title: The cAMP receptor protein, SyCRP1 acts as a transcriptional repressor of CO2-concentrating mechanism genes at high inorganic carbon levels in cyanobacteria

city: Hyderabad

first: Suraj

last: Chauhan

state: Telangana

address: Prof. C.R. Rao Road, Central University P.O., Gachibowli

department: Biotechnology and Bioinformatics

country: India

institute: University of Hyderabad

summary: CO2-concentrating mechanism (CCM) is a unique adaptation that evolved in cyanobacteria for inorganic carbon (Ci) sequestration under limiting Ci levels. The CCM is based on several Ci uptake systems and the carboxysome in which RubisCO is confined in a high CO2 environment. Many CCM components are transcriptionally upregulated under low Ci levels through the combined action of the transcriptional factors NdhR, CmpR and the cAMP-binding SyCRP1. Here we show that, SyCRP1 senses the high Ci levels through high cAMP thereby repressing CCM genes. SyCRP1 possess low- and high-affinity cAMP binding sites. Further, the specific interaction of SyCRP1 with membrane lipids was shown. Flag-tagged SyCRP1, when ectopically expressed, was localized to the membrane and released to the cytosol upon cAMP binding under high Ci levels. Finally, ChIP-seq experiments revealed that SyCRP1 binds cis-acting elements at the promoters of multiple transcription units, mainly those involved in CCM. EMSA confirmed SyCRP1’s binding to target DNA-elements. Collectively, our results establish SyCRP1 as a transcriptional repressor of the cyanobacterial CCM under high Ci conditions.

overall_design: ChIP-seq of 3XFlag tagged SyCRP1 from Synechocystis PCC 6803 grown in BG11 with high CO2 condition. SyCRP1 was expresesed in BG11 that contains 0.17 µM cobalt. Cells grown till 1 OD (730 nm) and for high CO2  condition, 5% (v/v) was supplemented in sterile air for bublling the cultures.

first: Prakash

last: Jogadhenu


title: Crosstalk between EZH2 and m6A RNA methylation promotes prostate cancer progression through modulating an m6A autoregulation pathway

status: Public on Oct 05 2025

city: Chicago

first: Yang

last: Yi

state: IL

address: 303 E Superior St

department: Department of Urology

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: N6-methyladenosine (m6A), the most predominant RNA modification in humans, participates in various fundamental and pathological bioprocesses. Dynamic manipulation of m6A deposition in the transcriptome is critical for cancer progression, while how this regulation is achieved remains understudied. Here, we report that in prostate cancer (PCa), Polycomb group (PcG) protein Enhancer of Zeste Homolog 2 (EZH2) exerts an additional function in m6A regulation via its enzymatic activity. Mechanistically, EZH2 methylates and stabilizes FOXA1 proteins from degradation, which in turn facilitates the transcription of m6A reader YTHDF1. Through activating a m6A autoregulation pathway, YTHDF1 enhances the translation of METTL14 and WTAP, two critical components of the m6A methyltransferase complex (MTC), and thereby upregulates the global m6A level in PCa cells. We further demonstrate that inhibiting the catalytic activity of EZH2 suppresses the translation process globally through targeting the YTHDF1-m6A axis. By disrupting both the expression and interaction of key m6A MTC subunits, combinational treatment of EZH2 degrader MS8815 and m6A inhibitor STM2457 mitigates PCa tumor growth synergistically. Together, our study decodes a previously hidden interrelationship between EZH2 and RNA modification, which may be leveraged to advance the EZH2-targeting curative strategies in cancer.

overall_design: Nanopore Direct RNA sequencing of C4-2 cells after silencing EZH2 and METTL3, with two replicates each. RNA-sequencing of C4-2 cells after silencing YTHDF1 and treatment with EZH2 enzymatic inhibitor EPZ6438. In parallel, we performed ribosome profiling of both conditions using RiboLace library construction.

first: Joshua

last: Fry

first: Rendong

last: Yang

first: Qi

last: Cao


title: Tumour-associated tissue-resident memory T (TRM) cells and exhausted T cells are clonally and developmentally distinct populations

status: Public on Oct 06 2025

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

summary: CD8+ T cells serve as a key weapon in the therapeutic armamentarium against cancer. While CD8+ CD103+ T cells with a tissue-resident memory (TRM) phenotype have been favourably correlated with patient prognoses1-6, the tumour microenvironment comprises dysfunctional exhausted T (TEX) cells that exhibit a myriad of TRM-like features, leading to conflation of these cell types. Here, we deconvolute TRM and TEX cells within the intratumoural CD8+ CD103+ T cell pool across human cancers, ascribing markers and gene signatures that distinguish these CD8+ populations and enable their functional distinction. We found that while TRM cells exhibit superior functionality and are associated with long-term survival post tumour resection, TEX cells are associated with responsiveness to immune checkpoint blockade. Importantly, we show that tumour-associated TEX and TRM cells are clonally and developmentally distinct populations, with the latter predominantly comprised of low affinity and tumour-independent bystanders. Tumour-specific TRM cells may form in circumstances where specific tumour antigens are lost or inaccessible, and these TRM cells can be pushed towards exhaustion when cognate antigen is re-encountered. Thus, chronic T cell receptor signalling within tumours is the key distinction between tumour-associated TRM and TEX cells. Therefore, the most fruitful approaches to utilise TRM cells in anti-tumour therapies are likely embedded in the repurposing of tumour-independent TRM cells already present within tumours.

overall_design: Breast tissue from women with breast cancer and blood from healthy women was sampled and CD3+ cells sequenced.

first: Thomas

last: Burn

first: Laura

last: Mackay


title: Loss of aquaporin-1 triggers epithelial-mesenchymal transition in human cholangiocarcinoma

city: Austin

first: Sergio

last: Gradilone

address: 801 16th Avenue NE

department: The Hormel Institute

institute: University of Minnesota

summary: Background and Aims: Epithelial-mesenchymal transition (EMT) is involved in metastatic dissemination and associated with the progression of cholangiocarcinoma (CCA). Aquaporin-1 (AQP1) is a water channel expressed by cholangiocytes described to modulate cell proliferation and invasion in several cancers. However, the role of AQP1 in CCA remains unknown. Our aim was to study the function of AQP1 in CCA. Material and methods: AQP1 expression was evaluated in 39 human intrahepatic CCA (iCCA) by transcriptomic analysis. AQP1-KO in CCA cells, HucCCT1 was achieved by CRISPR/Cas9. Incucyte live-cell imaging system was used for functional studies. Next-generation sequencing (RNAseq) was used to further study the consequences of AQP1 KO. EMT and signaling pathways were evaluated by RT-qPCR, western blot, and immunostaining. In vivo experiments were performed using a xenograft CCA model.  Results: AQP1 expression correlated positively with overall survival in patients with iCCA and negatively with EMT, stemness, and proliferative signatures. In vitro, RNA-seq analysis of CCA cells depleted for AQP1 showed a downregulation of epithelial markers (CDH1 and KRT19; p< 0.001) and an upregulation of mesenchymal markers (VIM and FN1; p < 0.001). In these cells, we observed a phenotypic change with induction of cell scattering, a loss of cell-cell junction protein E-cadherin, and a higher expression of vimentin and ZEB1, an EMT-inducing transcription factor. Functionally, loss of AQP1 is associated with increased cell migration and proliferation. Moreover, we found an activation of the IGF2/IGF1R/IR pathway in AQP1-depleted CCA cells. In vivo, AQP1-depleted CCA cells displayed a higher tumorigenic potential and tumor burden than control cells.  Conclusion: Our data suggest that AQP1 acts as a tumor suppressor in CCA by acting both on cell proliferation and migration through an EMT process. Therefore, AQP1 might have an important role in the regulation of CCA progression.

overall_design: AQP1-KO in CCA cells, HucCCT1 was achieved by CRISPR/Cas9. Next-generation sequencing (RNAseq) was used to further study the consequences of AQP1 KO.

first: Cesar

last: Gaspari

first: Carine

last: Beaupere

first: Seth

last: Richard

first: Estanislao

last: Peixoto

first: Javier

last: Vaquero

first: Marie

last: Vallette

first: Ander

last: Arbelaiz

first: Corentin

last: Louis

first: Cedric

last: Coulouam

first: Raul

last: Marinelli

last: Fouassier

first: Juan

middle: E

last: Abrahante


title: WEE1 inhibition triggers GCN2-mediated activation of the integrated stress response.

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The WEE1 kinase negatively regulates the CDK1/2 kinases to control DNA replication and prevent premature entry into mitosis. Pharmacological inhibition of WEE1 (WEE1i) causes hyperactivation of CDK1 and CDK2, leading to premature mitosis in the presence of DNA lesions. WEE1i treatment is particularly cytotoxic in cells with oncogene-induced or treatment-induced replication stress. To uncover genetic factors that sensitize cancer cells to WEE1i, a genome-wide insertional mutagenesis screen was performed and identified that mutation of the alternative translation initiation factor EIF2A sensitized cells to WEE1i. WEE1i sensitivity of EIF2AKO cells was not explained by altered replication kinetics. Rather, WEE1i leads to a translational shut-down which is lethal in combination with the reduced translation in EIF2AKO cells. A genome-wide CRISPR-Cas9 screen in WEE1i-treated cells revealed that inactivation of the integrated stress response (ISR) kinase GCN2 rescued WEE1i-mediated cytotoxicity. In line with these findings, WEE1i resulted in GCN2 activation, ATF4 upregulation and a translational shutdown. Moreover, WEE1 inhibition leads to altered ribosome dynamics and increased ribosome collisions. Accordingly, cells lacking the collided ribosome sensor ZNF598 show increased sensitivity to WEE1i. This response was not restricted to cancer cells, but was also observed in peripheral blood monocytic cells. The GCN2-mediated ISR was not required for WEE1i to induce DNA damage in S-phase, premature mitotic entry nor the sensitizing effects to DNA damaging chemotherapeutics. Conversely, ISR activation and translational shut-down are independent on WEE1i-mediated activation of CDK1/2. WEE1i-mediated ISR activation was independent of the presence of WEE1, pointing at an off-target effect, which is shared by multiple chemically distinct WEE1 inhibitors. Importantly, WEE1 inhibition at doses that do not induce the ISR can still synergize with PKMYT1 inhibition. Taken together, pharmacological WEE1 inhibition triggers cytotoxic ISR activation and translational shutdown, which can be prevented by low-dose treatments, while retaining the cell cycle checkpoint-perturbing effects.

overall_design: RPE-1 hTERT TP53KO and EIF2AKO cells treated with 125nM WEE1i (6hr) cells subjected to a single pulse of EdU (10uM for 15 min). Next, cells were sorted in 384 well plates and subjected to scEdU-seq (van den Berg et al., 2024) .

