title: Tumor suppressors in Sox2-mediated lung cancers promote distinct cell intrinsic and immunologic remodeling [scRNA-seq]

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

summary: Non-small cell lung cancer (NSCLC) largely consists of lung squamous (LUSC) and lung adenocarcinoma (LUAD). While driver mutations are common in LUAD, LUSC has few if any actionable targetable drivers. Despite these distinct differences, alterations in the p53 and Pten tumor suppressors are common in both subtypes. While Sox2 is widely considered an LUSC proto-oncogene, the relationship of p53 and Pten with Sox2 is poorly understood. To evaluate the role of these tumor suppressors in Sox2-mediated NSCLC models on disease progression and the tumor microenvironment (TME), we deleted Trp53 or Pten in a C57BL/6J-Sox2hi, Nkx2-1-/-, Lkb1-/- (SNL) genetic background. In parallel, we generated a highly metastatic LUSC cell line (LN2A; derived from a Sox2high mouse model, followed by p53, Pten, and Cdkn2a deletion) that also grows in C57BL/6 mice. Histologic and single cell RNAseq analyses corroborated that SNL mice developed mixed tumors with both LUAD and LUSC histopathology while SNL-Trp53 and SNL-Pten mice developed LUAD and implanted LN2A tumors retained LUSC morphology. Compared with SNL mice, additional loss of p53 or Pten resulted in significantly reduced survival, increased tumor burden and altered tumor mucin composition. As the metastatic potential in the tumor models progressed from the least (SNL) to most (LN2A), we observed a progressive increase in cellular infiltrate, most notably high levels of recruited tumor-associated inflammatory monocytes (TIMs). We identified a sub-cluster of CD38+ TIMs in the LN2A model that significantly enriched for activation of the classical and alternative complement pathways. Importantly, Complement Factor B (Cfb) is associated with poor survival in LUSC patients, and we observed the LN2A model had significantly improved survival on a Cfb-/- background. Taken together, our findings demonstrate a cooperative role of p53 and Pten tumor suppressors in Sox2-mediated NSCLC tumor progression, mucin production, and remodeling of the immune TME.

overall_design: Single-cell RNA-Sequencing of tumors induced by four genetically engineered murine cell lines, consisting of: C57BL/6J-Sox2hi; Nkx2-1-/-; Lkb1-/- (SNL), Trp53 CRISPR deletion line in the SNL background (p53),  Pten CRISPR deletion line in the SNL background (PTEN), and a highly metastatic LUSC line,  LN2A.

first: Nisitha

last: Sengottuvel

first: Kristina

middle: M

last: Whately

first: Jennifer

last: Modliszewski

first: Rani

last: Sellers

first: William

middle: D

last: Green

first: Weida

last: Gong

first: Allison

middle: T

last: Woods

first: Eric

middle: W

last: Livingston

first: Katerina

last: Fagan-Solis

first: Gabrielle

last: Cannon

first: Lincy

last: Edatt

first: Hong

last: Yuan

first: Aaron

last: Chack

first: Yazmin

last: Sanchez

first: Katherine

last: Zhou

first: Alyaa

last: Dawoud

first: Jarred

last: Godfrey

first: Justin

middle: J

last: Milner

first: Gaorav

middle: P

last: Gupta

first: Chad

last: Pecot


title: Tumor suppressors in Sox2-mediated lung cancers promote distinct cell intrinsic and immunologic remodeling [RNA-seq]

status: Public on May 20 2025

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

country: USA

type: Expression profiling by high throughput sequencing

overall_design: Bulk RNA-Seq profiling of three murine LUSC cell lines, derived from a C57BL/6 background: JH716-18 (parental line),  LN1A (derivative of JH716-18), LN2A (highly metastatic derivative of LN1A)

first: Nisitha

last: Sengottuvel

first: Kristina

last: Whately

first: Jennifer

middle: L

last: Modliszewski

first: Rani

middle: S

last: Sellers

middle: C

first: Virginia

middle: V


title: Tumor suppressors in Sox2-mediated lung cancers promote distinct cell-intrinsic and immunologic remodeling

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

overall_design: Refer to individual Series


title: Satb1 directs the differentiation of TH17 cells through suppression of IL-2 expression [scMultiom ATAC/RNA-seq]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

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

type: Genome binding/occupancy profiling by high throughput sequencing

summary: TH17 cells play an important role in host defense especially in barrier organs. Altered functionality of TH17 cells is associated with dysregulated tissue homeostasis resulting in an increased susceptibility for the development of autoimmune diseases. Thus, it is critical to identify mechanisms governing physiological as well as pathophysiological TH17 cell differentiation and identify strategies targeting TH17 cell differentiation in disease settings. Here, we identified the genome organizer Special AT-rich sequence-binding protein 1 (Satb1) as a pioneering factor for TH17 cell development. Satb1 is highly expressed in TH17 cells and loss of Satb1 prevents the differentiation of TH17 cells. As a consequence, expression of Satb1 in CD4+ T cells is required for the formation of TH17 cell-driven autoimmune diseases. Mechanistically, Satb1 mediates TH17 cell development through regulating accessibility of the Il2 gene locus and thereby preventing IL-2 signaling early during TH17 cell differentiation. Thus, Satb1 is critical by suppressing IL-2 expression during the formation of TH17 cells and may be a novel therapeutic target for the treatment of TH17 cell-driven autoimmune diseases

overall_design: scMultiom ATAC/RNA-seq was performed following BD Rhapsody Express Single-Cell Analysis System. 4 Satb1fl/fl x CD4-CreERT2wt/+ mice and 4 Satb1fl/fl x CD4-CreERT2+/+ control mice received tamoxifen day 0 and day 3. on d7, spleen and LNs were isolated, processed, and naive CD4+ T cells were sorted (live single CD45+ CD3+ CD4+ CD62L+cells). Naive CD4⁺ T cells were differentiated under TH1 and TH17 conditions. Nuclei from TH1, TH17, and naive T cells were isolated and labeled with the nuclear Sample Tag reagent. After tagmentation, 40,000 labeled single nuclei from WT and KO cells were loaded onto a BD Rhapsody 8-Lane Cartridge

first: Mehnoush

last: Hadaddzadeh Shakiba

first: Tarek

last: Elmzzahi

first: Yuanfang

last: Li

first: Marc

last: Beyer


title: Unveiling the biological effects of DNA G-quadruplex ligands through multi-omics data integration

city: Naples

first: Nunzia

last: Iaccarino

address: Via Domenico Montesano, 49

department: Pharmacy

country: Italy

institute: University of Naples Federico II

summary: G-quadruplexes (G4s) are non-canonical DNA structures that have proved to play a pivotal role in various biological processes, including telomere maintenance and gene expression regulation. Owing to their prevalence in tumor cells, G4s have emerged as promising targets for cancer therapy, with a substantial body of research demonstrating the potential of G4 ligands as anti-cancer tools. However, a more comprehensive understanding of G4 binders’ mode of action is imperative to successfully translate them into therapeutic agents. Herein, we employed a multi-omics approach, integrating transcriptomics, proteomics and metabolomics, to identify key signaling pathways that mediate the anti-cancer effects of well-characterized G4-binding agents (berberine, PDS and RHPS4) on HeLa cancer cells. Our results revealed that, under the investigated experimental conditions, berberine treatment only had negligible cellular effects, whereas PDS-treated HeLa cells underwent significant changes at the transcriptomic, proteomic and metabolomic levels, with marked impairment in glycolysis, antioxidant capacity, lipids and nucleotides biosynthetic processes. Notably, RHPS4 could selectively affect mitochondrial activity, possibly through the specific stabilization of mitochondrial G-quadruplex structures. Overall, our findings provide a valuable multi-omics perspective on the cellular changes driven by G-quadruplex binders, that may accelerate the development of G4-targeted therapies.

overall_design: mRNA-seq profiling of HeLa cells treated with three different G-quadruplex ligands (Berberine, Pyridostatin, and RHPS4), compared to mRNA-seq profiling of untreated cells

first: Antonio

last: Randazzo

first: Anna

last: Di Porzio

first: Francesca

last: Romano

first: Carolina

last: Persico

first: Stefano

last: De Tito


title: FXR protects against neonatal sepsis via enhancing the immunosuppressive function of MDSCs

city: Guangzhou

first: Juan

last: He

state: Guangdong

address: No. 9, Jinshui Road

country: China

institute: Guangzhou Women and Children's Medical Center

summary: The presence of myeloid-derived suppressor cells (MDSCs) during the early postnatal period plays a protective role against neonatal inflammation. However, the mechanisms regulating neonatal MDSCs remain to be fully elucidated. In this study, we report that the bile acid receptor Farnesoid X receptor (FXR) acts as a pivotal positive regulator of neonatal MDSCs. Using FXR-deficient (FXR-/-) mice and FDA-approved FXR agonist obeticholic acid (OCA), we demonstrated that FXR deficiency impairs the immunosuppressive and antibacterial functions of neonatal MDSCs, thereby exacerbating the severity of neonatal sepsis. Adoptive transfer of MDSCs alleviates sepsis severity in FXR-/- neonatal pups. Mechanistic studies reveal that HIF1a, a well-established regulator of MDSCs, is a direct transcriptional target of FXR. Patients with neonatal sepsis displayed reduced MDSC frequencies and impaired expression of FXR and HIF-1α, which was negatively correlate with the clinical parameters. These observations highlight the important role of FXR in neonatal MDSCs and its therapeutic potential in neonatal sepsis.

overall_design: PMN-MDSCs sorted from spleens of FXR-/- and WT neonatal mice (7 days). PMN-MDSCs were resuspended in TRIzol for RNA extraction. Library preparation was performed using a SMARTer Ultra low RNA kit, and sequencing was conducted on an Illumina NovaSeq platform (150-bp paried-end).

first: Jie

last: Zhou

first: Yuxin

last: Zhang

first: Yuchao

last: Jing


title: Dynamic Multi-omics Profiling Unveils Bimodal Epigenetic Roles of Chromatin O-GlcNAc modification in Premature Senescence Program [ChIP-seq]

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

institute: Dalian University of Technology

summary: Cellular senescence, a recognized instigator of tumorigenesis and age-associated disorders, can be precipitated by characteristic alterations in gene expression profiles. However, the underlying mechanisms that precise orchestrate the expression of senescence-related genes are still elusive. Here, we employed a time-series approach using a chemical genomics multi-omics strategy to panoramically investigate the role of O-GlcNAc chromatin-associated proteins (OCPs) throughout the process of oncogene-induced senescence (OIS) in human primary fibroblasts. The progression of OIS is associated with the dynamic accumulation of chromatin O-GlcNAc modification, which facilitates cells commitment to senescence. Through the integration of dynamic analyses of transcriptome and epigenome profiles, we can demonstrate that OCPs experience genomic occupation shifts across diverse epigenetic chromatin states, and display bimodal sequential regulatory activity within the senescence transcriptome. Mechanistically, O-GlcNAc aids in the formation of bimodal epigenetic regulatory complexes (TF-SWI/SNF and NuRD), which dictate the gene expression patterns related to both the senescence-associated secretory phenotype (SASP) and cell cycle arrest. Additionally, we pinpointed O-GlcNAc JUN and GATAD2A as key regulators affecting the phenotypes of OIS in both in vitro and in vivo models of senescence and tumorigenesis. Our findings on the dynamic behavior and chromatin organization principles of O-GlcNAc epigenetic factors provide insights into the senescence process and enable potential therapeutic manipulation of the senescence phenotype.

