first: Ye-guang

last: Chen

summary:
Purpose:One goal of this bulk RNA-seq is to compare genome-wide transcriptome profiles in gastric organoids cultured in CM and differentiation media including Nog WD, BMP4, EB, Isx-9, BI, NRC and NRCA in mouse and EB, NRCSI and BIMDP in human. The other aim is to identify the differential biological process underpinning gastric epithelial cell differentiation and the conservative or divergent process between human and mouse.
Methods: For human and mouse gastric organids, we isolated and digested with Tryple and then extracted total RNA.  Bulk RNA-seq was performed using the Illumina Hiseq X. Sequence reads that passed quality filters were analysed at the transcript isoform level using two methods: Burrows-Wheeler Aligner (BWA) followed by ANOVA and TopHat followed by Cufflinks.
Results: By comparing RNA-seq data, we identified the signature genes involved in gastric epithelial cell lineage and enrichment of biological processes during differentiation.
Conclusion: EB is optimal medium for pit cell differentiation in both human and mouse, BI and BIMDP media are optimal media for parietal cell differentiation in human and mouse respectively, NRCS and NRCSI media are optimal media for chief cell differentiation in  human and mouse respectively.

overall_design: Bulk RNA profiles of organoids in CM and differentiation medium detected after 2 days culture.

first: Ye-Guang

first: Fan

last: Hong

first: Xiaodan

last: Wang

first: Shibo

last: Lin

first: Mengxian

last: Zhang

first: Haonan

last: Li

first: Yalong

first: Yuan

first: Hui

last: Liang


title: Chromatin accessibility assessment during RASMCs' transformation into macrophage-like cells [ATAC]

status: Public on May 29 2025

city: Xiamen

first: Wei

last: Shen

state: Fujian

address: 2999 Jinshan Rd, Huli District

country: China

institute: Xiamen University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the chromatin accessibility of rat vascular smooth muscle cell at de-differentiated state (induced by DAPT treatment), inflammatory state (induced by cholesterol treatment) and macrophage-like state (induced by combined treatment of DAPT and cholesterol)

overall_design: Primary rat aortic smooth muscle cells were treated by NOTCH inhibitor DAPT, soluble cholesterol or both of them for 48 hrs to achieve cell state transformations


title: Inactivation of GSK3b by Ser389 phosphorylation during early thymocyte development contributes to the diversity of the Tcrb and Tcra repertoire.

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

country: USA

institute: University of Colorado Anschutz Medical Campus

type: Expression profiling by high throughput sequencing

summary: During thymocyte development, double negative (DN) thymocytes go through consecutive rounds of Tcr and Tcr gene recombination that involve the generation of DNA double strand breaks (DSB), addition of N-nucleotides between coding ends, and DNA repair with the final goal of enhancing the diversity of the TCR repertoire. How DN thymocytes can survive such a genomic instability during this complex process and generate functional Tcr and Tcr genes remain unclear. Performing scRNAseq analyses of isolated DN3 and DN4 thymocytes we show here a defined trajectory from DN3 through DN4 stages that is delineated by a G1 cell cycle checkpoint, but also by a G2M cell cycle checkpoint to help DNA repair during recombination of Tcr and Tcr genes prior to cell proliferation. We have previously shown that inactivation of GSK3 by phosphorylation on Ser389 occurs selectively in response to DNA DSB to enhance survival during DNA repair. In this study we show that failure to inactivate GSK3 by Ser389-phosphorylation during the transition from DN3 to DN4 stages compromises Tcr and Tcr repertoire diversity. Inactivation of GSK3 during V(D)J recombination is needed to prevent cell death by necroptosis. Thus, cell cycle checkpoints to ensure proper DNA repair during V(D)J recombination as well as the use of unique survival pathways to avoid necroptosis during this process are critical to warrant a large diversity of pre-selection TCR repertoire.

overall_design: Single cell RNA-seq of DN3 and DN4 thymocytes from WT and GSK3B-knock-in mice

first: Felipe

last: Pereira

middle: M

first: Kent

middle: A

last: Riemondy

first: Mercedes

last: Rincon


title: Signaling basis of gastric epithelial cell differentiation revealed by human and mouse organoids [scRNA-Seq]

city: Beijing

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

summary:
Purpose:One goal of this single RNA-seq is to compare scRNA  profiles in gastric organoids cultured in CM and differentiation media including  EB,  BI and NRCA in mouse and EB, NRCSI and BIMDP in human. The other aim is to identify the differential biological process underpinning gastric epithelial cell differentiation and the conservative or divergent process between human and mouse.
Methods: For human and mouse gastric organids, we isolated and digested with Tryple and then were sorted by flow cytometry.ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: By comparing scRNA-seq data, we identified the signature genes involved in gastric epithelial cell lineage and enrichment of biological processes during differentiation.
Conclusion: EB is optimal medium for pit cell differentiation in both human and mouse, BI and BIMDP media are optimal media for parietal cell differentiation in human and mouse respectively, NRCS and NRCSI media are optimal media for chief cell differentiation in  human and mouse respectively.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell RNA profiles of organoids in CM and differentiation medium detected after 2 days culture.

last: Liu


title: Effect of HSD52 overexpression on gene expression in LN229 glioma cells

city: Harbin

first: Xiangqi

last: Meng

address: No. 157, Baojian Road

institute: Harbin Medical University

summary: In order to study the effect of HSD52 on the malignant progression and chemotherapy resistance of glioma, we examined the effect of HSD52 on the gene expression of brain glioma cells. We used lentiviral constructs to establish the LN229 cell line overexpressing HSD52. We subsequently performed gene expression profiling using RNA-seq data obtained from control LN229 cells and HSD52-overexpressing LN229 cells.

overall_design: Comparative gene expression profling analysis of RNA-seq data for control LN229 cells and LN229 cells with HSD52 overexpression

first: Jinquan

last: Cai

last: Sun


title: CircRNA of sugar beet in response to drought stress

city: Taigu

first: Chunlei

last: Zou

address: No.1 Mingxian Road

institute: Shanxi Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: We analyzed circRNAs from sugar beet leaves under water control treatment using high-throughput sequencing technology and bioinformatic approaches to explore the genome-wide quantity of circRNAs and their potential function in the regulation of drought responses.

overall_design: Sugar beet seedlings were divided into two groups: (1) well-watered (CK), (2) drought stress (DR).


title: Characterization of the meningeal leukocytes in 3xTg-AD mice

city: Verona

first: Gabriela

last: Constantin

state: Verona

address: Strada le Grazie 8

department: Department of Medicine, Division of General Pathology

country: Italy

institute: University of Verona

summary: We characterize the meningeal leukocyte (CD45+ cells) in wild-type and 3xTg-AD mice, a transgenic model of Alzheimer's disease (AD).

overall_design: Pools of 8 female mice (3xTg-AD or wild-type) were used for single-cell RNA-Seq (scRNAseq) analysis. Leukocytes isolated from the meninges were washed with PBS, and labeled with an anti CD45–BV480 antibody (Becton Dickinson). The cells were re-suspended in PBS supplemented with 10% FBS), and viable CD45HIGH cells were sorted on a FACSAria Fusion (Becton Dickinson). Both the 3xTg-AD and wild-type samples consisted of > 98% viable cells.

first: Constantin

last: Gabriela

first: Zenaro

last: Elena


title: Gastric niche in the regulation of the epithelial cell differentiation in the human and mouse

first: Ye-guang

last: Chen

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

overall_design: Refer to individual Series


title: Characterization of the brain infiltrating leukocytes in 3xTg-AD mice [Pools of 10 female mice brain]

summary: We characterize the brain infiltrating leukocyte (CD45high cells) in wild-type and 3xTg-AD mice, a transgenic model of Alzheimer's disease (AD).

overall_design: Pools of 10 female mice (3xTg-AD or wild-type) were used for single-cell RNA-Seq (scRNAseq) analysis. Leukocytes isolated from the brain were washed with PBS, and labeled with an anti CD45–BV480 antibody (Becton Dickinson). The cells were re-suspended in PBS supplemented with 10% FBS), and viable CD45HIGH cells were sorted on a FACSAria Fusion (Becton Dickinson). Both the 3xTg-AD and wild-type samples consisted of > 98% viable cells.

first: Elena

last: Zenaro


title: Small RNA of sugar beet in response to drought stress

summary: We analyzed Small RNAs from sugar beet leaves under water control treatment using high-throughput sequencing technology and bioinformatic approaches to explore the genome-wide quantity of Small RNAs and their potential function in the regulation of drought responses.


title: Macrophages amplify damaged sensory neuron spontaneous activity in a human co-culture model of neuropathic pain [human]

status: Public on May 28 2025

city: Glasgow

first: Paschalina

last: Chrysostomidou

address: University Avenue

country: United Kingdom

institute: University of Glasgow

summary: Neuropathic pain is a highly prevalent condition for which treatments are hampered by low efficacy and dose-limiting side-effects. Injury to the somatosensory nervous system causes maladaptive plasticity that initiates and maintains chronic pain. Emerging evidence suggests that inflammatory cells of the innate immune system shape the injured nervous system and drive pain pathogenesis. Data from preclinical models and human patient biopsies have specifically implicated peripheral macrophage populations for a pro-algesic role, yet how these cell types influence damaged sensory neurons and whether they directly sensitise their neuronal activity is unclear. Here, we have developed an iPSC co-culture system to study the interactions of macrophages and sensory neurons in a fully humanised experimental model. We found that analogous to endogenous counterparts, iPSC-derived macrophages (iMacs) display a dynamic molecular and functional profile that is highly dependent on neuronal context. Co-culture with injured iPSC-derived sensory neurons (iSNs) induces morphological, gene expression, and secretory profile changes in iMacs that are consistent with in vivo nerve injury datasets. iMacs in turn amplify spontaneous firing in damage sensory neurons, implicating macrophages in a cardinal feature of neuropathic pain. These results illustrate the utility of an iPSC-based model to study signalling between these two cell types; supporting a role for macrophages in directly amplifying damaged sensory neuron activity and suggesting that disrupting pathological signalling between these cell types could be a fruitful avenue for analgesic drug development.

overall_design: Macrophages were isolated from two sources (iPSCs and monocytes) and were cultured alone and co-cultured with naïve (3 and 7 days) or injured (7 days) iPSC-derived sensory neurons. Cells were stained with CITE-seq antibodies (HTO) and isolated using fluorescence activated sorting (FACS).

