title: Single-Cell RNA Sequencing Identifies Molecular Biomarkers Predicting Response to CDK4/6 Inhibition in Metastatic HR+/HER2- Breast Cancer

first: Ziyi

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

summary: Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i), combined with endocrine therapy, represent the standard treatment for metastatic HR+/HER2- breast cancer (mBC). Despite their established efficacy, intrinsic resistance affects approximately one-third of patients, posing a significant challenge and underscoring the importance of identifying reliable predictive biomarkers. This study utilizes single-cell RNA sequencing (scRNAseq) of metastatic site biopsies to unveil cellular and molecular biomarkers predictive of CDK4/6i response. Through this analysis, we have identified and validated the tumor-specific molecular biomarkers across two independent mBC patient cohorts using bulk RNAseq data from baseline fresh biopsies or FFPE slides of HR+/HER2- mBC patients prior to CDK4/6i treatment. Additionally, the data indicate that baseline predictors may include tumor-infiltrating cytotoxic NK and T lymphocytes, suggesting the potential utility of checkpoint inhibitors in CDK4/6i progressors. These potentially actionable insights underscore the importance of optimizing therapeutic strategies based on microenvironment-specific changes observed following disease progression.

overall_design: Metastatic tumor biopsies were obtained from HR+/HER2- BC patients pre-CDK4/6i treatment at baseline (BL) and/or at disease progression. BL samples were from CDK4/6i responders (n = 8, median progression-free survival [mPFS] = 17 months), while progressors were categorized as early-progressors (EP, n = 3, mPFS = 3 months) and late-progressors (LP, n = 8, mPFS = 10 months). Metastatic sites included liver (10), pleural effusions (6), ascites (2), and bone (1). InferCNV distinguished tumor cells, and functional analysis utilized the Molecular Signatures Database. Signature panel genes were validated in two independent cohorts (MDACC n = 89, Korean n = 61) with RNAseq data from baseline biopsies from HR+/HER2- mBC patients pre-CDK4/6i treatment.

first: Linjie

last: Luo


title: Single-Cell RNA Sequencing Identifies Molecular Biomarkers Predicting Late Progression to CDK4/6 Inhibition in Patients with HR+/HER2- Metastatic Breast Cancer [tissue]

status: Public on Feb 18 2025

city: Houston

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

country: USA

institute: University of Texas - MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary: This study addresses the critical need for predictive biomarkers in patients with hormone receptor–positive, HER2-negative (HR+/HER2-) metastatic breast cancer (mBC) who have been treated with cyclin-dependent kinase 4/6 inhibitors (CDK4/6is). Using single-cell RNA sequencing, we reveal differential mechanisms of early versus late progression, enhancing our understanding of resistance to CDK4/6is. We identify and validate tumor-specific molecular biomarkers and demonstrate that tumor-infiltrating cytotoxic natural killer and CD8+ T cells are predictive of therapeutic response. Additionally, increased immune activity suppression in late progressing tumors suggests that combining CDK4/6is with checkpoint inhibitors could be beneficial against drug resistance. Validation across 2 independent cohorts confirms the robustness and clinical relevance of our findings. These insights pave the way for optimizing therapeutic strategies based on microenvironment-specific changes, offering a personalized and effective approach to managing HR+/HER2- mBC and improving patient outcomes.

first: Peng

last: Yang

first: Sofia

last: Mastoraki

first: Xiayu

last: Rao

first: Yan

last: Wang

first: Nicole

middle: M

last: Kettner

first: Akshara

middle: S

last: Raghavendra

first: Debasish

last: Tripathy

first: Senthil

last: Damodaran

first: Kelly

middle: K

last: Hunt

first: Jing

last: Li


title: Role of VISTA in ILC2-mediated airway hyperreactivity

city: Los Angeles

first: Mohammad Hossein

last: Kazemi

state: CA

address: 1450 Biggy St.

department: Microbiology and Molecular Immunology

institute: University of Southern California

summary: Type-2 innate lymphoid cells (ILC2s) play a pivotal role in the development of airway hyperresponsiveness (AHR). However, the regulatory mechanisms governing ILC2 function remain inadequately explored. This study uncovers V-domain Ig suppressor of T cell activation (VISTA) as an inhibitory immune checkpoint crucial for modulating ILC2-driven lung inflammation. VISTA is upregulated in activated pulmonary ILC2s and plays a key role in regulating lung inflammation, as VISTA-deficient ILC2s demonstrate increased proliferation and function, resulting in elevated type-2 cytokine production and exacerbation of AHR. Mechanistically, VISTA stimulation activates Forkhead box O1 (FOXO1), leading to modulation of ILC2 proliferation and function. The suppressive effects of FOXO1 on ILC2 effector function were confirmed using FOXO1 inhibitors and activators. Moreover, VISTA-deficient ILC2s exhibit enhanced fatty acid oxidation and oxidative phosphorylation to meet their high energy demands. Therapeutically, VISTA agonist treatment reduces ILC2 function both ex vivo and in vivo, significantly alleviating ILC2-driven AHR. Our murine findings were validated in human ILC2s, where a VISTA agonist reduces their function ex vivo and in a humanized mouse model of AHR. Our studies unravel VISTA as a novel immune checkpoint for ILC2 regulation via the FOXO1 pathway, presenting potential therapeutic strategies for allergic asthma by modulating ILC2 responses.

overall_design: mRNA profiles of sorted mouse lung ILC2s lacking or not VISTA gene (Vsir) were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.

first: Mohammad

last: Hossein Kazemi


title: Gene expression signatures for highly effective dermal sheath cup cells

city: Yokohama

first: Yumiko

last: Ishimatsu-Tsuji

address: Nishi-ku

country: Japan

institute: Shiseido

summary: In order to identify genes that correlate with efficacy in clinical trials, titled Autologous cell–based therapy for male and female pattern hair loss using dermal sheath cup cells, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish efficacy. RNA was extracted from each DSC-cells  that was used in the clinical trial, and gene expression profiling by microarrays was performed. DSC cells derived from  representative 8 IDs of highly effective and less effecgive group were analyzed.  Signature was identified that distinguished between highly and less effective IDs.

overall_design: Gene expression was measured in dermal sheath cup cells derived from 8 highly or less effective individuals.


title: Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [eCLIP-seq]

city: Tucson

first: Kevin

last: Rhine

state: AZ

address: 1703 E Mabel St

department: Pharmacology & Toxicology

institute: University of Arizona

summary: Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged healthy donors directly into neurons, which retained their aging markers. Here we show that aged neurons are broadly depleted of RNA-binding proteins, especially spliceosome components. Intriguingly, splicing proteins – like the dementia and ALS-associated protein TDP-43 – mislocalize to the cytoplasm in aged neurons, which leads to widespread alternative splicing. Cytoplasmic spliceosome components typically are recruited to stress granules, but aged neurons suffer from chronic stress that prevents this sequestration. We link chronic stress to the malfunctioning ubiquitylation machinery, poor HSP90α chaperone activity, and the failure to respond to new stress events. Together our data demonstrates that aging-linked deterioration of RNA biology is a key driver of poor resiliency in aged neurons.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Enhanced immunoprecipitation and crosslinking followed by sequencing (eCLIP-seq) of RNA-binding proteins in neuron and tissues

first: Rachel

first: Hema

middle: E

last: Kopalle

first: Xuezhen

last: Ge

first: Elle

last: Epstein

first: Orel

last: Mizrahi

first: Assael

middle: A

last: Madrigal

first: Hsuan-Lin

last: Her

first: Trent

last: Gomberg

first: Anita

last: Hermann

first: Joshua

middle: L

last: Schwartz

first: Amanda

middle: J

last: Daniels

first: Uri

last: Manor

first: John

last: Ravits

first: Robert

last: Signer

first: Eric

last: Bennett

first: Gene

middle: W

last: Yeo


title: Single-Cell RNA Sequencing Identifies Molecular Biomarkers Predicting Late Progression to CDK4/6 Inhibition in Patients with HR+/HER2- Metastatic Breast Cancer [FFPE]

first: Khandan

last: Keyomarsi

first: Linjie

last: Luo

first: Peng

last: Yang

first: Sofia

last: Mastoraki

first: Xiayu

last: Rao

first: Yan

last: Wang

first: Nicole

last: Kettner

first: Akshara

last: Raghavendra

first: Debasish

last: Tripathy

first: Senthil

last: Damodaran

first: Kelly

last: Hunt

first: Jing

first: Ziyi

last: Li


title: Effect of the Mutated p.H222P A-type Lamins on Gene Expression in Both Patient-Derived Cardiomyocytes and Mouse Models of Dilated Cardiomyopathy

status: Public on Feb 17 2025

city: Paris

first: Marie

last: Kervella

address: 105 boulevard de l'Hôpital

country: France

institute: Inserm

summary: Mutation on A-type lamins encoding gene can lead to a wide-range of diseases called laminopathies, including dilated cardiomyopathy. Nuclear lamins are integral to a physical continuum connecting the extracellular environment and the nuclear interior, playing a crucial role in load-bearing tissues like  the heart to preserve mechanical integrity and genome stability. To investigate the impact of the LMNA p.H222P mutation on gene expression, we conducteed bulk RNA-seq in hiPSCs-derived cardiomyocytes and mouse cardiomyocytes, both carrying this mutation. Our results reveal that the LMNA p.H222P mutation leads to dysregulated gene expression, which may contribute to LMNA cardiomyopathy pathogenesis.

overall_design: bulk RNA-seq in hiPSCs-CMs (isogenic control and LMNA p.H222P cell lines) and heart sections from Lmna p.H222P/H222P and WT mice

first: Fiorella

middle: C

last: Grandi

first: Albano

last: Meli

first: Antoine

last: Muchir


title: Inflammatory Bowel Disease Leads to Long-Term Ovarian Dysfunction via Immune-Mediated Follicular Aging

city: Hong Kong

first: Yimeng

address: 21 Sassoon Road, Pokfulam Hong Kong

country: China

institute: The university of Hong Kong

summary: The rising global incidence of inflammatory bowel disease (IBD) is associated with reduced levels of anti-Müllerian hormone (AMH), a key biomarker for premature ovarian insufficiency (POI), highlighting reproductive risks for women of childbearing age. To investigate the connection between IBD and ovarian aging, we used a dextran sodium sulfate (DSS)-induced mouse model of IBD and assessed reproductive outcomes, including ovarian reserve, folliculogenesis, hormone profiles, and estrous cyclicity. Transcriptomic analysis of ovarian tissue showed that IBD upregulates genes associated with aging. Gene Ontology enrichment pointed to signaling pathways involved in cellular senescence, oxidative stress response, and senescence-associated secretory phenotypes. By integrating our ovarian transcriptomic data with single-cell RNA-seq datasets from young (3-month) and aged (9-month) mouse ovaries, we found significant parallels between IBD-induced transcriptional changes and natural ovarian aging. Flow cytometry confirmed elevated levels of T cells, CD8+ T cells, and macrophages in the ovaries, indicating localized immune activation. Similar systemic immune changes were observed in peripheral blood mononuclear cells, with expanded T cell and macrophage populations. TUNEL assays and qPCR further validated accelerated ovarian aging in IBD mice, showing increased granulosa cell apoptosis and upregulated aging-related markers. Notably, even after an 89-day recovery period following DSS treatment, persistent deficits in follicular counts, hormonal balance, and estrous regularity indicated irreversible ovarian dysfunction. Our findings demonstrate that IBD triggers ovarian inflammation, depletes ovarian reserve, and accelerates aging processes, leading to long-term reproductive impairment. This study elucidates the mechanistic links between IBD and POI, providing insights for therapeutic strategies to mitigate fertility risks in affected women.

