title: Activation of Fibroblast LRP1 by AT2-secreted MDK Affects OTUB1/SLC7A11 Ubiquitination to Inhibit Fibroblast Ferroptosis in Idiopathic Pulmonary Fibrosis.

status: Public on May 01 2026

city: Wuxi

first: Hua

last: Wenjie

address: NO.1800 Lihu Avenue

institute: Jiangnan University

summary: Idiopathic pulmonary fibrosis (IPF), a chronic interstitial fibrosing pneumonia of unknown cause, is characterized by an irreversible decrease in alveolar cells and an increase in fibroblasts. In our research, the numbers of AT2 cells and fibroblasts are abnormally regulated, but AT1 cells are significantly reduced in lung tissue sections from patients with IPF and mice. By analyzing the single-cell sequence from GEO database and experimental validation both in vivo and in vitro, it is found that the abnormally regulated AT2 cells secreting a large amount of MDK to activate the CTHRC1+ fibroblasts LRP1 receptor and inhibit the ferroptosis of fibroblasts. Further, by activating the LRP1 receptor in CTHRC1+ fibroblasts, the RNA-seq results reveal that the expression level of OTUB1 increased significantly. The ubiquitination experiment results showed that OTUB1, as a deubiquitinated molecule, can directly bind to the ferroptosis inhibitory protein SLC7A11, removing the ubiquitination modification of SLC7A11 and stabilizing its expression level to inhibit ferroptosis in fibroblasts. Meanwhile, this molecular pathway was verified in mice by dropping adenovirus through the airway, and the same experimental results as in vitro were verified. In conclusion, our study verified that IPF leads to abnormal regulation of AT2 secreting MDK, which activates LRP1 receptor and increases OTUB1 in fibroblasts. Deubiquitylation modification of OTUB1 stabilizes the expression level of SLC7A11, which results in a decrease in fibroblast ferroptosis, leading to an abnormal regulation of its programmed death, ultimately the deterioration of IPF.

overall_design: To investigate the effect of the LRP1 activated by MDK, we established the human lung primary fibroblast model stimulated with 15ug/ml MDK.

first: Wenjie

last: Hua

first: Zitao

last: Wang

first: Jingyu


title: Thyroid hormones act as a timer for the postnatal maturation of parvalbumin neurons in mouse neocortex [RUN125]

status: Public on Apr 22 2026

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

type: Expression profiling by high throughput sequencing

summary: A finely tuned balance between excitation and inhibition is essential for proper brain function. Disruptions in the GABAergic system, which alter this equilibrium, are a common feature in various types of neurological disorders. Understanding GABAergic neuron maturation processes is thus currently a major challenge in basic neuroscience. Thyroid hormones (THs) are required for proper maturation of parvalbumin-expressing GABAergic interneurons in the mouse neocortex. However, the timeline of this TH action has yet to be elucidated. Here, we used several mouse models expressing dominant negative mutations of the TH nuclear receptor α1 (TRα1), to better define the time window during which THs promote the postnatal maturation of parvalbumin neurons. Histological observations revealed that the action of TH during the first three postnatal weeks was necessary to initiate the expression of parvalbumin and the elaboration of a specialized extracellular matrix called the perineuronal net. By contrast, after the third postnatal week, TH action on parvalbumin neuron maturation appeared to be somewhat dispensable. Transcriptome analysis of neocortical GABAergic neurons two weeks after birth identified a small set of putative target genes for TRα1. These genes are at the origin of the postnatal remodeling of the repertoire of ions channels and the elaboration of perineuronal nets. These data suggest that THs act as a timer to define the temporal boundaries of the critical period of heightened cortical plasticity, which plays a fundamental role in the development of neuronal circuits.

overall_design: The Cre/loxP recombination system was used to restrict the expression of a reporter transgene which drives the expression of a nuclear fluorescent protein to GABAergic neurons. Two groups of mice were prepared: 1) One group of hypothyroid juvenile mice, generated by treating gestating females with propyl-thio-uracy (PTU group). 2) One group of hypothyroid mice which received a intraperitoneal injection of thyroid hormone 24h before brain collection (PTU+TH group). Nuclei were isolated from the cortical GABAergic neurons with a cell sorter. RNA was extracted from the sorted nuclei. 8 libraries were prepared for RNA-seq (4 hypothyroid, 4 hypothyroid +TH)

first: Juan

last: Ren

first: Suzy

last: Markossian

first: Romain

last: Guyot

first: Denise

last: Aubert

first: Jiemin

last: Wong

first: Sabine

last: Richard


title: Thyroid hormones act as a timer for the postnatal maturation of parvalbumin neurons in mouse neocortex [RUN54]

overall_design: The Cre/loxP recombination system was used to restrict the expression of two transgene: one is a reporter which drives the expression of a nuclear fluorescent protein. The other drives the expression of a mutation of the Thra gene, encoding a dominant negative nuclear receptor for thyroid hormone. A Cre driver additionnal transgene was used to restrict the expression to GABAergic neurons. Two groups of mice were prepared, one with the Thra mutation, the other without it as control. Fluorescent nuclei were sorted from the cerebral cortex of juvenile mice. RNA was extracted from the sorted nuclei. 8 libraries were prepared for RNA-seq (4 controls, 4 with Thra mutation).


title: Multisensory integration predated land plant colonization

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

summary: Land plant colonization was a pivotal event in the evolution of photosynthetic eukaryotes. The transition from aquatic to terrestrial environments required complex multisensory systems that enabled plants to perceive and integrate a broader range of environmental cues, such as light intensity and temperature. However, it remains unclear whether this ability was a pre-adaptation or an innovation during early plant terrestrialization. Here, we show that the aquatic streptophyte ancestor of land plants could integrate light and temperature through a complex regulatory network. A conserved regulatory nexus, comprising phytochromes and transcription factors, was active in the last common ancestor of land plants, allowing the first terrestrial colonizers to adapt and flourish on the harsh terrestrial surface of our planet. Thus, we propose that the multisensory integration that enables extant plants to achieve perceptual disambiguation and fine-tune growth in various ecological niches was a pre-adaptation encoded in the genomes of ancestral land plants.

sample_organism:
Marchantia polymorpha
Arabidopsis thaliana

overall_design: DAP-seq experiments

first: Bruno

last: Catarino

first: Fernando

last: Rodríguez-Marín

first: Cristina

last: Úrbez

first: Christina

last: Arvanitiou

first: Eva

last: Álvarez

first: Federico

last: Valverde

first: José

middle: M

first: Francisco

last: Romero-Campero

first: Miguel

middle: A

last: Blázquez


city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

country: USA

institute: Iowa State University

summary: Placenta enriched 1 (PLAC1) is a highly conserved X chromosome-linked gene prominently expressed in the mammalian placenta. The functions of PLAC1 in placentation have yet to emerge fully. The rat shares hemochorial placentation and deep intrauterine trophoblast cell invasion with the human. Herein, we investigated the expression and biological activities of PLAC1 in the rat and human placenta.  Plac1 transcripts were prominently expressed in the junctional zone of the rat placenta, a structure analogous to the extravillous trophoblast cell column of the human placentation site, and in invasive trophoblast cells. A PLAC1 mutant rat model was generated using CRISPR/Cas9 genome editing and used to investigate the role of PLAC1 in rat placentation. Plac1 mutant animals exhibited placentomegaly. Enlarged placentas were characterized by an expanded junctional zone, an irregular junctional zone-labyrinth zone boundary, and a prominent depletion of invasive trophoblast cells within the uterine parenchyma. PLAC1 was required for rat trophoblast stem (TS) cell differentiation. In human TS cell development, PLAC1 does not contribute to the regulation of the human invasive/extravillous trophoblast cell lineage, but instead, PLAC1 expression and actions were linked to syncytiotrophoblast differentiation. Thus, PLAC1 is critically involved in hemochorial placentation; however, the responsive trophoblast cell lineages and its contributions to placentation are fundamentally distinct in the rat versus human.

overall_design: CT27 Trophoblast stem (TS- Okae et.al.) cell transduced with control shRNAs (shSCR)  were used as controls. Cells transduced with  shRNAs targeting PLAC1 (shPLAC1) were used as treatment. RNA-seq was performed in control and treatment cells after 6 days of differentiaiton to syncytiotrophoblast (ST-3D). 3 biological replicates each conditions (shPLAC1 and shSCR)

first: Ayelen

last: Moreno-Irusta

first: Jovana

last: Rajovic

first: Khursheed

last: Iqbal

first: Arun

middle: S

last: Seetharam

first: Jackson

last: Nteeba

first: Regan

middle: L

last: Scott

first: Marija

last: Kuna

first: Masanaga

last: Muto

first: Keisuke

last: Kozai

first: Andjelka

last: Celic

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

first: Michael

middle: J

last: Soares


title: Fundamental and unique roles of PLAC1 in the regulation of rat and human trophoblast cell development

overall_design: gd 13.5 placental tissue from Plac1 mutant rats and wild type rats (5 biological replicates each)


overall_design: Rat Trophoblast stem (TS) cell transduced with control shRNAs (shSCR)  were used as controls. Cells transduced with  shRNAs targeting PLAC1 (shPLAC1) were used as treatment. RNA-seq was performed in control and treatment cells after 15 days of differentiaiton. 3 biological replicates each conditions (shPLAC1 and shSCR)


title: Gut Microbiota Modulation of Regulatory DNA Elements revealed by Massively Parallel Functional Characterization

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

summary: The human genome contains millions of DNA cis-regulatory elements (CREs) that regulate gene expression across different cell types. In liver hepatocytes, CREs enable adaptation to environmental changes by modifying transcriptomes, particularly in response to gut microbiome signals, which are linked to liver diseases. However, our understanding of the functionality of CREs and their responses to gut microbiota signals in vivo remains limited. To address this, we conducted a genome-wide multiplexed reporter assay (MPRA) to map functional CREs in the liver. Using this functional catalog, we discovered a rare functional variant associated with hepatocellular carcinoma in the Asian population that disrupts CRE activity. Additionally, we identify functional CREs regulated by gut microbiota. Overall, this study enhances our understanding of functional CREs and highlights the complex interactions between the gut microbiome and host gene regulation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Functional analysis of ~110,000 sequence regions was conducted utilizing massively parrallel reporter assays in mouse liver and human HepG2 cells.

