title: Expression data from drosophila ML3 gonads, pointed aga vs. Wt (Oregon R)

city: Sevilla

first: Alicia E.

last: Rosales-Nieves

state: Sevilla

address: HUVR. Edif. IBiS. Lab 109. Av Manuel Siurot S/N

institute: Instituto de Biomedicina de Sevilla-CSIC

summary:
pointed agametic mutation give rise to adults without germline. In this microrray we compare gondas from the pointed aga mutation to Wt gonads.
We used microarrays to detail the transcription profile in the agametic gonads

overall_design: 2 larval gonads (each gonad aproximately 2000-3000 cells) per sample (pointed aga and Wt) 3 biological replicates

first: Alicia

first: Acaimo

last: Gonzalez-Reyes


title: PROX1 Controls Cellular Patterning, Innervation and Differentiation in the Mouse Organ of Corti

status: Public on Jul 17 2025

city: Atlanta

first: Michael

last: Deans

address: 201 Dowman Drive Atlanta

country: USA

institute: Emory University School of Medicine

type: Expression profiling by high throughput sequencing

summary: The organ of Corti is divided into functional compartments responsible for hearing or cochlear amplification. A medial compartment containing inner hair cells innervated by Type I spiral ganglion neurons and a lateral compartment containing outer hair cells innervated by Type II spiral ganglion neurons. Supporting cells also differ, with lateral compartment pillar cells and Deiters’ cells developing specialized cellular structures to support outer hair cell electromotility. We bred organ of Corti-restricted Prox1 conditional knockout mice to study lateral compartment development because PROX1 is the first transcription factor expressed strictly in lateral compartment supporting cells. In the absence of Prox1, supporting cell numbers increased without corresponding changes in outer hair cells, and they appear incompletely differentiated based on morphological criteria. Outer hair cell number was not impacted but innervation was disrupted with many afferent neurons turning incorrectly towards the cochlear apex. RNAseq revealed no changes in gene expression that could account for the innervation phenotype. Therefore, we propose that PROX1 promotes pillar and Deiters’ cell differentiation and organization that has secondary effects on innervation but is not required for compartment specification.

overall_design: RNA-seq profiling of micro-dissected organ of Corti from wildtype and conditional Prox1 knock-out (Emx2-cre; floxed-Prox1) mice at P0

first: Shubham

last: Kale

first: Dimitri

last: Traenkner

first: Ellison

middle: J

last: Goodrich

first: Satish

middle: R

last: Ghimire

first: Thomas

middle: M

last: Coate


title: Adipocyte FMO3-derived TMAO induces WAT dysfunction and metabolic disorders by promoting inflammasome activation in ageing

city: Kowloon

first: Thashma

middle: Pemmanda

last: Ganapathy

address: 11 Yuk Choi Road

department: Health Technology and Information

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: Circulating trimethylamine N-oxide (TMAO) participates in the pathogenesis of cardio-metabolic diseases, with hepatic flavin-containing monooxygenase 3 (FMO3) originally regarded as the primary source of TMAO production. Here, we demonstrate that white adipose tissue (WAT) expressed FMO3 and its derived metabolic product TMAO causatively contribute to the systemic elevation of TMAO levels, WAT dysfunction, and metabolic diseases in ageing. We showed that FMO3 expression and TMAO levels are upregulated in WAT of naturally ageing animals and human subjects, as well as in a DNA damage-induced senescent adipocyte model, but not in the liver. This upregulation is due to p53 activation in mice and could be mitigated by calorie restriction in humans. Adipocyte-specific ablation of FMO3 attenuates TMAO accumulation in WAT and circulation, leading to enhanced glucose metabolism, energy homeostasis, and lipid regulation in aged and high-fat diet-induced obese mice. Transcriptomic and histological analysis link these metabolic improvements to reduced senescence, fibrosis, and inflammation in WAT as well as a decrease in adipose-resident macrophages. LiP-small molecule mapping (LiP-SMap) analysis identified numerous novel TMAO-interacting proteins implicated in inflammasome activation within white adipocytes and macrophages. Mechanistically, TMAO facilitates inflammasome activation by binding to the inflammasome adaptor protein apoptosis-associated speck-like protein containing A CARD (ASC), thereby inducing its expression, caspase-1 activation, and subsequent interleukin-1β (IL-1β) production. Our findings uncover a pivotal role for adipocyte FMO3 in modulating TMAO production and WAT dysfunction by promoting inflammasome activation in ageing via an autocrine and paracrine manner.

overall_design: To investigate the role of adipo-FMO3 during aging, we isolated epididymal adipose tissue (eWAT) from 105-week-old wild-type (WT) and adipo-FMO3 knockout (KO) mice on a C57BL/6 background. The isolated tissues were subjected to transcriptome sequencing to analyse gene expression profiles and elucidate the functional implications of adipo-FMO3 in the aging process.

middle: P

first: Juntao

last: Yuan

first: Kelvin

middle: K

last: Wu

first: Moinul

last: Hoque

first: Melody

middle: Y

last: Ho

first: Baomin

last: Wang

first: Xiaomu

last: Li

first: Wang

last: Kai

first: Martin

last: Wabitsch

first: Qizhou

last: Lin

first: Yongxia

last: Niu

first: Yuyan

last: Zhu

first: Kenneth

last: Cheng


title: Epigenetic metabolite lipid nanoparticles alleviate venous thrombosis via bone marrow reprogramming

status: Public on Jul 18 2025

city: Cleveland

first: Andrei

last: Maiseyeu

state: Ohio

address: 10900 Euclid Ave

department: Medicine

institute: Case Western Reserve University

summary: Targeting coagulation cascade is a mainstay approach to therapy of thrombosis. One of the most prevalent complications of anticoagulation is a significant bleeding risk that can result in hospitalization. Recent studies on immunothrombosis (i.e. inflammation-linked thrombosis) proposed myeloid cells, especially neutrophils, to actively participate in thrombus formation through neutrophil extracellular traps (NETosis) and activation of inflammatory pathways. Here, we developed lipid nanoparticles (LNPs) with coagulation cascade-independent action that target neutrophils to alleviate venous thrombosis. A single intravenous dose of immunomodulatory metabolite itaconate (ITA)-bearing LNPs (ITA-LNPs) targeted >90% of bone marrow-resident neutrophils, but not macrophages or T lymphocytes. ITA-LNPs significantly diminished inflammation in cultured neutrophils and macrophages and improved survival in the mouse model of endotoxemia. When tested in an inferior vena cava ligation model of deep vein thrombosis, ITA-LNPs decreased the size and weight of thrombi as compared to control LNPs (Ctrl-LNPs). In addition, the thrombi from ITA-LNPs injected mice had significantly reduced neutrophil infiltration, decreased NETosis and interleukin-1 beta (IL-1β) expression. Intriguingly, one of the mechanisms through which this occurred was histone H4K12ac deacetylation, resulting in chromatin condensation and transcriptional repression of inflammatory genes and transcription factors involved in DNA damage response. Finally, we found that ITA-LNPs were hemostatically safe and neither targeted nor activated platelets in vivo. In sum, our work explores an LNP technology with an epigenetic mode of action serving as an anti-immunothrombotic therapy that could improve clinical outcomes without additional hemorrhagic risk.

overall_design: RNA-seq was performed on primary, bone marrow-derived neutrophils isolated from C57BL/6 male mice 24 h after injection with control or ITA-LNPs followed by stimulation with lipopolisaccaride (100 ng/mL) in culture for 3 h.


title: Ptbp1 is not required for retinal neurogenesis and cell fate specification [scRNA-seq]

status: Public on Jul 16 2025

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust St.

department: Ophthalmology

institute: University of Pittsburgh

summary: The RNA-binding protein Ptbp1 has been proposed as a master regulator of neuronal fate, repressing neurogenesis through its effects on alternative splicing and miRNA maturation. While prior studies using RNA interference suggested that Ptbp1 loss promotes neurogenesis, recent genetic studies have failed to replicate glia-to-neuron conversion following Ptbp1 loss of function. To evaluate the role of Ptbp1 in developmental neurogenesis in vivo, we conditionally disrupted Ptbp1 in retinal progenitors. Ptbp1 was robustly expressed in both retinal progenitors and Müller glia but absent from postmitotic neurons, and efficient loss of function in mutant animals was confirmed using immunostaining for Ptbp1. Furthermore, bulk RNA-Seq at E16 revealed accelerated expression of late-stage progenitor and photoreceptor-specific genes and altered splicing patterns in Ptbp1 mutants, including increased inclusion of neuron- and retina-specific exons. However, we observed no defects in retinal lamination, progenitor proliferation, or cell fate specification in mature retina. ScRNA-Seq of mature mutant retinas revealed only modest transcriptional changes limited to Müller glia, recapitulating alterations seen following selective deletion of Ptbp1 in mature glia. Our findings demonstrate that Ptbp1 is fully dispensable for retinal development and suggest that its proposed role as a central repressor of neurogenesis should be reevaluated

overall_design: Single cell RNA-seq was performed on Chx10-Cre control and Chx10-Cre;Ptbp1lox/lox KO retinas at P30 using 10x Genomics Chromium Single Cell 3’ Reagents Kit v3.1.

first: Haley

last: Appel

first: Rogger

last: Carmen-Orozco

first: Thanh

last: Hoang

first: Seth

last: Blackshaw


title: Hexokinase 2 is an RNA-binding protein that regulates mRNA translation independently of glycolysis and induces melanoma cell proliferation

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

country: France

institute: Institut Curie

summary: Although metabolic benefits of glycolysis have been extensively described in tumor cells, the extra-metabolic functions linked to this energetic pathway in tumor growth and cell proliferation have not been clearly established yet. Recently, some key glycolytic enzymes, such as GAPDH and PKM2, were reported to regulate mRNA translation. Translational control of gene expression is considered as a critical effector in cancer biology, representing a highly promising area of research. Here, we report that Hexokinase 2 (HK2), a glucose kinase that catalyzes the first step of glycolysis at the outer mitochondrial membrane (OMM), is an RNA-binding protein (RBP) that regulates mRNA translation in melanoma cell lines. Polysome profiling experiments followed by RNA sequencing indicate that the translational regulation exerted by HK2 is partly independent of the metabolic status or the glycolytic pathway. We found that HK2 specifically regulates translation of the mRNA encoding SOX10, a transcription factor implicated in the regulation of tumor initiation, maintenance, and progression in melanoma. RNA-protein interaction assays, including crosslinking immunoprecipitation (CLIP), indicate that HK2 is an RBP whose interaction with RNA is independent of its enzymatic activity, its ability to bind glucose or its association with the OMM. HK2 directly interacts with the 5’ untranslated region (5’UTR) of the SOX10 mRNA through a stem-loop RNA secondary structure. Using RNA-protein proximity ligation assays and a fluorescence-based ribosome-bound mRNA mapping method (RIBOmap), we found that high glucose conditions, which promotes the release of HK2 from the OMM, induces an increase in HK2-SOX10 mRNA interaction and SOX10 mRNA translation in the cytoplasm. We further showed that HK2-dependent SOX10 mRNA translation is involved in melanoma cell proliferation and colony formation. Collectively, our data highlight a non-metabolic function of HK2 acting as an RBP and translation regulator.

overall_design: We performed transcriptome and translatome analysis (RNA-Seq) on A375 melanoma cells cultured in galactose- or glucose-containing medium depleted or not of the glycolytic enzymes HK2, GAPDH, PKM2.

