title: A novel oncolytic neutrophil phenotype is induced by IL-10R inhibition

city: New York

first: Yacine

last: Marouf

state: NY

address: 413 E 69th St

department: MCC

institute: Weill Cornell Medecine

summary: While the impact of neutrophils on antitumor T cells has been an active area of study, fewer studies have focused on the potential of neutrophils to directly impact tumor cells. Here we asked whether neutrophils have the capacity to directly kill tumor cells independently of T cells. We find that anti-CD40-based therapy, when combined with interleukin 10 (IL-10) receptor blockade, initiates a Batf3-dependent pathway in which IL-12 and interferon gamma (IFNγ) secretion results in oncolytic neutrophil activity. Using a combination of microscopy, single-cell, and functional assays, we observe that killing of tumor cells by neutrophils is dependent on physical contact and degranulation. This degranulation-mediated killing is associated with an atypical dynamic invasive neutrophil phenotype. In line with our preclinical findings, our phase 1 trial of anti-CD40 shows that circulating IL-12, IFNγ, and IL-10 increase in response to anti-CD40, while our phase 1b/2 PRINCE study shows that lower circulating IL-10 is associated with favorable overall survival specifically among anti-CD40-treated patients. Finally, we find that neutrophil expansion with granulocyte colony stimulating factor (G-CSF) is associated with improved overall survival specifically in patients treated with anti-CD40, suggesting that this pathway may be amenable to therapeutic intervention in patients with advanced cancer.

overall_design: C57BL/6 wild-type mice were intradermally inoculated with B16F10 murine melanoma cells on their flanks, and eight days later, they received Isotype control, anti-IL-10R alone, anti-CD40/Monophosphoryl Lipid A (CM), or a combination of anti-CD40/MPL/anti-IL-10R (CMI). Twelve hours post-treatment, the B16F10 tumors were harvested and processed into single-cell suspensions. Single-cell RNA sequencing (scRNA-Seq) was subsequently performed on these FACS-sorted cell suspensions.

first: Danny Nejad

last: Khalil

first: Ricardo

last: Gomez

first: Amit

last: Regev

first: Fadi

last: Samaan

first: Sadna

last: Budhu

first: Daniel

last: Hirschhorn

first: Isabell

last: Schulze

first: Jessica A.

last: Lavery

first: Nicholas

last: Ceglia

first: Samuel

last: Freeman

first: Vivien I.

last: Maltez

first: Jaynia

last: Garcia

first: Nathan

last: Suek

first: Chien-Huan (Gil)

last: Weng

first: Christopher R.

last: Cabanski

first: Sébastien

last: Monette

first: Yevgeniy

last: Romin

first: Yanyun

last: Li

first: Ronan

last: Chaligne

first: Michael

last: Yellin

first: Tibor

last: Keler

first: Deena M.

last: Maurer

first: Anne-Laure

last: Flamar

first: Lucia

last: Morgado-Palacin

first: Levi

last: Mangarin

first: James

last: Harding

first: Wungki

last: Park

first: Jaclyn P.

last: Lyman

first: Stephen

last: Maddock

first: Mark H.

last: O’Hara

first: Ghassan K.

last: Abou-Alfa

first: Robert H.

last: Vonderheide

first: Eileen M.

last: O’Reilly

first: Ronald N.

last: Germain

first: Jedd D.

last: Wolchok

first: Taha

last: Merghoub


title: Eupatilin Ameliorates Spinal Cord Injury by Inhibiting Damage-associated Microglia and Optimizing the Regenerative Microenvironment

status: Public on Aug 29 2025

city: Xi'an

first: Beibei

last: Yu

state: Shannxi

address: No. 157, Xiwu Road, Xincheng District, Xi'an City, Shaanxi Province

country: China

institute: Xijing hospital

type: Expression profiling by high throughput sequencing

summary: Microglia represent critical therapeutic targets in spinal cord injury (SCI), with damage associated microglia (DAM) playing key roles in neuroinflammation and tissue repair.Through integrated in-silico analysis of scRNA-seq and microarray datasets, we identified DAM subsets specific to acute SCI characterized by hub genes Fcer1g, Grn, and Gusb. Using a C57BL/6 mouse spinal cord contusion model, we validated increased DAM accumulation post-injury and demonstrated their propensity to transition toward homeostatic microglia (MG2). Eupatilin treatment promoted DAM-toMG2 differentiation, as confirmed through bulk and single-cell RNA sequencing analyses revealing supportive gene expression changes. These findings establish DAM as functionally distinct microglial populations in acute SCI and identify Eupatilin as a therapeutic agent that facilitates beneficial microglial polarization. This work provides mechanistic insights into microglial dynamics during SCI and suggests targeted modulation of DAM-to-MG2 transitions as a promising therapeutic strategy for promoting inflammation resolution and functional recovery.

overall_design: Prior to surgery, mice were fasted for 6 hours received anesthesia with a single intraperitoneal injection of 270-330 mg/kg Avertin (Sigma-Aldrich, MO, USA, T48402). The T9 lamina was surgically exposed while preserving the integrity of the dura mater, followed by a 30-second aneurysm clip compression for all injured groups. The muscle and skin were then sutured closed. Following SCI, manual bladder  expression was performed 3 times daily until bladder function recovered. For the first 3 days, intrathecal injections were administered: the treatment group received Eupatilin (30 μl, 1.5 mg/mL, Bide, Shanghai,  China, BD298186), while the SCI control group received an equivalent volume of saline.

first: Weitao

last: Man

first: Zide

last: Wang


title: Physiological and functional characterization for high-throughput optogenetic skeletal muscle exercise assays

city: Cambridge

first: Ritu

last: Raman

state: MA

address: 77 Massachusetts Avenue

department: Mechanical Engineering

country: USA

institute: Massachusetts Institute of Technology

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

overall_design: Refer to individual Series

first: Ronald

last: Heisser

first: Angel

last: Bu


title: Preadipocyte uncoupling protein 1 expression invoked by fibroblast growth factors imprints on post-differentiation white and brown adipocyte function [2]

city: Freising

first: Katharina

last: Küllmer

state: Bavaria

address: Gregor-Mendel Straße 2

country: Germany

institute: Technical University of Munich

summary: The presence of uncoupling protein 1 (UCP1) is a hallmark of thermogenic adipocytes and enables heat production by dissipating energy from mitochondrial proton motive force as heat. The purpose of its recently discovered presence in preadipocytes in response to certain fibroblast growth factors (FGFs) remains elusive. In this study, we systematically investigated the potential of all paracrine FGFs to invoke Ucp1 expression in murine preadipocytes derived from interscapular brown and inguinal white adipose tissue. The factors FGF2, FGF4, FGF8, and FGF9 induced Ucp1 expression in undifferentiated preadipocytes, with FGF2 acting most potently and rapidly. This premature Ucp1 induction did not translate into increased Ucp1 thermogenic activity after full adipogenic differentiation. Notably, preadipocyte treatment with FGFs and parallel Ucp1 expression led to a sustained suppression of interferon-stimulated genes after differentiation. Preadipocyte Ucp1 was required and sufficient for this lasting imprint. Thus, FGF-induced Ucp1 expression in preadipocytes programs a lasting post-differentiation anti-inflammatory status.

overall_design: Stromal vascular fraction (SVF) cells were isolated from interscapular brown adipose tissue (iBAT) of C57BL/6N wild-type and Ucp1 knockout mice. Cells were cultured to 70–80% confluency and treated at the preadipocyte stage with either 5.5 nM FGF2, 250 nM of the FGFR inhibitor LY (LY2874455), or left untreated for 48 hours. Subsequently, differentiation into mature brown adipocytes was induced (Gantert et al. 2021). Total mRNA was extracted using the SV Total RNA Isolation System (Promega). For each condition, mRNA from three biological replicates was pooled prior to library preparation and sequencing, which were performed by Novogene.

last: Kuellmer

first: Tobias

last: Fromme


title: Preadipocyte uncoupling protein 1 expression invoked by fibroblast growth factors imprints on post-differentiation white and brown adipocyte function [1]

overall_design: We used 20-day-old male C57BL/6N wild-type (WT) and Ucp1 knockout (Δ/Δ) mice. For each genotype, interscapular brown adipose tissue (iBAT) from three animals was pooled to generate one sample. Total mRNA was isolated using the Promega kit, and library preparation and sequencing were performed by Novogene.


title: Integrated Single-Cell Lung Cancer Atlas Revealed Distinct Fibroblast Phenotypes between Adenocarcinoma and Squamous Cell Carcinomas

city: Minato-ku

first: Yuta

last: Hirano

state: Tokyo

address: 3-25-8 Nishi-shimbashi

department: Internal Medicine

country: Japan

institute: The Jikei University School of Medicine

summary: The tumor microenvironment (TME) not only influences cancer progression but has also been shown to have a significant impact on patient prognosis. One of the major TME components is cancer-associated fibroblasts (CAFs), of which several subtypes are identified in tumor tissues. Although scRNA-seq technology is a powerful tool to investigate the cellular proportion and composition in tissues, large-scale datasets are required to analyze a small number of cell populations. Here, we constructed an integrated single-cell RNA-seq dataset for non-small cell lung cancer (NSCLC) by compiling publicly-available data and demonstrated differences in TME heterogeneity and cellular composition between lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Particularly, we identified significant differences in CAF subtypes between LUAD and LUSC. Inflammatory CAFs (iCAFs) were dominantly found in LUAD, while myofibroblastic CAFs (mCAFs) were more common in LUSC. Co-culture analysis with lung fibroblasts confirmed that LUAD cells induced iCAF phenotype and, in contrast, LUSC promoted myofibroblastic differentiation. Correlation analysis with patient prognosis identified mCAF as a poor prognostic factor in both LUAD and LUSC, but iCAF was found to be a poor prognostic factor only in LUSC, and vice versa in LUAD. This work highlights important considerations on CAF subtype dominance in LUAD and LUSC, which may relate to patient prognosis.

overall_design: Normal embryonic lung fibroblast (MRC5) were either mono-cultured or indirect co-cultured with Lung adenocarcinoma (Calu-3) and Lung squamous cell carcinoma (LC1). Total RNA was extracted after 5days culture.

first: Yusuke

last: Yamamoto

first: Yu

last: Fujita


title: TGF-β induces an atypical EMT to evade immune mechanosurveillance in lung adenocarcinoma dormant metastasis

first: Zhenghan

address: 417 East 68th St

department: CBG

institute: Memorial Sloan Kettering Cancer Centerr

summary: The heterogeneity of epithelial-to-mesenchymal transition (EMT) programs is manifest in the diverse EMT-like phenotypes occurring during tumor progression. However, little is known about the mechanistic basis and functional role of specific forms of EMT in cancer. Here we address this question in lung adenocarcinoma (LUAD) cells that enter a dormancy period in response to TGF-β upon disseminating to distant sites. LUAD cells with the capacity to enter dormancy are characterized by expression of SOX2 and NKX2-1 primitive progenitor markers. In these cells, TGF-β induces growth inhibition accompanied by a full EMT response that subsequently transitions into an atypical mesenchymal state of round morphology and lacking actin stress fibers. TGF-β induces this transition by driving the expression of the actin-depolymerizing factor gelsolin, which changes a migratory, stress fiber-rich mesenchymal phenotype into a cortical actin-rich, spheroidal state. This transition lowers the biomechanical stiffness of metastatic progenitors, protecting them from killing by mechanosensitive cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. Inhibiting this actin depolymerization process clears tissues of dormant metastatic cells. Thus, LUAD primitive progenitors undergo an atypical EMT as part of a strategy to evade immune-mediated elimination during dormancy. Our results provide a mechanistic basis and functional role of this atypical EMT response of LUAD metastatic progenitors and further illuminate the role of TGF-β as a crucial driver of immune evasive metastatic dormancy.

