title: MicroRNA-mediated changes contributing to susceptibility for benzo[a]pyrene toxicity in a 3D respiratory model for asthma

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary: There is increased emphasis on understanding how non-chemical stressors that contribute to inflammation in the lung may influence adverse health outcomes after chemical exposures.  Prior studies in an in vitro respiratory model of type 2 asthmatic inflammation found cells from the asthmatic phenotype respond uniquely to benzo[a]pyrene (BAP) treatment compared to normal cells across multiple endpoints related to mucus production, goblet cell hyperplasia, mucociliary dysfunction and airway remodeling. To further understand how cellular response to BAP is regulated in a model of inflammation-based disease, this study examines changes in miRNA and mRNA regulation following BAP exposure in primary human bronchial epithelial cells (HBECs) cultured at the air-liquid interface with normal and interlukin-13 (IL-13) induced asthmatic phenotypes.  Primary 3D HBECs differentiated in the presence and absence of 10ng/mL IL-13 were treated on day 25 with 158 uM BAP for 48 hours.  Differentially expressed (q<0.01) miRNA and mRNA were analyzed to predict miRNA target interactions and assess the functional consequences of miRNAs in each phenotype. While BAP-treated HBEC with the IL-13 asthmatic phenotype had a similar number of differentially expressed miRNA (93 up- and 100 down-regulated) compared to BAP-treated normal HBEC (93 up- and 94 down-regulated), IL-13 HBEC treated with BAP were shown to have unique overrepresentation of miRNA targets involved in up-regulation of cell cycle processes and down-regulation of processes related to NOTCH, WNT, and Hedgehog signaling. These data are the first to provide insight into the role of miRNAs as regulators of chemical toxicity in a respiratory model of inflammation-based disease.

overall_design: Fully differentiated bronchial epithelial cells (n=4 replicates) were treated with 40 µg/ml benzo[a]pyrene (BAP) or vehicle control (PBS with 1% DMSO) for 48 hrs.   In addition bronchial epithelial cells differentiated in the presence of 10 ug/mL interluekin-13 were treated with 40 µg/ml benzo[a]pyrene (BAP) or vehicle control (PBS with 1% DMSO) for 48 hrs.  Isolated mRNA were sequenced on DNBseq platform


title: Single cell transcriptome profiling of mouse pancreatic α-lineage cells

status: Public on Dec 01 2025

city: Sagamihara City

first: Naoya

last: Shimizu

state: Kanagawa

address: 1-15-1, Kitasato

country: Japan

institute: Kitasato University Graduate School of Medical Sciences

type: Expression profiling by high throughput sequencing

summary:
As a strategy for regenerative medicine in diabetes, α-to-β reprogramming, which involves differentiating α cells into β cells, is an important option. However, while there are many reports on β cell differentiation, there are insufficient reports on α cell differentiation. There are still many unknowns regarding how α cells mature.
In this study, we used the Gcg-Timer mouse model, which enables high temporal resolution to evaluate the development process of α cells. We sorted newly generated and more differentiated α cells from E17.5 Gcg-Timer and performed single-cell RNA sequencing. As a result, we found six clusters within the endocrine population and revealed transcriptional heterogeneity. In addition, the fluorescent characteristics of Gcg-Timer (newly generated and more differentiated cells) did not match the pseudotime information, which was in contrast to the results of our previous analysis of transcriptional characteristics during β-cell development using Ins1-eGFP;Timer. Furthermore, on the pseudotime axis of Gcg-Timer, Gcg mRNA showed a transient expression pattern, which was different from the expression pattern of Ins1 mRNA in Ins1-eGFP;Timer. These results suggest that (1) α-cell differentiation is probabilistic and (2) glucagon mRNA activation is probabilistic. Thus, evaluating the expression patterns of Gcg mRNA during α-cell development will lead to a deeper understanding of α-cell differentiation in the future.

overall_design: This study characterizes the single-cell transcriptomes of mouse pancreatic α-lineage cells.

first: Miwa

last: Himuro

first: Francis

middle: C

last: Lynn

first: Shugo

last: Sasaki

first: Takeshi

last: Miyatsuka


title: RNA-sequencing reveals growth phase specific differences in global transcriptional thermoregulation in Pseudomonas aeruginosa

city: Atlanta

first: Rachel

middle: Evans

last: Robinson

state: GA

address: 1510 Clifton Road NE

department: Pediatrics

country: USA

institute: Emory University

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

overall_design: Refer to individual Series

middle: E

first: Michael

middle: J

last: Gebhardt

first: Joanna

middle: B

last: Goldberg


title: RNA-seq of PAO1 and ΔlasR grown at 37°C or 25°C at stationary phase

summary: Pseudomonas aeruginosa is a highly versatile bacterium capable of surviving and often thriving in stressful environmental conditions. Here we studied the effect of two environmental conditions, temperature and growth phase, on the P. aeruginosa PAO1 transcriptome. As P. aeruginosa is well-known for its growth-phase dependent phenotypes and gene regulation, our goal was to determine how temperature altered global gene expression at exponential versus stationary phase and to characterize how growth phase affects thermoregulation. To do this, we grew PAO1 in parallel at 25°C and 37°C and sampled the same populations first at exponential phase and then again at stationary phase and assessed gene expression by RNA-sequencing. We also grew PAO1 and an isogenic DlasR mutant at 25°C and 37°C and sampled populations at stationary phase to define LasR-regulated genes at each temperature by RNA-sequencing. This work provides a comprehensive thermoregulon for PAO1 at two distinct growth phases, as well as growth phase transcriptomics at two temperatures, and expands our understanding of quorum sensing regulation under different environmental conditions that P. aeruginosa encounters.

overall_design: PAO1 was grown in parallel at two temperatures, 37°C or 25°C, and cultures were sampled for RNA-seq first at exponential phase and then again at stationary phase.                          PAO1 and an isogenic ΔlasR mutant were also grown at 37°C and 25°C to stationary phase and sampled for RNA-seq.


title: Therapeutic effects of telomerase-derived peptide GV1001 in experimental autoimmune encephalomyelitis: inhibiting neuroinflammation and promoting remyelination

city: Daegu

first: Jong-Heon

last: Kim

address: 680 Gukchaebosang Street, Jung-gu

department: Brain Science & Engineering Institute

country: South Korea

institute: Kyoungpook National University

summary: GV1001, a peptide derived from human telomerase reverse transcriptase, exhibits anti-cancer and anti-inflammatory actions, yet its impact on experimental autoimmune encephalomyelitis (EAE)—an established mouse model of multiple sclerosis—remains unknown. This study assessed the therapeutic potential and mechanism of GV1001 in EAE. Subcutaneous administration of GV1001 reduced clinical scores, inflammatory cytokine transcripts, and spinal cord pathology in EAE mice. Spinal cord RNA-seq showed that GV1001 suppressed immune and neuroinflammatory genes, particularly in microglia. Experiments in cultured mouse and human glia cells identified microglia as the principal cellular target. Mechanistically, GV1001 increased the NF-κB antagonist PRMT1 and boosted microglial insulin-like growth factor-1, promoting oligodendrocyte progenitor cell survival and maturation. Co-culture assays confirmed that GV1001 blunts microglial neurotoxicity and facilitates remyelination during inflammation. Collectively, the data indicate that GV1001 modulates microglial activity to attenuate neuroinflammation and foster spinal cord repair, underscoring its promise as a multitarget therapy for inflammatory demyelinating diseases such as multiple sclerosis.

overall_design: RNA-seq profiling of spinal cords from naïve control, EAE, and EAE treated with GV1001 mice

first: Anup

last: Busal

first: Jiwon

last: Kwon

first: Jun-Yeong

last: Lee

first: Min-Soo

last: Song

first: Won-Ha

first: Long Tai

last: Zheng

first: Sangjae

first: Kyoungho

last: Suk


title: Conditional Knockout of Fshr in Osteocytes Restores Bone Mass and Accelerates Fracture Healing in Ovariectomized Mice

city: taiyuan

first: Zemin

last: Liu

state: shanxi

address: wuyi street number 382

department: Orthopedics

country: China

institute: Second Hospital of Shanxi Medical University

summary: Building on our previous observation that osteocytes express FSH receptors (FSHR), we generated Dmp1-CreERT; Fshrfl/fl mice and subjected them to ovariectomy (OVX), followed by weekly tamoxifen administration to achieve osteocyte-specific Fshr deletion. Osteocyte-specific Fshr knockout mice exhibited increased bone mineralization alongside elevated bone resorption. RNA-seq of femoral cortical bone revealed enhanced coupling of bone formation and resorption, which was associated with PI3K/Akt pathway activation. Digital PCR and ELISA confirmed up-regulation of osteoblast- and osteoclast-related genes. In vitro, Fshr deletion abolished FSH-mediated inhibition of the PI3K/Akt pathway and restored osteogenic mineralization of bone-marrow mesenchymal stem cells (BMSCs). In a closed femoral-fracture model, osteocyte-specific Fshr knockout accelerated callus maturation and fracture healing, and three-point bending tests demonstrated improved biomechanical properties. These findings identify osteocytes as direct FSH-responsive cells within bone. Osteocyte-specific Fshr deletion enhances PI3K/Akt signaling, enhancing formation–resorption coupling, and accelerates fracture repair in ovariectomized mice. Our study provides mechanistic insights and potential therapeutic strategies for postmenopausal osteoporosis and fracture management.

overall_design: In the study, femur samples were collected from three mice in the tamoxifen - induced FGF21 knockout group (A1-A3) and three mice in the corn oil - injected control group (B1-B3) for subsequent RNA extraction and high - throughput sequencing procedures.

first: Hongjie

last: Zhou

first: Liben

last: Cheng

first: Xiaoli

last: Li

first: Dong

last: Wang

first: Juan

first: Min

first: Yan

first: Yonghong

last: Zhang


title: Single-nucleus RNA sequencing reveals cellular heterogeneity in the lateral septal area of mice with different immune backgrounds

city: Shanghai

first: xia

middle: wen

last: Gao

state: Shanghai

address: No. 500 Zhen Nan Road

department: School of Medicine

institute: Tongji University

summary: We employed single-nucleus RNA sequencing (snRNA-seq) using the 10x Genomics platform to investigate the cellular heterogeneity and gene expression changes in the lateral septum (LS) region of mice with different immune backgrounds. The LS serves as a central hub for regulating emotional responses in the brain and may be influenced by the host’s immune status. Notably, C57J, BALB/c, and nude mice exhibit distinct behavioral differences in open field and fear memory tests. To further explore the underlying molecular mechanisms, we performed snRNA-seq analysis on the LS region of these three mouse strains, aiming to elucidate how immune background shapes the cellular architecture and transcriptional landscape of the LS.

overall_design: The lateral septum (LS) regions were microdissected from C57J, BALB/c, and nude mice under a stereomicroscope and immediately snap-frozen at −80 °C for preservation. Prior to sequencing, the frozen tissues were thawed and processed for single-nucleus isolation, followed by single-nucleus RNA sequencing (snRNA-seq) analysis.