first: Ana

middle: L

last: Dian

first: Lucilla

last: Fabbri

first: Antoine

last: Moya-Plana

first: Giuseppina

last: Claps

first: Juliana

middle: C

last: Ferreira

first: Virginie

last: Quidville

first: Sylvain

last: Martineau

first: Dorothée

last: Baille

first: Laetitia

last: Besse

first: Cédric

last: Messaoudi

first: Séverine

last: Roy

last: Raynal

last: Baulande

first: Wael

last: Rabeh

first: Caroline

last: Robert

first: Stéphan

last: Vagner


title: Direct sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution unravels their distinct roles in Alzheimer’s disease [RNA-Seq]

city: Shanghai

first: Zixin

last: Wang

address: Siping Road

country: China

institute: Tongji University

summary: 5-hydroxymethylcytosine (5hmC) constitutes up to 20% of 5-methylcytosine (5mC) in mammalian cells. As conventional bisulfite sequencing is unable to distinguish 5hmC from 5mC, several methods have been proposed to detect 5hmC and infer 5mC levels by subtracting 5hmC from whole-genome bisulfite sequencing data. This subtraction approach, however, can lead to the underestimation of 5mC levels at sites with high 5hmC abundance. Here, we present two orthogonal methods: CMD1-Deaminase sequencing and CMD1-TET bisulfite sequencing, which enable the direct and independent detection of 5mC. In combination with ACE-seq or TAB-seq, these techniques facilitate an accurate distinction between 5mC and 5hmC, eliminating the need for subtraction. Using these approaches, we generated a comprehensive landscape of 5mC and 5hmC in the hippocampus of the Alzheimer's disease (AD) model mice. Notably, while 5hmC levels were substantially reduced in the AD mice, 5mC levels remained largely unchanged, suggesting a critical role for 5hmC as an independent epigenetic mark in the pathogenesis of AD.

overall_design: RNA-seq in hippocampus of WT and Alzheimer's disease model mice

first: Faying

last: Chen

first: Baodan

last: He

first: Fanchen

first: Jiaxue

last: Cha

first: Yu

last: Song

first: Weiying

last: Meng

first: Yutao

last: Fu

first: Wanyue

last: Zou

first: Shuxia

last: Sun

first: Keyao

last: Zhao

first: Haoming

last: Jiang

first: Zhiyan

first: Yujun

last: Hou

first: Jiejun

last: Shi

first: Jianhuang

last: Xue


title: Comparative analysis of Ad5, mRNA, and protein vaccines reveals context-dependent immune responses

city: Boston

first: Pablo

last: Penaloza-MacMaster

state: MA

address: 3 Blackfan Circle

department: CVVR

institute: Beth Israel Deaconess Medical Center

summary: Despite the widespread use of adenovirus, mRNA, and protein-based vaccines during the COVID-19 pandemic, their relative immunological profiles and protective efficacies remain incompletely defined. Here, we compared antigen kinetics, innate and adaptive immune responses, and protective efficacy following Ad5, mRNA, and protein vaccination in mice. Ad5 induced the most sustained antigen expression, but mRNA induced the most potent interferon responses, associated with robust antigen presentation and costimulation. Unlike Ad5 vaccines, which were hindered by pre-existing vector immunity, mRNA vaccines retained efficacy after repeated use. As a single-dose regimen, Ad5 vaccines elicited superior immune responses. However, as a prime-boost regimen, and particularly in Ad5 seropositive mice, mRNA vaccines outperformed the other vaccine platforms. These findings highlight strengths of each vaccine platform and underscore the importance of vaccination context in determining optimal vaccine performance.

overall_design: C57BL/6 mice were immunized intramuscularly with each respective vaccine (Ad5, mRNA, and protein vaccines). At day 1 post-vaccination, lymph nodes from five mice were pooled and MACS-sorted with a CD45 MACS positive selection kit (STEMCELL) and used for single-cell sequencing. A naive group with no vaccination was used as control.

first: Bakare

last: Awakoaiye

first: Shiyi

last: Li

first: Sarah

last: Sanchez

first: Tanushree

last: Dangi

first: Nahid

last: Irani

first: Laura

last: Arroyo

first: Gabriel

last: Arellano

first: Shadi

last: Mohammadabadi

first: Malika

last: Aid


title: NanoString BC360 gene signatures in luminal breast cancer

city: Munich

first: Guokun

last: Zhang

address: Marchioninistr. 15

country: Germany

institute: IBE LMU

summary: We analyzed a cohort of 220 early breast cancer patients with ER-positive and/or progesterone receptor (PR)-positive, HER2-negative tumors.

overall_design: RNA was submitted for NanoString BC360 analysing. Nanostring profiling was accomplished following the protocol provided along with the kits including hybridization, purification and immobilization, counting and analysis. It included 728 specific genes.

first: Clarissa

last: Gerhäuser

first: Hans

middle: H

last: Kreipe

first: Nadia

last: Harbeck


title: RCC2 and CD24 Cooperate to Modulate Prostate Cancer Progression Through Vimentin Ubiquitination and β-Catenin Pathway Activation

status: Public on Jul 21 2025

city: Birmingham

first: Lizhong

last: Wang

address: 740 20th St S

institute: UAB

summary: CD24 plays a crucial role in tumor growth and metastasis, including in prostate cancer. While CD24 stimulates prostate cancer cell growth by controlling the ARF-NPM interaction and p53 inactivation, the mechanism of CD24-mediated metastasis remains elusive. This study identifies a direct interaction between CD24 and RCC2 with roles in prostate cancer cell proliferation and migration. Immunohistochemical analysis of primary prostate cancer samples showed expression of CD24 in 49% of samples and RCC2 in 82%, with a positive correlation between their protein levels. Their co-expression, particularly the binding of CD24 to the C-terminal domain of RCC2, supports their direct interaction, which may regulate cell motility and adhesion. Functional assays revealed that knockout (KO) of RCC2 in DU145 and PC3 prostate cancer cells inhibited cell proliferation but unexpectedly enhanced cell migration and invasion, while CD24 KO reduced proliferation and migration. Notably, dual KOs of CD24 and RCC2 led to a significant decrease in cell proliferation but showed mixed effects on migration, indicating a complex interplay between these proteins. In vivo, RCC2 KO in prostate cancer cells promoted spontaneous lung metastasis without significantly altering primary tumor growth, contrasting with CD24 KO, which reduced tumor growth and metastasis. Mechanistically, RCC2 was shown to ubiquitinate and degrade Vimentin, influencing cytoskeletal dynamics and migratory behavior. Furthermore, CD24 was found to ubiquitinate and degrade RCC2, leading to modulation of the β-catenin signaling pathway. RCC2 KO increased β-catenin activation and decreased the expression of its inhibitors AXIN2 and APC, while CD24 KO led to β-catenin inactivation. This opposing regulation of β-catenin signaling by CD24 and RCC2 underscores their differential roles in prostate cancer cell migration. These findings provide new insights into the molecular mechanisms underlying prostate cancer growth and metastasis and identify the CD24-RCC2 axis as a potential therapeutic target for controlling tumor growth and metastasis in prostate cancer.

overall_design: Total RNA expression by deep-sequencing in DU145 cells sorted for different levels of CD24 gene knockout and RCC2 gene knockot.

first: Runhua

last: Liu

first: Xuelian

last: Cui


title: Dual targeting of CDK6 and LSD1 is synergistic and overcomes differentiation blockade in AML [ATACseq_MV4_11]

city: Marseille

first: Sophie

last: Lopez

address: 27 Bd Lei Roure

institute: INSERM

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The heterogeneity of leukemic cells is the main cause of resistance to therapy in acute myeloid leukemia (AML). Consequently, innovative therapeutic approaches are critical to target a wide spectrum of leukemic clones, regardless of their genetic and non-genetic complexity. In this report, we leverage the vulnerability of AML cells to CDK6 to identify a combination therapy capable of targeting common biological processes shared by all leukemic cells, while sparing non-transformed cells. We demonstrate that the combined inhibition of CDK6 and LSD1 restores myeloid differentiation and depletes the leukemic progenitor compartment in AML samples. Mechanistically, this combination induces major changes in chromatin accessibility, leading to the transcription of differentiation genes and diminished LSC signatures. Remarkably, the combination is synergistic, induces durable changes in the cells, and is effective in PDX mouse models. While many AML samples exhibit only modest responses to LSD1 inhibition, co-targeting CDK6 restores the expected transcription response associated with LSD1 inhibition. Given the availability of clinical-grade CDK6 and LSD1 inhibitors, this combination holds significant potential for implementation in clinical settings through drug repositioning.

overall_design: ATACseq profiling of MV4-11 cells treated for 4 days with the combination (Palbociclib + TCP), the single molecule (Palbociclib or TCP) or vehicle control (DMSO)

first: Lise

last: Brault

first: Edwige

last: Voisset

first: Mathieu

last: Desaunay

first: Antonia

last: Boudet

first: Paraskevi

last: Kousteridou

first: Sébastien

last: Letard

first: Nadine

last: Carbuccia

first: Armelle

last: Goubard

first: Rémy

last: Castellano

first: Yves

last: Collette

first: Julien

last: Vernerey

first: Isabelle

last: Vigon

first: Jean-Max

last: Pasquet

first: Patrice

last: Dubreuil

first: Paulo

last: De Sepulveda


title: Dual targeting of CDK6 and LSD1 is synergistic and overcomes differentiation blockade in AML [RNAseq_patients]

overall_design: RNAseq profiling of primary AML samples treated for 4 days with the combination (Palbociclib + TCP), the single molecule (Palbociclib or TCP) or vehicle control (DMSO)


title: Dual targeting of CDK6 and LSD1 is synergistic and overcomes differentiation blockade in AML [RNAseq_MV4_11]


title: RNA sequencing of primary bone marrow-derived macrophages from MAPL KO and control mice.

status: Public on Jul 23 2025

city: Berkeley

first: Olesia

last: Ignatenko

state: CA

address: Morgan Hall

institute: UC Berkeley

summary: Differential expression analysis

overall_design: untreated, LPS+Ifny 4.5 hours, LPS+Ifny 24 hours

first: Heidi

last: McBride

first: Mai

last: Nguyen

first: Jack

last: Collier


title: Polyamine Depletion Inhibits Ewing Sarcoma Metastasis by Inducing Ferroptosis

city: Baltimore

first: Da

last: Peng

state: Maryland

address: 733 North Broadway, MRB 653

institute: Johns Hopkins University

summary: Polyamine metabolism and signaling play important roles in multiple cancers including neuroblastoma and breast cancer but have not previously been studied in Ewing sarcoma.  Prior work in our lab suggested that tumor microenvironment affects arginase expression -- orthotopically implanted hindlimb tumors with enhanced metastatic potential demonstrate diminished arginase expression compared to subcutaneously implanted tumors that do not metastasize.  As arginase catalyzes the conversion of arginine to ornithine, the precursor for polyamine synthesis, this suggested a potential role for polyamine synthesis in Ewing sarcoma metastasis and a target for therapeutic intervention.  Here, we show that blocking polyamine synthesis with D, L-alpha-difluoromethylornithine (DFMO) causes a G1 cell cycle arrest, dose-dependent decreases in sarcosphere formation from Ewing sarcoma cell lines growing in non-adherent conditions and a decrease in clonogenic growth in soft agar.  Further, we utilized our orthotopic implantation/amputation model of Ewing sarcoma metastasis to investigate the impact of disrupting polyamine synthesis on tumor growth and metastasis.  When mice were treated with low dose DFMO, there was no effect on primary tumor growth or metastatic potential; however, at higher concentrations, systemic DFMO slowed primary tumor growth in addition to limiting metastasis.  RNA sequencing demonstrated gene expression patterns consistent with induction of ferroptosis caused by polyamine depletion, and this was confirmed experimentally.  Collectively, these results reveal a novel mechanism by which DFMO prevents metastasis – induction of ferroptosis due to polyamine depletion, and our results suggest that DFMO may be a readily translatable and well-tolerated treatment to prevent metastatic recurrence in patients with high-risk Ewing sarcoma.

