title: ZSTK3744, a Novel Aryl Hydrocarbon Receptor Agonist, Overcomes Chemotherapy Resistance in Triple-Negative Breast Cancer [RNA-seq]

city: Hachioji-shi

first: Takahio

last: Ohashi

state: Tokyo

address: 7-1, Minamiosawa 4-chome

institute: Zenyaku Kogyo Co., Ltd.

summary: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by a poor prognosis owing to the lack of therapeutic targets, including hormone receptors and HER2. Systemic chemotherapy remains the primary treatment option; however, its efficacy is frequently limited by chemotherapy resistance, a substantial challenge in clinical management. In the present study, we aimed to develop a novel anticancer drug that overcomes chemotherapy resistance in TNBC. First, chemotherapy-resistant MDA-MB-468 cells derived from TNBC were developed via long-term exposure to adriamycin or paclitaxel. Compared with wild-type cells, these resistant cells exhibited reduced sensitivity to paclitaxel, adriamycin, and eribulin in the viability assays. Various compounds were screened for their cell growth-inhibitory activity against these resistant cells to identify novel therapeutic agents; ZSTK3744 was a promising candidate and showed significant anti-tumor activity in vitro and in vivo. Mechanistically, ZSTK3744 upregulated CYP1A1, CYP1B1, and TIPARP expression in MDA-MB-468 cells but exhibited no cell growth-inhibitory activity in aryl hydrocarbon receptor (AhR) knockout cells, indicating that ZSTK3744 act as an AhR agonist. Notably, ZSTK3744 demonstrated superior tumor inhibition and lower pulmonary toxicity in ex vivo and in vivo models than other AhR agonists. These results suggest that ZSTK3744 combines robust cell growth-inhibitory activity with a favorable safety profile. In conclusion, ZSTK3744 is a promising candidate for overcoming chemotherapy resistance in TNBC, addressing the urgent need for more effective treatment options for this aggressive cancer subtype. This study represents the first demonstration of the anti-tumor activity of an AhR agonist on chemotherapy-resistant TNBC.

overall_design: RNA-seq profiling was performed to compare gene expression between wild-type MDA-MB-468 breast cancer cells and chemo-resistant derivatives. Chemo-resistant cells were generated by long-term exposure to either adriamycin or paclitaxel.

first: Takahiro

first: Tsubasa

last: Nagasaki

first: Kayoko

last: Kawai-Asami

first: Kotomi

last: Akatsuka

first: Yuko

last: Nagata

first: Sayuri

last: Terada

first: Shinsuke

last: Hiramoto

first: Eika

last: Higashi

first: Ryuichiro

last: Ohshita

first: Kuramochi

last: Mizuki

first: Makoto

last: Furuya

first: Mai

last: Todoroki

first: Hisashi

last: Yoshimi

first: Keiko

last: Fukushima


title: ZSTK3744, a Novel Aryl Hydrocarbon Receptor Agonist, Overcomes Chemotherapy Resistance in Triple-Negative Breast Cancer [microarray]

status: Public on Dec 31 2025

country: Japan

overall_design: mRNA expression profiling was conducted to compare gene expression between wild-type MDA-MB-468 breast cancer cells and their chemo-resistant derivatives. The chemo-resistant cells were generated through long-term exposure to either adriamycin or paclitaxel.


title: Chemical Reprogramming of Human Blood Cells to Pluripotency under Serum-Free Conditions

city: Beijing

first: Ruoqi

last: Cheng

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

country: China

institute: Peking University

type: Expression profiling by high throughput sequencing

summary: Small molecule-based chemical reprogramming provides a fundamentally innovative approach for generating human chemically induced pluripotent stem cell. Our recent work has successfully applied this chemical strategy to efficiently reprogram human blood cells to pluripotency. However, the absence of serum-free conditions for blood cell reprogramming significantly limited the further clinical translation. Here, we established a robust and defined serum-free condition that enable the stable reprogramming of human blood cells into hCiPS cells. This method has been reliably reproduced across over 10 different donors and can generate hCiPS cells within 20 days. The serum-free blood derived-hCiPS cells exhibit typical characteristics of human pluripotent stem cells. Furthermore, this approach allows for efficient generation of hCiPS cells even from a small volume of fingerstick blood. In summary, this study established a powerful and defined conditions for deriving hCiPS cells from blood cells, thereby greatly facilitating their further clinical applications in regenerative medicine.

overall_design: A total of 26 bulk RNA-seq data were analyzed, including those from EPC, hCiPSC, and S1 cells. Each condition has 2 biological replicates.

first: Xiaodi

last: Fu

first: Fangqi

last: Peng

first: Ruyi

last: Cai

first: Yanglu

last: Wang

first: Jingyang

last: Guan

first: Hongkui

last: Deng


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

city: Townsville

first: Lionel

last: Hebbard

state: QLD

address: 1 James Cook Dr, Douglas QLD 4811

country: Australia

institute: James Cook University

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

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

first: Rhys

last: Gillman

first: Eun

middle: J

last: Sun

first: Miriam

last: Wankell

first: Matt

middle: A

last: Field

first: Ulf

last: Schmitz


title: Dissect the organ-specific cytotoxicity mechanism of streptokinase- streptodornase in canine cell lines

city: Jeongeup-Si

first: Ju Young

last: Lee

address: 30 Baekhak 1 Gil,

country: South Korea

institute: Korea institute of toxicology

summary: As streptokinase-streptodornase (SKD) can be used to treat respiratory diseases in dogs, we evaluated the cytotoxicity and related mechanisms of SKD in CF52.Tr and Madin–Darby canine kidney (MDCK) cells. The IC50 (half maximal inhibitory concentration) was observed at a concentration of 10 mg/mL of SKD in both cell lines. mRNA sequencing showed that SKD regulates 133 differentially expressed genes (DEGs) in CF52.Tr and 22 DEGs in MDCK (p<0.05, |log2 fold change| ≥ 1). The cytotoxicity induced by SKD in CF52.Tr cells are linked to increased inflammation and decreased cell cycle progression, as confirmed by the expression of cyclin-dependent kinases (CDKs). Furthermore, SKD-induced cytotoxicity in MDCK cells was associated with an increased cytoskeleton, as confirmed by the distribution of F-actin, and decreased cell cycle progression, as confirmed by cell cycle phase analysis. Notably, cell cycle progression in CF52.Tr is controlled by the transcription factor Forkhead box M1 (FoxM1). In summary, SKD-induced cell type-specific cytotoxicity is caused by the upregulation of inflammatory or cytoskeleton-related genes and the downregulation of cell cycle regulators.

overall_design: To identifiy toxciological DEG profiles in MDCK and CF52.Tr cells treated with 10mg/mL of streptokinase-streptodornase

first: Han Na

last: Suh

first: Hyeong Ryeol

last: Cho

first: Sung Ho

first: Young Bin

last: Park

first: Jeong Ho

last: Hwang


title: Single-cell transcriptomic profiling of lung and mediastinal lymph node from SARS-CoV-2 Omicron-infected cynomolgus macaques

city: Cheong-ju

first: Dong-yeon

last: Kim

address: Yeongudangi-ro

institute: KRIBB

summary: This study provides single-cell transcriptomic datasets from the lung and mediastinal lymph node tissues of cynomolgus macaques following primary or secondary infection with the SARS-CoV-2 Omicron variant. The dataset captures

overall_design: A total of 12 samples were collected from the lung and mediastinal lymph nodes of SARS-CoV-2 Omicron-infected cynomolgus macaques. Samples were obtained at baseline, and day 21 post-infection, Single-cell RNA sequencing was

first: Jung Joo

last: Hong


title: A single-cell map of intratumoral heterogeneity during combination treatment of anti-PD1 and chemotherapy in triple-negative breast cancer

city: Suzhou

first: Siying

last: Zhou

address: Pinghai Road 899

institute: The First Affiliated Hospital of Soochow University

summary: Triple-negative breast cancer (TNBC) is the most malignant subtype of breast cancer (BC), which exhibited a poor prognosis due to the highly tumor microenvironmental heterogeneity and specific mutations. Recent studies have investigated the different celltypes in TNBC microenvironment, however, the effects of immunotherapy and chemotherapy combination therapy on TNBC are largely unknown. Here we explored the changes of TNBC microenvironment upon immunotherapy and chemotherapy combination therapy by scRNA-seq. We found that the insensitive (PCPAi) patient exhibited high CNV score in tumor cells, lower cytotoxicity in CD8+ T cells, higher quiescence and exhaustion characteristics CD4+ T cells, compared to sensitive (PCPAs) patient. Meanwhile, the PCPAi patient showed more complex fibroblasts and tumor-associated macrophages heterogeneity. We also found the key ligand-receptor based cellular interactions, such as SPP1 and TGFβ. These results provide a research basis for us to understand the microenvironment changes and therapeutic efficacy of triple negative breast cancer after chemotherapy combined with immunotherapy.

overall_design: The tumor samples were collected from 12 female patients who were diagnosed with TNBC and treated with combination therapy of immunotherapy and chemotherapy, which were used for mIHC and analyzed using scRNA-seg.

first: Lei


title: A Novel LysR Transcriptional Regulator in Burkholderia pseudomallei: Insights from Transcriptomic and Functional Analyses

city: Bangi

first: Sylvia

last: Chieng

state: Selangor

address: Faculty of Science & Technology

department: Department of Biological Sciences & Biotechnology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

summary: Burkholderia pseudomallei is a Gram-negative pathogen responsible for melioidosis, a life-threatening disease throughout the region of Southeast Asia. LysR-type transcriptional regulators (LTTRs) are key regulators of bacterial virulence and metabolism, yet many remain uncharacterized. This study investigates the function of a novel LTTR, UKMD286_5923, in B. pseudomallei UKM D286. A deletion mutant was constructed, and transcriptomic analysis via RNA sequencing identified 45 upregulated and 22 downregulated genes in the mutant compared to the wild type. Functional enrichment analysis highlighted significant roles in nitrogen metabolism, host entry, and transcriptional regulation. Biofilm formation assays revealed increased biofilm production in the mutant, suggesting a regulatory role in bacterial adhesion.

