosis and proposes c-MET inhibitors as a potential therapeutic strategy for ARID1A-deficient CRC.

overall_design: RNA-seq

first: Joongsup

last: Shim

first: Xu

last: Zhang

first: Yijiang

last: Song


title: Single-cell RNA analysis reveals reduced frequency and activity of CXCR5+ atypical memory B cells in islet xenotransplantation treated with clinically applicable immunosuppressants including Belimumab

city: Seoul

first: Yuji

last: Lee

state: Soul-t'ukpyolsi

address: #308, Convergence building, Seoul National University College of Medicine, 103 D

institute: Seoul National University

summary:
Background
Porcine-to-human islet xenotransplantation offers a promising solution to type 1 diabetes. This study investigates the use of belimumab, a human monoclonal antibody that inhibits B cell activating factor (BAFF) as part of an immunosuppressive regimen in porcine-to-non-human primate xenotransplantation.
Methods
Porcine islets were transplanted into Rhesus monkeys with an immunosuppressant regimen. Blood samples were collected from the monkeys pre- and post-treatment, and single-cell RNA sequencing was performed to investigate immune cell landscape changes, focusing on B cells.
Results
UMAP clustering of B cells identified five distinct subsets. Notably, belimumab treatment significantly reduced the proportion of both CXCR5+ and CXCR5- atypical memory B cells, which possess the potential to differentiate into antibody-secreting cells. Furthermore, differentially expressed gene (DEG) analysis revealed a comprehensive functional impairment, along with significant downregulation of activation markers such as CD69 and CD83, across all B cell subsets.
Conclusions
Our study elucidates the mechanism of action of belimumab in non-human primate models, serving as preclinical subjects for B-cell-targeted therapy research in a xenotransplantation context. Significantly, our data indicate that belimumab not only reduces the proportion of antibody-secreting atypical memory B cells but also induces functional impairment across all B cell subsets. Given the potential pathogenic roles of atypical memory B cells in autoimmunity and other related settings, their reduction by belimumab could play a crucial role in regulating B cell-mediated immune responses in pig-to-nonhuman primate pancreatic islet xenotransplantation. Thus, our findings highlight the prospective utility of belimumab as a B cell suppressant in future clinical xenotransplantation applications.

first: Ji-Hwan

last: Moon

first: Hyun-Je

last: Kim

first: Daesik

first: Yong-Hee

first: Jong-Min

first: Chung-Gyu

last: Park


title: Ecologically designed three-member microbial consortia promote growth in Brassicaceae members by modulating growth-defense tradeoff

city: singapore

first: Hitesh

last: Tikariha

address: 5A Engineering Drive 1, #02-03 T-Lab Building

country: Singapore

institute: National university of singapore

summary: Both microbiological and genomics approaches demonstrated the significant PGP potential and stability of bacterial consortia SAB, which outperformed its members. Phenotypic data indicated that SAB treatment positively impacted shoot and root biomass growth. Furthermore, greenhouse experiments confirmed the consistent and significant performance of SAB treatment on choy sum plants in various soil conditions. Transcriptomics data of boht root and shoot at two different time point revealed that SAB triggered a parallel activation of growth and defense response in shoot that by pass the growth defense tread-off through microbiome mediated signaling and beneficial services.

overall_design: A three-membered bacterial consortium (SAB) was formulated by considering the natural interactions among its members through genome-scale metabolic modeling along with the PGPR properties. The consortium was found to promote growth in several leafy vegetables like Choy-sum and Kai-lan in both laboratory and greenhouse conditions. Transcriptome analysis was carried out from the leaves and root system of the consortium-treated Choy-sum plants at 8 and 18 days of their growth in pots with peat-moss soil, with their respective untreated control.  The seeds were treated with SAB consortium and sowed in peat-moss soil.  Plants were grown in a controlled environment with a 16/8-hour light and dark cycle at 22 degrees Celsius temperature.

first: Mrinmoy

last: Mazumdar

first: Mayalagu

last: Sevugan

first: Shruti

last: Pavagadhi

first: Sanjay

last: Swarup


title: Evolutionary adaptations to the hormonal regulation of vascular tissue development

city: ghent

first: Wei

last: Xiao

address: Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium

country: Belgium

institute: VIB-UGent Center for Plant Systems Biology

summary: Vascular tissues connect shoot and root organs in the vascular plant lineage, providing significant adaptive advantages. Although the crosstalk between auxin and cytokinin in promoting both vascular cell proliferation and differentiation has been well studied in angiosperms such as Arabidopsis thaliana, little is known about this regulation in other vascular plant lineages. Here, we found that unlike the hormonal cross talk found in all other species under study, the lycophyte Selaginella moellendorffii shows clear task separation with auxin driving vascular cell proliferation only, and cytokinin specifically triggering cell differentiation. Using a cross-species transcriptomics approach, we found members of the AUXINs/INDOLE-ACETIC ACIDs (Auxs/IAAs) and CYTOKININ OXIDASEs (CKXs) gene families exhibited divergent expression patterns in response to auxin and cytokinin. Despite these regulatory differences, we show that AtIAA/SmIAA and AtCKX/SmCKX proteins are functionally conserved. Taken together, our findings suggest an evolutionary adaptation to the hormonal regulation of vascular tissue development in which core protein functions are conserved, but regulatory circuits diverged in Lycophytes.

sample_organism:
Arabidopsis thaliana
Selaginella moellendorffii

overall_design: For Arabidopsis thaliana, the plants (Col-0) were grown on 1/2 Ms plates for 4 days and transferred to mock, 10μM NAA or 10μM BAP for 2h. Next, the 0,2 cm root tips were harvested for RNA-seq. For Selaginella moellendorffii, the experimental setup 1: the plants (WT) were grown on 1/2 Ms plates for 14 days and transferred to mock, 10μM NAA or 10μM BAP for 2h. Next, the 0.2 cm root tips were harvested for RNA-seq. The experimental setup 2:  the plants (WT) were grown on 1/2 Ms plates for 14 days and transferred to 1μM NAA or Mock (directly harvest after the treatment) for 7d. Next, the plants were transferred to Mock for 0h, 3h, 6h, 12h, and 24h. The plants were harvest 0.2 cm root tips for RNA-seq in each indipendent time point.

first: Bert

last: De Rybel


title: A transient tumoral challenge is sufficient to negatively im-print the generated memory CD8 T cells

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

country: France

institute: AltraBio

summary: The objective of this study is to compare the transcriptome of memory CD8 T cells generated following an acute viral infection (VV-CD8) or a transient tumoral challenge with a tumor that is eleminated by the immune system (EL4-CD8), in quiescent condition or following a brief in vitro stimulation with their cognate peptide. Naive CD8 T cells were used as control.

