title: Cerebrospinal fluid from HAM/TSP patients with rapid evolution affects mitochondrial DNA transcription and structure in human glioblastoma cell lines

city: Rio de Janeiro

first: Otávio

middle: de Melo

last: Espíndola

state: RJ

address: Av. Brasil, 4365

country: Brazil

institute: FIOCRUZ

summary: Human T-lymphotropic virus 1 (HTLV-1)-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a progressive neurodegenerative disease impacting motor and sensorial functions. While the cerebrospinal fluid (CSF) alterations have been used to identify biomarkers for this disease, the effects of HTLV-1 CSF on neural cells remain unexplored. Herein, we investigated the impact of CSF from HTLV-1 infected patients on glioblastoma cell lines. CSF samples were obtained from HTLV-1 asymptomatic carriers (HAC) (n=13), and HAM/TSP patients (n=21) categorized according to the speed of disease progression: very slow (HAMvs), typical (HAMt), and rapid (HAMr). RNA sequencing of glioblastoma cells treated with HTLV-1 CSF revealed notable gene expression changes, particularly with HAMr CSF, which caused significant downregulation of mitochondrial DNA transcripts. Confocal microscopy showed phenotypical changes in the mitochondrial network: astrocytes exposed to HAMr CSF exhibited a less complex mitochondrial network compared to CSF from other patient groups. It is characterized by reduced mitochondrial branching, fewer junctions per branch length, and slightly increased branch diameter. Compared to untreated cells, HTLV+ CSF disturbed mitochondrial metabolism. However, these changes are limited at the metabolic level and do not appear to vary significantly with HTLV donor status. In conclusion, our findings suggest that HTLV+ CSF induces mitochondrial reorganization in glioblastoma cells, potentially helping to compensate for the stress caused by the CSF exposure.

overall_design: Bulk RNA-seq profiling of U87-MG cells incubated for 6 hours and 24 hours with cerebrospinal fluid from HAM/TSP patients with different speed of disease progression.

first: Yago

middle: C

last: Gomes

first: Alice

last: Bongers

first: Patricia

last: Jeannin

first: Ana Carolina

last: Vicente

first: Antoine

last: Gessain

first: Philippe

last: Afonso

first: Otavio

last: Espindola


title: KRIT1 heterozygous mutations are sufficient to induce a pathological phenotype in patient-derived iPSC models of Cerebral Cavernous Malformation

status: Public on Apr 15 2025

city: Uppsala

first: Peetra

middle: Ulrica

last: Magnusson

address: Dag Hammarskjoldsv 20

department: Immunology, Genetics and Pathology (IGP)

country: Sweden

institute: Uppsala University

type: Expression profiling by high throughput sequencing

summary: Cerebral Cavernous Malformation (CCM) is a neurovascular disease distinguished by clusters of leaky, mulberry-like blood vessels. KRIT1 biallelic loss-of-function mutations in endothelial cells are known to trigger brain cavernomas, however, human pre-clinical models are needed to unveil the importance of germline KRIT1 heterozygous mutations in CCM pathogenesis. We generated three iPSCs from CCM patients with hereditary KRIT1 heterozygous mutations. Patient-derived vascularized organoids exhibited intricate and abnormal vascular structures with cavernoma-like morphology, and iPSCs-derived endothelial cells displayed phenotypic abnormalities at the junctional and transcriptional level. Upon injection into brain explants, CCM-endothelial cells integrated into the normal vasculature and created vascular anomalies. Lastly, transcriptional analysis showed that the endothelial progenitor marker PEG3 was highly expressed in iPSCs-derived CCM endothelial cells and further confirmed in familial and sporadic cavernoma biopsies. Overall, our study enlightens the molecular consequence of KRIT1 heterozygous mutations in endothelial cells and the potential implications in cavernoma pathogenesis.

overall_design: CCM patient-derived and one healthy control iPSCs were differentiated towards endothelial cells using a ETV2 tetracycline inducible vector. Furthermore, the same cells (only patient CCM01 and Healthy control) were co-cultured with brain explants ex vivo.

first: Maximiliano

last: Arce

first: Fan

last: Yang

middle: U


title: The therapeutic mechanism of baritinib in idiopathic granulomatous mastitis treatment elucidated by single-cell RNA sequencing

city: Hangzhou

first: Lifeng

last: Ma

address: Yuhangtang Road No.388

country: China

institute: Zhejiang University

summary: The pathogenesis of idiopathic granulomatous mastitis (IGM) remains poorly understood. Based on compelling clinical evidence, we have discovered that baricitinib, a widely prescribed medication for autoimmune disorders, exhibits remarkable efficacy in alleviating the symptoms associated with IGM. To gain a more comprehensive understanding of the underlying mechanism of baricitinib in IGM, we performed single-cell RNA sequencing (scRNA-seq) analysis and observed an augmented presence of lip-macrophages and plasma cells_IGHG in patients with IGM. Our results indicated that IGM may possess autoimmune characteristics, potentially triggered by an upregulation of plasma cells. And plasma cells were undergoing class-switch recombination from IGHA to IGHG to lead to development of autoimmunity in IGM. Our data also revealed that lip-macrophages involved in maintaining breast homeostasis are associated with pathways related to phagocytosis, endocytosis, and lipid metabolism

overall_design: Over 50,000 cells from normal and inflamed tissue regions of five patients with idiopathic granulomatous mastitis

first: Yuan

last: Liao

first: Haiyan

last: Wei

first: Di

last: Zhang


title: Pathophysiology of microglial-driven neurodegeneration in Histiocytosis [Proj_11769]

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

country: USA

institute: Memorial SLoan-Kettering Cancer Center

summary: L-Histiocytosis is a clonal myeloid disease characterized by BRAFV600E somatic mutations and increased risk of neurodegeneration, the mechanism of which is poorly understood. We report that microglia from histiocytosis patients is characterized by a high mutational load, dominated by the BRAFV600E variant. Genetic bar-coding analysis of the patients’ microglia, blood and/or bone marrow suggest that most microglia clones are generated or expanded locally. A diagnosis of neurodegeneration was linked to larger and more widespread clusters of mutant microglia. Microglial clones preferentially accumulate in the patients’ hippocampus and brainstem, attributable in part to a local proliferative advantage over time in mouse models. snRNAseq showed that BRAFV600E microglia cause neuro-inflammation, a neurotoxic astrocyte response, and preferential loss of pons glutamatergic and GABAergic neurons. Early treatment with CSF1R-inhibitor depleted mutant microglia, limited neuronal loss, improved symptoms, and prolonged survival in mice, suggesting that preventive treatment may alleviate neurodegeneration in Histiocytosis.

overall_design: Analysis of BRAFVE and WT microglia from cortex and brainstem from 2 months and end-stage mice

first: Frederic

last: Geissmann


title: Pathophysiology of microglial-driven neurodegeneration in Histiocytosis

overall_design: RNAseq analysis of human brain samples.


title: Transcriptome analysis of fetal kidney RNA from GR-null and control mice at E18.5

city: Melbourne

first: Mehran

last: Piran

state: VIC

address: 19 Innovation Walk

department: Anatomy and Developmental Biology

country: Australia

institute: Monash University

summary: Glucocorticoid steroid hormones play essential roles for maturation and growth of many fetal organs including the lung and heart, yet the kidney-specific roles are not well characterised. Glucocorticoids activate the intracellular glucocorticoid receptor (GR) that acts primarily as nuclear transcriptional regulators. We analysed the effect of loss of GR expression on the fetal kidney transcriptome at E18.5 by RNA sequencing. Total RNA was extracted from control (n=4) and GR-null (n=3) kidneys. Loss of GR expression resulted in 2473 differentially expressed genes (FDR < 0.05), 288 genes with absolute LogFC > 1 & FDR < 0.05, which identified 16 upregulated and 25 downregulated primary ciliary genes (FDR < 0.05). Primary cilia are cell signalling and environment sensing organelles that protrude from cell membranes and play important roles during embryogenesis and tissue homeostasis. Little is known of the cellular pathways regulating ciliogenesis. Our findings indicate a role of glucocorticoid signalling in primary cilia formation in renal tubular cells of the developing mouse kidney.

overall_design: Total RNA was isolated from embryonic kidneys using TRIzolTM reagent (Invitogen, USA) according to the manufacturer’s instructions. Total RNA was analysed using a Bioanalyzer 2100 (Agilent Technologies, USA) and Next generation RNA sequencing (NGS RNA-seq) was performed by Genewiz Biotechnology, Suzhou, China. RNA sequencing (20 million reads) was performed on the Illumina Hiseq platform, in a 2 x 150 bp paired-end format.

first: Kelly

middle: L

last: Short

first: Jianshen

last: Lao

first: Rachel

last: Lam

first: Julie

last: Moreau

first: Judy

last: Ng

first: Alexander

middle: N

last: Combes

first: Denny

last: Cottle

first: Timothy

middle: J

last: Cole


title: Auxin affects gene editing efficiency through regulating chromatin accessibility

city: wuhan

first: yu

last: zhang

address: Gaonong International Phase II, No. 888 Gaoxin Avenue, Donghu High-tech Zone, Wuhan

institute: biorun

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ATAC-seq of tobacco callus cells cultured by different NAA concentrations during in vitro tissue culture illustrates the landscape of chromatin openness across the entire genome，which provides a novel direction and theoretical basis for improving gene editing efficiency in plants by modulating chromatin accessibility through auxin signaling and tissue culture conditions.

overall_design: Approximately 80 tobacco explants were harvested from the media containing 0.1 mg/L or 0.5 mg/L NAA after 2 weeks culture for nuclei isolation. The ATAC-seq was performed according to the guidelines of the ATAC-Seq Library Prep Kit for Illumina®


title: Placental mitochondrial calcium uniporter modulates offspring susceptibility to obesity in a sex-dependent manner

city: Minneapolis

first: Emilyn

last: Alejandro

state: MN

address: 2231 6th Street SE

institute: University of Minnesota

summary: Mitochondria regulate bioenergetics, metabolism, and calcium storage, but their role in the placenta and how they may shape offspring metabolic health remains unclear despite associations with pregnancy complications. We examined this relationship by using a murine model with placenta-specific deletion of the mitochondrial calcium uniporter (Pl-MCUKO). We found that female placental trophoblasts exhibited higher respiration rates than males at baseline. MCU deletion impaired mitochondrial function specifically in female placentas, accompanied by changes in metabolomic profiles of amino acid and lipid catabolism. Transcriptome analysis indicated reduced placental cellular growth, which was supported by smaller placentas and reduced embryonic body weights in PI-MCUKO. These deficits normalized postnatally, with body weight and glucose metabolism remaining comparable to the controls under normal chow diet. Notably, under a metabolic challenge of high-fat-diet feeding, Pl-MCUKO females showed reduced weight gain, improved glucose and insulin tolerance, smaller fat depots and increased ambulatory activity, compared to controls. These results provide direct evidence linking placental mitochondrial function to offspring metabolic health.