overall_design: RNA-seq profiling of wild-type B. pseudomallei UKM D286 and ukmd286_5923 deletion mutant after overnight growth in LB broth.

first: Maryam Shawkee

last: Ashraf

first: Shu Sian

last: How


title: IL-36γ Armored CAR T Cells Reprogram Neutrophils to Induce Endogenous Antitumor Immunity

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

country: USA

institute: Roswell Park Comprehensive Cancer Center

summary: Chimeric antigen receptor (CAR) T cells are ineffective against solid tumors due to obstacles of antigen heterogeneity and the immunosuppressive tumor microenvironment (TME). Previous efforts focused on enhancing cytotoxicity and persistence of CAR T cells, while the feasibility of improving their therapeutic efficacy by leveraging the modulatory effects of CAR T cells on host anti-tumor immunity remains unclear. Here, we report that IL-36γ armored CAR T cells eradicated primary solid tumors and enabled rejection of rechallenged antigen-negative tumors. IL-36γ armored CAR T cells favorably modulated the TME and reprogrammed unique neutrophil subsets with tumoricidal ability and antigen-(cross)presenting functions, resulting in the induction of endogenous T cells recognizing tumor antigens beyond CAR-targeted antigens. Our study demonstrates that neutrophil engagement by CAR T cells is a critical step in the establishment of the cancer-immunity cycle and introduces a broadly applicable method to overcome key barriers to adoptive cell therapies for solid tumors.

overall_design: Mouse SCLC tumors were collected four days after CAR T cell treatment. CD45⁺ live cells were then isolated using a BD FACSAria cell sorter for single-cell sequencing analysis.

first: Yihan

last: Zuo

first: Renier

last: Brentjens


title: The microbial tryptophan metabolite indole acts on the gastrointestinal tract to improve glucose homeostasis by enhancing GLP-1 secretion and L-cell differentiation

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Aims/hypothesis: Growing evidence implicates gut microbiota-derived metabolites in metabolic homeostasis. Indole, a microbial tryptophan metabolite, has been reported to enhance Glucagon-like peptide-1 (GLP-1) secretion in vitro, and its derivatives have been inversely associated with risk of type 2 diabetes (T2D). We hypothesised that indole acts via the gastrointestinal tract to modulate glucose homeostasis, and aimed to test this hypothesis using in vitro and in vivo models. Methods: The acute effects of indole on GLP-1 secretion in vitro, and on glucose tolerance and hormone secretion in mice, were determined. Subsequently, the effects of indole on intestinal epithelial cell fate and L-cell differentiation in murine ileal organoids and in vivo were studied. Finally, the utility of chronic indole administration in a murine model of T2D was explored. Results: Indole stimulated in vitro GLP-1 secretion in a concentration-dependent manner, and improved acute glucose control in vivo. Additionally, we demonstrate that indole drives enteroendocrine L-cell differentiation in murine ileal organoids, resulting in increased L-cell density and longer-term glucoregulatory benefits in vivo. Finally, sub-chronic indole administration improved glucose tolerance and insulin sensitivity in diabetic mice. Conclusions/interpretation: Our findings identify indole as an anti-diabetic molecule that acts on the gut, and raise the possibility of incorporating indole into nutraceutical supplements to aid in the treatment or prevention of T2D. This highlights the importance of gut microbiota-derived metabolites in metabolic health and opens new avenues for developing novel strategies to combat T2D.

overall_design: RNASeq profiling of mouse liver tissue after subchronic treatment with either Indole (20mg/kg) or water (vehicle control)

first: Phyllis

last: Phuah

first: Kevin

middle: G

last: Murphy

first: Giles

middle: S

last: Yeo

middle: Y


title: Spatial and single-nucleus transcriptomic profiling of CHB liver biopsies

city: Foster City

first: Ricardo

last: Ramirez

state: CA

address: 333 Lakeside Drive

institute: Gilead Sciences

summary: A modified spatial transcrptomics workflow was used to profile liver tissues to compare viral and host-transcript profiles

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The assay was tested on H&E stained FFPE samples from: 1) HBV infected uPA/SCID humanized mouse livers (one vehicle treated and one Tenofovir alafenamide treated), 2) cell pellets from PLC/PRF/5 cell line and primary human hepatocytes which where unifected or infected with genotypes C and B versions of HBV, and 4) commercially procured liver biopsy samples (2 healthy donors, 4 chronic HBV patients)

first: Sangeetha

last: Mahadevan

first: Hatef

last: Mehrabian

first: Subhra

last: Chaudhuri

first: Hsiu-Chun

last: Chuang

first: Kai-Hui

last: Sun

first: Anjali

last: Rao


title: Molecular mechanisms underlying the megakaryocyte developmental defects caused by the ETV6 p.R369W variant

city: Amsterdam

first: Emile

last: van den Akker

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin Research Amsterdam

summary: In this study, we explored the function of the transcription factor ETV6 in megakaryopoiesis and assessed the impact of the pathogenic variant ETV6 p.R369W on megakaryocyte and platelet development. We hypothesized that ETV6 p.R369W acts in a dominant-negative manner, mimicking the molecular consequences of ETV6 deficiency. To investigate this, we overexpressed both wild-type ETV6 and the ETV6 p.R369W variant in Meg01 cells. Transcriptomic analysis revealed that ETV6 p.R369W upregulated genes associated with hematopoietic progenitor states and platelet activation, closely resembling the gene expression changes observed in ETV6 knockout cells.

overall_design: To investigate this, we transduced Meg01 cells with lentiviral constructs encoding either empty vector (EV), wild-type ETV6, or the ETV6 p.R369W variant. Cells were harvested three days post-transduction for RNA sequencing, with three biological replicates included per condition.

first: Huan

last: Zhang

first: Elise J

last: Huisman

first: Simon

last: Rouschop

first: Lucas

last: Kuijpers

first: Chantal

middle: C

last: Clark

first: Arthur F

last: Svendsen

first: Carmen

last: van der Zwaan

first: Nynke

last: Gillemans

first: Wilfred

middle: F

last: van IJcken

first: Marjon H

last: Cnossen

first: Sjaak

last: Philipsen

first: Arie

last: Hoogendijk


title: Comparison of enzymatic and bisulfite-based methods for sequencing-based cell-free DNA methylation profiling

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

type: Methylation profiling by high throughput sequencing

summary: We generated high-throughput sequencing data using cfRRBS (n = 2) and EM-Seq (n = 2) from healthy human plasma samples.

overall_design: cfDNA methylation profiling by high-throughput sequencing.

first: Mark

last: O. Ezegbogu

first: Peter

last: Stockwell

first: Glen

last: Reid

first: Ben

last: Brockway

first: Rajiv

last: Kumar

first: Euan

last: J. Rodger


title: Transcriptomic analysis of light-induced circadian disruption in C. elegans dark adaptation

city: Kunming

first: Jiahong

last: Duan

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

department: Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences

institute: Yunnan University

summary: This study investigates the molecular mechanisms of disrupted dark adaptation in C. elegans under light/dark cycles. RNA-seq analysis comparing constant darkness (NL) with 12h-light/12h-dark cycles (DL) revealed significant transcriptomic changes, including dysregulation of circadian rhythm genes.

overall_design: Synchronized C. elegans N2 wild-type worms were cultured under standard dark conditions (NL control) until the young adult stage. For the experimental group, worms were exposed to 12-hour light followed by 12-hour dark cycles (DL), while controls remained in constant darkness. After treatment, worms were collected for RNA-seq analysis.

first: Chenggang

last: Zou

first: Yicheng

last: Ma

first: Xinyue

last: Tang


title: 3D-printed nHA/PA66 porous scaffold: Regulating immune balance and vascularization synergistically promotes bone regeneration

city: 南充市

first: Cai-Ping

last: Yan

state: sichuan

address: No. 1 The South of Maoyuan Road

department: orthopedics

institute: North sichuan medical college

summary: 3D-printed porous scaffolds have emerged as a potential solution for treating critical-sized bone defects, yet localized inflammatory imbalance leads to suboptimal therapeutic outcomes. This study utilized nHA/PA66 composite material as the foundation, employing APF additive manufacturing technology to fabricate a three-dimensional porous scaffold (HP) suitable for local bone filling, and functionalized the porous scaffold through modification with polydopamine and magnesium ions (Mg2+) (HPDM). First, the physicochemical properties and biosafety of the HPDM scaffold were verified, followed by a comparative analysis of its effects on macrophage phenotype transformation, vascular endothelial cell differentiation, and pre-osteoblast differentiation differences. The HPDM scaffold achieves coordinated balance in the transformation between M1 and M2 macrophages through sustained release of polydopamine and Mg2+. Mg2+ plays a crucial role in inflammatory regulation by downregulating the NF-κB signaling pathway. Furthermore, several experiments demonstrated that the HPDM scaffold regulates orderly inflammatory responses to promote intercellular interactions, stimulating angiogenesis and osteogenic regeneration. In New Zealand rabbits' femoral condyle bone defect model, the HPDM porous scaffold achieved significant vascularized bone regeneration. This study confirms that the functionalized HPDM porous scaffold prepared using nHA/PA66 as the base material has significant potential in regulating immune responses and enhancing vascularized bone regeneration.

overall_design: MC3T3-E1 cells were co-cultured with HP, HPD, HPDM scaffolds and HPDM@Hu/Ra for 7 days.