first: Yi Eve

last: Sun

first: Wei

last: Chen

first: Wenxia

first: Yian

first: Wenmin

last: Zhu


title: RNA-seq of PAO1 at two temperatures and at two growth phases

first: Rachel

last: Robinson

first: Michael

last: Gebhardt

first: Joanna

last: Goldberg


title: Role of CDCP1 and Cardiac Fibrosis in a Mouse Model of Dilated Cardiomyopathy (DCM)

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: Cardiac fibrosis is a common pathological feature of various cardiac diseases that contributes significantly to heart failure progression and poor clinical outcomes. Recent genetic studies have shown that lower expression of CUB domain-containing protein 1 (CDCP1) is linked to myocardial recovery, but its direct role in cardiac pathophysiology remains unkown. In this study, we investigated the functional contribution of CDCP1 to pressure overload-induced cardiac remodeling and fibrosis. CDCP1 deletion attenuated Ang II/PE-induced cardiac dysfunction as demonstrated by reduced left ventricular mass index and improved cardiac function compared to wild-type controls. Histological analysis revealed significantly decreased cardiac fibrosis in CDCP1-KO mice. Transcriptomic profiling revealed that CDCP1 KO attenuates cardiac fibrosis through downregulation of matrix metalloproteases, collagen biosynthesis and limiting the pathological remodeling extracellular matrix. Spatial transcriptomics further revealed region-specific alterations in fibrotic and inflammatory signatures among the subtypes of cardiomyocytes and fibroblasts, suggesting localized CDCP1-dependent effects on cardiac remodeling. Our findings establish CDCP1 as a critical regulator of pressure overload-induced cardiac fibrosis and dysfunction. Our work provides direct evidence supporting CDCP1 inhibition as a potential therapeutic strategy for cardiac fibrosis.

overall_design: CDCP1-knockout (KO) mice and wild-type littermates underwent chronic angiotensin II/phenylephrine (Ang II/PE) infusion via osmotic minipumps. Cardiac structure and function were assessed by serial echocardiography, and cardiac fibrosis was assessed by histology. We used bulk RNA sequencing and spatial transcriptomics to study the underlying molecular mechanisms.

first: Rachad

last: Ghazal

first: Akshatha

middle: N

last: Sriniva

first: Li

first: Irene

last: Marín-Goñ

first: August

last: John

first: Hridyansh

last: Vyas

first: Carolyn

last: Roos

first: Runqing

last: Huang

first: Tamas

last: Ordog

first: Chen

first: Richard

last: Weinshilboum

first: Duan

first: Laura

last: Lambert

first: Jordan

last: Miller

first: Daniel

last: Tschumperlin

first: Naveen

middle: L

last: Pereira


title: Histone lactylation during host–pathogen interaction: An intimate and persistent affair between Pseudomonas aeruginosa quorum-sensing signaling and host lactate [CUT&RUN]

city: Boston

first: Laurence

middle: G

last: Rahme

state: MA

address: 50 Blossom Street

department: Surgery

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Bacteria can stimulate host lactate production, aiding their colonization and virulence. However, the role of pathogen-driven host lactate remains underexplored. We show that Pseudomonas aeruginosa (PA)-secreted quorum-sensing (QS) signaling molecule 2’-aminoacetophenone (2-AA) elevates and sustains lactate in PA-infected immune-cells and animal tissues. In support, 2-AA increases the protein abundance of the lactate transporter, MCT4, and lactyl-coenzyme A synthetase (guanosine triphosphate (GTP)-specific SCS (GTPSCS)), and GTPSCS’s interaction with the transcriptional coactivators CREB-binding protein (CBP) and p300. Lactate augmentation drives histone H3 lysine 18 lactylation (H3K18la) enrichment at the regulatory regions of key immune and metabolic genes. H3K18la and consequent transcriptional changes promote PA survival in macrophages. Inhibition of lactate or 2-AA synthesis impedes lactate augmentation and H3K18la and reduces PA survival in macrophages. The uncovered QS-driven H3K18la represents a seminal interplay during host-pathogen interaction. Targeting this QS-epigenetic axis may offer a viable therapeutic approach for chronic PA infection.

overall_design: CUT&RUN of RAW 267.4 cells treated with 200 µM/sample of Pseudomonas aeruginosa UCBPP-PA14 secreted quorum sensing molecule 2'-AA (2-aminoacetophenone).

first: Arijit

last: Chakraborty

first: Shifu

last: Aggarwal

first: Filip

last: Kovacic

first: Arunava

last: Bandyopadhyay

first: Sujin

last: Cha

first: Lai Ping

last: Wong

first: Vijay

last: Singh

first: Asel

last: Kabashi

first: Rashmi

last: Richa

first: Myung Whan

last: Oh

first: Alexandra

last: Dimitrou

first: Ruslan

last: Sadryev

first: Amy

last: Tsurumi


title: Age-associated G-quadruplex accumulation and DDX5 loss shape chromatin landscapes in human astrocytes [CUT&Tag]

city: San Diego

first: Christopher

last: Hartl

address: Pacific Heights Blvd

department: Cell Biology

institute: Epigenome Technologies

summary: Aging disrupts genome organization and transcriptional fidelity, but the role of non-canonical DNA structures in the aging process remains unclear. G-quadruplexes (G4s), stable guanine-rich DNA and RNA structures are established regulators of gene expression and genome integrity, yet their contribution to physiological aging is unknown. Using primary human astrocytes derived from individuals spanning early to late adulthood (22–73 years) and fluorescent imaging, we observed increased G4 accumulation and reduced nuclear expression of the G4-resolving helicase DDX5 in older cells. To investigate how these changes relate to genome architecture, we performed ATAC-seq and G4 CUT&Tag across all astrocyte cultures. Older cells exhibited global chromatin compaction and focal G4 enrichment, with gains occurring in both accessible and closed chromatin regions, indicating locus-specific and context-dependent regulation. To determine whether DDX5 modulates these features, we overexpressed DDX5 in young astrocytes and identified transcriptional targets involved in chromatin organization and genome maintenance. Acute DDX5 knockout caused focal G4 accumulation without widespread chromatin changes, indicating that DDX5 maintains and modulates G4 dynamics at defined genomic regions. Together, these findings reveal G4s as dynamic, age-sensitive features of the genome with potential roles in epigenetic regulation and establish DDX5 as a modulator of G4 dynamics and genome integrity during human brain aging.

overall_design: RNA-seq, ATAC-seq, G4 Quadruplex CUT&Tag in resection-derived human astrocytes across the human age span, and with DDX5 over-expression and knockout

middle: M

last: Kumar

first: Rocio

middle: D

last: Escarcega

first: Ellery

last: Wheeler

first: Nitin

last: Tandon

first: David

last: Monchaud

first: Andrey

middle: S

last: Tvetkov


title: Histone lactylation during host–pathogen interaction: An intimate and persistent affair between Pseudomonas aeruginosa quorum-sensing signaling and host lactate

first: Laurence

last: Rahme

overall_design: RNA sequencing of RAW 267.4 cells infected with Pseudomonas aeurginosa UCBPP-PA14, and the quorum sensing regulator isogenic deletion mutant strain  mvfR and mvfR mutant supplemented with 200 µM of 2'-AA (2-aminoacetophenone).Uninfected cells served as controls.

first: Arijit

last: Chakraborty

first: Shifu

last: Aggarwal

first: Filip

last: Kovacic

last: Bandyopadhyay


title: Epidermal cell fusion promotes the transition from an embryonic to a larval transcriptome in C. elegans

city: Laramie

first: Owen

last: Funk

address: 1000 E. University Ave

institute: University of Wyoming

summary: Cell fusion is a fundamental process in the development of multicellular organisms, but its precise influence on gene regulation during critical developmental stages remains largely unknown. The Caenorhabditis elegans epidermis, a powerful model for studying cell fusion, forms 8–10 syncytial cells. The largest of these, hyp7, integrates 139 individual nuclei via cell–cell fusion mediated by the fusogenic protein EFF-1. To explore the effects of cell fusion on developmental progression and associated gene expression changes, we conducted transcriptomic analyses of eff-1 knockout and fusion-deficient C. elegans mutants. Our RNAseq findings showed widespread transcriptomic changes including enrichment for epidermal genes and key molecular pathways involved in epidermal function during larval development. Subsequent single-molecule fluorescence in situ hybridization validated the altered expression of mRNA transcripts, confirming quantifiable changes in gene expression in the absence of embryonic epidermal fusion. These results underscore the significance of cell–cell fusion in shaping transcriptional programs during development and raise questions regarding the precise identities and specialized functions of different subclasses of nuclei within developing syncytial cells and tissues.

overall_design: RNAseq of L1 wildtype and mutant larva

first: Funk

last: Owen


title: Unique sequence features define epigenetic longevity of inflammatory memory [scATAC-seq]

city: New York

first: Luis

middle: F

last: Soto-Ugaldi

state: NY

institute: The Rockefeller University

summary: Many tissues harbor epigenetic memories of inflammation, which heighten sensitivity to diverse future assaults. Whether and how these adaptations are sustained through time and cell division remain poorly understood. Here, we show that epidermal stem cells store functional epigenetic records of a psoriatic skin flare that last a lifetime. Applying deep learning to interrogate these chromatin dynamics, we unearth CpG dinucleotide density as a major driver of memory persistence. Molecularly, while unnecessary for stress-induced chromatin opening, CpG dinucleotides thereafter become essential, reinforcing accessibility across cellular generations through a signature integrating DNA demethylation, methylation-sensitive transcription factors, sequence-intrinsic nucleosome disaffinity and nucleosome-destabilizing histone variant H2A.Z. Thus, inherent CpG enrichment within DNA sequence confers enduring adaptability to environmentally sensitive cis-regulatory elements, with profound consequences to long-term tissue fitness.

overall_design: D30: EpdSCs (CD49f+, Sca-1+, CD29+, CD34-, CD45-, CD117-, CD140a-, CD31-) and immune cells (CD45+, Ly6G-) were FACS isolated and mixed at a 1:1 ratio to perform 10x Chromium Next GEM single cell multiome ATAC + Gene expression after following 10x protocol for nuclei extraction. Following nuclei extraction downstream processing was performed by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center. Downstream processing was only performed on scATAC-seq data. Y1: EpdSCs (CD49f+, Sca-1+, CD29+, CD34-, CD45-, CD117-, CD140a-, CD31-) were FACS isolated and nuclei extracted using 10x protocol for nuclei extraction. Following nuclei extraction downstream processing was performed by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center where single cell ATAC-seq was performed.

last: Cowley

first: Sairaj

last: Sajjath

first: Elaine

last: Fuchs


title: P-bodies control circadian rhythms by regulating the translational repression and decay of period mRNAs.

