title: Stromal Transcriptomics Uncover LIF as a Key Effector in High Tumor Budding Triple-Negative Breast Cancer

city: Bangkok

first: Pimchanok

last: Phankeaw

state: Bangkok

address: 2 Wanglang Rd., Bangkok Noi, Siriraj

department: Immunology

country: Thailand

institute: Mahidol University

summary: The overexpressed genes in FAP-positive CAFs from high TB-TNBCs included ZNF235, ANKRD30B, SLC26A2, SPDYC, CDKN1C, LIF, and FAM83A. The secreted LIF was found in 41.1% of TNBC cases with high levels detected in CAFs, while 26.2% of cases showed high LIF production in cancer cells. The recombinant LIF significantly promoted breast cancer cell migration and enhanced PD-L1 expression, effects that were attenuated by EC359. This study highlights the correlation of high TB in TNBC with poor prognosis and upregulation of key signaling pathways in CAFs. FAP-positive CAFs overexpress genes like LIF, which promotes cell migration and PD-L1 expression. LIF inhibition reduces these effects, suggesting LIF as a potential therapeutic target in TB-associated TNBC progression and immunotherapy.

overall_design: The 170 formalin-fixed paraffin-embedded TNBC tissues were assessed for TB by pan-cytokeratin immunohistochemistry (IHC). Its clinicopathological correlations were examined through univariate and multivariate analyses, with overall survival (OS) evaluated using Kaplan-Meier analysis. CAFs whole transcriptomic profiles of 13 TNBCs was conducted using Templated Oligo-Sequencing and the differential expression was analyzed in R studio with the DESeq2 package. Pathways associated with differentially expressed genes were identified using the Enrichr package. The level of leukemia inhibitory factor (LIF) was explored by IHC in 141 TNBCs, and its prognostic significance was determined. The induction of TNBC cell migration and expression of programmed death-ligand 1 (PD-L1) by a recombinant LIF, along with attenuation by EC359, a LIF inhibitor, were investigated using Transwell assay and flow cytometry.

first: Suparada

last: Khanaraksombat

first: Warapan

last: Numprasit

first: Pranisa

last: Jamjuntra

first: Punn

last: Augsornworawat

first: Malee

last: Warnnissorn

first: Peti

last: Thuwajit

first: Chanitra


title: Androgen deprivation-mediated activation of AKT is enhanced in prostate cancer with TMPRSS2:ERG fusion [microarray]

status: Public on Sep 10 2025

city: Boston

first: Steven

last: Balk

state: MA

address: 3 Blackfan circle

country: USA

institute: BIDMC

summary: The TMPRSS2:ERG gene fusion (T:E fusion) in prostate adenocarcinoma (PCa) puts ERG under the androgen receptor (AR) regulated expression of TMPRSS2. The T:E fusion is frequently associated with PTEN loss, and is highly correlated with decreased expression of INPP4B, both of which may compensate for ERG-mediated suppression of PI3K/AKT signaling. We confirmed in PCa cells and a mouse PCa model that ERG suppresses AKT activation, and that one potential mechanism is through downregulation of IRS2. In contrast, ERG knockdown did not increase INPP4B, suggesting its decreased expression is indirect and reflects selective pressure to suppress INPP4B function. Notably, INPP4B expression is similarly decreased in PTEN-intact and PTEN-deficient T:E fusion tumors, suggesting selection for a function distinct from regulation of PI3K activity. As ERG expression in T:E fusion tumors is AR regulated, we further assessed the extent to which AR inhibition increased AKT activity in T:E fusion tumors. T:E fusion positive versus negative PDXs had greater increases in AKT activity after castration. Moreover, in a neoadjuvant trial of AR inhibition prior to radical prostatectomy we similarly found greater increases in AKT activation in the T:E fusion tumors. Together these findings indicate that AKT activation may mitigate the efficacy of AR targeted therapy in T:E fusion PCa, and that these patients may most benefit from combination therapy targeting AR and AKT.

overall_design: 6 samples

first: Fen

last: Ma

first: Sen

last: Chen

first: Carla

last: Calagua

first: Seiji

last: Arai

first: Fang

last: Xie

first: Olga

last: Voznesensky

first: Larysa

last: Poluben

first: Eva

last: Corey

first: Changmeng

last: Cai

first: Yuzhuo

last: Wang

first: David

middle: J

last: Einstein

first: Mary-Ellen

last: Taplin

first: Huihui

last: Ye

first: Adam

middle: G

last: Sowalsky

first: Joshua

middle: W

last: Russo

first: Xin

last: Yua

middle: P


title: The effect of inhibiting the cGAS-STING pathway in a chronic liver disease mouse model

status: Public on Sep 09 2025

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

type: Expression profiling by high throughput sequencing

summary: Hepatocellular carcinoma (HCC) mostly develops on the background of a chronic liver disease (CLD). The hallmarks of CLD includes increased hepatocyte apoptosis, compensatory proliferation and DNA damage. Mice with MCL-1 deficiency in hepatocytes (Mcl-1Dhep mice ) recapitulated these key features of CLD and developed HCC later in life. However, it is unclear how MCL-1 deficiency drives tumorigenesis. We analysed replication stress and the activation the cGAS-STING pathway in Mcl-1Dhep mice. 2-month-old Mcl-1Dhep mice showed increased replication stress, micronucleated hepatocytes and increased cytosolic DNA sensing. We found that an increase in extrachromosomal circular DNA in Mcl-1Dhep liver promoted a crosstalk between hepatocytes and immune cells to drive the immune response which was dependent on the canonical cGAS-STING pathway. We then generated Mcl-1Dhep/STING-/- double knockout mice to study the effects of inhibiting the cGAS-STING pathway in liver homeostasis and tumorigenesis. In fact, deletion of STING in Mcl-1Dhep mice reduced immune cell chemotaxis, as well as tumor incidence. Our findings indicate that the cytosolic DNA sensing pathway may play an important role in inflammation-driven liver carcinogenesis.

overall_design: Knockout mice were generated by crossing transgenic mice with different genetic background.

first: Peter

last: Leary

first: Lap Kwan

last: Chan

first: Achim

last: Weber


title: Elevated PRKD2 Promotes Progression and Poor Prognosis of Multiple Myeloma

city: Xuzhou

first: Guihua

last: Zhang

address: Xuzhou

department: Hematology

country: China

institute: Xuzhou Cancer Hospital

summary: This study aimed to address the challenges in treating multiple myeloma (MM) and its advanced stage, relapsed and refractory multiple myeloma (RRMM), by identifying new therapeutic targets. Clinical data were collected from 132 MM patients. Through propensity score matching, bone marrow samples from 24 MM patients and 6 control individuals were selected for RNA sequencing analysis. Western blot validation was performed in cell lines to investigate the role of serine/threonine-protein kinase D2 (PRKD2) in MM and RRMM. Additionally, gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, immune infiltration analysis, and drug sensitivity screening were conducted. The study found PRKD2 to be significantly upregulated in MM and RRMM, suggesting its potential as a therapeutic target. Functional assays indicated that disrupting PRKD2 inhibited myeloma cell proliferation, and pathway analysis revealed immune-related pathway alterations associated with PRKD2 expression. Drug sensitivity analysis identified Axitinib as a potential therapeutic agent targeting PRKD2, highlighting its promise for MM treatment.

overall_design: To study the PRKD2 in Nrelapsed and refractory multiple myeloma

first: Hong

last: Liu

first: Jiaqian

last: Qi

first: Zhenyu

last: Li


title: Loss-of-function variants in ciliary genes confer high risk for Tetralogy of Fallot [RNA-Seq]

city: Nanjing

first: Jimiao

last: Gao

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

summary: Tetralogy of Fallot (TOF), the most common severe cyanotic congenital heart disease, has poorly understood genetic causes. Through next-generation sequencing in 131 nonsyndromic TOF patients, we identified an increased burden of rare deleterious variants in ciliary genes and cilium pathway, and observed a multigenic inheritance pattern, with an OR of 1.672 for more than two deleterious variants and a cumulative OR of 3.158 for six variants. Functional validation in single- and double-heterozygous mouse models carrying these variants recapitulated TOF-like phenotypes and impaired normal cilia structure and function, particularly disrupting Hedgehog signaling in cardiomyocytes, downregulating key transcription factors Gata4 and Nkx2-5.

overall_design: RNA-Seq analysis of mice E10.5 hearts from wild-type and ciliary gene knockout/mutant littermates of each strain.

first: Yayun

last: Gu

first: Yuan

last: Lin

first: Zhibin

last: Hu


title: Deciphering the cis-regulatory code of alternative splicing in human cell lines

status: Public on Sep 08 2025

city: seattle

first: Samantha

last: Koplik

email: skoplik@uw.edu, kopliksam@gmail.com

state: Washington

address: 185 Stevens Way

department: Electrical and Computer Engineering

institute: University of Washington

summary: Alternative splicing (AS) is a key mechanism of gene expression diversity, and dysregulation of AS is implicated in many human diseases. Identifying variants that disrupt splicing and characterizing their impact on isoform abundance across different cell types remains challenging. Here, we perform massively parallel reporter assays (MPRAs) to measure splicing phenotypes of over 87,000 sequence variants in five cell lines of different tissue origin. The MPRA encompasses 2,096 short human exons from 1,733 genes and tens of thousands of single and double variants. Our measurements identify variants that strongly modulate splicing but are currently classified as variants of unknown significance or have not yet been described. We systematically identify putative RNA-binding protein (RBP) binding motifs and quantify effect sizes associated with the disruption of these motifs, suggesting possible mechanisms for variant impact.  A comparison across cell lines enables the identification of variants that differentially modulate splicing.

overall_design: Massively parallel splicing reporter assay (MPRA) testing ~87,000 exon and variant sequences cloned into a Citrine–SMN2 minigene backbone. Constructs were transfected into five human cell lines (HEK293, HeLa, K562, MCF7, HMC3) with biological replicates. Sequencing was used to quantify exon inclusion (PSI) across replicates, and processed PSI values are reported.

middle: E

first: Angela

middle: M

last: Yu

first: Georg

last: Seelig


title: Persistent open chromatin state in early-life stress-activated cells of the VTA

city: Princeton

first: Catherine

middle: Jensen

last: Peña

state: NJ

address: Princeton Neuroscience Institute, Washington Road, Lot 20

institute: Princeton Neuroscience Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Early-life stress sensitizes individuals to subsequent stressors to increase lifetime risk for psychiatric disorders. Within the ventral tegmental area (VTA), a mesolimbic brain region implicated in stress response and mental health, early-life stress causes long-lasting changes in gene expression and chromatin modifications that in turn cause latent physiological and behavioral sensitivity to stress. These molecular consequences of early-life stress are indicative of epigenetic priming, a form of molecular memory in which developmental or environmental cues open chromatin at enhancers to facilitate transcriptional response to stimuli. However, the long term impact of early-life stress on chromatin architecture in the VTA was not yet known. Using a combination of activity-dependent cellular tagging and ATAC-sequencing, we find that early-life stress opens chromatin specifically in stress-activated cells of the VTA, that this remodeling persists into adulthood, and that opening chromatin at cis-regulatory elements
including enhancers augments transcriptional response to adult stress. Together, this data supports enhancer priming within ELS-responsive cells in the VTA as a biological mechanism for lifelong stress sensitivity.

