title: Single-cell RNA-seq and spatial transcriptomics characterize CD8+ exhausted T cells in pancreatic ductal adenocarcinoma

city: Huzhou

first: Yan

last: qiang

address: No. 1558, North Third Ring Road, Wuxing District, Huzhou City.

institute: huzhou central hospital

summary: Pancreatic cancer resists immunotherapy due to a suppressive immune microenvironment where CD8⁺ T cells play a key role. Using single‑cell RNA sequencing and spatial transcriptomics, we characterized CD8⁺ exhausted T (Tex) cells in pancreatic ductal adenocarcinoma (PDAC). We generated single‑cell profiles from PDAC tumors and matched peripheral blood mononuclear cells, and performed T cell sub‑analysis. We found CXCL13 upregulated and GZMK downregulated in CD8⁺ Tex cells. Cell‑cell interaction analysis showed that T cells most frequently interacted with myeloid cells and cancer cells via ligand‑receptor pairs; INHBA⁺ macrophages and cancer cells communicated most with CD8⁺ Tex cells. Two key LR pairs (SPP1–integrin α4β1 and PLAUR–integrin α4β1) mediated crosstalk between cancer cells and CD8⁺ Tex cells, confirmed by immunofluorescence, spatial mapping, and protein docking. High SPP1 and PLAUR expression correlated with poor prognosis in TCGA‑PAAD. These findings provide a resource for understanding CD8⁺ T cell exhaustion in PDAC.

overall_design: To elucidate the relationship between cancer cells and CD8+Tex cells in the tumor microenvironment and to analyze the mechanism of exhaustion. Deep sequencing of pancreatic tissue was performed. In this study, scRNA-seq was performed on 5 fresh PDAC tumor tissue samples and 5 matched peripheral blood samples, and spatial transcriptome sequencing was performed on 5 formalin fixed paraffin-embedded (FFPE) sections of PDAC tumor tissue from the same five patients, enabling integrated analysis of the same tumors. Our findings reveal the heterogeneity and communication pathway of CD8+Tex cells in the PDAC tumor microenvironment and peripheral blood mononuclear cells (PBMCs) of patients. It is expected to provide new targets and strategies for the comprehensive treatment of pancreatic cancer.

first: Jing

last: Mao

first: Chenxin

last: Yan

first: Ying

last: Mei

first: Yanjun

last: Yao

first: Xingxia

last: Zhuang

first: Kuai

last: Yu

first: Gangzhao

last: Gu

first: Hengzhi

first: Yu

last: Zheng

first: Yunyao

last: Wei

first: Shuwen

last: Han

first: Qiang


title: The extreme diversity of retinal amacrine cells has deep evolutionary roots [axolotl]

status: Public on Jun 16 2026

city: Berkeley

first: Dario

last: Tommasini

address: 242 Stanley Hall

country: USA

institute: UC Berkeley

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Amacrine cells (ACs) comprise a heterogeneous class of inhibitory neurons in the vertebrate retina, exhibiting morphological and functional complexity rivaling that of cortical interneurons. Here, we integrate single-cell and single-nucleus transcriptomic atlases from 24 vertebrate species to reconstruct the evolutionary origins of this extreme diversity. We identify 42 orthologous AC types (oACs), most of which exhibit a one-to-one correspondence across amniotes and, in many cases, across vertebrates. While core molecular identities are conserved, AC types vary in abundance and gene expression across species, likely reflecting adaptations to distinct visual ecologies. AC diversity scales with that of retinal ganglion cells (RGCs), indicative of co-evolution. Finally, we suggest that ACs arose from an AC-RGC hybrid precursor, with glycinergic ACs diverging early in vertebrate evolution, followed by a bifurcation between RGCs and GABAergic ACs. Together, these findings establish a unified evolutionary framework for understanding the diversity, development, and function of a class of inhibitory neurons across vertebrates.

overall_design: Retinas were collected from 5 wild type axolotls between 4-8 months old, as well as 5 6-month-old wild type Iberian ribbed newts. Salamander retinas were dissected in cold amphibian PBS (PBS + 25% volume water) and snap-frozen by submerging in an isopentane bath cooled on liquid nitrogen. Nuclei were isolated according to the described protocol (PMID: 39240519) using 30 seconds of lysis incubation. Isolated nuclei were resuspended in 1X Diluted Nuclei Buffer (10X Genomics; PN- 2000207) and 8000-16000 nuclei were loaded per reaction for downstream assays. Single-nucleus transcriptomes were generated using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10X Genomics cat. PN-1000285) following 10X Genomics protocol CG000338 Rev F. Libraries were sequenced at the Novogene Sequencing Core (Sacramento, CA & Beaverton, OR) on the NovaSeq X Plus instrument (Illumina). Read alignment and cell calling were performed using CellRanger-ARC (10X Genomics).

first: Aboozar

last: Monavarfeshani

first: Vishruth

last: Dinesh

first: Josh

last: Hahn

first: Jared

last: Tangeman

first: Olivier

last: Marre

first: Seth

last: Blackshaw

first: Teresa

last: Puthussery

last: R. Sanes

first: Karthik

last: Shekhar


title: The extreme diversity of retinal amacrine cells has deep evolutionary roots [newt]


title: Effect of keratinocyte-intrinsic VISTA deletion on UV-induced type I interferon and inflammatory gene expression in mouse epidermis

city: LEBANON

first: SLADJANA

last: SKOPELJA-GARDNER

address: ONE MEDICAL CENTER DR

institute: DARTMOUTH COLLEGE

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

overall_design: Refer to individual Series


title: Effect of keratinocyte-intrinsic VISTA deletion on UV-induced type I interferon and inflammatory gene expression in mouse epidermis [scRNA-seq]

summary: Type I interferon (IFN-I) signaling is a central driver of cutaneous lupus erythematosus (CLE), but the keratinocyte-intrinsic checkpoints that restrain UV-triggered IFN-I responses remain poorly defined. Here we report that the immune checkpoint VISTA (encoded by Vsir) is expressed in epidermal keratinocytes and acts cell-intrinsically to suppress cGAS–STING–dependent IFN-I induction following ultraviolet (UV) exposure. Conditional deletion of Vsir in keratinocytes (K14Cre-Vsir^fl/fl^) results in markedly elevated expression of interferon-stimulated genes (ISGs), chemokines, and antigen presentation machinery at baseline and is further amplified by acute UVB irradiation. Co-deletion of STING (Sting1) abrogates this hyperinflammatory transcriptional program, placing VISTA upstream of the cGAS–STING–IFN-I axis. Mechanistically, our data support a model in which VISTA restrains EGFR/LRIG1/NUMB-dependent stabilization of phosphorylated (pY245) STING, thereby tuning the magnitude of UV-induced IFN-I output. These findings identify a keratinocyte-intrinsic role for VISTA in suppressing sterile cutaneous inflammation and have translational relevance for photosensitive autoimmune skin disease and for cutaneous immune-related adverse events of VISTA-targeted therapies.

overall_design:
Bulk RNA-seq profiling of mouse skin isolated from K14Cre-Vsir^fl/fl^ (keratinocyte VISTA cKO), Vsir^−/−^ (whole-body KO), and littermate control mice, harvested at baseline(NoUV) and 3 h post-acute UVB exposure (500 mJ/cm²). N = 3-4  biological replicates per genotype × treatment condition.
DD1A_4815_NOUV,BC001,
DD1A_4976_NOUV,BC002,
DD1A_4978_NOUV,BC003,
DD1A_4979_NOUV,BC004,
KRTCRE_4810_NOUV,BC005,
KRTCRE_4811_NOUV,BC006,
KRTCRE_4975_NOUV,BC007,
KRTCRE_4980_NOUV,BC008,
DD1A_4977_UVD1,BC009,
DD1A_4839_UVD1,BC010,
DD1A_5311_UVD1,BC011,
DD1A_5313_UVD1,BC012,
KRTCRE_5109_UVD1,BC013,
KRTCRE_5111_UVD1,BC014,
KRTCRE_5396_UVD1,BC015,
KRTCRE_5397_UVD1,BC016,

first: Zachary

last: Peters

first: Sladjana

last: Skopelja-Gardner


title: Hyperosmotic stress induces a large-scale rewiring of 3D chromatin interactions [RNA-seq]

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

summary: Cells rapidly adapt to hyperosmotic stress through coordinated molecular responses. To determine how three-dimensional (3D) chromatin structure contributes to this process, we profiled chromatin interactions, architectural protein occupancy, and transcriptional dynamics in human cells exposed to sorbitol-induced hyperosmotic stress. We performed time-resolved Hi-C to measure stress-induced remodeling of chromatin loops and domains, CUT&Tag to quantify CTCF, RAD21, YAP1, and H3K27ac occupancy at loop anchors, and RNA-seq to capture stress-responsive transcriptional programs. These data reveal global loss of pre-existing chromatin contacts and concurrent formation of de novo, transient loops enriched for retained CTCF and cohesin, as well as transcriptional responses that are temporally layered and largely decoupled from loop remodeling. This dataset provides a resource for investigating how nuclear architecture and transcriptional regulation respond to hyperosmotic stress.

overall_design: HEK293 eGFP-YAP cells were serum-starved for 1 hour and then exposed to 200 mM sorbitol to induce hyperosmotic stress. Chromatin organization was profiled by in situ Hi-C at eight time points (0 min, 10 min, 30 min, 1 h, 3 h, 6 h, 12 h, and 24 h) to capture the formation, loss, and recovery of chromatin interactions. To assess the generality of chromatin remodeling, additional Hi-C experiments were performed in HEK293 wild-type and HCT116 cells with and without 1 hour of sorbitol treatment. Transcriptional responses were measured by stranded RNA-seq across a time course (0 h, 1 h, 3 h, 6 h, 9 h, 12 h, and 24 h). To quantiy changes in architectural protein occupancy, CUT&Tag for CTCF and RAD21 was performed in untreated and 1-hour sorbitol-treated HEK293 cells.

first: JP

first: Andrea A.

last: Perreault

first: Zack

last: Drum

first: Chenxi

last: Xu

first: Doris

last: Cruz Alonso

first: Gelila

last: Petros

first: Yijia

last: Wu

first: Ivana Y.

last: Quiroga-Barber

first: Isha

last: Sahasrabudhe

first: Justin

last: Demmerle

first: Gang Greg

last: Wang

first: Danfeng

last: Cai

first: Douglas

last: Phanstiel


title: Effect of keratinocyte-intrinsic VISTA deletion on UV-induced type I interferon and inflammatory gene expression in mouse epidermis [bulk RNA-seq]

first: SLADJANA

summary: (abstract)Type I interferon (IFN-I) signaling is a central driver of cutaneous lupus erythematosus (CLE), but the keratinocyte-intrinsic checkpoints that restrain UV-triggered IFN-I responses remain poorly defined. Here we report that the immune checkpoint VISTA (encoded by Vsir) is expressed in epidermal keratinocytes and acts cell-intrinsically to suppress cGAS–STING–dependent IFN-I induction following ultraviolet (UV) exposure. Conditional deletion of Vsir in keratinocytes (K14Cre-Vsir^fl/fl^) results in markedly elevated expression of interferon-stimulated genes (ISGs), chemokines, and antigen presentation machinery at baseline and is further amplified by acute UVB irradiation. Co-deletion of STING (Sting1) abrogates this hyperinflammatory transcriptional program, placing VISTA upstream of the cGAS–STING–IFN-I axis. Mechanistically, our data support a model in which VISTA restrains EGFR/LRIG1/NUMB-dependent stabilization of phosphorylated (pY245) STING, thereby tuning the magnitude of UV-induced IFN-I output. These findings identify a keratinocyte-intrinsic role for VISTA in suppressing sterile cutaneous inflammation and have translational relevance for photosensitive autoimmune skin disease and for cutaneous immune-related adverse events of VISTA-targeted therapies.

