title: Isolation, Phylogenetics, and Characterization of a New PDCoV Strain that Affects Cellular Gene Expression in Human Cells

city: Jinzhong

first: Bo

last: Yang

state: Shanxi

address: No.1 Mingxian South Road，Taigu District, Jinzhong City, Shanxi Province

institute: Shanxi Agricultural University

summary: Porcine deltacoronavirus (PDCoV) is an enteropathogenic coronavirus that causes acute diarrhea, vomiting, dehydration, and even death in piglets, resulting in serious economic losses to the pork industry worldwide. PDCoV has received much attention owing to its broad host range, including humans, posing a potential threat to public health. However, the prevalence, characteristics, and host cellular gene expression of PDCoV remain poorly understood. In this study, a new PDCoV strain (CHN/SX-Y/2023, GenBank number PQ373831) was successfully isolated, identified, and subjected to phylogenetic tree and transcriptome analyses in human hepatoma (Huh7) cells following PDCoV infection. The results showed that the CHN/SX-Y/2023 strain belongs to the Chinese lineage and causes cytopathic effects in the cells of various species. Based on transcriptome analysis, 1799 differentially expressed genes (DEGs) were upregulated and 771 were downregulated during PDCoV infection. Among the upregulated genes, FCGR1A, VSIG1, TNFRSF9, and PLCXD3 are associated with immunity, inflammation, and lipid catabolism. Moreover, Kyoto Encyclopedia of Genes and Genomes analysis revealed that the upregulated DEGs were significantly enriched in the MAPK, TNF, and NF-κB signaling pathways and viral protein interactions with cytokines and cytokine receptors. Protein-protein interaction networks showed that the upregulated genes CXCL8, DUSP1, PTGS2, and IL15 were associated with inflammation and immunity. In addition, the protein levels of ACSL4, LC3-II, and p-IRF3 increased, suggesting that PDCoV infection in Huh7 cells induces an intrinsic immune response, cellular autophagy, and ferroptosis. Collectively, our findings provide new insights into the characteristics and mechanisms of PDCoV infection.

overall_design: RNA-seq profilling of Huh 7 cells and PDCOV-infected Huh 7 cells at 24 hpi

first: Xiaozhu

first: Hanwei

last: Yin

first: Mengyuan

last: Liu

first: Xuemei

last: Wang

first: Tao

last: Song

first: Aiai

first: Yibo

last: Xi

first: Ting

first: Zilong

first: Wei

first: Sheng

last: Niu

first: Farwa

last: Zainab

first: Chenyang

first: Ding

first: Haidong


title: Subtyping Burkitt Lymphoma by DNA Methylation

status: Public on Apr 16 2025

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University and Ulm University Medical Center

summary: Burkitt lymphoma (BL) is an aggressive germinal center B-cell-derived malignancy. Historically, sporadic, endemic, and immunodeficiency-associated epidemiological variants were distinguished which differ in the frequency of Epstein-Barr virus (EBV) association. Aiming at identifying subgroups based on DNA methylation patterns we here profiled 96 primary BL cases, 17 BL cell lines and 6 lymphoblastoid cell lines using Illumina BeadChip arrays. DNA methylation clustered the cases into each two subgroups according to EBV status, with each showing two underlying subgroups (EBV-positive: BL-mC1, BL-mC2 and EBV-negative: BL-mC3, BL-mC4). The subgroups BL-mC1/2 enriched for EBV-positive cases showed increased DNA methylation, epigenetic age and in part increased proliferation history compared to BL-mC3/4. CpGs hypermethylated in EBV-positive BLs were enriched for polycomb repressive complex 2 marks, while the CpGs hypomethylated in EBV-negative BLs were linked to B-cell receptor signaling. EBV-associated hypermethylation affected regulatory regions of genes frequently mutated in BL (e.g. CCND3, TP53), and impacted superenhancers, suggesting that hypermethylation may compensate for the lower mutation burden of oncogenic drivers in EBV-positive BLs. Though minor, but significant differences were also observed between EBV-positive endemic and sporadic cases (e.g. at the SOX11 and RUNX1 loci), our findings suggest that EBV status, rather than epidemiological variants, drive the DNA methylation-based subgrouping of BL.

overall_design: We collected 113 samples from patients with Burkitt lymphoma (sBL: n=70; eBL: n=20), Burkitt lymphoma-derived cell lines (n=17) and lymphoblastoid cell lines (n=6). The samples were analyzed using the Infinium HumanMethylation450 BeadChip array.

first: Reiner

last: Siebert


title: Spatiotemporal Proteomic and Transcriptomic Landscape of DAT+ Dopaminergic Neurons Development and Function

city: Shanghai

first: Heyu

last: Zhao

address: No.131 Dongan Road

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary: Dopaminergic (DA) neurons marked by the dopamine transporter (DAT) have multiple physiological functions and are involved in the regulation of mental and neurological diseases, prompting in-depth studies into their development and functions. This research explores the spatiotemporal proteomic and transcriptomic changes in DAT+ DA neurons within key brain regions involved in DA signaling—the nucleus accumbens (NAc), substantia nigra (SNc), and ventral tegmental area (VTA). Utilizing cutting-edge multi-omics techniques, such as ultrasensitive trace sample proteomics and SMART_x0002_seq2 for transcriptomics, we examine the DA neuronal system at critical postnatal milestones: postnatal day 7 (P7), postnatal day 30 (P30), and postnatal day 60 (P60). The study reveals unique molecular profiles within DA neuron populations, showcasing their varied functional roles and developmental progression. Immunofluorescence mapping illustrates these molecular distributions, validating the quantitative data and highlighting the dynamic molecular structure of DA neurons. Our findings notably highlight a marked increase over time in Aldh1a1 expression, an essential enzyme for retinoic acid production, suggesting its evolving role in neuronal development and specific functions. This comprehensive analysis offers a profound molecular perspective on DAT+ DA neuron development, enhancing our understanding of their functional diversity and potential relevance in DA-related diseases.

overall_design: we outlined a stepwise approach for multi-omics profiling of brain dopaminergic neuron development. We used mice at different ages to represent various developmental stages: P7, representing infancy (n=5); P30, juvenile phase (n=5); and P60, adulthood (n=5). We focused on three specific brain regions rich in DAT+ neurons within these developmental groups: the NAc, SNc, and VTA. After dissecting and isolating the brain region tissues (Fig. 1C), we dissociated the tissue samples to obtain single-cell suspensions and then performed flow cytometry to isolate the DAT+ neuron populations.Once isolated, the DAT+ neurons from each region and developmental stage were simultaneously analyzed through proteomic and transcriptomic techniques

first: Peipei

last: Chen

first: Xia

last: Gao

first: Zhili

last: Huang

first: Pengyuan

first: Huali

last: Shen


title: A Dual-Mechanism Luminescent Antibiotic for Bacterial Infection Identification and Eradication

city: Singapore

first: Guobin

last: Qi

address: 5A Engineering Drive 1

country: Singapore

institute: NUS，Chemical & Biomolecular Engineering

summary: Due to the rapid emergence of antibiotic-resistant bacteria, there is a growing need to discover antibacterial agents. Herein, we design and synthesize a compound of TPA2PyBu that kills both Gram-negative and Gram-positive bacteria with an undetectably low drug resistance. Comprehensive analyses reveal that the antimicrobial activity of TPA2PyBu proceeds via a unique dual mechanism by damaging bacterial membrane integrity and inducing DNA aggregation. TPA2PyBu could provide imaging specificity that differentiates bacterial infection from inflammation and cancer. Importantly, high in vivo treatment efficacy of TPA2PyBu was achieved in methicillin-resistant S. aureus infection mouse models. This promising antimicrobial agent suggests that combining multiple mechanisms of action into a single molecule can be an effective approach to address challenging bacterial infections.

overall_design: The RNA-seq profiling of Staphylococcus aureus was conducted to analyze the gene expression patterns before and after treatment with the compound TPA2PyBu.

first: Xianglong

first: Hao

last: Li

first: Yunyun

last: Qian

first: Can

first: Jiahao

last: Zhuang

first: Leilei

last: Shi

first: Bin


title: Differentially Expressed MiRNAs Associated with Circulating Tumor Cell Status in Metastatic Colorectal Cancer

city: Bursa

first: Dilek

last: Pirim

address: Görükle

country: Turkey

institute: Bursa Uludag University

summary: Colorectal cancer (CRC) ranks as the third most prevalent cancer worldwide. Recent studies suggest the promising potential of microRNAs (miRNA) in predicting the status of circulating tumor cells (CTC), and their combined analyses could pave the way for significant advancements in assessing the risk of metastatic cancer. Here, we investigate the circulating miRNA signatures associated with CTC status in metastatic CRC (mCRC). The CTC status was assessed using AdnaTest ColonCancer technology, which detects tumor cells using an immunomagnetic approach and characterizes them based on colon-specific surface markers. The miRNA profiles were then analyzed using the Agilent miRNA microarray platform in 8 CTC-positive, 8 CTC-negative, and eight healthy individuals. The functional implications of dysregulated miRNAs and their interactions with target mRNAs, TFs, and lncRNAs were determined through a comprehensive in silico analysis. We identified two groups of downregulated miRNAs associated with CTC status/metastasis and multiple candidate biomarkers in suggested miRNA regulatory networks. Four miRNAs (miR-181c-5p, miR-199a-5p, miR-500b-5p, miR-769-5p) were prioritized as findings were consistent with their tissue expressions in TCGA datasets. Our findings reveal candidate biomarkers with potential for CTC status and mCRC-associated CTC detection, providing insights for new translational medicine applications in mCRC management.

overall_design: Microarray analysis of miRNA expression level is performed on 24 whole blood samples from 16 mCRC patients (8 CTC positive mCRC and 8 CTC negative mCRC) and 8 matching healthy individuals.


title: AML induces TTCR-C4 NK-like transcriptional  skewing associated with low persistence and dysfunction

city: Seattle

first: Aude

last: Chapuis

state: WA

address: 1100 Fairview Ave

country: USA

institute: Fred Hutchinson Cancer Center

summary:
This dataset includes single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (bulk RNA-seq) data generated to investigate T cell responses in the context of acute myeloid leukemia (AML) and WT1-specific TCR-T cell therapy.

The scRNA-seq dataset comprises peripheral blood (PB) and bone marrow (BM) samples from AML patients treated with WT1-specific TCR-engineered T cells (TCR-T). We specifically profiled both endogenous CD8⁺ T cells and TCR-T cells to characterize their transcriptional states and assess the impact of AML on T cell differentiation and function. In-depth analysis of samples from a patient with a durable clinical response provided insights into the transcriptional profiles of TCR-T cells over time, including after Azacitidine treatment.

