title: PCSK5M452I is a recessive hypomorph exclusive to MCF10DCIS.com cells

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

summary: The most widely used cell line for studying ductal carcinoma in situ (DCIS) premalignancy is the transformed breast epithelial cell line, MCF10DCIS.com. During its original clonal isolation and selection, MCF10DCIS.com acquired a heterozygous M452I mutation in the proprotein convertase PCSK5, which has never been reported in any human cancer. The mutation is noteworthy because PCSK5 matures GDF11, a TGFβ-superfamily ligand that suppresses progression of triple-negative breast cancer. We asked here whether PCSK5M452I and its activity toward GDF11 might contribute to the unique properties of MCF10DCIS.com. Using an optimized in-cell GDF11 maturation assay, we found that overexpressed PCSK5M452I was measurably active but at a fraction of the wildtype enzyme. In a PCSK5–/– clone of MCF10DCIS.com reconstituted with different PCSK5 alleles, PCSK5M452I was mildly defective in anterograde transport. However, the multicellular organization of PCSK5M452I addback cells in 3D matrigel cultures was significantly less circumscribed than wildtype and indistinguishable from a PCSK5T288P null allele. Growth of intraductal MCF10DCIS.com xenografts was similarly impaired along with the frequency of comedo necrosis and stromal activation. In no setting did PCSK5M452I exhibit gain-of-function activity, leading us to conclude that it is hypomorphic and thus compensated by the remaining wildtype allele in MCF10DCIS.com.

overall_design: RNAseq profiling of day 8 3D cultures of PCSK5-/- MCF10DCIS.com cells with inducible addback of PCSK5 alleles (wildtype, M452I, or T288P) without added GDF11 or T288P allele addback cultured with 250 ng/ml recombinant GDF11.

first: Taylor

last: Marohl

first: Lixin

last: Wang


title: Antibiotic adjuvant effects in VRSA-1

status: Public on Dec 10 2025

city: High Point

first: Heather

middle: Bennett

last: Miller

state: NC

address: One University Parkway

department: Chemistry

country: USA

institute: High Point University

type: Expression profiling by high throughput sequencing

summary: Methicillin-resistant Staphylococcus aureus (MRSA) is a major threat to human health. Rather than depend on creating new antibiotics (to which bacteria will eventually become resistant), we are employing antibiotic adjuvants that potentiation existing antibiotics. To gain biological insight into how lead compounds potentiate antibiotics and inhibit biofilms, we used RNA-seq on treated VRSA-1 cultures to examine antibiotic adjuvant effects transcritome-wide.

overall_design: Differential gene expression was examined between VRSA-1 cultures either untreated, treated with oxacillin only, treated with vancomycin only, treated with an antibiotic adjuvant (loratadine or compound 8), or cotreated with oxacillin or vancomycin and either loratadine or compound 8. Each of the treatments was performed with biological triplicates.

middle: B


title: Transcriptomic analysis of neuroblastoma cells in response to RORB over-expression

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

country: China

institute: Union Hospital of Tongji Medical College

summary: Neuroblastoma, the most common extracranial solid malignancy in infants and young children, originates from aberrant neural crest cells and accounts for 10-15% of childhood cancer deaths. However, the underlying mechanisms regulating neuroblastoma progression remain to be determined. To investigate the mechanisms regulating tumorigenesis and aggressiveness, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma SK-N-BE(2) cells in response to over-expression of RAR-related orphan receptor B (RORB). The results showed that 2027 and 1549 genes were respectively elevated or reduced in SK-N-BE(2) cells following RORB over-expression. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to RORB over-expression in human neuroblastoma cells, and these findings will help us understand the pathogenesis of neuroblastoma progression.

overall_design: RNA-seq profiling of human neuroblastoma SK-N-BE(2) cells stably transfected with empty vector (mock) or RORB construct.

first: Liduan

last: Zheng


title: Immune transcriptomic changes in Australian Gulf War Veterans

city: Southport

first: Natalie

last: Eaton-Fitch

state: Queensland

address: Parklands Dr

country: Australia

institute: Griffith University

overall_design:
Gene expression analysis of RNA was performed using the commercially available NanoString® nCounter Immune Exhaustion gene expression panel (NanoString Technologies, Seattle, WA, USA). This panel contains 785 genes to elucidate mechanisms behind T cell, B cell and NK cell exhaustion in disease.
Ribonucleic acid (RNA) was extracted from peripheral blood mononuclear cells (PBMCs) isolated from Gulf War Illness (GWI, n=20), and healthy control (HC; n=15) participants. Veterans with GWI were classified according to the Kansas Criteria.

first: Sonya

last: Marshall-Gradisnik


title: Fucosyltransferase 8-derived circular RNA drives M2 polarization of macrophages through ENO1-TNF signaling axis to promote lung cancer progression

city: Shanghai

first: Feng

last: Li

address: 2901 Caolang Highway

institute: Shanghai Public Health Clinical Center

summary: CircFUT8 (hsa_circ_0003028) was significantly upregulated in lung cancer tissues, correlating with advanced stages and poor prognosis. It enhanced lung cancer cell proliferation, migration, and invasion while inhibiting apoptosis in cellular and animal models.     Mechanistically, circFUT8 directly binds ENO1 to form an RNA-protein complex, promoting M2 macrophage polarization. Silencing circFUT8 reversed these effects by suppressing ENO1 and M2 polarization, inhibiting tumor progression.

overall_design: To further explore the downstream pathways and functions regulated by circFUT8, we used RNA-seq to detect the functional enrichment and pathway changes of downstream genes regulated by circFUT8 silencing in A549 and H1299 cells.

first: Yang

last: Ren

first: Yidan

last: Shen

first: Yinzhong


title: scRNA-seq of MC38 syngeneic colorectal tumors after FAP-CAR mRNA-LNP therapy

city: Suita

first: Sikun

last: Meng

state: Osaka

address: Yamadaoka 2-2

country: Japan

institute: the Universiy of Osaka

summary: This study investigates the therapeutic potential of an mRNA–lipid nanoparticle (LNP)-based strategy delivering fibroblast activation protein (FAP)-specific chimeric antigen receptor (CAR) mRNA in colorectal cancer. Syngeneic colorectal mouse tumor models were treated with FAP-CAR mRNA-LNPs, and single-cell RNA sequencing (scRNA-seq) of tumor tissues was performed. The analysis aimed to explore mechanisms of tumor relapse following treatment, with a particular focus on the MIF–CD74 signaling axis. The data revealed heterogeneous immune and stromal cell states, highlighting immunosuppressive pathways associated with relapse.

overall_design: MC38 syngeneic colorectal tumors were established in C57BL/6 mice and treated with FAP-CAR mRNA-LNPs in combination with 5-fluorouracil (5-FU), anti-PD1, and anti-CTLA4 antibodies. Tumor tissues were collected from two relapse cases and one untreated control for single-cell RNA sequencing (scRNA-seq).

first: Tomoaki

last: Hara

first: Tetsuya

last: Sato

first: Shotaro

last: Tatekawa

first: Yasuko

last: Arao

first: Yoshiko

last: Saito

first: Toshiro

last: Hirai

first: Daisuke

last: Motooka

first: Sarah

last: Rennie

first: Taroh

last: Satoh

first: Kazuhiko

last: Ogawa

first: Yutaka

last: Miura

first: Masaki

last: Mori

first: Yuichiro

last: Doki

first: Hidetoshi

last: Eguchi

first: Hideshi

last: Ishii


title: AI-assisted Drug Re-purposing  for Human Liver Fibrosis

city: PALO ALTO

first: YUAN

last: GUAN

state: CA

address: 1701 Page Mill Road

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Liver fibrosis is a severe disease with few treatment options due to the poor quality of the available animal and in vitro models. To address this, human hepatic organoids were grown in microwells (i.e., microHOs) to provide a robust, live cell imaging platform for serially evaluating the anti-fibrotic effects of drug candidates. Here, we developed a multi-parameter image analysis workflow that enabled anti-fibrotic efficacy and drug toxicity to be serially assessed in microHOs, and endpoint analyses (flow cytometry and scRNA-Seq) were used to characterize drug effects on different cell types. Transcriptomic analysis revealed that the efficacy of five anti-fibrotic agents occurred via two different mechanisms: two inhibited TGF-induced intracellular signaling while three altered TGF-induced mesenchymal cell differentiation. microHO data facilitated drug re-purposing by enabling the effects of different drugs to be directly compared. This study provides a first demonstration that a hypothesis generating multi-agent AI system (AI co-scientist) can assist in re-purposing drugs for a disease with few treatment options. Two of three AI co-scientist-recommended drugs targeting epigenomic modifiers exhibited significant anti-fibrotic activity; and one is an FDA-approved drug (Vorinostat) that also promoted liver parenchymal cell regeneration. Hence, the use of AI co-scientist coupled with this enhanced microHO platform identified a new generation of liver fibrosis treatments that also promote liver regeneration.

overall_design: scRNA-seq and scATAC-seq profiling microHO treated with TGFb1 and TGFb1 plus different anti-fibrosis drugs.

first: Yuan

last: Guan


title: Control samples for study "hiv-seq reveals global host gene expression differences between hiv-transcribing cells from viremic and suppressed people with hiv"

city: San Francisco

first: Julie

last: Frouard

state: California

address: 1650 Owens street

department: Virology

institute: Gladstone Institutes

summary: In our study, we aimed to improve the identification of active reservoir cells producing HIV in individuals undergoing antiretroviral therapy (ART). We developed a technique called HIV-Seq to enhance the efficiency of capturing HIV transcripts during single-cell RNA sequencing (scRNAseq) analysis. By applying this technique, we compared the transcriptional features of HIV RNA+ cells before and after ART initiation. Our findings highlight distinct transcriptional signatures of active reservoir cells during viremia and suppression, demonstrating the utility of HIV-Seq in elucidating the mechanisms underlying reservoir persistence during ART.

overall_design: CD4⁺ T cells from two HIV-negative donors were subjected to both the standard scRNA-seq protocol and the HIV-seq protocol in parallel. This was done to validate that the addition of HIV-specific primers in the HIV-seq method does not result in false-positive detection of HIV transcripts. Peripheral blood mononuclear cells (PBMCs) were thawed, and CD4⁺ T cells were isolated by negative selection using the EasySep™ Human CD4⁺ T Cell Enrichment Kit (StemCell Technologies). These purified cells were then used to generate gene expression (GEX) libraries following either the standard 10x Genomics 5′ scRNA-seq protocol or the modified HIV-seq protocol.

first: Sushama

last: Telwatte

first: Xiaoyu

last: Luo

first: Natalie

last: Gill

first: Reuben

last: Thomas

first: Douglas

last: Arneson

first: Pavitra

last: Roychoudhury

first: Rebecca

last: Hoh

first: Steven

middle: G

last: Deeks

first: Sulggi

middle: A

last: Lee

first: Nadia

middle: R

last: Roan

last: Yukl


title: Genome-wide occupancy of RORB in neuroblastoma cells.

first: Qiangsong

last: Tong

summary: Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. To investigate the mechanisms underlying the tumor suppressive functions of RAR-related orphan receptor B (RORB), we employed the Illumina HiSeq X Ten as a discovery platform to analyze the genome-wide occupancy of RORB on target genes in human SK-N-BE(2) cells. The results showed that 1637 target genes were regulated by transcriptional regulator RORB, especially those involved in regulation of NF-κB signaling pathway. Furthermore, we validated the ChIP-seq results by real-time PCR with high identity. Overall, our results provided fundamental information about the genomic enrichment of RORB in human NB cells, and these findings will help us understand the pathogenesis of NB.