overall_design: B6 mice were transferred with naive CD8 T cells from F5 transgenic mice. The next day, mice were challenge with vaccinia virus (VV) or EL4 tumor cells, both expressing NP68 peptide. CD45.1+ F5 memory cells were sorted from the spleens of VV- or EL4-immunised mice 9 weeks after the primary challenge. Naive F5 cells were sorted from the spleen of F5 x CD45.1 mice. Enriched CD8 T cells were stimulated (VV-CD8_R, EL4-CD8_R, naive_R)  or not (VV-CD8, EL4-CD8, Naive) with NP68 peptide (10 nM) for 2h at 37 °C.

first: Daphné

last: Laubreton

first: Margaux

last: Prieux

first: Sophia

last: Djebali

first: Maxence

last: Dubois

first: Olivier

last: Gandrillon

first: Christophe

last: Arpin

first: Jacqueline

last: Marvel


title: Antigen specificity of clonally-enriched CD8+ T cells in multiple sclerosis

city: San Francisco

first: Joseph

last: Sabatino

address: 1651 4th St, Room 421A

institute: UCSF

summary: CD8+ T cells are the dominant lymphocyte population in multiple sclerosis (MS) lesions where they are highly clonally expanded.  The clonal identity, function, and antigen specificity of CD8+ T cells in MS are not well understood.  Here we report a comprehensive single-cell RNA-seq and T cell receptor (TCR)-seq analysis of the cerebrospinal fluid (CSF) and blood from a cohort of treatment-naïve MS patients and control participants.  A small subset of highly expanded and activated CD8+ T cells were enriched in the CSF in MS that displayed high activation, cytotoxicity and tissue-homing transcriptional profiles.  Using a combination of unbiased and targeted antigen discovery approaches, MS-derived CD8+ T cell clonotypes recognizing Epstein-Barr virus (EBV) antigens and multiple novel mimotopes were identified.  No CD8+ T cell cross-reactivity was found between the EBV epitopes and self-antigens, but EBV DNA was detected in CSF, including in the same individuals with highly expanded CD8+ T cells.   These findings shed vital insight into the role of CD8+ T cells in MS and lend further support an important role of EBV in MS immunopathology.

overall_design: Cross-sectional single-cell sequencing analysis of blood and CSF from a cohort of MS patients and control subjects

first: Kristen

last: Mittl

first: Fumie

last: Hayashi

first: Ravi

last: Dandekar

first: Ryan

last: Schubert

first: Ebtesam

last: Hassan

first: Josiah

last: Gerdts

first: Lindsay

last: Oshiro

first: Rita

last: Loudermilk

first: Ariele

last: Greenfield

first: Danillo

last: Augusto

first: Akshaya

last: Ramesh

first: Edwina

last: Tran

first: Kanishka

last: Koshal

first: Kerry

last: Kizer

first: Joanna

last: Dreux

first: Alaina

last: Cagalingan

first: Florian

last: Schustek

first: Lena

last: Flood

first: Tamson

last: Moore

first: Lisa

last: Kirkemo

first: Tiffany

last: Cooper

first: Meagan

last: Harms

first: Refujia

last: Gomez

first: Leah

last: Sibener

first: Bruce

last: Cree

first: Stephen

last: Hauser

first: Jill

last: Hollenbach

first: Marvin

last: Gee

first: Michael

last: Wilson

first: Scott

last: Zamvil


title: Divergent tumor immunity determined by bacteria-cancer cell engagement

city: HangZhou

first: Xiaoqin

last: Liu

state: ZheJiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

institute: Westlake University

summary: Intratumor bacteria represent an understudied yet influential component of the cancer ecosystem, critically impinging cancer progression. In PyMT breast tumors, we find intracellular bacteria, when residing in cancer cell cytosol, promote metastasis by triggering cytosolic double-stranded DNA (dsDNA) accumulation, which in turn activates the tumor intrinsic cGAS-STING-interleukin (IL)-17B pathway and redirects neutrophils toward a protumor phenotype that inhibits cytotoxic T cells. By contrast, the same strain of bacteria, when present extracellularly, induces antitumor neutrophil activity without engaging the STING pathway. Physiologically, eliminating intracellular bacteria, or therapeutically introducing extracellular bacteria components, abrogates immunosuppression and prevents postsurgical metastatic recurrence in preclinical models. Clinically, the bacteria invasion signature we have developed is associated with poor prognosis in patients with breast cancer. In summary, the spatial interplay between bacteria and host cells in metastatic niches can shape divergent tumor immunity, highlighting bacterial-host engagement as a crucial determinant of cancer immune regulation and a potential therapeutic target.

overall_design: For FVB mouse experiment, lungs were harvested from PBS(injected PBS), Bacteria(injected bacteria), woBac(injected tumor cell co-cultured with bacteria which showed negative bacteria signal) , withBac(injected tumor cell co-cultured with bacteria which showed positive bacteria signal). For germ free mouse experiment, lungs were harvested from WT(wild type), Control(injected tumor cells co-cultured with bacteria) and ATBx(injected tumor cell co-cultured with bac but use Antibiotics treated) mice at the end of point of experiment. Then lungs were dissected into single cells. Live cells were sorted by FACS to do 10X scRNA-seq. For RNA seq experiment, tumor cells co-cultured with live or dead bacteria. Then tumor cell containing live or dead bacteria were sorted by FACS to do bulk RNA-seq.

first: Bingqing

last: Yao

first: Kanghui

last: Ruan

first: Xiunan

last: Fang

first: Shang

last: Cai


title: The role of suv4-20h1 in Xenopus multiciliogenesis

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

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

overall_design: Refer to individual Series


title: CRISPLD2 regulates adipocyte function

city: OKC

first: David

last: Sparling

state: OK

address: 1200 Children’s Avenue, Suite 4D

department: Section of Pediatric Diabetes and Endocrinology

institute: Oklahoma Children’s Hospital OU Health

summary: Obesity with accompanying adipose fibrosis is associated with worsening insulin resistance. Weight loss and adipose tissue turnover are conversly associated with improved insulin signaling and overall health. We previously found the secreted protein CRISPLD2 up-regulated in adipocytes during weight loss; CRISPLD has been suggested regulate inflammation and tissue turnover. As loss of CRISPLD2 is embryonic lethal, we developed mice with adipocyte-specific inducible CRISPLD2 overexpression to explore its function. Single-cell RNAseq analysis of the stromal vascular fraction (SVF) during long-term adipocyte CRISPLD2 overexpression demonstrated broad down-regulation of collagen transcription across multiple cell types; we found similar down-regulation of fibrosis via picosirius red staining of adipose tissue overexpressing CRISPLD2, along with a decrease in adipocyte cell size in chow-fed animals.