The bulk RNA-seq dataset was generated using an in vitro model of AML-induced T cell dysfunction. CD8⁺ transgenic WT1-specific T cells (TTCR37-45) recognizing the HLA-A0201-restricted WT137-45 epitope were repeatedly challenged with WT1-expressing HLA-A0201-transduced K562 AML cells. Loss of tumor control by day 13 was associated with a transition from a naïve/stem-like transcriptional state to one enriched in effector, activation/exhaustion, and NK-like/Temra gene signatures. By day 23, activation/exhaustion markers declined while NK-like/Temra-associated genes persisted or increased, highlighting a phenotypic shift in dysfunctional T cells.

overall_design:
Single-cell RNA-sequencing: Following TCR-T cell infusion we performed scRNAseq on patients peripheral blood (5 patients, 13 samples) and bone marrow (1 patient, 2 samples).

Bulk RNA-sequencing: RNA-sequencing of sorted TTCR37-45 at day 0, day 13 and day 23

first: Francesco

last: Mazziotta

first: Laure

last: Martin

first: Valentin

last: Voillet


title: Effect of BCL7 gene mutation and BRM014 treatment on DNA accessibility in K-562 cells

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal of this study was to determine the effect of muations in the three BCL7 genes (BCL7A, BCL7B and BCL7C) on DNA accessibility in K-562 cells.

overall_design: K-562 cells were edited using CRISPR/Cas9 to introduce mutations in the genes BCL7A, BCL7B and BCL7C. Parental cells were used as controls. Cells were treated with BRG1/BRM ATPase inhibitor BRM014 or left untreated. Cells were harvested for ATAC-sequencing.

first: Stephanie

first: Elisa

last: Bergamin


title: Microarray data from simple and effective differentiation-switching model using long-term-expanded prostate primary cells

city: Nagakute

first: Akihito

last: Inoko

state: Aichi

address: 1-1 Yazakokarimata

department: Pathology

country: Japan

institute: Aichi Medical University School of Medicine

summary: We developed a long-term expansion method for primary prostate cells using a set of compounds. Moreover, we established a simple and effective epithelial differentiation method by simply removing the compounds. As a benefit of this convenient differentiation-switching technique, we obtained microarray data comparing each differentiation state and confirmed many genes that  determine differentiation states at the cellular level. This culturing method can be useful in future epithelial cell biology, physiology, and regeneration research.

overall_design: Microarray data sets were obtained from primary human prostate epithelial cells (PrEC, donor1) cultivated in YDAC-containing F medium and in YDAC removed F medium for 2 days (Pre and 48H, respectively)

first: Inoko

last: Akihito

first: Soga

last: Norihito

first: Suzuki

last: Minako


title: RBM24 regulates apoptosis rates by modulating global transcriptome profile in CAL27 cells [iRIP-seq]

city: Zhengzhou

first: Wang

last: Shuyuan

state: Hennan

address: 100 Science Avenue, High-tech Zone, Zhengzhou, China

department: Academy of Medical Sciences,

institute: Zhengzhou University

summary: RNA binding proteins (RBPs) are key factors regulating post-transcriptional events. Categorized as RBPs, RBM24 expression levels have been shown to be a prognosis-related pivotal gene in oral squamous cell carcinoma. We analyzed the binding targets and regulated post-transcriptional events of RBM24 in RBM24-overexpressing cell lines and controls using iRIP-seq and RNA-seq. RBM24-overexpressing cells showed significant changes in gene expression, which are involved in biological pathways related to apoptosis and immune inflammation. RBM24-regulated genes that undergo alternative splicing are primarily engaged in biological processes related to DNA damage repair and RNA metabolism. More notably, we found that RBM24 binds to lncRNAs in addition to pre-mRNAs. These results indicated that RBM24 could play a key role in cancer progression by finding clinical therapeutic targets for Oral squamous cell carcinoma.

overall_design: Cal27 cells with excessively expressed RBM24 to filtrate different expression genes and analyze for RBM24-regulated AS by RNA-seq. Next,iRlP-seq was employed to examine RBM25-binding sites.Then we used RT-qPCR to validate specific genes modulated by RBM24.

first: Zhenjie

last: Gao

first: Shuyuan

last: Wang

first: Shumin

last: Peng

first: Jingjing

last: Sun


title: RBM24 regulates apoptosis rates by modulating global transcriptome profile in CAL27 cells [RNA-seq]


title: Topical TLR7 agonist and radiotherapy in patients with metastatic breast cancer

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

summary: This study explores the safety and efficacy of combining topical Imiquimod (IMQ), a TLR-7 agonist, with local radiotherapy (RT) for metastatic breast cancer. The phase I/II clinical trial (NCT01421017) aimed to assess systemic and local anti-tumor responses using immune-related response criteria (irRC). Patients were divided into three cohorts: (1) IMQ + RT + cyclophosphamide, (2) IMQ + RT, and (3) RT + cyclophosphamide (control). Cutaneous metastases were treated with IMQ+RT (area A) or IMQ alone (area B). Tumor biopsies were obtained at baseline and after treatment for gene expression profiling. Results demonstrated safety and promising systemic anti-tumor responses, with transcriptional analyses revealing a T-helper 1 immune orientation and DNA-repair gene downregulation associated with complete responses in IMQ+RT-treated areas.

overall_design:
The study involved longitudinal transcriptional analysis of tumor biopsies from 24 patients treated with topical IMQ (cohorts 1 and 2) and 7 control patients treated with RT alone (cohort 3). Tumor samples were collected at baseline, week 2, and week 3 post-treatment. Gene expression profiling was performed using Affymetrix microarrays to identify immune activation and DNA repair signatures associated with treatment response. A total of 84 samples were processed for transcriptional analyses.

Submitter states: raw data not available for this series due to file loss.

first: Sylvia

last: Adams

first: Sandra

last: Demaria

first: Ena

first: Davide

last: Bedognetti

first: Silvia

last: Formenti


title: Inhibiting CXCR4 Reduces Immunosuppressive Effects of Myeloid cells in Breast Cancer Immunotherapy

city: ann arbor

first: gary

last: luker

state: MI

address: 109 zina pitcher place

department: radiology

institute: university of michigan

summary: The goal of this experiment is to understand effects of combining CXCR4 inhibitor balixafortide with an anti-PD-1 immune checkpoint inhibitor on response to therapy in a mouse model of triple-negative breast cancer.

overall_design: There are triplcate samples of isolated cancer and tumor-infilatrating immune cells from mouse breast cancer E0771 tumors.

first: Gary

last: Luker

first: Aasia

last: Rehman

first: Nicholass

last: Ciavattone

first: Kathryn


title: RNA-seq analysis of resistant ER+ breast cancer cell lines

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

institute: University of Colorado Denver Anschutz Medical Campus

summary: This study aims to identify transcriptional differences between parental ER+ breast cancer cell lines and those that are resistant to several common endocrine therapies, including tamoxifen, fulvestrant, and aromatase inhibition. To mimic aromatase inhibitors, cells were grown in estrogen withdrawl (EWD) conditions, using phenol red free media and charcoal-stripped serum. Cells were kept in their respective treatments until RNA was procured.

overall_design: Long-term treatments of T47D or UCD4 cells with 1 uM tamoxifen, 100 nM fulvestrant, or estrogen withdrawl using stripped serum and phenol red free media.

first: Kiran

middle: V

last: Paul

first: Duncan

last: Riley

first: Peter

last: Kabos

first: Carol

middle: A

last: Sartorius


title: Transcriptomic characterization of CD206- and CD206+ macrophages in human pancreatic islets and exocrine tissue

city: Uppsala

first: Anders

middle: Roger

last: Hedin

state: Uppland

address: Dag Hammarskjölds väg 20.

department: Clinical immunology

country: Sweden

institute: Uppsala University

summary: Macrophages reside in all organs and participate in homeostatic- and immune regulative processes. Little is known about pancreatic macrophage gene expression. CD206 is an endocytic receptor with prior use in subclassifying macrophages. In the present study, global gene expression was characterized in human pancreatic macrophage subpopulations. Flow cytometry was used to sort CD206-    and CD206+ macrophages separately from pancreatic islets and exocrine tissue to high purity. RNA-seq generated transcriptomic profiles were then analyzed. Comparing CD206- with CD206+ macrophages, CD206- showed enrichment in proliferation and nucleic acid processing, glycolysis, pro-inflammatory and SPP1-associated gene sets while CD206+ showed enrichment in complement-, IL-10 and IL-2RA immune regulation, as well as scavenging-related gene sets. Two sets involved in immune regulation were enriched in islet CD206-, while various sets including some proinflammatory sets were enriched in exocrine CD206- macrophages. Fewer differences were found between CD206+ macrophages, with enrichment in two IL2-RA related gene sets in islets and eight gene sets in exocrine samples. Comparing macrophages between individuals with normoglycemia, elevated HbA1c or type 2 diabetes, only a few diverse differentially expressed genes were identified. This work characterizes global gene expression and identifies differences between CD206- and CD206+ macrophage populations within the human pancreas.

overall_design: To investigate pancreatic macrophages, fresh pancreases from donors without diabetes(ND), Type 1 Diabetes(T1D), Type 2 Diabetes(T2D) and Intermediade glycemic status(IGM) were dispersed and sorted into exocrine and pancreatic fraction.  Flow cytometry was used to sort macrophages from other cell types; Macrophages were then sorted into  CD206-    and CD206+ macrophages separately from pancreatic islets and exocrine tissue to high purity. RNA-seq generated transcriptomic profiles were then analyzed

first: Alexander

last: Jonsson

first: Olle

last: Korsgren


title: Disruption of the Integrator complex triggers the Integrated Stress Response through formation of double-stranded RNA [48h_INTS8_RNAseq]

city: Boston

first: Apoorva

last: Baluapuri

state: MA

address: 45 Shattuck St.

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Acute loss of INT induces transcription factors that initiate stress-responses like the Integrated Stress Response (ISR). Inefficient elongation upon INT loss enables termination in introns and dsRNA formation. dsRNA is recognized by PKR, which persistently activates the ISR in samples from patients with INT mutations

first: Nicole

middle: C

last: Zhao

first: Kai-Lieh

last: Huang

first: Ryan

middle: J

last: Marina

first: Maria

middle: E

last: Amodeo

first: Chad

middle: B

last: Stein

first: Eric

last: Wagner

first: Karen

last: Adelman


title: Transcriptome Analysis of Corneal Endothelial Cells in Col8a2Q455K/Q455K/Tcf4+/- compared to Col8a2Q455K/Q455K FECD Mouse Model

city: Kyotanabe

first: Taisuke

last: Numao

state: Kyoto

department: Department of Biomedical Engineering, Faculty of Life and Medical Sciences

institute: Doshisha University

summary: This study investigated transcriptional changes in corneal endothelial cells with and without Tcf4 heterozygous knockout in Col8a2Q455K/Q455K FECD mouse model. RNA-seq analysis was performed on corneal endothelial cells isolated from Col8a2Q455K/Q455K and Col8a2Q455K/Q455K/Tcf4+/- mice. Principal component analysis and hierarchical clustering demonstrated distinct gene expression patterns between the two groups, identifying 1,053 differentially expressed genes. These genes showed significant changes in pathways related to ion transport and TNF signaling.

overall_design:
To investigate the effects of Tcf4 heterozygous knockout on corneal endothelial cells in FECD model mice, we examined corneal endothelium from Col8a2Q455K/Q455K mice, an established FECD model, and Col8a2Q455K/Q455K/Tcf4+/- mice, in which Tcf4 was heterozygously knocked out in the FECD model mice.
We then performed gene expression profiling analysis using RNA-seq data obtained from corneal endothelial cells of Col8a2Q455K/Q455K (n=3) and Col8a2Q455K/Q455K/Tcf4+/- (n=3) mice.
Comparative gene expression profiling analysis of RNA-seq data between Col8a2Q455K/Q455K mice and Col8a2Q455K/Q455K/Tcf4+/- mice revealed distinct transcriptional profiles.

first: Suguru

last: Ito

first: Yuki

last: Oyama

first: Taichi

last: Yuasa

first: Koki

last: Amano

first: Kotaro

last: Onishi

first: Ayaka

last: Izumi

first: Albert

middle: S

last: Jun

first: Masahito

last: Ikawa

first: Noriko

last: Koizumi

first: Naoki

last: Okumura


title: Gene expression profiling of colorectal cancer liver metastases from liver transplantation.