overall_design: RNA seq profiling of ovaries from four groups of wildtype C57BL/6J mice and dextran sodium-induced mice was performed at the end of modeling and after 89 days of rest in both groups.

first: Xiaofan

last: Guo

first: Yanhui

last: Liu

first: Huashan

last: Zhao


title: Differential gene expression in Nintedanib-treated 3D skin rafts with Scleroderma (SSc) skin and healthy fibroblasts

city: Ann Arbor

first: Priyanka

last: Verma

state: MI

address: 2800 Plymouth Rd,

institute: University of Michigan

summary: This study examines differential gene expression in 3D skin organoids treated with Nintedanib.

overall_design: Human SSc/ healthy fibroblast samples (400,000 cells/ml) were resuspended in a buffered solution of rat tail type I collagen (4 mg/ml, from BD Biosciences) and seeded in 12-well cell culture plates. The dermal collagen plugs were allowed to polymerize for 30 minutes and then supplemented with 20% Fetal Bovine Serum (FBS) in Dulbecco's Modified Eagle Medium (DMEM) overnight. 1 mL of primary human epidermal keratinocytes (600,000 cells/ml) were seeded on top of the dermal collagen plug in E medium. After 48 hours of incubation, the skin equivalents were transferred to the top of a metal grid raised above the surface of a 60-mm tissue culture dish and exposed to air to promote epidermal stratification. Approximately 2 hours prior to this, the media was changed for fresh E media supplemented with epidermal growth factor (5ng/ml). E media without epidermal growth factor was used to replace media every other day for up to 10 days. Rafts were treated with either Nintedanib (2uM) or vehicle every day. After 10 days, the rafts were harvested in RNAlater stabilization solution prior to RNA isolation.

first: Kris

last: Shah

first: Timothy

last: Hamill

first: John

last: Varga

first: Swati

last: Bhattacharyya


title: A niche-dependent redox rheostat regulates epithelial stem cell fate in the distal colon II

city: Boston

first: Jay

middle: R

last: Thiagarajah

state: MA

address: 300 Longwood Avenue

department: Division of Gastroenterology, Hepatology and Nutrition

institute: Boston Childrens Hospital

summary: The niche environment surrounding intestinal stem cells (ISCs) varies along the length of intestine and provides key cues that regulate stem cell fate. Here, we investigated the role of cellular redox balance in colonic ISC function. We show that hypoxia and Wnt signaling synergize to restrict the reactive oxygen species (ROS) generating enzyme NADPH oxidase 1 (NOX1) to the crypt base in the distal colon. NOX1 function maintains a more oxidative cell state that licenses cell cycle entry, altering the balance of asymmetric stem cell self-renewal and directing lineage commitment. Mechanistically, cell redox state directs a self-reinforcing circuit that connects hypoxia inducible factor 1 (HIF1a)-dependent signaling with regulation of the metabolic enzyme isocitrate dehydrogenase 1 (IDH1). Our studies show that cellular redox balance is a central and niche-dependent regulator of epithelial homeostasis and regeneration and provide a basis for understanding disease propensity in the distal large intestine.

overall_design: RNA seq of colonoids from WT and NOX1 KO mice.

first: Chen

last: Xi

first: Thiagarjah

last: Jay


title: A Cryogel-Based Dendritic Cell Vaccine for Post-Surgical Breast Cancer Immunotherapy

city: Hsinchu City

first: ShengLiang

last: Cheng

address: No. 101, Sec. 2, Guangfu Rd., East Dist.

department: Institute of Biomedical Engineering

country: Taiwan

institute: National Tsing Hua University

summary: Triple-negative breast cancer (TNBC) is an aggressive malignancy with high mortality and limited treatment options. While surgical resection removes the primary tumor, it often fails to prevent recurrence or metastasis, and despite the promise of immunotherapy, the response to immune checkpoint blockade remains poor. Here, we develop a cryogel-based dendritic cell (DC) vaccine that integrates gold nanodot-lipopolysaccharide (AuLPS)-loaded DCs, doxorubicin (Dox), and a PD-1 immune checkpoint blockade, effectively enhancing anti-tumor immunity in the post-surgical setting. The AuLPS nanoparticles (NPs) stabilize LPS assembly, optimizing Th1 adjuvant activity, thereby improving DC vaccine efficacy while minimizing adverse effects. The cryogel enables the sustained localized release of therapeutic agents at the surgical site, preserving DC viability, migration, and functionality within the tumor microenvironment. This strategy enhances DC activation and potentiates robust T-cell activation in both tumor-draining lymph nodes and tumor beds, leading to durable anti-tumor immunity. When administered at the post-surgical site in an orthotopic TNBC model, the aPD-1+Dox+AuLPS@DC cryogel vaccine significantly delays tumor recurrence, reduces distant metastases, and prolongs survival. These findings highlight cryogel-based DC vaccines as a promising post-surgical immunotherapy to overcome the limited response to immune checkpoint blockade and improve TNBC outcomes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine TNBC tumors with or without treatment of DOX and AuNP treated BMDC co-loaded cryogel

first: Yunching

last: Chen

first: Shu-Yi

last: Lin

first: Jane

last: Wang


title: IRF5 produced by kidney macrophages promotes polycystic kidney disease

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

summary: We show that Pkd1 mice have higher levels of kidney IRF5 compared to control mice and that IRF5 expression is found predominantly in macrophage populations in the kidney. Suppressing IRF5 with an antisense oligonucleotide (ASO) decreased kidney IRF5, the total number of kidney macrophages, pro-inflammatory cytokine production, and attenuated kidney cyst growth.

overall_design: CrePlus and CreMinus Pkd1 mice with and without unilateral nephrectomy were compared for differential gene expression by RNASeq methods.

first: E

last: Hazard

first: Takamitsu

last: Saigusa


title: DISC1 Protects Against Zika Virus Infection and Long-Term Neurological Damage Through AMPK-mTOR-Mediated Autophagy

city: Shenzhen

first: Shengze

last: Zhang

state: Guangdong

address: No. 66, Gongchang Road

institute: Sun Yat-sen University

summary: Disrupted in Schizophrenia 1 (DISC1) is essential for neuronal development and has been implicated in various psychiatric disorders. However, its role in Zika virus (ZIKV) infection, particularly in congenital Zika syndrome (CZS) and ZIKV-induced long-term neurodevelopmental defects, remains unexplored. In this study, we demonstrate that DISC1 suppresses ZIKV infection in human placental and neuroglia cells, as well as in murine macrophages. DISC1 also limits ZIKV dissemination from peripheral tissues to key organs of mice, including the uterus, testis, and brain, thereby reducing fetal abortion rates and intrauterine growth restriction. Notably, DISC1 is associated with long-term ZIKV effects, including memory loss, reduced anxiety and depression, declines in sociability and social novelty. Mechanistically, DISC1 activates autophagy by enhancing AMPKα phosphorylation and reducing mTOR phosphorylation, protecting against ZIKV infection. Additionally, DISC1 interacts with LC3 to further activate autophagy, partially contributing to inhibit ZIKV infection. In conclusion, DISC1 plays a critical factor in controlling ZIKV infection and mitigating CZS and ZIKV-induced neurocognitive decline.

overall_design: U251 cells were infected with ZIKV GZ01 (MOI of 1.0) post pcDNA or HA-DISC1 transfection for 24 hours.


title: Lamin B1 and LAP2β resist cytoskeletal force to maintain lamin A/C meshwork organization and preserve nuclear integrity

city: San Francisco

first: Yewande

last: Alabi

state: California

address: 555 Mission Bay Boulevard South Rm 312A

institute: UCSF

summary: The nuclear lamins are extremely long-lived proteins in most cell types. As a consequence, lamin function cannot be effectively dissected with temporal precision using standard knock-down approaches. Here, we apply the auxin inducible degron (AID) system to rapidly deplete each lamin isoform within one cell cycle and reveal the immediate impacts of lamin loss on the nucleus . Surprisingly, neither acute lamin A/C (LA/C), lamin B1 (LB1), nor lamin B2 (LB2) depletion altered nuclear shape or induced nuclear blebbing, indicating that acute lamin loss is not sufficient to alter nuclear morphology. LB1 depletion is immediately followed by LA/C meshwork disorganization due to actin cytoskeletal forces on the lamina, yet neither LA/C nor LB1 depletion induced nuclear rupturing. We found that the abundant inner nuclear membrane protein LAP2β protects nuclear integrity in the absence of LB1, as depletion of both LB1 and LAP2β induced severe LA/C disorganization and frequent nuclear rupturing. Depolymerization of the actin cytoskeleton halts nuclear rupture in LAP2β- and LB1-depleted nuclei. We conclude that both LB1 and LAP2β resist cytoskeletal force to maintain regular lamin A/C meshwork organization and preserve nuclear integrity.

overall_design: RNA-seq profiling of DLD1 cells expressing Lamin A/C, Lamin B1 or Lamin B2 endogenously tagged with an N-terminal auxin inducible degron tag. Cells were treated with auxin for 0, 16, or 96 hours. Non-tagged DLD1 parental cells were also treated with auxin for 0, 16, or 96 hours to generate a list of auxin responsive genes.

first: Vasilisa

last: Aksenova

first: Alexei

last: Arnaoutov

first: Harold

last: Marin

first: Mary

last: Dasso

first: Abby

last: Buchwalter


title: A niche-dependent redox rheostat regulates epithelial stem cell fate in the distal colon

first: Jay

last: Thiagarajah


title: OTX2 controls  chromatin accessibility to direct somatic versus germline differentiation [ATAC-Seq]

city: Edinburgh

first: Elisa

last: Barbieri

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The choice between somatic and germline fates is essential for species survival. This choice occurs in embryonic epiblast cells, as these cells are competent for both somatic and germline differentiation. Transcription factors (TFs) play a central role in this process by binding to specific chromatin loci to modulate gene expression and determine cell identity. The TF OTX2 regulates the choice between somatic and germline fates, as Otx2-null epiblast-like cells (EpiLCs) form primordial germ cell-like cells (PGCLCs) with enhanced efficiency.  However, the mechanisms by which OTX2 achieves this function are not fully characterized. Here we show that OTX2 controls chromatin accessibility to enable somatic differentiation. By performing CUT&RUN for OTX2 and ATAC-seq in wild-type and Otx2-null embryonic stem cells and EpiLCs, we identified regions where OTX2 binding opens chromatin. Enforced OTX2 expression maintains accessibility at these regions and induces opening of 4,000 additional somatic-associated regions in the presence of PGC-inducing cytokines. Once cells have acquired germline identity, the 4,000 additional somatic associated regions do not respond to OTX2 and remain closed. Our results indicate that OTX2 works in cells with dual competence for both somatic and germline differentiation to increase accessibility of somatic regulatory regions and induce the somatic fate at the expense of the germline.

overall_design: Chromatin accessiblity profiling by ATAC-seq of WT and OTX2-/- ESCs, EpiLCs, PGCLC or somatic cell aggregates. Chromatin profiling of OTX2-/- EpiLCs and aggregates after enforced expression of OTX2 using a tamoxifen-induced system.

