title: Inhibiting FKBP5 might alleviate obstetric antiphospholipid syndrome by regulating macrophage polarization.

city: Jinan

first: Yu

last: Xia

state: Shandong

address: 324 Jingwu Street

department: Department of Central Laboratory

institute: Shandong Provincial Hospital affiliated to Shandong University

summary: The disturbance of immune balance at the maternal-fetal interface is a significant contributor to obstetric antiphospholipid syndrome (OAPS); however, the precise mechanisms underlying this disturbance remain unclear. This study investigates the immune regulatory role of FK506-binding protein 5 (FKBP5) to elucidate its molecular mechanisms in pathological pregnancies associated with OAPS. We conducted RNA sequencing (RNA-seq) analysis and immune cell typing on decidual tissue from OAPS patients and healthy controls. The results indicated that the FKBP5 gene and inflammation-related pathways were significantly expressed in the maternal-fetal interface of OAPS patients, characterized by an increase in M1 (iNOS+/CD86+) macrophages and a decrease in M2 (Arg-1+/CD206+) macrophages. In vitro experiments demonstrated that FKBP5 promotes M1-like polarization of macrophages via the JAK1/STAT1 pathway while inhibiting M2-like polarization through the PPARγ/STAT6 pathway. Using a macrophage-trophoblast cell co-culture model, we found that FKBP5-induced abnormal macrophage polarization at the maternal-fetal interface negatively impacted the migration, invasion, and proliferation of trophoblast cells. In a mouse model of OAPS, the knockout of FKBP5 regulated the abnormal polarization of macrophages between M1 and M2 phenotypes, facilitated epithelial-to-mesenchymal transition (EMT), and mitigated antiphospholipid antibodies (aPLs)-mediated placental pathological damage. Notably, SAFit2, a small molecule inhibitor of FKBP5, effectively improved adverse pregnancy outcomes in OAPS mice. The immune microenvironment imbalance at the maternal-fetal interface, driven by FKBP5-regulated macrophage polarization, constitutes a critical immunological basis for aPLs-mediated placental damage. Therefore, FKBP5 presents a potential therapeutic target for OAPS.

overall_design: Samples from the OAPS patient group (n=4) and the HC group (n=4), who chose to terminate their pregnancies for non-medical reasons, were collected. The decidual tissues were isolated, and differences in gene expression between the decidual tissues of the OAPS group and the HC groupwere assessed using RNA-seq sequencing.

first: Mingjie

last: Song


title: STAT3 signalling drives tissue expansion during postimplantation mouse development

status: Public on Apr 06 2025

city: Edinburgh

first: Takuya

last: Azami

address: Crewe Road

department: Institute of Genetics and Cancer

country: United Kingdom

institute: The University of Edinburgh

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: ERG activates a stem-like proliferation-differentiation program in prostate epithelial cells with mixed basal-luminal identity [scATAC-seq]

status: Public on Apr 07 2025

city: New York

first: Erik

last: Ladewig

state: New York

address: 435 East 65th Street

country: USA

institute: MSKCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Performed scATAC-seq in 3 timepoints of an autochthonous mouse model.  A proliferative population is characterized by an ERG-specific chromatin state enriched for NFkB, AP-1, STAT and NFAT binding, with implications for TF cooperativity. ERG is enriched in a small stem-like population implicates the chromatin context of these cells as a critical variable for unmasking its oncogenic activity.

overall_design: A Rosa26-ERGLSL/LSL; Ptenflox/flox;Pb-Cre4 (EPC) mouse model, using single cell sequencing (scATAC-seq), at an early timepoint to capture changes associated with cancer initiation. At age 4 weeks, 3 months, and 6 months EPC mice have small foci of invasive cancer which subsequently progress to highly penetrant glandular invasion within 6 months

first: Weiran

last: Feng


title: Decitabine Induces Cell Differentiation and Growth Inhibition that Accompanies Up-regulation of microRNA-143 and MS4A3 in MDS-derived leukemic cell line, MDS-L.

city: Fukui

first: Rie

last: Nishi

address: 23-3 Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun

country: Japan

institute: University of Fukui

type: Methylation profiling by genome tiling array

summary: Myelodysplastic syndromes (MDS) are a group of clonal myeloid neoplasms characterized by ineffective hematopoiesis and cytopenia. Hypomethylating agents (HMAs) play a central role in the treatment of high-risk MDS, but their mechanisms of action are diverse and not fully understood. To investigate the molecular mechanisms of HMA, an MDS cell line (MDS-L) was cultured with a non-toxic concentration of decitabine for 6 months and drug sensitivity, cell differentiation, and DNA methylation profiles were evaluated. Cells with long-term exposure to decitabine (MDS-L-DAC) were morphologically mature with nuclear lobulation and cytoplasmic granulation, accompanied by decreased expression of the CD34 surface antigen. MDS-L-DAC cells exhibited decreased WT1 expression and intense induction of apoptosis by DAC. DNA methylation array analysis revealed the demethylation of the membrane spanning 4-domains A3 (MS4A3) genes and microRNA-143 (MIR143) in MDS-L-DAC cells. MIR143 functions as a tumor suppressor through the MAPK/ERK pathway, and in MDS-L-DAC cells, decreased expression of KRAS and β-catenin was observed in response to the increased expression of MIR143. The differentiation of MDS cells and decreased expression of WT1 induced by long-term incubation with DAC may involve the restoration of function via demethylation of the MIR143 and MS4A3 gene promoters, which may contribute to eliminating the malignant phenotype through reductions in KRAS and β-catenin expression.

overall_design:
We investigated the mechanisms of DAC-induced demethylation and expression restoration of tumor suppressor genes via studies in the MDS-derived leukemic cell line MDS-L. Long-term culture with DAC was conducted for downstream methylation array analysis and the identification of factors involved in cell differentiation and cell death. When DAC was applied at a low concentration, the intracellularly converted active metabolite 5-aza-dCTP was subsequently incorporated into DNA, resulting in the inhibition of DNA synthesis and the consequent induction of apoptosis. Our results may indicate the mechanism underlying HMA-induced expression restoration and differentiation in MDS-L cells.

Submitters state that output from Illumina's GenomeStudio (HM450_Report_191-1.txt) is provided as raw data since IDAT files are unavailable.

first: Naoko

last: Hosono

first: Kaoru

last: Thoyama

first: Takahiro

last: Yamauchi


title: STAT3 signalling drives tissue expansion during postimplantation mouse development [scRNA-seq]

summary: STAT3 has been studied extensively in the context of self-renewal of naïve pluripotent mouse embryonic stem cells (mESCs). Although STAT3 is required to maintain ICM lineages when maternally eliminated, the role of STAT3 during gastrulation is unclear as the conventional knockout of Stat3 develops until E6.5. In this study, we observed that zygotic loss of Stat3 on CD1 genetic background leads to consistent developmental retardation from implantation to mid-gestation, beginning with a significant reduction in the number of epiblast cells by the time of implantation. Remarkably, mutants appear to scale normally and resemble non-affected embryos from the previous day at all postimplantation stages examined. Bulk RNA-seq analysis using isolated epiblast cells revealeed that E6.5 null epiblasts were intermediate between WT E5.5 and E6.5; E7.5 null epiblasts grouped more closely with WT E6.5 than E7.5 epiblasts. Gene ontology analysis revealed lipid metabolism was compromised in Stat3 null embryos as early as E6.5. Interestingly, Socs3, downstream target of STAT3, was not induced in WT rpiblast cells until E7.5. We found Y705 phospholylated STAT3 was not exist postimplantation epiblast, but S727 phoshorylated STAT3 was abundant over the time, suggesting postimplantation specific roles of S727 phosphorylated STAT3 in growth and differentiation. Our study revealed that while Stat3 null epiblast cells progress along a near normal differentiation trajectory, Stat3 deletion compromises lipid metabolism as early as E6.5.

overall_design: Single-cell RNA sequencing on chimeric Stat3 null / WT embryos. Chimeras were generated by injecting WT blastocysts with tdTomato+ Stat3 null ESC. Chimeras were collected in multiple pools (replicates) at E7.5, E8.5, or E9.5, followed by dissociation to create single-cell suspensions. These cells were then sorted on  tdTomato to separate out the WT (tdTom-) and Stat3 null (tdTom+) cells within each pool. After sorting, cells were processed for scRNA-seq using 10x genomics 3' v3 kit.

first: Jennifer

last: Nichols

first: Bart

last: Theeuwes

first: Berthold

last: Gottgens


title: Human iPSC-derived cardiomyocyte from a patient with dilated phase of hypertrophic cardiomyopathy

city: Tsukuba

first: Nobuyuki

last: Murakoshi

address: 1-1-1 Tennoudai

institute: University of Tsukuba

summary: Hypertrophic cardiomyopathy (HCM) is an inherited cardiac disorder characterized by ventricular wall hypertrophy and diastolic dysfunction. Most patients with HCM are often a slowly progressive disease and may be asymptomatic; however, some progress to the dilated phase of HCM (D-HCM), and have a poorer prognosis. This study established disease-specific human induced pluripotent stem cells (iPSCs) from a patient with D-HCM harboring a truncating mutation in MYBPC3, and compared transcriptomes of iPSCs-derived cardiomyocytes between healthy control and D-HCM.

overall_design: We established D-HCM patient-derived iPSCs, and purchased two cell lines, HPS3354 and HPS3386, from the RIKEN BioResource Center and used as healthy control cells. To differentiate iPSCs into cardiomyocytes, iPSCs were treated with 8 µM CHIR99021 (GSK3β inhibitor) during 24 hours (day 0). At day 3, the cells were treated with 2 µM Wnt-C59 (Wnt inhibitor) during 48 hours. After purification and maturation, iPSC-CMs were collected approximately 50 days after cardiac differentiation (Days 45-55), and total RNA was extracted.

first: Murakoshi

last: Nobuyuki


title: Nuclear matrix associated protein SMAR1 attenuated acute graft-versus-host disease by targeting JAK-STAT signaling in CD4+ T cells [RNA-Seq]

city: Wuhan

first: Zhenli

last: Huang

address: 1277 Jiefang Avenue,

country: China

institute: Huazhong University of Science and Technology

summary: To investigate the function of nuclear matrix associated protein SMAR1 in the CD4+T cell, human primary CD4+ T cells were transfected with the SMAR1 lentivirus vector or empty vector. We performed mRNA gene expression profiling analysis using data obtained from RNA-seq.

overall_design: We divided CD4+ T cells into negative control group (Ctrl group) and SMAR1-overexpression group (OE group) according to the different transfection vectors. RNA samples were extracted from each group with 2 replicates.

first: Yao

last: Teng

first: Linghui


title: Nuclear matrix associated protein SMAR1 attenuated acute graft-versus-host disease by targeting JAK-STAT signaling in CD4+ T cells [ATAC-Seq]

summary: As a chromatin remodeling factor, SMAR1 might promote local chromatin changes, leading to the activation or inhibition of specific gene subsets in T cells. We performed high-resolution ATAC-seq on primary CD4+ T cells with SMAR1 overexpression (OE) and control (Ctrl), conducting a genome-wide analysis to map the locations and profile the accessibility of diverse regulatory elements.

overall_design: Analysis of  ATAC-seq data in CD4+T cells with SMAR1 overexpression. Each group has 3 replicates.


title: Effect of Rnf111 S254D mutant on gene expression on embryo at E7.5

city: Beijing

first: Zhiqiang

last: Peng

address: 38 Life Science Park Road

institute: State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics

summary: Transcriptome analysis of RNAs extracted from embryos of wild type or Rnf111 S254D knockin mice at E7.5.

