title: ARID1A recruits TRIM28 for the essential remodeling of heterochromatin independent of SWI/SNF.

city: Shanghai

first: Yihao

last: Wang

state: State

address: Zhizaoju Road 833, Shanghai

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary: ARID1A functions as a vital tumor suppressor whose activity usually depends on the SWI/SNF chromatin remodeling complex. ARID1A is highly mutated across human cancers, and its deficiency has been found to promote immunogenicity through impaired mismatch repair and elevated tumor mutation burden. However, little is known about the SWI/SNF-independent function of ARID1A and the subsequent consequences. Here, we report a novel mechanism of action that ARID1A maintains heterochromatin integrity and silences endogenous satellite/retroelements, independent of SWI/SNF and microsatellite instability. Mechanistically, ARID1A recruits TRIM28 to keep the rigidity of heterochromatin. Loss of ARID1A displaces SETDB1 from TRIM28-contraining heterochromatin complex to induce the derepression of H3K9me3 at endogenous satellite/retroelement regions. The unleashed satellites and retroelements resulting from impaired ARID1A-TRIM28 interaction trigger type-I interferon immune responses, promoting tumor progression and sensitivity to PD1 blockade through both RNA- and DNA-sensing pathways. Our results shed light on the SWI/SNF-independent function of ARID1A to necessarily maintain heterochromatin integrity and safeguard the immunogenicity, potentiating the disruption of ARID1A-TRIM28 interaction as a strategy to convert ARID1A-wildtype tumors into hot to strengthen the therapeutic efficacies.

overall_design: ATAC-seq of control (shCtrl; n=3) and ARID1A-loss (shARID1A; n=3) HCT116 cells.

first: Qian

last: Li

first: Zhe

first: Xiangdong

last: Peng


title: CUL5 E3 ubiquitin ligase regulates the evasion of bladder cancer cells to CD8+ T cell-mediated killing by inhibiting autophagy

status: Public on Jan 29 2026

city: Wuhan

first: Xincheng

last: Gao

state: Hubei

address: 1277 Jiefang Avenue

department: Urology

country: China

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

type: Expression profiling by high throughput sequencing

summary: CD8+ T cells are capable of specifically targeting and eliminating malignant tumor cells, but tumor cells can develop resistance mechanisms to escape CD8+ T cell-mediated killing. Here, we performed a whole genome CRISPR-Cas9 knockout screen under CD8+ T cells pressure and identified the E3 ubiquitin ligase CUL5 as an essential factor required for escaping CD8+ T cells killing in bladder cancer cells. We found that CUL5 knockout promoted the sensitivity of bladder cancer cells to CD8+ T cell-mediated killing both in vivo and in vitro. Mechanistically, CUL5 loss reduced the ubiquitination of PTBP1, which regulated alternative splicing of RUBCN pre-mRNA and led to an increase in the levels of the RUBCN-S isoform, thereby preventing immune evasion of bladder cancer cells by inhibiting autophagy. Importantly, CUL5 knockout significantly enhanced the efficacy of anti-PD-1 immunotherapy in a xenograft model. Collectively, these findings reveal a novel mechanism of bladder cancer immune evasion, providing potential targets for cancer immunotherapy.

overall_design: Considering that PTBP1 acts as a classical splicing factor, we conducted high-throughput sequencing of RNA (RNA-Seq) on the CUL5-WT and CUL5-KO T24 cells to analyze the changes of alternative splicing (AS).

first: Hui

last: Zhang

first: Guosong

last: Jiang


title: Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers

city: Los Angeles

first: Marty

middle: G

last: Yang

state: CA

address: 615 Charles E Young Dr S

department: Biological Chemistry

country: USA

institute: University of California, Los Angeles

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We present a genome-scale method to map the single-molecule co-occupancy of structurally distinct nucleosomes, subnucleosomes, and other protein-DNA interactions via long-read high-resolution adenine methyltransferase footprinting. Iteratively Defined Lengths of Inaccessibility (IDLI) classifies nucleosomes on the basis of shared patterns of intranucleosomal accessibility, into: i.) minimally-accessible chromatosomes; ii.) octasomes with stereotyped DNA accessibility from superhelical locations (SHLs) +/-1 through +/-7; iii.) highly-accessible unwrapped nucleosomes; and iv.) subnucleosomal species, such as hexasomes, tetrasomes, and other short DNA protections. Applying IDLI to mouse embryonic stem cell (mESC) chromatin, we discover widespread nucleosomal distortion on individual mammalian chromatin fibers, with >85% of nucleosomes surveyed displaying degrees of intranucleosomally accessible DNA. We observe epigenomic-domain-specific patterns of distorted nucleosome co-occupancy and positioning, including at enhancers, promoters, and mouse satellite repeat sequences. Nucleosome distortion is programmed by the presence of bound transcription factors (TFs) at cognate motifs; occupied TF binding sites are differentially decorated by distorted nucleosomes compared to unbound sites, and degradation experiments establish direct roles for TFs in structuring binding-site proximal nucleosomes. Finally, we apply IDLI in the context of primary mouse hepatocytes, observing evidence for pervasive nucleosomal distortion in vivo. Further genetic experiments reveal a role for the hepatocyte master regulator FOXA2 in directly impacting nucleosome distortion at hepatocyte-specific regulatory elements in vivo. Our work suggests extreme—but regulated—plasticity in nucleosomal DNA accessibility at the single-molecule level. Further, our study offers an essential new framework to model transcription factor binding, nucleosome remodeling, and cell-type specific gene regulation across biological contexts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-molecule long-read adenine methyltransferase footprinting of protein-DNA contacts in vivo with PacBio sequencing. Datasets include E14 (wild-type), CTCF-AID, and SOX2-FKBP mouse embryonic stem cell (mESC) lines, as well as primary hepatocytes isolated from C57BL/6J (wild-type) and heterozygous FOXA2-dHx knock-in mice.

first: Vijay

last: Ramani

first: Hannah

last: Richter


title: Transcriptomic changes in primary CD4+ T cells upon infection with HIV-1 harboring an intact or defective vpr open-reading frame

city: Tübingen

first: Morgana

last: Barroso Oquendo

address: Otfried-Müller-Straße 37

department: Quantitative Biology Center (QBiC)

country: Germany

institute: University of Tuebingen

summary: We performed unbiased RNA sequencing (RNA-seq) analyses of primary CD4+ T cells infected with HIV-1 harboring an intact or defective Vpr open reading frame and analyzed which genes are deregulated in a Vpr-dependent manner. Our transcriptome analyses showed that NFAT controls 46.5% of 1083 Vpr-deregulated genes in primary CD4+ T cells. Gene set enrichment analyses revealed that Vpr upregulated processes related to T cell signaling, proliferation, and immune function, while downregulating cell cycle progression, ribosome activity, and cytoskeleton organization. qRT-PCR confirmed Vpr-mediated modulation of specific genes, including the upregulation of NEIL1, TNFS4 and CXCL10, and the downmodulation of CCNB1, CDC20, CENPA and PLK1. Hence, a significant portion of Vpr-deregulated genes in primary CD4+ T cells are controlled by NFAT, affecting pathways related to T cell activation, cell cycle progression, cytoskeleton, and chromosome organization.

overall_design: PHA-prestimulated CD4+ T cells were infected with purified and concentrated HIV-1 stocks via spinoculation and analyzed at 48 hours post infection by flow cytometry to assess infection rates. Upon confirmation of similarly high infection rates, CD4+ T cells of three healthy donors were subjected to RNA extraction and RNA-seq. Sequencing yielded 21 to 51 million reads per sample.

first: Darius

last: Anthea

first: Vanegas-Torres

last: Carlos Alberto

first: Schindler

last: Michael

first: Oquendo

last: Morgana Barroso


title: Molecular responses of amaranth species to abiotic stresses

city: Irapuato

first: Alfredo

middle: Heriberto

last: Herrera

state: Guanajuato

address: Libr.  Norte Carr. Leon Km 9.6

department: LANGEBIO

country: Mexico

institute: LANGEBIO

summary: Abiotic stress triggered by Drought or soil salinity impacts  negatively on crop production. To better understand amaranth responses to those environmental stresses, transcriptomics approaches were applied to investigate changes at molecular level in leaves of two Amaranthus species: A. hybridus, a wild species that grows in saline soils and A. hypochondriacus, the most cultivated species for grain production. Under control conditions, A. hybridus showed up-regulation of organic hydroxyl and sulfur compound processes, while A. hypochondriacus showed up-regulation of genes related to photosynthetic process, amino acids, fatty acids, and secondary metabolism. Under salt stress, significantly fewer DEGs were observed in A. hybridus, interestingly those were related to phosphonate and phosphinate metabolism, phosphorous mobilization, and steroid biosynthesis. In contrast, A. hypochondriacus response to salt stress was characterized by starch, sucrose, and trehalose metabolism, porphyrin, monoterpenoid and organonitrogen compounds biosynthetic process.Under water deficit, both species showed similar transcriptional response by up-regulation of LEAs, dehydrins, and genes related to the biosynthesis of Raffinose Family Oligosaccharides. A. hypochondriacus better adaptation to grow under drought and salt stress could be due to its fast response observed by the up-regulation of MAPK signaling pathways, ABC transporters, and production of defense compounds such as glucosinolates. The common response in both amaranth species to both type of stresses was observed by modulation of secondary metabolism, which was directed towards cell wall modification, cuticle and wax metabolism, and the production of antimicrobial and antifungal metabolites

sample_organism:
Amaranthus hybridus
Amaranthus hypochondriacus

overall_design: RNAseq of A. hybridus or A. hypochondriacus plants well watered (Control) or subjected to saline (salinity stress) or water stress (drought) were sequenced by triplicate. Differentially expressed genes were obtained from stress vs control treatments in each amaranth species.

first: Ana

middle: P

last: Barba

first: José

last: Cetz

first: Esaú

last: Bojorquez

first: Jose

last: Martinez

first: Antonio

middle: D

last: Leon

first: Eduardo

last: Espitia


title: Effect of MAX.16H5 and Cyclosporin A treatment on gene expression of CD4+ T cells after stimulation in a one-way mixed lymphocyte reaction.

city: Leipzig

first: Kristina

last: Roth

state: Outside USA

address: Perlickstraße 1

institute: Fraunhofer IZI

summary: We aimed at investigating molecular changes stimulated CD4+ T cells undergo after anti-human CD4 mAb (MAX.16H5) treatment in order to study mechanisms of immune tolerance induction. Non-specific immunosuppression by Cyclosporin A is used as a reference treatment.

overall_design: Unbiased gene expression analysis of stimulated CD4+ T cells after MAX.16H5 and Cyclosporin A treatment compared to the untreated control using five biological relpicates per group.

first: Dennis

last: Loeffler

first: Conny

last: Blumert

first: Alexander

last: Scholz

first: Kristin

last: Reiche

first: Nandja

last: Hilger

first: Uta

middle: S

last: Tretbar

first: Ulrike

last: Köhl

first: Stephan

last: Fricke

first: Ulrich

last: Blache


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and FAD4T thyroid Transcriptomes，Young and Aging thyroid Transcriptomes

first: Junjie

last: Gao

address: 600 Yishan Road

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

summary: A recent study showed thyroid function of both humans and animals decrease as they age. Muchmore, the incidence of thyroid dysfunction was also higher in patients with Alzheimer's disease than in normal people. The goals of this study were to study the molecular mechanism of thyroid dysfunction in FAD4T and aging by transcriptome profiling (RNA-seq). Therefore, we collected the thyroids from 2 month-old wild-type (WT) and 18-month natural aging mouse, 2-month-old WT and 2-month FAD4T mouse, 8-month-old WT and 8-month FAD4T mouse, and then performed RNA sequencing.

