title: Integrative single cell analysis of progressive multiple sclerosis induced neural stem cells reveals epigenetically dysregulated type-I-interferon signaling [scATAC-seq]

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: Multiple sclerosis (MS) is a chronic demyelinating disease of the central nervous system, which currently lacks effective therapies that provide regeneration and stop disease progression. A suggested link is anticipated between the development of progressive MS (PMS) and aging, as suggested by recent work identifying hallmarks of cellular senescence in numerous cell types both in vitro with patient cell lines and in vivo in the post-mortem MS brain, including neural stem cells (NSCs). Using an inducible system, directly reprogramming human fibroblasts into induced NSCs (iNSCs), we generated control and PMS iNSC cell lines, which was found to maintain epigenetic age. Here we performed multi-omics, including bulk RNA, single-cell (sc) RNA, single-nucleus (sn) RNA and ATAC, and whole genome bisulfite sequencing. Here, we show that PMS iNSCs have overall increases in senescence and inflammatory associated genes using bulk sequencing. We next identified a unique subcluster of cells within the PMS iNSCs that have a pro-inflammatory and senescent phenotype, associated with interferon gene activation using sc-RNA seq. Within this specific subcluster there is higher expression of genes associated with inflammatory protein secretion, as well as the senescence associated secretory phenotype (SASP). A similar clustering pattern was observed in the ATAC-seq data, a large main cluster and a small inflammatory cluster primarily comprising of PMS iNSCs. Differentially accessible regions within the PMS cluster revealed promoter sites of inflammatory-associated genes to be more accessible correlating with gene expression. Our results highlight a novel cellular mechanism in PMS wherein NSCs are interferon-responsive and senescent-like which may impact other cells within the lesion leading to chronic inflammation.

overall_design:
iNSC lines, between passages 25-30, were plated at 500,000 cells per well in a growth factor reduced matrigel coated 6 well plate. After 24 hours, the media was changed to fresh media. Cells were harvested in RLT lysis buffer 72 hours after plating then frozen at -80C until extraction.
Please note that processed data files (generated from both Lane1 and Lane2) are linked to the corresponding *Lane1 sample records.

first: Bongsoo

last: Park

first: Alexandra

last: Nicaise

first: Dimitrios

last: Tsitsipatis

first: Liviu

last: Pirvan

first: Andi

last: Munteanu

first: Lopez

last: De Novales

first: Pranathi

last: Prasad

first: Julia

last: Whitten

first: Luka

last: Culig

first: Joseph

last: Llewellyn

first: Rosana-Bristena

last: Ionescu

first: Jinshui

last: Fan

first: Supriyo

last: De

first: Marta

last: Suarez Cubero

first: Tommaso

last: Leonardi

first: Valentina

last: Fossati

first: Frank

last: Edenhofer

first: Myriam

last: Gorospe

first: Isabel

last: Beerman

first: Stefano

last: Pluchino


title: Integrative single cell analysis of progressive multiple sclerosis induced neural stem cells reveals epigenetically dysregulated type-I-interferon signaling [scRNA-Seq]

status: Public on Oct 10 2025

first: Irina

last: Mohorianu

country: United Kingdom

type: Expression profiling by high throughput sequencing

overall_design: iNSC lines, between passages 25-30, were plated at 500,000 cells per well in a growth factor reduced matrigel coated 6 well plate. After 24 hours, the media was changed to fresh media. Cells were harvested in RLT lysis buffer 72 hours after plating then frozen at -80C until extraction.

first: Bongsoo

last: Park

first: Alexandra

middle: M

last: Nicaise

first: Dimitrios

last: Tsitsipatis

first: Liviu

last: Pirvan


title: Integrative single cell analysis of progressive multiple sclerosis induced neural stem cells reveals epigenetically dysregulated type-I-interferon signaling

overall_design: iNSC lines, between passages 25-30, were plated at 500,000 cells per well in a growth factor reduced matrigel coated 6 well plate. After 24 hours, the media was changed to fresh media. Cells were harvested in RLT lysis buffer 72 hours after plating then frozen at -80°C until extraction. RNA extraction was performed according to the RNeasy kit followed by DNase treatment (Qiagen). This accession refers to the bulk mRNAseq data.

first: Andi

last: Munteanu


title: Impact of AIM2 on Head and Neck Squamous Cell Carcinoma Development

city: Tucson

first: Justin

last: Wilson

state: AZ

address: 1515 N Campbell Ave

department: Immunobiology

country: USA

institute: The University of Arizona

summary: Head and neck squamous cell carcinoma (HNSCC) constitutes 90% of head and neck cancers. HNSCC development is linked to chronic inflammation through mechanisms that are not fully understood. The cytosolic double-stranded DNA sensor Absent in Melanoma 2 (AIM2) is an inflammasome-forming protein that also has inflammasome-distinct roles in restricting tumorigenesis. We performed bulk RNA sequencing on tongue tissue from wild type (WT) and Aim2-/- mice treated with the carcinogen 4NQO in drinking water as a model of experimental HNSCC to uncover gene signatures regulated by AIM2 during HNSCC development.

overall_design: Wild type and Aim2-/- mice were treate with 4NQO for 20 weeks. Mouse tongues were excised and processed to extrat bulk RNA for sequencing.

first: Dakota M

last: Reinartz

first: Justin E


title: Therapeutic potential of heat-killed Enterococcus faecalis (EC-12) Para-Probiotic in reversing maternal separation-triggered social deficit in Mice

city: Tokyo

first: Eman

middle: Abdo

last: Mady

address: Harumicho

department: veterinary medicine

country: Japan

institute: Tokyo university Of Agriculture and technology

summary: Maternal separation (MS) stress in early life was established as a model of triggering lifelong mental disorders. It can disrupt the gut-brain axis (GBA) and induce neurobiological illnesses in the adult stage. Diverse probiotics were utilized to reverse the encountered alterations. However, the employment of heat-killed Enterococcus faecalis (EC-12) to reverse the psychological abnormalities following MS has not been investigated yet. Hence, we aim to study the effectiveness of EC-12 as a potential therapy for MS mice. Our study illustrates the potential use of heat-killed EC-12 as a novel Para-Probiotic that could reverse the social abnormalities induced at the adult stage by exposure to MS in early life.

overall_design: RNA-seq profiling from prefrontal cortex of brainsamples of wildtype adult male mice Following 5 consecutive weeks of EC-12 supplementation

middle: A


title: Spatiotemporal hepatocyte heterogeneity impacts in vivo gene engineering

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

summary: The liver is a central organ for metabolism and hepatocytes are the main cell type responsible for most of its functions. Several previous studies investigated the cell types involved in tissue homeostasis and regeneration, however, the mechanisms underlying post-natal liver growth and establishment of the mature hepatocyte phenotypes remain to be fully understood. Here we investigate liver tissue dynamics in mice during growth and adulthood, by spatial transcriptomics, clonal analysis, and lineage tracing. We observe the progressive establishment of metabolic zonation of hepatocytes following weaning, with the specification of the centrilobular identity only in adults. We report that only a fraction of hepatocytes proliferate in the newborn liver, generating most of the adult tissue, and that preferential gene editing of the more proliferating hepatocytes allows expansion of the genetically engineered liver area. We also describe age-dependent differences in the efficiency and distribution of lentiviral in vivo gene delivery, with higher efficiency of gene transfer in young compared to adult animals and a skewed localization within the liver lobule. We identify high proteasome activity in the peri-central lobular area as the major determinant of the observed outcome and successfully revert it by proteasomal inhibition before vector administration. Overall, our findings provide new insights into the spatiotemporal dynamics of hepatocytes during post-natal growth, which extend our understanding of liver biology and have important implications for therapeutic applications.

overall_design: Liver samples from 3 mice per age (2 and 8 weeks old) were collected on ice. Single nuclei suspension was obtained from the livers by Singleron Biotechnologies and then equally pooled into a single sample for each age group to be processed for single nuclei RNA sequencing.

first: Michela

last: Milani

first: Francesco

last: Starinieri

first: Marco

last: Monti

last: Beretta

first: Alessio

last: Cantore


title: Androgenic Effects of 11-Oxygenated Androgens in Castration-Resistant Prostate Cancer

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

country: Canada

institute: Laval University

summary: Investigations of CRPC cell models demonstrate that both 11oxygenated androgens 11Ketotestesterone (11KT) and 11-hydroxytestosterone (11OHT) drive robust AR-mediated proliferative responses and significantly modulate gene and protein expression profiles, paralleling canonical androgens. They also exhibit unique transcriptional and post-transcriptional effects that include potential AR-independent pathways. Furthermore, the AR antagonist enzalutamide effectively inhibits their androgenic actions, suggesting they are primarily AR-mediated.

overall_design: RNA-seq profiling of the prostate cancer cell lines DU145, LAPC4, VCaP exposed to R1881 or 11ketotestosterone or 11hydroxytestosterone with or without co-exposure to the androgen receptor inhibitor enzalutamide

first: Michèle

last: Rouleau

first: Vincent

last: Gélinas


title: Transcriptomic profiling during normothermic machine perfusion of human kidneys reveals a pro-inflammatory cellular landscape and gene expression signature associated with prolonged delayed graft function after transplantation [bulk RNA-seq]

first: Irina

last: Mohorianu

summary: Assessment and treatment of severe ischaemia-reperfusion-injury (IRI) remains an unmet challenge in kidney transplantation. Normothermic machine perfusion (NMP) recapitulates IRI ex situ, but there is limited understanding of the transcriptional pathways, and the associated cellular landscape, driving IRI during NMP and determining its severity. Such knowledge is essential for therapeutic targeting and organ resuscitation during machine perfusion. Using tissue obtained at the time of NMP from kidneys subsequently transplanted as part of a randomised controlled trial, we undertook in-depth transcriptomic analyses comparing kidneys suffering severe IRI, manifesting clinically as the development of delayed graft function (DGF), to kidneys with mild IRI (defined by immediate graft function, IGF) post-transplantation. We validated upregulation of previously described pro-inflammatory and immune transcriptomic pathways, including TNFa via NFkB signaling, Allograft Rejection and Inflammatory Response. Going further, we identified innate immune system driven processes at the core of the transcriptional signature in kidneys suffering severe IRI, such as recruitment and migration of myeloid leucocytes, macrophage activation, phagocytosis and inflammasome activation. Deconvolution using single-cell-RNAseq data showed kidneys with severe IRI and post-transplant DGF were enriched for pro-inflammatory mononuclear phagocytes, myofibroblasts and fibroblasts, but depleted of tubuloepithelial, cell signatures. These transcriptional findings were recapitulated in tissue biopsies obtained during NMP from an external cohort comparing kidneys with high acute tubular injury and severe IRI to kidneys with low acute tubular injury and mild IRI; these kidneys were histologically similar to the DGF/IGF kidneys, respectively. Together, our study characterises the transcriptional signature of severe IRI during NMP, suggesting the role of pro-inflammatory innate/pro-fibrotic cells in this process. We describe a transcriptomic signature that may support future prospective therapeutic trials as a potential efficacy endpoint, and highlight potential cellular targets for therapeutic intervention during NMP in an era of precision medicine.