overall_design: RNA-seq profiling of WT or Rnf111 S254D KI embryo at E7.5

first: Lingqiang

last: Zhang

first: Cuihua

last: Liu


title: Liver mRNA profiles of 39w-46w old wild type (WT) and Lmln-/- mice

first: Akihiro

last: Kuno

state: Ibaraki

address: 1-1-1 Tennodai

summary: NOT PROVIDED; REQUESTED

first: Satoru

last: Takahashi


title: Combining high-risk ADRD mutations across genetically distinct mice

status: Public on Apr 05 2025

city: BAR HARBOR

first: Amy

middle: R

last: Dunn

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Alzheimer’s disease and related dementias (ADRD), including Alzheimer’s disease (AD), frontotemporal dementia (FTD), Lewy body dementia (LBD), and mixed dementia are characterized by diverse pathologies and etiologies. ADRDs are typically distinguished based on combinations of associated pathologies in the brain such as amyloid, tau, TDP-43 inclusions, alpha-synuclein aggregates, and cerebral amyloid angiopathy, and these pathologies often co-occur even in cases clinically diagnosed as one disease. The heterogeneity of ADRDs presents significant challenges in model development for disease mechanism elucidation, drug discovery, and preclinical testing. Current animal models of ADRD fail to incorporate mixed pathologies and demonstrate low concordance with the diverse genetic, molecular, pathological, and cognitive features of human disease. Further, genetic background is critical for accurately modeling the complex genetic, molecular and cognitive features of late-onset AD in mice, and that incorporation of genetic diversity significantly improves concordance between mouse models and human patients in these parameters. Using CRISPR genome editing, we knocked-in several known human disease-causing mutations into C57BL/6J mice. Through serial breeding, we combined these KI mutations into various 3X, 4X, 5X and 6X knock-in models. We then crossed these 3X-5X models to various genetic backgrounds (C57BL/6J, DBA/2J, FVB/NJ, WSB/EiJ) to achieve a diverse F1 panel of genetically altered mice. Our goal was to maintain physiological expression levels of genes that induce commonly co-occurring pathologies in brain and peripheral tissues, while addressing these critical concerns often overlooked in most mouse models of neurodegenerative diseases (i.e., genetic diversity, late symptom onset, systemic expression of mutations, etc).

overall_design: Frontal cortex was isolated from mouse ADRD models. Samples were flash-frozen and mRNA was isolated from those samples for bulk RNA sequencing.

first: Harpreet

last: Kaur

first: Andrew

last: Tooley

first: Mouse

last: Boucher

first: Zoey

last: Bridges

first: Aamir

last: Zuberi

first: Cathleen

last: Lutz

first: Catherine

last: Kaczorowski

first: Kristen

last: O'Connell


title: Nuclear matrix associated protein SMAR1 attenuated acute graft-versus-host disease by targeting JAK-STAT signaling in CD4+ T cells

first: Zhenli


title: CDK2 Inhibition Produces a Persistent Population of Polyploid Cancer Cells

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

summary: Aneuploidy, a cancer hallmark, drives chromosomal instability, drug resistance, and clinically-aggressive tumors. Cyclin-dependent kinase 2 (CDK2) antagonism with independent inhibitors or CDK2 knock-down triggered anaphase catastrophe. This disrupts supernumerary centrosome clustering, causing multipolar division and apoptosis. Time-lapse fluorescent microscopy of FUCCI cell cycle probes transduced into aneuploid lung cancer cells revealed distinct fates of bipolar and polyploid cells after CDK2 inhibition. Apoptosis occurred in multipolar progeny but was repressed in persistent polyploid cancer cells. RNA-seq analyses after CDK2 inhibition of 4N versus 2N lung cancer cells were enriched for CDK1 pathway and KIF family members. The Cancer Genome Atlas (TCGA) analysis of lung cancers indicated CDK1 and KIF family member overexpression was associated with an unfavorable survival. Intravital microscopy of transplanted lung cancer cells in mice extended findings from the in vitro to in vivo settings. CDK2 inhibition of tumor-bearing mice produced polyploid cancer cells in vivo.  These cancer cells were resistant to apoptosis and proliferated despite CDK2 inhibition. In contrast, polyploid populations were rarely detected in CDK2 inhibited human alveolar epithelial cells.  These findings are translationally relevant. Combined targeting of CDK2 with CDK1 or kinesin family member antagonists should eliminate polyploid cancer cells, promote apoptosis and augment antineoplastic effects.

overall_design: ED1SQ4 lung cancer cells treated with vehicle as a control or CYC065 (0.5M) for 72 hours were stained with Vybrant™ DyeCycle™ Green Stain (#V35005, ThermoFisher) for 1 hour. Cells were then washed with phosphate buffered saline (PBS) and then sorted for diploid and for polyploid populations by S3e Cell Sorter (Bio-RAD) based on DNA quantification.

first: Liliya

last: Tyutyunyk-Massey

first: Xi

first: Ethan

last: Dmitrovsky


title: Transcriptomic profiling of A375 and PC9 cells following knockdown of the VCX gene family

city: Shanghai

first: Xunrui

last: Xunrui

address: No. 115, Jinzun Road, Beicai Town, Pudong New District

institute: Shanghai Jiao Tong University

summary: To investigate the role of the VCX gene family in cancer cells at the transcriptomic level,  we selected VCX gene family-positive A375 (melanoma) and PC9 (lung adenocarcinoma) cell lines. Stable cell lines with lentiviral shRNA targeting the conserved sequences shared by all VCX family members were generated, and cells treated with non-targeting shRNA were used as controls. Total RNA was extracted from cells at the logarithmic growth phase for RNA-seq library construction and sequencing. Differential expression genes and pathway analysis were performed to assess the transcriptomic alterations following VCX gene family knockdown. This dataset provides insights into the potential role of the VCX gene family in multiple cancer types.

overall_design: We employed a 2×2 factorial design examining the following variables: cell type (A375 melanoma cells vs. PC9 lung adenocarcinoma cells) and treatment (lentiviral shRNA targeting VCX gene family vs. non-targeting shRNA control). VCX knockdown was achieved using shRNAs targeting conserved sequences shared by all VCX family members. Each condition was performed in biological triplicate.

last: Chen


title: RNA-seq for High and low EPA+DHA group in the F2 population of the C. gigas and C.angulata crosses

city: Qingdao

first: Qingyuan

last: Li

address: Haijun road 88

institute: IOCAS

summary: To examine the candidate genes for GWAS at the transcriptional level, we selected 40 individuals each of EPA+DHA extreme phenotypes in the F2 population for mixed-pool transcriptome sequencing

overall_design: In this study, a total of 458 oysters from the F2 population resulting from the crossbreeding of C. angulata and C. gigas were utilized for liquid microarray genotyping. The F1 population were established through the crossbreeding of the 30 female C. angulata from Zhangzhou, Fujian (117°41'35 "E, 23°56'42 "N) and 30 male C. gigas from Jiaonan, Qingdao (119°57'3 "E, 35°43'20 "N), involving 30 or more oysters for both male and female parents. The F2 population was subsequently produced by the mating of the 30 female and 30 male F1 individuals and then cultured in Jiaonan, Qingdao, China. At the age of 11 months, a total of 458 F2 individuals were sampled in situ.Two extreme phenotype groups, H (high EPA+DHA) and L (low EPA+DHA), were selected from the GWAS population for transcriptomic analysis. Each group consisted of a total of 40 oyster individuals, and their total RNA was mixed equally for three technical replicates.


title: Effect of SIRT7 deletion on gene expression during skeletal muscle regeneration

city: Kyoto

first: Tatsuya

last: Yoshizawa

state: Kyoto

address: 1－5 Shimogamohangi-cho, Sakyo-ku

institute: Kyoto Prefectural University of Medicine

summary: Muscle satellite cell (MuSCs)-specific Sirt7 knockout (KO) mice display impaired muscle regeneration after injury. To evaluate the effect of SIRT7 deficiency on the early stages of muscle regeneration in vivo, we performed RNA-seq analysis for tibialis anterior (TA) muscle of control and MuSCs-specific Sirt7 KO mice at the early stages of myogenesis, day 3 post injury.

overall_design: RNA-seq data for TA muscle from 7-week-old WT; Pax7-CreERT2 (Control) and Sirt7fl/fl; Pax7-CreERT2 (Sirt7 scKO) mice at day 3 post injury by BaCl2.

first: Tomonori

last: Tsuyama

first: Hitoshi

last: Gotoh


title: Cooperation of a polymerizing SAM domain and an intrinsically disordered region enables full SAMD1 function on chromatin

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

summary: Transcription factors orchestrate gene expression through a myriad of complex mechanisms, encompassing collaborations with other transcription factors and the formation of multimeric complexes. The chromatin-binding protein SAMD1 [sterile alpha motif (SAM) domain-containing protein 1] binds to unmethylated CpG-rich DNA utilizing its N-terminal winged-helix (WH) domain. Additionally, its C-terminal SAM domain, which mediates interactions with itself and with L3MBTL3, is crucial for chromatin binding. The precise role of the SAM domain in this process remains unclear. Using structural analyses, we elucidated the distinct homopolymerization modes within the SAM domains of L3MBTL3 and SAMD1, alongside their heterodimerization architecture. Interestingly, SAMD1 necessitates not only the WH and SAM domain but also a proline/alanine-rich intrinsically disordered region (IDR) for efficient chromatin binding. The IDR is essential for the ability of SAMD1 to form large polymers, with its functionality determined by integrity rather than the specific sequence. Mutagenesis studies underscore the critical role of arginines within the IDR for polymerization, chromatin binding, and the biological function of SAMD1. These findings propose a model in which structured and unstructured regions of SAMD1 cooperate in a coordinated fashion to facilitate chromatin binding. This work provides new insights into the diverse mechanisms transcription factors employ to interact with chromatin and regulate gene expression.

overall_design: ChIP-Seq of various FLAG-tagged SAMD1 versions, ectopically expressed in SAMD1 KO mouse ES cells

first: Merle

last: Geller

first: Bastian

last: Stielow

first: Andrea

last: Nist


title: USP9X integrates TGF-β and hypoxia signalings to promote ovarian cancer chemoresistance via HIF-2α-maintained stemness

city: Tianjin

first: Zhenlei

last: Zhang

address: Qixiangtai Road 22

institute: Tianjin Medical University

summary: Widespread intraperitoneal metastases and chemoresistance render ovarian cancer the leading cause of gynecological malignancy–related deaths, wherein TGF-β signaling plays the pivotal role by promoting cancer stem cells (CSCs) activity. The activation mechanism and key protumorigeneic events downstream of TGF-β signaling remain incompletely understood. Here, we identify hypoxic tumor microenvironment as an initiator of TGF-β signaling to promote HIF-2α positive CSC-mediated chemoresistance in high-grade serous ovarian cancer (HGSOC). Mechanistically, deubiquitinase USP9X, as a TGF-β downstream effector, stabilizes HIF-2ɑ in a hydroxylation- and ubiquitylation-dependent manner, thus promoting stemness reprogramming. Hypoxia and TGF-β signals converge on USP9X-HIF-2ɑ axis via multi-level regulations, which in turn facilitates Smad/HIF responses. Clinically, USP9X expression correlates with TGF-β signatures, CSCs characteristics, EMT behaviors, and chemotherapy responsiveness, along with HIF-2ɑ. Antagonizing USP9X efficiently represses tumor formation, metastasis, CSCs occurrence, while increasing chemosensitivity in orthotopic tumors, patient derived xenograft (PDX), organoid, and chemoresistant cell models, in part via restricting TGF-β and hypoxia activities. This study deciphers the critical role of hypoxic niche in stimulating TGF-β signaling, and a downstream USP9X-HIF-2ɑ proteostatic regulatory axis in priming the HGSOC stemness, thereby provides novel targeting venues to counteract TGF-β signaling in CSCs and meliorate clinical chemoresistance.