first: Rinskje

last: Tjeerdsma

first: Marcel

last: van Vugt


title: Palmitate suppresses CD8+ T cell antitumoral response by disrupting mitochondrial metabolism

city: Milano

first: Teresa

last: Manzo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: IEO

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: WEE1 inhibition triggers GCN2-mediated activation of the integrated stress response

first: Michael

last: VanInsberghe

overall_design: Ribosome profiling and RNA-seq in RPE-1 hTERT TP53-KO cells that were untreated or treated with AZD1775 WEEi inhibitor

middle: B

first: Timothy

middle: F

last: Ng

first: Maurits

last: Roorda

first: Danielle

last: Bianchi

first: Sora

last: Yang

first: Clara

last: Bonnet

first: Marieke

last: Everts

first: Femke

middle: J

last: Bakker

first: Rolf

last: de Boer

first: Nathalie

last: Moatti

first: Nicole

last: Hustedt

first: Matthew

last: Leibovitch

first: Krzysztof

last: Szkop

first: Shannon

last: Mclaughlan

first: Lisa

last: Hoeg

first: Ivan

last: Topisirovic

first: Ola

last: Larsson

first: Alexander

last: van Oudenaarden

first: Steven

last: de Jong

first: Marvin

last: Tanenbaum

first: Thijn

middle: R

last: Brummelkamp

first: Daniel

last: Durocher

middle: A


title: Cancer-derived exosomal DPP3 promotes lung metastasis by activating the RAP1 signaling pathway

city: wuhan

first: Wei

last: Yan

state: Hubei

address: Bayi Street 229 in Wuchang district

department: College of life science

country: China

institute: Wuhan University

summary: Metastasis is the leading cause of breast cancer-related death, with lung metastasis occurring in more than 60% of breast cancer (BRCA) patients. Small extracellular vesicles (sEVs) play crucial roles in breast cancer metastasis. Dipeptidyl peptidase 3 (DPP3) is an enzyme that hydrolyzes various peptides, and its dysregulation contributes to multiple pathology processes. However, the role of DPP3 in breast cancer lung metastasis is poorly understood. In this study, we discovered a novel mechanism whereby DPP3, packaged in small extracellular vesicles (sEVs) from breast cancer, is delivered to lung tissue to remodel the vascular niche to promote lung metastasis.

overall_design: To investigate the mechanism of breast cancer-secreted exosomal DPP3 on lung metastasis, we subcutaneously injected MDA-MB-231 and MDA-MB-231/DPP3 KO cells into the fourth mammary fat pat of NSG mice to construct orthotopic xenograft.After 5 weeks, mice were sacrificed, and lung tissue was collected for gene expression profiling analysis.

first: Xu

last: Li


title: Longitudinal single-cell transcriptomics of monocytes, Tfh and gd Tcells following a control human malaria infection.

city: Brisbane

first: Zuleima

last: Pava Imitola

state: Queensland

address: 300 Herston road

institute: QIMR Berghofer

summary:
Malaria infection drives tolerogenic cell responses which protects from high inflammation and immunopathogenesis but reduces  parasite control and adaptive immunity. Here, we comprehensively map responses across innate and adaptive cells.
The results of this Controlled Human Malaria Infection study are presented in three independent publications.

Blood samples from 4 donors were collected prior to infection (day 0), at peak infection (day 8) and 14 or 15 and 27-36 days (end of study, EOS) after inoculation (in analyses these time points are grouped as 0, 8, 14/15 and EOS).  Participants were healthy malaria naïve adults with no prior exposure to malaria or residence in malaria-endemic regions.  For trials NCT02867059, NCT02783833, NCT02431637 all participants received the same study drug (no-randomization) and 3D7-strain parasites. For NCT02431650, participants were randomized 1:1 to receive study drug or control and 3D7-strain parasites. Samples used here were from samples opportunistically collected from volunteers who consented to donate blood for immunological studies within the parent clinical trial. As such, no sample size estimation was performed for this immunology study.

overall_design:
In brief, healthy malaria naïve adults with no prior exposure to malaria or residence in malaria-endemic regions underwent CHMI with 2800 viable P. falciparum parasitized RBCs, and peripheral parasitaemia was measured at least daily by qPCR as described previously (53). Participants were treated with antimalarial drugs at day 8 of infection when parasitaemia reaches approximately 20,000 parasites/ml.
PBMCs were isolated by Ficoll-Paque (Sigma, USA) density gradient centrifugation, isolated PBMCs were cryopreserved in 10% DMSO/FBS. Monocytes, Tfh and GD-T cells from 4 individuals with P. falciparum infection were collected at day of infection (day 0), peak parasitaemia and before treatment at (day8), and day 16 and 36 days post-infection. PBMCs were isolated by Fluorescence-activated cell sorting (FACS) and analysed using droplet-based scRNAseq.”

first: Michelle

last: Boyle

first: Nick

last: Dooley

first: Megan

last: Soon

first: Jessica

last: Loughland

last: Pava

first: Julianne

last: Hamelink

first: Kiana

last: Berry

first: Dean

last: Andrew

first: Arya

last: SheelaNair

first: Kim

last: Piera

first: Timothy

last: Williams

first: Bridget

last: Barber

first: Matt

last: Grigg

first: Chris

last: Engwerda

first: Alejandro

last: Lopez

last: Anstey


title: Synergistic targeting of TWIST1 and HOXA9 in MLL-AF9+ AML via combination of SD70 and MI-503

city: TianJin

first: Xiao Tong

last: Ma

state: TianJin

address: Blood hospital, 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

summary: To identify the downstream targets of TWIST1 or Hoxa9, we carried out RNA sequencing to characterize transcriptional changes upon Twist1 deletion or Hoxa9 knockdown in LSCs from MLL-AF9+ AML mice.

overall_design: a) RNA-seq in Twist1-deleted and control leukemia stem cells from MLL-AF9+ AML mice; b) RNA-seq in  Hoxa9 knockdown and control leukemia stem cells from MLL-AF9+ AML mice.

first: Xiaotong

last: Wang

first: Jing

last: Yin

last: You


title: Elimination of dormant cancer stem cells by disrupting glucocorticoid mediated lipid metabolism in glioblastoma

city: Heidelberg

first: Chunxuan

last: Shao

address: Im Neuenheimer Feld 581

country: Germany

institute: Deutsches Krebsforschungszentrum

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Elimination of dormant cancer stem cells by disrupting glucocorticoid mediated lipid metabolism in glioblastoma [shRNA KD]

summary: Little progress has been made in therapeutic treatment of glioblastoma (GBM) in the last decade despite rapid progress in molecular understanding of brain tumors. Targeting cancer stem cells was considered as a strategy to treat GBM. Here we show that the stress hormone glucocorticoid is essential for the maintenance of brain tumor stem cells (BTSCs), which are resistant to conventional therapy. The glucocorticoid receptor (GR) regulates metabolic plasticity and chemoresistance of the dormant BTSC via controlling expression of GPD1 (glycerol-3-phosphate dehydrogenase 1), which is an essential regulator of lipid metabolism in BTSCs.  Genomic, lipidomic and cellular analysis confirm that GR/GPD1 regulation is essential for BTSCs metabolic plasticity and survival. We further demonstrate that the GR agonist dexamethasone (DEXA), which is commonly used to treat GBM edema, abolishes the effect of chemotherapy drug temozolomide (TMZ) by upregulating GPD1 and thus promoting tumor cell dormancy and TMZ resistance, this provides a mechanistic explanation and thus settle the debate of steroid usage in brain tumor patient edema control. Pharmacological inhibition of GR/GPD1 pathway disrupts metabolic plasticity, induces ferroptosis and immune activation thus prolongs animal survival, which is superior to standard chemotherapy. This study identifies an important mechanism regulating cancer stem cell dormancy and provides a new opportunity for GBM treatment.

overall_design: Comparative gene expression profiling analysis of GPD1KO, GRKO, dexamethasone, mifepristone in NCH601, NCH710 cell lines

first: Yonghe

last: Wu

first: Haikun

last: Liu


title: Heat stress and SCA48 mutations reveal the metamorphic structure and function of the ubiquitin ligase CHIP

city: Durham

first: Kenneth

last: Scaglione

address: 3 Genome Court

institute: Duke

summary: This data set compares the transcriptome of CHIP and CHIP-KO MEFs either at 37 degrees Celsius or after 1 hour at 43 degrees Celsius.

overall_design: RNA was isolated from the described conditions prior to RNAseq analysis performed by Novogene.


title: Transcriptomic changes in selenite-stimulated lens epithelial cells after RORα overexpression.

city: Beijing

last: Tao

address: NO.1 Dongjiaominxiang Street

institute: Beijing Tongren Hospital, Beijing Ophthalmology and Visual Science Key Lab, Capital Medical University

summary: This trancriptomic analysis identified the genes in selenite-stimulated lens epithelial cells regulated by RORα.

overall_design: Human lens epithelial cells (SRA01-04) were transfected with plasmids expressing RORα or empty plasmids, and then the cells were treated with 10 μM selenite for 24 h after 48-h cell transfection.

first: Zhenyu

first: Jinda

first: Xuemin

last: Li

first: Yu

last: Wan


title: Gene expression profile at single cell level of tumor-infiltrating leukocytes upon anti-OX40 agonist antibody treated mice.

city: Tel Aviv

first: Tomer

last: Weiss

state: Tel-Aviv-Jaffa

address: Klachkin 9

country: Israel

institute: Tel Aviv University

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of tumor-infiltrating leukocytes in the skin of B16F10-bearing mics.

overall_design: live (DAPI+) leukocytes (CD45+) of the B16F10-bearing mice were isolated by Fluorescence-activated cell sorting (FACS)  and analyzed using scRNAseq.

first: Amar

last: Sarah

first: Kaminitz

last: Ayelet

first: Madi

last: Asaf


title: Elimination of dormant cancer stem cells by disrupting glucocorticoid mediated lipid metabolism in glioblastoma I

first: Yang

last: Aoxue

first: Shao

last: Chunxuan

first: Liu

last: Haikun


title: Effect of  gyrification  on  regional specific gene expression of ferret neocortex germinal zone between lateral gyrus and lateral sulcus

city: Shanghai

first: Youning

last: Lin

address: Rm 4027 Research Building II, Dong'an Rd. Xuhui District.

institute: Fudan University

summary: To investigate the candidate genes for gyrification of ferret neocortex,we used bulk RNA sequencing (bulk RNA-seq) to analyze the different gene expression between gyrus and sulcus of ferret neocortex.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of paired lateral gyrus and lateral sulcus at postnal day 4.
Comparative gene expression profiling analysis of RNA-seq data for germinal zone of lateral gyrus  and lateral sulcus.


title: Circular RNA expression profile and its potential regulative role in Chronic total occlusion

city: Chongqing

first: Gege

address: No.76, Linjiang Road, Yuzhong District

department: Cardiovascular Medicine

institute: The Second Hospital of Chongqing Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Objectives: CircRNAs, a novel class of noncoding RNAs, have been reported in many diseases. However, their role in coronary CTO remains unclear. Here, we aimed to determine the circRNA expression profile in coronary CTO patients and further construct a circRNA–miRNA network. It provides a new way to study the pathogenesis of coronary CTO.
Methods: Plasma circRNA expression profiles were screened by circRNA microarrays. The CircRNA–miRNA network was established to predict the circRNA targets. Gene ontology (GO) analysis and KEGG, Reactome pathway analysis were applied for further enrichment of data. Finally, quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to confirm these results.
Results: We collected the peripheral blood of 4 adult patients with coronary CTO and 4 adult patients with normal coronary arteries, and found 11,562 circRNAs by sequencing. 652 circRNAs were significantly differentially expressed, of which 196 were significantly up-regulated and 456 were significantly down-regulated. Through bioinformatics analysis, we analyzed and predicted the potential biological functions of circRNAs. Further studies found that differently expressed circRNAs are mainly involved in the occurrence and development of coronary CTO by participating in inflammatory response, angiogenesis, calcification in lesions, regulation of lipid metabolism, insulin secretion and other pathways. Finally, the over-expression of hsa_circ_0045503, hsa_circ_0125975 and under-expression of  hsa_circ_0102054 were further validated by qRT-PCR. Hsa-circ-0125975 exhibited significant up-regulation in patients with coronary CTO, which was in line with the sequencing data.
Conclusions: The results of this study may provide a new biomarker and therapeutic target for the diagnosis and treatment of coronary CTO.