city: Ann Arbor

first: Swathi

last: Yadlapalli

address: 109 Zina Pitcher Pl

institute: University of Michigan

summary: Circadian clocks are cell-autonomous timekeepers that regulate 24-hour oscillations in gene expression through conserved transcription-translation feedback loops. Although the core components of these clocks are well-characterized, other regulators remain underexplored. To address this, we used BioID-based proximity labeling to identify proteins near the Period repressor in Drosophila melanogaster clock neurons. Surprisingly, among approximately 700 high-confidence hits, genes linked to processing bodies (p-bodies), such as pacman (pcm) and maternal expression at 31B (me31b), showed significant enrichment. Fluorescence microscopy revealed that p-body condensates associate with Period protein during the late activation phase of the circadian cycle. We found that per mRNAs localize to p-bodies, promoting their translational repression. Disruption of p-body proteins, including the 5’–3’ exoribonuclease Pcm or the DEAD-box RNA helicase Me31b, in clock neurons caused persistent accumulation of PER/TIM nuclear condensates, eliminating the delay between activation and repression phases and disrupting ~24-hour circadian rhythms. Additionally, p-body proteins are essential for the decay of core clock mRNAs during the repression phase. Incorporating the Period 3’ untranslated region (UTR) into reporter transcripts was sufficient to recruit them to p-bodies, reducing both transcript and protein levels. Thus, p-bodies play a critical dual role in translational repression and mRNA decay, indispensable for maintaining 24-hour circadian rhythms. These findings provide novel insights into circadian regulation and underscore broader principles of post-transcriptional control in gene expression.

overall_design: polyA RNA sequencing of Drosophila melanogaster adult whole head lysate (tim-GAL4>UAS-RpL3-3XFLAG). For each biological replicate, two samples were collected and sequenced: 1) INPUT, a portion of lysate collected immediately after head homogenization, 2) FLAG, co-immunoprecipitated RNA prepared from the remaining lysate using anti-FLAG magnetic beads.

first: Yangbo

last: Xiao

first: Ye

last: Yuan


title: Tubacin alleviate the reproductive toxicity of deoxynivalenol in mouse oocytes and zygotes via strengthening microtubule stability

city: Nanjing

first: Jianhua

last: Chen

state: Jiangsu

address: 101 Longmian Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

summary: Deoxynivalenol (DON) is one of the most common food contaminants, widely present in grain products. Studies using murine and porcine models show deoxynivalenol exposure impairs oocyte maturation and mitochondrial function; however, the exact mechanisms remain unclear. In the present study, we found DON exposure markedly altered the microtubule nucleation-associated proteins expression pattern of oocytes, while supplementation of Tubacin recovered the progress of oocyte maturation, as well as the expression of KIF11 and TPX2, which are key factors for microtubule nucleation and spindle stabilization. More importantly, with the in vivo TUBB8 oocyte-specific knock-in model which introduced the human β-tubulin isotype into the most widely used mouse model, we found inhibition of HDAC6 activity reconstructed morphologically normal spindles and drastically recovered polar-body extrusion rate by culturing with the specific HDAC6 inhibitor Tubacin in DON-exposed oocytes. Mechanistically, DON represses mRNA translation and disrupts ribosomal function. In our investigation, DON interfered with fertilized egg cleavage by disrupting microtubule and microfilament networks, and Tubacin enhanced microtubule acetylation, stabilizing the network and rescuing developmental arrest. Taken together, these findings elucidated the rescue effects of Tubacin on DON-induced reproductive toxicity in oocytes,  and validated our TUBB8 oocyte-specific knock-in mouse model as a rapid evaluation of exposure and potential treatment of environmental pollutants to female reproductive health.

overall_design: Five oocytes per sample were collected from the Control, DON-treated, and DON+Tubacin for RNA-sequencing. Each sample was lysed with 1 µL lysis buffer, and immediately used for cDNA synthesis via the SMART-seq2 method.

first: Ruizhi

last: Feng

first: Hui

last: Luo


title: Childhood brain tumours instruct cranial haematopoiesis and immunotolerance [scRNAseqTCR postTx]

city: Cambridge

first: Elizabeth

last: Cooper

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

summary: Recent research has revealed a remarkable role for immunosurveillance in healthy and diseased brains, dispelling the notion that this organ is a passive immune-privileged site. Better understanding of how this immunosurveillance operates could improve the treatment of neurological diseases. Here, using a novel genetically engineered mouse model of ZFTA-RELA ependymoma–a childhood brain tumour–we characterised an immune circuit between the tumour and antigen presenting, haematopoietic stem/progenitor cells (HSPCs) in the skull bone marrow. The presentation of antigens in the cerebrospinal fluid (CSF) by HSPCs to CD4+ T cells, biased HSPCs lineages toward myelopoiesis and polarised CD4+ T-cells to regulatory T cells (T-regs), culminating in tumour immunotolerance. Remarkably, a single infusion of antibodies directed against cytokines enriched in the CSF of mice bearing ZFTA-RELA ependymomas, choroid plexus carcinomas or Group-3 medulloblastoma–all aggressive childhood brain tumours–disrupted this process and caused profound tumour regression. These data unmask a mechanism by which skull bone marrow-derived HSPCs and CD4+ T cells cooperate to promote the immunotolerance of childhood brain tumours. Antibodies that disrupt this immunosurveillance could prove an effective therapy for these cancers that are less toxic than current treatments.

overall_design: Tumour/brain samples from age-matched 6-8 week-old EPZFTA-RELA  (NestinCreERT2;Fus1;RFPTdT) mice were mechanically dissociated using sterile surgical scalpels into ∼1 mm3 cubes, and dissociated using the mouse tumour dissociation kit (Miltenyi Biotec) using the gentleMACS Octo Dissociator (Miltenyi Biotec). After dissociation, the samples were then filtered through 100 µm meshes and washed with 2% fetal bovine serum in RPMI, spun down 420 g for 5 minutes. Samples were resuspended in 40% percoll and centrifuged at 600 x g for 10 minutes. Supernatant was removed and washed with 2% fetal bovine serum in RPMI and resuspended on 0.05% BSA PBS solution. Samples were stained with DAPI (0.2 µg/ml). Samples were centrifuged, resuspended in FACS buffer with anti-CD16/32 (FC block; Biolegend) diluted 1:50 in FACS buffer and fluorescently conjugated antibodies (CD45-PE and anti-Ter 119 FITC)  at 4°C, followed by for 20 minutes. Cells were sorted using the Influx Cell Sorter (BD Biosciences) or FACsAria II (BD Biosciences) into 1% BSA coated 1.5 mL Eppendorf tubes with 500 μL of DMEM


title: MOIRA is required for clock protein and gene clustering and normal circadian rhythms in Drosophila [ATAC-seq]

summary: Circadian clocks are ~24-hour timekeepers that orchestrate daily rhythms in the expression of a multitude of genes, thereby influencing a wide array of physiological processes from sleep to metabolism. The chromatin at clock-controlled genes undergoes rhythmic modifications facilitated by the activities of histone modifiers and chromatin-remodeling proteins. However, despite its significance, this area of research remains relatively under explored. Our recent investigations unveiled that Moira, a component of ATP-dependent chromatin remodeling complex SWI/SNF complex is essential for generating ~24-h circadian rhythms in Drosophila Melanogaster. Moira functions specifically as a repressor for clock regulated genes by compacting chromatin in clock neurons. The rhythm of chromatin accessibility is completely abolished in the absence of Moira. Further, Moira is organized into ~10 positionally static, discrete nuclear foci at the inner nuclear envelope across all Drosophila cells, and clock regulated genes are localized to one of these Moira foci throughout the circadian cycle specifically in the clock neurons. Our study will lead to a significant advancement in our understanding of how SWI/SNF complexes regulate chromatin structure and subnuclear localization of clock-regulated genes, and ultimately affect circadian rhythms.

overall_design: 1) polyA RNA sequencing of Drosophila melanogaster clock neurons in control and mor-RNAi knockdown, and 2) ATAC-seq of Drosophila melanogaster clock neurons in control and mor-RNAi knockdown. Cells were isolated by fluorescence-activated cell sorting (FACS) using Clk-GAL4>UAS-GFP-NLS line developed in the lab. GFP-positive and DAPI-negative cells were sorted to be clock neurons.

first: Qianqian


title: Childhood brain tumors instruct cranial haematopoiesis and immunotolerance [endpoint Fus1 GEX]

summary: Recent research has revealed a remarkable role for immunosurveillance in healthy and diseased brains, dispelling the notion that this organ is a passive immune-privileged site1–3. Better understanding of how this immunosurveillance operates could improve the treatment of neurological diseases. Here, using a novel genetically engineered mouse model of ZFTA-RELA ependymoma4–a childhood brain tumour–we characterised an immune circuit between the tumour and antigen presenting, haematopoietic stem/progenitor cells (HSPCs) in the skull bone marrow. The presentation of antigens in the cerebrospinal fluid (CSF) by HSPCs to CD4+ T cells, biased HSPCs lineages toward myelopoiesis and polarised CD4+ T-cells to regulatory T cells (T-regs), culminating in tumour immunotolerance. Remarkably, a single infusion of antibodies directed against cytokines enriched in the CSF of mice bearing ZFTA-RELA ependymomas, choroid plexus carcinomas or Group-3 medulloblastoma–all aggressive childhood brain tumours–disrupted this process and caused profound tumour regression. These data unmask a mechanism by which skull bone marrow-derived HSPCs and CD4+ T cells cooperate to promote the immunotolerance of childhood brain tumours. Antibodies that disrupt this immunosurveillance could prove an effective therapy for these cancers that are less toxic than current treatments.

overall_design: Tumour/brain samples from age-matched 6-8 week-old EPZFTA-RELA (NestinCreERT2;Fus1) (n=5) and NestinCreERT2 (n=4) mice were mechanically dissociated using sterile surgical scalpels into ∼1 mm3 cubes, and dissociated using the mouse tumour dissociation kit (Miltenyi Biotec) using the gentleMACS Octo Dissociator (Miltenyi Biotec). After dissociation, the samples were then filtered through 100 µm meshes and washed with 2% fetal bovine serum in RPMI, spun down 420 g for 5 minutes. Samples were resuspended in 40% percoll and centrifuged at 600 x g for 10 minutes. Supernatant was removed and washed with 2% fetal bovine serum in RPMI and resuspended on 0.05% BSA PBS solution. Samples were stained with DAPI (0.2 µg/ml). Samples were centrifuged, resuspended in FACS buffer with anti-CD16/32 (FC block; Biolegend) diluted 1:50 in FACS buffer and fluorescently conjugated antibodies (anti-Ter 119 FITC)  at 4°C, followed by for 20 minutes. Cells were sorted using the Influx Cell Sorter (BD Biosciences) or FACsAria II (BD Biosciences) into 1% BSA coated 1.5 mL Eppendorf tubes with 500 μL of DMEM


title: MOIRA is required for clock protein and gene clustering and normal circadian rhythms in Drosophila [RNA-seq]


title: P-bodies control circadian rhythms by regulating the translational repression and decay of period mRNAs

overall_design: polyA RNA sequencing of Drosophila melanogaster clock neurons in 1) control and pcm-RNAi knockdown, and 2) control and me31B-rABE adenine base editor overexpression conditions. Cells were isolated by fluorescence-activated cell sorting (FACS) using Clk-GAL4>UAS-GFP-NLS line developed in the lab. GFP-positive and DAPI-negative cells were sorted to be clock neurons.