overall_design: TC-71 cells were cultured, and 100 cells were suspended in Matrigel 1:1 dilution with phosphate-buffered saline in a total volume of 0.1 ml. This suspension was injected into the subcutaneous space of the flank of NSG mice using a 25-gauge needle. When tumors reached 1.5 cm in diameter, Ewing sarcoma cells were recovered from lungs, bone marrow, and the primary tumor by flow cytometry

first: Rachel

last: Offenbacher

first: Kyle

middle: W

last: Jackson

first: Masanori

last: Hayashi

first: Jinghang

last: Zhang

first: Yuqi

last: Tan

first: Tracy

last: Stewart

first: Paul

last: Ciero

first: Jackson

last: Foley

first: Robert

middle: A

last: Casero Jr

first: Patrick

last: Cahan

first: David

last: Loeb


title: Strain-Specific Variation in the Complement Resistome of Pseudomonas aeruginosa

city: Grenoble

first: Manon

last: Janet-Maitre

address: 71 Avenue des Martyrs

institute: IBS

summary: Determination of molecular factors involved in P. aeruginosa survival to human plasma by Tn-seq performed in 3 strains of P. aeruginosa

overall_design: Tn-seq analysis of transposon insertion mutants enriched in plasma compared to heat inactivated plasma in Pseudomonas aeruginosa strains CHA, YIK and PA14, in biological duplicates

first: Ina

last: Attrée


title: Direct sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution unravels their distinct roles in Alzheimer’s disease [BS-Seq]

first: Zixin

last: Wang

type: Methylation profiling by high throughput sequencing

overall_design: CD-seq、CT-seq、ACE-seq and TAB-seq in hippocampus of WT and Alzheimer's disease model mice.

first: Faying

last: Chen

first: Baodan

last: He

first: Fanchen

first: Jiaxue

last: Cha

first: Yu

last: Song

first: Weiying

last: Meng

first: Yutao

last: Fu

first: Wanyue

last: Zou

first: Shuxia

last: Sun

first: Keyao

last: Zhao

first: Haoming

last: Jiang

first: Zhiyan

first: Yujun

last: Hou

first: Jiejun

last: Shi

first: Jianhuang

last: Xue


title: Longitudinal liquid biopsy identifies an early predictive biomarker of immune checkpoint blockade response in head and neck squamous cell carcinoma [scRNA-seq]

status: Public on Jul 15 2025

city: Gaithersburg

first: Binbin

state: MD

address: 408 Suffield Dr

institute: NATIONAL CANCER INSTITUTE, NIH

summary: Immune checkpoint blockade (ICB) has improved outcomes in head and neck squamous cell carcinoma (HNSCC), yet there is an unmet need for predictive, blood-based biomarkers to guide treatment. We longitudinally profiled peripheral immune responses in a mouse HNSCC model treated with anti–PD-1, using single-cell and bulk RNA sequencing with paired TCR sequencing. Early expansion of effector memory T cells (Tem) and B cells was associated with ICB response. Here, we show that the LiBIO score, a composite of Tem and B cell signatures, robustly predicts ICB response in HNSCC blood and tumor cohorts, outperforming existing biomarkers. Furthermore, the LiBIO score generalizes to melanoma, non-small cell lung cancer, and breast cancer, demonstrating potential as a clinically applicable blood-based biomarker for ICB response across multiple cancer types.

overall_design:
We employed our previously characterized 4MOSC carcinogen-induced orthotopic HNSCC preclinical model to evaluate immune dynamics during ICB therapy. Two cohorts of mice were used, with one cohort comprising 45 mice for bulk RNA sequencing (RNA-seq) and the other comprising 16 mice for single-cell RNA sequencing (scRNA-seq) and single-cell TCR sequencing. Lesions developed consistently at expected time points. Blood samples were collected at four key intervals: pre-treatment (Day 4) and three on-treatment time points (Days 9, 17, and 24), aligned with the administration of anti-PD-1 therapy. Tumor growth and immune responses were monitored longitudinally to assess treatment efficacy. Bulk RNA-seq provided an overview of immune dynamics in the larger cohort, while scRNA-seq and scTCR sequencing in the smaller cohort delivered high-resolution insights into immune repertoire changes, supporting the study’s focus on peripheral immune biomarkers for predicting ICB outcomes.

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first: Robert

last: Saddawi-Konefka

first: Lauren

last: Clubb

first: Shiqi

last: Tang

first: Di

last: Wu

first: Sumit

last: Mukherjee

first: Sahil

last: Sahni

first: Saugato

last: Rahman-Dhruba

first: Xinping

last: Yang

first: Sumeet

last: Patiyal

first: Chi-Ping

last: Day

first: Parth

last: Desai

first: Clint

last: Allen

first: Kun

first: Silvio

last: Gutkind

first: Eytan

last: Ruppin


title: Direct sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution unravels their distinct roles in Alzheimer’s disease [BS-Seq mESC]

first: Zixin

last: Wang

overall_design: CD-seq and CT-seq of mESC genomic DNA.

first: Faying

last: Chen

first: Baodan

last: He

first: Fanchen

first: Jiaxue

last: Cha

first: Yu

last: Song

first: Weiying

last: Meng

first: Yutao

last: Fu

first: Wanyue

last: Zou

first: Shuxia

last: Sun

first: Keyao

last: Zhao

first: Haoming

last: Jiang

first: Zhiyan

first: Yujun

last: Hou

first: Jiejun

first: Jianhuang


title: Nrf2 regulates activation driven-expansion of CD4+T-cells by differentially modulating glucose and glutamine metabolism [RNA-Seq]

city: Kansas City

first: Kalyani

last: Pyaram

state: KS

address: 2060 W 39th Ave

institute: University of Kansas Medical Center

summary: Upon antigenic stimulation, CD4+T-cells undergo clonal expansion elevating their bioenergetic demands and utilization of nutrients like glucose and glutamine The nuclear factor erythroid 2-related factor2 (Nrf2) is a well-known regulator of oxidative stress, but its involvement in modulating the metabolism of CD4+T-cells remain unexplored. We report that Nrf2 protein levels are temporally regulated in activated CD4+T-cells, with elevated expression during early activation followed by a decline. T-cell-specific constitutive activation of Nrf2 by deletion of its regulator Keap1, enhances early activation and IL-2 secretion, upregulates TCR-signaling, and increases activation-driven expansion of CD4+T-cells. Metabolically, high Nr2 alters glucose metabolism and promotes glutamine metabolism via glutaminolysis to support increased CD4+T-cell proliferation. Mechanistically, elevated Nrf2 activity in activated CD4+T-cells leads to increased chromatin accessibility and proliferation-associated gene expression. In summary, we elucidate the role of Nrf2 beyond traditional antioxidation in modulating the activation-driven expansion of CD4+T-cells by influencing their nutrient metabolism.

overall_design: Mouse naïve CD4+T-cells were activated in vitro in presence of anti-CD3 and anti-CD28 to mimic T-cell activation for 24 and 48h. After 24 and 48 hours, total RNA was extracted using RNeasy Plus Micro kit (Qiagen) and processed at the Genomics Core Facility at the University of Kansas Medical Center. 100ng of the RNA was used to perform Agilent TapeStation QC analysis to verify RNA integrity and generate RNA Integrity number (RIN). Using Nova-Seq 6000 S1 200 cycle reagent kit, 25 million pair-ended reads were recorded for construction of mRNA libraries. For bioinformatic analysis, following quality check through fastQC data were aligned to human reference genome using RSEM (RNA-Seq by Expectation Maximization) resulting in the generation of gene count matrix. Further differential expression analysis was performed between Keap1-KO (KKO) and WT CD4+T-cells for gene ontology (GO) enrichment using ClusterProfiler R-package, to identify significant biological processes, molecular pathways and metabolic pathways associated with the samples. The enrichment results were prioritized based on significance and the top GO terms were visualized using dotplots. Box-plots for genes were also generated using ggplot2 to illustrate the variability of the genes between the 2 groups with mean P-values annotated on each plot, respectively.

first: Aprajita

last: Tripathi

first: Debolina

last: Dasgupta

first: Michael

middle: S

last: Dahabieh

first: Rachel

last: Griffard-Smith

first: Anil

last: Pant

first: Ashlyn

last: Bugbee

first: Nanda

last: Kumar Yellapu

first: Emily

last: Burt

first: Ben

last: Choi

first: Ryan

middle: D

last: Sheldon

first: Shailendra

last: Giri

first: Devin

last: Koestler

first: Russell

middle: G

last: Jones

first: Viveka

last: Nand Yadav


title: Nrf2 regulates activation driven-expansion of CD4+T-cells by differentially modulating glucose and glutamine metabolism [ATAC-Seq]

overall_design: Stimulated CD4+T-cells from WT and Keap1-KO mice were harvested after 36 h. Cells were transferred to a 15mL or 50mL conical tube and centrifuged at 500 x g for 5 minutes. The media was aspirated, and cells were resuspended in 10mL of pre-warmed growth media, followed by the addition of 1:100 volume of 100x DNase buffer and DNase solution (250mM MgCl2 and 50mM CaCl2 in dH2O). Incubated the cells at 37°C for 30 minutes and centrifuged again at 500 x g for 5 minutes at 4°C, resuspended in 5mL ice-cold PBS (or 500µL for Eppendorf tubes), and 300,000 cells were quantified using a hemocytometer for cryopreservation. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. The cells were then thawed in a 37oC water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif cat# 53150). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the iSeq (Illumina) and sequenced with PE42 sequencing on the NovaSeq 6000 sequencer (Illumina). Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Signal maps and peak locations were used as input data to Active Motif’s proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations, and gene annotations.


title: Ptbp1 is not required for retinal neurogenesis and cell fate specification [RNA-seq]

first: Clayton

last: Santiago

overall_design: Bulk RNA-seq was performed on Chx10Cre control (WT) , Chx10Cre;Ptbp1lox/WT (HET), and Chx10Cre;Ptbp1lox/lox (KO) retinas at E16 and sequenced on the Illumina NovaSeq X platform

first: Haley

last: Appel

first: Rogger

last: Carmen-Orozco

first: Thanh

last: Hoang

first: Seth

last: Blackshaw


title: ULK1 as a novel therapeutic target in Myeloproliferative Neoplasms [RNA-Seq]

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

summary: We provide evidence that genetic or pharmacological targeting of ULK1 delays disease progression in Jak2V617F-mutant MPN in vivo models. Mechanistically, the ULK1 anti-neoplastic effects were found to be associated, at least in part, with the transcriptional regulation of genes involved in myeloid malignancies and hematopoietic stem cell differentiation, leading to a reduced number of early-stage erythroid progenitors in both spleen and bone marrow, decreased levels of hemoglobin, hematocrit and red blood cells and spleen size in MPN in vivo models. These findings reveal a novel pro-tumorigenic role for ULK1 downstream of the hyperactive JAK2 signaling characteristic of MPNs and highlight the potential of targeting this kinase as a new therapeutic strategy for MPN patients.

overall_design: RNA-Seq profiling of HEL cells treated for 6 hours with either vehicle-control (DMSO) or with 5µM of the ULK1 inhibitors SBI-0206965 or ULK101.

