title: Genome-wide DNA Methylation Profiling in Methamphetamine Addiction

city: Ningbo

first: Qingxiao

last: Hong

state: Zhejiang province

address: No.1 Zhuangyu South Road

department: Department of psychiatry

institute: Afffliated Kangning Hospital of Ningbo University

summary: Methamphetamine addiction is a chronic brain disorder involving significant neuroadaptive changes, with recent research emphasizing the role of epigenetic mechanisms, particularly DNA methylation. This study aims to evaluate the diagnostic potential of gene methylation by identifying and validating differentially methylated genes in methamphetamine-dependent individuals versus healthy controls.A genome-wide differentially methylated analysis was conducted using methylation microarray technology.

overall_design: 4 men from Ningbo addiction research and Treatment center were recruited for the present study, they all met the Diagnostic and Statistical Manual of Mental Disorders (Fifth Edition) criteria for methamphetamine dependence. Four healthy participants were recruited as the healthy controls from Ningbo Health Screening Centre.Illumina iScan system was used to detect methylation patterns using the Infinium Methylation EPIC Bead Chip.

first: Shanshan

last: Chen

first: Zhongze

last: Lou

first: Weisheng

first: Han

last: Du

first: Longhui

first: Xiaohu

last: Xie

first: Wenjin

last: Xu

first: Wenhua

last: Zhou

first: Huifen

last: Liu


title: Monitoring systemic immune responses to checkpoint inhibition in breast cancer reveals host responses and mechanisms of resistance

status: Public on Dec 17 2025

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

country: USA

institute: Vanderbilt University Medical Center

type: Expression profiling by high throughput sequencing

summary: Immune checkpoint inhibitors (ICI) have improved survival in various cancers, but their success in breast cancer, specifically triple-negative breast cancer (TNBC), remains limited, benefiting less than 10% of patients. We modeled ICI response in vivo to unravel the mechanisms underlying immunotherapy efficacy, identify mechanisms of resistance in non-responsive tumors, and ascertain the therapeutic benefits of different chemotherapeutic combinations with ICI in breast cancer. We investigated the impact of ICI as monotherapy and in combination with other therapeutics in mouse models of mammary cancer, which we found robustly suppressed primary tumor growth and extended survival. Interestingly, even within a single model, responses to ICI were highly variable. Resistance was not reliably retained by transplantation into syngeneic hosts, suggesting a role for systemic host immunity rather than tumor-autonomous mechanisms. Transcriptomic analysis of the primary tumor landscape by fine-needle aspiration revealed that upregulated cytotoxic T cell response and inflammatory interferon signaling (both at baseline and post anti-PD-L1 administration) corresponded to favorable response to ICI. Longitudinal analysis of the peripheral blood uncovered enhanced myeloid cell recruitment in resistant mice, prior to therapy initiation. Similar effects were observed through longitudinal assessment of peripheral blood in ICI-treated human breast cancer patients. Blocking myeloid cell recruitment with navaraxin (CXCR1/2 inhibitor) improved ICI responses, further suppressing tumor growth and improving survival. These findings provide insight into resistance mechanisms and suggest the potential for minimally invasive strategies (sampling of systemic immune cells from peripheral blood) to identify patients likely to respond to ICI. This approach may help inform de-escalation strategies to mitigate therapeutic toxicities and limit unnecessary treatments.

overall_design: RNA-sequencing to profile longitudinal peripheral blood (collected via submandibular vein) and tumor samples (via fine-needle aspiration) of BALB/c mice inoculated with EMT6 mammary tumor cells and treated with mIgG1 or anti-PD-L1 (clone 6E11)

first: Ann

last: Hanna

first: Xiaopeng

last: Sun

first: Quanhu

last: Sheng

first: Paula

middle: I

last: Gonzalez-Ericsson

first: Elizabeth

middle: C

last: Wescott

first: Brandie

last: Taylor

first: Jacey

middle: L

last: Marshall

first: Susa

middle: R

last: Opalenik

first: Abigail

last: Toren

first: Violeta

last: Shanchez

first: Carly

middle: M

last: Fielder

first: Melinda

middle: E

last: Sanders

first: Justin

last: Balko


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

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

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

first: Rachel

last: Marcone

first: Yahya

last: Mohammadzadeh

first: Michele

last: De Palma


title: SBFI inhibitors reprogram transcriptomic landscape of prostate cancer leading to cell death [SBFI-103]

city: Stony Brook

first: Agnieszka

middle: B.

last: Bialkowska

state: New York

address: HSC-T17 Room 090

department: Dept. of Medicine

institute: Stony Brook University

summary: Prostate cancer (PCa) remains the second leading cause of cancer-related deaths in the United States. Fatty acid-binding protein 5 (FABP5), a member of a class of intracellular lipid transporters, promotes PCa progression via enhanced lipid metabolism and trafficking of lipid ligands. Previous work from our group has shown that the small molecule FABP5 inhibitors based on the truxillic-acid monoester (TAMEs) scaffold reduce PCa growth. In the current study, we demonstrate that the third-generation FABP5 inhibitor SBFI-1143 significantly inhibited the viability and proliferation of PCa cells by arresting cells at the G0/G1 and G2/M phases of the cell cycle and inducing apoptosis and cell death compared to 1st and 2nd generation inhibitors. Stinkingly, SBFI-1143 efficiently inhibited the growth of PCa spheroids compared to its predecessor, SBFI-103. RNA sequencing and Gene Set Enrichment Analysis (GSEA) demonstrated that SBFI-1143 more effectively suppressed the activity of pathways involved in cell cycle progression, cell cycle division, and chromosome organization, while upregulated genes associated with the endoplasmic reticulum (ER) stress, responses to the topologically incorrect folded proteins, and regulating apoptosis compared to the SBFI-103. We further show that SBFI-1143 inhibits oxidative phosphorylation, a process on which PCa depends during cancer initiation and progression. Notably, SBFI-1143 treatment downregulated genes attributed to the subpopulation of PCa cells characterized by the lineage plasticity-related signature leading to trans-differentiation, recurrence, and poor cancer prognosis. Our findings demonstrate that SBFI-1143 significantly modifies the transcriptomic landscape of PCa and may serve as a potentially effective therapeutic option for PCa.

overall_design: To investigate the mechanism of action and efficacy of SBFI-103 in vitro, we treated the human prostate cancer cell line, PC-3, with vehicle control (DMSO) and 15uM of SBFI-103 for 24 hours. Total RNA was isolated and RNA-seq was conducted. We then performed differential gene expression analysis using RNA-seq data from three biological replicates of each treatment condition to characterize significant transcriptomic changes in response to treatments.

first: Shubhra

last: Rajput

first: Joseph F

last: LaComb

first: Chris

last: Gordon

first: Hehe

last: Wang

first: Martin

last: Kaczocha

first: Agnieszka B

first: Iwao

last: Ojima


title: Retinoic acid signaling activation in early intermediate mesoderm differentiation promotes dual lineage of intermediate mesoderm specification and enhances full-segment kidney organoid generation

city: Daejeon

first: In Hwan

last: Tae

address: 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: During kidney development, an intermediate mesoderm (IM) give rise to distinct structures: the ureteric bud (UB) and the metanephric mesenchyme (MM). These structures differentiate further into the collecting duct and nephron, forming a mature kidney. Generating functional kidney organoids has been challenging due to incomplete development of the UB. Researchers have overcome this limitation by differentiating UB and MM separately and co-culturing them to generate kidney organoids. However, this study developed a co-culture-free method using retinoic acid (RA), plays important role in the anterior IM differentiation and BMP7 secreted by UB in vivo development. This protocol provided not only simplifies the complexity of kidney organoid generation but also advances our understanding of the crucial signaling pathways involved in kidney development.

overall_design: Pluripotent stem cells were cultured with 10 uM CHIR99021 for 4 days for inducing premitive streak differentiation. And then cells were exposed 0.1uM retinoic acid for 2 days with 100ng/ml FGF9 and withdrawn the retinoic acid for 1 day for inducing intermediate mesoderm cells.

first: Hyun-Mi

last: Kang


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

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

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

last: Monti

first: Giancarlo

last: Ruocco

first: Emanuele

last: Rodolà

first: Alessio

last: Colantoni

first: Gian Gaetano

last: Tartaglia


title: Gene expression profiles of skin basal layer in young, aged, and Tunicamycin treated killifish

city: Suita

first: Daneil

last: Semmy

state: Osaka

address: Yamadaoka 3-1

department: Homeostatic Regulation

country: Japan

institute: Osaka University Research Institute for Microbial Diseases

summary: The endoplasmic reticulum (ER) stress-response is an adaptive cellular mechanism activated by unfolded protein accumulation within the ER. Although recent evidence shows that ER stress-response is activated in aged tissues and therefore ER stress is considered as a candidate driver of aging, the spatiotemporal regulation and roles of the ER stress-response during aging remains unclear, especially in vertebrates. Using imaging, analysis we discovered that the expression of Ire1-Xbp1s in the basal layer of epidermis decline during aging, suggesting that ER stress response is involved in epidermal basal layer regulation. Furthermore, treatment with tunicamycin, a pharmacological ER stress inducer, significantly increase cell proliferation, while genetic abaltion decrease cell proliferation in epidermal basal layer. To uncover the mechanism in which Ire1-Xbp1s regulates epidermal stem cell proliferation, a novel spatial transcriptomics, the Photo-Isolation Chemistry (PIC) is conducted in young, aged, and tunicamycin treated aged epidermal basal layer of the killifish. As a result, we identified that the Ire1-Xbp1s pathway maintains young epidermal stem cell proliferation through activating a cell cycle regulator Vcp, while the age-dependent decline of glucose metabolism reduces the Ire1-Xbp1s activity, which consequently downregulates stem cells proliferation. Collectively, our study shows a previously unidentified role of ER stress-response in skin aging, which can offer insights into therapeutic targets for promoting healthy skin.

overall_design: Aged killifish were treated with 1µg/mL Tunicamycin for one night alongside with young and control aged killifish treated in DMSO. Trunk and fin were cryosectioned, and RNA expression in the basal layer epidermis of the fin were read using Photo-Isolation Chemistry (PIC) method, described in the following sections.

first: Daniel

first: Tohru

last: Ishitani

first: Mizuki

last: Honda

first: Shinya

last: Oki

first: Yasuyuki

last: Okawa


title: Paeonol Affects Hepatocellular Carcinoma Cell Proliferation and Apoptosis via the CLGN/NF-κB Pathway Under Endoplasmic Reticulum Stress

city: hefei

first: yan

last: sitong

address: 安徽医科大学第一附属医院研工部

country: China

institute: 安徽医科大学

summary: In order to reveal the core role of CLGN in the ERS-induced drug resistance of liver cancer

overall_design: Comparalive gene expression profling analysis ofRNA-seg data for Hep-G2 cells and its KD deriaives (shCLGN).