overall_design: bulk ATAC-seq (assay for transposase accessible chromatin) from the ventral tegmental area (VTA) of adult (>postnatal day 60) Mus musculus.

first: Rebekah

middle: L

last: Rashford

first: Michael

last: DeBerardine

first: Shu

last: Dan

first: Shannon

middle: N

last: Bennett


title: Tissue localization of Natural Killer Cell cells dictates surveillance of lung metastasis

first: Marijne

last: Vermeer

institute: University of Zurich

summary: The lung is a common metastatic site for various cancer types. Successful immune surveillance of lung metastasis depends on Natural Killer (NK) cells, but the underlying mechanisms are elusive. Here, we show that the pulmonary vasculature recruits and maintains highly cytotoxic and differentiated CD11bhigh NK cells through the integrins Lymphocyte Function-associated Antigen 1 (LFA-1) and Very Late Antigen (VLA-4). These NK cells rapidly eradicate metastasizing tumor cells within the vasculature. However, after the initial clearing phase, pulmonary NK cells fail to track extravasated tumor cells and remain intravascular, outside of the emerging nodules. In contrast, metastatic nodules are preferentially infiltrated with bloodborne and less differentiated CD27high NK cells. Within the metastatic lung, CD11bhigh NK cells undergo a rapid impairment of their migratory and cytotoxic features, while the intranodular CD27high subset transitions towards a transforming growth factor β (TGF-β)-driven state with reduced capacity to persist in the tumor tissue. Our findings demonstrate that the compartmentalization of NK cells is key for effective tumor cell surveillance in lung metastasis and that the use of TGF-β-resistant CD27high NK cells might be a novel strategy to enhance local anti-tumor activity.

overall_design: Lungs were dissociated and Live NK1.1+NKp46+  cells were sorted from both lungs and blood. Lung and blood NK cells were distinguished with unique barcodes (Totalseq B0304 and B0306, Biolegend)  before scRNA-seq using 10x Genomics platform.


title: SETBP1 variants outside the degron disrupt DNA-binding, transcription and neuronal differentiation capacity to cause a heterogeneous neurodevelopmental disorder [induced neurons]

city: Nijmegen

first: Maggie MK

last: Wong

address: Wundtlaan 1

department: Language and Genetics

country: Netherlands

institute: Max Planck Institute for Psycholinguistics

summary: Different types of germline de novo SETBP1 variants cause clinically distinct and heterogeneous neurodevelopmental disorders: Schinzel-Giedion syndrome (SGS, via missense variants at a critical degron region) and SETBP1-haploinsufficiency disorder. However, due to the lack of systematic investigation of genotype-phenotype associations of different types of SETBP1 variants, and limited understanding of its roles in neurodevelopment, the extent of clinical heterogeneity and how this relates to underlying pathophysiological mechanisms remain elusive. This imposes challenges for diagnosis. Here, we present a comprehensive investigation of the largest cohort to-date of individuals carrying SETBP1 missense variants outside the degron region (n=18). We performed thorough clinical and speech phenotyping with functional follow-up using cellular assays and transcriptomics. Our findings suggest that such variants cause a clinically and functionally variable developmental syndrome, showing only partial overlaps with classical SGS and SETBP1-haploinsufficiency disorder. We provide evidence of loss-of-function pathophysiological mechanisms impairing ubiquitination, DNA-binding, transcription, and neuronal differentiation capacity and morphologies. In contrast to SGS and SETBP1 haploinsufficiency, these effects are independent of protein abundance. Overall, our study provides important novel insights into diagnosis, patient care, and aetiology of SETBP1-related disorders.

overall_design:
RNA-seq profiling of induced neurons generated from human skin fibroblasts from healthy controls and patients with SETBP1-related disorders. Three biological replicates, i.e. differentiation experiments, were included.

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

first: Maggie

first: Simon

last: Fisher


title: RNA-seq of dTAG-NUDT21 HCT116 cells treated with DMSO+JTE-607 or dTAGV1+JTE-607.

city: Pittsburgh

first: Hun-Way

last: Hwang

state: PA

address: 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

summary: We performed RNA-seq on dTAG-NUDT21 HCT116 cells treated with DMSO+JTE-607 or dTAGV1+JTE-607 for 48 hours with 4 biological replicates

overall_design: We assessed differential RNA expression by treatment conditions (DMSO+JTE-607 vs. dTAGV1+JTE-607)


title: Slc22a17 governs postnatal neurogenesis by maintaining the iron homeostasis in hippocampus [RNA-Seq hippocampus]

city: Beijing

first: Ligong

last: Chen

address: Shuangqing Road No.30

institute: tsinghua university

summary: Iron transporters are essential for maintaining cellular iron homeostasis. Among them, SLC22A17 mediates lipocalin-2 (LCN-2)-dependent iron transport, but its precise role in the brain remains unclear. Here, we show that Slc22a17 is critical for postnatal neurogenesis by regulating hippocampal iron balance. Conditional knockout of Slc22a17 in the murine brain causes early postnatal lethality, growth retardation, neural stem cell apoptosis, and cognitive deficits, largely due to oxidative stress from iron overload. Mechanistically, Slc22a17 interacts with p62 to modulate Nrf2 activity. Its loss aberrantly activates the Nrf2/HO-1 pathway, disrupting iron efflux and promoting accumulation of reactive oxygen species (ROS). These findings establish Slc22a17 as a key regulator of neuronal development and a potential therapeutic target for neurological disorders linked to iron dysregulation.

overall_design: RNAseq profiling of C57BL/6 mice at postnatal day 14, and total RNA was extracted for sequencing.

first: Lei

last: Tao

first: Long

last: Teng


title: HIF1A regulated genes in MCF10A cells after treatment with Oncostatin M or control ligands

city: Portland

first: Laura

last: Heiser

state: OR

address: 2730 S Moody Ave

department: Biomedical Engineering

institute: Oregon Health and Science University

summary: We employed a single-cell RNA sequencing approach to study the role of Oncostatin M (OSM) in inducing collective cell migration in MCF10A cells and its upregulation of HIF1A. To identify HIF1A-dependent transcriptional programs, we stably knocked down HIF1A using shRNA and treated cells with OSM.

overall_design: MCF10A breast epithelial cells stably expressing shHIF1A or control shSCR were grown in vitro and treated with Oncostatin M (OSM), epidermal growth factor (EGF), or a combination of EGF and interferon gamma (IFNG) for 24 hours prior to single-cell RNA sequencing.

first: Ian

middle: C

last: McLean

first: Sean

last: Gross

first: Tiera

last: Liby

first: Mark

middle: A

last: Dane

first: Daniel

middle: S

last: Derrick


title: Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids [RNAseq_concentration]

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

institute: EPFL

summary: Understanding the interplay between cell fate specification and morphogenetic changes remains a central challenge in developmental biology. Gastruloids, self-organizing pseudo-embryos that mimic post-implantation mammalian development, provide a powerful platform to address this question. Here, we show that physical parameters, particularly system size, critically influence the timing and outcomes of morphogenetic processes. Larger gastruloids exhibit delayed symmetry breaking, increased multipolarity, and prolonged axial elongation, with morphogenesis driven by system size. Despite these variations, transcriptional programs and cell fate composition remain remarkably stable across a broad size range. Notably, extreme sizes show distinct transcriptional modules and clear shifts in gene expression patterns. Intriguingly, size perturbation experiments rescued the morphogenetic and pattern phenotypes observed in extreme sizes, demonstrating the remarkable adaptability of gastruloids to their effective system size. These findings establish gastruloids as versatile models for studying spatiotemporal dynamics in mammalian embryogenesis and reveal how physical constraints decouple transcriptional from morphogenetic programs.

overall_design: RNA-seq on hydrogel embedded gastruloids (0.7mM, 0.8mM, 1mM)

first: Alexandre

last: Mayran

first: Pierre

last: Osteil

first: Jérôme

last: Ng Wong

first: Judith

last: Pineau

first: Thomas

last: Gregor

first: Denis

last: Duboule


title: Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids

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

overall_design: Refer to individual Series


title: Intratumoral bacteria are immunosuppressive and promote immunotherapy resistance in head and neck squamous cell carcinoma

city: Cleveland

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

summary: Despite the promise of immune checkpoint blockade (ICB) in head and neck squamous cell carcinoma (HNSCC), mediators of response are poorly understood. To address this, we analyzed oropharyngeal HNSCCs treated with neoadjuvant durvalumab (anti-PD-L1) alone or in combination with tremelimumab (anti-CTLA-4) from the CIAO clinical trial (NCT03144778). We found that only the total abundance of intratumoral bacteria predicted ICB response, which was validated in multiple independent patient cohorts. High intratumoral bacteria abundance was associated with an immunosuppressive tumor microenvironment, characterized by an accumulation of neutrophils coupled with depletion of T cells and other adaptive immune cells. Experimental elevation or reduction of intratumoral bacteria abundance in orthotopic models of HNSCC in female mice recapitulated immunological associations observed in patient tumors. Increasing intratumoral bacteria abundance was sufficient to induce resistance to anti-PD-L1 immune checkpoint blockade, irrespective of bacterial species tested. Together, these findings demonstrate that high intratumoral bacteria abundance is a key suppressor of anti-tumor immunity and promotes immunotherapy resistance.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For the transcriptome analysis, cells were either mock infected or infected with Fusobacterium or Prevotella at an MOI of 200 for four hours prior to harvesting RNA using a Qiagen RNeasy Mini Kit for RNA sequencing.


title: Slc22a17 governs postnatal neurogenesis by maintaining the iron homeostasis in hippocampus [RNA-Seq neurosphere]

last: Chen

overall_design: RNAseq of neurospheres derived from wild-type (WT) and Slc22a17-conditional knockout (cKO) mice


title: mRNA-Seq of Arabidopsis thaliana tho2-8 mutant

status: Public on Sep 07 2025

city: Nan Jing

first: La

middle: yu

last: mei

state: Jiang Su

address: XuanWu

institute: Nanjing Agricultural University

summary: The mechanistic connection between the THO/TREX complex and RdDM remains poorly understood. To address this, we performed EMS mutagenesis in a transgenic Col-0 background harboring pro2×35S::LUC and pro2×35S::NPTII reporters and homozygous for rdr6, and identified a low-fluorescence mutant, tho2-8. Unlike null alleles, tho2-8 is a viable homozygous allele, offering a unique opportunity to explore THO2 function in DNA methylation. Here, we report that THO2 is required for proper siRNA accumulation and RdDM activity, revealing a previously uncharacterized role for the THO/TREX complex in epigenetic gene silencing. This study expands our understanding of the molecular coordination between RNA metabolism and epigenetic regulation in plants.