overall_design: RNASeq profiling of embryonic day 17.5 placenta from male and female, control and placenta specific MCU knockout samples

first: Juan

last: Abrahante Llorens

first: Megan

last: Beetch

first: Seokwon

last: Jo


title: Antigenic cancer persister cells survive direct T cell attack

city: La Jolla

first: Matthew

last: Hangauer

state: CA

address: 9500 Gilman Drive #0869

department: Dermatology

institute: University of California, San Diego

summary: Drug-tolerant cancer persister cells were reported fifteen years ago as cells in a quiescent, reversible cell state which tolerates unattenuated cytotoxic drug stress. It remains unknown whether a similar phenomenon contributes to immune evasion. Here we report an antigenic persister state which survives weeks of cytotoxic T lymphocyte (CTL) attack. In contrast to immune evasion mechanisms that limit immune detection or activation, antigenic persisters robustly activate CTLs which deliver Granzyme B, secrete IFNγ, induce tryptophan starvation, and initiate persister cell apoptosis. However, instead of dying, persisters paradoxically leverage apoptotic stress to suppress inflammatory death and acquire mutations and epigenetic changes which enable outgrowth of CTL-resistant cells. Furthermore, persister cells undergoing sublethal apoptosis are enriched in inflamed human and mouse tumors which have regressed during immunotherapy. These findings reveal that adaptive evolution mediated by persister cells surviving direct T cell attack presents a barrier to complete immune-mediated tumor rejection.

overall_design: Untreated A375 melanoma cells (parental) or residual A375 melanoma cells that survived 15 days of NY-ESO-1 CTL coculture (CTL-tolerant persister cells) were analyzed using scRNAseq.

first: Michael

middle: X

last: Wang

first: Brandon

middle: E

last: Mauch

first: August

middle: F

last: Williams


title: CCR8+ decidual regulatory T cells maintain maternal-fetal immune tolerance during early pregnancy

city: Jinan

first: Pinxin

last: Si

state: Shandong

address: Wenhua West Road, Lixia District

institute: Shandong University

type: Non-coding RNA profiling by high throughput sequencing

summary: Regulatory T cells (Tregs) play crucial roles in maintaining maternal immune tolerance to the semi-allogeneic fetus during pregnancy, but Treg population heterogeneity and tissue-specific functions in human decidua remain largely unknown. Here, we conducted single-cell transcriptomic and T cell receptor sequencing of CD4+ T cells from first-trimester decidua and matched peripheral blood of pregnant women. These analyses identified a highly activated, immunosuppressive CCR8+ Treg subset specifically enriched in decidua (dTregs). CCR8+ dTregs are decreased in recurrent pregnancy loss (RPL) patients and abortion-prone model mice. Depletion of this subset with anti-CCR8 antibodies alters the decidual immune profile, increasing susceptibility to fetal loss. The CCR8 ligand, CCL1, is mainly produced by decidual CD49a+ NK cells and is also significantly decreased in RPL patients. By characterizing the landscape of dTregs in human early pregnancy, we identified CCR8+ dTregs as crucial for maintaining maternal-fetal tolerance, suggesting new potential strategies for RPL diagnosis and therapy.

overall_design: We performed scRNA-seq and TCR sequencing of decidual and matched peripheral blood of normal pregnancy women and analyze the gene expression profiles.

first: Zhuqing

last: Li

first: Tingting

last: Meng

first: Chendi

last: Zhu

first: Dunfang

last: Zhang

first: Nianyu

first: Ran

last: Liu

first: Xiaoran

last: Zhao

first: Tianxiang

last: Ni

first: Junhao

last: Yan

first: Hongchang

first: Ning

first: Xiao

last: Yu

first: Yingying

last: Qin

first: WanJun

last: Chen

first: Zi-Jiang

first: Xue

last: Jiao


title: Mesenchymal Stromal Cell Senescence Induced by Dnmt3a-Mutant Haematopoietic Cells is a Targetable Mechanism Driving Clonal Haematopoiesis and Initiation of Leukemia

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Clonal haematopoiesis (CH) is a benign age-related condition occurring due to somatic genetic variation in haematopoietic stem and progenitor cells (HSPCs). In some individuals, CH is a precursor condition for haematologic malignancy, but the mechanisms driving progression of CH to malignancy are incompletely understood. Given that malignant cells reprogram their microenvironment to create a self-reinforcing niche, we hypothesized that HSPCs carrying CH mutations have microenvironment-remodelling properties that promote their clonal advantage and contribute to malignant progression. By single-cell RNA-seq profiling of the non-haematopoietic bone marrow microenvironment in a mouse model of DNMT3A-mutant CH, we identified strong enrichment of a cellular senescence signature in bone marrow mesenchymal stromal cells (MSCs). We find that Dnmt3a-mutant HSPCs induce markers of senescence including SA-b-gal, BCL-2, BCL-xL, Cdkn1a (p21), and Cdkn2a (p16) selectively in MSCs using ex vivo and in vivo assays. This senescence induction phenotype is cell contact-independent and reproduced by IL-6 and TNFa, both of which are soluble factors produced by Dnmt3a-mutant HSPCs. Removal of senescent MSCs using Navitoclax reduced the selective growth advantage of Dnmt3a-mutant hematopoietic cells and reduced myeloproliferation in a Dnmt3a;Npm1-mutant model of myeloid neoplasms. Together, our data demonstrate that Dnmt3a-mutant HSPCs produce specific factors that reprogram their microenvironment through senescence induction, and that this process creates a self-reinforcing niche favouring their growth advantage and progression to malignancy.

overall_design: Hematopoietic and bone marrow microenvironment cell populations were enriched using cell sorting 16 weeks post transplantation from 4 Dnmt3a- mutant and 4 Fgd5- control mice transplanted into middle aged CD45.1 recipient mice for single cell RNA-seq.

first: Mistry

last: Jayna

first: Young

last: Kira

first: Trowbridge

last: Jennifer


title: Role of clonal inflammatory microglia in histiocytosis-associated neurodegeneration

first: Bic

last: MSKCC

summary: Langerhans cell Histiocytosis (LCH) and Erdheim-Chester disease (ECD) are clonal myeloid disorders, associated with MAP-Kinase activating mutations and increased risk of late-onset neurodegeneration. Surprisingly, we found microglia mutant clones associated with microgliosis, astrocytosis, and neuronal loss, predominantly in the grey nuclei of the rhombencephalon, in patients with LCH and ECD whether or not they presented with clinical symptoms of neurodegeneration at the time of death. The presence of clinical symptoms was associated with a longer evolution of the disease and a larger size of PU.1+ clones (p= 0.0003), indicating a phase of subclinical incipient neurodegeneration. Depletion of mutant microglia by a CSF1R-inhibitor in a mouse model of incipient disease limited neuronal loss and improved survival. Disease topography was attributable to a local proliferative advantage of mutant microglia. Genetic bar-coding analysis suggest that mutant clones originate from either definitive or yolk sac hematopoiesis depending on patients. These studies characterize a progressive neurodegenerative disease associated with clonal proliferation of inflammatory microglia (CPIM), and a preclinical stage of incipient disease which represents a therapeutic window for prevention of neuronal death.

overall_design: snRNAseq from microglia from Alzheimer's disease patients with and without pathogenic mutations and contols

first: Frederic

last: Geissmann

first: Rocio

last: Vicario


title: Reprogramming deaminase substrate specificity for single nucleobase editing

status: Public on Apr 14 2025

city: CHICAGO

first: Yuan

last: Wu

state: Illinois

address: 929 E 57th St, GCIS E535

department: Chemistry

institute: University of Chicago

summary: In this study, we set out to reprogram deaminase context specificity to pinpoint editing. We identified multiple nucleic acid-recognition hotspots in the E. coli tRNA-specific adenosine deaminase (TadA). Strategically sampling these recognition hotspots, we first accessed multipotency for C in TadA and subsequently eliminate its A-deamination activity. We further reprogrammed TadAC context specificity through 16 evolution campaigns, each aimed at a defined NCN context, and isolated hundreds of thousands of context-specific cytosine deaminases. Our panel of 16 NCN-specific deaminases covers the full spectrum of all possible minus1 and plus 1 contexts for a target C, offering on demand deaminase choices for editor customization. Our context-specific CBEs corrected 5,866 of 7,196 disease-associated T:A-to-C:G transitions documented by ClinVar with higher accuracy than existing CBEs, often achieving selective editing of a single cytosine out of multiple cytosines in the protospacer without compromising editing potency. We also showcased the application of context-specific base editing for modeling disease-associated C:G-to-T:A transitions using two cancer driver mutations, KRASG12D and TP53R248Q, each demanding selective editing of one cytosine in two consecutive cytosines (ACC and CCG). These context-specific editors, as expected, showed tightly controlled off-target profiles by rejecting most cytosines at potential off-target sites. Bystander-free, single-nucleobase editing, as enabled by reprogramming deaminase context specificity, complements our current editor portfolio and unlocks new potential in base editing.

overall_design: Various CBE variants was transfected to cells which harbors 12,000 Disease-related-A paired sgRNA-target library. After 72h, genomic DNA was extracted and target was amplified using pcr. Amplicon library was submitted to Nextseq 2000 for sequencing.

first: Wu

last: Yuan

last: Yulan

first: Tang

last: Weixin


title: Cutaneous lupus features specialized stromal niches and altered retroelement expression

city: New Haven

first: Jeff

middle: R

last: Gehlhausen

state: CT

address: 333 Cedar St LCI 501

department: Yale Dermatology

institute: Yale School of Medicine

summary: Single-cell RNA and spatial sequencing of lesional and non-lesional cutaneous lupus skin compared to healthy controls. The study includes 12 single-cell samples (cutaneous lupus patients with non-lesional (5) and lesional (4) skin biopsies with healthy controls (3)) and 4 spatial transcriptomics samples (cutaneous lupus patient pre/post-Anifrolumab treatment, 1 additional CLE patient, and 1 healthy control).

overall_design: Overall design: Single-cell RNA-seq was performed on 12 samples: 5 non-lesional cutaneous lupus (CLE) samples, 4 lesional (NL) skin samples from CLE patients, and 3 healthy control (HC) samples. Additionally, 10x Visium spatial transcriptomics was performed on 4 samples: 1 from a patient with subacute cutaneous lupus (SCLE) before and after Anifrolumab treatment, 1 from a patient with discoid lupus erythematosus (DLE), and 1 healthy control sample. The study aims to investigate pathophysiology of cutaneous lupus, including interferon signatures, specialized fibroblast populations, and retroelement expression.