title: Staphylococcus aureus intoxicates stem cells to accelerate repair [16S rRNA-seq]

city: New York

first: Dr. Shruti

last: Naik

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

summary: Pathogens are typically viewed as barriers to healing—but Staphylococcus aureus defies this paradigm. We identify its secreted toxin LukED as an unexpected accelerator of tissue repair. Through functional screening and bacterial genetics, we uncover LukED as a pro-repair virulence factor that enhances both epithelial and muscle healing. In skin, LukED drives migratory and senescence-associated programs in wound-edge epidermal stem and progenitor cells. Using organoid models and primary epithelial cultures, we show that LukED acts directly on skin epithelia to promote repair. Remarkably, this activity is independent of pore formation, revealing a noncanonical function for an otherwise cytolytic toxin. Our findings redefine microbial influence on host physiology and introduce microbial DAMPs (mDAMPs) as a new class of pro-reparative effectors.

sample_organism:
human skin metagenome
air metagenome

platform_organism:
human skin metagenome
air metagenome

overall_design: 16S microbial sequencing from wounded skin and contralateral normal skin site

first: Ikjot

last: Sidhu

first: Rachel

last: Kratofil

first: Ujunwa

last: Okoye-Okafor

first: Shruti


title: The transcription factor EGR2 plays an important role in the expansion and function TCRα + CD4 - CD8 - double negative T cells in lpr lupus mice

city: Blacksburg

first: Zhuang

last: Wang

state: VA

address: 1739 Autumn Splendor Way

institute: VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY

summary: Single cell RNA sequencing of CD3+CD4-CD8- double negative T cells of EGR2fl/fl Cre-/- (EF) B6/lpr and EGR2fl/fl Cre+/- (EK) B6/lpr mice.

overall_design: Comparison of splenic CD3+CD4-CD8- double negative T cells from EF and EK B6/lpr mice

first: Ansar

last: Ahmed

first: Rujuan

last: Dai


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

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

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

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

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

first: Maxime

last: Bigotte

first: Adam

middle: M

last: Groh

first: Elia

last: Afanisiev

first: Vincent

last: Wong

first: Kevin

last: Lancon

first: Moein

last: Yaqubi

first: Finn

last: Creeggan

first: Craig

last: Moore

first: Adil

last: Harroud

first: Raphael

last: Schneider

first: Philippe

last: Séguéla

first: Charabati

last: Marc

first: Tea

last: Fiona

first: Fournier

last: Antoine

first: Yu Chang

first: Ragoussis

last: Ioanis

first: Alexandre

last: Prat

first: Simon

last: Thebault

first: Stephanie

last: Zandee

first: Jo Anne


title: Paternal over- and under-nutrition program fetal and placental development in a sex-specific manner

city: Manchester

first: Hannah

middle: L

last: Morgan

address: Oxford Road

institute: University of Manchester

summary: Under- and over-nutrition are directly linked to poor physiological, metabolic and reproductive health. While the association between paternal diet and offspring well-being is becoming established, the underlying mechanisms are yet to be fully defined. The aim of this study was to establish and compare the impact of over- and under-nutrition on male reproductive fitness and post-fertilisation development, with the additional exploration of the role that specific micronutrient supplementation may play in ameliorating any detrimental effects of poor paternal diet. Male C57/BL6J mice were fed either control diet (CD), isocaloric low protein diet (LPD), ‘Western’ diet (WD) or LPD or WD supplemented with methyl-donors and carriers (MD-LPD or MD-WD respectively) for 8 weeks before mating with virgin C57/BL6J females maintained on standard mouse chow. Placental tissue was collected at embryonic day (E)8.5 to assess early placental morphology and metabolism or E17.5 for sex-specific transcriptomic profiling. Post-mating male tissues were harvested for assessment of testicular morphology, gene expression and metabolic profiling and fecal microbiome was analysed. This study found significant increases in adiposity, hepatic cholesterol and FFAs in WD and MDWD fed males, alongside an increase in the abundance of Defferibacteres, Proteobacteria and reduction TM7 abundance in fecal samples compared to CD fed males. Analysis of testicular gene expression revealed 402 (267 down-regulated, 135 upregulated) genes and 285 (187 down-regulated, 98 up-regulated) genes differentically expressed in WD and MD-WD-fed males, respectively, with minimal changes observed in LPD and MD-LPD groups compared to CD-fed males. Placenta from LPD fed fathers had a significant reduction in lactate production at E8.5 and significant sex-specific influences of paternal diet on late gestation fetal and placental growth were observed in both LPD and MD-LPD groups, which had a significantly higher proportion of fetuses with weights below the 10th centile when compared to CD fetuses. We also identified a significant reduction in sexually dimorphic gene expression in response to paternal diet, with 301, 13, 0, 14 and 15 placental genes to be differentially expressed between males and females in the CD, LPD, MD-LPD, WD and MD-WD. We observed that males consuming a high fat/sugar diet (WD and MD-WD), displayed a series of physiological changes in their metabolic health, gut bacterial profiles and testicular morphology and gene expression. While both over- and under-nutritional regimens had no impact on fundamental male fertility, we observed a significant loss in sexual-dimorphism in the late gestation placenta in response to our experimental diets. Such loss of sexual- dimorphism could provide one process through which poor paternal diet programs offspring ill-health in adulthood.

overall_design: To investigate the impact sub-optimal diet fed males had on the placental RNA profiles of their offspring. We fed male mice either control diet (CD; 18% casein, 21% sucrose, 0% milk fat, 0% cholesterol), isocaloric low protein diet (LPD; 9% casein, 24% sucrose, 0% milk fat, 0% cholesterol), ‘Western’ diet (WD; 19% casein, 34% sucrose, 20% milk fat, 0.15% cholesterol) or LPD or WD supplemented with methyl-donors and carriers (5 g/kg diet choline chloride, 15 g/kg diet betaine, 7.5 g/kg diet methionine, 15 mg/kg diet folic acid, 1.5 mg/kg diet vitamin B12; termed  MD-LPD or MD-WD respectively) for a minimum of 8 weeks before males were mated with standard chow fed females. At gestational day 17.5 females were euthanised and placentae were collected, fetal DNA was sexed using 3 primer sets specific for regions on the Y (Sry and Zfy) and X (Dxnds3) chromosomes and placental RNA was extracted from 1 placenta per litter (N=8, with 4 male and 4 female placenta in each diet group)

first: Nader

last: Eid

first: Nadine

last: Holmes

first: Matthew

last: Carlile

first: Sonal

last: Henson

first: Fei

last: Sang

first: Victoria

last: Wright

first: Marcos

last: Castellanos-Uribe

first: Iqbal

last: Khan

first: Nazia

last: Nazar

first: Sean

middle: T

last: May

first: Rod

last: Mitchel

first: Federica

last: Lopes

first: Robert

last: Robinson

first: Antônio

last: Augusto Coppi

first: Roger

last: Sturmey

first: Vipul

last: Batra

first: Adam

last: Watkins


title: Linear Ubiquitination in Keratinocytes Amplifies Psoriatic inflammation via TNF-α/NF-κB Signaling [RNA-seq]

city: Kyoto

first: Satoshi

last: NAKAMIZO

state: Kyoto

address: 54 Shogoin-Kawahara, Sakyo

institute: Kyoto University

summary: Psoriasis is a chronic inflammatory skin disorder driven by dysregulated immune signaling and keratinocyte activation. While the importance of proinflammatory cytokines such as TNF-α, IL-23, and IL-17 in psoriasis is well established, the upstream mechanisms amplifying these pathways, particularly within keratinocytes, remain incompletely defined. Here, we investigate the role of linear ubiquitination—a post-translational modification catalyzed by the linear ubiquitin chain assembly complex (LUBAC)—in psoriasis pathogenesis using a transgenic mouse model (HOIL-1LΔRING1) with enhanced LUBAC activity. In the imiquimod-induced psoriasis model, HOIL-1LΔRING1 mice exhibited exacerbated skin inflammation characterized by increased epidermal thickness, leukocyte infiltration, and elevated expression of Tnf and Il23a. Transcriptomic and pharmacologic analyses showed that linear ubiquitination amplified TNF-α/NF-κB signaling, and TNF-α blockade ameliorated disease severity. BM chimera experiments demonstrated that this effect was mediated by radio-resistant skin cells, particularly keratinocytes. Flow cytometry and in vitro assays confirmed that keratinocyte-intrinsic linear ubiquitination promotes TNF-α production, which was suppressed by a LUBAC inhibitor. Finally, analyses of human psoriatic skin confirmed elevated linear ubiquitination and LUBAC component expression in keratinocytes. These findings identify linear ubiquitination in keratinocytes as a key amplifier of psoriatic inflammation and a potential therapeutic target.

overall_design: RNA-seq of ear skin from wild-type and HOIL1 ΔRING1 mice 1 day after imiquimod treatment.

first: Ken I

last: Kosaka

last: Nakamizo

first: Kenji

last: Kabashima


title: Function-Driven Design of a Surrogate Interleukin-2 Receptor Ligand

city: Shanghai

first: Ziwei

last: Tang

address: 393 Huaxia Middle Road, Pudong New Area

institute: ShanghaiTech University

summary: We developed an artificial signaling system to enable the assembly of cytokine receptor surrogate ligands. A JAK-STAT5 signaling module—comprising the JAK3-specific γc receptor and a functional IL-2Rβ receptor—was stably expressed in a STAT-deficient cell line. Using a combinatorial antibody library, we screened for receptor binders with selective emphasis on IL-2Rβ affinity. Among various bispecific scaffolds, the single-chain diabody (scDb) format demonstrated superior potency and efficacy, effectively recapitulating native IL-2 ligand activity by inducing functional dimerization of IL-2Rβ and γc receptors. The lead scDb-2d (also termed J9H4) agonist antibody functioned as a surrogate IL-2 receptor ligand, selectively driving Teff and NK cell proliferation and activation.

overall_design: Human NK cells were purified using EasySep™ Human NK Cell Isolation Kit (STEMCELL Technologies, #17955), then the cells were proliferated with irradiated (100 Gy) wild type K562 cells (feeder cell to NK cell ratio of 1:1) adding 20 nM natural cytokine (IL-2, IL-15) or antibody (scDb-2d) for 7 days then stimulation with 20 nM natural cytokine and antibody for another 6 days, natural cytokine and antibody were refreshed every 2 days. Then the cells were washed and rested overnight for another 24h stimulation by 20 nM IL-2/IL-15 or scDb-2d.

first: Fulian

last: Wang


title: RNAseq analysis of differentiated rat PAC1 pulmonary artery smooth muscle cells (SMCs)  compared to proliferative cells, and the RBPMS knockdown and MBNL1&2 knockdown in differentiated PAC1 cells.

