title: Central nervous system-compartmentalized pathogenic B cells promote neurological inflammation relapses

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

summary: B cells have emerged as a critical player in autoimmune disorders of the central nervous system (CNS), such as multiple sclerosis (MS). While locally educated B cells with a CNS non-self-reactive immune repertoire are observed at the brain borders, the specific function of these CNS-compartmentalized B cells in the neuroinflammation pathogenesis remains unclear. Here we demonstrated that autoreactive B cells promoted neuroinflammation through local cognate interaction with pathogenic T cells in the meninges. By selectively perturbing B cell compositions in the CNS through intra-cisterna magna injection, we found that CNS-compartmentalized autoreactive T-B interactions drove the influx of pro-inflammatory phagocytes and initiated vascular inflammation responses, which were dependent on the expression of class II major histocompatibility complex molecules. Selective targeting of B cells in the CNS effectively alleviated relapses of neurological inflammation. These findings elucidate the pathogenic functions of CNS-compartmentalized B cells, highlighting their potential as therapeutic targets for relapsing MS.

overall_design: We induced experimental autoimmune encephalomyelitis (EAE) in C57BL/6J mice by intravenously transferring pathogenic 2D2 pathogenic T-helper 17 (pTh17) cells. On day 3 following the T cell transfer, we transferred wild type (WT) or myelin oligodendrocyte glycoprotein (MOG)-specific mature naïve B cells into the recipients via intracisternal magna (ICM) injection. Subsequently, on day 6 after the T cell transfer, we collected subdural brain tissues and enzymatically digested them to obtain a single-cell suspension. The harvested cells were then labeled with flow antibodies and hashtag antibodies. We specifically sorted and pooled blood endothelial cells (BECs) (CD45–CD31+) and fibroblasts (CD45–PDPN+) for single-cell RNA sequencing using the 10X Genomics platform.

first: Yan

last: Wang

first: Shaorui

last: Liu

first: Danyang

last: He


title: Subcellular Trafficking of Oncoprotein FOXK1 Reverses Insulin Resistance-induced Circadian Disruption and Promotes Sensitivity of Metformin in Tumor Therapy

status: Public on Jul 16 2025

city: Beijing

first: Zhao

middle: Ming

last: hui

address: You'anmen

country: China

institute: Capital Medical university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The pathophysiological function of the FOXK family-member FOXK1 remains to be explored. Although tumors classically induce abnormalities in the insulin pathway, clinical trials have failed to establish insulin receptors as potential targets for tumor therapy. Metformin, so far has been identified as an effective treatment in several clinical oncology trials; however, metformin may fail to benefit all patients, and some even suffer from many side effects and drug resistance. Herein, we report that FOXK1 expression correlates with the sensitivity to metformin treatment in a variety of tumors. FOXK1 translocates into the nucleus in response to insulin stimulation and recruits multiple class I HDAC-containing complexes that regulate the expression of genes, such as PER2 and OGT, known to be critically involved in circadian rhythm and insulin resistance. Furthermore, high insulin levels associated with cancer could disturb the subcellular localization and epigenetic regulatory functions of FOXK1. Glycosylation modifications stabilize FOXK1 in the nucleus. Elevated nuclear FOXK1 competes with CLOCK for binding with BMAL1, leading to the deregulation of circadian rhythm, which, in turn, enhanced tumor cell proliferation in vitro and promoted tumor development in vivo. Correspondingly, elevated expression of nuclear FOXK1 was observed during tumor progression and was associated with a poor prognosis. Interestingly, both in vitro and in vivo experiments confirmed that cells with high FOXK1 expression were highly responsive to metformin stimulation. Collectively, these findings revealed that nuclear FOXK1 promotes tumorigenesis by disrupting circadian rhythm under insulin resistance, and its expression may serve as a potential indicator for the adjuvant treatment of tumors using metformin.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for FOXK1 in MCF-7 cells.

first: Lin

last: Shan

first: Zhaohan

last: Zhang

first: Minghui

last: Zhao

first: Qian

first: Geyu

last: Ze


title: Set1 is a critical transcriptional regulator in response to external signals [ChIP-seq]

city: Chuncheon-si, Gangwon-do

first: Jueun

last: Kim

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

summary: Set1-mediated methylation of histone H3 at lysine 4 (H3K4) is a well-established marker of active transcription in eukaryotes. However, absence of Set1 did not significantly alter the overall gene expression; interestingly, some genes exhibited enhanced expression in Candida albicans. The present study aimed to elucidate the role of Set1 in transcription of genes that exhibited increased expression levels in its absence. Ideally, these genes should be repressed and activated in response to specific signals. The hypha-specific genes of C. albicans were expressed in the absence of Set1, even without any external activating signals. These inducible genes displayed atypical H3K4 modification patterns. During the initial induction stages, H3K4 methylation was not involved in the rapid and explosive expression of these genes; instead, acetylation of the same residue was involved. H3K4 acetylation significantly increased in the absence of H3K4 methylation, allowing genes that did not receive external transcriptional signals to initiate mRNA expression, leading to morphological changes. With continued exposure to induction signals, the heightened H3K4 acetylation decreased while H3K4 methylation increased in these genes. Thus, inducible genes receive a positive feedback for stable and sustainable expression. In conclusion, Set1 is a key regulator of transcription in response to external environment changes.

overall_design: Chromatin immunoprecipitation (ChIP) sequencing for histone H3K4me1, H3K4me2, H3K4me3, H3, and H3K4 acetylation in Candida albicans wild-type, Δset1, and Δgcn5 under normal yeast and hypha-inducing conditions were generated by deep sequencing, in duplicate, by Illumina HiSeq 2500

first: Jiyeon

last: Park

first: Eun-Jin

last: Lee

first: Yong-Joon

last: Cho

first: Jung-Shin


title: Transcriptomic analysis of the left and right ventricles in a rat model of pulmonary hypertension

city: Parma

first: Alessia

last: Caputo

state: Parma

address: Parco Area delle Scienze 23/A

country: Italy

institute: University of Parma

type: Expression profiling by high throughput sequencing

summary: Pulmonary hypertension (PH) encompasses a diverse spectrum of disorders characterized by elevated pulmonary arterial pressure presenting substantial morbidity and mortality challenges. Despite significant advancements in understanding its underlying pathophysiology therapeutic options remain limited particularly in cases where patients exhibit elevated pulmonary pressures despite maintaining a preserved left ventricular ejection fraction. The traditional focus on right ventricular (RV) function in PH has led to the underestimation of the impact on the left ventricle (LV) due to the absence of high-resolution modalities capable of monitoring the electromechanical coupling in both ventricles. We present here the results of an integrated histology and transcriptome analysis  used to improve our understanding of the pathophysiology of pulmonary hypertension and identify the different molecular responses due to MCT-induced PH.

overall_design: Male rats, upon reaching a weight of 250g, were injected with a dose of monocrotaline (MCT) 60 mg/kg or saline (day 0 - 4) and sacrificed upon reaching a discomfort score (DS) greater than or equal to 7. Transcriptome profiling by RNAseq was performed on total RNA extracted from the right and left ventricles.

first: Francesco

middle: P

last: Lo Muzio

first: Michele

last: Miragoli

first: Barbara

last: Montanini


title: Investigating JUNB and CXCR4 expression in Circulating Tumor Cells and exosomes derived from Small Cell Lung Cancer (SCLC) patients

city: Patras

first: Athanasios

middle: Nasir

last: Shaukat

state: Western Greece

address: Asklipiou 1

department: Department of Biochemistry

country: Greece

institute: University of Patras

type: Non-coding RNA profiling by high throughput sequencing

summary: The enhanced metastatic ability of small-cell lung cancer warrants the discovery of prognostic biomarkers to support decisions during the course of the disease. We have previously demonstrated the clinical significance of JUNB and CXCR4 expression in circulating tumor cells (CTCs) from breast and non-small cell lung cancer (NSCLC). patients. In the present study, we aimed to explore the expression levels of the aforementioned biomarkers in patients’ CTCs and plasma-derived exosomes. One hundred SCLC patients at baseline were enrolled in the study; exosome isolation was performed in 58 of them. Cytospins were analyzed using the VyCAP system and exosomes were characterized based on their molecular and transcriptomic profile. JUNB and CXCR4 were expressed in the majority of the CTCs. Protein exosomal expression of both biomarkers in patients was significantly different compared to healthy donors (p = 0.003 and p = 0.027, respectively), while a high discriminative ability was observed in patients overexpressing JUNB and CXCR4 in their exosomes (c-statistic = 0.949 and c-statistic = 0.903 respectively). The presence of JUNB and/or CXCR4 in CTCs was associated with poorer OS (p = 0.025). CXCR4 exosomal overexpression correlated with the presence of CTCs and their phenotypes. Lastly, miRNA profiling on 4 SCLC patients, indicated a multitude of biological processes and signaling pathways implicated in SCLC pathogenesis. Our study is the first attempt to evaluate two different aspects of liquid biopsy (CTCs and exosomes) in SCLC patients, regarding JUNB and CXCR4 expression, aiming to provide a potential new prognostic and/ or diagnostic approach.

overall_design: miRNA-seq on the Ion Torrent Genestudio S5 platform with Ion Chef (Ion torrent) on plasma-derived exosome from one healthy donor and four Small Cell Lung Cancer (SCLC) patients

first: Dimitrios

last: Papakonstantinou

first: Argyro

last: Roumeliotou

first: Evangelia

last: Pantazaka

middle: N

first: Constantinos

last: Stathopoulos

first: Galatea

last: Kallergi


title: microRNA regulates alveolar macrophage maintanance and function during pulmonary fibrosis

city: Detroit

first: Qing-Sheng

last: Mi

state: Michigan

address: One Ford Place

department: Dermatology

country: USA

institute: Henry Ford Health System

summary: Alveolar macrophages (AMs) are important for maintaining lung homeostasis and involved in many lung diseases such as pulmonary fibrosis. Tissue-resident AMs (TR-AMs) derived from embryonic progenitors can self-renew locally in the steady state independently of hematopoiesis. During fibrogenesis, circulating monocytes rapidly migrate into the lung and become monocyte-derived AMs (Mo-AMs). MicroRNAs (miRNAs) are non-coding small RNAs that are essential for regulating gene expression and processed by ribonuclease Dicer. However, the role of miRNAs in regulation of TR-AMs and Mo-AMs during pulmonary fibrosis remains poorly understood. Bulk RNA-seq analysis revealed divergent transcriptomic and pathway changes caused by miRNA deficiency in the two AM subgroups after BLM injury. We propose that miRNAs are key epigenetic mediators that differentially regulate TR-AM and Mo-AM maintenance and function in the pathogenesis of pulmonary fibrosis.