overall_design: bulkRNA samples of Kidnay biopsies for patients that underwent NMP

first: Harry

middle: V

last: Spiers

first: Sarah

last: Hosgood

first: Miguel

last: Larraz

first: Lukas

middle: J

last: Stadler

first: Ying

last: Zhai

first: Haeun

last: Moon

first: Serena

last: MacMillan

first: Michael

middle: L

last: Nicholson

first: Vasilis

last: Kosmoliaptsis


title: The effect of exposure to PM2.5 from the cowshed environment on the ovaries of rats

city: Changchun

first: Zhenhua

last: Ma

state: Jilin

address: Xincheng Street

department: College of Veterinary Medicine

country: China

institute: Jilin Agricultural University

summary: Fine particulate matter (PM2.5) is toxic to reproduction and can cause a range of reproductive disorders. However, the underlying mechanisms of female reproductive impairment due to cowshed PM2.5 exposure are unclear. The aim of this study was the investigation of the effects of PM2.5 on rat ovaries and its molecular mechanisms. Therefore, this study established a whole-body exposure model of PM2.5 in female rats to investigate the effects of PM2.5 on the ovaries. Exposure of rats to PM2.5 using a small animal whole-body PM2.5 exposure system. The device effectively simulates the exposure of animals or humans to PM2.5 within the barn environment, thereby offering enhanced scientific reference data. To put it briefly, for 30 days, the rats were exposed to six hours a day at four times the actual ambient PM2.5 concentration. Adult rats' respiratory coefficient, single-breath volume, and respiratory frequency were used to quantify their daily exposure to PM2.5. To study the effects of PM2.5 exposure on the ovaries of rats, the rats were divided into 2 groups: rats living in clean air were the Control group (Control), which received no additional treatments, and rats exposed to PM2.5 were the PM2.5-exposed group (PM2.5).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for adult female rat ovaries

first: Yunhang

last: gao


title: Modeling NRF2-Driven Anti-inflammatory, Tumor-promoting Macrophages In Vitro II

city: Zurich

first: Florence

last: Vallelian

address: Rämistrasse 100

country: Switzerland

institute: University Hospital Zürich

summary: We employed 3D spheroid co-cultures to explore the paracrine and direct cell-contact effects of NRF2-driven macrophages on MC38 tumor growth. We seeded equal numbers of GFP+ MC38 cells and macrophages (WT or Keap1 KO) in ultra–low-adherence plates to form multicellular spheroids. Live-cell imaging showed that spheroids containing NRF2high macrophages reached significantly larger sizes over 120 hours compared to spheroids with WT macrophages. With multiplexed scRNA-seq of spheroids collected at 24 and 120 hours post-formation, we defined the directed effects of NRFhigh stress-TAMs on tumor cells. UMAP density projections visualize that the macrophage genotype did not affect tumor cell gene expression within the first 24 hours despite persistent NRF2-driven macrophage phenotypic diversity. However, by 120 hours, tumor cell transcriptomes diverged markedly, as visualized by an unequal shift in cell densities, which was much more pronounced in the spheroids containing Keap1 KO macrophages. Leiden clustering and subsequent cluster-based GSEA revealed that while most tumor cells co-cultured with wild-type macrophages remained in a proliferative state, those co-cultured with Keap1 KO macrophages transitioned into an epithelial-mesenchymal transition (EMT) state, indicative of high metastatic potential.

overall_design: We seeded equal numbers of GFP+ MC38 cells and macrophages (WT or Keap1 KO) in ultra–low-adherence plates to form multicellular spheroids. We collected these spheroids after 24 and 120 hours post-formation and analyzed them with multiplexed scRNAseq.

first: Dominik

last: Schaer

first: Livio

last: Baselgia

first: Elena

last: Duerst


title: Spatial Zonation of Pro- and Anti-inflammatory Tumor Macrophages After Anti-CD40 II

summary: Because necrosis can be induced by multiple therapeutic modalities, we next analyzed irradiated MC38 tumors to see if they similarly exhibit Spp1+–Cxcl9+ polarization. Therefore, we conducted a spatial RNA-seq analysis on MC38 tumors at 24 hours and 7 days post–irradiation with 12 Gy. As observed under anti–CD40–mediated immunotherapy, we discovered that phenotype heterogeneity among Lyz2+ features increased over time, reproducing the bifurcated polarization trajectory along the Spp1–Cxcl9/Cxcl10 axis. High-resolution macrophage profiling similarly confirmed the regional segregation of Cxcl10+ (better detected in these samples than Cxcl9) and Spp1+ cells.

first: Nadja

last: Schulthess-Lutz


title: Spatial Zonation of Pro- and Anti-inflammatory Tumor Macrophages After Anti-CD40

summary: Seeking to understand how local tissue factors reinforce these divergent TAM phenotypes, we next investigated their spatial distribution in MC38 tumors following anti-CD40 treatment (days 6 and 8 post-inoculation). We performed high-definition spatial transcriptomics at a spatial resolution of ~2 µm on a formalin-fixed, paraffin-embedded (FFPE) section. H&E-staining  revealed dense leukocyte infiltrates and a large necrotic core. Spatial mapping showed a clear partition in macrophage phenotypes. The peripheral zone was rich in antigen-presenting and proinflammatory macrophages, while antiinflammatory macrophages were concentrated close to the necrosis-proximal region. This pattern was consistent with the accumulation of Cd74+ and Cxcl9+ macrophages at the tumor edges and Spp1+ macrophages clustering toward the necrotic center. Cells co-expressing pro- and anti-inflammatory markers (Cxcl9+ / Cd74+ and Spp1+) were scattered between the single-positive populations, suggesting a continuous gradient of macrophage states driven by local stress.

overall_design: MC38 cells in culture medium were mixed with Geltrex and injected subcutaneously into the mouse flanks. Agonistic anti-CD40 treatment was administered intravenously according to treatment protocol. Mice were euthanized, and tumors were collected at defined timepoints after antibody administration. The tumor was analyzed using spatial transcriptomics.


title: Modeling NRF2-Driven Anti-inflammatory, Tumor-promoting Macrophages In Vitro

summary: To determine whether NRF2-mediated anti-inflammatory differentiation and its downstream consequences on tumor immunology are intrinsic macrophage processes, we conducted a series of in vitro studies. First, we performed scRNA-seq studies of WT, Keap1 KO, and Nrf2 KO BMDMs after short-term culture with GM-CSF for 5 days to capture a broad spectrum of differentiation and polarization states across the macrophage lineage trajectory.

overall_design: scRNA-seq study of WT, Keap1 KO, and Nrf2 KO BMDMs after short-term culture with GM-CSF for 5 days


title: NRF2 Engenders Anti-inflammatory Stress Macrophages

summary: We evaluated the function of NRFhigh stress-TAMs and how they respond to immunostimulatory cues. scRNA-seq of CD45+ tumor-infiltrating leukocytes from Keap1flox/flox VavCre and WT mice (n=2 per group) revealed that macrophages were the most abundant leukocyte population in both genotypes. Differential expression, gene set enrichment analysis (GSEA), and cell-by-cell functional scoring indicated a pronounced upregulation of oxidative-stress defense and metabolic adaptation in Keap1 KO macrophages, accompanied by reduced MHC II expression, suppressed interferon-response pathways, and impaired antigen presentation capacity. Despite major shifts in oxidative stress defense and antigen presentation, key macrophage-defining functions such as phagocytic capacity remained comparable between WT and Keap1 KO TAMs. Transcription factor motif analysis further identified NRF2 as a top activated factor and STAT1 as a repressed factor in Keap1 KO TAMs.


title: Next Generation Sequencing analysis of the global expression profiling in bone marrow-derived macrophages (BMDMs) from wild-type and RBP4-deficient mice.

city: Taian

first: Yingli

last: Shang

state: Shandong

address: No. 61, Daizong Street

institute: Shandong Agricultural University

summary: To investigate the influence of retinol-binding protein 4 (RBP4) deficiency on the expression of genes related to cholesterol metabolism, we examined the expression profiling of global genes in BMDMs from wild-type(WT) and RBP4-deficient mice (RBP4-KO) by RNA-seq. The results revealed that expression of 71 genes were greater than twofold in RBP4-KO BMDMs relative to their expression levels in WT cells.In addition, the expression of 158 genes were lower than in RBP4-KO BMDMs compared to that of WT cells. Clustering analysis suggested that deficiency of RBP4 suppressed the expression of a subset of cholesterol uptake-associated genes without affecting the expression of genes related to cholesterol synthesis or efflux, indicating that RBP4 is likely involved in regulating cholesterol homeostasis.

overall_design: mRNA profiles of BMDMs from WT and RBP4-deficient mice.

first: Hejiao

last: Zhao


title: Metabolic Dependency on De Novo Pyrimidine Synthesis in Platinum Resistant Ovarian Cancer

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: Recurrent high grade serous ovarian cancer (OC) is mostly lethal due to development of resistance to platinum-based chemotherapy. We used cisplatin resistant (Cis-R) cells generated by repeat cisplatin treatment of sensitive (Cis-S) OC cell lines, and metabolomics to identify critical factors associated with platinum resistance. Pathway analysis of differentially abundant metabolites in Cis-R vs. Cis-S OVCAR5 and COV362 cells identified enrichment of pyrimidine metabolism (FDR<0.05) produced by increased de novo pyrimidine synthesis which was subsequently confirmed by flux analysis. Inhibition of this pathway using the DHODH inhibitor brequinar (BRQ) decreased viability, and produced expression changes in genes of the mitochondrial electron transport in Cis-R compared with Cis-S cells. Oxygen consumption rate (OCR) measured with a Seahorse assay indicated lower (P<0.05) OCR (baseline, ATP-related, and maximal) and spare respiratory capacity (SRC) in Cis-R vs. Cis-S OVCAR5 cells. In addition, BRQ had dose-related inhibitory effects on OCR across assay conditions in both Cis-R and Cis-S cells, SRC however, was inhibited by BRQ only in Cis-R cells. In vivo, BRQ attenuated growth of intraperitoneal (ip) Cis-R tumor xenografts but did not alter Cis-S tumors. Similarly, tumor growth was inhibited (p<0.01) by BRQ in a Cis-R PDX model. BRQ plus carboplatin enhanced (p<0.05) the inhibitory effects of carboplatin alone on total tumor weight and numbers of Cis-R ip tumor xenografts. Results indicate that Cis-R cells develop mechanisms that enhance de novo pyrimidine synthesis and maintain relatively low levels of mitochondrial oxidation, however these changes make Cis-R cells vulnerable to inhibitors of these processes.

overall_design: To determine the relevance of de novo pyrimidine synthesis in resistance to cisplatin in ovarian cancer cells, we performed RNA-seq analysis of cisplatin resistant vs. cisplatin sensitive OVCAR5 cells treated with vehicle (control) or the DHODH inhibitor, brequinar (n=3 samples per group).

first: Horacio

last: Cardenas

first: Guangyuan

first: Ana Maria

last: Isac

first: Wenan

last: Qiang


title: CD8+ T cell recall cytotoxicity during chronic treated HIV-1 infection is associated with limited reservoir size and activity

first: Jonathan

middle: Morris

last: Urbach

state: Massachusetts

address: 400 Technology Sq Rm 851

institute: Ragon Institute of MGH, MIT and Harvard

summary: The combination of replication-competent HIV-1 proviral persistence and virus-specific immune dysfunction prevents virus clearance during antiretroviral therapy (ART), resulting in rebound viremia after treatment interruption. Functional impairment of HIV-specific CD8+ T cells during chronic infection is typically not reversed by ART but has recently been shown to improve in some individuals after prolonged treatment. To evaluate the impact of cellular immune function on viral persistence, we mapped and functionally characterized HIV-1 epitope-specific CD8+ T cell responses and virus reservoirs in sixty people with HIV-1 (PWH) who initiated prolonged ART during chronic progressive infection. In 17% of participants, recall cytotoxicity of proliferative CD8+ T cells targeting one or more autologous proviral epitopes was comparable to responses in spontaneous HIV-1 controllers. These responses were associated with smaller and less transcriptionally active HIV-1 reservoirs during prolonged ART. Treatment interruption in one participant with moderately high HIV-specific CD8+ T cell proliferative and cytolytic capacity resulted in a rapid reduction of rebound viremia coincident with in vivo HIV-specific CD8+ T cell expansion and secondary cytotoxic effector cell differentiation. Collectively, these results highlight a potential role for recall cytotoxicity in limiting HIV-1 persistence during ART and attenuating rebound viremia after treatment interruption, which may inform strategies to elicit durable post-ART immune control.

overall_design:
HLA-B*44-restricted HIV Gag AEQASQEVKNW-specific CD8+ T cells were isolated from PBMCs by FACS using barcoded fluorescent peptide-HLA tetramer across six longitudinal samples during analytical treatment interruption in one participant. Each sample was also stained with a unique barcoded hashing antibody and a panel of commercially available library of barcoded surface antibodies prior to isolation. Gene expression (GEX), antibody-derived tags (ADT), and T cell receptor (VDJ) sequencing libraries were prepared using 10X NextGEM 5’ single-cell RNA-sequencing with feature barcode technology before sequencing via the Illumina NextSeq 2000 platform.

