title: ChIP-seq of ESCC Cells Overexpressed TFAP2β or its LLPS-deficient Mutants

summary: This dataset contains raw ChIP-seq data from esophageal squamous cell carcinoma (ESCC) cells overexpressing TFAP2β or its LLPS-deficient mutants (ΔIDR3 or Mut_IDR3). The experiment aims to explore the chromatin binding profiles of TFAP2β and its phase separation-deficient mutants to uncover the role of TFAP2β's LLPS activity in regulating gene expression in ESCC. Data were collected from the genomic binding of TFAP2β and its LLPS-deficient mutants, providing insights into the regulatory networks controlled by TFAP2β in cancer progression.

overall_design: ChIP-seq of TFAP2β or LLPS-deficient mutants (ΔIDR3 or Mut_IDR3) in ESCC cells KYSE150 to understand the chromatin binding dynamics and regulatory activity associated with TFAP2β’s phase separation mechanism.


title: The role of low-complexity repeats in RNA–RNA interactions and a deep learning framework for duplex prediction

status: Public on Dec 17 2025

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

type: Expression profiling by high throughput sequencing

summary: RNA-RNA interactions (RRIs) are fundamental to gene regulation and RNA processing, yet their molecular determinants remain unclear. In this work, we analyzed several large-scale RRI datasets and identified low-complexity repeats (LCRs), including simple tandem repeats, as key drivers of RRIs. Our findings reveal that LCRs enable thermodynamically stable interactions with multiple partners, positioning them as key hubs in RNA-RNA interaction networks. RNA-sequencing of the interactors of the Lhx1os lncRNA allowed to validate the importance of LCRs in shaping interactions potentially involved in neuronal development. Recognizing the pivotal role of sequence determinants, we developed RIME, a deep learning model that predicts RRIs by leveraging embeddings from a nucleic acid language model. RIME outperforms traditional thermodynamics-based tools, successfully captures the role of LCRs and prioritizes high-confidence interactions, including those established by lncRNAs. RIME is freely available at https://tools.tartaglialab.com/rna_rna.

overall_design: RNA sequencing of two independent Lh1xos pull-down experiments, which allowed the isolation of the Lhx1os lncRNA using 20 nt-long antisense biotinylated oligonucleotide probes in mESC-derived motor neurons. The experiments were performed employing two sets of probes, ODD and EVEN, targeting all the Lhx1os isoforms. A third set of probes, targeting the LacZ mRNA, was used as a negative control (LacZ). The enrichment in each pull-down sample was assessed by comparing it with the Input sample.

first: Adriano

last: Setti

first: Giorgio

last: Bini

first: Flaminia

last: Pellegrini

first: Valentino

last: Maiorca

first: Gabriele

last: Proietti

first: Dimitrios

last: Miltiadis-Vrachnos

first: Angelo

last: D'Angelo

first: Alexandros

last: Armaos

first: Julie

last: Martone

first: Michele

last: Monti

first: Giancarlo

last: Ruocco

first: Emanuele

last: Rodolà

first: Alessio

last: Colantoni

first: Gian Gaetano

last: Tartaglia


title: Coordinate tumor-antigen uptake and dendritic cell activation by chimeric antigen receptors. [RNA-seq]

city: Geneva

first: Nadine

last: Fournier

state: Geneva

address: CMU, Rue Michel-Servet 1

department: Faculty of Medicine

country: Switzerland

institute: University of Geneva

summary: Effective anti-tumor immunity requires dendritic cells (DCs) to internalize, process and present tumor antigens to T cells. Adoptive transfer of DCs loaded ex vivo with tumor antigens has been shown to stimulate anti-tumor immunity in patients with cancer, but clinical responses have been mixed. To address limitations of traditional DC-based therapies, we constructed and functionally screened a panel of chimeric antigen receptors (CARs) optimized for expression and activity in DCs. Through this screening, we identified key functional components that informed the design of an inducible platform centered on an instructive chimeric antigen receptor (iCAR). This platform enables the DCs to (i) recognize a surface molecule present on cancer cells or their extracellular vesicles (EVs), such as GD2 and HER2, thereby promoting the acquisition of tumor-derived material that contains putative tumor antigens; (ii) undergo immunostimulatory activation to prime antigen-specific T cells via both cross-dressing and cross-presentation; and (iii) transactivate the expression of a therapeutic gene (IL-12) in response to antigen uptake. The iCAR converted melanoma-derived EVs from immune-suppressive to stimulatory cues for DCs. Moreover, systemic administration of iCAR-DCs enhanced antigen-specific T cells, expanded low-frequency T cell clonotypes, and delayed tumor growth in immunotherapy-resistant melanoma models without the need for ex vivo antigen loading or cell maturation. iCAR-DCs provide a platform for antigen-agnostic cancer immunotherapy that integrates antigen uptake with programmable DC activation.

overall_design: Comparative gene expression profiling of MutuDCs (Ctrl-iCAR or iCAR) treated with GD2+ EVs or untreated.

first: Yahya

last: Mohammadzadeh

last: De Palma


title: LINE-1 locus transcription nucleates oncogenic chromatin architecture

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

country: USA

institute: St. Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: Functional Remodeling of iNKT Cells by Sulfatide-Reactive Type II NKT Cells Reprograms Alveolar Macrophages to Alleviate Lung Ischemia-Reperfusion Injury

status: Public on Dec 16 2025

city: Guangzhou

first: Wen

last: Zheng

address: No. 2 Lujing Road, Yuexiu District

department: Dermatology Hospital

country: China

institute: Southern Medical University

summary: Lung ischemia-reperfusion injury (LIRI) is a serious complication in critical clinical situations. Despite its importance, the specific role of type II natural killer T (NKT) cells in LIRI remains unclear.

overall_design: In this study, we establish a LIRI mouse model and demonstrate that sulfatide-reactive type II NKT cells promote M2 polarization of alveolar macrophages (AMs) and alleviate LIRI through AMs-mediated mechanisms. This protective effect is absent in Jα18-/- mice, indicating the essential role of invariant NKT (iNKT) cells. Further analysis shows that interleukin-10 (IL-10) secreted by iNKT cells upregulates AT-rich interaction domain 3A (Arid3a) in macrophages, which then promotes the transcription of DNA damage inducible transcript 4 (DDIT4). This cascade enhances M2 polarization of macrophages, potentially contributing to lung protection and alleviating LIRI. These findings suggest that NKT cells may offer a therapeutic target for LIRI in the future.

first: Qingqing

last: Li


title: Cell-specific effects of acute sleep deprivation on transcriptomic signatures of non-neuronal cells in the mouse hippocampus and prefrontal cortex

city: Iowa City

first: Junko

last: Kasuya

state: IA

address: 169 Newton Rd

department: Neuroscience and Pharmacology

institute: University of Iowa

summary: Sleep is essential for maintaining cognitive, emotional, metabolic, and immune functions in animals. Although much research on sleep homeostasis has focused on neurons, non-neuronal cells are also critical. We performed transcriptomic analyses on nuclei isolated from non-neuronal cells in the hippocampus and prefrontal cortex of mice subjected to acute sleep deprivation (SD). We demonstrate that acute SD elicits robust, cell-type and region-specific transcriptional reprogramming in astrocytes and oligodrocytes. The most striking changes are in astrocyes, with reductions in cholesterol biosynthesis genes across both regions, but opposite changes in genes regulating mitochodrial and neurodegeneration-related pathways. Strikingly, we see the induction of genes associated with primary cilia in cortical astrocytes.  Within oligodendrocytes, genes encoding cell-adhesion molecules are down regulated.  This work highlights the importance of focusing our gene expression studies on specific cell populations and reveals new potential mechanisms for the regulation of sleep and sleep function by non-neuronal cells.

overall_design: Cell-specific effects of acute sleep deprivation on transcriptomic profiles were analyzed in non-neuronal cells from mice hippocampus using single nuclear RNAseq

first: Yutong

last: Wong

first: Yann

last: Vanrobaeys

first: Marcos

last: Frank

first: Ted

last: Abel


title: Coordinate tumor-antigen uptake and dendritic cell activation by chimeric antigen receptors.

first: Rachel

last: Marcone


title: Combination immunotherapy induces post-intervention control of HIV

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: Study examining the efficacy of combination immunotherapy including HIV vaccination, immune stimulation/latency reversal, and passive transfer of broadly neutralizing antibodies (bNAbs) in humans

overall_design: We performed a proof-of-concept combination study of these three approaches in ten people with HIV on ART that included (1) therapeutic vaccination with an HIV/Gag conserved element (CE)-targeted DNA+IL-12 prime/MVA boost regimen followed by (2) administration of two bNAbs (10-1074 and VRC07-523LS) and a toll-like receptor 9 (TLR9) agonist (lefitolimod) during ART suppression, followed by (3) repeat bNAb administration at the time of ART interruption

first: Leanne

middle: S

last: Whitmore

first: Demi

last: Sandel

first: Elise

last: Smith

first: Jennifer

last: Tisoncik-Go

last: Gale Jr.

