title: TMAO Aggravates Myocardial Ischemia-Reperfusion Injury by Sustaining PERK/eIF2α Activation and Impairing FDXR-Dependent Mitochondrial Function

first: Chongbin

last: Zhong

address: No 253, Middle Gongye Avenue

department: Department of Cardiology

institute: Zhujiang Hospital, Southern Medical University

summary: Alleviating myocardial ischemia-reperfusion injury (MIRI) is pivotal for improving acute myocardial infarction (AMI) prognosis. Identifying risk factors exacerbating MIRI may provide novel mitigation strategies. Previous clinical studies demonstrate that individuals with elevated plasma trimethylamine N-oxide (TMAO) levels suffer worse myocardial injury following AMI. However, whether TMAO promotes MIRI remained undefined. This study addressed this question and demonstrated that exogenous TMAO administration exacerbated MIRI in both in vivo mouse ischemia-reperfusion (IR) models and in vitro primary cardiomyocyte hypoxia/reoxygenation (HR) models. RNA sequencing (RNA-Seq) and gene set enrichment analysis (GSEA) indicated that TMAO suppressed mitochondrial function-related pathways. Further in vitro and in vivo experiments confirmed TMAO aggravated mitochondrial dysfunction during IR, manifested as ultrastructural damage, reduced mitochondrial membrane potential (ΔΨm), elevated ROS overproduction, and profound energy metabolism impairment. Mechanistically, TMAO-induced mitochondrial dysfunction was mediated through FDXR suppression, as FDXR overexpression reversed TMAO-mediated injury. TMAO directly bound PERK and sustained PERK/eIF2α pathway activation during IR. Pharmacological inhibition of PERK/eIF2α signaling (using GSK2606414 and ISRIB) reversed TMAO-induced FDXR suppression, mitochondrial dysfunction, and MIRI exacerbation, establishing the dependence of these effects on PERK/eIF2α signaling. Taken together, TMAO exacerbates MIRI by maintaining PERK/eIF2α activation, thereby driving FDXR-dependent mitochondrial dysfunction. This identifies TMAO as a risk factor for MIRI and the PERK/eIF2α/FDXR axis as a therapeutic target for TMAO-mediated injury.

overall_design: Male C57BL/6 mice were used to model IR via thoracotomy with transient ligation of the left anterior descending coronary artery (LAD) for 45 min, followed by 24 h reperfusion. 0.12% TMAO preconditioning was supplemented ad libitum in drinking water for 4 weeks before and during IR. Total RNA was isolated from myocardial tissues in the IR regions of TMAO+IR and IR group mice following IR modeling and subjected to RNA-seq analysis.

first: Pingzhen

last: Yang


title: The effect of nitrogen on wheat during drought and recovery after rehydration.

status: Public on Jul 10 2026

city: Qingdao

first: Junyi

last: Mu

address: No. 72, Binhai Road, Jimo District, Qingdao City

country: China

institute: Shandong Unoversity

type: Expression profiling by high throughput sequencing

summary: For transcriptomic analysis under drought, re-watering (RW), and re-watering with nitrate (RWN) conditions, wheat seedlings were germinated and transplanted into soil tanks once the first leaf emerged from the coleoptile, then irrigated with 2 L of wheat growth medium containing 5 mM nitrate, after which no further water was added. When soil moisture fell below 5%, seedlings were subjected to drought for one day before being re-watered with 2 L of medium containing either 0 mM (RW) or 5 mM (RWN) nitrate per tank. Leaf samples were collected from wheat seedlings during well-watered, drought, and at 3 hours, 1 day, and 5 days post-RW/RWN, and RNA was extracted for subsequent RNA-Seq analysis.

overall_design: Well-watered (WW),Drought(Dr), rewatering for 3h(RW3h), rewatering for 1d(RW1d), rewatering for 5d(RW5d), rewatering with nitrogen for 3h(RWN3h), rewatering with nitrogen for 1d(RWN1d), rewatering with nitrogen for 5d(RWN5d)


title: Drosha in mesangial cells regulates Glomerular Capillary Tufts Formation Through Drosha/Ribosome/Gata3 Axis

city: Guangzhou

first: Xin

last: Li

state: Guangdong

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

institute: Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary:
CAKUT (congenital anomalies of the kidney and the urinary tract) is one of the most prevalent birth defects, affecting around 1% of newborns. However, the genetic factors underlying the majority of CAKUT are unknown. Drosha, the microRNA-processing ribonuclease, has been reported to regulate the nephric cap meschyme development, and its mutations are implicated in Wilms tumor, a pediatric kidney cancer. Here, we investigated the role of Drosha in mesangial cells and its impact on glomerular capillary tuft formation. Deletion of Drosha in mesangial cells (DroshacKO) disrupted the glomerular capillary tufts formation, leading to dysplastic glomeruli, proteinuria, oliguria, reduced looping of glomerular capillaries and capillary dilation. Drosha-knockdown (KD) in mesangial cells (SV40 MES 13) leads to decreased cell proliferation and reduced Gata3 protein level. Transcriptome analysis by RNA-seq shows decreased level of ribosome protein gene (RPG)s but unaltered mRNA level of major genes affecting kidney development, including Gata3, Pax2, Atn1, Wt1 etc. in Drosha-KD compared to Control SV40 MES13 cells. Further analysis indicates Drosha regulates the translation of Gata3 in mesangial cells via regulating RPG transcription. Our work, for the first time, reveals that Drosha in mesangial cells orchestrates the formation of glomerular capillary tufts by regulating Gata3 translation. It identifies the critical role of DROSHA in nephric development and proposes DROSHA as a novel potential causal gene for CAKUT.

[miRNA-Seq] This study investigates the role of DROSHA in microRNA biogenesis using the mouse renal mesangial cell line ME13 sv40. Small RNA sequencing was performed to compare microRNA expression profiles between DROSHA knockdown cells and control cells. The results aim to elucidate how DROSHA depletion alters microRNA expression patterns, which may provide insights into post-transcriptional regulation in renal mesangial cells.

overall_design:
Drosha-knockdown (KD) SV40 MES 13 cell line (a mouse mesangial cell line) , generated by shRNA, was used as an in vitro model to elucidate the specific biological function of Drosha in mesangial cells

[miRNA-Seq] This study utilized the mouse renal mesangial cell line ME13 sv40, which was divided into two groups: a DROSHA knockdown group (genetically modified to reduce DROSHA expression) and a control group (unmodified or scrambled control). Small RNA sequencing was performed for both groups to profile microRNA expression, with biological replicates included for each condition to ensure statistical reliability. Differential microRNA expression analysis was then conducted to compare the two groups.

first: Zixuan

last: Fan

first: Lang

last: Qin

first: Jiajia

first: Tingxuan

last: Xu

first: Wenjun

last: Xiao

first: Jin

last: Tang

first: Yonghui

last: He

first: Weiqian

last: Chen

first: Chuwen

last: Lin

first: Xuan

last: Jiang


title: Fenofibrate-mediated inhibition of tumor proliferation and progression by modulating the PTPN14/MARK/Hippo signaling axis

city: Beijing

first: Yang

last: Liu

address: No. 49, Huayuan North Road, Haidian District, Beijing

institute: Peking University Third Hospital

summary: PTPN14 is a non-receptor tyrosine phosphatase that functions as a tumor suppressor through negative regulation of the Hippo signaling pathway, making it a potential therapeutic target for cancer. Despite its therapeutic potential, no PTPN14-targeting small-molecules have been developed to date. In this study, we discovered fenofibrate (FF), a small-molecule commonly used as a lipid-lowering agent, exhibits potent anti-proliferative and anti-migratory properties. Mechanistically, FF was found to directly bind the PPEY motif of PTPN14, facilitating formation of a complex with LATS1 and MARK3, which promotes cytoplasmic sequestration of YAP. Furthermore, genetic knockdown of PTPN14 or pharmacological inhibition of MARK3 substantially abolished the FF-mediated inhibition of malignant phenotypes, indicating the critical role of the PTPN14/MARK3/Hippo signaling axis in tumor progression. Notably, our data provide evidence for the potential of FF to sensitize the efficacy of conventional chemotherapeutics across melanoma, colorectal and ovarian carcinoma models. In conclusion, our results demonstrate that PTPN14 is a promising target for drug development in treating melanoma. These findings broaden our understanding of FF beyond its conventional functions, presenting a promising novel therapeutic strategy for treating melanoma.

overall_design: B16F10 melanoma cells were treated with 50 μM fenofibrate. Total RNA was extracted from treated and control cells, followed by RNA sequencing (RNA-seq) to assess fenofibrate-induced transcriptional changes (biological triplicates).

first: Xuedi

last: Cao

first: Tengrui

last: Zhang

first: Jianling

first: Xiaotong

last: Yu

last: Zhen

first: Yinjia

last: Ye

last: Zhou

first: Kewu

last: Zeng

first: Lixiang

last: Xue


title: Bulk transcriptome analysis of wildtype, TREM2 knockout, GPR34 knock-out or TREM2/GPR34 double knock-out iPSC-derived human microglia treated either with PBS or myelin.

status: Public on Jul 21 2026

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

country: USA

institute: Denali Therapeutics

summary: Microglia are broadly implicated in modifying disease risk in the central nervous system (CNS). Identifying regulators of microglia state is critical for elucidating their role in disease and identifying novel drug targets. GPR34 is a G-protein coupled receptor expressed in homeostatic microglia where its function is not well understood. Like TREM2, GPR34 detects lipid ligands. Here, we report that GPR34 knockout (KO) maintains lipid homeostasis and rescues dysregulated cholesterol metabolism in TREM2 KO human iPSC-derived microglia (iMG). Loss of GPR34 reduced ERK signaling in iMG, which has been implicated as a signaling pathway dysregulated in AD, with GPR34 agonism shown to promote GPR34 interaction with ERK in a matter consistent with endosomal signaling. In both healthy and amyloid mouse models, Gpr34 KO accelerated microglial state transcriptionally and histologically consistent conversion of homeostatic microglia to a disease-associated microglia (DAM) state. Shifts in microglial state were accompanied by increased expression of multiple metabolic gene sets.

overall_design: Human induced pluripotent stem cells (iPSC) were differentiated into microglia. Four lines with the following genotypes were included in the experiment: 1) wildtype, 2) TREM2 knockout, 3) GPR34 knockout, 4) TREM2+GPR34 double-knock-out. Microglia were treated with either PBS (control) or 25 µg/ml myelin for 24 hours. The entire experiment was replicated 4 times, e.g. cells were treated on 4 different days.