overall_design: mRNA profiles of mouse ovarian cancer cell line ID8 Control and USP9X knocked-down were generated by deep sequencing, in duplicate, using Illumina novaseq6000.

first: Li

first: Shukai

last: Yuan


title: TATA-binding Associated Factors have distinct roles during early mammalian development

city: Amherst

first: Jesse

last: Mager

state: Massachusetts

address: 661 N Pleasant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts Amherst

summary: Early embryonic development is a finely orchestrated process that requires precise regulation of gene expression coordinated with morphogenetic events. TATA-box binding protein-associated factors (TAFs), integral components of transcription initiation coactivators like TFIID and SAGA, play a crucial role in this intricate process. Here we show that disruptions in TAF5, TAF12 and TAF13 individually lead to embryonic lethality in the mouse, resulting in overlapping yet distinct phenotypes. Taf5 and Taf12 mutant embryos exhibited a failure to implant post-blastocyst formation, and Taf5 mutants have aberrant lineage specification within the inner cell mass. In contrast, Taf13 mutant embryos successfully implant and form egg-cylinder stages but fail to initiate gastrulation. Strikingly, we observed a depletion of pluripotency factors in TAF13-deficient embryos, including OCT4, NANOG and SOX2, highlighting an indispensable role of TAF13 in maintaining pluripotency. Transcriptomic analysis revealed distinct gene targets affected by the loss of TAF5, TAF12 and TAF13. Thus, we propose that TAF5, TAF12 and TAF13 convey locus specificity to the TFIID complex throughout the mouse genome.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse embryos from a WT, Taf5KO, Taf12KO, or Taf13KO transgenic background.

first: Xinjian

middle: D

last: He

first: Kaito

middle: A

last: Hioki

first: Prabin

last: Mahji


title: PTIR1 acts as a suppressor of immunoproteasome and promotes cancer immune resistance [TILs 10x scRNA-seq]

first: Jia

last: Song

state: China

address: Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

summary: Cancer cells evade host immune surveillance by virtue of poor immunogenicity. We identify a novel oncogene that acts as a promotor of tumor immune resistance, designated as PTIR1. Tumor-intrinsic PTIR1 is induced by RNA splicing and highly correlated with poor outcome of patients with cancer.

overall_design: Study of  tumor infiltration lymphocytes in colon cancers with or without PTIR1 expressing using 10x scRNA-seq technologies.

first: Dan

last: Lu

first: Xin


title: Identification and regulation of circulating tumor TCR-matched cytotoxic CD4+ lymphocytes by KLRG1 in bladder cancer

status: Public on Apr 04 2025

city: San Francisco

first: David

last: Oh

state: CA

address: 513 Parnassus Ave, HSE301, Box 0519

institute: University of California, San Francisco

summary: While cytotoxic CD4+ tumor-infiltrating lymphocytes have anti-cancer activity in patients, whether these can be non-invasively monitored and how these are regulated remains obscure. By matching single cells with T cell receptors (TCR) in tumor and blood of bladder cancer patients, we identified distinct pools of tumor-matching cytotoxic CD4+ T cells in the periphery directly reflecting the predominant antigenic specificities of intratumoral CD4+ TILs. On one hand, the granzyme B (GZMB)-expressing cytotoxic CD4+ subset proliferated in blood in response to PD-1 blockade, but was separately regulated by the killer cell lectin-like receptor G1 (KLRG1) which inhibited their killing by interacting with E-cadherin. Conversely, a clonally related, granzyme K (GZMK)-expressing circulating CD4+ population demonstrated basal proliferation and a memory phenotype that may result from activation of GZMB+ cells, but was not directly mobilized by PD-1 blockade. As KLRG1 marked the majority of circulating tumor TCR-matched cytotoxic CD4+ T cells, this work nominates KLRG1 as a means to isolate them from blood and provide a window into intratumoral CD4+ recognition, as well as a putative regulatory receptor to mobilize the cytolytic GZMB+ subset for therapeutic benefit. Our findings also underscore the ontogenic relationship of GZMB- and GZMK-expressing populations and the distinct cues that regulate their activity.

overall_design:
For single-cell analysis of circulating immune responses, the sample set was available matched blood samples from 6 of 7 patients with localized, muscle-invasive bladder cancer whose tumor and normal adjacent tissue (NAT) scRNAseq was previously published (Oh DY, Kwek SK et al. Cell 2020). These patients included 3 patients ("Anti-PD-L1 B", "Anti-PD-L1 C", "Anti-PD-L1 D") who were treated with neoadjuvant atezolizumab prior to cystectomy on a clinical trial (NCT02451423, see "Clinical trial design"); 1 patient treated with neoadjuvant chemotherapy before cystectomy as standard of care; and 2 patients untreated with any systemic therapy before cystectomy as standard of care. Blood samples from an additional patient from the neoadjuvant trial ("Anti-PD-L1 E"), as well as three separately sequenced technical replicates from a single healthy donor, were also analyzed but without matching tumor data. For standard of care, there was a single blood draw the same day as surgery. For trial patients, a baseline blood draw was taken prior to starting (pre-treatment) and after neoadjuvant atezolizumab (post-treatment) for the trial.  All post-treatment blood draws except 1 were prior to surgery, and most were within 1-2 weeks of the surgery date. scRNAseq/TCRseq were conducted as described below and as previously published, and jointly analyzed with the previously published tumor scRNAseq/TCRseq data. All available blood timepoints, and a single tumor timepoint (surgery), were combined for clustering and initial analysis. Connected CD4+ between the blood and TILs were identified in the blood based on matching, paired TCR sequences in single cells, and downstream analyses characterized these circulating, tumor-matching cytotoxic CD4+ T cells.

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

middle: S

last: Kwek

first: Hai

last: Yang

first: Tony

first: Arielle

last: Ilano

first: Eric

last: Chow

first: Hewitt

last: Chang

first: Diamond

last: Luong

first: Averey

last: Lea

first: Matthew

last: Clark

first: Alec

last: Starzinski

first: Yimin

last: Shi

first: Elizabeth

last: McCarthy

first: Sima

last: Porten

first: Maxwell

middle: V

last: Meng

first: Chun

middle: J

last: Ye

first: Lawrence

last: Fong

middle: Y


title: Identification of known and novel long non-coding RNAs potentially responsible for the effects of BMD GWAS loci [hFOB RNA-seq]

city: Charlottesville

first: Charles

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

summary: Osteoporosis, characterized by low bone mineral density (BMD), is the most common complex disease affecting bone and constitutes a major societal health problem. Genome-wide association studies (GWASs) have identified over 1100 associations influencing BMD. It has been shown that perturbations to long non-coding RNAs (lncRNAs) influence BMD and the activities of bone cells; however, the extent to which lncRNAs are involved in the genetic regulation of BMD is unknown. Here, we combined the analysis of allelic imbalance (AI) in human acetabular bone fragments with a transcriptome-wide association study (TWAS) and expression quantitative trait loci (eQTL) colocalization analysis using data from the Genotype-Tissue Expression (GTEx) project to identify lncRNAs potentially responsible for GWAS associations. We identified 27 lncRNAs in bone that are located in proximity to a BMD GWAS association and harbor SNPs demonstrating AI. Using GTEx data we identified an additional 31 lncRNAs whose expression was associated (FDR correction<0.05) with BMD through TWAS and had a colocalizing eQTL (regional colocalization probability (RCP)>0.1). The 58 lncRNAs are located in 43 BMD associations. To further support a causal role for the identified lncRNAs, we show that 23 of the 58 lncRNAs are differentially expressed as a function of osteoblast differentiation. Our approach identifies lncRNAs that are potentially responsible for BMD GWAS associations and suggest that lncRNAs play a role in the genetics of osteoporosis.

overall_design: RNA-seq profiling of hFOB 1.19 cells at days 0, 2, 4, 6, 8, and 10 of osteogenic differentiation.

first: Abdullah

last: Abood

first: Larry

last: Mesner

first: Will

last: Rosenow

first: Basel

middle: M

last: Al‐Barghouthi

first: Nina

last: Horowitz

first: Elise

middle: F

last: Morgan

first: Louis

middle: C

last: Gerstenfeld


title: Discovery of BMS-986408, a First-In-Class Dual DGK⍺ and DGK𝛇 Inhibitor That Unleashes PD-1 Checkpoint and CAR-T Cell Immunotherapies

city: Cambridge

first: Siqi

last: Liu

state: MA

address: 250 WATER STREET

department: Oncology

institute: BMS

summary: DGKα and DGKζ are lipid kinases that negatively regulate T cell signaling through diacylglycerol (DAG) metabolism, making them attractive targets for next-generation immunotherapy. Here, we disclose the discovery and pre-clinical characterization of the first clinical-stage DGKα and DGKζ lipid kinase inhibitor, BMS-986408. BMS-986408 binds to the accessory subdomain of the catalytic domain and inhibits DGKα/ζ through a mechanism of action that includes DAG-substrate competitive inhibition, subcellular translocation to plasma membrane, and proteosome-dependent degradation. DGKα/ζ inhibition markedly improved the therapeutic benefit of PD-1 therapy by unleashing T cell responses in the tumor while also uniquely amplifying the priming and expansion of tumor-reactive T cells in the tumor-draining lymph nodes. Importantly, simultaneous inhibition of both DGKα and DGKζ was required to maximize combination benefit with PD-1 therapy. DGKα and DGKζ were broadly expressed in NSCLC tumor-infiltrated T cells and combination therapy invigorated a robust cytokine response in NSCLC patient-derived organotypic tumors supporting the clinical evaluation of this combination in NSCLC patients. BMS-986408 also markedly improved CD19-targeted CAR-T cell therapy efficacy by overcoming hypo-functionality, insufficient expansion, and lack of co-stimulatory ligands. BMS-986408 represents the first critical step towards evaluating the broad immunotherapy potential of DGKα/ζ inhibitors in cancer patients.

overall_design: MC38 tumors were injected into female C57BL/6 mice and grown to a mean tumor volume of ~100 mm3. Animals were then randomized into anti-PD1, BMS-986408, combination anti-PD1/BMS-986408, or vehicle isotype control arms (n = 5 per arm) and tumors were collected seven days after the initiation of treatment. We generated bulk RNA sequencing libraries to profile gene expression changes induced by each treatment and differential expression analysis was performed between different treatment arms.