middle: T

first: Diana

last: Saleiro

first: Leonidas

last: Platanias


title: Airway Epithelial SARS-CoV-2 Infectious and Repair Responses: Relationships to Age, Sex, and Post-COVID Pulmonary Syndromes

city: Chapel Hill

first: Hong

last: Dang

state: North Carolina

address: 125 Mason Farm Rd, Cb#7248

institute: University of North Carolina at Chapel Hill

summary: This study investigated the acute and reparative responses as a function of age and sex in primary human bronchial epithelial (HBE) cultures over a 14-day post-SARS-CoV-2 infection (dpi) protocol. Methods: Bulk RNA-seq was performed on well-differentiated human bronchial epithelial (HBE) cell culture lysates with/without SARS-CoV-2 inoculation. Results: SARS-SoV-2 infection peaked at 3 dpi with an ~ 2 log titer suppression at 14 dpi. Airway epithelia repaired to an abnormal mucus metaplastic/inflammatory state that reflected potentially beneficial and adverse consequences at 14 dpi. No age- or sex-dependent effects on SARS-CoV-2 infection were detected. Conclusions: Human airway epithelial repair post-SARS-CoV-2 is prolonged and incomplete in vitro over 14 days, and persistently abnormal repair may contribute to phenotypes of people with long-COVID pulmonary syndrome.

overall_design:
HBE cells were maintained >4 weeks on air-liquid interface culture until they are well-ifferentiated. Then the cells were inoculated with SARS-CoV-2 (G614D strain) apically at MON=0.5 for two hours. Cell lysates for bulk RNA-seq were obtained at 1-, 3- 7- and 14-day post inoculation from mock- and virus-inoculated cutures.
All samples from GSE210223, which came from 14 donors, were combined with additional samples from 9 donors (GSE299837), and were processed together from the raw FASTQ files to generate combined processed gene expression data and were analyzed as a whole set, which achieved balanced design with regard to age group, and sex. All final statistical analysis of the combined data included batch as a covariate. Therefore, all samples from GSE210223 were re-used in this study.

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

first: Caitlin

middle: E

last: Edwards

first: Takafumi

last: Kato

first: Boris

last: Reidel

first: Camille

last: Ehre

first: Rita

middle: M

last: Meganck

first: Yu

last: Mikami

first: Takanori

last: Asakura

first: Padraig

last: Hawkins

first: Charles

middle: R

last: Esther Jr

first: Minako

last: Furusho

first: Jeffrey

last: Myers

first: Kristine

last: Konopka

first: Raymond

middle: J

last: Pickles

first: Sabra

last: Klein

first: Scott

last: Randell

first: Wanda

last: O'Neal

first: Ralph

last: Baric

first: Richard

last: Boucher


title: Longitudinal liquid biopsy identifies an early predictive biomarker of immune checkpoint blockade response in head and neck squamous cell carcinoma [bulk RNA-seq]

first: Binbin

last: Wang

overall_design: We employed our previously characterized 4MOSC carcinogen-induced orthotopic HNSCC preclinical model to evaluate immune dynamics during ICB therapy. Two cohorts of mice were used, with one cohort comprising 45 mice for bulk RNA sequencing (RNA-seq) and the other comprising 16 mice for single-cell RNA sequencing (scRNA-seq) and single-cell TCR sequencing. Lesions developed consistently at expected time points. Blood samples were collected at four key intervals: pre-treatment (Day 4) and three on-treatment time points (Days 9, 17, and 24), aligned with the administration of anti-PD-1 therapy. Tumor growth and immune responses were monitored longitudinally to assess treatment efficacy. Bulk RNA-seq provided an overview of immune dynamics in the larger cohort, while scRNA-seq and scTCR sequencing in the smaller cohort delivered high-resolution insights into immune repertoire changes, supporting the study’s focus on peripheral immune biomarkers for predicting ICB outcomes.

first: Robert

last: Saddawi-Konefka

first: Lauren

last: Clubb

first: Shiqi

last: Tang

first: Di

last: Wu

first: Sumit

last: Mukherjee

first: Sahil

last: Sahni

first: Saugato

last: Rahman-Dhruba

first: Xinping

last: Yang

first: Sumeet

last: Patiyal

first: Chi-Ping

last: Day

first: Parth

last: Desai

first: Clint

last: Allen

first: Kun

first: Silvio

last: Gutkind

first: Eytan

last: Ruppin


title: ULK1 as a novel therapeutic target in Myeloproliferative Neoplasms

first: Elizabeth

last: Bartom

overall_design: HEL cells were treated with either vehicle (DMSO), 5mM of ULK101 or 5mM of SBI-0206965 for 4 hours and assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed.

first: Diana

last: Saleiro

first: Leonidas

last: Platanias


title: INSM1 governs a neuronal progenitor state that drives glioblastoma in a human stem cell model

city: Saint Louis

first: Patrick

last: DeSouza

state: MO

address: 4515 McKinley Ave.

department: Neurosurgery

institute: Washington University School of Medicine

summary: Glioblastoma (GBM) is an aggressivea lethal brain tumorcancer marked by functional plasticity driven by the interplay between tumor cell-intrinsic mutations and -extrinsic heterogeneity, enabling rapid evolutiontheir interplay with developmental programs. To investigate how canonical GBM glioblastoma mutations promote functional plasticity, we have developeded an isogenic human neural stem cell (NSC) model of glioblastoma GBM by sequential addition of TERT promoter, TP53, and PDGFRA point mutations. TP53 loss-of-function increasesd TERT TERT expression during serial mutagenesis, but only triple mutant NSCs reliably formed lethal brain tumors in vivo that recapitulate glioblastomaGBM. Tumor cell evolution triggersed stress-related metabolic changes and transitionsed toward a neuronal progenitor network driven by transcription factor INSM1. INSM1 is highly expressed in human glioblastoma GBM tumors and, during cortical development, in intermediate progenitor cells (IPC), which give rise to neurons. Remarkably, INSM1 knockdown in triple mutant NSCs and primary glioblastoma GBM cells disrupted disrupts oncogenic gene expression and function and inhibited inhibits the in vivo tumorigenicity of triple mutant NSCs, highlighting the functional importance of an intermediate progenitor cellIPC-like cell state in glioblastoma GBM pathogenesis.

overall_design: Proneural in vitro serial mutagenesis scRNA-seq: H1 human embryonic stem cells (hESCs) were CRISPR edited to create single mutant TERTp C228T and double mutant TERTp+TP53 G743A hESCs. Cells exposed to CRISPR reagents but non-mutagenized were wildtype (WT) controls. WT, single, and double mutant hESCs were differentiated to neural stem cells and transduced with empty vector or mutPDGFRA D842V expression construct to create 4 Proneural genotypes: WT, single mutant TERTp, double mutant TERTp+TP53, and triple mutant TERTp+TP53+mutPDGFRA (PRO) engineered neural stem cells (eNSCs). Proneural genotypes were uniquely labeled with hashtag oligos (HTOs) and pooled for multiplexed scRNA-seq. Proneural in vitro multiomic scRNA+scATAC-seq: 2 biological replicates (independent differentiation, same genetic clone) of WT and PRO eNSCs were profiled for joint gene expression and chromatin accessibility at single cell resolution. Each condition was submitted independently for sequencing. Proneural in vivo scRNA-seq: PRO eNSCs were intracranially xenografting in the striatum of athymic nude mice, which formed tumors and caused animal death within 109 days. Tumors harvested from 3 mice (mouse-35, mouse-38, mouse-42) 100 days post-injection were dissociated into single cells and tumor cells were isolated by FACS for double human nuclear antigen+/CD45- populations. Tumors cells from each mouse were submitted independently for scRNA-seq. PRO eNSC in vitro RNAi scRNA-seq: PRO eNSCs were transduced with two independent RNA inhibition (RNAi) lentivirus constructs targeting transcription factors INSM1, TCF4, or SOX4, versus non-target control plasmid. For each gene, RNAi conditions (shCtrl vs. 2x RNAi) were uniquely labeled with HTOs and pooled for multiplexed scRNA-seq, resulting in 3 datasets with 3 samples each.

first: Jeffrey

last: Millman

first: Albert

last: Kim


title: Spatial joint profiling of DNA methylome and transcriptome in tissues

city: Philadelphia

first: Hongxiang

last: Fu

state: PA

address: 3501 Civic Center Blvd

institute: University of Pennsylvania

summary: We introduce a high-resolution, genome-wide co-mapping technology that spatially resolves DNA methylation and transcriptome profiles simultaneously. This method combines microfluidic deterministic barcoding strategy to analyze DNA methylation and gene expression on the same tissue section at the cellular level.

overall_design: Gene expression and DNA methylation spatial profiling through high throughput sequencing of four mouse C57 embryos at E11 & E13 and one P21 juvenile mouse brain tissue.

first: Chin

middle: N

last: Lee

first: Angelysia

last: Cardilla

first: Wanding

last: Zhou

first: Yanxiang

last: Deng


title: De Novo Pyrimidine Synthesis Is a Collateral Metabolic Vulnerability in NF2-deficient Mesothelioma

city: Nanjing

first: Tong

last: Hu

address: No. 300 Guangzhou Road

institute: Nanjing Medical University

summary: Pleural mesothelioma (PM) is one of the deadliest cancers, with limited therapeutic options due to its therapeutically intractable genome, which is characterized by the functional inactivation of tumor suppressor genes (TSGs) and high tumor heterogeneity, including diverse metabolic adaptations. However, the molecular mechanisms underlying these metabolic alterations remain poorly understood, particularly how TSG inactivation rewires tumor metabolism to drive tumorigenesis and create metabolic dependencies. Through integrated multi-omics analysis, we identify for the first time that NF2 loss of function defines a distinct PM subtype characterized by enhanced de novo pyrimidine synthesis, which NF2-deficient PM cells are critically dependent on for sustained proliferation in vitro and in vivo. Mechanistically, NF2 loss activates YAP, a downstream proto-oncogenic transcriptional coactivator in the Hippo signalling pathway, which in turn upregulates CAD and DHODH, key enzymes in the de novo pyrimidine biosynthesis pathway. Our findings provide novel insights into metabolic reprogramming in PM, revealing de novo pyrimidine synthesis as a synthetic lethal vulnerability in NF2-deficient tumors. This work highlights a potential therapeutic strategy for targeting NF2-deficient mesothelioma through metabolic intervention.

overall_design: RNA-seq profiling of wild-type and NF2-kockout(KO) H2452 mesothelioma cells.

first: Duo

last: Xu


title: Tetrandrine regulates the gut microbiota-associated CYP51 metabolism and improves cognitive dysfunction in SAH rats through the TLR4/NF-κB pathway

city: Hengyang

first: Rui

last: Chen

address: No. 336 Dongfeng Road

institute: Nanhua Hospital Affiliated to University of South China

summary: Tet restored gut microbiota imbalance in SAH rats

overall_design: Considering that Tet improved cognitive function in SAH rats, potentially involving the gut microbiota, fecal samples were collected to determine differences in gut microbiota composition among the experimental groups.