first: Zoe

last: Hore

first: Domenico

last: Somma

first: Julia

last: Vlachaki Walker

first: Katy

last: Diallo

first: Heather

middle: F

last: Titterton

first: Aziza

last: Elmesmari

first: Mariola

last: Kurowska-Stolarska

first: Franziska

last: Denk

first: Greg

last: Weir


title: Characterization of the brain infiltrating leukocytes in 3xTg-AD mice [Pools of 8 female mice brain]

overall_design: Pools of 8 female mice (3xTg-AD or wild-type) were used for single-cell RNA-Seq (scRNAseq) analysis. Leukocytes isolated from the brain were washed with PBS, and labeled with an anti CD45–BV480 antibody (Becton Dickinson). The cells were re-suspended in PBS supplemented with 10% FBS), and viable CD45HIGH cells were sorted on a FACSAria Fusion (Becton Dickinson). Both the 3xTg-AD and wild-type samples consisted of > 98% viable cells.


title: Inflammation drives TGFβ1 activation via the αvβ6 integrin-mechanotransduction pathway in human skin

city: geneva

first: Wolf

middle: Henning

last: Boehncke

address: Rue Michel servet 1

country: Switzerland

institute: Univeristy of Geneva

summary: Transforming growth factor β (TGFβ) is a critical regulator of skin homeostasis and is implicated in skin inflammation, including psoriasis. We investigated the molecular mechanisms of TGFβ1 regulation during cutaneous inflammation using reconstructed human epidermis. We report a mechanosensitive positive feedback loop, that occurs downstream of inflammatory stimuli and involves TGFβ-mediated activation of mechanotransduction pathways, further promoting αvβ6 integrin-dependent TGFβ1 activation in keratinocytes.

overall_design: N/TERT-1 keratinocytes were cultured to create 3D reconstituted human epidermis model (10 days at the air-liquid interphase), and then stimulated with 10ng/ml TGFβ1 for 3 days.

first: Xuewei

last: Jiang

first: Sihem

last: Sellami

first: Jérémy

last: Kessler

first: Michael

last: Bachmann

first: Fanny

last: Noulet

first: Barbara

last: Russo

first: Nicolo

middle: C

last: Brembilla

first: Guerkan

last: Kaya

first: Andrei

middle: I

last: Ivanov

first: Bernhard

last: Wehrle-Haller

first: Wolf-Henning

first: Maria

middle: S

last: Shutova


title: Synergistic Targeting of Vemurafenib-Resistant Melanoma via Network-Guided Drug Combination and Biophysical Validation

city: Warszawa

first: Tomasz

last: Gambin

address: Nowowiejska 15/19

country: Poland

institute: Warsaw University of Technology

summary: Vemurafenib, a selective inhibitor targeting the BRAF V600E mutation, has improved outcomes in advanced melanoma. However, resistance frequently emerges, limiting its long-term effectiveness and highlighting the need for combination therapies. This study aimed to identify synergistic drug combinations to overcome vemurafenib resistance in BRAF-mutant melanoma using an integrative computational approach. We applied a modified version of SynGeNet, which combines gene expression data with protein–protein interaction networks, to predict effective drug combinations in the vemurafenib-resistant A375 melanoma cell line. The analysis identified sorafenib and pioglitazone as the most promising candidates. Sorafenib is a multi-kinase inhibitor targeting signaling pathways involved in proliferation and angiogenesis, while pioglitazone activates PPARγ and modulates stress responses. Transcriptomic profiling of resistant cells revealed enrichment in nucleotide metabolism, protein trafficking, and corticosteroid response pathways, alongside suppression of mitotic and cell cycle processes. In vitro validation confirmed that the sorafenib/pioglitazone combination reduces cell viability with a strong synergistic effect. We further applied a novel biophysical platform integrating QCM-D and lectin–glycan interaction analysis to assess glycosylation dynamics. The combination treatment reduced the glycan viscoelastic index, suggesting a shift toward a less metastatic phenotype.

overall_design: The experimental design integrates computational drug synergy prediction, transcriptomic profiling, and biophysical glycan analysis. A375 human melanoma cells, either vemurafenib-sensitive or -resistant, were treated with sorafenib and pioglitazone individually and in combination. Resistance was induced by gradual vemurafenib exposure. RNA-Seq was performed on biological replicates from each condition. Libraries were prepared from total RNA and sequenced on an Illumina platform in paired-end mode. Gene expression data were used to evaluate transcriptional responses and pathway enrichment. Additionally, whole-cell glycomic profiling was conducted using a quartz crystal microbalance with dissipation monitoring (QCM-D) and lectin-binding analysis. Changes in the glycan viscoelastic index (gVI) served as a surrogate for metastatic potential and phenotypic plasticity under treatment. The approach supports the identification of therapeutic synergies and biomarkers associated with resistance and EMT-like transitions.

first: Matteo

last: Italia

first: Swamy

last: Kasarla

first: Anna

last: Sobiepanek

last: Kujawa

first: Konstancja

last: Bobecka-Wesołowska

first: Fabio

last: Dercole

last: Kobiela


title: RELA haploinsufficiency manifesting as an atypical phenotype of Crohn’s disease

city: Hod hasheon

first: Noa

last: Tal

address: Kaplan 14

country: Israel

institute: Schneider children hospital

summary: Mutations in RELA, a key component of NF-κB signaling, are associated with dysregulated immune responses and inflammatory disorders. While immunodeficiency phenotypes associated with RELA haploinsufficiency have been reported, gastrointestinal manifestations remain poorly described. We aimed to characterize the clinical, genomic, and immunological features of a patient presenting with an atypical Crohn’s-like phenotype driven by RELA haploinsufficiency. We report a case of RELA haploinsufficiency in a 17-year-old male presenting with a Crohn’s-like phenotype, including pan-enteric inflammation, perianal disease, chronic mucocutaneous candidiasis, and lymphopenia. Whole exome sequencing revealed a heterozygous RELA missense variant (p.V196A), which might impaired RelA protein stability and function. Functional assays showed reduced NF-κB activity and protein expression. Immune profiling by CyTOF and scRNA-seq demonstrated Treg deficiency, high IFN-γ levels, a strong interferon signature, and aberrant activation of MAIT and cytotoxic CD4+ T cells with upregulation of IL23R and ADAM12.

overall_design: Whole exome sequencing was performed and results confirmed by Sanger sequencing. Protein modeling, Western blot, immunofluorescence, and nuclear extract-based NF-κB activation assays were conducted to assess the functional impact of the identified mutation. Immune profiling was performed using mass cytometry time of flight (CyTOF) and single-cell RNA sequencing (scRNA-seq) and compared to controls.

first: Liran

last: Baram

first: Arne

last: Gehlhaar

first: Weihong

last: Gu

first: Siqi

last: Guo

first: Eduardo

last: Gonzalez Santiago

first: Atar

last: Lev

first: Ortal

last: Barel

first: Raanan

last: Shamir

first: Raz

last: Somech

first: Liza

last: Konnikova

first: Dror

last: Shouval


title: TEAD1 condensates are transcriptionally inactive storage sites on the pericentromeric heterochromatin

city: Baltimore

first: Danfeng

last: Cai

address: 615 N Wolfe St

institute: Johns Hopkins Bloomberg School of Public Health

summary: TEA domain transcription factor 1 (TEAD1), a Hippo pathway transcription factor important in cellular homeostasis and development, is increasingly implicated in cancer biology. Here, we reveal a novel role for TEAD1 in organizing nuclear condensates, independent of active transcription. Using high-resolution imaging, ChIP-seq, RNA-seq and proximity-based proteomics, we demonstrate that in patient-derived renal cell carcinoma cells, TEAD1 forms micron-sized foci by binding to the heterochromatic pericentromeric regions using its DNA-binding domain. These TEAD1 foci do not mediate transcription but instead serve as depots for excess TEAD1. This contrasts with TEAD1 organization in other genomic regions of both RCC and normal kidney cells, where TEAD1 associates with markers of active transcription. Our findings provide a mechanistic framework for TEAD1’s dual regulatory roles, offering new insights into its contribution to transcriptional dysregulation and tumor progression.

overall_design: Chromatin immunoprecipitation (Ch-IP) was performed based on previous studies81. In general, 108 cells are used per each ChIP-seq experiment. HK2 and UOK cells were first treated with 1% formaldehyde in UOK media, followed by the addition of 0.125M glycine to halt cross-linking. The cells, washed in ice-cold PBS, were then lysed in cell lysis buffer, with subsequent nutation at 4°C. Cells were treated by dounce homogenization on ice, followed by centrifuge at 500 x g for 10min. The supernatant was discarded, and the pellets was resuspended using nuclear lysis buffer. Nuclear lysates were then sheared by Covaris E220 to achieve average chromatin length of 300-400 bp. The protein/chromatin complexes are captured using antibodies specific to the TEAD1, H3K9me3, YAP1, H3K27ac, and mouse IgG, and the mixtures were incubated overnight on nutator at 4°C.


title: Cell Cycle Arrest of a ‘Zippering’ Epithelial Cell Cluster Mediates Face Morphogenesis in Mice and Humans and is Unleashed in Craniofacial Disorders

city: New York

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

summary: Facial features identify individuals, but the mechanisms shaping the human face remain elusive. Orofacial clefting (OFC), the most common craniofacial abnormality, results from failed fusion of the facial prominences, partly caused by persistence of the cephalic epithelium. Using mouse models to guide our studies, here we uncover the identity, behaviors, and molecular blueprints of a novel craniofacial epithelial population, Zippering Lambda (ZL), similarly characterized by cell cycle arrest in mouse and human embryos. Remarkably, in Pbx1/2 and p63 mutant mice with OFC cell cycle is unleashed in ZL epithelium. Intersecting ZL-enriched genes with human OFC whole-genome sequencing datasets identifies ZFHX3 variants in affected individuals and cephalic epithelial Zfhx3 deletion results in murine OFC. Our findings further demonstrate that ZFHX3 and PBX1 synergistically regulate cell cycle inhibitor genes acting within a complex in embryonic faces. Collectively, we deconstruct new mechanisms that pattern the face, connecting cell cycle arrest to developmental tissue fusion.

