title: Heightened DOT1L-AF10 enriches H3K79me3 to promote pro-atherogenic inflammatory endothelial phenotype through NF-κB p65

city: Pilani

first: Syamantak

last: Majumder

state: Rajasthan

address: Vidhya Vihar, 1264 MALVIYA BHAVAN

department: Biological Sciences

country: India

institute: BITS Pilani, Pilani Campus

summary: DOT1L-catalyzed H3K79 methylation is a hallmark of actively transcribed genes and has been extensively studied in developmental and disease contexts. While DOT1L inhibition has emerged as a promising therapeutic strategy in cancer, its role in pro-atherogenic endothelial inflammation remains unclear. To investigate this, we utilized an in vivo partial carotid artery ligation model and observed increased DOT1L expression and H3K79me3 level. Consistently, in vitro studies employing a 3D-printed human coronary artery model and TNF-α stimulation corroborated these results, showing elevated DOT1L expression and H3K79me3 deposition, while levels of H3K79me and me2 remained unchanged. Further analyses identified key DotCom complex components, AF10 and AF9 (upregulated) and AF17 (downregulated), as contributors to the enhanced H3K79me3 landscape. CUT&RUN sequencing showed prominent H3K79me3 enrichment at the RELA (NF-κB p65) promoter, corresponding with increased NF-κB p65 expression and activation. Notably, inhibition/knockdown of the methyltransferase DOT1L or overexpression of the demethylase FBXL10 significantly reduced H3K79me3 levels, thereby suppressing NF-κB p65 expression and attenuating endothelial inflammation, independent of canonical NF-κB p65 activation. These findings establish DOT1L-mediated H3K79me3 as a crucial epigenetic regulator of endothelial inflammation, highlighting a potential therapeutic avenue for mitigating NF-κB p65-driven pro-atherogenic endothelial dysfunction.

overall_design: CUT&RUN-seq of histone modification H3K79me3  in untreated (control) and 4 h TNF-α treated HUVEC

first: Yash

last: Katakia

first: Ritobrata

last: Bhattacharyya

first: Sushmitha

last: Duddu

first: Nivedha

last: Suresh

first: Nehal

last: Gupta

first: Suchit

last: Chebolu

first: Soumitra

last: Ghosh

first: Praphulla

last: Shukla


title: Mouse digit fibroblast AAV gene delivery platform regulates regenerative outcome

status: Public on Dec 16 2025

city: Boston

first: Jessica

middle: A

last: Lehoczky

state: MA

address: 60 Fenwood Rd.

department: Orthopedic Surgery

country: USA

institute: Brigham and Women's Hospital

type: Expression profiling by high throughput sequencing

summary: The mouse digit tip robustly regenerates post-amputation, a process facilitated by the formation of a blastema. Fibroblasts constitute most of this structure, with specific subtypes contributing significantly more to the blastema. However, it remains unclear whether these fibroblast subpopulations and their associated genes are unique to regeneration or part of a broader wound-healing response. In this study, we performed single-cell RNA sequencing of non-regenerating digits to computationally identify fibroblast subpopulations and genes associated with regeneration and fibrosis. Furthermore, we developed a robust adeno-associated virus (AAV)-based gene delivery system to functionally assess the impact of newly identified candidate pro-fibrotic and pro-regenerative genes on wound healing outcomes.

overall_design: Cohorts of adult wildtype FVB/NJ mice underwent P2 mid-digital (non-regenerative) digit amputation; 12, 17, and 28 days post-amputation, fibrosing digit tissues were collected and used for single cell RNA sequencing and analysis. An unamputated, homeostatic mid-digital sample was also collected.


title: Gut resident T-bet expressing Tr1 cells driven by dietary signals dominate the small intestinal immune landscape IV

city: San Diego

first: Eduardo

last: Ansaldo

address: 15550 Torrey Pines Rd

department: IMM

institute: Scripps Research

summary: Intestinal immunity provides defense against enteric pathogens, mediates symbiotic relationships with the resident microbiota, and provides tolerance to food antigens, safeguarding critical nutrient absorption and barrier functions of this mucosal tissue. Despite the large abundance of tissue resident activated T cells, how T cell immunity contributes to these various roles remains poorly understood. Here we describe a previously uncharacterized dominant T-bet expressing Tr1 T cell population in the small intestine lamina propria present at homeostasis. Importantly, this IL-10 secreting CD4^+^T-bet^+^ T cell population appears in the small intestine at the time of weaning independently of the resident microbiota, presenting similar accumulation, functional capacity, and TCR repertoire in germ free conditions. Instead, small intestinal T-bet^+^ Tr1 T cells respond to dietary signals driving their accumulation, suppressive program, and clonal selection; and depend on cDC1s, IL-27 signaling, and T-bet, but not IL-12. Altogether, this work uncovers a previously unappreciated dominant player in homeostatic small intestinal immunity with the potential to play critical suppressive roles in oral tolerance to dietary antigens, raising important implications for the understanding of food allergy and celiac disease.

overall_design: SILP CD4^+^ T cells (Live, CD45+CD90.2+, TCRb+, CD4+) from SPF or GF T-bet-ZsGreen mice that received aCD3 or isotype as described in the corresponding methods section were sorted using a Sony MA900 sorter. RNA was extracted using the Qiagen miRNeasy kit, and sequencing library was prepared using Tecan SoLo total RNA kit for mouse according to manufacturer's instructions. Libraries were sequenced as 1 x 150bp reads on a Illumina NextSeq 2000 using the P3 200 cycle kit.\*

first: Eduard

first: Daniel

last: Yong

first: Nathan

last: Carrillo

first: Taryn

last: McFadden

first: Mahnoor

last: Abid

first: Dan

last: Corral

first: Claudia

last: Rivera

first: Taylor

last: Farley

first: Nicolas

last: Bouladoux

first: Inta

last: Gribonika

first: Yasmine

last: Belkaid


title: Gene expression profile Predictor on chemical Structures (GPS): Deep Learning-based platform to screen and design novel therapeutics

city: Grand Rapids

first: Bin

last: Chen

state: Michigan

address: 400 Monroe Ave NW

department: Department of Pediatrics and Human Development

institute: MICHIGAN STATE UNIVERSITY

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

overall_design: Refer to individual Series


title: Whole-genome bisulfite sequencing of whole blood cells in dog lymphomas cases

city: Fujimino

first: Miyuki

last: Nakamura

state: Saitama

country: Japan

institute: KDDI research Inc

type: Methylation profiling by high throughput sequencing

summary: DNA methylation patterns reflect the status of individual tissues in mammals, including factors such as cell composition, age, and local environment. These patterns can be leveraged to predict an individual's health status. The aim of this experiment is to discover the signature of lymphoma using DNA methylation from blood samples of dogs. We compared whole-genome DNA methylation data from individuals diagnosed with lymphoma to that from a control group. After adjusting for differences in age and breed, we detected differentially methylated regions.

overall_design: Whole-genome bisulfite sequencing was performed with whole blood obtained from twenty individual dogs diagnosed with lymphoma. The breeds of subjects were Poodle (Toy,Standard), Shiba, Dachshund (Miniature), Bichon Frise, Boston Terrier, Cavalier King Charles Spaniel, Chihuahua, French Bulldog, Golden Retriever, Norfolk Terrier, Papillon, Pug, Shetland Sheepdog, and Yorkshire Terrier.


title: Gut resident T-bet expressing Tr1 cells driven by dietary signals dominate the small intestinal immune landscape III

overall_design: SILP CD4^+^T-bet^+^ T cells (Live, CD45+CD90.2+, TCRb+, CD4+, T-bet-ZsGreen+) from GF T-bet-ZsGreen mice raised on casein, amino acid, or regular chow diet were sorted from samples labeled with TotalSeqC hashtags antibodies (Biolegend) using a Sony MA900 sorter. Sorted cells were pooled during sorting and 40000 cells per lane (total of 4 lanes) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets. The gene expression (GEX), hashtag oligonucleotide (HTO) and VDJ (TCR) sequencing libraries were prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq1000 platform (NextSeq 1000/2000 P2 reagents)


title: Feed-forward regulatory loops by NR5A2 ensure robust gene activation during pre-implantation development [ATAC-seq]

city: Martinsried

first: Siwat

last: Ruangroengkulrith

state: Bavaria

address: Am Klopferspitz 18

department: Totipotency

country: Germany

institute: Max Planck Institute of Biochemistry

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The pioneer transcription factor NR5A2 plays multiple roles in regulating zygotic genome activation and expression of lineage-determining factor during mouse pre-implantation development. However, how NR5A2 differentially regulates transcriptional networks at distinct developmental stages remains unknown. Here, we demonstrate the dynamics of chromatin binding profiles of NR5A2 from the 2-cell to morula stage, which corresponds to totipotency-to-pluripotency transition. Our NR5A2 CUT&Tag analysis identifies lineage-determining factor KLF and GATA families as co-regulators for NR5A2. We find that KLF5 cooperates with NR5A2 to enhance H3K27ac deposition, and NR5A2 predominantly promotes chromatin accessibility. NR5A2 regulates Xist expression either directly or indirectly through its role in up-regulating GATA factor expression. In vitro assays reveal that NR5A2 co-binds to nucleosomes with KLF5 or GATA6, suggesting that these pioneer transcription factors can simultaneously binds to the chromatin. Our findings highlight the role of NR5A2 in ensuring robust gene activation in pre-implantation development through feed-forward regulatory loops with lineage-determining transcription factors.

overall_design: Omni-ATAC-seq of preimplantation embryos and Nr5a2 and Klf5 knockdown 8-cell stage embryos.

first: Wataru

last: Kobayashi

first: Eda

middle: N

last: Arslantas

first: Adarsh

last: Mohanan

first: Kikuë

last: Tachibana


title: Feed-forward regulatory loops by NR5A2 ensure robust gene activation during pre-implantation development [CUT&Tag, CUT&RUN, TIP-seq]

overall_design: CUT&Tag of transcription factors (Nr5a2, Klf5, and Gata6 in mouse preimplantation embryo)


title: Feed-forward regulatory loops by NR5A2 ensure robust gene activation during pre-implantation development [RNA-seq]

overall_design: RNA-seq profiling of Nr5a2 and Klf5 knockdown 8-cell stage embryos.


title: Comparative Analysis of microRNA Expression in Serum and Plasma in Patients Screened for BRCA1 or BRCA2 Mutations - dataset 1

city: Lodz

first: Urszula

last: Smyczynska

address: 15, Mazowiecka Street

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

type: Non-coding RNA profiling by high throughput sequencing

summary: This dataset was created in order to evaluate the concordance of miRNA expression between serum and plasma in humans. miRNA expression was quantified in both biological materials using sequencing. Differential expression and correlations analysis were used to evaluate similarities and differences between miRNAs abundance in plasma and serum. Concurrently, miRNA quantification in the subset of these samples was performed by qPCR, the results of which belong to the separate submission to GEO. Generation of this dataset was supported by The Gray Foundation grant “Circulating microRNAs for assessment of risk beyond the BRCA genes and early detection of breast cancer in high-risk families” awarded to Dipanjan Chowdhury and Polish National Research Center grant OPUS “Predictive Potential of Circulating MicroRNA Biomarkers in Patients with High Familial or Genetic Risk of Cancer” (2023/49/B/NZ5/03835) awarded to Wojciech Fendler.