first: Ian

last: Chambers


title: OTX2 controls  chromatin accessibility to direct somatic versus germline differentiation [CUT&Run]


title: RNA splicing patterns contribute to burst size variation among HIV-1 infected Jurkat cell clones

first: Alice

last: Telesnitsky

address: 1150 W. Medical Center Drive, 6714 MSII

department: Microbiology & Immunology

summary: Jurkat T cells were infected with barcoded HIV-1, and the resulting polyclonal pool was analyzed to identify factors contributing to burst size variation among HIV-1 infected cell clones.

overall_design: Amplicon-seq of barcoded HIV-1 present in cellular chromosomal DNA, cellular total and affinity capture RNA, and extracellular viral RNA.

first: Kamya

last: Gopal

first: Cleo

last: Burnett

first: Ann

last: Emery

first: Edmond

last: Atindaana

first: Ronald

last: Swanstrom

first: Jeffrey

last: Kidd


title: Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies [scCAR-seq]

city: Nanjing

first: Yuxin

last: Wang

address: 163 Xianlin Road

institute: Nanjing University

summary: Chimeric antigen receptor-engineered macrophages (CAR-Ms) hold great promise for solid tumor immunotherapy. The intracellular domains ICDs of CARs determine the phenotypic output of therapeutic macrophages but remain largely unexplored. Here, we constructed a library of CARs containing 131 unique signaling domains derived from native immune receptors and revealed 17 ICDs that enhanced macrophage phagocytosis, the inflammatory response and tumor infiltration in vitro and in vivo. We further developed a scalable 3’ barcode technology, CARode, to uniquely label and trace ICD variants in a large-scale combinatorial signaling domain CAR library and applied it to perform single-cell RNA sequencing and single-cell CAR analysis to measure the synergetic effects of ICD combinations in promoting macrophage activation. This platform includes a novel CD40-LY9-FCRL1 chimeric receptor that modulates the tumor microenvironment and improves solid tumor clearance. In conclusion, pooled screening facilitates the discovery of complex ICD constructs to program macrophage functions for therapeutic applications.

overall_design: The CoSDC lentiviral library was generated and transduced to THP-1 cells at a MOI of 0.3 to minimize multiple integrations per cell. The EGFP+ cells were sorted, PMA-induced and cocultured with high PSMA-expressing tumor cell PC3-PSMA at an E/T ratio of 1/1 for 24 h. Immediately after coculture, EGFP+ CAR-Ms were sorted by FACS and subjected to scRNA-seq.

first: Shiman

last: Zuo


title: A germline mutation in human Oxidation Resistance 1 gene causes developmental delay, epilepsy and cerebellar atrophy

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

summary:
Purpose: The Oxidation Resistance 1 gene (OXR1) confers neuroprotection against oxidative stress. Oxr1 deficiency in mice resulted in cerebellar neurodegeneration. Genetic causes account for the most proportion of neurodegenerative disorders (early) onset in children. However, the pathological consequence of Oxr1 deficiency in human remains unclear. To assess the effect of OXR1 on the whole transcriptome during neuronal differentiation, we conducted RNA-sequencing of iPS cells, neural aggregates and neurons derivated from OXR1 deficient patient fibroblast and compared with healthy control.
Methods: The iPS cells (iPSC) were generated from fibroblast cells of  health control (WT) and OXR1 deficient patient (OX), and induced 2 days to form neural aggregate (NA) following to be differentiated into neuron cells in day 20. Total RNA was pooled from triplicate samples in each group  and performed RNA sequencing on an Illumina HiSeq2500 platform. The sequence reads that passed quality filters were analyzed at gene level. The GOseq program was used to generate gene ontology (GO) annotation of differentially expressed genes (DEGs). The pathway enrichments were identified by KEGG Pathway Enrichment Analysis. qRT–PCR validation was performed using SYBR Green assays.
Results:Totally 1595 DEGs were identified at neuron stage due to Oxr1 disruption, 874 DEGs at iPSC stage and 388 DEGs at NA stage. Among them, there are 61 DEGs commonly regulated by Oxr1 throughout all of the three stages . Further gene oncology (GO) analysis of biological process showed there was a significant enrichment for DEGs related to cell adhesion and extracellular matrix organization (ECM), cell development, cell differentiation, organ development caused by Oxr1 deficiency throughout all developmental stages. Especially neurogenesis and differentiation, axonogensis and guidance, brain and nerves system development  were among the top of 50 items when entering neuron stage. In addition, a set of DEGs was significantly enriched in positive regulation of intrinsic apoptotic signaling pathway and regulation of cellular response to stress.
Conclusions: Oxr1 regulates transcriptional networks required for modulating oxidative stress, apoptosis and neurogenesis during neuronal differentiation of iPS cells.

overall_design: The cells were collected from three stages including iPSC, NA and neuron. The differencial expression profiles were generated by comparsion between health control and OXR1 difficent group in each stage.

first: Xiaolin

last: Lin

first: Wei

first: Nadirah

last: Damseh

first: Agata-Antonina-Rita

last: Impellizzeri

first: Richard

last: Siller

first: Maher

last: Shahrour

first: Barak

last: Yaacov

first: Motee

last: Al-Ashhab

first: Bassam

last: Abu-Libdeh

first: Simon

last: Edvardson

first: Lars

last: Eide

first: Gareth

last: Sullivan

first: Orly

last: Elpeleg

first: Magnar

last: Bjoras


title: Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies [RNA-Seq]

first: Yuxin

overall_design: mRNA profiling of CAR-Ms (LY9 or CD247 signaling domain) from 3 different healthy donors following 24 h of co-culture with PSMA+ or PSMA- K562 cells.


title: Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies

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

overall_design: Refer to individual Series


title: A Novel EBF2 Nonsense Variant Drives Adipose Tissue Fibrosis and Dysfunction in Partial Lipodystrophy Syndrome

city: ANN ARBOR

first: Tae-Hwa

last: Chun

address: 2800 PLYMOUTH RD, NCRC B10-A186, NCRC B10-A186

department: Internal Medicine

summary: Heterozygous Ebf2 p.E165X knock-in (KI) mice exhibited restricted adipogenesis and excess extracellular matrix (ECM) deposition during post-weaning AT expansion and high-fat-diet (HFD)-induced obesity.

overall_design: Bulk RNA-seqeuding of inguinal white adipose tissues (IWAT) isolated from  4-week-old wildtype (Ebf2+/+) and knock-in (Ebf2 p.E165X/+) male mice on regular chow diet.

first: Donatella

last: Gilio

first: Weisheng

last: Wu

first: Maria

last: Foss-Freitas


title: Granulosa cell expression of Fos is critical for regulating ovulatory gene expressions in the mouse ovary

city: Lexington

first: Jacqueline

middle: Nichole

last: Southall

state: KY

address: 800 Rose Street

department: OB/GYN

institute: University of Kentucky

summary: A previous study showed that female Fos null mice fail to ovulate even when given gonadotropins, suggesting that ovarian expression of Fos is critical for successful ovulation. However, the expression of FOS and function of FOS have not been determined in the mouse ovary. FOS, a member of the Fos family (Fos, Fosb, Fosl1, and Fosl2), functions as a transcription factor by forming a heterodimer complex with a member of Jun family (Jun, Junb, and Jund). The present study demonstrated rapid increases in Fos, along with other Fos and Jun family members, after hCG administration in the ovary of immature PMSG-primed mice and after the LH surge of naturally cycling animals. ChIP-seq analysis identified 1965 FOS-binding genes in granulosa cells collected at 3h post-hCG, including Pgr, Ptgs2, Tnfiap6, and Edn2, genes known to be involved in the ovulatory process. When super-ovulation was induced, the number of oocytes released was significantly reduced in Esr2cre/+ - driven granulosa cell-specific Fos knockout (gcFosKO) mice. This reduction was accompanied by lower expression of Pgr, Ptgs2, Ptgs1, and Edn2 in preovulatory follicles of gcFosKO mice compared to those in control litter mates. In addition, gcFosKO mice showed a trend of decreasing average litter size. Together, this study provided a comprehensive characterization of the tightly controlled up-regulation of all Fos and Jun family members in mouse preovulatory follicles after the LH surge or ovulatory hCG administration and revealed FOS’s role in regulating the expression of key ovulatory genes in the mouse ovary.

overall_design: in vivo 3 h post-human chorionic gonadatropin (hCG) injection granulosa cells collected from female mice ChIP-Seq with FOS antibody (Santa Cruz, sc-7202, I1012)

first: Southall

last: Jacqueline

first: Park

last: Shawn

first: Choi

last: Yohan

first: Jeon

last: Hayce

first: Ko

last: Chemyong

first: Jo

last: Misung


title: Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies [scRNA-seq]

last: Wang

overall_design: PSMA-positive prostate tumors were bilaterally inoculated into the subcutaneous flanks of NCG mice. After confirmation of tumor engraftment, human peripheral blood mononuclear cells (PBMCs) were transplanted to reconstitute the immune system. UTD or COMB7 CAR-Ms were injected intratumorally into either the right or left flank. Four days later, the tumors were harvested and the human CD45-positive cells were sorted and subjected to scRNA-seq.

first: Shiman

last: Zuo


title: Macrophage junctional adhesion molecule-like protein (JAML) promotes NLRP3 inflammasome activation in the development of atherosclerosis

city: Jinan

first: huiliang

last: cui

address: 07 Wenhua xi road, Jinan, Shandong

institute: Qilu hospital Shandong University

summary: Inflammation plays a crucial role in the progression of atherosclerosis. Junctional adhesion molecule-like protein (JAML), a type-I transmembrane glycoprotein, activates downstream signaling pathways. However, the precise role of macrophage-derived JAML in inflammation and atherosclerosis remains unclear. This study aimed to generate mice with macrophage-specific deletion or overexpression of JAML, with the focus of assessing its impact on macrophage function and elucidating its regulatory mechanism in atherosclerosis. High-throughput data screening was employed to investigate JAML expression in atherosclerosis, and macrophage-specific JAML-knockout and transgenic mice models were utilized to examine the effects of JAML on atherosclerosis. Furthermore, the role of JAML was assessed using Oil Red O staining, RNA-sequencing analysis, and co-immunoprecipitation techniques. Increased JAML expression was observed in macrophages from both mice and patients with atherosclerosis. Macrophage-specific JAML deletion attenuated atherosclerosis and inflammation, whereas macrophage-specific JAML overexpression exacerbated these conditions. Mechanistically, JAML deletion inhibited lipopolysaccharide (LPS) or ox-LDL-induced inflammation by decreasing nuclear translocation of pyruvate kinase M2 (PKM2) and PKM2/p65 complex formation, which consequently suppressed the nuclear factor kappa B (NF-κB) pathway and NLRP3 inflammasome activation. Taken together, these findings demonstrate that macrophage-expressed JAML facilitates the progression of atherosclerosis by activating the NF-κB pathway and NLRP3 inflammasome through nuclear migration and phosphorylation of PKM2. Notably, our study revealed a novel mechanism for the regulation of NLRP3 inflammasome activation in atherosclerosis. Therefore, targeting JAML may be an effective treatment strategy for atherosclerosis, a condition characterized by chronic inflammation.

