title: Targeting the ADAR1 p150 isoform triggers tumor growth inhibition and antitumor immunity to overcome immunotherapy resistance

city: Shanghai

first: Zhichao

last: Ai

state: Shanghai

address: 371 Lishizhen Road

department: Oncology

institute: China Innovation Center of Roche (CICoR)

summary: Cancer immunotherapy efficacy is often limited by primary and acquired resistance. The RNA- editing enzyme ADAR1 has emerged as a key regulator of tumor immune evasion, yet therapeutic targeting is challenged by the essential physiological roles of its constitutively expressed p110 isoform. Here, we identify the interferon-inducible p150 isoform and its Zα domain as a critical therapeutic vulnerability. We demonstrate that ADAR1 p150 is frequently overexpressed in human cancers and correlates with an immunosuppressive tumor microenvironment. Genetic ablation of ADAR1 p150 intrinsically inhibits tumor proliferation and extrinsically triggers a robust type I interferon response and profound remodeling of the tumor immune landscape, converting immunologically "cold" tumors to "hot." Furthermore, we establish that myeloid-specific ADAR1 deletion synergizes with anti-PD-1 therapy by enhancing antigen presentation and fostering a pro-inflammatory microenvironment. Crucially, we delineate the Zα domain as the essential structural determinant for dsRNA editing selectivity. Targeted disruption of this domain alone, without affecting the catalytic deaminase domain, is sufficient to recapitulate the potent antitumor effects of complete ADAR1 ablation, leading to accumulation of immunogenic dsRNA, activation of cytosolic sensors (MDA5/PKR), and potent anti-tumor immunity. Our work provides a compelling rationale for selectively targeting the ADAR1 p150-Zα axis to reverse malignant RNA editing and overcome resistance to immunotherapy, offering a refined strategy with a potentially superior therapeutic index.

overall_design: We performed 150bp paired-end RNA-seq on 2 biological replicates of WT vs KO cells_x000D_

first: Yuying

first: Gang


title: Targeting the ADAR1 p150 isoform to overcome immunotherapy resistance

status: Public on Apr 12 2026

country: China

type: Expression profiling by high throughput sequencing

summary: Cancer immunotherapy efficacy is often limited by primary and acquired resistance. The RNA-editing enzyme ADAR1 has emerged as a key regulator of tumor immune evasion, yet therapeutic targeting is challenged by the essential physiological roles of its constitutively expressed p110 isoform. Here, we identify the interferon-inducible p150 isoform and its Zα domain as a precise therapeutic vulnerability. We demonstrate that ADAR1 p150 is frequently overexpressed in human cancers and correlates with an immunosuppressive tumor microenvironment. Genetic ablation of ADAR1 p150 intrinsically inhibits tumor proliferation and extrinsically triggers a robust type I interferon response and profound remodeling of the tumor immune landscape, converting immunologically "cold" tumors to "hot." Furthermore, we establish that myeloid-specific ADAR1 deletion synergizes with anti-PD-1 therapy by enhancing antigen presentation and fostering a pro-inflammatory microenvironment. Crucially, we delineate the Zα domain as the essential structural determinant for dsRNA editing fidelity. Targeted disruption of this domain alone, without affecting the catalytic deaminase domain, is sufficient to recapitulate the potent antitumor effects of complete ADAR1 ablation, leading to accumulation of immunogenic dsRNA, activation of cytosolic sensors (MDA5/PKR), and potent anti-tumor immunity. Our work provides a compelling preclinical rationale for selectively targeting the ADAR1 p150-Zα axis to reverse malignant RNA editing and overcome resistance to immunotherapy, offering a refined strategy with a potentially superior therapeutic index.

overall_design: There are 4 mouse samples, consisting of tumour samples collected from mouse beared with WT or Za mutant MC38 colon adenocarcinoma treated with anti-PD1 therapy, with whole tissue single cell sequencing.


title: Lineage plasticity of the integrated stress response is a hallmark of lung cancer evolution. [RNA-Seq]

city: Montréal

first: Antonis

last: Koromilas

state: QC

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

country: Canada

institute: Lady Davis Institute - McGill University

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

overall_design: To investigate the role of integrated stress response, specifically p-eIF2, in LUAD evolution, we conducted scRNA-seq on GFP+/CD45- lung tumor cells isolated by Fluorescence-Activated Cell Sorting (FACS). The isolated tumor cells were treated with siCHCHD10 or shATF4 and then subjected to RNA-seq.

first: Shiqi

last: Diao

first: Jia

last: Zou

middle: E


title: Gene expression in Erm-minus and Erm-proficient Staphylococcus aureus strains under sublethal and lethal doses of erythromycin

city: Chicago

first: Mee-Ngan

middle: F.

last: Yap

state: IL

address: 320 E Superior St

department: Microbiology-Immunology

country: USA

institute: Northwestern University Feinberg School of Medicine

summary: Differential gene expression between five S. aureus strains were determined by RNA-seq. The five strains are ermB_minus parental JE2(WT), ermB_proficient strain (ALS77),  ermB_proficient delta_rae1 mutant (ALS101), ermB_minus delta_purR mutant (MNY221), and ermB_proficient delta_purR mutant (ALS97).

overall_design: Investigate how inactivation of purR and rae1 in Staphylococcus aureus promotes macrolide resistance with and without erythromycin exposure

first: Alexandre

last: Le Scornet

first: Jonathan

last: Winkelman

middle: F


title: Laurocapram inhibits Salmonella infection via dual mechanisms

city: changchun

first: rundong

last: shu

address: xinzhu road

institute: jilin university

summary: In response to the escalating challenge of antibiotic resistance, this study aims to explore novel antimicrobial agents, and we demonstrated that Laurocapram inhibits intracellular replication of Salmonella; to investigate its mechanism, we conducted RNA sequencing (RNA-seq) on murine macrophage-like RAW264.7 cells under four conditions: untreated control, Laurocapram treatment alone, Salmonella Typhimurium infection, and S. Typhimurium infection with concurrent Laurocapram treatment, with the goal of identifying key host genes and cellular pathways manipulated by the pathogen during infection and elucidating how Laurocapram counteracts Salmonella infection by modulating these targets.

overall_design: The experiment consisted of four treatment groups: Control(B), LRP-treated (Y), S. Typhimurium-infected (X), and S. Typhimurium-infected with LRP treatment (D).

first: Rundong

first: Hongtao

last: Liu

first: Jiazhang

last: Qiu


title: High-resolution spatial transcriptomics of DARLIN mouse [CRISPR array amplicon]

city: Hangzhou

first: Li

last: Li

state: Zhejiang

address: Shilongshan ST #18, Xihu District

institute: Westlake University

summary: Spatially-resolved single-cell lineage tracing is a powerful approach for studying cell lineages and fate decisions in situ. However, existing studies are limited to specific cell types such as lymphocytes and cancer cells. We recently developed DARLIN, a lineage tracing mouse model that has massive lineage barcodes and efficient barcode recovery. Here, we present Spatio-DARLIN, a generic spatial lineage tracing tool that integrates sequencing-based spatial transcriptomics with DALRIN mouse. Applying it to the small intestine, we observed a high-quality transcriptome with nearly single-cell resolution and recovered ~25% cells with reliable lineage barcodes, resulting in ~7000 clones with >1 cell per tissue section. These clones showed highly reproducible spatial localization across adjacent tissue sections, confirming their accuracy. With this high-throughput approach, we observed that intestinal epithelial clones were localized along the crypt-villus axis and underwent vertical expansion over a longer tracing period. Since DARLIN is publicly available and labels cells across most tissues, Spatio-DARLIN offers an accessible and efficient approach for spatial lineage tracing across various mouse tissues with high resolution.

overall_design:
DARLIN mice were generated by crossing homozygous Col1a1tetO-Cas9–TdT-gRNAs:Rosa26M2-rtTA mice with Col1a1CA:TigreTA:Rosa26RA mice, which were maintained separately.
For the proof-of-concept experiment, one 8-week-old DARLIN mouse was administered doxycycline (Dox) for one week, and the proximal small intestine was collected one week after Dox induction.
For the time-course experiment, two 4-week-old DARLIN mice were treated with Dox for one week, and proximal small intestines were collected at 2 and 3 weeks after Dox induction, respectively.
For the clone verification experiment, one 8-week-old DARLIN mouse was induced with Dox for one week, and the small intestine was collected one week post-induction, then dissected into proximal, middle, and distal regions. Three adjacent tissue sections (20 μm apart) from the middle region were collected for spatial transcriptomics.
For the brain development application, one E10 DARLIN mouse was induced with Dox for 12h, and the brain was collected after 8 weeks (7 weeks old) post-induction.

first: Jianing

last: Gao

first: Daolong

last: Chen

first: Zhanhao

last: Zhang

first: Shouwen

last: Wang


title: High-resolution spatial transcriptomics of mouse intestine [Spatial-RNAseq]

overall_design:
DARLIN mice were generated by crossing homozygous Col1a1tetO-Cas9?TdT-gRNAs:Rosa26M2-rtTA mice with Col1a1CA:TigreTA:Rosa26RA mice, which were maintained separately.
For the proof-of-concept experiment, one 8-week-old DARLIN mouse was administered doxycycline (Dox) for one week, and the proximal small intestine was collected one week after Dox induction.
For the time-course experiment, two 4-week-old DARLIN mice were treated with Dox for one week, and proximal small intestines were collected at 2 and 3 weeks after Dox induction, respectively.
For the clone verification experiment, one 8-week-old DARLIN mouse was induced with Dox for one week, and the small intestine was collected one week post-induction, then dissected into proximal, middle, and distal regions. Three adjacent tissue sections (20??m apart) from the middle region were collected for spatial transcriptomics.
For the brain development application, one E10 DARLIN mouse was induced with Dox for 12h, and the brain was collected after 8 weeks (7 weeks old) post-induction.


title: SIRT6 Overexpression Counteracts Chromatin Aging [RNA-Seq]

city: Ramat-Gan

first: Haim

middle: Yosef

last: Cohen

address: Max & Anna Webb

country: Israel

institute: Bar-Ilan University

summary: Aging is associated with detrimental changes in chromatin structure and gene expression, contributing to inflammation, metabolic decline and tissue dysfunction. SIRT6, a histone deacetylase, plays a key role in maintaining chromatin integrity and promoting longevity. Here, we show that aging leads to increased chromatin accessibility in the murine liver, accompanied by upregulation of inflammation and downregulation of metabolic pathways. Remarkably, SIRT6 overexpression reversed these changes, reducing inflammation and enhancing metabolic function. Notably, ETS family members were enriched in regions with increased accessibility during aging, while liver-enriched transcription factors (LETFs) were enriched in regions with reduced accessibility. ChIP-seq analyses of H3K9ac and H3K56ac binding showed that H3K9ac, but not H3K56ac, is associated with increased accessibility during aging, and that SIRT6 can reverse this effect. Furthermore, AAV-mediated SIRT6 overexpression in aged mice demonstrated that SIRT6 not only slows age-related chromatin changes but can also reverse them, rejuvenating chromatin accessibility to a youthful state.