first: Huan

last: Liu

first: Qin

last: Zou

first: Tao

last: Xiang

last: Zhu

first: Zigui


title: An Open-Source QIIME2 and R Pipeline for Multi-Amplicon 16S rRNA Profiling: Validation and Application in Pediatric Microbiome Studies

status: Public on Jul 14 2025

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: This study presents a validated, open-source QIIME2- and R-based pipeline for 16S rRNA gene profiling using multi-amplicon sequencing. It aims to overcome the limitations of commercial, closed-source tools by offering a standardized and reproducible workflow. The pipeline was benchmarked against proprietary software using five mock communities and 12 child–caregiver fecal sample pairs, showing nearly identical microbial profiles, greater sequencing depth, and improved taxonomic resolution. High reproducibility (R = 0.99, p < 0.0001) was achieved across all datasets. Application to pediatric cancer samples revealed distinct Bifidobacterium variants in children whose microbiota closely matched their caregivers’. This highlights the pipeline’s utility in studying microbial relationships. Overall, the pipeline supports transparent, adaptable, and accurate microbiome analysis, advancing research in both clinical and experimental settings while promoting open-source solutions for reproducible science.

overall_design: The experimental design included sequencing five mock microbial communities and 12 fecal sample pairs from pediatric cancer patients and their caregivers. A multi-amplicon approach (V2–9) was used with semiconductor-based sequencing. Data were analyzed using both the newly developed open-source pipeline and commercial software for benchmarking and a validation set of fecal specimens from 90 cases.


title: Chromatin factor YY1 controls fetal hematopoietic stem cell migration and engraftment in mice [CUT&Tag]

status: Public on Jul 11 2025

city: Madison

first: Xuan

last: Pan

state: WI

address: 4470 Veterinary Medicine Building

institute: University of Wisconsin

summary: Fetal liver is a major organ for generating hematopoietic stem cells (HSCs) during embryonic development. Many questions remain unanswered regarding how transition of hematopoiesis from the fetal liver to the bone marrow (BM) is regulated. We demonstrate that mammalian Polycomb Group (PcG) protein Yin Yang 1 (YY1) is required for this transition, as a conditional knockout of Yy1 in the hematopoietic system during fetal development results in exhaustion of fetal HSC pools and neonatal death. Yy1 deficient fetal HSCs have diminished capacity to migrate to and engraft the adult BM, and consequently fail to reconstitute blood. YY1 deficiency leads to distinct transcriptomic changes in fetal hematopoietic stem progenitor cells (HSPCs) compared with adult HSPCs. The genetic networks governing cell motility and adhesion are distinctly deregulated by YY1 in fetal HSPCs. Notably, YY1 regulates mobility of fetal HSPCs largely through an indirect mechanism as it does not directly bind to the promoters of dysregulated genes involved in control of  mobility. Instead, it regulates broader transcriptional mechanisms by modulating the genes in chromatin remodeling complexes that impact HSPC mobility. Our study provides a framework to further decipher how temporal epigenomic configurations determine HSC fetal-to-adult transition during development.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) targetting Yin Yang 1 (YY1) in E14.5 fetal liver Lin- cells. Trimethylation of Histone H3 at Lysine 4 (H3K4me3) was used as positive controls. To ensure reproducibility, four biological replicates were obtained to determine YY1 binding.


title: CRISPR screens identify EXO1 as a therapeutic target for cancers with Fanconi anemia pathway and BRCA1-A complex deficiencies [PM20138]

city: London

first: Simon

last: Boulton

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: EXO1 is a conserved multi-functional exonuclease that performs roles in mismatch repair, homologous recombination, nucleotide excision repair, translesion DNA synthesis, resection of stalled replication forks and processing of Okazaki fragments. However, EXO1 loss is well tolerated, suggesting the existence of compensatory mechanisms that could be exploited therapeutically in DNA damage repair (DDR) deficient cancers. Using CRISPR screening, we find that EXO1 loss is synthetic lethal with many somatically inactivated DDR genes identified as frequent vulnerabilities in cancers, including Fanconi anemia (FA) pathway and BRCA1-A complex genes. We also identify the spliceosome factor and tumour suppressor ZRSR2 as synthetic lethal with loss of EXO1 and show that ZRSR2-deficient cells are attenuated for FA-pathway activation, exhibiting cisplatin sensitivity and radial chromosome formation, which we attribute to discreet splicing defects that compromise FA pathway genes. Finally, we show that vulnerabilities caused by mutations in FA or ZRSR2 genes depend on the catalytic activity of EXO1 and can be further sensitised in combination with either PARP inhibitors or ionising radiation. Altogether, we establish the rationale for development of EXO1 inhibitors for treatment across a broad spectrum of cancers with distinct DDR vulnerabilities, which are not effectively targeted with current therapeutic approaches.

overall_design: To investigate synthetic lethal interactions with EXO1 loss, we performed a genome-wide CRISPR-Cas9 dropout screen. Wild type and EXO1 KO cell lines were transduced with Brunello library from Addgene containing sgRNAs targeting 19114 genes, with 4 sgRNAs per gene, and with 1000 non-targeting sgRNAs. Transductions (performed in a biological triplicate on cells that were passaged separately through expansion) were achieved through transduction of 100 x 10^6 cells in 12 well plates at MOI of 0.4 for 500x representation of each sgRNA (titer required for both cell lines was determined prior to experiment). Cells with viruses were spun at 290 x g for 90 minutes at 37 degrees. The following day cells were trypsinised to transfer into 5-layer flasks and puromycin was added for selection. 40 x 10^6 cells for each replicate was passaged onwards every two days to ensure that sgRNA representation is maintained. Replicates were then treated with doxycycline (1ug/ml final concentration) for 6 days. Samples were collected at day 6 and day 16 for library preparation and sequencing (harvesting 60 x 10^6 cells per sample). Genomic DNA was extracted with the PureLink Genomic DNA Mini Kit (Invitrogen; 16 columns per sample). 200ug gDNA was used for PCRs with Ex Taq polymerase (TaKaRa) to prepare sgRNA amplicon libraries following Broad Institute’s protocol with P5 mix of oligos and barcoded P7 oligos. Libraries (sgRNA amplicons) were gel purified with QIAquick Gel Extraction Kit (QIAGEN), followed by MinElute PCR Purification kit (QIAGEN) for buffer exchange, and analysed with Agilent 2100 Bioanalyzer.

first: Marija

last: Maric

first: Harshil

last: Patel


title: Transcriptomic analysis of the planktonic growth of Streptococcus pneumoniae serotype 1 reveals serotype-specific gene regulation

city: Dublin

first: Karsten

last: Hokamp

state: Dublin

address: Stephen's Green

department: Genetics

country: Ireland

institute: Trinity College Dublin

summary: Streptococcus pneumoniae is an opportunistic pathogen that colonizes the mucosal surfaces of the human upper respiratory tract. To the exception of very few studies, all previous transcriptomic analyses on the pneumococcus were carried out using lab-adapted strains such as D39 or TIGR4. Our study is one of the first to investigate the transcriptomes of serotype 1 (S1) pneumococci. We took the most basic approach of growing S. pneumoniae in brain heart infusion medium using three distinct strains, i.e. sequence type ST306, ST217 and ST615, as representative isolates of the European, African and South American S1 clusters. As a follow-up to our recent studies on these three lineages, we sought to investigate their respective in vitro transcriptomic profiles in comparison to D39. In total, 292 genes showed significant differential expression in the exponential growth phases of all three S1 isolates compared to D39. A total of 151 genes showed higher transcription levels while 141 genes presented lower expression. The most prominent functional groups showing higher expression included the competence pathway and purine metabolism, while lactose metabolism and iron/amino acid transport presented lower expression in serotype 1 strains. Our study provides novel insight into the signature gene expression associated with hypervirulent pneumococci S1 and highlight the need to perform transcriptomic analysis on pneumococcal strains other than lab-adapted strains.

overall_design:
To investigate the Streptococcus S1-specific transcriptional profile we carried out RNA-seq on three S1 strains and one S2 strain over different growth stages and compared the exponential phase samples.

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

first: Pongchaikul

last: Pisut

first: Hokamp

last: Karsten

first: Yahya

last: Reham

first: Bricio-Moreno

last: Laura

first: O'Brien

last: Marie

first: Kadioglu

last: Aras


title: Lentiviral Vectors for Hematopoietic Stem Cell Gene Therapy Restore α-Globin Expression in  α-Thalassemia Red Blood Cells

status: Public on Jul 10 2025

city: Los Angeles

first: Eva

last: Segura

address: Terasaki Life Sciences Building, Room 3163

department: Department of Microbiology, Immunology & Molecular Genetics

institute: University of California, Los Angeles

summary: Alpha thalassemia major (ATM) is an inherited blood disorder caused by the absence of all four α-globin genes (HBA2/1), resulting in severe anemia and lifelong transfusion dependence. While allogeneic hematopoietic stem cell transplant (HSCT) offers a potential cure, donor availability remains limited. We present a gene therapy approach for autologous HSCT, using lentiviral vectors (LVs) to deliver HBA2 under the regulation of optimized β-globin locus control region (LCR) enhancers, restoring α-globin expression. The best-performing LVs, EV-α and EV-α-UV, achieved 90-100% transduction efficiency in human hematopoietic stem and progenitor cells (HSPCs), optimal vector copy numbers, and a safe integration profile. ATM-derived HSPCs from three donors treated with these LVs yielded α/β-globin mRNA and chain ratios within the therapeutic range (~0.5+), and restored hemoglobin levels by 50 to 100%. These findings establish the safety and clinical potential of EV-α and EV-α-UV as a promising autologous stem cell gene therapy for ATM.

overall_design: Erythroid cells differentiated from bone marrow derived hematopoietic stem and progenitor cells from 2 healthy donors and 1 donor with alpha thalassemia major. Some conditions from the alpha thalassemia major cells were transduced with different alpha globin lentiviral vectors desgined and produced in our laboratory.

first: Kevyn

last: Hart

first: Beatriz

last: Campo Fernandez

first: Devin

last: Brown

first: Kevin

last: Tam

first: Andrea

last: Guiterrez Gracia

last: Seigneurbieux

first: Karen

last: Li

first: Emma

last: Blakely

first: Katelyn

last: Masiuk

first: Roshani

last: Sinha

first: Devesh

last: Sharma

first: John

last: Everett

first: Matthew

last: Hogenauer

first: Kyle

last: Cromer

first: Frederick

last: Bushman

first: Tippi

last: MacKenzie

first: Donald

middle: B

last: Kohn


title: Combined aerobic and resistance exercise training alters the spatial transcriptome of skeletal muscle in young adults

city: Tarrytown

first: Michael

last: Stec

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

summary: Chronic exercise training substantially improves skeletal muscle function and performance. The repeated demands and stressors of each exercise bout drive coordinated molecular adaptations within multiple cell types in muscle tissue, leading to enhanced neuromuscular recruitment and contractile function, stem cell activation, myofiber hypertrophy, mitochondrial biogenesis, and angiogenesis, among others. To comprehensively profile molecular changes induced by combined resistance and endurance exercise training, we employed spatial transcriptomics coupled with immunofluorescence and computational approaches to resolve effects on myofiber and mononuclear cell populations in human muscle. By computationally identifying fast and slow myofibers using immunofluorescence data of spatially sequenced tissue sections, we identified fiber type-specific, exercise-induced gene expression changes that correlated with muscle functional improvements. Additionally, spatial transcriptome profiling and integration of human muscle single cell RNAseq data identified an exercise-induced shift in interstitial cell populations coincident with angiogenesis. Overall, these data provide a unique spatial molecular profiling resource for exploring muscle adaptations to exercise, and provide a pipeline and rationale for future studies in human muscle.

overall_design: Sendentary and chronic exercise skeletal muscle samples from five health young donors

first: Miachel

first: Zachary

last: Graham

first: Qi

last: Su


title: CUT&RUN of the kidneys from diabetic mice with MAT2A inhibitor I

status: Public on Jul 09 2025

first: Yalu

last: Zhou

address: 303 E Superior St

department: Department of Medicine

institute: Northwestern University

summary: H3K27me3 was enhanced in the gene loci related to the inflammatory pathway.