overall_design: designBulk RNA-seq profiling of mouse skin isolated from K14Cre-Vsir^fl/fl^ (keratinocyte VISTA cKO), Vsir^−/−^ (whole-body KO), and littermate control mice, harvested at baseline(NoUV) and 3 h post-acute UVB exposure (500 mJ/cm²). N = 3-4  biological replicates per genotype × treatment condition.


title: RNA-seq analysis of Eleutheroside E-treated MASH mouse liver

city: nanjing

first: xin

last: Qian

address: No. 24 Tongjia Lane, Gulou District, Nanjing, Jiangsu Province, P.R.China

country: China

institute: China Pharmaceutical University

summary: This study investigated the effects of Eleutheroside E on hepatic gene expression in metabolic dysfunction-associated steatohepatitis (MASH). A high-fat diet-induced MASH mouse model was established, and liver tissues from control, MASH model, Eleutheroside E-treated MASH, and resmetirom-treated MASH groups were collected for RNA-seq analysis.

overall_design: C57BL/6J mice were divided into four groups: normal control group, high-fat diet-induced MASH model group, Eleutheroside E-treated MASH group, and resmetirom-treated MASH group. After 8 weeks of model establishment, mice in the Eleutheroside E-treated group were orally administered Eleutheroside E at 100 mg/kg for 4 weeks, and mice in the resmetirom-treated group were orally administered resmetirom at 3 mg/kg for 4 weeks. Mice in the normal control group and MASH model group were orally administered 0.5% CMC-Na as vehicle control for 4 weeks. At the end of treatment, liver tissues were collected for RNA extraction, library construction, and high-throughput RNA sequencing.


title: Acquired resistance to the RAS(ON) multi-selective inhibitor daraxonrasib guides rational combination therapy strategies in pancreatic cancer

city: Redwood City

first: Ximo

last: Pechuan-Jorge

state: CA

address: 700 Saginaw Drive

institute: Revolution Medicines

summary: Daraxonrasib is an orally bioavailable RAS(ON) multi-selective tri-complex inhibitor of the oncogenic mutant and wild-type variants of N, H and KRAS. We previously reported encouraging efficacy in a Phase 1/2 clinical trial evaluating daraxonrasib monotherapy at clinically active dose levels in patients with previously treated, RAS mutant metastatic pancreatic adenocarcinoma (PDAC), providing the basis for confirmatory evaluation in the randomized Phase 3 RASolute 302 clinical trial  . Here, we report mechanisms of acquired resistance to daraxonrasib monotherapy observed through targeted sequencing of over 800 genes in paired pre- and end of treatment ctDNA samples from 44 patients in the Phase 1/2 clinical trial. Treatment-emergent genomic alterations in the RAS signaling pathway were observed in more than half (26/44; 59%) of these patients including, most notably, mutant KRAS amplifications in one third (16/44; 36%), as well as alterations in receptor tyrosine kinase (RTK) (4/44, 9%), MAPK (11/44, 25%) and PI3K (4/44, 9%) pathways. Notably, no acquired secondary KRAS mutations were observed, distinct from resistance profiles of mutant-selective KRAS G12C(OFF) inhibitors. To corroborate these clinical findings, we found or mechanistically established concordant mechanisms of daraxonrasib resistance in human and murine preclinical models of PDAC, including mutant KRAS and MYC amplification, and RTK upregulation, with these alterations guiding various combination therapy concepts. Notably, daraxonrasib combined with agents targeting DNA Damage Response (DDR), receptor tyrosine kinases (RTKs), or with the mutant-selective RAS(ON) G12D inhibitor zoldonrasib, averted resistance in preclinical models. Collectively, these results show that most daraxonrasib genomic resistance mechanisms drive reactivation of RAS pathway signaling and guide potential combination strategies in PDAC for further investigation.

overall_design: We report mechanisms of acquired resistance to daraxonrasib monotherapy observed through targeted sequencing of over 800 genes in paired pre- and end of treatment ctDNA samples from 44 patients in the Phase 1/2 clinical trial, with these alterations guiding various combination therapy concepts. Most daraxonrasib genomic resistance mechanisms drive reactivation of RAS pathway signaling and guide potential combination strategies in PDAC for further investigation.

first: Ida

last: Aronchik

first: Sumit

last: Kar

first: Yongxian

last: Zhuang

first: Ethan

last: Ahler

first: Lick

middle: P

last: Lai

first: Vidya

last: Seshadri

first: Yu

middle: C

last: Yang

first: Ashenafi

last: Bulle

first: Marie

last: Menard

first: Biswadeep

last: Nayak

first: Mark

last: Labrecque

first: Julien

last: Dilly

first: Eejung

last: Kim

first: Lingyan

last: Jiang

first: Jason

last: Yano

first: Urszula

middle: N

last: Wasko

first: Ciara

last: Helland

first: Sean

last: Bredeson

first: Brett

last: Garrick

first: Yevgeniy

last: Gindin

first: Brad

last: Sickler

first: Xing

last: Wei

first: Kyle

last: Seamon

first: Jingjing

first: Kian

last: Huat-Lim

first: Matthew

last: Holderfield

first: Elsa

last: Quintana

first: Aparna

last: Hegde

first: Zeena

last: Salman

first: Alexander

last: Starodub

last: Spira

first: Wungki

last: Park

first: David

middle: S

last: Hong

first: Minal

last: Barve

first: Meredith

last: Pelster

last: Sommerhalder

first: Salman

middle: R

last: Punekar

first: Ignacio

last: Garrido-Laguna

first: Brian

last: Wolpin

first: Anirban

last: Maitra

first: Clay

last: Gustafson

first: Steve

last: Kelsey

first: Jacqueline

middle: A


title: SOX9-BAF multi-omics profiling in human colon cancer cell models

city: Boston

first: Nilay

last: Sethi

state: Massachusetts

address: 450 Brookline Avenue, D742

department: MCO

institute: Dana-Farber cancer institute

summary: This study combines matched ATAC-seq, RNA-seq, and CUT&RUN profiling in human colon cancer cell models to track SOX9 degradation/recovery, BAF subunit perturbation, histone-mark occupancy, ARID1A/ARID1B knockdown, and SOX9-variant chromatin accessibility. The main time-course series uses HT29-dTAG cells; the SOX9-variant ATAC-seq subset uses LS180 cells.

overall_design: Matched high-throughput sequencing profiles were generated across multiple assay types in human cell-line systems. The main HT29-dTAG series covers a full SOX9 degradation/recovery time course (DMSO, D2, D4, D5, D7, D10, and D13), including ATAC-seq, RNA-seq, a first CUT&RUN time course, a second CUT&RUN batch with fewer time points and additional BAF subunits, and a multi-time-point histone-mark CUT&RUN series. A separate ATAC-seq batch profiles ARID1A/ARID1B perturbation, and a final ATAC-seq batch profiles SOX9 variants in LS180 cells.

first: Zhixin

last: Li


title: Spatial transcriptomic analysis of patient- and cell line-derived high grade serous ovarian cancer spheroids

city: London

first: Fred

last: Dick

state: Ontario

address: 790 Commissioners Road East

department: Pathology & Laboratory Medicine

country: Canada

institute: Western University

summary: In vitro models of high grade serous ovarian cancer spheroids are often used to study mechanisms of cell dormancy and resistance to chemotherapy, but their ability to accurately mimic spheroid biology in patients is unclear. We performed spatial transcriptomic profiling of in vitro cell line- and in vivo patient-derived high grade serous ovarian cancer spheroids to profile spheroid cell composition and gene expression programs between models. Our analysis reveals the predominant cell types that make  up patient spheroids and common expression patterns that shared between models.

overall_design: 3 High Grade Serous Ovarian Cancer Cell Lines (HeyA8, OVCAR8 and iOvCa147) were used to generate cell-line derived spheroid samples. Cell lines growing on adherent cell culture plates were transferred on to ultra low attachment plates and incubated for 7 days to allow spheroid formation. Patient-derived high grade serous ovarian cancer spheroids were isolated from ascites fluid obtained from debulking surgery of 3 patients (526, 530, 498). Patient spheroids were prepared by filtering the ascites fluid through a 100 um mesh filter. Both cell line- and patient-derived spheroid samples were washed with PBS, fixed in 10% formalin and embedded into paraffin blocks to generate tissue microarrays (TMA_1-A = cell lines, TMA_2-B = patient samples)

first: Michael

last: Roes

first: Joon

last: Kim


title: Gene expression alterations in left atrial tissue were identified by RNA sequencing (RNA-seq) in a murine model of myocardial infarction–induced atrial fibrillation.

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Artesunate exhibits well-documented anti-inflammatory, antioxidant, and anticancer properties. While its therapeutic potential in ameliorating myocardial infarction (MI) has been well established, its role in MI-induced atrial fibrillation (AF) remains poorly understood.

overall_design: Mice were randomly assigned to three experimental groups: Sham + Vehicle, MI + Vehicle, and MI + ART. The myocardial infarction (MI) model was established via left anterior descending coronary artery ligation. Starting two days prior to MI surgery and continuing until day 7 post-surgery, ART (10 mg/kg) was administered intraperitoneally every other day. Total RNA was isolated with TRIzol (Invitrogen) from left atrial tissues (n=3 per group) at each time point according to the manufacturer's instructions.

first: Yun-Long

last: Zhang

first: Xiao

last: Han


title: Epigenome analysis of DU145 samples

city: Guangzhou

first: Bo

last: Xuan

address: No.280, Outer Ring East Road, Higher Education Mega Center, Panyu District, Guangzhou City

department: School of Basic Medical Science

institute: Guangdong Pharmaceutical University

type: Methylation profiling by genome tiling array

summary: The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles in DU145 cell samples.

overall_design: Genomic DNA was isolated from DU145 cells and bisulfite conversion was performed. Add 0.1 N NaOH to the sample to denature the DNA to single-stranded DNA. After neutralization, add the whole genome amplification reagent, and incubate overnight at 37 °C. The DNA fragments were precipitated by adding isopropanol, and the fragmented DNA was enriched by centrifugation at 4 °C and purified. After the precipitated DNA is dried in the air, a hybridization buffer reagent is added to re-dissolve the DNA precipitate. Hybridize the resuspended DNA sample with the prepared chip and place it in a hybridization oven overnight. Wash away unhybridized and non-specifically hybridized DNA for subsequent staining and extension. Using the captured DNA as a template, a single-base extension reaction is performed on the chip, and a detectable label group is added to the chip to distinguish the methylation of the sample. Put the reaction-completed chip into XC4 reagent and then put it in a vacuum environment to dry for 1 hour. Put the processed chip into a scanner, use laser to excite the fluorescent group of the single-base extension product on the chip, and the scanner obtains the fluorescence emitted by the fluorescent group and generates a high-resolution picture. The data thus obtained is directly imported into GenomeStudio software for analysis, so as to obtain the methylation data of each sample. Samples included normal and UHRF1 knockdown DU145 cell samples, Each sample is repeated three times.