overall_design: scRNAseq of Mouse stromal vascular fraction from control and CRISPLD2 overexpression mice. This was performed on 2 males of each genotype, Tg and Double Tg. A double transgenic mouse was developed by crossing mice carrying a the inducible crispld2 plasmid with C57BL/6-Tg(Adipoq-rtTA)2Zvw/J mice from Jackson lab (RRID:IMSR_JAX:033448) (CLD2AD).  Single transgenic mice carrying only the TRE-mCLD2 served as the control group. These mice were fed Teklad Rodent Diet plus doxycycline to induce the crispld2 transgene. Single Cell experiment was done on the stromal vascular fraction of these mice following isolation. Cell ranger and Parktek Software was used to visualize the data,, quality control was performed then cell types were identified and additioanl analsis of gene expression in those populations was analyzed.

first: Beth A

last: Griesel

first: Kylie

last: Williams

first: Nagib

last: Ahsan

first: Philipp E

last: Scherer

first: Ann Louise

last: Olson

first: David P


title: The role of suv4-20h1 in Xenopus multiciliogenesis [RNA]

summary: Histone post-translational modifications (PTM) greatly influence gene expression and are widely considered to regulate progression through development. However, the function of some PTMs remain elusive. H4K20 is sequentially methylated in concert with the cell cycle. In proliferating cells, SET8/KTM5A writes the monomethyl mark in G2/M phase, which then is converted to the di- and trimethylated states by SUV4-20H1/H2 (KMT5B/KMT5C) methyltransferases in the next G1 and S phase. In quiescent, differentiated cells, H4K20me2 represents the most abundant histone modification present in vertebrate chromatin. To address the function of H4K20 methyl states in development, we blocked the deposition of H4K20me2 and H4K20me3 by depleting the SUV4-20H1 in Xenopus embryos. This results in a severe ciliogenic defect in multiciliated cells (MCCs), as well as the repression of hundreds of cytoskeleton and cilium related genes. Further, we demonstrate that this defect can be rescued by wildtype, but not catalytically inactive SUV4-20h1, as well as by overexpressing PHF8, an H4K20me1-specific histone demethylase. Ciliogenic defects cannot be rescued by master regulators of ciliogenesis on the phenotypic or transcriptional levels. Taken together, this indicates that SUV4-20H1 plays a critical role in multiciliogenesis.

overall_design: To investigate the effect of suv4-20h1/2 knockdown on Xenopus animal caps, we injected embryos with translation blocking morpholinos again suv4-20h1 and suv4-20h2 and then cut epidermal explants (animal caps). Separately, we were interested in the effect of multicilin overexpression in conjunction with suv4-20h1 depletion, so we co-injected hormone inducible multicilin mRNA (mci-hGR) and induced with dexamethasone. At NF 16, we harvested animal caps and performed RNA-seq.

first: Janet

last: Tait

first: Ralph

last: Rupp


title: The role of suv4-20h1 in Xenopus multiciliogenesis [ATAC]

overall_design: To investigate the effect of suv4-20h1 knockdown on Xenopus animal caps, we injected embryos with translation blocking morpholinos again suv4-20h1 and cut epidermal explants (animal caps).  At NF 16, we harvested animal caps and performed ATAC-seq to profile changes in chromatin accessibility upon suv4-20h1 depletion.


title: MIC-Drop-seq: Scalable single-cell phenotyping of mutant vertebrate embryos

status: Public on Jan 02 2026

city: SALT LAKE CITY

first: Clayton

last: Carey

state: UT

address: 1390 President's Circle

department: Biology

institute: University of Utah

summary: Pooled perturbation screens can reveal cellular regulatory networks, yet scaling these techniques for large-scale screens in animals remains challenging. To address this, we developed MIC-Drop-seq, which combines high-throughput CRISPR gene disruption in zebrafish embryos with phenotyping by multiplexed single-cell RNAseq. In one MIC-Drop-seq experiment, we simultaneously identified changes in gene expression and cell abundance across 74 cell types resulting from loss of function of 50 transcription factors. These observations recapitulated many known phenotypes, while also uncovering novel functions in brain and mesoderm development. A key advantage of whole-animal screens is that they reveal how changes in one cell type affect the development of other cell types. Surprisingly, such cell-extrinsic phenotypes were abundant, indicating that transcription factors frequently exert effects beyond the cells where they are expressed to adjacent cells. We propose that MIC-Drop-seq will facilitate efforts to dissect the complete gene regulatory networks that guide animal development.

overall_design:
This submission includes single-cell RNA sequencing data from pooled CRISPR-perturbed zebrafish embryos and amplicon sequencing for CRISPR validation.
Dataset 1 contains 1 scRNA-seq sample from 40 pooled embryos at 24 hpf, each injected with MIC-Drop droplets targeting one of 8 genes (tbx16, tbxta, cdx4, foxa2, hoxb1b, rx3, hand2, tyr). Genotypes are multiplexed via gRNA capture using 10X feature barcoding.
Dataset 2 contains amplicon sequencing of genomic DNA from MIC-Drop injected embryos and wild-type controls to validate CRISPR editing efficiency at target loci.
Dataset 3 contains 16 scRNA-seq samples (4 biological replicates × 4 technical pools) from a screen of 50 transcription factors. Each pool contains ~250 embryos at 24 hpf, with each embryo injected with droplets targeting one of 50 genes.

first: Saba

last: Parvez

first: Zachary

last: Brandt

first: Brent

last: Bisgrove

first: Christopher

last: Yates

first: Randall

last: Peterson

first: James

last: Gagnon


title: Assessment of innate immune regulators in pancreatic cancer

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

summary: Pancreatic ductal adenocarcinoma (PDAC) accounts for 90% of all pancreatic cancer cases, and is among the most aggressive and lethal malignancies worldwide. PDAC is driven by genetic alterations in the pancreatic epithelium (e.g. KRAS, TRP53) coupled with a dysregulated innate immune response, the latter leading to an inflammatory tumor microenvironment enriched in innate immune cells (e.g. macrophages). However, immune-based treatment regimens for PDAC patients have primarily focused on immunotherapy with adaptive immune checkpoint inhibitors (e.g. PD-1) which disappointingly have yielded minimal clinical benefit. Thus, there is an unmet clinical need to identity disease-associated innate immune regulators as therapeutic targets in PDAC.  Innate immune responses depend on a series of cell surface, endosomal and cytosolic pattern recognition receptors (PRRs) that are expressed in immune and non-immune cells. PRRs are classified into several structurally and functionally conserved subfamilies, including Toll-like receptors (TLRs), Absent in melanoma 2 (AIM2)-like receptors (ALRs), and Nod-like receptors (NLRs). A subset of NLRs and AIM2 are also well documented for their formation of multiprotein complexes called ‘inflammasomes’ - comprising the adaptor ASC and Caspase-1 - which direct the maturation and release of bioactive pro-inflammatory cytokines, IL-18 and IL-1beta. However, the role of these critical innate immune regulators in PDAC has been underexplored, and is virtually unknown. Here, using the genetically engineered KPC PDAC mouse model, we performed whole transcriptome profiling to identify unique ASC-inflammasome driven downstream molecular networks associated with a range of oncogenic cellular processes in pancreatic tumorigenesis.