last: Rutishauser


title: In vivo CRISPR screening identifies SAGA complex members as a key regulators of hematopoiesis [ATAC]

city: Philadelphia

last: Haney

state: PA

address: 422 Curie Boulevard

institute: University of Pennsylvania, Perelman School of Medicine, Department of Pathology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The biological mechanisms that sustain the vast blood production required for healthy life remain incompletely understood. To search for novel regulators of hematopoiesis, we performed a genome-wide in vivo hematopoietic stem and progenitor cell (HSPC)-based CRISPR knockout screen for regulators of hematopoiesis. We discovered SAGA complex members, including Tada2b and Taf5l, as key regulators of hematopoiesis. Loss of Tada2b or Taf5l strongly inhibited hematopoiesis in vivo, causing a buildup of immature hematopoietic cells in the bone marrow. The SAGA complex deposits histone H3 lysine 9 acetylation (H3K9ac) and removes histone H2B ubiquitination (H2Bub). Loss of Tada2b led to reductions in H3K9ac levels and altered H2Bub enrichment in HSPCs, implicating disruption of SAGA complex activity. This was associated with upregulation of interferon pathway genes, reduced mitochondrial activity, and increased megakaryocyte progenitor cell commitment. Loss of these factors also enhanced the cell outgrowth and the interferon pathway in an in vivo human myelodysplastic syndrome cell line model. In summary, this study has identified the SAGA complex as an important regulator of hematopoiesis.

overall_design: ATAC-seq of HSPCs in vitro including Tada2b KO HSPCs

first: Adam

last: Wilkinson

first: Christy

last: Munson

first: Ian

last: Hsu


title: In vivo CRISPR screening identifies SAGA complex members as a key regulators of hematopoiesis [scRNA]

overall_design: Single Cell-seq of HSPCs in vitro including Tada2b, Taf5l KO HSPCs

first: Haney

last: Michael


title: Coordinate tumor-antigen uptake and dendritic cell activation by chimeric antigen receptors. [TCR-seq]

first: Nadine

last: Fournier

overall_design: TCRB sequencing of B16F10 tumors with iCAR conditions. Tumors from mice in different conditions were harvested and TCRbeta sequencing was performed.

first: Yahya

last: Mohammadzadeh

first: Michele

last: De Palma


title: Transcriptomic Signature-Guided Depletion of Intermediate Alveolar Epithelial Cells Ameliorates Pulmonary Fibrosis in Mice

city: New Orleans

first: Yong

last: Zhou

state: LA

address: 333 S Liberty St

department: Medicine - Pulmonary Diseases

institute: Tulane University

summary: scRNA-seq was used to profile transitional AT2 cells in bleomycin-injured mouse lungs. Using an RNA-sensing strategy, Sprr1a-expressing cells corresponding to Krt8⁺ alveolar differentiation intermediates (ADIs) were selectively labeled and analyzed. scRNA-seq revealed that Sprr1a+ cells display transcriptomic features of transitional epithelial states. These datasets provide a resource to study the role of transitional epithelial populations in lung fibrosis.

overall_design: C57BL/6 mice were treated with bleomycin to induce lung fibrosis. At the fibrotic stage, AAV6.2FF vectors encoding Sprr1a sensor RNAs fused to EGFP were delivered to label Sprr1a+ transitional AT2 cells. Labeled (EGFP+) and unlabeled cells were isolated for scRNA-seq using the 10x Genomics Fixed RNA Profiling platform with a custom EGFP probe. Libraries were sequenced on an Illumina NextSeq 2000 and analyzed with Cell Ranger and Scanpy to define Sprr1a+ cell states and compare them with known Krt8+ ADIs.

first: Fei

last: Peng

first: Chun-sun

last: Jiang

first: Zhen

last: Zheng

first: Shaharam

last: Aliyari

first: Dan

last: Shan

first: Aaryan

last: Sabharwal

first: Qinyan

last: Yin

first: Shigeki

last: Saito

first: Chao

last: He

first: Ivan

middle: O

last: Rosas

first: Joseph

middle: A

last: Lasky

first: Victor

middle: J

last: Thannickal


title: Spatiotemporally Controlled Restoration of GAS6 Signaling via mRNA Therapy Promotes Scarless Healing in Preclinical Models

city: hangzhou

first: Yan

state: 浙江省

address: hangzhou

institute: 浙江大学医学院附属第二医院

summary: Deep cutaneous injuries in adult mammals often lead to fibrotic scarring, a process exacerbated by inflammatory fibroblasts that amplify immune recruitment. Early modulation of immune-fibroblast crosstalk represents a promising therapeutic strategy. Here we show that GAS6 is a key regulator of this interaction and can be therapeutically targeted using a spatiotemporally controlled lipid nanoparticle (LNP)-mRNA hydrogel platform. We engineer LNP-GAS6 mRNA to enhance macrophage efferocytosis and suppress inflammatory fibroblasts, then encapsulate it in a thermosensitive hydrogel for localized delivery. In murine, rabbit ear, and Bama minipig wound models, this treatment significantly accelerates wound closure and reduces fibrotic scarring. These results demonstrate that restoring GAS6 signaling via mRNA-based delivery promotes scarless healing and offers an effective therapeutic approach for fibrotic skin disorders.

overall_design: Male C57BL/6 mice (6-8 weeks) underwent dorsal full-thickness 6-mm circular excisions under intraperitoneal injection anesthesia, stabilized with silicone rings and 3M Tegaderm film (inhibiting wound contraction). Treatments included hydrogel + LNP and hydrogel + GAS6 mRNA-LNP. Peri-wound tissues were harvested at day 3.


title: PTEN regulates vagal-insulin signaling to optimize autonomic output determining peripheral inflammatory and metabolic homeostasis

city: Toronto

first: Minna

last: Woo

state: Ontario

address: 10-601D, College Street

department: Department of Medicine

country: Canada

institute: University of Toronto

summary: The vagus nerve (VN) is a major component of the parasympathetic nervous system that regulates glucose and energy homeostasis. However, the specific molecular signaling pathways mediated by the VN that regulates homeostasis remain unclear. Here, we show that vagal neuron-specific deletion of phosphatase and tensin homolog (Pten), the endogenous negative regulator of PI3K, led to increased vagal output. Intriguingly, dopaminergic signaling genes were upregulated, correlating with elevated sympathetic nerve density and increased norepinephrine levels in adipose tissue of Pten-deficient mice. These mice were also protected against high-fat diet-induced obesity, insulin resistance, and systemic inflammation. To investigate insulin-specific PI3K signaling within the VN, we generated mice with vagal neuron-specific insulin receptor deletion that resulted in exacerbation of metabolic defects, which was rescued by concomitant Pten deletion. In summary, we show that insulin-PI3K-PTEN axis within vagal neurons is essential in optimizing the autonomic output that determines peripheral inflammatory and metabolic homeostasis.

overall_design: Overall experimental design: P-PTEN WT and P-PTEN KO animals were weaned at 4 weeks of age and allowed to acclimatize to newly separated littermates for 2 weeks prior to performing baseline insulin/glucose tolerance tests. Following the 2 weeks, the animals and subsequently separated into chow or high fat diet consisting of 60% fat content cohorots and were maintained on their respective diets for 3 months. Following the 3 months, the animals were assessed for their vagal output , endpoint itt/gtts and metabolic parameters via metabolic caging. Animals were then subsequently euthanized and their adipose, liver and muscle tissue were collected for molecular analysis including western blot, real-time PCR alongside histological analysis Single-nucleus rna-sequencing design: Animals were fed for 2 weeks of HFD after 6 weeks of age where the body weights start to diverge between our P-PTEN WT and P-PTEN KO. Animals were subsequently euthanized and both their left and right cervical vagus nerves which contained the nodose ganglion were collected. 14 vagus nerves collected from 7 animals were then subsequently pooled into a single sample from both cohorts of mice. Nuclei were then extracted per sample and single nucleus rna-sequencing was performed. The Seurat and Harmony programs were used in RStudio version 4.2.2 to annotate and cluster different cell populations and to generate the list of genes enriched within the different cellular populations. The samples are separated into WT and KO data respectively

first: Yu Zhe

last: Li

first: Joe Eun

last: Son

first: Nathaniel

last: Vo

first: Catherine

last: Bellisimo

first: Ju Hee

last: Lee

first: Joshua

last: Rapps

first: Evan

last: Pollock-Tahari

first: Martha

last: Ghebreselassie

first: Chuck Tsu

last: Chen

first: Richard P

last: Bazinet

first: Fillio

last: Billia

first: Akira

last: Suzuki

first: Chi-Chung

last: Hui

first: Tak W

last: Mak

first: Hoon-Ki

last: Sung

first: Paul

last: Yoo


title: Connectome-seq: High-throughput Mapping of Neuronal Connectivity at Single-Synapse Resolution via Barcode Sequencing [snRNA-seq, ssRNA-seq]

city: Urbana

first: Boxuan

last: Zhao

state: IL

address: 505 S Goodwin Ave

institute: UIUC

summary: Understanding neuronal connectivity at single-cell resolution remains a fundamental challenge in neuroscience, with current methods constrained by an inherent trade-off between throughput and synaptic precision. Here we present Connectome-seq, a high-throughput method that combines engineered synaptic proteins, RNA barcoding, and single-compartment sequencing to map neuronal connectivity at single-synapse resolution. We validate this approach in the mouse pontocerebellar circuit, successfully identifying thousands of connections including the predominant excitatory projections from pontine neurons to cerebellar granule cells, while also revealing potentially novel synaptic partnerships. By enabling systematic mapping of neuronal connectivity across brain regions with single-cell precision, Connectome-seq provides a scalable platform for comprehensive circuit analysis across different experimental conditions and biological states. This advance in connectivity mapping methodology opens new possibilities for understanding circuit organization in complex mammalian brains.

overall_design:
Pons and cerebellum tissue was obtained from Sun1-sfGFP-Myc mice, and nuclei and synaptosomes were subsequently isolated via fluorescence-activated cell sorting, selecting based on GFP, HA, or V5 signals, before undergoing single-nucleus and single-synaptosome RNA sequencing (snRNA-seq, ssRNA-seq) analysis.
mRNA library: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode


title: Dgat1 detoxifies androgen receptor signaling to promote antitumor CD8+ T cell responses