first: Sitong

last: Yan

first: Anqi

last: Wang


title: IFN-gamma exposure of MOLM-13 cells enhances HLA gene expression

city: Munich

first: Monika

last: Sponheimer

address: Feodor-Lynen-Strasse 25

department: Gene Center

country: Germany

institute: LMU Munich

summary: Challenges to developing immunotherapies for acute myeloid leukemia (AML) include the identification of suitable target antigens due to on-target-off-leukemia toxicity. CD70, expressed on  AML bulk and leukemic stem cells with limited expression on healthy cells, has emerged as a promising target. This study evaluated CD70 as a target for NK-cell-based immunotherapy using a sugar-engineered antibody (SEA-CD70). Flow cytometry revealed CD70 expression ranging from 0.2% to 89.6% (median = 7.0%, n = 86) in primary AML cells across genetic subgroups; this expression remained stable at relapse (median  = 3.9%, n = 14). SEA-CD70 showed potent, dose-dependent cytotoxicity against AML cell lines, primary cells and in an SCID mouse model, which correlated with CD70 expression levels. Notably, AML cells exposed to conditioned medium (CM) from activated T cells upregulated CD70. TNF-a was identified as the driver of CD70 upregulation, translating into enhanced antibody dependent cellular cytotoxicity (ADCC) against AML cells (cytotoxicity w/o TNF-a = 17.9% vs. with TNF-a = 34.3%, n = 13–15). Conversely, IFN-g exposure led to reduced ADCC (cytotoxicity w/o IFN-g = 17.9% vs. with IFN-g = 9.2%, n = 15), which is attributed to increased expression of NK inhibitory receptor ligands (HLA-ABC, HLA-E). Blocking of the corresponding inhibitory NK receptors (KIR/CD158b and NKG2A) partially reversed this effect. Similar findings were observed with a CD33-directed antibody, indicating a universal resistance mechanism against ADCC-based immunotherapy in AML. These findings suggest that IFN-g-dependent upregulation of HLA molecules contributes to resistance to NK-cell based therapy, warranting further biomarker studies from clinical trials.

overall_design: RNA bulk sequecing profile of AML cell line MOLM-13 wildtype and IFNGR1 knock out clones after exposure to TNF-alpha and/or IFN-gamma

first: Marion

last: Subklewe


title: Extracellular matrix flow guides emergent morphogenesis

city: Vienna

first: Abdel Rahman

last: Abdel Fattah

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Morphogenesis of vertebrate embryos requires extracellular matrix (ECM) in multiple developmental contexts1. Symmetry-breaking events in initially homogenous tissues trigger collective cellular dynamics which follow fluid-like behaviors, and the ECM, which is in constant engagement with morphing tissues, also undergoes fluid-like motion2–4. Cell and ECM deformations require coordination, however the interplay between them at cellular and tissue-scale remains largely unexplored. Here, we reveal a novel mechanism coupling morphogenetic events and epithelia-driven ECM flow. We show that exposure to ECM components triggers periodic morphogenesis of dome-shaped structures in human pluripotent stem cell monolayers, driven by directional ECM flow towards the sites of morphogenesis. We show that this flow is initiated by local symmetry-breaking events, is driven by microvilli and requires unperturbed flow conditions and cytoskeletal contractility. A theoretical model shows that a reaction-diffusion-like mechanism is responsible for organizing local morphogenesis into global tissue-wide events. The cell patterning landscape predicted by the model is experimentally recapitulated during mesoderm differentiation. We further validate ECM flow in 3D gastruloids and in quail embryos during primitive streak formation. These results uncover a new role for the ECM: in addition to being a site of cell adhesion, structural support and mechanical force generation5, as is currently established, we show that directional transport of ECM, termed ECM flow, is a major contributor in sustaining epithelial morphogenesis and differentiation.

overall_design: Human pluripotent stemcell cultures were culture to confluence then exposed to media containing 10% Matrigel for 24 h. Along with Matrigel-free media condition, both samples were dissociated using TrypLE and analyzed separately using scRNA-seq

first: Deniz

last: Conkar

first: Myriam

last: Roussigne

first: Francesca

last: Sgualdino

first: Lorenzo

last: Mattolini

first: Suresh

last: Poovathingal

first: Kristofer

last: Davie

first: Katlijn

last: Vints

first: Natalia

middle: V

last: Gunko

first: Giulio

last: Superti-Furga

first: Jesse

last: Veenvliet

first: Bertrand

last: Bénazéraf

first: Adrian

last: Ranga


title: Differential DNA methylation in infants with Ig E mediated and non-Ig E mediated cow’s milk allergy and its association with acquired tolerance

city: Madrid

first: Jose Antonio

last: Cañas

state: Madrid

address: Av. Reyes Catolicos 2

department: Inmunology

country: Spain

institute: Health Research Institute Fundación Jiménez Díaz (IIS-FJD), UAM

summary: Background: Cow's milk allergy (CMA) is one of the most common food allergies (FA) in childhood. This condition can be IgE-mediated, non-IgE-mediated, or a combination of both. Diagnosis involves clinical history in conjunction with sensitization tests. However, these tests have limited predictive value, making the oral food challenge (OFC) the gold standard for diagnosis. Recent research has focused on identifying biomarkers, including DNA methylation patterns, for FA diagnosis. The aim of this study is to investigate the differences in DNA methylation associated with distinct patterns of CMA, to identify novel diagnostic biomarkers.  Methods: Genome-wide DNA methylation profiling was performed on blood samples from infants with IgE-mediated CMA (CMAIE), non-IgE-mediated CMA (CMANIE), and non-allergic controls, at baseline and after 6 months of a exclusion diet in CMA groups. These results were then correlated with tolerance acquisition following the restrictive diet.  Results: A total of 19 infants were enrolled (10 CMAIE, 6 CMANIE, and 3 controls). Significant differentially methylated regions (DMRs) annotated to both genes and promoters were identified in all groups, and a clear separation of the samples into their respective groups was observed. Furthermore, DMRs in promoters and genes were identified in tolerant CMAIE children after the exclusion diet, being associated to tolerance.  Discussion: Differential DNA methylation in CMA children is a useful diagnostic biomarker, and it could also be valuable in predicting the resolution of such pathologies.

overall_design: The aim of our study is to investigate differences in DNA methylation associated with distinct patterns of CMA, namely IgE-mediated and non-IgE-mediated, with the goal of identifying novel diagnostic biomarkers for CMA in infants. To achieve this, we used whole genome-wide methylation analysis. The results of this study will contribute to a better understanding of the epigenetic mechanisms involved in CMA and to the search for novel diagnostic biomarkers.

first: José

middle: A

first: Genoveva

last: del Río Camacho

first: Victoria

last: del Pozo

first: Rebeca

last: López Gómez


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

institute: St. Jude Children's Research Hospital

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

overall_design: Refer to individual Series


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

city: Chengdu

first: Lu

last: Pu

state: Sichuan

address: #37 Guoxue Alley, Wuhou District

institute: west china hospital

summary: This dataset contains raw RNA-seq data from esophageal squamous cell carcinoma (ESCC) cells overexpressing GFP-TFAP2β, its LLPS-deficient mutants (ΔIDR3 and Mut_IDR3) or GFP control. The experiment aims to explore the downstream genes 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: RNA-seq of TFAP2β, its LLPS-deficient mutants (ΔIDR3 and Mut_IDR3) or GFP control in ESCC cells KYSE150 to understand the downstream genes and regulatory activity associated with TFAP2β’s phase separation mechanism.


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

type: Genome binding/occupancy profiling by high throughput sequencing

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: Compromised Intestinal Barrier Resilience to Disruption in People with HIV [ileum]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: People living with HIV (PLWH) experience chronic intestinal barrier dysfunction (gut leakage), which persists despite viral suppression by antiretroviral therapy (ART) and contributes to chronic inflammation and its comorbidities. The mechanisms underlying this phenomenon remain unclear and are likely multifactorial. We hypothesize that living with HIV compromises the intestinal barrier’s resilience to injurious agents, increasing susceptibility to leakage upon exposure to common exogenous or endogenous disruptors, such as alcohol or pro-inflammatory cytokines, respectively. Using 3D intestinal organoids (colonoids and enteroids) derived from PLWH on ART and HIV-negative controls, we assessed the impact of alcohol and inflammatory cytokines on barrier integrity. Organoids from PLWH exhibited reduced resilience to disruption compared to controls, correlating with alterations in pathways critical to epithelial integrity, including epithelial-mesenchymal transition, DNA repair, and oxidative stress-related pathways. These findings reveal a novel mechanism underlying intestinal dysfunction in PLWH and highlight potential molecular targets to mitigate these complications.

overall_design: RNAseq profilling of organoids from colon biopsies from people living with HIV (PLWH) and people living without HIV (PLWoH)

first: Maliha

middle: W

last: Shaikh

first: Shalini

last: Singh

first: Ali

last: Keshavarzian

first: Mohamed

last: Abdel-Mohsen


title: Compromised Intestinal Barrier Resilience to Disruption in People with HIV


title: CXCR4/CXCR7-SDF1 Axis-Based Targeting Treatment of Huntington’s Disease with Blood-Brain Barrier Permeable Neural Stem Cell-Derived Nanovesicles Reinforced by Biomimetic Nanozymes

city: Guangzhou

first: Yanteng

state: Guangdong

address: 600# Tianhe Road

department: Centre for Nanomedicine

institute: The Third Affiliated Hospital of Sun Yat-sen University

summary: Commencing with the production of toxic mutant huntingtin protein, many pathogenic factors, including mitochondrial dysfunction, overproduced reactive oxygen species (ROS) and neuroinflammation interactively accelerate the progression of Huntington’s disease (HD), causing the dysfunction and death of neurons, especially striatal medium spiny neurons. In light of that, we developed versatile neural stem cells (NSCs)-derived nanovesicles incorporating ultrasmall citrate modified-manganese oxide nanoparticles (CMnNZs) as well as pre-stimulating with IFNγ (MnINNVs). CMnNZs and IFNγ markedly increased the level of therapeutic factors in MnINNVs. Furthermore, MnINNVs are able to bypass the blood-brain barrier and target the inflammatory sites of HD through the SDF1-CXCR4/CXCR7 axis. After being uptake by neurons, microglia, and astrocytes, MnINNVs alleviate HD-like mice phenotype by scavenging ROS, promoting the conversion of microglia and astrocytes phenotypes to reduce neuroinflammation, and further rescuing neurons. Our study not only offers a novel therapy for HD but also presents new strategies to enhance the wholesome effects of NSCs-based therapies.