overall_design: Mice on a mixed 129Sv x C57BL/6 background were aged 20 weeks, and pancreas was collected and snap-frozen.

first: Bassam

middle: F

last: Kashgari

first: Brendan

last: Jenkins

first: Linden


title: Incorporation of genomic determinants improves diagnostic accuracy of oligomonocytic chronic myelomonocytic leukemia

status: Public on Dec 31 2025

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

summary: Recent updates to the monocyte count thresholds for diagnosing chronic myelomonocytic leukemia (CMML) have been implemented to recognize oligomonocytic CMML (OM-CMML) as an early stage within the CMML spectrum. However, the clinical validity of these changes remains uncertain without considering biological factors. In this study, we compared a large cohort of patients (N=911) with OM-CMML (n=249), CMML (n=359), and myelodysplastic syndromes (n=303) using unsupervised clustering to assess the role of genomic determinants in improving CMML diagnostic accuracy. Our findings show that CMML molecular signatures, characterized by biallelic TET2 mutations or SRSF2-TET2 co-mutations, are associated with a distinct transcriptome, monocytic bias, classical monocytosis, and progression to overt CMML in OM-CMML cases. By developing a weighted and reproducible model, we demonstrate that genomic features, combined with bone marrow monocyte frequencies, can reliably predict CMML progression in OM-CMML. These results support the integration of genomic determinants into the CMML diagnostic framework to enhance diagnostic accuracy and suggest that incorporation of our proposed clinic-ready diagnostic workflow into clinical practice might reliably identify early stage CMML with oligomonocytic features.

overall_design: Bulk RNA sequencing in bone marrow CD34+ cells from patients with CMML, MDS and OM-CMML

first: Guillermo

last: Montalban Bravo


title: Comparative analysis of the cardiac structure and transcriptome of scallop and snail, perspectives on heart chamber evolution

city: Qingdao

first: Long

last: Zhao

address: 5 Yushan Rd

institute: Ocean University of China

summary: As a vital organ to pump blood in the circulatory system, the heart has undergone gradual refinement in its structure and functional efficiency along animal evolution. The occurrence of cardiac chambers, the atrium and the ventricle, is an important event during heart evolution.The two-chambered heart, consisting of a single atrium and a single ventricle, first appeared among mollusks, prior to the evolution of multi-chambered hearts in higher vertebrates. The molecular bases driving the evolution of cardiac chambers, however, are largely unknown. In this study, we studied two common mollusks, the giant African snail (Lissachatina fulica) and scallops (Mizuhopecten yessoensis), to explore the gene profiles of atrium vs. ventricle in mollusks. By examining their heart structures, we found that the snail heart possesses a more compact muscle layer than the scallop heart. Then, RNA sequencing and differentially expressed genes (DEGs) analysis of the atrium and ventricle revealed that these two chambers are distinct in gene expression preference and functional features. Moreover, by comparing with the zebrafish heart, a typical two-chambered heart in vertebrates, mollusk ventricles share similar gene function enrichments with the zebrafish ventricle, but their atria exhibit obvious variation in functional clusters from the zebrafish atrium. Interestingly, we also found that the scallop hearts contain a high amount of collagens, which could be beneficial for heart repair after damage. Together, our work presented novel gene profiling data in the mollusk atria and ventricles, thereby providing new insights into the evolution of cardiac chambers.

sample_organism:
Mizuhopecten yessoensis
Lissachatina fulica

overall_design: To systematically profile the cardiac gene expression in adult scallop and snail hearts, their atria and ventricles were separately  collected, and RNA sequencing for these samples was performed.

first: Meina

last: Lu

first: Xuejiao

last: Zhang


title: Gene expression analysis using the NanoString nCounter® Human AutoImmune Profiling Panel for T cells from PRAAS patients carrying a de novo PSMB8 variant

city: Greifswald

first: Sophie

last: Wolfgramm

address: Ferdinand-Sauerbruch Straße

department: Medical Biochemistry and Molecular Biology

institute: University Medicine Greifswald

summary:
Elucidation of a heterozygous de novo PSMB8 variant on transcriptional level using the NanoString nCounter® Human Autoimmune Profiling panel
Two seperate analyses were performed for normalization (1st and 2nd batch). HD_A-C and Pt A,B, and C were analyzed together and represents the first batch. HD_E, HD_F, β5i_IH_A, and β5i_IH_B were analyzed together and reprensent the second batch.

overall_design: Isolated peripheral blood mononuclear cells (PBMCs) from patients and healthy controls were co-cultured with irridated feeder cells and stimulated with interleukin-2 (IL-2) and phytohemmagglutinin-L (PHA-L) for T cells expansion. Isolated RNA from T cells were used for NanoString measurements.

first: Frédéric

last: Ebstein


title: Cell-dependent contributions of thrombospondin-1 to the rupture of abdominal aortic aneurysm in mice

city: Madison

first: Bo

last: Liu

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin - Madison

summary: Rationale: Abdominal aortic aneurysms (AAA) rupture is a life-threatening event with unclear molecular mechanisms. Our previous work demonstrated elevated levels of the matricellular protein thrombospondin-1 (TSP1, encoded by Thbs1) in human and mouse AAA tissues. Single-cell RNA sequencing analysis identified macrophages, endothelial cells, and smooth muscle cells as the major TSP1-expressing cells in aneurysmal tissues. Global Thbs1 deletion reduces aneurysm formation by inhibiting vascular inflammation. Aims: To investigate how TSP1 deficiency in different cell types affects AAA rupture. Methods and Results: AAA and rupture were induced by angiotensin II infusion in hypercholesterolemic mice. In global Thbs1 deficient mice, hypercholesterolemia was achieved by crossing them with Apoe knockout mice. To generate cell type–specific TSP1 deficient mice, Thbs1 flox/flox mice were crossed with VE-cadherin-Cre, SMMHC-iCreERT2, and Lyz2-Cre mice to target endothelial cells, smooth muscle cells, and myeloid cells, respectively. In these conditional knockout models, hypercholesterolemia was induced via AAV-PCSK9. We found that both global and myeloid-specific Thbs1 deletion increased rupture rate over twofold, whereas endothelial- or smooth muscle cell–specific deletion had no significant effect. Endothelial-specific Thbs1 deletion reduced aneurysm size in the CaCl₂ model. Single-cell RNA sequencing and histology in myeloid-specific Thbs1 knockout aortas revealed broad suppression of inflammation and extracellular matrix production. Conclusions: Myeloid-derived TSP1 plays a critical role in inhibiting aneurysm rupture in mice, likely by promoting matrix repair phenotypes in vascular smooth muscle cells, enhancing vascular wall integrity.