overall_design: RNA-sequencing of TR-AMs and Mo-AMs sorted from Cd11cCre+Dicerfl/fl and Cd11cCre-Dicerfl/fl adult mice on day 14 after bleomycin treatment

first: Yi

last: Yao

first: Namir

last: Khalasawi

first: Congcong

last: Yin

first: Qiong

last: Zhang

first: Indra

last: Adrianto

first: Aakash

last: Hans

first: Li

last: Zhou


title: 5' Untranslated regions tune Toxoplasma translation [MPRA]

status: Public on Jul 15 2025

city: Cambridge

first: Sebastian

last: Lourido

state: MA

address: 455 Main Street

institute: Whitehead Institute

summary: Some of the longest 5′ untranslated regions (UTRs) documented in eukaryotes belong to parasites of the phylum Apicomplexa. Translational regulation plays prominent roles in the development of these parasites, including the agents of toxoplasmosis (Toxoplasma gondii) and malaria. To understand the function of 5′ UTRs in apicomplexan translation, we performed high-resolution ribosome profiling of T. gondii in human fibroblasts. We show that parasite translation efficiency (TE) is largely controlled by 5′ UTR features and tuned by the number of upstream AUGs (uAUGs). Examination of ribosome occupancy reveals that, despite widespread engagement of uAUGs, parasite ribosomes seldom translate uORFs. These features are reaffirmed in a massively parallel reporter assay examining the effect of more than 30,000 synthetic 5′ UTRs in T. gondii. A model trained on these results accurately predicted the TE of newly designed 5′ UTRs. Together, this work defines the regulatory language of T. gondii translation, providing a framework to understand the evolution of exceptionally long 5′ UTRs in apicomplexans.

overall_design: Massively parallel reporter assay (MPRA) of 5' UTRs driving mNeonGreen, with a constitutive mKate marker. Reporter construct was stably integrated into Toxoplasma gondii (RH) and parasites were subjected to FACS based on mKate positivity and mNG intensity. Targeted DNA and RNA sequencing was performed on the plasmid library, bulk parasite, populations and 4 sorted bins.

first: Michelle

middle: L

last: Peters

first: Aditi

last: Shukla

first: Zoe

middle: A

last: Gotthold

first: Dylan

middle: M

last: McCormick

first: Kehui

last: Xiang

first: David

last: Bartel


title: 5' Untranslated regions tune Toxoplasma translation [Ribosome Profiling]

sample_organism:
Toxoplasma gondii
Homo sapiens

platform_organism:
Toxoplasma gondii
Homo sapiens

overall_design: Paired ribosome footprinting and RNAseq of acute-stage ME49 Toxoplasma gondii and host human foreskin fibroblasts (HFF).


title: H3K9me3 regulates T cell effector function and colon tumor liver metastasis

city: Augusta

first: Kendra

last: Fick

address: 1410 Laney Walker BLVD CN1109N

institute: Medical College of Georgia

summary: Patients with the microsatellite stable (MSS) subset of colorectal cancer, which accounts for 85-90% of all human colorectal cancer cases, do not respond to PD-(L)1 immune checkpoint inhibitor immunotherapy. Metastasis accounts for over 90% of human colorectal cancer mortality and liver metastasis accounts for 90% of human colorectal cancer metastasis. The mechanism underlying colorectal tumor cell immune evasion and the resultant liver metastasis is incompletely understood. The SUV39H1-H3K9me3 epigenetic pathway has emerged as a key regulator of CTL persistence and effector function in anti-tumor immunity. We therefore aimed at testing the hypothesis that H3K9me3 induces CTL dysfunction to promote colorectal tumor liver metastasis. Using a mouse MSS colon tumor experimental liver metastasis model, we observed that PD-1 blockade immunotherapy does not induce CTL activation in the liver metastases and exhibits no significant efficacy in suppression of liver metastasis. CTL adaptive transfer increased accumulation of the tumor-specific CTLs in liver metastases but also exhibited no significant efficacy in suppression of liver metastasis. However, pharmacological inhibition of H3K9me3-specific histone methyltransferases with the small molecule F5446 significantly suppressed liver metastasis in mice. scRNA-seq analysis of liver metastases-infiltrating immune cells revealed that F5446 therapy does not increased total level of T cell tumor infiltration. Instead, inhibition of H3K9me3 increased Tex and decreased Tcm in liver metastases. Analysis of human colon tumor scRNA-Seq datasets identified Tex, Tcm and Tem-like clusters in both primary and liver metastasis with higher level of Tex subset of T cells in liver metastases than primary tumor. Our findings determine that colon tumor cells induce H3K9me3 to regulate T cell differentiation and effector function in liver metastases microenvironment and targeting H3K9me3 is a promising approach for suppression of CRC liver metastasis.

overall_design: CT26 cells were injected to spleens of BALB/c mice to form liver metastases. The tumor-bearing mice were treated with vehicle control of F5446 (10 mg/kg body weight) 4 days after tumor cell injection every 2 days for 5 times. Livers were harvested and underwent single cell suspension. CD45 cells were isolated from the samples using mouse CD45 positive selection beads before sequencing.

first: Fick

last: Kendra

first: Liu

last: Kebin


title: Reassessing in vivo conversion of Müller cells to retinal ganglion cells

city: Shanghai

first: Jinhai

last: Huang

address: 83 Fenyang Road, Xuhui District

institute: EYE & ENE Hospital of Fudan University

summary: The conversion of Müller cells (MGs) to retinal ganglion cells (RGCs) in vivo is a potential regeneration-based therapeutic strategy for optical nerve injury. It has been reported that Ptbp1 knockdown can efficiently convert MGs into RGCs. However, another study reported that mislabeling could have yielded a possible false positive. No previous studies have examined gene expression at single-cell resolution after Ptbp1 knockdown in MGs. Here, using CasRx-mediated knockdown of Ptbp1 in optic nerve crush model mice, we observed MG-to-RGC conversion in vivo and found that this conversion attenuated the symptoms of visual impairment caused by the loss of RGCs. ScRNA-seq revealed that a cluster of retinal progenitor cells (RPCs) underwent MG-to-RGC conversion after Ptbp1 knockdown. Our study confirmed the presence of intermediate cells during the MG-to-RGC conversion process after Ptbp1 knockdown and discovered transcription regulators including Nfix, Nfia, Crx, Rax, and Neurod1 are functionally involved in regulating this process.

overall_design: Retinal mRNA profiles of  8 weeks after injection with AAV virus B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J mice.

first: Zhenhai

last: Zeng

first: Yujun

last: Xu

first: Zhongxing

last: Chen

first: Yini

last: Li

first: Siheng

first: Zhilin

last: Zou

first: Jun

first: Qing

last: Wang

first: Qingyi

last: Gao

first: Shuangzhe

first: Yifan

last: Feng

first: Ziqian

first: Mingyu

last: Yao

first: Xinyi

first: Meimin

last: Lin

first: Xinyu

last: Liu

first: Rongrong

first: Jing

last: Zhao

first: Sisi

first: Xiangjia

last: Zhu

first: Wenyi

last: Wu

first: Xingtao

first: Lijia

last: Ma


title: Whole transcriptome analysis reveals ELK3 as a key driver of metastasis through regulation of 3D migration and stemness in triple-negative breast cancer cells

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

summary: To investigate the key mechanisms regulated by the transcription factor ELK3 relevant for cancer metastasis, we emplyed whole-genome microarray expression profiling as a discovery tool to identify the signaling networks affected by ELK3 knockdown. MDA231 breast cancer cells with ELK3 knockdown (ELK3-KD) were generated by lentiviral mediated transduction. ELK3-KD significantly altered the expression of 2.156 genes (p<0.05), among which 740 showed a fold regulation (FR) greater than |±1.3|.  ELK3 inhibition impacted key cancer-related functional signaling networks, including cellular movement, cell cycle regulation, cell death and survival, as well as cell-to-cell communication, and structural organization.

overall_design: MDA231 breast cancer cells with ELK3 knockdown and corresponding mock controls were generated by lentiviral mediated transduction in 4 biological relpicates. More then 95% of cells for all biological replicates were geneticaly modified after transduction. The whole transcriptome analysis  was implemented on all four biological replicates in ELK3-KD vs. CTR-KD cells.

first: Daniel

last: Cruceriu

first: Loredana

last: Balacescu

first: Oana

last: Sava

first: Stefan

last: Miron

first: Irma-Lidia

last: Szigyarto

first: Alexandrina

last: Burlacu

first: Manuela

last: Banciu

first: Ovidiu


title: Single-Cell Atlas of Pan-Cancer Immunotherapy Reveals the Role of Ferroptosis in Exhausted Macrophages and Immune Therapy Resistance

city: Guangzhou

first: Xinyu

last: Pan

address: No. 135 West Xingang Road, Haizhu District

institute: Sun Yat-Sen University Department of Biochemistry

summary: SLC40A1 (also known as ferroportin) is a key iron exporter that maintains intracellular iron homeostasis and regulates macrophage function. In this study, we found that a metabolically reprogrammed SLC40A1+ subset of tumor-associated macrophages (TAMs), characterized by ferroptosis resistance and immunosuppressive features, is enriched in patients who do not respond to PD-1 immune checkpoint blockade therapy. To further investigate the regulatory role of SLC40A1 in macrophage immune function and ferroptosis resistance, we performed RNA sequencing on differentiated THP-1 macrophages transfected with either SLC40A1-targeting siRNA or negative control siRNA.

overall_design: RNA-seq of THP-1-derived macrophages transfected with si-SLC40A1-1, si-SLC40A1-2, or negative control siRNA following PMA-induced differentiation.

first: Yuanyan

last: Xiong

first: Zhijie

last: Hu


title: Modulating SPARC Expression in Mesenchymal Stem Cells Improves Secretome-Mediated Skin Regeneration and Wound Repair

city: Escobar

first: Antonella

last: Lombardi

state: Buenos Aires

address: Ruta 9 Km 54

country: Argentina

institute: FLENI

summary: Mesenchymal stem cells (MSCs) have garnered significant attention over the past three decades due to their robust regenerative potential, primarily mediated by their paracrine activity by releasing soluble bioactive factors and extracellular vesicles (EVs). The MSC secretome plays a pivotal role in wound healing by influencing cellular migration, inflammation, angiogenesis, extracellular matrix (ECM) remodeling, and re-epithelialization. SPARC (Secreted Protein Acidic and Rich in Cysteine), a multifunctional ECM glycoprotein involved in tissue repair and remodeling, regulates key processes such as cell migration, proliferation, angiogenesis, and survival. Despite its known role in ECM dynamics, the impact of SPARC expression on the regenerative properties of MSCs remains underexplored. In this study, we hypothesized that SPARC overexpression in MSCs enhances their secretome's regenerative capacity. Using lentiviral systems, we generated SPARCoverexpressing (+SPARC) and SPARC-knockdown (KD-SPARC) MSCs to investigate SPARC's role in wound healing. Conditioned media (CM) derived from these MSCs were analyzed in vitro for their effects on human skin keratinocytes and fibroblasts. Our results revealed that SPARC expression significantly influences cell-specific migration and cell cycle. Furthermore, in an in vivo wound healing model, CM from +SPARC MSCs accelerated regeneration, while SPARC absence in MSCs CM delayed the healing process. These findings underscore the critical role of SPARC in modulating MSC secretome composition and enhancing its regenerative efficacy. This study highlights SPARC as a promising therapeutic target for the development of advanced regenerative therapies aimed at improving cutaneous wound healing outcomes

overall_design: Wild type (WT), SPARC Knock Down (Kd) and SPARC Overexpressed (S) cells Bulk RNA was analyzed to assess changes in their capacity to condition culture media.

first: A.

first: J.