overall_design: RNA-seq of liver from WT and SIRT6 tg, young (5-7 mo) and old (18-21 mo) mice

first: Ron

last: Nagar

first: Zacharia

last: Scwartz

middle: Y


title: GPR56 as a Key Modulator of the Androgen-Responsive Transcriptome in Prostate Cancer Cells

city: Gurugram

first: Gargi

last: Bagchi

state: HARYANA

address: Amity University Haryana. Amity Education Valley Gurugram (Manesar), Haryana 122 413

country: India

institute: Amity University Haryana

summary: To investigate the role of GPR56 in androgen-mediated gene regulation, RNA sequencing was performed in LNCaP (prostate cancer cells) wild-type or GPR56-knockdown (LNCaP cells transfected with GPR56 siRNA, GPR56-KD), following testosterone stimulation. Transcriptomic analysis revealed extensive androgen-responsive gene expression in LNCaP-WT cells, including established androgen target genes, which was markedly reduced upon GPR56 knockdown. These findings suggest that GPR56 is required for optimal androgen response of androgen-dependent transcriptome in prostate cancer cells.

overall_design: LNCaP cells were transiently transfected with GPR56 or scrambled siRNA and subsequently treated with 10nM testosterone. Each experimental group consisted of three biological replicates (3 different Batches). High-quality total RNA was isolated, assessed for integrity, and DNase-treated prior to library preparation. A small aliquot from each batch was used to check GPR56 expression. RNA sequencing was performed on an Illumina HiSeq 2500 platform to generate single-end reads for transcriptomic analysis from each batch.

last: Bagchi*

first: Versha

last: Dahiya

first: Ravi

last: Sharma


title: SIRT6 Overexpression Counteracts Chromatin Aging [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ATAC-seq of liver from 24 months old mice injected with AAV8 SIRT6 or GFP for hepatocyte specific expression


title: hnRNPC engages mature RNAs during metaphase: RNA-seq and fCLIP in proTAME-arrested HeLa/HeLa S3 cells

city: Tel Aviv

first: Daniel

last: Benhalevy

address: Chaim Levanon St 55

institute: Tel Aviv University

summary: Proper progression through mitosis requires coordinated changes in RNA metabolism, but the specific contributions of individual RNA-binding proteins remain unclear. Heterogeneous nuclear ribonucleoprotein C (hnRNPC) is a ubiquitous RBP that normally binds uridine-rich sequences to influence pre-mRNA processing and stability. Here we investigated the role of hnRNPC in mitotic cells by profiling both global RNA abundance and hnRNPC–RNA interactions during metaphase arrest. To this end, we combined bulk RNA-seq with fluorescent crosslinking and immunoprecipitation (fCLIP) in proTAME-arrested HeLa S3 cells. This dataset enables the characterization of hnRNPC binding to mature RNAs during mitosis, the evaluation of biochemical fractionation (low-density vs high-density complexes), and the assessment of binding site resolution across distinct RNase digestion conditions. Together, the study provides a resource for exploring how hnRNPC contributes to RNA stability and gene expression control during cell division

overall_design: proTAME-arrested HeLa cells: (i) Total extract RNA-seq (2 replicates), (ii) Low-density hnRNPC fCLIP (2 replicates), (iii) High-density hnRNPC fCLIP (2 replicates). fCLIP replicates were performed using different RNase I concentrations (low RNase 0.015U/µL and high RNase 0.15U/µL).

first: Liat

last: Lev-Ari

first: Sandra

last: Laster

first: Andrea

last: Atzmon

last: Blumenkrants

first: Orna

last: Elroy-Stein


title: Effects of PAK4 deficiency on the transcriptome of hepatic stellate cells

city: Jeonju

first: Chang Yeob

last: Han

address: 20, Geonji-ro, Deokjin-gu

department: School of Pharmacy

country: South Korea

institute: Jeonbuk National University

summary: Hepatic stellate cell (HSC) activation plays a pivotal role in the progression of liver fibrosis. We investigated how the loss of p21-activated kinase 4 (PAK4), an emerging therapeutic target, influences key features of HSCs. To elucidate the underlying molecular mechanisms, we carried out RNA-sequencing using PAK4-deficient HSCs.

overall_design: During HSC activation, PAK4 expression was silenced through siRNA-mediated knockdown, and subsequent RNA-sequencing analysis was performed.

first: Gil-Hwan

last: Kim

first: Hyunsoo

last: Rho


title: A Pilot Phase II Study of Neoadjuvant Fulvestrant plus Abemaciclib in Women with Advanced Low-Grade Serous Carcinoma

city: Houston

first: Sanghoon

last: Lee

state: TX

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

summary: Neoadjuvant chemotherapy shows limited activity in low-grade serous carcinoma of the ovary, fallopian tube, and peritoneum (LGSOC). Given LGSOC’s similarities to hormone receptor-positive (HR+) breast cancer, including clinical benefit from endocrine therapies, we conducted a phase II pilot study to assess the clinical benefit of neoadjuvant treatment with fulvestrant and abemaciclib for women with advanced LGSOC. Women with untreated, unresectable stage III or IV LGSOC were eligible. Patients received fulvestrant (500 mg IM on day 1 and 15 of the first 28-day cycle, then day 1 of subsequent cycles) and abemaciclib 150 mg orally BID. Pre/perimenopausal patients received goserelin 10.8 mg subcutaneously every 12 weeks for ovarian suppression. Imaging re-assessment was performed every 8 weeks using RECIST 1.1 until deemed resectable. Following interval cytoreductive surgery (ICS), patients received 4 cycles of adjuvant fulvestrant and abemaciclib followed by maintenance letrozole. Patients with progressive disease were removed from the study and received standard chemotherapy. The primary endpoint is best overall response clinical benefit rate (BOR CBR). Fifteen patients were enrolled and evaluable for efficacy. BOR CBR in the neoadjuvant setting was 100%, with 9/15 patients (60%) achieving partial response (PR), and 6/15 patients (40%) showing stable disease (SD). One patient with radiologic PR had pathologic complete response at ICS. Nine of fifteen patients (60%) underwent ICS – 5 (55.5%) with complete gross resection, 2 (22.2%) with <1cm residual disease, and 2 (22.2%) with suboptimal cytoreduction. Median time on study prior to surgery was 8.38 months. Neoadjuvant treatment with fulvestrant and abemaciclib was tolerable and demonstrated unprecedented response and CBR rates in this pilot study. These results compare favorably with published outcomes of neoadjuvant chemotherapy in LGSOC.

overall_design: Three pairs of pre- and post-treatment samples were subject to RNA sequencing.

first: Yibo

last: Dai

first: Linghua

last: Wang

first: Lauren P.

last: Cobb

first: Amir A.

last: Jazaeri


title: METTL3-Driven RNA Modifications: A Key Mechanism and Potential Therapeutic Target in Pancreatic Acinar Cell Carcinoma in Mice [MeRIP]

city: Suita

first: Shotaro

last: Tatekawa

state: Osaka

address: 2-2(D10), Yamadaoka, Suita-city

department: Departments of Radiation Oncology,

country: Japan

institute: The University of Osaka Graduate School of Medicine

summary: Pancreatic acinar cell carcinoma (ACC) represents a rare and aggressive malignancy with poorly understood molecular mechanisms. N6-methyladenosine (m6A) RNA modification, particularly through the methyltransferase METTL3, has emerged as a critical regulator in various cancers. This study investigates the role of METTL3-mediated RNA methylation in ACC development and progression. We utilized transgenic mouse models over-expressing Mettl3 and SV40 large T antigen under the pancreatic Elastase I promoter. Comprehensive analyses included m6A-methylated RNA immunoprecipitation sequencing (MeRIP-seq), single-cell RNA sequencing (scRNA-seq), and functional studies with the METTL3 inhibitor STM2457. SAM-binding domain deletion mutants were generated to assess functional requirements. Mettl3 overexpression significantly accelerated ACC development and enhanced tumor aggressiveness. The SAM-binding domain proved essential for tumor formation, as deletion mutants failed to promote carcinogenesis. MeRIP-seq revealed preferential methylation of cell cycle and DNA replication genes in Mettl3-overexpressing tumors. scRNA-seq analysis demonstrated enhanced malignancy signatures, including epithelial-to-mesenchymal transition and TGF-β signaling. METTL3 promoted PRSS1-mediated signaling from ACC cells to inflammatory cancer-associated fibroblasts, creating a feed-forward loop involving IGF1 that amplifies tumor growth. Conditional Mettl3 deletion induced rapid tumor apoptosis. Pharmacological inhibition with STM2457 similarly triggered caspase-3/7-dependent apoptosis in pancreatic tumors. METTL3-mediated RNA methylation drives ACC pathogenesis through tumor-intrinsic cell cycle regulation and tumor-extrinsic stromal interactions. These findings establish METTL3 as a promising therapeutic target and provide mechanistic insights supporting clinical development of METTL3 inhibitors for pancreatic cancer treatment.

overall_design: RIP-seq data using m6A antibody for the following mouse tumor and liver samples: Kras/Mettl3, TAg/Mettl3, TAg/Mettl3-depleted, and TAg

first: Tomoaki

last: Hara

first: Sikun

last: Meng

first: Tetsuya

last: Sato

first: Hideshi

last: Ihii


title: Spinal cord regeneration deploys cell-type specific developmental and non-developmental strategies to restore neuron diversity

status: Public on Apr 11 2026

city: Seattle

first: Avery

last: Angell Swearer

state: Washington

address: UW Box 357350, 1705 NE Pacific St.

department: Biochemistry

institute: University of Washington

summary: A major goal of spinal cord injury research is to develop a path to endogenous regeneration. This approach has been heavily informed by animal models of natural regeneration. An unresolved question is whether these models rebuild the spinal cord by exclusively accessing developmental mechanisms of neuron differentiation. To address this question, we contrasted single-cell gene expression during regeneration with stage-matched controls in the conditionally regenerative frog Xenopus tropicalis. We generated an expanded atlas of neuronal diversity, annotating several neurons in Xenopus for the first time. From this atlas, we found that the neuron composition of the developing and regenerating spinal cord differ. So do the strategies employed, which favor waves of early cell-type specific neurite projection and guidance, then later proliferative neurogenesis during regeneration. Low levels of early neurogenesis are then compensated by movement of post-mitotic neurons. Our work highlights the use of distinct developmental versus regenerative paths to heal post-injury.

overall_design: Aggregated FASTQ file of 8 single-cell RNA Sequencing samples from Xenopus tropicalis tadpoles: tail tip, uninjured 1 day post amputation (un1dpa), un3dpa, un7dpa, mid-trunk, injured 1 day post amputation (1dpa), 3dpa, and 7dpa. tail tip/mid-trunk was collected at stage 41, and following stages were collected at indicated timepoints. Samples were dissociated, FACs for pax6:GFP+ cells, and processed using 10X Genomics GEM-X v4 before sequencing with Illumina. Samples were aggregated using CellRanger.