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

summary: Investigation of the regulation of RNA binding proteins RBPMS and MBNL1 via the global-scale analysis of alternative splicing changes in rat artery smooth muscle cells; as well as the alternative splicing changes in differentiated and proliferative PAC1 cells. Bulk mRNA-Seq was carried out after panel knockdown of RBPMS and MBNL1&2 in differentiated PAC1 cells.

overall_design: RBPMS and MBNL1&2 were parallel knockdown in differentiated PAC1 cells. RBPMS knockdown was treated with RBPMS-specific siRNA; MBNL1&2 knockdown was treated with MBNL1 and MBNL2 specific siRNA.  The differentiated and proliferative PAC1 negative control samples were treated with control siRNA.

first: Yuling

last: Huang

first: Aishwarya

last: Jacob

first: Rafael

last: Kollyfas

first: Chris

last: Smith


title: A single intraarticular injection of placental‐expanded, mesenchymal-like stromal cells halts progression of experimental primary osteoarthritis through a combined modulation of inflammation and cartilage homeostasis

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: Background: Osteoarthritis (OA) is a highly prevalent degenerative joint disease, yet no effective disease-modifying treatments for OA are clinically available. The anti-inflammatory, immunomodulatory, and tissue regenerative properties of placenta-expanded mesenchymal-like adherent stromal cells (PLX-PAD) address several targets of osteoarthritic disease, suggesting a potential therapeutic role of PLX-PAD in primary OA. Objective: To evaluate the safety and therapeutic efficacy of PLX-PAD cell therapy in primary knee OA (KOA) using the Dunkin Hartley (DH) guinea pig model, with a focus on inflammation, cartilage structure, extracellular matrix (ECM) homeostasis, and subchondral bone remodeling. Methods: PLX-PAD cells were characterized for differentiation capacity, secretome, and immunomodulatory properties in vitro, as well as paracrine effects using ex vivo co-culture with human OA cartilage. Two-month-old healthy animals (n = 10) were used to validate the DH model as a primary KOA model. Six-month-old DH guinea pigs (n = 30) received a single intra-articular (IA) injection of PLX-PAD cells at two different doses or Dulbecco's Phosphate Buffered Saline (DPBS). Safety was assessed via MRI at 7 and 12 months. OA progression and treatment efficacy were evaluated through histological and immunostaining analyses, transcriptomic profiling, and matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI)-based proteomics, and micro-computed tomography (μCT). Results: PLX-PAD cells exhibited negligible differentiation capacity and secreted anti-inflammatory mediators in vitro, and shifted OA cartilage toward a pro-anabolic, anti-catabolic profile ex vivo. Age-related KOA progression in the DH model was confirmed by histological and molecular comparisons of two-month-old healthy and DPBS-treated animals at twelve months. PLX-PAD treatment reduced joint inflammation and preserved cartilage integrity. Transcriptomic analysis revealed that differentially expressed genes were significantly enriched in inflammatory and catabolic pathways, including TNF and Wnt signaling, along with reduced Adamts4 and Mmp13 expression and protein levels in cartilage following PLX-PAD treatment. MALDI-MSI analysis revealed decreased fibronectin fragmentation and restored ECM peptide distribution in PLX-PAD groups. μCT analysis indicated reduced subchondral bone sclerosis and improved trabecular structure in PLX-PAD-treated animals, with greater improvements in bone mineral density at the higher dose, indicating partial dose-dependent effects. No adverse events were registered. Conclusion: PLX-PAD therapy exhibits disease-modifying effects in primary KOA by attenuating inflammation, preserving cartilage, and improving ECM and bone remodeling at both molecular and structural levels. Clinical investigations are currently underway to explore PLX-PAD’s potential translational applications and long-term efficacy.

overall_design: RNA-seq profiling of knee cartilage from Dunkin Hartley guinea pigs 6 months after receiving intra-articular injections of DPBS or PLX-PAD cells at different doses.

first: Tazio

last: Maleitzke

first: Sijia

last: Zhou

first: Florian N.

last: Fleckenstein

first: Bin

last: Chen

first: Alexander

last: Hildebrandt

first: Dominik

last: Geisel

first: Rene

last: Hägerling

first: Christian F.

last: Thudium

first: Michal

last: Sheleg

first: Gilad

last: Kunis

first: Marta

last: Grzeski

first: Daniela

last: Aschenbrenner

first: Oliver

last: Klein

first: Georg N.

last: Duda

first: Sven

last: Geissler

first: Tobias

last: Winkler


title: Integrative Analysis Reveals Shegan-Mahuang Decoction Modulates Immunometabolism and Inflammatory Response in Asthma [RNA-seq]

city: Chongqing

first: huina

last: lu

address: No. 6 Panxi Seventh Branch Road, Jiangbei District, Chongqing

institute: CHONGQING TRADITIONAL CHINESE MEDICINE HOSPITAL

summary: SMD alleviated lung injury in asthmatic mice with a significant reduction in leukocytes and recovered inflammatory marker levels. Mice treated with SMD showed higher microbial diversity and reversed metabolic imbalances compared to the asthma group. SMD acted primarily by modulating gene expression enriched in inflammatory processes in the lungs. Analysis of intercellular interactions revealed changes in the interaction network between different cell types during SMD treatment. Particularly, macrophages and T cells showed diversity in differentiation, suggesting the role of cellular heterogeneity and their interactions in immune response to asthma. ELISA results showed that SMD reduced asthma-induced inflammatory factors and IgE levels.

overall_design: After 7 days of acclimatization, mice were randomly assigned to four experimental groups containing 15 mice in each group: control, model, SMD and Prednisone (PDN) groups.lung tissues were taken from all four groups for RNA seq.

first: Huina

last: Lu

first: Yu

first: Xia

first: Chao

last: Yuan

first: Youhua

first: Xin

last: Liu

first: Mingming

last: Yang


title: An epigenetic basis for sustained inflammatory epithelial progenitor cell states in Crohn’s disease

city: Philadelphia

first: Yusen

last: Zhou

state: PA

address: 3401 Civic Center Blvd

department: Department of Biomedical and Health Informatics

institute: Children's Hospital of Philadelphia

summary: Defining consequential differences in intestinal epithelial stem cells in healthy humans versus those with inflammatory bowel disease (Crohn’s disease (CD) and ulcerative colitis) is essential for the development of therapies to restore the epithelial barrier and maintain its fidelity post-injury. Our study objective was to define transcriptomic, epigenomic, and functional divergence between healthy and CD epithelium.

overall_design:
We used single cell RNA sequencing and single nuclei ATAC-sequencing (n= 27 CD, 26 control) to evaluate transcriptomic and epigenomic differences in non-inflamed CD epithelium. Matched patient organoids from the same specimens were used to investigate durable epithelial-intrinsic changes at transcriptional and functional levels.
This submission contains scRNA-Seq submission.

first: Tatiana

last: A Karakasheva

first: Clara

last: Morral Martinez

first: Jingya

last: Qiu

first: Kathryn

last: E. Hamilton


title: Visualize and quantify rDNA instabilities in mammalian cells and mouse models

first: Shan

last: Zha

address: 1130 Saint Nicholas Ave.

institute: Columbia University

summary: Ribosomal DNA (rDNA) encodes the 18S, 5.8S, and 28S RNA components of ribosomes, accounting for up to 70% of cellular transcription activities. Despite its central role in cellular function and known association with cancer and aging, quantifying rDNA instability in mammals remains challenging due to its repetitive organization and inherent heterogeneity. In this study, we developed murine rDNA FISH probes and genomic tools tailored for laboratory strains. The results confirmed the locations of rDNA clusters, uncovered marked inter-/intra-strain and inter-cell heterogeneity at rDNA loci in inbred mice and unstressed cells, and identified sources of spontaneous, replication-associated DNA double-strand breaks within rDNA. Focused mini-screens using DNA repair-deficient cells uncovered distinct contributions of homologous recombination, non-homologous end-joining, and the ATM-mediated DNA damage response in safeguarding rDNA stability. Together, these findings and tools provide a robust framework for assessing rDNA instability in mammalian cells and animal models with utility in aging and cancer research.

overall_design: End-Seq of purified and activated (24 or 28 h with anti-CD40 and IL4) (S phase) or quiescent (G1 phase) CD43–splenic B cells to map replication-dependent single-ended DNA DSB in primary cells, without external DNA damage.

first: Xiaolu

last: Zhu

first: Demis

last: Menolfi

first: Brian

last: Lee


title: TM9SF1 aggravates liver ischemia-reperfusion injury by promoting autophagy

city: Zhengzhou

first: Tongtong

last: Wu

address: 1 Jianshe East Road

institute: Zhengzhou University

summary: Liver transplantation (LT) stands as the sole effective approach for addressing end-stage liver disease. Autophagy plays an indispensable role in liver ischemia-reperfusion（I/R）. Transmembrane 9 superfamily member 1 (TM9SF1) is a transmembrane protein that has been shown to be associated with autophagy. However, the role and mechanism of this protein in liver I/R injury have not been explored. We found that TM9SF1 expression increased in liver I/R injury mice and AML12 cells after hypoxia-reoxygenation (H/R). Then, we constructed TM9SF1 adeno-associated virus overexpression and knockdown (KD) mice and constructed a liver I/R injury model. The results showed that TM9SF1-overexpressing mice had increased liver damage, inflammation, and autophagy levels. The opposite changes were observed in knockdown mice. Mechanistically, we found that TM9SF1 and Annexin A2 (ANXA2) interacted and jointly affected the expression of autophagy levels during liver I/R injury. Based on the construction of TM9SF1-overexpressing mice , we interfered with the expression of ANXA2 and found that the degree of liver damage was reduced, the level of inflammation decreased, and the level of autophagy decreased. Finally, we performed virtual screening on the FDA-approved molecular library and found that lomitapide can reduce the expression of TM9SF1, thereby alleviating liver ischemia-reperfusion injury. In general, our findings indicated that TM9SF1 and ANXA2 interact with each other, affecting autophagy levels through the mitogen-activated protein kinase (MAPK) pathway, thereby aggravating liver I/R injury. Targeting TM9SF1-ANXA2 may be a potential therapeutic strategy.