overall_design: Male Thbs1fl/fl/Lyz2-Cre and Thbs1wt/wt/Lyz2-Cre mice (8-12 weeks of age) were subjected to the PCSK9-AAV/Angiotensin II model of AAA. Abdominal aortas were collected after 7 days of Angiotensin II infusion and digested into a single-cell suspension. For each genotype, cells from five mice were pooled into one sample and subjected to scRNA-seq.

first: Ting

last: Zhou

first: Huan

last: Yang


title: CsdA-LaeB Regulatory Hub Contributes to Aspergillus fumigatus Virulence via Fumiquinazoline C Biosynthesis

city: Beijing

first: Zili

last: Song

address: Beichen West Road 1

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Fungal secondary metabolism plays a critical role in pathogen-host interactions, yet the regulatory networks linking metabolic reprogramming to virulence remain poorly understood. This study identifies a conserved regulatory hub in the human pathogen Aspergillus fumigatus, where the RNA-binding protein (RBP) CsdA interacts with the global regulator LaeB in the nucleus to control biosynthesis of the secondary metabolite fumiquinazoline C (FqC). Disruption of the CsdA-LaeB interaction hyperactivates FqC production, enhancing fungal colonization and lethality in murine invasive aspergillosis models. Integrative metabolomic and transcriptomic analyses reveal that CsdA and LaeB function as co-regulators of a broader secondary metabolic gene cluster network, with FqC emerging as an effector that mediates virulence in vivo. Genetic validation confirms that FqC is strictly required for the increased virulence phenotype of CsdA- or LaeB-deficient strains, while analyses of clinical isolates demonstrate a striking inverse correlation: reduced CsdA and LaeB expression coincides with elevated FqC production, showing consistency with the infection outcomes of the deletion mutants. This work identifies the RBP-based interaction that coordinates fungal metabolic virulence, shedding new light on the post-transcriptional regulatory logic linking secondary metabolism to pathogenicity and offering alternative strategies for diagnostic development and therapeutic intervention in invasive fungal diseases.

overall_design: RNA-seq profile of wildtype CEA17 and their knockdown derivatives (csdA and laeB) at Day5 of metabolic differentiation.

first: Hongjiao

first: Wen-Bing

last: Yin


title: Oncolytic virotherapy and platinum-based chemotherapy synergize to potentiate anti-tumor immunity through targeted engagement of chemo-persistent bystander CD8+ T cells

city: Chongqing

first: shuai

last: yue

state: Chongqing

address: Gaotanyan street

institute: army medical university

summary: The efficacy of combined chemotherapy and PD-1 immune checkpoint blockade (ICB) is constrained by a fundamental pharmacological conflict, as chemotherapy indiscriminately eliminates the proliferating tumor-specific CD8+ T (TTST) cells that PD-1 ICB aims to expand. To overcome this limitation, we targeted the chemotherapy-resistant bystander CD8+ T (TBYS) cell niche. We found that within the tumor microenvironment, CD8+ TBYS cells persist in a quiescent state, in stark contrast to chemotherapy-susceptible TTST cells. Leveraging this, we developed an oncolytic virus (OV-BYTE) engineered to redirect TBYS cells against tumors. In preclinical models and patient-derived organoids, OV-BYTE synergized with chemotherapy to control tumor progression. This synergy stemmed from direct engagement of the TBYS cell reservoir and concurrent restoration of TTST cell function via reduced apoptotic susceptibility and promotion of a polyfunctional effector state. Importantly, integrating OV-BYTE into standard chemo-PD-1 ICB regimens yielded superior anti-tumor efficacy. Collectively, our work establishes TBYS cells as a pivotal therapeutic target and presents OV-BYTE as a translatable strategy that resolves a core constraint in current cancer therapy, unlocking more effective combination regimens.

overall_design: The library preparation for single-cell RNA sequencing (scRNA-seq) using the BD Rhapsody platform to study P14/OT1 CD8+ T cells in tumor when undergoing OV-BYTE treatment w/o chemotherapy. Here, we further demonstrate that OV-BYTE and chemotherapy activate tumor-specific and bystander T cells in pre-clinical models, thus jointly killing tumor cells. This study gives a transcriptome profiles of P14/OT1 CD8+ T cells in tumor with administration of OV-BYTE treatment and chemotherapy.

first: Yang

last: yang

first: Shuai

last: Yue

first: Junjian

last: He

first: Lilin

last: Ye

first: Xiangyu

last: Chen


title: Safe focused ultrasound-mediated blood-brain barrier opening is driven primarily by transient reorganization of tight junctions

city: New York

first: Elisa

middle: E

last: Konofagou

department: Biomedical Engineering

institute: Columbia University

summary: Single-cell sequencing performed on endothelial cells after exposure to focused ultrasound in vivo to determine the transcriptomic signature of the response to intervention.

overall_design: Focused Ultrasound Blood-Brain Barrier Opening was performed in eGFP-Cldn5 mice targeting the striatum and putamen.  The animals were sacrificed after 1 or 72 hours and the targeted brain tissue was dissected out and prepared for FACS. The cells were sorted based on eGFP expression to isolate endothelial cells using FACS, and the cells were submitted for single cell RNA sequencing.

first: Rebecca

last: Noel

first: Sanjid

last: Shahriar

first: Dritan

last: Agai


title: Molecular Characterisation of the A52 Murine Hepatocellular Carcinoma Cell Line

city: Townsville

first: Lionel

last: Hebbard

state: QLD

address: 1 James Cook Dr, Douglas QLD 4811

institute: James Cook University

summary:
Background: To combat hepatocellular carcinoma (HCC) disease heterogeneity and growing mortality, there is an urgent need for targeted and personalised therapeutics. While syngeneic mouse models are commonly used for preclinical validation of these therapeutics, the lack of genetically characterised murine cell lines adds uncertainty to the study of drug-gene interactions in these models. We previously generated a novel murine cell line, A52, from a diethylnitrosamine (DEN)-induced adiponectin-knockout mouse model. Here, we present a comprehensive genomic and transcriptomic characterisation of the A52 cell line.
Methods: A52 cells were grown in various culture medium compositions to investigate robustness to simple media. Whole-genome sequencing (WGS) and RNAseq were performed on A52 cells from both cell culture and syngeneic tumour tissue, as well as a reference cell line representing non-tumour cells, AML-12.
Results: A52 was found to show robust growth in all medium compositions. Substantial chromosomal instability was observed in A52, including trisomy 15 and notable amplifications of oncogenic loci such as Myc and Cd274 (PDL-1), alongside frequent small variants and structural rearrangements. Notably, the cell line harbours the common HCC driver Braf V584E mutation, and a novel Plk1 p.R364W variant predicted as a driver mutation. Transcriptomic profiling defined a distinct "A52 gene signature" enriched in EGFR-ERBB signalling and cell migration pathways. Integrative analyses demonstrated that the A52 gene signature aligns closely with a subset of human HCC lacking CTNNB1 mutations.
Conclusion: This study provides a critical genetic resource, facilitating more precise preclinical modelling and therapeutic validation in HCC.