overall_design: The striatum tissues were isolated from the freshly sampled brains of the Normal (N), HD (H), and MnINNV-treated (T) groups without perfusion or fixation using PFA on ice, followed by immediate freezing in liquid nitrogen. The total RNA was extracted from the frozen striatum tissues through homogenization in Trizol. Subsequently, the RNA purification, fragmentation, reverse transcription, PCR, library construction, and sequencing using the Novaseq 6000 system (Illumina, USA) were performed at LC-Bio Technology (Hangzhou, China).

first: Ling

last: Long

first: Hao

last: Tian

first: Yixin

last: Zhang

first: Yu

last: Tao

first: Mingqiang

last: Li


title: Cell-specific Inducible Human APOL1 Risk Variant Expression Cause Hypertension and Renal Damage

city: PHILA

first: Fang

address: 3400 CIVIC CENTER BLVD, Smilow Translational Center 12-188

institute: University of Pennsylvania

summary: African Americans bear a disproportionate burden of hypertension (HTN) and hypertension-attributed chronic kidney disease (H-CKD). The role of Apolipoprotein L1 (APOL1) risk variants (G1 and G2) in these conditions have been proposed, but genetic and observational studies have shown inconsistent results.Here, we investigated the causal role of APOL1 risk variants using patient samples, transgenic animal models, and in vitro cellular experiments.In the human kidney, APOL1 was highly expressed by glomerular podocytes and endothelial cells. Mice with podocyte-specific expression of the APOL1 risk variant (G2APOL1), but not those with the reference allele (G0), developed severe secondary HTN following albuminuria and kidney disease. Mice expressing endothelial-specific G2APOL1 RV developed mild hypertension with aging, which exacerbated following uninephrectomy and a high-salt diet. This condition induced slight alterations in kidney function. In vitro and in vivo experiments demonstrated that the APOL1 risk variant activates the cytosolic nucleotide sensor STING, leading to increased production of endothelin 1. Notably, mice with endothelial-specific STING knock-out or those treated with an endothelin inhibitor were protected from G2APOL1 RV-mediated hypertension. These findings indicate the role of G2APOL1 in HTN development through STING and endothelin 1 activation, offering new precision therapeutics for addressing hypertension in Black communities carrying APOL1 risk variants.

overall_design: We performed unilateral nephrectomy (UNX) surgery on WT, EC/G0APOL1, and EC/G2APOL1 mice at 6 weeks of age and maintained them on a high salt (4% salt) diet following the surgery.

first: Bibek

last: Poudel

first: Magaiver

last: Andrade Silva

first: Xiaoqiang

last: Ding

first: Amin

last: Abedini

first: Konstantin A

last: Klötzer

first: Katalin

last: Susztak


title: Ceramides Drive Mitochondrial Dysfunction and Tubular Injury in AKI

city: Salt Lake City

first: Scott

last: Summers

state: UT

institute: University of Utah

summary: Perturbations in proximal tubule mitochondrial function and lipid metabolism potentiate kidney dysfunction in acute kidney injury (AKI). We identified the bioactive lipid ceramides as drivers of proximal tubule pathology in AKI. Ceramide synthesis was upregulated in humans and mice with AKI. We utilized a proteome-wide thermal shift assay to observe that ceramides interact with proximal tubule proteins involved in lipid and mitochondrial metabolism. Mechanistic studies revealed that ceramides altered assembly of the inner mitochondrial membrane MICOS complex and respiratory supercomplexes in proximal tubule cells leading to acute impacts on mitochondrial respiration, cristae architecture, and mitochondrial morphology. Effects of ceramides on complex assembly and mitochondrial function were dependent on the presence of the 4-5 trans double bond incorporated by dihydroceramide desaturase 1 (DES1). Blunting ceramide synthesis, via genetic or pharmacologic inhibition of DES1, prevented kidney injury in mice following renal ischemia reperfusion injury. Ceramides may be a novel therapeutic target to combat mitochondrial disruption during AKI.

overall_design: Bulk RNA sequencing of kidney cortex tissue from Degs1 inducible global knockout (Degs1iGKO) mice or Degs1 fl/fl controls 24 hours after challenge with bilateral ischemia reperfusion injury or sham operations.

first: Rebekah

last: Nicholson

first: Luis

last: Cedeño-Rosario

first: Chris

last: Stubben

first: Liping

last: Wang

first: William

last: Holland

first: Nirupama

last: Ramkumar


title: ‘FATLESS’ MICE REVEAL FUNDAMENTAL ASPECTS OF ADIPOSE TISSUE REQUIREMENTS FOR FEMALE REPRODUCTION

city: Pittsburgh

first: Bokai

last: Zhu

address: Bridgeside Point 1, 5th Floor, 100 Technology Drive

institute: Aging Institute of UPMC/University of Pittsburgh School of Medicine

summary: Here, we show the transcriptional changes resulting from sex-specific and early adaptive thermogenic responses to adipocyte specific knockout of Ubc9 in mice compared to littermate controls.

overall_design: Subcutaneous and visceral fat depots were collected from 2-week-old normal chow fed female mice with adipose tissue specific knockout of Ubc9 and littermate controls.

first: Elizabeth

last: Vrazel

last: Dion

first: Sean

last: Hartig


title: Single-cell transcriptomics of myeloid milieu reveals an angiogenic niche in triple-negative breast cancer

city: Seoul

first: Minkyu

last: Shim

address: 103, Daehak-ro, Jongno-gu

institute: Seoul National University

summary: Intratumoral myeloid cells are highly heterogeneous in terms of development and function and are pivotal for forming and regulating the tumor microenvironment. However, the myeloid milieu in triple-negative breast cancer (TNBC) remains poorly understood. To elucidate this myeloid milieu, we integrated in house and public single-cell RNA-sequencing data. We detected diverse neutrophil and mononuclear-phagocyte subtypes and delineated their developmental trajectories and functions. Of particular interest were the VEGFAhi neutrophil and SPP1hi macrophage subtypes, which displayed pro-tumoral functions including angiogenesis. Spatial transcriptomics revealed that they colocalized with epithelial cancer cells and APLNhi endothelial tip cells in a hypoxic region forming an angiogenic niche. Moreover, SPP1hi macrophage enriched TNBC patients showed poor prognosis, which worsened in patients who also displayed abundant VEGFAhi neutrophils. These subtypes were also conserved in multiple murine TNBC models. This comprehensive analysis of the myeloid population in TNBC thus reveals novel therapeutic targets and provides a  foundation for translational research.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: scRNA-seq of CD11b+ cells from TNBCs

first: Juhee

last: Jeong

first: Duk Ki

last: Kim


title: m6A mRNA Methylation Decorates Genes Involved in Fibrinogen Synthesis to Regulate Liver Regeneration in Mice

city: Boston

first: Jonathan

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: The role of m6A RNA methylation in liver regeneration is unclear. This study aimed to determine the role of m6A methylation in liver regeneration after a 70% hepatectomy (HEPA) using liver specific Mettl 14 KO male mice. Analysis was conducted on post-operative days 1, 3, or 7 (HEPA1, 3, or 7) in control (FLOX) mice. In Flox mice, CyclinD1 protein expression was highest on postoperative day 3 (HEPA3) consistent with a dynamic increase in hepatocyte replication. The abundance of Mettl14 protein presented a similar pattern on HEPA3. Then, we performed hepatectomy in Mettl14 KOs (M14KO) and Flox controls and observed significantly higher post-surgical mortality in mutants. In Flox mice, CyclinD1 protein levels and Ki67 were markedly increased on HEPA3 compared to SHAM, while being downregulated in M14KO. Characterizing the m6A epitranscriptomic changes in Flox mice after hepatectomy and contrasting them to hepatectomy in M14KO in HEPA3 revealed enrichment for gene ontology terms associated with endoplasmic reticulum, inflammation, and apoptosis. Differentially methylated genes in M14KO compared to Flox on HEPA3 were also enriched for PPAR and AMPK signaling. Finally, we identified hypomethylated transcripts involved in fibrinogen synthesis, such as Fga, Fgb, and Fgg, by comparing differentially m6A-decorated genes in M14KO versus Flox on HEPA3. Knockdown of fibrinogen leads to suppression of proliferation via activation of p21 protein in AML12 cells. Together, m6A RNA methylation decorates genes involved in fibrinogen synthesis pointing to an important role in liver regeneration consistent with recent work demonstrating the significance of fibrinogen in liver regeneration.

overall_design: Four groups of mice: HEPA3-FLOX, HEPA3-Mettl14KO, SHAM3-FLOX, SHAM3-Mettl14KO with n=4 per group, where each sample was run as input (usual bulk RNA-seq) and with IP using anti-m6A antibody as m6A.

first: Tomohiko

last: Kimura

first: Dario

middle: F

last: De Jesus


title: Non-alcoholic fatty liver disease exacerbates the advancement of renal fibrosis by modulating renal CCR2+PIRB+ macrophages through the ANGPTL8/PIRB/ALOX5AP axis

city: Shenzhen

first: Donglin

last: Sun

state: None Selected

address: Xinhu Road, Bao'an District

institute: Southern Medical University

summary: Renal fibrosis is a key pathological feature of chronic kidney disease, and non-alcoholic fatty liver disease (NAFLD) is associated with its progression. Our previous experimental results indicate that NAFLD exacerbates UUO-induced renal fibrosis. However, the specific role and mechanisms of NAFLD in renal fibrosis remain unclear. To further investigate the underlying mechanisms, we used single-cell transcriptome sequencing to construct a single-cell atlas of the kidney. Single-cell RNA sequencing analysis and our further experimental results showed that high-fat-induced hepatocytes releasing significant levels of ANGPTL8, which activates renal CCR2+PIRB+ macrophages. These specialized macrophages promote the activation and proliferation of Th17 cells, which could further worsen renal fibrosis. The ANGPTL8/PIRB/ALOX5AP axis is thus a crucial signaling pathway between the liver and kidneys, with CCR2+PIRB+ macrophages playing a pivotal role in the progression of NAFLD-induced renal fibrosis.