first: Chadmirah

last: Zaratiana

first: Tiffany

last: Liu

first: Yong-An

last: Lee

first: Agnes

last: Ong

first: Samantha

last: Chang

first: Torsten

last: Wuestefeld

first: Poshen

middle: B


title: Species-specific gene utilization in the regulation of hemochorial placentation [PLAC1_JZ_18.5]

first: Geetu

last: Tuteja

overall_design: RNA-seq was performed in the junctional zone of the Wild Type or PLAC1 mutant placentation at gd 18.5.gd  (5 biological replicates for mutants and 4 for wildtype)

first: Ayelen

last: Moreno-Irusta

first: Jovana

last: Rajovic

first: Khursheed

last: Iqbal

first: Arun

last: Seetharam

first: Jackson


overall_design: CT29 Trophoblast stem (TS- Okae et.al.) cell transduced with control shRNAs (shSCR)  were used as controls. Cells transduced with  shRNAs targeting PLAC1 (shPLAC1) were used as treatment. RNA-seq was performed in control and treatment cells after 6 days of differentiaiton to syncytiotrophoblast (ST-3D). 3 biological replicates each conditions (shPLAC1 and shSCR)

last: Nteeba

first: Regan

last: Scott

first: Marija

last: Kuna

first: Masanaga

last: Muto

first: Keisuke

last: Kozai

first: Andjelka

first: Hiroaki


overall_design: Choriocarcinoma-derived BeWo cells transduced with control shRNAs (shSCR)  were used as controls. Cells transduced with  shRNAs targeting PLAC1 (shPLAC1) were used as treatment. RNA-seq was performed in control and treatment cells after 6 days of differentiaiton to syncytiotrophoblast (ST-3D). 3 biological replicates each conditions (shPLAC1 and shSCR)BeWo_PLAC1_KD samples with 3 biological replicates each for 2 conditions (control and KD)

last: Celic

last: Okae

first: Takahiro

last: Arima

first: Michael

last: Soares


title: Development of novel Hepatocellular Carcinoma drugs, JNK-IN-5A derivatives simultaneously induce Apoptosis and Necrosis

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

summary: In our previous study, we repurposed JNK-IN-5A to targeting PKLR gene which most co-related to hepatocellular carcinoma (HCC). Here, We showed anti HCC effect of JNK-IN-5A and its six derivative compounds SET135, SET156, SET158, SET159, SET171, and SET172 in HepG2 human HCC cell line. Compare to multi-target kinase inhibitor sorafenib and regorafenib, JNK-IN-5A and its 6 derivatives showed p53 induced cell cycle arrest, autophagy, apoptosis and reduced invasiveness. We found two derivatives which also has its own necrotic cell death pathway. SET135 showed p62/SQSTM1 induced autophgic necrotic cell death, and SET171 increased cellular ROS and lipid peroxidation induced necrotic cell death. Bioinformatics analysis also confirmed new derivatives has distinctive different cellular effect with stronger cell cycle arrest and apoptosis compare to sorafenib and regorfenib. Our new derivatives of JNK-IN-5A which has apoptotic and necrotic cell death inducer can be suggested as a new HCC drug candidate.

overall_design: 400,000 HepG2 WT cells were prepared in 6well plate and compounds were treated for 2days at 10μM.RNA samples for RNA sequencing were extracted with RNeasy Plus Mini Kit (74134, QIAGEN). RIN score of total RNA samples were measured using RNA 6000 Nano kit (5067-1511, Agilent). 2100 Bioanalyzer Instrument (G2939BA, Agilent) was used for RIN score test using electrophoresis. Samples with Rof IN score more than 8 were submitted to SZA Omics, Istanbul for RNA sequencing analysis.

first: Woonghee

last: Kim

first: Cheng

last: Zhang

first: Adil

last: Mardinoglu


title: Tunable Gene Control via RNA Splicing with clinically approved small molecule

status: Public on Apr 30 2026

city: Basel

first: Mateusz

last: Mendel

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd

summary: Precise transgene regulation is crucial for safe and effective gene and cell therapies. Current inducible systems often rely on immunogenic exogenous proteins or non-clinically approved inducers, hindering clinical translation. We developed RisdiON, a compact inducible system controlled by risdiplam, a clinically approved oral drug that acts via splicing modulation. RisdiON utilizes risdiplam-responsive sequences for precise transgene control via endogenous splicing machinery, bypassing exogenous protein regulators, while its 'split-ATG' architecture ensures the expression of native, tag-free proteins. This approach provides robust, dose-dependent induction with minimal leakiness. RisdiON demonstrated broad utility, controlling various transgenes in immortalized cell lines and hiPSCs, enabling inducible CAR expression in primary T cells, and regulating Cas9 for precise gene editing. Additionally, adeno-associated virus (AAV)-delivered RisdiON achieved reversible transgene expression in vivo. The platform is modular and functional across diverse promoters, offering a safe, titratable, and reversible tool when coupled with an orally bioavailable drug to advance next-generation therapies.

overall_design: Targeted DNA amplicon sequencing was performed on a pooled CRISPR Cas9 HDR mutagenesis screen in HEK293T cells expressing a low copy SMN2 GFP splicing reporter. Following editing, cells were treated with 150 nM risdiplam for 48 hours and sorted by FACS into distinct GFP based splicing response populations, and variant frequencies were quantified to determine the effect of reporter sequence variation on drug induced SMN2 splicing.

first: Dominic

last: Schwarz

first: Tao

last: Sun

first: Sophia

last: Tan

first: Asia

last: Franceschetti

first: Daria

last: Majcher

first: Simone

last: Lang

first: Dario

last: Venetz

first: Hasane

last: Ratni

first: Ravi

last: Jagasia

first: Martin

last: Ebeling

first: Filip

last: Roudnicky

first: Lina

last: Schukur


title: Wounding activates HSFA1 to promote cellular reprogramming in Arabidopsis

city: Yokohama

first: Duncan

middle: Peter

last: Coleman

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

country: Japan

institute: Riken

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mechanical injury is a primary trigger for cellular reprogramming during organ regeneration, yet the transcriptional mechanisms that link wounding to reprogramming remain poorly understood. In this study we identify the HEAT SHOCK FACTOR A1 (HSFA1) class of transcription factors, key regulators of the heat stress response, as a central player in wound-induced callus formation and shoot regeneration in Arabidopsis. Loss of HSFA1 function in the hsfa1abd triple mutants severely impairs cellular reprogramming, reducing callus formation from wounded hypocotyls and shoot regeneration from explants. Conversely, overexpression of a gain-of-function HSFA1d variant markedly enhances regeneration. Time-series RNA-seq and ChIP-seq analyses revealed that HSFA1 directly activates key reprogramming regulators, WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1), PLETHORA 3 (PLT3) and ZINC FINGER OF ARABIDOPSIS THALIANA 6 (ZAT6). Furthermore, we demonstrate that the HSFA1d activity is attenuated by SIZ1-mediated SUMOylation, linking post-translational modification to the regulation of wound responses. Our findings establish HSFA1 as an early transcriptional hub that integrates wound signals to activate a broad gene network that drives cellular reprogramming, thereby providing a mechanistic framework for understanding how stress-responsive transcription factors control regeneration.

overall_design: ChIP-seq analysis of pHSFA1d-HSFA1d-GFP plants following heat stress or wounding

first: Takamasa

last: Suzuki

first: Keiko

last: Sugimoto

first: Ayako

last: Kawamura


title: Gene expression profile at single cell level of testicular cells from the adult zebrafish testis

city: suzhou

first: Taole

last: LIU

state: JIANGSU

address: Renai Road 199

department: center for circadian clock

country: China

institute: Soochow University

summary: Testicular cells include somatic cells and germ population in zebrafish. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of testicular cells in zebrafish.

overall_design: Whole testes of adult zebrafish males were sampled and analyzed using scRNAseq.

last: Liu

first: Han

last: Wang


title: Chromatin insulators homie and nhomie can interact with distant copies either together or separately, with distinct outcomes for enhancer-promoter interactions

status: Public on Apr 21 2026

city: Princeton

first: Wenfan

last: Ke

state: New Jersey

address: South Drive, Carl Icahn Laboratory

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Chromatin insulators, a.k.a. boundary elements, separate regions of the chromosome with distinct chromatin characteristics, including distinct histone modifications.  This activity affects gene expression by allowing chromatin domains to be stably regulated and maintained.  Insulators also block enhancer-promoter interactions and, somewhat paradoxically, facilitate other interactions, particularly when they stitch together distant regions of the chromosome by pairing with specific partners.  Here we explore how long-range interactions facilitated by insulator pairing are affected by the presence of two potentially competing partners.  Our results show that when two partners are present, they can reduce each other's effects on distant gene expression, suggesting that enhancer-promoter interactions are best facilitated by pairwise insulator interactions.  When a distant copy of an eve insulator (homie or nhomie) is present, it can interact with either or both endogenous insulators.  But when one endogenous insulator is removed, the remaining one interacts more strongly with the transgenic copy, biasing the induced enhancer-promoter interactions toward those nearest the remaining endogenous insulator.  On the other hand, physical interaction data suggest that strictly pairwise interactions are not the rule, suggesting a more complex model involving tripartite interactions.  We further show that removing one or both endogenous eve insulators significantly reduces endogenous eve function at a critical early stage of development, and that the eve Polycomb domain expands in both directions when its insulator boundaries are removed, showing that insulators in their native context are required for each of the main functions that have been ascribed to them based on transgene assays.

overall_design: microC for Drosophila st14 whole embryo samples, 2-3 independent replicates for each genotype

first: Fujioka

last: Miki

first: Ke

last: Wenfan

first: Schedl

last: Paul

first: Jaynes

last: James


title: Stable global repertoire architecture masks short- term clonal remodeling in intratumoral TCR repertoires

city: Odense M

first: Sofie

last: Traynor

address: Fioniavej 36

country: Denmark

institute: University of Southern Denmark

summary: Background: Tumor-in ltrating T cell receptor repertoires are increasingly pro led to assess intratumoral T cell dynamics and inform prognosis and treatment response. Most analyzes rely on aggregate diversity metrics, such as Shannon index or clonality, which describe overall repertoire structure but do not resolve changes in clonotype identity over time. Thus, intrinsic temporal dynamics of intratumoral T cell receptor repertoires during tumor progression remain incompletely de ned. Methods: In a bilateral murine cancer model, one tumor was surgically removed, and the paired tumor was collected 11 days later. The T cell receptor repertoires of these tumors, and of synchronously harvested bilateral tumors from separate control animals, were analyzed using diversity metrics, Morisita–Horn similarity, and clonal tracking approaches. Results: Time-matched bilateral tumors exhibited highly similar clonotype composition and abundance. In contrast, time-separated tumors showed reduced clonal overlap, increased fractions of private clonotypes, and redistribution of dominant clones. These changes occurred despite preserved global repertoire metrics, including clonotype number, Shannon diversity, and Gini coef cient. Conclusion: Short-term tumor progression is associated with clear changes in the composition of the intratumoral T cell receptor repertoire, even when overall diversity appears stable. These results suggest that relying solely on global diversity metrics can obscure active clonal remodeling, underscoring the importance of monitoring individual T cell clonotypes to accurately capture intratumoral T cell dynamics over time.