overall_design: Examination of the transcriptomic profiles of macrophages isolated from JAML-WT or JAMLM-KO mice after LPS (8 h, 100 ng/ml) and ATP (30 min, 5 mM) stimulation.

first: Jianmin

last: Yang

first: Wencheng

last: Zhang

first: Huiliang

last: Cui

first: Cheng

last: Cheng

first: Fei

last: Xue

first: Lin

last: Xie

first: Zhenguo


first: Tae-Hwa

last: Chun

summary: In vitro disease modeling of an erly B cell factor 2 (EBF2) nonsense variant (EBF2 8:26033143 C>A, c.493G>T, p.E165X) demonstrates that the EBF2 variant impairs adipogenesis causing excess accumulation of extracelluar matrix protein and inflammatory myeloid cells.

overall_design: Human subcutaneous pre-adipocytes were transfected with lentivirus constructs encoding full length EBF2 (575 aa),  truncated EBF2 variant (aa. 1-164), or empty lentivirus expressing GFP. Bulk RNA-sequencing was performed for those cells after adipogenesis induction along with coontrol cells without lentivirus trasnduction (control_no-lentivirus).

first: Maria

last: Foss-Freitas

first: Weisheng

last: Wu

first: Donatella

last: Gilio


title: scATAC-seq of OT-1 CD8+ T cells from different time-course of Lm-OVA infected mice

city: Guangzhou

first: Zhonghui

last: Tang

address: No. 74 Zhongshan Second Road, Guangzhou

summary: scATAC-seq from OT-1 CD8+ T cells after Lm-OVA infection at day 0 (Naïve), day 2 (D2),  and day 8 (D8) post infection

overall_design: CD45.1+ OT-1 cells were sorted from mice infected with Lm-OVA 0, 2, and 8 post infection. scATAC-seq libraries were prepared using 10x Genomics kits.

first: Qiao

last: Liu

first: Wei

last: Dong


title: Cardiac resident macrophage-derived legumain improves cardiac repair via promoting clearance and degradation of apoptotic cardiomyocytes after myocardial infarction

city: Shanghai

first: Si

middle: qin

last: Chen

address: No. 180 of Road Fenglin, District Xuhui.

institute: Fudan university

summary: During the acute inflammatory phase of MI, the amount of necrotic and apoptotic cardiomyocytes is a critical determinant of the severity of adverse remodeling that leads HF. The inefficient clearance of dying cardiomyocytes is important to suboptimal tissue remodeling after MI. Macrophages are the main immune cells after MI, playing important roles in clearance of necrotic and apoptotic cardiomyocytes. LGMN is specifically required for the clearance and degradation of dying adult cardiomyocytes. LGMN deficiency impact the ability of macrophages to clearing apoptotic cardiomyocytes after MI. We used RNA sequencing to examine the gene expression profiles of the macrophages sorted from the hearts of LGMN-KO and WT mice after MI, especially genes associated with phagocytic function.

overall_design: MRNA profiles of  cardiac macrophages of  Lgmn-KO and WT mice after MI

first: Daile

last: Jia

first: Siqin

first: Aijun

last: Sun

first: Junbo

last: Ge


title: CX3CR1-Fractalkine Dysregulation Affects Retinal GFAP Expression, Inflammatory Gene Induction, and LPS Response in a Mouse Model of Hypoxic Retinopathy

city: San Antonio

first: Astrid

last: Cardona

address: One UTSA Circle

department: Molecular Microbiology and Immunology

institute: University of Texas at San Antonio

summary: Diabetic retinopathy (DR) causes vision loss due to sustained inflammation and vascular dam-age. The vascular damage is characterized fibrinogen leakage, angiogenesis, and hypoxia exac-erbating retinal damage. Neuronal regulation of microglia via the CX3CL1 (FKN)-CX3CR1 pathway also play a significant role in retinal pathology; here defects in the FKN-CX3CR1 pathway exacerbate inflammation, vascular damage and vision impairment. However, the con-tribution of hypoxic astrocytes to the pathological process of DR is unclear.

overall_design: We tested how microglia dysregulation affected the retinal transcriptome under conditions of short duration (7-days) hypoxia-induced retinopathy. Age matched wild type (WT) and CX3CR1 knockout (CX3CR1-KO, CX3KO) mouse were housed under control  (22.1% oxygen) or hypoxic (7.5% oxygen) conditions.


title: Rapamycin limits CD4+ T cell proliferation in simian immunodeficiency virus-infected rhesus macaques on antiretroviral therapy

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: We report on the impact of rapamycin on the transcriptome profile (RNA-seq) of simian immunodeficency virus-infected rhesus macaques on antiretroviral therapy

overall_design: We analyzed 42 samples in 14 animals at 3 timepoints, with 21 rapamycin treated animals and 21 control animals

first: Benjamin

last: Varco-Merth

first: William

last: Brantley

first: Alejandra

last: Marenco

first: Derick

middle: D

last: Duell

first: Devin

middle: N

last: Fachko

first: Brian

last: Richardson

first: Kathleen

last: Busman-Sahay

first: Danica

last: Shao

first: Walter

last: Flores

last: Engelman

first: Yoshinori

last: Fukazawa

first: Scott

last: Wong

first: Rebecca

last: Skalsky

first: Jeremy

last: Smedley

first: Michael

last: Axthelm

first: Jeffrey

last: Lifson

first: Jacob

last: Estes

first: Paul

middle: T

last: Edlefsen

first: Louis

last: Picker

first: Cheryl

last: Ainslie Cameron

first: Timothy

last: Henrich

first: Afam

last: Okoye


title: Chromatin landscape alteration uncovers multiple transcriptional circuits during memory CD8+ T cell differentiation

first: Zhonghui

last: Tang


title: Gene expression profile at single cell level of total mammary primary cells from 6-8 weeks old female mice

city: Wuhan

first: Weizhen

last: Chen

state: Hubei

address: 115#, Donghu road

department: Medical Research Institute

institute: Wuhan University

summary: Using the Gpm6a knockout mouse model, we found that Gpm6a deficiency leads to the abnormal mammary duct development, and insufficient postpartum milk production. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of total mammary gland primary cells from WT or Gpm6a knockout mice.

overall_design: Total mammary primary cells of the WT and Gpm6aKO mice were isolated by Fluorescence-activated cell sorting (FACS) according to DAPI- cells and analyzed using scRNAseq.

first: Cheguo

last: Cai

first: Gaosong

last: Wu


title: RNA sequencing to identify UNC-49-regulated genes in C. elegans defense against pathogen P. aeruginosa infection

city: Changsha

first: Xibin

last: Tian

address: Tianma Road

institute: Hunan University

summary:
Purpose: To gain molecular insights on how UNC-49 regulates C. elegans innate immunity, we used RNA sequencing to profile gene expression in unc-49(e407) animals relative to wild-type animals with or without P. aeruginosa (PA14) infection.
Methods: Synchronized L1 worms were placed onto NGM plates seeded with E. coli OP50 and grown at 20 °C until the L4 stage. Worms were washed off the plates, collected with M9 solution and subsequently transferred to modified NGM plates containing E. coli OP50 or P. aeruginosa PA14 for 24 h at 25 °C. Then, the animals were washed off the plates with M9 solution and frozen in TRIzol (Transgen, ER501-01, China) with liquid nitrogen. Total RNA was isolated using a TransZol Up Plus RNA kit (Transgen, ER501-01, China).
Results: RNA seq analyses shows enriched and signficant changed immune genes and pathways that are dependent of  GABAergic neuromuscular junctions.
Conclusion: Our studies uncover that lack of UNC-49-mediated suppression in unc-49(e407) animals contributes to their improved survival against P. aeruginosa infection.

overall_design: Three replicates of four groups of RNA samples (unc-49(e407) and wild-type L4-stage animals with or without exposure to P. aeruginosa for 24 hrs) were sequenced. Gene expression was compared between groups to identify UNC-49-regulated genes under fed on OP50 or exposed to PA14.

first: Haijun

last: Tu


title: scATAC-seq of antigen-specific CD8+ T cells from different time-course of LCMV-Armstrong infected mice

summary: scATAC-seq from LCMV-specific P14 CD8+ T cells after LCMV-Armstrong at day 0 (Naïve), day 2 (D2), day 8 (D8-1 and D8-2), and day 180 (D180) post infection

overall_design: LCMV-specific P14 cells were sorted from mice infected with LCMV-Armstrong days 0, 2, 8 and 180 post infection. scATAC-seq libraries were prepared using 10x Genomics kits.

first: Qiao

last: Liu

first: Wei

last: Dong


title: ChIA-PET from naïve and in vitro-induced antigen-specific effector and memory CD8+ T cells

summary: The scATAC-seq approach identifies cell type-specific cis- and trans-regulatory elements in a genome-wide manner. However, which genes targeted by the identified cis-regulatory elements (CREs) remain unresolved, regarding CREs usually putatively assigned to their nearest genes in bioinformatic analysis. Additionally, it is important to characterize CREs that play essential roles in gene regulation from non-functional “parking spots”. To this end, we applied ChIA-PET approach to mapping RNAPII-mediated enhancer-promoter chromatin interactions between enhancers and their target genes genome-wide.

overall_design: We performed ChIA-PET on antigen specific naïve CD8+ T cells and in vitro-induced antigen specific effector and memory CD8+ T cells.

first: Rong


title: Poxvirus attack of anti-viral defense pathways unleashes an effector-triggered NF-κB response

status: Public on Feb 16 2025

city: Berkeley

first: Brenna

last: Remick

address: 415 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Effector-triggered immunity (ETI) is a form of pathogen sensing that involves detection of pathogen-encoded virulence factors or “effectors”. To discover novel ETI pathways in mammals, we developed a screening approach in which individual virulence factors are expressed in human monocytes and transcriptional responses are assessed by RNA-seq. Using this approach, we identify a poxvirus effector, myxoma virus M3.1, which elicits an anti-viral NF-κB response. We find that NF-κB is unleashed by an ETI pathway that senses M3.1 attack of two anti-viral complexes: ZAP and TBK1. NF-κΒ activation occurs because the proteins inhibited by M3.1—N4BP1, ZC3H12A, and TBK1—are negative regulators of NF-κB. Our results illustrate how negative regulators can function as pathogen sensors and establish a systematic approach for the discovery of ETI pathways.

overall_design: RNA-seq of MYD88–/–TRIF–/– BLaER1 monocytes expressing doxycycline-inducible myxoma virus M003.1 or mCherry, treated with doxycycline for 24 hours

first: Russell

last: Vance


title: Small molecule RNA therapeutics to target prostate cancer [RNA-seq]

first: Duygu

last: Kuzuoglu Ozturk

address: 1450 3rd Street, Helen Diller Cancer Building

summary: Tuning protein expression by targeting RNA structure using small molecules is an unexplored avenue for cancer treatment. To understand whether this vulnerability could be therapeutically targeted in the most lethal form of prostate cancer, castrate-resistant prostate cancer (CRPC), we used a clinical small molecule, zotatifin, that targets the RNA helicase and translation factor eIF4A. Zotatifin repressed tumorigenesis in patient-derived and xenograft models and prolonged survival in vivo alongside hormone therapy. Genome-wide transcriptome, translatome, and proteomic analysis revealed two important translational targets: Androgen Receptor (AR), a key oncogene in CRPC, and hypoxia-inducible factor 1A (HIF1A), an essential cancer modulator in hypoxia. We solved the structure of the 5’UTRs of these oncogenic mRNAs and strikingly observed complex structural remodeling of these select mRNAs by this small molecule. Remarkably, tumors treated with zotatifin become more sensitive to radiotherapy, usually blunted by HIF1A. Therefore, ‘translatome therapy’ opens new avenues to treat the deadliest cancers.