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

summary: We have performed gene expression profiling by exon-resolution microarrays of liver metastases from patients treated by liver transplantation for unresectable metastatic colorectal cancer.

overall_design: This series consists of tumor tissue samples from the liver explants of 48 patients with metastatic colorectal cancer. All samples were analyzed on Affymetrix Human Transcriptome 2.0 Arrays. A subset of the samples (n=14) were excluded from analyses due to no/low tumor cell content.

first: Seyed

middle: H

last: Moosavi

first: Ragnhild

last: Lothe


title: Single-cell temporal characterization of RSV infection

city: San Francisco

first: Sara

last: Sunshine

address: 1700 4th Street

institute: University of California, San Francisco

summary: Respiratory syncytial virus (RSV) is a prevalent pathogen globally, can cause severe disease in older adults, and remains the leading cause of bronchiolitis and pneumonia in the United States for children during their first year of life. Despite its prevalence worldwide, RSV specific pharmacologic interventions remain unavailable for most infected patients. Although vaccines are available for a subset of adults, further investigation of the molecular interactions between RSV and the host remains essential to understanding this prolific pathogen. To aid our understanding of the host response in both RSV infected cells, and uninfected bystanders, we utilized single-cell RNA sequencing.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We infected A549 cells with Respiratory Syncytial Virus (MOI 0.3) and performed single-cell RNA sequencing at 0, 4, 8 and 12 hours post-infection.

first: Joseph

middle: L

last: DeRisi


title: Multiple Phenotypes and Epigenetic Profiles in a Three-Generation Family History with GATA2 Deficiency [WES]

city: L'Hospitalet de Llobregat

first: Alessandra

last: Giorgetti

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: PCMRC

country: Spain

institute: IDIBELL

summary: Germline heterozygous GATA2 mutations cause GATA2 deficiency, a complex disorder characterized by bone marrow failure, immunodeficiency, and a high risk of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). The disease evolves variably among patients, leading to anxiety for families. Due to phenotypic diversity and clinical overlap, timely diagnosis is often challenging. GATA2 carriers exhibit variable expressivity, with some developing early-onset MDS while others remain asymptomatic, suggesting that genetic and epigenetic factors influence disease progression. While advances in diagnostics through whole-exome sequencing (WES) and whole genome sequencing (WGS) have been made, few epigenetic studies have focused on GATA-related MDS. We present a familial case of four GATA2 carriers, two of whom are asymptomatic and two have developed MDS. Notably, we conducted a longitudinal epigenome analysis of one patient, tracking progression from asymptomatic to MDS, providing key insights with potential clinical applications

overall_design: Whole exome sequencing (WES) of peripheral blood mononuclear cells DNA of patients was performed to identify somatic mutations

first: Damia

last: Romero-Moya

first: Joan

last: Pera


title: Multiple Phenotypes and Epigenetic Profiles in a Three-Generation Family History with GATA2 Deficiency

type: Methylation profiling by genome tiling array

overall_design: We analyzed the genomic methylation profiles of Peripheral Blood mononuclear cells. This analysis was performed using the Infinium Human Methylation EPIC 850K platform (Illumina). This work include 6 samples from patients and 3 healthy donors.


title: Single-Cell transcriptional landscape of lung cells from PCV2d-infected mice

city: xianyang

first: chen

middle: yun

last: long

state: shaanxi

address: yangling

institute: Northwest A & F University

summary: Porcine Circovirus (PCV2) infection is prevalent in pig farming and causes significant economic losses. In recent years, the PCV2d subtype has become the main prevalent genotype in China. Compared with other subtypes, it exhibits stronger virulence, leading to more severe viremia and organ damage. Therefore, studying the biological characteristics of the PCV2d subtype holds great significance. We established a PCV2d infection model using BALB/c mice and employed single-cell RNA sequencing (scRNA-seq) to systematically analyze the transcriptome of 10 cell types in the lung tissue of infected mice. Notably, we developed a valuable marker gene catalog for these cell types. Compared to uninfected mice, PCV2d infection induced extensive viral replication and immunosuppressive responses in most cell types. More importantly, we suggest that monocyte macrophages with high levels of viral replication, proinflammatory cytokines, and various cell population interactions occurring through CD40_CD40L and CXCL14_CXCR4, as well as predominantly mediating antigen presentation and processing pathways in vivo to participate in the immune response, may contribute to PCV2driven inflammatory lung injury. Our data uncovered a complex yet unique immune response scenario in the lung tissue of mice post PCV2d infection and deciphered the potential mechanisms underlying PCV2d-driven inflammatory responses in mice. Furthermore, this study provides a rich database for the molecular basis of different cell types' responses to PCV2d infection.

overall_design: We divided 6-week-old mice into two groups of three mice each, male and female randomized to PCV2d attack and mock control. After the thirtieth day, mouse lung tissues were taken and mixed and prepared to send samples for sequencing.

first: Chen

middle: Y

last: Long

first: Fan

last: Gan

first: Yang

last: Bin

middle: X

last: Yi

first: Lou

last: Jiao

first: Ma

middle: Z

last: Yuan

first: Xu

last: Mei

first: Wang

last: Yan

first: Zhang

last: Qiang


title: PLK1-mediated PDCD4 degradation confers resistance to enzalutamide in prostate cancer

city: lexington

first: Jia

last: Peng

address: 760 press ave

institute: University of Kentucky

summary: Enzalutamide, a second-generation androgen receptor inhibitor, is utilized for treating patients with metastatic castration-resistant prostate cancer (mCRPC). However, acquired resistance to enzalutamide presents a significant clinical challenge, necessitating novel strategies for overcoming this resistance. In this study, we demonstrated that PLK1 phosphorylates PDCD4 at serine 239 (S239), leading to PDCD4 degradation by enhancing its binding to βTRCP2, thereby promoting enzalutamide resistance both in vitro and in vivo. Mechanistically, phosphorylation of PDCD4 at S239 upregulates the expression of UDP-glucuronosyltransferase 2B15 (UGT2B15) through activation of the c-MYC-Hedgehog axis. This pathway circumvents the androgen receptor, thereby reducing cellular sensitivity to enzalutamide treatment. Inhibition of UGT2B15 enhances enzalutamide-induced cell apoptosis and growth arrest in a manner dependent on PDCD4-S239 phosphorylation. Our findings provide a insight into the role of PLK1-mediated PDCD4 phosphorylation in enzalutamide resistance and suggest a potential therapeutic strategy to overcome resistance in prostate cancer.

overall_design: To determine the underlying mechanisms of PLK1-mediated PDCD4 phosphorylation for enzalutamide resistance, PDCD4 was knocked down by shRNA in 22RV1 cells, followed by rescue of wild-type PDCD4, PDCD4-S239A variant, and PDCD4-S239D variant. Cells were sent for RNA-seq, the gene set enrichment analysis was performed to determine the difference between wild-type PDCD4 and PDCD4 variants (S239A and S239D).


title: The adaptation of key bacterial vaginosis-associated bacteria to a medium simulating vaginal tract secretions: a transcriptomic analysis

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

summary: Bacterial vaginosis (BV), the most common vaginal infection among women worldwide, is characterized by an imbalance in the vaginal microbiota with a reduction of protective Lactobacillus species and overgrowth of facultative and strictly anaerobic bacteria. Although the development of a polymicrobial biofilm on the vaginal epithelium is a hallmark of BV, interactions between key BV-associated bacteria (BVAB) [i.e. Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia] present in the biofilm remain largely unexplored. In this study, we aimed to analyze the transcriptome of triple-species biofilms growing in a medium simulating vaginal tract secretions (mGTS) compared to a rich medium, New York City III (NYCIII). As such, triple-species biofilms formed by G. vaginalis, F. vaginae, and P. bivia were grown in either NYCIII or mGTS in anaerobic conditions. After that, RNA was extracted and cDNA libraries were constructed and sequenced. We first characterized the biofilm composition in both media by qPCR and observed that G. vaginalis was the most prevalent species in both conditions. RNA-sequencing data analysis revealed a total of 964, 596, and 656 differentially expressed genes in G. vaginalis, F. vaginae, and P. bivia, respectively, when comparing the transcriptome of biofilms in mGTS versus NYCIII. We identified 927 upregulated and 37 downregulated genes for G. vaginalis, 492 upregulated and 104 downregulated for F. vaginae, and 166 upregulated and 490 downregulated for P. bivia. Gene ontology enrichment showed that metabolic and biosynthetic processes were common within upregulated genes for G. vaginalis, while downregulated genes were associated with transmembrane transporters. For F. vaginae, transmembrane transporters were identified among upregulated genes, while downregulated genes were related to metabolism and cellular process, in which several KEGG pathways linked to metabolism were recognized. For P. bivia, upregulated genes were associated with transmembrane processes while downregulated genes were associated with metabolic processes; KEGG pathways were also identified. This work highlighted the adaptation of 3 key BVAB growing on a medium that simulates in vivo conditions and will contribute to a better understanding of bacterial interactions that are important in the pathogenesis of incident BV.

sample_organism:
Gardnerella vaginalis
Prevotella bivia
Fannyhessea vaginae

overall_design: To analyze transcriptomic alterations on three bacterial vaginosis-associated bacteria, namely Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia when growing in a medium simulating vaginal tract secretions, compared to a rich medium.

first: Lúcia

last: Sousa

first: Angela

first: Vânia

last: Pinheiro

first: Christina

last: Muzny

first: Nuno

last: Cerca


title: Blood Gene Expression Profiling in Patients with Idiosyncratic Drug-Induced Liver Injury