overall_design: We collected the peripheral blood of 4 adult patients with coronary CTO and 4 adult patients with normal coronary arteries to perform circRNA microarrays.

first: Yunqing

last: Chen

first: Bing

last: Deng


title: Transcriptome profiling of pitp-1 mutant and pitp-1(RNAi)-treated Caenorhabditis elegans

status: Public on Oct 04 2025

city: HsinChu

first: Yen-Hung

state: East district

address: No. 101, Section 2, Kuang-Fu Road

department: Institute of Biotechnology

country: Taiwan

institute: National Tsing Hua University, Taiwan

summary: This dataset contains the transcriptome profiling results of Caenorhabditis elegans under pitp−1 regulation. The experiment was designed to identify the transcriptional mechanisms underlying the pitp−1 suppression-mediated lifespan extension. Transcriptomic analysis was performed on pitp−1 mutant and pitp−1(RNAi)-treated worms at Day 3 of Adulthood (D3A). Bioinformatic pathway analysis (IPA) of the resulting differential expression profiles revealed a significant and coordinated downregulation of genes associated with the IIS (Insulin/IGF-1 Signaling) and TOR signaling pathways. This dataset therefore provides key molecular insight into how PITP−1 transcriptionally affects the major longevity regulatory networks.

overall_design: Transcriptome profiling was performed on D3A worms with two biological replicates for each condition. Samples included pitp-1 mutant (pitp-1(pe1297) and its wild-type control (N2), as well as pitp-1(RNAi)-treated N2 worms and their Empty Vector(EV) control.

first: Tsiu-Ting

last: Ching

first: Chiou-Hwa

last: Yuh

first: Horng-Dar

last: Wang


title: HDAC5 Deficiency Induces Intrinsic Resistance to KRASG12D Inhibition by Disrupting c-Myc Acetylation-Ubiquitination Homeostasis [ChIP-Seq]

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

summary: We found that HDAC5 deletion significantly enhances intrinsic resistance to MRTX1133 in KRASG12D mutant pancreatic cancer. Mechanistic studies show that HDAC5 deletion promotes resistance to KRASG12D inhibitors by sustaining the activation of the MAPK signaling pathway.

overall_design: ChIP-seq was performed on PANC-1 cells transfected with shControl-1,shControl-2,shHDAC5-1, or shHDAC5-2 to investigate the impact of HDAC5 knockdown on MYC chromatin binding.

first: Zhou

last: Yingke

last: Haixin


title: HDAC5 Deficiency Induces Intrinsic Resistance to KRASG12D Inhibition by Disrupting c-Myc Acetylation-Ubiquitination Homeostasis [RNA-seq]

overall_design: RNA-seq analysis was performed on AsPC-1 cells, transfected with shNC or shHDAC5 and treated with DMSO or MRTX1133, to investigate their effects on the transcriptome.

first: Yu


title: Interferons inhibit Ebola virus infection of human keratinocytes

city: Iowa City

first: Jonah

last: Elliff

state: Iowa

address: 51 Newton Rd

institute: University of iowa

summary: Orthoebolavirus zairense, or Zaire Ebola virus (EBOV) is a species within the virus family Filoviridae, a group of viruses that can cause severe disease in humans characterized by hemorrhagic shock, coagulation abnormalities, and severe inflammation. While tissue macrophages are critical targets early during EBOV infection, other cell types support viral replication as disease progresses. At late stages of infection, infectious EBOV is found on the surface of the skin, which may be a critical source of infectious virus transmitted be-tween individuals during outbreaks. Human skin contains a number of cellular targets of EBOV, including keratinocytes. Here, we demonstrate EBOV infection of telomer-ase-immortalized normal human skin keratinocytes (NHSK-1) as well as EBOVΔVP30 in-fection of NHSK-1 cells that were stably complemented with the EBOV transcription factor VP30. Infection with EBOVΔVP30 did not elicit detectable endogenous interferon re-sponses, however, exogenous pre-treatment of NHSK-1 cells with type I, II, and III inter-feron (IFN) inhibited EBOVΔVP30 infection and infection of an additional low contain-ment model of EBOV, rVSV/EBOV GP, in a dose-dependent manner. Analysis of the transcriptome of IFN-treated keratinocytes identified multiple genes unique to each IFN and a subset of ISGs upregulated by each IFN. Our results indicate that ISGs induced by IFN pre-treatment of keratinocytes can reduce infection, underlining possible anti-EBOV ISGs for development of EBOV-targeting therapeutics.

overall_design: RNA-seq profiling of the transcriptome of telomerase-immortalized human keratinocytes at 6 or 24 hours following treatment with IFN-β, IFN-γ, IFN-α, or IFN-λ.

first: Hanora

last: Van Ert

first: Kristina

last: Sevcik

first: Marija

last: Djurkovic

first: Danielle

last: Rudd

first: Francoise

last: Gourronc

first: Aloysius

last: Klingelhutz

first: Olena

last: Shtanko

first: Wendy

last: Maury


title: SPARC Upregulation Mediates Podocyte Injury in Alport Syndrome Mice

first: Dongxuan

last: Chi

state: China

address: No.5 Le Yuan Road, Daxing District

institute: Peking University First Hospital

summary: Alport syndrome (AS) is a hereditary kidney disease with no curative treatment, which characterized by hematuria, proteinuria, and progressive kidney failure. Podocyte injury has been observed in AS, whereases, the mechanism is still unclear. Reported studies showed the expression level of secreted protein acidic and rich in cysteine (SPARC) correlated with podocyte injury in chronic kidney diseases, yet its mechanism still unknown. Especially, its role in AS-related podocyte injury is unclear. Therefore, the kidney of Col4a3-/- AS mice was used to detect SPARC expression, location, and podocyte injury, and mouse podocyte cell line (MPC5) was used to explore the mechanism of SPARC-induced podocyte injury. Besides, SPARC expression in both urine and kidney samples from AS patients were analyzed. The results showed, SPARC upregulated and located in podocytes were detected in Col4a3-/- AS mice, and increased inflammatory cytokines, impaired podocyte structure and function were identified in SPARC-overexpression MPC5, importantly, knockdown adhesion G protein-coupled receptor B1 (ADGRB1) exerted a protective effect. In AS patients, urinary increased level of SPARC was detected, SPARC deposition in glomeruli of kidney sections was identified. Our findings identified SPARC as a key mediator of podocyte injury in AS, with ADGRB1 acting as its downstream effector.

overall_design: RNA-seq profiling of  wild type mouse podocyte cell line (MPC5) and transfected SPARC-overexpression plasmid (SPARCoe) MPC5 at 24 hours after transfection.

first: Hongyuan

last: Chu

first: Fang

first: Jing

last: Nie


title: Targeting PTPN2 enhances human CAR T cell efficacy and the development of long-term memory [RNA-seq]

city: Melbourne

first: Tony

last: Tiganis

address: 23 Innovation Walk, Monash University, Clayton

institute: Monash University

summary: CAR T cells have been ineffective against solid tumors, where the hostile tumor microenvironment limits CAR T cell function and persistence. Here we have used CRISPR/Cas9 gene-editing, or a small molecule inhibitor to target protein tyrosine phosphatase N2 (PTPN2) in human CAR T cells specific for the Lewis Y (LeY) neo-antigen. Targeting PTPN2 increased CAR and cytokine signaling and enhanced the activation and cytotoxicity of anti-LeY CAR T cells. The deletion or the systemic inhibition of PTPN2 in human CAR T cells repressed the growth of human tumor xenografts or patient-derived xenografts in mice and prolonged survival. PTPN2 deletion or inhibition promoted the generation and intratumoral accumulation of stem cell memory CD8+ CAR T cells that are associated with persistent CAR T cell-mediated tumor repression and improved clinical outcomes in patients. These findings support the use of gene-editing or small molecule inhibitors for targeting PTPN2 in human CAR T cells to combat solid tumors.

overall_design:
CAR T cells specific to Lewis Y antigen, derived from donor PBMCs, with or without CRISPR/Cas9-mediated deletion of PTPN2. stimulated with plate-coated anti-idiotype antibody (1 ?g/ml) to crosslink the LeY CAR for 6h. RNA-seq libraries were prepared from RNA using the Quant-seq 3 mRNA-seq Library Prep Kit for Illumina (Lexogen) as per the manufacturer’s instructions. NextSeq (Illumina, Inc., San Diego, CA) sequencing was performed to generate single-end, 75-bp RNA-seq short reads and subsequently CASAVA 1.8.2 was used for base calling.

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there are privacy concerns regarding public access to the raw data
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first: Eamon

last: Coughlan


title: Targeting PTPN2 enhances human CAR T cell efficacy and the development of long-term memory [scRNA-Seq]

overall_design:
CAR T cells specific to Lewis Y antigen, derived from donor PBMCs, with or without CRISPR/Cas9-mediated deletion of PTPN2, extracted from spleen of OVCAR-3 tumour-bearing NSG mice 14 days after adoptive transfer.

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there are privacy concerns regarding public access to the raw data.
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title: Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus

city: New Haven

first: Rong

last: Fan

state: CT

address: 55 Prospect Street

department: Biomedical Engineering

institute: Yale University

summary: DBiTplus utilizes in situ reverse transcription, in-tissue delivery of DNA oligos for spatial barcoding, and RNaseH-mediated selective cDNA retrieval, preserving tissue architecture to enable highly multiplexed protein imaging and spatial transcriptomics on the same slide. Computational pipelines seamlessly integrates these modalities, allowing imaging-guided deconvolution to generate genome-scale, single-cell-resolved spatial transcriptome atlases. DBiTplus was demonstrated across diverse samples including mouse embryos, normal human lymph nodes, and formalin-fixed paraffin-embedded (FFPE) human lymphoma tissues, highlighting its compatibility with challenging clinical specimens. Applying DBiTplus to human lymphoma samples reveals key mechanisms driving lymphomagenesis, progression, and notably, the progression of indolent marginal zone lymphoma (MZL) or the transformation from chronic lymphocytic leukemia (CLL) to diffuse large B-cell lymphoma (DLBCL), including uniquely, the spatially resolved involvement of microRNAs in modulating the transformation dynamics. Thus, DBiTplus is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.

overall_design: DBiT-seq spatial transcriptomics is performed on a tissue section followed by RNaseH-mediated selective cDNA retrieval. Multiplexed immunofluorescence imaging (using the PhenoCycler Fusion or CellScape) on the same tissue.

first: Archibald

last: Enninful

first: Oliver

last: Braubach

first: Zongming

last: Ma

first: Zhaojun

last: Zhang

first: Mina

last: Xu


title: Integration of scRNA-seq and scATAC-seq reveals malignant characteristics of clear cell renal cell carcinoma with sarcomatoid differentiation