overall_design: Transcriptional landscape of 22Rv1 cells under normoxia and hypoxia conditions, treated with eIF4A inhibitor zotatifin was investigated by RNAseq

last: Kuzuoglu-Ozturk

first: Vishvak

last: Subramanyam

first: Davide

last: Ruggero

first: Isabelle


title: Poxvirus attack of anti-viral defense pathways unleashes an effector-triggered NF-κB response [RNAseq_2]

overall_design: RNA-seq of BLaER1 monocytes deficient for N4BP1, ZC3H12A, TRIM25, or ZC3H12A/N4BP1 treated with doxycycline for 24 hours to induce expression of doxycycline-inducible myxoma virus M003.1 or mCherry.


title: Small molecule RNA therapeutics to target prostate cancer [Ribo-seq]

overall_design: Translational landscape of 22Rv1 cell xenografts upon eIF4A inhibitor zotatifin were analyzed by performing Riboseq. Three independent replicates are used for each sample.


title: RNA sequencing analysis of JAG1 overexpressed Ink4a-/- murine astrocytes

city: Seoul

first: Nayoung

last: Hong

address: Anam-ro 145

country: South Korea

institute: Korea University

summary: Notch signaling is a signaling pathway related to development and homeostasis of tissue. Jagged 1 (JAG1), which is one of the ligand of NOTCH, is highly expressed in tumor and induce proliferation, survival and tumor aggressiveness of cancer cells. This study demonstrate the biological function of JAG1 in tumor progression. To elucidate the role of JAG1, JAG1 was overexpressed in murine Ink4a-/- astrocytes. Our results provide the clue of molecular mechanism in tumor aggressiveness.

overall_design: Ink4a-/- murine astrocytes were transfected with pcDNA3.1-puro (Con) or pcDNA3.1-JAG1-puro (JAG1).

first: Seok

last: Ham

first: Jung

middle: Y

last: Kim

first: Hyunggee


title: Small molecule RNA therapeutics to target prostate cancer [DMS MaP-seq]

overall_design: DMS MaP-Seq analysis of endogenous AR, HIF1A, DNAJA1, APEX1 and RPS5 5'UTRs were analyzed under different conditions (Control, Zotatifin or Enzalutamide treatment) in 22Rv1 prostate cancer cells. For each condition, two independent replicates were used.


title: Effect of DIS3 knockdown on circRNA expression

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: To investigate the effect of DIS3 KD on circRNA expression in 293T cell line

overall_design: Ribosomal RNA depleted (ribo-) RNA-seq for 9 samples (3 biological replicates sets of 293T cells treated with scramble shRNA, DIS3-sh1 shRNA or DIS3-sh2 shRNA)

first: Ling-Ling

first: Xiao

last: Tao

first: Si-Nan

last: Zhai

first: Jia

last: Wei

first: Yi-Lin

last: Guo

first: Chu-Xiao


title: Locolization of circRNA with DIS3 WT or D146N mutant in sucrose density gradient centrifugation assay

summary: To investigate the locolization between DIS3 and circRNA in fractions form sucrose density gradient centrifugation (SDGC) assay for 293T cells

overall_design: Ribosomal RNA depleted (ribo-) RNA-seq for 12 samples (3 biological replicates sets of fractions 3,4,7 and 8 in SDGC assay for DIS3 KD+DIS3-WT 293T cells ) and 12 samples  (3 biological replicates sets of fractions 3,4,7 and 8 in SDGC assay for DIS3 KD+DIS3-D146N 293T cells )

last: Chen


title: EPAS1 induction drives myocardial degeneration in Desmoplakin-cardiomyopathy [TOMO-seq]

status: Public on Feb 15 2025

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

summary: Arrhythmogenic cardiomyopathy (ACM) is frequently attributed to desmosomal mutations, such as those in the desmoplakin (DSP) gene. Patients with DSP- cardiomyopathy are predisposed to myocardial degeneration and arrhythmias. Despite advancements, the underlying molecular mechanisms remain incompletely understood, thus limiting therapeutic options. Here, we employed spatial transcriptomics on an explanted heart from a patient with a pathogenic DSP variant. Our transcriptional analysis revealed endothelial PAS domain-containing protein 1 (EPAS1) as a potential regulator of mitochondrial homeostasis in stressed cardiomyocytes. Elevated EPAS1 levels were associated with mitochondrial dysfunction and hypoxic stress in both human-relevant in vitro ACM models and additional explanted hearts with genetic cardiomyopathy. Collectively, cardiomyocytes bearing pathogenic DSP variants exhibit mitochondrial dysfunction, increased apoptosis, and impaired contractility, which are linked to the increased EPAS1 levels. These findings implicate EPAS1 as a key regulator of myocardial degeneration in DSP-cardiomyopathy, which expand to other forms of ACM.

overall_design:
Spatial transcriptomics by RNA-tomography (TomoSeq) on 20um sections on diseased heart. After isolation, we cryosectioned samples, extracted RNA from the individual sections, and amplified and barcoded mRNA using the CEL-seq protocol as in (Junker 2014, PMID: 25417113). Libraries were sequenced on Illumina NextSeq 500 using 75p paired end sequencing.

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

last: Kyriakopoulou

first: Eva

last: van Rooij


title: Single-cell profiling of the nucleus pulposus (NP) supports the Shh+ cells as NP stem cells

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

summary: The physiological function of the intervertebral disc (IVD) depends on the cellular and molecular composition of the nucleus pulposus (NP), which plays a key role in managing the mechanical loading of the IVD.We conducted single-cell RNA sequencing (scRNA-seq) analysis to better characterize the NP cells, particularly the Shh-tdTom+ NP cells, in the adult Shh-CreER; Rosa26tdTomato mice.

overall_design: After five consecutive Tamoxifen injections to the 1-month-old Shh-CreER; Rosa26tdTomato mice, lumbar and coccygeal IVDs were harvested 2 weeks later. CD45+ immune cells were removed by Fluorescence-Activated Cell Sorting (FACS) to focus on the non-immune cells in the IVD. The digested IVD cells were then subjected to 10X Genomics scRNA-seq.

first: Guoyan

last: Liang

first: Yu

last: Jin

first: Qian

last: Cong

first: Yizhong

last: Hu

first: Tao

last: Yu

first: Yingzi


title: Effects of peptidomimetic PD00 on OVA-induced immune cells and their metabolic pathways in mouse lung tissue by single-cell transcriptome sequencing

first: Shumei

last: Ma

address: No. 1111, Zhongshan North 1st Road

institute: Shanghai Institute of Pharmaceutical Industry Co., Ltd.

summary: OVA-induced allergic asthma in mice shares many similar features with human asthma. The peptidomimetic PD00 can significantly improve OVA-induced asthma symptoms in mice. However, the molecular mechanism by which it works is still unclear. The metabolic status of immune cells affects their functional status, so single-cell transcriptome sequencing was used to explore the effect of PD00 on immune cell subsets and their metabolic pathways in OVA-treated mouse lung tissue.

overall_design: Three samples from mouse lung tissue

first: Li


title: A Spatially Resolved Transcriptome Landscape during Thyroid Cancer Progression

last: Zeng

address: Fangsong Street

institute: Shanghai Jiaotong University

summary: Thyroid cancer ranks as the ninth most common cancer type in terms of incidence worldwide. Furthermore, the global incidence of thyroid cancer has been on the rise over the past decades.Spatial transcriptomics technology systematically profiles gene expression across tissue space by combing high-throughput RNA sequencing and imaging techniques. The applications of ST have revealed high-resolution spatial architecture and cellular crosstalk in many tumor types, advancing the discovery of new targets for diagnosis and therapy. However, the spatial architecture in thyroid cancer and the structural differences in the TME among papillary thyroid cancer (PTC), locally advanced thyroid cancer (LPTC), and Anaplastic thyroid carcinoma (ATC) have been little investigated. Herein , we applied ST and scRNA-seq data to reveal the spatial difference of TME in PTC, LPTC, and ATC samples.

overall_design: Specimens collected for single-cell transcriptomics and spatial transcriptomics were from twelves thyroid cancer patients undergoing surgery at Fudan University Shanghai Cancer Center. All the patients signed informed consent before sample collection. In total, 4 para-tumors (N), 4 early thyroid cancer (PTC), 4 locally advanced thyroid cancer (LPTC), and 4 anaplastic thyroid cancer (ATC) were used for spatial transcriptomics. Three out of 4 N, 3 out of 4 PTC, and 3 out of 4 LPTC samples were collected for single-cell transcriptomics. Two experienced pathologists confirmed the pathology of each sample.

first: Shengli

last: Li

first: Tian

last: Liao


title: Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming

city: Leuven

first: Anyi

last: Zhang

address: Naamsestraat 61/bus 4049

country: Belgium

institute: KU Leuven

summary: Unlike mammals, zebrafish can regrow axons after injury and restore circuit function in the central nervous system (CNS). Mitochondria have been identified as key players in this process, but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells (RGCs) after optic nerve crush injury, we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously, the thioredoxin antioxidant system is upregulated, likely to limit oxidative damage. Additionally, we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases, possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved, as it also occurs in the pro-regenerative mammalian Pten and Socs3 co-deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth, suggesting that targeting these pathways could enhance CNS regeneration in mammals.

overall_design: Bulk RNA sequencing of FAC-sorted adult Tg(isl2b:eGFP)zc7Tg zebrafish retinal ganglion cells under the uninjured (naive) condition and at 1, 3, 6, 10, and 14 days post-optic nerve crush injury.

first: Steven

last: Bergmans

first: Annelies

last: Van Dyck

first: An

last: Beckers

first: Lieve

last: Moons

first: Luca

last: Masin


title: A Novel Rescue Strategy for Bone Marrow Hematopoietic Failure via Microenvironment Reconstruction with Reduced HSC Dependency

status: Public on Feb 14 2025

city: chongqing

first: Debao

address: No. 13, Tianchi Avenue, Mudong Town, Banan District, Chongqing

institute: Chongqing International Institute for Immunology

summary: Hematopoietic stem cell transplantation (HSCT) represents the most effective therapeutic approach for hematopoietic malignancies, bone marrow (BM) failure syndromes, and primary immunodeficiency diseases. However, the clinical demand for HSCT is constrained by current limitations in HSC sources and expansion technologies. The BM niche is crucial providing a supportive microenvironment for the self-renewal and differentiation of HSCs, and its rejuvenation is essential for rapid and effective hematopoietic recovery. In this study, we demonstrate that costal-cartilage-derived stem cells (CDSCs) can achieve hematopoietic reconstruction comparable to HSCT, even with a significantly reduced number of hematopoietic stem and progenitor cells (HSPCs), while exhibiting low chimerism. We further show that transplanted CDSCs differentiate into various cell types, including bone marrow stromal cells (BMSCs), endothelial cells, and osteoblasts, and secrete pro-hematopoietic factors that restore the damaged BM niche. Moreover, in vitro-expanded CDSCs exhibit elevated expression of BMSC markers and enhance hematopoietic recovery in injury models. Notably, the combination of CDSCs with cyclosporine A is effective in treating aplastic anemia in mouse models. Collectively, these findings propose a novel strategy for treating BM hematopoietic failure through microenvironmental restoration and broaden the potential therapeutic scope of HSCT.