first: Wichroski

last: Michael

first: Liu

last: Si-Qi

first: Longmire

last: Tyler

first: Powles

last: Ryan

first: Font Tello

last: Alba

first: Drokhlyansky

last: Eugene

first: Lees

last: Emma


title: IKK in mesothelioma

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

summary: perform gene expression silencing for both IKKs in AE17, AB2 and KPM1 cells using lentiviral shRNA pools. After validating gene silencing, RNA was extracted from both parental (shC) and daughter cells (shChuk, shIkbkb) and was send for RNAsequencing in order to define possible target genes, up or down regulated upon gene expression manipulation with lentiviral shRNA. These cell lines (parental and daughter) were evaluated in vitro for the role of IKKs in cell proliferation, survival and clonogenicity and in vivo for their impact in MPM development upon intrapleural injection in mice

overall_design: The purpose of this study was to functionally examine the main NF-κB activating kinases IKKα and ΙΚΚβ in mouse models of human and murine malignant pleural mesothelioma (MPM). First, we induced MPM in C57BL/6 and Balb/c mice by intrapleural injections of syngeneic AE17 and AB2 MPM cells respectively

first: M

last: Pepe

first: G

first: I

last: Giopanou


title: An enantiomer-dependent and modification-free DNA matrix as a novel adjuvant platform for subunit vaccines

first: Cuifeng

last: Li

address: Qinghua Yuan Street

institute: Tsinghua University

summary: We introduce a novel dynamic DNA supramolecular matrix material assembled from five unmodified, short DNA strands, serving as a safe and effective adjuvant platform. Our findings demonstrate that this DNA matrix material elicits robust humoral response in an enantiomer-dependent but CpG-independent manner, effectively generating potent neutralizing antibodies and conferring robust protection against diverse pathogen infections, including both SARS-CoV-2 and Streptococcus pneumoniae. Remarkably, DNA matrix exhibits minimal adverse effects in comparison to the commonly used aluminum material. In stark contrast to its soluble DNA components, the dynamic colloidal feature of DNA matrix material prolongs the in vivo retention of both DNA and antigen by spontaneously disintegrating into nanoparticles in hundreds of nanometers range, facilitating lymphatic-targeted transportation and accumulation. This process leads to a robust pro-inflammatory response in both vaccinated local tissue and draining lymph node (dLN), which in turn promotes the recruitment and activation of diverse immune cells, ultimately leading to a rapid and robust antigen-specific antibody response. Surprisingly, mechanistic investigation uncovers that the enhancing function of this DNA matrix material is not dependent on DNA-sensor machineries including cGAS, ZBP1, AIM2 and STING, relying instead on the TLR9-MyD88 signaling axis. Cell-lineage specific MyD88 knockout experiments underscore the critical role of this axis in DCs, but not in B cells and keratinocytes. Unexpectedly, the antibody-enhancing function of this DNA matrix material is also strongly dependent on the right-handed chirality of the building block DNA strands, forming D-DNA matrix. In marked contrast, the left-handed L-DNA matrix, despite inheriting identical physiochemical properties as a material and the ability to disintegrate into nanoparticles as D-DNA matrix, completely fails to promote immune activations in vitro and in vivo. Thus, this injectable, self-assembling, CpG- and modification-free DNA matrix material functions as a novel, all-in-one subunit vaccine adjuvant platform, opening up promising avenues in next-generation vaccine design.

overall_design: RNA seq prolife of dLN of mice 12 hours post immunized  with PBS, Alum or DNA matrix

first: Yuxin

first: Bini

last: Zhou

first: Tong

first: Dongsheng

first: Wanli


title: The bone marrow niche and hematopoietic system are distinctly remodeled by CD45-targeted astatine-211 radioimmunotherapy

city: Seattle

first: Matthew

last: Hagen

state: WA

address: 1100 Fairview Ave N.

department: Translational Science and Therapeutics

institute: Fred Hutchinson Cancer Center

summary: Radioimmunotherapy (RIT) is used to treat patients with hematological malignancies known to infiltrate the bone marrow (BM) microenvironment. RIT uses target-specific monoclonal antibodies stably conjugated to radionuclides to deliver cytotoxic radiation to cells of interest. While RIT is effective at delivering radiation to cancer cells, normal tissue is also exposed to radiation upon RIT, the consequences of which are largely unknown. Here, we studied the cellular and molecular effects of CD45-targeted astatine-211 (211At) RIT, IgG non-targeted 211At RIT, and Cesium-137 total-body irradiation (TBI) on hematopoietic cells and their BM niche in wild-type immunocompetent mice. Relative to non-targeted RIT or TBI, CD45-targeted RIT significantly delayed hematopoietic regeneration overall in the peripheral blood and BM and reduced hematopoietic stem/progenitor cell recovery and colony-forming ability. While BM endothelial cells (ECs) do not express the CD45 antigen, CD45-targeted RIT significantly depleted BM ECs compared to non-targeted RIT or TBI. RNA sequence analysis revealed significantly different transcriptomic profiles of BM ECs from CD45-RIT-treated mice compared to non-targeted RIT or TBI. ECs from CD45-RIT-treated mice, but not TBI or IgG-RIT-treated mice, were transcriptionally enriched for TGFβ, NOTCH, and IFNα signaling pathways compared to untreated mice. Collectively, our study indicates that CD45-targeted RIT severely impacts hematopoietic and EC niche recovery compared to non-targeted approaches. Future studies are required to determine the long-term consequences of such RIT-driven effects on BM niche physiology and how BM niche reprogramming by RIT affects cancer cells.

overall_design: RNA sequencing of flow-sorted bone marrow endothelial cells from endothelial reporter (Cdh5 Cre Rosa26 TdTomato) mice treated with either: 500 cGy total body irradiation, 20 µCi IgG non-targeted radioimmunotherapy, 20 µCi CD45-targeted radioimmunotherapy, or non-treated controls.

middle: W

first: Nicollette

last: Setiawan

first: Shannon

last: Dexter

first: Kelsey

last: Woodruff

first: Francesca

last: Gaerlan

first: Johnnie

last: Orozco

first: Christina

last: Termini


title: ScRNA-Seq of Human MDS and AML Bone Marrow Marrow Microenvironment.

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: Single Cell RNA-Sequencing was performed on enzymatically digested and magnetically depleted CD45- cells from the bone marrow aspirates of MDS and AML patients.

overall_design: Bone marrow aspirates were obtained from MDS/ AML patients after written informed concent. CD45- cells were magnetically sorted and processed for scRNA-Seq.

first: Sonali

last: Sharma

first: Jeevisha

last: Bajaj

first: John

last: Ashton


title: Illumina Infinium MethylationEPIC data for Glioma

first: ARIJIT

last: PANDA

state: MINNESOTA

address: 200 1st street SW

institute: MAYO CLINIC

summary: Methylation profiling by Illumina Infinium MethylationEPIC microarray of glioma subjects

overall_design:
The goal of this project was to examine the methylation pattern of glioma and correlate with germline and somatic alterations

Please note that additional sample information is provided in the 'Methylation_deidentify.csv'. Sample-specific genotype details are available in the dbGaP submission phs003041.v1.p1, and the RNA-seq/ChIP-seq datasets are available under GEO accession GSE167806.

first: Robert

middle: B

last: Jenkins

first: Jeanette

middle: E

last: Eckel-Passow

first: Kristen

middle: L

last: Drucker


title: 16p11.2 copy number variants drive convergent cell-type specific disruptions in corticogenesis

city: La Jolla

first: Summer

last: Fair

address: 2880 Torrey Pines Scenic Drive

institute: UC San Diego

summary: Here, Van Enoo et al. generate isogenic CRISPR/Cas9-engineered iPSC-derived cortical organoids (COs) to investigate the cellular and molecular consequences of 16p11.2 copy number variants (CNVs) during early human neurogenesis. Single-nuclei RNA sequencing reveals progenitor depletion, premature cell cycle exit, and accelerated gliogenesis, leading to the emergence of a neuronal subpopulation enriched for neurodevelopmental disorder (NDD) risk genes.

overall_design: Single-nucleus RNA sequencing was performed on cortical organoids derived from induced pluripotent stem cell (iPSC) lines carrying 16p11.2 copy number variants (deletion or duplication) and isogenic wild-type controls. Organoids were harvested at 2 months of differentiation to capture dynamic changes during cortical development. All samples were processed using the 10x Genomics Chromium platform and sequenced on a NovaSeq 6000. The experimental design enables comparative analysis of transcriptomic profiles across genotypes.

first: Alicia

last: Van Enoo

first: Issac Alexander

last: Chaim

first: Eugene

last: Yeo


title: NaBH4-sequencing of MVC infected WRD cells

city: Wuhan

first: Xueyan

last: Zhang

address: 湖北省武汉市武昌区水果湖街道

institute: wuhan institute of virology

summary: RNA modifications play crucial roles in RNA metabolism, structure, and functions. N4-acetylcytidine (ac4C) modifications have been shown to enhance stability and translation efficiency of mRNAs and viral RNAs. However, the relationship between ac4C and alternative RNA processing remains unexplored. Here, N-acetyltransferase 10 (NAT10) and its catalyzed ac4C modifications on minute virus of canines (MVC) was shown to regulate viral DNA replication and RNA processing, including both the alternative RNA splicing and polyadenylation. Through acRIP-seq and RedaC:T-seq, functional ac4C-modified residue 3311 was identified and characterized, which affected MVC RNA processing, rather than altered the viral RNA stability. Ac4C modification at nt 3311 was revealed to participate in NP1-mediated viral RNA processing without influencing RNA affinity of NP1. Meanwhile, CPSF5 was identified to interact with NP1 and mediate viral RNA processing in an ac4C-dependent manner. Further in vitro assays showed that NP1 recruited CPSF5 to MVC RNAs and the ac4C modification promoted specific binding of CPSF5 to the target region, which ensured precise alternative MVC RNA processing. This study not only reveals the functions of NAT10 and ac4C, but also elucidates the mechanisms by which RNA modifications orchestrate MVC proteins and host factors for efficient viral replication and alternative RNA processing.

overall_design: The changes of ac4C modification in WRD cells after MVC infection were investigated by NaBH4 sequencing.

first: Wuxiang

last: Guan

first: Shuangkang

last: Qin

first: Fang

last: Huang


title: RNA-seq analysis of Trpm7-deficient muscle satellite cells

city: Shizuoka

first: Kotaro

last: Hirano

state: Shizuoka

address: Suruga Ward 52-1 Yada

institute: University of Shizuoka

summary: Muscle satellite cells (MuSCs), skeletal muscle-resident stem cells, are crucial for regeneration of myofibers. Molecular factors such as cations that trigger the transition of MuSCs from a quiescent to an active state remain largely unidentified. In this study, we identified TRPM7, a Mg2+-permeable ion channel, as a critical determinant for myofiber regeneration. We investigated gene profiles of Trpm7-deficient MuSCs to understand the role of TRPM7 during myogenesis. Our results suggest that TRPM7 governs the myogenesis, cell-cycle progression and mitochondrial biosynthesis in satellite cells to regulate crucial events (ie, activation, proliferation, and myogenesis) during skeletal muscle regeneration.

overall_design: control or Trpm7-/- MuSCs were isolated by FACS (fluorescence activated cell sorting) as a population of YFP+ve cells from Pax7-CreERT2; Rosa26-YFP mice. Total RNA samples were isolated from MuSCs 3 days post cardiotoxin (CTX) injury.

first: Kaori

last: Tanaka

first: Yasuyuki

last: Ohkawa

first: Yuji

last: Hara


title: Acetylated RIP-sequencing of MVC infected WRD cells

address: 湖北省武汉市武昌区水果湖街道

overall_design: The levels of ac4C modification of MVC RNA in WRD cells after virus infection were investigated by acRIP sequencing.