Funding by Howard Hughes Medical Institute, Clinical Translational Science Award 1UL1TR002541.

first: David

middle: R

last: Collins

first: Mpho

last: Olatotse

first: Tyler

last: Lilie

first: Xianbao

last: He

first: Bridget

last: Coffey

first: Umar

last: Arshad

first: Zachary

last: Racenet

first: Jennifer

last: Davis

first: Hannah

middle: C

last: Jordan

first: Manish

last: Sagar

first: Emanuele

last: Mazzola

first: Bruce

middle: D

last: Walker

first: Athe

last: Tsibris


title: Targeted protein evolution in the gut microbiome by diversity-generating retroelements

city: Los Angeles

first: Benjamin

last: Macadangdang

state: CA

address: 10833 Le Conte Ave, MDCC B2-375

institute: University of California, Los Angeles

summary: Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting they play adaptive roles in this environment. We identified >1,100 unique DGRs among human-associated Bacteroides species and discovered a subset that diversify adhesive components of Type V pili and related proteins. We show that Bacteroides DGRs are horizontally transferred across species, that some are highly active while others are tightly controlled, and that they preferentially alter the functional characteristics of ligand-binding residues on adhesive organelles. Specific variable protein sequences are enriched when Bacteroides strains compete with other commensal bacteria in gnotobiotic mice. Analysis of >2,700 DGRs from diverse phyla in mother-infant pairs shows that Bacteroides DGRs are preferentially transferred to vaginally delivered infants where they actively diversify. Our observations provide a foundation for understanding the roles of stochastic, targeted genome plasticity in shaping host-associated microbial communities.

sample_organism:
Bacteroides thetaiotaomicron VPI-5482
Bacteroides ovatus ATCC 8483
Bacteroides uniformis ATCC 8492
Bacteroides fragilis 638R
Bacteroides finegoldii CL09T03C10

overall_design: To investigate if Bacteroides DGR activity is controlled at the transcriptional level, we grew five strains of Bacteroides in culture that each had varying levels of DGR activity for 24 hours for gene expression profiling.

first: Umesh

last: Ahuja

first: Bennett

last: Shaw

first: Jeff

last: Miller


title: CD8+ T cell stemness precedes post-intervention control of HIV viremia

first: Jonathan

last: Urbach

summary: Interventions to induce lasting HIV remission are needed to obviate the requirement for lifelong antiretroviral therapy (ART). Durable post-intervention control (PIC) of viremia has been achieved in a subset of individuals following broadly neutralizing anti-HIV-1 antibody (bNAb) administration and analytical treatment interruption (ATI)1-4. Prior studies support a role for CD8+ T cells5-9 but the precise features of CD8+ T cells involved in PIC remain unclear. Here we mapped and functionally profiled CD8+ T cell responses to autologous HIV epitopes using longitudinal samples from four ATI trials in bNAb recipients. PIC was associated with superior pre-intervention HIV-specific CD8+ T cell proliferative capacity, stem cell-like memory phenotype, and recall cytotoxicity against autologous HIV peptide-pulsed CD4+ T cells. CD8+ T cell stemness was further increased following bNAb administration without emergence of new clonotypes targeting defined HLA-optimal epitopes. Multimodal single-cell analyses revealed molecular features associated with PIC and HIV-specific CD8+ T cell stemness, including signatures of metabolic fitness and reduced T cell exhaustion. These results identify immune features that precede subsequent PIC to inform the development of combination immunotherapies that will elicit durable HIV remission.

overall_design:
HIV and CMV epitope-specific CD8+ T cells were isolated from participant PBMCs by FACS using combinations of barcoded fluorescent peptide-HLA tetramers among longitudinal samples collected before (pre) and/or following (post) infusion of broadly-neutralizing antibodies against HIV-1 and analytical treatment interruption. Each sample was also stained with a unique barcoded hashing antibody (HTO) and a panel of commercially available library of barcoded surface antibodies prior to isolation. Gene expression (GEX), antibody-derived tags (ADT), and T cell receptor (VDJ) sequencing libraries were prepared using 10X GEM-X 5’ single-cell RNA-sequencing with feature barcode technology before sequencing via the Illumina NextSeq 2000 platform.

Funding by Howard Hughes Medical Institute.

first: Zahra

last: Kiani

last: Wisner

first: Daniel

middle: Y

last: Chang

first: Joshua

last: Acklin

first: Alicja

last: Piechocka-Trocha

first: Nathalie

last: Bonheur

first: Ashok

last: Khatri

first: Mathias

last: Lichterfeld

first: Jesper

last: Gunst

first: Ole

middle: S

last: Sogaard

first: Marina

last: Caskey

first: Michel

last: Nussenzweig

first: David

last: Collins


title: Cellular and molecular dysregulation of the esophageal epithelium in systemic sclerosis

first: Matthew

last: Dapas

address: 240 E Huron St

department: Medicine

summary: Individuals with systemic sclerosis (SSc)  often suffer from chronic acid reflux and dysphagia due to loss of esophageal motility. However, the pathogenesis of esophageal dysmotility in SSc is poorly understood. To determine whether distinct changes in esophageal epithelial cells contribute to impaired motility in SSc, we investigated the stratified squamous esophageal epithelium from proximal and distal biopsies using single-cell RNA sequencing (n=306,372 cells) in individuals with SSc compared those with gastroesophageal reflux disease (GERD) as well as healthy controls.

overall_design:
Single-cell RNA-seq of esophageal mucosa biopsies from scleroderma, GERD, and healthy controls

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

first: Deborah

last: Winter

first: Marie-Pier

last: Tetreault


title: METTL1 relays the tumor-promoting signal flow from senescent CAFs by modulating RNA m7G modifications with SASP-related cytokines

city: guangzhou

first: Ze

last: Yuan

state: guangdong

address: yuancun

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

summary: Colorectal cancer (CRC) remains a significant contributor to global cancer-related mortality. The significant role of senescent cancer-associated fibroblasts (S-CAFs) in the progression of CRC has been acknowledged, while the mechanisms remain unclear. We employed RNA sequencing, m7G-MeRIP sequencing, and Luminex liquid suspension chip assays to elucidate the epigenetic changes induced by S-CAFs. Our findings revealed a significant downregulation of METTL1 in CRC tissues, particularly in older patients, which correlates with poor prognosis. S-CAFs modulate METTL1 expression and m7G methylation, leading to epigenetic reprogramming that enhances tumor proliferation and invasion. The secretion of SASP cytokines PDGF-BB and TNF-α by S-CAFs was identified as key mediators of this process. The use of inhibitors such as rapamycin, Typhostin, and Infliximab demonstrated the potential to reverse epigenetic changes and inhibit CRC progression. Our study investigated the role of METTL1-mediated transcriptome reprogramming in the crosstalk between cancer cells and S-CAFs, offering novel insights into the complex mechanisms underlying tumor progression and providing a foundation for developing targeted therapies. Furthermore, our research paved the way for innovative therapeutic strategies that may improve outcomes for CRC patients, especially those with early-onset disease.

overall_design: Total RNA was collected from DLD1 cells co-cultured with S-CAFs, DLD1 cells co-cultured with CAFs, DLD1 cells with stable METTL1-knockdown and control cells (two replications, which were labeled as sh2 and shnc, respectively) using TRIzol reagent (Invitrogen, CA).

first: Jingrong

last: Weng

first: Zhenghua

last: Chen

first: Huichuan

last: Yu


city: Shanghai

first: Ke

last: Tang

address: Tongji University, No. 1239, Siping Road, Shanghai

institute: Tongji University

summary: To quantitively evaluate MetroSCREEN’s performance in predicting MRs, we performed CRISPR knockout (CRISPR KO) screens on the PC cell line, targeting four well-known MRs: CTNNB159, ATF460, MYC61, and JUN62.

overall_design: CRISPR knockout (CRISPR KO) screens on the PC cell line, targeting four well-known MRs: CTNNB, ATF, MYC, and JUN. After lentiviral library infection and puromycin selection, the sequences encoding the sgRNAs were PCR-amplified from the transduced cells and quantified by high-throughput sequencing. We conducted the screen with 10x Genomics droplet-based 3’ scRNA-seq and direct sgRNA capture.


title: Rebound Polarization of Monocyte-derived Tumor Macrophages Under Repeated Anti-CD40 Immunotherapy II

first: Florence

last: Vallelian

summary: To confirm that both pro-inflammatory and immunosuppressive subsets arise from common monocyte precursors, we employed Ms4a3-Cre Rosa26-tdTomato fate-mapping mice. Flow cytometry of dissociated tumors showed that most F4/80+ macrophages were tdTomato+, with subpopulations differing in MHC class II expression. scRNA-seq of sorted CD45+tdTomato+ cells confirmed a bifurcated differentiation trajectory that yields pro-inflammatory, MHC II–high macrophages (Cxcl9+, H2-Eb1), as well as Spp1+ Arg1+ immunocompromised phenotypes.

first: Dominik

last: Schaer

first: Livio

last: Baselgia

first: Elena

last: Duerst


title: Rebound Polarization of Monocyte-derived Tumor Macrophages Under Repeated Anti-CD40 Immunotherapy

summary: To investigate TAM phenotypes and potential stress-induced feedback mechanism upon immunotherapy, we treated MC38 tumor-bearing C57BL/6 mice with a single dose of agonistic anti-CD40 or isotype control on day 11 (1× anti-CD40) or with repeated doses on days  11,  13, and  15 (3× anti-CD40). Twenty-four hours after the last injection, tumors were harvested for flow cytometry and single-cell RNA sequencing (scRNA-seq). A single anti-CD40 injection significantly elevated CD45+F4/80+ macrophage numbers. PCA on CD45+F4/80+ cell RNAseq data , followed by gene set enrichment analysis (GSEA) and transcription factor enrichment, revealed a pronounced transcriptional transformation. After the first round of immunotherapy, most macrophages shifted toward an IFN–STAT1–driven, immune-activated phenotype—reflecting a robust antitumor response. However, repeated anti-CD40 doses induced a rebound in macrophage gene expression, reverting toward the original “tumor-conditioned” state highlighted by strong Spp1 expression. This rebound raised questions about stress signals in the local tumor environment driving macrophage immunosuppression. Across all conditions, we detected a striking polarity along a phenotype gradient from Spp1+ immunocompromised TAMs towards immune-activated Cxcl9+ Cxcl10+ MHC class II macrophages.