overall_design: The primary and cultured CDSCs at passaged P2-P3 underwent single cell RNA-seq (scRNA-seq) (MobiDrop, China).

first: Rui

last: Dong

first: zhiguo

last: Ling


title: Simultaneous single cell CRISPR, RNA, and ATAC-seq enables multiomic CRISPR screens to identify gene regulatory relationships

city: San Francisco

first: Scot

middle: M

last: Federman

address: 499 Illinois St

department: Biochemistry

institute: UCSF

summary: Identifying gene functions and interactions in specific cellular contexts has been greatly enabled with functional genomics studies. CRISPR-based genetic screens have been proven invaluable in elucidating gene function in mammalian cells. Single cell functional genomics methods, such as Perturb-seq and Spear-ATAC, have made it possible to achieve high-throughput mapping of the functional effects of gene perturbations by profiling transcriptomes and DNA accessibility, respectively.  Combining single-cell chromatin accessibility and transcriptomic data via multiomics technologies facilitates the discovery of novel cis-regulatory and gene regulatory interactions, however, bulk readouts complicate this analysis due to a heterogeneous response of cells to the same genetic perturbation/s, which could be mitigated by using transcriptional profiles of single cells to subset the ATAC-seq data. Existing methods to capture CRISPR guide RNAs to simultaneously assess the impact of genetic perturbations on RNA and ATAC profiles either require cloning gRNA libraries in specialized vectors or use complex protocols with multiple rounds of barcoding. Here, we introduce CAT-ATAC, a technique that simply captures CRISPR gRNAs within the 10X Genomics Multiome assay, generating paired transcriptome, chromatin accessibility and perturbation identity data from the same cells. We demonstrate up to 77% guide capture efficiency for both arrayed and pooled lentiviral transductions of sgRNAs in induced pluripotent stem cells (iPSCs) and cancer cell lines. This capability allows us to construct gene regulatory networks (GRNs) in cells under drug and genetic perturbation. We identified a GRN associated for dasatinib resistance, indirectly activated by the HIC2 gene. Using loss of function experiments, we further validated that the gene, ZFPM2, a component of the predicted GRN, also contributes to dasatinib resistance. CAT-ATAC can thus be used to generate high-content multidimensional genotype-phenotype maps to reveal novel gene and cellular interactions and functions.

overall_design: 10x Multiome seq with CRISPR guide capture: Single nuclei were extracted following manufacturers instructions. scRNAseq and scATACseq libraries were prepared following 10x protocol. CRISPR guide libraries were prepared using a custom protocol.

first: Kaivalya

last: Shevade

first: Yeqing

last: Yang

first: Kevin

last: Feng

first: Karl

last: Mader

first: Volkan

last: Sevim

first: Jacob

last: Parsons

first: Gunisha

last: Arora

first: Hasnaa

last: Elfawy

first: Rachel

last: Mace

first: Rustam

last: Esanov

first: Shawn

last: Shafer

first: Eric

last: Chow

first: Laralynne

last: Przybyla


title: fmo-4 promotes longevity and stress resistance via ER to mitochondria calcium regulation in C. elegans

city: Ann Arbor

first: Angela

last: Tuckowski

address: 109 Zina Pitcher Place

department: Molecular and Integrative Physiology

institute: University of Michigan

summary: Flavin-containing monooxygenases (FMOs) are a conserved family of xenobiotic enzymes upregulated in multiple longevity interventions, including nematode and mouse models. Previous work supports that C. elegans fmo-2 promotes longevity, stress resistance, and healthspan by rewiring endogenous metabolism. However, there are five C. elegans FMOs and five mammalian FMOs, and it is not known whether promoting longevity and health benefits is a conserved role of this gene family. Here, we report that expression of C. elegans fmo-4 promotes lifespan extension and paraquat stress resistance downstream of both dietary restriction and inhibition of mTOR. We find that overexpression of fmo-4 in just the hypodermis is sufficient for these benefits, and that this expression significantly modifies the transcriptome. By analyzing changes in gene expression, we find that genes related to calcium signaling are significantly altered downstream of fmo-4 expression. Highlighting the importance of calcium homeostasis in this pathway, fmo-4 overexpressing animals are sensitive to thapsigargin, an ER stressor that inhibits calcium flux from the cytosol to the ER lumen. This calcium/fmo-4 interaction is solidified by data showing that modulating intracellular calcium with either small molecules or genetics can change expression of fmo-4 and/or interact with fmo-4 to affect lifespan and stress resistance. Further analysis supports a pathway where fmo-4 modulates calcium homeostasis downstream of activating transcription factor-6 (atf-6), whose knockdown induces and requires fmo-4 expression. Together, our data identify fmo-4 as a longevity- promoting gene whose actions interact with known longevity pathways and calcium homeostasis.

overall_design: RNA-seq profiling of WT and fmo-4 overexpression C. elegans worms collected at day 1 of adulthood grown on OP50 bacteria on NGM plates.

first: Safa

last: Beydoun

first: Elizabeth

middle: S

last: Kitto

first: Ajay

last: Bhat

first: Marshall

middle: B

last: Howington

first: Aditya

last: Sridhar

first: Mira

last: Bhandari

first: Kelly

last: Chambers

first: Scott

middle: F

last: Leiser


title: Gene expression-based, comparison of mouse tumors co-injected macrophages with different PIM kinase phenotypes

city: Tucson

first: Amber

last: Clements

address: 1515 N Campbell Ave

institute: University of Arizona

summary: Changes in gene expression were used to compare immune infiltration in tumors co-injected with PIM modified macrophages

overall_design: Wild-type (WT), PIM1 KO, and triple knockout (TKO; knockout of PIM1/2/3) MEFs were injected with MyC-CaP cells. After tumor growth for 2 wks, tumors were harvested and RNA was extracted from FFPE tissue

first: Noel

middle: A

last: Warfel


title: Characteristics of microRNA expression in osteoblasts exposed to high dose rate of alpha particle radiation

city: Hirosaki

first: Satoru

last: Monzen

state: Aomori

address: Hon-cho 66-1

institute: Hirosaki University

summary: Osteoblast is one of the bone marrow cells and not only play a central role in bone turnover, but also play a role as supporting cell for hematopoietic stem/progenitor cells. In the field of radiotherapy, internal radiotherapy using radioactive isotopes that emit alpha particles is performed, and antitumor effect is expected by radioisotopes (such as 223-Ra) when the primary cancer cells metastasize to bone marrow. In general, higher dose rates of ionising radiation can induce cell death through DNA damage. However, the extent of DNA damage and repair (radiosensitivity) varies between tissue cell types. In the bone marrow environment, there are many unknowns regarding the radiosensitivity and the its related gene expression in osteoblast, especially the expression status of micro RNAs (miRNAs). The purpose of this study is to reveal the expression pattern of miRNAs in osteoblasts exposed to alpha particle radiation and to identify miRNAs associated with radiosensitivity. Osteoblastic cell line, MC3T3-E1 cell was exposed to 0.223 Gy/min alpha particles (total dose: 0.5 Gy and 1 Gy) and extracted total RNAs after the incubation of 24 h. A significantly up- or down-regulated 21 miRNAs were observed in comparison to non-irradiated control. Using omicsnet data analysis system, we focused on 5 miRNAs (miR-467f, miR-362-3p, miR-5119, miR-292a-5p, miR-466h-3p) and validated them using RT-qPCR. As a result, A higher expression of miR-362-3p after exposure of alpha particle irradiation was reproducibly observed. These results suggested that osteoblastic cell irradiated to alpha particle radiation has a unique miRNA expression pattern.

overall_design: The pattern of micro RNA expressions in MC3T3-E1 cell exposed to 0.5 Gy or 1 Gy alpha particles (0.22 Gy/min) was analyzed using micro RNA microarray. The data analysis had been performed duplicate samples.

first: Takamasa

last: Yamanaka

first: Andrzej

last: Wojcik


title: Functional reprogramming of neutrophils within tumors by hypoxia-driven histone lactylation [scRNA-seq]

city: Tampa

first: Xiaoxian

last: Liu

state: FL

address: 13131 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: We used scRNAseq to study the mechanism underlying the functional reprogramming in brain tumors. scRNA-seq of FACS-sorted neutrophils was performed on mice with brain tumors (SB28). We showd that the immunosuppressive ability of brain-tumor infiltrating neutrophils was exclusively mediated by a population of highly glycolytic neutrophils expressing the transferrin receptor CD71.

overall_design: We FACS-sorted neutrophils (CD45+ CD11b+ LY6Ghigh LY6Clo/-) from blood and tumors of mice with brain tumors (SB28) at late stage (day 18) and processed them for sc-RNAseq using the 10x Genomics Chromium platform.

first: Xiaoqing

last: Yu

first: Alessio

last: Ugolini

first: Filippo

last: Veglia


title: Genetic Variability and Sex Affect the Response of Skeletal Muscle to Extended Immobilization

city: Richmond

first: Jessica

middle: Rose

last: Williamson

address: 70 S Madison St

department: Biomedical Engineering

institute: Virginia Commonwealth University

summary: Extended periods of mechanical disuse can cause changes to the musculoskeletal system, particularly impacting the composition and strength of the affected muscle. Genetics are known to play a role in the proportion of lean mass and risk for sarcopenia with age, though the role of genetic variability in muscle adaptation to disuse is largely unknown. A total of 77 DO mice were casted using the single limb immobilization for three weeks, then hindlimb muscle morphology and performance were quantified. Total RNAseq was performed on gastrocnemius muscles, then Ingenuity Pathway Analysis was used to analyze sequencing data. We found that casting decreased body mass and hindlimb muscle mass (p<0.0001). Analyzing skeletal muscle morphology, we found an increase in cross-sectional area and volume in males but not females (p<0.0001). Additionally, we found immobilized limbs had greater twitch torque, but there was no effect on tetanus torque (p<0.0001). RNA sequencing identified 47 total significant differentially expressed genes. Finally, pathway analysis revealed a sex-dependent response to immobilization. Taken together, these results indicate that single limb immobilization incudes physiological changes to skeletal muscle and changes gene expression in a sex-dependent manner. Ultimately, this work will allow researchers to develop treatments to combat disuse-induced muscle loss.

overall_design: 16 week old Diversity Outbred (DO) mice were casted via single limb immobilization for a period of 3 weeks. RNA was isolated from gastrocnemius muscles and sequenced.

first: Michael

last: Friedman

first: John

middle: L

last: McKean

first: Henry

last: Donahue

first: Priscilla

last: Hwang


title: Characterization of the genes that were regulated by feeding Lactiplantibacillus sp. MH-1

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

summary: In the present study, we investigated the effects of feeding Lactiplantibacillus sp. MH-1 using Caenorhabditis elegans as a model animal. The healthspan of the adult C. elegans fed MH-1 was significantly longer than that of unfed animals (control).

overall_design: Transcriptional profiling of four-day-old worms that were fed Lactiplantibacillus sp. MH-1  or E. coli OP50 (control) for one day, by deep sequencing, using Illumina NextSeq2000.