overall_design: We constructed a liver ischemia-reperfusion model and detected the expression of TM9SF1. In vivo, we constructed TM9SF1 overexpression and knockdown mice, and detected the degree of liver damage and changes in autophagy through experimental methods such as TUNEL, DHE, and TEM. In vitro, we constructed knockdown and overexpression AML12 cell lines, and verified the changes in cell damage and autophagy through Hoechst 33342/PI, ROS, and TEM methods. At the same time, sequencing and mass spectrometry were performed on stably transfected cell lines to explore the mechanism of TM9SF1 in liver ischemia-reperfusion injury.

first: Wendong

last: Li

first: Ying

first: Xudong

first: Hongwei

last: Tang

first: Mingjie

last: Ding

first: Wenzhi

last: Guo


title: Tet2 and p53 cooperate to promote leukemia and modulate response to inflammation [Copy number]

first: Alan

last: Shih

address: 1 Gustave L Levy Place

institute: Icahn School  of Medicine at Mount Sinai

summary: TET2, a regulator of DNA methylation, is amongst the most commonly mutated genes in acute myeloid leukemia (AML) and is linked to enhanced inflammatory responses. The ability to respond to TP53 activation and inflammatory response has been linked to clonal advantage in hematopoietic stem-progenitors. These mutations combine and affect the pyroptosis pathway.

overall_design: Mouse tissue- bone marrow, spleen, and tail tissue was isolated and DNA extracted using Qiagen DNA isolation kit. Genomic DNA was used for mouse select exome sequencing. Copy number variations compared to pooled normal reads was determined.

first: Pablo

last: Sanchez-Vela

first: Jonathan

last: Foox

first: Ross

last: Levine

middle: H


title: Lipidomic changes in persister cancer cells drive enhanced ferroptosis sensitivity

city: W 120 St

first: Brent

middle: R

last: Stockwell

state: New york

department: Biology

summary: Persister cancer cells (PSs) are implicated in minimal residual disease from which cancer relapse occurs. PSs are sensitive to and present a critical point through which identification and targeting of PSs may be possible. To identify biomarkers for such cells, the drivers of ferroptosis sensitivity in PSs should be identified. Here, we first derived PSs from the lung carcinoma cell line PC9 (PSPC9), performed transcriptomic analysis, and observed enrichment of lipid and sugar metabolism gene expression in PSPC9. We performed untargeted and targeted lipidomics, revealing enrichment within PSPC9 for ferroptosis-driving diPUFA phospholipids (diPUFA-PL), as well as polyunsaturated free fatty acids (PUFA FFAs). Upon PSPC9 reversion to the ferroptosis-resistant parental state (PC9PS -> PC9), this lipid signature reverted. We generated two additional PS-like cell models: PS-like prostate carcinoma (PSLNCaP) from LNCaP and PS-like fibrosarcoma (PSHT1080) from HT1080. These PS-like models individually had features consistent with PS, including increased labile-iron pool, reversibility, and enhanced ferroptosis sensitivity. We performed lipidomics in these cell models, and identified lipid features consistent with those in PSPC9. Finally, we found that in PSHT1080, mitochondrial elimination partially abrogated ferroptosis sensitivity and altered the PSHT1080 lipid profile. In summary, we found that lipidomic changes dependent on the presence of mitochondria are key for the ferroptosis sensitivity of drug-tolerant persister cancer cells.

overall_design: PC9 and 6 day erlotinib derived PS were submitted in triplicate per condition with follow on DGE analysis and GSEA to explore pathways that may be enriched between the persister vs parental state.

first: Eduard

last: Reznik

first: Fereshteh

last: Zandkarimi

first: Joleen

last: Csuka

first: Qiulin

first: Jenny

last: Jin

first: Taruna

middle: V

last: Neelakantan

first: Jiewen

last: Zhang

first: Vasiliki

last: Polychrondiou

first: Mark

last: Fongheiser

first: Ashley

last: Brown

first: Baiyu

first: Megan

last: Rodriguez

first: Lela

last: Devine

first: Prem

last: Subramaniam

first: Andrea

last: Califano


title: Cell type-specific RNAs signatures in midbody remnants: insights from cancer, stem and differentiated cells

city: Madison

first: Finn

last: Kuusisto

state: WI

address: 1205 University Ave

institute: University of Wisconsin-Madison

summary: This study investigates the differences in mRNA payloads between midbody remnants (MBRs) and whole cell of origin for six cell types, in order to determine type-specific and common enriched genes in MBRs. RNA-seq was performed by the Skop lab for all six cell types. Ribo-seq was performed by the Iwasaki lab on one of the cell types to assess translational differences. Data include raw FASTQ files, processed count tables, and metadata describing each sample.

overall_design: RNA-seq profiling of midbody remnants (MBRs) versus whole cell type of origin for six different cell types. Additional Ribo-seq profiling of MBR versus whole cell type of origin for one of the six cell types.

first: Dantong

last: Zhu

first: Kotaro

last: Tomuro

first: Elizabeth

last: Torr

first: Yuichi

last: Shichino

first: Benjamin

last: Minkoff

first: Sophie

last: Lusty

first: John

last: Favate

first: Randall

middle: D

last: Dahn

first: Premal

last: Shah

first: Michael

last: Sussman

first: Justin

last: Wolter

first: Shintaro

last: Iwasaki

first: Ahna

last: Skop


title: Contemporary highly pathogenic avian influenza (H5N1) viruses retain neurotropism in human cerebral organoids

city: Hamilton

first: Emmie

last: de Wit

state: MT

address: 903 S 4th St

institute: NIAID

summary: Background Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) H5N1 viruses are widely circulating in North America with unprecedented transmission into novel host species. A high incidence of neurologic disease is observed in carnivores infected with clade 2.3.4.4b HPAI H5N1 viruses and historical outbreaks of HPAI H5N1 in humans are also associated with neurologic complications, raising concerns about neurotropism and neurovirulence of clade 2.3.4.4b HPAI H5N1 viruses. Methods We analyzed virus replication kinetics, cellular tropism, and host responses to infection in human cerebral organoids (hCOs) inoculated with clade 2.3.4.4b HPAI H5N1 viruses compared to a historical clade 1 HPAI H5N1 virus and a seasonal influenza A virus. Results HPAI H5N1 viruses replicated to high titers in hCOs, but replication of the seasonal influenza A virus was not detected. Viral antigen and RNA were detected primarily in neuron- and astrocyte-like cells. Interferon responses to infection with HPAI H5N1 viruses were observed in a small population of bystander cells. Higher levels of cell death and proinflammatory cytokines and chemokines were observed in organoids inoculated with the historical HPAI H5N1 isolate. Conclusions Clade 2.3.4.4b HPAI H5N1 viruses exhibit similar neurotropism compared to a historical clade 1 HPAI H5N1 virus. Lower levels of cell death and inflammatory cytokine production induced by clade 2.3.4.4b viruses may indicate reduced neuropathogenic potential of these viruses in humans.

sample_organism:
Homo sapiens
Influenza A virus

platform_organism:
Homo sapiens
Influenza A virus

overall_design: Human cerebral organoids (hCOs) were inoculated with historical HPAI H5N1 isolate VN2004, contemporary HPAI H5N1 isolates mMT2024 or bOH2024, seasonal influenza A virus isolate BR2007, or mock-inoculated. scRNA-seq aanlysis was conducted at 1 or 3 days post-inoculation. Libraries were prepared using PIPseq T2 3’ Single Cell RNA kit v4.0 PLUS (Fluent Biosciences). Samples were indexed using the PIPseq UDI-96 kit (Fluent Biosciences), pooled, and sequenced on an Illumina NextSeq instrument.

first: Kerry

last: Goldin

first: Meaghan

last: Flagg

first: Tessa

last: Lutterman

first: Bridget

last: Brackney

first: Katie

last: Williams

first: Cathryn

last: Haigh


title: Lower Elastic Modulus of Novel Zr58Cu25Al14Nb3 Dental Implants Improves Stress Distribution and Osteogenesis in Peri-implant Alveolar Bone Under Physiological Loading

city: Beijing

first: Yunshu

last: Wu

address: No.22 Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

summary: While implant materials with bone-mimetic elastic moduli are theoretically advantageous for reducing the stress shielding effect, the underlying mechanism remains incompletely understood, particularly in alveolar bone applications. In this study, we investigate the mechanism of excellent peri-implant bone quality of a Zr58Cu25Al14Nb3 bulk metallic glass (Nb3) dental implant in terms of its lower elastic modulus than commercial pure titanium (cpTi) and the stress distribution under masticatory mechanical loading. In vitro, Nb3 exhibits enhanced osteogenic potential over cpTi. In vivo, rat maxillary molar implants are subjected to a controllable cyclic loading program (10 N, 3 Hz, 0.12 s duration, 1800 cycles/day). The animal model coupled finite element analysis confirms that the lower elastic modulus of Nb3 implants promotes the more physiological stress distribution, and thus reduces stress concentration while increasing strain energy density in peri-implant bone. Histomorphometry reveals that loaded Nb3 implants significantly accelerate mineral apposition rate, upregulate collagen III, and increase osteoblast density while reducing osteocyte number, demonstrating improved mechano-adaptation. Transcriptomics identify coordinated upregulation of osteogenic, angiogenic, and mechanosensitive markers in Nb3-loaded bone. Immunohistochemistry validates elevated expression of osteopontin and periostin, key mediators of mechanical signaling. These findings establish that Nb3’s optimal elastic modulus enhances peri-implant bone quality through biomechanical optimization of stress transfer that further activates mechanotransductive osteogenesis, providing a material-based solution to stress shielding.