title: Asparagine alleviates naphthalene-induced lens opacity in SRA cells

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

summary: Cataract is characterized by lens opacity, often leading to vision loss. The primary clinical treatment is lens replacement, which usually yields good results. Although cataract surgery is a common ophthalmic treatment, it still carries surgical risks, such as infection, bleeding, and dislocation of the intraocular lens. Therefore, researching drugs that can delay or treat cataract holds significant social and scientific importance. This study found that asparagine can improve lens opacification in rats exposed to naphthalene. Consequently, in vitro, SRA01/04 cells were treated with the naphthalene metabolite 1,2 - dihydroxynaphthalene (1,2 - DHN), and RNA - sequencing technology was employed to investigate the cellular mechanisms underlying the therapeutic effects of asparagine.Through systematic experiments and analyses, we have dissected the cellular changes following treatment with 1,2 - DHN, comprehensively presenting the molecular network affected thereby. Simultaneously, we have also paid particular attention to the signaling pathways activated by Asn during this process.

overall_design: RNA-seq was used to detect the differences in SRA01/04 cells among the normal group, the normal group supplemented with asparagine, the 1,2-DHN treatment group, and the 1,2-DHN plus asparagine treatment group after 24 hours of treatment.

first: Tingting

last: Cui


title: Control of Circadian Glucose Metabolism through BMAL1-HIF Axis in Obesity

city: Chicago

first: Clara

middle: Bien

last: Peek

state: IL

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

institute: Feinberg School of Medicine - Northwestern University

summary: Disruptions of circadian rhythms is widespread in modern society and leads to accelerated and worsened symptoms of metabolic syndrome. In healthy mice, the circadian clock factor BMAL1 is required for skeletal muscle function and metabolism. However, the importance of muscle BMAL1 in the development of metabolic diseases, such as diet-induced obesity (DIO), remains unclear. Here, we demonstrate that skeletal muscle-specific BMAL1-deficient mice exhibit worsened glucose tolerance upon high fat diet feeding, despite no evidence of increased weight gain. Metabolite profiling from Bmal1-deficient muscles revealed impaired glucose utilization specifically at early steps in glycolysis that dictate the switch between anabolic and catabolic glucose fate. We provide evidence that this is due to abnormal control of the nutrient stress-responsive hypoxia inducible factor (HIF) pathway. Genetic HIF1α stabilization in muscle Bmal1-deficient mice restores glucose tolerance and expression of approximately 30% of dysregulated genes during DIO, including glycolytic enzymes. Together, these data indicate that during DIO, skeletal muscle BMAL1 is an important regulator of HIF-driven glycolysis and metabolic flexibility, which influences the development of high fat diet-induced glucose intolerance.

overall_design: Gene expression profiling from gastrocnemius muscle tissue from regular chow and high-fat diet fed wildtype or skeletal muscle-specific BMAL1 KO mice.

first: Claire

last: Chaikin


title: Sex differences in DNMT3A-mutant clonal hematopoiesis and the effects of estrogen [scRNA-Seq]

city: Boston

first: Julia

last: Stomper

address: 360 Longwood Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Blood cancers are generally more common in males, and the prevalence of most mutations that drive clonal hematopoiesis and myeloid malignancies is higher in males. In contrast, hematopoietic DNMT3A mutations are more common in females. We sought to investigate if sex hormones might contribute to the female predominance of DNMT3A mutations. We used single-cell RNA- and ATAC-sequencing in murine models to examine genotype-specific sex differences and sex hormone effects on hematopoietic stem and progenitor cells.

overall_design: Single-cell RNA-sequencing was performed of hematopoietic stem and progenitor (Lineage- Sca-1+ c-kit+ [LSK]) cells from unmanipulated male and female mice with wild-type (WT) or Dnmt3a-mutant backgrounds, and from ovariectomized mice transplanted with WT or Dnmt3a-mutant bone marrow cells and treated with a single dose of estradiol, dihydrotestosterone (DHT), or vehicle. Single-cell ATAC-sequencing was performed of LSK cells from unmanipulated female WT or Dnmt3a-mutant mice.

first: Abhishek

last: Niroula

first: Roger

last: Belizaire

first: Marie

last: McConkey

first: Benjamin

last: Ebert


title: Gene expression profile at single cell level of skin cells from back skin of control and Piezo1 inducible knock-out mice

first: Rui

last: Yi

state: Illinois

address: 765 N FAIRBANKS CT

department: Pathology, Feinberg School of Medicine

institute: Northwestern University

summary: Piezo1 is a mechanoactive calcium ion channel and is expressed in skin cells. We used single cell RNA sequencing (ScRNAseq) to analyze the functions of mechanical sensing by Piezo1 in hair follicle cells.

overall_design: Back skin cells of control and Piezo1 inducible knock-out mice were isolated by collagenase and trypsin digestion.

first: Jingjing

last: Wang


title: Diabetic ischaemic cardiomyopathy: Characterising the left ventricular myocardial molecular profile in advanced human heart failure

city: Panania

middle: John

last: Hunter

state: NSW

address: 118 Horsley Rd

department: School of Medical Sciences

country: Australia

institute: The University of Sydney

summary: Ischaemic cardiomyopathy (ICM) is the most common cause of heart failure (HF) and often coexists with diabetes mellitus (DM). Yet, their combined effects are seldom investigated and are poorly understood. Herein, we performed multi-omic analyses of end-stage ICM with DM (ICM-DM) against ICM-No DM, non-ischaemic (dilated) cardiomyopathy with DM (NICM-DM), NICM-No DM, and healthy age-matched donors (AMD). Tissue was sourced from pre-mortem human left ventricular myocardium. Though fatty acid oxidation (FAO) proteins were down-regulated in ICM-DM relative to AMD and other HF, the unique ICM-DM down-regulation of acylcarnitines, perilipin, and ketone body, amino acid, and glucose metabolising proteins indicated FAO may not be entirely impaired. Oxidative phosphorylation appeared reduced in HF but exacerbated in ICM-DM, consistent with purportedly increased oxidative stress. Extracellular matrix proteins including collagens were up-regulated principally in ICM-DM despite the absence of macroscopic scar tissue. These findings were supported histologically and in metabolomic and RNA sequencing analyses.

overall_design: The aim of this study was to perform multi-omics analyses on cryopreserved pre-mortem human left ventricular myocardium to uncover the influence of DM in end-stage HF, and the molecular characteristics of ICM with DM (ICM-DM), thereby creating a comprehensive molecular resource of diabetes related heart failure.

first: Yunwei

last: Zhang

first: Dylan

last: Harney

first: Holly

last: McEwen

first: YenChin

last: Koay

first: Michael

last: Pan

first: Cassandra

last: Malecki

first: Jasmine

last: Khor

first: Robert

last: Hume

first: Giovanni

last: Guglielmi

first: Alicia

last: Walker

first: Shashwati

last: Dutta

first: Vijay

last: Rajagopal

first: Anthony

last: Don

first: Mark

last: Larance

first: John

last: O’Sullivan

first: Jean

last: Yang

first: Sean

last: Lal


title: Transcriptomic Differences between Oral and Skin Keratinocytes

first: Chen

last: Han

address: 801 S. Paulina St.

department: Center for Wound healing and Tissue Regeneration

institute: University of Illinois Chicago

summary: Compared to skin wounds, oral mucosal wounds heal more rapidly with less inflammation, faster re-epithelialization, and minimal scarring. One cell type that may be a differentiating factor is keratinocytes. Using immortalized skin and oral keratinocytes, HaCaT and TIGK, respectively, we found that oral keratinocytes have an enhanced migratory and proliferative capacity. To examine the transcriptomic differences that underlie the improved healing abilities of oral keratinocytes, we generated an RNA-sequencing (RNA-seq) gene expression dataset utilizing HaCaT and TIGK. Differentially expressed genes (DEGs) were identified between HaCaT and TIGK at baseline and throughout the injury response. Gene Ontology (GO) or Reactome enrichment analysis was performed to understand the biological significance of DEGs. Processes related to inflammation and migration were uniquely enriched in TIGK. Additionally, TIGK retained its enhanced migratory capacity when grown on various basement membrane (BM) and extracellular matrix (ECM) substrates. This may be due to the differential expression of matrix metalloproteinases (MMPs) and integrins between HaCaT and TIGK. We also identified genes differentially over or under-expressed in HaCaT and TIGK following injury when compared to each respective cell type’s unwounded gene expression levels. Lastly, we showed that the post-injury secretome of TIGK promotes keratinocyte migration. Our comparative analyses suggest specific transcriptomic differences between oral and skin keratinocytes at unwounded baseline and in response to injury may underlie the distinct wound healing phenotypes seen in these two tissues. This work also provides a source of HaCaT and TIGK gene expression data over healing that can be used for future analyses.

overall_design:
To examine the transcriptomic differences that underlie the improved healing abilities of oral keratinocytes, we generated an RNA-sequencing (RNA-seq) gene expression dataset utilizing skin and oral keratinocyte cell lines, HaCaT and TIGK, at 3 distinct time points following in vitro wounding.
We first performed comparative gene expression analysis between HaCaT and TIGK to determine differentially down- or upregulated genes in HaCaT relative to TIGK at unwounded baseline  (0 h) and throughout healing (6 h and 24 h). Downregulated genes in HaCaT relative to TIGK were considered upregulated in TIGK.
Then, to compare the injury responses of HaCaT and TIGK, we studied the differentially expressed genes in HaCaT or TIGK at 6 h or 24 h relative to their 0 h.


title: SMIM20 promotes complex IV biogenesis and Ca2+ Signalling in mice heart

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Mitochondria are key to cellular energetics, metabolism, and signaling. Their dysfunction is linked to devastating diseases including mitochondrial disorders, diabetes, neurodegenerative diseases, cardiac disorders, and cancer. Here, we present a novel knockout mouse model lacking the complex IV assembly factor SMIM20/MITRAC7. SMIM20-/- mice display cardiac pathology with reduced heart weight and cardiac output. Heart mitochondria present with reduced levels of complex IV associated with increased complex I activity, have altered fatty acid oxidation, and display elevated levels of ROS production. Interestingly, mutant mouse ventricular myocytes show unphysiological Ca2+ handling, which can be attributed to the increase in mitochondrial ROS production. Our study presents a new example of a tissue-specific phenotype in the context of OXPHOS dysfunction. Moreover, our data suggest a link between complex IV dysfunction and Ca2+ handling at the endoplasmic reticulum through ROS signaling.

overall_design: To compare differences in gene expression between WT and SMIM20-/- mouse heart RNA samples

first: Angela

last: Boshnakovska

first: Julius

middle: R

last: Pronto

first: Tanja

last: Gall

first: Abhishek

last: Aich

first: Jan

last: Prochazka

first: Zuzana

last: Nichtova

first: Radislav

last: Sedlacek

first: Izzatullo

last: Sobitov

first: Sofia

last: Ainatzi

first: Christof

last: Lenz

first: Dörthe

last: Katschinski

first: Henning

last: Urlaub

first: Niels

last: Voigt

first: Peter

last: Rehling

first: Laura

last: Kremer


title: T cell - DAM feedback loop drives CNS inflammation and neurodegenration in SPG15 at an early age [CD45+]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: The immune system is an emerging cause of neuroinflammation and is suspected to be involved in neurodegeneration. The role of microglia, the macrophages of the Central Nervous System (CNS), was extensively researched in CNS neuropathologies. However, we only start to understand the role of T cells in diseases like Alzheimer’s Disease (AD) and Huntington’s Disease (HD) and how microglial – T cell crosstalk contributes to these pathologies. Here we tackle these topics in a rare and less investigated disease called Spastic Paraplegia 15 (SPG15) using a Zfyve26-/- mouse model. We were able to show, that CD8+ T cells and microglia potentiate a pro-inflammatory response through bidirectional communication in SPG15 KO and not WT mouse brains. The increase of CD8+ T cells in SPG15 KO animals also required a TCR dependent component. These findings are in line with previous reports on neurodegenerative disease which hints at cross-condition mechanisms involved in CD8+T cell responses in CNS, when encountering accumulation of non-degradable material in the brain.