overall_design: We performed bulksequencing of live cells from the pooled lambdoidal junctions from E11.5 from wild-type and Pbx1/2 knock out genetic background

first: T

last: Qu

first: B

last: Chacon

first: L

first: M

last: Losa

first: R

last: Hernandez Martinez

first: K

last: Robinson

first: A

last: Jones

first: J

last: De Anda

last: Risolino

first: G

last: Panagiotakos

first: E

middle: J

last: Leslie-Clarkson

first: I

last: Adameyko

last: Selleri


title: Repetitive sequences drive the condensation of H3K9me3 Methyltransferase complex to promote epigenetic inheritance in Caenorhabditis elegans [mutants]

city: Guangzhou

first: shiyu

last: cai

address: No. 135 Xingang Xi Road, Haizhu District

institute: Sun Yat-sen University

summary: Histone H3K9 trimethylation (H3K9me3) plays a pivotal role in the establishment and maintenance of heterochromatin and is essential for facilitating epigenetic inheritance. H3K9me3 is often biasedly deposited and associated with repetitive sequence region, although the underlying mechanism remain poorly understood. In this study, we identify two proteins, SECP-1 and SECP-2, as crucial cofactors for the genome-wide deposition of H3K9me3 in Caenorhabditis elegans. SECP-1 interacts directly with SECP-2 and the primary H3K9me3 methyltransferase, SET-25, forming a protein complex that bridges SECP-2 with SET-25. This complex assembles in the cytoplasm and is transported into the nucleus through SET-25. Once in the nucleus, the complex is recruited to and concentrated at SET-25’s genomic targets in an interdependent manner. The accumulation of this complex correlates with the formation of condensates at repetitive sequences, the perinuclear localization of heterochromatin, and the epigenetic inheritance of small RNA-mediated gene silencing. The introduction of transgenic arrays leads to the redistribution of the SECP-1/SECP-2/SET-25 complex to the transgene locus, a genome-wide decrease in H3K9me3 levels, and an increase in repetitive sequence expression. We propose that repetitive sequences drive the formation of condensates containing H3K9me3 methyltransferase complexes, which in turn causes a biased deposition of H3K9me3 at these genomic regions.

overall_design: ChIP-seq of histone modification H3K9me3 in Caenorhabditis elegans embryo

first: Shiyu

first: Xinru

last: Li


title: Next Generation Sequencing Facilitates Quantitative Analysis of control and PS micro-/nanoplastics stressed E. faecalis OG1RF , E. faecalis OG1RS , E. coli DH5α and pCF10 plasmid Transcriptomes

city: Shenzhen

first: Yuanyuan

last: Kang

address: No. 6 Pingshan 1st Road, Taoyuan Street, Nanshan District

department: School of Civil and Environmental Engineering

institute: Harbin Institue of Technology

summary: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of E. faecalis OG1RF , E. faecalis OG1RS , E. coli DH5α and plasmid pCF10, and their mRNA response under the exposure of different sizes of Polystyrene (PS), including 20 nm, 120 nm and 1 μm. The concentrations were 0.1, 1, 10 mg/L for every size of PS. The group without adding PS was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these 3 sizes of PS on transcriptional levels can be revealed. Illumina HiSeq PE150 was applied. NEBNextő Ultra II Directional RNA Library Prep Kit for Illumina was used for library construction. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. faecalis OG1RF reference genome (NC_017316.1), E. coli DH5α reference genome (GCF_000982435.1), and plasmid pCF10 reference genome (NC_006827.2) using Bowtie2. RSeQC was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

overall_design: Bacterial mRNA profiles of E. faecalis OG1RF , E. faecalis OG1RS , E. coli DH5α and plasmid pCF10 in response to 0.1 mg/L 20 nm PS, 1 mg/L 20 nm PS, 10 mg/L 20 nm PS, 0.1 mg/L 120 nm PS, 1 mg/L 120 nm PS, 10 mg/L 120 nm PS, 0.1 mg/L 1 μm PS, 0.1 mg/L 1 μm PS, and 10 mg/L 1 μm PS for 2 hours, bacteria and plasmid without adding PS are the control group, in triplicate, using Illumina HiSeq PE150.

first: Shu-Hong

last: Gao

first: Yusheng

last: Pan

first: Tianyao

first: Rui

first: Yue

last: Wang

first: Jianhua

last: Guo

first: Jianqiang

last: Su

first: Aijie

first: Zhigang

last: Qiu


title: Macrophages amplify damaged sensory neuron spontaneous activity in a human co-culture model of neuropathic pain [mouse]

first: Paschalina

last: Chrysostomidou

summary: Neuropathic pain is a highly prevalent condition for which treatments are hampered by low efficacy and dose-limiting side-effects. Injury to the somatosensory nervous system causes maladaptive plasticity that initiates and maintains chronic pain. Emerging evidence suggests that inflammatory cells of the innate immune system shape the injured nervous system and drive pain pathogenesis. Data from preclinical models and human patient biopsies have specifically implicated peripheral macrophage populations for a pro-algesic role, yet how these cell types influence damaged sensory neurons and whether they directly sensitise their neuronal activity is unclear. Here, we have developed an iPSC co-culture system to study the interactions of macrophages and sensory neurons in a fully humanised experimental model. We found that analogous to endogenous counterparts, iPSC-derived macrophages (iMacs) display a dynamic molecular and functional profile that is highly dependent on neuronal context. Co-culture with injured iPSC-derived sensory neurons (iSNs) induces morphological, gene expression, and secretory profile changes in iMacs that are consistent with in vivo nerve injury datasets. iMacs in turn amplify spontaneous firing in damaged sensory neurons, implicating macrophages in a cardinal feature of neuropathic pain. These results illustrate the utility of an iPSC-based model to study signalling between these two cell types; they support a role for macrophages in directly amplifying damaged sensory neuron activity and highlight disrupting pathological signalling between these cell types as a promising strategy for future analgesic drug development.

overall_design: Myeloid lineage cells extracted from mouse sciatic nerve were processed for single cell sequencing 1 or 15 weeks after surgically induced nerve injury (Crush, PSNL or Sham).

first: Julia

last: Vlachaki Walker

first: Zoe

last: Hore

first: Franziska

last: Denk


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

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 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.

first: Sidrit

last: Uruci

first: Daphne

middle: E

last: Boer

first: Paul

middle: W

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

middle: P

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: Research on the role and mechanism of stress liver regulation of negative emotions

city: Hefei

first: Shuaijie

last: Sun

address: The First Affiliated Hospital of USTC

institute: Department of Anesthesiology,First Affiliated Hospital of USTC

summary: Post-stress hepatic metabolic dysfunction is a critical factor in the development of negative emotional states after liver transplantation (NEALT), severely impairing postoperative patient recovery. However, its pathological mechanisms remain unclear. Microglia (Mg), as central immune cells, express numerous sensory receptors on their membranes and serve as a key link between peripheral organ stress and brain nucleus regulation. By constructing microglia-specific gene knockout mice, liver transplantation, and restraint stress models, combined with behavioral tests and multi-omics analysis, we found that transplanting a stressed donor liver into a non-stressed recipient mouse could mimic clinical NEALT symptoms. The anterior cingulate cortex (ACC) is a key brain region regulating emotional responses and sensory perception. Mechanistic studies revealed that stress-induced liver detoxification dysfunction leads to elevated bilirubin levels, which acts as a ligand to activate the TRPM2 receptor in ACC microglia, enhancing their impact on glutamatergic synapses and ultimately leading to decreased neuronal activity and NEALT development. We propose a hypothesis: stressed livers drive microglia to excessively engulf glutamatergic synapses via the liver-brain-Mg TRPM2 signaling axis. Evaluating interventions targeting this axis holds significant potential for NEALT prevention and treatment, providing significant insights into its mechanisms and therapeutic strategies.

overall_design: Freshly dissociated single-cell suspensions were loaded to 10X Genome GenCode Single-cell instrument to generate GEMs (Gel Bead-In-EMlusion). ScRNA-seq libraries were subsequently prepared following the manufacturer’s protocol of Chromium Next GEM Single Cell 3’ Regent Kits v3.1. Libraries were then sequenced using the Novaseq 6000 platform with paired-end sequencing (PE150) mode.

first: Hongrui

last: Zhu


title: Synthetic lethality from the combination of a histone methyltransferase, SUV39H2 inhibitor, and a poly (ADP-ribose) polymerase inhibitor for uterine leiomyosarcoma [ChIP-Seq]

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

summary: Background: Uterine leiomyosarcoma (uLMS) has a poor prognosis owing to its resistance to chemotherapy. Therefore, novel therapeutic targets for uLMS should be identified. Suppressor license of variegation 3-9 homolog 2 (SUV39H2) is a histone methyltransferase that promotes the repair of double-stranded DNA breaks by recruiting phosphorylated H2AX (γH2AX). In this study, we investigated the potential therapeutic targets of SUV39H2 in uLMS and the mechanism of synthetic lethality between PARP inhibitors and the SUV39H2 inhibitor OTS186935. Methods: First, we analyzed the mRNA and protein expression of SUV39H2 in the clinical tissues of uLMS, normal myometrium, and leiomyomas using real-time polymerase chain reaction and immunohistochemistry, respectively. Next, we conducted drug sensitivity assays for OTS186935 alone and in combination with olaparib, a poly (ADP-ribose) polymerase inhibitor, using the uLMS cell lines SK-LMS-1 and SK-UT-1. We performed Western blotting, immunofluorescence, and chromatin immunoprecipitation sequencing (ChIP-seq) to investigate γH2AX following OTS186935 treatment in addition to in vivo experiments using nude mice with subcutaneously implanted uLMS. Results: SUV39H2 expression in uLMS was significantly higher than that in the normal myometrium and leiomyomas. OTS186935 decreased the viability of both cell lines, and its combination with olaparib resulted in synthetic lethality in SK-UT-1 cells (combination index = 0.88). After treatment with OTS186935, γH2AX accumulation decreased. ChIP-seq also showed downregulation of γH2AX following OTS186935 treatment. Notably, the combination of OTS186935 and a PARP inhibitor was significantly more effective in vivo. Conclusion: OTS186935 inhibited double-stranded DNA break repair, as evidenced by γH2AX downregulation by ChIP-seq and other assays. OTS186935 combined with olaparib induces synthetic lethality in patients with uLMS.

overall_design: ChIP-seq was conducted for SK-UT-1 cell line under four conditions: 0.1% DMSO (negative control), 1 µM OTS186935, 0.5 µM doxorubicin, and a combination of 1 µM OTS186935 with 0.5 µM doxorubicin.