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: Clear cell renal cell carcinoma (ccRCC) is the most common histological type of kidney cancer. The appearance of spindle cell proliferation is generally considered as sarcomatoid differentiation. To further understand the malignant characteristics of this special histological type of ccRCC, it is a promising direction to study it at the level of genetics, cellular and molecular levels. In this study, we integrated scRNA-seq, scATAC-seq and WES analysis on a sample of sarcomatoid ccRCC, and discovered the characteristics of malignant progression. These findings provided a new reference for the diagnosis and treatment of ccRCC with sarcomatoid differentiation in the future.

overall_design: clear cell renal cell carcinoma with sarcomatoid differentiation was used for scRNA-seq and scATAC-seq by 10X Genomics.

first: Wenhao

last: Lu

first: Yixuan

last: Liu

first: Jizhen

last: Cen

first: Shengzhu

last: Huang

first: Zheng

last: Wen

first: Jiaping

last: Li

first: Zengnan

last: Mo

first: Xuefang

last: Liang

first: Cheng

last: Su


title: Integrated Transcriptomics and Metabolomics Analysis Promotes the Understanding of Adventitious Root Formation in Toxicodendron succedaneum (L.) Kuntze

city: Kunming

first: cai

last: wang

address: qingyun street

institute: Southwest forestry university

summary: Toxicodendron succedaneum is an important economic tree species. In the process of establishing a regeneration system for the T. succedaneum, it was found that the axillary buds that are produced from the same tender branch after cutting are inserted into a rooting medium, with a rooting rate of 1%. When the main stem segments of the rooted tissue culture seedlings were placed on the same rooting medium, the rooting rate could reach 100%, and the complete tissue culture seedlings could be obtained. This study is based on the transcriptome and metabolome analysis, combined with the dynamic changes of endogenous hormones, investigates the key molecules, and potential mechanism in the process of adventitious root formation of TSE and TSW in T. succedaneum. The combination of transcriptomics and metabolomics revealed that the differentially expressed genes and differential metabolites in TSE and TSW were significantly enriched in plant hormone signal transduction pathway and alpha-linolenic acid metabolism pathway after 12 hours of cultivation. In the metabolome, the level of jasmonic acid in TSW is significantly lower than in TSE, and the expression levels of key genes in the JA biosynthetic pathway are also significantly lower than those in TSE. Therefore, it can be preliminarily inferred that the reduction in jasmonic acid content in TSW may be an important reason for its rooting. Furthermore, the JA content in TSE was consistently higher than it in TSW at 0,6,12 and 24 hours. Examining the dynamics of hormonal changes, When the jasmonic acid content reaches a certain concentration, it can inhibit the synthesis of auxins, thereby suppressing the formation of adventitious roots. Exogenous application of jasmonic acid and diethofencarb revealed that both high and low concentrations of JA suppress the root growth of T. succedaneum. The impact of diethofencarb treatment on the rooting of T. succedaneum is that high concentrations suppress it while low concentrations promote it. The molecular mechanism of jasmonic acid on AR formation in the T. succedaneum revealed in this study, provides a more comprehensive understanding of the AR formation mechanism in the T. succedaneum and other plants.

overall_design: The transcriptome, metabolome, and endogenous hormones of T. succedaneum stems cultured in rooting medium for varying times were measured with the aim to evaluate the differences in adventitious root development of stems with varying rooting abilities. The levels of differentially expressed genes, metabolites, and endogenous phytohormones in the adventitious root development of T. succedaneum were further analyzed within a way explore the differences of lilac in adventitious root development at the physiological, biochemical, and molecular levels and to lay the groundwork for T. succedaneum stem genetic analysis.

first: Dan

last: Zong

first: ChengZhong

last: He

first: Cai

last: Wang

first: Dongxiao


title: RNA-seq Analysis of Wild-Type and Dcaf8 Knockout LT-HSCs in Mice

first: Pengfei

address: Ruijin Rd. II

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Hematopoietic stem cell aging leads to dysfunction of hematopoietic and immune systems, which in return contribute to organismal aging and the development of aging-related diseases. Understanding the molecular mechanisms of HSC aging is critical for developing interventions to treat and prevent aging-related diseases. Here, we show that DCAF8, a substrate receptor of E3 ubiquitin ligases, is highly expressed in HSCs and undergoes a progressive decline with age. Loss of DCAF8 in mice results in aging-like phenotype in HSCs, characterized by increased number of HSCs, decreased self-renewal capacity, cellular senescence and elevated DNA damage. Mechanistically, DCAF8 mediates the degradation of DOCK11, a guanine nucleotide exchange factor for CDC42. In the absence of DCAF8, DOCK11 accumulates, leading to elevated CDC42 activity and consequential loss of polarity of HSCs. Knocking out of Dock11 mitigates the senescence, DNA damage, and self-renewal defects of Dcaf8-/- HSCs. This study highlights a critical role of DCAF8 in regulating HSC aging via the DOCK11-CDC42 axis and suggests potential therapeutic targets for preventing the age-related decline in HSC functions.

overall_design: To explore the mechanisms by which Dcaf8 knockout leads to functional defects in HSCs, we performed RNA-sequencing on LT-HSCs sorted from 3 Dcaf8 knockout mice and 3 WT controls at young ages.

first: Xiuli

first: Donghe

first: Ruibao

last: Ren

first: Ping


title: Elimination of dormant cancer stem cells by disrupting glucocorticoid mediated lipid metabolism in glioblastoma [treatment]

first: Chunxuan

last: Shao

overall_design: Comparative gene expression profiling analysis of GPD1KO, GRKO, dexamethasone, mifepristone in NCH601, NCH710 cell lines

first: Yonghe

last: Wu

first: Haikun


title: Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq)

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

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

overall_design: Refer to individual Series

first: Kaivalya

last: Walavalkar

first: Shivani

last: Gupta

first: Jelena

last: Kresoja-Rakic

first: Mathieu

last: Raingeval

first: Chiara

last: Mungo

first: Philip

last: Rubin


title: Sox11 overexpression restores embryonic pro-growth transcription in mature corticospinal tract neurons.

city: Milwaukee

first: Murray

last: Blackmore

state: WI

address: 561 N 16th St

department: Biomedical Sciences

institute: Marquette University

summary: Neurons in the central nervous system (CNS) display a high capacity for axon growth during early development but mostly lose this ability during a key stage of differentiation marked by synaptic maturation, circuit integration, and a profound shift in gene transcription. Once mature, neurons largely fail to reverse this transcriptional switch after axon injury, fundamentally constraining their intrinsic capacity for repair. Here, we show with single-nucleus RNA sequencing that forced expression of the transcription factor Sox11 in adult corticospinal tract neurons produces large-scale and stable changes in gene expression that are highly enriched for growth-relevant processes, and which strongly resemble those of pre-synaptic embryonic stages. Moreover, Sox11 is equally effective when delivered to chronically injured CST neurons. These data reveal Sox11’s ability to reverse a critical step of neuronal maturation even in otherwise unperturbed neurons, clarifying the transcriptional underpinnings and highlighting Sox11’s potential as a pro-regenerative stimulus.

overall_design: In adult mouse samples, corticospinal tract (CST) neurons were transduced with a retrograde, nuclear-localized fluorophore (mGl) and control or Sox11-expressing virus by retrograde transduction from cervical spinal cord. Animals recevied either no injury or a cervical contusion injury six weeks prior to tissue collection. Animals that received Sox11 and no injury were collected at four time points: 1 week, 2 weeks, 4 weeks, or 6 weeks after viral delivery, with each time point uniquely barcoded and pooled in the same sequencing reaction. Embryonic cortex was collected at embryonic day 18. For all samples, single nucleus RNA sequencing was performed. Adult samples were pre-purified using fluorescent activated nuclei sorting prior to library preparation. E18 embryonic libraries were prepared from ixed cortical tissue.

first: Elizabeth

last: Batsel

first: Zimei

last: Otten

first: Rabia

last: Mohammad

first: Paula

last: Pascal

first: Darby

last: O'Shea

first: Jose

last: Rosas

first: Pantelis

last: Tsoulfas


title: Nitric oxide required for transition to slower hepatic protein synthesis rates during long-term caloric restriction

city: St Louis

first: Hector

middle: H

last: Palacios

state: MO

address: 00201 West Building

institute: Washington University School of Medicine

summary: Caloric restriction (CR) extends maximal lifespan and maintains cellular homeostasis in various animal models. We have previously shown that CR induces a global reduction in protein fractional synthesis rates (FSRs) across the hepatic proteome in mice, but the timing and regulatory mechanisms remain unclear. Nitric oxide (NO), a bioactive molecule upregulated during CR, is a potential regulator of protein synthesis. To explore the role of NO in hepatic proteome fluxes during CR, we used in vivo deuterium labeling from heavy water and LC/MS-based flux proteomics in wild-type and NO-deficient (NO-) mice. We found a transition to reduced global protein FSRs that occurred rapidly between days 25 to 30 of CR. NO deficiency, whether genetic or pharmacological, disrupted the slowing of proteome-wide fluxes and the beneficial effects on body composition and physiology. Administering the NO donor molsidomine restored the reduction in hepatic FSRs in NO-deficient mice. Further, inhibiting NO pharmacologically, whether starting on day 1, day 14, or day 24 of CR, mitigated the reduction in hepatic protein FSRs at day 32, highlighting NO's critical role during the transition period. These results underscore the importance of NO in CR-induced changes in proteostasis and suggest NO as a potential CR-mimetic target, while offering a specific time window for identifying other signals and testing therapeutic interventions.

overall_design: Examines the impact of caloric restriction (CR) on hepatic gene expression before and after a threshold event that elucidates a unique slowdown in hepatic protein synthesis rates under CR.


title: Subtle changes in brain expression modules in Alzheimer’s disease TREM2 carriers compared to non-carriers

city: London

first: Guillermo

last: Carbajosa

address: Guy’s Hospital, St Thomas Street

department: Medical and Molecular Genetics

country: United Kingdom

institute: King's College London

summary:
Background: Rare heterozygous coding variants with a large effect on the risk of developing late-onset Alzheimer's disease (similar to ApoE4, OR 2.90-5.05) have been identified in the Triggering Receptor Expressed on Myeloid cells 2 (TREM2) gene. However, little is known about the mechanisms through which Trem2 maladjustment may lead to AD
Methods: We performed differential expression and co-expression network analysis on samples obtained from 5 (mainly 2) brain areas from individuals carrying the TREM2 variant known to increase the risk of Alzheimer’s and others using RNA-Seq to obtain a systems level view of the effects of the TREM2 mutation
Results: The absence of Trem2 has a stronger effect at an earlier age with the number of differential expressed (DE) genes being 17-fold greater at 4 months than at 8 months in cortex. By integrating DE genes and network analysis we discovered gene clusters associated with the disruption of blood vessel formation at 4 months of age and protein targeting primarily affecting the hippocampus at 8 months. Further integration of cell type and ontology information revealed a large disruption of a gene module enriched for endothelial cell markers coinciding with the module enriched for neuron cell markers having weaker connections to modules with oligodendrocyte and astrocyte identities. The module with neuronal identity has decreased expression only in the KO where it has closer association with a new module enriched for phagocytic functions
Conclusions: Combining gene co-expression and differential expression analysis on brains of carriers of TREM2 mutations we demonstrate that the presence of damaging TREM2 mutation produce subtle disruptions.