overall_design: mRNA-Seq of tho2-8;Col-LUC

first: Yumei

last: La

first: Honggui


title: Gene expression following myocardial infarction in mice with Stimulated by retinoic acid gene 6 (Stra6) germline deletion, Vitamin A deficiency, and the combination of both

status: Public on Sep 06 2025

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary: mRNA expression of hearts obtained from mice with Stimulated by retinoic acid gene 6 (Stra6) germline deletion, Vitamin A deficiency (VAD) induced by lecithin-retinol acyltransferase (Lrat) germline deletion and feeding with vitamin A-deficient diet, and the combination of both. Mice were subjected to myocardial infarction (MI) or Sham surgery.

overall_design: C57/Bl6J mice were subjected to myocardial infarction or Sham surgery and sacrificed 3-days post-surgery. mRNA was extracted from the infarct border zone, and libraries were prepared for high throughput sequencing.

first: Christian

last: Riehle


title: SETBP1 variants outside the degron disrupt DNA-binding, transcription and neuronal differentiation capacity to cause a heterogeneous neurodevelopmental disorder [fibroblast]

first: Maggie MK

last: Wong

overall_design:
RNA-seq profiling of human skin fibroblasts from healthy controls and patients with SETBP1-related disorders. Three technical replicates were included per cell line and are listed as CELL LINE NAME_1, CELL LINE NAME_2, CELL LINE NAME_3

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

first: Maggie

first: Simon

last: Fisher


title: Xcr1+ type 1 conventional dendritic cells are essential mediators for atherosclerosis progression

city: Xinxiang

first: Tianhan

last: Li

state: Henan

address: No.601, Hualan Road

institute: Xinxiang Medical University

summary: Atherosclerosis is characterized by lipid accumulation within plaques, leading to foam cell formation and inflammatory response within the aortic lesions. Lipid disorders have been extensively investigated, however the cellular and molecular mechanisms that trigger the inflammatory response in atherosclerotic plaques remain far from being fully understood. Xcr1+ cDC1 cells are newly identified antigen-presenting cells in activating immune cells. However, the role of cDC1 cells in atherosclerosis development remains highly controversial. We first confirmed the presence of cDC1 within human atherosclerotic plaques and discovered a significant association between the increasing cDC1 numbers and atherosclerosis progression in mice. Subsequently, we established Xcr1Cre-Gfp Rosa26LSL-DTA Apoe–/– mice, a novel and complex genetic model, in which cDC1 was constitutively depleted in vivo during atherosclerosis development. Intriguingly, we observed a notable reduction in atherosclerotic lesions in hyperlipidemic mice, alongside suppressed T cell activation of both CD4+ and CD8+ subsets in the aortic plaques. Notably, aortic macrophages and serum lipid levels were not significantly changed in the cDC1-depleted mice. Single-cell RNA sequencing revealed heterogeneity of Xcr1+ cDC1 cells across the aorta and lymphoid organs under hyperlipidemic conditions. As Xcr1 is the sole receptor for Xcl1, we next explored to target Xcr1+ cDC1 cells via Xcl1 by establishing Xcl1–/–Apoe–/– mice. Xcl1–/–Apoe–/– mice exhibited decreased atherosclerotic plaque formation and reduced aortic cDC1 accumulation, indicating that Xcl1 contributes to cDC1-mediated atherosclerotic lesion development. Our results reveal crucial roles of cDC1 in atherosclerosis progression and provide insights into the development of immunotherapies by targeting cDC1 through Xcl1.

overall_design: Eight-week-old male Apoe–/– mice were fed with 20-week ND or HFD. The single cell suspension of spleen, lymph node and aorta were obtained according to the flow cytometry analysis section. Single cell suspension from spleens and lymph nodes were firstly removed the CD5+, CD19+ and CD11b+ cells via SAV conjugated beads. Then two million live cells from spleen and lymph node were stained with mix1 (CD45.2-PE-Cy7, CD11c-PE-Cy5.5, CD172α-FITC, MHCII- APC-eFluor780 and Xcr1-APC), and all cells from aorta were stained with mix2 (CD45.2-PE-Cy7, CD11b-super bright 600, CD11c-PE-Cy5.5, MHCII- FITC, CD3- Alexa Fluor 700, CD19- Alexa Fluor 700, Ly6G- Alexa Fluor 700 and Xcr1-APC) for 30 minutes at 4 °C. After washing with 1 mL FACS buffer two times, cells from different organs were stained with different anti-CD45 antibodies conjugated with barcode oligos from BD™ Ms Single Cell Sample Multiplexing Kit (BD Bioscience, Cat: 633793). Finally, cells were resuspended with Sytox blue and CD11c+ MHCII+ Xcr1+ cells were sorted and subjected to the BD Rhapsody Express system. Then cDNA and sample tag libraries were built with BD Rhapsody whole transcriptome amplification (WTA) reagent kit (BD Bioscience, Cat: 633733, 633773, 633801, 664887) following manufacturer’s instructions, and sequenced on an illumine Novaseq 600 sequencer. Pair-end Fastq files of sample tag and WTA data were processed via BD RhapsodyTM analysis pipeline v2.0, and the resultant dataset was mainly analysis using SeqGeqTM software, which contain Lex-BDSMK and Seurat v4.04 plugin components. This experiment was performed once, and both raw data and processed data were uploaded into GEO (Accession number: GSE279370).

first: Juanjuan

last: Qiu

first: Xin

last: Dong

first: Liaoxun

last: Lu

first: Yinming

last: Liang

first: Lichen

last: Zhang


title: Slc22a17 governs postnatal neurogenesis by maintaining the iron homeostasis in hippocampus [ATAC-Seq]

first: Ligong

overall_design: ATAC sequencing (ATAC-seq) on neurospheres derived from wild-type (WT) and Slc22a17-conditional knockout (cKO) mice.

first: Lei

last: Tao

first: Long

last: Teng


title: DeepWheat: Predicting the Effects of Genomic Variants on Gene Expression and Regulatory Activities Across Tissues and Varieties in Wheat Using Deep Learning [ChIP-Seq]

status: Public on Sep 05 2025

first: Zefu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

summary: Accurate prediction of genomic variant effects and gene expression is essential for identifying functional variations and enabling precise genome editing of cis-regulatory elements (CREs). Spatiotemporal gene expression patterns are fundamental to the formation of key traits, yet tissue-specific predictions remain inaccurate, particularly in large-genome crops like wheat. In this study, we developed DeepWheat, a suite of two models for predicting epigenomic features and gene expression in wheat. DeepEXP, a deep learning model, integrates epigenomic and transcriptomic data across various wheat tissues, achieving Pearson correlation coefficients (PCC) over 0.8 and outperforming sequence-only models, especially for tissue-specific genes. DeepEPI predicts epigenomic features from DNA sequences, helping identify regulatory sequences and facilitating model transfer across wheat varieties. Using chromatin accessibility and transcriptomic data from 9 additional wheat varieties, we validated the model’s accuracy and transfer efficiency. Our analysis further revealed that indels have a greater impact on gene expression than SNPs, and that, compared to promoter regions, the 5’UTR, 3’UTR, and introns exert even stronger regulatory effects on gene expression. These models also identified mutations that alter gene expression, supporting precise CRE editing. They provide valuable tools for tissue-specific predictions, regulatory sequence identification, and saturation mutagenesis to pinpoint high-effect sites.

overall_design: RNA-seq, ATAC-seq and Chip-seq in multiple wheat different tissues

first: Zhigang

last: Ma

first: Jiazi

first: Hongcui

last: Pei

first: Yanhong

last: Lui

last: Wang


title: DeepWheat: Predicting the Effects of Genomic Variants on Gene Expression and Regulatory Activities Across Tissues and Varieties in Wheat Using Deep Learning [ATAC-seq]

overall_design: ATAC-seq  in multiple wheat different tissues


title: sRNA-Seq of Arabidopsis thaliana tho2-8 mutant

first: La

last: mei

type: Non-coding RNA profiling by high throughput sequencing

overall_design: sRNA-Seq of tho2-8;Col-LUC

first: Yumei

last: La

first: Honggui


title: Antecedent enhancer activity predicts future susceptibility to seizures in mice

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

institute: Washington University in St. Louis

summary: Wide variation of responses to identical stimuli presented to genetically inbred mice suggests the hypothesis that stochastic non-genetic variation, such as in chromatin state or enhancer activity during neurodevelopment, can mediate such phenotypic differences. However, this hypothesis is largely untested since capturing pre-existing molecular states requires non-destructive, longitudinal recording. Therefore, we tested the potential of Calling Cards (CC) to record transient neuronal enhancer activity during postnatal development, and thereby associate such non-genetic variation with a subsequent phenotypic presentation – degree of seizure response to the pro-convulsant pentylenetetrazol. We show that recorded differences in enhancer activity at 243 loci predict a severe vs. mild response, and that these are enriched near genes associated with human epilepsy. We also validated pharmacologically a seizure-modifying role for two novel genes, Htr1f and Let7c. This proof-of-principle supports using CC broadly to discover predisposition loci for other neuropsychiatric traits and behaviors.  Finally, as human disease is also influenced by non-genetic factors, similar epigenetic predispositions are possible in humans.

overall_design: Calling Cards viral reagents were injected transcranially into neonatal mouse brains. At one month of age, acute seizures were induced with PTZ and brains were collected. Cortical tissue was split into up to six pieces, from which bulk Calling Cards libraries were prepared independently. Sample names contain animal ID as the first two integers, followed by tissue piece number. e.g. CT14-5_piece_2 indicates animal CT14-5, tissue piece 2.

first: Benjamin

last: Boros

first: Mariam

last: Gachechiladze

first: Juanru

last: Guo

first: Dylan

last: Galloway

first: Shayna

last: Mueller

first: Mark

last: Shabsovich

first: Allen

last: Yen

first: Xuhua

last: Chen

first: Alexander

last: Cammack

first: Tao

last: Shen

first: Robi

last: Mitra

first: Timothy

last: Miller


title: CCL28 contributes to angiogenesis and cardiac repair by CCR10+ endothelial cells after myocardial infarction

city: Hangzhou

first: Rifeng

last: Gao

state: Zhejiang

address: No. 88 Jiefang Road

institute: Zhejiang University

summary: Secretome-based therapies targeting angiogenesis are promising in ischemic heart disease (IHD). The effects of Chemokine C-C motif ligand (CCL) 28 on IHD remain unclear. This study investigated the role of CCL28 in angiogenesis in IHD. The myocardial infarction (MI) and hindlimb ischemia (HI) models were constructed on male wild-type and CCL28-knockout mice. AAV9-TIE1-sh-CCR10 induced endothelial specific CCR10 deficiency in mice by tail vein injection. Recombinant CCL28 protein was used to treat MI and HI in wild-type and db/db mice. Serum levels of CCL28 were evaluated in a cohort of 416 consecutive chronic total occlusions (CTO) patients. The upregulated CCL28/ C-C motif receptor (CCR)10 axis was observed in myocardial and hindlimb ischemia. Additionally, CCL28 was mainly secreted by macrophages and CCR10 was highly expressed in endothelial cells (ECs). Compared to CCR10- ECs, CCR10+ ECs exhibited robust proangiogenic capacity, which are induced by CCL28 through the CCR10/ERK/SOX5 positive feedback signaling. Deletion of CCL28 results in impaired angiogenesis in the ischemic models while the use of recombinant CCL28 protein has therapeutic potential for myocardial and hindlimb ischemia, including in diabetes. Endothelial specific CCR10 deficiency impairs angiogenesis and blocks the therapeutic effect of rCCL28 in the myocardial and hindlimb ischemia. Serum CCL28 levels exhibited the predictive effect on coronary collateral vessels (CCV) in CTO patients. CCR10+ endothelial cells (ECs) are characterized with the enhanced proangiogenic capacity and beneficial for angiogenesis. CCL28 promotes angiogenesis by increasing CCR10+ ECs via the CCR10/ERK/SOX5 positive feedback signaling. This study highlights the angiogenic role of CCL28 and recombinant CCL28 protein might be a potential therapeutic option to attenuate myocardial and hindlimb ischemia, including in diabetes.