first: Karthik

last: Raju

first: Sophia

middle: M

last: Guldberg

first: David

last: Tatarakis

first: Shan

middle: V

last: Andrews

first: Connie

last: Ha

first: Joseph

middle: W

last: Lewcock

first: Jim

last: Ray

first: Kathryn

last: Monroe


title: BCAT1 as a critical regulator of human chondrosarcoma progression and differentiation through enzymatic and non-enzymatic mechanisms

city: Kyoto

first: Yoshiki

last: Yamamoto

address: 53 Shogoin Kawahara-cho, Sakyo-ku

country: Japan

institute: Kyoto University

summary: Human chondrosarcoma is a malignant bone tumor with a poor prognosis due to its resistance to conventional therapies. In this study, we investigated the role of Branched-Chain Amino Acid Transaminase 1 (BCAT1) in chondrosarcoma pathogenesis. BCAT1 depletion impairs proliferation and tumorigenicity both in vitro and in vivo in a xenograft model, underscoring its oncogenic role. Transcriptome analyses revealed that BCAT1 suppresses the chondrocyte differentiation pathway by inhibiting the expression of SOX9, a master regulator of normal chondrogenesis, through epigenetic regulation. This process depends on BCAT1’s enzymatic activity to generate α-ketoglutarate, which subsequently alters histone methylation status. Additionally, the CXXC motif of BCAT1 scavenges reactive oxygen species (ROS) independently of its enzymatic activity, maintaining G2/M checkpoint signaling and preventing ROS-induced cellular senescence. Finally, knockdown experiments in patient-derived primary cells confirm the clinical significance of BCAT1 function in human chondrosarcoma. These findings establish BCAT1 as a critical moonlighting enzyme in chondrosarcoma proliferation and differentiation, presenting a potential therapeutic target for this challenging cancer.

overall_design: RNA-seq profiling of chondrosarcoma cell lines (HT-1080, JJ012, NDCS-1) and their knockdown derivatives (shCtrl, shBCAT1)

first: Ayuna

last: Hattori

first: Makoto

last: Nakagawa

first: Kazuya

last: Ichihara

first: Akinobu

last: Matsumoto


title: Integrative single-cell analysis reveals malignant archetypes and proliferative hierarchies in multiple myeloma [Part 2 of 4: Illumina NextSeq 500; MARS]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Multiple myeloma (MM) is a plasma cell malignancy characterized by substantial genomic and biological heterogeneity, limiting disease classification and development of more targeted therapies. Here, we present a population-level single-cell atlas of MM and detailed clinical annotations from 342 patients representing MM disease and treatment continuum. Our analysis identifies five distinct malignant transcriptional archetypes (MM1–MM5), and a proliferative module variably expressed across archetypes. This proliferation signature emerges as a context-dependent program with independent prognostic value across archetypes. Combined archetype classification with proliferation scoring defines therapeutic resistance, genomic instability, and clinical outcomes. External validation using the CoMMpass cohort confirms the biological robustness and prognostic relevance of this stratification across platforms. Leveraging the resolution of our single-cell atlas, we applied a computational pipeline for therapeutic target discovery based on malignancy, cell-type specificity and tissue restriction. This approach highlights FCRL2 as a promising MM-specific therapeutic target, with selective expression in malignant plasma and B cells at both transcriptomic and protein levels. This integrative analysis provides a clinically actionable blueprint for patient-specific stratification and precision medicine in plasma cell malignancies.

overall_design: this submission includes single-cell RNA sequencing data from bone marrow aspirates collected from 322 multiple myeloma patients plus 20 healthy donors from hip surgery as controls. Samples represent patients with pre-myeloma stages (MGUS, SMM), newly diagnosed multiple myeloma (treatment-naive) and relapsed/refractory multiple myeloma with various prior treatment exposures, compared to normal bone marrow from healthy controls. Disease stage information is available for all samples, while additional clinical data including survival, FISH results, treatment response, and treatment history are available for subsets of samples. The study focuses on plasma cells, with tumor microenvironment cells captured but not analyzed in this dataset.

first: Mor

last: Zada

first: Anna

last: Kurilovich

first: Noam

last: Shapira

first: Shuang-Yin

last: Wang

first: Reut

last: Sharet-Eshed

first: Paulina

last: Chalan

first: Florian

last: Ingelfinger

first: Shlomit

last: Kfir-Erenfeld

first: Nathalie

last: Asherie

first: Chamutal

last: Gur

last: Gurevich-Shapiro

first: Iuliana

last: Vaxman

first: Rotem

last: Shalita

first: Maya

last: Ben Yehuda

first: Pascale

last: Zwicky

first: Michelle

last: von Locquenghien

first: Kfir

last: Mazuz

first: Eyal

last: David

first: Natan

last: Melamed

first: Irit

last: Avivi

first: Assaf

last: Weiner

first: Polina

last: Stepensky

first: Yael

last: Cohen


title: Spatial transcriptomic profiling of alveoli and granuloma regions in patients with active pulmonary tuberculosis

city: Los Angeles

first: Jonathan

last: Perrie

state: CA

address: 610 Charles E Young Dr S

department: Bioinformatics

institute: University of California, Los Angeles

summary: Spatial transcriptomic profiling was performed using the GeoMx DSP Whole Transcriptome Atlas to measure expression of over 18,000 genes in alveoli and granuloma core and mantle regions from patients with active pulmonary tuberculosis. Differential gene expression revealed region-specific transcriptional profiles, including signatures related to antimicrobial response and lipid metabolism.

overall_design: Spatial transcriptomic data was generated from lung tissue sections by profiling geometric segments as ROIs using the GeoMx DSP Whole Transcriptome Atlas. After quality filtering, 10,968 genes were retained across 59 ROIs spanning alveoli, core, and mantle regions. Region-specific transcriptional programs were analyzed by pairwise differential expression.

first: Rosane

last: Teles

first: Chaouki

last: Benabdessalem

first: Matteo

last: Pellegrini

first: Robert

last: Modlin


title: Rapamycin, but not propranolol, can partially revert CCM phenotype in brain endothelial cells and ameliorates chronic cavernoma development in combination with lapatinib

city: Santiago de Compostela

first: Juan

last: Zalvide

state: A Coruña

address: CIMUS, Avda de Barcelona s/n

department: Physiology

country: Spain

institute: Universidad de Santiago de Compostela

summary: Brain microvascular endothelial cells (mBMEC) deficient in Ccm3 were used to model CCMs in vitro. Cells were treated with propranolol (10 µM) and rapamycin (100 nM) for various durations. RNAseq was employed to analyze gene expression. Propranolol did not significantly affect the CCM phenotype in mBMEC, failing to revert gene expression changes. Rapamycin partially reversed gene expression changes caused by Ccm3 deficiency, affecting genes such as Nos3, Adamts1, and Thbs1, known to be important for cavernoma pathogenesis in endothelial cells deficient for Ccm3. Propranolol's lack of efficacy in brain endothelial cells raises questions about its mechanism of action and potential benefits in CCM treatment.

overall_design: RNAseq profiling of CCM3 wild-type and KO brain endothelial cells either untreated or treated with 10 µM propranolol or 100 nM rapamycin for 24 hours

first: Mar

last: García-Colomer

first: José E

last: Martínez

first: Luis

last: Díaz

first: Miriam

last: Sartages

first: Eva M.

last: Esquinas-Román

first: Cristina

last: Riobello

first: David

first: Miguel

last: Fidalgo

first: Marta

last: Varela-Rey

first: Celia M

last: Pombo


title: RNA sequencing of HUVEC, HCMEC and human primary skeletal muscle cells in response to in vitro mechanical loading

city: Jyväskylä

first: Riikka

last: Kivelä

address: Rautpohjankatu 8

country: Finland

institute: University of Jyväskylä

summary: Our objective was to profile and compare the transcriptomes of mechanically loaded vs. static cells in three different human cell lines: Human umbilical vein endothelial cells (HUVEC), Human cardiac microendothelial cells (HCMEC) and primary human skeletal muscle cells (HSkM). Cells were mechanically loaded for 5h and total RNA was collected immediately after. The mechanical loading experiment was conducted for all three cell lines separately, with 6 biological replicates in the experimental group and 6 replicates as static controls, resulting in a total of 12 samples per cell line.

overall_design: RNA-Seq profiling of HUVEC, HCMEC and human myotube monocultures in response to in vitro mechanical loading compared to non-loaded controls.

last: Kivela

first: Erik

last: Niemi


title: Type I interferon–activated myeloid states are associated with less fibrotic stages in idiopathic pulmonary fibrosis

city: Oxford

first: Ling-Pei

last: Ho

address: Headley Way

department: MRC Human Immunology Unit

country: United Kingdom

institute: University of Oxford

summary: Early immune processes in idiopathic pulmonary fibrosis (IPF) are  poorly defined. Here, we integrate single cell transcriptomics of lung digest and bronchoalveolar-lavaged cells (n=108 patients), subcellular-resolution tissue spatial transcriptomics, and single-cell phospho-CyTOF of blood cells to define myeloid states associated with early stages of fibrosis. Two distinct myeloid gene transcriptional programmes are increased in IPF compared to non-diseased controls - type I interferon-activated and fibrotic remodelling programme. At cell,  organ and patient levels, cell types with increased type I interferon-activated programme (FABP4hi alveolar macrophages, classical monocytes, interstitial macrophages and non-classical monocytes) are associated with architecturally better-preserved lung tissue, the alveolar barrier and less fibrotic lung, or less severe disease. Circulating monocytes exhibited heightened type I interferon responsiveness that inversely correlated with severity of clinical disease. Our findings show that myeloid cells with increased type I interferon-activated gene programmes are associated with less fibrotic stages of IPF.

overall_design: We investigate the role of myeloid cells in early IPF pathogenesis by performing a step-wise multi-compartment single cell level analysis across lung digest, alveolar barrier , blood and intact lung tissue. We first assembled an integrated single-cell transcriptomic atlas from four independent studies of IPF explant lung digest (Morse 2021, Adam 2020, Reyfman 2019 ,Habermann 2020) and bronchoalveolar lavage (BAL) samples (Oxford Cohort A) enabling high-resolution characterisation of lung myeloid cell populations and unbiased comparison of their transcriptional programmes to non-diseased lungs. We then examined the BAL compartment (Oxford Cohort A) separately to determine usage of these transcriptional programmes in alveolar barrier-associated macrophage states, compared upper versus lower lobe tissue profiles (Morse 2021) to examine association with disease stage at the organ level, and finally, in a group of patients undergoing diagnostic biopsies (Oxford Cohort E),  we performed subcellular-resolution Xenium spatial transcriptomics on lung tissue to define association of myeloid cell types and states with multicellular neighbourhoods. These analyses were complemented by blood-based single-cell phospho-CyTOF signalling studies and monocyte immunophenotyping (Oxford Cohort C and D).

first: Vishal

last: Nathwani

first: Praveen

last: Weeratunga

first: Jeongmin

last: Woo

first: Laura

last: Denney

first: Chaitanya

last: Vuppusetty

first: Tian

last: Hu

first: Sabrina

last: Zulfikar

first: Andrew

last: Achaiah

first: Leila

last: Baghaarabani

first: Harriet

last: Parker

first: Huei-Wen

last: Chuang

first: Michalina

last: Mazurczyk

first: Aleksandr

last: Fedorov

first: Alison

last: Simmons

first: Colin

last: Clelland

first: Jan

last: Rehwinkel

first: Agne

last: Antanaviciute


title: Deep learning identifies Pbx1 as a network hub of hematopoietic stem cell aging [26hr ATAC-seq]

city: Sendai

first: Keiyo

last: Takubo

address: 2-1 Seiryo-machi Aoba-ku

department: Graduate School of Medicine

institute: Tohoku University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hematopoietic stem cells (HSCs) constitute a well-structured hematopoietic system that undergoes an age-related bias toward myeloid/platelet differentiation. The mechanism by which this aging hallmark is deeply embedded in intrinsic HSC programs is unknown. Using single-cell RNA-seq data, old HSCs harbor two distinct transcriptional programs: one shared with megakaryocytes and the other associated with the most primitive HSCs. By employing a transformer-based model that captures higher-order differences between young and aging HSCs and integrating time-series transcriptomic analyses, epigenetic studies, and comprehensive transcription factor screens, we identified Pbx1 as a central gene controlling both age-related transcriptional programs and differentiation defects in old HSCs. Pbx1 suppresses erythroid differentiation by repressing Gata1 expression. In addition, we found that the histone methyltransferase G9a/GLP acts as an epigenetic regulator that specifically inhibits Gata1 expression and erythroid differentiation. These findings provide insight into the differentiation defects associated with stem cell aging and potential strategies for rejuvenation.