overall_design: To investigate the genetic changes of peri-implant bone with or without cyclic loading. Mini implants of titanium and novel material Nb3 were inserted at rat's maxillary first molar site. Implants of the loading group were subjected to cyclic loading for 2 weeks, while implants of the non-loading group remained static. Φ4mm of peri-implant bone tissues were collected for RNA sequencing.

first: Feifei

last: Wang

first: Yuan

last: He

first: Kinon

last: Chen

first: Baoan

last: Sun

first: Yuchun


title: Moderate Elevation of Ambient Temperature Enhances Phosphorus Deficiency Tolerance in Lotus japonicus under Hydroponic Conditions

city: Higashi-Hiroshima

first: Lydia

middle: Ratna

last: Bunthara

state: Hiroshima

address: Kagamiyama 1-7-1

department: Graduate School of Integrated Sciences for Life

institute: Hiroshima University

summary: The combined effects of high temperature stress from global warming and phosphorus (P) deficiency due to limited P rock reserves pose a critical threat to modern agriculture. However, the understanding of the effect of the combined stress on plants are limited. Here, we performed hydroponic culture to investigate the physiological and transcriptional response of the model legume Lotus japonicus to simultaneous moderate high temperature and low P conditions. While both elevated temperature and low P individually reduced shoot biomass, their combination alleviated growth reduction, with greater shoot biomass observed under combined stress than under low P alone. Lotus japonicus enhanced root-secreted acid phosphatase activity in response to low P alone and increased organic acid exudation rate, such as malate and citrate, under elevated temperature, regardless of P supply. We explored root transcriptome, and detected an up-regulated PEPC1 gene, encoding phosphoenolpyruvate carboxylase which suggested to be related with organic acid root exudation. Additionally, elevated temperature also increased metal ion translocation and absorption, anthocyanin levels, and carbohydrate transport in shoots. Transcriptomic analysis revealed that low P stress altered heat shock protein (HSP) expression, likely due to reduced ATP availability. This study demonstrates that L. japonicus employs distinct and overlapping strategies to adapt to the combined stresses of elevated temperature and P deficiency, including adjustments in exudation patterns, nutrient transport, and stress-responsive gene expression.

overall_design: RNA-Seq analysis to understand the transcriptomic profiles of L. japonicus cultivated under the stress combination of low phosphorus supply and elevating temperature after three weeks of treatment

first: ZePeng

last: Sheng

first: Hirotsuna

last: Yamada

first: Toshihiro

last: Watanabe

first: Jun

last: Wasaki


title: Histamine H4 receptor antagonists prevent receptor-mediated and EBV-induced B cell proliferation [RNA-Seq]

city: Lyon

first: Marlène

middle: Lucie

last: Roy

address: 21 Avenue Tony Garnier

department: Centre International de Recherche en Infectiologie (CIRI)

country: France

institute: Hormae Pharma

summary: Epstein-Barr virus (EBV) infects over 90% of individuals worldwide and establishes lifelong latency in memory B cells. While this latency is typically controlled by the immune system in healthy people, it can reactivate leading to cell immortalization and post-transplant lymphoproliferative disorders (PTLD), a frequent and potentially life-threatening condition in immunosuppressed patients. Surprisingly, we show that specific antagonists of the histamine H4 receptor (H4R), a G protein-coupled receptor expressed in immune cells, prevent the activation and proliferation of B cells following antigenic-like stimulation (BCR, TLR9, or CD40 ligands) or EBV infection. The lead compound, A943931, inhibited transcriptional but not epigenetic programs associated with B cell activation. Key metabolic genes, were downregulated, with a marked inhibition of glycolysis and oxidative phosphorylation. EBV-driven B cell immortalization was also blocked by H4R antagonists. A943931 similarly impaired energy production in lymphoblastoid cell lines, albeit to a lesser extent than in receptors-stimulated B cells. Finally, A943931 inhibited the growth of the Burkitt lymphoma Daudi xenografted in NSG mice and the development of B cell lymphoma in EBV-infected humanized mice. These findings highlight promising therapeutic potential of some H4R antagonists for EBV-induced lymphoproliferations such as PTLD and, more broadly, for EBV-linked autoimmune disorders.

overall_design: Gene expression profiling was performed using RNA-seq on purified human CD19⁺ B cells subjected to various stimulation and treatment conditions. Cells were stimulated for 24 hours with 5 µg/mL CpG-B ODN2006 (InvivoGen) and 10 µg/mL anti-human IgG + IgM (H+L) antibodies (Oxyme), or left unstimulated as controls. Simultaneously, cells were treated with either 10 µM A-943931 or left untreated (DMSO only).

first: Patrice

last: André

first: Pierre-Olivier

last: Vidalain

first: Vincent

last: Lotteau

first: Laurent

last: Genestier

first: Emilie

last: Bardel

first: Fabrice

last: Chatonnet


title: Transport stress induces paradoxical increases in airway inflammatory responses in beef stocker cattle

city: Fort Collins

first: Grace

middle: Marie

last: Jakes

state: CO

address: 2500 Flintridge Pl

department: Microbiology, Immunology, Pathology

institute: Colorado State University

summary: The development of Bovine Respiratory Disease (BRD ) in beef cattle is associated with stressful events, including auction and transport. In addition to the effects of commingling on pathogen exposure, stress also impacts immune function and has classically been associated with an immunosuppressed state. Much of the research on cattle immunity in stress has focused on peripheral blood immune functionality rather than mucosal immune responses. To characterize immunity at the primary site of pathogen colonization in BRD, we evaluated stress responses  in lung cells from beef stocker cattle to understand mucosal immune changes. Stocker calves were sampled via bronchoalveolar lavage fluid collection within 24 hours of auction and transport to a new facility (Stressed, n=12), or allowed to acclimate for 2 months at the new facility before sampling (Acclimated, n=7). Lavage cellular RNA was extracted and sequenced for bulk RNA-seq gene expression. Differential gene expression analysis of RNA sequencing data demonstrated a profound  upregulation of inflammatory genes in Stressed calves compared to Acclimated calves, including expression of CXCL8, CSF3R, IL1B, and CCL22. Top pathway upregulation in Stressed calves involved neutrophil migration and chemotaxis, and cytokine signaling. To predict cellular population proportions from the data, CIBERSORTx was used to deconvolute bulk RNA-seq gene counts. This analysis showed that Stressed calves had significantly increased BALF neutrophils compared to Acclimated calves (p =0.003). Neutrophilic infiltration occurred in the absence of pathogen colonization of the lungs in most calves, as demonstrated by a multi-pathogen respiratory qPCR screen. As such, the stress induced an inflammatory response in lungs not explained by pathogen exposure. This study provides strong evidence that shipping stress in beef stocker calves can paradoxically  trigger increased rather than suppressed inflammatory pulmonary mucosal immune responses, which has important implications for the pathogenesis of BRD.

overall_design: RNA-seq profiling of Stressed beef calves immediately after auction and transport, and Acclimated calves on pasture for two months.

first: Dylan

last: Ammons

first: Randy

last: Hunter

first: Steven

last: Dow

first: Sarah

last: Raabis


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

city: Strasbourg

first: Stefano

last: Marzi

address: 2 allée Konrad Roentgen

department: UPR9002 - IBMC

institute: CNRS

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

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

first: Maximilian

middle: P

last: Kohl

first: Roberto

last: Bahena-Ceron

first: Béatrice

last: Chane-Woon-Ming

first: Maria

last: Kompatscher

first: Matthias

last: Erlacher

first: Pascale

last: Romby

first: Bruno

last: Klaholz


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

overall_design: For the MNase as well as the RNase 1 Ribo-Ret experiments, two biological replicates were analyzed for Retapamulin-treated and untreated samples. These samples were processed and analyzed by our method for ribosome profiling in S. aureus.


title: Intracellular C3 regulates the immune response to infection via NF-κB signaling

city: Malmo

first: Vaishnavi

last: Dandavate

address: Inga-Marie Nilssons gata 53

country: Sweden

institute: Lund University

summary: Complement factor C3 is one of the most abundant proteins in the bloodstream and a central part of the complement system. Upon activation, C3 facilitates bacterial recognition and clearance of bacteria in the extracellular environment. Initially regarded as a serum effector component, C3 is also emerging as an intracellular protein regulating basic cellular processes. Previously, we reported that intracellular, cytosolic C3 can opsonize bacteria and impact their virulence. In this study, we show that cells lacking C3 exhibit altered gene expression that influences immune responses to infection and inflammation. We observed decreased cytokine secretion in C3-deficient cells, which was rescued by expression of non-canonical, cytosolic C3. Further investigation revealed that C3 deficiency impairs signal transduction within the NF-κB signaling pathway which is attributed to decreased expression of Toll-like receptors. This effect is reversed in cells expressing cytosolic C3, where receptor expression and pathway activation are restored. Therefore, we propose a novel role of intracellular, cytosolic C3 in shaping immune responses by modulating the expression of receptors critical to pathogen recognition.

overall_design: RNA-seq profiling of human type II alveolar epithelial cell line A549, including wild-type and gene-edited variants deficient of C3 (C3 KO) or expressing only cytosolic C3 (ΔATG1), 4 individual clones per genotype

first: Kuska

last: Katarzyna

first: Blom

last: Anna

first: Dandavate

last: Vaishnavi


title: Multi-omics analysis highlights the link of aging-related cognitive decline with systemic inflammation and alterations of tissue-maintenance