first: Yusuke

last: Toyohara

first: Kenbun

last: Sone

first: Reo

last: Maruyama


title: Repetitive sequences drive the condensation of H3K9me3 Methyltransferase complex to promote epigenetic inheritance in Caenorhabditis elegans [transgenes]

first: shiyu

last: cai

first: Shiyu

last: Cai

first: Xinru

last: Li


title: Cell and nuclear size are associated with chromosomal instability and tumorigenicity in cancer cells that undergo whole genome doubling

city: Blacksburg

first: Mathew

last: Bloomfield

state: VA

address: 1015 Life Science Circle

department: Biological Sciences

institute: Virginia Tech

summary: Whole genome doubling (WGD) is a frequent event in cancer evolution associated with chromosomal instability, metastasis, and poor prognosis. While the genomic consequences of WGD are well documented, the effects of non-genetic alterations that accompany WGD, such as changes to cell and nuclear size, on tetraploid (4N) cancer cell physiology are less understood. Here, we show that cell and nuclear volume do not always scale with DNA content after WGD in cancer cells, resulting in 4N cells that differ in size. We find that small size is associated with enhanced cell fitness, mitotic fidelity, and tumorigenicity in 4N cancer cells and with poor patient survival in WGD-positive human cancers. Overall, these results suggest that cell and nuclear size contribute to the tumorigenic potential of 4N cancer cells and could be an important prognostic marker in human tumors that undergo WGD.

overall_design: Single cell tetraploid clones that differ in cell and nuclear size, but not ploidy, were generated from near-diploid breast and colorectal cancer cell lines. Tetraploidy was induced in DLD1 by exposing cells to 1.5ug/mL dihydrocytochalasin for 20 hr. In HCT116 and CAL51, cytokinesis failure was induced by adding 75 µM blebbistatin to the culture medium for 20 hr. Drugs were washed out four times in media. The cells were allowed to recover for 48 hr before performing single cell cloning via limiting dilution in 96-well plates. Transcriptional profiling was performed on the small and large tetraploid clones to identify differences in gene expression.

first: Daniela

last: Cimini


title: Synthetic lethality from the combination of a histone methyltransferase, SUV39H2 inhibitor, and a poly (ADP-ribose) polymerase inhibitor for uterine leiomyosarcoma [RNA-Seq]

overall_design: RNA-seq was conducted for SK-LMS-1 and SK-UT-1 cell lines treated with DMSO


title: Gene regulatory programs of NK cells show that NCAM1 (CD56) and KIRs are controlled by genetically polymorphic distal regulatory elements

city: Columbus

first: Patrick

last: Collins

state: Ohio

address: 460 West 12th Avenue, Biomedical Research Tower 770

department: Microbial Infection and Immunity

institute: The Ohio State University

type: Genome binding/occupancy profiling by array

overall_design: Refer to individual Series


title: Effect of depletion of hepcidin-1 on gene expression  of mouse hepatic Kupffer cells

city: Hangzhou

first: yihang

last: Pan

state: Zhejiang

address: erkang road

institute: Zhejiang University

summary: To investigate the effect of hepcidin-1 deficiency on gene expression of mouse hepatic Kupffer cells, we isolated hepatic non-parenchymal cells from hepcidin-1 knockout mice (KO) and wild type (WT) mice with C57BL/6 genetic background, and then obtained fluorescence-activated cell sorting (FACS) sorted-Kupffer cells (gated on live CD45+ F4/80+ CD11bint hepatic nonparenchymal cells). We then performed switching mechanism at the 5′ end of the RNA transcript (SMART-seq) analysis of isolated Kufpffer cells.

overall_design: Comparative gene expression profiling analysis of SMART-seq data for Kupffer cells isolated from  hepcidin-1 knockout mice (KO) and wild type (WT) mice.

first: Yihang

first: Qixing

last: Chen


title: ABHD18 is essential for cardiolipin remodeling and its inhibition restores mitochondrial function in Barth Syndrome

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

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


title: RNA sequencing of BM-MDSCs exposed to high potassium

city: hangzhou

first: zhiqi

last: xie

address: huzhou street 51

institute: Hangzhou city university

summary: Total RNA was extracted from BM-MDSCs treated with or without additional 34.7 mM KCl. Libraries were prepared according to standard Illumina protocols. RNA sequencing was performed by Shanghai Biotechnology Corporation (Shanghai, China). The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4). The fragments of genes were counted using stringtie (v1.3.3b) followed by TMM (trimmed mean of M values) normalization. Differential gene expression analysis was conducted using DESeq2 (version 1.20.0), with a significance threshold of a corrected p-value < 0.05 and an absolute fold change ≥ 2. The distribution of differentially expressed genes in KEGG pathways was analyzed using the clusterProfiler R package (version 3.8.1) to identify key biological mechanisms.

overall_design: BM cells were isolated from C57BL/6J mice and stimulated with 40 ng/mL recombinant granulocyte-macrophage colony-stimulating factor (GM-CSF, Peprotech) for four days. Cells were cultured either in the absence or presence of additional 34.7 mM KCl (Sigma)

first: Zhiqi

last: Xie


title: Integrative Computational and Experimental Analysis of Curly Su Mutations in Drosophila melanogaster

city: Washington

first: Shaolei

last: Teng

state: District of Columbia

address: 415 College St. NW

department: Biology

institute: Howard University

summary: The Curly Su (dMPO) protein, a homolog of the human myeloperoxidase (hMPO), is critical for wing development in Drosophila melanogaster. Like human peroxidases, dMPO is involved in various cellular and physiological processes, producing significant quantities of reactive oxygen species that contribute to both development and immunity in the fruit fly. Given the significant sequence and structural similarities between dMPO and hMPO, dMPO serves an ideal model for studying peroxidase functions and related pathologies. We performed saturated computational mutagenesis on dMPO, analyzing the effects of 11,191 missense mutations on its stability. Notably, the G378W mutation exhibited the greatest destabilizing effect, while the W621R, potentially pathogenic, also reduced dMPO stability. To investigate these effects in vivo, we used genome editing to generate the transgenic Drosophila with G378W, W621R, and deletion of residues 305-687. Remarkably, G378W mutants displayed significant alterations in wing morphology and reduced lifespan. RNA-seq analysis of transgenic and wild-type flies revealed differentially expressed genes (DEGs), as interpreted through gene ontology analysis. Our integrated computational and genetic approach identified dMPO mutations that disrupt protein stability and alter gene expression. These findings offer new insight into how single-point mutations can lead to systemic biological changes.

overall_design: RNA-seq was conducted on adult Drosophila carrying G378W, W621R, or Del305–687 dMPO mutations and wild-type controls, with three biological replicates per group.

first: Adebiyi

last: Sobitan

first: Md Shah

last: Jalal

first: Qiaobin

last: Yao

first: Jinrui

last: Xu

first: Ginger

last: Hunter

first: Atanu

last: Duttaroy


title: NDF/GLYR1 Promotes RNA Polymerase II Processivity via Pol II Binding and Nucleosome Destabilization

city: Piscataway

first: Jia

last: Fei

state: NJ

address: 604 Allison Rd

department: Department of Molecular Biology and Biochemistry

institute: Rutgers University

summary: The Nucleosome Destabilizing Factor (NDF) facilitates transcription through chromatin, but its precise mechanism remains incompletely understood. Here, we identify a critical region (amino acids 140-160) within NDF that specifically interacts with phosphorylated RPB1, the largest subu-nit of elongating RNA Polymerase II (Pol II). Mutations in this region disrupt Pol II interaction and impair Pol II elongation both in vitro and in cells, yet do not affect NDF's ability to destabilize nu-cleosomes, establishing a functional separation between these two activities. Cellular studies re-veal that NDF knockout cells display faster Pol II elongation rates but produce fewer nascent tran-scripts, demonstrating NDF's primary role in maintaining transcriptional processivity through-out gene bodies. Our findings demonstrate that NDF uses distinct mechanisms to ensure productive transcription elongation rather than simply enhancing elongation speed, offering new insights in-to how transcription efficiency is maintained in chromatin.

overall_design: ChIP-seq analysis of NDF in NDF WT, MT2 and MT4 rescued SW480 KO cells; ChIP-seq analysis of Pol II in NDF WT and KO Hela cells across the conditions: DRB transcription arrested, DRB released for 5, 10 and 20 mins respectively.

first: Ziwei


title: A spatio-cellular map of the mouse nodose ganglia

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: The vagus nerve is a key component of the parasympathetic nervous system, innervating multiple abdominal organs to monitor and regulate their function. It forms the main neural pathway between the gastrointestinal tract and the brain, playing a major role in the regulation of energy homeostasis. The cell bodies for vagal sensory neurons reside in the nodose ganglia, with the left and right ganglia reported to have distinct roles in food intake and reward. Here, we have integrated our own single nucleus RNA sequencing data with multiple publicly available datasets to create a database of 108,482 nuclei and cells, and combined this with spatial transcriptomics to present a spatio-cellular transcriptional map of the mouse nodose ganglia, the ‘NodoMap’. Nodose ganglia neuronal cells clustered into twenty-two different subtypes, all found in both left and right nodose ganglia, but with significant differences in gene expression between left and right ganglia across multiple neuronal subtypes. Overnight fasting modulated gene expression across specific neuronal subtypes, including nutrient responsive pathways. Spatial transcriptomics showed that while vagal neuronal types were highly interspersed, patterns of organisation into cellular ‘neighbourhoods’ could be observed, with neighbourhoods identified of predominantly non-neuronal cells and of different neuronal populations accompanied by glial-like cells. Thus, NodoMap provides a detailed atlas of the mouse nodose ganglia in a spatial context, providing a platform for vagovagal neurocircuit analysis, and serving as an important resource to identify targets for pharmacotherapies for metabolic disease.

overall_design: We performed single nucleus RNA sequencing on left and right mouse nodose ganglia  from mice fed ad libitum, and mice that were subjected to an overnight fast. After nucleus dissociation, samples were barcoded using the 10X Genomics cellplex kit and pooled. A single libraries was generated containing 4 samples (left adlibitum, right adlibitum, (10 nodose ganglia per pool). We additionally performed Curio seeker spatial transcriptomics on left and right nodose ganglia (3 nodose ganlia per tile, 3 tiles). A total of 3 libraries were generated: 2 from left nodose ganglia and 1 from right nodose ganglia.

first: Sijing

last: Cheng

first: Georgina KC

last: Dowsett

first: Giles SH

last: Yeo

first: Kevin G

last: Murphy

first: Brian YH


overall_design: TT-seq analysis of nascent RNA and elongation speed in NDF WT and KO Hela cells, cells were treated with DRB and released for 5 and 10 min; Bru-seq analysis of nascent RNA in  NDF KO SW480 cells rescued with NDF WT, MT2 or MT4.

last: Li


title: Exploration of predictive factors based on oral and intestinal bacterial flora for treating patients with urothelial carcinoma