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: The role of fatty acid (FA) oxidation 31 in T cell responses has been extensively studied, but whether FA esterification to triacylglycerol (TAG) regulates T cell exhaustion is unknown. Dgat1 catalyzes the rate-limiting step in TAGsynthesis. Here,we showthat deficiency in Dgat1 improvedmitochondrial metabolic fitness and expanded the pool of progenitors of CD8+ exhausted T (Tex) cells to sustain antitumor responses in femalemice. Inmalemice, however, Dgat1 deficiency synergized with androgen receptor (AR) signaling to cause FA peroxidation, endoplasmic reticulum (ER) stress, and Tex cell death. Deletion of Ar, overexpression of glutathione peroxidase 4 (Gpx4), or inhibition of ER stress-induced cell death rescued Dgat1-deficient CD8+ T cell survival and promoted antitumor responses in male mice. This study suggests that Dgat1 detoxifies AR signaling to protect against ER stress-induced cell death and maintain T cell stemness in males, and highlights sex-specific metabolic adaptations in the tumormicroenvironment.

overall_design: Male and female C57BL/6N mice (6-8 weeks old) were subcutaneously inoculated with 3e5 B16-GP33 cells. On day 15 post-inoculation, P14 WT and Dgat1 KO mice were sacrificed, and splenocytes were isolated and cultured for 72 hours with GP33 peptide (10 ng/mL) and IL-2 (10 ng/mL). Activated splenocytes from KO and WT mice were mixed while maintaining equal numbers of CD8+ T cells in both groups. The mixture was intravenously injected into tumor-bearing mice. Four days later, mice were euthanized. TILs were enriched by gradient centrifugation, and WT and KO P14 donor cells were FACS-sorted.

first: Alaa

last: Madi

first: Guoliang

last: Cui


title: High-resolution mapping and transcriptional profiling of coronary-cardiomyocyte interactions during zebrafish heart development

city: Montreal

first: Rubén

last: Marín-Juez

address: 3175 Chem. de la Côte-Sainte-Catherine

institute: CHU Sainte-Justine

summary: We used a 10X Genomics single-cell RNA sequencing approach to study transcriptional profiling of coronary developmental stages in zebrafish comparing data from initiation (10 mm), establishment (14 mm), expansion (18 mm) and maturation (28 mm).

overall_design: One pool of ventricles per developmental stage, initiation (10 mm) 25 ventricles, establishment (14 mm) 18 ventricles, expansion (18 mm) 12 ventricles and maturation (28 mm) 5 ventricles were extracted for single-cell dissociation and library preparation.

last: Marin-Juez

first: Muhammad Abdul

last: Rouf

first: Gülsüm

last: Kayman-Kürekçi

first: Shaoqiu

last: Zhang

first: Stéphanie Larrivée

last: Vanier

first: Sarah M.

last: Kamel

first: Ann Nee


title: The Lysine Demethylase Kdm4C is an Oncogenic Driver and Regulates ERK Activity in KRAS Mutant Pancreatic Ductal Adenocarcinoma

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine


title: Neuronal Idol deletion ameliorates amyloid pathology

city: Indianapolis

first: Jungsu

last: Kim

state: IN

address: 320 W. 15th Street

institute: Indiana University School of Medicine

summary: Earlier studies demonstrated that overexpression of the low-density lipoprotein receptor (LDLR) decreases apolipoprotein E (APOE) levels in the brain and alleviates amyloid-beta (Aβ) pathology. We hypothesized that inhibiting the Inducible Degrader of LDLR (IDOL)- an E3 ubiquitin ligase that ubiquitinates LDLR for degradation- would increase endogenous LDLR levels and decrease amyloid pathology. Previously, we demonstrated that the deletion of Idol increased LDLR levels and reduced amyloid deposition in a transgenic mouse model of Aβ-amyloidosis. However, the cellular mechanisms underlying these beneficial effects were unknown. Here, we investigate the cell-type-specific contribution of Idol deletion to amyloid pathology by generating Idol conditional knock-out mouse models. We demonstrate that deletion of neuronal, but not microglial, Idol reduces amyloid accumulation in the 5XFAD transgenic mouse model. Furthermore, only neuronal Idol deletion alters brain LDLR and APOE levels, pointing to the critical role of the neuronal LDLR-APOE axis in modulating Aβ accumulation.

overall_design: Quant-seq (3' mRNA-seq) analysis of cerebral cortices of female 5xFAD mice with Camk2a-Cre Idol WT vs. cKO genotypes at 4 months of age

first: Hande

last: Karahan

first: Kelly

last: Hartigan

first: Md Mamun

last: Al-Amin

first: Sutha K

last: John

first: Brianne

last: McCord

first: H.R. Sagara

last: Wijeratne

first: Dominic J

last: Acri

first: Daniel C

last: Smith

first: Luke C

last: Dabin

first: Hannah M

last: Rondon Cordero

first: Byungwook

first: Do-Hun

last: Lee


title: Vaginal and gut microbiome pilot in the Carolina Endometrial Cancer

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

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

institute: University of North Carolina at Chapel Hill

summary: Characterization of the microbiome in vaginal and stool samples self-sampled from endometrial cancer survivors enrolled in the Carolina Endometrial Cancer Study.

overall_design: Observational Cohort

first: Hazel

middle: B

last: Nichols

first: Mu

last: Jin


title: Differential expression of VA opsin transcript variants in tissues linked to photoperiodic time measurement in Svalbard rock ptarmigan

city: Tromsø

first: Jana

last: Kalinova

address: Postboks 6050 Stakkevollan

country: Norway

institute: UiT The Arctic University of Norway

summary: Photoperiodic time measurement is the process through which annual changes in daylength are integrated to synchronize seasonal physiological and behavioral responses. Unlike mammals, which detect light exclusively through the eyes, birds possess multiple photoreceptive sites including the eyes, pineal gland, and deep brain photoreceptors (DBPs) located within the hypothalamus. The cellular and molecular identity of the DBPs mediating avian photoperiodic time measurement remains a matter of debate, however. Vertebrate ancient opsin (VA opn) is considered a strong DBP candidate, based on its anatomical localization and spectral response characteristics. Here, we used three different RNA profiling methods to evaluate VA opn expression across photosensitive structures in the Svalbard rock ptarmigan, a highly photoperiodic galliform species adapted to the extreme light conditions of the High Arctic. In the pineal gland, over 60% of transcripts encoded a full-length VA opn, containing all seven transmembrane domains considered necessary for photoreceptor function. In vitro analysis demonstrated that the full-length VA opn has peak spectral sensitivity at approximately 500 nm, consistent with published work in other galliform species. By contrast, in the hypothalamus and retina, the majority of VA opn transcripts are predicted to encode non-functional proteins lacking at least 2 out of 7 transmembrane domains. In the hypothalamus, single-nuclei RNA-sequencing analysis showed that VA opn transcript variants are predominantly expressed in cells of the oligodendrocyte lineage. These data support a model in which, in the Svalbard rock ptarmigan, VA opn contributes to the photosensitivity of the pineal gland, but not to hypothalamic DBP function.

overall_design: RNA-profiling of photosensitive tissues (hypothalamus, retina, pineal gland) of the Svalbard rock ptarmigan across 4 seasonal states.


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [CP-9mo-m-022]

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating aging effects on the epigenomic features of brain is critical to understand brain functional decline and neurodegeneration. Single nucleus methylation sequencing was applied to brain regions of mouse at the age of 2, 9 and 18 months. We use these data to identify the epigenomic changes with aging in mouse brains.

overall_design:
Apply snmC-seq3 to mouse brain regions to identify aging effects on epigenomics

Processed data for these samples are available at:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE313770

first: Q

last: Zeng

first: Wei

last: Tian

first: Anna

last: Bartlett

first: J

last: Nery

first: Rosa

last: Gomez Castanon

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: N

middle: D

last: Johnson

first: M

last: Kenworthy

first: C

last: Valadon

first: Huaming

last: Chen

middle: M

last: Behrens


title: The Lysine Demethylase Kdm4C is an Oncogenic Driver and Regulates ERK Activity in KRAS Mutant Pancreatic Ductal Adenocarcinoma [ChIP-seq]

first: Anirban

last: Maitra

summary: Deregulation of proteins involved in chromatin regulation is common in pancreatic ductal adenocarcinoma (PDAC). Lysine demethylase 4C (Kdm4C) is one of the chromatin-modifying proteins frequently overexpressed across multiple solid cancers and is linked to chromatin instability, increased cell proliferation, and enhanced stem cell-like behavior. We observed upregulation of Kdm4C protein in a panel of human PDAC cell lines and patient samples compared to non-neoplastic controls. CRISPR/Cas9-mediated deletion of KDM4C in human and murine PDAC cells reduced proliferation, clonogenicity and increased survival of orthotopically implanted murine PDAC allografts. Transcriptomic and proteomics analyses revealed that loss of Kdm4C in both human and murine PDAC cell lines was associated with reduction of activated phospho-Erk, a pivotal effector downstream of mutant Ras. Using proximity labeling, we identified the histone deacetylase SIRT1 as a novel interacting protein with Kdm4C via the latter’s Tudor reader domain. SIRT1-mediated deacetylation leads to repression of downstream targets, including the dual specificity phosphatase DUSP2, which is known to inactivate Erk via dephosphorylation. In vitro propagation of KDM4C-null PDAC lines eventually led to adaptation and restitution of Erk signaling via compensatory upregulation of other KDM4 family members. To bypass this genetic compensation, we tested a preclinical pan-KDM4 inhibitor TACH107 and confirmed its efficacy in in vitro and in vivo PDAC models including those resistant to the covalent KRASG12D inhibitor MTRX1133.  Our studies identify Kdm4C as an oncogenic molecule that sustains Erk signaling in KRAS-mutant PDAC and can be broadly targeted via small molecule inhibitors.