last: Smucler

last: Palma

last: Iribarne

last: La Greca

last: García

last: Sevlever

last: Miriuka

last: Luzzani


title: Transcriptionally and phenotypically dysfunctional neutrophils have a suppressive role in macrophage activation syndrome

city: Cincinnati

first: Kairavee

last: Thakkar

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Macrophage activation syndrome (MAS) is a life-threatening cytokine storm syndrome that complicates rheumatic diseases including systemic juvenile idiopathic arthritis (SJIA). Though neutrophil expansion and activation are key features of SJIA, MAS is associated with neutropenia. As the functional contribution of neutrophils to MAS is largely unexplored, we aimed to define neutrophil dynamics in the TLR9-induced MAS mouse model. Mice with TLR9-MAS showed a transient increase in immature neutrophils during MAS and persistent decrease of mature neutrophils through resolution, even after other MAS features were normalized. Single-cell RNA sequencing confirmed increased proportions of both interferon-stimulated gene-high and immature neutrophils during MAS. We also detected an enhanced interferon signature with upregulation of CD274 (PD-L1), suggesting immunosuppressive roles but distinct form myeloid-derived suppressor cells (MDSC). Furthermore, most of the interferon signature normalized at resolution, but prolonged suppression of IL-1 related genes persisted. Neutrophils from both acute and resolution phases of MAS showed in vitro suppression of pro-inflammatory responses upon LPS stimulation. Notably, antibody mediated neutrophil depletion exaggerated clinical, laboratory, and immunologic features of MAS. Overall, neutrophils in MAS show dynamic changes in subpopulations, including transcriptional and phenotypic dysfunction. These findings suggest that mature neutrophils may play anti-inflammatory roles in MAS and highlights an underappreciated role for neutrophil functions in the pathogenesis of cytokine storm syndromes.

overall_design: We pooled and sequenced neutrophils from 4 mice each from acute MAS, resolution, and control treatments. After quality control and removal 19 of contaminated cells , we obtained 29,760 single cells (control: 10,481, MAS: 8, 278, Resolution: 11, 001 cells) and resolved six distinct blood neutrophil cell populations.

first: Natsumi

last: Inoue

first: Nathan

last: Salomonis

first: Grant

middle: S

last: Schulert


title: CHIP protects lysosomes from CLN4 mutant-induced membrane damage

city: Bethesda

first: Yihong

last: Ye

state: MD

address: 5 Center Drive

institute: NIH

summary: Understanding how cells mitigate lysosomal damage is critical for unraveling pathogenic mechanisms of lysosome-related diseases. Here we generated and characterized iPSC-derived neurons (i3Neuron) bearing Ceroid Lipofuscinosis Neuronal 4 (CLN4)-linked DNAJC5 mutations, which revealed extensive lysosomal abnormality in mutant neurons. In vitro membrane-damaging experiments establish lysosome damages, caused by lysosome-associated CLN4 mutant aggregates, as a critical pathogenic linchpin in CLN4-associated neurodegeneration. Intriguingly, in non-neuronal cells, a ubiquitin-dependent microautophagy mechanism downregulates CLN4 aggregates to counteract CLN4-associated lysotoxicity. Genome-wide CRISPR screens identify the ubiquitin ligase CHIP as a central microautophagy regulator that confers ubiquitin-dependent lysosome protection. Importantly, CHIP’s lysosome protection function is transferrable: ectopic CHIP improves lysosomal function in CLN4 i3Neurons and effectively alleviates lipofuscin accumulation and cell death in a Drosophila CLN4 disease model. Our study establishes CHIP-mediated microautophagy as a key organelle guardian that preserves lysosome integrity, offering new insights into therapeutic development for lysosome-related neurodegenerative diseases.

overall_design: 293T cells stably expressing either mKeima-tagged human DNAJC5 wild type or J-domain deleted mutant (delJ or DJ) were infected with GeckoV2 libraries. Keima neutral (3% of cells) and Keima acidic (97%) were sorted by a FACS Ariall cell sorter. Genomic DNA was extracted for amplification of sgRNAs by PCB. Amplified sgRNAs were deep-sequenced by an Illumina platform.

first: Juhyung

last: Lee

first: Natalie

last: Chin

first: Jizhong

last: Zou

first: Wan

last: Mazli

first: Michal

last: Jarnik

first: Layla

last: Saidi

first: Yue

last: Xu

first: Eutteum

last: Jeong

first: Jessica

last: Suh

first: John

last: Replogle

first: Michael

middle: E

last: Ward

first: Juan

last: Bonifacino

first: Wei

last: Zheng

first: Ling

last: Hao


title: Longitudinal liquid biopsy identifies an early predictive biomarker of immune checkpoint blockade response in head and neck squamous cell carcinoma [bulk RNA-seq]

city: Gaithersburg

first: Binbin

last: Wang

address: 408 Suffield Dr

institute: NATIONAL CANCER INSTITUTE, NIH

summary: Immune checkpoint blockade (ICB) has improved outcomes in head and neck squamous cell carcinoma (HNSCC), yet there is an unmet need for predictive, blood-based biomarkers to guide treatment. We longitudinally profiled peripheral immune responses in a mouse HNSCC model treated with anti–PD-1, using single-cell and bulk RNA sequencing with paired TCR sequencing. Early expansion of effector memory T cells (Tem) and B cells was associated with ICB response. Here, we show that the LiBIO score, a composite of Tem and B cell signatures, robustly predicts ICB response in HNSCC blood and tumor cohorts, outperforming existing biomarkers. Furthermore, the LiBIO score generalizes to melanoma, non-small cell lung cancer, and breast cancer, demonstrating potential as a clinically applicable blood-based biomarker for ICB response across multiple cancer types.

overall_design: We employed our previously characterized 4MOSC carcinogen-induced orthotopic HNSCC preclinical model to evaluate immune dynamics during ICB therapy. Two cohorts of mice were used, with one cohort comprising 45 mice for bulk RNA sequencing (RNA-seq) and the other comprising 16 mice for single-cell RNA sequencing (scRNA-seq) and single-cell TCR sequencing. Lesions developed consistently at expected time points. Blood samples were collected at four key intervals: pre-treatment (Day 4) and three on-treatment time points (Days 9, 17, and 24), aligned with the administration of anti-PD-1 therapy. Tumor growth and immune responses were monitored longitudinally to assess treatment efficacy. Bulk RNA-seq provided an overview of immune dynamics in the larger cohort, while scRNA-seq and scTCR sequencing in the smaller cohort delivered high-resolution insights into immune repertoire changes, supporting the study’s focus on peripheral immune biomarkers for predicting ICB outcomes.

first: Robert

last: Saddawi-Konefka

first: Lauren

last: Clubb

first: Shiqi

last: Tang

first: Di

last: Wu

first: Sumit

last: Mukherjee

first: Sahil

last: Sahni

first: Saugato

last: Rahman-Dhruba

first: Xinping

last: Yang

first: Sumeet

last: Patiyal

first: Chi-Ping

last: Day

first: Parth

last: Desai

first: Clint

last: Allen

first: Kun

first: Silvio

last: Gutkind

first: Eytan

last: Ruppin


title: Immunosuppressive tumor microenvironment of osteosarcoma [Spatial transcriptomics]

city: Farmington

first: Ching

middle: C

last: Lau

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

summary: Osteosarcoma is the most common malignant bone tumor in children, characterized by a high degree of genomic instability, resulting in copy-number alterations and genomic rearrangements without disease-defining recurrent mutations. Clinical trials based on molecular characterization have failed to find new effective therapies or improve outcomes over the last 40 years. To better understand the immune microenvironment of osteosarcoma, we performed single-cell RNA sequencing on six tumor biopsy samples, combined with a previously-published cohort of six samples. Additional osteosarcoma samples were profiled using spatial transcriptomics for validation of discovered subtypes and to add spatial context. Analysis revealed immunosuppressive cells, including myeloid-derived suppressor cells (MDSCs), regulatory and exhausted T-cells, and LAMP3+ dendritic cells. Using cell-cell communication modeling, we identified robust interactions between MDSCs and other cells, leading to NF-κB upregulation and an immunosuppressive microenvironment, as well as interactions involving regulatory T-cells and osteosarcoma cells that promoted tumor progression and a proangiogenic niche.

overall_design: Formalin-fixed, paraffin-embedded (FFPE) samples of two primary OS pre-treatment biopsy tissue samples (Patients A and B) were obtained from CCMC and stored at 4 °C in the dark. Prior to Visium transcriptomics, RNA quality of FFPE samples was determined by DV200 score using Agilent (Santa Clara, California) TapeStation 4200 High Sensitivity DNA ScreenTape. Tissue blocks with DV200 scores above 50% were used for downstream processing.  Briefly, FFPE sections were placed on a 10x Visium FFPE Gene Expression slide, deparaffinized, H&E stained, then imaged in brightfield using a NanoZoomer SQ (Hamamatsu Photonics, Shizuoka, Japan) slide scanner, followed by incubation with human-specific probe sets provided by the manufacturer for subsequent mRNA labeling and library generation per the manufacturer's protocol (10x Genomics, CG000407). Libraries were pooled for sequencing on an Illumina NovaSeq 6000 200-cycle S4 flow cell using a 28-10-10-90 read configuration, targeting 100,000 read pairs per spot covered by tissue.

first: Aaron

last: Taylor

first: Jianting

last: Sheng

first: Patrick

middle: K

last: Ng

first: Jeffrey

last: Harder

first: Parveen

last: Kumar

first: Ju Young

last: Ahn

first: Yuliang

last: Cao

first: Alissa

last: Dzis

first: Nathaniel

last: Jillette

first: Andrew

last: Goodspeed

first: Avery

last: Bodlak

first: Qian

first: Michael

last: Isakoff

first: Joshy

last: George

first: Jessica

middle: D

last: Grassmann

first: Diane

last: Luo

first: William

middle: F

last: Flynn

first: Elise

middle: T

last: Courtois

first: Paul

last: Robson

first: Masanori

last: Hayashi

first: Alini

last: Paolillo

first: Sergio

last: Petrilli

first: Silvia Regina

last: Caminada de Toledo

first: Fabiola

last: Balarezo

first: Adam

last: Lindsay

first: Bang

last: Hoang

first: Stephen

last: Wong


title: Immunosuppressive tumor microenvironment of osteosarcoma [scRNA-seq]

first: Ching

last: Lau

overall_design: Primary, treatment-naïve pediatric osteosarcoma biopsies were gathered from six patients at Connecticut Children's Medical Center or Children's Hospital Colorado. Tissues were dissociated into individual cells for single-cell RNA sequencing. Data was combined with single-cell RNA sequencing of six additional treatment-naïve pediatric osteosarcoma biopsy samples previously described in Liu et al. (Front Oncol, 2021) downloaded from the Gene Expression Omnibus (GSE162454).

first: Aaron

last: Taylor

first: Jianting

last: Sheng

first: Patrick

last: Ng

first: Jeffrey

last: Harder

first: Parveen

last: Kumar

first: Ju Young

last: Ahn

first: Yuliang

last: Cao

first: Alissa

last: Dzis

first: Nathaniel

last: Jillette

first: Andrew

last: Goodspeed

first: Avery

last: Wu


title: In vivo efficacy study of BMS-986365 and enzalutamide in mCRPC PDX models

city: San Diego

first: Celia

last: Fontanillo

state: CA

address: 10300 Campus Point Dr

institute: Bristol Myers Squibb

summary: This study is aimed to explore in vivo trascriptional response of BMS-986365 and enzalutamide in mCRPC PDX models CTG-2441 and CTG-2440 which were derived from bone metastases of the same patient following progression on ADT or ADT plus abiraterone treatments, respectively.