overall_design: 2-month FAD4T (n=3), 2-month WT (n=3), 8-month FAD4T (n=3), and 8-month WT (n=3) female mice and the same number male mice as above, and 2-month WT (n=3), 18-maonth WT (n=3) male mice

first: Siyuan

last: Zhu

first: Yidan

last: Pang


title: Hnf1a mutation in endocrine pancreas affect cell function and identity

city: Bergen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

summary:
Purpose: Hnf1a is an important regulator of pancreas development. Mutation in this gene in humans lead to Maturity Onset Diabetes of the Young 3. Previous studies have shown that Hnf1a is important in function of insulin producing cells. However, they have not payed attention to islet cell identity, which we have focused on.
Methods: WT mice or mice carrying a floxed version of the Hnf1a gene in all islet endocrine cells controlled by NGN3-cre were maintainted in normal housing condition and glyceamia were monitored twice a week. Islet cells were isolated from adult mice of each group and mRNA were extracted before shipping to Qiagen for analysis.
Results: Mice carrying the floxed Hnf1a in all endocrine cells were severly hyperglyceamic with alterations in expression of important cell identiy genes.

overall_design: mRNA from pancreatic islets from Ngn3-cre Hnf1a flox mice

first: Thomas

middle: A

last: Legøy

first: Andreas

middle: F

last: Mathisen

first: Luiza

last: Ghila


title: Sympathetic-Epithelial Crosstalk Governs Regionalized CD8+ TRM Cell Immunosurveillance in the Skin [scRNA-seq]

city: Hangzhou

first: Zhang

middle: Zhou

last: melanoma

state: China

address: 西湖大学医学院

institute: Westlake University

summary: Epithelial cells, immune cells, and nerves converge at barrier tissues to collaboratively defend against pathogens and malignancies, but the mechanisms mediating their coordination remain poorly understood. Here we show that in the skin, sympathetic nerves interact with epidermal stem cells (EpiSCs) to regulate CD8+ tissue-resident memory T (TRM) cell density, thereby modulating local immunosurveillance against developing melanoma. Sympathetic nerves anchor on skin epithelium and establish synapse-like connections with EpiSCs, modulating their secretion of chemokine ligand CXCL16 via norepinephrine-ADRB2 signaling. Reduced sympathetic tone elevates CXCL16 secretion, increasing CD8+ TRM cell abundance in the skin epithelium and enhancing local cancer immunosurveillance. Conversely, heightened sympathetic activity during acute stress decreases CD8+ TRM cell number, allowing nascent cancer cells to evade elimination and propagate. Our study unveils a neuro-epithelial-immune axis that governs CD8+ TRM cell dynamics at barrier tissues, and illustrates how regional immunosurveillance can be influenced by systemic neuronal inputs and mental status.

overall_design: To investigate the phenotypes of CD8+ T cells and epidermal cells, we treated Gi-DREADD and control mice with CNO for 3 days to suppress the activity of sympathetic neurons. Then CD45+ cells were isolated by CD45-biotin and Anti-Biotin MicroBeads (Miltenyi Biotec 130-090-485). The remaining cells were designated as P1. The purified immune cells were then sorted by FACS, and the following cell populations were isolated and purified: P2: CD45+, CD3+, TCRβ+, CD8+ (CD8+ T cells), P3: CD45+CD3− (non-T immune cells), P4: CD45+, CD3+, TCRβ− (γδ T and DETC). The P1, P2, and P3 populations from each sample were mixed at a 3:3:2 ratio, respectively.


title: Single-cell landscape of piglet lung response with Actinobacillus pleuropneumoniae

city: Changchun

first: Liancheng

last: Lei

state: Jilin

address: 5333, Xi'an Road

institute: Jilin university

summary: Actinobacillus pleuropneumoniae can cause lethal porcine infectious pleuropneumonia, resulting in substantial economic losses for the pig industry. The lung is the main target organ of A. pleuropneumoniae. However, the lung-specific immune responses against the pathogen remain unclear. In this study, single-cell RNA sequencing analysis of the transcriptome of the piglet lung with or without A. pleuropneumoniae infection identified 18 subpopulations with different phenotypes. Monocytes, neutrophils, and plasmacytoid dendritic cells (pDC) were enriched in the lung post-infection and played anti-infection roles by promoting the expression of interferon-induced factors (such as IL-18) and inflammatory response-associated genes. A. pleuropneumoniae reduced the number of macrophages by inhibiting monocyte differentiation into interstitial macrophages (IM) and alveolar macrophages (AM) and triggering AM endogenous apoptosis. Additionally, A. pleuropneumoniae lowered the amount of various T cell subsets and induced CD8A+ γδ T exhaustion and apoptosis. Furthermore, we identified dramatically augmented pathological fibroblast-¬like cells contributing to rapidly developing pulmonary fibrosis, whereas epithelial cells were significantly decreased, and included those with features of epithelial‐mesenchymal transition differentiated into fibroblasts through the signaling of TGFB1 and HIF1A. Cell-to-cell communication analysis further revealed that the interaction between the EMT-epithelial, vascular endothelial, pDC, and fibroblast subsets, except for COL3A1 fibroblasts, were enhanced, mainly via CD74/(COPA or MIF) receptor ligands after infection, whereas COL3A1 fibroblasts interacted via EGFR/MIF and EGFR/TGFB1 pairs. In summary, our study is the first time to systematically analyze the cell response of piglet lung under the status of physiology and A. pleuropneumoniae infection, deepening the understanding of the molecular basis of pathogenesis, and providing a wealth of resources for the prevention and treatment of A. pleuropneumoniae and other fibrotic lung diseases.

overall_design: Single-cell RNA sequencing (10X Genomics) was used to profile the transcriptomes signatures of lung tissue from three Actinobacillus pleuropneumoniae-infected and three healthy pigs.

first: Junhui

last: Li

first: Xuan

last: Jiang

first: Chuntong

last: Bao

first: Fengyang

first: Rining


title: Cruciform-forming AT/TA repeats are acted upon by structure selective endonucleases and Rad51 prior to repositioning to the nuclear periphery for repair

status: Public on Jan 28 2026

city: New York

first: Bertrand

last: Theulot

state: NY

address: 100 WASHINGTON SQ E, Attn: Duncan Smith

institute: NYU

summary: Structure-forming DNA repeats can pose a barrier to DNA replication and repair and create chromosomal fragile sites. An (AT/TA) 34 DNA repeat, derived from the Flex1 region of human common fragile site FRA16D, can form hairpin and cruciform structures which interfere with DNA replication. When inserted into the S. cerevisiae genome, the Flex1(AT) 34 repeat stimulates chromosome deletions in a manner dependent on the Mus81-Mms4 nuclease and the SLX4 nuclease scaffold. It was previously found that hairpin forming CAG/CTG repeats move to the nuclear periphery to maintain genomic stability. We show that the structure forming AT/TA repeat also relocalizes to the nuclear periphery in late S/G2 phase in a replication and length-dependent manner. In contrast to the CAG repeat, this shift in nuclear positioning is dependent on polySUMOylation and the activity of the Mus81-Mms4 nuclease. Thus, different replication barriers may have differing dependencies for processing and repositioning to the nuclear periphery to protect genome integrity. Processing by the Mre11 nuclease and Rad51 strand exchange occurs prior to repositioning. Replication analysis shows that the replisome likely bypasses the AT structure-induced barrier leaving an under-replicated region that requires resolution. We conclude that AT/TA repeats form post-replicative DNA structures that are targeted for nuclease cleavage and require hairpin processing and repositioning to the nuclear periphery for homologous recombination-dependent repair.

overall_design: OK-seq was performed in Saccharomyces cerevisiae strains carrying either an (AT/TA)_34 DNA repeat or a Flex1 control cassette inserted on chromosome VI or chromosome X, in RAD52+ and rad52Δ genetic backgrounds

first: Jan L

last: Boer

first: Sara M.

last: Crippen

first: Amelia J.

last: Kim

first: Daphne N.

last: Kramer

first: Daniel

last: Dovrat

first: Amir

last: Aharoni

first: Duncan J.

last: Smith

first: Catherine H.

last: Freudenreich


title: Nascent transcriptome changes in response to CDK12/13 inhibition in gliomas

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: To assess changes in the nascent  and steady state transcriptomes after treatment with the CDK12/13 inhibitor THZ531, we performed SLAM-seq in the G7 glioblastoma derived cell line after DMSO treatment or treatment with 500 nM THZ531 for 6 hrs.

overall_design: G7 glioblastoma cells were treated with 500 nM THZ531 for 6 hrs or DMSO for 6 hrs.

first: Silje

last: Lier

first: Deo

last: Pandey


title: Metabolic changes of human induced pluripotent stem cell-derived cardiomyocytes and teratomas after transplantation

city: Tokyo

first: Yusuke

last: Soma

address: Haneda-kuko 1-1-4, Ota-ku

country: Japan

institute: Fujita Health University

summary: Cardiac regenerative therapy using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) has been applied in clinical settings. Herein, we aimed to investigate the in vivo metabolic profiles of hiPSC-CM grafts. RNA sequencing and imaging mass spectrometry were performed in the present study, which revealed that hiPSC-CM grafts matured metabolically over time after transplantation. Glycolysis, which was active in the hiPSC-CM grafts immediately after transplantation, shifted to fatty acid oxidation. Additionally, we examined the metabolic profile of teratomas that may form when non-CMs, including undifferentiated hiPSCs, remain in transplanted cells. The upregulated gene expression of amino acid transporters and the high accumulation of amino acids, such as methionine and aromatic amino acids, were observed in the teratomas. We show that subcutaneous teratomas derived from undifferentiated hiPSCs can be detected in vivo using positron emission tomography with [18F]fluorophenylalanine. These results provided insights into the clinical application of cardiac regenerative therapy.

overall_design: We evaluated gene expressions of human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) tissues and hiPSC-derived teratomas by using RNA-seq two, four and twelve weeks after transplantation of hiPSC-CMs or hiPSCs to the hearts of immunodeficient mice.