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: Accurate diagnosis, assessment, and prognosis of idiosyncratic drug-induced liver injury (IDILI) is problematic, in part due to the shortcomings of traditional biomarkers. Studies in rodents and healthy volunteers have supported that RNA transcript changes in whole blood may address some of these shortcomings.  In this study, we conducted RNA-Seq analysis on peripheral blood samples collected from 55 patients with acute IDILI and 17 patients with liver injuries not attributed to IDILI. Three  differentially expressed genes (DEGs; CFD, SQLE, and INKA1) were identified as significantly associated with IDILI vs other liver injuries. No DEGs were identified comparing IDILI patients to the 5 patients with autoimmune hepatitis, supporting common underlying mechanisms. Two genes (VMO1 and EFNA1) were significantly associated with hepatocellular injury compared to mixed/cholestatic injury. When patients with severe vs milder IDILI were compared, we identified over 500 DEGs.  The top pathways identified  from these DEGs  had in common down regulation of multiple T-cell specific genes.  Further analyses confirmed that these changes could largely be accounted for by a fall in the concentration of circulating T-cells during severe DILI, perhaps due to exhaustion or sequestration of these cells in the liver. Exploration of DEGs specific for the individual causal agents was largely unsuccessful, but isoniazid-induced IDILI demonstrated 25 DEGs compared to other non-isoniazid IDILI cases.  Finally, among the 14 IDILI patients that had hepatocellular jaundice (i.e. Hy’s Law ases), we identified 39 DEGs between the 4 patients with a fatal or liver transplantation outcomes compared to those that recovered.  These findings suggest the potential for blood-based transcriptomic biomarkers to aid in the diagnosis and prognostic stratification of IDILI.

overall_design:
To explore genes differentially expressed in IDILI,  whole blood was collected into PAXgene tubes from individuals with suspected DILI who were enrolled into the DILIN registry within 2 weeks of the recognition of their liver injury and while injury was ongoing.
Transcript profiling and pathway analysis was performed using data obtained from RNA-seq was conducted in RNA isolated from whole blood of 55 indiviauls with IDILI and 17 individuals who had liver injury not caused by IDILI
To explore reduction gene related to T cell biology, CIBERSORTx analysis using a built-in immune cell training dataset, was conducted.

first: Church

last: Rachel

first: Watkins

last: Paul


title: Characterization of POP mixture redistribution and identification of their molecular signature in xenografted fat mice

city: Paris

first: Min Ji

last: Kim

address: 45 rue des saints-Pères

country: France

institute: Inserm 1124

summary: Persistent organic pollutants (POPs) are associated with many adverse health effects in humans, including cancers, immune, reproductive, neurological disorders and metabolic diseases. These chemicals are known to accumulate in fatty tissues, from which they can be released in other tissue compartments of living organisms, in particular, upon weight loss. This dynamic distribution of POPs remains, however poorly investigated. In this study, a xenografted POP-contaminated adipose tissue (AT) model was used to assess 1) their concentrations in the ATs, the liver and the brain and 2) their associated effects by transcriptomics, metabolomics and lipidomics approaches. In the ATs, the liver and the brain of mice grafted with POP-contaminated fat pad, most of POPs were detected 3 days and 21 days after the graft with the highest concentrations in the ATs and the lowest concentrations in the brain. Conversely, per- and polyfluoroalkyl substances presented a distinct profile as they persist in the liver but not in the ATs or in the brain. In the AT of POP-exposed mice, the most dysregulated pathways were related to mitochondrial functions, endobiotic (carbohydrate, lipid, amino acid) and xenobiotic metabolism and inflammatory response. In the liver of grafted mice, many pathways related to mitochondrial functions and metabolism were dysregulated. These results support that realistic mixture of POPs that accumulate in AT and liver induces a systemic metabolic dysfunction which may represent the mechanisms by which the POPs can promote metabolic diseases such as obesity, type 2 diabetes and cardiovascular diseases.

overall_design: To assess the toxic effects of a POP mixture released from an internal source, we used a a mouse model of grafted adipose tissue contaminated by a mixture of 10 POPs and determined their signature by RNA sequencing in the adipose tissue and the liver.


title: Genome-wide DNA methylation profile of blood samples from patients with major depressive disorder.

city: Shinjuku-ku, Tokyo

first: Yae

last: Kanai

address: 35, Shinano-machi

institute: Keio University School of Medicine

summary: In the present study, to identify DNA methylation alterations correlating to the heterogeneity of symptoms of major depressive disorder, 283 blood samples were subjected to genome-wide DNA methylation analysis using the latest high-density bead array.

overall_design: The aim of this study was to clarify the significance of DNA methylation profile of the blood samples in the heterogeneity of symptoms of major depressive disorder (MDD). Genome-wide DNA methylation analysis was performed using the Infinium MethylationEPIC BeadChip in 283 blood samples. Patients with MDD were recruited at the National Center of Neurology and Psychiatry Hospital, Tokyo, Japan, and control participants were recruited from the community through advertisements in a free local magazine and our website announcement, between May 2006 and April 2019. Participants were excluded if they had a history of central nervous system disease, severe head injury, or substance abuse.

first: Eri

last: Arai

first: Yukiko

last: Nagao

first: Mao

last: Fujimoto

first: Hiroshi

last: Kunugi

first: Kotaro

last: Hattori


title: The effect 10 mM MgCl2 on gene expression during osteogenic differentiation of hPDLSCs

city: Bangkok

first: Supanat

last: Lumbikanada

address: Thanon Henri Dunant

country: Thailand

institute: Chulalongkorn University

summary: hPDLSCs showed the decreasing of osteogenic differentiaion following with 10 mM MgCl2. The RNA sequencing of treated group reported the various of signaling pathway related to the chemokine and cellular calcium.

overall_design: hPDLSCs were treated with osteogenic differentiaion medium supplemeted with or without 10 mM MgCl2 and RNA were collected

last: Lumbikananda

first: Worachat

last: Namangkalakul

first: Thanaphum

last: Osathanon


title: CRISPR targeting of FOXL2 c.402C>G mutation reduces malignant phenotype

city: Majadahonda

first: Maria

last: Barrero

state: Madrid

address: Crta. Majadahonda-Pozuelo KM 2.2

institute: ISCIII

summary: FOXL2 is a transcription factor essential for sex determination and ovary development and maintenance. Mutations in this gene are implicated in syndromes involving premature ovarian failure and granulosa cell tumors (GCTs). This rare cancer accounts for less than 5% of diagnosed ovarian cancers and is causally associated with the FOXL2 c.402C>G, p.C134W mutation in 97% of the adult cases (AGCTs). In this study, we employed CRISPR technology to specifically eliminate the FOXL2 c.402C>G mutation in granulosa tumor cells. Our results show that this Cas9-mediated strategy selectively targets the mutation without affecting the wild-type allele. Granulosa cells lacking the FOXL2 c.402C>G exhibit a reduced malignant phenotype, with significant changes in cell proliferation, invasion, and cell death. Furthermore, these modified cells are more susceptible to Dasatinib and Ketoconazole. Transcriptomic and proteomic analyses reveal that CRISPR-modified granulosa tumor cells shift their expression profiles towards a wild-type like phenotype. Additionally, this altered expression signature has led to the identification of new compounds with antiproliferative and pro-apoptotic effects on granulosa tumor cells. Our findings demonstrate the potential of CRISPR technology for the specific targeting and elimination of a mutation causing granulosa cell tumors, highlighting its therapeutic promise for treating this rare ovarian cancer.

overall_design: To explore the potential therapeutic effect of eliminating  the FOXL2 C134W mutation in the human ovarian granulosa cell line KGN we eliminated the mutant allele using CRISPR technology and compared the transcriptomic profile of parental and CRISPR-Cas9 edited clones.

first: Ignacio

last: Perez de Castro

first: Sandra

last: Amarilla-Quintana

first: Isabel

last: Cuesta


title: Selective NSD2 Inhibition Reveals an Epigenetic Dependency of KRAS-Driven Cancers

city: Houston

first: Pawel

last: Mazur

state: Texas

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

summary: NSD2, through generation of the epigenetic modification histone H3 di-methylated at lysine 36 (H3K36me2), is a candidate convergent downstream effector of oncogenic KRAS-signaling. However, whether NSD2 targeting represents a therapeutic vulnerability of KRAS-driven cancers is unknown. Here, we characterize a first-in-class, clinical grade small molecule catalytic NSD2 inhibitor (NSD2i) series and find pharmacological targeting of NSD2 constitutes an epigenetic dependency with broad therapeutic efficacy in KRAS-driven pre-clinical cancer models. NSD2i inhibits NSD2 potently, with single digit nM IC50 values, and shows high selectively for NSD2 versus NSD1, NSD3, and other similar enzymes. Structural analyses reveal the molecular basis of NSD2i specificity for NSD2, which includes S-adenosylmethionine (SAM)-competitive binding and catalytic disruption via a dual-channel obstruction mechanism. Proteo-epigenomic and single cell strategies in pancreatic ductal adenocarcinoma (PDAC) and lung adenocarcinoma (LUAD) samples support a model in which durable NSD2i exposure reverses H3K36me2-driven pathologic chromatin plasticity, re-establishing silencing at H3K27me3-legacy loci to curtail KRAS-regulated and oncogenic-associated gene expression programs. Accordingly, NSD2i treatment inhibits PDAC and LUAD cell viability and patient-derived xenograft tumor growth. Further, NSD2 inhibition, which is well tolerated in vivo, is equally effective as KRAS inhibition (sotorasib) treatment in prolonging survival in advanced stage autochthonous KRASG12C-driven PDAC and LUAD mouse tumor models. Moreover, in these models, NSD2 inhibition and sotorasib co-treatment synergize to confer sustained survival with extensive tumor nodule regression and elimination. Together, our work uncovers targeting of the NSD2-H3K36me2 axis as an actionable vulnerability in KRAS-driven cancers and provides a mechanistic rationale for testing NSD2i-KRAS inhibition combination therapies in the clinic.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on fresh, micro-dissected lung adenocarcinoma (LUAD) tumor samples from KRAS(G12C); p53(flox) mice treated with selective catalytic NSD2 inhibitor (NSD2i).

first: Xiaoyin

last: Lu

middle: K


title: The oligosaccharyltransferase complex is an essential component of multiple myeloma plasma cells that regulates bortezomib resistance

city: Cluj-Napoca

first: Oana

last: Tudoran

address: Str. Republicii 34-36

department: Department of Genetics

country: Romania

institute: The Oncology Institute “Prof. Dr. Ion Chiricuță” in Cluj-Napoca

summary: Multiple myeloma (MM) is an incurable malignancy characterized by mutated plasma cell clonal expansion in the bone marrow, leading to severe clinical symptoms. Thus, identifying new therapeutic targets for MM is crucial. We identified the oligosaccharyltransferase (OST) complex as a novel vulnerability in MM cells. Elevated expression of this complex is associated with relapsed, high-risk MM, and poor prognosis. Disrupting the OST complex suppressed MM cell growth, inducing cell cycle arrest and apoptosis. Combined inhibition with bortezomib synergistically eliminated MM cells in vitro and in vivo, via suppressing genes related to bortezomib-resistant phenotypes. Mechanistically, OST complex disruption downregulated pathological gene signatures (NF-kB signaling, mTORC1 pathway, glycolysis, MYC targets, and cell cycle), induced TRAIL-mediated apoptosis and inflammatory pathways. MYC translation was robustly suppressed upon inhibiting the OST complex. Collectively, the OST complex presents a novel target for MM treatment, and combining its inhibition with bortezomib offers a promising approach for relapsed MM patients.