title: Differential immune cell distribution between arterial and venous blood in healthy rats

city: Wuhan

first: Longpeng

address: No. 461 Luoyu Rd. Hongshan District, Wuhan

institute: Wuhan Sports University

summary: We previously identified differentially expressed miRNAs between arterial and venous blood in rats; however, whether immune cell composition and transcriptional states differ along the arterial–venous axis remains unclear. Here, single-cell RNA sequencing of 119,481 PBMCs, complemented by flow cytometry and protein-level validation, were performed to characterize immune heterogeneity between arterial and venous blood. Cell composition analysis showed enrichment of T cells in arterial blood, whereas B cells, NK cells, and monocytes were more abundant in venous blood. At the subset level, naïve T cells were enriched in arterial blood, while CD8⁺ effector memory T cells were increased in venous blood. NK cell analysis demonstrated enrichment of cytotoxic NK subsets in venous blood and resting NK subsets in arterial blood, whereas monocyte subset proportions were comparable between compartments. Transcriptomic analysis revealed reduced JAK–STAT signaling in venous PBMCs, consistent with decreased STAT3 and NF-κB phosphorylation. Subset-specific analysis further showed reduced TNF/NF-κB signaling and enrichment of ribosome-associated pathways in venous T cells, enhanced cytotoxic, chemokine, and NF-κB–related programs in venous NK cells, and attenuated TNF/NF-κB signaling with increased ribosome-associated activity in monocytes, indicating functional reprogramming without compositional changes. Collectively, these findings demonstrate coordinated but cell type–specific immune adaptations along the arterial–venous axis, identifying blood sampling site as a critical determinant of immune readouts and a previously underappreciated source of variability in immunological studies.

overall_design: We performed single-cell RNA sequencing on paired arterial and venous peripheral blood mononuclear cells (PBMCs) from five rats.

first: Sijie

last: Lai

first: Shufan

last: Yang

first: Shaohui

last: Jia

first: Qinghua

last: Cui


title: Genome-wide Screening Identifies Unique Host-Directed Drugs and Pro-viral Signalling Pathways for SARS-CoV-2

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

institute: University of Saskatchewan

summary: SARS-CoV-2 is a positive-sense RNA virus that was responsible for the devastating COVID-19 pandemic. Although the current disease burden is less severe, there are limited treatment options, and a looming threat of the emergence of variants and future pandemics. To address these challenges, we performed genome-wide CRISPR knockout screens in a novel human lung cell line NCI-H23ACE2, as well as in HEK293TACE2 cells, with SARS-CoV-2 Wuhan strain, and identified several host-dependency factors including NRAS, KAT5, HTR3E and GNL3L. Drugs targeting some of these dependency factors, donepezil, dH-ergocristine, trametinib and sorafenib, showed effective pan-coronaviral inhibition in cell lines. Trametinib also showed inhibition of SARS-CoV-2 Delta variant in primary human airway tissue model (ALI). We also demonstrate that SARS-CoV-2 inhibits IFN-β induction through an NRAS/Raf/MEK/ERK signaling pathway dependent mechanism. Our study highlights the efficiency of a bilateral approach of gene silencing and antiviral screening to identify host-dependency factors and effective antivirals.

overall_design: genome-wide CRISPR knock-out screen for H23 and HEK93 cell lines with ACE2 overexpression. Total of 12 samples

first: Juveriya

middle: Q

last: Khan

first: Karthic

last: Rajamanickam

first: Frederick

first: Darryl

last: Falzarano

first: Anil

last: Kumar

first: Joyce

last: Wilson


title: RNA-seq analysis of Ythdf1-deficient SVF-derived adipocytes

city: Hangzhou

first: Shun

last: Chen

address: No. 866 Yuhangtang Road, Hangzhou, Zhejiang Province, China

institute: Zhejiang University

summary: This dataset contains bulk RNA-seq profiles of stromal vascular fraction (SVF)-derived adipocytes isolated from wild-type and Ythdf1 knockout mice. SVF cells were induced to undergo adipogenic differentiation in vitro, and RNA-seq was performed to identify transcriptomic changes associated with Ythdf1 deficiency.

overall_design: SVF cells were isolated from inguinal white adipose tissue of wild-type and Ythdf1 knockout mice and differentiated in vitro. RNA-seq was performed on three biological replicates per genotype. Differential gene expression was analyzed between Ythdf1 knockout and wild-type SVF-derived adipocytes.


title: Genome-wide characterization of extrachromosomal circular DNA and its functional role in colon cancer carcinogenesis and progression [Circle-Map]

city: Suzhou

first: Wenbo

state: Jiangsu Province

address: No.199 Ren'ai Road

institute: Soochow University

summary: Extrachromosomal circular DNAs (eccDNAs) are defined as distinct genomic entities of circular and mobile DNA molecules, but their molecular functions in and impact on breast cancer (BC) are rarely known. This study used Circle-seq to analyze eccDNAs from 19 BC tissues and 17 adjacent normal tissues. We found that eccDNAs are present on all chromosomes and enriched in seven eccDNA hotspot genes (HSGs) associated with the BC pathway. Several eccDNAs harboring entire genes (eccGenes) and eccDNAs harboring miRNAs (eccMIRs) were identified and linked to cancer-relevant pathways. Synthetic eccMIR6748, eccMIR6508, and eccMIR3142 elevated miRNA expression in MCF-7 cells, with eccMIR6748 promoting BC cell migration and invasion by upregulating miR-6748, which suppresses tumor suppressor candidate factor 5 (TUSC5) at the post-transcriptional level. eccMIR6748 also influences BC progression via the p38 mitogenactivated protein kinase (MAPK) signaling pathway. These findings suggest that eccDNAs, which contain functional genomic segments, play a role in BC initiation and progression, offering a dynamic source of genomic plasticity and potential as biomarkers and therapeutic targets.

overall_design: This study includes three complementary sequencing assays on human samples to investigate circular DNA, microRNA, and mRNA expression profiles.A total of 6 samples were analyzed, comprising two experimental groups with 3 biological replicates per group. A: Circle seq (circular DNA). Paired end 150 bp sequencing on Illumina NovaSeq 6000. Linear DNA was removed by exonuclease treatment, followed by rolling circle amplification. Clean reads were aligned to the reference genome (HG38) using BWA, and circular DNAs were identified with circle map. Differential expression was analyzed with edgeR. B: miRNA seq. Single end sequencing. Small RNA libraries were constructed and sequenced. Reads were trimmed with cutadapt, aligned to miRBase pre miRNAs (v22) plus newly predicted pre miRNAs using Novoalign. miRNA expression was normalized by TPM. Novel miRNAs were predicted with miRDeep2. Differential expression was calculated using edgeR. C: mRNA seq. Paired end 150 bp sequencing on Illumina NovaSeq 6000. mRNA was enriched via poly A selection, strand specific libraries were prepared. Raw reads were preprocessed with fastp, aligned to HG38 using HISAT2, and gene counts were obtained with featureCounts. Differential expression was analyzed with edgeR). All differential analyses were followed by GO and KEGG pathway enrichment. Data visualization was performed with IGV, cluster heatmaps, scatter plots, and volcano plots.

first: Ji

last: Wang

first: Kehan


title: Obesity Increases Atherosclerosis Susceptibility via Inter-tissue miR-30e-SLC7A11 Axis

city: Xi'an

first: Chen

address: Yanta West Road No.277

institute: The First Affiliated Hospital of Xi’an Jiaotong University

summary: With obesity as a risk factor for atherosclerotic disease, recent research suggests that adipose tissue in obese animal models and humans can generate endocrine-like molecules that affect arterial health. Previous studies showed that microRNA-30e (miR-30e) level is elevated in atherosclerosis and solute carrier family 7 member 11 (SLC7A11), a cystine/glutamate transporter, is involved in atherogenesis. However, whether an endocrine-like link between the adipose-derived miR-30e-5p and SLC7A11 in the vascular endothelium can lead to obesity-caused atherosclerosis is unknown.MiRNA data mining and RT-PCR validations were used to demonstrate the positive association among serum level of miR-30e-5p, obesity, and coronary arterial disease in human patients. Transcriptomics (bulk RNA-seq and single-nucleus RNA-seq), metabolomics, and in silico analysis were used to establish a miR-30e-5p–SLC7A11 regulation of central carbon metabolism, mitochondrial and endothelial cell (EC) function. Mouse models with EC-specific Slc7a11 knockout (EC-Slc7a11-/-) and gain- or loss-of- function of miR-30e-5p were used to elucidate the detrimental role of this endocrine-like axis in obesity-related atherosclerosis.Our multi-omics approaches demonstrate that the adipose-derived miR-30e-5p downregulated SLC7A11 mRNA in ECs via tissue crosstalk. The resulting EC dysfunction led to obesity-related atherosclerosis in mice. These findings underscore a causality between obesity and atherosclerosis in the context of cardiovascular-kidney-metabolic syndrome.

overall_design: Eight-week-old male Apoe-/- mice were fed an high-fed diet (HFD) or chow diet (CD) for 12 weeks. The epididymal WAT (eWAT) collected from 3 animals in each of the two groups, and all samples were run for single-nucleus RNA-sequencing (snRNA-seq).

first: Jianqing

last: She

first: John

last: Shyy

first: Zu-yi

last: Yuan


title: Transcriptome and small RNA landscapes of tree shrew testes and epididymides during reproductive and non-reproductive seasons

city: Kunming

first: xu

last: dai

state: Yunnan

address: No. 452 Fenyuan Road, Panlong District

institute: Yunnan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: The treeshrew (Tupaia belangeri), as a species closely related to primates, exhibits significant seasonal reproductive traits in adult males, including cyclical changes in testicular morphology and spermatogenesis between the breeding and non-breeding seasons. However, comprehensive and systematic data resources on the molecular expression features associated with this physiological phenomenon are still lacking. In this study, we utilized the Illumina high-throughput sequencing platform to perform RNA-seq and small RNA-seq on testicular (Testis), caput epididymis (Caput), and caudal epididymis (Cauda) tissues collected from male tree shrews during both breeding (R) and non-breeding (NR) seasons. These analyses were performed to generate a paired transcriptomic and small RNA dataset covering multiple tissues and seasonal states. RNA-seq analysis identified 21,299 expressed genes, and weighted gene co-expression network analysis (WGCNA) was performed to identify modules and candidate genes significantly associated with reproductive status. The small RNA-seq data systematically characterized the composition and expression landscapes of miRNAs and piRNAs, leading to the identification of 263 novel miRNAs, 59,590 piRNAs, and 139 piRNA clusters. Differential expression analyses and computational predictions were further integrated to construct a miRNA–candidate gene–piRNA association network. The multi-omics data generated in this study provide a systematic and reusable molecular resource for deciphering the gene expression and small RNA characteristics associated with seasonal reproduction in male tree shrews. This dataset can serve as an important reference for investigating dynamic changes in mammalian reproductive tissues.

overall_design: This study investigated the transcriptome and small RNA landscapes of tree shrew (Tupaia belangeri) male reproductive tissues across two physiological states. Testis (TESTIS), caput epididymis (CAPUT), and caudal epididymis (CAUDA) tissues were collected from sexually mature male tree shrews (1.5–2 years old) during the non-reproductive season (NR; mid-December 2023) and the reproductive season (R; mid-April 2024), yielding six groups in total (TESTIS-NR, TESTIS-R, CAPUT-NR, CAPUT-R, CAUDA-NR, CAUDA-R). For each group, three biological replicates were used. Two sequencing libraries were constructed per sample: a poly(A)-selected RNA-seq library (PE150, Illumina NovaSeq 6000) for mRNA profiling, and a small RNA-seq library (SE50, Illumina NovaSeq 6000) for miRNA and piRNA profiling. Differential expression analysis between reproductive and non-reproductive seasons was performed for each tissue type using DESeq2.