overall_design: Entorhinal cortex  and BA9 were selected because they represent tissues affected in AD at early and late stages, respectively. CTRLs, non-TREM2-variant carrier AD samples and TREM2-variant-AD samples  were used. RNA-Seq was used to profile the transcriptomes for each sample.


title: A small CRISPR/Cas-associated RNA regulates ferrous iron transport in Neisseria meningitidis

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

summary: In this study the RNA targetome of the endonuclease Cas9, the trans-activating crRNA (tracrRNA) and a CRISPR-associated small RNA (scaRNA/NMnc0040) was determined in Neisseria meninigitidis serogroup C strain 8013 by RNA-seq.

overall_design: To uncover the RNA targetome of Cas9, tracrRNA and scaRNA of Neisseria meningitidis (N.meninigitidis), bacterial samples were collected of three biological replicates of N.meninigitidis strain 8013 wt and cas9, tracrRNA and scaRNA deletion in which the CDS of Cas9 and the sequences of tracrRNA and scaRNA was replaced by an antibiotics cassette. Bacterial cultures grown to OD600nm of 0.5 in cell culture medium (EMEM+++) were snapfrozen in liquid nitrogen prior to total RNA-extraction with the hot phenol method and DNase digestion.

first: Denise

last: Müller

first: Thorsten

last: Bischler

first: Christoph

last: Schoen


title: Linker histone regulates the myeloid versus lymphoid bifurcation of multipotent hematopoietic stem and progenitors

status: Public on Oct 03 2025

first: Shangqin

last: Guo

address: 10 Amistad Street

department: Department of Cell Biology

summary: Myeloid-biased differentiation of multipotent hematopoietic stem and progenitor cells (HSPCs) occurs with aging or exhaustion. The molecular mechanism(s) responsible for this fate bias remain unclear. Here we report that linker histone regulates HSPC fate choice at the lymphoid versus myeloid bifurcation. Linker histones package nucleosomes and compact chromatin. HSPCs expressing a doxycycline (dox) inducible H1.0 transgene favor the lymphoid fate, display strengthened nucleosome organization and reduced chromatin accessibility at subsets of genomic regions. The genomic regions showing reduced chromatin accessibility host many known marker genes of myeloid biased HSCs. The transcription factor Hlf is located in one of the most differentially closed regions, whose chromatin accessibility and gene expression are reduced in H1.0high HSPCs. Failure to reduce Hlf expression in multipotential HSPCs abrogates the H1.0-endowed lymphoid potential. Furthermore, HSPCs display aspartyl protease dependent H1.0 decreases, especially in response to interferon alpha (IFNa). Aspartyl protease inhibitors preserve endogenous H1.0 levels and promote the lymphoid fate of wild type HSPCs. Thus, our work elucidates a molecular scenario how myeloid bias arises and uncovers a point of intervention for correcting myeloid skewed hematopoiesis.

overall_design: ATAC seq of Lin- Sca1+ cKit+ (LSK) cells isolated from WT or iH1.0-GFP mice treated with Dox water for 3 weeks

first: Kutay

last: Karatepe

first: Bruna

last: Mafra de Faria

first: Jian

last: Zhang


title: Tanshinone IIA inhibits heat-induced growth of p53-mutant Huh-7 hepatocellular carcinoma by modulating osmotic homeostasis and glycolysis through targeting ALDH7A1

city: Zhengzhou

first: Xuhua

last: Duan

address: No. 1 Longhu Middle Ring Road, Jinshui District

institute: The First Affiliated Hospital of Zhengzhou University

summary: Thermal ablation offers minimally invasive treatment options for hepatocellular carcinoma (HCC) therapy. However, local recurrence due to sublethal temperatures enhances tumor cell survival. This study aims to investigate the tumor-promoting effects of hyperthermia on HCC cells, the role of tanshinone IIA (Tan IIA) in mitigating these effects, and the underlying mechanisms involved. We observed that temperature at 44 °C increased the aggressiveness of HCC cells, and Tan IIA inhibited cell viability and cell invasion, and induced cell cycle arrest and apoptosis of heat-pretreated HCC cells. ALDH7A1 was identified as a target of Tan IIA, and its altered expression resulted in dysregulation of cell viability, invasion, apoptosis, ATP production, glycolysis, osmolyte levels, and reactive oxygen species (ROS). Under hyperosmotic conditions, ALDH7A1 knockdown sensitized heated Huh-7 cells, while its overexpression promoted cell survival and invasion, with corresponding changes in energy metabolism and enzymatic products. Tan IIA and the specific ALDH7A1 inhibitor, 4-diethylaminobenzaldehyde, demonstrated similar effects on gene expression patterns, glycolysis, osmotic regulation, and ROS levels in heated Huh-7 cells. Moreover, Tan IIA is able to direct interact with ALDH7A1 protein. In vitro, Tan IIA combined with hyperosmotic stress significantly inhibited cell invasion and induced apoptosis in heat-induced Huh-7 cells and ALDH7A1 overexpression partially reversed the effects of Tan IIA. In vivo, Tan IIA combined with hyperosmotic stress or glycolysis inhibitor yielded better therapeutic efficacy for HCC. In conclusion, Tan IIA sensitizes HCC cells to sublethal heat by targeting ALDH7A1, leading to disrupted glycolytic and osmolytic balance, subsequently hindering tumor cell survival and increasing apoptosis. These findings highlight a potentially novel strategy for preventing or treating recurrent HCC post-thermal ablation using Tan IIA with hyperosmotic reagents.

overall_design: Total RNA was extracted from Huh-7 and Hep-G2 cells using the TRIzol reagent (Invitrogen). The cells were treated under various conditions as described: a blank control; exposure to 8 μM Tan IIA for 48 hours; treatment with 8 μg/mL 4-diethylaminobenzaldehyde (DEAB) for 48 hours; shALDH7A1 infection for 48 hours; preheating at 44 °C (Huh-7) or 45 °C (Hep-G2) for 10 min; and 8 μM Tan IIA treatment for 48 hours following preheating at 44 °C for 10 min.

first: Hao

last: Li

first: Shuguang

last: Ju

first: Jiacheng

last: Wang

first: Donglin

last: Kuang

first: Pengfei

last: Chen

first: Mengfan

first: Ruijie

last: Qian

first: Chao

last: Liang

first: Daqian

last: Han


title: TOR inhibition drives accumulation of amino acids through transcriptional activation in algae

city: Berkeley

first: Shivani

last: Upadhyaya

address: Koshland Hall

institute: University of California Berkeley

summary: Cellular homeostasis is maintained by the balance between energy production and breakdown and is fundamental to all forms of life. The conserved, ancient target of rapamycin (TOR) kinase is a central metabolic regulator in eukaryotes that integrates carbon and nitrogen to maintain homeostasis and promote growth and development through protein synthesis. While TOR regulatory mechanisms of amino acid accumulation are well known in yeast and mammals, they remain unknown in photosynthetic organisms. Here, we developed the unicellular green alga Chromochloris zofingiensis as a simpler model system for understanding TOR function. Multiomics experiments showed that TOR inhibition leads to an increase in amino acid levels independent of hexokinase-mediated glucose signaling. We observed upregulation of selective amino acid biosynthesis pathways at the transcript and protein levels as potential mechanisms driving the increase in amino acids. Transcriptomics and proteomics experiments identified a basic helix-loop-helix (bHLH) transcription factor with rapid upregulation during TOR inhibition. DAP-seq analysis demonstrated that bHLH can bind directly to the promoters of amino acid biosynthesis genes, potentially regulating their transcription in response to TOR inhibition. We found high conservation of the bHLH-binding motif in the genomes of other green algae and plants, suggesting a conserved regulatory mechanism for amino acid biosynthesis across Viridiplantae. Phosphoproteomics experiments also revealed novel conserved targets that are not currently recognized as part of the TOR pathway. Altogether, our findings elucidate the transcriptional regulation of amino acid metabolism and explain how TOR regulates nitrogen metabolism to support growth and development in photosynthetic organisms.

overall_design: RNA-seq profiling of wild type Chromochloris zofingiensis cells under different treatment conditions of TOR inhibition by AZD treatment and glucose addition.


title: Macrophage MERTK restrains GRAMD1A‑driven mitochondrial cholesterol trafficking to limit colitis

city: nanjing

first: Juanhan

last: Liu

state: jiangsu

address: Medical School of Nanjing University

institute: nanjing university

summary: Failed clearance of apoptotic cells drives pathogen persistence, tissue damage, and damage associated molecular patterns accumulation, fueling immune remodeling. Despite its pathophysiological significance, the precise immunometabolic reprogramming underlying impaired phagocytic signaling in macrophages remains poorly defined. Here, we reveal a correlation between Crohn’s disease (CD) activity and MERTK⁺ macrophage abundance, establishing a previously unrecognized link between MERTK signaling and the orchestrated regulation of mitochondrial bioenergetics and cholesterol homeostasis. MERTK deficiency activates cholesterol biosynthesis in the endoplasmic reticulum (ER) and disrupts the protein degradation of the cholesterol transporter GRAM Domain Containing 1A (GRAMD1A) localized to the ER. Combined live-cell imaging and metabolomics show enhanced ER-to-mitochondria cholesterol trafficking, oxysterol accumulation, and impaired oxidative phosphorylation. Critically, this mitochondrial dysfunction activates innate immune signaling cascades by releasing mtDNA and dsRNA. Our findings define an elegant mechanistic axis linking defective efferocytosis to metabolic reprogramming and inflammatory disease pathogenesis.

overall_design: 16sRNA-seq of colon samples from control and DSS-induced model in WT or Mertk-/- mouse (n=4)

first: Yun

last: Zhao

first: Jianan

last: Ren

first: Xiuwen

last: Wu


title: Bile acid receptor Tgr5 prevents macrophage hyperinflammation during bacterial sepsis through metabolic and epigenetic silencing

city: Magdeburg

first: Tobias

last: Franz

address: Leipziger Str. 44

department: Molecular and Clinical Immunology

institute: Otto-von-Guericke University Magdeburg

summary: Tgr5 is a membrane-bound bile acid receptor that negatively regulates immune cells, although the molecular mechanisms behind this observation remain elusive. Here we report that Tgr5 is upregulated in macrophages during stimulation with Listeria monocytogenes and that Tgr5-deficient macrophages are hyperinflammatory and mice with myeloid Tgr5 deficiency are more susceptible to Listeria monocytogenes sepsis. Unexpectedly, Tgr5-deficient macrophages show reduced glycolysis and ATP citrate lyase expression, which cumulates in Acetyl-CoA deficiency and metabolic-epigenetic gene silencing, driving macrophages towards a hyperinflammatory phenotype during bacterial sepsis

overall_design: RNA-Seq profiling of wildtype and Tgr5⁻/⁻ bone marrow-derived macrophages (BMDMs) after 6 h stimulation with Listeria monocytogenes.

first: Maria

last: Reich

first: Sascha

last: Kahlfuß

first: Verena

last: Keitel


title: HDAC5 Deficiency Induces Intrinsic Resistance to KRASG12D Inhibition by Disrupting c-Myc Acetylation-Ubiquitination Homeostasis [RNA-Seq]

first: Haixin

last: Yu

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

summary: We found that HDAC5 deletion significantly enhances intrinsic resistance to MRTX1133 in KRASG12D mutant pancreatic cancer. Mechanistic studies show that HDAC5 deletion promotes resistance to KRASG12D inhibitors by sustaining the activation of the MAPK signaling pathway.