overall_design: Mice were fed either a high-fat diet or a normal diet to establish NAFLD mouse models and control groups. In the 11th week of feeding, unilateral ureteral obstruction (UUO) surgery was performed. After seven days, in the 12th week, the mice were euthanized, and kidneys from the ligated side (HU, WU) were collected for single-cell transcriptome sequencing.

first: Jing

last: Guo

first: Shuqi

last: Wei

first: Diwen

last: Shou


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.

first: Rachel

last: Rutishauser


title: Thyroid hormone augmentation accelerates hair cell maturation in human cochlear organoids

city: Indianapolis

first: Tsubasa

last: Saeki

state: IN

address: 980 W Walnut St

department: Otolaryngology-Head and Neck Surgery

institute: Indiana University School of Medicine

summary: Outer and inner hair cells in the cochlea are essential for hearing, but are vulnerable to damage by genetic mutations and environmental insults, resulting in irreversible sensorineural hearing loss. Investigating these processes requires access to large numbers of human cochlear hair cells and the ability to precisely control genetic, biochemical, and environmental conditions. We recently established a new organoid system that recapitulates human cochlear differentiation. However, maturation of cochlear organoid cultures is inefficient, requiring several months to express the mature outer hair cell marker Prestin. To efficiently obtain fully functional outer hair cells, we tested the effects of the thyroid hormone thyroxine on hair cell maturation in human cochlear organoids. Thyroxine supplementation significantly increased the percentages of Prestin-positive hair cells in an age-dependent manner. Additionally, transcriptomic analyses revealed upregulation of mature outer hair cell genes and downregulation of immature hair cell genes in thyroxine-treated hair cells. Furthermore, some of the treated hair cells exhibited electromotility, a functional hallmark of mature outer hair cells. These results suggest that thyroid hormones accelerate the maturation of hair cells in human cochlear organoids, thereby useful for establishing an improved in vitro model for pre-clinical investigation on sensorineural hearing loss.

overall_design: We conducted three scRNA-seq analyses to compare the transcriptome of cochlear organoids treated without thyroxine (T4) (CTR d109), with 20 days of T4 treatment (T4 d109), and with 50 days of T4 treatment (T4 d140).

first: Saeki

last: Tsubasa

first: Ueda

last: Yoshitomo

first: Aristizábal-Ramírez

last: Isabel

first: Moore

middle: T

last: Stephen

first: Frolenkov

last: Gregory

first: Hashino

last: Eri


title: Identification of neoadjuvant chemotherapy response transcriptomic meta-signatures in invasive breast cancer in Latino patients

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: Breast cancer is a highly heterogeneous disease with varying incidences and mortality rates among women from different populations worldwide. Neoadjuvant chemotherapy (NAC) is the standard treatment for locally advanced breast cancer; however, its efficacy differs significantly among breast cancer subtypes. This study aimed to investigate the genes linked to response to NAC in Colombian women with invasive breast cancer. RNA sequencing was performed on formalin-fixed paraffin-embedded tissues from 58 patients, categorized into 29 NAC responders and 29 non-responders. Differentially expressed genes (DEGs) were identified for each molecular subtype and their prognostic performance was evaluated using risk scores. Functional enrichment analysis revealed pathways related to the immune system in the non-responders. Cytokine target activity and immune cell population changes were assessed to understand the role of the TME in the response to treatment. APOD, CCL19, GPR132, FGF10, and HBB were identified as independent predictors of NAC response, with APOD showing a protective effect in LuminalB/Her2- patients. RT-PCR and immunohistochemistry were used to validate these findings. Drug sensitivity analysis showed varying sensitivities to potential therapeutic drugs among the non-responders. This study highlights the importance of identifying specific gene expression profiles and immune cell population changes to predict NAC response in patients with breast cancer, potentially leading to personalized and effective treatment strategies for the Colombian population

overall_design: After obtaining informed consent, patients with a histologically confirmed diagnosis of breast cancer and scheduled chemotherapy were recruited for this study. Histopathological review of pre- and post-chemotherapy biopsies was performed by an expert pathologist who reviewed the slides and outlined the tumor tissue. Following completion of the neoadjuvant regimen, treatment response was evaluated using surgical specimens obtained by a pathologist. A pCR was established according to the most accepted definition: the absence of infiltrating components in the breast and lymph nodes (ypT0/is or ypN0). Patients were classified as responders if they showed pCR and non-responders if they did not present with pCR. RNA sequencing was performed on formalin-fixed paraffin-embedded pretreatment (baseline) tissues from 58 patients (29 NAC responders and 29 non-responders). Differentially expressed genes (DEGs) were identified between the responders and non-responders for each molecular subtype.

first: Hedda

last: Guevara-Nieto

first: Rafael

last: Parra Medina

first: Carlos

last: Orozco

first: Sandra

last: Diaz Casas

first: Jone

last: Garai

first: Liliana

last: Lopez-Kleine

first: Alba

last: Combita


title: BTA3 control tiller angle formation and shoot gravitropism in rice

city: Shenyang

first: Xiaoxue

last: Wang

state: Liaoning

address: 120 Dongling Road, Shenhe District

department: Rice Research Institute

institute: Shenyang Agricultural University

summary: To explore the roles of BTA3 in regulating tiller angle, we performed RNA high-throughput sequencing analysis. The response of wild type (WT) and bta3-1 mutant to gravity stimulation was investigated in the study.

overall_design: Two group of seedlings were used for RNA-seq with two biological replicates. One group is the vertical-grown 7-day-old WT and bta3-1 seedlings serving as no gravity stimulation control, named YJWC1,  YJWC2; YJBC1, YJBC2. The other group is the 7-day-old WT and bta3-1 seedlings, which were vertical-grown for 4 days and transferred to horizontal-grown status for another 3 days serving as gravity stimulation treatment, named YJWT1, YJWT2; YJBT1, YJBT2.

first: Yanjuan

last: Hu


title: Compromised Intestinal Barrier Resilience to Disruption in People with HIV [colon]

first: Priyankara

last: Wickramasinghe

first: Maliha

last: Shaikh

first: Shalini

last: Singh

first: Ali

last: Keshavarzian

first: Mohamed

last: Abdel-Mohsen


title: Transcriptional regulation of T cell exhaustion in immune checkpoint blockade resistance at single-cell resolution [ex vivo-scRNA]

city: Taipei

first: Hsueh-Fen

last: Juan

address: No. 1, Sec. 4, Roosevelt Rd.

department: Life Science

country: Taiwan

institute: National Taiwan University

summary: Tumor-specific CD8+ T lymphocytes are crucial for anti-cancer immunity but can lose cytotoxic function in the immunosuppressive tumor microenvironment. Immune checkpoint blockades (ICB), like anti-PD-1 therapy, enhance and prolong anti-tumor T cell responses. Despite its widespread clinical use, resistance to ICB develops in some patients, characterized by the proliferation of exhausted T cell (Tex). Here, we establish two single-cell murine hepatocellular carcinoma (HCC) models to explore regulatory network in Tex with ICB resistance. We uncover distinct T cell compositions, including both early and terminal Tex subsets, following prolonged ICB treatment, and reveal the differentiation trajectory of Tex subsets. Finally, we not only identify transcription factor Runx2 and its downstream targets as contributors to T cell exhaustion in both models, but discover ICB response correlates to Runx2 level in human tumor-infiltrating lymphocytes. These findings elucidate Runx2 regulates T cell exhaustion in response to prolonged ICB treatment, influencing ICB effICBency, and suggest potential targets for combination therapy alongside ICB in HCC.

overall_design: To generate exhausted CD8+ T cells, we used P14 mice in which CD8+ T cells could specifically recognize gp33 peptide, repeatedly taking splenocytes with gp33 peptide to stimulate CD8+ T cell exhaustion. On different conditions, we generated four types of T cells: naïve, active, exhausted (72 h) and exhausted (96 h), respectively. CD8+ T cells from each group were collected by cell sorter (BD FACSAria III) and separated for single-cell multiome sequencing, including scRNA-seq and scATAC-seq. For sequencing, CD8+ T cells underwent nuclei isolation followed by the use of the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) according to the instruction provided by the manufacturer. Sequencing was then conducted on Illumina NovaSeq 6000 platform to generate the single-cell multiome dataset.

first: Tzu-Yang

last: Tseng

first: Ching-Huang

last: Hsieh

first: Chia-Lang

last: Hsu

first: Yu-Ching

last: Wu

first: Chiun

first: Hsuan-Cheng

last: Huang

first: Da-Liang

last: Ou


title: Transcriptional regulation of T cell exhaustion in immune checkpoint blockade resistance at single-cell resolution [ex vivo-scATAC]


title: Changes in DNA Methylation in Cow Blood Associated With Age and Disease

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is among the most promising biomarkers for age prediction, enabling the development of epigenetic clocks that correlate methylation profiles with chronological age. In this study, we investigated the relationship between ageing and disease susceptibility, focusing on both nuclear and mitochondrial DNA methylation in dairy cows. Genome-wide DNA methylation profiling was performed using enzymatic methyl-seq, covering 53 million CpG sites. The dataset included 96 cows with different phenotypes, sampled cross-sectionally and ranging from 2 to 9 years of age. We applied elastic net regression to identify the most predictive CpG sites for age estimation, achieving a mean absolute error of 111 days with a strong correlation to chronological age r = 0.97. Beyond chronological age prediction, we assessed the impact of disease status on epigenetic ageing. Our results revealed accelerated epigenetic ageing in cows susceptible to diseases, suggesting a link between health-related stress and disrupted DNA methylation dynamics. We further identified age-associated promoter methylation changes, particularly in MAB21L1, which may play a role in molecular ageing mechanisms. Additionally, we observed a decline in mitochondrial DNA methylation with age, notably in genes encoding Cytochrome c oxidase (COX), indicating a possible connection between mitochondrial dysfunction and epigenetic regulation. An inverse correlation between D-loop methylation and mtDNA copy number was also observed. This study demonstrates the potential of epigenetic models for biological age prediction in livestock, while recognizing that their accuracy may vary among species with different lifespans.