overall_design: Immune cells from old (15 months) and Zfyve26-/- (KO) or Zfyve26+/- (WT) mouse brains were isolated using Fluorescence-activated cell sorting (FACS). All animals were of B57BL/6 𝐶𝑋𝐶𝑅4;𝐶𝑟𝑒𝐸𝑅(𝑇2)−𝐼𝑅𝐸𝑆−𝐺𝐹𝑃;𝑅26𝐶𝐴𝐺−𝐿𝑆𝐿−𝑡𝑑𝑇 background and treated with tamoxifen at the age of 4-6 weeks.  3' counting scRNAseq was performed on CD45+ cells using SeqWell ^s3. These cells were stained with CITE-seq antibodies (ADTs and HTOs).  Full length scRNAseq libraries were generated via SmartSeq2. To that purpose, CD3+ cells were sorted into 384 well plates.

first: Aleksej

last: Frolov

first: Hao

last: Huang

first: Collins

last: Osei-Sarpong

first: Thomas

last: Ulas

first: Elvira

last: Mass

first: Marc

last: Beyer


title: A Tetramer of BCL11A is Required for Stable Protein Production and Fetal Hemoglobin Silencing

first: Stuart

last: Orkin

address: 1 Blackfan Circle

department: Hematology and Oncology

institute: Boston Childrens Hospital

summary: Down-regulation of BCL11A protein reverses the fetal (HbF, a2g2) to adult (HbA, a2β2) hemoglobin switch and is exploited in gene-based therapy for hemoglobin disorders. Due to reliance on ex vivo cell manipulation and marrow transplant, such therapies cannot lessen disease burden. To develop novel small molecule approaches, we interrogated the state of BCL11A protein in erythroid cells. We report that tetramer formation mediated by a single zinc-finger (ZnF0) is required for production of steady-state protein. Beyond its role in protein stability, the tetramer state is necessary for g-globin gene repression, as an engineered monomer fails to engage a critical corepressor complex. These aspects of BCL11A protein production identify tetramer formation as a vulnerability for HbF silencing, and provide opportunities for drug discovery.

overall_design: ATAC-seq experiments were performed in HUDEP-2 cells expressing wild-type BCL11A (WT), BCL11A with biallelic deletions of ZnF1 (DZnF1), BCL11A with biallelic deletions of both ZnF0 and ZnF1 (DZnF01), BCL11A knock-out (KO), or BCL11A with biallelic deletions of the NuRD-binding motif (DN) to assess their chromatin accessibility at various differentiation days.  To assess DNA binding of WT and DZnF01 BCL11A, CUT&RUN experiment was performed using BCL11A antibody in WT and DZnF01 HUDEP-2 cells on day 7 of differentiation.  Occupancy of NF-Y was analyzed in WT, DZnF0, DZnF1, and DZnF01 HUDEP-2 cells by CUT&RUN using NF-Y antibody on day 6 of differentiation. Occupancy of MTA2 was analyzed in WT, DN, DZnF0, DZnF1, DZnF01 HUDEP-2 cells by CUT&RUN using MTA2 antibody on day 7 of differentiation. RNAseq: We compared the gene expression profiles in WT, DZnF1, and DZnF01 HUDEP-2 cells by RNA-Seq on days 0 and 7 of differentiation.  We compared the gene expression profiles in WT and DN HUDEP-2 cells by RNA-Seq on days 0 and 4 of differentiation.

first: Ge

last: Zheng

first: Stacy

last: Wang


title: Guided Differentiation of Pluripotent Stem Cells for Cardiac Cell Diversity

first: Erik

last: McIntire

address: 920 E. 58th Street, CLSC 317

department: Department of Human Genetics

institute: University of Chicago

summary: Develop a new guided induced pluripotent stem cell differentiation protocol that rapidly generates diverse range of cardiac-relevant cell types.

overall_design:
Expression analysis of 10x scRNA-seq data from guided differentiation cell cultures (from 3 iPSC lines) for cell annotation and characterization.

Grant ID: T32 GM139782
Grant title: Genetic Mechanisms and Evolution Training Grant
Grantee: Erik McIntire
Funding source: National Institute of General Medical Sciences

Grant ID: T32 HL007381
Grant title: Cardiovascular Sciences Training Grant
Grantee: Erik McIntire
Funding source: National Heart, Lung, and Blood Institute

first: Kenneth

last: Barr

first: Yoav

last: Gilad


title: Effect of Gemcitabine and nab-paclitaxel in pancreatic cancer cachexia

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

summary: The aim of the study is to test if Gemcitabine in combination with nab-paclitaxel can prevent muscle wasting and cardiac dysfunction in a mouse model of pancreatic cancer cachexia.

overall_design: The study had three groups- Sham surgery group (control, group 1), KPC group- mice orthotopically impanted with pancreatic cancer cells (group 2) and KPC group receiving gemcitabine and nab-paclitaxel (group 3). RNA sequencing was performed in skeletal muscle and heart.

first: Ashok

last: Narasimhan

first: Yunlong

last: Liu

first: Leonidas

middle: G

last: Koniaris


title: The effect of SLC6A6 Knock-down on bcCML leukemia

first: Cameron

last: Baker

summary: RNA sequencing analysis was performed on leukemia cells sorted from sex and age matched SLC6A6 WT and KO leukemic mice

overall_design: Spleen from mice transplanted with bcCML leukemia ( BCR-ABL and NUP98-HOXA9) were extracted .Leukemia cells were sorted and processed for RNA sequencing

first: Sonali

last: Sharma

first: Benjamin

last: Rodems

first: Jeevisha

last: Bajaj

first: John

last: Ashton


title: The effect of bcCML leukemia progression on the bone marrow microenvironment

summary: Single Cell RNA-Sequencing was performed on CD45-Ter119- cells from leukemic mice at different stages of leukemic progression.

overall_design: Bone and bone marrow from mice transplanted with bcCML leukemia (BCR-ABL and NUP98-HOXA9) were extracted at timepoints 0, 2, 4, 7, 8, 11, and 14 days post transplant. CD45- Ter119- cells were sorted and processed for scRNA-Seq.


title: Inhibition of cytosolic translation mitigates mitochondrial dysfunction in C. elegans

city: Worcester

first: Rui

last: Li

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

summary: The mitochondrial unfolded protein response (UPR mt ) is regulated by the bZIP protein ATFS-1 which promotes mitochondrial protein homeostasis (proteostasis) and mitochondrial biogenesis in Caenorhabditis elegans . Upon mitochondrial perturbation, the ATFS-1-dependent transcriptional program promotes gene expression, leading to mitochondrial recovery. Conversely, atfs-1 -deletion worms harbor dysfunctional mitochondria, are developmentally impaired, and short-lived. However, atfs-1 -deletion worms develop to adults suggesting the presence of other signaling pathways that promote mitochondrial function and biogenesis in the absence of atfs-1 . We hypothesized that additional transcription factors regulate, or promote, mitochondrial function in the absence of atfs-1 . Here, we screened for transcription factors that could reduce the decline in mitochondrial function in the atfs-1 mutants when inhibited. Here, we demonstrate that inhibition of the nuclear hormone receptor NHR-180 re-establishes a functional mitochondrial network in atfs-1(null) worms, increases mtDNA content, and improves the developmental rate of wildtype worms. NHR-180 increases transcription of genes required for cytosolic protein synthesis in response to mitochondrial perturbation. Inhibition of the S6 kinase homolog, rsks-1 , in atfs-1(null) worms leads to a recovery of the mitochondrial network and mtDNA content consistent with nhr-180 regulating expression of protein synthesis components. Consistent with the observations in C. elegans , S6 kinase inhibition also increased mitochondrial biogenesis in mammalian atf5 -knockout cells that harbor severely impaired mitochondria. Intriguingly, nhr-180 or S6 kinase inhibition also rescues mitochondrial dysfunction caused by mutations in multiple genes required for oxidative phosphorylation. Combined, these studies suggest that increased protein synthesis contributes to the mitochondrial dysfunction caused by perturbations in OXPHOS gene expression and suggest a relatively straightforward approach to reducing the impact of mitochondrial dysfunction.

overall_design: Worms were collected at the L4 stage. RNA was extracted using Trizol reagent.

first: Avijit

last: Mallick

first: Cole

last: Haynes


title: T cell - DAM feedback loop drives CNS inflammation and neurodegenration in SPG15 at an early age

first: Joachim

last: Schultze

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

overall_design: Refer to individual Series


title: T cell - DAM feedback loop drives CNS inflammation and neurodegenration in SPG15 at an early age via CCR5-CCL5 interaction [CD3+]

overall_design: Immune cells from old (15 months) and Zfyve26-/- (KO) or Zfyve26+/- (WT) mouse brains were isolated using Fluorescence-activated cell sorting (FACS). All animals were of B57BL/6 𝐶𝑋𝐶𝑅4;𝐶𝑟𝑒𝐸𝑅(𝑇2)−𝐼𝑅𝐸𝑆−𝐺𝐹𝑃;𝑅26𝐶𝐴𝐺−𝐿𝑆𝐿−𝑡𝑑𝑇 background and treated with tamoxifen at the age of 4-6 weeks.  3' counting scRNAseq was performed on CD45+ cells using SeqWell v2. These cells were stained with CITE-seq antibodies (ADTs and HTOs).  Full length scRNAseq libraries were generated via SmartSeq2. To that purpose, CD3+ cells were sorted into 384 well plates.

first: Aleksej

last: Frolov

first: Hao

last: Huang

first: Collins

last: Osei-Sarpong

first: Thomas

last: Ulas

first: Elvira

last: Mass

first: Marc

last: Beyer


title: Sex differences in DNMT3A-mutant clonal hematopoiesis and the effects of estrogen [scATAC-Seq]

first: Julia

last: Stomper

first: Abhishek

last: Niroula

first: Roger

last: Belizaire

first: Marie

last: McConkey

last: Ebert


title: Oncogene cooperation in human leukemia

first: Cameron

last: Baker

institute: University of Rochester

summary: Validation of previously defined oncogene cooperativity signature across various human leukemia types. Additionaly, to characterize functional impact of these genes and defined network interactions that drive leukemia progression and survival.

overall_design: identify cohort of leukemia specimens, inlcuding AML and bcCML along with non-leukemia, healthy specimens to use as the baseline comparator.


title: Stress attenuation by the adrenergic-specific lncRNA NESPR prevents cell death in neuroblastoma cells [ATAC-seq]

status: Public on Apr 03 2025

city: Gent

first: Louis

last: Delhaye

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

summary: Neuroblastoma is a pediatric cancer of the sympathetic nervous system characterized by heterogeneous cell states that mirror normal differentiation trajectories. Each state is governed by a core regulatory transcriptional circuitry that reinforces cell identity through an autoregulatory feedforward loop. We identified the long non-coding RNA NESPR as specifically expressed in adrenergic neuroblastoma cells. NESPR expression correlates with high-risk neuroblastoma clinical parameters and poor patient survival. NESPR is located within an insulated gene neighborhood alongside PHOX2B, a master transcription factor of the adrenergic identity. NESPR depletion reduced cell proliferation and increased caspase activity in neuroblastoma cell lines, and NESPR knockout in a neuroblastoma zebrafish model led to reduced tumor penetrance. Subcellular localization revealed NESPR to be a cytosolic long non-coding RNA, suggesting a trans-regulatory function. RNA-sequencing following NESPR depletion revealed a shift from an adrenergic to a mesenchymal cell state, due to proteotoxic stress-induced molecular reprogramming. These findings suggest NESPR as a regulator of neuroblastoma cell identity with potential therapeutic opportunities in high-risk neuroblastoma cases.