overall_design: Examination O-GlcNAc protein bound chromatin loci in human primary fibroblasts cells (oncogene induce senescence time D0, D2, D4, D10).Epigenetic modification,include histone modification analysis in human primary fibroblasts cells(oncogene induce senescence time D0, D2, D4, D10).

first: Nana

first: Jianing


title: Deciphering the role of histone modifications in memory and exhausted CD8 T cells [RNA-seq]

city: Philadelphia

first: Shelley

middle: L.

last: Berger

state: PA

address: 3400 Civic Center Blvd

department: Penn Epigenetics Institute

institute: University of Pennsylvania

summary: Exhausted CD8 T cells (TEX) arising during chronic infections and cancer have reduced functional capacity and limited fate flexibility that prevents optimal disease control and response to immunotherapies. Compared to memory (TMEM) cells, TEX have a unique open chromatin landscape underlying a distinct gene expression program. How TEX transcriptional and epigenetic landscapes are regulated through histone post-translational modifications (hPTMs) remains unclear. Here, we profiled key activating (H3K27ac and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in naive CD8 T cells (TN), TMEM and TEX. We identified H3K27ac-associated super-enhancers that distinguish TN, TMEM and TEX, along with key transcription factor networks predicted to regulate these different transcriptional landscapes. Promoters of some key genes were poised in TN, but activated in TMEM or TEX whereas other genes poised in TN were repressed in TMEM or TEX, indicating that both repression and activation of poised genes may enforce these distinct cell states. Moreover, narrow peaks of repressive H3K9me3 were associated with increased gene expression in TEX, suggesting an atypical role for this modification. These data indicate that beyond chromatin accessibility, hPTMs differentially regulate specific gene expression programs of TEX compared to TMEM through both activating and repressive pathways.

overall_design: LCMV Armstrong (Arm) and LCMV clone 13 (Cl13) were grown in house and titrated. PBMCs were isolated from the peripheral blood of naive P14 donor mice. 1000 naive P14 cells were adoptively transferred i.v. into sex-matched recipient mice. P14 cells were isolated from donor mice of a distinct congenic background than recipient mice to enable donor P14 cells to be distinguished from recipient CD8 T cells. Recipient mice were infected with LCMV Arm or LCMV Cl13 one day following adoptive cell transfer. Spleens were collected at d30 of LCMV Arm and d32 of LCMV Cl13 infection.

first: E. John

last: Wherry

first: Shelley L.


title: GLIOBLASTOMAS ARE CHARACTERIZED BY A REDUCED NUMBER OF M6A SITES IN LNCRNAs

city: Kaunas

first: Giedrius

last: Steponaitis

address: Eiveniu str. 4

department: Neuroscience Institute

country: Lithuania

institute: Lithuanian University of Health Sciences

summary: Recent studies have suggested the potential role of posttranscriptional N6-methyladenosine (m6A) RNA modifications in diverse biological processes, including tumor development. In contrast to intensively studied mRNA modifications, insufficient information is known so far about the epitranscriptome of long non-coding RNAs (lncRNAs). Furthermore, an epitranscriptome of LncRNAs in glioma pathogenesis has not been previously presented. Thus, this study aimed to profile m6A modifications within lncRNAs in different grades of gliomas using direct RNA long-read sequencing, with the goal of yielding both nucleotide and transcript-resolved m6A hits as biomarkers for tumor progression.  Here we explored ONT direct RNA-seq to detect N6-methyladenosine (m6A) sites within lncRNAs' RRACH motifs in 26 glioma tumor tissues. Generally, 98.5% of m6A-modified RRACH motifs were detected in mRNA transcripts, and 1.16% in lncRNAs. We identified 60-748 unique m6A-modified lncRNAs for individual gliomas. On average, 15.84% of all RRACH motifs within lncRNAs were modified in glioblastomas (GB), while the m6A frequency reached 23.73% in the low-grade glioma (LGG) group. Unsupervised clustering analysis based on lncRNAs' m6A status resulted in three m6A clusters. Patients within the highly modified lncRNAs cluster (C3) experienced significantly longer survival compared to patients with lower methylation rates who were clustered into C1/C2 (2901 days in C3 vs 439 days in C1, log-rank test p=0.019).   In summary, we discovered that lncRNAs are highly modified in LGG while multiple epi-marks, found in low-grade gliomas, are absent in GB tissues revealing m6A contribution to glioma pathology.

overall_design: Post-surgical tumor samples (17 glioblastoma (GB) and 9 diffuse astrocytoma (LGG)) sequenced using direct RNA sequecning approach for the detection of RNA expression and m6A modifications.  Differences of RNA expression and m6A modifications were compared between GB and LGG groups.

first: Rugile

last: Dragunaite

first: Rytis

last: Stakaitis

first: Vytenis Pranas

last: Deltuva

first: Amit

last: Sharma

first: Daina

last: Skiriutė


title: Transcriptomic profiling of Sox11 wildtype and mutant intestinal organoids upon  treatment with TGF-β1

city: Freiburg

first: Andreas

last: Hecht

address: Stefan-Meier-Str. 17

institute: Albert-Ludwigs-Universität Freiburg

summary: Colorectal cancer (CRC) cells infiltrating surrounding tissue commonly undergo partial epithelial-mesenchymal transitions (pEMT) and employ a collective mode of invasion. How these phenotypic traits are regulated and possibly interconnected remains underexplored. Here, we used intestinal organoids with CRC driver mutations as model system to investigate the mechanistic basis of TGF‑β1-induced pEMT and collective invasion. By scRNA-seq we identified multiple cell subpopulations representing a broad pEMT spectrum, where the most advanced pEMT state correlated with the transcriptional profiles of leader cells in collective invasion and a poor prognosis mesenchymal subtype in human CRC. Bioinformatic analyses pinpointed Sox11 as a transcription factor whose expression peaked in the potential leader/pEMThigh cells. Immunofluorescence staining confirmed Sox11 expression in cells at the invasive front of TGF‑β1-treated organoids. Loss-of-function and overexpression experiments showed that Sox11 is necessary, albeit not sufficient, for TGF-β1-induced pEMT and collective invasion. In human CRC samples, elevated Sox11 expression was associated with advanced tumor stages and worse prognosis. Unexpectedly, aside from orchestrating the organoid response to TGF-β1, Sox11 controlled expression of genes related to normal gut function and tumor suppression. Apparently, Sox11 is embedded in several, distinct gene regulatory circuits, contributing to intestinal tissue homeostasis, tumor suppression, and TGF-β-mediated cancer cell invasion.

overall_design: Sox11 wildtype and knockout small intestinal organoids (lines 931 and 1308; Apc-/-, KrasG12D/+, Trp53R172H/+ )were treated with solvent or TGF-β1 for 72 h, followed by bulk RNA-seq analysis.

first: Yu-Hsiang

last: Teng

first: Bismark

last: Appiah

first: Geoffroy

last: Andrieux

first: Monika

last: Schrempp

first: Katja

last: Rose

first: Angelika

last: Hofmann

first: Manching

last: Ku

first: Sven

last: Beyes

first: Melanie

last: Boerries


title: Exosomal miR-432-5p, miR-4433b-5p and miR-599 as Biomarkers for Monitoring the Severity of Anti-N-methyl-D-aspartate Receptor Encephalitis

city: Beijing

first: Zhuxiao

last: Xie

address: NO.1 Dongjiaomin Lane

institute: Beijing Tongren Hostipal

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: The diagnosis and monitoring of Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis typically rely on clinical manifestations and the detecting of anti-NMDAR antibodies. However, several studies have found that anti-NMDAR IgG in serum is not entirely specific and can be detected in about 3% of healthy individuals. Objective: To identify novel biomarkers that can accurately monitor the severity of anti-NMDAR encephalitis. Methods: We enrolled 9 patients with anti-NMDAR encephalitis and categorized them into an acute-phase group and a stable-phase group based on the duration of illness and disease severity. The clinical severity of the patients was assessed using the modified Rankin Scale (mRS) and the clinical assessment scale for autoimmune encephalitis (CASE). Then, we isolated exosomal miRNAs from plasma samples and analysed the differentially expressed miRNAs through next-generation sequencing. The sequencing results were validated using RT-qPCR. Furthermore, we conducted correlation analyses between miRNAs and clinical severity. Finally, we performed the functional pathways analysis to explore the underlying mechanisms in anti-NMDAR encephalitis. Results: We have found that exosomal miR-432-5p, miR-4433b-5p and miR-599 exhibited significant differences between patients with anti-NMDAR encephalitis and healthy controls, as well as at different stages of the disease. The expressions of miR-432-5p and miR-4433b-5p were negatively correlated with both the mRS and the CASE. We further identified that the pathways involved in rhythmic processes and neuroinflammation, as well as glutamatergic signaling, play significant roles in the pathogenesis of anti-NMDAR encephalitis. Conclusions: Our research indicates that exosomal miR-432-5p, miR-4433b-5p and miR-599 were highly correlated with the severity of anti-NMDAR encephalitis and can serve as potential biomarkers for disease monitoring. We further identified the pathways play significant roles in anti-NMDAR encephalitis. By modulating the functions of these crucial pathways, we can potentially uncover novel therapeutic targets and improve patient outcomes.

overall_design: Peripheral blood samples were collected from patients with anti-NMDAR encephalitis and healthy people for the isolation of extracellular vesicles. RNA extraction and miRNA sequencing were performed on extracellular vesicles

first: Lei

last: Liu

first: Yanjun

last: Guo

first: Hanqiu

last: Jiang

first: Lin

last: Li

first: Zhixin

last: Qiao

first: Jing

last: Zhang

first: Jingxiao

first: Yatong

first: Jiawei

last: Wang


title: CDK4/6 inhibitors plus RANKL inhibitors in syngeneic TNBC model

city: Lisbon

first: Sandra

last: Casimiro

address: Av. Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

summary: CDK4/6i alone have proven to be largely ineffective in breast cancer, even in the presence of functional retinoblastoma protein (pRB). In this study, we investigated the role of the RANK pathway in the response to CDK4/6i in pRB-proficient TNBC. Transcriptomic analysis of allografts revealed that combining CDK4/6i with RANKLi more effectively mounts an anti-tumoral immune response.

overall_design: The transcriptomic profiles of tumor tissue from 4T1 xenografts implanted in NSG mice, collected after 12 days of treatment with Vehicle, OPG-Fc, Palbociclib or Palbociclib+OPG-Fc, were analyzed by RNASeq. 2-3 tumors per group were included.

first: Inês

last: Gomes

first: Luis

last: Costa


title: Deciphering the role of histone modifications in memory and exhausted CD8 T cells [CUT&Run]

first: Shelley

last: Berger

first: E. John

last: Wherry

first: Shelley L.