overall_design: RNA-seq was performed on CD45-CD31+ ECs magnetic bead sorted from WT and Ccl28-KO mice

first: Kun

last: Yang


title: WGBS of Arabidopsis thaliana tho2-8 mutant

first: La

last: mei

type: Methylation profiling by high throughput sequencing

overall_design: BS-seq of tho2-8;Col-LUC;ros1-7.

first: Yumei


title: IL-1β priming triggers an adaptive stress response that enhances pancreatic β-cell resilience to subsequent cytotoxic inflammatory insult

city: Pilar

first: Marcelo

middle: Javier

last: Perone

state: Buenos Aires

address: Av. Juan Domingo Perón 1500

country: Argentina

institute: Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral

summary: In this study, we explored the role of IL-1β-mediated hormesis in defending β-cells against dysfunction and death induced by pro-inflammatory cytokines (CYT). Preconditioning β-cells with physiological circulating levels of IL-1β (IL-1βlow) induced a resilient state, protecting them from CYT-induced cell death while preserving glucose-stimulated insulin secretion through hormesis. IL-1βlow-treated INS-1E cells reduced CYT-induced NO secretion by suppressing NF-κB signaling and decreasing iNOS expression, correlating with reduced β-cell death. IL-1βlow conditioning reduced ER stress and upregulated p-eIF2a in response to CYT, thereby enhancing the expression of ER chaperones and biomarkers linked to improved β-cell identity/functionality.

overall_design: RNA-seq profiling of INS-1E cells conditioned with IL-1β 10 pg/ml for 72h (IL-1βlow), with fresh cytokine added every 24h without replacing the culture media. Then, the culture media was renewed, and cells were challenged with a proinflammatory cytokine mixture (CYT: IL-1β 100 pg/ml + IFN-γ 5 ng/ml) for 16h. Experimental conditons: untreated, IL-1βlow, CYT, IL-1βlow + CYT. Three biological replicates were included for each condition.

first: Carolina

last: Sétula

first: Ingrid

last: Pensado Evans

first: Andrea

last: Scelza Figueredo

first: Miranda

last: Orellano

first: Ignacio

last: Rodríguez-Valero

first: Eduardo

last: Spinedi

first: Raghavendra

last: Mirmira

first: Luz

last: Andreone


title: Gene expression profile at single cell level of endothelial cells (ECs) from the WT and Apoa1bp-/- mice adductors with femoral artery ligation (FAL) injury

city: Changsha

first: Lingping

last: Zhu

address: Xiangya Road

institute: Xiangya hospital

summary: Establishment of collateral circulation (CC) is crucial for the treatment of ischemic disease, such as peripheral artery disease (PAD). We performed single-cell transcriptomic analysis to explore the cellular mechanism underlying CC.

overall_design: Adductors from WT or Apoa1bp-/- mice were collected for scRNA-seq on the day7 of FAL injury.

first: Yong

last: Bai

first: Long

middle: H

last: Fang


title: Glycerol metabolism modulates antibiotic tolerance in Pseudomonas aeruginosa

city: Birmingham

first: Jessica

last: Scoffield

state: Alabama

address: 1720 2nd Ave S

department: Microbiology

institute: The University of Alabama at Birmingham

summary: Chronic infections with Pseudomonas aeruginosa are a leading cause of morbidity and mortality in persons with cystic fibrosis (pwCF). P. aeruginosa persists in the CF lung by utilizing adaptation strategies to cause infection, including altering the expression of metabolic genes to acquire nutrients that are abundant in the CF airway. Glycerol in the airway is imported and metabolized by the glp regulon, which is under the control of the GlpR repressor. It has been shown that the loss of GlpR results in increased biofilm development in P. aeruginosa CF isolate compared to a wound isolate. Based on the increased biofilm phenotype observed and because biofilms are associated with increased antibiotic tolerance, we questioned whether GlpR plays a role in mediating antibiotic resistance of P. aeruginosa. We measured tobramycin tolerance in wild-type and glpR-defective P. aeruginosa isolates from the CF airway (FRD1) and a wound (PAO1). Cultures were grown in lysogeny broth or synthetic cystic fibrosis sputum consisting of the base formula of primarily amino acids (SCFM1) or supplemented with mucins and DNA (SCFM2), with dose-dependent concentrations of tobramycin. We tested the impact of a glpR mutation on P. aeruginosa adherence on bronchial epithelial cells from pwCF (CFBE) in the presence of tobramycin. CFBE cells were inoculated at an MOI of ~1:20 for 1 hour, given fresh apical media for 5 more hours, then apical and basal media was replaced with media containing 20 µg/ml tobramycin. We measured colony forming units (CFUs) and lactate dehydrogenase (LDH) release for cytotoxicity. Loss of glpR increased tolerance to tobramycin in both the PAO1 and FRD1 backgrounds in vitro at a concentration of 0.625 µg/mL in lysogeny broth and SCFM1. On both CFBE’s and 16HBE’s, the antibiotic resistance phenotype was more prominent in FRD1 glpR with a 2-log increase in viable bacteria when grown on cells and treated with 20 ug/ml tobramycin. However, changes in cytotoxicity where not observed between wildtype and GlpR mutants as LDH measurements were not significantly different. Our results indicate that GlpR may regulate antibiotic tolerance, in addition to biofilm development and glycerol metabolism. Additional studies are necessary to determine the mechanism of how GlpR modulates biofilm development and antibiotic tolerance.

overall_design: Transcriptome comparison of Pseudomonas aeruginosa strains PA01 and FRD1, with and without GlpR, the glycerol repressor, with and without treatment with 5 μg/mL tobramycin. All samples were grown in SCFM2 until mid-exponential phase, ~8 hours for untreated PA01 and ~20 hours for the FRD1 and treated cultures, then harvested for RNA-seq.

first: Nicholas

last: Evans


title: Alpha hemolysin enhances the immune response by modulating dendritic cell differentiation via ADAM10-Notch signaling

status: Public on Sep 04 2025

city: Chongqing

first: Ke

last: Wang

address: No. 30, Gaotan Yanzheng Street, Shapingba District, Chongqing

institute: Army Medical University

summary: In this study, we used PA0833 a novel protective antigen from Pseudomonas aeruginosa (P. aeruginosa) as the target antigen to evaluate the immune protective effect of the carrier antigen HlaH35A. The transcriptional profiling of bone marrow derived dendritic cells (BMDCs)  from mice indicated that HlaH35A predominantly modulates DC maturation, cytokine production, and subsequent T-cell activation. Structural prediction (AlphaFold-Multimer) and fluorescence confocal microscopy confirmed that the specific binding of HlaH35A to ADAM10 enhanced its antigen uptake capacity in dendritic cells. Meanwhile, this interaction between HlaH35A and ADAM10 further activated the downstream Notch signaling transduction in dendritic cells. The HlaH35A-ADM10–Notch axis in cDCs drives their differentiation into type2 cDCs (cDC2s)—particularly the Notch2-dependent cDC2—rather than involving monocyte-derived dendritic cells. This process promotes Th17 and T follicular helper (Tfh) cell responses in draining lymph nodes, leading to elevated antigen-specific IgG1 titers and robust protection against acute Pseudomonas aeruginosa lung infection. Thus, HlaH35A enhances immune response against acute lung infection by modulating cDC differentiation to amplify Th17 and T follicular helper responses, providing a promising Th17/Tfh-oriented vaccine design strategy.

overall_design: We collected bone marrow cells from the femurs and tibias of BALB/c mice. The cells were then cultured in RPMI-1640 medium supplemented with 10% FBS, penicillin and streptomycin and human recombinant Flt3L. The cells were harvested on day 8 and stimulated for 7.5 h. The cells were then subjected to bulk RNA-seq sequenced on the DNBSEQ platform (BGI).


title: Modeling arrhythmogenic cardiomyopathy fattyfibro pathology through the use of PKP2-deficient human iPSC-derived epicardial cells

city: Tucson

first: Jared

last: Churko

state: Arizona

address: 1501 N CAMPBELL AVE LSN 461

department: CMM

institute: University of Arizona

summary: Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disease characterized by progressive fatty-fibro replacement of the ventricular myocardium leading to arrhythmias and an increased risk of sudden cardiac death. To date, the cell types and signaling mechanisms involved in fatty-fibro infiltration of the myocardium have yet to be fully resolved. However, given that fatty-fibro replacement is initiated within the subepicardial layer, epicardial cells are predicted to contribute to the development of this pathology. To investigate the epicardial contributions to the development of ACM, we generated human induced pluripotent stem cell (hiPSC) lines from ACM patients harboring either a PKP2 1849C>T or a PKP2 2013delC mutation alongside CRISPR/Cas9 gene-edited isogenic control lines and a PKP2 knockout line. Epicardial cells derived from patient and knockout conditions displayed enhanced epithelial-to-mesenchymal transition characteristics, dysregulated Wnt and interferon signaling, increased lipid accumulation, and an enhanced fibrotic phenotype when converted to epicardial-derived fibroblasts. Transcriptomic analysis revealed upregulation of insulin growth factor 2 (IGF2) in ACM hiPSC-EPCs as well as in human ACM heart tissue. Subsequent treatment with exogenous IGF2 enhanced expression of the adipogenic transcription factors CEBPA and PPARG in hiPSC-EPCs, suggesting insulin growth factor signaling contributes to ACM fatty-fibro remodeling.

overall_design: We generated hiPSC lines from two ACM families carrying either a PKP2 1849C>T or PKP2 2013delC mutation, corrected each by CRISPR/Cas9 to create isogenic controls, and produced a PKP2 knockout line. All lines were differentiated into epicardial cells, then assayed for EMT markers, cell migration, lipid accumulation (Nile Red), and fibrotic marker expression. Epicardial-derived fibroblasts versus non-epicardial fibroblasts were compared under adipogenic induction. RNA-seq profiled global transcriptional changes; key findings were functionally validated by IGF2 treatment and IGF-1R inhibition.