overall_design: The experiment was performed in 30 pairs of human serum and plasma samples collected at the same time. Each sample title indicates the patient, so pairs of samples are identified. All samples came from healthy women, but some of them harbored germinal BRCA1/2 mutations as this experiment is a part of a larger study about changes in miRnome induced by BRCA mutations or the presence of BRCA-related cancers (especially ovarian and breast cancer).

first: Wojciech

last: Fendler

first: Dipanjan

last: Chowdhury

first: Aleksander

last: Rycerz


title: Erucamide regulates retinal neurovascular crosstalk

city: La Jolla

first: Guoqin

last: Wei

state: CA

address: 10550 North Torrey Pines Rd, MB216

institute: The Scripps research institute

summary: Neurovasculoglial crosstalk is critical in establishing and maintaining a functional neurovascular unit. Breakdown in the unit is central to many neurodegenerative disorders of the CNS of which the retina is a component. A growing literature indicated that primary fatty acid amides (PFAMs) can regulate this crosstalk between vasculature and neuronal tissues. In this study we describe a central role for erucamide, a 22:1 mono-unsaturated omega-9 fatty acid amide, in degenerating retinal tissues. Using high-resolution global mass spectrometry-based metabolomics, we cataloged metabolites in murine models of retinal degeneration and show that while PFAMs, in general, are highly dysregulated, erucamide is the one most significantly diminished during photoreceptor atrophy. Using rodent models of retinal degeneration and novel organosilane-modified porous silicon nanoparticles (pSiNPs) for the in vivo delivery of erucamide, we demonstrate that erucamide activates CD11b+ myeloid cells, leading to the upregulation of angiogenic and neurotrophic cytokines that stabilize retinal degeneration. We identified TMEM19 as a novel binding protein for erucamide that is crucial for human iPSC-derived macrophage precursor cells activation and subsequent neurotrophic and angiogenic factor production. These findings reveal a previously unknown PFAM pathway that is modulated during retinal degenerative diseases, demonstrating that erucamide or functional analogues and their action through TMEM19 may be useful as a therapeutic alternative to neuroprotective and stem cell-based approaches for the treatment of retinal degenerative diseases.

overall_design: To investigate the function of erucamide in myeloid cells and signaling pathways mediated by erucamide through TMEM19, we conducted a bulk RNA sequencing experiment. iPSC-MPCs cells were treated with a combination of erucamide (Eru-C18-pSi) or not (C18-pSi), with (using scrambled siRNA) or without (using siTMEM19) TMEM19. Differential expression analysis was performed to compare the treatment combinations.

first: Shreyosree

last: Chatterjee

first: Qinglin

last: Yang

first: Daisuke

last: Ogasawara

first: Sarah

last: Giles

first: Peter

last: Westenskow

first: Junhua

last: Wang

first: Ruhan

last: Fan

first: Helena

last: Pham

first: Edith

last: Aguilar

first: Jacob

last: Robinson

first: Ayumi

last: Usui-Ouchi

first: Roberto

last: Bonelli

first: Kevin

last: Eade

first: Gary

last: Siuzdak

first: Benjamin

last: Cravatt

first: Michael

last: Sailor

first: Dale

last: Boger

first: Martin

last: Friedlander


title: Transcriptomics-based Screening and Novel compound for Hepatocellular Carcinoma

first: Bin

last: Chen

summary: HCC is the sixth most common cancer and the third leading cause of cancer-related death worldwide. It has a high mortality rate, yet lacks effective treatment options. We used our Gene expression profile Predictor on chemical Structures (GPS) platform to discover novel and selective anti-HCC drug candidates. GPS is a deep learning-based drug discovery system for the screening of a large compound library and de novo designing of novel compounds that can reverse transcriptional phenotype. To achieve this, a previously defined HCC signature was queried against the GPS-generated transcriptomic profiles for compounds in the ZINC library with almost seven million drug-like compounds.  Top-ranked compounds were nominated for testing their cytotoxicities in HCC cell lines in vitro, and their efficacy in vivo.

overall_design: Here we include samples and processed data (HCC_CDX_TPM.csv,HCC_CDX_RAWCOUNT.csv) for Huh7 xenograft samples treated with our novel compound MSU45302 or DMSO. In addition, we also provide raw and processed data (HUH_4852_TPM.csv,HUH_4852_RAWCOUNT.csv) for Huh7 cellline treated with compound PB56874852 (two concentrations 4μM and 10μM) and DMSO. We designed MSU45302 by substituting specific structural components of PB56874852, optimizing its properties for enhanced efficacy.

first: Jing

last: Xing

first: Mingdian

last: Tan

first: Shreya

last: Paithankar

first: Mei-Sze

last: Chua

first: Rama

last: Shankar

first: Dmitry

last: Leshchiner


title: Engineered Enucleated Mesenchymal Stem Cells Regulating Immune Microenvironment and Promoting Wound Healing

city: Hangzhou

first: Zhengtai

state: zhejiang

address: 88 Jie Fang Road, Hangzhou

country: China

institute: The Second Affiliated Hospital, Medical School, Zhejiang University

summary: We conducted a transcriptomic analysis to evaluate DEK expression levels in the uninjured skin of healthy mice, wound tissue of healthy mice, and diabetic mice. Our findings revealed a significant upregulation of DEK in diabetic mouse wounds, with Gene Ontology (GO) analysis indicating enrichment in pathways related to neutrophil migration. Moreover, principal component analysis (PCA) results indicated that there are significant differences in gene expression between these two groups (Fig. 2D). Differential expression gene (DEG) analysis revealed 508 downregulated and 359 upregulated genes in the diabetic group compared with the health group. These downregulated genes are associated with skin, chondrocyte, and cartilage development, suggesting that the wound repair process is impaired in diabetic mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for skin tissue from uninjured skin of healthy mice, wound tissue of healthy mice, and diabetic mice.

first: Hanxaio

last: Sun

first: Yan

last: He

first: Kai

last: Ye


title: Nuclear exosome targeting complex safeguards hematopoietic stem cell self-renewal and genomic integrity through resolving R loops

first: Aiwei

last: Wu

state: Zhejiang

address: 2318 Yuhangtang Road

department: School of Basic Medical Sciences

institute: Hangzhou Normal University

summary: Pervasive transcription of the mammalian genome produces a vast repertoire of non-functional nascent transcripts, generating R loops and R-loop-induced DNA breaks. Such a coupling between continual transcription and a burst of R-loop formation, however, presents a challenge for hematopoietic stem cells (HSCs) to maintain their genome integrity. Here, we show that the nuclear exosome targeting (NEXT) complex, an RNA adaptor that targets non-functional nascent transcripts to the RNA exosome for decay, plays a pivotal role in overcoming this challenge. Hematopoietic-specific deletion of ZCCHC8, a core subunit of NEXT, not only leads to impaired HSC self-renewal but also causes elevated DNA lesions and upregulated DNA repair pathways in HSCs due to accumulated R loops. Moreover, dysregulation of ZCCHC8 occurs frequently in diffuse large B cell lymphoma (DLBCL) and is associated with poor clinical outcomes. Collectively, our findings highlight NEXT as a novel protector of HSCs and position it as a potential therapeutic target for DLBCL.

overall_design: RNA-seq experiment was performed to analyze the effects of ZCCHC8 depletion on transcriptome in LT-HSCs.

first: Yinghao

last: Pan

first: Hongna

last: Zuo

first: Hu

last: Wang


title: Transcriptomics-based Screening of Repurposing Drug for Idiopathic Pulmonary Fibrosis

summary: IPF is a pathological condition resulting from injury to the lungs and an ensuing fibrotic response leading to thickening of the alveolar walls and the obliteration of the alveolar space. The etiology of IPF and the role of the microenvironment in disease progression are largely unknown. We first used the repurposing pipeline to explore disease biology for the identification of relevant cell populations and then applied the screening pipeline to discover novel compounds. Using various types of RNAseq data from multiple datasets, we constructed signatures that capture different aspects of IPF biology, such as those related to cell type-specific transcriptional changes and those associated with disease development in animal models. We predicted and tested drugs targeting various IPF signatures and identified Pyrithyldione as our top candidate for reduction of fibrosis in the human precision-cut lung slices PCLS model and RNAseq was conducted on treated and untreated paired adjacent patient samples to determine its the effects on gene expression.

overall_design: IPF lung explant samples were obtained from 6 patients, undergoing lung transplantation at Richard Devos Heart and Lung Transplantation Center, Corewell Health Butterworth Hospital, Grand Rapids, Michigan. Pathologic assessment confirmed the findings of advanced usual interstitial pneumonia (UIP) in the IPF subjects. All protocols were performed in compliance with relevant ethical regulations approved by local Institutional Review Board (IRB #: CHW 2017-198); Written informed consent was obtained from all patients who participated in the current study. Differential gene expression analysis of RNA-seq data for IPF Patients  was performed between samples treated with  a. Pyrithyldione or  b. DMSO.

first: Katie

last: Uhl

first: Li

last: Huang

first: Mohamed

last: Abdelgied

first: Reda

last: Girgis

first: Xiaopeng

last: Li


title: Single-cell screens identify ADAM12 as a fibroblast checkpoint impeding anti-tumor immunity - scRNA-seq of murine KPC models

city: Beijing

first: Qile

last: Guo

state: Beijing

address: Yiheyuan Road

department: BIOPIC

institute: Peking University

summary: Clinical trials targeting cancer-associated fibroblasts (CAFs)—crucial pro-tumoral factors in cancer—have almost all failed. This may be ascribed to their intrinsic functional plasticity and the opaque regulatory circuits underlying their heterogeneous phenotypes within tumors. We address these by developing a systematic screening approach for patient-derived fibroblasts using complementary CRISPR interference (CRISPRi) and activation (CRISPRa)-based Perturb-seq . An anti-tumoral interferon (IFN)-I response-associated program is identified as the primary antagonism axis counteracting TGFβ-driven pro-tumoral myofibroblast activation. ADAM12 emerges as a molecular checkpoint mediating this relationship. Its ablation elicits IFN-I responsive programs, reconfigures myofibroblast population structures into progenitor-like states, revitalizes T cell-based immune responses, and induces tumor rejection across various murine models. Further combined with human genomics data analysis, our findings position ADAM12 as a potential target for fibroblasts, paving the way for actionable therapeutic interventions.

overall_design: scRNA-seq of samples from Adam12 pCKO and control murine KPC models.


title: Single-cell screens identify ADAM12 as a fibroblast checkpoint impeding anti-tumor immunity


title: Single-cell screens identify ADAM12 as a fibroblast checkpoint impeding anti-tumor immunity - scRNA-seq of co-injection murine models

overall_design: scRNA-seq of samples from C57BL/6 murine models which were co-injected with MC38 cells and ex vivo cultured fibroblasts,either control Rosa26 (Ctrl) or Adam12 knockout (sgAdam12).


title: Single-cell screens identify ADAM12 as a fibroblast checkpoint impeding anti-tumor immunity - RNA-seq of C57BL/6 murine models

overall_design: RNA-seq of different tissues from Adam12 pCKO and control C57BL/6 murine models.