title: Massively parallel quantification of mutational impact on IAPP amyloid formation

city: Barcelona

first: Marta

last: Badia-Graset

address: Baldiri i Reixac, 14

country: Spain

institute: Institute for Bioengineering of Catalonia

summary: Amyloid fibrils formed by the islet amyloid polypeptide (IAPP) cause pancreatic beta-cell damage, resulting in reduced insulin secretion and Type 2 diabetes (T2D). Variations in the primary amino acid sequence of IAPP can influence its aggregation rate and animals expressing IAPP variants that do not form amyloids, do not develop T2D. Conversely, specific single amino -acid changes in IAPP are enough to accelerate its aggregation rate. Understanding how mutations impact IAPP aggregation can help gain mechanistic understanding into the process of pathogenic amyloid formation of this peptide and preventively identify mutations that may contribute to the risk of developing T2D. Here, we employ deep mutational scanning to measure the ability to nucleate amyloids for 1663 IAPP variants, including substitutions, insertions, truncations and deletions and identify variants that increase amyloid formation in all mutation classes. Our results point at a continuous stretch of residues (15-32) which likely is structured in IAPP amyloids and that matches the core of the early aggregated species formed by IAPP in vitro. Inside this region, mutations have a more drastic effect in the 21-27 NNFGAIL segment, suggesting tighter structural constraints for this stretch in IAPP amyloids. Finally,  by comparing this mutational atlas to that of another amyloid, Amyloid beta (Aβ42), the peptide that aggregates in Alzheimer’s Disease, we find that the effects of mutations that slow down nucleation correlate between the two amyloids, but that when it comes to mutations that accelerate nucleation one single amyloid dataset cannot be used to predict mutational effects in the other.

overall_design: Systematic measurement of the nucleation of single amino acid substitutions, single amino acid insertions, variants generated through polymerase slippage, deletions and truncations in IAPP.

first: Benedetta

last: Bolognesi

last: Badia


title: TNBC response to CDK4/6 inhibitors plus RANKL inhibitors

summary: CDK4/6i alone have proven to be largely ineffective in TNBC, even in the presence of functional retinoblastoma protein (pRB). In this study, we investigated the role of the RANK pathway in the response to CDK4/6i in pRB-proficient TNBC. Transcriptomic analysis of xenografts revealed that combining CDK4/6i with RANKLi more effectively arrested the cell cycle.

overall_design: The transcriptomic profiles of tumor tissue from MDA-MB-231 xenografts implanted in NSG mice, collected after 21 days of treatment with Vehicle, OPG-Fc, Palbociclib or Palbociclib+OPG-Fc, were analyzed by RNASeq. 2-3 tumors per group were included.


title: Expression data from human PDAC-derived cancer-associated fibroblast (CAF) treated with isorhamnetin

city: Tsukuba

first: Munkhzul

last: Ganbold

state: Ibaraki Prefecture

address: 1 Chome-1-1 Tennodai

country: Japan

institute: AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL)

summary:
Human pancreatic ductal adenocarcinoma (PDAC) derived cancer-associated fibroblast (CAF) treated or not with isorhamnetin
We used microarrays to detail the global hallmarks, gene ontology, and KEGG pathway terms affected by isorhamnetin treatment of CAF derived from human PDAC

overall_design: PDAC derived CAFs were immortalized and treated with 20 µM isorhamnetin for 96 h, followed by total RNA extraction and hybridized on Applied Biosystems Clariom S array


title: Age-associated adipose-derived stem cell activity is dictated by IGF2BP3-dependent regulation of glutamine and BCAA catabolism

city: Xi'an

first: Yifu

last: Zhu

address: 陕西省西安市新城区长乐西路169号

institute: 中国人民解放军空军军医大学

summary: Cultured human adipose-derived stem cells(hASCs) are considered as a homogeneous population in vitro. We used single cell RNA sequencing (scRNA-seq) to reveal the cellular heterogeneity of hASCs and identify aging-related cell clusters in hASCs.

overall_design: The hASCs for scRNA-seq were isolated from the discarded abdominal subcutaneous fat (SAT) from 3 healthy infants (<3 years old) and 3 elderly (>75 years old).

first: Zichao

first: Liangliang

last: Shen

first: Dahai

last: Hu


title: Nuclear functions of CFAP20 in transcription and replication [DRIP-seq]

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

summary: Fine-tuning DNA replication and transcription co-occurrence is vital to avoid collisions between their machineries. This is especially relevant near promoters, where RNAPII initiates transcription and often arrests, forming R-loops. Arrested RNAPII poses a roadblock for DNA replication, which evolutionarily initiates near promoters. The mechanisms that salvage arrested RNAPII during elongation to avoid conflicts with incoming replisomes remain unaddressed. In this study, employing genome-wide and proteomic approaches, we identify and characterize CFAP20 as part of a protective pathway that rescues arrested RNAPII in promoter-proximal regions, diverting it from the path of co-directional replisomes. CFAP20-deficient cells accumulate R-loops specifically near promoters, displaying defects in replication origin firing and fork progression. Co-depletion of the Mediator coactivator complex or removal of RNAPII engaged with R-loops rescues these replication phenotypes. Therefore, we propose that CFAP20 salvages arrested RNAPII under conditions of high Mediator-driven transcription to promote RNAPII elongation, thereby preventing collisions with co-directional replisomes.

overall_design:
To explore the role of CFAP20 in R-loop resolution, we performed DRIP-seq experiments in RPE1 cells being either wild type (WT) or CFAP20-KO.
NOTE: The records have been updated for data processing steps, contributor lists, replacement/addition of processed data files on May 30, 2025.

first: Sidrit

last: Uruci

first: Daphne

middle: E

last: Boer

first: Paul

last: Chrystal

first: Maxime

last: Lalonde

first: Andreas

last: Panagopoulos

first: George

last: Yakoub

first: Idil

last: Kirdök

first: Klaas

last: de Lint

first: Melanie

last: van der Woude

first: Tiemen

last: Wendel

first: Sem

last: Brussee

first: Annelotte

last: Wondergem

first: Nila

middle: K

last: van Overbeek

first: Jolanthe

last: Lingeman

first: Mats

last: Ljungman

first: Alexander

last: van Oudenaarden

first: Haico

last: van Attikum

first: Alfred

last: Vertegaal

first: Sylvie

last: Noordermeer

first: Rob

last: Wolthuis

first: Matthias

last: Altmeyer

first: Stephan

last: Hamperl

first: Vincent

last: Tropepe

first: Jeroen

last: van den Berg

first: Diana

last: van den Heuvel


title: RNA-seq Reveals Paxillin as a Key Facilitator of Endothelial Cell Migration and Angiogenesis after Spinal Cord Injury

city: Delhi

first: Jaidev

last: Sharma

state: Delhi

address: Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, near Govind Puri Metro Station, New Delhi, Delhi 110020

department: Computational Biology

country: India

summary: Spinal cord injury (SCI) is a catastrophic condition resulting in significant neurological deficits. To map the altered pathways within the lesion epicenter and the surrounding rostro-caudal segments, we employed RNA-seq on injured spinal cord tissue. We sequenced samples from three level (rostral, epicenter, and caudal) at days 1, 14, and 28 post-injury to systematically define the transcriptomics profile, aiming to identify pathways related to angiogenesis after SCI. Gene set enrichment analysis (GSEA) revealed enriched pathways, including hepatocyte growth factor (HGF) receptor signalling and alpha-6 beta-4 signaling pathway, suggesting an active angiogenic signature. Furthermore, the participating genes in HGF receptor signaling were validated by qPCR analysis, demonstrating that HGF receptor signaling is involved in the pathological remodeling following SCI. Subsequently, we investigated paxillin as a candidate gene promoting endothelial cell migration through HGF receptor signaling. Immunohistochemistry data suggest paxillin’s role in mediating the endothelial cell migration and proliferation post-SCI. In summary, our findings indicate that paxillin is a key mediator of endothelial cell proliferation and migration in response to angiogenic factors like HGF following SCI. However, extensive mechanistic studies are required to fully establish paxillin’s role in endothelial cell migration and proliferation after SCI.

overall_design: Transcriptomics alterations were validated spatiotemporally in contusion model of spina cord injury at DPI-1, DPI-14, and DPI-28.

first: Manjeet

last: Chopra

first: Aditya

middle: A

last: Singh

first: Zarna

last: Pathak

first: Priyanka

last: Vats

first: Vibhor

last: Kumar

first: Amit

last: Mandoli

first: Hemant


title: Aging-Related Increase in Hepatic Microbiota and Glutamine Promotes M2 Polarization of Macrophage in the Aging Liver

city: changzhi

first: Pu

last: wang

state: shanxi

address: jiefang road 163

institute: changzhi medical college

summary: In the aging liver, a distinct senescence-associated secretory phenotype (SASP) and a concomitant influx of inflammatory cells are observed. Traditionally considered an immune-privileged site, the etiology of pronounced immune cell infiltration into the liver during senescence remains inadequately understood. The potential contribution of microbial entities to this age-related hepatic inflammation is not well-characterized. Through the analysis of clinical liver specimens and aged murine models, we documented a notable augmentation in hepatic bacterial load that paralleled the progression of aging, concomitant with a marked decline in the diversity of the hepatic microbiome. With advancing senescence, we detected an upregulation of glutamine biosynthesis within the liver. Furthermore, our findings reveal that enhanced glutamine availability preferentially skews macrophage differentiation toward an anti-inflammatory M2 phenotype, rather than a pro-inflammatory M1 phenotype. Utilizing the glutaminase inhibitor BPTES, we demonstrated that attenuation of glutamine catabolism leads to a substantial reduction in both hepatic bacterial abundance and inflammatory cell infiltration, while simultaneously impeding the M2 macrophage polarization. Our study provides new insights into the dynamic relationship between shifts in hepatic microbial populations, glutamine metabolic pathways, and immune regulatory mechanisms throughout liver aging. These findings lay the groundwork for pioneering therapeutic approaches targeting the mitigation of liver pathologies associated with the aging process.

overall_design: AGING MICE AND AGING MICE TREAT WITH BPTES, LATTERLY LIVER WAS ISOLATED AND THE TOTAL RNA was isolated for RNA-sequence


title: Nuclear functions of CFAP20 in transcription and replication [BrU-seq]

first: Martijn

last: Luijsterburg

overall_design:
To explore spatial connections between transcription and replication at the genome-wide level, as well as the role of CFAP20 in these processes, we mapped RNA polymerase II (RNAPII) and CFAP20 occupancy using chromatin immunoprecipitation (ChIP)-seq, nascent transcription by bromouridine (BrU)-seq and TTchem-seq, and R-loops by DNA-RNA hybrid immunoprecipitation (DRIP)-seq in RPE1 cells being either wild type (WT), CFAP20-KO, CFAP20-KO rescued with CFAP20-GFP, or CFAP20/CCNC-dKO.