overall_design: MM1S cells were cultured and treated with NGI-1 and then harvested after 0, 2, 3 and 5 days. 200ng total RNA was extracted then sent for sequencing.

first: Hong

middle: P

last: Nguyen

first: Enze

last: Liu

first: Brian

last: Walker

first: Ngoc

middle: T

last: Tran


title: The role of microfibril-associated glycoprotein-1 in experimental liver fibrosis [bulk RNA-seq]

city: Beijing

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

institute: Capital Medical University

summary: Microfibril-associated glycoprotein-1 (MAGP-1), a critical component of extracellular matrix (ECM) microfibrils, plays a pivotal role in liver fibrosis, although its precise function in this process remains elusive. Our research underscores that MAGP-1 (Mfap2) is predominantly expressed in activated hepatic stellate cells (HSCs) and exhibits heightened levels in advanced liver fibrosis. Deletion of MAGP-1 showcased limited impact on overall collagen deposition following CCl4 stimulation. However, it notably heightened intrahepatic inflammatory infiltration within lobular regions, hastened ECM stabilization through the upregulation of insoluble matrisome constituents within the ECM, and triggered focal adhesion (FA) signaling in HSCs, hindering the regression of liver fibrosis upon cessation of CCl4 treatment.

overall_design: Bulk RNA-seq analysis was conducted on frozen livers from CCl4-treated Mfap2+/+ and Mfap2-/- mice (8W, n=4 for each group of mice) and from Mfap2+/+ and Mfap2-/- mice  undergoing fibrosis reversal (4W, n=4 for each group of mice) . Additionally, scRNA-seq was performed on liver NPCs isolated from CCl4-injected Mfap2+/+ and Mfap2-/- mice (8 weeks).

last: You

first: Wen

last: Zhang

first: Wenyu

last: Wu


title: The role of microfibril-associated glycoprotein-1 in experimental liver fibrosis [scRNA-seq]

overall_design: scRNA-seq was performed on liver nonparenchymal cells  isolated from CCl4-injected Mfap2+/+ and Mfap2-/- mice (8 weeks).


title: Enabling adenosine signaling to promote aged fracture healing

first: Shyni

last: Varghese

state: NC

address: 203 Research Drive

department: Department of Biomedical Engineering

institute: Duke University

summary: Despite its regenerative capacity, the healing potential of bone tissue declines with aging. With the increase in global aging population, bone fractures pose a tremendous burden to the healthcare system. Therapeutic interventions that circumvent age-associated impairments and promote bone tissue regeneration are attractive options for geriatric fracture repair. We and others have demonstrated the role of extracellular adenosine in bone homeostasis and regeneration. Herein, we examined the changes in extracellular adenosine with aging and the potential of local delivery of adenosine to promote fracture healing using aged mice as a model system. Extracellular adenosine level was significantly lower in aged bone tissue compared to those from young mice. Concomitantly, the ecto-5′-nucleotidase CD73 expression was also found to be lower in the aged bone tissue.  Local delivery of adenosine using injectable, in situ curing microgel delivery units yielded a pro-regenerative environment and promoted fracture healing in aged mice. This study offers new insights into age-related physiological changes in adenosine levels and demonstrates the therapeutic potential of adenosine supplementation to circumvent the compromised healing of geriatric fractures.

overall_design: Calluses from mice treated with either 1) adenosine-containing microgel or 2) empty microgel were harvested seven days after treatment and analyzed using scRNA-seq

first: Hunter

last: Newman

first: Yu-Ru

middle: V

last: Shih

first: Jiaul

last: Hoque

first: Yuze

last: Zeng

first: Naveen

middle: R

last: Natesh

first: Gavin

last: Gonzales

first: Wendi

last: Guo

first: Vijitha

last: Puviindran

first: Colleen

first: Benjamin

last: Alman


title: Lipid droplet efferocytosis attenuates proinflammatory signaling in macrophages via TREM2 and MS4A7-dependent mechanisms

city: Ann Arbor

first: Linkang

last: Zhou

state: Michigan

address: Mary Sue Coleman Hall 210 Washtenaw Avenue

institute: University of Michigan

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is characterized by the injury of steatotic hepatocytes, triggering the release of endogenous danger-associated molecular patterns (DAMP). The nature of the danger signals and their role in engaging the innate immune cells like macrophage remain to be fully delineated. Recent work demonstrated that exposed lipid droplets (LD) serve as a disease-associated danger signal that promotes monocyte infiltration and its maturation into TREM2+ macrophages within the MASH liver. In this study, we explored the nature of LD-mediated danger signaling and its impact on inflammatory signaling in macrophages. We found that efferocytosis of LDs triggers a global transcriptional response and dampens pro-inflammatory signaling in cultured macrophages. LD treatments attenuated proinflammatory signaling and NLRP3 inflammasome activation via mechanisms independent of lipid hydrolysis by macrophages. TREM2 is required for the attenuation of inflammatory response, whereas MS4A7 downregulation contributes to the dampening effects of LD treatments. These results underscore the dual role of LD-mediating danger signaling in MASH liver by promoting monocyte infiltration and TREM2+ macrophage induction and dampening pro-inflammatory response in macrophages.

overall_design: For bulk RNA sequencing, BMDMs were treated with LD for 3 hrs, Subsequently, the LD was removed and the cells were cultured for additional 8 hrs before being harvested. RNA extraction was performed using a kit (Invitrogen, Cat: 12183025) and the samples were sent for sequencing.


title: Disruption of the Integrator complex triggers the Integrated Stress Response through formation of double-stranded RNA

city: Boston

first: Apoorva

last: Baluapuri

address: 45 Shattuck St.

institute: Harvard Medical School

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

overall_design: Refer to individual Series


title: Disruption of the Integrator complex triggers the Integrated Stress Response through formation of double-stranded RNA [RNAseq]

summary: Acute loss of INT induces transcription factors that initiate stress-responses like the Integrated Stress Response (ISR). Inefficient elongation upon INT loss enables termination in introns and dsRNA formation. dsRNA is recognized by PKR, which persistently activates the ISR in samples from patients with INT mutations

overall_design: RNA-seq performed with or without degradation of INTS1 for 0, 4 or 12 hours.

first: Nicole

last: Zhao

first: Kai-Lieh

last: Huang

first: Ryan

last: Marina

first: Maria

last: Amodeo

first: Chad

last: Stein

first: Eric

last: Wagner

first: Karen

last: Adelman


title: Disruption of the Integrator complex triggers the Integrated Stress Response through formation of double-stranded RNA [RIPseq]

overall_design: RIP-seq using J2 or PKR antibody in presence or absence of acute degradation of INTS1.


title: Disruption of the Integrator complex triggers the Integrated Stress Response through formation of double-stranded RNA [PROseq]

overall_design: PROseq performed in presence or absence of acute degradation of INTS1 in HEK293T cells. Cells were permeabilized as in Mimoso et al. 2024; run-ons were performed with biotinylated NTPs and then purified. Purified biotinylated RNAs were ligated to sequencing adapters and amplified by PCR.


title: Pan AMPK-activator O304 ameliorates oxidative stress in MASLD, reverses lipid zonation and reveal lobular metabolic heterogeneitites in the murine live

city: Umeå

first: Emanuel

last: Holm

address: Johan Bures Väg 12

department: MTB

institute: Umeå University

summary: Therapeutic activators of the AMP-Activated Protein Kinase (AMPK) have been proposed as a potential treatment for metabolic dysfunction-associated steatotic liver disease, the most common chronic liver disease worldwide. This study investigates the effect of pan-AMPK activator O304 in a preclinical mouse model of progressive fatty liver disease and demonstrate that O304 reduces body fat mass, blood cholesterol and liver steatosis, as well as ameliorate development of liver fibrosis. These beneficial effects are accompanied by a shift in the metabolic program of the liver including increased lipid oxidation, reduced lipid synthesis, as well as changes in cholesterol and lipid transport. In addition, we detect lobular heterogeneities in the response to O304 and a consistent switch in the zonal distribution of lipid droplets upon treatment. Taken together, our data suggest that O304 is a promising candidate for treatment of MASLD also in human patients

overall_design:
5w old C57Bl6 mice were fed with either standard chow (Special Diet Service #801730) or choline deficient high-fat diet (CD-HFD, D05010402, Research diets). After 3w (short-term cohort) or 21w (long-term cohorts) half of the mice fed CD-HFD were switched to CD-HFD supplemented with 1 mg/g O304 (CD-HFD+O304). Short-term mice were sacrificed 7w after diet-switch while long-term cohorts were sacrificed after 10w or 24w of treatment.
Approximately 30 mg of frozen liver were used for total RNA extraction using the RNeasy Plus Universal minikit (Qiagen, #73404). Integrity and quality of RNA and was determined on a Bioanalyzer (Agilent, #5067-1511). Poly(A) RNA was purified with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and RNA-seq libraries was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) following the manufacturer’s instructions.

first: Holm

last: Emanuel

first: Vermeulen

last: Isabeau

first: Parween

last: Saba

first: López-Pérez

last: Ana

first: Cillero-Pastor

last: Berta

first: Vandenbosch

last: Michiel

first: Remeseiro

last: Silvia

first: Hörnblad

last: Andreas


title: Disruption of the Integrator complex triggers the Integrated Stress Response through formation of double-stranded RNA [TTseq]

first: Apoorva

last: Baluapuri

overall_design: TT-seq performed after 10' labelling in presence or absence of acute degradation of INTS1.


title: Metabolic shifts during growth deceleration in Drosophila imaginal wing discs

city: London

first: Gavin

last: Kelly

state: London

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick institute

summary: Growth during development is often characterised by progressive deceleration, as organisms, tissues, and organs approach their final size. Using transcriptomics analysis, we show that, during their two-day period of growth deceleration, wing imaginal discs of Drosophila undergo a progressive metabolic shift away from oxidative phosphorylation and towards glycolysis. We then develop a sensitive reporter of HIF-1a activity (a proxy for hypoxia), which allows us to show that imaginal discs become mildly, though increasingly, hypoxic during normal development, in normoxic conditions. As a result, HIF-1a dampens growth via transcriptional activation of scylla/REDD1, a negative regulator of TOR signalling. We find that overactivation of TOR signalling triggers a marked hypoxia response both cell-autonomously and in surrounding tissues. This suggests that, in wildtype animals, TOR activity imposes increasing pressure on oxygen supplies. Indeed, in the absence of HIF-1a, TOR signalling triggers JNK signalling, a marker of cellular stress. Moreover, TOR-induced stress is alleviated by a small increase is oxygen supplies. Our results suggest that, during normal development, Sima/HIF-1α prevents growth-induced demand from exceeding available supplies, which become increasing scarce as tissue size increases.

overall_design: We performed bulk RNA-Sequencing (RNA-Seq) on precisely timed third larval instar (L3) wing imaginal discs at seven developmental time points, ranging from 80 to 118 hours after egg laying (AEL). For each time point, three biological replicates and two technical replicates were included.