title: Osteocyte Parvalbumin Mediates Mechanotransduction to Attenuate Osteoarthritis

city: Shanghai

first: Jiansen

last: Su

address: No. 600, Yishan Road, Shanghai

institute: Shanghai Sixth People's Hospital

summary: Osteoarthritis (OA) is a leading cause of disability among the elderly, characterized by aberrant subchondral bone remodeling that precedes cartilage degeneration. We identify parvalbumin (Pvalb) in osteocytes as a critical mechanosensory regulator of this pathological process. Pvalb expression is significantly reduced in osteocytes from both OA patients and male murine models of the disease. Conditional deletion of Pvalb in osteocytes accelerates OA progression, whereas bone-targeted restoration of Pvalb expression mitigates disease manifestations. Mechanistically, Pvalb maintains calcium homeostasis by competing with CaMKIV for calmodulin binding. Under excessive mechanical loading, Pvalb expression is suppressed, leading to activation of the Ca²+-CaMKIV-CREB signaling pathway, increased RANKL production, and subsequent osteoclast activation and pathological bone remodeling. These findings identifies an osteocyte-mediated mechanotransduction pathway in OA pathogenesis and underscore Pvalb as a promising therapeutic target.

overall_design: To investigate the impact of excessive mechanical loading on the subchondral bone during the development of osteoarthritis and the role of Pvalb in this process, we performed Sham or Destabilization of the medial meniscus (DMM) surgeries on 8 - week - old wild - type or Pvalb osteocyte - specific knockout mice, respectively. Eight weeks after DMM, we collected the subchondral bones from WT+SHAM, WT+DMM, and Pvalb cKO+DMM mice for RNA - seq analysis and compared their gene expression profiles.


title: Endometrial transcriptomic responses associated with a 17α-hydroxyprogesterone caproate-containing formulation and progesterone in Holstein cows: an exploratory RNA-seq analysis

city: Towada

first: Masaki

last: Watanabe

department: School of Veterinary Medicine

country: Japan

institute: Kitasato University

summary: 17α-hydroxyprogesterone caproate (17-OHPC) is included in a veterinary depot formulation approved in Japan for the prevention of implantation failure and abortion in cattle, but its molecular effects on the bovine endometrium remain unclear. In this exploratory RNA-seq study, six Holstein cattle were assigned to a 17-OHPC-containing formulation group (100 mg 17-OHPC plus 10 mg progesterone [P4]; n = 3) or a P4-alone group (100 mg P4; n = 3). Endometrial samples were collected during an untreated synchronized cycle on days 4 and 7, and during a second synchronized cycle on day 7 after treatment on day 4. RNA-seq was used to characterize treatment-associated endometrial transcriptomic profiles and gene-set enrichment patterns between the 17-OHPC/P4 formulation and P4-alone arms.

overall_design: Bulk mRNA-seq was performed on 18 bovine endometrial samples from six Holstein cattle. Animals A-C were assigned to the 17-OHPC/P4 formulation arm and animals D-F to the P4-alone arm. For each animal, sample suffix _1 denotes day 4 of the untreated control cycle, _2 denotes day 7 of the untreated control cycle, and _3 denotes day 7 of the treatment cycle. During the treatment cycle, animals A-C received a depot formulation containing 100 mg 17-OHPC and 10 mg P4 on day 4, while animals D-F received 100 mg P4 on day 4; endometrial samples were collected on day 7. The design supports within-arm comparisons to the untreated control cycle and a direct day 7 comparison between treatment arms.

first: Okami

last: Kiseki

first: Watanabe

last: Masaki

first: Yamasaki

last: Noe

last: Toru

first: Momozawa

last: Kenji

first: Sasaki

last: Nobuya

first: Nagano

last: Masashi


title: DMD-Null Mice Exhibit Severe Muscle Weakness, Impaired Regeneration, and Deficient Satellite Cell Function

city: Edmonton

first: Toshifumi

last: Yokota

state: Alberta

department: Medical Genetics

institute: University of Alberta

summary: The DMD gene encodes for dystrophin, a large structural protein found in muscles that plays a critical role in muscular strength and stability. The absence of dystrophin is associated with Duchenne muscular dystrophy (DMD), a fatal diseases characterized by muscle weakness and ddgeneration. Interestingly, DMD harbors multiple intragenic promoters that lead to alternative splicing and the production of various short isoforms of dystrophin, with distinct expression patterns and roles. Recent studies have found that the expression of these short isoforms may partially modulate the DMD phenotype. Here, we aimed to assess the contributions of short dystrophin isoforms to gene expression. Bulk RNA sequencing was performed on muscles from mdx mice, which fail to produce full-length dystrophin but still express short isoforms, and on DMD-Null mice, which have a complete DMD deletion preventing the expression of any dystrophin isoform.

overall_design: Bulk sequencing was performed on tibialis anterior muscles from naïve 6-month old wild-type, mdx, and DMD-Null mice. N=4 per group.

first: Harry

last: Wilton-Clark


title: Engineered heart tissues facilitate functional characterization of noncoding variants implicated in Hypertrophic and Dilated Cardiomyopathy [ATAC-seq]

city: Chicago

first: Zachary

middle: Thomas

last: Weber

state: Illinois

department: Human Genetics

institute: University of Chicago

summary: Inherited cardiomyopathies frequently arise from rare, highly penetrant coding variants with variable clinical expressivity. Recent biobank-scale genome-wide association studies (GWAS) suggest significant polygenic contributions to cardiovascular diseases, including cardiomyopathy. Most GWAS loci map to noncoding regions, which are poorly conserved across species, requiring a human genome context for experimental validation. We created engineered heart tissues (EHTs) from human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes and primary cardiac fibroblasts. We assayed single-cell gene expression and chromatin accessibility to generate comprehensive genome-wide regulatory maps. Open chromatin regions (OCRs) were integrated with chromatin contact information and used to functionally fine-map single nucleotide polymorphisms (SNPs) in cardiomyopathy GWAS. SNPs and their associated regulatory regions were assessed using reporter assays, genome editing, and expression profiling. Single-cell RNA-seq of EHTs confirmed populations recapitulating major cell types found in hearts, with advanced cardiomyocyte maturation compared to monolayer hiPSC-cardiomyocytes. More than 400,000 OCRs were resolved to cell type and assayed for canonical transcription factor footprints. Functional fine-mapping of GWAS loci prioritized 5817 variants, and reporter assays on select variants validated allele-specific enhancer activity. We identified a locus harboring significant GWAS signals from both dilated cardiomyopathy and left ventricle ejection fraction in an intergenic region at chr3p25.1. Several of these variants lie in OCRs participating in long range chromatin interactions with SLC6A6 and GRIP2.  Haplotype-resolved and synthetic reporter assays confirmed enhancer activity and narrowed candidate SNPs. CRISPR-deletion of this region reduced expression of both SLC6A6 and GRIP2, indicating the enhancer regulates the expression of more than one gene. EHTs with the enhancer deletion displayed markedly reduced contractile function, confirming the necessity of this enhancer region for normal contractility.  Taken together, EHTs derived from hiPSCs are an experimentally tractable platform for testing the function of noncoding variants as modifiers of cardiomyopathy. Variants fine-mapped from cardiomyopathies using EHT regulatory maps have functional consequences and provide a set of prioritized sites to advance the study of polygenic heart failure liability.

overall_design: We created engineered heart tissues (EHTs) from human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes and primary cardiac fibroblasts. Briefly, cardiomyocytes were differentiated for 10 days from human induced pluripotent stem cells stably expressing eGFP from the AAVS1 safe harbor locus. Cardiomyocytes were isolated using column based purification and mixed with human cardiac fibroblasts in a collagen-based scaffold on custom plates to cast engineered heart tissues. EHTs were matured for an additional 20 days. EHTs were dissociated and pooled across 2x 48-well plates. Cells for sorted for eGFP expression using fluorescence-assisted cell sorting (FACS) to generate cardiomyocyte enriched and fibroblast enriched fractions for ATAC-Seq. For comparison to EHTs, we also collected day 10 differentiated cardiomyocytes purified according to the same protocol for EHT preparation, and generated three libraries for and ATAC-Seq.

middle: T

first: Tanner

middle: O

last: Monroe

first: Elizabeth

middle: M

last: McNally

first: Marcelo

last: Nobrega


title: Engineered heart tissues facilitate functional characterization of noncoding variants implicated in Hypertrophic and Dilated Cardiomyopathy [Bulk RNA-Seq]

overall_design: Cardiomyocytes were differentiated in monolayers for 10 days from human induced pluripotent stem cells using standard protocols using small molecule modulation of WNT signaling. The cells were then isolated using column-based purification, re-plated for 48 hours and lysed for RNA collection. CRISPR edited cells were nucleofected with Cas9-guide RNPs targeting an intergenic enhancer at chr3p25.1. Isogenic lines were obtained via limited dilution cloning and confirmed with Sanger sequencing. Lines were then differentiated to cardiomyocytes using the same strategy as above.


title: Effect of RSL3 and IFN-γ on gene expression in 526MEL cells

city: Nagasaki

first: Daisuke

last: Ehara

address: 1-12-4 Sakamoto

department: Dermatology

institute: Nagasaki University Graduate School of Biomedical Sciences

summary: Tumor masses often exhibit heterogeneity, including escape variant clones that lack antigen-presenting machinery and/or tumor antigens, which poses a major challenge to immunotherapy. Ferroptosis, a form of regulated cell death driven by iron-dependent lipid peroxidation, has been shown to effectively induce cell death in various tumor cells. Recent studies have reported that IFN-γ suppresses the expression of System Xc-, thereby enhancing the induction of ferroptosis. Based on this, we hypothesized that combining immunotherapy with ferroptosis inducers could enhance antitumor effects against both antigen-positive and antigen-negative tumor cells. Consistent with this hypothesis, we comprehensively analyzed mRNA expression changes in 526MEL cells treated with the combination of RSL3 and IFN-γ using RNA sequencing. Our data suggest that multiple ferroptosis-related pathways, including the CoQ-dependent membrane repair pathway (FSP1–CoQ axis), the DHODH–CoQ mitochondrial redox pathway (DHODH–CoQ axis), the CYB5R–cytochrome b5 lipid redox pathway (CYB5R axis), and the thioredoxin–peroxiredoxin repair pathway (PRDX/TXN axis), may contribute to the synergistic effects of combined RSL3 and IFN-γ treatment in human melanoma cell lines.

overall_design: Total RNA was isolated from two biological replicates of control 526MEL cells, 526MEL cells treated with RSL3 alone, IFN-γ alone, or a combination of IFN-γ and RSL3, as well as 526MEL cells treated with conditioned supernatants collected from co-cultures of 526MEL cells and MART-1–specific TCR-engineered T cells, either in the presence or absence of RSL3.