overall_design: Each replicate (n = 2 biological replicates per group) consisted of a pool of 12 young mice (14 weeks old) and 2 old mice (25 and 28 months old). In each group, 30,000 CD150+CD48-LSK cells were sorted and either immediately subjected to ATAC-seq for the fresh group or cultured for 26 hours under SF-O3 conditions supplemented with 4% BSA, 1 ng/mL SCF, 100 ng/mL TPO, and 1% O₂, followed by ATAC-seq for the culture group.

first: Hiroshi

last: Kobayashi

first: Shintaro

last: Watanuki

first: Naoya

last: Takayama

first: Motohiko

last: Oshima

first: Atsushi

last: Iwama


title: Deep learning identifies Pbx1 as a network hub of hematopoietic stem cell aging

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

overall_design: Refer to individual Series


title: Seed endophytic bacterium induces a priming-like drought transcriptomic state in an invasive plant prior to stress exposure

city: Gwangju

first: Jeong

last: Seorin

address: 123, Cheomdangwagi-ro, Buk-gu

country: South Korea

institute: Gwangju Institute of Science and Technology

summary: Seedborne endophytes may facilitate plant establishment by modifying host responses to environmental stress, but the mechanisms underlying these effects remain poorly understood. This may be particularly important for invasive plants, whose establishment in novel habitats often depends on tolerance to abiotic stress. Here, we examined whether the seed endophytic bacterium Erwinia tasmaniensis YJ6 induces priming-like drought-associated gene expression in the invasive plant Lactuca serriola. We compared the growth and root transcriptomes of uninfected and YJ6-infected plants grown under benign and drought conditions. YJ6-infected plants maintained shoot dry weight, root dry weight, and relative leaf growth under drought at levels comparable to those under benign water conditions, whereas these traits decreased in uninfected plants. Under benign water conditions, YJ6 infection induced 1,114 differentially expressed genes, including 317 genes that overlapped with drought-responsive genes in uninfected plants. Functional enrichment analyses showed that bacterial infection under benign conditions and drought exposure in uninfected plants affected several common pathways, including plant hormone signal transduction, phenylpropanoid biosynthesis, and nitrogen metabolism. YJ6 infection also affected genes associated with ABA-related signaling, gibberellin biosynthesis, and soluble sugar metabolism. These results are consistent with the establishment of a priming-like transcriptomic state before drought exposure, providing a potential mechanism by which seedborne microbes enhance stress tolerance in invasive plants.

overall_design: To investigate the drought stress-ameliorating mechanism of Erwinia tasmaniensis YJ6 on xerophytic invasive plant Lactuca serriola, we compare the gene expression of L. serriola under benign and stress condition, with or without YJ6. Triplicates were analyzed for each treatment using RNA-Seq with Illumina NovaSeq X.

first: Seorin

last: Jeong

first: Tae-Min

last: Kim

first: Byungwook

last: Choi

first: Yousuk

first: Eunsuk


title: Targeting the oncohistone-ASCL1 axis disrupts plasticity and suppresses pediatric gliomas [RNA-seq]

first: Alan

last: Jiao

state: MA

address: Old Road Campus Research Building

institute: Ludwig Institute for Cancer Research, Oxford University

summary: Phenotypic plasticity, a hallmark of cancer facilitated by epigenomic reprogramming, represents a significant challenge but also therapeutic opportunity for cancer treatment. How plasticity is regulated in diffuse midline gliomas (DMGs), incurable pediatric brain tumors characterized by oncogenic H3K27M histone mutations, is not understood. Here we demonstrate that H3K27M-driven plasticity requires the lineage-specific, pioneer transcription factor (TF) ASCL1. Prolonged differentiation reveals clinically relevant plasticity in DMGs, which segregate into ASCL1-high, neural progenitor cell (NPC)-like gliomaspheres and ASCL1-low, mesenchymal (MES)-like adherent subpopulations. Direct transcriptional activation by ASCL1 enables super enhancers to sustain NPC programs de-repressed by H3K27M. H3K27M loss induces an irreversible MES-like state, suppresses plasticity by abolishing the ASCL1-high state, and is largely phenocopied by loss of ASCL1. Knocking out ASCL1 in DMG lines robustly inhibited tumor growth and significantly extended survival of recipient mice. Our results suggest targeting epigenetic plasticity to suppress master TF-driven progenitor states as a general therapeutic opportunity in cancer.

overall_design:
To investigate the cooperative effects of ASCL1 and K27M on glioma plasticity, we established Control (expressing non-targeting guide RNA), ASCL1-KO, K27M-KO, and double knockout (DKO) DIPG-XIII cell lines
We treated cells with differentiation medium containing 10% FBS
Total RNA was collected at Day 0 (from cultures in tumor stem medium), and at Day3 and Week10 of differentiation. We compared gene expression profiles between Control and KO lines at each time point.

first: Jiao

last: Alan

first: Shi

last: Yang


title: Targeting the oncohistone-ASCL1 axis disrupts plasticity and suppresses pediatric gliomas [CUT&TAG]

overall_design:
To investigate the cooperative effects of ASCL1 and K27M on glioma plasticity, we established Control (expressing non-targeting guide RNA), ASCL1-KO, K27M-KO, and double knockout (DKO) DIPG-XIII cell lines
Cells were treated with differentiation medium containing 10% FBS

first: Yang

last: Shi


title: Cerebrospinal fluid-linked periventricular gradient pathology in multiple sclerosis associates with ependymal cell reactivity and cell adhesion disruption

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

summary: Cerebrospinal fluid (CSF)-adjacent brain surfaces – namely the subpial cortical and ependyma-adjacent periventricular regions – are uniquely vulnerable to diffuse pathology in multiple sclerosis (MS). So-called surface-in gradients, which predict disease relapses independent of white matter lesions, are thought to arise from CSF-borne cytotoxic factors and represent a distinct therapeutic target. Yet, how such factors access the brain, particularly at the ventricular border, remains unclear. While ependymal injury in MS has been suggested, a comprehensive assessment of cell health in the disease is lacking. Using ultra-high-field MRI-guided histology, electron microscopy, and single-nucleus multiomics, we deeply profiled human ependymal cells in MS. We found that ependymal pathology correlates with periventricular gradients and involves an immune-reactive state marked by transporter and junctional protein dysregulation. We then further defined the gene regulatory networks underpinning the MS ependymal state, predicted ligands known to be enriched in MS CSF that could drive the emergence of this state, and tested one candidate in vivo. IFNγ increased murine ependymal permeability and conditional knockout of its receptor (Ifngr1) reversed this effect. These findings implicate ependymal dysfunction in periventricular pathology and highlight how CSF ligands modulate ependymal function and regional inflammation.

overall_design:
Single nuclei were extracted from frozen human brain tissue. Joint snRNA- and snATAC libraries were prepared using the 10x Genomics platform.

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

first: Adam MR

last: Groh

first: Elia

last: Afanasiev

first: Risavarshni

last: Thevakumaran

first: Liam

last: Callahan-Martin

first: Finn

last: Creeggan

first: Moein

last: Yaqubi

first: David A

last: Rudko

first: Jo Anne


title: Targeting the oncohistone-ASCL1 axis disrupts plasticity and suppresses pediatric gliomas [CUTAC]

overall_design:
To investigate the cooperative effects of ASCL1 and K27M on glioma plasticity, we established Control (expressing non-targeting guide RNA), ASCL1-KO, K27M-KO, and double knockout (DKO) DIPG-XIII cell lines
Cells were treated with differentiation medium (DM) containing 10% FBS
CUTAC was performed in Day 0 (TSM) and at Day 3 in DM


title: Targeting the oncohistone-ASCL1 axis disrupts plasticity and suppresses pediatric gliomas [CUT&RUN]


title: Epigenetic landscape, key transcriptional regulators, and in vivo identification of human Tr1 cells [scMultiome]

city: Stanford

first: Laura

last: Amaya

address: 269 Campus Drive

institute: Stanford University

summary: Type 1 regulatory T (Tr1) cells are CD4+ T cells with immunoregulatory function, which are induced from mature peripheral CD4+ T cells in response to persistent extra-thymic antigens. The role of human Tr1 cells in disease is not completely understood, because transcription factors that regulate their antigen-driven differentiation are not known, and there is lack of consensus on how to best identify them in the tissue, where antigen interactions occur. Here, we leveraged comprehensive bulk and single-cell (sc) transcriptomic, epigenomic, and TCR repertoire profiling of human antigen-induced Tr1 cells, complemented with CRISPR-based functional genomics, to uncover the role of transcription factors IRF4, BATF and MAF in human Tr1 cell differentiation and function. In addition, we identify a Tr1 cell transcriptional signature that can reveal Tr1-like cells in sc-RNA-seq datasets of peripheral blood CD4+ T cells of patients treated with Tr1 therapy, and within tumor-resident CD4+ T cells in patients with clear-cell renal cell carcinoma, triple-negative breast cancer, and colorectal cancer. These data enable further development of Tr1 therapies and Tr1-targeting treatments, and provide new insights into human Tr1 cell biology.

overall_design: Purified peripheral blood CD4+ T cells from two healthy donors and one patient at 9 months post-T-allo10 infusion and allo-HSCT were processed with sc-multiome (sc-ATAC + RNA-seq; 10X Genomics).

first: Alma-Martina

last: Cepika

first: Colin

last: Waichler

first: Mansi

last: Narula


title: Chip seq data of transcription factor ELF-1 in mouse BMDM derived macrophages.

status: Public on Jul 09 2026

first: Zhaoqi

last: Zhang

state: Beijing

address: Peking University People’s Hospital

institute: Peking University People’s Hospital

summary: Acute kidney injury (AKI) is an unavoidable complication following renal transplantation and a critical determinant of patient prognosis. M1-polarized macrophages are known to exacerbate the progression of AKI. Preliminary clinical data reveal a positive correlation between the expression level of E74-like ETS transcription factor 1 (ELF-1) in macrophages from post-transplant patients and the levels of pro-inflammatory cytokines. However, the role of ELF-1 in M1 macrophage polarization and the pathogenesis of AKI remains unclear. In this study, we aim to investigate the role of ELF-1 in M1 macrophage polarization and AKI pathogenesis by employing ELF-1-deficient murine macrophages and performing ChIP-seq to identify downstream genes regulated by ELF-1.

overall_design: BMDMs from WT or Elf-1 KO mice were induced by LPS for 6 hours to obtain M1 macrophages for ChIP-seq assay. The ChIP-seq assay was performed by Wuhan Igenebook Biotechnology Co. Ltd (China). Trimmomatic (version 0.36) was used to filter out low-quality reads. Clean reads were mapped to the GRCm38 genome by Bowtie2. Samtools rmdup was used to remove potential PCR duplicates. The results were visualized using IGV_Win_2.3.92.