overall_design: H3K27Ac and H3K36me3 ChIP-seq profiling of wildtype AsPC1 cells, and their early passage KDM4C knockout derivatives.

first: Mennatallah

last: Shaheen

first: Sarah

last: Dhebat

first: Kimal

middle: I

last: Rajapakshe

first: Bidyut

last: Ghosh

first: Benson

middle: C

last: Selvanesan

first: Shariq

last: Ansari

first: Cara

last: Haymaker

first: Dorsay

last: Sadeghian

first: Huamin

last: Wang

first: Haoqiang

last: Ying


title: Small RNA profiling under HIF1alpha control

status: Public on Dec 15 2025

city: Tainan

first: Jie

middle: ning

last: Li

state: Please select an option below

address: No1. University road

department: Department of Medical Laboratory Science and Biotechnology

country: Taiwan

institute: National Cheng Kung University

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

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

first: Jie-Ning


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

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

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

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

first: Masahiro

last: Wakita

first: Koyu

last: Ito

first: Hideka

last: Miyagawa

first: Kaho

last: Fuji

first: Dai

last: Sakamoto

first: Takumi

last: Mikawa

first: Sho

last: Sugawara

first: Xiangyu

last: Zhou

first: Jeong

middle: H

last: Park

first: Emi

last: Ogasawara

first: Akiko

last: Takahashi

first: Hiroshi

last: Kondoh

first: Naotada

last: Ishihara

first: Eiji

last: Hara


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

city: Los Angeles

first: Jason

middle: Michael

last: Link

address: 650 Charles E Young Dr S

department: Surgery

institute: University of California, Los Angeles

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

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

first: Zev

last: Wainberg

first: Timothy

last: Donahue


title: Identification of a Lipid Oxygen Radical Defense pathway and its epigenetic control [ChIP-Seq]

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

institute: EPFL

summary: Membrane phospholipids are vulnerable to oxidative radicals, and uncontrolled lipid peroxidation affects cell viability. Cells have evolved quality control and defense mechanisms, of which the genetic regulation is not fully understood. Here, we identify what we have coined the Lipid Oxygen Radical Defense (LORD) pathway. It is epigenetically repressed by a complex comprising the KRAB-zinc finger protein ZNF354A, the scaffold protein KAP1/TRIM28, the histone methyltransferase SETDB1, and the transcriptional activator ATF2. Upon lipid peroxide accumulation, p38- and JNK-dependent phosphorylation of ATF2, KAP1/TRIM28, and ZNF354A leads to disassembly of the repressive complex, releasing ZNF354A from specific DNA loci and activating a network of protective genes, including NRF2 targets. The pathway affects the cellular sensitivity to oxidative stress and ferroptosis, revealing a previously uncharacterized layer of epigenetic control in lipid quality control and damage repair. This positions the LORD pathway as a promising therapeutic target for diseases linked to chronic inflammation, neurodegeneration and cancer.

overall_design: ChIP-seq in K562 cells expressing GFP or doxycycline-induced ZNF354A-HA, with or without 50 µM H₂O₂ for 4 h. Chromatin was crosslinked, sonicated, and immunoprecipitated with anti-HA beads (Pierce: 88837). Libraries were prepared with the NEBNext Ultra II kit and sequenced on the Element Aviti platform (PE150). Four replicates per condition.

first: Francisco S

last: Mesquita

first: Laurence

last: Abrami

first: Romain

last: Forey

first: Béatrice

last: Kunz

first: Charlène

last: Raclot

first: Lucie

last: Bracq

first: Danica

last: Milovanovic

first: Olga

last: Rosspopoff

first: Filipe

last: Martins

first: Didier

last: Trono

first: Gisou

last: van der Goot


title: Identification of a Lipid Oxygen Radical Defense pathway and its epigenetic control [RNA-Seq]

overall_design: U2OS human osteosarcoma cells were transfected with control siRNA (siCtrl) or siRNA targeting ZNF354A (siZNF354A). Four independent biological replicates were prepared per condition. Total RNA was extracted 72 hours after transfection for mRNA sequencing to identify transcriptional changes upon ZNF354A depletion. For human ZNF354A, 3 different siRNA in 3’-UTR were tested and validated, from Qiagen: ZNF354A (TACATCCTTGAGAGAGATGTA), from Santa Cruz (sc-91974), ZNF354A (GTCACGTGATCATCAGAAA), and from Origene , ZNF354A (GAGGTTTATCCATGGAATTAAATACCT). A control siRNA, a sequence targeting the viral glycoprotein VSV-G (5’-ATTGAACAAACGAAACAAGGA-3’) was used.

first: Charlene


title: Glc7/PP1 triggers Paf1 complex dissociation from RNA polymerase II to enable transcription termination

city: Pittsburgh

first: Karen

middle: M.

last: Arndt

state: Pennsylvania

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

summary: The mechanisms that control the dynamic composition of RNAPII elongation complexes govern major transitions in the transcription cycle yet are poorly understood. Here, we show that the transcription elongation factor Spt5 determines elongation complex composition to promote productive elongation and the transition to termination. Using an unbiased genetic screen and genomic approaches in Saccharomyces cerevisiae, we provide evidence that dephosphorylation of the Spt5 C-terminal repeat domain (CTR) by Glc7/PP1 is required to dislodge the Paf1 complex (Paf1C) from RNAPII near the cleavage and polyadenylation site (CPS). Mutations in Paf1C or the Spt5 CTR that dissociate Paf1C from RNAPII bypass the requirement for two critical regulators of Glc7 in the cleavage and polyadenylation factor that promote Glc7 enrichment at the 3’ ends of genes. Depletion of Glc7 causes aberrant retention of Paf1C past the CPS and a dramatic increase in readthrough transcription, which is fully suppressed by Paf1C mutations. Our results demonstrate that Paf1C retention antagonizes transcription termination and that Glc7-mediated restructuring of the RNAPII elongation complex to evict Paf1C at the CPS is a critical step in the transition from elongation to termination.

overall_design: Saturated Transposon Analysis in Yeast using WT, spt5∆5, spt5∆CTR and spt5-S1-15A mutant S. cerevisiae strains. After transposition induction over 18-20 days, the genomic DNA regions flanking the transposon insertion site were sequenced.

first: Sanchirmaa

last: Namjilsuren


title: METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [RNA-Seq 22Rv1 M3 writing]

city: TORONTO

first: Xin

last: Xu

address: 101 COLLEGE ST EAST TOWER 11-601D

institute: Princess Margaret Cancer Center

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

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

first: Yujuan

last: Wang

first: Helen

last: Zhu

first: Housheng

last: He


title: Comparison of Multi-MiRNA Models from Donor-Matched Plasma and Cerebrospinal Fluid as Candidate Biomarkers for Alzheimer’s Disease Prediction

city: Portland

first: Julie

last: Saugstad

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Anesthesiology & Perioperative Medicine

institute: Oregon Health & Science University

type:
Expression profiling by RT-PCR
Non-coding RNA profiling by array

summary:
To validate candidate miRNA biomarkers for AD in donor and date matched CSF and plasma from a cohort of healthy control and AD donors;
We obtained 320 donor- and date-matched normal control (NC) and AD CSF and plasma samples from the AD Neuroimaging Initiative 2, then analyzed 57 potential AD miRNA biomarkers in both biofluids by RT-qPCR.

overall_design:
CSF and plasma samples from 160 participants (80 AD and 80 NC; 320 total) were obtained from ADNI 2.
We used CSF and plasma samples from living donors obtained from the Alzheimer's Disease Neuroimaging Initiative 2 to validate the expression of 57 candidate Alzheimer's Disease vs Healthy control miRNA biomarkers. The miRNAs were quantified on custom Taqman Low Density miRNA Arrays from ThermoFisher Scientific.
Please note that 32 samples are excluded from the final analysis as detailed in the sample data processing field (i.e. normalized_data.txt contains

first: Ursula

last: Sandau

first: Joseph

last: Quinn

first: Jack

last: Wiedrick

first: Siting

last: Chen

first: Trevor

last: McFarland


title: LINE-1 locus transcription nucleates oncogenic chromatin architecture [L1CaP-C]

city: Memphis

first: Jian

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

summary: Retrotransposons are a prolific class of genomic parasites frequently upregulated in human cancers, where their spontaneous mobility can generate insertional mutations and structural variations. However, whether retrotransposon-derived gene products contribute to cancer beyond retrotransposition remains unclear. Here, we identify an oncogenic, chromatin-associated function of RNAs produced by Long Interspersed Element-1 (LINE-1), the only autonomous human retrotransposon. Sequencing analysis of subcellular fractions revealed that LINE-1 RNAs primarily exist as nascent transcripts expressed from full-length, cell type-specific genomic copies of evolutionarily young LINE-1 subfamilies. Through developing a long-read sequencing-based chromosome conformation assay, we uncovered a class of highly interactive LINE-1 loci essential for gene expression across cancer subtypes, establishing an unexpected regulatory link between LINE-1 locus transcription and oncogenic gene expression via long-range chromatin interactions. Depleting LINE-1 RNAs disrupted LINE-1-centric chromatin interactions, leading to the downregulation of associated genes, whereas inserting a LINE-1 element into an endogenous genomic locus induced de novo chromatin interactions in a transcription-dependent manner. Therefore, retrotransposons not only mutagenize linear genetic content but also regulate cancer gene expression through transcription-dependent nucleation of chromatin architecture.