overall_design: RNA-seq analysis was performed on tumors from KPC WT and Hdac5 KO mice, as well as on PANC-1 cells transfected with shNC or shHDAC5, to investigate transcriptomic changes following HDAC5 knockdown.

first: Yingke

last: Zhou


title: Dysregulation of AGO2-miRNA dynamics underlies the AGO2-associated Lessel-Kreienkamp syndrome

city: Hamburg

first: Jan Broder

last: Engler

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

institute: Universitätsklinikum Hamburg-Eppendorf


title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - MERSCOPE Data

city: Cambridge

first: Samouil

middle: L

last: Farhi

state: MA

address: 75 Ames St

department: Spatial Technology Platform

institute: Broad Institute of MIT and Harvard

summary: Emerging imaging spatial transcriptomics (iST) platforms and coupled analytical methods can recover cell-to-cell interactions, groups of spatially covarying genes, and gene signatures associated with pathological features, and are thus particularly well-suited for applications in formalin fixed paraffin embedded (FFPE) tissues. Here, we benchmark the performance of three commercial iST platforms—10X Xenium, Vizgen MERSCOPE, and Nanostring CosMx—on serial sections from tissue microarrays (TMAs) containing 17 tumor and 16 normal tissue types for both relative technical and biological performance. On matched genes, we find that Xenium consistently generates higher transcript counts per gene without sacrificing specificity. Xenium and CosMx measure RNA transcripts in concordance with orthogonal single-cell transcriptomics.  All three platforms can perform spatially resolved cell typing with varying degrees of sub-clustering capabilities, with Xenium and CosMx finding slightly more clusters than MERSCOPE, albeit with different false discovery rates and cell segmentation error frequencies. Taken together, our analyses provide a comprehensive benchmark to guide the choice of iST method as researchers design studies with precious samples in this rapidly evolving field.

overall_design: In this study, we compared currently available FFPE-compatible iST platforms on matched tissue samples. We prepared a set of samples representative of typical archival FFPE tissues, comprised of 33 different tumor and normal tissue types, and acquired matched data from sequential sections according to the manufacturer’s best practices at the time of writing, generating a dataset of > 5.0 M cells. We analyzed the relative sensitivity and specificity of each method on shared transcripts and further quantified the concordance of the iST data across each platform with paired scRNA-seq data collected by 10x Chromium Single Cell Gene Expression FLEX. Then we focused on cell-level comparisons, evaluating the out-of-the-box segmentation for each platform based on detected genes and transcripts and coexpression patterns of known disjoint markers. Finally, we cross-compared the ability of each platform to identify cell type clusters with breast and breast cancer tissues as an example use case. Taken together, our work provides the first head-to-head comparison of these platforms across multiple archival healthy and cancerous FFPE tissue types.

first: Huan

last: Wang

first: Ruixu

last: Huang

first: Jack

last: Nelson

first: Ce

last: Gao

first: Miles

last: Tran

first: Anna

last: Yeaton

first: Sachi

last: Krishna

first: Kristen

last: Felt

first: Kathleen

last: Pfaff

first: Teri

last: Bowman

first: Scott

last: Rodig

first: Kevin

last: Wei

first: Brittany

last: Goods


title: A single-cell transcriptomic atlas of inner ear morphogenesis in zebrafish

first: Ian

last: Swinburne

state: CA

address: Weill Hall, Room 585

department: Molecular and Cell Biology

institute: UC Berkeley

summary: The inner ear constitutes different cell types next to one another: the sensory patches whose hair cells synapse with neurons, the thin channels of three semicircular canals whose perpendicular organization enables detection of directional head rotation, and the endolymphatic duct and sac whose conditional epithelial barrier relieves excess pressure and promotes fluid pressure homeostasis. How the ear’s component cell states are established during development has remained unknown. We use single-cell RNA sequencing to distinguish cell states within the developing ear with wild-type zebrafish embryos and lmx1bb mutants that exhibit defects in canal and sac morphogenesis. We identify the earliest marker for the semicircular canal-genesis zone (ccn1l1), unexpected genes in the endolymphatic sac that suggest a role for tissue contraction in its function (smtnb), parallel gene sets for sensory patches in the neuromast and ear, and a conserved role for cell-cycle pausing (cdkn1bb expression in the canals and sac as previously observed in the developing mouse ear). This atlas provides the most comprehensive transcriptional profiling of the developing inner ear, identifying new molecular leads to understand ear morphogenesis.

overall_design: Blocks of tissue enriched for the inner ear were dissected and collected from wild-type zebrafish at 40, 48, 60, and 72 hours post fertilization (hpf) were collected, and from lmx1bb mutant zebrafish at 60 and 7 hpf. Single-cells were captured and transcriptome libraries were prepared by the single-cell core at Harvard Medical School with established protocols (Klein et al. 2015; Wagner et al. 2018). Libraries were pooled in a manner to evenly distribute samples and prevent overlapping of barcodes. Assembled libraries were then sequenced with paired end reads using 21 flow cells of 75 cycles on an Illumina NextSeq 500. As described previously, cDNA reads were mapped using the GRCz11 zebrafish genome assembly (Wagner et al. 2018).  We provide the raw data (.fastq files) and the entire pooled and filtered data after removing doublets as EarAtlas_FullProcessed.h5ad.  Information about pooling libraries and library indices is provided in Swinburne_EarAtlas_PoolingSamples.xlsx.

first: Akankshi

last: Munjal

first: Kalki

last: Kukreja

first: Sean

last: Megason


title: Downregulation of CBX7 induced by EZH2 upregulates FGFR3 expression to reduce sensitivity to cisplatin in bladder cancer

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

summary: Cisplatin-based cytotoxic chemotherapy is considered to be the first-line therapy for advanced bladder cancer (BC), but resistance to cisplatin limits its antitumor effect. Fibroblast growth factor receptor 3 (FGFR3) has been reported to contribute to the progression and cisplatin resistance of BC. Meanwhile, chromobox protein homolog 7 (CBX7) was reported to inhibit BC progression. And our previous RNA-seq data on CBX7 (GSE185630) suggested that CBX7 might repress FGFR3，but the underlying mechanism and other cancer-related functions of CBX7 are still unknown.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the ccRCC cells and bladder cancer cells after kncokdown of CBX7.

first: Xin

last: Jin

first: Wei

last: Li


title: Investigating the Molecular Impact of GGMSC on Redox and Metabolic Pathways in Pancreatic Cancer Cells [HPAF-II]

city: Stockholm

first: Mehran

last: Ghaderi

state: Huddinge

address: Forskningsgatan 46

department: Clintech

country: Sweden

institute: Karolinska Institutet

summary: Pancreatic ductal adenocarcinoma (PDAC) remains a highly aggressive malignancy with limited treatment options. Targeting metabolic vulnerabilities and disrupting redox stress pathways has gained increasing attention as a potential therapeutic strategy. γ-Glutamyl-selenomethylselenocysteine (GGMSC) is a selenium-containing compound structurally related to seleno-L-methylselenocysteine (MSC), which has shown anticancer potential in preclinical models, although its molecular effects in PDAC are not well defined. In this study, we investigated the transcriptomic response to high-dose GGMSC in two PDAC cell lines, CAPAN-2 and HPAF-II. RNA sequencing and cytotoxicity assays revealed marked sensitivity to GGMSC in CAPAN-2 cells, associated with activation of oxidative stress and ferroptosis-related pathways, alongside downregulation of metabolic and cell cycle genes. Conversely, HPAF-II cells displayed limited transcriptional alterations and maintained proliferative and metabolic programs. These findings offer insights into the molecular mechanisms underlying GGMSC-induced transcriptional responses in PDAC and suggest potential avenues for future investigations of selenium-based therapies in pancreatic cancer.

overall_design: RNA-seq of pancreatic ductal adenocarcinoma (PDAC) cell line, HPAF-II was performed to assess differential gene expression induced by 500 µM GGMSC at 8 h and 20 h.

first: Ghaderi

last: Mehran

first: Selvam

last: Arun kumar


title: Dysregulation of AGO2-miRNA dynamics underlies the AGO2-associated Lessel-Kreienkamp syndrome [RNA-Seq, 2]

first: Jan Broder

last: Engler

summary: Mutations in human Argonaute genes, AGO1 and AGO2, are associated with neurodevelopmental disorders. Although multiple patients have been identified, the underlying molecular basis for pathogenesis remains unclear. Here, we biochemically examined five AGO2 mutations (p.L192P, p.A367P, p.T357M, p.F182del, and p.G733R) linked to different clinical severities. Except for G733R, all AGO2 mutant proteins maintained a stable fold, capable of binding and using microRNA (miRNA) guides. Kinetic studies showed that the L192P, A367P, and T357M mutants have prolonged dwell times on target RNAs, indicating impaired target release. The L192P and A367P variants also display slow target RNA association kinetics. RNA Bind-n-Seq experiments showed that in vitro, the L192P, A367P, T357M, and F182D mutants are prone to mis-targeting. In cultured murine cortical neurons, the L192P mutant altered the miRNA complement associated with AGO2, altered guide strand selectivity, and increased the accumulation of 3' isomiRs, suggesting altered miRNA loading and increased miRNA 3' end exposure. In vivo, mice carrying the p.L192P variant, but not p.G733R, demonstrated strongly reduced breeding ability, altered cortical transcriptomes, and over-repression of miRNA targets. The combined results suggest patient mutations impact AGO2 targeting dynamics in a gain-of-function manner, leading to deregulation of the neuronal transcriptome and the observed neurodevelopmental anomalies.

overall_design: RNA was extracted from cerebral cortex tissue of heterozygous Ago2 G733R mutant mice and wildtype controls. Isolated RNA was subjected to RNA-sequencing.

first: Debora

last: Tibbe

first: Hans-Jürgen

last: Kreienkamp

first: Davor

last: Lessel


title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - Xenium Data

first: Samouil

last: Farhi

first: Huan

last: Wang

first: Ruixu

last: Huang

first: Jack

last: Nelson

first: Ce

last: Gao

first: Miles

last: Tran

first: Anna

last: Yeaton

first: Sachi

last: Krishna

first: Kristen

last: Felt

first: Kathleen

last: Pfaff

first: Teri

last: Bowman

first: Scott

last: Rodig


title: Single-cell RNA-seq of human bone marrow cells by TAS-Seq

city: Noda City

first: Aisa

last: Suzuki

state: Chiba

address: Yamasaki 2669

country: Japan

institute: Tokyo University of Science

summary: The TCF3::HLF fusion protein defines a subtype of incurable B cell acute lymphoblastic leukemia (B-ALL). Here, we identified self-reinforcing IL-1b networks in TCF3::HLF B-ALL cells using a newly-established mouse model that fully recapitulates human TCF3::HLF B-ALL, including osteolysis. We found significant upregulation of several inflammatory cytokines, including IL1B, IL6 and IFNG in the B-ALL mice. Deletion of IL1B or IL1R1 strongly inhibited the growth of the human TCF3::HLF B-ALL cells, reduced the expression of RANKL and ameliorated the destruction of bone in the transplanted mice. Genetic and epigenetic analyses identified a previously unknown regulatory region of the IL1B gene locus, where TCF3::HLF directly binds. Importantly, single cell RNA-seq profiling of TCF3::HLF B-ALL patients revealed a dramatic upregulation of IL1B at relapse compared to the time of diagnosis. These findings suggest a critical role of TCF3::HLF-IL-1b axis for the progression of TCF3::HLF B-ALL.