first: Yangxiao

last: Hou


title: Sequential-GAM constructs the single-cell geometric 3D genome structure

first: Yongge

last: Li

state: Haidian

address: FIT 1-108, Tsinghua University, Haidian District

institute: Tsinghua University

summary: The three-dimensional genome structure plays important role in cell identity and gene regulation. We used a new method to construct the diploid geometric structure of genome in single cells. Using the structure, we determine the radial positioning of distinct genomic features and epigenetic markers and the variance in single cells.

overall_design: We used a new method to construct 10 single cell structure in F123 Mouse ES cell.

first: Kaili

last: Wang

first: Minglei

first: Juntao

last: Gao

first: Michael

middle: Q


title: TNFAIP3/A20 dysfunction drives innate and sterile hyperinflammation

city: Zwijnaarde

first: Bart

last: Lambrecht

address: Technologiepark

department: IRC

country: Belgium

institute: VIB

summary: Feedback mechanisms regulate immune activation and prevent excessive tissue damage. TNFAIP3, also known as A20, serves as a crucial brake on inflammation, and mutations or haploinsufficiency of this gene are linked to diseases characterized by inappropriate inflammation. In this study, we document highly conserved patterns of cell type-specific gene expression, regulation, and induction of TNFAIP3, and employ transgenic and gnotobiotic mouse models to investigate how adaptive immunity and the gut microbiome contribute to pathology arising from impaired A20 function. Contrary to our expectations, systemic inflammation resulting from Tnfaip3 deficiency in CD11c (Itgax)-expressing cells developed independently of autoreactive antibodies, B cells, and T cells. The microbiome also proved dispensable for disease manifestations in these models. These findings suggest that in diseases caused by insufficient TNFAIP3/A20 activity, autoantibodies may reflect a downstream consequence of disease rather than a causative driver, suggesting autoinflammatory rather than autoimmune pathology. These insights carry therapeutic implications for the treatment of TNFAIP3-associated diseases.

overall_design: We carried out single-cell RNA sequencing on magnetic activated (MACS) and fluoresence-activated cell sorted (FACS) splenocytes of 3 wild-type and 3 A20 CD11c-ko female C57BL/6 mice

first: Karel

middle: F

last: Van Damme

first: Dorine

last: Sichien

first: Katrien

last: Van der Borght

middle: N


title: Monocarboxylate Transporter 2 (MCT2) Mitigates Lung Tumor Progression by Shaping the Immune Microenvironment [snRNA-Seq]

city: Huntington

first: Yen On

last: Chan

state: WV

address: Arthur Weisberg Family Applied Engineering Complex, Suite # 4103, 1676 Third Avenue

department: Department of Biomedical Sciences

institute: Marshall University

summary: Monocarboxylate transporter 2 (MCT2; SLC16A7) is a high-affinity pyruvate transporter implicated in cancer metabolism. However, its role in lung cancer progression and the tumor microenvironment remains unclear. This study examined the effects of MCT2 loss on tumor growth and cell type-specific transcriptional changes within the tumor microenvironment. MCT2 loxP/loxP mice were crossed with mCre-Tg mice, and MCT2 deletion was induced by tamoxifen. Control (CO) mice received vehicle treatment. TC1 cells (100,000 cells/mouse) were injected subcutaneously, and tumors were harvested after 24 days. Single-nucleus RNA sequencing (snRNA-seq) was performed on isolated tumor nuclei (4,000 nuclei/sample; n = 3 per group) using the 10x Genomics Chromium platform. Data were processed with Cell Ranger v3.0.2 and Seurat v5.2.1, followed by differential expression and pathway enrichment analyses integrated with macrophage bulk RNA-seq data. MCT2-deficient tumors grew significantly faster than control tumors, supporting a tumor-suppressive role for MCT2. Transcriptomic analysis generated high-quality profiles from 7,840 CO and 10,175 KO nuclei. Clustering identified 10 cellular populations, including nine annotated cell types. MCT2 deficiency altered pathways involved in glycolysis, the tricarboxylic acid cycle, oxidative phosphorylation, and fatty acid metabolism across multiple populations. Macrophages showed prominent transcriptional changes, including enrichment of MAPK, PI3K-Akt, IgSF-CAM, and cell adhesion molecule signaling pathways. These findings were supported by macrophage bulk RNA-seq data. MCT2 deficiency enhances tumor growth and induces widespread transcriptional remodeling of the tumor microenvironment. Altered metabolic and immune-related pathways, particularly in macrophages, may contribute to lung cancer progression and represent potential therapeutic targets.

overall_design: Eight-week-old MCT2 conditional knockout mice were treated with tamoxifen for five consecutive days to induce MCT2 knockout, while control mice received the corresponding vehicle without tamoxifen. Two days after the final treatment, TC1 tumor cells were injected subcutaneously into the lower right flank and allowed to grow for 24 days. Tumors were then harvested from CO and KO mice, nuclei were isolated from whole tumor tissues, and single-nucleus RNA sequencing was performed to compare cell populations, gene-expression profiles, and pathway changes between CO and KO tumors.

first: Zhuanhong

last: Qiao

first: Trupti

last: Joshi

first: David

last: Gozal

first: Abdelnaby

last: Khalyfa


title: Monocarboxylate Transporter 2 (MCT2) Mitigates Lung Tumor Progression by Shaping the Immune Microenvironment [bulk RNA]

overall_design: Eight-week-old MCT2 conditional knockout mice were treated with tamoxifen to generate the KO group, while control mice received vehicle treatment. Two days later, TC1 tumor cells were injected subcutaneously into the lower right flank and allowed to grow for 24 days. At endpoint, tumors were excised from CO and KO mice, tumor-associated macrophages were purified, and RNA was extracted from the purified macrophages for bulk RNA sequencing to identify differentially expressed genes and enriched pathways between CO and KO groups.


title: RNA-seq based correlation analysis of producer cell and STV-C8

city: Neuherberg

first: Florian

last: Giesert

state: Bavaria

address: Ingolstaedter Landstrasse 1

department: Stem Cell Department

country: Germany

institute: Helmholtz Munich

summary: Synthetic transport vehicles (STVs) are fully engineered, non-viral protein nanoparticles designed to deliver functional RNA cargos with high efficiency while enabling precise control over their molecular composition. Comprehensive RNA profiling demonstrated that STVs package predominantly the intended therapeutic RNA while strongly minimizing the incorporation of endogenous cellular transcripts, highlighting the ability of engineered RNA-protein interactions to direct selective cargo loading. This highly defined RNA composition underpins the robust delivery performance of STVs, enabling efficient transfer of diverse functional RNAs, including mRNAs encoding transcription factors, gene editors, and antiviral effectors, across multiple cell types and in vivo models.

overall_design: TV-C8 particles (supernatant) and corresponding producer cells (cells) were processed for RNA isolation (Monarch Total RNA Miniprep Kit, NEB). Library preparation, sequencing, and analysis were performed by Azenta (Leipzig)

first: Christoph

last: Gruber

first: Wolfgang

last: Wurst


title: Plasma multi-miRNA models classify Alzheimer’s, Parkinson’s, and Lewy body dementia

city: Portland

first: Julie

middle: A

last: Saugstad

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Anesthesiology & Perioperative Medicine

institute: Oregon Health & Science University

summary: We obtained 289 human plasma samples from national repositories in order to examine whether miRNAs could serve as biomarkers to distinguish diagnostic groups with similar clinical presentations and co-pathologies from each other. The participant groups included Alzheimer’s disease (AD), Parkinson’s disease (PD), and dementia with Lewy bodies (DLB). We also examined plasma miRNAs in normal control participants (NC).

overall_design: Plasma samples and data from 289 participants were obtained from the Alzheimer’s Disease Neuroimaging Initiative 2 (ADNI 2), the Oregon Alzheimer’s Disease Research Center (OADRC), and the Veterans Health Administration (VHA) Puget Sound Health Care System. RT-qPCR was used to quantify plasma expression levels of 64 miRNAs that included 57 AD-associated miRNAs, 1 spike-in miRNA for exogenous calibration, 4 endogenous control miRNAs for normalization, and 2 negative control miRNAs using custom TaqMan Low Density miRNA Arrays from Thermo Fisher Scientific.

first: Ursula

middle: S

last: Sandau

first: Jack

middle: T

last: Wiedrick

first: Trevor

middle: J

last: McFarland

first: Dora

last: Yearout

first: Cyrus

middle: P

last: Zabetian

first: Shu-Ching

last: Hu

first: Debby

last: Tsuang

first: Joseph

last: Quinn


title: Spatial transcriptomics reveals D2-associated synaptic transcriptional attenuation in the chronically stressed dorsal striatum

city: Seoul

first: Jinhee

last: Bae

address: 5, Hwarang-ro 14-gil

institute: KIST

summary: Chronic stress alters striatal functions involved in motivation, action selection, and behavioral adaptation, yet cell-type-associated transcriptional organization in the dorsal striatum remains unclear. We used RNAscope-guided GeoMx spatial transcriptomics to compare D1- and D2-enriched neuronal compartments within anatomically matched dorsal striatal regions after chronic restraint stress. Chronic restraint stress engaged both populations and produced comparable numbers of differentially expressed genes. Pathway-level analysis revealed partially overlapping transcriptional attenuation in D1 and D2 neurons, whereas D2 responses showed more coherent organization around receptor-trafficking and synaptic signaling programs. CRS-downregulated D2 genes further resolved into synapse-centered functional categories, including glutamatergic synapse, postsynaptic organization, and dendritic spine.

overall_design: Male heterozygous Drd2-Cre mice on a C57BL/6 background were assigned to a control group (n = 10) or a chronic restraint stress group (n = 9). Mice in the stress group were restrained for 6 h per day for 21 consecutive days, whereas control mice were handled for approximately 3 min per day. Brains were collected 3 days after the final restraint session. One anatomically matched dorsal striatal region of interest was selected from each mouse. Each region was segmented into paired D1- and D2-enriched neuronal compartments using endogenous Drd1 and Drd2 RNAscope signals, yielding 38 total segments. Transcriptomic profiling was performed using the GeoMx Mouse Whole Transcriptome Atlas probe set, followed by next-generation sequencing on an Illumina NovaSeq 6000.

first: Heh-In

last: Im


title: OASL Regulates Endothelial Function via USP39-Mediated Deubiquitination of CDK1 to Promote Large Full-Thickness Skin Defect Healing

city: Beijing

first: zhiyang

last: xie

address: No. 33, Badachu Road, Shijingshan District

department: Plastic Surgery Hospital

institute: Chinese Academy of Medical Sciences / Peking Union Medical College

summary: Large full-thickness skin defects (LFSDs) remain a major clinical challenge due to insufficient vascular regeneration and impaired tissue repair. Emerging evidence suggests that oligoadenylate synthase-like protein (OASL), an interferon-stimulated protein, contributes to endothelial homeostasis and vascular function; however, its role in endothelial regeneration and wound healing has not been elucidated. Here, we investigated the molecular mechanism by which OASL regulates endothelial regeneration and explored its therapeutic potential for LFSD repair.

overall_design: Human Umbilical Vein Endothelial Cells (HUVECs) with stable OASL overexpression or knockdown were established to evaluate endothelial proliferation, migration, and angiogenic capacity. Recombinant OASL protein was administered to wild-type HUVECs to further assess its biological effects. RNA sequencing, immunoprecipitation–mass spectrometry (IP/MS), and ubiquitination assays were integrated to identify downstream targets and elucidate the molecular mechanisms underlying OASL-mediated endothelial regeneration. The therapeutic efficacy of recombinant OASL1 was further evaluated in a C57BL/6 mouse LFSD model using an injectable F127DA hydrogel delivery system.