title: Transcriptome-wide analysis of 5-methylcytosine modification and expression profiles in a mouse model of cerebral ischemia

city: WUHAN

first: chao

last: zhang

state: HUBEI

address: donghu

institute: Zhongnan Hospital of Wuhan University

summary: Stroke is one of the leading causes of death and disability, surpassing heart disease and respiratory diseases, and has become the primary cause of disability-adjusted life years lost in patients. Ischemic stroke (IS) accounts for 87% of all stroke cases. Epigenetics refers to the heritable and modifiable processes that regulate gene expression without altering the DNA sequence. This includes DNA methylation or hydroxymethylation, histone modifications, chromatin remodeling, and RNA methylation. 5-methylcytosine (m5C) is one form of RNA methylation that has been reported to be widely present in various RNAs. Studies have shown that m5C modification is involved in several fields, including cancer, cardiovascular diseases, reproductive diseases, and neurological diseases. However, the specific role of m5C methylation in stroke remains unclear. Therefore, We set up the mouse cerebral ischemia model (Middle Cerebral Artery Occlusion, MCAO) to study the epigenetic modifications and potential biological functions of relevant RNAs after stroke.

overall_design: First, we build the cerebral ischemia model of the male c57 mice, divided into a sham surgery group (Sham) and a stroke group (MCAO). After model establishment, we validated the model using TTC staining, TUNEL staining, and immunofluorescence staining. We assessed the extent of nerve damage in mice after MCAO using the Longa neurological deficit score. We used methylated RNA immunoprecipitation sequencing (MeRIP-Seq) to identify m5C peaks in the mouse transcriptome (lncRNA, circRNA, mRNA), and simultaneously constructed RNA libraries through RNA-Seq to study the expression profile. We analyzed the differentially methylated lncRNA, circRNA, and mRNA, and studied their potential biological functions through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The final validation was performed using RT-PCR

first: Dan

last: Xiong

first: Chao

last: Zhang

first: Jian

last: Xia


title: Aberrant Cell Fate and Functional Impairment in Developing Human Liver Organoids Exposed to Nanoplastics

city: Chuncheon-si

first: Kim

last: Wijin

address: Kangwondaehak-gil

institute: kangwon national university

summary: Nanoplastics represent an emerging class of global environmental contaminants; however, their potential to interfere with human developmental processes remains largely unexplored. This study investigated the impact of exposure to polystyrene nanoplastics (PS-NP) on the de novo formation, differentiation, and function of human liver organoids derived from induced pluripotent stem cells (hiPSCs), a sophisticated model of early organogenesis.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of liver organoids subjected to stepwise liver organoids differentiation with and without PS-NPs

first: Wijin

last: Kim

first: Ju-Hyun

last: Park


title: Stem cell specification and niche formation in developing incisor depend on actomyosin forces

city: Zurich

first: Anamaria

last: Balic

address: Plattenstr. 11

department: Institute of Oral Biology

country: Switzerland

institute: University of Zurich Center for Dental Medicine

summary: The precise timing of stem cell specification and niche formation during murine incisor development is poorly understood, and it is unclear whether these processes occur simultaneously or in a sequential manner. Functional dental epithelial stem cells are marked by the expression of Sox2, a transcription factor that is broadly expressed in the dental epithelium at the dentition onset and restricted to stem cells in fully developed incisor. Using genetic lineage tracing in Sox2CreERT2/+; R26RmT/mGand Sox2CreERT2/+; R26RtdT/+embryos along with a single-cell RNA sequencing at different stages of incisor development, we investigated the timing of the stem cell specification and its temporal relationship with niche formation. Our results reveal the presence of a Sox2-expressing stem cell-like population prior to formation of the functional niche. These cells localize to the leading edge of the advancing incisor epithelium where they are maintained in an undifferentiated state. Our data demonstrate presence of actomyosin network and a generation of a contractile tension which helps confine Sox2+ stem cells to the leading edge. This mechanical confinement likely plays an important role in maintaining their stemness until the niche is functionally and structurally established. Partial or complete disruption of the actomyosin network disables the clustering of Sox2-expressing cells, potentially triggering their premature differentiation, and ultimately leads to impaired formation of the functional stem cell niche and abnormal growth of the incisor.

overall_design: Expression profiling by high throughput sequencing: scRNAseq of developing wild type murine incisor at E11.5, E14.5 and E16.5


title: Bulk RNASeq S64F MAFA male islets

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

summary: Mice harboring the S64F mutation in the endogenous MafA gene ("Het") on a mixed genetic background (SJL x C57/Bl6J) show impaired glucose tolerance then overt diabetes by 5 weeks of age. Moreover, when backcrossed to the C57/Bl6J background, mutant Het mice are euglycemic similar to their wild type littermates, suggesting compensation which can prevent diabetes.

overall_design: Male mouse islets isolated at 5.5 weeks of age and submitted for sequencing. Each sample was produced from islets from one unique mouse

first: Jeeyeon

last: Cha

first: Zach

last: Loyd

first: Dongsoo

last: Lee


title: Unique sequence features define epigenetic longevity of inflammatory memory

first: Luis

last: Soto-Ugaldi

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: E2F4/SETD1A axis-mediated METTL3 methylation promotes tumor immune evasion through impeding endogenous retroelements expression

city: Wuhan

first: Haijie

last: Li

address: no.1095 Jiefang Avenue

department: Tongji Hospital

institute: Huazhong University of Science and Technology

summary: Colorectal cancer (CRC) progression and recurrence persist as major clinical challenges despite standard therapies. Emerging evidence underscores that tumor relapse arises from crosstalk between malignant cells and the immunosuppressive microenvironment, yet the role of non-histone lysine methylation in this interplay remains unclear. Here, we identify di-methylation of lysine 513 (K513) on methyltransferase-like 3 (METTL3) as a key epigenetic modification associated with CRC progression and recurrence. Mechanistically, we reveal that SETD1A catalyzes METTL3 K513 methylation, enhancing its binding affinity to S-adenosylmethionine (SAM) and augmenting RNA m⁶A deposition. Strikingly, METTL3 methylation suppresses endogenous retroelements expression, leading to impaired type I interferon responses and tumor immune evasion. We further uncover a fluorouracil-induced E2F4/SETD1A/METTL3 regulatory axis, wherein E2F4 self-regulation activates SETD1A to drive METTL3 methylation. Targeting this axis through pharmacological inhibition of E2F4 or genetic disruption of METTL3 methylation synergizes with immune checkpoint blockade (ICB), significantly suppressing tumor growth. Our findings unveil a methylation-dependent regulatory mechanism that reshapes the tumor immune microenvironment, offering a novel therapeutic strategy for CRC.

overall_design: To determine the biological importance of METTL3 methylation at K513, we conducted methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-sequence on METTL3 WT and K513R LoVo cells


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [MSKPCA3 Bulk RNA-Seq]

city: Baltimore

first: Yangzhenyu

last: Gao

state: MD

address: 2917 Saint Paul

department: Oncology

institute: johns hopkins university

summary: Castration-resistant prostate cancer (CRPC) is largely dependent on the androgen receptor (AR) for growth and often exhibits hyperactive PI3K signaling, most frequently due to PTEN loss. Therapeutic pressure from anti-AR therapies can induce trans-differentiation toward an AR-independent phenotype. Recently, different subtypes of AR-independent CRPC have been redefined, with the stem cell-like (SCL) subtype emerging as one of the most prevalent. Elucidation of the epigenetic mechanisms controlling the maintenance of these distinct CRPC cell states could pave the way for effective combinatorial therapies for CRPC. In this study, we identified a key role for the histone methyltransferase KMT2D in establishing the chromatin competence necessary for the recruitment of AR and FOXA1 transcription factors (TFs) that are essential for the AR transcriptional output in AR-dependent CRPC cell lines, patient derived organoids, and patient samples. Unexpectedly, KMT2D maintained the identity of the AR-low CRPC-SCL subtype and controlled activity of AP-1 TFs such as FOSL1, which acts as a master regulator of this subtype. Single cell transcriptomics and chromatin assays underscored the role of KMT2D in sustaining a mixed lineage cell state via AP-1 and FOXA1. The combined suppression of PI3K/AKT and KMT2D reduced cell proliferation in prostate cancer cells and patient-derived organoids in both CRPC-AR and CRPC-SCL subtypes. Altogether, these results unveil KMT2D as a major mediator of the epigenetic landscape in subtype-specific CRPC, contributing to tumor growth and therapeutic response.

overall_design: Bulk RNA-Seq was performed in MSKPCA3 AR-low patient-derived organoids with doxycycline-inducible knockdown of KMT2D

first: Eneda

last: Toska

first: Wouter

last: Karthaus

first: Srushti

last: Kittane

first: Erik

last: Ladewig

first: Taibo


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [LNCaP Bulk RNA-Seq]

overall_design: Bulk RNA-Seq was performed in LNCAP AR-high prostate cancer cells with doxycycline-inducible knockdown of KMT2D


title: Metabolic Reprogramming during Human Neuron Differentiation Identifies Glutaminase as a Key Determinant in Fragile X Syndrome

city: Worcester

first: Sneha

last: Shah

state: Massachusetts

address: 373 Biotech II, Suite 204, Plantation Street

department: Molecular Medicine

institute: UMASS CHAN MEDICAL SCHOOL

summary: Metabolic homeostasis gone awry is a contributor to, if not an underlying cause of, several neurologic disorders. Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by a trinucleotide repeat expansion in FMR1 and consequent loss of the encoded protein FMRP, which results in downstream molecular, neurologic, and mitochondrial deficits that are linked to cognitive impairment. In human postmortem brain, many metabolites and solute carrier proteins are coordinately dysregulated, which also occurs during differentiation of human iPSCs into excitatory neurons. Metabolic tracing in FXS neurons demonstrates a dearth of glutamine deamidation to glutamate, which reduces anaplerosis into the TCA cycle, consequently hindering bioenergetic and biosynthetic functions of mitochondria. Mechanistically, aberrant expression of glutaminase isoforms in FXS is responsible for reduced glutaminolysis, thereby altering glutamate levels which may contribute to FXS.

overall_design: RNA-seq of age matched male post-mortem cortex tissues from 5 Typlically developing (TD) and FXS individuals.

first: Botao

last: Liu

first: Maurice

last: Swanson

first: Tenzin

last: Tseyang

first: Thang

last: Do

first: Jodi

last: Bubenik

first: Suna

last: Jung

first: Mina

last: Anadolu

first: Verónica

last: Martínez-Cerdeño

first: Elizabeth

last: Berry-Kravis

first: Jessica

last: Spinelli

first: Joel

last: Richter


title: Effect of MetAP2 Inhibitor Evexomostat (SDX-7320) on Gene Expression in MC38 Tumors from Lean and Obese Mice

city: WESTON

first: Pierre

middle: Jean

last: Dufour

address: 273 CONANT RD.