title: Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids [RNAseq_time]

first: Lucille

last: Lopez-Delisle

overall_design: RNA-seq on hydrogel embedded gastruloids (1mM and 1.5mM, at 72h vs 96h)

first: Alexandre

last: Mayran

first: Jérôme

last: Ng Wong

first: Judith

last: Pineau

first: Thomas

last: Gregor

first: Denis

last: Duboule


title: Developmental regulation of long-range neuroblast migration by Eph/ephrin signaling

city: Storrs

first: Daria

last: Yeroshenko

state: Connecticut

address: 75 North Eagleville Road

department: PNB

institute: University of Connecticut

summary: In the developing mouse anterior forebrain, the rostral migratory stream (RMS) supports continued proliferation and efficient transportation of large quantities of neuroblasts from the ventricular-subventricular (V-SVZ) stem cell niche to the olfactory bulb (OB). Astrocytes aid this migration by providing a glial network through which chains of fasciculated neuroblasts move. The largest receptor tyrosine kinase family, Eph receptors, and their ephrin ligands have been implicated in controlling neuroblast migration and astrocyte organization within this pathway. However, a clear understanding of the regulatory mechanisms underlying Eph/ephrin signaling remains elusive, in part due to the complexity of heterogeneous expression patterns in both neuroblasts and astrocytes, as well as the cytoarchitectural changes that occur during postnatal development. Our studies provide a framework to deconvolute and characterize Eph and ephrin signaling as the RMS changes from a diffuse stream of migratory neuroblasts to a highly constricted pathway of neuroblast chains within astrocytic networks. Specifically, we identify temporally regulated, cell type-specific receptor-ligand interactions, revealing the prevalence and dynamic shifts of neuroblast-neuroblast, neuroblast-astrocyte, astrocyte-astrocyte interactions.

overall_design: Mice were harvested at P6, P12, or P60 ages. Their brains were harvested, and the rostral migratory stream was microdissected. Live cells were sorted by FACS from dead cells and debris and analyzed using scRNA seq.

first: Chamalka

last: De Silva

first: Anika

last: Burli

first: Sarah

last: Bellizzi

first: Vijender

last: Singh

first: Joanne

last: Conover


title: Anti-Leukemic Effects of Velcrin in SLFN12-Expressing Acute Myeloid Leukemia

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

summary: Schlafen 12 (SLFN12) is a member of the Schlafen (SLFN) family of proteins, a group of interferon-stimulated genes with diverse roles in cellular regulation with implications for human malignancies. Accumulating evidence indicates that SLFN family proteins may serve as prognostic markers across various cancer types. In acute myeloid leukemia (AML), SLFN12 is notably overexpressed, which prompted us to investigate its potential as a therapeutic target. Employing a panel of leukemia cell lines, we explored the effects of velcrins, a class of small molecules able to modulate SLFN12 biological activity. Mechanistic studies showed that velcrin treatment increases expression of SLFN12 and promotes SLFN12 complex formation with PDE3A or PDE3B. Functionally, these effects were associated with growth inhibition and induction of apoptosis. Further, velcrin treatment induced potent suppressive effects on the clonogenic capability of primary human AML progenitors and suppressed tumor growth and significantly extended survival in a mouse AML xenograft model. Taken together, these findings highlight the potential of using velcrins as a promising therapeutic strategy for the treatment of AML patients.

overall_design: Animal experiment protocols were approved by the Northwestern University Institutional Animal Care and Use Committee and performed accordingly. 5–6-week-old NU/NU nude female mice were acquired from Charles River laboratories (Strain Code 088). To induce flank tumors, 5x106 early passage HEL cells in the logarithmic growth phase were collected, washed, and resuspended in a final volume of 100 µL in PBS and loaded into a U-100 insulin syringe with an attached 27-gauge needle and injected into the right flank.  Approximately 13 days after injection, once tumors were palpable, tumor measurements were collected and mice were randomized into two treatment groups: vehicle control or treatment with a velcrin (BAY 2666605), with 5 mice per group. Mice were treated with vehicle control or BAY 2666605 (5 mg/kg), which was administered orally, twice daily for 2 weeks, with two days off. Tumor size was measured three times per week by caliper and the formula was calculated as follows (D × d2)* π/6, where D is the longest diameter and d is the shorter diameter.  Body weights and clinical observations were recorded 3 times per week.  For survival, mice were observed daily and all animals were compassionately euthanized 30 minutes following the last treatment dose. Tumor sections (n=4 per experimental group) were subsequently processed for SDS page or RNA-seq analysis.

first: Jamie N

last: Guillen Magaña

first: Markella

last: Zannikou

first: Aneta

last: Baran

first: Elspeth

last: Beauchamp

first: Matthew

last: Schipma

first: Elizabeth

middle: T

last: Bartom

first: Leonidas

last: Platanias


title: AS03-adjuvanted chimeric HA-based influenza vaccine induces long-lived stalk-specific plasma cells in bone marrow and lymph nodes of non-human primates

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Current influenza vaccines face challenges due to antigenic evolution of the circulating virus and waning immunity in humans. Here, we investigated the durability of humoral immunity induced by an AS03-adjuvanted chimeric hemagglutinin (cHA) based influenza vaccine in non-human primates (NHPs). Two groups of NHPs (n=7 or 8) received two doses of a seasonal quadrivalent influenza vaccine (QIV) on weeks 0 and 4, followed by sequential immunization with split virus cHA vaccines cH8/1N1 (week 21), and cH5/1N1 (weeks 33 and 94). One group received cHA immunizations with AS03 adjuvant. We monitored serum antibodies and long-lived plasma cells in bone marrow for nearly 2 years after the final vaccination. The seasonal QIV vaccine induced poor HA stalk-specific antibodies and failed to give rise to detectable long-lived plasma cells in bone marrow. In contrast, cHA vaccines significantly induced stalk-specific antibody responses. Importantly, the addition of AS03 enhanced both the magnitude and durability of humoral immunity by establishing the persistence of long-lived plasma cells in the bone marrow and lymph nodes for nearly 2 years. Passive transfer of NHP serum provided protection against challenge with heterologous influenza A virus strains in mice. This study highlights the potential of the AS03-adjuvanted chimeric HA vaccine strategy to provide durable and broadly protective humoral immunity.

overall_design: Ten male Rhesus macaques were innoculated with cH5/1N1, five in an un-adjuvanted group and 5 adjuvanted with AS03, following a common immunization with QIV. Blood samples were collected at Days 0, 1, 2, 4 and 7 post-innoculation for RNA-Seq analysis.

first: Akil

last: Akhtar

first: Tiffany

last: Styles

first: Chunyang

last: Gu

first: André

last: León

first: Kasey

last: Stokdyk

first: Anass

last: Abbad

first: Cora

last: Hirst

first: Shirin

last: Strohmeier

first: Gabriele

last: Neumann

first: Sara

last: Richey

first: James

last: Ferguson

first: Hasan

last: Ahmed

first: Julianna

last: Han

first: Juan

last: Carreño

first: Carl

last: Davis

first: Rustom

last: Antia

first: Peter

last: Palese

first: Andrew

middle: B

last: Ward

first: Yoshihiro

last: Kawaoka

first: Florian

last: Krammer

first: Rafi

first: Rama

middle: R

last: Amara


title: BamA self-insertion drives inner-to-outer membrane remodelling in diderm Firmicutes

city: Vancouver

first: Elitza

last: Tocheva

state: BC

address: 2350 Health Sciences Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

summary: Exclusive to Firmicutes, endospore formation is a complex process that results in the release of a mature spore after the mother cell lyses. The spore is protected by multiple layers, including inner and outer spore membranes (IsM and OsM), both originating from the mother cell's inner membrane (IM). While well understood in monoderm bacteria like Bacillus subtilis, less is known about diderm sporulators such as Acetonema longum, which retain and remodel their OsM into a functional outer membrane (OM) during germination. Here, we demonstrate that outer membrane proteins (OMPs), including the essential BAM complex component BamA and the LPS translocon protein LptD, are present in vegetative and germinating cells but absent from mature spores, indicating that OM biogenesis occurs without pre-existing OMPs. Growth-stage proteomics and expression profiling identify two previously uncharacterized proteins, SonA and SonB, co-expressed with BamA and in a conserved operon among diderm Firmicutes. SonA is a β-barrel OMP with three POTRA domains, while SonB is a predicted OM lipoprotein. In vitro, BamA and SonA spontaneously fold and insert into liposomes, supporting a model where BamA and/or SonA initiate self-insertion into the OsM, driving its stepwise transformation into a fully functional OM.

overall_design: RNAseq profiling of Acetonema longum APO-1 (DSM 6540) across discrete stages of the sporulation cycle: vegetative growth (3 day subcultures in exponential phase), sporulation (5 day subcultures in stationary phase) and germination (pure germinating spores at 16 hours post-inoculation).

first: Polina

last: Beskrovnaya

first: Ameena

last: Hashimi

first: Danielle L.

last: Sexton

first: Gregory E.

last: Nikas

first: Elitza I.


title: Transcriptomic profiile of A375 melanoma cell treated with Olive oil and Ozoanted olive oil

city: Sapporo-shi

first: Seong-jin

last: An

state: Hokkaido

address: Kita 12 nishi 6, kita-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Hokkaido university

summary: To investigate the transcriptional effects of ozonated olive oil, we performed a comprehensive gene expression analysis of A375 human melanoma cells treated with either ozonated olive oil or olive oil as a control.

overall_design: A375 cells were treated with olive oil or ozonated olive oil for 6 h and gene expression profile was analyzed by NGS.

first: Jun-ichi

last: Kashiwakura

first: Sumihito

last: Togi

first: Tadashi

last: Matsuda


title: Role of GPNMB in Foam Cells Formation and Atherosclerosis Progression

city: Beijing

first: Huan

last: Wang

address: 38 Life Science Park Road

institute: National Center for Protein Sciences, Beijing

summary: Currently, both reliable biomarkers for disease monitoring and specific therapeutic targets are needed to combat atherosclerosis, one of the dangerous lipid metabolism disorders. We observed attenuation of atherosclerosis in a GPNMB auto-mutant (GpnmbR150X) mouse model as well as in a myeloid-specific Gpnmb-knockout mouse model. Furthermore, in GpnmbR150X BMDMs, we observed that impaired lipid droplet formation, enhanced lipid oxidative metabolism, and more robust lipid degradation by the lysosomal pathway suppressed the macrophage foaming, thereby reducing the atherosclerotic burden of excess OxLDL.

overall_design: To investigate how GPNMB affected the macrophage foaming, we performed bulk RNA-seq analysis of BMDMs from GpnmbR150X mouse or control mouse and OxLDL-treated BMDMs from GpnmbR150X mouse or control mouse.