overall_design: LINE-1 Capture Pore-C (L1CapC) was performed on wild-type MCF7, K562, and T47D cell lines. It was also conducted on MCF7 cells treated with either a scrambled antisense oligonucleotide (ASO) or a LINE-1-targeting ASO. Additionally, LINE-1 Capture Pore-C was carried out on MCF7 cells stably expressing either a transgenic LINE-1 element or an "empty vector" TagBFP, both integrated at the "Rogi2" safe harbor locus (chr3:22,746,757).

first: Michael

last: Lee Jr.

first: Yuannyu

last: Zhang


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

city: NAGOYA

first: XINGXING

last: WANG

state: 愛知県

address: 65 Tsurumai-cho, Showa-ku

department: cancer biology

institute: Nagoya University

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

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

first: Kohei

last: Kumegawa

first: Keiko

last: Shinjo

first: Xingxing

first: Akinori

last: Kanai

first: Shota

last: Takashima


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

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

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

first: Reo

last: Maruyama


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

first: Daisuke

last: Motooka

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

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

first: Masahiro

last: Wakita

first: Koyu

last: Ito

first: Hideka

last: Miyagawa

first: Kaho

last: Fuji

first: Dai

last: Sakamoto

first: Takumi

last: Mikawa

first: Sho

last: Sugawara

first: Xiangyu

last: Zhou

first: Jeong

last: Park

first: Emi

last: Ogasawara

first: Akiko

last: Takahashi

first: Hiroshi

last: Kondoh

first: Naotada

last: Ishihara

first: Eiji

last: Hara


title: Characteristics of senescent cells resistant to ABT263 and ARV825

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

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


title: The Lysine Demethylase Kdm4C is an Oncogenic Driver and Regulates ERK Activity in KRAS Mutant Pancreatic Ductal Adenocarcinoma [RNA-Seq]

first: Anirban

last: Maitra

overall_design: RNA-seq profiling of wildtype AsPC1 cells, and their early passage KDM4C knockout, or late passage KDM4C knockdown derivatives.

first: Mennatallah

last: Shaheen

first: Sarah

last: Dhebat

first: Kimal

last: Rajapakshe

first: Bidyut

last: Ghosh

first: Benson

last: Selvanesan

first: Shariq

last: Ansari

first: Cara

last: Haymaker

first: Dorsay

last: Sadeghian

first: Huamin

last: Wang

first: Haoqiang

last: Ying


title: Hippocampal Cofilin and CFL1 gene variants are linked to Alcohol Use Disorder phenotypes

city: Warsaw

first: Katarzyna

last: Radwańska

state: Prowincja

address: ul. L. Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology (PAS)

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

overall_design: The total hippocampus and amygdala of adult (6-7 month-old) female mice that exhibit alcohol use disorder (AUD)-like phenotype characterised by excessive alcohol seeking during withdrawal (high drinkers) and those who limit alcohol seeking during alcohol non-availability periods (low drinkers) were used to the experiment. Tissue from alcohol-naive age-matched female mice was used as a control.

first: Roberto

last: Pagano

first: Ahmad

last: Salamian

first: Edyta

last: Skonieczna

first: Bartosz

last: Wojtas

first: Bartek

last: Gielniewski

first: Galip

middle: Y

last: Ünlü

first: Anna

last: Cały

first: Robbert

last: Havekes

first: Ted

last: Abel

first: Liubov

last: Kalinichenko

first: Monika

last: Puchalska

first: Małgorzata

last: Grochowicz

first: Zofia

last: Harda

first: Christiane

last: Mühle

first: Bernd

last: Lenz

first: Johannes

last: Kornhuber

first: Anbarasu

last: Lourdusamy

first: Christian

middle: P

last: Müller

first: Kasia

last: Radwanska


title: Oxidative Stress Signaling and Regenerative Responses in a Larval Zebrafish Model of Retinal Light Damage

city: Messina

first: Luigi

last: Donato

state: Italy

address: via Consolare Valeria, 1

department: BIOMORF

institute: University of Messina

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

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

first: Ignacio

last: Babiloni-Chust

first: S.

last: Sartori

first: Darin

last: Zerti

first: Matthias

last: Carl

first: Rosalia

last: D’Angelo

first: Rita

last: Maccarone

first: Lucia

last: Poggi


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

city: San Diego

first: Xingxiu

last: Pan

state: California

address: 6868 Nancy Ridge Dr

institute: Scintillon institute

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

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

first: Valentin

last: Cracan


title: RNA-seq of human ovarian clear cell carcinoma PDX tumors

city: kyoto

first: MENGXIN

last: JIANG

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Department of Gynecology and Obstetrics

institute: Kyoto University

summary: This dataset contains RNA-seq profiles of patient-derived xenograft (PDX) tumors established from human ovarian clear cell carcinoma (OCCC). Tumor tissues were collected without any therapeutic treatment and used to generate xenografts in immunodeficient mice. Total RNA was extracted from the PDX tumors and sequenced on the Illumina NovaSeq 6000 platform using 150 bp paired-end reads. These data represent the baseline transcriptomic landscape of OCCC tumors and may serve as a resource for studying tumor biology and preclinical model characterization.

overall_design: This experiment was designed to profile the baseline transcriptomic landscape of human ovarian clear cell carcinoma (OCCC) using patient-derived xenograft (PDX) models. Tumor tissues from OCCC patients were implanted into immunodeficient mice to establish PDX models. No therapeutic treatment was applied. Tumors were harvested at the baseline timepoint, and total RNA was extracted and sequenced using paired-end 150 bp reads on the Illumina NovaSeq 6000 platform. The resulting data provide a reference transcriptomic map for human OCCC in PDX models.

first: Mengxin

last: Jiang

first: Ken

last: Yamaguchi

first: Kohei

last: Hamada

first: Yuko

last: Hosoe

first: Yuka

last: Mise

first: Sachiko

last: Kitamura

first: Zhihong

last: Liu

first: Hairong

last: Wei

first: Zhenhai

last: Gao

first: Mana

last: Taki

first: Koji

last: Yamanoi

first: Ryusuke

last: Murakami

first: Rin

last: Mizuno

first: Taito

last: Miyamoto

first: Junzo

last: Hamanishi

first: Masaki

last: Mandai


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

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

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

institute: The University of Chicago

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

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

first: Yiyi

last: Ji

first: Lei

last: Chen

first: Jiangbo


title: Neural crest cell derived DKK1 modulates Wnt signalling in the second heart field to orchestrate cardiac outflow tract development.

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

summary: Heart morphogenesis is highly complex, and depends on the generation of diverse cell types which interact with each other in an orchestrated manner to remodel the primitive heart tube into a functional organ. Cardiac outflow tract formation critically depends on continued contribution of cardiac progenitor cells from the anterior second heart field to ensure proper growth of the outflow tract. Prior to entering the outflow tract, neural crest cells migrate in close apposition to the second heart field and may play important roles in regulating second heart field growth dynamics, however the molecular mechanisms by which neural crest cells interact with the second heart field have remained elusive. Here, we discover that neural crest cells are a primary source of Dickkopf1 (DKK1), a secreted Wnt signalling inhibitor, which modulates Wnt signalling activity in the second heart field to impose a balance between progenitor maintenance and differentiation. Further, we identify the ubiquitin ligase NEDD4 as a critical regulator of DKK1 levels, with disruption of Nedd4 activity leading to outflow tract defects. In the context of disease pathogenicity, we show a novel human congenital heart disease variant of NEDD4 has lost the ability to ubiquitinate DKK1, and is associated with heart defects in a mouse model of the genetic variant. Our findings point to an unexpected role for neural crest cells acting as a rheostat of Wnt signalling activity in cardiac progenitors, identifying a new molecular pathway underpinning correct outflow tract morphogenesis, and a new causative factor of congenital heart disease.

overall_design: Tissue sections from embryonic day E9.5 mouse embryos were acquired and subjected to laser capture microdissection. A region containing the anterior second heart field and associated neural crest and pharyngeal endoderm tissue was laser dissected, and total RNA prepared. This was done from 3 independent wildtype and Wnt1-Cre;Nedd4fl/fl embryos. Prepared RNA was subjected to bulk RNAseq.

first: Sophie

last: Wiszniak

first: Quenten

last: Schwarz


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

city: Aarhus

first: Lasse

middle: Sommer

last: Kristensen

address: Wilhelm Meyers Allé 4

department: Biomedicine

country: Denmark

institute: Aarhus University

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

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

first: Ulvi

last: Ahmadov

first: Charlotte

middle: W

last: Udengaard

first: Stine

last: Vissing

first: Silke

last: Nielsen

first: Kim-Gwendolyn

last: Dietrich

first: Benedicte

last: Ulhøi

middle: S


title: Molecular Signatures and Signaling Interactions of the Hair Follicle Stem Cell Niche

city: New York

first: Michael

last: Rendl

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

summary: Signaling interactions between the dermal papilla (DP) and neighboring stem cells in the hair germ (HGSCs) and bulge (BuSCs) regulate new follicle growth in the hair cycle. To study these interactions, the three populations had been profiled together by now-outdated microarrays or separately by bulk RNA-sequencing. Recent single-cell transcriptomics established signatures of DP, BuSCs and HGSCs, but low detection sensitivity limited the depth of gene expression discovery. Here, we define the transcriptomes of DP, BuSCs, HGSCs, epidermal, follicle and dermal fibroblast cells – after flow-sorting each population from four neighboring mouse back skin regions – to gain deeper insights into the unique gene expression programs of SCs and their instructive niche. With cross-comparisons of 56 whole-transcriptome measurements, we classify cell type-specific molecular signatures of enriched genes with unprecedented sensitivity. Joint analysis with signatures from 15 leading studies published in the last 20 years revealed many previously undescribed DP, BuSC and HGSC genes in mouse and human counterparts. With ligand-receptor mapping and CellChat analyses we then uncover comprehensive cell-cell communication insights. Finally, we provide a new installment of our Hair-Gel repository along with numerous signature and other gene tables for easy exploration of gene expression in hair follicle SCs and their niche.