title: RNAseq data from myotubes after treatment with iAM373 in vitro

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Sarcopenia represents an important health challenge with reduced quality of life and increased mortality.  Gut microbiota have been suggested to contribute to this age-associated muscle wasting but the underlying mechanisms are still unclear. We uncovered the quorum sensing peptide iAM373 as a hitherto unknown contributor to sarcopenia. The involved pathways resulting in a decreased muscle metabolism were explored by RNA sequencing of C2C12 and human myotubes after treatment with iAM373 or placebo. Gene-set enrichment analysis (GSEA) with terms from Gene ontology (GO) biological processes, and KEGG, Biocarta and Reactome canonical pathways revealed an enrichment in gene sets involved in striated muscle development and differentiation in iAM373 treated samples. Most of these gene sets were downregulated by iAM373. The proteasome degradation pathway was also enriched, i.e., upregulated in murine and human myotubes after QSP incubation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Murine (C2C12) or human (AB678C53Q) myotubes were treated with quorum sensing peptide iAM373 or placebo for 8 hours or 24 hours in vitro. RNA sequencing was conducted for pathway analysis. N=10 for each condition at specific timepoint (N=40 in total)

first: Anton

last: De Spiegeleer

first: Julie

last: Coudenys


title: Il7rKO Single Cell

city: San Francisco

first: James

last: Gardner

address: 513 Parnassus Ave

institute: University of California, San Francisco

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

overall_design: We obtained lymph nodes (mesenteric,cervical, inguinal, axillary, brachial, and para-aortic) from WT and IL7rKO mice and FACS-sorted tdTmt+ MHCII+ cells for subsequent scRNA-seq.

first: Im Hong

last: Sun

first: Anita

last: Qualls

first: Han

last: Yin


title: Synaptic vesicle endocytosis deficits underlie GBA-linked cognitive dysfunction in Parkinson’s disease and Dementia with Lewy bodies

first: Sreeganga

middle: S.

last: Chandra

address: 295 Congress Avenue

department: Departments of Neurology and Neuroscience

summary: GBA mutations are major risk factors for Parkinson’s disease (PD) and Dementia with Lewy Bodies (DLB), two common α-synucleinopathies associated with cognitive impairment. Here, we investigated the role of GBA mutations in cognitive decline by utilizing Gba L444P mutant mice, SNCA transgenic (tg), and Gba-SNCA double mutant mice. Notably, Gba mutant mice showed early cognitive deficits but no PD-like motor deficits up to 12 months old. Conversely, SNCA tg mice displayed age-related motor deficits but no cognitive abnormalities. Gba-SNCA mice exhibited exacerbated motor deficits and cognitive decline.  Immunohistological analysis revealed cortical phospho-α-synuclein pathology in SNCA tg mice, which was exacerbated in Gba-SNCA mice, especially in layer 5 cortical neurons. Significantly, Gba mutant mice did not show α-synuclein pathology. Single-nucleus RNA sequencing of cortices instead uncovered selective synaptic vesicle cycle defects in excitatory neurons of Gba mutant and Gba-SNCA mice, via robust downregulation in gene networks regulating synapse vesicle cycle and synapse assembly. Meanwhile SNCA tg mice displayed broader synaptic changes. Immunohistochemical and electron microscopic analyses validated these findings. Together, our results indicate that Gba mutations, while exacerbating pre-existing α-synuclein aggregation and PD-like motor deficits, contribute to cognitive deficits through α-synuclein-independent mechanisms, likely involving dysfunction in synaptic vesicle endocytosis. Additionally, Gba-SNCA mice are a valuable model for studying cognitive and motor deficits in PD and DLB

overall_design: Mice: Gba mutant mice have been previously described in Mistry et al. (2010)1 and Taguchi et al. (2017)2. These mice have a copy of the Gba L444P mutant allele and a Gba KO allele, with Gba expression rescued in skin to prevent early lethality. SNCA tg mice overexpress the human α-synuclein A30P transgene (heterozygous), and have also been previously described. Gba mutant mice were crossed to SNCA tg to obtain Gba-SNCA double mutant mice. Age and sex matched WT mice were used as normal controls. We performed single nucleus RNA sequencing (snRNA-seq) on cortical brain tissue from adult mice belonging to the four genotypes (n=14) 3-4 mice per genotype were used: 4 Gba mutant mice (192, 193, 185, and 201), 3 SNCA tg mice (729, 754, 740), 3 Gba-SNCA double mutant mice (187, 191, 184) and 4 WT (normal control) mice of the B6 strain. We chose to perform this analysis on 12-month-old mice, as Gba-SNCA mice show enhanced behavioral deficits and α-synuclein pathology, while lacking gross neuronal loss or degeneration in the cortex, allowing us to investigate disease relevant mechanisms. Nuclei isolation from cerebral cortex: Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications. All procedures were carried out on ice or at 4 degrees C. Cortical snRNA expression was analysed in mice with a pathogenic mutation - i.e., Gba mutant mice, SNCA tg mice, and Gba-SNCA double mutant mice - and compared, respectively, with WT mice cortical snRNA expression.

first: David

last: Bäckström

first: Vidyadhara

last: Devarunda Jaganath

first: Risha

last: Chakraborty

first: Jiapeng

last: Ruan

first: Jae-Min

last: Park

first: Pramod

middle: K

last: Mistry

middle: S


title: COCA-seq: genome-wide mapping of O-GlcNAc-associated open chromatin [RNA-Seq]

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

institute: Dalian University of Technology

summary: O-GlcNAcylation, a prevalent reversible post-translational modification, intricately alters non-histone proteins, influencing the organization of gene transcriptional regulation within the accessible chromatin environment. This nucleoplasmic landscape, characterized by histone-free regions, fundamentally enables O-GlcNAc-mediated modulation through dynamic accessibility. However, unraveling the O-GlcNAc-open chromatin interplay that governs sophisticated transcriptional regulatory networks remains constrained by current techniques, which lack the resolution to probe this spatiotemporal crosstalk. Here, we reported a general strategy to systematically and chemoselectively profile O-GlcNAc-associated chromatin accessibility on a genome-wide scale (COCA-seq). Through comprehensive validation across low- and high-throughput levels, we demonstrated COCA-seq's dual fidelity in both O-GlcNAc chemoselectivity and open chromatin specificity. We employed it to delve into doxorubicin resistance for breast cancer, scrutinizing pivotal regulatory genes and transcription factors implicated in this complex biological event, such as NRF1 and XBP1. By integrating bulk RNA-seq with COCA-seq, we offered a multiomics perspective, shedding light on related biological processes and pathways like drug efflux and stress homeostasis, thereby uncovering potential mechanisms by which O-GlcNAc-associated open chromatin orchestrates tumor drug resistance. COCA-seq emerges as a general and versatile tool across various biological contexts, poised to reveal the landscape of O-GlcNAc-associated open chromatin regions across the genome and decipher the significance of glycosylation behind it.

overall_design: We employed a chemoselective metabolic labeling strategy coupled with DNase I treatment to profile open chromatin regions bound by O-GlcNAc-modified non-histone proteins. Briefly, human breast cancer cells (MCF-7) and their doxorubicin-resistant counterparts (MCF-7/DOX) were metabolically labeled with 200 μM 1,6-Pr2GalNAz. The O-GlcNAz-modified chromatin was crosslinked, digested with 5 U/mL DNase I, and enriched via bioorthogonal chemistry. Genomic DNA fragments associated with O-GlcNAc-modified proteins were then de-crosslinked, size-selected (100-750 bp), and processed for next-generation sequencing (Chemoselectively O-GlcNAc-Chromatin Accessibility Sequencing, COCA-seq). In parallel, we performed RNA-seq to analyze differential gene expression between MCF-7 and MCF-7/DOX cells. Two biological replicates of COCA-seq and RNA-seq were both performed.

first: Chang

last: Ge

first: Hongyu

last: Jiang

first: Wenwen

last: Fang

first: Wei

last: Wang


title: RBM15-mediated Metabolic Reprogramming Boosts Immune Response in Colorectal Cancer

city: Shanghai

first: Chen

address: Xianxia Rd 1111, Changning District

department: Department of Gastroenterology

institute: Shanghai Jiaotong University School of Medicine Affiliated Tongren Hospital

summary: Immune checkpoint blockade (ICB) offers therapeutic options for patients with advanced colorectal cancer; however, only a subset of patients with microsatellite instability-high (MSI-H) tumors respond to treatment. Therefore, strategies to enhance immunotherapy sensitivity are urgently needed. In this study, we demonstrate that RBM15 is highly expressed in colorectal cancer and is associated with poor prognosis. Loss of RBM15 increases the expression of fumarate hydratase (FH), leading to a reduction in its substrate fumarate, which acts as a suppressor of anti-tumor immunity. Notably, RBM15 depletion delays tumor growth by promoting CD8+ T cell infiltration. Our findings identify RBM15 as a key suppressor of anti-tumor immunity, suggesting that targeting RBM15 could be a promising therapeutic strategy in colorectal cancer.

overall_design: To reveal the tumor-intrinsic functional role of RBM15 in colorectal cancer, we utilized the CRISPR/Cas9 gene editing system to knock out (KO) RBM15 in the human colorectal cancer cell line HCT15. We then performed differential gene expression analysis using data obtained from RNA-seq of WT or RBM15 knockout cells.

first: Min

last: Shi


title: Neuregulin-1 prevents death from a normally lethal respiratory viral infection.

city: Columbus

first: Syed-Rehan

middle: A

last: Hussain

state: Ohio

address: 700 Children's Dr.

department: Abigail Wexner Research Institute

institute: Nationwide Children's Hospital

summary: Respiratory infections with RNA viruses such as respiratory syncytial virus (RSV) and influenza lead to significant morbidity and mortality. Using a natural rodent pathogen, Sendai virus (SeV), which is similar to RSV, mice made atopic with house dust mite survived a normally lethal SeV infection. Since we previously demonstrated a critical role for CD11c+ cells in the immune axis linking SeV to post-viral airway disease we posited that some of the protection against lethal SeV infection could be due to CD11c+ cells from atopic mice. Therefore, we performed RNA-seq analysis of CD11c+ cells isolated from atopic and non-atopic (NA) mouse lungs. While there were several dysregulated genes, one gene product whose expression was increased several-fold in atopic CD11c+ cells was neuregulin-1(NRG1) whose protein was found to be markedly elevated in the lungs and bronchoalveolar lavage fluid of atopic mice. When NRG1 was administered to naïve (non-atopic) mice it protected them from death with both SeV and mouse adapted influenza A virus (IAV). Survival was associated with reduced alveolar epithelium permeability and reduced phosphorylation of mixed lineage kinase domain-like (MLKL) protein indicating inhibition of necroptosis. In conclusion, our data demonstrate a unique function of NRG1 in respiratory viral infections by reducing alveolar leak, inhibiting epithelial necroptosis, and promoting homeostatic regulation of airway epithelium, all of which associate with markedly reduced mortality to the respiratory viral insult.

overall_design:
To investigate the role of CD11c positive cells in providing survival advantage in atopic mice we isolated CD11c+ cells from HDM sensitized and challenged mice vs PBS control control
We then performed gene expression profiling analysis of CD11c+ cells that occur as a result of making mice atopic. FACS was performed to isolate CD11c+ cells from both atopic and NA mouse lung and RNA-seq performed.
Comparative gene expresssion analysis was performed of RNA-seq data for CD11c+ cells from atopic (HDM group) vs non-atopic (PBS treated group) two days after the last HDM challenge.

first: Hussain

last: Syed-Rehan

first: Mitchell

middle: H

last: Grayson


title: COCA-seq: genome-wide mapping of O-GlcNAc-associated open chromatin


title: RNA sequencing of peripheral blood mononuclear cells (PBMCs) from fetal sheep exposed to lipopolysaccharide (LPS).