overall_design: Mice bearing subcutaneous (s.c.) MC38 tumors were treated intravenously (i.v.) with either isotype control (ctrl)l or agonistic anti-CD40 on day 11 (single injection; 1xCD40) or on days 11, 13, and 15 (multiple injections, 3xCD40). Twenty-four hours after the final injection, tumors were harvested, and CD45+F4/80+ cells were FACS-sorted for multiplexed scRNA-seq.


title: Targeting De Novo Cholesterol Synthesis as a Therapeutic Strategy in Rhabdomyosarcoma

city: Helsinki

first: Nebeyu

middle: Yosef

last: Gizaw

state: Helsinki

address: Haartmaninkatu

department: Biomedicine

country: Finland

institute: University of Helsinki

summary: Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children, but outcomes for high-risk patients remain dismal, underscoring the critical need for novel therapeutic strategies. Our study demonstrates that RMS exhibits elevated de novo cholesterol biosynthesis. Silencing key cholesterol biosynthesis genes, such as DHCR7, disrupts cell cycle progression by inducing G2/M phase arrest. Additionally, inhibiting this pathway triggers endoplasmic reticulum (ER) stress, activates the unfolded protein response (UPR), and leads to apoptosis. These findings emphasize the essential role of de novo cholesterol synthesis in RMS and highlight a novel therapeutic strategy that targets this metabolic pathway to suppress tumor growth and promote apoptosis.

overall_design: To investigate the role of cholesterol biosynthesis in RMS tumorigenesis, we established an RD cell line with DHCR7 knockdown using shRNA. We then perform RNA sequencing (RNA-seq) analysis of four biological replicates of DHCR7 silenced (75% deletion) and control RD cells.

first: Riikka

last: Kivelä


title: DuShen Decoction protects rats from sepsis and hemorrhagic shock and alleviates sepsis-induced acute lung injury by inhibiting HSPs mediated endoplasmic reticulum stress

first: Yisa

last: Wang

address: 1035 Boshuo Rd., Nanguan District

institute: Changchun University of Chinese Medicine

summary: Our study confirmed that DSD reduced the transcription level of HSPs in lungs of CLP rats by inhibiting the expression and nuclear translocation of HSF1 and HSF2, as well as the DNA binding activity of HSF, thereby inhibiting ERs to alleviate sepsis-induced lung injury.

overall_design: Male SD rats were randomly divided into Sham, CLP, and DSD groups. The CLP and DSD groups underwent cecal ligation puncture for 12 hours, while the DSD group was oraly gavaged 3g/kg DSD before modeling. In the end stage, rats were euthanized and their lung tissue was preserved, and RNA was extracted for transcriptome analysis after rapid freezing in liquid nitrogen.

first: Xiangyan

last: Li


title: Spatiotemporal liver dynamics shapes hepatocellular heterogeneity and impacts in vivo gene engineering [MERFISH]

first: Ivan

last: Merelli

summary: Hepatocytes are the main liver cells, pivotal for metabolism and relevant in vivo gene therapy targets. While prior research has explored liver homeostasis and regeneration, growth and maturation are not fully elucidated. Here, by single-cell and spatial transcriptomics, and clonal analysis we discovered that a subset of clonogenic hepatocytes (15-20%) in newborns generates >90% of the adult tissue and co-localizes with hematopoietic islands in a spatial niche. Gene editing of these clonogenic hepatocytes resulted in an expansion of the gene-engineered area, a finding supporting their role in liver growth. Age-dependent hepatocellular heterogeneity also influenced the efficiency of lentiviral gene delivery in vivo and its distribution within the liver lobule. Progressive establishment of metabolic zonation post-weaning and high proteasome activity in the peri-central area in adults determined the observed age-related outcomes. These insights into the spatiotemporal hepatocyte dynamics advance our understanding of liver biology and have implications for therapeutic strategies.

overall_design: Mice bearing established liver metastases were treated with TA33 or TA33.Combo. After 10 days mice were eutanized and the liver was collected to perform spatial transcriptomics.

first: Michela

last: Milani

first: Francesco

last: Starinieri

first: Marco

last: Monti

first: Stefano

last: Beretta

first: Alessio

last: Cantore


title: CNTNAP2-203 interaction with EGFR modulates E2F1 activity and promotes tumorigenesis in oral squamous cell carcinoma.

city: Hengyang City

first: Suzhen

last: Ma

state: Hunan Province

address: 28 Changsheng West Road, Hengyang City, Hunan Province

institute: University of South China

summary: CNTNAP2 has two isoforms with clear evidence of expression: CNTNAP2-201 and CNTNAP2-203. Extensive research has centered on the full-length CNTNAP2-201, as a neuronal adhesion molecule, due to its association with numerous neurodevelopmental disorders, the role of CNTNAP2-203 in disease pathology has remained largely unexplored. Oral squamous cell carcinoma (OSCC) is a major malignancy in the head and neck region with high mortality and morbidity, partially due to a limited understanding of molecular mechanisms underlying its onset and progression. This study reveals that CNTNAP2-203 mRNA and protein levels are significantly elevated in OSCC tissues compared to their adjacent normal tissues, and high CNTNAP2-203 expression is closely associated with worsened clinical outcomes in OSCC patients. Functionally, CNTNAP2-203 plays a role in driving OSCC cell proliferation in vitro and tumor growth in vivo by modulating E2F1 activity. Mechanistically, CNTNAP2-203 interacts with the epidermal growth factor receptor (EGFR) and amplifies EGFR signal activities, promoting OSCC tumorigenesis through the EGFR-E2F1 axis. Notably, OSCC cells with elevated CNTNAP2-203 demonstrate increased sensitivity to Gefitinib, either alone or in combination with Cisplatin, suggesting patients with high CNTNAP2-203 levels may achieve better outcomes when treated with such regimens. Therefore, this study not only elucidates the pathogenic role of CNTNAP2-203 in OSCC but also highlights the potential of using CNTNAP2-203 as a biomarker for guiding therapeutic strategies in OSCC management.

overall_design: To investigate the mechanisms by which CNTNAP2-203 promotes OSCC cell proliferation, we performed RNA-seq analysis on CAL27 cells with CNTNAP2-203 OE.

first: Lin

last: Zhu

first: Danling


title: Combination of AgNPs and DOC in PC3

city: Beijing

first: Tianxiao

last: Xu

address: 52 Fucheng Road, Haidian District, Beijing

institute: Peking University Cancer Hospital

summary: In order to better understand the effects of combination treatment with silver nanoparticles and chemotherapy in human castration-resistant prostate cancer cells, RNA sequencing was performed to explore transcriptome alteration.

overall_design: RNA sequencing in PC3 cell line with AgNPs or/and DOC treatment


title: Single-cell Transcriptome Analysis Reveals Mechanical Properties of Leukemic Stem Cells in AML.

city: Hefei

first: Mingming

state: Anhui

address: No.96, JinZhai Road Baohe District,

department: life sciences and medicine

institute: University of Science and Technology of China

summary: Leukemic stem cells (LSCs) are crucial drivers of leukemia, yet the mechanisms underlying their function remain poorly understood. Here, we investigated the physical properties of LSCs and their potential role in LSCs function. single-cell RNA-sequencing analysis has revealed that small-sized LSCs aberrantly overexpress ALDH1A1, a crucial regulator of stem cell function. Lastly, ALDH1A1 inhibition increases cell stiffness and suppresses leukaemogenesis in patient-derived xenograft models. Our findings establish a novel link between the biomechanics of LSCs and their function in leukemia, providing a compelling rationale for targeting therapy-resistant LSCs by inhibiting G3BP. Overall, our study provides valuable insights into the mechanisms of LSCs function and has significant implications for the development of more effective therapies for this devastating disease.

overall_design: In order to explore the mechanism of the function in mechanical properties of LSCs, we isolated small cells and large cells derived from bone marrow lin- cells of 4 AML patients.For the scRNA-seq analysis of human lin- small and large cells ,we pooled 4 sample from the small group in one tube and 4 sample from the large group in another tube. We then counted and resuspended the pooled cells at a concentration of 1000 cells/µL, targeting an estimated 6000 cells per library, following the instructions of the Single Cell 3ʹ Solution v3 Kit (10X Genomics). Single-cell libraries were constructed strictly according to the manufacturer's standard protocol. Libraries were sequenced on the Illumina NovaSeq 6000 System.

first: Haoxiang

last: Yang

first: Tingting

last: Liang

first: Beibei

last: Huang

first: Hongyuan

last: Jiang

first: Fang

last: Ni


title: Exploration of Key Gene Mining and Formation Mechanisms for the White-Shelled Egg Trait in Chickens

first: Bingjie

last: Zhang

address: Beijing HaiDian District, Mingyuanxilu No.2

institute: China Agricultural University

summary: In this study, we investigated the production of white-shelled eggs at physiological and molecular levels using a F2 resource population as major samples.

overall_design: From the 600K Affymetrix panel, 571,185 high-quality and segregating SNPs were retained for 201 samples.

first: Guoying

last: Hua


title: Development of mRNA expression signatures for Nao Yi Kang decoction in treating  intracerebral hemorrhage

city: Changsha

first: Zhe

last: Yu

address: Kaifu District, Xiangya Road, No.87

institute: Central South University

summary: To identify the potential mRNA asscociated with Nao Yi Kang decoction (NYKD) in treating  intracerebral hemorrhage (ICH), we have employed mRNA expression profiling. 2405 and 1806 mRNAs were identified in the ICH vs sham group and the NYKD vs ICH group, respectively. Specifically, 294 DEmRNAs were intersected among the three groups.

overall_design: Mice were randomly divided into 3 groups (n=5): the Sham, ICH, and NYKD-M groups. The gavage administration started on the 1st day after the surgery for 3 consecutive days. Brain samples were dectected at 3 d after ICH.

first: Teng

last: Li

first: Tao

last: Tang

first: En

last: Hu


title: Construction of immune profiles in PBMC of bacteremia mice with different outcomes

city: Harbin

first: xinyang

last: zhang

address: 678 Haping Road, Xiangfang District, Harbin City, Heilongjiang Province

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

summary: We used mice as an experimental model to establish two animal infection models of bacteremia with different outcomes. In the low-dose infection group, the bacteria within the mice are cleared by the immune system, allowing the mice to survive. In contrast, the high-dose infection group leads to sepsis and ultimately results in the death of the mice. We aim to utilize single-cell sequencing technology to study the changes in the transcriptomes of various immune cells during different stages and outcomes of mammalian bacteremia, in order to understand the host's response to bacteremia.