first: Junqi

first: Xiaoping

last: Chen

first: Li

last: Tang


title: Saikosaponin‑D triggers cancer death by targeting the PIM1/c-Myc axis to rewire oncogenic alternative splicing

city: Shanghai

first: Fuwen

last: Yuan

state: 上海

address: Cailun Road #1200, Pudong New area

institute: Shanghai University of Traditional Chinese Medicine

summary: Saikosaponins (SSs, including SSA, SSB, SSC, and SSD), the major bioactive compounds in the traditional medicine Radix Bupleuri (RB), are emerging agents exhibiting anti-tumor efficacy in several cancers. However, the respective anti-tumor efficacy of these agents and mechanisms in cancers such as gastric and prostate cancer remains unclear. In this study, we demonstrated that SSD, among SSs, possessed a significant anti-tumor role in vivo and in vitro. Transcriptome analysis revealed a down-regulation of alternative splicing factors and rewiring of oncogenic alternative splicing events such as CYP1A1, whose transcript-specific ablation with CIRSPR-Cas13 significantly abolished SSD-induced cell growth inhibition. Specifically, we showed that SSD binds to PIM1 and down-regulates its expression, thus restraining PIM1-mediated serine 62 phosphorylation of Myc, which is critical for its transcription activity. This results in decreasing the expression of Myc-governed alternative splicing factors that are responsible for the regulation of oncogenic alternative splicing events. These studies demonstrated the potent anti-tumor efficacy of SSD and exposed a PIM1/Myc pathway that drives the expression of an essential alternative splicing regulatory network that mediates SSD’s anti-tumor role in cancers.

overall_design: mRNA profiles of AGS cells treated with vehicle, SSD were generated by deep sequencing, in triplicate, using Illumina HiSeq6000

first: Xuehui

last: Li


title: Sulfatide deficiency-induced astrogliosis and myelin lipid dyshomeostasis are independent of Trem2-mediated microglial activation_Male cerebrum study

city: SAN ANTONIO

first: Sijia

last: He

state: Texas

address: 7703 Floyd Curl Dr.

institute: uthealth sa

summary: This study investigates the impact of central nervous system sulfatide (ST) deficiency on gene expression in the male mouse cerebrum tissues, both in the presence and absence of Trem2, using the NanoString Neuroinflammation panel.

overall_design: The measurement set contains 12 samples, composed of 4 genotypes (Cre-/Trem2 WT, Cre-/Trem2 KO, Cre+/Trem2 WT, and Cre+/Trem2 KO) in triplicates. Note that Cre- indicate mice with ST, Cre+ indicate mice of adult-onset ST-deficiency.

first: Namrata

last: Mittra

first: Xianlin

last: Han


title: High throughput CRISPR perturbation screens identify epigenetic regulators impacting primordial germ cell development [RNA-seq]

city: Ithaca

first: Jingyi

last: Gao

state: NY

address: 618 Tower road

department: BMS

institute: Cornell University

summary: There is concern that environmental factors underlie reported declines in fertility and reproductive parameters such as the number and quality of sperm and eggs. One possible mechanism is the perturbation of epigenetic landscapes in the germline. To explore this possibility, we utilized a highly scalable in vitro platform for the differentiation of embryonic stem cells (ESCs) into primordial germ cell-like cells (PGCLCs) to conduct a CRISPRi screen of epigenetic-related genes to identify those that specifically perturb the efficiency of PGCLC formation. This platform leveraged an ESC line containing 4 inducible transcription factors (Prdm1, Prdm14, Tfap2c, and Nanog) and a PGC reporter (Stella-eGFP) that enabled highly efficient, cytokine-free differentiation and quantification en masse. A total of 701 genes with distinct sgRNAs were screened, and 53 genes were identified that decreased the efficiency of PGCLC formation. NCOR2, a transcriptional repressor that acts via recruitment of Class I and Class IIa histone deacetylases (HDACs) to gene targets, was particularly potent in suppressing PGCLC differentiation. Consistent with evidence that histone deacetylation is crucial for germline differentiation, we found that HDAC inhibitors (HDACi), including the anti-convulsive drug valproic acid (VPA) and widely-available dietary supplement sodium butyrate (SB), also suppressed ESC>PGCLC differentiation. Transcriptome analyses of HDACi-treated, differentiating ESC>PGCLC cultures revealed suppression of germline-associated pathways and enhancement of somatic pathways. Additionally, exposure of developing mouse embryos to SB or VPA caused hypospermatogenesis. This work demonstrates the feasibility of conducting large scale functional screens of genes, chemical agents and possibly genetic variants that impact germline development and epigenome.

overall_design: RNA-seq to evaluate the effect of HDACi, sodium butyrate (SB) and valproic acid (VPA), exposure on PGCLC development.

first: Liangdao

first: Dain

last: Yi

first: Alex

middle: P

last: Sheft

first: John

last: Schimenti

first: Xinbao

last: Ding


title: Sulfatide deficiency-induced astrogliosis and myelin lipid dyshomeostasis are independent of Trem2-mediated microglial activation_Female spinal cord study

summary: This study investigates the impact of central nervous system sulfatide (ST) deficiency on gene expression in the female mouse spinal cord tissues, both in the presence and absence of Trem2, using the NanoString Neuroinflammation panel.


title: High throughput CRISPR perturbation screens identify epigenetic regulators impacting primordial germ cell development [CRISPRi]

overall_design: Using a CRISPR inhibition (CRISPRi) screen to identify essential epigenetic regulators of PGC development.


title: Sulfatide deficiency-induced astrogliosis and myelin lipid dyshomeostasis are independent of Trem2-mediated microglial activation_Female cerebrum study

summary: This study investigates the impact of central nervous system sulfatide (ST) deficiency on gene expression in the female mouse cerebrum tissues, both in the presence and absence of Trem2, using the NanoString Neuroinflammation panel.

overall_design: The measurment set contains 12 samples, composed of 4 genotypes (Cre-/Trem2 WT, Cre-/Trem2 KO, Cre+/Trem2 WT, and Cre+/Trem2 KO) in triplicates. Note that Cre- indicate mice with ST, Cre+ indicate mice of adult-onset ST-deficiency.


title: Scalable and Efficient Generation of Mouse Primordial Germ Cell-like Cells

summary: Primordial germ cells (PGCs) are the founder cells of the germline. The ability to generate PGC-like cells (PGCLCs) from pluripotent stem cells has advanced our knowledge of gametogenesis and holds promise for developing infertility treatments. However, generating an ample supply of PGCLCs for demanding applications such as high-throughput genetic screens has been a limitation. Here, we demonstrated that simultaneous overexpressing 4 transcriptional factors – Nanog and three PGC master regulators Prdm1, Prdm14 and Tfap2c - in suspended mouse epiblast like cells (EpiLCs) and formative embryonic stem cells (ESCs) results in efficient and cost-effective production of PGCLCs. The overexpression of Nanog enhances the PGC regulatory network and suppresses differentiation of somatic lineages, enabling a significant improvement in the efficiency of PGCLC production. Transcriptomic analysis reveals that differentiated PGCLCs exhibit similarities to in vivo PGCs and are more advanced compared to cytokine-induced PGCLCs. These differentiated PGCLCs could be sustained over prolonged periods of culture, and could differentiate into spermatogonium-like cells in vitro. Importantly, the ability to produce PGCLC differentiation at scale enables biochemical and functional genomic screens to dissect mechanisms of germ cell development and infertility.

overall_design: RNA-seq for 4 transcriptional factor (i.e., Prdm1, Prdm14, Tfap2c and Nanog) induced PGCLC at day 2, 4 and 6, as well as EpiLC and ESC.


title: Targeting Liver Epsins Ameliorates Dyslipidemia in Atherosclerosis through Inhibition of Proprotein Convertase Subtilisin/Kexin Type 9-Mediated Low-density Lipoprotein Receptor Degradation

city: Boston

first: Krishan

last: Gupta

state: MASSACHUSETTS

address: 300 Longwood Avenu, Boston children's Hospital

institute: Boston Children's Hospital/Harvard Medical School

summary:
Background: The low-density lipoprotein receptor (LDLR) in the liver plays a crucial role in clearing low-density lipoprotein cholesterol (LDL-C) from the bloodstream. This process takes place mainly in the liver. Under atherogenic conditions, Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9), secreted by the liver, binds to LDLR on hepatocytes, preventing its recycling and enhancing its lysosomal degradation. This process reduces LDL-C clearance, promoting hypercholesterolemia. Epsins, a family of ubiquitin-binding endocytic adaptors, are key regulators of atherogenesis in lesional cells, including endothelial cells and macrophages. Given epsins' canonical role in regulating endocytosis of cell surface receptors, we aimed to determine whether and  how liver epsins contribute to PCSK9-mediated LDLR endocytosis and degradation, thereby impairing LDL-C clearance and accelerating atherosclerosis.
Methods: Liver-specific epsin knockout (Liver-DKO) atherosclerotic models were generated in ApoE-/- and PCSK9-AAV8-induced atheroprone mice fed on a Western diet. We utilized single-cell RNA sequencing, along with molecular, cellular, and biochemical analyses, to investigate the physiological role of liver epsins in PCSK9-mediated LDLR degradation. Additionally, we explored the therapeutic potential of nanoparticle-encapsulated siRNAs targeting epsins 1 and 2 in ApoE-/- mice with established atherosclerosis.
Results: Western diet (WD)-induced atherosclerosis was significantly attenuated in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls, as well as in PCSK9-AAV8-induced Liver-DKO mice compared with PCSK9-AAV8-induced wild-type (WT) mice accompanied by reductions in blood cholesterol and triglyceride levels. Mechanistically, single-cell RNA sequencing of hepatocytes and aortas isolated from atherosclerotic ApoE-/- and ApoE-/-/Liver-DKO mice revealed epsin-deficient Ldlrhi hepatocytes with diminished lipogenic potential. Notably, pathway analysis of hepatocytes showed increased LDL particle clearance and enhanced LDLR-cholesterol interactions under WD treatment in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls, correlating with decreased plasma LDL-C levels. Furthermore, pathway analysis of the aortas showed attenuated inflammation and endothelial activation, coupled with reduced lipid uptake, and enhanced cholesterol efflux under WD treatment in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls. Moreover, the absence of liver epsins led to an upregulation of LDLR protein expression in hepatocytes. We further demonstrated that epsins bind LDLR via the ubiquitin-interacting motif (UIM), enabling PCSK9-mediated LDLR degradation. Depleting epsins abolished this degradation, thereby preventing atheroma progression. Lastly, targeting liver epsins with nanoparticle-encapsulated epsins siRNAs effectively ameliorates dyslipidemia and inhibits atherosclerosis progression. These results are consistent with findings showing an increased epsin1 and epsin2 expression in atherosclerotic cardiovascular disease patients.
Conclusions: Liver epsins drive atherogenesis by promoting PCSK9-mediated LDLR degradation, thereby elevating circulating LDL-C levels and heightening lesional inflammation. As such, targeting epsins in the liver represents a promising therapeutic strategy to mitigate atherosclerosis by preserving LDLR and enhancing LDL-C clearance in the liver.

overall_design: In this study, all animal procedures were performed in compliance with institutional guidelines and mouse protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of Boston Children’s Hospital, MA, USA.