city: Tucson

first: Sean

middle: W

last: Limesand

state: AZ

address: 4101 N Campbell Ave

department: Animal & Comparative Biomedical Sciences

institute: University of Ariziona

summary: Differential gene expression of PBMCs at day 1 (pre-LPS exposure) and day 5 following Repeated LPS administration to sheep fetuses

overall_design: LPS boluses were administered intravenously to fetal sheep. Four LPS boluses were given with increasing doses of 0.3µg, 1.5µg, 3µg, and 15µg on day 1, 3, 4, and 5 respectively. Physiological responses were assessed at  0,1, 3, and 5 hours relative to the LPS bolus. PMBCs were isolated from whole blood on day 1 and 5 prior to the daily LPS bolus.


title: Gene expression in PNPT1 knockout A549 cell and wild type A549 cells

city: Nanjing

first: HONGWEI

last: LIANG

state: Jiangsu Province

address: Qixia District, Xianlin Road No.163

institute: Nanjing University

summary: To investigate the gene expression regulated by PNPT1, we have employed whole genome microarray expression profiling as a discovery platform to identify genes expression in PNPT1 knockout A549 cell and wild type A549 cells

first: Hongwei

last: Liang


title: A second genetic screen for gurken mRNA mislocalisation reveals novel phenotypes of the piRNA pathway mutants in Drosophila [ncRNA-seq]

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

institute: The Australian National University

summary: Transposon silencing is essential for germ line development. In Drosophila oogenesis, DNA damage caused by transposon activation affects microtubule-dependent mRNA localisation in the oocyte and impairs embryonic axes formation. Our previous EMS mutagenesis screen for gurken mRNA mislocalisaiton on Chromosome 3L of Drosophila melanogaster identified several piRNA pathway mutants (PMID: 24531791). Here we report the screen for Chromosome 3R. We identified 10 mutation groups disrupting gurken mRNA localisation and other mutations affecting different aspects of oogenesis. We found that mutations in karyopherin-b3 affect localisation and translation of gurken mRNA in a transposon silencing-independent manner. Characterisation of the new mutation in vreteno revealed that the piRNA pathway is essential for the basal stalk development, the process of holding the ovariole and encapsulating the first egg chambers. Females transheterozygous for vreteno and armitage mutations both showed abnormal basal stalks, defective egg chamber formation and loss of germ line cells. We also found that the mutation in the Zinc Finger motif of Spindle-E shows a hypomorphic transposon activation phenotype, consistent with the previous study (PMID: 25239103). Further characterisation showed that the Zinc Finger is required for robust ping-pong piRNA biogenesis and the nuage localisaiton of AGO3, but not of Aubergine, suggesting that it is involved in a specific step of ping-pong biogenesis.

overall_design: The study characterises the phenotype of the mutations affecting gurken mRNA localisation in Drosophila oocytes. Of those, we focused on the piRNA pathway mutations and examined their impacts on piRNA production in the ovaries. We generated oxidised small RNA sequencing libraries from freshly dissected ovaries and sequenced them by single-read 150bp mode on Illumina Novaseq.


title: The m6A demethylase FTO controls activation-induced cell death in effector CD8+ T cells by modulating Fas expression

city: xian

first: Cangang

last: Zhang

state: State...

address: Yanta district, xi 'an city, shaanxi province

institute: xian jiaotong university

summary: Functional CD8+ T cell immune response is critical for immune surveillance and host defense against infection and tumor. Epigenetic mechanisms associated with RNA modification in controlling CD8+ T cell response remain poorly understood. Here, by T cell-specific deletion of fat mass and obesity-associated protein (FTO), a critical N6-methyladenosine (m6A) demethylase, we revealed that FTO was indispensable for sufficient CD8+ T cell immune response and protective function. FTO ablation led to considerable cell death in activated CD8+ T cells, which was attributed to apoptosis. MeRIP-seq analysis identified the upregulated m6A modification on Fas mRNA in FTO deficient CD8+ T cells. Loss of FTO promoted Fas expression via enhancing the Fas mRNA stability dependent on m6A reader IGF2BP3. Mutation of the Fas m6A sites or knockdown IGF2BP3 could rescue the upregulated Fas expression and cell apoptosis caused by FTO ablation in CD8+ T cells. Our findings defined a novel epigenetic regulatory mechanism of FTO-mediated m6A modification in supporting CD8+ T cell immune responses, providing new insights into understanding the post-transcriptional regulation in CD8+ T cell immunological functions.

overall_design: WT and FTO KO CD8+ T cells (OT-1+) transferred into recipient mice before infection with LM-OVA for 5 days. WT and FTO KO CD8+ T cells (OT-1+) transferred into recipient mice before infection with LM-OVA for 5 days. WT and KO CD8+ T cells were isolated for  RNA-seq and MeRIP-seq. m6A immunoprecipitation and sequencing were performed at the LC Sciences, LLC on an Illumina Novaseq™ 6000 platform with 2×150bp paired-end sequencing (PE150).

first: Lina

last: Sun

first: Tianzhe

first: Yanhong

last: Su

first: Baojun


title: Single-cell transcriptomics and translatomics dual-omics analysis reveals the potential mechanism of HFD-induced maternal RNA degradation abnormalities

city: Zhengzhou

first: Lin-Li

last: Yang

state: Henan

address: No. 1, Jianshe East Road, Erqi District

department: department of obstetrics and gynecology

institute: The First Affiliated Hospital of Zhengzhou University

summary: This study explores the impact of high-fat diet (HFD)-induced obesity on maternal RNA degradation and its implications for oocyte quality and development in mice, using a novel transcriptome and translatome sequencing (T&T-seq) strategy. By combining RiboLace for translatome profiling and Smart-seq for transcriptome analysis, the research investigates how HFD disrupts RNA degradation pathways during oocyte maturation, particularly from the germinal vesicle (GV) to metaphase II (MII) stages. The findings reveal that HFD impairs the degradation of key transcripts such as BTG4 and CNOT7, and alters the translation efficiency of meiotic regulators, which are crucial for proper meiotic progression. This study provides new insights into how maternal dietary factors influence oocyte quality at the molecular level, with potential implications for fertility and embryonic development.

overall_design: We employed T&T-seq (translatome and transcriptome sequencing) to comprehensively analyze gene expression profiles in GV oocytes and MII oocytes from both high-fat diet (HFD) and normal diet (ND) mice.To achieve absolute quantification of transcript abundance, we performed spike-in calibrated single-cell transcriptomics on GV and MII oocytes from both dietary groups.Furthermore, to investigate the functional role of translation initiation in oocyte gene regulation, we conducted EIF2B1 knockdown in GV-stage oocytes using siRNA-mediated gene silencing. Both EIF2B1-KD oocytes and negative control (NC) oocytes were subjected to spike-in incorporated single-cell transcriptomic analysis to precisely quantify transcriptome changes resulting from translational perturbation.

first: Linli

first: Yingying

last: Chen

first: Huan

last: Yao

last: Lei

first: Xianlan

last: Zhao

first: Qingling

first: Yingpu


title: P301S Mutant Tau-Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3β Inhibitors with Anti-Neurodegenerative Efficacy

city: ShanTou

first: juan

middle: juan

last: Luo

address: Xinling street 22

institute: ShanTou University

summary: Spatial transcriptome sequencing technology has provided high-resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease-like pathological changes in zebrafish, providing a unique insight into the pathogenesis of tau pathology-mediated cell-cell interactions in AD.

overall_design: This study utilized four Danio rerio lines: wild-type (WT) and three transgenic lines (AD3, AD4, AD5) expressing human Tau protein with the P301S mutation (Tau-P301S). All transgenic lines were generated via stable integration of the human TAU P301S transgene.

first: Juanjuan


title: A second genetic screen for gurken mRNA mislocalisation reveals novel phenotypes of the piRNA pathway mutants in Drosophila [RNA-seq]

overall_design: The study characterises the phenotype of the mutations affecting gurken mRNA localisation in Drosophila oocytes. Of those, we focused on the piRNA pathway mutations and examined their impacts on transposon mRNA expression in the ovaries. We generated poly-A selected RNA sequencing libraries from freshly dissected ovaries and sequenced them by paired-end 150bp mode on Illumina Novaseq.

first: Azusa


title: NAT10-mediated β-hydroxybutyrylation Facilitates DNA Replication, Reduces Replication Stress and Genomic Instability

city: Chongqing

first: Yaqi

last: Sui

state: --- Select One ---

address: Chongqing

institute: Chongqing University

summary: Accurate DNA replication is essential for genome integrity, with dysregulated replication dynamics, replication stress and genomic instability-hallmarks of cancer and aging. Here, we identify NAT10-mediated β-hydroxybutyrylation (Kbhb) of histones that safeguards replication fork progression, alleviates replication stress, and preserves genomic stability. DNA fiber analyses show β-hydroxybutyrate (BHB) treatment enhances replication efficiency while maintaining fork symmetry, effects abolished by NAT10 depletion or inhibition. BrdU/EdU labeling, FACS analyses reveal that NAT10-mediated Kbhb accelerates replication fork velocity and shortens S-phase duration. LC-MS/MS profiling shows no significant changes in origin firing following BHB treatment. Mechanistically, NAT10-mediated Kbhb modulates chromatin association, thereby modulating chromatin accessibility to establish a replication-permissive environment. This epigenetic remodeling mitigates replication stress markers and genomic instability. Conserved effects in transformed and primary cell models position NAT10 as a metabolic-epigenetic nexus linking nutrient signaling to replication fidelity. Our findings suggest targeting Kbhb signaling as a potential therapeutic strategy against replication stress-associated pathologies.

overall_design: ATAC-seq     Sample A siCtrl Sample B siCtrl+BHB Sample C siNAT10 Sample D siNAT10+BHB

first: Rui

last: Zhou

first: Kun

last: Liu

first: Yonghong

last: Wang

first: Yingming

first: Yanchang

last: Li

first: Wenhui

last: zhao


title: The gut microbiome enhances breast cancer immunotherapy following bariatric surgery

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

institute: UTHSC

summary: Bariatric surgery is associated with improved breast cancer (BC) outcomes, including greater immunotherapy effectiveness in a pre-clinical BC model. A potential mechanism of bariatric surgery-associated protection is through the gut microbiota. Here, we demonstrate the dependency of improved immunotherapy response on the post-bariatric surgery gut microbiome via fecal microbial transplant. Cecal contents were isolated from either obese controls that received sham surgery or formerly obese mice following bariatric surgery-induced weight loss and transferred by FMT to lean recipients. Response to αPD-1 immunotherapy was significantly improved following FMT from formerly obese bariatric-surgery treated mice. Microbes can impact tumor burden through microbially derived metabolites produced or modified by gut microbiota including branched chain amino acids (BCAA). Circulating BCAA correlated significantly with NK T cell content in the tumor microenvironment in both donor mice after bariatric surgery and in FMT recipients of donor cecal content after bariatric surgery compared to obese sham controls. Findings implicate a role of microbially-derived BCAA in activating anti-tumor immunity that is dependent upon bariatric surgery. Importantly, when stool from a patient who exhibited 25% weight loss post-bariatric surgery was transplanted into recipient mice and compared to the patient’s pre-bariatric surgery stool transplant. Patient samples post bariatric surgery significantly reduced tumor burden by 2.4-fold and immunotherapy effectiveness was doubled. Taken together, findings suggest that reinvigorating anti-tumor immunity may be dependent upon microbially derived metabolites such as BCAA.