NOTE: The records have been updated for data processing steps, contributor lists, replacement/addition of processed data files on May 30, 2025.

first: Sidrit

last: Uruci

first: Daphne

last: Boer

first: Paul

last: Chrystal

first: Maxime

last: Lalonde

first: Andreas

last: Panagopoulos

first: George

last: Yakoub

first: Idil

last: Kirdök

first: Klaas

last: de Lint

first: Melanie

last: van der Woude

first: Tiemen

last: Wendel

first: Sem

last: Brussee

first: Annelotte

last: Wondergem

first: Nila

last: van Overbeek

first: Jolanthe

last: Lingeman

first: Mats

last: Ljungman

first: Alexander

last: van Oudenaarden

first: Haico

last: van Attikum

first: Alfred


title: RNA-seq of Satb1 conditional KO in CD4+ na ve T cells reveals role of Satb1 in developing Th17 T cells through suppression of IL-2 expression

first: Joachim

last: Schultze

summary: TH17 cells play an important role in host defense especially in barrier organs. Altered functionality of TH17 cells is associated with dysregulated tissue homeostasis resulting in an increased susceptibility for the development of autoimmune diseases. Thus, it is critical to identify mechanisms governing physiological as well as pathophysiological TH17 cell differentiation and identify strategies targeting TH17 cell differentiation in disease settings. Here, we identified the genome organizer Special AT-rich sequence-binding protein 1 (Satb1) as a pioneering factor for TH17 cell development. Satb1 is highly expressed in TH17 cells and loss of Satb1 prevents the differentiation of TH17 cells. As a consequence, expression of Satb1 in CD4+ T cells is required for the formation of TH17 cell-driven autoimmune diseases. Mechanistically, Satb1 mediates TH17 cell development through regulating accessibility of the Il2 gene locus and thereby preventing IL-2 signaling early during TH17 cell differentiation. Thus, Satb1 is critical by suppressing IL-2 expression during the formation of TH17 cells and may be a novel therapeutic target for the treatment of TH17 cell-driven autoimmune diseases.

overall_design: RNA-Seq was performed comparing 4 conditional KO samples of naive CD3+CD4+CD25-CD44low/-CD62L+ T cells from Satb1fl/fl x CD4-CreERT2wt/+  mice treated with tamoxifen to 4  untreated (WT) samples of of naive CD3+CD4+CD25-CD44low/-CD62L+ T cells from Satb1fl/fl x CD4-CreERT2wt/+  mice.

first: Maren

last: Koehne

first: Jonas

last: Schulte-Schrepping

first: Marc

last: Beyer


title: Nuclear functions of CFAP20 in transcription and replication [FLASH-seq]

first: Martijn

last: Luijsterburg

overall_design: To explore whether CFAP20 is an RNA-binding protein, we performed FLASH-seq in RPE1 cells being either CFAP20-KO (negative control) or CFAP20-KO expressing FLASH-BIO-CFAP20.

first: Daphne

last: Boer

first: Sidrit

last: Uruci

first: Ibrahim

last: Ilik

first: Tugce

last: Aktas

first: Diana

last: van den Heuvel


title: Single-cell RNA-seq of CNS T cells derived from Satb1-deficient and Satb1-sufficient animals in EAE model

summary: TH17 cells play an important role in host defense especially in barrier organs. Altered functionality of TH17 cells is associated with dysregulated tissue homeostasis resulting in an increased susceptibility for the development of autoimmune diseases. Thus, it is critical to identify mechanisms governing physiological as well as pathophysiological TH17 cell differentiation and identify strategies targeting TH17 cell differentiation in disease settings. Here, we identified the genome organizer Special AT-rich sequence-binding protein 1 (Satb1) as a pioneering factor for TH17 cell development. Satb1 is highly expressed in TH17 cells and loss of Satb1 prevents the differentiation of TH17 cells. As a consequence, expression of Satb1 in CD4+ T cells is required for the formation of TH17 cell-driven autoimmune diseases. Mechanistically, Satb1 mediates TH17 cell development through regulating accessibility of the Il2 gene locus and thereby preventing IL-2 signaling early during TH17 cell differentiation. Thus, Satb1 is critical by suppressing IL-2 expression during the formation of TH17 cells and may be a novel therapeutic target for the treatment of TH17 cell-driven autoimmune diseases

overall_design: scRNA-seq was performed following BD Rhapsody Express Single-Cell Analysis System. Six Satb1fl/fl x CD4-CreERT2wt/+ mice and two Satb1fl/fl x CD4-CreERT2+/+ control mice received tamoxifen day -7 and day -3 before induction of EAE. Brain and spinal cord were isolated, processed, and CD4+ T cells were sorted (live single CD45+ CD3+ CD4+ cells). CD4+ T cells were multiplexed using oligo-tagged anti-CD45 antibodies before sorting, and cells corresponding to the same genotype were pooled after sort. CD4+ T cells were loaded on a BD Rhapsody cartridge, with cells corresponding to each genotype being loaded on two independent cartridges.

first: Tarek

last: Elmzzahi


title: Satb1 directs the differentiation of TH17 cells through suppression of IL-2 expression

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

overall_design: Refer to individual Series


title: ATAC-seq of Satb1 conditional KO in CD4+ naïve T cells reveals epigenetic role of Satb1 in developing Th17 T cells by controlling the accessibility of Il2, thereby inhibiting IL-2 signaling in the initial stages of T cell differentiation.

overall_design: ATAC-Seq was performed following Buenrostro et al., 2013 comparing 5 conditional KO samples of naive CD3+CD4+CD25-CD44low/-CD62L+ T cells from Satb1fl/fl x CD4-CreERT2wt/+  mice treated with tamoxifen to 5 untreated (WT) samples of of naive CD3+CD4+CD25-CD44low/-CD62L+ T cells from Satb1fl/fl x CD4-CreERT2wt/+  mice.


title: Pain may be related to pathogen phenotype: Transcriptome analysis of Staphylococcus aureus isolated from PJI with different VAS scores

city: Fuzhou

first: Xinyu

last: Fang

address: Chazhong road

institute: The First Affiliated Hospital of Fujian Medical University

summary: To explore whether S. aureus contributes to the mechanism of pain, we assayed S. aureus isolates from 3 severe pain PJI (sp-PJI) and 3 mild pain PJI (mp-PJI) by RNA-sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sp-PJI and mp-PJI.


title: Whole genome bisulfite sequence in heat treated rice seeds

city: Fukuoka

first: Yushi

last: Ishibashi

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Department of Bioresource Sciences

institute: Kyushu University, Faculty of Agriculture

type: Methylation profiling by high throughput sequencing

summary: We report the relationship between transgenerational growth and  profiling of DNA methylation in rice seeds treated with heat.

overall_design: Examination of DNA methylation in seeds treated with heat.

first: Ishibashi

last: Yushi

first: Suriyasak

last: Chetphilin


title: Chronic paternal morphine exposure increases sensitivity to morphine-derived antinociception

first: Mathieu

last: Wimmer

address: 1701 N 13th Street

institute: Temple University

summary: Preclinical studies suggest that parental exposure to drugs of abuse such as opioids can have  profound and long-lasting effects on reward processing and drug sensitivity across generations.  However, little is known about the impact of long-term paternal morphine exposure on sensitivity  to morphine-derived antinociception in offspring. We developed a novel sub-second pain scale with statistical modeling and machine learning to  measure mechanical nociception in Long Evans and Sprague Dawley male and female rats. Next,  we used this rat pain scale with a multigenerational paternal morphine exposure paradigm to  determine whether chronic paternal morphine exposure impacts pain sensitivity in offspring.  Finally, we used RNA sequencing to identify potential molecular correlates of sire exposure to  morphine on offspring. Surprisingly, we found that von Frey hair filaments (VFHs), the most commonly-used noxious  mechanical stimuli to test pain sensitivity, are not painful to rats as measured by this novel rat  pain scale. Male progeny produced from morphine-treated sires did not exhibit any baseline  changes in sensitivity to noxious mechanical stimuli but had greater sensitivity to the  antinociceptive properties of morphine. Changes in gene expression within the periaqueductal  gray, including primary members of the RGS family of proteins, were identified that may play a  role in modified sensitivity to morphine within offspring. These findings reveal nuanced responses to VFHs that should be considered in future pain  studies and demonstrate that long-term paternal exposure to morphine increases sensitivity to  morphine-derived analgesia in the subsequent male generation.

overall_design: 12 samples from the periaqueductal grey were analyzed, including 6 control and 6 experimental.

first: Andre

last: Toussaint

first: William

last: Foster

first: Jessica

last: Jones

first: Samuel

last: Kaufmann

first: Meghan

last: Wachira

first: Robert

last: Hughes

first: Angela

last: Bongiovanni

first: Sydney

last: Famularo

first: Benjamin

last: Dunham

first: Ryan

last: Schwark

first: Reza

last: Karbalaei

first: Carmen

last: Dressler

first: Charlotte

last: Bavley

first: Nathan

last: Fried

first: Ishmail

last: Abdus-Saboor


title: Regulatory circuits of mitophagy restricts cell death for mounting memory CD8+ T cell formation

city: Epalinges

first: Ping-Chih

last: Ho

address: Ch. des Boveresses 155

country: Switzerland

institute: Ludwig Cancer Institute, UNIL

summary: Mitophagy, a central guarding process to maintain mitochondrial quality, is commonly impaired in human diseases, but its impacts in adaptive immunity remains unclear. Here, we found that Parkinson’s patients have reduced CD8+ memory T cell abundance and failed to form memory T cells upon COVID-19 vaccination. We further unveiled that regulators of mitophagy, including Parkin and NIX, were upregulated in response to IL-15 for supporting memory T cell formation. Our results indicate that the mitophagy machinery orchestrate survival and metabolic dynamics required for memory T cell formation.

overall_design: Examination of transcriptomes changes of antigen specific CD8 T cell with Parkin knockout in acute infection.

first: Fabien

last: Franco


title: The miR-3648/FRAT1-FRAT2/c-Myc feedback loop modulates the metastasis and invasion of gastric cancer cells

first: Jide

last: Wang

address: 1838 Guangzhou Avenue North

department: Department of Gastroenterology

institute: Nanfang Hospital, Southern Medical University

summary: RNA-seq were used to screen differentially expressed genes in AGS  transfected with NC and miR-3648 mimics.

overall_design: In the experiments, we performed RNA-sequencing of AGS cells transfected with NC or miR-3648 mimics. 3 replicates were setted per group.Then screened for up-regulated or down-regulated genes in AGS cells using NC as a control.


title: Integrating Reproductive States and Social Cues in the Control of Sociosexual Behaviors (scRNAseq data)

first: Kun

last: Li

address: HaiDian

institute: Tsinghua University

summary: Female sociosexual behaviors, essential for survival and reproduction, are modulated by ovarian hormones and triggered in the context of appropriate social cues. Here we identify primary estrous-sensitive Cacna1h-expressing medial prefrontal cortex (mPFCCacna1h+) neurons that integrate hormonal states with recognition of potential mates to orchestrate these complex cognitive behaviors. Bidirectional manipulation of mPFCCacna1h+ neurons shifts opposite-sex-directed social behaviors between estrus and diestrus females via anterior hypothalamic outputs. In males, these neurons serve opposite functions compared to estrus females. Miniscope imaging reveals mixed-representation of self-estrous states and social target sex in distinct mPFCCacna1h+ subpopulations, with biased-encoding of opposite-sex cues in estrus females and males. Mechanistically, ovarian hormone-induced Cacna1h upregulation enhances T-type rebound excitation after oxytocin inhibition, driving estrus-specific activity changes and the sexually dimorphic function of mPFCCacna1h+ neurons. These findings uncover a prefrontal circuit that integrates internal hormonal states and target-sex information to exert sexually bivalent top-down control over adaptive social behaviors.

overall_design: To characterize the molecular features of mPFC neurons responsive to estrous cycle and sex, the mPFC tissues were extracted from two estrous female mice, two diestrous female mice, and two male mice, and the cells were isolated for 10x Genomics scRNAseq analyzing.