overall_design: SGTL2 WT and MT mice were fed with HFD for 18 weeks.

first: Hiroshi

last: Maekawa

first: Yuki

last: Aoi


title: Gene expression profile at single cell level of kidney from Sglt2 WT and mutant mice fed with normal diet and high-fat diet.

summary: Analysis of scRNA seq data showed emergence of a new cluster of proximal tubular cells with a distinct molecular fingerprint, predominantly found in WT-HFD mice.

overall_design: SGLT2 MT and WT mice (10 weeks old) were fed with fed with high fat diet (60% Cal) or normal diet for 8 weeks.

first: Margaret

last: Fain

first: Susan

last: Quaggin


title: Bulk RNAseq of the kidneys from diabetic mice with MAT2A inhibitor

summary: These analysis detected the Loci of genes regulated in a SAM-dependent manner.

overall_design: SGTL2 WT and MT mice were fed with HFD for 8 weeks, then they were treated with placebo (DMSO) or (E)-4-(2-Chloro-6-fluorostyryl)-N-methylaniline (MAT2Ai, 10 mg/kg BW) through the intraperitoneal route three times per week for 8 weeks.


title: Diabetic mice with MAT2A inhibitor

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

overall_design: Refer to individual Series


title: Integration of multiomics reveals the mechanism of Lycium barbarum polysaccharides inhibit MCF-7 cell proliferation

city: Ningxia

first: feng

middle: xu

last: fu

address: Shengli Street

institute: Ningxia Medical University

summary: Background：Breast cancer, as a highly prevalent malignant tumor among women, has a consistently high mortality rate due to metastasis and drug resistance. Lycium barbarum polysaccharides (LBP), which have been reported to have significant anti-tumor activity, have not yet had their molecular mechanism and signaling pathways against breast cancer clearly defined. Methods and Results：In this study, the CCK-8 assay determined that treatment with 8 mg/mL LBP for 48 h was the optimal condition for subsequent multi-omics analysis. The results demonstrated that a high concentration of LBP significantly reduced the viability of MCF-7 cells and inhibited cell proliferation. Transcriptome sequencing revealed that LBP markedly altered the expression levels of the genes HO-1, FTH1, FTL, and TFRC. Metabolomics analysis further indicated that LBP significantly impacted glutathione metabolism, glycerophospholipid metabolism, and the alanine-aspartate-glutamate metabolic pathway. Further integration of transcriptomic and metabolomic data suggests that LBP may suppress cell proliferation by activating the ferroptosis pathway via the NRF2/HO-1 axis. To further validate this hypothesis, we conducted additional experiments to detect the NRF2/HO-1 signaling pathway and markers associated with ferroptosis. The results demonstrated that LBP treatment significantly upregulated the expression of NRF2 and its downstream effector molecule HO-1. Moreover, the specific NRF2 inhibitor ML385 was able to reverse the alterations in GSH, Fe2+, and MDA levels induced by LBP. Conclusion：In conclusion, our research results indicate that LBP induces ferroptosis by activating the NRF2/HO-1 signaling pathway.

overall_design: RNA-seq profiling of MCF-7 cells and MCF-7 cells treated with LBP(8 mg/mL).

first: Li

middle: y

last: Ding

first: Yi

middle: t

last: Shang

first: Zhen

last: Zhang

first: Hong

last: Yang

first: Yu

last: Deng

first: Tian

last: He

first: Guo

middle: q

first: Jia

middle: x

last: Ma

first: Xu

middle: f

last: Fu

first: Xing

last: Du


title: CUT&RUN of the kidneys from diabetic mice with MAT2A inhibitor II

overall_design: MAT2Ai (10 mg/kg BW) was injected into intraperitoneal cavity of SGLT2 MT mice with prior exposure to HFD for eight weeks.


title: CRISPR screens identify EXO1 as a therapeutic target for cancers with Fanconi anemia pathway and BRCA1-A complex deficiencies [PM22329]

first: Simon

last: Boulton

overall_design: To investigate drivers of synthetic lethal interactions between EXO1 and FANCG or EXO1 and ZRSR2, we performed genome-wide CRISPR rescue screens. eHAP iCas9 EXO1 KO cells, that were previously transduced with Brunello library in triplicate for the dropout screen and frozen, were recovered and transduced with lenti-sgRNA-Hygro with sgRNAs for either FANCG or ZRSR2 or non-targeting control (at MOI of 1 based on predetermined titer). Transduced cells were selected with hygromycin and Cas9 expression was induced with doxycycline. Cells were passaged every 2-3 days (keeping 40 x 10^6 cells representation) and samples were collected 10 days after Cas9 expression induction. Genomic DNA was extracted with the PureLink Genomic DNA Mini Kit (Invitrogen; 16 columns per sample). 200ug gDNA was used for PCRs with Ex Taq polymerase (TaKaRa) to prepare sgRNA libraries following Broad Institute’s protocol with P5 mix of oligos and barcoded P7 oligos. Libraries (sgRNA amplicons) were gel purified with QIAquick Gel Extraction Kit (QIAGEN), followed by MinElute PCR Purification kit (QIAGEN) for buffer exchange, and analysed with Agilent 2100 Bioanalyzer.

first: Marija

last: Maric

first: Tyler

last: Stanage


title: Comparative Evaluation of miRNA Detection in Plasma, Urine, and Liquid-Based Cytology (LBC) for High-Grade Cervical Intraepithelial Neoplasia

status: Public on Jul 08 2025

city: Barretos

first: Stéphanie

last: Calfa

state: São Paulo

address: Antenor Duarte Viléla, 1331 - Dr. Paulo Prata

country: Brazil

institute: Barretos Cancer Hospital

summary: We profiled 798 miRNAs using NanoString technology in plasma, urine, and liquid-based cytology (LBC) from 24 women with and without high-grade cervical lesions (CIN2/3). LBC showed the highest detection efficiency and consistency, with the lowest proportion of low-count miRNAs and the highest expression levels, supporting its utility as the most effective specimen type for miRNA-based screening.

overall_design: In the study presented here, matched plasma, urine, and liquid-based cytology (LBC) samples were collected from 24 women—12 with high-grade cervical intraepithelial neoplasia (CIN2/3) and 12 controls. Expression profiling of 798 miRNAs was performed using the NanoString nCounter Human v3 miRNA panel to compare detection performance across specimen types.

first: Ana Julia

middle: A

last: Freitas

first: Welinton

last: Hirai

first: Rhafaela

middle: L

last: Causin

first: Júlio César

last: Possati-Resende

first: Ricardo

last: Reis

first: Rui

first: Márcia Maria

middle: C

last: Marques


title: CRISPR screens identify EXO1 as a therapeutic target for cancers with Fanconi anemia pathway and BRCA1-A complex deficiencies


title: Deep indel mutagenesis reveals the regulatory and modulatory architecture of alternative exon splicing

city: Heidelberg

first: Pablo

last: Baeza Centurion

address: Im Neuenheimer Feld 580

institute: DKFZ

summary: Altered splicing is a frequent mechanism by which genetic variants cause disease. However, the regulatory architecture of human exons remains poorly understood, making the therapeutic modulation of splicing in disease challenging. Here we show that deep indel mutagenesis (DIM) provides an efficient strategy to chart the regulatory landscape of human exons and to rapidly identify effective splice-modulating oligonucleotides. DIM defines a minimal exon length, uncovers a mechanism for the evolutionary birth of unusually short microexons and the repression of transmembrane domain-encoding exons, and reveals a checkerboard architecture of sequential enhancers and silencers in a model alternatively spliced exon. Accurate prediction of the effects of deletions using deep learning provides a resource, DANGO, that maps the splicing regulatory landscape of all human exons and predicts effective splice-altering antisense oligonucleotides genome-wide.

overall_design: Deep insertion-deletion mutagenesis of a model human alternatively-spliced exon (FAS exon 6).

last: Baeza-Centurion

first: Belén

last: Miñana

first: Andre

last: Faure

first: Mike

last: Thompson

first: Sophie

last: Bonnal

first: Ben

last: Lehner

first: Juan

last: Valcárcel


title: Spatiotemporal profiling reveals the impact of caloric restriction in the aging mammalian brain

city: New York

first: Zehao

last: Zhang

address: 1230 York Ave, The Rockefeller University

institute: The Rockefeller University

summary: Aging induces functional declines in the mammalian brain, increasing its vulnerability to cognitive impairments and neurodegenerative disorders. Among various interventions to slow aging and delay age-related diseases, caloric restriction (CR) consistently extends lifespan across species. However, the specific molecular and cellular mechanisms through which CR benefits the aging brain remain unclear. In this study, we performed spatiotemporal profiling of mouse brains to uncover detailed mechanisms underlying the anti-aging effects of CR. We analyzed the transcriptional states of over half million single cells from mouse brain samples across various ages and in response to CR treatment. Monitoring the dynamics of over 300 transcriptionally distinct cellular states, we captured the temporal dynamics of cellular states particularly vulnerable to aging and those rescued by CR (e.g., CR delays the expansion of inflammatory glia and preserves neurogenesis cells). Further spatial transcriptome analysis revealed gene expression and cellular dynamics across brain regions in aged mice upon CR treatment, uncovering region-specific anti-aging effects. In summary, our spatiotemporal mouse brain profiling delineated highly cell-type-specific molecular pathways in response to aging and CR, shedding light on the nuanced regulatory roles of CR across different cell types and brain regions.

overall_design:
Single nucleus RNA-seq profiling for caloric restricted and ad libitum C57BL/6 mouse brain cells at 12,18,24 months.
Spatial transcriptomic profiling for caloric restricted and ad libitum C57BL/6 mouse brain cells at 24 months.

first: Alexander

last: Epstein

first: Chloe

last: Schaefer

first: Abdulraouf

last: Abdulraouf

first: Weirong

last: Jiang

first: Wei

last: Zhou

first: Junyue

last: Cao


title: Comparing gene expression effects of Hnrnpf knockout in mESCs while they are pluripotent vs. after they have been differentiating for 4 days due to LIF removal [RNA-seq]

city: tianjin

first: Duan

middle: Xiao

last: wei

address: China

institute: Nankai

summary: The ERK (extracellular signal-regulated kinase) signaling pathway plays a crucial role in maintaining the self-renewal and regulating the differentiation of mouse embryonic stem cells (ESCs). However, the underlying mechanisms by which ERK exerts these effects remain incompletely understood. In this study, we identified heterogenous nuclear ribonucleoprotein F (HNRNPF) as a novel ERK2-interacting protein and phosphorylation substrate. We demonstrated that ERK2 phosphorylates HNRNPF on Ser346 and Tyr356. Hnrnpf knockout (KO) ESCs manifested impaired self-renewal, due to downregulation of CDK1 and CCNB1. Notably, phosphorylation of HNRNPF rescued CDK1 and CCNB1 expression, leading to restoring self-renewal capacity of Hnrnpf KO ESCs. Additionally, loss of HNRNPF promoted ESC differentiation toward mesoderm and trophectoderm lineages, a phenotype attributed to reduced EED expression and diminished H3K27me3 levels. Phosphorylation of HNRNPF restored EED expression and H3K27me3 levels, thereby mitigating differentiation bias in Hnrnpf KO ESCs. Collectively, our findings uncover a critical role for HNRNPF as a downstream effector of ERK2 signaling in regulating ESC self-renewal and differentiation.

overall_design: To evaluate the differentiation potential of Hnrnpf KO ESCs, we performed RNA sequencing (RNA-seq) to profile global transcriptional changes in both differentiated and undifferentiated ESCs following HNRNPF deletion.