first: Kiyoshi

last: Yasui

first: Mitsuhiro

last: Yoneda

first: Deng

last: Situo

first: Hiroaki

last: Ikeda


title: Convergent evolution of metabolic regulation governs redox adaptation in Toxoplasma

city: Cambridge

first: Sebastian

last: Lourido

address: 455 Main Street Room 661G

department: Biology

institute: Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology

summary: Diverse organisms adjust metabolic gene expression during crowding as they encounter nutrient scarcity, oxidative stress, and waste accumulation. Apicomplexan parasites experience these stresses during intracellular growth in host cells, yet lack known regulators of metabolic adaptation. We screened the apicomplexan Toxoplasma gondii to identify genes that support parasite fitness during crowding. NAD(P)+ biosynthesis was required at high parasite density along with several parasite-specific factors, including an RNA-binding protein named T. gondii Parasite Response to Oxidation (TgPRO). TgPRO loss elevated reactive oxygen species under ambient conditions, which was rescued by growth at low oxygen. TgPRO regulates expression of specific transcripts involved in carbon metabolism and iron-sulfur cluster assembly. Regulation of the iron-sulfur cluster assembly protein ISCU relies on TgPRO binding to the transcript’s 3′ UTR. Through convergent evolution, TgPRO performs a role analogous to known metabolic regulators from other species, representing the first dedicated regulator of metabolic gene expression in apicomplexans.

overall_design: RNA-seq profiling of T. gondii tachyzoites expressing a conditional wild-type (cWT) or conditional TgPRO knockout (cMUT) allele, treated with actinomycin D (5 ug/mL, 4 h) or DMSO vehicle, 3 biological replicates per condition (12 libraries total). Libraries were prepared from poly(A)-selected RNA and sequenced paired-end (75x75 bp) on an Element Biosciences AVITI platform.

first: Christopher

last: Giuliano

first: Chinmay

last: Kalluraya

first: Joachim

last: Kloehn

first: Megan

last: Sloan

first: Molly

middle: E

last: Bunkofske

last: Hunter

first: Dominique

last: Soldati-Favre

first: Clare

last: Harding


title: Engineered heart tissues facilitate functional characterization of noncoding variants implicated in Hypertrophic and Dilated Cardiomyopathy

first: Zachary

last: Weber

overall_design: We created engineered heart tissues (EHTs) from human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes and primary cardiac fibroblasts. Briefly, cardiomyocytes were differentiated from human induced pluripotent stem cells for 10 days and isolated using column based purification. Cardiomyocytes were mixed with human cardiac fibroblasts in a collagen-based scaffold on custom plates to cast engineered heart tissues. EHTs were matured for an additional 20 days. EHTs were dissociated and pooled across 2x 48-well plates, and sequenced. The protocol was then repeated with independent differentiations of cardiomyocytes to generate a replication experiment using the same procedure. Cells were sequenced for single cell gene expression using chromium 10X 3’ V3 system.

last: Monroe


title: 4T1 Cut&Run

city: West Lafayette

first: Sagar

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

summary: Mammalian SWI/SNF or BAF are multi-subunit complexes that regulate cell-type specific gene expression by modulating chromatin accessibility, in coordination with transcription factors and other chromatin regulators. PBRM1 is the complex defining subunit of PBAF class of SWI/SNF complexes. It is mutated in ~40% of clear cell renal cell carcinoma cases but also associated with cancer progression and therapy resistance, indicating context-dependent function. We have previously reported that loss of PBRM1 in normal epithelial cells results in a partial Epithelial-to-Mesenchymal Transition (EMT). In this study, we have utilized epigenomic and transcriptomic approaches to understand the mechanistic role of PBRM1 in EMT-regulated gene expression, and its relationship to genome-wide histone modifications.

overall_design: Cut&Run was performed on control and PBRM1 KO 4T1 cells with and without 4 days of TGFβ1 treatments

first: Emily

last: Dykhuizen

first: Alisha

last: Dhiman


title: 4T1 ATAC-seq

overall_design: ATAC-seq was performed on control and PBRM1 KO 4T1 cells with or without 4 days of TGFbeta treatments.


title: Astrocyte redox imbalance underlies prelimbic neuronal hypoactivity and affective behavior in epilepsy [Astrocyte_MACS]

city: Baltimore

first: Akira

last: Sawa

state: Maryland

address: 600 N Wolfe St Meyer 3-166

institute: Johns Hopkins University

summary: A fundamental but unanswered question in neuropsychiatry is whether the psychiatric symptoms of epilepsy are caused by the same or a separate pathophysiology as seizures. To address this question, we investigated a monogenic form of epilepsy (pyridoxine-dependent epilepsy) caused by aldehyde dehydrogenase 7a1 (ALDH7A1) mutations. ALDH7A1 global knockout mice exhibited both seizure-associated and affective behavioral phenotypes. However, seizure phenotypes were caused by ALDH7A1 deletion in hepatocytes whereas affective behaviors were caused by ALDH7A1 deletion in astrocytes. Deletion in astrocytes disrupted astrocyte redox homeostasis, impairing regulation of extracellular ion concentrations and reducing neuronal activity in the prelimbic cortex. Sulforaphane, which activates the NRF2 antioxidant pathway, restored prelimbic neuronal activity and rescued affective behaviors in ALDH7A1 knockout mice, but did not prevent seizures. These studies implicate astrocyte redox homeostasis and prelimbic hypoactivity in the psychiatric manifestations of a congenital form of epilepsy, which are mechanistically and therapeutically separate from the seizure pathophysiology.

overall_design: RNA sequencing analysis of MACS-isolated astrocytes obtained from the cerebral cortex of male, P70 astrocyte-specific ALDH7A1 conditional knockout mice (cKO-Astro; Slc1a3-CreER/+; Aldh7a1-Flox/Flox) and control littermates (Con-Astro; Aldh7a1-Flox/Flox) injected with 4-hydroxytamoxifen at P3-P4 and fed either a control diet or a diet containing sulforaphane from P21 to P70.

first: Travis

last: Faust

first: Kun

last: Yang

first: Ho

last: Namkung

first: Lindsay

last: Hayes

first: Hanna

last: Jaaro-Peled


title: Astrocyte redox imbalance underlies prelimbic neuronal hypoactivity and affective behavior in epilepsy

overall_design: RNA sequencing analysis of brain tissue homogenate of the cerebral cortex obtained from male P70 ALDH7A1-/- mice (ALDH7A1 global knockout) and wild-type littermate controls


title: Developmental dynamics of the cortical cellular and molecular landscapes in autism spectrum disorder models

city: Klosterneuburg

first: Gaia

last: Novarino

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (ISTA)

summary: Recent research has identified over 100 causal genes in autism spectrum disorder (ASD), raising the question of how mutations in genes with diverse functions result in similar clinical presentations. Here, we profiled 251 samples from eleven monogenic ASD mouse models using single-nucleus multi-omic sequencing across three developmental stages, both sexes, and two brain regions. We discovered that, despite wide genetic heterogeneity, ASD-linked mutations converged on perturbations of the radial glial cell lineage. This converging alteration primarily reflects a transient developmental delay rather than a lasting lineage misspecification and resolves by postnatal stages. Molecularly, the largest transcriptional differences emerged in neurons at early postnatal stages. These changes included downregulation of synaptic and ion channel-related genes, consistent with homeostatic adaptation or delayed maturation. Network analysis indicated that molecular convergence is strong across models within each developmental stage, suggesting that diverse ASD mutations impinge on common, stage-specific processes. Convergence becomes less pronounced by postnatal day 14, highlighting the dynamic nature of ASD-associated changes. Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology corroborated this pattern: mutants generally showed altered neuronal excitability and synaptic properties with model-specific nuances. Our study also highlighted sex-specific gene expression alterations, with females often displaying larger effect sizes than males. Altogether, our findings provide a comprehensive view of the developmental cellular and molecular dynamics across ASD models.

overall_design: Simultaneous profiling of gene expression and chromating accessibility using a single-nuclei multi-omics approach with combined mutliplexing. Single-nuclei RNA- and single-nuclei ATAC-seq profiles of the cortex of 11 mouse lines, in both sexes, and across three time points of corticogenesis: E14.5, P4 and P14. Additionally, profiling of the cerebellum of male P4 mice of all 11 mouse lines was performed. Overall, 251 samples were profiled.

first: Lena A.

last: Schwarz

first: Christoph P.

last: Dotter

first: Sergey

last: Isaev

first: Christoph

last: Büschl

first: Sabrina

last: Ladstätter

first: Igor

last: Adameyko

last: Bock


title: PBRM1 RNA-seq [4T1]

last: Utturkar

overall_design: RNA-seq was performed on control or PBRM1 KO 4T1 cells with or without 4 days of TGFbeta treatment


title: miR-339-5p impairs myogenic proliferation and differentiation by repressing contractile gene programs in skeletal muscle

city: Stockholm

first: Nicolas

last: Pillon

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

summary: MicroRNAs (miRNAs) are critical regulators of skeletal muscle development and adaptation, orchestrating the balance between proliferation, differentiation, and tissue repair. Here, we identify miR-339-5p as a previously unrecognized, conserved regulator of skeletal muscle remodeling. Transcriptomic analysis from human, mouse, and rat studies revealed that miR-339-5p is consistently upregulated in skeletal muscle under conditions of stress or injury and declines during myogenic differentiation in vitro. Gain-of-function experiments demonstrated that miR-339-5p overexpression impairs expression of genes associated with myogenic differentiation and promotes expression of proliferative markers in both primary human myotubes and mouse C2C12 cells. Transcriptomic profiling confirmed widespread repression of pathways involved in cytoskeletal organization, myofibrillar assembly, and mitochondrial function. In vivo, electroporation-mediated overexpression of miR-339-5p in mouse tibialis anterior altered regeneration-associated gene expression and increased the number of immature fibers, therefore modulating tissue remodeling during post-injury growth. Integrated analyses combining target prediction algorithms, differentiation-associated correlations, and overexpression datasets identified seven conserved high-confidence miR-339-5p targets, among which the autophagy-associated phosphatase MTMR3 emerged as the most consistently regulated candidate. Collectively, our data demonstrate that miR-339-5p functions as a conserved inhibitor of myogenic progression, linking injury-induced stress responses to delayed differentiation and altered muscle remodeling. These findings establish miR-339-5p as a potential therapeutic target in conditions characterized by impaired muscle regeneration or dysregulated tissue remodeling.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNAseq profiling of human primary skeletal muscle cells and mouse C2C12 muscle cells with or without overexpression of miR-339-5p

first: Xue

last: Yu

first: Elena

last: Caria


title: Eomes sustains progenitor CD4⁺ T helper cells to promote anti-tumor immunity during immunotherapy

city: Toulouse

first: Anne

last: Dejean

state: Midi-Pyrenees

address: CHU Purpan – BP 3028

country: France

institute: Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)

summary: CD4⁺ T helper (Th) cells contribute to tumor immunity, yet the subsets and differentiation programs involved remain unclear. Here, we show that the transcription factor Eomesodermin (Eomes) is essential for Th–mediated anti-tumor immunity by orchestrating the differentiation and maintenance of an exhausted-like Th cell lineage, which is transcriptionally and functionally distinct from conventional effector or memory Th subsets. This Eomes-dependent program is further enhanced by 4-1BB stimulation, promoting effective Th cell–mediated tumor control. The precursor subset of this lineage (pTh) expresses stemness-associated transcription factors, displays self-renewal capacity, and can differentiate into effector cells capable of controlling tumor growth. At the transcriptional level, Eomes supports the survival, metabolic fitness, and apoptotic resistance of this lineage. Notably, Eomes⁺ pTh cells are directly relevant to human cancer, being detected across multiple tumor types, exhibiting conserved transcriptional features, and representing the most expanded Th cell population upon immune checkpoint blockade therapy.