first: Zhao

last: Yifan

first: Alexandre

last: Cyrille

first: Kelly

last: Gavin

first: Perez-Mockus

last: Gantas

first: Vincent

last: Jean-Paul


title: Type 1 Diabetes Human Enteroid Studies Reveal Major Changes In The Intestinal Epithelial Compartment

city: Nashik

first: Vishwesh

last: Bharadiya

state: Maharashtra

address: Plot No. 27, Vishwesh Children Hospital, Tidke Colony

country: India

institute: Johns Hopkins University School of Medicine

summary: Lack of understanding of the pathophysiology of gastrointestinal (GI) complications in type 1 diabetes (T1D), including altered intestinal transcriptomes and protein expression represents a major gap in the management of these patients. Human enteroids have emerged as a physiologically relevant model of the intestinal epithelium but establishing enteroids from individuals with long-standing T1D has proven difficult. We successfully established duodenal enteroids using endoscopic biopsies from pediatric T1D patients and compared them with aged-matched enteroids from healthy subjects (HS) using bulk RNA sequencing (RNA- seq), and functional analyses of ion transport processes. RNA-seq analysis showed significant differences in genes and pathways associated with cell differentiation and proliferation, cell fate commitment, and brush border (BB) membrane. Further validation of these results showed higher expression of enteroendocrine cells, and the proliferating cell marker Ki-67, significantly lower expression of NHE3, lower epithelial barrier integrity, and higher fluid secretion in response to cAMP and elevated calcium in T1D enteroids. Enteroids established from pediatric T1D duodenum identify characteristics of an abnormal intestinal epithelium and are distinct from HS. Our data supports the use of pediatric enteroids as an ex-vivo model to advance studies of GI complications and drug discovery in T1D patients.

overall_design:
To investigate the gastrointestinal epithelial changes in type 1 diabetic enteroids, we established 2 duodenal enteroids  from T1D patients and compared them with 3 age-matched enteroids from healthy subjects using bulk RNA sequencing

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first: Varsha

last: Singh

first: Mark

last: Donowitz


title: SPL13 controls a root apical meristem phase change by triggering oriented cell divisions

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

summary: Oriented cell divisions are crucial for determining the overall morphology and size of plants, but what controls the onset and duration of this process remains largely unknown. Here, we identified a small molecule that activates root apical meristem (RAM) expression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE13 (SPL13) a known player in the shoot's juvenile-to-adult transition. This expression leads to oriented cell divisions in the RAM through SHORT ROOT (SHR) and cell cycle regulators. We further show that the RAM has distinct juvenile and adult phases typed by morphological and molecular characteristics and that SPL factors are crucially required for this transition in Arabidopsis and rice (Oryza sativa). In summary, we provide molecular insights into the age-dependent morphological changes occurring in the RAM during phase change.

overall_design: 5 DAG Col-0 plants were transferred to ½ MS plates containing 50μM coral7 and solvent control plates and were sampled at the following time points: 0h, 6h, 12h and 24h. Three biological repeats per time point were used.

first: Baojun

last: Yang

first: Yanbiao

last: Sun

first: Max

last: Minne

first: Yanhua

last: Ge

first: Qianru

last: Yue

first: Vera

last: Goossens

first: Eliana

last: Mor

first: Brenda

last: Callebaut

first: Kevin

last: Bevernaege

first: Johan

middle: M

last: Winne

first: Dominique

last: Audenaert


title: Development of an AAV-RNAi strategy to silence the dominant variant GNAO1 c.607G>A linked to encephalopathy

city: Moscow

first: Evgenii

last: Lunev

address: Ulitsa Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology

summary: RNA interference (RNAi)-based gene therapy is a promising strategy for dominant neuropathological conditions. Adeno-associated virus (AAV) vectors are used to deliver RNAi triggers into the central nervous system. The safety of the AAV-RNAi drugs should be closely addressed due to unintended effects on the transcriptome and associated toxicity. In this study, we developed a mutation-specific gene therapy candidate called AAV-sh1500 for the neurodevelopmental disorder caused by the GNAO1 c.607G>A (p.G203R) variant. We assessed the non-intended changes in gene expression induced by AAV infection, activation of RNAi machinery, and sh1500 off-target effects in patient-specific GABAergic neurons in vitro. RNAseq analysis identified 19 downregulated and 59 upregulated genes in neurons treated with AAV-sh1500 compared to non-infected cells. AAV transduction and RNAi activation were found to be the main contributors to the differentially expressed genes. Furthergene ontology analysis showed that AAV transduction downregulates genes related to neuronal differentiation pathways, while RNAi affects genes associated with the apoptotic and protein phosphorylation pathways. The sh1500 sequence-dependent effects were limited to 8 genes. Among these genes, upregulation of SERPINE1, FIP1L1-PDGFRA, PALM2-AKAP2, and COL1A1 has been previously observed in a variety of tumors except the central nervous system. Dysregulation of other off-targets has not been described in pathological processes.

overall_design: The patient-specific GABAergic neurons were transduced with the gene therapy candidate AAV-sh1500. To discriminate sh1500-specific effects per se from changes induced by AAV transduction or RNAi activation, we used non-infected control and neurons infected with AAV-eGFP devoid of shRNA or with non-targeting shRNA (shSCR).

middle: A

first: Ksenia

last: Anufrieva

first: Egor

last: Volovikov

first: Marina

last: Utkina

first: Sergey

last: Popov

first: Natalia

last: Klementieva

first: Tatiana

last: Egorova

first: Maryana

last: Bardina


title: A ketogenic diet mitigates the hippocampal astrogliosis in the Epileptic Brain

city: Los Angeles

first: Hugo

middle: Jae Mun

last: Kim

state: CA

address: 4760 Templeton St, Unit 3113

department: Neuroscience

institute: UNIVERSITY OF CALIFORNIA, SAN DIEGO

summary: The ketogenic diet (KD) is an established treatment for patients with medically intractable epilepsy and is chiefly characterized by the production of ketone bodies (KB) such as β-hydroxybutyrate (BHB). However, after more than a century of clinical use, the mechanisms underlying its efficacy remain unclear. While prior investigations have examined the effects of the KD and its metabolic substrates on synaptic transmission, few studies have explored a potential connection between astrocytic ion channels and seizure genesis. One essential function of astrocytes is spatial potassium buffering which influences passive potassium conductance (PPC), and when impaired, can result in neuronal hyperexcitability. In the present study, we demonstrate that the KD can mitigate hippocampal astrogliosis in the Kcna1-null (KO) mouse model of developmental epilepsy. Specifically, we observed a significant increase in GFAP expression in KO mice fed a control diet compared to wild-type (WT) animals, and that the KD prevented this change. Furthermore, we noted a reduction in hippocampal astrocytic PPC in epileptic mice, whereas KD-treated KO animals exhibited nearly normal passive conductance levels. In this regard, we also provide evidence for the role of Kir4.1 channels in mediating astrocytic PPC, and the activation of these inwardly rectifying potassium channels by BHB. To further explore these findings at a molecular level, we conducted bulk RNA-seq analysis which revealed down-regulation of factors linked to hippocampal astrogliosis, notably those involved with neuroinflammation, consistent with earlier reports highlighting the anti-inflammatory effects of the KD and its metabolic substrates such as BHB. Our findings indicate that the KD protects against epilepsy-associated astrogliosis and astrocytic PPC changes, underscoring a novel mechanism of KD action, and the potential functional role of extracellular potassium in neuronal-glial interactions in the epileptic brain.

overall_design: We collected mouse brain from kcna1 KO and WT treated with Standard or Ketogenic Diet

first: Jae Hyouk

last: Choi

middle: J

first: Jong

last: Rho


title: The effect of ABCF1 overexpression on Hepg2 cell line [RNA]

city: Taizhou

first: yin

last: yuan

state: jiangsu

address: 210 Yingchun Road, Hailing District, Taizhou City, Jiangsu Province

country: China

institute: Nanjing Medical University Affiliated Taizhou People's Hospital

summary: The aim of this study is to investigate the effect of high expression of ABCF1 lactate on Hepg2 cells

overall_design: Construction of Hepg2 stable transgenic strains overexpressing ABCF1 K to R mutations, followed by RNA-seq, ATAC-seq and ChIP-seq

first: yuan

last: yin


title: The effect of ABCF1 overexpression on Hepg2 cell line [ATAC]


title: The effect of ABCF1 overexpression on Hepg2 cell line [ChIP]


title: Microarray data from simple and effective differentiation-switching model using long-term-expanded mammary primary cells

city: Nagakute

first: Akihito

last: Inoko

state: Aichi

address: 1-1 Yazakokarimata

institute: Aichi Medical University School of Medicine

summary: We developed a long-term expansion method for primary mammary basal cells using a set of compounds. Moreover, we established a simple and effective epithelial differentiation method by simply removing the compounds. As a benefit of this convenient differentiation-switching technique, we obtained microarray data comparing each differentiation state and confirmed that the transcription factors EGR1 and ELF3 determine mammary differentiation states at the cellular level. This culturing method is an effective tool for verifying molecular mechanisms that determine mammary differentiation state and can be useful in future epithelial cell biology, physiology, and regeneration research.

overall_design: Microarray data sets were obtained from primary human mammary epithelial cells (HMEC, donor1) cultivated in YDAC-containing F meduim and in YDAC removed F medium for 2 days (Pre and 48H, respectively)

first: Norihito

last: Soga

first: Minako

last: Suzuki


title: Multi-omics sequencing reveals the signature of the genome, cell composition and transcriptome of nodal RDD [ST]

city: Nanjing

first: Xinyi

last: Xia

state: Jiangsu

address: 138 XianLin Road, Nanjing, JiangSu, China

institute: Nanjing University of Chinese Medicine

summary: RDD is a poorly understood disease with low incidence. Here, we performed whole genome sequencing, single cell RNA-seq and spatial transcriptome sequencing of a nodal RDD, describing its cell composition, spatial arrangement and molecular characteristics from a multi-omics perspective. By integrating single cell RNA-seq data, we found that compared with lymph node and LCH, RDD harbors completely different cell composition and molecular feature. Compared with lymph node, a subset of ion-responded macrophage appeared in RDD. Compared with LCH, macrophages in RDD are enriched for RHO GTPase pathway. And RHO GTPase high macrophages have unique cell-cell interactions and are the most actively proliferating cells in RDD. Our results provide a valuable insight for understanding the molecular basis of nodal RDD.