overall_design:
Blood samples were collected from cows at a Vancouver farm between November 2020 and February 2021. Two years later, we selected 48 cows that had been culled due to complications related to infertility (BFR, n=6), mastitis (BMS, n=6), lameness (BFL, n=12), metabolic disorders (BMT, n=6), or low production (n=18), which were not identified at the time of sampling. This culling reason was recorded in farm management logs and represented the primary cause for culling. These cows formed the “diseased group.” For comparison, we selected a second group of 48 cows that remained in the herd without any health issues. This second group represented the “control group.” The ages of the cows in both groups ranged from 1.8 to 9.2 years.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Lotfi

last: Bouzeraa

first: Camila

middle: B

last: Lima

first: Helene

last: Martin

first: Jessica

last: Marques

first: Ronaldo

last: Cerri

last: Oudihat

first: Marc-Andre


title: Explore tumor intrinsic factors regulating immunotherapy response in ovarian cancer

city: Houston

first: Weiyi

last: Peng

state: TX

address: 3455 Cullen Blvd., Suite 342

department: Department of Biology and Biochemistry

institute: University of Houston

summary: Despite approval of immunotherapy for the treatment of ovarian cancer patients, the majority of patients fail to respond to immunotherapy or relapse following initial response. These failures may be attributed to immunosuppressive mechanisms co-opted by tumor cells. However, it is challenging to use conventional methods to systematically evaluate the potential of tumor intrinsic factors to act as immune regulators in patients with cancer. To identify immunosuppressive mechanisms in non-responders to cancer immunotherapy in ovarian cancer , we firstly performed an unbiased genome-wide CRISPR immune screens to explore tumor intrinsic factors which regulates ovarian cancer cell lines response to T cell mediated killing. Then we integrated the in vitro CRISPR screen results with multi-omics clinical data to generate a sub-library including top candidates for in vivo CRISPR screen to further evaluate the role of potential tumor intrinsic factors in regulating ovarian cancer cell response to immunotherapy with using the immune checkpoint blocker. Collectively, the data provide a rich resource of novel targets for rational immuno-oncology combinations.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design:
To explore the potential tumor intrinsic factors regulating T cell mediated killing, we performed both in vitro and in vivo immune screens.
For in vitro screens: gRNA-expressing ID8/GC cells were cultured with or without gp100-specific T cells from pmel mice. Experimental groups are listed below. Equal amount of barcoded genomic DNA samples from all groups were pooled and sequenced into 4 individual sequencing lanes.
1.ID8/GC cells transduced with genome-wide gRNA library without T cell treatment: Ctrl 1_1,Ctrl1_2, Ctrl2_1 and Ctrl2_2;
2. ID8/GC cells transduced with genome-wide gRNA library with T cell treatment at ET ratio=0.2: ET02-2,ET02-3 and ET02-4;
3. ID8/GC cells transduced with genome-wide gRNA library with T cell treatment at ET ratio=1: ET1-2, ET1-3 and ET1-4;
For in vitro screens: sub-library expressing ID8/GC cells(ID8/GCSL) were inoculated in NSG or C57BL/6 mice. Tumor bearing mice were treated with or without anti-PD-1. Experimental groups are listed below. Equal amount of barcoded genomic DNA samples from all groups were pooled and sequenced into 4 individual sequencing lanes.
1. ID8/GCSL tumor tissue which were from tumor-bearing NSG mice: NSG-1~5;
2. ID8/GCSL tumor tissue which were from  tumor-bearing C57/BL6 mice receiving mock treatment: Mock-1~5;
3. ID8/GCSL tumor tissue which were from  tumor-bearing C57/BL6 mice receiving anti-PD-1 treatment: PD1-1~10
4. Plasmid of for in vivo gRNA sub-library: plasmid_ICB sub-library;
5. ID8/GCSL cells after 2-day puromycin selection: Ref-1;
6. ID8/GCSL cells after 7-day puromycin selection: Ref-2;

first: Yiwen

last: Chen

first: Jiakai

last: Hou

first: Yanjun

last: Wei


title: Transcriptional regulation of T cell exhaustion in immune checkpoint blockade resistance at single-cell resolution

first: Hsueh-Fen

last: Juan

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

overall_design: Refer to individual Series


title: In vivo gene editing of human hematopoietic stem and progenitor cells using envelope-engineered virus-like particles

city: Seattle

first: Keylie

last: Gibson

state: Washington

address: 188 East Blaine Street Suite 400

institute: Sana Biotechnology

summary:
Engineered virus-like particles (VLPs) are a promising technology for in vivo
gene editing of human hematopoietic stem and progenitor cells (HSPCs).
Here we design and test two different VLP envelopes for human HSPC editing
in vitro and in vivo. The first is an optimized version of the baboon envelope
BaEVTR, which efficiently transduces human HSPCs in vitro. We show that
the optimized BaEVTR VLP enables in vivo editing of β2 microglobulin
in long-term human HSPCs (31% at 8 weeks after dosing) and editing of
two hemoglobinopathy-relevant loci, BCL11A and HBG1/2 (26% and 7.5%,
respectively, at 5 days after dosing), inducing fetal hemoglobin. Our second VLP
design uses a CD133-targeted envelope designed to reduce the transduction of
mature blood cells and achieves higher in vivo specificity for HSPCs compared
to the optimized BaEVTR VLP. As avoiding delivery in filter organs such as the
liver would enhance efficiency and safety, we also demonstrate that both VLPs
avoid human hepatocytes in a humanized liver model.

overall_design: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

first: Vladimir

last: Botchkarev Jr

first: Sean

last: Harrington

first: Matteo

last: Stoppato

first: Alexander

last: Justen

first: Casey

last: Kimber

first: Anjali

last: Kapuria

first: Chi-Shuen

last: Chu

first: Yuanxin

last: Xu

first: Kelsey

last: Haugh

first: Ramya

last: Ankala

first: Nathan

last: Kipniss

first: Andre

last: DeGroot

first: Emerson

last: Moore

first: Rowena

last: de Jesus

first: Funmi

last: Adewale

first: Kathy

last: Daniels

first: Samantha

last: Crocker

first: Anna

last: Liang

first: Shannon

last: Joyce

first: Nicole

last: Roberto

first: Pamela

last: Angel

first: Derek

last: Smith

first: Athena

last: Wong

first: Nick

last: Adler

first: Valeria

last: Berlfein

first: Shirisha

last: Amatya

first: Patricia

last: Cruite

first: Shariq

last: Usmani

first: Albert

last: Ruzo

first: Benjamin

last: Ferland

first: Sundeep

last: Chandra

first: Edward

last: Rebar

first: Jagesh

last: Shah

first: Kyle

last: Trudeau

first: Luca

last: Biasco


title: Differential nucleosome organization in human interphase and metaphase chromosomes [RNA-seq]

city: Evanston

first: Xiaozhong

last: Wang

state: IL

address: 2200 Campus Dr

department: Molecular Biosciences

institute: Northwestern University

summary: Mitosis induces profound changes in chromosome structure, impacting nucleosome organization. Here, we employed chemical mapping to achieve single-base-pair resolution of nucleosome positioning in human interphase and metaphase chromosomes, unveiling distinct organizing principles between the two states. During interphase, we observe greater variability in internucleosome spacing, with a higher abundance of shorter linkers compared to metaphase, reflecting the genome's adaptability in accommodating nucleosome arrays for gene expression. Local analyses further uncover differential nucleosome landscapes at key euchromatin landmarks, including promoters, enhancers, and insulators, in each state. Moreover, we analyzed the relationship between DNA cyclizability and dyad positioning during mitosis. Our results indicate that in metaphase, nucleosomes exhibit significantly higher cyclizability around the dyad, whereas during interphase, nucleosomes more frequently position DNA with higher cyclizability in the nucleosome shoulder near regulatory genomic regions. Together, this study offers novel insights into the intricate interplay between DNA mechanics and nucleosome dynamics during mitosis.

overall_design: Total RNA-seq of Hela S3 cells were performed as a complimentary data for the analysis of nuclesome mapped by chemical mapping

first: Keren

last: Li

first: Irem

last: Unlu

first: Lilien

middle: N

last: Voong

first: Xiaotian

last: Ma

first: Yiren

last: Tu

first: Ji-ping


title: Differential nucleosome organization in human interphase and metaphase chromosomes [Mnase-seq]

overall_design: MNase digestion of nucleosomal DNA in interphase and metaphase HeLa S3 cells was performed as described previously.


title: In vivo gene editing of human hematopoietic stem and progenitor cells using envelope-engineered virus-like particles [cell line panel]

first: Keylie

last: Gibson

summary: Engineered virus-like particles (VLPs) are a promising technology for in vivo gene editing of human hematopoietic stem and progenitor cells (HSPCs). Here we design and test two different VLP envelopes for human HSPC editing in vitro and in vivo. The first is an optimized version of the baboon envelope BaEVTR, which efficiently transduces human HSPCs in vitro. We show that the optimized BaEVTR VLP enables in vivo editing of β2 microglobulin in long-term human HSPCs (31% at 8 weeks after dosing) and editing of two hemoglobinopathy-relevant loci, BCL11A and HBG1/2 (26% and 7.5%, respectively, at 5 days after dosing), inducing fetal hemoglobin. Our second VLP design uses a CD133-targeted envelope designed to reduce the transduction of mature blood cells and achieves higher in vivo specificity for HSPCs compared to the optimized BaEVTR VLP. As avoiding delivery in filter organs such as the liver would enhance efficiency and safety, we also demonstrate that both VLPs avoid human hepatocytes in a humanized liver model.

overall_design:
We performed an RNA-seq analysis of untreated immortalized and non-hematopoietic primary cell lines to investigate the expression levels of known target receptors.
This study includes a reanalysis of the raw data for Samples GSM5822305 (GSE193832) and GSM7134569 (GSE200120).

first: Vladimir

last: Botchkarev Jr

first: Sean

last: Harrington

first: Matteo

last: Stoppato

first: Alexander

last: Justen

first: Casey

last: Kimber

first: Anjali

last: Kapuria

first: Chi-Shuen

last: Chu

first: Yuanxin

last: Xu

first: Kelsey

last: Haugh

first: Ramya

last: Ankala

first: Nathan

last: Kipniss

first: Andre

last: DeGroot

first: Emerson

last: Moore

first: Rowena

last: de Jesus

first: Funmi

last: Adewale

first: Kathy

last: Daniels

first: Samantha

last: Crocker

first: Anna

last: Liang

first: Shannon

last: Joyce

first: Nicole

last: Roberto

first: Pamela

last: Angel

first: Derek

last: Smith

first: Athena

last: Wong

first: Nick

last: Adler

first: Valeria

last: Berlfein

first: Shirisha


title: Nuclear translocation of Cx43 promotes CRC progression by CAF via activating β-catenin through TGF-β and phosphorylation

city: Hangzhou

first: Shuo

last: Wang

address: Zijingang Campus

institute: Zhejiang University

summary: The tumor microenvironment (TME) significantly influences intercellular communication, wherein a lot of secreted factors are known to activate both tumor cells and fibroblasts. Connexin43 (Cx43), a critical gap junction protein, is recognized for its regulatory role in tumorigenesis. However, the underlying regulation mechanisms of Cx43 in colorectal cancer (CRC) is not fully understood. Here, we systematically identified Cx43 as a promoter in CRC carcinogenesis. We found that Wnt signaling pathway was activated in the co-culture of CRC cells and fibroblasts. Concurrently, we noted an upregulation of Cx43 expression, which was subsequently confirmed as a pro-oncogenic factor through survival prognostic analysis of patient samples. Intriguingly, nuclear translocation of Cx43 occurred during malignant progression and had a significant effect in metastasis and being regulated by secreted TGF-β. This process involves the interaction between Cx43 with β-catenin, facilitating the nuclear translocation of β-catenin and consequently activating the Wnt signaling pathway. Furthermore, we found different situation on nuclear translocation of Cx43 in different CRC cell lines, which determined by S368 phosphorylation. Collectively, these findings highlight the novel mechanism of nuclear translocation of Cx43 as a pro-carcinogenic factor in CRC and enhancing our understanding of the interplay between TME and CRC progression.