overall_design: To enable the simultaneous collection of samples exposed to different TGF-β treatment durations (0 h (control), 3 h, 1 d, 3 d, 5 d, and 7 d) for scRNA-seq analysis, the start of cell culture and TGF-β administration for these samples were correspondingly staggered. Specifically, H2087-BrM cells were plated in 10 cm petri dishes for each treatment condition and incubated overnight for attachment. Subsequently, the medium was replaced with fresh MLM medium supplemented with 10 pg/mL TGF-β for the specified durations, with the medium changed every 2 days, before being harvested for scRNA-seq analysis. Two experimental replicates (Samples 1 and 2) were collected and processed for scRNA-seq on consecutive days, following the same protocol as decribed. The two samples showed strong agreement, confirming their reproducibility as replicates, and were therefore combined for downstream analysis. In both samples, TotalSeq-A0251 and A0252 were used together to label cells following TGF-β treatment at 0 h (control), while A0253, A0254, A0255, A0256, and A0257 were used for the 3 h, 1 d, 3 d, 5 d, and 7 d time points, respectively.

first: Siting

last: Gan

first: Joan

last: Massagué


title: Effects of Acute and Chronic Type I Interferon Stimulation on Human Cardiomyocytes

city: Beverly Hills

first: Caroline

last: Jefferies

state: CA

address: 121 N San Vicente Blvd

department: Kao Autoimmunity Institute

institute: Cedars-Sinai Medical Center

summary: Persistent type I interferon activity is a hallmark of systemic lupus erythematosus (SLE) and contributes to extra-renal organ injury, yet the temporal transcriptomic response of human cardiomyocytes has not been mapped. To address this gap, AC16 ventricular cardiomyocytes were stimulated with recombinant IFN-α (1 000 U mL⁻¹) under three time courses: a single 24 h pulse (acute), a 24 h pulse followed by a 5-day recovery (chronic-hold), and two 24 h pulses separated by a 4-day recovery (repeat). Triplicate RNA-seq profiles captured robust induction of canonical interferon-stimulated genes immediately after exposure, whereas expression largely returned to baseline after the recovery periods, indicating that the cardiomyocyte interferon response is transient rather than self-sustaining. The dataset comprises raw FASTQ files, md5 checksums, gene-level count tables, and TPM matrices, providing a reference for benchmarking innate immune–cardiac interactions, validating bioinformatic pipelines, and integrating multi-omics studies. Proteomic and metabolomic measurements from the same biological replicates are being deposited separately in public repositories and can be cross-referenced to extend analyses of interferon kinetics.

overall_design: AC16 cells (ATCC CRL-4021) were cultured in DMEM/F-12 plus 10 percent FBS at 37 °C with 5 percent CO₂ and treated with IFN-α or vehicle under the three regimens described above, with three independent biological replicates per condition. Total RNA (325 ng) was poly-A–enriched using the NEBNext Poly(A) Magnetic Isolation Module, and strand-specific libraries were prepared with the IDT xGen Broad-Range RNA Library Prep Kit (12 PCR cycles). Library size and concentration were verified on an Agilent 4200 TapeStation and Qubit fluorometer, pooled, and sequenced on an Illumina NovaSeq X (single-end 1 × 75 bp, target 30 million reads per sample). Reads were quality-trimmed with Trim Galore, aligned to GRCh38 using STAR 2.7.11a, and quantified at the gene level with featureCounts against Gencode v41; TPM normalization, differential expression with DESeq2, and PCA were performed in R. Library preparation and lane assignment were randomized to minimize batch effects, and standard QC metrics confirmed library complexity and alignment quality. Matching cell pellets were retained for proteomic and metabolomic analysis, which will be released through PRIDE and MetaboLights to facilitate multi-layer interrogation of interferon-driven pathways in SLE-relevant cardiac models.

first: Arati

last: Naveen Kumar

first: Trinitee

last: Oliver


title: Hepatitis virus-associated B cell non-Hodgkin’s lymphoma involves dysregulated epigenetic and RNA-mediated regulatory gene expression and altered snoRNA transcription

city: Bethesda

first: Amanda

last: Henning

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: Infection with HBV and its satellite virus HDV remain a significant global health issue due to their involvement in hepatic and extrahepatic diseases, including B cell non-Hodgkin’s lymphoma (BNHL). Clinical and epidemiological evidence support a causal role for HBV in BNHL development, although mechanistic insight is lacking and the role of HDV infection in this process is unknown. We performed RNA-sequencing on peripheral B cells from patients with HBV mono-infection, HBV/HDV co-infection, BNHL, and HBV/HDV-associated BNHL to identify unique and shared transcriptional profiles associated with transformation. Our data suggest dysregulated epigenetic and miRNA-mediated regulatory gene expression may be a potential common pathway for lymphomagenesis among viral- and non-viral-associated lymphoma. We also observed wide-spread upregulation of snoRNAs in B cells from virally infected patients, supporting a role for these non-coding RNAs in viral infection and, potentially, viral-associated lymphomagenesis.

overall_design: RNA-sequencing of peripheral B cells isolated from patients with chronic HBV infection (n=4), HBV/HDV co-infection (n=7), B cell non-Hodgkin's lymphoma (n=6), HBV/HDV-associated B cell non-Hodgkin's lymphoma (n=3), and healthy donors (n=6)

middle: N

first: Valeria

last: De Giorgi


title: Native CFTR codon bias controls translation rate to balance off-pathway aggregation and channel function by conformational imprinting

city: Lexington

first: Jae Seok

last: YOON

address: 44 Hartwell Avenue

department: CFFT Lab

institute: Cystic Fibrosis Foundation

summary: Protein folding in vivo is biologically tuned to minimize off-pathway events and optimize native folding outcomes.  A key factor in this process is biased synonymous codon usage, in which synonymous codons modulate local translation rate while maintaining the native amino acid sequence.  Here, we demonstrate that native codon usage within the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) induces a translational pause during a critical window of synthesis that is important for CFTR folding, processing, and function.  Eliminating this pause by substituting synonymous codons increased the aggregation propensity of immature CFTR and induced conformational and functional changes that persisted during CFTR processing and plasma membrane expression.  Interestingly, the resulting mature CFTR protein at the plasma membrane exhibited enhanced ATP-dependent chloride channel gating.  Thus, during protein synthesis, cotranslational events dictated by codon usage can imprint persistent conformational and functional properties upon CFTR.  Our findings suggest that CFTR codon usage has evolved and adapted to balance a compromise between protein aggregation and a modest loss of channel function.

overall_design: Ribosome profiling of heterologously expressed CFTR variants with different synonymous codons in HEK293 cells

last: Yoon

first: Hongyu

last: Li

first: Yonjung

last: Kim

first: Hideki

last: Shishido

first: David

last: Sheppard

first: Min Goo

last: Lee

first: William

middle: R

last: Skach


title: Physiological and functional characterization for high-throughput optogenetic skeletal muscle exercise assays [30min]

first: Ritu

last: Raman

summary: Exercise has long been considered an essential part of human health and longevity. Recent physiological studies have expanded muscle’s role beyond simply acting as an actuator, revealing muscle’s exercise-mediated paracrine and endocrine relationships with other organ systems. In vitro engineered skeletal muscle models can address physiological questions about exercise adaptation with the precision of cell biology. Optogenetic tools have enabled a noninvasive approach to stimulating muscle contraction that avoids the potential off-target effects of electrical stimulation techniques. In this article we propose high-throughput culture and optical exercise protocols to generate statistically robust cellular exercise response datasets. We characterize optical rheobase for 2D muscle tissue morphology, finding that optical intensities as low as 5 μW mm-2 can trigger contraction. We then analyze bulk RNA sequencing data collected from high throughput, acute exercise protocols and find a rich display of transcriptional behavior that is consistent with experimental observations. The spontaneous contractility of our tissue constructs introduced oxygen diffusion challenges when maintained in a 24 well plate, and our analysis shows divergent myogenic and pathological transcriptional consequences of hypoxia. We believe our techniques provide a practical foundation for conducting future high-precision in vitro exercise studies of skeletal muscle.

overall_design: ChR2 C2C12 myoblasts (optogenetic) grown on a fibrin hydrogel and differentiated for about two weeks before RNA extraction. This cohort underwent daily optical stimulation for 30 minutes at a variety of frequencies (none-control, 1Hz, 4Hz, and 10Hz).

first: Ronald

last: Heisser

first: Angel

last: Bu


title: ENA1, a transporter of nicotianamine that mediates secretion in the root of Arabidopsis

city: taipei

first: Yitze

last: Chen

address: 128 Academia Road, Section 2, Nankang,

country: Taiwan

institute: Academia Sinica

summary:
• Nicotianamine (NA), a key chelator in plant heavy metal homeostasis, plays a pivotal role in managing Zn bioavailability. In the Zn/Cd hyperaccumulator Arabidopsis halleri, NA is secreted into the rhizosphere, forming stable complexes with Zn to reduce its bioavailability and prevent rapid uptake. However, the NA transporter responsible for this secretion remains unidentified.
• Transcriptome analysis of A. halleri and A. thaliana roots with further characterization led to the identification of EFFLUX TRANSPORTER OF NA1 (ENA1) as a plasma membrane-localized NA efflux transporter. ENA1 expression is significantly higher in A. halleri compared to A. thaliana and is induced by excess Zn only in A. halleri.
• Increased ENA1 expression promotes NA secretion from roots into the rhizosphere without altering NA accumulation or long-distance root-to-shoot NA transport. Using 67Zn uptake experiments, we found that enhanced NA secretion alleviates Zn toxicity by reducing excess Zn uptake.
• Promoter and in situ expression studies showed distinct root expression patterns of ENA1 between A. halleri and A. thaliana, aligning with the species-specific Zn detoxification strategies.
• This discovery advances our understanding of Zn homeostasis mechanisms and provides a foundation for developing phytoremediation technologies to manage heavy metal contamination.

sample_organism:
Arabidopsis thaliana
Arabidopsis halleri subsp. gemmifera

overall_design: RNA-Seq profilings of roots of hydroponic grown Arabidopsis halleri ssp. gemmifera and A. thaliana.

first: Yi

middle: T

first: Kuo

middle: C

last: Yeh


title: Single cell spatial transcriptome and RNA-seq analysis in human lung tissues with mycobacterial infection: RNA-seq analysis

city: Tokyo

first: Harutaka

last: Katano

address: 1-23-1 Toyama, Shinjuku

department: Department of Pathology

institute: National Institute of Infectious Diseases

summary: Tuberculosis and non-tuberculous mycobacterial (NTM) diseases are infections caused by Mycobacterium tuberculosis and non-tuberculous mycobacteria, leading to the formation of granulomatous lesions with caseous necrosis in the lungs. We applied spatial transcriptomics at single-cell resolution (CosMx Spatial Molecular Imaging) to human lung samples from patients with mycobacterial infections. RNA-seq was also performed on the samples.