overall_design: TCR sequencing of murine bilateral tumors in a time-matched or time-separated setting with or without treatment with decitabine. Three mice included per group

first: Pernille

middle: G

last: Pedersen

first: Odd

last: Gammelgaard

first: Christina

last: Ruhlmann

first: Aida

last: Hansen

first: Henrik

last: Ditzel

first: Morten

middle: F

last: Gjerstorff

first: Mikkel

last: Terp


title: RANKL inhibits macrophage pro-inflammatory Toll-like receptor 2 and 4 signaling and impairs killing of intracellular bacteria

city: Nashville

first: James

last: Cassat

state: TN

address: 1161 21st Ave S

institute: Vanderbilt University Medical Center

summary: Monocyte-macrophage lineage cells, crucial components of the innate immune system, can uniquely form bone-resorbing osteoclasts upon exposure to the cytokine receptor activator of NF-κB ligand (RANKL) in the bone microenvironment. Recent studies have also begun to uncover extensive extraskeletal roles of RANKL. However, how monocyte-macrophage lineage cells respond to RANKL outside of the bone, and the impact that this signaling pathway exerts on the host immune response, is not fully understood. In this study, we sought to define how RANKL exposure shapes the macrophage inflammatory response to pathogens by using the model intracellular bacterium Salmonella enterica serovar Typhimurium (STm), which co-opts macrophages to cause life-threatening infections. We found that exposing both mouse and human macrophages to sub-osteoclastogenic levels of RANKL increased intracellular STm burdens and decreased pro-inflammatory cytokine production. RNA sequencing revealed downregulation of pattern recognition receptor (PRR) signaling pathways in RANKL-treated macrophages during the early stages of infection. Therefore, we hypothesized that RANKL impairs PRR-dependent signaling pathways that are important for pro-inflammatory cytokine production. We discovered that RANKL-treated macrophages exhibit reduced NF-κB and IRF3 activation, specifically in response to Toll-like receptor (TLR) 2 and TLR4 stimulation. We determined that prior RANKL exposure decreases abundance of the TLR2 and TLR4 adaptor proteins TRAM and TIRAP. Together, these data suggest that RANKL exposure negatively impacts the macrophage TLR-mediated inflammatory response to bacteria.

overall_design: RNAseq profiling of bone marrow-derived macrophages after 4h or 24h of infection with Salmonella enterica serovar Typhimurium following treatment with or without 100ng/mL of RANKL.

first: Clara

middle: D

last: Si

first: Christopher

middle: T

last: Peek

first: Sana

middle: R

last: Fatah

first: Andrew

last: Beaudoin

first: Anton

last: Zhelonkin

first: Kara

last: Eichelberger

first: Stacy

last: Hahn

first: Robert

middle: O

last: Watson

first: Denis

last: Mogilenko

middle: E


title: NanoString nCounter Mouse PanCancer Immune Profiling of CT26 tumors following chronic in vitro PMS2 inhibition and in vivo anti-PD-1 treatment

city: Altrincham

first: Maria T.

last: Rodriguez Plata

state: Cheshire

address: 3rd Floor, 1 Ashley Road

country: United Kingdom

institute: NeoPhore Ltd.

summary: NanoString nCounter immune profiling revealed that PMS2 inhibitor NP1867-pretreated tumours mounted an enhanced immune response to anti-PD-1 therapy, characterized by increased infiltration of lymphocytes, including T cells and cytotoxic populations, together with enrichment of multiple immune-related pathways. These included adaptive immune responses, antigen processing and presentation, MHC signaling, and interferon pathways, indicating that NP1867 pretreatment primes tumors for improved immunological responsiveness to PD-1 blockade.

overall_design:
CT26 cells were treated in vitro with PMS2 inhibitor NP1867 or vehicle control (DMSO) for 40 weeks. Cells were implanted subcutaneously into immunocompetent (BALB/c) syngeneic mice. Animals were randomized on day 7 post-implantation, when the mean tumor volume was approximately 50 mm³, into two groups per condition and treated with anti-PD-1 (rat IgG2a, κ, clone RMP1-14) or isotype control (rat IgG2a, κ, clone 2A3) administered intraperitoneally (i.p.) twice weekly, for a total of four doses. On day 19, 24 h after the fourth and final dose of anti–PD-1 or isotype control, animals with tumors representative of the group mean tumor volume were assigned to a satellite group (n = 6 per group) for tumor sampling. Tumors were formalin-fixed and paraffin-embedded (FFPE) prior to NanoString nCounter Mouse PanCancer Immune Profiling analysis.
(contributor) NeoPhore Ltd.

first: Maria


title: Dual Activation of CD8+ and CD4+ T cells by a PD-1 targeted IL-15 Mutein in Viral Infection

city: Salt Lake City

first: Jaroslav

last: Zak

state: UT

address: 1950 Circle of Hope Dr

department: Department of Radiation Oncology, Huntsman Cancer Institute

institute: University of Utah

summary: Immune checkpoint inhibitors have transformed cancer therapy, yet many patients fail to achieve durable responses, in part due to insufficient T cell reinvigoration. Cytokines remain promising additions to immunotherapy to improve response rates; however, the low therapeutic index and associated side effects have hindered progress. In response to these challenges, immunocytokines, engineered fusion proteins that combine the specificity of antibodies with the immune-stimulatory properties of cytokines, have been employed to enable targeted delivery of cytokine signals to immune cells or the tumor microenvironment to minimize pathological consequences. Here, we describe SAR445877 (SAR’877), a novel PD-1-targeted immunocytokine that fuses a high-affinity anti-PD-1 antibody with a detuned IL-15/IL-15Rα sushi domain complex. SAR’877 simultaneously blocks PD-1/PD-L1 and PD-1/PD-L2 interactions and delivers IL-15 signals selectively to PD-1+ T cells. This design enhances the proliferation and activation of antigen-experienced CD8⁺ and CD4⁺ T cells, as well as NK cells, while limiting systemic inflammatory cytokine release. Mechanistically, SAR’877 preferentially activates STAT5 signaling in PD-1⁺ lymphocytes and restores effector function in exhausted T cells in vitro. A murine surrogate of SAR’877 accelerated viral clearance and reinvigorated exhausted T cells in the chronic LCMV Clone-13 infection model. In multiple syngeneic tumor models, the surrogate induced robust anti-tumor immunity by expanding cytotoxic CD8⁺ T cells and promoting Th1 polarization. Notably, SAR’877 outperformed combination therapy with anti-PD-1 and untargeted IL-15, underscoring the therapeutic potential of targeted IL-15 delivery to PD-1+ cells. These findings position SAR’877 as a promising next-generation checkpoint immunotherapy that augments efficacy while reducing cytokine-associated toxicities.

overall_design: In this single-cell transcriptomic experiment, mice infected with LCMV Clone 13 were treated with mouse SAR'877 (1 mg/kg), anti-PD1 (1 mg/kg), mouse IL-15 mutein (1 mg/kg), anti-PD1+mouse IL-15 mutein (1 mg/kg each) or isotype control (1 mg/kg). At day 30 post infection, splenic T cells were subjected to flow sorting, labeling with DNA-barcoded antibodies and single-cell transcriptome library preparation following the hashtag-multiplexed 10X Genomics 3' sequencing protocol.

first: Isaraphorn

last: Pratumchai

first: John

last: Teijaro

first: Kristi

last: Marquardt


title: Dynamic NFκB control during B-lymphopoiesis ensures proteostasis to enable phased proliferation and differentiation decisions

city: Los Angeles

first: Apeksha

last: Singh

state: CA

address: 570 Boyer Hall

institute: University of California, Los Angeles

summary: Aging and inflammation reduce the bone marrow B cell output. While myeloid bias among multipotent progenitors is one cause, how the developmental cascade of B-committed progenitors is affected remains less well characterized. Here, we identify dynamic modulation of NFκB as a hallmark of healthy lymphopoiesis, which is diminished in aged, B-lymphopenic mice. Indeed, dysregulated NFκB dynamics result in severe B-lymphopenia. Model-aided analysis of in vivo progenitor populations and ex vivo experimental time courses reveal that accelerated differentiation of pro-B cells results in skipping critical proliferative phases. Single-cell transcriptomics confirmed premature cell-state transitions, characterized by inappropriate activation of NFκB target genes that cause wholesale increases in protein synthesis rates. This imbalanced proteostasis leaves little spare energetic capacity to support population expansion and impairs the functionality of the few B cells that do emerge. Our findings indicate that developmental NFκB dynamics pace and safeguard B-lymphopoiesis, thereby identifying additional mechanistic causes of age-associated humoral immune deficiency.

overall_design: Bone marrow from a C57BL/6J and an IκB – mouse was isolated and lymphoid progenitors were magnetically enriched as previously described using the biotinylated antibodies at a concentration of 1:50 in staining panel 12. Following enrichment of the lymphoid progenitors, the cells were surface marker-stained using staining panel 9 as previously described. The cells were then sorted with the BD FACSAriaIII sorter in UCLA Janis V. Flow Cytometry Core Laboratory with adequate compensation setup by using UltraComp eBeads™ Compensation Beads and live cells with staining antibodies prior to actual sample sorting. We sorted approximately 204,000 WT and IκB – fraction A-B cells and added 10ng of yeast RNA (strain BY7473, generous gift from T.L. Johnson lab) per 100,000 cells as an internal control. The RNA samples were then submitted to UCLA Technology Center for Genomics & Bioinformatics for library preparation and were sequenced using Novaseq X Plus 10B (1250M/lane). Raw data were filtered for adaptor sequences with cutadapt 4.1 69 with Python 3.10.8. Reads were processed by first concatenating the murine GRCm39 and yeast R64 genomes and annotations, and then aligning with STAR 2.7.1a. Default parameters were used except outFilterType BySJout, outFilterMultimapNmax 20, alignSJoverhangMin 8, alignSJDBoverhangMin 1, and seedSearchStartLmax 30. Aligned reads were filtered based on mapping score (MAPQ≥30) by Samtools 1.9 and transcript counts were quantified using featureCounts v1.6.5. Data were then normalized by dividing counts for each mouse gene by the total number of yeast transcripts and scaling by 1e6.

first: Valentina

last: Alonso

first: Yu-sheng

last: Lin

first: Alexander

last: Hoffmann


title: CD8 T-cells, CD86+ macrophages, and TNF-α signaling pathways are correlated with fetlock osteoarthritis in racehorses

city: Ithaca

first: Erica

last: Secor

state: NY

address: 960 Campus Rd

institute: Cornell University

summary:
Background: There is emerging evidence for the role of the immune system in osteoarthritis (OA) pathophysiology; however, little is known about how immune cells and the synovial transcriptome are altered in naturally occurring equine OA.

Objectives: To evaluate synovial fluid (SF) and synovial membrane (SM) immune cell populations and the SM transcriptome in racehorses with fetlock osteoarthritis.

Methods: Fetlock joints from racehorses euthanized on NY racetracks were considered for inclusion. SF and SM were analyzed by flow cytometry using T-cell (CD3, CD4, CD8) and macrophage (CD14, CD86, CD206) surface markers. OA severity was characterized by gross joint evaluation and SM histology. Bulk RNA-sequencing of SM was performed to identify differentially expressed genes. Flow cytometry data was analyzed with mixed linear modeling, including OA severity as a fixed effect and horse as a random effect. RNA-sequencing was evaluated with mixed linear and quadratic modeling using DREAMSeq method to capture differential gene expression over the range of OA severity.