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

summary: Purpose The role of intestinal flora in carcinogenesis and chemotherapy efficacy has been increasingly studied; however, comparisons between oral and intestinal flora remain limited. This study aimed to identify the microbial changes in urothelial carcinoma (UC) by analyzing oral saliva and stool samples from healthy individuals and patients. We also examined the association between microbial composition and immune checkpoint inhibitor (ICI) response. Methods A total of 20 healthy individuals and 38 patients with UC were analyzed. Among them, 27 patients with UC underwent ICI treatment. Oral saliva and stool samples were analyzed for 16S rRNA sequences to assess bacterial composition. Operational taxonomic units were generated, and phylogenetic analysis was performed using the 16S Metagenomics app  whithin the Illumina BaseSpace Sequence Hub. Results Patients with UC showed higher Veillonellaceae and Prevotellaceae levels in saliva and stool, with lower levels of these bacteria associated with more prolonged overall survival and progression-free survival, particularly Veillonellaceae in stool. A higher neutrophil-to-lymphocyte ratio correlated with increased levels of these bacteria. Conclusion Veillonellaceae and Prevotellaceae are potential microbial biomarkers of survival outcomes and ICI efficacy in patients with UC. Non-invasive oral microbial sampling may facilitate personalized cancer treatment strategies.

sample_organism:
human gut metagenome
human oral metagenome

overall_design: To investigate microbial changes associated with UC, we performed 16S rRNA sequencing using genomic DNA extracted from saliva and stool samples of UC patiants and healthy controls.

first: Yuichi

last: Matsumoto

first: Yukihiro

last: Hitaka

first: Hiroshi

last: Hirata

first: Yoshiaki

last: Yamamoto

first: Keita

last: Kobayashi

first: Naohito

last: Isoyama

first: Toshio

last: Matsubara

first: Kenji

last: Watanabe

first: Shin

last: Nakagawa

first: Katsumi

last: Mishima

first: Koji

last: Harada

last: Shiraishi


title: O-Desmethyltramadol Enhanced Anti-Cancer Efficacy over Tramadol through Non-μ-Opioid Receptor and Differential Cellular Contexts of Human Breast Cancer Cells

city: Taipei

first: Zih-Syuan

last: Wu

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 114201, Taiwan

country: Taiwan

institute: National defense medical center

summary: Tramadol, a widely used analgesic, has recently been explored for its potential anti-cancer effects. However, the antitumor dosage of tramadol is over its current clinical application. Its primary metabolite, O-desmethyltramadol, has a higher affinity for the μ-opioid receptor and exhibits stronger pharmacological activity. Hence, we sought to examine whether the cytotoxic effect of O-desmethyltramadol was better than tramadol on breast cancer cells. Our results showed that O-desmethyltramadol significantly reduced cell viability in MDA-MB-231 and MCF-7 breast cancer cells, at least, ten-fold efficacy than tramadol. The presence of a μ-opioid receptor antagonist alvimopan did not alter these cytotoxic effects of tramadol and O-desmethyltramadol, indicating a non-opioid receptor-mediated mechanism. Compared with antitumor activity of tramadol mediated through ER stress, we confirmed that O-desmethyltramadol induced endoplasmic reticulum stress proteins, p-eIF2α/ eIF2α ratio, ATF4, and CHOP in western blot analysis and ATF4, DDIT3, and CHAC1 mRNAs in real-time polymerase chain reaction. Beyond the opioid receptor-mediated pathway, we further analyzed the differential functions of O-desmethyltramadol than tramadol using the RNA-seq analysis. The pathway enrichment analyses revealed that O-desmethyltramadol influenced immune and inflammatory pathways, such as TNF and IL-6/JAK/STAT3 signaling in MDA-MB-231 cells, while in MCF-7 cells, it affected metabolic and transcriptional pathways, including mTOR and MAPK signaling. Gene Set Enrichment Analysis further highlighted O-desmethyltramadol’s role in interferon response and tumor microenvironment modulation. Four upregulated genes and five downregulated genes were modulated by O-desmethyltramadol in MDA-MB-231 and MCF-7 cells. Overall, our findings indicated that O-desmethyltramadol exerted potent anti-cancer effects through multiple non-opioid mechanisms, with distinct response from tramadol depending on breast cancer subtype.

overall_design: In this study, RNA sequencing analysis was employed to investigate the effects of 0.05 mg/ml O-Desmethyltramadol in comparison to 0.5 mg/ml tramadol on gene expression in MDA-MB-231 and MCF-7 cells.

first: Yi-Hsuan

last: Huang

first: Shih-Ming


title: Induced B Cell Receptor Diversity Predicts PD-1 Blockade Immunotherapy Response

city: Stanford

first: Yonglu

last: Che

state: CA

address: 269 Campus Dr

department: Dermatology

institute: Stanford University

summary: Immune checkpoint inhibitors such as anti-PD-1 antibodies (aPD1) can be effective in treating advanced cancers. However, many patients do not respond and the mechanisms underlying these differences remain incompletely understood. In this study, we profile a cohort of patients with locally-advanced or metastatic basal cell carcinoma undergoing aPD-1 therapy using single-cell RNA sequencing, high-definition spatial transcriptomics in tumors and draining lymph nodes, and spatial immunoreceptor profiling, with long-term clinical follow-up. We find that successful responses to PD-1 inhibition are characterized by an induction of B-cell receptor (BCR) clonal diversity after treatment initiation. These induced BCR clones spatially co-localize with T-cell clones, facilitate their activation, and traffic alongside them between tumor and draining lymph nodes to enhance tumor clearance. Furthermore, we validated aPD1-induced BCR diversity as a predictor of clinical response in a larger cohort of glioblastoma, melanoma, and head and neck squamous cell carcinoma patients, suggesting that this is a generalizable predictor of treatment response across many types of cancers. We discover that pre-treatment tumors harbor a characteristic gene expression signature that portends a higher probability of inducing BCR clonal diversity after aPD-1 therapy, and we develop a machine learning model that predicts PD-1-induced BCR clonal diversity from baseline tumor RNA sequencing. These findings underscore a dynamic role of B cell diversity during immunotherapy, highlighting its importance as a prognostic marker and a potential target for intervention in non-responders.

overall_design: 35 total samples of Xenium in situ on human FFPE tissue. Specimens include 4 tumor-draining lymph nodes post PD-1 inhibitor treatment, 8 treatment-naïve BCC tumor specimens, 2 perilesional skin samples post PD-1 inhibitor treatment, and 21 post PD-1 inhibitor treatment BCC tumor specimens

first: Howard

middle: Y

last: Chang


title: Gene expression changes induced by repeated administration of intravenous cell therapy in dystrophic skeletal muscle

city: Los Angeles

first: Russell

last: Rogers

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: We compared the effects of long-term cell therapy on dystrophic skeletal muscle gene expression

overall_design: 8-week-old mdx mice were administered cardiosphere-derived cells or vehicle once-monthly for one year. The soleus was extracted and prepared for RNA-seq

middle: G


title: High-throughput screen reveals that atypical antipsychotics promote continual efferocytosis by antagonizing dopamine signaling and promoting vitamin A-dependent Arginase 1 upregulation

city: SHANGHAI

first: Fudi

last: Wang

state: SHANGHAI

address: 320, YUEYANG ROAD

summary: Programmed cell removal, or efferocytosis, has been proposed as a method to dispose of unwanted cells that accumulate and promote diseases such as cancer, infection, and atherosclerosis. Several pro-efferocytic therapies are currently in development, but toxicity related to the off-target clearance of healthy tissue has led to the premature termination of multiple first-generation clinical programs. To identify new pro-efferocytic therapies with established risk profiles, we conducted a high-throughput screen of about 3000 FDA-approved drugs and compounds. This allowed us to identify the atypical antipsychotic drug, thiothixene, as a promising candidate for clinical translation. Leveraging thiothixene’s known inhibitory effects on a wide range of neurotransmitters and catecholamines, we found that dopamine has a potent inhibitory effect on efferocytosis, which thiothixene could partially offset. Mechanistic studies revealed that thiothixene’s pro-phagocytic effects were not mediated by alterations in so-called ‘eat me’ molecules or efferocytic receptors, but instead occurred due to the induction of a process known as continual efferocytosis. RNA-sequencing revealed that these effects occurred via alterations in the retinol binding receptor, Stra6L, which enhanced vitamin A-dependent signaling and drove upregulation of the continual efferocytosis mediator, Arginase 1. Taken together, this unbiased screen identified the unanticipated anti-efferocytic properties of dopamine, while highlighting the translational potential of a generic, FDA-approved anti-psychotic drug which has been in use for more than 50 years. This therapy may represent a novel approach for promoting continual efferocytosis and the removal of diseased tissue that otherwise could promote a range of clinical disorders.

overall_design: BMDMs were prepared from three mice. At day4 of differentiation, 7x10^5 macrophages were seeded into 6-well plates, and cells were treated with 2µM thiothixene or DMSO for 24 hours at day 6. Drug-treated macrophages were washed with PBS once and cells were lysed with 0.5 ml TRIzol™ Reagent. Total RNA was extracted according to the protocol from manufacturer and qualified on a NanoDrop™ OneC Microvolume UV-Vis Spectrophotometer (Thermo Scientific™ 840274200). Three biological replicates per treatment group with a total of 200 ng RNA per sample were sent to Novogene Co. (Sacramento, CA, USA) for sample quality control, library preparation, and sequencing.

first: Yoko

last: Kojima

first: Nicholas

last: Leeper


title: Gene expression in droughted and well-watered maize roots in diverse, differentially conditioned soil microbiomes

city: Lawrence

first: Maggie

middle: R

last: Wagner

state: KS

address: 1200 Sunnyside Avenue

institute: University of Kansas

summary: The goal of this growth chamber experiment was to investigate the effects of diverse soil microbial communities on the transcriptional responses of plants to drought. Specifically, we sought to understand how soil microbiomes' past exposure to water-limited conditions (either long-term exposure to dry conditions in low-precipitation sites, or recent acute drought) impacted their interactions with plants. Six soils collected from remnant prairies  crossing a steep precipitation gradient in Kansas, USA were used as the starting microbial communities. Thirty-two pots (or mesocosms) of each soil were divided among four treatments: droughted or well-watered, and with or without a host plant (Tripsacum dactyloides) in a factorial design. The soil mesocosms were "conditioned" in these treatments for five months. (Metagenome and metatranscriptome data from the baseline soils and the post-conditioning soils are available in a separate BioProject on NCBI SRA and GEO). Then, a microbial slurry extracted from each of the 192 conditioned soils was used to inoculate 4 plants in a subsequent experiment (the “Test Phase”): one pot per combination of watering treatment (droughted or control) and host species (Zea mays or Tripsacum dactyloides). After 4 weeks (for maize) or 5 weeks (for eastern gamagrass) we harvested one crown root per plant for 16S rRNA sequencing and another crown root for RNA-seq. The 16S and RNA-seq data for these plants (both species) are contained in this BioProject. Note that 16S rRNA sequencing data are available for all plants in this experiment, but we conducted RNA-seq only for a subset (all plants grown in microbiomes originating from the 2 driest and 2 wettest collection sites).