overall_design: FFPE samples ( 5 MTB, 7 NTM, 12 granulomatous diseases including 2 RN, 3 Aspergillosis, 3GPA, 3SA, and 1 aspiration pneumonia, 4 control lung, and 4 tonsils) were analyzed with RNA-seq to reveal RNA expression profile in each sample.

first: Yoshihiko

last: Hoshino


title: Ischemic injury induces hematopoietic aging and facilitates tumor growth [scRNA-seq]

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

summary: Background: Cancer patients are at increased risk of cardiovascular disease (CVD). In turn, myocardial infarction can accelerate cancer progression in mice and humans. Many mechanisms driving CVD-cancer communication remain poorly understood, including the impact of ischemic injury on cancer development. Objectives: To evaluate breast cancer growth and anti-tumoral immunity following peripheral ischemic insult in mice. Methods: Hind limb ischemia (HLI) by femoral artery ligation or sham surgery was performed on C57BL/6J mice three days after orthotopic implantation of E0771 mammary cancer cells and tumor growth was monitored. Immune cell composition in tumors, circulation, and the bone marrow was assessed by flow cytometry. The influence of ischemia on chromatin accessibility and gene expression in hematopoietic stem and progenitor cells (HSPC) was evaluated by single cell (sc)ATAC- and (sc)RNA-seq. Bone marrow transplant from HLI or sham mice was performed to assess altered responsiveness of HSPCs and their myeloid progeny in restricting tumor growth. Results: Peripheral ischemia accelerated breast cancer growth and increased the accumulation of immunosuppressive regulatory T cells and myeloid cells within tumors. Ischemia also increased monocyte and neutrophil output from the bone marrow at the expense of lymphocytes. Multiomic analyses revealed an increase in myeloid-biased bone marrow HSPCs and a gene signature consistent with inflammation (NLRP3 inflammasome) and aging (Neogenin-1, Thrombospondin-1). This HLI-induced phenotype, including accelerated tumor growth and myeloid-skewing, was transmissible by bone marrow transplantation to naïve recipients, indicating long-term reprogramming of innate immune responses. Conclusions: Peripheral ischemia promotes inflammaging of hematopoietic stem cells and long-lasting alterations to anti-tumoral immunity to accelerate breast tumor growth.

overall_design: The effects of ischemic injury on bone marrow hematopoietic stem and progenitor cells were under investigation, compared to sham surgery controls, and using a total of four hashtagged replicates per group.


title: Single cell spatial transcriptome and RNA-seq analysis in human lung tissues with mycobacterial infection: Single cell spatial transcriptome

summary:
Tuberculosis and non-tuberculous mycobacterial (NTM) diseases are infections caused by Mycobacterium tuberculosis and non-tuberculous mycobacteria, leading to the formation of granulomatous lesions with caseous necrosis in the lungs.
We applied spatial transcriptomics at single-cell resolution (CosMx Spatial Molecular Imaging) to human lung samples from patients with mycobacterial infections. RNA-seq was also performed on the samples.

overall_design: CosMx technology [CosMx Human Universal Cell Characterization RNA Panel (1000-plex) genes; Nanostring, USA] was applied to 7 FFPE samples: 3 Mycobacterium tuberculosis (MTB) and 4 non-tuberculous mycobacterial (NTM) patients with a mean of 30.9 fields of view (FoVs) per sample. The mean area explored was 4.6 mm2 per sample. The following cell surface markers were used for morphology visualization: B2M/CD298, PanCK, CD45, CD3 antibodies and DAPI.


title: Ischemic injury induces hematopoietic aging and facilitates tumor growth [multiome]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: The effects of ischemic injury on bone marrow hematopoietic stem and progenitor cells were under investigation and compared to sham surgery controls.

middle: A

first: Alexandra

last: Newman

first: Gabriel

last: Duran

first: Kathryn

middle: J

last: Moore


title: Single cell RNAseq of human neuroblastoma

city: 天津市

first: zhe

last: nian

state: 天津市

address: 天津市和平区气象台路22号

institute: Tianjin Medical University

summary: To study heterogenous cellular function and behaviors, we isolated individual cells from freshly resected and dissociated eight human neuroblastoma samples including 2 paired samples of primary tumors and bone marrow metastases, removed the inflammatory infiltrate and DAPI-positive dead cells  , and performed single cell analysis using the 10x Genomics Chromium platform.

first: Zhe

last: Nian

last: Liu


title: Gene expression profile at single cell level of tumor infiltrated CD45+ cells in liver tumors

city: Shanghai

first: Yuetong

last: Wang

address: 320 Yue Yang Road, Room 713

department: Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences

institute: Chinese Academy of Sciences

summary: CD45+ cells are considered as important componants of tumor immuno microenvironment. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of CD45+ cells in liver tumor treated with ARF1 inhibitor.

overall_design: liver cancer infiltrated CD45+ cells from MYC-ON mice were isolated by Fluorescence-activated cell sorting (FACS) according to the CD45 staining and analyzed using scRNAseq.

first: Steven

middle: X

last: Hou

first: Qiaoming

last: Li


title: Intestinal and mesenteric artery formation by intestine-derived prearterial endothelial cells

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

institute: Max Planck Institute for Molecular Biomedicine

summary: The cellular and molecular mechanisms mediating arterial development remain little understood for most organs. Here, we show that a small subpopulation of endothelial cells inside the intestinal villi of the embryonic mouse, characterized by the expression of endothelial cell-specific molecule 1 (Esm1/endocan), serves as an arterial progenitor population. The specification of arterial progenitors is initiated inside the villus capillary network and contributes to the formation of intestinal and mesenteric arteries during development.

overall_design: E18.0 embryos were collected following Esm1-CreERT2-mediated lineage tracing for 24 hours. Unsorted total intestinal cells and unsorted total mesenteric cells were isolated from 3 pooled embryos and CD31+GFP+ and CD31+GFP- FACS-sorted intestinal blood ECs were isolated from 13 pooled embryos. Single cell RNA isolation was performed utilizing BD rhapsody.

first: Esther

last: Bovay

first: Emma

last: Watson

first: Vishal

last: Mohanakrishnan

first: Mark

middle: L

last: Kahn

first: Ralf

middle: H

last: Adams


title: Adipocyte heterogeneity regulated by the Bithorax Complex-Wnt signaling crosstalk in Drosophila

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

summary: Adipocytes distributed throughout the body are essential for lipid metabolism and energy homeostasis, with regional differences affecting their functions and disease susceptibility. However, the mechanisms driving this regional heterogeneity remain poorly understood. Here, we show that the interactions between Wnt/Wingless signaling and Bithorax Complex (BX-C) genes – specifically abdominal A (abd-A) and Abdominal B (Abd-B) – drive regional differences in Drosophila larval adipocytes. Abdominal adipocytes, expressing abd-A and Abd-B, differ from thoracic ones, with active Wnt signaling further amplifying these differences. Depleting abd-A and Abd-B, genes in adipocytes reduces fat accumulation, delays larval-pupal transition, and leads to pupal lethality, while also attenuating Wnt signaling-induced lipid mobilization. Moreover, Wnt signaling stimulates abd-A and Abd-B, transcription, creating a feedforward loop that intensifies the interaction between Wnt signaling and BX-C genes. These findings elucidate how the crosstalk between cell-autonomous BX-C gene expression and Wnt signaling defines adipocyte heterogeneity in Drosophila larvae.

overall_design: RNA-seq on fat bodies of control or axn/abd-A/Abd-B depleted animals. Following principal component analysis (PCA), we excluded two outlier samples from subsequent analyses: dcg+4 from the dcg+ group and dcg-AiBi-1 from the dcg-AiBi group.


title: Gene expression-based, individualized outcome prediction for surgically treated  patients with acanthosis nigricans

city: Changsha

first: Jianyun

last: Lu

state: Hunan

address: Tongzipo Road, Yuelu District

institute: Third Xiangya Hospital, Central South University

type:
Non-coding RNA profiling by array
Expression profiling by array
Methylation profiling by array

summary: To investigate the potential mechanism of m6A modification in the development of obesity-related AN

overall_design: In the study presented here, m6A ArrayStar apparent transcriptome sequencing was performed in lesional skin and normal human skin tissues collected from patients with AN

first: JIanyun


title: Myocardial Reprogramming by HMGN1 Underlies Heart Defects in Trisomy 21 (CutnRun)

status: Public on Aug 28 2025

city: San Francisco

first: Angelo

last: Pelonero

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

summary: Congenital heart defects (CHD) are the most common form of developmental abnormalities, occurring in ~1% of live births, and can arise due to altered dosage of genes essential for cardiogenesis. Aneuploidy accounts for nearly 15% of CHD and the most frequent form involves trisomy of chromosome 21 (Ch21), resulting in Down Syndrome (DS). Here we used single cell RNA-seq, CRISPR-activation with single cell RNA-seq, single cell ATAC-seq and Cut&Tag epigenomic profiling to define the molecular disruptions occuring with Trisomy 21 and upregulation of the Ch21 epigenetic factor HMGN1. These experiments were performed in human pluripotent stem cells (hiPSCs) or in directed differentiation to cardiomyocyte lineages at days 10 and 20.

overall_design: Cut and Run samples for HMGN1-Flag. Cardiomyocytes differentiated from human induced pluripotent stem cells (hiPSCs) were collected at day 20 for CUT&RUN analysis. Cells were dissociated using 0.25% Trypsin-EDTA (1X) (Gibco, 25200-072) and neutralized with 1% FBS in PBS. For each condition, 150,000 cells per sample were processed according to the manufacturer’s instructions using the CUTANA™ CUT&RUN Kit (Epicypher, 14-1048). Cells were first washed and bound to activated Concanavalin A (ConA)–coated magnetic beads in the Bead Activation Buffer. Nuclei were permeabilized with Digitonin-containing buffer, and all buffers were supplemented with cOmplete™ Mini, EDTA-free Protease Inhibitor Cocktail (Millipore Sigma, 11836170001).  Samples were incubated with 0.5 µg of H3K4me3 primary positive control antibody (Epicypher 13-0060), 1 µL of IgG control antibody, and 1 µg of Monoclonal ANTI-FLAG M2 antibody (Sigma-Aldrich, F1804-200 µG) per sample at 4 °C overnight on a rotating mixer. After antibody binding, samples were washed by cell permeabilization buffer. Protein A-MNase fusion enzyme was added to each sample and incubated at 4 °C for 1 hour with mixing. Targeted chromatin digestion was initiated by adding calcium-containing digestion buffer and incubating at 0 °C for 30 minutes. Reactions were stopped with Stop Buffer supplemented with glycogen and RNase A, followed by incubation at 37 °C for 10 minutes to release digested chromatin fragments.  DNA was purified using phenol-chloroform extraction or DNA Clean & Concentrator kit (Zymo Research), followed by SPRIselect bead cleanup (Beckman Coulter, B23317) and 80% ethanol washes. Elution was performed with 0.1X TE buffer, and DNA concentration was measured using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32851). Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645), indexed with i5/i7 dual indices, and amplified by PCR. Library DNA size distribution was assessed using the Agilent Bioanalyzer High Sensitivity DNA kit (Agilent, 5067-4626). Final libraries were pooled and sequenced on an Illumina NextSeq 500/550 using the Mid Output v2 kit (Illumina, 20024904) with the following cycle configuration: Read 1: 75 bp, Index 1: 8 bp, Index 2: 8 bp, Read 2: 75 bp.