first: Shugo

last: Tohyama

first: Akiko

last: Kubo

first: Tomoteru

last: Yamasaki

first: Noriko

last: Kabasawa

first: Hidenori

last: Tani

first: Yuika

last: Morita-Umei

first: Tomohiko

last: C Umei

first: Otoya

last: Sekine

first: Masashi

last: Nakamura

first: Kotaro

last: Haga

first: Taijun

last: Moriwaki

first: Sho

last: Tanosaki

first: Shota

last: Someya

first: Yujiro

last: Kawai

first: Masatoshi

last: Ohno

first: Yoshikazu

last: Kishino

first: Hideaki

last: Kanazawa

first: Jun

last: Fujita

first: Ming-Rong

last: Zhang

first: Makoto

last: Suematsu

first: Keiichi

last: Fukuda

first: Masaki

last: Ieda


title: Inhibition of Cxcr4 chemokine receptor signaling improves habituation learning in a zebrafish model of Neurofibromatosis

city: Madison

first: Andrew

middle: H

last: Miller

state: WI

address: 1111 Highland Ave

department: Neuroscience

institute: University of Wisconsin-Madison

summary: Neurofibromatosis type 1 (NF1) is a neurogenetic disorder caused by loss of function mutations in the gene neurofibromin 1 (NF1). NF1 encodes neurofibromin, a multifunctional tumor suppressing protein that regulates Ras, cAMP, and dopamine signaling. NF1 predisposes patients to a wide range of symptoms, including peripheral nerve tumors, brain tumors, and cognitive dysfunction. Despite considerable work using animal models to investigate the role of neurofibromin in behavior, translating research into treatment for NF1-associated cognitive dysfunction has not yet been successful. Here, we provide evidence that Cxcr4 chemokine receptor signaling is a regulator of habituation learning and modulator of cAMP-PKA signaling in nf1 mutant larval zebrafish. Combining a small-molecule drug screen and RNAseq analysis, we show that cxcr4b expression is increased in nf1 mutants and that pharmacological inhibition of Cxcr4 with AMD3100 (Plerixafor) improves habituation learning. We further demonstrate that Plerixafor activates cAMP-PKA pathway signaling but has limited effects on Ras-Raf-MEK-ERK pathway signaling in the nf1 mutant brain. CXCR4 was previously identified as a potential therapeutic target for neurofibromin-deficient tumorigenesis. Our results suggest that Cxcr4 signaling also regulates neurofibromin-dependent cognitive function.

overall_design: Bulk RNA-seq profiling of wild-type (Tüpfel long fin background) and putative nf1 double homozygous (nf1a-/-;nf1b-/-) mutant zebrafish. Samples were isolated from groups of 20 whole zebrafish larvae at 5 days post-fertilization, including 8 biological replicates from each group.

first: Yeng

last: Yang

first: Natalie

last: Schmidt

first: Jaffna

last: Mathiaparanam

first: Mark

middle: E

last: Berres

first: Mary

middle: C

last: Halloran


title: Genome-wide changes in RNAPII occupancy and phosphorylation in response to CDK12/13 inhibition in gliomas

first: Mads

last: Lerdrup

summary: To assess RNA Pol II (RNAPII) enrichment and modification state after treatment with the CDK12/13 inhibitor THZ531, we performed Cut&Run using antibodies against RNAPII as well as phosphorylated Serine 2 (S2P) or Serine 5 (S5P) in the c-terminal domain of RNAPII in the G7 glioblastoma derived cell line after DMSO treatment or treatment with THZ531 for 1 hr or 6 hrs. In addition, we performed Cut&Run of the H3K27me3 and H3K27Ac histone marks in untreated cells.

overall_design: Cut&Run of RNAPII and modifications (S2P, S5P) in G7 glioblastoma cells. Treatment with 500 nM THZ531 for 1 hr or 6 hrs or DMSO control (6 hrs).

first: Silje

last: Lier

first: Deo

last: Pandey


title: Cell confinement memory initiates heritable loss of chromosomes and a persistently dysregulated division program

city: Philadelphia

first: Dennis

last: Discher

state: Pennsylvania

address: 129 Towne Bldg

institute: University of Pennsylvania

summary: Heritable genetic changes continually arise in cancer, especially in solid tumors where cells sometimes appear compressed. Rare heritable losses of chromosomes in live cells are quantified here with chromosome reporters (ChReporters) that show similar losses after mild or strong compression. Mild compression (to <40% of interphase height) perturbs mitotic spindles and prolongs pro/metaphase but ruptures few nuclei compared to strong compression. Unexpectedly, chromosome mis-segregation into micronuclei emerges only after release from mild confinement, but arrest and death predominate. All such effects are phenocopied by Nocodazole washout that induces a ‘memory’ of prolonged mitosis. The results differ from transient inhibition of the spindle assembly checkpoint and cell cycle entry with a CDK4/6-inhibitor – both of which quickly generate micronuclei. Single-cell-RNA-sequencing confirms chromosome loss days after confinement and reveals persistent upregulation of chromosome segregation. The results suggest a mitotic memory of confinement, addressing a significant gap in mechanobiology and cancer evolution.

overall_design: Our focus on the very rare cells that are ChReporter-negative (~1-per-500 cells). Therefore we sorted live cells for ChReporter loss after the 48h recovery from confinement or 2D controls, and then we used single-cell RNA-seq (scRNAseq) to quantify transcript changes.  RNA libraries were constructed using the Chromium Single Cell Gene Expression kit (v3.1, single index, Catalog no. PN-1000128; PN-1000127; PN-1000213) from 10X Genomics per the manufacturer's instructions. The libraries were submitted to the University of Pennsylvania's Next Generation Sequencing Core for sequencing using NovaSeq 6000 (100 cycles) from Illumina. Raw base call (BCL) files were analyzed using CellRanger (version 5.0.1) to generate FASTQ files and the ‘count’ command was used to generate raw count matrices aligned to GRCh38 provided by 10X genomics.

first: Mai

last: Wang


title: Genomic accesssment of patients with HR+/HER2- metastatic breast cancer treated with palbociclib (PROMISE_study)

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

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

overall_design: Refer to individual Series


title: A spatial transcriptomics comparison of the adult versus metamorphosed axolotl brain

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: The Mexican axolotl (Ambystoma mexicanum) is an established model for studying tetrapod regeneration and development. Notably, axolotls exhibit remarkable brain regeneration as adults, a trait rarely observed in other adult vertebrates. Adult axolotls can undergo metamorphosis, a process that induces dramatic remodeling of multiple organs and is accompanied by a gradual decline in regenerative capacity and lifespan. However, systematic studies on whole-brain cellular dynamics and molecular mechanisms in both adult and metamorphosed individuals remain lacking. Here, we profiled five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals. Our work reveals metamorphosis-associated changes in cell types and molecular profiles across brain regions.

overall_design: We generated Stereo-seq spatial transcriptomes from five representative brain regions of both Adult and Meta. axolotls.  This dataset, comprising 19 sections, surveys the major regions of the adult axolotl brain.

first: Shuai

first: Sulei

last: Fu


title: Impact of NPAS2 on mPFC dopamine synthesis and nap behavior

city: GuangZhou

first: Haobin

last: CEN

address: 232 Outer Ring East Road, University Town, Panyu District, Guangzhou City

institute: Guangzhou University of Chinese Medicine

summary: The biological basis of afternoon nap, a widespread yet poorly understood phenomenon, has remained elusive. Here we identify NPAS2, among core circadian regulators, as a sex-independent determinant of the nap behavior in mice. Specifically, medial prefrontal cortex (mPFC)-expressed NPAS2 orchestrates nap regulation through circadian modulation of local dopaminergic activity. We demonstrate that tyrosine hydroxylase-positive (TH+) neurons in mPFC exhibit time-of-day dependent wake-promoting activity, showing minimal excitation precisely during nap hours. Mechanistically, NPAS2 achieves this circadian suppression through a POU2F2-TH regulatory pathway: 1) transcriptional activation of the transcription repressor POU2F2, and 2) consequent downregulation of TH expression (a rate-limiting enzyme for dopamine synthesis) and dopamine production in mPFC TH+ neurons. These findings establish an endogenous circadian mechanism where mPFC NPAS2 periodically inhibits wake-promoting dopaminergic activity to drive nap behavior, providing fundamental insights into the neural and molecular regulation of nap biology.

overall_design: To elucidate the molecular mechanisms by which mPFC NPAS2 regulates sleep-wake cycles and nap behavior, we performed a comparative single-nucleus transcriptomic analysis using Npas2 KO mice and wild-type littermate controls. Medial prefrontal cortex (mPFC) tissues were harvested from four mice per genotype at circadian time ZT20 (the peak of nap behavior) and pooled by genotype to ensure robust biological representation. Nuclei were isolated using the Shbio Cell Nuclear Isolation Kit (52009-10) in combination with NP-40 lysis buffer to obtain high-quality single-nucleus suspensions. Single-nucleus libraries were then constructed using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit v3.1, followed by high-depth sequencing on the Illumina NovaSeq 6000 platform with a paired-end 150 bp (PE150) configuration.

first: Lianxia

last: Guo

last: Cen

first: Yuwei

last: Huang

first: Zanjin

last: Li

first: Kengran

last: Zeng

first: Zicong

last: Wu

first: Jiaxian

last: Weng

first: Xiaocao

first: Di

last: He

first: Xinyu

last: Liu

first: Zhehan

first: Haiman

last: Xu

first: Tingying

last: Hao

first: Binbin

last: Wei

first: Xingxing

last: Diao

first: Baojian


title: Genome-wide changes in RNAPII occupancy, RNAPII phosphorylation, and transcription in response to CDK12/13 inhibition in gliomas

first: Mads

last: Lerdrup


title: Genomic accesssment of patients with HR+/HER2- metastatic breast cancer treated with palbociclib (PROMISE study) paired

first: Xiaojia

last: Tang

summary: Biomarker studies for cyclin-dependent 4/6 kinase inhibitors (CDK4/6i) are often limited by tissue availability and narrow genomic assessments. We conducted a multicenter prospective study to obtain an unbiased 'omics’ assessment of tumors derived from women commencing 1st line (1L) palbociclib plus letrozole for HR+ HER2- MBC. We generated RNA and DNA data from baseline and a subset of progression samples. Patient-derived xenograft models were established from 10 samples. Genome-wide analyses and semi-supervised assessments of RB1-genes were conducted using whole exome and RNA sequencing data from baseline and progression tumors. Genes (FAT1, MYC, CDK2, and AMBRA1) known to drive CDK4/6i response, were confirmed to be associated with progression free survival (PFS). Novel CDK4/6i response genes including TIMELESS, SAE1, CENPU, SPAG5, and EXO1, as well as copy alterations in cytobands 12q21.2; 11q24.2; 1p22.3; 11p15.1, and 4q22.2 were observed to be associated with PFS. Paired baseline/progression samples demonstrated enrichment of genes involved in lipid metabolic processes, particularly beta oxidation as well as frequent intrinsic subtype switching. An RB1 signature, associated with shorter PFS (HR=2.72, p=0.006) and lack of cell cycle arrest in the NeoPalana study, may identify a subgroup of patients with de novo endocrine resistance.

overall_design:
PROMISE (A Prospective Study to Evaluate the Role of Tumor Sequencing in Women Receiving Palbociclib for Advanced HR+ Breast Cancer [NCT0281902]) is a multicenter clinical study that enrolled pre- or post-menopausal women with HR+ HER2- MBC commencing palbociclib in combination with the aromatase inhibitor, letrozole, or the selective estrogen receptor degrader, fulvestrant, in the 1L or 2L metastatic setting, respectively. Eligible patients underwent tumor biopsies and collection of research blood draws (ctDNA), stool, and urine samples prior to the start of treatment (baseline), after two cycles of treatment (EOC2), and at progression of disease (PD). Patient derived xenografts (PDXs) were also generated from tumor biopsies collected at these time points. In collaboration with Tempus, both WES (exome capture) and RNA-seq used the Integrated DNA Technologies xGen Exome Research Panel v1.0 capture kit. Specically, paired RNA seq samples for 1L PROMISE patients at baseline and at progression are reported here.