first: Gupta

last: Krishan

first: Zhu

last: Bo

first: Chen

last: Hong

last: Kaifu


title: Deer Antler ASCs Exosomes Ameliorate Osteoarthritis via miR-140/MMP13 Axis-Mediated Dual Modulation of Inflammation and Cartilage Regeneration

status: Public on Sep 03 2025

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

summary: Osteoarthritis (OA) is a progressive degenerative joint disorder characterized by chondrocyte dysfunction and extracellular matrix degradation. While stem cell therapies have been constrained by immunological rejection risks, their derived extracellular vesicles (Exos) emerge as a promising alternative therapeutic approach. Antler, a remarkable regenerative organ with extraordinary regenerative capacity and chondrogenic potential, offers a unique biological resource. Antler Stem Cells (ASCs) provide an innovative extracellular vesicle source (ASC-Exos) that presents a compelling therapeutic strategy for addressing OA's complex pathogenesis. To investigate the therapeutic effects and mechanism of ASC-Exos in OA treatment. ASCs characteristics were confirmed through immunofluorescence and tri-lineage differentiation, while exosomes were validated using transmission electron microscopy, nanoparticle tracking analysis, and Western blot. A rat OA model was established to evaluate therapeutic effects of ASC-Exos via different administration routes. Small RNA sequencing identified key extracellular vesicle components, while dual-luciferase reporter assays confirmed regulatory interactions between miR-140 and metalloproteinase-13(MMP13). Stable miR-140 overexpressing ASCs were generated through lentiviral transduction. An IL-1β-stimulated chondrocyte OA model was employed to assess the impact of miR-140-engineered ASC-Exos (miR-140-Exos) on cellular proliferation, migration, and apoptosis. The therapeutic potential was further evaluated in in vivo animal models. We successfully isolated and characterized ASCs and ASC-Exos. Intra-articular injection of ASC-Exos demonstrated superior cartilage repair efficacy. The critical extracellular vesicle component miR-140 was identified. In vitro studies revealed that miR-140-Exos significantly enhanced chondrocyte proliferation and migration while reducing cellular apoptosis. Dual-luciferase assays confirmed miR-140 directly targets MMP13, with MMP13 overexpression partially reversing miR-140-mediated cellular effects. In vivo investigations demonstrated that miR-140-modified ASC-Exos effectively inhibited COL II degradation and suppressed NLRP3 elevation, thereby providing anti-inflammatory benefits and promoting cartilage regeneration. miR-140-Exos represent an innovative therapeutic approach for osteoarthritis, effectively promoting cartilage regeneration and alleviating inflammation through MMP13 inhibition, presenting a novel therapeutic strategy for OA treatment.

overall_design: ASC-Exos and chondrogenic-induced Chr-ASC-Exos  were collected. Total RNA pooled was collected from ASC-Exos and chondrogenic-induced Chr-ASC-Exos to construct a cDNA library. ASC-Exos and chondrogenic-induced Chr-ASC-Exos miRNAs were analyzed by Illumina NovaSeq 6000 for high-throughput deep sequenc.

first: Yuhao

last: Song

first: Xue

last: Wang

first: Xin


title: Transcriptomic profiile of B16F10 melanoma cell treated with Olive oil and Ozoanted olive oil

first: Seong-jin

last: An

summary: To investigate the transcriptional effects of ozonated olive oil, we performed a comprehensive gene expression analysis of B16F10 murine melanoma cells treated with either ozonated olive oil or olive oil as a control.

overall_design: B16F10 cells were treated with olive oil or ozonated olive oil for 6 h and gene expression profile was analyzed by NGS.

first: Jun-ichi

last: Kashiwakura

first: Sumihito

last: Togi

first: Tadashi

last: Matsuda


title: Exogenous Delivery of Sphingomyelinase Mediates Mesenchymal Stromal Cell-Extracellular Vesicle Biogenesis, Alters Cargo Sorting, and Therapeutic Potency in vitro

first: Daniel

last: Shah

state: Ga

address: 315 Ferst Dr.

institute: Georgia Institute of Technology

summary: Mesenchymal stromal cells (MSCs) are multipotent stromal cells with regenerative, immunomodulatory, and anti-inflammatory properties, making them a promising tool in cell-based therapies. Increasing evidence suggests the therapeutic effects of MSCs are largely mediated by secreted paracrine factors and extracellular vesicles (EVs), which facilitate extracellular communication by transferring bioactive molecules such as proteins, lipids, and nucleic acids to target cells. The lipid composition of EVs is critical for their stability, uptake, and functional activity. Sphingomyelinase (SMase), an enzyme that hydrolyzes sphingomyelin into ceramide, plays a key role in EV biogenesis by influencing membrane curvature allowing for invagination and budding of multivesicular bodies (MVBs). However, the impact of SMase treatment on the characteristics and therapeutic potential of MSC-derived EVs remains largely unexplored. In this study, human MSCs were cultured with SMase for 24 hours and EVs were isolated via ultracentrifugation. EV size distribution was analyzed using nanoparticle tracking analysis (NTA), microRNA (miRNA) profile was determined using RNA-sequencing, while lipidomic and proteomic profiling were assessed using mass spectrometry. Functional assays were conducted to assess changes in bioactivity. NTA revealed a shift in EV production, with a higher vesicle concentration in SMase induced MSCs compared to untreated cells. SMase treatment significantly altered MSC-EV composition, leading to increased ceramide and glycosphingolipids. In addition, the modifications in protein and miRNA EV cargo were found to be associated with pathways involving TNF-α signaling, vesicle trafficking, wound healing, and angiogenesis. Functional assays indicated greater suppression of TNF-α in activated macrophages and greater tubular network formation in HUVECS. These findings provide new insights into distinct biophysical and biochemical changes in MSC-derived EVs following SMase stimulation, potentially enhancing their therapeutic properties and may inform strategies for optimizing future EV-based therapies.

overall_design: MSCs were treated with SMase for 24 hours and the miRNA profile of MSCs and their derived EVs was sequenced.

first: S'Dravious

last: DeVeaux

first: Edward

last: Botchwey


title: Transcriptomic and functional responses of the cystic fibrosis airway epithelium to CFTR modulator therapy

city: Aurora

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: Elexacaftor/tezacaftor/ivacaftor (ETI) CFTR modulator therapy has led to rapid and substantial improvements in cystic fibrosis (CF) airway disease. Underlying molecular and cellular mechanisms, long-term efficacy, and ability to reverse airway epithelial remodeling in established disease remain unclear. Longitudinal nasal brushes from an adult CF cohort were used to evaluate gene expression, cellular composition, stem cell function, and microbiome changes at baseline and at six months and two years after ETI. The baseline to six month span showed a massive downregulation of extensive neutrophilic inflammatory gene expression programs that correlated with increased pulmonary function and decreased sinusitis. Primary airway epithelial stem cell cultures from matched donor samples showed partially improved differentiation and barrier capacity at six months. Although clinical outcomes remained stable during the six month to two year span, transcriptional changes revealed a resurgence of baseline inflammatory programs. Time course gene expression was consistent with ongoing normalization of epithelial remodeling. Relative abundance of Pseudomonas also decreased during the time course. These data suggest that ETI rectifies inflammation, epithelial remodeling, and bacterial infection in the airways, but resurgence of inflammatory gene expression may indicate ongoing inflammation, potentially presaging disease progression with long-term therapy.

overall_design: Longitudinal nasal brushes from an adult cystic fibrosis cohort were used to evaluate gene expression changes using RNA-seq at baseline and at six months and two years after Elexacaftor/tezacaftor/ivacaftor CFTR modulator therapy.

first: Eszter

last: Vladar


title: Tumor nutrient stress gives rise to a drug tolerant cell state in pancreatic cancer

first: Alex

last: Muir

email: amuir@berkeley.edu, amuir@uchicago.edu

state: Illinois

department: Ben May Department for Cancer Research

institute: University of Chicago

summary: Cytotoxic chemotherapy remains the standard-of-care treatment for patients with pancreatic ductal adenocarcinoma (PDAC). However, chemotherapy only has modest effects at improving overall survival due to primary or rapidly acquired chemoresistance. The biological underpinnings of PDAC therapy resistance are incompletely defined, but the tumor microenvironment is known to be a major contributor to chemoresistance. We have found chemoresistance is imprinted on PDAC cells by the tumor microenvironment and persists for a period of days after PDAC cells are removed from tumors. However, PDAC chemoresistance is lost upon long term culture in standard laboratory conditions. Interestingly, culture of PDAC cells in Tumor Interstitial Fluid Medium (TIFM), a culture medium we developed to recapitulate the nutrient availability of the tumor microenvironment, maintains PDAC cells in a chemoresistant state even after long term culture ex vivo. These findings suggest that microenvironmental metabolic stress keeps PDAC cells in a physiologically relevant, therapy resistant cell state that standard culture models fail to maintain. Using TIFM culture, we sought to understand how PDAC cells in this state resist chemotherapeutic challenge. We found that chemotherapy drugs largely retain on-target activity within TIFM medium but fail to activate cell death, enabling a “chemotolerant” cell state, which is also observed in PDAC tumors. This chemotolerant state is driven by suppression of apoptotic priming and can be overcome by targeting the anti-apoptotic regulator BCL-xL. Taken together, these findings suggest that reprogramming of cell death mechanisms by the PDAC nutrient microenvironment is a key contributor to therapy resistance in this disease.

overall_design: Murine pancreatic cancer cells (mPDAC1) were grown in RPMI-1640 or in tumor interstitial fluid medium (TIFM). Cells in each medium were treated with either vehicle or 125nM gemcitabine for 24 hours. RNA was then extracted and sent for library prep and sequencing with the University of Chicago Genomics Core.

first: Colin

last: Sheehan


title: The effect of ZIKV and MBD-mutant ZIKVs infection on neonatal mouse brains

first: Rui-Ting

last: Li

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

summary: To compare the impact of WT and MBD ZIKVs on the developing brain at the molecular level, we carried out global tanscriptome analyses (RNA-seq) on one-day-old neonatal mouse brains infected with Mock, WT or MBD2 ZIKV at 3 days post-infection.

overall_design: RNA sequencing (RNA-seq)-based transcriptional profiling experiments were conducted using Mock, WT and MBD2 ZIKV infected one-day-old neonatal mouse brains at 3 days after infection.

first: Xiang

last: Chen


title: Effect of hepatocytic RKIP depletion on HFD-induced MASLD

city: Hangzhou

first: Mengjie

address: Institute of Immunology and Bone Marrow Transplantation Center, The First 6 Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, 7 China.

institute: Zhejiang University

summary: High-fat diet (HFD) is a risk factor for metabolic dysfunction-associated steatotic liver disease (MASLD), yet the molecular pathways that connect dietary fats to liver dysfunction remain unclear. Hepatocyte-specific RKIP depletion in male mice exacerbates ER stress, resulting in lipid droplets accumulation and MASLD progression.

overall_design: RNA-seq profiling of liver tissues from HFD-fed RKIPf/f and Albcre-RKIPf/f mice.