institute: SynDevRx, Inc

summary: The objective of this study was to test the anti-tumor activity of the MetAP2 inhibitor evexomostat (SDX-7320) on sub-cutaneous MC38 allografts in lean and obese mice. Mice with established MC38 tumors were treated with evexomostat (SDX-7320) 6 mg/kg by sub-cutaneous injection every 4 days beginning when tumors were 75-100 mm3 for a total of 5 doses. Upon study termination, mice were euthanized and tumor tissue from N=4 mice/group was dissected, weighed, and placed into RNAlater for subsequent isolation of polyA+ RNA, cDNA library construction and sequencing.

first: Peter

last: Cornelius


title: Post-transcriptional splicing of timeless drives ~24-hour circadian rhythms in Drosophila

first: Swathi

last: Yadlapalli

summary: Circadian clocks drive ~24-hour rhythms in physiology and behavior through precisely timed gene expression cycles1-4. Here, we reveal an unexpected role for intron splicing in tuning the ~24-hour circadian period in Drosophila. Using RNA Fluorescent In Situ Hybridization and RNA-sequencing, we demonstrate that ~50% of timeless (tim) mRNAs—a core clock transcript—remain nuclear throughout the circadian cycle due to retention of a specific intron, termed intron P. Unlike other tim introns, spliced during transcription, intron P—lacking a canonical branch point—is spliced inefficiently post-transcriptionally near nuclear speckles, thereby limiting tim mRNA export and TIM protein synthesis. CRISPR deletion of intron P results in all tim mRNAs being fully spliced and exported, accelerating TIM production and shortening the circadian period to ~22.5 hours. Inserting intron P into reporter genes promotes their nuclear retention in both Drosophila neurons and human U2OS cells, which is reversed by adding a canonical branch point sequence. A genetic screen identified the KH-domain RNA-binding protein Qkr58E-2 (a Sam68 homolog5) as an intron P splicing activator, and HnRNP proteins Hrb27c and Squid6 as repressors. Together, these findings uncover a novel regulatory role for intron splicing dynamics in circadian timing and further suggest that introns have the potential to act as critical regulatory elements in other temporally regulated biological processes, including developmental transitions and stress responses.

overall_design: polyA RNA sequencing of Drosophila melanogaster clock neurons in control and Prp3-RNAi knockdown conditions. Cells were isolated by fluorescence-activated cell sorting (FACS) using Clk-GAL4>UAS-GFP-NLS line developed in the lab. GFP-positive and DAPI-negative cells were sorted to be clock neurons.

first: Ye

last: Yuan


title: TREM2 expression level is critical for microglial state, metabolic capacity and efficacy of TREM2 agonism.

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

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

summary: Triggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator of microglial activity and sequence variants are major risk factors for late onset Alzheimer’s disease (LOAD). To better understand the molecular and functional changes associated with TREM2 signalling, we generated a TREM2 reporter mouse model and observed a gradual upregulation of reporter expression with increasing plaque proximity. Isolated microglia were sorted based on reporter expression and their transcriptomic profiles acquired in both wildtype and APP transgenic animals, allowing us to disentangle TREM2 versus pathology-specific effects. Bulk RNA36 sequencing highlighted TREM2 level-dependent changes in major immunometabolic pathways, with enrichment of genes in oxidative phosphorylation and cholesterol metabolism in microglia with increased TREM2 expression. To confirm these findings, we next analysed uptake of fluorodeoxyglucose (FDG) and examined metabolomic and lipidomic profiles. Again, independent of Aβ pathology, TREM2 expression correlated with uptake of FDG as well as increased cellular redox, energetics, and cholesterol homeostasis. Finally, we performed chronic treatment with a brain penetrant TREM2 agonist and identified a window of TREM2 expression where microglia are most responsive. Thus, our data provide novel insights into TREM2-mediated regulation of microglial metabolic function and informs current efforts to bring TREM2 agonists into clinical application.

overall_design: A C57Bl/6J based mouse model with mKate2 fluorescence reporter for the expression of TREM2 was created. The experimental mice expressed the reporter heterozygous while AppSAA and the hTfR knock in were homozygous. 8-month-old Trem2-mKate2KI/wt APPSAA/SAA.hTfRKI/KI mice were injected with 1 mg/kg Trem2 agonist (4D9) coupeled with an antibody transport vehicle (ATV:4D9), monthly until 11 months. At 12 months, mice were injected with 30 mg/kg FDG, 641 perfused 1 hour later and the extracted microglia were then sorted into low, mid and high mKate2 expressing populations with FACS. The cells were stored in Trizol until RNA-Seq. The samples include longtime treated ATV:4D9 microglia and control treated miicroglia sorted into mKate2(Trem2) low, mid and high expressing cells.

first: Astrid

last: Feiten

first: Kilian

last: Dahm

first: Thomas

last: Ulas

first: Pia

last: Grundschoettel

first: Kathryn

last: Monroe

first: Christian

last: Haass


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [MSKPCA2 Bulk RNA-seq]

first: Yangzhenyu

last: Gao

overall_design: Bulk RNA-Seq was performed in MSKPCA2 AR-high patient-derived organoids with doxycycline-inducible knockdown of KMT2D

first: Eneda

last: Toska

first: Wouter

last: Karthaus

first: Srushti

last: Kittane

first: Erik

last: Ladewig

first: Taibo

last: Li

first: Wanlu

last: Chen


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [H3K4me2 ChIP-Seq]

overall_design: H3K4me2 ChIP-Seq was performed in LNCaP AR-high cells with doxycycline-inducible knockdown of KMT2D


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [PC3 Bulk RNA-seq]

overall_design: Bulk RNA-Seq was performed in PC3 AR-neg prostate cancer cells with doxycycline-inducible knockdown of KMT2D


title: Tau impedes glioma progression via enhancing fatty acid β-oxidation induced cellular senescence

city: Xiamen

first: Wanhong

last: Han

address: No.  55, Zhenhai Road, Siming District

institute: the First Affiliated Hospital of Xiamen University,School of Medicine, Xiamen University

summary: Tau (MAPT) gene and protein levels exhibit a negative correlation with glioma malignancy and reduced survival rates. However, the molecular mechanisms underlying this correlation require to be further investigated. In this study, we observed tau impedes glioma cell growth both in vitro and in vivo. Mechanistically, tau enhanced fatty acid β-oxidation, which induces DNA damage and glioma cellular senescence. Furthermore, we identified that the molecular mechanism by which tau regulates lipid metabolism is its binding to CPT1A and promoting CPT1 activity. Our findings highlight the biological role of tau in regulating lipid metabolism and cellular senescence in a CPT1 activity-dependent manner. These results suggest that tau may serve as a promising therapeutic target for glioma in the future.

overall_design: U87 cell which overexpresdsed control vector or tau were used forRNA-Seq analysis to identify tau induced different genes

first: Wujie

last: Zhao

first: Jiawei

last: He

first: Wenpeng

first: Hanwen

last: Lu

first: Zhenwei

first: Xiansheng

last: Qiu


title: Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT

city: Würzburg

first: Alexander

last: Westermann

address: Josef-Schneider Straße 2

institute: HIRI

summary: Salmonella virulence chiefly relies upon two major pathogenicity islands, SPI-1 and SPI-2, which enable host cell invasion and intracellular survival, respectively. There has been increasing evidence for post-transcriptional control of SPI gene expression by Hfq-dependent small RNAs (sRNAs) such as PinT. This 80-nucleotide sRNA is highly expressed after Salmonella enters host cells and modulates the transition from the SPI-1 to SPI-2 program by targeting different virulence factor mRNAs. It has been elusive, however, how PinT activity could be counteracted when virulence gene suppression were to be relieved. To identify putative inhibitors of PinT, we have mapped the RNA interactome of Salmonella recovered from infected macrophages, using an optimized version of the RIL-seq method. Next to offering an unprecedented view of Hfq-mediated RNA interactions during Salmonella’s intracellular infection stage, RIL-seq uncovered the 3’ end-derived sRNA InvS as a direct negative regulator of PinT. Biochemical and genetic experiments suggest a decoy mechanism whereby InvS lifts the PinT-mediated repression of virulence factors. Additionally, InvS acts as an mRNA repressor of the host cell adhesion protein, MipA, and PinT interaction with InvS relieves mipA repression. Together, our work identifies a unique pair of antagonistic sRNAs in a growing post-transcriptional network of virulence gene regulation.

sample_organism:
Mus musculus
Salmonella enterica

platform_organism:
Mus musculus
Salmonella enterica

overall_design: We have used the RIL-seq technique (Melamed et al. 2016) to map the global RNA-RNA interactome on the sRNA chaperone Hfq in Salmonella enterica under infection conditions (SPI-2 medium or mouse macrophage 20 h post infection).

first: Hoda

last: Kooshapour

first: Gianluca

last: Matera

first: Elisa

last: Venturini

first: Thorsten

last: Bischler

first: Jörg

last: Vogel


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [PC3 Bulk ATAC-seq]

first: Yangzhenyu

last: Gao

overall_design: Bulk ATAC-Seq was performed in PC3 AR-neg prostate cancer cells with doxycycline-inducible knockdown of KMT2D

first: Eneda

last: Toska

first: Wouter

first: Srushti


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [AR ChIP-Seq]

overall_design: AR ChIP-Seq was performed in LNCaP AR-high cells with doxycycline-inducible knockdown of KMT2D

last: Karthaus

last: Kittane

first: Erik

first: Taibo


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [MSKPCA3 Bulk ATAC-seq]

overall_design: Bulk ATAC-Seq was performed in MSKPCA3 AR-low patient-derived organoids with doxycycline-inducible knockdown of KMT2D

last: Ladewig

last: Li


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [DU145 Bulk ATAC-seq]

overall_design: Bulk ATAC-Seq was performed in DU145 AR-neg prostate cancer cells with doxycycline-inducible knockdown of KMT2D


title: Gene expression profile in diet-induced HFpEF rat model

city: Nagoya-shi

first: Yuka

last: Kono

state: Aichi

address: 2-1723, Omori, Moriyama-ku

institute: Kinjo Gakuin University

summary: To investigate gene expression changes associated with the development of HFpEF and the preventive effects of pharmacological interventions against HFpEF onset, Wistar rats were administered N(G)-Nitro-L-arginine methyl ester, an inhibitor of nitric oxide synthase, and fed a high-fat diet for 8 weeks. Cardiac tissues were collected at the time of sacrifice.

overall_design: The rats were divided into four groups: a normal group, an HFpEF group, a group treated with the RAS inhibitor captopril (Cap) group, and a group treated with sacubitril/valsartan (Sac/Val) group.

first: Kunihiro

last: Sonoda

first: Shogo

last: Watanabe


title: Single cell RNA sequencing of the steroidogenic lineage in the male adrenal cortex