overall_design: Bulk RNA-seq was performed on FACS isolated Dermal Papilla (DP), Dermal Fibroblasts (DF), Epidermis (Epi), Follicle Cells (Foll), Bulge Stem Cells (BuSC) and Hair Germ Stem Cells (HGSC), and a negative fraction (Neg) from 4 individual back skin sections Z1-Z4 at P22 of 2 biological replicates using the IlluminaHiSeq 2000 platform.

first: Sangeeta

last: Ghuwalewala

first: Jenny

last: Cao

first: Amelie

last: Rezza

first: Martina

last: Rangl

first: Alexia

last: Brown

first: Laura

last: Grisanti

first: Nicholas

last: Heitman

first: Markus

last: Schober

first: Zichen

last: Wang

first: Avi

last: Ma’ayan

first: Axel

last: Almet

first: Maksim

last: Plikus


title: METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [CRISPR screen_H358]

first: Xin

last: Xu

state: Ontario

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

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

first: Yujuan

first: Helen

last: Zhu

first: Housheng

last: He


title: RNA sequence for RMG1 cells with HIF2A knockdown under 1.5% O₂ for 24 hours

first: MENGXIN

last: JIANG

summary: We performed RNA-seq analysis on ovarian clear cell carcinoma (OCCC) cell lines to investigate the transcriptional effects of HIF2A knockdown. Hypoxia-inducible factor 2 alpha (HIF2A) plays a key role in cellular adaptation to low oxygen environments and has been implicated in tumor progression. In this study.A human OCCC cell line,  RMG1, was cultured under hypoxic conditions following lentiviral transduction with shHIF2A or a control vector. This dataset provides insights into the downstream gene expression changes and mitochondrial function modulated by HIF2A suppression.

overall_design: RMG1 cell line was transduced with lentiviral vectors expressing either shHIF2A or shcontrol. After selection, the cells were cultured in F-12 with 10% FBS under 1.5% O₂ for 24 hours. Total RNA was extracted and subjected to paired-end sequencing using the Illumina NovaSeq 6000 platform. Each condition included biological replicates.

first: Mengxin

last: Jiang

first: Ken

last: Yamaguchi

first: Kohei

last: Hamada

first: Yuko

last: Hosoe

first: Yuka

last: Mise

first: Sachiko

last: Kitamura

first: Zhihong

last: Liu

first: Hairong

last: Wei

first: Zhenhai

last: Gao

first: Mana

last: Taki

first: Koji

last: Yamanoi

first: Ryusuke

last: Murakami

first: Rin

last: Mizuno

first: Taito

last: Miyamoto

first: Junzo

last: Hamanishi

first: Masaki

last: Mandai


title: Glc7/PP1 triggers Paf1 complex dissociation from RNA polymerase II to enable transcription termination

first: Karen

last: Arndt

summary: The mechanisms that control the dynamic composition of RNAPII elongation complexes govern major transitions in the transcription cycle yet are poorly understood. Here, we show that the transcription elongation factor Spt5 determines elongation complex composition to promote productive elongation and the transition to termination. Using an unbiased genetic screen and genomic approaches in Saccharomyces cerevisiae, we provide evidence that dephosphorylation of the Spt5 C-terminal repeat domain (CTR) by Glc7/PP1 is required to dislodge the Paf1 complex (Paf1C) from RNAPII near the cleavage and polyadenylation site (CPS). Mutations in Paf1C or the Spt5 CTR that dissociate Paf1C from RNAPII bypass the requirement for two critical regulators of Glc7 in the cleavage and polyadenylation factor that promote Glc7 enrichment at the 3’ ends of genes. Depletion of Glc7 causes aberrant retention of Paf1C past the CPS and a dramatic increase in readthrough transcription, which is fully suppressed by Paf1C mutations. Our results demonstrate that Paf1C retention antagonizes transcription termination and that Glc7-mediated restructuring of the RNAPII elongation complex to evict Paf1C at the CPS is a critical step in the transition from elongation to termination.

overall_design: 4tU-seq to investigate nascent transcription in mAID-Spt5 depletion strains, spt5 mutants, HA-Glc7 mutants and Glc7-anchor-away strains.

first: Sanchirmaa

last: Namjilsuren


title: Decoding the heterogeneity of human undifferentiated spermatogonia reveals RAS-dependent regulation of stem cell fate

city: La Jolla

first: Kun

last: Tan

address: 9500 Gilman Drive # 0695

department: Dept. of Obstetrics, Gynecology & Reproductive Science

institute: UCSD

summary: Spermatogonial stem cells (SSCs) are essential for long-term spermatogenesis and hold therapeutic potential for treating male infertility. While rodent SSCs are well characterized, human SSCs remain poorly understood. Here, we screen antibodies against proteins encoded by genes enriched in specific subsets of human undifferentiated spermatogonia (uSPG) identified by single-cell RNA sequencing. We characterize four markers labeling distinct uSPG subsets: PIWIL4 marks primitive, quiescent uSPG; EGR4 marks uSPG at a proliferative crossroads; and PPP1R36 and NANOS3 label distinct proliferative subsets poised for differentiation. The most and least advanced subsets-PIWIL4+ and NANOS3+ cells-do not overlap. Comparative transcriptomics uncover candidate pathways involved in uSPG fate transitions, including RAS signaling. Using FSD1, a pan-uSPG cell-surface marker identified here, we purify the entire uSPG population and demonstrate that RAS signaling maintains the primitive uSPG state. These findings provide a framework for human uSPG identity, with broad implications for reproductive biology and regenerative medicine.

overall_design: FSD1+ cells were purified from testis biopsies from four individuals by FACS and performed bulk RNAseq. For comparison, bulk RNAseq analysis was performed in parallel on unfractionated human testicular cells from the same donors.

first: Chiara

last: Capponi


overall_design: ChIP-seq to probe occupancies of RNA polymerase II and elongation factors in mAID-Spt5 depletion strains, spt5 mutants, HA-Glc7 mutants and Glc7-anchor-away strains.


title: Mitochondrial protease Afg3l2 regulates the homeostasis of mouse hematopoietic stem and progenitor cells through Mmadhc [proteomics]

city: Indianapolis

first: Bin

last: Guo

state: Indiana

address: 950 W. Walnut Street

department: Microbiology & Immunology

institute: Indiana University

summary: In order to study how mitochondrial proteases function on mouse hematopoietic stem cells, the article constructed Afg3l2 knockout mice. When Afg3l2 was knocked out, mouse hematopoietic stem cells showed HSC depletion accompanied by amino acid accumulation and TCA overactivation. We performed transcriptome and proteome sequencing analysis on cells from wild-type (WT) and Afg3l2-KO mice, and differential gene analysis revealed the Mmadhc protein. Further verification showed that Mmadhc is a substrate of the mitochondrial protease Afg3l2, and overexpression of Mmadhc can mimic the amino acid accumulation and TCA overactivation caused by Afg3l2 knockout. Overall, the mitochondrial protease Afg3l2 affects the homeostasis of hematopoietic stem cells by regulating the level of Mmadhc.

overall_design: Comparative gene expression profiles were performed using proteomics data from WT and Afg3l2 KO LK(Lin−c-Kit+) cells.

first: Meng

last: Zhang

first: Xiashiyao

first: Jun

last: Wan


title: Mitochondrial protease Afg3l2 regulates the homeostasis of mouse hematopoietic stem and progenitor cells through Mmadhc [RNA-Seq]

overall_design: Comparative gene expression profiling was performed using RNA-seq data from WT and Afg3l2 KO LSK(Lin−Sca-1+c-Kit+) cells.


title: Ancient co-option of LTR retrotransposons as yeast centromeres

city: Dortmund

first: Max

last: Haase

address: Otto-Hahn-Str. 11

country: Germany

institute: Max Planck Institute of Molecular Physiology

summary:
Centromeres ensure accurate chromosome segregation, yet their DNA evolves rapidly across eukaryotes, leaving the origin of new centromere architectures unresolved. In the brewer’s yeast Saccharomyces cerevisiae (order Saccharomycetales), compact, genetically defined “point” centromeres replaced large, repeat-rich, epigenetically specified centromeres, but how this transition occurred has been unclear. Competing models have proposed either descent with modification from ancestral epigenetic centromeres or acquisition from selfish plasmid DNA.

Here we map and characterize centromeres in the sister order Saccharomycodales and identify evolutionarily related “proto-point” centromeres that bridge repeat-rich and point centromeres. Proto-point centromeres contain a single centromeric nucleosome positioned over an AT-rich core, but retain relaxed organization and sequence variability in flanking cis-elements. In two species, including Saccharomycodes ludwigii, proto-point centromeres are embedded within clusters of Ty5 long terminal repeat (LTR) retrotransposons, and their core CDEII and flanking motifs share sequence similarity to Ty5 LTR sequence.