first: Angell Swearer

last: Avery

first: Samuel

last: Perkowski

first: Iba

last: Husain

first: Thiago

last: Figueiredo

first: Morgan

last: McCartney

last: Wills


title: SIRT6 Overexpression Counteracts Chromatin Aging [ChIP-Seq]

first: Haim

last: Cohen

overall_design: H3K9ac, H3K56ac and H3K27ac ChIP-seq of liver from WT and SIRT6 tg, young (5-7 mo) and old (18-21 mo) mice

first: Ron

last: Nagar

first: Zacharia

last: Scwartz


title: METTL3-Driven RNA Modifications: A Key Mechanism and Potential Therapeutic Target in Pancreatic Acinar Cell Carcinoma in Mice [scRNA]

overall_design: Single-cell RNA-seq data for the following mouse tumor samples: WTg (TAg/Mettl3) and EL (TAg)


title: The role of PurR purine transcriptional repressor and Rae1 endoribonuclease in Erm-mediated macrolide resistance in methicilin-resistant Staphylococcus aureus.

first: Mee-Ngan

last: Yap

summary: Differential gene expression between six S. aureus strains were determined by RNA-seq in 3 biological replicates.The six strains are ermB_minus parental JE2(WT), ermB_proficient strain (KES29), ermB_minus rae1 mutant (MNY205), ermB_proficient rae1 mutant (MNY212), ermB_minus purR mutant (MNY221), and ermB_proficient purR mutant (MNY224). Two culture media were used: A indicates tryptic soy broth (TSB), B indicates RPMI_1640 supplemented with 1% casamino acids.

overall_design: Investigate how inactivation of purR and rae1 in Staphylococcus aureus promotes macrolide resistance.

first: Alexandre

last: Le Scornet


title: Leukaemia cell intrinsic and extrinsic factors cooperate to facilitate the survival and proliferation of KMT2A-rearranged B-ALL in the CNS niche.

city: Edinburgh

first: Alasdair

last: Duguid

address: 5 Little France Drive

department: Institute for Regeneration and Repair

country: United Kingdom

institute: University of Edinburgh

summary: Infant B-cell acute lymphoblastic leukaemia (B-ALL) is a rare, aggressive entity characterised by KMT2A-rearrangements and poor outcomes. One of the unique features of KMT2A-rearranged infant ALL contributes to these poor outcomes is a particularly high rate of central nervous system (CNS) involvement. In this study we used an immune competent KMT2A-AFF1+ infant B-ALL murine model (https://doi.org/10.1182/blood.2020006610) to explore the cell-intrinsic and cell-extrinsic mechanisms that underpin this clinically significant complication. We show novel functional impacts on leukaemia propagating cells (LPCs) following exposure to the CNS niche which results in unique leukaemia repopulation dynamics. Transcriptomic and immune cell profiling comparisons by niche showed differences in the immune microenvironment between the CNS and bone marrow (BM) niches. We observe the CNS niche demonstrates supressed T cell and macrophage activity which may be part of a wider CNS niche-specific immune escape mechanism. Our transcriptomic comparisons by niche also led us to explore the role of PI3K pathway activation in the propagation of leukaemia cells within the CNS niche. We identify miR-93 as a possible master regulator of this process. The importance of miR-93 is emphasised as it is shown to be upregulated in CNS leukaemia cells across multiple murine KMT2A-AFF1 B-ALL model systems and in primary KMT2A-AFF1 B-ALL patient samples. We conclude by showing impaired CNS engraftment of leukaemia cells upon miR-93 knockdown, cementing its importance in CNS leukaemia biology.

overall_design: BM and CNS cells from miR-128a overexpression Kmt2a-AFF1+ mouse model of infant pro-B ALL, described in Malouf et al. 2021, were harvested. These cells were FACS-sorted into different LPC populations (LSK-IL7R+: Lin- Sca1+ cKit+ IL7R+ and LK/CLP: Lin- Sca1- cKit+) for RNA extraction and bulk sequencing. Transcriptomic comparisons were made by LPC type and by niche.

first: Camille

last: Malouf

first: Katrin

last: Ottersbach


title: Endothelial Parkin safeguards coronary microcirculation in myocardial ischemia/reperfusion injury

city: wenzhou

first: jia

last: sun

address: 109 Xueyuan West Road, Lucheng District,

institute: The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University

summary: Gaining a deeper insight into the signals and molecular mechanisms that govern the function of coronary endothelial cells after MI/R could pave the way for the discovery of new preventative and therapeutic approaches. The functional role of Parkin in coronary microvascular injury in response to MI/R is unclear. Here, we investigated the upstream regulators and downstream effectors of Parkin against MI/R damage and examined the underlying mechanisms.

overall_design: we performed RNA sequencing analysis of MI/R and Sham mouse hearts between WT and endothelial cell-specific Parkin knockout mice

first: Chao

last: Niu

first: Jia

last: Sun


title: Transcriptomic and Accessibilty characterization of Wild type mouse Embryonic Stem Cells (mESCs),  β-actin Knock out mESC and upon rescue with a nuclear localization signal  β-actin

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: abu dhabi

address: NYUAD Saadiyat Island

country: United Arab Emirates

institute: Biology

summary: Pluripotency and lineage commitment in embryonic stem cells depend on coordinated regulation of chromatin architecture and extracellular matrix (ECM) signaling. Here, we identify nuclear β-actin as a key regulator linking these processes in mouse embryonic stem cells. Loss of β-actin disrupts core pluripotency factors, including Oct4 and Sox2, and causes broad transcriptional changes, while nuclear re-expression rescues these defects. Chromatin accessibility analysis revealed reduced accessibility at regulatory regions of pluripotency genes, consistent with impaired chromatin remodeling. β-actin depletion also altered ECM-related gene expression, matrix properties, and cellular biomechanics, leading to impaired self-renewal, skewed lineage specification, and defective differentiation, particularly reduced neuronal potential and increased mesodermal-like fate bias. In vivo, β-actin loss restricted teratoma growth and compromised tri-lineage differentiation. Together, these results define nuclear β-actin as an important regulator of chromatin accessibility, ECM-dependent signaling, and stem cell fate.

overall_design: ATAC seq of WT, beta actin KO, and NLS  for mouse Embryonic stem cells.

first: Nadine

last: Hosny El Said

first: Colin

last: Campbell

first: Amani

last: Nuairi

first: Sabrina

last: Desbordes


title: Polymicrobial extracellular vesicles reduce the innate immune response of human cystic fibrosis bronchial epithelial cells

city: Hanover

first: Lily

last: Charpentier

state: New Hampshire

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

type: Non-coding RNA profiling by high throughput sequencing

summary: Adults with cystic fibrosis (CF) have chronic antibiotic-resistant polymicrobial lung infections, the leading cause of death in CF. We developed a polymicrobial culture model containing four genera that represents a ‘pulmotype’ detected in ~34% of lung infections in people with CF (pwCF), and accounts for 27% of the variability in lung function. This community, comprised of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis, and Prevotella melaninogenica, is grown in synthetic CF media (SCFM2) under anoxic conditions that mimic the environment in mucus plugs in CF. We have shown that Pseudomonas in monoculture communicates with primary human bronchial epithelial cells (pHBEC) by secreting bacterial extracellular vesicles (bEVs) that diffuse through mucus and deliver virulence factors, DNA, and RNA to pHBEC. We report herein that each bacterial genus in the polymicrobial community secretes bEVs containing proteins and RNAs predicted to promote the establishment of chronic infection by enhancing virulence and biofilm formation, and upregulating the stress response and pro-inflammatory pathways in pHBEC. This response is most pronounced in CF pHBEC. Trikafta, a highly effective drug, does not ameliorate the response or return it to WT levels. Bacterial EVs also inhibited Trikafta-stimulated CFTR Cl- currents by CF pHBEC. These studies provide insight into why Trikafta does not eliminate polymicrobial lung infections and a hyperinflammatory lung environment in pwCF.

sample_organism: Staphylococcus aureus subsp. aureus str. Newman

overall_design: RNA-seq profiling of bacterial extracellular vesicles from a polymicrobial culture containing Pseudomonas aeruginosa PA14, Staphylococcus aureus Newman, Streptococcus sanguinis SK36, and Prevotella melaninogenica ATCC 25845.

middle: A

first: Bruce

last: Stanton


title: Multimodal Transcriptomic Profiling of T Cell Responses to Triple-Negative Breast Cancer-Derived Exosomes

city: Indiana University

first: Reza

last: Shahbazi

address: 980 W Walnut st

institute: Indiana University

summary: Triple-negative breast cancer (TNBC) is a highly aggressive and immunogenic subtype that lacks effective targeted therapies. Although tumor-derived exosomes are known to influence immune responses, their direct role in shaping human T cell plasticity and antigen specificity remains insufficiently characterized. In this study, we performed an integrative single-cell multiomic analysis of primary human T cells following exposure to exosomes isolated from 17 genomically distinct TNBC cell lines. By combining single-cell transcriptomics, T cell receptor (TCR) V(D)J sequencing, non-coding RNA profiling, and both bulk and single-cell cytokine analyses, we identified conserved and subtype-specific immunoregulatory programs elicited by TNBC-derived exosomes.

overall_design: Single-cell RNA sequencing and TCR V(D)J profiling were performed on primary T cells from 17 exosome-treated samples and one untreated control. Non-coding RNA profiles were obtained from exosomes isolated from 17 triple-negative breast cancer (TNBC) cell lines. Additionally, plasma-derived exosomes were isolated from 28 breast cancer patients and 7 healthy donors to evaluate circulating exosomal non-coding RNA signatures.

first: Samaneh

last: Maleknia

first: Sanam

last: Rezaei Benam

first: Kent

last: Williams

first: Lionel

last: Apetoh


title: Increased competition for eIF4 factors or 40S ribosomal subunits disfavors translation preinitiation complex assembly on poorly translated mRNAs with high G/A nucleotide ratios in 5’ leaders

status: Public on Apr 13 2026

city: Bethesda

first: Jon

middle: R.