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

institute: Christian-Albrechts-University Kiel

summary: Aging-related cognitive decline is associated with changes across different tissues and the gut microbiome, including dysfunction of the gut-brain axis. However, only few studies have linked multi-organ alterations to cognitive decline during aging. Here we report a multi-omics analysis integrating metabolomics, transcriptomics, DNA methylation, and metagenomics data from hippocampus, liver, colon, and fecal samples of mice, correlated with cognitive performance in the Barnes Maze spatial learning task across different age groups. We identified 734 molecular features associated with cognitive rank within individual data layers, of which 227 features remain when integrating all data layers with each other. Among the single-layer predictors, several host and microbial features were highlighted, with host-associated markers being predominant. Host features associated with cognitive function mainly belong to innate and adaptive inflammatory activity (inflammaging) and developmental processes. Our findings suggest that cognitive decline in aging is tightly coupled to systemic, age-associated inflammation, potentially initiated by microbiome-driven gastrointestinal inflammatory activity, emphasizing a link between peripheral tissue alterations and brain function.

overall_design: RNA sequencing with Illumina’s TruSeq stranded kit, with polyA enrichment, 100 bp paired end sequencing of 83 total RNA samples from male mice’s (C57BL/6J/Ukj) brains and livers at different ages: 3 (n = 16), 9 (n = 16), 15 (n = 16), 24 (n = 17), and 28 (n = 18) months.

last: Flor

first: Thomas

last: Dost

first: Madlen

last: Haase

first: Rowena

last: Simon

first: Marie-Luise

last: Ederer

first: Samer

middle: A

last: Kadibalban

first: Jan

last: Taubenheim

first: Maja

last: Olecka

first: Alesia

last: Walker

first: Johannes

last: Zimmermann

first: Georgios

last: Marinos

first: Sören

last: Franzenburg

first: Philippe

last: Schmitt-Kopplin

first: John

last: Baines

first: Konstantin

last: Riege

first: Steve

last: Hoffmann

first: Christiane

last: Frahm

first: Christoph

last: Kaleta


title: Integrative Analysis Reveals Shegan-Mahuang Decoction Modulates Immunometabolism and Inflammatory Response in Asthma [scRNA-seq]

first: huina

last: lu

overall_design: After 7 days of acclimatization, mice were randomly assigned to four experimental groups containing 15 mice in each group: control, model, SMD and Prednisone (PDN) groups.Lungs tissues from model and SMD groups were taken for scRNA-seq.

first: Huina

last: Lu

first: Yu

last: Zhou

first: Xia

last: Chen

first: Chao

last: Yuan

first: Youhua

first: Xin

last: Liu

first: Mingming

last: Yang


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

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

institute: Washington University in St. Louis

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

first: Leland

last: Sudlow

first: Junwei

last: Du

first: Kiana

last: Shahverdi

first: Haiyin


title: Integrative Analysis Reveals Shegan-Mahuang Decoction Modulates Immunometabolism and Inflammatory Response in Asthma [16S-seq]

overall_design: After 7 days of acclimatization, mice were randomly assigned to four experimental groups containing 15 mice in each group: control, model, SMD and Prednisone (PDN) groups.Stools were taken from all four groups for 16s sequencing.


title: Gene expression profiling of surgically treated pancreatic cancer patients using NanoString nCounter.

city: Tokyo

first: Manabu

last: Takamatsu

address: 3-8-31 Ariake Koto-ku

institute: Cancer Institute

summary: Differential expression analysis of 770 genes in the tumor component of pancreatic cancer.

overall_design: FFPE samples were dissected according to image clusters derived through AI analysis using UMAP.


title: mRNA profiling of human effector Type 1 T helper (Th1) cells for autoimmune gene signatures using the nCounter Nanostring platform [autoimmunity panel]

city: Rochester

first: Adebowale

last: Bamidele

state: Minnesota

address: Medicine, 200 First Street SW, Guggenheim 10

department: Medicine

institute: Mayo Clinic

summary: Human naïve CD4 T cells were purified from healthy volunteers' peripheral blood using commercially available kits and differentiated into effector Th1 in vitro by culturing for 6 days in the presence of anti-CD3 and CD28 antibodies (2 µg/ml each) and IL-12 (20 ng/ml). Human effector Th1 cells were harvested on day 6 post-differentiation and treated with either vehicle, LY (0.0125 µM), or Methyl Pyruvate (MePyr, 5 mM) in complete RPMI media for 24 hours.

overall_design: Gene expression profiling. Effector Th1 cells from four biological replicates (donors) were used and treated separately as indicated in the summary. An equal amount of total RNA from each replicate was used for gene expression analysis.

first: Shravan

middle: K

last: Mishra

middle: O


title: Mapping the Cellular Landscape of Calvarial Bone Repair Accelerated by Sympathetic Nerve Inhibition

city: Shanghai

first: Lei

last: Zhao

state: Shanghai

address: 500 Zhennan Road

institute: Tongji University

summary: Understanding the dynamic changes of cells during calvarial bone repair is crucial for identifying novel therapeutic targets to enhance bone regeneration. However, the cellular changes and intercellular communication during calvarial defect repair remain poorly understood. To address this, we performed single-cell RNA sequencing on tissues collected at different time points post-defect. Our analysis revealed a significant enhancement in intercellular communication following defect, particularly among stem cells, endothelial cells, pericytes, and macrophages. Pathways related to neurogenesis were significantly enriched after defect. Furthermore, we found that inhibiting sympathetic nerves promoted calvarial bone repair. Mechanistically, sympathetic nerve inhibition enhanced angiogenesis and osteogenesis by promoting interactions between pericytes and endothelial cells, generating a novel senescenced  Arg1+ macrophages, which contributed to bone repair by secreting osteogenesis-related cytokines. Besides, inhibition of sympathetic nerves promotes the generation of Shisa3+ suture cell subpopulation and enhances osteogenic differentiation capacity. Importantly, senolytics abrogated the repair benefits brought about by sympathetic nerve inhibition, underscoring the critical role of senescent macrophages in the repair process.

overall_design: To further investigate how sympathetic nerve inhibition promotes calvarial bone defect repair, single-cell RNA sequencing was performed on calvarial bone samples collected 7 and 14 days after frontal bone defect induction with or without sympathetic nerve inhibition.

first: Zhaoning

last: Xu

first: Yiyun

last: Wang


title: Growing iPSC-derived neuronal precursor cells (NPCs) of MT-ATP6 patients and of normal controls under physiological glucose concentrations of 4.5 mM with and without 1 µM or 10 µM Sildenafil for 6 or 24 hours.

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

summary: Mitochondrial diseases are a group of rare inherited disorders that affect mitochondrial function. A severe untreatable form of mitochondrial disease is Leigh syndrome (LS), which is characterized by psychomotor regression and acute metabolic crises during which patients quickly deteriorate. To accelerate drug discovery for mitochondrial diseases, we focused on drug repurposing and used induced pluripotent stem cell (iPSC)-derived neuronal precursor cells (NPCs) from LS patients to screen a library of 5,632 repurposable compounds. We identified phosphodiesterase 5 inhibitors (PDE5i) as leads capable of normalizing mitochondrial polarization in NPCs of LS patients. Among the PDE5i, we prioritized Sildenafil due to its established safety profile in children and adults. Sildenafil restored key pathways regulating nervous system development, enhanced neurite outgrowth in LS neurons, and mitigated abnormal calcium responses in LS brain organoids under metabolic stress. Chronic off-label compassionate treatment of six LS patients with Sildenafil showed good tolerability and clear clinical improvements. Our findings highlight the potential of iPSC-driven drug discovery for rare diseases and position Sildenafil as a promising drug candidate for patients with mitochondrial diseases.

overall_design: RNA-profiling of Neuronal Precursor Cells (NPC) generated from iPSCs from control individuals and from patients with Maternally Inherited Leigh Syndrome (MILS) carrying mutations in the MT-ATP6 gene in the presence and absence of 1 µM or 10 µM Sildenafil after an incubation period for 6 and for 24 hours at a physiological glucose concentration of 4.5 mM.

first: Marie-Thérèse

last: Henke

first: Alessandro

last: Prigione


title: Transcriptional profile of tumor-associated macrophages from control-diet- and high-fat-diet-fed C57BL/6 mice with colorectal liver metastasis.

city: Guangzhou

first: Yizhi

last: Zhan

state: Guangdong

address: 1023 South Shatai Road Baiyun District

department: Department of Pathology

institute: Nanfang Hospital Southern Medical University

summary: The obesity epidemic is associated with increased incidence of colorectal cancer liver metastasis (CRLM) and the local recurrence following CRLM resection. Here, we demonstrate that M2 type tumor-associated macrophages (TAMs) significantly accumulate within liver metastases in high-fat-diet-induced obese mice, and thus accelerating the development of CRLM. The TAMs from mice with high-fat diet facilitate the expansion of lipid droplets by upregulating SLC27A1, and as a result, M2 polarization is promoted. Mechanistically, SLC27A1 binds with PLIN2, a lipid droplet coat protein, to inhibit its degradation via chaperone-mediated autophagy. Moreover, the number of SLC27A1+ TAMs is significantly increased in obese patients with CRLM, suggesting that the mechanism revealed here likely plays a role in the progression of human CRLM and represents a potential target for treatment.

overall_design: C57BL/6 mice were fed a control diet (CD, 10% kcal from fat)) and a high-fat diet (HFD, 60% kcal from fat)) for 6 weeks. We then performed an intrasplenic injection of 5 × 105 MC38 cells to induce liver metastasis. The liver metastases from 4 CD-fed and 4 HFD-fed mice were utilized for flow cytometry sorting 19 days post tumor implantation. The TAMs were characterized as CD45/CD11b/F4/80-positive cells through sorting, and then were subjected to RNA sequencing.