overall_design: Spatial transcriptomics profiles of human Rosai-Dorfman disease (n=1)

first: Qiyang

last: Shen

first: Hanjun

last: Yin

first: Lifeng

last: Zhu

first: Chunlei

last: Zhou

first: Sirui

last: Pan

last: Xie

first: Jianfeng

first: Tao

last: Li


title: Transcriptional responses of T cells activated via CD22-specific T cell receptor compared to CD22-specific chimeric antigen receptor

city: Bethesda

first: Kazusa

last: Ishii

state: MD

address: 10 Center Drive, Building 10, Room 5B05

institute: National Cancer Institute, National Institutes of Health

summary: Chimeric antigen receptor (CAR) T cells are effective against B-cell malignancies but are associated with cytokine-driven inflammatory toxicities such as cytokine release syndrome (CRS). Historically, T cell receptor (TCR) engineered T cell therapies are rarely associated with CRS. However, it is challenging to compare diverse cell products utilized in different clinical contexts and against different antigens. In this study, TCR and CAR were made to target the same source of antigen, CD22, expressed by B-cell malignancies: the TCR recognizes CD22-derived peptide processed and presented in the context of HLA-A*02:01, and the CAR recognizes CD22 protein expressed on the cell surface. In vivo studies comparing the CD22 TCR-T cells to CD22 CAR-T cells demonstrated that the TCR-T cells could clear leukemia without inducing systemic proinflammatory cytokine elevation, whereas CD22 CAR-T cells induced high levels of circulating proinflammatory cytokine reminiscent of CRS. T cells activated through either the TCR or CAR by an identical leukemia cell line demonstrated differential transcriptional responses. T cells activated via the CAR had disproportionate and significant upregulation of inflammatory gene sets compared to T-cells activated via the TCR.

overall_design: From human peripheral blood mononuclear cells (PBMCs), CD8+ and CD4+ T cells were isolated. CD8+ and CD4+ T cells were each transduced to express either the CD22 TCR or the CD22 CAR. In some groups, CD22 TCR-transduced T cells were then co-transduced to express exogenously added CD8alpha-beta heterodimers (exCD8). Each transduced T cell product was co-cultured with HLA-A*02:01 and CD22 positive leukemia cell line, BV173, at an E:T ratio of 1:1 (2e7 cells each per well) in 24-well plate. After 6 hours of co-culture, residual leukemia cells were depleted using magnetic isolation technique. The purity of T cells in the post-leukemia-depletion samples were confirmed with flow cytometry analysis. Non-stimulated control T cells (without co-culture with leukemia cells) also underwent identical magnetic isolation processes for the purpose of equalizing the condition. Bulk RNA was extracted from each sample. Experiment was set up in three biological replicates and RNA extraction was performed in a single batch.

first: Zhihui

last: Liu


title: Activated stroma dictates response to gemcitabine in combination with nab-paclitaxel in pancreatic ductal adenocarcinoma patient derived xenografts (PDAC-PDX) [murine Agilent microarray]

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: Transcription profiling of PDAC-PDX orthotopically engrafted  in the pancreas of immunodeficient mice.

overall_design: Extracted RNA fro 4 samples at different passages was hybridized on murine Agilent microarrays in order to investigate the transcriptional profiling of the stroma counterpart.


title: Activated stroma dictates response to gemcitabine in combination with nab-paclitaxel in pancreatic ductal adenocarcinoma patient derived xenografts (PDAC-PDX) [human Agilent microarray]

summary: Transcription profiling of PDAC-PDX orthotopically engrafted in the pancreas of immunodeficient mice.

overall_design: Extracted RNA from 5 samples at different passages was hybridized on human Agilent microarrays.


title: Activated stroma dictates response to gemcitabine in combination with nab-paclitaxel in pancreatic ductal adenocarcinoma patient derived xenografts (PDAC-PDX).

overall_design: Refer to individual Series


title: RBPMS in Heart Failure during aging

first: Haobo

address: MEDR410 / Lunder Bldg Dock, 255 Charles St

department: Department of Anesthesia, Critical Care, and Pain Medicine

country: USA

institute: Massachusetts General Hospital and Harvard Medical School

summary:
To investigate the role of RBPMS in endothelial cells, endothelial cells were isoldated from 18-month-old mice hearts and treated with lentivirus expressing empty vector or lentivirus overexpressing RBPMS.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for endothelial cells treated with vector control or RBPMS overexpression.

first: Anthony

last: Rosenzweig


title: Multi-omics sequencing reveals the signature of the genome, cell composition and transcriptome of nodal RDD [scRNA-seq]

overall_design: single cell mRNA profiles of human Rosai-Dorfman disease (n=1)


title: PARP9 in Heart Failure during aging

summary:
To investigate the role of PARP9 in endothelial cells, endothelial cells were isoldated from 18-month-old mice hearts and treated with scrambled control or PARP9 siRNA gene knockdown.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for endothelial cells treated with scrambled control or PARP9 siRNA gene knockdown.


title: Cardiopulmonary bypass with deep hypothermic circulatory arrest results in organ-specific transcriptomic responses in pediatric swine

status: Public on Apr 15 2025

city: Aurora

first: Christopher

middle: Andrew

last: Mancuso

state: CO

address: 13001 East 17th Place

department: Department of Biostatistics and Informatics

institute: University of Colorado Anschutz Medical Campus

summary: The organ-level molecular response to cardiac surgery with cardiopulmonary bypass (CPB) remains inadequately understood and may be heterogeneous. Here, we measured organ-specific gene expression in a piglet model of CPB with deep hypothermic circulatory arrest (DHCA). Infant piglets underwent peripheral CPB with 75 min of DHCA and 6 h of critical care after separation from CPB. Mechanically ventilated animals served as controls. Tissue was obtained from the lung, kidney, liver, heart, and ileum. RNA sequencing was performed using NovaSeq 6000 and evaluated via differentially expressed gene (DEG) and pathway/network analyses. CPB/DHCA induced significant transcriptomic alterations, with greater changes seen in liver (2,166 DEGs), heart (775 DEGs), and kidney (1,759 DEGs) compared to lung (401 DEGs) and ileum (11 DEGs), and little overlap across organs (<20 % differentially expressed in >1 organ). Key upregulated systems included ribosomal proliferation and mitochondrial assembly in the liver, oxidative stress response and proximal tubular repair in the kidney, myofilament structural genes and pro-hypertrophy pathways in the heart, and solute channels and arginine metabolism in the lung. Downregulation of adaptive immunity genes occurred in multiple organs. Transcriptomics could inform the investigation of targeted therapies and adverse event screening after cardiac surgery.

overall_design: Infant swine model with 8 animals serving as anesthesiology controls, 7 animals who underwent CPB/DHCA with no treatment and 4 animals who underwent CPB/DHCA and were administered the drug Linrodostat (75 mg). For animals undergoing CPB/DHCA the circulatory arrest time was 75 minutes.

first: Jesse

last: Davidson

first: John

last: Iguidbashian

first: Ludmila

last: Khailova

first: Tanner

last: Lehmann

first: Alejandro

last: Suarez-Pierre

first: Lindsay

last: Thomson

first: Jack

last: Zakrzewski

first: Eiman

last: Ali

first: Schuyler

last: Lee

first: Benjamin

last: Frank

first: Richard

last: Ing

first: Matthew

last: Stone

first: Suzanne

last: Osorio Lujan

first: Sierra

last: Niemiec


title: Humoral determinants of checkpoint immunotherapy: anti-TL1A treatment has a synergistic effect with anti-PD-1 treatment

city: San Francisco

first: YILE

last: DAI

state: California

address: 590 Minnesota St., Apt. 342

institute: Yale University

summary: While the role of cellular immunity in checkpoint immunotherapy (CPI) for cancer is well established, the impact of antibody-mediated humoral immunity is comparably underexplored. Here we used rapid extracellular antigen profiling (REAP) to map the autoantibody reactome within a cohort of 374 cancer patients treated with CPIs and 131 healthy controls for autoantibodies against 6,172 extracellular and secreted proteins (the ‘exoproteome’). Globally, CPI-treated cancer patients harbored an exquisite diversity of autoreactivities that were elevated relative to controls, but changed minimally with treatment. Autoantibody signatures within CPI-treated patients strikingly distinguished them from controls. While associations of specific autoantibodies with immune-related adverse events (irAE) were sparse, we detected numerous individual autoantibodies that were associated with dramatically altered odds ratios (ORs) for response to therapy. These included autoantibodies against immunomodulatory proteins, such as cytokines, growth factors, and immunoreceptors, as well as tumor surface proteins. Functional evaluation of several autoantibody responses indicated that they neutralized the activity of their target proteins including type-I IFN (IFN-I), IL-6, OSM, TL1A, and BMPR1A/BMPR2. Modeling the effects of autoantibodies against IFN-I and TL1A in preclinical mouse tumor models resulted in enhanced CPI efficacy, consistent with their effects in patients. This single-cell RNA sequencing dataset evaluates the synergistic effect between anti-PD-1 and anti-TL1A treatments.

overall_design: Mice used for single RNA sequencing were engrafted with MC38b and treated with anti-mouse PD-1 and anti-mouse TL1A. Mice were euthanized 24 hours after the 2nd dose of saline, anti-mouse PD-1 and/ or anti-mouse TL1A and tumors were harvested for analysis. Tumor tissues were digested. Cell surface staining of single-cell suspensions from tumors was performed after two times wash with FACS buffer (PBS supplemented with 2% FBS). All samples were first stained with LIVE/DEAD™ Fixable Blue to exclude dead cells and incubated with Fc receptor blocking antibody (Biolegend, #101320). Then, cells were stained with anti-CD45 (30-F11) and anti-CD3 (17A2). Biological replicates for saline control (n=2) and treated group (n=4) were individually processed. Biological replicates were then pooled together at the single cell suspension stage before sorting with equivalent number of cells from each replicate. The following populations were sorted: P1: CD45+CD3+ (TIL cells), P2: CD45+CD3− (non-TIL immune cells), P3: CD45−CD3− (tumor and stromal cells). P1, P2, and P3 for each sample were then mixed back together at a 9:9:2 ratio, respectively. 20,000 cells from each treatment condition were loaded onto the 10x Genomics Chromium System. Library preparation was performed with 10x Genomics reagents according to the manufacturer’s instructions by the Yale Center for Genome Analysis (YCGA). Libraries were then sequenced with an Illumina NovaSeq 6000 at the YCGA.

first: Yile

last: Dai

first: Kai

last: Qin

first: Aaron

last: Ring


title: Research on the effect of PRMT5 on the genomic binding sites of ΔNp63α and its impact on the global transcriptomic regulation in the human tongue squamous cell carcinoma cell line UM1.

city: Cheng du

first: Yu cheng

last: Qi

state: Sichuan

address: No. 24, South Section of First Ring Road

institute: Sichuan University

summary: By performing PRMT5 knockdown in the human tongue squamous cell carcinoma cell line UM1, we analyzed the effects of this treatment on the global gene transcription level and its impact on the genomic binding capacity of the transcription factor ΔNp63α. Using genomic binding data supplemented with the histone activation marker H3K27ac, we identified a significant impact of PRMT5 on the transcriptional regulatory capability of ΔNp63α.

overall_design: To investigate how PRMT5 affects the transcriptional regulatory capacity of ΔNp63α, we performed RNA-seq and CUT&Tag analyses on UM1 cells under control (shGFP) and PRMT5 knockdown (shPRMT5) conditions.