overall_design: RNA -Seq data from bulk tumor (orthotopically injected with E0771 Mouse Triple Negative Breast Cancer Cells) in specific pathogen-free C57BL/6J mice, treated with obese fecal microbial transplant (with αPD-1 immune checkpoint blockade N = 4 or IgG2a isotype control N = 6) or vertical sleeve gastrectomy fecal microbial transplant (with αPD-1 immune checkpoint blockade N = 4 or IgG2a isotype control N = 5), grown for 17 days, excised, and snap frozen.

first: Margaret

last: Bohm

first: Sydney

middle: C

last: Joseph

first: Laura

middle: M

last: Sipe

first: Minjeong

last: Kim

first: Cameron

middle: T

last: Leathem

first: Tahliyah

last: Mims

first: Nathaniel

middle: B

last: Willis

first: Joel

last: Elasy

first: Ubaid

last: Tanveer

first: Emily

last: Grey

first: Madeline

last: Pye

first: Zeid

last: Mustafa

first: Barbara

last: Harper

first: Logan

middle: G

last: McGrath

first: Deidre

last: Daria

first: Jelissa

last: Myers

first: Brenda

last: LandvoigtSchmitt

first: Patricia

middle: P

last: Newman

first: Brandt

middle: D

last: Pence

first: Marie

last: VanderMerwe

first: Matthew

last: Davis

first: Joseph

last: Pierre


title: Excitatory Neuron-Derived Interleukin-34 Controls Cortical Developmental Microglia Function

city: Durham

first: Benjamin

last: Devlin

state: North Carolina

address: 210 Research Drive

department: Psychology and Neuroscience

institute: Duke University

summary: Neuron-microglia interactions dictate the development of neuronal circuits in the brain. However, the factors that support and broadly regulate these processes across developmental stages are largely unknown. Here, we find that IL34, a neuron-derived cytokine, is upregulated in development and plays a critical role in supporting and maintaining neuroprotective, mature microglia in the anterior cingulate cortex (ACC) of mice. We show that IL34 mRNA and protein is upregulated in neurons in the second week of postnatal life and that this increase coincides with increases in microglia number and expression of mature, homeostatic markers, e.g., TMEM119. We also found that IL34 mRNA is higher in excitatory (compared to inhibitory) neurons. Global genetic KO of IL34 reduced microglia numbers and prevented the functional maturation of microglia, and excitatory-neuron specific KO of IL34 similarly impacted microglia and increased aberrant microglial phagocytosis of excitatory thalamocortical synapses in the ACC. Acute, low dose blocking of IL34 at postnatal day (P)15 in mice decreased microglial TMEM119 protein and also increased microglial phagocytosis of excitatory thalamocortical synapses during an inappropriate time in development. In contrast, viral overexpression of IL34 early in life (P1-P8) caused early maturation of microglia and prevented microglial phagocytosis of thalamocortical synapses during the appropriate neurodevelopmental refinement window. Taken together, these findings establish IL34 as a key regulator of neuron microglia crosstalk in postnatal brain development, controlling both microglial maturation and synapse engulfment.

overall_design: IL34 Het and KO mice, as well as WT mice treated with blocking antibodies against IL34 or control, we saline perfused and their forebrain harvested for sequencing. One hemisphere was processed for bulk RNASeq and the other hemisphere went through a CD11b+ magentic bead based isolation method to isolate microglia before sequencing.

first: Staci

last: Bilbo


title: Defective autophagy in CD4 T cells drives liver fibrosis via type 3 inflammation

city: CLICHY

first: Camille

last: PIGNOLET

address: 100 Bd du Général Leclerc

department: CRI U1149

country: France

institute: INSERM

summary: Abstract: Conventional CD4 T cells represent a major source of inflammatory mediators that drive progression of chronic liver disease to fibrosis and to end-stage cirrhosis. Identification of T cell pathways that limits the inflammatory response could thus have therapeutic relevance. Here we show, using both human samples and mouse models, that autophagy is deficient in CD4 T cells from patients with advanced fibrosis, and that loss of autophagy following genomic deletion of ATG5 in T cells is associated with the emergence of pathogenic IL-17A+IFN-g+ Th17 T cells that drive liver fibrosis in mice. Mechanistically, liver CD4 T cells lacking autophagy display a Th17 glycolytic phenotype associated with enhanced type 3 cytokine (i.e. IL-17A and GM-CSF) release, shifting hepatic myofibroblasts, hepatocytes and macrophages toward a proinflammatory phenotype. We also show that autophagy can be rescued in CD4 T cells from patients with extensive liver fibrosis, leading to decreased frequency of pathogenic Th17 cells and reduced GM-CSF levels; in addition, limited fibrosis is observed in mice in which Rubicon, a negative regulator of autophagy, is deleted specifically in their T cells. Our findings thus implicate autophagy in CD4 T cells as a key therapeutic target to control inflammation-driven fibrosis during chronic liver injury.

overall_design: Experimental design:  RNA-seq profiling of liver autophagy-deficient (ATG5TLymph-/-) or wildtype (ATG5fl/fl) CD4 T cells isolated from mice with liver fibrosis. Mice were chronically injected with CCl4 for 5 weeks and liver CD4 T cells were sorted using BD FACSMelodyTM Cell Sorter.

first: Lotersztajn

last: Sophie

first: AlSayegh

last: Rola

first: Nicolle

last: Rémy

first: Pignolet

last: Camille


title: Hepatic miR-93 promotes the pathogenesis of metabolic dysfunction-associated steatotic liver disease by suppressing SIRT1

city: Eonyang-eup, Ulju-gun

first: Bukyung

last: Baik

state: Ulsan

department: Department of Biological Science

country: South Korea

institute: Ulsan National Institute of Science and Technology

summary: The molecular mechanisms underlying the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD) remain largely unclear. Emerging evidence suggests that microRNAs (miRNAs) play a critical role in transcriptional regulation by targeting genes involved in MASLD and other metabolic disorders, this study aims to elucidate the role of miR-93 in lipid metabolism and its impact on MASLD progression.

overall_design: Analysis of differential expression (DE) caused by miR-93 Knockout (KO) compared to the wild-type (WT).

first: Yo Han

last: Lee

first: Jang Hyun

last: Choi

first: Dougu

last: Nam


title: Fructose activates a stress response shared by methylglyoxal and hydrogen peroxide in streptococcus mutans

city: Gainesville

first: Alejandro

last: Riveros Walker

state: Fl

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: Fructose catabolism by Streptococcus mutans is initiated by three PTS transporters yielding either fructose-1-phoshate (F-1-P) or fructose-6-phosphate (F-6-P). Deletion of one such F-1-P-generating PTS, fruI, has been shown to reduce the cariogenicity of S. mutans in rats fed a high-sucrose diet. Moreover, a recent study linked fructose metabolism in S. mutans to a reactive electrophile species (RES) methylglyoxal. Here, we conducted a comparative transcriptomic analysis of exponentially grown S. mutans shocked with 50 mM fructose, 50 mM glucose, 5 mM methylglyoxal, or 0.5 mM hydrogen peroxide (H2O2). The results revealed a striking overlap between the fructose and methylglyoxal transcriptomes, totaling 176 genes, 61 of which were also shared with the H2O2 transcriptome. This core of genes encompassed many of the same pathways affected by exposure to low pH or zinc intoxication. Consistent with these findings, fructose negatively impacted metal homeostasis of a mutant deficient in a zinc exporter and the growth of a mutant of the major oxidative stress regulator SpxA1. We further demonstrated the induction of the superoxide dismutase (sodA) and the fruRKI operon by different levels of fructose. Finally, fructose metabolism lowered culture pH at a faster pace, allowed better survival under acidic and nutrient-depleted conditions, and enhanced the competitiveness of S. mutans against Streptococcus sanguinis, although a moderated level of F-1-P might further boost some of these benefits. In conclusion, fructose metabolism is integrated into the stress core of S. mutans and regulates critical functions required for survival in both the oral cavity and during systemic infections.

overall_design: 3 replicates for Glucose control, Glucose 50 mM, Fructose 50 mM, Methylglyoxal 5 mM


title: Morphogenic accommodations for unidirectional airflow in the chicken lung

city: Cincinnati

first: Guolun

last: Wang

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: Unidirectional airflow in the avian lung enables gas exchange during both inhalation and exhalation. Stereo-seq spatial transcriptomics reveal a third, chicken-specific alveolar cell type expressing KRT14, hereby named luminal cells. Luminal, alveolar type 2, and alveolar type 1 cells sequentially occupy concentric zones radiating from the parabronchial lumen. Our study explores the evolutionary space of lung diversification and lays the foundation for functional analysis of species-specific genetic determinants.

overall_design: E20 chicken lungs were harvested, and flash frozen in Tissue-Tek OCT medium in ethanol/dry ice bath, and then stored at -80°C until used for a Stereo-seq experiment. Cryo-sections were cut at the thickness of 10 μm and mounted on Stereo-seq permeabilization chips.

first: Kamryn

last: Gerner-Mauro

first: Lisandra

last: Vila Ellis

first: Jichao

last: Chen


title: Profiling immune cells in the mammary gland during pregnancy and lactation

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: The mammary gland undergoes profound structural and cellular changes during pregnancy and lactation, yet the changes in immunocyte populations are incompletely understood. We identified changes in all immunocyte populations including B cells, NK cells, myeloid cells, and T cells, specifically increases in CD4+ and CD8+ T effector cells in late pregnancy and lactation that are partly dependent on microbial signals.

overall_design: Single-cell RNA seq of CD45+ immune cells from the mammary gland during different stages of pregnancy and lactation (nulliparous, gestation, lactation, involution, and regression). Includes Balb/c and germ-free mice to analyze changes in different backgrounds.

first: Deepshika

last: Ramanan

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Galectin3: a novel biomarker of glycogen storage disease type III

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

summary: Glycogen storage disease type III (GSDIII) is a rare genetic disease caused by mutations in the AGL gene, resulting in glycogen debranching enzyme (GDE) deficiency. There is currently no cure. Among various symptoms, skeletal muscle impairment represents a key target for the development of therapies. Identifying reliable biomarkers is crucial for evaluating new therapies, yet muscle-specific biomarkers for GSDIII are lacking. In this study, we generated GSDIII skeletal muscle cells derived from human-induced pluripotent stem cells that recapitulate the glycogen accumulation phenotype. A comparative gene expression analysis was carried out using RNA sequencing to identify novel biomarkers. Our results reports a significant overexpression of galectin-3 in both human and mouse models and patient biopsies, and a significant decrease in mice treated by an AAV gene therapy. Together, our results propose galectin-3 as a biomarker to assess therapeutic efficacy and GSDIII pathological monitoring in the muscle.