first: Zhiyang

last: Xie


title: The spatial transcriptomics of the mouse brain 3 days after tMCAO

city: shanghai

first: Yong

middle: hui

last: Chen

address: 160, Pujian Road

institute: Renji hospital

summary: This study employed spatial transcriptomics to profile the expression and spatial distribution of Htr2b, P2ry12, Mrc1, and Ms4a7 in mouse brains 3 days after transient middle cerebral artery occlusion (tMCAO). By capturing genome‑wide transcriptional data with spatial coordinates, we aimed to map the regional expression patterns of these genes across the ischemic core, penumbra, and remote areas, and to delineate their co‑localization relationships with distinct immune and glial cell populations. This spatially resolved approach will provide insights into the topographic organization of serotonergic signaling and neuroimmune interactions during the acute phase of ischemic stroke.

overall_design: Adult Ms4a3creERT2-Ai14 mice were subjected to transient middle cerebral artery occlusion (tMCAO) for 60 minutes, followed by 3 days of reperfusion. At the endpoint, brains were harvested, rapidly frozen, and sectioned coronally at 20 µm thickness. Spatial transcriptomic profiling was performed using the 10× Genomics Visium platform, capturing genome‑wide gene expression while preserving spatial coordinates. Tissue sections spanning the ischemic core, penumbra, and contralateral homologous regions were selected for analysis.

first: Yueman

last: Zhang

first: Yonghui

first: Yue

last: Cheng


title: Transcriptional response to RfxCas13d with mCherry targeting crRNA in HEK293T

city: Melbourne

first: Honglin

state: VIC

address: 305 Grattan St, North Melbourne VIC

country: Australia

institute: PeterMacCallum Cancer Centre

summary: Collateral RNA cleavage by CRISPR-Cas13 effectors presents a critical obstacle to their application in biological research and therapeutics, yet the molecular determinants of this activity remain poorly understood. Here, we systematically investigate the collateral activity of various Cas13 variants in human cells in vitro and zebrafish embryos in vivo. Among these nucleases, RfxCas13d displays robust collateral activity that is highly dependent on target abundance. Targeting moderately expressed RNAs activates only a limited subset of RfxCas13d molecules, resulting in selective degradation of ectopically expressed transcripts, while endogenous RNAs remain largely protected. This selectivity indicates higher accessibility to exogenous RNAs through spatial proximity and temporal colocalization with activated RfxCas13d nuclease domains. In contrast, the recognition of highly abundant RNA targets drives simultaneous activation of a large fraction of cellular RfxCas13d, leading to widespread collateral cleavage of cellular RNAs, disruption of proteome homeostasis, and consequent cell toxicity and developmental defects in zebrafish embryos. Notably, transgenic zebrafish with target RNA expression restricted to endothelial or neuronal cell lineages exhibit localized collateral activity, leading to tissue-specific developmental abnormalities and motility deficits. These findings reveal that RfxCas13d’s collateral activity is threshold-dependent, with abundant target RNA acting as a molecular switch for widespread collateral RNA degradation. This work underscores the need for careful consideration of target abundance when deploying RfxCas13d, and highlights PspCas13b as an alternative for RNA silencing free of collateral activity.

overall_design: RNA-seq of HEK293T cells comparing non-targeting control (NT) versus mCherry-targeting condition (TAR), three biological replicates per condition (six libraries total). Total RNA, paired-end sequencing on Illumina NextSeq.


title: The midbrain–hindbrain boundary region is defined by cellular heterogeneity

city: Aurora

first: rebecca

middle: L

last: orourke

state: CO

institute: University of Colorado Anschutz SOM

summary: Background: During vertebrate embryogenesis, the isthmic region spans the midbrain-hindbrain boundary of the neural tube and includes an organizer (IsO) that is essential for proper formation of adjacent brain regions, yet the molecular and cellular composition of the isthmic region remains unresolved. Results: We employed combined single-nucleus ATAC-seq and RNA-seq (scMultiome) in 13 and 16 hours post-fertilization zebrafish embryos to molecularly resolve cell populations in the isthmic region and we validated our findings in vivo by RNA fluorescence in situ hybridization. We identified two distinct isthmic cell populations – isthmic midbrain (IsMB) and isthmic hindbrain (IsHB) – that share expression of canonical isthmic genes, but that differ in their expression of midbrain vs hindbrain genes. We also uncovered a previously unrecognized heterogeneity within the IsHB, reflecting a canonical fgf8-expressing population anteriorly (IsO/r0a), and a novel fgf8-negative population posteriorly (r0p). We find that inhibition of Fgf signaling disrupts formation of the isthmic region, leading to loss of cell populations except a residual population categorized by a mixed neural identity. Conclusions: Using transcriptional and epigenetic characterization, we expand on prior anatomical and genetic analyses of the isthmic region to refine our understanding of its cellular organization and demonstrate that it consists of several subdomains.

overall_design: Multiome-seq: Single nuclei were extracted from 13 hours post-fertilization (hpf) zebrafish embryos after treatment of the Fgf signaling pathway molecule inhibitor SU5402 beginning at 7 hpf. DMSO was used for vehicle control samples. Joint snRNA- and scATAC libraries were prepared using the 10x Genomics platform.

first: Sylvia

last: Nunez

first: Yong-Il

last: Kim

first: Rebecca

last: O’Rourke

first: Charles

middle: G

last: Sagerström


title: A transcriptomic atlas of the parasitoid wasp Nasonia vitripennis across ploidy, sex, and tissue [RNA-seq WGDL]

city: Nanjing

first: Xuan

last: Li

address: No. 666, Binjiang Avenue, Jiangbei New Area

institute: Nanjing Agricultural University

summary: The parasitoid wasp Nasonia vitripennis is a major insect model for morphology, behavior, and genetics. It has haplodiploid sex determination: unfertilized eggs develop into haploid males and fertilized eggs develop into diploid females. Additionally, polyploids (diploid males, triploid females) occur in Nasonia, representing gene expression mechanisms regulating sexual maintenance outside of standard haplodiploidy. Here, we generated a transcriptomic atlas for N. vitripennis across two tissues (head and abdomen) for typical haploid males and diploid females and polyploid diploid males and triploid females. These data are a resource for analyses on transcriptomic differences across sex, tissue type, ploidy, strain, and temporal change.

overall_design: The WGDL line is an artificially induced neo-polyploid line, resulted from colchicine-induced whole genome duplication. For transcriptome sequencing, diploid and triploid females from generations F2 and F14, and haploid and diploid males from generations F5 and F15 were used. Both head and abdomen tissues were sampled.

first: Kelley

last: Leung


title: Noncoding SNP rs17728461 regulates the malignant progression of lung cancer [RNA-seq]

city: Tianjin

first: Xiaoling

last: Tian

state: Tianjin

address: Tianjin Medical University 22 Qixiangtai Road, Heping Distric

institute: Tianjin Medical University

summary: To study the effect of rs17728461 on lung cancer cells, we performed RNA-seq in H1155 and A549 cells carrying different genotypes of rs17728461.

overall_design: The RNA-seq of H1155 and A549 cells carrying different genotypes of rs17728461.

first: Xinyue

last: Lei


title: Noncoding SNP rs17728461 regulates the malignant progression of lung cancer [4C-seq]

summary: To examine target genes that interact with different alleles of rs17728461 in H155 (C/G) cells.

overall_design: H1155 (C/G) cells were used to performed allele-specific 4C. Hind III and Dpn II were used in the experiments.


title: Fecal miRNome profile of young individuals from two areas of the Campania region

status: Public on Jul 20 2026

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

summary: Recent studies highlighted fecal microRNAs as promising non-invasive biomarkers for investigating the effects of environmental factors on the gut, while also strengthening the association between fecal microRNAs and the gut microbiota. In this study, we explored the fecal miRNome and gut microbiome of 54 young, healthy individuals living in a high-pollution (Land of Fires, LF) or a low-pollution area (Valley of Sele) in Italy’s Campania region.

overall_design: Small RNA-Seq data of fecal samples from healthy subjects

first: Paola

last: De Lisa

first: Alessio

last: Naccarati

first: Barbara

last: Pardini

first: Sonia

last: Tarallo

first: Luigi

last: Montano


title: Patient tumor bulk RNA-seq analysis of the pre-axi-cel treatment tumor microenvironment in large B cell lymphoma

city: TAmpa

first: Yonghong

last: Zhang

state: FL

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

summary: We examined the tumor immune infiltrate and its relationship with clinical outcomes in patients with LBCL receiving Axicabtagene ciloleChimeric antigen receptor (CAR) T cell therapies have revolutionized B cell malignancy treatment, but many patients with large B cell lymphoma (LBCL) experience primary resistance or relapse. To uncover resistance mechanisms, we examined pre-infusion tumor biopsies and observed that increased immunoregulatory macrophages correlate with poor clinical responses. In murine models, CAR T cell-produced interferon-gamma (IFN-) upregulates inducible nitric oxide synthase (iNOS, NOS2) in immunoregulatory macrophages, impairing CAR T cell function. Proteomic profiling revealed that iNOS-expressing macrophages promote apoptosis and cell cycle arrest while downregulating protein synthesis machinery in CAR T cells. Metabolically, CAR T cells exhibit reduced glycolytic intermediates and altered tricarboxylic acid (TCA) cycle activity. Pharmacological inhibition of iNOS enhances CAR T cell treatment efficacy in vivo. Notably, elevated levels of iNOS+CD14+ monocytes in leukaphereses are associated with non-durable responses to CAR T cells. Targeting iNOS in immunoregulatory macrophages, potentially by modulating CAR T-produced IFN-, could improve LBCL outcomes.

overall_design:
RNA-seq of 19 samples and 24 samples from GSE153437 was performed on patient tumor biopsies taken before lymphodepletion and CAR T cell treatment.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Michael

middle: D

last: Jain

first: Marco

last: Davila

first: Sae

last: Bom


title: A transcriptomic atlas of the parasitoid wasp Nasonia vitripennis across ploidy, sex, and tissue [RNA-seq TRA]

overall_design: The TRA line is an artificially induced neo-polyploid line, resulted from knocking down transformer (tra). For transcriptome sequencing, diploid and triploid females from generations F2 and F14, and haploid and diploid males from generations F3 and F15 were used. Both head and abdomen tissues were sampled.