title: Single-cell screens identify ADAM12 as a fibroblast checkpoint impeding anti-tumor immunity  - RNA-seq of B16F10 lung melanoma murine models

overall_design: RNA-seq of lung fibroblasts and endothelial cells from Adam12 pCKO and control B16F10 lung melanoma murine models.


title: Comparative Analysis of microRNA Expression in Serum and Plasma in Patients Screened for BRCA1 or BRCA2 Mutations - dataset 2

first: Urszula

last: Smyczynska

summary: This dataset contains serum miRNA expression of 94 healthy women, among which 56 harbored germline BRCA1 or BRCA2 mutations. MicroRNA abundance was quantified with sequencing and qPCR, the latter being the subject of separate GEO submission. Data was analyzed with the aim of assessing concordance between two miRNA assays and the possibility of translating miRNA biomarkers from sequencing to qPCR panel. Generation of this dataset was supported by The Gray Foundation grant “Circulating microRNAs for assessment of risk beyond the BRCA genes and early detection of breast cancer in high-risk families” awarded to Dipanjan Chowdhury and Polish National Research Center grant OPUS “Predictive Potential of Circulating MicroRNA Biomarkers in Patients with High Familial or Genetic Risk of Cancer” (2023/49/B/NZ5/03835) awarded to Wojciech Fendler.

overall_design: The experiment was performed in 94 samples of human serum. All samples came from healthy women, but 56 of them were carriers of germinal BRCA1/2 mutations as this experiment is a part of a larger study about changes in miRnome induced by BRCA mutations or the presence of BRCA-related cancers (especially ovarian and breast cancer). In this technical comparison between miRNA quantification methods we included only cancer-free individuals.

first: Wojciech

last: Fendler

first: Dipanjan

last: Chowdhury

first: Aleksander

last: Rycerz


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [snRNA-seq]

city: Yuseong-gu, Daejeon-si

first: Taejun

last: Seol

address: 291, Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology (KAIST)

summary: The transcriptional coregulators YAP and TAZ control tissue homeostasis as downstream effectors of the Hippo signaling pathway. The molecular mechanisms by which they regulate cell differentiation or dedifferentiation have remained unclear, however. Here we reveal how YAP/TAZ regulates the transcription and genomic activity of the adipocyte lineage-specification factor PPARγ at the chromatin level. TAZ binds to the Pparg2 genomic region and to PPARγ target gene enhancers, thereby inducing chromatin reprogramming and transcriptional repression. Binding to TEAD transcription factors is essential for this repressive action of TAZ, but direct protein interaction with PPARγ via the WW domain of TAZ is not. Single-nucleus genomic analyses of mouse adipose tissue revealed that YAP/TAZ hyperactivation drives extensive epigenetic changes and the dedifferentiation of adipocytes. Collectively, our findings indicate that YAP/TAZ determine adipocyte fate by modulating the expression of a key transcription factor and the enhancer landscape of its target genes.

overall_design: single nucleus RNA-seq data obtained from ingunal white adipose of Lats1/2-floxed (Control) or Lats1/2-floxed; Adipoq-Cre (LAKO) mice

first: Ju-Gyeong

last: Kang

first: Dae-Sik

last: Lim


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [ChIP-seq]

overall_design: ChIP-seq data obtained from C3H10T1/2 cell during adipogenic cocktail treatment.


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [snATAC-seq]

overall_design: single nucleus ATAC-seq data obtained from ingunal white adipose of Lats1/2-floxed (Control) or Lats1/2-floxed; Adipoq-Cre (LAKO) mice


title: Targeting serotonin-driven histone serotonylation suppresses lineage plasticity and progression of NEPC

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

summary: Neuroendocrine prostate cancer (NEPC) is an aggressive, therapy-resistant subtype of prostate cancer characterized by lineage plasticity. While metabolic and signaling molecules are increasingly recognized as modulators of tumor progression, their role in cell fate transition remains unclear. NEPC tumors produce and accumulate serotonin (5-HT), a neurotransmitter that regulates diverse physiological processes. Here, we identify a tumor-intrinsic 5-HT axis as a key driver of NEPC lineage commitment and progression. NEPC endogenously synthesize serotonin via aromatic L-amino acid decarboxylase (DDC) and reuptake through the transporter SLC6A4, independent of serotonin receptor activity. Mechanistically, high level of intracellular 5-HT promotes neuroendocrine differentiation and suppresses androgen receptor (AR) signaling through histone serotonylation at H3K4me3Q5. This epigenetic modification reconfigures the H3K4me3 chromatin landscape and sustains NEPC-specific transcriptional programs. Pharmacological inhibition of 5-HT synthesis using the FDA-approved DDC inhibitor carbidopa significantly impairs tumor growth and prolongs survival in both genetically engineered and patient-derived xenograft models, highlighting histone serotonylation as a druggable vulnerability in NEPC.

overall_design:
RNA-seq profiling was performed on PC3 cells overexpressing DDC, SLC6A4, or an empty vector.
ChIP-seq was performed for H3K4me3, H3K4me3Q5ser, and input controls in PC3 cells overexpressing DDC, SLC6A4, or an empty vector.
CUT&Tag was performed in human prostate cancer cells using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903), followed by paired-end sequencing on Novaseq X. Raw sequencing reads were processed using FastQC for quality control and aligned to the human reference genome (GRCh38.release108) using Bowtie2(50). PCR duplicates have been removed. Peak calling was performed using MACS2(51), and annotation of binding sites was conducted using HOMER and in-house scripts.

first: Yiyi

last: Ji

first: Lei

last: Chen

first: Jiangbo

last: Wei


title: Comprehensive transcriptome analysis of skeletal muscle in the NADS knockout mice.

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

summary: Nicotinamide adenine dinucleotide (NAD+) is a pivotal molecule involved in various biological processes, including energy production, protein post-translational modification, DNA repair, calcium mobilization, and 5’-capping of mRNA. Accumulating evidence has revealed that NAD+ declines with age by disturbing the balance between its synthesis and degradation. Decreased NAD+ levels result in deterioration of physiological functions in multiple tissues, including the liver, muscle, kidney, and brain. Contrarily, the repletion of NAD+ levels by supplementation of NAD+ precursors have beneficial effects on lifespan, physiological aging, and aging-associated diseases. However, it is unknown whether declined NAD+ levels in young age affect aging processes. Therefore, in this study, to better understand the effect of NAD+ levels on the aging processes, we performed the RNA-sequencing using skeletal muscle samples from young and old wild-type and NAD synthetase (NADS)-deficient mice.

overall_design: mRNA profiles of  skeletal muscles were generated by RNA sequencing using the Illumina NovaSeq 6000  (Illumina).

first: Mariam

last: Karim

first: Takashi

last: Nakagawa


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [CUT&Tag]

overall_design: CUT&Tag data obtained from ingunal white adipose of Lats1/2-floxed (Control) or Lats1/2-floxed; Adipoq-Cre (LAKO) mice


title: PKM2/STAT1 pathway governs naïve B cell fate in germinal center formation within Peyer’s patches and gut mucosal immunity

city: Chengdu

first: Li

last: Zeng

state: China

address: Guoxuexiang 37, West China Hospital, Chengdu, Sichuan.

institute: West China Hospital, Sichuan University

summary: This study investigates the effects of high-protein diets on intestinal B cell development and their role in Crohn’s disease (CD) pathogenesis. Our results demonstrate that a high-protein diet (HPD) combined with low-dose dextran sulfate sodium (DSS) effectively models CD in juvenile mice, leading to disrupted B cell development in Peyer’s patches (PPs). This is characterized by a reduction in germinal center (GC) B cells and an increase in plasma cells in PPs, accompanied by downregulation of the PKM2/STAT1 signaling pathway in B cells, as validated through single-cell RNA sequencing (scRNA-seq), BCR sequencing (scBCR-seq) and flow cytometry.

overall_design: Juvenile (3 weeks old) and adult (11 weeks old) male C57BL/6J mice were were randomly assigned to either the colitis group or control group. In the colitis group, mice were fed diets with protein levels of 14% (low protein), 20% (normal protein), 30% (moderately high protein), or 40% (high protein) for one week of adaptive feeding, followed by three cycles of low-dose DSS-induced injury. Control mice were fed either a 20% or 40% protein diet without DSS exposure, receiving normal drinking water throughout. After three cycles of interventions, the three largest visible PPs closest to the ileocecal junction were collected. Samples from three mice were pooled for each group, resulting in eight PP groups for sc-RNA and sc-BCR sequencing: juvenile groups (SD, HPD, SD+DSS, HPD+DSS) and adult groups (SD, HPD, SD+DSS, HPD+DSS).

first: Zhiyin

last: Huang


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [ATAC-Seq]

overall_design: ATAC-seq data obtained from C3H10T1/2 cell during adipogenic cocktail treatment


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [RNA-Seq]

overall_design: RNA-seq data obtained from C3H10T1/2 cell during adipogenic cocktail treatment


title: Single-Cell RNA-Sequencing of Murine KPC Pancreatic Tumors

city: NAGOYA

first: XINGXING

last: WANG

state: 愛知県

address: 65 Tsurumai-cho, Showa-ku

department: cancer biology

institute: Nagoya University

summary: Single-cell RNA-sequencing analyses were performed on unfractionated live cell mixtures from pancreatic tumors of KPC mice and wild-type mice to detect different myCAF subpopulations

overall_design: Unfractionated live cell mixtures from pancreatic tumors of two KPC mice and two parental wild-type KPC mouse were collected and analyzed by 10x single-cell RNA-sequencing. All mice were 12-week-old males.

first: Kohei

last: Kumegawa

first: Keiko

last: Shinjo

first: Xingxing

last: Wang

first: Akinori

last: Kanai

first: Shota

last: Takashima


title: Single-Cell ATAC-Sequencing of Murine KPC Pancreatic Tumors

summary: Single-cell ATAC-sequencing analyses were performed on unfractionated live cell mixtures from pancreatic tumors of KPC mice and wild-type mice to better understand the epigenetic characteristics of different cell populations

overall_design: Unfractionated live cell mixtures from pancreatic tumors of two KPC mice and one parental wild-type KPC mouse were collected and analyzed using single-cell chromatin accessibility sequencing. All mice were 12-week-old males.

first: Reo

last: Maruyama


title: Epithelial WNT secretion drives niche escape of developing gastric cancer

city: Daejeon

first: Bon-Kyoung

last: Koo

state: Yuseong-gu

address: Expo-ro 55

department: Center for genome engineering

institute: Institute for Basic Science

summary: Recent studies have shed light on the signaling pathways required for gastric tissue maintenance and how aberrations in these key pathways lead to gastric cancer development. Although it has been shown that the WNT pathway is important for gastric epithelial homeostasis, the identity and source of the responsible canonical WNT ligands remain unknown. Furthermore, it is unclear how gastric cancer acquires WNT niche independence - an important early step in tumorigenesis. Using human and mouse gastric organoids andin vivomouse models, we found that mesenchymal WNT2B and WNT7B maintain gastric epithelium in homeostasis. Next, mouse genetic studies and single-cell multi-omics analyses revealed that activation of MAPK signaling induces secretion of WNT7B in the epithelium itself. We further confirmed that in human gastric cancer, MAPK pathway activation through HER2 overexpression or copy number gains ofWNT2confers WNT independence. Importantly, the epithelium-intrinsic WNT expression could be therapeutically inhibited. Taken together, our results reveal that normal gastric epithelial turnover relies on WNT ligands secreted by niche mesenchymal cells, while transformation involves acquisition of a WNT secretory phenotype in the epithelium - representing a potential target for therapeutic interventions.