overall_design: To investigate the influence on overexpressed Cx43 in RKO cells. For stable overexpression of Cx43, cDNA of Cx43 were linked to the overexpression vector pCDNA3.1. RKO cells were selected for  stable transfection. The control group was EV, and the experimental group was OVER43

first: Ziling

last: Zhu

first: Jing

last: Tan

first: Hong

last: Deng


title: Differential nucleosome organization in human interphase and metaphase chromosomes [Chemical Mapping]

first: Xiaozhong

overall_design: Through PiggyBac transgenic expression of an shRNA directed against a shared DNA sequence present in all human H4 genes and RNAi-resistant H4S47C cDNA, we generated H4S47C-substituted HeLa S3 stable cell lines suitable for efficient chemical cleavage of nucleosomes. Using these cells, we performed chemical nucleosome mapping experiments in both interphase and synchronized mitotic cells, with two replicates for each condition.

first: Keren

last: Li

first: Irem

last: Unlu

first: Lilien

last: Voong

first: Xiaotian

last: Ma

first: Yiren

last: Tu

first: Ji-ping


title: Tamoxifen improves muscle structure and function of Bin1- and Dnm2-related centronuclear myopathies

city: Illkirch-Graffenstaden

first: Jocelyn

last: Laporte

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: Congenital myopathies define a genetically heterogeneous group of disorders associated with severe muscle weakness, for which no therapies are currently available. Here we investigated the repurposing of tamoxifen in mouse models of mild or severe forms of centronuclear myopathies due to mutations in BIN1 (encoding amphiphysin 2) or DNM2 (encoding dynamin 2), respectively. Exposure to a tamoxifen-enriched diet from 3 weeks of age resulted in significant improvement in muscle contractility without increase in fibre size in both models, underlying an increase in the capacity of the muscle fibres to produce more force. In addition, the histological alterations were fully rescued in the BIN1-centronuclear myopathies mouse model. To assess the mechanism of the rescue, transcriptome analyses and targeted protein studies were performed. Although tamoxifen is known to modulate the transcriptional activity of the oestrogen receptors, correction of the disease transcriptomic signature was marginal on tamoxifen treatment. Conversely, tamoxifen lowered the abnormal increase in dynamin 2 protein level in both centronuclear myopathies models. Of note, it was previously reported that dynamin 2 increase is a main pathological cause of centronuclear myopathies. The Akt/mTOR muscle hypertrophic pathway and protein markers of the ubiquitin–proteasome system (the E3 ubiquitin ligase cullin 3) and autophagy (p62) were increased in both models of centronuclear myopathies. Normalization of dynamin 2 level mainly correlated with the normalization of cullin 3 protein level on tamoxifen treatment, supporting the idea that the ubiquitin–proteasome system is a main target for the tamoxifen effect in the amelioration of these diseases. Overall, our data suggest that tamoxifen antagonizes disease development probably through dynamin 2 level regulation. In conclusion, the beneficial effect of tamoxifen on muscle function supports the suggestion that tamoxifen may serve as a common therapy for several autosomal forms of centronuclear myopathies.

overall_design: RNA-seq profiling of tibialis anterior muscle in WT, Dnm2S619L/+, and Bin1mck-/- mice treated with Tamoxifen diet supplementation or placebo

first: Charlotte

last: Gineste

first: Alix

last: Simon


title: RNA G-quadruplex(rG4) exacerbates cellular senescence by mediating ribosome pausing [G4P-RIP-seq]

city: guangzhou

first: haoxian

last: zhou

address: zhongshan 2nd Road

institute: guangdong people hosptial

summary: Ribosome pausing plays a crucial role in the collapse of proteostasis, which is a prominent characteristic of cellular senescence. However, the understanding of ribosome pausing in senescent cells remains limited. In this study, we utilized ribosome profiling and G-quadruplex RNA immunoprecipitation sequencing techniques to investigate the impact of RNA G-quadruplex (rG4) on the translation efficiency of genes in senescent cells. Our findings reveal a decrease in the translation efficiency of genes enriched with rG4 in senescent cells. Meanwhile, we developed a dual fluorescence reporter system to demonstrate the ability of rG4 to halt ribosome translation both in vivo and in vitro. Moreover, a noteworthy augmentation in the prevalence of rG4 abundance was observed in senescent cells, and the reinforcement of the rG4 structure further exacerbates the process of cellular senescence. Additionally, the RNA helicase DHX9 was identified as a crucial regulator of rG4 abundance, and its reduced expression in senescent cells exacerbates the occurrence of ribosome pausing. Intriguingly, we also observed an augmented abundance of rG4, an imbalance in protein homeostasis, and a decrease in DHX9 expression in the fibroblast cells and highly aged tissues of aging mice. In summary, our findings reveal a novel biological role of rG4 and DHX9 in the regulation of ribosome translation and proteostasis, potentially providing implications for the postponement of cellular senescence and ageing.

overall_design: G4P-RIP-seq: create stable express G4P bj cell line, and collect young and senescence cell to do the RIP.

first: Haoxian

last: Zhou


title: RNA G-quadruplex(rG4) exacerbates cellular senescence by mediating ribosome pausing [RNA-seq]

overall_design: cPDS-RNA-seq：young BJ fibroblast cell treated with DMSO or cPDS(2 μM) for 48 h, then collect cell to do the RNA-seq.


title: Single-cell RNA Sequencing dissects cellular phenotypes linked to dysregulated mucosal wound healing in diabetes and aging

city: Philadelphia

first: Leticia

last: Rojas

institute: University of Pennsylvania

summary: Aging and diabetes exert a disruptive wound healing process. We use single-cell RNA-sequencing (scRNA-seq) data from palatal oral wounds in young, aged and diabetic mice to investigate immune and stromal cells heterogeneity to understand their role in wound repair.

overall_design: Type-I diabetes mellitus was induced in mice using streptozotocin. A 1-mm excisional punch biopsy wound was created in the palate of young (3-6-months), diabetic (4-6-months) and old (16-22-months) mice. Cells were isolated from 7-day oral gingival wounds, FACS-sorted and scRNA-sequenced in 10x Genomics platform. For each experimental condition, a pool of 6 mice was use, with no replicates. Young mice were use as control in some pair-wise analysis.

first: Adolfo

first: Zhe

last: Lyu

first: Hamideh

last: Azfali

first: Jane

last: Yang

first: Min

last: Liu

first: Erick

last: Armingol

first: Michael

last: Troka

first: Patricio

last: Smith

first: Vinicius

last: Coutinho-Maracaja

first: Kang

last: Ko

first: Dana

last: Graves


title: Transcriptional regulation of T cell exhaustion in immune checkpoint blockade resistance at single-cell resolution [in vivo]

first: Hsueh-Fen

last: Juan

summary: Tumor-specific CD8+ T lymphocytes are crucial for anti-cancer immunity but can lose cytotoxic function in the immunosuppressive tumor microenvironment. Immune checkpoint blockade (ICB), like anti-PD-1 therapy, enhance and prolong anti-tumor T cell responses. Despite its widespread clinical use, resistance to ICB develops in some patients, characterized by the proliferation of exhausted T cell (Tex). Here, we establish two single-cell murine hepatocellular carcinoma (HCC) models to explore regulatory network in Tex with ICB resistance. We uncover distinct T cell compositions, including both early and terminal Tex subsets, following prolonged ICB treatment, and reveal the differentiation trajectory of Tex subsets. Finally, we not only identify transcription factor Runx2 and its downstream targets as contributors to T cell exhaustion in both models, but discover ICB response correlates to Runx2 level in human tumor-infiltrating lymphocytes. These findings elucidate Runx2 regulates T cell exhaustion in response to prolonged ICB treatment, influencing ICB effICBency, and suggest potential targets for combination therapy alongside ICB in HCC.

overall_design: To uncover the crucial gene regulatory network that causes T cell exhaustion. We designed a mice model to examine the differential effects of anti-PD-1, an ICB targeting PD-1, on T cell. We inoculated C57BL/6 mice subcutaneously with 2 x 106 cells of hepatocellular carcinoma cell line, Hepa1-6. Mice were randomly assigned to two groups, anti-PD1 treatment or isotype, respectively, when tumors grew to reach an average volume of 200 mm3. For the short-term treatment experiment, either anti-mouse PD1 antibody (clone RMP1–14) or isotype control antibody (clone 2A3) was administered once per two days from day 15 to day 19, and the mice were sacrificed on day 20. Conversely, in the long-term treatment experiment, treatments were given every other day from day 15 to day 19 and then once per week starting from day 20, with the mice being sacrificed on day 57.

first: Tzu-Yang

last: Tseng

first: Ching-Huang

last: Hsieh

first: Chia-Lang

last: Hsu

first: Yu-Ching

last: Wu

first: Chiun

first: Hsuan-Cheng

last: Huang

first: Da-Liang

last: Ou


title: Effects of RNA splicing on hepatocyte fate decision

city: Jinan

first: Yachun

last: An

address: 44 Wenhua West Road, Lixia District, Jinan City

institute: Shandong university


title: Combinatorial codes of presynaptic organizer neurexins orchestrate precise olfactory axon targeting

city: Worcester

first: I-Hao

last: Wang

address: 370 Sunderland Rd, Unit D24

department: PMM

institute: UMMS

summary: Precise neural wiring is essential for the formation of complex neural circuitry within the mammalian brain, particularly in the olfactory system. While trans-interactions between synaptic membrane proteins have emerged as crucial elements in orchestrating the elaborate assembly of neural circuitry, identifying which specific synaptic surface proteins are involved in the wiring processes has remained elusive. Here, we uncover neurexins, the indispensable presynaptic receptors crucial neurotransmission, as novel wiring players using unbiased approaches based on single-cell transcriptomes of olfactory sensory neurons (OSNs). The distinctive expression of neurexin isoforms in OSNs synergistically cooperates the regulation of axon innervation, guiding OSNs to their designated glomeruli, in collaboration with their postsynaptic partners which display unique patterns of expression in mitral and tufted (M/T) cells. Our findings suggest a novel mechanism underpinning the precise assembly of the olfactory circuitry, facilitated by the trans-interaction between neurexins and their partnering elements. Beyond advancing our understanding of wiring processes in the olfactory system, this study holds the promise of unveiling the intricacies that govern higher brain structure and function.