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

first: Ciara

last: O’ Sullivan

first: Krishna

middle: R

last: Kalari

first: Matthew

last: Goetz


title: Single-cell RNA sequencing of circulating mock-electroporated CD2 wild-type and CD2-knockout 41BBzeta CART19 cells

first: Marco

last: Ruella

state: PA

address: 3400 Civic Center Blvd

summary: Single-cell gene expression of 4-1BBzeta CART19 cells in both the peripheral blood of OCI-Ly18 DLBCL-bearing mice. Cells were captured and processed using 10X 5' v2 Chemistry GEX

overall_design: CART19 cells generated from a healthy human donor were administered to mice bearing OCI-Ly18 tumors. Briefly, on day −10, 5 × 10^⁶ luciferase-expressing OCI-Ly18 cells were implanted subcutaneously into NSG mice. On day 0, tumor-bearing mice received an infusion of 4 × 10^⁶ CART19 cells that were either CD2 wild-type (n = 8, mock electroporated) or CD2 knockout (n = 6). On day 16, peripheral blood was collected via the retro-orbital sinus. Human T cells from individual mice were subsequently barcoded, pooled according to experimental group (WT or CD2 KO), and isolated by FACS based on CD3⁺CD2⁺CD5⁺ expression.

first: Guruprasad

last: Puneeth

first: Carturan

last: Alberto

first: Ruella

last: Marco


title: Dual Therapy Targeting Cellular Bioenergetics as Treatment for Pancreatic Cancer

city: Duarte

first: James

last: Figarola

address: 1500 E. Duarte Road

department: Diabetes-Metabo Res Inst-BRI

institute: City of Hope

summary: Pancreatic cancer (PC) is a highly aggressive malignancy with a dismal prognosis. Approximately 95% of cases are pancreatic ductal adenocarcinoma (PDAC), which represents the most prevalent histological subtype and is currently the third leading cause of cancer-related mortality in the United States. The limited efficacy of existing therapies highlights an urgent need for novel therapeutic strategies. Metabolic reprogramming is a hallmark of cancer that enables tumor cells to sustain their energetic and biosynthetic demands, thereby supporting uncontrolled proliferation and survival. Targeting these metabolic adaptations represents a promising therapeutic avenue for PDAC. Mitochondrial oxidative phosphorylation (OxPhos) and glycolysis are the two principal energy-producing pathways in mammalian cells, including PDAC cells. Although numerous metabolic inhibitors have been developed for pancreatic and other cancers, clinical trials employing single-agent metabolic therapies have shown limited success, in part due to the pronounced metabolic heterogeneity and plasticity of PDAC. Cancer cells can dynamically shift between glycolysis and OxPhos in response to changes in nutrient and oxygen availability within the tumor microenvironment, thereby evading metabolic stress. We hypothesized that simultaneous inhibition of both glycolysis and OxPhos would overcome this metabolic plasticity and produce enhanced antitumor efficacy. In this study, we evaluated the in vitro effects of two small-molecule metabolic inhibitors, SR4 and lonidamine (LND), targeting OxPhos and glycolysis, respectively, in PDAC models. SR4 is a novel mitochondrial uncoupler that functions as a fatty acid–activated proton transporter, whereas LND inhibits aerobic glycolysis primarily through suppression of mitochondrial-associated hexokinase II, which catalyzes the first committed step of glycolysis. Combined treatment with SR4 and LND produced highly synergistic cytotoxic effects and significantly suppressed proliferation, clonogenic survival, migration, and invasion across PDAC cell lines with distinct metabolic phenotypes. Mechanistically, the dual therapy markedly inhibited glycolysis, mitochondrial OxPhos, and overall cellular bioenergetic capacity, independent of baseline metabolic dependency. The combination treatment also increased reactive oxygen species (ROS) levels and induced mitochondrial membrane depolarization. Furthermore, flow cytometry, protein expression and RNA transcriptomic analyses revealed that dual inhibition more effectively triggered cell cycle arrest, cellular senescence, autophagy/mitophagy, and apoptosis compared with either agent alone. Collectively, these findings demonstrate that concurrent targeting of mitochondrial uncoupling and glycolytic inhibition disrupts cellular bioenergetics and adaptive metabolic responses in PDAC, supporting this dual-metabolic strategy as a promising therapeutic approach for PC.

overall_design: RNA sequence profiling of PDAC human cell lines (BXPC3 and PANC1 ) after 24 h  treatment of  vehicle control , SR4 , Lonidamine and their combination

middle: L

first: Jyotsana

last: Singhal

first: Min-Hsuan

last: Chen

first: Yate-Ching

last: Yuan


title: RBOHD-dependent apoplastic oxidative burst plays a protective role against the necrotrophic fungus Botrytis cinerea

city: Kaiserslautern

first: Alejandra

last: VIelba Fernández

state: Rhineland-Palatinate

address: Paul-Ehrlich-Straße 22

department: BIology

institute: RPTU

summary: The necrotrophic fungus Botrytis cinerea rapidly kills host tissue with its secreted proteins and metabolites. Necrotrophs can trigger the hypersensitive response (HR), which is accompanied by reactive oxygen species (ROS) production, but it remains unclear whether this ROS burst promotes or restricts B. cinerea infection. We have combined Arabidopsis RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) mutant analysis, luminol-based in vivo assays, and the use of CRISPR-Cas generated B. cinerea ROS detoxification mutants to analyze the toxic effect of the ROS burst. In addition, RNA-sequencing, expression analyses and redox imaging were used to study RBOHD-dependent signaling and redox homeostasis. RBOHD mutants showed increased susceptibility to B. cinerea infection, and the apoplastic ROS burst was dependent on RBOHD. Fungal mutants confirmed the importance of SUPEROXIDE DISMUTASE 1 (SOD1) and ACTIVATOR PROTEIN 1 (AP1) for ROS detoxification and virulence. Unexpectedly, the transcriptomes of B. cinerea-infected Arabidopsis Col-0 and RBOHD mutant were highly similar, providing no evidence for a connection of extracellular ROS production and intracellular ROS-induced transcriptional signaling. Nevertheless, RBOHD activity was found to be involved in the maintenance of cellular redox homeostasis under phytotoxic stress. Our results demonstrate an exclusive and protective role of the RBOHD-dependent oxidative burst, but B. cinerea counteracts this response via different detoxification mechanisms.

overall_design: Arabidopsis Col-0 and RBOHD S39A/S339A/S343A were infected with B. cinerea and mock (semisolid Gamborg medium) and incubated in a humid chamber for 48 hours. After this time, samples from at least 5 different plants were harvested and the RNA extracted. 3 different biological replicates were performed, each one consisting in at least 5 plants per genotype and 3 leaves infected per plant.

last: Vielba-Fernández

first: Lea

last: Sommer

first: Désirée

last: Ross

first: Julian

last: Ingelfinger

first: Thorsten

last: Wachtmeister

first: Jochen

last: Hecht

first: Nassim

last: Safari

first: Stefanie J

last: Müller-Schüssele

first: Matthias

last: Hahn


title: Degradation of perineuronal nets in hippocampal CA2 explains the loss of social cognition memory in Alzheimer's disease

city: Charlottesville

first: Harald

last: Sontheimer

state: VA

address: 409 Lane Rd

institute: University of Virginia

summary: Loss of social cognition memory impairs Alzheimer's disease (AD) patients to recognize family members, friends, and caregivers. We investigate the role of perineuronal nets (PNNs), specialized coats of extracellular matrix around hippocampal CA2 neurons in AD‐associated social memory impairments.

overall_design: 3 month and 7 month comparison of bulk RNA profiles from CA2 hippocampus of 5xFAD positive or 5xFAD negative mice

first: Chaunsali

last: Lata

first: Li

last: Jiangtao

first: Fleischel

last: Erik

first: Prim

last: Courtney

first: Kasprzak

last: Izabela

first: Jiang

last: Shan

first: Hou

last: Silky

first: Escalante

last: Miguel

first: Cope

last: Elise

first: Olsen

last: Michelle

first: Tewari

last: Bhanu

first: Sontheimer

last: Harlad


title: 3D-Printed GelMA/Hydroxyapatite/Barium Titanate Piezoelectric Hydrogels for Bone Tissue Engineering

city: 北京

first: Yunfeng

last: Zhao

state: --- Select One ---

address: Beijing

institute: Air Force Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Bone defect repair remains a major clinical challenge. This study presents a novel strategy using a 3D-printed piezoelectric hydrogel scaffold—composed of gelatin methacrylate (GelMA), hydroxyapatite (HA), and barium titanate (BTO)—for functional bone tissue engineering. The GelMA/HA/BTO (GelHABT) scaffold exhibited a well-defined porous structure, enhanced mechanical stability, and, crucially, reliable piezoelectric responsiveness. This key feature enables the material to convert external mechanical stimuli, such as low-intensity pulsed ultrasound (LIPUS), into endogenous electrical signals. In vitro, the scaffold promoted BMSCs adhesion, proliferation, and osteogenic differentiation, with performance significantly enhanced under LIPUS stimulation. Mechanistic insights revealed that the piezoelectric microenvironment remodeled the cellular miRNA expression profile, particularly up-regulating osteogenesis-related miR-29b-3p and activating the AMPK signaling pathway. Collectively, this ultrasound-responsive, gene-regulating scaffold represents a promising approach for treating bone defects by leveraging piezoelectricity to actively stimulate bone regeneration.

overall_design: Based on the results of previous in vitro experiments of materials, GelHA group, as a classical bone repair material, has been widely studied, and its miRNAs expression pattern is relatively mature, which is suitable for use as the control group, and GelHABT group as the experimental group. Both groups of materials were treated under LIPUS conditions to enhance the piezoelectric effect. Each group of BMSCs was seeded on the surface of the material with a density of 1×10⁵ cells/mL, 48-well plate with 500 µL per well, and cultured in a 37°C 5% CO₂ incubator for 24 h. Then, the medium was replaced by osteogenic induction medium for 14 days, and the medium was changed every two days. LIPUS stimulation was given once a day for 10 min.

first: Meng

last: Li

first: Yifei

last: Zhang

first: Wanmin

first: Ying

first: Qian

last: Liu

first: Chufan

last: Ma


title: Genomic accesssment of patients with HR+/HER2- metastatic breast cancer treated with palbociclib (PROMISE study)

first: Xiaojia

last: Tang

summary: Biomarker studies for cyclin-dependent 4/6 kinase inhibitors (CDK4/6i) are often limited by tissue availability and narrow genomic assessments. We conducted a multicenter prospective study to obtain an unbiased 'omics’ assessment of tumors derived from women commencing 1st line (1L) palbociclib plus letrozole for HR+ HER2- MBC. We generated RNA and DNA data from baseline and a subset of progression samples. Patient-derived xenograft models were established from 10 samples. Genome-wide analyses and semi-supervised assessments of RB1-genes were conducted using whole exome and RNA sequencing data from baseline and progression tumors. Genes (FAT1, MYC, CDK2, and AMBRA1) known to drive CDK4/6i response, were confirmed to be associated with progression free survival (PFS).  Novel CDK4/6i response genes including TIMELESS, SAE1, CENPU, SPAG5, and EXO1, as well as copy alterations in cytobands 12q21.2; 11q24.2; 1p22.3; 11p15.1, and 4q22.2 were observed to be associated with PFS. Paired baseline/progression samples demonstrated enrichment of genes involved in lipid metabolic processes, particularly beta oxidation as well as frequent intrinsic subtype switching. An RB1 signature, associated with shorter PFS (HR=2.72, p=0.006) and lack of cell cycle arrest in the NeoPalana study, may identify a subgroup of patients with de novo endocrine resistance.

overall_design:
PROMISE (A Prospective Study to Evaluate the Role of Tumor Sequencing in Women Receiving Palbociclib for Advanced HR+ Breast Cancer [NCT0281902]) is a multicenter clinical study that enrolled pre- or post-menopausal women with HR+ HER2- MBC commencing palbociclib in combination with the aromatase inhibitor, letrozole, or the selective estrogen receptor degrader, fulvestrant, in the 1L or 2L metastatic setting, respectively. Eligible patients underwent tumor biopsies and collection of research blood draws (ctDNA), stool, and urine samples prior to the start of treatment (baseline), after two cycles of treatment (EOC2), and at progression of disease (PD). Patient derived xenografts (PDXs) were also generated from tumor biopsies collected at these time points.  In collaboration with Tempus, both WES (exome capture) and RNA-seq used the Integrated DNA Technologies xGen Exome Research Panel v1.0 capture kit.  Specically, RNA seq from the baseline samples for 1L PROMISE patients are reported here.