Results: Twenty-four fetlocks from 12 horses met inclusion criteria. CD8+ T-cells (R2 = 0.25 for SM, 0.35 for SF) and CD86+ macrophages (R2 = 0.14 for SM) were positively correlated with OA severity, while CD4+ T-cells (R2 = 0.17 for SM, 0.31 for SF) were negatively correlated. Macrophages co-expressing CD86 and CD206 correlated with OA severity in SM (R2 = 0.31). Pathways including those associated with TNF-α signaling, connective tissue development, and cell and neuron projection organization/development were differentially regulated in SM with greater OA scores.

Main Limitations: Limited sample size, particularly of horses with severe OA.

Conclusions: CD8+ T-cells, CD86+ macrophages, and macrophages co-expressing CD206 and CD86 are enriched in horses with more advanced OA. Gene set analysis suggests the importance of TNF-α signaling and disinhibition of neuron and cell projection development in OA pathogenesis.

overall_design: Cross-sectional cadaver study

first: Erik

last: Chow

first: Matthew

last: Thomas

first: Lynn

last: Johnson

last: Siefert

first: Bettina

last: Wagner

first: Julie

last: Engiles

first: Heidi

last: Reesink


title: Gallic acid chemoprevention of oral carcinogenesis

city: Columbus

first: Steve

last: Oghumu

address: 1841 Neil Ave

institute: Ohio State University

summary: Naturally derived phytochemicals such as gallic acid (GA) exhibit multitargeted anticancer properties and favorable safety profiles, yet the molecular mechanisms underlying their chemopreventive effects in head and neck squamous cell carcinoma (HNSCC) remain incompletely defined. Using a 4 nitroquinoline 1 oxide (4NQO) induced oral carcinogenesis mouse model, we evaluated GA’s effects on tumor progression, and related molecular pathways. Phenotypic outcomes were assessed by histopathology, and proliferation markers. Transcriptomic changes were profiled by RNA sequencing, pathway enrichment and validation using RT qPCR. We report GA as a key modulator of transcriptional programs associated with oral carcinogenesis in a 4-nitroquinoline-1-oxide–induced mouse model. Comparative RNA sequencing of wild-type vehicle-treated (WtVeh) and GA-treated (WtGal) oral tissues revealed GA-dependent reprogramming of immune and stress-response pathways. Our data identifies unique molecular pathways associated with GA mediated oral cancer chemoprevention.

overall_design: Mice were administered with 4-nitroquinoline 1-oxide (4NQO) in their drinking water at a concentration of 100 µg/mL. 4NQO exposure continued for 16 weeks, after which mice were provided regular drinking water until the time of terminal sacrifice. Four weeks after the initiation of 4NQO exposure, mice were randomly assigned to receive either GA or vehicle control. Mice in the treatment group received GA at 100 mg/kg body weight via oral gavage five times per week, while control animals received an equal volume of vehicle using the same schedule. Treatment continued until the day of terminal sacrifice. At terminal sacrifice, tongue samples from GA treated and vehicle treated 4NQO mice were processed for bulk RNA seq

first: Puja

last: Upadhaya

first: Felipe

last: Lamenza

first: Ravi

last: Ramalingam

first: Kishan

last: Nyati


title: Single-nucleus RNA sequencing of human visceral adipose tissue biopsies from 11 Italian participants.

first: Kyla

last: Gelev

email: kylagelev@gmail.com, kzg@g.ucla.edu

address: 695 Charles E. Young Drive South

summary: We performed single-nucleus RNA-sequencing on visceral adipose tissue biopsies from 11 Italian donors from the Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA) cohort.

overall_design: Frozen visceral adipose tissue biopsies (300mg per sample) were manually minced. Nuclei were isolated separately per sample using the 10x Genomics nuclei isolation protocol. Nuclei were then loaded into the 10x Chromium Chip in preparation of library construction. Single Cell 3’ v3.1 chemistry was used for library construction. Two lanes of the NovaSeq 6000 S4 were used for sequencing, and we targeted 50,000 reads per nucleus.

middle: Z

first: Päivi

last: Pajukanta

first: Stefano

last: Romeo


title: Mechanisms governing interaction of the chromosomal protein SMCHD1 with chromatin determined by live-cell and single molecule imaging

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: The chromosomal protein SMCHD1 is a GHKL-ATPase that plays important roles in epigenetic silencing, including on the inactive X chromosome (Xi) and at the D4Z4 macrosatellite linked to regulation of DUX4 expression in the disorders FSHD2 and BAMS. In this study we use live-cell and single-molecule imaging approaches to investigate SMCHD1 interactions with chromatin and its function in epigenetic silencing. We show that chromatin binding of SMCHD1 genome wide, including on Xi, is critically dependent on the protein LRIF1 that mediates interaction with H3K9me2/3 modified nucleosomes. Using engineered mutations in the GHKL ATPase domain we show that ATP hydrolysis is required for SMCHD1 function on chromatin and gene silencing, but is dispensable for chromatin binding.  A gain of function mutation, G137E, that occurs in BAMS patients, results in accelerated Xi recruitment and greater Xi chromosome compaction.  Together, our findings advance mechanistic understanding of SMCHD1 function on Xi and at other target sites in the genome.

overall_design: To investigate Xist-mediated chromosomal silencing in the presence of various SMCHD1 mutants, chromatin-associated RNAs (ChrRNA) were isolated to assess allelic gene expression. ChrRNAs were isolated from cells with an endogenous inducible Xist model (iXist-ChrX), derived from mouse embryonic stem cells. The allelic ratios of X-linked genes were systematically and comprehensively compared.

first: Flavia

last: Constantinescu

first: Neil

last: Brockdorff


title: Small RNA production in E13.5 placenta of intra-cytoplasmic sperm injection(ICSI)-F2 offspring

city: Kyoto

first: mito

last: shinohara

state: Kyoto

address: Sakyo-ku, Yoshida Konoe

department: Medicine

institute: Kyoto University

type: Non-coding RNA profiling by high throughput sequencing

summary: Various behavioural abnormalities were observed in the F2 offspring of ICSI (Kanatsu-Shinohara et al., 2023, J. Clin. Invest. 133(22):e170140). The data presented here aim to clarify the cause of these abnormalities, and gene expression in the neonatal brain was investigated using RNA sequencing (RNAseq). ICSI was performed using C57BL/6 epididymal sperm and oocytes. Males from the F1 generation were naturally mated with C57BL/6 females to produce the F2 generation. Small RNA production in E13.5 placenta of ICSI-F2 offspring was examined. Each group contains 5 biological replicates.

overall_design: Neonatal brain tissue was prepared from male F2 offspring of the C57BL/6 strain, produced by natural mating from male ICSI-F1 offspring. Control brain samples were prepared from a neonate born via natural mating to wild-type C57BL/6 parents. Total RNA samples were extracted using a miRNeasy Mini Kit (Qiagen, Cat. No. 217084), followed by treatment with RNase-free DNase (Qiagen, Cat. No. 79254). cDNA libraries were generated using a TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA, USA). Sequencing was performed using a NextSeq 550 (Illumina) with a single-read sequencing length of 76 bp. A total of ten samples were analysed.

first: Mito

last: Kanatsu-Shinohara

first: Yusuke

last: Shiromoto

first: Takashi

last: Shinohara

first: Narumi

last: Ogoniki

first: Kimiko

last: Inoue

first: Atsuo

last: Ogura


title: Single-nucleus RNA sequencing of human visceral adipose tissue biopsies from 63 Italian participants.

summary: We performed single-nucleus RNA-sequencing on visceral adipose tissue (VAT) biopsies from 63 Italian donors from the Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA) cohort.

overall_design:
Frozen VAT biopsies (n=63) were pooled and batched into 8 batches. There were 7-8 VAT samples per batch. We randomly assigned samples to batches to minimize associations with phenotypes of interest. We isolated nuclei in groups of two samples (50 mg per sample) prior to pooling all samples into their respective batch using the 10x Genomics nuclei isolation protocol. Batches of nuclei were then loaded into the 10x Chromium Chip, and library construction was performed using the Single Cell 3’ v3.1 chemistry. Sequencing was performed across two lanes of the Novaseq X Plus 25B. We targeted 70,000 reads per nucleus.

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There are patient privacy concerns regarding public access to the raw data
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title: Expression data of E13.5 placenta from intra-cytoplasmic sperm injection(ICSI)-F2 offspring

summary: Various behavioural abnormalities and congenital anomalies were observed in the F2 offspring of ICSI (Kanatsu-Shinohara et al., 2023, J. Clin.). Invest. 133(22): e170140). The data presented here aim to clarify the cause of these abnormalities. Gene expression in the ICSI-F2 placenta was investigated using RNA sequencing (RNA-seq). ICSI was performed using C57BL/6 epididymal sperm and oocytes. Male ICSI-F2 offspring was mated with wild-type C57BL/6 female, and placentae recovered from pregnant females at E13.5 were examined for gene expression. Each group contains five biological replicates.

overall_design: ICSI was performed with C57BL/6 wt female mice sere mated naturally to ICSI-F1 male, and placenta was recovered from pregnant female by caesarean section at E13.5. Control placenta samples were prepared from pregnant female at the same stage after natural mating with C57BL/6 wt male. Total RNA samples were extracted using a miRNeasy Mini Kit (Qiagen, Cat. No. 217084), followed by treatment with RNase-Free DNase (Qiagen, Cat. No. 79254). cDNA libraries were generated using a TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA). Sequencing was performed using a NextSeq 550 (Illumina) with a single-read sequencing length of 76 bp. A total of ten samples were analysed.

first: Takuya

last: Yamamoto


title: Expression data of neonatal brain from male intra-cytoplasmic sperm injection(ICSI)-F2 offspring

summary: Various behavioural abnormalities were observed in the F2 offspring of ICSI (Kanatsu-Shinohara et al., 2023, J. Clin. Invest. 133(22):e170140). The data presented here aim to clarify the cause of these abnormalities, and gene expression in the neonatal brain was investigated using RNA sequencing (RNAseq). ICSI was performed using C57BL/6 epididymal sperm and oocytes. Males from the F1 generation were naturally mated with C57BL/6 females to produce the F2 generation. Gene expression in the neonatal brains of male ICSI-F2 offspring was examined. Each group contains four biological replicates.

overall_design: Neonatal brain tissue was prepared from male F2 offspring of the C57BL/6 strain, produced by natural mating from male ICSI-F1 offspring. Control brain samples were prepared from a neonate born via natural mating to wild-type C57BL/6 parents. Total RNA samples were extracted using a miRNeasy Mini Kit (Qiagen, Cat. No. 217084), followed by treatment with RNase-free DNase (Qiagen, Cat. No. 79254). cDNA libraries were generated using a TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA, USA). Sequencing was performed using a NextSeq 550 (Illumina) with a single-read sequencing length of 76 bp. A total of eight samples were analysed.


title: Expression data of E19.5 placenta from intra-cytoplasmic sperm injection(ICSI)-F1/F2 offspring

summary: Various behavioural abnormalities and congenital anomalies were observed in the F2 offspring of ICSI (Kanatsu-Shinohara et al., 2023, J. Clin.). Invest. 133(22): e170140). The data presented here aim to clarify the cause of these abnormalities. Gene expression in the ICSI-F1/F2 placenta was investigated using RNA sequencing (RNA-seq). ICSI was performed using C57BL/6 epididymal sperm and oocytes. The ICSI-F2 generation was produced using the sperm of the ICSI-F1 generation via in vitro fertilisation. Placentae recovered by caesarean section at E19.5 were examined for gene expression. Each group contains four biological replicates.