overall_design: To collect PBMC from animals in lethal and non-lethal bacteremia models for scRNA-seq, groups of 6 mice were infected with E.coli at high (lethal dose, H group) and low (non-lethal dose, L group) doses, respectively. For L group, four time points, 2, 4, 8, and 12 hpi, were selected to indicate different stages of infection; while for the high dose infection group, two time points, 2, and 6 hpi, were selected to indicate early and late moribund stages of infection.Isolated PBMC were then subjected to scRNA-seq with 10× Genomics platform.

first: Xinyang

first: Wentong

last: Cai

first: Ganwu


title: A single cell atlas of E4.5 Control and Sox2 MZ KO mouse embyros

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

summary: Here, we molecularly defined Sox2 KO at single-cell resolution, revealing hidden transcriptional dynamics that govern epithelial morphogenesis via tight junction assembly and organisation of actomysin, cadherin and integrin-mediated binding.

overall_design: Approximately 13 blastocysts from each replicate – one replicate of control and an two replicates of Sox2 MZ KO embryos from E4.5 were collected and analyzed using sc-RNA seq.

first: Deepthi

last: Chandramohan

first: Katja

last: Mueller

first: Rongge

last: Yan

first: Ivan

last: Bedzhov


title: S-SETMAR in the biogenesis of glioblastoma : a protective role ?

city: Tours

first: Sylvaine

last: Renault

address: 10 bld Tonnelé

country: France

institute: INSERM U1253

summary: Born 45 million years ago, SETMAR is a fusion gene only present in higher primates. It is made of three exons, the two first given by the SET gene and coding for methyltransferase functions, the third given by the Hsmar1 transposase gene and coding for recombinase functions. The full length SETMAR protein (FL-SETMAR) is described as a genome keeper, expressed in main tissues, but with different levels. In cancer cells, the SETMAR gene is over-expressed, and FL-SETMAR sustains oncogenic processes, probably through its involvement in DNA repair by Non-Homologous End-Joining (NHEJ), replication stress response and chromosome decatenation. Under certain circumstances, SETMAR pre-mRNA undergoes alternative splicing, leading to the production of shorter proteins, enriched in cancer stem cells. One of them, S-SETMAR, was first discovered in glioblastoma (GB), and more recently in colorectal cancers. S-SETMAR lacks a part of the pre-SET domain and the whole SET domain, both encoded by exon 2. As a result, S-SETMAR is unable to methylate proteins, as does FL-SETMAR with a moderate efficiency. Little is known about the role of S-SETMAR. It has been recently shown that S-SETMAR, when enriched in tissues surrounding GB, correlates with an increased patient’s survival. In order to understand how S-SETMAR can have a protective role in glioblastoma biogenesis, the transcriptomes of established glioblastoma cell line expressing or not S-SETMAR were compared. This allowed the identification of deregulate pathways.

overall_design: 8MGBA glioblastoma cells were stably transfected with vector encoding S-SETMAR under the control of pE1F promoter (8MGBA S-SETMAR).  Gene expression was compared between  8MGBA as reference  and 8MGBA S-SETMAR cell lines. Three biological replicates were performed

first: Sarah-Anne

last: David

first: Sara

last: Benharrat

first: Jerome

last: Jaillet

first: Corinne

last: Augé


title: Small RNA-Seq analysis of liver tissues in AAV9-Tnnt2-Cre and AAV9-Tnnt2-Cre-miR122 injected mice

first: Luzi

last: Yang

address: 38 Xueyuan Road, Haidian District

institute: Peking University Health Science Ce

type: Non-coding RNA profiling by high throughput sequencing

summary: The cardiac troponin T (Tnnt2) promoter is broadly utilized for cardiac specific gene expression, particularly via adeno-associated virus (AAV)-based gene transfer. However, these vectors drive lower-level ectopic gene expression in other tissues, most notably in the liver. Whether the AAV-Tnnt2 vectors remain tissue-specific in applications sensitive to low or transient gene expression, such as gene editing, remains unclear. Inclusion of target sequences for microRNA-122, a highly expressed, liver-specific microRNA, in the AAV transgene’s 3’ untranslated region (3’ UTR) markedly reduced ectopic transgene expression, genome editing and AAV integration in the liver. The heavily used AAV-Tnnt2 system exhibits liver leakiness that severely impairs the cardiac specificity of AAV-based genetic manipulation. This problem can be mitigated via miR122-mediated liver detargeting.

overall_design: To investigate the impact of AAV-promotor-miR122 on the micro-RNA of murine livers.

first: Zhanzhao

last: Liu

first: Yuxuan

last: Guo


title: MicroRNA-122-mediated liver detargeting enhances the tissue specificity of cardiac genome editing

summary: We use base editing to eliminate the CaMKII-delta, a major driver of heart disease. We found that insertion of microRNA122 target sequence (miR122 TS) in the 3' UTR of the vector eliminates editing in the liver, in combination with heart-specific promoters to specifically edit in heart.

overall_design: We delivered AAV-Tnnt2-SaCas9(-miR122) and AAV-Tnnt2-SPRY-ABE8e(-miR122) to mice. We harvested the murine hearts and livers to investigate the gene edit effect.

first: L

first: Z


title: Discovery of golcadomide (CC-99282) as a promising drug candidate for diffuse large B-cell lymphoma (DLBCL)

city: San Diego

first: Antonia

last: Lopez-Girona

state: California

address: 10300 Campus Point Drive

department: Protein Homeostasis TRC

institute: Bristol Myers Squibb

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Diffuse large B-cell lymphoma (DLBCL) is an aggressive, heterogeneous disease with poor prognosis associated with high-risk molecular features. We report the discovery of golcadomide (CC-99282), a novel cereblon-modulating agent, that induces faster and deeper degradation of hematopoietic transcription factors Ikaros/Aiolos compared with first-generation degraders such as lenalidomide. In vitro, golcadomide induced interferon-stimulated genes, promoted apoptosis, robust antiproliferation, and immunogenic cell death, independent of clinical outcome determinators observed with standard care treatment. In vivo, golcadomide exhibited enhanced antitumor activity, resulting in significant tumor regression and tumor-free animals in lymphoma xenograft models. Pharmacological and CRISPR-based screenings demonstrated that targeting apoptosis, cell cycle progression, NF-kB signaling, and nuclear cytoplasmic transport increased antitumor efficacy of golcadomide. In summary, these data represent the discovery of golcadomide as a promising drug candidate for DLBCL and highlight the rationales for future golcadomide-based combination regimens that could improve clinical outcomes for patients.

overall_design: Cleavage Under Targets and Release Using Nuclease (CUT&RUN)  for Ikaros and Aiolos in SUDHL-2 with DMSO vs compound treatment

first: Diana

last: Jankeel

first: Yan

last: Kai


title: Bulk RNA-Seq analysis of liver tissues in AAV9-Tnnt2-Cre and AAV9-Tnnt2-Cre-miR122 injected mice

overall_design: To investigate the influence of the AAV-Tnnt2-miR122 vectors in the liver tissues, we performed mRNA-Seq analysis to compare liver tissues that were transduced by either Tnnt2-Cre or Tnnt2-Cre-miR122TS AAVs.


title: miR122

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

overall_design: Refer to individual Series


title: HOTAIR-YTHDF3 interaction in promoting breast cancer cell metastasis [ATAC-seq]

city: Guangzhou

first: Li

last: Xinhui

address: Guangzhou

institute: Sun Yat-sen university

summary: Long noncoding RNA HOTAIR (HOX antisense intergenic RNA) is an important regulator of breast cancer metastasis. Studies showed that HOTAIR reprograms chromatin state through interacting with Polycomb Repressive Complex 2 (PRC2) to promote breast cancer metastasis. However, it is unclear if there exist other HOTAIR-binding factors which participate in promoting breast cancer metastasis. In the current study, we utilized mass spectrometry (ChIRP-MS) to comprehensively identify RNA-binding proteins (RBPs) associated with HOTAIR. We also performed a high-throughput CRISPR screen to investigate HOTAIR-interacting proteins involved in cell metastasis. We found that many m6A-reader proteins were involved in this progress, including YTHDF3, which is a newly identified HOTAIR partner. We further demonstrated that HOTAIR and YTHDF3 co-regulated the expression of several metastasis-associated genes by modifying their chromatin accessibility in breast cancer cells. Altogether, our work detailed the functional interactome of HOTAIR involved in promoting breast cancer cell metastasis, and suggested a mechanism whereby HOTAIR regulates chromatin state in cooperation with the m6A-reader YTHDF3.

overall_design: Chromatin accessibility profiles of HOTAIR-Ctrl, HOTAIR-OE, HOTAIR-Ctrl YTHDF3-KO cells were generated by ATAC-seq using the illumina novaseq platform.

first: Liuyi

first: Xinhui

last: Li

first: Jin

last: Xu

first: Qing

last: Ma


title: HOTAIR-YTHDF3 interaction in promoting breast cancer cell metastasis [RNA-seq]

overall_design: Total RNA of HOTAIR-Ctrl, HOTAIR-OE, HOTAIR-Ctrl YTHDF3-KO and HOTAIR-OE YTHDF3-KO cells were extracted and sequenced using DNBSEQ Platform with 100 bp paired-end Reads.


title: HOTAIR-YTHDF3 interaction in promoting breast cancer cell metastasis


title: RNA-Sequencing Analysis of of  heart tissue from murine model of endotoxemia

city: changsha

first: yan

last: tan

address: 138 Tongzpo Road

institute: XiangYa School of Medicine

summary:
Cardiac dysfunction, an early complication of sepsis and endotoxemia, is the major cause of death in intensive care units. To explore the key mechanism in the “double-hit” endotoxemia heart, we performed bulk RNA sequencing and analyses of heart tissue from healthy C57BL/6J mice with endotoxin exposure at early or late stage.
The RNA-seq analyses revealed the canonical and non-canonical inflammasome activation is involved in  endotoxin-induced cardiac injury.

overall_design: Bulk RNA sequencing of heart tissue from healthy C57BL/6J mice (n=6, eight weeks-age) at baseline, after 7-hour poly(I:C) priming,

first: Jingjing

last: Cai

last: Tang

first: Junru

last: Wu

first: Xuejing

last: Sun

first: Wenbo

first: Yunmin

last: Shi

first: Tian

last: He

first: Siyu

last: Yin

first: Lun

first: Yuanyuan

last: Chen

first: Qian

last: Tan

first: Youxiang

last: Jiang

first: Wenjing

first: Wei

last: Huang

first: Chunyan

last: Weng

first: Qi

first: Yao

last: Lu

first: Hong

last: Yuan

first: Qingzhong

last: Xiao

first: Qingbo

first: Timothy

last: Billiar


title: Expression profiling of Photomorphogenic Arabidopsis seedlings

city: Taipei

first: Meng-Chun

last: Lin

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Institute of Plant and Microbial Biology

summary: We revisited the transcriptomes of Arabidopsis seedlings by analyzing alternatively spliced variants during early photomorphogenesis. Half of the expressed transcripts have alternatively spliced forms; many were previously uncharacterized. Light regulated AS for 19.2% of the genes expressed, intron retention being the most prevalent type of alternative splicing. We observed distinct groups of transcripts with differential expression levels or with AS, which implies that transcription and AS target different sets of genes. More than one-third of the AS transcripts with retained introns were translatable. In summary, these AS variants could play regulatory roles and increase the proteome complexity in photomorphogenic Arabidopsis

overall_design: Examination of 2 replicates of Arabidopsis seedlings transcriptomes in Dark, 4 hours Dark (D4h) and 4 hours Light (L4h).