overall_design: Male NOG immunocompromised mice were implanted subcutaneously into the left flank with tumor fragments from CTG-2441 and CTG02440 prostate cancer models. Mice were dose with 7 days of QD dosing by oral gavage of vehicle, BMS-986365 (60 mg/kg), and ENZ (50 mg/kg) and carried out at Champions Oncology (Rockville, MD, USA).  At 6 hours post final dose, tumor samples were collected and RNA-seq was performed.

first: Marwa

last: Khater

first: Raju

last: Kandimala

first: Shuichan

last: Xu


title: ATAC-seq of oxaliplatin resistant HCT116

city: Houston

first: Stephen

middle: Qi Rong

last: Wong

state: Texas

address: 6670 Bertner Ave

institute: Houston Methodist

summary: Drug resistance and distant metastases are leading causes of mortality in colorectal cancer (CRC), yet the molecular mechanisms linking these processes remain elusive. In this study, we demonstrate that acquired resistance to oxaliplatin, a first-line chemotherapeutic in CRC, enhances metastatic potential through transcriptional reprogramming. Using a clinically relevant dosing regimen, we generated oxaliplatin-resistant CRC cells that displayed increased metastatic potential. Integrated transcriptomic and phenotypic analyses revealed that dysregulated cholesterol biogenesis amplifies TGF-b signaling, which in turn drives expression of SERPINE1, that serves as a key effector of both oxaliplatin resistance and metastasis. Furthermore, we uncovered a SERPINE1-associated nine-gene expression signature, RESIST-M, that robustly predicts overall and relapse-free survival across distinct patient cohorts. Notably, RESIST-M stratifies a high-risk subtype of CMS4/iCMS3-fibrotic patients that display the poorest prognosis, underscoring its clinical relevance. Targeting of SERPINE1 or cholesterol biosynthesis re-sensitized resistant, pro-metastatic cells to oxaliplatin in mouse xenograft models. Altogether, this study uncovers a mechanistic link between metabolic rewiring and transcriptional plasticity underlying therapy-induced metastasis in primary CRC. Additionally, it also reveals actionable vulnerabilities that offer both prognostic value and therapeutic potential.

overall_design: HCT116 cells were treated with 0.5 uM (low dose; LD), 5 uM (mid dose; MD) or 80 uM (high dose; HD) for 72 hours before changing to drug free media. Cells were then subcultured and treated again with the same dose for 72 hours. Cells were treated for 10 cycles. Cells were subsequently cultured in drug free media and used for ATAC-seq.

middle: Q

first: Jia Min

last: Loo

first: Tenzin

last: Kenzom

first: Hui Wen

last: Chua

first: Mohua

last: Das

first: Shirgaonkar

last: Niranjan

first: Dasgupta

last: Ramanuj


title: microRNA expression profile of human thymus populations corresponding to 8 sequential T-cell developmental stages isolated from 3 independent pediatric thymus samples.

city: Madrid

first: María

last: Toribio

state: Madrid

address: Calle Nicolás Cabrera, 1. Campus Cantoblanco

department: Interactions with the environment

country: Spain

institute: Centro de Biología Molecular Severo Ochoa (CSIC-UAM)

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy arising from the neoplastic transformation of immature T cells during their development in the thymus. Deciphering the developmental programs whose dysregulation leads to T-ALL pathogenesis is critical for the development of novel targeted therapies, which remain an urgent unmet need for the treatment of this disease. MicroRNAs (miRNAs) have emerged as key post-transcriptional regulators of numerous physiological processes and cancer. However, the specific role of miRNAs in human T-cell development and T-ALL pathogenesis remains largely unexplored. In this study, we comprehensively evaluated miRNA expression profiles across human T-cell development by microarray analysis and identified a dynamic expression pattern of miR-16-2, which is upregulated across early pre-T cell proliferative stages up to the resting state of immature thymocytes immediately preceding TCR expression, and decreased thereafter. We confirmed the coordinated regulation of miR-15b expression, consistent with the reported clustered genomic location of both miRNAs. Notably, functional studies identified the miR-15b/16-2 cluster as a negative regulator of early thymocyte proliferation, and showed that overexpression of miR-15b/16-2 in T-ALL cells impaired leukemic growth in vitro and tumor progression in patient-derived xenotransplantation assays. Mechanistically, miR-15b/16-2 expression represses the genes encoding BCL-2 and CYCLIN D3, leading to T-ALL apoptosis and cell cycle dysregulation, with an accumulation of G0-phase cells and a defective transition to the G2/M phase. Overall, these findings support a novel function for miR-15b/16-2 as tumor suppressors in T-ALL, highlighting their role as promising targets for T-ALL therapy.

overall_design: Thymocyte subpopulations corresponding to sequential T-cell developmental stages were isolated by immunomagnetic sorting from 3 independent pediatric thymus samples (aged 1 month to 4 years). Sortings were performed based on the surface expression markers characteristic of each T-cell developmental stage using Dynabeads (Dynal, Invitrogen) or Microbeads and AutoMACs (Miltenyi Biotec). Individual population purity (>95%) was confirmed by flow cytometry.

first: M

first: S

last: González-García


title: DNA break formation induces Scc2/cohesin-dependent recruitment of condensin to meiotic chromosomes

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

summary: Meiotic chromosome pairing, recombination, and fertility depends on the conserved loop-axis architecture of meiotic chromosomes. This architecture is modulated by condensin, a structural maintenance of chromosome (SMC) complex that catalyzes chromatin loop formation. Here, we investigated how condensin is recruited to meiotic chromosomes in Saccharomyces cerevisiae. We show that double-strand break (DSB) formation, the initiating event of meiotic recombination, causes condensin redistribution from the nucleolus to DSB hotspots, pericentromeric regions and axis attachment sites. Hotspot association of condensin correlates weakly with break probability but does not depend on local DSB formation, whereas association with axis sites and pericentromeric regions depends on the Scc2-associated pool of cohesin, another SMC complex. Intriguingly, Scc2 distribution also changes in response to DSB formation. As condensin and Scc2-cohesin both catalyze chromatin loop extrusion, their redistribution upon DSB formation implies a profound change in chromatin loop dynamics that may help promote proper chromosome pairing and DNA repair.

overall_design: ChIP-seq analysis of condensin binding dynamics in S. cerevisiae in meiosis. Each bedgraph file is the results from paired Input and ChIP samples.

first: Adhithi

middle: R

last: Raghavan

first: Tovah

last: Markowitz

first: Jonna

last: Heldrich


title: Mouse embryo limb bud regeneration

city: Montpellier

first: Jholy

last: De la cruz

state: hérault

address: 80 avenue Augustin Fliche

country: France

institute: INSERM U1183

summary: Mouse embryos at the E10.5 stage display the ability to regenerate their limb buds, however this is quickly lost during embryogenesis . In the present study, we identified the E12.5 stage as the stage at which regeneration is lost. To deepen our understanding of the transcriptomic programs established during regeneration we generated microarray data from post-amputation tissues at E10.5 and E12.5 stages with a particular focus on early response to amputation observed at 1 and 3hpa. We believe this dataset will help understand how regeneration works in mammals as well as the key differences in a non-regenerative context.

overall_design: Microarray data was generated from 0,1 and 3 hours post-amputation for both E10.5 and E12.5 stages containing 3 biological replicates for each sample type.

first: Béryl

last: Laplace-Builhé

first: Gautier

last: Tejedor

first: Farida

last: Djouad


title: Longitudinal liquid biopsy identifies an early predictive biomarker of immune checkpoint blockade response in head and neck squamous cell carcinoma [scRNA-seq]

first: Binbin

last: Wang

overall_design:
We employed our previously characterized 4MOSC carcinogen-induced orthotopic HNSCC preclinical model to evaluate immune dynamics during ICB therapy. Two cohorts of mice were used, with one cohort comprising 45 mice for bulk RNA sequencing (RNA-seq) and the other comprising 16 mice for single-cell RNA sequencing (scRNA-seq) and single-cell TCR sequencing. Lesions developed consistently at expected time points. Blood samples were collected at four key intervals: pre-treatment (Day 4) and three on-treatment time points (Days 9, 17, and 24), aligned with the administration of anti-PD-1 therapy. Tumor growth and immune responses were monitored longitudinally to assess treatment efficacy. Bulk RNA-seq provided an overview of immune dynamics in the larger cohort, while scRNA-seq and scTCR sequencing in the smaller cohort delivered high-resolution insights into immune repertoire changes, supporting the study’s focus on peripheral immune biomarkers for predicting ICB outcomes.

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first: Robert

last: Saddawi-Konefka

first: Lauren

last: Clubb

first: Shiqi

last: Tang

first: Di

last: Wu

first: Sumit

last: Mukherjee

first: Sahil

last: Sahni

first: Saugato

last: Rahman-Dhruba

first: Xinping

last: Yang

first: Sumeet

last: Patiyal

first: Chi-Ping

last: Day

first: Parth

last: Desai

first: Clint

last: Allen

first: Kun

first: Silvio

last: Gutkind

first: Eytan

last: Ruppin


title: KRAS G12C inhibition combined with CD47 and immune checkpoint blockage overcomes intrinsic resistance to concomitant KRAS G12C and immune checkpoint inhibitor therapy

city: Nagoya

first: Hiromichi

last: Ebi

state: Aichi

address: 1-1, Kanokoden, Chikusa-ku

department: Division of Molecular Therapeutics

country: Japan

institute: Aichi Cancer Center Research Institute

summary: Although KRAS G12C inhibitors have altered the treatment strategy of patients with KRAS G12C mutant lung cancer, their efficacy is insufficient to eliminate tumors. Here, we identified that inhibition of mutant KRAS promotes escape from macrophage phagocytosis by upregulating the expression of ‘don’t eat me’ signal proteins, including CD47. CD47 was induced by the binding of FOXA1 to the super-enhancer of CD47. The addition of an anti-CD47 antibody restored macrophage phagocytosis and phenotype of macrophages.

overall_design: LLC Nras KO syngeneic lung tumors were treated with vehicle, sotorasib (100mg/kg), anti-CD47 (100μg/body), or the combination of these drugs at the same doses for 3 days. Tumors were harvested and subjected to spatial transcriptomics analyses.

first: Kentaro

last: Hirade

first: Noritaka

last: Tanaka

first: Rui

last: Yamaguchi


title: De Novo Pyrimidine Synthesis Is a Collateral Metabolic Vulnerability in NF2-deficient Mesothelioma

city: Nanjing

first: Tong

last: Hu

address: No. 300 Guangzhou Road

institute: Nanjing Medical University

summary: Pleural mesothelioma (PM) is one of the deadliest cancers, with limited therapeutic options due to its therapeutically intractable genome, which is characterized by the functional inactivation of tumor suppressor genes (TSGs) and high tumor heterogeneity, including diverse metabolic adaptations. However, the molecular mechanisms underlying these metabolic alterations remain poorly understood, particularly how TSG inactivation rewires tumor metabolism to drive tumorigenesis and create metabolic dependencies. Through integrated multi-omics analysis, we identify for the first time that NF2 loss of function defines a distinct PM subtype characterized by enhanced de novo pyrimidine synthesis, which NF2-deficient PM cells are critically dependent on for sustained proliferation in vitro and in vivo. Mechanistically, NF2 loss activates YAP, a downstream proto-oncogenic transcriptional coactivator in the Hippo signalling pathway, which in turn upregulates CAD and DHODH, key enzymes in the de novo pyrimidine biosynthesis pathway. Our findings provide novel insights into metabolic reprogramming in PM, revealing de novo pyrimidine synthesis as a synthetic lethal vulnerability in NF2-deficient tumors. This work highlights a potential therapeutic strategy for targeting NF2-deficient mesothelioma through metabolic intervention.