overall_design: RNA-seq data from crown roots of maize plants inoculated with microbial slurries originating from 4 different sites. Each microbial slurry had been conditioned for 5 months under droughted or well-watered conditions and with or without a plant host (see abstract). Each independent slurry was used to inoculate 4 plants (2 maize, 2 eastern gamagrass), which were then drought-treated or well-watered, in a factorial design).

first: Nichole

last: Ginnan

first: Natalie

last: Ford


title: Gene expression in droughted and well-watered eastern gamagrass roots in diverse, differentially conditioned soil microbiomes


title: Epigenetic priming of embryonic enhancer elements coordinates developmental gene networks

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute


title: Robust generation of photoreceptor-dominant retinal organoids from porcine induced pluripotent stem cells.

city: Madison

first: David

last: Gamm

state: WI

address: 1500 Highland Ave

department: Department of Ophthalmology and Visual Sciences

institute: University of Wisconsin School of Medicine and Public Health

summary: Outer retinal degenerative diseases (RDDs) and injuries leading to photoreceptor (PR) loss are prevailing causes of blindness worldwide. While significant progress has been made in the manufacture of human pluripotent stem cell (hPSC)-derived PRs, robust production of PSC-PRs from pigs, a popular preclinical large animal model, would provide an avenue to collect conspecific functional and safety data to complement human xenograft studies. Toward this goal, we describe the highly efficient generation of PR-dominant pig induced PSC (piPSC)-derived retinal organoids (ROs) using modifications of our established hPSC-RO differentiation protocol. Pig iPSC-ROs were characterized using immunocytochemistry (ICC) and single cell RNA-sequencing (scRNA-seq), which revealed the presence and maturation of major neural retina cell types, including PRs and retinal ganglion cells, that possess molecular signatures akin to those found in hPSC-ROs. In late piPSC-ROs, a highly organized outer neuroepithelium was observed with rods and cones possessing outer segments and axon terminals expressing pre-synaptic markers adjacent to dendritic terminals of bipolar cells. The existence of piPSC lines and protocols that support reproducible, scalable production of female and male ROs will facilitate transplant studies in pig models of retinal injury and RDD unconfounded by immunological and evolutionary incompatibilities inherent to human xenografts.

overall_design:
Porcine iPSC-derived retinal organoids at day 40 and d120 of differentiation were dissociated. At each designated timepoint, 5 piPSC-ROs from n=3 independent differentiations were pooled for scRNA-seq analysis.
Please note that the processed data files generated from both *L001 ad *L002 samples are linked to the corresponding *L001 sample record.

first: Kimberly

middle: L

last: Edwards

first: Bethany

middle: M

last: Moore

first: Praveen

last: Susai Manickam

first: Ron

last: Stewart


title: Investigating AtcS in the Two Component Regulatory System of Treponema denticola

city: Richmond

first: Daniel

last: Miller

state: Virginia

address: 1101 E Marshall Street

department: Microbiology and Immunology

institute: Virginia Commonwealth University

summary: The ability of T. denticola to thrive during disease progression arises from its ability to adapt to changing environmental, immunological, and physicochemical conditions. Two component regulatory (TCR) systems are found in most bacteria and are used as sensory systems that allow bacteria to respond to changing environmental conditions. TCR systems consist of a histidine kinase and response regulator and when the appropriate stimulus occurs, the kinase autophosphorylates at a conserved histidine residue. The phosphate is transferred to a conserved aspartate residue in the receiver domain of the response regulator which results in conformational changes in the output domain. These conformational changes impact DNA binding, protein-protein interactions, or enzymatic activities that influence transcriptional and cellular activity. While AtcS sensor kinase and AtcR response regulator have shown to have growth-phase-regulated global regulatory potential, the molecular mechanisms and responses regulated by AtcSR need further elucidation. This study utilized genetic manipulation strategies in order to characterize the knockout of AtcS in T. denticola. RNAseq was utilized to compare differential gene expression between T. denticola wild-type (Wt) and knockout strain (KO) which showed downregulated genes involved in motility and chemotaxis. Motility and chemotaxis assays showed reduced motile and chemotactic capabilities in the KO. We have demonstrated the importance of AtcS in the regulation of virulence factors linked to motility, chemotaxis, and glycine-specific metabolism.

overall_design: We performed atcS (TDE0032) genetic manipulation of Treponema denticola strain 35405 using erthromycin B resistance cassette allelic exchange. Electroporation was done with chemically competent Td cells, and subsurface plating was done with NOS-Noble agar medium containing erythromycin.  We then performed gene expression profile analysis using data obtained from RNA-seq of T. denticola wild-type 35405 and atcS knockout strain where cultures were grown up to 4 days.

first: Annie

middle: N

last: Hinson

first: Bin

last: Zhu


title: Characterization of H3K4me3 profile in circulating neutrophils from COPD patients [ChIP-Seq]

city: Verona

first: Barbara

last: Mariotti

address: strada le grazie 8

department: Medicine

institute: University of Verona

summary: The aim of this study is to comprehensively charatcterizethe transcriptional and epigenetic profile of circulating neutrophils from COPD patients and to explore correlations with neutrophils’ functional dysregulation and clinical disease parameters.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K4me3 in circulating neutrophils from COPD patients and sex- and age-matched control donors.

first: Bazzoni

last: Flavia

first: Mariotti

last: Barbara


title: Characterization of the transcriptional profile of circulating neutrophils from COPD patients [RNA-Seq]

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data from circulating neutrophils purified from COPD patients and sex- and age-matched control donors.


title: Profile in circulating neutrophils from COPD patients

overall_design: Refer to individual Series


title: IGF2BP3-mediated m6A modification of RASGRF1 promoting joint injury in rheumatoid arthritis [MeRIP-seq]

city: beijing

first: Cheng

last: Xiao

state: beijing

address: yinghua road

institute: China japan friendship hospital

summary: With the deepening of epigenetic research, more and more studies have shown that N6- methyladenosine (m6A) is closely related to the occurrence and development of rheumatoid arthritis (RA), but the specific mechanism still needs to be further elucidated. In the study, we collected synovial tissues from normal controls and patients with OA or RA. The levels of m6A and inflammation were analyzed by immunofluorescence and western blot. The role of IGF2BP3 in cell proliferation and inflammatory activation was explored using transfection and RNA immunoprecipitation assays. IGF2BP3-/- mice were established, which were used to construct a mouse model of arthritis by transferring serum from adult arthritis K/BxN mice. Histological analysis and micro-CT were performed to determine joint damage. m6A level was markedly increased in RA patients and mouse models, and the expression of IGF2BP3 was upregulated in RA and related to inflammatory markers. IGF2BP3 played an important part in RA-fibroblast-like synoviocytes (FLS) by promoting cell proliferation, migration, invasion, inflammatory cytokine release, and inhibiting autophagy. In addition, IGF2BP3 inhibited autophagy to reduce the production of ROS, thereby decreasing inflammatory activation in macrophages. More importantly, RASGRF1-mediated mTORC1 activation played a crucial role in the ability of IGF2BP3 to promote cell proliferation and inflammatory activation. Based on the arthritis model of IGF2BP3-/- mice, IGF2BP3 knockdown Inhibited RA-FLS proliferation and inflammatory infiltration, and further improved RA joint injury. Our study revealed the important role of IGF2BP3 in RA progression. The targeted inhibition of IGF2BP3 reduced cell proliferation and inflammatory activation and limited RA development in a mouse model of arthritis, providing a potential strategy for RA therapy.

overall_design: MeRIP-seq of synovial tissue in OA or RA patients

first: Qishun

last: Geng


title: Dominant RDH12-retinitis pigmentosa impairs photoreceptor development and cone function in retinal organoids

city: LONDON

first: Mariya

last: Moosajee

address: 1 Midland Rd

institute: The Francis Crick Institute

summary: Retinal dehydrogenase 12 (RDH12) is a photoreceptor NADPH-dependent retinal reductase enzyme, which converts all-trans-retinal to all-trans-retinol. In rare cases, heterozygous variants in RDH12 are associated with a mild, late-onset autosomal dominant (AD) retinitis pigmentosa (RP). There are no dominant RDH12 animal models, hence, we generated retinal organoids from human induced pluripotent stem cells (hiPSC) derived from dermal fibroblasts from a RDH12-AD patient with the heterozygous pathogenic variant c.759del p.(Phe254Leufs*24) and an unrelated unaffected individual (WT). Retinal organoids were characterised at different stages of differentiation; at 18-weeks there were no differences in rod and cone photoreceptors with correct localisation of RDH12 in the photoreceptor inner segments in both WT and RDH12-AD. Transmission electron microscopy on week 37 retinal organoids showed a normal outer limiting membrane and mitochondria, but photoreceptors were 1.8 times less abundant and shorter in RDH12-AD mutant compared to WT. Transcriptomic analyses on week 44 retinal organoids revealed visual cone function, retinol biosynthesis and the vitamin A pathway are highly affected in RDH12-AD retinal organoids. Our study is the first to describe a human RDH12 retinal organoid model, and we found subtle differences between the WT and mutant at later stages of photoreceptor differentiation. This is in keeping with the milder disease course seen in humans, but it provides insights into the aetiology and possible targets for future therapeutic development.

overall_design: Inherited eye diseases is a clinically and genetically heterogenous group of stationary and progressive diseases, with limited treatment options. To understand these pathologies, we developed retinal organoids derived from human induced pluripotent stem cells, obtained from skin biopsies of patients affected with inherited eye diseases. We would like to identify transcriptomic signatures for any intracellular and molecular pathophysiology associated with autosomal dominant [AD] retinitis pigmentosa).

first: Cécile

last: Méjécase

first: Pablo

last: Soro-Barrio


title: IGF2BP3-mediated m6A modification of RASGRF1 promoting joint injury in rheumatoid arthritis [RIP-seq]

overall_design: RIP-seq of synovial tissue in OA or RA patients


title: Methyl-seq analysis for endometrium and serous classification of endometrial cancer

city: Asan

first: Jeong-An

last: Gim

address: 22 Suncheonhyang-ro

country: South Korea

institute: Soonchunhyang University

type: Methylation profiling by high throughput sequencing

summary: In order to classify the endometrium and serous of endometrial cancer, we try to find genes expressed differently between the two groups.