first: Xiaowei

last: Duan

first: Lingyi

last: Chen


title: Comprehensive analysis of microRNA expression provides mechanistic insights into transcriptomic alteration in primary and metastatic testicular germ cell tumors

city: Baltimore

first: Taibo

last: Li

address: 1830 E Monument Street, Suite 2-300

institute: Johns Hopkins School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNA (miRNA) dysregulation is implicated in testicular germ cell tumor (TGCT) pathogenesis. Here, we characterized miRNA expression profiles across TGCT histologic subtypes using miRNA-sequencing on 43 formalin-fixed paraffin-embedded (FFPE) tissue samples (30 primary, 13 metastases) from 32 patients to identify diagnostic markers and their regulatory functions. From 20 seminomas (SEM), 14 non-seminomatous germ cell tumors (N-SEM), and 9 teratomas, we profiled a total of 2,606 miRNAs. Compared to teratomas, 154 miRNAs (targeting 657 genes) were enriched in SEM, and 141 miRNAs (targeting 358 genes) in N-SEM. miR-200-3p, targeting the DNA methyltransferase DNMT3B, was enriched in N-SEM versus SEM. Our findings showed high concordance with The Cancer Genome Atlas (TCGA)-TGCT data (Pearson R > 0.66, p < 1e-10). miRNA expression was largely similar between primary and metastatic tissues and between chemotherapy-treated and untreated teratomas, reflecting teratoma chemo-resistance. Using novel candidates, miRNA-based logistic regression classifiers distinguished viable GCT (SEM/N-SEM) from teratoma (Area Under the Curve [AUC] > 0.99) and SEM from N-SEM (AUC = 0.99), outperforming well-known miRNA markers. Target gene analysis implicated FOXO and RUNX1 regulation, somatotroph signaling, and height-related pathways. Overall, our comprehensive tissue-level miRNA profiling in TGCTs identified potential diagnostic biomarkers for histologic subtypes, offering insights into miRNA-mediated transcriptional dysregulation.

overall_design: miRNA-seq of 43 formalin-fixed paraffin-embedded (FFPE) tissue samples from 32 patients (30 primary, 13 metastases) with testicular cancer

first: Anirudh

last: Yerrapragada

first: Stephan

last: Bronimann

first: Carlos

last: Rivera Lopez

first: Joseph

last: Cheaib

first: Yasser

last: Ged

first: Ezra

last: Baraban

first: Shawn

last: Lupold

first: Nirmish

last: Singla


title: Differential gene expression in mouse liver with lamin A/C KO in adipocytes

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Lmna mutations can result in lipodystrophic syndromes including fat atrophy (lipoatrophy) and metabolic alterations resulting from insulin resistance (glucose tolerance abnormalities, dyslipidemia, non-alcoholic fatty liver disease).

overall_design: RNA-seq profiling of female mouse liver with Lmna-KO genotype treated with vehicle (6 replicates), Lmna-KO genotype treated with rescue (8 replicates),  Lmna-WT genotype treated with vehicle (7 replicates), Lmna-WT genotype treated with rescue (3 replicates)

first: Ormond

last: MacDougald

first: Jessica

last: Maung


title: Comprehensive profiling of RNAs enriched in small extracellular vesicles of colorectal cancer patients

status: Public on Jul 07 2025

city: Brno

first: Robin

last: Jugas

address: Kamenice 5

country: Czech Republic

institute: CEITEC MU

summary:
The main objective of this project was to determine RNA expression profiles in small extracellular vesicles isolated from low volumes of blood serum of colorectal cancer (CRC) patients and to compare the data with those of healthy controls (HC) in order to identify molecules (mainly lncRNAs and protein-coding genes) that could serve as novel non-invasive biomarkers for early diagnosis of CRC.
In total, we have identified 4,014 transcripts to be differentially expressed between two studied groups (adjusted P < 0.05). From those, 1,469 were assigned to lncRNAs (36.6%), while protein-coding genes represented the second most common gene biotype (1,166 transcripts; 29%). The hierarchical clustering proved that it is possible to distinguish CRC samples from HC based on the expression of all significantly deregulated genes as well as protein coding genes and lncRNAs, separately or in combination. As this study was primarily focused on lncRNAs, more stringent criteria concerning several different parameters were set to identify lncRNAs with the highest potential to discriminate the two groups of samples. In total, we got 21 molecules, which met our requirements and thus were chosen for further evaluation in the training phase of the study by RT-qPCR.

overall_design: In total, 150 samples were involved in the study including 100 serum samples of CRC patients and 50 serum samples of HC. No replicates were involved.

first: Petra

last: Vychytilova-Faltejskova

first: Lucie

last: Pifkova

first: Tina

last: Catela Ivkovic

first: Milana

last: Sachlova

first: Ondrej

last: Slaby


title: Targeting VRK2 Enhances the Efficacy of Anti-PD-1 Therapy in Hepatocellular Carcinoma by Reducing Direct Phosphorylation and Stability of MYC，CUT-TAG sequencing for MYC in hepatocellular carcinoma cells [CUT&Tag]

city: Wuhan

first: chen

last: su

address: No. 1095, Jiefang Avenue

institute: Huazhong University of Science and Technology

summary: VRK2–MYC axis, a transcription-dependent regulatory axis, could be a prognostic indicator and potential therapeutic target in liver cancer.

overall_design: Cleavage Under Targets and Tagmentation (CUT&TAG) sequencing was then performed on MYC in cells from different treatment groups,

first: Chen

last: Su

first: Zhibin

last: Liao

first: Jie

last: Mo

first: Furong

last: Liu

first: Zhanguo

last: Zhang

first: Peng

last: Zhu

first: Bixiang


title: Nur77 induces GSDMC-mediated pyroptosis

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

summary: Pyroptosis is a type of lytic cell death executed by members of the gasdermin family. It has been demonstrated that induction of pyroptosis can effectively inhibit tumor growth, which implicates a new strategy for clinical tumor therapy, especially for those tumors (such as melanoma) that are insensitive or resistant to the induction of apoptosis.By means of a chemical compound DBIC, designed and identified by our group recently, to induce GSDMC-mediated pyroptosis in melanoma cells.

overall_design: To investigate the mechanism of pyroptosis induced by DBIC based on the fact that hemin inhibted DBIC-induced pyroptosis. We then performed gene expression profiling analysis data obtained from RNA-seq of four groups.Comparative gene expression profiling analysis of RNA-seq data for Ctrl, DBIC, Hemin and DBIC+Hemin.

first: Liu-zheng

last: Wu

first: Ya-ying

last: Huang

first: Hai-jing

last: Hu


title: Uncover the molecular mechanisms underlying HNRNPF functions in ESCs [RIP-seq]

first: Duan

last: wei

overall_design: To uncovered the molecular mechanisms underlying HNRNPF functions in ESCs, we conducted RNA immunoprecipitation (RIP) experiments followed by sequencing in the FLAG-tagged HNRNPF overexpressed (OE) cell line.

first: Xiaowei

last: Duan

first: Lingyi

last: Chen


title: The kinase PLK1 promote melanoma progression in the BRAFV600E/PTEN-deficient mouse

status: Public on Jul 06 2025

city: Lexington

first: Xiaoqi

state: KY

address: 760 Press Avenue, Research Building 2, Room 330

institute: University of Kentucky

summary: To investigate the role of PLK1 in melanoma progression, we introduced the overexpression of PLK1 to the BRAFV600E/PTEN-deficeint melanoma mouse model. After tumor induction, we harvested the tumors and performed the RNA-seq to analyze the expression profile of tumors from either cohort respectively.

overall_design: RNA-seq profilling of tumors from BrafCA/+ / Ptenloxp/loxp and BrafCA/+ / Ptenloxp/loxp / Plk1  mouse

first: Mao

last: Fengyi

first: Liu

last: Xiaoqi


title: INTESTINAL EPITHELIAL-DERIVED IL-34 REGULATES MACROPHAGE POLARIZATION AND GASTROINTESTINAL TRACT GRAFT VERSUS HOST DISEASE

city: Milwaukee

first: Anthony

middle: Elston

last: Zamora

state: Wisconsin

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Gastrointestinal (GI) tract graft versus host disease (GVHD) is a major complication after allogeneic hematopoietic stem cell transplantation (HSCT) and is attributable to dysregulation that occurs between the effector and regulatory arms of the immune system.  Whereas regulatory T cells have a primary role in counterbalancing GVHD-induced inflammation, identifying and harnessing other pathways that promote immune tolerance remains a major goal in this disease.  Herein, we have identified interleukin 34 (IL-34) as a tissue-intrinsic regulatory cytokine that is able to mitigate the severity of GVHD within the GI tract.  Specifically, we observed that absence of recipient IL-34 production exacerbated GVHD lethality, promoted intestinal epithelial cell death, and compromised barrier integrity.  Mechanistically, the absence of host IL-34 skewed donor macrophages towards a proinflammatory phenotype and augmented the accumulation of pathogenic CD4+ GM-CSF+ T cells within the colon.  Conversely, the administration of recombinant IL-34 significantly reduced GVHD mortality and inflammation in the GI tract which was dependent upon the expression of apolipoprotein E (ApoE) in donor macrophages.  Complementary genetic and imaging approaches demonstrated that intestinal epithelial cells were the biologically relevant source of IL-34.  Colonic biopsies from patients with GVHD also revealed expression of IL-34 in intestinal epithelial cells, as well as ApoE in lamina propria macrophages, validating similar cellular localization in humans.  Thus, these studies define IL-34 as an intestinal epithelial-derived cytokine that regulates macrophage polarization in an ApoE-dependent manner, positioning this cytokine as a key regulator of GVHD in the GI tract and a potential therapeutic target for amelioration of this disease.

overall_design: Cells were isolated from the colons of mice that were transplanted with Bone marrow (BM) alone or BM plus adjunctive spleen cells (GVHD). To delineate macrophage populations within colon microenvironment, scRNAseq was performed on sorted donor derived CD11b+ CD64+ macrophages from the colons of BM and GVHD mice. To define the effect of IL-34 on the regulation of macrophages, scRNAseq was performed on sorted donor CD11b+ CD64+ macrophages from the colons of WT and IL-34-/- transplant recipients. To address the question of whether IL-34 binding to CSF-1R on macrophages affects the emergenece of proinflammatory T cells in GVHD target organs, scRNAseq was performed on donor derived sorted T cells.

first: Aditya

last: Rayasam

first: Alison

last: Moe

first: Ravi

middle: K

last: Shah

first: Chengyin

last: Yuan

first: James

last: Miller

first: Mary

last: Rau

first: Mollie

last: Patton

first: Marco

last: Colonna

first: William

last: Drobyski


title: Regional differences in neonatal enterocytes

city: Durham

first: Staci

last: Bilbo

address: 207 Research Dr, GSRB2

department: Psychology and Neuroscience

institute: Duke University

summary: We report bulk scRNAseq data obtained from 2 P6 mice. Input was isolated epithelium cells of the small intestine in a 2cm segment of  the jejunum and 2 cm segment in the ileum of the same mouse, 1 male and 1 female were included in the analysis.

overall_design: A 2 cm segment of jejunum and ileum was isolated from the same mouse. The segments were incubated in EDTA to separate intestinal epthelial cells from the intestinal wall and then incubated in dispase to generate a single cell suspension. Cells were barcoded using PIP-Seq technology.