overall_design: ChIP-seq assay of genome-wide occupancy of transcriptional factor RORB in neuroblastoma SK-N-BE(2) cells.

first: Liduan

last: Zheng


title: Human Subcutaneous ABD/GLU/Thi adipose tissue RNAseq - NYC sample

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Bulk RNAseq of adipose tisssues of healthy men and women

overall_design: Our goal was to collect preliminary data on sex differences in gene expression in three subcutaneous depots:  abdominal, gluteal and thigh (anterior).

first: Kalyspo

last: Karastergiou

first: Jeanine

last: Albu

first: Susan

middle: K

last: Fried


title: A Serum-free Culture Medium for Long-term Expansion of Human Airway Basal Stem Cells

city: Guangzhou

first: Mingyue

last: Jiang

address: No. 74, Zhongshan Second Road, Yuexiu District, Zhongshan University North Campus

institute: Sun Yat-sen University

summary: Background: Human basal stem cells, with their self-renewal and multilineage differentiation capacity, are essential tools for modeling airway diseases and advancing regenerative medicine. However, existing culture systems often rely on undefined components like serum, bovine pituitary extract, or feeder cells, limiting reproducibility and clinical translation. To address this limitation, we developed a well-defined culture medium that enables the long-term expansion of human airway basal stem cells while preserving their proliferative and differentiation potential. Methods: We formulated a novel medium (sfBSC) comprising 14 defined components, including basal media, supplements, growth factors (EGF, FGF10), and signaling inhibitors (Y-27632, A-83-01, DAPT, DMH1). Human bronchial and small airway epithelial cells were cultured over multiple passages in sfBSC and assessed for morphology, population doublings, marker expression, and differentiation capacity via air-liquid interface and organoid cultures. RNA-seq was performed to explore molecular changes across passages. Results: Bronchial and small airway epithelial cells were expanded up to 17 and 24 passages, respectively, with stable morphology and consistent cell size (10-15 μm). Cells maintained expression of canonical BSC markers (TP63, KRT5, NGFR) throughout long-term culture. Differentiation assays confirmed the ability to generate ciliated, goblet, and club cells. Optimized concentrations of EGF (1 ng/mL) and FGF10 (0.4 ng/mL) were critical for sustained proliferation. RNA-seq revealed stable marker expression and metabolic changes over time.Conclusions: sfBSC medium offers a defined, reproducible, and scalable platform for basal stem cell culture, enabling applications in disease modeling, regenerative medicine, and clinical-grade cell production.

overall_design: RNA-seq pofiling of HBECs (P3, P6, P9, and P13) and HSAECs (P2, P7, P14, and P21) cultured in a novel medium (sfBSC)


title: Gene expression analysis of murine normal mammary gland fibroblasts (mNFs) after perturbing the expression of ASPA (silencing and over-expression)

city: Santander

first: Fernando

last: Calvo

state: Cantabria

address: C. Albert Einstein, 22

country: Spain

institute: IBBTEC

summary: Metabolic reprogramming is a hallmark of cancer, and the field has predominantly focused on investigating metabolic alterations in tumour cells. However, the relevance, mechanism and consequences of metabolic adaptations in stromal cells remains largely unexplored. Here, we identify Aspartoacylase (ASPA) as a metabolic enzyme consistently repressed in tumour stroma and cancer-associated fibroblasts (CAFs). Loss of ASPA is associated with the accumulation of its substrate, N-acetylaspartate (NAA), and we corroborate the relevance of this metabolite in the control of macrophage polarization. Importantly, we report an unprecedented reciprocal crosstalk of ASPA with TGFβ signalling. TGFβ suppresses ASPA expression, whereas ASPA restrains TGFβ-dependent myofibroblast conversion and the generation of aggressive pro-tumoral responses in fibroblasts. Analyses of human specimens revealed a strong negative prognostic value for ASPA in different tumour types, associated with pro-tumoral macrophages and TGFβ signalling levels. Our findings unveil ASPA expression in fibroblasts as a previously unknown gatekeeper of TGFβ responses and activation in cancer, and shed light into the intratumoral metabolic crosstalk that governs the process of cancer progression.

overall_design: RNA-seq profiling of murine mammary normal fibroblasts (mNF1) after silencing ASPA with two independent shRNAs. Scramble shRNA (shC) and two individual shRNA targeting Aspa (Sh3-ASPA and Sh4-ASPA), under doxycyclin control, were transfected in mNF1, and selection was performed using Blasticidin at 10 μg/mL final concentration. Stable clones were cultured in subconfluency in full DMEM (10% FBS) and treated with 300ng/mL of doxycyclin for 5 days, and RNA was extracted. In addition, RNA-seq profiling of mNF1 control and over-expressing a wild-type form of ASPA, after treatment with vehicle or TGF-beta1 , on duplicates. mNF1 were stably transfected with a doxycyclin-inducible cDNA for ASPA and selected using Blasticidin at 10 μg/mL final concentration. Stable clones were cultured in full DMEM (10%FBS) and treated with Vehicle (control) or with 300ng/mL of doxycyclin for 5 days to induce ectopic ASPA expression (mNF1-ASPA). Cells were then exposed to vehicle (Vh) or to 10 ng/mL of TGF-beta1 for 24 h, and RNA extracted.

first: Catalina

last: Capó-Serra

first: Miguel

last: Juliá


title: Super-enhancer-driven core transcription factor FOXP1 delays endothelial cell senescence via phase separation-mediated SESN3 activation_cuttag seq

city: dongguan

first: Lushuang

last: Mao

state: guangdong

address: No.1 Xincheng Avenue, Songshan Lake Science and Technology Industrial Park

department: 2.Dongguan Key Laboratory of Aging and Anti-Aging

institute: Guangdong Medical University

summary: Rationale: Endothelial cell senescence leads to endothelial dysfunction, thereby promoting the progression of atherosclerosis. Super-enhancers are crucial epigenetic cis-regulatory elements whose extensive reprogramming drives aberrant transcription in human diseases. However, the underlying mechanisms of super-enhancer on endothelial cell senescence remain unclear.

overall_design: This study reveals the effect of liquid-liquid phase separation (LLPS) of the super-enhancer-driven core transcription factor FOXP1 on endothelial cell senescence. Methods: The landscape of super-enhancers, chromatin accessibility, and transcriptome profiling were  characterized during endothelial cell senescence by conducting CUT&Tag-seq with antibodies against H3K27ac, H3K4me1, and  H3K4me3, along with assays for ATAC-seq and RNA-seq. The Coltron algorithm was used to identify core transcription factors during the process of endothelial cell senescence. Fluorescence recovery after photobleaching (FRAP), dCas9-KRAB CRISPRi, and the Optodroplet assay were utilized to confirm the phase separation properties of  FOXP1. Functional experiments were employed to elucidate the effect of FOXP1 on endothelial cell senescence through LLPS.


title: Ly6G+Nur77+ macrophages initiate the type-2 immune response to allergens in the lung

city: Bethesda

first: Beatriz

last: León

state: Maryland

address: Building 10, Room 11N240A, 10 Center Drive

department: NIAID

institute: NIH

summary: The mechanisms of allergen sensing and type 2 immune response initiation remain unclear. Using a house dust mite (HDM)-induced allergic airway model, we demonstrated that host detection of protease activity in HDM was crucial for initiating T helper type 2 (Th2) responses. This process was driven by the major allergen Der p 1, a cysteine protease, which was sensed by protease-activated receptor 2 (PAR2) on a novel population of perivascular lung macrophages expressing Ly6G and nuclear receptor Nur77. These macrophages required PAR2 and Nur77 for activation and accumulation and regulated conventional dendritic cell (mDC) migration to draining mediastinal lymph nodes (mLN) via cysteinyl leukotriene (CysLTs) production. CysLTs enhanced CCR7-driven migration of mDCs toward its ligand, CCL21, facilitating arrival to mLNs for T cell priming and expansion. Inhibiting CysLTs biosynthesis reduced mDC migration and dampened Th2 allergic responses, highlighting new therapeutic paths and mechanisms in type 2 immunity.

overall_design: This study aims to compare allergen-activated Ly6G⁺ macrophages (Ly6G⁺ MΦ) and non-classical monocytes in the lung using single-cell RNA sequencing (scRNA-seq). Eight-week-old C57BL/6J mice (Mus musculus) were treated intranasally with 10 µg of the cysteine protease papain in a 100 µL volume. After 24 hours, lungs were processed into a single-cell suspension, and two distinct cell populations were isolated by fluorescence-activated cell sorting (FACS): Ly6G⁺Ly6C⁺CX3CR1⁺CD11b^hi SIGLEC-F⁻ macrophages (Ly6G⁺ MΦ) and Ly6G⁻Ly6C⁻CX3CR1⁺CD11b⁺SIGLEC-F⁻CD16.2^hi non-classical monocytes. The sorted cells were subjected to scRNA-seq to characterize their transcriptional profiles. This dataset provides insights into the relationship and functional differences between these allergen-responsive myeloid subsets in the lung.

first: Audrey

last: Meloun

first: Holly

last: Bachus

first: Crystal

last: Lewis

first: Brittany

last: Dulek

first: Shivangi

last: Dave

first: Dave

last: Durell Hill

first: Gabriela

last: Pessenda

first: Jose

last: Carlos Gonzalez

first: P’ng

last: Loke

first: Alexander

middle: F

last: Rosenberg


title: Epithelial-Mesenchymal Plasticity is Associated with Immunosuppressive Features in Canine Mammary Carcinomas

city: Ithaca

first: Kimaya

middle: Milind

last: Bakhle

state: NY

address: 930 Campus Road VRT T7012

department: Department of Biomedical Sciences

institute: Cornell University

summary: Epithelial-mesenchymal plasticity (EMP) is a cellular process activated in carcinoma cells to drive invasiveness, metastasis, and chemoresistance. Recently, we have demonstrated that activation of the EMP program also results in the assembly of an immunosuppressive tumor microenvironment and resistance to immunotherapy in an immunocompetent orthotopic murine model. However, it has yet to be shown whether these findings can be translated to canine carcinomas. Here, we show that in spontaneous canine mammary carcinomas (CMCs), which share similar histopathologic, molecular, and clinical features with human breast cancers, EMP activation is linked to the recruitment of immunosuppressive cells including regulatory T-cells and M2-like macrophages. Additionally, through transcriptomic profiling of CMCs, we identify that the glycoprotein CD109 is associated with EMP-mediated immunosuppression across canine, murine, and human breast cancer models. CD109 has been previously associated with tumorigenicity, but not immunosuppression in cancers of any species. Finally, we identified upregulation of several immunosuppressive paracrine factors across multiple canine carcinomas, including oral squamous cell carcinoma, urothelial carcinoma, and pulmonary carcinoma samples. These findings demonstrate for the first time that the EMP program is associated with immunosuppression in canine carcinomas, with direct translational implications for human breast cancers.

overall_design: RNA-seq data from 15 formalin-fixed paraffin-embedded canine mammary carcinoma samples across three states: epithelial, heterogeneous, and quasi-mesenchymal.