first: Sanjeev

last: Ranade

first: Deepak

last: Srivastava


title: Gene expression of hepatocellular carcinoma tissue in China Medical University Hospital (CMUH) cohort of Taiwanese patients

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

institute: China Medical University

summary: It’s unknown what, how, and why lipid metabolites involve in cancer prognosis. This work implementing multi-omics measurement in hepatocellular carcinoma (HCC) patient cohort to associate tumoral lipidome, transcriptome, and serological metabolome to disease prognosis. Data indicating that dietary related ether-lipids, e.g., PC O- and PE O-, promote cell mobility and poor prognosis through TRPV2-related cytoskeletal rearrangement. In addition, downregulation of Peroxisome Proliferator-Activated Receptorα (PPARα) and consequential lipophagic deficit increase ether-lipids in cancer cells. Unfortunately, pathological coupling of Very Low-Density Lipoprotein Receptor (VLDLR) overexpression in HCC patients, concordantly deteriorates ether-lipid accumulation and facilitate HCC prognosis via VLDL entrance, the diet direct responding lipoprotein. Knocking out hepatic VLDLR reduce HCC burden in human etiology-related spontaneous HCC mouse model, which demonstrated the pathological causality in HCC. At last, administration of VLDL-Mimicking Nanoparticle encapsulating Lenvatinib, or fenofibrate (PPAR αagonist) could effectively diminished tumor anarchy.

overall_design:
To investigate the role of VLDLR in the poor prognostic HCC, we cooperate with China Medical University Hospital to collect HCC specimens.
Tissue was collected from HCC patients receiving surgery at China Medical University Hospital for 2011-2013. The specimens was keep in RNA-Keeper buffer and sotred in －80℃ freezers. The RNA was obtained from HCC patients (n=71) for analysis. All of RNA samples were assessed on next-generation sequencing.

first: Wen-Lung

last: Ma

first: Pei-Yin

last: Liao

first: Wen-Jen

last: Lin


title: Safety and Regenerative Properties of Immortalized Human Mesenchymal Stromal Cell Secretome

city: Moscow

first: Vadim

last: Chechekhin

address: Leninskie gory 1

country: Russia

institute: Lomonosov Moscow State University

summary: The secretome of mesenchymal stromal cells (MSCs) can efficiently stimulate regeneration and therefore is a tempting remedy for “cell-free cellular therapy”. However, the usage of primary MSC cultures as secretome-producers for translation studies has obvious obstacles, including rapid aging of MSC cultures, the need for a large number of verified donors and donor-to-donor variability of secretome content. MSCs immortalization allows to overcome those limitations and to obtain secretome-producing cultures with prolonged lifetime. However, the efficacy and safety of such secretomes are critical issues, which limit their usage as therapeutic agents. In this study we have tested in large detail how the immortalization of MSC cultures affects the content, biological activity and safety of their secretome. MSCs immortalization via overexpression of human TERT gene does not significantly alter the qualitative and quantitative composition of their secretome or its activity according to the results of proteomic analysis, ELISA, qPCR and functional tests in vitro. Moreover, we have demonstrated that the secretome of immortalized MSCs does not contain detectable amounts of telomerase and does not possess any transforming activity. Altogether, our data suggest that immortalized MSC cultures may become a reliable source for obtaining standardized active secretome in large-scale quantities for clinical use.

overall_design: To assess the potential ability of iMSC secretome to alter expression of pro- and anti-oncogenes in target cells, we analyzed the transcriptome of primary human dermal fibroblasts treated with the secretome of pMSCs and iMSCs. For this purpose, we used cultures of primary human dermal fibroblasts of 5-8 passages of 80-90% confluent. In experimental groups growth medium was replaced with the non-concentrated secretome of pMSCs or iMSCs. In the negative control group, cells were cultured in complete fibroblast growth medium, and in the positive control groups mutagen solutions (3mM sodium nitrite or 0.01% DMS in complete fibroblast growth medium) were used [32,33]. In the DMS group, 6 hours after the start of the experiment, the DMS solution was replaced with the complete fibroblast growth medium. Test solutions were renewed every 3 days, and 7 days after the start of the experiment, the fibroblast cultures were lysed for total RNA isolation as described above. About 800 ng of total RNA (for each group) was utilized for library construction employing the NЕВNext® Poly(А) mRNА Magnetiс Isоlatiоn Mоdulе alongside the NЕВNext® Ultra II™ Dirесtiоnal RNА Librаry Prер Kit for Illuminа (Nеw Еnglаnd Biоlаbs), following the manufacturer’s guidelines. Libraries integrity and quality were evaluated using the Biоаnalyzеr 2100 (Аgilеnt), and confirmed by quantitative PCR. Sequencing was conducted on an Illuminа NоvаSеq 6000 platform with 61 bр pаirеd-end reads. Subsequent data processing and analysis were performed using the SТАR aligner, Subrеаd, and DЕSеq2 software tools. The resulting gene lists were annotated using the g:Profiler resource.

first: Maxim

last: Karagyaur


title: Scalers hypothesis and its confirmation in sea urchin embryos

first: Fedor

middle: M

last: Eroshkin

address: 16/10 Miklukho-Maklaya str.

institute: IBCH RAS

summary: The phenomenon of embryonic scaling, the ability of embryos to regulate their structure in proportion to size, is a fascinating yet underexplored area of study. First described in sea urchin embryos by Hans Driesch, this phenomenon is now recognized as a striking example of how living organisms use non-equilibrium self-organization to generate pattern-determining morphogen gradients that scale with embryo size. Although specific molecular mechanisms for scaling morphogens gradients have been described in some cases, a general approach for the targeted identification  such mechanism had not been elaborated until recently. In search of a solution, we hypothesized the obligatory participation in the scaling mechanisms of special genes, which we named scalers, with their expression being sensitive to the size of the embryo and their protein products regulating the scale of morphogen gradients. As proof of principle, we recently identified scalers by detecting differentially expressing genes in wild-type and half-size Xenopus laevis gastrula embryos. We also described a novel mechanism by which one of the identified scalers, the gene encoding metalloproteinase 3 (Mmp3), modulates gradients of the morphogenic protein Bmp and its antagonists Chordin and Noggin1/2 based on Xenopus laevis embryo size. To test the universality of the scalers hypothesis, we now applied our method of identifying scalers that adjust Bmp/Chordin gradients to the size of the sea urchin embryo, Strongylocentrotus droebachiensis. Our results show that at least two members of the gene cluster encoding astacin proteinases of the Span family, namely bp10 and Span, exhibit properties characteristic of scalers in the embryos of this species. Notably, their expression increases in half-size embryos, and their protein products specifically digest Chordin. Additionally, we found that the loss of function of bp10 and span lead to contraction of the ventral domain of the Bmp signaling nuclear effector, pSmad1/5. These findings not only validate the scalers hypothesis but also uncover a novel mechanism by which Span proteinases fine-tune Chordin and Bmp morphogen gradients in sea urchins, offering promising avenues for future research into scaling mechanisms across biological systems.

overall_design: Three biological replicates were analyzed for 2 conditions (intact embryos vs their siblings divided at two-blastomere stage and grown to mesenchyme blastula stage)

first: A

middle: G

last: Zaraisky

first: F


title: Single-cell analysis of castration-resistant prostate cancers to identify potential biomarkers for diagnosis and prognosis of neuroendocrine prostate cancer

city: Taipei

first: Pei-Ching

last: Chang

address: No. 155, Sec. 2, Linong Street, Beitou District

department: Institute of Microbiology and Immunology

institute: National Yang Ming Chiao Tung University

summary: The high heterogeneity and low percentage of neuroendocrine cells in prostate cancer limit the utility of traditional bulk RNA sequencing and even single-cell RNA sequencing to find better biomarkers for early diagnosis and stratification. Re-clustering of specific cell-type holds great promise for identification of intra-cell-type heterogeneity. However, this has not yet been used in studying neuroendocrine prostate cancer heterogeneity. Neuroendocrine cluster(s) were individually identified in each castration-resistant prostate cancer specimen and combined for trajectory analysis. Three neuroendocrine states were identified. Neuroendocrine state 2 with the highest AR score was considered the initial starting state of neuroendocrine transdifferentiation. State 1 and state 3 with distinct high neuroendocrine scores and marker genes enriched in N-Myc and REST target genes, respectively, were considered as two different types of neuroendocrine differentiated cancer cells. These two states contained distinct groups of prostate cancer biomarkers and a strong distinguishing ability of normal versus cancerous prostate across different pathological grading was found in the N-Myc-associated state. Our data highlight the central role of N-Myc and REST in mediating lineage plasticity and classifying neuroendocrine phenotypes.

overall_design: A lymph node metastasis of prostate cancer was obtained from a 60-year-old male patient. The resulting cell suspension was enriched for viable cells using Ficoll density gradient centrifugation and subsequently analyzed by single-cell RNA sequencing.

first: Tzu-Ping


title: ImmuniT Platform for Improved Neoantigen Prediction in Lung Cancer

city: Irvine

first: Stephanie

middle: Jeanelle

last: Hachey

address: 2400 Biological Sciences III

institute: UC Irvine

summary:
Background: Lung cancer remains the leading cause of cancer-related mortality, with many patients responding poorly to immunotherapy due to limited tumor recognition. Neoantigen-based strategies offer a promising solution, but current discovery methods often miss key targets, particularly those with low or heterogeneous expression. To address this, we developed ImmuniT, a three-phase platform for enhanced neoantigen discovery and validation. Methods: Under an IRB-approved protocol, patients with lung cancer consented to tumor collection for ex vivo processing to modulate antigen expression. Autologous T cells from matched blood were co-cultured with treated cancer cells to expand tumor-reactive populations. The nextneopi pipeline integrated mutational, transcriptomic, and HLA data to predict candidate neoantigens, which were validated using MHC epitope tetramer staining. Results: In five patient samples, ImmuniT identified a broader spectrum of neoantigens and induced stronger T cell activation in vitro compared to conventional approaches. Notably, in one case, two neoantigens missed by standard methods were confirmed to elicit tumor-specific T cell responses in both the tumor-infiltrating and peripheral compartments. Conclusions: These findings highlight ImmuniT’s potential to expand the repertoire of actionable tumor antigens and improve personalized immunotherapy strategies, particularly for patients with limited response to existing treatments.
Note: This submission provides de-identified, summary-level results from NSCLC patient samples, including normalized RNA-seq counts, differential expression (DE) results, and copy number variation (CNV) calls. Raw sequencing files (FASTQ/BAM/VCF) are not deposited due to informed consent limitations; see README.

overall_design:
Case-series of 5 lung cancer samples; processed-only GEO submission with per-sample normalized counts and CNV calls; study-level DE results.