overall_design: RNA-seq profiling of wild-type and NF2-kockout(KO) H2452 mesothelioma cells.

first: Duo

last: Xu


title: Genomic profiles of oxidative stress-induced renal cell carcinomas developed in wild-type and BRCA2+/- SD rats

first: Shinya

last: Toyokuni

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

summary: Fenton reaction-based repeated oxidative stress via ferric nitrilotriacetate (Fe-NTA) causes renal cell carcinoma (RCC) with genetic alterations similar to those in humans. We conducted high-resolution microarray comparative genomic hybridization with Fe-NTA induced RCC obtained from both wild-type and BRCA2+/- rats to evaluate the involvement of BRCA2 haploinsufficiency in carcinogenesis.

overall_design: The carcinogenesis protocol was started with 28 wildtype and 22 BRCA2+/- male Jcl: SD rats. 37 rats developed a renal cell carcinoma in total. Genomes of 8 samples from RCCs for each genotype (16 in total) were profiled on Agilent 180K rat genome CGH microarrays.

first: Yuki

last: Maeda

last: Akatsuka

first: Yashiro

last: Motooka


title: ULK1 as a novel therapeutic target in Myeloproliferative Neoplasms [RNA-Seq]

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

summary: We provide evidence that genetic or pharmacological targeting of ULK1 delays disease progression in Jak2V617F-mutant MPN in vivo models. Mechanistically, the ULK1 anti-neoplastic effects were found to be associated, at least in part, with the transcriptional regulation of genes involved in myeloid malignancies and hematopoietic stem cell differentiation, leading to a reduced number of early-stage erythroid progenitors in both spleen and bone marrow, decreased levels of hemoglobin, hematocrit and red blood cells and spleen size in MPN in vivo models. These findings reveal a novel pro-tumorigenic role for ULK1 downstream of the hyperactive JAK2 signaling characteristic of MPNs and highlight the potential of targeting this kinase as a new therapeutic strategy for MPN patients.

overall_design: RNA-Seq profiling of HEL cells treated for 6 hours with either vehicle-control (DMSO) or with 5µM of the ULK1 inhibitors SBI-0206965 or ULK101.

first: Diana

last: Saleiro

first: Leonidas

last: Platanias


title: Nrf2 regulates activation driven-expansion of CD4+T-cells by differentially modulating glucose and glutamine metabolism [RNA-Seq]

city: Kansas City

first: Kalyani

last: Pyaram

state: KS

address: 2060 W 39th Ave

institute: University of Kansas Medical Center

summary: Upon antigenic stimulation, CD4+T-cells undergo clonal expansion elevating their bioenergetic demands and utilization of nutrients like glucose and glutamine The nuclear factor erythroid 2-related factor2 (Nrf2) is a well-known regulator of oxidative stress, but its involvement in modulating the metabolism of CD4+T-cells remain unexplored. We report that Nrf2 protein levels are temporally regulated in activated CD4+T-cells, with elevated expression during early activation followed by a decline. T-cell-specific constitutive activation of Nrf2 by deletion of its regulator Keap1, enhances early activation and IL-2 secretion, upregulates TCR-signaling, and increases activation-driven expansion of CD4+T-cells. Metabolically, high Nr2 alters glucose metabolism and promotes glutamine metabolism via glutaminolysis to support increased CD4+T-cell proliferation. Mechanistically, elevated Nrf2 activity in activated CD4+T-cells leads to increased chromatin accessibility and proliferation-associated gene expression. In summary, we elucidate the role of Nrf2 beyond traditional antioxidation in modulating the activation-driven expansion of CD4+T-cells by influencing their nutrient metabolism.

overall_design: Mouse naïve CD4+T-cells were activated in vitro in presence of anti-CD3 and anti-CD28 to mimic T-cell activation for 24 and 48h. After 24 and 48 hours, total RNA was extracted using RNeasy Plus Micro kit (Qiagen) and processed at the Genomics Core Facility at the University of Kansas Medical Center. 100ng of the RNA was used to perform Agilent TapeStation QC analysis to verify RNA integrity and generate RNA Integrity number (RIN). Using Nova-Seq 6000 S1 200 cycle reagent kit, 25 million pair-ended reads were recorded for construction of mRNA libraries. For bioinformatic analysis, following quality check through fastQC data were aligned to human reference genome using RSEM (RNA-Seq by Expectation Maximization) resulting in the generation of gene count matrix. Further differential expression analysis was performed between Keap1-KO (KKO) and WT CD4+T-cells for gene ontology (GO) enrichment using ClusterProfiler R-package, to identify significant biological processes, molecular pathways and metabolic pathways associated with the samples. The enrichment results were prioritized based on significance and the top GO terms were visualized using dotplots. Box-plots for genes were also generated using ggplot2 to illustrate the variability of the genes between the 2 groups with mean P-values annotated on each plot, respectively.

first: Aprajita

last: Tripathi

first: Debolina

last: Dasgupta

first: Michael

last: Dahabieh

first: Rachel

last: Griffard-Smith

first: Anil

last: Pant

first: Ashlyn

last: Bugbee

first: Nanda

last: Kumar Yellapu

first: Emily

last: Burt

first: Ben

middle: H

last: Choi

first: Ryan

last: Sheldon

first: Shailendra

last: Giri

first: Devin

last: Koestler

first: Russell

middle: G

last: Jones

first: Viveka

last: Nand Yadav


title: Nrf2 regulates activation driven-expansion of CD4+T-cells by differentially modulating glucose and glutamine metabolism [ATAC-Seq]

overall_design: Stimulated CD4+T-cells from WT and Keap1-KO mice were harvested after 36 h. Cells were transferred to a 15mL or 50mL conical tube and centrifuged at 500 x g for 5 minutes. The media was aspirated, and cells were resuspended in 10mL of pre-warmed growth media, followed by the addition of 1:100 volume of 100x DNase buffer and DNase solution (250mM MgCl2 and 50mM CaCl2 in dH2O). Incubated the cells at 37°C for 30 minutes and centrifuged again at 500 x g for 5 minutes at 4°C, resuspended in 5mL ice-cold PBS (or 500µL for Eppendorf tubes), and 300,000 cells were quantified using a hemocytometer for cryopreservation. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. The cells were then thawed in a 37oC water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif cat# 53150). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the iSeq (Illumina) and sequenced with PE42 sequencing on the NovaSeq 6000 sequencer (Illumina). Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Signal maps and peak locations were used as input data to Active Motif’s proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations, and gene annotations.


title: Effect on gene expression when SMN-1 is deleted in specific tissues (muscle, intestine, neurons, global) in C. elegans

city: Riverside

first: Anusha

last: Iyengar

address: 900 University Ave

department: Biochemistry

institute: University of California, Riverside

summary: SMN is known to be implicated in various RNA metabolism roles.  Deleting smn-1 results in neuromuscular phenotypes and has been shown to primarily affect motor neurons.  However, the role of smn-1 in non-neuronal tissues has yet to be further studied.  Here, we sought to study the effect on gene expression when SMN-1 is deleted in a tissue-specific manner.

overall_design: To investigate the role of SMN-1 in specific tissues, we used FLP/Frt to knockout SMN-1 in muscle (myo-3), intestine (elt-2), pan-neuronal (rgef-1) and global (mex-5).  We then extracted total RNA from whole worms in triplicate and performed RNA-sequencing

first: Adam

last: Norris

first: Lindsey

last: Philips


title: ULK1 as a novel therapeutic target in Myeloproliferative Neoplasms

first: Elizabeth

last: Bartom

overall_design: HEL cells were treated with either vehicle (DMSO), 5mM of ULK101 or 5mM of SBI-0206965 for 4 hours and assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed.

first: Diana

last: Saleiro

first: Leonidas

last: Platanias


title: Effect of LINE1 intervention on vascular calcification （RNA-seq）

city: Shenzhen

first: Ma

last: Jianshuai

address: No. 3025, Shennan Middle Road, Futian District

department: the Eighth Affiliated Hospital

institute: Sun Yat-sen University

summary: In this study, we report the protective effect of LINE1 intervention on vascular calcification. To elucidate the molecular mechanisms underlying the protective role of LINE1 inhibition, we employed RNA sequencing to identify gene expression changes under LINE1 suppression conditions. Our findings provide insights into the pathways involved in modulating vascular calcification and highlight LINE1 as a potential therapeutic target.

overall_design: Human vasculr smooth muscle cells  exposed to Pi for 7 days and transfected with si-scr or si-LINE1, or treated with NRTIs or not. RNA seq was employed to identify downstream targets of LINE1 inhibition in vascular calcification. Gene expression levels were calculated using the Fragment Per Kilobase of Million mapped reads, and differential expression was assessed using the DEGseq package.

first: Jianshuai

last: Ma

first: Dayu

last: He

first: Aoran

last: Huang

first: Ziting

last: Zhou


title: Single-cell RNA-sequencing of undifferentiated pleomorphic sarcoma, myxofibrosarcoma, and liposarcoma samples from patients participating in a clinical trial studying BO-112 plus Nivolumab and hypofractionated pre-operative radiotherapy.

city: Boston

first: Stefano

last: Testa

state: Massachusetts

address: 330 Brookline Avenue

institute: Beth Israel Deaconess Medical Center

summary: Here we analyzed through single cell RNA sequencing multiple samples derived from patients with three different types of soft tissue sarcoma, including liposarcoma, undifferentiated pleomorphic sarcoma, and myxofibrosarcoma, participating in a clinical trial that evaluates the efficacy of intra-tumoral BO-112 injection with or without Nivolumab and pre-operative radiation therapy. The goal of this study is to analyze the changes in the tumor-microenvironment associated with the treatments administered.

overall_design: Single cell RNA-sequencing was performed on 10 soft tissue sarcomas from 9 patients.

first: Kalbasi

last: Anusha

first: Moding

last: Everett

first: Testa

last: Stefano


title: Populus tremula x alba 717-1B4 Laccaria bicolor S238N  ectomycorrhiza

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

institute: INRAE

summary: Illumina  technology was used to generate mRNA profiles of  Populus tremula x alba 717-1B4 control roots and  Laccaria bicolor S238N ectomycorrhiza. Total RNA was extracted, TruSeq mRNA Stranded libraries were constructed and and sequenced  (2 x 150 bp Illumina HiSeq3000) at the Genotoul sequencing facilities (Toulouse, France).  Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the Populus trichocarpa v4.1 primary transcripts available at Phytozome (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1l) using CLC Genomics Workbench v24.