middle: M

first: Sophie

last: Nelissen

first: Lynna

last: Li

first: Ioannis

last: Ntekas

first: Iwijn

last: De Vlaminck

first: Santiago

last: Peralta

first: Andrew

middle: D

last: Miller

first: Anushka

last: Dongre


title: Super-enhancer-driven core transcription factor FOXP1 delays endothelial cell senescence via phase separation-mediated SESN3 activation_atac seq

first: Lushuang

last: Mao


title: Safety, feasibility and pharmacodynamic activity of intratumoral injections of the agonist anti-CD137 (4-1BB) mAb urelumab in combination with nivolumab

city: Pamplona

first: David

last: Ruiz Guillamón

state: Navarra

address: Av. de Pío XII, 55

department: Programa de Inmunología e Inmunoterapia

institute: Centro de Investigación de Medicina Aplicada (CIMA) - Clínica Universidad de Navarra

summary: Intravenous dosing of the anti-CD137 (4-1BB) agonist monoclonal antibody urelumab is limited to 8 mg flat doses due to liver toxicity, thus reducing bioavailability. Here we explored intratumoral delivery of urelumab to increase bioavailability at the tumor, while reducing systemic exposure, in combination with systemic nivolumab (clinical trial INTRUST, NCT03792724).

overall_design: Bulk RNA-seq of biopsy samples from clinical trial patients at different timepoints.

first: Miguel

last: Sanmamed

last: Ruiz-Guillamón

first: Carlos

middle: E

last: de Andrea

middle: L

last: Perez-Gracia

first: Ignacio

last: Melero


title: RPL22 Expression Identifies a Transcriptional Subset of MLH1 Deficient Endometrial Cancers that Impacts Tumor Infiltrating Lymphocytes [protein]

city: Chapel Hill

last: Gladden

address: 160 N. Medical Drive

department: Pathology & Laboratory Medicine

institute: The University of North Carolina at Chapel Hill

summary: RPL22 expression is lost is ~30% of MSI-high endometrial cancers, and the consequences of RPL22 loss are still unknown. The purpose of this study was to determine the consequences of RPL22 loss in both the tumor and immune microenvironment of MSI-high endometrial cancers. We determined that the number of CD8+ T cells in RPL22 negative tumors is significantly lower than in RPL22 positive tumors and that beta-2-microglobulin protein is significantly reduced in RPL22 negative tumors.

overall_design: Sixteen formalin-fixed, paraffin embedded MLH1 deficient endometrial tumors were analyzed with digital spatatial proteomics using the GeoMx Immuno-Oncology protein pannel . Eleven tumors were RPL22 positive. Of these, 5 were immune high (as determined by quanitifying CD8+ T cells in the whole tumor) and 6 were immune low. Five tumors were RPL22 negative and immune low. Six regions of interest (ROIs) were chosen for each tumor. Three ROIs were of tumor cells, and 3 ROIs were of immune cells in the periphery of the tumor.

first: Macy

last: Osborne-Frazier

first: Savannah

last: LaBuda

first: Molly

last: Parrish

first: Hannah

last: Atkins

first: Russell

last: Broaddus


title: RPL22 Expression Identifies a Transcriptional Subset of MLH1 Deficient Endometrial Cancers that Impacts Tumor Infiltrating Lymphocytes [transcript]

summary: RPL22 expression is lost is ~30% of MSI-high endometrial cancers, and the consequences of RPL22 loss are still unknown. The purpose of this study was to determine the consequences of RPL22 loss in both the tumor and immune microenvironment of MSI-high endometrial cancers. We determined that the number of CD8+ T cells in RPL22 negative tumors is significantly lower than in RPL22 positive tumors and thatRPL22 positive tumors have distinct transcriptional profiles characterized by upregulation of immune pathways.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Sixteen formalin-fixed, paraffin embedded MLH1 deficient endometrial tumors were analyzed using whole transcriptome digital spatial analysis. Eleven tumors were RPL22 positive. Of these, 5 were immune high (as determined by quanitifying CD8+ T cells in the whole tumor) and 6 were immune low. Five tumors were RPL22 negative and immune low. Six regions of interest (ROIs) were chosen for each tumor. Three ROIs were of tumor cells, and 3 ROIs were of immune cells in the periphery of the tumor.


title: RPL22 Expression Identifies a Transcriptional Subset of MLH1 Deficient Endometrial Cancers that Impacts Tumor Infiltrating Lymphocytes

type:
Other
Protein profiling by protein array

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

overall_design: Refer to individual Series


title: Functional interplay between (p)ppGpp and RNAP in Acinetobacter baumannii

city: Namur

first: Regis

last: Hallez

address: 61 Rue de Bruxelles

country: Belgium

institute: UNamur

summary: The (p)ppGpp-dependent stress response is required for pathogenic bacteria to survive both outside and inside the host but the mechanisms behind this survival are mostly unknown. In this study, we characterize the (p)ppGpp metabolism in the opportunistic pathogen multi-drug-resistant Acinetobacter baumannii. We show that two stressful conditions potentially encountered during infection – iron starvation and polymyxin exposure – induce (p)ppGpp production. The absence of (p)ppGpp led to multiple consequences on the physiology of A. baumannii, including an increase of surface motility, a decrease in catalase activity, a poor survival upon nutrient starvation, a rapid killing during desiccation and a strong attenuation in a Galleria mellonella model of infection. Using a motility suppressor screen, we isolated multiple independent stringent mutations in rpoB and rpoC that suppress the (p)ppGpp-dependent phenotypes. By combining the suppressor screen with deep sequencing, we isolated dozens of additional mutants, expanding the list of putative stringent RNAP mutations described so far. Furthermore, our transcriptomic data reveal that (p)ppGpp deeply impacts the transcriptional landscape of A. baumannii on solid surface to induce many stress-related genes, including catalase and hydrophilins critical for tolerance to desiccation. This work highlights the functional interplay between (p)ppGpp and RNAP in the successful survival of A. baumannii in the environment but also during infection.

overall_design: Determination of (p)ppGpp-dependent regulons in Acinetobacter baumannii WT, DrelA and DrelA rpoB_R557C suppressor mutant cells grown on LB low agar plates and in LB liquid medium

first: Anthony

last: Perrier

first: Aurélie

last: Budin-Verneuil

first: Régis


title: Allele-Specific Expression of PAXIP1-AS1 at rs112651172 in Schizophrenia and Bipolar Disorder Contributes to Synaptic Dysfunction and Behavioral Abnormalities in Mice

first: Cunyou

last: Zhao

state: Guangdong

address: No. 1023-1063, South Sha-tai Road, Baiyun District

institute: Southern Medical University

summary: Schizophrenia (SCZ) and bipolar disorder (BPD) are highly heritable psychiatric disorders with complex genetic and environmental underpinnings. Allele-specific expression (ASE) has emerged as a critical mechanism linking noncoding genetic variants to disease risk through epigenetic and environmental modulation. Here, we performed whole-genome and transcriptome analyses of monozygotic twin pairs discordant for BPD or SCZ and identified that noncoding genetic variants drive differential ASE patterns of long noncoding RNA (lncRNAs) in affected individuals compared to their unaffected co-twins. We identified rs112651172 (C/G) as a functional ASE variant regulating PAXIP1-AS1 expression via allele-specific transcription factor binding: SMC3 binds the C allele, while CEBPB binds the G allele, resulting in G allele-specific upregulation in patients. In mice, G allele overexpression in the prefrontal cortex induced anxiety- and depression-like behaviors, social deficits, memory impairments, sensorimotor gating abnormalities, and synaptic dysfunction characterized by reduced neuronal excitability. Mechanistically, PAXIP1-AS1 promotes CNTNAP3 expression by sequestering the transcriptional repressor ZGPAT. Knockdown of CNTNAP3 in PAXIP1-AS1-overexpressing mice rescued synaptic and behavioral phenotypes. These findings establish rs112651172 as a functional noncoding variant that contributes to psychiatric phenotypes through ASE-driven, lncRNA-mediated regulation, highlighting the relevance of lncRNAs and ASE as potential molecular mechanisms and therapeutic targets in SCZ and BPD.

overall_design: RNA-seq profiling of female wild type mice overexpressing the PAXIP1-AS1 reference C allele (Ref),  female wildtype mice overexpressing the PAXIP1-AS1 alternative G allele (Alt) and their control (Ctr) .

first: Chaoying

last: Ni

first: He

last: Chen

first: Qiaqi

first: Yangyang

last: Liao

first: Yunqian

last: Wang

first: Linyan

last: Ye

first: Xiaohui

last: Wu

first: Hongyu

first: Tingyun

last: Jiang

first: Shufen

last: Li

first: Qiong

last: Yang

first: Hong

last: Xue

first: Zhongju

first: Feng

last: Yi


title: Intergenerational Regulation of Mosaic Supernumerary Chromosomes: Evidence for a Developmental Correction Mechanism from Clinical and Computational Models

city: Shanghai, China

first: Yang

last: Lily

address: No.1239, Siping Road, Yangpu District, Shanghai

institute: Tongji University

summary: Objective This study presents a rare case of father-to-offspring mosaic transmission of a supernumerary marker chromosome (SMC) and, through integration of literature analysis and computational modeling, proposes a novel embryonic selection-based regulatory mechanism. Methods Karyotyping and SNP-array were performed on amniotic fluid, cord blood, and parental samples. A systematic review identified 35 additional mosaic SMC transmission cases. Four computational frameworks—agent-based simulation, logistic regression, Bayesian inference, and Markov chain modeling—were used to test the hypothesis of selective regulation during early embryogenesis. Results The father carried a mosaic SMC at 11p11 (57%), transmitted to the fetus (38% in amniotic fluid, 45% in cord blood), with both individuals phenotypically normal and no pathogenic CNVs detected. Literature analysis showed consistent patterns of equal or reduced mosaicism in offspring. Modeling revealed that mild selection pressures could replicate observed retention patterns, supporting a non-random, developmentally regulated mechanism. Conclusion The combined clinical, literature-based, and computational evidence supports a model in which early embryos selectively eliminate SMC+ cells to maintain mosaicism at non-pathogenic levels. This proposed “Shepherd Mechanism” may underlie intergenerational mosaic regulation and provides a theoretical foundation for improved prenatal counseling in mosaic cases.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from Amniotic Fluid or peripheral blood samples.


title: Surgical revision of S. aureus infection increases virulence factor expression and activates a multi-tissue inflammatory response

city: Philadelphia

first: Theresa

last: Freeman

state: PA

address: 1015 Walnut Street

department: Orthopedic Surgery Research

institute: Thomas Jefferson University

summary: Surgical revision of infection can involve multiple procedures. Each revision activates a tissue injury response and disrupts the established bacterial biofilm. However, it is not well understood how the bacteria, immune system, and overall tissue environment coordinate their response to revision. Our results show that immunological niches already compromised by infection – such as the bone marrow, lymph nodes, and circulating blood – further upregulate pro-inflammatory programs in response to revision surgery. This enhanced inflammation at the incision site has no effect on reducing bacteria numbers. Instead, it leads to increased expression of virulence factors, enhanced tissue remodeling, and damage including bone osteolysis and muscle fibrosis. Whereas muscle fibrosis appears to resolve 14 days post-revision, osteolysis continues to progress. These findings show that revision surgery negatively impacts all tissues within the surgical site. It is therefore essential to question the risks and benefits of each revision on a case-by-case basis. Further, understanding the timing and tissue changes associated with revision of infected orthopedic sites will help inform the design of additional interventions to minimize tissue damage and maximize bactericidal effects.