overall_design: we performed a bulk RNA sequencing of the 3 CTRLs and the 4 GSDIIIPatients generated skMt. (Quantseq)

first: Lucille

last: Rossiaud

first: Quentin

last: Miagoux

first: Manon

last: Benabidès

first: Océane

last: Reiss

first: Louisa

last: Jauze

first: Margot

last: Jarrige

first: Pascal

last: Laforêt

first: Edoardo

last: Malfatti

first: Giuseppe

last: Ronzitti

first: Xavier

last: Nissan

first: Lucile

last: Hoch


title: Identification of a novel forkhead transcription factor MtFKH1 for cellulase and xylanase gene expression in Myceliophthora thermophila (ATCC 42464)

city: Auckland

first: Yapeng

last: Lai

address: 55 Wellesley Street East,  Auckland Central

department: School of Science

country: New Zealand

institute: Auckland University of Technology

summary: Myceliophthora thermophila, a thermophilic fungus, has been utilized to produce industrially important enzymes in biorefineries. In filamentous fungi, the mechanisms underlying cellulase and xylanase expression have been explored, which uncovered the complex networks controlled by numerous transcription factors (TFs). However, the TFs regulating cellulase and xylanase gene expression and production remain unclear in M. thermophila. Here, we identified and characterized a novel cellulase and xylanase regulator MtFKH1 (MYCTH_2307931) in M. thermophila through comparative transcriptomic and genetic analyses. Comparative transcriptome analyses of M. thermophila grown on Avicel and glucose screened eight potential transcription factor encoding genes and five of them were successfully deleted by newly developed CRISPR/Cas9 system, which caused the identification of a forkhead TF MtFKH1. The disruption of Mtfkh1 remarkably elevated cellulolytic and xylanolytic enzyme activities, whereas the overexpression of Mtfkh1 led to considerable decrease in cellulase and xylanase production in M. thermophila cultivated on Avicel. Loss of Mtfkh1 also exhibited an impairment in sporulation but normal mycelia growth compared with WT. Real-time quantitative reverse transcription PCR (RT-qPCR) showed that MtFKH1 regulated the expression of essential cellulase and xylanase genes, and electrophoretic mobility shift assays (EMSAs) demonstrated that MtFKH1 could specifically bound to the promoter regions of genes encoding β-glucosidase (bgl1/MYCTH_66804), cellobiohydrolase (cbh1/MYCTH_109566), and xylanase (xyn1/MYCTH_112050). Further DNase I footprinting analysis identified binding motif of MtFKH1 in the upstream region of Mtbgl1, which exhibited strongest binding affinity. Finally, transcriptomic profiling and Gene Ontology (GO) enrichment analyses of Mtfkh1 deletion mutant revealed that the regulon of MtFKH1 were significantly prevalent in hydrolase activity (acting on glycosyl bonds), polysaccharide binding, and carbohydrate metabolic process functional categories. These findings enlarge our knowledge of how forkhead transcription factor regulate lignocellulose degradation and provide a novel target for engineering of fungal cell factories with the hyperproduction of cellulases and xylanases.

sample_organism: Thermothelomyces thermophilus ATCC 42464

overall_design: The transcription factor MtFKH1 regulates cellulase and xylanase production in M. thermophila. To comprehensively clarify the regulation of MtFKH1, we conducted transcriptional profiling analysis of the WT and ΔMtfkh1 strains cultured on Avicel for 48 h after transferring from glucose.

first: Juan

last: Wang

first: Gang

last: Liu

first: Donnabella

last: Lacap-Bugler


title: Cathepsin X is a conserved cell death protein involved in algal response to environmental stress

city: Rehovot

first: Avia

last: Mizrachi

address: 234 Herzl St.

department: Plant and Environmental Sciences

country: Israel

institute: Weizmann Institute of Science

summary: Phytoplankton play a crucial role in global primary production and can form vast blooms in aquatic ecosystems. Bloom demise and the rapid turnover of phytoplankton are suggested to involve programmed cell death (PCD) induced by diverse environmental stressors. However, fundamental knowledge of the PCD molecular components in algae and protists in general remains elusive. Previously, we revealed that early oxidation in the chloroplast predicted subsequent cell death or survival in isogenic subpopulations that emerged in response to H2O2 in the diatom Phaeodactylum tricornutum. Here, we performed transcriptome analysis of sorted sensitive oxidized cells and resilient reduced cells, to discover genes linked to their contrasting fates. By cross-comparison with a large-scale mutant screen in the green alga Chlamydomonas reinhardtii, we identified functionally relevant conserved PCD gene candidates, including the cysteine protease cathepsin X/Z (CPX). CPX mutants in P. tricornutum CPX1 and C. reinhardtii CEP12 both exhibited profound resilience to oxidative stress, supporting a conserved function in algal PCD. P. tricornutum cpx1 mutants, generated using CRISPR-Cas9, also exhibited resilience to the toxic diatom-derived infochemical cyanogen bromide. Phylogenetic and predictive structural analyses show that CPX is highly conserved in eukaryotes, and algae of the green and red lineages exhibit strong structural similarity to human cathepsin CTSZ. CPX is expressed by diverse algae across the oceans and during toxic Pseudo-nitzschia blooms, supporting its ecological importance. Elucidating PCD components in algae sheds light on the evolutionary origin of PCD in unicellular organisms, and on the cellular strategies employed by the population to cope with stressful conditions.

overall_design: To investigate the genes involved in cell fate determination in the diatom P. tricornutum, we performed transcriptome analysis using the bulk MARS-seq method of sorted sensitive and resilient subpopulations. P. tricornutum cells expressing chloroplast-targeted roGFP were treated with 80 µM H2O2, and 2.7 h later sensitive oxidized cells and resilient reduced cells were FACS sorted for transcriptome analysis based on roGFP oxidation as well as control untreated cells.

first: Assaf

last: Vardi


title: Molecular characterisation of ameloblastoma with RNA-sequencing

city: Puerto Montt

first: Constanza

last: Marin Marquez

address: Lago Panguipulli 1390

department: Oral Pathology

country: Chile

institute: Universidad San Sebastián

summary: The aim of the study was to characterise the transcriptome profile of ameloblastoma in order to identify relevant genes involved in its pathogenesis by carrying out high-throughput gene expression.

overall_design: Total RNA from 12 fresh tumour samples of ameloblastomas were RNA-sequenced on Illumina NovaSeq 6000 S4, paired-end 150 bp. The key findings were verified by quantitative real-time PCR (QPCR) and immunohistochemistry. The experiment type was an expression profiling by RNA-sequencing.

last: Marin

first: Keith

last: Hunter

first: Janine

last: Kirby

first: Akinyele

middle: O

last: Adisa


title: Surfaceome analysis of extracellular vesicles from senescent cells uncovers uptake repressor DPP4

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Senescent cells are beneficial for repairing acute tissue damage, but they are harmful when they accumulate in tissues, as occurs with advancing age.  Senescence-associated extracellular vesicles (S-EVs) can mediate cell-to-cell communication and export intracellular content to the microenvironment of aging tissues.  Here, we studied the uptake of EVs from senescent cells (S-EVs) relative to proliferating cells (P-EVs).  Interestingly, P-EVs were readily taken up by other proliferating cells (fibroblasts and cervical cancer cells) while S-EVs were not; by contrast, macrophages selectively engulfed all EVs (P-EVs, S-EVs).  We thus investigated the surface proteome (surfaceome) of P-EVs relative to S-EVs derived from cells that had reached senescence via replicative exhaustion, exposure to ionizing radiation, or treatment with etoposide.  We discovered that relative to P-EVs, S-EVs from all senescence models were enriched in proteins DPP4, ANXA1, ANXA6, S10AB, AT1A1, and EPHB2.  Among them, DPP4 was found to dictate selective uptake by proliferating cells, as ectopic overexpression of DPP4 in HeLa cells rendered DPP-expressing EVs that were no longer taken up by other proliferating cells.  We propose that DPP4 on the surface of S-EVs makes these EVs refractory to internalization by proliferating cells, advancing our knowledge of the impact of senescent cells in aging-associated processes.

overall_design: We studied the uptake of EVs from senescent cells (S-EVs) relative to proliferating cells (P-EVs) and thus, we investigated the surface proteome (surfaceome) of P-EVs relative to S-EVs derived from cells that had reached senescence via replicative exhaustion, exposure to ionizing radiation, or treatment with etoposide.

first: Qiong

last: Meng

first: Chen

last: Chen

last: Yang

first: Olesia

last: Gololobova

first: Changyou

last: Shi

first: Martina

last: Rossi

first: Jennifer

middle: L

last: Martindale

first: Michael

last: Delannoy

first: Krystyna

last: Mazan-Mamczarz

first: Chang

last: Shin

first: Kenneth

last: Witwer

first: Arya

last: Biragyn

first: Payel

last: Sen

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe


title: The TET2 methylcytosine dioxygenase regulates early and late transitions in exhausted CD8+ T-cell differentiation

city: Philadelphia

first: Gregory

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Epigenetic reprogramming of CAR T-cells by targeting TET2, a methylcytosine deoxygenase that mediates active DNA demethylation, has shown therapeutic potential; however, the role of TET2 in TEX development is unclear. In both CAR T-cell exhaustion models in vitro and chronic LCMV infection in vivo, TET2 drove the conversion from memory-like, self-renewing TEX progenitors towards effector (TEFF)-like and terminally differentiated TEX. TET2-deficient terminally differentiated TEX retained aspects of TEX progenitor biology, including decreased expression of the transcription factor TOX, suggesting that TET2 is required for terminal exhaustion.

overall_design: Mice with chronic LCMV infection received WT or TET2KO P14 T cells. Naive and D15 T cells were isolated; D15 T cells were assessed in bulk, as well as in sorted subsets of Ly108+ and Ly108-. Bulk RNA-Seq and ATAC Seq were performed. Separately, human CAR T cells targeting CD19 were co-cultured with irradiated K562-CD19+ cells at a 1:1 ratio for 5 days, with fresh R10 media and newly irradiated K562 cells for 4-5 additional stimulations. Bulk RNA-Seq was performed.

first: Alexander

middle: J

last: Dimitri

first: Amy

middle: E

last: Baxter

first: Martha

last: Jordan

first: Joseph

last: Fraietta


title: MapID-based Quantitative Mapping of Chemical Modifications and Expression of Human Transfer RNA

city: Chestnut Hill

first: Huiqing

last: Zhou

state: Massachusetts

address: 2609 Beacon St.

department: Chemistry

institute: Boston College

summary: Transfer RNAs (tRNAs) carry abundant chemical modifications, and growing evidence shows dysregulation of chemical modifications on human tRNAs causes an expanding number of diseases including cancers, diabetes, neurological diseases, and mitochondrial disorders. Sensitive and robust detection and quantification of chemical modifications are critical to discovering functionally relevant and regulatory tRNA chemical modifications. Here we report a method “MapID-tRNA-seq” deploying a recently evolved processive reverse transcriptase to map modifications in human tRNAs and MapID-based data processing pipeline for de novo modification identification and tRNA expression quantification. MapIDs refer to consolidated sequences of human tRNA genes with reduced redundancy and annotations of genetic variation sites. MapID-based data processing largely improved the accuracy of modification detection and expression quantification by tRNA-seq, which otherwise got compromised from reads mis- and multi-alignment to the highly redundant human tRNA genome. “MapID-tRNA-seq” robustly detected the occurrence and stoichiometries of N1-methyladenosines, providing insights into the function and biosynthesis of N1-methyladenosine in human tRNAs. Our data revealed unique signatures of the evolved reverse transcriptase against N1-methyladenosine and four other types of chemical modifications. “MapID-tRNA-seq” provides a generalizable platform for de novo identification and quantitation of chemical modifications in human tRNAs to elucidate their functions in biology and diseases.

overall_design:
Mapping of chemical modifications in tRNAs extracted from HEK-293T cells.