first: Qiang

last: Qin

first: Xiaojian


title: Using constraint-based metabolic modeling to elucidate drug-induced metabolic changes in a cancer cell line

city: Trondheim

first: Åsmund

last: Flobak

state: Norway

address: Prinsesse Kristinas gt 1, Gastrosenteret

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology - NTNU

summary: Since the discovery of the Warburg effect, metabolism has become a crucial cancer hallmark, for cancer cells change the activity of metabolic pathways to satisfy the demand of biomolecules and energy required to sustain continuous growth. Specially, gastric cancer (GC) still remains a growing burden of society, and often require the development of targeted and personalized interventions, including the use of combinatorial drug therapies that allow for synergistic interactions. However, the mechanism underlying synergistic interactions between multiple drugs remain poorly understood. The objective of this study is to use genome-scale metabolic models (GEMs) and transcriptomic data to investigate potential synergistic mechanisms in the GC cell line AGS following treatment with three kinase inhibitors and their combinations. To explore the metabolic phenotype of AGS cells, we curated and used a set of descriptions of metabolic functions (metabolic tasks) based on the latest iteration of the Human-GEM, and we used the Task Inferred from Differential Expression (TIDE) framework to infer the metabolic changes in AGS cells. Additionally, we expanded and complemented the TIDE framework by integrating essential genes from metabolic tasks, allowing for a more robust analysis. The results revealed a complex metabolic response in AGS cells after kinase inhibitor treatments, particularly in amino acid  and nucleotide metabolism, and characterized by the down-regulation of metabolic functions. Using two definitions of synergistic effects, we identified significant metabolic shifts in combinatorial treatments, including a combination-specific increase in ornithine levels, potentially linked to an antiproliferative effect on AGS cell growth. These findings highlight the potential of using transcriptomic data to infer the metabolic phenotype of AGS cells  and the role of metabolic alterations in cancer progression. In addition, we developed a Python library for Metabolic Task Enrichment Analysis, making the TIDE frameworks accessible to other researchers.

overall_design: RNA-seq profiling of AGS cells under different treatment conditions with a control and three kinase inhibitors and their combinations at 24 hours post-exposure. Each treatment condition had four biological replicates.

first: Xavier

last: Benedicto

first: Miguel

last: Ponce-de-León

first: Alfonso

last: Valencia


title: The Integrated Stress Response Pathway Improves Aged Murine Muscle Stem Cell Activation and in vivo Regeneration

city: San Francisco

first: Andrew

last: Brack

state: CA

address: 35 Medical Center Way

department: Orthopaedic Surgery

institute: UCSF

summary: For efficient regeneration, muscle stem cells (MuSCs) transition out of quiescence through a series of progressively more activated states. During MuSC aging, transition through the earliest steps is the slowest and delayed, with the molecular regulators that govern this transition not well characterized. Here, we found that aged MuSCs have increased baseline integrative stress response (ISR) activity in quiescence that does not increase during activation to levels observed in adult MuSCs. Rapid and transient pharmacological ISR activation in vitro was sufficient to increase aged MuSC activation rate through ISR-activator (ISR-a) and migratory behavior and also alter the transcriptional states toward an adult phenotype. ISR activation also improved aged MuSC potency and aged mouse muscle regeneration in vivo. Therefore, pharmacological activation of the ISR has therapeutic potential to improve MuSC function and skeletal muscle repair during aging.

overall_design: RNA seq profiling of adult (4 month), aged (22 month) and ISR-activator treated of activated (18h) Murin Muscle Stem Cells to investigate the effects of ISR activation on activated muscle stem cells.

first: Samiha

last: Mahin

last: Brown


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

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

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: RNA isolated from Hermes4B cell lines treated with siRNA control (siNT),  against CDH3-AS1 (siCDH3-AS1) or against CDH3 RNA isolated from Hermes4B cell lines treated with control siRNA (siNT), siRNA targeting CDH3-AS1 (siCDH3-AS1), or siRNA targeting CDH3 (siCDH3).

first: Manon

last: Chadourne

first: Crystal

last: Griffiths

first: Xiaonan

last: Xu

first: Emily

last: Brennan

first: Olga

last: Vera

first: Nicol

last: Mecozzi

first: Kaizhen

last: Wang

last: Jaeger

first: Florian

last: Karreth


title: CRISPR/Cas9-Mediated PTPRZ1 Knockout Suppresses LUSC Proliferation with Genome-Wide Off-Target Analysis

status: Public on Sep 02 2025

city: Xi'an

first: Yihui

last: Zhang

state: Shanxi

address: No.229 Taibai North Road

institute: Northwest University

summary: To investigate the potential role of the PTPRZ1 in tumor development, we leveraged CRISPR/Cas9 to perform knockout experiments in two distinct LUSC cell lines, H520 and HCC95, both characterized by high cellular expression of the gene. Following the disruption of PTPRZ1, we observed a significant reduction in the proliferation of both LUSC cell lines, as indicated by the Cell Counting Kit-8 (CCK-8) assay .To comprehensively assess potential off-target effects of the CRISPR/Cas9 editing, we conducted whole-genome sequencing comparing the HCC95-NC and HCC95-KO-PTPRZ1cell lines, which enabled genome-wide evaluation of editing specificity

overall_design: WGS of the HCC95-NC and HCC95-KO-PTPRZ1 cells.

first: Jie

first: Yongqiang

last: Ning


title: The contribution of the transcription factors Crz1 and Rim101 to the response to alkalinization in Komagataella phaffii

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

summary: In the industrially relevant yeast Komagataella phaffii, as in other yeasts, alkalinization of the medium results in fast and extensive transcriptional remodeling. This response has been useful to design novel methanol-free, regulatable platforms for heterologous protein expression. However, its molecular bases are fully unknown. Crz1 and Rim101/PacC are transcription factors known to contribute to the alkaline pH transcriptional responses in many fungi. We identified here the transcription factors Crz1 and Rim101 in K. phaffii and used CRISPR/Cas9 techniques to create single and double mutant strains. Phenotypic characterization shows that crz1 cells are strongly sensitive to Ca2+ ions, mildly sensitive to alkaline pH and hypertolerant to SDS. In contrast, rim101 cells are markedly hypersensitive to Na+ and Li+ ions, to alkaline pH and to SDS. RNA-seq transcriptomic analysis revealed that mutation of RIM101 affects 55% of genes whose expression is altered at pH 8.0, whereas lack of Crz1 alters only 11% of these. Thirty-eight genes are co-regulated by both Crz1 and Rim101. The PMC1 vacuolar Ca+2-ATPase is regulated by Crz1, whereas the ENA2 Na+-ATPase, the PHO89 and PHO84 phosphate transporters, and diverse genes involved in iron homeostasis are Rim101-dependent. These effects were confirmed by proteomic analyses after 3 h of alkalinization. Therefore, while Rim101 appears as a major player in the transcriptional response to alkalinization, nearly 40% of the alkaline pH transcriptional response in K. phaffii is controlled still unknown pathways.

overall_design: Comparison of mRNA levels by RNA-Seq between Komagataella phaffii yeast cells grown  on YP-glycerol at pH 5.5 (reference) and 8.0 (alkaline pH) for wild-type GS115 strain and cell mutated for PAS_chr3_0625 (RIM101) and PAS_chr2-2_0202 (CRZ1) transcription factors. Samples were taken after 0, 15, 30 and 60 min  upon alkalinization of the medium.

first: Joaquin

last: Arino

first: Marcel

last: Albacar

first: Antonio

last: Casamayor

first: Asier

last: González


title: Divergent functions of master TFs in LUSC [RNA-seq]

summary: To examine the essential role of these four TFs particularly the two novel ones KLF5 and GRHL2, we depleted individual factors with siRNA in a human LUSC cell line HCC95. The results consistently showed that cells deficient of any of these 4 factors except SOX2 were revealed with most prominent deficiency in epidermal cell development which is important features of LUSC development . Note that SOX2 is known also to play a primary role in neuron development, and the depletion indeed caused disturbance in regulation of nervous system development. The pathways involved in epidermal cell development involving regulating keratinization and epithelial-mesenchymal transition influencing tumor behavior, aggressiveness, and response to treatment.

overall_design: RNA-seq of TP63/SOX2/KLF5/GRHL2-targeting siRNA (siTP63, siSOX2, siKLF5, siGRHL2) compared to negative control siRNA (siNC) in HCC95 cells.


title: Supplement and refinement the standard and analysis of primary human hepatocytes.

first: Xinyang

last: Jia

address: haike street 501

institute: Shanghai Institute of Materia Medica

summary: We use high-throughout single-cell RNA sequencing technology to analyze primary human hepatocytes, combining with LC-MS/MS for drug-metabolizing function research. We measure the enzymatic metabolic function of PHH and perform a correlation analysis with the values documented in the quality inspection report. Furthermore, we assess functions beyond cellular metabolism as specified in the PHH standards. These additional functions include bile secretion, albumin (ALB) secretion, and cell purity, which are not addressed in the quality inspection report. Additionally, we examine the impact of donor characteristics such as body weight, age, underlying health conditions, and lifestyle habits (including smoking and alcohol consumption) on cellular function. We aim to conduct a comprehensive analysis of the factors that influence cellular function. This research not only seeks to supplement and refine the standards of PHH but also aspires to provide a crucial reference for the application of PHH in the domains of disease research and drug development in the future.

overall_design: scRNA-seq of six donors of primary human hepatocytes to profile gene expression and facilitate the verification of cell purity and asses differences in drug-metabolizing enzyme function.

first: Zhaoliang

last: Peng


title: TGFβ signaling in cancer-associated fibroblasts drives a hepatic gp130-dependent pro-metastatic inflammatory program in colorectal cancer

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

summary: The Consensus Molecular Subtype 4 (CMS4) of colorectal cancer (CRC) has the worst prognosis and  the highest frequency of hepatic metastases. It is characterized by abundant cancer-associated fibroblasts (CAFs) in the tumor microenvironment and active TGFβ signaling, but the molecular drivers of metastasis remain unclear. Here, we show that TGFβ signaling in CRC patient-derived CAFs from the primary tumor induces production of IL-6 family cytokines, particularly IL-6 and IL-11. These cytokines stimulate hepatocytes to express myeloid chemoattractants, including SAA1, through gp130-dependent JAK/STAT signaling. This promotes neutrophil recruitment to the liver, potentially creating a pro-metastatic niche. This IL-6 family-JAK/STAT stromal signaling axis is active in both a murine model of CMS4 as well as in human CRC patients in vivo. Combined, our data reveal that TGFβ-driven CAF signaling actively contributes to the formation of a neutrophil-dependent, pre-metastatic hepatic niche in the metastatic phenotype of CMS4 CRC.

overall_design: Bulk RNA seq of murine wild type colon tissue, organoid lines and colonic tumors from intracolonic transplants of these lines.

first: Mark

last: White

first: Tamsin

last: Lannagan

first: Rene

last: Jackstadt

first: Michael

last: Gillespie

first: Owen

last: Sansom