overall_design: Gene expression was compared between uninfected and infected surgical incisions in Sprague-Dawley rats at a pre-revision surgery timepoint and between infected pre-revision rats and infected rats at three different timepoints (6 hours, 4 days, and 14 days post-revision). An index surgery created an initial incision, and revision surgery (and the pre-revision surgery timepoint) occurred 7 days after index. The rats were euthanized either pre-revision (7 days post index), 6 hours post-revision (7 days + 6 hours post-index), 4 days post-revision (11 days post-index), or 14 days post-revision (21 days post-index). The biceps femoris muscle was excised on the day of euthanasia for each rat and snap frozen. RNA was extracted from the snap-frozen muscle and sequenced at Novogene.

first: Carly

middle: J

last: Smith

first: Arianna

last: Moniodes

first: Amanda

last: Watkins

first: Autumn

last: Melvage

first: Thomas

middle: P

last: Thompson

first: Eirene

last: Choi

first: Abigail

last: Lucas

first: Brendan

last: Gilmore

last: Schaer

first: Noreen

last: Hickok


title: Tracing the molecular route to progression in miRNA biogenesis-defective thyroid lesions [Spatial_transcriptomics]

city: Hospitalet de Llobregat

first: Barbara

last: Rivera

address: Granvia de l'Hospitalet de Llobregat, 199

institute: IDIBELL

summary: Germline and somatic alterations in DICER1 and DGCR8 microprocessors confer risk of developing benign and malignant thyroid lesions, yet the molecular events driving malignant transformation remain unclear. We trace the molecular trajectories from benignity to malignancy in DICER1/DGCR8-mutated thyroid lesions using multi-omic profiling on 27 DICER1/DGCR8-mutated samples. Our findings reveal a progressive, specific, and linear accumulation of genetic alterations, which when combined with enhanced downregulation of miRNAs distinguished DICER1/DGCR8-malignant lesions from their benign counterparts. Compensatory hypomethylation of miRNA encoding genes characterised DICER1/DGCR8-benign lesions, but as the tumors progressed to malignancy, methylation was partly reimposed, reversing the attempts to activate miRNA-encoded genes and further compromising miRNA production. Transcriptomic analyses revealed mutation-specific effects on the microenvironment, whereby DICER1 mutations activated canonical thyroid cancer progression pathways, whereas altered DGCR8 associated with immune-related alterations. This work unveils specific molecular events underlying malignant progression of miRNA-biogenesis related thyroid tumors and identifies potential biomarkers and disease etiology mechanisms.

overall_design: We explored the spatial transcriptonal profiles of 1 sporadic DICER1-mutated case and 1 germline DGCR8-mutated case, capturing different histological components in each case. For the DICER1-case, this included a tumour core from a DICER1-mutated PDTC, the tumor’s capsule (DICER1-wildtype), a non-neoplastic nodular area (DICER1-wildtype benign thyroid lesion) and a norma lthyroid area (DICER1-wildtype). For the DGCR8-case, this included a tumour core from a DGCR8-mutated micropapillary thyroid carcinoma, a normal thyroid area adjacent to the tumour (DGCR8-mutated, 3 non-neoplastic nodular areas (DGCR8-mutated benign thyroid lesions) and a normal thyroid area (DGCR8-mutated). Each histological component was further segmented into PanCK+ (representing the epithelial population of the histological component) and VIM+ areas (representing the stroma-enriched population of the histological component). Differential expression analyses were performed between the different histological components at the region of interest level (PanCK+/VIM+), the epithelial level (PanCK+/VIM-) and stromal level (PanCK-/VIM+).

first: Anne-Sophie

last: Chong


title: The NF-Y Transcription Factor Complex as a Regulator of the Cholangiocyte Proliferation-Associated Phenotype in a Model of Murine Cholestasis

city: Rochester

first: Alexander

middle: Quinn

last: Wixom

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: Ductular reactive (DR) cells proliferate and contribute to liver injury during cholestasis by promoting myeloid cell derived inflammation. How DR cells promote this inflammation is unclear, and therefore, our aim was to gain insight into the DR cell-initiated signaling mechanisms contributing to this pathophysiologic process. Mice were fed a DDC diet for 10 days to induce liver injury and then switched to a chow diet to permit recovery, designated as R days. Profiling of isolated intrahepatic leukocytes by mass spectrometry revealed an abundant CX3CR1+ macrophage population on the DDC diet which declined during the recovery period. This observation was confirmed using Cx3cr1GFP mice to more specifically distinguish this recruited macrophage population. CX3CL1, the ligand for CX3CR1, in DR cells was expressed by cholangiocytes from DDC fed mice.  Next, cholangiocytes were isolated from control, DDC and R15 mice, and RNA-seq performed. IPA pathway analysis revealed activation of the pathogen induced cytokine storm pathway in cholangiocytes activated from DDC fed mice, and resolution of this pathway in R15 isolated cholangiocytes. SCENIC regulon analysis identified that NF-Y, a transcription factor complex, was activated only on the DDC diet, but not in control or R15 mice. Finally, normal human cholangiocytes (NHC) were treated with an siRNA of NF-YA and chemokine expression assessed by PCR. Expression of CX3CL1 and other chemokines decreased following transfection of NHC cells with siRNA targeting NF-YA as assessed by NanoString analysis. Collectively, these observations implicate NF-Y as a participant transcription factor in the proliferation-associated secretory phenotype.

overall_design: Wildtype C57BL/6 male mice, between 14-16 weeks of age, were fed the chow diet (control group), DDC diet for 10 days (DDC group), or DDC diet for 10 days and then transferred to a chow diet for 15 days (R15 group). Cholangiocytes were isolated from the livers and sequenced.

first: Kirsta

last: Olson

first: Anuradha

last: Krishnan

first: Patrick

last: Splinter

middle: Q

first: Maria Eugenia

last: Guicciardi

first: Kevin

last: Pavelko

first: Nidhi

last: Jalan-Sakrikar

first: Adiba

last: Azad

first: Nicholas

last: LaRusso

first: Gregory

last: Gores


title: PARP  and CLK/DYRK inhibition in therapy resistant high grade serous carcinoma

city: Denver

first: Benjamin

last: Bitler

state: CO

department: OB-GYN

institute: The University of Colorado

summary: Therapy-resistant high grade serous carcinoma tumors treated with control, olaparib and/or SM08502. The goals of the project were to determine differential gene expression and differential splicing in treated tumors.

overall_design: HGSC PDX model grown in NSG mice were treated with control, olaparib (50 mg/kg, daily, oral gavage), SM08502 (25 mg/kg, daily, oral gavage) or in combination.

first: Bradley

last: Corr

first: Thomas

last: Danhorn


title: Glutamine Synthetase Loss in β-Catenin-Mutant Hepatocellular Carcinoma Rewires Glutamine Metabolism to Promote Immunosuppressive Macrophage Adaptation [dataset3.scRNAseq]

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Recent therapeutic strategies using immune checkpoint inhibitors (ICIs) to treat hepatocellular carcinoma (HCC) have shown modest success. Response to ICIs is heterogeneous, and while mutational burden may predict stable responses, some HCCs with poor prognostic markers (e.g., CTNNB1 mutations) may still respond under favorable tumor immune microenvironment (TIME) conditions. We show that β-catenin-mutated HCCs lacking glutamine synthetase (GS) exhibit aggressive disease due to altered glutamate/glutamine (Glu/Gln) availability, driving macrophage adaptation that promotes immunosuppression. Loss of HCC Glul (encoding GS) forces hepatic macrophages to redistribute effort from immunologic to metabolic functions. Notably, depleting macrophages in GS-deficient, β-catenin-mutant HCC models improves survival. Additionally, HCC GS loss results in macrophage GS overexpression that maintains mTOR signaling in tumors, which is targetable. These findings reveal a metabolic dynamic between HCCs and the TIME which suggests that metabolic profiling, including GS expression, may refine patient selection for ICI therapies and improve outcomes under current standards of care.

overall_design: Single-cell sequencing from non-tumor bearing control and GS-KO mice in mouse liver samples. 11 week-old Glulf/f mice were infected with either AAV8-GFP or AAV8-Cre.

first: Evan

last: Dalgado

first: Panari

last: Patel

first: Junyan

last: Tao

first: Yekaterina

last: Krutsenko

first: Silvia

first: Daniel

last: Green

first: Raghad

last: Alzubali

first: Brandon

last: Lehrich

first: Jia-Jun

first: Tyler

last: Yasaka

first: Minakshi

last: Poddar

first: Sucha

last: Singh

first: Vik

last: Meadows

first: Aaron

middle: W

last: Bell

first: Aatur

last: Singhi

first: Satdarshan

last: Monga


title: Tracing the molecular route to progression in miRNA biogenesis-defective thyroid lesions [miRNA_profiling_data]

first: Barbara

last: Rivera

overall_design: In the study presented here, a cohort of 23 DICER1-/DGCR8-mutated thyroid lesions (10 benign and 13 malignant) was used to identify unique and shared miRNA profiles of mutant benign (DICER1, N=4; DGCR8, N=6) and malignant  (DICER1, N=10; DGCR8, N=3) thyroid lesions distinguishing them from  6 benign and 9 malignant non-DICER1/non-DGCR8 follicular-patterned thyroid lesions. This was performed with a total of 540 mature miRNAs.


title: Single-cell RNA sequencing of microglia derived from C9orf72 mutant and isogenic control human iPSCs

city: Paris

first: Michela

last: Deleidi

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine, INSERM UMR1163

summary: This study characterizes transcriptional differences in human iPSC-derived microglia carrying the C9orf72 hexanucleotide repeat expansion (C9) compared to isogenic controls.

overall_design: Human iPSCs were differentiated into microglia using a modified version of an established protocol involving embryoid body (EB) formation, hematopoietic induction, and microglial maturation. The differentiation process included sequential exposure to key cytokines and growth factors (BMP4, VEGF, SCF, IL-3, M-CSF, IL-34, and GM-CSF). After 3–4 weeks of maturation, floating microglia-like cells were collected and cultured for terminal differentiation. Single-cell RNA sequencing (scRNA-seq) was then performed to investigate cell-type composition and transcriptional changes associated with the C9orf72 mutation. This dataset enables exploration of C9-related molecular phenotypes in a human microglial context and provides a resource for studying neuroinflammatory mechanisms in ALS/FTD.

first: Insa

last: Hirschberg

first: Maria Jose

last: Perez J.


title: Single cell RNA sequencing reveals dynamic changes in the peritoneal microenvironment of patients undergoing dialysis for 3 years and provides new insights for peritoneal fibrosis

first: Siqi

last: Zheng

state: Guangdong province

address: Zhongshan 2nd Road

department: nephrology

institute: Guangdong Provicial People's Hospital

summary: Peritoneal dialysis related fibrosis (PD-related fibrosis) is one of the most common complications of PD and one of the main reasons for patients to stop PD, occurring almost exclusively in all long-term PD patients. The mechanism of PD-related fibrosis is currently not fully understood. Previous studies have shown that it is related to frequent peritonitis and the epithelial-mesenchymal transition (more accurately, mesothelial-mesenchymal transition) of peritoneal mesothelial cells caused by high glucose and high osmotic non physiologically compatible PD fluid. Due to the lack of effective prevention and treatment methods for PD-related fibrosis, the study of its mechanism is of great clinical significance. Collecting dialysis fluid from patients after 3 years of PDfor single-cell sequencing can help observe changes in the peritoneal environment and structural composition during dialysis, providing a new perspective for the prevention and treatment of PD-related fibrosis.

overall_design: We collected 2 liters of overnight PD fluid from a patient who underwent continuous ambulatory peritoneal dialysis (CAPD) for 3 years. Dialysis fluid is obtained within 1 hour after the patient's dialysis fluid flows out. Obtain exfoliated cells from dialysate by centrifugation at 3000rpm for 15 minutes, wash the cells twice with phosphate buffered saline (PBS) buffer, and finally resuspend the cells in culture medium containing 10% bovine serum albumin (BSA).