first: Shijie

last: Fan

first: Yucheng

first: Chenghua

last: Li


title: RNA-Protein Cargo Delineates Distinct Subpopulations of Cancer-Derived Extracellular Vesicles

city: Trento

first: Francesca

last: Demichelis

state: TN

address: Via Sommarive, 9

department: Department for Cellular, Computational and Integrative Biology - CIBIO

institute: University of Trento

summary: Extracellular vesicles (EVs) are membrane-encapsulated particles that vary greatly in size and content. Although both normal and tumor cells produce an array of small EVs (S-EVs), only tumor cells have been found to release a population of atypically large EVs (L-EVs), also known as large oncosomes (LO). Little is known about the cargo of L-EVs, and how it differs from the S-EVs. Given the potential for tumor-derived L-EVs to provide insights into disease mechanisms and course, we performed proteomic analysis of L- and S-EVs derived from three cancer models followed by comparative proteomic and transcriptomic analysis of EVs from the prostate cancer model. 1) We identified both common and model-specific protein signatures for L- and S-EVs. 2) A subset of the proteins enriched in prostate cancer cell-derived L-EVs were also identified in L-EVs isolated from plasma of patients with metastatic prostate cancer. 3) Proteins enriched in L-EV that were also identified at the transcript level were mostly mitochondrial in origin, as confirmed by single vesicle RNA-Seq. Additionally, the L-EV mitochondrial signature was detected in plasma-derived L-EVs and distinguished patients with prostate cancer from cancer-free individuals as well as patients with metastatic prostate cancer from those with localized disease, corroborating the relevance of an integrative multi-analyte approach focused on L-EVs for liquid biopsy.

overall_design: Large EVs (L-EVs) were enriched from the PC3 cell conditioned medium by differential centrifugation and purified by iodixanol density gradient; the number of particles was quantified by qNano using NP2000 and the L-EV  sample was diluted to contain 10,000 particles total to enable encapsulation of single L-EVs into individual droplets.

first: Yari

last: Ciani

first: Emily

last: Ko

first: Tatyana

last: Vagner

first: Dolores

last: Di Vizio


title: Long-range massively parallel reporter assay reveals rules of distal enhancer-promoter interactions

city: St. Louis

first: Barak

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

summary: Long-range activation is an essential property of enhancers, yet the features determining long-range enhancer activities have not been systematically investigated due to a lack of high-throughput methods to measure long-range enhancer activities efficiently. To address this gap, we present a long-range massively parallel reporter assay (long-range MPRA), a genome-integrated assay allowing the measurement of hundreds of enhancers at multiple distances away from a promoter in parallel. The long-range MPRA assay features two independent landing pads, which allow for modular control over the genome-integrated promoter and enhancer libraries. We showcased the capability of long-range MPRA by testing over 300 K562 enhancers, as well as a set of enhancer combinations, at distances up to 100kb. We found that enhancers’ long-range activities are primarily determined by their intrinsic strength, with strong enhancers retaining more activity over long distances, while weak enhancers rapidly lose activity. Additionally, we found that GATA1-bound enhancers are more resistant to distance-dependent loss of activity, suggesting that TF binding also modulates long-range function. Finally, testing long-range enhancer activities with three different promoters (HBE, HBG and GAPDH) revealed that long-range E-P interactions rely on not only enhancer properties but also promoter responsiveness.

overall_design: Genome-integrated, long-range massively parallel reporter assays of enhancers in K562 cells. To explore features of long-range enhancers, we designed two enhancer libraries: (1) GATA1/non-GATA1 enhancer library which contains 383 enhancers (249bp) selected from the K562 genome based on their GATA1 binding status; (2) LCR HS combination library which contains differet combinations of four DNase hypersensitive sites (HS1-4) in the beta-globin locus. For both libraries, we tagged each library member with a 10 bp unique enhancer barcode (eBC) and a 16bp random barcode (rBC). We also made a series of long-range landing pad cells, consisting of a promoter landing pad at a fixed location (chr18:58014732) and an enhancer landing pad at 0,3,10,20,50 or 100kb upstream. The promoter landing pad contains an mScarlet fluorescence reporter to report enhancer activity, and the enhancer landing pad contains counterselection markers for further selection of enhancer integrations. Each enhancer landing pad is tagged with a 12 bp distance barcode (dBC) to specificy the E-P distance. To measure enhancer activity at selected distances, we first mixed long-range landing pad cells with selected E-P distances in equal ratios and then integrated the enhancer library using Flpase-mediated site-directed recombination. We sorted cells into four bins based on their mScarlet levels, and sequenced the barcodes in each sorted population.

first: Yawei

last: Wu

first: Jie

first: Emma

last: Bartley-Dier

first: Cassidy

last: Pitts


title: Anatomical and Molecular Characterization of the Zebrafish Meninges

first: Madeleine

last: Kenton

address: 10 CENTER DR

department: NICHD

institute: NIH

summary: The meninges are a set of connective tissue layers that surround the central nervous system, protecting the brain from mechanical shock, supporting its buoyancy, guarding it from infection and injury, and maintaining brain homeostasis. Despite their critical role, the molecular identity, developmental origins, and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here, we show that the zebrafish, a genetically and experimentally accessible vertebrate, possesses an easily imaged mammalian-like meninges. Anatomical and cellular characterization of its composition via histology, electron microscopy, and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double-layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics, we define the molecular identities of meningeal cell populations, including a unique ependymin (epd)-expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges, provide a foundational description for future zebrafish meningeal research, and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges.

overall_design: Single cell expression profiling by high throughput sequencing

first: Marina

last: Venero Galanternik

first: Daniel

last: Castranova

first: Ryan

middle: D

last: Gober

first: Tuyet

last: Nguyen

middle: I

first: Brant

last: Weinstein


title: Gene expression changes in NAT10-knockdown primary human endometrial stromal cells (hESCs) compared to control cells

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

summary: To portray the molecular mechanism for NAT10 function in hESCs, cell treated with siNAT10 and siNC were subjected to RNA-seq analysis.

overall_design: The hESCs treated with siNAT10 and siNC were subjected to RNA-seq analysis


title: Global ac4C-modified mRNAs in the uterus of wild-type mouse on gestational day 4

summary: Global ac4C-modified mRNAs in the uterus of wild-type mouse were analyzed by using ac4C RNA immunoprecipitation sequencing (acRIP-seq)

overall_design: We investigated global ac4C-modified mRNAs in the uterus of wild-type mouse by using acRIP-seq


title: Gene expression changes in Nat10-deleted mouse uterus on PND21

summary: We specifically deleted Nat10 in the female reproductive tract using the Pgr-Cre driver. To portray the molecular mechanism for Nat10 function in uterus, uterine tissues were collected from Nat10f/f and Nat10d/d mice on PND21 and subjected to RNA-seq analysis.

overall_design: Uterine tissues were collected from Nat10f/f and Nat10d/d mice on PND21 and subjected to RNA-seq analysis.


title: Global ac4C-modified mRNAs in the human endometrium at mid-secretory phase

summary: Global ac4C-modified mRNAs  in the human endometrium were analyzed by using ac4C RNA immunoprecipitation sequencing (acRIP-seq)

overall_design: We investigated global ac4C-modified mRNAs in the human endometrium by using acRIP-seq


title: Designed NGF mimetics with reduced nociceptive signatures in neurons

city: Seattle

first: Damien

last: Detraux

state: Washington

address: 850 Republican St

institute: University of washington

summary: The clinical use of Nerve Growth Factor (NGF) for neural regeneration has been hampered by pain sensitization side effects. NGF signals through the receptor tyrosine kinase TrkA and the co-receptor p75NTR; pain sensitization is thought to involve p75NTR. We sought to overcome this limitation by de novo design of a TrkA agonist that does not bind p75. We designed homodimeric TrkA engaging constructs that bring together two TrkA subunits in a variety of geometries, and identified those eliciting the strongest signaling. The resulting designed agonists are able to stimulate transdifferentiated neurons and neuroblastoma cell lines, leading to neurite outgrowth and neuronal differentiation, with considerably reduced transcription of inflammation and pain related genes. Although detailed in vivo characterization will be required to fully understand their therapeutic potential, these agonists are promising candidates for inducing neural regeneration with reduced pain side effects.

overall_design: RNA-seq profile for total RNA for two-weeks transdifferentiated neurons (iNs) treated for 48h with vehicle, 10 nM NGF or 10 nM 237 desgined agonist

first: Thomas

last: Schlichthaerle

first: Aerin

last: Yang

first: David

middle: E

last: Johnson

first: Chloe

last: Peach

first: Natasha

last: Edman

first: Catherine

last: Sniezek

first: Charles

last: Williams

first: Sonali

last: Arora

first: Neerja

last: Katiyar

first: Irene

last: Chen

first: Ali

last: Etemadi

first: Andrew

last: Favor

last: Lee

first: Connor

last: Kubo

first: Brian

last: Coventry

first: Buwei

last: Huang

first: Stacey

last: Gerben

first: Nathan

last: Ennist

first: Lukas

last: Milles

first: Banumathi

last: Sankaran

first: Alex

last: Kang

first: Hannah

first: Asim

last: Bera

first: Babak

last: Negehdari

first: Nobuhiko

last: Hamazaki

first: Devin

last: Schweppe

first: Lance

last: Stewart

first: Hannele

last: Ruohola-Baker

first: Julie

last: Mathieu

first: Christopher

last: Garcia

first: Siobhan

last: Pattwell

last: Baker


title: Knockdown of xenotropic and polytropic retrovirus receptor 1 in thyroid cancer cells

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

summary: Xenotropic and polytropic retrovirus receptor 1 (XPR1), initially identified as a receptor for murine leukemia viruses, has been shown to function as a phosphate exporter, maintaining inorganic phosphate homeostasis in cells. Recently, XPR1 was recognized as a late-stage neoantigen-related gene in thyroid cancer; however, its functions in this context have not been well characterized.

overall_design: Thyroid cancer cell line TPC-1 was transfected with either a control siRNA or an siRNA targeting XPR1. Total RNA was extracted and subjected to RNA-seq.


title: AireDTR Single Cell

first: James

last: Gardner

address: 513 Parnassus Ave

institute: University of California, San Francisco

summary: The immune system must distinguish pathogens from innocuous dietary antigens, but the precise mechanisms and cellular actors involved are unclear. Here, we demonstrate that RORγt-lineage antigen-presenting cells (APCs) expressing the Autoimmune Regulator (Aire) gene – referred to as RORγt eTACs – are required for oral tolerance. Using lineage tracing and single-cell sequencing, we show that RORγt eTACs are of a myeloid-derived lineage and establish consensus identities for all RORγt-lineage APCs. We found that RORγt eTACs, but not type 3 innate lymphoid cells, are necessary and sufficient for oral tolerance induction. Upon depletion of RORγt eTACs, mice fail to develop food-specific Tregs and display severe delayed-type hypersensitivity responses. These findings establish RORγt eTACs as critical mediators of oral tolerance and suggest novel targets to modulate immune tolerance.

overall_design: We obtained lymph nodes (mesenteric,cervical, inguinal, axillary, brachial, and para-aortic) from AireDTR mice and FACS-sorted tdTmt+ MHCII+ cells for subsequent scRNA-seq.

first: Sun

last: Im Hong

first: Qualls

last: Anita

first: Yin

last: Han