title: Transcriptional stratification of necrotizing enterocolitis identifies distinct disease subtypes

status: Public on May 19 2025

city: Seoul

first: Murim

last: Choi

address: 103 Daehakro, Jongrogu

country: South Korea

institute: Seoul National University

summary: Necrotizing enterocolitis (NEC) is a severe inflammatory disorder of the intestine that affects neonatal babies, with a mortality rate of 30–50%. Despite the severe nature of the disease, its rare incidence and early onset prevent further understanding of its etiology and the development of treatment strategies. To further understand the pathogenic mechanism of this disease, we subjected intestinal tissues from ten NEC patients and three control individuals to RNA-sequencing. Clustering of the affected tissues revealed three clusters, each with a distinct transcriptional profile characterized by the expression of genes enriched in inflammatory pathways related to lipid binding and no obvious expression signature. The three subtypes displayed distinct gene expression patterns specific to the cell types composing the small intestine layers. Our results elucidate the genetic rationale underlying patient-specific symptoms, prognosis.

overall_design: RNA-seq profiling of Necrotizing enterocolitis patients and non-NEC patients

first: Jean

last: Lee

first: So Hyun

last: Nam

first: Da young

last: Ko

first: Joong kee

last: Youn

first: Jaemoon

last: Koh

first: Hee Beom

last: Yang

first: Hyun-Young

last: Kim


title: Proximal TCR signaling by endogenous self-peptides modifies gene expression without amplifying distal signaling in CD4 T cells

city: Bethesda

first: Jianfei

last: Hu

state: MD

address: BG NIHBC T40 RM 101A-09

department: VRC

institute: NIH

summary: The goal of the study was to characterize the molecular signatures of lymph node T cell of TCR transgenic mouse under different treatment. We compared the transcriptome profiles of mouse lymph node T cells under different treatment (NP (no peptide), GP (self-peptide), MCC (agonist), GP+MCC).

overall_design: Mouse lymph node T cell populations were sorted and whole transcriptome analysis was performed using an Illumina NovaSeq 6000 machine

first: Gideon

last: Wolf


title: Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks [MPRA]

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Genetic variants associated with autoimmune diseases are highly enriched within putative cis-regulatory regions of CD4+ T cells, suggesting that they alter disease risk via changes in gene regulation. However, very few genetic variants have been shown to affect T cell gene expression or function. Here, we tested >18,000 autoimmune disease-associated variants for allele-specific expression using massively parallel reporter assays in primary human CD4+ T cells. We find 545 variants that modulate expression in an allele-specific manner (emVars). Primary T cell emVars greatly enrich for probable causal variants, are mediated by common upstream pathways, and their putative target genes are highly enriched within a lymphocyte activation network. Using bulk and single-cell CRISPR-interference screens, we confirm that emVar-containing T cell cis-regulatory elements modulate both known and previously unappreciated target genes that regulate T cell proliferation, providing plausible mechanisms by which these variants alter autoimmune disease risk.

overall_design: This project contains MPRA data of 18,312 variants identified from 578 GWAS index variants (representing 531 distinct GWAS loci) associated with autoimmune disease in which T-cells are known to play a role. Additonally, it includes and 91 positive enhancer controls and 506 negative controls. The dataset includes 5 samples of plasmid DNA barcode sequencing and 7 samples of mRNA barcode sequencing read replicates from human primary T cells.

first: Ching-Huang

first: Maxwell

last: Dippel

first: Meghan

last: McQuade

first: LeAnn

last: Nguyen

first: Arpit

last: Mishra

first: Stephan

last: Pribitzer

first: Samantha

last: Hardy

first: Harshpreet

last: Chandok

first: Florence

last: Chardon

first: Troy

last: McDiarmid

first: Hannah

last: DeBerg

first: Jane

middle: H

last: Buckner

first: Jay

last: Shendure

first: Carl

middle: G

last: de Boer

first: Michael

last: Guo

first: Ryan

last: Tewhey

first: John

last: Ray


title: Stress during lactation: a hidden link to offspring bone health

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

summary: Early life resource limitation is one factor that could have a major impact on child health and development. Thus, using a rat model of limited bedding and nesting (LBN), we investigated the postnatal bone development, mineralization, and microarchitecture. Pregnant Sprague-Dawley rats were subjected to a LBN model to induce chronic early life stress (CES), while a control group was maintained under standard conditions. The offspring were assessed at postnatal day (PND) 10, 21, and 35. Tibial length was measured, and tibial and lumbar vertebral bone mineral density (BMD), content (BMC), and area (BMA) were assessed using dual-energy X-ray absorptiometry (DXA). Bone microarchitecture was examined using microcomputed tomography (μCT). Changes in gene expression from the lumbar vertebrae were analyzed by transcriptome. At PND 10, there were no significant differences in BMD and BMC between the treatment groups, but tibial length was significantly decreased by CES. By PND 21, tibial BMC and BMA were significantly reduced in the CES group, indicating impaired bone mineral accumulation. At PND 35, tibial length remained significantly reduced by CES, while BMD and BMC differences were less affected. Vertebral BMA and BMC were reduced by CES. μCT analysis of tibial cortical bone showed significant changes in cortical thickness and bone volume at PND 10 and 21, respectively. For the lumbar vertebrae, μCT data indicated significant increases in the degree of anisotropy and structural model index at PND 21 and 35, respectively. Transcriptome analyses revealed significant differential expression of genes involved in immune response, cellular repair, and stress adaptation at PND 21 but not at PND 10 and PND 35. CES significantly disrupts BMC, BMD, length and microarchitecture differently at various stages of postnatal development. Transcriptome analyses suggest that these changes are mediated by alterations in gene expression related to immune function and cellular repair. Future research should focus on tracking the longitudinal impacts of CES on bone health from infancy into adulthood, and exploring nutritional interventions, stress reduction programs, and molecular studies that can mitigate the negative effects of CES on bone.

overall_design: Animal experiments were performed at Arkansas Children’s Research Institute as approved by the Institutional Animal Care and Use Committee of the University of Arkansas for Medical Sciences (Little Rock, AR). Rats were housed in 12-hour light/dark conditions with ad libitum access to a standard rodent chow (Lab diets, Prolab RMH1800, St. Louis. MO) and water.  Timed pregnant Sprague-Dawley rats (Charles River, Wilmington, MA) were delivered to the vivarium on gestational day 18.  Dams delivered pups without intervention on PND 0. On PND 2, the dams were randomly transferred to cages containing a standard plexiglass cage with ample sawdust and 3 paper towels to use as nesting material (STD), or an impoverished cage (CES) which had limited sawdust which was inaccessible to the dam by a wire mesh platform which sat 2cm above the cage floor and one half of one paper towel was provided as nesting material (Figure 1). Pups were randomly distributed to dams until each litter contained 12 pups with equal male: female ratio. These cages then remained undisturbed for 7 days. On  PND 10, all litters were transferred to and maintained in standard cages until offspring were weaned on PND 21. On PND 10, 21 and 35, equal numbers of offspring were anesthetized with isoflurane and euthanized by decapitation. The bilateral tibia and lumbar vertebra were collected and stored at -80°C until analyses.

first: Ranjitha

last: Chandrashekar

first: Bharath K.

last: Mulakala

first: Manoj

last: Gurung

first: Geetanjali

last: Venna

first: Jolene R.

last: Rearick

first: Brenda

last: Onyekweli

first: Meghan L.

last: Ruebel

first: Jasmine

last: Dada-fox

first: Jasmina A.

last: Zeledon

first: Rachelanne

last: Talatala

first: Kayleigh

last: Rodriguez

first: Laura R.

last: Osborn

first: Mary Grace

last: Bishop

last: Smith

first: Kimberly E.

last: Stephens

first: Edralin A.

last: Lucas

first: Laxmi

last: Yeruva


title: Innate immune responses between low DIPs and high DIPs LAIV inoculations in the mouse upper respiratory tract revealed by bulk RNA-seq

city: Changchun

first: Weiheng

last: Su

address: Qianjin Street, 2699

institute: Jilin University

summary: To investigate the innate immune responses of low DIPs and high DIPs H3N2 LAIVs in mouse turbinate tissues, the transcriptomes at multiple timepoints were analyzed using bulk RNA-seq.

overall_design: Female 6–8-week-old BALB/c mice were intranasally immunized with of low DIPs LAIV or high DIPs LAIV. The turbinate and adjacent mucosal tissues were isolated at 8 hpi, 2 dpi, 4 dpi, and 6 dpi, respectively for bulk RNA-seq.

first: Min

last: Wu

first: Peihan

last: Wang

first: Fei

last: Chen


title: TNFR2 loss prevents TOX upregulation in CD8+TIM3+ T cells and affords improved responses to tumor and chronic LCMV

city: Durham

first: Aditya

middle: Anand

last: Mohan

address: 126 Constitution Drive

institute: Duke University

summary: Preview PDF Abstract Exhaustion represents a collection of programmed T cell differentiation states and an important mode of T cell dysfunction. T cell progression from progenitor to terminal exhaustion is associated with upregulation of the transcription factor TOX and expression of TIM3. Our understanding of factors regulating TOX expression and the transition from progenitor to terminal exhaustion, however, remains incomplete. We reveal here that T cell upregulation of tumor necrosis factor receptor type II (TNFR2) coincides with the gain of phenotypic markers and functions reflective of terminal exhaustion. Meanwhile, knocking out TNFR2 affords a novel population of T cells that express TIM3 but possess diminished TOX levels and functional characteristics of both progenitor and terminally exhausted cells. TIM3+ TNFR2 KO T cells exhibit reduced exhaustion transcriptional programs and enhanced AP1 pathway signatures. Finally, TNFR2 KO mice demonstrate improved T cell-dependent control of tumor and chronic lymphocytic choriomeningitis viral (cLCMV) infection, while pharmacologic antagonism of TNFR2 licenses responses to checkpoint blockade in multiple tumor models.

overall_design: To investigated transcriptional differences in WT and TNFR2 KO CD8+ T cells, terminally (TIM3+ ) exhausted T cells were sorted from cLCMV-infected spleens. Cells were lysed using the TRI reagent (Zymo, cat # R2050-1-50) and RNA was isolated using the Direct-Zol MinPrep kit from Zymo (Cat # R2050), including the optional DNaseI treatment step. RNA was eluted in 25µL RNase- and DNase-free water. mRNA was purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, cat # E7490). Samples were processed using the NEBNext Ultra-II RNA library prep kit from New England Biolabs (cat # E7775S) and the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer pairs) (NEB, cat # E6440S) according to manufacturer’s protocol.


title: Transcriptomic atlas of the morphologic development of the fungal pathogen Coccidioides reveals key phase-enriched transcripts

city: San Francisco

first: Christina

last: Homer

state: CA

address: 513 Parnassus Ave, S472

institute: University of California, San Francisco


title: PDK1 regulates metabolic balance in osteosarcoma stem cells

city: Gifu

first: Kazuya

last: Tokumura

address: 1-25-4 Daigakunishi

department: Bioactive Molecules

institute: Gifu Pharmaceutical University

summary: 143B cells cultured under tumorsphere (OSCs) and adherent (non-OSCs) conditions

overall_design: To investigate the mechanism of stemness regulation by PDK1 in osteosarcoma stem cells, we used the PDK1 knockdown 143B cells under tumor spheroid conditions.

last: Fukasawa

first: Jiro

last: Ichikawa

first: Koki

last: Sadamori

first: Manami

last: Hiraiwa

first: Eiichi

last: Hinoi


title: Aging-Related Decline of Astrocytic APOE Expression via Extracellular Vesicle

city: Seongnam

first: Jae Hyun

last: Park

state: Gyeonggi-do

address: 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-

institute: CHA University

summary: APOE, a well-established genetic risk factor for Alzheimer’s disease, is also closely associated with the aging process. Previous studies have demonstrated age-related declines in APOE expression within astrocytes. To investigate the mechanisms underlying this reduction, in this study, we performed small RNA sequencing on extracellular vesicles (EVs) derived from human fetal brain astrocytes. Our findings reveal miR-let-7b, enriched in astrocyte-derived EVs, as a key mediator of age-related APOE downregulation. Furthermore, we uncover a novel role for APOE in regulating astrocyte senescence, providing new insights into the molecular interplay between aging and neurodegenerative disorders.