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

first: Ciara

last: O’ Sullivan

first: Krishna

last: Kalari

first: Matthew

last: Goetz


title: Viral and host mRNA expression during HSV- 1 infection

city: Kuopio

first: Henri

last: Niskanen

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary: Herpes simplex virus type 1 (HSV-1) infection extensively remodels the host nucleus, marginalizing chromatin to the nuclear periphery and forming prominent viral replication compartments (VRCs). Nuclear speckles, nuclear bodies enriched with RNA-processing factors, are repositioned adjacent to VRCs and undergo structural changes, including enlargement and rounding up. While viral mRNAs are transcribed within VRCs and host transcription is largely suppressed, the nuclear pathways that viral and upregulated host transcripts take en route to the cytoplasm and their relationship with nuclear bodies, remain poorly understood. Furthermore, it is unclear why the infected nucleus continues to uphold these nuclear bodies as the nucleus restructures. Here, we demonstrate that immediate-early (IE) viral transcripts uniquely accumulate within nuclear speckles prior to export, a phenomenon not observed for early or late viral transcripts, highlighting a selective nuclear speckle-dependent processing pathway. Host mRNAs transcriptionally upregulated during infection similarly traffic into nuclear speckles after transcription. Structural remodeling of nuclear speckles includes removal of the long non-coding RNA MALAT1 from nuclear speckles, and increased dynamics of the core nuclear speckle protein SRRM2. Additionally, inhibiting mRNA export results in the accumulation of IE viral mRNAs in nuclear speckles, and disassembling nuclear speckles significantly impairs IE viral mRNA export, effectively blocking downstream viral gene expression, confirming nuclear speckles as critical intermediate hubs for viral transcript processing and nuclear export. Altogether, these findings establish nuclear speckles as indispensable and dynamic regulatory centers that selectively facilitate the processing and export of immediate-early viral mRNAs during HSV-1 infection.

overall_design: HeLa cells were infected with HSV1 and samples for GRO-Seq were collected 4 or 8 hours post infection.

first: Salla

last: Mattola

first: Minna

last: Kaikkonen

first: Maija

last: Vihinen-Ranta


title: Transcriptome changes in trigeminal ganglia in the mouse chronic constriction injury of the infraorbital nerve model - role of TRPM3.

city: Leuven

first: Andrei

last: Segal Stanciu

address: Herestraat 49/801

department: Cellular and Molecular Medicine

country: Belgium

institute: KU Leuven

summary: In this project, we performed bulk RNAseq of mouse trigeminal ganglia at different time points following a constriction of the infraorbital nerve (IoN-CCI model). Samples include both ipsilateral and contralateral samples, as well as samples from sham-operated mice. To evaluate a possible role of TRPM3, trigeminal ganglia were isolated from both wild type and TRPM3-knockout mice. Our data indicate profound and time-dependent transcriptomic changes induced by the IoN-CCI model, but did not reveal IoN-CCI-specific differences between  wild type and TRPM3-knockout mice.

overall_design: Bulk RNAseq of isolated trigeminal ganglia from sham and IoN-CCI wild type and TRPM3 knockout mice, taken at days 0, 3, 11, 18, 25 and 42 after the CCI or sham procedure.

first: Thomas

last: Voets

last: Segal

first: Silvia

last: Pinto

first: Kristof

last: Deseure

first: Nele

last: Van Ranst

first: joris

last: Vriens


title: Stratifying High-Risk Prediabetes Clusters Using Blood-Based Epigenetic Markers

city: Potsdam

first: Amandeep

last: Singh

state: Brandenburg

address: Arthur-Scheunert-Allee 114-116

department: EOD

institute: German Institute of Human Nutrition

type: Methylation profiling by genome tiling array

summary: Previously, we identified six prediabetes clusters, three at moderate and three at high-risk for type 2 diabetes and/or complications. While this novel classification could enable earlier and improved disease prevention, it relies on intensive clinical phenotyping.

overall_design: Here, we developed a machine learning workflow to identify blood-based epigenetic markers to distinguish between prediabetes clusters. DNA methylation was profiled in blood cells of different cohorts including individuals that belong to clusters 2 (low-risk), 3, 5, and 6 (each high-risk) and data was subjected to a machine learning workflow.  In a discovery cohort (n = 187), we identified 1,557 CpG sites as predictors for clusters 2, 3, 5, and 6. These CpGs were sufficient to distinguish between individuals belonging to the high-risk clusters 3, 5 and 6 in an independent replication cohort (n = 146) with an accuracy of 92%.

first: Reiner

last: Jumpertz von Schwartzenberg

first: Robert

last: Wagner

first: Leontine

last: Sandforth

first: Arvid

first: Markus

last: Jähnert

first: Marlene

last: Ganslmeier

first: Stefan

last: Kabisch

first: Nikolaos

last: Perakakis

first: Hubert

last: Preißel

first: Andreas

last: Fritsche

first: Norbert

last: Stefan

first: Dirk

last: Walther

first: Meriem

last: Ouni

last: Birkenfeld

first: Annette

last: Schürmann


title: High-throughput measurements of protein domain functions using magnetic separation

city: Stanford

first: Abby

last: Thurm

address: 443 Via Ortega Rm 036

institute: Stanford University

summary: High-throughput screening of protein domains enables systematic discovery of protein sequences that encode specific cellular functions. Fluorescence-activated cell sorting (FACS)-based assays have been the standard readout for such screens but remain time- and resource-intensive, imposing practical limits on library size and coverage. Here, we describe a scalable magnetic separation-based workflow that provides a simple and quantitative alternative to FACS for screening large protein libraries. We engineered a modular synthetic surface marker, consisting of an IgG1 Fc-PDGFRβ transmembrane fusion, that allows cells to be magnetically separated based on surface reporter expression using Protein G-coated magnetic beads. This approach involves pooled library cloning, lentiviral delivery, magnetic separation, and sequencing-based quantification, enabling reproducible screening of over 200,000 protein domain variants. We have applied the method to transcriptional and RNA-regulatory effector domain screens, identifying new functional domains, and to the selection of improved transmembrane domains for efficient protein surface display. The entire workflow, from library design to data analysis, can be completed in three to four weeks and requires only basic cell culture, molecular cloning, and computational skills. This accessible, high-throughput protocol enables identification of functional protein domains across different phenotypes and provides an alternative screening readout for researchers without access to FACS facilities.

overall_design: High-throughput protein domain screening in K562 cells, using magnetic separation to produce Bound and Unbound fractions each containing cells expressing different protein library members. Enrichment scores are calculated by the ratio of library member counts in each fraction. Libraries were designed as systematic mutations of the 'flexi-NR box' motif, LxxLL, and fused directly to the inducible DNA-binding domain rTetR. After recruitment to synthetic reporter genes under the control of either a minimal or a constitutively active promoter, protein domains were assessed for transcriptional activation or repression capacity.

first: Josh

last: Tycko

first: Connor

last: Ludwig

first: Mark

last: Ragheb

first: Nicole

last: Delrosso

first: Gaelen

middle: T

last: Hess

first: Michael

last: Bassik

first: Lacramioara

last: Bintu


title: Transcriptome profiling of hPDLSCs following Enterococcus LTA stimulation

city: Changsha

first: yue

last: guo

address: 139 Renmin Middle Road

institute: the Second Xiangya Hospital

summary: This study investigates gene expression changes in human periodontal ligament stem cells (hPDLSCs) following exposure to microbial components. hPDLSCs were cultured under osteogenic induction conditions and treated with Enterococcus-derived lipoteichoic acid (LTA) at 10 μg/mL for 7 days. Total RNA was extracted and subjected to RNA-seq on the Illumina NovaSeq 6000 platform. The processed data include gene-level FPKM expression values. These data provide a resource for exploring how microbial components influence the transcriptional responses of hPDLSCs under osteogenic induction.

overall_design: RNA-seq profiling of human periodontal ligament stem cells (hPDLSCs) with or without Enterococcus-derived LTA stimulation (10 μg/mL) after 7 days of treatment. Three biological replicates were included per group.

first: Yue

last: Guo


title: Candida tropicalis biofilm formation under secondary bile salt sodium deoxycholate

city: Itabashi-ku

first: Takahiro

last: Namiki

state: Tokyo

address: 30-1 Oyaguchikamicho

department: Pathology and Microbiology

institute: Nihon University School of Medicine

summary: Candida species are components of the normal intestinal microbiota and are under constant exposure to bacterial metabolites, including secondary bile salts. Here, we examined the effect of a secondary bile salt, sodium deoxycholate (NaDCA), on the formation of biofilms by Candida tropicalis. In contrast to C. albicans, C. tropicalis tended to maintain its absolute biofilm biomass and surface hydrophobicity in the presence of NaDCA. Fluorescent 3D microscopic imaging of the biofilm revealed that NaDCA treatment reduced filamentous projection to the top of the biofilm. RNA-seq analysis revealed that some genes, especially those associated with iron metabolism, were differentially expressed in NaDCA-treated C. tropicalis. Although NaDCA altered the appearance of C. tropicalis biofilms, analysis of the expression of key virulence factor genes encoding agglutinin-like sequences and candidalysin revealed that these genes were less affected by NaDCA in C. tropicalis than in C. albicans. High-iron exposure had a negative effect on C. tropicalis biofilm biomass. These results suggest a difference in the intestinal niche occupied by C. albicans and C. tropicalis according to the local availability of secondary bile salts.