title: Expanding the map of Pol III transcriptome: eCLIP and ROPE-seq of POLR3A

city: Urbana

first: Ruiying

last: Cheng

state: IL

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

institute: The University of Illinois Urbana-Champaign

summary: RNA polymerase III (Pol III) synthesizes noncoding RNAs essential for translation, RNA processing, and transcription regulation. Its activity aligns with cellular growth and nutrient availability, and its dysregulation is linked to diseases like breast cancer and leukodystrophy. Here we use eCLIP and ROPE-seq to identify short-lived Pol III transcripts

overall_design: eCLIP seq and ROPE seq of HEK293T expressing FLAG-eGFP as control and POLR3A

first: Kevin

last: Van Bortle


title: Indirubin inhibits RSL3-induced ferroptosis and ameliorates acute lung injury by activating the Wnt/β-catenin signaling pathway

city: Bengbu City, Anhui Province

first: Bohan

address: 安徽省蚌埠市东海大道2600号

department: School of Pharmacy

institute: Bengbu Medical University

summary: Acute lung injury (ALI) is a severe clinical condition with high morbidity and mortality, yet effective pharmacotherapies remain limited. Ferroptosis, a form of regulated cell death driven by iron‑dependent lipid peroxidation, has been implicated in the pathogenesis of ALI. Indirubin (ID), a natural bisindole alkaloid with established anti‑inflammatory properties, has been reported to activate the Wnt/β‑catenin signaling pathway; however, its role in ferroptosis‑associated ALI remains unexplored. This study aimed to investigate whether indirubin alleviates RSL3‑induced ferroptosis in ALI and to elucidate the involvement of the Wnt/β‑catenin pathway. A cellular model of ALI was established by treating human alveolar epithelial cells with RSL3, a specific GPX4 inhibitor. Cells were treated with indirubin or the ferroptosis inhibitor ferrostatin‑1 (Fer‑1). Protein expression levels of GPX4, SLC7A11, Wnt5a and β‑catenin were assessed by Western blotting; transcriptomic profiling was performed by RNA‑sequencing to identify differentially expressed genes and enriched pathways; ferroptosis‑associated ultrastructural changes were evaluated by transmission electron microscopy (TEM); and molecular docking was performed using MOE software to investigate the direct binding interaction between indirubin and β‑catenin. RSL3 treatment markedly downregulated GPX4 and SLC7A11 expression and suppressed the Wnt/β‑catenin pathway, as evidenced by decreased Wnt5a and β‑catenin levels. Co‑treatment with indirubin dose‑dependently activated the Wnt/β‑catenin pathway, which was accompanied by restored expression of GPX4 and SLC7A11. Transcriptomic analysis confirmed that indirubin enhanced Wnt/β‑catenin signaling components and corrected RSL3‑induced gene expression alterations in ferroptosis‑related pathways. TEM showed that RSL3‑induced mitochondrial shrinkage and increased membrane density were ameliorated by indirubin, and molecular docking revealed that indirubin directly binds to β‑catenin, providing a structural basis for pathway activation. Our findings demonstrate that indirubin attenuates RSL3‑induced ferroptosis and ameliorates ALI by activating the Wnt/β‑catenin signaling pathway, suggesting that indirubin represents a promising therapeutic candidate for acute lung injury.

overall_design: To gain a genome‑wide perspective on the molecular changes induced by ID, we performed RNA‑sequencing on control, RSL3‑treated, and RSL3 + ID treated cells.


title: Inhibition of H3K27M-enhanced ATM signaling increases radiation efficacy in diffuse midline glioma

city: Ann Abor

first: Carl

last: Koschmann

address: 100 Washtenaw Ave.

institute: University of Michigan

summary: H3K27-altered diffuse midline glioma (DMG) is an aggressive and treatment-resistant form of pediatric high-grade glioma (pHGG). The disease is defined by point mutations in histone H3 that convert lysine 27 to methionine (termed H3K27M), resulting in genome-wide epigenetic changes that drive tumorigenesis. While radiation therapy is the standard of care, subsequent recurrence, often within the high dose radiation field, is universal. We found that the apical DNA damage response kinase Ataxia Telangiectasia-Mutated (ATM) was uniquely upregulated in H3K27M-expressing patient tumor samples compared to pHGG expressing only wild type histone H3. Using a panel of H3K27 isogenic cell lines, we further found that H3K27M was associated with reduced H3K27me3 within the ATM promoter, increased ATM mRNA levels, and elevated DNA damage response (DDR) signaling, even in the absence of radiation-induced DNA damage. In assessing the effect of these changes on the ability of AZD1390, a clinical-grade, CNS-penetrant ATM inhibitor, to sensitize cells to radiation, we found that while exogenous expression of H3K27M conferred preferential radiosensitization by AZD1390, CRISPR/Cas9 deletion of H3K27M did not attenuate the efficacy of AZD1390 in patient derived DMG cell lines. Finally, AZD1390 sensitized orthotopic H3K27M mutant tumors to radiotherapy in both immune deficient and syngeneic immune competent hosts with minimal adverse effects. Taken together, these data provide a direct mechanistic link between the H3K27M mutation and ATM expression and support the recently initiated clinical investigation of AZD1390 with radiotherapy in newly diagnosed pHGG.

overall_design: ChIP-seq of H3K27me3, H3K4me3, H3K27ac, and H3K36me3 on murine glioma cells containing H3WT ("PPW"), H3K27M ("PPK"), or H3G34R ("PPG").

first: Erik

middle: R

last: Peterson

first: Leslie

last: Parsels

first: Dana

last: Messinger

first: Viveka

last: Yadav

first: Tingting

last: Qin

first: Meredith

last: Morgan


title: RNASET2 degrades mRNAs that protect against lipotoxicity

city: Austin

first: Alan

last: Lambowitz

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

summary:
Abstract/objective: RNASET2 is a lysosomal RNase whose enzymatic function is required for early events in lipotoxicity. However, the endogenous RNA substrates of RNASET2 that modulate lipid-induced cell death are not known. The purpose of this study was to identify RNASET2 substrates that impact lipotoxic stress.
Methods: RNA sequencing was used to identify RNAs that increase in abundance in human cells upon RNASET2 knockdown, and actinomycin D assays were used to show that RNASET2 impacted decay rates of these RNAs. We tested for the presence of these RNAs in immunoisolated lysosomes and determined the contribution of the lysosomal membrane transporter SIDT2 in delivery of these RNAs to the lysosome. A role for these RNAs in lipotoxic cell death was directly tested in loss- and gain of function analysis.
Results: RNASET2 knockdown increased steady-state abundance of UCHL3, PFN2 and PRDX3 mRNAs and prolonged their decay rate, leading to increased protein expression. These mRNAs were delivered to the lysosomal lumen by the lysosomal membrane transporter SIDT2 that mediates RNautophagy. While UCHL3 and PFN2 have not previously been implicated in lipotoxic responses, expression of these proteins protected against lipid-induced cell death.
Conclusions: Our study identified specific mRNA substrates of RNASET2 and uncovered a previously unexplored function for lysosomes and RNautophagy in regulation of the response to metabolic stress. Moreover, we demonstrate that RNautophagy selectively regulates turnover of specific endogenous RNAs and thereby impacts regulation of gene expression.

overall_design: TGIRT-seq profiling of wildtype HEK293T cells and their RNASET2 knockdown derivatives under BSA or Palmitate treatment.

first: Shuiling

last: Zhao

first: Stevens

last: Bontemps

first: Ryan

middle: M

last: Nottingham

first: Jun

last: Yao

first: Mariana

last: Acuña

first: David

middle: E

last: Cohen


title: small RNA seq: POLR3G and POLR3GL knockout in THP-1 and POLR3G knockdown in HEK293T

first: Ruiying

summary: RNA polymerase III (Pol III) synthesizes noncoding RNAs essential for translation, RNA processing, and transcription regulation. Its activity aligns with cellular growth and nutrient availability, and its dysregulation is linked to diseases like breast cancer and leukodystrophy. Here we explot the effect of POLR3G and POLR3GL knockout in THP-1 and POLR3G knockdown in HEK293T to small RNA expression

overall_design: POLR3G and POLR3GL knockout in THP-1 and POLR3G knockdown by treating the cell using 200nM of POLR3G targeting ASO for 48h in HEK293T


title: Brain-sensing synNotch-CAR T-cells enable precise targeting and clearance of diffuse midline glioma in multiple preclinical models

city: San Francisco

first: Hideho

last: Okada

department: Neurological Surgery

institute: University of California, San Francisco

summary: Diffuse midline glioma (DMG) is a lethal pediatric brain tumor with limited therapeutic options and a poor prognosis. The ultimate success of chimeric antigen receptor (CAR) T-cell therapy requires improving T-cell tumor infiltration, and persistence, and reducing the risk of on-target/off-tumor toxicity. Here, we adapt and advance a brain-restricted CAR T-cell platform, previously validated in glioblastoma, to address the distinct anatomical and biological challenges of DMG. We engineer  we test whether a strategy developed for  glioblastoma can also be effective against DMG. We evaluated a T- cell circuit in which a brain-specific sensor -- the synthetic Notch (synNotch) receptor recognizingagainst Brevican (BCAN) -- induces CAR the expression against of a CAR targeting either EphA2 or IL-13Rα2 (“B-SYNC”), enabling multi-antigen tumor recognition tumor recognition through multiple antigens while restricting CAR expression to the CNS. In immunodeficient DMG models, a single infusion of B-SYNC T- cells, either by intravenousintravenously (IV) or intracerebroventricularly (ICV) infusion, led to tumor infiltration, sustained persistence, robust anti-tumor activity, and significantly extended survival. An alternative BCAN-primed circuit CAR inducing a CAR targeting eithertargeting  B7-H3 or IL-13Rα2 (“B-SYNC-B/I”) similarly improved therapeutic efficacy when delivered IV. However, ICV administration triggered fatal neurotoxicity due to low-level B7-H3 expression in non-tumor CNS regions, indicating that rapid CNS exposure via ICV delivery can amplify off-tumor toxicity. In contrast, in an immunocompetent syngeneic DMG model, both IV and ICV delivery of a murinized BCAN-gated B7-H3 CAR (mB-SYNC-B7-H3) achieved durable tumor clearance and resistance to rechallenge, without any detectable neurotoxicity. Mechanistically, synNotch-primed CAR T--cells exhibited reduced exhaustion, enhanced activation, and enrichment of naïve and stem- cell memory-like subsets. , supporting superior functional durability in the DMG microenvironment. These findings demonstrate that brain-sensing synNotch CAR T circuits represent a generalizable and translatable strategy for targeting multiple CNS malignancies, including DMG.

overall_design: Bulk RNA sequencing was performed on CD4+ and CD8+ T cells (2 cell types) transduced with either a constitutive CAR or B-SYNC construct (2 transduction conditions). Experiments were performed using cells generated from two independent donors (biological replicates, n = 2). For each donor, cell type, and transduction condition, three technical replicates (n = 3) were prepared and sequenced.

first: Senthilnath

last: Lakshmanachetty

first: Takahide

last: Nejo

first: Wendell

last: Lim


title: Paneth cell TNF-receptor 1 controls zinc deficiency induced hiarrha

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

summary: In humans, mild to severe Zn2+ deficiency is manifested by intestinal health issues such as diarrhea, and Zn2+-based therapies are beneficial in such diseases. We established a mouse model, based on a Zn2+ deficient diet (ZDD), and focused on Paneth cells, the most critical cells controlling intestinal microbiota. Eight weeks of ZDD, compared to standard diet (StD), has mild effects on fecal consistency, Paneth cell morphology and Paneth cell transcriptome, but 16S reveals important changes in ileal microbiome composition. The latter renders mice significantly more sensitive to challenges, involving critical functions of intestinal bacteria, such as peritoneal sepsis and TNF-induced systemic inflammatory response syndrome (SIRS). While studying the role of TNF receptor P55 of Paneth cells in this latter finding, we observed that P55PanethKO mice, on a ZDD, display severe diarrhea. The transcriptome in Paneth cells in such mice, compared to P55PanethWT controls on ZDD, suggests the induction of a strong IFN response in these cells and complete absence of Unfolded Protein Response (UPR) and a further skewing of microbes, towards diarrhea-causing Enterococcus gallinarum. We suggest that in wild type mammals, biological activity of TNF on Paneth cells is essential to protect these cells against excessive IFN responses and to prevent diarrhea. Potential underlying mechanisms are discussed.