overall_design: 5' scRNAseq was performed with olfactory epithelial cells isolated from wild-type mice

first: SungJin

last: Park

first: Paul

last: Greer


title: Effect of knockdown NR1D1 on gene expression of Xp11.2 translocation renal cell carcinoma cell lines UOK109 and  UOK120

city: Nanjing

first: Yanwen

last: Lu

state: jiangsu

address: No. 22 Hankou Rd., Gulou District, Nanjing, Jiangsu 210093, P.R.China

institute: Nanjing University

summary: To study the function of NR1D1 in cell cycle in Xp11.2 translocation renal cell carcinoma, we interfered NR1D1 in UOK109 and UOK120, then RNA-seq was performed to evaluate the expression of gene on cell cycle, cell cycle was enriched in GSEA enrichment analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for UOK109 and UOK120 and their KD derivatives (shNR1D1).

first: Shuoming

last: Zhou

first: Yi

last: Chen

first: Wenliang

last: Ma


title: Gene expression profile at single cell level of bone metastases from triple-negative breast cancer in mice.

city: jiangsu

first: Yiqiu

last: Liu

state: State...

address: 140 hanzhong road, nanjing city, jiangsu province, Chin

institute: Nanjing Medical University

summary: Triple-negative breast cancer (TNBC) bone metastasis has been lacking targeted therapy options. Our research has identified the androgen receptor (AR) as a potential driver of TNBC bone metastasis. To investigate the role of AR in TNBC bone metastasis, we utilized the iliac artery injection method to establish mouse models of bone metastasis. Subsequently, we administered PBS/DHT injections to explore the effects of AR on TNBC bone metastasis in mice.

overall_design: BALB/c Nude mice were subjected to iliac artery injection of MDA-MB-231 tumor cells. Subsequently, every three days, intraperitoneal injections of PBS/DHT were administered. After three weeks, bone metastatic tumor tissues were harvested and lysed to obtain single-cell suspensions for single-cell sequencing analysis.

first: Xiaoxiang

last: Guan

first: Lingling

last: Fan


title: In vivo gene editing of human hematopoietic stem and progenitor cells using envelope-engineered virus-like particles (PHH cells)

first: Keylie

last: Gibson

overall_design:
We investigated the changes in nature of PHHs upon thawing and in vitro culture prior to vector exposure becase we observed negligible transduction in the humanized liver of the FRG mice.
Gene expression profiling analysis of RNA-seq data was compared between freshly thawed PHH and PHH cultured in vitro for 24h (time of vector dosing for the in vitro titration experiments) or human hepatocytes freshly isolated from FRG mice prior to vector dosing.

first: Vladimir

last: Botchkarev Jr

first: Sean

last: Harrington

first: Matteo

last: Stoppato

first: Alexander

last: Justen

first: Casey

last: Kimber

first: Anjali

last: Kapuria

first: Chi-Shuen

last: Chu

first: Yuanxin

last: Xu

first: Kelsey

last: Haugh

first: Ramya

last: Ankala

first: Nathan

last: Kipniss

first: Andre

last: DeGroot

first: Emerson

last: Moore

first: Rowena

last: de Jesus

first: Funmi

last: Adewale

first: Kathy

last: Daniels

first: Samantha

last: Crocker

first: Anna

last: Liang

first: Shannon

last: Joyce

first: Nicole

last: Roberto

first: Pamela

last: Angel

first: Derek

last: Smith

first: Athena

last: Wong

first: Nick

last: Adler

first: Valeria

last: Berlfein

first: Shirisha

last: Amatya

first: Patricia

last: Cruite

first: Shariq

last: Usmani

first: Albert

last: Ruzo

first: Benjamin

last: Ferland

first: Sundeep

last: Chandra

first: Edward

last: Rebar

first: Jagesh

last: Shah

first: Kyle

last: Trudeau

first: Luca

last: Biasco


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

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

first: Rachel

last: Marcone

first: Yahya

last: Mohammadzadeh

first: Michele

last: De Palma


title: Redirecting microglia phenotype via inhibition of NFAT1 ameliorates deficits in mouse model of synucleinopathies

city: Bethesda

first: Changyoun

last: Kim

state: Maryland

address: 35 Convent Dr. Rm 1A-1002

department: Molecular Neuropathology Unit

institute: National Institute on Aging, National Institutes of Health

summary: We evaluated the potential of NFAT1 inhibition as a new therapeutic strategy for synucleinopathies utilizing in vitro and in vivo synucleinopathy models.

overall_design: Gene expression profiling analysis of RNA-seq data following NFAT inhibition in mouse brain microglia.

first: Yeon-Joo

last: Lee


title: Ileal Enterocyte Brush Border Abnormalities Associate with Progressive Disease Course in Pediatric Crohn’s Disease

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

summary: Objective: There is a critical need for biomarkers to predict prognosis and guide clinical care in pediatric Crohn’s disease (CD). Our previous studies of adult CD indicated ileal microvillus length as a potential prognostic biomarker for therapy response. Here, we tested if short microvillus length predicted progression of disease behavior or bowel resection surgery in pediatric CD. Design: We obtained H&E-stained ileal histology samples from 3 pediatric CD cohorts. Average microvillus length was determined for 59 Control and 377 CD samples and tested for associations with patient demographic and clinical data, RNA-seq molecular profiles, histological inflammation scores, and clinical outcomes. Results: Relative to Controls, the average microvillus length was shorter in CD samples collected at diagnostic or follow-up colonoscopy procedures. Microvillus length was generally not associated with demographic data or clinical activity indices. The CD molecular signature was functionally enriched for transporter activity and brush border membrane among the genes positively associated with microvillus length and for extracellular matrix, inflamed macrophages, and fibroblasts among the genes negatively associated with microvillus length. Microvillus length negatively correlated with histologic inflammation score, but short microvillus length phenotype could cooccur with low histologic inflammation. There was a higher likelihood of stricturing disease behavior or bowel resection surgery, but not fistulizing disease behavior, in follow-up CD samples with short microvillus length. Conclusion: Short microvillus length can predict the development of stricturing disease behavior and bowel resection surgery in pediatric CD, further supporting the potential use of this histological phenotype as a biomarker for CD prognosis.

overall_design: 138 Crohn’s disease (CD) and 14 control human ileum biopsies

first: Yael

last: Haberman

first: Erin

last: Bonkowski

first: Katherine

last: Simpson

first: Ta-Chiang

last: Liu

first: Subra

last: Kugathasan

first: Lee

last: Denson

first: Kelli

last: VanDussen


title: Epigenomic landscape of endothelial differentiation from human pluripotent stem cells

city: Beijing

first: Yonglin

last: Zhu

state: Beijing

address: D115, School of Medicine

institute: Tsinghua University

summary:
We performed transcriptome, open chromatin and genome binding of histone H3K4me3 H3K27ac, and H3K27me3 profiling of different endothelial populations during human pluripotent stem cell differentiation. Through integrative analysis,  we identified transcription factor BCL6B as a novel regulator of arterial and venous endothelial cell fate.  We also generated and characterized the transcriptome and chromatin state of BCL6B KO hECs to reveal the mechanism of its function.
Methods: undifferentiated hESC (H1) cells, vascular mesoderm cells (VMCs), endothelial progenitor cells (EPCs), and endothelial cells (ECs) were sorted. Transcriptome profiling was done using the SMART-seq2 protocol; ATAC-seq and  CUT&Tag methods were used to profile the chromatin accessibility and  the genome-wide binding of histone H3K4me3, H3K27ac, H3K27me3 marks. BCL6B KO ECs were generated and the change in global gene expression was investigated by RNA-seq.  ChIP-seq was performed to reveal the binding sequences of BCL6B.
Results: By integrative analysis the transcriptome and epigenetic landscape of undifferentiated hESC (H1) cells, vascular mesoderm cells (VMCs), endothelial progenitor cells (EPCs), and endothelial cells (ECs). We depicted the epigenomic roadmap of human EC fate establishment, and identified BCL6B as a novel regulator of EC fate.  We also characterized the differentially-expressed genes in wide-type and BCL6B knock-out ECs, inferred the potential target genes of BCL6B and the mechanism of BCL6B function.
Conclusions: This study depicted the epigenomic lanscape of hPSC-EC differentiation, predicted transcription factors involved in EC fate specification and uncovered that BCL6B is a novel regulator of arterial and venous EC fate decision.

overall_design: Perform RNA-seq, ATAC-seq, and ChIP-seq (H3K4me3, H3K27me3, and H3K27ac) of undifferentaited hESC, hESC-derived VMC, EPC, and EC.

first: Jie


title: BEAS_2B Human lung cell : Control vs transfected with E6E7 HPV16

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

summary: Transcriptional profiling of BEAS_2B lung cell transfected with E6E7 HPV-16 genes using pLXSN vector. Control cells were transfected with the empty pLXSN  vector

overall_design: Two-condition experiment, BEAS_2B E6E7 vs BEAS_2B V. Two dye-swap Cy3/Cy5 replicate per array.

first: Nelson

last: Peña

last: Urzúa

first: Francisco

last: Aguayo


title: Inhibition of Wnt signaling in primary human hepatocytes promotes Plasmodium falciparum liver stage development

city: Nijmegen

first: Richard

last: Bartfai

state: Gelderland

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

summary: After infection of the human host, the first stage of the Plasmodium falciparum (Pf) lifecycle takes place in the liver. However, understanding of host-parasite interactions in this stage has been limited by the rapid loss of functionality in cultured primary human hepatocytes (PHHs), the natural host source for Pf liver stage parasites. Here, we link loss of hepatic functionality to a drastic loss in Pf permissiveness, which we can effectively prevent by using a novel medium containing serum-replacement and signal transduction inhibitors. Integrating transcriptomic analysis and phenotypic assessment of infection outcome, we identified several host signaling pathways that influence Pf liver stage development via modulating the host cell environment. Inhibition of the Wnt pathway in particular has a major impact on the size and maturity of Pf liver stage schizonts, by retaining the metabolic activity and epithelial nature of PHHs. Understanding how alteration of the host cellular state via signalling pathways determine Pf liver stage permissiveness provides insight into host-parasite interactions and may accelerate development of novel therapeutic strategies via improved in vitro liver stage models.