last: Lorsch

state: MD

address: 49 Convent Dr Building 49 RM 2C08

department: NICHD

institute: NIH

summary: The ribosome concentration model (RCM) posits that reducing the concentration of ribosomal subunits re-programs translation initiation to favor mRNAs with high rates of 48S preinitiation complex (PIC) assembly over mRNAs with low assembly rates.  We tested the RCM using the yeast reconstituted initiation system by measuring PIC assembly on all native mRNAs in parallel (Rec-Seq) at different 40S subunit concentrations. We found broad agreement with the RCM, as mRNAs with the largest decreases in PIC assembly when 40S subunits became limiting tend to be the least efficient in PIC assembly at the lowest [40S]/[mRNA] ratio. Likewise, reductions in PIC assembly at limiting 40S in Rec-Seq correlated with translational efficiencies (TE) of mRNAs in WT yeast determined by ribosome profiling (Ribo-Seq). Conclusions in line with the RCM also emerged from Rec-Seq conducted in the absence or presence of mRNA-recruitment factors eIF4E-eIF4G or eIF4B and by Ribo-Seq analysis of a tif3Δ mutant lacking eIF4B, wherein mRNAs least efficient for PIC assembly or translation in absence of the factor generally showed the greatest impairment when it is missing . Remarkably, occurrence of G nucleotides in 5’UTRs is associated with low PIC assembly and TE in vivo and confers heightened sensitivity to limiting 40S, eIF4E-eIF4G, eIF4B or eIF4A in Rec-Seq reactions, and to the elimination/depletion of eIF4B and eIF4E in vivo. We speculate that G residues impede processive ribosomal scanning in a manner overcome by eIF4 factors and high rates of 43S PIC attachment at mRNA 5’ ends.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae BY4741

overall_design: we tested the recruitment of yeast total mRNA at different 40S ribosome concentrations (5 nM, 15 nM, 30 nM and 60 nM) and also eIF4G/eIF4E concentrations (0 nM, 5 nM, 15 nM, 60 nM, 120 nM and 240 nM) and conditions with or without 300 nM eIF4B.

first: Fujun

last: Zhou

first: Meizhen

last: Hou

middle: R

first: Alan

middle: G

last: Hinnebusch


title: SIRT6 Overexpression Counteracts Chromatin Aging [ATAC-Seq_tg]

first: Haim

last: Cohen

overall_design: ATAC-seq of liver from WT and SIRT6 tg, young (5-7 mo) and old (18-21 mo) mice

first: Ron

last: Nagar

first: Zacharia

last: Scwartz


title: Lenvatinib exacerbates colitis by inhibiting intestinal vascular endothelial MAdCAM-1-mediated B cell trafficking.

first: Fang

last: Yue

address: No. 866 Yuhangtang Road

institute: Zhejiang University

summary: The use of lenvatinib (Lenv) in advanced hepatocellular carcinoma (HCC) patients is associated with a range of adverse events, including gastrointestinal toxicities, yet the underlying mechanisms remain poorly understood. Here, we demonstrated that Lenv exacerbated both acute and chronic colitis in mouse models by impairing intestinal B cell homeostasis, leading to reduce intestinal B cells and plasma cells, along with decreased IL-10 and IgA secretion. Mechanistically, Lenv decreased MAdCAM-1 expression in intestinal vascular endothelial cells via the VEGFR/PLCγ/PKC/p65 signaling, thereby disrupting B cell homing to the gut. Notably, blockade of either p65 or MAdCAM-1 abrogated Lenv-induced B cell loss and colitis exacerbation. Furthermore, in both tumor-bearing mice and HCC patients receiving Lenv treatment, decreased serum sMAdCAM-1 levels correlated with reduced serum IgA and disruption of intestinal immune homeostasis. Thus, our results show a mechanism for Lenv disrupts intestinal immune homeostasis and implicate serum sMAdCAM-1 may serve as a potential biomarker for monitoring B cell-mediated intestinal immune dysfunction during Lenv therapy.

overall_design: RNA-seq profiling of B cells sorted from colons of mice received dmso and lenvatinib treatment


title: Lenvatinib exacerbates colitis by inhibiting intestinal vascular endothelial MAdCAM-1-mediated B cell trafficking

overall_design: RNA-seq profiling of colon of mice received dmso and lenvatinib treatment


title: Gene expression in whole seedlings (wild-type, nlp6nlp7-KO)

city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

state: Tokyo

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

institute: The University of Tokyo

summary: To examine differential effect of the mutation of Arabidopsis NLP6 and NLP7 on the gene expressions, we performed microarray analysis using root tissue of seedlings of wild-type and nlp6nlp7 double mutant.

overall_design: whole seedlings from 9 day-old wild-type and nlp6nlp7-KO seedlings grown under potassium-sufficient and potassium-defficient conditions

first: Shuichi

last: Yanagisawa


title: Genome-Wide Dual-Selection Unveils Novel Self-Cleaving Ribozymes in the Human Genome

city: Shenzhen

first: Zhe

last: Zhang

state: Guangdong

address: Gaoke Innovation Center

department: Institute of Physical and Systems Biology

institute: Shenzhen Bay Laboratory

summary: The landscape of catalytic RNAs in complex eukaryotes remains poorly charted. Although self-cleaving ribozymes are widespread in microbial and viral genomes, their existence and functional roles in humans remain largely unknown. Here, we introduce a generalizable, genome-wide discovery platform that integrates high-throughput signals from two complementary adapter ligation assays—3P-seq and 5OH-seq—to specifically capture RNA fragments bearing cleavage signatures (2′,3′-cyclic phosphate/3′-phosphate and 5′-hydroxyl termini). By applying a dedicated computational scoring algorithm to human genomic data, we systematically identified four previously unrecognized self-cleaving ribozymes. These ribozymes localize to diverse genomic features: an exon of WDFY1, an intron of PLD5 embedded within a repetitive element, an LTR retrotransposon, and the antisense strand of an SYNJ2BP intron. Truncation analyses and mutational profiling defined minimal functional cores of 21–55 nucleotides, and experiment-assisted secondary structure prediction suggests that they adopt simple structural architectures. Despite their short sequences and simple architectures, we demonstrated that these ribozymes possess robust cleavage activity under multiple biochemical conditions. Most importantly, our experimental results indicate that three of them exhibit significant self-cleavage activity within the cellular environment. Our work establishes a powerful strategy for genome-wide mining of self-cleaving ribozymes, expands the catalogue of human ribozymes from 6 to 10, and reveals new layers of functional complexity in the human RNA world.

overall_design: To profile RNA cleavage products, we generated a protease/RNase-free genomic RNA library through in vitro transcription. RtcB ligase and terminally modified RNA linkers were utilized to selectively capture and distinguish fragments bearing 2′,3′-cyclic phosphate or 5′-OH ends, followed by streptavidin bead enrichment and sequencing library construction. The newly identified ribozyme sequences were used for subsequent mutational‑scanning experiments. A random mutagenesis library was generated using a commercial Random Mutagenesis Kit. Barcode sequences were appended to the library in three PCR cycles. Approximately 10⁶ barcoded molecules were used as template to amplify the final mutant DNA library. The final mutant DNA library served as template for constructing the DNA‑seq library. The barcoded DNA library was transcribed with T7 RNA Polymerase. In vitro transcribed RNA was reverse transcribed with template‑switch oligo. The purified cDNA was used as the template for RNA-seq library amplification.

first: Jian

last: Zhan

first: Yaoqi


first: Lily

last: Charpentier

overall_design: RNA-seq profiling of WT and CF primary human bronchial epithelial cells treated with either polymicrobial bacterial extracellular vesicles or processed control.

first: Bruce

last: Stanton


title: Blocking NKp46-CCR6-ILC3 autophagy alleviates necrotizing enterocolitis by restoring energy metabolism balance [RNA-seq]

city: Guangzhou

first: Junyu

last: He

address: School of Basic Medicine, Southern Medical University, Guangzhou

institute: School of Basic Medical Sciences, Southern Medical University

summary: Group 3 innate lymphoid cells (ILC3s) play a crucial role in intestinal inflammatory disorders such as necrotizing enterocolitis (NEC) in neonates; however, the mechanisms by which ILC3s contribute to NEC remain unclear. In this study, single-cell transcriptomics, in vivo experiments on T cell-deficient mice, and targeted cell interventions demonstrated that NKp46−CCR6− (double-negative, DN) ILC3 autophagy significantly impacts NEC development by regulating intracellular metabolism. Mice lacking ATG5 or treated with autophagy inhibitors exhibited reduced ILC3 abundance and impaired ILC3 function, alleviating NEC. Mechanistically, ATG5 deficiency enhanced fatty acid metabolism while reducing glycolysis. Conversely, inhibiting fatty acid oxidation or supplementing with lactate restored the quantity and functionality of ATG5-deficient DN ILC3s, exacerbating NEC. Lipid metabolism analyses combined with a mouse model of NEC indicated that phosphatidylcholine supplementation alleviated intestinal inflammation by inhibiting DN ILC3 autophagy. Clinically, patients with NEC showed elevated ILC3 levels and significant enrichment of autophagy genes. These findings highlight the importance of DN ILC3 autophagy in metabolic adaptation, suggesting potential strategies for managing NEC.

overall_design: Comparison of DN ILC3s gene expression between Atg5fl/fl mice and RorccreAtg5fl/fl mice

first: Yumei

first: Yuxiong

last: Guo

first: Kai

last: Wu

first: Laiqin

last: Peng

first: Qiqiong

last: Wang

first: Xinyao

last: Li


title: RNA-seq analysis of pulmonary arterial smooth muscle cells (PASMCs), bronchial smooth muscle cells(BSMCs) and venous SMCs in the lung

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Information about the differences among arterial, venous, and bronchial smooth muscle cells (SMCs) in the lung is particularly valuable, as these distinct SMC populations are differentially affected in pulmonary diseases such as asthma, chronic obstructive pulmonary disease (COPD), and pulmonary arterial hypertension (PAH). To directly compare these SMC subtypes, we employed a combination of genetic tools and fluorescence-activated cell sorting (FACS) isolation strategies.We generated an ASMC-effector mouse line by combining Cspg4/Acta2 intersectional genetics, enabling specific targeting of vascular SMCs, including pulmonary arterial SMCs (PASMCs). To target non-vascular SMCs, including bronchial SMCs (BSMCs), we generated the NVSMC-effector mouse line using Chrm2/Acta2 intersectional genetics. As no driver specific to venous vascular SMCs (VVSMCs) is currently available, we used the transgenic reporter line [Tg(Acta2-GFP)], which labels all pulmonary SMCs, including venous SMCs.

overall_design: To directly compare the different pulmonary SMC types, we isolated PASMCs from ASMC-effector mice, BSMCs from NVSMC-effector mice, and total pulmonary SMCs—including venous SMCs—from [Tg(Acta2-GFP)] mice using FACS.

first: Lei

first: Guenther

last: Stefan

first: Kuenne

last: Carsten

first: Andre

last: Schneider


title: RNA-seq analysis of non-vascular smooth muscle cells (NVSMCs) isolated from the lung, intestine and bladder

summary: None of the currently available Cre recombinase-expressing mouse lines allows for exclusive and specific manipulation of non-vascular smooth muscle cells (NVSMCs). To address this, we focused on the Chrm2 gene, which encodes the M2 muscarinic acetylcholine receptor (M2R), a G protein-coupled receptor (GPCR) previously reported to be expressed selectively in NVSMCs and also in CD45-positive immune cells. In contrast, Acta2 is broadly and strongly expressed in all smooth muscle cells (SMCs), including both vascular and non-vascular populations. To achieve specific labeling of NVSMCs, we generated NVSMC-effector mice by combining Chrm2-Dre with Acta2-Rox-CreER and R26-LoxP-GFP alleles. Following tamoxifen administration, we observed robust GFP fluorescence specifically in NVSMCs of the lung, stomach, and intestine. Notably, GFP labeling was virtually absent in vascular SMCs across multiple organs, confirming the specificity of this genetic strategy.