first: Shanshan

last: Deng

first: Guanglan

last: Li

first: Yan

last: Ying

first: Jiaying

first: Ganyuan

last: He

first: Wenxue

last: Hu

first: Xinling

last: Liang


title: Fibrin defines tissue stiffness and biomechanical signalling in regenerating zebrafish hearts as revealed by high-resolution stiffness mapping

city: Potsdam

first: Juliane

last: Münch

state: Brandenburg

address: Karl-Liebknecht-Strasse 24-25

department: Biochemistry and Biology

country: Germany

institute: University of Potsdam

summary: The infarction of the human heart leads to irreversible scar formation, which permanently impairs its mechanical properties and physiological functions. Interestingly, the zebrafish heart is capable of resolving scar tissue and regenerating injured myocardium, offering a unique opportunity to study the interplay between scar tissue and cardiac mechanical properties during regeneration. In this study, we developed a novel method combining atomic force microscope-based nanoindentation with confocal microscopy to generate an elasticity map of the zebrafish heart. This high-resolution mapping revealed distinct regions of stiffness within the injury site, despite the overall global mechanical properties remaining unaffected. Specifically, we identified a stiff area that is cell-poor and fibrin-rich, contrasting with the center of injury, which is as soft as the surrounding myocardium. Extensive whole transcriptome analyses uncovered several components of the coagulation and fibrinolysis cascade in the regenerating heart. Pharmacological inhibition of Serpine1, a regulator of fibrinolysis, demonstrated that reduced fibrin-mediated stiffness impacts the activation of biomechanical Hippo pathway signaling in adjacent endocardial cells. Our approach characterizes the mechanical properties of different regions in the zebrafish ventricle, highlighting fibrin as the stiffest element influencing biomechanical signaling. This suggests it may play a structural role in the regeneration process. The methodology presented here offers a detailed view of the biomechanical environment and mechanotransductive signaling in regenerating cardiac tissue, which is crucial for understanding regenerative mechanisms.

overall_design: RNAseq profiling of apexes of zebrafish hearts. Unijured hearts or hearts upon 1.5, 3, 7 and 14 days post cryoinjury were taken.

first: Salim

last: Abdelilah-Seyfried


title: Glutamine Synthetase Loss in β-Catenin-Mutant Hepatocellular Carcinoma Rewires Glutamine Metabolism to Promote Immunosuppressive Macrophage Adaptation [dataset2.scRNAseq]

first: Shuchang

last: Liu

overall_design: Single-cell sequencing from tumor bearing control and GS-KO mice in mouse liver samples. Tumor bearing Glulf/f mice infected with either AAV8-GFP or AAV8-Cre were used 7-weeks post-virus infection.

first: Evan

last: Dalgado

first: Panari

last: Patel

first: Junyan

last: Tao

first: Yekaterina

last: Krutsenko

first: Silvia

first: Daniel

last: Green

first: Raghad

last: Alzubali

first: Brandon

last: Lehrich

first: Jia-Jun

first: Tyler

last: Yasaka

first: Minakshi

last: Poddar

first: Sucha

last: Singh

first: Vik

last: Meadows

first: Aaron


title: Glutamine Synthetase Loss in β-Catenin-Mutant Hepatocellular Carcinoma Rewires Glutamine Metabolism to Promote Immunosuppressive Macrophage Adaptation


title: Sandfly saliva reprogrammes skin fibroblasts to enhance arbovirus infection

city: York

first: Yonca

last: Keskek Turk

address: Heslington Road

department: Skin Research Centre

country: United Kingdom

institute: University of York

summary: Arbovirus transmission by sand flies is a growing public health concern, yet the early skin events shaping infection outcomes remain undefined. We establish a new mouse model of Toscana virus (TOSV) infection that incorporates sand fly salivary factors to mimic natural transmission. Saliva from two distinct sand fly genera significantly enhanced infection and promoted neurological signs and joint inflammation, recapitulating key features of human TOSV disease. In the skin, dermal macrophages and fibroblasts were the main infected cell types, but only fibroblasts generated infectious virus. Saliva reprogrammed fibroblasts into a wound-healing state permissive to viral replication, driving local viral amplification, systemic spread, and thereby clinical disease. These findings identify skin fibroblasts as central determinants of host susceptibility and reveal that sand fly saliva actively remodels the skin to exacerbate viral pathogenesis. This work redefines the skin’s role in sand fly-transmitted infection and highlights new targets for therapeutic and vaccine development.

overall_design: Resting fibroblast cells isolated by Magnetic Activated Cell Sorting (MACS) were compared with fibroblast cells treated with sandfly salivary gland extract using RNA-seq

first: Sandy

last: Macdonald


title: A role for the cholinergic neuron circadian clock in RNA metabolism and mediating neurodegeneration

city: Chicago

first: Sharon

last: Tam

state: IL

address: 303 E Chicago Ave, Rm 13-270

institute: Northwestern University


title: Androgen receptors promote mitochondrial oxidative phosphorylation, carnitine metabolism, and resistance to palmitate lipotoxicity in ER-mutant breast cancer.

city: Aurora

first: Andrew

last: Goodspeed

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: The effect of androgen receptor (AR) in ER+ breast cancer remains controversial. We find that AR promotes tumor cell growth, oxidative phosphorylation, and fatty acid oxidation under conditions mimicking long-term aromatase inhibition. AR also promotes expression of the mitochondrial and peroxisomal acylcarnitine synthesis enzyme CRAT. AR inhibition decreases CRAT expression and CRAT knockdown is sufficient to inhibit OXPHOS. AR inhibition does not elicit a broad anti-OXPHOS transcriptomic signature, but does affect the expression of a few key metabolic enzymes. AR antagonism also induces a metabolomic signature consistent with severe OXPHOS dysfunction. This work identifies AR as a regulator of CRAT and OXPHOS in ER+ breast cancer.

overall_design: To identify how AR antagonism affects OXPHOS in ER-mutant breast cancer, we performed bulk mRNA sequencing on Y537S ER-mutant CRISPR knock-in breast cancer cells treated with DMSO or 30 uM Enzalutamide for 96 hours.

first: Sessions

last: Dane

first: Spoelstra

last: Nicole

first: Caino

last: Cecilia

first: Yu

last: Min

first: Goodspeed

last: Andrew

first: Richer

last: Jennifer


title: LOSS OF MFAP5 AND ITS EFFECT ON SKIN HOMEOSTASIS AND WOUND HEALING

first: Chen

last: Han

address: 801 S. Paulina St.

department: Center for Wound healing and Tissue Regeneration

institute: University of Illinois Chicago

summary: MFAP5, also known as microfibrillar-associated glycoprotein-2 (MAGP2), may influence parameters of skin wound healing related to scar formation. To further elucidate its role in skin wound healing, we assessed skin wound repair in Mfap5-/- mice. Loss of MFAP5 significantly reduced wound closure rates and angiogenesis while enhancing neutrophil and macrophage influx into wounds. Loss of MFAP5 also reduced the deposition of total and mature collagen in uninjured normal skin (NS), but not in wounds. Furthermore, NS dermis of Mfap5-/- mice was thinner without any reduction in tensile strength. Single-cell RNA-sequencing of NS and wounds from Mfap5+/+ and Mfap5-/- mice revealed two fibroblast subclusters that express MFAP5 more highly than other subclusters. Enrichment analysis of the differentially expressed genes (DEGs) in these two subclusters suggests these fibroblasts engage in extracellular matrix (ECM) deposition and angiogenesis. Mfap5+/+ and Mfap5-/- fibroblasts also exhibit transcriptomic differences throughout in vivo wound healing, though as healing progressed, fewer differences were evident. To examine the direct effect of MFAP5 on fibroblasts outside of the wound space, fibroblasts were isolated from Mfap5+/+ and Mfap5-/- mice for in vitro analysis. MRNA-sequencing of Mfap5+/+ and Mfap5-/- fibroblasts found genes involved in cellular migration and proliferation, ECM synthesis, and angiogenesis to be downregulated in Mfap5-/- fibroblasts vs Mfap5+/+ fibroblasts. Functionally, Mfap5-/- fibroblasts exhibited reduced migration, contractility, proliferation, and ECM deposition. Our findings indicate that MFAP5 is a multifunctional glycoprotein in skin wound healing as it promotes angiogenesis and collagen deposition, inhibits inflammatory cell influx, and promotes pro-scarring fibroblast behavior.

overall_design: The effects that the loss of MFAP5 has on the fibroblast transcriptome may be obscured during in vivo healing, as a myriad of cell-cell, cell-ECM, and cell-cytokine interactions may compensate for the loss of MFAP5. Thus, to assess intrinsic changes to the fibroblast transcriptome and infer mechanisms for the functional deficits observed following the loss of MFAP5, we performed mRNA-sequencing on Mfap5+/+ and Mfap5-/- fibroblasts cultured in vitro. Differential expression analysis of the raw count data generated by Novogene (Novogene America) was performed with the DESeq2 package (v1.20.0) in R [51]. Only genes with an average raw count of at least 10 across all samples were analyzed. P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate (FDR). Genes with an adjusted p-value (p.adj) < 0.05 were assigned as being differentially expressed after DESeq2 analysis.  In this study, we assessed differentially regulated genes in Mfap5+/+ and Mfap5-/- fibroblasts at baseline using the following parameters: p.adj < 0.01 and log (fold change) > 0.25 or log(foldchange) < -0.25. Genes with a negative log(foldchange) were considered upregulated in Mfap5+/+ fibroblasts, while genes with a positive log(fold change) were considered upregulated in Mfap5-/- fibroblasts.


title: Glutamine Synthetase Loss in β-Catenin-Mutant Hepatocellular Carcinoma Rewires Glutamine Metabolism to Promote Immunosuppressive Macrophage Adaptation [dataset1.Spatial.Transcriptomics]

first: Shuchang

last: Liu

overall_design: Spatial transcriptomics data was measured by Resolve Biosciences Molecular Cartography on non-tumor (AAV8-GFP control) and tumor (AAV8-Cre) samples. Each condition includes 8 slides.

first: Evan

last: Dalgado

first: Panari

last: Patel

first: Junyan

last: Tao

first: Yekaterina

last: Krutsenko

first: Silvia

first: Daniel

last: Green

first: Raghad

last: Alzubali

first: Brandon

first: Jia-Jun

last: Bell

first: Aatur

last: Singhi

first: Satdarshan

last: Monga


title: AMPK-dependent epigenetic regulation of metabolism mediates the anti-cancer action of pterostilbene in hepatocellular carcinoma.