sample_organism:
Plasmodium falciparum
Homo sapiens

platform_organism:
Plasmodium falciparum
Homo sapiens

overall_design:
In vitro cultured primary human hepatocytes (either uninfected and infected with NF135/NF54 strain of Plasmodium falciparum) were kept under mock/IWP2/5C treatment till harvest at day 5 post-infection cognate timepoints. All samples, including freshly isolated hepatocytes, were preserved in TRIzol reagent for RNA isolation.
Total RNA was isolated using the Zymo Research RNA extraction kit. Stranded mRNA sequencing library was prepared with the Kapa mRNA HyperPrep Kit. 36bp paired-ended sequencing was performed on the Illumina NextSeq 550 platform.
Differential gene expression analysis was performed between freshly isolated and mock vs IWP2 treated hepatocytes.

first: Abhishek

last: Kanyal

first: Geert-Jan

last: van Gemert

first: Haoyu

last: Wu

first: Alex

last: van der Starre

first: Johannes

middle: H

last: de Wilt

first: Teun

last: Bousema

first: Robert

last: Sauerwein

first: Annie

last: Yang


title: Spatial transcriptomics reveals spatial remodling of hepatic lobule during liver regeneration

first: Yachun

last: An

summary: In this study, we explored the effects of RNA splicing on hepatocyte fate decision. We found spatial remodeling of hepatic lobule during liver regeneration by  spatial transcriptome analysis in regenerative and control mouse model. We also reported cell heterogeneity of hepatocyte-organoids and found that splicing factors reprogram hepatocytes from single-cell resolution. To explore the detailed function of splicing factors, splicing inhibitors (Pladienolide B) were used to treated organoids, then total RNA were harvest for bulk RNA sequence. In summary, we found that splicing factors can promote the transformation of hepatocytes from metabolic state to proliferative state by spatial transcriptome, single-cell RNA sequencing, and bulk RNA sequencing.

overall_design: Undamaged and injuried mouse liver tissues were used for spatial transcriptome analysis: undamaged (Und), 24 hours after hepatectomy (PHx24h), 48 hours after hepatectomy (PHx48H) and chornic carbon tetrachloride injuried (CCl4).

first: Wenjing

last: Wei

first: Jiabei

last: Lian

first: Longxin

last: Qiao

first: Yao

last: Lu

first: Yunuo

last: Mao

first: Chunyang

last: Li

first: Fan

last: Yi

first: Hans

last: Clevers

first: Huili

last: Hu


title: RNA G-quadruplex(rG4) exacerbates cellular senescence by mediating ribosome pausing [Ribo-seq]

first: haoxian

last: zhou

overall_design: Ribo-seq: collect young and replicate sensescence BJ fibroblast cell to do the ribo-seq.

first: Haoxian

last: Zhou


title: Gene expression profile at single cell level of hepatocytes from hepatocyte derived liver organoid

overall_design: Mouse hepatocytes were obtained by two-step collagenase perfusion and culture into hepatocyte-organoids for 6 days. We performed single cell RNA sequencing of organoids for exploring detailed cell heterogeneity of hepatocytes of organoids.


title: Study of the effects of RNA splicing inhibitor Pladienolide B on hepatocyte proliferation in vitro

overall_design: To investigate function of RNA splicing  in regulating hepatocytes fate determination,  Pladienolide B and DMSO were used to treat hepatocyte-organoid. We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different samples containing 3 DMSO treated and 3 Pladienolide B treated.


title: Elucidation of gene clusters underlying withanolide biosynthesis in ashwagandha through yeast metabolic engineering

status: Public on Dec 16 2025

city: Cambridge

first: Erin

last: Reynolds

address: 455 Main St

institute: Whitehead Institute

summary: Withanolides are medicinally important steroidal lactones produced by Withania somnifera (ashwagandha) amongst other Solanaceae family plants, known for their anti-inflammatory, anti-cancer, and adaptogenic properties. However, the biosynthetic pathway to withanolides is largely unknown, preventing scale-up and hindering pharmaceutical applications. Here, we generate a chromosome-scale assembly of the W. somnifera genome and identify two withanolide biosynthetic gene clusters that exhibit a segmented tissue-specific expression pattern. Using metabolic engineering in yeast, complemented by heterologous expression in Nicotiana benthamiana and virus-induced gene silencing in W. somnifera, we elucidate the withanolide biosynthetic pathway to an intermediate with all characteristic chemical features of withanolides. We report two cytochromes P450 (CYP87G1 and CYP749B2) and a short-chain dehydrogenase (SDH2) responsible for lactone ring formation and two P450s (CYP88C7 and CYP88C10) and a sulfotransferase (SULF1) that generate the characteristic A-ring structure of withanolides, featuring a C1 ketone and C2-C3 unsaturation. Identifying SULF1 as a core pathway enzyme challenges the conventional paradigm of sulfotransferases as tailoring enzymes and suggests a wider role for this enzyme family in plant specialized metabolism. This work opens new avenues for the sustainable production of withanolides through biomanufacturing and for drug development leveraging the withanolide scaffold.

overall_design: RNA-seq profiling of leaf, young leaf (<2 cm size), root, and berry tissue of Withania somnifera. Biological replication n=3.

first: Jing-Ke

last: Weng


title: Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

city: Seattle

first: Sanjay

last: Srivatsan

state: WA

address: 1100 Fairview Ave N. Mailstop A2-119

institute: Fred Hutchinson Cancer Center

summary: Spatial genomics technologies include imaging- and sequencing-based methods. Sequencing-based spatial methods typically require surfaces coated with coordinate-associated DNA barcodes, but the physical registration of these barcodes to spatial coordinates is challenging, necessitating either high density printing of oligonucleotides or in situ sequencing/probing of randomly deposited, DNA-barcode-bearing beads. As a consequence, the surface areas available to sequencing-based spatial genomic methods are constrained by the time, labor, cost, and instrumentation required to either print or decode a coordinate-tagged surface. To address this challenge, we developed SCOPE (Spatial reConstruction via Oligonucleotide Proximity Encoding), an optics-free, DNA microscopy-inspired method. With SCOPE, the relative positions of DNA-barcoded beads within a 2D shape, 2D image or 3D volume are inferred from the ex situ sequencing of chimeric molecules formed from diffusing “sender” and tethered “receiver” oligonucleotides. To demonstrate the potential of this approach, we applied SCOPE to reconstruct 2D shapes, 2D images or 3D volumes defined by 104-106 x 20-100 µm DNA barcoded beads, including an asymmetric “swoosh” resembling the Nike logo (44 mm2), a “color” Snellen eye chart (704 mm2) and the surface topology of 3D molds of a teddy bear, star, butterfly or block letter (75-100 mm3). Each of the resulting “DNA barcode proximity graphs” was computationally reconstructed in an automated fashion, across fields of view and at resolutions that were determined by sequencing depth, bead size, and diffusion kinetics, rather than by microarray or microscope instrument time. Because the ground truth shapes are known, these datasets may be particularly useful for the further development of computational algorithms by this nascent field.

overall_design: The SCOPE reaction involves subjecting the hydrogel-encased monolayer of polyacrylamide beads to a temperature-controlled, two-phase reaction mediated by a single reaction volume containing two enzymes. In the first phase (37°C; 15’), sender-messengers are released from beads by the USER enzyme, which cleaves at the dU present at the stem of a subset of DNA barcodes. Sender-messengers diffuse away and hybridize to receiver-messengers, of the same bead type but opposite strand, tethered to adjacent beads. Because the complementary regions reside in the functional cap (Fig. 1A), senders and receivers are expected to hybridize at their 3’ ends. In the second phase (55°C; 15’), reverse transcriptase, which can mediate both RNA- and DNA-templated DNA polymerization, drives overlap extension and the generation of a chimeric molecule that includes both the sender-messenger and receiver-messenger derived DNA barcodes (or, alternatively, chimeras of decoders and proximate hashing oligos). Sender-receiver chimeras are then PCR amplified and subjected to massively parallel sequencing, which yields a sparse matrix of interaction counts between a large number of DNA barcode-defined beads.

first: Hanna

last: Liao

last: Kottapalli

first: Yuqi

last: Huang

first: Matthew

last: Chaw

first: Jase

last: Gehring

first: Olivia

last: Waltner

first: Melissa

last: Phung-Rojas

first: Riza

last: Daza

first: Frederick

last: Matsen IV

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: A simple and effective method for mature kidney organoid containing a collecting duct using retinoic acid and bone morphogenetic protein 7

city: Daejeon

first: In Hwan

last: Tae

address: 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: During kidney development, an intermediate mesoderm (IM) give rise to distinct structures: the ureteric bud (UB) and the metanephric mesenchyme (MM). These structures differentiate further into the collecting duct and nephron, forming a mature kidney. Generating functional kidney organoids has been challenging due to incomplete development of the UB. Researchers have overcome this limitation by differentiating UB and MM separately and co-culturing them to generate kidney organoids. However, this study developed a co-culture-free method using retinoic acid (RA), plays important role in the anterior IM differentiation and BMP7 secreted by UB in vivo development. This protocol provided not only simplifies the complexity of kidney organoid generation but also advances our understanding of the crucial signaling pathways involved in kidney development.

overall_design: Two-dimensional (2D)-cultured IM cells were collected, dissociated using accutase, seeded in a 96-well ultra-low attachment plate (Corning; 1 × 105 cells/well), and gently centrifuged thereafter. The cell aggregates were cultured with 100 ng/mL FGF9, 1 μg/mL heparin, and 5 μM Y27632 (Tocris) in basal differentiation medium for 1 day. After incubation at 37 °C (5% CO2), 5–6 cell aggregates were transferred to a collagen-coated Transwell (#3491, Corning) and treated with 5 μM CHIR99021 in basal differentiation medium for 1 h. The medium was replaced by basal differentiation medium containing 100 ng/mL FGF9 and 100 ng/mL BMP7 (Peprotech), and the cells were cultured for 10–14 days. The medium was replaced daily with care taken so that the cultured medium did not overflow over the membrane.

first: Hyun

last: Kang