overall_design: small RNA profiling of EVs released from human fetal brain-derived astrocytes


title: Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks

first: Stephanie

last: Osmond


title: A dietary intervention following incretin analog treatment restores adipose tissue functions in diet-induced obese mice

city: Leuven

first: Mitsugu

last: Shimobayashi

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: Obesity is associated with the development of type 2 diabetes. In recent years, incretin analogs are prescribed at a high rate for treatment of obesity and diabetes due to their potent effects on lowering bodyweight and improving glucose homeostasis. However, many patients do not stay on incretin analog therapy and thereby rapidly regain bodyweight. The non-compliance of patients to incretin analog therapy is not only due to drug shortage but also insufficient knowledge on the long-term effects of the therapy. To address this knowledge gap, we examined the effects of incretin analog treatment and withdrawal on adipose tissue functions in high fat diet (HFD)-induced obese mice. Our transcriptome data suggest that incretin analog treatment restored most of obesity-mediated deregulated gene expression in adipose tissue. However, genes encoding lipogenic enzymes, downregulated by HFD, were not restored by incretin analog treatment. Interestingly, a dietary intervention with normal chow diet (ND) feeding, but not calorie-matched HFD feeding, restored the expression of lipogenic enzymes. Upon incretin therapy withdrawal, mice displayed rapid bodyweight regain, impaired adipose tissue function, and glucose intolerance. In contrast, a ND intervention following incretin analog therapy withdrawal restored lipogenic gene expression in adipose tissue, maintained glucose homeostasis, and minimized body weight regain. This study revealed the effects of incretin analog therapy and therapy withdrawal on adipose tissue and highlights the importance of the dietary composition during and after incretin analog therapy. Thus, our findings may contribute to the development of long-term therapy guidelines of incretin analog therapy for patients with obesity.

overall_design: To check which genes remain deregulated and which genes are restored upon incretin analog treatment, we performed RNA seq analysis in subcutaneous white adipose tissue (sWAT) obtained from ND-fed mice, HFD-fed mice, HFD-fed mice treated with semaglutide, HFD-fed mice treated with tirzepatide and HFD-fed mice that received a dietary intervention (diet switch from HFD to ND). 8 samples from each group were sequenced, making a total of 40 samples.


title: Transcriptomic profiles of neutrophils during pediatric cardiac surgery

city: Boston

first: Koichi

last: Yuki

state: MA

address: 300 Longwood Avenue

institute: Boston Children's Hospital

summary: Pediatric cardiac surgery is associated with signficant inflammatory responses. In this study, we tried to dissect transcriptomic signatures of neutrophils in the perioperative period.

overall_design: We obtained blood neutrophils from pediatric patients and subjected to bulk RNA sequencing experiments.

first: Wiriya

last: Maisat


title: Single-cell RNA-sequencing identifies anti-cancer immune phenotypes in the early lung metastatic niche during breast cancer

city: Ann Arbor

first: Ian

last: Schrack

state: MI

address: 1600 Huron Parkway

department: Biomedical Engineering

institute: University of Michigan

summary: We performed single-cell RNA sequencing (scRNA-seq) to analyze the immune microenvironment at both the natural metastatic site in the lung and a synthetic metastatic site within a biomaterial implant (scaffold) using the 4T1 murine model of metastatic triple-negative breast cancer.

overall_design: Lungs, spleens, and biomaterial scaffold implants were isolated from both time-matched healthy, and 4T1-tumor bearing mice receiving throughout the normal course of metastatic progression - 7, 14, and 21 days post 4T1-inoculation. Lungs, spleens, and scaffolds were processed into a single cell suspension and analyzed by scRNAseq following standard DropSeq protocols.

first: Sophia

middle: M

last: Orbach

first: Michael

middle: D

last: Brooks

first: Yining

last: Zhang

first: Scott

last: Campit

first: Joseph

last: Decker

first: Ryan

last: Rebernick


title: Multi-omics Profiling of the Lateral Ventricle Choroid Plexus Reveals Temporal Cellular Remodeling, Early Immune Gene Activation, and a Novel Epithelial Subtype [snMultiome]

city: Stockholm

first: Mónica

middle: da Silva

last: Fernandes

address: Nobels väg 6

country: Sweden

institute: Karolinska Institutet

summary: Healthy brain development and function highly depend on the choroid plexus. Temporal alterations in the cellular landscape and gene expression of choroid plexus cells, whether in health or disease, can alter immune cell trafficking in the brain and cerebrospinal fluid composition, ultimately impacting brain dynamics. Here, we performed a comprehensive multi-omics analysis—including bulk and single-cell transcriptomics and epigenomics—of the lateral ventricle choroid plexus across early postnatal and adult stages in mice and rats. We uncovered striking fluctuations in the choroid plexus cellular composition from neonatal to adult stages, accompanied by transcriptional remodeling of all main cell types. Immune profiling revealed a marked increase in immune cells in adulthood and an altered cell-type diversity through time. Surprisingly, we observed an early activation of host-defense genes in choroid plexus cell, beginning in the neonatal period and progressively increasing into young adulthood.  Epithelial cells exhibited subtype diversity and plasticity, with distinct gene expression programs and chromatin accessibility profiles emerging over time. Notably, we identified a previously unrecognized epithelial cell subtype with unique gene markers suggesting a specialized function. Ligand-receptor interaction analysis revealed a progressive remodeling of cellular crosstalk networks during CP maturation, suggesting dynamic intercellular signaling as the tissue develops. Our study offers a comprehensive atlas of gene activity and chromatin accessibility in the lateral ventricle CP cells, providing a valuable resource to guide future efforts in targeting gene expression at the CP for therapeutical purposes.

overall_design: We have collected the choroid plexus from the lateral ventricles of C57BL/6 mice at the following developmental time points: postnatal day  (P11) and P60.  We then performed scMultiome (scRNA-seq together with scATACseq) analysis.

first: Lili

last: Li

first: Eduarda

last: Correia

first: Alice

last: Vieira

first: Diana

last: Afonso

first: Jonas

last: Campos

first: Neemat

last: Mahmud

first: Mandy

last: Meijer

first: Eneritz

last: Agirre

first: Nobrega

last: Claudia

first: Fernanda

last: Marques

first: Gonçalo

last: Castelo-Branco

first: João Carlos

last: Sousa

first: Ana Mendanha

last: Falcão


title: KDM5 demethylases suppress R-loop-mediated “viral mimicry” and DNA damage in breast cancer cells [CUT&Tag_S96]

city: San Diego

first: Marie

last: Classon

address: 10555 Science Center Dr

institute: Pfizer

summary: Tumors with low expression of Interferon-Stimulated Genes (ISG) and Antigen Presentation (AP) genes respond relatively poorly to current immunotherapies. One of the early hallmarks of cancer is DNA hypomethylation in genomic repeat regions, resulting in the expression of normally silenced endogenous “viral” elements.  Such epigenetic changes have the potential to augment anti-tumor immune responses as well as reduce tumor cell fitness through the generation of aberrant nucleic acid species (NAS) and consequent activation of NAS-sensing pathways.  Therefore, tumor evolution should favor additional selective events that suppress NAS generation, possibly yielding specific therapeutic vulnerabilities.  Here, we show that the Lysine Demethylase 5 (KDM5) family of epigenetic regulatory enzymes suppress R-loop formation in genomic repeat regions in cancer cells.  We find that KDM5 inhibition in luminal breast cancer cells results in R-loop-mediated DNA damage, reduced cell fitness and an increase in ISG and AP signatures as well as cell surface Major Histocompatibility Complex (MHC) class I, mediated by RNA:DNA hybrid activation of the CGAS/STING pathway. KDM5 inhibition does not result in DNA damage or activation of the CGAS/STING pathway in normal breast epithelial cells, suggesting that KDM5 inhibitors may enable a wide therapeutic window in this setting, as compared to STING agonists or Type I Interferons. These findings provide new insights into the interplay between epigenetic regulation of genomic repeats, R-loop formation, innate immunity, and cell fitness in the context of cancer evolution and therapeutic vulnerability.

overall_design: Cut-and-Tag profiling of R-loops using S9.6 antibody in HCC1428 cells treated with KDM5 inhibitor C48 for 5 days

first: Lena

last: Lau

first: Kurt

last: Henderson

first: Ahu

last: Turkoz

first: Sara

last: Linker

first: Dorte

last: Schlesinger

first: Brad

last: Townsley

first: Brian

last: Egan

first: Shoba

last: Regunathan

first: Robert

last: Rollins

first: Xianju

last: Bi

first: Zhijian

last: Chen

first: Oleg

last: Brodsky

first: Clifford

last: Restaino

first: Murali

last: Gururajan

first: Kristen

last: Jensen-Pergakes

first: Anders

last: Malarstig

first: Chames

last: Kermi

first: Paul

last: Moore


title: KDM5 demethylases suppress R-loop-mediated “viral mimicry” and DNA damage in breast cancer cells [RNA-Seq]

first: Marie

last: Classon

overall_design: RNA-seq profiling of HCC1428 cells treated with KDM5 inhibitor C48 for 2 and 7 days

first: Lena

last: Lau

first: Kurt

last: Henderson


title: A bovine 3D endometrium-on-a-chip revelas the role fo conceptus-derived factors CAPG and PDI in conceptus-endometrium communication

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

country: United Kingdom

institute: University of Leeds

summary: Early embryo loss affects all mammalian species, including humans and agriculturally important food-producing mammals such as cattle. The developing conceptus (embryo and extra-embryonic membranes) secretes factors which modify the endometrium and can be critical for early pregnancy processes such maternal recognition of pregnancy (MRP) and enhancing uterine receptivity to implantation. For example, a competent bovine conceptus secretes IFNT to initiate MRP. The bovine conceptus also secretes other proteins at the time of MRP, including CAPG and PDI, which are highly conserved among placental mammals. We have previously shown that these proteins act upon the endometrium to modulate receptivity, embryo development, and implantation in species with different implantation strategies (humans and cattle). We hypothesise that developing a novel 3D bovine endometrium on a chip system will enhance our understanding of the role of conceptus-derived factors in altering the endometrium and/or ULF secretion. Here we have developed a 3D bovine endometrium on a chip system, comprising both stromal and epithelial cell culture combined with culture medium flow better mimics the in vivo endometrium and exposure to conceptus-derived factors than conventional 2D endometrial cell culture. We have demonstrated that the conceptus-derived proteins CAPG and PDI modulate the endometrial transcriptome and secretory response to promote pathways associated with early pregnancy and alter ULF composition. This work highlights the critical need for more robust and in vivo-like culture systems to study endometrial-conceptus interactions in vitro to further investigate the role of conceptus derived factors for pregnancy success.

overall_design: Primary bovine endometrial epithelial and stromal cells were co-cultured in a 3D endometrial organ on a chip. They were exposed on the epithelial-side to the conceptus-derived factors CAPG and PDI for 24 hours under microfluidic flow, alongside controls (N=3). Conditioned medium was collected and analysed for proteomics alongside unconditioned controls. Cells were removed, RNA extracted, and RNA sequenced.