overall_design: ICSI was performed with C57BL/6 wt female mice sere mated naturally to ICSI-F1 male, and placenta was recovered from pregnant female by caesarean section at E19.5. Control placenta samples were prepared from pregnant female at the same stage after  natural mating. Total RNA samples were extracted using a miRNeasy Mini Kit (Qiagen, Cat. No. 217084), followed by treatment with RNase-Free DNase (Qiagen, Cat. No. 79254). cDNA libraries were generated using a TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA). Sequencing was performed using a NextSeq 550 (Illumina) with a single-read sequencing length of 76 bp. A total of eight samples were analysed.

first: Keiji

last: Mochida


title: A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain

city: Boston

first: David

last: Brann

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

summary: Although topographical maps organize many peripheral sensory systems, mouse olfactory sensory neurons (OSNs) are thought to randomly choose which one of ~1,100 possible olfactory receptors (ORs) to express, with spatial organization in the olfactory epithelium limited to a handful of broad anatomical zones that modestly restrict OR choice. Here we reveal that each OR is instead expressed at a unique mean dorsoventral position, thereby instantiating a stereotyped receptor map in the olfactory epithelium. OSN dorsoventral identities are encoded by a coherent gene expression program, which includes key transcription factors and axon guidance molecules; use of this program reflects a dorsoventral gradient in retinoic acid signaling, translates each physical location into a spatially appropriate distribution of potential OR choices, and aligns receptor maps in the nose and brain. Spatial order in the olfactory system, therefore, arises from a continuously varying transcriptional code that precisely organizes the many discrete channels responsible for smell.

platform_organism:
Mus musculus
synthetic construct

overall_design:
281 replicates of single cell RNA-seq libraries using 10X genomics chromium single cell 3' v3.1 library reagents, 4 replicates with the GEM-X 3' v4 kits. The strain/genotype is given for each sample. Note, analyses and processed data also include data publicly available in GEO accession GSE173947 and bioproject PRJNA727597
Multiplexed error-robust fluorescence in situ hybridization (MERFISH) was performed using the Vizgen MERSCOPE platform. Four replicates of coronal samples from the main olfactoy epithelium (MOE) from young (4-5 week) mice were processed according to the manufacturer's user guides (Vizgen 91600002 Rev E and 91600112 Rev C) with a 300-plex gene panel containing olfactory receptors, marker genes, and dorsoventral genes.
Two replicates of stereo-seq spatial transcriptomics data, from 10 µm coronal sections of the mouse main olfactory epithelium (MOE).

middle: H

first: Tatsuya

last: Tsukahara

first: Sandeep

last: Datta


title: RNA Folding Energy Regulates Discontinuous Transcription in Coronaviruses

first: Stephen

middle: Joseph

last: Ross

state: Massachusetts

address: 72 E Concord St

institute: Boston University School of Medicine

summary: Coronaviruses use discontinuous transcription to generate subgenomic RNAs (sgRNAs) that encode structural and accessory proteins. However, the factors regulating sgRNA abundance remain unclear. Here, we combined strand-specific RNA sequencing, RNA:RNA interaction mapping, thermodynamic modeling, and targeted mutagenesis to define the regulation of (-) sgRNA synthesis in SARS-CoV-2 infection. We demonstrate that the relative (-) sgRNA abundance across viral genes is stable throughout infection and strongly correlates with corresponding (+) sgmRNA levels. Through meta-analysis of published SPLASH data, we found that the frequency of long-range interactions between the 5′ genomic transcription regulatory sequence (TRS)-Leader and downstream TRS-Body sequences correlates with sgRNA abundance. Notably, the thermodynamic stability (ΔG) of these duplexes quantitatively predicts (-) sgRNA transcript levels. Mutations in non-coding regulatory regions that altered the ΔG resulted in corresponding changes in (-) sgRNA expression, establishing a causal role for TRS duplex stability in transcriptional regulation. Analysis of naturally occurring mutations near regulatory sites further suggests that modulation of duplex stability may also serve as an evolutionary mechanism to fine-tune viral gene expression. Together, our findings identify TRS-Leader:TRS-Body thermodynamics as a key determinant of discontinuous transcription and reveal how RNA structure encodes gene expression levels in the coronavirus genome.

sample_organism:
Chlorocebus aethiops
Mus musculus

platform_organism:
Chlorocebus aethiops
Mus musculus

overall_design: SARS-CoV-2 and rMHV NGS RNA-Sequencing by bulk and poly(A) Sequencing

first: Chengjin

last: Ye

first: Simon

last: Moxon

first: Elke

last: Mühlberger

first: Luis

last: Martinez-Sobrino

first: Daniel

last: Cifuentes


title: FABP4 Mediated Fatty Acid Transport Promotes Proliferation and Survival of Platinum-Resistant Ovarian Cancer Cells

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: Background: Ovarian cancer (OC) depends on fat as fuel for metastasis and growth. We previously demonstrated that cisplatin resistant (Pt-R) OC cells uptake higher amounts of fatty acids (FAs) compared to sensitive (Pt-S) cells– a process which facilitates cancer cell survival under cisplatin-induced oxidative stress. Results: Here we report that Pt-R OC cells are dependent on unsaturated FAs compared to Pt-S cells and upregulate key lipid transporters to allow increased uptake of FAs. Cell viability assays showed Pt-R cells were less viable under serum depletion, with oleic acid (OA, unsaturated) promoting proliferation of OC cells. OA alone rescued the inhibition of cell proliferation under conditions of serum depletion exerting more significant effects in Pt-R vs Pt-S cells. OA also reduced apoptosis, as shown by Annexin V assays, and decreased Caspase-3 and -8 cleavage. RNA-sequencing analysis linked OA-rescued cell proliferation to upregulation of cell cycle-related pathways, including G2/M checkpoints, driven by E2F1. OA increased S- and G2/M phase cell populations (6.95% to 11.6%; p<0.05), while E2F1 inhibition reduced OA-induced cell proliferation. Pt-R cells also expressed higher levels of FA transporter proteins FABP4 and CD36. Inhibiting FABPs reduced the IC50 to Pt and blocked OC growth in vivo. FABP4 was overexpressed in metastatic and recurrent vs. primary ovarian tumors. Implication: Pt-R OC cells are dependent on unsaturated FAs compared to Pt-S cells and upregulate key transporters to increase FAs uptake. OA supports proliferation of Pt-R cells by promoting cell cycle progression from G1 to S- and G2/M phases. Inhibiting FA transport reduces OC progression in vivo.

overall_design: To study the mechanism through which OA rescued the proliferation of OC cells, we performed RNA-seq in OVCAR5 Pt-S and Pt-R cells that were first cultured under starvation (induced by reducing the level of Fetal Bovine Serum from 10% down to 1%) for 24 h, and then supplemented with 50 uM OA for further 24 h. There were two experimentel groups: control group (cells starved for total 48h) and the OA group [cells starved for 24h, then supplemented with OA for further 24h (total: 48h)]. The RNA was then extracted and the RNA-seq libraries prepared. We compared the Pt-S cells cultured under starvation vs OA supplementation (n=3), and Pt-R cells cultured under starvation vs OA supplementation (n=3).  Later, we also performed RNA-seq investigating the effects of palmitic acid (PA) in OVCAR5 Pt-S cells. The experimental conditions were identical the previous experiment: Pt-S cells were first cultured under starvation (1% FBS) for 24 h, and then supplemented with 50 uM PA for further 24 h. The RNA was then extracted and the RNA-Seq libraries prepared. We compared the Pt-S cells cultured under starvation vs PA supplementation (n=3).

first: Ana Maria

last: Isac

first: Andres

last: Valdivia

first: Ujin

last: Kim

first: Yinu

last: Wang

first: Jian-Jun

last: Wei

first: Guangyuan

last: Zhao

first: Vanessa

last: Hernandez

first: Chinamyee

middle: V

last: Prabhu Dessai

first: Sandra

last: Orsulic

first: Ji-Xin

last: Cheng


title: TCA cycle rewiring underpins histone acetylation sourcing and cell-fate transitions during exit from naive pluripotency

city: Copenhagen

first: Jan

middle: Jakub

last: Żylicz

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW

institute: University of Copenhagen

summary: Metabolism has emerged as a crucial regulator of development and stem cell epigenome. This coupling is particularly evident during the in vitro exit from naïve pluripotency. However, our understanding of the dynamic metabolic rewiring at this developmental stage remains rudimentary. In this study, we reconstruct intracellular metabolite routings in pre- and post-implantation mouse embryos and their dynamic stem cell models. Our findings reveal that, instead of a simple TCA cycle shutdown, there is spatio-temporally programmed TCA cycle rewiring at implantation. Focusing on the pluripotency spectrum, we identify pyruvate as a key metabolic nexus. Indeed, pyruvate carboxylase and malic enzyme activity is essential for maintaining a balanced metabolic and transcriptional state as well as timely exit from naïve pluripotency. Additionally, we discover that formative and primed pluripotent cells exhibit increased glutamine uptake, reduced oxidative TCA activity, and reciprocal reductive glutamine metabolism. This metabolic rewiring supports increased histone acetylation turnover, primarily using glutamine as a carbon source, supplemented by pyruvate cycling. Thus, we uncover diverse nutrient strategies that are functionally coupled to epigenome programming and dynamic pluripotency cell state transitions at the time of implantation.

overall_design: RNA sequencing of control (negative/scramble) and following the repression of all three Pcx, Me1 and Me2 (3xKD) in ESCs and EpiLCs day 2

first: Eleni

last: Kafkia

first: David

last: Pladevall-Morera

first: Jan Jakub

last: Zylicz


title: A temporal map of B cell diversification mechanisms in mice

city: Melbourne

first: Oliver

middle: Philip

last: Skinner

state: VIC

address: 792 Elizabeth Street

department: Microbiology and Immunology

country: Australia

institute: Peter Doherty Institute, University of Melbourne

summary: Naive B cells diversify via clonal expansion, immunoglobulin isotype switching, phenotypic variation and somatic hypermutation (SHM). Diversity in antigenic targets, functional classes and the production kinetics of antibodies affects immunity to malaria. Here we show that individual clones diversify over time during Plasmodium infection. During the first week, amid widespread bystander activation, isotype switching initiates soon after Myc upregulation and overlaps with clonal expansion, resulting in isotype variegation among clones. During the second week, expanded clones seeding germinal centers (GC) bifurcate into extrafollicular plasmablasts, exhibit isotype variegation and initiate SHM, indicating substantial intraclonal diversification. Over the following month, GC clones exhibit SHM at approximately four mutations per week. Antimalarial intervention does not impede SHM, instead exerting quantitative limits on GC size, plasma cell emergence, circulating antibody levels and protection against reinfection. Finally, contemporaneous B cell development relocates from bone marrow to spleen. Thus, multiple temporally overlapping mechanisms combine in vivo to diversify and safeguard humoral immune responses.