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

city: Leuven

first: Yoke Chin

last: Chai

state: Leuven

address: Herestraat 49, ON5

department: Development & Regeneration

country: Belgium

institute: KU Leuven

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

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

first: Karan

last: Ahuja

first: Roya

last: Ramezankhani

first: Xinyu

first: Thibaut

last: Burg

first: Giulia

last: Amos

first: Katrien

last: Neyrinck

first: Alessio

last: Silva

first: Geethika

last: Arekatla

first: Eleanor

last: Eva Cassidy

first: Arefe

last: Nami

first: Joke

last: Terryn

first: Keimpe

last: Weirda

first: Katlijn

last: Vints

first: Niels

last: Van Damme

first: Suresh

last: Kumar Poovathingal

first: Ivo

last: Lambrichts

first: Johan

last: Swinnen

first: Ludo

last: Van Den Bosch

first: Lies

last: De Groef

first: Lieve

last: Moons

first: Catherine

last: Verfaillie

last: Neyts

first: Dirk

last: Jochmans

first: Yoke

last: Chin Chai


title: Abiotic stress responses of aldehyde dehydrogenase mutants in moss Physcomitrium patens focused on members linked to the GABA shunt pathway

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: We constructed three moss aldh5F2, aldh10A1 and aldh21A1 knockouts to obtain complementary information on the importance of each family for the regulation of GABA shunt and levels of metabolites in TCA cycle.

overall_design: Physcomitrium patens "Grandsen 2004" WT and three independent mutant lines of chosen ALDH genes were cultivated in modified Knop medium, enriched with trace element solution, vitamins and tartrate with 1% plant Agar and 300mM NaCl in 24-well plates.

first: David

middle: J

last: Kopečný

first: Martina

last: Kopečná

first: Miroslav

last: Valárik

last: Müller


title: ECRG4 as a novel diagnostic plasma marker detected in the early phase of Alzheimer’s disease

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku

institute: Hokkaido University

summary: Current therapeutic methods for Alzheimer’s disease (AD) aim to delay its progression; therefore, developing a reliable method for diagnosing the early phases of the disease (EAD) is crucial. Based on the finding that the secretory protein Esophageal Cancer-Related Gene 4 (ECRG4) is elevated in the hippocampus of AD patients, we developed a new ECRG4 ELISA system. Here, we show that ECRG4 peptides, particularly those containing amino acids 108 to 132, are increased in the plasma of approximately 25% of mild cognitive impairment and half of AD patients, compared to non-dementia individuals. RNA sequencing analysis of the plasma revealed decreased levels of CHST3 mRNA, which is highly expressed in oligodendrocyte-lineage cells, in ECRG4-positive patients. We demonstrate that amino acids 71 to 107 exert cytotoxicity to oligodendrocytes in culture and decrease the intensity of the oligodendrocyte marker in the corpus callosum when injected into the brain. This results in extravascular IgG leakage due to the accumulation of oligodendrocyte precursor cells (OPCs), which regenerate myelin, around the blood vessels. Given that similar phenomena were detected in the brains of EAD patients, these results suggest that ECRG4 is involved in the progression of AD through vascular destruction in a manner dependent on oligodendrocyte defects.

overall_design: EDTA-treated plasma (plasma) and cerebrospinal fluid (CSF) samples were obtained from patients diagnosed with dementia, including AD and normal pressure hydrocephalus, as well as those with MCI and non-dementia neurological disorders, such as multiple system atrophy and myopathy, using standard methods.


title: Break-Seq to map DNA double stranded breaks in WT S. cerevisiae post treatment with six different replication inhibitors

city: Syracuse

first: Wenyi

last: Feng

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

summary: Replication–transcription conflicts have long been identified as a source of genome instability, leading to DNA double-strand break (DSBs) formation at the site of encounter.  The encounter between replication and transcription is significantly increased when cells encounter stress, such as by treatment with agents that alter either of these processes.  Alterations in either of these processes increase the probability of their encounter, ultimately inducing DSBs.  Previous studies with hydroxyurea (HU)-treated synchronous cell cultures showed that HU-induced DSBs are a result of replication-transcription collisions.  Here, we sought to determine whether replication-transcription collision is a general phenomenon used by replication inhibitors to induce DSBs.  In our study, we used six different replication inhibitors, HU, methyl methane sulfonate (MMS), camptothecin (CPT), actinomycin D (AD), doxorubicin (DOX), and methotrexate (MTX), each of which acts differently.  The replication inhibitor-specific DSBs tend to be enriched at gene exons and are also well correlated with the origins of replication.  Gene expression around these DSBs tends to be upregulated, thus increasing the probability of encounter between the two. These results support our hypothesis that DSBs result from replication-transcription conflicts.  We also observed enrichment in the transcription-dependent histone mark deposition-H3K4me3 and H3K36me3 at one DSB locus.  Taken together, these results suggest that replication inhibitor treatment induces the expression of certain genes, depositing active histone marks, which upon encountering the incoming replication fork result in collision.  Overall, our study maps the genome-wide location of DSBs as well as the gene expression profile induced by different replication inhibitors and provides insight into the role of chromatin architecture in regulating genome integrity.

overall_design: Asynchronously grown WT cells from the W303 background were treated with  six different replication (HU,MMS,CPT, AD,DOX,MTX) inhibitors at their IC50 concentration. DSBs were mapped in each of the replication inhibitor treatment as well as its vehicle control. Two independent experiments were performed for each with each having a technical replicate (4 total experiments per each replication inihibitor and vehivle control).

first: Ishita

last: Joshi


title: The oncogenic potential of YAP requires Y357 phosphorylation in cholangiocytes but not in hepatocytes

first: Chantal

last: McCabe

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

summary: The transcriptional cofactor yes-associated protein (YAP) functions as a proto-oncogene and a key effector of the canonical Hippo pathway. Phosphorylation at serine 127 (S127) by core Hippo kinases inhibits YAP activity, while phosphorylation at tyrosine 357 (Y357) by SRC-family kinases promotes its activation. YAP activation has been implicated in many cancers, including primary liver cancers (PLCs). Owing to the inherent plasticity of the liver, PLCs may arise from different cells of origin. However, it is unknown whether the level of YAP activation favors liver tumorigenesis from specific cells of origin or instead promotes lineage commitment in a single cell of origin across the PLC spectrum. To assess the role of YAP tyrosine phosphorylation in liver tumorigenesis, C57BL/6 mice underwent biliary transfection with the Sleeping Beauty transposon system to deliver myr-AKT and YAP S127A (YAP-S) or YAP S127A/Y357F (YAP-SY). While YAP-S mice represent an established model of intrahepatic cholangiocarcinoma (iCCA), unexpectedly, a shift in tumor phenotype to hepatocellular carcinoma (HCC) was identified in YAP-SY mice. Transcriptome and pathway analysis revealed differential activation of cytokines and growth factors (e.g., TGFB1, TNF, IL1B, IL4, and INFG) and transcription factors (e.g., STAT3, PGR, AHR, STAT1, and NFKB) associated with this phenotypic switch. To determine the cell of origin, tumors were generated in lineage tracing mice (ROSA26mT/mG mice treated with AAV8-TBG-Cre), which demonstrated that HCC originated from hepatocytes and iCCA from cholangiocytes in the biliary transfection model. Finally, two tumor-derived cell lines with YAP-SY and constitutive AKT expression were isolated, representing a novel, transplantable murine syngeneic model with mixed features of HCC and iCCA.

overall_design: From previously established mouse models (YAP-S and YAP-SY), bulk RNA sequencing was conducted. Transcriptomic and pathway analyis was conducted to investigate biological processes and investigate phenotypic switch.

first: Muhammed

last: Aksu

first: Jayla

last: Millender

middle: E

first: Ryan

last: Watkins

first: Jennifer

last: Yonkus

first: EeeLN

last: Buckarma

first: Nathan

middle: W

last: Werneburg

first: Daniel

last: O’Brien

first: Rondell

last: Graham

first: Gregory

last: Gores

first: Rory

last: Smoot

first: Caitlin

middle: B

last: Conboy


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

city: Chengdu

first: Hua

last: He

state: Sichuan

address: 2222 Xinchuan Rd

institute: West China Second University Hospital Sichuan University

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

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


title: ChIP-Seq to map DNA double stranded breaks in WT S. cerevisiae post treatment with five different replication inhibitors

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Replication–transcription conflicts have long been identified as a source of genome instability, leading to DNA double-strand break (DSBs) formation at the site of encounter.  These encounter between replication and transcription is significantly increased when cells encounter stress, such as by treatment with agents that alter either of these processes.  Alterations in either of these processes increase the probability of their encounter, ultimately inducing DSBs.  Previous studies with hydroxyurea (HU)-treated synchronous cell cultures showed that HU-induced DSBs are a result of replication-transcription collisions.  Here, we sought to determine whether replication-transcription collision is a general phenomenon used by replication inhibitors to induce DSBs.  In our study, we used six different replication inhibitors, HU, methyl methane sulfonate (MMS), camptothecin (CPT), actinomycin D (AD), doxorubicin (DOX), and methotrexate (MTX), each of which acts differently.  The replication inhibitor-specific DSBs tend to be enriched at gene exons and are also well correlated with the origins of replication.  Gene expression around these DSBs tends to be upregulated, thus increasing the probability of encounter between the two. These results support our hypothesis that DSBs result from replication-transcription conflicts.  We also observed enrichment in the transcription-dependent histone mark deposition-H3K4me3 and H3K36me3 at one DSB locus.  Taken together, these results suggest that replication inhibitor treatment induces the expression of certain genes, depositing active histone marks, which upon encountering the incoming replication fork result in collision.  Overall, our study maps the genome-wide location of DSBs as well as the gene expression profile induced by different replication inhibitors and provides insight into the role of chromatin architecture in regulating genome integrity.

overall_design: Asynchronously grown WT cells from the W303 background were treated with  five different replication (HU,MMS,CPT,DOX,MTX) inhibitors at their IC50 concentration. ChIP-seq for transcription deposited histone marks (H3K4me3 and H3K36me3) were mapped in each of the replication inhibitor treatment as well as its vehicle control. Two independent experiments were performed for each (2 total experiments per each replication inihibitor and vehivle control).