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


title: CREPT aggravates liver fibrosis through TGF-β activated-Smad2/3 but not Smad4 in hepatocytes

city: Beijing

first: Ming

middle: han

last: wang

address: Haidian road

institute: Tsinghua university

summary: Background & Aims: Liver fibrosis, a serious medical condition with limited therapies, frequently progresses to cirrhosis and other severe complications. Here, we report that cell cycle-related and expression elevated protein in tumor (CREPT) is up-regulated in liver fibrosis. CREPT preferentially enhances transforming growth factor-β (TGF-β)-activated Smad2/3, rather than the canonical Smad2/3-Smad4 complex, thereby facilitating liver fibrosis progression. Methods: We analyzed public transcriptomic and proteomic datasets from patients with liver fibrosis. Human tissue arrays and mouse models of fibrosis were used to investigate CREPT expression patterns. Hepatocyte-specific overexpression (TG-CREPT) and deletion (CREPThep-/-) mice were subjected to acute liver injury (24 h, high-dose CCl4), chronic fibrosis (28 d, low-dose CCl4), and bile duct ligation (BDL) to induce liver fibrosis. Histological, biochemical, and RNA-sequencing (RNA-seq) analyses and CUT&Tag experiments were conducted. Results: CREPT is predominantly enriched in hepatocytes and upregulated in fibrotic liver tissues from patients and mice induced by CCl4 or BDL. Overexpression of CREPT in hepatocytes exacerbates liver injury and fibrosis in mice under acute or chronic CCl4 exposure and BDL challenge. In contrast, hepatocyte-specific deletion of CREPT significantly alleviates liver fibrosis. Mechanistically, CREPT aggravates TGF-β/Smad signaling pathway, preferentially interacting with Smad2/3, but not Smad4, to promote inflammatory responses, and up-regulates fibrogenic genes, including Cebpd, Fosl2 and Fn1. Intriguingly, targeting CREPT with LNP-delivered siRNA (LNP-siCREPT) and GalNAc-delivered siRNA (GalNAc-siCREPT) significantly reduces pre-existing liver fibrosis in mice. Conclusions: Our findings identify a promoting effect of CREPT on liver fibrosis through TGF-β-activated Smad2/3 but not Smad4. Targeting CREPT represents a potential therapeutic strategy for liver fibrosis.

overall_design: CUT& Tag of CREPT, Smad2/3 and Smad4 in fibrotic livers of hepatocyte-specific deletion (CREPThep-/-) mice with bile duct ligation (BDL).

first: Minghan

last: Wang

first: Yinan

last: Duan

first: Renbo


title: Dual role of ZIC2 during neural induction: from pioneer transcription factor to enhancer activator [ChIP-Seq]

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria

summary: ZIC2, a member of the Zinc Finger of the Cerebellum family of transcription factors (TFs), plays crucial roles during neural development. In humans, defects in ZIC2 cause holoprosencephaly, a congenital brain malformation characterized by the defective cleavage of cerebral hemispheres due to problems in midline patterning. However, the gene regulatory network (GRN) controlled by ZIC2 and the regulatory mechanisms it employs during neural development remain largely unexplored. Here, we combined a mouse embryonic stem cell (mESC) in vitro differentiation model towards anterior neural progenitors (AntNPCs) with genome editing approaches, bulk and single cell (i.e. Multiome scATAC + scRNAseq) genomic methods to elucidate the precise GRN controlled by ZIC2 and the underlying mechanisms. We found that ZIC2 shows widespread binding throughout the genome already in mESC as well as upon pluripotency exit and neural induction. Despite its extensive binding in mESC, ZIC2 function is dispensable in pluripotent cells due to compensation by ZIC3. In contrast, ZIC2 plays a major regulatory function during neural induction, directly controlling the expression of master regulators implicated in the patterning and morphogenesis of specific brain regions, such as the midbrain (e.g., En1, Lmx1b, Pax2, Wnt1) and the roof plate (e.g., Lmx1a, Wnt3a). Mechanistically, ZIC2 plays a dual role in neural differentiation: (i) during pluripotency exit, ZIC2 acts as a pioneer TF, binding de novo to distal enhancers and promoting their chromatin accessibility; (ii) during neural induction, ZIC2 is essential for the activation of a subset of the previously primed enhancers, which in turn control the expression of major neural patterning regulators and signaling pathways (i.e. WNT) that prevent the premature differentiation of neural progenitors. Overall, our work shows that, by sequentially acting as a promiscuous pioneer and selective activator of enhancer elements, ZIC2 canalizes pluripotent cells towards neural progenitors with rostro-dorsal identities.

overall_design: Genome-wide binding profiles of ZIC3 were mapped by ChIP-seq specifically in mouse embryonic stem cells (mESCs, day 0 of differentiation, D0). In addition, ZIC2 binding was assessed through in vitro differentiation of an endogenously tagged Zic2Flag-HA (Z2FH) mESC line in both wild-type (WT) and, where applicable, Zic2-/- (Z2KO) backgrounds. ChIP-seq experiments were performed at three differentiation stages:  day 0 (D0, mESCs), day 3 (D3, early progenitors), and day 6 (D6, anterior neural progenitors, AntNPCs). In parallel, ChIP-seq for selected histone modifications was carried out in WT and Z2KO cells at the same timepoints to define the genome-wide profiles of the different histone marks examined.

first: Víctor

last: Sánchez-Gaya

first: María

last: Mariner-Faulí

first: Álvaro


title: Spatially Resolved Microglial Expression Around Aβ Plaques in Human Alzheimer’s Disease Tissue

city: London

first: Jack

last: Wood

state: County

address: Gower Street

department: Neuroscience, Physiology and Pharmacology

country: United Kingdom

institute: University College London

summary: Using microglia-enriched spatial transcriptomics on human Alzheimer’s disease tissue, we identify distinct gene expression changes across microglia located in direct contact with plaques, in periplaque regions, and in areas distant from plaques. We define a group of plaque contact–only microglial (PCOM) genes whose expression increases exclusively in microglia directly contacting plaques. These genes show significant overlap with previously reported gene sets, suggesting that plaque-contacting microglia correspond to the well-characterised disease-associated microglia (DAM) and other AD-related gene-expression signatures. We further identify distinct co-expression networks associated with disease-relevant covariates, including an immune module linked to APOE genotype and a synaptic–mitochondrial module negatively associated with Braak stage. Finally, we compare the human dataset to our previously published data from 18-month-old AppNL-F mice, generated using the same experimental paradigm and demonstrate cross-species concordance in gene expression within plaque-contacting microglia.

overall_design: NanoString GeoMx Digital Spatial Profiler (DSP) was applied to FFPE human hippocampus to profile microglia-enriched gene expression from donors with Alzheimer’s disease (AD) and cognitively unimpaired, amyloid-positive (CU-AP) controls. For each tissue, gene expression was captured from microglia directly contacting amyloid plaques (“plaque-associated”), (ii) microglia in the peri-plaque region, and (iii) microglia distant from plaques.

middle: I

first: Georgia

last: Ppasia

first: Paul

last: Rolland-Du-Roscoat

first: Sneha

last: Desai

first: Shamim

last: Choudhury

first: Aya

last: Balbaa

first: Daria

last: Gavriouchkina

first: Modesta

last: Blunskyte

first: John

last: Hardy

first: Damian

last: Cummings

first: Dervis

last: Salih

first: Jörg

last: Hanrieder

first: Frances

last: Edwards


title: Silencing AADAC enhances trophoblast invasion and reveals a protective angiogenic role in severe preeclampsia

city: Changwon

first: Hyo Jung

last: An

address: 11 samjeongja-ro, seongsan-gu

country: South Korea

institute: Gyeongsang National University Changwon Hospital

summary:
Background: Preeclampsia (PE) is a serious complication of pregnancy characterized by hypertension and organ dysfunction. The pathogenesis involves impaired trophoblast invasion and inadequate spiral artery remodeling, but the exact molecular mechanisms are not fully understood.
Methods: This study aimed to investigate the role of arylacetamide deacetylase (AADAC) in the pathogenesis of PE and its effects on trophoblast function. Placental tissues were collected from 30 PE patients and 15 controls. RNA sequencing was performed for 6 severe PE samples and 6 control samples. AADAC expression in primary trophoblasts was validated via semiquantitative PCR and Western blotting. To investigate AADAC function under hypoxia, HTR8/SVneo cells were treated with CoCl2, and AADAC expression was manipulated through siRNA knockdown and overexpression. Invasion and tube formation assays were conducted to assess trophoblast function.
Results: RNA sequencing revealed upregulated AADAC expression in placental tissue from PE patients. AADAC mRNA levels were significantly greater in placental cells from PE patients than in those from controls (p<0.01), whereas AADAC protein expression was lower (p<0.01). Subjecting HTR8/SVneo cells to hypoxia for 18 hours significantly increased AADAC mRNA and protein expression (p<0.001) and HIF1-alpha protein levels (p<0.05). Compared with those in control cells, the invasion (p<0.01) and tube formation (p<0.01) of hypoxia-treated HTR8/SVneo cells were greater after AADAC silencing. AADAC overexpression reduced tube formation (p<0.001) but did not significantly affect invasion.
Conclusions: This study demonstrated that under hypoxic conditions, AADAC expression is significantly altered in human PE placental tissues and may play a role in trophoblast invasion and angiogenesis, which are key processes in the pathogenesis of PE. While further research is needed to elucidate the underlying mechanisms and confirm its clinical relevance, these findings suggest that AADAC could be a potential factor involved in the management of PE.

overall_design: RNA-seq profiling of placental samples from women with normal pregnancies and placental samples from women with severe preeclampsia


title: Integrated Base Editing and Microfluidics Boost Microbial Lipid Production from Lignin

city: Tianjin

first: Jinyang

last: Li

address: No. 32, Xiqi Road, Tianjin Airport Economic Park

summary: Lignin, a recalcitrant aromatic biopolymer, represents a promising feedstock for sustainable biorefining. In this study, we characterized the transcriptional response of the fungus Curvularia clavata J1 to alkali lignin (AL) and developed a Cu2+-inducible MCM5–AID base editing system for genome-wide C-to-T and G-to-A mutagenesis. Transcriptomic analysis revealed that AL exposure triggered upregulation of genes involved in electron transport, lipid catabolism, and iron homeostasis. Using droplet microfluidics, we conducted ultrahigh-throughput screening and identified a mutant strain, M6, exhibiting superior phenotypic traits. When cultivated in lignosulfonate medium, M6 showed a 33–36% increase in lipid production and a 75–87% enhancement in laccase activity. Transcriptional profiling further indicated reinforced metabolic pathways related to fatty acid, steroid, and glycerolipid biosynthesis, redirecting carbon flux toward the formation of oil-enriched single-cell protein. This study establishes an integrated platform for lignin valorization and underscores the synergy between synthetic biology and microfluidics for precision engineering of fungal hosts.

overall_design: For comparative transcriptomic analysis of the wild-type (WT) strain under alkaline lignin (AL) conditions, mycelia were inoculated in 100 mL of minimal medium (MM) containing either 1% (w/v) AL (WT_L) or 1% glucose (WT_G) as the carbon source, and cultured at 30°C with shaking at 200 rpm for four days. To compare the transcriptional profiles of the M6 mutant and WT grown on lignosulfonate, both strains were cultivated in MM supplemented with 0.3% (w/v) glucose and 1% (w/v) lignosulfonate under the same conditions. After incubation, mycelia were harvested, washed two times with sterilized water, and processed for RNA extraction. Biological triplicates were prepared for each experimental condition.