overall_design: Mouse Gastric oragnoids from Anxa10-CreERT2; Rnf43f/f; Znrf3f/f mice (RZ sample) and Anxa10-CreERT2: Rnf43f/f: Znrf3f/f: Kraslsl-G12D mice (RZK sample). The oragnoids were cultured on WEN medial which contains Wnt3A, mEGF, and mNoggin.

first: Jaehun

last: Lee

first: Soomin

first: Youngchul

last: Oh

first: Jihoon

first: Stephan

middle: R

last: Jahn

first: Isaree

last: Teriyapirom

first: Yeongjun

first: Sang-Min

first: Tim

last: Schmäche

first: Jungmin

first: Somi

first: Anne-Marlen

last: Ada

first: Andrea

last: Català-Bordes

first: Youngwon

last: Cho

first: Jinho

first: Amanda

last: Andersson-Rolf

first: Sebastian

last: Merker

first: Joo Yeon

last: Lim

first: Ji-Yeon

last: Park

first: Thomas

middle: M

last: Klompstra

first: Ki-Jun

last: Yoon

first: Ho-Seok

first: Jong Kyoung

first: Eunyoung

last: Choi

first: James

last: Goldenring

first: Jae-Ho

last: Cheong

first: Hyunki

first: Daniel

middle: E

last: Stange

first: Heetak

first: Ji-Hyun


title: Molecular fingerprints of alcohol craving in the hippocampus

city: Warsaw

first: Katarzyna

last: Radwańska

state: Prowincja

address: ul. L. Pasteura 3

institute: Nencki Institute of Experimental Biology (PAS)

summary: Differentially expressed transcripts in High and Low-alcohol drinkers mice were characterise to identify affected molecular pathways in the hippocampus and amygdala

overall_design: The hippocampus and amygdala of mice that exhibit AUD-like phenotype characterised by excessive alcohol seeking during withdrawal (high drinkers) and those who limit alcohol seeking during alcohol non-availability periods (low drinkers) were used to the experiment.

first: Roberto

last: Pagano

first: Ahmad

last: Salamian

first: Edyta

last: Skonieczna

first: Bartosz

last: Wojtas

first: Bartek

last: Gielniewski

first: Malgorzata

last: Piechota

first: Anna

last: Cały

first: Robbert

last: Havekes

first: Ted

last: Abel

first: Kasia

last: Radwanska


title: The mechano-biological microenvironment of pancreatic ductal adenocarcinoma

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: GelMA hydrogels of different stiffness (5% and 7.5%) provide a microenvironment capable of directing not only pancreatic cancer cell growth but also stiffness- and matrisome-related gene programs. BxPC-3 and PANC-1 cells were chosen for this analysis as representative epithelial and mesenchymal-like cell lines respectively. Transcriptomic signatures of GelMA-embedded cells were compared against those of cells cultured in commonly-used collagen hydrogels (Col).

overall_design: RNA sequencing was performed on the pancreatic cancer cell lines BXPC3 and PANC1 embedded in GelMA or in collagen hydrogels. Two replicates per condition were analysed per cell line.

first: Eleonora

middle: F

last: Peerani

first: Juliana

last: Candido

first: Daniela

last: Loessner


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation

first: Taejun

last: Seol

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

overall_design: Refer to individual Series


title: CircRNAs expression analysis of HCC tumor and peri-tumor

first: He

last: Luyun

address: 15 DaTun Road, Chaoyang District

institute: IBP

summary: Investigation of differentially expressed circRNAs in  HCC tumors

overall_design: CircRNAs expression profiling using HCC tumor and peri-tumor tissues. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and circRNA array were performed.

first: Luyun

last: He

first: Zusen

last: Fan


title: Integrative Multi-Omics Analysis Identifies a Functional Enhancer Driving Tumorigenesis in Head and Neck Squamous Cell Carcinoma

status: Public on Dec 15 2025

city: Shanghai

first: Xu

last: Pengfei

state: Shanghai

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

summary: Bulk RNA-seq of CRISPR-edited cells identified 742 differentially expressed genes enriched in multi pathways related to cancer, highlighting the widespread regulatory influence of this enhancer. Quantitative PCR validation confirmed consistent expression changes of key genes across multiple mutant cell lines. Collectively, our study demonstrates that GH05J001312 functions as an enhancer with broad impact on oncogenic transcriptional networks, providing a potential therapeutic target in HNSCC.

overall_design: Bulk RNA-seq of CRISPR-edited cells

first: Pengfei

last: Xu

first: Xiaorong

last: Liu

first: Xiaoling

last: Lu

first: Qianhui

last: Jiang

first: Dan

last: Yu

first: Bin

last: Yan


title: Impact of Fc engineering on the transcriptional profile of monocytes and interstitial macrophages in the lungs of Hu-FcgR Tg mice after MA30 infection

first: Michael

middle: S.

last: Diamond

state: MO

address: 425 S. Euclid Ave

department: Immunology and Pathology

institute: Washington University School of Medicine

summary: As the SARS-CoV-2 pandemic progressed, many monoclonal antibodies (mAbs) that neutralized infection against initial strains lost potency against later variants due to accumulation of mutations in the spike protein. Nonetheless, some mAbs, including S309, the parent of the therapeutically used sotrovimab, remained protective in animals against Omicron variants despite reduced neutralizing potential, with Fc-mediated effector functions likely sustaining inhibitory activity. Here, we identify Fc variants of S309 that confer enhanced protection against SARS-CoV-2 infection in a humanized Fcg receptor transgenic (Hu-FcgR Tg) mouse model of infection. Versions of S309 that are afucosylated (AFUC) and contain a G236A (GA) mutation in the Fc region showed increased binding to FcgRs IIA, IIIA, and IIIB and enhanced phagocytic activity in cell culture-based assays. Treatment with S309-GA-AFUC resulted in less viral burden, inflammation, and pulmonary ventilatory dysfunction in the lungs of Hu-FcgR Tg mice challenged with SARS-CoV-2 strains compared to the parental S309 mAb or a variant (S309-GRLR) lacking Fc effector functions. The enhanced protection in the lung conferred by S309-GA-AFUC required trafficking of CCR2-expressing monocytes to reduce SARS-CoV-2 viral burden and lung injury. Flow cytometry and RNA sequencing analyses showed that compared to the parental S309 mAb, S309-GA-AFUC treatment reduced the inflammatory state and induced a reparative transcriptional signature in monocytes and interstitial macrophages. Overall, our findings demonstrate that Fc engineering to increase antibody binding to activating FcgRs can strengthen effector functions, shape myeloid transcriptional profiles, and enhance protection against SARS-CoV-2 infection in vivo.

overall_design: RNA-seq profiling of monocytes and interstitial macrophages in the lungs of Hu-FcgR Tg day 3 following MA30 infection

first: Samantha

last: Mackin

first: Courtney

last: Karl

first: Chieh-Yu

last: Liang

first: Maksim

last: Kleverov

first: Mehak

middle: Z

last: Khan

first: Thendral

last: Selvam

first: Matthias

last: Mack

first: Galit

last: Alter

first: Barbara

last: Guarino

first: Davide

last: Corti

last: Schmid

middle: S


title: Circulating Th1, Th1/17, and Th17 cell bulk RNA sequencing from endometriosis patients and controls

city: Kingston

first: Chandrakant

last: Tayade

state: Ontario

address: 18 Stuart Street

country: Canada

institute: Queen's University

summary: We aimed to gain a comprehensive understanding of transcriptional profiles of circulating Th1, Th1/17, and Th17 cells in endometriosis patients (n=10) as compared to healthy controls (n=12). Briefly, fresh peripheral blood was collected from subjects, peripheral blood mononuclear cells (PBMCs) were isolated using density centrifugation and then cryopreserved until later bulk analysis. PBMCs were later thawed, CD4+ T cells were magnetically isolated (#17952, StemCell Technologies, Canada) and stimulated with 30ng/mL of PMA and 1ug/mL of Ionomycin and incubated for 4hrs. Cells were then stained for FACS and sorted into viable populations of Th17 (CD3+CD4+IFNg-IL-17+), Th1/17 (CD3+CD4+IFNg+IL-17+), and Th1 (CD3+CD4+IFNg+IL-17-) cells using BD FACSAria™ III. RNA was then isolated from Th1, Th1/17, and Th17 cell populations from patients and controls using a commercially available kit (#74004, Qiagen, Canada). Samples were then quality checked and sent for bulk RNA sequencing (RNAseq) at McGill Genome Centre (MGC, Canada) using Illumina NovaSeq X Plus 10B (Illumina, USA) and subsequent bioinformatic analyses, as per standard pipelines. Briefly, analyses included principal component analysis (PCA), unsupervised and supervised clustering, heatmap generation, differential expression analysis (DEG), volcano plots, fold-change distribution, and Gene Ontology (GO) enrichment analyses. RNA sequencing revealed extensive Th subset reprogramming in endometriosis, most predominately in Th17 cells (2,220 DEGs). Collectively, our findings reveal significant immune remodeling in endometriosis and highlight a distinct, aberrant Th17 cell phenotype, contributing to endometriosis pathophysiology. Ultimately, this work supports the repurposing of IL-23- and IL-17-targeted therapeutics to provide novel options for endometriosis patients, as these therapeutics have been successfully used in other chronic inflammatory diseases and may also target endometriosis-associated comorbidities.

overall_design: RNA-seq profiling of circulating Th1, Th1/17, and Th17 cells isolated from female endometriosis patients and healthy female controls.

first: Danielle

middle: J

last: Sisnett

first: Katherine

middle: B

last: Zutautas

first: Jaelis

middle: P

last: Holmes

first: Jessica

last: Pudwell

first: Kira

last: King

first: Olga

last: Bougie


title: Gene expression signature of liver of mice with and without functional NNT

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

summary: Global RNA sequencing analysis of liver of chow and high-fat diet fed WT and NNT KO mice (both sexes)

overall_design: At the age of 11-13 weeks, half of the mouse cohort (female as well as male mice) were switched from chow to a 45 kcal% Fat (ssniff E15744-347, according to research diets D12451). After 11 weeks of HFD feeding, mice were sacrificed 2–4,5 h after the lights went on, and serum and tissue samples were collected.

first: S

last: Keipert

first: D

first: M

last: Jastroch

last: Kutschke

last: Liedtke

first: K

last: Makris


title: Loss of NADPH-producing enzymes accelerates pancreatic precancerous lesions

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

institute: University of Michigan

summary: Acinar-to-ductal metaplasia (ADM) is a reversible cell state that facilitates pancreas repair following injury. Oncogenic KRAS mutations can progress ADM to pancreatic intraepithelial neoplasia (PanIN) and pancreatic ductal adenocarcinoma. Metabolism is extensively reprogrammed in cancer, but the metabolic alterations in precancerous lesions are understudied. Using RNA-sequencing and targeted metabolomics from isolated acinar cells we identified global changes in central carbon metabolism genes and metabolites during ADM formation.