first: Guan

middle: H

first: Sim

last: Lim

first: Shu-Hsing


title: Cellular and Spatial Drivers of Unresolved Injury Link to Functional Decline in the Human Kidney

status: Public on Oct 09 2025

city: Saint Louis

first: Madhurima

last: Kaushal

address: 1 Brookings Dr

institute: Washington University in St Louis

summary: Building upon a foundational Human Kidney resource, we present a comprehensive multi-modal atlas that defines spatially resolved versus unresolved repair states and mechanisms in human kidney disease. Homeostatic interactions between injured kidney epithelium and its surrounding milieu determine successful repair outcomes, while pathogenic signaling promotes unresolved inflammation and fibrosis leading to chronic disease. We integrated multiple single-cell and spatial modalities across ~700 samples from >350 patients (~250 research biopsies), analyzing ~1.7 million cells alongside complementary mouse multi-omic profiles spanning acute-to-chronic injury and aging (>300,000 cells) and spatial transcriptomic analysis of 150 human biopsies. This cross-species atlas delineates functional pathways and druggable targets across the nephron and defines gene regulatory networks and chromatin landscapes governing tubular, fibroblast, and immune cell transitions from injury to either recovery or failed repair states. We identified distinct cellular states associated with specific pathological features that show dynamic distributions between acute kidney injury (AKI) and chronic kidney disease (CKD), organized within unique spatial niches that reveal progression mechanisms from early injury to unresolved disease. Gene regulatory analyses prioritized key transcription factor activities (SOX4, SOX9, NFKB1, REL, KLFs) and their target networks establishing disease states and tissue microenvironments. These regulatory programs were directly linked to clinical outcomes, identifying molecular signatures of recovery and secreted biomarkers predictive of AKI-to-CKD progression, providing a key resource for therapeutic development and precision medicine approaches in kidney disease.

overall_design: Multiome data for 18 wildtype mouse kidney samples collected from male and female mice across lifespan (16 weeks, 48 weeks, and 80 weeks old).

first: Blue

middle: B

last: Lake

first: Kun

last: Zhang

first: Sanjay

last: Jain


title: Alzheimer's disease-associated PLCG2 variants alter microglial state and function in human iPSC-derived microglia-like cells

city: Indianapolis

first: Logan

middle: Michael

last: Bedford

state: Indiana

address: 350 W 14th Street

department: Pharmacology and Toxicology

institute: Indiana University School of Medicine

summary: BACKGROUND: Variants of PLCG2, a key microglial immune signaling protein, are genetically linked to Alzheimer’s disease (AD) risk. Understanding how PLCG2 variants alter microglial function is critical for identifying mechanisms that drive neurodegeneration or resiliency in AD. METHODS: iPSC-derived microglia carrying the protective PLCG2P522R or risk-conferring PLCG2M28L variants, or loss of PLCG2, were generated to ascertain the impact on microglial transcriptome and function. RESULTS: Protective PLCG2P522R microglia showed significant transcriptomic similarity to isogenic controls. In contrast, risk-conferring PLCG2M28L microglia shared similarities with PLCG2KO microglia, with functionally reduced TREM2 expression, blunted inflammatory responses, and increased proliferation and cell death. Uniquely, PLCG2P522R microglia showed elevated cytokine secretion after LPS stimulation and were protected from apoptosis. DISCUSSION: These findings demonstrate that PLCG2 variants drive distinct microglia transcriptomes that influence microglial functional responses that could contribute to AD risk and protection. Targeting PLCG2-mediated signaling may represent a powerful therapeutic strategy to modulate neuroinflammation.

overall_design: RNA-seq profiling of basal iPSC derived microglia-like cells homozygous for WT, P522R, M28L, or KO PLCG2.

first: Kaylee

last: Tutrow

first: Karly

last: Hooper

first: Evan

last: Messenger

first: Melody

last: Hernandez

first: Bruce

last: Lamb

first: Jason

last: Meyer

last: Richardson

first: Stephanie

last: Bissel


title: Patterns of hypermutation shape gliomagenesis and immunotherapy response in mismatch repair deficient glioma

city: Toronto

first: Uri

last: Tabori

state: Ontario

address: 170 Elizabeth St

department: Haematology/Oncology

institute: Sick Kids

type: Methylation profiling by genome tiling array

summary: Primary mismatch-repair deficient (priMMRD) gliomas are lethal tumours characterized by hypermutation, resistance to chemoradiation, and variable response to immunotherapy.To investigate the mechanisms governing the emergence of driver mutations and their impact on gliomagenesis and outcome, we analyzed genomic and clinical data of 162 priMMRD gliomas. We identified three subgroups defined by secondary driver mutations in replicative DNA polymerases or IDH1. These subgroups converge on glioma drivers through distinct combinations of genomic instability-generating mechanisms, displaying an inverse correlation between point mutation and copy number alteration. MMRD signaturesdrive the emergence of specific mutations in TP53 and IDH1, notably excluding common pediatric glioma drivers. Global hypomethylation stratifies priMMRD gliomas into a unique methylation cluster. DNA-polymerasemut priMMRD gliomas exhibit ultrahypermutation, an immune-hot microenvironment, and immunotherapy responsiveness, whereas IDH1mut priMMRD gliomas are immune-cold and immunotherapy resistant. MMRD-driven gliomagenesis defines the role of non-random mutagenesis-patterns in cancer development, providing frameworks for targeted and immune-therapeutics.

overall_design: This study evaluated methylation profiling through the Illumina 450K or EPIC array platforms for n = 77 primary MMRD glioma. Comparisons were made between global methylation profiles on the basis of three priMMRD glioma subgroups (priMMRD-1/2/3) and in comparison to previously published mismatch repair proficient glioma cohorts.

first: Tabori

last: Uri

first: Hawkins

last: Cynthia


title: Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells (RNA-Seq)

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: The RNA-binding protein PARP13 is a primary factor in the innate antiviral response. PARP13 can suppress translation and drive decay of bound viral and host RNA. PARP13 interacts with many proteins encoded by interferon-stimulated genes (ISG) to perform its antiviral activities, such as activation of the pathway mediated by post-translational addition ISG15 or ISGylation. The RNA-binding domains of both PARP13 and its primary cofactor, TRIM25, are required for antiviral activity. Here we perform enhanced crosslinking immunoprecipitation (eCLIP) and RNA-seq to investigate the role of PARP13 expression and RNA binding in transcriptome regulation within human cells. We find that PARP13 regulates the transcriptome in basal and antiviral states and that the antiviral response shifts PARP13 target localization, but not its binding preferences. We demonstrate that PARP13 expression supports the expression of ISGylation-related genes, including TRIM25. Using the common targets PARP13 and TRIM25 share, we assess their spatial relationship along transcripts and show that PARP13 and TRIM25 associate in part via RNA-protein interactions. Evidence from genomic data and molecular biology experiments provide insight into the geometry of PARP13's interface with its cofactor TRIM25 and implicates PARP13 in creating and maintaining a cellular environment poised for an antiviral response.

overall_design: RNA-seq was performed on WT and PARP13 KO HEK293T cells 24 h after transfection with either an ssRNA control or a 3p-RNA viral mimic in duplicate.

first: Veronica

middle: F

last: Busa

first: Yoshinari

last: Ando

first: Stefan

last: Aigner

first: Brian

last: Yee

middle: W

first: Anthony

last: Leung


title: pS6-IP RNA-seq of mouse olfactory epithelium upon binary odor mixture stimulation under different delivery methods

city: Dalseong-gun

first: Minseok

last: Kim

state: Daegu

address: 333, Techno jungang-daero, Hyeonpung-eup

department: Department of Brain Sciences

country: South Korea

institute: Daegu Gyeongbuk Institute of Science & Technology

summary: Phosphorylation of ribosomal protein S6 (pS6) serves as a molecular marker of neuronal activation by external stimuli. In this study, olfactory epithelium tissues were obtained from mice exposed to binary odor mixtures consisting of acetophenone–decanal or octanal–cis-3-hexenol. To examine how different delivery methods of odor presentation influence neural responses, two paradigms for binary mixtures were employed. In the “+” condition, the two odorants were directly combined on a single piece of filter paper, allowing interaction prior to volatilization. In contrast, in the “&” condition, the odorants were applied separately to two filter papers placed in close proximity (~1 mm apart), such that the components mixed only in the air upon evaporation. Using these approaches, four experimental odor groups were generated (A+D, A&D, O+C, and O&C), along with a no-odor control, resulting in a total of five groups. Following stimulation, pS6-associated ribosome complexes were isolated from olfactory epithelium lysates through immunoprecipitation, selectively enriching mRNAs undergoing active translation in odor-activated cells. RNA sequencing of these samples enabled transcriptomic profiling within activated neuronal populations, providing insights into gene expression programs associated with distinct delivery methods of binary odor stimulation.

overall_design: C57BL/6J wild-type male mice (8 weeks old) were individually housed in sealed, odor-proof containers and habituated in an odorless environment for 4 hours prior to stimulation. Mice were then exposed for 90 minutes to binary odor mixtures delivered by two different methods. In the “+” condition, both odorants were applied to a single piece of filter paper, allowing direct mixing prior to volatilization. In the “&” condition, the odorants were applied separately to two filter papers placed in close proximity (~1 mm apart), enabling mixing in the air without physical contact on the filter. These procedures generated four binary mixture groups (A+D, A&D, O+C, and O&C), along with a no-odor control. Immediately following stimulation, olfactory epithelium tissues were collected, perfused, and homogenized. pS6-associated ribosome complexes were isolated from the homogenates through immunoprecipitation, selectively enriching ribosome-bound mRNAs from odor-activated cells. Three biological replicates were obtained for each condition, and the immunoprecipitated mRNAs were subsequently purified and processed for RNA sequencing.

first: Han Kyoung

last: Choe


title: Origin of Ewing sarcoma by embryonic reprogramming of neural crest to mesoderm

city: Los Angeles

first: Claire

last: Arata

email: carata@usc.edu, clairearata@gmail.com

address: 1425 San Pablo St

department: Stem Cell

institute: University of Southern California

summary: Ewing sarcoma is a malignant small round blue cell tumor of bones and soft tissues, predominantly affecting children, adolescents and young adults. Ewing sarcoma is caused by chromosomal translocations that generate aberrant chimeric transcription factors, most frequently EWSR1::FLI1. Ewing sarcomas exhibit features of both neural and mesenchymal cells. The cell of origin of Ewing sarcoma and the mechanisms of EWSR1::FLI1-driven cell transformation are the subjects of long-standing debates, largely due to the absence of a representative animal model. By developing a robust Ewing sarcoma model in zebrafish, we provide evidence for a neural crest origin of this cancer. We show that neural crest-derived cells (NCCs) uniquely tolerate expression of the human EWSR1::FLI1 oncofusion protein in vivo and that targeted expression of the oncofusion in NCCs is sufficient to generate Ewing sarcoma tumors. In the trunk, EWSR1::FLI1 reprogrammed NCCs to a mesoderm-like state, including upregulation of the early mesoderm specifier tbxta (Brachyury/T) and mesenchymal genes pdgfra, twist1a, and prrx1a. Mesodermal reprogramming of trunk neural crest was evident by the ability of EWSR1::FLI1-expressing cells to induce ectopic fins throughout the body. Single-nucleus analysis of RNA expression and chromatin accessibility, combined with genome-wide profiling of EWSR1::FLI1 binding, revealed that EWSR1::FLI1 targets single GGAA-containing ETS sites in mesodermal developmental enhancers for neural crest to mesoderm reprogramming during cancer initiation, also binding  to GGAA repeats in established tumors. These findings show that EWSR1::FLI1 hijacks normal ETS-dependent developmental pathways in embryonic NCCs to drive initiation of Ewing sarcoma.