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

country: Canada

institute: The University of British Columbia

summary: Scope: Disrupted metabolism, often implicated in hepatocellular carcinoma (HCC), is linked to aberrant epigenetic patterns. Dietary polyphenols, including pterostilbene (PTS), have been demonstrated to remodel epigenetic landscapes and restore metabolic homeostasis by regulating the activity of AMP-activated protein kinase (AMPK), a protein recently shown to orchestrate a diverse set of networks to epigenetically mediate transcription. We therefore explored the mechanistic involvement of AMPK in the epigenetic effects of PTS in HCC. Methods and Results: We incorporated PTS into a choline-deficient amino acid defined HCC-inducing diet (CDAA) in male Fisher-344 rats and found significant attenuation in HCC development compared to CDAA alone. Transcriptomics by RNA-sequencing revealed PTS-upregulated targets, that were enriched in key metabolic processes, including the folate (Aldh1l1), methionine (Bhmt) and sarcosine (Dmdgh) cycles. PTS-mediated gene upregulation was linked to lower levels of histone H3-methylation at lysine 27 (H3K27me3) at gene promoters. Mechanistic studies in HCC HepG2 cells revealed that AMPK inhibition abolished epigenetic gene activation in response to PTS, which was accompanied by diminished binding of H3K27me3-demethylase KDM6A at promoters of PTS-target genes. Conclusion: Our findings provide evidence for new disease vulnerabilities that arise from epigenetic/metabolic changes and constitute novel opportunities for preventative and therapeutic success in HCC.

overall_design: Male F344 rats were housed two per cage in a temperature-controlled environment (24°C) with a 12-hour light/dark cycle and were provided ad libitum access to water and food. Upon arrival at the animal facility at 4 weeks of age, the rats underwent one week acclimation period during which they were maintained on a choline-sufficient L-amino acid-defined (CSAA) diet. Following acclimation, the rats were randomly assigned to one of four experimental groups: Group 1 (CSAA), Group 2 (choline-deficient L-amino acid-defined, CDAA), Group 3 (CDAA supplemented with RSV, CDAA+PTS), and Group 4 (CDAA supplemented with PTS, CDAA+PTS), with n=6 rats per group. As shown in the scheme in Figure 1A, Group 1 and 2 were on CSAA diet for first 3 weeks, whereas Group 3 and 4 were on CSAA diet supplemented with RSV or PTS, respectively, for first 3 weeks of the experiment. The CSAA and CDAA diets were obtained from Dyets Inc. (Bethlehem, PA, USA) and prepared in pellet form. RSV and PTS were obtained from Biotang Inc. (Albuquerque, NM, USA) and incorporated into the respective diets by Dyets Inc. at a dose of 1.2 and 1.34 g/kg of diet, respectively. The concentration of RSV and PTS in diets was measured using liquid chromatography-mass spectrometry (LC-MS) as described by Moser et al. [29], with modification of calibration with authentic standards for RSV and PTS. Body weight and food intake were recorded weekly throughout the 60-week experimental period. At the conclusion of the study, the rats were killed by carbon dioxide asphyxiation followed by cervical dislocation. Liver tissues, including tumors, nodules, or normal tissue in the absence of tumors, were collected for subsequent analyses. Tumor and nodule volumes were calculated using the formula: volume = (length × width^2)/2. The study design and all procedures followed strictly the animal use protocol #1112000342 approved by the Institutional Animal Care and Use Committee at the involved institutions. RNA-seq data on CDAA and CSAA is deposited under GSE199443.

first: Cayla

last: Boycott

first: Megan

last: Beetch

first: Katarzyna

last: Lubecka-Gajewska

first: Benjamin

middle: S

last: Ramsey

first: Sandra

last: Torregrosa-Allen

first: Bennett

last: Elzey

first: Abigail

last: Cox

first: Nadia

last: Atallah Lanman

first: Aline

last: de Conti

first: Min

last: Li

first: Mario

last: Ferruzzi

first: Igor

last: Pogribny

last: Stefanska (corresponding author)


first: Chen

last: Han

overall_design: Wound tissues were collected from male and female Mfap5+/+ or Mfap5-/- mice (n=4-5 animals for each sex and each experimental group) on days 0 (D0), 3 (D3), and 7 (D7) post-wounding. A total of 48-60 mice were used for single-cell RNA-sequencing. Collected wound tissues were pooled separately based on sex, experimental group, and time post-wounding. Tissue collected from D0 was considered NS. After collection and pooling, tissues were micro-dissected, minced, and incubated at 37°C in a dispase (Worthington Biochemical Corporation, Lakewood, NJ, Catalog # 9001-92-7)/liberase (Roche, Basel, Switzerland, Catalog # 5401135001) solution supplemented with DNAse I (Sigma-Aldrich, Catalog # D5025) and penicillin-streptomycin (Gibco, Waltham, MA, Catalog # 15-140-122) for 60 min with constant rotation. The final concentrations for each solution component were 3.6 mg/mL dispase, 30 µg/mL liberase, 100 µg/mL DNAse I, and 100 Units/mL-100 µg/mL penicillin-streptomycin. Post-incubation, cell suspensions were passed through a 40 µM cell strainer (ThermoFisher Scientific, Waltham, MA). Single-cell suspensions were treated with 1x RBC lysis buffer (Biolegend, San Diego, California, Catalog # 420301), washed, and resuspended in cold PBS before debris removal using the Debris Removal Solution (Miltenyi Biotec, North Rhine-Westphalia, Germany, Catalog # 130-109-398) according to the manufacturer’s protocol. All cells were then frozen in a mixture of 70% DMEM (Corning Inc, Corning, NY), 30% Fetal Bovine Serum (FBS) (GeminiBio, Sacremento, CA), and 10% DMSO (Sigma-Aldrich) before being sent to Novogene (Novogene America, Sacramento, CA). Thawed cell suspensions underwent dead cell removal, and only samples with >100,000 cells, >70% viability, and minimal to no cell clumps were used for single-cell RNA sequencing. GEM generation, barcoding, post-GEM-RT cleanup, cDNA amplification, and cDNA library construction were performed using Single-cell 3′ v3 chemistry (10X Genomics, Pleasanton, California). Libraries were then sequenced on an Illumina NovaSeq 6000 (Illumina, San Diego, CA). Dead cell removal, cell counting and viability testing, GEM generation, barcoding, post-GEM-RT cleanup, cDNA amplification, library preparation, quality control, and sequencing were all performed by Novogene (Novogene America). Transcripts were mapped to the mouse reference genome (GRCm38/mm10) using Cell Ranger Version 7.0.0. Before downstream analyses, low-quality cells were removed and data integration was performed using the RPCA method. Quality control metrics included keeping genes present in at least 10 cells and cells with at least 200 genes, while removing cells with either a mitochondrial gene expression greater than 10% or a multiplet likelihood score greater than 0.25. Post-quality control, 72,876 cells remained for downstream bioinformatic analyses. All data quality control and downstream analyses were done by us using R version 4.4.1 with Bioconductor v3.20. Clustering of cells was performed using the Seurat R package. In brief, digital gene expression matrices were column-normalized and log-transformed. Principal component analysis (PCA) was first performed on the list of highly variable genes to identify cell clusters. Genes were selected for inclusion in PCA with an average expression > 0.01 and dispersion > 1.0. We used the Jackstraw method in Seurat to identify significant principal components (PCs). The top 10 PCs were used for clustering with the Louvain modularity-based community detection algorithm to generate cell clusters (FindClusters function, 18 clusters with resolution = 0.2). Cell cluster marker genes were identified using the FindAllMarkers() function according to the following criteria: adjusted p-value (p.adj) < 0.05 and log(fold-change) (Log2FC) > 0.25. To present high-dimensional data in a two-dimensional space, we performed UMAP analysis using the results of PCA with significant PCs as input. Differentially expressed marker genes used for cell type identification were selected using the following criteria: p.adj < 0.05, log(fold-change) > 2, pct.1 > 0.40 (percentage of cells where the gene is detected within the cluster), and pct.2 < 0.20 (percentage of cells where the gene is detected in other clusters). Differentially expressed marker genes meeting these cut-offs were input into EnrichR, and likely cell types were identified using the top 5 enrichments from the following cell marker curated databases: 1) CellMarker 2024, Tabula Muris, and PanglaoDB. Known marker genes used for skin cell types in previously published single-cell RNA-sequencing studies were also used. We followed the same procedures as above for the sub-clustering analysis of fibroblasts. The top 15 PCs were used for clustering, and 6 subclusters (subclusters 0-5) were obtained with a resolution = 0.1. Fibroblast subcluster marker genes were identified using FindAllMarkers() function according to the following criteria: p.adj < 0.05 and log(fold-change) > 0.25. To present high-dimensional data in two-dimensional space, we performed UMAP analysis using the results of PCA with significant PCs as input. DEG signatures for each fibroblast subcluster were analyzed to determine if a unique fibroblast subcluster differentially expressed MFAP5 as a marker gene in NS and during wound healing in vivo. Gene ontology (GO) enrichment for biological processes (BP) terms and Reactome pathway enrichment analysis was performed on DEGs with a p.adj < 0.05 and log(fold-change) > 1 for the fibroblasts subclusters that differentially expressed MFAP5 relative to other fibroblast subclusters via the EnrichR package in R. GO BP terms with a p.adj < 0.05 following Benjamini and Hochberg's approach for controlling the false discovery rate (FDR) were considered statistically significantly enriched terms, and only the top 25 significantly enriched terms based on p.adj were included in our analyses. We used the FindAllMarkers() function to identify DEGs between fibroblasts isolated from Mfap5+/+ or Mfap5-/- mice at each time point. We identified DEGs between Mfap5+/+ or Mfap5-/- fibroblasts based on the following criteria: p.adj < 0.01, average Log2FC> 0.25, and the percentage of cells where the gene is detected in either Mfap5+/+ or Mfap5-/- fibroblasts (pct.1) is more than 25% (pct.1 > 0.25). GO BP and Reactome pathway term enrichment analysis was performed on the list of differentially upregulated and downregulated genes in Mfap5-/- fibroblasts relative to Mfap5+/+ fibroblasts via the EnrichR package in R version 4.4.1. GO terms with a p.adj < 0.05 following Benjamini and Hochberg's approach for controlling the FDR were considered statistically significantly enriched, and only the top 25 significantly enriched terms based on p.adj were included in our analysis.


title: Enhancement of activation-induced T cell proliferation by SIRPG in a CD47-independent manner

city: Boston

first: Flavien

last: Marguerie

address: 60 Fenwood Road

department: Rheumatology and Immunology

institute: Brigham and Women's Hospital

summary: SIRPG, a primate-specific type 1 transmembrane protein in the Signal Regulatory Protein (SIRP) family, is predominantly expressed in T cells. It contains a short cytoplasmic domain, which does not contain any known signaling motif, and its only known ligand is CD47. Several genetic variations in SIRPG, including the V263A (rs6043409) polymorphism, linked to increased type 1 diabetes risk, highlight its potential importance. However, its expression and physiological role remain largely unclear due to its absence in rodents. Here, we demonstrate that SIRPG and GzmB exhibit near mutually exclusive expression in resting peripheral CD8+ T cells. We further show that SIRPG serves as a valuable marker for GzmK-expressing CD8+ T cells in peripheral blood and inflamed synovial fluid and that its expression in both CD4+ and CD8+ T cells is upregulated by anti-CD3 stimulation, with further enhancement by the TNFα inhibitor adalimumab, but not certolizumab. While SIRPG ablation minimally affects T cell activation and IFNγ/TNFα production, it impairs the expression of mitosis-regulating genes like UBE2C and TOP2A, leading to reduced proliferation, and alters the expression of certain activation-induced surface molecules, including CRTAM. Notably, SIRPG-mediated proliferation and CRTAM expression are cell-autonomous and CD47-independent. Structural and functional analyses reveal that SIRPG-driven proliferation is independent of its extracellular D1 domain, not significantly affected by the V263 variant, but dependent on its cytoplasmic domain. Collectively, our findings offer novel insights into the expression, function, and mechanism of action of SIRPG in T cells.