title: CosMx 6175 human gene for human kidney delayed graft function (DGF) and immediate graft function (IGF)

city: Sacramento

first: Yongheng

last: Wang

address: 3101 Clinical Lab Building (Research II), UC Davis Medical Center, 4625 2nd Ave.

institute: University of California Davis

summary: This dataset includes CosMx spatial transcriptomic data from human kidney biopsies collected one hour post-transplantation. Patients were then monitored and categorized into two groups: those with immediate graft function (IGF) and those with delayed graft function (DGF). DGF refers to cases where patients required dialysis for one or more weeks before kidney function was restored. The biopsies were formalin-fixed, paraffin-embedded, and sectioned using a microtome. Sample processing followed NanoString's standard protocol, utilizing a pre-made 6175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

overall_design: This study contains human kidney biopsies form 2 groups: immediate graft function (IGF) and those with delayed graft function (DGF).

first: Siyu

last: Lin

first: Weidi

last: Zhang

first: Kuang-Yu

last: Jen

first: Peter

last: Than

first: Aijun


title: Functional reprogramming of neutrophils within tumors by hypoxia-driven histone lactylation [RNA-seq]

summary: We used bulk RNAseq to study the mechanism underlying the functional reprogramming in brain tumors.

overall_design: FACS-sorted neutrophils from in vitro cultures and mouse brain tumors


title: ATF4 mediates cold-induced adipose tissue browning by regulating MTHFD2 expression

city: 천안시

first: Rehna

middle: Paula

last: Ginting

state: 충청남도

address: 25 Bongjeong-ro, Dongnam-gu

department: Integrated Biomedical Science

institute: Soonchunhyang University

summary: In mammals, adaptation to cold environments involves browning of inguinal white adipose tissue (iWAT) to enhance adaptive thermogenesis and maintain body temperature. Immune cells that reside in the adipose tissue are involved in iWAT browning. However, the mechanism by which thermogenesis regulates immune cell composition remains elusive. Here, we revealed that cold-induced activating transcription factor 4 (ATF4) is necessary for maintaining the immune cell composition and supporting iWAT browning. ATF4 and integrated stress response-related genes were highly expressed in iWAT following acute cold exposure. Mice lacking ATF4 exhibited less cold-induced iWAT browning and lower CL316,243-induced oxygen consumption. Mechanistically, the depletion of ATF4 leads to the accumulation of mitochondrial oxidative stress due to the reduction of MTHFD2, a mitochondrial one-carbon metabolism enzyme that contributes to the maintenance of the mitochondrial redox balance. This leads to higher levels of pro-inflammatory cytokines and shifts in adipose tissue macrophage polarization. Together, our findings highlight the critical role of ATF4 in maintaining oxidative stress and adipose tissue inflammatory signaling, thus supporting iWAT browning.

overall_design:
To investigate the function of ATF4 in adipocyte in response to cold temperature, we generated adipocyte specific knockout of ATF4 (Atf4AKO) by bred Atf4floxed mice (Atf4WT) with AdipoqCre mice. Furthermore, we challenged the mice into cold temperature (5⁰C) for 12 hours and collect their iWAT for further analysis
We then performed gene profiling analysis from iWAT collected from WT (Cre-) and AKO (Cre+) mice

middle: P

first: Hoang-Anh

last: Pham-Bui

first: Siti

last: Fuad

first: Noverya

last: Netanya

first: Jaeseok

last: Han

first: Mihye

last: Lee

first: Min-Woo


title: Gene expression profile at single level of embryonic kidney cells 16 weeks post-transplantation

city: Tokyo

first: Satoshi

last: Hatsuse

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

summary: Embryonic kidney (metanephros) is known to mature after in vivo transplantation. We used scRNA-seq to analyze the maturity of embryonic kidney cells after transplantation.

overall_design: Embryonic kidneys transplanted in 8-week-old syngeneic rat were urinary-reconstructed 3 weeks post-transplantation, collected 16 weeks post-transplantation, and  analyzed using scRNA-seq.


title: Plasma histidine as biomarker for recurrent atrial fibrillation after catheter ablation

city: Beijing

first: Hongxuan

last: Xu

address: No.8 Xishiku Street

department: Cardiology

institute: Peking university first hospital

summary: Atrial fibrillation (AF) is associated with complex and multifaceted etiology including neural modulation that alters atrial electrophysiology. To explore potential biomarkers for AF and AF recurrence. Peripheral histidine levels in PeAF were significantly higher compared to those in the right atrium and coronary sinus. Receiver operating characteristic (ROC) analysis revealed that peripheral histidine was predictive of AF recurrence, with an optimal cutoff value of ≤ 4.71 µg/mL, yielding a sensitivity of 76.3% and a specificity of 76.5%. The area under the ROC curve (AUC) was 0.75 (95% CI, 0.59–0.90). Peripheral His was robustly associated with lower incidence of AF recurrence after covariates adjustment (OR 0.34, 95% CI 0.14- 0.71, p=0.01).

overall_design: To investigate the cardiac effect of histidine, we isolated neonatal rat cardiomyocytes and stimulated these cells with 100nM histidine for 72 h hours with or without 1 μM doxorubicin .

first: Lin

last: Wu


title: Single-cell RNA sequencing reveals the transcriptional landscape and heterogeneity of macrophages in intestinal tissue of WT and CD163+ macrophage-deficient mice.

city: Tianjin

first: Yun Huan

last: Gao

address: 94 Weijin Road, Nankai District, Tianjin

institute: Nankai University

summary: CD163 macrophages, which markedly accumulated in inflammation and tumor tissues possessed markedly immunosuppressive functions on immune cells, especially effective cells such as CD8 cells. However, the mechanism of CD163 macrophages in regulating immune responses remains to be illusive. Using single cell-sequence techniques, we identified CD163 macrophage subset in the colon tissues. Meanwhile, we also characterized CD163 macrophage associated immune cell populations and subpopulations in mouse colon tissues. We found that CD163+ macrophage subset in the colon was related to gut microbiota. Deletion of CD163+ macrophage subset could markedly increase the proportions of the immune cell subsets such as CD8 and NK cells. Mechanistically, gut microbiota mediated CD163+ macrophage subpopulations can down-regulate CD8 and NK cells through inhibitory molecules CD94/NKG2a (Kird1/Kirc1 in mice) and their ligand HLA-E /QA-1 (Human/mice) on the surface of CD163+ macrophages.

overall_design: 10X Genomics scRNA-seq was performed to better assess immune cell heterogeneity in gut lamina propria (LP).

first: yunhuan

last: gao

first: yi

last: shi


title: Sequence composition dictates chromatin assembly, activity, folding and compartmentalization [CRAC-seq]

city: Paris

first: Romain

last: Koszul

address: 25 Rue du Dr Roux

department: Genetics and Genomics

institute: Institut Pasteur

summary: Genomic sequences co-evolve with chromatin-associated proteins to ensure that long DNA molecules are folded in the nucleus in an orderly and functional manner. In eukaryotes, this multiscale folding involves several molecular complexes and structures, ranging from nucleosomes to large cohesin-mediated DNA loops. To explore the causal relationships between the DNA sequence composition and the spontaneous loading and activity of these complexes, we circumvented the boundaries imposed by the evolved, fine-tuning of chromosome regulation by using yeast strains that carry artificial bacterial chromosomes that have diverged from eukaryotic sequences for over 1.5 billion years. By combining this chimeric? synthetic genomics approach with a deep learning-based in silico analysis, we show that sequence composition precisely dictates the whole spectrum of chromatin assembly, transcriptional activity, folding, and compartmentalization in a given cellular context. These results are a first step to understand the molecular events at stake during synthetic chromosome engineering as well as natural horizontal gene transfers.

overall_design: We explored whether PolII-associated RNA were detected along bacterial chromosomes integrated in a eukaryotic environment by performing CRAC-seq analysis of yeast strains containing linearized and telomerized bacterial chromosomes.

first: Jacques

last: Serizay


title: An adult clock component links circadian rhythms to pancreatic β-cell maturation

city: Philadelphia

first: Mai

last: Liu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: The circadian clock attunes metabolism to daily energy cycles, but how it regulates metabolic tissue maturation is not well understood. Here we show that DEC1, a clock transcription factor induced in adult islet β cells, coordinates their glucose responsiveness by synchronizing energetic and secretory rhythms. DEC1 binds maturity-linked genes regulating integration of energy metabolism and insulin exocytosis, and β-cell Dec1 ablation disrupts their transcription synchrony. Dec1-disrupted mice develop lifelong glucose intolerance and insulin deficiency, despite normal islet formation and intact CLOCK/BMAL1 genes. Metabolic dysfunction upon β-cell Dec1 loss stems from poor coupling of insulin secretion to glucose metabolism, reminiscent of fetal/neonatal immaturity. We find that stunted maturation reflects an energetic deficit, marked by reduced glycolysis and compromised mitochondrial dynamics and respiration, which is rescued by increasing metabolic flux. Thus, DEC1 links circadian clockwork to β-cell metabolic maturation, revealing a hierarchy for how the clock programs metabolic tissue specialization.

overall_design: ChIP-sequencing of fixed Beta-TC6 cells


title: Transcriptome analysis of ovaries by subcutaneous injections of olaparib in wild-type and BRCA1+/- rats.

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

summary: BRCA1 pathogenic variant may have the negative impact on ovarian function. Poly (adenosine diphosphate–ribose) polymerase (PARP) inhibitor, olaparib exploit the principle of synthetic lethality to selectively kill the cells that have a deficiency in homologous recombination repair. To evaluate the effect to olaparib on ovaries, we performed the study of subcutaneous olaparib injections for 2 weeks in wild-type and BRCA1+/- rats. We compared the microarray gene expression profiles of rat ovary tissues  from the study.

overall_design: The olaparib protocol in ovaries was started with 8 wildtype and 8 BRCA1+/- female Jcl: SD rats. A total of 16 microarrays (Whole Rat Genome Microarray) were used for screening purpose: 8 microarrays for wildtype SD rats, and 8 for BRCA1+/- SD rats.

first: Reina

last: Sonehara

first: Yashiro

last: Motooka

last: Akatsuka

last: Kaseki


title: Transcriptomic change related to abdominal aortic aneurysm pathogenesis

first: Yaozhong

state: MICHIGAN

address: 2800 Plymouth Road

summary: Angiotensin II (Ang II)-induced abdominal aortic aneurysm model was established in low-density lipoprotein receptor-deficient mice, and the gene expression profiles in abdominal aortic tissues exhibiting varying degrees of severity were analyzed.