Mapping of chemical modifications in tRNAs extracted from MCF10A, MCF7 and MDA-MB-231 cells

first: Mtichel

last: Tepe

first: Yitan

last: Chen

first: Allison

last: Carso


title: Human giant GTPase GVIN1 forms an antimicrobial coatomer around the intracellular bacterial pathogen Burkholderia thailandensis

first: Jörn

last: Coers

state: NC

address: 3 Genome Ct

summary: Several human pathogens exploit the kinetic forces generated by polymerizing actin to power their intracellular motility. Human cell-autonomous immune responses activated by the cytokine interferon-gamma (IFNγ) interfere with such microbial actin-based motility, yet the underlying molecular mechanisms are poorly defined. Here, we identify the IFNγ-inducible human giant GTPases GVIN1 as a novel host defense protein that blocks the bacterial pathogen Burkholderia thailandensis from high-jacking the host's actin polymerization machinery. We found that GVIN1 proteins form a coatomer around cytosolic bacteria and prevent Burkholderia from establishing force-generating actin comet tails. Coatomers formed by a second IFNγ-inducible GTPase, human guanylate binding protein 1 (GBP1), constitute a GVIN1-independent but mechanistically related anti-motility pathway. We show that coating with either GVIN1 or GBP1 displaces the Burkholderia outer membrane protein BimA, an actin nucleator that is essential for actin tail formation. Both GVIN1 and GBP1 coatomers require additional IFNγ-inducible co-factors to disrupt the membrane localization of BimA, demonstrating the existence of two parallel-acting IFNγ-inducible defense modules that evolved to target a virulence trait critical for the pathogenesis of numerous bacterial infectious agents.

overall_design: RNA-seq profiling of A549, HeLa, T24, THP1, and U937 cell lines in standard media or treated with 100 units per milliliter interferon-gamma (IFNg) for 6 hours.


title: Tracheal aspirate bulk and single cell RNA sequencing from patients with ARDS

city: San Francisco

first: Aartik

last: Sarma

state: CA

address: 513 Parnassus Ave

institute: University of California, San Francisco

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

overall_design: Refer to individual Series


title: Identification of a novel forkhead transcription factor MtFKH1 for cellulase and xylanase gene expression in Myceliophthora thermophila ATCC 42464

first: Yapeng

last: Lai

platform_organism: Thermothelomyces thermophilus ATCC 42464

overall_design: Transcription factors (TFs) play a pivotal regulatory role in fugal lignocellulolytic enzymes synthesis. We speculated that TFs may be responsible for significantly improved cellulase and xylanase activities of M. thermophila that observed under Avicel culture compared to glucose condition. Therefore, the transcriptomes of M. thermophila wild type (WT) cultured on Avicel (A_RNA) and Glucose (G_RNA) at 36 hours were screened for potential regulators of cellulolytic and xylanolytic genes expression. All RNA sequencing data were generated from three biological replicates.

first: Juan

last: Wang

first: Gang

last: Liu

first: Donnabella

last: Lacap-Bugler


title: Tracheal aspirate bulk RNA sequencing from patients with ARDS [bulk RNA-seq]

summary: Trachel aspirates samples were collected from an observational cohort of mechanically ventilated patients to compare respiratory tract gene expression in previous-descried ARDS molecular phenotypes. Patient charts were reviewed by two physicians and patients with ARDS were identified using the Berlin Definition. Control subjects were mechanically ventilated for neurologic indications, were not immunosuppressed, and had no evidence of pulmonary disease. ARDS molecular phenotypes were defined using a previously-described 3-variable classifier (Sinha 2020)

overall_design:
Tracheal aspirates were collected from mechnically ventilated patients admitted to the intensive care units.
***Please note that the UCSF IRB has restricted sharing the raw data because some of the samples were collected under a waiver of consent and could in theory be identifiable. Therefore, raw data is not provided***

first: Charles

middle: R

last: Langelier

first: Carolyn

last: Calfee


title: Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles, affecting ocular and neurobehavioral function

city: Corvallis

first: Dante

last: Perone

state: Oregon

institute: Oregon State University

summary: Cytochrome P450 1B1 (CYP1B1) is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma (PCG), however CYP1B1’s role in PCG development and related eye disorders is poorly understood. To explore CYP1B1’s role an in vivo zebrafish (Danio rerio) model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line (wh5) was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays, untargeted metabolomics, and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid, steroid, amino acid, and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi-omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays, however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs.

overall_design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line (wh5) was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex, genotype (WT or KO (wh5)), and organ for a total of 40 samples.

first: Andrew

last: Annalora

first: Jared

middle: V

last: Goldstone

middle: N

last: Dickey

first: Matthew

last: Salanga

first: Rene

last: Francolini

first: Fred

last: Wright

first: Craig

last: Marcus

first: Robyn

last: Tanguay

first: Manuel

last: Garcia-Jaramillo


title: Genome-Wide Analysis Reveals the Roles of lncRNA in Se accumulation and detoxification in alfalfa (Medicago sativa L.)

city: China

first: Meiling

last: Xiang

address: 100 Science Avenue

institute: Zhengzhou university

summary: Medicago sativa L. is the most extensively cultivated and high biomass forage. Selenium is an essential microscale mineral for humans and animals and is a beneficial element for plants, which could increase yields under low concentration and have a poisoning effect under high concentration. LncRNA is involved in diverse biological processes such as flowering, photomorphogenesis, vernalization and stress response in the plants. To study the possible role of lncRNAs in Se accumulation and detoxification underlying alfalfa, we identified and analyzed lncRNAs in alfalfa leaves under 0 mg L-1, 100 mg L-1, 500 mg L-1 based on the degradome deep sequencing. We identified a total of 64,684 novel lncRNAs, from which 3155 were differentially expressed lncRNAs (DELs). The expression patterns of some lncRNAs can be significantly differentially expressed between high and low concentrations. The results of GO and KEGG analysis suggested that sulfate transporter and ABC transporter might be a contributor to Se accumulation in alfalfa. The jasmonic acid (JA) promoted by lipoxygenase and allene oxide synthase may play an important role in Se resistance. The high expression of some key genes of selenocompound metabolism may be beneficial to remove excess Se. The phenylpropanoid, flavonoid, isoflavonoid, and anthocyanidin biosynthesis and autophagy may alleviate the Se toxicity by scavenging reactive oxygen. The expression patterns of nine lncRNAs and their protein-coding genes were validated by qRT-PCR. The same expression pattern was observed between most lncRNAs and their target genes. This study has excavated potential lncRNAs and will give new insight and rich genetic resources to Se-enriched breeding.

overall_design: Research of 3 different selenite concentration in alfalfa leaf

first: Qingdong

first: Huafeng

last: Hu


title: Characterization of 5-hmC DNA Methylation Patterns in the Hippocampus of an Experimental Model of Epilepsy

city: Birmingham

first: Farah

last: Lubin

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: University of Alabama at Birmingham

type: Methylation profiling by high throughput sequencing

summary: Temporal lobe epilepsy is one of the most common refractory epilepsies in the world. Epilepsy progression is controlled through the expression of epilepsy permissive genes, ultimately resulting in a hyperexcitable network and spontaneous seizures. DNA methylation has been explored as a potential epigenetic regulatory mechanism of gene expression in epilepsy, however, the role of 5-hydroxymethylcytosine (5-hmC) has been underexplored to date. 5-hmC is a stable epigenetic mark most abundantly expressed in the brain. In this study, we show that 5-hmC but not 5-methylcytosine (5-mC) is lost in temporal lobe epilepsy. Using 5-hmC meDIP-sequencing, we characterized epileptic 5-hmC distribution in the rat kainic acid model of temporal lobe epilepsy. We identified the correlation of 5-hmC loss and gain with epilepsy-associated gene ontology pathways and implicate the potential involvement of multiple cell types with 5-hmC regulation of temporal lobe epilepsy. Overall, we show that 5-hmC has the potential to be a crucial regulator of epilepsy and epileptic gene expression and are the first to characterize the genomic distribution of 5-hmC in a model of epilepsy.

overall_design: Using hmeDIP-sequencing, we characterized 5-hmC distribution in the hippocampus of rat kainic acid model of temporal lobe epilepsy.

first: Rudhab

last: Bahabry

first: Rebecca

last: Hauser

first: Richard

last: Sanchez

first: Silvienne

last: Sint Jago

first: Lara

last: Ianov

first: Remy

last: Stuckey

first: R

last: Parrish

first: Lawrence

last: Ver Hoef


title: RNA-seq of ST2+ and ST2- Tregs in the omentum from naïve and tumor-bearing mice

first: Mingyong

last: Liu

address: SHEL 531, 1825 University Blvd

department: Clinical Immunology and Rheumatology

summary: To determine how the transcriptomes of ST2+ and ST2- Tregs in the omentum are different from each other, we purified these two subsets from naïve and tumor-bearing mice and performed RNAseq analysis.

overall_design: Transcriptomes of ST2+ and ST2- Tregs from the tumor-free or tumor-bearing omentum

first: Troy

last: Randall

first: Selene

last: Meza-Perez


title: Tetrahydrobenzimidazole TMQ0153 Targets OPA1 and Restores Drug Sensitivity in AML via ROS-Induced Mitochondrial Metabolic Reprogramming

status: Public on Apr 13 2025

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

institute: Seoul National University

summary: Abstract Background: Acute myeloid leukemia (AML) is a highly aggressive cancer with a 5-year survival rate of less than 35%. It is characterized by significant drug resistance and abnormal energy metabolism. Mitochondrial dynamics and metabolism are crucial for AML cell survival. The mitochondrial fusion protein optic atrophy (OPA)1 is upregulated in AML patients with adverse mutations and correlates with poor prognosis. Method: This study investigated targeting OPA1 with TMQ0153, a tetrahydrobenzimidazole derivative, to disrupt mitochondrial metabolism and dynamics as a novel therapeutic approach to overcome treatment resistance. Effects of TMQ0153 treatment on OPA1 and mitofusin (MFN)2 protein levels, mitochondrial morphology, and function in AML cells. In this study, reactive oxygen species (ROS) production, oxidative phosphorylation (OXPHOS) inhibition, mitochondrial membrane potential (MMP) depolarization, and apoptosis were examined. Additionally, metabolic profiling was conducted to analyze the changes in metabolic pathways. Results: TMQ0153 treatment significantly reduced OPA1 and mitofusin (MFN)2 protein levels and disrupted the mitochondrial morphology and function in AML cells. This increases ROS production and inhibits OXPHOS, MMP depolarization, and caspase-dependent apoptosis. Metabolic reprogramming was observed, shifting from mitochondrial respiration to glycolysis and impaired respiratory chain activity. Profiling revealed reduced overall metabolism, alongside changes in the glutathione (GSH)/oxidized glutathione (GSSG) and NAD⁺/NADH redox ratios. TMQ0153 treatment reduces tumor volume and weight in MV4-11 xenografts in vivo. Combination therapies with TMQ0153 and other AML drugs significantly reduced the leukemic burden and prolonged survival in NOD scid gamma (NSG) mice xenografted with U937-luc and MOLM-14-luc cells. Conclusion: TMQ0153 targets mitochondrial dynamics by inhibiting OPA1, inducing metabolic reprogramming, and triggering apoptosis in AML cells. It enhances the efficacy of existing AML therapies, providing a promising combination treatment approach that exploits mitochondrial vulnerability and metabolic reprogramming to improve treatment outcomes in AML

overall_design: To capture gene alterations both preceding and during the execution of cell death, two distinct time points were selected for each cell line: 1 h after treatment to observe early molecular events prior to cell death initiation and a later time point prior to the onset of significant cell death: 6 h for MV4-11 and 48 h for U937 cells.