overall_design: Mice WT and KO for P55 (Tnfrsf1a) in paneth cells were placed on standard chow or a zinc deficient diet and treated with TNF or PBS control. This experiment was run in parrallel with GSE237759 and uses the same control mice, of which several samples were sequenced in this dataset to correct for batch effects

first: Somara

last: De Beul

first: Tineke

last: Vanderhaeghen

first: Natalia

last: Garcia Gonzalez

first: Charlotte

last: Wallaeys

first: Jolien

last: Vandewalle

first: Riet

last: De Rycke

first: Fabien

last: Thery

first: Francis

last: Impens

first: Serge

last: Verbanck

first: Filip

last: Van Immerseel

last: Boyens

first: Takao

last: Iwawaki

first: Richard S

last: Blumberg

first: Claude

last: Libert


title: APOE3 and APOE4 Human Astrocytes Differentially Modulate Alzheimer’s Disease Pathology and Microglial Responses in Chimeric Mice

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary: To investigate how APOE3 and APOE4 human iPSC-derived astrocytes influence the gene expression profile of the mouse host microglia in vivo, we performed bulk RNA sequencing of cortical regions adjacent to transplanted astrocytes in AD chimeric mice. Human iPSC-derived astrocytes (APOE3 or APOE4) were transplanted into neonatal Alzheimer's disease model mice and analyzed 6-7 months post-transplantation. Mouse-specific transcripts were analyzed to compare the transcriptomic profiles of host microglia in AD chimeric mice engrafted with APOE4 versus APOE3 human astrocytes.

overall_design: Bulk RNA-seq performed on cortical tissue from 12 AD chimeric mice (6 APOE3, 6 APOE4 astrocyte recipients) 6 months after transplantation of human iPSC-derived astrocyte progenitors. Libraries prepared from 10ng total RNA using SMARTer Stranded Total RNA-seq Kit v3 Pico Input Mammalian (Takara Bio) and sequenced on Illumina NovaSeq 6000 (150 bp paired-end). Ribosomal RNA reads (~50%) were removed using SortMeRNA v4.3.6 prior to alignment. Mouse-specific read count matrices analyzed using DESeq2 v1.44.0, with RIN and total RNA input as covariates.

first: Leire

last: Ruiz

first: Nuria

last: Galbis-Gramage

first: Lorea

last: Cortes

first: Laura

last: Escobar

first: Pranav

last: Preman

first: An

last: Snellinx

first: Takashi

last: Saito

first: Takaomi C

last: Saido

last: Saiz-Auz

first: Alberto

last: Rabano-Gutierrez

first: Ana M

first: Ibai

last: Diez

first: Julia

last: TCW

first: Alison

last: Goate

first: Bart

last: De Strooper

first: Elena

last: Alberdi

first: Amaia M

last: Arranz


title: miRNA expression profiling in MIA PaCa-2 pancreatic cancer cells after sotorasib exposure

city: Kagoshima

first: Ayako

last: Nagat

state: Kagoshima

address: 8-35-1 Sakuragaoka

department: Department of Digestive Surgery, Breast and Thyroid Surgery

institute: Kagoshima University

summary: Sotorasib is a selective inhibitor of KRAS G12C. In this study, miRNA expression changes in response to sotorasib exposure were analyzed by sequencing in MIA PaCa-2 pancreatic cancer cells harboring a KRAS G12C mutation.

overall_design: MIA PaCa-2 cells were treated with 1 μM sotorasib for 0, 6, 24, and 48 hours. RNA was collected at each time point and subjected to sequencing analysis.

first: Atsushi

last: Furoi

first: Naohiko

last: Seki

last: Nagata


title: Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors

city: Cambridge

first: Nir

last: Hacohen

address: 415 Main Street, Room 6032

department: Cell Circuits Program / Center for Cell Circuits

institute: Broad Institute

summary: Stem-like TCF7+ CD8 T cells sustain anti-tumor responses and support immune checkpoint blockade. We systematically identified regulators of this cell state using genome-wide CRISPR screens in primary T cells in vitro. Using random barcodes to link clonal relationships with guide identity and transcriptional states in single cells, we inferred differentiation trajectories and differentiation rates of CD8 T cells in tumors, while mitigating confounding clonal bias. We found that Trim28-deficient T cells in tumors were enriched in the TCF7+ cell state, depleted in cycling and terminal effector states, and uniquely generating a tissue resident memory (TRM)-like state with increased chromatin accessibility at known TRM loci as well as repeat elements. Despite the increase in TCF7+ CD8 T cells, loss of Trim28 did not improve tumor control, likely because of reduced effector differentiation, highlighting the need for tuning the balance and dynamics of stem-like versus effector states for effective tumor clearance.

overall_design: Naive Cas9 x OT-I CD8 T cells were transduced with a Trim28/Setdb1 construct library, transferred into B16-OVA tumor-bearing mice, harvested from tumors or draining lymph nodes, mouse-hashtagged, pooled by tissue and harvest batch, and profiled with 10x Genomics gene-expression, CRISPR guide-capture, feature-barcode, and clonal-barcode information.

first: Marc

last: Schwartz

first: Dillon

last: Lue

first: Mohammed

last: Mutaher

first: Miriam

last: McNerney

first: Oluwatomisin

last: Olajide

first: Arnav

last: Mehta

first: Jared

last: Rowe

first: Ryan

last: Park

first: Juan

last: Dubrot

first: Aziz

last: Al’Khafaji

first: Matthew

last: Bakalar

first: Lynn

last: Bi

first: Martin

last: LaFleur

first: Kathleen

last: Yates

first: Robert

last: Manguso

first: John

last: Doench

first: Arlene

last: Sharpe

first: Yuri

last: Pritykin


title: Transcriptional profiling of the Epidermis of Naked Mole-RatsTreated with DMBA and TPA

city: Boston

first: Vladimir

last: Botchkarev

address: 609 Albany Street

institute: Boston University

summary: We compared expressions of cancer-related genes (tumor suppressor genes and oncogenes) in the skin epidermis between Naked mole-rats treated with DMBA/TPA and control animals. Bulk RNA-seq analyses revealed that in contrast to control animals, epidermis of Naked mole-rats treated with DMBA/TPA is characterized by increased expression of anti-cancer genes, activation of genes controlling ferroptosis, as well as by downregulation of numerous oncogenes including components of NF-kB, Wnt and tyrosine kinase signaling pathways.

overall_design: Dorsal skin was collected from 6-7 month-old Naked mole-rats treated with DMBA or DMBA/TPA, or from aceton-treated control animals. Skin epidermis was separated from the dermis. RNA was isolated and processed for RNA-seq analyses. Naked mole-rat RNA-seq libraries were sequenced by LC Sciences (Houston, TX), while mouse libraries were sequenced by Med Genomics (Foster City, CA).

first: Iqra

last: Fatima

first: Elena

last: Rozhkova

first: Andrey

last: Sharov


title: Transcriptional profiling of Mouse Epidermis Treated with DMBA and TPA

summary: We compared expressions of cancer-related genes (tumor suppressor genes and oncogenes) in the skin epidermis between FVB mice treated with DMBA/TPA and control animals. Bulk RNA-seq analyses revealed that in contrast to control animals, epidermis of mice treated with DMBA is characterized by upregulation of the genes enriched for immune response pathways, whereas downregulated genes were involved in the control of extracellular matrix remodeling and wound healing. In mouse epidermis treated by DMBA/TPA, transcriptional response to DMBA/TPA at the pre-tumor stage was accompanied by upregulation of the genes controlling epidermal differentiation, oncogenes including the components of Wnt signaling pathway, as well as of selected tumor suppressor genes.

overall_design: Dorsal skin was collected from 7-8 week-old -old FVB mice treated with DMBA or DMBA/TPA, or from aceton-treated control animals. Skin epidermis was separated from the dermis. RNA was isolated and processed for RNA-seq analyses. Mouse RNA-seq libraries were sequenced by Med Genomics (Foster City, CA).


title: Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors [Multiome]

first: Nir

last: Hacohen

overall_design: Cas9 x OT-I x CD45.1 Trim28-knockout donor CD8 T cells and Cas9 x OT-I x CD45.2 NT donor CD8 T cells were mixed, transferred into recipients, recovered from B16-OVA tumors, and profiled using 10x Genomics Chromium Single Cell Multiome gene-expression and chromatin-accessibility libraries.

first: Marc

last: Schwartz

first: Dillon

last: Lue

first: Mohammed

last: Mutaher

first: Miriam

last: McNerney

first: Oluwatomisin

last: Olajide

first: Arnav

last: Mehta


title: Transcriptional profiling of epidermal keratinocytes from Naked mole-rats and mice

summary: We compared expressions of cancer-related genes (tumor suppressor genes and oncogenes) between homeostatic epidermal keratinocytes from Naked mole-rats and FVB mice. Bulk RNA-seq analyses revealed that homeostatic epidermal keratinocytes in Naked mole-rats maintain high expression of tumor suppressor genes that inhibit cell proliferation and activity of pro-oncogenic Wnt, IGF and Hedgehog signaling pathways, stimulate apoptosis and DNA repair, which is associated with downregulation of several key oncogenes stimulating skin carcinogenesis. In contrast to Naked mole-rats, mouse keratinocytes predominantly express tumor suppressor genes linked to cell adhesion, growth factors signaling, nuclear receptors and transcriptional regulators, as well as show decreased expression of oncogenes driving carcinogenesis outside of the skin.

sample_organism:
Mus musculus
Heterocephalus glaber

platform_organism:
Mus musculus
Heterocephalus glaber

overall_design: Dorsal skin was collected from normal homeostatic 6–7 month-old Naked mole-rats and 7-8 week-old FVB mice, skin epidermis was separated from the dermis and epidermal keratinocytes were FACS-sorted using anti-Cd49f (integrin a6) antibody. RNa was isolated and processed for RNA-seq analyses. Naked mole-rat RNA-seq libraries were sequenced by LC Sciences (Houston, TX), while mouse libraries were sequenced by Med Genomics (Foster City, CA).


title: RNA Polymerase III inhinition leads to changes in protein coding gene expression

first: Ruiying

last: Cheng

summary: RNA polymerase III (Pol III) produces small noncoding RNAs essential for diverse cellular processes, including translation (tRNA, 5S rRNA, 7SL RNA), RNA processing (U6 snRNA, RPPH1, RMRP), and transcription regulation (7SK snRNA). Here we explore the unexpected effect of Pol III repression on protein coding gene expression.

overall_design: For POLR3A KD Hek293T cells are transfected with either control siRNA or POLR3A siRNA, and cells are collected 2 days after knockdown. For Pol III small molecule inhibition, Hek293T cells are treated with either DMSO (vehicle, 0.1%) or ML60218 (25uM). HEK 293T cells are treated with various ASO or siRNA targeting Pol III subunit POLR3G and POLR3GL, as well as overexpression of Pol III inhibitor MAF1; THP-1 cells are treated with Pol III inhibitor ML-60218, in combindation protein synthesis inhibitor. Libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche) and sequenced on two 25B lanes for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits.

first: Kevin

last: VanBortle


title: BACH1 acts as a pioneer repressor to enable macrophage plasticity and adaptation across tissues and inflammatory contexts [RNA-seq/ATAC-seq]