Comparative genomics, synteny, and phylogenetic analyses across multiple yeast orders show that Ty5-cluster centromeres are ancient genomic features and support a model in which proto-point and point centromeres evolved by co-option of Ty5 LTR sequences in an ancestor with retrotransposon-rich centromeres, rather than by horizontal transfer from the 2-µm plasmid. These results indicate that yeast point centromeres are direct descendants of retrotransposons and illustrate how transposable elements can be repurposed to create genetically encoded centromeres.

overall_design: Cse4 was mapped by MNase-ChIP-sequencing of a mNeonGreen-tagged Cse4 variant.

first: Luciana

last: Lazar-Stefanita

first: Lyam

last: Baudry

first: Aleksandra

last: Wudzinska

first: Xiaofan

last: Zhou

first: Antonis

last: Rokas

first: Chris

last: Hittinger

first: Boris

last: Pfander

first: Andrea

last: Musacchio

first: Jef

last: Boeke


title: HIF-1α+ CD4 T cells coordinate a tissue resident immune cell network in the lung [Xenium]

city: Basel

first: Carolyn

last: King

address: Hebelstrasse 28

department: Department of Biomedicine

institute: University of Basel

summary: Pulmonary infection leads to the development of CD4+ T resident helper (TRH) cells in the lung. TRH cells generated after influenza infection support local humoral responses and exhibit differentiation plasticity following infectious challenge. A subset of TRH cells is enriched for expression of the transcription factor HIF-1α which has unknown function in the lung. Here we find that inducible deletion of HIF-1α in CD4 T cells leads to decreased numbers of CXCR6+ tissue resident T cells with minimal impact on peripheral lymphoid responses. At the same time, HIF-1α deletion impairs the replenishment of tissue resident macrophages and NK cells, as well as influenza specific IgA titers. These seemingly disparate responses converge upon a requirement for IL-21 produced by HIF-1α+ CD4 T cells. A similar HIF-1α dependent network is engaged in a lung adenocarcinoma model, highlighting novel roles for HIF-1α+ CD4 T cells in coordinating protective immunity during infection and cancer.

overall_design: WT mouse infected with influenza strain PR8. Harvest at day 14 and day 30 post infection


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

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

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

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

first: Alexandra

middle: T

last: Tankka

first: Jaclyn

last: Einstein

first: Catherine

middle: J

first: Vivian

last: Pham

first: Yuhan

first: Jack

last: Naritomi

first: Grady

middle: G

last: Nguyen

first: Orel

last: Mizrahi

first: Mark

last: Perelis

first: Joseph

last: Sarsam

first: Fred

middle: E

first: Dan

last: Kaufman

first: Corina

last: Antal

first: Gene

last: Yeo


title: A critical role of GABAergic neurons in driving CGG repeat toxicity associated with Fragile X Premutation Carriers [scRNA-Seq]

city: Atlanta

first: Yulin

last: Jin

state: GA

address: 615 Micheal Street

department: Human Genetics

institute: Emory University

summary: Fragile X-associated tremor/ataxia syndrome (FXTAS) is a neurodegenerative disorder caused by a CGG repeat expansion (55-200) in the 5′ UTR of the fragile X messenger ribonucleoprotein 1 (FMR1) gene. The molecular mechanisms of FXTAS involve the toxic effects of the expanded CGG repeat RNA and the repeat-associated non-AUG (RAN) translation product, the FMRpolyG peptide. To gain deeper insights into the pathogenesis of FXTAS, we performed comprehensive transcriptomic profiling of the brain of an FXTAS mouse model at both bulk and single-cell levels, which revealed pronounced dysregulation in inhibitory neurons of FXTAS animals. Further, conditional FXTAS mouse models demonstrated that the expression of expanded CGG repeats in GABAergic neurons alone was sufficient to induce key features associated with the expression of FMR1 premutation CGG repeats. Many of the dysregulated mRNAs in GABAergic neurons were found to be bound by hnRNPA2/B1, an RNA-binding protein sequestered by CGG repeat RNA.

overall_design: To gain deeper insights into the cellular perturbations associated with the pathogenesis of FXTAS, we applied snRNA-seq to the prefrontal cortex of FXTAS animals and littermate controls at the onset of the phenotype stage (3-4m).

first: Yiqu

last: Cao

first: Wenjing

last: Ma

first: Peng


title: Mismatch repair deficiency drives malignant progression and alters the tumor immune microenvironment of glioblastoma

city: NEW YORK

first: Alexander

last: Tsankov

state: New York

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Mutations in DNA mismatch repair (MMR) pathway genes (MSH2, MSH6, MLH1, and PMS2) have been associated with acquired resistance to temozolomide and with a high tumor mutation burden (TMB) in high-grade gliomas (HGG), including glioblastoma (GBM). However, the specific roles of individual MMR genes in the initiation, progression, increased TMB and microsatellite instability (MSI), and resistance to temozolomide (TMZ) in glioma have not been extensively studied. In the present study, we developed de novo mouse models of germline and somatic MMR-deficient (MMRd) HGG. Surprisingly, we found that loss of Msh2 or Msh6 does not lead to a high TMB and MSI nor confer response to anti-PD-1 in GBM. Our data also revealed that germline MMRd leads to the transition from low to high-grade glioma. Additionally, we show that mice with germline MMRd had reduced survival compared to MMR-proficient (MMRp) tumor-bearing mice. This effect was tumor cell intrinsic but was associated with MMRd in the tumor immune microenvironment, which led to increased immunosuppressive pathways in myeloid cells, reduced lymphoid infiltration, and increased exhaustion of CD8+ T cells. We have found that both MMR-reduced (MMRr) and MMRd GBM are resistant to TMZ, unlike MMRp tumors. Our study shows that KL-50, a new imidazotetrazine-based DNA targeting agent designed to induce DNA interstrand cross-links, is effective in treating both germline and somatic MMRr and MMRd GBM-bearing mice. These findings present a new treatment option for HGG patients with inherited or acquired MMRd who are resistant to TMZ.

overall_design: Using immunocompetent de novo mouse models of GBM, we generated PDGFB+shp53-driven tumors in the right-frontal striatum of Msh2 WT, HET and KO mice. At human endpoint of these mice, tumor cells were isolated and sc-RNA seq was conducted to compare the difference between genotypes.

first: Dolores

last: Hambardzumyan

first: Puigdelloses Vallcorba

last: Montserrat

first: Nishant

last: Soni


title: The hegemonic EWSR1::ETS oncogene overrules core regulatory circuitry mechanisms in Ewing sarcoma [ChIP-seq]

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: Ewing sarcoma is an aggressive bone tumor of adolescence characterized by a hallmark EWSR1::FLI1 fusion oncogene. This chimeric protein drives tumorigenesis by reshaping transcriptional and epigenetic landscapes. However, how it is transcriptionally regulated and whether additional master transcription factors (MTFs) form a core regulatory circuit (CRC) in Ewing sarcoma remain unclear. Here, using an extensive panel of Ewing sarcoma cell lines and primary tumors, we mapped super-enhancers and identified strong enrichment of GGAA microsatellites, confirming their specificity to Ewing sarcoma as compared to other pediatric cancers and normal tissues. Integrating transcriptomic, epigenetic, 3D chromatin conformation, and dependency data, we predicted a set of MTFs potentially comprising a CRC. However, functional validation demonstrated that these MTFs neither establish auto-regulatory loops nor confer proliferative dependencies typical of CRC s in other pediatric tumors. Instead, EWSR1::FLI1 emerged as an “hegemonic” oncogene, regulating the expression of these MTFs without reciprocal regulation. Knockdown (KD) of EWSR1::FLI1 strongly reduced Ewing sarcoma cell proliferation and shifted H3K27ac profiles toward mesenchymal states, whereas silencing of individual or combined MTFs did not alter cell growth or EWSR1::FLI1 expression. These findings highlight the absence of a classical CRC in Ewing sarcoma and emphasize EWSR1::FLI1 as the dominant oncogene but also as a major vulnerability in this disease.

overall_design: ChIP-seq (H3K27ac and FLI1) were performed to complete the actual catalog of Ewing sarcoma cell line. We also generate H3K27ac profile after inhibiting the oncogene EWSR1::ETS and in some MSC models. Some transcription factors defined as CRC candidates were also sequenced (IKZF2, POU3F2, SOX6)

first: Sandrine

last: Grossetete

first: Sakina

last: Zaidi

first: Karine

last: Laud-Duval

first: Didier

last: Surdez


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

first: Brian

last: Yee

overall_design: RNA-seq of MCF10A, MDA-MB-231, MDA-MB-436, and SUM-149 cells following PUF60 knockdown; RNA-seq of MDA-MB-231 cells expressing an L140P PUF60 mutant

first: Alexandra

last: Tankka

first: Jaclyn

last: Einstein

first: Catherine

last: Zhou

first: Vivian

last: Pham

first: Yuhan

last: Zhang

first: Jack

last: Naritomi

first: Grady

last: Nguyen

first: Orel

last: Mizrahi

first: Mark

last: Perelis

first: Joseph

first: Fred

last: Tan


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

overall_design: eCLIP of PUF60 in MDA-MB-231, MDA-MB-436, SUM-149, and MCF10A cells and eCLIP of V5-tagged L140P mutant PUF60 in MDA-MB-231 cells, in duplicate

last: Sarsam

first: Dan

last: Kaufman

first: Corina

last: Antal

first: Gene

last: Yeo


title: wrn-deficient zebrafish exhibit premature malnutrition

city: Sagamihara

first: Kota

last: Ujibe

address: 5-10-1, Fuchinobe, Chuo-ku

institute: Aoyama Gakuin University

summary: To establish Werner syndrome model, we established wrn knockout mutant zebrafish. We performed time-course individual RNA-Seq to elucidate cause of death of mutant.

overall_design: Wild-type and mutant zebrafish larvae were sacrificed at 13 time point between 4 and 35 dpf with 4-13 biological replicates.