overall_design: Eomes-GFP and Eomes-TKO mice, both crossed to Foxp3-Thy1.1 mice, were injected i.v. with NK1.1-depleting mAbs (50µg/mice, days -2 and 5), engrafted with Vk12653 MM cells (2.10 millions, day 0), subsequently treated with 4-1BB agoniste or control IgG mAbs (20µg/mice, days 10, 13, 16) and mice were euthanized at day 18. At day 18, CD4+ Th cells (Thy1.1neg) were isolated from the spleen and sorted by FACS (TCR+, CD4+, Thy1.1neg, GFPpos or GFPneg) Aria Fusion (BD Biosciences).

first: Arantxa

last: Agesta

first: Chloé

last: Ferrand

first: Anne-Louise

last: Le Dorze

first: Adeline

last: Chaubet

first: Margot

last: Zahm


title: Bulk RNA-seq profiling of primary mouse tubular epithelial cells following AdvCre-mediated ELF3 deletion under TNFα and IFNγ stimulation

city: PHILADELPHIA

first: Yanjuan

last: Hou

state: PA

address: 3400 civic center blvd

department: Perelman School of Medicine, Department of Medicine

institute: university of pennsylvania

summary: Primary mouse renal tubular epithelial cells were subjected to adenoviral Cre recombinase (AdvCre)-mediated deletion of ELF3 or control treatment. Cells were stimulated with TNFα and IFNγ to model inflammatory activation. Bulk RNA sequencing was performed to characterize transcriptional changes associated with ELF3 loss under proinflammatory conditions. This dataset enables analysis of ELF3-dependent gene regulatory programs in cytokine-stimulated tubular epithelial cells.

overall_design: Primary mouse renal tubular epithelial cells were isolated and cultured under standard conditions. Cells were infected with adenovirus expressing Cre recombinase (AdvCre) to induce ELF3 deletion or corresponding control virus. Following viral transduction, cells were stimulated with TNFα and IFNγ prior to RNA extraction. Total RNA was isolated and processed for bulk RNA sequencing to assess differential gene expression between control and ELF3-deficient cells.

first: Katalin

last: Susztak


title: Transcriptomic profiling of human RPTECs following TNFα and IFNγ stimulation at early and late time points

summary: Renal proximal tubule epithelial cells (RPTECs) were stimulated with TNFα, IFNγ, or a combination of TNFα and IFNγ to characterize cytokine-induced transcriptional responses. Bulk RNA sequencing was performed at 3 h and 12 h following treatment to capture early and sustained gene expression changes. This dataset enables analysis of inflammatory signaling dynamics and cytokine-specific versus cooperative transcriptional programs in human tubular epithelial cells

overall_design: Immortalized human renal proximal tubule epithelial cells (hTERT-RPTECs) were treated with TNFα, IFNγ, or TNFα + IFNγ. Cells were harvested at 3 h and 12 h post-stimulation. Untreated cells served as controls. Total RNA was extracted and subjected to bulk RNA sequencing to assess differential gene expression associated with cytokine exposure and time-dependent responses.


title: CUT&RUN profiling of ELF3 and NFKB2 binding landscapes in primary mouse tubular epithelial cells under TNFα and IFNγ stimulation

summary: Primary mouse renal tubular epithelial cells were cultured and stimulated with TNFα and IFNγ to model inflammatory activation. CUT&RUN assays were performed using antibodies targeting ELF3, NFKB2, and IgG control to define genome-wide chromatin binding profiles. This dataset enables characterization of ELF3- and NFKB2-associated regulatory regions in cytokine-stimulated tubular epithelial cells.

overall_design: Primary mouse renal tubular epithelial cells were isolated and cultured under standard conditions. Cells were treated with TNFα and IFNγ prior to CUT&RUN experiments. CUT&RUN was conducted using validated antibodies against ELF3 and NFKB2, with IgG serving as a negative control. Sequencing libraries were prepared from released DNA fragments and subjected to high-throughput sequencing to identify transcription factor binding sites.


title: Transcriptional Response to Pool Human Milk Exosomes in Infant Ileal Intestinal Enteroids

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

summary: RNA sequencing was used to compare the transcriptional response of human infant ileal intestinal enteroids following exposure to human milk exosomes. Exosome-exposed enteroids were compared to enteroids not exposed to exosomes in the same 72 hour period.

overall_design: Human infant ileal intestinal enteroids from three individuals were used for total RNA sequencing.

first: Kacie

last: Waiters

first: Grace

last: Adeniyi-Ipadeola

first: Micah

last: Castillo

first: Preethi

last: Gunaratne

first: Hoa

last: Nguyen-Phuc

first: Sasirekha

last: Ramani

first: Tasneem

last: Bawa-Khalfe


title: Transcriptomic analysis of macrophages

first: Mengyu

last: Chang

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

summary: The clinical efficacy of cytotoxic nanomedicines is often limited by rapid hepatic clearance, yet the endogenous biological regulators of this process remain incompletely understood. Here, we identify the gut microbiota as a central determinant of nanomedicine biodistribution, acting through transcriptional programming of liver-resident macrophages rather than modulation of adaptive immunity. Using germ-free mice, fecal microbiota transplantation, and targeted microbial perturbation, we show that the nitroimidazole antibiotic metronidazole reconfigures gut microbial ecology and reprograms Kupffer cells into a reduced-uptake state. This shift suppresses hepatic sequestration and enhances tumour accumulation of clinically deployed nanomedicines across multiple cancer models and nanoparticle formulations. Single-cell RNA sequencing reveals a coordinated downregulation of phagocytic and scavenger receptor pathways in Kupffer cells, while metabolomic profiling identifies microbiota-dependent changes in bile acid availability. Restoration of this altered microbial state through fecal transfer is sufficient to transmit the low-clearance phenotype, demonstrating causal and transferable host control of nanomedicine fate. Together, these findings position the gut-liver axis as a tuneable checkpoint for cytotoxic drug pharmacokinetics and introduce microbiome-directed interventions as a distinct strategy to improve nanomedicine delivery.

overall_design: Specific pathogen-free (SPF) mice were divided into two groups and given either control drinking water or metronidazole-infused water for three consecutive weeks. Each group consisted of three mice. After treatment, liver immune cells were isolated from each mouse, and cells from the same group were pooled together to generate one sample for single-cell RNA sequencing (scRNA-seq) analysis.


title: ACSS2 aggravates Metabolic dysfunction associated steatohepatitis (MASH) by regulating AIF1 mediated inflammation

city: Chongqing

first: Xiao

last: Wen

address: Medical College Road

department: Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)

institute: Chongqing Medical University

summary: Metabolic dysfunction associated steatohepatitis (MASH) is one of the most common types of liver disease, which is caused by hepatotoxicity caused by metabolic disorder. The incidence rate and mortality are very high, but the current treatment drugs are still limited. The role of ACSS2 in regulating inflammation in MASH is unclear. This study aims to explore the role and potential mechanisms of ACSS2 in the progression of MASH.

overall_design: To explore the role of ACSS2 in metabolic dysfunction associated steatohepatitis (MASH), we prepared liver cell specific knockout ACSS2 mice and performed liver transcriptome analysis


title: NMuMG PBRM1 ChIP-seq

first: Sagar

last: Utturkar

overall_design: ChIP-seq was performed on control and PBRM1 KO NMuMG cells with 0, 24 and 48h of TGFβ1 treatments

last: 24 and 48h of TGFβ1 treatments

first: Emily

last: Dykhuizen

first: Alisha

last: Dhiman


title: Ultra-sensitive profiling of CRISPR-Cas off-target effects with Tracking-seq2

first: Zhu

last: Ming

address: No. 500, Dongchuan Road

institute: East China Normal University

summary: Accurate detection of off-target activity in patient-derived cells is critical for ensuring the safety of gene therapeutics. Here, we present Tracking-seq2—the most sensitive, cell-based, and clinically applicable off-target detection technology to date, capable of profiling diverse genome editors. Crucially, we reveal that genomic variations drive distinct off-target heterogeneity across different cells, highlighting the necessity for personalized safety assessment in clinical genome editing therapies

overall_design: Enhanced Tracking-seq2 for off-target detection of various genome-editing tools and cell types


title: Fucci-G1 insertion partially disrupts Shh expression

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

summary: The Fucci mouse lines are valuable tools for tracing cell cycle stages during development and in postnatal tissues; however, the insertion loci for the transgenes remain unidentified. Here, we report the genomic insertion sites of both the Fucci-G1 and -S/G2/M transgenes, identified through whole genome sequencing. Interestingly, the Fucci-G1 transgene is located proximal to the Shh lung gut enhancer (SLGE) on chromosome 5. Homozygous Fucci-G1 embryos survive until embryonic day 18.5 (E18.5), exhibiting craniofacial and foregut-related defects, but are perinatal lethal. Expression of Shh and canonical targets are down-regulated in the pharyngeal arches of E11.5 homozygous Fucci-G1 embryos. Furthermore, in situ hybridization analysis showed diminished Shh expression in the pharyngeal ectoderm and foregut endoderm, consistent with disruptions to SLGE activity. Our results indicate that heterozygous Fucci-G1 mice are suitable for cell cycle studies; however, we caution potential genetic interference when investigating SHH-related pathways.

overall_design: The pharyngeal arches of 18 embryonic day 11.5 embryos were collected from two litters by microdissection and stored in TRIzol. Following genotype confirmation (6 wild type, 7 Fucci-G1 heterozygotes, and 5 Fucci-G1 homozygotes), RNA was extracted using the manufacturer's protocol. Purified total RNA were used for poly(A)-enriched, non-directional RNA-sequencing (Novogene Corporation, USA). FASTQ files were aligned to the mouse genome, mm10, using STAR (version 2.7.10a) and differential expression analysis was performed using edgeR (version 3.40.2) and limma (version 3.54.2) using genotype and litter information as covariates. Significant changes were defined as an FDR less than 0.05. Pathway analysis was performed using Enrichr.

first: Yuka

last: Morikawa

first: James

middle: F

last: Martin


title: Tumor-borne ADAMTSL4 drives cancer cachexia via TGFβ signaling pathway

city: Munich

first: Mauricio

last: Berriel Diaz

state: Bavaria

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Cancer

country: Germany

institute: Helmholtz Center Munich

summary: Cancer cachexia (CCx) is a multifactorial wasting disorder in patients with cancer characterized by involuntary body weight loss. Whereas CCx is associated with reduced quality of life and poor survival, no approved pharmacological intervention exists. Here we show that elevated circulating levels of the tumour-derived glycoprotein ADAMTSL4 were associated with weight loss in various preclinical CCx models as well as in cachectic patients with different cancers. ADAMTSL4 overexpression in non-cachexia-inducing tumour cells conferred cachexia-inducing properties upon exposure of cultured myocytes and adipocytes as well as implantation in mice. Reversely, genetic ADAMTSL4 deletion in cachexia-inducing cancer cells markedly repressed wasting phenotypes both in vitro and in vivo. Ligand-receptor capture technology identified the latency-associated peptide of TGF-β1 as ADAMTSL4 target on muscle cell surface. ADAMTSL4 mediated muscle atrophy and adipose tissue wasting through local TGF-β1 activation, sensitive to inhibition of TGFβR1 or knockdown of proTGF-β1. Given the conserved correlation between circulating ADAMTSL4 and skeletal muscle TGF pathway component expression in an independent human cancer patient cohort, our data suggest that blockade of ADAMTSL4 function represents a first rational approach towards efficient cancer cachexia pharmacotherapy.