sample_organism:
Candida albicans
Candida tropicalis

platform_organism:
Candida albicans
Candida tropicalis

overall_design: Five different strains of Candida tropicalis (JCM1541, A, 8, 1712, 1822) incubated in RPMI1640 medium with 10% FBS with/without sodium deoxycholate in 37ºC+5% CO2 chamber for 6 hours

first: Kazuhide

last: Takada

first: Satoshi

last: Hayakawa

first: Shihoko

last: Komine-Aizawa


title: Rab37-mediated OPN secretion enriches SPP1+ macrophages through autocrine–paracrine signaling to drive lung tumor progression

city: Tainan

first: You-En

last: Yang

address: No.1, University Road, Tainan 701

department: Department of Pharmacology

country: Taiwan

institute: National Cheng Kung University

summary: Tumor-associated Macrophages (TAMs) are highly plastic immune cells that shape the tumor microenvironment (TME) and influence cancer progression. However, the molecular determinants governing their functional heterogeneity remain incompletely understood. In this study, we identify Rab37 as a key regulator that remodels the states of macrophages within the lung TME. Single-cell RNA sequencing revealed that Rab37 wild-type (WT) tumors were enriched in immunosuppressive Spp1+ TAMs, whereas Rab37 knockout (KO) tumors contained a higher proportion of Thbs1+ TAMs, suggesting Rab37-dependent shifts in macrophage programming. Mechanistically, Rab37 promoted osteopontin (OPN) secretion, which activated STAT3 signaling to establish an autocrine feedback loop that sustained Spp1 expression and induced M2-like polarization. Paracrine OPN signaling further enhanced lung cancer cell proliferation, migration, and invasion. In clinical lung cancer specimens, CD163+/Rab37+/OPN+ TAMs correlated with recurrence and poor survival, and multivariate analysis confirmed their independent prognostic value. Together, these findings demonstrate that Rab37 governs macrophage phenotype and function by orchestrating OPN/STAT3 signaling, thereby reinforcing an immunosuppressive TME and promoting lung cancer progression. Targeting the Rab37–OPN axis may thus represent a promising therapeutic strategy.

overall_design: CD45+ immune cells were isolated from Rab37 WT and KO C57BL/6 mice injected with Matrigel (Matrigel-injected) or tumor cells (LLC-injected) 14 days after tumor establishment. Single-cell suspensions were subjected to scRNA-seq using the 10x Genomics Chromium platform according to the manufacturer’s instructions.

first: Yu-An

last: Lin

first: Lun-Ling

last: Ling

first: I-Ying

last: Kuo

first: Wan-Ting

first: Hsuan

last: Liu

first: Yi-Ching

last: Wang


title: Multi-Omics SMR and Experimental supportive analyses Decipher Causal Drivers Hepatocellular Carcinoma

city: Beijing

first: Tingyang

last: Li

address: No. 16 Dongzhimen Inner South Street, Dongcheng District

department: Institute of Chinese Materia Medica

institute: China Academy of Chinese Medical Sciences

summary: Hepatocellular carcinoma (HCC) is a highly prevalent and fatal digestive system malignancy, challenging to treat due to its latent onset and non-specific symptoms in advanced stages. Somatic mutations play a crucial role in hepatocarcinogenesis, with nearly half of HCC patients carrying oncogenic driver mutations such as TP53, CTNNB1, or TERT. In parallel, germline susceptibility variants identified by genome-wide association studies (GWAS) — including loci near TERT, MBOAT7, TM6SF2, and PNPLA3 — reveal inherited predisposition that shapes the molecular landscape for HCC development. Despite recent therapeutic advancements, long-term survival remains suboptimal, necessitating a deeper understanding of its pathogenesis and the identification of precise molecular targets. Traditional genomic studies, such as genome-wide association studies (GWAS), have successfully identified associated variants; however, due to their statistical design, they do not provide direct causal inference, functional supportive analyses, or comprehensive insight into multi-level molecular regulation and tumor microenvironment heterogeneity, serving instead as a critical starting point for subsequent functional and integrative analyses.

overall_design: To address these gaps, this study employed an integrated multi-omics approach combining HCC GWAS summary data (FinnGen) with expression (eQTL from GTEx V8), methylation (mQTL), and protein (pQTL from ARIC, UKBPPP, DECODE) quantitative trait loci data. We utilized Summary-data-based Mendelian Randomization (SMR) to infer causal associations between molecular traits and HCC risk, prioritizing candidates with higher clinical translation potential. To refine SMR-based prioritization of candidate genes, bulk transcriptome sequencing and ELISA-based quantification were performed as complementary analyses on peripheral blood samples from 10 HCC patients and 10 healthy controls. Following SMR-based gene prioritization, bulk transcriptome and spatial transcriptomic analyses were first used to refine candidate selection and guide subsequent quantification, thereby avoiding unnecessary assays and optimizing the use of clinical samples and research resources. These analyses aimed to assess whether expression changes were directionally consistent with eQTL and pQTL effects, providing supportive—rather than confirmatory—evidence for the inferred genetic associations. Spatial transcriptomics was applied to HCC tissue sections to map region-specific expression patterns of candidate genes. Finally, publicly available single-cell RNA sequencing (scRNA-seq) data was analyzed to resolve cell composition changes, cell-type-specific expression, and intercellular communication networks within the HCC tumor microenvironment.


title: Omacetaxine reduces c-Myc expression and demonstrates antitumor effects in osteosarcoma

city: Fort Collins

first: Sunetra

last: Das

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: Omacetaxine mepesuccinate (OMX), formerly known as homoharringtonine, is a protein translation inhibitor approved for use in human chronic myeloid leukemia.  Recent studies suggest that OMX may be effective against other cancer types, and may be successful against protein targets that are otherwise difficult to inhibit by reducing their translation rates.  Using canine, human, and mouse osteosarcoma (OS) cell lines, we investigated the antineoplastic effects of OMX against OS by evaluating growth inhibition, migration and invasion, apoptosis, expression of c-Myc, changes in gene expression, and in vivo efficacy.  OMX induced dose-dependent growth inhibition and apoptosis of OS cells with IC50 values in the low nanomolar range.  OMX also reduced migration and Matrigel invasion.  Strikingly, levels of c-Myc protein were reduced in most canine, human, and mouse OS cell lines after OMX exposure, and Myc target RNA transcripts were also reduced with treatment. OMX significantly inhibited tumor growth in and metastasis in two separate orthotopic mouse OS models.  OMX is a promising candidate for treatment of OS in both dogs and humans, and potentially other c-Myc-driven cancers.

sample_organism:
Canis lupus familiaris
Mus musculus

platform_organism:
Canis lupus familiaris
Mus musculus

overall_design: RNA-seq profiling of DLM8 and Gracie cells with 6 hours of 50 nM omacetaxine exposure and untreated control cells.

first: Kristen

middle: B

last: Farrell


title: Mutated fibroblast growth factor receptor 1 is an oncogenic driver and therapeutic target in high-risk neuroblastoma

city: Cologne

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Department of Experimental Pediatric Oncology

institute: University Children’s Hospital of Cologne

summary: Fibroblast growth factor receptor 1 (FGFR1) is recurrently mutated at p.N546 in neuroblastoma. We here sought to examine whether mutant FGFR1 is an oncogenic driver, a predictive biomarker, and an actionable vulnerability in this malignancy. FGFR1 mutations at p.N546 were associated with high-risk disease and rapid tumor progression, resulting in dismal outcome of neuroblastoma patients bearing this alteration. Ectopic expression of FGFR1N546K induced constitutive down-stream signaling and interleukin-3-independent growth in Ba/F3 cells, indicating oncogene addicted proliferation. In FGFR1N546K;MYCN transgenic mice, neuroblastoma developed within the first days of life with fatal outcome within 3 weeks, reflecting the devastating clinical phenotypes of FGFR1 mutant high-risk neuroblastoma patients. Treatment with FGFR inhibitors impaired proliferation and pathway activation in FGFR1N546K-expressing Ba/F3 and patient-derived FGFR1N546K mutant neuroblastoma cells, and inhibited tumor growth in FGFR1N546K;MYCN transgenic mice and in a chemotherapy-resistant patient-derived xenograft mouse model. In addition, partial regression of FGFR1N546K mutant tumor lesions occurred upon treatment with the FGFR inhibitor futibatinib and low-intensity chemotherapy in a patient with refractory neuroblastoma. Together, our data demonstrate that FGFR1N546K is a strong oncogenic driver in neuroblastoma that is associated with failure of current standard chemotherapy, and suggest potential clinical benefit of FGFR-directed therapies in FGFR1 mutant high-risk patients.

overall_design: RNA-seq and gene expression analysis of 8 FGFR1N546K and 11 FGFR1N546K;MYCN transgenic mice. RNA-seq data of the mice transgenic for ALKF1174L;MYCN were previously published under GSE254751.

first: Lisa

last: Werr


title: MNK3 cells with CRISPR interference or activation at the CLN3 gene

city: London

first: Mikhail

last: Spivakov

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: This RNA-seq data in MNK3 cells with CRISPRi/a at CLN3 accompanies the manuscript: "High resolution promoter interaction analysis in Type 3 Innate Lymphoid Cells implicates Batten Disease gene CLN3 in Crohn's Disease aetiology".

overall_design: RNA-seq of MNK3 cells with CLN3 gene perturbed with either CRISPRi or CRISPRa approach, and their respective scramble controls. Cells were either unstimulated or stimulated with IL-23 and IL1B. Each condition has three replicates.

first: Rachel

last: Green

first: Gene

last: Oltz

first: Helen

last: Ray-Jones

first: Valeriya

last: Malysheva


title: Gene Expression Changes Induced by YTHDC1 knockdown in triple-negative breast cancer cells

city: guangzhou

first: zhenghao

last: Lai

address: yanjiang road

institute: sun yat-san memorial hospital

summary: To investigate the role of YTHDC1 in triple-negative breast cancer, we performed YTHDC1 knockdown in triple-negative breast cancer cell lines MDA-MB-231 and Hs578T, followed by transcriptome sequencing using next-generation sequencing technology.

overall_design: We randomly divided MDA-MB-231 and Hs578T cells into two groups, each comprising three replicate samples. One group was treated with siYTHDC1, while the other received siNC treatment as the control group. Following successful knockdown of YTHDC1, total RNA was extracted using the Trizol method. After RNA quality control, transcriptome sequencing was performed.


title: A new mouse mutant with a discrete mutation in Pcdhgc5 reveals that the Protocadherin gC5 isoform is not essential for dendrite arborization in the cerebral cortex

city: Bar Harbor

first: Robert

last: Burgess

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: There are ~60 clustered protocadherin (cPcdh) isoforms expressed from three gene clusters (Pcdha, Pcdhb, Pcdhg) arrayed in tandem across nearly 1 Mb in mammals. cPcdhs are homophilic cell adhesion molecules (CAMs) critical for a host of neural developmental functions consistent with a role in cell-cell recognition. Indeed, isoforms make recognition modules in combination to generate recognition diversity far exceeding the ~60 individual CAMs. However, there is also growing evidence for specialized functions for specific isoforms, particularly the C-type isoforms found at the 3’ ends of the Pcdha cluster (aC1 and aC2) and at the 3’ end of the Pcdhg cluster (gC3, gC4, and gC5). We have previously described unique roles for gC3 in dendrite arborization in the cerebral cortex and neural circuit formation in the spinal cord, as well as for gC4 in neuronal survival. Here we report a new mouse mutant specifically targeting the Pcdhgc5 exon encoding gC5. Unlike the rest of the Pcdhg cluster, expression of this isoform does not begin until postnatal stages of mouse development, increasing in the second week of life, suggesting specialized roles. We found significant expression changes in gene pathways involved in synaptic activity, learning and memory, and cognition. Despite this, we saw no major disruption in the cerebral cortex in neuronal organization, survival, dendritic arborization, or synaptic protein expression in these mutants. This new model will be an important tool for future studies delineating specific functions for gC5.