sample_organism:
Laccaria bicolor
Populus tremula x Populus alba

overall_design: mRNA profiles of control roots and Laccaria bicolor S238N-Populus tremula x alba 717-1B4 in vitro ectomycorrhiza after 14 days of contact were generated by Illumina HiSeq 3000 (2x150bp).

first: Joske

last: Ruytinx

first: Francis

last: Martin


title: Utilizing combined spatial transcriptomics to elucidate localized immune responses within human coronary arteries throughout the progression of atherosclerosis [CosMx]

city: Birmingham

first: Claudio

last: Mauro

address: University of Birmingham

department: Institute of Immunology and Immunology

country: United Kingdom

institute: University of Birmingham

summary:
Atherosclerosis is a complex inflammatory disease characterized by the accumulation of lipids and immune cells in the arterial wall, leading to the narrowing and stiffening of blood vessels. The involvement of both innate and adaptive immunity in the pathogenesis of human atherosclerosis is increasingly recognised. However, the spatial organization and specific roles of immune cells during the various stages of disease progression remain poorly understood, underscoring the necessity for additional research to elucidate their functions throughout the disease course. A better understanding of the immune response’s contribution to atherosclerosis progression could unveil novel therapeutic targets to mitigate plaque development and rupture, ultimately reducing the burden of cardiovascular events.
In this study, we utilised NanoString GeoMx® and CosMx™ technologies to analyse serial sections of human coronary arteries from patients with varying degrees of atherosclerotic lesion severity. Our work consists of a series of investigations, and integrated findings from both the GeoMx® and CosMx™ datasets, including pathway analyses, cell typing, and neighbourhood analysis. This workflow underscores the power of combining these spatial transcriptomics platforms to elucidate biological processes at the single-cell level, hence unbiasedly providing molecules and pathways of relevance to aid in the understanding of disease pathogenesis and assessing the opportunity of novel therapies.

overall_design: We analysed in this study a total of 9 coronary artery cross-sections (3 cross-sections from each donor). During CosMx SMI acquistion, we placed a total of 235 Fields Of View (FOVs) in order to sample the full thickness of the coronary arteries, atherosclerotic plaques, and immune cell infiltration areas. All samples were hybridized with a panel of 970 RNA probes, including negative control probes.

first: Joana

last: Campos

first: Jack

last: McMurray

first: Michelangelo

last: Certo

first: Ketaki

last: Hardikar

first: Chris

last: Morse

first: Clare

last: Corfield

first: Melanie

last: Weigand

first: Desley

last: Neil

first: Pasquale

last: Maffia


title: DNA methylation profiles of F2 mice testis of the control group and arsenic group [testis]

city: Tsukuba

first: Takehiro

last: Suzuki

state: Ibaraki

address: 16-2 Onogawa

institute: National Institute for Environmental Studies

type: Methylation profiling by high throughput sequencing

summary: Pregnant C3H mice were given tap water (control group) and tap water containing 85 ppm sodium arsenite from gestational day 8 to 18 (arsenic group), respectively. The DNA methylomes of testis of F2 mice were investigated by RRBS method.

overall_design: Comparative DNA methylation analysis of RRBS data for control group and arsenic group

first: Keiko

last: Nohara


title: Transcriptome analysis uncovers the drought responses of two contrasting sorghum (Sorghum bicolor (L.) Moench) cultivars

city: 太原市

first: Chunlei

last: Zou

state: 山西省

address: 山西省晋中市太谷区铭贤南路1号

institute: 山西农业大学

summary: We analyzed genes from sorghum leaves under water control treatment using high-throughput sequencing technology and bioinformatic approaches to explore the genome-wide quantity of genes and their potential function in the regulation of drought responses.

overall_design: There were two levels of drought treatment: normal water supply (CK) and drought stress (DR), and two sorghum cultivars Sanchisan (SCS) and Jinliang 5 (JL).


title: DNA methylation profiles of F2 mice sperm of the control group and arsenic group [sperm]

summary: Pregnant C3H mice were given tap water (control group) and tap water containing 85 ppm sodium arsenite from gestational day 8 to 18 (arsenic group), respectively. The DNA methylomes of sperm of F2 mice were investigated by RRBS method.


title: Utilizing combined spatial transcriptomics to elucidate localized immune responses within human coronary arteries throughout the progression of atherosclerosis

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: In this study, we performed spatial transcriptomics analysis in a total of 9 cross-sections of human coronary arteries from 3 donors with varying degrees of atherosclerotic lesions.


title: Single-Cell Spatial Transcriptomics Unveils Platelet-Fueled Cycling Macrophages for Kidney Fibrosis

city: Su Zhou

first: Jun

last: Liu

address: No.92, Zhongnan Street, Industrial Park District

institute: Children’s Hospital of Soochow University

summary: With the increasing incidence of kidney diseases, there is an urgent need to develop therapeutic strategies to combat post-injury fibrosis. Immune cells, including platelets, play a pivotal role in this repair process, primarily through their released cytokines. However, the specific role of platelets in kidney injury and subsequent repair remains underexplored. Here, our research underscores the detrimental role of platelets in renal recovery following ischemia/reperfusion injury. We show that depleting platelets accelerates injury resolution and significantly reduces fibrosis. Employing advanced single-cell and spatial transcriptomic techniques, we identify macrophages as the primary mediators modulated by platelet signals. We uncover a novel subset of macrophages, termed "cycling M2", which exhibit an M2 phenotype combined with enhanced proliferative activity. This subset emerges in the injured kidney during the resolution phase and is shaped by platelet-derived thrombospondin 1 (THBS1) signaling, acquiring profibrotic characteristics. Conversely, strategic inhibition of THBS1, achieved through either genetic deletion or pharmacologic suppression, markedly downregulates the cycling M2 macrophage, thereby mitigating fibrotic progression. Overall, our findings highlight the adverse role of platelet THBS1-boosted cycling M2 macrophages in renal injury repair and suggest platelet THBS1 as a promising therapeutic target for alleviating inflammation and kidney fibrosis.

overall_design: To elucidate the comprehensive molecular alterations in kidneys exposed to ischemia-reperfusion (I/R), we generated a mouse model of bilateral I/R-induced acute kidney injury (AKI) and followed by injection of R300, a platelets-depleting antibody. Subsequently, we performed single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (stRNA-seq) on the mouse kidneys of sham and I/R-treated ones.


title: Adverse proinflammatory responses in the kidney after FGF23 administration in murine kidney disease models

city: Bern

first: Matthias

middle: B.

last: Moor

address: Freiburgstrasse

country: Switzerland

institute: University Hospital Bern

summary: FGF23 is a biomarker associated with morbidity and mortality, but controversies remain if a causative link exists between FGF23 excess and adverse renal consequences in chronic kidney disease (CKD).  Here, we investigated renal FGF23 signaling in kidney disease models in mice, with a focus on adverse pro-inflammatory effects assessed in bulk transcriptomes.

overall_design: To investigate renal effects of FGF23 hormone in kidney disease, we assessed bulk transcriptomes in kidney of FGF23 or vehicle treated mice that were i) healthy males or males with anti-glomerular basement membrane disease receiving 6 days of treatments, ii) healthy females or females with adriamycin nephroathy receiving 24h of treatment, and iii) adenine nephropathy mouse kidney tissue receiving ex vivo treatment for 1h in precision-cut kidney slices (PCKS).

middle: B

first: Mikhail

last: Burmakin

first: Jaakko

last: Patrakka

first: Hannes

last: Olauson


title: Astragaloside IV improves autism-like behaviors in BTBR mice by modulating CAMK2N2-dependent OXPHOS and neurotransmission in the mPFC

city: chongqing

first: jiahui

last: shi

address: 30 Gaotanyan Street

department: Department of Military Cognitive Psychology

institute: Third Military Medical University (Army Medical University)

summary: Autism spectrum disorder (ASD) represents a multifaceted set of neurodevelopmental conditions marked by challenges with social interaction and communication, restricted and repetitive behavior. Astragaloside IV (ASIV), a natural compound derived from the traditional Chinese herb Astragalus membranaceus, exhibits robust neuroprotective effects. However, whether ASIV can ameliorate behavioral deficits in ASD remains unknown. The present study found that ASIV treatment significantly reduced social deficits and repetitive behaviors in the BTBR T+tf/J (BTBR) mouse model of autism in a dose-dependent manner. The ASIV treatment normalized the neurotransmitter levels (GABA and glutamate) and their corresponding vesicular transporters (vGAT, vGlut1) in the medial prefrontal cortex (mPFC). Furthermore, whole-cell patch-clamp recordings showed that the imbalance between excitatory and inhibitory synaptic transmission in layer V of mPFC was reversed after ASIV administration. Mechanistically, bulk RNA-seq and PPI network analysis identified the CAMK2N2 as the crucial bridging gene regulating both oxidative phosphorylation and neurotransmission. CAMK2N2 overexpression in the mPFC abolished the beneficial effects of ASIV on autistic symptoms in BTBR mice via the CAMK2/CREB pathway. These findings suggest that ASIV may serve as a promising therapeutic option for ASD and imply that the CAMK2N2/CAMK2/CREB axis could be a potential target for these patients.

overall_design: To investigate  whether drug ASIV has an improving effect on neurotransmitter transmission in the BTBR model of autism, and to explore potential therapeutic mechanisms based on experimental results

first: Mei

last: Chen

first: Jiahui

last: Shi

first: Tianyao

first: Xiaotang

last: Fan


title: Infarcted brain tissues from Hilpda cKO brains at 3 days post-tMCAO

city: Shanghai

first: Weijie

last: Vhen

address: 160, Pujian Road

institute: Renji hospital

summary: Hypoxia-inducible protein 2 (HIG2), encoded by the gene hypoxia-inducible lipid droplet associated (Hilpda) is an important regulator of intracellular lipid metabolism and immune response. We conducted single cell RNA-seq transcriptome analysis of infarcted brain tissues from wild-type (WT) and conditional Hilpda knockout (cKO) mice at 3 days post-stroke to study the funtion of Hilpda in myeloid cells.

overall_design: Infarcted brain tissues were dissected from the WT or Hilpda cKO brains at 3 days post-tMCAO.

first: Peiying

last: Li


title: Spatial joint profiling of DNA methylome and transcriptome in tissues

city: Philadelphia

first: Hongxiang

last: Fu

state: PA

address: 3501 Civic Center Blvd

institute: University of Pennsylvania

summary: We introduce a high-resolution, genome-wide co-mapping technology that spatially resolves DNA methylation and transcriptome profiles simultaneously. This method combines microfluidic deterministic barcoding strategy to analyze DNA methylation and gene expression on the same tissue section at the cellular level.

overall_design: Gene expression and DNA methylation spatial profiling through high throughput sequencing of four mouse C57 embryos at E11 & E13 and one P21 juvenile mouse brain tissue.

first: Chin

middle: N

last: Lee

first: Angelysia

last: Cardilla

first: Wanding

last: Zhou

first: Yanxiang

last: Deng


first: Hiromichi

last: Ebi

institute: Aichi Cancer Center Research Institute

summary: THP-1 derived macrophage samples with phagocytosis and non-phagocytosis of tumor cells (duplicates for each condition).

overall_design: THP-1 derived M0 macrophages were co-culture with NCI-H358 for 24 hours and sorted into phagocytic macrophages and non-phagocytic macrophages.