overall_design: Tissue from GFP+ embryos expressing EWSR1-FLI1 at 24hpf and tumors were dissociated and processed for CUT&RUN using Cell Signaling Technology's CUT&RUN Assay Kit #86652.

first: Elena

last: Vasileva

middle: E

first: Gage

last: Crump

first: James

last: Amatruda


title: Vagal Sensing of Altered Gut Microbiota Links to Externalizing Behaviors

city: Daejeon

first: Min Joung

last: Lee

address: Munhwa-ro 266

department: Department of Biochemistry

institute: Chungnam National University School of Medicine

summary:
Background and Aims
Interoceptive impacts on the brain triggered by changes in the intestinal microbial ecosystem influence mood-related behaviors such as anxiety and depression. Although changes in the gut microbiome can be driven by genetic mutations in the host, how alterations in the gut microbiome caused by host genetic variations affect behavioral outcomes is not fully understood. To investigate how host genetic variation affects interoceptive responses, we analyzed the gut microbiota and investigated gut–brain interactions in sirtuin 3 (Sirt3)-knockout (KO) mice.
Methods
We evaluated the composition of the gut microbiome and behavior in Sirt3-KO and wild-type (WT) mice. To distinguish microbiome-driven effects from genetic influences, we conducted cohousing experiments and compared results with heterozygous littermates. Region-specific changes in gene expression in the brain were identified by transcriptomic profiling of the limbic system. We also analyzed metabolites in the nucleus of the solitary tract (NTS) generated by gut microbiome–vagal signaling. The role of the vagus nerve in the gut-brain axis was further examined through vagotomy, alongside comparative choline analysis in both mood disorder patients and mice.
Results
Mood-related neurobehavioral changes and alterations in synaptic plasticity-related genes in the amygdala and bed nucleus of the stria terminalis (BNST) of Sirt3-KO mice appeared to be dependent on gut microbiome composition. Elevated plasma choline levels in both mood disorder patients and Sirt3-KO mice, together with reduced neurotransmitter-related metabolites (e.g., -aminobutyric acid [GABA] in the NTS), suggested that externalizing behaviors in Sirt3-KO mice are mediated by vagus nerve-dependent gut–brain axis signaling. Consistent with this, vagotomy abolished these changes, including GABA in the NTS, as well as alterations in synaptic plasticity in the amygdala and BNST.
Conclusions
Our findings suggest the novel finding that an altered gut microbiome caused by a host genetic change, namely a Sirt3 deficiency, is sensed in the NTS of the brain via the vagus nerve, leading to externalizing behaviors.

overall_design: 16-week-old SIRT3 WT and KO male mice and co-housed WT and KO mice (beginning at 3 weeks of age) - amygdala, BNST in brain

first: Jun Young

last: Heo


title: ERBB2 signaling drives immune cell evasion and resistance against immunotherapy in small cell lung cancer II

city: Erlangen

first: Lydia

last: Meder

state: Bavaria

address: Glückstr. 6

department: Experimentelle Medizin 1

summary: Small cell lung cancer (SCLC) represents ~15% of all lung cancers and is characterized by its highly aggressive phenotype and its dismal outcome. Though the addition of immune checkpoint blockade to carboplatin and etoposide treatment has improved outcome in SCLC patients, SCLC cells finally acquire the ability to evade immunosurveillance and resistance against immune checkpoint blockade. To elaborate molecular mechanisms that mediate SCLC immune evasion, we performed high dimensional profiling of human and murine SCLC specimens. We herein comprehensively analyzed matched human samples of primary and metastatic SCLC and found a loss of MHC-I in SCLC metastases indicating that MHC-I loss mediates SCLC immune evasion. Silencing MHC-I in SCLC cells drastically diminished immune cell infiltration and facilitated the formation of metastasis in mice by circumventing immune surveillance. Using mass spectrometry and phospho-tyrosine kinase analysis, we discovered that ERBB2 signaling suppresses MHC-I expression in SCLC cells and stimulates immune modulating transcripts. Mechanistically, genetic and/or pharmacologic blockade of the ERBB2 signaling axis was sufficient to induce MHC-I expression and to prevent immune evasion in autochthonous murine SCLC in a STING-dependent manner. Finally, we demonstrate that the ERBB2 signaling axis regulates MHC-I expression on SCLC cells and is critical in maintaining immune evasion in SCLC. Most strikingly, we here uncover synergistic treatment efficacy by combining ERBB2 inhibition with PD-1 blockade eliciting profound responses in preclinical SCLC models and circumventing MHC-I loss under immunotherapy, suggesting this combination for future clinical trials in patients with SCLC.

overall_design: We used an autochthonous Rb1/Trp53-deleted mouse model to generate tumor-derived cell lines. Three cell lines were established from primary lung tumors of individual mice, and one from a liver metastasis of a separate mouse. All were cultured under identical conditions and subjected to bulk RNA sequencing to compare transcriptional profiles between primary and metastatic tumor-derived cells.

first: Charlotte

middle: I

last: Orschel

first: Cyrielle

last: Bouchez

first: Rahil

last: Gholamipoorfard

first: Claudia

middle: V

first: David

last: Stahl

first: Christoph

last: Kreer

first: Mirjam

last: Koker

first: Xinlei

last: Zhao

first: Marieke

last: Nill

first: Ilayda

middle: G

last: Kocak

first: Ka-Won

last: Noh

first: Leon

last: Ullrich

first: Björn

last: Häupl

first: Josefine

last: Jakob

first: Marie-Lisa

last: Eich

first: Alexandra

last: Florin

first: Holger

last: Grüll

first: Jürgen

last: Wolf

first: Reinhard

last: Büttner

first: Thomas

last: Oellerich

first: Florian

last: Klein

first: Johannes

last: Brägelmann

first: Christian

last: Reinhardt

first: Nima

last: Abedpour

first: Roland

middle: T


title: pS6 immunoprecipitation RNA-seq of mouse olfactory epithelium in response to single odorants, binary mixtures, and complex fragrances

first: Minseok

last: Kim

summary: Phosphorylation of ribosomal protein S6 (pS6) serves as a molecular marker of neuronal activation by external stimuli. In this study, olfactory epithelium tissues were collected from mice exposed to single odorants (acetophenone, decanal, octanal, and cis-3-hexenol), binary mixtures (acetophenone–decanal and octanal–cis-3-hexenol), or complex fragrances (floral, mint, and floral–mint combination). To selectively capture transcripts undergoing active translation in odor-activated cells, pS6-associated ribosome complexes were isolated from tissue lysates through immunoprecipitation. The enriched mRNAs were subsequently purified and subjected to RNA sequencing, enabling transcriptomic profiling specifically within odor-activated neuronal populations, particularly olfactory sensory neurons. This approach provides a targeted view of gene expression programs induced by diverse odor stimulation paradigms in the heterogeneous olfactory epithelium.

overall_design: C57BL/6J wild-type male mice (8 weeks old) were individually housed in sealed, odor-proof containers and habituated in an odorless environment for 4 hours prior to stimulation. Mice were then exposed for 90 minutes to one of the following conditions: single odorants (acetophenone, decanal, octanal, cis-3-hexenol), binary mixtures (acetophenone–decanal, octanal–cis-3-hexenol), or complex fragrances (floral, mint, floral–mint). Immediately following exposure, olfactory epithelium tissues were collected, perfused, and homogenized. pS6-associated ribosome complexes were isolated from the homogenates through immunoprecipitation, selectively enriching ribosome-bound mRNAs from odor-activated cells. Three biological replicates were obtained for each condition, and the immunoprecipitated mRNAs were subsequently purified and processed for RNA sequencing.

first: Jeongyoon

last: Lee

first: Han Kyoung

last: Choe


title: Identification of KIF20A as a vulnerability for breast cancer stem-like cells in triple negative breast cancer

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

summary: Triple-negative breast cancer (TNBC), being both aggressive and highly lethal, poses a significant challenge in terms of treatment. Its heterogeneity and lack of hormone receptors or HER2 expression further restrict the availability of targeted therapy. Breast cancer stem cells (BCSCs), known to fuel TNBC malignancy, are now being exploited as the vulnerability for TNBC treatment. Here, we dissected the transcriptome of BCSCs and identified Kinesin Family Member 20A (KIF20A) as an essential gene for BCSC survival and TNBC tumorigenesis. Depletion or pharmacologic inhibition of KIF20A impairs BCSC viability, tumor initiation and development in vitro and in vivo. Mechanistically, KIF20A regulates BCSC stemness through modulating the oxidative phosphorylation (OXPHOS) pathway in mitochondria, which is repressed by a member of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex, SMARCA4. Therapeutically, treatment with a KIF20A inhibitor sensitizes TNBC xenograft tumors to standard-of-care chemotherapy. Our study highlights the significance of targeting KIF20A to exploit BCSC vulnerabilities in TNBC.

overall_design: RNA-seq analyses between breast cancer stem cells (BCSCs) and non-BCSCs from Hs578T and HCC70 cells. RNA-seq analyses between control sgRNA (sgCtrl) and KIF20A sg1, or KIF20A overexpression (OE) and empty vector (EV) in MDA-MB-231 cells.

first: Weilong

last: Chen

first: Yayoi

last: Adachi

first: Chengheng

last: Liao

first: Qing

last: Zhang


title: Dibromoacetonitrile exposure induces neurobehavioral toxicity in adult zebrafish via disruption of multiple neural pathways

city: Zhenjiang

first: Xinwei

last: Xu

state: Jiangsu

address: Xiangshan Street 301 Xuefu Road

department: School of Medicine

institute: Jiangsu University

summary: Disinfecting drinking water is a good public health strategy to stop the spread of contagious waterborne illnesses. However, during the disinfection process, some organic compounds in water react with disinfectants to produce disinfection by-products, such as haloacetonitriles (HANs) and halonitromethanes. Among HANs, the detection frequency of dibromoacetonitrile (DBAN) is high, which has attracted wide attention from scholars. It is not known whether DBAN exposure will harm the ecological environment by damaging aquatic biological nerves. In this paper, adult zebrafish were used as model animals, and blank control groups and different dose groups (1.6, 8, 40, 200, and 1000 μg/L DBAN) were set up to be exposed for 8 consecutive weeks. During the period, the health status of zebrafish in each group was observed and recorded. After the exposure, behavioral tests and transcriptome sequencing were performed to comprehensively investigate the effects of different doses of DBAN exposure on the neurotoxicity of zebrafish and explore the related mechanisms. The results showed that 200-1000 μg/L DBAN exposure could reduce the survival rate of zebrafish, and the survival rate of male zebrafish was lower than that of female zebrafish. Exposure to 1.6-200 μg/L DBAN for 8 weeks also affected the behavior of zebrafish, resulting in delayed movement of zebrafish, significantly reduced swimming distance and range, and decreased maximum acceleration and swimming vitality. Transcriptome sequencing showed that the number of differentially expressed genes up-regulated or down-regulated in male zebrafish was much higher than that in female zebrafish after 8 weeks of exposure to 40 μg/L DBAN. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that DBAN affected neurobehavioral-related genes such as ion imbalance, inhibition of synaptic neurodevelopment and neurotransmitter release in zebrafish, as well as light transduction, mitogen-activated protein kinase (MAPK) signaling pathway, ferroptosis, mammalian target of rapamycin (mTOR) signaling pathway, Wnt signaling pathway, calcium signaling pathway and other pathways, and the effects on female and male zebrafish were different. For male zebrafish, the MAPK signaling pathway and calcium signaling pathway are particularly affected. For female zebrafish, the MAPK signaling pathway and the phototransduction signaling pathway are most affected. The above results indicate that during the 8-week exposure period, 200 μg/L DBAN exposure can cause zebrafish death, 1.6 μg/L DBAN exposure can affect the behavioral ability of zebrafish, and involves multiple nerve-related pathways, such as the MAPK pathway genes and light conduction pathways.