first: Le

last: Gao

first: Xin

last: Wu


title: Myocardial Reprogramming by HMGN1 Underlies Heart Defects in Trisomy 21 [scRNA-seq]

first: Angelo

last: Pelonero

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We used human pluripotent stem cells (hIPSCs) from an individual who was mosaic for Down Syndrome. Thus we compare cells that are trisomic for Ch21 with cells that are isogenically similar and disomic for Ch21. As well, we generated a CRISPR-activation knock-in to disomic cells and used sgRNAs directed to chromosome 21 genes. Sample replicates are defined and all single cell samples were processed with 10X Genomics pipelines. Cut&Run samples were processed with Epicypher reagents. All samples were isolated with Accutase or Trypsin reagents.

first: Sanjeev

last: Ranade

first: Deepak

last: Srivastava


title: The genetic architecture of the human bZIP interaction network

city: Basel

first: Alexandra

middle: Michaela

last: Bendel

address: Maulbeerstr. 66

department: Genome Regulation

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: nderstanding the complexity of the genetic architecture underlying protein function is key to 20building accurate predictive models for therapeutic and bioengineering applications. Here, we systematically mutagenized all 54 human basic-leucine zipper (bZIP)domains and quantified their interactions with each other using bindingPCA, a quantitative deep mutational scanning assay. This resulted in ~2 million interaction measurements, capturing the effect of all single amino acid substitutions at each of the 35 interfacial positions. We found that mutation effects 25are largely additive in the vicinity of each wild-type bZIP, but diverge across the family, indicating strong context dependency. A global additive thermodynamic model provided moderate prediction of mutation effects, while individual models per bZIP achieved higher performance, supporting a model of local simplicity and global complexity. A convolutional neural network trained on this dataset accurately predicted binding scores from sequence alone. 30Furthermore, the model enabled the design of synthetic bZIPs with high target specificity, demonstrating practical applicability for bioengineering purposes. Our study shows that capturing family-wide diversity is essential to reveal context dependencies and train accurate quantitative models of protein-protein interactions.

sample_organism:
Escherichia coli
Saccharomyces cerevisiae

overall_design: Deep Mutational Scanning of the entire human bZIP domains and measurement of the effect on protein-protein interactions. Provided is NGS data that serves as readout for protein interaction.

first: Bastian

last: Eichenberger

first: Georg

last: Kempf

first: Dominique

last: Klein

first: Kenji

last: Shimada

first: Marcella

last: Franco

first: Sebastian

last: Jaaks-Kraatz

first: Sevi

last: Durdu

first: Vivian

last: Herrmann

first: Gregory

last: Roth

first: Charlotte

last: Soneson

first: Sebastien

last: Smallwood

first: Nicolas

last: Thomä

first: Dirk

last: Schübeler

first: Michael

last: Stadler

first: Friedemann

last: Zenke

first: Guillaume

last: Diss


title: Single-cell RNA-seq of MMTV-PyMT mouse lungs treated with long-term systemic tamoxifen treatment

city: Seoul

first: Mi-Ock

last: Lee

address: 1 Gwanak-ro

department: College of Pharmacy

institute: Seoul National University

summary: Estrogen receptor (ER)-positive breast cancer (BC) patients face constant threat of distant recurrence up to 20 years of diagnosis, reaching a total of 30% recurrence and a mortality rate of more than 25%. Here, we examined the influence of long-term tamoxifen treatment in metastatic niche formation in vivo. To test this, placebo or tamoxifen pellets were inoculateded in the 8-week old MMTV-PyMT mouse model and analyses were conducted 5-weeks after the treatment. Despite a reduction in primary tumor size compared to the placebo-treated group, lung metastasis was increased in the tamoxifen-treated mouse. At this point, scRNA-seq was also performed in mouse lungs of either placebo or tamoxifen-treated MMTV-PyMT mouse lungs, which revealed an increase in an interstitial macrophage subpopulation in the tamoxifen-treated group. This Prg4+ macrophages had enhanced lipid metabolic gene signatures and strongly interacted with fibroblasts via TGFβ1 signaling pathway, potentially contributing to lung fibrosis. This study identifies long-term tamoxifen treatment as a risk factor for promoting breast cancer cell resistance and altering the lung microenvironment, thereby facilitating lung metastasis.

overall_design: FVB/NJ mice mammary tumor virus–polyoma middle tumor-antigen (MMTV-PyMT; designated as PyMT) (RRID: IMSR_JAX:002374) at 8-weeks-old were separated randomly into two groups (n=2 for each group) and implanted with tamoxifen pellets (5 mg, 60-day release) (Innovative Research of America, SE-361) or placebo pellets (SE-111). Tumor diameter was measured with caliper two times a week, and tumor volumes were estimated using the following formula: tumor volume (cm3) = (length x width2) x 0.5. After 5 weeks of implantation, mice were sacrificed and lungs were removed after perfusion with sterile saline from the right to the left ventricle of the heart.

first: Minsoo

last: Noh

first: Seung-Su

last: Kim

first: Seungchan

last: An


title: RNA-seq of in vivo B7H3_CAR_T cells loaded with oncolytic virus VSVΔ51

city: Guangzhou

first: Fan

last: Xing

address: Zhongshan Road

institute: Guangdong Provincial People's Hospital

summary: To investigate the in vivo functions of CR2/3-CAR-T loaded with VSVΔ51 after infiltrating tumor microenvironment, we  analyzed the transcriptomic signatures at early stage after CAR-T infiltrating into tumor tissue. We isolated the CAR-T cells from the mouse tumor and used RNA sequence to study the global gene expression. We identified differentially expressed genes in B7H3-CAR-T cells and CR2/3-B7H3-CAR-T cells loaded with loading VSVΔ51, aiming to identify the changed pathways that are influenced by the cross-connection between VSV-G protein and CR2/3-CAR moiety.

overall_design: For CAR-T cell construction, the activated CD3 positive human T lymphocytes were transduced with lentivirus carrying the B7H3-CAR and CR2/3-B7H3-CAR. To preload VSVΔ51, B7H3-CAR-T or CR2/3-B7H3-CAR-T cells were co-incubated with VSVΔ51 (MOI=10) on ice for 1 hour. The CAR-T cells were injected into the NCG mice bearing U87 tumor,  then CAR-T cells were isoalted from the  tumor tissue  after 16 house post injection. The samples used in the RNA sequence analysis were in triplicates.


title: FOXO1 links KRAS G12D and G12V alleles to glutamine and nitrogen metabolism in colorectal cancer

city: Uxbridge

first: Alessandro

last: Esposito

state: Select a State/County

address: Kingston Lane

department: Centre for Genome Engineering and Maintanance

institute: Brunel University of London

summary: Mutations in KRAS, particularly at codon 12, are frequent in adenocarcinomas of the colon, lungs and pancreas, driving carcinogenesis by altering cell signalling and reprogramming metabolism. However, the specific mechanisms by which different KRAS G12 alleles initiate distinctive patterns of metabolic reprogramming are unclear. Using isogenic panels of colorectal cell lines harbouring the G12A, G12C, G12D and G12V heterozygous mutations and employing transcriptomics, metabolomics, and extensive biochemical validation, we characterise distinctive features of each allele. We demonstrate that cells harbouring the common G12D and G12V oncogenic mutations significantly alter glutamine metabolism and nitrogen recycling through FOXO1-mediated regulation compared to parental lines. Moreover, with a combination of small molecule inhibitors targeting glutamine and glutamate metabolism, we also identify a common vulnerability that eliminates mutant cells selectively. These results highlight a previously unreported mutant-specific effect of KRAS alleles on metabolism and signalling that could be potentially harnessed for cancer therapy.

overall_design: We have done RNA sequencing (transcriptomics) to reveal differences between different KRAS mutants. We used a commercially available isogenic cell line based on the colorectal cancer SW48 line with heterozygote knockin mutations G12A, G12C, G12D and G12V. Having identified FOXO1 as a possible mediator of metabolic reprogramming induced by KRAS mutants, we have repeated the work in low nutrient conditions, and with a FOXO1 inhibitor.

first: Suzan

last: Ber

first: Khushali

last: Patel

first: Annie

last: Howitt

first: Shamith

last: Samarajiwa


title: Brain pericytes and Wnt/β-catenin signaling induce functional blood-brain barrier phenotype in human iPSC-derived model

city: Amsterdam

first: Henrique

last: Nogueira Pinto

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

summary: The blood-brain barrier (BBB), formed by brain microvascular endothelial cells (BMECs), restricts vascular permeability by establishing tight junctions, reducing vesicular transport, and regulating molecular trafficking via dedicated transporters. In disease, BBB dysfunction leads to barrier disruption and neuroinflammation. Existing human in vitro BBB models recapitulate some but not all of these key BMEC features. Here, we present a method to differentiate human induced pluripotent stem cells (hiPSCs) into BMECs (hiBMECs) by co-culturing hiPSC-derived endothelial cells with brain pericytes (hiBPCs) and activating the Wnt/β-catenin pathway. The resulting hiBMECs exhibit barrier properties, functional efflux transporters, and appropriate inflammatory responses. RNA sequencing revealed a transcriptomic profile in hiBMECs closely matching the adult human BBB. Mechanistically, hiBPCs and Wnt/β-catenin signaling provided complementary cues that converged on ETS1, SMAD3/4, and PPARγ transcriptional networks. These findings reveal a synergistic mechanism by which brain pericytes and Wnt/β-catenin signaling orchestrate human BMEC differentiation and function, providing mechanistic insight into human BBB development and an improved hiPSC-derived BBB model for future drug screening and disease modeling.

overall_design: RNA-seq profiling of hiBMEC, hiEC, hiEC+hiBPC, hiEC+CHIR, hiBPC, hiBPC+hiEC and hiBPC+hiBMEC, with or without inflammatory stimulation with TNFa and IFNg (25 IU/mL, 16h).

first: Nine R

last: Kok

first: Philipp C

last: Hauger

first: Manon

last: Kersten-van Diepen

last: de Kok

first: Nanne J

last: Paauw

first: Susanne MA

last: van der Pol

first: Joline P

last: Nugteren-Boogaard

first: Peter L

last: Hordijk

first: Stephanie D

last: Beekhuis-Hoekstra

first: Susan

last: Gibbs

first: Nienke M

last: de Wit

first: Helga E

last: de Vries


title: IL-25-induced effector-memory ILC2s mediate small intestinal adaptation

first: Victor

middle: S

last: Cortez

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

summary: This study used bulk ATAC sequencing of epitheilal crypt organoids grown for 6 days, which were isolated from proximal small intestines of wild type mice +50 days after an IL-25 regimen or PBS regimen to study chromatin accessibility.

overall_design: Mice (wild type) were injected i.p. with IL-25 (500ng) or PBS 3x a week for 4 weeks and then rested for 50+ days. Epithelial crypts were isolated from the proximal small intestine, grown under standard organoid conditions for 6 days, and organoids isolated from Matrigel and dissociated as detailed below. Cells were washed with basal medium containing 10% FBS, stained in FACS wash buffer containing antibodies for flow cytometry (EpCAM+), then resuspended in FACS wash buffer containing DAPI. Single, live EpCAM+ cells were sorted and 100k cells per sample were used as input for ATAC libraries. Cells were then used for bulk ATAC sequencing.