first: Kentaro

last: Hirade

first: Rui

last: Yamaguchi


title: Three FT-like proteins controls internode elongation during flowering via the gene PINE1, a chromatin remodeler transcription factor responsible for the mainteinance of unelongated internodes.

city: Milano

first: Vittoria

last: Brambilla

state: Milano

address: Via Celoria, 26

department: Agricoltural and environmental sciences

institute: University of MIlan

summary: RNA-seq performed on rice stem. The comparison is made to discover differentially expressed genes between Nipponbare wild-type unelongated stems (samples were taken 20 days after germination, when internodes are still compressed at the base of the plant) and pine1 knockout mutants, which show internode elongation even though floral induction didn't occur.

overall_design: three Nipponbare wild-type and three pine1-1a stem sample were prepared. Samples consisted of around 1cm of the basal portion of a plant, at 20 days after germination. Such portion contains the stem and the shoot apical meristem. 8 plants were taken for each sample.

first: Giulio

last: Vicentini


title: ATAC-seq of  NCI-H358 cells treated with KRAS G12C inhibitor sotorasib

city: Nagoya

address: 1-1, Kanokoden, Chikusa-ku

summary: ATAC-seq of  sotorasib-resistant NCI-H358 cells treated with sotorasib

overall_design: NCI-H358 cells were treated with DMSO or 1uM sotorasib for 72 hour

first: Takaomi

last: Sanda


title: Human neuron subtype programming through combinatorial patterning with scSeq readouts

city: Basel

first: Jasper

last: Janssens

address: Mattenstrasse 26

department: DBSSE

institute: ETH Zurich

summary: iPSCs were induced into neuronal fate using either NGN2 or ACL1/DLX2 under different conditions. Single-cell RNA-sequencing was used to measure diversity of acquired neuronal fates. Single-cell multiome (RNA+ATAC) was performed on patterned iPSCs.

overall_design: TF expression was induced by Dox, patterning was acquired using different morphogen concentrations of Retinoic Acid (RA), FGF8, XAV, CHIR, BMP4, SHH and CycA. Prepatterned samples were also exposed to different media.

first: Hsiu-Chuan

last: Lin

first: Gray

last: Camp

first: Barbara

last: Treutlein


title: Cell Density Regulates Neural Stem Cells of Cellular Contact and Differentiation in 3D Hydrogel Culture System

city: Changsha

first: Chaoyong

last: He

address: Tianma road

institute: Hunan university

summary: Neural Stem Cells (NSCs) of biological behaviors are frequently regulated by the three-dimensional (3D) niches that they located in. The impact of cell density cue inside niche on cellular outcomes are usually underestimated and understudied. In this study, a facile NSCs of 3D culture system was developed using collagen self-assembled fibril hydrogel. We used RNA sequencing and molecular biology technologies to investigate the NSCs of cell contacts and differentiations in developed 3D hydrogel culture system with low (0.75 million/mL), medium (1.5 million/mL), and high (3 million/mL) cell packing density. Compared with low cell density system, cytoskeletal spreading, gap junction, and tight junction mediated cell contacts were significantly improved in high cell density culture. Moreover, high cell density increased NSCs differentiation into immature (Tuj1) neuron, while there is no discrepancy of NSCs differentiation into astrocytes in different cell densities of 3D culturing system. This study provides new understanding in the regulation of 3D cultured NSCs behaviors through niche of cell density cue.

first: Yuyun

last: Liang

first: Xiaonan

last: Wang

first: Jing

last: Yang

first: Ziyan

last: Chen

first: Hexu

last: Zhang

first: Cheng

last: Zhao

first: Liyang

last: Shi


title: Single-nuclear RNA sequencing of imiquimod-applied psoriasis-like mouse skin samples

city: Xiamen

first: Lingjuan

address: Xiangan South Street

institute: Xiamen University

summary: Here we performed single-nuclei RNAseq of the imiquimod-induced psoriasis-like mouse skin samples. This data will be useful supplementary data to the single-cell RNAseq data (GSE238086) of the imiquimod-treated mouse skin samples. Because  large cells, such adipocytes, are often lost through enzymatic digestion in scRNA-seq. SnRNAseq can maximally capture and characterize the immune responses of these large cells.

overall_design: Skin biopsies were collected from adult mice (C57BL/6, 2 month, female) topically applied with imiquimod for 5 days. Nuclear suspensions were extracted from skin biopsies, and nuclei were purified by FACS sorting prior to being subjected to 10x Genomics single nuclei cDNA library prep and sequenced on an Illumina Novaseq6000 platform.

first: Ling-juan

first: Rundong

last: Wu


title: Multi-omics Prediction from High-content Cellular Imaging with Deep Learning

city: Stevenage

first: Carl

last: Fishwick

address: Gunnels Wood Road

institute: GSK

summary: High-content cellular imaging, transcriptomics, and proteomics data provide rich and complementary views on the molecular layers of biology that influence cellular states and function. However, the biological determinants through which changes in multi-omics measurements influence cellular morphology have not yet been systematically explored, and the degree to which cell imaging could potentially enable the prediction of multi-omics directly from cell imaging data is therefore currently unclear. Here, we address the question of whether it is possible to predict bulk multi-omics measurements directly from cell images using Image2Omics -- a deep learning approach that predicts multi-omics in a cell population directly from high-content images stained with multiplexed fluorescent dyes. We perform an experimental evaluation in gene-edited macrophages derived from human induced pluripotent stem cell (hiPSC) under multiple stimulation conditions and demonstrate that Image2Omics achieves significantly better performance in predicting transcriptomics and proteomics measurements directly from cell images than predictors based on the mean observed training set abundance. We observed significant predictability of abundances for 5903 (22.43%; 95% CI: 8.77%, 38.88%) and 5819 (22.11%; 95% CI: 10.40%, 38.08%) transcripts out of 26137 in M1 and M2-stimulated macrophages respectively and for 1933 (38.77%; 95% CI: 36.94%, 39.85%) and 2055 (41.22%; 95% CI: 39.31%, 42.42%) proteins out of 4986 in M1 and M2-stimulated macrophages respectively. Our results show that some transcript and protein abundances are predictable from cell imaging and that cell imaging may potentially, in some settings and depending on the mechanisms of interest and desired performance threshold, even be a scalable and resource-efficient substitute for multi-omics measurements.

overall_design: For transcriptomic profiling we utilised a multiplexed 3' RNA-seq approach based on DRUG-seq (https://doi.org/10.1038/s41467-018-06500-x). 384-well plates of iPSC-monocyte precursors were subjected to genetic perturbation using CRISPR-Cas9 to knock out (KO) single genes per well or control conditions without CRISPR or non-targeting control gRNAs. Cells were then exposed to macrophage differentaiation stimuli before being stimulated with  M0/M1/M2 skewing conditions with the exception of column 13 which was always M0 to provide a baseline control  in each plate. Replicate groups in the supplementary csv files denominate triplicates of CRISPR gene targets per plate, positive control=drive stimulation phenotype, negative control= attenuate stimulation phenotype, neutral=no change in phenotype. Each 384-well plate results in 4x pairs of R1 and R2 reads due to amplification of the cDNA library with 4x pairs of primers.

first: Rahil

last: Mehrizi

first: Arash

last: Mehrjou

first: Maryana

last: Alegro

first: Yi

first: Benedetta

last: Carbone

first: Johanna

last: Vappiani

last: Bi

first: Siobhan

last: Sandford

first: Hakan

last: Keles

first: Marcus

last: Bantscheff

first: Cuong

last: Nguyen

first: Patrick

last: Schwab


title: Phosphate depletion in mammalian cells

city: Salt Lake City

first: Jordan

middle: A

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

institute: University of Utah

summary: Comparison of different cell lines membrane potential responded or not to -Pi (HEK293 and A375 has increased mp in -Pi, but not U2OS)

overall_design: HEK293, A375, U2Os depleted of phosphate for 1 day

first: Yeyun

last: Ouyang

first: Nikolett

last: Sziszkosz

first: Jared

last: Rutter


title: Decoding the protein with CD44 of serum-starved and normal nucleus pulposus cells

city: Chongqing

first: Jianmin

last: Li

address: shapingba xinqiaozhengjie 183

institute: Army Medical University

summary: In our experiment, we found that there was a nuclear translocation of CD44 in the nucleus pulposus cells after serum starvation. In order to further clarify the role of CD44 molecules after nuclear translocation, we analyzed the CD44 binding regions and related genes between serum starved nucleus pulposus cells and normal nucleus pulposus cells by chromatin immunoprecipitation technique.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for two groups : serum starvation group and control group cultured in a 10% serum medium.

first: Bo

last: Huang


title: Human brain organoids: a new model to study Cryptococcus neoformans neurotropism

status: Public on Jul 14 2025

city: Boston

first: Jatin

last: Vyas

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

summary: With the rise in immunocompromised individuals and patients with immune-related comorbidities such as COVID-19, the rate of fungal infections is growing. This increase, along with the current plateau in anti-fungal drug development, has made understanding the pathogenesis and dissemination of these organisms more pertinent than ever. The mouse model of fungal infection, while informative on a basic science level, has severe limitations in terms of translation to the human disease. Here we present data supporting the implementation of the human cerebral organoid model, which is generated from human embryonic stem cells and accurately recapitulates relevant brain cell types and structures, to study fungal infection and dissemination to the central nervous system (CNS). This approach provides direct insight into the relevant pathogenesis of specific fungal organisms in human tissues where in vivo models are impossible. With this model system we assessed the specific brain tropisms and cellular effects of fungal pathogens that are known to cross the blood brain barrier such as Cryptococcus neoformans. We determined the effects this fungal pathogen has on the overall gross morphology, cellular architecture, and cytokine release of these model organoids. Furthermore, we demonstrated that C. neoformans can penetrate and invade the organoid tissue and remain present throughout the course of infection. These results demonstrate the utility of this new model to the field and highlight the potential for this system to elucidate fungal pathogenesis to new therapeutic strategies to prevent and treat the terminal stages of fungal diseases such as cryptococcal meningitis.

overall_design: RNA-seq profiling of human cerebral organoids 3- and 7-days post infection with either C. neoformans, C. auris, S. cerevisiae, as well as an uninfected control

first: Alfred

last: Harding

first: Lee

last: Gehrke

first: Hannah

last: Brown Harding


title: MYDGF Governs Endothelial Homeostasis in Hypertension

city: Ethnicity

first: Xiaohan

last: Liu

address: 44#, Whenhua Xi Road

institute: Shandong University

summary: Myeloid-derived growth factor (MYDGF) demonstrates well-established cardioprotective properties. However, its endothelial-specific functions and potential therapeutic applications in hypertension remain largely unexplored. Through comparative RNA sequencing analysis of Ang II-treated endothelial cells with versus without MYDGF overexpression, we identified genes associated with endothelial functional modulation.

overall_design: The gene expression of 5 samples from  48 h Ang II induced AD-MYDGF endothelial cell line was compared to 5  samples from 48 h Ang II  induced AD-NC samples by RNA sequencing.