overall_design: RNAseq profiling of murine hepatocellular carcinoma cell line (A52) grown in culture and tumour tissue derived from a subcutaneous transplanted syngeneic mouse model derived from A52 cells. WGS profiling of A52 cell line grown in culture.

first: Rhys

last: Gillman

first: Eun

last: Sun

first: Miriam

last: Wankell

first: Matt

last: Field

first: Ulf

last: Schmitz


title: GVH_transcriptomic_validation_cohort

city: Paris

first: David

last: Michonneau

address: 1 avenue Claude Vellefaux

department: Hematology and transplantation

institute: Assistance Publique des Hôpitaux de Paris

summary: Transcriptomic analysis from patient's samples after hematopoietic stem cell transplantation with or without acute GVHD

overall_design: PBMC samples of patients treated with haematopoietic stem cell transplant, presenting with or without aGVHD

first: Sophie

last: Le Grand

first: Nicolas

last: Vallet

first: Yannick

last: Marie

first: Delphine

last: Bouteiller

first: Margo

last: Fernandez

first: Gwendolyn

last: Marguerit

first: Émeline

last: Mundwiller

first: Émilie

last: Robert

first: Régis

last: Peffault de Latour

first: Gérard

last: Socié


title: Cerebrospinal fluid-driven ependymal motile cilia defects are implicated in multiple sclerosis

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

institute: McGill University

summary:
Background: Multiple sclerosis is a neurodegenerative autoimmune disorder of the central nervous system (CNS) in which autoreactive immune cells migrate through a damaged blood brain barrier, resulting in focal demyelinating lesions of both the white and grey matter. Of increasing interest is the repeated observation that beyond focal lesions, there are also diffuse, surface-in gradients of pathology in MS, wherein damage is most severe directly adjacent to cerebrospinal fluid (CSF)-contacting surfaces, such as the subpial and periventricular areas. This observation suggests that toxic factors within MS CSF may be contributing to the emer-gence and/or evolution of surface-in gradients. Directly separating the CSF from the periventricular parenchyma are ependymal cells – a glial epithelium that expresses tufts of motile cilia which are critical for circulating CSF solutes and regulating local fluid flow. While damage to ependymal cilia has the potential to drastically modify CSF homeostasis and thus contribute to the damage of CSF exposed regions, these motile cellular structures have yet to be investigated in the context of MS.
Methods: We first conducted single cell RNA sequencing of fresh human periventricular brain tissue containing ependymal cells from MS patients and non-MS disease controls. We subse-quently collected CSF from MS patients and exposed cultured rodent ependymal cells to this CSF in order to evaluate impact on ependymal ciliary function. To complement our direct eval-uation of cilia in the context of MS, we also confirmed whether cilia were altered in a classic animal model of MS, experimental autoimmune encephalomyelitis (EAE), and also designed a novel transgenic animal model to evaluate the cellular and behavioural effect(s) of adult ep-endymal ciliary disruption.
Results: Single cell RNA sequencing analysis of human ependymal cells in MS demonstrated largescale dysregulation of ciliary genes; in situ stains of MS brain tissue confirmed a loss of ependymal cilia in MS compared to control. Exposure of ependymal cells to MS CSF led to transcriptional modification of ciliary gene expression and reduced ciliary beating frequency. Likewise, analysis of ependymal cells in EAE also demonstrated altered cilia gene expression. Conditional knockout of the critical cilia-associated gene Ccdc39 in ependymal cells led to transient ventricular enlargement, increased periventricular microglial density, and alterations in nesting behaviour.
Conclusion: These data suggest that cilia are dysregulated in CNS autoimmunity. More im-portantly, however, they provide evidence to suggest that ependymal cilia disruption could play an active role in the development of periventricular pathology in MS, and can lead to behav-ioural deficits that may underlie aspects non-motor MS symptomatology.

overall_design:
Tissue samples were collected from 4 MS patients and 4 controls (CTRL; 3 amyotrophic lateral sclerosis (ALS) and 1 hereditary spastic paraplegia (HSP) patients) under the medical assistance in dying (MAID) program of Quebec at the Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CR-CHUM). single cell RNAeq Joint library was then prepared using the 10x Genomics platform. Complete sample ID information is provided in the associated metadata table (.csv file).

UPDATE: [Apr-09-2026] The supplementary files were updated.

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

last: Bigotte

first: Adam

last: Groh

first: Elia

last: Afanisiev

first: Vincent

last: Wong

first: Kevin

last: Lancon

first: Moein

last: Yaqubi

first: Finn

last: Creeggan

first: Craig

last: Moore

first: Adil

last: Harroud

first: Raphael

last: Schneider

first: Philippe

last: Séguéla

first: Charabati

last: Marc

first: Tea

last: Fiona

first: Fournier

last: Antoine

first: Yu Chang

last: Wang

first: Ragoussis

last: Ioanis

first: Alexandre

last: Prat

first: Simon

last: Thebault

first: Stephanie

last: Zandee

first: Jo Anne


title: Effects of Oxaliplatin on Hematopoietic Pathways with Implications for Chronic Pain