overall_design: scRNAseq (gene expression and VDJ) of sorted B cells from splenocytes of female mice at various timepoints post-Plasmodium infection with or without anti-malarial drug treatment. Experiment 1: scRNAseq and BCRseq B cells at timepoints, 4-, 7-, 10-, 14-days post infection. Each timepoint contains 5x hashtagged individual mouse samples. Note, timepoint 4 days post infection includes one uninfected mouse sample. Experiment 2: scRNAseq and BCRseq B cells at timepoints 10-, 14-, 21-, 28-, 35-, 42-days post infection. At each timepoint, there are 7 hashtagged individual mouse samples: 3x samples infection only, 3x samples infection with anti-malarial drug treatment and 1x uninfected sample. Experiment 3: scRNAseq of sorted GC B cells and ASCs from a single day 14 Plasmodium infected mouse spleen. Spatial transcriptomics using Stereo-seqv1.2 was also performed on day 21 Plasmodium infected mouse spleens from two independent mice.

middle: P


title: Syrah: a pipeline to maximize spatial transcriptomics data output

city: Kansas City

first: Alejandro

last: Sánchez Alvarado

institute: Stowers Institute for Medical Research

summary: Spatial analysis of gene expression patterns has been a key technique for revealing the functions of genes. Traditionally, these analyses were constrained to examining only a few candidate genes per sample. However, the advent of spatial transcriptomic techniques like Slide-seqV2 has transformed this field, enabling unbiased and massively parallel exploration of gene expression patterns within their tissue contexts through RNA sequencing. Despite its potential, Slide-seq datasets often suffer from low read counts, loss of data points, and poor quality. We have identified that a significant source of these errors stems from the chemical synthesis of mRNA capture oligonucleotides used in Slide-seqV2. To address this issue, we have developed "Syrah," an analysis pipeline designed to correct these errors. Syrah can dramatically enhance Slide-seqV2 datasets by recovering nearly 30% more reads. Unlike other dataset improvement methods that rely on complex mathematical imputation or single-cell RNA-seq references, Syrah operates independently, requiring no additional datasets or intricate calculations. This innovative technique promises to salvage previously unusable Slide-seq datasets by restoring valuable reads that were inadvertently discarded during analysis.

overall_design: Comparison of standard and Syrah spatial transcriptomic data processing, including previously published Slide-seqV2 and Curio Seeker data, as well as a novel planarian Slide-seqV2 dataset.

first: Carolyn

last: Brewster

first: Frederick

last: Mann Jr

first: Blair

last: Benham-Pyle


title: Multisensory integration at the dawn of land plant evolution

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

summary: Land plant colonization was a pivotal event in the evolution of photosynthetic eukaryotes. The transition from aquatic to terrestrial environments required complex multisensory systems that enabled plants to perceive and integrate a broader range of environmental cues, such as light intensity and temperature. However, it remains unclear whether this ability was a pre-adaptation or an innovation during early plant terrestrialization. Here, we show that the aquatic streptophyte ancestor of land plants could integrate light and temperature through a complex regulatory network. A conserved regulatory nexus, comprising phytochromes and transcription factors, was active in the last common ancestor of land plants, allowing the first terrestrial colonizers to adapt and flourish on the harsh terrestrial surface of our planet. Thus, we propose that the multisensory integration that enables extant plants to achieve perceptual disambiguation and fine-tune growth in various ecological niches was a pre-adaptation encoded in the genomes of ancestral land plants.

sample_organism:
Marchantia polymorpha
Arabidopsis thaliana
Ostreococcus tauri
Mesotaenium endlicherianum

overall_design: To assess the integration of light and temperature at a transcriptomic level in different plant species, we grew Arabidopsis thaliana, Marchantia polymorpha, Mesotaenium endlicherianum and Ostreococcus tauri in different combinations of light and temperature conditions.

first: Bruno

last: Catarino

first: Fernando

last: Rodríguez-Marín

first: Cristina

last: Úrbez

first: Christina

last: Arvanitidou

first: Eva

last: Álvarez

first: Federico

last: Valverde

first: José

middle: M

last: Franco-Zorrilla

first: Francisco

last: Romero-Campero

first: Miguel

middle: A

last: Blázquez


title: Single cell variant to enhancer to gene map for coronary artery disease [ChIP-seq]

city: Singapore

first: Roger

last: Foo

address: 14 Medical Drive, MD6

institute: National University of Singapore

summary: Although genome wide association studies (GWAS) in large populations have identified hundreds of variants associated with common diseases such as coronary artery disease (CAD), most variants lie within non-coding regions of the genome, rendering it difficult to determine the downstream causal gene and cell type. Here, we performed paired single nucleus gene expression and chromatin accessibility profiling from 44 human coronary arteries. To link disease variants to molecular traits, we developed a meta-map of 88 samples and discovered 11,182 single-cell chromatin accessibility quantitative trait loci (caQTLs). Heritability enrichment analysis and disease variant mapping demonstrated that smooth muscle cells (SMCs) harbor the greatest genetic risk for CAD. To capture the continuum of SMC cell states in disease we used single cell caQTL modeling for the first time in tissue to uncover QTLs which are cell state aware and expand our insight into gene regulation in heterogenous cell populations. We identified a variant in the COL4A1/COL4A2 CAD GWAS locus which becomes a caQTL as SMCs de-differentiate through a transcription factor binding site change for EGR1/2. To unbiasedly prioritize functional candidate genes, we built a genome-wide single cell variant to enhancer to gene (scV2E2G) map in human CAD to link disease variants to causal genes in cell types. Using this approach, we found several hundred genes predicted to be linked to disease variants in different cell types. We validated these predictions using enhancer targeted perturb sequencing (TAP-seq). Next, we performed genome-wide HiC in 16 human coronary arteries to build tissue specific gene regulatory networks and map disease variants to integrated chromatin hubs and distal target genes not previously implicated. Using this approach, we show that rs4887091 within the ADAMTS7 GWAS locus modulates function of a super chromatin interactome through a change in a CTCF binding site. Finally, by integrating human genetics with single cell multi-omics we show that CAD genetic risk is enriched in de-differentiated fibromyocytes. Collectively we provide a disease agnostic framework to translate human genetic findings to identify pathologic cell states and genes driving disease, producing a comprehensive scV2E2G map with genetic and tissue level conviction for future mechanistic and therapeutic studies.

overall_design:
One million human coronary artery smooth muscle cells (HCASMC) and human coronary endothelial cells (HCAEC) from the same lot used for HiChIP experiments were crosslinked with 1% Formaldehyde for 10 min at room temperature and quenched with glycine (125mM) for 5 min.
The cells were rinsed twice with cold 1XPBS and sonicated in nuclei lysis buffer (50mM HEPES-KOH, pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X, 0.1% Sodium deoxycholate, 1% SDS, Takara, 1x protease inhibitor) using the Bioruptor sonicator to obtain chromatin fragments between 200 to 500 bp.
The fragmented chromatin was immunoprecipitated overnight at 4ºC, with 5 μg of H3K27ac antibody (Abcam, ab4729) and 50 μl of protein G beads (Invitrogen, 10004D). Subsequently, the beads were washed and immunoprecipitated DNA was de-crosslinked and eluted in elution buffer (50 mM Tris-HCI, pH7.5, and 10 mM EDTA). Eluted ChIP fragments were isolated using Phenol-Chloroform extraction method, and DNA was purified by ethanol precipitation.

first: Chang Jie Mick

last: Lee

first: Anene-Nzelu

last: Chukwuemeka

first: Amrute

last: Junedh

first: Stitziel

last: Nathan


title: Glutathione induces trap closure for carnivory in Cape sundew

city: Beijing

first: daoxin

last: Xie

address: Tsinghua University Haidian District

institute: Tsinghua University

summary: Charles Darwin was infinitely fascinated with Drosera (sundew plants), which have behaved as the most sagacious animals and evolved as flesh-eaters with modified leaves, called traps, to catch and digest insects. However, the molecular basis underlying movement of carnivorous plants remains very limited. Here, we uncover glutathione (GSH) as a signaling molecule in sundew plants that induces trap movement for carnivory. To better understanding the molecular basis of sundew carnivory, we further performed transcriptomic profiling of closed sundew traps stimulated by living fruit flies and GSH.

overall_design: Trap closure of Cape sundew was indued either by feeding living fruit fly on leaf or applying 100 mM GSH on to the leaf petiole. Such closed sundew traps as well as the mock control sundew traps were collected and further subjected to transcriptome profiling.

first: Rui

last: Li

first: Yongfang

last: Yang

first: Jianbin

last: Yan

first: Qinggang

last: Liao

first: Haidong

last: Chen

first: Xiaoyi

last: Shan

first: Daoxin


title: Functional evolution, modification, and derivatization of mammalian developmental enhancers

status: Public on Apr 20 2026

city: Seattle

first: Tony

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: This dataset encompasses two complementary massively parallel reporter assay (MPRA) studies that together dissect the functional architecture and evolutionary dynamics of mammalian cis-regulatory elements (CREs) at nucleotide resolution, using five parietal endoderm enhancers as a model system. The first study maps the functional evolution of these enhancers by testing orthologous sequences from 480 extant and ancestrally reconstructed mammalian genomes (Zoonomia/Cactus). Using a model-driven reconstitution strategy guided by deep learning predictions of chromatin accessibility, we traced causal transcription factor binding site (TFBS) changes across lineages, revealing pervasive context-dependent epistasis and diverse modes of evolutionary divergence. Targeted enhancer editing further demonstrated a striking asymmetry: ablation of enhancer activity required as few as one to seven mutations, whereas activity enhancement was constrained by element-specific ceilings. The second study subjects the same five enhancers to intensive sequence perturbation, assaying over 35,000 variants organized into four classes: dense multi-size tiling, multi-hit saturation mutagenesis, model-guided compaction, and TFBS-anchored sequence derivatization including synthetic thripsis. This dissection revealed sharp non-additivity between fragment size and activity, a spectrum of mutational robustness, rare but consequential inter-TFBS epistasis, and a strong influence of background sequence on enhancer output independent of TFBS arrangement. Together, these datasets provide a comprehensive resource for understanding how enhancer sequences encode function, robustness, and evolvability across the mammalian phylogeny.

overall_design: To link molecular barcodes (mBCs) to their corresponding CRE sequences, we performed CRE-BC association mapping. Using paired-end Illumina sequencing, each mBC and its associated CRE were captured within a single amplicon, generating a lookup dictionary for each library prior to massively parallel reporter assay (MPRA) experiments.

first: Jean--Benoit

last: Lalanne

first: Jay

last: Shendure


title: Spatially Resolved Obesity-Driven Molecular Changes in Early Breast Cancer