overall_design: To investigate NVSMC heterogeneity across different tissues, we isolated NVSMCs from the lung, intestine and bladder by fluorescence-activated cell sorting (FACS) and performed RNA sequencing (RNA-seq) analysis.


title: Longitudinal multi-organ transcriptomic atlas of salt-induced hypertension

city: Tampa

first: Ratnakar

last: Tiwari

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida

summary: Salt-sensitive hypertension is a common form of hypertension characterized by an exaggerated blood pressure response to dietary salt intake. The molecular mechanisms linking salt-induced hypertension to multi-organ damage remain poorly defined. To address this issue, we generated a longitudinal multi-organ transcriptomic atlas by performing RNA sequencing on the kidney cortex, kidney medulla, liver, and heart across four stages of hypertension in male Dahl salt-sensitive rats. These data provide a valuable resource for identifying organ-specific transcriptional responses involved in the pathogenesis of salt-induced hypertension.

overall_design: Animals were maintained on a normal-salt diet (0.4% NaCl, #D113755, Dyets Inc.). To induce hypertension, 9- to 11-week-old male Dahl salt-sensitive rats were switched to a high-salt diet (4% NaCl, #D113756, Dyets Inc.) for 7, 14, 21, or 35 days. Multiple tissues were collected at each time point, and extracted RNA was used for sequencing and downstream analysis.

first: Alexander

last: Staruschenko


title: RNA-seq analysis of pulmonary arterial smooth muscle cells (PASMCs) and bronchial smooth muscle cells (BSMCs) after pulmonary arterial hypertension (PAH) treatment

summary: Previous studies to determine transcriptional changes in PASMCs during PAH were affected by the inevitable contamination with BSMCs and venous SMCs.  To specific target ASMCs, we generated an ASMC-effector mouse line by combining Cspg4/Acta2 intersectional genetics, enabling specific targeting of vascular SMCs, including PASMCs. To target non-vascular SMCs, including BSMCs, we generated the NVSMC-effector mouse line using Chrm2/Acta2 intersectional genetics.  The development of ASMC-effector mice, excluding venous and BSMCs, enabled us to avoid such problems and determine PASMC-specific reactions after induction of PAH.

overall_design: Eight-week-old mice were administered tamoxifen (five intraperitoneal injections) to induce Cre-mediated recombination. Twenty-one days after the final tamoxifen injection, mice were randomized into two experimental groups. Mice assigned to the hypoxia group received a single intraperitoneal injection of the VEGFR inhibitor SU5416 (20 mg/kg body weight; Sigma, St. Louis, MO), followed by continuous exposure to hypoxia (10% oxygen) for 21 days. To sustain VEGFR inhibition, two additional doses of SU5416 were administered on days 7 and 14 after the initiation of hypoxia. Control mice received vehicle (DMSO) instead of SU5416 and were maintained under normoxic conditions (21% oxygen) for the same duration. These mice also received two additional doses of vehicle on days 7 and 14 after treatment initiation to match the injection schedule of the hypoxia group. At the end of the 21-day treatment period, PASMCs and BSMCs were isolated using fluorescence-activated cell sorting (FACS) strategies.

first: Maximilian

last: Staps


title: Berry-derived gold nanoparticles induce integrated oxidative stress-mediated apoptosis, immune modulation, and transcriptomic remodeling in 4T1 triple-negative cancer cells

city: Wilmington

first: Oladapo

middle: Fisoye

last: Fagbohun

state: OH

address: 1870 Quaker Way

department: Biology

institute: Wilmington College

summary: Comprehensive molecular and phenotypic characterization of tumor models is still needed for robust understanding of breast cancer mechanisms and therapies. Here, we explore genome, transcriptome, and proteome of treated and untreated 4T1 triple-negative breast cancer cells. Nanoencapsulation (AuNPs) of berry-derived polyphenolic compounds was influenced by limited clinical use due to poor stability and bioavailability. Several physicochemical characterizations employed include TEM, FTIR, and targeted UPLC/MS-QQQ assays. We identified significant mutations to breast cancer-related tumor suppressor genes (Trp53, Brca2, Bard1, Cdh1, Nf1, and Chek2) and deciphered the function consequences leveraging on the higher throughput Illumina NovaSeq X and NextSeq 1000 sequencers and highly accurate predicting power of AlphaFold. We found ~5700000 single nucleotide variations (SNVs) and 329448 indels achieving an important upgrade over previous literature data. Key findings from differentially expressed gene  enrichment analyses (GSEA) revealed positive gene enrichments of DNA repair regulators and TGF-β signaling while having negative enrichments of cell adhesion, cadherin and MAPK signaling via PI3K/AKT/MAPK/Wnt pathways, potentially influencing apoptosis and immune evasion intrinsic to cancer. Notably, decreased expression of PIK3CG, PALLD, PTPRZ1, and CDH8 and increased expression of SEMA6C, WWOX, NHEJ1, and MAML3 suggested suppression of epithelial-to-mesenchymal transition (EMT) and metastatic potential. Further assessment of immunohistochemical, immunofluorescent, and flow cytometric data revealed that berry-derived nanoparticles can modulate oncogenic transcription factors and induce caspase-dependent execution-phase ROS-mediated apoptosis through pPAK1Thr212 dephosphorylation, downregulation of pPI3Kp85αγ(Tyr467/199)/pAKT1Thr450/mTOR signaling, and modulation of pJAK3Tyr785/STAT3 pathway supporting transcriptomic and transcriptional reprogramming of 4T1 treated cells. Together, our findings uncover a new strategy to capture berry-derived polyphenols required to regulate apoptosis, autophagy, immune response, and metastasis-related gene networks in breast cancer thereby underscoring the therapeutic potential of functionalized AuNPs as delivery platforms for dietary phytochemicals.

overall_design: mRNA libraries were prepared using the flowing reagents from QIASeq FastSelect RNA Lib HMR and QIA UX96 Index UDI-B (96) 331825 Kits (Qiagen Inc., Santa Clarita, CA, USA; Cat#: 334235) with primers N6-T RT and ODT-RT. The quality of the libraries was evaluated with fluorometry by DeNovix QFX fluorometer (DeNovix Inc., Wilmington, DE, USA; S/N: S-04083) and with 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA; S/N: DE72903137). A total of 100 ng total RNA was used for the sequencing. Ribosomal RNA was removed by enzymatic digestion and then fragmented for 3 min. The libraries were sequenced with Illumina NovaSeq X plus 10B (Illumina Inc., San Diego, CA, USA), with sequence coverage ranging between PF clusters 35 million to 50 million paired reads. Raw data were converted into FASTQ format, demultiplexed, and filtered for reads passing QC filters. Adapter and low-quality sequences were trimmed and only sequences with Q30 or higher quality were used. RNA Seq FASTQ files were processed and mapped to reference. RNA sequencing reads were aligned to the published Mus musculus reference genome. Mapping rates and coverage statistics of the samples were reported.

first: Adewale

last: Oladipo

first: Chengyu

last: Gao

first: Babatunde

last: Olawoye

first: Rachel

last: Berry

first: Jaylah

last: Captain

first: Olive

last: Iragena

first: Xavier

last: McDougle

first: Randy

last: Harris

first: Amanda

last: Rollins

first: Jitcy

last: Joseph

first: Olatomide

last: Fadare

first: Russell

last: Kincaid


title: Molecular phenotyping of diverse human skeletal muscles with CAGE-Seq

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

summary: Different skeletal muscles have distinct gene expression profiles, yet, in humans, the skeletal muscle transcriptome has been explored only in a few muscle types. In this study, we applied cap analysis of gene expression (CAGE-Seq) to autopsy samples of 75 skeletal muscles and quantitatively profiled thousands of transcribed regulatory elements.

overall_design: 228 autopsy samples were obtained from 76 sites of 4 individuals. The samples correspond to 75 skeletal muscles and septum intermusculare brachii laterale.

first: Andrey

middle: I

last: Buyan

first: Oleg

last: Gusev

first: Guzel

last: Gazizova

first: Elena

last: Shagimardanova

first: Yulia

middle: P

last: Sergeeva

first: Leyla

last: Shigapova


title: PP2A Regulates Senescence and Immunogenicity in Medulloblastoma

city: San Francisco

first: Rongze

middle: Olivia

last: Lu

state: CA

address: 1450 3rd St, 4th floor

department: Department of Neurological Surgery

institute: University of California, San Francisco

summary: Medulloblastoma (MB) is the most common malignant pediatric brain tumor. Current treatments carry significant morbidity, and prognosis remains poor in subgroups with TP53 mutations or relapse, underscoring the need for new therapeutic strategies. Senescence is a tumor-suppressive program disrupted in MB. We hypothesized that restoring senescence through p53-independent mechanisms could be therapeutic. Here, we identify Protein Phosphatase 2A (PP2A) as a key regulator of senescence in MB. Genetic ablation of the PP2A catalytic subunit (PP2Ac) or knockdown of the regulatory subunit PP2A-B56α induces robust senescence in TP53-mutant MB models. Senescent PP2Ac-deficient cells show increased MHC-I expression and enhanced immunogenicity. In a syngeneic orthotopic model, PP2Ac loss prolongs survival in an immune- and CD8-dependent manner, indicating enhanced immune-mediated tumor clearance. Analysis of MB patient datasets links senescence signatures with improved survival, and integrative single-cell analysis reveals reduced PP2A activity in immunogenic senescent clusters. Although the PP2A inhibitor LB-100 is under clinical investigation, it fails to cross the blood-brain barrier. To overcome this, we developed a lipid nanoparticle (LNP) formulation delivering siRNA against PP2Ac. LNP-siPP2Ac efficiently silences PP2Ac in vitro and, when locally delivered in vivo, extends survival and increases tumor MHC-I expression. These findings establish PP2A as a central modulator of senescence and immunogenicity in MB and support a therapeutic strategy that induces tumor cell senescence and enhances anti-tumor immunity for treatment of MB.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
PP2Ac knockout D425 and SJ (#2416) cells were generated using CRISPR. For #2416, cells were harvested for bulk RNAseq. For D425 cells were also treated sham or radiation (10Gy) before being harvested for bulk RNAseq.
PP2Ac knockout in Group 3 medulloblastoma syngeneic CTD cells was generated using CRISPR, and total RNA was harvested for bulk RNA‑seq.