first: Carina

last: Block

first: Michel

last: Bagnat

first: Cagla

last: Eroglu

first: Kristina

last: Sakers


title: Effect of EGR1 on gene expression during SFTSV-infeced HUVECs

city: Nanjing

last: Jiang

address: Hankou Road

institute: Nanjing University

summary: During viral infections, EGR1 expression can facilitate either an anti-viral or pro-viral cellular state, depending on the virus and the transcriptional events regulated by EGR1. We here report that SFTSV infection could promote the EGR1 expression. Our observations revealed similar results to other studies, underscoring the biological relevance and general importance of EGR1 in viral infections.

overall_design: To determine the mechanism underlying the inducible expression of sVEGFR1，we performed a transcriptome analysis in SFTSV-infected or mock-infected HUVECs.

first: Zhiwei

last: Wu


title: Loss of NR2F6 reduces tissue-resident macrophages and protects from Salmonella typhimurium infection

city: Innsbruck

first: Johannes

last: Woelk

address: Peter-Mayr-Str. 1a

department: Cell Genetics

country: Austria

institute: Medical University of Innsbruck

summary: Nuclear receptors regulate key functions of mononuclear phagocytes and are critical components of the innate immune system, acting as regulators of organ health and disease. In healthy mice, NR2F6 deficiency alters tissue-resident macrophage populations in the liver, lung, and spleen. In response to Salmonella Typhimurium infection, mice deficient in the nuclear receptor NR2F6 exhibit improved clinical outcomes, characterized by reduced weight loss, bacterial loads in the spleen and liver, and decreased plasma pro-inflammatory cytokines. Despite unchanged basal iron metabolism in the spleen and liver, iron regulatory proteins and the IL-6-hepcidin axis are altered in Nr2f6-deficient mice during Salmonella infection, reducing hypoferremia. Transcriptomic analysis of splenic red pulp macrophages reveals significant alterations of phagocytosis-related genes, including upregulation of Sirpa. In vitro, phagocytosis of red blood cells, regulated by the inhibitory CD47-Sirp axis, and Salmonella Typhimurium phagocytosis is significantly impaired in Nr2f6-deficient splenic macrophages. Blocking Sirp in vitro restores the phagocytic activity of Nr2f6-deficient macrophages to wild-type levels. In vivo, Salmonella Typhimurium loads are partially increased post-infection in anti-Sirp treated Nr2f6-deficient mice. These findings uncover a previously unrecognized role of NR2F6 in host-pathogen interactions, positioning it as a potential therapeutic target for infectious diseases.

overall_design: RPMs were sorted from the spleen of wild-type C57BL/6 mice or Nr2f6-deficient mice. RPM were identified as live/CD45+/Lin-CD11bmid/F4/80+/CD64-/CD169-/CD106+ on a FACS Aria III. We sequenced RNA from RPM lysates of 3 wild-type and 2 Nr2f6-deficient mice.

first: Woelk

last: Johannes

first: Pfeifhofer-Obermair

last: Christa

first: Benz

last: Julia

first: Brigo

last: Natascha

first: Bamberger

last: Milena

first: Kleiter

last: Alexeja

first: Hermann

last: Martin

first: Weiss

last: Günther

first: Hermann-Kleiter


title: Regional differences in enterocyte function across development

summary: The medial (jejunum) and distal (ileum) regions of the small intestine undergo dramatic functional changes after weaning. However, how these changes differ by region and developmental stage remains unclear. To address this, we performed bulk RNA sequencing on isolated epithelial cells from the jejunum and ileum of mice at postnatal day 6 (P6) and day 36 (P36) to analyze region- and age-dependent transcriptional changes

overall_design: A 2 cm segment of jejunum and ileum was isolated from the same mouse. The segments were incubated in EDTA to separate intestinal epthelial cells from the intestinal wall. 4 mice age were utlized including both male and female mice.

first: Block

last: Carina

first: Bagnat

last: Michel

first: Eroglu

last: Cagla

first: Sakers

last: Kristina


title: Transcriptional differences in jejunum and ileum of a conditional knockout of Dab2 in the intestine

status: Public on Jul 05 2025

first: Staci

last: Bilbo

summary: We report bulk RNAseq data obtained from P6 mice. Input was isolated epithelium cells of the small intestine in a 2cm segment of  the jejunum and 2 cm segment in the ileum of P6 Dab2 cWT and Dab2 cKO mice. Conditional deletion of Dab2 wa

last: Carina L


title: Modelling HNSCC in mice with hyperactivated NRF2 pathway

city: Houston

first: Mitchell

last: Frederick

state: Texas

address: One Baylor Plaza

department: Otolaryngology

institute: Baylor College of Medicine

summary: Purpose: Alterations in the KEAP1/NFE2L2 (NRF2)/CUL3 pathway occur in ~20% of human head and neck squamous cell carcinomas (HNSCC) and are associated with resistance to standard-of-care therapy. However, this pathway's role in radiotherapy resistance in HNSCC has not been well-studied. Experimental Design: We generated genetically engineered mouse models and developed primary murine cancer cell lines harboring mutations commonly observed in human HNSCC, including inducible activation of PIK3CA and deletion of Trp53, with or without Keap1 loss. Primary tumors were initiated via 4-hydroxytamoxifen injection ± the tobacco carcinogen benzo[a]pyrene (BAP) into the oral buccal mucosa. Tumors were analyzed using Western blotting, immunohistochemistry, RNA sequencing (RNA-seq), and subjected to fractionated radiation therapy to investigate the role of the KEAP1/NRF2 pathway in radioresistance and modulation of the tumor immune microenvironment. Results: BAP exposure accelerated primary tumor formation within one month, with histological analysis confirming invasive squamous cell carcinoma, validated by cytokeratin and differentiation marker expression. Primary cell lines derived from Keap1-haploinsufficient tumors exhibited upregulation of NRF2 target genes and a radioresistant phenotype, which was reversed post-Nrf2 knockdown in vitro. Bulk RNA-seq revealed that Keap1 haploinsufficiency correlated with NRF2 pathway activation, increased myeloid infiltration, and enhanced angiogenic signatures. In vivo, Keap1 haploinsufficiency promoted accelerated tumor growth and decreased survival. Finally, using fractionated radiotherapy, we showed that Keap1 haploinsufficient primary tumors were significantly more radioresistant than Keap1-proficient tumors, regardless of BAP exposure. Conclusion: These data demonstrate that Keap1 haploinsufficiency in HNSCC is linked to unfavorable tumor immune microenvironment, aggressive growth, and a radioresistant phenotype.


title: A Simple and Efficient Method for the Robust Expansion of Human ILC2s to Prevent Acute GvHD [RNA-seq]

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

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

institute: University of North Carolina at Chapel Hill

summary: Reconstitution of stem cells and enhancement of the barrier function of the gastrointestinal (GI) tract is critical to the resolution of intestinal acute graft-versus-host disease (aGvHD). Previously, our group has shown in murine models that type II innate lymphoid cells (ILC2) cells generate proteins in the GI tract that enhanced GI tract barrier function and diminished the expansion and function of pro-inflammatory donor cells when given to allogeneic stem cell transplant recipients. Therefore, the infusion of donor ILC2 cells could treat or prevent GI tract acute GvHD, but for this approach to be clinically applicable, robust expansion of a homogenous population of human ILC2 cells is needed. Here, we describe a method for the rapid expansion of a uniform population of human ILC2 cells which decrease GvHD in (NOD scid gamma mouse) NSG mice. The addition of IL-4 to the culture was critical to prevent the expansion of pro-inflammatory ILC1-like cells. Our approach should allow for the evaluation of human ILC2 cells to treat therapy-resistant GI tract acute GvHD.

overall_design:
Cells were enriched via Rosette separation and expanded in complete a-MEM media with 10-50 ng/ml IL-7, IL-2, IL-4, IL-25, and IL-33 for 21 days.

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

first: Danny

middle: W

last: Bruce

first: Sonia

last: Laurie

first: Yan

last: Xing

first: Heather

middle: E

last: Stefanski

first: Keli

last: Hippen

first: Alec

middle: D

last: Wilkinson

first: Mark

middle: G

last: Woodcock

first: James

middle: M

last: Coghill Jr

first: Karen

middle: P

last: McKinnon

first: Bruce

last: Blazar

first: Jonathan

middle: S

last: Serody


title: A Simple and Efficient Method for the Robust Expansion of Human ILC2s to Prevent Acute GvHD [ATAC-seq]

middle: J

middle: R


title: Identification of Neuritin 1 as a local metabolic regulator of brown adipose tissue

status: Public on Jul 04 2025

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Brown adipose tissue (BAT) plays a key role in metabolic homeostasis through its thermogenic effects and the secretion of regulatory molecules. Here we report that RAP250 haploinsufficiency stimulates BAT in mice, thus contributing to a decrease in fat accumulation. Local in vivo AAV-mediated RAP250 silencing in BAT reduces body weight and fat mass and enhances glucose oxidation, thereby indicating that RAP250 participates in the regulation of BAT metabolic activity.   Analysis of the mechanisms  led to the finding that Neuritin 1 is produced and released by brown adipocytes, it plays a key metabolic role, and it participates in the enhanced BAT metabolic activity under RAP250 deficiency.  Forced overexpression of Neuritin 1 in UCP1-expressing cells markedly decreases fat mass and body weight gain in mice and induces the expression of thermogenic genes in BAT. Neuritin 1-deficient brown adipocytes also shows a reduced b-adrenergic response. We demonstrate a metabolic role of BAT-derived Neuritin 1 acting through an autocrine/paracrine mechanism.  Based on our results, Neuritin-1 emerges as a potential target for the treatment of metabolic disorders.

overall_design: Vector plasmid pAAV-UCP1-m-NRN1 contains the mouse Neuritin 1 (gene ID 68404, RefSeq# BC035531, ORF size 429 bp, protein 142 Aa).

first: Manuela

last: Sánchez-Feutrie

first: Antonio

last: Zorzano

first: Vanessa

last: Hernández

first: Óscar

last: Reina


title: TET1 modulates trophoblast function by regulation of ODC1 in preeclampsia

status: Public on Jul 03 2025

city: Jinan

first: Chao

last: Fan

address: No. 9-7, Jiang Shui Quan Road, Lixia District

institute: Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University

summary: Analysis of trophoblast cell line HTR8/SVneo knocking down the DNA hydroxymethylase TET1. The results provide insights into genes that undergo expression changes in trophoblast cells due to DNA hydroxymethylation.

overall_design: RNA-seq profiling of wildtype HTR8/SVneo cells and their knockdown derivatives (siTET1).

last: Kang

first: Zhenya

last: Fang

first: Lixia

last: Liu

first: Chunying

last: Wang

first: Man

last: Zhao

first: Li

last: Xiao

first: Changqing

last: Zhang


title: mRNA expression profile in the liver after overexpressed tsRNA-Glu-CTC oligos in C57BL/6 mice with mRNA-seq method

status: Public on Jul 02 2025

city: Riverside

first: Xiuchun

last: Li

address: 900 University Avenue

institute: UCR

summary: Purpose: To  reveal mRNA profiles in the liver using mRNA-seq method. Methods: 8 week old C57BL/6 male mice were injected Control Oligos and tsRNA-Glu-CTC oligos for two weeks. Liver RNA was extracted with Trizol methods. Results:mRNA-seq revealed upregulation of lipids metabolism related genes in overexpressed tsRNA-Glu-CTC oligos mice. Importantly, cholesterol synthesis key genes SREBP2 and HMGCR are significantly upregulation.

overall_design: Liver mRNA were sequenced from C57BL/6 male mice with I.P. injection of Control Oligo and tsRNA-Glu-CTC Oligo-1 for two weeks

first: Changcheng

last: Zhou

first: Tong