overall_design: ATAC-seq of SK-N-BE(2)c with and without ASO treatment (2 NESPR-targeting ASOs, 1 negative control ASO).

first: Pieter

last: Mestdagh

first: Julliette

last: Roels

last: Van Vlierberghe


title: Stress attenuation by the adrenergic-specific lncRNA NESPR prevents cell death in neuroblastoma cells [4C-seq]

overall_design: 4C-seq of the NESPR-PHOX2B loci in neuroblastoma cell lines in SK-N-BE(2)c with ASO treatment (1 NESPR-targeting ASO, 1 negative control ASO).

first: Eva

last: D'haene

first: Sarah

last: Vergult

first: Bjorn

last: Menten


title: Stress attenuation by the adrenergic-specific lncRNA NESPR prevents cell death in neuroblastoma cells [RNA-seq]

overall_design: RNA-seq for neuroblastoma cell lines (IMR32, NGP, SK-N-BE(2)c) with and without ASO treatment (3 NESPR-targeting ASOs, 1 negative control ASO).

first: Dries

last: Rombaut


title: Potential mechanisms by which Jiawei Lianpu Yin inhibits Helicobacter pylori colonization and alleviates gastric mucosal inflammation and damage: Integrated transcriptomics, network pharmacology, and experimental validation

first: Xinyue

last: Zhang

address: No. 95 Luoyu Road, Luonan Street, Hongshan District, Wuhan

institute: The Affiliated Hospital of Wuhan Sports University

summary:
Ethnopharmacological relevance: Helicobacter pylori (H.pylori) infection is the leading cause of gastric mucosal damage and inflammation, and persistent infection is one of the major risk factors for gastric cancer. Eradication of H.pylori remains a clinical challenge, and therefore, it is urgently necessary to identify more drugs that can interfere with H.pylori colonization and promote its clearance. Jiawei Lianpu Yin (JWLPY) is a compound formula composed of natural drugs used to treat gastric diseases associated with H.pylori infection. However, the underlying mechanisms of its action are still unclear.
Aim of the study: The aim of this study was to investigate whether JWLPY can inhibits H.pylori colonization and alleviates gastric mucosal inflammation and damage and to explore its mechanism of action.
Materials and METHODS: The effects of JWLPY on Helicobacter pylori and gastric mucosa injury were studied by using Helicobacter pylori induced gastritis model in rats. Transcriptomics, network pharmacology and bioinformatics were used to determine the mechanism of JWLPY
Results: JWLPY inhibited the aggregation of inflammatory cells and preserved the integrity of the mucosal barrier, reducing autophagy and apoptosis in gastric mucosal epithelial cells. Network pharmacology and transcriptomics analysis revealed that JWLPY promotes the assembly and synthesis of MUC5AC in the endoplasmic reticulum by activating the IRE1-XBP1 signaling pathway, which enhances the process of protein assembly in the endoplasmic reticulum, thereby inhibiting H.pylori colonization in the gastric mucosa.
Conclusion: This study is the first to demonstrate that JWLPY inhibits H.pylori colonization in the gastric mucosa, alleviates gastric inflammation and damage, and is a potential drug for the treatment of H.pylori -related gastritis.

overall_design:
The effect of JWLPY on Helicobacter pylori and gastric mucosa injury in vivo was studied by using Helicobacter pylori induced gastritis model in rats. Transcriptomics, network pharmacology and bioinformatics were used to determine the mechanism of JWLPY
Control* samples refer to the group that did not receive any intervention during the experiment.
Model-* samples refer to the group in which gastritis was induced in rats using Helicobacter pylori infection.
LPY-* samples refer to the group that received intragastric administration of Jiawei Lianpu Yin treatment based on the gastritis model.

first: Lingyan

last: Wang

first: Lei

last: Huang

first: Guojun

last: Cao

first: Chaoqun

first: Yanjun

last: Duan

first: Wenliang

last: Lyu


title: The impact of NR1H3 deficiency on gene expression in ovarian cancer cells

city: Hefei

first: Yifan

last: Feng

state: Anhui

address: Jixi Road 218

institute: The Anhui Medical University

summary: NR1H3 is significantly influences cancer progression. Here, we identified the critical role of NR1H3 in the diagnosis and prognosis of ovarian cancer through bioinformatics analysis. Further functional experiments demonstrated that NR1H3 significantly promotes ovarian cancer progression through RPL29. RNA-seq analysis revealed that differentially expressed genes downstream of NR1H3 are significantly enriched in the TNF signaling pathway, which was validated by Western blot. In summary, our data provide new molecular insights into ovarian cancer.

overall_design: The NR1H3 SINC, NR1H3 SI, NR1H3 OENC and NR1H3 OE ovarian cancer cell lines were used for 3v3v3v3 RNA-seq.

first: Min

last: Li


title: Comprehensive Multi-Omics and Biochemical Analysis to Elucidate the Molecular Response Mechanisms of Gill and Kidney Tissues Under Acute Salinity Stress in Pseudobagras ussuriensis

city: Taigu

first: libo

last: gu

state: shanxi

address: No. 1 Xianming South Road

department: College of Animal Science

institute: Shanxi Agricultural University

summary: Saline is a key environmental parameter in aquaculture. Research on acute salinity stress can help farmers determine the optimal salinity level to reduce stress responses in fish larvae, improve survival rates, and increase production efficiencies. It can also aid in the selection or breeding of species suited to environments with specific salinities. However, the molecular mechanisms underlying the negative effects of high salinity on Pseudobagras ussuriensis and the regulatory mechanisms underlying its tolerance remain unclear. In this study, Pseudobagras ussuriensis was exposed to 10 g/L NaCl for 96 h, and the physiological and biochemical changes in the gill and kidney tissues were continuously monitored. Transcriptomic and metabolomic analyses of the gill and kidney tissues were conducted at 24 h to elucidate the molecular adaptation mechanisms to salt stress. A total of 2,554 differentially expressed genes (DEGs) were identified in gill and 1,066 DEGs in the kidney tissue, respectively. Compared with the control group, 826 genes were upregulated and 1,728 were downregulated in the gill tissue under acute salinity stress at 24 h, whereas 508 genes were upregulated and 558 were downregulated in the kidney tissue. These DEGs were involved in oxidative stress, energy metabolism, ion transport, and immune responses. Metabolomic analysis showed that compared to the control group, 85 differential metabolites (DMs) were identified in the gill tissue, with 49 upregulated and 36 downregulated, whereas 433 DMs were identified in the kidney tissue, with 252 upregulated and 181 downregulated. Notably, the levels of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) in the kidney and phosphatidic acid (PA) and PC in the gills were significantly increased, while sphingomyelin (SM) decreased. Integrated analysis of metabolomics and transcriptomics through the KGML network map revealed the downregulation of ALDH, ALDH7A1, AOX, and HADHA in the gill, and ENPP1_3, CD203, L-glutamine (downregulated), and Succinic Acid (upregulated) in the kidney. This study combined metabolomics, transcriptomics, and physiological-biochemical analyses to provide new insights into the molecular mechanisms of oxidative stress, energy metabolism, and immune regulation in gill and kidney tissues under acute salinity stress.

overall_design: Compare gene expression levels between gill and kidney

first: Yu

last: Liu

first: Libo

last: Gu


title: Oncometabolism Drives Autophagy Activation in Skeletal Muscle

city: Los Angeles

first: Anja

last: Karlstaedt

state: California

address: 127 San Vincente Blvd

department: Cardiology

institute: Cedars Sinai Medical Center

summary: We hypothesize that the oncometabolite D2-HG activates autophagy in skeletal muscle.

overall_design: Examination of gene expression in skeletal muscle from mice treated with the oncometabolite D2-HG for 30-days.


title: G-quadruplex profiling in complex tissues using single-cell CUT&Tag

city: Solna

first: Simon

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: G-quadruplexes (G4) are non-canonical DNA structures that gained increasing attention for their potential roles in gene regulation, with implications in neurodegenerative diseases and cancer. Despite their biological significance, G4 structures have not been studied systematically across tissues and cell types. In this study, we employ G4 single-cell CUT&Tag (G4 scCUT&Tag) to characterize G4 landscapes in postnatal mouse brain cells, leveraging single-cell analytical approaches commonly used in scRNA-Seq and scATAC-Seq datasets. Using conventional single-cell omics workflows to process and explore our data, we distinguished different cell types based on G4 heterogeneity. Furthermore, we performed uncoupled multi-omics integration of G4 scCUT&Tag data with scRNA-Seq gene expression profiles, using both a covariance-based technique (canonical correlation analysis) and a transfer learning-based deep learning approach. These integrations not only revealed significant co-enrichment of G4 and gene expression signals, but demonstrated that G4 scCUT&Tag enables detailed examination of G4 heterogeneity in complex tissues and supports integrative analysis of G4 profiles with other omics layers, offering new insights into the epigenomic landscapes of the developing central nervous system.

overall_design: mouse ESC and NIH-3T3 were subjected to bulk and single cell G4 CUT&Tag (two biological replicates), and mouse brain were subjected to single cell G4 CUT&Tag

first: Jing

first: Szabolcs

last: Hetey

first: Gonçalo

last: Castelo-Branco

first: Marek

last: Bartosovic


title: A gel-top model for characterizing the mesenchymal features of glioblastoma cells

first: Yuanzhong

last: Pan

address: 1002 Childs Way

institute: University of Southern California

summary: Glioblastoma (GBM) remains one of the most aggressive adult cancers, with limited treatment options due to an incomplete understanding of its biology. GBM exhibits different transcriptional subtypes, among which the mesenchymal (mGBM) variant is associated with particularly aggressive nature and poor outcomes. Developing models that capture mGBM phenotypes could offer new insights into its biology and therapeutic vulnerabilities. However, the lack of in vitro models for mGBM has posed challenges in investigating the aggressive GBM subtype. Here, we present a gel-top culture model in which GBM cells exhibit MES features, including distinct transcriptomic profiles, invasive phenotypes, cell morphology, cytoskeletal organization, and gene expression linked to cell-extracellular matrix interactions. Furthermore, co-culturing GBM cells with microglia in this system revealed enhanced microglial recruitment and interaction, effectively recapitulating the tumor microenvironment of mGBM that traditional 2D culture fails to model. Using the bioinformatic tool Small Molecule Suite, we identified casein kinase 2 (CK2) as a targetable molecule in GBM cells within our system, potentially driving MES features. Notably, CK2 inhibitors reduced the mesenchymal signature of mGBM cells, suggesting their potential as a targeted therapy for mGBM. Together, our findings suggest that the gel-top culture model replicates key features of mGBM, serving as a valuable platform for studying its biology and identifying novel therapeutic strategies.

overall_design: Two glioblastoma cell lines, T387 and MGG31, were used in the study. Cells were cultured  on plastic surface and on top of basement membrane estract type 2 to compare the gene expression between different culture methods. In drug treatment experiments, MGG31 was treated with three CK2 inhibitors, GO289, CX4945, and SGC-CK2-1. Three repeates were performed for each group.