overall_design: Acinar cells were isolated from KrasLSL-G12D/+;Ptf1a-CreERTM/+ pancreas (n=3 individual pancreata; labeled as KC2, KC3, and KC5) or Ptf1a-CreERTM/+ control pancreas (n=1; labeled as CA2). 4-hydroxytamoxifen (2uM) was used to induce KrasG12D in cells over three days and compared with vehicle treatment after one day.

first: Costas

last: Lyssiotis

first: Megan

middle: D

last: Radyk


title: A Microphysiological Model of Human MASLD Reveals Paradoxical Response to Resmetirom

city: Cambridge

first: Dominick

last: Hellen

state: MA

address: 32 Vassar St

institute: Massachusetts Institute of Technology

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic disease with multiple etiologies, stemming from the interplay between local and systemic genetic, diet, and gene-environment interactions. To understand the progression of MASLD in a controlled setting, we utilized a human liver microphysiological system (MPS) to establish a physiologically relevant metabolic baseline and probe how primary human hepatocytes respond to perturbations in insulin, glucose, and free fatty acids (FFAs). Replicate liver MPS were maintained in media with either 200 pM or 800 pM insulin for up to 3 weeks alone and in combination with standard glucose (5.5 mM), hyperglycemia (11 mM glucose), normal (20µM) and elevated FFA (100 µM). Together, hyperinsulinemia along with elevated glucose and FFAs, induces the release of pro-inflammatory chemokines, accumulation of triglycerides, and predisposes hepatocytes to insulin resistance. Treatment with the thyroid receptor ß agonist resmetirom normalizes hepatic fat content and partially rescues insulin sensitivity, but paradoxically induces higher CXCL1 and IL8 expression in male and female donors. In aggregate, our enhanced in vitro MPS model establishes a metabolic baseline and perturbed condition that recapitulates a spectrum of phenotypes observed in MASLD, offering improved quantification and insight into disease progression with relevance to human physiology.

overall_design:
Microphysiological modeling of MASLD with human hepatocytes in the CN-Bio LiverChip system.

*** Raw data not provided due to the human cells, along with their sequencing data, were provided as part of a contractual agreement and data-ownership restriction between an organization (NovoNordisk) and MIT. The raw sequencing data are owned and controlled by the sponsor in this case. Under this contract, we are able to share processed, non-identifiable gene-level count data. ***

last: Ungerleider

first: Erin

last: Tevonian

first: Pierre

last: Sphabmixay

first: Priyatanu

last: Roy

first: Nikolaos

last: Meimetis

first: Federico

last: Presutti

first: Ashleigh

last: Williams

first: Ryan

last: Ogi

first: Caroline

last: Lewis

first: Jacob

last: Jeppesen

first: Sixian

last: You

first: Damien

last: Demozay

first: Linda

last: Griffith


title: Characteristics of senescent cells resistant to ABT263 and ARV825

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: ABT263 and ARV825 were identified as promising senolytic drugs based on our criteria. However, 20–30% of senescent cells survived treatment with these agents. To clarify why a subset of senescent cells remained resistant, we performed RNA-seq to characterize the surviving population. Several SASP factors were upregulated compared with untreated senescent cells, suggesting that incomplete senolysis may diminish therapeutic benefits and that more effective elimination of senescent cells is required. In addition, AKR1C1–3, which are involved in detoxifying reactive carbonyl species and reducing oxidative stress, were also upregulated. These results suggest that the surviving cells may overcome mitochondrial stress by preserving mitochondrial membrane potential and limiting ROS accumulation.

overall_design: RNA-seq profiling of doxorubicin-induced senescent TIG-3 cells with ABT263, ARV825, or vehicle (DMSO) for 7days.

first: Masahiro

last: Wakita

first: Koyu

last: Ito

first: Hideka

last: Miyagawa

first: Kaho

last: Fuji

first: Dai

last: Sakamoto

first: Takumi

last: Mikawa

first: Sho

last: Sugawara

first: Xiangyu

last: Zhou

first: Jeong

middle: H

last: Park

first: Emi

last: Ogasawara

first: Akiko

last: Takahashi

first: Hiroshi

last: Kondoh

first: Naotada

last: Ishihara

first: Eiji

last: Hara


title: Identification of NOTCH-driven matrisome-associated genes as prognostic indicators of multiple myeloma patient survival

city: Wuerzburg

first: Carsten

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

institute: University of Wuerzburg

summary:
Multiple myeloma (MM) provides a permissive tumor microenvironment (TME), supporting tumor cell growth and dissemination, and conferring therapy resistance. RNAseq in the human MM cell lines RPMI 8226 and MM.1S after knockdown of NOTCH1 (N1) and NOTCH2 (N2) was performed to identify genes and pathways that are specifically regulated through NOTCH signaling and contribute to the permissive TME.
GSEA confirmed previous findings that NOTCH signaling stimulates the expression of cytokines involved in inflammation, defining an immunosuppressive TME promoting cell viability and migration in MM. Furthermore, a downregulation of “receptor signaling pathway via JAK-STAT” after N1 or N2 knockdown and “regulation of bone resorption” and “regulation of bone remodeling” after N1 knockdown was found.
Moreover, our results showed that the expression of multiple core matrisome and matrisome-associated proteins was altered, revealing N1 and N2 as key regulators of extracellular matrix (ECM) remodeling in the bone marrow niche. This process destroys the ECM abundance and integrity and has prognostic relevance. The identification of novel ECM targets will help to develop new treatment strategies that preserve the ECM in a less permissive niche.

overall_design: RNA-seq of MM.1S and RPMI-8226 cells with a shRNA mediated knockdown of Notch1 or Notch2 were performed to identify Notch target genes and genes regulated by the Notch pathway.

first: Franziska

last: Jundt

first: Daniela

last: Maichl

first: Julius

last: Kirner

first: Thorsten

last: Bischler

first: Susanne

last: Beck

first: Dirk

last: Hose

first: Anja

last: Seckinger

first: Martin

last: Kuric

first: Regina

last: Ebert


title: Heterogeneity of senescent cells underlies resistance to ABT263 and ARV825

first: Daisuke

last: Motooka

summary: ABT263 and ARV825 emerged as promising senolytic candidates based on our criteria. Nevertheless, 20–30% of senescent cells persisted after treatment with these compounds. To investigate why a subset of cells remained refractory, we examined scRNA-seq to profile the surviving population. Notably, several genes encoding V-ATPase subunits—such as ATP6V0E1, which are essential for lysosomal degradation of damaged organella—were consistently enriched in both ABT263- and ARV825-resistant senescent cells. These findings indicate that cells exhibiting elevated V-ATPase activity may evade senolytic action by more efficiently clearing damaged organelles, including mitochondria.

overall_design: RNA-seq profiling of early-passage pre-senescent TIG-3 cells and doxorubicin-induced senescent TIG-3 cells with ABT263, ARV825, or vehicle (DMSO) for 7days.

first: Masahiro

last: Wakita

first: Koyu

last: Ito

first: Hideka

last: Miyagawa

first: Kaho

last: Fuji

first: Dai

last: Sakamoto

first: Takumi

last: Mikawa

first: Sho

last: Sugawara

first: Xiangyu

last: Zhou


title: Small RNA profiling under HIF1alpha control

city: Tainan

first: Jie

middle: ning

last: Li

state: Please select an option below

address: No1. University road

department: Department of Medical Laboratory Science and Biotechnology

country: Taiwan

institute: National Cheng Kung University

summary: This study investigates the expression of miRNA and snoRNA in HIF-1alpha manipulating  breast cancer cells

overall_design: miRNAs and snoRNAs expression were analyzed in HIF-1 alpha and HLH-truncated HIF-1 alpha overexpressing MCF-7 cells and HIF-1 'alpha knockdown MDA-MB-231 cells.

first: Jie-Ning


title: Neoadjuvant modified FOLFIRINOX plus nivolumab in borderline-resectable pancreatic ductal adenocarcinoma: a pilot phase 1 trial

city: Los Angeles

first: Jason

middle: Michael

last: Link

state: CA

address: 650 Charles E Young Dr S

department: Surgery

institute: University of California, Los Angeles

summary: Combination therapies of chemotherapy and immune checkpoint inhibitors have failed to improve survival in pancreatic ductal adenocarcinoma (PDAC), except in rare MSI-H cases, despite their success in other solid tumors.  Most prior studies have been conducted in advanced disease. Here, we present clinical, pathologic, and translational results from a phase 1b/2 investigator-initiated study evaluating neoadjuvant modified FOLFIRINOX (mFFX) plus nivolumab in patients with borderline-resectable (BR) PDAC.   Among 28 patients enrolled, 22 (79%) proceeded to surgery. Treatment was well tolerated with no significant delays or surgical complications, meeting the primary endpoint. Among patients who underwent surgical resection, median disease-free survival was 19.7 months, median progression-free survival was 26 months (95% CI: 14.7-34.3) and median overall survival was 38 months (95% CI: 27.9-not reached). The regimen demonstrated an acceptable safety profile, with all Grade 3-4 treatment-related adverse events due to chemotherapy and no Grade 3 immune related adverse events observed.  Treatment effects were assessed using paired pre- and post-treatment samples and by comparing post-treatment tumors from the nivolumab cohort to historical BR mFFX-only controls. In paired analyses, intra-tumoral CD8 T cells and plasma cells increased together; in between-group comparisons, plasma cells were significantly higher in the nivolumab cohort, with a modest CD8 T cell increase. Immunohistochemistry revealed that plasma cell abundance correlated with dense intra-tumoral lymphoid aggregates lacking germinal center-like morphology, a pattern consistent with extrafollicular B cell differentiation. Single-cell spatial transcriptomics identified irregular lymphoid aggregates with high plasma cell to B cell ratios that were enriched for terminally exhausted CD8 T cells and de-enriched for progenitor exhausted CD8 T cells and central memory CD4 T cells. Together, these findings implicate intra-tumoral LA disorganization and skewed T cell subsets as complementary features associated with limited efficacy of PD-1-based chemoimmunotherapy in PDAC. (Clinicaltrials.gov identifier: NCT03970252).

overall_design: Xenium 5K Prime was applied to six archival resected PDAC patient tumors post treatment with FOLFIRINOX and nivolumab

first: Zev

last: Wainberg

first: Timothy

last: Donahue


title: Understanding tumor heterogeneity in HNSCC by gene-expression

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Head and neck squamous cell carcinoma (HNSCC) encompasses a heterogeneous group of distinct malignancies. Established prognostic factors are based on clinical and biological characteristics, including disease stage and site, performance status, comorbidities, smoking history, and human papillomavirus (HPV) status. Nonetheless, even when patients are categorized according to these parameters, significant variability in clinical behavior and treatment response remains.    Recent advances in genomic technologies have enabled the identification of a range of genomic and epigenomic alterations that arise during tumor initiation and progression. A deeper understanding of this complex tumor heterogeneity is expected to pave the way for more personalized therapeutic approaches and the development of targeted treatments. One effective strategy for dissecting cancer heterogeneity is to identify molecularly defined subtypes and establish classifiers capable of predicting the subtype of new patient samples.