first: Winson

last: Ho

first: Isha

last: Mondal

first: Jingjing

last: Liu

first: Rayond

last: Sun

first: Jiyang

last: Yu


title: Dopaminergic neurons are vulnerable to dysregulation of YEATS2-dependent calcium homeostasis

city: Chiang Mai, Thailand

first: Ranchana

last: Yeewa

state: State/Province

address: Faculty of Medicine, Chiang Mai University 110 Intawaroros Road, Si Phum, Muang, Chiang Mai

country: Thailand

institute: Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University

summary: YEATS2, a chromatin-associated factor, is essential for maintaining dopaminergic (DA) synaptic integrity, but the underlying mechanism remains unclear. Using Drosophila, we show that neuronal depletion of YEATS2 alters brain transcriptomes, downregulating metabolic genes and upregulating G protein–coupled receptors (GPCRs). This correlates with elevated intracellular calcium levels, leading to neurobehavioral deficits and selective DA neuron loss. Crucially, genetic or pharmacological inhibition of the store-operated calcium entry channel Orai restores calcium balance and rescues DA neuron survival. These findings reveal a YEATS2-dependent epigenetic–calcium axis critical for dopaminergic neuron vulnerability.

overall_design: RNA-seq profiling of heads of nSyb>mCherry IR (NTC IR-1), nSyb>dYEATS2 IR (dYEATS2-IR), nSyb>Luciferase IR (NTC IR-2), and nSyb>dENL/AF9 IR (dENL/AF9 IR) at 3-day-old.

first: Luca

last: Lo Piccolo

first: Pitiporn

last: Noisagul

first: Arnaud

last: Monteil

first: Vorasuk

last: Shotelersuk

first: Salinee

last: Jantrapirom


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice  [part24]

city: South San Francisco

first: Mitchell

last: Rezzonico

address: 1 DNA Way

institute: Genentech

summary: The central nervous system represents a uniquely immune-privileged environment, with inflammatory responses involving several resident CNS-specific cell types. While stereotyped cellular and transcriptional responses recur across varied diseases, relevant signaling pathways and regulatory networks are not fully understood. Here, we describe a screening platform based on high-throughput RNA-seq analysis and glial cell state gene set scores that enables multimodal investigation of inflammatory networks at scale. As proof-of-concept, we investigate genetically heterogeneous mice from a large-scale chemical mutagenesis screen to identify novel functionally relevant variants in six genes previously linked to human CNS disorders: Nrros, Ctsd, Smpd1, Idua, Nlrp1a, and Inpp5d . We leverage the rich and readily-interpretable data from our study to demarcate distinct inflammatory states arising from each mutation. In all, our work provides a methodology for discovering novel regulators of CNS neuroimmune homeostasis and provides a validated analysis framework for identifying discrete neuroinflammatory modules that are engaged divergently across disease contexts.

overall_design:
RNA-seq was performed on brain RNA from a large cohort of ENU-mutagenized mice. Brain RNA was converted into a 3' cDNA library using  SMART-Seq® v4 3’ DE Kits and sequenced as 1152-plex libraries on Illumina instruments. RNA-seq data was mined to identify abnormal inflammation states, and exome sequencing of genomic DNA was utilized to identify candidate causal variants.

Processed data for samples in this series are available on GSE294998. Use the file "sample_lookup.xlsx" to locate the processed data file containing the data for each sample.

first: Christopher

middle: J

last: Bohlen

first: Lisa

last: Miosge

first: Brad

last: Friedman


title: RNA-seq analysis of arterial smooth muscle cells (ASMCs) isolated from the lung, heart, aorta, stomach, intestine, kidney and bladder

first: Stefan

last: Günther

summary: None of the currently available Cre recombinase-expressing mouse lines allows exclusive and specific manipulation of arterial smooth muscle cells (ASMCs). To enable targeted manipulation of ASMCs, we generated two knock-in mouse lines: one carrying a Dre recombinase cassette inserted into the Cspg4 locus (Cspg4-Dre) and another carrying a Rox-Stop-Rox-CreER cassette inserted into the Acta2 locus (Acta2-Rox-CreER). These two lines (hereafter referred to as ASMC-effector mice) were crossed with R26-LoxP-GFP reporter animals, and the offspring were treated with three doses of tamoxifen to induce recombination. This strategy resulted in robust and specific labeling of ASMCs in virtually all arteries examined.To further enhance specificity, we generated an additional line in which a tamoxifen-inducible DreERT cassette was inserted into the Cspg4 locus. This Cspg4-DreERT line also enabled specific labeling of ASMCs in distinct organs.

overall_design: To investigate ASMC heterogeneity across different tissues, we isolated ASMCs from the lung, heart, aorta, stomach, intestine, kidney and bladder by fluorescence-activated cell sorting (FACS) and performed RNA sequencing (RNA-seq) analysis.

first: Lei

last: Wang

first: Guenther

last: Stefan

first: Kuenne

last: Carsten

first: Andre

last: Schneider


title: Identifying Norrin-induced genes in bEnd.3 cells

city: Minneapolis

first: Ha-Neul

last: Jo

state: Minnesota

address: 2001 6th St SE, Lions research building. Room 310

department: Ophthalmology and Visual Neuroscience

institute: University of Minnesota

summary: To identify genes induced by Norrin in bEnd.3 cells (mouse brain endothelial cell line), we treated the cells with recombinant Norrin. It is known that the Norrin ligand induces beta-catenin-dependent (also known as canonical) signaling through binding to a receptor complex containing Frizzled4 (FZD4). First, we confirmed that receptor complex components, FZD4, LRP5/6, and TSPAN12, were expressed in bEnd.3 cells. Next, we observed that Norrin treatment strongly induces Axin2, a beta-catenin-dependent signaling response gene. Multiple norrin-induced DEGs were identified, including P2ry1. However, it is noted that many DEGs identified in previous scRNAseq studies on retinal vascular cells in Ndp and Tspan12 KO mice are not induced in bEnd.3. cells. This observation suggests that bEnd.3 cells are a good model system for studying signal initiation and signal transduction; however, they may not capture all aspects of cellular behavior.

overall_design: RNA-seq of bEnd.3 cells with either vehicle (PBS, 0.1% BSA) or recombinant Norrin treated bEnd.3 cells. Biological quadruplicate of each control (minus Norrin) and Norrin-treated cells (plus Norrin)

first: Harald

last: Junge


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part22]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part19]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part21]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part23]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part18]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part10]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part20]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part14]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice[part11]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part16]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part13]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part12]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part17]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part6]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice[part5]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part15]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part1]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part7]


title: NanoString nCounter study of ICCR-engineered human T cells compared to nontransduced T cells.

city: Houston

first: Irene

middle: M

last: Min

address: 6565 Fannin Street

department: Radiology

institute: Houston Methodist Research Institute

summary: This study aimed to investigate the targeting efficacy of ICAM1-specific chimeric costimulatory receptor (ICCR)-T cells on solid tumor and to study the molecular changes that underlie ICCR functional activity. This objective was addressed by demonstrating superior ICCR-T cell targeting efficacy using allogeneic and autologous ICCR-T cells on anaplastic thyroid cancer (ATC) cells in vitro. ICCR-T cell activity was also tested in vivo using ATC xenografts. We delineated the mechanism by which ICCR enhances T cell proliferation and selective activation by analyzing downstream signal pathway activation, gene expression, and TCR sequencing.

overall_design: Two donor T cells (healthy donor 5 and anaplastic thyroid cancer (ATC) patient RM) were manufactured to express ICCR (ICCR-T) or not (Nontransduced, NT). We had two conditions (unstimulated or target tumor-stimulated). Healthy donor 5 derived T cells (NT and ICCR-T) was stimulated with 8505C ATC cells and 8505C tumor. RM-ATC T cells (NT and ICCR-T) were stimulated with autologous RM-ATC cells.


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part2]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part3]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part9]


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part8]


title: Early cell autonomous and niche-mediated alveolar epithelial response to influenza infection in primary lung organoids

status: Public on Apr 10 2026

city: CINCINNATI

first: William

last: Zacharias

address: 3333 BURNET AVE

institute: Cincinnati Children's Hospital Medical Center

summary: Influenza A virus (IAV) infection is a significant cause of morbidity and mortality for patients worldwide. Alveolar type 2 (AT2) cells are the preferential target of IAV as part of the pathogenesis of viral pneumonia and acute respiratory distress syndrome (ARDS). Early IAV infection of alveolar cells has been challenging to model both in vitro and in vivo. To address this challenge, we used a combination of murine and human primary alveolar organoids to define methods for robust IAV infection and evaluated cell-autonomous consequences of IAV using a temporal series of multiome paired single nuclei RNA/ATAC sequencing. Infected AT2 cells undergo conserved changes defined by early loss of surfactant secretion, decreased lipid biogenesis, a rapid burst of antiviral response, and late viral-mediated suppression. Surprisingly, uninfected AT2 cells undergo substantial transcriptional and epigenomic changes in IAV-treated cultures,  leading to transition to damage-associated cell states within hours via a process driven by the inflammatory milieu of murine organoids. Together, these data provide new methods for high-fidelity modeling of IAV infection in alveolar cells and define a conserved AT2 cell response signature to IAV with implications for ARDS pathogenesis.

overall_design: Nuclei were extracted from murine and human alveolar epithelial organoids harvested following 8, 16, or 24 hours of suspension with or without exposure to PR8 IAV. Joint snRNA- and snATAC-seq libraries were prepared using the 10x Genomics platform.

first: Amber

last: Elitz


title: miRNA expression profiles in plasma-derived exosomes of patients with premature ovarian failure

first: Jiaqiong

last: Lin

address: Guangzhou dadaobei 1838

institute: South medical university

summary: Exosomes are extracellular vesicles that have been shown to have therapeutic effects. However, the role of plasma-derived exosomal miRNA in premature ovarian failure (POF) remains ambiguous. To investigate the epigenetic pathogenesis in POF, we analyzed the expression profile of miRNA in exosomes derived from plasma of health control and POF patients using RNA sequencing.

overall_design: A total of 10 samples were collected, including 4 healthy control subjects and 6 patients with POF.

first: Yanhui

last: Liu

first: Fu

last: Xiong


title: Gene expression profiling in the rmt1∆, rmt5∆, rmt1∆rmt5∆ and gis2∆ mutants of Cryptococcus neoformans.

city: Buffalo

first: John

middle: C.

last: Panepinto

state: NY

address: 955 Main Street Suite 5240

institute: University at Buffalo

summary: This study aimed to investigate transcriptomic changes in Cryptococcus neoformans mutants. We report transcriptome wide remodeling in the rmt1∆, rmt5∆, rmt1∆rmt5∆ and gis2∆ mutants compared to wildtpe cells. We also report transcriptome remodeling following fluconazole treatment in wildtype and gis2∆ cells.

overall_design: Cells were grown to midlog growth stage at 37˚C, then indicated samples were treated with fluconazole (FLUC) at 3.75 mg/mL for 3 hours. Cells were pelleted and total RNA were extracted, DNase treated and sequenced using Illumina HiSeq platform.

middle: C

first: Murat

last: Kalem


title: Cyclin-dependent kinase-9 and oxidative phosphorylation inhibition overcome ibrutinib resistance in mantle cell lymphoma