first: Dedeepya

last: Vaka

first: Dario

last: Boffelli

first: Sara

last: Viragova


title: Microarray analysis of peripheral blood mononuclears of breast cancer patients

city: Tomsk

first: Alexei

last: Sleptcov

address: Ushaika 10

department: Research Institute of Medical Genetics

institute: Tomsk National Research Medical Center

summary: This study aimed to perform microarray analysis of the peripheral blood mononuclear cell (PBMC) transcriptome to evaluate differential lncRNA expression in women with luminal A breast cancer

overall_design: A one-color microarray analysis was conducted using SurePrint G3 Human Unrestricted 8×60K arrays and a SureScan Microarray Scanner

first: Renata

last: Savchenko

first: Varvara

last: Minina


title: Modeling hereditary distal renal tubular acidosis using patient-derived iPSCs with WDR72 mutations

city: Khon Kaen

first: ์Narissara

last: Kaewboonlert

state: Khon Kaen

address: Mittraphap Rd

department: Department of Biochemistry, Faculty of Medicine

country: Thailand

institute: Khon Kaen University

summary: Distal renal tubular acidosis (dRTA) is a rare genetic disorder characterized by impaired urine acidification. The WDR72 gene has recently been implicated in dRTA, though its precise functional mechanisms remain unclear. In this study, we generated induced pluripotent stem cell (iPSC) from a patient with WDR72 mutations to model the disease. Upon differentiation into renal tubular epithelial cells, the wild-type and mutant cells (variants c.1777A>G and c.2522T>A) were analyzed for RNA expression, protein localization, and H+-ATPase trafficking. The results indicated no significant changes in these parameters, with the mutant protein retaining its role in acid-base homeostasis. Transcriptomic analysis revealed the top 10 differentially expressed genes (DEGs) were predominantly associated with the collagen-containing extracellular matrix, suggesting a potential link between WDR72 function and extracellular matrix composition. These findings highlight the value of iPSC-derived cellular models in advancing personalized research on dRTA.

overall_design: RNA-seq profiling of wild-type and mutant (c.1777A>G and c.2522T>A) WDR72 in iPSC-derived renal tubular epithelial cells at day 14 of differentiation.

first: Narissara

first: Methichit

last: Wattanapanitch

first: Oranud

last: Praditsap

first: Prapaporn

last: Thamtarana

first: Chutima

last: Chanprasert

first: Pucharee

last: Songprakhon

first: Nunghathai

last: Sawasdee

first: Choochai

last: Nettuwakul

first: Pa-thai

last: Yenchitsomanus

first: Nanyawan

last: Rungroj


title: Chronic periodontitis induces neurobehavioral deficits via microbiota–glia–endocrine interactions

city: Tokyo

first: YUJIN

last: OHSUGI

address: 1-5-45, Yushima, Bunkyo-ku

department: Oral Biology

institute: Institute of Science Tokyo

summary: Periodontitis is increasingly linked to diverse brain disorders, yet causal mechanisms remain elusive. Here we demonstrate that ligature-induced oral dysbiosis in mice is sufficient to perturb central function. Six weeks of periodontitis produced anxiety-like behavior and motor deficits, accompanied by microglial depletion, reduced neuronal activity and region-selective transcriptional down-regulation in the frontal cortex. Pharmacological microglial ablation phenocopied, and glucocorticoid-receptor blockade rescued, these abnormalities, implicating microglia and activation of the hypothalamic–pituitary–adrenal axis. 16S rRNA gene sequencing revealed significant shifts in oral and gut microbiota that were partially normalized by a broad-spectrum antibiotic cocktail. Antibiotics alone elevated corticosterone but did not affect microglia or behavior, indicating that dysbiosis and glucocorticoids act synergistically on the brain dysfunction. Antibiotic treatment restored microglial density and behaviors in ligature mice, despite plasma corticosterone levels remaining elevated and comparable to those in antibiotic-treated controls. Our findings suggest oral dysbiosis as a tractable driver of neuroimmune dysfunction and redefine periodontitis as a systemic disorder with direct consequences for brain health.

overall_design: Spatial tramscriptomics of prefrontal cortex at 6 weeks after ligature induced periodontitis model (C57BL/6J mice) creation

first: Yujin

last: Ohsugi

first: Sayaka

last: Katagiri

first: Tomomitsu

last: Hirota


title: Chronic periodontitis induces neurobehavioral deficits via microbiota–glia–endocrine interactions [RNA-Seq]

overall_design: RNA-seq profiling of frontal cortex and cerebellum at 6 weeks after ligature induced periodontitis model (C57BL/6J mice) creation


title: Comparison of human pluripotent stem cell-derived cardiomyocyte subtypes

city: Okayama

first: Yukihiro

last: Sato

address: 2-5-1 Shikata-cho Kita-ku

institute: Okayama University

summary: Different subtypes of cardiomyocytes were induced from human induced pluripotent stem cells.

overall_design: Human induced pluripotent cells were basically differentiated using cardic differentiation protocol with a GSK3 inhibitor and a Wnt inhibitor (GiWi). Cells were purified using no glucose medium supplemented with lactate. Standard GiWi mainly produced NKX2-5-positive/TBX5-positive cardiomyocytes and modified GiWi mainly produced NKX2-5-positive/TBX5-negative cardiomyocytes.

last: Saito

first: Dai

last: Kusumoto

first: Shinsuke

last: Yuasa


title: RNA-seq of tomato leaves under JCK1241 treatment and/or Ralstonia solanacearum challenge

city: Busan

first: Young-Su

last: Seo

address: Geumjeong-Gu

department: Microbiology

institute: Pusan National University

summary: This study performed RNA sequencing (RNA-seq) of tomato (Solanum lycopersicum, cultivar Seokwang) leaves to investigate transcriptional responses under treatment with JCK1241 and/or challenge with the bacterial wilt pathogen Ralstonia solanacearum. A total of 12 samples were analyzed, including control, pathogen-infected, treatment-only, and combined treatment-plus-pathogen conditions

overall_design: Tomato leaves were sampled from cultivar PNU 01 grown under controlled conditions. Four groups were studied: (i) control, (ii) R. solanacearum-infected, (iii) JCK1241-treated, and (iv) JCK1241 treatment plus pathogen infection. Three biological replicates were included per group. RNA was extracted, sequenced using Illumina paired-end sequencing, and analyzed for differential gene expression, annotation, and clustering

first: Mohamed

last: Mannaa


title: Genome level identification of transcription start sites by nanoCAGE sequence in soybean (Glycine max).

city: Weifang

first: haiying

last: yang

state: Shandong

address: 699 Binhu Road, Xiaoshan Ecological Economic Development Zone

institute: Weifang Modern Agriculture Laboratory of Shandong Province

summary: Identification of the transcription start sites (TSS) of genes is critical for understanding promoter regions and transcription initiation. One well characterized and widely used method to determine TSSs is CAGE (Cap Analysis of Gene Expression). CAGE has been commonly used in animal studies, yet in plants species, the precise TSS and core promoter landscape is not sufficient yet, no experiment has been taken on soybean to identify TSS neither. Soybean is one economically valuable species used for both food supply and oil. In this study, we present the main results of nanoCAGE-seq to reveal the genome-wide TSS conducted on shoot and root in soybean Williams 82.

overall_design: Soybean (Wm 82) was grown under white light condition (300 µmol•m-2•s-1) with a 12 h light/12 h dark circadian rhythm for 2 weeks. Shoots and roots were collected separately and used for nanoCAGE library construction.


title: Comparative transcriptomic profiling between wild-type and FvMATE51 mutant (a vacuolar membrane protein) strawberry fruits at 26 DPA

city: Be

first: Keru

last: Wang

state: 未付

address: No.20 Nanxincun, XIangshan, Haidian District

department: Institute of botany

institute: University of Chinese Academy of Sciences

summary: To explore the molecular mechanisms of FvMATE51 during fruit development and ripening, we generated CRISPR/Cas9-mediated gene knockout mutants Fvmate51. Then, we performed comparative transcriptome analysis through RNA sequencing (RNA-seq) using fruits of the wild-type and the mutant lines (Fvmate51-1 and Fvmate51-2) at 26 days post anthesis. Three independent biological replicates were applied for the RNA-seq analysis, using Illumina Nova seq 6000

overall_design: Total RNA was extracted from fruits of 26 DPA WT fruits and FvmMATE1 mutants (Fvmate51-1 and Fvmate51-2) at 26-day postanthesis using HiPure HP Plant RNA Mini Kit (Magen, China).Double-stranded cDNA libraries were prepared from poly(A)+ mRNA, subjected to Illumina high-throughput sequencing after quality control and pooling.

first: Guozheng

last: Qin


title: The type 6 secretion system immunity protein RhsFI has been repurposed for small RNA regulation in pathogenic E. coli

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: RNA-binding proteins (RBPs) play key roles in regulating virulence gene expression in pathogenic, enterohaemorrhagic E. coli (EHEC). Under virulence-inducing conditions total RNA associated protein purification (TRAPP) identified 443 RNA-associated proteins. These included 35 encoded within pathogenicity islands, with RNA-binding confirmed in vitro for a sub-set that included RhsFI. In vivo RNA targets for RhsFI included regulatory small RNAs (sRNAs) encoded in 3’ UTRs. The rhsF-rhsFI locus encodes effector and immunity proteins for the type 6 secretion system (T6SS). T6SS expression is repressed in EHEC, but internal initiation generates a transcript encoding a truncated toxin (RhsFint) and downstream RhsFI. Modelling predicted that RhsFint can dimerise with RhsFI. Deletion of rhsFint rhsFI alters the expression of multiple operons in which embedded sRNAs are direct RhsFI targets. Loss of RhsFint:RhsFI dramatically reduced adhesion to bovine cells in vitro, altered cell morphology and increased acid resistance, phenotypes that impact host colonisation.

overall_design: RNA seq was performed on biological triplicate cultures of E. coli O157:H7 str. Sakai (stx-) and an isogenic rhsF rhsFI (ECs0605 ECs0604) double deltion strain, and mutant complemented with rhsFint rhsFI (pZE12::rhsFint rhsFI) grown in MEM-HEPES media supplemented with 250nM FeNO3 and 0.1% glucose. In addition, UV-crosslinking and sequencing of RNAs (CRAC) bound to RhsFI was performed on rhsFI-His-TEV-FLAG expressed from pBADmycHis in EHEC. CRAC was performed as previously (Tree et al Molecular Cell 2014) in biological duplicate and the parental EHEC strain was included as a control.