overall_design: RNA-seq profiling of healthy donor PBMCs and their CRISPR-mediated SIRPG knockout derivatives (SIRPG+ and SIRPG-) at Day 2 (D2) and Day 4 (D4). The cells were first activated with anti-CD3 and anti-CD28 for CRISPR editing. SIRPG+ and SIRPG- were maintained in IL-2 at the same density for 3 days before being stimulated again with a-CD3 and IL-2. On D2 and D4 after restimulation, the live population (7AAD-) was sorted into CD3+ CD4+ or CD3+ CD8+ T cell subsets

first: Mohammad

last: Saifi

last: Greary

first: David

last: Barnes

first: Anna

middle: H

last: Jonsson

first: I-Cheng

last: Ho


title: Study of the mechanism of action of 4-octyl itaconate in attenuating myocardial ischemia-reperfusion injury after heart transplantation

city: wuhan

first: hao

last: tian

state: hubei

address: No.9, Zhangzhidong Road, Wuchang District

institute: Renmin Hospital of Wuhan University

summary: It is important to mitigate myocardial ischemia-reperfusion (IR) injury for improving the success of heart transplantation (HT) and the quality of life of patients.4-OI is a derivative of itaconate with similar chemical properties and biological activities as itaconate. However, 4-OI could overcome the limitations of itaconate in in vivo applications such as inefficient cellular uptake and rapid metabolism, making it more suitable for exploratory studies in the therapeutic direction.In our study, we demonstrated that 4-OI is an effective therapeutic strategy against myocardial ischemia-reperfusion injury after heart transplantation.

overall_design: We established a syngeneic cervical heterotopic heart transplantation model in recipient mice undergoing cardiac transplantation with or without intraperitoneal injection of 4-OI (50 mg/kg) 12 h before and 2 h after reperfusion, and the recipient mice were then executed 24 h after reperfusion to remove the transplanted hearts.

first: Hao

last: Tian

first: Yonghong

last: Xiong

first: Zongyuan

last: Xia


title: Inhibition of Scarb1 on endothelial cells attenuates pressure overload-induced heart failure progression

city: Shinjuku-ku

first: Toshiomi

last: Katsuki

state: Tokyo

address: Shinanomachi 35

department: Cardiology

institute: Keio University Hospital

summary: RNA sequencing for human heart microvascular endothelial cells with and without BLT-1 treatment.

overall_design: mRNA profiles of human heart microvascular endothelial cells with and without BLT-1 treatment. Three samples for each group.


title: Single cell and single nucleus transcriptomics of precision-cut liver slices

city: Trieste

first: Davide

last: Selvestrel

address: Padriciano 99

country: Italy

institute: International Centre for Genetic Engeneering and Biotechnology (ICGEB)

summary: We performed single cells and single nucleus RNA sequencing of an organotypic ex vivo model of ductular reaction (DR) based on precision-cut liver slices (PCLS) from mouse and human livers, which faithfully preserves the native tissue architecture and key hepatic cell types. This system enables ex vivo propagation of DR from previously injured livers, as well as de novo induction of reactive BECs in uninjured tissues, providing an experimental framework for mechanistic dissection in disease-relevant settings.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mouse and human PCLS were embedded in basement membrane extract (BME) and cultured on transwell inserts in expansion medium. Mouse PCLS were harvested after 96 hours, while human PCLS were collected after 144 hours of culture. At the respective timepoints, samples were processed for transcriptomic analysis. For single-nucleus RNA sequencing (snRNA-seq), PCLS were snap-frozen in liquid nitrogen and stored at –80 °C prior to nuclei isolation and library preparation. In contrast, for single-cell RNA sequencing (scRNA-seq), freshly collected PCLS were immediately dissociated and processed for single-cell suspension preparation and downstream library construction.

first: Beatrice

last: Anfuso

first: Suresh

last: Velnati

first: Giovanni

last: Sorrentino


title: Loss of EGFR prevents the synergistic early-phase impact of obesity-associated metabolic and humoral stress on primary VSMC – stressor synergy, sex-dependence

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

summary: RNAsequencing was performed for murine primary aortic smooth muscle cells (SMC) and endothelial cells (EC) from wildtype animals (WT) and animals with conditional EGFR knockout in VSMC (KOsmc) after exposing the cells to obestity-associated stress factors.

overall_design: Cells were exposed to for 24h  to 20 mM glucose + 100 µM free fatty acids (HG+FFA) or 30 nM angiotensin II + 300 nM epinephrine (AII+NA) or all four stressors together (ALL).

first: Sindy

last: Rabe

first: Narjes

last: Ansari-Nasiri

first: Michael

last: Kopf

first: Sigrid

last: Mildenberger

first: Gerald

last: Schwerdt

first: Barbara

last: Schreier

last: Gekle


title: Gene expression profiling of tunicamycin-induced ER stress in HepG2 hepatoma cells

city: Tartu

first: Tiit

last: Örd

address: Riia 23b/2

department: Institute of Genomics

country: Estonia

institute: University of Tartu

summary: Endoplasmic reticulum (ER) stress, a disruption of ER homeostasis, is involved in the pathophysiology of several human diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD). MASLD, formerly known as nonalcoholic fatty liver disease (NAFLD), is characterized by an excessive accumulation of hepatic lipids. To characterize ER stress-induced changes in the expression of genes involved in lipid metabolism, HepG2 human hepatoma cells  were exposed to tunicamycin, followed by transcriptome profiling. Among genes involved in lipid biosynthesis, GPAT3 was strongly activated by tunicamycin while many other genes involved in this process (e.g., DGAT2, AGPAT2, AGPAT3, GPAT1, DGAT1 and GPAT4) were downregulated. Since GPAT proteins catalyze rate-limiting step in the de novo synthesis of glycerophospholipids and triglycerides, the unique expression pattern of GPAT3 potentially links it to ER stress-associated accumulation of lipids in hepatic cells.

overall_design: RNA-Seq of HepG2 cells treated with tunicamycin or mock treated as control. Five replicate experiments done on separate days.

first: Daima

first: Tõnis


title: BCL-11 enables adaptive stress responses to environmental challenges

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1/99

institute: DZNE, German Center for Neurodegenerative Diseases

summary: This study investigated the transcriptional impact of hypomorphic bcl-11 mutations.

overall_design: RNAseq profiling of eggs extracted from daf-2(e1370), daf-2(e1370); bcl-11(bon125) and daf-16(mu86); daf-2(e1370);bcl-11(bon125) adults. Worms were fed with OP50-1 at 20℃. Eggs were incubated at 27℃ for two hours after bleaching.

first: Patrizia

last: Niedworok

first: Rossella Erminia

last: Ciliberti

first: Beijia

last: Xie

first: Amal John

last: Mathew

first: Elena

last: De-Domenico

first: Stefan

last: Paulusch

first: Marc

last: Beyer


overall_design: RNAseq anaylsis of adult wildtype, bcl-11(bon125), bcl-11(bon144), daf-2(e1370), daf-2(e1370);bcl-11(bon125) and daf-2(e1370);bcl-11(bon144) mutant Caenorhabditis elegans.


title: MLL1 complex is a critical regulator of fetal hemoglobin repression

city: Bethesda

first: Yang

last: Du

state: MD

address: 4301 Jones Bridge Road

department: Pediatrics

institute: Uniformed Services University of the Health Sciences

summary: Increasing fetal-type hemoglobin (HbF) expression in adult erythroid cells holds promise in the treatment of sickle cell disease (SCD) and -thalassemia. We have identified MLL1 complex as a critical regulator of fetal and embryonic hemoglobin repression. Knockdowns of MEN1 and KMT2A, encoding essential components of the complex, caused a significant downregulation of BCL11A expression and a substantial increase in - and -globin mRNA levels in HUDEP-2 cells. Significant binding of MEN1 and KMT2A were readily detected at the promoter and a critical enhancer of BCL11A in HUDEP-2 cells, suggesting that BCL11A is a direct transcriptional target of MLL1 complex. Consistent with these results, MEN1 or KMT2A knockdown in normal human CD34+ hematopoietic stem and progenitor cells (HSPCs) induced to undergo erythroid differentiation also significantly decreased their BCL11A expression and increased their - and -globin expression and the production of F cells in the culture. Treatment of these cells with MENIN inhibitors yielded similar results and promoted erythroid differentiation with minimal effects on their growth. These findings underscore a critical role of MLL1 complex in regulating fetal and embryonic hemoglobin expression and suggest that MENIN inhibitors could offer a promising therapeutic approach for sickle cell disease and -thalassemia.

overall_design: RNA-seq profiling of HUDEP-2 cells transduced with a lentiviral shRNA targeting MEN1 and a non-targetting control shRNA at 72 hours after transduction.


title: GLMP promotes EGFR-TKI resistance by activating autophagy and RhoA pathway in non-small cell lung cancer

city: Nanjing

first: Renhua

last: Guo

state: Jiangsu

address: 101 longmian Avenue

institute: Nanjing Medical University

summary: Here, we report that the EGFR-TKI resistance mechanism is mediated by lysosome-related regulation. We established an osimertinib-resistant cell line, designated PC9OR, derived from the parental PC9 cells. The overexpression of glycosylated lysosomal membrane protein (GLMP) in PC9OR promotes resistance to Osimertinib. Mechanistically, GLMP could regulate the ubiquitination of RhoA and promote resistance by activating the epithelial-mesenchymal transition (EMT). Our findings provide a potential therapeutic strategy to overcome resistance to EGFR-TKIs.

overall_design: RNA-seq analysis was performed after knockdown of GLMP in PC9OR cell line.

first: Xiao

last: Liang

first: Jiali

last: Xu

first: Erbao

last: Zhang


title: Impacts of VTC3 and VTC2 on transcriptome under illumination in Arabidopsis

city: Matsue

first: Takanori

last: Maruta

address: 1060 Nishikawatsu

institute: Shimane University

summary: VITAMIN C DEFECTIVE 3 (VTC3) is a distinctive protein with both kinase and phosphatase domains and is essential for ascorbate accumulation in Arabidopsis. In the vtc3 mutant, ascorbate levels are approximately 50% of those in the wild type, and light-induced increases in the ascorbate pool size are markedly suppressed. The regulation of the ascorbate pool size by light involves GDP-L-galactose phosphorylase (VTC2), a key biosynthetic enzyme. To elucidate the physiological function of VTC3, we compared the transcriptomes of vtc3, wild-type, and vtc2 plants. Contrary to expectations, the loss of VTC3 had minimal impact on the transcriptome. Among the few genes upregulated in the vtc3 mutant, several were related to pathogen responses.

overall_design: RNA-seq profiling of wild type, vtc2, and vtc3 shoots under illumination. After 48 hours of dark adaptation, the plants were exposed to light for 6 hours.

first: Yasuhiro

last: Tanaka

first: Takahiro

last: Ishikawa


title: A SET domain-containing protein and HCF-1 maintain transgenerational epigenetic memory

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

institute: University of Cambridge

type: Non-coding RNA profiling by high throughput sequencing

summary: Epigenetic information can be inherited through a process known as transgenerational epigenetic inheritance (TEI). TEI can be initiated and maintained by small RNAs and histone modifications. The latter includes histone methylation, deposited by proteins with methyltransferase activity, including SET domain-containing proteins. Other SET domain-containing proteins with no catalytic methyltransferase activity, also adopt roles in chromatin and gene expression regulation. Here, we describe SET-24, a SET domain-containing protein in Caenorhabditis elegans that belongs to a family of catalytically inactive SET proteins. SET-24 localises to germline nuclei and is required for germline immortality. Additionally, the inheritance of small RNA-driven epigenetic silencing is compromised in set-24 mutants. Using quantitative proteomics and yeast two-hybrid assays, we found that SET-24 interacts with Host Cell Factor 1 (HCF-1), a protein involved in epigenetic regulation and associated with known chromatin remodelling complexes, like COMPASS, which deposits H3K4me3. In set-24 mutants, hundreds of genes display increased H3K4me3 levels at their transcription start sites. While these changes are not matched at the transcriptional level, small RNA production is disrupted in approximately one fifth of those genes, which are normally targeted by small RNA pathways. We propose that SET-24 is a factor required to maintain epigenetic memory in the germline by maintaining a chromatin environment permissible to small RNA biogenesis over generations.