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 2720 S Moody Ave

department: Department of Biology Medical Engineering

institute: Oregon Health Science University

summary: Resistance to Bruton tyrosine kinase inhibitors (BTKi) is inevitable in mantle cell lymphoma (MCL). Cyclin-dependent kinase-9 (CDK9), a key regulator of oncogenic transcription, is a promising therapeutic target. Here we studied a selective CDK9 inhibitor, AZD4573, in MCL. AZD4573 suppressed growth of MCL cell lines and primary cells and reduced expression of key oncogenic programs including MYC and MCL1. However, CDK9 inhibition also induced metabolic adaptation, with increased oxidative phosphorylation (OxPhos), ATP production, and reactive oxygen species in ibrutinib-resistant models. In an ibrutinib-resistant MCL PDX model, AZD4573 produced modest survival benefit and suppressed TNFα/NF-κB and mTORC1 signaling, but OxPhos remained elevated. To define treatment-associated transcriptional changes at cellular resolution, we analyzed PBMCs from patients receiving AZD4573 using single-cell RNA sequencing. In a responding MCL patient, malignant B cells showed sustained downregulation of MYC targets and OxPhos, whereas refractory patients showed the opposite pattern, with upregulation of MYC-associated and OxPhos programs. Consistent with these findings, the OxPhos inhibitor IACS-010759 synergized with AZD4573 in vitro. Together, these results support CDK9 inhibition as a therapeutic strategy in BTKi-resistant MCL and highlight single-cell transcriptomics as a powerful approach to reveal response-associated malignant cell states and rational combination vulnerabilities.

overall_design:
PBMCs from peripheral blood was collected from patients (AZ01 and AZ06) treated with AZD4573 at the prespecified timepoints: baseline 0 hours, 4 hours, 24 hours, and cycle 1 day 8 (C1D8). AZ01_0hr: CMO301, AZ01_4hr: CMO302, AZ01_24hr: CMO303, AZ01_C1D8: CMO304; AZ06_0hr: CMO305, AZ06_4hr: CMO306, AZ06_24hr: CMO307, AZ06_C1D8: CMO308.

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

first: Carly

last: Roleder

first: Xiaofan

last: Zhao

first: Vi

last: Lam

first: Edward

last: Dominguez

first: Canping

last: Chen

first: Sonia

last: Rodgriguez-Rodriguez

first: Lili

first: Tycel

last: Phillips

first: Alexey

last: Danilov


title: Single-cell RNA sequencing of ancestral and evolved Saccharomyces cerevisiae across 20 environmental conditions

city: Chciago

first: Annisa

last: Dea

state: IL

address: 929 E 57th St

institute: University of Chicago

summary: We performed single-cell RNA sequencing (scRNA-seq) of Saccharomyces cerevisiae cells across 20 environmental conditions using a lab w303 strain (ancestral) and an evolved strain grown in KCl under continuous directed evolution (derived). Cells were grown in each of 20 stress environments (18 for the derived strain) to log phase and harvested for scRNA-seq using the 10x Genomics Chromium platform. This dataset enables comparison of the variances in transcriptional responses across environments and between ancestral and evolved strains at single-cell resolution to reveal an adaptive hierarchy in stress response prioritization that collapses under continuous selection in a constant environment

overall_design: Ancestral strain: Cells were grown overnight to saturation in YPD, diluted to OD600 0.05 in each of 20 environmental conditions, grown to log phase, and harvested for scRNA-seq. Evolved (derived) strain: Generated by continuous directed evolution using the eVOLVER system in synthetic dextrose media with 0.8M KCl over 9 months (automated dilution OD600 0.58 to 0.08), then subjected to the same growth/harvesting protocol across 18 conditions.

first: Yongqing

last: Lan

first: Valeryia

last: Aksianiuk

first: David

last: Pincus

first: Arjun

middle: S

last: Raman


title: GPR34 regulation of disease-associated microglial states in iMGL

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

summary: GPR34 is a microglia-enriched GPCR whose expression is downregulated under several disease conditions, including Alzheimer’s disease (AD) and multiple sclerosis (MS). Despite this, its function is poorly understood in normal or disease conditions, as is its contribution to disease-related microglia states. Using RNA-sequencing, we find that microglia from global Gpr34 knockout (KO) mouse brains exhibited transcriptional shifts toward disease-associated microglia (DAM) and inflammatory profiles, partially mirroring the microglial phenotype seen in 5xFAD AD model mice. Notably, when Gpr34 KO mice were crossed with 5xFAD mice, DAM transcriptional profiles and glial pathology were further exacerbated despite the already robust DAM signature driven by amyloidosis. This occurred without affecting amyloid plaque burden. In human stem cell-derived microglia (iMGLs), GPR34 KO strongly reduced calcium (Ca²⁺) and phosphorylated ERK (pERK) signaling in response to known GPR34 agonists, including lyso-phosphatidylserine (lysoPS) and myelin, and caused transcriptional alterations linked to immune regulation and cell proliferation. Interestingly, GPR34 loss selectively impaired phagocytosis of myelin but not amyloid-β or E. coli. Furthermore, GRP34 KO diminished, but did not abolish, the transcriptional response elicited by myelin. Together, these findings suggest that GPR34 is important for maintaining microglia homeostasis, mediating phagocytosis of and transcriptional response to myelin, and restraining microglial response to neurodegenerative disease conditions.

overall_design: RNA-seq profiling of control (non-targeting CRISPR guide) and GPR34 knockout human microglia-like cells (iMGLs) at day 40 under basal conditions and following myelin treatment (6 μg/mL) for 2 or 24 hours.

first: Ana

last: Geller

first: Min Jee

last: Kwon

first: Sean

last: Simmons

first: Qihong

last: Xu

first: William

last: Martenis

first: Jordan

last: Doman

first: Sahana

last: Natarajan

first: Katherine

last: Stalnaker

first: Constanze

last: Depp

first: Steven

last: Carr

last: McKinney

first: Alexandra

last: Gould

first: Evan

last: Lebois

first: Michel

last: Weiwer

first: Matthew

last: Johnson

first: Yan-Ling

last: Zhang

first: Nader

last: Morshed

first: Deeksha

last: Misri

first: Diana

last: Bohannon

first: Elena

last: Longhi

first: Hasmik

last: Keshishian

last: Demers

first: Donovan

last: Batzli

first: Antia

last: Valle-Tojeiro

first: Christy

last: Biji

first: Sameer

last: Aryal

first: Horai

last: Pribiag

first: Jixiang

first: Xian

last: Adiconis

first: Trang

last: Nguyen

first: Morgan

last: Sheng

first: Prabhat

last: Kunwar


title: Neurodevelopmental disorder genes

city: New Haven

first: Huanyao

last: Gao

state: Connecticut

address: 300 George St., Suite 901

department: Department of Psychiatry

institute: Yale University

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

overall_design: Refer to individual Series


title: Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part4]

first: Mitchell

last: Rezzonico

first: Christopher

last: Bohlen

first: Lisa

last: Miosge

first: Brad

last: Friedman


title: Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells

city: Palo Alto

first: Lattice

last: Data Coordination

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

summary: Primary human myeloid cells are promising candidates for immunotherapy, yet efficient and scalable technologies for genetic engineering and screening in these cells are limited. Here we present a virus-like particle (VLP)-based toolkit that delivers diverse CRISPR genome editing modalities to human monocytes, macrophages, and dendritic cells with high efficiency while preserving viability and innate immune responsiveness. VLP-mediated delivery of ribonucleoprotein payloads supports gene knockout, base editing, and epigenetic silencing. Furthermore, in combination with AAV-mediated donor delivery, this approach enables site-specific integration of large DNA sequences via homology-directed repair. We also developed SLICeVLP, a system combining sgRNA delivery via VPX-lentivirus with Cas9 protein delivery via engineered virus-like particles (eVLPs), and applied it to perform pooled loss-of-function screens and Perturb-seq in human macrophages.  We uncovered regulators of TNF production and CD80 expression in human macrophages, converging on TNFAIP3 as a central regulator of inflammatory polarization. TNFAIP3 ablation promoted a pro-inflammatory cell state that is resistant to suppressive polarization, and augmented cytotoxicity in engineered HER2 CAR-macrophages. Taken together, this platform enables unbiased functional genomics in primary human myeloid cells, with direct implications for myeloid cell therapy design.

overall_design: scRNA-seq with lentiviral delivery CRISPR interference in human monocytes, macrophages, and dendritic cells. Perturb-seq in human marophages.

first: Hyuncheol

last: Jung

first: Pascal

last: Devant

first: Carter

last: Ching

first: Mineto

last: Ota

first: Emma

last: Dann

first: Ronghui

last: Zhu

first: Chandrima

last: Modak

first: Ana

last: Vasquez-Ibarra

first: Jennifer

last: Hamilton

first: Zachary

last: Steinhart

first: Wayne

last: Ngo

first: Luis

last: Sandoval

first: Jae

last: Hyung Jung

first: Jenny

last: Lee

first: Da

last: Xu

first: Meirui

last: An

first: Esha

last: Urs

first: Peixin

last: Amy Chen

first: Vincent

last: Allain

first: Takuya

last: Tada

first: Brian

last: Shy

first: Jonathan

last: Pritchard

first: James

middle: K

last: Nuñez

first: Nathaniel

last: Landau

first: David

last: Liu

first: Justin

last: Eyquem

last: Doudna

first: Alexander

last: Marson

first: Julia

last: Carnevale


title: Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [SMRT]

city: Rennes

first: Samuel

last: Bastos Serra Trinca

address: 2 avenue du professeur Léon Bernard

country: France

institute: University of Rennes

summary: The aim of this study is to benchmark methods for immunoglobulin repertoire profiling using human B-cell samples. We compare targeted VDJ mRNA sequencing and repertoire reconstruction from bulk RNA-seq data to PCR-independent full-length transcript sequencing using Single-Molecule Real-Time technology. The objective is to assess methodological biases and establish a robust reference framework for immunoglobulin repertoire analysis.

overall_design: Transcriptome Sequencing

first: Steve

last: Genebrier

first: Ophélie

last: Dézé

first: Marie

last: Cornic

first: Maiwenn

last: Pineau

first: Karin

last: Tarte

first: Michel

last: Cogné


title: Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [RNA-Seq]


title: DYRK1A enhances antitumor immunity in type 1 conventional dendritic cells via mTORC1 activation [tumor-infiltrating type 1 conventional dendritic cells]

city: Xiamen

first: Hongjiao

last: Wang

address: xiangannanlu

institute: xiamen university

summary: Type 1 conventional dendritic cells (cDC1s) play an integral role in mediating immune responses and maintaining homeostasis, yet the molecular mechanisms underlying their functions remain poorly understood. In this study, we identified dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) as a key kinase that responded to TLR and growth factor stimulation and acted as an essential regulator of cDC1 function. Genetic ablation of Dyrk1a specifically in cDC1s impaired antitumor immunity and accelerated tumor progression in murine models. Mechanistically, DYRK1A mediated the phosphorylation of the mTORC1 inhibitor TSC2 at serine 540, triggering the degradation of TSC2 and promoting the mTORC1 signaling in cDC1s. Notably, Tsc2 deletion in Dyrk1a-deficient cDC1s remarkably restored their antitumor immune functions. Furthermore, DYRK1A-mediated mTORC1 signaling in cDC1s positively correlated with effector T-cell responses across multiple human cancers. Our findings highlight a critical role for the DYRK1A-TSC2-mTORC1 signaling pathway in regulating cDC1 functions in antitumor immunity, offering potential strategies to improve cancer immunotherapy.