overall_design: Bulk RNAseq was used to examine differential gene expression in the cerebral cortex of mice lacking the Pcdhgc5 isoform of the gamma-protocadherin (Pcdhg) gene cluster.  Six homozygous mutant animals (3 male, 3 female) were compared to 6 wild type littermates (5 male, 1 female).

first: Andrew

middle: M

last: Garrett

middle: W

first: Abigail

last: Tadenev


title: Zinc deficiency contributes to blunted myogenesis in chronic kidney disease

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

institute: University of Kentucky

summary: Frailty in patients with chronic kidney disease (CKD) greatly exacerbates disease comorbidities and increases probability of death. Prior research underscores molecular alterations in skeletal muscle physiology that may underly frailty and poor intervention response in this patient population. CKD can negatively affect satellite cell abundance and function, reducing skeletal muscle injury resilience and adaptive capacity. Pathogenic drivers of compromised satellite cell abundance and activity in patients with CKD remain largely unknown. To address this gap in knowledge, we isolated primary myogenic progenitor cells (MPCs) from patients with CKD and control participants. We also sought to define cell-extrinsic and intrinsic processes that may underlie myogenic deficits. We performed RNA sequencing on MPCs from control participants cultured in control serum, MPCs from control participants cultured in CKD serum, and MPCs from CKD participants cultured in control serum. We identified zinc mishandling as a shared pathway between control cells treated with CKD serum and CKD cells treated with control serum. Consistent with these observations, we found zinc deficiency and attenuated myogenesis in MPCs from patients with CKD. Finally, we showed that zinc supplementation partially restores the myogenic capacity of MPCs from patients with CKD. Together, these data highlight the importance of zinc metabolism in myogenesis and identify a novel mechanism whereby CKD pathogenesis impedes MPC differentiation.

overall_design: Myogenic progenitor cell (MPC) RNA sequenced from control subjects cultured in control serum,  control subjects cultured in CKD serum, and CKD subjects cultured in control serum.

first: Sara

last: Gonzalez-Velez

first: Helena

last: Weiss

first: Karen

last: Zuluaga-Osorio

first: William

last: Paredes

first: Sally

last: Duran

first: Kehao

last: Zhang

first: Allison

last: Owen

first: Matthew

middle: K

last: Abramowitz

first: Christopher

last: Fry


title: T cell receptor-engineered T cells targeting the TP53R248Q neoantigen elicit antitumor effects in human cancer models

city: Shanghai

first: lianghua

last: shen

state: Shanghai

address: Wujin Road No.85

institute: Shanghai General Hospital

summary: Malignant tumors with TP53 mutations exhibit poor therapeutic outcomes and high recurrence rates. T cell receptor (TCR)-based T cell therapy shows great promise for targeting intracellular cancer neoantigens. However, the immunogenic potential of TP53 hotspot mutations remain poorly characterized. Here, we identify a immunogenic neoantigen derived from the recurrent TP53R248Q mutation, presented by the prevalent Human Leukocyte Antigen (HLA)-A*11:01 allele. Additionally, we isolated a TP53R248Q reactive TCR that specifically recognize the TP53R248Q mutation without any discernable cross-activity to cognate wild-type TP53 or other TP53 mutants at the same codon position. Functional characterization revealed that TP53R248Q TCR-T cells exhibited selectively cytotoxicity against tumor cells expressing both TP53R248Q mutation and HLA-A*11:01 in vitro. Importantly, the adoptive transfer of TP53R248Q TCR-T cells exhibited significant anti-tumor activity in a clinically relevant patient-derived xenograft (PDX) model engrafted with TP53R248Q/HLA-A*11:01 positive human tumor tissues. Collectively, our study validates the immunogenicity of the TP53R248Q hotspot mutation and provides a TCR with high therapeutic potential for the development of T cell therapies targeting TP53R248Q/HLA-A*11:01 positive cancers.

overall_design: FACS-sorted CD8+/Tetramer+ cells were harvested, final cell concentration was determined by cell count on a hemocytometer, and the cell concentration was adjusted to approximately 1,000 cells per microliter with a cell viability greater than 98%. Prepare sorted CD8+/Tetramer+ T cells for 10× Genomics single-cell sequencing of rearranged VDJ according to manufacturer’s instructions. Detailed quality control metrics were generated and evaluated using single-cell analysis packages from Bioconductor, including DropletUtils, scater and scran. Genes detected in fewer than three cells and cells where fewer than 200 genes had non-zero counts were filtered out and excluded from subsequent analysis. Low-quality cells with more than 15% of the read counts derived from the mitochondrial genome were also discarded. After single-cell sequencing and analysis, the TCR sequences were evaluated using the Loupe VDJ browser (Cell Ranger, 10× Genomics), and the top ten rankings were performed according to the frequency of TCRs, and the top three ranked human TCR sequences were selected for subsequent functional experiments.

first: Lianghua

last: Shen

first: Ziyu

last: Chen

first: Jian

last: Xu

first: Xiaodan

last: Ding

first: Pengran

last: Wang

first: Xianmin

last: Song

first: Yan


title: High Frequency Loss of 17q11.2 and Downregulation   of the Cancer Metastasis Suppression microRNA miR-193a-3p in Prostate Cancer Bone Metastasis

first: Yong-Jie

last: Lu

address: Barbican

institute: Queen Mary University of London

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Metastasis is the main cause of death from prostate cancer (PCa), a common malignant disease. 90% of PCa metastasis occurs in the bone, thus understanding the genetic chang-es underlying bone preference is critical. However, due to the difficulty in getting samples from the bone and other reasons, limited bone metastasis specific genomic alteration pro-files, particularly at individual sample level, have been published. Here we generated in-dividually genomic change profiles for six PCa bone metastasis samples and identified bone metastasis specific genomic changes. One of them, loss of 17q11.2 genomic region, was further confirmed by another genetic method in further 14/21 PCa bone metastasis samples but only in 9/151 localized PCa. The function of a well-established tumor sup-pressor, miR-193a-3p, located in this lost genomic region, was reduced in bone metastasis,  leading to overaction of two well-established genes to promote cancer metastasis. It pro-vides new insight into bone metastasis development.

overall_design: DNA was extracted from six fresh frozen bone metastases. Samples preparation for hybridization onto Affymetrix SNP 6.0 array chips (Affymetrix, Santa Clara, CA, USA) was performed according to the manufacturer’s protocols.

first: Elzbieta

last: Stankiewicz

first: Sarah

last: McCarley

first: Xueying

last: Mao

first: Sakunthala

last: Kudahetti

first: Tim

last: Oliver

first: Jonathan

last: Shamash

first: Trevor

last: Graham

first: Daniel

last: Berney


title: Heterogeneity study on miRNAs expression in islet cells of rat pancreatic head and tail

city: Fuzhou

first: Jinyan

address: No.7 Wusi Road

institute: Fufian Academy of Medical Sciences

summary: Background：As a vital endocrine organ, the pancreas, which has differences in terms of anatomical structure and microenvironment between the pancreatic head and tail. However, it is currently unclear whether there is heterogeneity in miRNAs expression within the islet cells of these two regions and what biological significance this heterogeneity might bring. Methods：In this study, high-throughput sequencing was applied to analyze the miRNA expression profiles in the islet cells from the pancreatic head and tail in rats. The TargetScan and miRDB databases were used to predict target genes of the differentially expressed miRNAs (DEmiRNAs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were utilized to analysis the target genes. Then the key miRNA was verified by qRT-PCR. Result：A total of 445 miRNAs were detected in the islet cells of the pancreatic head and tail, among which 69 showed significant differences (|log2 fold change|＞0.585 and P＜0.05). Comparing with the pancreatic tail, 28 miRNAs were upregulated and 41 miRNAs were downregulated in the pancreatic head. Bioinformatics analysis revealed that these target genes were significantly enriched in functions such as negative regulation of cellular process, anatomical structure development, intracellular organelle, pancreatic cancer, insulin resistance, MAPK signaling, Wnt signaling, Hippo signaling. In addition, KEGG analysis of target genes showed that miR-124-3p was in several pathways, such as insulin signaling pathway, endocrine resistance, small cell lung cancer, and other pathways in cancer. qRT-PCR results showed that miR-124-3p was significantly upregulated in the pancreatic head. Conclusions：Our research exhibits novel insights on the molecular mechanisms underlying pancreatic cancer and offered potential targets for future diagnostic and therapeutic strategies.

overall_design: miRNA profiles in the islet cells from the pancreatic head and tail of 24-week-old male SD rats were generated by high-throughput sequencing, in six copies, using Illumina NextSeq 500.

first: Xuehua

first: Yunlu

last: Liu

first: Peng

last: Huang

first: Kun

first: Junyong

last: Han


title: Ythdc1-p300-Klf5 complex-mediated Golgi dysfunction promotes aortic aneurysm [Hi-Chip]

city: Shijiazhuang

first: siming

last: Bu

state: CHINA

address: Zhongshan East Road

institute: Hebei Medical university

summary: Klf5 and Golph3l-mediated regulation of Golgi morphology has been implicated in the development of apoptosis induced by diverse stress stimuli, and the loss of VSMCs caused by VSMCs apoptosis is a major factor leading to aortic wall thinning and aneurysm development. However, the molecular link between Klf5, Golph3l, and Golgi morphology alteration in the context of the aortic aneurysm is unclear. Here, we show that apoptosis-induced proliferation (AIP) in VSMCs occurs in AD and AAA tissues of humans and mice. The upregulation of Golph3l by Klf5 facilitates TNF-α and TNFSF12 secretion from AngII-stimulated VSMCs by inducing the compaction of the Golgi, which is essential for AIP and aneurysm development. Mechanistic studies reveal that AngII-induced elevation of global m6A RNA level, especially m6A-Gm40097, is responsible for Golph3l upregulation and AIP in VSMCs. Further, m6A-Gm40097 mediates Klf5 interaction with Ythdc1 and p300 to form a transcription complex on the Golph3l promoter, unveiling a novel lncRNA m6A modification-dependent regulatory mechanism of chromatin remodeling and transcription activation.

overall_design: ApoE−/− mice, Tgln-cre mice, and Golph3l-flox mice containing loxP sites flanking exons 2 and 3 were purchased from Suzhou Cyagen Biotechnology Co., Ltd. Smooth muscle cell–specific Golph3l knockout (smcGolph3l−/− mice) by crossing Golph3l-flox mice and Tgln-cre mice (Golph3l-flox mice served as controls). Mice were kept under a 12-hour light/dark cycle at 23℃ with ad libitum access to food and water.

first: Wenli

first: Zhixue

first: Siming

first: Dong

last: Ma


title: The integrated stress response promotes immune evasion through Lipocalin 2