first: Thomas

last: Zammit

first: Brandon

last: Sy


title: Ischemic injury induces hematopoietic aging and facilitates tumor growth

city: New York

first: Michael

last: Gildea

address: 550 1st avenue

institute: NYU Langone Health

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

overall_design: Refer to individual Series


title: Altered pathways in Cockayne syndrome: Involvement of MAPK, PI3K-Akt, extracellular matrix, inflammation, and neuronal signaling

city: São Paulo

first: Gustavo

middle: Satoru

last: Kajitani

state: SP

address: Rua itapiru 53, ap 25

department: Departamento de Morfologia e Genética

country: Brazil

institute: Universidade Federal de São Paulo

summary: Cockayne syndrome (CS), a disorder characterized by neurodegeneration and a segmental progeroid phenotype, is caused by mutations in CSA or CSB genes, which codify proteins necessary for the DNA repair pathway known as transcription-coupled nucleotide excision repair (TC-NER). To further elucidate the biological pathways associated with this aging-related neurodegenerative phenotype, we analyzed CS transcriptome datasets. We performed RNA-seq on the brains of one Csa-/- mouse model and a respecitive wild-type mouse (C57-Black6J background) in three different age timepoints (45 days, 12 months, 24 months). RNA-seq was performed in 5 lanes using AB SOLiD system.

overall_design: RNA-seq profiling of Csa-/- mice and their respective wild-type counterparts in different timepoints (45 days, 12 months and 24 months) during their lifespan.

first: Camila

last: Garcia

first: Carlos

middle: F

last: Menck


title: The antisense RNA CDH3-AS1 regulates expression of the melanoma suppressor P-cadherin

city: Tampa

first: Alex

last: Jaeger

state: FL

address: 12902 Magnolia Dr

department: Molecular Oncology

institute: Moffitt Cancer Center

summary: Thousands of regulatory noncoding RNAs (ncRNAs) have been annotated; however, their functions in gene regulation and contributions to cancer formation remain poorly understood. To gain a better understanding of the influence of ncRNAs on gene regulation during melanoma progression, we mapped the landscape of ncRNAs in melanocytes and melanoma cells. Nearly half of deregulated genes in melanoma are ncRNAs, with antisense RNAs (asRNAs) comprising a large portion of deregulated ncRNAs. CDH3-AS1, the most significantly downregulated asRNA, overlaps the CDH3 gene, which encodes P-cadherin, a transmembrane glycoprotein   involved in cell adhesion that was also reduced in melanoma. Overexpression of CDH3-AS1 increased cell aggregation and reduced xenograft tumor growth, mimicking the tumor-suppressive effects of CDH3. CDH3-AS1 interacted with CDH3 mRNA and enhanced P-cadherin protein levels. Interestingly, secondary structures at the CDH3 5’ end regulated P-cadherin translation, and ribosome profiling revealed that CDH3-AS1 promotes ribosome occupancy at the CDH3 5’UTR. Notably, 5’UTR ribosome occupancy was generally increased in mRNAs having cognate asRNA. Taken together, this study revealed the CDH3-AS1-mediated enhancement of P-cadherin translation, underscoring the broader potential of asRNAs as regulators of protein-coding genes and their role in diseases like melanoma.

overall_design: Comparison of Ribosome density in Hermes melanocytes treated with either control siRNA or siRNA targeting CDH3-AS1.

first: Manon

last: Chadourne

first: Emily

last: Brennan

first: Florian

last: Karreth


title: KRAS Inhibition Activates an Actionable CD24 “Don’t Eat Me” Signal in Pancreatic Cancer

city: Houston

first: Zhenzhen

last: Xun

state: TX

address: 7007 Bertner Ave

institute: MD Anderson Cancer Center

summary: KRASG12C inhibitors (G12Ci) have produced encouraging, albeit modest and transient, clinical benefit in pancreatic ductal adenocarcinoma (PDAC). Identifying and targeting resistance mechanisms to G12Ci treatment is therefore crucial. To better understand the function of KRASG12C and possible G12Ci bypass mechanisms, we developed an autochthonous KRASG12C-driven PDAC model. Compared to the classical KRASG12D PDAC model, the G12C model exhibits slower tumor growth, yet similar histopathological and molecular features. Aligned with clinical experience, G12Ci treatment of KRASG12C tumors produced modest impact despite stimulating a ‘hot’ tumor immune microenvironment. Immunoprofiling revealed that CD24, a ‘don’t eat me’ signal, is significantly upregulated on cancer cells upon G12Ci treatment. Blocking CD24 enhanced macrophage phagocytosis of cancer cells and significantly sensitized tumors to G12Ci treatment. Similar findings were observed in KRASG12D-driven PDAC. Together, this study reveals common and distinct oncogenic KRAS allele-specific biology and identifies a clinically actionable adaptive mechanism that may improve the efficacy of oncogenic KRAS inhibitor therapy in PDAC.

overall_design: Tumor samples from vehicle (n=3) or AMG 510 (n=3) treated PDAC KRAS G12C mutant orthotopic mice tumor tissues were dissected, and single-cell suspensions were obtained. CD45+ enriched samples were preserved in PIPseq™ T20 3′ Single Cell Capture and Lysis Kit and processed on an Illumina NextSeq sequencer.

first: Yongkun

last: Wei

first: Minghui

last: Liu

first: Jun

last: Yao

first: Han

last: Liang

first: Wantong

first: Haoqiang

last: Ying


title: Satellite Cells Choreograph an Immune Cell-Fibrogenic Cell Circuit During Mechanical Loading in Geriatric Skeletal Muscle

city: Fayetteville

first: Kevin

last: Murach

state: Arkansas

address: 155 Stadium Drive

institute: University of Arkansas

summary: Muscle stem cells, or satellite cells, decline in number with age and may become senescent. Whether and how satellite cells contribute to muscle adaptation in the oldest-old is unclear. Using short-term mechanical overload in geriatric satellite cell replete and depleted mice (28 months of age) combined with single cell RNA-sequencing, we show: 1) subsets of geriatric satellite cells show signs of senescence as well as normal fate progression during overload, 2) satellite cells express markers that may contribute to the regulation of innervation, 3) the presence of satellite cells during overload globally enhances intercellular communication and causes upregulation of the cell surface receptor gene Cd74 in immune cells, 4) Mif, the primary ligand for CD74, is produced by fibrogenic cells and is more pronounced in the absence of satellite cells - perhaps to help normalize dysregulated fibrotic signaling, and 5) satellite cells drive fate directive transcript splicing that promotes the canonical macrophage response to hypertrophic loading. Our findings expose the behavior of satellite cells in response to mechanical loading in the oldest-old and reveal a satellite cell-macrophage-fibrogenic cell circuit in geriatric muscle that may promote extracellular matrix remodeling

overall_design: 28-month-old Pax7-DTA mice with satelite cells depleted via tamoxifen treatment  ("SC-" in study, "t" in file names) or satellite cells retained via sunflowerseed oil treatment vehicle ("SC+" in study, "v" in file names) 2-weeks prior to 96-hours of mechnical overlaod via removal of gastrocnemius and soleus muscles.

first: Nicholas

last: Thomas

first: Yuan

last: Wen

first: Christopher

last: Fry


title: Trans-generational adaptation to maternal climate through hormone transport in plants

city: Norwich

first: Xiaochao

last: Chen

address: Norwich Research Park, Colney Ln

department: Crop Genetics

institute: John Innes Centre

summary: Whether and how organisms can inherit environmental information from their parents is a major question in evolutionary theory. Plants have evolved to link reproductive development to seasonal environmental cues and seed dormancy is highly contingent on the environmental temperature during seed set, although the mechanism by which seeds acquire seasonal timing information is unclear. Here we show that loss of maternal like heterochromatin protein 1 (LHP1) causes an inability of progeny seeds to sense temperature and that this is linked mechanistically to reduced ABA levels in seeds and hyperaccumulation of free nitrate. Remarkably, single cell transcriptomics reveals that in both maternal fruit and seed tissues, the effect of small changes in temperature closely phenocopies the lhp1 mutant phenotype and ABA biosensor imaging reveal large fluxes of maternal ABA into seeds is modulated by temperature cues. We show that temperature activates ABA production in leaves and that maternal ABA is necessary and sufficient for progeny seeds to acquire seed dormancy. Thus, we reveal that the climate experience of mother plants causes adaptation of progeny behaviour via hormone transport during seed set.

overall_design: Col-0 plants were grown at 22°C till bolting, then half plants were transferred to 16°C. At bent stage, siliques from 2 different temperature were dissected to separate fruit tissue and seed tissue which were sequenced seperately.

first: William

last: Bezodis

first: Steven

last: Penfield


title: Post-transcriptional control of homeostatic B- cell signalling by HuR is required for innate B cell maintenance and function. [RNA-Seq]

city: Toulouse

first: Manuel

middle: D

last: Diaz-Munoz

address: CHU Purpan, BP3028

country: France

institute: INSERM

summary: Innate B-1 cells constitute a self-maintained layer of defence for early detection of bacteria, clearance of apoptotic cell debris and removal of autoantigens driving autoimmunity. B-1 cells are originated from foetal tissues but, as opposed to B-2 cells, the molecular mechanisms behind their development and homeostatic maintenance remain largely unknown. Here we demonstrate that post-transcriptional regulation by the RNA binding protein HuR is essential for the homeostatic self-replenishment of innate B-1 cells, the expansion of B-1 cell clones targeting self-antigens and the production of natural autoantibodies. HuR KO B-1 cells fail to express the high levels of surface BCR, TACI and BAFFR required for tonic signalling and cell survival. Mechanistically, HuR binds to the 3’UTRs of mRNAs encoding these surface receptors and of pro-survival molecules, like BCL-2 and MCL-1, promoting their translation into protein. In summary, we reveal the need of post-transcriptional regulation in BCR expression, tonic signalling and homeostatic maintenance of functional B-1 cells.

overall_design: Individual cross-linking immunoprecipitation (iCLIP) and sequencing for HuR in B cells isolated from the peritoneal cavity of C57BL/6 mice.

first: Dunja

last: Capitan-Sobrino

first: Mailys

last: Mouysset

first: Orlane

last: Maloudi

first: Yann

last: Aubert

first: Ines

last: Osma-Garcia

first: Maia

last: Nestor-Martin

first: Trang-My

last: Nguyen

first: Greta

last: Dunga


title: Cell-targeted PD-1 agonists are potent NK cell inhibitors

city: Abingdon

first: Alice

last: Newey

address: 92 Park Dr, Milton

institute: Immunocore

summary: We have generated a novel targeted bispecific PD-1 molecule, to achieve tissue-specific immune suppression for the treatment of immune-mediated inflammatory diseases. These targeted PD-1 agonists have shown potent T cell inhibition and here we describe an additional effect on NK cell activation. We show that PD-1 pathway activation modifies NK cell gene expression and decreases their inflammatory and cytotoxic functions. Targeted PD-1 agonist molecules, inhibiting T cells and NK cells in a tissue-specific manner offer a new promising treatment for autoimmune and inflammatory diseases.

overall_design: Pope, C, Harriet

first: Chiodetti

last: Ana

first: Newey

last: Alice

first: Rieunier

last: Guillaume

first: Overton

last: David

first: Mateos-Diaz

last: Eduardo

first: Mahon

last: Tara

first: Bossi

last: Giovanna

first: Al-Mossawi

last: Hussein

first: Viant

last: Charlotte


title: Post-transcriptional control of homeostatic B- cell signalling by HuR is required for innate B cell maintenance and function.

first: Manuel

last: Diaz-Munoz

first: Dunja

last: Capitan-Sobrino

first: Mailys

last: Mouysset

middle: C