overall_design: Cryopreserved bone marrow samples were obtained from two TCF3::HLF-positive B-ALL patients at diagnosis and at relapse. Healthy donor bone marrow mononuclear cells (BM MNC) were used as controls.

first: Tsukasa

last: Shigehiro

first: Mayumi

last: Hirakawa

first: Risa

last: Hirano

first: Minori

last: Tamai

first: Koshi

last: Akahane

first: Kazuo

last: Okamoto

first: Satoshi

last: Ueha

first: Toshimori

last: Kitami

first: Masatoshi

last: Takagi

first: Dai

last: Keino

first: Takeshi

last: Inukai

first: Tomokatsu

last: Ikawa


title: CUT&Tag chromatin profiling of HLF-deficient YCUB2 cells

overall_design: YCUB2 cells constitutively expressing Cas9 were transduced with sgRNA vectors containing the designed sequences, and sorted cells were cultured for 3 days prior to analysis.


title: Transcriptomic  shift in ethanol and amino acid metabolic genes regulated by Med15 during fermentation

city: Indianapolis

first: David

last: Cooper

state: IN

address: 350 PHSB, 4600 Sunset Ave.

institute: Butler University

summary: Wine yeast are specialized strains that are adapted to survive in the wine making environment while producing high concentrations of ethanol. In addition to large genomic changes that differentiate wine yeast from yeast used in other industries, single nucleotide and polyglutamine tract polymorphisms in the transcriptional regulator Med15 are associated with the fermentation efficiency and stress response phenotypes of wine yeast. In this study we investigated the transcriptional differences during wine fermentation in transgenic lab strain yeast having integrated wine yeast MED15 alleles. Compared to the lab strain, a strain with a MED15 allele from a palm wine yeast strain, exhibited enhanced expression of glycolytic, fermentation, and amino acid biosynthesis genes. Our experimental data confirms the importance of arginine biosynthetic genes during the fermentation process and suggests that the improvement in fermentation efficiency in strains with MED15 alleles from wine yeast strains may be related to the role of Med15 in expression of the genes of the arginine biosynthetic pathway. The global benefit conferred by polymorphisms in a single transcriptional regulator, makes Med15 a prime target for engineering of strains devoted to various types of alcohol production.

overall_design: Individual fermentation reactions in 5 mL supplemented white grape juice were prepared for two biological replicates each of the med15Δ strain and integrants of the LAB, WY7, WY15, and WY23 MED15 alleles. Weight loss was monitored, and RNA was extracted from yeast at the 35% weight loss point (~37 hours for MED15 strains, and 48 hours for med15Δ strains).

middle: G

first: Jan

middle: S

last: Fassler


title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - CosMx Data

first: Samouil

last: Farhi

first: Huan

last: Wang

first: Ruixu

last: Huang

first: Jack

last: Nelson

first: Ce

last: Gao

first: Miles

last: Tran

first: Anna

last: Yeaton

first: Sachi

last: Krishna

first: Kristen

last: Felt

first: Kathleen

last: Pfaff

first: Teri

last: Bowman

first: Kevin

last: Wei

first: Brittany

last: Goods


title: Dysregulation of AGO2-miRNA dynamics underlies the AGO2-associated Lessel-Kreienkamp syndrome [miRNA-Seq]

first: Jan Broder

last: Engler

summary: Mutations in human Argonaute genes, AGO1 and AGO2, are associated with neurodevelopmental disorders. Although multiple patients have been identified, the underlying molecular basis for pathogenesis remains unclear. Here, we performed an extensive investigation of five AGO2 mutations (p.L192P, p.A367P, p.T357M, p.F182del, and p.G733R) linked to different clinical severities.

overall_design: Primary mouse cortical neurons were transduced with AAVs to express EGFP-AGO2-WT or EGFP-AGO2-L192P and immunoprecipitation against EGFP was performed to enrich AGO2-bound miRNA for subsequent miRNA sequencing.

first: Debora

last: Tibbe

first: Hans-Jürgen

last: Kreienkamp


title: Bulk RNA-seq analysis of murine and human TCF3-fusion B-ALL cells

first: Aisa

last: Suzuki

overall_design: RNA-seq profiling was performed on bone marrow pro-B cells from wild-type (WT) mice and B-ALL mice transplanted with TCF3::PBX1-positive or TCF3::HLF-positive iLS cells. Additionally, RNA-seq profiling was conducted on YCUB2 cells and IL1B-knockout YCUB2 cells.

first: Tsukasa

last: Shigehiro

first: Mayumi

last: Hirakawa

first: Risa

last: Hirano

first: Minori

last: Tamai

first: Koshi

last: Akahane

first: Kazuo

last: Okamoto

first: Satoshi

last: Ueha

first: Toshimori

last: Kitami

first: Masatoshi

last: Takagi

first: Dai

last: Keino

first: Takeshi

last: Inukai

first: Tomokatsu

last: Ikawa


title: The syntenic lncRNA DANCR is a human melanoma oncogene and an essential regulator of zebrafish development

city: Bath

first: Keith

middle: William

last: Vance

state: Somerset

address: University of Bath

department: Department of Biology and Biochemistry

institute: University of Bath

summary: Long non-coding RNAs (lncRNAs) play crucial roles in regulating gene expression. Some are essential for organismal development and physiology, and they can contribute to diseases such as cancer. Whilst most lncRNAs exhibit little sequence similarity, conservation of lncRNA transcription relative to neighbouring protein-coding genes suggests potential functional significance. Nevertheless, most positionally equivalent lncRNAs are uncharacterized and it remains unclear whether they exert similar roles in distant species. Here, we identified syntenic melanoma-associated lncRNAs predicted to be components of the MITF gene regulatory network in human melanoma, with positionally equivalent transcripts in zebrafish. Among these, we prioritized Differentiation Antagonizing Non-Protein Coding RNA (DANCR), a cancer-associated lncRNA critical for maintaining somatic progenitor cells in human models, for functional investigation. Dancr is a multi-exonic, cytoplasmically enriched lncRNA transcribed from syntenic regions in the human and zebrafish genomes. MITF and c-MYC, key melanoma transcription factors, regulate human DANCR expression and melanoma patients with high DANCR display significantly decreased survival. DANCR is a melanoma oncogene that controls cancer-associated gene expression networks and promotes human melanoma cell proliferation and migration. Zebrafish dancr is dynamically expressed across multiple different cell types in the developing embryo, regulates genes involved in cell death, and is essential for embryonic development. Our work suggests that cancer-critical lncRNAs such as Dancr, expressed from similar regions in vertebrate genomes, may regulate related genes and processes involved in both embryonic development and tumorigenesis across species.

overall_design: RNA-sequencing of DANCR loss-of-function human melanoma cells and whole zebrafish embryos and controls

first: Stephanie

middle: M

last: Jones

first: Elizabeth

last: Coe

first: Michael

last: Shapiro

first: Igor

last: Ulitsky

first: Robert

middle: N

last: Kelsh

middle: W


title: RNA-seq reveals differentially expressed genes involved in the hypothalamus and pituitary function affecting divergent residual feed intake in slow-growing Korat chicken

city: Mueang Nakhon Ratchasima

first: Panpradup

last: Sinpru

state: Nakhon Ratchasima

address: 111 University Ave.

country: Thailand

institute: Suranaree University of Technology

summary: Feed efficiency (FE) is crucial in poultry production due to the high costs of feed. Korat chicken (KRC), a slow-growing breed, is known for its unique meat flavor and nutritional value, with genetic variation in feed efficiency (FE). Since the brain parts, i.e., the hypothalamus and pituitary gland, act as a convergent and integrative center for multiple nutrient-related signals, understanding the genetic basis of neuronal signaling regulating FE is essential to improve the genetic potential of KRC. Thus, this study aimed to identify genes related to neuronal signaling that influence FE using RNA sequencing in the hypothalamus and pituitary gland from low and high residual feed intake (RFI) groups.

overall_design: RNA was extracted from 20 hypothalamic tissues of males of KRC in the low residual feed intake (low RFI; n=10) and high residual feed intake (high RFI; n=10) groups, and five RNA pools were created from 10 each group. A total of 10 transcriptome libraries were constructed, and candidate genes for FE traits were screened and identified. For the pituitary gland, total RNA was isolated from pituitary samples of 8 chickens from each group (LRFI or HRFI). To increase the quantity of RNA and reduce variation from dissection, an equal mass of RNA from 2 birds was pooled for each sample in each group, yielding a total of n = 4 pools for each of the LRFI and HRFI groups. Pools were defined according to ranked RFI values (e.g., pairs of samples with successive RFI values were pooled). Subsequently, a total of 8 transcriptome libraries were constructed (n=4/treatment), and candidate genes for FE traits were screened and identified.

first: Panpradub

first: Phocharapon

last: Pasri

first: Boonyarit

last: Kamkrathok

first: Orapin

last: Jantasaeng

first: Saknarin

last: Pengsanthia

first: Tom

last: Porter

first: Wittawat

last: Molee

first: Amonrat


title: Endothelial BMP6 Drives Hemodynamic-Dependent VSMCs Calcification in Carotid Atherosclerosis

city: zhengzhou

first: Shen

last: Li

address: No. 1 East Jianshe Road

department: The Department of Neurology

institute: The Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China

summary: Carotid atherosclerosis (CAS) is a major contributor to ischemic stroke, with vascular calcification driving disease progression. However, the molecular mechanisms driving vascular calcification in CAS remain unelucidated. Previous studies have confirmed that bone morphogenetic proteins (BMPs) play essential roles in calcification; however, the regulatory mechanisms of BMP6 signaling in vascular calcification remain unclear. This study aimed to investigate the role of BMP6 in vascular calcification in CAS and the underlying mechanisms. A subset of endothelial cells (ECs) with high BMP6 expression, which interacted with specific vascular smooth muscle cells (VSMCs) via the BMP signaling pathway, was identified using single-cell RNA sequencing of human CAS plaque samples. In vitro experiments demonstrated BMP6-induced osteogenic differentiation of VSMCs. Moreover, BMP6 activated the p-SMAD1/5/8 signaling pathway by binding to the ACVR1–BMPR2 receptor complex, and pharmacological inhibition of this pathway attenuated osteogenic differentiation. Experimental results from endothelium-specific BMP6 knockout (BMP6ECKOApoE-/-) and overexpression (AAV-Cdh5-BMP6) mice confirmed that BMP6 exacerbated vascular calcification, whereas its knockdown reduced calcific lesions. Additionally, disturbed flow conditions upregulated BMP6 expression by suppressing Krüppel-like factor 4 and linking hemodynamic forces to BMP6-mediated calcification. These findings suggest that BMP6 is a key regulator of vascular calcification in CAS, driven by EC–VSMC interactions and hemodynamic stress

overall_design: 12 CAS plaques obtained following carotid endarterectomy (CEA) and carotid arteries from mice were isolated by  fluorescence-activated cell sorting and analyzed using ScRNA-seq

first: Shuang

last: Cao

first: Peipei

first: Yongjun

last: Wang

first: Zongping

last: Xia

first: Jie

last: Xu

first: Yuming


title: A florigen-expressing subpopulation of phloem companion cells expresses other small proteins and reveals a nitrogen-sensitive FT repressor

city: Seattle

first: Josh

last: Cuperus

state: WA

address: 3720 15th Ave NE, Foege Building Room s310

institute: University of Washington

summary: The precise onset of flowering is crucial to ensure successful plant reproduction. The gene FLOWERING LOCUS T (FT) encodes florigen, a mobile signal that is produced in leaves and initiates flowering in the shoot apical meristem. FT is highly expressed in phloem companion cells that reside in distal leaf regions. Thus far, a detailed molecular characterization of the FT-expressing phloem companion cells has been lacking. Here, we used single-nuclei RNA-seq to investigate gene expression in FT-expressing cells and other phloem companion cells. We discovered that companion cells with high FT expression form a unique cluster and express other genes encoding small proteins, including the anti-florigen BROTHER OF FT (BFT). The promoters of FT and the genes co-expressed with FT were enriched for the consensus binding motif of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR1 (NIGT1). Overexpression of the paralogs NIGT1.2 and NIGT1.4 in transgenic Arabidopsis lines significantly delayed flowering under nitrogen-rich conditions, consistent with NIGT1s acting as nitrogen-dependent FT repressors. Taken together, our results demonstrate that FT-expressing cells show a distinct expression profile that suggests that these cells produce multiple systemic signals to regulate plant growth and development.