first: Haidee

last: Tinning

first: Elton

last: Vasconcelos

first: Dapeng

last: Wang

first: Niamh

last: Forde


title: OTTR ribosome profiling in Mettl14 knockout mESC

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

summary: Degradation of mRNA containing N6-methyladenosine (m6A) is essential for cell growth, differentiation, and stress responses. Here, we show that m6A markedly alters ribosome dynamics and that these alterations mediate the degradation effect of m6A on mRNA. We find that m6A is a potent inducer of ribosome stalling, and these stalls lead to ribosome collisions that form a unique conformation unlike those seen in other contexts. We find that the degree of ribosome stalling correlates with m6A-mediated mRNA degradation, and increasing the persistence of collided ribosomes correlates with enhanced m6A-mediated mRNA degradation. Ribosome stalling and collision at m6A is followed by recruitment of YTHDF m6A reader proteins to promote mRNA degradation. We show that mechanisms that reduce ribosome stalling and collisions, such as translation suppression during stress, stabilize m6A-mRNAs and increase their abundance, enabling stress responses. Overall, our study reveals the ribosome as the initial m6A sensor for beginning m6A-mRNA degradation.

overall_design: OTTR ribosome profiling was performed using OTTR cDNA library construction kit (Karnateq, R2201001S). Briefly, cells were grown in a 150 mm dish to 70% confluency. Cells were washed with ice-cold PBS supplemented with 100 μg/mL cycloheximide and 100 μg/mL tigecycline. Cells were lysed in 300 μL lysis buffer [20 mM Tris-HCl, pH 7.4, 150 mM NaCl, 5 mM, MgCl2, 1 mM DTT, 1 % Triton X, 100 μg/mL cycloheximide, 100 μg/mL tigecycline, and 15 U/mL DNaeI (ThermoFisher, 89836)]. Lysates were passed through a 25-gauge needle five times, incubated on ice for 20 min, and clarified by centrifugation for 10 min at 20,000 x g at 4 °C. RNA in the lysate was quantified using Qubit™ RNA Broad Range kit (ThermoFisher, Q10211) on Qubit4 Fluorometer. 30 μg RNA was digested using 600 U P1 nuclease (NEB, M0660S) in 400 μL supplemented with 42 μL 0.2 M Bis-Tris, pH 6.0 (Life Technologies, J62686.AE) at 37 °C for 1 h. OTTR ribosome profiling libraries were prepared using mirRICH small RNA enrichment method according to the manufacturer’s instruction. Final library quality was assessed on Agilent TapeStation4200 using D1000 ScreenTape (Agilent, 5067-5582). Library was quantified on Qubit4 Fluorometer using Qubit 1X dsDNA HS Assay Kit (ThermoFisher, Q33231). Libraries were sequenced with single-end 100 cycles on Illumina NovaSeq 6000.

first: Shino

last: Murakami

middle: R


title: Mismanagement of Cellular Iron Leads to Ferroptosis Susceptibility in Cancer Cells Surviving Chemotherapy

city: Baltimore

first: Sarah

last: Amend

address: 600 N Wolfe St

department: Brady Urological Institute

institute: Johns Hopkins University

summary: Despite centuries of research, metastatic cancer remains incurable due to resistance against all conventional cancer therapeutics. Alternative strategies leveraging non-proliferative vulnerabilities in cancer are required to overcome cancer recurrence. Ferroptosis is an iron dependent cell death pathway that has shown promising pre-clinical activity in several contexts of therapeutic resistant cancer. However, ferroptosis sensitivity is highly variable across tissue types and cell state posing a challenge for clinical translation. We describe a convergent phenotype induced by chemotherapy where cells surviving chemotherapy have similar transcriptomic signatures and dysregulated iron homeostasis, regardless of initial cell type or chemotherapy used. Elevated labile iron levels are counteracted by NRF2 signaling that does not alleviate the amount of labile iron. Selectively inhibiting GPX4 leads to uniform susceptibility to ferroptosis in surviving cells, highlighting the common reliance on lipid peroxidation defenses. Cellular iron dysregulation is a vulnerability of chemoresistant cancer cells that can be leveraged by triggering ferroptosis

overall_design: PC3 (prostate cancer cell line) were treated with cisplatin and surviving cells were analyzed 1, 5 and 10 days following chemotherapy (DPT). PC3 cells were treated with docetaxel and surviving cells were analyzed 1, 5, 10 days following chemotherapy. SIngle cell RNA sequencing was performed on untreated cell lines and surviving cells 1, 5, and 10 DPT in biological triplicate. Parse Biosciences sequencing is done by combinatorial barcoding, whereby cells from every sample type is present in each sublibrary. Sublibraries are sequenced and individual cells called by barcode identifier.

first: Luke

last: Loftus

first: Christopher

last: Cherry

first: Michael

last: Patatanian


title: Visceral adipocyte metabolic dysfunction in obesity related to altered chromatin accessibility to thyroid hormone receptor [ATAC-seq]

city: nanjing

first: Hao

last: Zhu

address: 300 guangzhou road

institute: nanjing medical university

summary: Adipocyte dysfunctuon exacerbates obesity, yet the onset of adipocyte dysfunction is still unclear. Here, we employed RNA-seq and ATAC-seq on visceral adipose tissue from individuals with obesity or normal weight.Our research identified differentially expressed genes (DEGs) of VAT from individuals with normal wight or obesity enriched in pathways related to adipocyte metabolic function, thyroid hormone receptor binding sites were discovered in the accessible chromatin regions of these DEGs, including STAT5B. Motif enrichment, CHIP assay and in vitro cell experiments confirmed the decreased activation of STAT5B by triiodothyronine (T3) through binding with thyroid hormone receptor alpha (THRa) in obesity. In addition, RNA interference revealed STAT5B as a key transcription factor in maintaining the metabolic function of VAT. In conclusion, the impaired metabolic function of VAT is associated with altered chromatin accessibility to thyroid hormone (TH) in obesity. STAT5B is a key transcription factor at the core of the disrupted thyroid-adipose signaling and might be a promising target to improve obesity.

overall_design: RNA-seq and ATAC-seq on visceral adipose tissue from 3 human individuals with normal weight and 3 human inviduals with obesity.

first: Wen-Na

last: Zhang

first: Xiao-dong


title: Transcranial direct current stimulation promotes post-SCI motor recovery via miR-298-5p/ LC3-dependent autophagy activation

city: Nanning

first: Zhenxing

state: Guangxi

address: Zhongshan Street

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medicla University

summary: While transcranial direct current stimulation (tDCS) has been shown to contribute to motor recovery after spinal cord injury (SCI), the mechanisms remain unclear. This study investigated whether tDCS exerts neuroprotective effects by regulating apoptosis and autophagy. To achieve this aim, SCI was induced in rats using a modified Allen’s method with tDCS treatment. Otherwise,Furthermore, tDCS-responsive miRNAs were detected by using microRNA (miRNA) sequencing and validated via RT-qPCR. Similarly, tDCS regulatory mechanisms were verified through dual-luciferase assays and miRNA overexpression. Subsequently, H₂O₂-treated PC-12 cells simulated SCI in vitro to examine miR-298-5p's effects on apoptosis and autophagy. The findings revealed that miR-298-5p was upregulated post-SCI and downregulated after tDCS. In vitro, miR-298-5p silencing promoted autophagy and reduced apoptosis, whereas overexpression exacerbated neuronal injury. LC3 was a direct of miR-298-5p, and tDCS enhanced autophagy, reduced apoptosis, improved nerve regeneration, and minimized motor deficits after SCI. Notably, all tDCS-induced effects were counteracted after the overexpression of miR-298-5p by agomir. In summary, this study showed that while miR-298-5p could be detrimental to SCI, tDCS could increase autophagy flux and inhibit neuronal apoptosis by negatively regulating miR-298-5p, thereby improving the recovery of function in SCI.

overall_design: The experiment utilized a randomized controlled design with two parallel groups: control group (SCI-1, SCI-2, SCI-3) and experimental group (tDCS-1, tDCS-2, tDCS-3), each comprising three biological replicates (n=3 per group). Samples were randomly assigned to either group to ensure balanced allocation. This design aligns with standard protocols for interventional comparisons, where the experimental group receives transcranial direct current stimulation (tDCS) treatment, while the control group undergoes placebo procedures. Both groups were analyzed under identical conditions to minimize confounding variables

first: Qinhe

last: Pan

first: Jianmin

last: Chen

first: Weifeng

last: Zuo

first: Jianwen

last: Xu


title: Multi-omics Profiling of the Lateral Ventricle Choroid Plexus Reveals Temporal Cellular Remodeling, Early Immune Gene Activation, and a Novel Epithelial Subtype [bulkRNA-seq]

first: Mónica

last: Fernandes

overall_design: We have collected the choroid plexus from the lateral ventricles of C57BL/6 mice at the following developmental time points: postnatal day (P)2/3, P11 and P60.  We then performed scRNA-seq analysis.

first: Lili

last: Li

first: Eduarda

last: Correia

first: Alice

last: Vieira

first: Diana

last: Afonso

first: Jonas

last: Campos

first: Neemat

last: Mahmud

first: Mandy

last: Meijer

first: Eneritz

last: Agirre

first: Nobrega

last: Claudia

first: Fernanda

last: Marques

first: Gonçalo

last: Castelo-Branco

first: João Carlos

last: Sousa

first: Ana Mendanha

last: Falcão


title: FUT8 is a critical driver of prostate tumour growth and can be targeted using fucosylation inhibitors

city: Newcastle Upon Tyne

first: Margarita

last: Orozco-Moreno

address: Newcastle University, International Centre for Life

department: Biosciences Institute

institute: Newcastle University

summary:
To identify signalling pathways altered by FUT8 in prostate cancer cells, we established luciferase-tagged CWR22Rv1 stable cell lines in which FUT8 was overexpressed (OE) and luciferase-tagged PC3 cell lines in which FUT8 was knocked down (KD).
We then performed differential gene expression, Gene Ontology and GSEA analyses using data obtained from RNA-seq of the control and FUT8 overexpression, and the control and knockdown cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Lenti-ORF negative control CWR22Rv1 cells vs CWR22Rv1 cells with FUT8 overexpression, and from lenti shControl PC3 cells vs PC3 cells with FUT8 knockdown.