overall_design: We perfomed RNASequencing, ChIP sequencing and small RNA sequencing to discover the function of set-24

first: Chenming

last: Zeng

first: Giulia

last: Furlan

first: Miguel

last: Vasconcelos Almeida

first: Juan

last: C. Rueda-Silva

first: Jonas

last: Mars

first: Pedro

last: Rebelo-Guiomar

first: Meng

last: Huang

first: Shouhong

last: Guang

first: Falk

last: Butter

first: Eric

last: Miska


title: Intestinal adaptations increase basolateral intestinal glucose uptake and glycolysis in a Cystic Fibrosis mouse model

city: Cleveland

first: Aura

last: Perez

state: OH

address: 10900 Euclid Avenue

institute: CWRU

summary: The intestinal manifestations of Cystic Fibrosis (CF) continue to be a source of morbidity despite major advances in CF therapies over the past several years. CF intestinal disease may include obstruction at birth or throughout the lifespan, dysmotility, constipation, small intestinal bacterial overgrowth, and abdominal pain and discomfort. People with CF also have a five to ten-fold increased risk of developing gastrointestinal cancers earlier in life, the reason for which remains largely unknown. The mechanisms underlying the intestinal manifestations of CF are not fully understood. Impaired chloride and bicarbonate ion transport due to absent or dysfunctional CFTR results in dehydrated, viscous mucus that coats the intestinal lumen and altered pH. These changes are thought to create an environment that hinders digestive enzymatic and immune function to promote dysbiosis, dysmotility, and obstruction. The other major organs of digestion, including the pancreas and hepatobiliary system, are also affected in CF, which can result in a variety of symptoms mainly related to fat malabsorption, in addition to various hepatic and biliary pathologies. Most of what is known about the CF intestines has been garnered from studies on the luminal function pertaining to digestion, absorption, mucus accumulation, and bacterial dysbiosis, but little has been described regarding the serosal side. In the process of evaluating systemic carbohydrate utilization in CF mice, we identified the intestine as a key site of increased glucose uptake from circulation in CF. Consequently, we employed a series of complementary in vivo and ex vivo, transcriptional and functional approaches to characterize intestinal glucose demand and metabolism in a mouse model of CF to gain new insights into mechanisms of intestinal disease.  We show elevated GLUT1 (Slc2a1) expression in both CF intestinal tissue and isolated crypts, suggesting GLUT1 is responsible for the increased intestinal glucose uptake from the circulation in CF mice. We also identified concomitant increases in glycolysis, in addition to evidence of a proliferative adaptive response in the CF intestine. Taken together, these results are indicative of an increased intestinal glucose demand in CF to maintain intestinal homeostasis and offer a novel approach to understanding CF intestinal disease that may result in new markers of disease status and potentially new critical insight into cancer risk in people with CF. Our findings emphasize a continued need to investigate how the interplay of numerous digestive and absorptive defects in CF contribute to disease pathogenesis to develop more effective therapies for the gastrointestinal manifestations of CF.

overall_design: RNA-seq profile of whole tissue duodenum, jejunum, and ileum, and jejunum crypts from WT mice and G542X mice

first: Alexander

last: Lesser

first: Chunying

last: Wu

first: Shuyu

last: Hao

first: Bernadette

last: Erokwu

first: Derek

last: Host

first: Anjum

last: Jafri

first: Elisha

last: Barbato

first: Jean

last: Eastman

first: Senthilkumar

last: Sankararaman

first: Chris

middle: A

last: Flask

first: Mitchell

last: Drumm


title: Ly6G+Nur77+ perivascular macrophages initiate type-2 immune responses to allergens in the lung

city: BETHESDA

first: Beatriz

last: León

address: 10 CENTER DR

department: Division of Intramural Research (DIR)

institute: National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH)

summary: The mechanisms of allergen sensing and type 2 immune response initiation remain unclear. Using a house dust mite (HDM)-induced allergic airway model, we demonstrated that host detection of protease activity in HDM was crucial for initiating T helper type 2 (Th2) responses. This process was driven by the major allergen Der p 1, a cysteine protease, which was sensed by protease-activated receptor 2 (PAR2) on a novel population of perivascular lung macrophages expressing Ly6G and nuclear receptor Nur77. These macrophages required PAR2 and Nur77 for activation and accumulation and regulated conventional dendritic cell (mDC) migration to draining mediastinal lymph nodes (mLN) via cysteinyl leukotriene (CysLTs) production. CysLTs enhanced CCR7-driven migration of mDCs toward its ligand, CCL21, facilitating arrival to mLNs for T cell priming and expansion. Inhibiting CysLTs biosynthesis reduced mDC migration and dampened Th2 allergic responses, highlighting new therapeutic paths and mechanisms in type 2 immunity.

overall_design: three groups of samples: 1) lung perivascular macrophages isolated after 24h papain treatment (4 mouse replicates), 2) lung perivascular macrophages isolated from untreated mice (3 mouse replicates), 3) CCR2+ bone marrow monocytes isolated from untreated mice (3 mouse replicates)

first: Audrey

last: Meloun

first: Holly

last: Bachus

first: Crystal

last: Lewis

first: Brittany

last: Dulek

first: Shivangi

last: Dave

first: Dave

last: Hill

first: Gabriela

last: Pessenda

first: Jose

middle: C

last: Gonzales

first: P'ng

last: Loke

last: Rosenberg


title: Effect of anti-IL-4 and anti-IL-13 vaccination in a mouse model of atopic dermatitis

city: Toulouse

first: Aurélie

last: Mougel

address: Avenue des arènes romaines CHU Purpan 31300 Toulouse

institute: INSERM

summary: The effect of anti-mouse IL-4 and/or anti-mouse IL-13 Kinoid vaccines was assessed in a model of atopic dermatitis. Mice were immunized with IL-4 and/or IL13 Kinoids (or the carrier protein CRM197 alone as control). Atopic dermatitis-like pathology was induced by repeated epicutaneous exposures to house dust mite and the enterotoxin B from Staphylococcus aureus (SEB). Lesional skin biopsies were collected for bulk RNA sequencing analysis.

overall_design:
Bulk RNAseq on back skin of vehicle or HDM-SEB-treated mice (immunized with Kinoids® or control) at D56 (end of the model) (n = 30 samples).
RNA extraction was performed using RNeasy Lipid Tissue Kit (Qiagen). Libraries were produced using the llumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina), according to the manufacturer’s instructions. RNA sequencing was performed on one S4 lane of the Illumina NovaSeq 6000 instrument (Illumina, San Diego, CA, USA), using the NovaSeq 6000 S4 v1.5 Reagent Kit (300 cycles) and a paired-end 2 ×150 pb strategy. Raw reads were processed with the nf-core/rnaseq workflow v3.12.0 using Nextflow v22.12.0-edge. Analyses on raw counts are performed on R v4.2.2. The DESeq2 package (v1.38.3) was used to normalize data and run the differential expression analyses. Differentially expressed genes were defined as genes with an adjusted p-value below 0.05 and an absolute log2 Fold Change above 1.

first: Margot

last: Zahm

first: Adeline

last: Chaubet

first: Katia

last: Lemdani

first: Vincent

last: Serra

first: Laurent

last: Reber


title: SHMT2 modulates the transcriptome and metabolism profiles to promote the tumor phenotypes of bladder cancer HT-1376 cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

institute: Nissi Biotech

summary: Bladder cancer (BLCA) is a common malignant tumor of the urinary system. The development and progression of BLCA are controlled by multiple regulatory molecules, which have not been widely investigated. In this study, we explored the functions and downstream targets of serine hydroxy methyltransferase 2 (SHMT2) by silencing its expression using small interference RNA (siSHMT2) in HT-1376 cells. Whole transcriptome and metabolism profiles were deeply analyzed to identify the molecular targets of SHMT2. We found that siSHMT2 significantly reduced the proliferation rate and altered the cell cycle stages of HT-1376 cells. Moreover, siSHMT2 can modulate the expression of hundreds of genes (DEGs), including 126 upregulated and 106 downregulated DEGs. We then found that the most significant DEGs were tightly associated with progression of cancers, including PTMA, HNRNPR, RAPH1, TRAF3IP1, CNBP, and PRR15. At the same time, the alternative splicing profile was also regulated by siSHMT2, including the skipped exon as the dominant AS types. Finally, we identified the differential metabolites (DMs), and found the metabolism profile was significantly regulated by siSHMT2. Besides the purine metabolism, we observed that valine, leucine and isoleucine biosynthesis and degradation, TCA cycle, and propanoate metabolism were among the top pathways of DMs. In summary, we highlight the important roles of SHMT2 in HT-1376 cells and identified its downstream molecular targets, which are associated with the development of BLCA and can be used as therapeutic targets of BLCA in future.

first: Xiaobo

last: Guo

first: Gang

last: Li


title: Obese adipose tissue extracellular vesicles activate mitochondrial fatty acid -oxidation to drive colonic stemness

city: Denver

first: Parsa

last: Haque

state: Colorado

address: 1635 Aurora Ct, Aurora, CO 80045

institute: University of Colorado Anschutz Medical Campus

summary: Obesity increases the risk of colorectal cancer (CRC) development and accelerates disease progression. Obesity adversely affects the visceral adipose tissue (VAT) leading to increased secretion of extracellular vesicles (EVs). However, the crosstalk between VAT and CRC tumor cells still remains unclear. EVs are lipid-membraned particles that transfer cargo to and/or induce signaling in other cells. Here, human VAT-derived non-obese (N-OB) and obese (OB) EVs through proteomics and investigated the functional interaction between CRC cells and EVs through RNA-seq analysis of EV-treated CRC cells. EVs were isolated from VAT obtained from obese (BMI>30) and non-obese patients (BMI<30). Unbiased proteomics revealed that compared to N-OB EVs, OB EVs were enriched with glycolytic enzymes like triose phosphate isomerase (TPI1). This enrichment was associated with increased TPI1 protein levels in CRC cells and elevated glycolytic activity. OB EV-treated cells also exhibited increased stemness-associated genes, 3D-spheroid formation and Apcmin/+ tumoroid self-renewal capacity. In vivo, mice with an adipocyte-specific knockout of EV cargo sorting protein, Tsg101 (Tsg101ΔAd), have altered EV cargo composition with reduced glycolytic enzyme levels. Functionally, Tsg101ΔAd-EVs were able to protect against high-fat diet (HFD)-induced increase in glycolysis and stem-like ability. Moreover, Apcmin/+:Tsg101ΔAd mice were protected against HFD-induced enhanced tumorigenesis. Collectively, this study identifies adipocyte EVs, and its metabolic cargo, as an important regulator of CRC cell metabolism and function, promoting intestinal tumorigenesis.

overall_design: Human CRC cell line HCT-116 was treated with vehicle, N-OB EV (BMI 25) and OB-EV (BMI 46) for 48 hrs. RNA was isolated for RNA-seq, with n=3 TECHNICAL REPLICATES.

first: Arianne

last: Theiss