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

summary: To achieve single-cell characterization of the adrenal cortex transcriptome, we selectively labeled the steroidogenic adrenocortical cells using a transgenic Cre-LoxP approach. We combined Sf1-Crehigh mice with Rosa26mTmG animals to obtain mice expressing fluorescent reporter proteins at the cell membrane (mTmG) of cells that express or have expressed the transcription factor SF-1 (Steroidogenic Factor 1, also AdBP4, encoded by NR5A1). We prepared a single-cell suspension by combining mechanic and enzymatic dissociation at low temperatures to preserve the viability of steroid cells and their transcriptional states. Fluorescence-activated cell sorting (FACS) was then used to isolate GFP-positive cells representing the steroidogenic lineage. GFP-positive cells include the progenitor populations as well as differentiated cells (zona glomerulosa and zona fasciculata cells).

overall_design: A total of 26 male mouse adrenals (15 week-old) was harvested and dissociated into single cell suspension. Steroidogenic cells were isolated by FACS and analyzed by single cell RNAsequencing.

first: Typhanie

last: Dumontet


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer

address: 1830 E Monument Street, Suite 2-300

institute: Johns Hopkins School of Medicine

overall_design: Single nuclei were harvested from MSKPCA3 patient-derived organoids upon KMT2D knockdown at 7 days post-doxycycline administration, with controls at day 0 and day 7 without KMT2D knockdown. Joint single-nucleus RNA and ATAC libraries were prepared using the 10x platform.


title: m1A methylase TRMT6 promotes neuroblastoma development by demethylating SST mRNA in an m1A/YTHDF2-dependent manner

city: shenzhen

first: Xin

middle: xin

last: Zhang

state: china/guangdong

address: No.7 pengfei road Dapend

department: agricultural genomics institute at shenzhen

institute: chinese academy of agricultural science

summary: m1A, a prevalent RNA modification found in various RNA species, was recently reported to modulate cancer progression; However its effects in neuroblastoma have not been investigated. In this study, we observed a significantly elevated expression of m1A transmethylase TRMT6 in high-risk and late-stage neuroblastoma patients. Silence and regain of function studies demonstrated that TRMT6 promotes neuroblastoma cell malignancy, tumor growth, and metastasis in vitro and in vivo. Omics analysis and cancer malignancy assay revealed that somatostatin (SST) is the functional downstream target of TRMT6, which determined the pro-tumor role of TRMT6 in neuroblastoma. Mechanistically, TRMT6 reduces SST mRNA levels by inhibiting its mRNA stability in an m1A-YTHDF2-dependent manner, which revealed the crosstalk of the m1A methylase TRMT6 in neuroblastoma. Moreover, SST analog octreotide suppresses neuroblastoma cell malignancy, tumor growth, and metastasis. Targeting TRMT6 provides a novel potential diagnosis and therapeutic target for neuroblastoma

overall_design:
Silence TRMT6  to detect the m1A modification variation in SK-N-AS neuroblastoma cells.
m1A-seq

first: Xinxin

first: Huiran

last: Lin

first: Huimin

last: Yin

first: Yufeng

last: Han

first: Liping

last: Chen

first: Mengzhen

first: Hongxia

first: Zhenjian

last: Zhuo

first: Jing

last: He


title: scRNAseq on tumor-draining lymph nodes (tdLN) migratory DC and CD4+ T cells in primary melanoma-bearing BP (TyrCre-ERT2Tg/0 BrafLSL-V600E/+ Ptenlox/lox) and BPT (TyrCre-ERT2Tg/0 BrafLSL-V600E/+Ptenlox/lox Tslp-/-) mice

city: ILLKIRCH

first: Mei

address: 1 Rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire

summary: Characterization of migratory DC and CD4 T cells in tdLN from primary melanoma of BP and BPT mice

overall_design: We performed multiplexed scRNAseq to characterize migDC and CD4 T cells enriched from tdLN of BP and BPT mice. Hashtag oligos (HTO) were used to label 4 populations for multiplexing.

first: Alicia

last: Perrin

first: Antoine

last: Braud

first: Marine

last: Guivarch

first: Tao

last: Ye


title: single-cell transcriptomic analysis of mouse haematopoietic stem cells upon Nat10 deletion

city: GuangZhou,GuangDong Province

first: Feng

last: Huang

state: China

institute: Guangzhou Laboratory

summary: Epigenetic regulation exerts a crucial role in maintaining the balance between self-renewal and differentiation of hematopoietic stem cells (HSCs), thereby sustaining normal hematopoiesis. Although emerging evidence has demonstrated the contribution of RNA N4-acetylcytidine (ac4C) modification and its catalytic enzyme Nat10 to numerous biological processes, particularly tumorigenesis, the landscape and function of ac4C in normal hematopoiesis remain unexplored. In this study, we characterize the landscape of ac4C across the hierarchy of hematopoietic stem and progenitor cells (HSPCs)  tracked by single-cell transcriptomic analysis and reveal a key role of Nat10 in the maintenance of HSCs.

overall_design: To  investigate the role of Nat10-mediated ac4C in HSC maintenance and differentiation, we performed 10×Genomics single-cell RNA sequencing (scRNA-seq) on sorted lineage-negative cells (HSPCs) from the bone marrow (BM) of five independent WT or Nat10 cKO mice.

first: Hengyou

last: Weng

first: Huilin

first: Yushuai

last: Wang


title: Dynamic ac4C landscape across mouse hematopoietic stem and progenitor hierarchy using the ultra-low input acRIP-seq (ULAC-seq)

summary: Epigenetic regulation exerts a crucial role in maintaining the balance between self-renewal and differentiation of hematopoietic stem cells (HSCs), thereby sustaining normal hematopoiesis. Although emerging evidence has demonstrated the contribution of RNA N4-acetylcytidine (ac4C) modification and its catalytic enzyme Nat10 to numerous biological processes, particularly tumorigenesis, the landscape and function of ac4C in normal hematopoiesis remain unexplored. In this study, we characterize the landscape of ac4C across the hierarchy of hematopoietic stem and progenitor cells (HSPCs) using  the ultra-low input acRIP-seq (ULAC-seq) and reveal a key role of Nat10 in the maintenance of HSCs.

overall_design: To further investigate the role of Nat10-mediated ac4C in HSC maintenance and differentiation, we developed an ultra-low input acRIP-seq (ULAC-seq) method, capable of handling varying amounts of input, as low as 500 ng of total RNA. We subsequently profiled ac4C modification in six distinct sorted hematopoietic populations, including HSCs, MPP, CMP, GMP, MEP, and CLP from wild-type (WT) mouse BM using ULAC-seq. We also applied ULAC-seq in Nat10 knockout BM lin- cells and control BM lin- cells to characterize Nat10 targets.


title: Global mRNA profiling (RNA-seq) across mouse hematopoietic hierarchy

summary: Epigenetic regulation exerts a crucial role in maintaining the balance between self-renewal and differentiation of hematopoietic stem cells (HSCs), thereby sustaining normal hematopoiesis. Although emerging evidence has demonstrated the contribution of RNA N4-acetylcytidine (ac4C) modification and its catalytic enzyme Nat10 to numerous biological processes, particularly tumorigenesis, the landscape and function of ac4C in normal hematopoiesis remain unexplored. In this study, we characterize the landscape of ac4C across the hierarchy of hematopoietic stem and progenitor cells (HSPCs) using RNA-seq and reveal a key role of Nat10 in the maintenance of HSCs.

overall_design: To understand the role of epigenetic regulation in the establishment and maintenance of HSC fate decisions, we sorted distinct hematopoietic populations including long-term HSCs (LT-HSCs), short-term HSCs (ST-HSCs), multipotent progenitors (MPP), common myeloid progenitors (CMP), granulocyte-macrophage progenitor (GMP), megakaryocyte/erythroid progenitors (MEP), and the mature cells from the bone marrow (BM) using fluorescence-activated cell sorting (FACS), followed by RNA sequencing (RNA-seq) analysis.


title: Paeonol Alleviates Skin Inflammation and Pruritus in Atopic Dermatitis by Inhibiting the TRPV3/NF-κB/CCL3 Axis of Keratinocytes

city: Nanjing

first: xin

last: sun

address: 138 Xianlin Avenue

institute: Nanjing University of Chinese Medicine

summary: Background: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by eczematous lesions and intense pruritus. Skin inflammation mediated by transient receptor potential vanillin 3 (TRPV3) in keratinocytes is a key mechanism driving the progression of AD. Paeonol is a bioactive phenolic compound extracted from the root bark of the Paeonia genus, which has demonstrated anti-inflammatory activities. Whether paeonol alleviates skin inflammation by inhibiting TRPV3 in the treatment of AD remains unclear.Objective: This study aims to investigate the therapeutic efficacy of paeonol against AD and its underlying anti-inflammatory mechanism.Methods: The therapeutic effects of paeonol were evaluated in a mouse model of AD induced by MC903 or carvacrol, as well as in tumor necrosis factor-alpha (TNF-α)-stimulated HaCaT cell line. Itch-related behaviors, hematoxylin-eosin (H&E) staining and toluidine blue staining were assessed in AD mice to evaluate the anti-atopic activity of paeonol. TRPV3 expression and function in keratinocytes were examined by Quantitative Real-time-PCR (qPCR), WB, immunofluorescence (IF) and Ca2+ imaging experiments. The anti-inflammation effect and its mechanisms of paeonol were measured by RNA sequencing (RNA-seq), H&E staining, qPCR and ELISA. Whole-cell patch-clamp were used to measure the excitability of trigeminal ganglion (TG) neurons treated by Chemokine (C-C motif) ligand 3 (CCL3).Results: Paeonol significantly alleviated MC903 and carvacrol-induced pruritus, epidermal hyperplasia and skin inflammation. Paeonol inhibited the expression and function of TRPV3 in keratinocytes, thereby inhibiting the activating of nuclear factor κB (NF-κB) pathway and reducing the secretion of CCL3. Downregulation of CCL3 expression in keratinocytes reduces the number of macrophages in the skin and inhibits their polarization to the M1 type. Moreover, paeonol also reversed the hyperexcitability of TG induced by increased CCL3, thus alleviated pruritus. Conclusion: Our study demonstrated that the activation of TRPV3 in keratinocytes aggravated skin inflammation and pruritus by promoting the secretion of CCL3. Paeonol alleviated AD by inhibiting the TRPV3/NF-κB/CCL3 axis in keratinocytes, thereby reducing macrophage-related skin inflammation, and inhibiting the hyperexcitability of TG neurons. These findings provide a novel therapeutic mechanism of paeonol in treating AD.

overall_design: RNA-seq and analysis were conducted on mouse ear tissues from control, MC903 and MC903 + paeonol (200mg/kg) groups.

first: Xin

last: Sun

first: Shuo

last: Cheng

first: Zongxiang

last: Tang


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [KMT2D ChIP-seq]

first: Yangzhenyu

last: Gao

overall_design: KMT2D ChIP-Seq was performed in LNCaP AR-high cells treated with 1μM PI3K inhibitor.