first: Makoto

last: Kashima

first: Miku

last: Kataoka

first: Rintaro

last: Shimada

first: Masashige

last: Okamoto

first: Isao

last: Kobayashi

first: Seiji

last: Wada

first: Hiroki

last: Matsuda

first: Akira

last: Sakamoto

first: Hiromi

last: Hirata


title: A roadmap to human hippocampal neurogenesis in adulthood, aging and AD

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: In the rodent, hippocampal neurogenesis plays critical roles in learning and memory, is tightly regulated by inhibitory neurons and contributes to memory dysfunction in Alzheimer’s disease (AD) mouse models. In contrast, the mechanisms regulating neurogenesis in the adult human hippocampus, the dynamic shifts in the transcriptomic and epigenomic profiles in aging and AD and putative niche interactions within the cellular environment, remain largely unknown. Using single nuclei multi-omics of postmortem human hippocampi we map the molecular mechanisms of hippocampal neurogenesis across aging, cognitive decline, and AD neuropathology. Transcriptomic and epigenetic profiling of neural stem cells (NSCs), neuroblasts and immature neurons suggests that the earliest shift in the characteristics of neurogenesis takes place in NSCs in aging.  Cognitive impairment was associated with changes in neuroblast profile. In AD, there was a widespread cessation of the transcription machinery in immature neurons, with robust downregulation of genes regulating ribosomal and mitochondrial function. Further, there was substantial loss of parvalbumin+ inhibitory neurons in the hippocampus in aging. The number of the rest of inhibitory neurons were reduced as a function of age and diagnosis. Notably, a similar system-level effect was observed between immature and inhibitory neurons in the transition from aging to AD, manifested by common molecular pathways that were ultimately lost in AD. The numbers of neuroblasts, immature and GABAergic neurons inversely correlated with extent of neuropathology. Using CellChat and NeuronChat, we inferred the ligands and receptors by which neurogenic cells communicate with their cellular environment. Loss of synaptic adhesion molecules and neurotransmitters, either sent or received by neurogenic cells, was observed in AD. Together, this study delineates the molecular mechanisms and dynamics of human neurogenesis, functional association with inhibitory neurons and a mechanism of hippocampal hyperexcitability in AD.

overall_design: Nuclei isolated from the hippocampus of young adults (YA, n=2), aging with no cognitive impairments (NCI, n=4), mild cognitive impairments/early dementia (MCI, n=4) and Alzheimer’s disease dementia (AD, n=4) were sequenced for multi-ome single nuclei RNA sequencing (snRNAseq) and single nuclei Assay for Transposase-Accessible Chromatin (snATACseq) analysis. Machine learning label transfer algorithm scANVI was used to transfer labels from two scRNAseq datasets, a human developmental forebrain and an adult human hippocampal dataset to ensure unbiased cell annotation.  Single-cell trajectory analysis ( CytoTRACE, Pseudotime) were used t infer and confirm the different developmental paths through the cell populations. Differential gene and peak expression as well as Motif analysis were used to assess the alterations in transcriptomic profiles of diffenet neurogenic niches accross diagnosis. Lastly, CellChat and NeuroChat to infer putative interaction of the neurogenic niches with their cellular niche in the human brain and the ligand-receptor pathways that may play a role in a decline in cell-cell interaction as a function of pathology in immature neurons

first: Ahmed

last: Disouky

middle: A

last: Sanborn

first: Mostafa

last: Mostafa

first: K

middle: R

last: Sabitha

first: Aimee

last: Schantz

first: Namhee

last: Kim

first: Szymon

last: Pawlowski

first: William

last: Honer

first: David

last: Bennett

first: Yi

last: Zhou

first: C

middle: D

last: Keene

first: Jalees

last: Rehman

first: Orly

last: Lazarov


title: Single cell RNA-seq analysis reveals the crucial role of Collagen triplex helix repeat containing-1 (Cthrc1) cardiac fibroblasts for ventricular remodeling after myocardial infarction

city: Pamplona

first: Núria

last: Planell

address: Pio XII, 55

country: Spain

institute: CIMA - UNAV

summary: Cardiac fibroblasts have a central role during the ventricular remodeling process associated to different types of cardiac injury. Recent studies have shown that fibroblasts do not respond homogeneously to heart damage, suggesting that the adult myocardium may contain specialized fibroblast subgroups with specific functions. Due to the limited set of bona fide fibroblast markers, a proper characterization of fibroblast population dynamics in response to cardiac damage is still missing. Using single cell RNA-seq we have identified and characterized a fibroblast subpopulation that emerges in response to myocardial infarction (MI) in a murine model. These activated fibroblasts exhibit a clear pro-fibrotic signature, and localize to the wounded myocardium. Combining epigenomic profiling with functional assays, we unveil important candidate regulators mediating their response to cardiac damage.

overall_design: Time-course of study of cardiac fibroblasts after myocardial infarction. Samples include 3 and 5 days after myocardial infarction.

first: Silvia

middle: C

last: Hernandez

first: Juan

last: Romero

first: Marina

last: Ainciburu

first: Nuria

first: Amaia

last: Vilas-Zornoza

first: Patxi

last: San Martin-Uriz

first: Elena

last: Iglesias

first: Gloria

last: Abizanda

first: Diego

last: Alignani

last: Gomez-Cabrero

first: Adrian

last: Ruiz-Villalba

first: Felipe

last: Prosper


title: A critical role of GABAergic neurons in driving CGG repeat toxicity associated with Fragile X Premutation Carriers

first: Yulin

last: Jin

overall_design: To investigate the molecular signatures associated with the expression of expanded CGG repeats, we performed RNA-Seq on brain tissues from the FXTAS mouse model, which expresses both FMRpolyG and CGG repeat RNA. Samples were collected from the cortex, cerebellum, and hippocampus of FXTAS mice and control animals at two key stages: the onset of phenotypic presentation (3–4 months) and the full phenotype stage (6–7 months). Additionally, to gain deeper insights into the molecular signatures of GABAergic neurons during disease progression, we performed anti-HA Targeted TRAP (Translating Ribosome Affinity Purification), followed by RNA sequencing (TRAP-seq). This analysis was conducted on the cortex and cerebellum of FMRpolyG+RNA(+/-);Gad2-Tagger mice and their littermate controls.

first: Yiqu

last: Cao

first: Peng


title: Open chromatin, HIF binding and mRNA expression analysis in primary tubule and ccRCC cells [CUT&Tag]

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

institute: RWTH Aachen University Medical School

summary: Inactivation of the von Hippel-Lindau tumor suppressor leads to stabilization of HIF transcription factors and subsequent oncogenic HIF-2 signaling in ccRCC. However, little is known about the transcriptional mechanisms leading to dysregulation of HIF-2α mRNA in renal cancer. Epigenetic analysis of the EPAS1 locus (coding for HIF-2α) using ATAC-seq, ChIP-seq and RNA-seq revealed an oncogenic enhancer that maintains a HIF-dependent feed-forward circuit of HIF-2α regulation in renal tumor cells.

overall_design: This study consists of ATAC-seq, ChIP-seq, CUT&Tag-seq and RNA-seq samples from primary tubular and primary ccRCC cells as well as genetically modified 786-0 and RCC4 cells.

first: Johannes

last: Schödel

first: Stephanie

last: Naas


title: Open chromatin, HIF binding and mRNA expression analysis in primary tubule and ccRCC cells [ChIP-seq]

overall_design:
This study consists of ATAC-seq, ChIP-seq, CUT&Tag-seq and RNA-seq samples from primary tubular and primary ccRCC cells as well as genetically modified 786-0 and RCC4 cells.

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Access to unprocessed raw data of primary cells is restricted to protect the privacy and intent of research participants consistent with the informed consent agreements provided by individual research participants.
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title: METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [ATAC-Seq]

city: TORONTO

first: Xin

last: Xu

address: 101 COLLEGE ST EAST TOWER 11-601D

institute: Princess Margaret Cancer Center

summary: To investigate the molecular role of CHD9 in prostate cancer, we knockdown CHD9 gene by two different shRNAs in 22Rv1 cells.

overall_design: Differential gene expression analysis of RNA-seq data for KD control cells and KD CHD9 cells

first: Yujuan

last: Wang

first: Helen

last: Zhu

first: Housheng

last: He


title: Immune polarization of type 1 and type 2 human eosinophils

city: Scottsdale

first: Elizabeth

middle: A.

last: Jacobsen

state: AZ

address: 13400 E. Shea Blvd.

institute: Mayo Clinic

summary: Eosinophils have specific immune phenotypes in type 2 and type 1 environments both in vitro and in translational models of disease in vivo. RNA sequencing was completed on human blood eosinophils cultured with cytokines that represent a Th2 (IL-33, IL-4, GM-CSF) or Th1 (TNFα/IFNγ)-associated environment cytokines.

overall_design: Eosinophils were isolated from the blood of  otherwise healthy human donors (no allergy, atopy, pregnancy, 0r autoimmunity) and cultured for 18 hrs in different conditions prior to RNA isolation for RNA sequencing. Eosinophils were cultured at 2 million cells per ml in standard RPMI-1640+10% FBS + 1X streptomycin-penacllin-glutamine and split into three conditions: E0: [IL-5 (1ng/mL)], E1: [IL-5 (1ng/mL)+ TNF-alpha (15ng/mL) + IFN-gamma (15ng/,L);  E2: [ Il-5 (1ng/mL) +IL-4 (10ng/mL )+ GM-CSF (10ng/mL) + IL-33 (50ng/mL) for 18 hrs and then isolated for RNA and RNA sequencing.