first: Kayla

last: Bastian

first: Huw

last: Thomas

first: Kirsty

last: Hodgson

first: Eline

last: Visser

first: Emiel

last: Rossing

first: Johan

middle: F

last: Pijnenborg

first: Nienke

last: Eerden

first: Laura

last: Wilson

first: Hasvini

last: Saravannan

first: Oliver

last: Hanley

first: Grace

last: Grimsley

first: Fiona

last: Frame

first: Ziqian

last: Peng

first: Bridget

last: Knight

first: Paul

last: McCullagh

first: John

last: McGrath

first: Malcom

last: Crundwell

first: Lorna

last: Harries

first: Norman

middle: J

last: Maitland

first: Rakesh

last: Heer

first: Ning

last: Wang

first: Ethan

last: Goddard-Borger

first: Ramon

last: Hurtado-Guerrero

first: Thomas

last: Boltje

first: Richard

last: Drake

first: Emma

last: Scott

first: David

last: Elliott

first: Jennifer

last: Munkley


title: U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation

first: Ana

last: Fiszbein

address: 24 Cummington Mall, LSE(Life Science and Engineering) Building

department: Biology

institute: Boston University

summary: Transcription and splicing are intricately linked processes, with emerging evidence highlighting the involvement of splicing factors mediating their coupling. U1 small nuclear ribonucleoprotein particle (U1 snRNP), a key splicing factor, not only serves as the initial component of the spliceosome but also plays a crucial role in preventing premature cleavage and polyadenylation, facilitating long-distance transcription elongation. Here, we show that U1 snRNP regulates alternative promoter usage through inhibition of premature polyadenylation. Inhibiting U1 snRNP with antisense oligonucleotides or introducing a premature polyadenylation leads to a significant decrease in downstream promoter activity in genes with premature polyadenylation sites in between two promoters. Conversely, restoring U1 snRNP activity or inhibiting premature polyadenylation sites using a gene-specific U1 snRNP rescues downstream promoter activity. Mechanistically, U1 snRNP inhibition correlates with reduced chromatin accessibility and serine 5 phosphorylation levels of RNA polymerase II at downstream promoters. Our findings propose a model where U1 snRNP facilitates productive transcription from upstream promoters, triggering downstream promoter activation by destabilizing nucleosomes and promoting promoter escape.

overall_design: Six samples with two distinct experimental conditions were investigated by Precision Run-On Sequencing (PRO-seq): 3 biological replicate sets of cells treated with a Control antisense morpholino oligonucleotides (Control ASO) and 3 biological replicate sets of cells treated with a U1 antisense morpholino oligonucleotides  (U1 ASO).


title: KDM5 demethylases suppress R-loop-mediated “viral mimicry” and DNA damage in breast cancer cells [CUT&Tag_H3K4me3]

first: Marie

last: Classon

overall_design: Cut-and-Tag profiling of the histone modification H3K4me3 in HCC1428 cells treated with KDM5 inhibitor C48 for 5 days

first: Lena

last: Lau

first: Kurt

last: Henderson

first: Ahu

last: Turkoz

first: Sara

last: Linker

first: Dorte

last: Schlesinger

first: Brad

last: Townsley

first: Brian

last: Egan

first: Shoba

last: Regunathan

first: Robert

last: Rollins

first: Xianju

last: Bi

first: Zhijian

last: Chen

first: Oleg

last: Brodsky

first: Clifford

last: Restaino

first: Murali

last: Gururajan

first: Kristen

last: Jensen-Pergakes

first: Anders

last: Malarstig

first: Chames

last: Kermi

last: Moore


title: Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks [gRNA]

city: Seattle,

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Genetic variants associated with autoimmune diseases are highly enriched within putative cis-regulatory regions of CD4+ T cells, suggesting that they alter disease risk via changes in gene regulation. However, very few genetic variants have been shown to affect T cell gene expression or function. Here, we tested >18,000 autoimmune disease-associated variants for allele-specific expression using massively parallel reporter assays in primary human CD4+ T cells. We find 545 variants that modulate expression in an allele-specific manner (emVars). Primary T cell emVars greatly enrich for probable causal variants, are mediated by common upstream pathways, and their putative target genes are highly enriched within a lymphocyte activation network. Using bulk and single-cell CRISPR-interference screens, we confirm that emVar-containing T cell cis-regulatory elements modulate both known and previously unappreciated target genes that regulate T cell proliferation, providing plausible mechanisms by which these variants alter autoimmune disease risk.

overall_design: We created gRNA libraries targeting on average 14 gRNAs to each variant CRE (within 100 bp of each variant), 120 positive control gRNAs targeting known regulators of T cell proliferation and effector function, and 992 non-targeting control gRNAs We activated primary human T cells and delivered dCas9- ZIM3 and the gRNA library using lentivirus infection. We harvested half of the transduced cells directly post-puromycin treatment (day 2) and the remainder of the cells after 21 days of proliferation (day 21).

first: Ching-Huang

last: Ho

first: Maxwell

last: Dippel

first: Meghan

middle: S

last: McQuade

first: LeAnn

middle: P

last: Nguyen

first: Arpit

last: Mishra

first: Stephan

last: Pribitzer

first: Samantha

last: Hardy

first: Harshpreet

last: Chandok

first: Florence

last: Chardon

first: Troy

last: McDiarmid

first: Hannah

last: DeBerg

first: Jane

last: Buckner

first: Jay

last: Shendure

first: Carl

last: de Boer

first: Michael

last: Guo

first: Ryan

last: Tewhey

first: John

last: Ray


title: Studying Inner ear development through the use of the CARLIN mouse model to label progenitor cells, identifying the potency of early cell types in the otocyst

city: Houston

first: Joel

last: Nelson

email: Joel.Nelson@bcm.edu, joeln@bcm.edu

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: This experiment focuse on utilizing the CARLIN mouse model. The CARLIN system (CRISPR Array Repair Lineage tracing IN situ) is a genetic barcoding and lineage tracing tool developed to track the lineage and fate of individual cells in vivo over time. It was designed to allow researchers to reconstruct cell lineages and study progenitor cell behavior, especially in complex tissues like the hematopoietic system, the brain, and during development. Utilizing an inducible Cas9, it allows for temporal control of marking cells with unique heritable barcodes

overall_design: For this experiment, timed matings were performed, and plugs were checked the next morning. Doxycycline injection were performed on the pregnant dams at E7.5 and 8.5. The pups were collected for dissection at P4, 2-weeks post injections. Blunt dissection to remove and isolate the inner ear was performed, followed by single cell dissociation and EpCAM-focused FACS. Then, library prep of the collected cells were performed, and both bulk and single-cell sequencing was performed on this sample.

middle: C

first: Fengshuo

last: Liu

first: Andrew

last: Groves

first: Xiang

last: Zhang


title: Multiomics coupled with vibrational spectroscopy identify early mechanisms of experimental aortic valve stenosis [miRNA]

city: Athens

first: Nikolaos

last: Anousakis-Vlachochristou

address: Vas Sofias 114 Ave

department: First Department of Cardiology, Athens Medical School

country: Greece

institute: National and Kapodistrian University of Athens

summary: Calcific aortic valve stenosis (CAVS), characterized by calcium deposition in the aortic valve in a multiannual process, is associated with high mortality and morbidity. To understand phenomena at its early stages, reliable animal models are needed. Here, we used a critically revised high-fat vitamin D2 diet rabbit model to unveil the earliest in vivo-derived mechanisms linked to CAVS progression. We modeled the inflammation-calcification temporal pattern seen in human disease and investigated molecular changes before inflammation. Coupling comprehensive multiomics and vibrational spectroscopy revealed that among the many procedures involved, mechanotransduction, peroxisome activation, DNA damage-response, autophagy, phospholipid signaling,  native ECM proteins upregulation, protein cross-linking and self-folding, are the most relevant driving mechanisms. Activation of Complement 3 receptor, Immunoglobulin J and TLR6 were the earliest signs of inflammation. Among several identified key genes were AXIN2, FOS, and JUNB. Among 10 identified miRNAs, miR-21-5p and miR-204-5p dominated fundamental cellular processes, phenotypic transition, inflammatory modulation, and were validated in human samples. The enzymatic biomineralization process mediated by TNAP was complemented by V-type proton ATPase overexpression, and the substitution of Mg-pyrophosphate with Ca-pyrophosphate. These data extend our understanding on CAVS progression, facilitate the refinement of pathophysiological hypotheses and provide a basis for novel pharmaceutical therapy investigations.

overall_design: New Zealand male rabbits received a diet supplemented by 1% cholesterol plus 3500 International Units ergocalciferol per Kg per day, or normal diet. The experimental groups were: E (experimentals, having received the experimental diet) obtained after 2 weeks, 4 weeks, and 7 weeks of diet, and C (controls, having received regular diet), which are pooled from 2 weeks and 4 weeks. Before the analysis, to account for possible minimal myocardial contamination in the aortic valve dataset, we extracted RNA from the left ventricular myocardium and ascending aorta (just below the head and neck vessels) and sequenced the RNA (from 3 control and 3 experimental animals), filtered out the genes that were present in both the myocardium and the aortic valve but not in the ascending aorta (2.22% of genes).

first: Giannis

last: Vatselas

first: Marios

last: Miliotis

first: Manolis

last: Mavroidis

first: Artemis

last: Hatzigeorgiou

first: C

last: Anagnostopoulos

first: Dennis

last: Cokkinos

first: Konstantinos

last: Toutouzas


title: Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing

city: Columbus

first: Benjamin

middle: Z.

last: Stanton

state: OH

address: 575 Children's Crossroad

department: Center for Childhood Cancer Research

institute: Nationwide Children's Hospital

summary: Quantitative comparison of ChIP-seq profiling between experimental conditions or samples remains technically challenging for the epigenetics field. Here, we report a strategy combining the use of well-defined cellular spike-in ratios of orthologous species’ chromatin and a bioinformatic analysis pipeline to facilitate highly quantitative comparisons of 2D chromatin sequencing across experimental conditions. We find that the PerCell methodology results in efficient and consistent levels of spike-in vs. experimental genomic reads. We demonstrate use of the method and pipeline to enable quantitative, internally normalized chromatin sequencing on zebrafish embryos and human cancer cells. Overall, we propose the PerCell method to enable cross-species comparative epigenomics and promote uniformity of data analyses and sharing across labs.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for 1) H3K27ac histone modification in Rh4 rhabdomyosarcoma cells treated with DMSO, 0.5 μM A485, or 0.5 μM Entinostat; and 2) CTCF in Rh4 rhabdomyosarcoma cells with 100%, 75%, 50%, or 25% of spike-in mouse reads retained.

first: Alexi

last: Tallan

first: Jack

last: Kucinski

last: Sunkel

first: Cenny

last: Taslim

first: Stephanie

last: LaHaye

first: Qi

first: Jun

last: Qi

first: Meng

last: Wang

first: Genevieve

last: Kendall

middle: Z


title: Multiomics coupled with vibrational spectroscopy identify early mechanisms of experimental aortic valve stenosis [RNA]

first: Nikolaos

last: Anousakis-Vlachochristou


title: Comparative study of transcriptome expression in water extract and ethanol extract of Schisandra chinensis

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

institute: Korean Institute of Oriental Medicine

summary: This study aimed to identify the mode of action of Schisandra chinensis water extracts (SCW) and  Schisandra chinensis ethanol extracts (SCE) in SW1783 cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SCW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), SCE (310 ug/mL, 62 ug/mL, and 12.4 ug/mL) and vehicle control (DMSO).


title: Transcriptomes of WT and cry2 mutant and flΔ4 mutant in different light conditions

city: Shanghai

first: Desheng

last: Zeng

address: 300 Feng Lin Road

institute: CAS Center for Excellence in Molecular Plant Science

summary: This sequencing was designed to identify the downstream genes that were regulated by CRY2 in darkness and blue light or regulated by FL1/FL3 in darkness.

overall_design:
For the comparison between WT and cry2 mutant, 4-day-old seedlings grown either in darkness or transferred from darkness to blue light for 30 minutes were harvested and rapidly frozen in liquid nitrogen. Subsequently, the frozen samples were used for mRNA-seq analysis.
For the comparison between WT and flΔ4 mutant, 4-day-old seedlings grown in darkness were harvested and rapidly frozen in liquid nitrogen. Subsequently, the frozen samples were used for mRNA-seq analysis.

first: Hongtao

last: Liu