overall_design: The suprarenal abdominal aorta was defined as no aneurysm (maximal diameter < 1.2 mm), dilation (maximal diameter ≥ 1.2 mm without dissection), and dissection (intramural hemorrhage), with saline-infusion group as control

first: Huilun

last: Wang

first: Haocheng

last: Lu

first: Yanhong

last: Guo

first: Eugene

last: Chen


title: Comparative Transcriptomic Analysis of Perfluoroalkyl Substances-Induced Responses of Exponential and Stationary Phase Escherichia coli

city: Gaithersburg

first: Molly

last: Wintenberg

state: MD

address: 100 Bureau Dr

department: Biosystems and Biomaterials Division

institute: National Institute of Standards and Technology

summary: Per- and polyfluoroalkyl substances (PFAS) are highly stable chemical contaminants of emerging concern for human and environmental health due to their non-natural chemistry, widespread use, and environmental persistence. Despite conventional metrology, mitigation strategies, and removal technologies, the complexity of this growing problem necessitates the need for alternative approaches to tackle the immense challenges associated with complex environmental PFAS contamination. Recently, biology has emerged as an alternative approach to detect and mitigate PFAS and understand the molecular-level responses of living organisms, including microorganisms, to these compounds. However, further study is needed to understand how microorganisms in different environments and growth phases respond to PFAS. In this study, we performed RNA sequencing at mid-exponential, early stationary phase, and late stationary phase of bacterial growth to determine the global transcriptional response of a model chassis, Escherichia coli MG1655, induced by two PFAS, perfluorooctanoic acid (PFOA) and perfluorododecanoic acid (PFDoA), and equivalent non-fluorinated carboxylic acids (NFCA), octanoic acid and dodecanoic acid. Differential gene expression analysis revealed PFOA and PFDoA induced distinct changes in gene expression throughout cultivation. Specifically, we identified significant changes in expression of the formate regulon and sulfate assimilation at mid-exponential phase and ferrous iron transport, central metabolism, the molecular chaperone network, and motility processes during stationary phase. Importantly, many of these changes are not induced by NFCAs. In summary, we found PFAS induced a system-level change in gene expression, and our results expand the understanding of bacterial-PFAS interactions that could enable the development of future real-time environmental monitoring and mitigation technologies.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Comparative gene expression analysis of RNA-Seq data for E. coli MG1655 treated with PFCAs or equivalent non-fluorinated carboxylic acids (NFCAs) to an untreated control group at three time points within the growth cycle was performed to investigate the transcriptional response of E. coli to PFAS.

middle: E

first: Olga

last: Vasilyeva

first: Samuel

middle: W

last: Schaffter


title: Phenotypic rescue via mTOR inhibition in neuron-specific Pten knockout mice reveals AKT and mTORC1-site specific changes

city: Boston

first: Kellen

last: Winden

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

summary: Phosphatase and Tensin Homolog (PTEN) is a dual-specific protein and lipid phosphatase that regulates AKT and downstream signaling of the mechanistic target of rapamycin (mTOR). PTEN functions as a tumor suppressor gene whose mutations result in PTEN Hamartoma Tumor Syndrome (PHTS) characterized by increased cancer risk and neurodevelopmental comorbidity. Here, we generated a novel neuron-specific Pten knock-out mouse model (Syn-Cre/Pten HOM) to test the ability of pharmacologic mTOR inhibition to rescue Pten mutation-associated disease phenotypes in vivo and in vitro. We found that treatment with the mTOR inhibitor, everolimus, increased the survival of Syn-Cre/Pten HOM mice while some neurologic phenotypes persisted. Transcriptomic analyses revealed that in contrast to mice harboring a neuron-specific deletion of the Tuberous Sclerosis Complex 2 gene (Syn-Cre/Tsc2 KO), genes that are under AKT regulation were significantly increased in the Syn-Cre/Pten HOM mice. In addition, genes associated with synapse, extracellular matrix, and myelination were broadly increased in Syn-Cre/Pten HOM mouse neocortex. These findings were confirmed by immunostaining of cortical sections in vivo, which revealed excessive immunoreactivity of myelin basic protein and perineuronal nets (PNN), the specialized extracellular matrix surrounding fast-spiking parvalbumin (PV) interneurons. We also detected increased expression of Synapsin I/PSD95 positive synapses and network hyperactivity phenotypes in Syn-Cre/Pten HOM mice neurons compared to wild-type (WT) neurons in vitro. Strikingly, everolimus treatment rescued the number of synapses and network hyperactivity in the Syn-Cre/Pten HOM mice cortical neuron cultures. Taken together, our results revealed in vivo and in vitro molecular and neuronal network mechanisms underlying neurological phenotypes of PHTS. Notably, pharmacologic mTOR inhibition by everolimus led to successful downstream signaling rescue, including mTOR complex 1 (mTORC1) site-specific suppression of S6 phosphorylation, correlating with phenotypic rescue found in our novel neuron-specific Syn-Cre/Pten HOM mice.

overall_design: Pten homozygous and heterozygous mutant mice of the indicated genotypes were sacrificed at P45 (n=4 HET, 4 HOM), and the cortex was collected. RNA extraction was performed using TRIzol (Invitrogen). Total RNA was used as an input for cDNA library preparation using the NEBNext Ultra II RNA Library Prep Kit by Illumina, as per manufacturer’s protocols. Sequencing was performed on an Illumina analyzer, and 150bp paired-end reads were obtained. Reads passing quality filters were mapped using Hisat2 (http://daehwankimlab.github.io/hisat2/; v2.0.5) onto the mouse genome. For differential expression, raw gene counts from protein coding genes from heterozygous and homozygous animals were used as input for EdgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html). Functional annotation was performed using DAVID (https://david.ncifcrf.gov/summary.jsp), and redundant or non-specific categories were manually removed. Comparison with ASD candidate genes was performed by comparing differentially expressed genes to SFARI genes (category 1-3). For RNA sequencing of Tsc2 model (previously described by Yuan and colleagues29), mice from the indicated genotypes were sacrificed at P30 and frontal cortex was dissected. Total RNA was isolated using a Qiagen RNAeasy kit, and cDNA sequencing libraries were constructed with the Kapa Hyperprep library kit using polyA selection (Roche). Sequencing was performed on an Illumina analyzer, and 75bp single-end reads were obtained. Reads passing quality filters were mapped onto the mouse genome using Hisat2. For WGCNA, the WGCNA package from CRAN was used, and gene counts from protein coding genes from both Pten mutant and Tsc2 mutant mice were normalized using log2 counts per million separately. Co-expression networks were created from genes with a coefficient of variation > 0.005 using b=6, and clusters were isolated using the cutreeDynamic package. Module overlap was determined by calculating the Pearson correlation of the kME between two modules.

first: Angelica

last: D'Amore

first: Maria

last: Sundberg

first: Rui

last: Lin

first: Ella

last: Lubbers

first: Lucy

last: Yu

first: Kinga

last: Gawlinska

first: Dawid

last: Gawlinski

first: Sam

last: Lopez

first: Yongho

last: Choe

first: Emma

last: Wightman

first: Yini

last: Liang

first: Meera

last: Modi

first: Christopher

last: Yuskaitis

first: Henry

last: Lee

first: Alexander

last: Rotenberg

first: Mustafa

last: Sahin


title: Inhibition of histone methyltransferase EZH2 for immune-interception of colorectal cancer in Lynch syndrome

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: This study investigates the potential of EZH2 inhibition as a preventive strategy for colorectal cancer in Lynch Syndrome (LS) by modulating the immune system. Using a mouse model of LS and colonic organoids, researchers treated the mice with the EZH2 inhibitor GSK503 and observed increased CD4+ and CD8+ T cells in both spleen and colon tissue. Over a 9-week period, the inhibitor reduced adenoma formation, indicating its preventive efficacy. RNA sequencing and ChIPseq analyses revealed that EZH2 inhibition activated immune and apoptotic markers and decreased H3K27 methylation, leading to changes in gene regulation. These findings suggest that EZH2 inhibitors hold promise for cancer prevention in LS by reprogramming immune responses and gene expression patterns.

overall_design: A mouse model of LS colorectal carcinogenesis and ex vivo colonic organoids were utilized to assess the effects of an EZH2 inhibitor (GSK503) on regulatory pathways of adaptive immunity, tumorigenesis, and epigenetic reprogramming using RNA sequencing.


title: Inhibition of Histone Methyltransferase EZH2 for Immune-Interception of Colorectal Cancer in Lynch Syndrome


title: Cancer-associated fibroblasts reveal aberrant DNA methylation across different types of cancer [Array]

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

type: Methylation profiling by genome tiling array

summary: Cancer-associated fibroblasts (CAFs) are critical components of the tumor microenvironment. Several studies demonstrated molecular differences between CAFs and normal tissue-associated fibroblasts (NAFs). In this study, we isolated CAFs and NAFs from liver tumors and analyzed their DNA methylation profiles. A subset of the CAFs exhibited aberrant DNA methylation, which was also reflected on gene expression level. The DNA methylation at liver-CAF-specific CG dinucleotides (CpGs) was associated with survival in liver cancer data. An integrative analysis with public datasets of CAF versus NAF in different cancer types, including lung, prostate, esophagus, and gastric cancer, revealed overlapping epigenetic aberrations. CpGs with common aberrations in DNA methylation included cg09809672 (EDARADD), cg07134930 (HDAC4), and cg05935904 (intergenic). Aberrant DNA methylation at these sites was associated with prognosis in several cancer types. Thus, activation of CAFs by the tumor environment is associated with characteristic epigenetic modifications that could be used as biomarkers for disease stratification.

overall_design: DNA methylation analysis of cancer associated fibroblasts (CAFs) and normal-tissue associated fibroblasts (NAFs) of human liver tumor samples. NAFs were isolated form neighboring tumor-free tissue. DNA methylation profiles were analyzed with EPIC BeadChip microarray (Illumina, San Diego, USA) by Life & Brain company (Bonn, Germany).

first: Marco

last: Schmidt

first: Tiago

last: Maié

first: Thorsten

last: Cramer

first: Ivan

middle: G

last: Costa


title: Sequence composition dictates chromatin assembly, activity, folding and compartmentalization [ATAC-Seq]

first: Romain

last: Koszul

overall_design: We explored whether chromatin accessible sites were able to form on bacterial chromosomes integrated in a eukaryotic environment by performing ATAC-seq analysis of yeast strains containing linearized and telomerized bacterial chromosomes.

first: Jacques

last: Serizay


title: Formation of malignant, metastatic small cell lung cancers through overproduction of cMYC protein in TP53 and RB1 depleted pulmonary neuroendocrine cells derived from human embryonic stem cells [bulk RNA-seq]

city: New York

first: Yajas

last: Shah

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: We recently described our initial efforts to develop a model for small cell lung cancer (SCLC) derived from human embryonic stem cells (hESCs) that were differentiated to form pulmonary neuroendocrine cells (PNECs), a putative cell of origin for neuroendocrine-positive SCLC. Although reduced expression of the tumor suppressor genes TP53 and RB1 allowed the induced PNECs to form subcutaneous growths in immune-deficient mice, the tumors did not display the aggressive characteristics of SCLC seen in human patients. Here we report that the additional, doxycycline-regulated expression of a transgene encoding wild-type or mutant cMYC protein promotes rapid growth, invasion, and metastasis of these hESC-derived cells after injection into the renal capsule. Similar to others, we find that the addition of cMYC encourages the formation of the SCLC-N subtype, marked by high levels of NEUROD1 RNA. Using paired primary and metastatic samples for RNA sequencing, we observe that the subtype of SCLC does not change upon metastatic spread and that production of NEUROD1 is maintained. We also describe histological features of these malignant, SCLC-like tumors derived from hESCs and discuss potential uses of this model in efforts to control and better understand this recalcitrant neoplasm.

overall_design: Bulk and single cell RNA sequencing of cell lines and mouse xenografts

first: Eric

last: Gardner

first: Huanhuan

middle: J

last: Chen

first: Harold

last: Varmus