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

institute: University of Oklahoma Health Sciences Center

summary: Obesity is an established risk factor for invasive breast cancer; however, the specific molecular heterogeneity distinguishing invasive ductal carcinoma (IDC) from ductal carcinoma in situ (DCIS) within the obese tumor microenvironment is not well defined. In the current study, spatially resolved transcriptomics was utilized to profile the epithelial, stromal, and immune compartments of DCIS and IDC lesions stratified by host body mass index, categorized as non-obese (≤29.9 kg/m2) or obese (≥30 kg/m2). These analyses reveal that the transcriptional signatures defining the invasive state differ significantly across BMI categories. In non-obese patients, IDC lesions exhibited canonical profiles driven by proliferation and epithelial-to-mesenchymal transition, compared with DCIS. Conversely, the obese setting was characterized by a distinct "stress-adaptive" phenotype, enriched for metabolic adjustment, oxidative stress response, and inflammatory signaling. The epithelial component was accompanied by a fibro-inflammatory stromal signature and an immunosuppressive niche characterized by B cell depletion and M2 macrophage enrichment. Furthermore, SULF2, an extracellular endosulfatase involved in extracellular matrix organization and signaling, was consistently upregulated within the obese epithelium, providing a plausible link between metabolic stress and structural remodeling. Collectively, these data indicate obesity-associated differences consistent with an alternative invasive transcriptional program that is less dominated by classical proliferative drivers in this cohort. Consequently, standard prognostic markers may be context-dependent, highlighting the need to integrate metabolic health into precision risk stratification.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Each sequenced library corresponds to a single GeoMx Digital Spatial Profiler region-of-interest segment or technical control collected into an individual well of a 96-well plate. The submitted dataset contains libraries from formalin-fixed, paraffin-embedded human breast tissue sections from ductal carcinoma in situ and invasive ductal carcinoma cases stratified by body mass index, including epithelial (cytokeratin-positive), stromal/myoepithelial (alpha-smooth muscle actin-positive), and immune (CD45-positive) segments, together with a no-template control. ROI-level metadata include slide number, ROI identifier, segment identity, area, nuclei count when available, scan coordinates, and panel annotation.

first: Cole

last: Hladik

first: Malika

last: Sekhri

first: Haoning-Howard

last: Cen

first: Suganthapriya

last: Elayapillai

first: Schuyler

first: Bifeng

last: Gao

first: William

last: Dooley

first: Ty

last: Milligan

first: Haddon

last: Hill

first: Alexander

last: Filatenkov

first: Elizabeth

last: Wellberg

middle: N


title: RNA-seq profiling of non-muscle invasive bladder cancer (NMIBC) tumors

city: Bothell

first: Joseph

last: Dekker

state: Washington

institute: Pfizer

summary: Bulk RNA-seq was performed on fresh-frozen non-muscle invasive bladder cancer (NMIBC) tumor biopsies obtained from commercial biobanks (BioIVT and Proteogenex). These data were generated to characterize the transcriptomic landscape of NMIBC tumors and support preclinical studies of integrin beta-6 (ITGB6)-targeted therapies. RNA was extracted from 25 untreated surgical specimens and sequenced using paired-end Illumina sequencing by Azenta Life Sciences.

overall_design: 25 fresh-frozen NMIBC tumor biopsies were profiled by paired-end RNA-seq. All samples are untreated clinical specimens sourced from BioIVT (n=14) and Proteogenex (n=11). No experimental treatment was applied.

first: Robert

last: Lawrence


title: Tectochrysin alleviates Ang II-induced pathological cardiac hypertrophy by binding to STING and inhibiting STING/NFκB-mediated inflammation

city: Chongqing

first: Yanghao

last: Chen

address: No. 288, Tianwen Avenue, Nan'an District, Chongqing

institute: Chongqing Medical University

summary: Angiotensin II (Ang II)-induced cardiac inflammation plays a pivotal role in the pathogenesis of pathological cardiac hypertrophy and hypertension-related heart failure. Tectochrysin (Tec) is a flavonoid natural compound exhibiting significant anti-inflammatory activity. However, the role of Tec in hypertensive heart failure and its molecular targets remain unclear. The therapeutic efficacy of Tec was assessed in the Ang II-induced mouse model using echocardiography, histopathological staining, and serological tests. Its anti-hypertrophic effect was further examined in vitro by phalloidin staining. Investigate the mechanism of action of Tec through transcriptome sequencing. The interaction of Tec with STING was detected by DARTS, CETSA, and SPR assays. Western blotting assay detected the effect of Tec on Ang II-induced activation of the STING/NFκB pathway. The functional dependency of Tec on STING was demonstrated using the STING inhibitor H151. In vivo experiments confirmed that Tec alleviates Ang II-induced myocardial inflammation, pathological hypertrophy, myocardial fibrosis, and cardiac dysfunction. Further in vitro studies revealed the efficacy of Tec in inhibiting cardiomyocyte hypertrophy. Mechanistically, Tec significantly suppressed Ang II-induced activation of the STING/NFκB signalling pathway by targeting STING. Crucially, administration of the STING inhibitor H151 alleviates pathological myocardial hypertrophy, however its use diminishes the therapeutic effect of Tec. Our findings confirmed STING as a critical therapeutic target in pathological ventricular remodeling, with Tec exerting its anti-hypertrophic effects through STING inhibition.

overall_design: we performed RNA sequencing analysis on the heart tissues of three Ang II mices and three Ang II mices treated by Tectochrysin

first: Zhiyu

last: Ling


title: Unique transcriptional profiles of adult human immature neurons in healthy aging, Alzheimer’s disease, and cognitive resilience

city: Amsterdam

first: Dilara

last: Ayyildiz

address: Meibergdreef 47

institute: Netherlands Institute For Neuroscience

summary: The existence and putative functional significance of immature neurons in the adult human brain, particularly in the context of neurodegenerative disorders, remains an open question. While rodent studies have highlighted active roles for adult-born immature neurons in the hippocampus under both healthy conditions and in Alzheimer’s disease (AD), evidence from the human brain is limited and lacks detailed molecular characterization. To address this gap, we performed single-nucleus RNA sequencing in aged healthy, AD and dementia-resilient human hippocampus to probe immature neuronal signatures and gene expression alterations associated with AD pathology and resilience. Employing a novel experimental and computational pipeline, we identified persistent populations of immature neurons across all donor groups, with transcriptional profiles reflecting ‘juvenile’ cellular functions, which are compromised in AD. Our findings suggest that the presence of these immature neuronal populations per se may actively contribute to maintaining homeostasis within the aged human hippocampus, and cognitive resilience in AD.

overall_design: Fresh frozen adult human hippocampal tissue blocks were sectioned into 300 μm thick slices using a cryostat. Sections were maintained on dry ice, and SGZ and GCL, extending from the molecular layer to the hilus were isolated under a stereomicroscope using a 0.5 mm-diameter biopsy puncher.Adjacent sections were stained with hematoxylin to facilitate the accurate identification of the dentate gyrus. Punched tissue samples were stored at -80°C until further processing. For the fetal samples, the region of the tissue containing the DG was identified by hematoxylin staining and sectioned into 50 μm-thick slices using a cryostat. Isolated nuclei samples were further processed for GEM generation, with targeted nuclei recovery of 10000 nuclei/sample by using 10x Genomics Single Cell 3` Reagent Kit (v3.1) according to manufacturer’s protocols (10x Genomics, CG000204_Rev_A).

first: Giorgia

last: Tosoni

first: Sarah

last: Snoeck

first: Elena P.

last: Moreno-Jiménez

first: Amber

last: Penning

first: Estibaliz

last: Santiago-Mujika

first: Olmo

last: Ruiz Ormaechea

first: Hyunah

last: Lee

first: Suresh

last: Poovathingal

first: Kristofer

last: Davie

first: Julien

last: Bryois

first: Will

last: Macnair

first: Jasper

last: Anink

first: Luuk E.

last: De Vries

first: Sahand

last: Farmand

first: Erik

last: Nutma

first: Dick F.

last: Swaab

first: Eleonora

last: Aronica

first: Jinte

last: Middeldorp

first: Sandrine

last: Thuret

first: Laurent

last: Roybon

first: Onur

last: Basak

first: Carlos P.

last: Fitzsimons

first: Paul J.

last: Lucassen

first: Evgenia

last: Salta


title: CD5L promotes phagocytic removal of Amyloid β oligomers and improves cognitive function in a mouse model of Alzheimer's disease [RNA-Seq]

city: Shinjuku

first: Natsumi

last: Maehara

state: Tokyo

address: 8-1, Kawata-cho

department: Department of Molecular Biomedicine for Pathogenesis

institute: The Institute for AIM Medicine

summary: Alzheimer's disease (AD), a neurodegenerative disorder, is the leading cause of dementia. Amyloid-beta (Aβ) and tau are major contributors to AD onset and progression. Here, we investigate the therapeutic potential of CD5L, a macrophage-specific secretory protein, in reducing Aβ accumulation and improving AD pathology. CD5L directly binds to Aβ, particularly the neurotoxic Aβ42, and blocks their aggregation. Moreover, CD5L enhances microglial phagocytosis against several forms of Aβ40 and Aβ42. In 5xFAD mice, a well-established AD murine model, forced expression of CD5L reduced Aβ plaque size and number. RNA sequencing revealed that CD5L promotes phagocytic activity in microglia within the 5xFAD mouse brain. Furthermore, adeno-associated virus (AAV)-mediated delivery of CD5L improved cognitive function, as demonstrated by enhanced performance in the T-maze test. These findings highlight the role of CD5L in inhibiting Aβ aggregation and facilitating Aβ clearance via enhanced phagocytosis, offering a promising therapeutic strategy for AD.

overall_design: Bulk RNA sequencing was performed to compare gene expression profiles between 5xFAD  mice, 5xFAD mice with forced expression of mouse CD5L via a transgene regulated by the human PDGF-B promoter (5xFAD/Cd5l tg/wt) and wild-type mice. Total RNA was extracted from brain tissues (cerebellum removed) and used for library preparation and sequencing.

first: Aika

last: Hirota

first: Kai

last: Kudo

first: Yuri

last: Yoshikawa

first: Satoko

last: Arai

first: Toru

last: Miyazaki


title: CD5L promotes phagocytic removal of Amyloid β oligomers and improves cognitive function in a mouse model of Alzheimer's disease


title: Acquired genetic and cell state changes in IDH-mutant glioma progression [coculture experiments]

city: New Haven

first: Kevin

middle: C

last: Johnson

state: CT

address: 333 Cedar Street

department: Neurosurgery

institute: Yale University

summary: Isocitrate dehydrogenase (IDH)-mutant gliomas are malignant brain tumors that typically arise in early- to mid-adulthood and nearly always recur following treatment. However, the genetic and cellular state changes that drive IDH-mutant glioma progression under treatment remain incompletely understood. Here, we integrated single-nucleus transcriptomic profiles, chromatin accessibility profiles and bulk DNA/RNA sequencing from 75 temporally separated gliomas across 35 patients comprising both the oligodendroglioma and astrocytoma IDH-mutant glioma tumor types. We show that malignant cell states transcriptionally resemble stages of normal glial-neuronal lineage development or a reactive mesenchymal-like state, mirroring states previously described in IDH-wildtype glioblastoma. Malignant cell states displayed distinct chromatin accessibility profiles that were comparable between both IDH-mutant glioma types. The abundance of less differentiated malignant cells increased with grade and with genetic alterations such as PDGFRA amplification. Longitudinal analysis highlighted two major malignant cell state transition patterns. First, reduced lineage differentiation and increased proliferative malignant cells at recurrence were pronounced in gliomas that acquired recurrence-associated genetic events, including treatment-associated hypermutation, increased copy number changes, and cell cycle alterations. Second, increased mesenchymal-like state abundance occurred independently of acquired genetic alterations and instead coincided with heightened macrophage expression. Overall, our findings provide an integrative model that traces the cell-intrinsic and extrinsic factors that shape cellular states during IDH-mutant glioma disease progression.

overall_design:
MGG152, a human IDH-mutant patient-derived glioma cell line, was profiled by 10x single-cell RNA sequencing  3' v4 (polyA) On-Chip Multiplexing (OCM) across 4 different environmental conditions each with 4 biological replicates. These conditions included MGG152 monoculture, MGG152 monoculture treated with irradiation, MGG152 co-culture with mouse macrophage cells, and MGG152 co-culture with mouse macrophage cells treated with irradiation.