overall_design: A single-center cohort of patients with locally and regionally advanced HNSCC, treated with curative intent and enrolled in the BD2Decide observational study, was retrospectively examined. Diagnoses were made between 2008 and 2017, with follow-up concluding in June 2019. Owing to the retrospective design, no formal sample size calculation was conducted. Instead, we applied specific selection criteria to achieve a numerical balance between long-term survivors and deceased patients: (i) for each primary HPV-negative tumor site (oral cavity, HPV-negative oropharynx, hypopharynx, and larynx), we included 20 patients: 10 who had died from the disease and 10 who were alive and disease-free with at least two years of follow-up; (ii) considering the more favorable prognosis of HPV-positive oropharyngeal cancer, we selected 20 patients—10 who experienced disease recurrence and 10 who were alive and disease-free with a minimum follow-up of two years.


title: Gel-free library preparation for next-generation RNA sequencing and small RNA quantification

first: Peter

middle: C.

last: Dedon

address: 77 Massachusetts Ave

department: Biological Engineering

summary: Next-generation RNA sequencing (RNA-seq) is hampered by “primer dimer” (PD) artifacts and its quantitative performance reduced by polymerase fall-off (PF) at RNA modifications and secondary structures. Here we improved RNA-seq efficiency by incorporating (i) a post-reverse-transcription (RT) digestion of excess primers with Escherichia coli exonuclease I for PD mitigation, thus obviating gel purification during RNA-seq library preparation, and (ii) a high-processivity reverse transcriptase to increase full-length reads. A full factorial experimental design was applied to absolute quantification RNA sequencing (AQRNA-seq), the most accurate NGS-based method for quantifying small RNAs, using cDNA libraries constructed from E. coli small RNAs (>85% tRNA) followed by sequencing, data processing, and data analysis. The novel PF and PD mitigation approaches increased AQRNA-seq sensitivity >10-fold by minimizing PF and maximizing target RNA reads. By increasing sensitivity and obviating gel electrophoresis for removing PD, AQRNA-seq and other NGS-based RNA-seq methods can now be automated to increase throughput and reduce RNA sample size.

overall_design: cDNA libraries for Escherichia coli strain BW25113 small RNAs were constructed following four variations of the library preparation protocols with three biological replicates. Constructed libraries were subjected to quality assessment using Fragment Analyzer and qPCR, followed by paired-end sequencing (PE75) on a Illumina MiSeq platform.

first: Ruixi

last: Chen

first: Daniel

last: Yim

first: Lili

last: Liu

first: Bo

last: Cao

middle: C


title: PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer [CRISPR]

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

summary: RNA-binding proteins (RBPs) regulate post-transcriptional gene expression, influencing key cancer pathways. Understanding how RBPs control these processes can uncover new treatment strategies, which is crucial for cancers that lack effective targeted therapies such as triple negative breast cancer (TNBC). Here, we employ dual in vitro and in vivo CRISPR/Cas9 screens to investigate the role of RBPs in TNBC, revealing the poly(U)-binding splicing factor 60 (PUF60) as a key modulator of TNBC cell survival. Integrated eCLIP and RNA-sequencing analysis identify that PUF60 drives exon inclusion within transcripts associated with cell cycle and genomic stability, thereby promoting proliferation. Furthermore, disrupting PUF60 splice site activity via a substitution in its RNA-binding domain causes widespread exon skipping, leading to the downregulation of proliferation-associated mRNAs and inducing apoptosis in TNBC cells. We demonstrate that this RNA-binding disruption inhibits TNBC cell proliferation and shrinks tumor xenografts, highlighting the molecular mechanism through which PUF60 supports cancer progression. Our work demonstrates functional in vivo screening of RBPs as an effective strategy for identifying unexpected cancer regulators. Here, we reveal a crucial role for PUF60-mediated splicing activity in supporting oncogenic proliferation rates and highlight its potential as a therapeutic target in triple negative breast cancer.

overall_design: RNA-Binding protein (RBP)-focused CRISPR screen in cultured MCF10As, MDAMB231s, MDAMB436s, and SUM149s (in vitro) and in MDAMB231, MDAMB436, and SUM149 subcutaneous tumor xenografts in athymic nude mice

first: Alexandra

middle: T

last: Tankka

first: Jaclyn

last: Einstein

first: Catherine

first: Vivian

last: Pham

first: Yuhan

last: Zhang

first: Jack

last: Naritomi

first: Grady

middle: G

last: Nguyen

first: Orel

last: Mizrahi

first: Mark

last: Perelis

first: Joseph

last: Sarsam

first: Fred

last: Tan

first: Dan

last: Kaufman

first: Corina

last: Antal

first: Gene

middle: W

last: Yeo


title: Spatial transcriptomic analysis of Naive or Yersinia pseudotuberculosis infected ileum reveals novel enterocyte transcriptional state

city: Philadlephia

first: Daniel

last: Beiting

state: Pennsylvania

address: 380 S. University Avenue

institute: University of Pennsylvania

summary:
As part of the mouse ileum infection single cell and spatial transcriptomic atlas, GutPath (GutPath.org), these data provide 10X Xenium spatially resolved transcriptional information about the intestine during infection. Yersinia pseudotuberculosis is a natural enteric pathogen that can become systemic in mice and people. In this study, we evaluate the finding that enterocytes are uniquely altered by Yersinia pseudotuberculosis infection and investigate the role of pyogranuloma strcutures in the spatial distribution of enterocyte transcriptional states.
The distal small intestine plays vital roles in host physiology by regulating nutrient and fluid homeostasis.  Despite being  impacted in Crohn’s disease and a major target for a range of infections, we know relatively little about the complexity of cellular responses and cell-cell communication in the ileum during infection.  Single cell and spatial transcriptomics have emerged as powerful technologies to study tissue complexity in the gut, but these tools have focused on the large intestine, in part due to the accessibility of this tissue for biopsies and its importance in cancer.  Here we present GutPath, an atlas of over 500,000 single cells that captures RNA and protein expression profiles for 91 cell states in the ileum across a range of model infectionsdiverse infectious archetypes.  We show that GutPath accurately captures established immune responses to infection while revealing pathogen-specific responses in enterocytes.  To highlight the discovery potential of this atlas, we identify a novel enterocyte cell state present during Yersinia pseudotuberculosis infection that is spatially linked to bacterial load and tissue pathology.  GutPath establishes a much-needed resource for the immunology community that will accelerate the study of the transcriptional diversity of cellular landscapes in the small intestine.

overall_design: Two Naive replicate mice and two replicate Yersinia pseudotuberculosis infected mice (5 days post infection) were used. 5 cm sections of the ileum from each mouse were Swiss rolled and fixed in 10% buffered formalin before paraffin embedding and Xenium imaging.

first: Andrew

last: Hart

first: Suhas

last: Bobba

first: Bethan

last: Wallbank

first: Igor

last: Brodsky


title: Compartmentalized RNA Surveillance Through Membraneless barriers

city: Worcester

first: GANGMING

last: ZHANG

address: 368 Plantation St, Asc5-2010

institute: RNA Therapeutics Institute, University of Massachusetts Chan Medical School

summary: Biomolecular condensates are thought to compartmentalize biochemical activities, yet how they control macromolecular access without membranes remains unclear. We show that C. elegans germline condensates have distinct RNA selectivity: P granules broadly admit RNA, whereas Mutator foci associate only with RNAs destined for silencing. The Mutator scaffold MUT-16 is required for this selectivity; charge-reversal substitutions in its C-terminal LOTUS-like domain disrupt RNA exclusion, reduce fertility, and elicit promiscuous RNA silencing. Synthetic RNAs bearing piRNA target sites silence a cognate reporter in a PRG-1 dependent manner, indicating both piRNA and PIWI protein facilitate targeted RNA entry into Mutator foci. These findings support a two-tier gate: P granules admit RNA while excluding translation and silencing effectors, whereas Mutator foci act as a physical RNA barrier, excluding transcripts except those marked for piRNA silencing. Thus, scaffold physical properties enable membrane-independent RNA gating. Our research broadens the concept of selective compartmentalization beyond membranes.

overall_design: Small-RNAs for whole worms  were cloned from WT, lambdaN tethered strains and multiple mut-16 mutants including lambdaN tethered different strains, mut-16(DE6R) and rde-3 mut-16(DE6R) worms.

first: Gangming

first: Craig

last: Mello


title: TGM2-deficient macrophages exhibited a significant upregulation of pro-inflammatory signatures.

city: Beijing

first: Zhaoqi

last: Zhang

address: Beijing China Institute of Zoology，Chinese Academy of Sciences

institute: University of Chinese Academy of Sciences

summary: Macrophages are essential for tissue homeostasis, orchestrating the initiation and resolution of both innate and adaptive immunity with profound impacts on protective immunity and immune-mediated pathological damage. Macrophages are heterogeneous subsets. During the inflammatory response, they include both pro-inflammatory subsets and subsets that promote inflammation resolution, and different macrophage subsets play distinct roles in the dynamic processes at different time points. In the current study, we found that a subset of TGM2+ macrophages with inflammation-resolving properties gradually increases during the inflammation resolution phase in the LPS-induced endotoxin shock model. The peak expression of the TGM2 gene occurs mainly during the inflammation resolution phase. Additionally, transcriptome analysis revealed that compared with wild-type (WT) macrophages, TGM2-deficient macrophages exhibited a significant upregulation of pro-inflammatory signatures and a marked downregulation of lipid metabolic synthesis processes. In lipid rescue experiments, we found that the elevated inflammation phenotype of TGM2-deficient macrophages could be restored. Moreover, a significant anti-inflammatory function of this macrophage subset was observed in mouse models of severe disease, enterocolitis, and endotoxin shock. We uncover an inflammatory remodeling of the neuro-metabolic landscape in macrophages, whereby serotonin induces TGM2-mediated serotonylation of in AKT1.

overall_design: Bone marrow cells were isolated from 6-8 week-old male wild-type (WT) and TGM2KO mice and then bone marrow-derived macrophages (BMDMs) were obtained and cultured with the stimulation of M-CSF (25ng/ml) for 7 days. BMDMs from WT and TGM2KO mice were either left unstimulated or polarized to a proinflammatory state by treatment with LPS (10ng/ml) for 6 hours. Total RNA was extracted from each sample (containing 1.0 × 106 macrophages) using TRIzol reagent, following the manufacturer's instructions and cDNA library preparation for RNA-sequencing analysis. cDNA library preparation and sequencing were both performed by Annoroad Gene Technology (Beijing) Co., Ltd.