first: Eneda

last: Toska

first: Wouter

last: Karthaus

first: Srushti

last: Kittane

first: Erik

last: Ladewig

first: Taibo

last: Li


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [FOXA1 ChIP-seq]

overall_design: FOXA1 ChIP-Seq was performed in LNCaP AR-high cells with doxycycline-inducible knockdown of KMT2D


title: Transcription factor NKX2-1 cooperates with RUNX1 and protects T-cell acute lymphoblastic leukemia cells from DNA damage [ChIP-seq]

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

summary: T-cell acute lymphoblastic leukemia (T-ALL) is characterized by ectopic expression of transcription factors such as TAL1, TLX1/3 and NKX2-1. NKX2-1 is overexpressed in 5% of T-ALL patients, driving transcriptional induction and metabolic addiction to the serine/glycine synthesis pathway in cancer cells. However, a more complete picture of the transcriptional targets of NKX2-1 and its role in T-ALL pathogenesis is missing. We generated a CRISPR-Cas9 NKX2-1 knockout (KO) model in the NKX2-1 expressing RPMI-8402 (RPMI) T-ALL cell line. KO of NKX2-1 in RPMI cells induced apoptosis while not affecting cell cycle progression. RNA-seq on RPMI WT versus NKX2-1 KO cells showed significant downregulation of gene sets related to T-cell differentiation upon NKX2-1 KO. Additionally, we observed that NKX2-1 promoted a more mature phenotype in RPMI cells, by mildly decreasing CD34 and increasing CD2 expression. Furthermore, gene sets related to epigenetics and DNA damage were enriched in the RNA-seq data. Interestingly, DNA damage machinery related proteins, such as RPA1, appeared among the binding partners of NKX2-1 in IP-MS, and this interaction was confirmed in PDX cells. In agreement with this, we found significantly lower levels of DNA damage marks gH2AX and H3K27me3 in the presence of NKX2-1. NKX2-1 expression was associated with decreased sensitivity to topoisomerase inhibitor etoposide, and to HDAC inhibitors vorinostat and romidepsin. Furthermore, these agents resulted in lower induction of gH2AX and H3K27me3 in NKX2-1 expressing cells. Finally, NKX2-1 positive T-ALL patients showed overexpression of DNA repair genes in public RNA-seq data compared to NXK2-1 negative T-ALL, further supporting a critical role of NKX2-1 in protecting cells against DNA damage. Mechanistically,  we identified RUNX1 as NKX2-1 binding co-factor through motif analysis of NKX2-1 ChIP-seq peaks and in our NKX2-1 IP-MS experiment. NKX2-1/RUNX1 binding was confirmed in RPMI and in PDX cells. Interestingly, NKX2-1 and RUNX1 IP-MS experiments revealed that most NKX2-1 binding partners also bound to RUNX1, and that presence of NKX2-1 altered the co-factors of RUNX1. Moreover, iRegulon performed on T-ALL patients revealed that genes that are differentially expressed in NKX2-1+ T-ALL samples were regulated by RUNX1. Finally, we observed that RUNX1 inhibitor, Ro5-3335, provoked a significantly higher cell death in the presence of NKX2-1. Summing up, in addition to induction of metabolic serine/glycine synthesis addiction, our data indicate that NKX2-1 is essential to protect T-ALL cells against DNA damage. Furthermore, we observed that NKX2-1 is a co-factor of RUNX1, regulating its binding partners and activity.

overall_design: NKX2-1 was knocked out in RPMI-8402 cells resulting in 4 WT clones (WT10, WT13, WT28 and WT30) and 4 KO clones (C12, C15, S04, S36). ChIP-seq was performed with a NKX2-1/TTF1 antibody (ab76013) to find out where this transcription factor binds.

first: Linde

last: van Aerschot

first: Kalina

last: Timcheva

first: Kim

last: De Keersmaecker

first: Cabrerizo Granados

last: David


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

overall_design: Refer to individual Series


title: Transcription factor NKX2-1 cooperates with RUNX1 and protects T-cell acute lymphoblastic leukemia cells from DNA damage [RNA-seq]

overall_design: NKX2-1 was knocked out in RPMI-8402 cells resulting in 4 WT clones (WT10, WT13, WT28 and WT30) and 4 KO clones (C12, C15, S04, S36). RNA-sequencing was performed to assess the transcriptional changes upon NKX2-1 KO comparing WT to KO clones.


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [LNCAP Bulk ATAC-seq]

summary: Castration-resistant prostate cancer (CRPC) is largely dependent on the androgen receptor (AR) for growth and often exhibits hyperactive PI3K signaling, most frequently due to PTEN loss. Therapeutic pressure from anti-AR therapies can induce trans-differentiation toward an AR-independent phenotype. Recently, different subtypes of AR-independent CRPC have been redefined, with the stem cell-like (SCL) subtype emerging as one of the most prevalent. Elucidation of the epigenetic mechanisms controlling the maintenance of these distinct CRPC cell states could pave the way for effective combinatorial therapies for CRPC. In this study, we identified a key role for the histone methyltransferase KMT2D in establishing the chromatin competence necessary for the recruitment of AR and FOXA1 transcription factors (TFs) that are essential for the AR transcriptional output in AR-dependent CRPC cell lines, patient derived organoids, and patient samples. Unexpectedly, KMT2D maintained the identity of the AR-low CRPC-SCL subtype and controlled activity of AP-1 TFs such as FOSL1, which acts as a master regulator of this subtype. Single cell transcriptomics and chromatin assays underscored the role of KMT2D in sustaining a mixed lineage cell state via AP-1 and FOXA1. The combined suppression of PI3K/AKT and KMT2D reduced cell proliferation in prostate cancer cells and patient-derived organoids in both CRPC-AR and CRPC-SCL subtypes. Altogether, these results unveil KMT2D as a major mediator of the epigenetic landscape in subtype-specific CRPC, contributing to tumor growth and therapeutic response.

overall_design: Bulk ATAC-Seq was performed in LNCAP AR-high prostate cancer cells treated with PI3K inhibitor, GDC0941

first: Xinyu

last: Guo


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [DU145 Bulk RNA-seq]

overall_design: Bulk RNA-Seq was performed in DU145 AR-neg prostate cancer cells with doxycycline-inducible knockdown of KMT2D


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [Monocytes_Ribo-seq]

city: Beijing

first: Xingxian

last: Liu

address: 30 Shuangqing Rd, Haidian District

institute: Tsinghua University

summary: Cytokine release syndrome (CRS) is a potentially life-threatening inflammatory condition. However, the defining features that distinguish it from self-resolving inflammation remain poorly understood. In this study, we identified monocyte/macrophage hyper-translation as a hallmark of CRS pathogenesis in patient samples. To uncover the molecular drivers of this phenomenon, a CRISPR screen followed by genetic validation pinpointed BCAP as a critical regulator of hyper-translation. Mechanistically, BCAP activated the RSK-EIF4B axis, fueling hyperactive translation in macrophages. Genetic ablation of RSK attenuated CRS-associated inflammation, and pharmacological inhibition of RSK alleviated CRS symptoms in a humanized mouse model. These findings establish hyper-translation as a key pathogenic feature of CRS and highlight protein translation as a druggable pathway, opening venues for therapeutic interventions of CRS and other inflammatory diseases.

overall_design: Ribo-seq and corresponding RNA-seq of KS (CRS model) stimulated human CD14-positive monocytes at 0h and 120h


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [BMDM_Ribo-seq]

overall_design: Ribo-seq and corresponding RNA-seq of LPS stimulated WT bone marrow derived macrophages (BMDM) at 0h, 6h and 24h


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [BMDM_RiboTag-seq]

overall_design: RiboTag-seq and corresponding RNA-seq of KS (CRS model) stimulated WT bone marrow derived macrophages (BMDM) at 0h , 24h and 72h


title: Latent MicroRNA Networks in Asthma Endotypes [HuGene-1_0]

city: New Haven

first: Jose

middle: Luis

last: Gomez

state: CT

address: 300 Cedar Street

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University

summary:
Transcriptome analysis of whole blood from subjects with asthma and controls
The presence or absence of type 2 inflammation (T2) biomarkers is used to identify T2-high and T2-low endotypes in the clinic. Despite the clinical relevance of these endotypes, the molecular mechanisms of T2-low asthma remain poorly understood. Specific microRNAs may regulate transcriptomic networks associated with asthma endotypes.

overall_design: Cross-sectional study of 88 participants with asthma stratified into T2-high and T2-low asthma by blood eosinophils or Fractional Exhaled Nitric Oxide (FeNO), combined with microRNA and mRNA of whole blood. DIABLO integrated omics of microRNA and mRNA profiles.

first: Maria

last: Ramirez

middle: P

last: Diaz

first: Ningya

last: Wang

first: Qing

first: Huan

first: Shannon

last: Kay

first: Jana

last: Zielonka

first: Gabriella

last: Wilson

first: Zuoheng

first: Xiting

last: Yan

first: Geoffrey

last: Chupp


title: Latent MicroRNA Networks in Asthma Endotypes [NS_H_miR_v3a]

last: Li


title: Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers [ChIP-Seq]

city: Boston

first: Mohamad Ali

last: Najia

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: Genes involved in the regulation of chromatin structure are frequently disrupted in cancer, contributing to an aberrant transcriptome and phenotypic plasticity. Yet, therapeutics targeting mutant forms of chromatin-modifying enzymes have yielded only modest clinical utility, underscoring the difficulty of targeting the epigenomic underpinnings of aberrant gene regulatory networks. Here, we sought to identify novel epigenetic vulnerabilities in diffuse large B-cell lymphoma (DLBCL). Through phenotypic screens and biochemical analysis, we demonstrated that inhibition of the H3K9 demethylases KDM4A and KDM4C elicits potent, subtype-agnostic cytotoxicity by antagonizing transcriptional networks associated with B-cell identity and epigenetically rewiring heterochromatin. KDM4 demethylases associated with the KRAB zinc finger ZNF587, and their enzymatic inhibition led to DNA replication stress and DNA damage-induced cGAS-STING activation. Broad surveys of transcriptional data from patients also revealed KDM4 family dysregulation in several other cancer types. To explore this potential therapeutic avenue, we performed high-throughput small molecule screens with H3K9me3 nucleosome substrates and identified novel KDM4 demethylase inhibitors. AI-guided protein-ligand binding predictions suggested diverse modes of action for various small molecule hits. Our findings underscore the relevance of targeting fundamental transcriptional and epigenetic mechanisms for anti-cancer therapy.