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

institute: Washington University in St. Louis

summary: Background: Oxaliplatin, a widely used chemotherapeutic agent, is associated with hematologic toxicities such as anemia, leukopenia, and thrombocytopenia. Despite their clinical relevance, the molecular mechanisms underlying lineage-specific bone marrow suppression remain poorly understood. Methods: We administered oxaliplatin to mice over eight weeks and performed bulk RNA-sequencing on bone marrow alongside peripheral blood analysis and cytokine profiling. Transcriptomic data were analyzed to identify differentially expressed genes (DEGs) and enriched pathways, with a focus on hematopoietic and immune lineages. Results: Oxaliplatin induced broad transcriptional suppression of erythropoiesis and lymphopoiesis, with 3,690 DEGs identified (FDR<0.05, |FC|>1.5). Upregulation of Cdkn1a and downregulation of E2f2 suggest G1/S cell cycle arrest, correlating with repression of key erythroid maturation genes (e.g., Spta1, Slc4a1, Alas2) and hemoglobin subunits (Hba-a12, Hbb-bs/t). Despite a ~3000-fold increase in renal Epo expression, bone marrow Epor was reduced, indicating erythropoietin resistance. B and T cell markers were also significantly downregulated, signifying a collapse in adaptive immunity. Notably, neutrophils were largely spared. Cytokine analysis revealed a pro-inflammatory shift with elevated TNF-α and CCL2 and reduced TGF-β, potentially exacerbating hematopoietic dysfunction. The data also point to a neuro-immune axis in which oxaliplatin-induced inflammation in the bone marrow contributes to peripheral nerve sensitization as seen with upregulation of nociceptive signaling components such as Tacr1. Conclusions: Oxaliplatin induces a lineage-dependent suppression of hematopoiesis, driven by coordinated cell cycle arrest, metabolic stress, and disrupted cytokine signaling. These findings provide mechanistic insights into oxaliplatin’s hematologic toxicity linking bone marrow failure and neuropathic pain via interconnected inflammatory and metabolic pathways and may inform therapeutic strategies to mitigate myelosuppression and peripheral neuropathy in cancer patients.

first: Leland

last: Sudlow

first: Junwei

last: Du

first: Kiana

last: Shahverdi

first: Haiyin

last: Zhou


title: A distinct mechanism governs translation initiation and its regulation in Staphylococcus aureus [RNA-Seq]

city: Strasbourg

first: Stefano

last: Marzi

address: 2 allée Konrad Roentgen

department: UPR9002 - IBMC

institute: CNRS

summary: Retapamulin-assisted ribosome profiling (Ribo-Ret) reveals translation initiation sites at a translatome-wide scale. Here we employed Ribo-Ret in S. aureus, utilizing either MNase or RNAse 1 for ribosomal protected footprint (RPF) generation, significanlty improving the obtainable resolution at translation start sites with the latter. The improved resolution helped to identify precise start codon selection, revealing distinct features of the S. aureus translation initiation mechanism as well as multiple unrecognized small open reading frames (sORFs). Furthermore, we identified novel regulators of the translation initiation step in this major human pathogen.

overall_design: For the MNase as well as the RNase 1 Ribo-Ret experiments, two biological replicates were analyzed for Retapamulin-treated and untreated samples. Total RNA was collected from each sample and processed for associated total RNA sequencing.

first: Maximilian

middle: P

last: Kohl

first: Roberto

last: Bahena-Ceron

first: Béatrice

last: Chane-Woon-Ming

first: Maria

last: Kompatscher

first: Matthias

last: Erlacher

first: Pascale

last: Romby

first: Bruno

last: Klaholz


title: Human Myelin Spheres for In Vitro Oligodendrocyte Maturation, Myelination and Neurological Disease Modeling

city: Leuven

first: Yoke Chin

last: Chai

state: Leuven

address: Herestraat 49, ON5

department: Development & Regeneration

institute: KU Leuven

summary: We used single nucleus RNA sequencing (10x genomics) to characterize a novel 3D spheroid model - Myelin Spheres (MyS). Neuron Monoculture Spheroids (NMS) as controls. MyS comprises of neuronal progenitor cells (NPCs) with oligodendrocyte progenitor cells (OPCs) while NMS were made of only NPCs. Both NPCs and OPCs were derived from human induced pluripotent stem cells (hiPSCs) with or without an inducible SOX10 casette integrated in the genome. We performed sequencing on MyS and NMS at week 8 and 15 respectively, to understand the temporal change in oligodendrocyte maturation.

overall_design: We used four to six spheroids for both MyS or NMS as one sample, for single nucleus extraction on week 8 and 15 seperately. Extracted nuclei were counted and checked for quality and were then used for library preparation and sequencing.

first: Karan

last: Ahuja

first: Roya

last: Ramezankhani

first: Xinyu

last: Wang

first: Thibaut

last: Burg

first: Giulia

last: Amos

first: Katrien

last: Neyrinck

first: Alessio

last: Silva

first: Geethika

last: Arekatla

first: Eleanor

last: Eva Cassidy

first: Arefe

last: Nami

first: Joke

last: Terryn

first: Keimpe

last: Weirda

first: Katlijn

last: Vints

first: Niels

last: Van Damme

first: Suresh

last: Kumar Poovathingal

first: Ivo

last: Lambrichts

first: Johan

last: Swinnen

first: Ludo

last: Van Den Bosch

first: Lies

last: De Groef

first: Lieve

last: Moons

first: Catherine

last: Verfaillie

last: Neyts

first: Dirk

last: Jochmans

first: Yoke

last: Chin Chai


title: FOXF2 regulates pericyte function required for pericyte-endothelial signaling during neonatal hyperoxic lung injury [RNA-Seq]

city: Chengdu

first: Hua

last: He

state: Sichuan

address: 2222 Xinchuan Rd

institute: West China Second University Hospital Sichuan University

summary: Pulmonary vascular development is essential for alveolarization, and disruption of this process contributes to bronchopulmonary dysplasia (BPD) pulmonary pathology. Proper vascular development requires an orchestration of many cell types within the lung. However, the mechanisms by which pericytes support the endothelium in the postnatal lung remain poorly understood. Here, we identify FOXF2 as a critical transcription factor that governs pericyte maturation and function during postnatal lung development and regeneration. FOXF2 expression in pericytes increases postnatally and is selectively downregulated following neonatal hyperoxic injury. Pdgfrb-CreER mediated Foxf2 deletion in pericytes leads to pericyte hyperplasia, impaired migration, reduced expression of angiogenic factors such as ANGPTL4, and exacerbated alveolar simplification in a neonatal murine model of BPD. Transcriptomic and genomic studies demonstrate that FOXF2 maintains chromatin accessibility at pro-angiogenic loci and modulates paracrine signaling essential for endothelial regeneration. Loss of FOXF2 disrupts pericyte–endothelial crosstalk, impairing angiogenesis and alveolar repair during injury. Our study identifies FOXF2 as a central transcriptional regulator of pericyte-driven vascular niche function in the neonatal lung and underscores the pathogenic role of dysfunctional pericytes in BPD.

overall_design: Bulk RNA sequencing was performed on CD140b+ cells, sorted by MACS, isolated from the lungs of Foxf2 KO (Foxf2f/f; Pdgfrb-CreER) and littermate control mice at postnatal day 7.