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

summary: ExCITE-Seq immune analysis of sorted CD45+ immune cell clusters from orthotopically transplanted KP LUAD with doxycycline-inducible shLcn2 and shCtr KP tumors 8 days after adding doxycycline

overall_design: Mice were sedated with ketamine and xylazine and then were injected with 2 ug of APC anti-CD45 (2 ug per mouse diluted in 100 uL PBS, Biolegend 30-F11) retro-orbitally 3 minutes prior to lung collection. The lung lobes were minced on a glass slide and then digested (collagenase IV (Sigma Aldrich C5138), DNAse I (Sigma Aldrich, DN25) in RPMI with 10% FBS) for 35 minutes at 37 degrees celsius. Digestion was stopped with EDTA (1 mM). Digested tissue were filtered into a single cell suspension through a 100 micron filter followed by red blood cell lysis (BD Pharm Lyse 555899). Cells were then washed and suspended in a staining buffer. Cells were then stained with live dead staining (Zombie UV fixabable viability dye, Biolegend #423107) and PeCy7 anti-CD45 (see flow cytometry methods section for staining protocol). Approximately 500,000 lung immune cells from each condition (2 mice per condition) were sorted as live+ IV-CD45 - CD45+ and 50,000 tumor cells were sorted as live+ CD45- GFP+. Sorted samples were multiplexed using cell hashing antibodies (Biolegend) and stained with ADTs (see antibody table). Cells from each sample were pooled and loaded into 10X Chromium.

first: Jozef

middle: P

last: Bossowski

first: Thales

last: Papagiannakopoulos


title: BMX-001, a selective radioprotector in phase II clinical trials, can reverse radiation-induced fibrosis when given three weeks after radiation [Bisulfite-seq]

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

type: Methylation profiling by high throughput sequencing

summary: Radiation provides excellent tumor control in prostate cancer yet unavoidably harms adjacent healthy tissue via the generation of reactive oxygen species (ROS). Radiation-induced ROS is known to impact fibroblasts long after radiation, resulting in radiation-induced fibrosis (RIF), which can cause incontinence and other side effects that reduce patient quality of life. BMX-001, a manganese porphyrin designed to mimic superoxide dismutase, is in clinical trials as a selective radioprotector when given before and during radiation therapy. However, there have been no studies evaluating BMX-001 when given after radiation for its impacts on RIF. Mice were given pelvic radiation (7.5 Gy for 5 consecutive days) followed by BMX-001 three weeks after radiation. Fibroblasts and tissues were isolated two months following radiation. We found that BMX-001 returned radiation-induced alterations in fibroblast morphology to normal and reversed markers of fibroblast activation and senescence. BMX-001 also decreased collagen deposition six months after radiation. We found that overall, radiation resulted in reduced methylation two months after radiation, and BMX-001 administered three weeks after radiation modulated radiation-altered methylation patterns back to normal and restored normal expression of a fibrosis-associated gene CAMK2beta. BMX-001 also decreased radiation-induced DNA adduct 8-hydroxy-2’-deoxyguanosine (8-OHdG), which is known to interfere with methylation. BMX-001 was able to prevent DNA oxidation and restore normal methylation patterns in an oligonucleotide model of DNA oxidation and methylation. This study reveals the feasibility of agents to reverse fibrosis in pelvic radiation and suggests that BMX-001 may be effective when given after radiation.

overall_design: Twelve RRBS bisulfite-seq methylation samples of four different treatments in mice with three replicates each: PBS, BuOE, PBS+raditation, and BuOE+radiation.

first: Molly

last: Myers

first: Elizabeth

last: Kosmacek

first: Chia Sin

last: Liew

first: Arpita

last: Chatterjee

first: Luis

last: Marky

first: Rebecca

last: Oberley-Deegan


title: Single-cell RNA sequencing for female Schistosoma mansoni to investigate BATT-induced sexual maturation.

first: Mengjie

last: Gu

address: 2005, Songhu Rd

institute: Fudan University

summary: Single-cell RNA sequencing (scRNA-seq) was performed on virgin/adult females using 10x Genomics to explore transcriptome change after BATT induction. Egg production by female Schistosoma is central to both the transmission and pathology of schistosomiasis, a neglected tropical disease affecting over 200 million people globally. Female sexual maturation depends on the male-derived pheromone β-alanyl-tryptamine (BATT), yet the molecular mechanisms underlying this process remain largely unknown.

overall_design: Virgins were cultured in A169 medium with either 50 μM BATT or 0.05% DMSO (vehicle control) for 2 days. For each condition, three biological replicates (~200 worms) were processed. In addition, approximately 60 adult females, freshly perfused from mice at 7 weeks post-infection, were processed for single-cell RNA sequencing.

first: Jipeng

last: Wang


title: Genetic background and transient prenatal disruption of vitamin A signaling determine susceptibility to airway hyperresponsiveness in mice

city: College Station

first: Masako

last: Suzuki

state: TX

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

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

overall_design: Refer to individual Series


title: NAT10-mediated ac4C-modification exacerbates ferroptosis by stabilizing HMOX1 in Deep vein thrombosis

city: Jinan

first: Yunhong

last: Zhang

state: Shandong

address: No. 4655, Daxue Road, Changqing District, Jinan, Shandong

institute: Shandong University of Traditional Chinese Medicine

summary: In our study, we aimed to identify the pathways closely related to the pathogenesis of deep vein thrombosis. Through microarray analysis, we discovered the important pathway of ferroptosis.

overall_design: The genome-wide analysis of mRNA expression of peripheral blood mononuclear cells in DVT patients (n= 6) and control subjects (n= 6) were performed using Human mRNA (4*180K, Design ID: 084410).

first: Zhen

first: Xinkui

last: Liu

first: Bin

first: Xia

last: Li


title: Pulmonary fibrosis after COVID-19 is characterized by airway abnormalities and elevated club cell secretory protein-16

first: David

state: NY

address: 650 W 168th Street, Room 905, New York, NY 10032

institute: Columbia University in the City of New York

summary: Prior studies testing biomarkers of residual lung abnormalities after COVID-19 are limited by sampling within the first year after acute COVID-19 illness and lack of external validation of findings. In three independent, international, racially and ethnically diverse prospective cohorts of survivors of moderate to critical COVID-19, we systematically tested 18 circulating biomarkers of inflammation, aging, endothelial activation, pulmonary epithelial function, fibrosis, and fibrinolysis. We found that only higher club-cell secretory protein-16 (CC16) levels are consistently associated with persistent fibrotic lung abnormalities in cross-sectional and longitudinal analyses for up to 3 years after acute COVID-19. Histopathological and single-cell RNA sequencing analyses of transbronchial biopsies of fibrotic lung abnormalities in COVID-19 survivors sampled between 3 and 4 years after acute illness and of COVID-19 lung explants suggest that circulating CC16 reflects underlying deranged pulmonary epithelial progenitor proliferation and anomalous CC16/MUC5B-related pro-fibrotic signaling in the distal airways. CC16 should be investigated further as a potential blood biomarker that may facilitate screening of COVID-19 survivors for pulmonary fibrosis and its progression.

overall_design: We compared single cell analyses of transbronchial lung biopsies of fibrotic-like abnormalities in study participants obtained between 3 and 4 years after acute COVID-19 to transbronchial biopsies from four asymptomatic lung transplant recipients done as part of routine surveillance during the first year after lung transplantation. Since there was no evidence of infection or rejection and normal appearing lung architecture in the lung transplant biopsies, these samples were used as healthy lung tissue controls. A thoracic pathologist (AS) reviewed all transbronchial biopsies and explant lung tissues.

first: Matthew

last: Baldwin

first: Ainsley

last: Jones

first: Chandan

last: Gurung

first: Zain

last: Khan

first: Anjali

last: Saqi

first: Xuehan

last: Yang

first: Ying

last: Wei

first: Renu

last: Nandakumar

first: Scarlett

last: Murphy

first: Claire

last: McGroder

first: Faisal

last: Shaikh

first: Selim

last: Arcasoy

first: Luke

last: Benvenuto

first: Harpreet

last: Grewal

first: Benjamin

last: Smith

first: Agnes

last: Yuen

first: Parteek

last: Johal

first: Chrisopher

last: Carlsten

first: Christopher

last: Ryerson

first: Brent

last: Richards

first: Alyson

last: Wong

first: Tomoko

last: Nakanishi

first: Aditi

last: Shah

first: Christine

last: Garcia


title: NAT10-mediated ac4C-modification exacerbates ferroptosis by stabilizing HMOX1 in Deep vein thrombosis [acRIP-Seq]

first: Yunhong

last: Zhang

summary: In our study, we aimed to identify the mechanisms closely related to ac4C. Through acRIP-seq analysis, we found that NAT10 enhances the stability of HMOX1 via ac4C modification, which leads to iron overload and lipid peroxides. This forms a positive feedback loop that exacerbates DVT.

overall_design: HUVECs were transfected with NC or si-NAT10.The RNA is first extracted from the sample (extracted using TRIzol), the RNA is quality controlled, and the concentration and purity of the RNA is detected. Total RNA was subjected to immunoprecipitation according the manufacturer’s instructions. The samples were sequenced using a NovaSeq platform (Illumina).

first: Zhen

first: Xinkui

last: Liu

first: Bin

last: Wang

first: Xia

last: Li


title: Genetic background and transient prenatal disruption of vitamin A signaling determine susceptibility to airway hyperresponsiveness in mice [RNA-Seq]

first: Masako

last: Suzuki

summary: Airway structural changes and hyperresponsiveness (AHR), hallmarks of asthma, are crucially influenced by genetic variations and adverse exposures. While intrauterine environmental perturbations leading to dysfunctional lung development have been linked to adult pulmonary disease, still little is known about the developmental events leading to these postnatal abnormalities. Here, we provide evidence of genetic background playing a key role in this process. Using A/J and C57BL/6J mice known for their distinct susceptibility to AHR, we show that A/J but not C57BL/6J develop an aberrant airway smooth muscle (SM) program and AHR in adulthood when exposed transiently to a vitamin A/retinoic acid (RA)-disrupted intrauterine environment in vivo by a maternal BMS493 administration. Single nuclei multiomics analysis identified a subpopulation of mesenchymal cells that overactivated TGFβ targets in response to BMS selectively in A/J, but not C57BL/6J, embryonic lungs. These cells, localized to sites of airway SM initiation, exhibited robust BMS-mediated upregulation of SMAD2/3 targets, including regulators of SM program Pdgfra and Tnc, and showed stable cell proportions despite the marked transcriptional rewiring following RA disruption. These findings identify TGFβ-activating mesenchymal cells as a critical niche responsive to RA signaling and reveal how genetic background determines developmental susceptibility to micronutrient perturbations with long-term impact on airway function.

overall_design: To identify the differentially expressed genes between the control group and the group treated with BMS493, we tested gene expression profiles in the lungs of male A/J and B6 mice at E14.5.

first: Takehiro

last: Otoshi

first: Ayyappa Kumar

last: Sista Kameshwar

middle: D

last: Kotton

first: Yoshinori

last: Seki

first: Zachary

last: Cardell

first: Ke

last: Xiangyi

first: Yuta

last: Matsuno

first: Pooja

last: Rajaram

first: Youn-Kyung

last: Kim

first: Loredana

last: Quadro

first: Wellington

middle: V

last: Cardoso


title: BMX-001, a selective radioprotector in phase II clinical trials, can reverse radiation-induced fibrosis when given three weeks after radiation

first: Jean-Jack

last: Riethoven

overall_design: Four total RNA-Seq samples of different treatments in mice: PBA, BuOE, PBS+raditation, and BuOE+radiation.

first: Molly

middle: S

last: Myers

first: Elizabeth

middle: A

last: Kosmacek

first: Chia Sin

last: Liew

first: Arpita

last: Chatterjee

first: Luis

last: Marky

first: Rebecca

last: Oberley-Deegan