first: Priscilla

last: Chan

first: Jeremy

middle: N

last: Rich

first: Steve

middle: A

last: Kay

first: Jinseok

last: Park


title: Artificial Light at Night Disrupts Circadian and Metabolic Gene Expression in the Green Anole Lizard (Anolis carolinensis): A Transcriptomic Analysis

city: Edinburgh

first: Violeta

last: Trejo-Reveles

address: Old College, South Bridge, Edinburgh

institute: The University of Edinburgh

summary: Artificial light at night (ALAN) disrupts natural light-dark cycles, posing ecological challenges for wildli in urban areas. Here we investigated the efcts of ALAN on gene expression in the brain, liver, skin, and gonads of green anole lizards (Anolis carolinensis) whose urban populations are increasingly exposed to light pollution. To identify genetic pathways impacted by ALAN exposure we analysed expression of genes associated with circadian and metabolic regulation at midday, midnight and at midnight with artificial light. Difrential expression analysis revealed that clock-related genes (PER1, NR1D1, CRY2) were significantly altered in the brain, liver, and skin following ALAN treatment and genes involved in glucagon regulation (GCG) and lipid metabolism (NOCT) were difrentially expressed in the liver, indicating metabolic disruptions. Skin exhibited unique responses to ALAN suggesting that repair responses may be altered as genes related to cellular processes, such as wound healing, were upregulated under normal light and dark conditions. Our findings also show that ALAN disrupts core circadian genes, impacting physiological processes including hormone regulation, glucose homeostasis, and potentially reproductive cycles. This study provides the first transcriptomic evidence of the efcts of light pollution on green anoles, highlighting the need to preserve natural light cycles in urban habitats. An interactive online database developed for this study allows further exploration of gene expression changes, to promote research on artificial light-polluted environments.

overall_design: Twenty-four free-living adult green anole lizards (Anolis carolinensis; twelve of each sex) were captured in the breeding season, in May 2024, on the urban campus of Trinity University in San Antonio, Texas, USA, during daylight hours. Green anole lizards were collected by using a dental floss loop attached to an extendable fishing pole or by hand and were transported individually to the Trinity University vivarium in cotton bags. On the day of capture, the body mass of each anole was measured to the nearest 0.1 g using a Pesola spring scale and snout-vent length measured to the nearest mm using a clear plastic ruler (Males: range 52-69mm, average 62mm; Females: range 51-57mm, average 55mm). Each individual was given a unique identification number on the lower jaw using a non-toxic permanent marker.  Each anole was then randomly assigned to one of three treatment groups: Midday, Midnight, or ALAN. Sex was determined by the presence of hemipenes and the size of the dewlap; four anoles of each sex were assigned to each treatment group. Green anole collection was performed under Scientific Permit SPR-0310-045 to Michele A. Johnson from Texas Parks and Wildli Department, with approval from Trinity University’s Animal Research Committee, protocol 051122-MJ2.Green anoles were rapidly decapitated without prior anaesthesia to avoid any confounding anaesthetic efcts on RNA expression. Brain (containing the pineal gland), eyes, dorsal skin, ventral skin, liver, and testes or ovaries were collected in under 7 min. 33 s and flash frozen on dry ice and stored at -80 oC until they were shipped to BGI Genomics (San Jose, CA, USA). Midday treatment dissections were performed between 12:48 to 13:45, and Midnight and ALAN treatment from 22:30 to 00:42.  Decapitation for the Midnight treatment group was performed in the dark under red torch light (HQRP, Harrison, NJ; emission peak in the red spectrum at 650 nm). To control for this additional illumination, ALAN treatment lizards were also illuminated by the same red torch light during decapitation.

first: Michele A

last: Johnson

first: Florissa F

last: Patterson

first: Grace E

last: Anderson

first: Zhou

last: Wu

first: Alex R.

last: Johnston

first: Simone L.

last: Meddle


title: Blood transcriptomic data from PRAM-D cohort

city: Brescia

first: Maria Grazia

last: Di Benedetto

address: Via Pilastroni 4

country: Italy

institute: IRCCS Centro San Giovanni di Dio Fatebenefratelli

summary:
Pregnant women suffering from depression show alterations in different biological systems, but the exact underlying mechanisms are still not clear.
We used microarrays to investigate the transcriptomic modulation in conditions such as depression and risk for developing depression during pregnancy.

overall_design: We explored the blood transcriptomic profile in 41 pregnant women with a current diagnosis of depression (depressed), 23 pregnant women, who were not depressed in pregnancy but, because of a history of depressive episodes, were considered at high risk of developing antenatal depression (history-only), and 28 pregnant women who had never experienced depression in their life, including the current pregnancy (controls).

first: Kristi M

middle: S

last: Priestley

first: Nadia

last: Cattane

first: Patrizia

last: Genini

first: Samantha

last: Saleri

first: Alessandra

last: Biaggi

first: Rebecca

middle: H

last: Bind

first: Susan

last: Conroy

first: Andrea

last: Du Preez

first: Katie

last: Hazelgrove

first: Sarah

last: Osborne

last: Pawlby

first: Vaheshta

last: Sethna

first: Carmine

last: Pariante

first: Annamaria

last: Cattaneo


title: Identification of miRNAs and Their Target Genes in juvenile Nicotiana benthamiana Plants [miRNA-Seq]

city: Hangzhou

first: fan

last: xiaoping

state: zhejiang

address: Hangzhou, China

institute: LC-Bio Technology Co.

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aims to identify and functionally characterize miRNAs and their target genes in juvenile Nicotiana benthamiana plants using miRNA sequencing (miRNA-seq) and degradome sequencing. miRNA-seq will be employed to profile the miRNA repertoire, while degradome sequencing will be used to identify miRNA-mediated mRNA cleavage sites and validate target genes. The combined approach will elucidate the regulatory roles of miRNAs in the early developmental stages of Nicotiana benthamiana and provide insights into their functional characteristics

overall_design: The miRNA and degradome sequencing data from 21-day-old Nicotiana benthamiana plants

first: Wenhao

last: Han

first: Fengbin

last: Zhang

first: Shunxia

last: Ji

first: Kailu

last: Liang

first: Junxia

last: Wang

first: Xiaoping

last: Fan

first: Shusheng

last: Liu

first: Xiaowei


title: Identification of miRNAs and Their Target Genes in juvenile Nicotiana benthamiana Plants [degradome]


title: Regulation of lung progenitor plasticity and repair by fatty acid oxidation [RNA-seq]

city: Columbus

first: Jhonny

last: Rodriguez Lopez

state: Ohio

address: Holly Ave 1383 203A

department: Internal medicine

institute: The Ohio State University

summary: Idiopathic pulmonary fibrosis (IPF) is an age-related interstitial lung disease, characterized by inadequate alveolar regeneration and ectopic bronchiolization. While some molecular pathways regulating lung progenitor cells have been described, the role of metabolic pathways in alveolar regeneration is poorly understood. We report that expression of fatty acid oxidation (FAO) genes significantly diminishes in alveolar epithelial cells of IPF lungs by single-cell RNA sequencing and tissue staining. Genetic and pharmacological inhibition in AT2 cells of carnitine palmitoyltransferase 1a (CPT1a), the rate-limiting enzyme of FAO, promoted mitochondrial dysfunction and acquisition of aberrant intermediate states expressing basaloid, and airway secretory cell markers SCGB1A1, and SCGB3A2. Further, mice with deficiency of CPT1a in AT2 cells show enhanced susceptibility to developing lung fibrosis with an accumulation of epithelial cells expressing markers of intermediate cells, airway secretory cells, and senescence. We found that deficiency of CPT1a causes a decrease in SMAD7 protein levels and TGF-β signaling pathway activation. These findings suggest that the mitochondrial FAO metabolic pathway contributes to the regulation of lung progenitor cell repair responses and deficiency of FAO contributes to aberrant lung repair and the development of lung fibrosis.

overall_design: To investigate the FAO pathway in AT2 cells, we collected IPF lung explants from patients diagnosed with IPF and undergoing transplantation. In parallel, we collected lung tissue from aged non-IPF individuals. Tissues were formalin-fixed and paraffin-embedded (FFPE) for preservation and used as input material for scRNA-Seq.

first: Quetzalli

middle: D

last: Angeles-López

last: Rodriguez-Lopez

first: Paula

last: Agudelo

first: Jazmin

last: Calyeca

first: Diana

last: Álvarez

first: Marta

last: Bueno

first: Lan

last: Tu

first: Myriam

last: Salazar-Terreros

first: Natalia

last: Vanegas-Avendaño

first: Jordan

last: Krull

first: Aigul

last: Moldobaeva

first: Srimathi

last: Bogamuwa

first: Stephanie

last: Scott

first: Victor

last: Peters

first: Brenda

last: Reader

first: Sruti

last: Shiva

first: Michael

last: Jurczak

first: Mahboobe

last: Ghaedi

first: Qin

last: Ma

first: Toren

last: Finkel

first: Mauricio

last: Rojas

first: Ana

last: Mora


title: mRNA profiling on CART19 cells treated with GM-CSF receptor alpha blockade or GM-CSF blockade

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: RNA sequencing was performed on three biological replicates of CART19 alone, GM-CSFRA Ab with CART19, or GM-CSF Ab with CART19

overall_design: T cells from normal donors were transduced with a replication-incompetent lentiviral vector expressing a second-generation chimeric antigen receptor (CAR) consisting of an anti-CD19 single chain variable fragment (FMC63) fused to 4-1BB and CD3ζ intracellular domains as previously described.  CART19 were cultured alone or with GM-CSFRA Ab or GM-CSF Ab (10ug/mL). Conditions each stimulated with irradiated NALM6 (CD19 antigen) for 24 hours. RNA was then isolated for sequencing.

first: Reona

last: Sakemura

first: Evandro

last: Bezerra

first: Michelle

last: Cox


title: Rorγt-positive dendritic cells are required for the induction of peripheral regulatory T cells in response to oral antigens

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine in St. Louis

summary: The intestinal immune system maintains tolerance to harmless food proteins and gut microbiota through peripherally-derived RORγt+Tregs (pTregs), which prevent food intolerance and inflammatory bowel disease. Recent studies suggested that RORγt+ antigen-presenting cells (APCs), which encompass rare dendritic cell (DC) subsets and type 3 innate lymphoid cells (ILC3s), are key to pTregs induction. Here, we developed a mouse with reduced RORγt+APCs by deleting a specific cis-regulatory element of Rorc encoding RORγt. Single-cell RNA-sequencing and flow cytometry analyses confirmed the depletion of a RORγt+DC subset and ILC3s. These mice showed a secondary reduction in pTregs, impaired tolerance to oral antigens and increase in Th2 cells. Conversely, newly and previously generated ILC3-deficient mice showed no pTregs or Th2 cells abnormalities. Lineage tracing revealed that RORγt+DCs share a lymphoid origin with ILC3s, consistent with their similar phenotypic traits. These findings highlight a unique role of lymphoid RORγt+DCs in maintaining intestinal immune balance and preventing conditions like food allergies.

overall_design: We performed single-cell RNA sequencing on sort purified CD3-B220-CD11c+MHC-II+ DCs extracted from mLNs and siLP of 15days old Gm38411-iCre-hCD2 reporter mice. Each tissue included three biological replicates, uniquely identified by the labeling of three distinct Hashtag antibodies.

first: Patrick

last: Fernandes Rodrigues