title: FOXF2 regulates pericyte function required for pericyte-endothelial signaling during neonatal hyperoxic lung injury [CUT&Tag]

overall_design: CUT&Tag and Cleavage Under Targeted Accessible Chromatin (CUTAC, a low salt version of CUT&Tag) using FOXF2 and H3K4me2 antibodies were performed on CD140b+ cells, sorted by MACS, isolated from the lungs of wild type mice, Foxf2 KO (Foxf2f/f; Pdgfrb-CreER) and littermate control mice at postnatal day 7.


title: Ptbp1 facilitates cytoskeletal organization through the mTOR-PKCα pathway in Sertoli cells thereby supporting spermatogenesis

city: Minato

first: Manabu

last: Ozawa

state: Tokyo

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

institute: The University of Tokyo

summary: Spermatogenesis is a highly coordinated process to produce mature spermatozoa. Somatic lineage Sertoli cells located in seminiferous tubule provide structural and paracrine support for spermatogenesis. Proper regulation of the Sertoli cell cytoskeleton dynamics is essential for this function; however, its regulatory mechanisms remain unclear. We show that the RNA-binding protein PTBP1 maintains cytoskeletal integrity in Sertoli cells via mTORC2 signaling. Sertoli cell–specific Ptbp1 deletion in mice results in germ cell loss, disrupted blood–testis barrier, and male infertility. Transcriptomic analysis of purified Sertoli cells revealed the dysregulation of cytoskeletal- and adhesion-related genes. RIP-seq demonstrated that PTBP1 binds to Rictor mRNA, which is a core mTORC2 component. PTBP1 loss reduced RICTOR protein levels and downstream PKCα activation, impairing the cytoskeletal structure. Rescue of cytoskeletal defects in PTBP1-deficient TM4 cells by constitutively active PKCα confirmed the functional relevance of the mTORC2–PKCα axis. These findings identify PTBP1 as a post-transcriptional regulator of mTORC2 signaling that supports Sertoli cell architecture and spermatogenesis, providing mechanistic insights into the regulation of male fertility.

overall_design: RNAseq of FACSed Sertoli cells; PTBP1-immunoprecipitated RNAseq

first: Hideto

last: Mori

first: Masafumi

last: Muratani

first: Takuya

last: Yamamoto


title: Single cell RNA-seq of myeloid immune cells in melanoma-draining lymph nodes

city: Mannheim

first: Volker

last: Ast

address: Theodor-Kutzer-Ufer 1-3

department: NGS Core Facility

institute: University Hospital Mannheim

summary: Tumor-draining lymph nodes are crucial for tumor immunity and immunotherapy outcomes. In this study, myeloid immune landscapes were profiled in lymph nodes draining either immunotherapy-sensitive or immunotherapy-resistant melanoma in mice.

overall_design: Myeloid immune cells expressing CD11b and/or CD11c were isolated from tumor-draining inguinal and axillary lymph nodes collected from mice bearing YUMM1.7 and YUMMER1.7 melanoma. Tumor-free animals served as naive control. Lymph nodes from multiple mice were pooled for each of the samples. Cells were subsequently subjected to single cell RNA-sequencing.

first: Lothar

middle: C

last: Dieterich


title: Next Generation Sequencing Facilitates Quantitative Analysis of Cornea Tissues from Lut Treated and Vehicle Control Treated EDE Mice

city: Shanghai

first: qian

last: yu

address: 1665 Kong Jiang Road

institute: Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: We had one goal to perform this study: transcriptome of cornea tissues from Lut treated and vehicle control treated EDE mice

overall_design: Comparison of transcriptome of cornea tissues from Lut treated and vehicle control treated EDE mice

first: Qian

last: Yu


title: Tumor-stromal crosstalk and macrophage enrichment is associated with chemotherapy response in bladder cancer

city: Aachen

first: Janik

last: Riese

address: Pauwelsstraße 30

department: Institute of Pathology

institute: UK Aachen

summary: This dataset provides a spatial transcriptomic atlas of bladder cancer tissue treated ex vivo with standard chemotherapy. Tumor specimens from eight bladder cancer patients were excised and treated for 48 hours with gemcitabine and cisplatin (GemCis) or medium control (MSC), followed by formalin fixation and paraffin embedding. Spatial gene expression profiling was performed using the NanoString GeoMx Digital Spatial Profiler Whole Transcriptome Atlas (WTA), capturing expression of over 18,000 transcripts. Tumor regions were identified by cytokeratin (CK) staining and analyzed alongside adjacent stroma (CK-negative). Chemotherapy treatment led to significant transcriptomic alterations, including downregulation of pathways related to substance uptake (e.g., endocytosis) and metabolism (e.g., glycolysis), and upregulation of cell death pathways. Cellular deconvolution using xCell revealed stromal M2 macrophage enrichment in chemotherapy-resistant samples, suggesting a microenvironmental contribution to resistance.

overall_design: Fresh tumor tissue from eight patients with bladder cancer was obtained and divided into two conditions: treatment with gemcitabine/cisplatin (GemCis) or medium control (MSC), incubated for 48 hours ex vivo. Post-treatment, tissues were formalin-fixed, paraffin-embedded, and processed using the NanoString GeoMx DSP Whole Transcriptome Atlas (WTA) assay. Regions of interest (ROIs) were selected based on immunohistochemical cytokeratin (CK) staining to distinguish tumor cells (CK-positive) from stroma (CK-negative). Two technical replicates per condition and region were collected. Standard GeoMx WTA workflow was applied, with downstream analysis including differential expression, pathway analysis, caspase-3 immunohistochemistry for treatment response classification, and xCell-based deconvolution to profile immune cell populations. The resulting data provide spatial resolution of transcriptomic changes in response to chemotherapy and insights into mechanisms of chemoresistance in bladder cancer.

first: Sophie

last: Leypold

first: Michael

last: Rose

first: Lancelot

last: Seillier


title: TET-dependent signaling of β-cell underlies intrauterine hyperglycemia-induced glucose intolerance in offspring [RRBS]

first: Jiahang

last: Mo

address: No.131 Dong'an Road

department: Institute of Reproduction and Development

institute: Obstetrics and gynecology Hospital of Fudan University

type: Methylation profiling by high throughput sequencing

summary: Epidemiologically, gestational diabetes mellitus (GDM) increases offspring’s diabetes risk. Intrauterine hyperglycemia (IHG) is a typical characteristic of GDM, impairing offspring’s glucose tolerance and insulin secretion, but the underlying mechanisms remain unclear. Here, we found IHG downregulates DNA demethylases Tet2/3 in fetal pancreatic islets. Pancreas-specific Tet2/3 double knockout (DKO) recapitulates the IHG effects.

overall_design: To investigate the mechanisms of impairing offspring’s glucose tolerance and insulin secretion in IHG offspring. Pancreatic islets from Tet2/3 double knockout mouse was analyzed using RRBS.