overall_design: Female zebrafish were exposed to 0, 40 and 200 μg/L dibromoacetonitrile (DBAN) for 56 days, and male zebrafish were exposed to 0 and 40 μg/L DBAN for 56 days. Then the brain tissue of zebrafish was taken for RNA-seq.

first: Jiahui

last: Gao

first: Guosheng

last: Shan

first: Lan

first: Guangqiao

last: Liang

first: Fang

last: Li


title: Total RNA-seq of mouse olfactory epithelium in response to single odorants and binary mixtures

summary: Total RNA was extracted from olfactory epithelium tissues of mice exposed to single odorants (acetophenone, decanal, octanal, and cis-3-hexenol) or binary mixtures (acetophenone–decanal and octanal–cis-3-hexenol). The extracted RNA was subjected to high-throughput sequencing to profile genome-wide transcriptional changes across all cell types of the olfactory epithelium following odor stimulation. This dataset provides a baseline reference for comparing odor-induced gene expression programs in the olfactory epithelium with transcriptomic profiles obtained from odor-activated neuronal populations enriched by pS6 immunoprecipitation.

overall_design: C57BL/6J wild-type male mice (8 weeks old) were individually housed in sealed, odor-proof containers and habituated in an odorless environment for 4 hours prior to stimulation. Mice were then exposed for 90 minutes to one of the following conditions: single odorants (acetophenone, decanal, octanal, cis-3-hexenol) or binary mixtures (acetophenone–decanal and octanal–cis-3-hexenol). Immediately following exposure, olfactory epithelium tissues were collected, perfused, and homogenized. Total RNA was extracted from the homogenates, purified, and processed for RNA sequencing. Three biological replicates were obtained for each condition.


title: mRNA Initiation and Termination are Spatially Coordinated I

city: Worcester

first: Athma

last: Pai

state: MA

address: 368 Plantation Street, AS5-2057

department: RNA Therapeutics Institute

institute: UMASS Medical School

summary: ABSTRACT: The expression of a precise mRNA transcriptome is crucial for establishing cell identity andfunction, with dozens of alternative isoforms produced for a single gene sequence. The regulationof mRNA isoform usage occurs by the coordination of co-transcriptional mRNA processingmechanisms across a gene. Decisions involved in mRNA initiation and termination underlie thelargest extent of mRNA isoform diversity, but little is known about any relationships betweendecisions at both ends of mRNA molecules. Here, we systematically profile the joint usage ofmRNA transcription start sites (TSSs) and polyadenylation sites (PASs) across tissues andspecies. Using both short and long read RNA-seq data, we observe that mRNAs preferentiallyusing upstream TSSs also tend to use upstream PASs, and congruently, the usage ofdownstream sites is similarly paired. This observation suggests that mRNA 5’ end choice maydirectly influence mRNA 3’ ends. Our results suggest a novel “Positional Initiation-TerminationAxis” (PITA), in which the usage of alternative terminal sites are coupled based on the order inwhich they appear in the genome.To examine the direct influence of promoter (AFE) choice on ALE decisions, we performed a series of CRISPR modulations on HEK293 cells to either activate or repress AFEs and measure the change in ALE usage.

overall_design: HEK293 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing D-Glucose (4.5 g/L), L-Glutamine and 10% fetal bovine serum (FBS). Cells were seeded into 6-well plates and transiently transfected ~16 hours later, at ~80% confluency, using lipofectamine3000 (Invitrogen L3000001) CRISPR activaton experiments were transfected with either UniSAM empty vector (Addgene #99866) or UniSAM vector containing sgRNA targeting the promoter region of the targeted first exon. CRISPR inteference experiments were transfected with either dCas9-P2A-EGFP empty vector (Addgene #159086) or dCas9-P2A-EGFP vector containing sgRNA targeting downstream of the transcription start site of the targeted first exon. 48 hours post transfection, total RNA was extracted using RNeasy Mini Kit according to the manufacturer’s instructions. Reverse transcription was performed in a reaction mix containing 1 μg of total RNA, using Maxima H Minus First Strand cDNA Synthesis Kit (Thermo Scientific, K1652) according to the manufacturer’s instructions. Two seperate batches with different experimental targets were sequenced. The first was sequenced xxxx. The second batch of Total RNA was sent to Novogene on dry ice. Novogene performed poly-A selection paired-end RNA-sequencing.Paired-end Illumina libraries were sequenced on Illumina Novaseq 6000.

first: Ezequiel

last: Calvo-Roitberg

first: Christine

middle: L

last: Carroll

first: GyeungYun

first: Valeria

last: Sanabria

first: Maritere

last: Uriostegui-Arcos

first: Joseph

last: Paquette

first: Steven

last: Mick

first: Sergey

last: Venev

first: Job

last: Dekker

first: Ana

last: Fiszbein

middle: A


title: Comparative analysis of mouse and human ovaries across age [human data]

city: San Francisco

first: Diana

middle: Matthew

last: Laird

address: 35 Medical Center Way RM913D

institute: University of California

summary: A combination of droplet based and plate based single cell sequencing was used to profile and compare all cell types in the mouse and human ovaries throughout the reproductive span.

overall_design: For each sample, the ovary was dissociated and cells were size filtered to separate large oocytes from small oocytes and somatic cells. Large oocytes were sequenced using SmartSeq2 while the suspension of small cells was sequenced using 10X Genomics.

first: Ryan

last: Samuel

first: Eliza

last: Gaylord

first: Mariko

last: Foecke


title: Potentiation of Noncanonical NF-𝛋B Signaling and Marginal Zone B Cell Expansion by CARD11-mediated Regulation of p100 Processing

city: Baltimore

first: Joel

last: Pomerantz

address: 733 N. Broadway

department: Biological Chemistry

institute: Johns Hopkins University School of Medicine

summary: Caspase recruitment domain-containing protein 11 (CARD11) is a multi-domain scaffolding protein critical for the adaptive immune response that is required for antigen receptor signaling to canonical NF-kB, mTOR, JNK, and AKT. Oncogenic gain-of-function (GOF) CARD11 mutants, implicated in a variety of lymphomas, bypass normal regulation and signal constitutively. In a mouse model expressing the lymphoma-associated GOF mutation CARD11 C49Y, we observed splenomegaly concomitant with B cell expansion that was most pronounced for Marginal Zone (MZ) B cells. CARD11C49Y/C49Y MZ B cells exhibited enhanced cell-autonomous survivability and elevated basal levels of the precursor NF-kB subunit p100, which was inducibly processed, leading to elevated nuclear p52 levels in response to BAFF. We show in a heterologous assay that active CARD11 variants can inhibit basal NIK-induced p100 processing to p52 independently of their ability to activate canonical NF-kB. Our results reveal an unexpected ability of CARD11 GOF mutants to potentiate the noncanonical NF-kB pathway through p100 accumulation, which likely contributes to the dysregulated B cell expansion observed in lymphomas that harbor CARD11 GOF variants.

overall_design: To analyze differentially expressed genes between CARD11+/+, CARD11+/C49Y and CARD11C49Y/C49Y Follicular (FO) and Marginal Zone (MZ) B cells both unstimulated and in response to stimulation. FO and MZ B cells were harvested from spleens of CARD11+/+, CARD11+/C49Y and CARD11C49Y/C49Y mice and stimulated under the following conditions: unstim; 4µg/mL anti-IgM (24hrs). Three replicates per stimulation condition per B cell type per genotype were included.

first: Anushka

last: Ghosh

first: Tyler

last: Jones

first: Sophie

last: Mackinnon

first: Shelby

middle: M

last: Hutcherson

first: Julia

last: Tritapoe

first: Piyusha

last: Mongia

first: Neha

last: Shah

first: Emma

last: Mehlhop

first: Nicole

last: Carter


title: ERBB2 signaling drives immune cell evasion and resistance against immunotherapy in small cell lung cancer [scRNA-Seq]

first: Lydia

last: Meder

summary: Small cell lung cancer (SCLC) represents ~15% of all lung cancers and is characterized by its highly aggressive phenotype and its dismal outcome. Though the addition of immune checkpoint blockade to carboplatin and etoposide treatment has improved outcome in SCLC patients, SCLC cells finally acquire the ability to evade immunosurveillance and resistance against immune check point blockade. To elaborate molecular mechanisms that mediate SCLC immune cell evasion we performed high dimensional profiling of human and murine SCLC specimens. We herein comprehensively analyzed matched human samples of primary and metastatic SCLC and found a loss of MHC-I in SCLC metastases indicating that MHC-I loss mediates SCLC immune cell evasion. Silencing MHC-I in SCLC cells drastically diminished immune cell infiltration and facilitated the formation of metastasis in mice by circumventing immune surveillance. Using mass spectrometry and phospho tyrosine kinase analysis we discovered that ERBB2 signaling suppresses MHC-I expression in SCLC cells and stimulates immune modulating transcripts. Mechanistically, genetic and/or pharmacologic blockade of the ERBB2 signaling axis was sufficient to induce MHC-I expression and to prevent immune evasion in autochthonous murine SCLC in a STING dependent manner. Finally, we demonstrate that ERBB2 signaling axis regulates MHC-I expression on SCLC cells and is critical in maintaining immune evasion in SCLC. Most strikingly, we here uncover synergistic treatment efficacy by combining ERBB2 with anti-PD-1 targeted treatment that elicits profound responses in preclinical SCLC models suggesting this combination for future clinical trials in patients with SCLC.

overall_design: Rb1/Trp53-deleted SCLC mice were randomized and systemically treated with vehicle, an anti-PD-1 inhibitor, an ERBB2 inhibitor, and with the combination of an ERBB2 inhibitor and an anti–PD-1 inhibitor. SCLC lung tumor was analyzed regarding antigen presentation, T-cell recruitment and restistance mechanisms..

first: Charlotte

last: Orschel

first: Cyrielle

last: Bouchez

first: Rahil

last: Gholamipoorfard

first: Claudia

first: David

last: Stahl

first: Christoph

last: Kreer

first: Mirjam

last: Koker

first: Xinlei

last: Zhao

first: Marieke

last: Nill

first: Leon

last: Ullrich

first: Marie-Lisa

last: Eich

first: Alexandra

last: Florin

first: Holger

last: Grüll

first: Jürgen

last: Wolf

first: Reinhard

last: Büttner

first: Florian

last: Klein

first: Johannes

last: Brägelmann

first: Christian

last: Reinhardt

first: Nima

last: Abedpour

first: Roland