overall_design: For RNA-seq profiling, tumor-infiltrating cDC1s (CD3-CD19-NK1.1-Ly6C-Ly6G-F4/80-CD11c+XCR1+) were sorted from tumor tissues of B16-F10 tumor-bearing Dyrk1a+/+-Cd11c-cre and Dyrk1afl/fl-Cd11c-cre mice (day 13 after tumor cell inoculation).

first: Songlin

last: He

first: Pan

last: Zhu

first: Zuliang

last: Jie


title: Biallelic UNC5C variants cause a recessive neurodevelopmental disorder with brain anomalies

city: Ankara

first: Efe

last: Dalli

address: Dogol Street

country: Turkey

institute: Ankara University

summary: Precise axon guidance is fundamental to neural circuit formation, yet the full spectrum of neurodevelopmental disorders arising from disruptions in this process remains undefined. Here, we describe a multi-ethnic cohort of eight patients from five independent families presenting with a neurodevelopmental disorder characterized by structural brain anomalies, distal limb contractures, developmental delay, intellectual disability, and additional variable features. All affected individuals carry biallelic deleterious variants in UNC5C, a gene encoding a conserved netrin receptor essential for axon guidance and neuronal migration. To investigate the functional consequences of these variants, we performed structural analyses, which indicated that the identified variants disrupt key functional domains, including the immunoglobulin-like (Ig), thrombospondin-1 type repeats (TSP), ZU5, UPA, and death domains. We then introduced disease-associated mutations into conserved residues of the Caenorhabditis elegans unc-5 orthologue using CRISPR/Cas9 genome editing and assessed phenotypic outcomes in vivo. Cell-type-specific rescue experiments revealed the observed motor defects are primarily neurogenic in origin. Consistent with the clinical features observed in patients, C. elegans carrying the corresponding human mutations exhibited defects in axon guidance, locomotion, and behaviour, supporting disruption of UNC-5–mediated signalling pathways. Together, our findings establish biallelic pathogenic variants in UNC5C as the cause of a previously unrecognized autosomal recessive neurodevelopmental disorder with structural brain anomalies and distal limb contractures. Our combined approach of human genetics and in vivo modelling defines a critical role for UNC5C in human neurodevelopment and expands the spectrum of disorders arising from disrupted axon guidance machinery.

overall_design: Synchronized populations of C. elegans wild type (n = 3) and unc-5(Cys348*) mutants (n = 3) were collected at the young adult stage. Total RNA was extracted using TRIzol with mechanical disruption, purified, and quality-checked (RIN > 8). RNA-seq libraries were prepared using poly(A) selection and sequenced on an Illumina platform. Reads were aligned to the WS288 reference genome using STAR, and gene-level counts were generated. Differential expression analysis between wild type and unc-5(Cys348*) mutants was performed using DESeq2, with genes considered significant at adjusted p < 0.05 and |log2 fold change| > 1. Functional enrichment analyses were conducted with clusterProfiler, and neuronal genes were identified based on known C. elegans gene annotations. R code is provided as a supplementary file.


title: Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [RACE_RepSeq]


title: C1q and immunoglobulins mediate activity-dependent synapse loss in the adult brain.

city: London

first: Emir

last: Turkes

address: Gower St

department: UK Dementia Research Institute

institute: University College London

summary: C1q, the initiator of the classical complement cascade, mediates synaptic elimination during development and disease, yet the triggers for C1q deposition on synapses in the adult brain remain unclear. Using in vivo chemogenetics, we demonstrate that neuronal hyperactivity acts as a trigger for region-specific C1q deposition and synapse loss in the adult hippocampus of wild-type mice; importantly, C1qa deficiency abolishes this activity-dependent synapse remodeling. Conversely, suppressing perforant pathway hyperactivity in a mouse model of Alzheimer’s disease lowers local Aβ levels, reduces C1q deposition, and partially rescues synapse loss. Further, using spatial transcriptomics, live cell tracking, super-resolution microscopy and other molecular and cellular tools, we report a surprising role for B lymphocyte lineage antibody-secreting cells in the activity-dependent C1q deposition and synapse loss in the non-diseased adult hippocampus. Overall, our work suggests a functional link between neuronal hyperactivity and C1q-mediated synapse loss in the adult brain and introduces immunoglobulins as players in this process.

overall_design: The Visium Gateway Package from 10x Genomics (PN-1000316, 10x Genomics) was used to generate spatial transcriptomic data from two coronal brain sections from two different hM3Dq-expressing CNO-treated mice. Experiments were performed in an RNase-free environment in line with the manufacturer’s recommendations and user guides. The brain was dissected immediately without PBS or PFA perfusion, and fresh frozen directly within an OCT mould in an isopentane bath submerged in liquid nitrogen. The lateral parts of the brain were trimmed during cryosectioning to allow 10 m-thick coronal sections including both dorsal hippocampi to be cryosectioned into the capture area (6.5 mm x 6.5 mm area) of the Visium Gateway Gene Expression Slide (10x Genomics). Cryosections were taken at 1.9 mm posterior to bregma, more than 2.5 mm anterior to the injection site at 4.6 mm posterior to bregma. Cryosections were also taken adjacent to the sections used for Visium and from MEC to confirm increased ipsilateral GFP and c-Fos immunostaining respectively.

first: Gerard

last: Crowley

first: Minjung

last: Kim

first: Nathanael

last: O’Neill

first: Fateme

last: Ghasemi

first: Luca

last: Giudice

first: Sebastiaan

last: De Schepper

first: Benjy J. Y.

last: Tan

first: Benito

last: Maffei

first: Laís S. S.

last: Ferreira

first: Julie

last: Rebejac

first: Javier

last: Rueda-Carrasco

first: Margarita

last: Toneva

first: John Christian

last: Fajardo

first: Judy Z.

last: Ge

first: Zhengyue Grace

last: Yang

first: Paula

last: Korhonen

first: Phillip

last: Muckett

first: Damaris

last: Bennett

first: Camille

last: Paoletti

first: Tammie T. M.

last: Sow

first: David A.

last: Posner

first: Annerieke

last: Sierksma

first: Dimitra

last: Sokolova

first: Viktoras

last: Konstantellos

first: Leen

last: Ali

first: Kiavash

last: Movahedi

first: Andrew

last: F. MacAskill

first: Victor L. J.

last: Tybulewicz

first: Tarja

last: Malm

first: Gabriele

last: Lignani

first: Menna

last: R. Clatworthy

first: Soyon

last: Hong


title: BATF3 regulates chromatin accessibility during CD8+ T lymphocyte differentiation

city: Nagoya

first: Seitaro

last: Terakura

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Hematology and Oncology

institute: Nagoya University Graduate School of Medicine

summary: CD8+ T lymphocytes differentiate from effector to memory cells following antigen clearance, with prolonged IL-2 production characterizing functional cytotoxic T lymphocytes (CTLs). To identify transcription factors associated with sustained IL-2 production, we compared influenza virus-specific and cytomegalovirus-specific CTLs, identifying Basic Leucine Zipper ATF-Like Transcription Factor 3 (BATF3) as a key candidate gene. BATF3 overexpression significantly enhanced cell proliferation in both virus-specific CTLs and CD19 chimeric antigen receptor T (CAR-T) cells while reducing cytokine production. ATAC-seq analysis revealed that BATF3 overexpression dynamically regulates chromatin accessibility, affecting diverse cellular processes including cytoskeletal organization, metabolic pathways, and cellular survival signaling. BATF3 specifically facilitated the critical transition from effector to memory phase. These findings establish BATF3 as a master regulator of CD8+ T cell fate determination through dynamic chromatin remodeling mechanisms.

overall_design: ATAC-seq was performed on CD8+ T cells transduced with BATF, BATF3, or untransduced control across a 14-day differentiation time course. 12 donor samples (6 pairs of technical duplicates) were collected at Day 0, Day 7, and Day 14, for a total of 36 samples.

first: Koji

last: Umemura

first: Yasuhiro

last: Kojima

first: Jakrawadee

last: Julamanee

first: Yusuke

last: Okuno

first: Yuki

last: Takeuchi

first: Fumiya

last: Ohara

first: Shihomi

last: Kuwano

first: Yoshitaka

last: Adachi

first: Ryo

last: Hanajiri

first: Hitoshi

last: Kiyoi


title: ADAR1 and ADAR2 associate with the RNA exosome and modulate RNA stability

city: Gosselies

first: Denis

middle: LJ

last: Lafontaine

state: Hainaut

address: Av Profs Jeneer & Brachet, 12

country: Belgium

institute: Universite libre de Bruxelles

summary: The adenosine deaminase acting on RNA (ADAR) enzymes deaminate adenosine to inosine in double-stranded (ds)RNA. Mammals express two catalytically active enzymes: ADAR1, which is ubiquitously expressed and essential for innate immune homeostasis, and ADAR2, which is enriched in the brain and vascular system. Here, we investigate the ADAR2 interactome and uncover a shared interaction network with ADAR1, including multiple components of the RNA exosome complex, a multi-subunit RNase involved in RNA processing, turnover, and surveillance. The interactions between ADARs and RNA exosome components is nuclear, and resistance to RNase A treatment implies their close proximity. We validated these interactions by immunoprecipitation of both endogenous and epitope tagged ADAR proteins in multiple cell lines and mapped the interaction interfaces to their dsRNA-binding domains. Exploiting an MS2–MCP tethering system, we show that recruitment of ADAR1 or ADAR2 to the 3’UTR of a reporter transcript decreases its stability. This decrease in RNA levels was reversed when EXOSC3 was depleted, demonstrating that this destabilizing effect of ADARs on RNA is via the RNA exosome complex. Finally, knockdown of ADARs perturbs rRNA processing, a canonical function of the nuclear exosome, demonstrating a cellular consequence of disrupting ADAR–exosome interactions.

overall_design: RiboMethSeq sequencing data from "Mock", "SCR", "ADAR1 #1", "ADAR1 #2,  and "ADAR2 #1" samples that refer to Supplementary Figure S7.

first: Dragana

last: Vukić

first: QiuPei

last: Du

first: Anna

last: Cherian

first: Damiano

last: Amoruso

first: Květoslava

last: Brožinová

first: Ludivine

last: Wacheul

first: Valentina

last: Lacovich

first: Christiane

last: Zorbas

first: Lenna

last: Yadav

first: Jiří

last: Sedmík

first: Salla

last: Keskitalo

first: Khadija

last: Hajji

first: Stanislav

last: Stejskal

first: Markku

last: Varjosalo

first: Denis LJ

first: Liam

last: Keegan

first: Mary

last: O'Connell