overall_design: Select CpG sites with statistically significant differences in expression through t-test between 1 samples classified as endometrium of endometrial cancer and 9 samples classified as serous.

first: Jin

middle: H

last: Hong


title: RNA-seq analysis for endometrium and serous classification of endometrial cancer

overall_design: Select genes with statistically significant differences in expression through t-test between 7 samples classified as endometrium of endometrial cancer and 9 samples classified as serous.


title: Genetic variation modulates aberrant DNA hypomethylation in naïve pluripotent stem cells

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

summary: Naïve pluripotent stem cells (nPSC) frequently undergo pathological and not readily reversible loss of DNA methylation marks at imprinted gene loci. This abnormality poses a hurdle for the use of pluripotent cell lines in biomedical applications and underscores the need to identify the causes underlying imprint instability in these cells. Here, we show that nPSCs from inbred mouse strains exhibit pronounced strain-specific susceptibility to locus-specific deregulation of imprinting marks during reprogramming to pluripotency and upon culture with MAP kinase inhibitors, the most common approach to maintain naïve pluripotency. Analysis of genetically highly diverse nPSCs from the Diversity Outbred (DO) stock confirms that genetic variation is a major determinant of epigenome stability in pluripotent cells. We leverage the variable DNA hypomethylation in DO lines to identify several trans-acting quantitative trait loci (QTLs) that determine epigenome stability at either specific target loci or genome-wide. Candidate factors encoded by two multi-target QTLs on chromosomes 4 and 17 suggest specific transcriptional regulators that contribute to methylation maintenance in nPSCs. We propose that genetic variants represent candidate biomarkers to identify pluripotent cell lines with desirable properties and might serve as entry points for the targeting engineering of nPSCs with stable epigenomes.

overall_design: We performed EM-seq + targeted enrichment to measure DNA methylation at a panel of ~400 genomic regions in naïve pluripotent stem cells. Our goal was to evaluate the variability in DNA methylation levels present among 80 naïve pluripotent stem cell lines derived from Diversity Outbred mouse stock

middle: A


title: Plasma fatty acids depletion: a metabolic signature related to colon cancer

city: Palma

first: Ramon

middle: Maria

last: Rodriguez

state: Balearic Islands

address: Edificio S, Hospital Universitario Son Espases, Carretera de Valldemossa, 79

department: Oncology and hematology

country: Spain

institute: Institut d'Investigació Sanitària Illes Balears

summary:
Understanding the complex interplay between tumor biology and host metabolism presents a formidable challenge with important clinical implications. At the local level, metabolic alterations of tumor cells and tumor microenvironment is a well-recognized process and constitute one of the major hallmarks of cancer cells. Consequently, research has largely isolated tumor biology from systemic metabolic dynamics, overlooking their potential interrelation. Nonetheless, cancer pathology is also very clearly associated with broad systemic metabolic disturbances, as exemplified by the frequent development of cachexia, which reaches up to 40% of colon cancer (CC) patients. Other metabolic alterations observed associated with cancer include insulin resistance, hypercalcemia, and amino acid metabolism, which underline the extensive systemic impact of cancer on the metabolic networks.   In addition to these alterations, another interesting yet less studied phenomenon in cancer pathology is the observation that cancer patients present alterations of their typical fatty acid profiles in circulation. Evidence of this phenomenon is limited and scattered across the literature, although some studies have identified this alteration in patients with colorectal and liver cancer. Nonetheless, discerning whether these lipid profile shifts signify an intrinsic metabolic alteration or are secondary to factors such as malnutrition, adipose tissue dynamics, or clinical parameters like tumor staging and location has yet to be determined. It is evident that addressing this issue requires a more comprehensive analysis of the possible factors involved.
Our study adopted an integrative methodology to study this process in CC, combining advanced body composition analysis, nutritional assessments, extensive clinical and transcriptomic data of the tumor, and precise profiling of esterified fatty acids in plasma. This multifaceted strategy has enabled us to confirm that the alteration of FA levels is a frequent phenomenon in patients with CC.

overall_design: A total of 107 frozen surgical colon specimens were used for transcriptomic analysis with  Clariom™ S Pico Assays.

first: Alice

last: Chaplin

first: Ramón

last: Rodríguez

first: Maria

last: Barceló-Nicolau

first: Marc

last: Gassió

last: Ramis

first: Elena

last: Usamentiaga

first: Dora

last: Romaguera

first: Gwendolyn

last: Barceló-Coblijn


title: Effect of genetic modification of extracellular matrix-related genes on B16F1 melanoma progression

city: Granada

first: Juan Carlos

last: Rodriguez-Manzaneque

state: Granada

address: Avda de la Ilustración 114

institute: GENYO. Centre for Genomics and Oncological Research

summary: Recent research highlighted the contribution of extracellular matrix, and particularly of ADAMTS proteases, in immune regulation. Now, our work with melanoma and mammary tumor models revealed that tumor blockade induced by the lack of Adamts1 led to an increased vascular deposition of its substrate, the basement membrane glycoprotein NIDOGEN-1 (NID1). Significantly, the overexpression of NID1 in the melanoma syngeneic model also blocked tumor progression, disclosing an overlapping phenotype with the absence of Adamts1. These tumors showed important alterations in their immune infiltrates, emphasizing an enhanced presence of antitumorigenic macrophages and a global inflammatory landscape. We corroborated in vitro that full length NID1, but not its fragments, promoted an M1-like macrophage polarization, mainly mediated by the αvβ3 integrin. Significantly, the projection of RNA-seq from our tumor models to two large human melanoma datasets allowed us to discover a new gene signature associated with good prognosis and the abundance of M1-like macrophages. These results support NID1 as a novel tumor suppressor with immunomodulatory properties, and unveil the existence of key oncological drivers in the extracellular scenario.

overall_design:
To investigate the effect of glycoprotein Nidogen-1 (NID1) on B16F1 melanoma progression from a transcriptomic perspective, we developed clones of B16F1 cell line overexpressing NID1 (referred as B16Nid1). We then conducted in vivo experiments by subcutaneously injecting B16Nid1 and parental B16F1 cells in C57BL/6 mice. At day 21, mice were sacrificed, and tumor were collected for bulk RNA isolation and RNA-sequencing. In parallel, CD11b+ cells were isolated from tumors, that were also processed to approach RNA-seq analysis.
To evaluate the impact of ADAMTS1 deficiency on B16F1 melanoma progression, we also injected B16F1 cells subcutaneously into ADAMTS1-knockout C57BL/6 mice. These tumors (identified as B16-Ats1KO) was also monitored until day 21, at which point mice were sacrified and RNA was isolated for sequencing.
RNA-seq was conducted on whole tumors (n=3 per group) from B16F1 (control), B16Nid1 and B16-Ats1KO tumors. Additionally, CD11b+ cells were isolated from three tumors of B16F1 and B16Nid1 groups for further transcriptomic analysis.

first: R

last: Caracuel-Peramos

first: F

middle: J

last: Rodríguez-Baena

first: JA

last: Villatoro-García

first: P

last: Carmona-Sáez

first: J

middle: C

last: Rodríguez-Manzaneque


title: Distinct Transcriptome Signatures Associated with Mortality and Prolonged Recovery Following Burn Injury

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: A dysregulated immune response after severe burn injury is associated with detrimental short and long-term clinical outcomes. Key changes to gene expression within the first 24 h after burn injury have been identified, but longitudinal data is lacking. Therefore, this study aims to characterize gene expression during the first 3 weeks after burn injury and identify specific genes and pathways associated with distinct clinical outcomes. Patients presenting within 4 h of injury had blood RNA isolated for microarray gene expression at admission and set timepoints to 21 days. Inter- and intra-group comparisons were performed between 4 groups (G1 died within 7 days; G2 died after 7 days; G3 discharged after 7 days; and G4 discharged within 7 days). A total of 17 289 transcripts were quantified from 116 patients. At admission, there were 110, 80, and 31 differentially expressed genes in G1, G2, and G3, respectively, compared to G4, and were largely nonoverlapping. Longitudinal intra-group analyses also showed distinct group- and time-dependent patterns. Upregulation of genes and pathways related to the innate immune response and unfolded protein response predominated during early time points, while persistent upregulation of coagulation pathways and downregulation of immune-related pathways were identified days to weeks following injury. Overall, burn injury induces widespread transcriptomic responses, with larger and more sustained changes observed in patients with worse clinical outcomes. These gene expression signatures reveal underlying molecular mechanisms that occur immediately following injury and may have prognostic and diagnostic utility in the care of burn-injured patients.

overall_design: Burn patients presenting to a regional center between 2012-2017 were prospectively enrolled. Blood was collected on admission and at predetermined timepoints. RNA was isolated and transcript levels were measure with a gene expression microarray.

first: Burook

last: Misganaw

first: Desiree

last: Pinto

first: Tuan

middle: D

last: Le

first: Anthony

last: Pusateri

first: Bonnie

last: Carney

first: Lauren

middle: T

last: Moffatt

first: Jeffrey

last: Shupp

first: Rasha

last: Hammamieh


title: Establishment of interpretable cytotoxicity prediction models using machine learning analysis of transcriptome features

city: Beijing

first: Ying

last: Guo

address: 1 Xian Nong Tan Street

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Cytotoxicity, usually represented by cell viability, is a crucial parameter for evaluating drug safety in vitro. Accurate prediction of cell viability/cytotoxicity could accelerate drug development in the early stage. In this study, by using machine learning algorithms on cellular transcriptome and cell viability data, highly accurate prediction models of 50% and 80% cell viability were developed with AUROCs of 0.90 and 0.84, respectively, which also showed good performance on diverse cell lines. With respect to the characterization of Feature Genes employed, the models can be interpreted, and the mechanisms of bioactive compounds with narrow therapeutic indices can also be analyzed. In summary, the models established in this study have the capacity to predict cytotoxicity highly accurately across cell lines and can be used for high safety substances screening efficiently. Moreover, the Cytotoxicity Signature genes from interpretability analysis is valuable for studying the mechanisms of action, especially for substances with narrow therapeutic indices.

overall_design: A549, HepG2 and HT-29 cells were seeded in 6-well plates and incubated with the test compounds or 0.1% v/v DMSO for 48 h. HT-29 cells (colon) were treated with cyclosporine A (CAS No: 59865-13-3 ) at a final concentration of 10 µM; A549 and HepG2 cells were treated with triptolide (CAS No: 38748-32-2) at final concentrations of 30 nM and 10 nM, respectively.