first: Yang

last: Zhao

first: Yong


title: Transcriptomic and Metabolic Insight into Flavonoid Biosynthesis Underlying Seed Coat Color Variation in Soybean (Glycine max)

city: Chuncheon

first: Beom-Soon

last: Choi

address: Kangwondaehak-gil 1

institute: NBIT

summary: Seed coat color in soybean (Glycine max) is determined by the accumulation of flavonoid-derived pigments. However, to date the molecular mechanisms driving natural variation remain poorly defined. This study integrated data from RNA sequencing (RNA-seq) with metabolite profiling via high-performance liquid chromatography (HPLC) to investigate genetic and metabolic differences between black and yellow seed coat soybean lines that share an identical genetic background. Transcriptomic analysis revealed that key anthocyanin biosynthesis genes, including flavanone 3-hydroxylase (F3H-3), anthocyanidin synthase (ANS), UDP-glucose:flavonoid 3-O-glucosyltransferase (UF3GT), UDP-glycosyltransferase (UGT79B6), and glutathione S-transferase (GSTF11), were more highly expressed in black seed coats, where we also observed increased anthocyanin and proanthocyanidin (PA) accumulation and antioxidant activity. In contrast, leucoanthocyanidin reductase (LAR) was strongly expressed in yellow seed coats but did not correspond to PA levels, likely due to the specific expression of laccase (LAC5) in black seeds, which facilitates PA polymerization. Elevated expression of cytochrome P450 enzymes (i.e., CYP73A5, cinnamate 4-hydroxylase; CYP82C4) in yellow seed coats suggested activation of the isoflavone biosynthesis pathway. Further transcriptional profiling also indicated that black-seed-specific MYB transcription factors (i.e., MYB111, MYB113, and MYB17) promoted anthocyanin production. This study is the first to provide evidence that small heat shock proteins (sHSPs) are implicated in the regulation of seed coat pigmentation and stress adaptation. Together, these findings elucidate the genetic and metabolic regulation of seed coat color in soybean and identify candidate genes relevant to functional breeding and genomics research.

overall_design: Identification of differentially expressed genes in black and yellow seed obtained in F9 from the cross of yellow (mother) and black ( father) soybeans

first: Kahee

last: Moon

first: Prakash

last: Basnet

first: Seung

last: Young

first: Grace

last: Lachica

first: Namil

last: Park

first: Taeyoung

last: Um

first: Ik-Young


title: Beyond canonical pathways: early retinal transcriptomic response to light-induced degeneration in the zebrafish larva

city: Messina

first: Luigi

last: Donato

state: Italy

address: via Consolare Valeria, 1

department: BIOMORF

institute: University of Messina

summary: The zebrafish (Danio rerio) is widely used to investigate the cellular and molecular mechanisms that support retinal regeneration. Although several adult injury paradigms have been established, models that capture the earliest stages of degeneration and Müller glia-mediated repair in larvae remain comparatively underexplored. Here, we validate a light-induced retinal degeneration (LIRD) paradigm at the larval stage as a tractable system to study acute phototoxic injury and early regenerative responses. This approach enables high-throughput RNA sequencing and provides a comprehensive transcriptomic view of retinal responses 48 hours after injury. At this timepoint, larvae display photoreceptor loss and robust Müller glia activation and proliferation, mirroring key features described in adult LIRD models. Transcriptomic analyses further highlight both canonical and previously undercharacterised pathways engaged during the early injury response. Together, this work establishes larval LIRD as a practical and informative model and provides a resource for hypothesis-driven studies aimed at dissecting the molecular events that initiate retinal regeneration.

overall_design: Two experimental groups were analyzed: control and light damage (LIRD) (n = 10–11 animals per group). Retinal RNA-seq was performed on Danio rerio (paired-end 150 bp, Illumina NovaSeq 6000). Differential expression and pathway analyses were conducted to assess the impact of LIRD.

first: Ignacio

last: Babiloni-Chust

first: S.

last: Sartori

first: Darin

last: Zerti

first: Matthias

last: Carl

first: Rosalia

last: D’Angelo

first: Rita

last: Maccarone

first: Lucia

last: Poggi


title: Epitranscriptomic Editing Screening Identifies Functional m6A Sites in Cancer [CRISPR screen_H358]

city: TORONTO

first: Xin

last: Xu

address: 101 COLLEGE ST EAST TOWER 11-601D

institute: Princess Margaret Cancer Center

summary: In this study, we used a targeted CRISPR/CasRx-METTL3 screen to identify m6A peaks that are critical for prostate and lung cancer.

overall_design: The CRISPR screen employed in our pooled sgRNA library consisted of ~12,045 sgRNAs targeting m6A peaks identified from prostate cancer and lung cancer patients, with 5 sgRNAs per gene on average. The sgRNAs were designed using the "cas13design". Stable dCasRx-METTL3-expressing 22Rv1 and H358 cell line was generated. dCasRx-METTL3-expressing cell lines was infected with the library at an MOI of ~ 0.3 and coverage of 400x. 24h post-infection, cells were selected with blasticidin for 5 days and part of cells were sujected to DNA extraction as day 0. Other cells were cultured in dish for ~16 days (day 16), maintaining 400x coverage prior to our screening assay. Genomic DNA was extracted from replicate samples and sgRNA inserts were amplified by PCR. The input amount of genomic DNA was calculated to achieve 400x coverage of the library and resulting libraries were sequenced on an Illumina HiSeq500.

first: Yujuan

last: Wang

first: Helen

last: Zhu

first: Housheng

last: He


title: Chromatin stability safeguards mitochondrial homeostasis and prevents mTORC1 hyperactivation

city: Memphis

first: R.

middle: Nicholas

last: Laribee

state: TN

address: 19 South Manassas

department: Pathology

institute: University of Tennessee Health Science Center

summary: Cells dynamically regulate chromatin in response to nutrient flux that promotes the transcriptional changes necessary for adaptation. The mechanistic target of rapamycin complex 1 (mTORC1) kinase integrates nutrient signaling with chromatin regulation, yet whether chromatin stability feeds back to mTORC1 activation and stress adaption remains unknown. We previously identified histone H3 at lysine 37 (H3K37) as essential for the cellular response to mTORC1 stress where mutation of H3K37 to alanine (H3K37A) causes cell death upon mTORC1 inhibition. Herein, we show that H3K37-dependent chromatin stability prevents proteasome-mediated histone degradation, restricts mTORC1 signaling, and safeguards mitochondrial homeostasis during mTORC1 stress. Genetic interaction analyses reveal that H3K37A combined with mutants that destabilize chromatin, including loss of the Set2 H3K36 methyltransferase, Rpd3S histone deacetylase, or multiple histone deposition pathways, causes synthetic lethality when mTORC1 is inhibited. Transcriptome analysis indicates that H3K37A misregulates the mitochondrial transcriptome during mTORC1 stress, which increases mitochondrial reactive oxygen species (ROS) and triggers lethal mitochondrial retrograde signaling. Inactivation of retrograde signaling, or ROS neutralization, rescues viability of H3K37A and chromatin stability mutants during mTORC1 stress. These findings establish chromatin stability as a key safeguard that restrains mTORC1 signaling and prevents toxic mitochondrial stress during metabolic adaptation.

overall_design: RNA seq profiling of H3WT and H3K37A mutant cells treated with mock or 20 nM rapamycin for 1 hour.

first: Vinoth

last: Sigamani

first: Mohd

last: Yousuf

first: Daniel

middle: L

last: Johnson

first: Brian

last: Strahl

first: Ronald

middle: N


title: Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies

city: Mölndal

first: Benjamin

last: Keith

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

summary: Recent developments in spatially resolved -omics have enabled studies linking gene expression and metabolite levels to tissue morphology, offering new insights into biological pathways. By capturing multiple modalities on matched tissue sections, one can better probe how different biological entities interact in a spatially coordinated manner. However, such cross-modality integration presents experimental and computational challenges. To align multimodal datasets into a shared coordinate system and facilitate enhanced integration and analysis, we propose MAGPIE (Multi-modal Alignment of Genes and Peaks for Integrated Exploration), a framework for co-registering spatially resolved transcriptomics, metabolomics, and tissue morphology from the same or consecutive sections. We illustrate the generalisability and scalability of MAGPIE on spatial multi-omics data from multiple tissues, combining Visium with both MALDI and DESI mass spectrometry imaging. MAGPIE was also applied to newly generated multimodal datasets created using a specialised experimental sampling strategy to characterise the metabolic and transcriptomic landscape in an in vivo model of drug-induced pulmonary fibrosis and to showcase the linking of small-molecule co-detection with endogenous responses in lung tissue. MAGPIE highlights the refined resolution and increased interpretability of spatial multimodal analyses in studying tissue injury, particularly in pharmacological contexts, and offers a modular, accessible computational workflow for data integration.

overall_design: A male Wistar Han rat (n=1) was subjected to daily inhalation exposure via snout-only administration for 14 days with 15 mg/kg/day of the AZX test formulation of AZX (10%), MPEG-2000-DSPE (1.25%), trileucine (5%), and trehalose (83.75%), in a flowpast exposure chamber. The rat was purchased from Charles River (Germany) at 7 weeks and were 10 weeks at the start of dosing. Animal handling conformed to standards established by the Council of Europe ETS123 AppA, the Helsinki Convention for the Use and Care of Animals, Swedish legislation, and AstraZeneca global internal standards. All mouse experiments were approved by the Gothenburg Ethics Committee for Experimental Animals in Sweden and conformed to Directive 2010/63/EU. The present study was approved by the local Ethical committee in Gothenburg (EA000680-2017) and the approved site number is 31-5373/11.

first: Eleanor

last: Williams

first: Lovisa

last: Franzén

first: Martina

last: Olsson Lindvall

first: Gregory

last: Hamm

first: Steven

last: Oag

first: Muntasir Mamun

last: Majumder

first: James

last: Denholm

first: Azam

last: Hamidinekoo

first: Javier

last: Escudero Morlanes

first: Marco

last: Vicari

first: Joakim

last: Lundeberg

first: Laura

last: Setyo

first: Trevor

middle: M

last: Godfrey

first: Livia

last: Eberlin

first: Aleksandr

last: Zakirov

first: Jorrit

last: Hornberg

first: Marianna

last: Stamou

first: Patrik

last: Ståhl

first: Anna

last: Ollerstam

first: Jennifer

last: Tan

first: Irina

last: Mohorianu


title: Epitranscriptomic Editing Screening Identifies Functional m6A Sites in Cancer [RNA-Seq 22Rv1 M3 writing]

first: Xin

last: Xu

summary: In this study, we used a targeted CRISPR/CasRx-METTL3 screen to identify m6A peaks that are critical for prostate cancer.

overall_design: The CRISPR screen employed in our pooled Epidrug library consisted of ~12,045 sgRNAs targeting m6A peaks in prostate cancer and lung cancer patients, with 5 sgRNAs per gene on average. The sgRNAs were designed using the "cas13design". Stable dCasRx-METTL3-expressing 22Rv1 and H358 cell line was generated. dCasRx-METTL3-expressing cell lines was infected with the library at an MOI of ~ 0.3 and coverage of 400x. 24h post-infection, cells were selected with blasticidin for 5 days and part of cells were sujected to DNA extraction as day 0. Other cells were cultured in dish for ~16 days (day 16), maintaining 400x coverage prior to our screening assay. Genomic DNA was extracted from replicate samples and sgRNA inserts were amplified by PCR. The input amount of genomic DNA was calculated to achieve 400x coverage of the library.

first: Yujuan

last: Wang

first: Helen

last: Zhu

first: Housheng

last: He


title: Cross-platform comparison of gene expression-based cancer molecular subtyping reveals discrepancies with exome capture methods

city: Chapel Hill

first: Jen Jen

last: Yeh

state: NC

address: 450 West Dr, CB7295

institute: University of North Carolina at Chapel Hill

summary: Gene expression profiling assays in precision oncology is increasing with uncertain validity across platforms. In this study, we examined the application of PurIST, a molecular subtyping algorithm for pancreatic ductal adenocarcinoma (PDAC), across different platforms. We compared PurIST calls between matched samples processed by whole transcriptome and commercial exome capture RNA-seq. In parallel, we compared subtypes between matched samples processed by NanoString and whole transcriptome RNA-seq from the PANCREAS trial (NCT04683315). Between whole transcriptome and exome capture, subtype agreement was 81% with significant increase in basal-like subtype with exome capture. Differences in overall survival in patients with basal-like tumors compared to classical tumors did not reach statistical significance using exome capture (log-rank P = 0.061), whereas with whole transcriptome it was significantly shorter (log-rank P < 0.0001). Subtype agreement between whole transcriptome RNA-seq and NanoString was higher at 95%. PurIST results should be interpreted with caution when using exome capture method.

overall_design:
For patients with pancreatic cancer who had their tumors sequenced with a commercial assay (Tempus xT/xR), matched tumors were also sequenced with whole-transcriptome RNA-seq in parallel.