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

summary: Transcriptional master regulators of the myeloid lineage (like PU.1, Cebpa/b, etc.) are believed to be the main drivers of chromatin reprogramming during differentiation and polarization. Such developmental transcription factors act via their pioneer ability to open chromatin de novo and bookmark genomic regulatory sites (enhancers and promoters) to later recruit signal-dependent TFs, co-factors, and the basal transcriptional machinery. However, recent studies by us and others challenged this “developmental TF-centric” mode as they suggested that signal-dependent TFs, particularly repressors, can also have a pioneer and thus safeguarding role in the MF epigenome at baseline and during acute inflammation. Such an expanded model predicts that active transcriptional repression and chromatin bookmarking by signal-dependent master regulators are key mechanisms for safeguarding the enhancer repertoire and proper priming, deployment, and resolution of an inflammatory response. Here, we show that BACH1, a heme-sensitive transcriptional repressor, acts as such a pervasive epigenomic safeguard to regulate tissue macrophage identity. We show that BACH1 is part of the core hardwired transcriptional program of ground-state macrophages shaping the chromatin accessibility of thousands of distal regulatory elements. Furthermore, BACH1 cistrome is extensive, not static but dynamic, and expanding upon different inflammatory stimuli and correlates with pre-formed and de novo formed enhancer-promoter networks. We further show that myeloid BACH1 is indispensable in vivo for tissue regeneration upon injury as it regulates the kinetics of Ly6C+ to Ly6C- transition of inflammatory macrophages and regulates the onset, the kinetics and magnitude of expression of critical inflammatory and repair-related genes. Finally, BACH1 was found to be required in vivo for competitive fitness and tissue adaptation of several tissue-resident macrophage populations (eg. lung, peritoneal macrophages), further supporting its pervasive role in acquiring and maintaining the functional specificity and diversity of tissue macrophages. Taken together, our data suggest that BACH1 acts as a signal-dependent master regulator that directly controls key transcriptional circuits during tissue macrophage subtype function, specification and inflammatory responses in vivo.

overall_design: Transcriptomic and epigenetic profiling of WT and Bach1-deficient mouse alveolar macrophages, using high throughput sequencing (RNA-seq, ATAC-seq).

first: Dora

last: Bojcsuk

first: Petros

last: Tzerpos


title: Comparison of iPSC lines during differentiation to intermediate mesoderm

city: Parkville

first: Kynan

middle: Thomas

last: Lawlor

address: Murdoch Children's Research Institute, Flemington Road

institute: Murdoch Children's Research Institute

summary: To examine variability in differentiation outcomes, distinct iPCS lines were differentiated to intermediate mesoderm following the protocol of Takasato et al (2015). Cells were treated with 4 or 5 days of CHIR followed by 4 days of FGF9, dissociated and profiled to generate bulk transcriptome data for each. Cell lines used were "MAFB-mtagBFP;GATA3-mCherry" described in Vanslambrouck et al, JASN, 2019; "NG-hiPSC line1B", D2MCBL01B, described in Novoa et al, Cytotherapy 2024; AICS-0061, "H2B-GFP AICS", a H2B-GFP reporter from the Allen Institute of Cell Science, Allen Cell Collection.

overall_design: 3 different iPSC lines differentiated to intermediate mesoderm by addition of CHIR for 4 days, followed by FGF9 for 3 or 4 days.

first: Kynan T

first: Mian

last: Xie

first: Melissa H

last: Little

first: Sean B

last: Wilson


title: Effect of GRP75 deficiency on gene expression in different subsets of CD8+ T cells

city: Hangzhou

first: Fan

last: Zhao

state: Zhejiang Province

address: 866 Yuhangtang Road, Xihu District

institute: Zhejiang University

summary: The development and functional maintenance of CD8+ T cells are metabolically regulated processes in which mitochondria serve as the central hub. Here, we identify glucose-regulated protein 75 (GRP75) as a critical mitochondrial regulator controlling these processes. Using T cell-specific Hspa9 (encodes GRP75) knockout mice, we demonstrate that GRP75 deficiency disrupts CD8+ T cell fate, leading to defective T cell homeostasis and impaired memory differentiation. Mechanistically, impaired mitochondrial function in GRP75-deficient CD8+ T cells leads to perturbation of IL-7R signaling and aberrant expression of effector-associated molecules. Further studies reveal that GRP75 deficiency leads to upregulation of Interferon regulatory factor 4 (IRF4), a critical transcription factor for effector versus memory fate, which in turn suppresses memory CD8+ T cell differentiation. Our findings establish GRP75 as a pivotal mitochondrial checkpoint that coordinates metabolic state and functional fate in CD8+ T cells.

overall_design: To investigate the role of GRP75 in different CD8+ T cell subsets, we isolated naive CD8+ T cells from 8-week-old WT and Hspa9 cKO mice, followed by in vitro differentiation into effector and memory subsets. RNA-seq was then performed on the naive, effector, and memory subsets for gene expression profiling analysis.

first: Pengfei

last: Wang

first: Zejin

last: Cui

first: Zhishan

first: Lize

last: Wu

first: Kaixiang

last: Zhu

first: Linrong

last: Lu


title: Leveraging TNFR2 for antitumour immunity: Treg depletion and myeloid reprogramming versus T cell costimulation

city: Lund

first: Björn

last: Frendeus

state: Skane

address: Ideongatan 1

country: Sweden

institute: BioInvent International

summary: We conducted single-cell RNA sequencing using the 10x Genomics Chromium Next-GEM Flex protocol to investigate the mechanism of action of two TNFR2-targeting antibodies—one ligand-blocking and the other agonistic. Our goal was to assess their anti-cancer potential in comparison to established immune checkpoint inhibitors, anti-PD1 and anti-CTLA4. These studies provide new insights and role of TNFR2 as a therapeutic target in cancer.

overall_design: BALB/c mice were inoculated subcutaneously with 1 million CT26 cells (ATCC). Mice were treated intraperitoneally with anti-mouse PD-1 (29F.1A12, rat IgG2a, 10 mg/kg, BioXcell), anti-mouse CTLA-4 (9H10, hamster IgG 10 mg/kg, BioXcell), anti-TNFR2 (3F10 mIgG2a, 10 mg/kg or 5A05 mIgG1, 10 mg/kg, both in-house) or isotype control (mIgG2a, 10 mg/kg, in-house) when the tumors reached a size of approximately 100 mm3. After start of treatment, CD45+ cells were isolated from the tumors day 2 (after 1 treatment) or day 8 (after 3 treatments) using Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Niyaz

last: Yoosuf

first: Petra

last: Holmkvist

first: Linda

last: Mårtensson

first: Ingrid

last: Teige


title: Integrated bulk and single-cell transcriptome analysis reveals the impact of cyclophosphamide on tumor microenvironment in triple-negative breast cancer models [scRNA-Seq]

city: Nantong,Jiangsu,China

first: Xiaorong

last: Zhou

state: Jiangsu province

address: 19 Qixiu Road

institute: Nantong University

summary: Triple-negative breast cancer (TNBC) remains a formidable clinical challenge. Although preclinical investigations utilizing TNBC mouse models have demonstrated that intermittent cyclophosphamide (CTX) treatment yields superior anti-tumor effects, partly through immune stimulation, mechanisms by which CTX modulates the tumor microenvironment (TME) are not yet fully understood. In this study, we assessed the impact of optimal (140 mg/kg every 6 days, C140) and suboptimal (100 mg/kg every 6 days, C100) CTX treatment regimens on 4T1 tumors, a widely utilized orthotopic TNBC mouse model. While the C100 regimen was better tolerated than the C140 regimen, it was less effective in inhibiting tumor growth. Through integrated bulk and single-cell RNA sequencing of tumor tissues, we discovered that CTX treatment not only inhibited cancer cell proliferation and epithelial-mesenchymal transition but also remodeled the TME by recruiting and reprogramming various immune cells, thereby enhancing the anticancer immune response in a dose-dependent manner. Although the C140 regimen demonstrated significant tumor suppression, it also induced notable extracellular matrix remodeling and led to the accumulation of cancer-associated fibroblasts within the tumor microenvironment. Furthermore, the C140 regimen caused considerable exhaustion of CD8+ T cells and was linked to increased expression of various immune checkpoint molecules, including PD-L1/PD-L2, CD39, and CD200. These effects may compromise therapeutic efficacy and potentially contribute to the development of drug resistance. Overall, our findings elucidate both cancer-cell-intrinsic and tumor microenvironment-dependent mechanisms of CTX action at both local and systemic levels, highlighting potential targets for optimizing chemoimmunotherapy in TNBC.

overall_design: In the subcutaneous tumor formation experiment, 4T1 cells resuspended in 100 μL PBS buffer were inoculated into the subcutaneous mammary gland area of each mice (1×10⁶ cells). Nine days later, when the tumor volume reached approximately 100 mm³, the mice were randomly divided into three groups according to the experimental grouping designing. The control group was intraperitoneally injected with 100 μL PBS, and the experimental groups were intraperitoneally injected with 100 or 140 mg/kg CTX in 100 μL PBS, respectively. All groups were injected once every 6 days. On the third day after the third treatment cycle, the mice were euthanized, and the tumor tissues were harvested for bulk RNA sequencing and scRNA-seq.

first: Ling

last: Zuo

first: Jia

last: Ge


title: Enhancing the therapeutic efficacy of gambogenic acid by modulating the NRF2/HSF1/HO-1 signaling pathway in cisplatin-resistant lung cancer cells

summary: Cisplatin is a cornerstone in cancer chemotherapy and chemoimmunotherapy protocols; however, the emergence of drug resistance poses a substantial challenge. Gambogenic acid (GNA), a natural compound derived from gamboge, has been documented to exert antitumor effects across a range of cancer types. Nonetheless, its clinical utilization is restricted by the necessity for high dosages to attain adequate bioactivity. In this study, we demonstrated that GNA could induce significant cell death in cisplatin-resistant A549/DDP cells. GNA treatment reduced NRF2 protein levels in A549/DDP cells, and both genetic and pharmacological inhibition of NRF2 further enhanced the cytotoxic effects of GNA. In addition, GNA treatment increased the expression of HO-1 through a mechanism independent of NRF2. Subsequent analyses indicated that GNA treatment elicited a heat-shock response, particularly in cells with NRF2 knockdown. While baseline HO-1 expression in A549/DDP cells is regulated by NRF2, the upregulation of HO-1 induced by GNA is dependent on HSF1, a key regulator of the heat-shock response. Furthermore, although treating cells with HO-1 inhibitors alone did not affect the viability of A549/DDP cells, it dramatically enhanced the GNA-induced cell death in combinational therapy. Collectively, our findings demonstrated that GNA possesses substantial cytotoxic activity in cisplatin-resistant lung cancer cells, and the effect can be augmented by disrupting the NRF2 and HSF1 signaling pathways, which jointly promote HO-1 expression in cells coping with GNA-induced acute stress. This study underscores a novel mechanism underlying the anticancer activity of GNA and suggests a potential strategy to overcome the translational challenges of GNA in lung cancer therapy.

overall_design: A549/DDP shNC and shNRF2 cells were cultured to reach 70% confluence，then treated with DMSO or 4 µM GNA for 24 h. After that, cells were harvested for bulk RNA sequencing and scRNA-seq.

first: Dandan

last: Cao