overall_design: ChIP-Seq for H3K27ac, H3K4me3, H3K9me2, and H3K9me3 in OCI-Ly1 cells treated with JIB-04 or DMSO

middle: T


title: Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers [RNA-seq]

overall_design: Transcriptional profiling via bulk RNA-Seq of OCI-Ly1 and TMD8 cells treated with JIB-04 or DMSO


title: Transcriptomic analysis of spinal cord in day 35 experimental autoimmune encephalomyelitis (EAE) model

city: Sacramento

first: Hyun Kyu

last: Kim

state: CA

address: 2425 Stockton Blvd

department: Neurology

institute: UCDAVIS

summary: Experimental autoimmune encephalomyelitis (EAE) is a widely used model for studying multiple sclerosis (MS), characterized by inflammation and demyelination in the central nervous system. This study investigates the transcriptional changes in the spinal cord of mice at day 35 post-induction of EAE. Bulk RNA sequencing was performed on spinal cord samples from three groups: (1) naïve mice, (2) mice treated with complete Freund’s adjuvant (CFA) and pertussis toxin (CFA control group), and (3) EAE-induced mice administered MOG peptide (amino acids 35–55) emulsified in CFA with pertussis toxin (MOG group). These findings provide insights into the spinal cord’s transcriptional response during EAE and advance our understanding of MS pathogenesis.

overall_design: Three-month-old C57BL/6 mice were received CFA and pertussis toxin (CFA control mice), or MOG peptide (35–55) emulsified in CFA and pertussis toxin to induce EAE. At day 35 post-induction, bulk RNA sequencing was performed from spinal cord of naïve mice, CFA control group and MOG group. Each group has 3 or 4 repeats.

first: Meina

last: Zhu

first: Yan

first: Fuzheng


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [BCAP_KO_BMDM_Ribo-seq]

first: Xingxian

overall_design: Ribo-seq and corresponding RNA-seq of KS (CRS model) stimulated WT and BCAP-deficient bone marrow derived macrophages (BMDM) at 0h and 24h


title: Nascent RNA m6A modification are involved in T cell activation gene signature under Hypoxia in CRPC-V16A

city: Shanghai

first: Yin

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

summary: In this study, we set out to identify m6A modified nascent transcription under Hypoxia in parallel with Normoxia by EU labeling coupled with MeRIP-seq. By comparing Hypoxia and Nomoxia, we identified 5,873 m6A sites specific under Hypoxia.

overall_design: We performed MeRIP-seq in CRPC-V16A cells under Hypoxia and Normoxia.

first: Yu-e


title: Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers


title: Syntaxin-6 mediated autophagy confers lenvatinib resistance in hepatocellular carcinoma

city: guangzhou

first: Zebing

last: Song

address: 250changgang road

institute: The Second Affiliated Hospital of Guangzhou Medical University

summary: Lenvatinib is the first-line therapy for inoperable HCC. However, intrinsic and acquired drug resistance occurs during the treatment period. Autophagy is an adaptive response that favors tumor survival under stress. In the present study, we aim to reveal the unknown autophagic engagement in lenvatinib resistance. Lenvatinib-resistant HCC cell lines and xenograft mouse HCC models were established to identify the key regulator of lenvatinib resistance in HCC. By in vitro functional restoration assays and autophagic flux detection, we demonstrated that the Syntaxin-6 (STX6) -mediated autophagy induced lenvatinib resistance of HCC cells. Mechanistically, Co-immunoprecipitation assay and mass spectrometry indicated that the interactions of STX6 with Beclin1, VTI1A, and VAMP3 facilitated autophagy, leading to the lenvatinib resistance. Additionally, STX6 enhanced the ability of proliferation, migration, and invasion of HCC in vitro and in vivo. Clinically, STX6 expression was significantly elevated in HCC tissues compared to it in para-tumor tissues. High STX6 expression predicted poor outcomes for patients following resection. Moreover, high expression of STX6 displayed low preventive efficacy of lenvatinib as a postoperative adjuvant treatment for HCC patients with a high risk of recurrence. Collectively, we identified that STX6-mediated autophagy was a pivotal determinant of lenvatinib resistance in HCC, providing a potential target to overcome lenvatinib resistance for HCC patients.

overall_design: To investigate the specific mechanism of STX6-induced lenvatinib resistance in hepatocellular carcinoma

first: Shaoqiang


title: scRNA-seq, ULAC-seq and RNA-seq across mouse hematopoietic hierarchy

first: Feng

last: Huang


title: Reduced TBX5 dosage causes human atrial disease by undermining developmental gene regulation of atrial cardiomyocyte identity [scATAC-seq]

city: San Francisco

first: Benoit

last: Bruneau

address: 1650 Owens St

institute: Gladstone Institutes

summary: In a TBX5-linked human cellular model of atrial disease, we examined the gene networks controlled by TBX5 during human atrial differentiation using single-cell RNA and ATAC sequencing.

overall_design: Wildtype, TBX5 heterozygous and homozygous mutant iPSCs were differentiated to atrial cardiomyocytes. At day 20 of differentiation, cells were harvested for single-cell ATAC sequencing. Two replicates per genotype per timepoint were harvested. Wildtype iPSCs were also differentiated to ventricular cardiomyocytes and cells were harvested at day 23 for single-cell ATAC sequencing.

first: Kavitha

last: Rao

first: Irfan

last: Kathiriya


title: Positive feedback regulation of E.coli metabolism by HU acetylation mediated by HDAH

city: Tianjin

first: Xinyun

last: Zhang

address: No22.Qixiangtai Rd.,Heping Dist

institute: Tianjin Medical University

summary: Lysine-acetylation (Kac) is a conserved protein post-translational modification (PTM) that plays a key role in regulating protein function in many biological processes such as gene transcription, nutrient metabolism and signal transduction. More and more acylation regulatory enzymes have been discovered in prokaryotes. Here we demonstrate HDAH in Escherichia coli as a potential Kac regulatory enzyme and illustrate the effects of HDAH on bacterial metabolism and growth by mediating Kac of histone-like protein Hu. By using a quantitative proteomic method stable isotope labeling by amino acids in cell culture (SILAC) to screen HDAH-regulated endogenous substrates, we found HDAH can catalyze the removal of HU lysine acetylation marks in vitro and in the cell through a series of biochemical experiments. Next, we used transcriptomic analysis in Escherichia coli and found that downstream genes regulated by HU were mainly related to metabolism. We further demonstrated that the acetylation of HU protein promotes the growth and migration of Escherichia coli by regulating its glucose metabolism. In summary, this study identified a new regulatory enzyme system in bacteria, analyzed the endogenous Kac substrate protein of HDAH, and elucidated the positive feedback regulation molecular mechanism of HU Kac-mediated glycometabolic reprogramming and bacterial proliferation.

overall_design: To investigate the effects of HDAH overexpression and HU knockout/mutation on gene expression in E. coli, we constructed BL21  (DE3) strains expressing HDAH using the pET-28a vector, as well as MG1655 strains expressing HU-K22Q and HU-ΔA for RNA-seq analysis.  The samples included E. coli strains overexpressing HDAH, control strains transformed with the empty pET-28a vector, and pET-28a-HU knockout complemented MG1655 strains.

first: Chen

last: Chen

first: Jianji


title: A Novel Foodstuff Restored Aberrant Dna Methylation Patterns In Western Diet Induced-MASLD Mice

city: Zapopan

first: Rebeca

last: Rosas Campos

state: Jalisco

address: Av. Gral Ramón Corona No 2514

department: EMCS

country: Mexico

institute: Tecnologico de Monterrey

type: Methylation profiling by genome tiling array

summary: Background: Aberrant DNA methylation patterns play an important role in the development of Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) development. Diets rich in fiber and antioxidants could potentially reverse these patterns. We have previously demonstrated that supplementation with AncestryR, a mixture of Mexican foods (nopal, cocoa, and crickets), exerts a curative effect on MASLD; however, the impact of Ancestry on DNA methylation remains unclear.

overall_design: Methods: Twenty-four male C57BL/6J mice were allocated into three groups: 1) control group on a normal diet (ND), 2) HF/FS group consuming a Western diet (high in fat and fructose/sucrose), and 3) AncestryR group, which followed a HF/FS diet for 10 weeks, and then switched to an HF/FS diet supplemented with AncestryR for an additional 8 weeks. DNA methylome analysis was performed using the Mouse Methylation BeadChip from liver tissues.

last: Rosas-Campos

first: Juan

last: Armendariz-Borunda


title: RNA-seq analysis identifies the impact of different organic components of fine particulate matter (PM2.5) on human nasal fibroblasts

first: Jiayao

last: Zhou

address: No. 600,  Yishan Road

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: In this study, high-throughput sequencing was used to analyze the effects of polar and non-polar organic components of PM2.5 on gene expression profiles in human nasal fibroblasts.

overall_design: Human nasal fibroblasts were treated with polar and non-polar organic components of PM2.5, and DMSO intervention was used as control. Gene expression profiles were analyzed by RNA-seq.

first: Weitian


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [RSK1_KO_RNA-seq]

last: Liu

overall_design: RNA-seq of KS (CRS model) stimulated WT and RSK1 KO bone marrow derived macrophages (BMDM) at 0h and 24h


title: HT-29 and SW620

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

institute: University Gent

overall_design: Refer to individual Series


title: Single nucleus RNA-seq of late embryonic and early postnatal mouse kidney.

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

summary: We are interested in changes to cell type composition of the developing kidney and so performed single nucleus RNA sequencing of whole kidney at E18.5 and P3.

overall_design: Nuclei were obtained from digestion of whole kidneys and analyzed with snRNA-seq.

first: Alexandria N.

last: Fusco

first: Jane N.

last: Warshaw

first: Denise K.

last: Marciano

first: Thomas J.


title: Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [CRISPR_screen]

first: Xingxian

overall_design: CRISPR screen of KS (CRS model) stimulated Cas9 transgenic marrow derived macrophages (BMDM) at 72h and isolation of IL-6 low population (top 5%) for sgRNA library construction and sequencing.


title: The role of Langerhans cells in the oral mucosa in oral innervation

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: Oral Langerhans cells (LCs) are well recognized for their immunological roles, but their involvement in other physiological processes remains poorly understood. This study identifies a novel function of oral LCs in regulating tongue epithelial innervation. Postnatal LC development coincides with the establishment of local innervation, and LC depletion impairs innervation and alters nociceptive responses, underscoring their neuroimmune function. This function is driven by LC-derived IL-1β, which stimulates basal epithelial cells to produce nerve growth factor (NGF), thereby promoting sensory nerve growth. Transcriptomic analyses revealed neuronal- related pathways enriched in LCs. Aging reduces LC frequency, NGF expression, and epithelial innervation, linking neuroimmune regulation to epithelial aging. While LC frequencies in the tongue remain unaffected in germ-free mice, the microbiota is essential for optimal LC function and NGF production. These findings expand our understanding of oral LCs, revealing their pivotal role in epithelial innervation beyond immune surveillance.

overall_design: Langerin-DTR mice were administered DT or PBS twice weekly from 2 weeks old to adulthood. Mice were sacrificed and tongue epithelium was excised and RNA was extracted using Qiagen RNAeasy mini kit.

first: Avi-Hai

last: Hovav

first: Yasmin

last: Netanely