first: You

last: Wu

first: Ke

last: Tang


title: Transcriptomic analysis of stage I endometrioid endometrial carcinoma (EEC)

city: Rio de Janeiro

first: Pedro

last: Nicolau Neto

state: RJ

address: 37 Andre Cavalcanti Street

department: PCM

country: Brazil

institute: INCA

summary: Transcriptome analysis aiming to identify differentially expressed genes from stage I EEC, comparing relapsed with non-relapsed tumors

overall_design: Transcriptomic analysis using Affymetrix microarray technology aiming to describe the expression profile of stage I endometrioid endometrial carcinomas

first: Claudia

last: Bessa

first: Tatiana

last: Simao

first: Luis

middle: F

last: Ribeiro-Pinto


title: METTL3-dependent m6A RNA methylation regulates activation of the NLRP3 inflammasome [RIP-Seq]

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

summary:
Inflammasomes are signalling complexes that are activated in response to infection, cellular stress and other cues to initiate an inflammatory response. The NLRP3 (NOD-, LRR- and pyrin domain-containing protein 3) inflammasome is a cytosolic sensor that mediates caspase-1-dependent maturation and release of the pro-inflammatory cytokines IL-1β and IL-18, and Gasdermin D-induced pyroptotic cell death. While a broad range of pathogens can activate the NLRP3 inflammasome, in most cases, it appears to be dispensable to fight infection.
In recent work, m6A has emerged as a key regulator of the immune response. However, the specific role played by METTL3 and RNA m6A methylation during inflammasome activation is still unknown. Using genetic manipulation and pharmacological inhibition, we demonstrate that METTL3 is essential for activation of the NLRP3 inflammasome in vitro and in vivo. We show that pharmacological inhibition of METTL3 attenuates NLRP3 hyperactivation in PBMCs isolated from patients affected by Cryopyrin Associated Periodic Syndrome (CAPS).

overall_design: Comparative m6A methylation analysis of  m6A-IP-Seq in THP-1-derived macrophages treated with LPS , Nigericin, Mettl3-deletion and untreated cells as control.

first: Natalia

last: Pinello

first: Quintin

last: Lee

first: Dan

last: Ye

first: Justin

last: Wong


title: METTL3-dependent m6A RNA methylation regulates activation of the NLRP3 inflammasome

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


title: Gene regulatory programs of NK cells show that NCAM1 (CD56) and KIRs are controlled by genetically polymorphic distal regulatory elements [CITE-seq]

status: Public on May 27 2025

city: Columbus

first: Patrick

last: Collins

state: Ohio

address: 460 West 12th Avenue, Biomedical Research Tower 770

institute: The Ohio State University

summary: Owing to their immunoprotective properties, natural killer (NK) cells are critical for the innate response to pathogens, as well as a new wave of cancer immunotherapy that harnesses natural cytotoxicity. We sought to understand the genetic and epigenetic drivers behind human specific NK cell receptors, so that we can better understand the underlying cellular function. Here, we present a transcriptomic, proteomic (CITE-seq), and chromatin (single nuclei ATAC-seq and Hi-C) analysis of human peripheral NK cell subsets, uncovering key regulatory programs governing NK cell differentiation. Through integrative multi-omics, we demonstrate that CD56bright versus CD56dim NK cell subsets have differential distal regulatory element (DRE) landscapes, with fewer accessible DREs in the CD56dim NK cells. We combine epigenetic, chromatin looping, and human genetic data to show mechanisms governing the NCAM1 (encoding CD56) and KIR loci. For example, we identify NCAM1 DREs that bind STAT in most NK cells, while identifying a genetic cohort that has motifs for binding repressive BLIMP1 at the DRE and resulting in less CD56 expression.  Together, our findings reveal novel epigenetic and transcriptomic systems for regulation of NK cells cytotoxicity and diversity, deepening our understanding of their function and how transcription factor networks govern CD56bright versus CD56dim phenotypes.

overall_design:
Natural killer (NK) cells were isolated from peripheral blood mononuclear cells (PBMCs) using the RosetteSep™ Human NK Cell Enrichment Cocktail (STEMCELL Technologies). ).  For tonsil NK isolation, Human innate lymphoid cells (ILCs) were enriched from fresh tonsil tissue.

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Submitter states that missing raw files are due to file loss.
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first: Aditi

last: Varkey

first: Matthew

last: Estrada

first: Caprice

last: Eisele

first: Aharon

last: Freud

first: Bethany

last: Mundy-Bosse


title: Tributyltin chloride alters the structural, genomic, and epigenomic integrity of postejaculatory mammalian sperm

city: Gainesville

first: Muhammad

middle: Sohail

last: Siddique

state: Florida

address: 1911 SW 40th Terrace Apt E

institute: Department of Animal Sciences

summary:
A global top priority for ameliorating male factor infertility includes identification of environmental factors and mechanisms that impact sperm function. Detection of endocrine disruptors (EDs) in seminal plasma and within the female reproductive tract has created an urgent need to understand how environmental stressors alter postejaculatory sperm function. Tributyltin chloride (TBT) is a model organotin, ED and epigenetic modifier that causes reproductive disorders in testicular sperm; however, consequences of TBT exposure on postejaculatory sperm prior to fertilization remain unknown. Our previous data indicate that TBT-exposed sperm affects initial cleavage and lowers embryo development potential. However, identifying reasons for idiopathic male factor subfertility is challenged by lack of routine clinical assessment for subtle phenotypes that compromise sperm function and therefore remain undetected with current diagnostic tools.
Results
The present study was aimed at identifying structural, genomic, and epigenomic consequences of TBT exposure to postejaculatory sperm in a temporal manner reflective of sperm transport prior to fertilization within the female reproductive tract. Bovine sperm were exposed to TBT (0 ,1, 10, 100nM) for 24 h under non-capacitating conditions at 25°C followed by quantification of sperm kinematics at 37°C, DNA integrity, and methylation status. No differences in sperm kinematics or capacitation status were detected after 24 h. However, acrosome integrity was compromised at both 0 and 24 h (P ≤ 0.05). Sperm DNA integrity was also negatively affected after 24 h. The methylation levels of select loci were quantified by PacBio single-molecule real-time (SMRT) long-read high-fidelity sequencing. Whole genome methyl-seq revealed 750 differentially methylated regions (DMRs) associated with exposure to TBT for 24 h. IPA and GO analyses identified embryo development, cell signaling, and transcriptional regulation as the most relevant bio-functions of TBT altered DMRs.
Conclusions
Postejaculatory mammalian sperm exposure to TBT negatively affects parameters important for sperm function while altering DNA integrity and the methylation profile of promotor regions. Consequences of sperm exposure to TBT include cellular and molecular mechanisms that are important for sperm function but remain undetected by routine clinical analyses. These findings provided new insight towards environmental impacts on postejaculatory sperm function.

overall_design: Frozen-thawed sperm from two different commercial bulls were used for all experiments except where stated otherwise. Four exposure level of TBT (100nm, 10nm, 1nM and 0nM) were used in all experimnets unless stated otherwise.In each replicate,sperm were isolated from four frozen straws on a discontinuous Percoll gradient (90:45%).DNA was isolated from TBT exposed sperm following TBT exposure at 24 h followed by enzymatic Methyl seq Conversion. The enzymatic methyl seq converted DNA from sperm were PCR amplified for three hypermethylated loci (PTK2B, HDAC11, PAK1) and three imprinted loci(SNRPN, H19, KCNQ1) and sequenced for loci specific PacBio single molecule real time long-read high-fidelity sequencing (SMRT).In SMRT sequencing, only two treatments (VC and TBT 10nM) were used (n = 2 bulls, 4 pooled independent reps/ bull/trt). For whole genome methyl-seq analysis, three treatments were used (VC, TBT 100nM and TBT 10nM) n = 1 bull, 4 pooled independent reps/bull/trt).Data were analyzed by logistic regression using a generalized linear mixed effect model. Treatment and time were considered fixed effects while bull and replicate were assigned as random effects.

middle: S

first: Santosh

last: Anand

first: Marie-Pierre

last: Gauthier

first: Brant

middle: O

last: Jason

first: Michael

middle: P

last: Kladde

first: Ramji

middle: K

last: Bhandari

first: Bradford

middle: W

last: Daigneault


title: RNA sequencing of (1) isolated retinal endothelial cells from wildtype and Zmiz1-KO endothelial cells and (2) control and Zmiz1 shRNA treated MS1 cells

city: new orleans

first: Rajan

last: K C

state: LA

address: 6602 Freret St

department: Cell and Molecular Biology

institute: Tulane University

summary:
Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 association with vascular system, its role in physiological and pathological angiogenesis is significantly unknown. Here, we use (1) MS1 cell line treated with control shRNA and Zmiz1 shRNA and (2) murine model to knockout Zmiz1 in endothelial cells using Cdh5CreERT2 and isolate retinal endothelial cells (iRECs) then performed RNA sequencing to profile transcriptional changes upon Zmiz1 deletion.
Retinal ECs were isolated from P7 pups as previously described (Patel et al., 2022. JCI Insight). Briefly, isolation of ECs from the retinas was performed using the Miltenyi Neural tissue Dissociation Kit (P) (Miltenyi, 130-092-628). For each sample, 8-10 retinas were pooled and digested to obtain a single cell suspension. CD31+ cells were separated from the cell mixture via magnetic activated cell sorting. MS1 cells were transfected with 20μM of either control-shRNA or Zmiz1-shRNA using Lipofectamine3000 (Thermofisher, L3000015).  Next, RNA was isolated from the cells and used for downstream RNA-sequencing.  RNA concentration and RNA integrity number were determined. RNA library was prepared, quantified, and verified using TruSeq RNA Library Prep Kit v2, Qubit dsDNA High Sensitivity Assay kit and Bioanalyzer DNA1000 assay kit respectively. Verified samples were sequenced on a Nextseq 500/550 platform. RNA-seq data analysis was performed using illumina BaseSpace Sequence Hub.
Results: For iRECs , we found 2,364 differentially expressed genes of which 834 genes were upregulated while 1530 genes were downregulated. Downregulated genes were enriched in biological processes such as angiogenesis, vascular development, and cell growth. For MS1 cells,  we found 1,711 differentially expressed genes of which 718 genes were upregulated while 993 genes were downregulated. Downregulated genes were enriched in biological processes such as regulation of angiogenesis.
Conclusions: We assessed changes in transcriptional landscape in MS1 and iRECs following Zmiz1 deletion.

overall_design: Transcriptional assessment on Zmiz1 depleted MS1 cells and deleted iRECs by RNA sequencing

first: Nehal

last: Patel

first: K C

last: Rajan

first: Stryder

last: Meadows