first: Min

first: Huiying

last: Jin


title: Protein arginine methyltransferase 7 regulates the cell cycle and promotes the progression of prostate cancer

city: Wuxi

first: Hongyuan

last: Wan

state: Jiangsu

address: Wuxi Medical College, Jiangnan University, Wuxi 214122, Jiangsu Province, China

summary: Background: Prostate cancer (PCa) is the second most common cancer in males worldwide. Arginine methyltransferase 7 (PRMT7) expression is associated with tumor proliferation, as it can drive tumor cell growth and promote its invasiveness in several types of cancer. However, its mechanism in PCa remains unknown. In this study, we investigated the function and related mechanism of PRMT7 in PCa cells. Method: The relationship between PRMT7 and PCa was analyzed using the TCGA online database. We used tissue chip techniques method to identify the clinical relevance of PRMT7 expression. PRMT7 expression levels in PCa tissues and cells were verified using RT-qPCR. Cell cycle, migration, proliferation, and apoptosis of PC3 and DU145 cells were observed using flow cytometry, CCK8, wound healing, plate cloning, and cell invasion assays. Gene set enrichment analysis and chip expression profiles were used to predict the potential signaling pathway involved in the action of PRMT7 in PCa. Results: First, TCGA, tissue microarray analysis, and RT-qPCR revealed that PRMT7 expression was increased in PCa tissues and cells. Furthermore, siRNA-mediated PRMT7 knockdown led to a significant reduction in the proliferation of cells, increased cell apoptosis, affected the cell cycle, and decreased cell migration and invasion. Additionally, PRMT7 regulated the functions of YY1, TP53, CCND2, CDK6, and RB1 in PCa. Conclusion: PRMT7 may promote proliferation, migration, and metastasis in PCa cells by regulating the activity of YY1,TP53,CCND2,CDK6, and RB1 in the cell cycle signaling pathway.

overall_design: RNA sequencing analysis was performed on PC3 cells with siPRMT7 and siCtrl knockdown.

first: Hangshen

last: Zhou

first: Jiandong

last: Gui

first: Dongjie

last: Yang

first: Lijie

last: Zhu

first: Ninghan

last: Feng

first: Yuanyuan

last: Mi


city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: The A3 adenosine receptor (AR) is an important inflammatory and immunological target. However, the underlying mecha-nisms are not fully understood. Here, we report the gene regulation in HL-60 cells treated acutely with highly selective A3AR agonist MRS5698, positive allosteric modulator (PAM) LUF6000, or both. Both pro- and anti-inflammatory genes, such  as  IL-1a,  IL-1β,  and  NFκBIZ,  are  significantly  upregulated.  During  our  observations,  LUF6000  alone  produced  a lesser effect, while the MRS5698 + LUF6000 group demonstrated generally greater effects than MRS5698 alone, consis-tent with allosteric enhancement. The number of genes up- and down-regulated are similar. Pathway analysis highlighted the  critical  involvement  of  signaling  molecules,  including  IL-6  and  IL-17.  Important  upstream  regulators  include  IL-1a, IL-1β, TNF-α, NF-κB, etc. PPAR, which modulates eicosanoid metabolism, was highly downregulated by the A3AR ago-nist. Considering previous pharmacological results and mathematical modeling, LUF6000’s small enhancement of genetic upregulation suggested that MRS5698 is a nearly full agonist, which we demonstrated in both cAMP and calcium assays. The smaller effect of LUF6000 on MRS5698 in comparison to its effect on Cl-IB-MECA was shown in both HL-60 cells endogenously  expressing  the  human  (h)  A3AR  and  in  recombinant  hA3AR-expressing  CHO  cells,  consistent  with  its HL-60 cell genetic regulation patterns. In summary, by using both selective agonists and PAM, we identified genes that are closely relevant to immunity and inflammation to be regulated by A3AR in differentiated HL-60 cells, a cell model of neutrophil function. In addition, we demonstrated the previously uncharacterized allosteric signaling-enhancing effect of LUF6000 in cells endogenously expressing the hA3AR.     (PDF) Genetic and functional modulation by agonist MRS5698 and allosteric enhancer LUF6000 at the native A3 adenosine receptor in HL-60 cells. Available from: https://www.researchgate.net/publication/378553124_Genetic_and_functional_modulation_by_agonist_MRS5698_and_allosteric_enhancer_LUF6000_at_the_native_A3_adenosine_receptor_in_HL-60_cells#fullTextFileContent [accessed Jul 07 2025].

overall_design: The genes expressed in four groups were compared with the (control group,G1, G2 and G!+G2) in three replications per gp

first: Zhanguo

last: Gao

first: Weiping

first: Ray

first: Kenneth

last: Jacobson


title: RNA-Seq of MCF7 treated with Cannabis extract CANN14 for 18 hrs

city: Haifa

first: Elazar

last: Besser

address: Kiryat Hatechnion

country: Israel

institute: Technion

summary: RNA sequencing of differentially expressed genes from MCF7 cells treated with a Cannabis extract or DMSO control. Hypothesis was ESR1 would be downregulated and genes related to estrogen signaling would be affected. We explored the gene expression profile of each sample to identify significant changes in gene expression between treatment and control groups. The differential expression analysis was conducted using 'DESeq2' R package.

overall_design: Analysis of up- and down-regulated genes in RNA-seq data of samples (in triplicates) from MCF7 cells following treatment with Cannabis extract CANN14 relative to DMSO control.

first: David

last: Meiri


title: RNA-seq and small RNA-seq data in boot mutant ovaries

city: Tokyo

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

institute: Tokyo Metropolitan Institute of Gerontology

summary: PIWI-interacting RNAs (piRNAs) silence transposons to maintain germline genome integrity in animal gonad. Most of piRNAs arise from piRNA clusters. In Drosophila, a Heterochromatin protein family member Rhino defines the germline piRNA clusters, so-called dual-strand clusters, and elicits the transcription. However, how the clusters are transcribed is largely unknown. Here, we characterized CG13741/Bootlegger (Boot) as an essential nuclear piRNA factor for piRNA production from the dual-strand clusters. Herein Boot is referred as Egret (Egt). Boot is indispensable for suppressing the splicing of the precursors through regulating Cuff function and furthermore for the recruitment of an RNA export factor Hel25E/UAP56 to the transcription sites in the nucleus. Our findings indicate that Boot acts in the transcription and the export of the precursors from dual-strand piRNA clusters.

overall_design: Genome-wide changes in RNA and small RNA expression levels in the boot mutant ovaries.


title: The quorum sensing molecule 2'-aminoacetophenone activates plant cell-surface immune receptors

city: Singpore

first: danxia

last: he

address: Jurong West St 61

country: Singapore

institute: School of biological sciences, Nanyang techolo

summary: Quorum sensing (QS) enhances bacterial pathogenesis. How plants perceive QS signals remains elusive. Here, we report that Arabidopsis thaliana perceives 2'-aminoacetophenone (2’-AA), a QS-regulated volatile compound emitted from Pseudomonas aeruginosa, through cell-surface pattern recognition receptor (PRR) complexes that require BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE (BAK1). 2’-AA activates PRR-mediated immunity and enhances plant resistance to Pseudomonas pathogens. The 2’-AA-activated immunity displayed structural specificity of the elicitor and genetic specificity of the PRR complexes. 2’-AA induces in vivo protein interactions between BAK1 and its co-functioning PPRs, meanwhile the plant transcriptome responded to 2’-AA similarly as to flg22, a bacterial immunogenic elicitor that activates BAK1-dependent immunity. Hence bacterial QS signals can be sensed by plant cell-surface immune receptors.

overall_design: Examination of 3 different samples of Col-0, each of samples contains 3 biological replicates. They are named as mock, flg22 and 2'-AA respectively..

first: Danxia

last: He

first: Miao

last: Wang


title: S100A8/A9 perturbation in bone marrow blunts antitumor immunity by promoting protumorigenic myelopoiesis in mouse models

city: Shapingba

first: Wen

last: Luo

state: Chongqing

address: No. 83, Xinqiao  street

institute: Xinqiao Hospital, Third Military Medical University

summary: S100A8/A9 plays a critical role in the formation of an immunosuppressive tumor microenvironment. Therefore, it is important to identify inhibitors targeting S100A8/A9 to enhance antitumor immunity. However, systemic targeting S100A8/A9 in clinical trials has shown minimal effects. Understanding the reasons underlying their underperformance is important for developing drugs targeting S100A8/A9 that could effectively reverse the immunosuppressive tumor microenvironment. In this study, using hematopoietic system-specific conditional knockout mice in heterotopic models of lung and colon cancer and systemic pharmacological interference, we demonstrated that S100A8/A9 perturbation in the hematopoietic system accelerates tumor progression by attenuating T cell-mediated antitumor immunity. Mechanistically, S100A8/9 perturbation triggered myeloid-biased differentiation in the bone marrow by promoting the production of abnormal granulocyte-monocyte progenitors. The local release of S100A8/A9 inhibitors using a tumor-targeted drug delivery system exhibited antitumor potential by avoiding myelopoiesis-promoting effects. These findings reveal a mechanism underlying the limited efficacy of systemic S100A8/A9 inhibition and propose a targeted strategy to enhance antitumor effects.

overall_design: This upload contains two single-cell sequencing files, namely the LLC tumor CD45+ cells, and the tumor-free bone marrow CD45+ cells, both from S100a8-cKO and WT mice.


title: Single-cell transcriptomic and 3D genome atlas of leukemia cells from patients with acute myeloid leukemia (AML)

city: Beijing

first: Menghan

last: Liu

address: Yiheyuan Road

institute: Peking University

summary: We applied a single-cell multi-omics assay named “Hi-C and RNA-seq employed simultaneously” (HiRES) to simultaneously profile chromatin structure and transcriptome within the same cell. In our study, this assay was conducted on CD34⁺CD117⁺CD38⁻ hematopoietic stem and progenitor cells (HSPCs) isolated from bone marrow aspirates of acute myeloid leukemia (AML) patients. This dataset represents the first application of single-cell HiRES in primary AML samples, providing paired 3D genome and gene expression information at single-cell resolution.

overall_design:
HiRES：Mononuclear cells were extracted from acute myeloid leukemia patients. Target cells were stained with CD34 and CD117 antibodies and isolated by Fluorescence-activated cell sorting (FACS). Final libraries were prepared strictly follwing HiRES protocol.

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

first: Yujing

last: Deng


title: Single cell ATAC-seq analysis of H3.3K4M WT and Hom brain samples (10X Genomics Multiome)

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

institute: NICHD

summary: Methylation of lysine4 on Histone H3 (H3K4) is require for promoter and enhancer activation at gene loci and presents distinct methylation patterns over developmental gene clusters. Disrupting in the writer, eraser and reader of H3K4 methylation is associated with developmental syndromes. However, less studies focus on the role of H3K4 methylation in development of interneuron and hypothalamus. Here, we explore the role of H3K4 methylation in the medial ganglionic eminence (MGE) derive interneuron and hypothalamus by directly mutating the lysine 4 on H3.3 to the methionine in mice.

overall_design: The Nkx2.1-Cre;H3.3K4M;Sun1-sfGFP mice were generated to harvest all Nkx2.1-lineage GFP+ nuclei via flow cytometry.  Single nuclei from embryonic and adult samples from each genotype were prepared using 10X Genomics Multiome pipeline. Samples: E13.5 MGE and hypothalamus as well as P60 cortex and hypothalamus of H3.3K4M WT and Hom. In addition, one replicate for male and female for each condition.

middle: J