first: Su-Jung

last: Park

first: M


title: IRG1 Promotes Neutrophil Reverse Migration and Alleviates Local Inflammation

city: Guangzhou

first: Jingjing

last: Ji

address: Liuhua Road

institute: General Hospital of Southern Theater Command of PLA

summary: Polymorphonuclear neutrophil (PMN) infiltration at inflammatory site plays a critical role in inflammation. PMN reverse migration (rM) describes the phenomenon that PMNs migrate away from inflammatory site back into the vasculature, and its role within inflammatory scenarios remains to be fully determined. This study aimed to investigate the mechanism underlying PMN rM and its role in inflammation. First, we demonstrated PMN rM in a mouse model of LPS-induced acute lung inflammation. By single-cell RNA sequencing (scRNA-seq), we demonstrated that reverse migrated (rM-ed) PMNs in blood expressed high level of immuneresponsive gene 1 (Irg1), the encoding gene of cis-aconitate decarboxylase (ACOD1).

overall_design: BALF and blood were collected from mice treated with LPS for 0, 6, and 24 h. CD45-positive cells in the BALF and blood were sorted for further scRNA-seq. The scRNA-seq libraries were generated by using Chromium Single Cell 3’ Library (10x Genomics) according to the manufacturer’s protocol.

first: Hanhui

last: Zhong

first: Yuehua

last: Li

first: Timothy

last: Billiar

first: Mark

middle: A

last: Wilson

first: Melanie

last: Scott

first: Jie

last: Fan


title: SKA1 promotes properties associated with tumor initiation and progression in OSCC and OLP

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Department of Medicine I

country: Austria

institute: Medical University of Vienna

summary: Global gene expression comparisons between OSCC and normal oral mucosa samples have been performed in more than 20 cohorts since 2004. Pathologically relevant genes (and associated pathways) are hypothesized to be deregulated in all studies. A bioinformatics analysis was performed to identify recurrently deregulated genes and pathways in OSCC compared to normal oral mucosa. Among the 629 consistently deregulated genes, genes related to mitosis and cell division were highly enriched. These included the gene spindle and kinetochore-associated complex subunit 1 (SKA1), which was consistently upregulated in OSCC and associated with poor survival of OSCC patients. SKA1 is part of the outer kinetochore and is required for proper chromosome segregation. An oncogenic role of SKA1 has been established in other solid tumor entities; however, its role in OSCC and in the transformation of premalignant cells to overt cancer cells has not been extensively studied. To investigate its role, SKA1 was overexpressed in the human OSCC cell line CAL-33 and the oral premalignant leukoplakia cell line MSK-Leuk1, and knocked down in the human OSCC cell line SCC-25. SKA1 promoted proliferation and 2D colony formation, and reduced the proportion of cells in metaphase by shortening the duration of this phase in OSCC cells. In addition, SKA1 promoted cell migration as assessed by the scratch assay. Growth and 3D colony formation in Matrigel® were enhanced by SKA1 expression. Its overexpression increased, and its knockdown decreased the radioresistance of OSCC cells, while resistance to chemotherapy drugs used in OSCC treatment remained unchanged. In the premalignant cell line MSK-Leuk1, SKA1 increased proliferation, 2D colony formation, migration, and 3D colony formation. RNA-sequencing of CAL-33 and MSK-Leuk1 cells overexpressing SKA1 and control cells showed that SKA1 promoted the activation of different signaling pathways in the two cell lines. In OSCC cells, EMT and inflammatory response-related pathways were enriched upon SKA1 overexpression, while in premalignant cells, genes associated with proliferation and with SKA1 expression in OSCC patients were most enriched. In conclusion, SKA1 is a novel oncogene in OSCC that enhances proliferation, migration, and resistance to irradiation in OSCC and premalignant cells.

overall_design: Gene expression profiles of CAL-33 SKA1 overexpression and CAL-33 control cell lines, and of MSK-Leuk1 SKA1 overexpression and SCC-25 control cell lines using Illumina HiSeq 2000.

first: Alexander

last: Grandits


title: Characterization of the vlVMH estrogen receptor α (ERα) neurons

status: Public on Apr 12 2025

city: Baton Rouge

first: Yanlin

last: He

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

summary: We report single-cell RNA-seq (patch-seq) data from the vlVMH ERα neurons

overall_design: 11-week old virgin female ERα-ZsGreen mice (n=3) in diestrus and PPD5 lactating ERα-ZsGreen dams (n=3) were used for sample collections. We collected the cellular component of each ERαvlVMH neuron after the recording. The samples were then transferred into a PCR tube. Samples were composed of one single neuron each.

first: He

last: Yanlin

first: Feng

last: Bing


title: Tracheal aspirate single cell RNA sequencing from patients with ARDS [scRNA-seq]

first: Aartik

last: Sarma

summary: Trachel aspirates samples were collected from an observational cohort of mechanically ventilated patients to compare respiratory tract gene expression in previous-descried ARDS molecular phenotypes. Patient charts were reviewed by two physicians and patients with ARDS were identified using the Berlin Definition. ARDS molecular phenotypes were defined using a previously-described 3-variable classifier (Sinha 2020)

first: Charles

last: Langelier

first: Carolyn

middle: S

last: Calfee


title: Selective NSD2 Inhibition Reveals an Epigenetic Vulnerability of KRAS-Driven Cancers [NicE-seq]

city: Stanford

first: Or

last: Gozani

address: 327 Campus Drive

department: Biology

institute: Stanford University

summary: NSD2, through generation of the epigenetic modification histone H3 di-methylated at lysine 36 (H3K36me2), is a candidate convergent downstream effector of oncogenic KRAS-signaling. However, whether NSD2 targeting represents a therapeutic vulnerability of KRAS-driven cancers is unknown. Here, we characterize a first-in-class, clinical grade small molecule catalyticNSD2inhibitor (NSD2i) series and find pharmacological targeting of NSD2 constitutes an epigenetic dependency with broad therapeutic efficacy in KRAS-driven pre-clinical cancer models. NSD2i inhibits NSD2 potently, with single digit nM IC50values, and shows high selectively for NSD2 versus NSD1, NSD3, and other similar enzymes. Structural analyses reveal the molecular basis of NSD2i specificity for NSD2, which includesS-adenosylmethionine (SAM)-competitive binding and catalytic disruption via a dual-channel obstruction mechanism. Proteo-epigenomic and single cell strategies in pancreatic ductal adenocarcinoma (PDAC) and lung adenocarcinoma (LUAD) samples support a model in which durable NSD2i exposure reverses H3K36me2-driven pathologic chromatin plasticity, re-establishing silencing at H3K27me3-legacy loci to curtail KRAS-regulated and oncogenic-associated gene expression programs. Accordingly, NSD2i treatment inhibits PDAC and LUAD cell viability and patient-derived xenograft tumor growth. Further, NSD2 inhibition, which is well toleratedin vivo, is equally effective as KRAS inhibition (sotorasib) treatment in prolonging survival in advanced stage autochthonous KRASG12C-driven PDAC and LUAD mouse tumor models. Moreover, in these models, NSD2 inhibition and sotorasib co-treatment synergize to confer sustained survival with extensive tumor nodule regression and elimination.Together, our work uncovers targeting of the NSD2-H3K36me2 axis as an actionable vulnerability in KRAS-driven cancers and provides a mechanistic rationale for testing NSD2i-KRAS inhibition combination therapies in the clinic.

overall_design: To investigate how NSDi affects chromosome accessibility in PDAC cell line, we treated MIA-PaCa2 cell line with either vehicle(DMSO) or NSD2i. We collected cells at day1, day5. We perfomed NicE-seq

first: Jinho

last: Jeong

first: Eric

last: Bareke

first: Jacek

last: Majewski


title: Transcriptomic profile of TLR7-induced DN2 B cell development with and without IL-4 Interference in vitro using B cells isolated from SLE patients.

first: Min

last: Gao

address: 1900 University Blvd, THT Building Suite #130G

summary: The effects of IL-4 on B cell development under an in vitro condition to polarize B cells into the double-negative 2 lineage were investigated.  Using single-cell RNA sequencing (scRNA-seq), we analyzed the transcriptomic profiles of B cells from systemic lupus erythematosus (SLE) patients treated with or without IL-4 at 4 hrs and 18 hrs following the stimulation.  Our results revealed that IL-4 pre-treatment led to a decrease in the expression of interferon response genes and DN2 signature genes, while promoting the emergence of a B cell population characterized by DN4 signature genes.  This has become evident at the 18 hr time point.

overall_design: B cells isolated from SLE patients were stimulated in RPMI with 10% FBS supplemented with or without IL-4 for 1 h. Cells were then stimulated with a combination of B cell polarication cocktail that exhibited a high potency to polarize B cells into the T-bet+ IgD-CD27- phenotype.  Cells were harvested at 4 and 18 hrs, followed by hash-tag antibody labeling and scRNA-seq analysis.

first: Changming

last: Lu

first: Shanrun

last: Liu

first: Winn

middle: W

last: Chatham

first: Hui-Chen

last: Hu

first: John

last: Mountz


title: ERG-driven gene expression in basal and luminal cells of mouse prostate organoids

first: Weiran

last: Feng

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

summary: ETS transcription factor ERG is aberrantly activated in ~50% of human prostate cancers. We found that ERG shows a preference of basal over luminal context to drive prostate cancer. However, the molecular basis of the cell context dependency remains elusive. Here we use ERG+/+;Pten-/- (EP) mouse prostate organoids with dual basal/luminal lineage reporters to profile ERG-driven gene expression programs from sorted basal vs luminal cells.

overall_design: ERG+/+;Pten-/- mouse prostate organoids treated with either NT sgRNA (N) or sgERG (E) were flow sorted to isolate basal (B) and luminal (L) cells a month post CRISPR. Sorted population were subject to RNA-seq profiling.