overall_design: Gene expression analysis of data obtained for a total of 22 samples of RNA extracted from GC muscle tissue of mice with ADAMTSL4 overexpressed in MC38 tumor (n=5), GFP expressed in MC38 tumor (n=5), ADAMTSL4 knockdown in C26 tumor (n=5), C26 tumor with control shRNA (n=5), and Non-tumor bearing mice injected with PBS (n=2). A total of 6 RNA samples were extracted from eWAT tissue with ADAMTSL4 knockdown in the C26 tumor (n=3) and C26 tumor carrying control shRNA (n=3). A total of 4 RNA samples were extracted from ingWAT tissue from C26 tumors with ADAMTSL4 knockdown (n=2) and from C26 tumors carrying control shRNA (n=2).

first: Juliano

last: Machado

first: Vignesh

last: Karthikaisamy

first: Pia

last: Benedikt-Kuehnast

first: Doris

last: Kaltenecker

first: Pauline

last: Morigny

first: Amit

last: Mhamane

first: Julia

last: Geppert

first: Lisa

last: Mehr

first: Hermine

last: Mohr

first: Estefania

last: Fernandes

first: Joanna

last: Lima

first: Anastasia

last: Georgiadi

first: Chris

last: Hermann

first: Achim

last: Krüger

first: Jose

last: Otoch

first: Marc

last: Martignoni

first: Inka

last: Zörnig

last: Szendrödi

first: Marilia

last: Seelaender

first: Olga

last: Prokopchuk

first: Maria

last: Rohm

first: Stephan

last: Herzig

middle: B

last: Diaz


title: Childhood Adversity, Allostatic Load, and Epigenetic Signatures in Pediatric and Adult-onset Multiple Sclerosis

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 651

department: Deparment of Human Genetics

country: Belgium

institute: KU Leuven

type: Methylation profiling by high throughput sequencing

summary:
Childhood adversity has an impact on multiple sclerosis (MS) onset, clinical severity and progression, but our understanding of potentially related biological pathways is limited. This study evaluated 60 individuals with either pediatric-onset MS (POMS) or adult-onset MS (AOMS) and tested the association between personal history of childhood adversity and clinical MS outcomes, current indicators of allostatic load, and epigenetic signatures. We conceptualized childhood adversity for each participant as a composite of individual, family, and socioeconomic measures captured, respectively, by the Adverse Childhood Experiences questionnaire, level of parental education, and estimated household income during childhood.
Our primary goal was to test the association between a history of childhood adversity and MS symptom severity, degree of neurologic impairment, biomarkers of allostatic load, and epigenetic changes.
We found that participants with a history of childhood adversity were more likely to have greater MS symptom burden and greater disability but did not differ in allostatic load. Among all patients, epigenetic signatures did not differ by history of childhood adversity. However, when we further analyzed by MS subtype (POMS vs. AOMS), we found that the POMS participants with childhood adversity had epigenetic signatures characterized by increased methylated regions. In contrast, AOMS individuals with childhood adversity showed decreased methylation compared to individuals without childhood adversity. None of the observed clinical and biologic differences were explained by differences in access to or timing of the onset of MS therapy or by the interval between symptom onset and diagnosis .
Our findings suggest that individuals with MS who experienced childhood adversity may have an increased MS symptom burden and greater neurologic deficits. A history of childhood adversity was associated with DNA methylation patterns specific to POMS vs. AOMS. These findings suggest that the biologic and clinical consequences of childhood adversity may have varying effects throughout the MS lifespan.

overall_design: This is a cross-sectional pilot study of 60 MS participants recruited during routine clinical care in an outpatient practice at the NYU Multiple Sclerosis Comprehensive Care Center in New York. A total of 30 POMS and 30 AOMS patients who met eligibility criteria were consecutively recruited and enrolled between August 2022 and March 2023. All were young adults, but recruitment was age-stratified so that patients were closely matched on disease duration. POMS participants were aged 18-25 years at time of enrollment and had MS onset before age 18 years. AOMS participants were aged 26-35 years at time of enrollment and had MS onset after age 21 years. All clinic visits were with clinicians that accepted the same health insurances. A pre-screening medical record review was performed by the study team on all MS patients who fit age range eligibility. The first three eligible patients of the day were approached for study inclusion, to improve temporal recruitment over multiple months. Eligibility criteria included a confirmed diagnosis of relapsing-remitting MS (RRMS), the ability to provide consent, and fluency in English language. Diagnosis of RRMS was made by a MS-trained neurologist according to international criteria (McDonald criteria 2017). Patients were excluded if they had another major neurologic, psychiatric, or medical condition other than MS judged by the treating clinician to be primary (e.g., uncontrolled seizure disorder, traumatic brain injury, cancer). Written consent was obtained from all participants in accordance with the Declaration of Helsinki and the study was approval by the NYU Institutional Review Board. Participants were compensated with a $100 gift card for their time.

first: Kimberly A.

last: O’Neill

first: Lauren

last: Krupp

first: Mirjana

last: Maletic-Savatic

first: Kian

last: Koh

first: Bernard K.


title: Opposing Functions of Dermal Antigen Presenting Cell Subsets in Wound Healing

first: Timothy

middle: Jon

state: IL

address: 1919 W Taylor Room 650

institute: University of Illinois at Chicago

summary: Monocytes and macrophages isolated from skin wounds on male BKS.Cg-Dock7m+/+Leprdb/J mice on day 3, 6, and 10 post-injury, subjected to enzymatic digestion to obtain single cells and pooled from two mice per time point. Fresh cells with viability over 70% processed using the 10x Chromium platform. Libraries sequenced on HiSeq with paired-end reads. Fastq files were generated and demultiplexed into single cells using Cell Ranger software

overall_design: Single cell RNA-seq data from 10X Chromium. Three samples: db_D3, db_D6, and db_D10

first: Timothy J

first: Jingbo

last: Pang

first: Mark

last: Maienschein-Cline

first: Brandon E

last: Lukas

first: Yang

last: Dai

first: Rita E

last: Roberts


title: Comparative scRNA-seq analysis of bone marrow stromal cells in control, naive, exhausted, aged, aged-injury condition

first: Yuki

last: Matsushita

state: Nagasaki

address: Sakamoto 1-7-1

institute: Nagasaki University

summary: Single-cell transcriptional profiles of femoral bone marrow stromal cells from control, naive (single-injured), exhausted (repeatedly injured), aged, and aged-injury (single-injured) mice labeled with Lepr-cre; tdTomato.

overall_design: Lepr-cre-tdTomato+ cells were FACS-isolated from from four groups: uninjured controls at 15 weeks, naive at 15 weeks (bone marrow ablation surgery at 13 weeks), exhausted at 15 weeks (surgeries at 9 and 13 weeks), aged at 18 months, and aged-injury at 18 months (1week after bone marrow ablation surgery). Cells were loaded onto the BD Rhapsody HT Xpress (BD Biosciences). cDNA or gDNA was sequenced by Illumina NovaSeq X Plus.

first: Sixun

last: Wu


title: The molecular basis for fate determination of nuclear polyadenylated RNA

city: Aarhus

first: Jerome

last: Rouviere

address: Universitetsbyen 81

country: Denmark

institute: Aarhus University

summary: Eukaryotic genomes generate a plethora of functional and non-functional polyadenylated (pA+) transcripts, that are all packaged with proteins into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA+ RNPs, such as protein-coding RNPs, are exported to the cytoplasm, while transcripts within non-functional pA+ RNPs are degraded in the nucleus. How cells distinguish these opposing outcomes remains unknown. The DExD-box ATPase UAP56/DDX39B is a central component of functional pA+ RNPs, promoting their docking to the nuclear pore complex (NPC). Here, the NPC-anchored ‘transcription and export complex 2 (TREX-2)’ triggers transcript release from UAP56, facilitating nuclear export. We now show that the ‘Poly(A) tail exosome targeting (PAXT)’ connection harbors a TREX-2-like module, releasing pA+ RNA from UAP56 for decay by the nuclear exosome. The core of this module consists of a LENG8-PCID2-SEM1 (LENG8-PS) trimer, which we show is structurally and functionally equivalent to the central GANP-PCID2-SEM1 (GANP-PS) trimer of TREX-2. Mutagenesis and transcriptomic data demonstrate that the nuclear fate of pA+ RNPs is governed by the contending actions of nucleoplasmic PAXT and NPC-anchored TREX-2, which interpret RNA-bound UAP56 as a signal for export or decay. As PAXT targets are generally short and intron-poor, we suggest an overall model for pA+ RNP fate determination where the distinct sub-nuclear localizations of PAXT and TREX-2 govern the degradation of short non-functional pA+ RNAs while allowing export of their longer and functional counterparts.

overall_design:
Total non polyA enriched RNAseq from RRP40-dTAG cells treated or not with dTAGv1
Please note that GSM9295324-GSM9295329 samples are re-used in the current study

first: Andrii

last: Bugai

first: Ulrich

last: Hohmann

first: Ana

last: Lorenzo

first: Max

last: Graf

first: Laura

last: Fin

first: Jérôme

last: Rouvière

first: Laszlo

last: Tirian

first: Yuhui

last: Dou

first: Marion

last: Le Rest

first: Patrik

last: Polak

first: Dennis

last: Johnsen

first: Lis

last: Jakobsen

first: Jens

last: Andersen

first: Julius

last: Brennecke

first: Clemens

last: Plaschka

first: Torben

middle: H

last: Jensen


title: Interaction between microglia and endothelial cell facilitates inflammatory BBB disruption in bacterial meningitis

city: Tianjin

first: zhiyue

last: Wu

address: No. 288 Nanjing Road, Heping District, Tianjin, China

institute: Institute of Hematology & Blood Diseases Hospital

summary: The blood-brain barrier (BBB) serves as a physiological and functional protective barrier between the brain parenchyma and the peripheral circulatory system, which protects the brain from bloodborne agents, including pathogens and toxins. Bacterial meningitis, a devastating disease occurring worldwide, remains a major cause of high mortality and morbidity, which can trigger BBB disruption and intense intracerebral inflammatory responses. Using single-cell RNA sequencing (scRNA-seq), we show that during neonatal meningitis Escherichia coli (NMEC) challenges, brain endothelial cells undergo pyroptosis and trigger the pyroptotic cascade through intercellular interactions, leading to inflammatory disruption of BBB and strong immune response within the brain. Analyses of the scRNA-seq dataset demonstrate that brian endothelial cells and microglia display the most sensitive to bacterial responses, and the crosstalk between brain vascular cells and immune cells remodels the central nervous system immune microenvironment. We employed a single-cell sequencing approach using 10x Genomics scRNAseq to study neonatal meningitis caused by Escherichia coli (NMEC) infection in mice. This study reveals that NMEC triggers pyroptosis in cerebral cortex cells, leading to inflammatory disruption of the BBB, activation of the apoptotic cascade, and triggering a strong immune response within the brain, disrupting the central nervous system's immune microenvironment. It helps us understand the immunopathological mechanisms of NMEC-induced meningitis and provides a theoretical basis for developing innovative therapeutic strategies targeting the function regulation of cortical cells or microglia and the apoptotic process, thus opening up new avenues for the prevention and treatment of neonatal meningitis.