overall_design: Promoters driving expression of the NTF reporter were used for FANS and subjected to 10x Genomics single-cell RNA-seq v3.1

first: Hiroshi

last: Takagi

first: Shogo

last: Ito

first: Jae

last: Shim

first: Akane

last: Kubota

first: Andrew

last: Hempton

first: Nayoung

last: Lee

first: Takamasa

last: Suzuki

first: Chansie

last: Yang

first: Christine

last: Nolan

first: Cristina

last: Alexandre

first: Daisuke

last: Kurihara

first: Yoshikatsu

last: Sato

first: Yasuomi

last: Tada

first: Takatoshi

last: Kiba

first: Jose

last: Pruneda-Paz

middle: T

last: Queitsch

first: Takato

last: Imaizumi


title: Dysregulation of AGO2-miRNA dynamics underlies the AGO2-associated Lessel-Kreienkamp syndrome [RNA-Seq]

first: Jan Broder

last: Engler

overall_design: RNA was extracted from cerebral cortex tissue of heterozygous AGO2 L192P mutant mice and wildtype controls. Isolated RNA was subjected to RNA-sequencing.

first: Debora

last: Tibbe

first: Hans-Jürgen

last: Kreienkamp


title: Nanomaterial- induced mitochondrial biogenesis enhances intercellular mitochondrial transfer efficiency

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 John Sharp Pkwy MREB II, Suite 4344

department: Cell Biology & Genetics

institute: Texas A&M University

summary: Intercellular mitochondrial transfer, the spontaneous exchange of mitochondria between cells, is a recently described phenomenon crucial for cellular repair, regeneration, and disease management. Enhancing this natural process holds promise for developing novel therapies targeting diseases associated with mitochondrial dysfunction. Here, we introduce a nanomaterial- based approach employing molybdenum disulfide (MoS2) nanoflowers with atomic- scale vacancies to stimulate mitochondrial biogenesis in cells to make them mitochondrial biofactories. Upon internalization, these nanoflowers result in a two- fold increase in mitochondrial mass and enhancing mitochondrial transfer to recipient cells by several- fold. This enhanced efficiency of transfer significantly improves mitochondrial respiratory capacity and adenosine triphosphate production in recipient cells under physiological conditions. In cellular models of mitochondrial and cellular damage, MoS2 enhanced mitochondrial transfer achieved remarkable restoration of cell function. This proof- of- concept study demonstrates that nanomaterial- boosted intercellular mitochondrial transfer can enhance cell survivability and function under diseased conditions, offering a promising strategy for treating mitochondrial dysfunction- related diseases.

overall_design: Paired-end Illumina RNA-seq of sorted smooth muscle cells (SMCs) alone, after coculture with hMSCs (Mito-Transfer), and after coculture with hMSCs pre-treated with MoS2 nanoflowers.

first: John

last: Soukar

first: Kanwar Abhay

first: Ari

last: Aviles

first: Sarah

last: Hargett

first: Harman

last: Kaur

first: Samantha

last: Foster

first: Feng

last: Zhao

first: Vishal

last: Gohil

first: Akhilesh

middle: K

last: Gaharwar


title: Pericytes orchestrate a tumor-restraining microenvironment in glioblastoma [scRNA-seq]

city: Lund

first: Kristian

last: Pietras

address: Sheelevägen 2

department: Division of Translational Cancer Research

institute: Lund University

summary: To functionally assess the role of pericytes in glioma development and progression, we study the effects of pericyte depletion in orthotopic and transgenic mouse models of high-grade glioma using single-cell and spatial transcriptomics. We present evidence that pericytes mitigate glioma development by orchestrating a tumor-suppressive microenvironment, challenging the concept of pericytes as merely pro-oncogenic cells, and underscoring the importance of pericyte preservation in future GBM therapies.

overall_design: High-grade gliomas were initiated by stereotactically delivering the glioma oncogenic drivers PDGFB and shp53 into the subventricular zone of transgenic adult Ntv-a mice that were either pericyte-poor (Pdgfbret/ret) or control (Pdgfbret/+). 7 Pdgfbret/+ and 4 Pdgfbret/ret mice were sacrificed when displaying severe symptoms. Single-cell RNA-seq libraries were prepared using 10x Chromium system.

first: Sebastian

last: Braun

first: Paulina

last: Bolivar

first: Clara

last: Oudenaarden

first: Jonas

last: Sjölund

first: Matteo

last: Bocci

first: Katja

last: Harbst

first: Mehrnaz

last: Talkhoncheh

first: Bengt

last: Phung

first: Eugenia

last: Cordero

first: Rebecca

last: Rosberg

first: Elinn

last: Johansson

first: Göran

last: Jönsson

first: Alexander


title: Dabigatran protection against lipopolysaccharide induced endotoxemia is not mediated through its anticoagulant function

city: Ann Arbor

first: Vinitha

last: Jacob

state: MI

address: 8200 Medical Science Research Building III,  III, 1153 West Medical Center Drive

institute: University of Michigan

summary: Endotoxemia is a key feature of sepsis pathogenesis and has also been found to mediate the pathophysiology of multiple chronic inflammatory conditions.  In this work, we expand upon a model of endotoxemia due to lipopolysaccharide (LPS) using zebrafish and demonstrate that this model displays activation of inflammatory and pro-coagulant genes, impaired coagulation in response to endothelial injury, and signs of organ dysfunction.  An in silico analysis revealed that there were multiple associations between the RNA-seq signature of LPS treated embryos and the RNA-seq signature of genes and drugs involving diverse pathways.  An in vivo screen involving >1,500 FDA approved drugs identified multiple compounds spanning several drug categories that partially or completely prevented endotoxemic death.  Three small molecules including one anticoagulant dabigatran were identified through both the in vivo and in silico analyses.  Dabigatran, a direct thrombin inhibitor, significantly reduced the upregulation of inflammatory cytokines and pro-coagulant genes and completely protected zebrafish from endotoxemic death due to LPS.  However, other anticoagulants argatroban (direct thrombin inhibitor), and rivaroxaban and apixaban, (factor Xa inhibitors), conferred no such protection.  Lastly, prothrombin mutant fish displayed no increase in survival when treated with LPS.  These data together suggest that dabigatran protects zebrafish from endotoxemia through a mechanism independent of its anticoagulant effect.  In summary, our in silico and in vivo analyses reveals that dabigatran and several other novel small molecules prevent LPS induced endotoxemia and warrant further therapeutic exploration in inflammatory conditions, both acute and chronic.

overall_design: Zebrafish larvae that were 3 days post fertilization (dpf) were incubated with a lethal dose of LPS from Salmonella typhi and collected 3 hours post treatment.  Gene expression changes were compared to control untreated larvae.

first: Murat

last: Yaman

first: Jordan

last: Shavit


title: NAD+ - and EVA1-C-dependent reversal of neurological deficits is mediated by differential alternative RNA splicing in tauopathic animal models

city: Guangzhou

first: Lipeng

last: Mao

state: Guangdong

address: No.601, West Huangpu Avenue

department: Department of Microbiology and Immunology

institute: Jinan University

summary: Aberrant alternative splicing events (ASEs) are emerging as a new hallmark of aging and are linked to age-related neurodegenerative pathologies such as Alzheimer’s disease (AD). AD brains are characterized by abundant intracellular proteinaceous aggregates, including neurofibrillary tangles (NFTs). Although NAD+ and related metabolites can slow down AD progression, the effects of NAD+ on ASEs in AD remain unclear. This study investigates the relationships between NAD+ metabolism, ASEs and AD or AD-like pathologies including tauopathies using deep-learning AI-based algorithms to predict protein structures and protein-protein interactions as well as experimental tauopathy models including hTau.P301S transgenic mice and transgenic hTau[P301L] Caenorhabditis elegans. Mouse transcriptomic data were mined to detect ASEs that were differentially induced in the presence of NAD+ precursor nicotinamide riboside (NR) with specific focus on the Eva1-C locus. The results reveal that the relative abundance of Eva1-C isoforms is sensitive to both the concentration of NR and to tauopathy genotype. NAD+ abundance/metabolic status modulates ASEs and the expression of EVA1-C isoforms, which in turn regulate the interaction with the key proteins, BAG-1 and HSP70, involved in orchestrating protein homeostasis. Importantly, EVA1-C is dramatically reduced in the postmortem entorhinal cortex and hippocampal neurons from 20 Braak 5/6 AD patients compared to 20 of cognitive normal humans. Thus, this study supports the novel idea that NAD+ metabolism modulates abundance of specific mRNA isoforms, and that ASEs influence disease progression in model tauopathies and potentially AD. These results could facilitate future development of NAD+-based splice-switching therapeutics for AD.

overall_design: To better understand how NAD+ precursor, NR, affects the hippocampus of mice in molecular pathways, we performed RNA sequencing in the hippocampal tissue of WT and P301S mice with or without NR treatment. We found that NR changed hippocampal neural activity and homeostasis.

first: Ruixue

last: Ai

first: Xurui

last: Jin


title: Characterization of the regulatory network of linc1393 in the maintenance of pluripotency provides the principles for lncRNA targets prediction [RNA-seq]

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

institute: College of Life Science,Northeast Agricultural University

summary: In the study, we screened the nuclear lncRNAs in mESCs, and demonstrate that linc1393 maintains mESCs pluripotency by recruiting SET1A nearby its binding sites, to establish H3K4me3 and activate the expression of specific pluripotent genes. Furthermore, we developed a computational framework, LncTargeter, to predict the binding sites and the target genes of a given lncRNA based on the XGBoost model.

overall_design:
The mechanism of linc1393 on the maintenance of pluripotency and development of LncTargeter
RNA-seq in mESCs

first: Weibo

last: Hou

first: Ming

last: Zong

first: Qi

last: Zhao

first: Meiling

last: Gao

first: Jianzhong

last: Su

first: Qingran

last: Kong