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

first: Jaewon

last: Lee


title: Analysis of previously reported BRD4 target genes related to mitochondrial function in senescent fibroblasts.

first: Daisuke

last: Motooka

summary: Because BRD4, a major target of ARV825, has been implicated in the regulation of mitochondrial gene expression in cardiomyocytes (DOI: 10.1161/CIRCULATIONAHA.120.047239), we examined whether ARV825-induced cell death in senescent cells is attributable to changes in the expression of mitochondria-related genes. Although senescent cells were eliminated within two days of ARV825 treatment, the mRNA expression levels of mitochondrial-related genes remained unchanged. In contrast, XRCC4— which functions together with DNA ligase IV in non-homologous end joining and has been reported to regulate senolysis (DOI: 10.1038/s41467-020-15719-6)— was downregulated, consistent with previous findings.

overall_design: RNA-seq profiling of doxorubicin-induced senescent TIG-3 cells with ARV825 or vehicle (DMSO) for 2days.

first: Masahiro

last: Wakita

first: Koyu

last: Ito

first: Hideka

last: Miyagawa

first: Kaho

last: Fuji

first: Dai

last: Sakamoto

first: Takumi

last: Mikawa

first: Sho

last: Sugawara

first: Xiangyu

last: Zhou

first: Jeong

last: Park

first: Emi

last: Ogasawara

first: Akiko

last: Takahashi

first: Hiroshi

last: Kondoh

first: Naotada

last: Ishihara

first: Eiji

last: Hara


title: A highly abundant circular RNA from the RMST locus plays a role in posterior fossa ependymoma pathogenesis

city: Aarhus

first: Lasse

middle: Sommer

last: Kristensen

address: Wilhelm Meyers Allé 4

department: Biomedicine

country: Denmark

institute: Aarhus University

summary: Pediatric ependymoma (EPN) is one of the most common central nervous system (CNS) cancers in children often accompanied by bad prognosis. The circular RNA, circRMST, is known to be upregulated in posterior fossa (PF) EPN, but its functional role in the disease has not been explored. We found that circRMST is abundantly expressed in the cytoplasm of cancer cells in PF EPN patients. Moreover, knockdown of circRMST in EPN cancer stem cells induced differentiation-related pathways while the expression of cell cycle-related pathways was reduced, suggesting that it acts as an oncogene. We further validated these findings using flow cytometry-based cell cycle analysis and an in vitro serum-induced differentiation assay. Furthermore, we found that high circRMST expression and low promoter methylation levels are associated with poor prognosis. In conclusion, this study identifies circRMST as a novel oncogene in PF EPN.

overall_design: Total RNA-seq 24h and 72h post circRMST knockdown (KD) in biological triplicates using two different dicer-substrate siRNA (DsiRNA) constructs (Negative control (NC), circRMST-KD1 and circRMST-KD2)

first: Ulvi

last: Ahmadov

first: Charlotte

last: Udengaard

first: Stine

last: Vissing

first: Silke

last: Nielsen

first: Kim-Gwendolyn

last: Dietrich

first: Benedicte

last: Ulhøi

middle: S


title: biocompatibility results for endovascular medical device

first: Youcheng

last: Yang

state: California

address: 430 Westwood Plaza, 5121 Engineering V, Box 951600, Attn (PI NAME): Li Lab

department: Bioengineering

institute: UCLA

summary: In this project, we developed an endovascular medical device. To evaluate its biocompatibility, the device (experimental) or a clinical medical device (control) was co-cultured with human immune cells. We further conducted single-cell RNA sequencing to examine potential immunogenic responses at the cellular level.

overall_design: We employed an in vitro co-culture model to compare immune responses to the developed device and a reference clinical medical device. Briefly, devices were incubated with human immune cells under controlled culture conditions for a defined exposure period. After co-culture, freshly collected samples were immediately transported for library preparation and processed using a standard single-cell workflow. The resulting single-cell profiles were analyzed to identify differences in cell composition and gene expression patterns. The integrated dataset was further processed using established pipelines for dimensionality reduction, clustering, and comparative analysis.

first: Jun

last: Chen

first: Yan Rui-de

last: Li


title: A genetically encoded bifunctional enzyme that mitigates redox imbalance and lipotoxicity via engineered Gro3P-Glycerol shunt

city: San Diego

first: Xingxiu

last: Pan

address: 6868 Nancy Ridge Dr

institute: Scintillon institute

summary: Dihydroxyacetone phosphate (DHAP), glycerol-3-phosphate (Gro3P) and reduced/oxidized nicotinamide adenine dinucleotide (NADH/NAD+) are key metabolites of the Gro3P shuttle system that forms a redox circuit, allowing transfer of reducing equivalents between cytosol and mitochondria. Targeted activation of Gro3P biosynthesis was recently identified as a promising strategy to alleviate reductive stress by promoting NAD+ recycling, including in cells with an impaired activity of the mitochondrial complex I. However, because Gro3P constitutes the backbone of triglycerides under some circumstances, its accumulation can lead to excessive fat deposition. As a step to alleviating redox imbalance while counteracting lipogenesis as a byproduct, we present the development of a novel genetically encoded tool based on a di-domain glycerol-3-phosphate dehydrogenase from algae Chlamydomonas reinhardtii (CrGPDH), which is a bifunctional enzyme that can recycle NAD+ while converting DHAP to Gro3P. Importantly, this enzyme also possesses an N-terminal domain which cleaves Gro3P into glycerol and inorganic phosphate (Pi) (in humans and other organisms, this reaction is catalyzed by a separate glycerol-3-phosphate phosphatase, a reaction also known as "glycerol shunt"). Here, we demonstrate that CrGPDH effectively operates both the alternative Gro3P shunt, which regenerates NAD⁺ and converts DHAP to Gro3P, and the glycerol shunt, which converts Gro3P to glycerol and Pi, across in vitro assays with recombinant proteins, transformed and primary mammalian cell cultures, and in vivo mouse liver experiments. In mammalian systems, CrGPDH rewires redox balance, carbon flux, and lipid metabolism in a cell type- and tissue- dependent manner. CrGPDH expression alone supported proliferation of HeLa cells under mitochondrial electron transport chain inhibition or hypoxia, and supported growth of patient-derived fibroblasts with mitochondrial dysfunction. Moreover, human kidney cancer cell lines, which exhibit abnormal lipid accumulation, had decreased triglycerides levels when expressing CrGPDH. Finally, our CrGPDH genetic tool modulated hepatic lipid metabolism in vivo, partially reversing ethanol-induced triglycerides accumulation. Our findings suggest that the coordinated boosting of the Gro3P-glycerol shunt may be a viable strategy to alleviate consequences of redox imbalance and associated impairment of lipogenesis in a wide repertoire of conditions, ranging from primary mitochondrial diseases to obesity, type 2 diabetes, and metabolic dysfunction-associated steatotic liver disease (MASLD).

overall_design: Desigh agenetically encoded bifunctional enzyme that mitigates NADH redox imbalance and clear Gro3P-linked lipotoxicity via engineered Gro3P-Glycerol shunt

first: Valentin

last: Cracan


title: RNA-seq profiling of wild-type E-mu-Myc-cells cultivated in vitro and of E-mu-Myc-cells-derived B-cell lymphoma treated with Vehicle and ASNase in vivo.

city: Nice

first: Johanna

last: CHICHE

address: 151 Route de Saint Antoine de Ginestière, Batiment Archimed

department: C3M, Inserm U 1065

country: France

institute: INSERM

summary: This dataset contains RNA-seq profiles of wild-type E-mu-Myc-lymphoma cells in two experimental contexts. First, E-mu-Myc-cells isolated from 12 individual transgenic Eµ-MycTg/+ mouse were cultured in vitro under standard growth conditions. Second, RNA-seq was also performed on bulk B-cell lymphomas of wild-type C57BL/6 mice engrafted with E-mu-Myc-#506 cells and treated with either Vehicle or L-asparaginase (ASNase) until disease endpoint. This dataset enables the comparison of transcriptional programs between in vitro–cultured E-mu-Myc-cells. It also evaluates the transcriptional responses to ASNase treatment in vivo in established B-cell lymphomas grown in C57BL/6 mice (n=1 BCL/group).

overall_design: Twelve different E-mu-Myc-cell lines generated from 12 individual trangenic Eµ-MycTg/+ mouse were cultured in vitro under standard growth conditions for 24 hours. Wild-type C57BL/6 mice were engrafted with E-mu-Myc-#506 cells and treated seven days post tumor-cell injection with either Vehicle or asparaginase (ASNase) until disease endpoint.

last: Chiche

first: Nicolas

last: Nottet

first: Jean-Ehrland

last: Ricci


title: Structural and Mechanistic Insights into the Dual-nuclease domain Defense Protein as a Single-Molecule Anti-Phage System

city: Hangzhou

first: Tong

last: Jiajing

address: Xiasha

institute: Zhejiang University of Technology

summary: Nucleic acid degradation is a common strategy for prokaryotic anti-phage systems, as exemplified by the CRISPR-Cas system. The PD-(D/E)-XK nucleases constitute a widely distributed family in these defenses. Notably, most members exhibit a single nuclease domain, while variants containing dual nuclease domains within a single polypeptide remain underexplored, and their molecular mechanisms largely obscure. Here, we biochemically and functionally study a single-molecule system containing an uncharacterized PD-(D/E)-XK defense protein (Upx). As revealed by single-particle electron cryo-microscopy (cryo-EM) structure, the C-terminal domain (CTD) harboring the conserved PD-(D/E)XK catalytic core is buttressed by the N-terminal domain (NTD) and the middle domain (MD). Functional assays demonstrate that the nucleic acid binding capability of the CTD is enhanced by the MD. Unexpectedly, the NTD also displays a noncanonical, minimalist version of exonuclease activity but is auto-inhibited by MD.IP-MS experiments identify Upx-interacting phage proteins, and substrate profiling defines its physiological preferences, collectively pointing to its potential physiological targets. Notably, the phage protein gp16 was found to relieve MD-mediated inhibition of the NTD, suggesting a virus-triggered mechanism for activating Upx’s dual nuclease activities. Together, these findings establish Upx as a single-protein dual-nuclease anti-phage system, expanding our understanding of bacterial immunity and informing antiviral strategy development.

overall_design: RNA-seq profiling of E. coli and their overexpression derivatives(UPX overexpressed) infected with Escherichia phage phiV-1.Samples were collected after infected for 20 minutes.