overall_design:
18-day-old wide type C57BL/6N mice were subjected to phosphate buffer saline (Control) or 1 × 10? CFU NMEC WT for 6 hours, via a tail vein. Brain tissues from the cerebral cortex and hippocampus were isolated at 6 hours post-infection, with sampling performed with reference to single-cell transcriptome sequencing protocols, and collected for ATAC-seq.
Frozen mouse brain tissues were thawed, and nuclei were isolated from tissue homogenates through density gradient centrifugation. A total of 50,000 nuclei per sample were subjected to Tn5 transposase-mediated tagmentation. Libraries were constructed, purified with AMPure beads, and sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads.

first: Yangyang

last: Zheng

first: Zhiyue

first: Haiqing

last: Xiong


title: Dietary effects on cytosolic and mitochondrial tRNA abundance and modification patterns across mouse tissues

city: Santa Cruz

first: Andrew

middle: David

last: Holmes

state: California

address: 1156 High Street

department: Molecular, Cell, and Developmental Biology

institute: UC Santa Cruz

summary: Transfer RNAs (tRNAs) play a central role in protein translation and are increasingly recognized as dynamic regulators of gene expression. Both physiological and environmental signals can modulate tRNA abundance and chemical modifications, yet the impact of dietary cues on the tRNA landscape remains poorly understood. Here, we investigated the effects of two distinct dietary interventions—low-protein and high-fat diets—on tRNA abundance and modification profiles across multiple mouse tissues. We conducted a comprehensive analysis of tRNA abundance and modification changes in response to these nutritional challenges using RNA mass spectrometry and Ordered Two-Template Relay sequencing (OTTR-seq), a modified-base-sensitive tRNA sequencing method. Our results reveal both shared and tissue-specific alterations in abundance and modifications of specific nuclear and mitochondrial genome-encoded tRNAs in response to dietary conditions at isotype, isoacceptor, and isodecoder levels. As many of the tissue-specific or diet-responsive tRNA modifications have been previously reported to affect decoding efficiency or translational fidelity, these results have implications for understanding translational adaptation in response to dietary conditions.

overall_design: OTTR-seq small-RNA sequencing of cells from mouse organs from mice fed with control, low-protein High-fat control and high-fat diets for  six months

first: Upasna

last: Sharma

first: Simeiyun

last: Liu


title: Single-cell omics analysis of age-related immune signatures induced by Omicron sublineage breakthrough infection

city: Beijing

first: Yanhua

last: Li

address: No.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Although COVID-19 is no longer a panic-inducing virus, immunocompromised populations, such as the elderly and those with underlying health conditions, remain at higher risk of severe illness. However, current data on population-level immunosenescence and its immune characteristics are scarce, leaving the impact of aging on antiviral immune responses largely unexplained. This study investigates the influence of age on immune responses by analyzing dynamic changes in blood indices, cytokine-related genes, T-cell receptors (TCRs), and B-cell receptors (BCRs) among COVID-19 patients of different age groups. The findings reveal that elderly patients exhibit significantly elevated levels of routine clinical indicators, such as white blood cells (WBC) and creatinine, along with marked increases in cytokines like interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) post-infection. Gene expression analysis shows that elderly patients have a greater number of differentially expressed genes (DEGs), particularly those associated with inflammatory and antiviral response pathways, with potential therapeutic targets such as CXCR4, IL2RG, and IFITM1 identified. Furthermore, TCR analysis indicates a decline in TCR diversity and a reduction in virus-specific TCRs among elderly patients, suggesting weakened adaptive immune system capabilities. Similarly, BCR analysis demonstrates decreased antibody secretion and restricted B-cell responses in the elderly, indicating impaired antiviral capacity. These findings underscore that age is a critical factor influencing antiviral immune responses, with elderly patients exhibiting more vulnerable immune functions. This study provides valuable insights for the development of personalized treatment and vaccination strategies tailored to the elderly.

overall_design:
We did single-cell RNA sequencing on 14 human samples with different ages that experienced BA.5.2 or BF.7 infection at 1-3 weeks post infection.

***************************************************************
Paired-end raw data has been deposited in the Genome Sequence Archive database (HRA008502)
***************************************************************

first: George

last: Gao

first: Shijie

last: Qin

first: Lei

last: Dong


title: NMuMG PBRM1 ATAC-seq

first: Sagar

last: Utturkar

address: 201 S University St

institute: Purdue University

summary: Mammalian SWI/SNF or BAF are multi-subunit complexes that regulate cell-type specific gene expression by modulating chromatin accessibility, in coordination with transcription factors and other chromatin regulators. PBRM1 is the complex defining subunit of PBAF class of SWI/SNF complexes. It is mutated in ~40% of clear cell renal cell carcinoma cases but also associated with cancer progression and therapy resistance, indicating context-dependent function. We have previously reported that loss of PBRM1 in normal epithelial cells results in a partial Epithelial-to-Mesenchymal Transition (EMT). In this study, we have utilized epigenomic and transcriptomic approaches to understand the mechanistic role of PBRM1 in EMT-regulated gene expression, and its relationship to genome-wide histone modifications.

overall_design: ATAC-seq was performed on control and PBRM1 KO NMuMG cells with 0, 24, 48, 72h of TGFbeta treatments. Related RNA-seq data is available under GEO accession GSE269428.

first: Emily

last: Dykhuizen

first: Alisha

last: Dhiman


title: Spatiotemporal Transcriptomics of Human Cardiovascular Progenitors in Pig Hearts Identifies MIDKINE as a Positive Regulator of Neovascularization

city: Singapore

first: Swarnaseetha

last: Adusumalli

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: In this study, we used time-series spatial transcriptomics to analyze the global gene expression profile of human pluripotent stem cell-derived cardiovascular progenitors (CVPs) transplanted into pigs at 1, 4, and 12 weeks post-chronic myocardial infarction (CMI).

overall_design: Hearts transplanted with cells (n = 2 biological replicates), hearts transplanted with medium as control (n =1) and sham hearts (n=1) were placed onto the 10x visium sldes for down stream seqeucning.

first: Lynn

last: Yap


title: The fetal specific gene LIN28B is essential for human fetal B-lymphopoiesis and initiation of KMT2A::AFF1 infant leukemia [RNA-seq]

city: Oxford

first: Rebecca

last: Ling

state: Select

address: MRC WIMM

department: Paediatrics

country: United Kingdom

institute: University of Oxford

summary: Infant ALL (iALL) is initiated in utero, most often by rearrangement of the KMT2A gene (KMT2Ar). It carries a very poor prognosis despite a lack of additional oncogenic driver mutations common in childhood ALL. Here, we aimed to identify specific properties of human fetal hematopoietic stem/progenitor cells (HSPC) that promote leukemic transformation in KMT2Ar iALL using molecular, functional and in vivo assays. First, by comparing transcriptomes of human fetal HSPC with adult HSPC we derived a fetal-specific gene signature and identified the fetal oncogene LIN28B and its downstream effectors among the top hits. These genes were also expressed in iALL. Functional assays revealed that LIN28B was essential in human fetal liver (FL) CD34+ cells to maintain proliferation and stemness, and support B- and NK-lymphopoiesis. To interrogate the role of LIN28B in iALL, we utilised a human FL-derived CRISPR-Cas9 KMT2A::AFF1 model. In this CRISPRKMT2A::AFF1 model, human FL CD34+ cells fail to transform upon induction of KMT2A::AFF1 translocation in the absence of LIN28B. In addition,  LIN28B-expressing CRISPRKMT2A::AFF1 leukemias were more proliferative in vitro and in vivo, with this advantage being lost upon LIN28B knockdown. Mechanistic studies showed that LIN28B acts by stabilizing key early B-lymphoid genes, epigenetic regulators, and cell cycle and anti-apoptotic genes. Thus, LIN28B has an essential role in normal human fetal B-lymphopoiesis, and is necessary for the initiation of KMT2A::AFF1 iALL in fetal cells in the absence of co-operating mutations. LIN28B activity may help explain why KMT2A::AFF1 leukemias are so aggressive, making it a potential target in LIN28B-expressing leukemias.

overall_design: RNAseq: (1) Adult bone marrow HSC, MPP and LMPP,Human fetal liver (FL)  CD34+ HSC, MPP and LMPP, (2) FL CD34+ control (EV) and LIN28B KD, (3) Xenografts(CRISPR-KMT2A::AFF1 ALL), (4) SEM cells control (EV) and LIN28B KD

first: Thomas

last: Jackson

last: Milne

first: Anindita

last: Roy


title: Epigenomic analysis of organoids from colorectal cancer peritoneal metastases uncovers a mechanism of resistance to doxorubicin

city: Rochester

first: Martin

last: Fernandez-Zapico

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: In this study, we generated patient-derived organoids (PDOs) from patients with colorectal cancer peritoneal mestasis and performed RNA- and ATAC-sequencing to study mechanisms for doxorubicin response.

overall_design: DNA was extracted from patient-derived organoids after growing for 3 passages and ATAC profiles were created using Illumina NovaSeq 6000.

first: Tara

middle: L

last: Hogenson


title: The fetal specific gene LIN28B is essential for human fetal B-lymphopoiesis and initiation of KMT2A::AFF1 infant leukemia [RIP-Seq]

overall_design: RIPseq: SEM cells, immunoprecipititation for with either LIN28B or IgG control


title: MicroRNA signature of lymphoblasts from amyotrophic lateral sclerosis patients as potential clinical biomarkers

city: Madrid

first: Eva

last: P. Cuevas

state: Madrid

address: Ramiro de Maeztu 9

department: Biomedicine

country: Spain

institute: CIB-CSIC

summary: MicroRNAs (miRNAs) are small, non-coding RNAs involved in different cellular functions that have emerged as key regulators of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). ALS is a fatal disease that lacks of not only effective treatments, but also presents delays in its diagnosis, since useful clinical biomarkers are unavailable. In recent years, high-throughput sequencing strategies have appeared to find new ALS biomarkers, to improve early diagnosis and to assess the efficacy of new treatments. Since immortalized lymphocytes obtained from peripheral blood are a suitable model to study pathological features of ALS, we use these samples with the aim of characterize the miRNAs dysregulated in ALS patients. Next-generation sequencing (NGS) was utilized in order to analyse miRNAs expression profiles in immortalized lymphocytes from healthy controls, sporadic ALS (sALS) and familial ALS with mutations in superoxide dismutase 1 (SOD1-ALS). The screening analysis of the NGS data identified a set of dysregulated miRNAs, of which we chose 9 candidates for qRT-PCR validation, identifying for the first time the possible importance of hsa-miR-6821-5p as ALS biomarker.

overall_design: miRNAs expression profiles in human immortalized lymphocytes from healthy controls, sporadic ALS (sALS) and familial ALS with mutations in superoxide dismutase 1 (SOD1-ALS)

middle: P

last: Cuevas

first: Enrique

last: Madruga

first: Ignacio

last: Valenzuela Martínez

first: David

last: Ramírez

first: Carmen

last: Gil

first: Siranjeevi

last: Nagaraj

first: Angeles

last: Martin-Requero

first: Ana

last: Martinez


title: Epigenomic analysis of organoids from colorectal cancer peritoneal and liver metastases uncovers a mechanism of resistance to doxorubicin

summary: In this study, we generated patient-derived organoids (PDOs) from patients with colorectal cancer peritoneal and liver mestases and performed RNA- and ATAC-sequencing to study mechanisms for doxorubicin response.

overall_design: mRNA was extracted from patient-derived organoids after growing for 3 passages and RNA profiles were created using Illumina NetSeq.