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

first: Linbin

last: Zhang

first: Anna

last: Lasorella

first: Roel

last: Verhaak


title: Spatial transcriptomics dissects mechanism of action of the PD-1 targeted IL15-mutein in B16-F10-OVA tumor-bearing mice

city: Cambridge

first: Julien

last: Tessier

address: 350 Water Street

institute: Sanofi US

summary: KD050 is an anti-PD-1/IL-15 bi-functional antibody with strong PD-1 antagonist function, but lower lymphocyte stimulation enabled by a novel mutation on the IL-15. Here, we spatially characterized at RNA level the effect of mKD050 surrogate I in B16-OVA (melanoma) mouse model, in comparison with anti-mPD1 and mouse non-targetKD050 (mntKD050).

overall_design: A total of 20 B16-F10-OVA tumors were characterized, with 5 samples per treatment groups (Isotype Control, anti-mPD-1, mIgG-mutmIL15 and anti-mPD-1-mutmIL15). For each tumor, we defined 3 compartments (“Leading Edge”, “Tumor” and “Necrosis”) based on morphological markers and H&E staining. For each compartment, we then harvested 8 circular (250μm in diameter) ROIs, so a total of 24 per tumor (23 ROIs per tumor for the isotype control group as the first well on each collection plate was dedicated to the no-template control). ROI placement for each compartment was done within the tumor boundaries, including for the “Leading Edge” one

first: Tessier

last: Julien

first: Lee

last: Joon Sang


title: Acquired genetic and cell state changes in IDH-mutant glioma progression

overall_design:
Two IDH-mutant glioma patient-derived neurosphere cell lines were treated with PDGFRA inhibitors or control. The experimental conditions per cell line were dimethyl sulfoxide (DMSO) control, dasatinib (broad SRC/ABL/PDGFR inhibitor), and CP-673451 (selective PDGFRα/β inhibitor). The doses for the PDGFRA inhibitors were 1µM and 5µM. These samples were profiled with single-cell RNA sequencing (10x Genomics, 3' v4).

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

first: Anuja

last: Lipsa

first: Kamil

last: Grzyb

last: Golebiewska


overall_design:
MGG152, an IDH-mutant patient-derived glioma cell line, was profiled by single-cell RNA sequencing (10x Genomics, 3' v3 (polyA)) across different experimental conditions. The conditions included a parental MGG152 cell line, MGG152 CDKN2A-/- single guide RNAs 1 & 3 (MGG152 CDKN2A-/- sgRNA1 and sgRNA3), and a non-targeting control (MGG152 NTC).

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

first: Ester

last: Calvo Fernández

first: Julie

middle: J

last: Miller

first: Hiroaki

last: Wakimoto

first: Daniel

last: Cahill

first: Mario

middle: L

last: Suvà


title: KAT6A  is essential for developmental control gene expression in neural stem and progenitor cells

city: Parkville

first: Nishika

last: Ranathunga

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

summary: Heterozygous mutations in the MYST family histone acetyltransferase gene, KAT6A (MOZ, MYST3) cause the human congenital disorders characterised by intellectual disability, Arboleda-Tham syndrome (KAT6A syndrome). In this dataset, we used neural stem cells isolated from Kat6a+/+, Kat6a+/– and Kat6a–/– E12.5 mouse embryos cultured under proliferating and differentiating conditions to assess the effects of loss of one or both alleles of Kat6a on neural stem and progenitor proliferation and differentiation.

overall_design: Proliferating and differentiating neural stem and progenitor cells isolated from the dorsal telencephalon of N = 4 Kat6a+/+, 4 Kat6a+/– and 4 Kat6a–/– E12.5 mouse embryos cultured under proliferating and differentiating conditions.

first: Alexandra

last: Garnham

first: Ranathunga

last: Nishika

first: Anne

middle: K

last: Voss

first: Tim

last: Thomas


city: Kyoto

first: Mamoru

last: Oyabu

address: 1-5 Shimogamo Hangicho, Sakyo Ward

department: Graduate School of Life and Environmental Sciences

institute: Kyoto Prefectural University

summary: Catabolic conditions, such as starvation, inactivity, and cancer cachexia, induce Forkhead box O (FoxO) transcription factor(s) expression and severe muscle atrophy via the induction of ubiquitin–proteasome system-mediated muscle proteolysis, resulting in frailty and poor quality of life. Microarray analysis of quadriceps muscle of fed or 24 h-fasted wild type mice and skeletal muscle-specific FoxO1,3,4 knockout mice identified the potential novel FoxOs-target genes in skeletal muscle including Redd1, Sestrin1, Castor2, Chac1, Depp1, Lat3, as well as Cebpd. This study comprehensively identifies novel potential FoxOs-target genes in skeletal muscle and clarifies the pathophysiological role of FoxOs, master regulators of skeletal muscle atrophy.

overall_design: Microarray profiling of quadriceps muscles of fed or 24 h-fasted male 8-week-old mFoxO1,3,4-/- (skeletal muscle specific FoxO1,3,4 knockout) mice and age-matched wild type (WT) mice. mFoxO1,3,4-/- mice were generated as previously described (PMID: 35061305). Briefly, Cre recombinase was driven by human α-actin (HSA) promoter to specifically delete FoxO1, FoxO3, and FoxO4 in skeletal muscle in mFoxO1,3,4-/- mice.

first: Yasutomi

last: Kamei


title: Instant fluorescence lifetime imaging microscopy reveals mechano-metabolic reprogramming of stromal cells in breast cancer peritumor microenvironment

city: Notre Dame

first: Julian

last: Najera

state: IN

address: 2031 McCourtney Hall East

institute: University of Notre Dame

summary: The breast peritumor microenvironment (pTME) is increasingly recognized as a mediator of breast cancer progression and treatment resistance. However, how tumor compressive forces (i.e., solid stresses) influence it remains unclear. Using instant fluorescence lifetime imaging microscopy (FLIM), we show that in vitro compression metabolically reprograms stromal cells found in the breast pTME. Namely, compression shifts fibroblasts and differentiated adipocytes toward a more glycolytic state, but promotes increased oxidative phosphorylation in undifferentiated adipocytes. Through RNA-sequencing, we confirmed that compression downregulates oxidative phosphorylation and upregulates glycolysis in fibroblasts. By elucidating tumor-host mechano-metabolic interactions, these results will inform the development of innovative treatment strategies to improve survival.

overall_design: RNA-seq profiling of NIH3T3 fibroblasts subjected to 0.14 kPa of compression or 0 kPa of compression (uncompressed).


title: Dual BCL-xL and BCL-2 Inhibition for Advanced Myeloid Neoplasms: A phase 1 dose-escalation study of Navitoclax, Venetoclax, and Decitabine

city: Boston

first: Hayden

last: Bell

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Background: The BCL-2 inhibitor venetoclax in combination with a hypomethylating agent is effective against most acute myeloid leukemia (AML) subtypes, but less so against other high-risk myeloid neoplasms. One resistance mechanism to BCL-2 inhibition is increased dependence on alternate BH3-only anti-apoptotic proteins, such as BCL-xL. Navitoclax is a BCL-2/BCL-xL inhibitor that has been previously studied in hematologic malignancies. Patients and methods: We conducted a Phase 1 study of dose-escalated navitoclax added to venetoclax/decitabine for subjects with 1) secondary (s-AML) or therapy-related AML, 2) accelerated- or blast-phase myelofibrosis (AP/BP-MF), 3) myelodysplastic syndrome (MDS)/myeloproliferative neoplasm (MPN) overlap syndromes with excess blasts, or 4) relapsed/refractory (R/R) MDS with excess blasts.  Results:Sixteen subjects were enrolled.  Dose-escalation for BP-MF and s-AML was not completed due to discontinued navitoclax supply.  Most common grade ≥3 treatment-emergent adverse events included neutropenia (69%), thrombocytopenia (69%), and febrile neutropenia (47%). No clinically significant bleeding was observed. One dose-limiting toxicity of delayed neutrophil recovery occurred. Among 15 evaluable subjects, the overall objective response rate was 60% (9/15). The recommended phase 2 dose was decitabine 20 mg/m2 days 1-5, venetoclax 400 mg/day days 1-14, and navitoclax 50 mg/day days 1-14 for AP-MF, MDS/MPN, and R/R MDS.  Correlative studies indicate preserved immature platelet fractions despite on-target reduction of mature platelets, a reduction in disease-associated aberrant monocytes in subjects with monocytic disease, and higher baseline myeloblast dependence on BCL-2 and BCL-xL as predictive of response.  Conclusion:Navitoclax added to venetoclax/decitabine is safely tolerable and is active in patients with high-risk myeloid malignancies.

overall_design:
Bone marrow aspirate mononuclear cells from patients with chronic myelomonocytic leukemia (CMML), including paired longitudinal samples from two unique study patients, underwent single cell multiome (scRNA-seq + scATAC-seq) sequencing. Patients were participants in a single-center, open-label nonrandomized phase 1 study (NCT05455294) investigating administration of navitoclax, venetoclax, and decitabine. Single nuclei were prepared and processed using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow. Libraries were sequenced on an Illumina NovaSeq 6000.

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

first: Evan

last: Chen

first: Yiwen

last: Liu

first: Jeremy

last: Ryan

first: Jason

last: Wu

first: Emma-Jayne

last: Minihane

first: Eric

middle: S

last: Winer

first: Marlise

last: Luskin

last: Roberts

first: Virginia

last: Volpe

first: Rahul

last: Vedula

first: Maximilian

last: Stahl

first: Matthew

last: Hersch

first: Dylan

last: Wilson

first: Jessica

last: Lee

first: Ilene

last: Galinsky

first: Mary

last: Gerard

first: Donna

last: Neuberg

first: Richard

last: Stone

last: DeAngelo

first: Anthony

last: Letai

first: Andrew

last: Lane

first: Jacqueline

last: Garcia